Repository: biopython/biopython

Issue:
HMMER Parser doesn't work with Windows
The regex defined here:

https://github.com/krdav/ANARCI_KD_copy/blob/5c4a17f6f0bc530b3e5154667e285eea1195a485/lib/python/anarci/Bio/SearchIO/HmmerIO/hmmer3_text.py#L24

Is unable to find any matches in this output banner from hmmscan:

'# C:\\msys64\\scr\\jou\\builds\\22-2\\build\\thirdparty\\bin\\Windows-x64\\hmmer\\bin\\hmmscan :: search sequence(s) against a profile database\n'

and as a result

https://github.com/biopython/biopython/blob/9965ece1d76adc8ee65904f87ea68c0b1206050a/Bio/SearchIO/HmmerIO/hmmer3_text.py#L20

Sometimes leaves query_start, query_end, hit_start, and hit_end as None. It's worse than assigning without correction, and should really be an error, or handled gracefully with its current downstream warning.


Discussion:
Hi Jonathan,

Could you provide us with a sample input we can reproduce the problem with?

Cheers,

João

A segunda, 17/07/2023, 21:26, Jonathan Jou ***@***.***>
escreveu:

> The regex defined here:
>
>
> https://github.com/krdav/ANARCI_KD_copy/blob/5c4a17f6f0bc530b3e5154667e285eea1195a485/lib/python/anarci/Bio/SearchIO/HmmerIO/hmmer3_text.py#L24
>
> Is unable to find any matches in this output banner from hmmscan:
>
> '#
> C:\msys64\scr\jou\builds\22-2\build\thirdparty\bin\Windows-x64\hmmer\bin\hmmscan
> :: search sequence(s) against a profile database\n'
>
> and as a result
>
>
> https://github.com/biopython/biopython/blob/9965ece1d76adc8ee65904f87ea68c0b1206050a/Bio/SearchIO/HmmerIO/hmmer3_text.py#L20
>
> Sometimes leaves query_start, query_end, hit_start, and hit_end as None.
> It's worse than assigning without correction, and should really be an
> error, or handled gracefully with its current downstream warning.
>
> —
> Reply to this email directly, view it on GitHub
> <https://github.com/biopython/biopython/issues/4361>, or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AABZ6EHP7RUZZYAOVBKFQD3XQXQ2RANCNFSM6AAAAAA2NVTXHM>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: ***@***.***>
>

It sounds like this input file has a full path to the hmmscan binary (a Windows path starting C:) but the regular expression in the parser is expecting just ``hmmscan`` alone. If so, this _might_ also break on Linux or macOS too if used with an explicit path to the binary?

But yes, a small sample output file would be useful. And if @bow thought it useful, ideally a test case we could add to Biopython's test suite.
Thanks for reporting this @jou-schrodinger.

Out of curiosity, can I ask how you did you execute `hmmscan`? Was `hmmscan` already in your `PATH` or did you have to refer to its absolute path as shown here?

Either way, seconding @JoaoRodrigues and @peterjc ~ we'd appreciate it if you have an example output. And with your permission, we might like to include it in our test suite :slightly_smiling_face:.
I've been working with @jou-schrodinger on this issue -- I've attached an hmmscan result file that reproduces it:
[6fr3_hmmscan_space_in_path.txt](https://github.com/biopython/biopython/files/13178955/6fr3_hmmscan_space_in_path.txt)

In this case, anarci was running hmmer with the following arguments:
```
['C:\\msys64\\scr\\byerly\\builds\\NB\\20231025 _\\thirdparty\\bin\\Windows-x64\\hmmer\\bin\\hmmscan', '-o', 'C:\\Users\\byerly\\AppData\\Local\\Temp\\tmpkslp61l0.txt', 'C:\\msys64\\scr\\byerly\\builds\\NB\\20231025 _\\internal\\lib\\site-packages\\anarci\\dat\\HMMs\\ALL.hmm', 'C:\\Users\\byerly\\AppData\\Local\\Temp\\tmpn5zlrimi.fasta']
```

So yes, surprisingly you do indeed appear to have a space in the path to ``hmmscan``, very odd:

``C:\msys64\scr\byerly\builds\NB\20231025 _\thirdparty\bin\Windows-x64\hmmer\bin\hmmscan``

This looks like an accident perhaps, why have the "date space underscore" as a folder name? But in general I would recommend avoiding using any file or folder as it makes life harder (extra steps to escape or quote paths), and sometimes leads to bugs where other people's code has not handled this.

@bow is this enough info for you to try to fix this?
yeah, this can happen if someone has a python installation in a nonstandard place, e.g. "Program Files" on Windows. The inclusion of a space is deliberate to make sure my testing is thorough.

I have a fix for this almost ready, just preparing a pull request now. I'm not super familiar with GitHub so it may take a little while!
@peterjc That should be enough for a PR ~ looks like @byerlyj has it under control :slightly_smiling_face:. Let us know if you need any help and feel free to ping me for the MR review.

Resolving patch:
diff --git a/Bio/SearchIO/HmmerIO/hmmer3_text.py b/Bio/SearchIO/HmmerIO/hmmer3_text.py
--- a/Bio/SearchIO/HmmerIO/hmmer3_text.py
+++ b/Bio/SearchIO/HmmerIO/hmmer3_text.py
@@ -17,7 +17,7 @@
 
 # precompile regex patterns for faster processing
 # regex for program name capture
-_RE_PROGRAM = re.compile(r"^# (\w*hmm\w+) :: .*$")
+_RE_PROGRAM = re.compile(r"^# .*?(\w?hmm\w+) :: .*$")
 # regex for version string capture
 _RE_VERSION = re.compile(r"# \w+ ([\w+\.]+) .*; http.*$")
 # regex for option string capture


Test patch:
diff --git a/Tests/Hmmer/README.txt b/Tests/Hmmer/README.txt
--- a/Tests/Hmmer/README.txt
+++ b/Tests/Hmmer/README.txt
@@ -19,6 +19,7 @@ text_30_hmmscan_007.out      single query, one match, no alignment
 text_30_hmmscan_008.out      single query, multiple matches, no alignment width
 text_30_hmmscan_009.out      single query, alignment block(s) with large gaps (bug 3399 in Redmine)
 text_30_hmmscan_010.out
+text_30_hmmscan_011.out      single query, multiple matches, windows-style hmmscan executable path with whitespace
 text_31b1_hmmsearch_001.out  multiple queries
 text_30_hmmsearch_001.out    single query, no match
 text_30_hmmsearch_002.out    single query, multiple matches, multiple hsps per match
diff --git a/Tests/Hmmer/text_30_hmmscan_011.out b/Tests/Hmmer/text_30_hmmscan_011.out
new file mode 100644
--- /dev/null
+++ b/Tests/Hmmer/text_30_hmmscan_011.out
@@ -0,0 +1,1425 @@
+# C:\msys64\scr\byerly\builds\NB\20231025 _\thirdparty\bin\Windows-x64\hmmer\bin\hmmscan :: search sequence(s) against a profile database
+# HMMER 3.1b2 (February 2015); http://hmmer.org/
+# Copyright (C) 2015 Howard Hughes Medical Institute.
+# Freely distributed under the GNU General Public License (GPLv3).
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# query sequence file:             C:\Users\byerly\AppData\Local\Temp\tmpt7psecrp.fasta
+# target HMM database:             C:\msys64\scr\byerly\builds\NB\20231025 _\internal\lib\site-packages\anarci\dat\HMMs\ALL.hmm
+# output directed to file:         C:\Users\byerly\AppData\Local\Temp\tmp2u1a0mw3.txt
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query:       6FR3  [L=202]
+Scores for complete sequence (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
+    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
+     3e-040  128.1   0.2   5.8e-040  127.2   0.0    1.6  2  human_A   
+   3.4e-038  121.4   0.5   8.4e-038  120.2   0.0    1.8  2  mouse_A   
+   5.4e-029   91.7   0.0   1.1e-028   90.7   0.0    1.5  2  human_D   
+   1.6e-028   90.6   0.2   4.7e-028   89.1   0.0    1.8  2  mouse_D   
+   1.4e-022   71.2   0.2   3.1e-022   70.0   0.0    1.6  2  mouse_B   
+   9.4e-021   65.1   0.0   2.2e-020   64.0   0.0    1.6  1  human_B   
+   2.8e-019   60.7   1.1     1e-018   58.9   0.1    2.0  2  rhesus_L  
+   4.6e-018   56.7   1.3   1.5e-017   55.0   0.1    2.0  2  human_L   
+   5.6e-017   53.2   0.9   1.2e-016   52.1   0.2    1.8  2  cow_L     
+   1.2e-016   52.3   0.1   1.2e-016   52.3   0.1    1.7  1  pig_L     
+   1.7e-016   51.5   0.6   2.4e-016   51.1   0.1    1.5  1  mouse_K   
+   2.2e-016   51.3   1.0   7.3e-016   49.6   0.2    1.9  2  rabbit_L  
+     1e-015   49.1   1.1     1e-015   49.1   0.1    1.5  1  rat_K     
+   2.2e-015   47.8   0.7   3.9e-015   47.0   0.1    1.7  2  human_K   
+   1.8e-014   45.1   0.5   3.9e-014   44.0   0.1    1.7  2  rat_L     
+   2.8e-014   44.3   0.8   4.4e-014   43.7   0.2    1.5  2  pig_K     
+     4e-014   43.9   0.1   8.2e-014   42.9   0.1    1.4  1  rhesus_K  
+   5.7e-014   43.3   0.1   1.3e-013   42.2   0.1    1.5  1  mouse_L   
+   1.7e-013   41.8   0.1   3.5e-013   40.8   0.1    1.5  1  cow_K     
+     2e-013   41.6   0.1   3.5e-013   40.8   0.1    1.4  1  rabbit_K  
+     3e-012   37.9   0.2   6.4e-012   36.9   0.0    1.6  2  rhesus_H  
+   5.5e-012   36.7   0.0   9.6e-011   32.7   0.0    2.1  2  mouse_G   
+   8.1e-012   36.4   0.1   1.9e-011   35.2   0.0    1.6  2  mouse_H   
+   1.4e-011   35.8   0.3   3.8e-011   34.4   0.0    1.8  2  human_H   
+     1e-010   33.1   0.2   5.1e-010   30.9   0.0    2.1  2  alpaca_H  
+   7.8e-010   30.1   0.0   1.8e-009   28.9   0.0    1.6  1  rabbit_H  
+   8.9e-010   30.1   0.1     2e-009   28.9   0.1    1.6  1  pig_H     
+   5.8e-009   27.1   0.3   1.6e-008   25.7   0.1    1.8  2  cow_H     
+   4.3e-008   24.2   0.1   1.5e-007   22.4   0.0    1.8  2  human_G   
+
+
+Domain annotation for each model (and alignments):
+>> human_A  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  127.2   0.0  5.8e-040  5.8e-040       1     128 []       2     111 ..       2     111 .. 0.97
+   2 ?   -2.6   0.0       7.9       7.9      93     103 ..     145     155 ..     134     166 .. 0.73
+
+  Alignments for each domain:
+  == domain 1  score: 127.2 bits;  conditional E-value: 5.8e-040
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_A   1 aqkveqspqslsvqEgesvtlnCtystsatlllllseylfWYkqepgkglqllikllsalldeeekkklllllgrlsatlnkseksssLkitasqlsdsAvY 102
+              +q+v+q p +lsv Ege++ lnC++++sa       ++l+W++q+pgkgl++l+ ++s+   ++e+++     grl+a+l+ks+ +s+L+i asq++dsA+Y
+     6FR3   2 KQEVTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQSS---QREQTS-----GRLNASLDKSSGRSTLYIAASQPGDSATY 89 
+              699**************************......9**********************8...999999.....***************************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_A 103 fCavsellllllkliFGkGTrLtVkp 128
+              +Cav     +++k++FG+GT+L+Vkp
+     6FR3  90 LCAVT----NFNKFYFGSGTKLNVKP 111
+              ****9....699************99 PP
+
+  == domain 2  score: -2.6 bits;  conditional E-value: 7.9
+              xxxxxxxxxxx RF
+  human_A  93 asqlsdsAvYf 103
+               sq +ds vY+
+     6FR3 145 VSQSKDSDVYI 155
+              46777888875 PP
+
+>> mouse_A  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  120.2   0.0  8.4e-038  8.4e-038       1     128 []       2     111 ..       2     111 .. 0.97
+   2 ?   -1.1   0.1       2.7       2.7      91     103 ..     143     155 ..     127     169 .. 0.74
+
+  Alignments for each domain:
+  == domain 1  score: 120.2 bits;  conditional E-value: 8.4e-038
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_A   1 gqkveqspesltvqegesvtlnCsystsavllllaseylfWYkqepgeglqlLlkivsalldeekkeslllllgrfeatlnkseksssLhitsvqlsDsAvY 102
+              +q+v+q p++l+v ege++ lnCs+++sa       ++l+W++q+pg+gl++Ll i s+   +++++s     gr++a l+ks+ +s+L i+++q+ DsA+Y
+     6FR3   2 KQEVTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQSS---QREQTS-----GRLNASLDKSSGRSTLYIAASQPGDSATY 89 
+              599**************************......8**********************7...888888.....***************************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_A 103 fCalsellllllkltFGkGTkLtvkp 128
+              +Ca++    +++k++FG+GTkL vkp
+     6FR3  90 LCAVT----NFNKFYFGSGTKLNVKP 111
+              *****....699************98 PP
+
+  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
+              xxxxxxxxxxxxx RF
+  mouse_A  91 itsvqlsDsAvYf 103
+               + +q +Ds vY 
+     6FR3 143 TNVSQSKDSDVYI 155
+              4567888998886 PP
+
+>> human_D  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   90.7   0.0  1.1e-028  1.1e-028       2     128 .]       3     111 ..       2     111 .. 0.95
+   2 ?   -2.7   0.0       8.9       8.9      16      27 ..     152     163 ..     140     180 .. 0.47
+
+  Alignments for each domain:
+  == domain 1  score: 90.7 bits;  conditional E-value: 1.1e-028
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_D   2 qkvtqsqpslsvqegeavtLnCsyetsasllllgnyylfWYkqepskeitflirqksslldkqekkedakklgrfsvkldkaaksasLkIsasqlgDsatYf 103
+              q+vtq +  lsv ege+ +LnCs++ sa+      y+l W++q p+k++t l+ ++ss   ++e+++     gr++ +ldk+   ++L I asq+gDsatY+
+     6FR3   3 QEVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS---QREQTS-----GRLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+              99**************************7......***************99999987...777777.....****************************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_D 104 CAleellllllqliFGkGtkliVep 128
+              CA+ +    +++++FG Gtkl V+p
+     6FR3  91 CAVTN----FNKFYFGSGTKLNVKP 111
+              ***86....89************97 PP
+
+  == domain 2  score: -2.7 bits;  conditional E-value: 8.9
+              xxxxxxxxxxxx RF
+  human_D  16 geavtLnCsyet 27 
+                  t +C  + 
+     6FR3 152 DVYITDKCVLDM 163
+              222333444444 PP
+
+>> mouse_D  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   89.1   0.0  4.7e-028  4.7e-028       2     128 .]       3     111 ..       2     111 .. 0.93
+   2 ?   -0.9   0.1       3.3       3.3      94     102 ..     146     154 ..     127     184 .. 0.56
+
+  Alignments for each domain:
+  == domain 1  score: 89.1 bits;  conditional E-value: 4.7e-028
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_D   2 qkvtqsqkslsvqegeevtldCsyetsdvllllknyalfWYkqlpsgslvllikqassllkkekkesdasklgrlsvkfqkkeksisLeisasqledsatYf 103
+              q+vtq +++lsv ege++ l+Cs++ s+       y l+W++q p+++l +l+  +ss    + +++     grl++ ++k+  +++L i+asq+ dsatY 
+     6FR3   3 QEVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS----QREQT---S-GRLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+              89**************************5......*****************999974....44444...3.9***************************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_D 104 CaleellllllklvFGtGielfVEP 128
+              Ca+ +    ++k +FG G++l V P
+     6FR3  91 CAVTN----FNKFYFGSGTKLNVKP 111
+              ****7....99************98 PP
+
+  == domain 2  score: -0.9 bits;  conditional E-value: 3.3
+              xxxxxxxxx RF
+  mouse_D  94 sqledsatY 102
+              sq +ds +Y
+     6FR3 146 SQSKDSDVY 154
+              333333333 PP
+
+>> mouse_B  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   70.0   0.0  3.1e-022  3.1e-022       2     126 ..       3     109 ..       2     110 .. 0.88
+   2 ?   -2.0   0.0       5.7       5.7      22      29 ..     158     165 ..     129     188 .. 0.61
+
+  Alignments for each domain:
+  == domain 1  score: 70.0 bits;  conditional E-value: 3.1e-022
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_B   2 agvtQtPrhlvkekGqkvtLkCeqksghllllllaeamyWYrqdlgkelkllvysqnglllkkaleksdlpkerfsasrplkksessLkiesaeledsavYl 103
+              ++vtQ P  l + +G+++ L+C+ + +         ++ W+rqd+gk+l+ l+ +q+        ++++++  r++as   ++ +s+L i + +++dsa+Yl
+     6FR3   3 QEVTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQS-------SQREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+              78**********************9999......799****************9999.......2333333.4666777767889***************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_B 104 CasselllllleqyFGeGtrLtV 126
+              Ca  +    +++ yFG+Gt+L V
+     6FR3  91 CAVTN----FNKFYFGSGTKLNV 109
+              ****9....89**********98 PP
+
+  == domain 2  score: -2.0 bits;  conditional E-value: 5.7
+              xxxxxxxx RF
+  mouse_B  22 kCeqksgh 29 
+              kC  ++++
+     6FR3 158 KCVLDMRS 165
+              34444444 PP
+
+>> human_B  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   64.0   0.0  2.2e-020  2.2e-020       2     126 ..       3     109 ..       2     110 .. 0.88
+
+  Alignments for each domain:
+  == domain 1  score: 64.0 bits;  conditional E-value: 2.2e-020
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_B   2 agvtQsPrykvtktgqkvtlrCsqisghllllllaetlyWYrqdlgqglelliysqegllleeatdksevpkdrfsaerplkkskstLklesaeledsavYl 103
+               +vtQ P  + + +g+++ l+Cs + +       + +l W+rqd+g+gl+ l+  q+    +++ + s     r +a+   ++ +stL + + +++dsa Yl
+     6FR3   3 QEVTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQS----SQREQTS----GRLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+              58*********************99999......899*************9999999....3333333....4456666656889***************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  human_B 104 CAsslllllllelyFGeGtrLtV 126
+              CA  +    +++ yFG+Gt+L V
+     6FR3  91 CAVTN----FNKFYFGSGTKLNV 109
+              ****9....89**********98 PP
+
+>> rhesus_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   58.9   0.1    1e-018    1e-018       2     126 ..       3     109 ..       2     110 .. 0.91
+   2 ?    0.4   0.1       1.2       1.2      10      43 ..     144     178 ..     137     188 .. 0.77
+
+  Alignments for each domain:
+  == domain 1  score: 58.9 bits;  conditional E-value: 1e-018
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_L   2 svltQppslvsaspgqsvrltCtgssskivlllgskyvsWyqqkpgqapklliyeksdlllsdskrpsgvpldRfsgskdasgntasLtisglqaeDEadY 102
+               +++tQ p+++s+  g++  l C+ + s+i      ++ +W++q pg+  + l+  +       s++ + ++  R+ +s d+s+ +++L i++ q+ D a Y
+      6FR3   3 QEVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ-------SSQREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATY 89 
+               689****99****************9996......89**********988888777.......45556677.799************************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_L 103 yCqswdlllllllvvFGeGTrLTv 126
+                C++++    ++   FG+GT+L v
+      6FR3  90 LCAVTN----FNKFYFGSGTKLNV 109
+               ******....78899*******86 PP
+
+  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
+               xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_L  10 lvsaspgqsvrlt..CtgssskivlllgskyvsWyq 43 
+               +vs+s+   v +t  C ++  ++  + ++++v+W  
+      6FR3 144 NVSQSKDSDVYITdkCVLDMRSM-DFKSNSAVAWSN 178
+               37888888888877799998886.577888899965 PP
+
+>> human_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   55.0   0.1  1.5e-017  1.5e-017       2     126 ..       3     109 ..       2     110 .. 0.90
+   2 ?    0.5   0.1       1.1       1.1      10      42 ..     144     177 ..     137     192 .. 0.79
+
+  Alignments for each domain:
+  == domain 1  score: 55.0 bits;  conditional E-value: 1.5e-017
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_L   2 svltqppslvsvspgqtvtltCtgsssevvlllgskyvsWyqqkpgkaPklliyeksdlllsdskrpsgvpldRfsgskdasgntasLtisglqaeDEadYY 103
+              +++tq p+++sv  g++  l C+ + s++      ++ +W+ q pgk  + l+  +       s++ + ++  R+ +s d s+ +++L i+  q+ D a Y 
+     6FR3   3 QEVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ-------SSQREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+              589****99***************99996......89**********999888888.......33444555.699*************************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  human_L 104 CaswdlllllllvvFGgGtkltv 126
+              Ca+++    ++   FG+Gtkl v
+     6FR3  91 CAVTN----FNKFYFGSGTKLNV 109
+              *****....77889*******88 PP
+
+  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
+              xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
+  human_L  10 lvsvspgqtvtlt..CtgsssevvlllgskyvsWy 42 
+              +vs+s  + v +t  C ++  ++  + ++ +v+W 
+     6FR3 144 NVSQSKDSDVYITdkCVLDMRSM-DFKSNSAVAWS 177
+              47888888888877799988886.58889999996 PP
+
+>> cow_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   52.1   0.2  1.2e-016  1.2e-016       3     126 ..       4     109 ..       2     110 .. 0.90
+   2 ?   -1.0   0.0       3.3       3.3      10      42 ..     144     177 ..     139     197 .. 0.70
+
+  Alignments for each domain:
+  == domain 1  score: 52.1 bits;  conditional E-value: 1.2e-016
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  cow_L   3 vLtqpsslvsgslGqtvsitCsgsssnvglllsensvsWyqqipgsaprtliyeksdlllsdskrasGvpldrfsgskdasgntatLtisglqaeDeaDYyCas 106
+            ++tq ++++s+  G++  + Cs ++s +      ++ +W+ q pg+++  l+  +     s+++++sG    r+ +s d s+  +tL i++ q+ D a Y Ca+
+   6FR3   4 EVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ----SSQREQTSG----RLNASLDKSSGRSTLYIAASQPGDSATYLCAV 93 
+            679*9999*****************997......799************999988....456777776....77899999************************ PP
+
+            xxxxxxxxxxxxxxxxxxxx RF
+  cow_L 107 adlllllllavFGsGttltv 126
+            ++    ++   FGsGt+l v
+   6FR3  94 TN----FNKFYFGSGTKLNV 109
+            **....66778******987 PP
+
+  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
+            xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
+  cow_L  10 lvsgslGqtvsit..CsgsssnvglllsensvsWy 42 
+            +vs+s    v it  C ++  ++  + s+  v W 
+   6FR3 144 NVSQSKDSDVYITdkCVLDMRSM-DFKSNSAVAWS 177
+            47777777777766677777775.36667777774 PP
+
+>> pig_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   52.3   0.1  1.2e-016  1.2e-016       1     126 [.       3     109 ..       3     110 .. 0.85
+
+  Alignments for each domain:
+  == domain 1  score: 52.3 bits;  conditional E-value: 1.2e-016
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  pig_L   1 qavliqePsllsvslgetvtltCalssgsvvlllssnyvsWyqqkPGrpPkyliyftfaslskdnsratgvplssfsgaillsgnkatLtisGlqaeDeaDyfC 104
+            q v +q P++lsv  ge   l C+++ + +      +++ W+ q PG+    l+  +  s  +++++  g    + s ++  s+ ++tL i+  q+ D a y C
+   6FR3   3 QEV-TQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ--SSQREQTS--GRL--NASLDK--SSGRSTLYIAASQPGDSATYLC 91 
+            566.9*********************9999......7************99999999..43444444..444..446666..77899***************** PP
+
+            xxxxxxxxxxxxxxxxxxxxxx RF
+  pig_L 105 allkllllllldrFGgGthLtv 126
+            a ++    ++   FG Gt+L v
+   6FR3  92 AVTN----FNKFYFGSGTKLNV 109
+            **99....66789*******98 PP
+
+>> mouse_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   51.1   0.1  2.4e-016  2.4e-016       3     127 ..       4     110 ..       2     111 .. 0.91
+
+  Alignments for each domain:
+  == domain 1  score: 51.1 bits;  conditional E-value: 2.4e-016
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_K   3 vltqspaslsvslgekvtisCkasqsilaskegssylaWyqqkpgqspklliyealllllllsnlasgvplsrfsgsgllsgtdftLtissveaedlatYyC 104
+               +tq pa lsv  ge+  ++C+ ++s         +l+W+ q pg+    l+          s++++  +  r+ +s   s    tL i   ++ d atY C
+     6FR3   4 EVTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQ-------SSQREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLC 91 
+              68********************99998......689**********999988888.......66777777.79999999999999***************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_K 105 qqsslllllllyTFGgGTKLEiK 127
+              + ++    ++ + FG+GTKL +K
+     6FR3  92 AVTN----FNKFYFGSGTKLNVK 110
+              *999....889**********99 PP
+
+>> rabbit_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   49.6   0.2  7.3e-016  7.3e-016       3     126 ..       4     109 ..       2     110 .. 0.90
+   2 ?    0.1   0.1       1.5       1.5       8      44 ..     142     179 ..     135     186 .. 0.79
+
+  Alignments for each domain:
+  == domain 1  score: 49.6 bits;  conditional E-value: 7.3e-016
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_L   3 vltqppslvsasLgqtarltCtlssgeivllleeyaveWyqqkpGkaPrlllykdtdllleikkrgsGvpldrFsgskdssgnsasLtisglqaeDeAdYy 103
+               ++tq p+++s+  g+   l C+ + + i      y ++W++q pGk  + ll  ++     +++++sG    r   s d+s+   +L i+  q++D A Y 
+      6FR3   4 EVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS----QREQTSG----RLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+               689*9999*************9998887......89***********9999888844....6778887....56899999********************* PP
+
+               xxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_L 104 CasaelllllllvvFGGGtqLtv 126
+               Ca+++    ++ + FG Gt+L v
+      6FR3  91 CAVTN----FNKFYFGSGTKLNV 109
+               ****9....77899*******98 PP
+
+  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
+               xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_L   8 pslvsasLgqtarlt..CtlssgeivllleeyaveWyqq 44 
+               +++vs s ++ + +t  C l+  ++  +  ++av W ++
+      6FR3 142 QTNVSQSKDSDVYITdkCVLDMRSM-DFKSNSAVAWSNK 179
+               5568999999999987798988886.5888899999765 PP
+
+>> rat_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   49.1   0.1    1e-015    1e-015       3     127 ..       4     110 ..       2     111 .. 0.89
+
+  Alignments for each domain:
+  == domain 1  score: 49.1 bits;  conditional E-value: 1e-015
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rat_K   3 qmtqspaslsvslgervtisCkasqdilksadgknylsWyqqkpgkspklliykalllllllsnlasgvplsrFsgsgllsgtdftltissleaedlavYyClq 106
+            ++tq pa lsv  ge+  ++C   ++         +l+W+ q pgk    l+          s+ ++  +  r  +s   s    tl i   ++ d a+Y C  
+   6FR3   4 EVTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQ-------SSQREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAV 93 
+            58*******************999998......567**********988777766.......56666667.79999998999999******************9 PP
+
+            xxxxxxxxxxxxxxxxxxxxx RF
+  rat_K 107 sklllllllltFGaGtkLElk 127
+            ++    ++ + FG+GtkL++k
+   6FR3  94 TN----FNKFYFGSGTKLNVK 110
+            99....78899********99 PP
+
+>> human_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   47.0   0.1  3.9e-015  3.9e-015       4     127 ..       5     110 ..       2     111 .. 0.84
+   2 ?   -1.7   0.0       4.7       4.7      85     105 ..     137     157 ..     120     178 .. 0.69
+
+  Alignments for each domain:
+  == domain 1  score: 47.0 bits;  conditional E-value: 3.9e-015
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_K   4 ltqsPsslsvsvgdrvtisCrasqsilesddgssylaWyqqkpgkapklliyaalllllllsslasGvPlsrfsGsGllsGtdftltissleaedvavyyCq 105
+              +tq P++lsv  g++  ++C  + s +       +l+W++q pgk  + l+          s+++      r+  s   s    tl i++ ++ d a+y C 
+     6FR3   5 VTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ------SSQREQTS--GRLNASLDKSSGRSTLYIAASQPGDSATYLCA 92 
+              8*******************9999984......56**********877666655......24444433..47777777777788****************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxx RF
+  human_K 106 qaklllllllltfGqGtkveik 127
+               ++    ++ + fG+Gtk+++k
+     6FR3  93 VTN----FNKFYFGSGTKLNVK 110
+              999....7889*********99 PP
+
+  == domain 2  score: -1.7 bits;  conditional E-value: 4.7
+              xxxxxxxxxxxxxxxxxxxxx RF
+  human_K  85 tdftltissleaedvavyyCq 105
+              tdf  + +  +++d  vy   
+     6FR3 137 TDFDSQTNVSQSKDSDVYITD 157
+              666666666667776666544 PP
+
+>> rat_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   44.0   0.1  3.9e-014  3.9e-014       3     126 ..       4     109 ..       2     110 .. 0.90
+   2 ?   -1.6   0.1       5.1       5.1      11      42 ..     145     177 ..     139     192 .. 0.64
+
+  Alignments for each domain:
+  == domain 1  score: 44.0 bits;  conditional E-value: 3.9e-014
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rat_L   3 vltqpnslvstslgstvklsCkrstgnitlllgsnYvnWyqqkedrsivtviykdllllllldkrpdgvpldrfsGsidsssnsaaLtitnvqieDeadYfCqs 106
+            ++tq ++++s+  g+ + l C+  + +i         +W++q +++ +++++  +       ++r +  +  r   s+d+ss++++L i   q  D a+Y C  
+   6FR3   4 EVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ------SSQREQ-TS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAV 93 
+            79999999*******************9......4589*************9988......466655.56.6******************************** PP
+
+            xxxxxxxxxxxxxxxxxxxx RF
+  rat_L 107 yslllllllPvfGGGtkLtv 126
+            ++    ++   fG GtkL v
+   6FR3  94 TN----FNKFYFGSGTKLNV 109
+            *9....66778*******98 PP
+
+  == domain 2  score: -1.6 bits;  conditional E-value: 5.1
+            xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
+  rat_L  11 vstslgstvkls..CkrstgnitlllgsnYvnWy 42 
+            vs s  s v ++  C+ +  ++  + +++ v W 
+   6FR3 145 VSQSKDSDVYITdkCVLDMRSM-DFKSNSAVAWS 177
+            5555556555544477777776.45666666665 PP
+
+>> pig_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   43.7   0.2  4.4e-014  4.4e-014       4     127 ..       5     110 ..       3     111 .. 0.83
+   2 ?   -2.7   0.0       9.6       9.6      85     103 ..     137     155 ..     118     173 .. 0.67
+
+  Alignments for each domain:
+  == domain 1  score: 43.7 bits;  conditional E-value: 4.4e-014
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  pig_K   4 ltqsPlslsvslGetvsiscrssqslesslygsnylaWyqqkpGksPk.lliyeallllllltnrasGvPldrfkGsgllsGtdftlkisrleaedvavyycqq 106
+            +tq P++lsv  Ge   + c  + s         +l+W++q pGk    ll+ ++       ++r+      r++ s   s    tl i+  +  d a+y c  
+   6FR3   5 VTQIPAALSVPEGENLVLNCSFTDSA------IYNLQWFRQDPGKGLTsLLLIQS-------SQREQTSG--RLNASLDKSSGRSTLYIAASQPGDSATYLCAV 93 
+            79******************999887......357**********8641555555.......34433333..6778877788899******************9 PP
+
+            xxxxxxxxxxxxxxxxxxxxx RF
+  pig_K 107 aklllllllvtfGsGtklelk 127
+            ++    ++ + fGsGtkl++k
+   6FR3  94 TN----FNKFYFGSGTKLNVK 110
+            99....7889********998 PP
+
+  == domain 2  score: -2.7 bits;  conditional E-value: 9.6
+            xxxxxxxxxxxxxxxxxxx RF
+  pig_K  85 tdftlkisrleaedvavyy 103
+            tdf  +    ++ d  vy 
+   6FR3 137 TDFDSQTNVSQSKDSDVYI 155
+            5555555555666666664 PP
+
+>> rhesus_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   42.9   0.1  8.2e-014  8.2e-014       4     127 ..       5     110 ..       3     111 .. 0.85
+
+  Alignments for each domain:
+  == domain 1  score: 42.9 bits;  conditional E-value: 8.2e-014
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_K   4 mtqspsslsvsvgervtlisCrasqsilesddgssylaWyqqkpgkaPklliykalllllllssresgvpldrfsGsgllsgtdftltisslepedvavyy 104
+               +tq p++lsv  ge+   + C  ++s         +l+W++q pgk    l+          s+re+  +  r++ s   s    tl i+  +p d a+y 
+      6FR3   5 VTQIPAALSVPEGENLV-LNCSFTDSA------IYNLQWFRQDPGKGLTSLLLIQ------SSQREQ-TS-GRLNASLDKSSGRSTLYIAASQPGDSATYL 90 
+               79***************.***999988......566**********988777666......244444.34.58888887888888**************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_K 105 CqqelllllllWtfGqGtkveik 127
+               C  +   +++ + fG Gtk ++k
+      6FR3  91 CAVT---NFNKFYFGSGTKLNVK 110
+               *999...788899*******999 PP
+
+>> mouse_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   42.2   0.1  1.3e-013  1.3e-013       4     126 ..       5     109 ..       2     110 .. 0.88
+
+  Alignments for each domain:
+  == domain 1  score: 42.2 bits;  conditional E-value: 1.3e-013
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_L   4 vtqesallttslGatvkltCrsstgavtllltsnyaeWvqekpdklfkgvigltkdlllgssnradGvPlarfsGsllliGdkaaltitgaqtedeaiyiCa 105
+              vtq  a+l++  G+  +l C  +  a+      +  +W+++ p k  + ++  +      ss+r +     r+  sl  +     l i+  q+ d a y+Ca
+     6FR3   5 VTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQ------SSQREQTS--GRLNASLDKSSGRSTLYIAASQPGDSATYLCA 92 
+              8999999*************8876666......899**********99999888......45555554..59999999999999****************** PP
+
+              xxxxxxxxxxxxxxxxxxxxx RF
+  mouse_L 106 lwylllllllyvfGgGtkvtv 126
+              + +    ++ + fG+Gtk+ v
+     6FR3  93 VTN----FNKFYFGSGTKLNV 109
+              ***....889********987 PP
+
+>> cow_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   40.8   0.1  3.5e-013  3.5e-013       4     127 ..       5     110 ..       2     111 .. 0.88
+
+  Alignments for each domain:
+  == domain 1  score: 40.8 bits;  conditional E-value: 3.5e-013
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  cow_K   4 ltqtPlslsvilGetvsisckstqslkysldgktylrWlqqkPGqsPklliyqvlllllllsnrytgvpldrftgsgllsetdftltissveaedaavyyclqd 107
+            +tq P+ lsv  Ge++ + c  t s  y+      l+W++q PG+   +l+          s+r  + +  r+ +s   s    tl i+  +  d+a+y c   
+   6FR3   5 VTQIPAALSVPEGENLVLNCSFTDSAIYN------LQWFRQDPGKGLTSLLLIQ------SSQRE-QTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVT 94 
+            89************************997......**********998887655......35555.555.699999999999*******************998 PP
+
+            xxxxxxxxxxxxxxxxxxxx RF
+  cow_K 108 tlllllllntfGqGtkveik 127
+                 ++   fG Gtk+++k
+   6FR3  95 N----FNKFYFGSGTKLNVK 110
+            8....566789******998 PP
+
+>> rabbit_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   40.8   0.1  3.5e-013  3.5e-013       3     127 ..       4     110 ..       2     111 .. 0.78
+
+  Alignments for each domain:
+  == domain 1  score: 40.8 bits;  conditional E-value: 3.5e-013
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_K   3 vltqtpasvsaavGGtvtincqasqsvylllldnsylswyqqkpGqppk.lliysalllllllsklasGvplsrfsGsGllsGtqftltisGvqcddaaty 102
+                +tq pa+ s + G  + +nc  ++s          l+w++q pG+    ll+ ++     +           r++ s   s  + tl i+  q  d+aty
+      6FR3   4 EVTQIPAALSVPEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTsLLLIQSSQREQTS---------GRLNASLDKSSGRSTLYIAASQPGDSATY 89 
+               58*******************9988753......48*********975414444442222222.........35555555555688*************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_K 103 ycqgsyllllllsltfGaGtkveik 127
+                c+ +     +++  fG+Gtk+++k
+      6FR3  90 LCAVTN----FNKFYFGSGTKLNVK 110
+               ***999....67789********99 PP
+
+>> rhesus_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   36.9   0.0  6.4e-012  6.4e-012      10     125 ..      10     108 ..       2     110 .. 0.82
+   2 ?   -2.5   0.1       9.6       9.6      87      97 ..     157     167 ..     136     184 .. 0.56
+
+  Alignments for each domain:
+  == domain 1  score: 36.9 bits;  conditional E-value: 6.4e-012
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_H  10 lglvkPggeslrlsCaaslGftfsllsssyalsWvrqapgkglewvgaisskaesgsteyadslklgrvtisrdtskntlylqlsslkaeDtAvyYCarll 110
+               ++l  P ge l l C+++   ++      y l+W rq pgkgl  +  i+s+         ++   gr+  s d+s     l +   +  D A+y Ca  +
+      6FR3  10 AALSVPEGENLVLNCSFT-DSAI------YNLQWFRQDPGKGLTSLLLIQSS-------QREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAV-T 94 
+               4788999********888.5555......9*******************999.......233445.8999****************************9.4 PP
+
+               xxxxxxxxxxxxxxx RF
+  rhesus_H 111 llllfdvWGqGvlvt 125
+               +++ f ++G G+ + 
+      6FR3  95 NFNKF-YFGSGTKLN 108
+               44444.678887765 PP
+
+  == domain 2  score: -2.5 bits;  conditional E-value: 9.6
+               xxxxxxxxxxx RF
+  rhesus_H  87 ntlylqlsslk 97 
+               ++++l++ s++
+      6FR3 157 DKCVLDMRSMD 167
+               33444444443 PP
+
+>> mouse_G  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   32.7   0.0  9.6e-011  9.6e-011      15     128 .]      16     111 ..       5     111 .. 0.84
+   2 ?    2.0   0.0      0.31      0.31       8      42 ..     142     177 ..     120     188 .. 0.73
+
+  Alignments for each domain:
+  == domain 1  score: 32.7 bits;  conditional E-value: 9.6e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_G  15 kdesaqisCkvslsvlklllsntaiHWYrqkkgqalerllyvstkllsevkvvekdfkdeklevsekfkdststlkinnvkeeDeatYYCAvWallllllhk 116
+              ++e+  ++C+ + s +        + W+rq +g+ l  ll  ++         ++++ + +l++s + ++ +stl i   +  D+atY CAv +    +++ 
+     6FR3  16 EGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS--------QREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTN----FNKF 99 
+              5667777777777776......4579**************99973........455678899***999************************99....5555 PP
+
+              xxxxxxxxxxxx RF
+  mouse_G 117 vFAeGtkLiviP 128
+               F  GtkL v P
+     6FR3 100 YFGSGTKLNVKP 111
+              79******8866 PP
+
+  == domain 2  score: 2.0 bits;  conditional E-value: 0.31
+              xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
+  mouse_G   8 elsvtrrkdesaqi..sCkvslsvlklllsntaiHWY 42 
+              +  v + kd+ ++i  +C + +  +  + sn+a+ W 
+     6FR3 142 QTNVSQSKDSDVYItdKCVLDMRSM-DFKSNSAVAWS 177
+              3445555666666622587777776.57788888885 PP
+
+>> mouse_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   35.2   0.0  1.9e-011  1.9e-011      14     126 ..      15     109 ..       4     111 .. 0.80
+   2 ?   -2.2   0.1       6.9       6.9      95     106 ..     147     158 ..     126     183 .. 0.63
+
+  Alignments for each domain:
+  == domain 1  score: 35.2 bits;  conditional E-value: 1.9e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_H  14 kpgaslklsCkasgftlsllatsyamsWvrqspgkglewigeisskaesgstkyneklklgratlsrdkskstlylqlssltsedtavyyCareallllllf 115
+                g+ l l C+ ++ ++      y+++W rq pgkgl  +  i+s+         e+   gr+  s dks+ +  l +   +  d+a+y Ca +    +++ 
+     6FR3  15 PEGENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS-------QREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVT----NFNK 98 
+              45788899999888888......9*******************999.......234445.7777788888777777778889**********93....3334 PP
+
+              xxxxxxxxxxx RF
+  mouse_H 116 dyWGqGttvtv 126
+               y+G Gt + v
+     6FR3  99 FYFGSGTKLNV 109
+              499****9987 PP
+
+  == domain 2  score: -2.2 bits;  conditional E-value: 6.9
+              xxxxxxxxxxxx RF
+  mouse_H  95 tsedtavyyCar 106
+              +s+d+ vy   +
+     6FR3 147 QSKDSDVYITDK 158
+              444555544433 PP
+
+>> human_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   34.4   0.0  3.8e-011  3.8e-011      16     124 ..      17     107 ..       5     110 .. 0.79
+   2 ?   -1.6   0.1       4.9       4.9      84      95 ..     156     167 ..     127     189 .. 0.57
+
+  Alignments for each domain:
+  == domain 1  score: 34.4 bits;  conditional E-value: 3.8e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_H  16 geslklsCaasGftlsllsssyalsWvrqapgkgLewvglisssaesgsteYaeslklgrvtisrdtskntlylqlsslraeDtavYyCarklllllllfdv 117
+              ge l l C++   ++      y l+W rq pgkgL  + li+ss  +      e+   gr+  s d+s     l +++ ++ D a+Y Ca +   +++   +
+     6FR3  17 GENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS--Q-----REQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVT---NFNK-FY 100
+              566667776665555......9*******************999..2.....23344.8999****************************93...2223.36 PP
+
+              xxxxxxx RF
+  human_H 118 WGqGtlv 124
+              +G Gt  
+     6FR3 101 FGSGTKL 107
+              7888865 PP
+
+  == domain 2  score: -1.6 bits;  conditional E-value: 4.9
+              xxxxxxxxxxxx RF
+  human_H  84 kntlylqlsslr 95 
+              +++ +l++ s++
+     6FR3 156 TDKCVLDMRSMD 167
+              233334444443 PP
+
+>> alpaca_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   30.9   0.0  5.1e-010  5.1e-010      16     126 ..      17     109 ..       7     111 .. 0.82
+   2 ?   -0.4   0.1       2.4       2.4      89     112 ..     141     163 ..     120     186 .. 0.73
+
+  Alignments for each domain:
+  == domain 1  score: 30.9 bits;  conditional E-value: 5.1e-010
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  alpaca_H  16 ggslrlscaasGstftlltssyamswvrqaPGkglelvaaisldllgGstyyadsvklgrftisrdnakntlylqlnslkpedtavyycakllllllllld 116
+               g+ l l c+ + s++      y ++w+rq PGkgl  +  i+++         +    gr+  s d++  +  l +++ +p d+a y ca     ++++  
+      6FR3  17 GENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS-------QREQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAV----TNFNKF 99 
+               666777776665555......**************999999988.......345555.99********9999999***************9....344445 PP
+
+               xxxxxxxxxx RF
+  alpaca_H 117 awGqGtlvtv 126
+               ++G Gt++ v
+      6FR3 100 YFGSGTKLNV 109
+               8999998876 PP
+
+  == domain 2  score: -0.4 bits;  conditional E-value: 2.4
+               xxxxxxxxxxxxxxxxxxxxxxxx RF
+  alpaca_H  89 lqlnslkpedtavyycakllllll 112
+                q n  +++d+ vy   k ++l +
+      6FR3 141 SQTNVSQSKDSDVYITDK-CVLDM 163
+               577777888888888877.33333 PP
+
+>> rabbit_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   28.9   0.0  1.8e-009  1.8e-009      16     122 ..      17     105 ..       4     110 .. 0.77
+
+  Alignments for each domain:
+  == domain 1  score: 28.9 bits;  conditional E-value: 1.8e-009
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_H  16 gdtLtltCtvsGfslslllssyavsWvrqapGkglewiglisssslsgstyyaswaklsrstisrntnentvtLkmtsltaaDtatyfCaralllllllld 116
+               g+ L l C  +  ++      y+++W rq pGkgl  + li+ss           ++ +r   s +++    tL +++    D aty+Ca +++    +  
+      6FR3  17 GENLVLNCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS---QR----EQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNF----NKF 99 
+               567888887777777......********************999...22....2334.777788888888999*****************9222....122 PP
+
+               xxxxxx RF
+  rabbit_H 117 lWGqGt 122
+                +G+Gt
+      6FR3 100 YFGSGT 105
+               356666 PP
+
+>> pig_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   28.9   0.1    2e-009    2e-009      30     109 ..      26      96 ..      11     110 .. 0.79
+
+  Alignments for each domain:
+  == domain 1  score: 28.9 bits;  conditional E-value: 2e-009
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  pig_H  30 fllllssyavswvrqapgkglewlaaissssysgstyyadsvklgrftisrddsqntaylqmnslrtedtaryycarlll 109
+            f +  + y+++w rq pgkgl +l  i+ss+        +    gr+  s d+s   + l + + +  d+a y ca +++
+   6FR3  26 F-TDSAIYNLQWFRQDPGKGLTSLLLIQSSQR-------EQTS-GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNF 96 
+            3.3456799********************933.......3445.9*******************************9332 PP
+
+>> cow_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   25.7   0.1  1.6e-008  1.6e-008      26     108 ..      27      95 ..       9     110 .. 0.76
+   2 ?   -1.9   0.0       5.1       5.1      26      42 ..     162     177 ..     137     193 .. 0.64
+
+  Alignments for each domain:
+  == domain 1  score: 25.7 bits;  conditional E-value: 1.6e-008
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  cow_H  26 sGfslllllssyavgwvrqapGkalewlGgissglllGstgynpalklsrlsitkdnsksqvslsvssvttedtatyycakvk 108
+            +        + y ++w rq pGk l  l  i+s     +t         rl  + d s  + +l +++  + d+aty ca ++
+   6FR3  27 TD------SAIYNLQWFRQDPGKGLTSLLLIQSS-QREQT-------SGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTN 95 
+            33......345999*****************999.22222.......2578888899999999*****************844 PP
+
+  == domain 2  score: -1.9 bits;  conditional E-value: 5.1
+            xxxxxxxxxxxxxxxxx RF
+  cow_H  26 sGfslllllssyavgwv 42 
+               s+  + s+ av+w 
+   6FR3 162 DMRSM-DFKSNSAVAWS 177
+            44444.44555566664 PP
+
+>> human_G  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   22.4   0.0  1.5e-007  1.5e-007      22     126 ..      23     109 ..      13     110 .. 0.75
+   2 ?   -2.1   0.0       5.8       5.8      22      41 ..     158     176 ..     140     181 .. 0.62
+
+  Alignments for each domain:
+  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-007
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_G  22 tCdlsvinillllsatyihWYlhqeGkapqrLlyydsdllnskvvlesGissgkyetdasperkslklilrnlienDsgvYYCatWdlllllliklfgsGtk 123
+              +C  +  +i        + W+++ +Gk    Ll ++s+    +  + sG    + +         ++l +      Ds++Y Ca+ +    +++  fgsGtk
+     6FR3  23 NCSFTDSAI------YNLQWFRQDPGKGLTSLLLIQSS----QREQTSG----RLNASLDKSSGRSTLYIAASQPGDSATYLCAVTN----FNKFYFGSGTK 106
+              444444443......5589****************999....4444555....44433333356788999999************99....67779****** PP
+
+              xxx RF
+  human_G 124 Liv 126
+              L v
+     6FR3 107 LNV 109
+              976 PP
+
+  == domain 2  score: -2.1 bits;  conditional E-value: 5.8
+              xxxxxxxxxxxxxxxxxxxx RF
+  human_G  22 tCdlsvinillllsatyihW 41 
+              +C+l   + + + s+  + W
+     6FR3 158 KCVLDMRS-MDFKSNSAVAW 176
+              47777777.46677777777 PP
+
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query sequence(s):                         1  (202 residues searched)
+Target model(s):                          29  (3712 nodes)
+Passed MSV filter:                        29  (1); expected 0.6 (0.02)
+Passed bias filter:                       29  (1); expected 0.6 (0.02)
+Passed Vit filter:                        29  (1); expected 0.0 (0.001)
+Passed Fwd filter:                        29  (1); expected 0.0 (1e-005)
+Initial search space (Z):                 29  [actual number of targets]
+Domain search space  (domZ):              29  [number of targets reported over threshold]
+# CPU time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00
+# Mc/sec: inf
+//
+Query:       6FR3  [L=244]
+Scores for complete sequence (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
+    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
+   1.1e-043  139.2   0.1   2.4e-043  138.2   0.1    1.5  1  human_B   
+   1.4e-038  122.9   0.1   3.3e-038  121.7   0.1    1.6  1  mouse_B   
+   6.2e-025   78.6   0.0   1.2e-024   77.7   0.0    1.5  1  human_A   
+     7e-025   78.4   0.1   1.2e-024   77.6   0.1    1.4  1  mouse_A   
+   6.8e-022   68.8   0.0   1.8e-021   67.4   0.0    1.7  2  human_D   
+   9.2e-022   68.7   0.5   3.5e-021   66.8   0.3    1.9  2  rhesus_L  
+   1.5e-020   64.7   0.4   4.8e-020   63.1   0.3    1.8  2  human_L   
+   1.4e-019   61.5   0.2   2.7e-019   60.7   0.2    1.4  1  cow_L     
+   4.3e-019   60.1   0.0   1.3e-018   58.6   0.0    1.7  2  mouse_D   
+   6.4e-019   59.4   0.4   4.4e-018   56.7   0.2    2.0  2  mouse_K   
+   2.1e-018   57.8   0.2   3.3e-018   57.2   0.2    1.3  1  rabbit_L  
+   4.3e-018   57.0   0.4   9.1e-018   56.0   0.2    1.6  1  pig_L     
+   7.5e-018   56.0   0.2   2.3e-017   54.4   0.1    1.7  2  rat_K     
+   1.1e-017   55.2   0.6   7.5e-017   52.6   0.4    2.0  2  human_K   
+   5.5e-016   49.9   0.3   1.9e-015   48.2   0.3    1.8  2  rhesus_K  
+   3.3e-015   47.3   0.1   5.9e-015   46.5   0.1    1.4  1  cow_K     
+   1.5e-014   45.2   0.4   2.6e-014   44.4   0.4    1.3  1  pig_K     
+   9.2e-014   42.6   0.1   2.1e-013   41.5   0.1    1.6  1  mouse_L   
+   1.7e-013   42.0   0.5   2.5e-013   41.4   0.1    1.5  1  rat_L     
+   2.8e-012   37.8   0.2   4.7e-012   37.1   0.2    1.4  1  rabbit_K  
+   1.3e-011   35.5   0.0   2.5e-011   34.6   0.0    1.4  1  mouse_G   
+   1.5e-011   35.5   0.0   3.7e-011   34.2   0.0    1.7  1  mouse_H   
+   1.6e-011   35.6   0.0   3.5e-011   34.5   0.0    1.6  1  human_H   
+     2e-011   34.9   0.0     3e-011   34.4   0.0    1.2  1  human_G   
+   2.9e-010   31.5   0.0   5.5e-010   30.6   0.0    1.5  1  rhesus_H  
+   7.1e-009   26.8   0.2   2.3e-008   25.1   0.0    1.9  2  cow_H     
+   1.1e-008   26.3   0.0   6.7e-008   23.8   0.0    2.0  2  rabbit_H  
+   5.9e-008   24.2   0.0   1.8e-007   22.6   0.0    1.8  1  alpaca_H  
+     3e-007   21.9   0.0   6.5e-007   20.8   0.0    1.6  1  pig_H     
+
+
+Domain annotation for each model (and alignments):
+>> human_B  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  138.2   0.1  2.4e-043  2.4e-043       1     127 [.       2     114 ..       2     115 .. 0.98
+
+  Alignments for each domain:
+  == domain 1  score: 138.2 bits;  conditional E-value: 2.4e-043
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_B   1 eagvtQsPrykvtktgqkvtlrCsqisghllllllaetlyWYrqdlgqglelliysqegllleeatdksevpkdrfsaerplkkskstLklesaeledsavY 102
+              +agvtQ+Pry+++++gq+vtl+Cs+isgh       ++++WY+q++gqgl++l+ + +    e++++k+++p  rfs +++ ++s+s+++++++el+dsa+Y
+     6FR3   2 KAGVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFS----ETQRNKGNFP-GRFSGRQF-SNSRSEMNVSTLELGDSALY 90 
+              599**************************.......**********************....**********.********.******************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_B 103 lCAsslllllllelyFGeGtrLtVl 127
+              lCAss    ++ +l+FG+GtrLtV+
+     6FR3  91 LCASSF-DSGNSPLHFGNGTRLTVT 114
+              *****7.99999************7 PP
+
+>> mouse_B  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  121.7   0.1  3.3e-038  3.3e-038       2     127 ..       3     114 ..       2     114 .. 0.97
+
+  Alignments for each domain:
+  == domain 1  score: 121.7 bits;  conditional E-value: 3.3e-038
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_B   2 agvtQtPrhlvkekGqkvtLkCeqksghllllllaeamyWYrqdlgkelkllvysqnglllkkaleksdlpkerfsasrplkksessLkiesaeledsavYl 103
+              agvtQtPr+l+k++Gq+vtL+C+++sgh        ++ WY+q++g++l++l+ + +    + + +k+++p  rfs ++  ++s+s+++++++el+dsa+Yl
+     6FR3   3 AGVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFS----ETQRNKGNFP-GRFSGRQF-SNSRSEMNVSTLELGDSALYL 91 
+              79**************************.......**********************....99********.********.********************* PP
+
+              xxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_B 104 CasselllllleqyFGeGtrLtVl 127
+              Cass    ++  + FG+GtrLtV+
+     6FR3  92 CASSF-DSGNSPLHFGNGTRLTVT 114
+              ****6.99999************6 PP
+
+>> human_A  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   77.7   0.0  1.2e-024  1.2e-024       3     127 ..       4     114 ..       2     115 .. 0.89
+
+  Alignments for each domain:
+  == domain 1  score: 77.7 bits;  conditional E-value: 1.2e-024
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_A   3 kveqspqslsvqEgesvtlnCtystsatlllllseylfWYkqepgkglqllikllsalldeeekkklllllgrlsatlnkseksssLkitasqlsdsAvYfC 104
+               v+q+p  l+ + g++vtl+C+  +         +++ WY+q pg+glq+l+++ s+   +++k +   + gr+s     s+++s ++++  +l+dsA Y+C
+     6FR3   4 GVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFSE--TQRNKGN---FPGRFSGRQ-FSNSRSEMNVSTLELGDSALYLC 92 
+              69*******************977666.......9********************97..6677777...889998753.3468999**************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  human_A 105 avsellllllkliFGkGTrLtVk 127
+              a s +  ++  l FG+GTrLtV+
+     6FR3  93 ASS-FDSGNSPLHFGNGTRLTVT 114
+              **9.899999***********96 PP
+
+>> mouse_A  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   77.6   0.1  1.2e-024  1.2e-024       3     127 ..       4     114 ..       2     115 .. 0.89
+
+  Alignments for each domain:
+  == domain 1  score: 77.6 bits;  conditional E-value: 1.2e-024
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_A   3 kveqspesltvqegesvtlnCsystsavllllaseylfWYkqepgeglqlLlkivsalldeekkeslllllgrfeatlnkseksssLhitsvqlsDsAvYfC 104
+               v+q+p  l  + g++vtl+Cs  + +       +++ WY+q+pg+glq+L++++s+  ++++k +   + grf+   + s+++s++++++ +l DsA+Y+C
+     6FR3   4 GVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFSE--TQRNKGN---FPGRFSG-RQFSNSRSEMNVSTLELGDSALYLC 92 
+              69*******************976666.......9*********************7..5555555...8899976.57788999***************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_A 105 alsellllllkltFGkGTkLtvk 127
+              a s +  ++  l+FG+GT+Ltv+
+     6FR3  93 ASS-FDSGNSPLHFGNGTRLTVT 114
+              ***.899999***********96 PP
+
+>> human_D  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   67.4   0.0  1.8e-021  1.8e-021       4     127 ..       5     114 ..       2     115 .. 0.87
+   2 ?   -2.2   0.0         6         6       9      29 ..     131     151 ..     127     168 .. 0.70
+
+  Alignments for each domain:
+  == domain 1  score: 67.4 bits;  conditional E-value: 1.8e-021
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_D   4 vtqsqpslsvqegeavtLnCsyetsasllllgnyylfWYkqepskeitflirqksslldkqekkedakklgrfsvkldkaaksasLkIsasqlgDsatYfCA 105
+              vtq++  l+   g++vtL+Cs          g++++ WY+q+p+++++fl+   s+   +++k +  +  grfs   + ++  + +++s  +lgDsa Y+CA
+     6FR3   5 VTQTPRYLIKTRGQQVTLSCSPI-------SGHRSVSWYQQTPGQGLQFLFEYFSE--TQRNKGN--FP-GRFSGR-QFSNSRSEMNVSTLELGDSALYLCA 93 
+              99******************843.......4789*****************99986..4555554..66.9***97.677888899**************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxx RF
+  human_D 106 leellllllqliFGkGtkliVe 127
+               + +  ++ +l FG Gt+l+V 
+     6FR3  94 SS-FDSGNSPLHFGNGTRLTVT 114
+              *8.79999************95 PP
+
+  == domain 2  score: -2.2 bits;  conditional E-value: 6
+              xxxxxxxxxxxxxxxxxxxxx RF
+  human_D   9 pslsvqegeavtLnCsyetsa 29 
+              ++  +++ +++tL C  ++  
+     6FR3 131 SEAEISHTQKATLVCLATGFF 151
+              566788889999999876655 PP
+
+>> rhesus_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   66.8   0.3  3.5e-021  3.5e-021       3     126 ..       4     113 ..       2     114 .. 0.89
+   2 ?   -1.0   0.0       3.3       3.3       7      28 ..     129     150 ..     124     169 .. 0.73
+
+  Alignments for each domain:
+  == domain 1  score: 66.8 bits;  conditional E-value: 3.5e-021
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_L   3 vltQppslvsaspgqsvrltCtgssskivlllgskyvsWyqqkpgqapklliyeksdlllsdskrpsg.vpldRfsgskdasgntasLtisglqaeDEadY 102
+                +tQ p ++ ++ gq+v+l+C+  s++       ++vsWyqq+pgq  + l  +      s+++r+ g  p  Rfsg +  s +++ + +s l+  D a Y
+      6FR3   4 GVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYF-----SETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALY 90 
+               68*******************999888.......57*************999998.....55888877256.******9.7777888************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_L 103 yCqswdlllllllvvFGeGTrLTv 126
+                C+s     ++    FG+GTrLTv
+      6FR3  91 LCASSF-DSGNSPLHFGNGTRLTV 113
+               **9988.78888999********9 PP
+
+  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
+               xxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_L   7 ppslvsaspgqsvrltCtgsss 28 
+               +ps +  s  q+++l C  +  
+      6FR3 129 EPSEAEISHTQKATLVCLATGF 150
+               6777888999999999977654 PP
+
+>> human_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   63.1   0.3  4.8e-020  4.8e-020       3     126 ..       4     113 ..       2     114 .. 0.89
+   2 ?   -1.8   0.0       5.7       5.7       7      25 ..     129     147 ..     125     162 .. 0.77
+
+  Alignments for each domain:
+  == domain 1  score: 63.1 bits;  conditional E-value: 4.8e-020
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_L   3 vltqppslvsvspgqtvtltCtgsssevvlllgskyvsWyqqkpgkaPklliyeksdlllsdskrpsg.vpldRfsgskdasgntasLtisglqaeDEadYY 103
+               +tq p ++ ++ gq+vtl+C+  s++       + vsWyqq+pg+  + l  + s     +++r+ g  p  Rfsg +  s +++ + +s l+  D a Y 
+     6FR3   4 GVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFS-----ETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYL 91 
+              589****9*************998888.......57***************99994.....5777776256.9*****9.8899999*************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  human_L 104 CaswdlllllllvvFGgGtkltv 126
+              Cas     ++    FG Gt+ltv
+     6FR3  92 CASSF-DSGNSPLHFGNGTRLTV 113
+              **998.78888999********9 PP
+
+  == domain 2  score: -1.8 bits;  conditional E-value: 5.7
+              xxxxxxxxxxxxxxxxxxx RF
+  human_L   7 ppslvsvspgqtvtltCtg 25 
+              +ps +  s  q++tl C  
+     6FR3 129 EPSEAEISHTQKATLVCLA 147
+              5676888999999999975 PP
+
+>> cow_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   60.7   0.2  2.7e-019  2.7e-019       3     126 ..       4     113 ..       2     114 .. 0.88
+
+  Alignments for each domain:
+  == domain 1  score: 60.7 bits;  conditional E-value: 2.7e-019
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  cow_L   3 vLtqpsslvsgslGqtvsitCsgsssnvglllsensvsWyqqipgsaprtliyeksdlllsdskrasG.vpldrfsgskdasgntatLtisglqaeDeaDYyCa 105
+             +tq + ++  + Gq+v+++Cs  s++        svsWyqq+pg++++ l         s+++r+ G  p  rfsg +  s+  + + +s+l+  D a Y Ca
+   6FR3   4 GVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYF-----SETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLCA 93 
+            67999999*************998887.......57*************998665.....67888888356.*****99.9*********************** PP
+
+            xxxxxxxxxxxxxxxxxxxxx RF
+  cow_L 106 sadlllllllavFGsGttltv 126
+            s     ++    FG Gt+ltv
+   6FR3  94 SSF-DSGNSPLHFGNGTRLTV 113
+            987.57777788********9 PP
+
+>> mouse_D  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   58.6   0.0  1.3e-018  1.3e-018       3     126 ..       4     113 ..       2     114 .. 0.87
+   2 ?   -1.5   0.0         5         5      10      44 ..     132     162 ..     128     199 .. 0.70
+
+  Alignments for each domain:
+  == domain 1  score: 58.6 bits;  conditional E-value: 1.3e-018
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_D   3 kvtqsqkslsvqegeevtldCsyetsdvllllknyalfWYkqlpsgslvllikqassllkkekkesdasklgrlsvkfqkkeksisLeisasqledsatYfC 104
+               vtq+++ l  + g++vtl+Cs  + +       ++++WY+q+p+++l++l++  s+     +++++    gr+s   q +++++ +++s+ +l dsa Y C
+     6FR3   4 GVTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFSE-----TQRNKGNFPGRFSGR-QFSNSRSEMNVSTLELGDSALYLC 92 
+              599*******************88877.......79*****************9974.....444433345888875.67788899**************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_D 105 aleellllllklvFGtGielfV 126
+              a++ +  ++  l FG G+ l+V
+     6FR3  93 ASS-FDSGNSPLHFGNGTRLTV 113
+              ***.599999***********9 PP
+
+  == domain 2  score: -1.5 bits;  conditional E-value: 5
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_D  10 slsvqegeevtldCsyetsdvllllknyalfWYkq 44 
+              + +++  +++tl C  ++       +   l+W+  
+     6FR3 132 EAEISHTQKATLVCLATGFFP----DHVELSWWVN 162
+              556677778888887665543....5667777755 PP
+
+>> mouse_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   56.7   0.2  4.4e-018  4.4e-018       4     126 ..       5     113 ..       2     114 .. 0.89
+   2 ?    0.4   0.0       1.1       1.1       8      42 ..     130     160 ..     125     169 .. 0.75
+
+  Alignments for each domain:
+  == domain 1  score: 56.7 bits;  conditional E-value: 4.4e-018
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_K   4 ltqspaslsvslgekvtisCkasqsilaskegssylaWyqqkpgqspklliyealllllllsnlasg.vplsrfsgsgllsgtdftLtissveaedlatYyC 104
+              +tq+p +l  + g++vt+sC+    i    +g+++++Wyqq pgq  + l  +        +++++g  p  rfsg   +s++   +++s++e  d a Y C
+     6FR3   5 VTQTPRYLIKTRGQQVTLSCSP---I----SGHRSVSWYQQTPGQGLQFLFEYF-----SETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLC 92 
+              8*******************86...5....35689****************999.....44555555277.******9.999******************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_K 105 qqsslllllllyTFGgGTKLEi 126
+              + s    ++  + FG GT+L +
+     6FR3  93 ASSF-DSGNSPLHFGNGTRLTV 113
+              **99.889999********965 PP
+
+  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_K   8 paslsvslgekvtisCkasqsilaskegssylaWy 42 
+              p+   +s  +k+t+ C a+        ++  l+W+
+     6FR3 130 PSEAEISHTQKATLVCLATGFF----PDHVELSWW 160
+              666789999*******998766....345566665 PP
+
+>> rabbit_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   57.2   0.2  3.3e-018  3.3e-018       4     127 ..       5     114 ..       2     115 .. 0.89
+
+  Alignments for each domain:
+  == domain 1  score: 57.2 bits;  conditional E-value: 3.3e-018
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_L   4 ltqppslvsasLgqtarltCtlssgeivllleeyaveWyqqkpGkaPrlllykdtdllleikkrgsGvpldrFsgskdssgnsasLtisglqaeDeAdYyC 104
+               +tq+p ++  + gq ++l+C+  sg+        +v+Wyqq+pG+  + l+ + ++    ++++    p  rFsg +  s+    + +s+l  +D A Y C
+      6FR3   5 VTQTPRYLIKTRGQQVTLSCSPISGHR-------SVSWYQQTPGQGLQFLFEYFSE----TQRNKGNFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLC 92 
+               699999999999*********999996.......7*****************9977....455555567.*****99.8888889**************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_L 105 asaelllllllvvFGGGtqLtvt 127
+               as+    ++    FG Gt Ltvt
+      6FR3  93 ASSF-DSGNSPLHFGNGTRLTVT 114
+               *997.7889999**********9 PP
+
+>> pig_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   56.0   0.2  9.1e-018  9.1e-018       4     126 ..       5     113 ..       2     115 .. 0.90
+
+  Alignments for each domain:
+  == domain 1  score: 56.0 bits;  conditional E-value: 9.1e-018
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  pig_L   4 liqePsllsvslgetvtltCalssgsvvlllssnyvsWyqqkPGrpPkyliyftfaslskdnsratgvplssfsgaillsgnkatLtisGlqaeDeaDyfCall 107
+            ++q P +l +  g++vtl+C+  sg          vsWyqq+PG+  ++l  +     s+ + +    p  +fsg + +s  ++ + +s l   D a y Ca+ 
+   6FR3   5 VTQTPRYLIKTRGQQVTLSCSPISGHRS-------VSWYQQTPGQGLQFLFEYF----SETQRNKGNFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLCASS 95 
+            69*******************9999885.......9**************9998....45566666677.9*****9.9***********************99 PP
+
+            xxxxxxxxxxxxxxxxxxx RF
+  pig_L 108 kllllllldrFGgGthLtv 126
+                ++    FG Gt+Ltv
+   6FR3  96 F-DSGNSPLHFGNGTRLTV 113
+            8.7888899*********9 PP
+
+>> rat_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   54.4   0.1  2.3e-017  2.3e-017       4     125 ..       5     112 ..       2     114 .. 0.89
+   2 ?   -1.7   0.0       5.2       5.2       8      27 ..     130     149 ..     128     165 .. 0.71
+
+  Alignments for each domain:
+  == domain 1  score: 54.4 bits;  conditional E-value: 2.3e-017
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rat_K   4 mtqspaslsvslgervtisCkasqdilksadgknylsWyqqkpgkspklliykalllllllsnlasg.vplsrFsgsgllsgtdftltissleaedlavYyClq 106
+            +tq+p  l  + g++vt+sC     i    +g++++sWyqq pg+  + l           +++++g  p  rFsg + +s++   +++s+le  d a Y C  
+   6FR3   5 VTQTPRYLIKTRGQQVTLSCSP---I----SGHRSVSWYQQTPGQGLQFLFEYF-----SETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLCAS 94 
+            8*******************64...6....57899*************998776.....45666666267.*****99.9***********************9 PP
+
+            xxxxxxxxxxxxxxxxxxx RF
+  rat_K 107 sklllllllltFGaGtkLE 125
+            s    ++  l FG Gt+L 
+   6FR3  95 SF-DSGNSPLHFGNGTRLT 112
+            98.888999********96 PP
+
+  == domain 2  score: -1.7 bits;  conditional E-value: 5.2
+            xxxxxxxxxxxxxxxxxxxx RF
+  rat_K   8 paslsvslgervtisCkasq 27 
+            p+   +s  +++t+ C a  
+   6FR3 130 PSEAEISHTQKATLVCLATG 149
+            56667889999999998865 PP
+
+>> human_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   52.6   0.4  7.5e-017  7.5e-017       4     126 ..       5     113 ..       2     114 .. 0.89
+   2 ?    0.1   0.0       1.3       1.3       8      29 ..     130     151 ..     126     168 .. 0.76
+
+  Alignments for each domain:
+  == domain 1  score: 52.6 bits;  conditional E-value: 7.5e-017
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_K   4 ltqsPsslsvsvgdrvtisCrasqsilesddgssylaWyqqkpgkapklliyaalllllllsslasG.vPlsrfsGsGllsGtdftltissleaedvavyyC 104
+              +tq+P  l  + g++vt+sC     i    +g+ +++Wyqq pg+  ++l           ++++ G  P  rfsG   +s     +++s+le  d a y C
+     6FR3   5 VTQTPRYLIKTRGQQVTLSCSP---I----SGHRSVSWYQQTPGQGLQFLFEYF-----SETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLC 92 
+              7*******************75...5....46789***************9988.....55666666267.******9.9999******************* PP
+
+              xxxxxxxxxxxxxxxxxxxxxx RF
+  human_K 105 qqaklllllllltfGqGtkvei 126
+                +    ++  l fG+Gt++ +
+     6FR3  93 ASSF-DSGNSPLHFGNGTRLTV 113
+              *998.888999********976 PP
+
+  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
+              xxxxxxxxxxxxxxxxxxxxxx RF
+  human_K   8 PsslsvsvgdrvtisCrasqsi 29 
+              Ps   +s  +++t+ C a+   
+     6FR3 130 PSEAEISHTQKATLVCLATGFF 151
+              88899999********987555 PP
+
+>> rhesus_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   48.2   0.3  1.9e-015  1.9e-015       4     125 ..       5     112 ..       3     114 .. 0.88
+   2 ?   -1.7   0.0       5.2       5.2       8      30 ..     130     151 ..     127     167 .. 0.71
+
+  Alignments for each domain:
+  == domain 1  score: 48.2 bits;  conditional E-value: 1.9e-015
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_K   4 mtqspsslsvsvgervtlisCrasqsilesddgssylaWyqqkpgkaPklliykalllllllssresg.vpldrfsGsgllsgtdftltisslepedvavy 103
+               +tq+p  l  + g++vt +sC     i    +g+ +++Wyqq pg+  ++l  +        ++r++g  p  rfsG   +s++   +++s le  d a y
+      6FR3   5 VTQTPRYLIKTRGQQVT-LSCSP---I----SGHRSVSWYQQTPGQGLQFLFEYF-----SETQRNKGnFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALY 90 
+               69***************.**965...5....46789**************99888.....45566655267.******9.999****************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_K 104 yCqqelllllllWtfGqGtkve 125
+                C  ++  ++    fG Gt+  
+      6FR3  91 LCASSFDSGNSPLHFGNGTRLT 112
+               *****99999*********975 PP
+
+  == domain 2  score: -1.7 bits;  conditional E-value: 5.2
+               xxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_K   8 psslsvsvgervtlisCrasqsi 30 
+               ps   +s  +++t + C a+  +
+      6FR3 130 PSEAEISHTQKAT-LVCLATGFF 151
+               7778889999999.999886544 PP
+
+>> cow_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   46.5   0.1  5.9e-015  5.9e-015       4     125 ..       5     112 ..       2     114 .. 0.89
+
+  Alignments for each domain:
+  == domain 1  score: 46.5 bits;  conditional E-value: 5.9e-015
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  cow_K   4 ltqtPlslsvilGetvsisckstqslkysldgktylrWlqqkPGqsPklliyqvlllllllsnrytgvpldrftgsgllsetdftltissveaedaavyyclqd 107
+            +tqtP +l  + G++v++sc     +    +g+  ++W+qq PGq  + l  +        ++r++g    rf+g + +s++   + +s +e  d+a y c  +
+   6FR3   5 VTQTPRYLIKTRGQQVTLSCSP---I----SGHRSVSWYQQTPGQGLQFLFEYF-----SETQRNKGNFPGRFSGRQ-FSNSRSEMNVSTLELGDSALYLCASS 95 
+            8*******************64...4....58899************9998777.....67888888766*******.9***********************99 PP
+
+            xxxxxxxxxxxxxxxxxx RF
+  cow_K 108 tlllllllntfGqGtkve 125
+                ++    fG Gt++ 
+   6FR3  96 F-DSGNSPLHFGNGTRLT 112
+            9.77777889*****975 PP
+
+>> pig_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   44.4   0.4  2.6e-014  2.6e-014       4     126 ..       5     113 ..       3     115 .. 0.87
+
+  Alignments for each domain:
+  == domain 1  score: 44.4 bits;  conditional E-value: 2.6e-014
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  pig_K   4 ltqsPlslsvslGetvsiscrssqslesslygsnylaWyqqkpGksPklliyeallllllltnrasGvPldrfkGsgllsGtdftlkisrleaedvavyycqqa 107
+            +tq+P  l  + G+ v++sc     +     g++ ++Wyqq pG+  ++l           t+r+ G    rf+G + +s     +++s le  d a y c  +
+   6FR3   5 VTQTPRYLIKTRGQQVTLSCSP---I----SGHRSVSWYQQTPGQGLQFLFEYF-----SETQRNKGNFPGRFSGRQ-FSNSRSEMNVSTLELGDSALYLCASS 95 
+            69******************64...4....467889************997544.....47888777544******9.9***********************99 PP
+
+            xxxxxxxxxxxxxxxxxxx RF
+  pig_K 108 klllllllvtfGsGtklel 126
+                ++  + fG+Gt+l +
+   6FR3  96 F-DSGNSPLHFGNGTRLTV 113
+            8.888999*******9975 PP
+
+>> mouse_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   41.5   0.1  2.1e-013  2.1e-013       2     126 ..       3     113 ..       2     115 .. 0.89
+
+  Alignments for each domain:
+  == domain 1  score: 41.5 bits;  conditional E-value: 2.1e-013
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_L   2 avvtqesallttslGatvkltCrsstgavtllltsnyaeWvqekpdklfkgvigltkdlllgssnradGvPlarfsGsllliGdkaaltitgaqtedeaiyi 103
+              a vtq   +l  + G+ v+l C   +g+ +       + W+q+ p +  + + +   +      n+++  P  rfsG   ++     + ++     d a+y+
+     6FR3   3 AGVTQTPRYLIKTRGQQVTLSCSPISGHRS-------VSWYQQTPGQGLQFLFEYFSE---TQRNKGN-FP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYL 91 
+              569999999999****************96.......99************9998844...5555554.78.9*****9.899999**************** PP
+
+              xxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_L 104 CalwylllllllyvfGgGtkvtv 126
+              Ca      ++    fG Gt++tv
+     6FR3  92 CASSF-DSGNSPLHFGNGTRLTV 113
+              **998.77888899********9 PP
+
+>> rat_L  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   41.4   0.1  2.5e-013  2.5e-013       4     126 ..       5     113 ..       2     115 .. 0.81
+
+  Alignments for each domain:
+  == domain 1  score: 41.4 bits;  conditional E-value: 2.5e-013
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rat_L   4 ltqpnslvstslgstvklsCkrstgnitlllgsnYvnWyqqkedrsivtviykdllllllldkrpdgvpldrfsGsidsssnsaaLtitnvqieDeadYfCqsy 107
+            +tq + ++  + g+ v+lsC+  +g+       + v+Wyqq +++ +  + ++     +   +r +g    rfsG  + s++++ + +  +++ D a Y C s 
+   6FR3   5 VTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFL-FEY----FSETQRNKGNFPGRFSGR-QFSNSRSEMNVSTLELGDSALYLCASS 95 
+            78888888889999999999877766.......78*********987655.444....456788888666******.68888899****************998 PP
+
+            xxxxxxxxxx.xxxxxxxxx RF
+  rat_L 108 slllllllPv.fGGGtkLtv 126
+                 ++ P  fG Gt+Ltv
+   6FR3  96 F--DSGNSPLhFGNGTRLTV 113
+            8..45555644********9 PP
+
+>> rabbit_K  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   37.1   0.2  4.7e-012  4.7e-012       4     126 ..       5     113 ..       2     115 .. 0.84
+
+  Alignments for each domain:
+  == domain 1  score: 37.1 bits;  conditional E-value: 4.7e-012
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_K   4 ltqtpasvsaavGGtvtincqasqsvylllldnsylswyqqkpGqppklliysalllllllsklasGvplsrfsGsGllsGtqftltisGvqcddaatyyc 104
+               +tqtp     + G  vt+ c               +swyqq pGq  ++l  +       + +     p  rfsG   +s  +  + +s ++  d+a y c
+      6FR3   5 VTQTPRYLIKTRGQQVTLSCSPIS-------GHRSVSWYQQTPGQGLQFLFEYF----SETQRNKGNFP-GRFSGRQ-FSNSRSEMNVSTLELGDSALYLC 92 
+               689999999999999999996533.......45689**********99997666....34444555678.******9.9********************** PP
+
+               xxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_K 105 qgsyllllllsltfGaGtkvei 126
+               ++s+   ++  l fG+Gt++ +
+      6FR3  93 ASSF-DSGNSPLHFGNGTRLTV 113
+               ****.7788889*******987 PP
+
+>> mouse_G  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   34.6   0.0  2.5e-011  2.5e-011       4     126 ..       5     113 ..       2     114 .. 0.83
+
+  Alignments for each domain:
+  == domain 1  score: 34.6 bits;  conditional E-value: 2.5e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_G   4 leqtelsvtrrkdesaqisCkvslsvlklllsntaiHWYrqkkgqalerllyvstkllsevkvvekdfkdeklevsekfkdststlkinnvkeeDeatYYCA 105
+              + qt  ++++ +++++++sC+              + WY+q +gq l+ l+ + +      ++++k+    ++  ++ f++s+s +++  ++  D+a+Y CA
+     6FR3   5 VTQTPRYLIKTRGQQVTLSCSPISGH-------RSVSWYQQTPGQGLQFLFEYFS-----ETQRNKGNFPGRFSGRQ-FSNSRSEMNVSTLELGDSALYLCA 93 
+              5688899*************854444.......479*************998875.....57888888888988765.6*********************** PP
+
+              xxxxxxxxxxxxxxxxxxxxx RF
+  mouse_G 106 vWallllllhkvFAeGtkLiv 126
+              +     ++    F +Gt+L v
+     6FR3  94 SSF-DSGNSPLHFGNGTRLTV 113
+              876.4555555699***9987 PP
+
+>> mouse_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   34.2   0.0  3.7e-011  3.7e-011      14     127 ..      15     114 ..       5     115 .. 0.79
+
+  Alignments for each domain:
+  == domain 1  score: 34.2 bits;  conditional E-value: 3.7e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  mouse_H  14 kpgaslklsCkasgftlsllatsyamsWvrqspgkglewigeisskaesgstkyneklklgratlsrdkskstlylqlssltsedtavyyCareallllllf 115
+                g+ ++lsC+         + +  +sW +q+pg+gl+++ e  s++++++ ++  ++  g     r+ s+s+  +++s+l+  d+a+y Ca  ++  ++  
+     6FR3  15 TRGQQVTLSCSPI-------SGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFS-G-----RQFSNSRSEMNVSTLELGDSALYLCAS-SFDSGNSP 102
+              4577888888642.......345579****************99998888888888888.4.....4567777779*****************.55555566 PP
+
+              xxxxxxxxxxxx RF
+  mouse_H 116 dyWGqGttvtvs 127
+                +G+Gt +tv 
+     6FR3 103 LHFGNGTRLTVT 114
+              678*******95 PP
+
+>> human_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   34.5   0.0  3.5e-011  3.5e-011      15     127 ..      16     114 ..       5     115 .. 0.77
+
+  Alignments for each domain:
+  == domain 1  score: 34.5 bits;  conditional E-value: 3.5e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  human_H  15 pgeslklsCaasGftlsllsssyalsWvrqapgkgLewvglisssaesgsteYaeslklgrvtisrdtskntlylqlsslraeDtavYyCarklllllllfd 116
+               g+ ++lsC+        +s + ++sW +q+pg+gL+++    s+++ ++ ++  ++        r+ s++   +++s+l+  D a+Y Ca + +  ++   
+     6FR3  16 RGQQVTLSCS-------PISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFS------GRQFSNSRSEMNVSTLELGDSALYLCASS-FDSGNSPL 103
+              4666666664.......33566789**************9988886666666665555......5678888899******************5.55555556 PP
+
+              xxxxxxxxxxx RF
+  human_H 117 vWGqGtlvtvs 127
+              ++G+Gt  tv 
+     6FR3 104 HFGNGTRLTVT 114
+              89******995 PP
+
+>> human_G  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   34.4   0.0    3e-011    3e-011      34     127 ..      28     114 ..       6     115 .. 0.83
+
+  Alignments for each domain:
+  == domain 1  score: 34.4 bits;  conditional E-value: 3e-011
+              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
+  human_G  34 lsatyihWYlhqeGkapqrLlyydsdllnskvvlesGissgkyetdasperkslklilrnlienDsgvYYCat.WdlllllliklfgsGtkLivt 127
+                  ++ WY++ +G+  q+L  y s+       ++ G  +g+++  +   ++ +++ +  l+  Ds+ Y Ca  +d   ++    fg+Gt+L vt
+     6FR3  28 SGHRSVSWYQQTPGQGLQFLFEYFSE-----TQRNKGNFPGRFSGRQF-SNSRSEMNVSTLELGDSALYLCASsFD--SGNSPLHFGNGTRLTVT 114
+              34679***************998877.....66788999*****9999.99999******************7366..6666778*********9 PP
+
+>> rhesus_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   30.6   0.0  5.5e-010  5.5e-010      12     126 ..      12     113 ..       4     115 .. 0.75
+
+  Alignments for each domain:
+  == domain 1  score: 30.6 bits;  conditional E-value: 5.5e-010
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rhesus_H  12 lvkPggeslrlsCaaslGftfsllsssyalsWvrqapgkglewvgaisskaesgsteyadslklgrvtisrdtskntlylqlsslkaeDtAvyYCarllll 112
+               l+k  g+ ++lsC+          s +  +sW +q+pg+gl+++ +  s++++++ ++      gr++  r+ s++   +++s l+  D A+y Ca  +  
+      6FR3  12 LIKTRGQQVTLSCSPI--------SGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFP-----GRFS-GRQFSNSRSEMNVSTLELGDSALYLCASSFDS 98 
+               6777788889998644........356779*************9988877555555555.....5554.6778888999*****************96544 PP
+
+               xx.xxxxxxxxxxxx RF
+  rhesus_H 113 ll.fdvWGqGvlvtv 126
+               ++    +G+G+++tv
+      6FR3  99 GNsPLHFGNGTRLTV 113
+               331335799999998 PP
+
+>> cow_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   25.1   0.0  2.3e-008  2.3e-008      20     127 ..      21     114 ..       6     115 .. 0.77
+   2 ?   -1.6   0.0       4.3       4.3      48      48 ..     164     164 ..     132     200 .. 0.54
+
+  Alignments for each domain:
+  == domain 1  score: 25.1 bits;  conditional E-value: 2.3e-008
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  cow_H  20 sltctvsGfslllllssyavgwvrqapGkalewlGgissglllGstgynpalklsrlsitkdnsksqvslsvssvttedtatyycakvkllllllvdawGrGlr 123
+            +l+c         +  +++v+w +q+pG+ l++l +  s+     t+ n +    r+s  ++ s s+  + vs++   d+a y ca  +  ++     +G+G r
+   6FR3  21 TLSC-------SPISGHRSVSWYQQTPGQGLQFLFEYFSE-----TQRNKGNFPGRFS-GRQFSNSRSEMNVSTLELGDSALYLCASSFDSGNSP-LHFGNGTR 110
+            3333.......23345789*****************9999.....7778877778888.577888888999****************66555554.57999999 PP
+
+            xxxx RF
+  cow_H 124 vtvs 127
+             tv+
+   6FR3 111 LTVT 114
+            9985 PP
+
+  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
+            x RF
+  cow_H  48 k 48 
+            k
+   6FR3 164 K 164
+            1 PP
+
+>> rabbit_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   23.8   0.0  6.7e-008  6.7e-008      20     127 ..      21     114 ..       8     115 .. 0.69
+   2 ?   -0.5   0.0       2.3       2.3      15      40 ..     137     158 ..     129     166 .. 0.68
+
+  Alignments for each domain:
+  == domain 1  score: 23.8 bits;  conditional E-value: 6.7e-008
+               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_H  20 tltCtvsGfslslllssyavsWvrqapGkglewiglisssslsgstyyaswaklsrstisrntnentvtLkmtsltaaDtatyfCaralllllllldlWGq 120
+               tl+C         +  + +vsW +q pG+gl+++    s++  ++ ++  + + +r       +++  ++++++l   D a y+Ca ++  ++  l  +G+
+      6FR3  21 TLSCS-------PISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPGRFS-GRQ-----FSNSRSEMNVSTLELGDSALYLCASSFDSGNSPL-HFGN 107
+               44443.......22345679************987666664555555555555.443.....3335556778888889*********777777776.58** PP
+
+               xxxxxxx RF
+  rabbit_H 121 GtLvtvs 127
+               Gt  tv+
+      6FR3 108 GTRLTVT 114
+               **99995 PP
+
+  == domain 2  score: -0.5 bits;  conditional E-value: 2.3
+               xxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  rabbit_H  15 pgdtLtltCtvsGfslslllssyavs 40 
+                ++  tl C ++Gf       + ++s
+      6FR3 137 HTQKATLVCLATGFFP----DHVELS 158
+               5667789999999855....444444 PP
+
+>> alpaca_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   22.6   0.0  1.8e-007  1.8e-007      17     127 ..      18     114 ..       6     115 .. 0.75
+
+  Alignments for each domain:
+  == domain 1  score: 22.6 bits;  conditional E-value: 1.8e-007
+               xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  alpaca_H  17 gslrlsca.asGstftlltssyamswvrqaPGkglelvaaisldllgGstyyadsvklgrftisrdnakntlylqlnslkpedtavyycakllllllllld 116
+               + + lsc+ +s         +  +sw++q+PG+gl+++    ++     t   +    grf+  r  +  +  +++++l+  d+a+y ca  +  ++    
+      6FR3  18 QQVTLSCSpIS--------GHRSVSWYQQTPGQGLQFLFEYFSE-----TQRNKGNFPGRFS-GRQFSNSRSEMNVSTLELGDSALYLCASSFDSGNSP-L 103
+               55555554223........34568*************9877777.....5555555558987.6888888889999***************55555555.5 PP
+
+               xxxxxxxxxxx RF
+  alpaca_H 117 awGqGtlvtvs 127
+                +G+Gt +tv+
+      6FR3 104 HFGNGTRLTVT 114
+               79*******96 PP
+
+>> pig_H  
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   20.8   0.0  6.5e-007  6.5e-007      35     126 ..      29     113 ..      12     115 .. 0.78
+
+  Alignments for each domain:
+  == domain 1  score: 20.8 bits;  conditional E-value: 6.5e-007
+            xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  pig_H  35 ssyavswvrqapgkglewlaaissssysgstyyadsvklgrftisrddsqntaylqmnslrtedtaryycarllllllllldswgrgvlvtv 126
+               +vsw +q+pg+gl++l    s      t+       grf+  r+ s+  + +++++l   d+a y ca  +  ++  l ++g+g+ +tv
+   6FR3  29 GHRSVSWYQQTPGQGLQFLFEYFSE-----TQRNKGNFPGRFS-GRQFSNSRSEMNVSTLELGDSALYLCASSFDSGNSPL-HFGNGTRLTV 113
+            45689**************876555.....5555555569997.56677788889999**************777776666.6899998887 PP
+
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query sequence(s):                         1  (244 residues searched)
+Target model(s):                          29  (3712 nodes)
+Passed MSV filter:                        29  (1); expected 0.6 (0.02)
+Passed bias filter:                       29  (1); expected 0.6 (0.02)
+Passed Vit filter:                        29  (1); expected 0.0 (0.001)
+Passed Fwd filter:                        29  (1); expected 0.0 (1e-005)
+Initial search space (Z):                 29  [actual number of targets]
+Domain search space  (domZ):              29  [number of targets reported over threshold]
+# CPU time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00
+# Mc/sec: inf
+//
+[ok]
diff --git a/Tests/test_SearchIO_hmmer3_text.py b/Tests/test_SearchIO_hmmer3_text.py
--- a/Tests/test_SearchIO_hmmer3_text.py
+++ b/Tests/test_SearchIO_hmmer3_text.py
@@ -1654,6 +1654,35 @@ def test_30_hmmscan_010(self):
         self.assertEqual(0, hit.domain_obs_num)
         self.assertEqual(0, len(hit))
 
+    def test_30_hmmscan_011(self):
+        """Parsing hmmscan 3.0 (text_30_hmmscan_011)."""
+        hmmer_file = get_file("text_30_hmmscan_011.out")
+        qresults = list(parse(hmmer_file, FMT))
+        assert len(qresults) == 2
+
+        result = qresults[0]
+        hit = result[-1]
+        assert len(result) == 29
+        assert hit.hsps[0].bitscore == 22.4
+
+        result = qresults[1]
+        hit = result[-1]
+        assert len(result) == 29
+        assert hit.hsps[0].bitscore == 20.8
+
+        # Test getting program name when preamble contains full path and whitespace
+        expected_db_target = (
+            "C:\\msys64\\scr\\byerly\\builds\\NB\\20231025 _\\internal\\lib\\"
+            "site-packages\\anarci\\dat\\HMMs\\ALL.hmm"
+        )
+        for idx, qresult in enumerate(qresults):
+            assert qresult.program == "hmmscan", (
+                "Expected program 'hmmscan' for item at index "
+                f"{idx}, found {qresult.program}"
+            )
+            # hmm db path also contains space
+            assert qresult.target == expected_db_target
+
 
 class HmmersearchCases(unittest.TestCase):
     """Test hmmsearch output."""