At2g14247.1/PDB

&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&&
Successfully read 2 file paths from WYRM_file_paths.txt
generic_input /usr/local/www/html/proteins/workspace/
generic_output /usr/local/www/html/proteins/htdocs/results/
======================================================
Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
Got here 3
Sequence 1
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14270-1nfda2.pir.txt
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Assigned types to 78 residues in Sequence 2-14247, 10 remain unknown
Assigned types to 69 residues in Sequence 1nfda2, 19 remain unknown
======================================================
Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
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Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 12 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 13 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 22 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 23 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 24 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 25 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 26 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 27 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 45 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 46 All residues are positively and negatively charged
Translated sequence file At2g14270-1nfda2.pir.txt into sequence alignment.
======================================================
>1NFD.pdb Made from 13688 ATOM records in 1NFD.pdb
DSVTQTEGLVTVTEGLPVKLNCTYQTTYLTIAFFWYVQYLNEAPQVLLKS
STDNKRTEHQGFHATLHKSSSSFHLQKSSAQLSDSALYYCALSEGGNYKY
VFGAGTRLKVIAHIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTM
ESGTFITDKTVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNATYPSSD
VPCDSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLI
QHYEKVERDKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLRW
GDEQYFGPGTRLTVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARG
FFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYSLSSRLRVSATFWHN
PRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADCDSVTQTEG
LVTVTEGLPVKLNCTYQTTYLTIAFFWYVQYLNEAPQVLLKSSTDNKRTE
HQGFHATLHKSSSSFHLQKSSAQLSDSALYYCALSEGGNYKYVFGAGTRL
KVIAHIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITD
KTVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNATYPSSDVPCDSGVV
QSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVER
DKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLRWGDEQYFGP
GTRLTVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVEL
SWWVNGKEVHSGVSTDPQAYKESNYSYSLSSRLRVSATFWHNPRNHFRCQ
VQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADCYELIQPSSASVTVGET
VKITCSGDQLPKNFAYWFQQKSDKNILLLIYMDNKRPSGIPERFSGSTSG
TTATLTISGAQPEDEAAYYCLSSYGDNNDLVFGSGTQLTVLRGPKSSPKV
TVFPPSPEELRTNKATLVCLVNDFYPGSATVTWKANGATINDGVKTTKPS
KQGQNYMTSSYLSLTADQWKSHNRVSCQVTHEGETVEKSLSPAECLEVYL
VESGGDLVQPGSSLKVSCAASGFTFSDFWMYWVRQAPGKGLEWVGRIKNI
PNNYATEYADSVRGRFTISRDDSRNSIYLQMNRLRVDDTAIYYCTRAGRF
DHFDYWGQGTMVTVSSATTTAPSVYPLAPACDSTTSTTDTVTLGCLVKGY
FPEPVTVSWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPKQPITC
NVAHPASSTKVDKKIEPRYELIQPSSASVTVGETVKITCSGDQLPKNFAY
WFQQKSDKNILLLIYMDNKRPSGIPERFSGSTSGTTATLTISGAQPEDEA
AYYCLSSYGDNNDLVFGSGTQLTVLRGPKSSPKVTVFPPSPEELRTNKAT
LVCLVNDFYPGSATVTWKANGATINDGVKTTKPSKQGQNYMTSSYLSLTA
DQWKSHNRVSCQVTHEGETVEKSLSPAECLEVYLVESGGDLVQPGSSLKV
SCAASGFTFSDFWMYWVRQAPGKGLEWVGRIKNIPNNYATEYADSVRGRF
TISRDDSRNSIYLQMNRLRVDDTAIYYCTRAGRFDHFDYWGQGTMVTVSS
ATTTAPSVYPLAPACDSTTSTTDTVTLGCLVKGYFPEPVTVSWNSGALTS
GVHTFPSVLHSGLYSLSSSVTVPSSTWPKQPITCNVAHPASSTKVDKKIE
PR
======================================================
Best alignment:
1NFD.pdb 165 KAMDSKSNGAI 175
 KA+D++ + A+
2-14247 43 KALDNEDHSAV 53
======================================================
Highlighted IDENTICAL residue LYS 171 index1 165 path 53 %Seq 100.00
Highlighted IDENTICAL residue ALA 172 index1 166 path 54 %Seq 100.00
Highlighted IDENTICAL residue ASP 174 index1 168 path 56 %Seq 100.00
Highlighted IDENTICAL residue ALA 180 index1 174 path 62 %Seq 100.00
Highlighted 4 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14270-1nfda2.pir.txt.1NFD.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14270-1nfda2.pir.txt PIR amino_acid 1NFD.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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