At2g14910.2/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/
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Sequence file type = 3
Sequence type = 3
Got here 1
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14910-2-1jadA.pir.txt
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Assigned types to 366 residues in Sequence 2-14910-2, 5 remain unknown
Assigned types to 221 residues in Sequence 1jadA, 150 remain unknown
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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 219 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 220 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 221 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 222 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 223 All residues are positively and negatively charged
Translated sequence file At2g14910-2-1jadA.pir.txt into sequence alignment.
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>1JAD.pdb Made from 3894 ATOM records in 1JAD.pdb
NKEVTQLPEPQTASLAELQQKLFLKLLKKQEKELKELERKGSKRREELLQ
KYSVLFLEPVYPRGLDSQVVELKERLEELIHLGEEYHDGIRRRKEQHATE
QTAKITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVRSTSD
KAAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQE
KEGQLQQEAVAEYEEKLKTLTVEVQEVKNYKEVFPNKEVTQLPEPQTASL
AELQQKLFLKLLKKQEKELKELERKGSKRREELLQKYSVLFLEPVYPRGL
DSQVVELKERLEELIHLGEEYHDGIRRRKEQHATEQTAKITELAREKQIA
ELKALKESSESNIKDIKKKLEAKRLDRIQVRSTSDKAAQERLKKEINNSH
IQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEKEGQLQQEAVAEYEE
KLKTLTVEVQEVKNYKEVFP
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Best alignment:
1JAD.pdb 6 QLPEPQTASLAELQQ-KLFLKLLKKQEKELKELERKGSKRREELLQKYSV 54
 QLPEPQTASLAELQQ KLFLKLLKKQEKELKELERKGSKRREELLQKYSV
1jadA 1 QLPEPQTASLAELQQMKLFLKLLKKQEKELKELERKGSKRREELLQKYSV 50
1JAD.pdb 55 LFLEPVYPRGLDSQVVELKERLE-ELIHLGEEYHDGIRRRKEQHATEQTA 103
 LFLEPVYPRGLDSQVVELKERLE ELIHLGEEYHDGIRRRKEQHATEQTA
1jadA 51 LFLEPVYPRGLDSQVVELKERLEMELIHLGEEYHDGIRRRKEQHATEQTA 100
1JAD.pdb 104 KITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQV--RSTSDK 151
 KITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQV RSTSDK
1jadA 101 KITELAREKQIAELKALKESSESNIKDIKKKLEAKRLDRIQVMMXXXXXK 150
1JAD.pdb 152 AAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEK 201
 AAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEK
1jadA 151 AAQERLKKEINNSHIQEVVQTIKLLTEKTARYQQKLEEKQAENLRAIQEK 200
1JAD.pdb 202 EGQLQQEAVAEYEEKLKTLTVEVQEV 227
 EGQLQQEAVAEYEEKLKTLTVEVQE+
1jadA 201 EGQLQQEAVAEYEEKLKTLTVEVQEM 226
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Highlighted IDENTICAL residue LEU 10 index1 7 path 64 %Seq 100.00
Highlighted IDENTICAL residue SER 17 index1 14 path 71 %Seq 100.00
Highlighted IDENTICAL residue LEU 30 index1 26 path 84 %Seq 100.00
Highlighted IDENTICAL residue GLU 35 index1 31 path 89 %Seq 100.00
Highlighted IDENTICAL residue LEU 61 index1 57 path 116 %Seq 100.00
Highlighted IDENTICAL residue LEU 76 index1 72 path 131 %Seq 100.00
Highlighted IDENTICAL residue GLU 78 index1 74 path 133 %Seq 100.00
Highlighted IDENTICAL residue LEU 80 index1 76 path 135 %Seq 100.00
Highlighted IDENTICAL residue GLY 88 index1 83 path 146 %Seq 100.00
Highlighted IDENTICAL residue ARG 97 index1 92 path 155 %Seq 100.00
Highlighted IDENTICAL residue THR 111 index1 106 path 177 %Seq 100.00
Highlighted IDENTICAL residue GLU 112 index1 107 path 178 %Seq 100.00
Highlighted IDENTICAL residue GLU 116 index1 111 path 182 %Seq 100.00
Highlighted IDENTICAL residue SER 131 index1 126 path 197 %Seq 100.00
Highlighted IDENTICAL residue LEU 145 index1 140 path 211 %Seq 100.00
Highlighted IDENTICAL residue ARG 147 index1 142 path 213 %Seq 100.00
Highlighted IDENTICAL residue ARG 163 index1 156 path 229 %Seq 100.00
Highlighted IDENTICAL residue LEU 164 index1 157 path 230 %Seq 100.00
Highlighted IDENTICAL residue LYS 181 index1 174 path 247 %Seq 100.00
Highlighted IDENTICAL residue LEU 202 index1 195 path 268 %Seq 100.00
Highlighted IDENTICAL residue ARG 203 index1 196 path 269 %Seq 100.00
Highlighted IDENTICAL residue GLU 207 index1 200 path 274 %Seq 100.00
Highlighted IDENTICAL residue LYS 208 index1 201 path 275 %Seq 100.00
Highlighted IDENTICAL residue LEU 212 index1 205 path 279 %Seq 100.00
Highlighted IDENTICAL residue ALA 216 index1 209 path 283 %Seq 100.00
Highlighted IDENTICAL residue GLU 219 index1 212 path 286 %Seq 100.00
Highlighted IDENTICAL residue GLU 222 index1 215 path 289 %Seq 100.00
Highlighted 27 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14910-2-1jadA.pir.txt.1JAD.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14910-2-1jadA.pir.txt PIR amino_acid 1JAD.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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