At2g03740.1/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/
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Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
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Sequence 1
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g03740-2ch7A0.pir.txt
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Assigned types to 189 residues in Sequence 2-03740, 8 remain unknown
Assigned types to 309 residues in Sequence 2ch7A0, 42 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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Translated sequence file At2g03740-2ch7A0.pir.txt into sequence alignment.
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>2CH7.pdb Made from 4630 ATOM records in 2CH7.pdb
GSHMKDVQTETFSVAESIEEISKANEEITNQLLGISKEMDNISTRIESIS
ASVQETTAGSEEISSATKNIADSAQQAASFADQSTQLAKEAGDALKKVIE
VTRMISNSAKDVERVVESFQKGAEEITSFVETINAIAEQTNLLALNAAIE
AARAGEAGRGFAVVADEIRKLAEESQQASENVRRVVNEIRSIAEDAGKVS
SEITARVEEGTKLADEADEKLNSIVGAVERINEMLQNIAAAIEEQTAAVD
EITTAMTENAKNAEEITNSVKEVNARLQEISASTEEVTSRVQTIRENVQM
LKEIVARYKSHMKDVQTETFSVAESIEEISKANEEITNQLLGISKEMDNI
STRIESISASVQETTAGSEEISSATKNIADSAQQAASFADQSTQLAKEAG
DALKKVIEVTRMISNSAKDVERVVESFQKGAEEITSFVETINAIAEQTNL
LALNAAIEAARAGEAGRGFAVVADEIRKLAEESQQASENVRRVVNEIRSI
AEDAGKVSSEITARVEEGTKLADEADEKLNSIVGAVERINEMLQNIAAAI
EEQNAAVDEITTAMTENAKNAEEITNSVKEVNARLQEISASTEEVTSRVQ
TIRENVQMLKEIVARYK
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Best alignment:
2CH7.pdb 157 AGRGFAVVADEIRKLAEESQQASENVRRVVNEIRSIAEDAGKVSSEITAR 206
 A +G ++ + L + S++AS V+ +E+ +++ G+ R
2-03740 51 AVKGAGNSPNDPKWLDDASEKASGYVKEKGSEVGNVSAQKGQELQNQMER 100
2CH7.pdb 207 VEEGTKLADEADEKLNSIVGAVERINEMLQNIAAAI-EEQTAAVDEITTA 255
 ++ + +A E ++S+ +R ++ + + EE T+ D+ 
2-03740 101 AKD--YIFGKAGEAMDSVAENAKRASDFVTEKGKEVKEETTSRTDKAKDF 148
2CH7.pdb 256 MTENAKNAEEITNSVKEVNAR 276
 + E A + ++ ++ ++
2-03740 149 IVEKAGDVKDTAMDMRNKTSK 169
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Highlighted IDENTICAL residue LEU 391 index1 171 path 71 %Seq 100.00
Highlighted IDENTICAL residue SER 395 index1 175 path 75 %Seq 100.00
Highlighted IDENTICAL residue ARG 404 index1 184 path 86 %Seq 100.00
Highlighted IDENTICAL residue ASN 407 index1 187 path 89 %Seq 100.00
Highlighted IDENTICAL residue VAL 419 index1 199 path 101 %Seq 100.00
Highlighted IDENTICAL residue GLU 429 index1 209 path 111 %Seq 100.00
Highlighted IDENTICAL residue GLU 436 index1 216 path 116 %Seq 50.00
Highlighted IDENTICAL residue ALA 437 index1 217 path 117 %Seq 100.00
Highlighted IDENTICAL residue ASN 442 index1 222 path 122 %Seq 100.00
Highlighted IDENTICAL residue VAL 448 index1 228 path 128 %Seq 100.00
Highlighted IDENTICAL residue GLU 449 index1 229 path 129 %Seq 100.00
Highlighted IDENTICAL residue ILE 451 index1 231 path 131 %Seq 100.00
Highlighted IDENTICAL residue GLU 453 index1 233 path 133 %Seq 100.00
Highlighted IDENTICAL residue ASN 457 index1 237 path 137 %Seq 50.00
Highlighted IDENTICAL residue ILE 458 index1 238 path 138 %Seq 100.00
Highlighted IDENTICAL residue ALA 461 index1 241 path 141 %Seq 100.00
Highlighted IDENTICAL residue ILE 462 index1 242 path 142 %Seq 100.00
Highlighted IDENTICAL residue THR 477 index1 257 path 158 %Seq 50.00
Highlighted IDENTICAL residue GLU 478 index1 258 path 159 %Seq 100.00
Highlighted 19 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03740-2ch7A0.pir.txt.2CH7.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03740-2ch7A0.pir.txt PIR amino_acid 2CH7.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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