At2g11810.1/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
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g11810-1vgv_A.pir.txt
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Assigned types to 465 residues in Sequence 2-11810, 21 remain unknown
Assigned types to 354 residues in Sequence 1vgv_A, 132 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 214 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 215 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 216 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 217 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 218 All residues are positively and negatively charged
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
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 270 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 271 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 272 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 273 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 274 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 275 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 276 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 277 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 351 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 365 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 366 All residues are positively and negatively charged
Translated sequence file At2g11810-1vgv_A.pir.txt into sequence alignment.
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>1VGV.pdb Made from 11450 ATOM records in 1VGV.pdb
KVLTVFGTRPEAIKAPLVHALAKDPFFEAKVCVTAQHRELDQVLKLFSIV
PDYDLNIQPGQGLTEITCRILEGLKPILAEFKPDVVLVHGDTTTTLATSL
AAFYQRIPVGHVEAGLRTGDLYSPWPEEANRTLTGHLAYHFSPTETSRQN
LLRENVADSRIFITGNTVIDALLWVRDQVSSDKLRSELAANYPFIDPDKK
ILVTGHRRESFGRGFEEICHALADIATTHQDIQIVYPVHLNPNVREPVNR
ILGHVKNVILIDPQEYLPFVWLNHAWLILTDSGGIQEEAPSLGKPVLVRD
TTERPEAVTAGTVRLVGTDKQRIVEEVTRLLKDENEYQASRAHNPYGDGQ
ACSRILEALKNNRISLKVLTVFGTRPEAIKAPLVHALAKDPFFEAKVCVT
AQHRELDQVLKLFSIVPDYDLNIQGLTEITCRILEGLKPILAEFKPDVVL
VHGDTTTTLATSLAAFYQRIPVGHVEAGLRTGDLYSPWPEEANRTLTGHL
AYHFSPTETSRQNLLRENVADSRIFITGNTVIDALLWVRDQVSSDKLRSE
LAANYPFIDPDKKILVTGHRRESFGRGFEEICHALADIATTHQDIQIVYP
VHLNPNVREPVNRILGHVKNVILIDPQEYLPFVWLNHAWLILTDSGGIQE
EAPSLGKPVLVRDTTERPEAVTAGTVRLVGTDKQRIVEEVTRLLKDENEY
QASRAHNPYGDGQACSRILEALKNNRISLKVLTVFGTRPEAIKAPLVHAL
AKDPFFEAKVCVTAQHRELDQVLKLFSIVPDYDLNIGQGLTEITCRILEG
LKPILAEFKPDVVLVHGDTTTTLATSLAAFYQRIPVGHVEAGLRTGDLYS
PWPEEANRTLTGHLAYHFSPTETSRQNLLRENVADSRIFITGNTVIDALL
WVRDQVSSDKLRSELAANYPFIDPDKKILVTGHRFGRGFEEICHALADIA
TTHQDIQIVYPVHLNPNVREPVNRILGHVKNVILIDPQEYLPFVWLNHAW
LILTDSGGIQEEAPSLGKPVLVRDTTERPEAVTAGTVRLVGTDKQRIVEE
VTRLLKDENEYQASRAHNPYGDGQACSRILEALKNNRKVLTVFGTRPEAI
KAPLVHALAKDPFFEAKVCVTAQHRELDQVLKLFSIVPDYDLNIQPGQGL
TEITCRILEGLKPILAEFKPDVVLVHGDTTTTLATSLAAFYQRIPVGHVE
AGLRTGDLYSPWPEEANRTLTGHLAYHFSPTETSRQNLLRENVADSRIFI
TGNTVIDALLWVRDQVSSDKLRSELAANYPFIDPDKKILVTGHRRESFGR
GFEEICHALADIATTHQDIQIVYPVHLNPNVREPVNRILGHVKNVILIDP
QEYLPFVWLNHAWLILTDSGGIQEEAPSLGKPVLVRDTTERPEAVTAGTV
RLVGTDKQRIVEEVTRLLKDENEYQASRAHNPYGDGQACSRILEALKNNR
I
======================================================
Best alignment:
1VGV.pdb 271 WLNHAWLILTDSG-GIQEEAPSLGKPVLVRD 300
 W+ I+T +G G EA G P+++ D
2-11810 351 WMGACDCIITKAGPGTIAEALICGLPIILND 381
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Highlighted IDENTICAL residue LEU 279 index1 272 path 373 %Seq 100.00
Highlighted IDENTICAL residue ILE 286 index1 278 path 379 %Seq 100.00
Highlighted IDENTICAL residue THR 288 index1 280 path 381 %Seq 100.00
Highlighted IDENTICAL residue GLY 291 index1 283 path 384 %Seq 100.00
Highlighted IDENTICAL residue GLY 292 index1 284 path 386 %Seq 100.00
Highlighted IDENTICAL residue GLU 296 index1 288 path 390 %Seq 100.00
Highlighted IDENTICAL residue ALA 297 index1 289 path 391 %Seq 100.00
Highlighted IDENTICAL residue GLY 301 index1 293 path 395 %Seq 100.00
Highlighted IDENTICAL residue PRO 303 index1 295 path 397 %Seq 100.00
Highlighted 9 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g11810-1vgv_A.pir.txt.1VGV.pdb.conservation.pml
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The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g11810-1vgv_A.pir.txt PIR amino_acid 1VGV.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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