At2g13810.1/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
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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/At2g13810-1j32_A.pir.txt
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Assigned types to 456 residues in Sequence 2-13810, 8 remain unknown
Assigned types to 378 residues in Sequence 1j32_A, 86 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 132 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 133 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 150 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 265 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 372 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 391 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 392 All residues are positively and negatively charged
Translated sequence file At2g13810-1j32_A.pir.txt into sequence alignment.
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>1J32.pdb Made from 5906 ATOM records in 1J32.pdb
MKLAARVESVSPSMTLIIDAKAKAMKAEGIDVCSFSAGEPDFNTPKHIVE
AAKAALEQGKTRYGPAAGEPRLREAIAQKLQRDNGLCYGADNILVTNGGK
QSIFNLMLAMIEPGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQFK
VSPEQIRQAITPKTKLLVFNTPSNPTGMVYTPDEVRAIAQVAVEAGLWVL
SDEIYEKILYDDAQHLSIGAASPEAYERSVVCSGFAKTYAMTGWRVGFLA
GPVPLVKAATKIQGHSTSNVCTFAQYGAIAAYENSQDCVQEMLAAFAERR
RYMLDALNAMPGLECPKPDGAFYMFPSIAKTGRSSLDFCSELLDQHQVAT
VPGAAFGADDCIRLSYATDLDTIKRGMERLEKFLHGILMKLAARVESVSP
SMTLIIDAKAKAMKAEGIDVCSFSAGEPDFNTPKHIVEAAKAALEQGKTR
YGPAAGEPRLREAIAQKLQRDNGLCYGADNILVTNGGKQSIFNLMLAMIE
PGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQFKVSPEQIRQAITP
KTKLLVFNTPSNPTGMVYTPDEVRAIAQVAVEAGLWVLSDEIYEKILYDD
AQHLSIGAASPEAYERSVVCSGFAKTYAMTGWRVGFLAGPVPLVKAATKI
QGHSTSNVCTFAQYGAIAAYENSQDCVQEMLAAFAERRRYMLDALNAMPG
LECPKPDGAFYMFPSIAKTGRSSLDFCSELLDQHQVATVPGAAFGADDCI
RLSYATDLDTIKRGMERLEKFLHGIL
======================================================
Best alignment:
1J32.pdb 58 QGKTRYGPAAGEPRLREAIAQKLQRDNGLCYGADNILVTNGGKQSIFNLM 107
 +G YG G LR+AIA+ RD L ++ + V++G + I L 
2-13810 103 EGYRGYGLEQGNKTLRKAIAETFYRD--LHVKSNEVFVSDGAQSDISRLQ 150
1J32.pdb 108 LAMIEPGDEVIIPAPFWVSYPEMVKLAEGTPVILPTTVETQ----FKVSP 153
 L ++ + + P + +Y + + T T + Q P
2-13810 151 L-LLGSNVTIAVQDPTFPAYIDSSVIIGQTGHFHEKTKKYQNVVYMPCGP 199
1J32.pdb 153 ---EQIRQAITPKTKLLVFNTPSNPTGMVYTPDEVRAIAQVAVEAGLWVL 200
 A+TP+T ++ F +P+NPTG V + ++ + A G ++
2-13810 200 NNSFFPDLAMTPRTDVIFFCSPNNPTGYVASRKQLHQLVDFAKTNGSIII 249
1J32.pdb 201 SDEIYEKILYDDAQHLSIGAASPEAYERSVVCSGFAKTYAMTGWRVGF-- 248
 D Y + +D SI P A E ++ S F+K TG R+G+ 
2-13810 250 FDSAYAAFI-EDGSPRSI-YEIPGAREVAIEVSSFSKFAGFTGVRLGWSI 297
1J32.pdb 248 ------LAGPVPLVKAATKIQGHSTSNVCTFAQYGAIAAYEN-SQDCVQE 291
 + P++ +I S + AQ G +A + ++ 
2-13810 298 IPDELLYSNGFPIINDFHRIVTTSFNGASNIAQAGGLACLSSGGLKEIRS 347
1J32.pdb 292 MLAAFAERRRYMLDALNAMPGLECPKPDGAFYMFPSIAKTGRSSLDFCSE 341
 + + E R+ ++D L ++ GL+ A Y++ + G S D +E
2-13810 348 VNNYYKENRKILMDTLVSL-GLKVYGGVNAPYLW--VHFKGSKSWDVFNE 394
1J32.pdb 342 LLDQHQVATVPGAAF--GADDCIRLSYATDLDTIKRGMERLEKFLH 385
 +L+ + TVPG+ F G ++ +R+S D I +RL+ F +
2-13810 395 ILENTHIITVPGSGFGPGGEEYLRISGFGRRDHIVEASKRLQNFFN 440
======================================================
Highlighted IDENTICAL residue GLY 59 index1 59 path 104 %Seq 100.00
Highlighted IDENTICAL residue TYR 63 index1 63 path 108 %Seq 100.00
Highlighted IDENTICAL residue GLY 64 index1 64 path 109 %Seq 100.00
Highlighted IDENTICAL residue GLY 68 index1 68 path 113 %Seq 100.00
Highlighted IDENTICAL residue LEU 72 index1 72 path 117 %Seq 100.00
Highlighted IDENTICAL residue ARG 73 index1 73 path 118 %Seq 100.00
Highlighted IDENTICAL residue ALA 75 index1 75 path 120 %Seq 100.00
Highlighted IDENTICAL residue ILE 76 index1 76 path 121 %Seq 100.00
Highlighted IDENTICAL residue ALA 77 index1 77 path 122 %Seq 100.00
Highlighted IDENTICAL residue ARG 82 index1 82 path 127 %Seq 100.00
Highlighted IDENTICAL residue ASP 83 index1 83 path 128 %Seq 100.00
Highlighted IDENTICAL residue VAL 95 index1 95 path 140 %Seq 100.00
Highlighted IDENTICAL residue GLY 98 index1 98 path 143 %Seq 100.00
Highlighted IDENTICAL residue ILE 103 index1 103 path 148 %Seq 100.00
Highlighted IDENTICAL residue PRO 122 index1 122 path 167 %Seq 100.00
Highlighted IDENTICAL residue TYR 127 index1 127 path 172 %Seq 100.00
Highlighted IDENTICAL residue THR 137 index1 137 path 182 %Seq 100.00
Highlighted IDENTICAL residue THR 144 index1 144 path 189 %Seq 100.00
Highlighted IDENTICAL residue GLN 148 index1 148 path 193 %Seq 100.00
Highlighted IDENTICAL residue VAL 151 index1 151 path 200 %Seq 50.00
Highlighted IDENTICAL residue SER 152 index1 152 path 201 %Seq 50.00
Highlighted IDENTICAL residue PRO 153 index1 153 path 202 %Seq 50.00
Highlighted IDENTICAL residue GLU 154 index1 154 path 206 %Seq 50.00
Highlighted IDENTICAL residue ALA 159 index1 159 path 211 %Seq 100.00
Highlighted IDENTICAL residue THR 161 index1 161 path 213 %Seq 100.00
Highlighted IDENTICAL residue PRO 162 index1 162 path 214 %Seq 100.00
Highlighted IDENTICAL residue THR 164 index1 164 path 216 %Seq 100.00
Highlighted IDENTICAL residue PHE 169 index1 169 path 221 %Seq 100.00
Highlighted IDENTICAL residue PRO 172 index1 172 path 224 %Seq 100.00
Highlighted IDENTICAL residue ASN 174 index1 174 path 226 %Seq 100.00
Highlighted IDENTICAL residue PRO 175 index1 175 path 227 %Seq 100.00
Highlighted IDENTICAL residue THR 176 index1 176 path 228 %Seq 100.00
Highlighted IDENTICAL residue GLY 177 index1 177 path 229 %Seq 100.00
Highlighted IDENTICAL residue VAL 179 index1 179 path 231 %Seq 100.00
Highlighted IDENTICAL residue ALA 192 index1 192 path 244 %Seq 100.00
Highlighted IDENTICAL residue GLY 196 index1 196 path 248 %Seq 100.00
Highlighted IDENTICAL residue ASP 202 index1 202 path 254 %Seq 100.00
Highlighted IDENTICAL residue TYR 205 index1 205 path 257 %Seq 100.00
Highlighted IDENTICAL residue ASP 212 index1 212 path 263 %Seq 100.00
Highlighted IDENTICAL residue SER 217 index1 217 path 269 %Seq 100.00
Highlighted IDENTICAL residue ILE 218 index1 218 path 270 %Seq 100.00
Highlighted IDENTICAL residue PRO 223 index1 223 path 275 %Seq 100.00
Highlighted IDENTICAL residue ALA 225 index1 225 path 277 %Seq 100.00
Highlighted IDENTICAL residue GLU 227 index1 227 path 279 %Seq 100.00
Highlighted IDENTICAL residue SER 233 index1 233 path 285 %Seq 100.00
Highlighted IDENTICAL residue PHE 235 index1 235 path 287 %Seq 100.00
Highlighted IDENTICAL residue LYS 237 index1 237 path 289 %Seq 100.00
Highlighted IDENTICAL residue THR 242 index1 242 path 294 %Seq 100.00
Highlighted IDENTICAL residue GLY 243 index1 243 path 295 %Seq 100.00
Highlighted IDENTICAL residue ARG 245 index1 245 path 297 %Seq 100.00
Highlighted IDENTICAL residue GLY 247 index1 247 path 299 %Seq 100.00
Highlighted IDENTICAL residue LEU 249 index1 249 path 309 %Seq 50.00
Highlighted IDENTICAL residue ALA 250 index1 250 path 310 %Seq 50.00
Highlighted IDENTICAL residue GLY 251 index1 251 path 311 %Seq 50.00
Highlighted IDENTICAL residue PRO 252 index1 252 path 312 %Seq 50.00
Highlighted IDENTICAL residue VAL 253 index1 253 path 313 %Seq 50.00
Highlighted IDENTICAL residue PRO 254 index1 254 path 314 %Seq 50.00
Highlighted IDENTICAL residue LEU 255 index1 255 path 315 %Seq 50.00
Highlighted IDENTICAL residue ILE 262 index1 262 path 322 %Seq 100.00
Highlighted IDENTICAL residue SER 266 index1 266 path 326 %Seq 100.00
Highlighted IDENTICAL residue ALA 274 index1 274 path 334 %Seq 100.00
Highlighted IDENTICAL residue GLN 275 index1 275 path 335 %Seq 100.00
Highlighted IDENTICAL residue GLY 277 index1 277 path 337 %Seq 100.00
Highlighted IDENTICAL residue ALA 280 index1 280 path 340 %Seq 100.00
Highlighted IDENTICAL residue ASN 284 index1 284 path 344 %Seq 50.00
Highlighted IDENTICAL residue GLU 298 index1 298 path 359 %Seq 100.00
Highlighted IDENTICAL residue ARG 300 index1 300 path 361 %Seq 100.00
Highlighted IDENTICAL residue ASP 305 index1 305 path 366 %Seq 100.00
Highlighted IDENTICAL residue LEU 307 index1 307 path 368 %Seq 100.00
Highlighted IDENTICAL residue GLY 312 index1 312 path 373 %Seq 100.00
Highlighted IDENTICAL residue LEU 313 index1 313 path 374 %Seq 100.00
Highlighted IDENTICAL residue ALA 321 index1 321 path 382 %Seq 100.00
Highlighted IDENTICAL residue TYR 323 index1 323 path 384 %Seq 100.00
Highlighted IDENTICAL residue GLY 332 index1 332 path 393 %Seq 100.00
Highlighted IDENTICAL residue SER 335 index1 335 path 396 %Seq 100.00
Highlighted IDENTICAL residue ASP 337 index1 337 path 398 %Seq 100.00
Highlighted IDENTICAL residue GLU 341 index1 341 path 402 %Seq 100.00
Highlighted IDENTICAL residue LEU 343 index1 343 path 404 %Seq 100.00
Highlighted IDENTICAL residue THR 350 index1 350 path 411 %Seq 100.00
Highlighted IDENTICAL residue VAL 351 index1 351 path 412 %Seq 100.00
Highlighted IDENTICAL residue PRO 352 index1 352 path 413 %Seq 100.00
Highlighted IDENTICAL residue GLY 353 index1 353 path 414 %Seq 100.00
Highlighted IDENTICAL residue PHE 356 index1 356 path 417 %Seq 100.00
Highlighted IDENTICAL residue GLY 357 index1 357 path 420 %Seq 50.00
Highlighted IDENTICAL residue ARG 363 index1 363 path 426 %Seq 100.00
Highlighted IDENTICAL residue SER 365 index1 365 path 428 %Seq 100.00
Highlighted IDENTICAL residue ASP 371 index1 371 path 434 %Seq 100.00
Highlighted IDENTICAL residue ILE 373 index1 373 path 436 %Seq 100.00
Highlighted IDENTICAL residue ARG 379 index1 379 path 442 %Seq 100.00
Highlighted IDENTICAL residue LEU 380 index1 380 path 443 %Seq 100.00
Highlighted IDENTICAL residue PHE 383 index1 383 path 446 %Seq 100.00
Highlighted 91 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13810-1j32_A.pir.txt.1J32.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13810-1j32_A.pir.txt PIR amino_acid 1J32.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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