At2g02740.1/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
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
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Got here 3
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Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g02740-1l3aA.pir.txt
======================================================
Assigned types to 268 residues in Sequence 2-02740, 0 remain unknown
Assigned types to 166 residues in Sequence 1l3aA, 102 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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Translated sequence file At2g02740-1l3aA.pir.txt into sequence alignment.
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>1L3A.pdb Made from 5435 ATOM records in 1L3A.pdb
TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAA
GVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRK
VLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVM
PYLLGWHTAVNSFKPETPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAF
KLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEF
FHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPV
TKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEAELETPKVFVGYSIYKGK
AALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFS
LSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHF
FNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFK
PESGAELEWNLEHHHHHHTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSG
AFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSC
EFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYI
PVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEGAELE
======================================================
Best alignment:
1L3A.pdb 327 NSFKPEAELETPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREG 376
 +S AE+ +P+ +VG+SIYKGKAALT+EPR+PEF L+SGAFKL++EG
2-02740 72 SSSSQNAEVSSPRFYVGHSIYKGKAALTIEPRAPEFVALESGAFKLTKEG 121
1L3A.pdb 377 MVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNK 426
 ++LQFAPAAGVRQYDWSRKQVFSLSVTEIG+++SLG ++SCEFFHDP K
2-02740 122 FLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPFK 171
1L3A.pdb 427 GR-SDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEF 475
 G+ SDEG+VRKVLKVEPLPDGSG FFNLSVQNKL+N+DE++YIP+TKAEF
2-02740 172 GKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEF 221
1L3A.pdb 476 AVLVSAFNFVMPYLLGWHTAVNSFKPESGAEL 507
 AVL+SAFNFV+P+L+GW NS KPE L
2-02740 222 AVLISAFNFVLPHLIGWSAFANSIKPEDSNRL 253
======================================================
Highlighted IDENTICAL residue ASN 249 index1 327 path 72 %Seq 50.00
Highlighted IDENTICAL residue SER 250 index1 328 path 73 %Seq 50.00
Highlighted IDENTICAL residue PHE 251 index1 329 path 74 %Seq 50.00
Highlighted IDENTICAL residue LYS 252 index1 330 path 75 %Seq 50.00
Highlighted IDENTICAL residue PRO 253 index1 331 path 76 %Seq 50.00
Highlighted IDENTICAL residue GLU 254 index1 332 path 77 %Seq 50.00
Highlighted IDENTICAL residue ALA 268 index1 333 path 78 %Seq 50.00
Highlighted IDENTICAL residue GLU 269 index1 334 path 79 %Seq 50.00
Highlighted IDENTICAL residue LEU 270 index1 335 path 80 %Seq 50.00
Highlighted IDENTICAL residue GLU 271 index1 336 path 81 %Seq 50.00
Highlighted IDENTICAL residue PRO 90 index1 338 path 83 %Seq 100.00
Highlighted IDENTICAL residue VAL 94 index1 342 path 87 %Seq 100.00
Highlighted IDENTICAL residue GLY 95 index1 343 path 88 %Seq 100.00
Highlighted IDENTICAL residue SER 97 index1 345 path 90 %Seq 100.00
Highlighted IDENTICAL residue ILE 98 index1 346 path 91 %Seq 100.00
Highlighted IDENTICAL residue TYR 99 index1 347 path 92 %Seq 100.00
Highlighted IDENTICAL residue LYS 100 index1 348 path 93 %Seq 100.00
Highlighted IDENTICAL residue GLY 101 index1 349 path 94 %Seq 100.00
Highlighted IDENTICAL residue LYS 102 index1 350 path 95 %Seq 100.00
Highlighted IDENTICAL residue ALA 103 index1 351 path 96 %Seq 100.00
Highlighted IDENTICAL residue ALA 104 index1 352 path 97 %Seq 100.00
Highlighted IDENTICAL residue LEU 105 index1 353 path 98 %Seq 100.00
Highlighted IDENTICAL residue THR 106 index1 354 path 99 %Seq 100.00
Highlighted IDENTICAL residue GLU 108 index1 356 path 101 %Seq 100.00
Highlighted IDENTICAL residue PRO 109 index1 357 path 102 %Seq 100.00
Highlighted IDENTICAL residue ARG 110 index1 358 path 103 %Seq 100.00
Highlighted IDENTICAL residue PRO 112 index1 360 path 105 %Seq 100.00
Highlighted IDENTICAL residue GLU 113 index1 361 path 106 %Seq 100.00
Highlighted IDENTICAL residue PHE 114 index1 362 path 107 %Seq 100.00
Highlighted IDENTICAL residue LEU 117 index1 365 path 110 %Seq 100.00
Highlighted IDENTICAL residue SER 119 index1 367 path 112 %Seq 100.00
Highlighted IDENTICAL residue GLY 120 index1 368 path 113 %Seq 100.00
Highlighted IDENTICAL residue ALA 121 index1 369 path 114 %Seq 100.00
Highlighted IDENTICAL residue PHE 122 index1 370 path 115 %Seq 100.00
Highlighted IDENTICAL residue LYS 123 index1 371 path 116 %Seq 100.00
Highlighted IDENTICAL residue LEU 124 index1 372 path 117 %Seq 100.00
Highlighted IDENTICAL residue GLU 127 index1 375 path 120 %Seq 100.00
Highlighted IDENTICAL residue GLY 128 index1 376 path 121 %Seq 100.00
Highlighted IDENTICAL residue LEU 132 index1 380 path 125 %Seq 100.00
Highlighted IDENTICAL residue GLN 133 index1 381 path 126 %Seq 100.00
Highlighted IDENTICAL residue PHE 134 index1 382 path 127 %Seq 100.00
Highlighted IDENTICAL residue ALA 135 index1 383 path 128 %Seq 100.00
Highlighted IDENTICAL residue PRO 136 index1 384 path 129 %Seq 100.00
Highlighted IDENTICAL residue ALA 137 index1 385 path 130 %Seq 100.00
Highlighted IDENTICAL residue ALA 138 index1 386 path 131 %Seq 100.00
Highlighted IDENTICAL residue GLY 139 index1 387 path 132 %Seq 100.00
Highlighted IDENTICAL residue VAL 140 index1 388 path 133 %Seq 100.00
Highlighted IDENTICAL residue ARG 141 index1 389 path 134 %Seq 100.00
Highlighted IDENTICAL residue GLN 142 index1 390 path 135 %Seq 100.00
Highlighted IDENTICAL residue TYR 143 index1 391 path 136 %Seq 100.00
Highlighted IDENTICAL residue ASP 144 index1 392 path 137 %Seq 100.00
Highlighted IDENTICAL residue TRP 145 index1 393 path 138 %Seq 100.00
Highlighted IDENTICAL residue SER 146 index1 394 path 139 %Seq 100.00
Highlighted IDENTICAL residue ARG 147 index1 395 path 140 %Seq 100.00
Highlighted IDENTICAL residue LYS 148 index1 396 path 141 %Seq 100.00
Highlighted IDENTICAL residue GLN 149 index1 397 path 142 %Seq 100.00
Highlighted IDENTICAL residue VAL 150 index1 398 path 143 %Seq 100.00
Highlighted IDENTICAL residue PHE 151 index1 399 path 144 %Seq 100.00
Highlighted IDENTICAL residue SER 152 index1 400 path 145 %Seq 100.00
Highlighted IDENTICAL residue LEU 153 index1 401 path 146 %Seq 100.00
Highlighted IDENTICAL residue SER 154 index1 402 path 147 %Seq 100.00
Highlighted IDENTICAL residue VAL 155 index1 403 path 148 %Seq 100.00
Highlighted IDENTICAL residue THR 156 index1 404 path 149 %Seq 100.00
Highlighted IDENTICAL residue GLU 157 index1 405 path 150 %Seq 100.00
Highlighted IDENTICAL residue ILE 158 index1 406 path 151 %Seq 100.00
Highlighted IDENTICAL residue GLY 159 index1 407 path 152 %Seq 100.00
Highlighted IDENTICAL residue SER 163 index1 411 path 156 %Seq 100.00
Highlighted IDENTICAL residue LEU 164 index1 412 path 157 %Seq 100.00
Highlighted IDENTICAL residue GLY 165 index1 413 path 158 %Seq 100.00
Highlighted IDENTICAL residue SER 169 index1 417 path 162 %Seq 100.00
Highlighted IDENTICAL residue CYS 170 index1 418 path 163 %Seq 100.00
Highlighted IDENTICAL residue GLU 171 index1 419 path 164 %Seq 100.00
Highlighted IDENTICAL residue PHE 172 index1 420 path 165 %Seq 100.00
Highlighted IDENTICAL residue PHE 173 index1 421 path 166 %Seq 100.00
Highlighted IDENTICAL residue HIS 174 index1 422 path 167 %Seq 100.00
Highlighted IDENTICAL residue ASP 175 index1 423 path 168 %Seq 100.00
Highlighted IDENTICAL residue PRO 176 index1 424 path 169 %Seq 100.00
Highlighted IDENTICAL residue LYS 178 index1 426 path 171 %Seq 100.00
Highlighted IDENTICAL residue GLY 179 index1 427 path 172 %Seq 100.00
Highlighted IDENTICAL residue SER 181 index1 429 path 175 %Seq 100.00
Highlighted IDENTICAL residue ASP 182 index1 430 path 176 %Seq 100.00
Highlighted IDENTICAL residue GLU 183 index1 431 path 177 %Seq 100.00
Highlighted IDENTICAL residue GLY 184 index1 432 path 178 %Seq 100.00
Highlighted IDENTICAL residue VAL 186 index1 434 path 180 %Seq 100.00
Highlighted IDENTICAL residue ARG 187 index1 435 path 181 %Seq 100.00
Highlighted IDENTICAL residue LYS 188 index1 436 path 182 %Seq 100.00
Highlighted IDENTICAL residue VAL 189 index1 437 path 183 %Seq 100.00
Highlighted IDENTICAL residue LEU 190 index1 438 path 184 %Seq 100.00
Highlighted IDENTICAL residue LYS 191 index1 439 path 185 %Seq 100.00
Highlighted IDENTICAL residue VAL 192 index1 440 path 186 %Seq 100.00
Highlighted IDENTICAL residue GLU 193 index1 441 path 187 %Seq 100.00
Highlighted IDENTICAL residue PRO 194 index1 442 path 188 %Seq 100.00
Highlighted IDENTICAL residue LEU 195 index1 443 path 189 %Seq 100.00
Highlighted IDENTICAL residue PRO 196 index1 444 path 190 %Seq 100.00
Highlighted IDENTICAL residue ASP 197 index1 445 path 191 %Seq 100.00
Highlighted IDENTICAL residue GLY 198 index1 446 path 192 %Seq 100.00
Highlighted IDENTICAL residue SER 199 index1 447 path 193 %Seq 100.00
Highlighted IDENTICAL residue GLY 200 index1 448 path 194 %Seq 100.00
Highlighted IDENTICAL residue PHE 202 index1 450 path 196 %Seq 100.00
Highlighted IDENTICAL residue PHE 203 index1 451 path 197 %Seq 100.00
Highlighted IDENTICAL residue ASN 204 index1 452 path 198 %Seq 100.00
Highlighted IDENTICAL residue LEU 205 index1 453 path 199 %Seq 100.00
Highlighted IDENTICAL residue SER 206 index1 454 path 200 %Seq 100.00
Highlighted IDENTICAL residue VAL 207 index1 455 path 201 %Seq 100.00
Highlighted IDENTICAL residue GLN 208 index1 456 path 202 %Seq 100.00
Highlighted IDENTICAL residue ASN 209 index1 457 path 203 %Seq 100.00
Highlighted IDENTICAL residue LYS 210 index1 458 path 204 %Seq 100.00
Highlighted IDENTICAL residue LEU 211 index1 459 path 205 %Seq 100.00
Highlighted IDENTICAL residue ASN 213 index1 461 path 207 %Seq 100.00
Highlighted IDENTICAL residue ASP 215 index1 463 path 209 %Seq 100.00
Highlighted IDENTICAL residue GLU 216 index1 464 path 210 %Seq 100.00
Highlighted IDENTICAL residue TYR 219 index1 467 path 213 %Seq 100.00
Highlighted IDENTICAL residue ILE 220 index1 468 path 214 %Seq 100.00
Highlighted IDENTICAL residue PRO 221 index1 469 path 215 %Seq 100.00
Highlighted IDENTICAL residue THR 223 index1 471 path 217 %Seq 100.00
Highlighted IDENTICAL residue LYS 224 index1 472 path 218 %Seq 100.00
Highlighted IDENTICAL residue ALA 225 index1 473 path 219 %Seq 100.00
Highlighted IDENTICAL residue GLU 226 index1 474 path 220 %Seq 100.00
Highlighted IDENTICAL residue PHE 227 index1 475 path 221 %Seq 100.00
Highlighted IDENTICAL residue ALA 228 index1 476 path 222 %Seq 100.00
Highlighted IDENTICAL residue VAL 229 index1 477 path 223 %Seq 100.00
Highlighted IDENTICAL residue LEU 230 index1 478 path 224 %Seq 100.00
Highlighted IDENTICAL residue SER 232 index1 480 path 226 %Seq 100.00
Highlighted IDENTICAL residue ALA 233 index1 481 path 227 %Seq 100.00
Highlighted IDENTICAL residue PHE 234 index1 482 path 228 %Seq 100.00
Highlighted IDENTICAL residue ASN 235 index1 483 path 229 %Seq 100.00
Highlighted IDENTICAL residue PHE 236 index1 484 path 230 %Seq 100.00
Highlighted IDENTICAL residue VAL 237 index1 485 path 231 %Seq 100.00
Highlighted IDENTICAL residue PRO 239 index1 487 path 233 %Seq 100.00
Highlighted IDENTICAL residue LEU 241 index1 489 path 235 %Seq 100.00
Highlighted IDENTICAL residue GLY 243 index1 491 path 237 %Seq 100.00
Highlighted IDENTICAL residue TRP 244 index1 492 path 238 %Seq 100.00
Highlighted IDENTICAL residue ASN 249 index1 497 path 243 %Seq 100.00
Highlighted IDENTICAL residue SER 250 index1 498 path 244 %Seq 100.00
Highlighted IDENTICAL residue LYS 252 index1 500 path 246 %Seq 100.00
Highlighted IDENTICAL residue PRO 253 index1 501 path 247 %Seq 100.00
Highlighted IDENTICAL residue GLU 254 index1 502 path 248 %Seq 100.00
Highlighted IDENTICAL residue SER 266 index1 503 path 249 %Seq 50.00
Highlighted IDENTICAL residue GLY 267 index1 504 path 250 %Seq 50.00
Highlighted IDENTICAL residue ALA 268 index1 505 path 251 %Seq 50.00
Highlighted IDENTICAL residue GLU 269 index1 506 path 252 %Seq 50.00
Highlighted IDENTICAL residue LEU 270 index1 507 path 253 %Seq 50.00
Highlighted 142 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02740-1l3aA.pir.txt.1L3A.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02740-1l3aA.pir.txt PIR amino_acid 1L3A.pdb A 100.0 BLOSUM62.dat 
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@