At2g02980.1/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 = 1
Read 2 amino_acid sequences from FASTA Sequence file /usr/local/www/html/proteins/workspace/At2g02980-1e3b_A.pir.txt
======================================================
Assigned types to 603 residues in Sequence P1;, 10 remain unknown
Assigned types to 378 residues in Sequence P1;, 235 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
======================================================
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 195 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 196 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 197 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 294 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 295 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 296 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 339 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 400 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 409 All residues are positively and negatively charged
Translated sequence file At2g02980-1e3b_A.pir.txt into sequence alignment.
======================================================
>1W3B.pdb Made from 5568 ATOM records in 1W3B.pdb
GPMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLD
RSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDF
IDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGR
LEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP
NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQ
GLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL
CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQ
QQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDGPMELAHREYQA
GDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQ
NPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALV
AAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAI
ETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNV
LKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRR
AIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSYRKAL
EVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNT
LKEMQD
======================================================
Best alignment:
1W3B.pdb 2 PMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDR 51
 PMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDR
P1; 1 PMELAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDR 50
1W3B.pdb 52 SAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFI 101
 SAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFI
P1; 51 SAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFI 100
1W3B.pdb 102 DGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRL 151
 DGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRL
P1; 101 DGYINLAAALVAAGDMEGAVQAYVSALQYNXXXYCVRSDLGNLLKALGRL 150
1W3B.pdb 152 EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN 201
 EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN
P1; 151 EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN 200
1W3B.pdb 202 FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQG 251
 FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQG
P1; 201 FLDAYINLGNVLKEARIFDRAVAAYLRXXXLSPNHAVVHGNLACVYYEQG 250
1W3B.pdb 252 LIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC 301
 LIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC
P1; 251 LIDLAIDTYRRAIELQPHFPXAYCNLANALKEKGSVAEAEDCYNTALRLC 300
1W3B.pdb 302 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ 351
 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQ
P1; 301 PTHADSLNNLANIKREQGNIEEAVRLYRKXLEVFPEFAXAHSNLASVLQQ 350
1W3B.pdb 352 QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDG 389
 QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD 
P1; 351 QGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD* 388
======================================================
Highlighted IDENTICAL residue GLU 28 index1 16 path 76 %Seq 100.00
Highlighted IDENTICAL residue LEU 37 index1 25 path 85 %Seq 100.00
Highlighted IDENTICAL residue LEU 85 index1 73 path 135 %Seq 100.00
Highlighted IDENTICAL residue LEU 95 index1 83 path 145 %Seq 100.00
Highlighted IDENTICAL residue GLU 97 index1 85 path 147 %Seq 100.00
Highlighted IDENTICAL residue LEU 108 index1 96 path 158 %Seq 100.00
Highlighted IDENTICAL residue ASP 111 index1 99 path 162 %Seq 100.00
Highlighted IDENTICAL residue LEU 119 index1 107 path 170 %Seq 100.00
Highlighted IDENTICAL residue ASP 128 index1 116 path 179 %Seq 100.00
Highlighted IDENTICAL residue ALA 132 index1 120 path 183 %Seq 100.00
Highlighted IDENTICAL residue ARG 162 index1 150 path 213 %Seq 100.00
Highlighted IDENTICAL residue GLU 165 index1 153 path 216 %Seq 100.00
Highlighted IDENTICAL residue ALA 166 index1 154 path 217 %Seq 100.00
Highlighted IDENTICAL residue GLY 195 index1 183 path 247 %Seq 100.00
Highlighted IDENTICAL residue LEU 199 index1 187 path 251 %Seq 100.00
Highlighted IDENTICAL residue ALA 207 index1 195 path 259 %Seq 100.00
Highlighted IDENTICAL residue LEU 221 index1 209 path 274 %Seq 100.00
Highlighted IDENTICAL residue ASP 232 index1 220 path 285 %Seq 100.00
Highlighted IDENTICAL residue ALA 234 index1 222 path 287 %Seq 100.00
Highlighted IDENTICAL residue VAL 235 index1 223 path 288 %Seq 100.00
Highlighted IDENTICAL residue TYR 259 index1 247 path 312 %Seq 100.00
Highlighted IDENTICAL residue GLY 263 index1 251 path 316 %Seq 100.00
Highlighted IDENTICAL residue ARG 274 index1 262 path 327 %Seq 100.00
Highlighted IDENTICAL residue GLN 279 index1 267 path 334 %Seq 100.00
Highlighted IDENTICAL residue PRO 280 index1 268 path 335 %Seq 100.00
Highlighted IDENTICAL residue LEU 289 index1 277 path 344 %Seq 100.00
Highlighted IDENTICAL residue ASN 291 index1 279 path 346 %Seq 100.00
Highlighted IDENTICAL residue ALA 292 index1 280 path 347 %Seq 100.00
Highlighted IDENTICAL residue GLY 297 index1 285 path 352 %Seq 100.00
Highlighted IDENTICAL residue VAL 299 index1 287 path 354 %Seq 100.00
Highlighted IDENTICAL residue GLU 301 index1 289 path 356 %Seq 100.00
Highlighted IDENTICAL residue GLY 331 index1 319 path 388 %Seq 100.00
Highlighted IDENTICAL residue ASN 332 index1 320 path 389 %Seq 100.00
Highlighted IDENTICAL residue GLU 334 index1 322 path 391 %Seq 100.00
Highlighted IDENTICAL residue ALA 336 index1 324 path 393 %Seq 100.00
Highlighted IDENTICAL residue LYS 342 index1 330 path 399 %Seq 100.00
Highlighted IDENTICAL residue LEU 344 index1 332 path 401 %Seq 100.00
Highlighted IDENTICAL residue PRO 348 index1 336 path 405 %Seq 100.00
Highlighted IDENTICAL residue LEU 357 index1 345 path 414 %Seq 100.00
Highlighted IDENTICAL residue LEU 367 index1 355 path 424 %Seq 100.00
Highlighted IDENTICAL residue ALA 370 index1 358 path 427 %Seq 100.00
Highlighted IDENTICAL residue TYR 388 index1 376 path 445 %Seq 100.00
Highlighted IDENTICAL residue ASN 393 index1 381 path 450 %Seq 100.00
Highlighted IDENTICAL residue GLY 13 index1 389 path 613 %Seq 100.00
Highlighted 44 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g02980-1e3b_A.pir.txt.1W3B.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g02980-1e3b_A.pir.txt FASTA amino_acid 1W3B.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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