At2g10836.1/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
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g10836-1fgu_A.pir.txt
======================================================
Assigned types to 282 residues in Sequence 2-10836, 37 remain unknown
Assigned types to 213 residues in Sequence 1fgu_A, 106 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 64 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 65 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 66 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 67 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 68 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 69 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 70 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 71 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 72 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 73 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 74 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 75 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 76 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 77 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 156 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 157 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 158 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 159 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 160 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 161 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 162 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 163 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 164 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 165 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 166 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 167 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 168 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 169 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 170 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 171 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 172 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 173 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 174 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 175 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 176 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 177 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 178 All residues are positively and negatively charged
Translated sequence file At2g10836-1fgu_A.pir.txt into sequence alignment.
======================================================
>1FGU.pdb Made from 3793 ATOM records in 1FGU.pdb
MSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES
GEIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTF
NNETSVMPCEDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDAT
KITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKG
ARVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSMSKV
VPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIR
ATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNET
SVMPCVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVA
KRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGARVSDFGGRSLS
VLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVS
======================================================
Best alignment:
1FGU.pdb 2 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG 51
 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG
1fgu_A 1 SKVVPIASLTPYQSKWTICARVXXXXXXXXXXXXXXEGKLFSLELVDESG 50
1FGU.pdb 52 EIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFN 101
 EIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFN
1fgu_A 51 EIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFN 100
1FGU.pdb 102 NETSVMPCEDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATK 151
 NETSVMPCEDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATK
1fgu_A 101 NETSVMPCEDXXXXXXXXXXXXXXXXXXXXXXXSLVDIIGICKSYEDATK 150
1FGU.pdb 152 ITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA 201
 ITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA
1fgu_A 151 ITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQPVLAIKGA 200
1FGU.pdb 202 RVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSMS 248
 RVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVS+S
1fgu_A 201 RVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSIS 247
======================================================
Highlighted IDENTICAL residue ILE 187 index1 7 path 47 %Seq 100.00
Highlighted IDENTICAL residue LEU 190 index1 10 path 50 %Seq 100.00
Highlighted IDENTICAL residue SER 195 index1 15 path 55 %Seq 100.00
Highlighted IDENTICAL residue GLU 225 index1 45 path 85 %Seq 100.00
Highlighted IDENTICAL residue VAL 227 index1 47 path 87 %Seq 100.00
Highlighted IDENTICAL residue GLY 231 index1 51 path 91 %Seq 100.00
Highlighted IDENTICAL residue ILE 233 index1 53 path 94 %Seq 100.00
Highlighted IDENTICAL residue ALA 235 index1 55 path 96 %Seq 100.00
Highlighted IDENTICAL residue LEU 262 index1 82 path 124 %Seq 100.00
Highlighted IDENTICAL residue ASN 274 index1 94 path 138 %Seq 100.00
Highlighted IDENTICAL residue PHE 280 index1 100 path 144 %Seq 100.00
Highlighted IDENTICAL residue THR 284 index1 104 path 148 %Seq 100.00
Highlighted IDENTICAL residue PRO 288 index1 108 path 152 %Seq 100.00
Highlighted IDENTICAL residue GLY 321 index1 141 path 185 %Seq 100.00
Highlighted IDENTICAL residue GLU 327 index1 147 path 191 %Seq 100.00
Highlighted IDENTICAL residue THR 330 index1 150 path 194 %Seq 100.00
Highlighted IDENTICAL residue VAL 334 index1 154 path 202 %Seq 100.00
Highlighted IDENTICAL residue ASN 337 index1 157 path 205 %Seq 100.00
Highlighted IDENTICAL residue THR 351 index1 171 path 219 %Seq 100.00
Highlighted IDENTICAL residue GLY 353 index1 173 path 221 %Seq 100.00
Highlighted IDENTICAL residue LYS 354 index1 174 path 222 %Seq 100.00
Highlighted IDENTICAL residue GLY 362 index1 182 path 230 %Seq 100.00
Highlighted IDENTICAL residue PHE 368 index1 188 path 236 %Seq 100.00
Highlighted IDENTICAL residue VAL 383 index1 203 path 267 %Seq 100.00
Highlighted IDENTICAL residue ASP 385 index1 205 path 269 %Seq 100.00
Highlighted IDENTICAL residue GLY 388 index1 208 path 272 %Seq 100.00
Highlighted IDENTICAL residue ARG 389 index1 209 path 273 %Seq 100.00
Highlighted IDENTICAL residue SER 392 index1 212 path 278 %Seq 100.00
Highlighted IDENTICAL residue SER 397 index1 217 path 283 %Seq 100.00
Highlighted IDENTICAL residue ILE 399 index1 219 path 285 %Seq 100.00
Highlighted IDENTICAL residue ASN 402 index1 222 path 288 %Seq 100.00
Highlighted IDENTICAL residue PRO 406 index1 226 path 292 %Seq 100.00
Highlighted IDENTICAL residue GLU 407 index1 227 path 293 %Seq 100.00
Highlighted IDENTICAL residue ARG 412 index1 232 path 298 %Seq 100.00
Highlighted IDENTICAL residue PHE 415 index1 235 path 303 %Seq 100.00
Highlighted IDENTICAL residue GLN 420 index1 240 path 308 %Seq 100.00
Highlighted 36 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g10836-1fgu_A.pir.txt.1FGU.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g10836-1fgu_A.pir.txt PIR amino_acid 1FGU.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@