At2g04360.1/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
Got here 3
Sequence 1
Got here 3
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Got here 3
Got here 4
Got here 3
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Sequence 2
Got here 3
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04360-1oe9A.pir.txt
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Assigned types to 320 residues in Sequence 2-4360, 34 remain unknown
Assigned types to 245 residues in Sequence 1oe9A, 109 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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Translated sequence file At2g04360-1oe9A.pir.txt into sequence alignment.
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>1OE9.pdb Made from 6925 ATOM records in 1OE9.pdb
ELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLDLEYCLKELPPL
RNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINP
YEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVS
GESGAGKTVSAKYAMRYFATVSNVEEKVLASNPIMESIGNAKTTRNDNSS
RFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVFQAEEERNYHIFYQLCAS
AALPEFKTLRLGNANYFHYTKQGGSPVIDGIDDAKEMVNTRQACTLLGIS
DSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIFCDLMGVDY
EEMAHWLCHRKLATYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKA
LHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKL
EQEEYMKEQIPDFYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQK
LYNTHLNKCALFEKPRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQ
IKVLKSSKKFKLLPELFHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKP
NDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVL
MKQKDVLSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIRA
DKLRAACIRIQKTIRGWLMRKKYMRMRRGDAFNKDQLEEFKEAFELFDRV
GDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLP
MLQAVAKYEDYLEGFRVFDGNGKVMGAELRHVLTTLGEKMTEEEVETVLA
GHEDSNGCINYEAFLKHILS
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Best alignment:
1OE9.pdb 90 YCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMA 139
 YCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMA
1oe9A 1 YCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMA 50
1OE9.pdb 140 RDERNQSIIVSGESGAGKTVSAKYAMRYFATV------SNVEEKVLASNP 183
 RDERNQSIIVSGESGAGKTVSAKYAMRYFATV +NVEEKVLASNP
1oe9A 51 RDERNQSIIVSGESGAGKTVSAKYAMRYFATVSGSASEANVEEKVLASNP 100
1OE9.pdb 184 IMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVF 233
 IMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVF
1oe9A 101 IMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVF 150
1OE9.pdb 234 QAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDD 283
 QAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDD
1oe9A 151 QAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDD 200
1OE9.pdb 284 AKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSD 328
 AKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSD
1oe9A 201 AKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSD 245
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Highlighted IDENTICAL residue GLY 104 index1 92 path 3 %Seq 100.00
Highlighted IDENTICAL residue LEU 116 index1 104 path 15 %Seq 100.00
Highlighted IDENTICAL residue PRO 117 index1 105 path 16 %Seq 100.00
Highlighted IDENTICAL residue ILE 118 index1 106 path 29 %Seq 50.00
Highlighted IDENTICAL residue TYR 119 index1 107 path 30 %Seq 50.00
Highlighted IDENTICAL residue GLN 130 index1 118 path 41 %Seq 100.00
Highlighted IDENTICAL residue PRO 137 index1 125 path 48 %Seq 100.00
Highlighted IDENTICAL residue HIS 138 index1 126 path 49 %Seq 100.00
Highlighted IDENTICAL residue ALA 141 index1 129 path 52 %Seq 100.00
Highlighted IDENTICAL residue ALA 146 index1 134 path 57 %Seq 50.00
Highlighted IDENTICAL residue TYR 147 index1 135 path 58 %Seq 50.00
Highlighted IDENTICAL residue LYS 148 index1 136 path 59 %Seq 50.00
Highlighted IDENTICAL residue GLN 149 index1 137 path 60 %Seq 50.00
Highlighted IDENTICAL residue MET 150 index1 138 path 61 %Seq 50.00
Highlighted IDENTICAL residue ALA 151 index1 139 path 62 %Seq 50.00
Highlighted IDENTICAL residue SER 165 index1 153 path 76 %Seq 100.00
Highlighted IDENTICAL residue LYS 174 index1 162 path 85 %Seq 100.00
Highlighted IDENTICAL residue PHE 180 index1 168 path 91 %Seq 50.00
Highlighted IDENTICAL residue ALA 181 index1 169 path 92 %Seq 50.00
Highlighted IDENTICAL residue THR 182 index1 170 path 93 %Seq 50.00
Highlighted IDENTICAL residue VAL 183 index1 171 path 94 %Seq 50.00
Highlighted IDENTICAL residue LEU 197 index1 179 path 108 %Seq 100.00
Highlighted IDENTICAL residue ALA 209 index1 191 path 120 %Seq 100.00
Highlighted IDENTICAL residue THR 211 index1 193 path 122 %Seq 50.00
Highlighted IDENTICAL residue THR 212 index1 194 path 123 %Seq 50.00
Highlighted IDENTICAL residue ARG 213 index1 195 path 124 %Seq 50.00
Highlighted IDENTICAL residue GLY 236 index1 218 path 155 %Seq 100.00
Highlighted IDENTICAL residue LEU 243 index1 225 path 162 %Seq 100.00
Highlighted IDENTICAL residue PHE 262 index1 244 path 184 %Seq 100.00
Highlighted IDENTICAL residue LEU 265 index1 247 path 187 %Seq 100.00
Highlighted IDENTICAL residue LEU 279 index1 261 path 202 %Seq 100.00
Highlighted IDENTICAL residue ASN 281 index1 263 path 204 %Seq 100.00
Highlighted IDENTICAL residue PHE 285 index1 267 path 208 %Seq 50.00
Highlighted IDENTICAL residue HIS 286 index1 268 path 209 %Seq 50.00
Highlighted IDENTICAL residue TYR 287 index1 269 path 210 %Seq 50.00
Highlighted IDENTICAL residue THR 288 index1 270 path 211 %Seq 50.00
Highlighted IDENTICAL residue LYS 289 index1 271 path 212 %Seq 50.00
Highlighted IDENTICAL residue GLN 290 index1 272 path 213 %Seq 50.00
Highlighted IDENTICAL residue GLY 291 index1 273 path 214 %Seq 50.00
Highlighted IDENTICAL residue GLY 292 index1 274 path 215 %Seq 50.00
Highlighted IDENTICAL residue SER 293 index1 275 path 216 %Seq 50.00
Highlighted IDENTICAL residue PRO 294 index1 276 path 217 %Seq 50.00
Highlighted IDENTICAL residue VAL 295 index1 277 path 218 %Seq 50.00
Highlighted IDENTICAL residue ILE 296 index1 278 path 219 %Seq 50.00
Highlighted IDENTICAL residue THR 313 index1 295 path 236 %Seq 50.00
Highlighted IDENTICAL residue LEU 314 index1 296 path 237 %Seq 50.00
Highlighted IDENTICAL residue LEU 315 index1 297 path 238 %Seq 50.00
Highlighted IDENTICAL residue GLY 316 index1 298 path 239 %Seq 50.00
Highlighted IDENTICAL residue ILE 317 index1 299 path 240 %Seq 50.00
Highlighted IDENTICAL residue SER 318 index1 300 path 241 %Seq 50.00
Highlighted IDENTICAL residue ASP 319 index1 301 path 242 %Seq 50.00
Highlighted IDENTICAL residue LEU 329 index1 311 path 252 %Seq 100.00
Highlighted IDENTICAL residue LEU 333 index1 315 path 256 %Seq 100.00
Highlighted IDENTICAL residue ASP 346 index1 328 path 269 %Seq 100.00
Highlighted 54 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04360-1oe9A.pir.txt.1OE9.pdb.conservation.pml
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The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04360-1oe9A.pir.txt PIR amino_acid 1OE9.pdb A 100.0 BLOSUM62.dat 
completed successfully.
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