At2g03050.1/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 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 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 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 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 Got here 4 Got here 3 Got here 4 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g03050-1lshA0.pir.txt

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Assigned types to 283 residues in Sequence 2-03050, 314 remain unknown Assigned types to 955 residues in Sequence 1lshA0, 20 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 At2g03050-1lshA0.pir.txt into sequence alignment.

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>1LSH.pdb Made from 9148 ATOM records in 1LSH.pdb FQPGKVYRYSYDAFSISGLPEPGVNRAGLSGEMKIEIHGHTHNQATLKIT QVNLKYFLGPWPSDSFYPLTGGYDHFIQQLEVPVRFDYSAGRIGDIYAPP QVTDTAVNIVRGILNLFQLSLKKNQQTFELQETGVEGICQTTYVVQEGYR TNEMAVVKTKDLNNCDHKVYKTMGTAYAERCPTCQKMNKNLRSTAVYNYA IFDEPSGYIIKSAHSEEIQQLSVFDIKEGNVVIESRQKLILEGIQSAPAA SQAASLQNRGGLMYKFPSSAITKMSSLFVTKGKNLESEIHTVLKHLVENN QLSVHEDAPAKFLRLTAFLRNVDAGVLQSIWHKLHQQKDYRRWILDAVPA MATSEALLFLKRTLASEQLTSAEATQIVASTLSNQQATRESLSYARELLN TSFIRNRPILRKTAVLGYGSLVFRYCANTVSCPDELLQPLHDLLSQSSDR AKEEEIVLALKALGNAGQPNSIKKIQRFLPGQGKSLDEYSTRVQAEAIMA LRNIAKRDPRKVQEIVLPIFLNVAIKSELRIRSCIVFFESKPSVALVSMV AVRLRREPNLQVASFVYSQMRSLSRSSNPEFRDVAAACSVAIKMLGSKLD RLGCRYSKAVHVDTFNARTMAGVSADYFRINSPSGPLPRAVAAKIRGQGM GYASDIVEFGLRAEGLQELLYDWKSVPEERPLASGYVKVHGQEVVFAELD KKMQEQIGAVVSKLEQGMDVLLTKGYVVSEVRYMQPVCIGIPMDLNLLVS GVTTNRANLSASFSSLPADMKLADLLATNIELRVAATTSMSQHAVAIMGL TTDLAKAGMQTHYKTSAGLGVNGKIEMNARESNFKASLKPFQQKTVVVLS TMESIVFVRDPSGSRILPVLPPKMTQKQIHDIMTARPVMRRKQSCSKSAA LSSKVCFSARLRNAAFIRNALLYKITGDYVSKVYVQPTSSKAQITKVELE LQAGSKPKVVIVLRAVRADGKQQGLQTTLYYGLTSNGLPKAKIVAVELSD LSVWKLCAKFRLSAHMKAKAAIGWGKNCQQYRAMLEASTGNLQSHPAARV DIKWGRLPSSLQRAKNALLENGAPVIASKLEMEIMPKANQKHQVSVILAA MTPRRMNIIVKLPKVTYFQQGILLPFTF

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Best alignment: 1LSH.pdb  837  SLKPFQQKTVVVLSTMESIVFVRDPSGSRILPVLPPKMTQKQIHDIMTAR   886 SL+    +VV + T+ S   +  P+  RIL + P  +T     +I+ 2-03050    55  SLRSAPISSVVSVETLLSSTGLSRPAVGRILDMFPDLLTSDPESEILPVL   104

1LSH.pdb  887  PVMRRKQSCS-KSAALSSKVCFSARLRNAAF-IRNALLYKITGDYVSKVY   934 + + S S +    S   C    + +  + +R AL +  T  +V + 2-03050   105  RFLSNEISISEQDIPKSISRCPRLLISSVDYQLRPALTFLKTLGFVGRDT   154

1LSH.pdb  935  VQPTSSKAQITKVELEL   951 +  ++   ++ VE  L 2-03050    155  ITSRNTVLLVSNVERTL   171

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Highlighted IDENTICAL residue LYS 914  index1  839  path  353  %Seq  50.00 Highlighted IDENTICAL residue PRO 915  index1  840  path  354  %Seq  50.00 Highlighted IDENTICAL residue PHE 916  index1  841  path  355  %Seq 100.00 Highlighted IDENTICAL residue GLU 928  index1  853  path  367  %Seq 100.00 Highlighted IDENTICAL residue ILE 930  index1  855  path  369  %Seq 100.00 Highlighted IDENTICAL residue VAL 933  index1  858  path  372  %Seq 100.00 Highlighted IDENTICAL residue ILE 941  index1  866  path  380  %Seq 100.00 Highlighted IDENTICAL residue PRO 946  index1  871  path  385  %Seq  50.00 Highlighted IDENTICAL residue MET 1008 index1  889  path  403  %Seq 100.00 Highlighted IDENTICAL residue LEU 1020 index1  901  path  416  %Seq 100.00 Highlighted IDENTICAL residue ARG 1029 index1  910  path  425  %Seq 100.00 Highlighted IDENTICAL residue ARG 1031 index1  912  path  435  %Seq 100.00 Highlighted IDENTICAL residue ALA 1034 index1  915  path  438  %Seq 100.00 Highlighted IDENTICAL residue ILE 1036 index1  917  path  441  %Seq 100.00 Highlighted IDENTICAL residue ASN 1038 index1  919  path  443  %Seq 100.00 Highlighted IDENTICAL residue LYS 1043 index1  924  path  448  %Seq 100.00 Highlighted IDENTICAL residue GLN 1062 index1  943  path  467  %Seq 100.00 Highlighted 17 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g03050-1lshA0.pir.txt.1LSH.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g03050-1lshA0.pir.txt PIR amino_acid 1LSH.pdb A 100.0 BLOSUM62.dat

completed successfully.

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