At2g03050.1/PDB

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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
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Sequence 1
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Sequence 2
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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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