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At2g03050.1/PDB

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&&&&&&&&&&&&&&&&&&&& 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

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

======================================================

Assigned types to 283 residues in Sequence 2-03050, 314 remain unknown
Assigned types to 955 residues in Sequence 1lshA0, 20 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

======================================================

Translated sequence file At2g03050-1lshA0.pir.txt into sequence alignment.

======================================================

>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

======================================================

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

======================================================

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

===============================================================================

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.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@

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