At2g14247.1/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 Sequence 2 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/At2g14270-1nfda2.pir.txt

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Assigned types to 78 residues in Sequence 2-14247, 10 remain unknown Assigned types to 69 residues in Sequence 1nfda2, 19 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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Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 12 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 13 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 22 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 23 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 24 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 25 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 26 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 27 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 45 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 46 All residues are positively and negatively charged

Translated sequence file At2g14270-1nfda2.pir.txt into sequence alignment.

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>1NFD.pdb Made from 13688 ATOM records in 1NFD.pdb DSVTQTEGLVTVTEGLPVKLNCTYQTTYLTIAFFWYVQYLNEAPQVLLKS STDNKRTEHQGFHATLHKSSSSFHLQKSSAQLSDSALYYCALSEGGNYKY VFGAGTRLKVIAHIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTM ESGTFITDKTVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNATYPSSD VPCDSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLI QHYEKVERDKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLRW GDEQYFGPGTRLTVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARG FFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYSLSSRLRVSATFWHN PRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADCDSVTQTEG LVTVTEGLPVKLNCTYQTTYLTIAFFWYVQYLNEAPQVLLKSSTDNKRTE HQGFHATLHKSSSSFHLQKSSAQLSDSALYYCALSEGGNYKYVFGAGTRL KVIAHIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITD KTVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNATYPSSDVPCDSGVV QSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVER DKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLRWGDEQYFGP GTRLTVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVEL SWWVNGKEVHSGVSTDPQAYKESNYSYSLSSRLRVSATFWHNPRNHFRCQ VQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADCYELIQPSSASVTVGET VKITCSGDQLPKNFAYWFQQKSDKNILLLIYMDNKRPSGIPERFSGSTSG TTATLTISGAQPEDEAAYYCLSSYGDNNDLVFGSGTQLTVLRGPKSSPKV TVFPPSPEELRTNKATLVCLVNDFYPGSATVTWKANGATINDGVKTTKPS KQGQNYMTSSYLSLTADQWKSHNRVSCQVTHEGETVEKSLSPAECLEVYL VESGGDLVQPGSSLKVSCAASGFTFSDFWMYWVRQAPGKGLEWVGRIKNI PNNYATEYADSVRGRFTISRDDSRNSIYLQMNRLRVDDTAIYYCTRAGRF DHFDYWGQGTMVTVSSATTTAPSVYPLAPACDSTTSTTDTVTLGCLVKGY FPEPVTVSWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPKQPITC NVAHPASSTKVDKKIEPRYELIQPSSASVTVGETVKITCSGDQLPKNFAY WFQQKSDKNILLLIYMDNKRPSGIPERFSGSTSGTTATLTISGAQPEDEA AYYCLSSYGDNNDLVFGSGTQLTVLRGPKSSPKVTVFPPSPEELRTNKAT LVCLVNDFYPGSATVTWKANGATINDGVKTTKPSKQGQNYMTSSYLSLTA DQWKSHNRVSCQVTHEGETVEKSLSPAECLEVYLVESGGDLVQPGSSLKV SCAASGFTFSDFWMYWVRQAPGKGLEWVGRIKNIPNNYATEYADSVRGRF TISRDDSRNSIYLQMNRLRVDDTAIYYCTRAGRFDHFDYWGQGTMVTVSS ATTTAPSVYPLAPACDSTTSTTDTVTLGCLVKGYFPEPVTVSWNSGALTS GVHTFPSVLHSGLYSLSSSVTVPSSTWPKQPITCNVAHPASSTKVDKKIE PR

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Best alignment: 1NFD.pdb  165  KAMDSKSNGAI   175 KA+D++ + A+ 2-14247    43  KALDNEDHSAV    53

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Highlighted IDENTICAL residue LYS 171  index1  165  path   53  %Seq 100.00 Highlighted IDENTICAL residue ALA 172  index1  166  path   54  %Seq 100.00 Highlighted IDENTICAL residue ASP 174  index1  168  path   56  %Seq 100.00 Highlighted IDENTICAL residue ALA 180  index1  174  path   62  %Seq 100.00 Highlighted 4 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14270-1nfda2.pir.txt.1NFD.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14270-1nfda2.pir.txt PIR amino_acid 1NFD.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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