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At2g14247.1/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

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

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

Assigned types to 78 residues in Sequence 2-14247, 10 remain unknown
Assigned types to 69 residues in Sequence 1nfda2, 19 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

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

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.

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

>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

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

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

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

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

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

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.

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


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