Fandom

Proteins Wiki

At2g01580.1/PDB

< At2g01580.1

47,923pages on
this wiki
Add New Page
Talk0 Share
&&&&&&&&&&&&&&&&&&&& 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
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
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01580_2bs2_C.pir.txt

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

Assigned types to 191 residues in Sequence 2-01580, 6 remain unknown
Assigned types to 180 residues in Sequence 2bs2_C, 21 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 41  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 173  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 200  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 201  All residues are positively and negatively charged

Translated sequence file At2g01580_2bs2_C.pir.txt into sequence alignment.

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

>2BS2.pdb  Made from 18272 ATOM records in 2BS2.pdb
MKVQYCDSLVIGGGLAGLRAAVATQQKGLSTIVLSLIPVKRSHSAAAQGG
MQASLGNSKMSDGDNEDLHFMDTVKGSDWGCDQKVARMFVNTAPKAIREL
AAWGVPWTRIHKGDRMAIINAQKTTITEEDFRHGLIHSRDFGGTKKWRTC
YTADATGHTMLFAVANECLKLGVSIQDRKEAIALIHQDGKCYGAVVRDLV
TGDIIAYVAKGTLIATGGYGRIYKNTTNAVVCEGTGTAIALETGIAQLGN
MEAVQFHPTPLFPSGILLTEGCRGDGGILRDVDGHRFMPDYEPEKKELAS
RDVVSRRMIEHIRKGKGVQSPYGQHLWLDISILGRKHIETNLRDVQEICE
YFAGIDPAEKWAPVLPMQHYSMGGIRTDYRGEAKLKGLFSAGEAACWDMH
GFNRLGGNSVSEAVVAGMIVGEYFAEHCANTQVDLETKTLEKFVKGQEAY
MKSLVESKGTEDVFKIKNRMKDVMDDNVGIFRDGPHLEKAVKELEELYKK
SKNVGIKNKRLHANPELEEAYRVPMMLKVALCVAKGALDRTESRGAHNRE
DYPKRDDINWLNRTLASWPNPEQTLPTLEYEALDVNEMEIAPGYRGYGAK
GNYIENPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMPYELPAKYKARN
ERLGDKMGRMLTIRVFKYDPQSAVSKPHFQEYKIEEAPSMTIFIVLNMIR
ETYDPDLNFDFVCRAGICGSCGMMINGRPSLACRTLTKDFEDGVITLLPL
PAFKLIKDLSVDTGNWFNGMSQRVESWIHAQKEHDISKLEERIEPEVAQE
VFELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDED
YYELIGDDDGVFGCMTLLACHDVCPKNLPLQSKIAYLRRKMVSVNMMTNE
SILESYSGVTPERKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILLG
DNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFLAMRKFPIN
YRQYLTFKTHKDLMRHGDTTLWWIQAMTGFAMFFLGSVHLYIMMTQPQTI
GPVSSSFRMVSEWMWPLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPDK
TRANLKKLKTLMSAFLIVLGLLTFGAYVKKGLEQTDPNIDYKYFDYKRTH
EMKVQYCDSLVIGGGLAGLRAAVATQQKGLSTIVLSLIPVKRSHSAAAQG
GMQASLGNSKMSDGDNEDLHFMDTVKGSDWGCDQKVARMFVNTAPKAIRE
LAAWGVPWTRIHKGDRMAIINAQKTTITEEDFRHGLIHSRDFGGTKKWRT
CYTADATGHTMLFAVANECLKLGVSIQDRKEAIALIHQDGKCYGAVVRDL
VTGDIIAYVAKGTLIATGGYGRIYKNTTNAVVCEGTGTAIALETGIAQLG
NMEAVQFHPTPLFPSGILLTEGCRGDGGILRDVDGHRFMPDYEPEKKELA
SRDVVSRRMIEHIRKGKGVQSPYGQHLWLDISILGRKHIETNLRDVQEIC
EYFAGIDPAEKWAPVLPMQHYSMGGIRTDYRGEAKLKGLFSAGEAACWDM
HGFNRLGGNSVSEAVVAGMIVGEYFAEHCANTQVDLETKTLEKFVKGQEA
YMKSLVESKGTEDVFKIKNRMKDVMDDNVGIFRDGPHLEKAVKELEELYK
KSKNVGIKNKRLHANPELEEAYRVPMMLKVALCVAKGALDRTESRGAHNR
EDYPKRDDINWLNRTLASWPNPEQTLPTLEYEALDVNEMEIAPGYRGYGA
KGNYIENPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMPYELPAKYKAR
NERLGDKMGRMLTIRVFKYDPQSAVSKPHFQEYKIEEAPSMTIFIVLNMI
RETYDPDLNFDFVCRAGICGSCGMMINGRPSLACRTLTKDFEDGVITLLP
LPAFKLIKDLSVDTGNWFNGMSQRVESWIHAQKEHDISKLEERIEPEVAQ
EVFELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDE
DYYELIGDDDGVFGCMTLLACHDVCPKNLPLQSKIAYLRRKMVSVNMMTN
ESILESYSGVTPERKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILL
GDNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFLAMRKFPI
NYRQYLTFKTHKDLMRHGDTTLWWIQAMTGFAMFFLGSVHLYIMMTQPQT
IGPVSSSFRMVSEWMWPLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPD
KTRANLKKLKTLMSAFLIVLGLLTFGAYVKKGLEQTDPNIDYKYFDYKRT
HE

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

Best alignment:
2BS2.pdb   453  SLVESKGTEDVFKIKNRMKDVM   474
                +L+ SK T++VFK  N  +DV+
2-01580    103  NLLNSKETDEVFK-ANINRDVL   123

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

Highlighted IDENTICAL residue LEU  454  index1  454  path  105  %Seq 100.00
Highlighted IDENTICAL residue LYS  458  index1  458  path  109  %Seq 100.00
Highlighted 2 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01580_2bs2_C.pir.txt.2BS2.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01580_2bs2_C.pir.txt PIR amino_acid 2BS2.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

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

Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.