Fandom

Proteins Wiki

At2g14340.1/PDB

< At2g14340.1

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
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
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14340-1zgmA.pir.txt

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

Assigned types to 220 residues in Sequence 2-14340, 17 remain unknown
Assigned types to 189 residues in Sequence 1zgmA, 48 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 55  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 92  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 93  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 94  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 95  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 135  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 136  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 137  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 138  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 139  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 140  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 141  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 171  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 172  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 176  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 177  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 183  All residues are positively and negatively charged

Translated sequence file At2g14340-1zgmA.pir.txt into sequence alignment.

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

>1ZGM=2FNO.pdb  Made from 3517 ATOM records in 1ZGM=2FNO.pdb
HHHEDGNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLDCGAE
KQPVAFGPPVLIDRERNFAISQPAIAIYLGERLDILPATVEGRTLSAKIV
NDANDVLDELTLNGGREWTPEKWQEFVPRLQKWIRIFADTGARNGLSAAS
GFLGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSRRVVAT
APLAALNSKSFEEYGNAYCGGEIEKSLRKVASDGNTFDLYYWPVPFRGQL
IRGILAHCGCSWDEHDVDAIEGLDCGAEKQPVAFGPPVLIDRERNFAISQ
PAIAIYLGERLDILPATVEGRTLSAKIVNDANDVLDELTLNGGREWTPEK
WQEFVPRLQKWIRIFADTGARNGLSAASGFLGTEKIGVADIVTAILWTTV
ADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGE
IEKSLRKVAS

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

Best alignment:
1ZGM=2FNO.pdb     2  HHEDG-NTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGL-DCGA    49
                     H EDG NTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGL DCGA
1zgmA             1  HMEDGMNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHXVDAIEGLMDCGA    50

1ZGM=2FNO.pdb    50  EKQPVAF-GPPVLIDRERNFAIS-QPAIAIYLGERLDILPATVEGRTLSA    97
                     EKQPVAF GPPVLIDRERNFAIS QPAIAIYLGERLDILPATVEGRTLSA
1zgmA            51  EKQPVAFMGPPVLIDRERNFAISQXXXXAIYLGERLDILPATVEGRTLSA   100

1ZGM=2FNO.pdb    98  KIVNDANDVLDELTLN-GGREWTPEKWQEFVPRLQKWIRIFADTGARNGL   146
                     KIVNDANDVLDELTLN GGREWTPEKWQEFVPRLQKWIRIFADTGARNGL
1zgmA           101  KIVNDANDVLDELTLNGXXXXXXXEKWQEFVPRLQKWIRIFADTGARNGL   150

1ZGM=2FNO.pdb   147  SAASGF-LGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSR   195
                     SAASGF LGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSR
1zgmA           151  SAAXXFMLXXEKIGVXDIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSR   200

1ZGM=2FNO.pdb   196  RVVATA   201
                     RVVATA
1zgmA           201  RVVATA   206

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

Highlighted IDENTICAL residue ILE   22  index1   23  path   40  %Seq 100.00
Highlighted IDENTICAL residue ILE   25  index1   26  path   43  %Seq 100.00
Highlighted IDENTICAL residue HIS   28  index1   29  path   46  %Seq 100.00
Highlighted IDENTICAL residue GLY   30  index1   31  path   48  %Seq 100.00
Highlighted IDENTICAL residue PRO   53  index1   53  path   71  %Seq 100.00
Highlighted IDENTICAL residue ARG   67  index1   66  path   85  %Seq 100.00
Highlighted IDENTICAL residue PHE   69  index1   68  path   87  %Seq 100.00
Highlighted IDENTICAL residue ILE   79  index1   77  path   97  %Seq 100.00
Highlighted IDENTICAL residue GLY   82  index1   80  path  100  %Seq 100.00
Highlighted IDENTICAL residue GLU   93  index1   91  path  111  %Seq 100.00
Highlighted IDENTICAL residue LEU  133  index1  130  path  151  %Seq 100.00
Highlighted IDENTICAL residue ARG  138  index1  135  path  156  %Seq 100.00
Highlighted IDENTICAL residue ILE  162  index1  158  path  180  %Seq 100.00
Highlighted IDENTICAL residue PHE  180  index1  176  path  202  %Seq 100.00
Highlighted IDENTICAL residue ILE  186  index1  182  path  208  %Seq 100.00
Highlighted IDENTICAL residue GLU  188  index1  184  path  210  %Seq 100.00
Highlighted IDENTICAL residue ASP  189  index1  185  path  211  %Seq 100.00
Highlighted IDENTICAL residue PRO  192  index1  188  path  214  %Seq 100.00
Highlighted IDENTICAL residue ARG  200  index1  196  path  222  %Seq 100.00
Highlighted IDENTICAL residue VAL  201  index1  197  path  223  %Seq 100.00
Highlighted 20 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14340-1zgmA.pir.txt.1ZGM=2FNO.pdb.conservation.pml

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

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14340-1zgmA.pir.txt PIR amino_acid 1ZGM=2FNO.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.