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