At2g01300.1/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/
======================================================
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/At2g01300_1orjA.pir.txt
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Assigned types to 156 residues in Sequence 2-01300, 7 remain unknown
Assigned types to 106 residues in Sequence 1orjA, 57 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 115 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 116 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 117 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 118 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 119 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 120 All residues are positively and negatively charged
Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 121 All residues are positively and negatively charged
Translated sequence file At2g01300_1orjA.pir.txt into sequence alignment.
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>1ORJ.pdb Made from 3847 ATOM records in 1ORJ.pdb
RNIAEAYFQNMVETATPLEQIILLYDKAIECLERAIEIYDQVNELEKRKE
FVENIDRVYDIISALKSFLDHEKGKEIAKNLDTIYTIILNTLVKVDKTKE
ELQKILEILKDLREAWEEVKKKVHHHPLEQIILLYDKAIECLERAIEIYD
QVNELEKRKEFVENIDRVYDIISALKSFLDHEKGKEIAKNLDTIYTIILN
TLVKVDKTKEELQKILEILKDLREAWEEVKKPLEQIILLYDKAIECLERA
IEIYDQVNELEKRKEFVENIDRVYDIISALKSFLDHEKGKEIAKNLDTIY
TIILNTLVKVDKTKEELQKILEILKDLREAWEEVKRNIAEAYFQNMVETA
TPLEQIILLYDKAIECLERAIEIYDQVNELEKRKEFVENIDRVYDIISAL
KSFLDHEKGKEIAKNLDTIYTIILNTLVKVDKTKEELQKILEILKDLREA
WEEVKKKVHH
======================================================
Best alignment:
1ORJ.pdb 194 IYTIILNTLVKVDKTKEELQKILEILKDLREAWEEVKKPLEQIILLYDKA 243
 + ++L+ + K K+ ++ ++ + + +++ +++ K 
2-01300 17 FHPLVLSQRAIIPKKKKMTMRVSAAASSGKDHYYGGGRLVDENMIVLRKR 66
1ORJ.pdb 244 IECLERAIEIYDQVNE-LEKRKEFVENIDRVY-DIISALKSFL 284
 I ++ Y+ + ++ K F + D V D + L+SFL
2-01300 67 IHEMKMVERNYEPPSHWMDWEKRFYNSYDSVICDSVGLLQSFL 109
======================================================
Highlighted IDENTICAL residue ILE 2085 index1 194 path 17 %Seq 50.00
Highlighted IDENTICAL residue TYR 2086 index1 195 path 18 %Seq 50.00
Highlighted IDENTICAL residue THR 2087 index1 196 path 19 %Seq 50.00
Highlighted IDENTICAL residue ILE 2088 index1 197 path 20 %Seq 50.00
Highlighted IDENTICAL residue ILE 2089 index1 198 path 21 %Seq 50.00
Highlighted IDENTICAL residue LEU 2090 index1 199 path 22 %Seq 50.00
Highlighted IDENTICAL residue ASN 2091 index1 200 path 23 %Seq 50.00
Highlighted IDENTICAL residue THR 2092 index1 201 path 24 %Seq 50.00
Highlighted IDENTICAL residue LEU 2093 index1 202 path 25 %Seq 50.00
Highlighted IDENTICAL residue VAL 2094 index1 203 path 26 %Seq 50.00
Highlighted IDENTICAL residue LYS 2095 index1 204 path 27 %Seq 50.00
Highlighted IDENTICAL residue VAL 2096 index1 205 path 28 %Seq 50.00
Highlighted IDENTICAL residue ASP 2097 index1 206 path 29 %Seq 50.00
Highlighted IDENTICAL residue LYS 2098 index1 207 path 30 %Seq 50.00
Highlighted IDENTICAL residue THR 2099 index1 208 path 31 %Seq 50.00
Highlighted IDENTICAL residue LYS 2100 index1 209 path 32 %Seq 50.00
Highlighted IDENTICAL residue GLU 2101 index1 210 path 33 %Seq 50.00
Highlighted IDENTICAL residue GLU 2102 index1 211 path 34 %Seq 50.00
Highlighted IDENTICAL residue LEU 2103 index1 212 path 35 %Seq 50.00
Highlighted IDENTICAL residue GLN 2104 index1 213 path 36 %Seq 50.00
Highlighted IDENTICAL residue LYS 2105 index1 214 path 37 %Seq 50.00
Highlighted IDENTICAL residue ILE 2106 index1 215 path 38 %Seq 50.00
Highlighted IDENTICAL residue LEU 2107 index1 216 path 39 %Seq 50.00
Highlighted IDENTICAL residue GLU 2108 index1 217 path 40 %Seq 50.00
Highlighted IDENTICAL residue LEU 2110 index1 219 path 42 %Seq 100.00
Highlighted IDENTICAL residue LYS 3028 index1 242 path 65 %Seq 100.00
Highlighted IDENTICAL residue ILE 3030 index1 244 path 67 %Seq 100.00
Highlighted IDENTICAL residue TYR 3040 index1 254 path 77 %Seq 100.00
Highlighted IDENTICAL residue LYS 3050 index1 264 path 88 %Seq 100.00
Highlighted IDENTICAL residue PHE 3052 index1 266 path 90 %Seq 100.00
Highlighted IDENTICAL residue ASP 3057 index1 271 path 95 %Seq 100.00
Highlighted IDENTICAL residue VAL 3059 index1 273 path 97 %Seq 50.00
Highlighted IDENTICAL residue ASP 3061 index1 275 path 100 %Seq 100.00
Highlighted IDENTICAL residue LEU 3066 index1 280 path 105 %Seq 100.00
Highlighted IDENTICAL residue SER 3068 index1 282 path 107 %Seq 100.00
Highlighted IDENTICAL residue PHE 3069 index1 283 path 108 %Seq 100.00
Highlighted IDENTICAL residue LEU 3070 index1 284 path 109 %Seq 100.00
Highlighted 37 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g01300_1orjA.pir.txt.1ORJ.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g01300_1orjA.pir.txt PIR amino_acid 1ORJ.pdb _ 100.0 BLOSUM62.dat 
completed successfully.
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