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 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

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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

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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

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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

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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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