At2g04400.1/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 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 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/At2g04400-1pii_.pir.txt

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Assigned types to 402 residues in Sequence 2-4400, 0 remain unknown Assigned types to 259 residues in Sequence 1pii_, 143 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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Translated sequence file At2g04400-1pii_.pir.txt into sequence alignment.

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>1PII.pdb Made from 3524 ATOM records in 1PII.pdb MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAF ILECKKASPSKGVIRDDFDPARIAAIYKHYASAISVLTDEKYFQGSFNFL PIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLA AVAHSLEMGVLTEVSNEEEQERAIALGAKVVGINNRDLRDLSIDLNRTRE LAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALMAHDDLHAAVR RVLLGENKVCGLTRGQDAKAAYDAGAIYGGLIFVATSPRCVNVEQAQEVM AAAPLQYVGVFRNHDIADVVDKAKVLSLAAVQLHGNEEQLYIDTLREALP AHVAIWKALSVGETLPAREFQHVDKYVLDNGQGGSGQRFDWSLLNGQSLG NVLLAGGLGADNCVEAAQTGCAGLDFNSAVESQPGIKDARLLASVFQTLR AY

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Best alignment: 1PII.pdb    2  QTVLAKIVADKAIWVEARKQQQPLASFQNEVQ--PSTRHFYDALQGA--R    47 + +L +I  K + V   K+  PL   +  V+  P TR F  AL+ A  R 2-4400     127  RNILEEITWYKDVEVSRMKELNPLDVLKKAVEDAPPTRDFVGALRMAHKR   176

1PII.pdb   48  TAF---ILECKKASPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYF    93 T F  I E KKASPS+G+++++FDP  IA  Y K  A+ +SVLTD+KYF 2-4400    177  TGFPGLIAEVKKASPSRGILKENFDPVEIAQAYEKGGAACLSVLTDQKYF   226

1PII.pdb   94  QGSFNFLPIVSQIAPQ-PILCKDFIIDPYQIYLARYYQADACLLMLSVLD   142 QG F L  +     + P+LCK+F++DP+QIY AR   ADA LL+ +VL 2-4400    227  QGGFENLEAIRSAGVKCPLLCKEFVVDPWQIYYARTKGADAVLLIAAVLA   276

1PII.pdb  143  DDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL-GAKVVGINNRDLRDL   191 D +  L  +   L +  L EV +E E  R + + G ++VGINNR L   2-4400     277  DLEITFLLKICKKLSLAALVEVHDEREMGRVLGIEGIELVGINNRSLETF   326

1PII.pdb  192  SIDLNRTREL   201 +D++ T++L 2-4400    327  EVDISNTKKL   336

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Highlighted IDENTICAL residue LEU   5  index1    5  path  130  %Seq 100.00 Highlighted IDENTICAL residue ILE   8  index1    8  path  133  %Seq 100.00 Highlighted IDENTICAL residue LYS  12  index1   12  path  137  %Seq 100.00 Highlighted IDENTICAL residue VAL  16  index1   16  path  141  %Seq 100.00 Highlighted IDENTICAL residue LYS  20  index1   20  path  145  %Seq 100.00 Highlighted IDENTICAL residue PRO  24  index1   24  path  149  %Seq 100.00 Highlighted IDENTICAL residue LEU  25  index1   25  path  150  %Seq 100.00 Highlighted IDENTICAL residue VAL  32  index1   32  path  157  %Seq 100.00 Highlighted IDENTICAL residue GLN  33  index1   33  path  158  %Seq  50.00 Highlighted IDENTICAL residue PRO  34  index1   34  path  161  %Seq 100.00 Highlighted IDENTICAL residue THR  36  index1   36  path  163  %Seq 100.00 Highlighted IDENTICAL residue ARG  37  index1   37  path  164  %Seq 100.00 Highlighted IDENTICAL residue PHE  39  index1   39  path  166  %Seq 100.00 Highlighted IDENTICAL residue ALA  42  index1   42  path  169  %Seq 100.00 Highlighted IDENTICAL residue LEU  43  index1   43  path  170  %Seq 100.00 Highlighted IDENTICAL residue ALA  46  index1   46  path  173  %Seq  50.00 Highlighted IDENTICAL residue ARG  47  index1   47  path  176  %Seq  50.00 Highlighted IDENTICAL residue THR  48  index1   48  path  177  %Seq  50.00 Highlighted IDENTICAL residue ILE  51  index1   51  path  183  %Seq 100.00 Highlighted IDENTICAL residue GLU  53  index1   53  path  185  %Seq 100.00 Highlighted IDENTICAL residue LYS  55  index1   55  path  187  %Seq 100.00 Highlighted IDENTICAL residue LYS  56  index1   56  path  188  %Seq 100.00 Highlighted IDENTICAL residue ALA  57  index1   57  path  189  %Seq 100.00 Highlighted IDENTICAL residue SER  58  index1   58  path  190  %Seq 100.00 Highlighted IDENTICAL residue PRO  59  index1   59  path  191  %Seq 100.00 Highlighted IDENTICAL residue SER  60  index1   60  path  192  %Seq 100.00 Highlighted IDENTICAL residue GLY  62  index1   62  path  194  %Seq 100.00 Highlighted IDENTICAL residue PHE  68  index1   68  path  200  %Seq 100.00 Highlighted IDENTICAL residue ASP  69  index1   69  path  201  %Seq 100.00 Highlighted IDENTICAL residue PRO  70  index1   70  path  202  %Seq 100.00 Highlighted IDENTICAL residue ILE  73  index1   73  path  205  %Seq 100.00 Highlighted IDENTICAL residue ALA  74  index1   74  path  206  %Seq 100.00 Highlighted IDENTICAL residue TYR  77  index1   77  path  209  %Seq 100.00 Highlighted IDENTICAL residue LYS  78  index1   78  path  211  %Seq  50.00 Highlighted IDENTICAL residue ALA  81  index1   81  path  214  %Seq 100.00 Highlighted IDENTICAL residue SER  85  index1   85  path  218  %Seq 100.00 Highlighted IDENTICAL residue VAL  86  index1   86  path  219  %Seq 100.00 Highlighted IDENTICAL residue LEU  87  index1   87  path  220  %Seq 100.00 Highlighted IDENTICAL residue THR  88  index1   88  path  221  %Seq 100.00 Highlighted IDENTICAL residue ASP  89  index1   89  path  222  %Seq 100.00 Highlighted IDENTICAL residue LYS  91  index1   91  path  224  %Seq 100.00 Highlighted IDENTICAL residue TYR  92  index1   92  path  225  %Seq 100.00 Highlighted IDENTICAL residue PHE  93  index1   93  path  226  %Seq 100.00 Highlighted IDENTICAL residue GLN  94  index1   94  path  227  %Seq 100.00 Highlighted IDENTICAL residue GLY  95  index1   95  path  228  %Seq 100.00 Highlighted IDENTICAL residue PHE  97  index1   97  path  230  %Seq 100.00 Highlighted IDENTICAL residue LEU 100  index1  100  path  233  %Seq 100.00 Highlighted IDENTICAL residue ALA 107  index1  107  path  240  %Seq  50.00 Highlighted IDENTICAL residue PRO 110  index1  110  path  244  %Seq 100.00 Highlighted IDENTICAL residue LEU 112  index1  112  path  246  %Seq 100.00 Highlighted IDENTICAL residue CYS 113  index1  113  path  247  %Seq 100.00 Highlighted IDENTICAL residue LYS 114  index1  114  path  248  %Seq 100.00 Highlighted IDENTICAL residue PHE 116  index1  116  path  250  %Seq 100.00 Highlighted IDENTICAL residue ASP 119  index1  119  path  253  %Seq 100.00 Highlighted IDENTICAL residue PRO 120  index1  120  path  254  %Seq 100.00 Highlighted IDENTICAL residue GLN 122  index1  122  path  256  %Seq 100.00 Highlighted IDENTICAL residue ILE 123  index1  123  path  257  %Seq 100.00 Highlighted IDENTICAL residue TYR 124  index1  124  path  258  %Seq 100.00 Highlighted IDENTICAL residue ALA 126  index1  126  path  260  %Seq 100.00 Highlighted IDENTICAL residue ARG 127  index1  127  path  261  %Seq 100.00 Highlighted IDENTICAL residue ALA 131  index1  131  path  265  %Seq 100.00 Highlighted IDENTICAL residue ASP 132  index1  132  path  266  %Seq 100.00 Highlighted IDENTICAL residue ALA 133  index1  133  path  267  %Seq 100.00 Highlighted IDENTICAL residue LEU 135  index1  135  path  269  %Seq 100.00 Highlighted IDENTICAL residue LEU 136  index1  136  path  270  %Seq 100.00 Highlighted IDENTICAL residue VAL 140  index1  140  path  274  %Seq 100.00 Highlighted IDENTICAL residue LEU 141  index1  141  path  275  %Seq 100.00 Highlighted IDENTICAL residue ASP 143  index1  143  path  277  %Seq 100.00 Highlighted IDENTICAL residue LEU 149  index1  149  path  283  %Seq 100.00 Highlighted IDENTICAL residue LEU 156  index1  156  path  290  %Seq 100.00 Highlighted IDENTICAL residue LEU 161  index1  161  path  295  %Seq 100.00 Highlighted IDENTICAL residue GLU 163  index1  163  path  297  %Seq 100.00 Highlighted IDENTICAL residue VAL 164  index1  164  path  298  %Seq 100.00 Highlighted IDENTICAL residue GLU 167  index1  167  path  301  %Seq 100.00 Highlighted IDENTICAL residue GLU 169  index1  169  path  303  %Seq 100.00 Highlighted IDENTICAL residue ARG 172  index1  172  path  306  %Seq 100.00 Highlighted IDENTICAL residue GLY 177  index1  177  path  312  %Seq 100.00 Highlighted IDENTICAL residue VAL 181  index1  181  path  316  %Seq 100.00 Highlighted IDENTICAL residue GLY 182  index1  182  path  317  %Seq 100.00 Highlighted IDENTICAL residue ILE 183  index1  183  path  318  %Seq 100.00 Highlighted IDENTICAL residue ASN 184  index1  184  path  319  %Seq 100.00 Highlighted IDENTICAL residue ASN 185  index1  185  path  320  %Seq 100.00 Highlighted IDENTICAL residue ARG 186  index1  186  path  321  %Seq 100.00 Highlighted IDENTICAL residue LEU 188  index1  188  path  323  %Seq 100.00 Highlighted IDENTICAL residue ASP 194  index1  194  path  329  %Seq 100.00 Highlighted IDENTICAL residue THR 198  index1  198  path  333  %Seq 100.00 Highlighted IDENTICAL residue LEU 201  index1  201  path  336  %Seq 100.00 Highlighted 87 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04400-1pii_.pir.txt.1PII.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04400-1pii_.pir.txt PIR amino_acid 1PII.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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