At2g14120.1/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 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 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/At2g14120-1jwyB.pir.txt

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Assigned types to 780 residues in Sequence 2-14120, 0 remain unknown Assigned types to 315 residues in Sequence 1jwyB, 465 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 At2g14120-1jwyB.pir.txt into sequence alignment.

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>1JWY.pdb Made from 8297 ATOM records in 1JWY.pdb DPIHDRTSDYHKYLKVKQFKLTVSDKRYIWYNPDPKERDSYECGEIVSET SDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNL RVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIF AISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGSGVLE QQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSAGFISGASIQSYL LEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGC VDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKG AGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVE KSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFK VNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQA TIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPR FSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLF NDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQ LPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNV PRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRI SEIDQLIPVINKLQDVFNTLGSDPLDLPQIVVVGSQSSGKSSVLENIVGR DFLPRPLILQLTHLPIADDGSQTQEWGEFLHKPNDMFYDFSEIREEIIRD TDISAQPINLKIYSPHVVNLTLVDLPGITDIEQQIRRMVMAYIKKQNAII VAVTPANTDLANSDALQLAKEVDPEGKRTIGVITKLDLMDKGTDAMEVLT GRVIPLTLGFIGVINRSQEDIIAKKSIRESLKSEILYFKNHPIYKSIANR SGTAYLSKTLNKLLMFHIRDTLPDLKVKVSKMLSTRGLV

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Best alignment: 1JWY.pdb  754  DQLIPVINKLQDVFNTLGS-DPLDLPQIVVVGSQSSGKSSVLENIVGRDF   802 +IP++NKLQD+F LGS   + LPQ+ VVGSQSSGKSSVLE +VGRDF 2-14120    19  SSVIPIVNKLQDIFAQLGSQSTIALPQVAVVGSQSSGKSSVLEALVGRDF    68

1JWY.pdb  803  LPRPLILQLTHLPIADDGSQTQEWGEFL-HKPNDMFYDFSEI   843 LP       RPL LQL     + DG   +EWGEFL H P    YDFSEI 2-14120    69  LPRGNDICTRRPLRLQLVQTKPSSDGGSDEEWGEFLHHDPVRRIYDFSEI   118

1JWY.pdb  844  REEIIRDTD-ISAQ---PINLKIYSPHVVNLTLVDLPGIT--   879 R EI +T+ +S +       PI LKI+SP+V++++LVDLPGIT 2-14120   119  RREIEAETNRVSGENKGVSDIPIGLKIFSPNVLDISLVDLPGITKVPVGD   168

1JWY.pdb  879  ---DIEQQIRRMVMAYIKKQNAIIVAVTPANTDLANSDALQLAKEVDPEG   926 DIE +IR M++ YIK+ + +I+AV+PANTDLANSDALQ+A  DP+G 2-14120   169  QPSDIEARIRTMILTYIKEPSCLILAVSPANTDLANSDALQIAGNADPDG   218

1JWY.pdb  927  KRTIGVITKLDLMDKGTDAMEVLTGRVIPLTLGFIGVINRSQEDIIAKKS   976 RTIGVITKLD+MD+GTDA  L G+ IPL LG++GV+NRSQEDI+  +S 2-14120   219  HRTIGVITKLDIMDRGTDARNHLLGKTIPLRLGYVGVVNRSQEDILMNRS   268

1JWY.pdb  977  IRESLKSEILYFKNHPIYKSIANRSGTAYLSKTLNKLLMFHIRDTLPDLK  1026 I+++L +E +F++ P+Y  + +R G   L+K LN++L+ HI+  LP LK 2-14120    269  IKDALVAEEKFFRSRPVYSGLTDRLGVPQLAKKLNQVLVQHIKALLPSLK   318

1JWY.pdb 1027  VKVSKML  1033 +++ L 2-14120    319  SRINNAL   325

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Highlighted IDENTICAL residue ILE   5  index1  757  path   22  %Seq 100.00 Highlighted IDENTICAL residue PRO   6  index1  758  path   23  %Seq 100.00 Highlighted IDENTICAL residue ASN   9  index1  761  path   26  %Seq 100.00 Highlighted IDENTICAL residue LYS  10  index1  762  path   27  %Seq 100.00 Highlighted IDENTICAL residue LEU  11  index1  763  path   28  %Seq 100.00 Highlighted IDENTICAL residue GLN  12  index1  764  path   29  %Seq 100.00 Highlighted IDENTICAL residue ASP  13  index1  765  path   30  %Seq 100.00 Highlighted IDENTICAL residue PHE  15  index1  767  path   32  %Seq 100.00 Highlighted IDENTICAL residue LEU  18  index1  770  path   35  %Seq 100.00 Highlighted IDENTICAL residue GLY  19  index1  771  path   36  %Seq 100.00 Highlighted IDENTICAL residue SER  20  index1  772  path   37  %Seq  50.00 Highlighted IDENTICAL residue LEU  25  index1  777  path   43  %Seq 100.00 Highlighted IDENTICAL residue PRO  26  index1  778  path   44  %Seq 100.00 Highlighted IDENTICAL residue GLN  27  index1  779  path   45  %Seq 100.00 Highlighted IDENTICAL residue VAL  30  index1  782  path   48  %Seq 100.00 Highlighted IDENTICAL residue VAL  31  index1  783  path   49  %Seq 100.00 Highlighted IDENTICAL residue GLY  32  index1  784  path   50  %Seq 100.00 Highlighted IDENTICAL residue SER  33  index1  785  path   51  %Seq 100.00 Highlighted IDENTICAL residue GLN  34  index1  786  path   52  %Seq 100.00 Highlighted IDENTICAL residue SER  35  index1  787  path   53  %Seq 100.00 Highlighted IDENTICAL residue SER  36  index1  788  path   54  %Seq 100.00 Highlighted IDENTICAL residue GLY  37  index1  789  path   55  %Seq 100.00 Highlighted IDENTICAL residue LYS  38  index1  790  path   56  %Seq 100.00 Highlighted IDENTICAL residue SER  39  index1  791  path   57  %Seq 100.00 Highlighted IDENTICAL residue SER  40  index1  792  path   58  %Seq 100.00 Highlighted IDENTICAL residue VAL  41  index1  793  path   59  %Seq 100.00 Highlighted IDENTICAL residue LEU  42  index1  794  path   60  %Seq 100.00 Highlighted IDENTICAL residue GLU  43  index1  795  path   61  %Seq 100.00 Highlighted IDENTICAL residue VAL  46  index1  798  path   64  %Seq 100.00 Highlighted IDENTICAL residue GLY  47  index1  799  path   65  %Seq 100.00 Highlighted IDENTICAL residue ARG  48  index1  800  path   66  %Seq 100.00 Highlighted IDENTICAL residue ASP  49  index1  801  path   67  %Seq 100.00 Highlighted IDENTICAL residue PHE  50  index1  802  path   68  %Seq 100.00 Highlighted IDENTICAL residue LEU  51  index1  803  path   69  %Seq 100.00 Highlighted IDENTICAL residue PRO  52  index1  804  path   70  %Seq 100.00 Highlighted IDENTICAL residue ARG  61  index1  805  path   79  %Seq 100.00 Highlighted IDENTICAL residue PRO  62  index1  806  path   80  %Seq 100.00 Highlighted IDENTICAL residue LEU  63  index1  807  path   81  %Seq 100.00 Highlighted IDENTICAL residue LEU  65  index1  809  path   83  %Seq 100.00 Highlighted IDENTICAL residue GLN  66  index1  810  path   84  %Seq 100.00 Highlighted IDENTICAL residue LEU  67  index1  811  path   85  %Seq 100.00 Highlighted IDENTICAL residue ASP  75  index1  819  path   93  %Seq 100.00 Highlighted IDENTICAL residue GLY  76  index1  820  path   94  %Seq 100.00 Highlighted IDENTICAL residue GLU  81  index1  825  path   99  %Seq 100.00 Highlighted IDENTICAL residue TRP  82  index1  826  path  100  %Seq 100.00 Highlighted IDENTICAL residue GLY  83  index1  827  path  101  %Seq 100.00 Highlighted IDENTICAL residue GLU  84  index1  828  path  102  %Seq 100.00 Highlighted IDENTICAL residue PHE  85  index1  829  path  103  %Seq 100.00 Highlighted IDENTICAL residue LEU  86  index1  830  path  104  %Seq 100.00 Highlighted IDENTICAL residue HIS  87  index1  831  path  106  %Seq  50.00 Highlighted IDENTICAL residue PRO  89  index1  833  path  108  %Seq 100.00 Highlighted IDENTICAL residue TYR  94  index1  838  path  113  %Seq 100.00 Highlighted IDENTICAL residue ASP  95  index1  839  path  114  %Seq 100.00 Highlighted IDENTICAL residue PHE  96  index1  840  path  115  %Seq 100.00 Highlighted IDENTICAL residue SER  97  index1  841  path  116  %Seq 100.00 Highlighted IDENTICAL residue GLU  98  index1  842  path  117  %Seq 100.00 Highlighted IDENTICAL residue ILE  99  index1  843  path  118  %Seq 100.00 Highlighted IDENTICAL residue ARG 100  index1  844  path  119  %Seq 100.00 Highlighted IDENTICAL residue GLU 102  index1  846  path  121  %Seq 100.00 Highlighted IDENTICAL residue ILE 103  index1  847  path  122  %Seq 100.00 Highlighted IDENTICAL residue THR 107  index1  851  path  126  %Seq 100.00 Highlighted IDENTICAL residue ALA 119  index1  855  path  131  %Seq 100.00 Highlighted IDENTICAL residue PRO 121  index1  857  path  140  %Seq 100.00 Highlighted IDENTICAL residue ILE 122  index1  858  path  141  %Seq 100.00 Highlighted IDENTICAL residue LEU 124  index1  860  path  143  %Seq 100.00 Highlighted IDENTICAL residue LYS 125  index1  861  path  144  %Seq 100.00 Highlighted IDENTICAL residue ILE 126  index1  862  path  145  %Seq 100.00 Highlighted IDENTICAL residue SER 128  index1  864  path  147  %Seq 100.00 Highlighted IDENTICAL residue PRO 129  index1  865  path  148  %Seq 100.00 Highlighted IDENTICAL residue VAL 131  index1  867  path  150  %Seq 100.00 Highlighted IDENTICAL residue LEU 136  index1  872  path  155  %Seq 100.00 Highlighted IDENTICAL residue VAL 137  index1  873  path  156  %Seq 100.00 Highlighted IDENTICAL residue ASP 138  index1  874  path  157  %Seq 100.00 Highlighted IDENTICAL residue LEU 139  index1  875  path  158  %Seq 100.00 Highlighted IDENTICAL residue PRO 140  index1  876  path  159  %Seq 100.00 Highlighted IDENTICAL residue GLY 141  index1  877  path  160  %Seq 100.00 Highlighted IDENTICAL residue ILE 142  index1  878  path  161  %Seq 100.00 Highlighted IDENTICAL residue THR 152  index1  879  path  162  %Seq 100.00 Highlighted IDENTICAL residue ASP 153  index1  880  path  172  %Seq 100.00 Highlighted IDENTICAL residue ILE 154  index1  881  path  173  %Seq 100.00 Highlighted IDENTICAL residue GLU 155  index1  882  path  174  %Seq 100.00 Highlighted IDENTICAL residue ILE 158  index1  885  path  177  %Seq 100.00 Highlighted IDENTICAL residue ARG 159  index1  886  path  178  %Seq 100.00 Highlighted IDENTICAL residue MET 161  index1  888  path  180  %Seq 100.00 Highlighted IDENTICAL residue TYR 165  index1  892  path  184  %Seq 100.00 Highlighted IDENTICAL residue ILE 166  index1  893  path  185  %Seq 100.00 Highlighted IDENTICAL residue LYS 167  index1  894  path  186  %Seq 100.00 Highlighted IDENTICAL residue ILE 173  index1  900  path  192  %Seq 100.00 Highlighted IDENTICAL residue ALA 175  index1  902  path  194  %Seq 100.00 Highlighted IDENTICAL residue VAL 176  index1  903  path  195  %Seq 100.00 Highlighted IDENTICAL residue PRO 178  index1  905  path  197  %Seq 100.00 Highlighted IDENTICAL residue ALA 179  index1  906  path  198  %Seq 100.00 Highlighted IDENTICAL residue ASN 180  index1  907  path  199  %Seq 100.00 Highlighted IDENTICAL residue THR 181  index1  908  path  200  %Seq 100.00 Highlighted IDENTICAL residue ASP 182  index1  909  path  201  %Seq 100.00 Highlighted IDENTICAL residue LEU 183  index1  910  path  202  %Seq 100.00 Highlighted IDENTICAL residue ALA 184  index1  911  path  203  %Seq 100.00 Highlighted IDENTICAL residue ASN 185  index1  912  path  204  %Seq 100.00 Highlighted IDENTICAL residue SER 186  index1  913  path  205  %Seq 100.00 Highlighted IDENTICAL residue ASP 187  index1  914  path  206  %Seq 100.00 Highlighted IDENTICAL residue ALA 188  index1  915  path  207  %Seq 100.00 Highlighted IDENTICAL residue LEU 189  index1  916  path  208  %Seq 100.00 Highlighted IDENTICAL residue GLN 190  index1  917  path  209  %Seq 100.00 Highlighted IDENTICAL residue ALA 192  index1  919  path  211  %Seq 100.00 Highlighted IDENTICAL residue ASP 196  index1  923  path  215  %Seq 100.00 Highlighted IDENTICAL residue PRO 197  index1  924  path  216  %Seq 100.00 Highlighted IDENTICAL residue GLY 199  index1  926  path  218  %Seq 100.00 Highlighted IDENTICAL residue ARG 201  index1  928  path  220  %Seq 100.00 Highlighted IDENTICAL residue THR 202  index1  929  path  221  %Seq 100.00 Highlighted IDENTICAL residue ILE 203  index1  930  path  222  %Seq 100.00 Highlighted IDENTICAL residue GLY 204  index1  931  path  223  %Seq 100.00 Highlighted IDENTICAL residue VAL 205  index1  932  path  224  %Seq 100.00 Highlighted IDENTICAL residue ILE 206  index1  933  path  225  %Seq 100.00 Highlighted IDENTICAL residue THR 207  index1  934  path  226  %Seq 100.00 Highlighted IDENTICAL residue LYS 208  index1  935  path  227  %Seq 100.00 Highlighted IDENTICAL residue LEU 209  index1  936  path  228  %Seq 100.00 Highlighted IDENTICAL residue ASP 210  index1  937  path  229  %Seq 100.00 Highlighted IDENTICAL residue MET 212  index1  939  path  231  %Seq 100.00 Highlighted IDENTICAL residue ASP 213  index1  940  path  232  %Seq 100.00 Highlighted IDENTICAL residue GLY 215  index1  942  path  234  %Seq 100.00 Highlighted IDENTICAL residue THR 216  index1  943  path  235  %Seq 100.00 Highlighted IDENTICAL residue ASP 217  index1  944  path  236  %Seq 100.00 Highlighted IDENTICAL residue ALA 218  index1  945  path  237  %Seq 100.00 Highlighted IDENTICAL residue LEU 222  index1  949  path  241  %Seq 100.00 Highlighted IDENTICAL residue GLY 224  index1  951  path  243  %Seq 100.00 Highlighted IDENTICAL residue ILE 227  index1  954  path  246  %Seq 100.00 Highlighted IDENTICAL residue PRO 228  index1  955  path  247  %Seq 100.00 Highlighted IDENTICAL residue LEU 229  index1  956  path  248  %Seq 100.00 Highlighted IDENTICAL residue LEU 231  index1  958  path  250  %Seq 100.00 Highlighted IDENTICAL residue GLY 232  index1  959  path  251  %Seq 100.00 Highlighted IDENTICAL residue GLY 235  index1  962  path  254  %Seq 100.00 Highlighted IDENTICAL residue VAL 236  index1  963  path  255  %Seq 100.00 Highlighted IDENTICAL residue ASN 238  index1  965  path  257  %Seq 100.00 Highlighted IDENTICAL residue ARG 239  index1  966  path  258  %Seq 100.00 Highlighted IDENTICAL residue SER 240  index1  967  path  259  %Seq 100.00 Highlighted IDENTICAL residue GLN 241  index1  968  path  260  %Seq 100.00 Highlighted IDENTICAL residue GLU 242  index1  969  path  261  %Seq 100.00 Highlighted IDENTICAL residue ASP 243  index1  970  path  262  %Seq 100.00 Highlighted IDENTICAL residue ILE 244  index1  971  path  263  %Seq 100.00 Highlighted IDENTICAL residue SER 249  index1  976  path  268  %Seq 100.00 Highlighted IDENTICAL residue ILE 250  index1  977  path  269  %Seq 100.00 Highlighted IDENTICAL residue LEU 254  index1  981  path  273  %Seq 100.00 Highlighted IDENTICAL residue GLU 257  index1  984  path  276  %Seq 100.00 Highlighted IDENTICAL residue PHE 261  index1  988  path  280  %Seq 100.00 Highlighted IDENTICAL residue PRO 265  index1  992  path  284  %Seq 100.00 Highlighted IDENTICAL residue TYR 267  index1  994  path  286  %Seq 100.00 Highlighted IDENTICAL residue ARG 273  index1 1000  path  292  %Seq 100.00 Highlighted IDENTICAL residue GLY 275  index1 1002  path  294  %Seq 100.00 Highlighted IDENTICAL residue LEU 279  index1 1006  path  298  %Seq 100.00 Highlighted IDENTICAL residue LYS 281  index1 1008  path  300  %Seq 100.00 Highlighted IDENTICAL residue LEU 283  index1 1010  path  302  %Seq 100.00 Highlighted IDENTICAL residue ASN 284  index1 1011  path  303  %Seq 100.00 Highlighted IDENTICAL residue LEU 287  index1 1014  path  306  %Seq 100.00 Highlighted IDENTICAL residue HIS 290  index1 1017  path  309  %Seq 100.00 Highlighted IDENTICAL residue ILE 291  index1 1018  path  310  %Seq 100.00 Highlighted IDENTICAL residue LEU 295  index1 1022  path  314  %Seq 100.00 Highlighted IDENTICAL residue PRO 296  index1 1023  path  315  %Seq 100.00 Highlighted IDENTICAL residue LEU 298  index1 1025  path  317  %Seq 100.00 Highlighted IDENTICAL residue LYS 299  index1 1026  path  318  %Seq 100.00 Highlighted IDENTICAL residue LEU 306  index1 1033  path  325  %Seq 100.00 Highlighted 160 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14120-1jwyB.pir.txt.1JWY.pdb.conservation.pml

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The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14120-1jwyB.pir.txt PIR amino_acid 1JWY.pdb _ 100.0 BLOSUM62.dat

completed successfully.

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