At2g01870.1/Structure

&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM//construct_homolog_PDB &&&&&&&&&&&&&&&&&&&&

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/

=
=========================================

Read 1 sequences from FASTA file At2g01870.fasta.txt; taking first sequence

>gi|18379315|ref|NP_565278.1| MVVVLGLQSLKWYTHGRIMETKKKRHLMRIVQATEREDSFQIDRDKAREA LKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEEPPEISGSFLTSS AFVLLALTLFYNILFITVIKPSMDGPESVPEENSVAMSDSDIVKFPLSSL PENTFKQ

Assigned types to 157 amino_acid residues in homolog_Sequence, 0 remain unknown

=
=========================================

Sequence file type = 3

Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g01870_1irjA.pir.txt

=
=========================================

>2-01870 MVVVLGLQSLKWYTHGRIMETKKKRHLMRIVQATER-EDSFQIDRD KAREALKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEEPPEISGS FLTSSAFVLLALTLFYNILFITVIKPSMDGPESVPEENSVAMSDSDIVKF PLSSLPENTFKQ

Assigned types to 157 residues in Sequence 2-01870, 5 remain unknown

=
=========================================

>1irjA [INUB:5] TCKMSQLERNIETIINTFHQXXXXXGHPDTLNQG EFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEE--- --FIMLMARL

Assigned types to 80 residues in Sequence 1irjA, 82 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

=
=========================================

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 37 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 38 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 39 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 40 All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment Path index 41 All residues are positively and negatively charged

Translated sequence file At2g01870_1irjA.pir.txt into sequence alignment.

=
=========================================

Generated FASTA sequence from the PDB file 1IRJ.pdb

>1IRJ.pdb Made from 5587 ATOM records in 1IRJ.pdb TCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLCKMSQLERNIETIIN TFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLD TNADKQLSFEEFIMLMARLKMSQLERNIETIINTFHQYSVKLGHPDTLNQ GEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMA RLMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKE NKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLKMSQLERNIETIINTF HQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTN ADKQLSFEEFIMLMARLCKMSQLERNIETIINTFHQYSVKLGHPDTLNQG EFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMAR LCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTCKMSQLERNIETII NTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDL DTNADKQLSFEEFIMLMARL

=
=========================================

gi|18379315|ref|NP_565278.1| vs        2-01870  (seq    1) 	Path length 157   Match score   787.000  Best   787.000 gi|18379315|ref|NP_565278.1| vs          1irjA  (seq    2) 	Path length 55    Match score    27.000  Best   787.000

=
=========================================

Best homolog alignment  Path 157

gi|18379315|ref|NP_565278.1|    1  MVVVLGLQSLKWYTHGRIMETKKKRHLMRIVQATEREDSFQIDRDKAREA    50 MVVVLGLQSLKWYTHGRIMETKKKRHLMRIVQATEREDSFQIDRDKAREA 2-01870                         1  MVVVLGLQSLKWYTHGRIMETKKKRHLMRIVQATEREDSFQIDRDKAREA    50

gi|18379315|ref|NP_565278.1|   51  LKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEEPPEISGSFLTSS   100 LKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEEPPEISGSFLTSS 2-01870                        51  LKQLDQQIESQADEKPRIINKTSSDVVRTNNDPIMFEEPPEISGSFLTSS   100

gi|18379315|ref|NP_565278.1|  101  AFVLLALTLFYNILFITVIKPSMDGPESVPEENSVAMSDSDIVKFPLSSL   150 AFVLLALTLFYNILFITVIKPSMDGPESVPEENSVAMSDSDIVKFPLSSL 2-01870                       101  AFVLLALTLFYNILFITVIKPSMDGPESVPEENSVAMSDSDIVKFPLSSL   150

gi|18379315|ref|NP_565278.1|  151  PENTFKQ   157 PENTFKQ 2-01870                       151  PENTFKQ   157

=
=========================================

1IRJ.pdb       vs         2-01870  (seq    1) 	Path length 47    Match score    30.000  Best    30.000 1IRJ.pdb       vs           1irjA  (seq    2) 	Path length 85    Match score   413.000  Best   413.000

=
=========================================

Best PDB     alignment   Path 85

1IRJ.pdb    1  TCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK    50 TCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKK 1irjA       1  TCKMSQLERNIETIINTFHQXXXXXGHPDTLNQGEFKELVRKDLQNFLKK    50

1IRJ.pdb   51  ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARL    85 ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARL 1irjA      51  ENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARL    85

=
=========================================

Matched T   2 (PDB     path    1) to T    1 (Alignment path   17) of 1irjA Matched R  17 (homolog path   17) to R   17 (Alignment path   17) of 2-01870 Matched C   3 (PDB     path    2) to C    2 (Alignment path   18) of 1irjA Matched I  18 (homolog path   18) to I   18 (Alignment path   18) of 2-01870 Matched K   4 (PDB     path    3) to K    3 (Alignment path   19) of 1irjA Matched M  19 (homolog path   19) to M   19 (Alignment path   19) of 2-01870 Matched M   5 (PDB     path    4) to M    4 (Alignment path   20) of 1irjA Matched E  20 (homolog path   20) to E   20 (Alignment path   20) of 2-01870 Matched S   6 (PDB     path    5) to S    5 (Alignment path   21) of 1irjA Matched T  21 (homolog path   21) to T   21 (Alignment path   21) of 2-01870 Matched Q   7 (PDB     path    6) to Q    6 (Alignment path   22) of 1irjA Matched K  22 (homolog path   22) to K   22 (Alignment path   22) of 2-01870 Matched L   8 (PDB     path    7) to L    7 (Alignment path   23) of 1irjA Matched K  23 (homolog path   23) to K   23 (Alignment path   23) of 2-01870 Matched E   9 (PDB     path    8) to E    8 (Alignment path   24) of 1irjA Matched K  24 (homolog path   24) to K   24 (Alignment path   24) of 2-01870 Matched R  10 (PDB     path    9) to R    9 (Alignment path   25) of 1irjA Matched R  25 (homolog path   25) to R   25 (Alignment path   25) of 2-01870 Matched N  11 (PDB     path   10) to N   10 (Alignment path   26) of 1irjA Matched H  26 (homolog path   26) to H   26 (Alignment path   26) of 2-01870 Matched I  12 (PDB     path   11) to I   11 (Alignment path   27) of 1irjA Matched L  27 (homolog path   27) to L   27 (Alignment path   27) of 2-01870 Matched E  13 (PDB     path   12) to E   12 (Alignment path   28) of 1irjA Matched M  28 (homolog path   28) to M   28 (Alignment path   28) of 2-01870 Matched T  14 (PDB     path   13) to T   13 (Alignment path   29) of 1irjA Matched R  29 (homolog path   29) to R   29 (Alignment path   29) of 2-01870 Matched I  15 (PDB     path   14) to I   14 (Alignment path   30) of 1irjA Matched I  30 (homolog path   30) to I   30 (Alignment path   30) of 2-01870 Matched I  16 (PDB     path   15) to I   15 (Alignment path   31) of 1irjA Matched V  31 (homolog path   31) to V   31 (Alignment path   31) of 2-01870 Matched N  17 (PDB     path   16) to N   16 (Alignment path   32) of 1irjA Matched Q  32 (homolog path   32) to Q   32 (Alignment path   32) of 2-01870 Matched T  18 (PDB     path   17) to T   17 (Alignment path   33) of 1irjA Matched A  33 (homolog path   33) to A   33 (Alignment path   33) of 2-01870 Matched F  19 (PDB     path   18) to F   18 (Alignment path   34) of 1irjA Matched T  34 (homolog path   34) to T   34 (Alignment path   34) of 2-01870 Matched H  20 (PDB     path   19) to H   19 (Alignment path   35) of 1irjA Matched E  35 (homolog path   35) to E   35 (Alignment path   35) of 2-01870 Matched Q  21 (PDB     path   20) to Q   20 (Alignment path   36) of 1irjA Matched R  36 (homolog path   36) to R   36 (Alignment path   36) of 2-01870 Matched Y  22 (PDB     path   21) to X   21 (Alignment path   37) of 1irjA Matched S  23 (PDB     path   22) to X   22 (Alignment path   38) of 1irjA Matched V  24 (PDB     path   23) to X   23 (Alignment path   39) of 1irjA Matched K  25 (PDB     path   24) to X   24 (Alignment path   40) of 1irjA Matched L  26 (PDB     path   25) to X   25 (Alignment path   41) of 1irjA Matched G  27 (PDB     path   26) to G   26 (Alignment path   42) of 1irjA Matched E  37 (homolog path   37) to E   37 (Alignment path   42) of 2-01870 Matched H  28 (PDB     path   27) to H   27 (Alignment path   43) of 1irjA Matched D  38 (homolog path   38) to D   38 (Alignment path   43) of 2-01870 Matched P  29 (PDB     path   28) to P   28 (Alignment path   44) of 1irjA Matched S  39 (homolog path   39) to S   39 (Alignment path   44) of 2-01870 Matched D  30 (PDB     path   29) to D   29 (Alignment path   45) of 1irjA Matched F  40 (homolog path   40) to F   40 (Alignment path   45) of 2-01870 Matched T  31 (PDB     path   30) to T   30 (Alignment path   46) of 1irjA Matched Q  41 (homolog path   41) to Q   41 (Alignment path   46) of 2-01870 Matched L  32 (PDB     path   31) to L   31 (Alignment path   47) of 1irjA Matched I  42 (homolog path   42) to I   42 (Alignment path   47) of 2-01870 Matched N  33 (PDB     path   32) to N   32 (Alignment path   48) of 1irjA Matched D  43 (homolog path   43) to D   43 (Alignment path   48) of 2-01870 Matched Q  34 (PDB     path   33) to Q   33 (Alignment path   49) of 1irjA Matched R  44 (homolog path   44) to R   44 (Alignment path   49) of 2-01870 Matched G  35 (PDB     path   34) to G   34 (Alignment path   50) of 1irjA Matched D  45 (homolog path   45) to D   45 (Alignment path   50) of 2-01870 Matched E  36 (PDB     path   35) to E   35 (Alignment path   51) of 1irjA Matched K  46 (homolog path   46) to K   46 (Alignment path   51) of 2-01870 Matched F  37 (PDB     path   36) to F   36 (Alignment path   52) of 1irjA Matched A  47 (homolog path   47) to A   47 (Alignment path   52) of 2-01870 Matched K  38 (PDB     path   37) to K   37 (Alignment path   53) of 1irjA Matched R  48 (homolog path   48) to R   48 (Alignment path   53) of 2-01870 Matched E  39 (PDB     path   38) to E   38 (Alignment path   54) of 1irjA Matched E  49 (homolog path   49) to E   49 (Alignment path   54) of 2-01870 Matched L  40 (PDB     path   39) to L   39 (Alignment path   55) of 1irjA Matched A  50 (homolog path   50) to A   50 (Alignment path   55) of 2-01870 Matched V  41 (PDB     path   40) to V   40 (Alignment path   56) of 1irjA Matched L  51 (homolog path   51) to L   51 (Alignment path   56) of 2-01870 Matched R  42 (PDB     path   41) to R   41 (Alignment path   57) of 1irjA Matched K  52 (homolog path   52) to K   52 (Alignment path   57) of 2-01870 Matched K  43 (PDB     path   42) to K   42 (Alignment path   58) of 1irjA Matched Q  53 (homolog path   53) to Q   53 (Alignment path   58) of 2-01870 Matched D  44 (PDB     path   43) to D   43 (Alignment path   59) of 1irjA Matched L  54 (homolog path   54) to L   54 (Alignment path   59) of 2-01870 Matched L  45 (PDB     path   44) to L   44 (Alignment path   60) of 1irjA Matched D  55 (homolog path   55) to D   55 (Alignment path   60) of 2-01870 Matched Q  46 (PDB     path   45) to Q   45 (Alignment path   61) of 1irjA Matched Q  56 (homolog path   56) to Q   56 (Alignment path   61) of 2-01870 Matched N  47 (PDB     path   46) to N   46 (Alignment path   62) of 1irjA Matched Q  57 (homolog path   57) to Q   57 (Alignment path   62) of 2-01870 Matched F  48 (PDB     path   47) to F   47 (Alignment path   63) of 1irjA Matched I  58 (homolog path   58) to I   58 (Alignment path   63) of 2-01870 Matched L  49 (PDB     path   48) to L   48 (Alignment path   64) of 1irjA Matched E  59 (homolog path   59) to E   59 (Alignment path   64) of 2-01870 Matched K  50 (PDB     path   49) to K   49 (Alignment path   65) of 1irjA Matched S  60 (homolog path   60) to S   60 (Alignment path   65) of 2-01870 Matched K  51 (PDB     path   50) to K   50 (Alignment path   66) of 1irjA Matched Q  61 (homolog path   61) to Q   61 (Alignment path   66) of 2-01870 Matched E  52 (PDB     path   51) to E   51 (Alignment path   67) of 1irjA Matched A  62 (homolog path   62) to A   62 (Alignment path   67) of 2-01870 Matched N  53 (PDB     path   52) to N   52 (Alignment path   68) of 1irjA Matched D  63 (homolog path   63) to D   63 (Alignment path   68) of 2-01870 Matched K  54 (PDB     path   53) to K   53 (Alignment path   69) of 1irjA Matched E  64 (homolog path   64) to E   64 (Alignment path   69) of 2-01870 Matched N  55 (PDB     path   54) to N   54 (Alignment path   70) of 1irjA Matched K  65 (homolog path   65) to K   65 (Alignment path   70) of 2-01870 Matched E  56 (PDB     path   55) to E   55 (Alignment path   71) of 1irjA Matched P  66 (homolog path   66) to P   66 (Alignment path   71) of 2-01870 Matched K  57 (PDB     path   56) to K   56 (Alignment path   72) of 1irjA Matched R  67 (homolog path   67) to R   67 (Alignment path   72) of 2-01870 Matched V  58 (PDB     path   57) to V   57 (Alignment path   73) of 1irjA Matched I  68 (homolog path   68) to I   68 (Alignment path   73) of 2-01870 Matched I  59 (PDB     path   58) to I   58 (Alignment path   74) of 1irjA Matched I  69 (homolog path   69) to I   69 (Alignment path   74) of 2-01870 Matched E  60 (PDB     path   59) to E   59 (Alignment path   75) of 1irjA Matched N  70 (homolog path   70) to N   70 (Alignment path   75) of 2-01870 Matched H  61 (PDB     path   60) to H   60 (Alignment path   76) of 1irjA Matched K  71 (homolog path   71) to K   71 (Alignment path   76) of 2-01870 Matched I  62 (PDB     path   61) to I   61 (Alignment path   77) of 1irjA Matched T  72 (homolog path   72) to T   72 (Alignment path   77) of 2-01870 Matched M  63 (PDB     path   62) to M   62 (Alignment path   78) of 1irjA Matched S  73 (homolog path   73) to S   73 (Alignment path   78) of 2-01870 Matched E  64 (PDB     path   63) to E   63 (Alignment path   79) of 1irjA Matched S  74 (homolog path   74) to S   74 (Alignment path   79) of 2-01870 Matched D  65 (PDB     path   64) to D   64 (Alignment path   80) of 1irjA Matched D  75 (homolog path   75) to D   75 (Alignment path   80) of 2-01870 Matched L  66 (PDB     path   65) to L   65 (Alignment path   81) of 1irjA Matched V  76 (homolog path   76) to V   76 (Alignment path   81) of 2-01870 Matched D  67 (PDB     path   66) to D   66 (Alignment path   82) of 1irjA Matched V  77 (homolog path   77) to V   77 (Alignment path   82) of 2-01870 Matched T  68 (PDB     path   67) to T   67 (Alignment path   83) of 1irjA Matched R  78 (homolog path   78) to R   78 (Alignment path   83) of 2-01870 Matched N  69 (PDB     path   68) to N   68 (Alignment path   84) of 1irjA Matched T  79 (homolog path   79) to T   79 (Alignment path   84) of 2-01870 Matched A  70 (PDB     path   69) to A   69 (Alignment path   85) of 1irjA Matched N  80 (homolog path   80) to N   80 (Alignment path   85) of 2-01870 Matched D  71 (PDB     path   70) to D   70 (Alignment path   86) of 1irjA Matched N  81 (homolog path   81) to N   81 (Alignment path   86) of 2-01870 Matched K  72 (PDB     path   71) to K   71 (Alignment path   87) of 1irjA Matched D  82 (homolog path   82) to D   82 (Alignment path   87) of 2-01870 Matched Q  73 (PDB     path   72) to Q   72 (Alignment path   88) of 1irjA Matched P  83 (homolog path   83) to P   83 (Alignment path   88) of 2-01870 Matched L  74 (PDB     path   73) to L   73 (Alignment path   89) of 1irjA Matched I  84 (homolog path   84) to I   84 (Alignment path   89) of 2-01870 Matched S  75 (PDB     path   74) to S   74 (Alignment path   90) of 1irjA Matched M  85 (homolog path   85) to M   85 (Alignment path   90) of 2-01870 Matched F  76 (PDB     path   75) to F   75 (Alignment path   91) of 1irjA Matched F  86 (homolog path   86) to F   86 (Alignment path   91) of 2-01870 Matched E  77 (PDB     path   76) to E   76 (Alignment path   92) of 1irjA Matched E  87 (homolog path   87) to E   87 (Alignment path   92) of 2-01870 Matched E  78 (PDB     path   77) to E   77 (Alignment path   93) of 1irjA Matched E  88 (homolog path   88) to E   88 (Alignment path   93) of 2-01870 Matched F  79 (PDB     path   78) to F   78 (Alignment path  107) of 1irjA Matched F 102 (homolog path  102) to F  102 (Alignment path  107) of 2-01870 Matched I  80 (PDB     path   79) to I   79 (Alignment path  108) of 1irjA Matched V 103 (homolog path  103) to V  103 (Alignment path  108) of 2-01870 Matched M  81 (PDB     path   80) to M   80 (Alignment path  109) of 1irjA Matched L 104 (homolog path  104) to L  104 (Alignment path  109) of 2-01870 Matched L  82 (PDB     path   81) to L   81 (Alignment path  110) of 1irjA Matched L 105 (homolog path  105) to L  105 (Alignment path  110) of 2-01870 Matched M  83 (PDB     path   82) to M   82 (Alignment path  111) of 1irjA Matched A 106 (homolog path  106) to A  106 (Alignment path  111) of 2-01870 Matched A  84 (PDB     path   83) to A   83 (Alignment path  112) of 1irjA Matched L 107 (homolog path  107) to L  107 (Alignment path  112) of 2-01870 Matched R  85 (PDB     path   84) to R   84 (Alignment path  113) of 1irjA Matched T 108 (homolog path  108) to T  108 (Alignment path  113) of 2-01870 Matched L  86 (PDB     path   85) to L   85 (Alignment path  114) of 1irjA Matched L 109 (homolog path  109) to L  109 (Alignment path  114) of 2-01870

Matched 80 residues of the homolog and PDB sequences

=
=========================================

Wrote 447 atoms into PDB file /usr/local/www/html/proteins/htdocs/results/At2g01870.fasta.txt.At2g01870_1irjA.pir.txt.1IRJ.pdb

=
=========================================

=
==================================================================

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM//construct_homolog_PDB At2g01870.fasta.txt At2g01870_1irjA.pir.txt PIR amino_acid 1IRJ.pdb A BLOSUM62.dat

completed successfully.

@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/pro