Results Summary:
The query matrix is available at here. The target database is scop40_genmatrix
This query finds 13 pdb hits containing 13 motifs (shown as below) spanning over 2 SCOP folds and 4 SCOP superfamilies
The ranking list of motif hits is shown as below. The description of each motif is formatted as:

• In the first line, the 1st column is ranking index, the 2nd column is pdbid links to PDB (e.g. 1sc6), the 3rd column is the description of this pdb (e.g. putative acylphosphatase) and the 4th column is the ranking score;
• The second line provides the SCOP domain id (1st column, e.g., d1sc6d3) and corresponding domain description (2nd column, e.g. Acylphosphatase) if the motif can be mapped to a SCOP domain;
• The third and the fourth line provide the SCOP superfamily and fold descriptions of the mapped scop domain, respectively (e.g. Acylphosphatase/BLUF domain-like and Ferredoxin-like);
• The last line is SSE array of the motif. It shows the pdb chain followed by the pdb residue numbering range of each secondary structure element(SSE).
  
Mouse-click on a structure motif downloads a PyMOL script to display the structure motif in protein structure (e.g. D:337-346,347-362,364-373,375-384,386-400,402-410).
The N-terminus of motif is colored in green, each SSE is colored in red and the start residiue of each SSE is colored in purple. Click here to downlaod the free version of PyMOL.

    1.  1y0y     Frv operon protein FrvX                                                           0.0815195
        d1y0ya1  Frv operon protein FrvX
                 Aminopeptidase/glucanase lid domain
                 Domain of alpha and beta subunits of F1 ATP synthase-like
                 A:73-81,83-90,99-107,111-119,139-143,160-163

    2.  2f1l     16S rRNA processing protein                                                       0.0773575
        d2f1la2  16S rRNA processing protein RimM, N-terminal domain
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:7-18,23-29,40-47,48-56,63-70,83-90

    3.  1w0j     ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOC                                     0.0718339
        d1w0ja2  F1 ATP synthase alpha subunit, domain 1
                 N-terminal domain of alpha and beta subunits of F1 ATP synthase
                 Domain of alpha and beta subunits of F1 ATP synthase-like
                 A:26-36,37-43,50-56,58-68,69-76,84-90

    4.  1jny     Elongation factor 1-alpha                                                         0.0638937
        d1jnya1  Elongation factor eEF-1alpha, domain 2
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:232-243,247-256,262-269,270-277,292-301,309-315

    5.  2gre     Deblocking aminopeptidase                                                         0.0634679
        d2grea1  Deblocking aminopeptidase YhfE
                 Aminopeptidase/glucanase lid domain
                 Domain of alpha and beta subunits of F1 ATP synthase-like
                 A:74-82,84-91,100-109,111-120,141-146,162-169

    6.  1wb1     TRANSLATION ELONGATION FACTOR SELB                                                0.0625234
        d1wb1a2  Elongation factor SelB, domains 2 and 4
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:390-401,402-408,420-428,429-441,442-450,455-464

    7.  1d1n     INITIATION FACTOR 2                                                               0.0617132
        d1d1na_  Initiation factor IF2/eIF5b, domains 2 and 4
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:146-159,163-172,179-186,193-201,212-219,228-234

    8.  1ylo     hypothetical protein SF2450                                                       0.0612033
        d1yloa1  Aminopeptidase YpdE
                 Aminopeptidase/glucanase lid domain
                 Domain of alpha and beta subunits of F1 ATP synthase-like
                 A:67-75,77-84,93-102,104-117,118-127,142-147

    9.  1kk1     eIF2gamma                                                                         0.0611546
        d1kk1a1  Initiation factor eIF2 gamma subunit, domain II
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:209-218,231-240,246-253,267-278,290-296,308-314

   10.  2jdi     ATP SYNTHASE SUBUNIT BETA                                                         0.0571396
        d2jdid2  F1 ATP synthase beta subunit, domain 1
                 N-terminal domain of alpha and beta subunits of F1 ATP synthase
                 Domain of alpha and beta subunits of F1 ATP synthase-like
                 D:10-18,19-25,32-39,45-54,56-64,71-78

   11.  1g7s     TRANSLATION INITIATION FACTOR IF2/EIF5B                                           0.0566187
        d1g7sa1  Initiation factor IF2/eIF5b, domains 2 and 4
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:232-242,246-255,262-269,270-283,304-312,320-327

   12.  2c78     ELONGATION FACTOR TU-A                                                            0.0529549
        d2c78a1  Elongation factor Tu (EF-Tu), domain 2
                 Translation proteins
                 Reductase/isomerase/elongation factor common domain
                 A:221-232,234-244,250-257,262-273,282-291,300-306

   13.  1bd0     ALANINE RACEMASE                                                                  0.0491256
        d1bd0a1  Alanine racemase
                 Alanine racemase C-terminal domain-like
                 Domain of alpha and beta subunits of F1 ATP synthase-like
                 A:246-260,276-284,295-300,301-307,312-319,325-332