Query         gi|254780287|ref|YP_003064700.1| iron-sulfur cluster assembly accessory protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 109
No_of_seqs    119 out of 3041
Neff          7.2 
Searched_HMMs 13730
Date          Wed Jun  1 02:06:07 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780287.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1s98a_ b.124.1.1 (A:) Fe-S sc 100.0 8.8E-30 6.4E-34  192.6  11.0   97    4-100     1-97  (97)
  2 d1nwba_ b.124.1.1 (A:) Hypothe  99.9 5.9E-28 4.3E-32  182.0   8.4   95    1-95      6-101 (101)
  3 d2p2ea1 b.124.1.1 (A:3-120) Pu  98.1 3.8E-06 2.8E-10   54.5   6.2   89    4-96      2-104 (118)
  4 d1sp2a_ g.37.1.1 (A:) Transcri  19.0      17  0.0012   15.7   0.9   10   99-108     3-15  (31)
  5 d2j0141 d.325.1.2 (4:1-50) Rib  15.1      32  0.0024   14.0   1.6   13   97-109    12-24  (50)
  6 d2j7ja2 g.37.1.1 (A:29-57) Tra  11.4      30  0.0022   14.2   0.6    8  102-109    10-17  (29)
  7 d1m0da_ c.52.1.17 (A:) Endonuc  10.5      42   0.003   13.4   1.0   10   89-98     75-84  (129)
  8 d1vsra_ c.52.1.15 (A:) Very sh   9.7      55   0.004   12.7   2.1   29   39-67     14-42  (134)
  9 d1vs6z1 d.325.1.2 (Z:1-70) Rib   8.9      59  0.0043   12.5   1.3   13   97-109    12-24  (70)
 10 d1ncsa_ g.37.1.1 (A:) SWI5 zin   8.5      43  0.0032   13.3   0.4    7  102-108    25-31  (47)

No 1  
>d1s98a_ b.124.1.1 (A:) Fe-S scaffold protein IscA (YfhF) {Escherichia coli [TaxId: 562]}
Probab=99.96  E-value=8.8e-30  Score=192.63  Aligned_cols=97  Identities=31%  Similarity=0.663  Sum_probs=92.7

Q ss_pred             CEEECHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEEHHHHCCCCCCCEECCCCEEEEECHHHHHHCCCCEEEEEE
Q ss_conf             03318899999999997289884799998368876514653332103521130046878999846776540687999872
Q gi|254780287|r    4 IIKITDAAATQIKTILESNSDKKALRITIEGGGCSGFSYKFDLESKQSEDDIVFEKNGAQIFIDKISLAYLTNSEIDFVD   83 (109)
Q Consensus         4 mi~iT~~A~~~i~~l~~~~~~~~~lRi~v~~gGCsG~~y~l~~~~~~~~~D~v~~~~gi~v~vd~~s~~~L~g~~IDy~~   83 (109)
                      -|+||++|+++|++++++++++.+|||+|++|||+||+|.|.|++++.++|.+++.+|++|+||+.|++||+|++|||++
T Consensus         1 ~I~iT~~A~~~i~~ll~~~~~~~~lRi~v~~gGCsG~~Y~l~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~G~~IDy~~   80 (97)
T d1s98a_           1 SITLSDSAAARVNTFLANRGKGFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKGVKVVVDGKSMQFLDGTQLDFVK   80 (97)
T ss_dssp             CCEECHHHHHHHHHHHHTTCCCCEEEEEEEEETTTEEEEEEEEESSCCTTEEEEEETTEEEEEEGGGHHHHTTCEEEEEC
T ss_pred             CEEECHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCEEEEEECCCCCCCCEEEECCCCEEEEEHHHHHHHCCCEEEEEE
T ss_conf             98989999999999997389981799999718977636776005458999699872899999827999873899998856


Q ss_pred             CCCCCEEEEECCCCCCC
Q ss_conf             78545238988888887
Q gi|254780287|r   84 NLLSKSFQIRNPNATSN  100 (109)
Q Consensus        84 ~~~g~gF~i~nPna~~~  100 (109)
                      +++++||+|+||||++.
T Consensus        81 ~~~~~gF~f~NPNak~e   97 (97)
T d1s98a_          81 EGLNEGFKFTNPNVKDE   97 (97)
T ss_dssp             SSTTCEEEEECTTSCCC
T ss_pred             CCCCCCEEEECCCCCCC
T ss_conf             68868469989888898


No 2  
>d1nwba_ b.124.1.1 (A:) Hypothetical protein Aq_1857 {Aquifex aeolicus [TaxId: 63363]}
Probab=99.94  E-value=5.9e-28  Score=181.95  Aligned_cols=95  Identities=38%  Similarity=0.730  Sum_probs=90.0

Q ss_pred             CCCCEEECHHHHHHHHHHHHHCC-CCCEEEEEEECCCCCCEEEEEHHHHCCCCCCCEECCCCEEEEECHHHHHHCCCCEE
Q ss_conf             98403318899999999997289-88479999836887651465333210352113004687899984677654068799
Q gi|254780287|r    1 MVPIIKITDAAATQIKTILESNS-DKKALRITIEGGGCSGFSYKFDLESKQSEDDIVFEKNGAQIFIDKISLAYLTNSEI   79 (109)
Q Consensus         1 M~~mi~iT~~A~~~i~~l~~~~~-~~~~lRi~v~~gGCsG~~y~l~~~~~~~~~D~v~~~~gi~v~vd~~s~~~L~g~~I   79 (109)
                      ...||+||++|+++|++++++++ +..+|||+|+++||+||+|.|+|++++.++|.+++.+|++|+||+.|++||+|++|
T Consensus         6 ~~~mi~iT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~D~v~~~~g~~i~id~~s~~~L~G~~I   85 (101)
T d1nwba_           6 QQFIFKVTDKAVEEIKKVAQENNIENPILRIRVVPGGCSGFQYAMGFDDTVEEGDHVFEYDGVKVVIDPFSMPYVNGAEL   85 (101)
T ss_dssp             CCCCCEECHHHHHHHHHHHHTTTCSSCEEEECCCCCCTTCCCCCCCEECSCCSSCCCCCCSSSEEEECTTTGGGSTTCEE
T ss_pred             CCCCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCCCCCCEEEECCCEEEEECHHHHHHHCCCEE
T ss_conf             28729988999999999998649988669999967999861588752245335745885088249998889868589999


Q ss_pred             EEEECCCCCEEEEECC
Q ss_conf             9872785452389888
Q gi|254780287|r   80 DFVDNLLSKSFQIRNP   95 (109)
Q Consensus        80 Dy~~~~~g~gF~i~nP   95 (109)
                      ||++++++++|+|+||
T Consensus        86 Dy~~~~~~~~F~f~NP  101 (101)
T d1nwba_          86 DYVVDFMGGGFTIRNP  101 (101)
T ss_dssp             EEEEETTEEEEEEECC
T ss_pred             EEEECCCCCEEEEECC
T ss_conf             9865698771899495


No 3  
>d2p2ea1 b.124.1.1 (A:3-120) Putative Fe-S biosynthesis protein LSL1730 {Lactobacillus salivarius [TaxId: 1624]}
Probab=98.06  E-value=3.8e-06  Score=54.53  Aligned_cols=89  Identities=21%  Similarity=0.367  Sum_probs=62.7

Q ss_pred             CEEECHHHHHHHHHHHHHCCCCCEEEEEE--------ECCCCC-CEEEEEHHHHC----CCCCCCEECCCCEEEEECHHH
Q ss_conf             03318899999999997289884799998--------368876-51465333210----352113004687899984677
Q gi|254780287|r    4 IIKITDAAATQIKTILESNSDKKALRITI--------EGGGCS-GFSYKFDLESK----QSEDDIVFEKNGAQIFIDKIS   70 (109)
Q Consensus         4 mi~iT~~A~~~i~~l~~~~~~~~~lRi~v--------~~gGCs-G~~y~l~~~~~----~~~~D~v~~~~gi~v~vd~~s   70 (109)
                      -||||+.|+++|++.+..+  ...|.+..        +++||+ |-.|.|-+.++    ..+-|..++.+-.+|++.+.+
T Consensus         2 ~ItiT~~A~~~L~~~~~~~--~~~L~L~~dDG~g~yS~gggC~i~g~f~L~~v~~~~~~~~~yd~~iesn~g~i~~~~~~   79 (118)
T d2p2ea1           2 KITVTDDAAKKLQRYTDDS--NAVLLLDFDDGVGALSKVGVCSLNSDFRILVVSKDMDYKKDYNEVIDSNIGKFYYKGYS   79 (118)
T ss_dssp             EEEECHHHHHHHHHHHTCT--TEEEEEEECSSCSGGGGSSCCCCSCCEEEEEEETTSSCTTTSCEEEEETTSCEEECGGG
T ss_pred             EEEECHHHHHHHHHHHCCC--CCEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCEEECCCCCCEEECCCC
T ss_conf             7898899999999862877--77799999179886455773025887899998077788964345601787557873531


Q ss_pred             HHHCC-CCEEEEEECCCCCEEEEECCC
Q ss_conf             65406-879998727854523898888
Q gi|254780287|r   71 LAYLT-NSEIDFVDNLLSKSFQIRNPN   96 (109)
Q Consensus        71 ~~~L~-g~~IDy~~~~~g~gF~i~nPn   96 (109)
                      ..|++ +++|||.+.  ...|..+.|+
T Consensus        80 ~~ffd~~m~ld~~~~--~~~l~LkSd~  104 (118)
T d2p2ea1          80 KMYMDDNMKISLNTN--NSLLRLTGDN  104 (118)
T ss_dssp             GGGSCSEEEEEECSS--SSCEEEEETT
T ss_pred             HHHCCCCCEEEECCC--CCEEEEECCC
T ss_conf             111289718988688--7879970797


No 4  
>d1sp2a_ g.37.1.1 (A:) Transcription factor sp1 {Human (Homo sapiens) [TaxId: 9606]}
Probab=19.01  E-value=17  Score=15.72  Aligned_cols=10  Identities=40%  Similarity=0.966  Sum_probs=7.5

Q ss_pred             CCC---CCCCCCC
Q ss_conf             877---8862246
Q gi|254780287|r   99 SNC---GCGTSFS  108 (109)
Q Consensus        99 ~~C---gCG~SF~  108 (109)
                      ..|   |||.+|+
T Consensus         3 f~C~~~~C~k~F~   15 (31)
T d1sp2a_           3 FMCTWSYCGKRFT   15 (31)
T ss_dssp             CBCCSTTCCCBCS
T ss_pred             CCCCCCCCCCCCC
T ss_conf             9990998791748


No 5  
>d2j0141 d.325.1.2 (4:1-50) Ribosomal protein L31p {Thermus thermophilus [TaxId: 274]}
Probab=15.08  E-value=32  Score=14.04  Aligned_cols=13  Identities=38%  Similarity=0.869  Sum_probs=8.2

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             8887788622469
Q gi|254780287|r   97 ATSNCGCGTSFSI  109 (109)
Q Consensus        97 a~~~CgCG~SF~~  109 (109)
                      .+-.|.||++|.+
T Consensus        12 v~~~cscg~~f~~   24 (50)
T d2j0141          12 ARIICGCGNVIET   24 (50)
T ss_dssp             TTTCTTSCGGGSC
T ss_pred             EEEEECCCCEEEE
T ss_conf             9999899999994


No 6  
>d2j7ja2 g.37.1.1 (A:29-57) Transcription factor IIIA, TFIIIA {Xenopus laevis [TaxId: 8355]}
Probab=11.42  E-value=30  Score=14.19  Aligned_cols=8  Identities=50%  Similarity=1.252  Sum_probs=0.0

Q ss_pred             CCCCCCCC
Q ss_conf             88622469
Q gi|254780287|r  102 GCGTSFSI  109 (109)
Q Consensus       102 gCG~SF~~  109 (109)
                      ||+.+|+.
T Consensus        10 gcdk~fs~   17 (29)
T d2j7ja2          10 GCDKRFSL   17 (29)
T ss_dssp             TCCCEESS
T ss_pred             CCCCCCCC
T ss_conf             75522227


No 7  
>d1m0da_ c.52.1.17 (A:) Endonuclease I (Holliday junction resolvase) {Bacteriophage T7 [TaxId: 10760]}
Probab=10.52  E-value=42  Score=13.39  Aligned_cols=10  Identities=0%  Similarity=0.082  Sum_probs=0.0

Q ss_pred             EEEEECCCCC
Q ss_conf             2389888888
Q gi|254780287|r   89 SFQIRNPNAT   98 (109)
Q Consensus        89 gF~i~nPna~   98 (109)
                      +|+|.|||++
T Consensus        75 RfvF~n~~~k   84 (129)
T d1m0da_          75 RIVFSSSRTK   84 (129)
T ss_dssp             EEEESCTTSB
T ss_pred             EEEEECCCCC
T ss_conf             9998577660


No 8  
>d1vsra_ c.52.1.15 (A:) Very short patch repair (VSR) endonuclease {Escherichia coli [TaxId: 562]}
Probab=9.72  E-value=55  Score=12.71  Aligned_cols=29  Identities=21%  Similarity=0.404  Sum_probs=0.0

Q ss_pred             CEEEEEHHHHCCCCCCCEECCCCEEEEEC
Q ss_conf             51465333210352113004687899984
Q gi|254780287|r   39 GFSYKFDLESKQSEDDIVFEKNGAQIFID   67 (109)
Q Consensus        39 G~~y~l~~~~~~~~~D~v~~~~gi~v~vd   67 (109)
                      |+.|.+...+-+..-|.++..-.+-|+||
T Consensus        14 G~RyR~~~k~lpG~PDiv~~~~k~aIfvd   42 (134)
T d1vsra_          14 GLAFRVQDASLPGRPDFVVDEYRCVIFTH   42 (134)
T ss_dssp             TCCCEESCTTSTTCCSEEEGGGTEEEEEE
T ss_pred             CCEEEECCCCCCCCCCEEECCCCEEEEEC
T ss_conf             98688648889999889633763899971


No 9  
>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]}
Probab=8.90  E-value=59  Score=12.52  Aligned_cols=13  Identities=38%  Similarity=0.997  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             8887788622469
Q gi|254780287|r   97 ATSNCGCGTSFSI  109 (109)
Q Consensus        97 a~~~CgCG~SF~~  109 (109)
                      ..-.|.||++|.+
T Consensus        12 v~~~~s~g~~f~~   24 (70)
T d1vs6z1          12 ITASCSCGNVMKI   24 (70)
T ss_dssp             CBCCCCSSCCCCC
T ss_pred             EEEEECCCCEEEE
T ss_conf             9999789999997


No 10 
>d1ncsa_ g.37.1.1 (A:) SWI5 zinc-finger domains {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=8.50  E-value=43  Score=13.29  Aligned_cols=7  Identities=43%  Similarity=1.222  Sum_probs=0.0

Q ss_pred             CCCCCCC
Q ss_conf             8862246
Q gi|254780287|r  102 GCGTSFS  108 (109)
Q Consensus       102 gCG~SF~  108 (109)
                      |||.+|+
T Consensus        25 ~C~k~F~   31 (47)
T d1ncsa_          25 GCTKTFK   31 (47)
T ss_dssp             TCCCEEC
T ss_pred             CCCCCCC
T ss_conf             8996045


Done!