Query         gi|254780252|ref|YP_003064665.1| 30S ribosomal protein S17 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 79
No_of_seqs    106 out of 1566
Neff          5.4 
Searched_HMMs 13730
Date          Tue May 24 06:26:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780252.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 d2uubq1 b.40.4.5 (Q:2-101) Rib 100.0 2.8E-32   2E-36  195.5   8.8   76    2-77      1-76  (100)
  2 d2gy9q1 b.40.4.5 (Q:5-82) Ribo 100.0 1.2E-30 8.5E-35  186.5  11.0   75    4-78      1-75  (78)
  3 d1ripa_ b.40.4.5 (A:) Ribosoma 100.0 2.5E-31 1.8E-35  190.2  -5.0   76    3-78      2-77  (81)
  4 d1a62a2 b.40.4.5 (A:48-125) Rh  30.2      16  0.0012   15.2   3.6   31   49-79     42-72  (78)
  5 d1c06a_ d.66.1.2 (A:) Ribosoma  20.5      17  0.0012   15.1   1.2   17   46-62     87-103 (159)
  6 d1ah9a_ b.40.4.5 (A:) Translat  17.5      30  0.0022   13.8   4.1   52    4-69      6-63  (71)
  7 d1e32a1 b.52.2.3 (A:21-106) Me  17.2      30  0.0022   13.7   2.0   13   50-62     73-85  (86)
  8 d2gy9d1 d.66.1.2 (D:2-205) Rib  16.2      21  0.0015   14.7   0.8   24   39-62    118-146 (204)
  9 d2ot2a1 b.40.14.1 (A:1-90) Hyd  15.1      29  0.0021   13.9   1.3   19   49-67     40-58  (90)
 10 d2z1ca1 b.40.14.1 (A:2-72) Hyd  15.0      24  0.0017   14.3   0.9   18   50-67     34-51  (71)

No 1  
>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]}
Probab=99.97  E-value=2.8e-32  Score=195.49  Aligned_cols=76  Identities=57%  Similarity=0.889  Sum_probs=74.8

Q ss_pred             CCEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEE
Q ss_conf             7347999999608986199999718878641308735103898688660406878999963775432039999764
Q gi|254780252|r    2 PKRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDSE   77 (79)
Q Consensus         2 ~~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~   77 (79)
                      |+|+|.|+|+|++|+|||+|+++|+++||+|+|+++++++|+||||+|+|++||.|.|.|||||||+|+|.|+|+.
T Consensus         1 pkr~l~G~Vvs~km~KTv~V~v~r~~~h~ky~K~~~r~kk~~vHD~~n~~k~GD~V~I~e~rPlSK~K~~~v~~Iv   76 (100)
T d2uubq1           1 PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLV   76 (100)
T ss_dssp             CCCEEEEEECCCCBTTEEEEEEEEEEEETTTEEEEEEEEEEEEECTTCCCCTTCEEEEEEEEEEETTEEEEEEEEE
T ss_pred             CCEEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEEE
T ss_conf             9818999999747997399999999954656789874079999998888999999999988678883579999998


No 2  
>d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]}
Probab=99.97  E-value=1.2e-30  Score=186.55  Aligned_cols=75  Identities=49%  Similarity=0.776  Sum_probs=72.9

Q ss_pred             EEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf             479999996089861999997188786413087351038986886604068789999637754320399997640
Q gi|254780252|r    4 RVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDSEG   78 (79)
Q Consensus         4 k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~~   78 (79)
                      ++|.|+|+|++|+||++|+++|+++||+|+|+++++++|+||||+|+|++||.|.|+|||||||+|+|.|+|+..
T Consensus         1 r~l~G~Vvs~km~KTv~V~v~r~~~h~ky~K~~~~~kky~aHDe~~~~~~GD~V~I~e~rPlSK~K~~~v~~iv~   75 (78)
T d2gy9q1           1 RTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVE   75 (78)
T ss_dssp             CEEEEEEEECCSSSEEEEEEEEEEECSSSCCEEEEEEEEEEECTTCCCCTTCEEEEEECSCSSSSCCEEEEEEEE
T ss_pred             CEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
T ss_conf             979999996689971999999999758667898853799999989777646499999867689928799999991


No 3  
>d1ripa_ b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stearothermophilus [TaxId: 1422]}
Probab=99.95  E-value=2.5e-31  Score=190.24  Aligned_cols=76  Identities=45%  Similarity=0.675  Sum_probs=73.7

Q ss_pred             CEEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf             3479999996089861999997188786413087351038986886604068789999637754320399997640
Q gi|254780252|r    3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVIDSEG   78 (79)
Q Consensus         3 ~k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~~~~~~~GD~V~i~e~rPiSK~K~~~vve~~~   78 (79)
                      ||+|.|+|+|++|+||++|+++|+++||+|+|+++++++|+||||+|+|++||.|.|.|||||||+|+|.|+|+..
T Consensus         2 rk~~~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~kr~kk~~aHd~~~~~~~GD~V~I~e~rPlSK~K~~~v~~Ii~   77 (81)
T d1ripa_           2 RKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVE   77 (81)
T ss_dssp             CSCBCCEESCCCSSSCSCCCBCCSCCCSCSSSCCCCSBCCCCCCCSTTCSSCEECCBCCCCCSSSCCCCCCCCCBS
T ss_pred             CCEEEEEEEECCCCCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEH
T ss_conf             8599999996179973999999999757467898860899999999888648899999866789976599999855


No 4  
>d1a62a2 b.40.4.5 (A:48-125) Rho termination factor, RNA-binding domain {Escherichia coli [TaxId: 562]}
Probab=30.20  E-value=16  Score=15.20  Aligned_cols=31  Identities=16%  Similarity=0.276  Sum_probs=27.2

Q ss_pred             CCCCCCCEEEEEECCCCCCCEEEEEEEEEEC
Q ss_conf             6040687899996377543203999976409
Q gi|254780252|r   49 NKYKVGDFVSIEESAPISKKKSWLVIDSEGV   79 (79)
Q Consensus        49 ~~~~~GD~V~i~e~rPiSK~K~~~vve~~~~   79 (79)
                      ..++.||.|.=.-..|...-|.|-++.++.|
T Consensus        42 fgLR~GD~V~G~vr~p~~~ek~~~L~~V~~V   72 (78)
T d1a62a2          42 FNLRTGDTISGKIRPPKEGERYFALLKVNEV   72 (78)
T ss_dssp             TTCCTTCEEEEEEECCCTTCCSEEEEEEEEE
T ss_pred             HCCCCCCEEEEEEECCCCCCCCEEEEEEEEE
T ss_conf             2998675899988889888875105899646


No 5  
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}
Probab=20.50  E-value=17  Score=15.11  Aligned_cols=17  Identities=18%  Similarity=0.294  Sum_probs=13.8

Q ss_pred             CCCCCCCCCCEEEEEEC
Q ss_conf             88660406878999963
Q gi|254780252|r   46 DENNKYKVGDFVSIEES   62 (79)
Q Consensus        46 D~~~~~~~GD~V~i~e~   62 (79)
                      =|+-.|++||.|.+.+-
T Consensus        87 iPSy~vk~GDvIsvkek  103 (159)
T d1c06a_          87 IPSYRVKPGQTIAVREK  103 (159)
T ss_dssp             CSSCCCCSSCEEEECGG
T ss_pred             ECCEEECCCCEEEECCC
T ss_conf             51215227848861200


No 6  
>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]}
Probab=17.55  E-value=30  Score=13.78  Aligned_cols=52  Identities=23%  Similarity=0.256  Sum_probs=36.6

Q ss_pred             EEEEEEEEEECCCCEEEEEEEEEEECCCCCEEECCCEEEEECCC------CCCCCCCCEEEEEECCCCCCCE
Q ss_conf             47999999608986199999718878641308735103898688------6604068789999637754320
Q gi|254780252|r    4 RVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDE------NNKYKVGDFVSIEESAPISKKK   69 (79)
Q Consensus         4 k~l~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~~~~kk~~vHD~------~~~~~~GD~V~i~e~rPiSK~K   69 (79)
                      ..+.|+|+....+..-.|+.+-             -....+|-+      .....+||.|.++ -+|..-+|
T Consensus         6 ie~~G~V~e~lg~~~f~V~l~n-------------g~~~~a~i~Gkmrk~ri~i~~GD~V~Ve-l~pyd~~k   63 (71)
T d1ah9a_           6 IEMQGTVLETLPNTMFRVELEN-------------GHVVTAHISGKMRKNYIRILTGDKVTVE-LTPYDLSK   63 (71)
T ss_dssp             EECCEEEEEECSSSEEEEEETT-------------SCEEEEEECSSGGGTTCCCCTTCEECCE-ECSSCTTE
T ss_pred             EEEEEEEEEECCCCEEEEEECC-------------CCEEEEECCCHHHEEEEEECCCCEEEEE-ECCCCCCC
T ss_conf             8999999998699889999679-------------9799998464343027996499999999-77667993


No 7  
>d1e32a1 b.52.2.3 (A:21-106) Membrane fusion ATPase p97 N-terminal domain , P97-Nn {Mouse (Mus musculus) [TaxId: 10090]}
Probab=17.20  E-value=30  Score=13.73  Aligned_cols=13  Identities=31%  Similarity=0.721  Sum_probs=7.5

Q ss_pred             CCCCCCEEEEEEC
Q ss_conf             0406878999963
Q gi|254780252|r   50 KYKVGDFVSIEES   62 (79)
Q Consensus        50 ~~~~GD~V~i~e~   62 (79)
                      -+.+||.|.|.+|
T Consensus        73 gv~iGD~V~V~p~   85 (86)
T d1e32a1          73 RVRLGDVISIQPC   85 (86)
T ss_dssp             TCCTTCEEEEEEC
T ss_pred             CCCCCCEEEEEEC
T ss_conf             9689999999969


No 8  
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}
Probab=16.19  E-value=21  Score=14.65  Aligned_cols=24  Identities=29%  Similarity=0.264  Sum_probs=16.5

Q ss_pred             CEEEEEC-----CCCCCCCCCCEEEEEEC
Q ss_conf             1038986-----88660406878999963
Q gi|254780252|r   39 SKRYAVH-----DENNKYKVGDFVSIEES   62 (79)
Q Consensus        39 ~kk~~vH-----D~~~~~~~GD~V~i~e~   62 (79)
                      +.+++|.     =|+-.|++||+|.+.|-
T Consensus       118 Hghi~VNgk~VnIPSy~vk~GDvIsvkek  146 (204)
T d2gy9d1         118 HKAIMVNGRVVNIASYQVSPNDVVSIREK  146 (204)
T ss_dssp             TTCEEESSSBCCCTTCBCCTTCBEEECTT
T ss_pred             HCCEECCCEEEEECCEEECCCCEEEECCC
T ss_conf             51164198899750076058977886221


No 9  
>d2ot2a1 b.40.14.1 (A:1-90) Hydrogenase expression/formation protein HypC {Escherichia coli [TaxId: 562]}
Probab=15.15  E-value=29  Score=13.87  Aligned_cols=19  Identities=21%  Similarity=0.357  Sum_probs=14.4

Q ss_pred             CCCCCCCEEEEEECCCCCC
Q ss_conf             6040687899996377543
Q gi|254780252|r   49 NKYKVGDFVSIEESAPISK   67 (79)
Q Consensus        49 ~~~~~GD~V~i~e~rPiSK   67 (79)
                      -+.++||+|.+.-.--+||
T Consensus        40 ~e~~vGDyVLVH~G~Ai~~   58 (90)
T d2ot2a1          40 GQPRVGQWVLVHVGFAMSV   58 (90)
T ss_dssp             SCBCTTCEEEEETTEEEEE
T ss_pred             CCCCCCCEEEEEHHHHHHH
T ss_conf             6468788999952177775


No 10 
>d2z1ca1 b.40.14.1 (A:2-72) Hydrogenase expression/formation protein HypC {Thermococcus kodakaraensis [TaxId: 311400]}
Probab=14.99  E-value=24  Score=14.31  Aligned_cols=18  Identities=33%  Similarity=0.477  Sum_probs=13.8

Q ss_pred             CCCCCCEEEEEECCCCCC
Q ss_conf             040687899996377543
Q gi|254780252|r   50 KYKVGDFVSIEESAPISK   67 (79)
Q Consensus        50 ~~~~GD~V~i~e~rPiSK   67 (79)
                      ++++||+|.+...--++|
T Consensus        34 e~~vGDyVLVh~G~Ai~~   51 (71)
T d2z1ca1          34 DTKPGDWVIVHTGFAIEK   51 (71)
T ss_dssp             TCCTTCEEEEETTEEEEE
T ss_pred             CCCCCCEEEEEECHHHHH
T ss_conf             999998999960324555


Done!