Query         gi|254781226|ref|YP_003065639.1| hypothetical protein CLIBASIA_05665 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 129
No_of_seqs    67 out of 69
Neff          3.8 
Searched_HMMs 13730
Date          Wed Jun  1 12:00:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781226.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 d2cuja1 a.4.1.18 (A:8-108) Tra  11.7      34  0.0025   11.8   0.9   16    2-17     30-45  (101)
  2 d1p65a_ d.254.1.1 (A:) Arteriv   9.8      40  0.0029   11.4   2.5   21    3-23      3-23  (57)
  3 d1ayia_ a.28.2.1 (A:) ImmE7 pr   6.9      54   0.004   10.6   2.4   15   42-56     65-79  (86)
  4 d1gxha_ a.28.2.1 (A:) ImmE8 (I   6.7      56  0.0041   10.6   1.9   15   42-56     63-77  (85)
  5 d2vlqa1 a.28.2.1 (A:4-84) ImmE   6.6      56  0.0041   10.6   2.4   15   42-56     61-75  (81)
  6 d1sf9a_ b.34.15.1 (A:) Hypothe   4.1      90  0.0066    9.4   1.4   12  109-120    27-38  (118)
  7 d1a62a1 a.140.3.1 (A:1-47) Rho   3.7   1E+02  0.0074    9.1   1.3   12  114-125     4-15  (47)
  8 d1di2a_ d.50.1.1 (A:) Double-s   3.7   1E+02  0.0074    9.1   2.4   19  100-118    51-69  (69)
  9 d1t4oa_ d.50.1.1 (A:) RNase II   3.3 1.2E+02  0.0086    8.7   2.2   21   98-118    55-75  (81)
 10 d1ekza_ d.50.1.1 (A:) Staufen,   3.0 1.3E+02  0.0094    8.5  -0.0   18  100-117    57-74  (76)

No 1  
>d2cuja1 a.4.1.18 (A:8-108) Transcriptional adaptor 2-like, TADA2L {Mouse (Mus musculus) [TaxId: 10090]}
Probab=11.68  E-value=34  Score=11.78  Aligned_cols=16  Identities=31%  Similarity=0.594  Sum_probs=13.1

Q ss_pred             CHHHHCHHHHHHHHHH
Q ss_conf             6233023301442399
Q gi|254781226|r    2 GRKVLTPEERMLCRRE   17 (129)
Q Consensus         2 ~r~~~~~~~r~~C~kE   17 (129)
                      |...|++.|..+|..-
T Consensus        30 ~~~lLs~~E~~LC~~l   45 (101)
T d2cuja1          30 GTEKLNEKEKELCQVV   45 (101)
T ss_dssp             TTTTSCHHHHHHHHHT
T ss_pred             CHHHCCHHHHHHHHHH
T ss_conf             8002699999999991


No 2  
>d1p65a_ d.254.1.1 (A:) Arterivirus nucleocapsid protein {PRRSV (Porcine reproductive and respiratory syndrome virus) [TaxId: 28344]}
Probab=9.77  E-value=40  Score=11.39  Aligned_cols=21  Identities=33%  Similarity=0.634  Sum_probs=16.2

Q ss_pred             HHHHCHHHHHHHHHHHHHHHH
Q ss_conf             233023301442399999999
Q gi|254781226|r    3 RKVLTPEERMLCRREYKRRYY   23 (129)
Q Consensus         3 r~~~~~~~r~~C~kE~~KkY~   23 (129)
                      |-.+++-||.+|..--+-++-
T Consensus         3 RHh~T~~er~lcl~siqtafN   23 (57)
T d1p65a_           3 RHHFTPSERQLCLSSIQTAFN   23 (57)
T ss_dssp             GGGCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHH
T ss_conf             443778899999999999985


No 3  
>d1ayia_ a.28.2.1 (A:) ImmE7 protein (Im7) {Escherichia coli [TaxId: 562]}
Probab=6.86  E-value=54  Score=10.65  Aligned_cols=15  Identities=13%  Similarity=0.235  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999999998738
Q gi|254781226|r   42 KDKIRESYHQYYLKN   56 (129)
Q Consensus        42 KEKIke~~Keyy~kN   56 (129)
                      ++-|.+-.++||..|
T Consensus        65 PegI~k~IKeWRa~n   79 (86)
T d1ayia_          65 PEGIVKEIKEWRAAN   79 (86)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             899999999999975


No 4  
>d1gxha_ a.28.2.1 (A:) ImmE8 (Im8) {Escherichia coli [TaxId: 562]}
Probab=6.66  E-value=56  Score=10.58  Aligned_cols=15  Identities=7%  Similarity=0.222  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999999998738
Q gi|254781226|r   42 KDKIRESYHQYYLKN   56 (129)
Q Consensus        42 KEKIke~~Keyy~kN   56 (129)
                      ++-|.+-.++||..|
T Consensus        63 PegIv~~IKeWRa~n   77 (85)
T d1gxha_          63 PEAVIKEIKEWRAAN   77 (85)
T ss_dssp             THHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             899999999999975


No 5  
>d2vlqa1 a.28.2.1 (A:4-84) ImmE9 protein (Im9) {Escherichia coli [TaxId: 562]}
Probab=6.65  E-value=56  Score=10.58  Aligned_cols=15  Identities=20%  Similarity=0.222  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999999998738
Q gi|254781226|r   42 KDKIRESYHQYYLKN   56 (129)
Q Consensus        42 KEKIke~~Keyy~kN   56 (129)
                      ++-|.+-.++||..|
T Consensus        61 PegIv~~IK~WRa~n   75 (81)
T d2vlqa1          61 PSGIVNTVKQWRAAN   75 (81)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             899999999999974


No 6  
>d1sf9a_ b.34.15.1 (A:) Hypothetical protein YfhH {Bacillus subtilis [TaxId: 1423]}
Probab=4.09  E-value=90  Score=9.39  Aligned_cols=12  Identities=50%  Similarity=0.559  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             998998754223
Q gi|254781226|r  109 LEREIARLKAKP  120 (129)
Q Consensus       109 ~~~e~~~~~~~~  120 (129)
                      |..||+.|+.|.
T Consensus        27 L~~EIa~L~EKa   38 (118)
T d1sf9a_          27 LNTEIALLSEKA   38 (118)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 7  
>d1a62a1 a.140.3.1 (A:1-47) Rho termination factor, N-terminal domain {Escherichia coli [TaxId: 562]}
Probab=3.74  E-value=1e+02  Score=9.11  Aligned_cols=12  Identities=50%  Similarity=0.847  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             875422399974
Q gi|254781226|r  114 ARLKAKPIEELI  125 (129)
Q Consensus       114 ~~~~~~~~~~~~  125 (129)
                      .-|+.+++++|.
T Consensus         4 seLk~k~~~EL~   15 (47)
T d1a62a1           4 TELKNTPVSELI   15 (47)
T ss_dssp             HHHHTSCHHHHH
T ss_pred             HHHHCCCHHHHH
T ss_conf             988159999999


No 8  
>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]}
Probab=3.71  E-value=1e+02  Score=9.09  Aligned_cols=19  Identities=21%  Similarity=0.233  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             5679999999989987542
Q gi|254781226|r  100 GMTKAEIEALEREIARLKA  118 (129)
Q Consensus       100 ~~~~~e~~~~~~e~~~~~~  118 (129)
                      ++..+|++|+..-+..|+.
T Consensus        51 sKK~Aeq~AA~~aL~~L~s   69 (69)
T d1di2a_          51 SKQVAKRVAAEKLLTKFKT   69 (69)
T ss_dssp             SHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHCC
T ss_conf             2999999999999998459


No 9  
>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=3.28  E-value=1.2e+02  Score=8.72  Aligned_cols=21  Identities=24%  Similarity=0.177  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             555679999999989987542
Q gi|254781226|r   98 PMGMTKAEIEALEREIARLKA  118 (129)
Q Consensus        98 ~~~~~~~e~~~~~~e~~~~~~  118 (129)
                      --|...+|++|+..-+..+++
T Consensus        55 g~SKK~AEq~AA~~aL~~~~~   75 (81)
T d1t4oa_          55 GRNIKIAGIRAAENALRDKKM   75 (81)
T ss_dssp             ESSHHHHHHHHHHHHHHCHHH
T ss_pred             CCHHHHHHHHHHHHHHHHCCH
T ss_conf             330108999999999983228


No 10 
>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}
Probab=3.01  E-value=1.3e+02  Score=8.51  Aligned_cols=18  Identities=22%  Similarity=0.344  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             567999999998998754
Q gi|254781226|r  100 GMTKAEIEALEREIARLK  117 (129)
Q Consensus       100 ~~~~~e~~~~~~e~~~~~  117 (129)
                      |.+.+|++|+..-+..|+
T Consensus        57 SKK~Aeq~AA~~al~~L~   74 (76)
T d1ekza_          57 GKKVSKKRAAEKMLVELQ   74 (76)
T ss_dssp             STTSSSHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             699999999999999987


Done!