Query         gi|254780894|ref|YP_003065307.1| hypothetical protein CLIBASIA_03955 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs    46 out of 48
Neff          3.9 
Searched_HMMs 13730
Date          Wed Jun  1 10:30:12 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780894.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 d1ykha1 a.252.1.2 (A:111-205)   61.6     4.9 0.00035   18.1   5.3   34    3-36     60-93  (95)
  2 d1vf6a_ a.194.1.1 (A:) Associa  13.1      36  0.0026   12.7   2.4   29   59-87     27-55  (58)
  3 d1r9wa_ d.89.1.2 (A:) Replicat  10.8      40  0.0029   12.3   1.0   10    2-11     83-92  (145)
  4 d1ku2a2 a.177.1.1 (A:93-272) S   8.8      50  0.0037   11.7   2.4   17   53-69    150-167 (180)
  5 d1w98b1 a.74.1.1 (B:228-357) G   7.8      55   0.004   11.5   2.0   32   30-70     31-64  (130)
  6 d2o4aa1 a.35.1.7 (A:370-452) D   7.8      55   0.004   11.5   0.9   11    3-13     53-63  (83)
  7 d1quua1 a.7.1.1 (A:1-124) alph   6.4      65  0.0047   11.0   8.8   37   63-99     88-124 (124)
  8 d1k4ta1 a.2.8.1 (A:641-712) Eu   5.8      70  0.0051   10.8   4.9   21   73-93      6-26  (72)
  9 d1hywa_ d.186.1.1 (A:) Head-to   5.7      71  0.0052   10.8   1.7   16   77-92     39-54  (58)
 10 d1wh8a_ a.35.1.7 (A:) Homeobox   5.1      77  0.0056   10.5   0.9   12    2-13     78-89  (111)

No 1  
>d1ykha1 a.252.1.2 (A:111-205) RNA polymerase II mediator complex protein MED7 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=61.59  E-value=4.9  Score=18.10  Aligned_cols=34  Identities=15%  Similarity=0.179  Sum_probs=28.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6788899999889999999999999999999999
Q gi|254780894|r    3 LQEQRTRLKEFRLNDERRQLQQLRATILEFRRIV   36 (103)
Q Consensus         3 sretLIRLk~fqVdEkRR~laql~~m~~ef~~~~   36 (103)
                      +|+|||-+=.-|+++||-.+.+++...+++..+.
T Consensus        60 AResLi~lme~Ql~~kr~~~~~i~~~~~~~~~~L   93 (95)
T d1ykha1          60 SRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKL   93 (95)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7999999999999999999999999999999876


No 2  
>d1vf6a_ a.194.1.1 (A:) Associated tight junction protein Pals-1 {Human (Homo sapiens) [TaxId: 9606]}
Probab=13.09  E-value=36  Score=12.66  Aligned_cols=29  Identities=24%  Similarity=0.180  Sum_probs=18.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             31899999999999999999999999999
Q gi|254780894|r   59 AYPILAKSARQRIDNLLLSIRDLLLRQES   87 (103)
Q Consensus        59 aY~tfAraa~~RRdnL~~Si~~l~~Q~e~   87 (103)
                      -+++.---.-..-=+|+.||..|+.|+..
T Consensus        27 lk~~LqSPLF~qiL~lQ~SiqqLk~Qvn~   55 (58)
T d1vf6a_          27 FYETLKSPLFNQILTLQQSIKQLKGQLNH   55 (58)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998687899999999999999999977


No 3  
>d1r9wa_ d.89.1.2 (A:) Replication initiation protein E1 {Human papillomavirus type 18 [TaxId: 333761]}
Probab=10.78  E-value=40  Score=12.35  Aligned_cols=10  Identities=0%  Similarity=-0.193  Sum_probs=6.8

Q ss_pred             CCHHHHHHHH
Q ss_conf             8678889999
Q gi|254780894|r    2 RLQEQRTRLK   11 (103)
Q Consensus         2 KsretLIRLk   11 (103)
                      |||+|+++|=
T Consensus        83 KsReTV~kLl   92 (145)
T d1r9wa_          83 KSRLTVAKGL   92 (145)
T ss_dssp             ECHHHHHHHH
T ss_pred             CCHHHHHHHH
T ss_conf             7889999999


No 4  
>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}
Probab=8.76  E-value=50  Score=11.72  Aligned_cols=17  Identities=12%  Similarity=0.256  Sum_probs=8.8

Q ss_pred             CCCC-CCCHHHHHHHHHH
Q ss_conf             7700-1431899999999
Q gi|254780894|r   53 YDKD-HFAYPILAKSARQ   69 (103)
Q Consensus        53 ~d~~-hFaY~tfAraa~~   69 (103)
                      .||. +|-.+|||.-|+.
T Consensus       150 fd~~~g~~f~tya~~~i~  167 (180)
T d1ku2a2         150 FEYKRRFKFSTYATWWIR  167 (180)
T ss_dssp             CCGGGCSCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHH
T ss_conf             399889977999899999


No 5  
>d1w98b1 a.74.1.1 (B:228-357) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]}
Probab=7.80  E-value=55  Score=11.46  Aligned_cols=32  Identities=38%  Similarity=0.419  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCC--CCCHHHHHHHHHHH
Q ss_conf             999999999999999999997157700--14318999999999
Q gi|254780894|r   30 LEFRRIVADLEKQIAIEERQVGIYDKD--HFAYPILAKSARQR   70 (103)
Q Consensus        30 ~ef~~~~~~LE~qI~~Ee~~agi~d~~--hFaY~tfAraa~~R   70 (103)
                      .+|.++++-||-=+         -|++  -|.|+..|.||.--
T Consensus        31 ~~fiq~aqLLDLC~---------LDi~sl~fsYsvLAAaAl~h   64 (130)
T d1w98b1          31 QIFIQIAELLDLCV---------LDVDCLEFPYGILAASALYH   64 (130)
T ss_dssp             HHHHHHHHHHHHHH---------HSGGGGGSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH---------HHHHHHCCCHHHHHHHHHHH
T ss_conf             99999999999999---------60235319659999999997


No 6  
>d2o4aa1 a.35.1.7 (A:370-452) DNA-binding protein SATB1 {Human (Homo sapiens) [TaxId: 9606]}
Probab=7.79  E-value=55  Score=11.46  Aligned_cols=11  Identities=18%  Similarity=0.317  Sum_probs=5.8

Q ss_pred             CHHHHHHHHHH
Q ss_conf             67888999998
Q gi|254780894|r    3 LQEQRTRLKEF   13 (103)
Q Consensus         3 sretLIRLk~f   13 (103)
                      ++++++|+..|
T Consensus        53 gre~f~Rm~~w   63 (83)
T d2o4aa1          53 LLVNLRAMQNF   63 (83)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
T ss_conf             77999999999


No 7  
>d1quua1 a.7.1.1 (A:1-124) alpha-actinin {Human (Homo sapiens) [TaxId: 9606]}
Probab=6.42  E-value=65  Score=11.03  Aligned_cols=37  Identities=14%  Similarity=-0.041  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999997
Q gi|254780894|r   63 LAKSARQRIDNLLLSIRDLLLRQESLESHLESESNSD   99 (103)
Q Consensus        63 fAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~~~   99 (103)
                      .+....++.+.|...-..|......=+..|..+.+++
T Consensus        88 ~~~~i~~~~~~l~~rW~~L~~~~~~R~~~L~~a~~ll  124 (124)
T d1quua1          88 DAVNVNDRCQKICDQWDRLGTLTQKRREALERMEKLL  124 (124)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             5899999999999999999999999999999987239


No 8  
>d1k4ta1 a.2.8.1 (A:641-712) Eukaryotic DNA topoisomerase I, dispensable insert domain {Human (Homo sapiens) [TaxId: 9606]}
Probab=5.83  E-value=70  Score=10.82  Aligned_cols=21  Identities=19%  Similarity=0.104  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999
Q gi|254780894|r   73 NLLLSIRDLLLRQESLESHLE   93 (103)
Q Consensus        73 nL~~Si~~l~~Q~e~a~~~L~   93 (103)
                      ||+.-|..-..|+.+|..+|-
T Consensus         6 nLq~KI~~Kk~qi~~a~~e~K   26 (72)
T d1k4ta1           6 NLQTKIDAKKEQLADARRDLK   26 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999


No 9  
>d1hywa_ d.186.1.1 (A:) Head-to-tail joining protein W, gpW {Bacteriophage lambda [TaxId: 10710]}
Probab=5.71  E-value=71  Score=10.77  Aligned_cols=16  Identities=31%  Similarity=0.264  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780894|r   77 SIRDLLLRQESLESHL   92 (103)
Q Consensus        77 Si~~l~~Q~e~a~~~L   92 (103)
                      ||.+|+.-|+.++..|
T Consensus        39 si~eL~~yI~~lE~~l   54 (58)
T d1hywa_          39 SVSDLKKYIAELEVQT   54 (58)
T ss_dssp             THHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             7999999999999875


No 10 
>d1wh8a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}
Probab=5.10  E-value=77  Score=10.53  Aligned_cols=12  Identities=17%  Similarity=0.274  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             867888999998
Q gi|254780894|r    2 RLQEQRTRLKEF   13 (103)
Q Consensus         2 KsretLIRLk~f   13 (103)
                      ++|++.||+..|
T Consensus        78 ~gR~~y~RM~~w   89 (111)
T d1wh8a_          78 KGREPFVRMQLW   89 (111)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
T ss_conf             888999999998


Done!