Query         gi|254781157|ref|YP_003065570.1| hypothetical protein CLIBASIA_05320 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 85
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 05:20:38 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781157.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01416 Rieske_proteo ubiqui  54.8     4.2 0.00011   21.3   0.4   10   65-74    154-163 (192)
  2 PRK13755 putative mercury tran  35.3      19 0.00048   17.9   1.3   18   51-68    124-141 (141)
  3 pfam09161 consensus             27.8      29 0.00075   16.9   1.2   27   31-57     32-58  (391)
  4 cd03470 Rieske_cytochrome_bc1   27.6      21 0.00052   17.7   0.4   13   63-75     87-99  (126)
  5 pfam10168 Nup88 Nuclear pore c  25.2      61  0.0016   15.2   2.5   32    3-34    504-537 (717)
  6 KOG0556 consensus               24.2      52  0.0013   15.5   2.0   23   63-85    495-517 (533)
  7 pfam09403 FadA Adhesion protei  20.7      65  0.0017   15.0   1.9   17    1-17      1-17  (126)
  8 PRK04607 consensus              17.7      38 0.00098   16.2   0.1   12   62-73    294-305 (330)
  9 PRK03877 consensus              16.7      41  0.0011   16.1   0.1   10   63-72    294-303 (328)
 10 pfam01249 Ribosomal_S21e Ribos  15.9      53  0.0013   15.5   0.5   16   15-30     18-33  (81)

No 1  
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit; InterPro: IPR006317   These sequences represent the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulphur subunit as found in ubiquinol-cytochrome c reductase. Not included in this group are the Rieske iron-sulphur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006118 electron transport.
Probab=54.82  E-value=4.2  Score=21.32  Aligned_cols=10  Identities=60%  Similarity=1.012  Sum_probs=7.7

Q ss_pred             CCCCCCCCHH
Q ss_conf             7334622456
Q gi|254781157|r   65 PDHGSKYDTR   74 (85)
Q Consensus        65 pdhgskydtr   74 (85)
                      |=|||+||+-
T Consensus       154 PCHGS~yD~a  163 (192)
T TIGR01416       154 PCHGSHYDLA  163 (192)
T ss_pred             CCCCCCCCCC
T ss_conf             6888960555


No 2  
>PRK13755 putative mercury transport protein MerC; Provisional
Probab=35.34  E-value=19  Score=17.88  Aligned_cols=18  Identities=28%  Similarity=0.604  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q ss_conf             555647874224897334
Q gi|254781157|r   51 VANKRCPNATKQTPPDHG   68 (85)
Q Consensus        51 vankrcpnatkqtppdhg   68 (85)
                      -++|||....-.+||.+|
T Consensus       124 Pa~~rC~~~~c~~p~~~~  141 (141)
T PRK13755        124 PAHRRCGPDSCELPAKRG  141 (141)
T ss_pred             CCCCCCCCCCCCCCCCCC
T ss_conf             632467988789986688


No 3  
>pfam09161 consensus
Probab=27.77  E-value=29  Score=16.85  Aligned_cols=27  Identities=33%  Similarity=0.468  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             776665679999997301755556478
Q gi|254781157|r   31 EQKRKETTVGFISRLVNKRPVANKRCP   57 (85)
Q Consensus        31 eqkrkettvgfisrlvnkrpvankrcp   57 (85)
                      ..|--.+++.||..||+.||+...||-
T Consensus        32 npkWL~~~~~firdLvssrPt~~gR~a   58 (391)
T pfam09161        32 NPKWLPCTFSFIRDLVSSRPTPAGRAA   58 (391)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             997015799999998734988467789


No 4  
>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=27.57  E-value=21  Score=17.68  Aligned_cols=13  Identities=46%  Similarity=0.682  Sum_probs=9.4

Q ss_pred             CCCCCCCCCCHHH
Q ss_conf             8973346224566
Q gi|254781157|r   63 TPPDHGSKYDTRE   75 (85)
Q Consensus        63 tppdhgskydtre   75 (85)
                      --|=|||+||+-.
T Consensus        87 ~CPCHGS~yD~aG   99 (126)
T cd03470          87 FCPCHGSHYDASG   99 (126)
T ss_pred             ECCCCCCCCCCCC
T ss_conf             0357687417888


No 5  
>pfam10168 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.
Probab=25.19  E-value=61  Score=15.18  Aligned_cols=32  Identities=31%  Similarity=0.385  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHCCCCCE--ECCCCCHHHHHHH
Q ss_conf             6799999999743258722--1354202457766
Q gi|254781157|r    3 KFVVRIMFLLSAISSNPIL--AANEHSSVSEQKR   34 (85)
Q Consensus         3 kfvvrimfllsaissnpil--aanehssvseqkr   34 (85)
                      -|...|--+|---++||||  .++..+|.+.|..
T Consensus       504 ~F~~~Ik~lL~R~~sqPIL~~~~dk~~sps~~E~  537 (717)
T pfam10168       504 SFEDHIRSILQRSVNNPILLRSADKDSSPPPEEC  537 (717)
T ss_pred             CHHHHHHHHHHCCCCCCHHHHCCCCCCCCCHHHH
T ss_conf             7899999997267877421203677779998999


No 6  
>KOG0556 consensus
Probab=24.23  E-value=52  Score=15.55  Aligned_cols=23  Identities=43%  Similarity=0.762  Sum_probs=17.1

Q ss_pred             CCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             89733462245668973605689
Q gi|254781157|r   63 TPPDHGSKYDTREVLMLFGGLNN   85 (85)
Q Consensus        63 tppdhgskydtrevlmlfgglnn   85 (85)
                      .||.-|.-..-..|.|||-||+|
T Consensus       495 ~PPHaGgGIGLERvvmlyl~L~n  517 (533)
T KOG0556         495 APPHAGGGIGLERVVMLYLGLNN  517 (533)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCC
T ss_conf             99877875159999999816775


No 7  
>pfam09403 FadA Adhesion protein FadA. FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices.
Probab=20.72  E-value=65  Score=15.02  Aligned_cols=17  Identities=35%  Similarity=0.544  Sum_probs=15.1

Q ss_pred             CHHHHHHHHHHHHHHCC
Q ss_conf             92679999999974325
Q gi|254781157|r    1 MSKFVVRIMFLLSAISS   17 (85)
Q Consensus         1 mskfvvrimfllsaiss   17 (85)
                      |-||.+-+|.++|++|-
T Consensus         1 MkK~ll~~~llls~~s~   17 (126)
T pfam09403         1 MKKILLCSMLILSSLSY   17 (126)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             91699999999999998


No 8  
>PRK04607 consensus
Probab=17.70  E-value=38  Score=16.25  Aligned_cols=12  Identities=33%  Similarity=0.623  Sum_probs=7.3

Q ss_pred             CCCCCCCCCCCH
Q ss_conf             489733462245
Q gi|254781157|r   62 QTPPDHGSKYDT   73 (85)
Q Consensus        62 qtppdhgskydt   73 (85)
                      .|-||||.-||-
T Consensus       294 RtS~dHGTa~dI  305 (330)
T PRK04607        294 RTSVDHGTALEL  305 (330)
T ss_pred             EECCCCCCHHHH
T ss_conf             778998704666


No 9  
>PRK03877 consensus
Probab=16.75  E-value=41  Score=16.06  Aligned_cols=10  Identities=50%  Similarity=0.976  Sum_probs=5.6

Q ss_pred             CCCCCCCCCC
Q ss_conf             8973346224
Q gi|254781157|r   63 TPPDHGSKYD   72 (85)
Q Consensus        63 tppdhgskyd   72 (85)
                      |-||||.-||
T Consensus       294 tSpdHGta~d  303 (328)
T PRK03877        294 TSVDHGTAFD  303 (328)
T ss_pred             ECCCCCCHHH
T ss_conf             7899870566


No 10 
>pfam01249 Ribosomal_S21e Ribosomal protein S21e.
Probab=15.92  E-value=53  Score=15.52  Aligned_cols=16  Identities=31%  Similarity=0.596  Sum_probs=13.6

Q ss_pred             HCCCCCEECCCCCHHH
Q ss_conf             3258722135420245
Q gi|254781157|r   15 ISSNPILAANEHSSVS   30 (85)
Q Consensus        15 issnpilaanehssvs   30 (85)
                      -.||.|++|.+|.||.
T Consensus        18 SatNriI~AKDHaSvQ   33 (81)
T pfam01249        18 SATNRLIGAKDHASVQ   33 (81)
T ss_pred             CCCCCCEECCCCCEEE
T ss_conf             2227624047732378


Done!