Query         gi|254780324|ref|YP_003064737.1| hypothetical protein CLIBASIA_01045 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 61
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 14:28:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780324.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG3667 PcoB Uncharacterized p  60.1     3.3 8.4E-05   22.6   0.6   33    1-33    146-178 (321)
  2 pfam08756 YfkB YfkB-like domai  55.8     1.2 3.2E-05   24.9  -2.1   19   20-38     27-45  (153)
  3 KOG3894 consensus               39.0      21 0.00054   18.1   2.0   24   19-42    286-311 (316)
  4 pfam10066 DUF2304 Uncharacteri  25.2      26 0.00066   17.6   0.6   32   18-51     27-58  (115)
  5 cd00929 Cyt_c_Oxidase_VIIc Cyt  23.9      43  0.0011   16.3   1.5   35   12-46      4-38  (46)
  6 TIGR02614 ftsW cell division p  23.1      73  0.0019   15.1   2.6   27   28-57     12-40  (370)
  7 KOG3393 consensus               22.6      75  0.0019   15.0   2.6   36   19-54     86-123 (157)
  8 pfam09499 RE_ApaLI ApaLI-like   22.1      38 0.00098   16.6   0.9   11   16-26    113-123 (191)
  9 TIGR01545 YfhB_g-proteo HAD su  21.7      24 0.00061   17.7  -0.2   26   21-46    109-139 (210)
 10 pfam05255 UPF0220 Uncharacteri  20.6      71  0.0018   15.1   2.1   51    1-51     73-126 (164)

No 1  
>COG3667 PcoB Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]
Probab=60.09  E-value=3.3  Score=22.56  Aligned_cols=33  Identities=36%  Similarity=0.565  Sum_probs=28.9

Q ss_pred             CCCCCCCEEEEECCCEEEEEECCCCHHHHHHHH
Q ss_conf             985210013430474888884264016887999
Q gi|254780324|r    1 MGNSVNSTILKAEGSIVNIKWRDANVWLLFGVV   33 (61)
Q Consensus         1 mgnsvnstilkaegsivnikwrdanvwllfgvv   33 (61)
                      .|.+.+.-.||+||.++.=+|.+|.|-+|||--
T Consensus       146 iGtdi~kl~lkaeGe~~~Gr~e~a~ve~L~gh~  178 (321)
T COG3667         146 IGTDISKLVLKAEGERVDGRWEKAEVEGLKGHA  178 (321)
T ss_pred             ECCCHHHEEEECCCCEECCCHHHHHHHHHHCCC
T ss_conf             245653503201572407621566655551575


No 2  
>pfam08756 YfkB YfkB-like domain. This protein is adjacent to YfkA in B. subtilis. In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=55.83  E-value=1.2  Score=24.93  Aligned_cols=19  Identities=47%  Similarity=0.938  Sum_probs=14.9

Q ss_pred             EECCCCHHHHHHHHHHHHH
Q ss_conf             8426401688799999863
Q gi|254780324|r   20 KWRDANVWLLFGVVMVYFS   38 (61)
Q Consensus        20 kwrdanvwllfgvvmvyfs   38 (61)
                      .-||.|+|.|||..-.|-.
T Consensus        27 d~Rd~~~WMLFGTLPfypC   45 (153)
T pfam08756        27 DIRDENVWMLFGTLPFYPC   45 (153)
T ss_pred             HCCCCCEEEEECCCCCCCC
T ss_conf             2669885788545553447


No 3  
>KOG3894 consensus
Probab=39.00  E-value=21  Score=18.07  Aligned_cols=24  Identities=33%  Similarity=0.567  Sum_probs=17.9

Q ss_pred             EEECCC--CHHHHHHHHHHHHHHHHH
Q ss_conf             884264--016887999998632035
Q gi|254780324|r   19 IKWRDA--NVWLLFGVVMVYFSISFS   42 (61)
Q Consensus        19 ikwrda--nvwllfgvvmvyfsisfs   42 (61)
                      ++|+.+  .+|++|+.++.-|++-|.
T Consensus       286 a~~~~~~~r~~~lf~llvlsf~lLFl  311 (316)
T KOG3894         286 AKRNNGGLRVFLLFFLLVLSFSLLFL  311 (316)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             99723553168999999999999988


No 4  
>pfam10066 DUF2304 Uncharacterized conserved protein (DUF2304). Members of this family of hypothetical archaeal proteins have no known function.
Probab=25.16  E-value=26  Score=17.56  Aligned_cols=32  Identities=22%  Similarity=0.487  Sum_probs=22.4

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8884264016887999998632035579998742
Q gi|254780324|r   18 NIKWRDANVWLLFGVVMVYFSISFSSRIVDYVDQ   51 (61)
Q Consensus        18 nikwrdanvwllfgvvmvyfsisfssrivdyvdq   51 (61)
                      .++++++-.|+.|+++++-+++--  .+.+++..
T Consensus        27 kl~~~~~l~Wl~~~~~~li~~ifP--~i~~~iA~   58 (115)
T pfam10066        27 RLSISDLLFWLFFWIVVLLFALFP--KISGRIAN   58 (115)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHCC--CHHHHHHH
T ss_conf             077999999999999999999875--18899999


No 5  
>cd00929 Cyt_c_Oxidase_VIIc Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIc subunit is found only in eukaryotes and its specific function remains unclear. Peroxide inactivation of bovine CcO coincides with the direct oxidation of tryptophan (W19) within subunit VIIc, along with other structural changes in other subunits.
Probab=23.90  E-value=43  Score=16.34  Aligned_cols=35  Identities=26%  Similarity=0.535  Sum_probs=28.1

Q ss_pred             ECCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04748888842640168879999986320355799
Q gi|254780324|r   12 AEGSIVNIKWRDANVWLLFGVVMVYFSISFSSRIV   46 (61)
Q Consensus        12 aegsivnikwrdanvwllfgvvmvyfsisfssriv   46 (61)
                      .||.--|+-..-.|-|.+.....+||.+.|+.--+
T Consensus         4 ~~gPg~NLPF~v~Nk~~l~a~~~~ffg~Gf~~PF~   38 (46)
T cd00929           4 GEGPGSNLPFSVTNKWRLTALFHLFFGSGFSAPFI   38 (46)
T ss_pred             CCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCHH
T ss_conf             88898877746545138799999999987424267


No 6  
>TIGR02614 ftsW cell division protein FtsW; InterPro: IPR013437    FtsW is an integral membrane protein with ten transmembrane segments . In general, it is one of two paralogs involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division. The FtsW designation is not used in endospore-forming bacteria (e.g. Bacillus subtilis), where these proteins are designated SpoVE, and three or more RodA/FtsW/SpoVE family paralogs are present. SpoVE acts in spore cortex formation and is dispensable for growth. Biological roles for FtsW in cell division include recruitment of penicillin-binding protein 3 to the division site.; GO: 0009252 peptidoglycan biosynthetic process, 0051301 cell division, 0016021 integral to membrane.
Probab=23.08  E-value=73  Score=15.05  Aligned_cols=27  Identities=33%  Similarity=0.481  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH
Q ss_conf             8879999986320355799987423--34667
Q gi|254780324|r   28 LLFGVVMVYFSISFSSRIVDYVDQK--HDLYH   57 (61)
Q Consensus        28 llfgvvmvyfsisfssrivdyvdqk--hdlyh   57 (61)
                      +.+|.||||   |-|+-+..+-...  ||-+|
T Consensus        12 ~~~GlvMV~---SaS~~~a~~~~~~d~~~~~~   40 (370)
T TIGR02614        12 LGIGLVMVY---SASAAVAERLGLSDEGDPFY   40 (370)
T ss_pred             HHHHHHHHH---HHHHHHHHHHCCCCCCCHHH
T ss_conf             999999999---76699998606888763689


No 7  
>KOG3393 consensus
Probab=22.59  E-value=75  Score=15.00  Aligned_cols=36  Identities=31%  Similarity=0.475  Sum_probs=26.7

Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf             884264016887999998632035--579998742334
Q gi|254780324|r   19 IKWRDANVWLLFGVVMVYFSISFS--SRIVDYVDQKHD   54 (61)
Q Consensus        19 ikwrdanvwllfgvvmvyfsisfs--srivdyvdqkhd   54 (61)
                      .--|.|..||++|-.|..=|+.-|  --|-+||-+.-|
T Consensus        86 sga~~AR~wLfiGF~l~fgsLias~wVli~~yv~~~~~  123 (157)
T KOG3393          86 SGARGARIWLFIGFALLFGSLIASIWVLIGKYVVKEYD  123 (157)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             22310256889999999701556678874898852778


No 8  
>pfam09499 RE_ApaLI ApaLI-like restriction endonuclease. This family includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognizes and cleaves the sequence GTGCAC.
Probab=22.11  E-value=38  Score=16.62  Aligned_cols=11  Identities=55%  Similarity=0.990  Sum_probs=8.1

Q ss_pred             EEEEEECCCCH
Q ss_conf             88888426401
Q gi|254780324|r   16 IVNIKWRDANV   26 (61)
Q Consensus        16 ivnikwrdanv   26 (61)
                      -..||||||..
T Consensus       113 AyEiKwRdAtT  123 (191)
T pfam09499       113 AYEIKWRDATT  123 (191)
T ss_pred             EEEEEEECCCC
T ss_conf             07988512677


No 9  
>TIGR01545 YfhB_g-proteo HAD superfamily (subfamily IF) hydrolase, YfhB; InterPro: IPR006435   This group describes a clade of sequences limited to the gamma proteobacteria. This group is a member of the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases and all of the conserved catalytic motifs are present . Although structurally similar to subfamily IA in that the variable domain is predicted to consist of five consecutive alpha helices (by PSI-PRED), it is sufficiently divergent to warrant being regarded as a separate sub-family (IF)..
Probab=21.74  E-value=24  Score=17.74  Aligned_cols=26  Identities=46%  Similarity=0.796  Sum_probs=20.2

Q ss_pred             ECCCCHHHHHH-----HHHHHHHHHHHHHHH
Q ss_conf             42640168879-----999986320355799
Q gi|254780324|r   21 WRDANVWLLFG-----VVMVYFSISFSSRIV   46 (61)
Q Consensus        21 wrdanvwllfg-----vvmvyfsisfssriv   46 (61)
                      -.||++||.-|     |-.|||.-.|-.|+-
T Consensus       109 ssda~~WlitGsPq~lve~vy~d~~~~~r~~  139 (210)
T TIGR01545       109 SSDAEVWLITGSPQRLVEAVYFDSNFLHRLR  139 (210)
T ss_pred             HCCCCEEEEECCCHHHHHHHHHCCHHHHHHH
T ss_conf             0577368974686788887750421577888


No 10 
>pfam05255 UPF0220 Uncharacterized protein family (UPF0220). This family of proteins is functionally uncharacterized.
Probab=20.61  E-value=71  Score=15.11  Aligned_cols=51  Identities=25%  Similarity=0.404  Sum_probs=30.4

Q ss_pred             CCCCCCCEEEEECCCEE-EEEECCCCHHHHHHHHHHHHHHHHHHH--HHHHHHH
Q ss_conf             98521001343047488-888426401688799999863203557--9998742
Q gi|254780324|r    1 MGNSVNSTILKAEGSIV-NIKWRDANVWLLFGVVMVYFSISFSSR--IVDYVDQ   51 (61)
Q Consensus         1 mgnsvnstilkaegsiv-nikwrdanvwllfgvvmvyfsisfssr--ivdyvdq   51 (61)
                      |=|+|+..-|..+..-- +.--+.|.+||..|-++..=++.-|--  +.+|+..
T Consensus        73 miN~V~k~~l~~d~~~~g~~~~~~ARvwLFiGF~l~fgglags~wvli~~yv~~  126 (164)
T pfam05255        73 MVNSIEKSRLRGDSLSEGSGGAWGARVWLFLGFALLFGSLAASIWVLILKYLVK  126 (164)
T ss_pred             HHCCCCHHHCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             523153865347877678765421102457999999988999999999998647


Done!