Query         gi|254780840|ref|YP_003065253.1| hypothetical protein CLIBASIA_03675 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 52
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 00:54:01 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780840.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam10255 Paf67 RNA polymerase  25.0      40   0.001   16.5   1.5   17   18-34     31-47  (402)
  2 KOG4128 consensus               24.7      32 0.00081   17.1   0.9   26    6-32    103-137 (457)
  3 pfam01687 Flavokinase Riboflav  22.2      32 0.00082   17.0   0.6   18    1-18      1-18  (125)
  4 TIGR03251 LAT_fam L-lysine 6-t  20.4     7.5 0.00019   20.4  -3.0   26    2-29     15-40  (431)
  5 TIGR03141 cytochro_ccmD heme e  17.7      61  0.0016   15.5   1.2   25    1-27      1-31  (45)
  6 pfam05452 Clavanin Clavanin. T  17.7      25 0.00065   17.6  -0.8   17    6-22     31-47  (80)
  7 pfam09983 DUF2220 Uncharacteri  16.0      87  0.0022   14.7   1.6   17    2-18     83-100 (179)
  8 TIGR00918 2A060602 transmembra  15.9      39   0.001   16.6  -0.2   18    2-22   1020-1037(1215)
  9 COG3114 CcmD Heme exporter pro  15.2      31 0.00079   17.1  -0.8   17    1-19     12-28  (67)
 10 KOG3491 consensus               14.2 1.2E+02  0.0031   13.9   2.6   21   15-35     41-61  (65)

No 1  
>pfam10255 Paf67 RNA polymerase I-associated factor PAF67. RNA polymerase I is a multisubunit enzyme and its transcription competence is dependent on the presence of PAF67. This family of proteins is conserved from worms to humans.
Probab=25.02  E-value=40  Score=16.53  Aligned_cols=17  Identities=41%  Similarity=0.929  Sum_probs=14.5

Q ss_pred             HHHHHHHCCHHHHHHHH
Q ss_conf             89998754169999999
Q gi|254780840|r   18 LFLWDVLDGRVFQFYRV   34 (52)
Q Consensus        18 lflwdvldgrvfqfyrv   34 (52)
                      ..|||.+|-=|+||.-.
T Consensus        31 ~WlWDiiDEFvYQfQsf   47 (402)
T pfam10255        31 SWLWDIIDEFVYQFQSF   47 (402)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             89999999999977889


No 2  
>KOG4128 consensus
Probab=24.66  E-value=32  Score=17.07  Aligned_cols=26  Identities=46%  Similarity=1.083  Sum_probs=18.3

Q ss_pred             EEEEEEHHHHHHHHHHHH---------HCCHHHHHH
Q ss_conf             252210212378899987---------541699999
Q gi|254780840|r    6 FYFWGKISHGIGLFLWDV---------LDGRVFQFY   32 (52)
Q Consensus         6 fyfwgkishgiglflwdv---------ldgrvfqfy   32 (52)
                      .+||.|... -..|||.+         +|||.+|+.
T Consensus       103 LFFwdKlEr-cnyFL~~vvd~a~r~ep~DgRlvq~L  137 (457)
T KOG4128         103 LFFWDKLER-CNYFLWTVVDLAMRCEPLDGRLVQNL  137 (457)
T ss_pred             HHHHHHHHH-HHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             999998888-89999999988862587521899999


No 3  
>pfam01687 Flavokinase Riboflavin kinase. This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism. This domain is thought to have kinase activity.
Probab=22.21  E-value=32  Score=17.02  Aligned_cols=18  Identities=33%  Similarity=0.713  Sum_probs=15.6

Q ss_pred             CCCCCEEEEEEHHHHHHH
Q ss_conf             987742522102123788
Q gi|254780840|r    1 MTGYPFYFWGKISHGIGL   18 (52)
Q Consensus         1 mtgypfyfwgkishgigl   18 (52)
                      |.|+||.+-|++.||-++
T Consensus         1 lLgr~y~~~G~Vv~G~~~   18 (125)
T pfam01687         1 LLGRPYSISGTVVHGKGR   18 (125)
T ss_pred             CCCCCEEEEEEEEECCCC
T ss_conf             969965898999978854


No 4  
>TIGR03251 LAT_fam L-lysine 6-transaminase. Characterized members of this protein family are L-lysine 6-transaminase, also called lysine epsilon-aminotransferase (LAT). The immediate product of the reaction of this enzyme on lysine, 2-aminoadipate 6-semialdehyde, becomes 1-piperideine 6-carboxylate, or P6C. This product may be converted subsequently to pipecolate or alpha-aminoadipate, lysine catabolites that may be precursors of certain seconary metabolites.
Probab=20.39  E-value=7.5  Score=20.40  Aligned_cols=26  Identities=27%  Similarity=0.483  Sum_probs=18.8

Q ss_pred             CCCCEEEEEEHHHHHHHHHHHHHCCHHH
Q ss_conf             8774252210212378899987541699
Q gi|254780840|r    2 TGYPFYFWGKISHGIGLFLWDVLDGRVF   29 (52)
Q Consensus         2 tgypfyfwgkishgiglflwdvldgrvf   29 (52)
                      .||||-  =.|.+|-|.+|||+.|||.+
T Consensus        15 ~~~p~~--i~i~rgeG~~l~D~~dG~~y   40 (431)
T TIGR03251        15 DGFDLV--LDLDRSRGSVLVDARDGRRY   40 (431)
T ss_pred             CCCCCC--EEEEEEECCEEEECCCCCEE
T ss_conf             389962--06886026999989999884


No 5  
>TIGR03141 cytochro_ccmD heme exporter protein CcmD. The model for this protein family describes a small, hydrophobic, and only moderately well-conserved protein, tricky to identify accurately for all of these reasons. However, members are found as part of large operons involved in heme export across the inner membrane for assembly of c-type cytochromes in a large number of bacteria. The gray zone between the trusted cutoff (13.0) and noise cutoff (4.75) includes both low-scoring examples and false-positive matches to hydrophobic domains of longer proteins.
Probab=17.73  E-value=61  Score=15.54  Aligned_cols=25  Identities=56%  Similarity=1.184  Sum_probs=15.5

Q ss_pred             CCCCCEEEEEEHHHHHH------HHHHHHHCCH
Q ss_conf             98774252210212378------8999875416
Q gi|254780840|r    1 MTGYPFYFWGKISHGIG------LFLWDVLDGR   27 (52)
Q Consensus         1 mtgypfyfwgkishgig------lflwdvldgr   27 (52)
                      |-||-||-|.  |-||.      +.+|...+.|
T Consensus         1 MGgya~YVW~--sygit~~~l~~li~~s~~~~r   31 (45)
T TIGR03141         1 MGGYAFYVWL--AYGITALVLAGLILWSLLDRR   31 (45)
T ss_pred             CCCCEEHHHH--HHHHHHHHHHHHHHHHHHHHH
T ss_conf             9986003779--999999999999999999999


No 6  
>pfam05452 Clavanin Clavanin. This family consists of clavanin proteins from the haemocytes of the invertebrate Styela clava, a solitary tunicate. The family is made up of four alpha-helical antimicrobial peptides, clavanins A, B, C and D. The tunicate peptides resemble magainins in size, primary sequence and antibacterial activity. Synthetic clavanin A displays comparable antimicrobial activity to magainins and cecropins. The presence of alpha-helical antimicrobial peptides in the haemocytes of a urochordate suggests that such peptides are primeval effectors of innate immunity in the vertebrate lineage.
Probab=17.66  E-value=25  Score=17.58  Aligned_cols=17  Identities=59%  Similarity=1.007  Sum_probs=13.4

Q ss_pred             EEEEEEHHHHHHHHHHH
Q ss_conf             25221021237889998
Q gi|254780840|r    6 FYFWGKISHGIGLFLWD   22 (52)
Q Consensus         6 fyfwgkishgiglflwd   22 (52)
                      |-|-|||-||||-|...
T Consensus        31 ~~~ig~iih~ig~~v~~   47 (80)
T pfam05452        31 FHFIGKIIHGIGHFVHG   47 (80)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             99999999723167643


No 7  
>pfam09983 DUF2220 Uncharacterized protein conserved in bacteria C-term(DUF2220). This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the C-terminus.
Probab=16.01  E-value=87  Score=14.70  Aligned_cols=17  Identities=41%  Similarity=1.173  Sum_probs=11.7

Q ss_pred             CCCCEEEEEEHH-HHHHH
Q ss_conf             877425221021-23788
Q gi|254780840|r    2 TGYPFYFWGKIS-HGIGL   18 (52)
Q Consensus         2 tgypfyfwgkis-hgigl   18 (52)
                      .+-|+|+||.|. ||...
T Consensus        83 ~~~~i~YWGDiDt~Gf~I  100 (179)
T pfam09983        83 HGKRIYYWGDIDTHGFAI  100 (179)
T ss_pred             CCCCEEEECCCCCCHHHH
T ss_conf             589458752666309999


No 8  
>TIGR00918 2A060602 transmembrane receptor Patched; InterPro: IPR004766   Patched (Ptc) is a Drosophila melanogaster (Fruit fly) membrane protein that plays a critical role in patterning embryonic and imaginal tissues. It constitutively inactivates the transcription of genes wingless, decapentaplegic, and patched itself. The secreted protein, hedgehog (Hh) induces transcription of genes by opposing the patched signaling pathway .    In humans, mutations affecting patched (Ptc) or smoothened (Smo) homologues that trigger ligand-independent activity of the Hedgehog (Hh) signalling pathway are associated with tumours such as basal cell carcinoma (BCC) and medulloblastoma .   Patched is associated with a complex belonging to the hedgehog pathway. Members of the complex include cubitus interruptus, sex-lethal, patched and smoothened. The complex is present at the plasma membrane and the association of patched changes depending on the activation state of the pathway . ; GO: 0008158 hedgehog receptor activity, 0016021 integral to membrane.
Probab=15.88  E-value=39  Score=16.56  Aligned_cols=18  Identities=44%  Similarity=0.975  Sum_probs=10.5

Q ss_pred             CCCCEEEEEEHHHHHHHHHHH
Q ss_conf             877425221021237889998
Q gi|254780840|r    2 TGYPFYFWGKISHGIGLFLWD   22 (52)
Q Consensus         2 tgypfyfwgkishgiglflwd   22 (52)
                      .||||-||-.-   +||=-|=
T Consensus      1020 sG~PFlFWEQY---~gLR~~l 1037 (1215)
T TIGR00918      1020 SGYPFLFWEQY---LGLRHSL 1037 (1215)
T ss_pred             CCCCCHHHHHH---HHHHHHH
T ss_conf             98860268889---9999999


No 9  
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=15.23  E-value=31  Score=17.11  Aligned_cols=17  Identities=47%  Similarity=1.091  Sum_probs=11.5

Q ss_pred             CCCCCEEEEEEHHHHHHHH
Q ss_conf             9877425221021237889
Q gi|254780840|r    1 MTGYPFYFWGKISHGIGLF   19 (52)
Q Consensus         1 mtgypfyfwgkishgiglf   19 (52)
                      |-||.||.|-  +-|+.+.
T Consensus        12 MGgyafyVWl--A~~~tll   28 (67)
T COG3114          12 MGGYAFYVWL--AVGMTLL   28 (67)
T ss_pred             CCCCHHHHHH--HHHHHHH
T ss_conf             3571689999--9999999


No 10 
>KOG3491 consensus
Probab=14.21  E-value=1.2e+02  Score=13.94  Aligned_cols=21  Identities=33%  Similarity=0.586  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHCCHHHHHHHHH
Q ss_conf             378899987541699999999
Q gi|254780840|r   15 GIGLFLWDVLDGRVFQFYRVV   35 (52)
Q Consensus        15 giglflwdvldgrvfqfyrvv   35 (52)
                      -+|||..-|....+||.-|.+
T Consensus        41 LlglFvFVVcGSa~FqIIr~~   61 (65)
T KOG3491          41 LLGLFVFVVCGSALFQIIRTA   61 (65)
T ss_pred             HHHHHHHHHHCHHHHHHHHHH
T ss_conf             988899986159999999998


Done!