Query         gi|254781183|ref|YP_003065596.1| hypothetical protein CLIBASIA_05450 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 94
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 05:37:26 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781183.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02890 spore_yteA sporulati  65.5     2.2 5.7E-05   23.9   0.6   27   46-72     89-115 (167)
  2 KOG4273 consensus               46.1      14 0.00036   19.4   2.0   36   35-70     72-108 (418)
  3 TIGR02538 type_IV_pilB type IV  36.6      10 0.00026   20.2   0.1   63   12-75    465-535 (577)
  4 pfam08885 GSCFA GSCFA family.   33.8      13 0.00034   19.5   0.3   12   77-88    211-222 (251)
  5 pfam10955 DUF2757 Protein of u  33.7      14 0.00035   19.5   0.3   42    9-53      3-60  (76)
  6 pfam05322 NinE NINE Protein. T  32.8     9.6 0.00025   20.3  -0.6   23   47-78     12-38  (60)
  7 pfam10596 U6-snRNA_bdg U6-snRN  31.4      18 0.00046   18.8   0.6   30   65-94     30-66  (160)
  8 pfam07652 Flavi_DEAD Flaviviru  30.1      33 0.00084   17.3   1.8   50   19-68     70-121 (146)
  9 pfam04875 DUF645 Protein of un  26.7      23 0.00059   18.2   0.5   21   48-68     27-47  (59)
 10 KOG0909 consensus               23.2      70  0.0018   15.5   2.5   43   11-55    162-204 (500)
 11 TIGR00387 glcD glycolate oxida  22.8      32 0.00081   17.4   0.6   16   25-46    347-362 (437)
 12 COG1734 DksA DnaK suppressor p  22.2      28 0.00071   17.8   0.2   24   45-68     80-103 (120)
 13 pfam05502 Dynactin_p62 Dynacti  22.1      36 0.00093   17.1   0.8   20   11-30      6-25  (476)
 14 pfam08965 DUF1870 Domain of un  20.9      54  0.0014   16.1   1.5   22   66-89     66-87  (117)
 15 pfam08421 Methyltransf_13 Hypo  20.7      61  0.0015   15.9   1.7   16   43-58     38-53  (78)
 16 KOG2560 consensus               20.7      17 0.00043   18.9  -1.1   20   37-56    104-123 (529)

No 1  
>TIGR02890 spore_yteA sporulation protein, yteA family; InterPro: IPR014240   This entry contains predicted regulatory proteins that are found in nearly every species of the endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria), with the exception of Clostridium perfringens. Some (but not all) of these proteins contain an unusual DksA/TraR C4-type zinc finger, where only one of the four key Cys residues is conserved. All members of this entry share an additional C-terminal domain. The function of proteins in this family is unknown. YteA is found in mature spores of Bacillus subtilis and its expression appeasr to be regulated by sigma-K ..
Probab=65.46  E-value=2.2  Score=23.86  Aligned_cols=27  Identities=33%  Similarity=0.455  Sum_probs=14.9

Q ss_pred             EEECCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             542366640256676535733556764
Q gi|254781183|r   46 GICENCGDLSLMAFQKWLPTKDINKAI   72 (94)
Q Consensus        46 gicencgdlslmafqkwlptkdinkai   72 (94)
                      ||||+||---=.-=-.-+||-..--+-
T Consensus        89 GICe~cG~~Ip~ERLEA~P~A~~c~~~  115 (167)
T TIGR02890        89 GICEVCGKPIPYERLEALPTATTCVEC  115 (167)
T ss_pred             EEECCCCCCCCHHHHHCCHHHHHHHHH
T ss_conf             000448787984442004178899987


No 2  
>KOG4273 consensus
Probab=46.06  E-value=14  Score=19.37  Aligned_cols=36  Identities=33%  Similarity=0.469  Sum_probs=25.0

Q ss_pred             HCCCCCCCEEEEEECCCCCH-HHHHHHHHCCHHHHHH
Q ss_conf             12575862355542366640-2566765357335567
Q gi|254781183|r   35 KAGNMHPTYAVGICENCGDL-SLMAFQKWLPTKDINK   70 (94)
Q Consensus        35 kagnmhptyavgicencgdl-slmafqkwlptkdink   70 (94)
                      .+-+-||.-|.-..-.-..+ .|.|.|.|||..|||.
T Consensus        72 n~~~a~pl~a~vmvfdlse~s~l~alqdwl~htdins  108 (418)
T KOG4273          72 NAEIAEPLQAFVMVFDLSEKSGLDALQDWLPHTDINS  108 (418)
T ss_pred             CCCCCCCEEEEEEEEECCCHHHHHHHHHHCCCCCCCC
T ss_conf             7644552026799985322010578875256655442


No 3  
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB; InterPro: IPR013374    This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE (IPR013369 from INTERPRO) of type II secretion systems (also referred to as the main terminal branch of the general secretion pathway). Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0009297 pilus biogenesis.
Probab=36.62  E-value=10  Score=20.18  Aligned_cols=63  Identities=22%  Similarity=0.483  Sum_probs=42.5

Q ss_pred             EEEHHCCC---CCCCCEEECCCCCHHHCC-CCCCCEEEEEECCCCCHHH----HHHHHHCCHHHHHHHHCCC
Q ss_conf             11201356---898420202555022125-7586235554236664025----6676535733556764030
Q gi|254781183|r   12 FCRHCSQK---NPNYGMCHAGVSKEEKAG-NMHPTYAVGICENCGDLSL----MAFQKWLPTKDINKAIGES   75 (94)
Q Consensus        12 fcrhcsqk---npnygmchagvskeekag-nmhptyavgicencgdlsl----mafqkwlptkdinkaiges   75 (94)
                      .|-||-+.   -|+-..-..|+..|+-+. ..+.--+|| |++|-.-..    =-||--.=+..|.++|=+.
T Consensus       465 LCs~CK~~~~~~p~~~Ll~lGF~~edL~~Pg~~ly~pvG-C~~C~~~GYKGRvGiYEVMp~~Eei~~~Il~g  535 (577)
T TIGR02538       465 LCSHCKAPVEEVPEEALLELGFTEEDLADPGLKLYGPVG-CEECSNTGYKGRVGIYEVMPISEEIAELILKG  535 (577)
T ss_pred             CCCCCCCCCCCCCHHHHHHCCCCHHHHCCCCCEECCCCC-CCCCCCCCCEEEEEEEEECCCCHHHHHHHHCC
T ss_conf             031368776646859998568886892699938617626-10037987201021366303358999998748


No 4  
>pfam08885 GSCFA GSCFA family. This family of proteins are functionally uncharacterized. They have been named GSCFA after a highly conserved N-terminal motif in the alignment.
Probab=33.76  E-value=13  Score=19.50  Aligned_cols=12  Identities=50%  Similarity=0.963  Sum_probs=8.9

Q ss_pred             HHHHHCCCHHHH
Q ss_conf             134427675664
Q gi|254781183|r   77 TKEEYFPSYEEF   88 (94)
Q Consensus        77 tkeeyfpsyeef   88 (94)
                      ..-.||||||-.
T Consensus       211 ~~v~YFPsyEiv  222 (251)
T pfam08885       211 DDVDYFPSYEIV  222 (251)
T ss_pred             CCCCCCCHHHHH
T ss_conf             897376527875


No 5  
>pfam10955 DUF2757 Protein of unknown function (DUF2757). Members in this family of proteins are annotated as YabK however currently no function is known.
Probab=33.68  E-value=14  Score=19.48  Aligned_cols=42  Identities=31%  Similarity=0.732  Sum_probs=21.6

Q ss_pred             EEEEEEHHCCCCCCCCEE--------ECCCCCHHH--------CCCCCCCEEEEEECCCCC
Q ss_conf             000112013568984202--------025550221--------257586235554236664
Q gi|254781183|r    9 LSIFCRHCSQKNPNYGMC--------HAGVSKEEK--------AGNMHPTYAVGICENCGD   53 (94)
Q Consensus         9 lsifcrhcsqknpnygmc--------hagvskeek--------agnmhptyavgicencgd   53 (94)
                      +--+||||.+|--..---        ---...||+        .|++   +.--|||.|-+
T Consensus         3 i~Y~CRHCg~~iG~l~~~~v~~~~LGf~~Lt~eEr~dmI~y~~nGdi---~Vk~ICEdCqe   60 (76)
T pfam10955         3 VHYYCRHCGQKIGSLTQVAVDSDKLGFFELTEEERNDMISYDQNGDI---HVKTICEDCQE   60 (76)
T ss_pred             EEEEECCCCCEEEEECCCCCCHHHCCCHHCCHHHHHHHHEECCCCCE---EEEEEHHHHHH
T ss_conf             16874157867776121214276557202798898667357579999---99975477799


No 6  
>pfam05322 NinE NINE Protein. This family consists of NINE proteins from several bacteriophages and from E. coli.
Probab=32.85  E-value=9.6  Score=20.32  Aligned_cols=23  Identities=65%  Similarity=0.954  Sum_probs=13.6

Q ss_pred             EECCCCCHHHHHHHHHCCHHH-HHHHH---CCCCHH
Q ss_conf             423666402566765357335-56764---030013
Q gi|254781183|r   47 ICENCGDLSLMAFQKWLPTKD-INKAI---GESQTK   78 (94)
Q Consensus        47 icencgdlslmafqkwlptkd-inkai---gesqtk   78 (94)
                      |||||         |+||||. +||--   -||+.|
T Consensus        12 icenc---------kylPTKRsrnk~kpip~es~vk   38 (60)
T pfam05322        12 ICENC---------KYLPTKRSRNKFKPIPQESMVK   38 (60)
T ss_pred             HHHHC---------EECCCCCCCCCCCCCCCHHHHH
T ss_conf             97344---------3056402334589988321333


No 7  
>pfam10596 U6-snRNA_bdg U6-snRNA interacting domain of PrP8. This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor.
Probab=31.37  E-value=18  Score=18.80  Aligned_cols=30  Identities=37%  Similarity=0.554  Sum_probs=23.2

Q ss_pred             HHHHHHHHCCC-------CHHHHHCCCHHHHHHHCCC
Q ss_conf             33556764030-------0134427675664220369
Q gi|254781183|r   65 TKDINKAIGES-------QTKEEYFPSYEEFYLSKAS   94 (94)
Q Consensus        65 tkdinkaiges-------qtkeeyfpsyeefylskas   94 (94)
                      .+|+..|+|.-       -.|..+||++|.++-.|+|
T Consensus        30 r~d~i~alGGve~ILeHtLfk~T~f~~weglfwekas   66 (160)
T pfam10596        30 RTDVIQALGGVETILEHTLFKATGFPSWEGLFWEKAS   66 (160)
T ss_pred             HHHHHHHCCCHHHHHHHHHCCCCCCCCCCCEEEECCC
T ss_conf             7999997303677776300256788862000111244


No 8  
>pfam07652 Flavi_DEAD Flavivirus DEAD domain.
Probab=30.05  E-value=33  Score=17.33  Aligned_cols=50  Identities=22%  Similarity=0.238  Sum_probs=39.7

Q ss_pred             CCCCCCEEECCCCCHHHCCCCCCCEEEEEECCC--CCHHHHHHHHHCCHHHH
Q ss_conf             689842020255502212575862355542366--64025667653573355
Q gi|254781183|r   19 KNPNYGMCHAGVSKEEKAGNMHPTYAVGICENC--GDLSLMAFQKWLPTKDI   68 (94)
Q Consensus        19 knpnygmchagvskeekagnmhptyavgicenc--gdlslmafqkwlptkdi   68 (94)
                      .+---.||||-...----+..-+.|.|-|...|  -|-+-+|+..|+-++.-
T Consensus        70 ~~ivdvmCHAT~t~r~l~~~~~~ny~viIMDE~H~~DP~SIAarG~~~~~~~  121 (146)
T pfam07652        70 REIVDVMCHATFTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVE  121 (146)
T ss_pred             CCEEEEECHHHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH
T ss_conf             8418897159888897368885644799985122389899998899998854


No 9  
>pfam04875 DUF645 Protein of unknown function, DUF645. This family includes several uncharacterized proteins from Vibrio cholerae.
Probab=26.66  E-value=23  Score=18.18  Aligned_cols=21  Identities=38%  Similarity=0.683  Sum_probs=17.9

Q ss_pred             ECCCCCHHHHHHHHHCCHHHH
Q ss_conf             236664025667653573355
Q gi|254781183|r   48 CENCGDLSLMAFQKWLPTKDI   68 (94)
Q Consensus        48 cencgdlslmafqkwlptkdi   68 (94)
                      --|.|.|+|-.|.-|.||...
T Consensus        27 tlnrgqlnldrfefW~~tSQl   47 (59)
T pfam04875        27 TLNRGQLNLDRFEFWQPTSQL   47 (59)
T ss_pred             HCCCCCCCHHHEECCCCHHHH
T ss_conf             136776561242125746678


No 10 
>KOG0909 consensus
Probab=23.17  E-value=70  Score=15.50  Aligned_cols=43  Identities=21%  Similarity=0.408  Sum_probs=31.7

Q ss_pred             EEEEHHCCCCCCCCEEECCCCCHHHCCCCCCCEEEEEECCCCCHH
Q ss_conf             011201356898420202555022125758623555423666402
Q gi|254781183|r   11 IFCRHCSQKNPNYGMCHAGVSKEEKAGNMHPTYAVGICENCGDLS   55 (94)
Q Consensus        11 ifcrhcsqknpnygmchagvskeekagnmhptyavgicencgdls   55 (94)
                      +-|+||.++.- -||-..+-..||+.++-. +--+-+|.-||.-+
T Consensus       162 PpC~~CG~et~-~~l~~~~p~eeE~~~Ga~-rVEiy~C~~C~~~~  204 (500)
T KOG0909         162 PPCNKCGGETS-SGLGNQPPNEEEKKFGAG-RVEIYKCNRCGTET  204 (500)
T ss_pred             CCCCCCCCCCC-CCCCCCCCCHHHHHCCCC-EEEEEEECCCCCCC
T ss_conf             98531024114-554688996467636875-48999835888766


No 11 
>TIGR00387 glcD glycolate oxidase, subunit GlcD; InterPro: IPR004490 The glc locus of Escherichia coli encodes the subunits of glycolate oxidase and the glc regulator protein. The subunit GlcD is similar to that of several D-lactate dehydrogenases, including that of E. coli. Glycolate oxidase has been found to have some D-lactate dehydrogenase activity.; GO: 0008891 glycolate oxidase activity, 0009339 glycolate oxidase complex.
Probab=22.84  E-value=32  Score=17.43  Aligned_cols=16  Identities=44%  Similarity=0.792  Sum_probs=10.8

Q ss_pred             EEECCCCCHHHCCCCCCCEEEE
Q ss_conf             0202555022125758623555
Q gi|254781183|r   25 MCHAGVSKEEKAGNMHPTYAVG   46 (94)
Q Consensus        25 mchagvskeekagnmhptyavg   46 (94)
                      .-|||      -||||||--.-
T Consensus       347 ~gHaG------DGNlHP~i~~d  362 (437)
T TIGR00387       347 VGHAG------DGNLHPLILTD  362 (437)
T ss_pred             EEECC------CCCCCCEEECC
T ss_conf             87417------78754322237


No 12 
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=22.19  E-value=28  Score=17.76  Aligned_cols=24  Identities=38%  Similarity=0.599  Sum_probs=15.8

Q ss_pred             EEEECCCCCHHHHHHHHHCCHHHH
Q ss_conf             554236664025667653573355
Q gi|254781183|r   45 VGICENCGDLSLMAFQKWLPTKDI   68 (94)
Q Consensus        45 vgicencgdlslmafqkwlptkdi   68 (94)
                      -|||+.||+---.+=-.-.|+-..
T Consensus        80 YG~Ce~cG~~Ip~~RL~A~P~A~~  103 (120)
T COG1734          80 YGICEECGEPIPEARLEARPTARL  103 (120)
T ss_pred             CCCHHCCCCCCCHHHHHHCCCHHH
T ss_conf             611433699688999850764277


No 13 
>pfam05502 Dynactin_p62 Dynactin p62 family. Dynactin is a multi-subunit complex and a required cofactor for most, or all, of the cellular processes powered by the microtubule-based motor cytoplasmic dynein. p62 binds directly to the Arp1 subunit of dynactin.
Probab=22.09  E-value=36  Score=17.10  Aligned_cols=20  Identities=25%  Similarity=0.458  Sum_probs=14.7

Q ss_pred             EEEEHHCCCCCCCCEEECCC
Q ss_conf             01120135689842020255
Q gi|254781183|r   11 IFCRHCSQKNPNYGMCHAGV   30 (94)
Q Consensus        11 ifcrhcsqknpnygmchagv   30 (94)
                      .|||||.|-.=++-.||--+
T Consensus         6 yfCe~C~qiRC~~CV~~EId   25 (476)
T pfam05502         6 LFCEDCHQIKCPRCVTEEIV   25 (476)
T ss_pred             EECCCCCCCCCCCCCCCCCC
T ss_conf             12256563579641572010


No 14 
>pfam08965 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins.
Probab=20.90  E-value=54  Score=16.12  Aligned_cols=22  Identities=36%  Similarity=0.770  Sum_probs=16.1

Q ss_pred             HHHHHHHCCCCHHHHHCCCHHHHH
Q ss_conf             355676403001344276756642
Q gi|254781183|r   66 KDINKAIGESQTKEEYFPSYEEFY   89 (94)
Q Consensus        66 kdinkaigesqtkeeyfpsyeefy   89 (94)
                      +.||..||+..  -.|||.|+.|-
T Consensus        66 ~kinnrIGnnT--mR~f~dl~aF~   87 (117)
T pfam08965        66 SEINNRIGNNT--YRYYPDLEAFQ   87 (117)
T ss_pred             HHHHHHHCCCH--HHHCCCHHHHH
T ss_conf             99987754131--24235799998


No 15 
>pfam08421 Methyltransf_13 Hypothetical methyltransferase. This domain is found at the N-terminus of bacterial methyltransferases.
Probab=20.74  E-value=61  Score=15.85  Aligned_cols=16  Identities=25%  Similarity=0.710  Sum_probs=12.6

Q ss_pred             EEEEEECCCCCHHHHH
Q ss_conf             3555423666402566
Q gi|254781183|r   43 YAVGICENCGDLSLMA   58 (94)
Q Consensus        43 yavgicencgdlslma   58 (94)
                      -.+++|++|+-+.|.-
T Consensus        38 L~l~~C~~C~lvQl~~   53 (78)
T pfam08421        38 LELVVCRDCGLVQLRE   53 (78)
T ss_pred             EEEEECCCCCEEEECC
T ss_conf             1798889998787887


No 16 
>KOG2560 consensus
Probab=20.70  E-value=17  Score=18.94  Aligned_cols=20  Identities=40%  Similarity=0.981  Sum_probs=13.9

Q ss_pred             CCCCCCEEEEEECCCCCHHH
Q ss_conf             57586235554236664025
Q gi|254781183|r   37 GNMHPTYAVGICENCGDLSL   56 (94)
Q Consensus        37 gnmhptyavgicencgdlsl   56 (94)
                      +-.-..|--|.|+|||..+-
T Consensus       104 ~~~atkyRKGACeNCGAmtH  123 (529)
T KOG2560         104 GSVATKYRKGACENCGAMTH  123 (529)
T ss_pred             CHHHHHHHHHHHHHHHHHHC
T ss_conf             21788876656643213103


Done!