Query         gi|254780736|ref|YP_003065149.1| hypothetical protein CLIBASIA_03115 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 60
No_of_seqs    109 out of 244
Neff          4.6 
Searched_HMMs 39220
Date          Sun May 29 21:46:45 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780736.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG3847 Flp Flp pilus assembly  99.8 3.7E-20 9.5E-25  123.2   7.3   58    1-58      1-58  (58)
  2 pfam04964 Flp_Fap Flp/Fap pili  99.7 4.3E-18 1.1E-22  112.7   5.2   47    8-54      1-47  (47)
  3 COG4961 TadG Flp pilus assembl  97.1 0.00081 2.1E-08   40.1   4.5   34    3-36     10-43  (185)
  4 pfam04021 Class_IIIsignal Clas  82.9     1.1 2.7E-05   24.3   2.7   23   12-34      1-23  (28)
  5 COG4966 PilW Tfp pilus assembl  73.6     3.4 8.7E-05   21.7   2.9   51    1-52      1-51  (318)
  6 pfam05307 Bundlin Bundlin. Thi  73.1     3.6 9.3E-05   21.6   3.0   31    9-39      8-38  (97)
  7 COG4537 ComGC Competence prote  72.5     6.5 0.00017   20.3   4.2   41    3-43      2-42  (107)
  8 COG0342 SecD Preprotein transl  53.7      21 0.00053   17.7   5.3   43   11-53    335-377 (506)
  9 TIGR01129 secD protein-export   50.9      23  0.0006   17.5   5.1   38   13-50    364-401 (522)
 10 pfam07811 TadE TadE-like prote  48.5      25 0.00063   17.3   3.6   23   14-36      1-23  (43)
 11 COG1991 Uncharacterized conser  40.0     4.2 0.00011   21.3  -1.5   34    1-34      1-34  (131)
 12 COG1681 FlaB Archaeal flagelli  36.3      37 0.00094   16.5   2.9   25   11-37      1-25  (209)
 13 TIGR01960 ndhF3_CO2 NAD(P)H de  33.5      41   0.001   16.3   2.7   23   24-46    282-304 (613)
 14 TIGR00411 redox_disulf_1 redox  26.6      15 0.00037   18.5  -0.5   15   10-24     39-53  (82)
 15 pfam12555 TPPK_C Thiamine pyro  26.5      61  0.0016   15.3   4.5   46    6-54      4-49  (53)
 16 PRK13024 bifunctional preprote  22.7      73  0.0019   15.0   5.1   40   11-50    254-293 (741)

No 1  
>COG3847 Flp Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]
Probab=99.81  E-value=3.7e-20  Score=123.19  Aligned_cols=58  Identities=43%  Similarity=0.721  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9799999950346823999999999999999999999855899999999853145325
Q gi|254780736|r    1 MINCMNKLLKDESGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAANRISNVKS   58 (60)
Q Consensus         1 M~~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~l~~a~~   58 (60)
                      |++.++||+|||+||||||||||++||++++|++++.+|+++++.|+++++.++++.+
T Consensus         1 m~~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~~l~~~l~~~ft~i~~al~~a~~   58 (58)
T COG3847           1 MKKLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGSTLGTALKGAFTAIGAALTGAAA   58 (58)
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9178999977456518999999999999999999999989999999999998704689


No 2  
>pfam04964 Flp_Fap Flp/Fap pilin component.
Probab=99.72  E-value=4.3e-18  Score=112.73  Aligned_cols=47  Identities=57%  Similarity=0.829  Sum_probs=45.4

Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             95034682399999999999999999999985589999999985314
Q gi|254780736|r    8 LLKDESGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAANRIS   54 (60)
Q Consensus         8 f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~l~   54 (60)
                      |+|||+|+||||||||++||+++||.+++.+|++++++|++++++++
T Consensus         1 F~kde~GaTAIEYgLIaalIav~iI~~~~~~g~~l~~~f~~i~~~l~   47 (47)
T pfam04964         1 FLKDESGATAIEYGLIAALIAVVIIAYVTTLGTALKTKFTSIGTALT   47 (47)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             96565641599999999999999999999970129889999886239


No 3  
>COG4961 TadG Flp pilus assembly protein TadG [Intracellular trafficking and secretion]
Probab=97.08  E-value=0.00081  Score=40.15  Aligned_cols=34  Identities=21%  Similarity=0.493  Sum_probs=28.4

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999995034682399999999999999999999
Q gi|254780736|r    3 NCMNKLLKDESGAAAIEYGMLVALIAVAIIAAVT   36 (60)
Q Consensus         3 ~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~   36 (60)
                      .+.+||++|++|+.|||.+|++-+..+++.+.+-
T Consensus        10 ~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve   43 (185)
T COG4961          10 GLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVE   43 (185)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999887648768999999999999999999999


No 4  
>pfam04021 Class_IIIsignal Class III signal peptide. This family of archaeal proteins contains. an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site. Two members of this family are cleaved by a type IV pilin-like signal peptidase.
Probab=82.92  E-value=1.1  Score=24.29  Aligned_cols=23  Identities=26%  Similarity=0.476  Sum_probs=17.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             46823999999999999999999
Q gi|254780736|r   12 ESGAAAIEYGMLVALIAVAIIAA   34 (60)
Q Consensus        12 e~GaTAIEYgLIaalIav~ii~a   34 (60)
                      .+|+.++||.++.+.+-++.+.+
T Consensus         1 ~kGQ~SlE~~lLi~~vlv~~~i~   23 (28)
T pfam04021         1 KKGQISLEFLLLILAVLVVAIIA   23 (28)
T ss_pred             CCCEEEHHHHHHHHHHHHHHHHH
T ss_conf             98654399999999999999771


No 5  
>COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=73.61  E-value=3.4  Score=21.74  Aligned_cols=51  Identities=27%  Similarity=0.339  Sum_probs=36.9

Q ss_pred             CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9799999950346823999999999999999999999855899999999853
Q gi|254780736|r    1 MINCMNKLLKDESGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAANR   52 (60)
Q Consensus         1 M~~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~   52 (60)
                      |++.-+...+..+|.+.||- ||+-+|+..++.++..+==.....|....+.
T Consensus         1 m~~~~~~~~rrqrG~SLIEL-MIallIglivL~av~s~y~~sr~~y~~~~~~   51 (318)
T COG4966           1 MLNHRRARPRRQRGFSLIEL-MIALLIGLIVLLAVGSLYLSSRQLYTTLADR   51 (318)
T ss_pred             CCCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHEEEEHHHHHHHHHHH
T ss_conf             97644355455577439999-9999999999997763034356778877666


No 6  
>pfam05307 Bundlin Bundlin. This family consists of several bundlin proteins from E. coli. Bundlin is a type IV pilin protein that is the only known structural component of enteropathogenic Escherichia coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localized adherence to epithelial cells.
Probab=73.09  E-value=3.6  Score=21.59  Aligned_cols=31  Identities=29%  Similarity=0.291  Sum_probs=26.1

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5034682399999999999999999999985
Q gi|254780736|r    9 LKDESGAAAIEYGMLVALIAVAIIAAVTMLG   39 (60)
Q Consensus         9 ~~De~GaTAIEYgLIaalIav~ii~av~~lG   39 (60)
                      -|.|.|-+.||-.+.+++++++|.+++--+-
T Consensus         8 kK~~kGlsLiE~~mVLal~A~vIAGvf~YY~   38 (97)
T pfam05307         8 KKYEKGLSLIESAMVLALAATVTAGVMFYYQ   38 (97)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHEEHH
T ss_conf             6675252199999999999999977510307


No 7  
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=72.52  E-value=6.5  Score=20.31  Aligned_cols=41  Identities=20%  Similarity=0.342  Sum_probs=33.0

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999950346823999999999999999999999855899
Q gi|254780736|r    3 NCMNKLLKDESGAAAIEYGMLVALIAVAIIAAVTMLGGSLK   43 (60)
Q Consensus         3 ~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~   43 (60)
                      ..+..||+++.|=|.||-=+....|++-++-.+..+-.+-.
T Consensus         2 ~~~~k~~~~~kgFTLvEMLiVLlIISiLlLl~iPNltKq~~   42 (107)
T COG4537           2 KKMKKFLKHKKGFTLVEMLIVLLIISILLLLFIPNLTKQKE   42 (107)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             16777777632625999999999999999997462544379


No 8  
>COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion]
Probab=53.75  E-value=21  Score=17.73  Aligned_cols=43  Identities=28%  Similarity=0.416  Sum_probs=32.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3468239999999999999999999998558999999998531
Q gi|254780736|r   11 DESGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAANRI   53 (60)
Q Consensus        11 De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~l   53 (60)
                      -+=|+.+++.|++++++++++|...-.+--.+-+....++.-+
T Consensus       335 psLG~~~i~~gi~Agl~g~~~V~vfm~~~Yr~~Gvia~ial~~  377 (506)
T COG0342         335 PTLGADSIKAGLIAGLIGLALVAVFMLLYYRLAGVIAAIALGL  377 (506)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4547678997899999999999999999998758999999999


No 9  
>TIGR01129 secD protein-export membrane protein SecD; InterPro: IPR005791    Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.     The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains . Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.     This entry describes the SecD family of transport proteins. Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed. SecD from Mycobacterium tuberculosis has a long Pro-rich insert. ; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=50.88  E-value=23  Score=17.48  Aligned_cols=38  Identities=26%  Similarity=0.353  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             68239999999999999999999998558999999998
Q gi|254780736|r   13 SGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAA   50 (60)
Q Consensus        13 ~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~   50 (60)
                      =|+-+||=|++|+++++++|...-.+-=.+-+.+..++
T Consensus       364 LG~d~i~~G~~A~~~Gl~lV~~FM~~yY~~~G~~A~~a  401 (522)
T TIGR01129       364 LGADSIEAGIKAGLIGLVLVLVFMIVYYRLFGLIAAIA  401 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             43899999999999999999999999976788999999


No 10 
>pfam07811 TadE TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues.
Probab=48.48  E-value=25  Score=17.35  Aligned_cols=23  Identities=26%  Similarity=0.632  Sum_probs=17.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             82399999999999999999999
Q gi|254780736|r   14 GAAAIEYGMLVALIAVAIIAAVT   36 (60)
Q Consensus        14 GaTAIEYgLIaalIav~ii~av~   36 (60)
                      |+.+||.+++.-++.+.+.+.+.
T Consensus         1 G~a~VEfalv~p~~l~l~~~~~~   23 (43)
T pfam07811         1 GAAAVEFALVLPVLLLLLFGIVE   23 (43)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             91699999999999999999999


No 11 
>COG1991 Uncharacterized conserved protein [Function unknown]
Probab=40.01  E-value=4.2  Score=21.29  Aligned_cols=34  Identities=24%  Similarity=0.462  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9799999950346823999999999999999999
Q gi|254780736|r    1 MINCMNKLLKDESGAAAIEYGMLVALIAVAIIAA   34 (60)
Q Consensus         1 M~~~~~~f~~De~GaTAIEYgLIaalIav~ii~a   34 (60)
                      |++.+..|..+.+|+-.-||.|....+-++.+.+
T Consensus         1 ~~~~i~~~~~~nkgQiSLEf~Ll~l~ivla~~i~   34 (131)
T COG1991           1 MTTYITKIILSNKGQISLEFSLLLLAIVLAASIA   34 (131)
T ss_pred             CCCEEEEEEECCCCCEEEEHHHHHHHHHHHHHHE
T ss_conf             9616625422466625641389999999973121


No 12 
>COG1681 FlaB Archaeal flagellins [Cell motility and secretion]
Probab=36.34  E-value=37  Score=16.49  Aligned_cols=25  Identities=36%  Similarity=0.515  Sum_probs=18.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             346823999999999999999999999
Q gi|254780736|r   11 DESGAAAIEYGMLVALIAVAIIAAVTM   37 (60)
Q Consensus        11 De~GaTAIEYgLIaalIav~ii~av~~   37 (60)
                      ||+|++-||=..  -|||.++++||-+
T Consensus         1 ~rrG~~GIgtlI--VfIAmVlVAAVaA   25 (209)
T COG1681           1 DRRGATGIGTLI--VFIAMVLVAAVAA   25 (209)
T ss_pred             CCCCCCCHHHHH--HHHHHHHHHHHHH
T ss_conf             984110432899--9999999999999


No 13 
>TIGR01960 ndhF3_CO2 NAD(P)H dehydrogenase, subunit NdhF3 family; InterPro: IPR010217   This family represents NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighbouring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=33.48  E-value=41  Score=16.26  Aligned_cols=23  Identities=39%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999855899999
Q gi|254780736|r   24 VALIAVAIIAAVTMLGGSLKGTF   46 (60)
Q Consensus        24 aalIav~ii~av~~lG~~l~~~f   46 (60)
                      .|+.++.+||+|+++|+++-..=
T Consensus       282 vA~~~li~IG~VTAig~SLiaIA  304 (613)
T TIGR01960       282 VALTVLIAIGSVTAIGASLIAIA  304 (613)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999989855788878899999


No 14 
>TIGR00411 redox_disulf_1 redox-active disulfide protein 1; InterPro: IPR004502 This group of proteins includes thioredoxins, glutaredoxins, protein-disulphide isomerases, and others, some of which have several such domains. The sequence of proteins in this group at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although overall the sequence seems closer to thioredoxins. Proteins may be involved in a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis.
Probab=26.59  E-value=15  Score=18.52  Aligned_cols=15  Identities=33%  Similarity=0.507  Sum_probs=11.7

Q ss_pred             HCCCCCCHHHHHHHH
Q ss_conf             034682399999999
Q gi|254780736|r   10 KDESGAAAIEYGMLV   24 (60)
Q Consensus        10 ~De~GaTAIEYgLIa   24 (60)
                      -||.-.-|+||||.+
T Consensus        39 ~~e~~~kA~~yGi~a   53 (82)
T TIGR00411        39 VMEDLKKALEYGIMA   53 (82)
T ss_pred             CCCCHHHHHHCCCCC
T ss_conf             454847887516352


No 15 
>pfam12555 TPPK_C Thiamine pyrophosphokinase C terminal. This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyses the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme.
Probab=26.50  E-value=61  Score=15.35  Aligned_cols=46  Identities=24%  Similarity=0.325  Sum_probs=31.2

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9995034682399999999999999999999985589999999985314
Q gi|254780736|r    6 NKLLKDESGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAANRIS   54 (60)
Q Consensus         6 ~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~l~   54 (60)
                      .++-|......++=--.+++|++++++..++..|+   ..|+.+.+.++
T Consensus         4 s~LYrsris~~~~~~lvla~Lva~~val~~s~~g~---~~~~~l~~~w~   49 (53)
T pfam12555         4 SRLYRSRISGGALLLLVLAALVALAVALLVSPAGQ---SFLDLLADRWN   49 (53)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHH---HHHHHHHHHHH
T ss_conf             88989227788999999999999999998084229---99999999987


No 16 
>PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=22.72  E-value=73  Score=14.96  Aligned_cols=40  Identities=30%  Similarity=0.404  Sum_probs=27.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3468239999999999999999999998558999999998
Q gi|254780736|r   11 DESGAAAIEYGMLVALIAVAIIAAVTMLGGSLKGTFEEAA   50 (60)
Q Consensus        11 De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~   50 (60)
                      -.-|+.+++.|+++++|++++|...-.+-=.+-+....++
T Consensus       254 ptLG~~si~~g~~A~~ig~~lV~lfMi~~Yr~~G~iA~ia  293 (741)
T PRK13024        254 PTLGQDAINAGIIAGIIGFALIALFMLLFYGLPGLIANIA  293 (741)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1310999999999999999999999999986769999999


Done!