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!