Query gi|254780732|ref|YP_003065145.1| hypothetical protein CLIBASIA_03095 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 58 No_of_seqs 102 out of 256 Neff 4.4 Searched_HMMs 39220 Date Sun May 29 21:13:26 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780732.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 1.3E-19 3.2E-24 117.4 7.1 56 3-58 2-57 (58) 2 pfam04964 Flp_Fap Flp/Fap pili 99.7 1E-18 2.6E-23 112.9 5.1 47 9-55 1-47 (47) 3 COG4961 TadG Flp pilus assembl 97.3 0.00037 9.5E-09 41.3 4.4 35 3-37 9-43 (185) 4 pfam04021 Class_IIIsignal Clas 82.1 1.2 3E-05 24.1 2.6 22 13-34 1-22 (28) 5 COG4537 ComGC Competence prote 72.5 6.6 0.00017 20.4 4.2 41 3-43 1-41 (107) 6 pfam05307 Bundlin Bundlin. Thi 71.8 4.1 0.0001 21.5 3.0 31 10-40 8-38 (97) 7 COG0342 SecD Preprotein transl 56.9 19 0.00049 18.2 5.3 42 12-53 335-376 (506) 8 TIGR01129 secD protein-export 53.6 22 0.00056 17.9 5.1 38 14-51 364-401 (522) 9 COG4966 PilW Tfp pilus assembl 52.7 13 0.00033 19.0 2.7 44 9-53 8-51 (318) 10 TIGR00872 gnd_rel 6-phosphoglu 50.3 7.3 0.00019 20.2 1.1 10 18-27 196-205 (341) 11 pfam07811 TadE TadE-like prote 49.2 24 0.00061 17.7 3.6 23 15-37 1-23 (43) 12 COG1681 FlaB Archaeal flagelli 40.5 28 0.00073 17.3 2.9 25 12-38 1-25 (209) 13 TIGR01960 ndhF3_CO2 NAD(P)H de 34.1 39 0.00099 16.7 2.7 24 25-48 282-305 (613) 14 TIGR00411 redox_disulf_1 redox 26.4 15 0.00038 18.7 -0.5 14 12-25 40-53 (82) 15 PRK13024 bifunctional preprote 25.7 67 0.0017 15.5 5.1 40 13-52 255-294 (741) 16 PRK13464 F0F1 ATP synthase sub 20.9 84 0.0021 15.0 2.5 40 4-43 2-41 (101) 17 pfam12301 CD99L2 CD99 antigen 20.3 75 0.0019 15.3 2.1 32 12-43 101-132 (154) No 1 >COG3847 Flp Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion] Probab=99.80 E-value=1.3e-19 Score=117.37 Aligned_cols=56 Identities=50% Similarity=0.771 Sum_probs=53.0 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 69999995023683299999999999999999999975489999999975212269 Q gi|254780732|r 3 MHIVKNFLQDESGATAIEYGLLASLIAVAIIASVTTLGGKLTAVFADISSKLNPKS 58 (58) Q Consensus 3 m~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~l~~at 58 (58) .++++||+|||+||||||||||+++|++++|+.++.+|+++++.|+.++++++.++ T Consensus 2 ~~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~~l~~~l~~~ft~i~~al~~a~ 57 (58) T COG3847 2 KKLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGSTLGTALKGAFTAIGAALTGAA 57 (58) T ss_pred CHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 17899997745651899999999999999999999998999999999999870468 No 2 >pfam04964 Flp_Fap Flp/Fap pilin component. Probab=99.75 E-value=1e-18 Score=112.92 Aligned_cols=47 Identities=66% Similarity=0.923 Sum_probs=45.5 Q ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 95023683299999999999999999999975489999999975212 Q gi|254780732|r 9 FLQDESGATAIEYGLLASLIAVAIIASVTTLGGKLTAVFADISSKLN 55 (58) Q Consensus 9 f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~l~ 55 (58) |+|||+|+||||||||+++|+++||.+++.+|++++++|++++++++ 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=97.28 E-value=0.00037 Score=41.34 Aligned_cols=35 Identities=26% Similarity=0.521 Sum_probs=29.4 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 69999995023683299999999999999999999 Q gi|254780732|r 3 MHIVKNFLQDESGATAIEYGLLASLIAVAIIASVT 37 (58) Q Consensus 3 m~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~ 37 (58) ..+.++|++|++|+.|||.+|++-+..+++.+.+- T Consensus 9 ~~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve 43 (185) T COG4961 9 RGLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVE 43 (185) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999887648768999999999999999999999 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=82.08 E-value=1.2 Score=24.09 Aligned_cols=22 Identities=27% Similarity=0.410 Sum_probs=16.7 Q ss_pred CCCCCHHHHHHHHHHHHHHHHH Q ss_conf 3683299999999999999999 Q gi|254780732|r 13 ESGATAIEYGLLASLIAVAIIA 34 (58) Q Consensus 13 e~GaTAIEYgLIaalIav~ii~ 34 (58) ++|+.++||.++.+.+-++.+. T Consensus 1 ~kGQ~SlE~~lLi~~vlv~~~i 22 (28) T pfam04021 1 KKGQISLEFLLLILAVLVVAII 22 (28) T ss_pred CCCEEEHHHHHHHHHHHHHHHH T ss_conf 9865439999999999999977 No 5 >COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion] Probab=72.45 E-value=6.6 Score=20.44 Aligned_cols=41 Identities=22% Similarity=0.391 Sum_probs=33.6 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 69999995023683299999999999999999999975489 Q gi|254780732|r 3 MHIVKNFLQDESGATAIEYGLLASLIAVAIIASVTTLGGKL 43 (58) Q Consensus 3 m~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l 43 (58) |.-++.|++++.|=|-||-=+....|++-++-.+..+...- T Consensus 1 m~~~~k~~~~~kgFTLvEMLiVLlIISiLlLl~iPNltKq~ 41 (107) T COG4537 1 MKKMKKFLKHKKGFTLVEMLIVLLIISILLLLFIPNLTKQK 41 (107) T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 91677777763262599999999999999999746254437 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=71.79 E-value=4.1 Score=21.47 Aligned_cols=31 Identities=19% Similarity=0.185 Sum_probs=26.1 Q ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5023683299999999999999999999975 Q gi|254780732|r 10 LQDESGATAIEYGLLASLIAVAIIASVTTLG 40 (58) Q Consensus 10 ~~De~GaTAIEYgLIaalIav~ii~av~~lG 40 (58) -+.|.|-+-||-.+..|+++++|.+++--.- 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 >COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion] Probab=56.85 E-value=19 Score=18.17 Aligned_cols=42 Identities=36% Similarity=0.452 Sum_probs=31.4 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 236832999999999999999999999754899999999752 Q gi|254780732|r 12 DESGATAIEYGLLASLIAVAIIASVTTLGGKLTAVFADISSK 53 (58) Q Consensus 12 De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~ 53 (58) -+=|+.+++.|++|++++.+.|.....+--.+-+.+..++.- T Consensus 335 psLG~~~i~~gi~Agl~g~~~V~vfm~~~Yr~~Gvia~ial~ 376 (506) T COG0342 335 PTLGADSIKAGLIAGLIGLALVAVFMLLYYRLAGVIAAIALG 376 (506) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 454767899789999999999999999999875899999999 No 8 >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=53.65 E-value=22 Score=17.90 Aligned_cols=38 Identities=29% Similarity=0.399 Sum_probs=33.0 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68329999999999999999999997548999999997 Q gi|254780732|r 14 SGATAIEYGLLASLIAVAIIASVTTLGGKLTAVFADIS 51 (58) Q Consensus 14 ~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~ 51 (58) =|+-+||=|++|+++++++|.....+-=.+-+.+..++ 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 9 >COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion] Probab=52.65 E-value=13 Score=18.98 Aligned_cols=44 Identities=18% Similarity=0.321 Sum_probs=31.4 Q ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 950236832999999999999999999999754899999999752 Q gi|254780732|r 9 FLQDESGATAIEYGLLASLIAVAIIASVTTLGGKLTAVFADISSK 53 (58) Q Consensus 9 f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~~ 53 (58) ..+..+|.+.||- ||+-+|++.++.++..+==+....|+..++. T Consensus 8 ~~rrqrG~SLIEL-MIallIglivL~av~s~y~~sr~~y~~~~~~ 51 (318) T COG4966 8 RPRRQRGFSLIEL-MIALLIGLIVLLAVGSLYLSSRQLYTTLADR 51 (318) T ss_pred CCCCCCCCCHHHH-HHHHHHHHHHHHHHHHEEEEHHHHHHHHHHH T ss_conf 5455577439999-9999999999997763034356778877666 No 10 >TIGR00872 gnd_rel 6-phosphogluconate dehydrogenase (decarboxylating); InterPro: IPR004849 This family resembles a larger family of bacterial and eukaryotic 6-phosphogluconate dehydrogenases (Gnd) but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain Gnd, and in Aquifex aeolicus. . Probab=50.33 E-value=7.3 Score=20.23 Aligned_cols=10 Identities=50% Similarity=1.145 Sum_probs=8.1 Q ss_pred HHHHHHHHHH Q ss_conf 9999999999 Q gi|254780732|r 18 AIEYGLLASL 27 (58) Q Consensus 18 AIEYgLIaal 27 (58) -||||+++|+ T Consensus 196 GIEYG~Maai 205 (341) T TIGR00872 196 GIEYGMMAAI 205 (341) T ss_pred CCHHHHHHHH T ss_conf 5138889999 No 11 >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=49.21 E-value=24 Score=17.70 Aligned_cols=23 Identities=26% Similarity=0.567 Sum_probs=18.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 83299999999999999999999 Q gi|254780732|r 15 GATAIEYGLLASLIAVAIIASVT 37 (58) Q Consensus 15 GaTAIEYgLIaalIav~ii~av~ 37 (58) |+.+||.+++.-++.+.+.+.+. 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 12 >COG1681 FlaB Archaeal flagellins [Cell motility and secretion] Probab=40.54 E-value=28 Score=17.32 Aligned_cols=25 Identities=36% Similarity=0.567 Sum_probs=17.2 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 236832999999999999999999999 Q gi|254780732|r 12 DESGATAIEYGLLASLIAVAIIASVTT 38 (58) Q Consensus 12 De~GaTAIEYgLIaalIav~ii~av~~ 38 (58) ||+|++-||=..+ +||.++++||.+ T Consensus 1 ~rrG~~GIgtlIV--fIAmVlVAAVaA 25 (209) T COG1681 1 DRRGATGIGTLIV--FIAMVLVAAVAA 25 (209) T ss_pred CCCCCCCHHHHHH--HHHHHHHHHHHH T ss_conf 9841104328999--999999999999 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=34.07 E-value=39 Score=16.67 Aligned_cols=24 Identities=33% Similarity=0.480 Sum_probs=19.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999997548999999 Q gi|254780732|r 25 ASLIAVAIIASVTTLGGKLTAVFA 48 (58) Q Consensus 25 aalIav~ii~av~~lG~~l~~~f~ 48 (58) .|+.++.+||+|+++|+++-..=| T Consensus 282 vA~~~li~IG~VTAig~SLiaIAQ 305 (613) T TIGR01960 282 VALTVLIAIGSVTAIGASLIAIAQ 305 (613) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 899999898557888788999999 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=26.39 E-value=15 Score=18.73 Aligned_cols=14 Identities=43% Similarity=0.657 Sum_probs=11.2 Q ss_pred CCCCCCHHHHHHHH Q ss_conf 23683299999999 Q gi|254780732|r 12 DESGATAIEYGLLA 25 (58) Q Consensus 12 De~GaTAIEYgLIa 25 (58) ||+-.-|+|||+.+ T Consensus 40 ~e~~~kA~~yGi~a 53 (82) T TIGR00411 40 MEDLKKALEYGIMA 53 (82) T ss_pred CCCHHHHHHCCCCC T ss_conf 54847887516352 No 15 >PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed Probab=25.75 E-value=67 Score=15.50 Aligned_cols=40 Identities=33% Similarity=0.402 Sum_probs=29.1 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3683299999999999999999999975489999999975 Q gi|254780732|r 13 ESGATAIEYGLLASLIAVAIIASVTTLGGKLTAVFADISS 52 (58) Q Consensus 13 e~GaTAIEYgLIaalIav~ii~av~~lG~~l~~~f~~i~~ 52 (58) .-|+.+++.|++|++|+.++|.....+-=.+-+....++= T Consensus 255 tLG~~si~~g~~A~~ig~~lV~lfMi~~Yr~~G~iA~iaL 294 (741) T PRK13024 255 TLGQDAINAGIIAGIIGFALIALFMLLFYGLPGLIANIAL 294 (741) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 3109999999999999999999999999867699999999 No 16 >PRK13464 F0F1 ATP synthase subunit C; Provisional Probab=20.88 E-value=84 Score=15.02 Aligned_cols=40 Identities=33% Similarity=0.416 Sum_probs=29.2 Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999995023683299999999999999999999975489 Q gi|254780732|r 4 HIVKNFLQDESGATAIEYGLLASLIAVAIIASVTTLGGKL 43 (58) Q Consensus 4 ~~~~~f~~De~GaTAIEYgLIaalIav~ii~av~~lG~~l 43 (58) .+--+++.+-.|.|+|--|++.++=++.--.+.+.+|++. T Consensus 2 ~m~~q~la~iq~~taia~~i~igl~AlGtaiG~GllggKf 41 (101) T PRK13464 2 DMSLQVLGNLNGLTAVAVALLISLPALGTAIGFGVLGGKY 41 (101) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7659999999989999999999999998788898873488 No 17 >pfam12301 CD99L2 CD99 antigen like protein 2. This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum. Probab=20.31 E-value=75 Score=15.25 Aligned_cols=32 Identities=16% Similarity=0.296 Sum_probs=21.3 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 23683299999999999999999999975489 Q gi|254780732|r 12 DESGATAIEYGLLASLIAVAIIASVTTLGGKL 43 (58) Q Consensus 12 De~GaTAIEYgLIaalIav~ii~av~~lG~~l 43 (58) |+..-+.-|-|+|+++++.+.++.+.++..-+ T Consensus 101 ~~~~~~~~~~G~IaGIvsAv~vAl~GAvSSyi 132 (154) T pfam12301 101 DGGPEGGAETGTIAGIVSAVAVALLGAVSSYI 132 (154) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 87765565776146799999999998899999 Done!