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!