Query gi|254781139|ref|YP_003065552.1| hypothetical protein CLIBASIA_05205 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 65 No_of_seqs 3 out of 5 Neff 1.5 Searched_HMMs 39220 Date Mon May 30 06:01:24 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781139.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 KOG2544 consensus 31.3 21 0.00052 18.5 0.9 33 12-44 665-697 (711) 2 TIGR00469 pheS_mito phenylalan 18.9 34 0.00088 17.4 0.1 26 31-56 106-132 (460) 3 PRK10202 ebgC cryptic beta-D-g 13.4 42 0.0011 16.9 -0.5 33 7-44 13-45 (149) 4 cd03591 CLECT_collectin_like C 12.8 1.1E+02 0.0028 14.7 1.5 30 29-58 22-51 (114) 5 pfam06869 DUF1258 Protein of u 10.4 1.5E+02 0.0037 14.1 1.4 31 32-62 74-104 (258) 6 pfam06212 GRIM-19 GRIM-19 prot 10.3 58 0.0015 16.2 -0.7 31 15-55 62-92 (130) 7 TIGR00505 ribA GTP cyclohydrol 9.8 1.2E+02 0.0031 14.5 0.9 19 27-45 50-71 (227) 8 PRK03600 nrdI ribonucleotide r 9.6 1.1E+02 0.0029 14.7 0.6 15 44-58 60-74 (136) 9 PRK02551 hypothetical protein; 9.4 1E+02 0.0026 14.9 0.3 16 43-58 80-95 (154) 10 COG5269 ZUO1 Ribosome-associat 9.2 99 0.0025 15.0 0.2 18 43-63 164-181 (379) No 1 >KOG2544 consensus Probab=31.31 E-value=21 Score=18.54 Aligned_cols=33 Identities=21% Similarity=0.403 Sum_probs=28.1 Q ss_pred HHHHCCEEEEHHCCHHHHCCCCEEEEECCCCHH Q ss_conf 643154100010004222056812011254078 Q gi|254781139|r 12 RKKNRDWQRIASIPVSILKDSHLLQAHTEGDDV 44 (65) Q Consensus 12 r~~~~dW~rvASiPlnvah~~~LvqAHsEGDD~ 44 (65) -++.|||..+|++.-.|+.+++.|+.|.--+-. T Consensus 665 ~akdRd~aT~A~Vta~Il~Ga~ivRVHdvk~~s 697 (711) T KOG2544 665 EAKDRDAATVACVTAGILFGANIVRVHDVKNNS 697 (711) T ss_pred CHHHHCCHHHHHHHHHHCCCCCEEEEEECHHHH T ss_conf 833301045665656650575259984012346 No 2 >TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=18.94 E-value=34 Score=17.37 Aligned_cols=26 Identities=38% Similarity=0.728 Sum_probs=20.0 Q ss_pred CCCEEEEECCCCHH-HHHHHHCCCCCC Q ss_conf 56812011254078-999970266641 Q gi|254781139|r 31 DSHLLQAHTEGDDV-WVNKWLNNRDNA 56 (65) Q Consensus 31 ~~~LvqAHsEGDD~-~VkrwLNn~DNr 56 (65) ..||+||||-.-.+ ...+-+||+||- T Consensus 106 ~~HLLR~HT~AH~~E~~~~~~~~sdni 132 (460) T TIGR00469 106 ETHLLRAHTSAHELELISKILDDSDNI 132 (460) T ss_pred CCHHHHHCCCHHHHHHHHCCCCCCCCC T ss_conf 300333302134545442223532111 No 3 >PRK10202 ebgC cryptic beta-D-galactosidase subunit beta; Reviewed Probab=13.43 E-value=42 Score=16.90 Aligned_cols=33 Identities=27% Similarity=0.299 Sum_probs=21.9 Q ss_pred HHHHHHHHHCCEEEEHHCCHHHHCCCCEEEEECCCCHH Q ss_conf 66666643154100010004222056812011254078 Q gi|254781139|r 7 CAMATRKKNRDWQRIASIPVSILKDSHLLQAHTEGDDV 44 (65) Q Consensus 7 cama~r~~~~dW~rvASiPlnvah~~~LvqAHsEGDD~ 44 (65) |--.-|||+|--..|++|+ |+..+ -+||-||+- T Consensus 13 ~yr~grkW~R~~EaI~~i~-~~~~g----v~ysIGDsl 45 (149) T PRK10202 13 IYASGKKWQRCVEAIENID-NIQPG----VAHSIGDSL 45 (149) T ss_pred ECCCCHHHHHHHHHHHHHC-CCCCC----CEEECCCEE T ss_conf 0267378999999986121-36877----468727747 No 4 >cd03591 CLECT_collectin_like C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CLECT_collectin_like: C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CTLDs of these collectins bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, or apoptotic cells) and mediate functions associated with killing and phagocytosis. MBPs recognize high mannose oligosaccharides in a calcium dependent manner, bind to a broad range of pathogens, and trigger cell killing by activating the complement pathway. MBP also acts directly as an opsonin. SP-A and SP-D in addition to functioning as host defense components, a Probab=12.84 E-value=1.1e+02 Score=14.74 Aligned_cols=30 Identities=3% Similarity=0.188 Sum_probs=23.9 Q ss_pred HCCCCEEEEECCCCHHHHHHHHCCCCCCEE Q ss_conf 205681201125407899997026664100 Q gi|254781139|r 29 LKDSHLLQAHTEGDDVWVNKWLNNRDNASW 58 (65) Q Consensus 29 ah~~~LvqAHsEGDD~~VkrwLNn~DNraW 58 (65) ..+.+|+.-+|+....++..++.......| T Consensus 22 ~~gg~La~i~s~~e~~~l~~~~~~~~~~~w 51 (114) T cd03591 22 EAGGTLAMPRNAAENAAIASYVKKGNTYAF 51 (114) T ss_pred HCCCEECCCCCHHHHHHHHHHHHCCCCCEE T ss_conf 769999363999999999998616797489 No 5 >pfam06869 DUF1258 Protein of unknown function (DUF1258). This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to C. elegans. Note that this family contains a number of conserved cysteine and histidine residues. Probab=10.41 E-value=1.5e+02 Score=14.12 Aligned_cols=31 Identities=23% Similarity=0.474 Sum_probs=24.6 Q ss_pred CCEEEEECCCCHHHHHHHHCCCCCCEEHHCC Q ss_conf 6812011254078999970266641000023 Q gi|254781139|r 32 SHLLQAHTEGDDVWVNKWLNNRDNASWRTSE 62 (65) Q Consensus 32 ~~LvqAHsEGDD~~VkrwLNn~DNraWRt~E 62 (65) ++.-..|.-+..-|-++|++..||.-|-+++ T Consensus 74 eg~n~~h~l~spffsk~~~~Es~n~l~ls~~ 104 (258) T pfam06869 74 EGRNSSHNLNSPFFSKKWLSESDNHLWLSTV 104 (258) T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCEEEEEEE T ss_conf 4787667656467766665407660578889 No 6 >pfam06212 GRIM-19 GRIM-19 protein. This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-# and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity. Probab=10.31 E-value=58 Score=16.18 Aligned_cols=31 Identities=26% Similarity=0.352 Sum_probs=23.7 Q ss_pred HCCEEEEHHCCHHHHCCCCEEEEECCCCHHHHHHHHCCCCC Q ss_conf 15410001000422205681201125407899997026664 Q gi|254781139|r 15 NRDWQRIASIPVSILKDSHLLQAHTEGDDVWVNKWLNNRDN 55 (65) Q Consensus 15 ~~dW~rvASiPlnvah~~~LvqAHsEGDD~~VkrwLNn~DN 55 (65) ..-|.|+|-+|+-. | |.|-+|++++.-|.+. T Consensus 62 E~~~aR~al~PlLq--------A--E~DR~~lr~~~~~~~~ 92 (130) T pfam06212 62 EDRSARNAILPLLQ--------A--ERDRRYLKQLRRNREE 92 (130) T ss_pred HHHHHHHHHHHHHH--------H--HHHHHHHHHHHHHHHH T ss_conf 99998999999998--------7--9999999999993999 No 7 >TIGR00505 ribA GTP cyclohydrolase II; InterPro: IPR000926 GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin. The enzyme converts GTP and water to formate, 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)- pyrimidine and pyrophosphate, and requires magnesium as a cofactor. It is sometimes found as a bifunctional enzyme with 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP_synthase) IPR000422 from INTERPRO. ; GO: 0003935 GTP cyclohydrolase II activity, 0009231 riboflavin biosynthetic process. Probab=9.81 E-value=1.2e+02 Score=14.50 Aligned_cols=19 Identities=32% Similarity=0.494 Sum_probs=13.9 Q ss_pred HHHCCCCEEEEECC---CCHHH Q ss_conf 22205681201125---40789 Q gi|254781139|r 27 SILKDSHLLQAHTE---GDDVW 45 (65) Q Consensus 27 nvah~~~LvqAHsE---GDD~~ 45 (65) +-+|..-|||-||| ||--| T Consensus 50 ~~a~~~~LvRiHSECLTGd~l~ 71 (227) T TIGR00505 50 SDAHNDVLVRIHSECLTGDALH 71 (227) T ss_pred CCCCCCEEEEEECCHHHHHHHH T ss_conf 3566880378831100222211 No 8 >PRK03600 nrdI ribonucleotide reductase stimulatory protein; Reviewed Probab=9.65 E-value=1.1e+02 Score=14.71 Aligned_cols=15 Identities=27% Similarity=0.355 Sum_probs=12.7 Q ss_pred HHHHHHHCCCCCCEE Q ss_conf 899997026664100 Q gi|254781139|r 44 VWVNKWLNNRDNASW 58 (65) Q Consensus 44 ~~VkrwLNn~DNraW 58 (65) .-|.+|||+.+|+.+ T Consensus 60 ~~v~~FL~~~~N~~~ 74 (136) T PRK03600 60 KQVIRFLNDEHNRKL 74 (136) T ss_pred HHHHHHHHCCCCHHH T ss_conf 899998837303546 No 9 >PRK02551 hypothetical protein; Provisional Probab=9.38 E-value=1e+02 Score=14.89 Aligned_cols=16 Identities=13% Similarity=0.225 Sum_probs=12.6 Q ss_pred HHHHHHHHCCCCCCEE Q ss_conf 7899997026664100 Q gi|254781139|r 43 DVWVNKWLNNRDNASW 58 (65) Q Consensus 43 D~~VkrwLNn~DNraW 58 (65) ..-|.+|||+.+||+. T Consensus 80 ~~~v~~FLn~~~Nr~~ 95 (154) T PRK02551 80 TTPLGEFIAYHNNAQR 95 (154) T ss_pred CHHHHHHHCCHHHHHH T ss_conf 3679988455554754 No 10 >COG5269 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones] Probab=9.21 E-value=99 Score=14.99 Aligned_cols=18 Identities=39% Similarity=0.671 Sum_probs=11.4 Q ss_pred HHHHHHHHCCCCCCEEHHCCC Q ss_conf 789999702666410000237 Q gi|254781139|r 43 DVWVNKWLNNRDNASWRTSEG 63 (65) Q Consensus 43 D~~VkrwLNn~DNraWRt~EG 63 (65) +-|-.-|-| -+||||||- T Consensus 164 e~FY~FW~n---FdSWRtFE~ 181 (379) T COG5269 164 EEFYEFWSN---FDSWRTFEP 181 (379) T ss_pred HHHHHHHHH---CCCCCCCCC T ss_conf 999999970---342103540 Done!