Query 537021.9.peg.759_1 Match_columns 58 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Wed May 25 08:01:29 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_759.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG3417 FlgN Collagen-binding 28.1 23 0.00059 18.4 0.7 14 8-21 180-193 (200) 2 TIGR02722 lp_ uncharacterized 24.0 30 0.00076 17.9 0.7 17 5-21 193-209 (215) 3 pfam07823 CPDase Cyclic phosph 18.9 97 0.0025 15.3 2.4 24 9-32 76-99 (192) 4 pfam06801 consensus 15.8 51 0.0013 16.7 0.4 10 38-47 6-15 (96) 5 COG3445 Acid-induced glycyl ra 15.8 77 0.002 15.8 1.3 19 12-30 47-65 (127) 6 TIGR00418 thrS threonyl-tRNA s 15.3 69 0.0018 16.0 1.0 24 30-53 9-32 (595) 7 KOG3703 consensus 14.1 34 0.00085 17.6 -0.9 37 17-56 646-682 (873) 8 TIGR01050 rpsS_bact ribosomal 13.4 1.1E+02 0.0029 14.9 1.7 21 18-39 56-86 (92) 9 COG0194 Gmk Guanylate kinase [ 13.4 1.2E+02 0.003 14.9 1.7 43 15-57 67-110 (191) 10 TIGR00340 zpr1_rel zinc finger 13.2 1.4E+02 0.0037 14.4 2.1 28 3-30 61-88 (168) No 1 >COG3417 FlgN Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only] Probab=28.12 E-value=23 Score=18.40 Aligned_cols=14 Identities=43% Similarity=0.776 Sum_probs=10.4 Q ss_pred HHEECCCCCEEEEE Q ss_conf 01101057424668 Q 537021.9.peg.7 8 LLIRRTTGEIEWQE 21 (58) Q Consensus 8 llirrttgeiewqe 21 (58) -|+-+.||||.|-. T Consensus 180 ~Lm~~qTGeIvWsd 193 (200) T COG3417 180 QLMLVQTGEIVWSD 193 (200) T ss_pred EEEEECCEEEEECC T ss_conf 66640210499747 No 2 >TIGR02722 lp_ uncharacterized lipoprotein; InterPro: IPR014094 Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby.. Probab=23.97 E-value=30 Score=17.86 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=12.3 Q ss_pred HHHHHEECCCCCEEEEE Q ss_conf 32001101057424668 Q 537021.9.peg.7 5 IAALLIRRTTGEIEWQE 21 (58) Q Consensus 5 iaallirrttgeiewqe 21 (58) +..-|.-..||||+|+. T Consensus 193 ~~l~Lmd~~TGli~W~d 209 (215) T TIGR02722 193 FTLRLMDLKTGLIVWSD 209 (215) T ss_pred EEEEECCCCCCCEEECC T ss_conf 13543135465268658 No 3 >pfam07823 CPDase Cyclic phosphodiesterase-like protein. Cyclic phosphodiesterase (CPDase) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft. Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site. Probab=18.87 E-value=97 Score=15.28 Aligned_cols=24 Identities=33% Similarity=0.584 Sum_probs=20.0 Q ss_pred HEECCCCCEEEEEEEEEECCCCCH Q ss_conf 110105742466899995588520 Q 537021.9.peg.7 9 LIRRTTGEIEWQEVYIEFSPTPTD 32 (58) Q Consensus 9 lirrttgeiewqevyiefsptptd 32 (58) +-+-++|..-+|-||+++.|||.= T Consensus 76 ~~~V~~G~~yfq~vYl~ve~tp~L 99 (192) T pfam07823 76 FDGVSSGDSYFQKVYLEVEPTPEL 99 (192) T ss_pred ECCEECCCEEEEEEEEEECCCHHH T ss_conf 431403776888999995599789 No 4 >pfam06801 consensus Probab=15.85 E-value=51 Score=16.67 Aligned_cols=10 Identities=60% Similarity=1.115 Sum_probs=6.9 Q ss_pred CCCEEEEEEE Q ss_conf 8632799999 Q 537021.9.peg.7 38 PDEKFAIFFL 47 (58) Q Consensus 38 pdekfaiffl 47 (58) ..-||||||. T Consensus 6 semkfaiffv 15 (96) T pfam06801 6 SEMKFAIFFV 15 (96) T ss_pred CCCEEEEEHH T ss_conf 5312533015 No 5 >COG3445 Acid-induced glycyl radical enzyme [General function prediction only] Probab=15.78 E-value=77 Score=15.77 Aligned_cols=19 Identities=37% Similarity=0.642 Sum_probs=16.0 Q ss_pred CCCCCEEEEEEEEEECCCC Q ss_conf 1057424668999955885 Q 537021.9.peg.7 12 RTTGEIEWQEVYIEFSPTP 30 (58) Q Consensus 12 rttgeiewqevyiefsptp 30 (58) ..-|+||+.||-+|..|+- T Consensus 47 s~lgqieyrevp~ev~p~v 65 (127) T COG3445 47 SKLGQIEYREVPVEVKPEV 65 (127) T ss_pred HHCCCEEEEECCEECCCEE T ss_conf 2236246543323037606 No 6 >TIGR00418 thrS threonyl-tRNA synthetase; InterPro: IPR002320 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 . Threonyl-tRNA synthetase (188.8.131.52 from EC) exists as a monomer and belongs to class IIa. The enzyme from Escherichia coli represses the translation of its own mRNA. The crystal structure of the complex between tRNA(Thr) and ThrRS show structural features that reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination . The zinc ion may act to ensure that only amino acids that possess a hydroxyl group attached to the beta-position are activated .; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006435 threonyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=15.26 E-value=69 Score=16.02 Aligned_cols=24 Identities=38% Similarity=0.538 Sum_probs=20.0 Q ss_pred CCHHHCCCCCCEEEEEEECHHHHH Q ss_conf 520100398632799999446655 Q 537021.9.peg.7 30 PTDFKNHYPDEKFAIFFLNEEGFK 53 (58) Q Consensus 30 ptdfknhypdekfaifflneegfk 53 (58) ....|.-||+++|++|-..|.||- T Consensus 9 ~~a~k~~~~~~~~~~gp~~e~GFy 32 (595) T TIGR00418 9 AEAVKQLYPDVKLAVGPVIEDGFY 32 (595) T ss_pred HHHHHHCCCCCEEEEECCCCCCCC T ss_conf 899970478718998255478754 No 7 >KOG3703 consensus Probab=14.05 E-value=34 Score=17.59 Aligned_cols=37 Identities=35% Similarity=0.667 Sum_probs=29.8 Q ss_pred EEEEEEEEEECCCCCHHHCCCCCCEEEEEEECHHHHHHHC Q ss_conf 2466899995588520100398632799999446655310 Q 537021.9.peg.7 17 IEWQEVYIEFSPTPTDFKNHYPDEKFAIFFLNEEGFKQAK 56 (58) Q Consensus 17 iewqevyiefsptptdfknhypdekfaifflneegfkqak 56 (58) |+| |.+|-|.|+.-...+-=||-|-+|-+|+.-|+|. T Consensus 646 idW---YMdfFP~psn~~tdf~FEKSAtYFdse~aPkraa 682 (873) T KOG3703 646 IDW---YMDFFPVPSNTTTDFLFEKSATYFDSEVAPKRAA 682 (873) T ss_pred HHH---HHHCCCCCCCCCCHHEEECCCCCCCCCCCCHHHH T ss_conf 114---7761778765553000211321237754530234 No 8 >TIGR01050 rpsS_bact ribosomal protein S19; InterPro: IPR005732 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The small ribosomal subunit protein S19 contains 88-144 amino acid residues. In Escherichia coli, S19 is known to form a complex with S13 that binds strongly to 16S ribosomal RNA. Experimental evidence has revealed that S19 is moderately exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=13.42 E-value=1.1e+02 Score=14.92 Aligned_cols=21 Identities=52% Similarity=0.877 Sum_probs=15.0 Q ss_pred EEEEEEE----------EECCCCCHHHCCCCC Q ss_conf 4668999----------955885201003986 Q 537021.9.peg.7 18 EWQEVYI----------EFSPTPTDFKNHYPD 39 (58) Q Consensus 18 ewqevyi----------efsptptdfknhypd 39 (58) .|-.||| ||+||-+ |+.|--+ T Consensus 56 ~~ipvyi~e~mVGhKLGEFapTR~-f~~H~~~ 86 (92) T TIGR01050 56 KFIPVYITEEMVGHKLGEFAPTRT-FKGHAKS 86 (92) T ss_pred EEEEEEEECCCCCCCCCCCCCCCC-CCCCCCC T ss_conf 674268603312420167554334-2345423 No 9 >COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism] Probab=13.39 E-value=1.2e+02 Score=14.86 Aligned_cols=43 Identities=23% Similarity=0.226 Sum_probs=28.4 Q ss_pred CCEEEEEEEEEECCCCCHHHCCCCCC-EEEEEEECHHHHHHHCC Q ss_conf 74246689999558852010039863-27999994466553106 Q 537021.9.peg.7 15 GEIEWQEVYIEFSPTPTDFKNHYPDE-KFAIFFLNEEGFKQAKN 57 (58) Q Consensus 15 geiewqevyiefsptptdfknhypde-kfaifflneegfkqakn 57 (58) .=+||.+++-.+.-||...-..-.++ +..|+=..-.|.+|.|+ T Consensus 67 ~fLE~a~~~gnyYGT~~~~ve~~~~~G~~vildId~qGa~qvk~ 110 (191) T COG0194 67 EFLEWAEYHGNYYGTSREPVEQALAEGKDVILDIDVQGALQVKK 110 (191) T ss_pred CCEEEEEECCCCCCCCHHHHHHHHHCCCEEEEEEEHHHHHHHHH T ss_conf 74788777197324868899999866990899985399999997 No 10 >TIGR00340 zpr1_rel zinc finger protein ZPR1 homolog; InterPro: IPR004470 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents ZPR1-type zinc finger domains. ZPR1 was shown experimentally to bind approximately two moles of zinc, and has two copies of a domain homologous to this protein, each containing a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this family by analogy may be suggested to play a role in signal transduction as proven for other Z-finger binding proteins. Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding. Probab=13.21 E-value=1.4e+02 Score=14.42 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=0.0 Q ss_pred CHHHHHHEECCCCCEEEEEEEEEECCCC Q ss_conf 0132001101057424668999955885 Q 537021.9.peg.7 3 KDIAALLIRRTTGEIEWQEVYIEFSPTP 30 (58) Q Consensus 3 kdiaallirrttgeiewqevyiefsptp 30 (58) +|+.|+.+|-+.|.|.-.|.=|.--|.| T Consensus 61 ~dL~t~V~RS~~a~I~IPElG~~IEPgp 88 (168) T TIGR00340 61 EDLFTRVVRSKSATIRIPELGIKIEPGP 88 (168) T ss_pred CCCCEEEEEECCCEEEEEEEEEEECCCC T ss_conf 9871127850457165112125779734 Done!