Query gi|254780907|ref|YP_003065320.1| hypothetical protein CLIBASIA_04030 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 88 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 00:23:49 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780907.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00059 L17 ribosomal protei 54.4 3 7.6E-05 22.2 -0.4 14 1-14 84-97 (125) 2 TIGR01804 BADH betaine aldehyd 44.1 9 0.00023 19.7 0.8 25 6-38 155-179 (471) 3 pfam03346 consensus 26.7 61 0.0016 15.4 3.1 52 13-68 12-70 (369) 4 TIGR02123 TRAP_fused TRAP tran 18.9 24 0.00061 17.5 -0.7 12 30-45 537-548 (681) 5 pfam07078 FYTT Forty-two-three 18.8 70 0.0018 15.1 1.7 19 68-86 25-43 (316) 6 pfam10231 DUF2315 Uncharacteri 18.0 48 0.0012 15.9 0.7 27 20-52 1-27 (127) 7 TIGR01481 ccpA catabolite cont 15.7 77 0.002 14.9 1.3 41 36-76 137-177 (332) 8 TIGR02408 ectoine_ThpD ectoine 11.9 1E+02 0.0027 14.2 1.1 17 28-44 230-246 (278) 9 pfam10668 Phage_terminase Phag 10.7 80 0.002 14.8 0.2 17 54-70 2-18 (60) 10 pfam07771 TSGP1 Tick salivary 8.8 1.5E+02 0.0039 13.3 1.0 33 27-59 86-118 (120) No 1 >TIGR00059 L17 ribosomal protein L17; InterPro: IPR000456 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 , . Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=54.38 E-value=3 Score=22.22 Aligned_cols=14 Identities=50% Similarity=0.819 Sum_probs=11.3 Q ss_pred CCHHHHHHHHHHHH Q ss_conf 93246543046542 Q gi|254780907|r 1 MKLLFSKIAPVFAM 14 (88) Q Consensus 1 mkllfskiapvfam 14 (88) |.-||++|||.|+- T Consensus 84 ~~kLF~~iaPry~~ 97 (125) T TIGR00059 84 LNKLFSEIAPRYAQ 97 (125) T ss_pred HHHHHHHHCCCCCC T ss_conf 99876530553234 No 2 >TIGR01804 BADH betaine aldehyde dehydrogenase; InterPro: IPR011264 Under osmotic stress, betaine aldehyde dehydrogenase oxidises glycine betaine aldehyde into the osmoprotectant glycine betaine, via the second of two oxidation steps from exogenously supplied choline or betaine aldehyde. This choline-glycine betaine synthesis pathway can be found in Gram-positive and Gram-negative bacteria. In Escherichia coli, betaine aldehyde dehydrogenase (betB) is osmotically co-induced with choline dehydrogenase (betA) in the presence of choline. These dehydrogenases are located in a betaine gene cluster with the upstream choline transporter (betT) and transcriptional regulator (betI) . Similar to E. coli, betaine synthesis in Staphylococcus xylosus is also influenced by osmotic stress and the presence of choline with genes localised in a functionally equivalent gene cluster . Organisation of the betaine gene cluster in Sinorhizobium meliloti and Bacillus subtilis differs from that of E. coli by the absence of upstream choline transporter and transcriptional regulator homologues , . Additionally, Bacillus subtilis co-expresses a type II alcohol dehydrogenase with betaine aldehyde dehydrogenase instead of choline dehydrogenase as in E. coli, Staphylococcus xylosus, and Sinorhizobium meliloti . Betaine aldehyde dehydrogenase is a member of the aldehyde dehydrogenase family. ; GO: 0008802 betaine-aldehyde dehydrogenase activity, 0006578 betaine biosynthetic process. Probab=44.06 E-value=9 Score=19.72 Aligned_cols=25 Identities=48% Similarity=0.650 Sum_probs=20.5 Q ss_pred HHHHHHHHHHHHHEECCCCCCCHHHCCCCCCCC Q ss_conf 543046542001023156668022147754787 Q gi|254780907|r 6 SKIAPVFAMGTALISCDSASDPAKKSNITPIPP 38 (88) Q Consensus 6 skiapvfamgtaliscdsasdpakksnitpipp 38 (88) -|+||-.|+|.++|- |-|.+||+.- T Consensus 155 WK~APALa~Gna~v~--------KPSE~TPLta 179 (471) T TIGR01804 155 WKSAPALAAGNALVF--------KPSEITPLTA 179 (471) T ss_pred HHCCHHHHHCCCEEE--------CCCCCCHHHH T ss_conf 401457770582553--------5888773689 No 3 >pfam03346 consensus Probab=26.68 E-value=61 Score=15.39 Aligned_cols=52 Identities=38% Similarity=0.634 Sum_probs=28.4 Q ss_pred HHHHHHEECC----CCCCCHHHCCCCCCCCCCEEECCCCC---CCCCCCCCCCCCCCHHHHEE Q ss_conf 4200102315----66680221477547876431026887---54326543234500012000 Q gi|254780907|r 13 AMGTALISCD----SASDPAKKSNITPIPPAPVALAAPPK---NKTEAPKTESSNKDKAKEIT 68 (88) Q Consensus 13 amgtaliscd----sasdpakksnitpippapvalaappk---nkteapktessnkdkakeit 68 (88) .-|..|..|. |.|.|--.|..||- |-.+||-- .|.|||+.+++.-++.|++. T Consensus 12 vaglvltacsgggssgss~kpnse~tpk----vDmsAPkAeqPKkEeaPqAd~pKae~PK~~A 70 (369) T pfam03346 12 VAGLVLTACSGGGSSGSSPKPNSESTPK----VDMSAPKAEQPKKEEAPQADSPKAEKPKSIA 70 (369) T ss_pred HHHHEEEECCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHC T ss_conf 7644255114788888899998777875----4555765668642226656686333750007 No 4 >TIGR02123 TRAP_fused TRAP transporter, 4TM/12TM fusion protein; InterPro: IPR011853 In some species, the 12-transmembrane spanning and 4-transmembrane spanning components of tripartite ATP-independent periplasmic (TRAP)-type transporters are fused. This entry describes such transporters, found in the archaea and in bacteria.. Probab=18.94 E-value=24 Score=17.52 Aligned_cols=12 Identities=75% Similarity=1.041 Sum_probs=7.0 Q ss_pred HCCCCCCCCCCEEECC Q ss_conf 1477547876431026 Q gi|254780907|r 30 KSNITPIPPAPVALAA 45 (88) Q Consensus 30 ksnitpippapvalaa 45 (88) -||||| |||||| T Consensus 537 ~a~iTP----PVALAA 548 (681) T TIGR02123 537 LADITP----PVALAA 548 (681) T ss_pred HHCCCC----CHHHHH T ss_conf 604884----179999 No 5 >pfam07078 FYTT Forty-two-three protein. This family consists of several mammalian proteins of around 320 residues in length called 40-2-3 proteins. The function of this family is unknown. Probab=18.83 E-value=70 Score=15.10 Aligned_cols=19 Identities=42% Similarity=0.646 Sum_probs=9.6 Q ss_pred EHHHHHHHHHHHHHHHHHC Q ss_conf 0132201035530003420 Q gi|254780907|r 68 TLDIIDLGIDLLTKEDKKE 86 (88) Q Consensus 68 tldiidlgidlltkedkke 86 (88) ++|-||...|-.-|-.||| T Consensus 25 ~~dKiDMSLDDIIkLNKkE 43 (316) T pfam07078 25 NLDKIDMSLDDIIKLNRKE 43 (316) T ss_pred CHHHHCCCHHHHHHHHHHH T ss_conf 1444215689998753676 No 6 >pfam10231 DUF2315 Uncharacterized conserved protein (DUF2315). This is a family of small conserved proteins found from worms to humans. The function is not known. Probab=18.03 E-value=48 Score=15.93 Aligned_cols=27 Identities=37% Similarity=0.469 Sum_probs=19.8 Q ss_pred ECCCCCCCHHHCCCCCCCCCCEEECCCCCCCCC Q ss_conf 315666802214775478764310268875432 Q gi|254780907|r 20 SCDSASDPAKKSNITPIPPAPVALAAPPKNKTE 52 (88) Q Consensus 20 scdsasdpakksnitpippapvalaappknkte 52 (88) |||-..-|-..|||-||--. .|.|.|+ T Consensus 1 s~D~igPPd~~SNlRPi~~~------~~~nEt~ 27 (127) T pfam10231 1 SHDWIGPPDPQSNLRPIVLH------IPENETP 27 (127) T ss_pred CCCCCCCCCCCCCCCCEECC------CCCCCCH T ss_conf 98867999941246531102------7999988 No 7 >TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377 Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription. Probab=15.70 E-value=77 Score=14.88 Aligned_cols=41 Identities=29% Similarity=0.432 Sum_probs=31.9 Q ss_pred CCCCCEEECCCCCCCCCCCCCCCCCCCHHHHEEHHHHHHHH Q ss_conf 78764310268875432654323450001200013220103 Q gi|254780907|r 36 IPPAPVALAAPPKNKTEAPKTESSNKDKAKEITLDIIDLGI 76 (88) Q Consensus 36 ippapvalaappknkteapktessnkdkakeitldiidlgi 76 (88) --|+||-||+---.+.+-|--.---+.-+||++...|+-|- T Consensus 137 rs~~PVVLAGt~D~~~~~pSVNIDy~~A~kEav~~l~~~Gh 177 (332) T TIGR01481 137 RSPVPVVLAGTVDKENELPSVNIDYKQATKEAVKELIAKGH 177 (332) T ss_pred CCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC T ss_conf 28998899535486546773101678999999999863358 No 8 >TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774 Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups. Probab=11.95 E-value=1e+02 Score=14.18 Aligned_cols=17 Identities=47% Similarity=0.608 Sum_probs=13.3 Q ss_pred HHHCCCCCCCCCCEEEC Q ss_conf 22147754787643102 Q gi|254780907|r 28 AKKSNITPIPPAPVALA 44 (88) Q Consensus 28 akksnitpippapvala 44 (88) .-.|||||.|-+-|-+. T Consensus 230 GSgsNItP~pRsNVF~V 246 (278) T TIGR02408 230 GSGSNITPYPRSNVFLV 246 (278) T ss_pred CCCCCCCCCCCCCEEEE T ss_conf 78888887543452678 No 9 >pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit. Probab=10.72 E-value=80 Score=14.80 Aligned_cols=17 Identities=35% Similarity=0.542 Sum_probs=13.0 Q ss_pred CCCCCCCCCHHHHEEHH Q ss_conf 54323450001200013 Q gi|254780907|r 54 PKTESSNKDKAKEITLD 70 (88) Q Consensus 54 pktessnkdkakeitld 70 (88) |...|.|.|+|+||-++ T Consensus 2 aR~RsP~RDkA~eiy~~ 18 (60) T pfam10668 2 ARQRSPDRDKAKEMWKE 18 (60) T ss_pred CCCCCCCHHHHHHHHHH T ss_conf 88889578899999998 No 10 >pfam07771 TSGP1 Tick salivary peptide group 1. This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis. Also present are peptides from a related tick species, Ixodes ricinus. They are characterized by a putative signal peptide indicative of secretion and conserved cysteine residues. Probab=8.81 E-value=1.5e+02 Score=13.32 Aligned_cols=33 Identities=24% Similarity=0.363 Sum_probs=13.6 Q ss_pred CHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCC Q ss_conf 022147754787643102688754326543234 Q gi|254780907|r 27 PAKKSNITPIPPAPVALAAPPKNKTEAPKTESS 59 (88) Q Consensus 27 pakksnitpippapvalaappknkteapktess 59 (88) |..-..-+|-|+...--..--..|++.||++|. T Consensus 86 P~~~~d~~~~pte~~k~kkkK~~k~k~~k~~s~ 118 (120) T pfam07771 86 PSHPDDHPPEPTEKPKKKKKKSKKTKKPKKSSK 118 (120) T ss_pred CCCCCCCCCCCCCCHHHHHHCHHHHHCCCHHHC T ss_conf 888243888887652333303344312202223 Done!