Query gi|255764475|ref|YP_003084341.1| hypothetical protein CLIBASIA_03592 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 59 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 29 17:11:41 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 255764475.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01524 ATPase-IIIB_Mg magne 39.8 14 0.00037 18.7 1.3 31 20-51 841-877 (892) 2 PRK06569 F0F1 ATP synthase sub 33.0 46 0.0012 15.9 3.7 29 30-58 6-34 (157) 3 TIGR02842 CyoC cytochrome o ub 28.9 49 0.0013 15.7 2.5 17 33-49 71-87 (180) 4 PRK09174 F0F1 ATP synthase sub 28.0 56 0.0014 15.4 3.8 31 28-58 47-77 (204) 5 pfam12062 HSNSD heparan sulfat 26.5 33 0.00084 16.7 1.3 12 42-53 129-140 (487) 6 TIGR02808 short_TIGR02808 cons 26.0 29 0.00075 17.0 1.0 10 30-39 14-23 (42) 7 TIGR01113 mtrE tetrahydrometha 25.0 29 0.00074 17.0 0.8 10 24-33 157-166 (298) 8 pfam04206 MtrE Tetrahydrometha 21.7 38 0.00097 16.4 0.8 17 22-42 151-167 (269) 9 PRK00972 tetrahydromethanopter 20.2 43 0.0011 16.1 0.8 19 20-42 155-173 (293) 10 pfam10798 YmgB Biofilm develop 16.5 85 0.0022 14.4 1.7 14 31-44 21-34 (60) No 1 >TIGR01524 ATPase-IIIB_Mg magnesium-translocating P-type ATPase; InterPro: IPR006415 This group describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms . These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis .; GO: 0015444 magnesium-importing ATPase activity, 0015693 magnesium ion transport, 0016021 integral to membrane. Probab=39.84 E-value=14 Score=18.69 Aligned_cols=31 Identities=42% Similarity=0.754 Sum_probs=17.4 Q ss_pred EEEEECCC-----CHHHHHHH-HHHHHHHHHHHHHHHH Q ss_conf 38970477-----21788769-9999999999988789 Q gi|255764475|r 20 VQISIPFP-----MPIVAMPA-IILWLIITLLRGYCRE 51 (59) Q Consensus 20 vqisipfp-----mpivampa-iilwliitllrgycre 51 (59) +-|+|||. .-..+.|. -.-|||.+|+ |||-- T Consensus 841 ~Gi~iPFsplg~~~gl~~LPlSYFPWLiaiLv-gYm~~ 877 (892) T TIGR01524 841 VGIIIPFSPLGASVGLEALPLSYFPWLIAILV-GYMLV 877 (892) T ss_pred HHHHCCCCCHHHHHCCCCCCCCHHHHHHHHHH-HHHHH T ss_conf 44213751002321022588750079999999-99999 No 2 >PRK06569 F0F1 ATP synthase subunit B'; Validated Probab=33.02 E-value=46 Score=15.89 Aligned_cols=29 Identities=28% Similarity=0.420 Sum_probs=21.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 78876999999999999887899987642 Q gi|255764475|r 30 IVAMPAIILWLIITLLRGYCREYIIFLSR 58 (59) Q Consensus 30 ivampaiilwliitllrgycreyiiflsr 58 (59) ..-.|.-+.||++|+.--|.--.-+++.| T Consensus 6 ~~~~~sQifWL~itF~~ly~~~sk~~lPr 34 (157) T PRK06569 6 IATYYSQIFWLIVTFGLLYIFVYKFITPK 34 (157) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 22408999999999999999999998604 No 3 >TIGR02842 CyoC cytochrome o ubiquinol oxidase, subunit III; InterPro: IPR014206 This entry represents subunit 3 (CyoC) of the cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilise cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant.. Probab=28.85 E-value=49 Score=15.72 Aligned_cols=17 Identities=47% Similarity=0.804 Sum_probs=14.5 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 76999999999999887 Q gi|255764475|r 33 MPAIILWLIITLLRGYC 49 (59) Q Consensus 33 mpaiilwliitllrgyc 49 (59) ...++.||.||.+=|-| T Consensus 71 ~~~v~~WL~iTF~LG~~ 87 (180) T TIGR02842 71 KKKVILWLAITFLLGLG 87 (180) T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 76899999999999999 No 4 >PRK09174 F0F1 ATP synthase subunit B'; Validated Probab=28.03 E-value=56 Score=15.41 Aligned_cols=31 Identities=26% Similarity=0.299 Sum_probs=22.3 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 2178876999999999999887899987642 Q gi|255764475|r 28 MPIVAMPAIILWLIITLLRGYCREYIIFLSR 58 (59) Q Consensus 28 mpivampaiilwliitllrgycreyiiflsr 58 (59) +-....|.-|.||+|++.-.|---.-+++.| T Consensus 47 ld~~t~~sQifWL~I~F~~lY~~~sk~~lPr 77 (204) T PRK09174 47 FDSTHYASQLLWLAITFGLFYLFLSRVILPR 77 (204) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9834508999999999999999999997603 No 5 >pfam12062 HSNSD heparan sulfate-N-deacetylase. This family of proteins is are heparan sulfate N-deacetylase enzymes. This protein is found in eukaryotes. This proteinenzyme is often found associated with pfam00685. Probab=26.48 E-value=33 Score=16.70 Aligned_cols=12 Identities=50% Similarity=0.916 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHH Q ss_conf 999998878999 Q gi|255764475|r 42 ITLLRGYCREYI 53 (59) Q Consensus 42 itllrgycreyi 53 (59) -.||.-|||||- T Consensus 129 R~LLDKYC~ey~ 140 (487) T pfam12062 129 RELLDKYCKEYG 140 (487) T ss_pred HHHHHHHHHHHC T ss_conf 999999999728 No 6 >TIGR02808 short_TIGR02808 conserved hypothetical protein TIGR02808; InterPro: IPR014175 This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966.. Probab=26.02 E-value=29 Score=16.97 Aligned_cols=10 Identities=60% Similarity=0.750 Sum_probs=7.0 Q ss_pred HHHHHHHHHH Q ss_conf 7887699999 Q gi|255764475|r 30 IVAMPAIILW 39 (59) Q Consensus 30 ivampaiilw 39 (59) --|||.|+|= T Consensus 14 Y~AMP~I~L~ 23 (42) T TIGR02808 14 YAAMPVIILS 23 (42) T ss_pred HHHHHHHHHH T ss_conf 6655799998 No 7 >TIGR01113 mtrE tetrahydromethanopterin S-methyltransferase, subunit E; InterPro: IPR005780 This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump.5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0006814 sodium ion transport, 0005737 cytoplasm, 0012506 vesicle membrane. Probab=25.03 E-value=29 Score=17.01 Aligned_cols=10 Identities=50% Similarity=1.338 Sum_probs=8.6 Q ss_pred ECCCCHHHHH Q ss_conf 0477217887 Q gi|255764475|r 24 IPFPMPIVAM 33 (59) Q Consensus 24 ipfpmpivam 33 (59) -|||.|..|+ T Consensus 157 HPFPLPllA~ 166 (298) T TIGR01113 157 HPFPLPLLAL 166 (298) T ss_pred CCCCHHHHHH T ss_conf 9973688999 No 8 >pfam04206 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. Probab=21.74 E-value=38 Score=16.35 Aligned_cols=17 Identities=47% Similarity=1.187 Sum_probs=12.6 Q ss_pred EEECCCCHHHHHHHHHHHHHH Q ss_conf 970477217887699999999 Q gi|255764475|r 22 ISIPFPMPIVAMPAIILWLII 42 (59) Q Consensus 22 isipfpmpivampaiilwlii 42 (59) +.-|||+|++++ +|=|. T Consensus 151 l~hPFplPlla~----iwGit 167 (269) T pfam04206 151 LKHPFPLPLLAM----IWGIT 167 (269) T ss_pred HCCCCCHHHHHH----HHHHH T ss_conf 059975159999----99884 No 9 >PRK00972 tetrahydromethanopterin S-methyltransferase subunit E; Provisional Probab=20.20 E-value=43 Score=16.07 Aligned_cols=19 Identities=42% Similarity=1.097 Sum_probs=13.1 Q ss_pred EEEEECCCCHHHHHHHHHHHHHH Q ss_conf 38970477217887699999999 Q gi|255764475|r 20 VQISIPFPMPIVAMPAIILWLII 42 (59) Q Consensus 20 vqisipfpmpivampaiilwlii 42 (59) +-+.-|||+|++++ +|=|. T Consensus 155 ~~l~hPFPlPlla~----iwGIt 173 (293) T PRK00972 155 VALGHPFPLPLLAL----IWGIT 173 (293) T ss_pred HHCCCCCCHHHHHH----HHHHH T ss_conf 86069975259999----99885 No 10 >pfam10798 YmgB Biofilm development protein YmgB/AriR. YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid which indicates that YmgB has an important function in acid-resistance. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole). Probab=16.46 E-value=85 Score=14.43 Aligned_cols=14 Identities=50% Similarity=0.472 Sum_probs=10.6 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 88769999999999 Q gi|255764475|r 31 VAMPAIILWLIITL 44 (59) Q Consensus 31 vampaiilwliitl 44 (59) |.-.+||+|||-.| T Consensus 21 vtNK~IIl~LI~~L 34 (60) T pfam10798 21 VSNKDIILKLIHKL 34 (60) T ss_pred CCHHHHHHHHHHHH T ss_conf 66599999999998 Done!