Query gi|255764464|ref|YP_003064771.2| Cytidine/deoxycytidylate deaminase, zinc-binding region [Candidatus Liberibacter asiaticus str. psy62] Match_columns 149 No_of_seqs 109 out of 4406 Neff 6.6 Searched_HMMs 39220 Date Sun May 29 15:26:08 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 255764464.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10860 tRNA-specific adenosi 100.0 0 0 357.6 17.0 147 3-149 18-164 (178) 2 COG0590 CumB Cytosine/adenosin 100.0 0 0 310.7 15.1 147 1-147 5-152 (152) 3 cd01285 nucleoside_deaminase N 100.0 3E-37 7.8E-42 244.7 11.2 107 8-114 1-108 (109) 4 PRK10786 ribD bifunctional dia 100.0 1.8E-34 4.7E-39 228.0 14.5 132 3-147 2-141 (367) 5 KOG1018 consensus 100.0 2.9E-34 7.3E-39 226.8 11.9 146 2-147 9-161 (169) 6 pfam00383 dCMP_cyt_deam_1 Cyti 100.0 6.2E-33 1.6E-37 218.8 10.4 102 1-102 1-104 (104) 7 TIGR00326 eubact_ribD riboflav 100.0 8E-33 2E-37 218.1 10.9 134 8-149 1-163 (393) 8 COG0117 RibD Pyrimidine deamin 100.0 1.8E-30 4.6E-35 204.0 14.1 134 3-149 5-146 (146) 9 cd01284 Riboflavin_deaminase-r 100.0 4.8E-29 1.2E-33 195.4 9.7 105 8-120 1-114 (115) 10 cd01286 deoxycytidylate_deamin 99.9 2.2E-25 5.6E-30 173.4 10.7 100 4-106 1-121 (131) 11 cd00786 cytidine_deaminase-lik 99.9 4.2E-24 1.1E-28 165.7 8.0 92 8-102 1-95 (96) 12 KOG2771 consensus 99.8 1.8E-21 4.6E-26 149.9 6.6 134 3-139 166-339 (344) 13 COG2131 ComEB Deoxycytidylate 99.8 5.7E-20 1.5E-24 140.9 9.8 116 3-121 8-145 (164) 14 KOG3127 consensus 99.6 2.9E-15 7.4E-20 112.6 7.9 98 2-104 65-183 (230) 15 TIGR02571 ComEB ComE operon pr 99.3 3.7E-12 9.4E-17 94.0 5.8 101 1-104 3-118 (151) 16 cd01283 cytidine_deaminase Cyt 98.3 9.2E-06 2.3E-10 55.5 9.1 95 9-106 2-103 (112) 17 PRK12411 cytidine deaminase; P 98.0 9.8E-05 2.5E-09 49.3 10.8 98 1-101 1-106 (132) 18 COG0295 Cdd Cytidine deaminase 97.8 0.00021 5.2E-09 47.4 8.3 93 8-102 9-108 (134) 19 PRK05578 cytidine deaminase; V 97.7 0.0008 2E-08 43.9 10.9 91 1-94 1-97 (132) 20 TIGR01354 cyt_deam_tetra cytid 97.6 0.00029 7.3E-09 46.5 6.9 90 6-95 2-102 (135) 21 PRK06848 hypothetical protein; 97.4 0.0038 9.8E-08 39.8 10.5 96 3-100 6-115 (139) 22 PRK08298 cytidine deaminase; V 97.3 0.0061 1.6E-07 38.6 10.8 101 1-104 1-111 (128) 23 KOG0833 consensus 95.6 0.15 3.8E-06 30.2 9.0 90 10-100 23-122 (173) 24 PRK09027 cytidine deaminase; P 94.6 0.29 7.5E-06 28.5 8.0 67 23-93 70-139 (295) 25 pfam08210 APOBEC_N APOBEC-like 93.2 0.14 3.5E-06 30.4 4.2 56 36-92 40-97 (116) 26 TIGR01355 cyt_deam_dimer cytid 86.4 2.3 5.8E-05 23.1 5.6 68 23-92 42-118 (311) 27 PRK04388 disulfide bond format 71.9 1.5 3.9E-05 24.2 0.8 12 77-88 32-43 (172) 28 smart00552 ADEAMc tRNA-specifi 71.4 9.2 0.00024 19.5 5.1 37 52-88 71-132 (374) 29 PRK01749 disulfide bond format 68.5 2 5.1E-05 23.5 0.8 12 77-88 35-46 (175) 30 pfam08211 dCMP_cyt_deam_2 Cyti 66.4 12 0.0003 18.8 5.3 60 4-64 33-94 (124) 31 PRK02110 disulfide bond format 62.3 3 7.7E-05 22.4 0.7 11 78-88 36-46 (169) 32 TIGR00707 argD acetylornithine 51.8 2.5 6.3E-05 22.9 -1.1 31 22-52 260-292 (402) 33 pfam02137 A_deamin Adenosine-d 50.3 13 0.00034 18.5 2.4 34 52-85 24-82 (325) 34 COG4827 Predicted transporter 43.1 20 0.0005 17.5 2.4 26 68-93 99-124 (239) 35 TIGR01885 Orn_aminotrans ornit 41.5 17 0.00044 17.8 1.9 37 17-53 274-314 (426) 36 TIGR02373 photo_yellow photoac 41.0 8.3 0.00021 19.7 0.2 29 14-44 16-46 (126) 37 cd06222 RnaseH RNase H (RNase 40.9 31 0.0008 16.3 4.7 55 25-81 16-71 (130) 38 pfam02600 DsbB Disulfide bond 38.6 12 0.00031 18.7 0.7 11 78-88 32-42 (159) 39 KOG1774 consensus 37.3 24 0.00061 17.0 2.1 35 5-39 47-83 (88) 40 pfam09930 DUF2162 Predicted tr 31.7 32 0.00082 16.2 2.0 25 69-93 94-118 (228) 41 cd01719 Sm_G The eukaryotic Sm 31.1 7.3 0.00019 20.1 -1.4 36 5-40 31-67 (72) 42 KOG1783 consensus 30.3 47 0.0012 15.2 4.3 35 5-40 37-73 (77) 43 cd06908 M14_AGBL4_like Peptida 29.5 40 0.001 15.6 2.2 29 38-66 108-136 (261) 44 PRK13907 rnhA ribonuclease H; 29.3 49 0.0012 15.1 4.5 57 19-78 9-68 (128) 45 KOG2777 consensus 28.5 50 0.0013 15.0 3.4 33 52-84 243-300 (542) 46 COG1624 Uncharacterized conser 28.4 49 0.0013 15.1 2.5 23 8-32 114-136 (247) 47 cd04673 Nudix_Hydrolase_15 Mem 28.1 51 0.0013 15.0 2.5 18 25-42 2-19 (122) 48 COG1495 DsbB Disulfide bond fo 28.0 24 0.0006 17.0 0.8 10 79-88 38-47 (170) 49 KOG1228 consensus 27.3 30 0.00078 16.3 1.2 15 71-85 73-87 (256) 50 KOG1682 consensus 24.7 59 0.0015 14.6 2.8 49 8-57 60-111 (287) 51 TIGR01407 dinG_rel DnaQ family 24.3 60 0.0015 14.6 3.2 69 25-107 22-91 (944) 52 pfam05988 DUF899 Bacterial pro 23.8 23 0.00057 17.1 0.0 14 80-93 82-95 (211) 53 PRK10811 rne ribonuclease E; R 23.7 19 0.00049 17.6 -0.4 17 72-88 393-409 (1063) 54 COG0353 RecR Recombinational D 23.4 29 0.00073 16.5 0.5 29 58-88 46-74 (198) 55 pfam01235 Na_Ala_symp Sodium:a 21.5 61 0.0016 14.5 1.8 18 132-149 386-403 (415) 56 KOG3752 consensus 21.2 49 0.0012 15.1 1.3 31 53-83 258-288 (371) 57 KOG1427 consensus 20.8 71 0.0018 14.1 2.4 27 30-56 125-151 (443) 58 TIGR02661 MauD methylamine deh 20.1 55 0.0014 14.8 1.4 63 19-89 30-92 (189) No 1 >PRK10860 tRNA-specific adenosine deaminase; Provisional Probab=100.00 E-value=0 Score=357.59 Aligned_cols=147 Identities=39% Similarity=0.570 Sum_probs=144.6 Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCC Q ss_conf 56999999999999887579980899998389099987347354488642511344566664148854541168861677 Q gi|255764464|r 3 KGNVFMSCALEEAQNAALRNEIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEP 82 (149) Q Consensus 3 ~d~~~M~~A~~~A~~a~~~g~~PvGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEP 82 (149) +|++||++||++|++|+..||+|||||||++|+||++|+|+++...|||+|||++||++|++.+++++|.+||||||||| T Consensus 18 ~de~fM~~Al~~A~~a~~~gevPVGaVIV~~g~IIa~g~N~~~~~~dpt~HAEi~Ai~~A~~~~~~~~L~~~tLYVTLEP 97 (178) T PRK10860 18 SHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEP 97 (178) T ss_pred CHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEECCC T ss_conf 99999999999999862179998899999899999997544336789986799999999999958976678479965487 Q ss_pred CHHHHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCCCCCCCEEEECCCHHHHHHHHHHHHHHHC Q ss_conf 6889899986088859997117988501741344431689999879928218999999899988409 Q gi|255764464|r 83 CTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISEQRSRQIIQDFFKERR 149 (149) Q Consensus 83 C~MC~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~~~~~~~v~~gvl~ee~~~Ll~~ff~~kR 149 (149) |+||++||+|+||+|||||+.||+.|++++..+++..+.+||+++|++|||++||.+||++||+++| T Consensus 98 C~MCa~Ai~~arI~rVv~ga~Dpk~g~~gs~~~~l~~~~~nh~ieV~~Gvle~E~~~Ll~~FF~~~R 164 (178) T PRK10860 98 CVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRR 164 (178) T ss_pred CHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHCCCCCCCCEEECCCCHHHHHHHHHHHHHHHH T ss_conf 6889999999097989996378999976538889755698999489848589999999999999997 No 2 >COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=310.68 Aligned_cols=147 Identities=46% Similarity=0.678 Sum_probs=142.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEC Q ss_conf 98569999999999998875799808999983-89099987347354488642511344566664148854541168861 Q gi|255764464|r 1 MKKGNVFMSCALEEAQNAALRNEIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVT 79 (149) Q Consensus 1 M~~d~~~M~~A~~~A~~a~~~g~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtT 79 (149) +++|+.||++|+++|+++.+.|++|||||||+ +|+|+++|+|.+.+.+|||+||||+||++|++.+++++|+||||||| T Consensus 5 ~~~~~~~m~~al~~A~~a~~~ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyvT 84 (152) T COG0590 5 SEKDEDFMREALKEAKKAGDEGEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVT 84 (152) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEE T ss_conf 45058899999999998887389977999991799889873377567788551499999999998608886787289986 Q ss_pred CCCCHHHHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCCCCCCCEEEECCCHHHHHHHHHHHHHH Q ss_conf 67768898999860888599971179885017413444316899998799282189999998999884 Q gi|255764464|r 80 LEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISEQRSRQIIQDFFKE 147 (149) Q Consensus 80 lEPC~MC~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~~~~~~~v~~gvl~ee~~~Ll~~ff~~ 147 (149) +|||+||++||+||||+|||||++||+.|++++..++...+..+|+++|++|++++||.+++++||.+ T Consensus 85 ~EPC~MCagAi~~ari~rvvyga~~~~~ga~g~~~~i~~~~~~~~~~~v~~g~~~~e~~~~l~~f~~~ 152 (152) T COG0590 85 LEPCPMCAGAIIWARIDRVVYGASDPKTGAIGSLLDILKDPRLNHRVEVYGGILEEECSALLSEFFRR 152 (152) T ss_pred CCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHC T ss_conf 68289999999984899499973258876656540210377779666766533007899999987419 No 3 >cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei Probab=100.00 E-value=3e-37 Score=244.68 Aligned_cols=107 Identities=50% Similarity=0.698 Sum_probs=102.4 Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHH Q ss_conf 9999999998875799808999983-890999873473544886425113445666641488545411688616776889 Q gi|255764464|r 8 MSCALEEAQNAALRNEIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCTMC 86 (149) Q Consensus 8 M~~A~~~A~~a~~~g~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC~MC 86 (149) |++||++|+++...|++|||||||+ +|+||+.|+|++.+.+|||.|||++||+++.++++.++++++|||||+|||+|| T Consensus 1 M~~Ai~~A~~a~~~g~~PvGaviv~~~g~ii~~g~N~~~~~~~~~~HaE~~ai~~a~~~~~~~~~~~~tly~TlEPC~mC 80 (109) T cd01285 1 MRLAIELARKALAEGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPMC 80 (109) T ss_pred CHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHH T ss_conf 97999999987357999999999938997999980764668998634899999999987188766773577488985999 Q ss_pred HHHHHHCCCCEEEEEECCCCCCEECCHH Q ss_conf 8999860888599971179885017413 Q gi|255764464|r 87 AAAISLARIRRLYYGASNPKGGGIENGT 114 (149) Q Consensus 87 ~~Ai~~agI~rVvyg~~d~~~g~~~~~~ 114 (149) ++||+|+||+|||||++||+.|++++.. T Consensus 81 ~~Ai~~~gI~~Vvyg~~~~~~g~~g~~~ 108 (109) T cd01285 81 AGALLWARIKRVVYGASDPKLGGIGFLI 108 (109) T ss_pred HHHHHHHCCCEEEEEECCCCCCCCEECC T ss_conf 9999995929899998489985502555 No 4 >PRK10786 ribD bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional Probab=100.00 E-value=1.8e-34 Score=227.99 Aligned_cols=132 Identities=25% Similarity=0.375 Sum_probs=118.2 Q ss_pred CHHHHHHHHHHHHHHH--HHCCCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECC Q ss_conf 5699999999999988--75799808999983890999873473544886425113445666641488545411688616 Q gi|255764464|r 3 KGNVFMSCALEEAQNA--ALRNEIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTL 80 (149) Q Consensus 3 ~d~~~M~~A~~~A~~a--~~~g~~PvGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTl 80 (149) +|++||++||++|+++ ....|++||||||++|+||++||++. .+..|||++||++|..+ .+|+|||||| T Consensus 2 ~d~~~M~~Al~lA~~~~g~t~pNP~VG~Vivk~g~iig~G~h~~----~G~~HAEv~Al~~a~~~-----~~gatlYVTL 72 (367) T PRK10786 2 QDEFYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQR----AGEPHAEVHALRMAGEK-----AKGATAYVTL 72 (367) T ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCEEEEEEECCC----CCCCCHHHHHHHHHHHH-----HCCCEEEEEE T ss_conf 87999999999998469987999999999998999999995788----99989999999971343-----1497699983 Q ss_pred CCCHH------HHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCCCCCCCEEEECCCHHHHHHHHHHHHHH Q ss_conf 77688------98999860888599971179885017413444316899998799282189999998999884 Q gi|255764464|r 81 EPCTM------CAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISEQRSRQIIQDFFKE 147 (149) Q Consensus 81 EPC~M------C~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~~~~~~~v~~gvl~ee~~~Ll~~ff~~ 147 (149) |||.+ |+.||+.+||+|||||..||+....|++...+...+ ++|..|++++||.+|++.||.. T Consensus 73 EPC~H~GkTpPC~~aIi~agI~rVvia~~DPnp~v~GkGi~~L~~aG----I~V~~g~l~~ea~~ln~~F~~~ 141 (367) T PRK10786 73 EPCSHHGRTPPCCDALIAAGVARVVAAMQDPNPQVAGRGLYRLQQAG----IDVSHGLMMSEAEALNKGFLKR 141 (367) T ss_pred CCCCCCCCCCHHHHHHHHHCCCEEEEECCCCCCCCCCCHHHHHHHCC----CEEEECCHHHHHHHHHHHHHHH T ss_conf 57346798945999999828988999688988212463699998769----8899742066799998999999 No 5 >KOG1018 consensus Probab=100.00 E-value=2.9e-34 Score=226.82 Aligned_cols=146 Identities=38% Similarity=0.535 Sum_probs=131.5 Q ss_pred CCHHHHHHHHHHHHHHHHHCC-CCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHH---HHHHCCCCCCCCEEE Q ss_conf 856999999999999887579-9808999983-89099987347354488642511344566---664148854541168 Q gi|255764464|r 2 KKGNVFMSCALEEAQNAALRN-EIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRM---GCRILSQEILPEVDL 76 (149) Q Consensus 2 ~~d~~~M~~A~~~A~~a~~~g-~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~---a~~~~~~~~l~~~tl 76 (149) .+|..||+.|+++|+++++.| ++|||||+|+ +|+|+++|+|.+++.+|||+|||+.+|+. .++.++.++++++|| T Consensus 9 ~~~~~~m~~a~eea~ka~d~~~~~pvg~vlV~~~g~v~a~g~n~~~~~~d~t~HaE~~~I~~~~~~~~~~~~~~ls~~tl 88 (169) T KOG1018 9 DHDIAFMVEAVEEAKKALDEGDEVPVGAVLVHMDGKVLASGGNMVNEKKDPTAHAEVIAIREEEVMCKSLRTIDLSETTL 88 (169) T ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEECCCCEECCCCCCCHHHHHHHHHHHHHHHHHCCCEECCCCEE T ss_conf 10479999999999861467778865799994798077215640024478104457887762777754307244148779 Q ss_pred EECCCCCHHHHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCC--CCCCCCEEEECCCHHHHHHHHHHHHHH Q ss_conf 86167768898999860888599971179885017413444316--899998799282189999998999884 Q gi|255764464|r 77 YVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLA--TCHHSPEIYPGISEQRSRQIIQDFFKE 147 (149) Q Consensus 77 YtTlEPC~MC~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~--~~~~~~~v~~gvl~ee~~~Ll~~ff~~ 147 (149) |||+|||+||++||.|+||++||||+.++++|+.++........ ...+.+...+|+..++...+++.|+.+ T Consensus 89 yvt~ePc~mC~gal~~~gv~~vv~G~~ne~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~f~~~ 161 (169) T KOG1018 89 YVTCEPCPMCAGALAQSGVKRVVFGASNERFGGIGFVLRGNKDFLKRLGASVISRDGIEKKEAQKLLIAFYVR 161 (169) T ss_pred EEEECCCHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEEEHHHHHCCCCCCEEECCCHHHHHHHHHHHHHCCC T ss_conf 9995544889999998699789980114531146244100012304678641762215667766677754120 No 6 >pfam00383 dCMP_cyt_deam_1 Cytidine and deoxycytidylate deaminase zinc-binding region. Probab=100.00 E-value=6.2e-33 Score=218.77 Aligned_cols=102 Identities=40% Similarity=0.512 Sum_probs=96.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHC-CCCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE Q ss_conf 985699999999999988757-99808999983-8909998734735448864251134456666414885454116886 Q gi|255764464|r 1 MKKGNVFMSCALEEAQNAALR-NEIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV 78 (149) Q Consensus 1 M~~d~~~M~~A~~~A~~a~~~-g~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt 78 (149) |+.|++||++|+++|++++.. +++|||||||+ +|+||+.|+|+++...|+|.|||++||.++.+......+++++||| T Consensus 1 ~~~de~~m~~A~~~A~~a~~~~~~~~VGaviv~~~g~ii~~g~N~~~~~~~~~~HAE~~Ai~~a~~~~~~~~~~~~~lyv 80 (104) T pfam00383 1 MEWDEYFMRLALEAAKRAYTPYSNFPVGAVIVKNDGGIIATGYNGENAGYDPTIHAERNAIRNAGRLGEGIKLEGATLYV 80 (104) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCEEEEEECEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEC T ss_conf 97899999999999986679889997899999279979998857075699963018999999999966997112632326 Q ss_pred CCCCCHHHHHHHHHCCCCEEEEEE Q ss_conf 167768898999860888599971 Q gi|255764464|r 79 TLEPCTMCAAAISLARIRRLYYGA 102 (149) Q Consensus 79 TlEPC~MC~~Ai~~agI~rVvyg~ 102 (149) |+|||+||+++|+|+||+|||||+ T Consensus 81 T~ePC~mC~~ai~~~gi~~Vvyg~ 104 (104) T pfam00383 81 TLEPCGMCRQAIIESGIKKVVFGT 104 (104) T ss_pred CCCCHHHHHHHHHHHCCCEEEECC T ss_conf 989769999999996919999809 No 7 >TIGR00326 eubact_ribD riboflavin biosynthesis protein RibD; InterPro: IPR004794 This entry describes the riboflavin biosynthesis protein (ribD) as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region that is shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins that may be related to the riboflavin biosynthesis protein contain only the C-terminal domain.; GO: 0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity, 0008835 diaminohydroxyphosphoribosylaminopyrimidine deaminase activity, 0009231 riboflavin biosynthetic process. Probab=100.00 E-value=8e-33 Score=218.13 Aligned_cols=134 Identities=28% Similarity=0.388 Sum_probs=120.1 Q ss_pred HHHHHHHHHHH--HHCCCCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCC---------------- Q ss_conf 99999999988--75799808999983-890999873473544886425113445666641488---------------- Q gi|255764464|r 8 MSCALEEAQNA--ALRNEIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQ---------------- 68 (149) Q Consensus 8 M~~A~~~A~~a--~~~g~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~---------------- 68 (149) |++|++||+++ ....|++||||||+ ||+|||.|++. +.|.| |||++||++|.++..+ T Consensus 1 M~~AL~lA~k~~g~T~PNP~VGcViv~~ng~IVG~G~H~--kaG~~--HAE~~Al~~AG~~aRPeisLPkeanaLhefiC 76 (393) T TIGR00326 1 MKRALDLAKKGQGTTHPNPLVGCVIVKKNGEIVGEGFHQ--KAGEP--HAEIHALRQAGENARPEISLPKEANALHEFIC 76 (393) T ss_pred CHHHHHHHHHCCCCCCCCCCEEEEEEECCCEEEEECCCC--CCCCC--HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf 935676664043100579860048983387587524669--77887--08999999976636886568513567888765 Q ss_pred ----CCCCCEEEEECCCCCHH------HHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCCCCCCCEEEECCCHHHHH Q ss_conf ----54541168861677688------98999860888599971179885017413444316899998799282189999 Q gi|255764464|r 69 ----EILPEVDLYVTLEPCTM------CAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISEQRSR 138 (149) Q Consensus 69 ----~~l~~~tlYtTlEPC~M------C~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~~~~~~~v~~gvl~ee~~ 138 (149) --++|+|+|||||||.| |+.||+.|||.|||++-.||+.-..|++.+.+...+ ++|..|+|.++|. T Consensus 77 knhqGvfKGat~yVTLEPCsH~GrTPPCa~aii~~Gi~kVv~~M~DpNplvaGkG~~~L~~aG----IeV~~~~l~~~a~ 152 (393) T TIGR00326 77 KNHQGVFKGATAYVTLEPCSHYGRTPPCAEAIIEAGIKKVVVSMQDPNPLVAGKGIERLKQAG----IEVTFGILKEEAE 152 (393) T ss_pred HCCCCEEECCEEEECCCCCCCCCCCHHHHHHHHHCCCEEEEEEEECCCCCCCCHHHHHHHHCC----CEEEECHHHHHHH T ss_conf 226741207767981576688888715689997386148988865087222341479998669----7254401589864 Q ss_pred HHHHHHHHHHC Q ss_conf 99899988409 Q gi|255764464|r 139 QIIQDFFKERR 149 (149) Q Consensus 139 ~Ll~~ff~~kR 149 (149) +|++.|.+.+| T Consensus 153 ~lnk~Fl~~~~ 163 (393) T TIGR00326 153 KLNKGFLKRMR 163 (393) T ss_pred HCCHHHHHHHC T ss_conf 00056788860 No 8 >COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism] Probab=99.97 E-value=1.8e-30 Score=203.96 Aligned_cols=134 Identities=29% Similarity=0.395 Sum_probs=119.3 Q ss_pred CHHHHHHHHHHHHHHH--HHCCCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECC Q ss_conf 5699999999999988--75799808999983890999873473544886425113445666641488545411688616 Q gi|255764464|r 3 KGNVFMSCALEEAQNA--ALRNEIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTL 80 (149) Q Consensus 3 ~d~~~M~~A~~~A~~a--~~~g~~PvGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTl 80 (149) .|+.||++||++|+++ ....++|||||||++|+||+.|++.. .++| |||..||++| .....|+|+|+|| T Consensus 5 ~~~~~M~~Al~lA~k~~g~T~pNP~VG~VIV~~~~Ivg~G~h~~--aG~p--HAEv~Al~~a-----g~~a~Gat~yVTL 75 (146) T COG0117 5 LDERYMERALELAEKGQGTTSPNPSVGCVIVKDGEIVGEGYHEK--AGGP--HAEVCALRMA-----GEAARGATAYVTL 75 (146) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCEEEEEEECCC--CCCC--CHHHHHHHHC-----CCCCCCCEEEEEE T ss_conf 79999999999998508667899966699988999986660377--8997--2899999975-----8555787899972 Q ss_pred CCCHH------HHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCCCCCCCEEEECCCHHHHHHHHHHHHHHHC Q ss_conf 77688------9899986088859997117988501741344431689999879928218999999899988409 Q gi|255764464|r 81 EPCTM------CAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATCHHSPEIYPGISEQRSRQIIQDFFKERR 149 (149) Q Consensus 81 EPC~M------C~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~~~~~~~v~~gvl~ee~~~Ll~~ff~~kR 149 (149) |||.+ |+.+|+.+||+|||++..||+....+.+...+.... ++|+.|+|++|+..|++.|+...| T Consensus 76 EPCsH~GrTPPC~~ali~agi~rVvva~~DPnp~Vag~G~~~L~~aG----i~V~~gil~~e~~~l~~~f~~~~~ 146 (146) T COG0117 76 EPCSHYGRTPPCADALIKAGVARVVVAMLDPNPLVAGGGLARLRAAG----IEVEVGILEEEAEKLNEGFLKRMR 146 (146) T ss_pred CCCCCCCCCCCHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHCC----CEEEEEHHHHHHHHHHHHHHCCCC T ss_conf 47666899964579999709888999952899301684699999769----869960408999998888870169 No 9 >cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain. Probab=99.96 E-value=4.8e-29 Score=195.40 Aligned_cols=105 Identities=33% Similarity=0.450 Sum_probs=89.7 Q ss_pred HHHHHHHHHHH--HHCCCCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCH Q ss_conf 99999999988--75799808999983-8909998734735448864251134456666414885454116886167768 Q gi|255764464|r 8 MSCALEEAQNA--ALRNEIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCT 84 (149) Q Consensus 8 M~~A~~~A~~a--~~~g~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC~ 84 (149) |++||++|+++ ....++|||||||+ +|+||++|||+ .+++.|||++||+++.+ ++++++|||||||||. T Consensus 1 M~~Ai~lA~~~~g~t~pnP~VGaViv~~~g~Iis~g~~~----~~g~~HAE~~Ai~~a~~----~~~~g~tlyvTLEPC~ 72 (115) T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGYHR----KAGGPHAEVNALASAGE----KLARGATLYVTLEPCS 72 (115) T ss_pred CHHHHHHHHHCCCCCCCCCCEEEEEEECCCEEEEEEECC----CCCCHHHHHHHHHHHHH----HCCCCCEEEEEECCCC T ss_conf 979999998537988999998999991799899988479----89974099999998523----1357976999867834 Q ss_pred H------HHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCC Q ss_conf 8------98999860888599971179885017413444316 Q gi|255764464|r 85 M------CAAAISLARIRRLYYGASNPKGGGIENGTQFYTLA 120 (149) Q Consensus 85 M------C~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~ 120 (149) | |+.+|+++||+|||||..||+....+++.+.+... T Consensus 73 ~~g~tp~Ca~ai~~~gI~~Vv~g~~DP~p~v~g~G~~~Lk~~ 114 (115) T cd01284 73 HHGKTPPCVDAIIEAGIKRVVVGVRDPNPLVAGKGAERLRAA 114 (115) T ss_pred CCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCHHHHHHHHC T ss_conf 789875499999983929999967594977488789999867 No 10 >cd01286 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor. Probab=99.93 E-value=2.2e-25 Score=173.41 Aligned_cols=100 Identities=34% Similarity=0.358 Sum_probs=82.9 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEEEECCEEEEEEECCCCCCC---------------------CCCCCCHHHHHHHH Q ss_conf 699999999999988757998089999838909998734735448---------------------86425113445666 Q gi|255764464|r 4 GNVFMSCALEEAQNAALRNEIPVGAVAVLNNKIISRAGNRNRELK---------------------DVTAHAEILAIRMG 62 (149) Q Consensus 4 d~~~M~~A~~~A~~a~~~g~~PvGaviv~~g~ii~~g~N~~~~~~---------------------d~t~HAEi~ai~~a 62 (149) |++||++|..+|+++.. ...+||||||++|+||+.|||..-... ..+-|||++||.++ T Consensus 1 De~fM~lA~~~A~rS~~-~~~~VGaVIV~~~~iIs~GyNG~p~g~~~~~~~~~~~~~~~~~~~~~~~~~iHAE~nAi~~a 79 (131) T cd01286 1 DEYFMAIARLAALRSTC-PRRQVGAVIVKDKRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQKCCRTVHAEQNAILQA 79 (131) T ss_pred CHHHHHHHHHHHHHCCC-CCCCEEEEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 98899999999986699-99986899997993896644899888887400033112444332322222178999999999 Q ss_pred HHHCCCCCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEECCCC Q ss_conf 64148854541168861677688989998608885999711798 Q gi|255764464|r 63 CRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPK 106 (149) Q Consensus 63 ~~~~~~~~l~~~tlYtTlEPC~MC~~Ai~~agI~rVvyg~~d~~ 106 (149) .+. ...+.|+|||||++||+||+.+|+++||+||||...-+. T Consensus 80 ~~~--~~~~~g~tlYvT~~PC~~Ca~~Ii~aGI~rVvy~~~y~~ 121 (131) T cd01286 80 ARH--GVSLEGATLYVTLFPCIECAKLIIQAGIKKVVYAEPYDD 121 (131) T ss_pred HHC--CCCCCCCEEECCCCCHHHHHHHHHHCCCCEEEECCCCCC T ss_conf 982--998888666607897799999999829999998997699 No 11 >cd00786 cytidine_deaminase-like Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Probab=99.90 E-value=4.2e-24 Score=165.69 Aligned_cols=92 Identities=26% Similarity=0.254 Sum_probs=83.7 Q ss_pred HHHHHHHHHHHHHC-CCCCEEEEEE--ECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCH Q ss_conf 99999999988757-9980899998--38909998734735448864251134456666414885454116886167768 Q gi|255764464|r 8 MSCALEEAQNAALR-NEIPVGAVAV--LNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCT 84 (149) Q Consensus 8 M~~A~~~A~~a~~~-g~~PvGaviv--~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC~ 84 (149) |+.|+++|++|+.. +++||||+|| ++|++|+.|+|..+...++|.|||++||.+|.+.. .+++++||+|+|||. T Consensus 1 m~~A~~~a~~ay~p~s~~pVGa~iv~~~~~~ii~~G~N~en~~~~~t~hAE~~Ai~~a~~~~---~~~~~tlyvtl~PC~ 77 (96) T cd00786 1 MTEALKAADLGYAKESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGSEG---DTKGQMLYVALSPCG 77 (96) T ss_pred CHHHHHHHHHCCCCCCCCCEEEEEEEECCCCEEECCCCEEECCCCCCCCHHHHHHHHHHHCC---CCCCEECEEECCCHH T ss_conf 97999999965698889988999998779979977646178667973379999999975225---876110787229919 Q ss_pred HHHHHHHHCCCCEEEEEE Q ss_conf 898999860888599971 Q gi|255764464|r 85 MCAAAISLARIRRLYYGA 102 (149) Q Consensus 85 MC~~Ai~~agI~rVvyg~ 102 (149) ||+++|+++||++||+-. T Consensus 78 ~C~q~I~e~gik~vvi~~ 95 (96) T cd00786 78 ACAQLIIELGIKDVIVVL 95 (96) T ss_pred HHHHHHHHHCCCCEEEEE T ss_conf 999999998899689996 No 12 >KOG2771 consensus Probab=99.85 E-value=1.8e-21 Score=149.89 Aligned_cols=134 Identities=19% Similarity=0.322 Sum_probs=113.9 Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCEEEEEEE--CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCC------------ Q ss_conf 569999999999998875799808999983--890999873473544886425113445666641488------------ Q gi|255764464|r 3 KGNVFMSCALEEAQNAALRNEIPVGAVAVL--NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQ------------ 68 (149) Q Consensus 3 ~d~~~M~~A~~~A~~a~~~g~~PvGaviv~--~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~------------ 68 (149) .+..+|+++|+.|..+... .|+|++|++ .+.|++.|...+-. .+|..|+-|++++...++... T Consensus 166 ~~~ri~e~~I~~a~~~~~~--~~~~a~I~~p~~~~Via~~~~~~~~-~~P~eh~~mv~v~~v~rrq~~~~~~~~~~~~~~ 242 (344) T KOG2771 166 EIARIGELLIAMATDGHAS--RPVSAAIVDPVMDRVIAAGTGEVCA-YNPIEHCVMVLVHFVARRQEEGTWDLHPIPLLI 242 (344) T ss_pred HHHHHHHHHHHHHHHHCCC--CCCCCEECCCCCCEEEECCCCCCCC-CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 9999998999998640025--6765045578613377447774223-474888899999999998753654444461001 Q ss_pred --------------------------CCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCCC Q ss_conf --------------------------545411688616776889899986088859997117988501741344431689 Q gi|255764464|r 69 --------------------------EILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLATC 122 (149) Q Consensus 69 --------------------------~~l~~~tlYtTlEPC~MC~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~~ 122 (149) +.+.|+++|.|+|||.||++|++|+||+||+|+..+..+|++++.+.++..+.+ T Consensus 243 f~~~~~~~~~~~~~v~~~D~~~d~~pYLCtgydv~ll~EPC~MCsMALvHsRikRvfy~~~~s~~G~L~s~~~i~~~k~L 322 (344) T KOG2771 243 FNAVSSPFYKQTVAVQLLDVSADSFPYLCTGYDVYLLHEPCAMCSMALVHSRIKRVFYCKPMSTAGGLGSLYRIHQRKSL 322 (344) T ss_pred CCCCCCHHHHHHCHHCCCCCCCCCCCEEEECCEEEEECCHHHHHHHHHHHHHHHHEEECCCCCCCCCCCCEEEEEECCCC T ss_conf 35200035553010004552236666364343378734738888999988764303653577777775412576302114 Q ss_pred CCCCEEEECCCHHHHHH Q ss_conf 99987992821899999 Q gi|255764464|r 123 HHSPEIYPGISEQRSRQ 139 (149) Q Consensus 123 ~~~~~v~~gvl~ee~~~ 139 (149) ||+++|+.+++++++.. T Consensus 323 Nhry~vfr~~~e~d~~~ 339 (344) T KOG2771 323 NHRYEVFRGYLEEDPIP 339 (344) T ss_pred CCCEEEEEEECCCCCCC T ss_conf 76147888505555500 No 13 >COG2131 ComEB Deoxycytidylate deaminase [Nucleotide transport and metabolism] Probab=99.82 E-value=5.7e-20 Score=140.88 Aligned_cols=116 Identities=30% Similarity=0.296 Sum_probs=88.9 Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCEEEEEEECCCCCCCC----------------------CCCCCHHHHHH Q ss_conf 56999999999999887579980899998389099987347354488----------------------64251134456 Q gi|255764464|r 3 KGNVFMSCALEEAQNAALRNEIPVGAVAVLNNKIISRAGNRNRELKD----------------------VTAHAEILAIR 60 (149) Q Consensus 3 ~d~~~M~~A~~~A~~a~~~g~~PvGaviv~~g~ii~~g~N~~~~~~d----------------------~t~HAEi~ai~ 60 (149) +|++||+.|.-.|.++-... .-||||||++++||+.|||..-...+ -+-|||+|||- T Consensus 8 wdeyfm~~A~l~a~Rstc~r-~~VGAvIvkd~rIiatGYNG~p~g~~~c~~~g~~~~~~~~~~~~~~~~r~vHAE~NAil 86 (164) T COG2131 8 WDEYFMAIAELVALRSTCPR-RQVGAVIVKDGRIIATGYNGAPSGEDHCIDRGCLRDKVVFVTTCGHCCRTLHAEQNAIL 86 (164) T ss_pred HHHHHHHHHHHHHHHCCCCC-CCEEEEEEECCEEEEEECCCCCCCCCCCCCCCCEECCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 99999999999998743866-54568998699599851388876567767667600122256623578899999999999 Q ss_pred HHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEECCCCCCEECCHHHHHHCCC Q ss_conf 6664148854541168861677688989998608885999711798850174134443168 Q gi|255764464|r 61 MGCRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASNPKGGGIENGTQFYTLAT 121 (149) Q Consensus 61 ~a~~~~~~~~l~~~tlYtTlEPC~MC~~Ai~~agI~rVvyg~~d~~~g~~~~~~~~~~~~~ 121 (149) +|.+..-. +.|+|||+|+.||.+|+..|+++||++|||+...+..-.......++...+ T Consensus 87 ~aa~~g~~--~~~atlYvt~~PC~~Cak~Ii~aGIk~Vvy~~~Y~~~~~~~~s~~l~~~ag 145 (164) T COG2131 87 QAARHGVG--LEGATLYVTHFPCSNCAKLIIQAGIKEVVYAEPYPTETVAPYSQELLEEAG 145 (164) T ss_pred HHHHCCCC--CCCCEEEEEECCCHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHHHCC T ss_conf 99864788--777089998246589999999828658995067775101377999998679 No 14 >KOG3127 consensus Probab=99.60 E-value=2.9e-15 Score=112.60 Aligned_cols=98 Identities=35% Similarity=0.405 Sum_probs=78.5 Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCEEEEEE-ECCEEEEEEECCCCCCC--C------------------CCCCCHHHHHH Q ss_conf 856999999999999887579980899998-38909998734735448--8------------------64251134456 Q gi|255764464|r 2 KKGNVFMSCALEEAQNAALRNEIPVGAVAV-LNNKIISRAGNRNRELK--D------------------VTAHAEILAIR 60 (149) Q Consensus 2 ~~d~~~M~~A~~~A~~a~~~g~~PvGaviv-~~g~ii~~g~N~~~~~~--d------------------~t~HAEi~ai~ 60 (149) ++|.+||++|.-.|+++.+.. .-|||+|| +++.|||.|||..-..- + -+-|||.+||. T Consensus 65 swd~yFM~iA~LsA~RSkDpn-tqVGaCiv~~~n~iVg~GYNgfP~gc~~~vfp~~~~~~~~~~~~k~~yv~HAE~NAi~ 143 (230) T KOG3127 65 SWDDYFMAIAFLSAKRSKDPN-TQVGACIVDRENRIVGTGYNGFPRGCSDDVFPWCKAALSTNLDLKYCYVVHAEENAIL 143 (230) T ss_pred CHHHHHHHHHHHHHHHCCCCC-CCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHH T ss_conf 689999999999998535965-6602699737987999603787677777777544344224877625888505778998 Q ss_pred HHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEECC Q ss_conf 66641488545411688616776889899986088859997117 Q gi|255764464|r 61 MGCRILSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASN 104 (149) Q Consensus 61 ~a~~~~~~~~l~~~tlYtTlEPC~MC~~Ai~~agI~rVvyg~~d 104 (149) .+. ..++.++++|+|+=||.-|+-.|+++||++|||+..+ T Consensus 144 ~~~----~~~~~~~~lYvtl~PC~~Ca~liiq~GIkeV~~~~~~ 183 (230) T KOG3127 144 NKG----RERVGGCSLYVTLCPCNECAKLIIQAGIKEVYYSSSY 183 (230) T ss_pred HHC----CCCCCCCEEEEEECCHHHHHHHHHHHHHHHEEECCCC T ss_conf 717----5504771689862456888999998545650422111 No 15 >TIGR02571 ComEB ComE operon protein 2; InterPro: IPR013404 This is encoded in the ComE operon for "late competence" as characterised in B. subtilis . The presence of a cytidine/deoxycytidine deaminase domain in these proteins means that they may perform this activity.. Probab=99.30 E-value=3.7e-12 Score=93.97 Aligned_cols=101 Identities=28% Similarity=0.385 Sum_probs=83.1 Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCEEEEEEECCCCCCCC---------------CCCCCHHHHHHHHHHH Q ss_conf 9856999999999999887579980899998389099987347354488---------------6425113445666641 Q gi|255764464|r 1 MKKGNVFMSCALEEAQNAALRNEIPVGAVAVLNNKIISRAGNRNRELKD---------------VTAHAEILAIRMGCRI 65 (149) Q Consensus 1 M~~d~~~M~~A~~~A~~a~~~g~~PvGaviv~~g~ii~~g~N~~~~~~d---------------~t~HAEi~ai~~a~~~ 65 (149) ..+|++||..+.-++.++.-. -..|||-||++.+||+-|||....... .|-||||+||-+.++. T Consensus 3 i~W~~yfm~q~~ll~~rstC~-rl~vGativ~d~riiaGGynGs~~G~~hC~~~GC~~~d~hC~rtihaemna~lqCak~ 81 (151) T TIGR02571 3 IKWDQYFMAQSHLLALRSTCT-RLSVGATIVRDKRIIAGGYNGSVAGEVHCIDEGCYVVDGHCVRTIHAEMNALLQCAKF 81 (151) T ss_pred CCHHHHHHHHHHHHHHHHHCC-HHEECEEEEECCEEEECCCCCEECCCCEEECCCCEEEECCEEEHHHHHHHHHHHHHHC T ss_conf 536788888888875420000-0000204542362662364530137723312773786174300367889999988640 Q ss_pred CCCCCCCCEEEEECCCCCHHHHHHHHHCCCCEEEEEECC Q ss_conf 488545411688616776889899986088859997117 Q gi|255764464|r 66 LSQEILPEVDLYVTLEPCTMCAAAISLARIRRLYYGASN 104 (149) Q Consensus 66 ~~~~~l~~~tlYtTlEPC~MC~~Ai~~agI~rVvyg~~d 104 (149) |.. -+++++|+|.-||.-|...|+++||+.|+|.-.- T Consensus 82 -G~~-t~~a~~yvt~fPCl~C~k~~~q~Gi~~~~y~~~y 118 (151) T TIGR02571 82 -GVS-TEEAEIYVTHFPCLQCTKSIIQAGIKKVYYAKDY 118 (151) T ss_pred -CCC-CCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHC T ss_conf -554-3663489850756789999998667874666632 No 16 >cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes. Probab=98.26 E-value=9.2e-06 Score=55.53 Aligned_cols=95 Identities=26% Similarity=0.238 Sum_probs=69.5 Q ss_pred HHHHHHHHHHHHCC-CCCEEEEEEEC-CEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEC-----CC Q ss_conf 99999999887579-98089999838-9099987347354488642511344566664148854541168861-----67 Q gi|255764464|r 9 SCALEEAQNAALRN-EIPVGAVAVLN-NKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVT-----LE 81 (149) Q Consensus 9 ~~A~~~A~~a~~~g-~~PvGaviv~~-g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtT-----lE 81 (149) +.|++...+++... +.||||+++.+ |+| -.|.|-.+.....+.|||..||.++...-... -..+++++ .. T Consensus 2 ~~a~~~~~~ay~pyS~f~Vga~~~~~~G~i-~~G~nvEna~~~~~~cAEr~ai~~~~~~g~~~--~~~~~~~~~~~~~~s 78 (112) T cd01283 2 EAALAAAEFAYAPYSNFTVGAALLTKDGRI-FTGVNVENASYGLTLCAERTAIGKAVSEGLRR--YLVTWAVSDEGGVWS 78 (112) T ss_pred HHHHHHHHCCCCCCCCCCEEEEEEECCCCE-EEEEEEECCCCCCCEEHHHHHHHHHHHCCCCC--EEEEEEEECCCCCCC T ss_conf 779999846768867991209999389989-99898706778875118899999999828985--499999938997568 Q ss_pred CCHHHHHHHHHCCCCEEEEEECCCC Q ss_conf 7688989998608885999711798 Q gi|255764464|r 82 PCTMCAAAISLARIRRLYYGASNPK 106 (149) Q Consensus 82 PC~MC~~Ai~~agI~rVvyg~~d~~ 106 (149) ||-+|...|....=+++.+-..+++ T Consensus 79 PCG~CrQ~l~Ef~~~~~~i~~~~~~ 103 (112) T cd01283 79 PCGACRQVLAEFLPSRLYIIIDNPK 103 (112) T ss_pred CCHHHHHHHHHHCCCCCEEEEECCC T ss_conf 7346899999867899689999799 No 17 >PRK12411 cytidine deaminase; Provisional Probab=98.05 E-value=9.8e-05 Score=49.34 Aligned_cols=98 Identities=17% Similarity=0.269 Sum_probs=67.9 Q ss_pred CCCHHHHHHHHHHHHHHHHHC-CCCCEEEEEE-ECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE Q ss_conf 985699999999999988757-9980899998-38909998734735448864251134456666414885454116886 Q gi|255764464|r 1 MKKGNVFMSCALEEAQNAALR-NEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV 78 (149) Q Consensus 1 M~~d~~~M~~A~~~A~~a~~~-g~~PvGaviv-~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt 78 (149) |++. ..++.|.+..++|+.. -+.||||+++ ++|+|. .|-|..+.....|.+||..||-++... +...+....+++ T Consensus 1 m~~~-~L~~~A~~a~~~AYaPYS~F~VGAall~~~G~i~-~G~NvEnasy~~t~CAEr~Ai~~avs~-g~~~~~~I~v~~ 77 (132) T PRK12411 1 MNSK-QLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVY-RGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVA 77 (132) T ss_pred CCHH-HHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEE-EEECCCCCCCCCCEEHHHHHHHHHHHC-CCCCEEEEEEEC T ss_conf 9889-9999999999718288679959999995899999-987415677887513377799999864-887689999986 Q ss_pred C----CCCCHHHHHHHHHCC--CCEEEEE Q ss_conf 1----677688989998608--8859997 Q gi|255764464|r 79 T----LEPCTMCAAAISLAR--IRRLYYG 101 (149) Q Consensus 79 T----lEPC~MC~~Ai~~ag--I~rVvyg 101 (149) . .-||-||-..|.... --+|+.. T Consensus 78 ~~~~~~~PCG~CRQvl~Ef~~~~~~i~~~ 106 (132) T PRK12411 78 DTKRPVPPCGACRQVMVELCKQDTKVYLS 106 (132) T ss_pred CCCCCCCCCHHHHHHHHHHCCCCCEEEEE T ss_conf 89986797388899999966899579998 No 18 >COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism] Probab=97.76 E-value=0.00021 Score=47.41 Aligned_cols=93 Identities=22% Similarity=0.179 Sum_probs=63.9 Q ss_pred HHHHHHHHHHHHHCC-CCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEC----CC Q ss_conf 999999999887579-9808999983-89099987347354488642511344566664148854541168861----67 Q gi|255764464|r 8 MSCALEEAQNAALRN-EIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVT----LE 81 (149) Q Consensus 8 M~~A~~~A~~a~~~g-~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtT----lE 81 (149) ...|.+.+..|+..- +.||||++.- +|+| -.|-|-.+.+.--|.|||..||-+|... +...+....+|.. .- T Consensus 9 ~~~a~~a~~~ay~PYS~F~VGAa~~t~~G~i-~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~~~~~s 86 (134) T COG0295 9 FALAPEAAANAYAPYSKFKVGAALRTKDGRI-YTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADTGKPVS 86 (134) T ss_pred HHHHHHHHHHCCCCCCCCCEEEEEEECCCCE-EEEEEEECCCCCCHHHHHHHHHHHHHHC-CCCCEEEEEEECCCCCCCC T ss_conf 9999999872448645782779999279979-9988660254552163899999999973-9971799999748999759 Q ss_pred CCHHHHHHHHHCC-CCEEEEEE Q ss_conf 7688989998608-88599971 Q gi|255764464|r 82 PCTMCAAAISLAR-IRRLYYGA 102 (149) Q Consensus 82 PC~MC~~Ai~~ag-I~rVvyg~ 102 (149) ||-||-.-|.... =...++-. T Consensus 87 PCG~CRQ~i~Ef~~~d~~ii~~ 108 (134) T COG0295 87 PCGACRQVLAEFCGDDTLIILL 108 (134) T ss_pred CCHHHHHHHHHHCCCCCEEEEE T ss_conf 8588999999866877459996 No 19 >PRK05578 cytidine deaminase; Validated Probab=97.72 E-value=0.0008 Score=43.86 Aligned_cols=91 Identities=22% Similarity=0.258 Sum_probs=62.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHC-CCCCEEEEEE-ECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE Q ss_conf 985699999999999988757-9980899998-38909998734735448864251134456666414885454116886 Q gi|255764464|r 1 MKKGNVFMSCALEEAQNAALR-NEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV 78 (149) Q Consensus 1 M~~d~~~M~~A~~~A~~a~~~-g~~PvGaviv-~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt 78 (149) |+.++. ++.|.+..++|+.. -+.+|||++. ++|+|+. |.|..+...-.+.+||..||-.|... +...+....++. T Consensus 1 ~d~~~L-~~~A~~a~~~AyaPYS~F~VGAall~~~G~i~~-G~NvEnasy~~~~CAEr~Ai~~avs~-g~~~i~~iav~~ 77 (132) T PRK05578 1 MDWKEL-IEAAVEASEKAYAPYSKFPVGAALLTDDGRIYT-GCNIENASYGLTNCAERTAIFKAISE-GGGRLVAIACVG 77 (132) T ss_pred CCHHHH-HHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEE-EEEEECCCCCCCCCHHHHHHHHHHHC-CCCCEEEEEEEC T ss_conf 978999-999999998366985688067999908998999-89760578887755779999999864-897378999984 Q ss_pred C----CCCCHHHHHHHHHCC Q ss_conf 1----677688989998608 Q gi|255764464|r 79 T----LEPCTMCAAAISLAR 94 (149) Q Consensus 79 T----lEPC~MC~~Ai~~ag 94 (149) . .-||-+|-..|.... T Consensus 78 ~~~~~~~PCG~CRQvl~Ef~ 97 (132) T PRK05578 78 ETGEPLSPCGRCRQVLAEFG 97 (132) T ss_pred CCCCCCCCCHHHHHHHHHHC T ss_conf 89982697524899999856 No 20 >TIGR01354 cyt_deam_tetra cytidine deaminase; InterPro: IPR006262 Cytidine deaminase is a small homotetrameric zinc metalloprotein. It is found in humans and most bacteria. A related homodimeric form, IPR006263 from INTERPRO, with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.; GO: 0004126 cytidine deaminase activity, 0046087 cytidine metabolic process. Probab=97.58 E-value=0.00029 Score=46.55 Aligned_cols=90 Identities=17% Similarity=0.162 Sum_probs=67.8 Q ss_pred HHHHHHHHHHHHHHHCC-CCCEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHH--CCCCC---CCCEEEEEC Q ss_conf 99999999999887579-9808999983890999873473544886425113445666641--48854---541168861 Q gi|255764464|r 6 VFMSCALEEAQNAALRN-EIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRI--LSQEI---LPEVDLYVT 79 (149) Q Consensus 6 ~~M~~A~~~A~~a~~~g-~~PvGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~--~~~~~---l~~~tlYtT 79 (149) .+++.|.+..++|+..= +.||||.++.++.-+-.|-|-.|.+--.|.+||..||.++-.. .+.++ +....++++ T Consensus 2 ~l~~~a~~a~~~aY~PYS~F~VGAa~~t~dg~~f~G~NvENASY~~~~CAEr~Ai~~~~~~yP~GG~r~G~f~~~~~~~~ 81 (135) T TIGR01354 2 KLFKAAQEALKKAYAPYSNFKVGAALLTKDGRVFTGVNVENASYGLTICAERSAIGKAISAYPAGGRRDGKFVAIAVAAS 81 (135) T ss_pred HHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEC T ss_conf 68889999998527876688116999856998898763421367670468999999998608878753551279998626 Q ss_pred C-----CCCHHHHHHHHHCCC Q ss_conf 6-----776889899986088 Q gi|255764464|r 80 L-----EPCTMCAAAISLARI 95 (149) Q Consensus 80 l-----EPC~MC~~Ai~~agI 95 (149) - -||=||=.-|..-.- T Consensus 82 ~~~D~~~PCG~CRQvl~EF~~ 102 (135) T TIGR01354 82 ANDDSVSPCGACRQVLAEFAK 102 (135) T ss_pred CCCCCCCCCCHHHHHHHHHCC T ss_conf 988832676035777887508 No 21 >PRK06848 hypothetical protein; Validated Probab=97.38 E-value=0.0038 Score=39.77 Aligned_cols=96 Identities=18% Similarity=0.149 Sum_probs=68.4 Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCEEEEEE-ECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE--- Q ss_conf 56999999999999887579980899998-38909998734735448864251134456666414885454116886--- Q gi|255764464|r 3 KGNVFMSCALEEAQNAALRNEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV--- 78 (149) Q Consensus 3 ~d~~~M~~A~~~A~~a~~~g~~PvGaviv-~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt--- 78 (149) +|...++.|++..++++...+.+|||.|. ++|+|+ .|-|..+.....+.-||..||-+|-.. +...+....... T Consensus 6 ~d~eLi~~A~~a~~~aY~ps~~~VgAAll~~dG~i~-tG~NvENasy~~~~CAEr~Ai~~Avs~-G~~~~~~iv~v~~~~ 83 (139) T PRK06848 6 EDYELIKAAEKVIEKRYRNDWHHVGAALRTKTGRIY-AAVHLEAYVGRITVCAEAIAIGKAISE-GDAGIDTIVAVRHPK 83 (139) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCEE-EEECCCCCCCCCCCCHHHHHHHHHHHC-CCCCEEEEEEEECCC T ss_conf 999999999999996589999973899993899999-986523676785517899999999987-997558999996058 Q ss_pred ---------CCCCCHHHHHHHHHCCCC-EEEE Q ss_conf ---------167768898999860888-5999 Q gi|255764464|r 79 ---------TLEPCTMCAAAISLARIR-RLYY 100 (149) Q Consensus 79 ---------TlEPC~MC~~Ai~~agI~-rVvy 100 (149) -+-||-+|-..|...+-. +|++ T Consensus 84 ~~~~~~~~~~~sPCG~CRQvl~Ef~~~~~viv 115 (139) T PRK06848 84 PHEDDREIRVVSPCGACRELISDYDKNTRVIV 115 (139) T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEE T ss_conf 88777765221782789999999789988999 No 22 >PRK08298 cytidine deaminase; Validated Probab=97.30 E-value=0.0061 Score=38.57 Aligned_cols=101 Identities=12% Similarity=0.063 Sum_probs=69.2 Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEE-ECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE- Q ss_conf 9856999999999999887579980899998-38909998734735448864251134456666414885454116886- Q gi|255764464|r 1 MKKGNVFMSCALEEAQNAALRNEIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV- 78 (149) Q Consensus 1 M~~d~~~M~~A~~~A~~a~~~g~~PvGaviv-~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt- 78 (149) |+.|....+.|+++-++.+..|.. ++|.|. ++|+|+. |-|--+.+...+..||..||-+|-+. +...+.-..+.. T Consensus 1 m~~~q~Lv~~A~~~~~~ry~~~~~-gaAAllt~dG~I~t-G~NvEnasy~~~lCAEr~Ai~~Avs~-G~r~~~~I~V~~~ 77 (128) T PRK08298 1 MNIEQALYDAAKELLEQRYPNGWG-GAAAMRTEDGTILT-SVAPEVINASTELCMETGAICEAHKL-QKRVTHSICVARE 77 (128) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCC-EEEEEEECCCCEEE-EECCCCCCCCCCCCHHHHHHHHHHHC-CCCEEEEEEEEEC T ss_conf 947899999999999974746675-38999947997999-74215566774515778999999976-9946999999916 Q ss_pred -------CCCCCHHHHHHHHHCCCC-EEEEEECC Q ss_conf -------167768898999860888-59997117 Q gi|255764464|r 79 -------TLEPCTMCAAAISLARIR-RLYYGASN 104 (149) Q Consensus 79 -------TlEPC~MC~~Ai~~agI~-rVvyg~~d 104 (149) -+-||-+|-..|...+=. +|+....| T Consensus 78 ~~~~~~~vl~PCG~CRQ~L~Efg~d~~V~v~~~d 111 (128) T PRK08298 78 NEHSPLKVLSPCGVCQERLFYWGPDVMVAVTNAD 111 (128) T ss_pred CCCCCEEEECCCHHHHHHHHHHCCCCEEEEECCC T ss_conf 8888726658977999999997999789996899 No 23 >KOG0833 consensus Probab=95.64 E-value=0.15 Score=30.20 Aligned_cols=90 Identities=18% Similarity=0.082 Sum_probs=55.9 Q ss_pred HHHHHHHHHHHC-----CCCCEEEEEEE-CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE----C Q ss_conf 999999988757-----99808999983-8909998734735448864251134456666414885454116886----1 Q gi|255764464|r 10 CALEEAQNAALR-----NEIPVGAVAVL-NNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV----T 79 (149) Q Consensus 10 ~A~~~A~~a~~~-----g~~PvGaviv~-~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt----T 79 (149) .-+.++++|... -+.||||++.- +|+| -.|-|-.+-...++-|||..||.++...--++....+.+-+ = T Consensus 23 ~L~~l~~~A~~~AyaPyS~fkVGA~~r~ssGri-f~G~NVEn~~~~~sIcAEr~ai~~l~l~g~~k~~~~aV~~~~~~~f 101 (173) T KOG0833 23 ELLKLARKAMKLAYAPYSKFKVGAAGRASSGRI-FLGVNVENASYHHSICAERFAIANLALNGERKFRAIAVVAYEDGDF 101 (173) T ss_pred HHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCE-EEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCCC T ss_conf 999999999985348855784478997059838-9851321467777621999999999970765414799995378876 Q ss_pred CCCCHHHHHHHHHCCCCEEEE Q ss_conf 677688989998608885999 Q gi|255764464|r 80 LEPCTMCAAAISLARIRRLYY 100 (149) Q Consensus 80 lEPC~MC~~Ai~~agI~rVvy 100 (149) ..||-.|-.-|..-+-.-.++ T Consensus 102 ~tPCG~CRQfl~Ef~~~~~l~ 122 (173) T KOG0833 102 TTPCGVCRQFLREFGNASLLL 122 (173) T ss_pred CCCCHHHHHHHHHHHHCCEEE T ss_conf 797588999999984140046 No 24 >PRK09027 cytidine deaminase; Provisional Probab=94.60 E-value=0.29 Score=28.46 Aligned_cols=67 Identities=24% Similarity=0.235 Sum_probs=46.2 Q ss_pred CCCEEEEEEE-CCEEEEEEECCCCC--CCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHC Q ss_conf 9808999983-89099987347354--48864251134456666414885454116886167768898999860 Q gi|255764464|r 23 EIPVGAVAVL-NNKIISRAGNRNRE--LKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAAISLA 93 (149) Q Consensus 23 ~~PvGaviv~-~g~ii~~g~N~~~~--~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC~MC~~Ai~~a 93 (149) +..||||-.- .|++ =.|-|.... ..+-|-|||-.||..|+.+-.+ .+ ..|.||--||-+|-.=+-.- T Consensus 70 ~F~VGAia~G~SG~~-Y~GaN~EF~g~~l~~sVHAEQ~aI~~Awl~gE~-~l--~~iaVn~~PCGHCRQFmnEL 139 (295) T PRK09027 70 HFNVGAIARGLSGNF-YFGANMEFAGAALQQTVHAEQSAISHAWLRGEK-GI--ADITVNYTPCGHCRQFMNEL 139 (295) T ss_pred CCEEEEEEECCCCCE-EEEECCCCCCCCCCCEEEHHHHHHHHHHHCCCC-CC--EEEEEECCCCHHHHHHHHHC T ss_conf 773558996388767-875044558998666311999999999973765-53--06885057745789999863 No 25 >pfam08210 APOBEC_N APOBEC-like N-terminal domain. A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). Probab=93.21 E-value=0.14 Score=30.42 Aligned_cols=56 Identities=25% Similarity=0.366 Sum_probs=37.5 Q ss_pred EEEEEECCCCCCCCCCCCCHHHHHHHHHH-H-CCCCCCCCEEEEECCCCCHHHHHHHHH Q ss_conf 99987347354488642511344566664-1-488545411688616776889899986 Q gi|255764464|r 36 IISRAGNRNRELKDVTAHAEILAIRMGCR-I-LSQEILPEVDLYVTLEPCTMCAAAISL 92 (149) Q Consensus 36 ii~~g~N~~~~~~d~t~HAEi~ai~~a~~-~-~~~~~l~~~tlYtTlEPC~MC~~Ai~~ 92 (149) .+..|+-+ ++..++-.|||+.-|.+... . .....-=.-|-|+|=.||.-|+..+.. T Consensus 40 ~~~~G~l~-n~~~~~~~HaE~~Fl~~~~~~~~~~~~~~y~VTwy~SWSPC~~Ca~~v~~ 97 (116) T pfam08210 40 SLDRGILR-NEVANTGCHAELCFLEWFGSLRLLPADQRYSVTWYVSWSPCANCAQKVAE 97 (116) T ss_pred CEECCEEC-CCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCHHHHHHHHHH T ss_conf 21002674-67788775289999999744346897776999999653876999999999 No 26 >TIGR01355 cyt_deam_dimer cytidine deaminase; InterPro: IPR006263 Cytidine deaminase is a homodimeric zinc metalloprotein found in Arabidopis and some Proteobacteria. A related, homotetrameric form with a much smaller subunit is found most bacteria and in animals, IPR006262 from INTERPRO. Both types may act on deoxycytidine as well as cytidine. ; GO: 0004126 cytidine deaminase activity, 0046087 cytidine metabolic process. Probab=86.44 E-value=2.3 Score=23.12 Aligned_cols=68 Identities=19% Similarity=0.187 Sum_probs=41.3 Q ss_pred CCCEEEEEE-ECCEEEEEEECCCCCCC--CCCCCCHHHHHHHHHHHCCCCCCCCEEEEEC------CCCCHHHHHHHHH Q ss_conf 980899998-38909998734735448--8642511344566664148854541168861------6776889899986 Q gi|255764464|r 23 EIPVGAVAV-LNNKIISRAGNRNRELK--DVTAHAEILAIRMGCRILSQEILPEVDLYVT------LEPCTMCAAAISL 92 (149) Q Consensus 23 ~~PvGaviv-~~g~ii~~g~N~~~~~~--d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtT------lEPC~MC~~Ai~~ 92 (149) +.+||||-. ..|++ =-|-|...... .-|=|||--+|-.++=+ +.+.|...++=.+ -.||.+|-.=+-. T Consensus 42 ~f~VgAvgrGsSGR~-YLGvNvEF~gl~l~~sIHAEQfli~hl~Ln-~Er~l~~lavs~ngdc~~F~~PCghCrQFl~E 118 (311) T TIGR01355 42 KFNVGAVGRGSSGRF-YLGVNVEFPGLPLHHSIHAEQFLISHLALN-NERGLNDLAVSSNGDCSVFAAPCGHCRQFLNE 118 (311) T ss_pred CCCEEEEEEECCCCE-EEEECEECCCCCCCCCCCHHHHHHHHHHHC-CCCCEEEEEEEECCCEEECCCCCCCHHHHHHH T ss_conf 343278998314764-200011047858786376148999999970-79850046785157653448878517789986 No 27 >PRK04388 disulfide bond formation protein B; Provisional Probab=71.93 E-value=1.5 Score=24.15 Aligned_cols=12 Identities=42% Similarity=1.013 Sum_probs=9.1 Q ss_pred EECCCCCHHHHH Q ss_conf 861677688989 Q gi|255764464|r 77 YVTLEPCTMCAA 88 (149) Q Consensus 77 YtTlEPC~MC~~ 88 (149) ..-+|||+||-. T Consensus 32 ~~gL~PCpLCI~ 43 (172) T PRK04388 32 HLGLEPCPLCIF 43 (172) T ss_pred HCCCCCCHHHHH T ss_conf 718888788999 No 28 >smart00552 ADEAMc tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase). Probab=71.41 E-value=9.2 Score=19.46 Aligned_cols=37 Identities=38% Similarity=0.460 Sum_probs=22.5 Q ss_pred CCCHHHHHHHHHHHC----------------------CCCCCC---CEEEEECCCCCHHHHH Q ss_conf 251134456666414----------------------885454---1168861677688989 Q gi|255764464|r 52 AHAEILAIRMGCRIL----------------------SQEILP---EVDLYVTLEPCTMCAA 88 (149) Q Consensus 52 ~HAEi~ai~~a~~~~----------------------~~~~l~---~~tlYtTlEPC~MC~~ 88 (149) .|||+.|.+-..+.+ +...|+ ..-||+|--||-=|+. T Consensus 71 ~HAEVlARRaf~r~Ly~el~~~~~~~~~sif~~~~~~~~~~Lk~~v~lhlYiS~~PCGDAsi 132 (374) T smart00552 71 CHAEILARRGFLRFLYSELQLFNSSSEDSIFEKNKEGGKYKLKSNVLFHLYISTLPCGDASI 132 (374) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCEEECCCCEEEEEECCCCCCCCCC T ss_conf 12999999999999999999871788885689878898357469838999967798620134 No 29 >PRK01749 disulfide bond formation protein B; Provisional Probab=68.49 E-value=2 Score=23.46 Aligned_cols=12 Identities=42% Similarity=1.007 Sum_probs=9.1 Q ss_pred EECCCCCHHHHH Q ss_conf 861677688989 Q gi|255764464|r 77 YVTLEPCTMCAA 88 (149) Q Consensus 77 YtTlEPC~MC~~ 88 (149) +.-+|||+||-. T Consensus 35 ~lgL~PCpLCI~ 46 (175) T PRK01749 35 VMLLKPCVMCIY 46 (175) T ss_pred HCCCCCCHHHHH T ss_conf 818886489999 No 30 >pfam08211 dCMP_cyt_deam_2 Cytidine and deoxycytidylate deaminase zinc-binding region. Probab=66.41 E-value=12 Score=18.82 Aligned_cols=60 Identities=12% Similarity=0.051 Sum_probs=43.0 Q ss_pred HHHHHHHHHHHHHHHHHCC-CCCEEEEEE-ECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 6999999999999887579-980899998-389099987347354488642511344566664 Q gi|255764464|r 4 GNVFMSCALEEAQNAALRN-EIPVGAVAV-LNNKIISRAGNRNRELKDVTAHAEILAIRMGCR 64 (149) Q Consensus 4 d~~~M~~A~~~A~~a~~~g-~~PvGaviv-~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~ 64 (149) ++...+.|++-|++++..- +.|+|++|. .+|+|. .|+|-.+-.-||+.-+--.||...-- T Consensus 33 ~d~L~~~Al~Aa~~syaPYS~~~~G~Al~~~~G~i~-~G~~~EnAAfnPSl~PlQaAL~~~~~ 94 (124) T pfam08211 33 SDALVQRALAAANRSHAPYSKSPSGVALEDKDGKVY-AGRYAENAAFNPSLPPLQAALVDFVA 94 (124) T ss_pred CCHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCEE-EEEEEECCCCCCCCCHHHHHHHHHHH T ss_conf 479999999999825588567960179993799999-85652302268983589999999997 No 31 >PRK02110 disulfide bond formation protein B; Provisional Probab=62.26 E-value=3 Score=22.38 Aligned_cols=11 Identities=27% Similarity=0.878 Sum_probs=8.6 Q ss_pred ECCCCCHHHHH Q ss_conf 61677688989 Q gi|255764464|r 78 VTLEPCTMCAA 88 (149) Q Consensus 78 tTlEPC~MC~~ 88 (149) .-+|||+||-. T Consensus 36 lgL~PC~LCI~ 46 (169) T PRK02110 36 KGEDPCPLCII 46 (169) T ss_pred CCCCCCHHHHH T ss_conf 08876576999 No 32 >TIGR00707 argD acetylornithine and succinylornithine aminotransferases; InterPro: IPR004636 This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from Escherichia coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (2.6.1.11 from EC), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism . Members of this family may also act on ornithine, like ornithine aminotransferase (2.6.1.13 from EC) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (2.6.1.17 from EC, DapC, an enzyme of lysine biosynthesis) . ; GO: 0008483 transaminase activity, 0006525 arginine metabolic process. Probab=51.81 E-value=2.5 Score=22.88 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=18.1 Q ss_pred CCCCEEEEEEEC--CEEEEEEECCCCCCCCCCC Q ss_conf 998089999838--9099987347354488642 Q gi|255764464|r 22 NEIPVGAVAVLN--NKIISRAGNRNRELKDVTA 52 (149) Q Consensus 22 g~~PvGaviv~~--g~ii~~g~N~~~~~~d~t~ 52 (149) |.+||||+|++. .+.+.-|-|-+-=.+||.+ T Consensus 260 gG~PiGA~~~~e~~a~~~~~G~HGsTFGGNPLA 292 (402) T TIGR00707 260 GGVPIGAVLAKEEVAEALTPGDHGSTFGGNPLA 292 (402) T ss_pred CCCHHHHHEEHHHHHHHCCCCCCCCCCCCCHHH T ss_conf 782022320236787315898986667873899 No 33 >pfam02137 A_deamin Adenosine-deaminase (editase) domain. Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. The region described in this family includes the catalytic domain, which has three active site sequence motifs characteristic of ADARs, each containing a cysteine or histidine that binds zinc. Probab=50.34 E-value=13 Score=18.51 Aligned_cols=34 Identities=41% Similarity=0.561 Sum_probs=20.4 Q ss_pred CCCHHHHHHHHHHHC----------------------CCCCCC---CEEEEECCCCCHH Q ss_conf 251134456666414----------------------885454---1168861677688 Q gi|255764464|r 52 AHAEILAIRMGCRIL----------------------SQEILP---EVDLYVTLEPCTM 85 (149) Q Consensus 52 ~HAEi~ai~~a~~~~----------------------~~~~l~---~~tlYtTlEPC~M 85 (149) .|||++|.+-..+.+ +...|+ ..-||+|--||-= T Consensus 24 ~HAEVlARR~f~r~Ly~el~~~~~~~~~~~~~~~~~~~~~~Lk~~v~lhlYiS~~PCGd 82 (325) T pfam02137 24 CHAEILARRGFLRFLYEELLLLANGGDKESSIFEAEEGKFRLKPGVKLHLYISTAPCGD 82 (325) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEECCCCEEEEEECCCCCCC T ss_conf 45999999999999999999974589887078757998647569838999966688876 No 34 >COG4827 Predicted transporter [General function prediction only] Probab=43.08 E-value=20 Score=17.48 Aligned_cols=26 Identities=15% Similarity=0.485 Sum_probs=20.1 Q ss_pred CCCCCCEEEEECCCCCHHHHHHHHHC Q ss_conf 85454116886167768898999860 Q gi|255764464|r 68 QEILPEVDLYVTLEPCTMCAAAISLA 93 (149) Q Consensus 68 ~~~l~~~tlYtTlEPC~MC~~Ai~~a 93 (149) ..|.++.+-..-.-|||-|.+|...+ T Consensus 99 ~~D~sK~~~~ais~PCPvCl~avavs 124 (239) T COG4827 99 KSDVSKHTFLAISMPCPVCLGAVAVS 124 (239) T ss_pred CCCHHHCEEEEEECCCCHHHHHHHHH T ss_conf 76312301478855870788999999 No 35 >TIGR01885 Orn_aminotrans ornithine--oxo-acid transaminase; InterPro: IPR010164 Ornithine aminotransferase catalyses the conversion of L-ornithine and a 2-oxo acid to L-glutamate 5-semialdehyde and an L-amino acid. This enzyme is found in low-GC bacteria, where it is responsible for the fourth step in arginine biosynthesis, and in the mitochondrial matrix of eukaryotes, where it controls L-ornithine levels in tissues. In human hereditary ornithine aminotransferase deficiency, the elevated levels of intraocular concentrations of ornithine are responsible for gyrate atrophy, which affects the CNS and peripheral nervous system ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding. Probab=41.50 E-value=17 Score=17.81 Aligned_cols=37 Identities=14% Similarity=0.068 Sum_probs=24.5 Q ss_pred HHHHCCCCCEEEEEEECCE--EEEEE--ECCCCCCCCCCCC Q ss_conf 8875799808999983890--99987--3473544886425 Q gi|255764464|r 17 NAALRNEIPVGAVAVLNNK--IISRA--GNRNRELKDVTAH 53 (149) Q Consensus 17 ~a~~~g~~PvGaviv~~g~--ii~~g--~N~~~~~~d~t~H 53 (149) ||+.-|=.||||||-+++- ++-=| .|.+-=.+||.+= T Consensus 274 KALsGGv~PiSa~la~~dim~vl~PGPF~HGSTfGGNPLAc 314 (426) T TIGR01885 274 KALSGGVYPISAVLADDDIMSVLKPGPFEHGSTFGGNPLAC 314 (426) T ss_pred HHHCCCCCCEEEEEECCCEEECCCCCCCCCCCCCCCCHHHH T ss_conf 23458946224366646401211764865677688757899 No 36 >TIGR02373 photo_yellow photoactive yellow protein; InterPro: IPR012130 Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by IPR012743 from INTERPRO is required for its biosynthesis. The modified Cys is in a PAS domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.; GO: 0009881 photoreceptor activity, 0007602 phototransduction, 0018298 protein-chromophore linkage. Probab=40.97 E-value=8.3 Score=19.75 Aligned_cols=29 Identities=24% Similarity=0.351 Sum_probs=19.1 Q ss_pred HHHHH-HHCCCCCEEEEEEE-CCEEEEEEECCC Q ss_conf 99988-75799808999983-890999873473 Q gi|255764464|r 14 EAQNA-ALRNEIPVGAVAVL-NNKIISRAGNRN 44 (149) Q Consensus 14 ~A~~a-~~~g~~PvGaviv~-~g~ii~~g~N~~ 44 (149) +|+.. ......|||||.++ .|.|+. ||+. T Consensus 16 la~m~~A~~d~LpfGAiqlD~~G~I~~--YN~a 46 (126) T TIGR02373 16 LARMGDAQLDSLPFGAIQLDGSGRILK--YNAA 46 (126) T ss_pred HCCCCCCCCCCCCCCEEEECCCCCHHH--HHCC T ss_conf 326898642255410488669883021--1011 No 37 >cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Probab=40.85 E-value=31 Score=16.25 Aligned_cols=55 Identities=16% Similarity=0.140 Sum_probs=32.2 Q ss_pred CEEEEEEECC-EEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCC Q ss_conf 0899998389-09998734735448864251134456666414885454116886167 Q gi|255764464|r 25 PVGAVAVLNN-KIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLE 81 (149) Q Consensus 25 PvGaviv~~g-~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlE 81 (149) -.|.++..++ .+....... . ......+||+.||..+.+..........++||--. T Consensus 16 G~g~v~~~~~~~~~~~~~~~-~-~~~s~~~aEl~Al~~al~~~~~~~~~~i~i~tDS~ 71 (130) T cd06222 16 GAGVVLRDPGGEVLLSGGLL-G-GNTTNNRAELLALIEALELALELGGKKVNIYTDSQ 71 (130) T ss_pred EEEEEEEECCCCEEEEEEEC-C-CCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHH T ss_conf 99999998995189997503-7-88652999999999999999868997799995569 No 38 >pfam02600 DsbB Disulfide bond formation protein DsbB. This family consists of disulfide bond formation protein DsbB from bacteria. The DsbB protein oxidizes the periplasmic protein DsbA which in turn oxidizes cysteines in other periplasmic proteins in order to make disulfide bonds. DsbB acts as a redox potential transducer across the cytoplasmic membrane and is an integral membrane protein. DsbB posses six cysteines four of which are necessary for it proper function in vivo. Probab=38.58 E-value=12 Score=18.71 Aligned_cols=11 Identities=45% Similarity=1.174 Sum_probs=8.1 Q ss_pred ECCCCCHHHHH Q ss_conf 61677688989 Q gi|255764464|r 78 VTLEPCTMCAA 88 (149) Q Consensus 78 tTlEPC~MC~~ 88 (149) --++||++|-. T Consensus 32 ~gl~PC~LCi~ 42 (159) T pfam02600 32 LGLEPCPLCIY 42 (159) T ss_pred CCCCCCHHHHH T ss_conf 38888565999 No 39 >KOG1774 consensus Probab=37.33 E-value=24 Score=16.96 Aligned_cols=35 Identities=14% Similarity=0.332 Sum_probs=24.9 Q ss_pred HHHHHHHHHHHHHHH--HCCCCCEEEEEEECCEEEEE Q ss_conf 999999999999887--57998089999838909998 Q gi|255764464|r 5 NVFMSCALEEAQNAA--LRNEIPVGAVAVLNNKIISR 39 (149) Q Consensus 5 ~~~M~~A~~~A~~a~--~~g~~PvGaviv~~g~ii~~ 39 (149) +.||.+.++.|.+-. ..+..|.|-++.++|.|-.. T Consensus 47 DEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli 83 (88) T KOG1774 47 DEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLI 83 (88) T ss_pred HHHHHHHHCCHHHCCCCCCCCCCCCCEEECCCCEEEE T ss_conf 8845531011532022135777013189738738999 No 40 >pfam09930 DUF2162 Predicted transporter (DUF2162). Members of this family of bacterial proteins are thought to be membrane transporters, but their exact function has not, as yet, been elucidated. Probab=31.67 E-value=32 Score=16.19 Aligned_cols=25 Identities=20% Similarity=0.515 Sum_probs=17.4 Q ss_pred CCCCCEEEEECCCCCHHHHHHHHHC Q ss_conf 5454116886167768898999860 Q gi|255764464|r 69 EILPEVDLYVTLEPCTMCAAAISLA 93 (149) Q Consensus 69 ~~l~~~tlYtTlEPC~MC~~Ai~~a 93 (149) ++.+..|-..=.=|||-|.+|+..| T Consensus 94 kd~s~~t~la~~~PCPvCl~A~~~S 118 (228) T pfam09930 94 KDVSKRTFLAMSAPCPVCLGAVILS 118 (228) T ss_pred CCCCCCHHEEEECCCHHHHHHHHHH T ss_conf 8887512303546870778999999 No 41 >cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Probab=31.07 E-value=7.3 Score=20.06 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=24.1 Q ss_pred HHHHHHHHHHHHHHHHCC-CCCEEEEEEECCEEEEEE Q ss_conf 999999999999887579-980899998389099987 Q gi|255764464|r 5 NVFMSCALEEAQNAALRN-EIPVGAVAVLNNKIISRA 40 (149) Q Consensus 5 ~~~M~~A~~~A~~a~~~g-~~PvGaviv~~g~ii~~g 40 (149) +.||.+.++.|.+-...+ ..+.|.++++.+.|+..+ T Consensus 31 D~~mNLVLdda~E~~~~~~~~~lG~~viRG~sVv~i~ 67 (72) T cd01719 31 DPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLE 67 (72) T ss_pred CCCCEEEEEEEEEECCCCCEEECCEEEECCCEEEEEE T ss_conf 7420277230588415797007028999789899997 No 42 >KOG1783 consensus Probab=30.32 E-value=47 Score=15.22 Aligned_cols=35 Identities=17% Similarity=0.340 Sum_probs=25.2 Q ss_pred HHHHHHHHHHHHHHHHCCCCC--EEEEEEECCEEEEEE Q ss_conf 999999999999887579980--899998389099987 Q gi|255764464|r 5 NVFMSCALEEAQNAALRNEIP--VGAVAVLNNKIISRA 40 (149) Q Consensus 5 ~~~M~~A~~~A~~a~~~g~~P--vGaviv~~g~ii~~g 40 (149) +-||.+|++.+..-. .|..| +|.+.+++..|+-.+ T Consensus 37 DgymNiaLe~tee~~-ngql~n~ygdaFirGnnVlyIs 73 (77) T KOG1783 37 DGYMNIALESTEEYV-NGQLKNKYGDAFIRGNNVLYIS 73 (77) T ss_pred HHHHHHHHHHHHHHH-CCCCCCCCCCEEECCCCEEEEE T ss_conf 447788888789986-6744231122366266079997 No 43 >cd06908 M14_AGBL4_like Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-4, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL4 and the mouse cytosolic carboxypeptidase (CCP)-6. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal Probab=29.46 E-value=40 Score=15.62 Aligned_cols=29 Identities=21% Similarity=0.106 Sum_probs=23.0 Q ss_pred EEEECCCCCCCCCCCCCHHHHHHHHHHHC Q ss_conf 98734735448864251134456666414 Q gi|255764464|r 38 SRAGNRNRELKDVTAHAEILAIRMGCRIL 66 (149) Q Consensus 38 ~~g~N~~~~~~d~t~HAEi~ai~~a~~~~ 66 (149) |...|+.+...|+..|.++-++++..+.+ T Consensus 108 G~dLNR~w~~p~~~~~P~i~~~k~li~~~ 136 (261) T cd06908 108 GHDLNRHWHDPSPWAHPTLHAVKNLLKEL 136 (261) T ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 89868687998945297999999999999 No 44 >PRK13907 rnhA ribonuclease H; Provisional Probab=29.35 E-value=49 Score=15.12 Aligned_cols=57 Identities=12% Similarity=0.033 Sum_probs=26.2 Q ss_pred HHCCCC-C--EEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEE Q ss_conf 757998-0--89999838909998734735448864251134456666414885454116886 Q gi|255764464|r 19 ALRNEI-P--VGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYV 78 (149) Q Consensus 19 ~~~g~~-P--vGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYt 78 (149) .++|++ | .|.+|..++.++..+.--...+.| -||..|+-.+.+..-....+...+|+ T Consensus 9 asrgNPG~ag~Gv~i~~~~~~~~~~~~lg~~TNN---~AEy~Ali~gL~~a~~~~~~~l~i~~ 68 (128) T PRK13907 9 ASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNH---EAEYHALLAALKYCTEHNYNIVSFRT 68 (128) T ss_pred CCCCCCCCEEEEEEEEECCEEEEEEEECCCCCCH---HHHHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 4799997706999999098679998614875577---99999999999999976998799982 No 45 >KOG2777 consensus Probab=28.48 E-value=50 Score=15.03 Aligned_cols=33 Identities=42% Similarity=0.554 Sum_probs=21.0 Q ss_pred CCCHHHHHHHHHHHC---------------------CC-CCCC---CEEEEECCCCCH Q ss_conf 251134456666414---------------------88-5454---116886167768 Q gi|255764464|r 52 AHAEILAIRMGCRIL---------------------SQ-EILP---EVDLYVTLEPCT 84 (149) Q Consensus 52 ~HAEi~ai~~a~~~~---------------------~~-~~l~---~~tlYtTlEPC~ 84 (149) .||||.|.|-..+.+ +. ..|+ -.-||+|--||- T Consensus 243 cHAEIlARR~llRfLy~eL~l~~~~~~~Sif~~~~~~~~~~LK~nv~fhLYiS~~PCG 300 (542) T KOG2777 243 CHAEILARRGLLRFLYSELQLYNSEKKDSIFEKSKEGGKFTLKENVLFHLYISTSPCG 300 (542) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCEECCCCCEEEEEECCCCCC T ss_conf 1099999999999999999986344887056556888733337880899996479997 No 46 >COG1624 Uncharacterized conserved protein [Function unknown] Probab=28.38 E-value=49 Score=15.09 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=13.5 Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 9999999998875799808999983 Q gi|255764464|r 8 MSCALEEAQNAALRNEIPVGAVAVL 32 (149) Q Consensus 8 M~~A~~~A~~a~~~g~~PvGaviv~ 32 (149) +..|++.|.++.+. -++||++|- T Consensus 114 ~i~ai~~av~~ls~--~kiGALivi 136 (247) T COG1624 114 LIDAIEKAVKGLSG--RKIGALIVI 136 (247) T ss_pred HHHHHHHHHHHHCC--CCCEEEEEE T ss_conf 99999999985257--861379999 No 47 >cd04673 Nudix_Hydrolase_15 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate Probab=28.09 E-value=51 Score=14.99 Aligned_cols=18 Identities=22% Similarity=0.326 Sum_probs=14.2 Q ss_pred CEEEEEEECCEEEEEEEC Q ss_conf 089999838909998734 Q gi|255764464|r 25 PVGAVAVLNNKIISRAGN 42 (149) Q Consensus 25 PvGaviv~~g~ii~~g~N 42 (149) -|||||+++|+||-.-.+ T Consensus 2 ~v~~ii~~~~kvLL~~R~ 19 (122) T cd04673 2 AVGAVVFRGGRVLLVRRA 19 (122) T ss_pred EEEEEEEECCEEEEEEEC T ss_conf 899999989999999969 No 48 >COG1495 DsbB Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones] Probab=27.96 E-value=24 Score=17.00 Aligned_cols=10 Identities=50% Similarity=1.218 Sum_probs=7.5 Q ss_pred CCCCCHHHHH Q ss_conf 1677688989 Q gi|255764464|r 79 TLEPCTMCAA 88 (149) Q Consensus 79 TlEPC~MC~~ 88 (149) -.|||++|.. T Consensus 38 g~~PC~LC~~ 47 (170) T COG1495 38 GLEPCPLCLY 47 (170) T ss_pred CCCCCHHHHH T ss_conf 8887197999 No 49 >KOG1228 consensus Probab=27.31 E-value=30 Score=16.34 Aligned_cols=15 Identities=33% Similarity=0.395 Sum_probs=12.2 Q ss_pred CCCEEEEECCCCCHH Q ss_conf 541168861677688 Q gi|255764464|r 71 LPEVDLYVTLEPCTM 85 (149) Q Consensus 71 l~~~tlYtTlEPC~M 85 (149) -.||.||+|+.||.. T Consensus 73 qgg~WLyVTHd~~a~ 87 (256) T KOG1228 73 QGGCWLYVTHDLCAK 87 (256) T ss_pred CCCEEEEEECCCCHH T ss_conf 774599995560010 No 50 >KOG1682 consensus Probab=24.72 E-value=59 Score=14.62 Aligned_cols=49 Identities=27% Similarity=0.403 Sum_probs=30.9 Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEE-ECCEEEEEEECCCCCCCCC--CCCCHHH Q ss_conf 999999999887579980899998-3890999873473544886--4251134 Q gi|255764464|r 8 MSCALEEAQNAALRNEIPVGAVAV-LNNKIISRAGNRNRELKDV--TAHAEIL 57 (149) Q Consensus 8 M~~A~~~A~~a~~~g~~PvGaviv-~~g~ii~~g~N~~~~~~d~--t~HAEi~ 57 (149) |-.+++-+-.. +..+.-+-+||+ .+|+|-+.|||..+-..+| --|||+- T Consensus 60 M~~~Lq~~ll~-d~d~~dlr~viita~GkifSaGH~LKELt~e~g~d~haevF 111 (287) T KOG1682 60 MMCALQDALLK-DKDNLDLRCVIITAQGKIFSAGHNLKELTNEPGSDIHAEVF 111 (287) T ss_pred HHHHHHHHHHH-CCCCCCEEEEEEECCCCCCCCCCCHHHHHCCCCCHHHHHHH T ss_conf 99999999851-24446515999935885224654577762475520789999 No 51 >TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310 These are a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of Escherichia coli. . Probab=24.29 E-value=60 Score=14.57 Aligned_cols=69 Identities=19% Similarity=0.137 Sum_probs=36.4 Q ss_pred CEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHH-HHHHHHHCCCCEEEEEEC Q ss_conf 0899998389099987347354488642511344566664148854541168861677688-989998608885999711 Q gi|255764464|r 25 PVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCTM-CAAAISLARIRRLYYGAS 103 (149) Q Consensus 25 PvGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC~M-C~~Ai~~agI~rVvyg~~ 103 (149) =||+|+|.||+||..=+..++ | |-++-.=-+..--+.+..+.++ |=.. |+.-|+ .-+.--||=|. T Consensus 22 qiGiV~v~DgeIv~~f~T~VN----P--~~~~pp~I~eLTGisd~~l~~A-------P~F~qVA~~i~-~~l~D~iFVAH 87 (944) T TIGR01407 22 QIGIVLVEDGEIVDTFATDVN----P--NEPIPPFIQELTGISDEQLKQA-------PYFSQVAQEIY-DLLEDGIFVAH 87 (944) T ss_pred EEEEEEEECCCEEEECCCCCC----C--CCCCCCHHHHHCCCCHHHHCCC-------CCHHHHHHHHH-HHHCCCEEEEE T ss_conf 998899855814320126778----8--9877611454228776864048-------88879999999-87429727761 Q ss_pred CCCC Q ss_conf 7988 Q gi|255764464|r 104 NPKG 107 (149) Q Consensus 104 d~~~ 107 (149) |-++ T Consensus 88 NV~F 91 (944) T TIGR01407 88 NVHF 91 (944) T ss_pred CHHC T ss_conf 0150 No 52 >pfam05988 DUF899 Bacterial protein of unknown function (DUF899). This family consists of several uncharacterized bacterial proteins of unknown function. Probab=23.76 E-value=23 Score=17.13 Aligned_cols=14 Identities=14% Similarity=0.199 Sum_probs=10.1 Q ss_pred CCCCHHHHHHHHHC Q ss_conf 67768898999860 Q gi|255764464|r 80 LEPCTMCAAAISLA 93 (149) Q Consensus 80 lEPC~MC~~Ai~~a 93 (149) -|||++|+..+-+. T Consensus 82 ~~~C~gCS~~~D~~ 95 (211) T pfam05988 82 EAGCPGCSFLADHF 95 (211) T ss_pred CCCCCCCHHHHHCC T ss_conf 89999722245275 No 53 >PRK10811 rne ribonuclease E; Reviewed Probab=23.70 E-value=19 Score=17.57 Aligned_cols=17 Identities=12% Similarity=0.159 Sum_probs=12.0 Q ss_pred CCEEEEECCCCCHHHHH Q ss_conf 41168861677688989 Q gi|255764464|r 72 PEVDLYVTLEPCTMCAA 88 (149) Q Consensus 72 ~~~tlYtTlEPC~MC~~ 88 (149) .-.-.-++.++||.|.| T Consensus 393 rpSL~es~~~~CP~C~G 409 (1063) T PRK10811 393 SPSLGESSHHVCPRCSG 409 (1063) T ss_pred CHHHHHHCCCCCCCCCC T ss_conf 14457542774888877 No 54 >COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Probab=23.40 E-value=29 Score=16.50 Aligned_cols=29 Identities=14% Similarity=0.307 Sum_probs=19.2 Q ss_pred HHHHHHHHCCCCCCCCEEEEECCCCCHHHHH Q ss_conf 4566664148854541168861677688989 Q gi|255764464|r 58 AIRMGCRILSQEILPEVDLYVTLEPCTMCAA 88 (149) Q Consensus 58 ai~~a~~~~~~~~l~~~tlYtTlEPC~MC~~ 88 (149) ||.+|.+++ ..++-|--+++-+||.-|+- T Consensus 46 al~~a~~~i--~~C~~C~~~te~d~C~ICsd 74 (198) T COG0353 46 ALLEAKENI--KHCSVCGNLTESDPCDICSD 74 (198) T ss_pred HHHHHHHCC--CCCCCCCCCCCCCCCCCCCC T ss_conf 999999738--63575678288986767698 No 55 >pfam01235 Na_Ala_symp Sodium:alanine symporter family. Probab=21.45 E-value=61 Score=14.54 Aligned_cols=18 Identities=6% Similarity=0.292 Sum_probs=15.2 Q ss_pred CCHHHHHHHHHHHHHHHC Q ss_conf 218999999899988409 Q gi|255764464|r 132 ISEQRSRQIIQDFFKERR 149 (149) Q Consensus 132 vl~ee~~~Ll~~ff~~kR 149 (149) .|..+..++++|||+|+| T Consensus 386 lL~~~v~~~~kdY~~q~k 403 (415) T pfam01235 386 LLSKVAYEALKDYERQLK 403 (415) T ss_pred HHHHHHHHHHHHHHHHHH T ss_conf 987999999999999996 No 56 >KOG3752 consensus Probab=21.22 E-value=49 Score=15.12 Aligned_cols=31 Identities=16% Similarity=0.092 Sum_probs=24.3 Q ss_pred CCHHHHHHHHHHHCCCCCCCCEEEEECCCCC Q ss_conf 5113445666641488545411688616776 Q gi|255764464|r 53 HAEILAIRMGCRILSQEILPEVDLYVTLEPC 83 (149) Q Consensus 53 HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC 83 (149) -||+.|+..|.++.......+.+|.|+.|== T Consensus 258 rAEl~Av~~ALkka~~~~~~kv~I~TDS~~~ 288 (371) T KOG3752 258 RAELIAAIEALKKARSKNINKVVIRTDSEYF 288 (371) T ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECHHHH T ss_conf 9999999999999984478747999466999 No 57 >KOG1427 consensus Probab=20.76 E-value=71 Score=14.14 Aligned_cols=27 Identities=15% Similarity=0.150 Sum_probs=14.0 Q ss_pred EEECCEEEEEEECCCCCCCCCCCCCHH Q ss_conf 983890999873473544886425113 Q gi|255764464|r 30 AVLNNKIISRAGNRNRELKDVTAHAEI 56 (149) Q Consensus 30 iv~~g~ii~~g~N~~~~~~d~t~HAEi 56 (149) +.+.|.+++-|+|+.-+.+-..+|+|+ T Consensus 125 ltdtG~v~afGeNK~GQlGlgn~~~~v 151 (443) T KOG1427 125 LTDTGQVLAFGENKYGQLGLGNAKNEV 151 (443) T ss_pred EECCCCEEEECCCCCCCCCCCCCCCCC T ss_conf 913775787216644541546544543 No 58 >TIGR02661 MauD methylamine dehydrogenase accessory protein MauD; InterPro: IPR013478 MauD appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulphide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulphide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded .; GO: 0030416 methylamine metabolic process. Probab=20.07 E-value=55 Score=14.79 Aligned_cols=63 Identities=16% Similarity=0.129 Sum_probs=36.9 Q ss_pred HHCCCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHH Q ss_conf 75799808999983890999873473544886425113445666641488545411688616776889899 Q gi|255764464|r 19 ALRNEIPVGAVAVLNNKIISRAGNRNRELKDVTAHAEILAIRMGCRILSQEILPEVDLYVTLEPCTMCAAA 89 (149) Q Consensus 19 ~~~g~~PvGaviv~~g~ii~~g~N~~~~~~d~t~HAEi~ai~~a~~~~~~~~l~~~tlYtTlEPC~MC~~A 89 (149) +.+-..|.||.|+|.|==||...=. . .=|+.-++++.|-.+.....+ .-|-=|.=-||.|-.. T Consensus 30 LHERS~P~GAM~~DHGPDvG~~aP~-F--~l~~f~G~~V~iG~~~a~~R~-----~LLMFTaPsCPvC~KL 92 (189) T TIGR02661 30 LHERSSPLGAMITDHGPDVGDAAPI-F--NLPDFDGEPVRIGGSIALGRP-----TLLMFTAPSCPVCDKL 92 (189) T ss_pred HHHCCCCCCCCCCCCCCCCCCCCCE-E--CCCCCCCCEEEECCCCCCCCC-----EEEEECCCCCCHHHHH T ss_conf 2203574213020258874555871-0--576667864561175567775-----0354438888532243 Done!