Query gi|254780714|ref|YP_003065127.1| tRNA (guanine-N(1)-)-methyltransferase [Candidatus Liberibacter asiaticus str. psy62] Match_columns 236 No_of_seqs 141 out of 1853 Neff 4.7 Searched_HMMs 39220 Date Sun May 29 19:47:06 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780714.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00088 trmD tRNA (guanine-N 100.0 0 0 772.4 18.4 231 3-234 1-237 (247) 2 PRK00026 trmD tRNA (guanine-N( 100.0 0 0 760.4 22.0 226 3-230 1-226 (226) 3 COG0336 TrmD tRNA-(guanine-N1) 100.0 0 0 751.0 21.5 230 3-235 1-231 (240) 4 PRK01037 trmD tRNA (guanine-N( 100.0 0 0 747.3 21.8 224 3-231 1-224 (357) 5 pfam01746 tRNA_m1G_MT tRNA (Gu 100.0 0 0 440.0 13.6 184 25-224 2-185 (185) 6 COG1576 Uncharacterized conser 96.1 0.15 3.9E-06 31.8 10.6 137 3-159 1-145 (155) 7 pfam02590 SPOUT_MTase Predicte 95.9 0.074 1.9E-06 33.9 8.2 135 3-158 1-145 (155) 8 PRK00103 SPOUT methyltransfera 95.7 0.056 1.4E-06 34.7 6.9 137 3-159 1-145 (156) 9 KOG3073 consensus 90.1 0.25 6.5E-06 30.3 2.7 63 78-143 153-218 (236) 10 COG1756 Mra1 Uncharacterized c 85.7 1.3 3.3E-05 25.6 4.1 62 86-148 149-210 (223) 11 pfam03587 EMG1 EMG1/NEP1 methy 85.4 1.4 3.7E-05 25.3 4.2 64 85-148 130-195 (202) 12 PRK04171 ribosome biogenesis p 82.8 3.4 8.8E-05 22.8 5.2 87 55-151 123-211 (221) 13 cd03108 AdSS Adenylosuccinate 69.5 11 0.00028 19.5 5.1 118 55-189 63-185 (363) 14 TIGR02874 spore_ytfJ sporulati 63.6 3.1 7.9E-05 23.1 1.0 20 50-69 69-88 (132) 15 KOG4066 consensus 63.1 14 0.00037 18.7 5.8 126 3-150 1-142 (177) 16 smart00226 LMWPc Low molecular 61.1 8.3 0.00021 20.3 2.8 15 14-28 9-23 (140) 17 COG3967 DltE Short-chain dehyd 53.4 19 0.00048 17.9 3.6 42 86-127 6-47 (245) 18 cd04259 AAK_AK-DapDC AAK_AK-Da 51.6 18 0.00045 18.1 3.2 102 56-159 6-133 (295) 19 cd04260 AAK_AKi-DapG-BS AAK_AK 49.5 24 0.00061 17.2 4.6 86 56-159 6-91 (244) 20 TIGR02895 spore_sigI RNA polym 48.8 2.8 7.2E-05 23.4 -1.2 18 114-138 30-47 (225) 21 PRK13786 adenylosuccinate synt 47.0 26 0.00067 17.0 3.8 79 58-139 66-149 (424) 22 TIGR01087 murD UDP-N-acetylmur 45.9 25 0.00064 17.1 3.3 44 56-99 410-459 (476) 23 PRK13784 adenylosuccinate synt 44.7 28 0.00072 16.8 3.7 79 58-139 68-151 (428) 24 PRK08210 aspartate kinase I; R 43.7 29 0.00075 16.7 5.9 82 56-158 8-92 (405) 25 COG0104 PurA Adenylosuccinate 41.0 32 0.00082 16.4 3.8 39 58-96 68-106 (430) 26 pfam02481 DNA_processg_A DNA r 39.8 12 0.0003 19.3 0.8 42 89-131 52-93 (210) 27 TIGR00619 sbcd nuclease SbcCD, 39.7 9.1 0.00023 20.0 0.2 28 191-218 82-109 (275) 28 KOG3638 consensus 38.6 10 0.00025 19.8 0.3 13 133-145 227-239 (414) 29 PRK07431 aspartate kinase; Pro 37.3 37 0.00093 16.0 4.6 80 56-158 8-87 (594) 30 PRK01117 adenylosuccinate synt 36.9 37 0.00095 16.0 3.8 42 57-98 67-108 (431) 31 COG0565 LasT rRNA methylase [T 36.5 38 0.00096 15.9 4.1 138 1-157 1-151 (242) 32 KOG4093 consensus 36.2 3.7 9.4E-05 22.6 -2.2 50 7-67 57-106 (144) 33 TIGR00596 rad1 DNA repair prot 36.1 14 0.00036 18.8 0.7 13 130-142 711-723 (939) 34 PRK05906 lipid A biosynthesis 36.1 29 0.00074 16.7 2.3 90 93-188 120-239 (454) 35 COG0420 SbcD DNA repair exonuc 34.8 37 0.00095 16.0 2.7 17 138-154 203-219 (390) 36 COG4270 Predicted membrane pro 33.8 15 0.0004 18.5 0.6 35 180-214 21-69 (131) 37 TIGR00636 PduO_Nterm ATP:cob(I 32.9 25 0.00064 17.1 1.6 48 112-160 87-136 (184) 38 cd04719 BAH_Orc1p_animal BAH, 32.7 17 0.00044 18.2 0.7 15 133-147 3-17 (128) 39 COG2425 Uncharacterized protei 32.6 43 0.0011 15.5 3.2 113 11-129 288-419 (437) 40 TIGR02169 SMC_prok_A chromosom 32.1 31 0.00078 16.5 1.9 21 141-161 1113-1135(1202) 41 COG0602 NrdG Organic radical a 32.0 44 0.0011 15.5 3.1 13 93-105 79-91 (212) 42 TIGR01717 AMP-nucleosdse AMP n 31.7 18 0.00045 18.1 0.7 32 103-143 289-321 (486) 43 PRK05665 amidotransferase; Pro 31.5 45 0.0012 15.4 5.8 87 1-87 1-94 (240) 44 KOG3039 consensus 30.6 46 0.0012 15.4 2.6 32 86-117 236-267 (303) 45 TIGR00571 dam DNA adenine meth 29.9 44 0.0011 15.5 2.4 35 94-128 184-220 (327) 46 KOG0365 consensus 29.7 32 0.00082 16.4 1.7 22 56-77 139-160 (423) 47 PRK01207 methionine synthase; 28.2 51 0.0013 15.0 3.0 11 152-162 194-204 (343) 48 smart00788 Adenylsucc_synt Ade 28.0 52 0.0013 15.0 3.7 60 57-117 65-129 (421) 49 pfam09276 Pertus-S5-tox Pertus 27.9 52 0.0013 15.0 2.8 40 13-67 49-88 (97) 50 cd01544 PBP1_GalR Ligand-bindi 27.5 53 0.0013 15.0 6.5 117 19-148 22-168 (270) 51 PRK02705 murD UDP-N-acetylmura 27.3 53 0.0014 14.9 3.2 33 86-118 110-144 (459) 52 TIGR02363 dhaK1 dihydroxyaceto 27.2 53 0.0014 14.9 4.2 45 65-112 84-128 (354) 53 PRK10433 putative RNA methyltr 26.9 54 0.0014 14.9 3.6 135 3-156 1-149 (228) 54 PRK13783 adenylosuccinate synt 26.8 54 0.0014 14.9 3.8 78 58-139 67-149 (404) 55 PRK08373 aspartate kinase; Val 26.6 43 0.0011 15.5 1.9 96 56-158 10-121 (359) 56 COG4658 RnfD Predicted NADH:ub 25.8 40 0.001 15.8 1.6 12 183-194 326-337 (338) 57 smart00391 MBD Methyl-CpG bind 25.7 42 0.0011 15.6 1.7 24 84-107 27-52 (77) 58 cd03275 ABC_SMC1_euk Eukaryoti 25.3 44 0.0011 15.5 1.7 73 93-175 105-195 (247) 59 pfam01429 MBD Methyl-CpG bindi 25.3 43 0.0011 15.5 1.7 24 84-107 29-54 (75) 60 pfam02598 DUF171 Uncharacteriz 25.3 58 0.0015 14.7 4.5 72 52-125 166-245 (283) 61 PRK13788 adenylosuccinate synt 24.6 59 0.0015 14.6 3.7 37 58-97 68-104 (404) 62 LOAD_tam consensus 24.0 46 0.0012 15.3 1.7 17 84-100 28-44 (75) 63 PRK02135 hypothetical protein; 23.6 62 0.0016 14.5 5.7 48 86-138 127-177 (199) 64 pfam01005 Flavi_NS2A Flaviviru 23.3 33 0.00084 16.3 0.8 22 142-164 58-79 (216) 65 cd06385 PBP1_NPR_A Ligand-bind 23.3 63 0.0016 14.5 5.5 43 98-141 192-234 (405) 66 pfam07005 DUF1537 Protein of u 22.9 64 0.0016 14.4 5.0 20 132-151 193-212 (224) 67 pfam07088 GvpD GvpD gas vesicl 22.8 64 0.0016 14.4 3.2 81 63-143 370-457 (484) 68 COG3444 Phosphotransferase sys 22.4 50 0.0013 15.1 1.6 44 19-67 42-85 (159) 69 cd03239 ABC_SMC_head The struc 21.8 52 0.0013 15.0 1.6 36 140-175 94-134 (178) 70 COG0527 LysC Aspartokinases [A 21.7 68 0.0017 14.3 5.4 98 56-158 8-132 (447) 71 pfam12147 Hydrolase_5 Putative 21.6 57 0.0015 14.7 1.7 35 88-122 189-223 (311) 72 COG3885 Uncharacterized conser 21.4 69 0.0018 14.2 3.9 41 67-108 23-63 (261) 73 TIGR00461 gcvP glycine dehydro 21.2 34 0.00085 16.3 0.5 14 88-101 778-791 (965) 74 TIGR02154 PhoB phosphate regul 21.2 63 0.0016 14.5 1.9 22 75-96 67-88 (226) 75 TIGR02275 DHB_AMP_lig 2,3-dihy 21.0 70 0.0018 14.2 2.9 35 93-127 21-60 (534) 76 COG3538 Uncharacterized conser 21.0 50 0.0013 15.1 1.3 24 139-163 52-75 (434) 77 COG3874 Uncharacterized conser 20.8 29 0.00073 16.7 0.1 41 51-97 59-99 (138) 78 TIGR01091 upp uracil phosphori 20.6 62 0.0016 14.5 1.7 24 70-94 145-170 (213) 79 PRK10437 carbonic anhydrase; P 20.1 46 0.0012 15.4 1.0 21 99-119 77-100 (220) 80 cd01396 MeCP2_MBD MeCP2, MBD1, 20.1 65 0.0017 14.4 1.8 18 83-100 24-41 (77) No 1 >TIGR00088 trmD tRNA (guanine-N1)-methyltransferase; InterPro: IPR002649 In transfer RNA many different modified nucleosides are found, especially in the anticodon region. tRNA (guanine-N1-)-methyltransferase 2.1.1.31 from EC is one of several nucleases operating together with the tRNA-modifying enzymes before the formation of the mature tRNA. It catalyses the reaction:S-adenosyl-L-methionine + tRNA -> S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine methylating guanosine(G) to N1-methylguanine (1-methylguanosine (m1G)) at position 37 of tRNAs that read CUN (leucine), CCN(proline), and CGG (arginine) codons. The presence of m1G improves the cellular growth rate and the polypeptide steptime and also prevents the tRNA from shifting the reading frame . The mechanism of the trmD3-induced frameshift involving mutant tRNA(Pro) and tRNA(Leu) species has been investigated . It has been suggested that the conformation of the anticodon loop may be a major determining element for the formation of m1G37 in vivo . ; GO: 0003723 RNA binding, 0008175 tRNA methyltransferase activity, 0008033 tRNA processing. Probab=100.00 E-value=0 Score=772.40 Aligned_cols=231 Identities=49% Similarity=0.821 Sum_probs=223.7 Q ss_pred EEEEEEEECHHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCCC Q ss_conf 45899851835644564033679999749659999602563589851353113068886177505889999987531147 Q gi|254780714|r 3 FHASILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTH 82 (236) Q Consensus 3 Mki~IITlFPe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~ 82 (236) |+|+||||||+||.++++.||++||+++++++++++|+||||.|||++|||+|||||||||||||||.+|++++++.. . T Consensus 1 mki~vLtLFP~~~~~~~~~sil~~A~~k~l~~~e~~n~RdFs~dKH~tvDD~pYGGG~GMvLk~ePi~~Al~~~~~~~-~ 79 (247) T TIGR00088 1 MKIDVLTLFPEMFKPYLESSILKKALEKNLVSFEVVNPRDFSKDKHKTVDDRPYGGGAGMVLKPEPIFDALESVKAAK-K 79 (247) T ss_pred CEEEEEECCHHHHHHHHCCCHHHHHHHCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-H T ss_conf 955677278777331203215899975470566753220003563452567533789765048678999998521043-2 Q ss_pred CCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHHHHHHHCCC Q ss_conf 78308998799876048999997302875999415011448999740453100334011173277999999999850574 Q gi|254780714|r 83 EDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGV 162 (236) Q Consensus 83 ~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~dai~RlipGv 162 (236) ..++|||+||||++|+|+.+++||+++|||||||||||||||+++++||+|||||||||||||||||++||||+|||||| T Consensus 80 ~~~~villsP~G~~~~Q~~~~~La~~~~lvLiCGrYEG~DeR~~~~~vD~e~SiGDfVLtGGEL~AL~lIDsv~Rli~GV 159 (247) T TIGR00088 80 EGAKVILLSPQGEKFDQALARELAKKEHLVLICGRYEGFDERIIELLVDEEISIGDFVLTGGELPALTLIDSVVRLIPGV 159 (247) T ss_pred CCCEEEEECCCCCCCCHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHCCEEEECCCEEECHHHHHHHHHHHHHHHHCCCC T ss_conf 58879997889964266899987412847899565036026645320786798366200104799999998898761773 Q ss_pred CCCCCCCCCCCH--HCCCCCCCCCCCHH----HCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCC Q ss_conf 678222334401--14884621116725----4089889843418998999999999999999876862686305634 Q gi|254780714|r 163 LGNQQSTIHESF--ENGLLEFPQYTRPQ----IWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKKGTLN 234 (236) Q Consensus 163 lg~~~S~~~eSf--~~~lLe~P~YTrP~----~~~g~~VP~VLlSGnH~~I~~Wr~~~s~~~T~~~RPDL~~~~~~~~ 234 (236) ||++.|+.+||| +|+||||||||||. +|+|.+||+|||||||++|++||++||+.||+++|||||+++...+ T Consensus 160 lg~~aSl~~eSFGv~~~LLd~PhYTRP~fkskd~~G~~VP~vLlSGnH~~I~~wRl~~s~~RT~~~RpDL~~~~~~~~ 237 (247) T TIGR00088 160 LGKEASLIEESFGVSNGLLDYPHYTRPYFKSKDLKGLKVPEVLLSGNHAKIEQWRLEQSLLRTKLRRPDLYKKYLALT 237 (247) T ss_pred CCHHHCHHHHCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCC T ss_conf 172101123213323666277744575410132068747832247776899998799998745311667899987506 No 2 >PRK00026 trmD tRNA (guanine-N(1)-)-methyltransferase; Reviewed Probab=100.00 E-value=0 Score=760.37 Aligned_cols=226 Identities=51% Similarity=0.866 Sum_probs=221.0 Q ss_pred EEEEEEEECHHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCCC Q ss_conf 45899851835644564033679999749659999602563589851353113068886177505889999987531147 Q gi|254780714|r 3 FHASILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTH 82 (236) Q Consensus 3 Mki~IITlFPe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~ 82 (236) |+|+|||||||||++++++||+|||+++|+|+++++|||||+.|||++|||+||||||||||||||+++|++++++. . T Consensus 1 Mki~iiTlFPe~f~~~l~~siigrA~~~~~i~i~~~nlRdf~~~kh~~VDD~PyGGG~GMVm~~epl~~ai~~i~~~--~ 78 (226) T PRK00026 1 MRIDVLTLFPEMFRAPLDDSILGRAVEKGLLELEVWNPRDFTTDKHRTVDDRPYGGGAGMVMKPQPLFDAIDAAKAA--R 78 (226) T ss_pred CEEEEEEECHHHHHHHHHCCHHHHHHHCCCEEEEEECHHHCCCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHC--C T ss_conf 97899998857533253342799999869669998784660789887647875789982176308999999998741--8 Q ss_pred CCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHHHHHHHCCC Q ss_conf 78308998799876048999997302875999415011448999740453100334011173277999999999850574 Q gi|254780714|r 83 EDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGV 162 (236) Q Consensus 83 ~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~dai~RlipGv 162 (236) ++.++|||||||++|||++|++||++++|+|||||||||||||+|+++|+|||||||||||||+|||+++||++||+||| T Consensus 79 ~~~~vI~lSP~G~~~~Q~~a~~ls~~~~liliCGrYEGiDeRvi~~~vd~eiSiGDyVLsGGEl~A~v~iDai~RllPGV 158 (226) T PRK00026 79 GYAKVIYLSPQGKPFTQADAKELAKEEHLIFLCGRYEGIDERVIELYVDEEISIGDYVLSGGELAALVLIDAVVRLLPGV 158 (226) T ss_pred CCCEEEEECCCCCCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHCCEEEEEECEEECCCHHHHHHHHHHHHHHCCCC T ss_conf 99749987999888448889988669987999546033628999850655876304885184499999999999857886 Q ss_pred CCCCCCCCCCCHHCCCCCCCCCCCHHHCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHH Q ss_conf 67822233440114884621116725408988984341899899999999999999987686268630 Q gi|254780714|r 163 LGNQQSTIHESFENGLLEFPQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKK 230 (236) Q Consensus 163 lg~~~S~~~eSf~~~lLe~P~YTrP~~~~g~~VP~VLlSGnH~~I~~Wr~~~s~~~T~~~RPDL~~~~ 230 (236) |||++|+.+|||+||||||||||||++|+|++||+|||||||++|++||++||+++|+++|||||+|. T Consensus 159 lgn~~S~~~eSF~~glLe~P~YTrP~~~~g~~VPeVLlSGnH~~I~~Wr~~~s~~~T~~~RPDL~~k~ 226 (226) T PRK00026 159 LGNEESAEEDSFSDGLLECPHYTRPEEFRGLKVPEVLLSGNHAKIRRWRLEQSLERTKLRRPDLLEKL 226 (226) T ss_pred CCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHC T ss_conf 68800200201323788898779942128999994024799799999999999999987695778539 No 3 >COG0336 TrmD tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=751.02 Aligned_cols=230 Identities=51% Similarity=0.889 Sum_probs=223.7 Q ss_pred EEEEEEEECHHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCCC Q ss_conf 45899851835644564033679999749659999602563589851353113068886177505889999987531147 Q gi|254780714|r 3 FHASILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTH 82 (236) Q Consensus 3 Mki~IITlFPe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~ 82 (236) |+|+|+|||||||++++++||+|||+++|+|+++++|+|||+.|||++|||+||||||||||||||+++|++++++.. T Consensus 1 mki~ilTlFPemf~~~~~~si~grA~~~g~~~~~~~n~Rdf~~dkh~~VDD~pyGGG~GMvmk~epi~~Al~~~~~~~-- 78 (240) T COG0336 1 MKIDILTLFPEMFDGYLGYSILGRAIEKGLLSLEVVNPRDFATDKHKTVDDTPYGGGAGMVMKPEPLFDALDSVKAAK-- 78 (240) T ss_pred CEEEEEEECHHHCHHHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCCCCCCCCCCCEECCHHHHHHHHHHHHCC-- T ss_conf 947689817544312422058999998695389962477835476753577657898861764288999999987235-- Q ss_pred CCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHHHHHHHCCC Q ss_conf 78308998799876048999997302875999415011448999740453100334011173277999999999850574 Q gi|254780714|r 83 EDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGV 162 (236) Q Consensus 83 ~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~dai~RlipGv 162 (236) +++||||||||++|||+.|++|++++||||||||||||||||++.++|+|||||||||||||+|||+++|||+||+||| T Consensus 79 -~~~vi~lsP~G~~f~Q~~a~eLa~~~~lv~iCGrYEGiDeRvi~~~vdeEiSIGDyVLtGGEl~AmvliDav~RlipGV 157 (240) T COG0336 79 -KAKVILLSPQGKPFTQARARELAKEEHLVLICGRYEGIDERVIELYVDEEISIGDYVLTGGELAAMVLIDAVVRLIPGV 157 (240) T ss_pred -CCEEEEECCCCCCCCHHHHHHHHCCCCEEEEECCCCCHHHHHHHHCCCEEEEECCEEECCCCHHHHHHHHHHHHHCCCC T ss_conf -8728998999883688999998658987999546445328988640633786336884186188999999999965523 Q ss_pred CCCCCCCCCCCHH-CCCCCCCCCCCHHHCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCC Q ss_conf 6782223344011-488462111672540898898434189989999999999999998768626863056346 Q gi|254780714|r 163 LGNQQSTIHESFE-NGLLEFPQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKKGTLNT 235 (236) Q Consensus 163 lg~~~S~~~eSf~-~~lLe~P~YTrP~~~~g~~VP~VLlSGnH~~I~~Wr~~~s~~~T~~~RPDL~~~~~~~~~ 235 (236) |||++|+++|||+ ||||||||||||++|+|++||+|||||||++|++||++||+++|+.+|||||+++.++.+ T Consensus 158 lg~~~S~e~dSF~~~gLLe~P~YTRP~~~~g~~VP~VLlSGnH~~I~~WR~~qsl~rT~~rRPDL~~~~~~~~~ 231 (240) T COG0336 158 LGNEESLEEDSFENNGLLEYPHYTRPREFEGMKVPEVLLSGNHAKIAQWRLEQSLERTKERRPDLLEAHKLTEE 231 (240) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCHH T ss_conf 38720101034456986678876783220799688123058679999999999999998739346665321255 No 4 >PRK01037 trmD tRNA (guanine-N(1)-)-methyltransferase/unknown domain fusion protein; Reviewed Probab=100.00 E-value=0 Score=747.31 Aligned_cols=224 Identities=43% Similarity=0.754 Sum_probs=219.1 Q ss_pred EEEEEEEECHHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCCC Q ss_conf 45899851835644564033679999749659999602563589851353113068886177505889999987531147 Q gi|254780714|r 3 FHASILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTH 82 (236) Q Consensus 3 Mki~IITlFPe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~ 82 (236) |+|+|||||||||++++++||+|||+++|+|++++||||||+.|||++|||+||||| ||||||||+++|+++++++ T Consensus 1 MkidIlTLFPe~f~~~L~~sIigRAiekgli~i~~~nlRDfs~dkhk~VDD~PYGGG-GMVm~~ePl~~Ai~~i~~~--- 76 (357) T PRK01037 1 MEIDILSLFPDYFDSPLQASILGRAIKQGLLDVQSRDIREFGLGKWKQVDDAPFNGE-GMLLMAEPVVQAIRSVRRE--- 76 (357) T ss_pred CEEEEEEECHHHHHHHHHCCHHHHHHHCCCEEEEEECCHHCCCCCCCCCCCCCCCCC-CEEEEHHHHHHHHHHHHHC--- T ss_conf 968999988565010211358999997797799987342026999988678698887-1184099999999986525--- Q ss_pred CCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHHHHHHHCCC Q ss_conf 78308998799876048999997302875999415011448999740453100334011173277999999999850574 Q gi|254780714|r 83 EDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGV 162 (236) Q Consensus 83 ~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~dai~RlipGv 162 (236) +.++|||||||++|||++|++||+.++|||||||||||||||+++++|+|||||||||||||+|||+++||++||+||| T Consensus 77 -~~~vI~lSPqGk~ltQ~~a~eLs~~~~LilICGRYEGIDeRvid~~vdeEISIGDyVLSGGElaAmvliDAv~RLiPGV 155 (357) T PRK01037 77 -KSKVIYLSPQGQLLTAKKSRELAACSHLILLCGHYEGIDERALESEVDEEISIGDYVLTNGGIAALVLIDALSRFIPGV 155 (357) T ss_pred -CCCEEEECCCCCCCCHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHCCEEEEECCEEEECCHHHHHHHHHHHHHHCCCC T ss_conf -9938998999985899999998669986999345433528999763545875335897282599999999999847886 Q ss_pred CCCCCCCCCCCHHCCCCCCCCCCCHHHCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHC Q ss_conf 678222334401148846211167254089889843418998999999999999999876862686305 Q gi|254780714|r 163 LGNQQSTIHESFENGLLEFPQYTRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRPDLLSKKG 231 (236) Q Consensus 163 lg~~~S~~~eSf~~~lLe~P~YTrP~~~~g~~VP~VLlSGnH~~I~~Wr~~~s~~~T~~~RPDL~~~~~ 231 (236) |||++|+.+|||+||||||||||||++|+|++||||||||||++|++||+++|+++|+++|||||.++- T Consensus 156 LGn~eS~~~ESF~ngLLE~PqYTRP~~~~G~~VPeVLLSGnH~kI~~WR~~qsl~rT~~rRPDLy~kYL 224 (357) T PRK01037 156 LGNQESAERDSLENGLLEGPQYTRPRVFEGKEVPEVLLQGDHQAIAQWRKQVSLERTRERRPDLYLQYL 224 (357) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHH T ss_conf 588430232522489888987899201299989974657887999999999999999876904899985 No 5 >pfam01746 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase. This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA. Probab=100.00 E-value=0 Score=439.99 Aligned_cols=184 Identities=36% Similarity=0.602 Sum_probs=175.1 Q ss_pred HHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHH Q ss_conf 99997496599996025635898513531130688861775058899999875311477830899879987604899999 Q gi|254780714|r 25 GKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQ 104 (236) Q Consensus 25 gkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ 104 (236) .+++++++++++++|+|+|+.|+|++|||+|||||+||||+|+|+.+|++++. +.++|++||+|++|+|+.+++ T Consensus 2 ~~m~ek~i~~l~~q~~R~ys~nr~~~vdd~~~ggG~gm~l~~~~~~~~~~~~~------~~~~i~~sp~g~~~~q~~~~~ 75 (185) T pfam01746 2 DLMIEKELVSLELQILRDYTANRRATVDDHLYGGGFGMVLKPEPDLEALKSVS------GWEVILLTPTGIPFSQELASE 75 (185) T ss_pred CCCCCCCCEEEEEECCHHCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCC------CCCEEEECCCCCCCCHHHHHH T ss_conf 65261786799978523204899988798768578885646558999997564------887899899987745789986 Q ss_pred HHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCCCC Q ss_conf 73028759994150114489997404531003340111732779999999998505746782223344011488462111 Q gi|254780714|r 105 LSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDAVVRLLPGVLGNQQSTIHESFENGLLEFPQY 184 (236) Q Consensus 105 ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~dai~RlipGvlg~~~S~~~eSf~~~lLe~P~Y 184 (236) |+++++||+|||||||+||||++.++ |+||||||++|||+|||+++|+++|++|||+ +.+|+..||| +|++||| T Consensus 76 l~~~~~lV~Lcg~yEgvderv~~~~~--~~sIGd~V~~gge~~a~~~id~~~r~~~Gv~-~~~~l~~~s~---ll~~p~y 149 (185) T pfam01746 76 LFKKEHLVYLTGDYEGVLERLDDDKA--EYIIGGIVDKGGEKGALTLIDAVVALLPGVL-NTASLPLDSF---LLGVPNY 149 (185) T ss_pred HCCCCCEEEEECCCCCHHHHCCCCCE--EEEECCEEECCCHHHHHHHHHHHHHCCCCCC-CCCCCCCCCC---CCCCCCC T ss_conf 23268779994898662320036762--8986579972960899999989998469988-8876785465---6489988 Q ss_pred CCHHHCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHCH Q ss_conf 6725408988984341899899999999999999987686 Q gi|254780714|r 185 TRPQIWEGLAIPPILNSGDHERIKKWRKEQSFALTKKHRP 224 (236) Q Consensus 185 TrP~~~~g~~VP~VLlSGnH~~I~~Wr~~~s~~~T~~~RP 224 (236) |||.+|+ .||||||||||++|++| ++|+.+|..+|+ T Consensus 150 trp~~~~--~VpeILlsg~h~~i~~W--~~a~~~t~~~Rk 185 (185) T pfam01746 150 TRPLTLN--QVPEILLSGNHAKIRNW--EEALLRTIPKRK 185 (185) T ss_pred CCCCCCC--CCCHHHCCCCHHHHHHH--HHHHHHHHHCCC T ss_conf 6876206--48077637775548899--999999985569 No 6 >COG1576 Uncharacterized conserved protein [Function unknown] Probab=96.08 E-value=0.15 Score=31.78 Aligned_cols=137 Identities=15% Similarity=0.249 Sum_probs=91.2 Q ss_pred EEEEEEEEC---HHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHH Q ss_conf 458998518---35644564033679999749659999602563589851353113068886177505889999987531 Q gi|254780714|r 3 FHASILTLY---PEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQ 79 (236) Q Consensus 3 Mki~IITlF---Pe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~ 79 (236) |+|.|+|+= |.+++.-+.. -.+|-- ....++.+.+-+....+..+ ++.+.+.-....-. T Consensus 1 Mki~iiaVGk~~~~~~~~g~~e-Y~KR~~--~~~~leliei~~~~~~~~~~---------------~~~~~~~E~~~il~ 62 (155) T COG1576 1 MKINIIAVGKKKPKYVKDGIAE-YLKRFP--RYLKLELIEIPEEKRGKNAS---------------AELIKKKEGEAILA 62 (155) T ss_pred CEEEEEEEECCCHHHHHHHHHH-HHHHHC--CCCCCEEEECCCCCCCCCCC---------------HHHHHHHHHHHHHH T ss_conf 9479999504463779999999-998725--13684278647766744248---------------89999999999998 Q ss_pred CCCCCCCEEEECCCCCEECHH-HHHHHHHCC----CEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHH Q ss_conf 147783089987998760489-999973028----759994150114489997404531003340111732779999999 Q gi|254780714|r 80 YTHEDIPRILMSPRGKTLTQK-RVRQLSQKL----GVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDA 154 (236) Q Consensus 80 ~~~~~~~vI~lSP~Gk~l~Q~-~a~~ls~~~----~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~da 154 (236) .-.++.++|.+..+||.++-. .|..+.... +|+|+-|-=+|.|+.+... +++-+|.|-..+.- .++-+++++. T Consensus 63 ~i~~~~~vi~Ld~~Gk~~sSe~fA~~l~~~~~~G~~i~f~IGG~~Gl~~~~~~~-a~~~~sls~lT~PH-ql~rlvL~EQ 140 (155) T COG1576 63 AIPKGSYVVLLDIRGKALSSEEFADFLERLRDDGRDISFLIGGADGLSEAVKAR-ADQVLSLSKLTLPH-QLVRLVLAEQ 140 (155) T ss_pred HCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHH-HHHHEECCCCCCHH-HHHHHHHHHH T ss_conf 369998599981468767759999999998734984899984755479999987-75510255666605-9899999999 Q ss_pred HHHHH Q ss_conf 99850 Q gi|254780714|r 155 VVRLL 159 (236) Q Consensus 155 i~Rli 159 (236) +-|-. T Consensus 141 iYRA~ 145 (155) T COG1576 141 IYRAF 145 (155) T ss_pred HHHHH T ss_conf 99999 No 7 >pfam02590 SPOUT_MTase Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases. Probab=95.87 E-value=0.074 Score=33.87 Aligned_cols=135 Identities=14% Similarity=0.244 Sum_probs=85.7 Q ss_pred EEEEEEEECH---HHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHH-HHHHHH Q ss_conf 4589985183---564456403367999974965999960256358985135311306888617750588999-998753 Q gi|254780714|r 3 FHASILTLYP---EMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKA-IDHAVS 78 (236) Q Consensus 3 Mki~IITlFP---e~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~a-i~~~~~ 78 (236) |+|.|+++=- ..+.. .-.--.+|- ++.+.++.+.+.+....+...+ +.+.+. -..+.+ T Consensus 1 Mki~ii~iGk~~~~~~~~-~~~~Y~kRl--~~~~~i~~iel~~~~~~~~~~~---------------~~~~~~E~~~i~~ 62 (155) T pfam02590 1 MKIRIIAVGKLKEKYVKD-GIAEYLKRL--SRYCKLELIELPDEKRPSAADI---------------EAIKEKEGERILA 62 (155) T ss_pred CEEEEEEECCCCCHHHHH-HHHHHHHHH--CCCCCCCEEEECCCCCCCCCCH---------------HHHHHHHHHHHHH T ss_conf 979999972759779999-999999981--7447885799378778775589---------------9999999999997 Q ss_pred HCCCCCCCEEEECCCCCEECHHHHHH-HHH-----CCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHH Q ss_conf 11477830899879987604899999-730-----287599941501144899974045310033401117327799999 Q gi|254780714|r 79 QYTHEDIPRILMSPRGKTLTQKRVRQ-LSQ-----KLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILL 152 (236) Q Consensus 79 ~~~~~~~~vI~lSP~Gk~l~Q~~a~~-ls~-----~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~ 152 (236) .. .++..+|.|.+.|+.+|-....+ +.+ ..+++|+-|==+|+|+-+.+. +|..+|+|+.+++ -|+|.++++ T Consensus 63 ~i-~~~~~~I~LDe~Gk~~sS~~fa~~i~~~~~~g~~~i~FiIGGa~G~~~~~~~~-a~~~~Sls~mT~p-H~larv~l~ 139 (155) T pfam02590 63 AI-PPGSYVIALDERGKELSSEEFAKLLEDLRLKGKSDITFVIGGSDGLSEEVLKR-ANEKLSLSKMTLP-HQLVRLLLA 139 (155) T ss_pred HC-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHH-HHHEEECCCCCCC-HHHHHHHHH T ss_conf 37-99998999937998378799999999998338975599983798869899975-6663441367650-899999999 Q ss_pred HHHHHH Q ss_conf 999985 Q gi|254780714|r 153 DAVVRL 158 (236) Q Consensus 153 dai~Rl 158 (236) |-+-|- T Consensus 140 EQiYRa 145 (155) T pfam02590 140 EQIYRA 145 (155) T ss_pred HHHHHH T ss_conf 999999 No 8 >PRK00103 SPOUT methyltransferase superfamily protein; Provisional Probab=95.67 E-value=0.056 Score=34.67 Aligned_cols=137 Identities=15% Similarity=0.213 Sum_probs=86.5 Q ss_pred EEEEEEEEC---HHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHH Q ss_conf 458998518---35644564033679999749659999602563589851353113068886177505889999987531 Q gi|254780714|r 3 FHASILTLY---PEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQ 79 (236) Q Consensus 3 Mki~IITlF---Pe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~ 79 (236) |+|.|+++= +..+....+. -.+| =+..+.++.+.+.+-...+...++ ....+--+.+.+. T Consensus 1 Mki~ii~iGK~~~~~~~~~i~~-Y~kR--l~~~~~i~~~el~~~~~~~~~~~~--------------~~~~~E~~~il~~ 63 (156) T PRK00103 1 MKIQLIAVGKLMPKWVKEGFAE-YAKR--LPRDCKLELIEIPDEKRGKNADIE--------------RIKAKEGERILAA 63 (156) T ss_pred CEEEEEEEECCCCHHHHHHHHH-HHHH--HCCCCCCCEEEECCCCCCCCCCHH--------------HHHHHHHHHHHHH T ss_conf 9799999707696799999999-9997--174258855894787776758999--------------9999999999984 Q ss_pred CCCCCCCEEEECCCCCEECHHHHHHHHH-----CCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHHHHH Q ss_conf 1477830899879987604899999730-----28759994150114489997404531003340111732779999999 Q gi|254780714|r 80 YTHEDIPRILMSPRGKTLTQKRVRQLSQ-----KLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALILLDA 154 (236) Q Consensus 80 ~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~-----~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~~da 154 (236) . .++..+|.|.+.|+.++-....++-+ ..+++|+-|==+|+|+-+.+. +++-+|+++.+++ -++|.++++|- T Consensus 64 ~-~~~~~~I~LDe~Gk~~sS~~fa~~l~~~~~~g~~i~FiIGGa~G~~~~~~~~-a~~~lSlS~mTfp-H~lar~il~EQ 140 (156) T PRK00103 64 I-PKGARVVALDIRGKPWTSEQFAKELERWRLDGRDVTFVIGGPEGLSPAVKKR-ADQSWSLSKLTLP-HQLVRLVLAEQ 140 (156) T ss_pred C-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHH-HHHEEEECCCCCC-HHHHHHHHHHH T ss_conf 7-9999899991799805769999999999863996699997888769899974-3228871367662-89999999999 Q ss_pred HHHHH Q ss_conf 99850 Q gi|254780714|r 155 VVRLL 159 (236) Q Consensus 155 i~Rli 159 (236) +-|-. T Consensus 141 iYRa~ 145 (156) T PRK00103 141 LYRAW 145 (156) T ss_pred HHHHH T ss_conf 99999 No 9 >KOG3073 consensus Probab=90.15 E-value=0.25 Score=30.32 Aligned_cols=63 Identities=25% Similarity=0.328 Sum_probs=46.7 Q ss_pred HHCCCCCCCEEEECCCCCEEC--HHHHHHHHHCCCEEEEECCC-HHHHHHHHHHCCCCCEEEHHEEECC Q ss_conf 311477830899879987604--89999973028759994150-1144899974045310033401117 Q gi|254780714|r 78 SQYTHEDIPRILMSPRGKTLT--QKRVRQLSQKLGVIIVCGRF-EGIDERIIEARDLEEISVGDYILSG 143 (236) Q Consensus 78 ~~~~~~~~~vI~lSP~Gk~l~--Q~~a~~ls~~~~liliCGrY-EGiDeRvid~~~d~eiSiGDyVLsG 143 (236) +..-..+++.|-||+.|..+. |++...+-..+.++|+-|-. +| .+-..|+|+.+||.||-||. T Consensus 153 tdHlPv~~~Ki~lSf~~p~l~~~~~lv~~~~~~~~~v~~Iga~ahg---~~~~ey~de~vsiSnYpLSa 218 (236) T KOG3073 153 TDHLPVNSRKIGLSFSGPKLSNVRDLVASLDDDDSVVFVIGAMAHG---KISVEYVDEKVSISNYPLSA 218 (236) T ss_pred CCCCCCCCCEEEECCCCCCCCCHHHHCCCCCCCCCEEEEEECCCCC---CCCHHHHHHHCCCCCCCCCH T ss_conf 2357998617761478763556776315447899789998131245---42111334434314686769 No 10 >COG1756 Mra1 Uncharacterized conserved protein [Function unknown] Probab=85.69 E-value=1.3 Score=25.64 Aligned_cols=62 Identities=24% Similarity=0.196 Sum_probs=45.0 Q ss_pred CEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHH Q ss_conf 089987998760489999973028759994150114489997404531003340111732779 Q gi|254780714|r 86 PRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAA 148 (236) Q Consensus 86 ~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a 148 (236) .+|.|+|.|....-+...+..... +.++-|-+--=|.+.-..++++++|||||=||---+++ T Consensus 149 ~~ill~e~G~~~~p~~~~~~l~~~-i~v~iG~fp~Gdf~~~~~~~~~~~si~~~pL~a~~v~~ 210 (223) T COG1756 149 VTILLHEKGELIPPKELISLLLKG-IAVIIGGFPHGDFREETEFVAEKYSIYDEPLSAWSVCS 210 (223) T ss_pred EEEEECCCCCCCCHHHHHHHHCCC-CEEEEECCCCCCCHHHHHHHHHEEEECCCCCCHHHHHH T ss_conf 389985788826889998640248-55999516777302444311013551588764999999 No 11 >pfam03587 EMG1 EMG1/NEP1 methyltransferase. Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases. Probab=85.39 E-value=1.4 Score=25.31 Aligned_cols=64 Identities=23% Similarity=0.264 Sum_probs=39.4 Q ss_pred CCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHH-H-HCCCCCEEEHHEEECCCCHHH Q ss_conf 308998799876048999997302875999415011448999-7-404531003340111732779 Q gi|254780714|r 85 IPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERII-E-ARDLEEISVGDYILSGGEPAA 148 (236) Q Consensus 85 ~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvi-d-~~~d~eiSiGDyVLsGGEl~a 148 (236) .++|.||++|++.+-+..-+-...+.++|+.|-.--=|-..- + ...++.+||++|-||.--..+ T Consensus 130 ~~~i~ls~~g~~~~~~~~~~~~~~~~~~~vIGaf~~G~~~~~~~~~~~~~~~sIs~~~Lsa~~v~s 195 (202) T pfam03587 130 SKKILLSEKGEKVSPKELASELKNEPVAFVIGAFPHGDFSDEVDYKKADESYSISNYPLSAWTVCS 195 (202) T ss_pred CEEEEECCCCCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCCCEECCCCEEEEECCCCCHHHHHHH T ss_conf 739997667876589999976057993899940456886642034046528998087704999999 No 12 >PRK04171 ribosome biogenesis protein; Provisional Probab=82.81 E-value=3.4 Score=22.82 Aligned_cols=87 Identities=20% Similarity=0.314 Sum_probs=51.4 Q ss_pred CCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCC-HH-HHHHHHHHCCCC Q ss_conf 3068886177505889999987531147783089987998760489999973028759994150-11-448999740453 Q gi|254780714|r 55 PAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRF-EG-IDERIIEARDLE 132 (236) Q Consensus 55 PyGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrY-EG-iDeRvid~~~d~ 132 (236) |-++.+=|=+.-.|+.+-+.. ...++|.+|++|+..+-+..-+-. ++++|+-|-+ .| +..-+. .+.|+ T Consensus 123 ~~~~~~Ll~v~k~~l~~~l~~-------~~~kii~ls~~g~~~~~~~~~~~~--~~~~~vIGaf~~G~f~~~~~-~~~d~ 192 (221) T PRK04171 123 PPGGEPLLELEDKSLSELLEE-------NPGKIILLSEKGEPVKPKELAKEL--ENPVVVIGGFPHGDFSSEVL-EKADK 192 (221) T ss_pred CCCCCCCEEEECCCHHHHHCC-------CCCEEEEECCCCCCCCHHHHHHHC--CCCEEEEEECCCCCCCCCCH-HCCCC T ss_conf 899950015663868997065-------898599983588672899997422--79769983016987660000-13684 Q ss_pred CEEEHHEEECCCCHHHHHH Q ss_conf 1003340111732779999 Q gi|254780714|r 133 EISVGDYILSGGEPAALIL 151 (236) Q Consensus 133 eiSiGDyVLsGGEl~a~v~ 151 (236) .+||++|-||+--..+-++ T Consensus 193 ~~SIs~~~Lsa~~v~~ri~ 211 (221) T PRK04171 193 KYSIYNEPLDAWTVVSRII 211 (221) T ss_pred EEEEECCCHHHHHHHHHHH T ss_conf 8998488769999999999 No 13 >cd03108 AdSS Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-phosphate group of GTP is transferred to the 6-oxygen atom of IMP. An aspartate then displaces this 6-phosphate group to form the product adenylosuccinate. Because of its critical role in purine biosynthesis, AdSS is a target of antibiotics, herbicides and antitumor drugs. Probab=69.47 E-value=11 Score=19.50 Aligned_cols=118 Identities=21% Similarity=0.246 Sum_probs=67.3 Q ss_pred CCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECH-----HHHHHHHHCCCEEEEECCCHHHHHHHHHHC Q ss_conf 306888617750588999998753114778308998799876048-----999997302875999415011448999740 Q gi|254780714|r 55 PAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQ-----KRVRQLSQKLGVIIVCGRFEGIDERIIEAR 129 (236) Q Consensus 55 PyGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q-----~~a~~ls~~~~liliCGrYEGiDeRvid~~ 129 (236) +-==|+|||+-|+.+.+-++.+.++.. .-...++.|++-..... ..+.|-++.+.-|==||| ||-.-..|+. T Consensus 63 ~~~Ig~G~vidp~~l~~Ei~~L~~~g~-~~~~rl~Is~~a~ii~p~H~~~D~~~E~~~~~~~iGTT~~--GIGPaY~dk~ 139 (363) T cd03108 63 TCVIGNGVVIDPPALFEEIDELEKKGG-DVTGRLFISDRAHLVFPYHILLDGLREEARGKKKIGTTKR--GIGPAYEDKA 139 (363) T ss_pred EEEECCCEEECHHHHHHHHHHHHHCCC-CCCCCEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCC--CCCHHHHHHH T ss_conf 177679779869999999999997499-9735789818855478421888999998728875355787--6625666555 Q ss_pred CCCCEEEHHEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCCCCCCHHH Q ss_conf 453100334011173277999999999850574678222334401148846211167254 Q gi|254780714|r 130 DLEEISVGDYILSGGEPAALILLDAVVRLLPGVLGNQQSTIHESFENGLLEFPQYTRPQI 189 (236) Q Consensus 130 ~d~eiSiGDyVLsGGEl~a~v~~dai~RlipGvlg~~~S~~~eSf~~~lLe~P~YTrP~~ 189 (236) .-.-|.++|. +...+ +-+| +.+.++..-|-=+.-||+--+=|-|.+ T Consensus 140 ~R~gir~~Dl-----d~~~~-l~~a--------~~~gk~iL~EGaQG~~LDid~GtYP~V 185 (363) T cd03108 140 ARRGIRVGDL-----DTSYL-INEA--------IQAGKKVLFEGAQGTLLDIDFGTYPFV 185 (363) T ss_pred HHCCCEEEEC-----CHHHH-HHHH--------HHCCCCEEEEECCHHCCCHHCCCCCCC T ss_conf 4218544506-----66999-9999--------976993899805222020201856666 No 14 >TIGR02874 spore_ytfJ sporulation protein YtfJ; InterPro: IPR014229 Proteins in this entry, exemplified by YtfJ of Bacillus subtilis, are encoded by bacterial genomes if, and only if, the species is capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF .. Probab=63.55 E-value=3.1 Score=23.13 Aligned_cols=20 Identities=30% Similarity=0.526 Sum_probs=15.6 Q ss_pred EEEECCCCCCCCEEEECHHH Q ss_conf 35311306888617750588 Q gi|254780714|r 50 SVDDTPAGGGAGMVLRVDIL 69 (236) Q Consensus 50 ~VDD~PyGGG~GMVlk~epi 69 (236) +--.+|||||+|==....|+ T Consensus 69 ~~~~~PFGGGSGaGVS~~Pv 88 (132) T TIGR02874 69 REQKLPFGGGSGAGVSVKPV 88 (132) T ss_pred HHHCCCCCCCCCCCEEECCE T ss_conf 64238886768887351315 No 15 >KOG4066 consensus Probab=63.13 E-value=14 Score=18.70 Aligned_cols=126 Identities=17% Similarity=0.188 Sum_probs=69.4 Q ss_pred EEEEEEEECHH------HHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHH Q ss_conf 45899851835------644564033679999749659999602563589851353113068886177505889999987 Q gi|254780714|r 3 FHASILTLYPE------MFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHA 76 (236) Q Consensus 3 Mki~IITlFPe------~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~ 76 (236) |..+++-+||| +|+...+.+=+.+-...|-++...+|++ .|+-|..++.|+..+ T Consensus 1 ~~~hilplfPe~~v~v~lfedVkNaaeir~ql~eg~id~AfIda~--------------------lil~pfq~ysAinra 60 (177) T KOG4066 1 MVVHILPLFPETQVHVFLFEDVKNAAEIREQLIEGNIDYAFIDAA--------------------LILYPFQVYSAINRA 60 (177) T ss_pred CCEEECCCCCCCEEEEEEHHHCCCHHHHHHHHHCCCCCCEEECHH--------------------HEECHHHHHHHHHHH T ss_conf 940102568886699986232124899999997058641553624--------------------400699999999999 Q ss_pred HHHCCCCCC--------CEEEECCCCCEECHHHHHHHH-HCCCEEEEECCCH-HHHHHHHHHCCCCCEEEHHEEECCCCH Q ss_conf 531147783--------089987998760489999973-0287599941501-144899974045310033401117327 Q gi|254780714|r 77 VSQYTHEDI--------PRILMSPRGKTLTQKRVRQLS-QKLGVIIVCGRFE-GIDERIIEARDLEEISVGDYILSGGEP 146 (236) Q Consensus 77 ~~~~~~~~~--------~vI~lSP~Gk~l~Q~~a~~ls-~~~~liliCGrYE-GiDeRvid~~~d~eiSiGDyVLsGGEl 146 (236) .......+. .+.-|||.-..=+ . ...+. +++.--|||-.++ |+|.-....+-+--+-=-..-++.||| T Consensus 61 lh~~k~nkMktRtL~sE~ilsLSP~~nISd-A-f~kFgI~~~st~Ii~vk~d~~~dke~~~e~l~k~VeG~~Vef~d~~L 138 (177) T KOG4066 61 LHDRKDNKMKTRTLHSEVILSLSPKTNISD-A-FRKFGITKKSTNIIVVKIDSKLDKEEEFERLDKLVEGNRVEFSDEEL 138 (177) T ss_pred HHHHHHCCCEECCCCCEEEEEECCCCCHHH-H-HHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCHH T ss_conf 999873611001001114787079864679-9-99828656886379999637744789999999883587433565316 Q ss_pred HHHH Q ss_conf 7999 Q gi|254780714|r 147 AALI 150 (236) Q Consensus 147 ~a~v 150 (236) |-.. T Consensus 139 pkf~ 142 (177) T KOG4066 139 PKFI 142 (177) T ss_pred HHHH T ss_conf 7664 No 16 >smart00226 LMWPc Low molecular weight phosphatase family. Probab=61.09 E-value=8.3 Score=20.31 Aligned_cols=15 Identities=0% Similarity=0.096 Sum_probs=6.7 Q ss_pred HHHHHHCCCHHHHHH Q ss_conf 644564033679999 Q gi|254780714|r 14 MFPGHLEKSVAGKAL 28 (236) Q Consensus 14 ~f~~~l~~sIigkA~ 28 (236) ...|++..++..+.. T Consensus 9 ~CRSpmAE~~~~~~~ 23 (140) T smart00226 9 ICRSPMAEALFKAIV 23 (140) T ss_pred HHHHHHHHHHHHHHC T ss_conf 659999999999857 No 17 >COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane] Probab=53.41 E-value=19 Score=17.94 Aligned_cols=42 Identities=17% Similarity=0.231 Sum_probs=32.8 Q ss_pred CEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHH Q ss_conf 089987998760489999973028759994150114489997 Q gi|254780714|r 86 PRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIE 127 (236) Q Consensus 86 ~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid 127 (236) ..|+.+-.|.-.--.+|++|++..+-+|||||-|--=+-+.. T Consensus 6 nTiLITGG~sGIGl~lak~f~elgN~VIi~gR~e~~L~e~~~ 47 (245) T COG3967 6 NTILITGGASGIGLALAKRFLELGNTVIICGRNEERLAEAKA 47 (245) T ss_pred CEEEEECCCCHHHHHHHHHHHHHCCEEEEECCCHHHHHHHHH T ss_conf 679993796436599999999838979996574999999986 No 18 >cd04259 AAK_AK-DapDC AAK_AK-DapDC: Amino Acid Kinase Superfamily (AAK), AK-DapDC; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the bifunctional enzyme AK - DAP decarboxylase (DapDC) found in some bacteria. Aspartokinase is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. DapDC, which is the lysA gene product, catalyzes the decarboxylation of DAP to lysine. Probab=51.55 E-value=18 Score=18.10 Aligned_cols=102 Identities=15% Similarity=0.044 Sum_probs=50.5 Q ss_pred CCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHH--HHHHHHCC-----------CEE----EEECCC Q ss_conf 0688861775058899999875311477830899879987604899--99973028-----------759----994150 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKR--VRQLSQKL-----------GVI----IVCGRF 118 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~--a~~ls~~~-----------~li----liCGrY 118 (236) |||-. |=.++-+.++.+-+++........+|..|+-|++-|+=. +......+ |+- +..-.+ T Consensus 6 FGGTS--v~~~~~~~~v~~ii~~~~~~~~~~vvVVSA~~gvTd~L~~~~~~~~~~~~~~~~~~i~~~h~~~~~~l~~~~~ 83 (295) T cd04259 6 FGGTS--VSSRARWDTIAKLAQKHLNTGGQPLIVCSALSGISNKLEALIDQALLDEHHSLFNAIQSRHLNLAEQLEVDAD 83 (295) T ss_pred ECHHC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCHH T ss_conf 68010--5879999999999998874799989997999998368999999875364466999999999999998521477 Q ss_pred HHHHHHHHHH-------CCCCCEE--EHHEEECCCCHHHHHHHHHHHHHH Q ss_conf 1144899974-------0453100--334011173277999999999850 Q gi|254780714|r 119 EGIDERIIEA-------RDLEEIS--VGDYILSGGEPAALILLDAVVRLL 159 (236) Q Consensus 119 EGiDeRvid~-------~~d~eiS--iGDyVLsGGEl~a~v~~dai~Rli 159 (236) .=+++++.+. ....|.| .=|+|++-||+-+..++-+..|-. T Consensus 84 ~~l~~~~~~l~~~l~~i~~~~~~~~~~~d~i~s~GE~lSa~l~a~~L~~~ 133 (295) T cd04259 84 ALLANDLAQLQRWLTGISLLKQASPRTRAEVLALGELMSTRLGAAYLEAQ 133 (295) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 89999999999999876640479888999999998999999999999967 No 19 >cd04260 AAK_AKi-DapG-BS AAK_AKi-DapG-BS: Amino Acid Kinase Superfamily (AAK), AKi-DapG; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional class enzyme found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis AKI is tetrameric consisting of two alpha and two bet Probab=49.53 E-value=24 Score=17.25 Aligned_cols=86 Identities=19% Similarity=0.198 Sum_probs=51.4 Q ss_pred CCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEE Q ss_conf 06888617750588999998753114778308998799876048999997302875999415011448999740453100 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEIS 135 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiS 135 (236) |||-. |=.++-+.++.+-+++........+|..|.-|+.-++....+|.+. +-..++-+..|. T Consensus 6 FGGtS--v~~~~~i~~va~iI~~~~~~~~~~vVVvSAmg~~~~~~~td~L~~l-----~~~~~~~~~~~~---------- 68 (244) T cd04260 6 FGGTS--VSTKERREQVAKKVKQAVDEGYKPVVVVSAMGRKGDPYATDTLINL-----VYAENSDISPRE---------- 68 (244) T ss_pred ECCCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHH-----HHHHCCCCCHHH---------- T ss_conf 18523--7999999999999988987799889997999999975899999999-----997530389899---------- Q ss_pred EHHEEECCCCHHHHHHHHHHHHHH Q ss_conf 334011173277999999999850 Q gi|254780714|r 136 VGDYILSGGEPAALILLDAVVRLL 159 (236) Q Consensus 136 iGDyVLsGGEl~a~v~~dai~Rli 159 (236) =|++++-||+-+..++-+..+-. T Consensus 69 -~D~l~s~GE~lSa~lla~~L~~~ 91 (244) T cd04260 69 -LDLLMSCGEIISAVVLTSTLRAQ 91 (244) T ss_pred -HHHHHHHCCHHHHHHHHHHHHHC T ss_conf -99999743099999999999964 No 20 >TIGR02895 spore_sigI RNA polymerase sigma-I factor; InterPro: IPR014244 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=48.76 E-value=2.8 Score=23.37 Aligned_cols=18 Identities=39% Similarity=0.912 Sum_probs=13.9 Q ss_pred EECCCHHHHHHHHHHCCCCCEEEHH Q ss_conf 9415011448999740453100334 Q gi|254780714|r 114 VCGRFEGIDERIIEARDLEEISVGD 138 (236) Q Consensus 114 iCGrYEGiDeRvid~~~d~eiSiGD 138 (236) +|||| ||.--|.|.|||= T Consensus 30 ~~~ry-------Id~~~DDE~SIGL 47 (225) T TIGR02895 30 VCKRY-------IDTKEDDELSIGL 47 (225) T ss_pred HHHHC-------CCCCCCCHHHHHH T ss_conf 86330-------6888883255889 No 21 >PRK13786 adenylosuccinate synthetase; Provisional Probab=46.99 E-value=26 Score=16.99 Aligned_cols=79 Identities=20% Similarity=0.300 Sum_probs=44.7 Q ss_pred CCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEC--HHH---HHHHHHCCCEEEEECCCHHHHHHHHHHCCCC Q ss_conf 88861775058899999875311477830899879987604--899---9997302875999415011448999740453 Q gi|254780714|r 58 GGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLT--QKR---VRQLSQKLGVIIVCGRFEGIDERIIEARDLE 132 (236) Q Consensus 58 GG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~--Q~~---a~~ls~~~~liliCGrYEGiDeRvid~~~d~ 132 (236) =|+|||+-|+.+.+-++.+.++.-.-....++.|++..... ++. +.|.++. .=|==||| ||-.-..|+..-. T Consensus 66 IG~GvVvdp~~L~~Ei~~L~~~Gi~~~~~rL~IS~rahli~P~H~~lD~~~E~~r~-~kiGTTgr--GIGPaY~DK~~R~ 142 (424) T PRK13786 66 IGPGVVLNPEVLAEEIAMLEKHGIKVDAEKLGIDAKTSIIMPYHIEMDGLREKARK-AKIGTTKR--GIGYAYIDKIARD 142 (424) T ss_pred ECCCEEECHHHHHHHHHHHHHCCCCCCCCCEEECCCCEECCHHHHHHHHHHHHHCC-CCCCCCCC--CCHHHHHHHCCCC T ss_conf 88978980999999999998669988701053369846726789987799898569-97786898--5358877540576 Q ss_pred CEEEHHE Q ss_conf 1003340 Q gi|254780714|r 133 EISVGDY 139 (236) Q Consensus 133 eiSiGDy 139 (236) -|-+||. T Consensus 143 giRv~DL 149 (424) T PRK13786 143 EVRMADL 149 (424) T ss_pred CCCHHHH T ss_conf 6601453 No 22 >TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC) and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales . This entry represents UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm. Probab=45.90 E-value=25 Score=17.12 Aligned_cols=44 Identities=23% Similarity=0.279 Sum_probs=30.1 Q ss_pred CCCCCCEEE------ECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECH Q ss_conf 068886177------50588999998753114778308998799876048 Q gi|254780714|r 56 AGGGAGMVL------RVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQ 99 (236) Q Consensus 56 yGGG~GMVl------k~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q 99 (236) +.+..+.+. ..+-+.+|+..+.+.....++-+|+|||.+--||| T Consensus 410 ~l~~~~~~~~~~~~~~~~~l~~Av~~a~~~~~~g~~d~vLLSPacASFDq 459 (476) T TIGR01087 410 LLKEIGLVVKYGEETLVESLEEAVQAAREVAKEGNADVVLLSPACASFDQ 459 (476) T ss_pred HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHH T ss_conf 86342764354653057789999999999712799767988864121777 No 23 >PRK13784 adenylosuccinate synthetase; Provisional Probab=44.70 E-value=28 Score=16.76 Aligned_cols=79 Identities=19% Similarity=0.187 Sum_probs=44.1 Q ss_pred CCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECH--HHH---HHHHHCCCEEEEECCCHHHHHHHHHHCCCC Q ss_conf 888617750588999998753114778308998799876048--999---997302875999415011448999740453 Q gi|254780714|r 58 GGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQ--KRV---RQLSQKLGVIIVCGRFEGIDERIIEARDLE 132 (236) Q Consensus 58 GG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q--~~a---~~ls~~~~liliCGrYEGiDeRvid~~~d~ 132 (236) =|+|||+-|+.+.+-++.+.++.-.-....++.|++.-.... +.+ +|-+..+ =|==||| ||-.-..|+..-. T Consensus 68 ig~GvVidp~~L~~Ei~~l~~~gv~~~~~~L~Is~ra~li~P~H~~lD~~~E~~~~~-kIGTTgr--GIGPaY~DK~~R~ 144 (428) T PRK13784 68 IGHGVVLDPVALDEEITRLQAKGIAISAENLFVSESCTIITSYHKLLDAVRESNTSE-KIGTTGK--GIGPAYEDKVSRK 144 (428) T ss_pred ECCCEEECHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHCCC-CCCCCCC--CCCHHHHHHHHCC T ss_conf 899499979999999999996199988777698188532885799989999874576-5565788--7217776554215 Q ss_pred CEEEHHE Q ss_conf 1003340 Q gi|254780714|r 133 EISVGDY 139 (236) Q Consensus 133 eiSiGDy 139 (236) -|-++|. T Consensus 145 giR~~DL 151 (428) T PRK13784 145 GIKFKHL 151 (428) T ss_pred CCCHHHH T ss_conf 5514542 No 24 >PRK08210 aspartate kinase I; Reviewed Probab=43.67 E-value=29 Score=16.66 Aligned_cols=82 Identities=16% Similarity=0.225 Sum_probs=48.3 Q ss_pred CCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEE---CHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCC Q ss_conf 068886177505889999987531147783089987998760---48999997302875999415011448999740453 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTL---TQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLE 132 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l---~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~ 132 (236) |||-. |=-++-+.++.+-+++.....+..++..|.-|+.= ......+|+.. .+.-...|- T Consensus 8 FGGtS--v~~~~~i~~v~~ii~~~~~~~~~~vVVvSAmg~~~~~~~td~L~~l~~~--------~~~~~~~~~------- 70 (405) T PRK08210 8 FGGTS--VSTEERRKMVVNKIKKALKEGYKVVVVVSAMGRKGDPYATDTLLSLVGE--------EFSDISKRE------- 70 (405) T ss_pred ECCCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHHHH--------HCCCCCHHH------- T ss_conf 68502--6999999999999987886699889997998989981149999999986--------502598788------- Q ss_pred CEEEHHEEECCCCHHHHHHHHHHHHH Q ss_conf 10033401117327799999999985 Q gi|254780714|r 133 EISVGDYILSGGEPAALILLDAVVRL 158 (236) Q Consensus 133 eiSiGDyVLsGGEl~a~v~~dai~Rl 158 (236) =|++||-||+-+..++-+..+- T Consensus 71 ----~D~l~s~GE~~S~~l~a~~L~~ 92 (405) T PRK08210 71 ----QDLLMSCGEIISSVVFSNMLNE 92 (405) T ss_pred ----HHHHHHHHHHHHHHHHHHHHHH T ss_conf ----9999877589999999999974 No 25 >COG0104 PurA Adenylosuccinate synthase [Nucleotide transport and metabolism] Probab=40.98 E-value=32 Score=16.39 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=25.9 Q ss_pred CCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCE Q ss_conf 888617750588999998753114778308998799876 Q gi|254780714|r 58 GGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKT 96 (236) Q Consensus 58 GG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~ 96 (236) =|+|||+-|+.+.+-++.+.++......-.++.|...-. T Consensus 68 IGnGvVvdP~~L~~Ei~~L~~~g~~~~~~rL~Is~~ahl 106 (430) T COG0104 68 IGNGVVVDPEVLLKEIEELEERGVDVVRDRLRISDRAHL 106 (430) T ss_pred ECCCEEECHHHHHHHHHHHHHCCCCCCCCEEEECCCCCC T ss_conf 638678879999999999986488666010787367662 No 26 >pfam02481 DNA_processg_A DNA recombination-mediator protein A. The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation. Probab=39.77 E-value=12 Score=19.30 Aligned_cols=42 Identities=29% Similarity=0.298 Sum_probs=35.0 Q ss_pred EECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCC Q ss_conf 9879987604899999730287599941501144899974045 Q gi|254780714|r 89 LMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDL 131 (236) Q Consensus 89 ~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d 131 (236) -.|+.|+.+.++.+++|++ .++++++|==.|||+-.-+...+ T Consensus 52 ~~s~~g~~~~~~~~~~l~~-~~~~VVSG~A~GiD~~ah~~aL~ 93 (210) T pfam02481 52 KPSAYGLRVARKLAAELAE-RGITIVSGLARGIDTAAHRAALE 93 (210) T ss_pred CCCHHHHHHHHHHHHHHHH-CCCEEEECCCCCHHHHHHHHHHH T ss_conf 8898699999999999987-89489967431447999999996 No 27 >TIGR00619 sbcd nuclease SbcCD, D subunit; InterPro: IPR004593 All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely to be homologous to the MRE11 family.; GO: 0004527 exonuclease activity, 0006259 DNA metabolic process. Probab=39.71 E-value=9.1 Score=20.01 Aligned_cols=28 Identities=14% Similarity=0.338 Sum_probs=20.8 Q ss_pred CCCCCCHHHCCCCHHHHHHHHHHHHHHH Q ss_conf 8988984341899899999999999999 Q gi|254780714|r 191 EGLAIPPILNSGDHERIKKWRKEQSFAL 218 (236) Q Consensus 191 ~g~~VP~VLlSGnH~~I~~Wr~~~s~~~ 218 (236) .+.+.|-||+||||-+-+.-...+++.+ T Consensus 82 ~~~R~p~Vvi~GNHD~~~~Ls~~~~Ll~ 109 (275) T TIGR00619 82 ANPRLPIVVISGNHDSADRLSAAKKLLK 109 (275) T ss_pred CCCCEEEEEECCCCCCHHHHCHHHHHHH T ss_conf 3896127870478887786111677897 No 28 >KOG3638 consensus Probab=38.56 E-value=10 Score=19.77 Aligned_cols=13 Identities=46% Similarity=1.058 Sum_probs=6.0 Q ss_pred CEEEHHEEECCCC Q ss_conf 1003340111732 Q gi|254780714|r 133 EISVGDYILSGGE 145 (236) Q Consensus 133 eiSiGDyVLsGGE 145 (236) |++||||||+-.+ T Consensus 227 el~iGD~Vla~~~ 239 (414) T KOG3638 227 ELSIGDYVLAADQ 239 (414) T ss_pred CCCCCCEEECCCC T ss_conf 7898984761266 No 29 >PRK07431 aspartate kinase; Provisional Probab=37.34 E-value=37 Score=16.02 Aligned_cols=80 Identities=21% Similarity=0.317 Sum_probs=48.7 Q ss_pred CCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEE Q ss_conf 06888617750588999998753114778308998799876048999997302875999415011448999740453100 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEIS 135 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiS 135 (236) |||-. |=.+|-+.+..+.+++.....+..++..|.-|+.- +...+|++.= + ...++|-. T Consensus 8 FGGTS--Va~~e~i~~va~~I~~~~~~g~~vvVVVSAmg~~T--d~L~~la~~i-----~---~~~~~re~--------- 66 (594) T PRK07431 8 FGGTS--VGSVERIQAVAQRIARTKEAGNDVVVVVSAMGKTT--DELVKLAEEI-----S---DNPPRREM--------- 66 (594) T ss_pred ECCCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHH--HHHHHHHHHH-----C---CCCCHHHH--------- T ss_conf 28765--79899999999999999875899999974998729--9999999987-----4---79998999--------- Q ss_pred EHHEEECCCCHHHHHHHHHHHHH Q ss_conf 33401117327799999999985 Q gi|254780714|r 136 VGDYILSGGEPAALILLDAVVRL 158 (236) Q Consensus 136 iGDyVLsGGEl~a~v~~dai~Rl 158 (236) |++||-||.-+..++-...+- T Consensus 67 --D~lls~GE~~S~~Lla~~L~~ 87 (594) T PRK07431 67 --DMLLSTGEQVSIALLSMALQE 87 (594) T ss_pred --HHHHHHHHHHHHHHHHHHHHH T ss_conf --999977599999999999996 No 30 >PRK01117 adenylosuccinate synthetase; Provisional Probab=36.91 E-value=37 Score=15.98 Aligned_cols=42 Identities=26% Similarity=0.250 Sum_probs=29.3 Q ss_pred CCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEC Q ss_conf 688861775058899999875311477830899879987604 Q gi|254780714|r 57 GGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLT 98 (236) Q Consensus 57 GGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~ 98 (236) ==|+|||+-|+.+.+-++.++++.-....-.++.|++-.... T Consensus 67 vIG~GvVidp~~L~~Ei~~L~~~Gi~~~~~rL~IS~rahli~ 108 (431) T PRK01117 67 VIGNGVVLDPEALLKEIDELEARGVDTVRERLRISERAHLIL 108 (431) T ss_pred EECCCEEECHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCC T ss_conf 857978986999999999999769998766689909984745 No 31 >COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis] Probab=36.46 E-value=38 Score=15.93 Aligned_cols=138 Identities=20% Similarity=0.220 Sum_probs=96.1 Q ss_pred CCEEEEEEEECHHHHHHHHCCCHHHHHHHC-CCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHH Q ss_conf 954589985183564456403367999974-9659999602563589851353113068886177505889999987531 Q gi|254780714|r 1 MTFHASILTLYPEMFPGHLEKSVAGKALAC-NLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQ 79 (236) Q Consensus 1 M~Mki~IITlFPe~f~~~l~~sIigkA~~~-gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~ 79 (236) |++++.|+=+-|+. .-+.|-+.||.++ |+=++-.+|+|+. -.-+-+-+-.|+.=|+-.--++..++++... T Consensus 1 ~~~~i~iVLVep~~---~gNIG~vARaMKNfGl~eL~LV~Pr~~-----~~eeA~a~A~gA~dile~A~i~~tL~eAl~d 72 (242) T COG0565 1 MLENIRIVLVEPSH---PGNIGSVARAMKNFGLSELRLVNPRAG-----LDEEARALAAGARDILENAKIVDTLEEALAD 72 (242) T ss_pred CCCCCEEEEECCCC---CCCHHHHHHHHHHCCCCEEEEECCCCC-----CCHHHHHHHCCCHHHHCCCEEECCHHHHHCC T ss_conf 98761799975888---752799999998679664899789889-----8899999864666665067664679999607 Q ss_pred CCCCCCCEEEECCCCCEE------CHHHHHHHHHC---CCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEEC---CCCHH Q ss_conf 147783089987998760------48999997302---8759994150114489997404531003340111---73277 Q gi|254780714|r 80 YTHEDIPRILMSPRGKTL------TQKRVRQLSQK---LGVIIVCGRFEGIDERIIEARDLEEISVGDYILS---GGEPA 147 (236) Q Consensus 80 ~~~~~~~vI~lSP~Gk~l------~Q~~a~~ls~~---~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLs---GGEl~ 147 (236) . ..+|.+|..-+.+ -...+..|... ..+-|+-|| || .-+-.+|+-.-||+++ .-|.| T Consensus 73 ~----~~v~aTtar~r~~~~~~~~P~e~~~~l~~~~~~~~vAlvFGR-----E~--~GLtNeEl~~c~~~v~IP~~p~Y~ 141 (242) T COG0565 73 C----DLVVATTARSRDLLRPLRTPREAAPELLEKAKGGKVALVFGR-----ER--VGLTNEELALCDVLVTIPANPDYP 141 (242) T ss_pred C----CEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECC-----CC--CCCCHHHHHHHHEEEECCCCCCCC T ss_conf 8----879980566676655656878789999987148976999788-----66--897889998502787367998654 Q ss_pred HHHHHHHHHH Q ss_conf 9999999998 Q gi|254780714|r 148 ALILLDAVVR 157 (236) Q Consensus 148 a~v~~dai~R 157 (236) +|-+.-||.= T Consensus 142 sLNLa~AV~i 151 (242) T COG0565 142 SLNLAQAVQV 151 (242) T ss_pred CCCHHHHHHH T ss_conf 3659999999 No 32 >KOG4093 consensus Probab=36.25 E-value=3.7 Score=22.63 Aligned_cols=50 Identities=28% Similarity=0.420 Sum_probs=40.4 Q ss_pred EEEECHHHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECH Q ss_conf 9851835644564033679999749659999602563589851353113068886177505 Q gi|254780714|r 7 ILTLYPEMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVD 67 (236) Q Consensus 7 IITlFPe~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~e 67 (236) +..-||++--+.++.+.++-|-.|..| |.|..-=.+.|||+-|| -+|+.+ T Consensus 57 fr~~Fp~l~v~~~t~~elKs~~aKe~W-------R~F~~~f~~kvdDyn~G----TLlR~d 106 (144) T KOG4093 57 FRSSFPELKVEEVTEDELKSAGAKEKW-------RPFCEKFEKKVDDYNFG----TLLRID 106 (144) T ss_pred HHHHCCCCCCCCCCHHHHHCCCHHHHH-------HHHHHHHHHHHCCCCCC----EEEEEC T ss_conf 987550104010688897241068889-------99999987431234542----356522 No 33 >TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167 All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues. This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologues of these genes, but the function of the Archaeal proteins is not known, so are not included in this family.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity, 0006281 DNA repair. Probab=36.11 E-value=14 Score=18.79 Aligned_cols=13 Identities=46% Similarity=0.695 Sum_probs=9.0 Q ss_pred CCCCEEEHHEEEC Q ss_conf 4531003340111 Q gi|254780714|r 130 DLEEISVGDYILS 142 (236) Q Consensus 130 ~d~eiSiGDyVLs 142 (236) +-..+.||||||| T Consensus 711 ~P~~L~VGDYILt 723 (939) T TIGR00596 711 IPCTLTVGDYILT 723 (939) T ss_pred EEEEEEECCEEEC T ss_conf 8778886267746 No 34 >PRK05906 lipid A biosynthesis lauroyl acyltransferase; Provisional Probab=36.10 E-value=29 Score=16.71 Aligned_cols=90 Identities=19% Similarity=0.369 Sum_probs=52.6 Q ss_pred CCCEECHHHHHHH----HHCCCEEEEECCCH--------------H-----------HHHHHHHHCCCCCEEEHHEEECC Q ss_conf 9876048999997----30287599941501--------------1-----------44899974045310033401117 Q gi|254780714|r 93 RGKTLTQKRVRQL----SQKLGVIIVCGRFE--------------G-----------IDERIIEARDLEEISVGDYILSG 143 (236) Q Consensus 93 ~Gk~l~Q~~a~~l----s~~~~liliCGrYE--------------G-----------iDeRvid~~~d~eiSiGDyVLsG 143 (236) +.+++.|..+.++ .+.+++|++|||+- | +|+++... .|.+=|--|-.+ T Consensus 120 ~eEv~~q~el~~~fs~l~~~~G~ILv~~H~aNWELpfl~it~~~pGlA~aKPlKnaRln~kI~sl---R~~~ggkIV~Pk 196 (454) T PRK05906 120 PEEVSSQQELEDTFSRLDEQEGAILFCGHQANWELPFLYITKRYPGLAFAKPIKNARLNKKIFSL---RESFKGKIVPPK 196 (454) T ss_pred CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCEEEEECCCCCCEEEECCCCHHHHHHHHHH---HHHHCCCEECCH T ss_conf 40021489899987420357735999624456403644564377741562002330678999999---987189125754 Q ss_pred CCHHHHHHHHHHHH-HHCCCCCCCCCCCCCCHHCCCCCCCCCCCHH Q ss_conf 32779999999998-5057467822233440114884621116725 Q gi|254780714|r 144 GEPAALILLDAVVR-LLPGVLGNQQSTIHESFENGLLEFPQYTRPQ 188 (236) Q Consensus 144 GEl~a~v~~dai~R-lipGvlg~~~S~~~eSf~~~lLe~P~YTrP~ 188 (236) +-+-.. +.|+-| -+=|.+|| +++..-||+-+++..+-+|-+. T Consensus 197 ~ai~~a--l~aL~~Ge~vgivGD-Qal~~ssys~P~fG~~AftTts 239 (454) T PRK05906 197 NGINQA--LRALHQGEVVGIVGD-QALLSSSYSYPLFGSQAFTTTS 239 (454) T ss_pred HHHHHH--HHHHHCCCEEEEECC-CCCCCCCCCCCCCCCCCCCCCC T ss_conf 789999--999745977999735-4354676332455762336656 No 35 >COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair] Probab=34.78 E-value=37 Score=15.98 Aligned_cols=17 Identities=18% Similarity=0.300 Sum_probs=8.2 Q ss_pred HEEECCCCHHHHHHHHH Q ss_conf 40111732779999999 Q gi|254780714|r 138 DYILSGGEPAALILLDA 154 (236) Q Consensus 138 DyVLsGGEl~a~v~~da 154 (236) |||.-|.---..++.+. T Consensus 203 ~YvALGHiH~~~~~~~~ 219 (390) T COG0420 203 DYVALGHIHKRQVIPKE 219 (390) T ss_pred CEEECCCCCCCCEECCC T ss_conf 56976888764000678 No 36 >COG4270 Predicted membrane protein [Function unknown] Probab=33.85 E-value=15 Score=18.49 Aligned_cols=35 Identities=26% Similarity=0.392 Sum_probs=23.0 Q ss_pred CCCCCCCHHHCCCCCCC-------HHHCCCCHH-------HHHHHHHHH Q ss_conf 62111672540898898-------434189989-------999999999 Q gi|254780714|r 180 EFPQYTRPQIWEGLAIP-------PILNSGDHE-------RIKKWRKEQ 214 (236) Q Consensus 180 e~P~YTrP~~~~g~~VP-------~VLlSGnH~-------~I~~Wr~~~ 214 (236) .--|||||+.|.+.--| .|+.||--+ -|..|+... T Consensus 21 Gi~HF~r~eqf~~IVPp~vP~p~tav~VSG~fEilgglaLlip~~s~~a 69 (131) T COG4270 21 GIGHFTRPEQFRRIVPPCVPLPKTAVLVSGIFEILGGLALLIPAPSQAA 69 (131) T ss_pred HHHHCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 2231156565324589988860468899789999704644247827988 No 37 >TIGR00636 PduO_Nterm ATP:cob(I)alamin adenosyltransferase; InterPro: IPR002779 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) . Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type , EutT-type and PduO-type . Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation , while EutT produces AdoCbl for ethanolamine utilisation . ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid ac-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process. Probab=32.90 E-value=25 Score=17.10 Aligned_cols=48 Identities=29% Similarity=0.367 Sum_probs=34.6 Q ss_pred EEEECCCHHHHHHHHHHCCCCCEEEHHEEECCCCHHHHHH--HHHHHHHHC Q ss_conf 9994150114489997404531003340111732779999--999998505 Q gi|254780714|r 112 IIVCGRFEGIDERIIEARDLEEISVGDYILSGGEPAALIL--LDAVVRLLP 160 (236) Q Consensus 112 iliCGrYEGiDeRvid~~~d~eiSiGDyVLsGGEl~a~v~--~dai~Rlip 160 (236) .|.--.=+.+++|| +.|--+.--+-.|||=||-.||..+ +=+|+|-.. T Consensus 87 ~~~~e~V~~LE~~I-~~Y~~~~~~l~~FvLPGGt~aAa~LHvaRTV~RRaE 136 (184) T TIGR00636 87 KITEEDVKFLEERI-DQYREELPPLKKFVLPGGTPAAAALHVARTVARRAE 136 (184) T ss_pred CCCHHHHHHHHHHH-HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 00599999999999-998653134430649996288999989999989999 No 38 >cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. Probab=32.66 E-value=17 Score=18.16 Aligned_cols=15 Identities=53% Similarity=0.895 Sum_probs=10.5 Q ss_pred CEEEHHEEECCCCHH Q ss_conf 100334011173277 Q gi|254780714|r 133 EISVGDYILSGGEPA 147 (236) Q Consensus 133 eiSiGDyVLsGGEl~ 147 (236) .|++|||||--|+=+ T Consensus 3 ti~vGdfVLVeg~D~ 17 (128) T cd04719 3 TIEVGDFVLIEGEDA 17 (128) T ss_pred EEEECCEEEEECCCC T ss_conf 888378999967876 No 39 >COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only] Probab=32.60 E-value=43 Score=15.53 Aligned_cols=113 Identities=16% Similarity=0.220 Sum_probs=72.2 Q ss_pred CHHHHHHHHCCCHHHHHHHCC------CEEEEEECCHHHCCCCCCEEE------ECCCCCCCCEEEECHHHHHHHHHHHH Q ss_conf 835644564033679999749------659999602563589851353------11306888617750588999998753 Q gi|254780714|r 11 YPEMFPGHLEKSVAGKALACN------LWSMDAIQIRNFSTDRHHSVD------DTPAGGGAGMVLRVDILGKAIDHAVS 78 (236) Q Consensus 11 FPe~f~~~l~~sIigkA~~~g------li~i~~~dlRdfs~~kh~~VD------D~PyGGG~GMVlk~epi~~ai~~~~~ 78 (236) ||+...-.+-..++..|...+ +++-.++++..|... +.++ -+-||||.- -.-|+.+|++.+++ T Consensus 288 ~~e~~AKAvalAl~~~alaenR~~~~~lF~s~~~~~el~~k~--~~~~e~i~fL~~~f~GGTD---~~~~l~~al~~~k~ 362 (437) T COG2425 288 FKEQWAKAVALALMRIALAENRDCYVILFDSEVIEYELYEKK--IDIEELIEFLSYVFGGGTD---ITKALRSALEDLKS 362 (437) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEECCCC--CCHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHC T ss_conf 288999999999999998843053899952520255505774--5799999999650689888---58999999998643 Q ss_pred HCCCCCCCEEEECCCCCEEC---HHHHHHHHHCC----CEEEEECCCHHHHHHHHHHC Q ss_conf 11477830899879987604---89999973028----75999415011448999740 Q gi|254780714|r 79 QYTHEDIPRILMSPRGKTLT---QKRVRQLSQKL----GVIIVCGRFEGIDERIIEAR 129 (236) Q Consensus 79 ~~~~~~~~vI~lSP~Gk~l~---Q~~a~~ls~~~----~liliCGrYEGiDeRvid~~ 129 (236) .. ..++..|+.|-.=-..+ +..++++++.. +-++|.|+-++==.||.|++ T Consensus 363 ~~-~~~adiv~ITDg~~~~~~~~~~~v~e~~k~~~~rl~aV~I~~~~~~~l~~Isd~~ 419 (437) T COG2425 363 RE-LFKADIVVITDGEDERLDDFLRKVKELKKRRNARLHAVLIGGYGKPGLMRISDHI 419 (437) T ss_pred CC-CCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHCEEEEEEECCCCCCCCCEECEEE T ss_conf 66-5677789980437665467899999998875434899996478986600011146 No 40 >TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent .. Probab=32.11 E-value=31 Score=16.54 Aligned_cols=21 Identities=43% Similarity=0.629 Sum_probs=15.3 Q ss_pred ECCCC--HHHHHHHHHHHHHHCC Q ss_conf 11732--7799999999985057 Q gi|254780714|r 141 LSGGE--PAALILLDAVVRLLPG 161 (236) Q Consensus 141 LsGGE--l~a~v~~dai~RlipG 161 (236) +|||| |+||.+|=||=|+-|- T Consensus 1113 MSGGEKSLtALsFIFAiQ~y~Ps 1135 (1202) T TIGR02169 1113 MSGGEKSLTALSFIFAIQRYKPS 1135 (1202) T ss_pred CCCCHHHHHHHHHHHHHHHCCCC T ss_conf 03838999999999999621898 No 41 >COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones] Probab=31.98 E-value=44 Score=15.46 Aligned_cols=13 Identities=31% Similarity=0.445 Sum_probs=5.4 Q ss_pred CCCEECHHHHHHH Q ss_conf 9876048999997 Q gi|254780714|r 93 RGKTLTQKRVRQL 105 (236) Q Consensus 93 ~Gk~l~Q~~a~~l 105 (236) .|+|+-|+.+.+| T Consensus 79 GGEP~~~~~l~~L 91 (212) T COG0602 79 GGEPLLQPNLLEL 91 (212) T ss_pred CCCCCCCCCHHHH T ss_conf 8864662239999 No 42 >TIGR01717 AMP-nucleosdse AMP nucleosidase; InterPro: IPR011271 This entry represents the AMP nucleosidase from proteobacteria but also including sequences from Corynebacterium, a Gram-positive organism. The Escherichia coli protein is the most well studied .. Probab=31.67 E-value=18 Score=18.09 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=21.6 Q ss_pred HHHHH-CCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEECC Q ss_conf 99730-287599941501144899974045310033401117 Q gi|254780714|r 103 RQLSQ-KLGVIIVCGRFEGIDERIIEARDLEEISVGDYILSG 143 (236) Q Consensus 103 ~~ls~-~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLsG 143 (236) ..||= -+|.=+.-||--|+|+|-. ||||||.- T Consensus 289 DHLAVLRP~~WlMiGHCaGLr~sq~---------iGDyvLAh 321 (486) T TIGR01717 289 DHLAVLRPHAWLMIGHCAGLRESQR---------IGDYVLAH 321 (486) T ss_pred HHHHHCCCCCEEEECCCCCHHHHHH---------HHHHHHHH T ss_conf 1022118874287222304123234---------31255520 No 43 >PRK05665 amidotransferase; Provisional Probab=31.52 E-value=45 Score=15.42 Aligned_cols=87 Identities=11% Similarity=0.010 Sum_probs=51.8 Q ss_pred CCEEEEEEE---ECHHHHHHHHCCCHHHHHH---HCCCEEEEEECCHHHCCC-CCCEEEECCCCCCCCEEEECHHHHHHH Q ss_conf 954589985---1835644564033679999---749659999602563589-851353113068886177505889999 Q gi|254780714|r 1 MTFHASILT---LYPEMFPGHLEKSVAGKAL---ACNLWSMDAIQIRNFSTD-RHHSVDDTPAGGGAGMVLRVDILGKAI 73 (236) Q Consensus 1 M~Mki~IIT---lFPe~f~~~l~~sIigkA~---~~gli~i~~~dlRdfs~~-kh~~VDD~PyGGG~GMVlk~epi~~ai 73 (236) |+|||-||- ..|++.+.+=+|+=.=+++ ..--+++.++|..+--.. .-...|-.-..|++-.|--.+|+...+ T Consensus 1 m~mki~IL~~d~~~~~~~~~~g~y~~mF~~ll~~~~~~~~~~~~~v~~ge~P~~~~~~dg~vITGS~~~vyd~~pWi~~L 80 (240) T PRK05665 1 MSLRICILETDVLRPELVAQYQGYGRMFEQLFARQPIAAEFVVYNVVQGDYPADDEKFDAYLVTGSKADSFGTDPWIQTL 80 (240) T ss_pred CCEEEEEEECCCCCHHHHHHCCCHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCHHHCCEEEEECCCCCCCCCCHHHHHH T ss_conf 97089999789998789977499889999999618998559999700687998977878999958987468996769999 Q ss_pred HHHHHHCCCCCCCE Q ss_conf 98753114778308 Q gi|254780714|r 74 DHAVSQYTHEDIPR 87 (236) Q Consensus 74 ~~~~~~~~~~~~~v 87 (236) .+...+....+.++ T Consensus 81 ~~~i~~~~~~~~pi 94 (240) T PRK05665 81 KTYLLKLYERGDKL 94 (240) T ss_pred HHHHHHHHHCCCCE T ss_conf 99999998769998 No 44 >KOG3039 consensus Probab=30.65 E-value=46 Score=15.38 Aligned_cols=32 Identities=28% Similarity=0.374 Sum_probs=19.8 Q ss_pred CEEEECCCCCEECHHHHHHHHHCCCEEEEECC Q ss_conf 08998799876048999997302875999415 Q gi|254780714|r 86 PRILMSPRGKTLTQKRVRQLSQKLGVIIVCGR 117 (236) Q Consensus 86 ~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGr 117 (236) +..+|+|.|-+++-..+.+|...+-+-.|||+ T Consensus 236 ~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~ 267 (303) T KOG3039 236 PCAVLRPSGHVVTKECVEKLIRKDMVDPVTDK 267 (303) T ss_pred CEEEECCCCCEEEHHHHHHHCCCCCCCCCCCC T ss_conf 13786167867549999986232462557798 No 45 >TIGR00571 dam DNA adenine methylase; InterPro: IPR012326 In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. There are 2 major classes of DNA methyltransferase that differ in the nature of the modifications they effect. The members of one class (C-MTases) methylate a ring carbon and form C5-methylcytosine (see IPR001525 from INTERPRO). Members of the second class (N-MTases) methylate exocyclic nitrogens and form either N4-methylcytosine (N4-MTases) or N6-methyladenine (N6-MTases). Both classes of MTase utilise the cofactor S-adenosyl-L-methionine (SAM) as the methyl donor and are active as monomeric enzymes . N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognize a specific sequence in DNA and methylate an adenine in that sequence. It has been shown , , , that A-Mtases contain a conserved motif Asp/Asn-Pro-Pro-Tyr/Phe in their N-terminal section, this conserved region could be involved in substrate binding or in the catalytic activity. The structure of N6-MTase TaqI (M.TaqI) has been resolved to 2.4 A . The molecule folds into 2 domains, an N-terminal catalytic domain, which contains the catalytic and cofactor binding sites, and comprises a central 9-stranded beta-sheet, surrounded by 5 helices; and a C-terminal DNA recognition domain, which is formed by 4 small beta-sheets and 8 alpha-helices. The N- and C-terminal domains form a cleft that accommodates the DNA substrate. A classification of N-MTases has been proposed, based on conserved motif (CM) arrangements . According to this classification, N6-MTases that have a DPPY motif (CM II) occuring after the FxGxG motif (CM I) are designated D12 class N6-adenine MTases.; GO: 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0006306 DNA methylation. Probab=29.92 E-value=44 Score=15.52 Aligned_cols=35 Identities=29% Similarity=0.437 Sum_probs=28.5 Q ss_pred CCEECHHHHHHHHHC-C-CEEEEECCCHHHHHHHHHH Q ss_conf 876048999997302-8-7599941501144899974 Q gi|254780714|r 94 GKTLTQKRVRQLSQK-L-GVIIVCGRFEGIDERIIEA 128 (236) Q Consensus 94 Gk~l~Q~~a~~ls~~-~-~liliCGrYEGiDeRvid~ 128 (236) -..++.+-.+.+|+. + +.+|+|+.|+-+.+.+... T Consensus 184 ~i~~~e~~~~~~~~~~~kn~~f~c~~F~~~~~~~~~~ 220 (327) T TIGR00571 184 IIIFDEKNLRNFSKKLQKNTTFLCGSFEKILEMVDRD 220 (327) T ss_pred HHCCCHHHHHHHHHHHHCCCEEEECCHHHHHHHCCCC T ss_conf 6427889999999986068157525667886230378 No 46 >KOG0365 consensus Probab=29.66 E-value=32 Score=16.38 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=19.4 Q ss_pred CCCCCCEEEECHHHHHHHHHHH Q ss_conf 0688861775058899999875 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAV 77 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~ 77 (236) ||||||-.=---|-++|+.++. T Consensus 139 fgGGPGQl~HLA~TYAAVnaL~ 160 (423) T KOG0365 139 FGGGPGQLPHLAPTYAAVNALC 160 (423) T ss_pred CCCCCCCCHHHHHHHHHHHHHH T ss_conf 7888764214567899988887 No 47 >PRK01207 methionine synthase; Provisional Probab=28.19 E-value=51 Score=15.05 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=3.9 Q ss_pred HHHHHHHHCCC Q ss_conf 99999850574 Q gi|254780714|r 152 LDAVVRLLPGV 162 (236) Q Consensus 152 ~dai~RlipGv 162 (236) +||+-+-+.|| T Consensus 194 v~a~~~~~~gv 204 (343) T PRK01207 194 VDSINKSVYGI 204 (343) T ss_pred HHHHHHHHCCC T ss_conf 99999984589 No 48 >smart00788 Adenylsucc_synt Adenylosuccinate synthetase. Adenylosuccinate synthetase plays an important role in purine biosynthesis, by catalyzing the GTP-dependent conversion of IMP and aspartic acid to AMP. Adenylosuccinate synthetase has been characterized from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present - one involved in purine biosynthesis and the other in the purine nucleotide cycle. The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central beta-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel beta-sheets, comprised of two strands and three strands each, 11 alpha-helices and two short 3/10-helices. Furt Probab=28.00 E-value=52 Score=15.03 Aligned_cols=60 Identities=23% Similarity=0.278 Sum_probs=35.9 Q ss_pred CCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECH--H---HHHHHHHCCCEEEEECC Q ss_conf 6888617750588999998753114778308998799876048--9---99997302875999415 Q gi|254780714|r 57 GGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQ--K---RVRQLSQKLGVIIVCGR 117 (236) Q Consensus 57 GGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q--~---~a~~ls~~~~liliCGr 117 (236) ==|+|||+-|+.+.+-++.+.++.- .-...++.|++.....- + .+.|.++...-|==||| T Consensus 65 vIG~GvVidp~~L~~Ei~~L~~~gi-~~~~rL~IS~rahli~P~H~~lD~~~E~~~g~~~IGTTgr 129 (421) T smart00788 65 VIGNGVVIDPEALFKEIDQLEAKGV-DVRDRLFISDRAHLILPYHIALDKLREKARGKKKIGTTGR 129 (421) T ss_pred EECCCEEECHHHHHHHHHHHHHCCC-CCCCCEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 8779689859999999999996289-9854889868744488314888899999738875566677 No 49 >pfam09276 Pertus-S5-tox Pertussis toxin S5 subunit. Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology. Probab=27.85 E-value=52 Score=15.01 Aligned_cols=40 Identities=25% Similarity=0.408 Sum_probs=28.8 Q ss_pred HHHHHHHCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECH Q ss_conf 5644564033679999749659999602563589851353113068886177505 Q gi|254780714|r 13 EMFPGHLEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVD 67 (236) Q Consensus 13 e~f~~~l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~e 67 (236) .+|+..+.+.|..-|++..+ .-+|.|.||-|-||-++.-+ T Consensus 49 twfdtmlgfaisayalksri---------------altvedspypgtpgdllelq 88 (97) T pfam09276 49 TWFDTMLGFAISAYALKSRI---------------ALTVEDSPYPGTPGDLLELQ 88 (97) T ss_pred HHHHHHHHHHHHHHHHHHCE---------------EEEECCCCCCCCCCCEEEEE T ss_conf 69999998999999865106---------------78842789997976661367 No 50 >cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi Probab=27.48 E-value=53 Score=14.97 Aligned_cols=117 Identities=14% Similarity=0.176 Sum_probs=60.0 Q ss_pred HCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEEC--CCCCE Q ss_conf 4033679999749659999602563589851353113068886177505889999987531147783089987--99876 Q gi|254780714|r 19 LEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMS--PRGKT 96 (236) Q Consensus 19 l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lS--P~Gk~ 96 (236) +-.||-..|.+.|. ++-+.+-.+-...--++|| |+++-...-.+.++.+.+. +.++|+.. +.+.. T Consensus 22 i~~gie~~a~~~Gy-~l~i~~~~~~~~~~~~~VD--------GiI~~~~~~~~~~~~l~~~----~~PvV~id~~~~~~~ 88 (270) T cd01544 22 IRLGIEKRAQELGI-ELTKFFRDDDLLEILEDVD--------GIIAIGKFSQEQLAKLAKL----NPNLVFVDSNPAPDG 88 (270) T ss_pred HHHHHHHHHHHCCC-EEEEEECCCCHHHHHCCCC--------EEEEECCCCHHHHHHHHHC----CCCEEEECCCCCCCC T ss_conf 99999999998099-9999968999999972899--------9999289999999999962----998999927678889 Q ss_pred E-----C-----HHHHHHHHHC--CCEEEEEC--------------CCHHHHHHHHHHCC--CCCEEEHHEEECCCCHHH Q ss_conf 0-----4-----8999997302--87599941--------------50114489997404--531003340111732779 Q gi|254780714|r 97 L-----T-----QKRVRQLSQK--LGVIIVCG--------------RFEGIDERIIEARD--LEEISVGDYILSGGEPAA 148 (236) Q Consensus 97 l-----~-----Q~~a~~ls~~--~~liliCG--------------rYEGiDeRvid~~~--d~eiSiGDyVLsGGEl~a 148 (236) + | ...++.|.+. +++.++.| |++|+-+-..++-. ...+..|+|-...|.-++ T Consensus 89 ~~~V~~Dn~~~~~~a~~~Li~~Ghr~I~~i~g~~~~~~~~~~~~~~R~~Gy~~al~~~g~~~~~~~~~~~~~~~~g~~~~ 168 (270) T cd01544 89 FDSVVPDFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGLYDPELIYIGDFTVESGYQLM 168 (270) T ss_pred CCEEEECHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHHHH T ss_conf 99899888999999999999779986999957766775122568999999999999859999644996689979999999 No 51 >PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional Probab=27.33 E-value=53 Score=14.95 Aligned_cols=33 Identities=24% Similarity=0.493 Sum_probs=18.2 Q ss_pred CEEEEC-CCCCEECHHHHHHHHHCCCE-EEEECCC Q ss_conf 089987-99876048999997302875-9994150 Q gi|254780714|r 86 PRILMS-PRGKTLTQKRVRQLSQKLGV-IIVCGRF 118 (236) Q Consensus 86 ~vI~lS-P~Gk~l~Q~~a~~ls~~~~l-iliCGrY 118 (236) ++|--| -.||+=+-.+...+.+..++ ..+||-. T Consensus 110 ~~IaVTGTnGKTTTt~ll~~iL~~~g~~~~~~GNI 144 (459) T PRK02705 110 PWVGITGTNGKTTVTHLLAHILQAAGLNAPMCGNI 144 (459) T ss_pred CEEEEECCCCCHHHHHHHHHHHHHCCCCCEEECCC T ss_conf 75777178972789999999999839985364013 No 52 >TIGR02363 dhaK1 dihydroxyacetone kinase, DhaK subunit; InterPro: IPR012736 In bacteria, dihydroxyacetone is formed by the oxidation of glycerol or the aldol cleavage of fructose-6-phosphate. Dihydroxyacetone kinase converts this compound to the glycolytic intermediate dihydroxyacetone phosphate. Two forms of this enzyme have been shown to exist, using either ATP or a phosphoprotein of the phosphoenolpyruvate: sugar phosphotransferase system (PTS) as phosphate donor. The ATP-dependent kinases (2.7.1.29 from EC) are single-subunit enzymes that are composed of two domains . The phosphoprotein-dependent kinases are composed of three subunits: DhaK and DhaL, which are homologous to the domains from the ATP-dependent enzyme; and DhaM which is a component of the PTS system . This entry represents the DhaK subunit of phosphoprotein-dependent dihydroxyacetone kinase. The model excludes the DhaK paralog DhaK2 (IPR012735 from INTERPRO) encoded in the same operon as DhaK in the firmicutes, with which it sometimes exists as a DhaK/DhaK2 fusion. This subunit is a homodimer which contains the dihydroxyacetone-binding site . The overall fold consists of two six-stranded mixed beta-sheets surrounded by nine alpha-helices and a beta-ribbon covering the exposed edge strand of one sheet. . Probab=27.22 E-value=53 Score=14.94 Aligned_cols=45 Identities=16% Similarity=0.170 Sum_probs=36.9 Q ss_pred ECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHCCCEE Q ss_conf 505889999987531147783089987998760489999973028759 Q gi|254780714|r 65 RVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKLGVI 112 (236) Q Consensus 65 k~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~~~li 112 (236) -||.|++|+.++- .+.....|.=.=.|-++|=.+|.|||..+.|. T Consensus 84 TPDqI~~AikAVD---~G~GVLLIVKNYtGDVmNFeMA~ElAE~eGI~ 128 (354) T TIGR02363 84 TPDQILEAIKAVD---QGAGVLLIVKNYTGDVMNFEMAAELAEAEGIK 128 (354) T ss_pred CCCHHHHHHHHHC---CCCCEEEEEECCCCCCCCHHHHHHHHHCCCCE T ss_conf 8548999898303---78913799853558835077899986227976 No 53 >PRK10433 putative RNA methyltransferase; Provisional Probab=26.86 E-value=54 Score=14.89 Aligned_cols=135 Identities=17% Similarity=0.182 Sum_probs=86.3 Q ss_pred EEEEEEEECHHHHHHHHCCCHHHHHHHC-CCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHHCC Q ss_conf 4589985183564456403367999974-965999960256358985135311306888617750588999998753114 Q gi|254780714|r 3 FHASILTLYPEMFPGHLEKSVAGKALAC-NLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVDILGKAIDHAVSQYT 81 (236) Q Consensus 3 Mki~IITlFPe~f~~~l~~sIigkA~~~-gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~ 81 (236) |+|.||=+=|.. +-+.|-+.||.++ |+-++..+++|+|....- +...-|+.=|+.---+++.++++.... T Consensus 1 m~i~iVLvep~~---p~NIGa~ARaMkN~G~~~L~LV~P~~~~~~~a-----~~~A~gA~diL~~a~v~~sL~eAl~d~- 71 (228) T PRK10433 1 MRLTIILVAPAR---AENIGAAARAMKTMGFSELRIVDSQAHLEPAA-----RWVAHGSGDILDNIEVFDTLAEALHDV- 71 (228) T ss_pred CEEEEEEECCCC---CCHHHHHHHHHHCCCCCCEEEECCCCCCCHHH-----HHHHCCHHHHHHHCCCCCCHHHHHHCC- T ss_conf 969999967999---75199999999728998169979999998889-----998347399997373337799998548- Q ss_pred CCCCCEEEECCCCCE-----ECHH-HHHHHHHC----CCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEEC---CCCHHH Q ss_conf 778308998799876-----0489-99997302----8759994150114489997404531003340111---732779 Q gi|254780714|r 82 HEDIPRILMSPRGKT-----LTQK-RVRQLSQK----LGVIIVCGRFEGIDERIIEARDLEEISVGDYILS---GGEPAA 148 (236) Q Consensus 82 ~~~~~vI~lSP~Gk~-----l~Q~-~a~~ls~~----~~liliCGrYEGiDeRvid~~~d~eiSiGDyVLs---GGEl~a 148 (236) ..+|-+|.+.+. ++-. .+..+... ..+-|+-||= | .-+-.+|++.-||+++ ..+.|+ T Consensus 72 ---~~vvgtTaR~r~~~~~~~~p~~~~~~~~~~~~~~~~valvFG~E-----~--~GLsneEl~~C~~~~~IPt~~~y~S 141 (228) T PRK10433 72 ---DFTVATTARSRAKYHYYATPAELVPLLEEKSSWMSHAALVFGRE-----D--SGLTNEELALADVLTGVPMAADYPS 141 (228) T ss_pred ---CEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCC-----C--CCCCHHHHHHCCEEEEEECCCCCCC T ss_conf ---98999645646688886899999999997323478479998886-----6--8989899986797898558999853 Q ss_pred HHHHHHHH Q ss_conf 99999999 Q gi|254780714|r 149 LILLDAVV 156 (236) Q Consensus 149 ~v~~dai~ 156 (236) |-+.-||. T Consensus 142 LNLaqAV~ 149 (228) T PRK10433 142 LNLGQAVM 149 (228) T ss_pred CCHHHHHH T ss_conf 21999999 No 54 >PRK13783 adenylosuccinate synthetase; Provisional Probab=26.84 E-value=54 Score=14.89 Aligned_cols=78 Identities=18% Similarity=0.275 Sum_probs=44.4 Q ss_pred CCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEC-H-HHHH---HHHHCCCEEEEECCCHHHHHHHHHHCCCC Q ss_conf 88861775058899999875311477830899879987604-8-9999---97302875999415011448999740453 Q gi|254780714|r 58 GGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLT-Q-KRVR---QLSQKLGVIIVCGRFEGIDERIIEARDLE 132 (236) Q Consensus 58 GG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~-Q-~~a~---~ls~~~~liliCGrYEGiDeRvid~~~d~ 132 (236) =|+|||+-|+.+.+-++.+.++.. .-...++.|++-.... . +.+. |-+..+ -|=-||| ||-.-..|+..-. T Consensus 67 IG~GvVidp~~L~~Ei~~L~~~g~-~~~~rL~Is~rahii~P~H~~lD~~~E~~rg~-~iGTT~r--GIGPaY~DK~~R~ 142 (404) T PRK13783 67 IGNGVVLDLEVLVEELEELKAKFP-DYSSRLYISELAHVVLPVHKELDEIIESVRKN-AIGTTKR--GIGPAYADKVMRV 142 (404) T ss_pred ECCCEEECHHHHHHHHHHHHHHCC-CCCCCEEECCCCCCCCHHHHHHHHHHHHHCCC-CCCCCCC--EECHHHHCCCCCC T ss_conf 889789969999999999997389-98778798188573786899988986554157-6675587--0427763424657 Q ss_pred CEEEHHE Q ss_conf 1003340 Q gi|254780714|r 133 EISVGDY 139 (236) Q Consensus 133 eiSiGDy 139 (236) -|-+||. T Consensus 143 giR~~Dl 149 (404) T PRK13783 143 GVRLADL 149 (404) T ss_pred CCEEEHH T ss_conf 8675412 No 55 >PRK08373 aspartate kinase; Validated Probab=26.55 E-value=43 Score=15.53 Aligned_cols=96 Identities=18% Similarity=0.193 Sum_probs=45.7 Q ss_pred CCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHCC--CEEEEECCCH------HHHHHHHH Q ss_conf 068886177505889999987531147783089987998760489999973028--7599941501------14489997 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQKL--GVIIVCGRFE------GIDERIIE 127 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~~--~liliCGrYE------GiDeRvid 127 (236) |||-.= ++.+.++.+-++ ....++..+|..|.-|..=| .+ -++++.. .+.-|.-+|+ |+|...+. T Consensus 10 FGGTSV----~~a~~~v~~iv~-~~~~~~~vvVVVSAm~gvTd-~L-i~~a~~~~~~~~~I~~~h~~~a~~l~~~~~~l~ 82 (359) T PRK08373 10 FGGSSV----RYDFEEAVELVK-SLSEEKEVIVVVSALKGVTD-CL-LKYANTDKSAALEIEKIHEEFAKEHGIDTEILS 82 (359) T ss_pred ECHHCC----HHHHHHHHHHHH-HHHCCCCEEEEECCCCCCHH-HH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 281013----328999999999-87528988999679999779-99-999976577789999999999998366677889 Q ss_pred HCCC--------CCEEEHHEEECCCCHHHHHHHHHHHHH Q ss_conf 4045--------310033401117327799999999985 Q gi|254780714|r 128 ARDL--------EEISVGDYILSGGEPAALILLDAVVRL 158 (236) Q Consensus 128 ~~~d--------~eiSiGDyVLsGGEl~a~v~~dai~Rl 158 (236) .... ..=++-|+++|-||+-+..++-+..+- T Consensus 83 ~~l~~l~~~~~~~~~~~~D~Ils~GE~lSa~Lla~~L~~ 121 (359) T PRK08373 83 PYLKELFNRPDFPSEALRDYILSIGERLSAVIFAEGLKI 121 (359) T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999998731138845766667767399999999999997 No 56 >COG4658 RnfD Predicted NADH:ubiquinone oxidoreductase, subunit RnfD [Energy production and conversion] Probab=25.77 E-value=40 Score=15.78 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=9.4 Q ss_pred CCCCHHHCCCCC Q ss_conf 116725408988 Q gi|254780714|r 183 QYTRPQIWEGLA 194 (236) Q Consensus 183 ~YTrP~~~~g~~ 194 (236) +||||+.|.+.+ T Consensus 326 yYtrpR~yG~~~ 337 (338) T COG4658 326 YYTRPRVYGHVK 337 (338) T ss_pred HHCCCCCCCCCC T ss_conf 744765468878 No 57 >smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain Probab=25.71 E-value=42 Score=15.63 Aligned_cols=24 Identities=33% Similarity=0.438 Sum_probs=16.4 Q ss_pred CCCEEEECCCCCEECHH--HHHHHHH Q ss_conf 83089987998760489--9999730 Q gi|254780714|r 84 DIPRILMSPRGKTLTQK--RVRQLSQ 107 (236) Q Consensus 84 ~~~vI~lSP~Gk~l~Q~--~a~~ls~ 107 (236) +.-|+|.||+|+.|-+. +++-|.+ T Consensus 27 k~dV~Y~sP~GkklRs~~ev~~YL~~ 52 (77) T smart00391 27 KFDVYYISPCGKKLRSKSELARYLHK 52 (77) T ss_pred EEEEEEECCCCCCCCCHHHHHHHHHH T ss_conf 06799989998540389999999997 No 58 >cd03275 ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for Probab=25.34 E-value=44 Score=15.52 Aligned_cols=73 Identities=30% Similarity=0.430 Sum_probs=45.6 Q ss_pred CCCEECHHHHHHHHHCC-------CEEEEECCCHHH------HHHHHHHCCCCCEEEHHEEECCCC--HHHHHHHHHHHH Q ss_conf 98760489999973028-------759994150114------489997404531003340111732--779999999998 Q gi|254780714|r 93 RGKTLTQKRVRQLSQKL-------GVIIVCGRFEGI------DERIIEARDLEEISVGDYILSGGE--PAALILLDAVVR 157 (236) Q Consensus 93 ~Gk~l~Q~~a~~ls~~~-------~liliCGrYEGi------DeRvid~~~d~eiSiGDyVLsGGE--l~a~v~~dai~R 157 (236) -|++-..+...++-... |.++-=|+-|-| +-|+.+. . -||||| ++|++++=|+-+ T Consensus 105 Ng~~vrlkdi~elf~~~gIgv~a~nflV~QG~Ve~Il~~~Pp~rRf~~~------~----~LSGGEKtl~alallFai~~ 174 (247) T cd03275 105 NGKVVSLKEYNEELEKINILVKARNFLVFQGDVESIASKNPPGKRFRDM------D----NLSGGEKTMAALALLFAIHS 174 (247) T ss_pred CCCCCCHHHHHHHHHHCCCCCCCCCEEEECCHHHHHHCCCCHHHCCCCH------H----HCCCCHHHHHHHHHHHHHHC T ss_conf 8972678999999876599977872389644488886379303100212------3----33820899999999999971 Q ss_pred HHCC---CCCCCCCCCCCCHH Q ss_conf 5057---46782223344011 Q gi|254780714|r 158 LLPG---VLGNQQSTIHESFE 175 (236) Q Consensus 158 lipG---vlg~~~S~~~eSf~ 175 (236) .-|- +|-.-+.+.+++-. T Consensus 175 ~~PsPF~vLDEVDAaLD~~Nv 195 (247) T cd03275 175 YQPAPFFVLDEVDAALDNTNV 195 (247) T ss_pred CCCCCEEEEECCCCCCCHHHH T ss_conf 289955887067634688999 No 59 >pfam01429 MBD Methyl-CpG binding domain. The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase. Probab=25.34 E-value=43 Score=15.54 Aligned_cols=24 Identities=29% Similarity=0.477 Sum_probs=16.4 Q ss_pred CCCEEEECCCCCEECHH--HHHHHHH Q ss_conf 83089987998760489--9999730 Q gi|254780714|r 84 DIPRILMSPRGKTLTQK--RVRQLSQ 107 (236) Q Consensus 84 ~~~vI~lSP~Gk~l~Q~--~a~~ls~ 107 (236) +.-|+|.||+|+.|-+. +++-|.+ T Consensus 29 k~DVyY~sP~GkklRs~~ev~~yL~~ 54 (75) T pfam01429 29 KVDVYYYSPTGKKFRSKSELIRYLEK 54 (75) T ss_pred CEEEEEECCCCCEECCHHHHHHHHHH T ss_conf 15699989999634189999999987 No 60 >pfam02598 DUF171 Uncharacterized ACR, COG2106. Probab=25.27 E-value=58 Score=14.71 Aligned_cols=72 Identities=22% Similarity=0.295 Sum_probs=44.3 Q ss_pred EECCCCCCC--CEEEE-CHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHH--HHCCCEEEEEC---CCHHHHH Q ss_conf 311306888--61775-0588999998753114778308998799876048999997--30287599941---5011448 Q gi|254780714|r 52 DDTPAGGGA--GMVLR-VDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQL--SQKLGVIIVCG---RFEGIDE 123 (236) Q Consensus 52 DD~PyGGG~--GMVlk-~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~l--s~~~~liliCG---rYEGiDe 123 (236) ...|++.|. |--.+ +.-+.+++..+.-... --.+|..|-.|+..++...+.. .+.+|+.++-| +.++.|+ T Consensus 166 p~~p~~~~~YwGY~Vr~a~sl~~v~~~~~~~~g--Yd~~I~tS~~G~~~~~~~~~~~~~~~~~~~lvVFG~~~~~~~~~~ 243 (283) T pfam02598 166 PAEPYGEGLYWGYKVRIASSLSDVFKKSPFPEG--YDVTIGTSRRGKDISEAELEIKLMENFKHILLVFGGWEPLKGSDE 243 (283) T ss_pred CCCCCCCCCCCCEEEEEECCHHHHHHCCCCCCC--CCEEEEECCCCCCCCHHHHCCCCCCCCCCEEEEECCCHHHHHHHH T ss_conf 656466788777579983689999623876788--886999899996463100011455677848999799436510344 Q ss_pred HH Q ss_conf 99 Q gi|254780714|r 124 RI 125 (236) Q Consensus 124 Rv 125 (236) .. T Consensus 244 ~~ 245 (283) T pfam02598 244 IL 245 (283) T ss_pred HH T ss_conf 41 No 61 >PRK13788 adenylosuccinate synthetase; Provisional Probab=24.64 E-value=59 Score=14.63 Aligned_cols=37 Identities=22% Similarity=0.358 Sum_probs=27.8 Q ss_pred CCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEE Q ss_conf 8886177505889999987531147783089987998760 Q gi|254780714|r 58 GGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTL 97 (236) Q Consensus 58 GG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l 97 (236) =|+|||+-|+.+.+-++.+.++.-. ..++.|++.... T Consensus 68 IG~GvVvdp~~L~~Ei~~L~~~Gi~---~rl~IS~rahli 104 (404) T PRK13788 68 LGDGMVIDPEKFQEERENLRKGGLD---PKLLISDRAHLV 104 (404) T ss_pred ECCCEEECHHHHHHHHHHHHHCCCC---CCEEEECCHHHC T ss_conf 7798898499999999999715989---978983532207 No 62 >LOAD_tam consensus Probab=23.98 E-value=46 Score=15.35 Aligned_cols=17 Identities=35% Similarity=0.389 Sum_probs=14.1 Q ss_pred CCCEEEECCCCCEECHH Q ss_conf 83089987998760489 Q gi|254780714|r 84 DIPRILMSPRGKTLTQK 100 (236) Q Consensus 84 ~~~vI~lSP~Gk~l~Q~ 100 (236) +.-|+|.||+|+.|-+. T Consensus 28 k~DvyY~sP~Gkk~Rs~ 44 (75) T LOAD_tam 28 KSDVYYYSPCGKKLRSK 44 (75) T ss_pred CEEEEEECCCCCEECCH T ss_conf 15799989999613089 No 63 >PRK02135 hypothetical protein; Provisional Probab=23.56 E-value=62 Score=14.50 Aligned_cols=48 Identities=19% Similarity=0.345 Sum_probs=22.5 Q ss_pred CEEEECCCCCEECHHHHHHHHHCCCEEEEECCCHHH---HHHHHHHCCCCCEEEHH Q ss_conf 089987998760489999973028759994150114---48999740453100334 Q gi|254780714|r 86 PRILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGI---DERIIEARDLEEISVGD 138 (236) Q Consensus 86 ~vI~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGi---DeRvid~~~d~eiSiGD 138 (236) .+++|...|+.+.+. ...++..||-|-=.|+ |+..++.+..+-||+|. T Consensus 127 ~~~~Ld~~G~~i~~~-----~~~~~~~FILsDh~~~~~~e~~~L~~~g~~~iSLGp 177 (199) T PRK02135 127 QLYYLHEDGEDIRDV-----EFPANPVFVLGDHIGMTKEEENLLKRLGAEKISLGP 177 (199) T ss_pred CEEEECCCCCCHHCC-----CCCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC T ss_conf 799988999950005-----689998799628999887899999870883165473 No 64 >pfam01005 Flavi_NS2A Flavivirus non-structural protein NS2A. NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex. Probab=23.32 E-value=33 Score=16.31 Aligned_cols=22 Identities=55% Similarity=0.771 Sum_probs=20.6 Q ss_pred CCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 17327799999999985057467 Q gi|254780714|r 142 SGGEPAALILLDAVVRLLPGVLG 164 (236) Q Consensus 142 sGGEl~a~v~~dai~RlipGvlg 164 (236) +|||+..++++ |+-.+-||.+. T Consensus 58 ~Ggdv~~Lali-AvFklRpgfl~ 79 (216) T pfam01005 58 SGGDVLHLALL-AVFKLRPGFLV 79 (216) T ss_pred CCHHHHHHHHH-HHHHCCHHHHH T ss_conf 08329999999-99843499999 No 65 >cd06385 PBP1_NPR_A Ligand-binding domain of type A natriuretic peptide receptor. Ligand-binding domain of type A natriuretic peptide receptor (NPR-A). NPR-A is one of three known single membrane-spanning natriuretic peptide receptors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. NPR-A is highly expressed in kidney, adrenal, terminal ileum, adipose, aortic, and lung tissues. The rank order of NPR-A activation by natriuretic peptides is ANPBNPCNP. Single allele-inactivating mutations in the promoter of human NPR-A are associated with hypertension and heart failure. Probab=23.29 E-value=63 Score=14.46 Aligned_cols=43 Identities=21% Similarity=0.304 Sum_probs=28.0 Q ss_pred CHHHHHHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEHHEEE Q ss_conf 48999997302875999415011448999740453100334011 Q gi|254780714|r 98 TQKRVRQLSQKLGVIIVCGRFEGIDERIIEARDLEEISVGDYIL 141 (236) Q Consensus 98 ~Q~~a~~ls~~~~liliCGrYEGiDeRvid~~~d~eiSiGDyVL 141 (236) -++..+++++...|||+|++-+-+.+=..+.+ .+...=||||. T Consensus 192 ~~~~L~~~~~~aRIIi~~~~~~~~r~im~~a~-~~gl~~g~Yvf 234 (405) T cd06385 192 YTTLLQDIKQKGRVIYVCCSPDIFRRLMLQFW-REGLPSEDYVF 234 (405) T ss_pred HHHHHHHHHHCCEEEEEECCHHHHHHHHHHHH-HCCCCCCCEEE T ss_conf 99999998747739999458999999999999-75999998899 No 66 >pfam07005 DUF1537 Protein of unknown function, DUF1537. This conserved region is found in proteins of unknown function in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Probab=22.86 E-value=64 Score=14.41 Aligned_cols=20 Identities=30% Similarity=0.596 Sum_probs=16.1 Q ss_pred CCEEEHHEEECCCCHHHHHH Q ss_conf 31003340111732779999 Q gi|254780714|r 132 EEISVGDYILSGGEPAALIL 151 (236) Q Consensus 132 ~eiSiGDyVLsGGEl~a~v~ 151 (236) +...++.+|+||||.+..|+ T Consensus 193 ~~~~~~~li~tGGDTs~av~ 212 (224) T pfam07005 193 EAAGVRRLIVAGGDTSGAVL 212 (224) T ss_pred HHCCCCEEEEECCHHHHHHH T ss_conf 72598879990778899999 No 67 >pfam07088 GvpD GvpD gas vesicle protein. This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation. Probab=22.83 E-value=64 Score=14.40 Aligned_cols=81 Identities=17% Similarity=0.101 Sum_probs=42.5 Q ss_pred EEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECH---HHHHHHHHC-CCEEEEECCCH---HHHHHHHHHCCCCCEE Q ss_conf 7750588999998753114778308998799876048---999997302-87599941501---1448999740453100 Q gi|254780714|r 63 VLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQ---KRVRQLSQK-LGVIIVCGRFE---GIDERIIEARDLEEIS 135 (236) Q Consensus 63 Vlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q---~~a~~ls~~-~~liliCGrYE---GiDeRvid~~~d~eiS 135 (236) -++-+|..+.++.+.++..++-.++|=+---=..|-- ..|+.++.. ...++||++=. -...||-|.+.-.+-| T Consensus 370 ~l~~~~~~e~~e~~r~qs~gp~l~iis~D~l~~~f~~~L~df~n~~a~~n~~~ilI~k~~~e~~~~a~~vaD~h~rl~~~ 449 (484) T pfam07088 370 RLKYDPYREIIEVKRAQSKGPLLHVISMDTAYLAFETRLGDFANYVALHNDGVILITKDGTELRTRADRVADMHFRLELS 449 (484) T ss_pred CCCCCHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHHHHEEEEECC T ss_conf 02553279999999863589829998568999987777889999998606728999758758878876421317886504 Q ss_pred EHHEEECC Q ss_conf 33401117 Q gi|254780714|r 136 VGDYILSG 143 (236) Q Consensus 136 iGDyVLsG 143 (236) -|+++|-| T Consensus 450 ~~~i~lYG 457 (484) T pfam07088 450 GNAIALYG 457 (484) T ss_pred CCEEEEEE T ss_conf 88089996 No 68 >COG3444 Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism] Probab=22.44 E-value=50 Score=15.11 Aligned_cols=44 Identities=9% Similarity=0.049 Sum_probs=17.2 Q ss_pred HCCCHHHHHHHCCCEEEEEECCHHHCCCCCCEEEECCCCCCCCEEEECH Q ss_conf 4033679999749659999602563589851353113068886177505 Q gi|254780714|r 19 LEKSVAGKALACNLWSMDAIQIRNFSTDRHHSVDDTPAGGGAGMVLRVD 67 (236) Q Consensus 19 l~~sIigkA~~~gli~i~~~dlRdfs~~kh~~VDD~PyGGG~GMVlk~e 67 (236) +..++++-|.-.| +.+.++++-+....-|+ --|++..=|++-.. T Consensus 42 ~rk~~lk~aaP~g-vk~~~~~v~k~i~~i~~----~~~~~~~v~ll~~~ 85 (159) T COG3444 42 VRKTLLKQAAPPG-VKLRFFSVEKAIDVINK----PKYDGQKVFLLFEN 85 (159) T ss_pred HHHHHHHHHCCCC-EEEEEEEHHHHHHHHCC----CCCCCEEEEEEECC T ss_conf 9999998416885-19999889999998628----77888179999789 No 69 >cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression. Probab=21.83 E-value=52 Score=15.01 Aligned_cols=36 Identities=36% Similarity=0.520 Sum_probs=25.9 Q ss_pred EECCCC--HHHHHHHHHHHHHHCC---CCCCCCCCCCCCHH Q ss_conf 111732--7799999999985057---46782223344011 Q gi|254780714|r 140 ILSGGE--PAALILLDAVVRLLPG---VLGNQQSTIHESFE 175 (236) Q Consensus 140 VLsGGE--l~a~v~~dai~RlipG---vlg~~~S~~~eSf~ 175 (236) .||||| +.|++++=|+-|+-|. +|--.+++.+++-. T Consensus 94 lLSGGEksl~alal~~ai~~~~p~p~~iLDEvdAaLD~~N~ 134 (178) T cd03239 94 ILSGGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNR 134 (178) T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHH T ss_conf 16752589999999999971389966998276554798899 No 70 >COG0527 LysC Aspartokinases [Amino acid transport and metabolism] Probab=21.72 E-value=68 Score=14.26 Aligned_cols=98 Identities=18% Similarity=0.179 Sum_probs=53.9 Q ss_pred CCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHC--------------------CCEEEEE Q ss_conf 06888617750588999998753114778308998799876048999997302--------------------8759994 Q gi|254780714|r 56 AGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQK--------------------LGVIIVC 115 (236) Q Consensus 56 yGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~--------------------~~liliC 115 (236) |||-. |=-++.+.++.+.+++.....+..++..|+-|. ..+..-+|++. ..--.+- T Consensus 8 FGGTS--va~~e~i~~va~iv~~~~~~g~~vVVVvSA~~~--vTd~Lv~~a~~~~~~~~~~~~~~~~~~~~el~~~~~~~ 83 (447) T COG0527 8 FGGTS--VADAERILRVADIVKEDSEEGVKVVVVVSAMGG--VTDLLVALAEGAESGRDAVAEQRHRDIASELILDPFIA 83 (447) T ss_pred ECCCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC--CHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCHHH T ss_conf 68755--388899999999998546339718999789877--45899999863314452057888999999874151045 Q ss_pred CCCHHHHHHHHHHC-----CCCCE--EEHHEEECCCCHHHHHHHHHHHHH Q ss_conf 15011448999740-----45310--033401117327799999999985 Q gi|254780714|r 116 GRFEGIDERIIEAR-----DLEEI--SVGDYILSGGEPAALILLDAVVRL 158 (236) Q Consensus 116 GrYEGiDeRvid~~-----~d~ei--SiGDyVLsGGEl~a~v~~dai~Rl 158 (236) .+.++++.++ ++. ...+. -.=|++||-||.-+..++-+..+- T Consensus 84 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~D~lls~GE~~Sa~lla~~L~~ 132 (447) T COG0527 84 ARLAEVIAEF-KKVLLGIALLGEVSPRERDELLSLGERLSAALLAAALNA 132 (447) T ss_pred HHHHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHHHHHHHHHHHHH T ss_conf 6676666666-676666664147987899999850548899999999996 No 71 >pfam12147 Hydrolase_5 Putative lysophospholipase. This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins. Probab=21.63 E-value=57 Score=14.75 Aligned_cols=35 Identities=20% Similarity=0.270 Sum_probs=28.1 Q ss_pred EEECCCCCEECHHHHHHHHHCCCEEEEECCCHHHH Q ss_conf 99879987604899999730287599941501144 Q gi|254780714|r 88 ILMSPRGKTLTQKRVRQLSQKLGVIIVCGRFEGID 122 (236) Q Consensus 88 I~lSP~Gk~l~Q~~a~~ls~~~~liliCGrYEGiD 122 (236) |.-=-+|.-||......+.-.++|++|+|=||=+- T Consensus 189 ia~Fe~gdAFd~~~la~l~p~P~l~IVSGLyELF~ 223 (311) T pfam12147 189 IARFEQGDAFDPASLAALTPAPTLAIVSGLYELFP 223 (311) T ss_pred HEEEEECCCCCHHHHHCCCCCCCEEEEECHHHHCC T ss_conf 00674057679767632699997899701266368 No 72 >COG3885 Uncharacterized conserved protein [Function unknown] Probab=21.36 E-value=69 Score=14.21 Aligned_cols=41 Identities=24% Similarity=0.266 Sum_probs=30.0 Q ss_pred HHHHHHHHHHHHHCCCCCCCEEEECCCCCEECHHHHHHHHHC Q ss_conf 588999998753114778308998799876048999997302 Q gi|254780714|r 67 DILGKAIDHAVSQYTHEDIPRILMSPRGKTLTQKRVRQLSQK 108 (236) Q Consensus 67 epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l~Q~~a~~ls~~ 108 (236) +-+.+|+..+-+...+.+ ..|..||+|..|+..+|--+++. T Consensus 23 ~~l~kA~k~i~~~~~~se-T~VvIsPHgi~ldd~iaviys~~ 63 (261) T COG3885 23 RKLNKAIKEIASDDKGSE-TYVVISPHGIRLDDYIAVIYSEY 63 (261) T ss_pred HHHHHHHHHHHCCCCCCC-EEEEECCCCEEEECHHHHHHHHH T ss_conf 999999999970567886-18998578525610146776876 No 73 >TIGR00461 gcvP glycine dehydrogenase; InterPro: IPR003437 This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T . The reaction catalysed by this protein is: Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0006544 glycine metabolic process, 0005961 glycine dehydrogenase complex (decarboxylating). Probab=21.23 E-value=34 Score=16.28 Aligned_cols=14 Identities=14% Similarity=0.207 Sum_probs=6.2 Q ss_pred EEECCCCCEECHHH Q ss_conf 99879987604899 Q gi|254780714|r 88 ILMSPRGKTLTQKR 101 (236) Q Consensus 88 I~lSP~Gk~l~Q~~ 101 (236) -+|=|+|=++.-.. T Consensus 778 ~MMG~eGL~kas~v 791 (965) T TIGR00461 778 KMMGAEGLKKASEV 791 (965) T ss_pred HHHCCCCCHHHHHH T ss_conf 85220135035577 No 74 >TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879 PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport. Probab=21.16 E-value=63 Score=14.46 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=16.1 Q ss_pred HHHHHCCCCCCCEEEECCCCCE Q ss_conf 8753114778308998799876 Q gi|254780714|r 75 HAVSQYTHEDIPRILMSPRGKT 96 (236) Q Consensus 75 ~~~~~~~~~~~~vI~lSP~Gk~ 96 (236) .+++.....+.|+|+||++|.- T Consensus 67 ~Lr~~~~Tr~iPIIMLTARGeE 88 (226) T TIGR02154 67 RLRREPETRAIPIIMLTARGEE 88 (226) T ss_pred HHCCCCCCCCCCEEEEECCCCC T ss_conf 7347633148881774055560 No 75 >TIGR02275 DHB_AMP_lig 2,3-dihydroxybenzoate-AMP ligase; InterPro: IPR011963 Siderophores are low molecular weight iron-chelating compounds synthesised by many bacteria to aid in the aquisition of this vital trace element . Proteins in this entry are adenylation components of non-ribosomal peptide synthases (NRPSs) involved in the biosynthesis of siderophores. These proteins belong to the AMP-binding family and are mostly thought to activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate. One of these proteins, however, is believed to differ in function, activating salicylate rather than DHB. The crystal structure of 2,3-dihydroxybenzoate-AMP ligase (P40871 from SWISSPROT) from Bacillus subtilis has been examined . This protein is composed of a large N-terminal domain (~420 aa) and a more compact C-terminal domain (~110 aa), with an overall "hammer-and-anvil" fold similar to that of firefly luciferase . The active site is located in a deep compartment located at the interface of the domains, with a p-loop thought to be involved in catalysis located at the entrance to the cavity. Relatively little conformational change was observed during catalysis.; GO: 0008668 (23-dihydroxybenzoyl)adenylate synthase activity, 0019290 siderophore biosynthetic process. Probab=21.03 E-value=70 Score=14.17 Aligned_cols=35 Identities=26% Similarity=0.518 Sum_probs=23.7 Q ss_pred CCCEECHHHHHHHHHC-CCEEEEEC----CCHHHHHHHHH Q ss_conf 9876048999997302-87599941----50114489997 Q gi|254780714|r 93 RGKTLTQKRVRQLSQK-LGVIIVCG----RFEGIDERIIE 127 (236) Q Consensus 93 ~Gk~l~Q~~a~~ls~~-~~liliCG----rYEGiDeRvid 127 (236) +||+|+--+-++=++. +.|.|||| +|.-+|+|.-. T Consensus 21 ~dkpLtD~L~~~A~~~PdaiAi~cGnr~~sY~eLd~~~~~ 60 (534) T TIGR02275 21 QDKPLTDILEKQAARRPDAIAIICGNRQFSYRELDQRADN 60 (534) T ss_pred CCCCHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHH T ss_conf 8860889999998328994378738753048999999999 No 76 >COG3538 Uncharacterized conserved protein [Function unknown] Probab=20.98 E-value=50 Score=15.13 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=18.0 Q ss_pred EEECCCCHHHHHHHHHHHHHHCCCC Q ss_conf 0111732779999999998505746 Q gi|254780714|r 139 YILSGGEPAALILLDAVVRLLPGVL 163 (236) Q Consensus 139 yVLsGGEl~a~v~~dai~RlipGvl 163 (236) |||| |+||||-+-||.+.+.|=+. T Consensus 52 FvlT-GDIPAmWLRDStaQvrPYL~ 75 (434) T COG3538 52 FVLT-GDIPAMWLRDSTAQVRPYLP 75 (434) T ss_pred EEEE-CCCHHHHHHCCHHHHCCCEE T ss_conf 7984-67417887412665265311 No 77 >COG3874 Uncharacterized conserved protein [Function unknown] Probab=20.82 E-value=29 Score=16.73 Aligned_cols=41 Identities=20% Similarity=0.342 Sum_probs=23.7 Q ss_pred EEECCCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCEE Q ss_conf 53113068886177505889999987531147783089987998760 Q gi|254780714|r 51 VDDTPAGGGAGMVLRVDILGKAIDHAVSQYTHEDIPRILMSPRGKTL 97 (236) Q Consensus 51 VDD~PyGGG~GMVlk~epi~~ai~~~~~~~~~~~~~vI~lSP~Gk~l 97 (236) --++|||||+|-=-+.+|+ |+--++ ....+++-++-.|..+ T Consensus 59 t~~~g~GGG~GaGa~I~Pi--Aflvl~----~d~vrml~l~~~g~~~ 99 (138) T COG3874 59 TGEKGFGGGAGAGASIEPI--AFLVLK----SDGVRMLPLDEKGHLL 99 (138) T ss_pred CCCCCCCCCCCCCCCCCEE--EEEEEE----CCCEEEEEECCCCCHH T ss_conf 5767878877776410304--899992----6987898725542089 No 78 >TIGR01091 upp uracil phosphoribosyltransferase; InterPro: IPR005765 The enzyme uracil phosphoribosyltransferase (UPRT, 2.4.2.9 from EC) catalyzes conversion of uracil to uridine 5'-monophosphate utilizing 5'-phosphoribosyl--1-pyrophosphate (PRPP).UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate ; GO: 0004845 uracil phosphoribosyltransferase activity, 0006223 uracil salvage. Probab=20.61 E-value=62 Score=14.53 Aligned_cols=24 Identities=25% Similarity=0.311 Sum_probs=9.8 Q ss_pred HHHHHHHHHHCCCCCCCE--EEECCCC Q ss_conf 999998753114778308--9987998 Q gi|254780714|r 70 GKAIDHAVSQYTHEDIPR--ILMSPRG 94 (236) Q Consensus 70 ~~ai~~~~~~~~~~~~~v--I~lSP~G 94 (236) ..||+.++++.. ++.++ |.=+|+| T Consensus 145 ~~a~~~lk~~g~-~~I~~~~~vAAPeG 170 (213) T TIGR01091 145 IAALDLLKKRGA-KKIKVLSIVAAPEG 170 (213) T ss_pred HHHHHHHHHCCC-CCEEEEEEEECHHH T ss_conf 999999985399-94499999825578 No 79 >PRK10437 carbonic anhydrase; Provisional Probab=20.10 E-value=46 Score=15.37 Aligned_cols=21 Identities=29% Similarity=0.518 Sum_probs=13.1 Q ss_pred HHHHHHHHHC---CCEEEEECCCH Q ss_conf 8999997302---87599941501 Q gi|254780714|r 99 QKRVRQLSQK---LGVIIVCGRFE 119 (236) Q Consensus 99 Q~~a~~ls~~---~~liliCGrYE 119 (236) -.-+-|+|-. =.-|+|||||. T Consensus 77 ~~aaIEYAV~~L~V~~IIVcGHs~ 100 (220) T PRK10437 77 CLSVVQYAVDVLEVEHIIICGHYG 100 (220) T ss_pred HHHHHHHHHHHCCCCEEEEECCCC T ss_conf 899999999974988799955876 No 80 >cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. Probab=20.10 E-value=65 Score=14.38 Aligned_cols=18 Identities=28% Similarity=0.455 Sum_probs=14.2 Q ss_pred CCCCEEEECCCCCEECHH Q ss_conf 783089987998760489 Q gi|254780714|r 83 EDIPRILMSPRGKTLTQK 100 (236) Q Consensus 83 ~~~~vI~lSP~Gk~l~Q~ 100 (236) .+.-|+|.||+|+.|-.. T Consensus 24 ~k~Dvyy~sP~Gkk~Rs~ 41 (77) T cd01396 24 GKFDVYYISPTGKKFRSK 41 (77) T ss_pred CCEEEEEECCCCCEEECH T ss_conf 850589989998676379 Done!