Query gi|254781204|ref|YP_003065617.1| hypothetical protein CLIBASIA_05555 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 707 No_of_seqs 6 out of 8 Neff 1.8 Searched_HMMs 39220 Date Mon May 30 06:42:10 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781204.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PHA02512 minor structural prot 100.0 0 0 756.2 32.5 357 318-682 448-842 (844) 2 KOG1142 consensus 64.4 9.7 0.00025 17.3 4.9 95 71-182 159-257 (258) 3 pfam09561 RE_HpaII HpaII restr 63.3 10 0.00026 17.2 5.6 199 441-665 140-350 (355) 4 PRK07008 acyl-CoA synthetase; 59.8 4.5 0.00011 19.6 1.3 43 626-671 401-443 (539) 5 PRK07374 dnaE DNA polymerase I 57.8 13 0.00032 16.6 9.0 168 297-472 509-722 (1171) 6 TIGR01129 secD protein-export 55.6 3.1 7.8E-05 20.7 -0.2 49 451-499 329-380 (522) 7 KOG1118 consensus 50.5 2.4 6E-05 21.5 -1.4 88 266-357 124-212 (366) 8 COG4468 GalT Galactose-1-phosp 44.5 20 0.00051 15.2 4.9 83 255-339 31-119 (503) 9 PRK06018 putative acyl-CoA syn 43.8 12 0.00031 16.7 1.4 45 625-671 400-444 (540) 10 PRK09489 rsmC 16S ribosomal RN 40.4 21 0.00053 15.1 2.2 64 484-547 225-317 (342) 11 PRK07786 acyl-CoA synthetase; 39.7 16 0.00041 15.9 1.5 39 630-671 400-438 (551) 12 PRK03640 O-succinylbenzoic aci 39.4 17 0.00043 15.7 1.6 38 630-671 354-392 (481) 13 pfam10682 UL40 Glycoprotein of 39.3 7.2 0.00018 18.2 -0.3 52 188-239 24-92 (220) 14 PRK08162 acyl-CoA synthetase; 39.0 18 0.00046 15.5 1.7 39 629-670 411-449 (545) 15 PRK10696 C32 tRNA thiolase; Pr 36.7 26 0.00067 14.4 4.1 53 184-236 122-177 (311) 16 COG1717 RPL32 Ribosomal protei 36.5 14 0.00036 16.3 0.8 52 351-405 70-128 (133) 17 PRK09089 consensus 36.3 21 0.00053 15.1 1.6 37 630-670 387-424 (517) 18 COG3492 Uncharacterized protei 35.9 25 0.00065 14.5 2.0 28 264-291 10-37 (104) 19 PRK07771 consensus 34.3 18 0.00045 15.6 1.0 37 628-666 403-439 (541) 20 KOG1177 consensus 34.2 23 0.00058 14.8 1.6 36 635-672 461-496 (596) 21 PRK06178 acyl-CoA synthetase; 33.9 17 0.00044 15.6 0.9 39 630-671 438-476 (567) 22 PRK08316 acyl-CoA synthetase; 33.6 28 0.0007 14.3 1.9 34 636-671 398-431 (525) 23 KOG1542 consensus 33.3 30 0.00076 14.0 2.5 109 520-666 226-340 (372) 24 pfam10749 DUF2534 Protein of u 33.0 30 0.00077 14.0 2.2 28 428-456 25-52 (85) 25 PRK08744 consensus 32.0 31 0.0008 13.9 9.6 32 439-470 689-732 (1195) 26 KOG1176 consensus 30.9 18 0.00046 15.5 0.6 40 629-671 402-442 (537) 27 TIGR02311 HpaI 2,4-dihydroxyhe 30.6 15 0.00039 16.0 0.2 116 8-140 90-212 (249) 28 pfam07527 Hairy_orange Hairy O 30.2 33 0.00085 13.7 3.2 33 251-285 9-41 (43) 29 TIGR02225 recomb_XerD tyrosine 30.2 33 0.00085 13.7 2.1 39 185-231 265-303 (305) 30 TIGR02143 trmA_only tRNA (urac 29.7 29 0.00075 14.1 1.5 17 616-632 289-306 (361) 31 TIGR02865 spore_II_E stage II 29.7 34 0.00087 13.7 1.8 32 636-667 662-695 (794) 32 PRK09736 5-methylcytosine-spec 29.5 34 0.00086 13.7 1.8 38 520-557 166-210 (350) 33 TIGR01187 potA polyamine ABC t 29.5 34 0.00088 13.6 2.5 26 285-312 129-154 (331) 34 PRK07470 acyl-CoA synthetase; 29.3 30 0.00077 14.0 1.5 39 630-671 390-428 (528) 35 pfam05693 Glycogen_syn Glycoge 29.0 4.7 0.00012 19.5 -2.7 12 191-202 263-274 (633) 36 PRK07116 flavodoxin; Provision 28.8 27 0.00068 14.3 1.2 21 595-615 12-32 (158) 37 TIGR02339 thermosome_arch ther 28.7 19 0.00049 15.3 0.4 107 5-117 70-178 (522) 38 PRK08974 long-chain-fatty-acid 28.4 33 0.00083 13.8 1.5 33 635-670 432-465 (559) 39 PRK09029 O-succinylbenzoic aci 27.5 37 0.00095 13.4 1.7 35 634-671 331-365 (458) 40 PRK06839 acyl-CoA synthetase; 27.3 34 0.00087 13.6 1.5 38 631-671 368-405 (496) 41 KOG1795 consensus 26.9 38 0.00097 13.3 3.5 222 147-381 544-828 (2321) 42 PRK06334 long chain fatty acid 26.0 39 0.001 13.2 2.0 36 634-671 409-444 (539) 43 smart00511 ORANGE Orange domai 25.2 41 0.001 13.1 3.7 35 250-287 8-43 (45) 44 TIGR00838 argH argininosuccina 25.1 41 0.001 13.1 2.7 62 519-605 285-360 (469) 45 PRK06188 acyl-CoA synthetase; 24.7 42 0.0011 13.1 1.7 35 630-667 387-422 (522) 46 PRK08512 consensus 24.6 42 0.0011 13.1 9.2 31 440-470 691-733 (1185) 47 TIGR01776 TonB-tbp-lbp TonB-de 23.9 16 0.0004 15.9 -0.7 32 99-130 579-611 (1163) 48 PRK07327 enoyl-CoA hydratase; 23.4 43 0.0011 13.0 1.4 69 4-80 15-83 (271) 49 TIGR01205 D_ala_D_alaTIGR D-al 23.4 44 0.0011 12.9 2.0 29 241-269 297-325 (375) 50 PRK06368 consensus 22.9 45 0.0011 12.8 1.8 30 636-666 405-434 (529) 51 TIGR02422 protocat_beta protoc 22.9 24 0.0006 14.7 -0.0 43 637-681 37-83 (224) 52 PRK06358 threonine-phosphate d 22.5 43 0.0011 13.0 1.2 18 249-266 204-221 (354) 53 PRK07529 acyl-CoA synthetase; 22.1 47 0.0012 12.7 1.8 36 634-671 444-479 (632) 54 PRK05850 acyl-CoA synthetase; 22.1 47 0.0012 12.7 1.6 35 633-670 438-472 (581) 55 PRK08751 putative long-chain f 21.9 47 0.0012 12.7 1.8 38 631-670 433-470 (560) 56 pfam02091 tRNA-synt_2e Glycyl- 21.7 40 0.001 13.2 1.0 130 23-190 30-159 (284) 57 KOG0905 consensus 21.6 29 0.00074 14.1 0.2 17 179-195 700-716 (1639) 58 PRK09348 glyQ glycyl-tRNA synt 21.5 43 0.0011 13.0 1.1 130 23-190 33-162 (291) 59 COG3836 HpcH 2,4-dihydroxyhept 21.1 18 0.00046 15.5 -0.9 99 8-121 95-200 (255) 60 TIGR02478 6PF1K_euk 6-phosphof 20.6 48 0.0012 12.6 1.2 41 298-347 496-536 (777) 61 pfam04690 YABBY YABBY protein. 20.5 49 0.0013 12.6 1.2 12 97-108 123-134 (170) 62 COG2042 Uncharacterized conser 20.3 51 0.0013 12.5 1.3 52 395-452 94-147 (179) 63 cd00733 GlyRS_alpha_core Class 20.2 51 0.0013 12.5 1.5 129 24-190 32-160 (279) 64 PRK08279 acyl-CoA synthetase; 20.2 48 0.0012 12.7 1.1 36 634-671 442-477 (602) 65 COG4972 PilM Tfp pilus assembl 20.1 48 0.0012 12.7 1.1 15 251-265 149-163 (354) 66 cd05491 Bromo_TBP7_like Bromod 20.0 46 0.0012 12.8 1.0 11 626-636 65-75 (119) No 1 >PHA02512 minor structural protein; Provisional Probab=100.00 E-value=0 Score=756.16 Aligned_cols=357 Identities=15% Similarity=0.211 Sum_probs=332.3 Q ss_pred CCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 33899988715013799999998756645645443235705799999740866667622102344456788999999999 Q gi|254781204|r 318 IPLEDYTQAYGVEQGTELYNLQQFKSVAAPDVARIKLMSTFDAKKFLQKIDDEYISNPSLSLASTMMATKYKEILEKSHR 397 (707) Q Consensus 318 ~~ldEFt~AYGv~eG~k~Y~~fq~~qiaG~DIatvq~MSt~~qtA~Leq~~P~~~~~pgegYAS~~~aaK~~DiLtKAhe 397 (707) -.+|||++||||++|+++|++|+++|+||+||+|||+|||++||||||+++|++++ +|||||+| |++||+|++|++ T Consensus 448 pt~def~~AyG~~~G~~~Ytef~ntq~~Gq~I~s~r~m~~ss~tA~ve~~~P~t~~-~gegya~r---a~~~d~v~~A~~ 523 (844) T PHA02512 448 PGEADFIAAYGVREGNLRYTEFRNTQIAGQYIGSFRNMPTSSITAYVEQLRPDTEE-TGEGYAAR---AALFDNVTAAAS 523 (844) T ss_pred CCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-CCCCHHHH---HHHHHHHHHHHH T ss_conf 86788999845351048999887668776566777528858899999850899898-87427999---888899999999 Q ss_pred HHHHHHHHCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCHHHHCHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 99998543775557653250754537988889999752033688898718860345878899999998605647789999 Q gi|254781204|r 398 QSMQELNQDAISWGIKYKQIDPLRFDTEESFADSLRQRAGFVKKIKDDYNLTTSHFNKTEENQLRTQLVKRPASESVDLI 477 (707) Q Consensus 398 ~vnt~RnsDPiqyaiE~gQIdPLdF~tpe~FtASLaqR~S~V~sLkr~YGt~laiFSkqEA~qLSqqVrkAPASQsI~LL 477 (707) +||++|++|||+|++++||++||||+++++|++||++|+|.|++|+|+||||++|||++||++|++++|++|+||+|.+| T Consensus 524 ~V~k~R~~dP~q~s~~~~q~kpidm~n~~~f~~~va~R~s~~~dlak~ygtpl~~fS~~Ea~~ig~~~r~ap~sqq~ayL 603 (844) T PHA02512 524 KVIKQRQADPFNAALAAGAAKPIAMNNKDDFGQEVALRAAQQEDLAKALGINAPFFSKDEAAAIGEFFRDAKDSNQAASL 603 (844) T ss_pred HHHHHHHCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 99998753837778763555764545867788899876301378998608985200676789999998638426678899 Q ss_pred HHHHHHCCCC--------------HHHHHHHHHHCCCCC---CCEEEEEH----HHHHCCCHHHHHHHHHHH---H---H Q ss_conf 9974204643--------------145788987406778---87027861----245088878999999823---5---4 Q gi|254781204|r 478 RGAYNTLSDS--------------DKEGVRSSFAHIEDN---GLSAVVRL----SSEFSDDAKNAAMVILSG---M---K 530 (707) Q Consensus 478 ~aI~qtLSns--------------~aeAyrA~l~qi~dN---gts~~V~~----Ss~i~~~p~~vA~vILsG---r---K 530 (707) +.|+|.+.+. ...||...|...|+| ||.|+|.+ |.+++++|.++|++||+| | + T Consensus 604 d~irq~~g~~~~y~~alqqis~na~saAvag~lm~kp~~~~~nt~~~~ae~~w~~~d~~v~p~~aaqtIl~Ga~arkg~~ 683 (844) T PHA02512 604 DQIMGKTGGAPAMMQAAQAIAANAAAAAVAAILLDKPDGQYDNTKPIIAEKNFFGPDPSMNKEDAAKTILAGAAALKGTD 683 (844) T ss_pred HHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC T ss_conf 99973127737899999986535717788899847988755664210221365688865388999999983066525754 Q ss_pred HCCC-----CCCCCCCHHHHHHHHHHHHHHHCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH Q ss_conf 2136-----57654311348888775567506801100000011035678888898763233202875520699999999 Q gi|254781204|r 531 HQKD-----TETRYNTDHKSNKFDSLYDSYINTPLTKLEQSTAGGNFNKDKEAIKLYLLGSMKDSGNYTLNRVRVSDAMQ 605 (707) Q Consensus 531 A~KD-----v~lp~dTdlK~~f~DqVGNsfansP~trl~~s~~synl~KdayAikaY~sG~ms~~Gn~t~Nsdrv~dAiq 605 (707) .+|+ +++|+|+|+|++|.|+|||+|++ +.++++.+|+++||+|||+++..|..+|+++-.+|+|+|++||+ T Consensus 684 ~~k~~~~~~i~mPkd~dLr~eF~D~VgdaFAg----daqga~~aYeiaKd~YAGvmakkG~vs~~~~ge~d~D~w~qAin 759 (844) T PHA02512 684 AAKDAGITPIPLPKDADLKLAFDDMVGDAFAG----DAQAAQLAYEIAKAAYAGIAAKKGDASMTKTDAADNDIVEKAAN 759 (844) T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH T ss_conf 21236766544886144569999987676358----86778889999999987888752776645566411489999886 Q ss_pred HHHCCCCCCCCCCEEEECCCCCHHHHHHH----HHHCCCCCC--CCCCEEEEEEECCCCEEEEEECCCCEECCCCCEEEE Q ss_conf 87268202477632520368883347777----531276556--525000434521785068983798104448987899 Q gi|254781204|r 606 IVLGNTPVNINESMLMPPRGMSKTDFEDR----LWYATKDTG--EYDPYTIKYMNVGSGKYMIIKNGNPKVDKEGKTIII 679 (707) Q Consensus 606 iaTGGiyk~~n~g~VmpPrGMDkstFkDR----l~y~~~~~g--~~~~~~i~~~~~g~~~y~i~~~~~~~~~k~g~~iii 679 (707) +||||+|++|++|+||+|||||+++|+|+ ++|+.+++| +..|..+|+||+||+|||+|.|+||+++|||+||+| T Consensus 760 vATGGV~d~~g~G~VllPwGM~~~qF~kqv~~a~~~~~~~~Gik~~~vg~~glqs~GdsQYlvklGsGyll~~dgtpvvi 839 (844) T PHA02512 760 VATGGVHDGFGGGDVLLPFGMDAEQFDDQVNAAANEALKDAGIKTNAVGNFGLQNIGDNQYLLKLGSGRLAKDDGSNEAI 839 (844) T ss_pred HHCCCEEECCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEECCEEEECCCCCCEEE T ss_conf 52265030489864552157888899899999998755155667799653151034774268872560574589985567 Q ss_pred EHH Q ss_conf 714 Q gi|254781204|r 680 NVE 682 (707) Q Consensus 680 ~~~ 682 (707) ||. T Consensus 840 dl~ 842 (844) T PHA02512 840 DLR 842 (844) T ss_pred EEC T ss_conf 511 No 2 >KOG1142 consensus Probab=64.42 E-value=9.7 Score=17.33 Aligned_cols=95 Identities=24% Similarity=0.321 Sum_probs=55.1 Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCC Q ss_conf 67765410121133321356888730023668999974212578999988876655655301660257323100000155 Q gi|254781204|r 71 DFHDFTNSLDTRDSLQAGDKIKEYVDGRIRSAYDRFLSSISHRDVRKKFQAQVEHDIRDYHTKGVDIQIGATQRAQEDNL 150 (707) Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (707) ..||+.--+|... +|.+-|.--+----|-|+++|.|+-++-- +|-|--.+..--.+-.-|.|+ T Consensus 159 kl~dLvqqId~~~------~LD~dVedlLleiADdFV~sii~~sC~LA-----------KHRKsdtlEvrDIqLhLEr~~ 221 (258) T KOG1142 159 KLDDLVQQIDGTT------KLDDDVEDLLLEIADDFVSSIIHRSCKLA-----------KHRKSDTVEVRDIQLHLERNF 221 (258) T ss_pred CHHHHHHHHCCCC------CCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHCCCCCCCHHHEEEEEECCC T ss_conf 0368999645756------45589999999999999999999999998-----------751667531010011221014 Q ss_pred CEEEEHHHHHHHCC----CCCCHHHHHHHHHHHHHH Q ss_conf 20200234554307----763049999998885310 Q gi|254781204|r 151 NMTVGLAAAHVLHD----PSNENYFQRVQSITDHIN 182 (707) Q Consensus 151 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~ 182 (707) ||.+.--++.-..- -..|.+-||+..|..-|. T Consensus 222 Nm~iPgf~sd~~~~~~k~~pTe~hkqr~a~i~k~~~ 257 (258) T KOG1142 222 NMEIPGFSSDEKRSKKKALPTEEHKQRLALIRKQIK 257 (258) T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 654787565555454566870999999999998642 No 3 >pfam09561 RE_HpaII HpaII restriction endonuclease. This family includes the HpaII (recognizes and cleaves C^CGG) restriction endonuclease. Probab=63.25 E-value=10 Score=17.18 Aligned_cols=199 Identities=14% Similarity=0.055 Sum_probs=126.9 Q ss_pred HHHHHHCCCHHHHCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEE-E-EHHHHHCCC Q ss_conf 88987188603458788999999986-05647789999997420464314578898740677887027-8-612450888 Q gi|254781204|r 441 KIKDDYNLTTSHFNKTEENQLRTQLV-KRPASESVDLIRGAYNTLSDSDKEGVRSSFAHIEDNGLSAV-V-RLSSEFSDD 517 (707) Q Consensus 441 sLkr~YGt~laiFSkqEA~qLSqqVr-kAPASQsI~LL~aI~qtLSns~aeAyrA~l~qi~dNgts~~-V-~~Ss~i~~~ 517 (707) |||+.+|-+.++||+..+..|-=.+. -.+++.+|+-+-+|.. ...++--+..+..+|+++- + +.+.-|..+ T Consensus 140 sIKS~LG~~~TLLNAg~aTNF~fei~g~~~~~~~i~~iN~i~~------~~ki~~r~~~i~~~Gg~L~y~~~~~~~F~~N 213 (355) T pfam09561 140 SIKSRLGSMPTLLNAGKTTNFKFEISGINLANPTIEKINAIST------PSKIKDRIKMIERLGGILKYLKVEDDVFRNN 213 (355) T ss_pred EEEECCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHCCCC------CHHHHHHHHHHHHCCCEEEEEECCHHHHHHC T ss_conf 8873358997210577753069996788778246787643787------1479999999985896599812244878757 Q ss_pred --------HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf --------789999998235421365765431134888877556750680110000001103567888889876323320 Q gi|254781204|r 518 --------AKNAAMVILSGMKHQKDTETRYNTDHKSNKFDSLYDSYINTPLTKLEQSTAGGNFNKDKEAIKLYLLGSMKD 589 (707) Q Consensus 518 --------p~~vA~vILsGrKA~KDv~lp~dTdlK~~f~DqVGNsfansP~trl~~s~~synl~KdayAikaY~sG~ms~ 589 (707) |.-.|+.++.--. --.+..+ +-+--.-..||+---++.+-.+--+|.+.=..|--+||+.- T Consensus 214 L~lID~~~p~ilae~l~~~y~-------~~~~~v~----~l~e~i~~~NPl~~~~~~~~~fYe~K~K~fL~a~alGM~Ps 282 (355) T pfam09561 214 LLLIDSHLPEILAEMVRLFYL-------DGISKLS----DLTEYIKEENPLKFKLENNHRFYEYKIKQFLTDVALGMRPS 282 (355) T ss_pred HHHHHHCCHHHHHHHHHHHHC-------CCCCCHH----HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 898982529999999999965-------7876199----99999986398656755776108999999999998268656 Q ss_pred CCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCHHHHHHHHHHCCC-CCCCCCCEEEEEEECCCCEEEEEEC Q ss_conf 287552069999999987268202477632520368883347777531276-5565250004345217850689837 Q gi|254781204|r 590 SGNYTLNRVRVSDAMQIVLGNTPVNINESMLMPPRGMSKTDFEDRLWYATK-DTGEYDPYTIKYMNVGSGKYMIIKN 665 (707) Q Consensus 590 ~Gn~t~Nsdrv~dAiqiaTGGiyk~~n~g~VmpPrGMDkstFkDRl~y~~~-~~g~~~~~~i~~~~~g~~~y~i~~~ 665 (707) . .|-- .--|+||++.--+.|+|+-=-=-+.+.|+|-|...|+ |++--+-+--|..---.|.|-++-| T Consensus 283 k--------~W~G-~~~A~gGyivVk~dGdvlcYh~y~r~~fedyL~~NtklE~~S~srh~~g~iy~eng~~y~kLN 350 (355) T pfam09561 283 K--------VWNG-HYDATGGYLIVKENGEVLCYHIYNRNQFEDYLFNNTKLETPSSSRHKFGELYRENGKLYFKLN 350 (355) T ss_pred C--------CCCC-CCCCCCCEEEEECCCCEEEEECCCHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCEEEEEEE T ss_conf 5--------3278-445765289995799789998233789999986545146776652354379998899999986 No 4 >PRK07008 acyl-CoA synthetase; Validated Probab=59.82 E-value=4.5 Score=19.57 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=29.1 Q ss_pred CCHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 8833477775312765565250004345217850689837981044 Q gi|254781204|r 626 MSKTDFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 626 MDkstFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) -+..+|.|. ||+|-|+|.+|.+-- +.-+|-.+-|||.+| +.++ T Consensus 401 ~~~~~~~dG-w~~TGDlg~~d~dG~-l~i~GR~kd~Ik~~G-~~V~ 443 (539) T PRK07008 401 GDASPLVDG-WFPTGDVATIDADGF-MQITDRSKDVIKSGG-EWIS 443 (539) T ss_pred CCCCCCCCC-CEECCCEEEECCCCC-EEEEECCCCEEEECC-EEEC T ss_conf 666655678-772798699878964-999872678899899-9999 No 5 >PRK07374 dnaE DNA polymerase III subunit alpha; Validated Probab=57.83 E-value=13 Score=16.57 Aligned_cols=168 Identities=16% Similarity=0.266 Sum_probs=77.2 Q ss_pred HHHHHHHHHH------CCCCEECHHHCCCHHHHHHHHCHHHHHHHHHHHHHHHHHH-----HHHHHHHCCCHHHH-HHHH Q ss_conf 7776435540------3770206123133899988715013799999998756645-----64544323570579-9999 Q gi|254781204|r 297 AQARRIDAQL------NHGITVKPSELIPLEDYTQAYGVEQGTELYNLQQFKSVAA-----PDVARIKLMSTFDA-KKFL 364 (707) Q Consensus 297 ~~~~~~~~~~------~~~~~~~~~~~~~ldEFt~AYGv~eG~k~Y~~fq~~qiaG-----~DIatvq~MSt~~q-tA~L 364 (707) .-|+++...- --|+-+-|. ||+||+--+--.+|. .-++|-...+-. =|+--.++|+.... -.++ T Consensus 509 ~~A~~LEGlpR~~g~HAaGvVIs~~---pL~~~vPl~~~~~g~-~vtQ~dk~dvE~~GLlK~DfLGLr~LtiI~~a~~~I 584 (1171) T PRK07374 509 DMAMRIEGTNKTFGVHAAGVVIASD---PLDELVPLQRNNDGQ-IITQYFMEDIESLGLLKMDFLGLKNLTMIEKTVELV 584 (1171) T ss_pred HHHHHHCCCCCCCCCCCCEEEECCC---CCCCCCCEEECCCCC-EEECCCHHHHHHCCCHHHHHHCCCCHHHHHHHHHHH T ss_conf 9999863873321235652573377---743136513578898-423035655887698366676368679999999999 Q ss_pred HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHC-------------CCC--CCCCCCHHHHH Q ss_conf 740866667622102344456788999999999999985437755576532-------------507--54537988889 Q gi|254781204|r 365 QKIDDEYISNPSLSLASTMMATKYKEILEKSHRQSMQELNQDAISWGIKYK-------------QID--PLRFDTEESFA 429 (707) Q Consensus 365 eq~~P~~~~~pgegYAS~~~aaK~~DiLtKAhe~vnt~RnsDPiqyaiE~g-------------QId--PLdF~tpe~Ft 429 (707) ++....-..-....+-. .|-|+.++++.+.+.=|+-|...+--+..= .|- |++..-...|. T Consensus 585 ~~~~g~~idl~~IpldD----~~t~~ll~~g~T~GVFQlES~gm~~~l~~lkP~~feDiva~~AL~RPGP~~~gmi~~yi 660 (1171) T PRK07374 585 EQSTGERIDPDNLPLED----EKTFELLGRGDLEGIFQLESSGMRQIVRDLKPSSLEDISSILALYRPGPLDAGLIPKFI 660 (1171) T ss_pred HHHHCCCCCCCCCCCCH----HHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHH T ss_conf 98549977713368661----99999985548788341366799999997199989999988842478755444338999 Q ss_pred HHHHHHC-------CCHHHHHHHHCCCH------------HHHCHHHHHHHHHHHHHCCHHH Q ss_conf 9997520-------33688898718860------------3458788999999986056477 Q gi|254781204|r 430 DSLRQRA-------GFVKKIKDDYNLTT------------SHFNKTEENQLRTQLVKRPASE 472 (707) Q Consensus 430 ASLaqR~-------S~V~sLkr~YGt~l------------aiFSkqEA~qLSqqVrkAPASQ 472 (707) +--..|. ...+-|+.-||+.. +=||-.||-.|++-|-|+...+ T Consensus 661 ~Rk~g~e~i~y~hp~L~~IL~~TyGvivYQEQVMqia~~~aGfslgeAD~LRRAmgKKk~~~ 722 (1171) T PRK07374 661 NRKHGREAIDFAHPLLEPILTETYGIMVYQEQIMKIAQDLAGYSLGQADLLRRAMGKKKVSE 722 (1171) T ss_pred HHCCCCCCCCCCCHHHHHHHCCCCCEEEEHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHH T ss_conf 85179978889989998654243787875999999999860699789999999875486889 No 6 >TIGR01129 secD protein-export membrane protein SecD; InterPro: IPR005791 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains . Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. This entry describes the SecD family of transport proteins. Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed. SecD from Mycobacterium tuberculosis has a long Pro-rich insert. ; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0009276 1-2nm peptidoglycan-based cell wall. Probab=55.57 E-value=3.1 Score=20.68 Aligned_cols=49 Identities=24% Similarity=0.293 Sum_probs=40.0 Q ss_pred HHHCHHHHHHHHHHHH--HCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHCC Q ss_conf 3458788999999986--0564778999999742046-43145788987406 Q gi|254781204|r 451 SHFNKTEENQLRTQLV--KRPASESVDLIRGAYNTLS-DSDKEGVRSSFAHI 499 (707) Q Consensus 451 aiFSkqEA~qLSqqVr--kAPASQsI~LL~aI~qtLS-ns~aeAyrA~l~qi 499 (707) |.||.+||.+|+-++| .=|+.=+|.--|.|+-+|= ++-..+..|++.++ T Consensus 329 P~Ft~~eA~dLA~~LR~GaLP~~~~~~e~r~iGP~LG~d~i~~G~~A~~~Gl 380 (522) T TIGR01129 329 PNFTAEEANDLALLLRSGALPAPLQILEERTIGPSLGADSIEAGIKAGLIGL 380 (522) T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEECHHHHHHHHHHHHHHHHHHH T ss_conf 8998899999999987751254607851022045643899999999999999 No 7 >KOG1118 consensus Probab=50.48 E-value=2.4 Score=21.45 Aligned_cols=88 Identities=20% Similarity=0.256 Sum_probs=38.0 Q ss_pred HHCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHCCCHHHHHHHHCHHHHHHHHHHHHHHHH Q ss_conf 100037899999975310-1233467767878777643554037702061231338999887150137999999987566 Q gi|254781204|r 266 DRLDDTKRRRLLEHLSSR-DNALNTKLRKETQAQARRIDAQLNHGITVKPSELIPLEDYTQAYGVEQGTELYNLQQFKSV 344 (707) Q Consensus 266 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ldEFt~AYGv~eG~k~Y~~fq~~qi 344 (707) |-|++.-+...|..|..- ++-|..--.+++.-..||.|-..- -+-+--||=||..+|---=+--++-.+-+--+. T Consensus 124 ~sl~~~vkq~FldpL~~l~~~elK~i~hh~KKLEgRRldyD~k----kkk~~K~~dEelrqA~eKfEESkE~aE~sM~nl 199 (366) T KOG1118 124 DSLDDNVKQNFLDPLQNLQLKELKDIQHHRKKLEGRRLDYDYK----KKKQGKIKDEELRQALEKFEESKELAEDSMFNL 199 (366) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999988867998766778889889998762122577888----877345870999999999888899999998988 Q ss_pred HHHHHHHHHCCCH Q ss_conf 4564544323570 Q gi|254781204|r 345 AAPDVARIKLMST 357 (707) Q Consensus 345 aG~DIatvq~MSt 357 (707) .--||-.|.+++- T Consensus 200 le~d~eqvsqL~~ 212 (366) T KOG1118 200 LENDVEQVSQLSA 212 (366) T ss_pred HHCCHHHHHHHHH T ss_conf 7448999999999 No 8 >COG4468 GalT Galactose-1-phosphate uridyltransferase [Carbohydrate transport and metabolism] Probab=44.48 E-value=20 Score=15.19 Aligned_cols=83 Identities=23% Similarity=0.309 Sum_probs=54.5 Q ss_pred HHHHHHCCCCHHHCCHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHCCCHHHHHHHHC Q ss_conf 6776522121010003789------9999975310123346776787877764355403770206123133899988715 Q gi|254781204|r 255 DVSKAIGLAGWDRLDDTKR------RRLLEHLSSRDNALNTKLRKETQAQARRIDAQLNHGITVKPSELIPLEDYTQAYG 328 (707) Q Consensus 255 ~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ldEFt~AYG 328 (707) .|-..+||.+|.+.++.-. ..+|+.|- +-|....+-..|+..-.-.||.|-.-+|-.|||+|--=.=++.+| T Consensus 31 rll~~lgl~~~~~v~~~~~~~~~~~~~ild~l~--~~A~e~~~i~d~~t~rd~l~a~lM~~~~p~Psevi~~F~e~y~~s 108 (503) T COG4468 31 RLLALLGLEDWEEVEEESDEPSKPLPDILDQLL--AIAVENGLIEDTVTERDLLDAELMNFITPRPSEVIRDFWELYQQS 108 (503) T ss_pred HHHHHHCCCCCCHHHHHCCCCCCCHHHHHHHHH--HHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCC T ss_conf 999983866623123312554544599999999--999873850023158888758986035788189999999998419 Q ss_pred HHHHHHHHHHH Q ss_conf 01379999999 Q gi|254781204|r 329 VEQGTELYNLQ 339 (707) Q Consensus 329 v~eG~k~Y~~f 339 (707) -.+.++.|-+| T Consensus 109 p~~At~~FY~l 119 (503) T COG4468 109 PKEATEYFYKL 119 (503) T ss_pred HHHHHHHHHHH T ss_conf 89999999998 No 9 >PRK06018 putative acyl-CoA synthetase; Provisional Probab=43.77 E-value=12 Score=16.67 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=30.2 Q ss_pred CCCHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 88833477775312765565250004345217850689837981044 Q gi|254781204|r 625 GMSKTDFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 625 GMDkstFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) +.++.+|++.-||+|-|+|.+|.+-- ..-+|-.+-|||.+| +.++ T Consensus 400 ~~~~~~~~~dGw~~TGDlg~~d~dG~-l~~~gR~kd~Ik~~G-~~V~ 444 (540) T PRK06018 400 RVDGEILDDDGFFDTGDVATIDADGY-MRITDRSKDVIKSGG-EWIS 444 (540) T ss_pred CCCCCCCCCCCCEECCCEEEECCCCE-EEEEECCCCEEEECC-EEEC T ss_conf 44110327787367585699878956-999973657899899-9999 No 10 >PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional Probab=40.38 E-value=21 Score=15.08 Aligned_cols=64 Identities=23% Similarity=0.274 Sum_probs=31.4 Q ss_pred CCCCHHHHHHHHHHCCCCCCCEEEEEHH----------HHHCCCHH---------HHHHHHHHH-HHHCCC--------- Q ss_conf 4643145788987406778870278612----------45088878---------999999823-542136--------- Q gi|254781204|r 484 LSDSDKEGVRSSFAHIEDNGLSAVVRLS----------SEFSDDAK---------NAAMVILSG-MKHQKD--------- 534 (707) Q Consensus 484 LSns~aeAyrA~l~qi~dNgts~~V~~S----------s~i~~~p~---------~vA~vILsG-rKA~KD--------- 534 (707) +.+.++-|+.++-+-+..|+....|.|| +.|..||| .+++.++.+ .+++|. T Consensus 225 l~Dv~a~Al~~ar~nl~~N~l~~~v~~sd~~~~v~~~fD~IvsNPPFH~G~~~~~~i~~~fi~~A~~~L~~gG~L~iVAN 304 (342) T PRK09489 225 LCDVSAPAVEASRATLAANGLEGEVFASNVFSEIKGRFDMIISNPPFHDGIQTSLDAAQTLIRGAVRHLNSGGELRIVAN 304 (342) T ss_pred EEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEC T ss_conf 99688999999999899809886899756445655678989968852157526589999999999986124988999981 Q ss_pred CCCCCCCHHHHHH Q ss_conf 5765431134888 Q gi|254781204|r 535 TETRYNTDHKSNK 547 (707) Q Consensus 535 v~lp~dTdlK~~f 547 (707) --|||+..+...| T Consensus 305 r~LpY~~~L~~~F 317 (342) T PRK09489 305 AFLPYPDLLDETF 317 (342) T ss_pred CCCCCHHHHHHHC T ss_conf 8989689999862 No 11 >PRK07786 acyl-CoA synthetase; Validated Probab=39.69 E-value=16 Score=15.87 Aligned_cols=39 Identities=23% Similarity=0.274 Sum_probs=26.2 Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 477775312765565250004345217850689837981044 Q gi|254781204|r 630 DFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 630 tFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .|.| -||+|-|+|.+|.+-- +.-+|-.+-|||.+ |+.++ T Consensus 400 ~f~~-gw~~TGDlg~~d~dG~-l~i~GR~dd~Ik~~-G~~I~ 438 (551) T PRK07786 400 AFAG-GWFHSGDLVRQDEEGY-VWVVDRKKDMIISG-GENIY 438 (551) T ss_pred HHCC-CCCCCCCEEEECCCCE-EEEEECCCCEEEEC-CEEEC T ss_conf 7549-9960487799989954-99997454889989-99988 No 12 >PRK03640 O-succinylbenzoic acid--CoA ligase; Provisional Probab=39.44 E-value=17 Score=15.71 Aligned_cols=38 Identities=26% Similarity=0.563 Sum_probs=26.1 Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCCEEC Q ss_conf 4777753127655652500043452-17850689837981044 Q gi|254781204|r 630 DFEDRLWYATKDTGEYDPYTIKYMN-VGSGKYMIIKNGNPKVD 671 (707) Q Consensus 630 tFkDRl~y~~~~~g~~~~~~i~~~~-~g~~~y~i~~~~~~~~~ 671 (707) .|.|. ||+|-|+|.+|.+ |+.- +|-.+-|||.+| +.++ T Consensus 354 ~f~dg-w~~TGDlg~~d~d--G~l~~~GR~~d~Ik~~G-~~I~ 392 (481) T PRK03640 354 TFQDG-WFKTGDIGYLDEE--GFLYVLDRRSDLIISGG-ENIY 392 (481) T ss_pred HHHCC-CCCCCCEEEECCC--CEEEEEECCCCEEEECC-EEEC T ss_conf 70089-8643763999899--44999971678899999-9999 No 13 >pfam10682 UL40 Glycoprotein of human cytomegalovirus HHV-5. This is glycoprotein UL40 from human cytomegalovirus or herpesvirus 5. The signal sequence of the UL40 polypeptide contains an HLA-E ligand identical with HLA-Cw*0304. The first 37 residues of UL40, including this ligand, are predicted to encode a signal peptide. The virus thus prevents the lysis by NK (natural killer) cells of the cell it has invaded. Probab=39.32 E-value=7.2 Score=18.17 Aligned_cols=52 Identities=37% Similarity=0.517 Sum_probs=32.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCC------CHHHHHHHHHHHHHCCC-----------CCCCCCCHH Q ss_conf 46578888888852170000012356------82689999999984589-----------987544123 Q gi|254781204|r 188 LRLKQKLLSEAKEKLNTNQIIGAHAR------DPRVFENFMRAFYKKGH-----------PPKDSTSLS 239 (707) Q Consensus 188 ~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~-----------~~~~~~~~~ 239 (707) |++...|-|.|.....|.--.-+|.. -|.|||.+.-|.|.||. .|||+.|.- T Consensus 24 l~i~~~l~spa~t~~ttagam~a~~pksntsyc~~vfegwvya~yhkg~m~lmtldv~ccr~~~~nsvv 92 (220) T pfam10682 24 LGIPGLLCSPAETPTTTAGAMFAHGPKSNTSYCPKVFEGWVYAMYHKGDMALMTLDVQCCRPKDNNSVV 92 (220) T ss_pred ECCCHHCCCCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHEEECCCCEEEEEEEEEECCCCCCCEE T ss_conf 357300058876751012216604887664323688855555102338814788876783367898400 No 14 >PRK08162 acyl-CoA synthetase; Validated Probab=38.97 E-value=18 Score=15.49 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=26.6 Q ss_pred HHHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEE Q ss_conf 347777531276556525000434521785068983798104 Q gi|254781204|r 629 TDFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKV 670 (707) Q Consensus 629 stFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~ 670 (707) ..|+|. ||+|-|+|.++.+- .+.-+|-.+-|||.+ |+.+ T Consensus 411 ~~f~dg-w~~TGDlg~~d~dG-~l~~~GR~~d~Ik~~-G~~V 449 (545) T PRK08162 411 EAFAGG-WFHTGDLGVLHPDG-YIKIKDRSKDIIISG-GENI 449 (545) T ss_pred HHHCCC-CCCCCCEEEECCCC-EEEEEECCCCEEEEC-CEEE T ss_conf 764477-77667479990896-399997555889989-9998 No 15 >PRK10696 C32 tRNA thiolase; Provisional Probab=36.68 E-value=26 Score=14.40 Aligned_cols=53 Identities=30% Similarity=0.471 Sum_probs=43.2 Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH---CCCCCCCCC Q ss_conf 76214657888888885217000001235682689999999984---589987544 Q gi|254781204|r 184 LPIDLRLKQKLLSEAKEKLNTNQIIGAHARDPRVFENFMRAFYK---KGHPPKDST 236 (707) Q Consensus 184 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ 236 (707) .-.--|++...|.+.-.+++.|.|-=+|-+|--+-.-||..||. ++-|||-.. T Consensus 122 CslCsRlRRg~Ly~~A~e~G~nKIALGHH~DDi~ETfLMNlf~gG~LktM~Pkl~~ 177 (311) T PRK10696 122 CSLCSRLRRGILYRTATELGATKIALGHHRDDILQTLFLNMFYGGKMKGMPPKLMS 177 (311) T ss_pred HHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHCCCCCCCCCEEEC T ss_conf 78999999999999999869987986065055899999999966876367976674 No 16 >COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis] Probab=36.51 E-value=14 Score=16.26 Aligned_cols=52 Identities=31% Similarity=0.333 Sum_probs=41.7 Q ss_pred HHHCCCHHHHH-------HHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 43235705799-------99974086666762210234445678899999999999998543 Q gi|254781204|r 351 RIKLMSTFDAK-------KFLQKIDDEYISNPSLSLASTMMATKYKEILEKSHRQSMQELNQ 405 (707) Q Consensus 351 tvq~MSt~~qt-------A~Leq~~P~~~~~pgegYAS~~~aaK~~DiLtKAhe~vnt~Rns 405 (707) -|+.|.|++-. +=||.++|++. +---||+.-|-|+-+|+.+|-+-+++++|- T Consensus 70 ~vRglhPSG~~~VlV~Nv~dLe~ldp~~~---aarIAs~VG~rKR~eI~~rA~elGikVlN~ 128 (133) T COG1717 70 AVRGLHPSGYEEVLVHNVKDLEKLDPETQ---AARIASTVGARKRIEILERARELGIKVLNP 128 (133) T ss_pred HHCCCCCCCCCEEEEECHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHCCEEECC T ss_conf 65256877660235516888742380467---999997641778999999999829177487 No 17 >PRK09089 consensus Probab=36.34 E-value=21 Score=15.10 Aligned_cols=37 Identities=27% Similarity=0.456 Sum_probs=27.1 Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCCEE Q ss_conf 4777753127655652500043452-1785068983798104 Q gi|254781204|r 630 DFEDRLWYATKDTGEYDPYTIKYMN-VGSGKYMIIKNGNPKV 670 (707) Q Consensus 630 tFkDRl~y~~~~~g~~~~~~i~~~~-~g~~~y~i~~~~~~~~ 670 (707) +|.| -||+|-|+|.+|.+ |+.- +|-.+-|||.+| ..| T Consensus 387 ~~~~-gw~~TGDlg~~d~d--G~l~~~GR~dd~Ik~~G-~~V 424 (517) T PRK09089 387 TIVN-GWLKTGDFGKIDEE--GFIYIVDRKKDLIISKG-INI 424 (517) T ss_pred HHHH-CCCCCCCEEEECCC--CCEEEEEECCCEEEECC-EEE T ss_conf 7530-77556977999899--51999882278899899-997 No 18 >COG3492 Uncharacterized protein conserved in bacteria [Function unknown] Probab=35.94 E-value=25 Score=14.52 Aligned_cols=28 Identities=43% Similarity=0.631 Sum_probs=17.9 Q ss_pred CHHHCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1010003789999997531012334677 Q gi|254781204|r 264 GWDRLDDTKRRRLLEHLSSRDNALNTKL 291 (707) Q Consensus 264 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 (707) --|+|+-.--|||++||-.|...-|..| T Consensus 10 q~~~leAAaFRrLv~HL~~rsdvQNIDL 37 (104) T COG3492 10 QRDRLEAAAFRRLVEHLQERSDVQNIDL 37 (104) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 9999899999999999998530001379 No 19 >PRK07771 consensus Probab=34.25 E-value=18 Score=15.56 Aligned_cols=37 Identities=27% Similarity=0.406 Sum_probs=26.2 Q ss_pred HHHHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECC Q ss_conf 334777753127655652500043452178506898379 Q gi|254781204|r 628 KTDFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNG 666 (707) Q Consensus 628 kstFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~ 666 (707) .++|+|. ||+|-|+|.+|.+- -+.-+|-.+-|||.+| T Consensus 403 ~~~~~dG-w~~TGDlg~~d~dG-~l~~~GR~~d~Ik~~G 439 (541) T PRK07771 403 PSKFDDG-WLRTGDVGRIDEDG-FITLTDRAKDVIKSGG 439 (541) T ss_pred CCCCCCC-CCCCCCEEEEECCC-EEEEEEEECCEEEECC T ss_conf 1324778-73148779991388-8999086228899899 No 20 >KOG1177 consensus Probab=34.17 E-value=23 Score=14.81 Aligned_cols=36 Identities=36% Similarity=0.469 Sum_probs=25.8 Q ss_pred HHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEECC Q ss_conf 53127655652500043452178506898379810444 Q gi|254781204|r 635 LWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVDK 672 (707) Q Consensus 635 l~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~k 672 (707) -||+|-|||-.+-.--. --||.++-||+| ||-.+|- T Consensus 461 rW~~TGDi~~m~enG~i-~iVGRskdmI~r-GGENVyP 496 (596) T KOG1177 461 RWYDTGDIAVMDENGTI-EIVGRSKDMIIR-GGENVYP 496 (596) T ss_pred CCEECCCEEEECCCCCE-EEEECCCCEEEE-CCCCCCH T ss_conf 01521766787378818-999725670775-8833576 No 21 >PRK06178 acyl-CoA synthetase; Validated Probab=33.92 E-value=17 Score=15.64 Aligned_cols=39 Identities=28% Similarity=0.345 Sum_probs=27.2 Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 477775312765565250004345217850689837981044 Q gi|254781204|r 630 DFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 630 tFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .|.|. ||+|-|+|.+|.+-- +.-+|-.+-|||.+ |+.++ T Consensus 438 ~f~dG-w~~TGDlg~~d~dG~-l~~~GR~~d~Ik~~-G~~I~ 476 (567) T PRK06178 438 SLRDG-WLHTGDIGIIDEQGF-LHYLGRRKEMLKVN-GMSVF 476 (567) T ss_pred EEECC-CCCCCCEEEECCCCE-EEEEEECCCEEEEC-CEEEC T ss_conf 44269-855487588869943-99998057989989-99988 No 22 >PRK08316 acyl-CoA synthetase; Validated Probab=33.56 E-value=28 Score=14.28 Aligned_cols=34 Identities=29% Similarity=0.423 Sum_probs=24.1 Q ss_pred HHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 312765565250004345217850689837981044 Q gi|254781204|r 636 WYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 636 ~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) ||+|-|+|.+|.+-- +.-+|-.+-|||.+| +.++ T Consensus 398 w~~TGDlg~~d~dG~-l~~~GR~~d~Ik~~G-~~I~ 431 (525) T PRK08316 398 WFHSGDLGVMDEEGY-LTVVDRKKDMIKTGG-ENVA 431 (525) T ss_pred CCCCCCEEEECCCCE-EEEEECCCCEEEECC-EEEC T ss_conf 986798578779984-999561578899899-9999 No 23 >KOG1542 consensus Probab=33.26 E-value=30 Score=14.04 Aligned_cols=109 Identities=20% Similarity=0.237 Sum_probs=62.6 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCHHH--HHHHHHHHHHHHCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC--C Q ss_conf 9999998235421365765431134--88887755675068011000000110356788888987632332028755--2 Q gi|254781204|r 520 NAAMVILSGMKHQKDTETRYNTDHK--SNKFDSLYDSYINTPLTKLEQSTAGGNFNKDKEAIKLYLLGSMKDSGNYT--L 595 (707) Q Consensus 520 ~vA~vILsGrKA~KDv~lp~dTdlK--~~f~DqVGNsfansP~trl~~s~~synl~KdayAikaY~sG~ms~~Gn~t--~ 595 (707) +|-+-|+.--.-+++...||.-+.. -.|++.---+++.+ .+.+-.+-..|.+++ ++.|-.+ + T Consensus 226 nA~~~~~~~gGL~~E~dYPY~g~~~~~C~~~~~~~~v~I~~----------f~~l~~nE~~ia~wL----v~~GPi~vgi 291 (372) T KOG1542 226 NAFKYIKKAGGLEKEKDYPYTGKKGNQCHFDKSKIVVSIKD----------FSMLSNNEDQIAAWL----VTFGPLSVGI 291 (372) T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCEEEEEC----------CEECCCCHHHHHHHH----HHCCCEEEEE T ss_conf 89999998179553354884366788532343363699703----------176378999999999----8549958997 Q ss_pred CHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCHHHHHHHHHH-CCCCCCCCCCEEEEEEECC-CCEEEEEECC Q ss_conf 069999999987268202477632520368883347777531-2765565250004345217-8506898379 Q gi|254781204|r 596 NRVRVSDAMQIVLGNTPVNINESMLMPPRGMSKTDFEDRLWY-ATKDTGEYDPYTIKYMNVG-SGKYMIIKNG 666 (707) Q Consensus 596 Nsdrv~dAiqiaTGGiyk~~n~g~VmpPrGMDkstFkDRl~y-~~~~~g~~~~~~i~~~~~g-~~~y~i~~~~ 666 (707) | ..+||--.||+.. |+ +| -+|..++-.|-++||-+.| ...|-|+||| T Consensus 292 N----a~~mQ~YrgGV~~---------P~-----------~~~Cs~~~~~HaVLlvGyG~~g~~~PYWIVKNS 340 (372) T KOG1542 292 N----AKPMQFYRGGVSC---------PS-----------KYICSPKLLNHAVLLVGYGSSGYEKPYWIVKNS 340 (372) T ss_pred C----HHHHHHHCCCCCC---------CC-----------CCCCCCCCCCCEEEEEEECCCCCCCCEEEEECC T ss_conf 2----0779985066567---------77-----------111781126736899950688988832899777 No 24 >pfam10749 DUF2534 Protein of unknown function (DUF2534). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. Probab=32.98 E-value=30 Score=14.01 Aligned_cols=28 Identities=32% Similarity=0.493 Sum_probs=23.6 Q ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHCHH Q ss_conf 89999752033688898718860345878 Q gi|254781204|r 428 FADSLRQRAGFVKKIKDDYNLTTSHFNKT 456 (707) Q Consensus 428 FtASLaqR~S~V~sLkr~YGt~laiFSkq 456 (707) +++++..|+-..+-+ .+||+|++..+.+ T Consensus 25 ia~tVvtrAtigGVi-eqYniP~s~Wt~s 52 (85) T pfam10749 25 IALTVVGRATFGGVI-EQYNMPLSHWTTS 52 (85) T ss_pred HHHHHHHHHHHHHHH-HHHCCCHHHHHHH T ss_conf 999998777755269-8718975441699 No 25 >PRK08744 consensus Probab=32.01 E-value=31 Score=13.90 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=22.2 Q ss_pred HHHHHHHHCCCH------------HHHCHHHHHHHHHHHHHCCH Q ss_conf 688898718860------------34587889999999860564 Q gi|254781204|r 439 VKKIKDDYNLTT------------SHFNKTEENQLRTQLVKRPA 470 (707) Q Consensus 439 V~sLkr~YGt~l------------aiFSkqEA~qLSqqVrkAPA 470 (707) .+-|+.-||+.. +=||-.||-.|++-|-|+.. T Consensus 689 e~iL~~TyGvivYQEQvMqia~~~agfslg~AD~lRrAmgKK~~ 732 (1195) T PRK08744 689 EVILKDTYGIMVYQEQVMQMAQIVGDYSLGGADLLRRAMGKKVP 732 (1195) T ss_pred HHHHHCCCCEEEEHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCH T ss_conf 98751358777529999999999957998789999998543678 No 26 >KOG1176 consensus Probab=30.87 E-value=18 Score=15.52 Aligned_cols=40 Identities=30% Similarity=0.530 Sum_probs=27.8 Q ss_pred HHHHHHHHHCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCCEEC Q ss_conf 34777753127655652500043452-17850689837981044 Q gi|254781204|r 629 TDFEDRLWYATKDTGEYDPYTIKYMN-VGSGKYMIIKNGNPKVD 671 (707) Q Consensus 629 stFkDRl~y~~~~~g~~~~~~i~~~~-~g~~~y~i~~~~~~~~~ 671 (707) .+|+|.=|+||-|+|-+|++- |.- ++-.|=|||.+ |+.++ T Consensus 402 ~~~~~~GW~~TGDiGy~D~DG--~l~IvdR~KdlIk~~-G~qv~ 442 (537) T KOG1176 402 EAFDDDGWFHTGDLGYFDEDG--YLYIVDRSKDLIKYG-GEQVS 442 (537) T ss_pred HHCCCCCCCCCCCEEEECCCC--EEEEEECCHHHEEEC-CEEEC T ss_conf 533457960417567885897--599962301443379-99868 No 27 >TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689 This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process. Probab=30.62 E-value=15 Score=15.96 Aligned_cols=116 Identities=27% Similarity=0.423 Sum_probs=73.7 Q ss_pred CCCHHHCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHH Q ss_conf 85001007763564311683343546777754488998764112320024541001238987767765410121133321 Q gi|254781204|r 8 KPLVEAVTPNQDAVRDSVNPQAGLRDLGDALGKATQFLEGIRRDNAFATANTRYTELSFKAVQDFHDFTNSLDTRDSLQA 87 (707) Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (707) -|.||.-.--..+|+-+--|-.|.|-.|-||-.|++|= |--|-.-+||..-.-| + -..||..|+- T Consensus 90 vPmi~~aeqA~~~V~A~rYPP~GiRGVGSALARASrwN---rIp~Ylq~AdeeiClL----l--------QVEtr~al~N 154 (249) T TIGR02311 90 VPMIETAEQAEAAVKATRYPPKGIRGVGSALARASRWN---RIPDYLQQADEEICLL----L--------QVETREALEN 154 (249) T ss_pred HHHHCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCC---CHHHHHCCHHHHEEHH----H--------HHHHHHHHHH T ss_conf 10303778999999850695195134007877632217---6125760521320232----3--------2657998862 Q ss_pred HHHHH--HHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEC Q ss_conf 35688--87300236-----6899997421257899998887665565530166025732 Q gi|254781204|r 88 GDKIK--EYVDGRIR-----SAYDRFLSSISHRDVRKKFQAQVEHDIRDYHTKGVDIQIG 140 (707) Q Consensus 88 ~~~~~--~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (707) =+.|- |=|||-.- ||-=-|+-.=||-+|+.-..--++. |+ -|-|-+-|-.. T Consensus 155 L~~Ia~VeGVDGVFiGPADLaasmGH~GnPsHPEV~~AI~~Ai~~-i~-a~gKAaGIL~~ 212 (249) T TIGR02311 155 LEEIAAVEGVDGVFIGPADLAASMGHLGNPSHPEVQDAIDDAIER-IK-AAGKAAGILTA 212 (249) T ss_pred HHHHHCCCCCCCEEECCHHHHHHCCCCCCCCCHHHHHHHHHHHHH-HH-HCCCCCCCCCC T ss_conf 157750178662475712443401568886961589999999999-98-54898654543 No 28 >pfam07527 Hairy_orange Hairy Orange. The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute. Probab=30.17 E-value=33 Score=13.70 Aligned_cols=33 Identities=33% Similarity=0.499 Sum_probs=22.4 Q ss_pred HHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHH Q ss_conf 99986776522121010003789999997531012 Q gi|254781204|r 251 EVVEDVSKAIGLAGWDRLDDTKRRRLLEHLSSRDN 285 (707) Q Consensus 251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 (707) |-+..|+.-+ ..-+..|+..+.||+.||.+.-+ T Consensus 9 eC~~Ev~rfL--~~~~~~~~~~~~rLl~HL~~~~~ 41 (43) T pfam07527 9 ECLNEVARFL--SSVEGVDPDVRARLLSHLASCLN 41 (43) T ss_pred HHHHHHHHHH--CCCCCCCHHHHHHHHHHHHHHHH T ss_conf 9999999996--25899986899999999999876 No 29 >TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932 Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This entry represents the chromosomally-encoded polypeptide XerD, which is closely related to, and interacts with, another chromosomally-encoded polypeptide, XerC (IPR011931 from INTERPRO). These proteins are site-specific tyrosine recombinases, which act by catalyzing the cutting and rejoining of the recombining DNA molecules . They form a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids. XerD is composed of two domains, an N-terminal alpha-helical domain, and a C-terminal domain composed mostly of alpha helices, with a three-stranded antiprallel beta sheet along one edge . The active site is found at the extreme C-terminal end of the polypeptide. Most of the C-terminal domain is structurally homologous to that of other "phage" integrases, but the active site regions of these enzymes are stucturally distinct.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division. Probab=30.16 E-value=33 Score=13.70 Aligned_cols=39 Identities=38% Similarity=0.514 Sum_probs=15.0 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 62146578888888852170000012356826899999999845899 Q gi|254781204|r 185 PIDLRLKQKLLSEAKEKLNTNQIIGAHARDPRVFENFMRAFYKKGHP 231 (707) Q Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (707) --|||.-|.||..| -+.|.||-- -|-.+.|+..|++-|| T Consensus 265 GADLR~VQeLLGHa--disTTQIYT------HV~~~~L~~~~~~~HP 303 (305) T TIGR02225 265 GADLRVVQELLGHA--DISTTQIYT------HVARERLKEVHKKHHP 303 (305) T ss_pred CCCHHHHHHHHCCC--HHHHHHHHH------HHHHHHHHHHHHHHCC T ss_conf 88276887774322--147889999------9879999999996288 No 30 >TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase; InterPro: IPR011869 This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of this entry belong to the Proteobacteria. ; GO: 0009021 tRNA (uracil-5-)-methyltransferase activity, 0008033 tRNA processing. Probab=29.74 E-value=29 Score=14.10 Aligned_cols=17 Identities=29% Similarity=0.643 Sum_probs=8.1 Q ss_pred CCCEEEECC-CCCHHHHH Q ss_conf 763252036-88833477 Q gi|254781204|r 616 NESMLMPPR-GMSKTDFE 632 (707) Q Consensus 616 n~g~VmpPr-GMDkstFk 632 (707) +.=-|=||| |||++|.| T Consensus 289 ~tiFVDPPRaGlD~~t~~ 306 (361) T TIGR02143 289 NTIFVDPPRAGLDPDTVK 306 (361) T ss_pred CEEEECCCCCCCCHHHHH T ss_conf 602677988888989999 No 31 >TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221 This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis.. Probab=29.70 E-value=34 Score=13.65 Aligned_cols=32 Identities=25% Similarity=0.398 Sum_probs=14.3 Q ss_pred HHCCCCCCCCCCEE--EEEEECCCCEEEEEECCC Q ss_conf 31276556525000--434521785068983798 Q gi|254781204|r 636 WYATKDTGEYDPYT--IKYMNVGSGKYMIIKNGN 667 (707) Q Consensus 636 ~y~~~~~g~~~~~~--i~~~~~g~~~y~i~~~~~ 667 (707) +|.|=|.-.+|-++ +..+-||+--=-||||+. T Consensus 662 ~FsTlDL~~iDL~~g~~~F~KvGavpSFiKRG~~ 695 (794) T TIGR02865 662 KFSTLDLSVIDLYTGQAEFVKVGAVPSFIKRGAK 695 (794) T ss_pred HHHHHHHHHHCCCCCEEEEEEECCCCCEEEECCE T ss_conf 0577678874477632789996161251666788 No 32 >PRK09736 5-methylcytosine-specific restriction enzyme subunit McrC; Provisional Probab=29.54 E-value=34 Score=13.68 Aligned_cols=38 Identities=8% Similarity=0.106 Sum_probs=20.1 Q ss_pred HHHHHHHHH---H-HHCCCCCCCC-CC--HHHHHHHHHHHHHHHC Q ss_conf 999999823---5-4213657654-31--1348888775567506 Q gi|254781204|r 520 NAAMVILSG---M-KHQKDTETRY-NT--DHKSNKFDSLYDSYIN 557 (707) Q Consensus 520 ~vA~vILsG---r-KA~KDv~lp~-dT--dlK~~f~DqVGNsfan 557 (707) .+|++||.| + ..++-.-..+ ++ .|...|-.+|++.|-. T Consensus 166 ~lc~Lil~~~l~t~~~G~~~~~~fl~d~~~M~~LFEkfV~~~yr~ 210 (350) T PRK09736 166 SVCKLIFNGLLPTENSGDKRLSDFEREEKEMSRLYEKFVRGFYRR 210 (350) T ss_pred HHHHHHHHCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 999999954385457874000351020579999999999999999 No 33 >TIGR01187 potA polyamine ABC transporter, ATP-binding protein; InterPro: IPR005893 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family comprises the spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belongs to the larger ATP-Binding Cassette (ABC) transporter superfamily. Polyamines like spermidine and putrescine play a vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included).; GO: 0015417 polyamine-transporting ATPase activity, 0015846 polyamine transport, 0016020 membrane. Probab=29.48 E-value=34 Score=13.63 Aligned_cols=26 Identities=42% Similarity=0.657 Sum_probs=22.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCEE Q ss_conf 2334677678787776435540377020 Q gi|254781204|r 285 NALNTKLRKETQAQARRIDAQLNHGITV 312 (707) Q Consensus 285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 312 (707) .||.-|||+.-|..-++|..|| |||+ T Consensus 129 sALD~kLR~~MQ~ELk~~~~~L--GiT~ 154 (331) T TIGR01187 129 SALDKKLRDQMQLELKTLQEQL--GITF 154 (331) T ss_pred HHHHHHHHHHHHHHHHHHHHHC--CCEE T ss_conf 2643898998899999998726--8289 No 34 >PRK07470 acyl-CoA synthetase; Validated Probab=29.32 E-value=30 Score=14.01 Aligned_cols=39 Identities=28% Similarity=0.480 Sum_probs=26.2 Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 477775312765565250004345217850689837981044 Q gi|254781204|r 630 DFEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 630 tFkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .|.|. ||+|-|+|.+|.+-- +.-+|-.+-|||.+ |+.++ T Consensus 390 ~f~dg-w~~TGDlg~~d~dG~-l~i~GR~~d~Ik~~-G~~I~ 428 (528) T PRK07470 390 AFRDG-WFRTGDLGHLDAQGF-LYITGRASDMYISG-GSNVY 428 (528) T ss_pred HHCCC-CCCCCCEEEECCCCC-EEEEEECCCEEEEC-CEEEC T ss_conf 65269-875696599989972-99998577889999-99999 No 35 >pfam05693 Glycogen_syn Glycogen synthase. This family consists of the eukaryotic glycogen synthase proteins GYS1, GYS2 and GYS3. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P). Probab=29.01 E-value=4.7 Score=19.45 Aligned_cols=12 Identities=42% Similarity=0.490 Sum_probs=5.1 Q ss_pred HHHHHHHHHHHC Q ss_conf 788888888521 Q gi|254781204|r 191 KQKLLSEAKEKL 202 (707) Q Consensus 191 ~~~~~~~~~~~~ 202 (707) -|+|-..+|+|+ T Consensus 263 fqnlh~~ak~ki 274 (633) T pfam05693 263 FQNLHAQNKEKI 274 (633) T ss_pred HHHHHHHHHHHH T ss_conf 889999999999 No 36 >PRK07116 flavodoxin; Provisional Probab=28.82 E-value=27 Score=14.35 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=10.6 Q ss_pred CCHHHHHHHHHHHHCCCCCCC Q ss_conf 206999999998726820247 Q gi|254781204|r 595 LNRVRVSDAMQIVLGNTPVNI 615 (707) Q Consensus 595 ~Nsdrv~dAiqiaTGGiyk~~ 615 (707) =|+.++++.|+..||+-..-+ T Consensus 12 GnTk~vA~~I~~~~gaDi~eI 32 (158) T PRK07116 12 GTTKKVAEKLAEVTGGDLYEI 32 (158) T ss_pred CCHHHHHHHHHHHHCCCEEEE T ss_conf 809999999999879997999 No 37 >TIGR02339 thermosome_arch thermosome, various subunits, archaeal; InterPro: IPR012714 Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacteria), a toroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding. Probab=28.72 E-value=19 Score=15.31 Aligned_cols=107 Identities=21% Similarity=0.272 Sum_probs=57.2 Q ss_pred CCCCCCHHHCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 058850010077635643116833435467777544889987641123200245-4100123898776776541012113 Q gi|254781204|r 5 TTNKPLVEAVTPNQDAVRDSVNPQAGLRDLGDALGKATQFLEGIRRDNAFATAN-TRYTELSFKAVQDFHDFTNSLDTRD 83 (707) Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (707) .+-|-|||.--.-..-|-|....-.=| -|.-|-||-..|| .+-..|.= .-|..-+-+|+.-+-+...+.+.-| T Consensus 70 PaAKmlVEVAktQd~EvGDGTTTAVVL--AG~LL~kAEdLL~----~~iHPTvI~~GYr~A~~~A~~~id~iA~~i~~~D 143 (522) T TIGR02339 70 PAAKMLVEVAKTQDAEVGDGTTTAVVL--AGELLEKAEDLLE----QDIHPTVIIEGYRKAAEKALEIIDEIATKIDVED 143 (522) T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHH--HHHHHHHHHHHHC----CCCCCEEEECHHHHHHHHHHHHHHHHCCCCCCCH T ss_conf 578999999986300006734889999--9899999998620----7998458733158889999999986246489885 Q ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH Q ss_conf 33213568887300236-68999974212578999 Q gi|254781204|r 84 SLQAGDKIKEYVDGRIR-SAYDRFLSSISHRDVRK 117 (707) Q Consensus 84 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 117 (707) .=+--.-..--..|..- ..+-..|+.+.-+-|+. T Consensus 144 ~~~L~K~A~Ts~tgK~~ae~~~d~La~lvv~AV~~ 178 (522) T TIGR02339 144 RDLLKKVAETSLTGKASAEETKDKLANLVVEAVKQ 178 (522) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999998762331344568899999999999998 No 38 >PRK08974 long-chain-fatty-acid--CoA ligase; Validated Probab=28.35 E-value=33 Score=13.77 Aligned_cols=33 Identities=33% Similarity=0.375 Sum_probs=24.6 Q ss_pred HHHCCCCCCCCCCEEEEE-EECCCCEEEEEECCCCEE Q ss_conf 531276556525000434-521785068983798104 Q gi|254781204|r 635 LWYATKDTGEYDPYTIKY-MNVGSGKYMIIKNGNPKV 670 (707) Q Consensus 635 l~y~~~~~g~~~~~~i~~-~~~g~~~y~i~~~~~~~~ 670 (707) -||+|-|.|.+|.+ |+ .-+|-.+-+||.+| +.+ T Consensus 432 gw~~TGDlg~~d~d--G~l~~~GR~dd~Ik~~G-~rI 465 (559) T PRK08974 432 GWLATGDIAVMDEE--GFLRIVDRKKDMILVSG-FNV 465 (559) T ss_pred CCCCCCCEEEECCC--CEEEEEECCCCEEEECC-EEE T ss_conf 98766875998799--64999987867799899-998 No 39 >PRK09029 O-succinylbenzoic acid--CoA ligase; Provisional Probab=27.50 E-value=37 Score=13.40 Aligned_cols=35 Identities=26% Similarity=0.540 Sum_probs=24.5 Q ss_pred HHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 75312765565250004345217850689837981044 Q gi|254781204|r 634 RLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 634 Rl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .-||+|-|+|.++ + =...=+|-.+-|||.+| +.++ T Consensus 331 dGw~~TGDlg~~d-d-G~l~~~GR~~d~Ik~~G-~~V~ 365 (458) T PRK09029 331 EGWFATRDRGEWQ-N-GELTILGRLDNLFISGG-ENIQ 365 (458) T ss_pred CCCCCCCCEEEEC-C-CEEEEEEECCCEEEECC-EEEC T ss_conf 7876678649987-9-93899045357899899-9999 No 40 >PRK06839 acyl-CoA synthetase; Validated Probab=27.31 E-value=34 Score=13.65 Aligned_cols=38 Identities=32% Similarity=0.420 Sum_probs=25.4 Q ss_pred HHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 77775312765565250004345217850689837981044 Q gi|254781204|r 631 FEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 631 FkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) |.|. ||+|-|.|-+|.+- -..-+|-.+-|||.+| +.++ T Consensus 368 ~~dg-w~~TGDlg~~d~dG-~l~~~GR~dd~Ik~~G-~~V~ 405 (496) T PRK06839 368 IQDG-WLCTGDLARVDEDG-FVYIVGRKKEMIISGG-ENIY 405 (496) T ss_pred HCCC-CCCCCCEEEECCCC-CEEEEEECCCEEEECC-EEEC T ss_conf 4489-86558579999996-2999872778899999-9999 No 41 >KOG1795 consensus Probab=26.91 E-value=38 Score=13.33 Aligned_cols=222 Identities=24% Similarity=0.258 Sum_probs=117.2 Q ss_pred CCCCCEEEEHHHHHHHCCCCCCHHHHH---HHHHHHHHHCCCCHHHHHHHHHHHHHH----------HCCCC----CCCC Q ss_conf 015520200234554307763049999---998885310176214657888888885----------21700----0001 Q gi|254781204|r 147 EDNLNMTVGLAAAHVLHDPSNENYFQR---VQSITDHINSLPIDLRLKQKLLSEAKE----------KLNTN----QIIG 209 (707) Q Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~----~~~~ 209 (707) ..-|.||--+..+||+---.|-.-||- +|-|-.|+.-|.--.|.|-||...-+- +.||+ .-.| T Consensus 544 REiLrl~KliVD~hVqfRlgnvDa~qLadgl~yi~nhVGqLTGmYRYKYklMrQIr~CKdlKhliyYrfn~gvgkgpgcg 623 (2321) T KOG1795 544 REILRLTKLVVDSHVQFRLGNVDAFQLADGLQYIFNHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGVGKGPGCG 623 (2321) T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 99999999986545210126731988712165898631333014688999999999865377777554315777898867 Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHH-HHHHHHHHH---------------------HHHHHHHHHHCCCCHHH Q ss_conf 23568268999999998458998754412322-134556568---------------------99986776522121010 Q gi|254781204|r 210 AHARDPRVFENFMRAFYKKGHPPKDSTSLSDV-SDSARERSL---------------------EVVEDVSKAIGLAGWDR 267 (707) Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~---------------------~~~~~~~~~~~~~~~~~ 267 (707) --|-.=||+-.|+|. |-|--..-|+.. +--+..|+- .|..|++..+ -+. T Consensus 624 fW~p~WRvWlfflRG-----~iPLLeR~lgnLl~RqfEGR~~~v~Kt~tKQRves~~DleLr~~vM~dildmm----peg 694 (2321) T KOG1795 624 FWAPGWRVWLFFLRG-----IIPLLERWLGNLLARQFEGRHSKVAKTVTKQRVESHFDLELRAAVMHDILDMM----PEG 694 (2321) T ss_pred CCCHHHHHHHHHHHC-----CHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHC----CCH T ss_conf 463468999999814-----06789999877778886266566564146664111335999999999998747----720 Q ss_pred CCHHHHHHHHHHHHHHHHH-----------H-----HHHHHHHH-HHHHHH-----HHHHHCCCCEE-CHHHCCCHHHHH Q ss_conf 0037899999975310123-----------3-----46776787-877764-----35540377020-612313389998 Q gi|254781204|r 268 LDDTKRRRLLEHLSSRDNA-----------L-----NTKLRKET-QAQARR-----IDAQLNHGITV-KPSELIPLEDYT 324 (707) Q Consensus 268 ~~~~~~~~~~~~~~~~~~~-----------~-----~~~~~~~~-~~~~~~-----~~~~~~~~~~~-~~~~~~~ldEFt 324 (707) ...+|-|++|.|||..=.. + |.-||--. .|..-. .-.....|-|| |.-++--|.-.| T Consensus 695 i~q~kaRtiLQHlsEAWRCWKANiPw~vpglp~pienmilRyvkskad~wt~~ahynrErirRgA~Vdkt~~kknLgRlt 774 (2321) T KOG1795 695 IKQNKARTILQHLSEAWRCWKANIPWKVPGLPIPIENMILRYVKSKADWWTNSAHYNRERIRRGATVDKTVCKKNLGRLT 774 (2321) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHEECCCHHHHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 11347999999989998875238985577887659999999872011330001303399875026621478988787899 Q ss_pred HHHCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH-HHHHHCCCCCCCCCCCCHHH Q ss_conf 8715013799999998756645645443235705799-99974086666762210234 Q gi|254781204|r 325 QAYGVEQGTELYNLQQFKSVAAPDVARIKLMSTFDAK-KFLQKIDDEYISNPSLSLAS 381 (707) Q Consensus 325 ~AYGv~eG~k~Y~~fq~~qiaG~DIatvq~MSt~~qt-A~Leq~~P~~~~~pgegYAS 381 (707) +-| +..-+++|-++++ -|++|.--.-.--...| -+||+++-.-+.-|-++|-. T Consensus 775 rl~-lk~eqErq~n~~k---~Gp~it~eEa~ai~t~tv~wlesR~f~pipfPpLsyk~ 828 (2321) T KOG1795 775 RLY-LKAEQERQHNYLK---DGPYITAEEAVAIYTTTVHWLESRRFSPIPFPPLSYKH 828 (2321) T ss_pred HHH-HHHHHHHHHHHHH---CCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC T ss_conf 999-8767788765662---28867889977888989999986316888899978613 No 42 >PRK06334 long chain fatty acid--[acyl-carrier-protein] ligase; Validated Probab=25.97 E-value=39 Score=13.22 Aligned_cols=36 Identities=22% Similarity=0.290 Sum_probs=26.5 Q ss_pred HHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 75312765565250004345217850689837981044 Q gi|254781204|r 634 RLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 634 Rl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .-||+|-|+|.+|.+- -+.=+|-.+-|||.+| +.++ T Consensus 409 ~~w~~TGDlg~~d~dG-~l~i~GR~kd~Ik~~G-~~I~ 444 (539) T PRK06334 409 ETWYVTGDLGYVDRHG-ELFLKGRLSRFVKIGA-EMVS 444 (539) T ss_pred CEEEECCCCCEECCCC-EEEEEECCCCEEEECC-EEEC T ss_conf 7046779852889996-6999872617899899-9999 No 43 >smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family. Probab=25.21 E-value=41 Score=13.13 Aligned_cols=35 Identities=40% Similarity=0.543 Sum_probs=23.6 Q ss_pred HHHHHHHHHHHC-CCCHHHCCHHHHHHHHHHHHHHHHHH Q ss_conf 899986776522-12101000378999999753101233 Q gi|254781204|r 250 LEVVEDVSKAIG-LAGWDRLDDTKRRRLLEHLSSRDNAL 287 (707) Q Consensus 250 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 (707) -|.+..|+.-+. +.|+ |+..|.||+.||.++-+.+ T Consensus 8 ~eC~~EVsrfLs~~~~~---~~~~~~rLl~HL~~~~~~~ 43 (45) T smart00511 8 RECANEVSRFLSQLPGT---DPDVRARLLSHLQTHLNQL 43 (45) T ss_pred HHHHHHHHHHHHCCCCC---CHHHHHHHHHHHHHHHHHH T ss_conf 99999999999628999---8699999999999999885 No 44 >TIGR00838 argH argininosuccinate lyase; InterPro: IPR009049 This entry represents argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. ; GO: 0004056 argininosuccinate lyase activity, 0042450 arginine biosynthetic process via ornithine. Probab=25.07 E-value=41 Score=13.11 Aligned_cols=62 Identities=23% Similarity=0.255 Sum_probs=38.4 Q ss_pred HHHHHHH------HHH-----HHHCCCCCCCCCCHH---HHHHHHHHHHHHHCCHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 8999999------823-----542136576543113---48888775567506801100000011035678888898763 Q gi|254781204|r 519 KNAAMVI------LSG-----MKHQKDTETRYNTDH---KSNKFDSLYDSYINTPLTKLEQSTAGGNFNKDKEAIKLYLL 584 (707) Q Consensus 519 ~~vA~vI------LsG-----rKA~KDv~lp~dTdl---K~~f~DqVGNsfansP~trl~~s~~synl~KdayAikaY~s 584 (707) ||||++| |+| +--||-.|+.||-|| ||..||.|...-.- .. T Consensus 285 PD~aELiRGK~Grv~G~L~g~L~~lKalP~aYNrDlQEdkE~LFD~v~t~~~~-------------------------~~ 339 (469) T TIGR00838 285 PDVAELIRGKTGRVIGNLTGLLTILKALPLAYNRDLQEDKEPLFDAVKTVELS-------------------------LE 339 (469) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH-------------------------HH T ss_conf 20799998755268999999999971123323510013783678899999999-------------------------99 Q ss_pred HHHHHCCCCCCCHHHHHHHHH Q ss_conf 233202875520699999999 Q gi|254781204|r 585 GSMKDSGNYTLNRVRVSDAMQ 605 (707) Q Consensus 585 G~ms~~Gn~t~Nsdrv~dAiq 605 (707) .++.+-.+++.|+.|.+.+++ T Consensus 340 ~~~~~l~~i~vn~er~~e~A~ 360 (469) T TIGR00838 340 VMTGMLDTIKVNKERMEEAAS 360 (469) T ss_pred HHHHHHHCCCCCHHHHHHHHH T ss_conf 999998308158789999864 No 45 >PRK06188 acyl-CoA synthetase; Validated Probab=24.74 E-value=42 Score=13.07 Aligned_cols=35 Identities=34% Similarity=0.483 Sum_probs=24.6 Q ss_pred HHHHHHHHCCCCCCCCCCEEEEEE-ECCCCEEEEEECCC Q ss_conf 477775312765565250004345-21785068983798 Q gi|254781204|r 630 DFEDRLWYATKDTGEYDPYTIKYM-NVGSGKYMIIKNGN 667 (707) Q Consensus 630 tFkDRl~y~~~~~g~~~~~~i~~~-~~g~~~y~i~~~~~ 667 (707) .|+|. ||+|-|+|-+|.+ |+. -+|-.+-|||.+|. T Consensus 387 ~f~~g-w~~TGDlg~~d~d--G~l~~~GR~~d~Ik~~G~ 422 (522) T PRK06188 387 TFRDG-WLHTGDLAREDED--GYYYIVDRKKDMIVTGGF 422 (522) T ss_pred HHCCC-CCCCCCEEEECCC--CEEEEEECCCCEEEECCE T ss_conf 33489-9757976998899--709999777578998999 No 46 >PRK08512 consensus Probab=24.59 E-value=42 Score=13.05 Aligned_cols=31 Identities=13% Similarity=0.260 Sum_probs=18.8 Q ss_pred HHHHHHHCCC------------HHHHCHHHHHHHHHHHHHCCH Q ss_conf 8889871886------------034587889999999860564 Q gi|254781204|r 440 KKIKDDYNLT------------TSHFNKTEENQLRTQLVKRPA 470 (707) Q Consensus 440 ~sLkr~YGt~------------laiFSkqEA~qLSqqVrkAPA 470 (707) +=|+.-||+. ++=||--||-.|++-|-|+.. T Consensus 691 ~IL~~TyGv~vYQEQVMqia~~lAGfslgeAD~LRRAmgKK~~ 733 (1185) T PRK08512 691 PILEPTYGVIVYQEQVMQIVQTIGGFSLGGADLVRRAMGKKDP 733 (1185) T ss_pred HHHCCCCCEEEEHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCH T ss_conf 9846778768779999999999827997778999998531768 No 47 >TIGR01776 TonB-tbp-lbp TonB-dependent lactoferrin and transferrin receptors; InterPro: IPR010948 This family of TonB-dependent receptors are responsible for import of iron from the mammalian iron carriers lactoferrin and transferrin across the outer membrane. These receptors are found only in bacteria which can infect mammals, examples are Moraxella, Mannheimia, Neisseria, Actinobacillus, Pasteurella, Haemophilus and Histophilus species.; GO: 0004872 receptor activity, 0005215 transporter activity, 0006810 transport, 0019867 outer membrane. Probab=23.91 E-value=16 Score=15.89 Aligned_cols=32 Identities=28% Similarity=0.387 Sum_probs=26.5 Q ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 36689-999742125789999888766556553 Q gi|254781204|r 99 IRSAY-DRFLSSISHRDVRKKFQAQVEHDIRDY 130 (707) Q Consensus 99 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (707) +.-.| |||.|.++|.|.+..|+.+.-++++-- T Consensus 579 ~~~G~RDkf~S~l~~~~~~~~~~~~~~~~~~~~ 611 (1163) T TIGR01776 579 LLLGYRDKFKSQLSRHDYLRQNAVQTYESIRGD 611 (1163) T ss_pred EEECEEEHHHHHCCCCCCHHHHHHCCEEECCCC T ss_conf 530302023531574653015544010011547 No 48 >PRK07327 enoyl-CoA hydratase; Provisional Probab=23.45 E-value=43 Score=13.00 Aligned_cols=69 Identities=17% Similarity=0.166 Sum_probs=32.1 Q ss_pred ECCCCCCHHHCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC Q ss_conf 30588500100776356431168334354677775448899876411232002454100123898776776541012 Q gi|254781204|r 4 ITTNKPLVEAVTPNQDAVRDSVNPQAGLRDLGDALGKATQFLEGIRRDNAFATANTRYTELSFKAVQDFHDFTNSLD 80 (707) Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (707) +....+=|--+|-|.-..+.+.+|+. ++.|.+++..+. .|......--+-..-+|-+-.|+..+....+ T Consensus 15 ~e~~~~GVa~itlnrP~~~Nals~~m-~~~l~~a~~~~~-------~d~~vrvvvltg~G~~FcaG~Dl~~~~~~~~ 83 (271) T PRK07327 15 FDRHPPGVLEIVLNRPEGLNAADARM-HRELADIWRDVD-------RDPDVRVVVIRGEGKAFSAGGDLALVEEMAG 83 (271) T ss_pred EEEECCCEEEEEECCCCCCCCCCHHH-HHHHHHHHHHHH-------HCCCCEEEEEECCCCCCCCCCCHHHHHHCCC T ss_conf 99808958999982898778989999-999999999997-------6899169999789986556756477763157 No 49 >TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase; InterPro: IPR005905 D-alanine--D-alanine ligase (6.3.2.4 from EC) is a bacterial enzyme involved in cell-wall biosynthesis. It participates in forming UDP-N-acetylmuramoyl pentapeptide, the peptidoglycan precursor. These enzymes are proteins of 300 to 360 amino acids containing many conserved regions. The N-terminal Gly-rich region could be involved in ATP-binding. This family of enzymes represent chromosomal versions of species not specifically resistant to glycopeptide antibiotics such as vancomycin. The mechanism of glycopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). This model attempts to exclude the VanA/VanB and VanC subfamilies while capturing most other D-Ala-D-Ala ligases above the trusted cut-off. However, changes in small numbers of amino acids, as demonstrated crystallographically, can alter specificity. In chlamydial species, this enzyme is found as a fusion protein with UDP-N-acetylmuramate--alanine ligase. ; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005737 cytoplasm. Probab=23.43 E-value=44 Score=12.91 Aligned_cols=29 Identities=28% Similarity=0.437 Sum_probs=15.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHCC Q ss_conf 21345565689998677652212101000 Q gi|254781204|r 241 VSDSARERSLEVVEDVSKAIGLAGWDRLD 269 (707) Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 269 (707) +++...+.--+...-+.+++|+.||-|.| T Consensus 297 L~~~~~~~i~~~a~~ay~~~~~~G~~R~D 325 (375) T TIGR01205 297 LDEELEEKIKELALKAYKALGCRGLARVD 325 (375) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCEEEEE T ss_conf 88899999999999999840887448998 No 50 >PRK06368 consensus Probab=22.89 E-value=45 Score=12.84 Aligned_cols=30 Identities=27% Similarity=0.357 Sum_probs=22.7 Q ss_pred HHCCCCCCCCCCEEEEEEECCCCEEEEEECC Q ss_conf 3127655652500043452178506898379 Q gi|254781204|r 636 WYATKDTGEYDPYTIKYMNVGSGKYMIIKNG 666 (707) Q Consensus 636 ~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~ 666 (707) ||+|-|+|-+|.+-- +.-+|-.+-|||.+| T Consensus 405 w~~TGDlg~~d~dG~-l~~~GR~dd~Ik~~G 434 (529) T PRK06368 405 WMHTGDLAVMDEYGY-IKIVDREKDAVKSGG 434 (529) T ss_pred CCCCCCEEEECCCCE-EEEEECCCCEEEECC T ss_conf 864497799868942-999963404899899 No 51 >TIGR02422 protocat_beta protocatechuate 3,4-dioxygenase, beta subunit; InterPro: IPR012785 Protocatechuate (3,4-dihydroxybenzene, PCA) is an aromatic compound which is a key intermediate in the degradation of the plant biopolymer lignin and other aromatic compounds. The key step of PCA degradation is the ring-cleavage performed by dioxygenases adding both atoms from molecular oxygen to specific carbon atoms within the ring. This step can be performed by two distinct mechanisms; intradiol cleavage and extradiol cleavage. In intradiol cleavage the oxygen atoms are added to the carbons carrying the hydroxyl groups, producing two carboxylate groups. In extradiol cleavage the oxygens are added to one carbon carrying a hydroxyl group and another carrying a hydrogen, resulting in the formation of a carboxylate group and an aldehydic group. For further information see . PCA dioxygenases fall into the broader category of catechol dioxygenases. These are metalloenzymes which bind non-haeme iron. The extradiol dioxygenases use Fe(II) to activate oxygen for nucleophilic attack on the aromatic substrate, while the intradiol dioxygenases use Fe(III) to activate the aromatic substrate for an electrophilic attack by oxygen . This entry represents the beta subunit of protocatechuate 3,4-dioxygenase, an enzyme which cleaves the PCA ring by an intradiol mechanism. It is composed of two subunits, alpha (IPR012786 from INTERPRO) and beta which are highly similar in structure and are thought to share a common ancestor , , . The core of each subunit is two four-stranded beta-sheets that fold upon each other to form a beta sandwhich. The active site cavity contains the Fe(III)-binding site and is located between the two subunits. All Fe(III) ligands are contributed by the beta subunit.; GO: 0005506 iron ion binding, 0018578 protocatechuate 34-dioxygenase activity, 0019619 protocatechuate catabolic process. Probab=22.87 E-value=24 Score=14.71 Aligned_cols=43 Identities=21% Similarity=0.475 Sum_probs=31.3 Q ss_pred HCCCCCCCCCCEEEE-EEECC-C--CEEEEEECCCCEECCCCCEEEEEH Q ss_conf 127655652500043-45217-8--506898379810444898789971 Q gi|254781204|r 637 YATKDTGEYDPYTIK-YMNVG-S--GKYMIIKNGNPKVDKEGKTIIINV 681 (707) Q Consensus 637 y~~~~~g~~~~~~i~-~~~~g-~--~~y~i~~~~~~~~~k~g~~iii~~ 681 (707) |-..++|+.|-|.|. |++-| . |+=+|+. |..||.+|+||==-| T Consensus 37 FG~~~~~~~DnDLt~N~~~~GE~pIGERI~V~--GrVlD~~GrPVp~~L 83 (224) T TIGR02422 37 FGHEDLGPLDNDLTKNFAHGGEEPIGERIIVH--GRVLDEDGRPVPNTL 83 (224) T ss_pred CCHHHCCCCHHHHHHHHHCCCCCCCCCEEEEE--EEEECCCCCCCCCCE T ss_conf 47322460001578876407888777757897--688658888588741 No 52 >PRK06358 threonine-phosphate decarboxylase; Provisional Probab=22.45 E-value=43 Score=12.99 Aligned_cols=18 Identities=17% Similarity=0.394 Sum_probs=12.5 Q ss_pred HHHHHHHHHHHHCCCCHH Q ss_conf 689998677652212101 Q gi|254781204|r 249 SLEVVEDVSKAIGLAGWD 266 (707) Q Consensus 249 ~~~~~~~~~~~~~~~~~~ 266 (707) .+-|+.-.||+.||+||- T Consensus 204 nlivlrSfSK~~glaGlR 221 (354) T PRK06358 204 NLIIIRAFTKFFAIPGLR 221 (354) T ss_pred CEEEEEECCHHHCCCCHH T ss_conf 668997251663676621 No 53 >PRK07529 acyl-CoA synthetase; Validated Probab=22.09 E-value=47 Score=12.73 Aligned_cols=36 Identities=31% Similarity=0.529 Sum_probs=26.1 Q ss_pred HHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 75312765565250004345217850689837981044 Q gi|254781204|r 634 RLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 634 Rl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .-||+|-|.|.+|.+-- +.-+|-.|-|||+|| +.++ T Consensus 444 dgW~rTGDlg~~D~dG~-l~i~GR~kD~Ii~gG-~nI~ 479 (632) T PRK07529 444 DGWLNTGDLGRIDADGY-FWLTGRAKDLIIRGG-HNID 479 (632) T ss_pred CCCCCCCCEEEECCCCE-EEEEECCCCEEEECC-EEEC T ss_conf 99703584689988921-999871767799899-9988 No 54 >PRK05850 acyl-CoA synthetase; Validated Probab=22.07 E-value=47 Score=12.73 Aligned_cols=35 Identities=23% Similarity=0.274 Sum_probs=23.4 Q ss_pred HHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEE Q ss_conf 77531276556525000434521785068983798104 Q gi|254781204|r 633 DRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKV 670 (707) Q Consensus 633 DRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~ 670 (707) +.-||+|-|.|-++-.- +.-+|-.|-|||.+ |+.+ T Consensus 438 ~g~w~rTGDlg~~~dG~--l~i~GR~kd~I~~~-G~~i 472 (581) T PRK05850 438 EGPWLRTGDLGFISEGE--LFIVGRIKDLLIVD-GRNH 472 (581) T ss_pred CCCEEECCCEEEEECCE--EEEEECCCCEEEEC-CEEE T ss_conf 98704758668987999--99983178979999-9998 No 55 >PRK08751 putative long-chain fatty acyl CoA ligase; Provisional Probab=21.88 E-value=47 Score=12.71 Aligned_cols=38 Identities=26% Similarity=0.289 Sum_probs=26.6 Q ss_pred HHHHHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEE Q ss_conf 7777531276556525000434521785068983798104 Q gi|254781204|r 631 FEDRLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKV 670 (707) Q Consensus 631 FkDRl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~ 670 (707) |+..-||+|-|+|.+|.+- -+.-+|-.+-|||.+| +.+ T Consensus 433 ~~~dGw~~TGDlg~~d~dG-~l~i~GR~~d~Ik~~G-~~I 470 (560) T PRK08751 433 MDADGWLHTGDIARMDEQG-FVYIVDRKKDMILVSG-FNV 470 (560) T ss_pred HCCCCCCCCCCEEEECCCC-EEEEEECCCCEEEECC-EEE T ss_conf 3046877789878986894-4999973767799899-999 No 56 >pfam02091 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit. Probab=21.67 E-value=40 Score=13.19 Aligned_cols=130 Identities=26% Similarity=0.313 Sum_probs=62.5 Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 11683343546777754488998764112320024541001238987767765410121133321356888730023668 Q gi|254781204|r 23 DSVNPQAGLRDLGDALGKATQFLEGIRRDNAFATANTRYTELSFKAVQDFHDFTNSLDTRDSLQAGDKIKEYVDGRIRSA 102 (707) Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (707) ...||..-||-||..--+ .-+.+--||- +..||.|-.- -+|.+|.|---+..- -+.| T Consensus 30 gT~~p~T~lr~lgp~pw~-~aYvqPsrRP-----~DgRYGenPn-Rlq~y~QfQVi~KPs-----p~n~----------- 86 (284) T pfam02091 30 GTFNPATFLRALGPEPWN-VAYVEPSRRP-----TDGRYGENPN-RLQHYYQFQVILKPS-----PDNI----------- 86 (284) T ss_pred CCCCHHHHHHHCCCCCCE-EEEECCCCCC-----CCCCCCCCCC-HHHHHEEEEEEECCC-----CHHH----------- T ss_conf 658889988631998641-5542467799-----9987778920-420022357897789-----4668----------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEEHHHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 99997421257899998887665565530166025732310000015520200234554307763049999998885310 Q gi|254781204|r 103 YDRFLSSISHRDVRKKFQAQVEHDIRDYHTKGVDIQIGATQRAQEDNLNMTVGLAAAHVLHDPSNENYFQRVQSITDHIN 182 (707) Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (707) -+-+|.|...-.+. ..+||||=.+..--.-.+||---.-|--|| . -.-+-=.|||.|-.|.-..- T Consensus 87 q~lYL~SL~~lgid-----~~~hDIrFveDnWEsPtLGAwGlGWEVwld------G----MEITQFTYFQQvGGi~c~pv 151 (284) T pfam02091 87 QELYLGSLKALGID-----PLDHDIRFVEDNWESPTLGAWGLGWEVWLD------G----MEITQFTYFQQVGGLECKPV 151 (284) T ss_pred HHHHHHHHHHCCCC-----CCCCCEEEEECCCCCCCCCCCCCCEEEEEC------C----EEEEEEEEEEEECCEECCCC T ss_conf 99999989983979-----543624786147878753102343399987------7----57764351201378214453 Q ss_pred CCCCHHHH Q ss_conf 17621465 Q gi|254781204|r 183 SLPIDLRL 190 (707) Q Consensus 183 ~~~~~~~~ 190 (707) +.-|..-| T Consensus 152 ~~EiTYGL 159 (284) T pfam02091 152 SGEITYGL 159 (284) T ss_pred CEEEEHHH T ss_conf 23310119 No 57 >KOG0905 consensus Probab=21.62 E-value=29 Score=14.12 Aligned_cols=17 Identities=35% Similarity=0.536 Sum_probs=8.9 Q ss_pred HHHHCCCCHHHHHHHHH Q ss_conf 53101762146578888 Q gi|254781204|r 179 DHINSLPIDLRLKQKLL 195 (707) Q Consensus 179 ~~~~~~~~~~~~~~~~~ 195 (707) -+|++||-.-||.-+|. T Consensus 700 ~~i~~lPREt~L~~tL~ 716 (1639) T KOG0905 700 RQICQLPRETRLTVTLF 716 (1639) T ss_pred HHHHHCCHHHEEEEEEE T ss_conf 88740771126999986 No 58 >PRK09348 glyQ glycyl-tRNA synthetase subunit alpha; Validated Probab=21.47 E-value=43 Score=12.97 Aligned_cols=130 Identities=25% Similarity=0.310 Sum_probs=60.6 Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 11683343546777754488998764112320024541001238987767765410121133321356888730023668 Q gi|254781204|r 23 DSVNPQAGLRDLGDALGKATQFLEGIRRDNAFATANTRYTELSFKAVQDFHDFTNSLDTRDSLQAGDKIKEYVDGRIRSA 102 (707) Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (707) ...+|..-||-||..--++ -+.+--||- +..||.|-.- -.|.++.|---|..- - ..|. T Consensus 33 gT~~p~Tflr~lgp~pw~~-aYvqPsrRP-----~DgRYGeNPN-Rlq~y~QfQVilKPs-----P--------~n~q-- 90 (291) T PRK09348 33 GTFHPATFLRALGPEPWNA-AYVQPSRRP-----TDGRYGENPN-RLQHYYQFQVILKPS-----P--------DNIQ-- 90 (291) T ss_pred CCCCHHHHHHCCCCCCCCE-EEECCCCCC-----CCCCCCCCCH-HHHHEEEEEEEECCC-----C--------CCHH-- T ss_conf 6588398885028876405-421345788-----8775468912-420105568997789-----7--------1399-- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEEHHHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 99997421257899998887665565530166025732310000015520200234554307763049999998885310 Q gi|254781204|r 103 YDRFLSSISHRDVRKKFQAQVEHDIRDYHTKGVDIQIGATQRAQEDNLNMTVGLAAAHVLHDPSNENYFQRVQSITDHIN 182 (707) Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (707) +-+|.|...-.+ -.-+||||=-...=-.-.+||---.-|--|| .- .-+--.|||.|-.|.-.-- T Consensus 91 -~lyL~SL~~lgi-----d~~~hDirFvED~WEsPtlGAwGlGWEVWld------GM----EitQFTYFQQvGGi~c~pv 154 (291) T PRK09348 91 -ELYLGSLEALGI-----DPLEHDIRFVEDNWESPTLGAWGLGWEVWLD------GM----EVTQFTYFQQVGGIECKPV 154 (291) T ss_pred -HHHHHHHHHHCC-----CCCCCCEEEEECCCCCCCCCCCCCCEEEEEC------CE----EEEEEEHHHHCCCCCCCCC T ss_conf -999999998088-----9753543786337778762342343499987------66----7652232011078015664 Q ss_pred CCCCHHHH Q ss_conf 17621465 Q gi|254781204|r 183 SLPIDLRL 190 (707) Q Consensus 183 ~~~~~~~~ 190 (707) +.-|..-| T Consensus 155 s~EiTYGL 162 (291) T PRK09348 155 TGEITYGL 162 (291) T ss_pred CEEEEHHH T ss_conf 34421319 No 59 >COG3836 HpcH 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism] Probab=21.14 E-value=18 Score=15.51 Aligned_cols=99 Identities=30% Similarity=0.419 Sum_probs=68.7 Q ss_pred CCCHHHCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHH Q ss_conf 85001007763564311683343546777754488998764112320024541001238987767765410121133321 Q gi|254781204|r 8 KPLVEAVTPNQDAVRDSVNPQAGLRDLGDALGKATQFLEGIRRDNAFATANTRYTELSFKAVQDFHDFTNSLDTRDSLQA 87 (707) Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (707) -|.|+.+.--...|+-+--|-.|.|.+|-+++.|..|- |..+.++.||.+-.-|- -..||..|.+ T Consensus 95 iPmV~s~eqAr~~V~A~rYPP~G~Rgvg~~~arAsr~~---~i~dyl~~An~~~~~lv------------qiEtr~gl~n 159 (255) T COG3836 95 IPMVDTAEQARQAVAATRYPPLGERGVGSALARASRFG---RIADYLAQANDEICLLV------------QIETRAGLDN 159 (255) T ss_pred EECCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC---CHHHHHHHCCCCEEEEE------------EECCHHHHHH T ss_conf 40358999999999961489977345441556665238---77899985360308887------------8734888977 Q ss_pred HHHHH--HHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH Q ss_conf 35688--873002366899-----99742125789999888 Q gi|254781204|r 88 GDKIK--EYVDGRIRSAYD-----RFLSSISHRDVRKKFQA 121 (707) Q Consensus 88 ~~~~~--~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~ 121 (707) =|-|- |-|||-.-..-| -++-+..|-+|+.-.+. T Consensus 160 LDaIaaveGVDgvFiGPaDLaas~G~~gn~~hpeV~~aI~~ 200 (255) T COG3836 160 LDAIAAVEGVDGVFIGPADLAASLGHLGNPGHPEVQAAIEH 200 (255) T ss_pred HHHHHCCCCCCEEEECHHHHHHHCCCCCCCCCHHHHHHHHH T ss_conf 88887157877698777887987499999998799999999 No 60 >TIGR02478 6PF1K_euk 6-phosphofructokinase; InterPro: IPR009161 Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (2.7.1.11 from EC) in which two tandem copies of the phosphofructokinase are found . Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal). Phosphofructokinase (PFK) catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate, which then enters the Embden-Meyerhof pathway. PFK is a key regulatory enzyme in glycolysis. For additional information please see , , .; GO: 0003872 6-phosphofructokinase activity, 0006096 glycolysis, 0005737 cytoplasm. Probab=20.60 E-value=48 Score=12.65 Aligned_cols=41 Identities=29% Similarity=0.399 Sum_probs=27.8 Q ss_pred HHHHHHHHHCCCCEECHHHCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHH Q ss_conf 77643554037702061231338999887150137999999987566456 Q gi|254781204|r 298 QARRIDAQLNHGITVKPSELIPLEDYTQAYGVEQGTELYNLQQFKSVAAP 347 (707) Q Consensus 298 ~~~~~~~~~~~~~~~~~~~~~~ldEFt~AYGv~eG~k~Y~~fq~~qiaG~ 347 (707) |.-+||+-|==| -.|=|+.+|--++.=+.|.+|+=-|++=| T Consensus 496 ~~~kiDgL~IIG---------GFEAf~al~qL~~aR~~YP~F~IPmv~iP 536 (777) T TIGR02478 496 QKHKIDGLLIIG---------GFEAFEALLQLEQAREKYPAFRIPMVVIP 536 (777) T ss_pred HHCCCCEEEEEC---------CHHHHHHHHHHHHHHHHCCCCCCCEEEEC T ss_conf 860988799976---------03688999999999861885578857866 No 61 >pfam04690 YABBY YABBY protein. YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs. Probab=20.49 E-value=49 Score=12.58 Aligned_cols=12 Identities=50% Similarity=0.974 Sum_probs=6.3 Q ss_pred HHHHHHHHHHHH Q ss_conf 023668999974 Q gi|254781204|r 97 GRIRSAYDRFLS 108 (707) Q Consensus 97 ~~~~~~~~~~~~ 108 (707) -|.-|||.||.- T Consensus 123 qRvPSAYNrFIK 134 (170) T pfam04690 123 QRVPSAYNRFIK 134 (170) T ss_pred CCCCHHHHHHHH T ss_conf 068367777799 No 62 >COG2042 Uncharacterized conserved protein [Function unknown] Probab=20.28 E-value=51 Score=12.49 Aligned_cols=52 Identities=13% Similarity=0.321 Sum_probs=25.3 Q ss_pred HHHHHHHHHHHCHHHHHHHHCCCCCCCCCCHHHHHHHHH--HHCCCHHHHHHHHCCCHHH Q ss_conf 999999985437755576532507545379888899997--5203368889871886034 Q gi|254781204|r 395 SHRQSMQELNQDAISWGIKYKQIDPLRFDTEESFADSLR--QRAGFVKKIKDDYNLTTSH 452 (707) Q Consensus 395 Ahe~vnt~RnsDPiqyaiE~gQIdPLdF~tpe~FtASLa--qR~S~V~sLkr~YGt~lai 452 (707) .|+----..+.||++|| +|...++.|+|+|.|- .+-.-+.+|-+.+.--.+| T Consensus 94 ~~R~LP~LvAaNPVNYG------kp~kLss~EAlaAaLYI~G~~deA~~lls~F~WG~~F 147 (179) T COG2042 94 EHRRLPFLVAANPVNYG------KPFKLSSAEALAAALYIVGFKDEASELLSKFKWGHTF 147 (179) T ss_pred CCCCCCHHHHCCCCCCC------CCCHHCHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHH T ss_conf 00222476634875668------7501044999999999827697999998427601889 No 63 >cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs. Probab=20.19 E-value=51 Score=12.48 Aligned_cols=129 Identities=26% Similarity=0.317 Sum_probs=62.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 16833435467777544889987641123200245410012389877677654101211333213568887300236689 Q gi|254781204|r 24 SVNPQAGLRDLGDALGKATQFLEGIRRDNAFATANTRYTELSFKAVQDFHDFTNSLDTRDSLQAGDKIKEYVDGRIRSAY 103 (707) Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 103 (707) ..||..-||-||..-- .+-|.+--||- +..||.|-.- -+|.++.|---+..- .+.| - T Consensus 32 T~hp~T~lr~lg~~pw-~~aYvqPsrRP-----~DgRYG~NPN-Rlq~y~QfQVilKPs-----p~n~-----------q 88 (279) T cd00733 32 TFHPATFLRALGPEPW-NVAYVEPSRRP-----TDGRYGENPN-RLQHYYQFQVIIKPS-----PDNI-----------Q 88 (279) T ss_pred CCCHHHHHHHCCCCCC-EEEEECCCCCC-----CCCCCCCCCC-HHCEEEEEEEEECCC-----CHHH-----------H T ss_conf 5888998863199863-15542467799-----9987778932-310003457998789-----5658-----------9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEEHHHHHHHCCCCCCHHHHHHHHHHHHHHC Q ss_conf 99974212578999988876655655301660257323100000155202002345543077630499999988853101 Q gi|254781204|r 104 DRFLSSISHRDVRKKFQAQVEHDIRDYHTKGVDIQIGATQRAQEDNLNMTVGLAAAHVLHDPSNENYFQRVQSITDHINS 183 (707) Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (707) +-+|.|...-.+. ..+||||=.+..--.-.+||---.-|--|| . -.-+-=.|||.|-.|.-..-+ T Consensus 89 ~lYL~SL~~igid-----~~~hDIrFveDnWEsPtLGAwGlGWEVwld------G----MEItQFTYFQQvGGi~c~pv~ 153 (279) T cd00733 89 ELYLESLEALGIN-----PKEHDIRFVEDNWESPTLGAWGLGWEVWLD------G----MEVTQFTYFQQVGGIPCKPIS 153 (279) T ss_pred HHHHHHHHHCCCC-----CCCCCEEEEECCCCCCCCCCCCCCEEEEEC------C----EEEEEEEEEEEECCEECCCCC T ss_conf 9999989984979-----543624786147878753102343499987------7----577643512113782144532 Q ss_pred CCCHHHH Q ss_conf 7621465 Q gi|254781204|r 184 LPIDLRL 190 (707) Q Consensus 184 ~~~~~~~ 190 (707) .-|..-| T Consensus 154 ~EiTYGL 160 (279) T cd00733 154 VEITYGL 160 (279) T ss_pred EEEEHHH T ss_conf 3310119 No 64 >PRK08279 acyl-CoA synthetase; Validated Probab=20.18 E-value=48 Score=12.68 Aligned_cols=36 Identities=19% Similarity=0.144 Sum_probs=25.0 Q ss_pred HHHHCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEC Q ss_conf 75312765565250004345217850689837981044 Q gi|254781204|r 634 RLWYATKDTGEYDPYTIKYMNVGSGKYMIIKNGNPKVD 671 (707) Q Consensus 634 Rl~y~~~~~g~~~~~~i~~~~~g~~~y~i~~~~~~~~~ 671 (707) .-||+|-|+|.+|.+-- +.-+|-.+-|||.+| +.++ T Consensus 442 dgw~rTGDlg~~D~dG~-l~i~GR~dD~Ik~~G-~rV~ 477 (602) T PRK08279 442 DAWFNTGDLMRDDGFGH-AQFVDRLGDTFRWKG-ENVA 477 (602) T ss_pred CCEECCCCEEEECCCCE-EEEEECCCCEEEECC-EEEC T ss_conf 84144786599868955-999867773687699-9998 No 65 >COG4972 PilM Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion] Probab=20.14 E-value=48 Score=12.66 Aligned_cols=15 Identities=53% Similarity=0.581 Sum_probs=5.3 Q ss_pred HHHHHHHHHHCCCCH Q ss_conf 999867765221210 Q gi|254781204|r 251 EVVEDVSKAIGLAGW 265 (707) Q Consensus 251 ~~~~~~~~~~~~~~~ 265 (707) |+||---.|.-+||. T Consensus 149 E~v~~ri~a~~~AGl 163 (354) T COG4972 149 EVVESRIDAFELAGL 163 (354) T ss_pred HHHHHHHHHHHHCCC T ss_conf 666788999997699 No 66 >cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi. TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. Probab=20.02 E-value=46 Score=12.75 Aligned_cols=11 Identities=45% Similarity=0.996 Sum_probs=3.7 Q ss_pred CCHHHHHHHHH Q ss_conf 88334777753 Q gi|254781204|r 626 MSKTDFEDRLW 636 (707) Q Consensus 626 MDkstFkDRl~ 636 (707) ||-++-+.||| T Consensus 65 mdl~~iEeRL~ 75 (119) T cd05491 65 MDLDTIEERLW 75 (119) T ss_pred CCHHHHHHHHH T ss_conf 66999999997 Done!