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!