Query         gi|254781160|ref|YP_003065573.1| 16S rRNA m3U1498 methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 245
No_of_seqs    113 out of 2755
Neff          7.5 
Searched_HMMs 39220
Date          Mon May 30 05:53:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781160.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11713 16S rRNA m3U1498 meth 100.0       0       0  441.0  20.2  235    7-245     1-243 (243)
  2 COG1385 Uncharacterized protei 100.0       0       0  421.9  18.7  237    5-243     1-246 (246)
  3 pfam04452 Methyltrans_RNA RNA  100.0       0       0  402.6  15.5  217   22-239     1-225 (225)
  4 TIGR00046 TIGR00046 conserved  100.0       0       0  384.0  18.4  236    5-244     2-256 (258)
  5 PRK02135 hypothetical protein;  93.8    0.12 3.1E-06   31.3   4.8   79  150-235   113-191 (199)
  6 pfam04013 DUF358 Protein of un  93.0    0.21 5.3E-06   29.8   4.8   79  150-235   113-192 (199)
  7 pfam00588 SpoU_methylase SpoU   91.6    0.48 1.2E-05   27.5   5.2  112   85-210     6-118 (142)
  8 COG1901 Uncharacterized conser  90.5     1.1 2.8E-05   25.1   6.3   89  142-237   103-192 (197)
  9 TIGR02775 TrbG_Ti P-type conju  84.9     2.3 5.9E-05   23.0   5.0   19  189-207   177-196 (220)
 10 pfam02590 SPOUT_MTase Predicte  83.6     2.9 7.4E-05   22.4   5.1   76  157-237    62-142 (155)
 11 pfam02598 DUF171 Uncharacteriz  81.0     2.1 5.2E-05   23.4   3.5   98  136-238   170-283 (283)
 12 COG1756 Mra1 Uncharacterized c  79.0     5.6 0.00014   20.5   5.5   83  150-242   137-221 (223)
 13 PRK01191 rpl24p 50S ribosomal   78.3     3.3 8.5E-05   22.0   3.9   51   23-73     31-83  (119)
 14 TIGR02203 MsbA_lipidA lipid A   75.7     1.4 3.5E-05   24.5   1.3   40    7-50    408-451 (603)
 15 PRK00103 SPOUT methyltransfera  74.9     6.4 0.00016   20.2   4.6   75  158-237    63-141 (156)
 16 PRK11181 23S rRNA (guanosine-2  74.6    0.26 6.8E-06   29.1  -2.5  140   82-241    97-238 (244)
 17 PRK10864 putative methyltransf  74.1     7.6 0.00019   19.6   5.1  141   80-241   200-342 (348)
 18 PRK11081 tRNA guanosine-2'-O-m  73.9     2.8 7.2E-05   22.4   2.6  118   78-210    16-135 (229)
 19 KOG3079 consensus               73.4     4.3 0.00011   21.3   3.4   79   78-156     6-103 (195)
 20 cd05828 Sortase_D_4 Sortase D   67.5     9.3 0.00024   19.1   4.1   69   18-89     42-110 (127)
 21 PTZ00194 60S ribosomal protein  65.1     6.9 0.00018   19.9   3.0   52   23-74     31-84  (143)
 22 COG4080 SpoU rRNA Methylase fa  61.9     3.6 9.1E-05   21.8   1.1  100  132-242    37-144 (147)
 23 CHL00194 ycf39 Ycf39; Provisio  61.9      12  0.0003   18.4   3.8  112   96-209    92-217 (319)
 24 pfam09895 DUF2122 RecB-family   60.3      11 0.00027   18.7   3.3   77  150-240    26-104 (105)
 25 cd05827 Sortase_C_3 Sortase C   58.0      16  0.0004   17.6   3.8   69   18-91     43-118 (131)
 26 PRK11572 copper homeostasis pr  57.1     8.3 0.00021   19.4   2.3  131   91-228    72-206 (248)
 27 TIGR00513 accA acetyl-CoA carb  56.7      13 0.00034   18.1   3.2  109   81-199    68-209 (329)
 28 cd06165 Sortase_A_1 Sortase A   56.0      12 0.00031   18.3   3.0   68   20-92     42-116 (127)
 29 cd05830 Sortase_D_5 Sortase D   55.8      17 0.00043   17.4   4.0   74   18-92     43-125 (137)
 30 TIGR01080 rplX_A_E ribosomal p  52.9      19 0.00048   17.1   4.5   70    6-75      6-80  (116)
 31 TIGR00630 uvra excinuclease AB  50.7     9.2 0.00024   19.1   1.6   17   91-107   215-231 (956)
 32 PTZ00066 pyruvate kinase; Prov  49.8      21 0.00054   16.8   4.2   72   36-110   152-228 (513)
 33 PRK04980 hypothetical protein;  49.8      19 0.00048   17.1   3.1   45   11-62     11-56  (102)
 34 cd00004 Sortase Sortases are c  48.3      14 0.00036   17.9   2.3   68   19-91     42-116 (128)
 35 TIGR02851 spore_V_T stage V sp  48.0      10 0.00026   18.8   1.6   28   32-59     21-49  (184)
 36 cd01724 Sm_D1 The eukaryotic S  47.6      23 0.00058   16.5   4.5   66   32-97      2-67  (90)
 37 cd06166 Sortase_D_5 Sortase D   46.5      24  0.0006   16.4   4.1   68   19-91     42-116 (126)
 38 cd01721 Sm_D3 The eukaryotic S  46.4      24 0.00061   16.4   3.7   65   33-97      2-66  (70)
 39 KOG3172 consensus               45.3      25 0.00063   16.3   3.5   65   33-97      7-71  (119)
 40 TIGR02109 PQQ_syn_pqqE coenzym  43.3      21 0.00053   16.8   2.5   74   79-152   145-231 (363)
 41 cd05829 Sortase_E Sortase E (S  42.3      27  0.0007   16.0   3.2   70   19-90     49-126 (144)
 42 PRK10039 hypothetical protein;  41.5      18 0.00046   17.2   2.0   18  195-212    78-95  (127)
 43 TIGR03531 selenium_SpcS O-phos  39.9      20 0.00052   16.8   2.0   23   94-116   191-213 (444)
 44 pfam02844 GARS_N Phosphoribosy  39.7      27  0.0007   16.0   2.7   29  191-222    64-92  (99)
 45 TIGR00699 GABAtrns_euk 4-amino  36.5      17 0.00044   17.3   1.2   14  195-208   154-167 (469)
 46 cd00429 RPE Ribulose-5-phospha  35.7      16 0.00042   17.5   1.0  137   78-228    58-202 (211)
 47 pfam04203 Sortase Sortase fami  35.3      35 0.00089   15.3   4.2   69   18-90     37-110 (122)
 48 COG3097 Uncharacterized protei  35.1      35  0.0009   15.3   3.4   45   11-62     12-57  (106)
 49 TIGR01672 AphA HAD superfamily  34.3      25 0.00065   16.2   1.8   33   20-53    112-144 (248)
 50 TIGR00958 3a01208 antigen pept  32.7      31 0.00078   15.7   2.0   15  186-200   557-571 (770)
 51 PRK13885 conjugal transfer pro  29.3      23 0.00059   16.5   0.9   20  188-207   241-261 (299)
 52 COG1660 Predicted P-loop-conta  28.2      18 0.00046   17.2   0.2   15  186-200   240-254 (286)
 53 PRK05784 phosphoribosylamine--  27.0      48  0.0012   14.5   2.2   22  124-145   318-339 (485)
 54 pfam05896 NQRA Na(+)-transloca  26.7      49  0.0012   14.4   5.6   97   17-117    24-135 (257)
 55 PRK04171 ribosome biogenesis p  26.4      49  0.0013   14.4   5.0   90  142-242   128-219 (221)
 56 pfam01081 Aldolase KDPG and KH  26.4      49  0.0013   14.3   5.2   95  127-227    89-183 (196)
 57 PRK10433 putative RNA methyltr  25.6      51  0.0013   14.3   2.8   25  186-210   104-129 (228)
 58 pfam00834 Ribul_P_3_epim Ribul  25.4      41   0.001   14.9   1.6  136   77-226    57-200 (201)
 59 TIGR00223 panD aspartate 1-dec  25.0      52  0.0013   14.2   4.8   57    3-63      6-63  (127)
 60 KOG2925 consensus               25.0      39 0.00099   15.0   1.4   60    6-68      2-62  (167)
 61 pfam06003 SMN Survival motor n  24.9      53  0.0013   14.2   3.9   37   36-72     67-105 (264)
 62 PRK10358 putative tRNA/rRNA me  24.6      53  0.0014   14.1   3.7  132   82-234     4-141 (157)
 63 pfam07236 Phytoreo_S7 Phytoreo  24.5      43  0.0011   14.7   1.6   20  191-210   283-302 (506)
 64 pfam01079 Hint Hint module. Th  24.4      54  0.0014   14.1   5.0   45   17-64     14-59  (214)
 65 COG2106 Uncharacterized conser  23.6      53  0.0014   14.1   1.9   96  142-241   165-266 (272)
 66 TIGR02311 HpaI 2,4-dihydroxyhe  22.9      26 0.00067   16.1   0.2   25   94-118    73-98  (249)
 67 cd01733 LSm10 The eukaryotic S  22.7      58  0.0015   13.9   3.8   68   29-96      7-74  (78)
 68 cd00452 KDPG_aldolase KDPG and  22.5      58  0.0015   13.9   4.6   90  127-223    85-174 (190)
 69 PRK13210 putative L-xylulose 5  22.5      43  0.0011   14.7   1.3   72   92-163    94-176 (284)
 70 PRK13668 hypothetical protein;  22.1      59  0.0015   13.8   3.4   10  131-140   145-154 (266)
 71 PRK12281 rplX 50S ribosomal pr  22.0      60  0.0015   13.8   3.4   27   36-62      5-31  (77)
 72 PRK00885 phosphoribosylamine--  21.7      60  0.0015   13.8   2.2   35   21-55    154-194 (424)
 73 PRK08745 ribulose-phosphate 3-  21.7      34 0.00087   15.4   0.6  136   77-228    62-207 (223)
 74 pfam05113 DUF693 Protein of un  20.8      63  0.0016   13.7   2.5   11  202-212   222-232 (311)
 75 TIGR02609 doc_partner putative  20.5      64  0.0016   13.6   4.0   39   21-63     11-51  (77)
 76 TIGR00185 rRNA_methyl_2 RNA me  20.4      56  0.0014   14.0   1.5   95   94-205    15-116 (161)
 77 KOG2589 consensus               20.2      55  0.0014   14.1   1.4   42   11-53    199-241 (453)
 78 TIGR01213 TIGR01213 conserved   20.1      65  0.0017   13.6   2.6   22  188-209   338-359 (450)
 79 CHL00141 rpl24 ribosomal prote  20.0      66  0.0017   13.5   3.4   29   34-62      8-36  (90)

No 1  
>PRK11713 16S rRNA m3U1498 methyltransferase; Provisional
Probab=100.00  E-value=0  Score=440.96  Aligned_cols=235  Identities=37%  Similarity=0.565  Sum_probs=203.8

Q ss_pred             CCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEEECCC-CCCCCCEE
Q ss_conf             8777408544788889987798759987035789888999977998798753023555-238997541355-55443135
Q gi|254781160|r    7 LKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQSRSQ-TKQSDVQY   84 (245)
Q Consensus         7 m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~~~~~-~~~~~i~l   84 (245)
                      |||||++.++..+..+.|+++++|||.+|||+++||.|.+|||+|+.|.|+|++++|+ +.+.+......+ .++++++|
T Consensus         1 m~r~fi~~~l~~~~~i~L~~~~~~Hl~~VlR~k~gd~i~v~dg~g~~~~a~I~~i~k~~~~~~i~~~~~~~~~~~~~i~L   80 (243)
T PRK11713          1 MPRLFVDAPLAAGETVILTGEEAHHLVRVLRLKEGDELRLFDGRGGEYLAEITEIGKKSVEVEILEKLEVEREPPLRLTL   80 (243)
T ss_pred             CCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCEEEEEEECCCCCCCCCCCEEEE
T ss_conf             97699687678999999788998899981608999999999798979999999955998999995122367899970799


Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             413445411567775444456656555542022011------22122335788999975123443433200000011233
Q gi|254781160|r   85 IFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKN  158 (245)
Q Consensus        85 ~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~  158 (245)
                      ++|++|+++|||+|||+|||||++|+|+.++||+++      .++++||++|+++|||||||+++|+|+.+.+|+++++.
T Consensus        81 ~~al~K~~~~e~il~k~tElGV~~i~p~~s~rs~~~~~~~~~~~k~eR~~~i~~eA~eQs~r~~lP~i~~~~~l~~~l~~  160 (243)
T PRK11713         81 AQALPKGDRLELIIQKATELGVSAIIPLITERSVVKLDGERADKKLERWQKIAIEAAEQSGRTRIPEIRPPVSLKELLEA  160 (243)
T ss_pred             EEEECCCHHHHHHHHHHHHHCCCEEEEEEHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCHHHHHHH
T ss_conf             99600755899999999872877799997000545212105666699999999999997099828776576799999953


Q ss_pred             CCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             32233321263000121102221003678835999888888888999999957995586368874004489999999999
Q gi|254781160|r  159 WDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ  238 (245)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als~~~  238 (245)
                      .......+++++....   ..........++++++||||||||++|+++|.++|| .++|||++|||||||+++|+|+++
T Consensus       161 ~~~~~~~~i~~~~~~~---~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~g~-~~vsLG~~ILR~ETA~i~als~l~  236 (243)
T PRK11713        161 LADGDLRLVLHPEANL---AAALKSLKPAGKVLLLIGPEGGFSPEEIELLREAGF-TPVSLGPRILRTETAALAALAALQ  236 (243)
T ss_pred             CCCCCCEEEECCCCCC---CCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             8677828998688775---432011257885899987888999999999998898-898679991357749999999999


Q ss_pred             HHHCCCC
Q ss_conf             9847869
Q gi|254781160|r  239 AICGDWY  245 (245)
Q Consensus       239 ~~~g~~~  245 (245)
                      +++|+|-
T Consensus       237 ~~~~~~~  243 (243)
T PRK11713        237 ALLGDLG  243 (243)
T ss_pred             HHHCCCC
T ss_conf             9855799


No 2  
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00  E-value=0  Score=421.88  Aligned_cols=237  Identities=37%  Similarity=0.554  Sum_probs=207.6

Q ss_pred             CCCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEEECC-CCCCCCC
Q ss_conf             778777408544788889987798759987035789888999977998798753023555-23899754135-5554431
Q gi|254781160|r    5 SHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQSRS-QTKQSDV   82 (245)
Q Consensus         5 ~~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~~~~-~~~~~~i   82 (245)
                      ++|+|+|++.++..+..+.++++++||+.+|||+++||++.+|||.|+.|.|+|..++|+ +.+.+...... ...+.++
T Consensus         1 ~~~~~~~v~~~~~~~~~~~l~~~~~~Hl~~VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i~~~~~~~~e~~~~i   80 (246)
T COG1385           1 MRMPRLFVDEELAEGATVILTGDEAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKIVEQLEPNPELPLKI   80 (246)
T ss_pred             CCCEEEEECCCCCCCCEEEECCHHHHHHHHEEECCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEECCCCCCCCCCEE
T ss_conf             97406863464467977997632443267446667899899995899699999810467716999864145677888607


Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHH--H---HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             354134454115677754444566565555420220112--2---12233578899997512344343320000001123
Q gi|254781160|r   83 QYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTH--Y---NMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLK  157 (245)
Q Consensus        83 ~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~--~---k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~  157 (245)
                      +|+++++|+++||+++||+|||||+.|+|++|+||+.+.  .   |++||++|+++|||||||+.+|+|..+.+|.++++
T Consensus        81 ~l~~~~~kg~k~d~iiqkatELGv~~i~p~~ter~~~k~~~~~~~kler~~ki~ieAaEQs~R~~vP~I~~~~~~~~~l~  160 (246)
T COG1385          81 TLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGKKAAKLERWQKIAIEAAEQSGRNVVPEIKPPESLKELLK  160 (246)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHCCCEEEEEEECEEEEEHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECHHHHHHHHH
T ss_conf             99996275188999999998718011798850126772001103689999999999998649986982623130999998


Q ss_pred             CCCCCC--CCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf             332233--321263000121102221003678835999888888888999999957995586368874004489999999
Q gi|254781160|r  158 NWDHNC--QIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMA  235 (245)
Q Consensus       158 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als  235 (245)
                      .++.++  .+.+++....+....... .....++++++||||||||++|++.|+.+|| .+|+|||||||||||+++|+|
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~iiIGPEGGfs~~Ei~~l~~~g~-~~v~LGprILRtETA~l~ala  238 (246)
T COG1385         161 EIDDEDALKLIYEEKAKEGLLALPLL-EALPEGKVLLIIGPEGGFSEDEIELLREAGF-TPVSLGPRILRTETAALAALA  238 (246)
T ss_pred             HCCCHHHHHHEECCCCCCCCCCCHHH-HCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEECCCCCEEEHHHHHHHHHH
T ss_conf             54630013322254454454333012-0156773899988998999899999997798-581378972007789999999


Q ss_pred             HHHHHHCC
Q ss_conf             99998478
Q gi|254781160|r  236 LVQAICGD  243 (245)
Q Consensus       236 ~~~~~~g~  243 (245)
                      ++++.+||
T Consensus       239 ~i~~~~~~  246 (246)
T COG1385         239 ALQALLGD  246 (246)
T ss_pred             HHHHHHCC
T ss_conf             99997349


No 3  
>pfam04452 Methyltrans_RNA RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation.
Probab=100.00  E-value=0  Score=402.61  Aligned_cols=217  Identities=35%  Similarity=0.554  Sum_probs=186.0

Q ss_pred             EEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEEECC-CCCCCCCEEEECCCCCCHHHHHHH
Q ss_conf             9987798759987035789888999977998798753023555-23899754135-555443135413445411567775
Q gi|254781160|r   22 GKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQSRS-QTKQSDVQYIFSPIKTNRLDYMIQ   99 (245)
Q Consensus        22 i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~~~~-~~~~~~i~l~~~~~k~~~~~~ilq   99 (245)
                      |.|+++++|||.||||+++||.|.+|||+|+.|.|+|++++++ +.+.+...... ..++++++|++|++|+++|||+||
T Consensus         1 i~L~~~~~hHl~kVlR~k~gd~i~v~dg~g~~~~~~I~~i~~~~~~~~i~~~~~~~~~~~~~i~l~~al~K~~~~~~il~   80 (225)
T pfam04452         1 VTLTDEEAHHLVRVLRLKEGDEIKLFDGDGGEYLAEIEEISKKSVLVKILEKLEVNKELPLKITLAQALPKGDRLELILQ   80 (225)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEHHCCCCCCCCCEEEEEEEEECCHHHHHHHH
T ss_conf             99868998899981858999999999798989999999951881899650002467899971799995007278999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHC
Q ss_conf             444456656555542022011------22122335788999975123443433200000011233322333212630001
Q gi|254781160|r  100 KSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCG  173 (245)
Q Consensus       100 k~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~  173 (245)
                      |+|||||++|+|++++||+.+      .++.+||++|+++|||||||+++|+|+.+.+|+++++.++....++++++...
T Consensus        81 k~tElGV~~i~p~~~ers~~k~~~~~~~~k~~R~~~i~~~A~eQs~r~~lP~I~~~~~l~~~l~~~~~~~~~i~~~~~~~  160 (225)
T pfam04452        81 KATELGVDRIVPLISERSVVKLDGKRADKKLERWQKIAIEAAEQSGRTRLPEVLPPISLKELLEELDDADKLILHEEAAK  160 (225)
T ss_pred             HHHHHCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCHHHHHHHCCCCCEEEEECCCCC
T ss_conf             99862876579998403545443034666599999999999997199828777266899999961866888999266554


Q ss_pred             CCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             211022210036788359998888888889999999579955863688740044899999999999
Q gi|254781160|r  174 SENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQA  239 (245)
Q Consensus       174 ~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als~~~~  239 (245)
                      ..............++++++||||||||++|+++|+++|| .+++||++|||||||+++|+|++++
T Consensus       161 ~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~g~-~~v~LG~~ILR~ETA~i~als~l~~  225 (225)
T pfam04452       161 SLGELSELLASLKGGKVLLIIGPEGGFSPEEIELLKEAGF-TPVSLGPRILRTETAALAALSALQA  225 (225)
T ss_pred             CCCCCHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHCCC-EEEECCCCCCCHHHHHHHHHHHHCC
T ss_conf             4321012321035784589988988999999999998899-8984799946078599999999619


No 4  
>TIGR00046 TIGR00046 conserved hypothetical protein TIGR00046; InterPro: IPR006700   Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry are predicted to belong to the family of Mtases, based on a crystal structure showing close structural homology to known methyltransferases ..
Probab=100.00  E-value=0  Score=384.05  Aligned_cols=236  Identities=27%  Similarity=0.404  Sum_probs=199.2

Q ss_pred             CCCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEEC-CCCEEEEEEECCCCC-CEEEEEEEECCC-CCCCC
Q ss_conf             778777408544788889987798759987035789888999977-998798753023555-238997541355-55443
Q gi|254781160|r    5 SHLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNG-KDGEWLSKISYVGKS-IRFKVEYQSRSQ-TKQSD   81 (245)
Q Consensus         5 ~~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg-~g~~~~~~I~~~~k~-~~~~i~~~~~~~-~~~~~   81 (245)
                      ++|+++|.+..+....++.|+++++|||.|||||+.||.+.++|+ +|..|.|++.+.+|+ +.+.+....... ..+.+
T Consensus         2 m~~~~~~~~~~~~~~~~i~l~~~~~~Hl~rVlR~~~gd~l~~~~~~~g~~y~~~~~~~~k~~~~~~~~~~~~~~~~~~~~   81 (258)
T TIGR00046         2 MRMRLVLHPEQLEEALIISLTEEEAHHLVRVLRLKKGDKLKLLDGKDGFIYKCEIKKISKKFVKVKLLEGESEERELPLK   81 (258)
T ss_pred             CEEEEEECCCCCCCCCEEEEEHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEECCCCEEEEEEEEEEHHCCCCCCC
T ss_conf             04777734200156525898000344346542158787145667589807987776414668899987100211457762


Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--
Q ss_conf             135413445411567775444456656555542022011------221223357889999751234434332000000--
Q gi|254781160|r   82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNT------HYNMDRVRTYTISAAEQCDILTLPFIYPPTTLE--  153 (245)
Q Consensus        82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~------~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~--  153 (245)
                      ++++++++|+.+||+|||++|||||..|.|++||||..+      .+|++||++|+++|||||+|.++|+|..+.+|.  
T Consensus        82 ~~~~~~~~~g~~~e~ii~~~~eLGv~~~~p~~~ers~~k~~~~~~~~K~~rw~KI~~eA~eQs~r~~~P~i~~~~~l~ql  161 (258)
T TIGR00046        82 IHLAIVLIKGKKMEKIIRKLTELGVSKIIPLNAERSVVKLDIERAIKKLERWQKIVIEAAEQSGRNIVPEIKVPKNLKQL  161 (258)
T ss_pred             EEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH
T ss_conf             89999753212342565456764678998888865304855778875778889999999862779989843205678999


Q ss_pred             -------CCCCCCCC-CCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             -------11233322-3332126300012110222100367883599988888888899999995799558636887400
Q gi|254781160|r  154 -------FLLKNWDH-NCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILR  225 (245)
Q Consensus       154 -------~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR  225 (245)
                             +++..... .....++...   ......+.+..+.+++.|+||||||||++|+.++.+.|| ++|+|||+|||
T Consensus       162 lqr~Q~~e~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~~GPEGGfse~E~~~~~~~~f-~~~~L~~~~LR  237 (258)
T TIGR00046       162 LQRMQDVEKLAESEEEALKLNFHPEA---SPLSANLEQIEQAGKIVIIIGPEGGFSEKEIQLLKEKGF-TPVLLGPRILR  237 (258)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCC---CHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHCCC-EECCCCCCCCH
T ss_conf             99865687641001013232210033---111200122005570489981699968889999988298-24137887021


Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             4489999999999984786
Q gi|254781160|r  226 SDTAAVAAMALVQAICGDW  244 (245)
Q Consensus       226 ~ETA~i~als~~~~~~g~~  244 (245)
                      ||||+++|+|++++.++|+
T Consensus       238 tETA~~~a~s~~~~~l~~l  256 (258)
T TIGR00046       238 TETAPVAALSILQALLEDL  256 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHC
T ss_conf             2268999999999986303


No 5  
>PRK02135 hypothetical protein; Provisional
Probab=93.85  E-value=0.12  Score=31.32  Aligned_cols=79  Identities=23%  Similarity=0.347  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHH
Q ss_conf             00001123332233321263000121102221003678835999888888888999999957995586368874004489
Q gi|254781160|r  150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTA  229 (245)
Q Consensus       150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA  229 (245)
                      .+|++.+..+.....+++.++...+.      .......+.+++.|=-=||+++|.+.+...|. ..+||||..|=+..+
T Consensus       113 ~~~e~~l~e~~~~~~~~~Ld~~G~~i------~~~~~~~~~~FILsDh~~~~~~e~~~L~~~g~-~~iSLGp~~L~a~~c  185 (199)
T PRK02135        113 GSFEDLLQELAEDGQLYYLHEDGEDI------RDVEFPANPVFVLGDHIGMTKEEENLLKRLGA-EKISLGPKMLHADHC  185 (199)
T ss_pred             CCHHHHHHHHHCCCCEEEECCCCCCH------HCCCCCCCCEEEEECCCCCCHHHHHHHHHCCC-CEEEECCHHHHHHHH
T ss_conf             89999999985379799988999950------00568999879962899988789999987088-316547388765058


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254781160|r  230 AVAAMA  235 (245)
Q Consensus       230 ~i~als  235 (245)
                      .+.+--
T Consensus       186 I~iiH~  191 (199)
T PRK02135        186 ITLIHN  191 (199)
T ss_pred             HHHHHH
T ss_conf             999999


No 6  
>pfam04013 DUF358 Protein of unknown function (DUF358). The proteins in this family are around 200 amino acids long with the exception of the Archaeoglobus fulgidus protein AF_1056 that has an additional 100 amino acids at its amino terminus. The function of these bacterial protein is unknown, however, they do contain several conserved histidines and aspartates that might form a metal binding site.
Probab=92.97  E-value=0.21  Score=29.83  Aligned_cols=79  Identities=18%  Similarity=0.259  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCC-CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHH
Q ss_conf             000011233322333212630001211022210036-7883599988888888899999995799558636887400448
Q gi|254781160|r  150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIA-HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDT  228 (245)
Q Consensus       150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ET  228 (245)
                      .+|++++..+.....+++.++...+..      ... ...+.+++.|=-=||+++|.+.++..+. ..+||||..|=+..
T Consensus       113 ~~fe~ll~e~~e~~~~~~Ld~~G~~i~------~~~~~~~~~~FiL~Dh~~~~~~e~~~L~~~~~-~~iSLGp~~L~a~h  185 (199)
T pfam04013       113 MGFEALIRELSEFKPLYYLHEDGGDIS------NVKIPPNNPVFILGDHIGLPEEDEKFLERILA-LKVSLGPLSLHASH  185 (199)
T ss_pred             CCHHHHHHHHHCCCCEEEECCCCCCCC------CCCCCCCCCEEEECCCCCCCHHHHHHHHHCCC-CEEEECCHHHHHHH
T ss_conf             899999999855897999978898432------35577889769855999988678888864488-21553738888757


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254781160|r  229 AAVAAMA  235 (245)
Q Consensus       229 A~i~als  235 (245)
                      +.+.+--
T Consensus       186 cI~ivH~  192 (199)
T pfam04013       186 CITLVHN  192 (199)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 7  
>pfam00588 SpoU_methylase SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet.
Probab=91.59  E-value=0.48  Score=27.47  Aligned_cols=112  Identities=21%  Similarity=0.236  Sum_probs=64.4

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             41344541156777544445665655554202201122122335788999975123443433200000011233322333
Q gi|254781160|r   85 IFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQ  164 (245)
Q Consensus        85 ~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~  164 (245)
                      +-.+-.+..+-.+++-+.-.|++.++.... ++.      +-|...+..++.- ..-++| +....+++++++.......
T Consensus         6 L~~i~~p~NlG~i~Rta~~fG~~~v~l~~~-~~~------~~~~~~~~r~s~g-a~~~i~-~~~~~~~~~~~~~~~~~~~   76 (142)
T pfam00588         6 LDEPQDPGNLGAIARTAAAFGADGLILVEP-RCA------DLYNPKAIRASAG-ALFHLP-LVIVDNLEEALKDLKEAGY   76 (142)
T ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCCCCCC-CCC------CCCCHHHHHHHCC-CCCCCC-CEEECCHHHHHHHHHHCCC
T ss_conf             957988776999999999839996435578-767------9777899999767-752378-3284339999999887495


Q ss_pred             CCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCC-CCCCHHHHHHHHH
Q ss_conf             212630001211022210036788359998888-8888899999995
Q gi|254781160|r  165 IVFADETCGSENSLEKLHAIAHIPNVAILIGPE-GGYHSEEKETLHS  210 (245)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPE-GGfs~~E~~~l~~  210 (245)
                      .++.-+. .+    +.+......+++.+++|+| .|.|+++.+....
T Consensus        77 ~i~~~~~-~~----~~~~~~~~~~~~~lv~G~E~~Gls~~~l~~~d~  118 (142)
T pfam00588        77 WIIATSL-KG----KPLYEIDFPKKVALVFGNEGTGLSNEVLELCDR  118 (142)
T ss_pred             EEECCCC-CC----CCHHHHCCCCCEEEEECCCCCCCCHHHHHHCCE
T ss_conf             0111344-67----487781468872899778778989999986997


No 8  
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=90.50  E-value=1.1  Score=25.09  Aligned_cols=89  Identities=24%  Similarity=0.340  Sum_probs=61.0

Q ss_pred             CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             4343320-000001123332233321263000121102221003678835999888888888999999957995586368
Q gi|254781160|r  142 TLPFIYP-PTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLG  220 (245)
Q Consensus       142 ~lP~i~~-~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG  220 (245)
                      ..|=+.- -.+|+.++........+++..+...+..      .....++.+++.|--=|+++++...++..+. ..+|||
T Consensus       103 ~~pGi~V~~~~~e~ll~~l~~~~~ly~L~E~G~DI~------~v~~~~np~FIlGDH~g~t~e~~k~L~r~~~-~~ISlG  175 (197)
T COG1901         103 VTPGIYVRNGGFEALLAELAEGRSLYYLHEDGRDIS------EVDLIPNPVFILGDHIGLTEEDEKLLERHAA-KKISLG  175 (197)
T ss_pred             CCCCEEEECCCHHHHHHHHHCCCCEEEECCCCCCHH------HCCCCCCCEEEEECCCCCCHHHHHHHHHHHC-CEEEEC
T ss_conf             379879925789999999865584799925786475------5556899669961788989789999998648-536727


Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             87400448999999999
Q gi|254781160|r  221 PRILRSDTAAVAAMALV  237 (245)
Q Consensus       221 ~~ILR~ETA~i~als~~  237 (245)
                      |.-|-|+.+.+++-..+
T Consensus       176 P~~lha~hcit~~h~~L  192 (197)
T COG1901         176 PLSLHADHCITLLHNLL  192 (197)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             66888888999999877


No 9  
>TIGR02775 TrbG_Ti P-type conjugative transfer protein TrbG; InterPro: IPR014142   The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbG is a homologue of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin, IPR014126 from INTERPRO) as well as the vir system VirB9 protein , ..
Probab=84.92  E-value=2.3  Score=23.03  Aligned_cols=19  Identities=32%  Similarity=0.821  Sum_probs=15.0

Q ss_pred             CEEEEECCCCC-CCHHHHHH
Q ss_conf             35999888888-88899999
Q gi|254781160|r  189 NVAILIGPEGG-YHSEEKET  207 (245)
Q Consensus       189 ~i~i~IGPEGG-fs~~E~~~  207 (245)
                      ..+++|||+|| |++++-++
T Consensus       177 P~LfVv~~~GGlftdd~~~L  196 (220)
T TIGR02775       177 PPLFVVGPDGGLFTDDENEL  196 (220)
T ss_pred             CEEEEEECCCCEEECCCCCE
T ss_conf             70168826886456378636


No 10 
>pfam02590 SPOUT_MTase Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases.
Probab=83.56  E-value=2.9  Score=22.37  Aligned_cols=76  Identities=17%  Similarity=0.159  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCCCHHCCCCCHHH---HHCC--CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHH
Q ss_conf             333223332126300012110222---1003--67883599988888888899999995799558636887400448999
Q gi|254781160|r  157 KNWDHNCQIVFADETCGSENSLEK---LHAI--AHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAV  231 (245)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~--~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i  231 (245)
                      +..+.++.+++.|+.....++.+-   +...  ...+++.++||.--||++.=.+   .+.  ..+|||+-++--+-|.+
T Consensus        62 ~~i~~~~~~I~LDe~Gk~~sS~~fa~~i~~~~~~g~~~i~FiIGGa~G~~~~~~~---~a~--~~~Sls~mT~pH~larv  136 (155)
T pfam02590        62 AAIPPGSYVIALDERGKELSSEEFAKLLEDLRLKGKSDITFVIGGSDGLSEEVLK---RAN--EKLSLSKMTLPHQLVRL  136 (155)
T ss_pred             HHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHH---HHH--HEEECCCCCCCHHHHHH
T ss_conf             7379999899993799837879999999999833897559998379886989997---566--63441367650899999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254781160|r  232 AAMALV  237 (245)
Q Consensus       232 ~als~~  237 (245)
                      +++=++
T Consensus       137 ~l~EQi  142 (155)
T pfam02590       137 LLAEQI  142 (155)
T ss_pred             HHHHHH
T ss_conf             999999


No 11 
>pfam02598 DUF171 Uncharacterized ACR, COG2106.
Probab=80.99  E-value=2.1  Score=23.35  Aligned_cols=98  Identities=10%  Similarity=0.152  Sum_probs=53.6

Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCHHCCCCCH-HHHHCCCCCCCEEEEECCCCCCCHHHHH-----
Q ss_conf             75123443433200000011233322---33321263000121102-2210036788359998888888889999-----
Q gi|254781160|r  136 EQCDILTLPFIYPPTTLEFLLKNWDH---NCQIVFADETCGSENSL-EKLHAIAHIPNVAILIGPEGGYHSEEKE-----  206 (245)
Q Consensus       136 eQsgr~~lP~i~~~~~l~~~l~~~~~---~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~i~IGPEGGfs~~E~~-----  206 (245)
                      ...|-.|=-.+....+|.+++...+.   ++..+...+........ .......+.+.++++.|   ||.+.+..     
T Consensus       170 ~~~~~YwGY~Vr~a~sl~~v~~~~~~~~gYd~~I~tS~~G~~~~~~~~~~~~~~~~~~~lvVFG---~~~~~~~~~~~~~  246 (283)
T pfam02598       170 YGEGLYWGYKVRIASSLSDVFKKSPFPEGYDVTIGTSRRGKDISEAELEIKLMENFKHILLVFG---GWEPLKGSDEILK  246 (283)
T ss_pred             CCCCCCCCEEEEEECCHHHHHHCCCCCCCCCEEEEECCCCCCCCHHHHCCCCCCCCCCEEEEEC---CCHHHHHHHHHHC
T ss_conf             6678877757998368999962387678888699989999646310001145567784899979---9436510344411


Q ss_pred             ------HHHHC-CCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             ------99957-995586368874004489999999999
Q gi|254781160|r  207 ------TLHSL-PFVTPLSLGPRILRSDTAAVAAMALVQ  238 (245)
Q Consensus       207 ------~l~~~-~~~~~vsLG~~ILR~ETA~i~als~~~  238 (245)
                            .|... ++  +-+-|.+..|+|-|...+||+++
T Consensus       247 ~~~~~~~fD~~lN~--~P~Qgs~tIRtEEAv~itLa~Ln  283 (283)
T pfam02598       247 DQGPKELFDGYLNT--PPNQGSRTIRTEEAVLIALSILN  283 (283)
T ss_pred             CCCCHHHCCEEEEC--CCCCCCCCEEHHHHHHHHHHHCC
T ss_conf             35625437878976--89988761367889999886119


No 12 
>COG1756 Mra1 Uncharacterized conserved protein [Function unknown]
Probab=79.02  E-value=5.6  Score=20.50  Aligned_cols=83  Identities=17%  Similarity=0.205  Sum_probs=48.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEEC--CCCCCCHHHHHHHHHCCCCEEEECCCCCCCHH
Q ss_conf             0000112333223332126300012110222100367883599988--88888889999999579955863688740044
Q gi|254781160|r  150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIG--PEGGYHSEEKETLHSLPFVTPLSLGPRILRSD  227 (245)
Q Consensus       150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IG--PEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~E  227 (245)
                      .++.++++..+ ...++|++. .....+.+........  ++++||  |+|.|+.+-....      ..+|+|+-=|-+.
T Consensus       137 ~~l~d~l~~~~-~~~ill~e~-G~~~~p~~~~~~l~~~--i~v~iG~fp~Gdf~~~~~~~~------~~~si~~~pL~a~  206 (223)
T COG1756         137 NPLTDLLPENN-KVTILLHEK-GELIPPKELISLLLKG--IAVIIGGFPHGDFREETEFVA------EKYSIYDEPLSAW  206 (223)
T ss_pred             CCHHHHCCCCC-CEEEEECCC-CCCCCHHHHHHHHCCC--CEEEEECCCCCCCHHHHHHHH------HEEEECCCCCCHH
T ss_conf             73888506347-638998578-8826889998640248--559995167773024443110------1355158876499


Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             899999999999847
Q gi|254781160|r  228 TAAVAAMALVQAICG  242 (245)
Q Consensus       228 TA~i~als~~~~~~g  242 (245)
                      |++--.+......+|
T Consensus       207 ~v~~ki~~~~E~~~g  221 (223)
T COG1756         207 SVCSKIVYAYERALG  221 (223)
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             999999999999865


No 13 
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=78.29  E-value=3.3  Score=21.98  Aligned_cols=51  Identities=24%  Similarity=0.228  Sum_probs=35.2

Q ss_pred             EECHHH-HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC-CCCEEEEEEEE
Q ss_conf             987798-7599870357898889999779987987530235-55238997541
Q gi|254781160|r   23 KASGDQ-YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQS   73 (245)
Q Consensus        23 ~L~~~~-~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~-k~~~~~i~~~~   73 (245)
                      .|+.+. ..|=++-++++.||+|.|.-|+..--.+.|..++ ++..+.++...
T Consensus        31 ~LSkeLr~ky~~Rs~~IrkgD~V~V~rG~~kG~~GkV~~V~~k~~~V~VEgv~   83 (119)
T PRK01191         31 PLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRYRIYVEGVT   83 (119)
T ss_pred             CCCHHHHHHHCCCCCCEECCCEEEEEECCCCCCCCEEEEEECCCCEEEEEEEE
T ss_conf             47988999848874435469999995527789623189997368899994369


No 14 
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917   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 consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=75.68  E-value=1.4  Score=24.51  Aligned_cols=40  Identities=23%  Similarity=0.300  Sum_probs=32.7

Q ss_pred             CCEEEECCCCCCCCEEEECHHH-HHHHHHHCCCC---CCCEEEEEECC
Q ss_conf             8777408544788889987798-75998703578---98889999779
Q gi|254781160|r    7 LKRLFVDFPLCIKTQGKASGDQ-YHYLAHVLRMK---EGDNILLFNGK   50 (245)
Q Consensus         7 m~R~f~~~~l~~~~~i~L~~~~-~hHl~kVlRlk---~Gd~i~i~dg~   50 (245)
                      +||||-++    .+.|.|||.+ .||..+-||-+   +++.|.+||+.
T Consensus       408 lPRFy~p~----~G~IllDG~~l~d~~L~~LR~q~alVsQ~V~LFdDT  451 (603)
T TIGR02203       408 LPRFYEPD----SGQILLDGVDLQDYTLADLRRQVALVSQDVVLFDDT  451 (603)
T ss_pred             CCCCCCCC----CCCEEECCCHHHHCCHHHHHHHHHHHCCCEEECCCC
T ss_conf             23660458----885652784044302663562300021523720532


No 15 
>PRK00103 SPOUT methyltransferase superfamily protein; Provisional
Probab=74.90  E-value=6.4  Score=20.15  Aligned_cols=75  Identities=16%  Similarity=0.096  Sum_probs=46.4

Q ss_pred             CCCCCCCCCCCCCHHCCCCCHHH---HHCC-CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHH
Q ss_conf             33223332126300012110222---1003-6788359998888888889999999579955863688740044899999
Q gi|254781160|r  158 NWDHNCQIVFADETCGSENSLEK---LHAI-AHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAA  233 (245)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ETA~i~a  233 (245)
                      ..+..+.+++.|+.....++.+-   +... ...+.+.++||.--||+++=.+.   +.  ..+|||+-++--+-|-+++
T Consensus        63 ~~~~~~~~I~LDe~Gk~~sS~~fa~~l~~~~~~g~~i~FiIGGa~G~~~~~~~~---a~--~~lSlS~mTfpH~lar~il  137 (156)
T PRK00103         63 AIPKGARVVALDIRGKPWTSEQFAKELERWRLDGRDVTFVIGGPEGLSPAVKKR---AD--QSWSLSKLTLPHQLVRLVL  137 (156)
T ss_pred             HCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHH---HH--HEEEECCCCCCHHHHHHHH
T ss_conf             479999899991799805769999999999863996699997888769899974---32--2887136766289999999


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254781160|r  234 MALV  237 (245)
Q Consensus       234 ls~~  237 (245)
                      +=++
T Consensus       138 ~EQi  141 (156)
T PRK00103        138 AEQL  141 (156)
T ss_pred             HHHH
T ss_conf             9999


No 16 
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=74.61  E-value=0.26  Score=29.14  Aligned_cols=140  Identities=11%  Similarity=0.099  Sum_probs=74.5

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             13541344541156777544445665655554202201122122335788999975123443433200000011233322
Q gi|254781160|r   82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDH  161 (245)
Q Consensus        82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~  161 (245)
                      +-++=.+-.+..+-.|++-|.-.||+.|+ +..+++..-...      .++.|   +|-.+...+....++.++++.+..
T Consensus        97 il~LD~I~DP~NlGaIiRsA~afGv~~vi-l~~~~~~~~~~~------v~k~S---~Ga~~~~pi~~~~nl~~~l~~lk~  166 (244)
T PRK11181         97 LLILDGVTDPHNLGACLRSADAAGVHAVI-VPKDRSAQLTAT------AKKVA---CGAAETVPLIRVTNLARTMRMLQE  166 (244)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCEEE-ECCCCCCCCCHH------HHHHH---HCHHHCCCEEEECCHHHHHHHHHH
T ss_conf             99981887873899999999981998999-789977854258------88874---142321881695899999999886


Q ss_pred             CCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCCEEEECCCCCCCHHH-HHHHHHHHHHH
Q ss_conf             3332126300012110222100367883599988888-888899999995799558636887400448-99999999999
Q gi|254781160|r  162 NCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHSLPFVTPLSLGPRILRSDT-AAVAAMALVQA  239 (245)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~~~~~~vsLG~~ILR~ET-A~i~als~~~~  239 (245)
                      ....++..+... .   ..+.+.....++.+++|-|| |.++.=   .+.+...-.+-+...+   |. -+-+|.+++.|
T Consensus       167 ~g~~i~g~~~~~-~---~~~~~~~~~~~~alvlGsE~~Gl~~~~---~~~~d~~v~Ip~~g~~---~SLNVsvAa~I~ly  236 (244)
T PRK11181        167 KNVWIVGTAGEA-D---HTLYQSKLTGPLALVMGAEGEGMRRLT---REHCDELISIPMAGSV---SSLNVSVATGICLF  236 (244)
T ss_pred             CCEEEEEECCCC-C---CCCCHHCCCCCEEEEECCCCCCCCHHH---HHHCCEEEEECCCCCC---CCHHHHHHHHHHHH
T ss_conf             596999524666-7---664101057876999877766658999---9759989980799998---55879999999999


Q ss_pred             HH
Q ss_conf             84
Q gi|254781160|r  240 IC  241 (245)
Q Consensus       240 ~~  241 (245)
                      .+
T Consensus       237 E~  238 (244)
T PRK11181        237 EA  238 (244)
T ss_pred             HH
T ss_conf             99


No 17 
>PRK10864 putative methyltransferase; Provisional
Probab=74.09  E-value=7.6  Score=19.64  Aligned_cols=141  Identities=9%  Similarity=0.063  Sum_probs=74.4

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             43135413445411567775444456656555542022011221223357889999751234434332000000112333
Q gi|254781160|r   80 SDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNW  159 (245)
Q Consensus        80 ~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~  159 (245)
                      +.+-++=.+-.+..+--||+-|.-.||+.|+.  .+++...   ..   ..++.|+  .+-.++|-+ ...++..+++.+
T Consensus       200 ~~lL~LDgV~DP~NlGAIiRSAaafGv~gVIl--~~~~~~~---s~---~avr~Sa--Ga~e~vpv~-~v~nl~~aL~~L  268 (348)
T PRK10864        200 DCVLALEDVGNPHNLGGIMRSCAHFGVKGVVV--QDAALLE---SG---AAIRTAE--GGAEHVQPI-TGDSIVDVLDDF  268 (348)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHCCCEEEE--CCCCCCC---CH---HHHHHHC--CHHCCCCEE-EECCHHHHHHHH
T ss_conf             85999789779715889999999858988997--9998774---37---8896633--222006359-977899999999


Q ss_pred             CCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCCEEEECCCCCCCHHH-HHHHHHHHH
Q ss_conf             223332126300012110222100367883599988888-888899999995799558636887400448-999999999
Q gi|254781160|r  160 DHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHSLPFVTPLSLGPRILRSDT-AAVAAMALV  237 (245)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~~~~~~vsLG~~ILR~ET-A~i~als~~  237 (245)
                      ......++.-.....    ..+......+++.|++|.|| |.|+.-.+.   +.+...+.+-..   +|. =+-+|.+++
T Consensus       269 k~aG~~Ivg~s~~~~----~~l~~~~l~~~~vLVlGsEg~GLs~~v~~~---cD~~V~IPm~g~---veSLNVSVAagIl  338 (348)
T PRK10864        269 RQAGYTIVTTSSHKG----KPLFKAELPAKMVLVLGQEYDGLSDAARSP---GDLSVKIDGTGN---VESLNVSVATGVL  338 (348)
T ss_pred             HHCCCEEEEECCCCC----CCHHHCCCCCCEEEEECCCCCCCCHHHHHH---CCEEEECCCCCC---CCCHHHHHHHHHH
T ss_conf             988968998547788----647563678988999899885506999975---888998279999---8578899999999


Q ss_pred             HHHH
Q ss_conf             9984
Q gi|254781160|r  238 QAIC  241 (245)
Q Consensus       238 ~~~~  241 (245)
                      .|.+
T Consensus       339 LyE~  342 (348)
T PRK10864        339 LAEW  342 (348)
T ss_pred             HHHH
T ss_conf             9999


No 18 
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=73.92  E-value=2.8  Score=22.45  Aligned_cols=118  Identities=14%  Similarity=0.184  Sum_probs=64.6

Q ss_pred             CCCCCEEEEC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             5443135413-445411567775444456656555542022011221223357889999751234434332000000112
Q gi|254781160|r   78 KQSDVQYIFS-PIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL  156 (245)
Q Consensus        78 ~~~~i~l~~~-~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l  156 (245)
                      +.+.++|+.- +-|+..+--|++-|--.||+.++.+......+.      ..+     +-+.-..|+|. ....++.+.+
T Consensus        16 Rq~dL~vvLD~V~dP~NlGAIiRTadA~Gv~~V~~v~~~~~~~~------~~~-----ta~Gs~~wv~v-~~~~~i~~~i   83 (229)
T PRK11081         16 RQPDLTVCLEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRMRT------MGS-----TAAGSNSWVQV-KTHRTIGDAV   83 (229)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCHHH------HHH-----HHHHHHCEEEE-EEECCHHHHH
T ss_conf             58986999768899850999999999838974689678752011------114-----43034400455-7847899999


Q ss_pred             CCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHH
Q ss_conf             333223332126300012110222100367883599988888-888899999995
Q gi|254781160|r  157 KNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHS  210 (245)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~  210 (245)
                      ..+.....-++..+..  ..+.. +.+..-.++.+|++|.|+ |.|++=.+....
T Consensus        84 ~~Lk~~G~~I~at~l~--~~avd-~~~~d~t~ptalVlGnE~~GiS~~~~~~aD~  135 (229)
T PRK11081         84 AHLKAQGMQILATHLS--DKAVD-FREIDYTRPTAILMGQEKTGISQEALALADQ  135 (229)
T ss_pred             HHHHHCCCEEEEEECC--CCCCC-HHHHCCCCCEEEEECCCCCCCCHHHHHHCCC
T ss_conf             9999749989999368--88640-7670456876999858777759999982895


No 19 
>KOG3079 consensus
Probab=73.36  E-value=4.3  Score=21.28  Aligned_cols=79  Identities=8%  Similarity=0.088  Sum_probs=40.1

Q ss_pred             CCCCCEEEECCC---CCCHHHHHHHHH--HHHHHHHHHHHHHHC--CCHH-----HH------HHHHHHHHHHHHHHHHC
Q ss_conf             544313541344---541156777544--445665655554202--2011-----22------12233578899997512
Q gi|254781160|r   78 KQSDVQYIFSPI---KTNRLDYMIQKS--VEMGMGAIRPVITRY--TQNT-----HY------NMDRVRTYTISAAEQCD  139 (245)
Q Consensus        78 ~~~~i~l~~~~~---k~~~~~~ilqk~--tELGV~~I~p~~~~r--s~~~-----~~------k~eR~~~ii~eA~eQsg  139 (245)
                      ..++|..+++-|   |+..++.|++|-  |-|.+..+---..++  |+.-     ..      -.+=....+.+|+.||+
T Consensus         6 ~~~~IifVlGGPGsgKgTqC~kiv~ky~ftHlSaGdLLR~E~~~~gse~g~~I~~~i~~G~iVP~ei~~~LL~~am~~~~   85 (195)
T KOG3079           6 DKPPIIFVLGGPGSGKGTQCEKIVEKYGFTHLSAGDLLRAEIASAGSERGALIKEIIKNGDLVPVEITLSLLEEAMRSSG   85 (195)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHCCCEEECHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             57988999768988822699999997695463287999998805467678999999986996748999999999999657


Q ss_pred             C-CCCCCCCCCCCCCCCC
Q ss_conf             3-4434332000000112
Q gi|254781160|r  140 I-LTLPFIYPPTTLEFLL  156 (245)
Q Consensus       140 r-~~lP~i~~~~~l~~~l  156 (245)
                      . .++-.=-.|.+.+++.
T Consensus        86 ~~~~fLIDGyPR~~~q~~  103 (195)
T KOG3079          86 DSNGFLIDGYPRNVDQLV  103 (195)
T ss_pred             CCCEEEECCCCCCHHHHH
T ss_conf             788388658988768899


No 20 
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=67.49  E-value=9.3  Score=19.08  Aligned_cols=69  Identities=10%  Similarity=0.024  Sum_probs=42.6

Q ss_pred             CCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCC
Q ss_conf             888899877987599870357898889999779987987530235552389975413555544313541344
Q gi|254781160|r   18 IKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPI   89 (245)
Q Consensus        18 ~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~   89 (245)
                      .+..+.|-|....|..+.-+++.||.|.+.+. ++.|..+|.+..-  .-.-......+.+...++|+=|.|
T Consensus        42 ~~GN~viaGH~~~~F~~L~~l~~GD~I~l~~~-~~~y~Y~V~~~~v--v~p~d~~~~~~~~~~~LTLiTC~P  110 (127)
T cd05828          42 EGGNIVIAGHRDTHFRFLGELEPGDIITLQTL-GGTYTYRVTSTRI--VDADDTSVLAPSDDPTLTLITCYP  110 (127)
T ss_pred             CCCCEEEEEECCCCCCCHHHCCCCCEEEEEEC-CEEEEEEEEEEEE--ECCCCCEECCCCCCCEEEEECCCC
T ss_conf             88869999506887767455747999999978-8399999977999--998771872579998799993688


No 21 
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=65.13  E-value=6.9  Score=19.90  Aligned_cols=52  Identities=12%  Similarity=0.151  Sum_probs=33.9

Q ss_pred             EECHHH-HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC-CCCEEEEEEEEC
Q ss_conf             987798-7599870357898889999779987987530235-552389975413
Q gi|254781160|r   23 KASGDQ-YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQSR   74 (245)
Q Consensus        23 ~L~~~~-~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~-k~~~~~i~~~~~   74 (245)
                      .|+.+. ..|=++-++++.||+|.|.-|.-.--.++|+.++ ++..+.++....
T Consensus        31 ~LSkELr~ky~~Rs~pIRkgDeV~V~RG~fkG~eGKV~~V~~kk~~I~VEgvt~   84 (143)
T PTZ00194         31 PLSKELRAKYNVRAMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHIDKVNR   84 (143)
T ss_pred             CCCHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEEEEEEEEEEEE
T ss_conf             269999998496310011599999985553687765999995000999951789


No 22 
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=61.92  E-value=3.6  Score=21.77  Aligned_cols=100  Identities=17%  Similarity=0.139  Sum_probs=51.2

Q ss_pred             HHHHHHHCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHH
Q ss_conf             9999751234434332--------00000011233322333212630001211022210036788359998888888889
Q gi|254781160|r  132 ISAAEQCDILTLPFIY--------PPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSE  203 (245)
Q Consensus       132 ~eA~eQsgr~~lP~i~--------~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~  203 (245)
                      ..++-|||-+...++.        ....++++++..+.+..++.. .....+..++....+.. .-..++-|-|+||+..
T Consensus        37 ~g~AAQsGIp~~~kla~k~G~~vlvf~dL~DAlevL~P~v~ll~~-~~~~~ek~~dp~e~ie~-~vliVf~ga~~gl~k~  114 (147)
T COG4080          37 KGSAAQSGIPEVLKLAFKLGKPVLVFPDLDDALEVLRPDVTLLVG-SASEGEKKLDPNEKIEG-RVLIVFSGAEPGLTKR  114 (147)
T ss_pred             CCHHHHHCCHHHHHHHHHHCCCEEEEHHHHHHHHHCCCCEEEEEC-CCCCCCCCCCCCCCCCC-EEEEEEECCCCCCCHH
T ss_conf             547666356889999998399479852277899745975699814-76443234794312463-3799992688775866


Q ss_pred             HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             999999579955863688740044899999999999847
Q gi|254781160|r  204 EKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAICG  242 (245)
Q Consensus       204 E~~~l~~~~~~~~vsLG~~ILR~ETA~i~als~~~~~~g  242 (245)
                      |.+.    |-..  +   -+-..+--++.+++++-|.++
T Consensus       115 El~l----g~~~--~---y~ve~~VG~~g~lAi~Lyell  144 (147)
T COG4080         115 ELEL----GADL--R---YIVEADVGELGALAIFLYELL  144 (147)
T ss_pred             HCCC----CCCE--E---EEEECCCHHHHHHHHHHHHHH
T ss_conf             6056----7727--9---998446417888999999987


No 23 
>CHL00194 ycf39 Ycf39; Provisional
Probab=61.88  E-value=12  Score=18.36  Aligned_cols=112  Identities=13%  Similarity=0.121  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCC
Q ss_conf             777544445665655554202201-12212233578899997512344343320000001123332----2333212630
Q gi|254781160|r   96 YMIQKSVEMGMGAIRPVITRYTQN-THYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWD----HNCQIVFADE  170 (245)
Q Consensus        96 ~ilqk~tELGV~~I~p~~~~rs~~-~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~----~~~~~~~~~~  170 (245)
                      .+++-|-+-||.+++.+..-.... .....-+++.-.....++||-+|. .+.+..-+..++.++.    ....++....
T Consensus        92 ~li~AAk~aGVkr~V~lS~lga~~~~~~p~~~~K~~~E~~L~~Sgl~~T-IlRPs~F~q~l~~~~a~pi~~~~~v~~~~~  170 (319)
T CHL00194         92 ALIEAAKAAKVKRFIFFSILNAEQYPQVPLMKIKSDIEEKLKQSGINYT-IFRLAGFFQGLISQYAIPILDSQTIWITGE  170 (319)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHHHHHHCCCCEEECCC
T ss_conf             9999999849988999613566668875677879999999986799859-984739999889987677630785776699


Q ss_pred             H---------HCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHH
Q ss_conf             0---------01211022210036788359998888888889999999
Q gi|254781160|r  171 T---------CGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLH  209 (245)
Q Consensus       171 ~---------~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~~l~  209 (245)
                      .         .-+......+........+.-+.||| -||.+|+-.+-
T Consensus       171 ~~~ia~I~~~DVA~~~a~aL~~~~~~gk~y~L~GP~-a~T~~EIa~l~  217 (319)
T CHL00194        171 STPIAYIDTQDAAKFALKSLSLPETKNKTFPLVGPK-SWNSSEIISLC  217 (319)
T ss_pred             CCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCC-CCCHHHHHHHH
T ss_conf             875288779999999999958977589899954986-38999999999


No 24 
>pfam09895 DUF2122 RecB-family nuclease (DUF2122). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=60.34  E-value=11  Score=18.66  Aligned_cols=77  Identities=17%  Similarity=0.225  Sum_probs=43.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCC-EEEEECCCCCCCHHHHHHHHHCCC-CEEEECCCCCCCHH
Q ss_conf             0000112333223332126300012110222100367883-599988888888899999995799-55863688740044
Q gi|254781160|r  150 TTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPN-VAILIGPEGGYHSEEKETLHSLPF-VTPLSLGPRILRSD  227 (245)
Q Consensus       150 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-i~i~IGPEGGfs~~E~~~l~~~~~-~~~vsLG~~ILR~E  227 (245)
                      ..++++++.+..+..+++.........  +   ..+...+ ..++-|-|.|||..|.+.    |- +....     +..+
T Consensus        26 ~dl~DAiEvL~P~~v~~i~~~~~~~~~--~---~l~~~~rvllvf~G~e~gfsk~El~~----g~~v~~~~-----v~~~   91 (105)
T pfam09895        26 PDLKDAIELLKPDVVYLLSRAAEGIKK--E---VLKVEGRVLLVFSGAEPGFSKIELEL----GEAVYIKG-----VESD   91 (105)
T ss_pred             CCHHHHHHHHCCCEEEEECCCCCCCCH--H---HHHCCCCEEEEECCCCCCCCHHHHCC----CCEEEEEC-----CCCC
T ss_conf             877889987298779997576656203--4---55305838999818988979656148----84478603-----6556


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             8999999999998
Q gi|254781160|r  228 TAAVAAMALVQAI  240 (245)
Q Consensus       228 TA~i~als~~~~~  240 (245)
                      .-++..++++-|.
T Consensus        92 iG~ig~~Ai~Ly~  104 (105)
T pfam09895        92 VGPIGALAIILYL  104 (105)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             6628899999950


No 25 
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is 
Probab=57.97  E-value=16  Score=17.60  Aligned_cols=69  Identities=9%  Similarity=0.098  Sum_probs=41.2

Q ss_pred             CCCEEEECHHH----HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCC
Q ss_conf             88889987798----7599870357898889999779987987530235---5523899754135555443135413445
Q gi|254781160|r   18 IKTQGKASGDQ----YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIK   90 (245)
Q Consensus        18 ~~~~i~L~~~~----~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k   90 (245)
                      .+....|.+..    ..|..+.-+++.||+|.+.+. ++.|..+|.+..   .+ ...   .......+..++|+=|.|.
T Consensus        43 ~g~n~viaGH~~~~~~~~F~~L~~l~~GD~I~l~~~-~~~y~Y~V~~~~iV~p~-d~~---~l~~~~~~~~LTLiTC~p~  117 (131)
T cd05827          43 KGTHSVITGHRGLPNAKLFTDLDKLKKGDKFYIHVL-GETLAYQVDQIEVVLPD-DTD---KLKIVPGKDLVTLLTCTPY  117 (131)
T ss_pred             CCCEEEEECCCCCCCCCCCCHHHCCCCCCEEEEEEC-CEEEEEEEEEEEEECCC-CCE---EEEECCCCCEEEEEEECCC
T ss_conf             767899980799999951010343878999999979-90999999889999976-225---8601599878999977799


Q ss_pred             C
Q ss_conf             4
Q gi|254781160|r   91 T   91 (245)
Q Consensus        91 ~   91 (245)
                      +
T Consensus       118 ~  118 (131)
T cd05827         118 G  118 (131)
T ss_pred             C
T ss_conf             9


No 26 
>PRK11572 copper homeostasis protein CutC; Provisional
Probab=57.09  E-value=8.3  Score=19.40  Aligned_cols=131  Identities=13%  Similarity=0.098  Sum_probs=63.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH---HCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             41156777544445665655554202201122122335788999975---123443433200000011233322333212
Q gi|254781160|r   91 TNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQ---CDILTLPFIYPPTTLEFLLKNWDHNCQIVF  167 (245)
Q Consensus        91 ~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQ---sgr~~lP~i~~~~~l~~~l~~~~~~~~~~~  167 (245)
                      -+.|..=++.+-++|++.|.+-.-.  ..-..+.++.++++..|--.   -+|.+=-.-++...++++++.  ..+.++-
T Consensus        72 ~~~M~~dI~~~~~~Ga~GvV~G~L~--~dg~iD~~~~~~Li~~a~~l~vTFHRAfD~~~dp~~ale~Li~l--G~~rILT  147 (248)
T PRK11572         72 FAAMLEDIRTVRELGFPGLVTGVLD--VDGHVDMPRMEKIMAAAGPLAVTFHRAFDMCANPLNALKNLAEL--GVARILT  147 (248)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEEC--CCCCCCHHHHHHHHHHHCCCEEEEECHHHCCCCHHHHHHHHHHC--CCCEEEC
T ss_conf             9999999999998699967996688--99984999999999974898079862022149999999999975--9998988


Q ss_pred             CCCHHCCCCCHHHHHCCCC-CCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHH
Q ss_conf             6300012110222100367-883599988888888899999995799558636887400448
Q gi|254781160|r  168 ADETCGSENSLEKLHAIAH-IPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDT  228 (245)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~-~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ET  228 (245)
                      .-........++.+..... .... + |=|-||.+++-+..|.+.|+ +.+++..+.-|..+
T Consensus       148 SG~~~~A~~G~~~L~~L~~~a~~~-i-Im~GgGV~~~Ni~~~~~tG~-~eiH~Sak~~~~s~  206 (248)
T PRK11572        148 SGQQSDAEQGLSLIMELIAQGDAP-I-IMAGAGVRAENLQKFLDAGV-REVHSSAGAWQPSP  206 (248)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCC-E-EEECCCCCHHHHHHHHHCCC-CEEEECCCCCCCCC
T ss_conf             999787778899999999844996-8-98789989999999997597-78973578644787


No 27 
>TIGR00513 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; InterPro: IPR001095 This entry contains the alpha subunit the acetyl coenzyme A carboxylase complex (). It catalyzes the first step in the synthesis of long-chain fatty acids which involves the carboxylation of acetyl-CoA to malonyl-CoA. The acetyl-CoA carboxylase complex () is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps:  Biotin carrier protein + ATP + HCO_3^- -> Carboxybiotin carrier protein + ADP + P_i   Carboxybiotin carrier protein + Acetyl-CoA -> Malonyl-CoA + Biotin carrier protein ; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=56.67  E-value=13  Score=18.07  Aligned_cols=109  Identities=23%  Similarity=0.356  Sum_probs=58.0

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHH-----------------HHHHHH--HHHH---HCCCHHHHH---------HHHHHH
Q ss_conf             313541344541156777544445-----------------665655--5542---022011221---------223357
Q gi|254781160|r   81 DVQYIFSPIKTNRLDYMIQKSVEM-----------------GMGAIR--PVIT---RYTQNTHYN---------MDRVRT  129 (245)
Q Consensus        81 ~i~l~~~~~k~~~~~~ilqk~tEL-----------------GV~~I~--p~~~---~rs~~~~~k---------~eR~~~  129 (245)
                      .+.|+=-+-||..||+|=--.+|-                 ||.+|-  |+.-   ++....+-|         .+-+|+
T Consensus        68 ~~qlARhP~RP~tLDYI~~i~~df~E~~GDRay~DD~AiVGG~Arldg~PV~viGhqKGr~tKek~~RNFGMP~P~GYRK  147 (329)
T TIGR00513        68 RLQLARHPDRPYTLDYIELIFDDFFELHGDRAYADDKAIVGGVARLDGRPVVVIGHQKGRDTKEKLLRNFGMPAPEGYRK  147 (329)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCHHHCCCCCCCCCCCCHHH
T ss_conf             99973088889768899998612200036778897822343211337812488621357540342112579887960479


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCC--CCCCCEEEEECCCCC
Q ss_conf             8899997512344343320000001123332233321263000121102221003--678835999888888
Q gi|254781160|r  130 YTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAI--AHIPNVAILIGPEGG  199 (245)
Q Consensus       130 ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~i~IGPEGG  199 (245)
                       +.-=++|+.|.-+|.|.+..|=    -.++.    +=+++..-++.-..++...  -..+.|+++|| |||
T Consensus       148 -ALrLm~~AerF~~PIi~fiDT~----GAYPG----igAEerGQsEAIA~NL~Ema~L~VPvic~vIG-EGG  209 (329)
T TIGR00513       148 -ALRLMKMAERFNLPIITFIDTP----GAYPG----IGAEERGQSEAIAKNLREMARLKVPVICTVIG-EGG  209 (329)
T ss_pred             -HHHHHHHHHHCCCCEEEEECCC----CCCCC----CHHHHHCCHHHHHHHHHHHHCCCCCEEEEEEC-CCC
T ss_conf             -9999987776179858865388----88756----20445052789999989971099887999852-686


No 28 
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=56.03  E-value=12  Score=18.30  Aligned_cols=68  Identities=16%  Similarity=0.196  Sum_probs=40.1

Q ss_pred             CEEEECHHHHHH----HHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCCCC
Q ss_conf             889987798759----9870357898889999779987987530235---552389975413555544313541344541
Q gi|254781160|r   20 TQGKASGDQYHY----LAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIKTN   92 (245)
Q Consensus        20 ~~i~L~~~~~hH----l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~   92 (245)
                      ..+.|.|....|    ..+.-++++||.|.+.+.. +.|..+|.+..   .+ ...+   .......+.++|+=|.|.+.
T Consensus        42 gN~viaGH~~~~~~~~F~~L~~l~~GD~I~v~~~~-~~~~Y~V~~~~iV~p~-d~~~---l~~~~~~~~lTLiTC~P~~~  116 (127)
T cd06165          42 GNYALAGHNMRNKGVLFSPLYKVKVGDKIYLTDKD-NVYEYKVTSKKIVDPT-RVDV---IDDVPGKKLITLITCDDATD  116 (127)
T ss_pred             CCEEEEECCCCCCCCCCCCHHHCCCCCEEEEEECC-CEEEEEEEEEEEECCC-CCEE---ECCCCCCCEEEEEEECCCCC
T ss_conf             86999936588676546676568999999999899-3999999489999988-7779---63169987899996589999


No 29 
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=55.78  E-value=17  Score=17.36  Aligned_cols=74  Identities=11%  Similarity=0.073  Sum_probs=43.7

Q ss_pred             CCCEEEECHHHHHH---HHHHCCCCCCCEEEEEECCCCEEEEEEECC---CCCCEEEEE---EEECCCCCCCCCEEEECC
Q ss_conf             88889987798759---987035789888999977998798753023---555238997---541355554431354134
Q gi|254781160|r   18 IKTQGKASGDQYHY---LAHVLRMKEGDNILLFNGKDGEWLSKISYV---GKSIRFKVE---YQSRSQTKQSDVQYIFSP   88 (245)
Q Consensus        18 ~~~~i~L~~~~~hH---l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~---~k~~~~~i~---~~~~~~~~~~~i~l~~~~   88 (245)
                      .+..+.|.|....|   ..+--++++||.|.+.++. +.|..+|+..   +..-.-.+.   ...........++|+=|.
T Consensus        43 ~~Gn~viaGHr~~~~~~F~~L~~l~~GD~I~v~~~~-~~~~Y~V~~~~iV~p~d~~vl~p~~~~~~~~~~~~~lTLiTC~  121 (137)
T cd05830          43 EVGNFAVAGHRTTYGAPFNDLDKLRPGDKIVVETAD-GWYTYVVRSSEIVLPTDVEVIAPVPGQPGAEPTDRYLTLTTCH  121 (137)
T ss_pred             CCCEEEEEECCCCCCCCCCCHHCCCCCCEEEEEECC-EEEEEEEEEEEEECCCCCEEECCCCCCCCCCCCCCEEEEEEEC
T ss_conf             997199997228977556013538999999999999-8999999749998976366873367745658998889999257


Q ss_pred             CCCC
Q ss_conf             4541
Q gi|254781160|r   89 IKTN   92 (245)
Q Consensus        89 ~k~~   92 (245)
                      |.+.
T Consensus       122 P~~~  125 (137)
T cd05830         122 PKFS  125 (137)
T ss_pred             CCCC
T ss_conf             9999


No 30 
>TIGR01080 rplX_A_E ribosomal protein L24; InterPro: IPR005756   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   Ribosomal protein L24 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. This entry represents the archaeal and eukaryotic branch of these proteins, known as the L26 family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=52.94  E-value=19  Score=17.07  Aligned_cols=70  Identities=20%  Similarity=0.293  Sum_probs=46.0

Q ss_pred             CCCEEEECCCCCCCC---EEEECHHH-HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC-CCCEEEEEEEECC
Q ss_conf             787774085447888---89987798-7599870357898889999779987987530235-5523899754135
Q gi|254781160|r    6 HLKRLFVDFPLCIKT---QGKASGDQ-YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQSRS   75 (245)
Q Consensus         6 ~m~R~f~~~~l~~~~---~i~L~~~~-~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~-k~~~~~i~~~~~~   75 (245)
                      +-+++++..|+..-.   +-.|+.+. ..|=.+.|+++.||.|.|.=|+=.-.+|+|..++ +...+.++..+..
T Consensus         6 K~Rk~~f~Apl~~Rr~lmsA~LSkeLr~~y~~r~lP~RkgD~V~i~RG~fkG~EGkv~~Vd~kr~~i~ve~~t~~   80 (116)
T TIGR01080         6 KQRKALFTAPLHVRRKLMSAPLSKELREKYGVRALPVRKGDKVRIVRGDFKGHEGKVLEVDLKRYRIYVEGVTKE   80 (116)
T ss_pred             CCCCEEEECCHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCC
T ss_conf             325135607722303222230246889872865376123987899746625875516887303888988131010


No 31 
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   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).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=50.68  E-value=9.2  Score=19.10  Aligned_cols=17  Identities=18%  Similarity=0.413  Sum_probs=7.6

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             41156777544445665
Q gi|254781160|r   91 TNRLDYMIQKSVEMGMG  107 (245)
Q Consensus        91 ~~~~~~ilqk~tELGV~  107 (245)
                      ..|+-.-+|++=++|-.
T Consensus       215 ~~RL~eSvEtaL~~~~G  231 (956)
T TIGR00630       215 RSRLAESVETALRLSEG  231 (956)
T ss_pred             CCHHHHHHHHHHHCCCC
T ss_conf             21168999999850587


No 32 
>PTZ00066 pyruvate kinase; Provisional
Probab=49.83  E-value=21  Score=16.76  Aligned_cols=72  Identities=18%  Similarity=0.187  Sum_probs=37.1

Q ss_pred             CCCCCCCEEEEEECCCCEEEEEEECCCCC-CEEEEEEE--ECC--CCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             35789888999977998798753023555-23899754--135--55544313541344541156777544445665655
Q gi|254781160|r   36 LRMKEGDNILLFNGKDGEWLSKISYVGKS-IRFKVEYQ--SRS--QTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIR  110 (245)
Q Consensus        36 lRlk~Gd~i~i~dg~g~~~~~~I~~~~k~-~~~~i~~~--~~~--~~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~  110 (245)
                      --+++||.|.+-||   ....+|.+++.+ +.+++..-  ...  .-.-|...+-++.+-..-.+.+++-+.+.||+-|.
T Consensus       152 ~~v~~Gd~IlidDG---~I~l~V~~v~~~~v~~~V~~gG~L~s~KgVnlP~~~l~lp~lTekD~~dil~fa~~~~vD~Ia  228 (513)
T PTZ00066        152 QSVKVGNIILIADG---SLSCEVLEVHDDHIVVKVLNSATIGERKNMNLPGVKVELPVIGEKDKNDILNFAIPMNCDFIA  228 (513)
T ss_pred             HHCCCCCEEEEECC---EEEEEEEEECCCEEEEEEEECCEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf             56788988999799---799999982297799999748397478643358986675547636889999999875999999


No 33 
>PRK04980 hypothetical protein; Provisional
Probab=49.80  E-value=19  Score=17.09  Aligned_cols=45  Identities=18%  Similarity=0.214  Sum_probs=34.9

Q ss_pred             EECCCCCCCCEEEE-CHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf             40854478888998-77987599870357898889999779987987530235
Q gi|254781160|r   11 FVDFPLCIKTQGKA-SGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG   62 (245)
Q Consensus        11 f~~~~l~~~~~i~L-~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~   62 (245)
                      |-+..++...+|.+ |.+|+|+       ++|+.+.++.-..+.|.|.|...+
T Consensus        11 fe~dIlsG~KTITIRD~SEsh~-------~~G~~l~V~t~E~~~~fc~IeIls   56 (102)
T PRK04980         11 FEADILAGRKTITIRDESESHF-------KPGDVLRVGTFEDDRYFCTIEVLS   56 (102)
T ss_pred             HHHHHHCCCCEEEECCCCCCCC-------CCCCEEEEEECCCCCEEEEEEEEE
T ss_conf             1678865984699525310456-------799889989835897899999999


No 34 
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=48.29  E-value=14  Score=17.92  Aligned_cols=68  Identities=15%  Similarity=0.171  Sum_probs=41.4

Q ss_pred             CCEEEECHHHH----HHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCCC
Q ss_conf             88899877987----599870357898889999779987987530235---55238997541355554431354134454
Q gi|254781160|r   19 KTQGKASGDQY----HYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIKT   91 (245)
Q Consensus        19 ~~~i~L~~~~~----hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k~   91 (245)
                      +..+.|.+...    .|..+.-++++||.|.+.++ ++.|..+|.+..   ..-.    .....+...+.++|+=|.+.+
T Consensus        42 ~gN~vIaGH~~~~~~~~F~~L~~l~~GD~i~i~~~-~~~y~Y~V~~~~iv~p~d~----~~~~~~~~~~~LTLiTC~p~~  116 (128)
T cd00004          42 NGNTVIAGHRGGDSGTVFSDLDNLKKGDKIYLTDG-GKTYVYKVTSILTVTPTDV----VVVNPPTGDPILTLITCTPPG  116 (128)
T ss_pred             CCCEEEEEEECCCCCCCCCCHHHCCCCCEEEEEEC-CEEEEEEEEEEEEECCCCC----EEECCCCCCCEEEEEEECCCC
T ss_conf             96099999818998844365545768998999999-9899999988999898864----781146998679999878999


No 35 
>TIGR02851 spore_V_T stage V sporulation protein T; InterPro: IPR014213   Members of this protein entry include the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB..
Probab=48.03  E-value=10  Score=18.77  Aligned_cols=28  Identities=32%  Similarity=0.512  Sum_probs=19.5

Q ss_pred             HHHHCCCCCCCEEEEEE-CCCCEEEEEEE
Q ss_conf             98703578988899997-79987987530
Q gi|254781160|r   32 LAHVLRMKEGDNILLFN-GKDGEWLSKIS   59 (245)
Q Consensus        32 l~kVlRlk~Gd~i~i~d-g~g~~~~~~I~   59 (245)
                      +.|.||+++||-+.+|. -+|...+=+.+
T Consensus        21 IRRTLRIrEGDPLEIF~Dr~GevILKKYS   49 (184)
T TIGR02851        21 IRRTLRIREGDPLEIFVDREGEVILKKYS   49 (184)
T ss_pred             CCCCCCCCCCCCCEEEEECCCCEEEEECC
T ss_conf             41101012599714888078978987107


No 36 
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation.  Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=47.56  E-value=23  Score=16.53  Aligned_cols=66  Identities=14%  Similarity=0.105  Sum_probs=40.3

Q ss_pred             HHHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHHH
Q ss_conf             987035789888999977998798753023555238997541355554431354134454115677
Q gi|254781160|r   32 LAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYM   97 (245)
Q Consensus        32 l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~i   97 (245)
                      |++-|+--.|+.|.|=--+|..|.+.+.+++....+.............+..+-...+|+....++
T Consensus         2 LV~fL~~l~g~~VtVELKng~~~~G~L~~vd~~MN~~L~~v~~t~~~~~~~~l~~~~IRGs~IRyi   67 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYF   67 (90)
T ss_pred             HHHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEEEEECCCCCEEECCEEEECCCCEEEE
T ss_conf             769787668987999987997999999881378201898899977999877877499957738999


No 37 
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=46.53  E-value=24  Score=16.43  Aligned_cols=68  Identities=13%  Similarity=0.191  Sum_probs=40.2

Q ss_pred             CCEEEECHHH----HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCCC
Q ss_conf             8889987798----7599870357898889999779987987530235---55238997541355554431354134454
Q gi|254781160|r   19 KTQGKASGDQ----YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIKT   91 (245)
Q Consensus        19 ~~~i~L~~~~----~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k~   91 (245)
                      +..+.|.|..    ..|..+.-+++.||+|.+.++ ++.|..+|.+..   .. ...+   .........++|+=|.|.+
T Consensus        42 ~gN~viaGH~~~~~~~~F~~L~~l~~GD~I~l~~~-~~~y~Y~V~~~~iV~p~-d~~~---l~~~~~~~~LTL~TC~p~~  116 (126)
T cd06166          42 NGNFAIAGHRSYTYGRIFNRLDEVEKGDEIKVTTK-NGTYKYKITSIFVVEPT-DTDV---LNQDKSKKEITLITCTPDG  116 (126)
T ss_pred             CCCEEEEEEECCCCCCCCCCHHHCCCCCEEEEEEC-CEEEEEEEEEEEEECCC-CCEE---ECCCCCCCEEEEEEECCCC
T ss_conf             96299997508887855200551858999999999-98999999779999976-5568---1347998889999747999


No 38 
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation.  Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=46.39  E-value=24  Score=16.42  Aligned_cols=65  Identities=9%  Similarity=0.100  Sum_probs=40.6

Q ss_pred             HHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHHH
Q ss_conf             87035789888999977998798753023555238997541355554431354134454115677
Q gi|254781160|r   33 AHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYM   97 (245)
Q Consensus        33 ~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~i   97 (245)
                      .++|+-..|..|.+=--+|..|.+.+..++.+..+.+..............+-...+|+....++
T Consensus         2 l~lL~~a~g~~VtVELKnG~~y~G~L~~~d~~MN~~L~~v~~t~~~g~~~~l~~v~IRGs~Ir~i   66 (70)
T cd01721           2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFF   66 (70)
T ss_pred             HHHHHHCCCCEEEEEECCCEEEEEEEEEEECCCCCEEEEEEEECCCCCEEECCEEEECCCEEEEE
T ss_conf             41675579988999988994999999887023674998999998899897566599907658999


No 39 
>KOG3172 consensus
Probab=45.28  E-value=25  Score=16.31  Aligned_cols=65  Identities=8%  Similarity=0.105  Sum_probs=39.3

Q ss_pred             HHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHHH
Q ss_conf             87035789888999977998798753023555238997541355554431354134454115677
Q gi|254781160|r   33 AHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYM   97 (245)
Q Consensus        33 ~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~i   97 (245)
                      +|+|--.+|-.|.+-.-.|..|.+++.+.+.+..+...........-.--++-+.+++++...|+
T Consensus         7 iKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFl   71 (119)
T KOG3172           7 IKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFL   71 (119)
T ss_pred             EEEEECCCCCEEEEEECCCCEEEEEEEEECCCCCEEEEEEEEECCCCCCEEEEEEEEECCEEEEE
T ss_conf             21210156718999933786660046783056440877789973588300202589706657899


No 40 
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843    This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.; GO: 0051539 4 iron 4 sulfur cluster binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=43.35  E-value=21  Score=16.78  Aligned_cols=74  Identities=12%  Similarity=0.099  Sum_probs=53.6

Q ss_pred             CCCCEEEECCCCC--CHHHHHHHHHHHHHHHHHHHHHHHCC----CHH------HHHHHHHHHHHHHHHHHH-CCCCCCC
Q ss_conf             4431354134454--11567775444456656555542022----011------221223357889999751-2344343
Q gi|254781160|r   79 QSDVQYIFSPIKT--NRLDYMIQKSVEMGMGAIRPVITRYT----QNT------HYNMDRVRTYTISAAEQC-DILTLPF  145 (245)
Q Consensus        79 ~~~i~l~~~~~k~--~~~~~ilqk~tELGV~~I~p~~~~rs----~~~------~~k~eR~~~ii~eA~eQs-gr~~lP~  145 (245)
                      -.+++|=+.+=|.  ++.+.||+.|.|||+++|=.=.+++=    .++      ...+++-.+++.+|-|-- |...+++
T Consensus       145 g~PltLN~V~HR~Ni~~i~~~i~La~~L~AdrvE~A~~QyYGWA~~NR~aLlPt~~Ql~~a~r~V~~aRer~~g~~~~~~  224 (363)
T TIGR02109       145 GLPLTLNFVLHRHNIDQIPEIIELAIELGADRVELATTQYYGWALLNRAALLPTREQLEEATRIVEEARERLKGQGNPLS  224 (363)
T ss_pred             CCCEEEEHCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             89817602002420213678999998638984888740202256774542489889999999999999999860799823


Q ss_pred             CCCCCCC
Q ss_conf             3200000
Q gi|254781160|r  146 IYPPTTL  152 (245)
Q Consensus       146 i~~~~~l  152 (245)
                      |..+..-
T Consensus       225 l~yV~PD  231 (363)
T TIGR02109       225 LDYVVPD  231 (363)
T ss_pred             EEEECCC
T ss_conf             6763487


No 41 
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=42.35  E-value=27  Score=16.02  Aligned_cols=70  Identities=13%  Similarity=0.106  Sum_probs=40.8

Q ss_pred             CCEEEECHHHHHH-----HHHHCCCCCCCEEEEEECCCCEEEEEEECCC---CCCEEEEEEEECCCCCCCCCEEEECCCC
Q ss_conf             8889987798759-----9870357898889999779987987530235---5523899754135555443135413445
Q gi|254781160|r   19 KTQGKASGDQYHY-----LAHVLRMKEGDNILLFNGKDGEWLSKISYVG---KSIRFKVEYQSRSQTKQSDVQYIFSPIK   90 (245)
Q Consensus        19 ~~~i~L~~~~~hH-----l~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~---k~~~~~i~~~~~~~~~~~~i~l~~~~~k   90 (245)
                      .....|.|.--.|     ..+.-++++||.|.+.+..|..+..+++...   |.. +.. ...-....+..++|+-|-..
T Consensus        49 ~Gn~ViaGH~d~~~~p~~F~~L~~l~~GD~I~v~~~~G~~~~Y~V~~~~~v~~~~-~p~-~~v~~~~~~~~LtLITC~g~  126 (144)
T cd05829          49 KGTAVLAGHVDSRGGPAVFFRLGDLRKGDKVEVTRADGQTATFRVDRVEVYPKDA-FPT-DAVYGDTGPPRLRLITCGGP  126 (144)
T ss_pred             CCCEEEEEEECCCCCCCHHHHHHCCCCCCEEEEEECCCCEEEEEEEEEEEECCHH-CCC-CEEECCCCCCEEEEEEECCC
T ss_conf             9889999970689987023244248999999999789959999998899987120-884-33676899986999970898


No 42 
>PRK10039 hypothetical protein; Provisional
Probab=41.55  E-value=18  Score=17.23  Aligned_cols=18  Identities=39%  Similarity=0.549  Sum_probs=15.0

Q ss_pred             CCCCCCCHHHHHHHHHCC
Q ss_conf             888888889999999579
Q gi|254781160|r  195 GPEGGYHSEEKETLHSLP  212 (245)
Q Consensus       195 GPEGGfs~~E~~~l~~~~  212 (245)
                      =+|||+|+-|...|++..
T Consensus        78 ~~EGGlSqVE~R~~~Ela   95 (127)
T PRK10039         78 MNEGGLSQVEERILHELA   95 (127)
T ss_pred             CCCCCCCHHHHHHHHHHH
T ss_conf             577882299999999997


No 43 
>TIGR03531 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein.
Probab=39.89  E-value=20  Score=16.84  Aligned_cols=23  Identities=17%  Similarity=0.182  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             56777544445665655554202
Q gi|254781160|r   94 LDYMIQKSVEMGMGAIRPVITRY  116 (245)
Q Consensus        94 ~~~ilqk~tELGV~~I~p~~~~r  116 (245)
                      ++.+-++.-|+|.++|..+.|--
T Consensus       191 v~~ie~~i~~~g~~~i~cVlSTT  213 (444)
T TIGR03531       191 VEDIERAIEEIGPENILCVLSTT  213 (444)
T ss_pred             HHHHHHHHHHHCCCCEEEEEECC
T ss_conf             99999999982867647998536


No 44 
>pfam02844 GARS_N Phosphoribosylglycinamide synthetase, N domain. Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam00289).
Probab=39.67  E-value=27  Score=16.01  Aligned_cols=29  Identities=24%  Similarity=0.575  Sum_probs=24.2

Q ss_pred             EEEECCCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             99988888888899999995799558636887
Q gi|254781160|r  191 AILIGPEGGYHSEEKETLHSLPFVTPLSLGPR  222 (245)
Q Consensus       191 ~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~  222 (245)
                      +++||||.=...-=.+.|.++|.  +| .||.
T Consensus        64 lviiGPE~pL~~Gl~D~l~~~gi--~v-fGP~   92 (99)
T pfam02844        64 LVVVGPEAPLVAGIVDALRAAGI--PV-FGPS   92 (99)
T ss_pred             EEEECCCHHHHHHHHHHHHHCCC--EE-ECCC
T ss_conf             99989606778788999986899--17-9928


No 45 
>TIGR00699 GABAtrns_euk 4-aminobutyrate aminotransferase; InterPro: IPR004631 4-aminobutyrate aminotransferase eukaryotic (2.6.1.19 from EC) is a class III pyridoxal-phosphate-dependent aminotransferase. The enzyme catalyses the conversion of 4-aminobutanoate and 2-oxoglutarate into succinate semialdehyde and L-glutamate. The degree of sequence difference between this set and known bacterial examples is greater than the distance between either set the most similar enzyme with distinct function, and so the prokaryotic and eukaryotic sets have been placed into separate families. This family describes known eukaryotic examples of the enzyme. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase.; GO: 0003867 4-aminobutyrate transaminase activity, 0009448 gamma-aminobutyric acid metabolic process.
Probab=36.45  E-value=17  Score=17.30  Aligned_cols=14  Identities=43%  Similarity=0.800  Sum_probs=8.5

Q ss_pred             CCCCCCCHHHHHHH
Q ss_conf             88888888999999
Q gi|254781160|r  195 GPEGGYHSEEKETL  208 (245)
Q Consensus       195 GPEGGfs~~E~~~l  208 (245)
                      ||++|||++|.+..
T Consensus       154 Gp~~~Fs~eE~~s~  167 (469)
T TIGR00699       154 GPERDFSEEENESC  167 (469)
T ss_pred             CCCCCCCHHHHHHH
T ss_conf             88753117887764


No 46 
>cd00429 RPE Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose phosphate pathway. In the Calvin cycle Ru5P is phosphorylated by phosphoribulose kinase to ribulose-1,5-bisphosphate, which in turn is used by RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) to incorporate CO2 as the central step in carbohydrate synthesis.
Probab=35.70  E-value=16  Score=17.47  Aligned_cols=137  Identities=21%  Similarity=0.234  Sum_probs=78.8

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             54431354134454115677754444566565555420220112212233578899997512344343320000001123
Q gi|254781160|r   78 KQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLK  157 (245)
Q Consensus        78 ~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~  157 (245)
                      -+..+||.+--|     +..+++..+.|++.|. +..|-+    ....++-..+++.-..+|=..-|.- +...+..+++
T Consensus        58 ~~~DvHLMv~~P-----~~~i~~~~~~g~d~I~-~H~E~~----~~~~~~i~~ik~~g~~~Glal~p~T-~~~~l~~~l~  126 (211)
T cd00429          58 LPLDVHLMVENP-----ERYIEAFAKAGADIIT-FHAEAT----DHLHRTIQLIKELGMKAGVALNPGT-PVEVLEPYLD  126 (211)
T ss_pred             CCEEEEEEECCH-----HHHHHHHHHHCCCEEE-ECCCCC----CCHHHHHHHHHHCCCCCEEEECCCC-CHHHHHHHHH
T ss_conf             970589987188-----7769999970998899-864322----0899999999973987235754899-9899999997


Q ss_pred             CCCCCCCCCCCCC-HHCC----CCCHHHHHCCC---CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCHHH
Q ss_conf             3322333212630-0012----11022210036---7883599988888888899999995799558636887400448
Q gi|254781160|r  158 NWDHNCQIVFADE-TCGS----ENSLEKLHAIA---HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDT  228 (245)
Q Consensus       158 ~~~~~~~~~~~~~-~~~~----~~~~~~~~~~~---~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~ET  228 (245)
                      ..+.  .+++.-+ ...+    ...++++...+   ......+.|.=.||-+.+-+..+.++|. ..+-.|..|.+.+.
T Consensus       127 ~~D~--vliMtV~PGf~GQ~f~~~~~~ki~~l~~~~~~~~~~~~I~vDGGI~~~~i~~l~~~Ga-d~~V~GS~iF~~~d  202 (211)
T cd00429         127 EVDL--VLVMSVNPGFGGQKFIPEVLEKIRKLRELIPENNLNLLIEVDGGINLETIPLLAEAGA-DVLVAGSALFGSDD  202 (211)
T ss_pred             HHCE--EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCCC-CEEEECHHHHCCCC
T ss_conf             5152--2798746887887545679999999999998649985999967859899999998599-99997937758999


No 47 
>pfam04203 Sortase Sortase family. The founder member of this family is S.aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall.
Probab=35.34  E-value=35  Score=15.31  Aligned_cols=69  Identities=10%  Similarity=0.080  Sum_probs=38.8

Q ss_pred             CCCEEEECHHH--HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECC---CCCCEEEEEEEECCCCCCCCCEEEECCCC
Q ss_conf             88889987798--759987035789888999977998798753023---55523899754135555443135413445
Q gi|254781160|r   18 IKTQGKASGDQ--YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYV---GKSIRFKVEYQSRSQTKQSDVQYIFSPIK   90 (245)
Q Consensus        18 ~~~~i~L~~~~--~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~---~k~~~~~i~~~~~~~~~~~~i~l~~~~~k   90 (245)
                      .+....|.|..  --|..+.-.++.||.|.+.+..|..|..+|...   ++.-. .   .......++.++|.=|.+.
T Consensus        37 ~~gn~viaGH~~~~~~F~~L~~l~~Gd~i~l~~~~~~~~~Y~V~~~~iv~~~~~-~---~~~~~~~~~~LtLiTC~p~  110 (122)
T pfam04203        37 EGGNTVIAGHRGGGTMFSRLDKLKKGDKIYVTTLDGKTYTYRVTSVEVVDPTDV-E---VLDPTPGDRLLTLITCTPF  110 (122)
T ss_pred             CCCCEEEEEEECCCCHHHHHHCCCCCCEEEEEECCCCEEEEEEEEEEEECCCCC-E---EECCCCCCCEEEEEEECCC
T ss_conf             987299998738992133565288999999997999799999999999987876-5---8623799988999975898


No 48 
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.14  E-value=35  Score=15.29  Aligned_cols=45  Identities=18%  Similarity=0.211  Sum_probs=33.8

Q ss_pred             EECCCCCCCCEEEE-CHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf             40854478888998-77987599870357898889999779987987530235
Q gi|254781160|r   11 FVDFPLCIKTQGKA-SGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG   62 (245)
Q Consensus        11 f~~~~l~~~~~i~L-~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~   62 (245)
                      |-+..++...+|.+ |.+++|+       ++||.+.|+.-+...|.|.|....
T Consensus        12 fe~dilagrKTITIRD~SEShf-------~~g~vlrV~r~Ed~~~fc~I~vl~   57 (106)
T COG3097          12 FEADILAGRKTITIRDKSESHF-------KPGDVLRVGRFEDDRYFCTIEVLA   57 (106)
T ss_pred             CCHHHHCCCCEEEEECCCHHCC-------CCCCEEEEEEECCCCEEEEEEEEE
T ss_conf             0077767872689703632037-------888789999924784899999987


No 49 
>TIGR01672 AphA HAD superfamily (subfamily IIIB) phosphatase, TIGR01672; InterPro: IPR010025   This family of proteins is a member of the IIIB subfamily (IPR001001 from INTERPRO) of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of subfamily III and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs , all of which are found conserved in this family.   AphA is a periplasmic acid phosphatase of Escherichia coli  belonging to class B bacterial phosphatases , which is part of the DDDD superfamily of phosphohydrolases. The crystal structure of AphA has been determined at 2.2A and its resolution extended to 1.7A. Despite the lack of sequence homology, the AphA structure reveals a haloacid dehalogenase-like fold. This finding suggests that this fold could be conserved among members of the DDDD superfamily of phosphohydrolases. The active enzyme is a homotetramer built by using an extended N-terminal arm intertwining the four monomers. The active site of the native enzyme hosts a magnesium ion, which can be replaced by other metal ions. The structure explains the non-specific behaviour of AphA towards substrates, while a structure-based alignment with other phosphatases provides clues about the catalytic mechanism . ; GO: 0003993 acid phosphatase activity, 0030288 outer membrane-bounded periplasmic space.
Probab=34.28  E-value=25  Score=16.22  Aligned_cols=33  Identities=18%  Similarity=0.305  Sum_probs=18.1

Q ss_pred             CEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCE
Q ss_conf             8899877987599870357898889999779987
Q gi|254781160|r   20 TQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGE   53 (245)
Q Consensus        20 ~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~   53 (245)
                      +...+..+-++.|+ -|-.+-||.|..+.|+..-
T Consensus       112 D~~SIPKe~A~qLI-~MH~~RGD~i~F~TGRt~g  144 (248)
T TIGR01672       112 DKYSIPKEVAKQLI-DMHQKRGDKIFFVTGRTAG  144 (248)
T ss_pred             CCCCCCHHHHHHHH-HHHHHHCCEEEEEECCCCC
T ss_conf             87777578999999-9887609879998468764


No 50 
>TIGR00958 3a01208 antigen peptide transporter 2; InterPro: IPR005293   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).     Proteins of this family are involved in the transport of antigens from the cytoplasm to a membrane-bound compartment for association with MHC class I molecules.; GO: 0005215 transporter activity, 0006810 transport.
Probab=32.72  E-value=31  Score=15.69  Aligned_cols=15  Identities=33%  Similarity=0.541  Sum_probs=6.7

Q ss_pred             CCCCEEEEECCCCCC
Q ss_conf             788359998888888
Q gi|254781160|r  186 HIPNVAILIGPEGGY  200 (245)
Q Consensus       186 ~~~~i~i~IGPEGGf  200 (245)
                      .+.++.-+|||-|+=
T Consensus       557 ~PG~vvALVGPsGsG  571 (770)
T TIGR00958       557 EPGEVVALVGPSGSG  571 (770)
T ss_pred             CCCEEEEEECCCCCC
T ss_conf             386259986589983


No 51 
>PRK13885 conjugal transfer protein TrbG; Provisional
Probab=29.33  E-value=23  Score=16.48  Aligned_cols=20  Identities=20%  Similarity=0.506  Sum_probs=14.5

Q ss_pred             CCEEEEECCCCC-CCHHHHHH
Q ss_conf             835999888888-88899999
Q gi|254781160|r  188 PNVAILIGPEGG-YHSEEKET  207 (245)
Q Consensus       188 ~~i~i~IGPEGG-fs~~E~~~  207 (245)
                      -..+++|||+|| |+++|-++
T Consensus       241 aP~LfVvg~dGgl~~d~e~~L  261 (299)
T PRK13885        241 APTLLVVRKEGGLFTDDETVM  261 (299)
T ss_pred             CCCEEEECCCCCCCCCCCCEE
T ss_conf             882899837887466784317


No 52 
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=28.20  E-value=18  Score=17.18  Aligned_cols=15  Identities=33%  Similarity=0.437  Sum_probs=11.7

Q ss_pred             CCCCEEEEECCCCCC
Q ss_conf             788359998888888
Q gi|254781160|r  186 HIPNVAILIGPEGGY  200 (245)
Q Consensus       186 ~~~~i~i~IGPEGGf  200 (245)
                      +..-++|+||+-||=
T Consensus       240 gks~lTIaIGCTGGq  254 (286)
T COG1660         240 GKSYLTIAIGCTGGQ  254 (286)
T ss_pred             CCEEEEEEECCCCCC
T ss_conf             974999997147986


No 53 
>PRK05784 phosphoribosylamine--glycine ligase; Provisional
Probab=27.00  E-value=48  Score=14.45  Aligned_cols=22  Identities=9%  Similarity=-0.241  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             2233578899997512344343
Q gi|254781160|r  124 MDRVRTYTISAAEQCDILTLPF  145 (245)
Q Consensus       124 ~eR~~~ii~eA~eQsgr~~lP~  145 (245)
                      +-|++.=+.+-+..|-...++.
T Consensus       318 Lp~L~sDl~~l~~a~~~g~L~~  339 (485)
T PRK05784        318 LYLYEGDFYELFELAATGKLHK  339 (485)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCC
T ss_conf             9874263999999998199887


No 54 
>pfam05896 NQRA Na(+)-translocating NADH-quinone reductase subunit A (NQRA). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration.
Probab=26.68  E-value=49  Score=14.38  Aligned_cols=97  Identities=13%  Similarity=0.133  Sum_probs=54.0

Q ss_pred             CCCCEEEECHHHHHHHHHHCCCCCCCEEE----EE-ECC--CCEE----EEEEECCC---CCCEEEEEEEEC-CCCCCCC
Q ss_conf             78888998779875998703578988899----99-779--9879----87530235---552389975413-5555443
Q gi|254781160|r   17 CIKTQGKASGDQYHYLAHVLRMKEGDNIL----LF-NGK--DGEW----LSKISYVG---KSIRFKVEYQSR-SQTKQSD   81 (245)
Q Consensus        17 ~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~----i~-dg~--g~~~----~~~I~~~~---k~~~~~i~~~~~-~~~~~~~   81 (245)
                      ....++.+.++++|.++=-|-+++||+|.    || |=+  +-.|    .++|.++.   |...+.++-+.. .....+.
T Consensus        24 ~~~~~~ai~p~Df~glkPkl~VkeGD~Vk~G~pLF~dK~np~i~f~SPvsG~V~~I~RG~kR~ilsivI~~d~~~~~~~~  103 (257)
T pfam05896        24 PAVRTVALLGEDYVGMKPKMLVKEGDKVKAGQPLFEDKKNPGVKFTAPASGTVVAINRGAKRVLQSVVIEVDGDEAVTFE  103 (257)
T ss_pred             CCCCEEEECCCCCCCCCEEEEEECCCEEECCCEEEEEECCCCCEEECCCCEEEEEECCCCCCCEEEEEEEECCCCCCCCC
T ss_conf             98757998460148873269983499985587579973698846856787389501056751015999993687430000


Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             135413445411567775444456656555542022
Q gi|254781160|r   82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYT  117 (245)
Q Consensus        82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs  117 (245)
                      -.=...+.+ -.-|.+.+.+.+-|   .||++-+|=
T Consensus       104 ~~~~~~~~~-ls~e~i~~~Ll~sG---lW~~~rqRP  135 (257)
T pfam05896       104 KYSAKDLSS-LSREAVKENLLESG---LWTALRTRP  135 (257)
T ss_pred             CCCCCCHHH-CCHHHHHHHHHHCC---CHHHHHCCC
T ss_conf             157224324-79999999998669---706754264


No 55 
>PRK04171 ribosome biogenesis protein; Provisional
Probab=26.44  E-value=49  Score=14.35  Aligned_cols=90  Identities=22%  Similarity=0.248  Sum_probs=49.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEEC--CCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             434332000000112333223332126300012110222100367883599988--888888899999995799558636
Q gi|254781160|r  142 TLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIG--PEGGYHSEEKETLHSLPFVTPLSL  219 (245)
Q Consensus       142 ~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IG--PEGGfs~~E~~~l~~~~~~~~vsL  219 (245)
                      .|.++.. .++.+++..  ...+++...+........+.....   ..++++||  |-|.|+.+-.+..   .  ..+|+
T Consensus       128 ~Ll~v~k-~~l~~~l~~--~~~kii~ls~~g~~~~~~~~~~~~---~~~~~vIGaf~~G~f~~~~~~~~---d--~~~SI  196 (221)
T PRK04171        128 PLLELED-KSLSELLEE--NPGKIILLSEKGEPVKPKELAKEL---ENPVVVIGGFPHGDFSSEVLEKA---D--KKYSI  196 (221)
T ss_pred             CCEEEEC-CCHHHHHCC--CCCEEEEECCCCCCCCHHHHHHHC---CCCEEEEEECCCCCCCCCCHHCC---C--CEEEE
T ss_conf             0015663-868997065--898599983588672899997422---79769983016987660000136---8--48998


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             88740044899999999999847
Q gi|254781160|r  220 GPRILRSDTAAVAAMALVQAICG  242 (245)
Q Consensus       220 G~~ILR~ETA~i~als~~~~~~g  242 (245)
                      ++.-|-|-+++--.++..-..||
T Consensus       197 s~~~Lsa~~v~~ri~~a~E~~~G  219 (221)
T PRK04171        197 YNEPLDAWTVVSRIIAAAERALG  219 (221)
T ss_pred             ECCCHHHHHHHHHHHHHHHHHHC
T ss_conf             48876999999999999999867


No 56 
>pfam01081 Aldolase KDPG and KHG aldolase. This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase)
Probab=26.40  E-value=49  Score=14.35  Aligned_cols=95  Identities=19%  Similarity=0.262  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHH
Q ss_conf             35788999975123443433200000011233322333212630001211022210036788359998888888889999
Q gi|254781160|r  127 VRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKE  206 (245)
Q Consensus       127 ~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~  206 (245)
                      +..-+.++|.+.+-+++|=+..|.......+.=-.. ..+|.-...+....++.+..  ..+.+-++  |=||.+.+-..
T Consensus        89 ~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G~~~-vKlFPA~~~Gg~~~lkal~~--p~p~~~f~--ptGGv~~~N~~  163 (196)
T pfam01081        89 LTADLLKHAVDVKIPLIPGVSTPSEIMLGLDLGLTR-FKFFPAEASGGVPAIKALAG--PFPQVRFC--PTGGIHPANVR  163 (196)
T ss_pred             CHHHHHHHHHHCCCCEECCCCCHHHHHHHHHCCCCE-EEECCCHHCCCHHHHHHHHC--CCCCCEEE--EECCCCHHHHH
T ss_conf             639999999973996637859999999999879998-99787310184999999857--79998699--80798988899


Q ss_pred             HHHHCCCCEEEECCCCCCCHH
Q ss_conf             999579955863688740044
Q gi|254781160|r  207 TLHSLPFVTPLSLGPRILRSD  227 (245)
Q Consensus       207 ~l~~~~~~~~vsLG~~ILR~E  227 (245)
                      .+-++|. ..+-.|..+..-+
T Consensus       164 ~yl~~g~-v~~~~GS~l~~~~  183 (196)
T pfam01081       164 DYLALPN-ILCVGGSWLVPAS  183 (196)
T ss_pred             HHHHCCC-EEEEECHHHCCHH
T ss_conf             9996898-6999893648988


No 57 
>PRK10433 putative RNA methyltransferase; Provisional
Probab=25.65  E-value=51  Score=14.26  Aligned_cols=25  Identities=24%  Similarity=0.401  Sum_probs=19.7

Q ss_pred             CCCCEEEEECCCC-CCCHHHHHHHHH
Q ss_conf             7883599988888-888899999995
Q gi|254781160|r  186 HIPNVAILIGPEG-GYHSEEKETLHS  210 (245)
Q Consensus       186 ~~~~i~i~IGPEG-Gfs~~E~~~l~~  210 (245)
                      ..+++.++.|+|. |.|.+|++.+..
T Consensus       104 ~~~~valvFG~E~~GLsneEl~~C~~  129 (228)
T PRK10433        104 WMSHAALVFGREDSGLTNEELALADV  129 (228)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHCCE
T ss_conf             47847999888668989899986797


No 58 
>pfam00834 Ribul_P_3_epim Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
Probab=25.44  E-value=41  Score=14.87  Aligned_cols=136  Identities=18%  Similarity=0.266  Sum_probs=73.1

Q ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             55443135413445411567775444456656555542022011221223357889999751234434332000000112
Q gi|254781160|r   77 TKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL  156 (245)
Q Consensus        77 ~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l  156 (245)
                      .-+..+||.+.-|     +..+++..+.|++.|. +..|-+.    ...+.-..++++-.++|=..-|. .+...++.++
T Consensus        57 ~~~~DvHLMv~~P-----~~~i~~~~~~g~d~i~-~H~E~~~----~~~~~i~~ik~~g~k~GlAlnP~-T~~~~l~~~l  125 (201)
T pfam00834        57 ELPLDVHLMVEEP-----DRIIPDFAEAGADIIS-FHAEASD----HPHRTIQLIKEAGAKAGLVLNPA-TPLDAIEYLL  125 (201)
T ss_pred             CCCEEEEEEEECH-----HHHHHHHHHCCCCEEE-ECHHHHH----CHHHHHHHHHHCCCEEEEEECCC-CCCHHHHHHH
T ss_conf             9963899998377-----6639999873998899-7544413----79999999986497268885699-8602888767


Q ss_pred             CCCCCCCCCCCCCCH-HCC----CCCHHHHHCCC---CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCH
Q ss_conf             333223332126300-012----11022210036---78835999888888888999999957995586368874004
Q gi|254781160|r  157 KNWDHNCQIVFADET-CGS----ENSLEKLHAIA---HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRS  226 (245)
Q Consensus       157 ~~~~~~~~~~~~~~~-~~~----~~~~~~~~~~~---~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~  226 (245)
                      +..+.-  +++.-+. ..+    ...++++...+   ..+...+.|.=.||-+.+-+..+.++|. ..+=.|.-|.++
T Consensus       126 ~~iD~V--LvMtV~PGf~GQ~f~~~~l~KI~~lr~~~~~~~~~~~I~vDGGIn~~ti~~l~~~Ga-d~~V~GSaiF~s  200 (201)
T pfam00834       126 DDLDLV--LLMSVNPGFGGQSFIPSVLPKIRKVRKMIDEGGLDTLIEVDGGVNLDNIPQIAEAGA-DVLVAGSAVFGA  200 (201)
T ss_pred             HHCCEE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCCC-CEEEECCEECCC
T ss_conf             427989--998866898876456779999999999998269980799989888999999998799-999978002459


No 59 
>TIGR00223 panD aspartate 1-decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process.
Probab=25.00  E-value=52  Score=14.18  Aligned_cols=57  Identities=19%  Similarity=0.214  Sum_probs=41.5

Q ss_pred             CCCCCCEEEEC-CCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCC
Q ss_conf             76778777408-54478888998779875998703578988899997799879875302355
Q gi|254781160|r    3 IHSHLKRLFVD-FPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK   63 (245)
Q Consensus         3 ~~~~m~R~f~~-~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k   63 (245)
                      ...|+||.-+- -+|..-.++.+|.|-.    +.-.+.+|++|.+.|-++|.-..+..-.+|
T Consensus         6 l~gKlHRa~vT~AnLnY~GSitIDeDl~----daag~lenekv~IvnvnNG~RfsTY~I~gk   63 (127)
T TIGR00223         6 LSGKLHRATVTEANLNYVGSITIDEDLL----DAAGLLENEKVDIVNVNNGKRFSTYVIAGK   63 (127)
T ss_pred             CCCCCCEEEEEECCCCEEEEEEHHHHHH----HHHHCCCCCEEEEEECCCCCCEEEEEECCC
T ss_conf             2176221576323674365332546799----985128998489986689971234665142


No 60 
>KOG2925 consensus
Probab=24.96  E-value=39  Score=15.03  Aligned_cols=60  Identities=13%  Similarity=0.127  Sum_probs=41.7

Q ss_pred             CCCEEEECCCCCCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEE-CCCCCCEEE
Q ss_conf             787774085447888899877987599870357898889999779987987530-235552389
Q gi|254781160|r    6 HLKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKIS-YVGKSIRFK   68 (245)
Q Consensus         6 ~m~R~f~~~~l~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~-~~~k~~~~~   68 (245)
                      .|.|=|+.+. ..+..+.|...+.-  .+|++++-...+.|.|.+|..+.+..- ...|++.++
T Consensus         2 atkkry~~q~-v~de~~~le~~q~I--aqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiR   62 (167)
T KOG2925           2 ATKKRYLKQA-VSDEDFTLEECQSI--AQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIR   62 (167)
T ss_pred             CCCHHHHCCC-CCCCCCCHHHHHHH--HHHHHCCCCCHHHHHHCCCCEEEEECCHHHHHCEEEE
T ss_conf             6311111000-25887431242568--9998457842323665177243001777651025785


No 61 
>pfam06003 SMN Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
Probab=24.90  E-value=53  Score=14.17  Aligned_cols=37  Identities=16%  Similarity=0.107  Sum_probs=27.0

Q ss_pred             CCCCCCCEEEEEE-CCCCEEEEEEECCC-CCCEEEEEEE
Q ss_conf             3578988899997-79987987530235-5523899754
Q gi|254781160|r   36 LRMKEGDNILLFN-GKDGEWLSKISYVG-KSIRFKVEYQ   72 (245)
Q Consensus        36 lRlk~Gd~i~i~d-g~g~~~~~~I~~~~-k~~~~~i~~~   72 (245)
                      ..-++||.....- .+|..|.|+|.+|+ |..++.+...
T Consensus        67 ~~wkVGD~C~A~yseDG~~YeAtI~SId~k~gtCvV~Y~  105 (264)
T pfam06003        67 KEWQVGDSCNAVWSEDGNLYTATITSIDQKRGTCVVFYT  105 (264)
T ss_pred             CEEECCCEEEEEECCCCCCCEEEEEEECCCCCCEEEEEE
T ss_conf             201118856766525785201367775267870689982


No 62 
>PRK10358 putative tRNA/rRNA methyltransferase YibK; Provisional
Probab=24.63  E-value=53  Score=14.14  Aligned_cols=132  Identities=8%  Similarity=0.077  Sum_probs=61.2

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCC
Q ss_conf             1354134454115677754444566565555420220-1122122335788999975123443--433200000011233
Q gi|254781160|r   82 VQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQ-NTHYNMDRVRTYTISAAEQCDILTL--PFIYPPTTLEFLLKN  158 (245)
Q Consensus        82 i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~-~~~~k~eR~~~ii~eA~eQsgr~~l--P~i~~~~~l~~~l~~  158 (245)
                      |.|+.+ -.+...-.|++-|.-.|+. ++.+.. .+- -.++++.       .    +|-.+.  ..+....+++.+++.
T Consensus         4 IVL~~P-~iP~N~G~i~R~ca~~g~~-L~LV~P-~gf~~~dk~lr-------R----Agldy~~~~~~~~~~~~~~f~~~   69 (157)
T PRK10358          4 IVLYEP-EIPPNTGNIIRLCANTGFR-LHIIEP-MGFAWDDKRLR-------R----AGLDYHEFTAVTRHHDYAAFLEA   69 (157)
T ss_pred             EEEECC-CCCCCHHHHHHHHHHCCCE-EEEEEC-CCCCCCCHHHH-------H----HCCCCHHEEEEEECCCHHHHHHH
T ss_conf             999589-8888289999999963998-999806-88787426665-------3----31630212689980899999974


Q ss_pred             CCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCCEEEECCCC--CCCHHHHHHHHH
Q ss_conf             3223332126300012110222100367883599988888-888899999995799558636887--400448999999
Q gi|254781160|r  159 WDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-GYHSEEKETLHSLPFVTPLSLGPR--ILRSDTAAVAAM  234 (245)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~~~~~~vsLG~~--ILR~ETA~i~al  234 (245)
                      ......+.+....   .....   ...-.+.-.++.|||+ |.+++..+.+.....+ .+-+-+.  -|=-.+|+.+++
T Consensus        70 ~~~~r~~~~tt~~---~~~~~---~~~~~~~d~llFG~Es~GLp~e~l~~~~~~~~i-~IPm~~~~rSLNLs~AvaIvl  141 (157)
T PRK10358         70 ENPQRLFALTTKG---TPAHS---AVSYQDGDYLMFGPETRGLPASILDALPAEQKI-RIPMVPDSRSMNLSNAVSVVV  141 (157)
T ss_pred             CCCCEEEEEECCC---CCCCH---HCCCCCCCEEEECCCCCCCCHHHHHCCCCCEEE-EEECCCCCCCHHHHHHHHHHH
T ss_conf             3897289972577---87610---023578988997776789899999517777499-830897985142999999999


No 63 
>pfam07236 Phytoreo_S7 Phytoreovirus S7 protein. This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins.
Probab=24.49  E-value=43  Score=14.73  Aligned_cols=20  Identities=20%  Similarity=0.388  Sum_probs=14.3

Q ss_pred             EEEECCCCCCCHHHHHHHHH
Q ss_conf             99988888888899999995
Q gi|254781160|r  191 AILIGPEGGYHSEEKETLHS  210 (245)
Q Consensus       191 ~i~IGPEGGfs~~E~~~l~~  210 (245)
                      -++|--++=||.+|.+.+.+
T Consensus       283 evFie~d~vFs~eE~s~lde  302 (506)
T pfam07236       283 EVFIEIDSVFSKEEHSKLDE  302 (506)
T ss_pred             CEEEECCCCCCHHHHHHHHH
T ss_conf             10460445656677878887


No 64 
>pfam01079 Hint Hint module. This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module.
Probab=24.40  E-value=54  Score=14.11  Aligned_cols=45  Identities=9%  Similarity=0.097  Sum_probs=30.7

Q ss_pred             CCCCEEEECHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEE-ECCCCC
Q ss_conf             788889987798759987035789888999977998798753-023555
Q gi|254781160|r   17 CIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKI-SYVGKS   64 (245)
Q Consensus        17 ~~~~~i~L~~~~~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I-~~~~k~   64 (245)
                      ..+.++.+.+....   .+--+++||.|...|.+|......+ ...+++
T Consensus        14 pg~a~V~l~~G~~k---~m~~L~~GD~Vla~d~~G~~~yS~Vi~Fldr~   59 (214)
T pfam01079        14 PGDATVTLEDGGTK---PMSDLRIGDRVLAADSDGKLVYSPVILFLDRD   59 (214)
T ss_pred             CCCCEEEECCCCEE---EHHHCCCCCEEEEECCCCCEEEEEEEEEEEEC
T ss_conf             99878993799888---93776888889986589999888579998217


No 65 
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=23.55  E-value=53  Score=14.14  Aligned_cols=96  Identities=20%  Similarity=0.260  Sum_probs=47.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHH-----HHH-HCCCCE
Q ss_conf             43433200000011233322333212630001211022210036788359998888888889999-----999-579955
Q gi|254781160|r  142 TLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKE-----TLH-SLPFVT  215 (245)
Q Consensus       142 ~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~-----~l~-~~~~~~  215 (245)
                      |==.+....+|.++++..+.+..++.... .+.....+.. .....+....+-||+.|.-+-...     .+. -.++ .
T Consensus       165 wGY~V~~~~~L~e~~~~~~~~~vvi~tsr-~g~~~~~e~~-~~~~~~~~~~fg~P~~gv~~~~~~~~~~~~~d~~~N~-~  241 (272)
T COG2106         165 WGYKVRIAKSLNELLKGFDLDVVVIATSR-YGPLDVRETE-APLKSKVTLVFGGPEKGVLEILKVGGVKLEFDIVVNF-I  241 (272)
T ss_pred             CCEEEEEHHHHHHHHHCCCCCCEEEEECC-CCCCEEEECC-CCCCCCCEEEECCCCCCHHEECCCCCCCCCCCEEEEE-C
T ss_conf             74799861458877633688735998435-5865001225-6667760589648655700011445666433615773-4


Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             86368874004489999999999984
Q gi|254781160|r  216 PLSLGPRILRSDTAAVAAMALVQAIC  241 (245)
Q Consensus       216 ~vsLG~~ILR~ETA~i~als~~~~~~  241 (245)
                      + .=|...-|+|-|.++.+++++.+.
T Consensus       242 p-~Qg~~~vrtEEavlatl~~ln~~~  266 (272)
T COG2106         242 P-GQGTETVRTEEAVLATLSILNILL  266 (272)
T ss_pred             C-CCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             8-755324660466788888888998


No 66 
>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=22.91  E-value=26  Score=16.13  Aligned_cols=25  Identities=20%  Similarity=0.381  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHH-HHHHHHCCC
Q ss_conf             5677754444566565-555420220
Q gi|254781160|r   94 LDYMIQKSVEMGMGAI-RPVITRYTQ  118 (245)
Q Consensus        94 ~~~ilqk~tELGV~~I-~p~~~~rs~  118 (245)
                      -=++|.+.=-+|+..+ .|++-.+-+
T Consensus        73 ~~~lIK~lLDIGAQTLLvPmi~~aeq   98 (249)
T TIGR02311        73 DPVLIKQLLDIGAQTLLVPMIETAEQ   98 (249)
T ss_pred             CCEEEEHHHHHHHHHHHHHHHCCHHH
T ss_conf             82021013223456643103037789


No 67 
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation.  Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet.  LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=22.69  E-value=58  Score=13.90  Aligned_cols=68  Identities=12%  Similarity=0.087  Sum_probs=42.6

Q ss_pred             HHHHHHHCCCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCHHHH
Q ss_conf             75998703578988899997799879875302355523899754135555443135413445411567
Q gi|254781160|r   29 YHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDY   96 (245)
Q Consensus        29 ~hHl~kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~k~~~~~i~~~~~~~~~~~~i~l~~~~~k~~~~~~   96 (245)
                      .+-|...|.--.|..+.+=--+|..+.+++.+++....+....-........+..+-...+++....+
T Consensus         7 ~~tLv~lL~~l~g~~VtVELkNg~~~~G~L~~vD~~MN~~L~~v~~t~~~g~~~~l~~~~IRGs~IRy   74 (78)
T cd01733           7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRY   74 (78)
T ss_pred             HCCHHHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEECCCCCEEECCEEEECCCEEEE
T ss_conf             46199999873897899997699899999998744626699459999379987787779991766899


No 68 
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase,  is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=22.54  E-value=58  Score=13.88  Aligned_cols=90  Identities=20%  Similarity=0.296  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCHHHHHCCCCCCCEEEEECCCCCCCHHHHH
Q ss_conf             35788999975123443433200000011233322333212630001211022210036788359998888888889999
Q gi|254781160|r  127 VRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGGYHSEEKE  206 (245)
Q Consensus       127 ~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEGGfs~~E~~  206 (245)
                      +..-+.+.|.+.+-+++|-+..|..+...++.=-+..+ +|.-+.. ..+-++.+...  .+.+.++  |=||.+.+-..
T Consensus        85 ~~~~v~~~a~~~~~~~iPGv~TpsEi~~A~~~G~~~vK-~FPa~~~-G~~~lkal~~p--fp~~~~~--ptGGI~~~N~~  158 (190)
T cd00452          85 LDPEVVKAANRAGIPLLPGVATPTEIMQALELGADIVK-LFPAEAV-GPAYIKALKGP--FPQVRFM--PTGGVSLDNAA  158 (190)
T ss_pred             CCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCCCCEEE-ECCCCCC-CHHHHHHHHCC--CCCCCEE--EECCCCHHHHH
T ss_conf             99999999998299665787999999999987999899-8955114-99999998554--8999389--96799988899


Q ss_pred             HHHHCCCCEEEECCCCC
Q ss_conf             99957995586368874
Q gi|254781160|r  207 TLHSLPFVTPLSLGPRI  223 (245)
Q Consensus       207 ~l~~~~~~~~vsLG~~I  223 (245)
                      .+-+.| +..|.+|...
T Consensus       159 ~yl~~g-v~avG~g~~l  174 (190)
T cd00452         159 EWLAAG-VVAVGGGSLL  174 (190)
T ss_pred             HHHHCC-CEEEEECHHC
T ss_conf             999689-9899954125


No 69 
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=22.50  E-value=43  Score=14.73  Aligned_cols=72  Identities=15%  Similarity=0.153  Sum_probs=37.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHCCCCC---------CCCCCCCCCCCCCCCCC
Q ss_conf             115677754444566565555420--2201122122335788999975123443---------43320000001123332
Q gi|254781160|r   92 NRLDYMIQKSVEMGMGAIRPVITR--YTQNTHYNMDRVRTYTISAAEQCDILTL---------PFIYPPTTLEFLLKNWD  160 (245)
Q Consensus        92 ~~~~~ilqk~tELGV~~I~p~~~~--rs~~~~~k~eR~~~ii~eA~eQsgr~~l---------P~i~~~~~l~~~l~~~~  160 (245)
                      +.++..++-|..||+..|...-.+  +........+|+..-+..+++.+.+.-+         |-+..+..+..+++..+
T Consensus        94 e~l~kaI~lA~~LGi~~I~l~g~dv~~~~~~~~~~~rf~e~l~~~~~~Ae~~gV~L~iE~~~~~f~~t~~~~~~~i~~v~  173 (284)
T PRK13210         94 EIMKKAIRLAQDLGIRTIQLAGYDVYYEEKDEETRQRFIEGLAWAVEQAAAAQVMLAVEIMDTPFMNSISKWKKWDEEID  173 (284)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCCCHHHHHHHHHHCC
T ss_conf             99999999999809978996887666686988999999999999999999839989999567655477999999999649


Q ss_pred             CCC
Q ss_conf             233
Q gi|254781160|r  161 HNC  163 (245)
Q Consensus       161 ~~~  163 (245)
                      +..
T Consensus       174 sp~  176 (284)
T PRK13210        174 SPW  176 (284)
T ss_pred             CCC
T ss_conf             983


No 70 
>PRK13668 hypothetical protein; Provisional
Probab=22.11  E-value=59  Score=13.82  Aligned_cols=10  Identities=10%  Similarity=-0.449  Sum_probs=3.5

Q ss_pred             HHHHHHHHCC
Q ss_conf             8999975123
Q gi|254781160|r  131 TISAAEQCDI  140 (245)
Q Consensus       131 i~eA~eQsgr  140 (245)
                      +.+.+.+--|
T Consensus       145 i~E~A~fNlr  154 (266)
T PRK13668        145 IREMALFNVR  154 (266)
T ss_pred             HHHHHHHHHH
T ss_conf             9999998886


No 71 
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=21.96  E-value=60  Score=13.80  Aligned_cols=27  Identities=30%  Similarity=0.368  Sum_probs=21.9

Q ss_pred             CCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf             357898889999779987987530235
Q gi|254781160|r   36 LRMKEGDNILLFNGKDGEWLSKISYVG   62 (245)
Q Consensus        36 lRlk~Gd~i~i~dg~g~~~~~~I~~~~   62 (245)
                      |+++.||.|.+.-|+..--.++|..+.
T Consensus         5 ~kIkkGD~V~VisGkdKGk~G~Vl~v~   31 (77)
T PRK12281          5 LHVKKGDMVKVIAGDDKGKTGKVLAVL   31 (77)
T ss_pred             EEEECCCEEEEEECCCCCCCEEEEEEE
T ss_conf             487589999994667899727899998


No 72 
>PRK00885 phosphoribosylamine--glycine ligase; Provisional
Probab=21.74  E-value=60  Score=13.77  Aligned_cols=35  Identities=9%  Similarity=0.006  Sum_probs=14.8

Q ss_pred             EEEECHHHHH-HHHHHCCCC----CCCEEEEEE-CCCCEEE
Q ss_conf             8998779875-998703578----988899997-7998798
Q gi|254781160|r   21 QGKASGDQYH-YLAHVLRMK----EGDNILLFN-GKDGEWL   55 (245)
Q Consensus        21 ~i~L~~~~~h-Hl~kVlRlk----~Gd~i~i~d-g~g~~~~   55 (245)
                      .|.=+.+++. .+..+|.-+    .|+.|.+=. -.|.++.
T Consensus       154 ~V~~~~~ea~~al~~i~~~~~fg~ag~~VvIEE~L~G~E~S  194 (424)
T PRK00885        154 VVAMTLEEAEAAVDDMLAGNKFGDAGARVVIEEFLDGEEAS  194 (424)
T ss_pred             EEECCHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCEEE
T ss_conf             76378999999999985033234568728999705883179


No 73 
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=21.67  E-value=34  Score=15.41  Aligned_cols=136  Identities=19%  Similarity=0.308  Sum_probs=73.6

Q ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             55443135413445411567775444456656555542022011221223357889999751234434332000000112
Q gi|254781160|r   77 TKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL  156 (245)
Q Consensus        77 ~~~~~i~l~~~~~k~~~~~~ilqk~tELGV~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP~i~~~~~l~~~l  156 (245)
                      ..+..+||.+..     -+..+++..+.|++.|. +..|-+    ....+.-..++++=.++|=.--|. .++..++.++
T Consensus        62 ~~plDvHLMv~~-----P~~~i~~~~~aGad~i~-~H~Ea~----~~~~~~i~~ik~~g~k~GlalnP~-T~~~~l~~~l  130 (223)
T PRK08745         62 TAPIDVHLMVEP-----VDRIVPDFADAGATTIS-FHPEAS----RHVHRTIQLIKSHGCQAGLVLNPA-TPVDILDWVL  130 (223)
T ss_pred             CCCEEEEEEECC-----HHHHHHHHHHCCCCEEE-EEECCC----CCHHHHHHHHHHCCCCEEEEECCC-CCHHHHHHHH
T ss_conf             975377898339-----89999999973997899-960644----299999999998398446774699-9879999988


Q ss_pred             CCCCCCCCCCCCCCH-HCCC----CCHHHHHCCC-----CCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEECCCCCCCH
Q ss_conf             333223332126300-0121----1022210036-----78835999888888888999999957995586368874004
Q gi|254781160|r  157 KNWDHNCQIVFADET-CGSE----NSLEKLHAIA-----HIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRS  226 (245)
Q Consensus       157 ~~~~~~~~~~~~~~~-~~~~----~~~~~~~~~~-----~~~~i~i~IGPEGGfs~~E~~~l~~~~~~~~vsLG~~ILR~  226 (245)
                      ...+.-  +++.-+. ..++    ..++++....     ....+.  |.=-||.+.+-+..+.++|. ..+=.|.-|++.
T Consensus       131 ~~~D~V--liMtV~PGf~GQ~f~~~~l~KI~~l~~~~~~~~~~~~--I~VDGGI~~~ti~~l~~aGa-d~~V~GSaiF~~  205 (223)
T PRK08745        131 PELDLV--LVMSVNPGFGGQAFIPSALDKLRAIRKKIDALGKPIR--LEIDGGVKADNIGAIAAAGA-DTFVAGSAIFNA  205 (223)
T ss_pred             HHCCEE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCE--EEEECCCCHHHHHHHHHCCC-CEEEECHHHHCC
T ss_conf             647989--9987569988754568899999999999986499945--99978879899999998699-999974177579


Q ss_pred             HH
Q ss_conf             48
Q gi|254781160|r  227 DT  228 (245)
Q Consensus       227 ET  228 (245)
                      +-
T Consensus       206 ~d  207 (223)
T PRK08745        206 PD  207 (223)
T ss_pred             CC
T ss_conf             99


No 74 
>pfam05113 DUF693 Protein of unknown function (DUF693). This family consists of several uncharacterized proteins from Borrelia burgdorferi (Lyme disease spirochete).
Probab=20.84  E-value=63  Score=13.65  Aligned_cols=11  Identities=18%  Similarity=0.229  Sum_probs=4.3

Q ss_pred             HHHHHHHHHCC
Q ss_conf             89999999579
Q gi|254781160|r  202 SEEKETLHSLP  212 (245)
Q Consensus       202 ~~E~~~l~~~~  212 (245)
                      +.+-+.|+..|
T Consensus       222 ~~~yk~LEDyg  232 (311)
T pfam05113       222 NAEYKALEDYG  232 (311)
T ss_pred             CCCHHHHHHHC
T ss_conf             52323366504


No 75 
>TIGR02609 doc_partner putative addiction module antidote; InterPro: IPR013432    This entry contains putative addiction module antidote proteins encoded by genes that appear recurrently in two-gene operons where the other gene encodes a Doc (death-on-curing) protein IPR006440 from INTERPRO. Note that these proteins tend to be found on bacterial chromosomes, not on plasmids..
Probab=20.55  E-value=64  Score=13.61  Aligned_cols=39  Identities=23%  Similarity=0.262  Sum_probs=27.0

Q ss_pred             EEEECHHHHHHHHHHCCCCCCCEE--EEEECCCCEEEEEEECCCC
Q ss_conf             899877987599870357898889--9997799879875302355
Q gi|254781160|r   21 QGKASGDQYHYLAHVLRMKEGDNI--LLFNGKDGEWLSKISYVGK   63 (245)
Q Consensus        21 ~i~L~~~~~hHl~kVlRlk~Gd~i--~i~dg~g~~~~~~I~~~~k   63 (245)
                      -+.|+.+-    ..-|+++.||+|  .++--+|+.-......+.+
T Consensus        11 vv~lpKE~----l~~L~~~~GDtl~i~~~~~~~g~~~~~~~~~~~   51 (77)
T TIGR02609        11 VVTLPKEV----LESLGLKEGDTLEIYVDEEEGGLRLKRADEVEK   51 (77)
T ss_pred             EEEECHHH----HHHCCCCCCCEEEEEEEECCCCEEEEEECCCHH
T ss_conf             26747488----974689999827899870799568998656723


No 76 
>TIGR00185 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 2; InterPro: IPR004440 The RNA methyltransferase, TrmH family, group 2 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification.; GO: 0008173 RNA methyltransferase activity, 0009451 RNA modification.
Probab=20.44  E-value=56  Score=13.97  Aligned_cols=95  Identities=8%  Similarity=0.126  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHH--HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCCCCCCCCCCCCCC-CCCC
Q ss_conf             5677754444566--56555542022011221223357889999751234434--33200000011233322333-2126
Q gi|254781160|r   94 LDYMIQKSVEMGM--GAIRPVITRYTQNTHYNMDRVRTYTISAAEQCDILTLP--FIYPPTTLEFLLKNWDHNCQ-IVFA  168 (245)
Q Consensus        94 ~~~ilqk~tELGV--~~I~p~~~~rs~~~~~k~eR~~~ii~eA~eQsgr~~lP--~i~~~~~l~~~l~~~~~~~~-~~~~  168 (245)
                      ---|++-|+--|.  +=|-|+-+.-..+.-++              +|=.+-+  .+..+.+++++++....... +++.
T Consensus        15 TGNI~R~Caat~~~LHLi~PlGF~~~DK~L~R--------------AGLdyw~fv~~~~H~s~E~fle~~~~~~~nlf~l   80 (161)
T TIGR00185        15 TGNIVRTCAATGTRLHLIKPLGFELDDKRLKR--------------AGLDYWEFVQLFYHKSWEEFLEAEKPQKGNLFLL   80 (161)
T ss_pred             CCHHHHHHHCCCCEEEEECCCCCCCCCCEEEE--------------CCCCCCCCEEEEECCCHHHHHHHCCCCCEEEEEE
T ss_conf             41120101115862456605786207814231--------------4787445232356255688886338997168888


Q ss_pred             CCHHC-CCCCHHHHHCCCCCCCEEEEECCCC-CCCHHHH
Q ss_conf             30001-2110222100367883599988888-8888999
Q gi|254781160|r  169 DETCG-SENSLEKLHAIAHIPNVAILIGPEG-GYHSEEK  205 (245)
Q Consensus       169 ~~~~~-~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~  205 (245)
                      ..... ..+...  -+........++.|+|- |. |..+
T Consensus        81 T~~G~~t~~~~~--~~~~~~d~~yl~fG~ET~GL-P~~~  116 (161)
T TIGR00185        81 TKKGDKTPDHIS--VTYQDGDELYLVFGQETKGL-PKSL  116 (161)
T ss_pred             EECCCCCCCCEE--EEECCCCCEEEEECCCCCCC-HHHH
T ss_conf             403887745046--65437861699836877551-2899


No 77 
>KOG2589 consensus
Probab=20.24  E-value=55  Score=14.05  Aligned_cols=42  Identities=21%  Similarity=0.312  Sum_probs=29.4

Q ss_pred             EECCCCCCCCEEEECHHHHHHHHHHCC-CCCCCEEEEEECCCCE
Q ss_conf             408544788889987798759987035-7898889999779987
Q gi|254781160|r   11 FVDFPLCIKTQGKASGDQYHYLAHVLR-MKEGDNILLFNGKDGE   53 (245)
Q Consensus        11 f~~~~l~~~~~i~L~~~~~hHl~kVlR-lk~Gd~i~i~dg~g~~   53 (245)
                      |++.+=..|=.+.-.|.+.-|+ |||| +++||+|.+|-|.|..
T Consensus       199 fINHDCrpnCkFvs~g~~tacv-kvlRDIePGeEITcFYgs~fF  241 (453)
T KOG2589         199 FINHDCRPNCKFVSTGRDTACV-KVLRDIEPGEEITCFYGSGFF  241 (453)
T ss_pred             HHCCCCCCCCEEECCCCCEEEE-EHHHCCCCCCEEEEEECCCCC
T ss_conf             6267778886650689860320-041227778536786225656


No 78 
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912    The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.  .
Probab=20.09  E-value=65  Score=13.55  Aligned_cols=22  Identities=18%  Similarity=0.143  Sum_probs=10.1

Q ss_pred             CCEEEEECCCCCCCHHHHHHHH
Q ss_conf             8359998888888889999999
Q gi|254781160|r  188 PNVAILIGPEGGYHSEEKETLH  209 (245)
Q Consensus       188 ~~i~i~IGPEGGfs~~E~~~l~  209 (245)
                      |..--+|=-++|-|++|++.+.
T Consensus       338 KvYrALV~~~~~v~d~dl~~l~  359 (450)
T TIGR01213       338 KVYRALVEVDDPVSDEDLEELV  359 (450)
T ss_pred             EEEEEEEEECCCCCHHHHHHHH
T ss_conf             1588868875997889999999


No 79 
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=20.04  E-value=66  Score=13.54  Aligned_cols=29  Identities=21%  Similarity=0.418  Sum_probs=22.8

Q ss_pred             HHCCCCCCCEEEEEECCCCEEEEEEECCC
Q ss_conf             70357898889999779987987530235
Q gi|254781160|r   34 HVLRMKEGDNILLFNGKDGEWLSKISYVG   62 (245)
Q Consensus        34 kVlRlk~Gd~i~i~dg~g~~~~~~I~~~~   62 (245)
                      +=|+++.||.|.+.-|+..--.++|..+.
T Consensus         8 ~K~kIkkGD~V~VisGkdKGk~G~Vl~v~   36 (90)
T CHL00141          8 KKMHVKKGDTVQVISGKDKGKIGEVLKII   36 (90)
T ss_pred             CCEEEECCCEEEEEECCCCCCCEEEEEEE
T ss_conf             14067089999991667899735799998


Done!