Query         gi|254780603|ref|YP_003065016.1| tRNA/rRNA methyltransferase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 282
No_of_seqs    133 out of 4339
Neff          8.0 
Searched_HMMs 39220
Date          Sun May 29 23:21:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780603.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG0566 SpoU rRNA methylases [ 100.0       0       0  412.6  17.5  251   24-282     3-259 (260)
  2 PRK11181 23S rRNA (guanosine-2 100.0       0       0  411.4  18.4  232   49-281     3-243 (244)
  3 PRK10864 putative methyltransf 100.0       0       0  400.5   9.0  235   45-281   107-347 (348)
  4 PRK11081 tRNA guanosine-2'-O-m 100.0       0       0  288.4   9.5  150  130-281    16-166 (229)
  5 KOG2506 consensus              100.0 2.8E-45       0  278.4  11.2  251   25-280   103-371 (371)
  6 pfam00588 SpoU_methylase SpoU  100.0 8.8E-44       0  270.3   8.7  141  133-274     1-142 (142)
  7 KOG0838 consensus              100.0 2.1E-38 5.3E-43  239.5  10.0  217   46-279    40-270 (271)
  8 PRK10358 putative tRNA/rRNA me 100.0 5.6E-36 1.4E-40  225.6   9.0  145  135-281     3-149 (157)
  9 TIGR00186 rRNA_methyl_3 RNA me 100.0 8.9E-33 2.3E-37  207.2   6.9  231   49-280     3-271 (271)
 10 COG0219 CspR Predicted rRNA me 100.0   4E-31   1E-35  197.7   9.0  147  134-281     3-150 (155)
 11 TIGR00185 rRNA_methyl_2 RNA me 100.0 2.3E-31   6E-36  199.1   5.6  148  134-281     2-156 (161)
 12 KOG0839 consensus               99.9 1.8E-25 4.5E-30  165.4   3.6  148  131-279  1324-1474(1477)
 13 PRK10433 putative RNA methyltr  99.9   2E-23 5.2E-28  153.6  10.0  141  134-279     3-158 (228)
 14 TIGR00050 rRNA_methyl_1 RNA me  99.9 1.8E-23 4.5E-28  153.9   9.1  145  133-279     4-166 (253)
 15 COG0565 LasT rRNA methylase [T  99.9 4.6E-22 1.2E-26  145.8   9.3  141  133-279     4-159 (242)
 16 pfam08032 SpoU_sub_bind RNA 2'  98.9 2.5E-09 6.4E-14   72.9   5.5   72   50-123     1-74  (75)
 17 COG4080 SpoU rRNA Methylase fa  97.9 7.7E-05   2E-09   47.1   8.5  141  133-279     2-146 (147)
 18 pfam09936 DUF2168 Uncharacteri  97.8 5.1E-05 1.3E-09   48.1   5.5  124  146-276    29-182 (185)
 19 PRK03958 tRNA 2'-O-methylase;   97.2  0.0013 3.4E-08   40.0   6.9  125  142-277    14-147 (175)
 20 COG1303 Uncharacterized protei  96.6  0.0022 5.7E-08   38.7   3.4  119  148-277    21-147 (179)
 21 PRK12703 tRNA 2'-O-methylase;   96.0   0.014 3.5E-07   34.2   4.8  124  142-276    13-141 (339)
 22 COG4752 Uncharacterized protei  95.5   0.021 5.4E-07   33.2   4.1   50  226-276   133-183 (190)
 23 COG1385 Uncharacterized protei  94.7    0.27 6.8E-06   26.8   7.9  138  132-272    77-236 (246)
 24 PRK11713 16S rRNA m3U1498 meth  94.5    0.29 7.4E-06   26.7   7.7  138  135-276    78-239 (243)
 25 pfam09895 DUF2122 RecB-family   94.4   0.065 1.7E-06   30.4   4.2   83  188-276    21-105 (105)
 26 pfam04452 Methyltrans_RNA RNA   93.8    0.21 5.3E-06   27.5   5.9  135  134-273    62-220 (225)
 27 PRK02135 hypothetical protein;  93.7   0.052 1.3E-06   31.0   2.7  115  143-280    79-197 (199)
 28 pfam01994 Trm56 tRNA ribose 2'  93.3   0.096 2.4E-06   29.4   3.5   81  191-277     9-93  (121)
 29 pfam04407 DUF531 Protein of un  91.5    0.28 7.1E-06   26.8   4.0  136  134-273     2-164 (174)
 30 pfam04013 DUF358 Protein of un  90.3     0.3 7.7E-06   26.6   3.3  118  143-279    79-197 (199)
 31 KOG0838 consensus               90.3   0.078   2E-06   29.9   0.2   53  222-275   133-189 (271)
 32 TIGR01362 KDO8P_synth 3-deoxy-  81.6    0.81 2.1E-05   24.1   1.6   56  139-203   200-271 (279)
 33 TIGR00046 TIGR00046 conserved   77.5     4.2 0.00011   20.0   4.2  130  132-262    79-240 (258)
 34 PRK04171 ribosome biogenesis p  74.1     6.5 0.00017   18.9   4.6   80  195-281   137-219 (221)
 35 pfam02590 SPOUT_MTase Predicte  72.3     7.2 0.00018   18.7   5.0   73  199-279    61-145 (155)
 36 COG1901 Uncharacterized conser  68.7     4.1  0.0001   20.1   2.4  114  143-280    79-196 (197)
 37 PRK00103 SPOUT methyltransfera  63.6      11 0.00028   17.6   4.4   73  200-279    62-144 (156)
 38 pfam04705 TSNR_N Thiostrepton-  55.5      15 0.00039   16.8   7.8   94   24-120     9-103 (115)
 39 PRK13398 3-deoxy-7-phosphohept  54.0     5.6 0.00014   19.3   1.0   32  136-167   199-233 (266)
 40 TIGR01456 CECR5 HAD-superfamil  53.3     3.8 9.7E-05   20.2   0.0   16  150-165    97-112 (325)
 41 KOG3925 consensus               52.8     4.4 0.00011   19.9   0.3   30  206-236   277-311 (371)
 42 COG3426 Butyrate kinase [Energ  51.0     7.6 0.00019   18.5   1.2   51  140-190   102-154 (358)
 43 COG2106 Uncharacterized conser  47.9      12  0.0003   17.4   1.8   63  195-258   175-245 (272)
 44 pfam02598 DUF171 Uncharacteriz  43.4      13 0.00033   17.2   1.5   66  189-255   180-261 (283)
 45 COG3222 Uncharacterized protei  43.4      12  0.0003   17.4   1.3   77  146-230    88-167 (211)
 46 COG1419 FlhF Flagellar GTP-bin  43.2      24 0.00061   15.7   3.0  120  132-258   202-342 (407)
 47 pfam09837 DUF2064 Uncharacteri  40.4      27 0.00068   15.4   2.9   77  141-225    39-119 (121)
 48 PRK11561 isovaleryl CoA dehydr  38.9      17 0.00042   16.6   1.4   25  218-242   266-290 (538)
 49 TIGR02894 DNA_bind_RsfA transc  38.6     6.5 0.00017   18.9  -0.7   28  135-178    30-57  (163)
 50 pfam07047 OPA3 Optic atrophy 3  37.7      25 0.00063   15.6   2.2   22  261-282    81-102 (134)
 51 KOG2882 consensus               37.7      14 0.00035   17.0   0.9   28   47-76     36-63  (306)
 52 COG1772 Uncharacterized protei  37.4      30 0.00076   15.1   3.3  135  134-272     2-163 (178)
 53 COG2242 CobL Precorrin-6B meth  35.8      32 0.00081   15.0   2.8   40  131-172    57-96  (187)
 54 KOG1618 consensus               35.6      24 0.00062   15.6   1.9   31   46-76     42-80  (389)
 55 TIGR01855 IMP_synth_hisH imida  34.2      32 0.00082   14.9   2.3   31  135-167     1-35  (211)
 56 pfam02784 Orn_Arg_deC_N Pyrido  33.7      32 0.00081   15.0   2.2   21  195-215   140-160 (245)
 57 cd06840 PLPDE_III_Bif_AspK_Dap  33.4      35 0.00088   14.7   4.2   13   51-63     63-75  (368)
 58 pfam05341 DUF708 Protein of un  33.3      35 0.00089   14.7   2.4   54  218-274    46-99  (105)
 59 TIGR01245 trpD anthranilate ph  32.6      27 0.00068   15.4   1.7   39  135-173   184-224 (331)
 60 TIGR01135 glmS glucosamine--fr  31.8      37 0.00094   14.6   5.2   76  203-281   527-612 (628)
 61 TIGR01055 parE_Gneg DNA topois  30.6      39 0.00099   14.5   5.0  120   44-179   423-543 (647)
 62 TIGR03565 alk_sulf_monoox alka  29.3      41   0.001   14.3   3.3   11  108-118   144-154 (346)
 63 pfam00851 Peptidase_C6 Helper   28.0      34 0.00087   14.8   1.6   28  212-239   291-318 (453)
 64 PRK13397 3-deoxy-7-phosphohept  27.9      40   0.001   14.4   1.9   31  143-173   134-164 (250)
 65 TIGR01678 FAD_lactone_ox sugar  26.6      42  0.0011   14.3   1.9   20  219-238   217-236 (505)
 66 PRK11052 malQ 4-alpha-glucanot  25.8      47  0.0012   14.0   2.7   39  140-178   160-207 (694)
 67 cd06843 PLPDE_III_PvsE_like Ty  25.3      48  0.0012   13.9   4.7   55   49-105    52-107 (377)
 68 TIGR00064 ftsY signal recognit  24.8      43  0.0011   14.2   1.6   78  130-216    79-175 (284)
 69 COG0187 GyrB Type IIA topoisom  24.4      50  0.0013   13.8   3.4   33   41-73    414-446 (635)
 70 PRK11440 hypothetical protein;  23.4      53  0.0013   13.7   2.9   65  134-200   122-186 (188)
 71 TIGR02303 HpaG-C-term 4-hydrox  23.3      25 0.00064   15.6   0.2   14  134-147   159-173 (249)
 72 TIGR02924 ICDH_alpha isocitrat  22.8      33 0.00083   14.9   0.7   95  145-244   291-394 (481)
 73 TIGR01607 PST-A Plasmodium sub  21.1      29 0.00075   15.2   0.2   21  196-216    64-84  (379)
 74 TIGR00750 lao LAO/AO transport  21.1      52  0.0013   13.7   1.4  114  145-259   123-275 (333)
 75 TIGR02080 O_succ_thio_ly O-suc  20.9      27  0.0007   15.3  -0.0   37  235-272   302-341 (383)
 76 TIGR01452 PGP_euk phosphoglyco  20.8      43  0.0011   14.2   0.9   32   47-80     16-47  (288)
 77 pfam07075 DUF1343 Protein of u  20.5      61  0.0015   13.4   2.3  133   52-205    13-164 (359)
 78 PRK13172 consensus              20.5      32 0.00081   15.0   0.2   11  157-167   125-135 (213)
 79 PRK10126 tyrosine phosphatase;  20.5      19 0.00049   16.2  -0.9   13  147-159    10-22  (147)
 80 pfam03308 ArgK ArgK protein. T  20.3      61  0.0016   13.3   3.1  115  144-263   107-241 (267)

No 1  
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=0  Score=412.63  Aligned_cols=251  Identities=32%  Similarity=0.478  Sum_probs=221.6

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHH--HHHCCCCEEEECHHHH
Q ss_conf             22376567776543112211128819998578899999789818999997378433543455--4326996999768998
Q gi|254780603|r   24 RRNHRDYKKMQSFNQKSRHTSQPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDA--NLPHPFPVKTVPPQTI  101 (282)
Q Consensus        24 ~~~n~~~k~~~~l~~k~k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~--~l~~~~~I~~v~~~~l  101 (282)
                      ++.|+..+.+.++      |.+.+.|++||.|+|.++|.+++ .+..+|++++...+..+..  ....+++++.++.+.+
T Consensus         3 s~~n~~~~~~~~~------r~~~~~~~~~G~~~v~~al~~~~-~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l   75 (260)
T COG0566           3 SPANPRVKALKKL------RGRAGEFLIEGEHAVLEALASGP-KIVRILVTEGRLPRFEELLALAAAKGIPVYVVSEAIL   75 (260)
T ss_pred             CCHHHHHHHHHHH------HCCCCCEEEECHHHHHHHHHCCC-CCEEEEEECCCCHHHHHHHHHHHHCCCCEEEECHHHH
T ss_conf             7214566899986------30577089971899999996797-7069998434321378999988765992899688999


Q ss_pred             HHHHCCCCCCCCCCEEEECCCCCCHHHCC---CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH
Q ss_conf             77524777777442024115555401126---650688723432068899999998642001100136863200000134
Q gi|254780603|r  102 DKIVGKEAVHQGLALETAPLLSPTLDAVR---NSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAK  178 (282)
Q Consensus       102 ~~i~~~~~~hqGi~a~~~~~~~~~l~~~~---~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~r  178 (282)
                      +++++.. +|||+++.+.+......+.+.   .++++|+||+|+||+|+|+|+|||+|||+++||++++++|+++++++|
T Consensus        76 ~~~~~~~-~hqGi~a~~~~~~~~~~~~~~~~~~~~~~lvLd~V~DP~NlGaIiRtA~a~Gv~~Vi~~~~~~~~~~~~v~r  154 (260)
T COG0566          76 DKLSGTE-NHQGIVAVVKKRRYPLLDDLLDAEAQPLLLVLDGVTDPHNLGAIIRTADAFGVDGVILPKRRADPLNPKVIR  154 (260)
T ss_pred             HHHHCCC-CCCEEEEEECCCCCCCHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHCCCEEEECCCCCCCCCHHHEE
T ss_conf             9875578-864057896355556524442024588699991787887124888759873898899889866774534325


Q ss_pred             HHHHHHHHHCCCCCCC-CCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCC
Q ss_conf             4433332110122232-211222222210000000123332211223689889997586789877999858939992789
Q gi|254780603|r  179 SASGALEHIPYIRISN-LTDALQKMHSWGFQTIGLSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMP  257 (282)
Q Consensus       179 as~Ga~~~l~~~~~~~-~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~  257 (282)
                      +|+|++|++|++++.| ...+++.+++.|||++|++.++..++++.++++|.+||||||++|||+++++.||.+|+|||.
T Consensus       155 ~s~Ga~~~vp~~~~~n~~~~~~~~~~~~G~~v~~t~~~~~~~~~~~~~~~~~aLvlG~Eg~Gls~~~~~~~D~~v~IPm~  234 (260)
T COG0566         155 ASAGAAFHVPVIRVTNLARTLLELLKEAGFWVVATSLDGEVDLYETDLPKKTALVLGNEGEGLSRLLLEHADQLVRIPMA  234 (260)
T ss_pred             ECCCCCCCCCEEEEECCHHHHHHHHHHCCCEEEEECCCCCCCHHHCCCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCC
T ss_conf             41771005735888077999999999769489998588874311026778779998789888589999517847993589


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             6874378999999999999876149
Q gi|254780603|r  258 GIIKALNVSNAAAVALYITQNHFAK  282 (282)
Q Consensus       258 ~~~~SLNvs~a~ai~l~~~~~~~~~  282 (282)
                      |.++|||||||+||+|||..||+..
T Consensus       235 G~v~SLNVsvAagI~Lye~~rq~~~  259 (260)
T COG0566         235 GKVESLNVSVAAGILLYEARRQRRA  259 (260)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             9865108999999999999986445


No 2  
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=100.00  E-value=0  Score=411.44  Aligned_cols=232  Identities=29%  Similarity=0.439  Sum_probs=209.3

Q ss_pred             EEEEEHHHHHHHHHCCCEEEEEEEECCCCCCC-CCHH--HHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCCCCC
Q ss_conf             99985788999997898189999973784335-4345--54326996999768998775247777774420241155554
Q gi|254780603|r   49 LFLYGVHTVSAALNNPSRKIFQLLATKNALAR-LDWD--ANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLLSPT  125 (282)
Q Consensus        49 ~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~-~~~~--~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~~~~  125 (282)
                      .+|||.|+|+|+|+++++.+..+|+.++...+ +...  .....++++..++++.|++++.. .+|||+++.+.|.....
T Consensus         3 e~IyG~haV~eaL~~~~~~i~~l~v~~~~~~~~~~~i~~~a~~~~I~v~~v~~~~l~~l~~~-~~HQGVva~v~~~~~~~   81 (244)
T PRK11181          3 EMIYGIHAVQALLERAPERFIEVFVLKGREDKRLLPLINELESQGVVIQLANRQTLDEKAEG-AVHQGIIARVKPAKQLN   81 (244)
T ss_pred             CEEEEHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCEEEECHHHHHHHCCC-CCCCEEEEEEECCCCCC
T ss_conf             88987999999983897646899985798776899999999976997799689999875168-87853799983245478


Q ss_pred             HHHC------CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             0112------6650688723432068899999998642001100136863200000134443333211012223221122
Q gi|254780603|r  126 LDAV------RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDAL  199 (282)
Q Consensus       126 l~~~------~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l  199 (282)
                      ..++      .+++++++||+||||+|+|+|+|||+|||+++|+++++++++++++++|+|+||.|++|++++.|+.+++
T Consensus        82 ~~~l~~~l~~~~~~lil~LD~I~DP~NlGaIiRsA~afGv~~vil~~~~~~~~~~~v~k~S~Ga~~~~pi~~~~nl~~~l  161 (244)
T PRK11181         82 ENDLDDLLASTEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLTATAKKVACGAAETVPLIRVTNLARTM  161 (244)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHCHHHCCCEEEECCHHHHH
T ss_conf             87899998357898799981887873899999999981998999789977854258888741423218816958999999


Q ss_pred             CCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             22222100000001233322112236898899975867898779998589399927896874378999999999999876
Q gi|254780603|r  200 QKMHSWGFQTIGLSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH  279 (282)
Q Consensus       200 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~  279 (282)
                      +.++++|||+||++.+++.++++.+++.|.+||||||++||++.+++.||+.|+|||.|.+||||||||+||+|||+.||
T Consensus       162 ~~lk~~g~~i~g~~~~~~~~~~~~~~~~~~alvlGsE~~Gl~~~~~~~~d~~v~Ip~~g~~~SLNVsvAa~I~lyE~~RQ  241 (244)
T PRK11181        162 RMLQEKNVWIVGTAGEADHTLYQSKLTGPLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQ  241 (244)
T ss_pred             HHHHHCCEEEEEECCCCCCCCCHHCCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             99886596999524666766410105787699987776665899997599899807999985587999999999999865


Q ss_pred             HC
Q ss_conf             14
Q gi|254780603|r  280 FA  281 (282)
Q Consensus       280 ~~  281 (282)
                      |.
T Consensus       242 R~  243 (244)
T PRK11181        242 RL  243 (244)
T ss_pred             CC
T ss_conf             05


No 3  
>PRK10864 putative methyltransferase; Provisional
Probab=100.00  E-value=0  Score=400.49  Aligned_cols=235  Identities=23%  Similarity=0.320  Sum_probs=214.2

Q ss_pred             CCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHH--HHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCC
Q ss_conf             28819998578899999789818999997378433543455--4326996999768998775247777774420241155
Q gi|254780603|r   45 QPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDA--NLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLL  122 (282)
Q Consensus        45 ~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~--~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~  122 (282)
                      ..+...|||.|+|.+++.+.++.+..+|++++...++...+  ...++..+..|+..+|+++++++ .||||++.+.+..
T Consensus       107 r~ee~~vyG~nA~~A~~~~rp~ai~Riw~t~e~~~r~~~~l~~~~a~~~~~~~V~~~eL~~~tgt~-hHqGi~l~v~~~~  185 (348)
T PRK10864        107 RAEETRVYGENACQALFQSRPDAIVRAWFIQSVTPRFKEALRWMAANRKAYHVVDEAELAKASGTE-HHGGVCFLIKKRN  185 (348)
T ss_pred             CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHCCC-CCCEEEEEECCCC
T ss_conf             103431022789999997292989999988876488999999999769759984899998874888-7340689976778


Q ss_pred             CCCHHHC----CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             5540112----665068872343206889999999864200110013686320000013444333321101222322112
Q gi|254780603|r  123 SPTLDAV----RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDA  198 (282)
Q Consensus       123 ~~~l~~~----~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~  198 (282)
                      ...++.+    ..++++|+||+|+||+|||+|+|||+|||+++||+++. ..++++.++|+|+|++|++|++++.|+.++
T Consensus       186 ~~~l~~~l~~~~~~~~lL~LDgV~DP~NlGAIiRSAaafGv~gVIl~~~-~~~~s~~avr~SaGa~e~vpv~~v~nl~~a  264 (348)
T PRK10864        186 GTDVQQWLAQAGAQDCVLALEDVGNPHNLGGIMRSCAHFGVKGVVVQDA-ALLESGAAIRTAEGGAEHVQPITGDSIVDV  264 (348)
T ss_pred             CCCHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCEEEECCC-CCCCCHHHHHHHCCHHCCCCEEEECCHHHH
T ss_conf             8799999960799985999789779715889999999858988997999-877437889663322200635997789999


Q ss_pred             CCCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             22222210000000123332211223689889997586789877999858939992789687437899999999999987
Q gi|254780603|r  199 LQKMHSWGFQTIGLSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQN  278 (282)
Q Consensus       199 l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~  278 (282)
                      |+.|+++|||+|+++.++..++++.+++.+++||||+|++||++.+++.||+.|+|||.+.+||||||||+||+|||..|
T Consensus       265 L~~Lk~aG~~Ivg~s~~~~~~l~~~~l~~~~vLVlGsEg~GLs~~v~~~cD~~V~IPm~g~veSLNVSVAagIlLyE~~R  344 (348)
T PRK10864        265 LDDFRQAGYTIVTTSSHKGKPLFKAELPAKMVLVLGQEYDGLSDAARSPGDLSVKIDGTGNVESLNVSVATGVLLAEWWR  344 (348)
T ss_pred             HHHHHHCCCEEEEECCCCCCCHHHCCCCCCEEEEECCCCCCCCHHHHHHCCEEEECCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999889689985477886475636789889998998855069999758889982799998578899999999999987


Q ss_pred             HHC
Q ss_conf             614
Q gi|254780603|r  279 HFA  281 (282)
Q Consensus       279 ~~~  281 (282)
                      |+.
T Consensus       345 Q~~  347 (348)
T PRK10864        345 QNK  347 (348)
T ss_pred             HHC
T ss_conf             316


No 4  
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=100.00  E-value=0  Score=288.37  Aligned_cols=150  Identities=23%  Similarity=0.337  Sum_probs=135.5

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             66506887234320688999999986420011001368632000001344433332110122232211222222210000
Q gi|254780603|r  130 RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQT  209 (282)
Q Consensus       130 ~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i  209 (282)
                      ..+.++|+||+|+||+|+|+|+|||+|||+++|.+.....+.  ....++|+|+.+++++..+.++.+++..||+.||++
T Consensus        16 Rq~dL~vvLD~V~dP~NlGAIiRTadA~Gv~~V~~v~~~~~~--~~~~~ta~Gs~~wv~v~~~~~i~~~i~~Lk~~G~~I   93 (229)
T PRK11081         16 RQPDLTVCLEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRM--RTMGSTAAGSNSWVQVKTHRTIGDAVAHLKAQGMQI   93 (229)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCH--HHHHHHHHHHHCEEEEEEECCHHHHHHHHHHCCCEE
T ss_conf             589869997688998509999999998389746896787520--111144303440045578478999999999749989


Q ss_pred             HHCCCC-CCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             000123-332211223689889997586789877999858939992789687437899999999999987614
Q gi|254780603|r  210 IGLSSD-SKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNHFA  281 (282)
Q Consensus       210 ~~~~~~-~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~~  281 (282)
                      ++++.. .+.++.++++++|++||||||++|||+++++.||+.|.|||.|.+|||||||||||+|||++|||.
T Consensus        94 ~at~l~~~avd~~~~d~t~ptalVlGnE~~GiS~~~~~~aD~~I~IPM~G~veSLNVSVAaaIiLyEa~RQR~  166 (229)
T PRK11081         94 LATHLSDKAVDFREIDYTRPTAILMGQEKTGISQEALALADQDIIIPMIGMVQSLNVSVASALILYEAQRQRQ  166 (229)
T ss_pred             EEEECCCCCCCHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9993688864076704568769998587777599999828957996899998862599999999999999898


No 5  
>KOG2506 consensus
Probab=100.00  E-value=2.8e-45  Score=278.37  Aligned_cols=251  Identities=19%  Similarity=0.268  Sum_probs=187.6

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEEEECHHHHHHH
Q ss_conf             23765677765431122111288199985788999997898189999973784335434554326996999768998775
Q gi|254780603|r   25 RNHRDYKKMQSFNQKSRHTSQPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVKTVPPQTIDKI  104 (282)
Q Consensus        25 ~~n~~~k~~~~l~~k~k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~~v~~~~l~~i  104 (282)
                      -..+.+-........+++|.++...+.||+.++.++|+.+-..-..+|-+.+.......+.  ..++.|+.|....+..+
T Consensus       103 lgd~~fs~~lt~v~srsf~~kqv~ii~egRrliqdaLk~g~~~ev~~Fs~~~qla~~p~e~--e~g~~i~kVks~d~K~w  180 (371)
T KOG2506         103 LGDRRFSIVLTIVKSRSFREKQVRIISEGRRLIQDALKGGVHREVCMFSTNKQLATTPIEC--EAGIRIVKVKSLDMKKW  180 (371)
T ss_pred             CCCCCHHHHHEEEECCCCHHHCCCCCCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCHHH--HCCEEEEECCHHHHHHH
T ss_conf             3763022220011014303322532223223688886246431378820444355568445--33704884238888887


Q ss_pred             HCCCCCCCCCCEE-EECCCC-----CCHHH---CCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHH
Q ss_conf             2477777744202-411555-----54011---26650688723432068899999998642001100136863200000
Q gi|254780603|r  105 VGKEAVHQGLALE-TAPLLS-----PTLDA---VRNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAV  175 (282)
Q Consensus       105 ~~~~~~hqGi~a~-~~~~~~-----~~l~~---~~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~  175 (282)
                      ++-. +++|+.+- ..|...     ...+.   ...-++.+|||+|+||||||||+|||+||+|+++++.++|||||++|
T Consensus       181 SsLv-SP~svmaIf~~P~d~hl~k~~a~~q~~~s~~lp~~lvcdnirdpgnlgti~rsaaa~~cs~v~lt~gccdpwe~k  259 (371)
T KOG2506         181 SSLV-SPESVMAIFLMPIDLHLDKDIATDQNKWSPSLPRVLVCDNIRDPGNLGTIVRSAAAFNCSGVFLTPGCCDPWEDK  259 (371)
T ss_pred             HCCC-CCCCHHHHCCCCCHHCHHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCEEECCCCCCCCCHH
T ss_conf             5156-871043321585000103537999860388887478853677885067899987507876136657767854246


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCHHHHCC-CCCCCC---CC--CCCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             13444333321101222322112---222222100000001-233322---11--2236898899975867898779998
Q gi|254780603|r  176 LAKSASGALEHIPYIRISNLTDA---LQKMHSWGFQTIGLS-SDSKKP---LE--QEIKNDKIALILGAEGKGLRPKTQE  246 (282)
Q Consensus       176 ~~ras~Ga~~~l~~~~~~~~~~~---l~~~~~~~~~i~~~~-~~~~~~---~~--~~~~~~~~~lv~G~E~~Gl~~~~~~  246 (282)
                      ++|+++||+|++||... +|+..   +.......+..+..+ +...++   +.  .-....+.|||+|+|++|+|++-.+
T Consensus       260 alrag~ga~fr~pi~~~-~w~~l~l~~pp~~ad~c~~~~a~t~qr~~~~~k~~e~ad~~~ap~~liigge~~gvseea~~  338 (371)
T KOG2506         260 ALRAGRGASFRLPIVSG-NWNHLKLLEPPFQADLCAGHPATTTQRLKPVSKLVEFADSLAAPLCLIIGGEGNGVSEEARK  338 (371)
T ss_pred             HHHCCCCCCEECCEECC-CHHHHHCCCCHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCEEEEECCCCCCCCHHHHH
T ss_conf             66435775066244568-65441213886677650476476665523203566777643676179974676774799998


Q ss_pred             HCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             5893999278968743789999999999998761
Q gi|254780603|r  247 TATSMAHLHMPGIIKALNVSNAAAVALYITQNHF  280 (282)
Q Consensus       247 ~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~  280 (282)
                      .| ..+.|||.+++||||||+|++|+|||.+|++
T Consensus       339 ~~-~lvgip~a~g~dslnva~a~~illfel~r~l  371 (371)
T KOG2506         339 VC-VLVGIPMAGGFDSLNVAVAGGILLFELQRLL  371 (371)
T ss_pred             HH-HHCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             99-9728764477213456777779998775139


No 6  
>pfam00588 SpoU_methylase SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet.
Probab=100.00  E-value=8.8e-44  Score=270.26  Aligned_cols=141  Identities=37%  Similarity=0.593  Sum_probs=134.6

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             0688723432068899999998642001100136-863200000134443333211012223221122222221000000
Q gi|254780603|r  133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTK-RYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIG  211 (282)
Q Consensus       133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~-~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~  211 (282)
                      |++|+||+++||+|+|+|+|||++||++.|++.+ .+++++++++.|+|+|+++++|+.++.|+.++++.+++.|+++++
T Consensus         1 p~~vvL~~i~~p~NlG~i~Rta~~fG~~~v~l~~~~~~~~~~~~~~r~s~ga~~~i~~~~~~~~~~~~~~~~~~~~~i~~   80 (142)
T pfam00588         1 PLIVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADLYNPKAIRASAGALFHLPLVIVDNLEEALKDLKEAGYWIIA   80 (142)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHCCCEEEC
T ss_conf             98999957988776999999999839996435578767977789999976775237832843399999998874950111


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             012333221122368988999758678987799985893999278968743789999999999
Q gi|254780603|r  212 LSSDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALY  274 (282)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~  274 (282)
                      ++..+ +++.+++++++.+||||+|++|||+++++.||+.|+|||.+.++|||||+|+||+||
T Consensus        81 ~~~~~-~~~~~~~~~~~~~lv~G~E~~Gls~~~l~~~d~~v~IP~~g~~~SLNvs~A~aI~ly  142 (142)
T pfam00588        81 TSLKG-KPLYEIDFPKKVALVFGNEGTGLSNEVLELCDRLVRIPMSGEVESLNVAVAAAIILY  142 (142)
T ss_pred             CCCCC-CCHHHHCCCCCEEEEECCCCCCCCHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             34467-487781468872899778778989999986997999749889963549999999969


No 7  
>KOG0838 consensus
Probab=100.00  E-value=2.1e-38  Score=239.47  Aligned_cols=217  Identities=32%  Similarity=0.441  Sum_probs=186.4

Q ss_pred             CCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCC-CHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCCCC
Q ss_conf             881999857889999978981899999737843354-3455432699699976899877524777777442024115555
Q gi|254780603|r   46 PENLFLYGVHTVSAALNNPSRKIFQLLATKNALARL-DWDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLLSP  124 (282)
Q Consensus        46 ~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~-~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~~~  124 (282)
                      .+...++|.++|.++|.++.+.+...|+.....-.- .....+.+  .+..+++..|+.++... .|||+++...     
T Consensus        40 ~~~e~~~G~~sv~~al~~~kR~~~~~~~~~~~~~~~~e~~~v~~~--~~~~~s~h~L~~~t~~r-~h~g~~leas-----  111 (271)
T KOG0838          40 LGGESVFGTHSVLAALSNGKRDCRGLLLQSATDFRSTEFELVLRR--DIEAVSKHDLNSLTDFR-PHNGILLEAS-----  111 (271)
T ss_pred             CCCCEEECHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEEHHHH--HHHCCCHHHHHHHHHHC-CCCCEEEEEE-----
T ss_conf             653112201566888753665412555201455576413313332--43305945677887631-2232687657-----


Q ss_pred             CHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             40112665068872343206889999999864200110013686320000013444333321101222322112222222
Q gi|254780603|r  125 TLDAVRNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHS  204 (282)
Q Consensus       125 ~l~~~~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~  204 (282)
                               ++++||++.||+|+|+|+|+|++||++++.+......+.++.+.++|+||.+++||.++.+..+|+...++
T Consensus       112 ---------l~vylde~tDp~n~gaI~rsA~~lg~~~v~lv~~n~s~lS~~vskss~gale~l~I~q~~~~~efl~vsva  182 (271)
T KOG0838         112 ---------LCVYLDEVTDPQNIGAIIRSAYFLGADGVLLVKGNSSPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVA  182 (271)
T ss_pred             ---------EEEECCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHCHHHEEEHHHCCCHHHHHHHHHH
T ss_conf             ---------77640575687506778776887467715897336887864677765021416638773888999899986


Q ss_pred             CCCHHHHCCCCC-------CCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCC------CCCCHHHHHHHHHH
Q ss_conf             100000001233-------32211223689889997586789877999858939992789------68743789999999
Q gi|254780603|r  205 WGFQTIGLSSDS-------KKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMP------GIIKALNVSNAAAV  271 (282)
Q Consensus       205 ~~~~i~~~~~~~-------~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~------~~~~SLNvs~a~ai  271 (282)
                      +|++++++..-.       ...+...++..|+++|+|||+.|+++.+++.||..++||++      +.++|||||+|+++
T Consensus       183 aG~~l~~t~~~~~~~~~~~~~~l~~~~~~~Pv~lv~Gneg~Gi~~~vl~~~d~~~si~~n~~~~d~~~v~SlNvSvaa~l  262 (271)
T KOG0838         183 AGIRLHGTCSWAPASKTISAVSLKFIDPEEPVALVLGNEGAGIRPGVLELCDLRVSIPGNGFEKDNGAVDSLNVSVAAGL  262 (271)
T ss_pred             CCEEEEEEECCCCCCCCCCCHHHHHCCCCCCEEEEECCCCCCCCHHHHHCCCEEEECCCCCCCCCCCCEEECCCHHHHHH
T ss_conf             75589996147677664030244301778974898546555447113424562675378762467763121110478889


Q ss_pred             HHHHHHHH
Q ss_conf             99999876
Q gi|254780603|r  272 ALYITQNH  279 (282)
Q Consensus       272 ~l~~~~~~  279 (282)
                      ++|++..+
T Consensus       263 l~~~~~~~  270 (271)
T KOG0838         263 LLYHFLNE  270 (271)
T ss_pred             HHHHHHHC
T ss_conf             88888506


No 8  
>PRK10358 putative tRNA/rRNA methyltransferase YibK; Provisional
Probab=100.00  E-value=5.6e-36  Score=225.56  Aligned_cols=145  Identities=19%  Similarity=0.185  Sum_probs=130.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCC
Q ss_conf             88723432068899999998642001100136863200000134443333211012223221122222221000000012
Q gi|254780603|r  135 LMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSS  214 (282)
Q Consensus       135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~  214 (282)
                      -|||.+++.|+|+|+|+|+|++||++.+++.+.+++..++++.||++++|+++.+....++.+|++..+.  -+++.++.
T Consensus         3 ~IVL~~P~iP~N~G~i~R~ca~~g~~L~LV~P~gf~~~dk~lrRAgldy~~~~~~~~~~~~~~f~~~~~~--~r~~~~tt   80 (157)
T PRK10358          3 NIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYAAFLEAENP--QRLFALTT   80 (157)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHCCCCHHEEEEEECCCHHHHHHHCCC--CEEEEEEC
T ss_conf             7999589888828999999996399899980688787426665331630212689980899999974389--72899725


Q ss_pred             CCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHH--CCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             333221122368988999758678987799985--8939992789687437899999999999987614
Q gi|254780603|r  215 DSKKPLEQEIKNDKIALILGAEGKGLRPKTQET--ATSMAHLHMPGIIKALNVSNAAAVALYITQNHFA  281 (282)
Q Consensus       215 ~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~--~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~~  281 (282)
                      .+...++++++....+||||+|+.|||+++++.  ||..|+|||.+.++|||+|+|++|++||+.||++
T Consensus        81 ~~~~~~~~~~~~~~d~llFG~Es~GLp~e~l~~~~~~~~i~IPm~~~~rSLNLs~AvaIvlYEa~RQ~~  149 (157)
T PRK10358         81 KGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLG  149 (157)
T ss_pred             CCCCCCHHCCCCCCCEEEECCCCCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             778761002357898899777678989999951777749983089798514299999999999998369


No 9  
>TIGR00186 rRNA_methyl_3 RNA methyltransferase, TrmH family, group 3; InterPro: IPR004441 The RNA methyltransferase, TrmH family, group 3 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=99.97  E-value=8.9e-33  Score=207.19  Aligned_cols=231  Identities=32%  Similarity=0.527  Sum_probs=199.2

Q ss_pred             EEEEEHHHHHHHHHCCCEEEEEEEECCCCCCC-C---CHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEEC----
Q ss_conf             99985788999997898189999973784335-4---345543269969997689987752477777744202411----
Q gi|254780603|r   49 LFLYGVHTVSAALNNPSRKIFQLLATKNALAR-L---DWDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAP----  120 (282)
Q Consensus        49 ~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~-~---~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~----  120 (282)
                      .+++|.+++.+++.+.++....++........ .   ........++.+..++...+++..... .|+|+++.+.+    
T Consensus         3 ~~~~g~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~   81 (271)
T TIGR00186         3 EYLYGVNAVLEALLNDPRRLSRLWILKLLLSGPKLKKLLELLKKKGVTIELVDRKKLDKLAKGG-NHQGVAAEVKPPKNK   81 (271)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHCC-CCCCEEEEECCCCHH
T ss_conf             1011257889875055357788877653112024678888887406504651303455554022-000001211221012


Q ss_pred             ---CCCCCHHH-------C------CC-CCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             ---55554011-------2------66-5068872343206889999999864200110013686320000013444333
Q gi|254780603|r  121 ---LLSPTLDA-------V------RN-SQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGA  183 (282)
Q Consensus       121 ---~~~~~l~~-------~------~~-~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga  183 (282)
                         .....++.       +      .. .++++++|+++||+|+|+++|||.++|+++++++.....+++..+.|+++|+
T Consensus        82 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~dp~~~g~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~g~  161 (271)
T TIGR00186        82 NLKYLYLDLEDENIPHELLLKTAKSKKKNPFLLLLDEITDPHNLGAILRTAEALGADGVVLPKRRSAPLTSTVLKTSAGA  161 (271)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCHHHCCCHHHHHHHHHHH
T ss_conf             22333211343345245666665202445147886133472023467665544121102420101001001344433102


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC--CCCCCCCC-----------CEEEEECCCCCCCCHHHHHHCCC
Q ss_conf             321101222322112222222100000001233322--11223689-----------88999758678987799985893
Q gi|254780603|r  184 LEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKP--LEQEIKND-----------KIALILGAEGKGLRPKTQETATS  250 (282)
Q Consensus       184 ~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~--~~~~~~~~-----------~~~lv~G~E~~Gl~~~~~~~~d~  250 (282)
                      .+++|+.++.++..++..+++.|+|+++++..+...  .+......           +.++++|+|++|++..+.+.||.
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~g~w~~~~~~~~~~~~~~~~~~~~~~~~~~g~c~~~~~~~~~g~~~~g~~~~~~~~~d~  241 (271)
T TIGR00186       162 LEYLPLARVTNLSRTLTKLKELGFWTLGTDLDGEDTPELYEKLLLKLHDLNGLCNELPLALVLGNEGEGLSRLLKKNCDF  241 (271)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHCCE
T ss_conf             34300233222588999887627547861344201245666554333322212311132457637653213455530661


Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999278968743789999999999998761
Q gi|254780603|r  251 MAHLHMPGIIKALNVSNAAAVALYITQNHF  280 (282)
Q Consensus       251 ~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~  280 (282)
                      .+.||+.+.++|||+++|+++++|+..+++
T Consensus       242 ~~~~p~~~~~~~l~~~~~~g~~~~~~~~~~  271 (271)
T TIGR00186       242 LIKIPLAGKVDSLNVSVAAGILLFEIKRQR  271 (271)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             676035666320024667787877665239


No 10 
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=99.97  E-value=4e-31  Score=197.72  Aligned_cols=147  Identities=20%  Similarity=0.234  Sum_probs=139.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf             68872343206889999999864200110013686320000013444333321101222322112222222100000001
Q gi|254780603|r  134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLS  213 (282)
Q Consensus       134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~  213 (282)
                      +.|+|.+++.|+|.|+|+|||+++|+.-.++-+-+++.-.+...||++.+|+.+.+.+.+++.+|+++.+. +-+++.++
T Consensus         3 ~~IvL~~PeIP~NTGNI~R~ca~tga~LhlI~PlGF~l~dk~lkRAGlDY~~~~~l~~h~s~e~fl~~~~~-~~rl~~~t   81 (155)
T COG0219           3 LNIVLYQPEIPPNTGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAGLDYHEKASLTEHDSLEAFLEAEPI-GGRLFALT   81 (155)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHCCCCHHHHCCEEEECCHHHHHHHCCC-CCEEEEEE
T ss_conf             07999789889845499999885297678974677765446645323451754662896889999863567-75399999


Q ss_pred             CCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCE-EEECCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             23332211223689889997586789877999858939-992789687437899999999999987614
Q gi|254780603|r  214 SDSKKPLEQEIKNDKIALILGAEGKGLRPKTQETATSM-AHLHMPGIIKALNVSNAAAVALYITQNHFA  281 (282)
Q Consensus       214 ~~~~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~-v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~~  281 (282)
                      ..+...+.+..+.....|+||.|+.|||+++++..... ++|||...++|||+|+++||++||+.||..
T Consensus        82 t~~~~~~~~~~f~~~d~llFG~Es~GLP~~i~~~~~~~~irIPm~~~~RSLNLsnsvavv~yEa~RQ~~  150 (155)
T COG0219          82 TKGTTTYTDVSFQKGDYLLFGPESRGLPEEILDAAPDRCIRIPMRPGVRSLNLSNTVAVVLYEALRQLG  150 (155)
T ss_pred             ECCCCCCCCCCCCCCCEEEECCCCCCCCHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             436666664567888789978888899999997393355983368787631088879999999999727


No 11 
>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=99.97  E-value=2.3e-31  Score=199.07  Aligned_cols=148  Identities=19%  Similarity=0.188  Sum_probs=135.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf             68872343206889999999864200110013686320000013444333321101222322112222222100000001
Q gi|254780603|r  134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLS  213 (282)
Q Consensus       134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~  213 (282)
                      +-|||..++-|.|.|+|+|||+|+|+.-.++.+-++.--+....||+..+|+++.+.+..++.+||+.-+..+-.+++++
T Consensus         2 ~~iVLy~PeIP~NTGNI~R~Caat~~~LHLi~PlGF~~~DK~L~RAGLdyw~fv~~~~H~s~E~fle~~~~~~~nlf~lT   81 (161)
T TIGR00185         2 LNIVLYEPEIPPNTGNIVRTCAATGTRLHLIKPLGFELDDKRLKRAGLDYWEFVQLFYHKSWEEFLEAEKPQKGNLFLLT   81 (161)
T ss_pred             EEEEEECCCCCCCCCHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCCCCEEEEECCCHHHHHHHCCCCCEEEEEEE
T ss_conf             15774078897884112010111586245660578620781423147874452323562556888863389971688884


Q ss_pred             CCC--CCCCCCCCCCCCE--EEEECCCCCCCCHHHHHHC--CCEEEECCCC-CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             233--3221122368988--9997586789877999858--9399927896-87437899999999999987614
Q gi|254780603|r  214 SDS--KKPLEQEIKNDKI--ALILGAEGKGLRPKTQETA--TSMAHLHMPG-IIKALNVSNAAAVALYITQNHFA  281 (282)
Q Consensus       214 ~~~--~~~~~~~~~~~~~--~lv~G~E~~Gl~~~~~~~~--d~~v~Ip~~~-~~~SLNvs~a~ai~l~~~~~~~~  281 (282)
                      ..|  ..+..++.+....  -||||.|.+|||+.+++..  +..|+|||.. .++|||+|.|+||++||+.||..
T Consensus        82 ~~G~~t~~~~~~~~~~~d~~yl~fG~ET~GLP~~~~~~~P~~~~~RiPm~~s~vRSlNLsn~va~~lYEa~rQ~~  156 (161)
T TIGR00185        82 KKGDKTPDHISVTYQDGDELYLVFGQETKGLPKSLLDNLPMEQKIRIPMTNSEVRSLNLSNSVAIVLYEALRQLG  156 (161)
T ss_pred             ECCCCCCCCEEEEECCCCCEEEEECCCCCCCHHHHHHCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             038877450466543786169983687755128998606321630325578884622468899999998787513


No 12 
>KOG0839 consensus
Probab=99.91  E-value=1.8e-25  Score=165.41  Aligned_cols=148  Identities=21%  Similarity=0.317  Sum_probs=126.6

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCCH
Q ss_conf             65068872343206889999999864200110013686320000013444333321101222--3221122222221000
Q gi|254780603|r  131 NSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRI--SNLTDALQKMHSWGFQ  208 (282)
Q Consensus       131 ~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~--~~~~~~l~~~~~~~~~  208 (282)
                      ...+|||-.-|..|.|+|.|+|||+.||++.+.+.+-.+- -++.---.|+-|--|+|+..+  +++..|++..|.+||.
T Consensus      1324 rssLIVVASLVDKppNLgGicRTcEVFgvs~LvVad~~vi-~DkQFk~lSVtAE~W~pieeVk~~~L~~fLq~kK~EGyT 1402 (1477)
T KOG0839        1324 RSSLIVVASLVDKPPNLGGICRTCEVFGVSLLVVADIKVI-NDKQFKNLSVTAERWMPIEEVKLDELASFLQEKKKEGYT 1402 (1477)
T ss_pred             CEEEEEEEECCCCCCCCCHHHHHHHHHCCCEEEEEEEEEE-CCHHHHHEEEEHHHCCCHHCCCHHHHHHHHHHHHHCCCE
T ss_conf             6159998520158986301445666617533787423452-252042224338756202226837789999986636827


Q ss_pred             HHHCCCCC-CCCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             00001233-322112236898899975867898779998589399927896874378999999999999876
Q gi|254780603|r  209 TIGLSSDS-KKPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH  279 (282)
Q Consensus       209 i~~~~~~~-~~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~  279 (282)
                      ++|++-.. ...+.++-||+|.+++||+|..|+|-.++...|.+|.||+.|-++||||.|++|+++||..||
T Consensus      1403 iIglEQTakSV~Ld~fqFPkKslilLG~EkEGIPvnLl~~LD~cvEIpQ~GviRSLNVHVsgAl~iweYTrQ 1474 (1477)
T KOG0839        1403 IIGLEQTAKSVKLDNFQFPKKSLILLGTEKEGIPVNLLSELDLCVEIPQFGVIRSLNVHVSGALIIWEYTRQ 1474 (1477)
T ss_pred             EEEEHHCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHEECCCCCEEEEEEEEHHHHHHHHHHHHH
T ss_conf             984232055011001347753268822653588377999976761321224455664104478899998888


No 13 
>PRK10433 putative RNA methyltransferase; Provisional
Probab=99.90  E-value=2e-23  Score=153.57  Aligned_cols=141  Identities=21%  Similarity=0.245  Sum_probs=111.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCHHHHC
Q ss_conf             688723432068899999998642001100136863200000134443333211012-2232211222222210000000
Q gi|254780603|r  134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYI-RISNLTDALQKMHSWGFQTIGL  212 (282)
Q Consensus       134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~-~~~~~~~~l~~~~~~~~~i~~~  212 (282)
                      +-+||.+++.|+|+|+++|.+..||++.+.+....+ ..++++.+.++||..-+.=. .++++.+++..+.    .++|+
T Consensus         3 i~iVLvep~~p~NIGa~ARaMkN~G~~~L~LV~P~~-~~~~~a~~~A~gA~diL~~a~v~~sL~eAl~d~~----~vvgt   77 (228)
T PRK10433          3 LTIILVAPARAENIGAAARAMKTMGFSELRIVDSQA-HLEPAARWVAHGSGDILDNIEVFDTLAEALHDVD----FTVAT   77 (228)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCEEEECCCC-CCCHHHHHHHCCHHHHHHHCCCCCCHHHHHHCCC----EEEEE
T ss_conf             999996799975199999999728998169979999-9988899983473999973733377999985489----89996


Q ss_pred             CCCCCC---C----------CC-CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             123332---2----------11-223689889997586789877999858939992789687437899999999999987
Q gi|254780603|r  213 SSDSKK---P----------LE-QEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQN  278 (282)
Q Consensus       213 ~~~~~~---~----------~~-~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~  278 (282)
                      +.....   +          +. .....++++||||+|..||+.+-++.||..++||.+....|||+|+|++|++||+..
T Consensus        78 TaR~r~~~~~~~~p~~~~~~~~~~~~~~~~valvFG~E~~GLsneEl~~C~~~~~IPt~~~y~SLNLaqAV~i~~YEl~~  157 (228)
T PRK10433         78 TARSRAKYHYYATPAELVPLLEEKSSWMSHAALVFGREDSGLTNEELALADVLTGVPMAADYPSLNLGQAVMVYCYQLAG  157 (228)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCEEEEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             45646688886899999999997323478479998886689898999867978985589998532199999999999987


Q ss_pred             H
Q ss_conf             6
Q gi|254780603|r  279 H  279 (282)
Q Consensus       279 ~  279 (282)
                      .
T Consensus       158 ~  158 (228)
T PRK10433        158 L  158 (228)
T ss_pred             H
T ss_conf             5


No 14 
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1; InterPro: IPR004384 These proteins are part of the trmH (spoU) family of rRNA methylases. The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases . TrmH is a tRNA (guanosine-2'-O-)-methyltransferase (2.1.1.34 from EC), which specifically methylates guanosine-18 in various tRNAs using S-adenosyl-L-methionine.; GO: 0008173 RNA methyltransferase activity.
Probab=99.90  E-value=1.8e-23  Score=153.93  Aligned_cols=145  Identities=21%  Similarity=0.271  Sum_probs=121.0

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             06887234320688999999986420011001368632000001344433332110-12223221122222221000000
Q gi|254780603|r  133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIP-YIRISNLTDALQKMHSWGFQTIG  211 (282)
Q Consensus       133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~-~~~~~~~~~~l~~~~~~~~~i~~  211 (282)
                      .+-|||=+++.|+|+|+|+|.+-.||+..++|.+.+++..+..+.-.|+||-+-|. ..-+++|.++|..+.-.  .++|
T Consensus         4 ~I~ivLVep~~~gNvG~~ARaMKnmGl~~L~Lv~p~~~~~~~eay~~A~~A~Di~~nA~vv~~L~Eal~sld~~--~~vg   81 (253)
T TIGR00050         4 NISIVLVEPKHSGNVGSIARAMKNMGLEELILVNPRVDILEEEAYALAAHAKDILENAKVVDDLDEALDSLDCD--LVVG   81 (253)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCEEECCHHHHHHHCCCC--EEEE
T ss_conf             24788861799864469999987627001256466225568789998720278658754742679998731997--0786


Q ss_pred             CC-CCCC--CCC------------CCCCCCC--CEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             01-2333--221------------1223689--88999758678987799985893999278968743789999999999
Q gi|254780603|r  212 LS-SDSK--KPL------------EQEIKND--KIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALY  274 (282)
Q Consensus       212 ~~-~~~~--~~~------------~~~~~~~--~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~  274 (282)
                      || ..|.  +.+            .-.....  ++++|||.|+.||+.|-++.||..|+||++...-|||+|+|++|++|
T Consensus        82 TsGaRGGd~r~l~~~~~~P~el~~~~~~~~g~~~~A~vFGREd~GL~NEEL~~Ch~~v~iP~~~~YPslNL~~AV~Vi~Y  161 (253)
T TIGR00050        82 TSGARGGDSRNLQRPLLTPRELADKILAKKGWMKVAIVFGREDSGLTNEELEKCHVLVSIPTSEEYPSLNLSHAVAVILY  161 (253)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHCCCEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             26788875434467777836668764242067214788524688876688964781552257788741148999999999


Q ss_pred             HHHHH
Q ss_conf             99876
Q gi|254780603|r  275 ITQNH  279 (282)
Q Consensus       275 ~~~~~  279 (282)
                      |+++.
T Consensus       162 eL~~~  166 (253)
T TIGR00050       162 ELRMA  166 (253)
T ss_pred             HHHHH
T ss_conf             99988


No 15 
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=99.87  E-value=4.6e-22  Score=145.81  Aligned_cols=141  Identities=22%  Similarity=0.319  Sum_probs=113.9

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCHHHH
Q ss_conf             0688723432068899999998642001100136863200000134443333211012-223221122222221000000
Q gi|254780603|r  133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYI-RISNLTDALQKMHSWGFQTIG  211 (282)
Q Consensus       133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~-~~~~~~~~l~~~~~~~~~i~~  211 (282)
                      .+.|||-+.+.|+|+|++.|.+.-||++.+++...++. .+..+...|+||-+-+.=. .++++.++|..+.    -++|
T Consensus         4 ~i~iVLVep~~~gNIG~vARaMKNfGl~eL~LV~Pr~~-~~eeA~a~A~gA~dile~A~i~~tL~eAl~d~~----~v~a   78 (242)
T COG0565           4 NIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDILENAKIVDTLEEALADCD----LVVA   78 (242)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCC-CCHHHHHHHCCCHHHHCCCEEECCHHHHHCCCC----EEEE
T ss_conf             61799975888752799999998679664899789889-889999986466666506766467999960788----7998


Q ss_pred             CCCCCC---CC----------C-CCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             012333---22----------1-122368988999758678987799985893999278968743789999999999998
Q gi|254780603|r  212 LSSDSK---KP----------L-EQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQ  277 (282)
Q Consensus       212 ~~~~~~---~~----------~-~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~  277 (282)
                      ++...-   .+          + .... ..+++||||.|..||+.+-+..||..++||++...-|||+|+|++|++||.+
T Consensus        79 Ttar~r~~~~~~~~P~e~~~~l~~~~~-~~~vAlvFGRE~~GLtNeEl~~c~~~v~IP~~p~Y~sLNLa~AV~ii~YEl~  157 (242)
T COG0565          79 TTARSRDLLRPLRTPREAAPELLEKAK-GGKVALVFGRERVGLTNEELALCDVLVTIPANPDYPSLNLAQAVQVILYELR  157 (242)
T ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHEEEECCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             056667665565687878999998714-8976999788668978899985027873679986543659999999999999


Q ss_pred             HH
Q ss_conf             76
Q gi|254780603|r  278 NH  279 (282)
Q Consensus       278 ~~  279 (282)
                      +.
T Consensus       158 ~~  159 (242)
T COG0565         158 KA  159 (242)
T ss_pred             HH
T ss_conf             86


No 16 
>pfam08032 SpoU_sub_bind RNA 2'-O ribose methyltransferase substrate binding. This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.
Probab=98.90  E-value=2.5e-09  Score=72.86  Aligned_cols=72  Identities=24%  Similarity=0.308  Sum_probs=57.7

Q ss_pred             EEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCC--HHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCEEEECCCC
Q ss_conf             998578899999789818999997378433543--45543269969997689987752477777744202411555
Q gi|254780603|r   50 FLYGVHTVSAALNNPSRKIFQLLATKNALARLD--WDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLALETAPLLS  123 (282)
Q Consensus        50 iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~--~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a~~~~~~~  123 (282)
                      +|||.|+|.|||++++. +..+|++++......  ......+++++..++++.|+++++ +.+|||+++.+.+..+
T Consensus         1 lI~G~~~V~eAL~~~~~-i~~l~i~~~~~~~~~~i~~~a~~~~i~v~~v~~~~l~~ls~-~~~hQGvva~v~~~~~   74 (75)
T pfam08032         1 LIEGRHAVEEALKSGPE-IEKLFVTEGRRDKRKELLKLAKKRGIKVIEVSEKVLDKLSG-TVNHQGVVAVVKPPEY   74 (75)
T ss_pred             CEEEEHHHHHHHHCCCC-EEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHCC-CCCCCEEEEEECCCCC
T ss_conf             97764799999977997-57999965751799999999998699856589999986469-9999848999417686


No 17 
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=97.93  E-value=7.7e-05  Score=47.13  Aligned_cols=141  Identities=19%  Similarity=0.273  Sum_probs=96.5

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC--CC-HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             06887234320688999999986420011001368632--00-0001344433332110122232211222222210000
Q gi|254780603|r  133 QLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSP--SE-SAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQT  209 (282)
Q Consensus       133 ~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~--~~-~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i  209 (282)
                      .+++++.++..++-+=-+.|++..||++.+++++-...  .- =|++.|-+--.  ..|+..+.++.++++-++-.-.-.
T Consensus         2 ev~vvlHN~~S~~rv~e~ariaygfg~k~lV~tka~g~AAQsGIp~~~kla~k~--G~~vlvf~dL~DAlevL~P~v~ll   79 (147)
T COG4080           2 EVIVVLHNVSSVQRVLEFARIAYGFGAKRLVLTKAKGSAAQSGIPEVLKLAFKL--GKPVLVFPDLDDALEVLRPDVTLL   79 (147)
T ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCCEEEEEECCCHHHHHCCHHHHHHHHHH--CCCEEEEHHHHHHHHHCCCCEEEE
T ss_conf             079999427755899999999713685389997125476663568899999983--994798522778997459756998


Q ss_pred             HHCCCCCCCCCCCCC-CCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             000123332211223-6898899975867898779998589399927896874378999999999999876
Q gi|254780603|r  210 IGLSSDSKKPLEQEI-KNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH  279 (282)
Q Consensus       210 ~~~~~~~~~~~~~~~-~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~  279 (282)
                      ++....+.+.+.-.+ ...++++||++-..|+++.-++.-+....| ..+.+-++   -++||+||++.+.
T Consensus        80 ~~~~~~~ek~~dp~e~ie~~vliVf~ga~~gl~k~El~lg~~~~y~-ve~~VG~~---g~lAi~Lyell~~  146 (147)
T COG4080          80 VGSASEGEKKLDPNEKIEGRVLIVFSGAEPGLTKRELELGADLRYI-VEADVGEL---GALAIFLYELLKA  146 (147)
T ss_pred             ECCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCHHHCCCCCCEEEE-EECCCHHH---HHHHHHHHHHHCC
T ss_conf             1476443234794312463379999268877586660567727999-84464178---8899999998704


No 18 
>pfam09936 DUF2168 Uncharacterized protein conserved in bacteria (DUF2168). This domain, found in various hypothetical prokaryotic proteins, has no known function. It is also found in a few prokaryotic tRNA (guanine-N(1)-)-methyltransferases.
Probab=97.78  E-value=5.1e-05  Score=48.15  Aligned_cols=124  Identities=22%  Similarity=0.278  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCC------------------CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC---
Q ss_conf             899999998642001100136863------------------20000013444333321101222322112222222---
Q gi|254780603|r  146 NIGAILRSAVAFSCDGIITTKRYS------------------PSESAVLAKSASGALEHIPYIRISNLTDALQKMHS---  204 (282)
Q Consensus       146 NlG~I~Rta~a~g~~~vil~~~~~------------------~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~---  204 (282)
                      -+=-|.|+|-.+|+.+.++...--                  ..+||.  |..  |+..+.+  ..++.++++...+   
T Consensus        29 DiHDIAR~~rTYgv~~yyiVtPl~~Q~~l~~ril~hW~~G~G~~~NP~--R~e--Al~~v~~--~~sle~ai~~i~~~~G  102 (185)
T pfam09936        29 DIHDIARSARTYGVGRYYIVTPLEAQQALVERILAHWQEGYGGEYNPD--RKE--ALSLVKV--VSSLEEAIEDIEKRTG  102 (185)
T ss_pred             CHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCC--HHH--HHHHHHH--HCCHHHHHHHHHHHHC
T ss_conf             477754555004776679956019999999999987325978666967--899--9857300--6029999999999619


Q ss_pred             CCCHHHHCCCC-C--CCCCCC---C--CCCCCEEEEECCCCCCCCHHHHHHCCCEEE-ECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             10000000123-3--322112---2--368988999758678987799985893999-2789687437899999999999
Q gi|254780603|r  205 WGFQTIGLSSD-S--KKPLEQ---E--IKNDKIALILGAEGKGLRPKTQETATSMAH-LHMPGIIKALNVSNAAAVALYI  275 (282)
Q Consensus       205 ~~~~i~~~~~~-~--~~~~~~---~--~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~-Ip~~~~~~SLNvs~a~ai~l~~  275 (282)
                      ..-.+++++.. .  ..++.+   .  +-.+|..|+||. |.||++++++.||..+. |--.+...-|.|=.|+||+|=.
T Consensus       103 ~~p~vvaTsAr~~~~~is~~~lr~~i~~~~~P~LllFGT-GwGL~~e~~~~~D~iLePI~g~~~yNHLSVRsAaAIilDR  181 (185)
T pfam09936       103 QRPLIVATSARKRPNTISYEELRKMIQEREKPVLLLFGT-GWGLAPEVLEQADYVLEPIRGAGDYNHLSVRSAAAIILDR  181 (185)
T ss_pred             CCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCEEEEECC-CCCCCHHHHHHCCEEECCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             997799804756899739999999984458818999658-7687799997468667056369997620499999999998


Q ss_pred             H
Q ss_conf             9
Q gi|254780603|r  276 T  276 (282)
Q Consensus       276 ~  276 (282)
                      +
T Consensus       182 L  182 (185)
T pfam09936       182 L  182 (185)
T ss_pred             H
T ss_conf             7


No 19 
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=97.24  E-value=0.0013  Score=40.02  Aligned_cols=125  Identities=14%  Similarity=0.061  Sum_probs=82.0

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH---HHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
Q ss_conf             2068899999998642001100136863200000134---4433332110122232211222222210000000123332
Q gi|254780603|r  142 NDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAK---SASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKK  218 (282)
Q Consensus       142 ~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~r---as~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~  218 (282)
                      +|+.=.--+.=||-|||++++++...  |+--...++   ..=|.-|.+.+  ..++..+++..++. -.++.+++-|..
T Consensus        14 RD~RiTTHv~LtaRAfGA~~i~l~~~--D~~~~etv~~V~~rwGG~F~~e~--~~~~~~~ir~~k~~-G~vVHLTMYG~~   88 (175)
T PRK03958         14 RDKRITTHVGLTARALGADKILFASE--DEHVKESVEDIVERWGGPFKVEV--TKSWKKYIREFKDG-GIVVHLTMYGEN   88 (175)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEECCC--CHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHHHHCCC-CEEEEEECCCCC
T ss_conf             67631358889888726876787688--76689999999986189669997--68979998630258-889998368886


Q ss_pred             ------CCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             ------21122368988999758678987799985893999278968743789999999999998
Q gi|254780603|r  219 ------PLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQ  277 (282)
Q Consensus       219 ------~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~  277 (282)
                            .+.+..-.++..+|+|.|-  +|.++-+.||+.|.|--...-|    -.|.||+|..++
T Consensus        89 i~~~~~~Ir~~~~~~~ilvVVGaeK--VP~evyelADyNVaVgNQPHSE----VAALAiFLDrl~  147 (175)
T PRK03958         89 INDVMDEIREAKTCKPLLIIVGAEK--VPREVYELADYNVAVGNQPHSE----VAALAVFLDRLF  147 (175)
T ss_pred             HHHHHHHHHHCCCCCCEEEEECCCC--CCHHHHHHCCCCEEECCCCCHH----HHHHHHHHHHHC
T ss_conf             6787767653057887899967886--9988974345415517887089----999999999860


No 20 
>COG1303 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.56  E-value=0.0022  Score=38.75  Aligned_cols=119  Identities=17%  Similarity=0.120  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCC---CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC---
Q ss_conf             9999998642001100136863---2000001344433332110122232211222222210000000123332211---
Q gi|254780603|r  148 GAILRSAVAFSCDGIITTKRYS---PSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLE---  221 (282)
Q Consensus       148 G~I~Rta~a~g~~~vil~~~~~---~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~---  221 (282)
                      --.+=||-|||+++++++..+-   ...=.++++ .=|.-|.+.  ...|+...+...++ |-.++.+++-|- ++.   
T Consensus        21 THV~LtARAfGA~gil~~~e~De~v~esv~dVv~-rwGG~F~v~--~~~nw~~~i~~wk~-gG~vvHLTMYG~-~i~dv~   95 (179)
T COG1303          21 THVALTARAFGADGILLDGEEDEKVVESVEDVVE-RWGGPFFVK--FGVNWRKVIREWKE-GGIVVHLTMYGL-NIDDVI   95 (179)
T ss_pred             HHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHH-HCCCCEEEE--ECCCHHHHHHHHHC-CCEEEEEEECCC-CCHHHH
T ss_conf             2333546861775479737643779999999998-549977999--72238999987404-877999996277-630341


Q ss_pred             -CCCCC-CCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             -22368-988999758678987799985893999278968743789999999999998
Q gi|254780603|r  222 -QEIKN-DKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQ  277 (282)
Q Consensus       222 -~~~~~-~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~  277 (282)
                       ++.-. ....+|+|.|-  +|.++-+.||..|.|--...-|   | .|.||.|..+.
T Consensus        96 ~ei~~~~k~~lvvVGaeK--Vp~evYelADyNV~VgnQPHSE---V-aaLAvFLDRl~  147 (179)
T COG1303          96 DEIRESKKDVLVVVGAEK--VPGEVYELADYNVSVGNQPHSE---V-AALAVFLDRLF  147 (179)
T ss_pred             HHHHHCCCCEEEEECCCC--CCHHHHHHCCCCEECCCCCCHH---H-HHHHHHHHHHH
T ss_conf             898746872799975662--8888964234413307876089---9-99999999971


No 21 
>PRK12703 tRNA 2'-O-methylase; Reviewed
Probab=95.96  E-value=0.014  Score=34.21  Aligned_cols=124  Identities=15%  Similarity=0.113  Sum_probs=73.9

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC--
Q ss_conf             20688999999986420011001368632000-001344433332110122232211222222210000000123332--
Q gi|254780603|r  142 NDPHNIGAILRSAVAFSCDGIITTKRYSPSES-AVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKK--  218 (282)
Q Consensus       142 ~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~-~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~--  218 (282)
                      +|+.=.--+.=||-|||++++++.+..-...+ -.-+-..=|.-|.+.     ...++...+++.+-.++.+++.|..  
T Consensus        13 RDkRITTHVaLtARAfGA~~il~~e~D~~v~etv~~V~~rwGG~F~ie-----~~~~w~~~~k~~~G~vVHLTMYG~~i~   87 (339)
T PRK12703         13 RDKRITTHVALTARAFGASSILVDERDETLENTIKKVVDNFGGSFEIK-----TGIEWKSEFKKFHGIRVHLTMYGRPIE   87 (339)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEE-----ECCCHHHHHHHCCCEEEEEECCCCCHH
T ss_conf             676212589899987168754436887678999999997349977997-----176799998735987999831688657


Q ss_pred             -CCCCCCC-CCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             -2112236-898899975867898779998589399927896874378999999999999
Q gi|254780603|r  219 -PLEQEIK-NDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYIT  276 (282)
Q Consensus       219 -~~~~~~~-~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~  276 (282)
                       -+.++.. .++..+|+|.|-  +|.++.+.+|+.|.|--...-|    -.|.||+|-.+
T Consensus        88 dvi~~Ir~~~k~ilVVVGaeK--VP~evYelADyNVaVgNQPHSE----VAALAIFLDRl  141 (339)
T PRK12703         88 DVIDEIRESGKDVMVLVGSEK--VPIEAYEIADYNVSVTNQPISE----VSALAIFLDRY  141 (339)
T ss_pred             HHHHHHHHCCCCEEEEECCCC--CCHHHHHHCCCCEEECCCCHHH----HHHHHHHHHHH
T ss_conf             877776512897799975885--9989985356534327988089----99999999986


No 22 
>COG4752 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.45  E-value=0.021  Score=33.17  Aligned_cols=50  Identities=20%  Similarity=0.265  Sum_probs=40.5

Q ss_pred             CCCEEEEECCCCCCCCHHHHHHCCCEEE-ECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             8988999758678987799985893999-27896874378999999999999
Q gi|254780603|r  226 NDKIALILGAEGKGLRPKTQETATSMAH-LHMPGIIKALNVSNAAAVALYIT  276 (282)
Q Consensus       226 ~~~~~lv~G~E~~Gl~~~~~~~~d~~v~-Ip~~~~~~SLNvs~a~ai~l~~~  276 (282)
                      .+++.++||. |.|||+++++.+|..+. |--.+...-|.|-.|+||++-.+
T Consensus       133 dkp~LilfGT-GwGlpde~m~~sDYiLEPIra~sd~NHLSVRaAvAIIlDRL  183 (190)
T COG4752         133 DKPWLILFGT-GWGLPDELMNTSDYILEPIRAASDWNHLSVRAAVAIILDRL  183 (190)
T ss_pred             CCCEEEEECC-CCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             7867999637-88998799877667232133057753153888899999998


No 23 
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.66  E-value=0.27  Score=26.85  Aligned_cols=138  Identities=20%  Similarity=0.268  Sum_probs=76.2

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHHH-------HHHHHHHHHHH-----HCCC-CCCCCC
Q ss_conf             5068872343206889999999864200110--0136863200000-------13444333321-----1012-223221
Q gi|254780603|r  132 SQLLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESAV-------LAKSASGALEH-----IPYI-RISNLT  196 (282)
Q Consensus       132 ~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~~-------~~ras~Ga~~~-----l~~~-~~~~~~  196 (282)
                      +..+-+.-.+-.+..+=.|++-|.-+|+..+  +.+++|..-|..+       --+....|.++     +|-+ ...++.
T Consensus        77 ~~~i~l~~~~~kg~k~d~iiqkatELGv~~i~p~~ter~~~k~~~~~~~kler~~ki~ieAaEQs~R~~vP~I~~~~~~~  156 (246)
T COG1385          77 PLKITLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGKKAAKLERWQKIAIEAAEQSGRNVVPEIKPPESLK  156 (246)
T ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEECEEEEEHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECHHHHH
T ss_conf             86079999627518899999999871801179885012677200110368999999999999864998698262313099


Q ss_pred             CCCCCCCCCCCHHHHCCCCCCCCCC-----CCCCCCCEEEEECCCCCCCCHHHHHHCCC--EEEECCCCCCCHHHHHHHH
Q ss_conf             1222222210000000123332211-----22368988999758678987799985893--9992789687437899999
Q gi|254780603|r  197 DALQKMHSWGFQTIGLSSDSKKPLE-----QEIKNDKIALILGAEGKGLRPKTQETATS--MAHLHMPGIIKALNVSNAA  269 (282)
Q Consensus       197 ~~l~~~~~~~~~i~~~~~~~~~~~~-----~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~--~v~Ip~~~~~~SLNvs~a~  269 (282)
                      ++++.........+.....+.....     +....++..+++|.|| |++++-.+....  ...|.+..++  |=.-+|+
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iiIGPEG-Gfs~~Ei~~l~~~g~~~v~LGprI--LRtETA~  233 (246)
T COG1385         157 ELLKEIDDEDALKLIYEEKAKEGLLALPLLEALPEGKVLLIIGPEG-GFSEDEIELLREAGFTPVSLGPRI--LRTETAA  233 (246)
T ss_pred             HHHHHCCCHHHHHHEECCCCCCCCCCCHHHHCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCEEECCCCCE--EEHHHHH
T ss_conf             9998546300133222544544543330120156773899988998-999899999997798581378972--0077899


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780603|r  270 AVA  272 (282)
Q Consensus       270 ai~  272 (282)
                      -.+
T Consensus       234 l~a  236 (246)
T COG1385         234 LAA  236 (246)
T ss_pred             HHH
T ss_conf             999


No 24 
>PRK11713 16S rRNA m3U1498 methyltransferase; Provisional
Probab=94.46  E-value=0.29  Score=26.65  Aligned_cols=138  Identities=20%  Similarity=0.271  Sum_probs=74.2

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHH-----H---HHHHHHHHH-----HHHC-CCCCCCCCCC
Q ss_conf             8872343206889999999864200110--013686320000-----0---134443333-----2110-1222322112
Q gi|254780603|r  135 LMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESA-----V---LAKSASGAL-----EHIP-YIRISNLTDA  198 (282)
Q Consensus       135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~-----~---~~ras~Ga~-----~~l~-~~~~~~~~~~  198 (282)
                      +.++-.+-.|..+=.+++-|.-+|++.+  +.++++...|..     +   .-|....|.     .++| +....++.++
T Consensus        78 i~L~~al~K~~~~e~il~k~tElGV~~i~p~~s~rs~~~~~~~~~~~k~eR~~~i~~eA~eQs~r~~lP~i~~~~~l~~~  157 (243)
T PRK11713         78 LTLAQALPKGDRLELIIQKATELGVSAIIPLITERSVVKLDGERADKKLERWQKIAIEAAEQSGRTRIPEIRPPVSLKEL  157 (243)
T ss_pred             EEEEEEECCCHHHHHHHHHHHHHCCCEEEEEEHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCHHHH
T ss_conf             79999600755899999999872877799997000545212105666699999999999997099828776576799999


Q ss_pred             CCCCCCCCCHHHHCCCCCCCC--CCCCCCCCCEEEEECCCCCCCCHHHHHHCCC--EEEECCCCCCCHHHHHH----HHH
Q ss_conf             222222100000001233322--1122368988999758678987799985893--99927896874378999----999
Q gi|254780603|r  199 LQKMHSWGFQTIGLSSDSKKP--LEQEIKNDKIALILGAEGKGLRPKTQETATS--MAHLHMPGIIKALNVSN----AAA  270 (282)
Q Consensus       199 l~~~~~~~~~i~~~~~~~~~~--~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~--~v~Ip~~~~~~SLNvs~----a~a  270 (282)
                      ++.....+..++ ++..+...  .......++.++++|.|| |.++.-++....  ...+.+..++  |=+.+    |+|
T Consensus       158 l~~~~~~~~~~i-~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~g~~~vsLG~~I--LR~ETA~i~als  233 (243)
T PRK11713        158 LEALADGDLRLV-LHPEANLAAALKSLKPAGKVLLLIGPEG-GFSPEEIELLREAGFTPVSLGPRI--LRTETAALAALA  233 (243)
T ss_pred             HHHCCCCCCEEE-ECCCCCCCCCCCCCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCEEEECCCCC--CHHHHHHHHHHH
T ss_conf             953867782899-8688775432011257885899987888-999999999998898898679991--357749999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780603|r  271 VALYIT  276 (282)
Q Consensus       271 i~l~~~  276 (282)
                      +++|.+
T Consensus       234 ~l~~~~  239 (243)
T PRK11713        234 ALQALL  239 (243)
T ss_pred             HHHHHH
T ss_conf             999985


No 25 
>pfam09895 DUF2122 RecB-family nuclease (DUF2122). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=94.38  E-value=0.065  Score=30.38  Aligned_cols=83  Identities=14%  Similarity=0.200  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC-CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEE-CCCCCCCHHHH
Q ss_conf             0122232211222222210000000123332211-223689889997586789877999858939992-78968743789
Q gi|254780603|r  188 PYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLE-QEIKNDKIALILGAEGKGLRPKTQETATSMAHL-HMPGIIKALNV  265 (282)
Q Consensus       188 ~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~-~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~I-p~~~~~~SLNv  265 (282)
                      ++....++.++++-++-.  .+|.++..+..... .....+++++||+....|+|+.-++.-+ .+++ -+...+-++  
T Consensus        21 ~llvl~dl~DAiEvL~P~--~v~~i~~~~~~~~~~~l~~~~rvllvf~G~e~gfsk~El~~g~-~v~~~~v~~~iG~i--   95 (105)
T pfam09895        21 SLLVLPDLKDAIELLKPD--VVYLLSRAAEGIKKEVLKVEGRVLLVFSGAEPGFSKIELELGE-AVYIKGVESDVGPI--   95 (105)
T ss_pred             CEEEECCHHHHHHHHCCC--EEEEECCCCCCCCHHHHHCCCCEEEEECCCCCCCCHHHHCCCC-EEEEECCCCCCCCH--
T ss_conf             589838778899872987--7999757665620345530583899981898897965614884-47860365566628--


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999999
Q gi|254780603|r  266 SNAAAVALYIT  276 (282)
Q Consensus       266 s~a~ai~l~~~  276 (282)
                       -++||+||++
T Consensus        96 -g~~Ai~Ly~l  105 (105)
T pfam09895        96 -GALAIILYLL  105 (105)
T ss_pred             -HHHHHHHHHC
T ss_conf             -8999999509


No 26 
>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=93.79  E-value=0.21  Score=27.47  Aligned_cols=135  Identities=21%  Similarity=0.343  Sum_probs=72.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCC------------HHHHHHHHHHH-HHHHC-CCCCCCCCC
Q ss_conf             68872343206889999999864200110--0136863200------------00013444333-32110-122232211
Q gi|254780603|r  134 LLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSE------------SAVLAKSASGA-LEHIP-YIRISNLTD  197 (282)
Q Consensus       134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~------------~~~~~ras~Ga-~~~l~-~~~~~~~~~  197 (282)
                      .+.++-.+-.|.++--+++-|.-.|++.+  +.++++...+            ..-++.|+.=+ -.++| +....++.+
T Consensus        62 ~i~l~~al~K~~~~~~il~k~tElGV~~i~p~~~ers~~k~~~~~~~~k~~R~~~i~~~A~eQs~r~~lP~I~~~~~l~~  141 (225)
T pfam04452        62 KITLAQALPKGDRLELILQKATELGVDRIVPLISERSVVKLDGKRADKKLERWQKIAIEAAEQSGRTRLPEVLPPISLKE  141 (225)
T ss_pred             EEEEEEEEECCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCHHH
T ss_conf             17999950072789999999986287657999840354544303466659999999999999719982877726689999


Q ss_pred             CCCCCCCCCCHHHHCCCCCCCC---CCC---CCCCCCEEEEECCCCCCCCHHHHHHCC--CEEEECCCCCCCHHHHHHHH
Q ss_conf             2222222100000001233322---112---236898899975867898779998589--39992789687437899999
Q gi|254780603|r  198 ALQKMHSWGFQTIGLSSDSKKP---LEQ---EIKNDKIALILGAEGKGLRPKTQETAT--SMAHLHMPGIIKALNVSNAA  269 (282)
Q Consensus       198 ~l~~~~~~~~~i~~~~~~~~~~---~~~---~~~~~~~~lv~G~E~~Gl~~~~~~~~d--~~v~Ip~~~~~~SLNvs~a~  269 (282)
                      +++.......  +.++.++...   ...   .....+.++++|.|| |.++.-.+..-  ....+.+..++  |=+-+|+
T Consensus       142 ~l~~~~~~~~--~i~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~l~~~g~~~v~LG~~I--LR~ETA~  216 (225)
T pfam04452       142 LLEELDDADK--LILHEEAAKSLGELSELLASLKGGKVLLIIGPEG-GFSPEEIELLKEAGFTPVSLGPRI--LRTETAA  216 (225)
T ss_pred             HHHHCCCCCE--EEEECCCCCCCCCCHHHHHCCCCCCEEEEECCCC-CCCHHHHHHHHHCCCEEEECCCCC--CCHHHHH
T ss_conf             9961866888--9992665544321012321035784589988988-999999999998899898479994--6078599


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254780603|r  270 AVAL  273 (282)
Q Consensus       270 ai~l  273 (282)
                      -.++
T Consensus       217 i~al  220 (225)
T pfam04452       217 LAAL  220 (225)
T ss_pred             HHHH
T ss_conf             9999


No 27 
>PRK02135 hypothetical protein; Provisional
Probab=93.75  E-value=0.052  Score=30.95  Aligned_cols=115  Identities=17%  Similarity=0.219  Sum_probs=74.7

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC
Q ss_conf             06889999999864200110013686320000013444333321101222322112222222100000001233322112
Q gi|254780603|r  143 DPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ  222 (282)
Q Consensus       143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~  222 (282)
                      |=.++...++.|..-...    +.+       ....++.|-     ++...++.+.++.+++.+ ++|-++.+|. ++.+
T Consensus        79 dERsia~~I~kaL~~~~~----~~~-------~~~e~~pGI-----~v~~~~~e~~l~e~~~~~-~~~~Ld~~G~-~i~~  140 (199)
T PRK02135         79 DERSLAALIKKALDASAG----IGE-------QEREVTPGI-----YVRTGSFEDLLQELAEDG-QLYYLHEDGE-DIRD  140 (199)
T ss_pred             CHHHHHHHHHHHHCCCCC----CCC-------CEEEECCCE-----EEECCCHHHHHHHHHCCC-CEEEECCCCC-CHHC
T ss_conf             379999999999758899----888-------347747998-----990889999999985379-7999889999-5000


Q ss_pred             CCCCCCEEEEECCCCCCCCHHHHHHC----CCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             23689889997586789877999858----93999278968743789999999999998761
Q gi|254780603|r  223 EIKNDKIALILGAEGKGLRPKTQETA----TSMAHLHMPGIIKALNVSNAAAVALYITQNHF  280 (282)
Q Consensus       223 ~~~~~~~~lv~G~E~~Gl~~~~~~~~----d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~  280 (282)
                      ..++++.+||+|- ..|++++-.+..    ...|++    +-.+|=.+++.+|+-|++.++-
T Consensus       141 ~~~~~~~~FILsD-h~~~~~~e~~~L~~~g~~~iSL----Gp~~L~a~~cI~iiH~~LD~~~  197 (199)
T PRK02135        141 VEFPANPVFVLGD-HIGMTKEEENLLKRLGAEKISL----GPKMLHADHCITLIHNELDRRG  197 (199)
T ss_pred             CCCCCCCEEEEEC-CCCCCHHHHHHHHHCCCCEEEE----CCHHHHHHHHHHHHHHHHHCCC
T ss_conf             5689998799628-9998878999998708831654----7388765058999999875037


No 28 
>pfam01994 Trm56 tRNA ribose 2'-O-methyltransferase, aTrm56. This family is an aTrm56 that catalyses the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin.
Probab=93.29  E-value=0.096  Score=29.41  Aligned_cols=81  Identities=16%  Similarity=0.041  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHCCCCCCC---CCCCCC-CCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHH
Q ss_conf             2232211222222210000000123332---211223-689889997586789877999858939992789687437899
Q gi|254780603|r  191 RISNLTDALQKMHSWGFQTIGLSSDSKK---PLEQEI-KNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVS  266 (282)
Q Consensus       191 ~~~~~~~~l~~~~~~~~~i~~~~~~~~~---~~~~~~-~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs  266 (282)
                      ...++..+++..++.|-.++.+++-|..   -+.++. ..++..+|+|.|-  +|.++-+.||+.|.|--...-|    -
T Consensus         9 ~~~~~~~~ir~~k~~~G~vVHLTMYG~~i~~~i~~Ir~~~~~ilvVVGaeK--VP~evye~ADyNVaVgNQPHSE----V   82 (121)
T pfam01994         9 FGVNWRSYIREWKEKGGIVVHLTMYGENIDDVIPEIRESGKDILVVVGAEK--VPGEVYELADYNVAVGNQPHSE----V   82 (121)
T ss_pred             ECCCHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEEECCCC--CCHHHHHHCCCCEEECCCCCHH----H
T ss_conf             767989999998763988999953688668877786503886799977873--8999984355415527887089----9


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999998
Q gi|254780603|r  267 NAAAVALYITQ  277 (282)
Q Consensus       267 ~a~ai~l~~~~  277 (282)
                      .|.||+|..+.
T Consensus        83 AALAiFLdrl~   93 (121)
T pfam01994        83 AALAVFLDRLF   93 (121)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999999861


No 29 
>pfam04407 DUF531 Protein of unknown function (DUF531). Family of hypothetical archaeal proteins.
Probab=91.52  E-value=0.28  Score=26.76  Aligned_cols=136  Identities=22%  Similarity=0.197  Sum_probs=73.4

Q ss_pred             EEEEECCCCCHH-----HHHHHHHH---HHHHHCCCCCCCCCCCCCCHHHHH-----HHHHHHH--HHHCCCCCCCCCCC
Q ss_conf             688723432068-----89999999---864200110013686320000013-----4443333--21101222322112
Q gi|254780603|r  134 LLMVLDHVNDPH-----NIGAILRS---AVAFSCDGIITTKRYSPSESAVLA-----KSASGAL--EHIPYIRISNLTDA  198 (282)
Q Consensus       134 ~~i~ld~i~dp~-----NlG~I~Rt---a~a~g~~~vil~~~~~~~~~~~~~-----ras~Ga~--~~l~~~~~~~~~~~  198 (282)
                      +.++|.+-.|+.     ++-+|+|.   |.|||++--++.=. ++......+     ..+.|.-  +...++. .|-..+
T Consensus         2 lTl~LyNtYd~~k~~e~H~RaIARAapic~Af~~~LAL~~FP-~~~~~~el~~~v~~~TtIG~~G~yl~~L~~-~nr~~i   79 (174)
T pfam04407         2 LTLGLYNTYDKKKVHEAHYRAIARAAPICYAFGFHLALFGFP-FDMTPKELAEYVADKTTIGESGKYLLELAE-SNKLHV   79 (174)
T ss_pred             EEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCC-CCCCHHHHHHHHHHCCCCCCCHHHHHHHHH-CCCEEE
T ss_conf             379998446877566089999984604766417877987798-877879999997642732776799999987-496789


Q ss_pred             CC----C-CCCCCCHHHHCC-CCCCCCC-----CCCCC-CCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHH
Q ss_conf             22----2-222100000001-2333221-----12236-89889997586789877999858939992789687437899
Q gi|254780603|r  199 LQ----K-MHSWGFQTIGLS-SDSKKPL-----EQEIK-NDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVS  266 (282)
Q Consensus       199 l~----~-~~~~~~~i~~~~-~~~~~~~-----~~~~~-~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs  266 (282)
                      ++    . ..+.|-.|+.++ ++.++..     .+... .++.++++|=-.+|||+++++.|++..-|-  |.-=||-..
T Consensus        80 ~d~p~k~fp~qfG~~IaTT~kPd~~K~~~p~eia~~~l~~~s~~lliGLGr~GLPk~i~~~a~yHldiT--gkgIsLETc  157 (174)
T pfam04407        80 IDFPKKGFPPQFGEVVATTSKPDEKKAITPEDVAREALRNKSFLLLIGLGRHGLPKELFESARYHLDIT--GKGVSLETC  157 (174)
T ss_pred             EECCCCCCCHHCCCEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHCHHHEEEC--CCCEEEEEC
T ss_conf             836300383320965887789984557897999998742886799994078888699986431106612--783136620


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254780603|r  267 NAAAVAL  273 (282)
Q Consensus       267 ~a~ai~l  273 (282)
                      +|-+.+-
T Consensus       158 TAiGaI~  164 (174)
T pfam04407       158 TAIGAIP  164 (174)
T ss_pred             HHHHHHH
T ss_conf             4561699


No 30 
>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=90.34  E-value=0.3  Score=26.55  Aligned_cols=118  Identities=14%  Similarity=0.145  Sum_probs=73.6

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC
Q ss_conf             06889999999864200110013686320000013444333321101222322112222222100000001233322112
Q gi|254780603|r  143 DPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ  222 (282)
Q Consensus       143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~  222 (282)
                      |-.+++.++|.|..-...    +.+.+       ..++.|-     ++...++.+.++++.+ ++++|-++.+|. ++.+
T Consensus        79 dERsiA~~I~kal~~~~~----~~~~~-------~e~~pGI-----~v~~~~fe~ll~e~~e-~~~~~~Ld~~G~-~i~~  140 (199)
T pfam04013        79 DERSIAILIKKALRAVKE----SGKQW-------RKVLPGI-----YVSRMGFEALIRELSE-FKPLYYLHEDGG-DISN  140 (199)
T ss_pred             HHHHHHHHHHHHHCCCCC----CCCCE-------EEECCCE-----EEECCCHHHHHHHHHC-CCCEEEECCCCC-CCCC
T ss_conf             388999999999716788----88743-------7846998-----9949899999999855-897999978898-4323


Q ss_pred             CCCC-CCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             2368-98899975867898779998589399927896874378999999999999876
Q gi|254780603|r  223 EIKN-DKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALYITQNH  279 (282)
Q Consensus       223 ~~~~-~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~  279 (282)
                      ..++ .+.+||+|-- .|++++-.+........+.+=+-.+|=.+++.+|+-|++.|.
T Consensus       141 ~~~~~~~~~FiL~Dh-~~~~~~e~~~L~~~~~~~iSLGp~~L~a~hcI~ivH~~LD~~  197 (199)
T pfam04013       141 VKIPPNNPVFILGDH-IGLPEEDEKFLERILALKVSLGPLSLHASHCITLVHNHLDRL  197 (199)
T ss_pred             CCCCCCCCEEEECCC-CCCCHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHHHHHCC
T ss_conf             557788976985599-998867888886448821553738888757999999987316


No 31 
>KOG0838 consensus
Probab=90.31  E-value=0.078  Score=29.91  Aligned_cols=53  Identities=25%  Similarity=0.259  Sum_probs=42.3

Q ss_pred             CCCCCCCEEEEECCCCCCCCHHHHHH---CCCEEEECCC-CCCCHHHHHHHHHHHHHH
Q ss_conf             22368988999758678987799985---8939992789-687437899999999999
Q gi|254780603|r  222 QEIKNDKIALILGAEGKGLRPKTQET---ATSMAHLHMP-GIIKALNVSNAAAVALYI  275 (282)
Q Consensus       222 ~~~~~~~~~lv~G~E~~Gl~~~~~~~---~d~~v~Ip~~-~~~~SLNvs~a~ai~l~~  275 (282)
                      .+-.-+++.++.|++ +++++.+.+.   |+..+.|++- ...+||||++|+++.++.
T Consensus       133 ~~lg~~~v~lv~~n~-s~lS~~vskss~gale~l~I~q~~~~~efl~vsvaaG~~l~~  189 (271)
T KOG0838         133 YFLGADGVLLVKGNS-SPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVAAGIRLHG  189 (271)
T ss_pred             HHHCCCCEEEEECCC-CCCCHHHHHHHHCHHHEEEHHHCCCHHHHHHHHHHCCEEEEE
T ss_conf             874677158973368-878646777650214166387738889998999867558999


No 32 
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase; InterPro: IPR006269   These sequences describe 2-dehydro-3-deoxyphosphooctonate aldolase. Alternate names include 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate.   phosphoenolpyruvate + D-arabinose 5-phosphate + H_2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate    In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. ; GO: 0008676 3-deoxy-8-phosphooctulonate synthase activity, 0008152 metabolic process, 0005737 cytoplasm.
Probab=81.63  E-value=0.81  Score=24.10  Aligned_cols=56  Identities=25%  Similarity=0.420  Sum_probs=39.4

Q ss_pred             CCCCCHH-----HHH-----------HHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             3432068-----899-----------999998642001100136863200000134443333211012223221122222
Q gi|254780603|r  139 DHVNDPH-----NIG-----------AILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKM  202 (282)
Q Consensus       139 d~i~dp~-----NlG-----------~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~  202 (282)
                      +-||-|+     =.|           +|+|+|.|.|++||++.-| .||-|.+.     .+--.+|+.   +|+.+|..+
T Consensus       200 HSvQ~PgGkkl~G~G~~SGG~refvp~LARAA~AVG~~GlF~EtH-~DP~~A~S-----DGp~mlpL~---~LE~Ll~~l  270 (279)
T TIGR01362       200 HSVQQPGGKKLDGLGGKSGGQREFVPTLARAAVAVGIDGLFIETH-PDPKNAKS-----DGPNMLPLD---ELEALLEKL  270 (279)
T ss_pred             CCEECCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEECC-CCCCCCCC-----CCCCCCCHH---HHHHHHHHH
T ss_conf             240376871225777767987434679999889862431466217-88777788-----884678988---999999999


Q ss_pred             C
Q ss_conf             2
Q gi|254780603|r  203 H  203 (282)
Q Consensus       203 ~  203 (282)
                      .
T Consensus       271 ~  271 (279)
T TIGR01362       271 L  271 (279)
T ss_pred             H
T ss_conf             9


No 33 
>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=77.49  E-value=4.2  Score=20.02  Aligned_cols=130  Identities=14%  Similarity=0.167  Sum_probs=73.5

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHHH-HHH------------HHHHHHHHHC-CCCCCCC
Q ss_conf             5068872343206889999999864200110--0136863200000-134------------4433332110-1222322
Q gi|254780603|r  132 SQLLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESAV-LAK------------SASGALEHIP-YIRISNL  195 (282)
Q Consensus       132 ~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~~-~~r------------as~Ga~~~l~-~~~~~~~  195 (282)
                      +.-+.+.-.+-++.++=.|+|-+.-.|+..+  +.++.|..-+... +.+            +-.+.--.+| |....++
T Consensus        79 ~~~~~~~~~~~~g~~~e~ii~~~~eLGv~~~~p~~~ers~~k~~~~~~~~K~~rw~KI~~eA~eQs~r~~~P~i~~~~~l  158 (258)
T TIGR00046        79 PLKIHLAIVLIKGKKMEKIIRKLTELGVSKIIPLNAERSVVKLDIERAIKKLERWQKIVIEAAEQSGRNIVPEIKVPKNL  158 (258)
T ss_pred             CCCEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH
T ss_conf             76289999753212342565456764678998888865304855778875778889999999862779989843205678


Q ss_pred             C------CCCCCCCCCCCHHHHCCCCCCCCCC--C---CCCCCCEEEEECCCCCCCCHHHHHHCC--CEEEECCCC---C
Q ss_conf             1------1222222210000000123332211--2---236898899975867898779998589--399927896---8
Q gi|254780603|r  196 T------DALQKMHSWGFQTIGLSSDSKKPLE--Q---EIKNDKIALILGAEGKGLRPKTQETAT--SMAHLHMPG---I  259 (282)
Q Consensus       196 ~------~~l~~~~~~~~~i~~~~~~~~~~~~--~---~~~~~~~~lv~G~E~~Gl~~~~~~~~d--~~v~Ip~~~---~  259 (282)
                      .      ++++++....-...-...+......  .   ++-.....+|+|.|| |+|+.-.....  ....|+...   +
T Consensus       159 ~qllqr~Q~~e~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~GPEG-Gfse~E~~~~~~~~f~~~~L~~~~LR  237 (258)
T TIGR00046       159 KQLLQRMQDVEKLAESEEEALKLNFHPEASPLSANLEQIEQAGKIVIIIGPEG-GFSEKEIQLLKEKGFTPVLLGPRILR  237 (258)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHCCCCCEEEEEECCC-CCCHHHHHHHHHCCCEECCCCCCCCH
T ss_conf             99999865687641001013232210033111200122005570489981699-96888999998829824137887021


Q ss_pred             CCH
Q ss_conf             743
Q gi|254780603|r  260 IKA  262 (282)
Q Consensus       260 ~~S  262 (282)
                      +|+
T Consensus       238 tET  240 (258)
T TIGR00046       238 TET  240 (258)
T ss_pred             HHH
T ss_conf             226


No 34 
>PRK04171 ribosome biogenesis protein; Provisional
Probab=74.07  E-value=6.5  Score=18.92  Aligned_cols=80  Identities=14%  Similarity=0.146  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCCCHHHHCCCCCCC-CCCCCCC-CCCEEEEECCCCCC-CCHHHHHHCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf             211222222210000000123332-2112236-89889997586789-87799985893999278968743789999999
Q gi|254780603|r  195 LTDALQKMHSWGFQTIGLSSDSKK-PLEQEIK-NDKIALILGAEGKG-LRPKTQETATSMAHLHMPGIIKALNVSNAAAV  271 (282)
Q Consensus       195 ~~~~l~~~~~~~~~i~~~~~~~~~-~~~~~~~-~~~~~lv~G~E~~G-l~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai  271 (282)
                      +.+.+..   .+-.+++++..|.. .+.++-- .++.++|+|.=.+| .+.++.+..|..++|--.    +|-.+++++-
T Consensus       137 l~~~l~~---~~~kii~ls~~g~~~~~~~~~~~~~~~~~vIGaf~~G~f~~~~~~~~d~~~SIs~~----~Lsa~~v~~r  209 (221)
T PRK04171        137 LSELLEE---NPGKIILLSEKGEPVKPKELAKELENPVVVIGGFPHGDFSSEVLEKADKKYSIYNE----PLDAWTVVSR  209 (221)
T ss_pred             HHHHHCC---CCCEEEEECCCCCCCCHHHHHHHCCCCEEEEEECCCCCCCCCCHHCCCCEEEEECC----CHHHHHHHHH
T ss_conf             8997065---89859998358867289999742279769983016987660000136848998488----7699999999


Q ss_pred             HHHHHHHHHC
Q ss_conf             9999987614
Q gi|254780603|r  272 ALYITQNHFA  281 (282)
Q Consensus       272 ~l~~~~~~~~  281 (282)
                      +++++-+..+
T Consensus       210 i~~a~E~~~G  219 (221)
T PRK04171        210 IIAAAERALG  219 (221)
T ss_pred             HHHHHHHHHC
T ss_conf             9999999867


No 35 
>pfam02590 SPOUT_MTase Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases.
Probab=72.35  E-value=7.2  Score=18.67  Aligned_cols=73  Identities=19%  Similarity=0.221  Sum_probs=46.2

Q ss_pred             CCCCCCCCCHHHHCCCCCCCCCCCC-----------CCCCCEEEEECCCCCCCCHHHHHHCCCEEEEC-CCCCCCHHHHH
Q ss_conf             2222221000000012333221122-----------36898899975867898779998589399927-89687437899
Q gi|254780603|r  199 LQKMHSWGFQTIGLSSDSKKPLEQE-----------IKNDKIALILGAEGKGLRPKTQETATSMAHLH-MPGIIKALNVS  266 (282)
Q Consensus       199 l~~~~~~~~~i~~~~~~~~~~~~~~-----------~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip-~~~~~~SLNvs  266 (282)
                      ++.++... .++.+|..|.. +...           .-..+.+|++|.- .|+++.+.+.||..+++- |.     +.=.
T Consensus        61 ~~~i~~~~-~~I~LDe~Gk~-~sS~~fa~~i~~~~~~g~~~i~FiIGGa-~G~~~~~~~~a~~~~Sls~mT-----~pH~  132 (155)
T pfam02590        61 LAAIPPGS-YVIALDERGKE-LSSEEFAKLLEDLRLKGKSDITFVIGGS-DGLSEEVLKRANEKLSLSKMT-----LPHQ  132 (155)
T ss_pred             HHHCCCCC-EEEEEECCCCC-CCHHHHHHHHHHHHHCCCCCEEEEEECC-CCCCHHHHHHHHHEEECCCCC-----CCHH
T ss_conf             97379999-89999379983-7879999999999833897559998379-886989997566634413676-----5089


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999876
Q gi|254780603|r  267 NAAAVALYITQNH  279 (282)
Q Consensus       267 ~a~ai~l~~~~~~  279 (282)
                      .|-.|++-+++|-
T Consensus       133 larv~l~EQiYRa  145 (155)
T pfam02590       133 LVRLLLAEQIYRA  145 (155)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999999


No 36 
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=68.66  E-value=4.1  Score=20.05  Aligned_cols=114  Identities=15%  Similarity=0.200  Sum_probs=69.6

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC
Q ss_conf             06889999999864200110013686320000013444333321101222322112222222100000001233322112
Q gi|254780603|r  143 DPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ  222 (282)
Q Consensus       143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~  222 (282)
                      |-.|+...+.-|...++.+-     ..-+       +.-|-     +++-..++..+..+ ..+..+|-++.+|. ++.+
T Consensus        79 dErs~a~~i~kAL~~~~~~~-----~~~~-------~~pGi-----~V~~~~~e~ll~~l-~~~~~ly~L~E~G~-DI~~  139 (197)
T COG1901          79 DERSLAILIKKALDAELGKE-----QTRE-------VTPGI-----YVRNGGFEALLAEL-AEGRSLYYLHEDGR-DISE  139 (197)
T ss_pred             CHHHHHHHHHHHHHHHCCCC-----CEEE-------CCCCE-----EEECCCHHHHHHHH-HCCCCEEEECCCCC-CHHH
T ss_conf             06778999999997431664-----2142-------37987-----99257899999998-65584799925786-4755


Q ss_pred             CCCCCCEEEEECCCCCCCCHHHH----HHCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             23689889997586789877999----85893999278968743789999999999998761
Q gi|254780603|r  223 EIKNDKIALILGAEGKGLRPKTQ----ETATSMAHLHMPGIIKALNVSNAAAVALYITQNHF  280 (282)
Q Consensus       223 ~~~~~~~~lv~G~E~~Gl~~~~~----~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~~~~~~~  280 (282)
                      .++..+.+||+|.- -|++++-.    +..+..|++-    --||-.+++..++-+++.+|.
T Consensus       140 v~~~~np~FIlGDH-~g~t~e~~k~L~r~~~~~ISlG----P~~lha~hcit~~h~~LD~~~  196 (197)
T COG1901         140 VDLIPNPVFILGDH-IGLTEEDEKLLERHAAKKISLG----PLSLHADHCITLLHNLLDRQG  196 (197)
T ss_pred             CCCCCCCEEEEECC-CCCCHHHHHHHHHHHCCEEEEC----CHHHHHHHHHHHHHHHHHHCC
T ss_conf             55689966996178-8989789999998648536727----668888889999998775225


No 37 
>PRK00103 SPOUT methyltransferase superfamily protein; Provisional
Probab=63.59  E-value=11  Score=17.62  Aligned_cols=73  Identities=15%  Similarity=0.164  Sum_probs=44.2

Q ss_pred             CCCCCCCCHHHHCCCCCCCCCCCCC----------CCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHH
Q ss_conf             2222210000000123332211223----------689889997586789877999858939992789687437899999
Q gi|254780603|r  200 QKMHSWGFQTIGLSSDSKKPLEQEI----------KNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAA  269 (282)
Q Consensus       200 ~~~~~~~~~i~~~~~~~~~~~~~~~----------~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~  269 (282)
                      +.++... .++.+|..|.. +....          -....+||+|.- .|+++++.+.||..+++--.-    +.=..|-
T Consensus        62 ~~~~~~~-~~I~LDe~Gk~-~sS~~fa~~l~~~~~~g~~i~FiIGGa-~G~~~~~~~~a~~~lSlS~mT----fpH~lar  134 (156)
T PRK00103         62 AAIPKGA-RVVALDIRGKP-WTSEQFAKELERWRLDGRDVTFVIGGP-EGLSPAVKKRADQSWSLSKLT----LPHQLVR  134 (156)
T ss_pred             HHCCCCC-EEEEEECCCCC-CCHHHHHHHHHHHHHCCCCEEEEEECC-CCCCHHHHHHHHHEEEECCCC----CCHHHHH
T ss_conf             8479999-89999179980-576999999999986399669999788-876989997432288713676----6289999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999876
Q gi|254780603|r  270 AVALYITQNH  279 (282)
Q Consensus       270 ai~l~~~~~~  279 (282)
                      -|++-+++|-
T Consensus       135 ~il~EQiYRa  144 (156)
T PRK00103        135 LVLAEQLYRA  144 (156)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 38 
>pfam04705 TSNR_N Thiostrepton-resistance methylase, N terminus. This region is found in some members of the SpoU-type rRNA methylase family (pfam00588).
Probab=55.49  E-value=15  Score=16.79  Aligned_cols=94  Identities=7%  Similarity=0.187  Sum_probs=63.6

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCC-CCCCCHHHHHHCCCCEEEECHHHHH
Q ss_conf             223765677765431122111288199985788999997898189999973784-3354345543269969997689987
Q gi|254780603|r   24 RRNHRDYKKMQSFNQKSRHTSQPENLFLYGVHTVSAALNNPSRKIFQLLATKNA-LARLDWDANLPHPFPVKTVPPQTID  102 (282)
Q Consensus        24 ~~~n~~~k~~~~l~~k~k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~-~~~~~~~~~l~~~~~I~~v~~~~l~  102 (282)
                      .+..|.++++..+-+.  .|-.....+||-..+..+++.+|-. +..+|..+.. ...........+++++..++...++
T Consensus         9 ~rSDPaVQRIiDvtk~--sRs~ikT~LiED~EPL~~~i~AGve-fieVYg~~~~p~~~~ll~~c~~r~i~vrli~~~i~N   85 (115)
T pfam04705         9 NRSDPAVQRIIDVTKH--SRSVIKTTLIEDIEPLMQSIRAGVE-FIEVYGSDTVPFPGDLLDLCEKRGIPVRLIDASIVN   85 (115)
T ss_pred             CCCCHHHHHHHHHHHC--CHHHHHEEEECCCHHHHHHHHCCCE-EEEEEECCCCCCCHHHHHHHHHCCCCEEEECHHHHH
T ss_conf             3776668889988644--2656410010375578998744707-989851157879848999998659841665588999


Q ss_pred             HHHCCCCCCCCCCEEEEC
Q ss_conf             752477777744202411
Q gi|254780603|r  103 KIVGKEAVHQGLALETAP  120 (282)
Q Consensus       103 ~i~~~~~~hqGi~a~~~~  120 (282)
                      ++...+.-+..+.....|
T Consensus        86 qlFk~erK~kvfGiArvP  103 (115)
T pfam04705        86 QLFKTERKAKVFGIARVP  103 (115)
T ss_pred             HHHHCCCCCCEEEEECCC
T ss_conf             987323566514574179


No 39 
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=54.02  E-value=5.6  Score=19.27  Aligned_cols=32  Identities=16%  Similarity=0.347  Sum_probs=18.6

Q ss_pred             EEEC---CCCCHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             8723---4320688999999986420011001368
Q gi|254780603|r  136 MVLD---HVNDPHNIGAILRSAVAFSCDGIITTKR  167 (282)
Q Consensus       136 i~ld---~i~dp~NlG~I~Rta~a~g~~~vil~~~  167 (282)
                      |++|   .+.+..-+-.+.|.|.++|++|+++.-+
T Consensus       199 Vi~D~SHs~G~r~~v~~la~aAva~G~dGlfiE~H  233 (266)
T PRK13398        199 IIVDPSHATGRRELVIPMAKAAIAAGADGLMIEVH  233 (266)
T ss_pred             EEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             89888533567999999999999839988999826


No 40 
>TIGR01456 CECR5 HAD-superfamily subfamily IIA hydrolase, TIGR01456, CECR5; InterPro: IPR006353 This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all eukaryotes. One sequence is called "Cat Eye Syndrome critical region protein 5" (CECR5) . This gene has been cloned from a pericentromere region of human chromosome 22 believed to be the location of the gene or genes responsible for Cat Eye Syndrome. This is one of a number of candidate genes. The Schizosaccharomyces pombe sequence is annotated as "phosphatidyl synthase," however this is due entirely to a C-terminal region of the protein (outside the region of similarity of this HMM) which is highly homologous to a family of CDP-alcohol phosphatidyltransferases. The physical connection of the phosphatidyl synthase and the HAD-superfamily hydrolase domain in S. pombe may, however, be an important clue to the substrate for the hydrolases in this equivalog..
Probab=53.29  E-value=3.8  Score=20.24  Aligned_cols=16  Identities=6%  Similarity=0.326  Sum_probs=6.5

Q ss_pred             HHHHHHHHHCCCCCCC
Q ss_conf             9999864200110013
Q gi|254780603|r  150 ILRSAVAFSCDGIITT  165 (282)
Q Consensus       150 I~Rta~a~g~~~vil~  165 (282)
                      ..-.|..+||..|+-.
T Consensus        97 v~~va~gyGF~nVv~~  112 (325)
T TIGR01456        97 VAEVAEGYGFKNVVSV  112 (325)
T ss_pred             HHHHHCCCCCCCEEEH
T ss_conf             6888516885220216


No 41 
>KOG3925 consensus
Probab=52.76  E-value=4.4  Score=19.90  Aligned_cols=30  Identities=20%  Similarity=0.409  Sum_probs=14.2

Q ss_pred             CCHH-HHCCCCCCCCCCCCC----CCCCEEEEECCC
Q ss_conf             0000-000123332211223----689889997586
Q gi|254780603|r  206 GFQT-IGLSSDSKKPLEQEI----KNDKIALILGAE  236 (282)
Q Consensus       206 ~~~i-~~~~~~~~~~~~~~~----~~~~~~lv~G~E  236 (282)
                      ||-+ ++++..|. .+.+..    -+....||||.=
T Consensus       277 GYD~~vg~s~rg~-~I~s~~~~~~t~~~iLlvfg~l  311 (371)
T KOG3925         277 GYDFVVGTSTRGS-AIASLSLEAETPPHILLVFGGL  311 (371)
T ss_pred             CCCEEEEECCCCC-CCCCCCCCCCCCCCEEEEEECH
T ss_conf             8446987246776-3000200258887189996030


No 42 
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=51.00  E-value=7.6  Score=18.54  Aligned_cols=51  Identities=22%  Similarity=0.192  Sum_probs=37.1

Q ss_pred             CCCCHHHHHHHH--HHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             432068899999--998642001100136863200000134443333211012
Q gi|254780603|r  140 HVNDPHNIGAIL--RSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYI  190 (282)
Q Consensus       140 ~i~dp~NlG~I~--Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~  190 (282)
                      +-+.+-|||+|+  |.|.++|+...|+.+-.+|...+.+.=+.+--+.+=.|+
T Consensus       102 ~G~haSnLGaiiA~~ia~~~gvPayIVDPvvVDEm~~~Ar~SG~p~i~RkSiF  154 (358)
T COG3426         102 QGEHASNLGAIIANRIAKALGVPAYIVDPVVVDEMEDVARFSGIPEIERKSIF  154 (358)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEEECCEEHHHCCHHHHHCCCCCCHHHHHH
T ss_conf             87551225679999876640997166675003220545510689662057788


No 43 
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=47.91  E-value=12  Score=17.42  Aligned_cols=63  Identities=16%  Similarity=0.162  Sum_probs=34.0

Q ss_pred             CCCCCCCCCCCCCHHHHCCCCCCCCCCCCC--CCCCEEEEECCCCCCCCHHHHH-----HCCCEEE-ECCCC
Q ss_conf             211222222210000000123332211223--6898899975867898779998-----5893999-27896
Q gi|254780603|r  195 LTDALQKMHSWGFQTIGLSSDSKKPLEQEI--KNDKIALILGAEGKGLRPKTQE-----TATSMAH-LHMPG  258 (282)
Q Consensus       195 ~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~--~~~~~~lv~G~E~~Gl~~~~~~-----~~d~~v~-Ip~~~  258 (282)
                      +.++++.....+ .+++++-.|..+..+..  ...+..++||+=..||.+-...     ..|..+. +|-.+
T Consensus       175 L~e~~~~~~~~~-vvi~tsr~g~~~~~e~~~~~~~~~~~~fg~P~~gv~~~~~~~~~~~~~d~~~N~~p~Qg  245 (272)
T COG2106         175 LNELLKGFDLDV-VVIATSRYGPLDVRETEAPLKSKVTLVFGGPEKGVLEILKVGGVKLEFDIVVNFIPGQG  245 (272)
T ss_pred             HHHHHHCCCCCC-EEEEECCCCCCEEEECCCCCCCCCEEEECCCCCCHHEECCCCCCCCCCCEEEEECCCCC
T ss_conf             887763368873-59984355865001225666776058964865570001144566643361577348755


No 44 
>pfam02598 DUF171 Uncharacterized ACR, COG2106.
Probab=43.40  E-value=13  Score=17.17  Aligned_cols=66  Identities=26%  Similarity=0.272  Sum_probs=33.5

Q ss_pred             CCCCCCCCCCCCCCCC-CCC-HHHHCCCCCCCCCCCCCC------C-CCEEEEECC--CCCCCCHH-----HHHHCCCEE
Q ss_conf             1222322112222222-100-000001233322112236------8-988999758--67898779-----998589399
Q gi|254780603|r  189 YIRISNLTDALQKMHS-WGF-QTIGLSSDSKKPLEQEIK------N-DKIALILGA--EGKGLRPK-----TQETATSMA  252 (282)
Q Consensus       189 ~~~~~~~~~~l~~~~~-~~~-~i~~~~~~~~~~~~~~~~------~-~~~~lv~G~--E~~Gl~~~-----~~~~~d~~v  252 (282)
                      +....++.+.++.+.- .|| .+++++..|. ++.+...      + ....+|||+  ...|.-+.     ..+.-|..+
T Consensus       180 Vr~a~sl~~v~~~~~~~~gYd~~I~tS~~G~-~~~~~~~~~~~~~~~~~~lvVFG~~~~~~~~~~~~~~~~~~~~fD~~l  258 (283)
T pfam02598       180 VRIASSLSDVFKKSPFPEGYDVTIGTSRRGK-DISEAELEIKLMENFKHILLVFGGWEPLKGSDEILKDQGPKELFDGYL  258 (283)
T ss_pred             EEEECCHHHHHHCCCCCCCCCEEEEECCCCC-CCCHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCHHHCCEEE
T ss_conf             9983689999623876788886999899996-463100011455677848999799436510344411356254378789


Q ss_pred             EEC
Q ss_conf             927
Q gi|254780603|r  253 HLH  255 (282)
Q Consensus       253 ~Ip  255 (282)
                      ..+
T Consensus       259 N~~  261 (283)
T pfam02598       259 NTP  261 (283)
T ss_pred             ECC
T ss_conf             768


No 45 
>COG3222 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.37  E-value=12  Score=17.44  Aligned_cols=77  Identities=21%  Similarity=0.195  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHHCCC---CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC
Q ss_conf             8999999986420011---0013686320000013444333321101222322112222222100000001233322112
Q gi|254780603|r  146 NIGAILRSAVAFSCDG---IITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKKPLEQ  222 (282)
Q Consensus       146 NlG~I~Rta~a~g~~~---vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~  222 (282)
                      .+|.=++-+..-++++   |++....|+..+...+-.+.-++..+|.+-..-    +    .-||++.|+......-+..
T Consensus        88 d~gdRlars~~~a~~~~~~VliIg~DcP~lt~elLa~a~taL~~~paVLGpa----~----dGGy~llgLrr~~pe~fe~  159 (211)
T COG3222          88 DLGDRLARSHVDAFDGSYPVLIIGMDCPGLTAELLADAFTALLQIPAVLGPA----F----DGGYYLLGLRRFAPELFEA  159 (211)
T ss_pred             CHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCEECCC----C----CCCEEEEEEECCCHHHHHC
T ss_conf             8889999999997568872799825897647999999999971476102222----2----5837899731048999950


Q ss_pred             CCCCCCEE
Q ss_conf             23689889
Q gi|254780603|r  223 EIKNDKIA  230 (282)
Q Consensus       223 ~~~~~~~~  230 (282)
                      ++|..+.+
T Consensus       160 ipwg~~~v  167 (211)
T COG3222         160 IPWGTPDV  167 (211)
T ss_pred             CCCCCCHH
T ss_conf             88887459


No 46 
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=43.17  E-value=24  Score=15.65  Aligned_cols=120  Identities=13%  Similarity=0.189  Sum_probs=76.3

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC---------C---CCCCCCC
Q ss_conf             506887234320688999999986420011001368632000001344433332110122---------2---3221122
Q gi|254780603|r  132 SQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIR---------I---SNLTDAL  199 (282)
Q Consensus       132 ~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~---------~---~~~~~~l  199 (282)
                      ++.+++|-|++--|-.-|++.-|+-|.   ..--...+...+-...|.  ||++++.++.         +   .++.+++
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~---~~~~~~kVaiITtDtYRI--GA~EQLk~Ya~im~vp~~vv~~~~el~~ai  276 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYV---MLKKKKKVAIITTDTYRI--GAVEQLKTYADIMGVPLEVVYSPKELAEAI  276 (407)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHH---HHCCCCCEEEEEECCCHH--HHHHHHHHHHHHHCCCEEEECCHHHHHHHH
T ss_conf             685799989988758879999999997---532576068997144115--289999999998699559963999999999


Q ss_pred             CCCCCCCCHHHHCCCCCCC---------CCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCC
Q ss_conf             2222210000000123332---------2112236898899975867898779998589399927896
Q gi|254780603|r  200 QKMHSWGFQTIGLSSDSKK---------PLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPG  258 (282)
Q Consensus       200 ~~~~~~~~~i~~~~~~~~~---------~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~  258 (282)
                      ..++....-++.+.+.+..         .+.+...+-.+.|||-.-.+.  +++.+.-++.-.+|..+
T Consensus       277 ~~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~--~dlkei~~~f~~~~i~~  342 (407)
T COG1419         277 EALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKY--EDLKEIIKQFSLFPIDG  342 (407)
T ss_pred             HHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCH--HHHHHHHHHHCCCCCCE
T ss_conf             9853188899968998833789999999997035662179998457646--88999999724588661


No 47 
>pfam09837 DUF2064 Uncharacterized protein conserved in bacteria (DUF2064). This domain, found in various prokaryotic proteins, has no known function.
Probab=40.36  E-value=27  Score=15.40  Aligned_cols=77  Identities=18%  Similarity=0.151  Sum_probs=49.9

Q ss_pred             CCCHHHHHHHHHHHHH----HHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf             3206889999999864----200110013686320000013444333321101222322112222222100000001233
Q gi|254780603|r  141 VNDPHNIGAILRSAVA----FSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDS  216 (282)
Q Consensus       141 i~dp~NlG~I~Rta~a----~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~  216 (282)
                      .|-.+|+|.=|+-|..    .|.+.|++....++.+++..++.+.-++.+-++        .+--..+-||+++|+....
T Consensus        39 ~Q~~gdLG~Rm~~a~~~~~~~g~~~v~lIGsD~P~l~~~~l~~A~~~L~~~d~--------VlgPa~DGGy~LiG~~~~~  110 (121)
T pfam09837        39 PQGGGDLGERMARAFRQAFAAGYRPVLLIGTDCPDLTAELLAQAFEALERHDA--------VLGPAEDGGYYLLGLRRPT  110 (121)
T ss_pred             ECCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCE--------EEEECCCCCEEEEEECCCC
T ss_conf             25999989999999999984389858998488465899999999998621997--------9997488999999747778


Q ss_pred             CCCCCCCCC
Q ss_conf             322112236
Q gi|254780603|r  217 KKPLEQEIK  225 (282)
Q Consensus       217 ~~~~~~~~~  225 (282)
                      ...+.++.|
T Consensus       111 ~~lF~~i~W  119 (121)
T pfam09837       111 PDLFEGVPW  119 (121)
T ss_pred             HHHCCCCCC
T ss_conf             887079998


No 48 
>PRK11561 isovaleryl CoA dehydrogenase; Provisional
Probab=38.85  E-value=17  Score=16.58  Aligned_cols=25  Identities=32%  Similarity=0.470  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCH
Q ss_conf             2211223689889997586789877
Q gi|254780603|r  218 KPLEQEIKNDKIALILGAEGKGLRP  242 (282)
Q Consensus       218 ~~~~~~~~~~~~~lv~G~E~~Gl~~  242 (282)
                      .+-.+..|.+-.++.+|.|++|+..
T Consensus       266 ~pSaEve~~gA~a~lvGeegrGv~~  290 (538)
T PRK11561        266 NASCEVEFQDAIGWLLGEEGEGIRL  290 (538)
T ss_pred             CCEEEEEECCCEEEEECCCCCCHHH
T ss_conf             8828999888079983578857899


No 49 
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243    This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. .
Probab=38.58  E-value=6.5  Score=18.91  Aligned_cols=28  Identities=36%  Similarity=0.425  Sum_probs=19.8

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH
Q ss_conf             88723432068899999998642001100136863200000134
Q gi|254780603|r  135 LMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAK  178 (282)
Q Consensus       135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~r  178 (282)
                      +-++|.|.|.=|     ||||||||-           ||..|-+
T Consensus        30 L~AFeEVG~~L~-----RT~AACGFR-----------WNa~VRk   57 (163)
T TIGR02894        30 LAAFEEVGDALN-----RTAAACGFR-----------WNAVVRK   57 (163)
T ss_pred             HHHHHHHCCCCC-----CCCHHCCCC-----------HHHHHHH
T ss_conf             778887331147-----873110253-----------3578758


No 50 
>pfam07047 OPA3 Optic atrophy 3 protein (OPA3). This family consists of several optic atrophy 3 (OPA3) proteins. OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity.
Probab=37.74  E-value=25  Score=15.58  Aligned_cols=22  Identities=27%  Similarity=0.221  Sum_probs=16.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             4378999999999999876149
Q gi|254780603|r  261 KALNVSNAAAVALYITQNHFAK  282 (282)
Q Consensus       261 ~SLNvs~a~ai~l~~~~~~~~~  282 (282)
                      |.+=-+||+++++||..|+..|
T Consensus        81 E~fIF~Va~~li~~E~~Rs~~k  102 (134)
T pfam07047        81 EAFIFSVAGGLLVYEYQRSSRK  102 (134)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999998424


No 51 
>KOG2882 consensus
Probab=37.71  E-value=14  Score=17.04  Aligned_cols=28  Identities=14%  Similarity=0.156  Sum_probs=14.5

Q ss_pred             CEEEEEEHHHHHHHHHCCCEEEEEEEECCC
Q ss_conf             819998578899999789818999997378
Q gi|254780603|r   47 ENLFLYGVHTVSAALNNPSRKIFQLLATKN   76 (282)
Q Consensus        47 ~~~iIeG~~~V~eaL~~~~~~i~~i~~te~   76 (282)
                      +.-.|+|.-...++|.+....  .+|+|.+
T Consensus        36 g~~~ipGs~e~l~~L~~~gK~--i~fvTNN   63 (306)
T KOG2882          36 GEKPIPGSPEALNLLKSLGKQ--IIFVTNN   63 (306)
T ss_pred             CCCCCCCHHHHHHHHHHCCCC--EEEEECC
T ss_conf             687888859999999973982--6999678


No 52 
>COG1772 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.39  E-value=30  Score=15.12  Aligned_cols=135  Identities=19%  Similarity=0.265  Sum_probs=71.7

Q ss_pred             EEEEECCCCCHHH-----HHHHHHH---HHHHHCCCCCCCCCCCCCC----HHHHHHHHHHHH--HHHCCCCCCCCCCCC
Q ss_conf             6887234320688-----9999999---8642001100136863200----000134443333--211012223221122
Q gi|254780603|r  134 LLMVLDHVNDPHN-----IGAILRS---AVAFSCDGIITTKRYSPSE----SAVLAKSASGAL--EHIPYIRISNLTDAL  199 (282)
Q Consensus       134 ~~i~ld~i~dp~N-----lG~I~Rt---a~a~g~~~vil~~~~~~~~----~~~~~ras~Ga~--~~l~~~~~~~~~~~l  199 (282)
                      +.+.|.+-.||.-     +-+|.|.   |.||+++-.++.=.+.+-.    .-.+.++.-|..  +-+-+. -.|....+
T Consensus         2 ltiglyNtYD~~r~heaH~RaIARAAPicyAF~fhLal~~FPf~~~~~Elae~va~~TTIGesG~yl~~L~-e~n~l~~~   80 (178)
T COG1772           2 LTIGLYNTYDKKRIHEAHLRAIARAAPICYAFNFHLALIDFPFKGTEKELAEEVAEKTTIGESGKYLLVLA-ESNKLHVI   80 (178)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCEEEEECCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHH-HCCCEEEE
T ss_conf             27997405683578899999987536535874242789778778987999999875170067732247568-63945885


Q ss_pred             CCCCCCCC-----HHHHCCCC--CCCCC-----C-CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHH
Q ss_conf             22222100-----00000123--33221-----1-223689889997586789877999858939992789687437899
Q gi|254780603|r  200 QKMHSWGF-----QTIGLSSD--SKKPL-----E-QEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVS  266 (282)
Q Consensus       200 ~~~~~~~~-----~i~~~~~~--~~~~~-----~-~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs  266 (282)
                      +. ..+||     .+++++..  ..+-+     . ...-++...+++|=-.+|||+++++.|-+-+-|.- .++ ||--.
T Consensus        81 D~-p~kgfp~qfG~vvaTTskPd~~k~i~p~dva~~~lr~ks~~~~iGLGr~GLPke~~~~~~YHLDiT~-kgv-SLETc  157 (178)
T COG1772          81 DK-PKKGFPPQFGEVVATTSKPDEKKAIKPIDVAEEALRGKSFTFLIGLGRHGLPKEMFKSAKYHLDITD-KGV-SLETC  157 (178)
T ss_pred             CC-CCCCCCHHHCCEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHCEEEEEECC-CCC-EEEEH
T ss_conf             16-6556971118555333689800145766679998468956999844777886999853024463136-731-02311


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780603|r  267 NAAAVA  272 (282)
Q Consensus       267 ~a~ai~  272 (282)
                      .|-+++
T Consensus       158 TAIGaI  163 (178)
T COG1772         158 TAIGAI  163 (178)
T ss_pred             HHHCCH
T ss_conf             243126


No 53 
>COG2242 CobL Precorrin-6B methylase 2 [Coenzyme metabolism]
Probab=35.80  E-value=32  Score=14.98  Aligned_cols=40  Identities=20%  Similarity=0.343  Sum_probs=29.4

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             650688723432068899999998642001100136863200
Q gi|254780603|r  131 NSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSE  172 (282)
Q Consensus       131 ~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~  172 (282)
                      ....++.+|  +|+.=+..|-|.|+.||++.+-+....++..
T Consensus        57 p~~~v~AIe--~~~~a~~~~~~N~~~fg~~n~~vv~g~Ap~~   96 (187)
T COG2242          57 PSGRVIAIE--RDEEALELIERNAARFGVDNLEVVEGDAPEA   96 (187)
T ss_pred             CCCEEEEEE--CCHHHHHHHHHHHHHHCCCCEEEEECCCHHH
T ss_conf             885599992--5888999999999984999679995464576


No 54 
>KOG1618 consensus
Probab=35.58  E-value=24  Score=15.63  Aligned_cols=31  Identities=19%  Similarity=0.273  Sum_probs=17.6

Q ss_pred             CCEEEEEEHHHHHHHHH--------CCCEEEEEEEECCC
Q ss_conf             88199985788999997--------89818999997378
Q gi|254780603|r   46 PENLFLYGVHTVSAALN--------NPSRKIFQLLATKN   76 (282)
Q Consensus        46 ~~~~iIeG~~~V~eaL~--------~~~~~i~~i~~te~   76 (282)
                      .+..++-|.+++-++.+        .+..+|-.+++|..
T Consensus        42 IDGVL~RG~~~i~~~~~Alr~L~~~~g~lkIP~vfLTNG   80 (389)
T KOG1618          42 IDGVLFRGHRPIPGALKALRRLVDNQGQLKIPFVFLTNG   80 (389)
T ss_pred             CCCEEEECCCCCCCHHHHHHHHHHCCCCEECCEEEEECC
T ss_conf             352798278878645889999973678710468999579


No 55 
>TIGR01855 IMP_synth_hisH imidazole glycerol phosphate synthase, glutamine amidotransferase subunit; InterPro: IPR010139   Imidazole glycerol phosphate synthetase (IGPS) is a key metabolic enzyme, which links amino acid and nucleotide biosynthesis: it catalyses the closure of the imidazole ring within histidine biosynthesis (fifth step), and provides the substrate for de novo purine biosynthesis. IGPS consists of two different subunits: HisH, a glutamine amidotransferase (glutaminase), and HisF, a synthase (cyclase). HisH functions to provide a source of nitrogen, which is required for the synthesis of histidine and purines. In the HisH glutaminase reaction, the hydrolysis of glutamine yields ammonia, which is then used by HisF in the subsequent synthase reaction. The X-ray structure of the HisH/HisF heterodimer of IGPS reveals a putative tunnel for the transfer of ammonia from HisH to HisF via a (beta-alpha)8 barrel fold within HisF that abuts HisH . Ammonia tunnels connect the glutaminase and synthase active sites.   HisH belongs to a large group of enzymes found in diverse and fundamental anabolic pathways. These enzymes share a common domain, referred to as the type-I glutamine amidotransferase (GATase) domain, which can occur either as single polypeptides (as with HisH) or as domains of large multifunctional proteins.; GO: 0016763 transferase activity transferring pentosyl groups, 0000105 histidine biosynthetic process, 0005737 cytoplasm.
Probab=34.16  E-value=32  Score=14.95  Aligned_cols=31  Identities=13%  Similarity=0.319  Sum_probs=19.1

Q ss_pred             EEEECCCCCHHHHHH----HHHHHHHHHCCCCCCCCC
Q ss_conf             887234320688999----999986420011001368
Q gi|254780603|r  135 LMVLDHVNDPHNIGA----ILRSAVAFSCDGIITTKR  167 (282)
Q Consensus       135 ~i~ld~i~dp~NlG~----I~Rta~a~g~~~vil~~~  167 (282)
                      |+|+|  ..+|||++    +-|.-..+|+...++.+.
T Consensus         1 i~viD--YG~GNL~SlyrGV~~Al~~~G~~~~v~~~~   35 (211)
T TIGR01855         1 IVVID--YGVGNLRSLYRGVKRALKRVGAEPVVVKDS   35 (211)
T ss_pred             CEEEE--CCCHHHHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             97874--371656889999999998449817996286


No 56 
>pfam02784 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.
Probab=33.69  E-value=32  Score=14.98  Aligned_cols=21  Identities=14%  Similarity=0.317  Sum_probs=10.1

Q ss_pred             CCCCCCCCCCCCCHHHHCCCC
Q ss_conf             211222222210000000123
Q gi|254780603|r  195 LTDALQKMHSWGFQTIGLSSD  215 (282)
Q Consensus       195 ~~~~l~~~~~~~~~i~~~~~~  215 (282)
                      +.+.++.+++.+.++.|++.+
T Consensus       140 ~~~~~~~~~~~~~~~~GlH~H  160 (245)
T pfam02784       140 AEALLKAAKELGLNVVGVHFH  160 (245)
T ss_pred             HHHHHHHHHHCCCCEEEEEEE
T ss_conf             999999998679975475565


No 57 
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=33.39  E-value=35  Score=14.75  Aligned_cols=13  Identities=8%  Similarity=0.064  Sum_probs=5.8

Q ss_pred             EEEHHHHHHHHHC
Q ss_conf             9857889999978
Q gi|254780603|r   51 LYGVHTVSAALNN   63 (282)
Q Consensus        51 IeG~~~V~eaL~~   63 (282)
                      +....-+..+++.
T Consensus        63 vaS~~El~~al~~   75 (368)
T cd06840          63 CVSIGELDLVLKL   75 (368)
T ss_pred             EECHHHHHHHHHH
T ss_conf             9899999999986


No 58 
>pfam05341 DUF708 Protein of unknown function (DUF708). This family consists of several uncharacterized nucleopolyhedrovirus proteins of unknown function.
Probab=33.33  E-value=35  Score=14.74  Aligned_cols=54  Identities=15%  Similarity=0.071  Sum_probs=43.3

Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             221122368988999758678987799985893999278968743789999999999
Q gi|254780603|r  218 KPLEQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKALNVSNAAAVALY  274 (282)
Q Consensus       218 ~~~~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SLNvs~a~ai~l~  274 (282)
                      ..+..||+.+|..+=+.+..-|+..+-+..+   ..=|..+..+++|++.+.-++.|
T Consensus        46 a~~EnFDYk~PI~Y~lk~k~L~i~ne~~~~A---Ln~P~~~~~~~~ni~~~~i~~~F   99 (105)
T pfam05341        46 ANLENFDYKQPIYYDLKRKQLLINNESVNKA---LNRPRYAVLDTLNISPIHIFLAF   99 (105)
T ss_pred             HHHHCCCCCCCEEEEECCCEEEECCHHHHHH---HCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             3112066889628980476887552899998---57986455675445508999999


No 59 
>TIGR01245 trpD anthranilate phosphoribosyltransferase; InterPro: IPR005940    In many widely different species, including Escherichia coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzyme is a C-terminal part of a multifunctional protein together with glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (4.1.3.27 from EC).; GO: 0004048 anthranilate phosphoribosyltransferase activity, 0000162 tryptophan biosynthetic process.
Probab=32.63  E-value=27  Score=15.39  Aligned_cols=39  Identities=10%  Similarity=0.019  Sum_probs=29.5

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCC-CCCC-CCCCCCH
Q ss_conf             8872343206889999999864200110-0136-8632000
Q gi|254780603|r  135 LMVLDHVNDPHNIGAILRSAVAFSCDGI-ITTK-RYSPSES  173 (282)
Q Consensus       135 ~i~ld~i~dp~NlG~I~Rta~a~g~~~v-il~~-~~~~~~~  173 (282)
                      -.-|=||.||.=++.+.+....+|.+.. ++.. ++-|..+
T Consensus       184 ~~qv~GVy~~~L~~~~A~aL~~LG~krAlVVhG~~GlDE~s  224 (331)
T TIGR01245       184 KYQVIGVYDPDLVEVMAEALKNLGVKRALVVHGEDGLDEIS  224 (331)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCEEE
T ss_conf             80278534688899999999861767089985788961453


No 60 
>TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase, isomerizing; InterPro: IPR005855    Glucosamine:fructose-6-phosphate aminotransferase (2.6.1.16 from EC) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars.   This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologs.; GO: 0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0016051 carbohydrate biosynthetic process, 0005737 cytoplasm.
Probab=31.76  E-value=37  Score=14.59  Aligned_cols=76  Identities=12%  Similarity=0.112  Sum_probs=54.1

Q ss_pred             CCCCCHHHHCCCCCC-C------CCCCCCCCCCEEEEECCC-CCCCCHHHHHHCCCEEEECCCCCCCH--HHHHHHHHHH
Q ss_conf             221000000012333-2------211223689889997586-78987799985893999278968743--7899999999
Q gi|254780603|r  203 HSWGFQTIGLSSDSK-K------PLEQEIKNDKIALILGAE-GKGLRPKTQETATSMAHLHMPGIIKA--LNVSNAAAVA  272 (282)
Q Consensus       203 ~~~~~~i~~~~~~~~-~------~~~~~~~~~~~~lv~G~E-~~Gl~~~~~~~~d~~v~Ip~~~~~~S--LNvs~a~ai~  272 (282)
                      =+.|++|++..+++. -      ++.|..--+-.+++|++| +.+..+.   .+|+.+.+|-.+..-+  +++.+..-++
T Consensus       527 id~~~PVva~ap~~~Gl~~K~~SNv~Ev~ARga~vi~~~~~~~~~~~~~---~~d~~i~~P~~~~~~~P~~~l~iplQLl  603 (628)
T TIGR01135       527 IDEGLPVVAIAPKDSGLLEKTKSNVEEVKARGARVIVLASEDDAELIAA---IADDIIKLPEVEELLAPIVYLTIPLQLL  603 (628)
T ss_pred             ECCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCC---CCCEEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             3188708998278898507778889988726963899825775324311---0545888468886304166767999999


Q ss_pred             HHHHHHHHC
Q ss_conf             999987614
Q gi|254780603|r  273 LYITQNHFA  281 (282)
Q Consensus       273 l~~~~~~~~  281 (282)
                      -|+.-..++
T Consensus       604 AYhiA~~kG  612 (628)
T TIGR01135       604 AYHIALAKG  612 (628)
T ss_pred             HHHHHHHHC
T ss_conf             999999708


No 61 
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=30.58  E-value=39  Score=14.47  Aligned_cols=120  Identities=16%  Similarity=0.187  Sum_probs=75.5

Q ss_pred             CCCCEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEEEECHHHHHHHHCCCCCCCC-CCEEEECCC
Q ss_conf             1288199985788999997898189999973784335434554326996999768998775247777774-420241155
Q gi|254780603|r   44 SQPENLFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVKTVPPQTIDKIVGKEAVHQG-LALETAPLL  122 (282)
Q Consensus        44 ~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqG-i~a~~~~~~  122 (282)
                      .++++|+|||.-+==.|=.+..|+.+.|+--.               .+|.-+-....+++......|.- |++.+.|..
T Consensus       423 e~TELFlVEGDSAGGSAKQAR~RE~QAilPL~---------------GKiLN~~~~~~~~vl~~~~i~D~~vAl~~~~~~  487 (647)
T TIGR01055       423 EKTELFLVEGDSAGGSAKQARDREYQAILPLK---------------GKILNTWEVSLDKVLNSQEIHDIEVALGIDPDS  487 (647)
T ss_pred             CCCEEEEEECCCCCCCHHHHCCCCCEEECCCC---------------CCEEEEECCCHHHHHCCCCCCEEEEEEECCCCC
T ss_conf             26427898325677521343053201214456---------------647763214644553124200021022248720


Q ss_pred             CCCHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             554011266506887234320688999999986420011001368632000001344
Q gi|254780603|r  123 SPTLDAVRNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKS  179 (282)
Q Consensus       123 ~~~l~~~~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ra  179 (282)
                      ...++++.-..++++-|.=.|---+.+++=+--..-+..++-. +....--|=..|-
T Consensus       488 ~~k~~~LRY~Ki~Il~DAD~DG~HIA~LL~~lF~~~~p~LV~~-GH~Y~A~PPLYR~  543 (647)
T TIGR01055       488 NDKLSQLRYGKIIILADADSDGLHIATLLCALFLKHFPKLVEE-GHVYVAKPPLYRI  543 (647)
T ss_pred             HHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHC-CCEEEECCCCEEE
T ss_conf             0036426722288984178880789999999999988888753-9078717872021


No 62 
>TIGR03565 alk_sulf_monoox alkanesulfonate monooxygenase, FMNH(2)-dependent. Members of this protein family are monooxygenases that catalyze desulfonation of aliphatic sulfonates such as methane sulfonate. This enzyme uses reduced FMN, although various others members of the same luciferase-like monooxygenase family (pfam00296) are F420-dependent enzymes.
Probab=29.26  E-value=41  Score=14.34  Aligned_cols=11  Identities=9%  Similarity=0.172  Sum_probs=4.9

Q ss_pred             CCCCCCCCEEE
Q ss_conf             77777442024
Q gi|254780603|r  108 EAVHQGLALET  118 (282)
Q Consensus       108 ~~~hqGi~a~~  118 (282)
                      ..+|+|=-..+
T Consensus       144 ~~~~~G~~~~v  154 (346)
T TIGR03565       144 TVDFDGKHIKV  154 (346)
T ss_pred             CCCCCCCEEEE
T ss_conf             70455875773


No 63 
>pfam00851 Peptidase_C6 Helper component proteinase. This protein is found in genome polyproteins of potyviruses.
Probab=27.97  E-value=34  Score=14.78  Aligned_cols=28  Identities=21%  Similarity=0.221  Sum_probs=20.8

Q ss_pred             CCCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             0123332211223689889997586789
Q gi|254780603|r  212 LSSDSKKPLEQEIKNDKIALILGAEGKG  239 (282)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~lv~G~E~~G  239 (282)
                      +..+|+.-++++..|.+--||+||-|.-
T Consensus       291 T~ddG~p~~S~~~~PTK~HLvIGnsgD~  318 (453)
T pfam00851       291 TLDDGKPIYSELKMPTKNHLVIGNSGDP  318 (453)
T ss_pred             ECCCCCEEEEECCCCCCCEEEECCCCCC
T ss_conf             6688987443133787684771578985


No 64 
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=27.86  E-value=40  Score=14.39  Aligned_cols=31  Identities=13%  Similarity=-0.073  Sum_probs=14.5

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH
Q ss_conf             0688999999986420011001368632000
Q gi|254780603|r  143 DPHNIGAILRSAVAFSCDGIITTKRYSPSES  173 (282)
Q Consensus       143 dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~  173 (282)
                      +|...-..+.-...+|.+.|+++++++..|+
T Consensus       134 s~~~~~~a~eki~~~Gn~~i~l~ERG~~gy~  164 (250)
T PRK13397        134 TIEEYLGALSYLQDTGKSNIILCERGVRGYD  164 (250)
T ss_pred             CHHHHHHHHHHHHHCCCCCEEEEECCCCCCC
T ss_conf             9999999999999659982899828987555


No 65 
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases; InterPro: IPR010031   This entry identifies a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesising ascorbic acid or a derivative. These include L-gulonolactone oxidase (1.1.3.8 from EC) from rat and D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by IPR006093 from INTERPRO.; GO: 0016899 oxidoreductase activity acting on the CH-OH group of donors oxygen as acceptor, 0009058 biosynthetic process.
Probab=26.62  E-value=42  Score=14.26  Aligned_cols=20  Identities=5%  Similarity=-0.069  Sum_probs=13.3

Q ss_pred             CCCCCCCCCCEEEEECCCCC
Q ss_conf             21122368988999758678
Q gi|254780603|r  219 PLEQEIKNDKIALILGAEGK  238 (282)
Q Consensus       219 ~~~~~~~~~~~~lv~G~E~~  238 (282)
                      -++=+.++++++++-|+-.+
T Consensus       217 Rv~wfPyt~~~v~wr~nkt~  236 (505)
T TIGR01678       217 RVLWFPYTEKVVVWRANKTE  236 (505)
T ss_pred             EEEEECCCCEEEEEECCCCC
T ss_conf             99871330418898447466


No 66 
>PRK11052 malQ 4-alpha-glucanotransferase; Provisional
Probab=25.80  E-value=47  Score=13.97  Aligned_cols=39  Identities=13%  Similarity=0.020  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCCC---------CCCCCCHHHHHH
Q ss_conf             432068899999998642001100136---------863200000134
Q gi|254780603|r  140 HVNDPHNIGAILRSAVAFSCDGIITTK---------RYSPSESAVLAK  178 (282)
Q Consensus       140 ~i~dp~NlG~I~Rta~a~g~~~vil~~---------~~~~~~~~~~~r  178 (282)
                      ||.|=+.|..+++.++..|++.|.+.+         ..+.||+|..-|
T Consensus       160 GiGDf~DL~~l~~~aa~~Gadfv~lNPlHA~~p~~P~~~SPYsPssRr  207 (694)
T PRK11052        160 GIGDFGDLKQMLVDVAKRGGDFIGLNPIHALYPANPESASPYSPSSRR  207 (694)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCEEEECCHHHCCCCCCCCCCCCCCCCCC
T ss_conf             877899999999999976998798671320678998999997952124


No 67 
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=25.25  E-value=48  Score=13.91  Aligned_cols=55  Identities=4%  Similarity=-0.055  Sum_probs=27.5

Q ss_pred             EEEEEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEE-EECHHHHHHHH
Q ss_conf             9998578899999789818999997378433543455432699699-97689987752
Q gi|254780603|r   49 LFLYGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVK-TVPPQTIDKIV  105 (282)
Q Consensus        49 ~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~-~v~~~~l~~i~  105 (282)
                      +=+....-+..++..++.  ..++.+............+..++... .-+..++.++.
T Consensus        52 ~DvaS~~El~~~~~~~~~--~~Iif~gp~K~~~~l~~a~~~gv~~i~~DS~~El~~i~  107 (377)
T cd06843          52 FEVASGGEIAHVRAAVPD--APLIFGGPGKTDSELAQALAQGVERIHVESELELRRLN  107 (377)
T ss_pred             EEEECHHHHHHHHHCCCC--CCEEECCCCCCHHHHHHHHHCCCCEEEECCHHHHHHHH
T ss_conf             898299999999853999--64798899999999999998799889988999999999


No 68 
>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390   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 includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=24.79  E-value=43  Score=14.20  Aligned_cols=78  Identities=13%  Similarity=0.154  Sum_probs=50.2

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCHHHHHHHHHHHHHHHCCC------------CC-CC
Q ss_conf             665068872343206889999999864200110--0136863200000134443333211012------------22-32
Q gi|254780603|r  130 RNSQLLMVLDHVNDPHNIGAILRSAVAFSCDGI--ITTKRYSPSESAVLAKSASGALEHIPYI------------RI-SN  194 (282)
Q Consensus       130 ~~~~~~i~ld~i~dp~NlG~I~Rta~a~g~~~v--il~~~~~~~~~~~~~ras~Ga~~~l~~~------------~~-~~  194 (282)
                      .+.|.++++-||.--|=.=||.--|..|--+|-  ++.  .+|     +.||  ||.++|..|            .. +|
T Consensus        79 ~~kp~Vil~VGVNG~GKTTTIaKLA~~l~~~Gk~V~la--AgD-----TFRA--AA~EQL~~Wa~R~gv~vi~~~~gn~D  149 (284)
T TIGR00064        79 EKKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLA--AGD-----TFRA--AAIEQLEVWAKRLGVDVIKQKEGNAD  149 (284)
T ss_pred             CCCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEE--CCC-----HHHH--HHHHHHHHHHHHHCCEEEECCCCCCC
T ss_conf             78977999984408860102889999998749908998--275-----2479--99999999898838755407889887


Q ss_pred             C----CCCCCCCCCCCCHHHHCCCCC
Q ss_conf             2----112222222100000001233
Q gi|254780603|r  195 L----TDALQKMHSWGFQTIGLSSDS  216 (282)
Q Consensus       195 ~----~~~l~~~~~~~~~i~~~~~~~  216 (282)
                      .    .+++++.+++||=++-.|+-|
T Consensus       150 PAaV~fDAi~~Ak~~niDvvliDTAG  175 (284)
T TIGR00064       150 PAAVIFDAIQAAKARNIDVVLIDTAG  175 (284)
T ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             17899998999987499789973475


No 69 
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=24.40  E-value=50  Score=13.82  Aligned_cols=33  Identities=15%  Similarity=0.239  Sum_probs=16.4

Q ss_pred             CCCCCCCEEEEEEHHHHHHHHHCCCEEEEEEEE
Q ss_conf             211128819998578899999789818999997
Q gi|254780603|r   41 RHTSQPENLFLYGVHTVSAALNNPSRKIFQLLA   73 (282)
Q Consensus        41 k~R~~~~~~iIeG~~~V~eaL~~~~~~i~~i~~   73 (282)
                      +...+..+|++||.-+==.|-....|..+.|+-
T Consensus       414 kd~~~~ELfiVEGDSAGGSAKqgRdR~~QAILP  446 (635)
T COG0187         414 KDPEKSELFLVEGDSAGGSAKQGRDREFQAILP  446 (635)
T ss_pred             CCCCCCEEEEEECCCCCHHHHHCCCCCCEEEEE
T ss_conf             882415599980477633244216866557720


No 70 
>PRK11440 hypothetical protein; Provisional
Probab=23.37  E-value=53  Score=13.70  Aligned_cols=65  Identities=14%  Similarity=0.141  Sum_probs=45.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             6887234320688999999986420011001368632000001344433332110122232211222
Q gi|254780603|r  134 LLMVLDHVNDPHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQ  200 (282)
Q Consensus       134 ~~i~ld~i~dp~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~  200 (282)
                      --|++.|+.-..=+-+-+|.|...|++-+++. +++.-+++...+++.-.++.. +..+.+..+.|.
T Consensus       122 ~~lvi~G~~T~~CV~sTardA~~~gy~v~vv~-Da~a~~~~e~h~~aL~~l~~~-~a~V~tt~eil~  186 (188)
T PRK11440        122 DTIVLCGISTNIGVESTARNAWELGFNLVIAE-DACSAASAEQHQNSMNHIFPR-IARVRSVEEILN  186 (188)
T ss_pred             CEEEEEEECCCHHHHHHHHHHHHCCCEEEEEC-CCCCCCCHHHHHHHHHHHHHC-EEEEEEHHHHHH
T ss_conf             98999322116569999999998899899810-234899999999999999854-579722999985


No 71 
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684    This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=23.32  E-value=25  Score=15.56  Aligned_cols=14  Identities=36%  Similarity=0.615  Sum_probs=12.1

Q ss_pred             EEEE-ECCCCCHHHH
Q ss_conf             6887-2343206889
Q gi|254780603|r  134 LLMV-LDHVNDPHNI  147 (282)
Q Consensus       134 ~~i~-ld~i~dp~Nl  147 (282)
                      .||| .+.|.||+||
T Consensus       159 Pw~VD~~dveDp~nL  173 (249)
T TIGR02303       159 PWIVDKEDVEDPMNL  173 (249)
T ss_pred             CEEEEECCCCCCCCC
T ss_conf             847851236785567


No 72 
>TIGR02924 ICDH_alpha isocitrate dehydrogenase; InterPro: IPR014273   This entry represents a group of isocitrate dehydrogenases found mainly in the alphaproteobacteria. Many of the species containing these proteins appear to have a TCA cycle lacking only a determined isocitrate dehydrogenase. The precise identity of the cofactor (NADH -- 1.1.1.41 from EC vs. NADPH -- 1.1.1.42 from EC) is unclear..
Probab=22.76  E-value=33  Score=14.89  Aligned_cols=95  Identities=16%  Similarity=0.081  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-CCC-
Q ss_conf             88999999986420-011001368632000001344433332110122232211222222210000000123332-211-
Q gi|254780603|r  145 HNIGAILRSAVAFS-CDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIGLSSDSKK-PLE-  221 (282)
Q Consensus       145 ~NlG~I~Rta~a~g-~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~-~~~-  221 (282)
                      .++-..+-.|+-== =|||    +++|.|+++.-+.=.|.-++-.=+ +.|+.+-=+.|++.-|..-+.+.+... .+. 
T Consensus       291 ~d~A~liynAwLKTLEdGv----HTADIy~~k~Sk~KVgTkeFA~aV-~~nlG~~P~~LP~~~~~f~~~~~~~~~~~~~~  365 (481)
T TIGR02924       291 KDIAQLIYNAWLKTLEDGV----HTADIYNEKTSKKKVGTKEFAEAV-VKNLGKKPEKLPKALISFSINSLKESKIDYER  365 (481)
T ss_pred             HHHHHHHHHHHHHHHHCCC----CHHHHCCCCCCCCCCCCHHHHHHH-HHHHCCCCCHHHHHHHHHHCCCEEECCCCCCC
T ss_conf             4689999877644421374----313321233666666525799999-98616781023686742303210101212440


Q ss_pred             CCCCC-----CCEEEEECCCCC-CCCHHH
Q ss_conf             22368-----988999758678-987799
Q gi|254780603|r  222 QEIKN-----DKIALILGAEGK-GLRPKT  244 (282)
Q Consensus       222 ~~~~~-----~~~~lv~G~E~~-Gl~~~~  244 (282)
                      ..++.     +-.++|==+++. ++.+-+
T Consensus       366 ~~~~~~k~LvG~Difi~wd~~~ld~~~l~  394 (481)
T TIGR02924       366 EQSYKVKVLVGVDIFIKWDGSSLDLNQLV  394 (481)
T ss_pred             CCCCCEEEEEEEEEEEEECCCCCCHHHHH
T ss_conf             36631148988778997367582489999


No 73 
>TIGR01607 PST-A Plasmodium subtelomeric family (PST-A); InterPro: IPR006494    These proteins represent a paralogous family of genes found in Plasmodium falciparum and Plasmodium yoelii that are closely related to various phospholipases and lysophospholipases of plants as well as generally being related to the alpha/beta-fold superfamily of hydrolases. These genes are preferentially located in the subtelomeric regions of the chromosomes of both P. falciparum and P. yoelii. .
Probab=21.14  E-value=29  Score=15.15  Aligned_cols=21  Identities=19%  Similarity=0.404  Sum_probs=16.8

Q ss_pred             CCCCCCCCCCCCHHHHCCCCC
Q ss_conf             112222222100000001233
Q gi|254780603|r  196 TDALQKMHSWGFQTIGLSSDS  216 (282)
Q Consensus       196 ~~~l~~~~~~~~~i~~~~~~~  216 (282)
                      .+|++.+-++||=|||+|.+|
T Consensus        64 dSWIE~fN~~GYSVYgLDLQG   84 (379)
T TIGR01607        64 DSWIEKFNKNGYSVYGLDLQG   84 (379)
T ss_pred             CEEEEECCCCCCEEEEEECCC
T ss_conf             825651167976387534356


No 74 
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129   Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK  resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=21.13  E-value=52  Score=13.75  Aligned_cols=114  Identities=13%  Similarity=0.114  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHH-------------------HHHHHHCCCCCCCCCCCCCCC--C
Q ss_conf             8899999998642001100136863200000134443-------------------333211012223221122222--2
Q gi|254780603|r  145 HNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSAS-------------------GALEHIPYIRISNLTDALQKM--H  203 (282)
Q Consensus       145 ~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~-------------------Ga~~~l~~~~~~~~~~~l~~~--~  203 (282)
                      .-.+..++-++|||||-||+--=++=...-.++++.=                   |=+|-=.|+-+ |-.+-=.+-  .
T Consensus       123 ~at~~~~~lldA~G~DVI~vETVGVGQSEVdi~~~aDT~v~v~~pg~GDd~Q~iKaG~mEiaDI~VV-NKaD~~~a~~v~  201 (333)
T TIGR00750       123 KATRELVKLLDAAGYDVILVETVGVGQSEVDIINMADTFVVVTIPGTGDDVQGIKAGVMEIADIYVV-NKADGEGAEEVK  201 (333)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHEEEEEEEE-ECCCCCCHHHHH
T ss_conf             9999999999863898799984157524878873415058985488783466665443023248788-168876658999


Q ss_pred             CCCCHHHHCCCC----------CC-----C-CCC--CCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCC
Q ss_conf             210000000123----------33-----2-211--22368988999758678987799985893999278968
Q gi|254780603|r  204 SWGFQTIGLSSD----------SK-----K-PLE--QEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGI  259 (282)
Q Consensus       204 ~~~~~i~~~~~~----------~~-----~-~~~--~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~  259 (282)
                      ..-...|.++.+          .+     + .++  +..|.-|++=..+-||+||.+-|-..-+|.=.+--+|.
T Consensus       202 ~~a~~~l~l~~esvqmlsqmthadearvq~G~~~~r~~gW~Ppv~~tsA~~G~Gi~EL~daI~eH~~~l~~~G~  275 (333)
T TIGR00750       202 TLARLMLALDLESVQMLSQMTHADEARVQKGEIYRREKGWRPPVLKTSAVEGRGIDELWDAIEEHKKFLTESGL  275 (333)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             99999888888899999865333344430265511010589963887335688716789999999999986360


No 75 
>TIGR02080 O_succ_thio_ly O-succinylhomoserine (thiol)-lyase; InterPro: IPR011821   Proteins in this entry are important in the interconversion of the sulphur-containing amino acids L-cysteine and L-methionine in bacteria. In bacteria, inorganic sulphur is reduced to sulphide, which is then used to displace the acetyl group of O-acetyl-L-serine to form the essential amino acid L-cysteine. Biosynthesis of L-methionine then occurs via the transsulphuration pathway which involves the sequential action of two pyridoxal 5'-phosphate (PLP) enzymes, cystathionine gamma-synthase (CGS) and cystathionine beta-lyase (CBL). Firstly CGS catalyses the formation of the intermediate cystathione from a homoserine ester and L-cysteine. This intermediate is then converted by CBL to L-homoserine, which is subsequently methylated by methionine synthase to form L-methionine. For more information see .   The CGS enzyme (P00935 from SWISSPROT) from Escherichia coli is, like other CGS enzymes, a homotetramer composed of two catalytically active dimers . The active site of each dimer is found at the interface between the monomers and involves residues from each monomer. Catalysis occurs by alpha,gamma-elimination/replacement reactions..
Probab=20.93  E-value=27  Score=15.33  Aligned_cols=37  Identities=19%  Similarity=0.195  Sum_probs=20.8

Q ss_pred             CCCCCCCHHHHHHCCC--EEEEC-CCCCCCHHHHHHHHHHH
Q ss_conf             8678987799985893--99927-89687437899999999
Q gi|254780603|r  235 AEGKGLRPKTQETATS--MAHLH-MPGIIKALNVSNAAAVA  272 (282)
Q Consensus       235 ~E~~Gl~~~~~~~~d~--~v~Ip-~~~~~~SLNvs~a~ai~  272 (282)
                      =|-+|=-+.+....+.  +.++- --|+|||| ||+++.|.
T Consensus       302 FEL~G~~~~v~~FL~~L~LFtLAESLGGVESL-iaHPATMT  341 (383)
T TIGR02080       302 FELKGGEEAVRRFLGKLSLFTLAESLGGVESL-IAHPATMT  341 (383)
T ss_pred             EEECCCHHHHHHHHHHCCCHHHHHHHCCHHHH-HCHHHCCC
T ss_conf             33218868999998431401212331551233-33010126


No 76 
>TIGR01452 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family; InterPro: IPR006349   This family of sequences represent 2-phosphoglycolate phosphatase which is limited to the eukaryotic lineage. PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In mammals, PGP is found in many tissues, notably in red blood cells where P-glycolate is and important activator of the hydrolysis of 2,3-bisphosphoglycerate, a major modifier of the oxygen affinity of hemoglobin. The PGPase enzyme described here is a member of the Haloacid dehalogenase superfamily of hydrolase enzymes. Unlike the bacterial PGP equivalog (IPR006346 from INTERPRO), which is a member of class (subfamily) I, this enzyme is a member of class (subfamily) II . These two enzymes have almost certainly arisen from convergent evolution (although these two ancestors may themselves have diverged from a more distant HAD superfamily progenitor). One of the sequences in the group comes from Chlamydomonas reinhardtii, a photosynthetic alga. The enzyme has been purified and characterised and these data are fully consistent with the assignment of function as a PGPase involved in photorespiration . Another, from Homo sapiens, is supported as a member of the family indirectly. Biochemical characterization of partially purified PGP's from various tissues including red blood cells  have been performed while one gene for PGP has been localized to chromosome 16p13.3 . The Homo sapiens sequence maps to chromosome 22. There is indeed a related gene on chromosome 16 (and it is expressed, since EST's are found) which shows 46 0dentity and 59603b08ositives by BLAST2 (E=1e-66). Presumably, these two genes are isoforms and have the same catalytic function while being expressed in different tissues and may be differently regulated. The sequence from Caenorhabditis elegans, is only supported by sequence similarity. This family is closely related to a family of bacterial sequences including the Escherichia coli NagD and Bacillus subtilus AraL genes which are characterised by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The Chlamydomonas reinhardtii PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this family have been annotated as pNPPases due to this association.; GO: 0016791 phosphoric monoester hydrolase activity, 0008152 metabolic process.
Probab=20.80  E-value=43  Score=14.24  Aligned_cols=32  Identities=19%  Similarity=0.290  Sum_probs=18.2

Q ss_pred             CEEEEEEHHHHHHHHHCCCEEEEEEEECCCCCCC
Q ss_conf             8199985788999997898189999973784335
Q gi|254780603|r   47 ENLFLYGVHTVSAALNNPSRKIFQLLATKNALAR   80 (282)
Q Consensus        47 ~~~iIeG~~~V~eaL~~~~~~i~~i~~te~~~~~   80 (282)
                      |.-.|+|.=-..+.|....+.+  +++|.|....
T Consensus        16 Ge~v~pG~Pelld~L~~~gK~~--~fvtNNstks   47 (288)
T TIGR01452        16 GEKVVPGAPELLDRLAKAGKKV--LFVTNNSTKS   47 (288)
T ss_pred             CCEECCCCHHHHHHHHHCCCEE--EEEECCCCHH
T ss_conf             8641378727899997459879--9981686410


No 77 
>pfam07075 DUF1343 Protein of unknown function (DUF1343). This family consists of several hypothetical bacterial proteins of around 400 residues in length. The function of this family is unknown.
Probab=20.54  E-value=61  Score=13.36  Aligned_cols=133  Identities=12%  Similarity=0.082  Sum_probs=67.6

Q ss_pred             EEHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHHHHCCCCEEEECHHHHHHHHCCCCCCCCCCE--EEECCCCCCHHHC
Q ss_conf             85788999997898189999973784335434554326996999768998775247777774420--2411555540112
Q gi|254780603|r   52 YGVHTVSAALNNPSRKIFQLLATKNALARLDWDANLPHPFPVKTVPPQTIDKIVGKEAVHQGLAL--ETAPLLSPTLDAV  129 (282)
Q Consensus        52 eG~~~V~eaL~~~~~~i~~i~~te~~~~~~~~~~~l~~~~~I~~v~~~~l~~i~~~~~~hqGi~a--~~~~~~~~~l~~~  129 (282)
                      .|.|.+..++++....+..+|..|.-.......     +..   ++ ...+.       ..|+-+  .-.....+..+.+
T Consensus        13 ~~~~~~d~L~~~~~v~l~~lF~PEHG~~G~~~a-----g~~---v~-~~~D~-------~tglpv~SLYg~~~~Pt~~~L   76 (359)
T pfam07075        13 DLEHLVDLLLAAPGVNLKALFGPEHGFRGDAQA-----GEK---VG-DYVDP-------KTGLPVYSLYGKTRKPTPEML   76 (359)
T ss_pred             CCCCHHHHHHHCCCCCEEEEECCCCCCCCCCCC-----CCC---CC-CCCCC-------CCCCEEEECCCCCCCCCHHHH
T ss_conf             987899999665698689981798787404214-----985---67-87688-------889908979899999999998


Q ss_pred             CCCCEEEEECCCCCHH--------HHHHHHHHHHHHHCCCCCCCCCCCCCCHH---------HHHHHHHHHHHHHCCCCC
Q ss_conf             6650688723432068--------89999999864200110013686320000---------013444333321101222
Q gi|254780603|r  130 RNSQLLMVLDHVNDPH--------NIGAILRSAVAFSCDGIITTKRYSPSESA---------VLAKSASGALEHIPYIRI  192 (282)
Q Consensus       130 ~~~~~~i~ld~i~dp~--------NlG~I~Rta~a~g~~~vil~~~~~~~~~~---------~~~ras~Ga~~~l~~~~~  192 (282)
                      ++-.  +++..|||-|        -++-+|..|+..|+.-++|...+  |.+.         ...+ |--+.+-+|+.+.
T Consensus        77 ~~iD--vlv~DiQDvG~R~YTyi~Tm~~~meaaa~~~~~~iVLDRPN--Pl~G~~veGpvl~~~~~-SFvG~~piP~~hG  151 (359)
T pfam07075        77 KGVD--VLVFDIQDVGVRFYTYISTLAYAMEAAAEAGKEFIVLDRPN--PLGGLYVEGPVLDPEFE-SFVGMYPIPVRHG  151 (359)
T ss_pred             HCCC--EEEEEEECCCEEEEEHHHHHHHHHHHHHHCCCCEEEECCCC--CCCCCCCCCCCCCHHHH-HCCCCCCCCCCCC
T ss_conf             3699--99997422761565459999999999997499589947899--88887665786487775-1234455660047


Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             3221122222221
Q gi|254780603|r  193 SNLTDALQKMHSW  205 (282)
Q Consensus       193 ~~~~~~l~~~~~~  205 (282)
                      -.+.+.-...++.
T Consensus       152 mTiGElA~~~n~e  164 (359)
T pfam07075       152 MTIGELALLFNGE  164 (359)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             7899999999871


No 78 
>PRK13172 consensus
Probab=20.49  E-value=32  Score=14.98  Aligned_cols=11  Identities=9%  Similarity=0.371  Sum_probs=4.5

Q ss_pred             HHCCCCCCCCC
Q ss_conf             20011001368
Q gi|254780603|r  157 FSCDGIITTKR  167 (282)
Q Consensus       157 ~g~~~vil~~~  167 (282)
                      .|+..|.....
T Consensus       125 ~GWn~i~~~~~  135 (213)
T PRK13172        125 IGWNELVSTSE  135 (213)
T ss_pred             ECHHHEECCCC
T ss_conf             01445332455


No 79 
>PRK10126 tyrosine phosphatase; Provisional
Probab=20.48  E-value=19  Score=16.19  Aligned_cols=13  Identities=38%  Similarity=0.409  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHC
Q ss_conf             9999999864200
Q gi|254780603|r  147 IGAILRSAVAFSC  159 (282)
Q Consensus       147 lG~I~Rta~a~g~  159 (282)
                      +|+|+||-.|-++
T Consensus        10 ~GNiCRSPmAE~i   22 (147)
T PRK10126         10 VGNICRSPTAERL   22 (147)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             9806189999999


No 80 
>pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
Probab=20.34  E-value=61  Score=13.34  Aligned_cols=115  Identities=15%  Similarity=0.111  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH-------CCCCC
Q ss_conf             68899999998642001100136863200000134443333211012223221122222221000000-------01233
Q gi|254780603|r  144 PHNIGAILRSAVAFSCDGIITTKRYSPSESAVLAKSASGALEHIPYIRISNLTDALQKMHSWGFQTIG-------LSSDS  216 (282)
Q Consensus       144 p~NlG~I~Rta~a~g~~~vil~~~~~~~~~~~~~ras~Ga~~~l~~~~~~~~~~~l~~~~~~~~~i~~-------~~~~~  216 (282)
                      +......++.|+|+|+|-||+..-++-.-.-.+...    ...+=++..+...+-++..|. |.--++       .|..+
T Consensus       107 s~~t~~~i~lleaaGfD~IivETVGVGQsE~~v~~~----aD~~llv~~Pg~GDeiQ~iKa-GImEiaDi~vVNKaD~~~  181 (267)
T pfam03308       107 SRATREAILLLDAAGFDVIIIETVGVGQSEVDIANM----ADTFVLVTIPGGGDDLQGIKA-GLMEIADIYVVNKADLPG  181 (267)
T ss_pred             CHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHH----CCEEEEEECCCCCHHHHHHHH-HHHHHCCEEEEECCCHHH
T ss_conf             476999999999779999999247777530355541----576899955887608889875-376535489996676476


Q ss_pred             ----------CCCC---CCCCCCCCEEEEECCCCCCCCHHHHHHCCCEEEECCCCCCCHH
Q ss_conf             ----------3221---1223689889997586789877999858939992789687437
Q gi|254780603|r  217 ----------KKPL---EQEIKNDKIALILGAEGKGLRPKTQETATSMAHLHMPGIIKAL  263 (282)
Q Consensus       217 ----------~~~~---~~~~~~~~~~lv~G~E~~Gl~~~~~~~~d~~v~Ip~~~~~~SL  263 (282)
                                .-.+   .+..|.-++..+-..++.|+.+-|....++.-.+-.+|..+..
T Consensus       182 A~~~~~~l~~~l~l~~~~~~~W~p~Vl~tSA~~g~Gi~el~~~I~~~~~~l~~sG~l~~r  241 (267)
T pfam03308       182 AERTARELRSALHLLTPKEAGWRPPVLTTSAVTGEGIDELWDAIEEHREFLTATGLLAAR  241 (267)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             999999999998517987789999989987478899999999999999999978869999


Done!