Query         gi|254780430|ref|YP_003064843.1| nitrogen fixation protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 189
No_of_seqs    141 out of 1544
Neff          5.9 
Searched_HMMs 39220
Date          Sun May 29 16:05:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780430.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG2358 consensus              100.0 6.4E-43       0  288.7   7.9  183    1-189    10-198 (213)
  2 pfam08712 Nfu_N Scaffold prote  99.9 6.9E-28 1.8E-32  195.0   8.0   86    3-88      1-87  (87)
  3 TIGR03341 YhgI_GntY IscR-regul  99.9 5.3E-25 1.4E-29  177.0   9.5   79  111-189   100-179 (190)
  4 COG0694 Thioredoxin-like prote  99.9 3.3E-25 8.5E-30  178.2   7.8   78  112-189     5-84  (93)
  5 PRK11190 putative DNA uptake p  99.9 4.6E-24 1.2E-28  171.1   9.5   79  111-189   101-181 (192)
  6 pfam01106 NifU NifU-like domai  99.9 1.9E-23 4.9E-28  167.3   8.6   68  121-189     1-68  (68)
  7 KOG2358 consensus               98.2 1.3E-06 3.4E-11   62.2   3.1   67  121-188    82-148 (213)
  8 pfam01883 DUF59 Domain of unkn  88.2       1 2.6E-05   25.5   4.7   67  119-187     3-73  (76)
  9 TIGR02000 NifU_proper Fe-S clu  83.6    0.72 1.8E-05   26.5   2.0   68  116-185   231-298 (302)
 10 TIGR02176 pyruv_ox_red pyruvat  74.0    0.97 2.5E-05   25.7   0.2   27  119-145   641-667 (1194)
 11 COG3086 RseC Positive regulato  61.9     8.1 0.00021   20.0   2.9   35  141-176     7-43  (150)
 12 PRK10862 SoxR reducing system   60.5     8.3 0.00021   19.9   2.8   24  141-164     7-32  (158)
 13 COG1308 EGD2 Transcription fac  58.0      16  0.0004   18.2   3.8   88   47-140    24-113 (122)
 14 cd04874 ACT_Af1403 N-terminal   56.6      18 0.00046   17.8   5.2   49  128-188    16-71  (72)
 15 cd07304 Chorismate_synthase Ch  56.5     7.4 0.00019   20.2   1.9   29  114-143   179-207 (344)
 16 PRK05382 chorismate synthase;   55.1     8.5 0.00022   19.8   2.0   28   38-65    230-257 (357)
 17 pfam04246 RseC_MucC Positive r  52.4     9.6 0.00025   19.5   2.0   20  143-162     2-23  (135)
 18 pfam01264 Chorismate_synt Chor  47.5      12  0.0003   18.9   1.8   26  115-141   178-203 (346)
 19 COG3435 Gentisate 1,2-dioxygen  44.8      16 0.00041   18.1   2.1   48  128-176    53-100 (351)
 20 COG0082 AroC Chorismate syntha  44.0      11 0.00028   19.2   1.2   63   37-99    227-298 (369)
 21 pfam03557 Bunya_G1 Bunyavirus   43.1     7.1 0.00018   20.3   0.1   30  135-165   738-767 (871)
 22 PRK12463 chorismate synthase;   42.2      17 0.00043   18.0   1.9   27   38-64    242-268 (390)
 23 TIGR02311 HpaI 2,4-dihydroxyhe  41.1      14 0.00035   18.5   1.3   47   43-89    156-205 (249)
 24 KOG1482 consensus               38.5      34 0.00088   16.1   4.0   50   38-87    296-356 (379)
 25 cd01815 BMSC_UbP_N BMSC_UbP (b  38.0      16 0.00041   18.1   1.3   30  154-183    12-41  (75)
 26 cd02969 PRX_like1 Peroxiredoxi  37.4      36 0.00091   15.9   3.5   27  160-186   136-162 (171)
 27 TIGR00033 aroC chorismate synt  36.5      21 0.00054   17.4   1.7   58   38-97    258-330 (391)
 28 PRK10128 putative aldolase; Pr  34.7      31  0.0008   16.3   2.3   56   36-91    138-196 (250)
 29 PRK11670 putative ATPase; Prov  34.6      40   0.001   15.7   7.1   42   41-82     29-75  (369)
 30 PRK09193 indolepyruvate ferred  34.1     7.8  0.0002   20.1  -0.8   16  152-167   435-450 (1155)
 31 PRK13030 2-oxoacid ferredoxin   33.3     8.3 0.00021   19.9  -0.8   17  152-168   434-450 (1168)
 32 PRK13029 2-oxoacid ferredoxin   33.1     8.8 0.00023   19.7  -0.7   17  152-168   451-467 (1186)
 33 pfam04320 DUF469 Protein with   32.9      42  0.0011   15.5   3.4   65  114-188    29-94  (102)
 34 COG2151 PaaD Predicted metal-s  31.7      44  0.0011   15.4   5.8   70  116-187    12-86  (111)
 35 TIGR00370 TIGR00370 conserved   31.6      44  0.0011   15.4   3.2   88   36-129    20-122 (217)
 36 COG3696 Putative silver efflux  30.8      46  0.0012   15.3   6.1  108   37-146    65-181 (1027)
 37 TIGR00852 pts-Glc PTS system,   30.6      35 0.00089   16.0   2.0   62  123-185    37-114 (312)
 38 pfam00873 ACR_tran AcrB/AcrD/A  30.2      47  0.0012   15.2   9.7   36  119-154   151-188 (1021)
 39 PRK10558 alpha-dehydro-beta-de  28.3      45  0.0011   15.3   2.2   36   38-78     28-63  (256)
 40 COG4551 Predicted protein tyro  27.8      52  0.0013   15.0   2.7   91   38-136    14-109 (109)
 41 TIGR01684 viral_ppase viral ph  27.0      53  0.0014   14.9   2.6   60   25-84    237-318 (323)
 42 PRK02269 ribose-phosphate pyro  23.6      62  0.0016   14.5   3.6   34  150-183   207-248 (321)
 43 TIGR02855 spore_yabG sporulati  23.4      18 0.00046   17.8  -0.5   48  116-164   149-223 (292)
 44 TIGR02916 PEP_his_kin putative  23.2      63  0.0016   14.4   3.5  108   39-151   558-691 (696)
 45 PRK08115 ribonucleotide-diphos  22.6      58  0.0015   14.6   1.9   37  132-171   820-856 (857)
 46 PRK10614 multidrug efflux syst  21.8      67  0.0017   14.2   9.3   34  121-154   154-189 (1025)
 47 KOG2679 consensus               21.5      68  0.0017   14.2   2.4  105   48-161   159-277 (336)
 48 pfam06954 Resistin Resistin. T  21.4      66  0.0017   14.3   2.0   44  112-164    26-69  (109)
 49 pfam08777 RRM_3 RNA binding mo  21.3      69  0.0018   14.2   4.1   29  129-158    18-48  (102)
 50 cd03009 TryX_like_TryX_NRX Try  20.8      70  0.0018   14.1   2.6   16  124-139   112-127 (131)

No 1  
>KOG2358 consensus
Probab=100.00  E-value=6.4e-43  Score=288.72  Aligned_cols=183  Identities=39%  Similarity=0.659  Sum_probs=166.0

Q ss_pred             CEEECCCCCCHHHHHHHCCCEEC-CCCCEECCCHHHCCCCHHHHHHHHCC-CCEEEEECCCEEEEEEC-C-CCCHHHHHH
Q ss_conf             91021148872243541797543-78864306966701346889874168-81079980877998314-6-682123489
Q gi|254780430|r    1 MFIQTEDTPNPATLKFIPGQVVL-VEGAIHFSNAKEAEISPLASRIFSIP-GIASVYFGYDFITVGKD-Q-YDWEHLRPP   76 (189)
Q Consensus         1 m~I~~e~TPNPn~lKFi~~~~i~-~~g~~~f~~~~~a~~spLa~~Lf~i~-GV~~Vfi~~nFITVtK~-~-~eW~~i~p~   76 (189)
                      |||+++.||||+++||.+++.++ ..++..|.+.-.+..+|||+++|.+. ||+++|+++|||||+|. + ..|..|+|.
T Consensus        10 ~~i~t~~tPn~~Sl~f~p~~~i~~~~~~~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~ee~~w~~L~p~   89 (213)
T KOG2358          10 MFIQTQITPNPSSLLFLPGKQILSERGLGDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTEENVWSVLDPE   89 (213)
T ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCHHHHHHHHHCCCCEEEEECCCEEEEECCCHHHHHHHHCHH
T ss_conf             24433489894210026898532321113345555311147889887525884798736973788455123447664405


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEC--CEEEEEE
Q ss_conf             99999999740143232321122222222233445440268899999999987777875289759996433--4799996
Q gi|254780430|r   77 VLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRD--GIVFLSM  154 (189)
Q Consensus        77 I~~~I~~~l~~g~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~~--g~v~v~~  154 (189)
                      +...+.++++.|.+.+......-.      .....++|.+....|+++|++||||.++.||||+.|.++++  |+|+++|
T Consensus        90 i~~~~sd~g~~g~pli~g~~~~~~------~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~y~g~e~g~g~v~lkl  163 (213)
T KOG2358          90 IPSLMSDGGNVGLPLIDGNIVVLK------LQGACESDPESTMTIKELIETRIRPKIQEDGGDEDYVGFETGLGLVSLKL  163 (213)
T ss_pred             HHHHHHCCCCCCCHHHCCCHHHHH------HCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHH
T ss_conf             678775224115602235134543------23444578258899999998753343110278304225557631578877


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             36646666689999999999999978970035539
Q gi|254780430|r  155 RGACSGCPSASETLKYGVANILNHFVPEVKDIRTV  189 (189)
Q Consensus       155 ~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~v  189 (189)
                      +|||++||||..|||+|||+||++|+|+|+.|+++
T Consensus       164 qgact~cpss~vtlk~Gie~mL~~y~~eVK~v~qv  198 (213)
T KOG2358         164 QGACTECPSSLVTLKNGIENMLEIYVPEVKGVIQV  198 (213)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHCCEEEEEEEC
T ss_conf             66651598310012014899998625000577850


No 2  
>pfam08712 Nfu_N Scaffold protein Nfu/NifU N terminal. This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters.
Probab=99.95  E-value=6.9e-28  Score=194.98  Aligned_cols=86  Identities=63%  Similarity=1.029  Sum_probs=83.6

Q ss_pred             EECCCCCCHHHHHHHCCCEECCCCCEECCCHHHCCCCHHHHHHHHCCCCEEEEECCCEEEEEEC-CCCCHHHHHHHHHHH
Q ss_conf             0211488722435417975437886430696670134688987416881079980877998314-668212348999999
Q gi|254780430|r    3 IQTEDTPNPATLKFIPGQVVLVEGAIHFSNAKEAEISPLASRIFSIPGIASVYFGYDFITVGKD-QYDWEHLRPPVLGMI   81 (189)
Q Consensus         3 I~~e~TPNPn~lKFi~~~~i~~~g~~~f~~~~~a~~spLa~~Lf~i~GV~~Vfi~~nFITVtK~-~~eW~~i~p~I~~~I   81 (189)
                      ||+|+|||||+|||++++.++..|+++|++.+++.++|||++||+++||++||++.|||||||+ +++|++|+|+|+++|
T Consensus         1 I~~e~TPNPn~lKf~~~~~l~~~gs~~f~~~~~a~~spLa~~Lf~i~gV~~Vf~~~nFITVtK~~~~~W~~l~~~I~~~I   80 (87)
T pfam08712         1 IQTESTPNPNTLKFLPGKEVLPEGTFEFKNADEAEGSPLAQKLFKIPGVKSVFFGDDFITVTKADDADWDDLKPEVLEAI   80 (87)
T ss_pred             CCCCCCCCCCCEEEECCCEECCCCCEEECCHHHCCCCHHHHHHHCCCCEEEEEEECCEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             94647989037678679764279867878978752687999984888803999858889997379999899999999999


Q ss_pred             HHHHHCC
Q ss_conf             9997401
Q gi|254780430|r   82 MEHFISG   88 (189)
Q Consensus        82 ~~~l~~g   88 (189)
                      ++||.+|
T Consensus        81 ~~~l~sG   87 (87)
T pfam08712        81 MEHLESG   87 (87)
T ss_pred             HHHHHCC
T ss_conf             9999649


No 3  
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=99.92  E-value=5.3e-25  Score=176.98  Aligned_cols=79  Identities=33%  Similarity=0.644  Sum_probs=74.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEE-ECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             54402688999999999877778752897599964-33479999636646666689999999999999978970035539
Q gi|254780430|r  111 IESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGY-RDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV  189 (189)
Q Consensus       111 ~~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~-~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~v  189 (189)
                      ...|+.+..+|+++|+++|||+|++|||||+|+++ ++|+|+|+|+|||+|||+|++|||+|||.+|++++|||++|+.+
T Consensus       100 ~~~d~~l~~~i~~vl~~ei~P~l~~hGG~v~lv~i~~~~~v~~~~~G~C~gC~~s~~Tlk~gvE~~l~~~~Pei~~V~d~  179 (190)
T TIGR03341       100 VADDAPLEERINYVLQSEINPQLASHGGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRDA  179 (190)
T ss_pred             CCCCCCHHHHHHHHHHHHCCHHHHHCCCEEEEEEEECCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             57776899999999986029357636998999999079789999575489983689999999999999869875358876


No 4  
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.92  E-value=3.3e-25  Score=178.24  Aligned_cols=78  Identities=47%  Similarity=0.939  Sum_probs=74.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEE--CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             44026889999999998777787528975999643--3479999636646666689999999999999978970035539
Q gi|254780430|r  112 ESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYR--DGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV  189 (189)
Q Consensus       112 ~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~--~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~v  189 (189)
                      ..++++.++++++|+++|||+|++||||++|++++  +|+|+++|+|||+|||||+.|||+|||++||+++|++++|+++
T Consensus         5 ~~~~~~~e~v~~~l~~~irP~l~~dGGdve~~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v   84 (93)
T COG0694           5 ETDAELLERVEEVLDEKIRPQLAMDGGDVELVGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQV   84 (93)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEEEECCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             01289999999999844571021049808999875689869999677578996628999999999999668865169973


No 5  
>PRK11190 putative DNA uptake protein; Provisional
Probab=99.91  E-value=4.6e-24  Score=171.11  Aligned_cols=79  Identities=30%  Similarity=0.643  Sum_probs=74.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEE-ECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCC-CCEEEEE
Q ss_conf             54402688999999999877778752897599964-334799996366466666899999999999999789-7003553
Q gi|254780430|r  111 IESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGY-RDGIVFLSMRGACSGCPSASETLKYGVANILNHFVP-EVKDIRT  188 (189)
Q Consensus       111 ~~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~-~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vp-ev~~V~~  188 (189)
                      ..+|+.+.++|+.+|+++|||+|++|||+|+|+++ ++|+|+|+|+|+|+|||+|.+|||+|||.+|++.+| ||++|+.
T Consensus       101 ~~~d~~l~~~i~~vl~~~i~P~l~~hGG~v~l~~i~~~~~~~~~~~G~C~gC~~~~~Tlk~gvE~~l~~~~P~ei~~V~d  180 (192)
T PRK11190        101 VADDAPLMERVEYVLQSQINPQLAGHGGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRD  180 (192)
T ss_pred             CCCCCCHHHHHHHHHHHHCCHHHHHCCCEEEEEEECCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCEEEE
T ss_conf             68875599999999987319567637987999998279889999666578986889999999999999869786705787


Q ss_pred             C
Q ss_conf             9
Q gi|254780430|r  189 V  189 (189)
Q Consensus       189 v  189 (189)
                      +
T Consensus       181 ~  181 (192)
T PRK11190        181 L  181 (192)
T ss_pred             C
T ss_conf             6


No 6  
>pfam01106 NifU NifU-like domain. This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
Probab=99.89  E-value=1.9e-23  Score=167.27  Aligned_cols=68  Identities=40%  Similarity=0.660  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             999999987777875289759996433479999636646666689999999999999978970035539
Q gi|254780430|r  121 IKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRTV  189 (189)
Q Consensus       121 i~~~l~~~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~v  189 (189)
                      |+++||+ |||+|++||||++|+++++|+|+|+|+|||+|||||+.||+++||++|++++|+++.|.+|
T Consensus         1 I~~~le~-IRP~l~~dGGdvelv~v~~~~v~v~l~GaC~gC~~s~~Tlk~~Ie~~L~~~vpev~~Vv~V   68 (68)
T pfam01106         1 IEEVIDE-IRPMLQRDGGDIELVDVDGDIVKVRLQGACGGCMSSTMTLKGGIERKLRERLGESLRVIPV   68 (68)
T ss_pred             CHHHHHH-HCHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             9779987-5648885599289999869999999812898981089999999999999878997669879


No 7  
>KOG2358 consensus
Probab=98.16  E-value=1.3e-06  Score=62.24  Aligned_cols=67  Identities=25%  Similarity=0.376  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999998777787528975999643347999963664666668999999999999997897003553
Q gi|254780430|r  121 IKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRT  188 (189)
Q Consensus       121 i~~~l~~~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~  188 (189)
                      ...+|+. ++|++.+|||+.-..-+.+.++.+.++|+|..||++++|+|.+||..+|..|||.-.+++
T Consensus        82 ~w~~L~p-~i~~~~sd~g~~g~pli~g~~~~~~~~~~~e~d~e~t~~ikelietRiRp~i~edggdi~  148 (213)
T KOG2358          82 VWSVLDP-EIPSLMSDGGNVGLPLIDGNIVVLKLQGACESDPESTMTIKELIETRIRPKIQEDGGDED  148 (213)
T ss_pred             HHHHHCH-HHHHHHHCCCCCCCHHHCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             4766440-567877522411560223513454323444578258899999998753343110278304


No 8  
>pfam01883 DUF59 Domain of unknown function DUF59. This family includes prokaryotic proteins of unknown function. The family also includes PhaH from Pseudomonas putida. PhaH forms a complex with PhaF, PhaG, and PhaI, which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. So members of this family may all be components of ring hydroxylating complexes.
Probab=88.19  E-value=1  Score=25.54  Aligned_cols=67  Identities=28%  Similarity=0.423  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHHHHHH---CCCCEEEEEEE-CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             99999999987777875---28975999643-34799996366466666899999999999999789700355
Q gi|254780430|r  119 QRIKEVLDNRVRPAVAR---DGGDIVFKGYR-DGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIR  187 (189)
Q Consensus       119 ~~i~~~l~~~IrP~l~~---dGG~i~~~~~~-~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~  187 (189)
                      ++|.+.|.+-+.|-+..   +=|-|.=+.++ +|.|.|.|.=.+.+||.+ ..+.+.++..++. +|.|.+|.
T Consensus         3 e~I~~aL~~V~DPEl~~~Iv~LGlI~~i~v~~~g~v~I~~~lT~~~CP~~-~~i~~~i~~~l~~-v~gv~~V~   73 (76)
T pfam01883         3 EAILEALKTVIDPELPVDIVDLGLVYEVDIDDDGNVKVKMTLTTPGCPLA-DLIALDVREALLE-LPGVEDVE   73 (76)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCH-HHHHHHHHHHHHC-CCCCEEEE
T ss_conf             89999982778999997800245368999857984999999589999837-8999999999983-99940789


No 9  
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU; InterPro: IPR010238   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents the NifU protein from the NIF system that is involved in nitrogenase maturation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly.
Probab=83.59  E-value=0.72  Score=26.52  Aligned_cols=68  Identities=35%  Similarity=0.567  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             6889999999998777787528975999643347999963664666668999999999999997897003
Q gi|254780430|r  116 AVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKD  185 (189)
Q Consensus       116 ~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~  185 (189)
                      .....+...+ ...+|..+.++|+..........+++.+.|+|.+|..+..++.. ++..+.........
T Consensus       231 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  298 (302)
T TIGR02000       231 QRIQLIVKVL-AELRPVLQADGGDVELLDVDGKIVYVSLTGACSGCSSSAATLAG-IQQKLVERLGEFVV  298 (302)
T ss_pred             HHHHHHHHHH-HHHCCHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCHHHHHHHH-HHHHHHHHCCCCCC
T ss_conf             0011111111-11100000012210000012221000011111110000111111-22211110011211


No 10 
>TIGR02176 pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxidoreductase; InterPro: IPR011895   The oxidative decarboxylation of pyruvate to acetyl-CoA, a central step in energy metabolism, can occur by two different mechanisms . In mitochondria and aerobic bacteria this reaction is catalysed by the multienzyme complex pyruvate dehydrogenase using NAD as electron acceptor. In anaerobic organisms, however, this reaction is reversibly catalysed by a single enzyme using either ferrodoxin or flavodoxin as the electron acceptor.   Pyruvate:ferrodoxin/flavodoxin reductases (PFORs) in this entry occur in both obligately and facultatively anaerobic bacteria and also some eukaryotic microorganisms. These proteins are single-chain enzymes containing a thiamin pyrophosphate cofactor for the cleavage of carbon-carbon bonds next to a carbonyl group, and iron-sulphur clusters for electron transfer. The Desulfovibrio africanus enzyme is currently the only PFOR whose three dimensional structure is known , . It is a homodimer where each subunit contains one thiamin pyrophosphate cofactor and two ferrodoxin-like 4Fe-S clusters and an atypical 4Fe-S cluster. Each monomer is composed of seven domains - domains I, II and VI make intersubunit contacts, while domains III, IV and V are located at the suface of the dimer, and domain VII forms a long arm extending over the other subunit. The cofactor is bound at the interface of domains I and VI and is proximal to the atypical 4Fe-S bound by domain VI, while the ferrodoxin-like 4Fe-S clusters are bound by domain V. Comparison of this enzyme with the multi-chain PFORs shows a correspondance between the domains in this enzyme and the subunits of the multi-chain enzymes.; GO: 0005506 iron ion binding, 0016903 oxidoreductase activity acting on the aldehyde or oxo group of donors, 0006118 electron transport.
Probab=73.96  E-value=0.97  Score=25.72  Aligned_cols=27  Identities=30%  Similarity=0.588  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             999999999877778752897599964
Q gi|254780430|r  119 QRIKEVLDNRVRPAVARDGGDIVFKGY  145 (189)
Q Consensus       119 ~~i~~~l~~~IrP~l~~dGG~i~~~~~  145 (189)
                      ....+...+=+||.+++.|-+|.+-.|
T Consensus       641 ~~~~eFV~nv~~pi~~q~GD~lpVS~~  667 (1194)
T TIGR02176       641 EDAPEFVKNVVRPIAAQEGDDLPVSAF  667 (1194)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf             747478999888886258898765777


No 11 
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=61.87  E-value=8.1  Score=19.98  Aligned_cols=35  Identities=20%  Similarity=0.416  Sum_probs=25.8

Q ss_pred             EEEEEECCEEEEEE--CCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             99964334799996--3664666668999999999999
Q gi|254780430|r  141 VFKGYRDGIVFLSM--RGACSGCPSASETLKYGVANIL  176 (189)
Q Consensus       141 ~~~~~~~g~v~v~~--~GaC~~Cpss~~Tl~~gie~~l  176 (189)
                      .++++++|.++|+-  +-+|+.|+|...-. .+..+-|
T Consensus         7 ~vv~~q~G~a~V~c~~~S~CgsC~a~~~CG-s~~l~kL   43 (150)
T COG3086           7 TVVSWQNGQAKVSCQRQSACGSCAARAGCG-SGLLSKL   43 (150)
T ss_pred             EEEECCCCEEEEEEECCCCCCCCHHHCCCC-HHHHHHH
T ss_conf             999733885999960467654542113422-6799985


No 12 
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=60.52  E-value=8.3  Score=19.89  Aligned_cols=24  Identities=21%  Similarity=0.638  Sum_probs=16.5

Q ss_pred             EEEEEECCEEEEEE--CCCCCCCHHH
Q ss_conf             99964334799996--3664666668
Q gi|254780430|r  141 VFKGYRDGIVFLSM--RGACSGCPSA  164 (189)
Q Consensus       141 ~~~~~~~g~v~v~~--~GaC~~Cpss  164 (189)
                      .++.+++|.++|+.  +.+|++|.+.
T Consensus         7 ~Vv~~~~g~a~Ve~~r~SaCg~C~a~   32 (158)
T PRK10862          7 TVVSWQNGQALVRCDVKASCSSCASR   32 (158)
T ss_pred             EEEEEECCEEEEEEEECCCCCCCCCC
T ss_conf             99999699899998526887678888


No 13 
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=58.03  E-value=16  Score=18.17  Aligned_cols=88  Identities=20%  Similarity=0.267  Sum_probs=44.9

Q ss_pred             HCCCCEEEEECC--CEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             168810799808--779983146682123489999999997401432323211222222222334454402688999999
Q gi|254780430|r   47 SIPGIASVYFGY--DFITVGKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLGDMKLDDMGSGDFIESDSAVVQRIKEV  124 (189)
Q Consensus        47 ~i~GV~~Vfi~~--nFITVtK~~~eW~~i~p~I~~~I~~~l~~g~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  124 (189)
                      .++||+.|-+-.  +-+.|.+..+.    ......+ ..|-.+|.+.. ..................++|=+++-.=..+
T Consensus        24 eld~v~~V~i~~kd~e~vi~~P~V~----~~~~~g~-~~yqi~g~~~~-~~~~~~~ee~~~d~~~i~eeDIkLV~eQa~V   97 (122)
T COG1308          24 ELDGVERVIIKLKDTEYVIENPQVT----VMKAMGQ-KTYQISGDPSA-KEAVKKPEEKTVDESDISEEDIKLVMEQAGV   97 (122)
T ss_pred             ECCCCEEEEEECCCCEEEEECCCEE----EEHHCCH-HHHHHHCCHHH-HCCCCCCHHCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             4267448999828953896189177----5510034-68988464345-3065561011245578988999999998189


Q ss_pred             HHHHHHHHHHHCCCCE
Q ss_conf             9998777787528975
Q gi|254780430|r  125 LDNRVRPAVARDGGDI  140 (189)
Q Consensus       125 l~~~IrP~l~~dGG~i  140 (189)
                      =.+..|-+|...|||+
T Consensus        98 sreeA~kAL~e~~GDl  113 (122)
T COG1308          98 SREEAIKALEEAGGDL  113 (122)
T ss_pred             CHHHHHHHHHHCCCCH
T ss_conf             9999999999838869


No 14 
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=56.55  E-value=18  Score=17.81  Aligned_cols=49  Identities=16%  Similarity=0.520  Sum_probs=33.4

Q ss_pred             HHHHHHHHCCCCEEEEEE---EC--CEEEEEECCCCCCCHHHHHHHHHHHHHHHH--HHCCCCEEEEE
Q ss_conf             877778752897599964---33--479999636646666689999999999999--97897003553
Q gi|254780430|r  128 RVRPAVARDGGDIVFKGY---RD--GIVFLSMRGACSGCPSASETLKYGVANILN--HFVPEVKDIRT  188 (189)
Q Consensus       128 ~IrP~l~~dGG~i~~~~~---~~--g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~--~~vpev~~V~~  188 (189)
                      +|--.++.|||+|.+...   ++  |..|+++.|-            .-++.+++  +.+|.|.+|+.
T Consensus        16 ~itgvIa~hg~NItytqqfi~~~g~~~iY~ElE~v------------~d~e~Li~~L~~~~~V~eVei   71 (72)
T cd04874          16 DLTGVIAEHGGNITYTQQFIEREGKARIYMELEGV------------GDIEELVEELRSLPIVREVEI   71 (72)
T ss_pred             HHHHHHHHCCCCEEEEEEEEECCCEEEEEEEEECC------------CCHHHHHHHHHCCCCEEEEEE
T ss_conf             98879986489869999998079828999999679------------998999999877995599994


No 15 
>cd07304 Chorismate_synthase Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway. Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway: the conversion of 5- enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a precursor for the biosynthesis of aromatic compounds. This process has an absolute requirement for reduced FMN as a co-factor which is thought to facilitate cleavage of C-O bonds by transiently donating an electron to the substrate, having no overall change its redox state. Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two classes: Enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctiona,l while those that can generate reduced FMN at the expense of NADPH, such as found in fun
Probab=56.47  E-value=7.4  Score=20.20  Aligned_cols=29  Identities=21%  Similarity=0.376  Sum_probs=15.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             026889999999998777787528975999
Q gi|254780430|r  114 DSAVVQRIKEVLDNRVRPAVARDGGDIVFK  143 (189)
Q Consensus       114 ~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~  143 (189)
                      |.+..+++.++|++ +|-.-.+-||-++++
T Consensus       179 d~~~~~~m~~~I~~-ak~~gDSlGG~ve~~  207 (344)
T cd07304         179 DPEAEEKMKELIDE-AKKEGDSVGGVVEVV  207 (344)
T ss_pred             CHHHHHHHHHHHHH-HHHCCCCCCCEEEEE
T ss_conf             98999999999999-854499987289999


No 16 
>PRK05382 chorismate synthase; Validated
Probab=55.10  E-value=8.5  Score=19.84  Aligned_cols=28  Identities=25%  Similarity=0.275  Sum_probs=20.2

Q ss_pred             CCHHHHHHHHCCCCEEEEECCCEEEEEE
Q ss_conf             3468898741688107998087799831
Q gi|254780430|r   38 ISPLASRIFSIPGIASVYFGYDFITVGK   65 (189)
Q Consensus        38 ~spLa~~Lf~i~GV~~Vfi~~nFITVtK   65 (189)
                      ++.||+.||.||.|+.|-++..|=....
T Consensus       230 da~La~a~msIpAvKgvEfG~Gf~~a~~  257 (357)
T PRK05382        230 DADLAHALMSINAVKGVEIGDGFEAARL  257 (357)
T ss_pred             HHHHHHHHHCCCCEEEEEECCHHHHHHC
T ss_conf             5789888617664236896451657526


No 17 
>pfam04246 RseC_MucC Positive regulator of sigma(E), RseC/MucC. This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions). In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonisation in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain pfam02424, w
Probab=52.38  E-value=9.6  Score=19.50  Aligned_cols=20  Identities=20%  Similarity=0.531  Sum_probs=9.9

Q ss_pred             EEEECCEEEEEE--CCCCCCCH
Q ss_conf             964334799996--36646666
Q gi|254780430|r  143 KGYRDGIVFLSM--RGACSGCP  162 (189)
Q Consensus       143 ~~~~~g~v~v~~--~GaC~~Cp  162 (189)
                      ++++++.++|+.  +.+|++|.
T Consensus         2 v~v~~~~~~V~~~r~saC~~C~   23 (135)
T pfam04246         2 VAVEGGWATVEAQRKSACGSCA   23 (135)
T ss_pred             EEEECCEEEEEEEECCCCCCCC
T ss_conf             8998999999982178662547


No 18 
>pfam01264 Chorismate_synt Chorismate synthase.
Probab=47.52  E-value=12  Score=18.93  Aligned_cols=26  Identities=19%  Similarity=0.350  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             268899999999987777875289759
Q gi|254780430|r  115 SAVVQRIKEVLDNRVRPAVARDGGDIV  141 (189)
Q Consensus       115 ~~~~~~i~~~l~~~IrP~l~~dGG~i~  141 (189)
                      .+..+++.+.|++ +|-.=.+-||-++
T Consensus       178 ~~~~~~m~~~I~~-ak~~gDSlGG~ve  203 (346)
T pfam01264       178 PEAEERMEELIDA-AKKEGDSLGGVVE  203 (346)
T ss_pred             HHHHHHHHHHHHH-HHHCCCCCCCEEE
T ss_conf             8999999999999-9753999871899


No 19 
>COG3435 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=44.79  E-value=16  Score=18.14  Aligned_cols=48  Identities=29%  Similarity=0.412  Sum_probs=20.7

Q ss_pred             HHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             8777787528975999643347999963664666668999999999999
Q gi|254780430|r  128 RVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANIL  176 (189)
Q Consensus       128 ~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l  176 (189)
                      .|||.|+.-|.-|.-.+=.--++++.=-| |.|-.|.+.||..|++-+|
T Consensus        53 ~ir~ll~~sgeli~~~~a~RRvi~L~NP~-l~g~ssiT~TLyAglQlil  100 (351)
T COG3435          53 EIRPLLLRSGELISAREAVRRVIYLENPG-LRGRSSITPTLYAGLQLIL  100 (351)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEEEEECCCC-CCCCCCCCHHHHHHHHEEC
T ss_conf             99999998642247445436899964888-8886633088886554045


No 20 
>COG0082 AroC Chorismate synthase [Amino acid transport and metabolism]
Probab=43.97  E-value=11  Score=19.16  Aligned_cols=63  Identities=22%  Similarity=0.323  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHCCCCEEEEECCCEEEEEE------CCCCCHH---HHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             13468898741688107998087799831------4668212---348999999999740143232321122
Q gi|254780430|r   37 EISPLASRIFSIPGIASVYFGYDFITVGK------DQYDWEH---LRPPVLGMIMEHFISGDPIIHNGGLGD   99 (189)
Q Consensus        37 ~~spLa~~Lf~i~GV~~Vfi~~nFITVtK------~~~eW~~---i~p~I~~~I~~~l~~g~~~i~~~~~~~   99 (189)
                      -++.||+.||.|+-|+.|-|+..|-...+      |...|++   -+..=..-|.--+.+|.|++...+...
T Consensus       227 Lda~lA~AlmsI~AvKGVEiG~GF~~a~~~GSe~~De~~~~~~~~~~tN~~GGilGGitnG~pIv~r~a~KP  298 (369)
T COG0082         227 LDAKLAHALMSIPAVKGVEIGDGFEAARMRGSEANDEITLDGGIVRKTNNAGGILGGITNGEPIVVRVAFKP  298 (369)
T ss_pred             CHHHHHHHHHCCCCCEEEEECCCHHHHHCCCCCCCCCEEECCCEEECCCCCCCEECCCCCCCCEEEEEEECC
T ss_conf             168999986076650057865516553156631168634078806724667763035458961799998677


No 21 
>pfam03557 Bunya_G1 Bunyavirus glycoprotein G1. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This family contains the G1 glycoprotein which is the viral attachment protein.
Probab=43.07  E-value=7.1  Score=20.33  Aligned_cols=30  Identities=33%  Similarity=0.595  Sum_probs=18.8

Q ss_pred             HCCCCEEEEEEECCEEEEEECCCCCCCHHHH
Q ss_conf             5289759996433479999636646666689
Q gi|254780430|r  135 RDGGDIVFKGYRDGIVFLSMRGACSGCPSAS  165 (189)
Q Consensus       135 ~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~  165 (189)
                      .+=||+.|..|.... -+...|.|+||+.-.
T Consensus       738 ~~lgd~~YK~~~~~~-~l~~~~~C~GC~~Cf  767 (871)
T pfam03557       738 AILGDIRYKTFAESI-DLEAEGKCVGCINCF  767 (871)
T ss_pred             EECCCHHHHCCCCCC-CEEEEEEECCCCCHH
T ss_conf             861502354056674-146503851663033


No 22 
>PRK12463 chorismate synthase; Reviewed
Probab=42.20  E-value=17  Score=17.97  Aligned_cols=27  Identities=26%  Similarity=0.289  Sum_probs=14.4

Q ss_pred             CCHHHHHHHHCCCCEEEEECCCEEEEE
Q ss_conf             346889874168810799808779983
Q gi|254780430|r   38 ISPLASRIFSIPGIASVYFGYDFITVG   64 (189)
Q Consensus        38 ~spLa~~Lf~i~GV~~Vfi~~nFITVt   64 (189)
                      ++-||+.||.||.|+.|-++..|=...
T Consensus       242 da~LA~A~mSIpAvKGvE~G~GF~~a~  268 (390)
T PRK12463        242 DAKLAGAIMSINAFKGAEIGVGFEAAR  268 (390)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCHHHHH
T ss_conf             299999862778502788635442300


No 23 
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689    This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process.
Probab=41.12  E-value=14  Score=18.50  Aligned_cols=47  Identities=13%  Similarity=0.211  Sum_probs=28.7

Q ss_pred             HHHHHCCCCEEEEECCCEEEEEE---CCCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf             98741688107998087799831---466821234899999999974014
Q gi|254780430|r   43 SRIFSIPGIASVYFGYDFITVGK---DQYDWEHLRPPVLGMIMEHFISGD   89 (189)
Q Consensus        43 ~~Lf~i~GV~~Vfi~~nFITVtK---~~~eW~~i~p~I~~~I~~~l~~g~   89 (189)
                      ..+..++||..||||+-=++=+=   -+-.=-++...|..+|+.=-..|+
T Consensus       156 ~~Ia~VeGVDGVFiGPADLaasmGH~GnPsHPEV~~AI~~Ai~~i~a~gK  205 (249)
T TIGR02311       156 EEIAAVEGVDGVFIGPADLAASMGHLGNPSHPEVQDAIDDAIERIKAAGK  205 (249)
T ss_pred             HHHHCCCCCCCEEECCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             57750178662475712443401568886961589999999999985489


No 24 
>KOG1482 consensus
Probab=38.54  E-value=34  Score=16.05  Aligned_cols=50  Identities=24%  Similarity=0.218  Sum_probs=36.6

Q ss_pred             CCHHHHHHHHCCCCEEEEECCC-EEEEEE----------CCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             3468898741688107998087-799831----------4668212348999999999740
Q gi|254780430|r   38 ISPLASRIFSIPGIASVYFGYD-FITVGK----------DQYDWEHLRPPVLGMIMEHFIS   87 (189)
Q Consensus        38 ~spLa~~Lf~i~GV~~Vfi~~n-FITVtK----------~~~eW~~i~p~I~~~I~~~l~~   87 (189)
                      ...+-+.|..++||++|.=-.= -||+.|          .+++|+.+..++++.|...+.-
T Consensus       296 ~~~~~~~l~~iegV~~VHdLhIWsiTv~k~~ls~Hv~i~~~ad~~~vL~~~~~~i~~~~~~  356 (379)
T KOG1482         296 FDKVKKGLLSIEGVKAVHDLHIWSITVGKVALSVHLAIDSEADAEEVLDEARSLIKRRYGI  356 (379)
T ss_pred             HHHHHHHHHHHCCEEEEEEEEEEEEECCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHCCE
T ss_conf             7899987742116468888888877427557899996168889899999999999742565


No 25 
>cd01815 BMSC_UbP_N BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins.  This CD represents the N-terminal ubiquitin-like domain.
Probab=38.04  E-value=16  Score=18.14  Aligned_cols=30  Identities=27%  Similarity=0.159  Sum_probs=26.4

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             636646666689999999999999978970
Q gi|254780430|r  154 MRGACSGCPSASETLKYGVANILNHFVPEV  183 (189)
Q Consensus       154 ~~GaC~~Cpss~~Tl~~gie~~l~~~vpev  183 (189)
                      +.|.|.-|.-+..||||-|-.+|...+|+=
T Consensus        12 e~gd~~~ggy~vs~lKQLia~~L~dS~PDP   41 (75)
T cd01815          12 ELGDVSPGGYQVSTLKQLIAAQLPDSLPDP   41 (75)
T ss_pred             CCCCCCCCCEEHHHHHHHHHHHCCCCCCCH
T ss_conf             777659983437899999975565469984


No 26 
>cd02969 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.
Probab=37.38  E-value=36  Score=15.94  Aligned_cols=27  Identities=15%  Similarity=0.150  Sum_probs=17.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             666689999999999999978970035
Q gi|254780430|r  160 GCPSASETLKYGVANILNHFVPEVKDI  186 (189)
Q Consensus       160 ~Cpss~~Tl~~gie~~l~~~vpev~~V  186 (189)
                      ....+..=|+++|+++|+-.-..+...
T Consensus       136 ~~~~~~~~l~~Ai~~~~~g~~i~~~~t  162 (171)
T cd02969         136 DPPVTGRDLRAALDALLAGKPVPVPQT  162 (171)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             998887999999999983899994676


No 27 
>TIGR00033 aroC chorismate synthase; InterPro: IPR000453 Chorismate synthase (4.2.3.5 from EC) catalyzes the last of the seven steps in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows ,  a high degree of sequence conservation. It is a protein of about 360 to 400 amino-acid residues.; GO: 0004107 chorismate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=36.46  E-value=21  Score=17.38  Aligned_cols=58  Identities=24%  Similarity=0.281  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHCCCCEEEEECCCEEEEEE------CCCCCH--HHHHHHHHHHHHH-------HHCCCCCCCCCCC
Q ss_conf             3468898741688107998087799831------466821--2348999999999-------7401432323211
Q gi|254780430|r   38 ISPLASRIFSIPGIASVYFGYDFITVGK------DQYDWE--HLRPPVLGMIMEH-------FISGDPIIHNGGL   97 (189)
Q Consensus        38 ~spLa~~Lf~i~GV~~Vfi~~nFITVtK------~~~eW~--~i~p~I~~~I~~~-------l~~g~~~i~~~~~   97 (189)
                      ++.||..||.|+=||.|-||..|=..+-      |...|+  +-...-  +..++       +..|.++.-+-+.
T Consensus       258 dA~LA~A~~SI~A~KGvEiG~GF~~a~~~GS~~~Def~~~KE~~~~i~--~ktNn~GGi~GGIt~G~~I~~r~a~  330 (391)
T TIGR00033       258 DAELASALMSIPAVKGVEIGDGFELASMRGSEANDEFVLEKEDDGGIR--RKTNNSGGILGGITNGEPIRVRIAV  330 (391)
T ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCE--EEECCCCCCCCCCCCCCCEEEEEEE
T ss_conf             588888873246211478757765022146422584046666288847--8734557423674017312898866


No 28 
>PRK10128 putative aldolase; Provisional
Probab=34.75  E-value=31  Score=16.31  Aligned_cols=56  Identities=14%  Similarity=0.166  Sum_probs=35.8

Q ss_pred             CCCCHHHHHHHHCCCCEEEEECCCEEEEEE---CCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             013468898741688107998087799831---46682123489999999997401432
Q gi|254780430|r   36 AEISPLASRIFSIPGIASVYFGYDFITVGK---DQYDWEHLRPPVLGMIMEHFISGDPI   91 (189)
Q Consensus        36 a~~spLa~~Lf~i~GV~~Vfi~~nFITVtK---~~~eW~~i~p~I~~~I~~~l~~g~~~   91 (189)
                      ...-.=+.+++++|||..+|+|++=++..-   .+.+..++...+...+...-..|.++
T Consensus       138 ~~av~nldeI~av~GvD~~fiGp~DLs~slG~pg~~~~p~v~~ai~~v~~~~~~~gk~~  196 (250)
T PRK10128        138 KTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAA  196 (250)
T ss_pred             HHHHHHHHHHHCCCCCCEEEECHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCE
T ss_conf             89998799985889988899884889986599999998699999999999999869976


No 29 
>PRK11670 putative ATPase; Provisional
Probab=34.59  E-value=40  Score=15.66  Aligned_cols=42  Identities=12%  Similarity=0.195  Sum_probs=23.6

Q ss_pred             HHHHHHHCCCCEEEEECCCEEEEEEC-C----CCCHHHHHHHHHHHH
Q ss_conf             88987416881079980877998314-6----682123489999999
Q gi|254780430|r   41 LASRIFSIPGIASVYFGYDFITVGKD-Q----YDWEHLRPPVLGMIM   82 (189)
Q Consensus        41 La~~Lf~i~GV~~Vfi~~nFITVtK~-~----~eW~~i~p~I~~~I~   82 (189)
                      |-+.|.++..|++|.+.++-++|+=. .    ..++.++.++...+.
T Consensus        29 ~~~~iv~lg~v~~i~i~~~~v~i~l~l~~~~~~~~~~~~~~~~~~l~   75 (369)
T PRK11670         29 LKHNLTTLKALHHVAWMDDTLHIELVMPFVWNSAFEELKEQCSAELL   75 (369)
T ss_pred             CCCCEECCCCEEEEEEECCEEEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             99880037970169997999999999688898879999999999998


No 30 
>PRK09193 indolepyruvate ferredoxin oxidoreductase; Validated
Probab=34.10  E-value=7.8  Score=20.07  Aligned_cols=16  Identities=38%  Similarity=0.706  Sum_probs=12.5

Q ss_pred             EEECCCCCCCHHHHHH
Q ss_conf             9963664666668999
Q gi|254780430|r  152 LSMRGACSGCPSASET  167 (189)
Q Consensus       152 v~~~GaC~~Cpss~~T  167 (189)
                      .+.--=|+|||..+.|
T Consensus       435 ~R~PyFCSGCPHNtST  450 (1155)
T PRK09193        435 ARTPYFCSGCPHNTST  450 (1155)
T ss_pred             CCCCCCCCCCCCCCCC
T ss_conf             8798677999997567


No 31 
>PRK13030 2-oxoacid ferredoxin oxidoreductase; Provisional
Probab=33.34  E-value=8.3  Score=19.90  Aligned_cols=17  Identities=35%  Similarity=0.604  Sum_probs=12.3

Q ss_pred             EEECCCCCCCHHHHHHH
Q ss_conf             99636646666689999
Q gi|254780430|r  152 LSMRGACSGCPSASETL  168 (189)
Q Consensus       152 v~~~GaC~~Cpss~~Tl  168 (189)
                      -|.--=|+|||..+.|-
T Consensus       434 ~R~P~FCSGCPHNtST~  450 (1168)
T PRK13030        434 RRTPYFCSGCPHNTSTK  450 (1168)
T ss_pred             CCCCCCCCCCCCCCCCC
T ss_conf             67873458999976654


No 32 
>PRK13029 2-oxoacid ferredoxin oxidoreductase; Provisional
Probab=33.06  E-value=8.8  Score=19.74  Aligned_cols=17  Identities=35%  Similarity=0.575  Sum_probs=12.5

Q ss_pred             EEECCCCCCCHHHHHHH
Q ss_conf             99636646666689999
Q gi|254780430|r  152 LSMRGACSGCPSASETL  168 (189)
Q Consensus       152 v~~~GaC~~Cpss~~Tl  168 (189)
                      -+.--=|+|||..+.|-
T Consensus       451 ~R~P~FCSGCPHNtST~  467 (1186)
T PRK13029        451 ERKPWFCSGCPHNTSTR  467 (1186)
T ss_pred             CCCCCCCCCCCCCCCCC
T ss_conf             67874468999964565


No 33 
>pfam04320 DUF469 Protein with unknown function (DUF469). Family of bacteria protein with no known function.
Probab=32.87  E-value=42  Score=15.49  Aligned_cols=65  Identities=26%  Similarity=0.411  Sum_probs=43.0

Q ss_pred             CHHHHHHHHHHHHHHHHH-HHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             026889999999998777-787528975999643347999963664666668999999999999997897003553
Q gi|254780430|r  114 DSAVVQRIKEVLDNRVRP-AVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIRT  188 (189)
Q Consensus       114 ~~~~~~~i~~~l~~~IrP-~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~~  188 (189)
                      ++.+..-+...|++.|.| .|.-+||+   ...-+|.|...-.|+|.-      .-+..|+.=|+. -|++++|+.
T Consensus        29 ~e~~D~~vD~fIde~Ie~ngL~~~Ggg---~~~~eG~Vc~~~~gs~tE------e~R~~V~~WL~~-r~ev~~v~v   94 (102)
T pfam04320        29 EEAIDAFVDAFIDEVIEANGLAFGGGG---YLEWEGFVCLQRYGSCTE------EDRAAVEAWLEA-RPEVKDVEV   94 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEECCC---CCEEEEEEEECCCCCCCH------HHHHHHHHHHHH-CCCCCEEEE
T ss_conf             899999999999998633683683487---422537998420579998------999999999970-987436886


No 34 
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=31.70  E-value=44  Score=15.37  Aligned_cols=70  Identities=27%  Similarity=0.439  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHC---CCCEEEEEEE--CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             688999999999877778752---8975999643--34799996366466666899999999999999789700355
Q gi|254780430|r  116 AVVQRIKEVLDNRVRPAVARD---GGDIVFKGYR--DGIVFLSMRGACSGCPSASETLKYGVANILNHFVPEVKDIR  187 (189)
Q Consensus       116 ~~~~~i~~~l~~~IrP~l~~d---GG~i~~~~~~--~g~v~v~~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~V~  187 (189)
                      +...+|.+.|.+=+.|.+--|   =|-|.=+.++  +|.++|.|...-.|||++.. +.+-+++.++. +|.++.|+
T Consensus        12 ~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~-i~~~v~~al~~-~~~v~~v~   86 (111)
T COG2151          12 VTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEV-IADQVEAALEE-IPGVEDVE   86 (111)
T ss_pred             HHHHHHHHHHHCCCCCCCCEEEEEECCEEEEEEECCCCEEEEEEECCCCCCCCHHH-HHHHHHHHHHH-CCCCCEEE
T ss_conf             66999999853477966660357631079999726774699999517888882078-89999999984-68813079


No 35 
>TIGR00370 TIGR00370 conserved hypothetical protein TIGR00370; InterPro: IPR010016   This is an uncharacterised family of proteins of unknown function..
Probab=31.64  E-value=44  Score=15.36  Aligned_cols=88  Identities=20%  Similarity=0.246  Sum_probs=51.4

Q ss_pred             CCCCHHHHHHHHC--CCCEEEEECCCEEEE-EECCC------------CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             0134688987416--881079980877998-31466------------82123489999999997401432323211222
Q gi|254780430|r   36 AEISPLASRIFSI--PGIASVYFGYDFITV-GKDQY------------DWEHLRPPVLGMIMEHFISGDPIIHNGGLGDM  100 (189)
Q Consensus        36 a~~spLa~~Lf~i--~GV~~Vfi~~nFITV-tK~~~------------eW~~i~p~I~~~I~~~l~~g~~~i~~~~~~~~  100 (189)
                      -.-.-+|++|-+-  ++|-.+..+.|-+|| ++|-+            -|++++.+|.+-+.+--+.-+.  + ...-+-
T Consensus        20 ~~~wa~A~~l~~~Pfp~~vE~ipgmnnlTVf~rd~~~~~k~l~qrl~~~wee~krdveerlaeiae~~e~--~-~R~iEI   96 (217)
T TIGR00370        20 KRVWALARRLEEEPFPDVVEVIPGMNNLTVFLRDMYEVYKDLVQRLERLWEEVKRDVEERLAEIAEALEV--E-SRFIEI   96 (217)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--C-CCEEEE
T ss_conf             5799999998746898758830175420000005689988767756567788754388899888765145--8-877873


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             22222233445440268899999999987
Q gi|254780430|r  101 KLDDMGSGDFIESDSAVVQRIKEVLDNRV  129 (189)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~i~~~l~~~I  129 (189)
                      ...-   ......|=+.+.+++++=.++|
T Consensus        97 PV~Y---GGe~GpDL~~VAk~~qlspe~v  122 (217)
T TIGR00370        97 PVVY---GGERGPDLEEVAKFNQLSPEEV  122 (217)
T ss_pred             EEEE---CCCCCCCHHHHHHHHCCCHHHE
T ss_conf             0475---7888989899997717884573


No 36 
>COG3696 Putative silver efflux pump [Inorganic ion transport and metabolism]
Probab=30.83  E-value=46  Score=15.28  Aligned_cols=108  Identities=20%  Similarity=0.273  Sum_probs=56.3

Q ss_pred             CCCHHHHHHHHCCCCEEE----EECCCEEEEE-ECCCC--CH-HHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCC
Q ss_conf             134688987416881079----9808779983-14668--21-2348999999999740143-23232112222222223
Q gi|254780430|r   37 EISPLASRIFSIPGIASV----YFGYDFITVG-KDQYD--WE-HLRPPVLGMIMEHFISGDP-IIHNGGLGDMKLDDMGS  107 (189)
Q Consensus        37 ~~spLa~~Lf~i~GV~~V----fi~~nFITVt-K~~~e--W~-~i~p~I~~~I~~~l~~g~~-~i~~~~~~~~~~~~~~~  107 (189)
                      ---|+-..+..+||++.|    +++-.+|||- ||.+|  |. .+-.+=.+..+..|..|-. .+.+....-...-... 
T Consensus        65 iT~Plet~m~G~pg~~tvRs~S~~g~S~VtViF~dgtDiY~ARq~V~ErL~~v~~~LP~g~~p~lgP~sTglG~i~~yt-  143 (1027)
T COG3696          65 VTYPLETAMMGLPGVKTVRSISKYGLSLVTVIFKDGTDLYWARQRVLERLSQVQSQLPEGVEPELGPDSTGLGWIYQYT-  143 (1027)
T ss_pred             CEEEEHHHHCCCCCCEEEECCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEE-
T ss_conf             1001067654799851541225577448999980785479999999999999997489988888488766762048999-


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             344544026889999999998777787528975999643
Q gi|254780430|r  108 GDFIESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYR  146 (189)
Q Consensus       108 ~~~~~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~  146 (189)
                       -..+++..-......+.|-.|||.|.+-.|=.+...+-
T Consensus       144 -l~~~~~~~~l~elr~lqdw~vrp~L~~vpGVaeV~s~G  181 (1027)
T COG3696         144 -LVDKSGKTDLDELRELQDWVVRPQLRSVPGVAEVASVG  181 (1027)
T ss_pred             -EECCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHCC
T ss_conf             -97588998889999988782689871599715531047


No 37 
>TIGR00852 pts-Glc PTS system, maltose and glucose-specific subfamily, IIC component; InterPro: IPR004719   Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family. These permeases show limited sequence similarity with members of the Fru family. Several of the Escherichia coli PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli. Most, but not all Scr permeases of other bacteria also lack a IIA domain. This HMM is specific for the IIC domain of the Glc family PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane.
Probab=30.64  E-value=35  Score=16.02  Aligned_cols=62  Identities=19%  Similarity=0.222  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEEEC-CEEEEE---------------ECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             9999987777875289759996433-479999---------------63664666668999999999999997897003
Q gi|254780430|r  123 EVLDNRVRPAVARDGGDIVFKGYRD-GIVFLS---------------MRGACSGCPSASETLKYGVANILNHFVPEVKD  185 (189)
Q Consensus       123 ~~l~~~IrP~l~~dGG~i~~~~~~~-g~v~v~---------------~~GaC~~Cpss~~Tl~~gie~~l~~~vpev~~  185 (189)
                      -.+..-+.=..+.+||+|+..++-. .+-.+.               ++|.|.+|..|...+ .-+|+.++..+|+...
T Consensus        37 p~~~~~~~~~~~~~~g~Ipv~~~~~~~~~~~~~~~~g~~~~agIkTLytg~v~pi~~~~~~~-~~~er~~~~~lP~~L~  114 (312)
T TIGR00852        37 PVLNNAMGVGAQAVGGEIPVWNFFGFEIAKVGFNNSGLTLGAGIKTLYTGVVGPIIVGAIAL-ALHERFLDKKLPDVLG  114 (312)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHCCCHHHHHHCCCHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHH
T ss_conf             99999999876316787102312243066653341455652453057778899999999999-9998884101002665


No 38 
>pfam00873 ACR_tran AcrB/AcrD/AcrF family. Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer.
Probab=30.24  E-value=47  Score=15.22  Aligned_cols=36  Identities=14%  Similarity=0.287  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCC--CEEEEEEECCEEEEEE
Q ss_conf             99999999987777875289--7599964334799996
Q gi|254780430|r  119 QRIKEVLDNRVRPAVARDGG--DIVFKGYRDGIVFLSM  154 (189)
Q Consensus       119 ~~i~~~l~~~IrP~l~~dGG--~i~~~~~~~g~v~v~~  154 (189)
                      ..+.++.+++++|.|.+--|  +|++.+..+..+.|++
T Consensus       151 ~~l~~~~~~~l~~~L~~v~gV~~V~~~G~~~~~i~I~~  188 (1021)
T pfam00873       151 TDLRDYADTNIKDQLSRIPGVGDVQLFGGSEYAMRIWL  188 (1021)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEE
T ss_conf             99999999999999847979069997589706999997


No 39 
>PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional
Probab=28.26  E-value=45  Score=15.35  Aligned_cols=36  Identities=11%  Similarity=0.346  Sum_probs=15.2

Q ss_pred             CCHHHHHHHHCCCCEEEEECCCEEEEEECCCCCHHHHHHHH
Q ss_conf             34688987416881079980877998314668212348999
Q gi|254780430|r   38 ISPLASRIFSIPGIASVYFGYDFITVGKDQYDWEHLRPPVL   78 (189)
Q Consensus        38 ~spLa~~Lf~i~GV~~Vfi~~nFITVtK~~~eW~~i~p~I~   78 (189)
                      .+|...+++..-|..-|+++..+-     -.+|+++.+.++
T Consensus        28 ~sp~~~Ei~a~~G~Dfv~iD~EHg-----~~~~~~l~~~i~   63 (256)
T PRK10558         28 SNPITTEVLGLAGFDWLVLDGEHA-----PNDVSTFIPQLM   63 (256)
T ss_pred             CCHHHHHHHHCCCCCEEEECCCCC-----CCCHHHHHHHHH
T ss_conf             998999999728989999837789-----999999999999


No 40 
>COG4551 Predicted protein tyrosine phosphatase [General function prediction only]
Probab=27.78  E-value=52  Score=14.95  Aligned_cols=91  Identities=14%  Similarity=0.236  Sum_probs=50.4

Q ss_pred             CCHHHHHHHH-CCCCEEEEECCCE---EEEEECCCCCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             3468898741-6881079980877---99831466821234899999999974014-32323211222222222334454
Q gi|254780430|r   38 ISPLASRIFS-IPGIASVYFGYDF---ITVGKDQYDWEHLRPPVLGMIMEHFISGD-PIIHNGGLGDMKLDDMGSGDFIE  112 (189)
Q Consensus        38 ~spLa~~Lf~-i~GV~~Vfi~~nF---ITVtK~~~eW~~i~p~I~~~I~~~l~~g~-~~i~~~~~~~~~~~~~~~~~~~~  112 (189)
                      .||-|..+|+ -+||+.--.|-+.   +.++++..+|.+|.--.-..-+..|+..- +.+-++...-.   +     .-+
T Consensus        14 rsptae~~Fa~~~~vetdSAGl~~dAe~Plt~e~leWAdiIfVMEr~HrqkL~krf~~~lk~kRviCL---D-----IPD   85 (109)
T COG4551          14 RSPTAEVMFATWPGVETDSAGLAHDAETPLTREQLEWADIIFVMERVHRQKLQKRFKASLKGKRVICL---D-----IPD   85 (109)
T ss_pred             CCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE---E-----CCC
T ss_conf             69516677512789754445566556787508886355634568999999999986687628848997---4-----885


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             402688999999999877778752
Q gi|254780430|r  113 SDSAVVQRIKEVLDNRVRPAVARD  136 (189)
Q Consensus       113 ~~~~~~~~i~~~l~~~IrP~l~~d  136 (189)
                      +..-..-..-++|+.++-|+|+.+
T Consensus        86 dy~yMq~eLi~lLkrkv~p~L~~~  109 (109)
T COG4551          86 DYEYMQPELIDLLKRKVGPYLRTY  109 (109)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHCCC
T ss_conf             476517999999998610142069


No 41 
>TIGR01684 viral_ppase viral phosphatase; InterPro: IPR007827 This family contains uncharacterised baculoviral proteins..
Probab=26.96  E-value=53  Score=14.86  Aligned_cols=60  Identities=17%  Similarity=0.267  Sum_probs=38.1

Q ss_pred             CCCEECCCH--HHCCCCH--HHHHHH--HCCCCEEEEEC----------CCEEEEEE-C---C-C-CCHHHHHHHHHHHH
Q ss_conf             886430696--6701346--889874--16881079980----------87799831-4---6-6-82123489999999
Q gi|254780430|r   25 EGAIHFSNA--KEAEISP--LASRIF--SIPGIASVYFG----------YDFITVGK-D---Q-Y-DWEHLRPPVLGMIM   82 (189)
Q Consensus        25 ~g~~~f~~~--~~a~~sp--La~~Lf--~i~GV~~Vfi~----------~nFITVtK-~---~-~-eW~~i~p~I~~~I~   82 (189)
                      ..+..++..  +.--+||  ...-|-  .+...+++.+-          ++||-|.| +   . . ||+....+|.+.|.
T Consensus       237 ~~pf~l~~~~~~~LPKSPrvVL~~L~~~G~~~~KsitLVDDL~~NN~~YDyfV~v~rCPDDn~P~NDW~~~~~~Iv~~~~  316 (323)
T TIGR01684       237 KTPFYLNLTDGKRLPKSPRVVLWYLADKGVNYIKSITLVDDLADNNFAYDYFVNVSRCPDDNVPVNDWDSYHDQIVSNLV  316 (323)
T ss_pred             ECCEECCCCCCCCCCCCCCHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             13335278742247998705453324669168644888604766785654438600077874288512577788888886


Q ss_pred             HH
Q ss_conf             99
Q gi|254780430|r   83 EH   84 (189)
Q Consensus        83 ~~   84 (189)
                      +|
T Consensus       317 ~Y  318 (323)
T TIGR01684       317 EY  318 (323)
T ss_pred             HH
T ss_conf             43


No 42 
>PRK02269 ribose-phosphate pyrophosphokinase; Provisional
Probab=23.64  E-value=62  Score=14.47  Aligned_cols=34  Identities=15%  Similarity=0.154  Sum_probs=21.2

Q ss_pred             EEEEECCCCCCCH--------HHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999636646666--------689999999999999978970
Q gi|254780430|r  150 VFLSMRGACSGCP--------SASETLKYGVANILNHFVPEV  183 (189)
Q Consensus       150 v~v~~~GaC~~Cp--------ss~~Tl~~gie~~l~~~vpev  183 (189)
                      ....+.|.+.|+-        ++..|+-+..+.+..+-...|
T Consensus       207 ~~~~~~gdV~Gk~vIIVDDiIdTGgTl~~aa~~Lk~~GA~~V  248 (321)
T PRK02269        207 EVMNIIGNVSGKKCILIDDMIDTAGTICHAADALAEAGATAV  248 (321)
T ss_pred             EECCCCCCCCCCEEEEECCHHHCHHHHHHHHHHHHHCCCCEE
T ss_conf             420357740697699966243142669999999984899827


No 43 
>TIGR02855 spore_yabG sporulation peptidase YabG; InterPro: IPR008764   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.     The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported.   This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of Bacillus subtilis ..
Probab=23.37  E-value=18  Score=17.78  Aligned_cols=48  Identities=19%  Similarity=0.441  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHH----------HHCCCCEEEEEEECC-----------------EEEEEECCCCCCCHHH
Q ss_conf             688999999999877778----------752897599964334-----------------7999963664666668
Q gi|254780430|r  116 AVVQRIKEVLDNRVRPAV----------ARDGGDIVFKGYRDG-----------------IVFLSMRGACSGCPSA  164 (189)
Q Consensus       116 ~~~~~i~~~l~~~IrP~l----------~~dGG~i~~~~~~~g-----------------~v~v~~~GaC~~Cpss  164 (189)
                      |--.+|.+||++ +||-+          .+-|+--.|..|++.                 -=.|-|.||||+|-=|
T Consensus       149 emPe~v~~L~~~-~~PDIlViTGHDa~~K~~~~~~DL~aYRhSkyFv~~V~~aR~~~P~lD~LVIFAGACQShfE~  223 (292)
T TIGR02855       149 EMPEKVLDLIEE-VRPDILVITGHDAYSKNKGNYGDLNAYRHSKYFVETVREARKYVPSLDQLVIFAGACQSHFES  223 (292)
T ss_pred             CCCHHHHHHHHH-HCCCEEEEECCCCEEECCCCHHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCHHHHHH
T ss_conf             180889999973-099789994666302167871136423665689999999863178753234332121445799


No 44 
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase; InterPro: IPR014265   Proteins in this entry are putative periplasmic sensor signal transduction histidine kinases. They all contain a GAF domain that is present in phytochromes and cGMP-specific phosphodiesterases, and which has been experimentally proven to be involved in protein:protein interactions. They also contain a C-terminal histidine kinase domain, which is composed of a dimerisation sub-domain and an ATP/ADP-binding phosphotransfer, or catalytic, sub-domain. The proteins in this entry are found strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system  common in Gram-positive bacteria, where members of IPR014264 from INTERPRO and IPR014266 from INTERPRO also occur..
Probab=23.21  E-value=63  Score=14.42  Aligned_cols=108  Identities=19%  Similarity=0.228  Sum_probs=56.3

Q ss_pred             CHHHHHHHHC----CCCEEEEE-CCCE-EEEEECCCCCHHHHHHHHHHHHHHHHCCCCC----CCCCCCC-CCCCCCCCC
Q ss_conf             4688987416----88107998-0877-9983146682123489999999997401432----3232112-222222223
Q gi|254780430|r   39 SPLASRIFSI----PGIASVYF-GYDF-ITVGKDQYDWEHLRPPVLGMIMEHFISGDPI----IHNGGLG-DMKLDDMGS  107 (189)
Q Consensus        39 spLa~~Lf~i----~GV~~Vfi-~~nF-ITVtK~~~eW~~i~p~I~~~I~~~l~~g~~~----i~~~~~~-~~~~~~~~~  107 (189)
                      +.|++++-+-    ..=-+|.+ +.+| ++|.   ++=+.++.-|-+.+.+++++..+-    +.-.... +...-+..+
T Consensus       558 ~~L~~~~~~~k~~q~p~~e~~~~~~~~rl~~~---a~~erl~rV~gHL~QNAlEAT~~~G~V~~~~~~~~~~~a~i~i~D  634 (696)
T TIGR02916       558 VDLLRRVIASKRAQQPRPEVSIEDTDFRLSVR---ADRERLERVLGHLVQNALEATPEEGRVKIRVERECGGAAVIEIED  634 (696)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCEEEEEE---ECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCEEEEEEEE
T ss_conf             99999999998631894489971754178887---528889999999999888604999628999874188822799986


Q ss_pred             CCCCCCCHHHHHHH-------H-------HHHHHHHHHHHHHCCCCEEEEEEEC-CEEE
Q ss_conf             34454402688999-------9-------9999987777875289759996433-4799
Q gi|254780430|r  108 GDFIESDSAVVQRI-------K-------EVLDNRVRPAVARDGGDIVFKGYRD-GIVF  151 (189)
Q Consensus       108 ~~~~~~~~~~~~~i-------~-------~~l~~~IrP~l~~dGG~i~~~~~~~-g~v~  151 (189)
                      +.+-=.++=+-++.       |       -+-|  .|-+++++||+|++.+..+ |+.+
T Consensus       635 ~G~GM~~~FiR~rLF~PF~tTK~~aGMGIG~YE--~~~yv~e~GG~i~V~S~pG~Gt~f  691 (696)
T TIGR02916       635 SGCGMSEAFIRERLFKPFDTTKGNAGMGIGVYE--CRQYVEELGGRIEVESTPGKGTIF  691 (696)
T ss_pred             CCCCCCHHHHHHHCCCCCCCCCCCCCCCCCHHH--HHHHHHHHCCCEEEEEECCCCEEE
T ss_conf             578998589984078997544566787201899--999999838905888635885488


No 45 
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.55  E-value=58  Score=14.63  Aligned_cols=37  Identities=19%  Similarity=0.409  Sum_probs=24.7

Q ss_pred             HHHHCCCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             7875289759996433479999636646666689999999
Q gi|254780430|r  132 AVARDGGDIVFKGYRDGIVFLSMRGACSGCPSASETLKYG  171 (189)
Q Consensus       132 ~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss~~Tl~~g  171 (189)
                      ..-.+.|++-=+.-++.+.-+   |+|.+|+.-..-||-|
T Consensus       820 ~~g~~~~~~cpvc~~g~i~~i---ggc~tc~~cg~q~~cg  856 (857)
T PRK08115        820 TIGSEIGNTCPICREGTVEEI---GGCNTCTNCGAQLKCG  856 (857)
T ss_pred             CCCCCCCCCCCCCCCCCEEEC---CCCCCCCCCHHHCCCC
T ss_conf             535334775875788870125---6876676440020048


No 46 
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=21.76  E-value=67  Score=14.24  Aligned_cols=34  Identities=15%  Similarity=0.232  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHCCC--CEEEEEEECCEEEEEE
Q ss_conf             999999987777875289--7599964334799996
Q gi|254780430|r  121 IKEVLDNRVRPAVARDGG--DIVFKGYRDGIVFLSM  154 (189)
Q Consensus       121 i~~~l~~~IrP~l~~dGG--~i~~~~~~~g~v~v~~  154 (189)
                      ..++.+.+++|.+.+--|  .+.+.+..+..+.|.+
T Consensus       154 l~~~a~~~l~~~L~~i~GV~~V~~~G~~~~ei~I~~  189 (1025)
T PRK10614        154 LYDFASTQLAQTIAQIDGVGDVDVGGSSLPAVRVGL  189 (1025)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEEE
T ss_conf             999999999999857989269997278707999997


No 47 
>KOG2679 consensus
Probab=21.48  E-value=68  Score=14.21  Aligned_cols=105  Identities=17%  Similarity=0.259  Sum_probs=49.9

Q ss_pred             CCCCEEEEECCCEEEE-EECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC---CCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             6881079980877998-31466821234899999999974014323232112---2222222233445440268899999
Q gi|254780430|r   48 IPGIASVYFGYDFITV-GKDQYDWEHLRPPVLGMIMEHFISGDPIIHNGGLG---DMKLDDMGSGDFIESDSAVVQRIKE  123 (189)
Q Consensus        48 i~GV~~Vfi~~nFITV-tK~~~eW~~i~p~I~~~I~~~l~~g~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~~i~~  123 (189)
                      +-+|.--++..+++|. +|+-++|+...|.+. .++..+..=+--+.+..+.   -..+....+..--....+       
T Consensus       159 ~f~v~~~~f~~d~~~~~~~~~ydw~~v~PR~~-~~~~~l~~le~~L~~S~a~wkiVvGHh~i~S~~~HG~T~e-------  230 (336)
T KOG2679         159 MFFVDTTPFMDDTFTLCTDDVYDWRGVLPRVK-YLRALLSWLEVALKASRAKWKIVVGHHPIKSAGHHGPTKE-------  230 (336)
T ss_pred             EECCCCCCCHHHHEECCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCEEEEECCCCEEHHHCCCCHHH-------
T ss_conf             31112441201101025523223446780889-9999999999999874325699942551001101598499-------


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEE----------ECCEEEEEECCCCCCC
Q ss_conf             9999877778752897599964----------3347999963664666
Q gi|254780430|r  124 VLDNRVRPAVARDGGDIVFKGY----------RDGIVFLSMRGACSGC  161 (189)
Q Consensus       124 ~l~~~IrP~l~~dGG~i~~~~~----------~~g~v~v~~~GaC~~C  161 (189)
                       |+++.+|.|++-|=|.-+-+.          +.++-|+.=+|+-..-
T Consensus       231 -L~~~LlPiL~~n~VdlY~nGHDHcLQhis~~e~~iqf~tSGagSkaw  277 (336)
T KOG2679         231 -LEKQLLPILEANGVDLYINGHDHCLQHISSPESGIQFVTSGAGSKAW  277 (336)
T ss_pred             -HHHHHHHHHHHCCCCEEEECCHHHHHHCCCCCCCEEEEEECCCCCCC
T ss_conf             -99988889986397579756545665215777770589407755456


No 48 
>pfam06954 Resistin Resistin. This family consists of several mammalian resistin proteins. Resistin is a 12.5-kDa cysteine-rich secreted polypeptide first reported from rodent adipocytes. It belongs to a multigene family termed RELMs or FIZZ proteins. Plasma resistin levels are significantly increased in both genetically susceptible and high-fat-diet-induced obese mice. Immunoneutralisation of resistin improves hyperglycemia and insulin resistance in high-fat-diet-induced obese mice, while administration of recombinant resistin impairs glucose tolerance and insulin action in normal mice. It has been demonstrated that increases in circulating resistin levels markedly stimulate glucose production in the presence of fixed physiological insulin levels, whereas insulin suppressed resistin expression. It has been suggested that resistin could be a link between obesity and type 2 diabetes.
Probab=21.38  E-value=66  Score=14.27  Aligned_cols=44  Identities=32%  Similarity=0.477  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCCCCCHHH
Q ss_conf             44026889999999998777787528975999643347999963664666668
Q gi|254780430|r  112 ESDSAVVQRIKEVLDNRVRPAVARDGGDIVFKGYRDGIVFLSMRGACSGCPSA  164 (189)
Q Consensus       112 ~~~~~~~~~i~~~l~~~IrP~l~~dGG~i~~~~~~~g~v~v~~~GaC~~Cpss  164 (189)
                      ..|+.+.++|++.+...+.|....-.  +.       -..|.=+|.=.+||+-
T Consensus        26 ~~d~~v~~KIke~~~~l~~ps~~~k~--L~-------C~SV~s~G~lasCPaG   69 (109)
T pfam06954        26 SLDSAVDKKIKEDLSSLEDPSAIRKT--LS-------CTSVKSRGRLASCPAG   69 (109)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCEE--EE-------EEEECCCCCEECCCCC
T ss_conf             27999999999988433662001203--78-------8875147842138997


No 49 
>pfam08777 RRM_3 RNA binding motif. This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.
Probab=21.26  E-value=69  Score=14.18  Aligned_cols=29  Identities=7%  Similarity=0.354  Sum_probs=20.8

Q ss_pred             HHHHHHHCCCCEEEEEEEC--CEEEEEECCCC
Q ss_conf             7777875289759996433--47999963664
Q gi|254780430|r  129 VRPAVARDGGDIVFKGYRD--GIVFLSMRGAC  158 (189)
Q Consensus       129 IrP~l~~dGG~i~~~~~~~--g~v~v~~~GaC  158 (189)
                      |+-.++.+| +|.|++|..  ..-||+|.-+.
T Consensus        18 iK~~f~~~g-~V~yVD~~~Gd~eg~vRf~~~~   48 (102)
T pfam08777        18 IKEAFSQHG-EVKYVDFLEGDKEGYVRFKTPE   48 (102)
T ss_pred             HHHHHHHCC-CEEEEEECCCCCEEEEEECCCC
T ss_conf             999998359-7568984278836999967921


No 50 
>cd03009 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the 
Probab=20.82  E-value=70  Score=14.12  Aligned_cols=16  Identities=31%  Similarity=0.420  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             9999877778752897
Q gi|254780430|r  124 VLDNRVRPAVARDGGD  139 (189)
Q Consensus       124 ~l~~~IrP~l~~dGG~  139 (189)
                      ++.+..|+.+.++|+|
T Consensus       112 IV~~~a~~~~~~~~~~  127 (131)
T cd03009         112 VVTTDARELVLEYGAD  127 (131)
T ss_pred             EEHHHHHHHHHHCCCC
T ss_conf             9817767788641744


Done!