Query         gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 129
No_of_seqs    107 out of 1080
Neff          5.7 
Searched_HMMs 39220
Date          Mon May 23 23:52:55 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780238.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05309 30S ribosomal protein 100.0       0       0  319.3  15.9  122    7-128     5-126 (126)
  2 PTZ00129 40S ribosomal protein 100.0 1.4E-45       0  299.3  14.6  128    1-128    10-146 (150)
  3 COG0100 RpsK Ribosomal protein 100.0 5.6E-45       0  296.3  14.7  129    1-129     1-129 (129)
  4 TIGR03632 bact_S11 30S ribosom 100.0 9.8E-45       0  294.6  14.5  108   19-126     1-108 (108)
  5 pfam00411 Ribosomal_S11 Riboso 100.0 1.3E-44       0  293.9  14.9  109   19-127     1-109 (109)
  6 PRK09607 rps11p 30S ribosomal  100.0 4.9E-44       0  290.4  14.6  116   13-128     1-125 (129)
  7 CHL00041 rps11 ribosomal prote 100.0 5.1E-43       0  284.1  14.9  114    8-121     3-116 (116)
  8 KOG0408 consensus              100.0 3.4E-39 8.7E-44  260.7  13.6  120    8-129    71-190 (190)
  9 TIGR03628 arch_S11P archaeal r 100.0 1.4E-37 3.5E-42  250.9  13.8  104   18-121     2-114 (114)
 10 KOG0407 consensus               99.9   9E-23 2.3E-27  160.2  11.6  114   15-128    13-135 (139)
 11 PTZ00090 40S ribosomal protein  99.2 4.3E-11 1.1E-15   88.7   6.2  109   20-129   101-214 (214)
 12 cd00432 Ribosomal_L18_L5e Ribo  97.6   0.001 2.6E-08   43.6   9.9   88   18-105    11-103 (103)
 13 CHL00139 rpl18 ribosomal prote  97.3  0.0033 8.4E-08   40.5   9.0   87   18-106    15-108 (109)
 14 PRK05593 rplR 50S ribosomal pr  97.2  0.0039 9.9E-08   40.1   8.7   86   17-106    24-114 (115)
 15 pfam00861 Ribosomal_L18p Ribos  97.0  0.0057 1.4E-07   39.1   8.1   90   17-106    22-118 (119)
 16 PRK08569 rpl18p 50S ribosomal   95.8   0.099 2.5E-06   31.5   8.6  100   20-129    34-143 (193)
 17 COG0256 RplR Ribosomal protein  95.8    0.12 3.1E-06   31.0   9.0   90   18-107    29-125 (125)
 18 TIGR00060 L18_bact ribosomal p  93.7    0.51 1.3E-05   27.1   7.8   89   19-107    25-118 (118)
 19 cd05313 NAD_bind_2_Glu_DH NAD(  87.9     1.5 3.8E-05   24.3   5.3   67   52-119    10-76  (254)
 20 cd01076 NAD_bind_1_Glu_DH NAD(  87.5     1.6 4.1E-05   24.1   5.3   65   51-116     2-66  (227)
 21 pfam00208 ELFV_dehydrog Glutam  85.0       2 5.2E-05   23.4   4.8   67   53-119     4-70  (237)
 22 TIGR01418 PEP_synth phosphoeno  84.4     1.1 2.7E-05   25.2   3.1   58   48-106   685-749 (877)
 23 PTZ00079 NADP-specific glutama  82.8     4.3 0.00011   21.5   5.7   77   37-119   214-290 (469)
 24 PRK09414 glutamate dehydrogena  81.7     4.8 0.00012   21.2   5.9   76   38-119   192-267 (446)
 25 cd05211 NAD_bind_Glu_Leu_Phe_V  69.6      10 0.00026   19.2   5.0   56   63-119     6-61  (217)
 26 pfam00044 Gp_dh_N Glyceraldehy  57.1      13 0.00034   18.5   3.3   16   75-92    108-123 (150)
 27 smart00846 Gp_dh_N Glyceraldeh  56.4      12 0.00032   18.6   3.1   16   75-92    108-123 (149)
 28 PTZ00032 60S ribosomal protein  55.9      18 0.00046   17.6   8.9   87   20-106   107-210 (211)
 29 pfam07733 DNA_pol3_alpha Bacte  50.0      13 0.00034   18.4   2.4   46   63-119    40-85  (381)
 30 PRK08356 hypothetical protein;  48.8      23  0.0006   17.0   4.5   27   83-111    96-122 (195)
 31 TIGR00423 TIGR00423 conserved   48.7      13 0.00033   18.5   2.1   58   28-92      5-65  (331)
 32 PRK07012 consensus              45.5      15 0.00039   18.1   2.1   23   23-45    997-1023(1173)
 33 COG0334 GdhA Glutamate dehydro  43.7      28 0.00071   16.5   5.9   65   54-119   181-245 (411)
 34 PRK08744 consensus              43.6      18 0.00046   17.6   2.2   11   30-40   1044-1054(1195)
 35 PRK08957 consensus              42.8      16 0.00041   18.0   1.9   17   24-40   1005-1024(1159)
 36 PRK09532 DNA polymerase III su  42.6      17 0.00044   17.8   2.0   12  101-112   195-206 (874)
 37 PRK07279 dnaE DNA polymerase I  41.2      14 0.00035   18.4   1.3   10   30-39    908-917 (1033)
 38 PRK08444 hypothetical protein;  41.2      19 0.00048   17.5   2.0   68   28-102    49-124 (353)
 39 pfam08901 DUF1847 Protein of u  39.6      32 0.00083   16.1   3.6   54   58-111    34-88  (157)
 40 PRK06658 consensus              39.2      19 0.00048   17.5   1.8   22   23-44    992-1018(1145)
 41 TIGR01534 GAPDH-I glyceraldehy  38.2      33 0.00083   16.1   2.9   32   83-115     1-40  (366)
 42 PRK06115 dihydrolipoamide dehy  37.0      32 0.00081   16.1   2.7   45   63-108   182-233 (466)
 43 PRK09074 consensus              36.7      18 0.00047   17.6   1.4   18   23-40   1001-1021(1149)
 44 PRK07374 dnaE DNA polymerase I  36.6      26 0.00067   16.6   2.2   11  102-112   198-208 (1171)
 45 PRK05673 dnaE DNA polymerase I  36.3      30 0.00076   16.3   2.4   22   23-44    993-1019(1143)
 46 PTZ00069 60S ribosomal protein  35.4      38 0.00097   15.7   9.0  105   11-125    41-183 (300)
 47 pfam00728 Glyco_hydro_20 Glyco  35.3      38 0.00097   15.7   5.3   73   26-100    31-103 (335)
 48 PRK06292 dihydrolipoamide dehy  34.5      39   0.001   15.6   3.0   26   63-89    177-202 (460)
 49 PRK06245 cofG FO synthase subu  34.5      39   0.001   15.6   3.9   55   28-88     12-66  (336)
 50 PRK06826 dnaE DNA polymerase I  33.9      29 0.00073   16.4   2.0   10   31-40   1021-1030(1157)
 51 PRK06920 dnaE DNA polymerase I  32.9      21 0.00054   17.2   1.2   16   25-40    959-977 (1107)
 52 PRK07135 dnaE DNA polymerase I  32.3      22 0.00057   17.1   1.3   27   90-119   289-315 (987)
 53 PRK05802 hypothetical protein;  31.7      44  0.0011   15.3   5.3   40   80-119   174-214 (328)
 54 PRK08010 pyridine nucleotide-d  31.2      44  0.0011   15.2   2.8   44   64-108   167-217 (441)
 55 PRK05898 dnaE DNA polymerase I  31.1      31  0.0008   16.2   1.8   27   90-119   292-318 (971)
 56 COG4782 Uncharacterized protei  29.9      47  0.0012   15.1   5.6   74   26-101   124-210 (377)
 57 TIGR03550 F420_cofG 7,8-dideme  29.5      37 0.00095   15.7   2.0   57   28-91      4-63  (322)
 58 PRK05249 soluble pyridine nucl  29.1      48  0.0012   15.0   2.8   42   66-108   187-235 (465)
 59 TIGR03551 F420_cofH 7,8-dideme  25.0      45  0.0011   15.2   1.7   58   28-92     39-99  (343)
 60 TIGR01438 TGR thioredoxin and   24.6      58  0.0015   14.5   4.9   23   63-86    196-218 (513)
 61 TIGR02183 GRXA Glutaredoxin, G  23.5      61  0.0016   14.4   3.0   34   58-91      9-44  (86)
 62 COG4911 Uncharacterized conser  23.2      62  0.0016   14.4   2.7   51   14-64     68-119 (123)
 63 PRK08013 hypothetical protein;  23.1      62  0.0016   14.3   4.1   10   92-101   165-174 (400)
 64 PRK01259 ribose-phosphate pyro  22.9      63  0.0016   14.3   6.6   59   66-126   223-282 (309)
 65 TIGR02684 dnstrm_HI1420 probab  22.3      41  0.0011   15.4   1.1   38   64-104    33-70  (91)
 66 TIGR02530 flg_new flagellar op  21.9      64  0.0016   14.3   2.1   21   19-39     78-98  (113)
 67 KOG4120 consensus               21.6      25 0.00064   16.7  -0.1   69   51-119   118-202 (426)
 68 pfam05990 DUF900 Alpha/beta hy  21.5      67  0.0017   14.2   3.2   78   21-101    23-113 (230)
 69 pfam01019 G_glu_transpept Gamm  21.5      67  0.0017   14.1   3.3   22   26-47    320-341 (506)
 70 smart00300 ChSh Chromo Shadow   21.4      67  0.0017   14.1   3.2   41   30-76     11-51  (61)

No 1  
>PRK05309 30S ribosomal protein S11; Validated
Probab=100.00  E-value=0  Score=319.35  Aligned_cols=122  Identities=57%  Similarity=0.926  Sum_probs=118.6

Q ss_pred             CCCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             43343001225218999917987799997089988997404443557754335203789999999999986981999999
Q gi|254780238|r    7 RIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKV   86 (129)
Q Consensus         7 ~~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i   86 (129)
                      +.+++.++.++.||+||++|+|||||||||++||+++|+|+|++||||++|+||||||++++.++++++++||+.|+|++
T Consensus         5 ~~~~~~k~~i~~GivhI~ss~NNTiitlTD~~Gn~l~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~Gi~~v~V~i   84 (126)
T PRK05309          5 KVRKKVKKNVSSGVAHIHATFNNTIVTITDRQGNAISWASAGGSGFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFV   84 (126)
T ss_pred             CCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             55655361377608999944798899998399999999807750258876566669999999999999972971999999


Q ss_pred             ECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             779986788877876369369999963889888868888678
Q gi|254780238|r   87 SGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR  128 (129)
Q Consensus        87 kG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR  128 (129)
                      +|+|+||+++|++|+.+||+|.+|+|+||+|||||||||+||
T Consensus        85 kG~G~GR~~air~L~~~gikI~~I~D~TpiphnGcRp~K~RR  126 (126)
T PRK05309         85 KGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKRRR  126 (126)
T ss_pred             ECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC
T ss_conf             778833899999998789889999989999978989899998


No 2  
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=100.00  E-value=1.4e-45  Score=299.31  Aligned_cols=128  Identities=34%  Similarity=0.511  Sum_probs=119.7

Q ss_pred             CCCCCCCCCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             98876443343001225218999917987799997089988997404443557754-33520378999999999998698
Q gi|254780238|r    1 MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSR-KNSPFAAQVATDDCSAKAQNHGM   79 (129)
Q Consensus         1 m~~~~~~~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~k-k~t~~Aa~~~a~~~~~~~~~~gi   79 (129)
                      |++.+.+...+.++.+++|++||++||||||||+||+.|+.+.|+|+|.++||+.+ |+||||||+++++++++++++||
T Consensus        10 ~~~~~~~~~~~~~~~~v~GvaHI~ASfNNTIVtvTD~~G~~t~~~sSGg~~~k~~r~ksTPyAAq~AAe~aa~~a~e~Gi   89 (150)
T PTZ00129         10 VPETPTTLGPQVKGEHVFGVAHVFASFNDTFIHITDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDAAARAKELGI   89 (150)
T ss_pred             CCCCCEECCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEEECCCCEEECCCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             63154003772236537799999824587189987399998999968972685787778879999999999999998198


Q ss_pred             CEEEEEEEC--------CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             199999977--------9986788877876369369999963889888868888678
Q gi|254780238|r   80 SSLEVKVSG--------LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR  128 (129)
Q Consensus        80 ~~v~v~ikG--------~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR  128 (129)
                      +.|+|+++|        ||+||+++||+|+.+||+|.+|+|+||+|||||||||+||
T Consensus        90 ~~v~V~vrg~Gg~~~k~PGpGresAIRaL~~~Gl~I~~I~DVTPiPHnGcRppk~RR  146 (150)
T PTZ00129         90 TAVHVKLRATGGTRSKTPGPGAQSALRSLARSGLKIGRIEDVTPIPTDSTRRKCGRR  146 (150)
T ss_pred             CEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC
T ss_conf             189999982478767889864667789987479889898877999999989899877


No 3  
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=5.6e-45  Score=296.29  Aligned_cols=129  Identities=53%  Similarity=0.882  Sum_probs=121.2

Q ss_pred             CCCCCCCCCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             98876443343001225218999917987799997089988997404443557754335203789999999999986981
Q gi|254780238|r    1 MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMS   80 (129)
Q Consensus         1 m~~~~~~~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~   80 (129)
                      |++.....+++.++.+..|++||++||||||||+||+.||.++|.|+|.+|||+++++||||||++++.+++.++++|++
T Consensus         1 ~~~~~~~~~~~~~~~i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~   80 (129)
T COG0100           1 MAKAKARKKKKVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGIK   80 (129)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEECCCCCCEEEEEECCCCEECCCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             97533343300012321315899726788589740789988999704762474788888689999999999999970854


Q ss_pred             EEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             9999997799867888778763693699999638898888688886789
Q gi|254780238|r   81 SLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI  129 (129)
Q Consensus        81 ~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RRi  129 (129)
                      .|+|+++|||+||+++||+|+..|++|.+|.|+||+|||||||||.||+
T Consensus        81 ~v~v~vkgpG~GreaAiraL~~ag~~i~~I~DvTPiphnG~Rppk~RR~  129 (129)
T COG0100          81 SVEVKVKGPGPGREAAIRALAAAGLKITRIEDVTPIPHNGCRPPKRRRV  129 (129)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC
T ss_conf             7999996899758999999987365587888868778899789887789


No 4  
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=100.00  E-value=9.8e-45  Score=294.63  Aligned_cols=108  Identities=56%  Similarity=0.957  Sum_probs=107.0

Q ss_pred             EEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHH
Q ss_conf             18999917987799997089988997404443557754335203789999999999986981999999779986788877
Q gi|254780238|r   19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR   98 (129)
Q Consensus        19 GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik   98 (129)
                      ||+||++|+|||||||||++||+++|+|+|++||||++|+||||||++++.++++++++||+.|+|+++|+|+||+++||
T Consensus         1 Gi~hI~~s~NNTiit~Td~~Gn~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~V~ikG~G~Gr~~air   80 (108)
T TIGR03632         1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGAGRESAIR   80 (108)
T ss_pred             CEEEEEECCCCEEEEEECCCCCEEEEEECCCEECCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHH
T ss_conf             98999935787899998799999999947733327765588899999999999999970961999999689974799999


Q ss_pred             HHHHCCCEEEEEEECCCCCCCCCCCCCC
Q ss_conf             8763693699999638898888688886
Q gi|254780238|r   99 ALRAIGFTIVSICDVTMIAHNGCRPRKR  126 (129)
Q Consensus        99 ~l~~~glkI~~I~D~T~ip~nGcRp~K~  126 (129)
                      +|..+||+|.+|+|+||+|||||||||+
T Consensus        81 ~l~~~glkI~~I~D~TpiphnGcRp~Kk  108 (108)
T TIGR03632        81 ALQAAGLEVTSIKDVTPIPHNGCRPPKR  108 (108)
T ss_pred             HHHHCCCEEEEEEECCCCCCCCCCCCCC
T ss_conf             9998898899999889999899898989


No 5  
>pfam00411 Ribosomal_S11 Ribosomal protein S11.
Probab=100.00  E-value=1.3e-44  Score=293.87  Aligned_cols=109  Identities=51%  Similarity=0.849  Sum_probs=108.2

Q ss_pred             EEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHH
Q ss_conf             18999917987799997089988997404443557754335203789999999999986981999999779986788877
Q gi|254780238|r   19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR   98 (129)
Q Consensus        19 GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik   98 (129)
                      ||+||++|+|||||||||++||+++|+|+|++||||++|+||||||++++.++++++++||+.|+|+++|+|+||++++|
T Consensus         1 Givhi~~t~NNTiitlTD~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr~~air   80 (109)
T pfam00411         1 GIAHIQASFNNTIVTVTDVIGRVVSWSSAGGCGFKGSRKSTPYAAQTAAENAAKIAKEQGIKALEVKIKGPGPGRESALR   80 (109)
T ss_pred             CEEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHH
T ss_conf             97999925788899998599899999957876558887689899999999999999981985999999889987899999


Q ss_pred             HHHHCCCEEEEEEECCCCCCCCCCCCCCC
Q ss_conf             87636936999996388988886888867
Q gi|254780238|r   99 ALRAIGFTIVSICDVTMIAHNGCRPRKRR  127 (129)
Q Consensus        99 ~l~~~glkI~~I~D~T~ip~nGcRp~K~R  127 (129)
                      +|+.+||+|.+|+|+||+|||||||||+|
T Consensus        81 ~l~~~gl~I~~I~D~TpiphnGcRp~K~R  109 (109)
T pfam00411        81 ALARSGLRIGRIRDVTPIPHNGCRPPKKR  109 (109)
T ss_pred             HHHHCCCEEEEEEECCCCCCCCCCCCCCC
T ss_conf             99877998999998599998996989899


No 6  
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=100.00  E-value=4.9e-44  Score=290.37  Aligned_cols=116  Identities=40%  Similarity=0.524  Sum_probs=111.2

Q ss_pred             EEECCCEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECC--
Q ss_conf             012252189999179877999970899-88997404443557754335203789999999999986981999999779--
Q gi|254780238|r   13 RKNIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGL--   89 (129)
Q Consensus        13 ~~~i~~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~--   89 (129)
                      ++++++||+||++||||||||+||++| +++.|+|+|+++|++++|+||||||+++|.++++++++||+.|+|+++|+  
T Consensus         1 krk~~~GivhI~asfNNTivtvTD~~G~~~~~~ssgg~~~k~~~kK~Tp~AAq~aae~~~~~a~~~Gi~~v~V~vkG~G~   80 (129)
T PRK09607          1 QRKEKWGIAHIYASFNNTIITITDLTGAETIAKVSGGMVVKADRDEPSPYAAMQAAFRAAELAKDKGITGVHIKVRAPGG   80 (129)
T ss_pred             CCCCEEEEEEEEECCCCEEEEEECCCCCEEEEEECCCCEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCC
T ss_conf             98540489999936898599998599996999947763004888768989999999999999997698589999983787


Q ss_pred             ------CCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             ------986788877876369369999963889888868888678
Q gi|254780238|r   90 ------GAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR  128 (129)
Q Consensus        90 ------G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR  128 (129)
                            ||||+++||+|+..||+|.+|.|+||+|||||||||+||
T Consensus        81 ~~~k~pGpGr~~air~l~~~Gl~I~~I~DvTpiPhNGcRp~K~RR  125 (129)
T PRK09607         81 NGSKTPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPGGRR  125 (129)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCC
T ss_conf             776788842899999998689789898870989989989899877


No 7  
>CHL00041 rps11 ribosomal protein S11
Probab=100.00  E-value=5.1e-43  Score=284.10  Aligned_cols=114  Identities=44%  Similarity=0.753  Sum_probs=111.8

Q ss_pred             CCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             33430012252189999179877999970899889974044435577543352037899999999999869819999997
Q gi|254780238|r    8 IRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVS   87 (129)
Q Consensus         8 ~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik   87 (129)
                      ..+|.+++++.|++||++|+|||||||||++||+++|+|+|++||||++|+||||||+++|.++++++++||+.|+|+++
T Consensus         3 ~~kk~k~~~~~Gi~hI~~t~NNTiitlTD~~Gn~l~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~a~~~Gi~~v~v~vk   82 (116)
T CHL00041          3 GSRKSKRKIPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGRRKGTPFAAQTAAENAIRTVIDQGMKRAEVMIK   82 (116)
T ss_pred             CCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEE
T ss_conf             65555555866799999447988999984999999998077311588876898899999999999999739849999997


Q ss_pred             CCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC
Q ss_conf             7998678887787636936999996388988886
Q gi|254780238|r   88 GLGAGRDSALRALRAIGFTIVSICDVTMIAHNGC  121 (129)
Q Consensus        88 G~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGc  121 (129)
                      |+|+||+++||+|+..||+|++|+|+||+|||||
T Consensus        83 G~G~GR~~aik~l~~~glkI~~I~D~TpiphNGC  116 (116)
T CHL00041         83 GPGLGRDTALRAIRRSGLKLSSIRDVTPMPHNGC  116 (116)
T ss_pred             CCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC
T ss_conf             8884589999999878988999998999999998


No 8  
>KOG0408 consensus
Probab=100.00  E-value=3.4e-39  Score=260.70  Aligned_cols=120  Identities=45%  Similarity=0.744  Sum_probs=115.9

Q ss_pred             CCCCEEEECCCEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             33430012252189999179877999970899889974044435577543352037899999999999869819999997
Q gi|254780238|r    8 IRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVS   87 (129)
Q Consensus         8 ~~~k~~~~i~~GiihI~~t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik   87 (129)
                      ...+..+++|  ++||++|+|||+||+||.+|.++.|+|||.+||+|++|+|++|||.++..+...++++|++.++|.+|
T Consensus        71 ~~g~~f~eiP--i~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrntrkgT~iAaQtaavaa~~r~v~~G~~~vrV~Vk  148 (190)
T KOG0408          71 FSGKNFREIP--IIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNTRKGTPIAAQTAAVAAIRRAVDQGMQTVRVRVK  148 (190)
T ss_pred             CCCCCCCCCC--EEEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEEE
T ss_conf             4786213054--68998537870899980688489885024201235666885067777789999999716369999984


Q ss_pred             CCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             799867888778763693699999638898888688886789
Q gi|254780238|r   88 GLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI  129 (129)
Q Consensus        88 G~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RRi  129 (129)
                      |+||||.+++++|...|+.|++|+|.||+|||||||+|+|||
T Consensus       149 GlGpGRmsa~kgl~m~Gl~vvsItD~Tp~~~ng~RPrK~Rrl  190 (190)
T KOG0408         149 GLGPGRMSALKGLRMGGLLVVSITDNTPMPHNGCRPRKKRRL  190 (190)
T ss_pred             CCCCCHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             588647888765521556999960688688789996412469


No 9  
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=100.00  E-value=1.4e-37  Score=250.90  Aligned_cols=104  Identities=44%  Similarity=0.582  Sum_probs=101.4

Q ss_pred             CEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEC--------
Q ss_conf             2189999179877999970899-8899740444355775433520378999999999998698199999977--------
Q gi|254780238|r   18 SGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG--------   88 (129)
Q Consensus        18 ~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG--------   88 (129)
                      +||+||++||||||||+||++| +++.|+|+|+++|++++|+||||||+++|.++++++++||+.|+|+++|        
T Consensus         2 ~Gi~hI~atfNNTiitvTD~~G~~~~~~ssgg~~~~~~~~K~Tp~AAq~aae~~a~~~~~~Gi~~v~V~ikG~G~n~~~~   81 (114)
T TIGR03628         2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS   81 (114)
T ss_pred             CEEEEEECCCCCEEEEEECCCCCEEEEEECCCCEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCC
T ss_conf             47999991689859999859999799996687465188877888999999999999999869849999999478787778


Q ss_pred             CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC
Q ss_conf             998678887787636936999996388988886
Q gi|254780238|r   89 LGAGRDSALRALRAIGFTIVSICDVTMIAHNGC  121 (129)
Q Consensus        89 ~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGc  121 (129)
                      +|||||++||+|+..||+|.+|.|+||+||||.
T Consensus        82 pGpGresAiral~~~Gl~I~~I~DvTPiPHNGt  114 (114)
T TIGR03628        82 PGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT  114 (114)
T ss_pred             CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCC
T ss_conf             986289999999868979999898799998988


No 10 
>KOG0407 consensus
Probab=99.89  E-value=9e-23  Score=160.21  Aligned_cols=114  Identities=36%  Similarity=0.512  Sum_probs=107.4

Q ss_pred             ECCCEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEC-----
Q ss_conf             2252189999179877999970899-8899740444355775433520378999999999998698199999977-----
Q gi|254780238|r   15 NIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG-----   88 (129)
Q Consensus        15 ~i~~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG-----   88 (129)
                      ..+.|++||++|||+||+++||+.| ++|...++||--....+.++||||+++++.++.+|+++||+.+++++++     
T Consensus        13 ~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh~klratgg~k   92 (139)
T KOG0407          13 EQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTK   92 (139)
T ss_pred             CEEEEEEEEEEECCCCEEEEECCCCCEEEEEEECCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEEEEECCCCC
T ss_conf             41335667664136616998615785688985076278604566886899998779999987628058999998238866


Q ss_pred             ---CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             ---9986788877876369369999963889888868888678
Q gi|254780238|r   89 ---LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR  128 (129)
Q Consensus        89 ---~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RR  128 (129)
                         +|||.++++|+|..+|++|-+|+|+||+|-.-.|.+.-||
T Consensus        93 tktpgpgaqsalralar~gmrigriedvtpip~d~trrkggrr  135 (139)
T KOG0407          93 TKTPGPGAQSALRALARSGMRIGRIEDVTPIPSDSTRRKGGRR  135 (139)
T ss_pred             CCCCCCCHHHHHHHHHHHCCEEEEECCCCCCCCCCHHHCCCCC
T ss_conf             6888963789999999715602101125558862011115745


No 11 
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=99.18  E-value=4.3e-11  Score=88.73  Aligned_cols=109  Identities=22%  Similarity=0.325  Sum_probs=97.6

Q ss_pred             EEEEEECCCCEEEEEECCCC--CEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHH
Q ss_conf             89999179877999970899--8899740444355775433520378999999999998698199999977998678887
Q gi|254780238|r   20 RAHVVSTFNNTRITITDPHG--NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSAL   97 (129)
Q Consensus        20 iihI~~t~NNTiitlTd~~G--n~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~i   97 (129)
                      .+-++.|+||.+.++.+..-  .+++.+-+|.+||......+.-.|+..+|.++++|+.+|+..++|.++-+- --+.++
T Consensus       101 ~~V~ttsKNNvhaqvvNkS~nyrTvfgsfAGnVG~~K~~qq~~kcAyRIGeniAkKcrRLGif~vdvkFRrim-Rve~vl  179 (214)
T PTZ00090        101 MLVLTTSKNNVHAQLVNRSKNYKTVFGSFAGNVGFTKKLQQSERCAYRIGENIAKKCKRLGIFAVDVKFRRIM-RVETVL  179 (214)
T ss_pred             EEEEECCCCCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEHHHHHHH-HHHHHH
T ss_conf             9999805774440110044440256531154210678876300689999889999988728221104689999-999999


Q ss_pred             HHHHHCCCEEEEEEECCCCCC---CCCCCCCCCCC
Q ss_conf             787636936999996388988---88688886789
Q gi|254780238|r   98 RALRAIGFTIVSICDVTMIAH---NGCRPRKRRRI  129 (129)
Q Consensus        98 k~l~~~glkI~~I~D~T~ip~---nGcRp~K~RRi  129 (129)
                      .++...||.|..|....++|-   |..||+++|||
T Consensus       180 qa~~a~~l~v~q~iheprlpk~g~n~~~pr~rrrv  214 (214)
T PTZ00090        180 QAFYANGLQVTQLIHEPRLPKTGLNSVRPRRRRRV  214 (214)
T ss_pred             HHHHHCCCCHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99997376246552377788667665684302469


No 12 
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e:  L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=97.60  E-value=0.001  Score=43.64  Aligned_cols=88  Identities=19%  Similarity=0.197  Sum_probs=69.1

Q ss_pred             CEEEEEEECCCCEEEEEECCC-CCEEEEECCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC-CH
Q ss_conf             218999917987799997089-98899740444355775--433520378999999999998698199999977998-67
Q gi|254780238|r   18 SGRAHVVSTFNNTRITITDPH-GNTIAWSSPKVVGFSGS--RKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA-GR   93 (129)
Q Consensus        18 ~GiihI~~t~NNTiitlTd~~-Gn~i~~~S~G~~gfkg~--kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~-GR   93 (129)
                      ...+.|+.|.+|+.+++.|.. +.+++.+|+-...+++.  ......||+.+++.+++++++.|+..+..-..|+-. ||
T Consensus        11 ~pRl~V~~Snk~i~aqiid~~~~~tl~sasT~~~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vvfDrg~~~yhgr   90 (103)
T cd00432          11 RPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRYHGR   90 (103)
T ss_pred             CCEEEEEEECCEEEEEEEECCCCCEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHH
T ss_conf             98899998189389999985999599999714065531236886299999999999999998799889986799976379


Q ss_pred             -HHHHHHHHHCCC
Q ss_conf             -888778763693
Q gi|254780238|r   94 -DSALRALRAIGF  105 (129)
Q Consensus        94 -~~~ik~l~~~gl  105 (129)
                       .+++.++...||
T Consensus        91 v~a~a~~~re~Gl  103 (103)
T cd00432          91 VKALAKGAREGGL  103 (103)
T ss_pred             HHHHHHHHHHCCC
T ss_conf             9999999998589


No 13 
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=97.25  E-value=0.0033  Score=40.52  Aligned_cols=87  Identities=21%  Similarity=0.247  Sum_probs=63.9

Q ss_pred             CEEEEEEECCCCEEEEEE-CCCCCEEEEECCCCCCCCCCCC--CCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC---
Q ss_conf             218999917987799997-0899889974044435577543--3520378999999999998698199999977998---
Q gi|254780238|r   18 SGRAHVVSTFNNTRITIT-DPHGNTIAWSSPKVVGFSGSRK--NSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA---   91 (129)
Q Consensus        18 ~GiihI~~t~NNTiitlT-d~~Gn~i~~~S~G~~gfkg~kk--~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~---   91 (129)
                      ...+.|+-|.+|...++. |..|.+|+.+|+=...++...+  ++-.||..+++.+++++++.||..| ++=+| |.   
T Consensus        15 rpRL~V~rSnkhiyaQiIDD~~g~tl~saST~~k~~~~~~~~~~n~e~A~~vG~~ia~~a~~~gI~~V-vFDRg-gy~YH   92 (109)
T CHL00139         15 RPRLSVFRSNKHIYAQIIDDTNGKTLVSCSTLDPDVKSNLSIGSTCDASKLVGQKLAKKSLKKGITKV-VFDRG-GKLYH   92 (109)
T ss_pred             CCEEEEEECCCEEEEEEEECCCCCEEEEEECCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCH
T ss_conf             88899997088189999987999899996233677765514786699999999999999998799999-98589-98422


Q ss_pred             CHH-HHHHHHHHCCCE
Q ss_conf             678-887787636936
Q gi|254780238|r   92 GRD-SALRALRAIGFT  106 (129)
Q Consensus        92 GR~-~~ik~l~~~glk  106 (129)
                      ||- ++--++...||+
T Consensus        93 GrVkalAd~aRe~GLk  108 (109)
T CHL00139         93 GRIKALAEAAREAGLQ  108 (109)
T ss_pred             HHHHHHHHHHHHCCCC
T ss_conf             1999999999984898


No 14 
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=97.17  E-value=0.0039  Score=40.07  Aligned_cols=86  Identities=23%  Similarity=0.240  Sum_probs=62.9

Q ss_pred             CCEEEEEEECCCCEEEEEECCC-CCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC---C
Q ss_conf             5218999917987799997089-98899740444355775433520378999999999998698199999977998---6
Q gi|254780238|r   17 VSGRAHVVSTFNNTRITITDPH-GNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA---G   92 (129)
Q Consensus        17 ~~GiihI~~t~NNTiitlTd~~-Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~---G   92 (129)
                      ....+.|+-|.+|..+.|.|.. |.+|+.+|+=...+++  ++.-.+|..+++.+++++.+.||+.| ++=+| |.   |
T Consensus        24 ~rpRL~VfrSnkhiyaQiIDD~~~~tl~saST~~k~~~~--~~n~~~A~~vG~~ia~~a~~~~I~~v-~FDR~-g~~YHG   99 (115)
T PRK05593         24 ERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDLKA--GGNKEAAKKVGKLIAERAKAKGIKQV-VFDRG-GYKYHG   99 (115)
T ss_pred             CCCEEEEEECCCEEEEEEEECCCCCEEEEEECCCHHHHC--CCCHHHHHHHHHHHHHHHHHCCCCEE-EECCC-CCCCCH
T ss_conf             986799996088279999986999799997414244416--88499999999999999998799889-98189-984223


Q ss_pred             HHHH-HHHHHHCCCE
Q ss_conf             7888-7787636936
Q gi|254780238|r   93 RDSA-LRALRAIGFT  106 (129)
Q Consensus        93 R~~~-ik~l~~~glk  106 (129)
                      |-.+ --++...||+
T Consensus       100 rvkalAd~aRe~Gl~  114 (115)
T PRK05593        100 RVKALADAAREAGLK  114 (115)
T ss_pred             HHHHHHHHHHHCCCC
T ss_conf             999999999984899


No 15 
>pfam00861 Ribosomal_L18p Ribosomal L18p/L5e family. This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of the rat 60S ribosomal protein L5 are necessary and sufficient to bind 5S rRNA in vitro. Suggesting that the entire family has a function in rRNA binding.
Probab=96.98  E-value=0.0057  Score=39.07  Aligned_cols=90  Identities=19%  Similarity=0.165  Sum_probs=64.1

Q ss_pred             CCEEEEEEECCCCEEEEEECCC-CCEEEEECCCCCCCCC----CCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC
Q ss_conf             5218999917987799997089-9889974044435577----5433520378999999999998698199999977998
Q gi|254780238|r   17 VSGRAHVVSTFNNTRITITDPH-GNTIAWSSPKVVGFSG----SRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA   91 (129)
Q Consensus        17 ~~GiihI~~t~NNTiitlTd~~-Gn~i~~~S~G~~gfkg----~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~   91 (129)
                      ....+.|+-|..|+.+.+.|.. +.++..+|+=...++.    ...+.-.||..+++.+++++++.|+..|..--.|+=.
T Consensus        22 ~rpRL~V~rSNkhiyaQiIdd~~~~tl~saSt~~k~lkk~~~k~~~~n~~aA~~vG~~ia~ka~~~gi~~v~fDR~g~~y  101 (119)
T pfam00861        22 ERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKKYGLKGGGNNTAAAYLVGLLLAKRALKKGIAVVVFDRGGYTY  101 (119)
T ss_pred             CCCEEEEEEECCEEEEEEEECCCCCEEEEEECCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
T ss_conf             99889999968948999998689988999973405677734446776499999999999999998799889983899844


Q ss_pred             -CH-HHHHHHHHHCCCE
Q ss_conf             -67-8887787636936
Q gi|254780238|r   92 -GR-DSALRALRAIGFT  106 (129)
Q Consensus        92 -GR-~~~ik~l~~~glk  106 (129)
                       || .++..++...||+
T Consensus       102 hGrvka~A~~aRe~Gl~  118 (119)
T pfam00861       102 HGRVFALAKGAREAGLN  118 (119)
T ss_pred             HHHHHHHHHHHHHCCCC
T ss_conf             59999999999983888


No 16 
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=95.81  E-value=0.099  Score=31.48  Aligned_cols=100  Identities=25%  Similarity=0.306  Sum_probs=73.2

Q ss_pred             EEEEEECCCCEEEEEEC--CCCC-EEEEECCC---CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--ECC--
Q ss_conf             89999179877999970--8998-89974044---43557754335203789999999999986981999999--779--
Q gi|254780238|r   20 RAHVVSTFNNTRITITD--PHGN-TIAWSSPK---VVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKV--SGL--   89 (129)
Q Consensus        20 iihI~~t~NNTiitlTd--~~Gn-~i~~~S~G---~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i--kG~--   89 (129)
                      .+-|..|.+++++.+..  +.|+ +++.+.+-   ..|.++..+++| ||+.++-.++.++.+.|+.+..+-+  .-+  
T Consensus        34 R~VVR~TN~~ii~Qiv~~~~~GD~v~~sa~s~eL~kyG~k~~~~N~p-AaYltGlL~gkral~~G~~eaiLDiGL~~~t~  112 (193)
T PRK08569         34 RLVVRKTNKHVIAQIVKYDPKGDRTLASAHSKELAKYGWKGDTGNTP-AAYLTGLLAGKKALKAGVEEAVLDIGLHRPTK  112 (193)
T ss_pred             EEEEEECCCCEEEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCCCCH-HHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC
T ss_conf             59999738847999998607898999997652375568478877208-99998999999999749763798405664655


Q ss_pred             CCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             9867888778763693699999638898888688886789
Q gi|254780238|r   90 GAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI  129 (129)
Q Consensus        90 G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~RRi  129 (129)
                      |.---+++|+....|+.         |||+--+-|..-||
T Consensus       113 G~rvfaalKGavDaGl~---------IPh~e~~fP~~dRi  143 (193)
T PRK08569        113 GSRVFAALKGAVDAGLE---------VPHGEEVLPDEDRI  143 (193)
T ss_pred             CCCHHHHHHCCCCCCCC---------CCCCCCCCCCHHHC
T ss_conf             62068866323245611---------67987768863231


No 17 
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=95.78  E-value=0.12  Score=30.95  Aligned_cols=90  Identities=18%  Similarity=0.145  Sum_probs=66.0

Q ss_pred             CEEEEEEECCCCEEEEEECCCC-CEEEEECCCCCCCCC--C--CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC-
Q ss_conf             2189999179877999970899-889974044435577--5--433520378999999999998698199999977998-
Q gi|254780238|r   18 SGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSG--S--RKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA-   91 (129)
Q Consensus        18 ~GiihI~~t~NNTiitlTd~~G-n~i~~~S~G~~gfkg--~--kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~-   91 (129)
                      ...+.|+-|.+|.++.+.|... -++..+|+=...+++  .  ..+.-.||..+++.+++++++.|++.+.+=..|+=+ 
T Consensus        29 rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr~g~~yh  108 (125)
T COG0256          29 RPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGGYKYH  108 (125)
T ss_pred             CCEEEEEEECCCEEEEEEECCCCCEEEEEECCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCC
T ss_conf             95799998089389999974899669998713677764032578987899999999999999985995899838988651


Q ss_pred             CH-HHHHHHHHHCCCEE
Q ss_conf             67-88877876369369
Q gi|254780238|r   92 GR-DSALRALRAIGFTI  107 (129)
Q Consensus        92 GR-~~~ik~l~~~glkI  107 (129)
                      || .++..+....||++
T Consensus       109 gRV~Ala~~AreaGL~f  125 (125)
T COG0256         109 GRVAALADGAREAGLEF  125 (125)
T ss_pred             HHHHHHHHHHHHCCCCC
T ss_conf             19999999999729679


No 18 
>TIGR00060 L18_bact ribosomal protein L18; InterPro: IPR004389   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This is the ribosomal protein L18 family. The archaebacterial and eukaryotic type rpL18 is not included in this family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=93.72  E-value=0.51  Score=27.13  Aligned_cols=89  Identities=19%  Similarity=0.168  Sum_probs=62.2

Q ss_pred             EEEEEEECCCCEEEEEECCCCC-EEEEECCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC-CHH
Q ss_conf             1899991798779999708998-8997404443557--75433520378999999999998698199999977998-678
Q gi|254780238|r   19 GRAHVVSTFNNTRITITDPHGN-TIAWSSPKVVGFS--GSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGA-GRD   94 (129)
Q Consensus        19 GiihI~~t~NNTiitlTd~~Gn-~i~~~S~G~~gfk--g~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~-GR~   94 (129)
                      ..+.|+-|.++....+-|..++ ||..+|+=....+  =.-.++..+|..+++.+|+++.++||..|.-==.|+=+ ||-
T Consensus        25 prl~VfrS~~hiYAQvIDd~~~~tlas~Stl~~~l~~~~~~~~n~~~a~~vG~~~A~rl~~kgi~~vvFDR~G~~YHGrv  104 (118)
T TIGR00060        25 PRLVVFRSNRHIYAQVIDDVKQVTLASASTLEKKLKEQLKSTGNKDAAKKVGKLVAERLIKKGINDVVFDRGGYKYHGRV  104 (118)
T ss_pred             CEEEEEEECCCEEEEEEECCCCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHH
T ss_conf             36899861681789999858884787315566887765103789889999999999999972772268526996223389


Q ss_pred             HHHH-HHHHCCCEE
Q ss_conf             8877-876369369
Q gi|254780238|r   95 SALR-ALRAIGFTI  107 (129)
Q Consensus        95 ~~ik-~l~~~glkI  107 (129)
                      +++- ++...||++
T Consensus       105 ~ALAeaaRE~Gl~f  118 (118)
T TIGR00060       105 AALAEAAREAGLNF  118 (118)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999999700359


No 19 
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=87.91  E-value=1.5  Score=24.30  Aligned_cols=67  Identities=15%  Similarity=0.158  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             57754335203789999999999986981999999779986788877876369369999963889888
Q gi|254780238|r   52 FSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        52 fkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      -.|+...|-+-...+++.+++.. ...++...|.+.|||.--..+-+-|...|.+|+-|.|.+.--||
T Consensus        10 s~gR~eATG~Gv~~~~~~~~~~~-~~~l~g~~vaIQGfGnVG~~aA~~l~e~GakvVaVsD~~G~i~~   76 (254)
T cd05313          10 SLIRPEATGYGLVYFVEEMLKDR-NETLKGKRVAISGSGNVAQYAAEKLLELGAKVVTLSDSKGYVYD   76 (254)
T ss_pred             CCCCCCEEHHHHHHHHHHHHHHC-CCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEEEC
T ss_conf             86877501088999999999967-96958999999897799999999999779979999857850887


No 20 
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids 
Probab=87.54  E-value=1.6  Score=24.09  Aligned_cols=65  Identities=23%  Similarity=0.311  Sum_probs=51.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCC
Q ss_conf             557754335203789999999999986981999999779986788877876369369999963889
Q gi|254780238|r   51 GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMI  116 (129)
Q Consensus        51 gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~i  116 (129)
                      |-.++...|-|-...+.+.+++.. ..+++...|.+.|||.=-..+.+-|...|-+|+.|.|.+..
T Consensus         2 Gs~gR~eATG~Gv~~~~~~~l~~~-~~~l~g~~v~IqG~GnVG~~~a~~L~~~Gakvv~vsD~~G~   66 (227)
T cd01076           2 GSLGREEATGRGVAYATREALKKL-GIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAVSDSDGT   66 (227)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHC-CCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCE
T ss_conf             999997332889999999999976-98978999999898899999999999879959999847873


No 21 
>pfam00208 ELFV_dehydrog Glutamate/Leucine/Phenylalanine/Valine dehydrogenase.
Probab=84.96  E-value=2  Score=23.45  Aligned_cols=67  Identities=16%  Similarity=0.245  Sum_probs=49.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             7754335203789999999999986981999999779986788877876369369999963889888
Q gi|254780238|r   53 SGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        53 kg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      .|+...|-|-...+.+.+++..-.-.++...|.+.|||.=-..+.+-|...|.+|+.+.|.+..-||
T Consensus         4 ~gR~eATg~Gv~~~~~~~~~~~~~~~l~g~~v~IqGfGnVG~~~a~~l~~~GakvvavsD~~G~i~~   70 (237)
T pfam00208         4 LGRPEATGYGVVYFVEEALKKLGGDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVAVSDSSGYIYD   70 (237)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEEEC
T ss_conf             9998341899999999999974999878999999898899999999999879969999828767999


No 22 
>TIGR01418 PEP_synth phosphoenolpyruvate synthase; InterPro: IPR006319   This family represents phosphoenolpyruvate synthase; also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. ; GO: 0008986 pyruvate water dikinase activity, 0006094 gluconeogenesis.
Probab=84.39  E-value=1.1  Score=25.19  Aligned_cols=58  Identities=16%  Similarity=0.346  Sum_probs=41.9

Q ss_pred             CCCCCCCCCCCCC--CH-HHHHHHHHHHHHH-HCCCCEEEEEE---ECCCCCHHHHHHHHHHCCCE
Q ss_conf             4435577543352--03-7899999999999-86981999999---77998678887787636936
Q gi|254780238|r   48 KVVGFSGSRKNSP--FA-AQVATDDCSAKAQ-NHGMSSLEVKV---SGLGAGRDSALRALRAIGFT  106 (129)
Q Consensus        48 G~~gfkg~kk~t~--~A-a~~~a~~~~~~~~-~~gi~~v~v~i---kG~G~GR~~~ik~l~~~glk  106 (129)
                      -|+||+|++|--.  |. |+.+=-++.++++ ++|+++|.|.|   |-+--|+. ++..|...||+
T Consensus       685 PMlG~RGasRY~s~~y~eaF~lE~~A~k~VR~eMGLtNV~vMiPFvRT~~E~~r-v~~im~~~GL~  749 (877)
T TIGR01418       685 PMLGWRGASRYYSESYEEAFRLECKAIKRVREEMGLTNVEVMIPFVRTPEEGKR-VLEIMAEEGLK  749 (877)
T ss_pred             CCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHH-HHHHHHHCCCC
T ss_conf             783324404026766047999999999988765085133113575488899999-99999972888


No 23 
>PTZ00079 NADP-specific glutamate dehydrogenase; Provisional
Probab=82.84  E-value=4.3  Score=21.45  Aligned_cols=77  Identities=14%  Similarity=0.199  Sum_probs=56.2

Q ss_pred             CCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCC
Q ss_conf             89988997404443557754335203789999999999986981999999779986788877876369369999963889
Q gi|254780238|r   37 PHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMI  116 (129)
Q Consensus        37 ~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~i  116 (129)
                      +.|+.+.|  +|+   .++..+|-|-....++.+++. ....++.-.|.+.|||+=-..+.+-|...|-+|+.+.|....
T Consensus       214 vTGKp~~~--GGs---~gR~eATG~G~vy~~~e~l~~-~~~~l~gk~vaIqGfGNVg~~aA~kl~e~GakVVavSDs~G~  287 (469)
T PTZ00079        214 LTGKNVKW--GGS---NIRPEATGYGAVYFVEEVLKS-LNIVVEKKTAVVSGSGNVAQYCVEKLLQLGAKVLTLSDSNGY  287 (469)
T ss_pred             EECCCCCC--CCC---CCCCCCHHHHHHHHHHHHHHH-CCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCE
T ss_conf             71887100--686---786762428899999999986-799857888999766738999999999769989999838943


Q ss_pred             CCC
Q ss_conf             888
Q gi|254780238|r  117 AHN  119 (129)
Q Consensus       117 p~n  119 (129)
                      -||
T Consensus       288 Iy~  290 (469)
T PTZ00079        288 IVE  290 (469)
T ss_pred             EEC
T ss_conf             988


No 24 
>PRK09414 glutamate dehydrogenase; Provisional
Probab=81.65  E-value=4.8  Score=21.18  Aligned_cols=76  Identities=13%  Similarity=0.166  Sum_probs=55.1

Q ss_pred             CCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCC
Q ss_conf             99889974044435577543352037899999999999869819999997799867888778763693699999638898
Q gi|254780238|r   38 HGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIA  117 (129)
Q Consensus        38 ~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip  117 (129)
                      .|+.+.|  +|++   ++...|-|-....++.+++. ....++.-.|.+.|||.=-..+.+-|...|-+|+.+.|.+..-
T Consensus       192 TGKp~~~--GGs~---gR~eATG~Gv~y~~~e~l~~-~g~~l~gk~v~IqGfGNVg~~aA~~l~e~GakvVavSDs~G~I  265 (446)
T PRK09414        192 TGKGLSF--GGSL---IRPEATGYGLVYFAEEMLKA-RGDSFEGKTVVVSGSGNVAIYAIEKAMELGAKVVTCSDSSGYV  265 (446)
T ss_pred             CCCCCCC--CCCC---CCCCCHHHHHHHHHHHHHHH-CCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEE
T ss_conf             8997210--6886---87653228999999999997-4999578879997777799999999997699799998378607


Q ss_pred             CC
Q ss_conf             88
Q gi|254780238|r  118 HN  119 (129)
Q Consensus       118 ~n  119 (129)
                      ||
T Consensus       266 y~  267 (446)
T PRK09414        266 YD  267 (446)
T ss_pred             EC
T ss_conf             88


No 25 
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms.  Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent.  As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=69.60  E-value=10  Score=19.19  Aligned_cols=56  Identities=20%  Similarity=0.203  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             789999999999986981999999779986788877876369369999963889888
Q gi|254780238|r   63 AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        63 a~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      ...+.+.+++. ....++...|.+.|||.=-..+.+-|...|.+|+.|.|.+.--||
T Consensus         6 v~~~~~~a~~~-~~~~l~g~~vaVqGfGnVG~~~a~~l~~~GakvvavsD~~G~i~~   61 (217)
T cd05211           6 VVVAMKAAMKH-LGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYD   61 (217)
T ss_pred             HHHHHHHHHHH-CCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCEEEC
T ss_conf             99999999997-696857999999898899999999999859989999857871778


No 26 
>pfam00044 Gp_dh_N Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.
Probab=57.05  E-value=13  Score=18.45  Aligned_cols=16  Identities=13%  Similarity=0.154  Sum_probs=7.2

Q ss_pred             HHCCCCEEEEEEECCCCC
Q ss_conf             986981999999779986
Q gi|254780238|r   75 QNHGMSSLEVKVSGLGAG   92 (129)
Q Consensus        75 ~~~gi~~v~v~ikG~G~G   92 (129)
                      .+.|.+.|.|  .+|.+.
T Consensus       108 l~~GaKkVii--SaP~~d  123 (150)
T pfam00044       108 LKAGAKKVII--SAPAKD  123 (150)
T ss_pred             HHCCCCEEEE--ECCCCC
T ss_conf             7579877999--579988


No 27 
>smart00846 Gp_dh_N Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.
Probab=56.38  E-value=12  Score=18.64  Aligned_cols=16  Identities=13%  Similarity=0.167  Sum_probs=8.4

Q ss_pred             HHCCCCEEEEEEECCCCC
Q ss_conf             986981999999779986
Q gi|254780238|r   75 QNHGMSSLEVKVSGLGAG   92 (129)
Q Consensus        75 ~~~gi~~v~v~ikG~G~G   92 (129)
                      .+.|.+.|  ++.+|.+.
T Consensus       108 l~~gakkV--iisaP~~d  123 (149)
T smart00846      108 LKAGAKKV--IISAPAKD  123 (149)
T ss_pred             HHCCCCEE--EECCCCCC
T ss_conf             64796769--98279889


No 28 
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=55.86  E-value=18  Score=17.64  Aligned_cols=87  Identities=21%  Similarity=0.198  Sum_probs=55.5

Q ss_pred             EEEEEECCCCEEEEEECC-CCCEEEEECC---------CCCCCCCC-----CCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             899991798779999708-9988997404---------44355775-----43352037899999999999869819999
Q gi|254780238|r   20 RAHVVSTFNNTRITITDP-HGNTIAWSSP---------KVVGFSGS-----RKNSPFAAQVATDDCSAKAQNHGMSSLEV   84 (129)
Q Consensus        20 iihI~~t~NNTiitlTd~-~Gn~i~~~S~---------G~~gfkg~-----kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v   84 (129)
                      .+-|+-|.|-...|+.|- .-.+++..++         |..--|..     .-++-.||+.+++.++++|.+.||+.|..
T Consensus       107 Rl~iK~Tnn~iyAtIvDDy~r~vlCf~cs~~~~lS~I~Gty~~k~tnr~~nnGg~i~aA~eVGk~IakkA~~kGI~~VvF  186 (211)
T PTZ00032        107 RLTLKNTNNQMYATIVDDYTRYVLCFTCTNFKYLSHIFGTYPTKATNRVRNNGGTIKAAYELGKLIGRKALSKGISKVRF  186 (211)
T ss_pred             CEEEECCCCEEEEEEECCCCCEEEEEECCCCCHHHHHHCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             06875267736787730200057999625882176663466666767375589765999999999999999879988998


Q ss_pred             EEECCCC-CHHHHHH-HHHHCCCE
Q ss_conf             9977998-6788877-87636936
Q gi|254780238|r   85 KVSGLGA-GRDSALR-ALRAIGFT  106 (129)
Q Consensus        85 ~ikG~G~-GR~~~ik-~l~~~glk  106 (129)
                      -=.|+=. ||-.++- +-...||+
T Consensus       187 DRggy~YHGRVkALAe~ARe~GL~  210 (211)
T PTZ00032        187 DRAHYKYAGKVEALAEGARAVGLQ  210 (211)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             799973202899999999971889


No 29 
>pfam07733 DNA_pol3_alpha Bacterial DNA polymerase III alpha subunit.
Probab=49.97  E-value=13  Score=18.41  Aligned_cols=46  Identities=28%  Similarity=0.409  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             789999999999986981999999779986788877876369369999963889888
Q gi|254780238|r   63 AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        63 a~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      .+++...+.+.|++.||-        .||||-++--+|..-   ..-|+|+-|++||
T Consensus        40 YFLiv~d~v~~a~~~gi~--------vgpgRGSaagSlV~y---~LgIT~vDPi~~~   85 (381)
T pfam07733        40 YFLIVWDLVKWAKDNGIP--------VGPGRGSAAGSLVAY---LLGITEVDPLKHD   85 (381)
T ss_pred             CHHHHHHHHHHHHHCCCE--------ECCCCCCHHHHHHHH---HHCCCCCCCCCCC
T ss_conf             479999999999987961--------379987379999999---8568240863147


No 30 
>PRK08356 hypothetical protein; Provisional
Probab=48.83  E-value=23  Score=16.95  Aligned_cols=27  Identities=11%  Similarity=0.409  Sum_probs=13.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHCCCEEEEEE
Q ss_conf             99997799867888778763693699999
Q gi|254780238|r   83 EVKVSGLGAGRDSALRALRAIGFTIVSIC  111 (129)
Q Consensus        83 ~v~ikG~G~GR~~~ik~l~~~glkI~~I~  111 (129)
                      .+++.|.-.-  .=+..|.+.+..++.|.
T Consensus        96 ~vVIdgiR~~--~Eve~lk~~~~~lI~V~  122 (195)
T PRK08356         96 NIAIDGVRSR--GEVEAIKRMGGKVIYVE  122 (195)
T ss_pred             CEEEECCCCH--HHHHHHHHCCCEEEEEE
T ss_conf             7899489988--99999996599799996


No 31 
>TIGR00423 TIGR00423 conserved hypothetical protein TIGR00423; InterPro: IPR005244    This entry describes a family of conserved hypothetical proteins with no known function. .
Probab=48.69  E-value=13  Score=18.54  Aligned_cols=58  Identities=21%  Similarity=0.302  Sum_probs=40.5

Q ss_pred             CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH---CCCCEEEEEEECCCCC
Q ss_conf             8779999708998899740444355775433520378999999999998---6981999999779986
Q gi|254780238|r   28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQN---HGMSSLEVKVSGLGAG   92 (129)
Q Consensus        28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~---~gi~~v~v~ikG~G~G   92 (129)
                      +|..|-.||     |+..-|.-|-|+..++. ..|..+-.+.+.+|+.+   .|.++|.+. -|..|.
T Consensus         5 VNRNINfTN-----IC~~~C~FCAF~~~~k~-~~~Y~Ls~eEI~~Kv~ea~~~G~tE~~iQ-GGlnP~   65 (331)
T TIGR00423         5 VNRNINFTN-----ICVGKCKFCAFRRREKD-KDAYVLSLEEILRKVKEAVAKGATEICIQ-GGLNPQ   65 (331)
T ss_pred             CCCCCCCCH-----HHHHCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHCCCEEEEEE-CCCCCC
T ss_conf             166567530-----02324796331134689-88814077999999999997198278852-342788


No 32 
>PRK07012 consensus
Probab=45.46  E-value=15  Score=18.07  Aligned_cols=23  Identities=13%  Similarity=0.143  Sum_probs=13.7

Q ss_pred             EEECCCC--EEEEEECCCC--CEEEEE
Q ss_conf             9917987--7999970899--889974
Q gi|254780238|r   23 VVSTFNN--TRITITDPHG--NTIAWS   45 (129)
Q Consensus        23 I~~t~NN--TiitlTd~~G--n~i~~~   45 (129)
                      ...|++.  .|+||-|..|  +++.|.
T Consensus       997 ~~~tk~G~maf~tleD~tg~~ev~vfp 1023 (1173)
T PRK07012        997 TQMTQRGKMVIALLDDGTGQCEITVFN 1023 (1173)
T ss_pred             ECCCCCCCEEEEEEEECCCCEEEEECH
T ss_conf             788887778999999799878999978


No 33 
>COG0334 GdhA Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]
Probab=43.71  E-value=28  Score=16.47  Aligned_cols=65  Identities=20%  Similarity=0.258  Sum_probs=46.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             754335203789999999999986981999999779986788877876369369999963889888
Q gi|254780238|r   54 GSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        54 g~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      ++...|.|-.....+ .+.+....++....|-+.|+|.=-..+.+-|...|-+|+.+.|....-||
T Consensus       181 ~r~~aTg~Gv~~~~~-~a~~~~g~~l~G~rVaVQG~GNVg~~aa~~l~~~GAkvv~~sds~g~i~~  245 (411)
T COG0334         181 GRSEATGYGVFYAIR-EALKALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAVSDSKGGIYD  245 (411)
T ss_pred             CCCCCCCEEEHHHHH-HHHHHCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCCEEC
T ss_conf             998651033079999-99998177768878999776289999999999749979999767884416


No 34 
>PRK08744 consensus
Probab=43.62  E-value=18  Score=17.63  Aligned_cols=11  Identities=18%  Similarity=0.401  Sum_probs=8.0

Q ss_pred             EEEEEECCCCC
Q ss_conf             79999708998
Q gi|254780238|r   30 TRITITDPHGN   40 (129)
Q Consensus        30 TiitlTd~~Gn   40 (129)
                      .|+||-|..|.
T Consensus      1044 af~tleD~tg~ 1054 (1195)
T PRK08744       1044 VFVQLEDGRGR 1054 (1195)
T ss_pred             EEEEEEECCCC
T ss_conf             99999968973


No 35 
>PRK08957 consensus
Probab=42.82  E-value=16  Score=17.96  Aligned_cols=17  Identities=24%  Similarity=0.231  Sum_probs=12.3

Q ss_pred             EECCCC---EEEEEECCCCC
Q ss_conf             917987---79999708998
Q gi|254780238|r   24 VSTFNN---TRITITDPHGN   40 (129)
Q Consensus        24 ~~t~NN---TiitlTd~~Gn   40 (129)
                      ..|+++   .|+|+-|..|.
T Consensus      1005 ~~tkkg~~maf~~leD~tg~ 1024 (1159)
T PRK08957       1005 MVTKRGNRIGICTLDDRSGR 1024 (1159)
T ss_pred             CCCCCCCEEEEEEEEECCCC
T ss_conf             57899898899999989986


No 36 
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=42.56  E-value=17  Score=17.77  Aligned_cols=12  Identities=42%  Similarity=0.722  Sum_probs=4.9

Q ss_pred             HHCCCEEEEEEE
Q ss_conf             636936999996
Q gi|254780238|r  101 RAIGFTIVSICD  112 (129)
Q Consensus       101 ~~~glkI~~I~D  112 (129)
                      ...++.++...|
T Consensus       195 ~~~~iplVATnd  206 (874)
T PRK09532        195 RELGIKIVATND  206 (874)
T ss_pred             HHHCCCEEECCC
T ss_conf             981999886186


No 37 
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=41.16  E-value=14  Score=18.36  Aligned_cols=10  Identities=10%  Similarity=0.321  Sum_probs=5.1

Q ss_pred             EEEEEECCCC
Q ss_conf             7999970899
Q gi|254780238|r   30 TRITITDPHG   39 (129)
Q Consensus        30 TiitlTd~~G   39 (129)
                      .|+||.|..|
T Consensus       908 af~tleD~tg  917 (1033)
T PRK07279        908 AFLSVNDTKK  917 (1033)
T ss_pred             EEEEEEECCC
T ss_conf             9999998998


No 38 
>PRK08444 hypothetical protein; Provisional
Probab=41.15  E-value=19  Score=17.54  Aligned_cols=68  Identities=15%  Similarity=0.228  Sum_probs=39.4

Q ss_pred             CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH---HHCCCCEEEEEEECCCCCH-----HHHHHH
Q ss_conf             87799997089988997404443557754335203789999999999---9869819999997799867-----888778
Q gi|254780238|r   28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKA---QNHGMSSLEVKVSGLGAGR-----DSALRA   99 (129)
Q Consensus        28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~---~~~gi~~v~v~ikG~G~GR-----~~~ik~   99 (129)
                      .|.+|.+|+     ++..+|+-|+|... ...+.|.....+.+.+++   .+.|.++|.+. -|..|--     +-.++.
T Consensus        49 ~n~~IN~TN-----iC~~~C~FCaF~r~-~~~~~aY~ls~eei~~~~~ea~~~G~tev~i~-GG~~P~~~~eyY~~l~r~  121 (353)
T PRK08444         49 INRHINPTN-----ICADVCKFCAFSAH-RKNPNPYTMSHEEILEIVKESVKRGIKEVHIV-SAHNPNYGYQWYLEIFKM  121 (353)
T ss_pred             ECCCCCCCC-----CCCCCCCCCCCCCC-CCCCCCEECCHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCHHHHHHHHHH
T ss_conf             205745664-----45688856756168-99998766699999999999997598789981-475989975889999999


Q ss_pred             HHH
Q ss_conf             763
Q gi|254780238|r  100 LRA  102 (129)
Q Consensus       100 l~~  102 (129)
                      +..
T Consensus       122 ik~  124 (353)
T PRK08444        122 IKE  124 (353)
T ss_pred             HHH
T ss_conf             998


No 39 
>pfam08901 DUF1847 Protein of unknown function (DUF1847). This family of proteins are functionally uncharacterized. THey contain 4 N-terminal cysteines that may form a zinc binding domain.
Probab=39.59  E-value=32  Score=16.07  Aligned_cols=54  Identities=19%  Similarity=0.340  Sum_probs=41.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEEEEE-ECCCCCHHHHHHHHHHCCCEEEEEE
Q ss_conf             35203789999999999986981999999-7799867888778763693699999
Q gi|254780238|r   58 NSPFAAQVATDDCSAKAQNHGMSSLEVKV-SGLGAGRDSALRALRAIGFTIVSIC  111 (129)
Q Consensus        58 ~t~~Aa~~~a~~~~~~~~~~gi~~v~v~i-kG~G~GR~~~ik~l~~~glkI~~I~  111 (129)
                      +..|.-..=.|.+.+.|+.+|++.+=|-+ -|+-.-.+.+.+.|...||.+.++.
T Consensus        34 ~~~Y~~~tRvEEii~FAk~mgykkiGiAfCiGL~~Ea~~~~~il~~~gFev~sV~   88 (157)
T pfam08901        34 GEGYGKLTRVEEIIEFAKRMGYKKIGIAFCIGLLNEARILAKILKAKGFEVYSVC   88 (157)
T ss_pred             HHHCCCHHHHHHHHHHHHHCCCCEEEEHHHHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             8641205659999999998599755302237389999999999997898898888


No 40 
>PRK06658 consensus
Probab=39.22  E-value=19  Score=17.50  Aligned_cols=22  Identities=18%  Similarity=0.243  Sum_probs=13.7

Q ss_pred             EEECCCC---EEEEEECCCCC--EEEE
Q ss_conf             9917987---79999708998--8997
Q gi|254780238|r   23 VVSTFNN---TRITITDPHGN--TIAW   44 (129)
Q Consensus        23 I~~t~NN---TiitlTd~~Gn--~i~~   44 (129)
                      ...|+++   .|+|+-|..|.  ++.|
T Consensus       992 ~~~tk~g~~maf~~leD~tg~~e~~~f 1018 (1145)
T PRK06658        992 VIQTKRGAKMAFGVFEDLKGAIDIVVF 1018 (1145)
T ss_pred             ECCCCCCCEEEEEEEEECCCCEEEEEC
T ss_conf             435799997899999968986899997


No 41 
>TIGR01534 GAPDH-I glyceraldehyde-3-phosphate dehydrogenase, type I; InterPro: IPR006424   This group of sequences represent glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilise NAD (1.2.1.12 from EC), NADP (1.2.1.13 from EC) or either (1.2.1.59 from EC). In some species, NAD- and NADP- utilising forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively . An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine . This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria . This enzyme is described by IPR006422 from INTERPRO. These two groups of sequences exhibit a close evolutionary relationship. There exists the possibility that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to possess a limited E4PD activity as well as a robust GAPDH activity ).; GO: 0008943 glyceraldehyde-3-phosphate dehydrogenase activity, 0051287 NAD binding, 0006006 glucose metabolic process.
Probab=38.25  E-value=33  Score=16.05  Aligned_cols=32  Identities=41%  Similarity=0.631  Sum_probs=22.1

Q ss_pred             EEEEECCCC-CHHHHHHH-HHHC----CCEE-EEEEEC-CC
Q ss_conf             999977998-67888778-7636----9369-999963-88
Q gi|254780238|r   83 EVKVSGLGA-GRDSALRA-LRAI----GFTI-VSICDV-TM  115 (129)
Q Consensus        83 ~v~ikG~G~-GR~~~ik~-l~~~----glkI-~~I~D~-T~  115 (129)
                      .|-|.|||. ||. ++|. +...    .|+| .-|-|. +-
T Consensus         1 kvgINGFGRIGRl-vlR~~~~~~~~g~~~~viv~inD~~~~   40 (366)
T TIGR01534         1 KVGINGFGRIGRL-VLRAILEKQGSGLDLEVIVAINDLSTD   40 (366)
T ss_pred             CEEEECCCHHHHH-HHHHHHCCCCCCCEEEEEEEECCCCCC
T ss_conf             9365147858999-999985057889705899831488768


No 42 
>PRK06115 dihydrolipoamide dehydrogenase; Reviewed
Probab=37.01  E-value=32  Score=16.13  Aligned_cols=45  Identities=16%  Similarity=0.023  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEECC--CC-----CHHHHHHHHHHCCCEEE
Q ss_conf             789999999999986981999999779--98-----67888778763693699
Q gi|254780238|r   63 AQVATDDCSAKAQNHGMSSLEVKVSGL--GA-----GRDSALRALRAIGFTIV  108 (129)
Q Consensus        63 a~~~a~~~~~~~~~~gi~~v~v~ikG~--G~-----GR~~~ik~l~~~glkI~  108 (129)
                      +-.++-.+++....+|. .|.+.-++.  -+     -.+.+.+.|...|++|.
T Consensus       182 gG~ig~E~A~~~~~lG~-~Vtlv~~~~~lL~~~D~~~~~~l~~~l~~~gi~i~  233 (466)
T PRK06115        182 AGVIGLELGSVWRRLGA-QVTVVEYLDRICPGTDGETAKTLQKALAKQGMRFK  233 (466)
T ss_pred             CCHHHHHHHHHHHHCCC-EEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCEEE
T ss_conf             85899999999986198-47899833421434341236888889987694999


No 43 
>PRK09074 consensus
Probab=36.71  E-value=18  Score=17.57  Aligned_cols=18  Identities=22%  Similarity=0.362  Sum_probs=11.5

Q ss_pred             EEECCCC---EEEEEECCCCC
Q ss_conf             9917987---79999708998
Q gi|254780238|r   23 VVSTFNN---TRITITDPHGN   40 (129)
Q Consensus        23 I~~t~NN---TiitlTd~~Gn   40 (129)
                      ...|++.   .|+||.|..|.
T Consensus      1001 ~~~tk~G~~maf~tleD~tg~ 1021 (1149)
T PRK09074       1001 ERKTKTGNKMGIVQLSDPTGQ 1021 (1149)
T ss_pred             ECCCCCCCEEEEEEEEECCCC
T ss_conf             535899997899999979985


No 44 
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=36.60  E-value=26  Score=16.64  Aligned_cols=11  Identities=18%  Similarity=0.601  Sum_probs=4.4

Q ss_pred             HCCCEEEEEEE
Q ss_conf             36936999996
Q gi|254780238|r  102 AIGFTIVSICD  112 (129)
Q Consensus       102 ~~glkI~~I~D  112 (129)
                      ..|+.++.--|
T Consensus       198 ~~~iplVATnd  208 (1171)
T PRK07374        198 ELGIKLIATND  208 (1171)
T ss_pred             HHCCCEEEECC
T ss_conf             80979899688


No 45 
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=36.31  E-value=30  Score=16.31  Aligned_cols=22  Identities=23%  Similarity=0.338  Sum_probs=13.0

Q ss_pred             EEECCCC---EEEEEECCCCC--EEEE
Q ss_conf             9917987---79999708998--8997
Q gi|254780238|r   23 VVSTFNN---TRITITDPHGN--TIAW   44 (129)
Q Consensus        23 I~~t~NN---TiitlTd~~Gn--~i~~   44 (129)
                      ...|+++   .|+|+.|..|.  ++.|
T Consensus       993 ~~~TkkG~~maf~tleD~tg~~e~vvf 1019 (1143)
T PRK05673        993 VRVTKRGNKMAIVTLEDRSGRIEVMLF 1019 (1143)
T ss_pred             ECCCCCCCEEEEEEEEECCCCEEEEEC
T ss_conf             511799898999999989984899997


No 46 
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=35.39  E-value=38  Score=15.67  Aligned_cols=105  Identities=18%  Similarity=0.108  Sum_probs=68.2

Q ss_pred             CEEEECCCEEEEEEECCCCEEEEEEC--CCCCEE-EEECC---CCCCCCCCCCCCCCHHHHHHHHHHHHHHHC-CC----
Q ss_conf             30012252189999179877999970--899889-97404---443557754335203789999999999986-98----
Q gi|254780238|r   11 RERKNIVSGRAHVVSTFNNTRITITD--PHGNTI-AWSSP---KVVGFSGSRKNSPFAAQVATDDCSAKAQNH-GM----   79 (129)
Q Consensus        11 k~~~~i~~GiihI~~t~NNTiitlTd--~~Gn~i-~~~S~---G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~-gi----   79 (129)
                      |.+-.-|+..+-|..|..++++.+..  ..|+.+ +.+.+   -..|++..-.+.+ ||+.++-.++..+... |+    
T Consensus        41 knKyntpKyRlVVR~TN~~iicQiv~a~~~GD~v~~aA~s~EL~kyG~k~gltNya-AAY~TGlLlarR~L~kl~ld~~y  119 (300)
T PTZ00069         41 KNKYNSPKYRLVVRITNKDIICQIVYAKIVGDKVVAAAYSHELPRFGIPVGLTNYA-AAYATGLLLARRTLKKLKLADKF  119 (300)
T ss_pred             CCCCCCCCCEEEEEEECCEEEEEEEEECCCCCEEEEEEECCHHHHCCCCCCCCCHH-HHHHHHHHHHHHHHHHCCCHHHH
T ss_conf             02358987449999877828999998506898999985112042358878877408-99998999999999860622331


Q ss_pred             ---CE------------------EEEEEE-C-----CCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCC
Q ss_conf             ---19------------------999997-7-----9986788877876369369999963889888868888
Q gi|254780238|r   80 ---SS------------------LEVKVS-G-----LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRK  125 (129)
Q Consensus        80 ---~~------------------v~v~ik-G-----~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K  125 (129)
                         .+                  +..++. |     .|.---+++++....||.         |||+-.|-|.
T Consensus       120 ~G~~e~~g~~~~v~e~~~~~~rpFka~LDvGL~rtTtG~RVFaaLKGAvDgGl~---------IPHs~krFpG  183 (300)
T PTZ00069        120 EGVKEADGSYYAVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLA---------IPHRPNRFPG  183 (300)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHCCCCCCCC---------CCCCCCCCCC
T ss_conf             575214575101222355787764799732544477653244532123357735---------7888875888


No 47 
>pfam00728 Glyco_hydro_20 Glycosyl hydrolase family 20, catalytic domain. This domain has a TIM barrel fold.
Probab=35.28  E-value=38  Score=15.66  Aligned_cols=73  Identities=22%  Similarity=0.251  Sum_probs=47.0

Q ss_pred             CCCCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHH
Q ss_conf             798779999708998899740444355775433520378999999999998698199999977998678887787
Q gi|254780238|r   26 TFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRAL  100 (129)
Q Consensus        26 t~NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l  100 (129)
                      -+|--|++|||-.|=.+...+=..+--+|+.+...|=.+.-...+.+.|.++|| .|.--|.-||-.+ +++++.
T Consensus        31 K~N~lhlHltD~~~~r~~~~~~p~l~~~ga~~~~~~yT~~ei~~lv~yA~~rgI-~viPEiD~PgH~~-a~~~~~  103 (335)
T pfam00728        31 KLNVLHWHLTDDQGWRLEIKAYPELTEVGAYRGSDFYTQEDIREIVAYAAARGI-EVIPEIDMPGHAR-AALKAY  103 (335)
T ss_pred             CCCEEEEEEECCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHCCC-EEEECCCCHHHHH-HHHHHC
T ss_conf             896799998537876201566644212367788876299999999999998599-8986256426789-999748


No 48 
>PRK06292 dihydrolipoamide dehydrogenase; Validated
Probab=34.51  E-value=39  Score=15.58  Aligned_cols=26  Identities=15%  Similarity=0.079  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEEEECC
Q ss_conf             789999999999986981999999779
Q gi|254780238|r   63 AQVATDDCSAKAQNHGMSSLEVKVSGL   89 (129)
Q Consensus        63 a~~~a~~~~~~~~~~gi~~v~v~ikG~   89 (129)
                      +-.++-.++..+..+|. .|.|+-++.
T Consensus       177 gG~ig~E~A~~l~~~G~-~Vtvv~~~~  202 (460)
T PRK06292        177 GGVIGLELGQALSRLGV-KVTVFERGD  202 (460)
T ss_pred             CCHHHHHHHHHHHHCCC-EEEEEEECC
T ss_conf             86788799999984698-699996247


No 49 
>PRK06245 cofG FO synthase subunit 1; Reviewed
Probab=34.50  E-value=39  Score=15.58  Aligned_cols=55  Identities=13%  Similarity=0.110  Sum_probs=30.9

Q ss_pred             CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEC
Q ss_conf             8779999708998899740444355775433520378999999999998698199999977
Q gi|254780238|r   28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSG   88 (129)
Q Consensus        28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG   88 (129)
                      .|.+|.+|+     ++...|+-|.|+......++=...-....++.+.+.|.+++.+. -|
T Consensus        12 ~n~~In~TN-----iC~~~C~fCaF~~~~~~a~~ls~eev~~~~~ea~~~G~tEvl~~-gG   66 (336)
T PRK06245         12 RNVFIPLTY-----ECRNRCGYCTFRPDPGEASLLSPEEVREILERGQDAGCTEALFT-FG   66 (336)
T ss_pred             CCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEE-CC
T ss_conf             862616775-----40268825867468875687799999999999997698399980-57


No 50 
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=33.93  E-value=29  Score=16.42  Aligned_cols=10  Identities=40%  Similarity=0.444  Sum_probs=7.8

Q ss_pred             EEEEECCCCC
Q ss_conf             9999708998
Q gi|254780238|r   31 RITITDPHGN   40 (129)
Q Consensus        31 iitlTd~~Gn   40 (129)
                      |+|+.|..|.
T Consensus      1021 f~tleD~tG~ 1030 (1157)
T PRK06826       1021 FITLEDLYGT 1030 (1157)
T ss_pred             EEEEEECCCC
T ss_conf             9999968986


No 51 
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=32.95  E-value=21  Score=17.23  Aligned_cols=16  Identities=25%  Similarity=0.237  Sum_probs=10.3

Q ss_pred             ECCCC---EEEEEECCCCC
Q ss_conf             17987---79999708998
Q gi|254780238|r   25 STFNN---TRITITDPHGN   40 (129)
Q Consensus        25 ~t~NN---TiitlTd~~Gn   40 (129)
                      .|+++   .|+|+-|..|.
T Consensus       959 ~tk~g~~maf~~leD~tg~  977 (1107)
T PRK06920        959 RTKKGQKMAFITFCDQNDE  977 (1107)
T ss_pred             ECCCCCEEEEEEEEECCCC
T ss_conf             3688996999999979986


No 52 
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=32.31  E-value=22  Score=17.05  Aligned_cols=27  Identities=30%  Similarity=0.445  Sum_probs=15.7

Q ss_pred             CCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             986788877876369369999963889888
Q gi|254780238|r   90 GAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        90 G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      ||||.++--+|..-   ..-|+|+-|+.||
T Consensus       289 GPGRGSaAGSLVaY---~LgIT~VDPi~y~  315 (987)
T PRK07135        289 GPGRGSASGSLVSY---LLEITSVNPLKYD  315 (987)
T ss_pred             CCCCCCHHHHHHHH---HHCCCCCCHHHCC
T ss_conf             68877378899999---9668763876548


No 53 
>PRK05802 hypothetical protein; Provisional
Probab=31.65  E-value=44  Score=15.29  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=32.6

Q ss_pred             CEEEEEEECCCCC-HHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             1999999779986-788877876369369999963889888
Q gi|254780238|r   80 SSLEVKVSGLGAG-RDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        80 ~~v~v~ikG~G~G-R~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      ...-|..+|+|.. --.++|-|...|=+|..|.|.+|..+|
T Consensus       174 ~k~LvIaRGIgqAP~vpVikkL~~n~NkV~vIid~~~~~~~  214 (328)
T PRK05802        174 GKSLVIARGIGQAPAVPVIKKLYSNGNKVIVILDKGPFENN  214 (328)
T ss_pred             CEEEEEECCCCCCCCHHHHHHHHHCCCEEEEEECCCCCCCH
T ss_conf             73999935623255559999998689979999858855316


No 54 
>PRK08010 pyridine nucleotide-disulfide oxidoreductase; Provisional
Probab=31.25  E-value=44  Score=15.25  Aligned_cols=44  Identities=16%  Similarity=0.126  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCC--C-----CHHHHHHHHHHCCCEEE
Q ss_conf             899999999999869819999997799--8-----67888778763693699
Q gi|254780238|r   64 QVATDDCSAKAQNHGMSSLEVKVSGLG--A-----GRDSALRALRAIGFTIV  108 (129)
Q Consensus        64 ~~~a~~~~~~~~~~gi~~v~v~ikG~G--~-----GR~~~ik~l~~~glkI~  108 (129)
                      -..+-.+++....+|. .|.|.-++.-  +     -.+.+.+.|...|+++.
T Consensus       167 G~ig~E~A~~~~~lG~-~Vtiie~~~~il~~~D~~~~~~l~~~l~~~Gi~i~  217 (441)
T PRK08010        167 GYIGVEFASMFANFGS-KVTILEAASLFLPREDRDIADNIATILRDQGVDII  217 (441)
T ss_pred             CHHHHHHHHHHHHCCC-EEEEEECCCCCCCCCHHHHHHHHHHHHHHCCEEEE
T ss_conf             5899999999997598-78897046732663114689999999987885997


No 55 
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=31.11  E-value=31  Score=16.17  Aligned_cols=27  Identities=41%  Similarity=0.539  Sum_probs=14.4

Q ss_pred             CCCHHHHHHHHHHCCCEEEEEEECCCCCCC
Q ss_conf             986788877876369369999963889888
Q gi|254780238|r   90 GAGRDSALRALRAIGFTIVSICDVTMIAHN  119 (129)
Q Consensus        90 G~GR~~~ik~l~~~glkI~~I~D~T~ip~n  119 (129)
                      ||||.++--+|..-   ...|+|+-|+.||
T Consensus       292 GPGRGSaAGSLVaY---~LgIT~iDPi~~~  318 (971)
T PRK05898        292 GPGRGSAAGSLIAY---LLHITDIDPIKYN  318 (971)
T ss_pred             CCCCCCHHHHHHHH---HHCCCCCCHHHCC
T ss_conf             78876269899999---9748775822158


No 56 
>COG4782 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.89  E-value=47  Score=15.11  Aligned_cols=74  Identities=22%  Similarity=0.331  Sum_probs=44.6

Q ss_pred             CCCCEEEE-------EECCCCC-----EEEEECCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCC
Q ss_conf             79877999-------9708998-----8997404443-557754335203789999999999986981999999779986
Q gi|254780238|r   26 TFNNTRIT-------ITDPHGN-----TIAWSSPKVV-GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAG   92 (129)
Q Consensus        26 t~NNTiit-------lTd~~Gn-----~i~~~S~G~~-gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~G   92 (129)
                      -|||+|.-       +....|+     +.+|-|.|.+ ||---|.++.|+.-....-+-..+.+.+.+.|+|.-.-.|. 
T Consensus       124 GfNntf~dav~R~aqI~~d~g~~~~pVvFSWPS~g~l~~Yn~DreS~~~Sr~aLe~~lr~La~~~~~~~I~ilAHSMGt-  202 (377)
T COG4782         124 GFNNTFEDAVYRTAQIVHDSGNDGVPVVFSWPSRGSLLGYNYDRESTNYSRPALERLLRYLATDKPVKRIYLLAHSMGT-  202 (377)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCHH-
T ss_conf             2587355778999988763189820699974788732000145556553389999999999747888628999854427-


Q ss_pred             HHHHHHHHH
Q ss_conf             788877876
Q gi|254780238|r   93 RDSALRALR  101 (129)
Q Consensus        93 R~~~ik~l~  101 (129)
                       -.+..+|+
T Consensus       203 -wl~~e~Lr  210 (377)
T COG4782         203 -WLLMEALR  210 (377)
T ss_pred             -HHHHHHHH
T ss_conf             -99999999


No 57 
>TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria.
Probab=29.54  E-value=37  Score=15.72  Aligned_cols=57  Identities=14%  Similarity=0.098  Sum_probs=31.5

Q ss_pred             CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH---HHHCCCCEEEEEEECCCC
Q ss_conf             8779999708998899740444355775433520378999999999---998698199999977998
Q gi|254780238|r   28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAK---AQNHGMSSLEVKVSGLGA   91 (129)
Q Consensus        28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~---~~~~gi~~v~v~ikG~G~   91 (129)
                      +|.+|.+|+     ++...|+-|.|... .+.+.|.....+.+.++   +.+.|.++|.+. -|..|
T Consensus         4 ~N~~In~TN-----iC~~~C~FCaF~r~-~~~~~ay~ls~eei~~~~~ea~~~G~tEv~i~-gG~~P   63 (322)
T TIGR03550         4 RNVFIPLTR-----LCRNRCGYCTFRRP-PGELEAALLSPEEVLEILRKGAAAGCTEALFT-FGEKP   63 (322)
T ss_pred             CCCCCCCCC-----CHHCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEC-CCCCH
T ss_conf             721568872-----03176967885168-99988774799999999999997798799964-88680


No 58 
>PRK05249 soluble pyridine nucleotide transhydrogenase; Provisional
Probab=29.11  E-value=48  Score=15.03  Aligned_cols=42  Identities=12%  Similarity=0.066  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHCCCCEEEEEEECCCC-------CHHHHHHHHHHCCCEEE
Q ss_conf             99999999998698199999977998-------67888778763693699
Q gi|254780238|r   66 ATDDCSAKAQNHGMSSLEVKVSGLGA-------GRDSALRALRAIGFTIV  108 (129)
Q Consensus        66 ~a~~~~~~~~~~gi~~v~v~ikG~G~-------GR~~~ik~l~~~glkI~  108 (129)
                      .+-.++.....+|. .|.|.-+....       -.+.+.+.|...|++|.
T Consensus       187 ig~E~A~~~~~lG~-~Vtiv~~~~~ll~~~d~~~~~~l~~~l~~~gI~i~  235 (465)
T PRK05249        187 IGCEYASIFRGLGV-KVDLINTRDRLLSFLDDEISDALSYHFRNSGVVIR  235 (465)
T ss_pred             CHHHHHHHHHHHCC-EEEEEECCCCCHHHCCHHHHHHHHHHHHHCCCEEE
T ss_conf             17999999996098-77897216600022189999999999998792999


No 59 
>TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit. This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases.
Probab=25.00  E-value=45  Score=15.22  Aligned_cols=58  Identities=17%  Similarity=0.294  Sum_probs=36.5

Q ss_pred             CCEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHH---HHHHHCCCCEEEEEEECCCCC
Q ss_conf             87799997089988997404443557754335203789999999---999986981999999779986
Q gi|254780238|r   28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCS---AKAQNHGMSSLEVKVSGLGAG   92 (129)
Q Consensus        28 NNTiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~---~~~~~~gi~~v~v~ikG~G~G   92 (129)
                      .|.+|.+|+     ++..+|+-|+|... .+.+.|....-+.+.   +.+.+.|.+++.+. -|..|-
T Consensus        39 ~n~~In~TN-----iC~~~C~fCaF~r~-p~~~~ay~lt~eei~~~~~~a~~~G~~Ei~~~-gG~~Pe   99 (343)
T TIGR03551        39 VNRNINFTN-----VCYGGCGFCAFRKR-KGDADAYLLSLEEIAERAAEAWKAGATEVCIQ-GGIHPD   99 (343)
T ss_pred             CCCCCCHHH-----HHHCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEE-CCCCCC
T ss_conf             500625526-----87478976778668-99986600799999999999997699689982-586878


No 60 
>TIGR01438 TGR thioredoxin and glutathione reductase; InterPro: IPR006338   This homodimeric, FAD-containing member of the pyridine nucleotide disulphide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-terminal arm of the protein is proposed to allow broad substrate specificity , .; GO: 0016654 oxidoreductase activity acting on NADH or NADPH disulfide as acceptor, 0050660 FAD binding, 0050661 NADP binding, 0006118 electron transport.
Probab=24.57  E-value=58  Score=14.52  Aligned_cols=23  Identities=22%  Similarity=0.341  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             789999999999986981999999
Q gi|254780238|r   63 AQVATDDCSAKAQNHGMSSLEVKV   86 (129)
Q Consensus        63 a~~~a~~~~~~~~~~gi~~v~v~i   86 (129)
                      |.=+|-.++=.+-.+|+ .|+|.+
T Consensus       196 asYVALECaGFL~~~g~-dV~V~V  218 (513)
T TIGR01438       196 ASYVALECAGFLAALGL-DVTVLV  218 (513)
T ss_pred             CCHHHHHHHHHHHHCCC-CEEEEE
T ss_conf             61423577889863399-649999


No 61 
>TIGR02183 GRXA Glutaredoxin, GrxA family; InterPro: IPR011902   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This entry includes the Escherichia coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase .; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis.
Probab=23.55  E-value=61  Score=14.40  Aligned_cols=34  Identities=9%  Similarity=0.372  Sum_probs=28.8

Q ss_pred             CCCCH--HHHHHHHHHHHHHHCCCCEEEEEEECCCC
Q ss_conf             35203--78999999999998698199999977998
Q gi|254780238|r   58 NSPFA--AQVATDDCSAKAQNHGMSSLEVKVSGLGA   91 (129)
Q Consensus        58 ~t~~A--a~~~a~~~~~~~~~~gi~~v~v~ikG~G~   91 (129)
                      +=||.  |.++||++....-+..+++|++.--|+.+
T Consensus         9 gC~YCVRA~~LaEkl~~~~~DF~fry~Di~AEGI~K   44 (86)
T TIGR02183         9 GCPYCVRAKQLAEKLAEELADFEFRYIDIHAEGISK   44 (86)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCH
T ss_conf             984023368889998864035562058887458871


No 62 
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=23.17  E-value=62  Score=14.36  Aligned_cols=51  Identities=18%  Similarity=0.203  Sum_probs=34.0

Q ss_pred             EECCCEEEEEEECCCCEEEEEECC-CCCEEEEECCCCCCCCCCCCCCCCHHH
Q ss_conf             122521899991798779999708-998899740444355775433520378
Q gi|254780238|r   14 KNIVSGRAHVVSTFNNTRITITDP-HGNTIAWSSPKVVGFSGSRKNSPFAAQ   64 (129)
Q Consensus        14 ~~i~~GiihI~~t~NNTiitlTd~-~Gn~i~~~S~G~~gfkg~kk~t~~Aa~   64 (129)
                      +.+..|++---+-.||-.+-+.=. ..|.+.++-.-..||+|+++-++|--+
T Consensus        68 rd~d~glVDFpa~~Ng~~~~lCWK~DE~~imywH~~~EGFrGRrr~~~~e~~  119 (123)
T COG4911          68 RDIDIGLVDFPAIINGKPAFLCWKIDENDIMYWHYMDEGFRGRRRLTGYEDI  119 (123)
T ss_pred             ECCCCCCCCCHHHHCCCEEEEEEECCCCCEEEEECCCCCCCCCCCCCHHHHH
T ss_conf             3254201215354379068999831786244332466212366668627656


No 63 
>PRK08013 hypothetical protein; Provisional
Probab=23.06  E-value=62  Score=14.34  Aligned_cols=10  Identities=40%  Similarity=0.418  Sum_probs=5.1

Q ss_pred             CHHHHHHHHH
Q ss_conf             6788877876
Q gi|254780238|r   92 GRDSALRALR  101 (129)
Q Consensus        92 GR~~~ik~l~  101 (129)
                      |+.+.+|...
T Consensus       165 G~~S~vR~~~  174 (400)
T PRK08013        165 GANSWLRNKA  174 (400)
T ss_pred             CCCCHHHHHC
T ss_conf             8761323313


No 64 
>PRK01259 ribose-phosphate pyrophosphokinase; Provisional
Probab=22.93  E-value=63  Score=14.33  Aligned_cols=59  Identities=8%  Similarity=-0.007  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHCCCCEEEEEE-ECCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCC
Q ss_conf             999999999986981999999-7799867888778763693699999638898888688886
Q gi|254780238|r   66 ATDDCSAKAQNHGMSSLEVKV-SGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR  126 (129)
Q Consensus        66 ~a~~~~~~~~~~gi~~v~v~i-kG~G~GR~~~ik~l~~~glkI~~I~D~T~ip~nGcRp~K~  126 (129)
                      +...+++.+++.|-+.|.+.. .|.-  -..++.-|..+++.=+-++|..|.|-+...++|-
T Consensus       223 Tl~~aa~~Lk~~GA~~V~~~~THglf--s~~A~~rl~~s~i~~iv~TnTip~~~~~~~~~kl  282 (309)
T PRK01259        223 TLCKAAEALKERGAKSVFAYATHPVL--SGGAAERIANSVLDELVVTDSIPLSEEIKKCPKI  282 (309)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEECHHC--CHHHHHHHHHCCCCEEEEECCCCCCHHHCCCCCC
T ss_conf             59999999975699669999876313--9459999870899889981896686222458981


No 65 
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057   Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=22.25  E-value=41  Score=15.44  Aligned_cols=38  Identities=26%  Similarity=0.369  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHCC
Q ss_conf             89999999999986981999999779986788877876369
Q gi|254780238|r   64 QVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIG  104 (129)
Q Consensus        64 ~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~l~~~g  104 (129)
                      -.+...++.-|+.+||+.|=   +-.|-+||+..|+|...|
T Consensus        33 ~~~~~ALG~iArArGMtqlA---~~tGlsREsLYkALs~~G   70 (91)
T TIGR02684        33 ALIAAALGVIARARGMTQLA---KKTGLSRESLYKALSGGG   70 (91)
T ss_pred             HHHHHHHHHHHHHCCHHHHH---HHHCCCHHHHHHHHCCCC
T ss_conf             89999988998651657899---982876788788735688


No 66 
>TIGR02530 flg_new flagellar operon protein; InterPro: IPR013367    Proteins in this entry are encoded in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function of this protein is unknown..
Probab=21.93  E-value=64  Score=14.26  Aligned_cols=21  Identities=43%  Similarity=0.305  Sum_probs=17.0

Q ss_pred             EEEEEEECCCCEEEEEECCCC
Q ss_conf             189999179877999970899
Q gi|254780238|r   19 GRAHVVSTFNNTRITITDPHG   39 (129)
Q Consensus        19 GiihI~~t~NNTiitlTd~~G   39 (129)
                      -.+-|-+.+|||-||+-|..-
T Consensus        78 d~ALVVs~KN~TVITamD~~~   98 (113)
T TIGR02530        78 DAALVVSVKNRTVITAMDKDE   98 (113)
T ss_pred             CCEEEEECCCCEEEEEECHHH
T ss_conf             851477235780542222331


No 67 
>KOG4120 consensus
Probab=21.62  E-value=25  Score=16.75  Aligned_cols=69  Identities=14%  Similarity=0.246  Sum_probs=47.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHH-------------HHHCCC---EEEEEEECC
Q ss_conf             5577543352037899999999999869819999997799867888778-------------763693---699999638
Q gi|254780238|r   51 GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRA-------------LRAIGF---TIVSICDVT  114 (129)
Q Consensus        51 gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~G~GR~~~ik~-------------l~~~gl---kI~~I~D~T  114 (129)
                      -||-.+|.+.|......+.+.+-+-+.=...++++|=|++||-.++.++             |..+||   ......|-+
T Consensus       118 ~~k~~kK~drfng~se~e~l~~tvPD~lc~NldiVIVGiNPGl~aayKGHhyagPgNhFWKcL~~sgL~e~q~t~~~Dh~  197 (426)
T KOG4120         118 LKKSVKKSDRFNGNSEDEALLQTVPDYLCENLDIVIVGINPGLTAAYKGHHYAGPGNHFWKCLNKSGLLEAQFTYLNDHD  197 (426)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHCCCHHHHCCCCEEEEECCCHHHHHHCCCCCCCCCCHHHHHHHHHCCCHHHHHCCCCCC
T ss_conf             16666555430475265788734745663576679994370155552367678984259999877101287750235555


Q ss_pred             CCCCC
Q ss_conf             89888
Q gi|254780238|r  115 MIAHN  119 (129)
Q Consensus       115 ~ip~n  119 (129)
                      -..|+
T Consensus       198 Lpk~G  202 (426)
T KOG4120         198 LPKHG  202 (426)
T ss_pred             CCCCC
T ss_conf             50015


No 68 
>pfam05990 DUF900 Alpha/beta hydrolase of unknown function (DUF900). This family consists of several hypothetical proteins of unknown function mostly found in Rhizobium species. Members of this family have an alpha/beta hydrolase fold.
Probab=21.53  E-value=67  Score=14.15  Aligned_cols=78  Identities=17%  Similarity=0.227  Sum_probs=44.4

Q ss_pred             EEEEECCCCEEEE----------EECCCCCE--EEEECCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             9999179877999----------97089988--997404443-5577543352037899999999999869819999997
Q gi|254780238|r   21 AHVVSTFNNTRIT----------ITDPHGNT--IAWSSPKVV-GFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVS   87 (129)
Q Consensus        21 ihI~~t~NNTiit----------lTd~~Gn~--i~~~S~G~~-gfkg~kk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik   87 (129)
                      ++|+ -|||++-.          ..+..|.+  ..|-|+|.. +|..-+.+..++....++-+...+.+.+.+.|+|.-.
T Consensus        23 vFVH-GyN~~f~~a~~r~aQl~~d~~~~g~~v~FSWPS~g~~~~Y~~D~~sa~~s~~~l~~~L~~l~~~~~~~~I~ilAH  101 (230)
T pfam05990        23 VFVH-GYNNSFEDAVYRFAQIAHDLGFPGVPVVFTWPSGASLFGYNYDRESANYSRDALERLLRYLATTPPVKRIHLIAH  101 (230)
T ss_pred             EEEC-CCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             9975-899998999999999998469997469996889996134487999999999999999999986669874899985


Q ss_pred             CCCCCHHHHHHHHH
Q ss_conf             79986788877876
Q gi|254780238|r   88 GLGAGRDSALRALR  101 (129)
Q Consensus        88 G~G~GR~~~ik~l~  101 (129)
                      ..|  -..+..+|.
T Consensus       102 SMG--~rl~~~aL~  113 (230)
T pfam05990       102 SMG--TWLVMEALR  113 (230)
T ss_pred             CCH--HHHHHHHHH
T ss_conf             817--899999999


No 69 
>pfam01019 G_glu_transpept Gamma-glutamyltranspeptidase.
Probab=21.50  E-value=67  Score=14.15  Aligned_cols=22  Identities=23%  Similarity=0.370  Sum_probs=17.6

Q ss_pred             CCCCEEEEEECCCCCEEEEECC
Q ss_conf             7987799997089988997404
Q gi|254780238|r   26 TFNNTRITITDPHGNTIAWSSP   47 (129)
Q Consensus        26 t~NNTiitlTd~~Gn~i~~~S~   47 (129)
                      ...-|++++.|..||.++..++
T Consensus       320 ~~~Tth~svvD~~GnaVS~t~S  341 (506)
T pfam01019       320 DGGTTHFSVVDRDGNAVSATSS  341 (506)
T ss_pred             CCCCEEEEEEECCCCEEEEECC
T ss_conf             9997899999089899988414


No 70 
>smart00300 ChSh Chromo Shadow Domain.
Probab=21.40  E-value=67  Score=14.14  Aligned_cols=41  Identities=17%  Similarity=0.223  Sum_probs=29.6

Q ss_pred             EEEEEECCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             79999708998899740444355775433520378999999999998
Q gi|254780238|r   30 TRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQN   76 (129)
Q Consensus        30 TiitlTd~~Gn~i~~~S~G~~gfkg~kk~t~~Aa~~~a~~~~~~~~~   76 (129)
                      -|+-.||.+|...+.     +.+|+ ....-..|..+-.++-+.+++
T Consensus        11 ~Iigatd~~G~l~fl-----~kWk~-de~~lvpa~~an~k~Pq~VI~   51 (61)
T smart00300       11 DIVGITKDDGELTFL-----IKWKD-DAASLVPNKEANVKCPQKVIR   51 (61)
T ss_pred             HHEEEECCCCEEEEE-----EEECC-CCCCEEEHHHHHHHCCHHHHH
T ss_conf             903567779979999-----99849-974321389987468699999


Done!