Query         gi|254780440|ref|YP_003064853.1| transcription elongation factor GreA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 158
No_of_seqs    135 out of 2199
Neff          6.5 
Searched_HMMs 39220
Date          Sun May 29 19:15:32 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780440.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01462 greA transcription e 100.0       0       0  385.1  16.0  151    6-156     1-155 (155)
  2 PRK00226 greA transcription el 100.0       0       0  361.3  18.6  157    1-157     1-157 (157)
  3 PRK01885 greB transcription el 100.0       0       0  355.7  17.8  156    1-157     3-158 (159)
  4 TIGR01461 greB transcription e 100.0       0       0  316.8  11.2  154    4-158     2-156 (157)
  5 PRK05892 nucleoside diphosphat 100.0 4.3E-44       0  301.6  17.6  152    2-157     5-159 (161)
  6 PRK06330 transcript cleavage f 100.0   5E-44       0  301.2  14.8  154    3-156   748-901 (906)
  7 COG0782 Uncharacterized conser 100.0 2.4E-42       0  290.5  16.0  151    7-158     1-151 (151)
  8 PRK06342 transcription elongat 100.0 3.2E-32 8.1E-37  226.1  14.7  134    3-156    27-160 (160)
  9 PRK05753 nucleoside diphosphat 100.0 2.6E-30 6.7E-35  213.9   7.4  123   27-157     4-127 (135)
 10 pfam01272 GreA_GreB Transcript  99.9 1.7E-22 4.3E-27  164.2   9.4   76   82-157     2-77  (77)
 11 pfam03449 GreA_GreB_N domain.   99.8 8.3E-21 2.1E-25  153.4   8.3   71    5-75      1-71  (71)
 12 PRK01490 tig trigger factor; P  91.5     1.3 3.3E-05   24.8   8.5   86   56-156   134-241 (435)
 13 COG0544 Tig FKBP-type peptidyl  74.5     7.8  0.0002   19.9   7.3   34  123-156   195-241 (441)
 14 cd06213 oxygenase_e_transfer_s  70.6     9.5 0.00024   19.3   5.1   65   86-150    28-96  (227)
 15 PRK05431 seryl-tRNA synthetase  69.7      10 0.00025   19.2   7.9   79   10-90     35-115 (422)
 16 pfam02359 CDC48_N Cell divisio  68.8      10 0.00027   19.1   5.1   69   70-143    14-83  (87)
 17 COG1047 SlpA FKBP-type peptidy  68.7     7.1 0.00018   20.1   3.7   28  118-145    38-65  (174)
 18 pfam11599 AviRa RRNA methyltra  68.1     8.4 0.00021   19.7   3.9   86    6-106    99-185 (249)
 19 PRK02195 V-type ATP synthase s  67.2      11 0.00029   18.9   8.5   69    1-77      1-75  (201)
 20 PRK04290 30S ribosomal protein  62.9      11 0.00027   19.0   3.7   27  119-145    18-44  (115)
 21 cd06165 Sortase_A_1 Sortase A   57.5      17 0.00043   17.8   4.0   27  131-157    62-88  (127)
 22 PRK10737 FKBP-type peptidyl-pr  57.4      17 0.00043   17.8   4.5   23  123-145    42-64  (196)
 23 cd06166 Sortase_D_5 Sortase D   56.1      18 0.00045   17.6   3.8   28  130-157    62-89  (126)
 24 COG5246 PRP11 Splicing factor   55.9      12 0.00031   18.6   3.0   73   44-117    94-167 (222)
 25 cd05828 Sortase_D_4 Sortase D   55.5      18 0.00046   17.6   3.9   26  132-157    61-86  (127)
 26 cd05830 Sortase_D_5 Sortase D   55.4      18 0.00046   17.5   4.1   36  121-157    55-90  (137)
 27 pfam00970 FAD_binding_6 Oxidor  53.6      19 0.00049   17.4   5.3   65   86-150    30-99  (99)
 28 COG3127 Predicted ABC-type tra  51.7      21 0.00053   17.2   4.7   38  119-157   598-635 (829)
 29 cd00004 Sortase Sortases are c  51.2      21 0.00054   17.1   3.9   29  130-158    62-90  (128)
 30 cd06210 MMO_FAD_NAD_binding Me  48.0      24  0.0006   16.8   5.5   64   87-150    36-103 (236)
 31 TIGR03007 pepcterm_ChnLen poly  47.7      24 0.00061   16.8   4.4   21   86-110   393-413 (510)
 32 cd06209 BenDO_FAD_NAD Benzoate  47.5      24 0.00061   16.8   5.4   64   86-149    31-97  (228)
 33 COG3764 SrtA Sortase (surface   46.8      25 0.00063   16.7   4.2   33  122-158   128-160 (210)
 34 pfam11160 DUF2945 Protein of u  45.5      26 0.00066   16.6   3.4   22  136-157     1-22  (62)
 35 PRK12306 uvrC excinuclease ABC  44.2      27 0.00069   16.4   6.8  130    6-146   169-328 (519)
 36 PTZ00066 pyruvate kinase; Prov  43.9      27  0.0007   16.4   6.0   87   60-156    83-175 (513)
 37 COG1018 Hmp Flavodoxin reducta  43.8      27  0.0007   16.4   4.8   65   85-150    34-105 (266)
 38 cd05827 Sortase_C_3 Sortase C   43.2      28 0.00072   16.3   4.0   29  128-156    62-90  (131)
 39 pfam06940 DUF1287 Domain of un  43.1      28 0.00072   16.3   3.2   23  132-154   106-128 (164)
 40 COG2960 Uncharacterized protei  42.4      29 0.00074   16.3   6.5   23   51-73     70-92  (103)
 41 pfam07798 DUF1640 Protein of u  41.7      30 0.00075   16.2   6.9   60    9-72     79-138 (177)
 42 COG3973 Superfamily I DNA and   41.1      30 0.00077   16.1   5.1   70   86-157    99-172 (747)
 43 COG3738 Uncharacterized protei  40.4      17 0.00044   17.7   1.7   31  125-155   133-163 (200)
 44 COG1188 Ribosome-associated he  39.8      30 0.00077   16.1   2.9   30   81-112    44-73  (100)
 45 cd06189 flavin_oxioreductase N  38.4      33 0.00085   15.9   5.4   64   86-150    26-93  (224)
 46 PRK09239 chorismate mutase; Pr  37.9      34 0.00086   15.8   5.3   54    1-57      1-60  (104)
 47 cd00986 PDZ_LON_protease PDZ d  36.6      35  0.0009   15.7   3.3   33  119-151    38-70  (79)
 48 COG2012 RPB5 DNA-directed RNA   35.2      30 0.00077   16.1   2.3   26  119-145    42-67  (80)
 49 TIGR01801 CM_A chorismate muta  34.3      38 0.00098   15.5   4.7   45   11-59      6-58  (104)
 50 cd02782 MopB_CT_1 The MopB_CT_  34.3      39 0.00098   15.5   4.6   31  122-152    36-66  (129)
 51 cd06193 siderophore_interactin  34.0      28 0.00071   16.4   2.0   61   86-149    27-115 (235)
 52 PRK05802 hypothetical protein;  33.9      39   0.001   15.4   3.1   66   77-144    87-157 (328)
 53 cd00508 MopB_CT_Fdh-Nap-like T  32.6      41   0.001   15.3   4.5   31  121-151    37-67  (120)
 54 cd06183 cyt_b5_reduct_like Cyt  32.4      41  0.0011   15.3   5.2   65   86-150    29-98  (234)
 55 PRK10465 hydrogenase 2-specifi  31.8      42  0.0011   15.2   3.1   83   58-154    15-98  (159)
 56 KOG3206 consensus               31.5      43  0.0011   15.2   7.6   97    1-129    94-194 (234)
 57 pfam11344 DUF3146 Protein of u  31.1      18 0.00047   17.5   0.7   41  114-154    35-79  (80)
 58 pfam01191 RNA_pol_Rpb5_C RNA p  30.9      44  0.0011   15.1   3.3   29  118-147    35-63  (74)
 59 pfam06152 Phage_min_cap2 Phage  30.4      45  0.0011   15.1   3.0   14    7-20      3-16  (361)
 60 PRK09570 rpoH DNA-directed RNA  29.8      46  0.0012   15.0   3.1   28  118-146    38-65  (79)
 61 COG2125 RPS6A Ribosomal protei  29.5      29 0.00074   16.2   1.4   18  123-140    22-39  (120)
 62 cd02775 MopB_CT Molybdopterin-  29.3      47  0.0012   14.9   4.5   34  119-152    23-56  (101)
 63 pfam10781 DSRB Dextransucrase   29.1      47  0.0012   14.9   3.1   23  134-156     2-25  (62)
 64 COG2139 RPL21A Ribosomal prote  28.9      43  0.0011   15.2   2.2   15  101-115    79-93  (98)
 65 TIGR01076 sortase_fam sortase   28.7      48  0.0012   14.9   3.9   31  128-158    59-89  (140)
 66 PRK10708 hypothetical protein;  28.6      48  0.0012   14.9   2.8   23  134-156     2-25  (62)
 67 PRK00558 uvrC excinuclease ABC  27.6      50  0.0013   14.7  11.0  135    6-146   183-348 (609)
 68 COG0853 PanD Aspartate 1-decar  27.3      50  0.0013   14.7   4.7   71   66-143     5-88  (126)
 69 pfam01092 Ribosomal_S6e Riboso  27.3      50  0.0013   14.7   4.2   20  126-145    23-42  (127)
 70 TIGR02160 PA_CoA_Oxy5 phenylac  26.7      42  0.0011   15.2   1.9   64   86-150    33-103 (371)
 71 KOG3129 consensus               26.2      53  0.0013   14.6   3.7   33  106-140   132-164 (231)
 72 cd02788 MopB_CT_NDH-1_NuoG2-N7  25.8      54  0.0014   14.5   4.4   31  121-151    31-61  (96)
 73 TIGR00875 talC transaldolase,   25.5      39   0.001   15.4   1.5   12    4-15     86-97  (216)
 74 KOG3026 consensus               25.1      55  0.0014   14.5   7.0   34   36-73     16-49  (262)
 75 pfam06273 eIF-4B Plant specifi  24.4      44  0.0011   15.1   1.6   38   61-104   341-378 (430)
 76 cd06190 T4MO_e_transfer_like T  24.2      57  0.0015   14.3   5.5   63   86-148    24-90  (232)
 77 cd06215 FNR_iron_sulfur_bindin  24.2      58  0.0015   14.3   4.4   64   86-149    28-97  (231)
 78 cd02790 MopB_CT_Formate-Dh_H F  23.6      59  0.0015   14.3   4.5   33  120-152    36-68  (116)
 79 PRK04778 septation ring format  22.7      62  0.0016   14.2   7.6   32   41-72    185-216 (569)
 80 pfam11939 DUF3457 Protein of u  22.6      62  0.0016   14.1   3.1   44  106-155    48-92  (158)
 81 KOG0534 consensus               22.5      62  0.0016   14.1   5.9   65   86-151    82-152 (286)
 82 TIGR01439 lp_hng_hel_AbrB tran  22.5      62  0.0016   14.1   3.5   33  117-150     7-40  (44)
 83 pfam02403 Seryl_tRNA_N Seryl-t  22.2      63  0.0016   14.1   7.7   58   10-73     36-93  (108)
 84 cd02778 MopB_CT_Thiosulfate-R-  22.1      63  0.0016   14.1   4.6   26  123-148    34-59  (123)
 85 KOG3227 consensus               21.1      66  0.0017   14.0   5.1   57    4-75     17-73  (231)
 86 KOG0493 consensus               20.9      67  0.0017   13.9   3.5   29    7-35    253-284 (342)
 87 cd06212 monooxygenase_like The  20.6      68  0.0017   13.9   5.2   65   86-150    30-98  (232)
 88 pfam06160 EzrA Septation ring   20.0      70  0.0018   13.8   7.7   31   42-72    182-212 (559)

No 1  
>TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359   Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes.    The 2.2 Å resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.  Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein.  ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=0  Score=385.14  Aligned_cols=151  Identities=50%  Similarity=0.844  Sum_probs=149.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-
Q ss_conf             1488999999999999987248999999999975176222430489998876879999999974444210472101332-
Q gi|254780440|r    6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD-   84 (158)
Q Consensus         6 ~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~-   84 (158)
                      |||++||++|++||++|++++||+++++|++||+||||||||||||||++|+++++||.+|+++|+||+||+++..++| 
T Consensus         1 ~~T~~g~~kL~~EL~~Lk~v~RpeI~~~I~~AR~~GDLsENAEY~AAKe~Q~~~E~RI~~le~~l~~A~vi~~~~~~~~g   80 (155)
T TIGR01462         1 PLTQEGYEKLKEELEYLKTVKRPEISEEIKEAREHGDLSENAEYHAAKEEQGFIEGRIAELEDLLANAEVIDDSKLSTDG   80 (155)
T ss_pred             CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEECCHHHCCCCC
T ss_conf             97888999999999885026118999999999851886556003899999999988999999887620623601004788


Q ss_pred             -CCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCC--EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEE
Q ss_conf             -1113657999534765235999963101334588--15013178998728888878999828971999999989
Q gi|254780440|r   85 -RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSG--LVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL  156 (158)
Q Consensus        85 -~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~--~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~  156 (158)
                       +|.|||+|+|.|.++|++.+|+|||++|+||+.|  +||+.||||+|||||++||.|+|++|+|.+.|+|++|+
T Consensus        81 d~V~~G~~V~~~~~~~~e~~~y~IVG~~EaD~~~giekIS~~SPlg~aL~Gkk~GD~~~v~~P~g~~~~~Il~i~  155 (155)
T TIGR01462        81 DKVSFGSTVTIKDEDTGEEETYTIVGSWEADPKEGIEKISIESPLGKALIGKKVGDEVEVQVPKGEKEYEILKIE  155 (155)
T ss_pred             CEEECCCEEEEEECCCCCEEEEEEECCCCCCHHCCCEEEECCCHHHHHHCCCCCCCEEEEEECCCEEEEEEEEEC
T ss_conf             377157589999838996489998345205533080782267702353337625877899858923799888737


No 2  
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=100.00  E-value=0  Score=361.32  Aligned_cols=157  Identities=52%  Similarity=0.839  Sum_probs=155.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99843148899999999999998724899999999997517622243048999887687999999997444421047210
Q gi|254780440|r    1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST   80 (158)
Q Consensus         1 M~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~   80 (158)
                      |++++|||++||++|++||++|++++||+++++|++||++|||||||+|++||++|+++++||++|+.+|++|+||+++.
T Consensus         1 m~~~~~lT~eg~~~L~~El~~L~~~~r~~i~~~i~~Ar~~GDlsENaeY~aAke~q~~~e~rI~~Le~~L~~A~iid~~~   80 (157)
T PRK00226          1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPTK   80 (157)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99773549999999999999998723689999999999869964057699999999999999999999998501458665


Q ss_pred             CCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             13321113657999534765235999963101334588150131789987288888789998289719999999897
Q gi|254780440|r   81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus        81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      .++|+|+|||+|++.|.++|+..+|+||||+|+||..|+||+.||||+||+|+++||+|+|++|+|..+|+|++|+|
T Consensus        81 ~~~~~V~~Gs~V~l~d~~~g~~~~y~iVG~~Ead~~~g~IS~~SPlg~ALlGk~~Gd~V~v~~P~G~~~~~I~~I~y  157 (157)
T PRK00226         81 PSSGKVKFGATVTIYDLDTDEEETYQIVGDDEADIKEGKISVNSPIARALIGKKVGDTVTVKAPGGEYEVEIVSVEY  157 (157)
T ss_pred             CCCCCEECCCEEEEEECCCCCEEEEEEECCCCCCCCCCEECCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC
T ss_conf             77884206758999985899679999913322456676524779899998289999989998499878999999889


No 3  
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=100.00  E-value=0  Score=355.73  Aligned_cols=156  Identities=34%  Similarity=0.572  Sum_probs=153.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99843148899999999999998724899999999997517622243048999887687999999997444421047210
Q gi|254780440|r    1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST   80 (158)
Q Consensus         1 M~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~   80 (158)
                      +|.++|||++||++|++||++|.+++||+++++|++||++||||||||||+||++|+++++||++|+.+|++|+||+++.
T Consensus         3 ~~~~~ylT~eg~~kL~~El~~L~~~~r~~~~~~i~~Ar~~GDlsENaeY~aAke~q~~le~rI~~Le~~L~~A~iid~~~   82 (159)
T PRK01885          3 AMKTNYITREGYERLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSP   82 (159)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             98654539999999999999987453045899999999859943026389999999999999999999987330357666


Q ss_pred             CCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             13321113657999534765235999963101334588150131789987288888789998289719999999897
Q gi|254780440|r   81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus        81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      .+.++|+|||+|+++| ++|++.+|+|||++|+||..|+||+.||||+||||+++||+|+|++|+|...|+|++|+|
T Consensus        83 ~~~~~V~~Gs~V~l~~-~~g~~~~y~iVG~~Ead~~~g~IS~~SPlg~ALlGkk~Gd~V~v~~P~G~~~~~Il~I~y  158 (159)
T PRK01885         83 QQEGKVFFGAWVEIEN-EDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEY  158 (159)
T ss_pred             CCCCEEECCCEEEEEE-CCCCEEEEEEECHHHCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC
T ss_conf             7788156240899986-689769999948244266678222469899998389999989998599978999999989


No 4  
>TIGR01461 greB transcription elongation factor GreB; InterPro: IPR006358   Bacterial GreA IPR006359 from INTERPRO and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase, allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue preexisting arrested complexes .    A 15 Å resolution helical reconstruction of the Escherichia coli core RNA polymerase (RNAP)/GreB complex that allows fitting of high-resolution RNAP and GreB structures. The model of the complex reveals a remarkable binding mode for GreB; the globular C-terminal domain binds RNAP at the edge of the active site channel, while the N-terminal coiled-coil domain extends 45 Å into a channel directly to the RNAP active site. The results point to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNAP active site to catalyse the transcript cleavage reaction, and mutational studies confirm that these positions are critical for Gre factor function. Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=0  Score=316.84  Aligned_cols=154  Identities=36%  Similarity=0.563  Sum_probs=150.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             43148899999999999998724899999999997517622243048999887687999999997444421047210133
Q gi|254780440|r    4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSG   83 (158)
Q Consensus         4 k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~   83 (158)
                      +.|+|++|+++|++||.+|++++||++.+.+.+|+++||+||||||.+.|.+++.+|+||++|..+|.+++|||++....
T Consensus         2 ~pliTpeG~~~Lk~EL~~Lw~~eRPevtq~V~wAA~lGDRSENadY~YgKkrlREIDrRvRfLtKrLEnlkvVd~~p~~~   81 (157)
T TIGR01461         2 TPLITPEGYEKLKDELYELWRKERPEVTQIVSWAAALGDRSENADYLYGKKRLREIDRRVRFLTKRLENLKVVDEEPREA   81 (157)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCEECCCCCCCC
T ss_conf             88717878999999999886232862113232442168712242100166000022112446555443001117653554


Q ss_pred             -CCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC
Q ss_conf             -211136579995347652359999631013345881501317899872888887899982897199999998979
Q gi|254780440|r   84 -DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI  158 (158)
Q Consensus        84 -~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi  158 (158)
                       ++|.||+||+|.+ ++|.+.+|.|||++|.|..+++||+.|||++||+++++||+|.+.||.|...+.|++|+||
T Consensus        82 t~~VfFGAwV~le~-~DG~~~r~rIVG~DEid~r~n~ISidSPlARaL~kke~gdevvvnTPaGe~~~~v~~iEY~  156 (157)
T TIGR01461        82 TDKVFFGAWVELED-DDGREQRYRIVGIDEIDTRKNKISIDSPLARALIKKEVGDEVVVNTPAGEEEWYVLSIEYV  156 (157)
T ss_pred             CCCEEEEEEEEEEC-CCCCCCCEEEEECCCCCCCCCCEEEECHHHHHHHCCCCCCEEEEECCCCCCEEEEEEEEEC
T ss_conf             57677225888653-8883202688605521235772014266788863012587778757888504788875206


No 5  
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=100.00  E-value=4.3e-44  Score=301.55  Aligned_cols=152  Identities=18%  Similarity=0.277  Sum_probs=139.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             98431488999999999999987248999999999975176222430489998876879999999974444210472101
Q gi|254780440|r    2 VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM   81 (158)
Q Consensus         2 ~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~   81 (158)
                      |+.-|||++||++|++||++|++++|+.+.+.+.+|+++|||||||||++||++|+++++||++|+.+|.+|.+   ...
T Consensus         5 ~~~p~lTpeG~~~L~~EL~~Lk~~rr~~v~~~~~~a~~~GDlSENaEY~~aK~eq~~ie~RI~~Le~~L~~a~~---~~~   81 (161)
T PRK05892          5 VESPGLADAARDHLAAELARLRQRRDRLEVEVKNDRGMIGDHGDAAEAIQRADELAILGDRINELDRRLRTGPT---PWS   81 (161)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCC
T ss_conf             57999799999999999999988263999999999997799456673999999999999999999999972888---778


Q ss_pred             CCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCC---CCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             3321113657999534765235999963101334---588150131789987288888789998289719999999897
Q gi|254780440|r   82 SGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADV---QSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus        82 ~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~---~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      ..+.|.||++|++.+ ++|+..+|+|||..++++   +.++||+.||||+|||||++||+|+|++|+|..+|+|++|+|
T Consensus        82 ~~~~v~~G~~Vti~~-edg~~~~~~iVg~~ee~~~~~~~~~IS~~SPlgrALlGk~~GD~V~v~tP~G~~~~~Il~Ik~  159 (161)
T PRK05892         82 GSETLPGGTEVTLRF-PDGEVVTMHVISIVEETPVGREAETLTARSPLGQALAGHQPGDTVTYSTPQGPNQVQLLAVKL  159 (161)
T ss_pred             CCCEEECCEEEEEEE-CCCCEEEEEEECCCCCCCCCCCCCEECCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC
T ss_conf             888784666999996-899889999973416574567676563679789998489899989997599757999999967


No 6  
>PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated
Probab=100.00  E-value=5e-44  Score=301.21  Aligned_cols=154  Identities=33%  Similarity=0.551  Sum_probs=151.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             84314889999999999999872489999999999751762224304899988768799999999744442104721013
Q gi|254780440|r    3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMS   82 (158)
Q Consensus         3 ~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~   82 (158)
                      +.+++|+++|++.+.||++|+.++.|+++++|++||++|||+|||||+||+|+|+++.+++..|+..|.+|+|+|+.+..
T Consensus       748 ~~liVT~~sl~kKKkELe~Lv~veipENSKdIg~ArelGDLRENAEYKaAkEkQ~~L~~~i~rLe~Ei~rArIlD~~~v~  827 (906)
T PRK06330        748 IGFLVTRRALNKKKKELEHLKNVEIPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIKSAKILDLTDVK  827 (906)
T ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCCCCCC
T ss_conf             52896189998889999998644555245779999863660120677889999999999999999985520622532032


Q ss_pred             CCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEE
Q ss_conf             32111365799953476523599996310133458815013178998728888878999828971999999989
Q gi|254780440|r   83 GDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL  156 (158)
Q Consensus        83 ~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~  156 (158)
                      +++|+|||+|++.|..+|+..+|+|+||||+||++|.|||.||+|++|||++.||++++.+|+....|+|++|+
T Consensus       828 T~kVg~GTkV~l~n~~tg~~etYtILGpWDaDPek~IISY~SP~G~~LLgkKtGd~~~~~~~~~~~~y~v~~I~  901 (906)
T PRK06330        828 TSKVGFGTKVKLKNESTGEEESYSILGPWESDPEKGIISYQSPLGKSLLGKKEGDSADFVINDTETRYTVLDIE  901 (906)
T ss_pred             CCEECCCEEEEEEECCCCCEEEEEEECCCCCCCCCCCEECCCHHHHHHHCCCCCCEEEEEECCCEEEEEEEEEE
T ss_conf             33440554899875577866789974476678212823401755476527876771699967846899998633


No 7  
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=100.00  E-value=2.4e-42  Score=290.52  Aligned_cols=151  Identities=46%  Similarity=0.756  Sum_probs=147.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             48899999999999998724899999999997517622243048999887687999999997444421047210133211
Q gi|254780440|r    7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRI   86 (158)
Q Consensus         7 lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V   86 (158)
                      ||.+|+++|+.||++|+.++||++.+.+.+|+++|||+|||+|++||++|+++++||.+|+.+|++|++++++..+. +|
T Consensus         1 ~T~~g~~~l~~el~~l~~~~rp~i~~~i~~ar~~gdl~enaey~aak~~q~~~e~ri~~le~~l~~a~vi~~~~~~~-~V   79 (151)
T COG0782           1 LTDEGFRKLKEELEYLKPVERPEIVEEIADARELGDLSENAEYRAAKEEQAFIERRIRLLEELLRNAQVIDDEKPPD-VV   79 (151)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCC-EE
T ss_conf             96027789999999765535226999999999715501083547899875101779999998860754158777789-78


Q ss_pred             CCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC
Q ss_conf             136579995347652359999631013345881501317899872888887899982897199999998979
Q gi|254780440|r   87 AFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI  158 (158)
Q Consensus        87 ~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi  158 (158)
                      .|||+|++.+.++|++.+|+||||+|+||++|+||+.||+|+||+|+++||+|.|.+|+|...|+|++|.|.
T Consensus        80 ~~Gs~V~~~~~~~ge~~~~~iVg~~ead~~~~~IS~~SPig~aLlGk~vGd~v~v~~p~g~~~~~I~~I~~~  151 (151)
T COG0782          80 TFGSTVTLENLDDGEEVTYTIVGPDEADPAKGKISVDSPLGRALLGKKVGDTVEVNTPGGEKEVEILSIEYQ  151 (151)
T ss_pred             ECCCEEEEEECCCCCEEEEEEECCCCCCCCCCCEECCCHHHHHHHCCCCCCEEEEECCCCEEEEEEEEEECC
T ss_conf             469889999879996899999824103601493304597789972899999899835996079999987129


No 8  
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=100.00  E-value=3.2e-32  Score=226.06  Aligned_cols=134  Identities=31%  Similarity=0.510  Sum_probs=121.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             84314889999999999999872489999999999751762224304899988768799999999744442104721013
Q gi|254780440|r    3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMS   82 (158)
Q Consensus         3 ~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~   82 (158)
                      .++|+|++||.+|++||..|.        ..+.+|...||.++|      |.+++.+++||++|..+|+.|+||++.. .
T Consensus        27 ~~NYvTP~G~~~L~~el~~l~--------~~~~~a~~~~d~~~~------k~~l~~i~R~iRyl~~Rl~~A~vv~~~~-~   91 (160)
T PRK06342         27 HPNLVTEAGLKALEDQLQQAR--------AAYEAAQAIEDVNER------RRQMARPLRDLRYLAARVRTAQLMPDPP-S   91 (160)
T ss_pred             CCCEECHHHHHHHHHHHHHHH--------HHHHHHHHCCCHHHH------HHHHHHHHHHHHHHHHHHHCCEEECCCC-C
T ss_conf             876108999999999999999--------999987516531576------8876326688999999872178848999-8


Q ss_pred             CCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEE
Q ss_conf             32111365799953476523599996310133458815013178998728888878999828971999999989
Q gi|254780440|r   83 GDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL  156 (158)
Q Consensus        83 ~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~  156 (158)
                      .++|.||+||++.+ ++|++.+|+|||++|+|+.+|+|||.||||+||||+++||+|++    |...|+|++|.
T Consensus        92 ~d~V~FGatVt~~~-e~g~~~t~~IVG~dEaD~~~g~IS~~SPlaraLlgk~vGD~V~v----G~~~~EI~~Is  160 (160)
T PRK06342         92 TDVVAFGSTVTFSR-DDGRVQTYRIVGEDEADPKAGSISYVSPVARLLMGKAVGDVVGV----GGQELEIIAIA  160 (160)
T ss_pred             CCEEEEEEEEEEEE-CCCCEEEEEEECHHHCCCCCCEEECCCHHHHHHHCCCCCCEEEE----CCEEEEEEEEC
T ss_conf             99899835999992-89999999996834447358967535989999838999998998----88279999859


No 9  
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=99.96  E-value=2.6e-30  Score=213.87  Aligned_cols=123  Identities=28%  Similarity=0.468  Sum_probs=109.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEE
Q ss_conf             89999999999751762224304899988768799999999744442104721013321113657999534765235999
Q gi|254780440|r   27 RPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQ  106 (158)
Q Consensus        27 r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~  106 (158)
                      ||.+.-...+++.++||.||++|++++.        ...|+..|++|+||+++.+|.|+|+|||+|+++|.++|++++|+
T Consensus         4 rP~I~it~~D~~rL~~L~e~a~~~~~~~--------a~~L~~eL~rA~Vvd~~~ip~dvV~~gS~V~~~d~~~g~~~~~~   75 (135)
T PRK05753          4 RPTIIINELDAERLDRLLEQPAYAGPPI--------AEALNAELDRAQVVPPAEMPADVVTMNSRVRFRDLSSGEERVVT   75 (135)
T ss_pred             CCCEEEEHHHHHHHHHHHHHHHHCCCHH--------HHHHHHHHCCCEEECHHHCCCCEEEECCEEEEEECCCCCEEEEE
T ss_conf             8978977788999999986565418689--------99999987487895822079998998989999988999899999


Q ss_pred             EECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCE-EEEEEEEEEE
Q ss_conf             96310133458815013178998728888878999828971-9999999897
Q gi|254780440|r  107 IVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGE-KTYEILQVLW  157 (158)
Q Consensus       107 lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~-~~~~Il~I~y  157 (158)
                      ||||+|+|+..|+||+.||+|+||||+++||+|+|++|+|. ..|+|++|.|
T Consensus        76 LV~p~ead~~~gkISv~SPiG~ALlG~~~Gd~i~~~~P~G~~~~l~I~~V~y  127 (135)
T PRK05753         76 LVYPADADISNGQVSVLAPVGAALLGLSVGQSIDWPLPGGKETHLTVLEVEY  127 (135)
T ss_pred             EECHHHCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEEE
T ss_conf             9490264944792010169999973899999999988999778999999988


No 10 
>pfam01272 GreA_GreB Transcription elongation factor, GreA/GreB, C-term. This domain has a FKBP-like fold.
Probab=99.88  E-value=1.7e-22  Score=164.18  Aligned_cols=76  Identities=46%  Similarity=0.850  Sum_probs=74.2

Q ss_pred             CCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             3321113657999534765235999963101334588150131789987288888789998289719999999897
Q gi|254780440|r   82 SGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus        82 ~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      |.|+|+|||+|+++|.+++++.+|+||||+|+|++.++||+.||||+||||+++||+|+|++|+|..+|+|++|+|
T Consensus         2 ~~d~V~~Gs~V~i~~~~~~~~~~~~iVg~~ea~~~~~~IS~~SPlg~ALlG~~~Gd~v~~~~p~G~~~~~I~~I~~   77 (77)
T pfam01272         2 PADVVTFGSTVTLEDLDDGEEETYTIVGPDEADPSKGKISVLSPLGRALLGKKVGDEVEVTAPSGEKKYEILKIEY   77 (77)
T ss_pred             CCCEEEECCEEEEEECCCCCEEEEEEECHHHCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC
T ss_conf             9999999989999999999899999979689282579228889889997399999999999699879999999999


No 11 
>pfam03449 GreA_GreB_N domain. This domain adopts a long alpha-hairpin structure.
Probab=99.84  E-value=8.3e-21  Score=153.39  Aligned_cols=71  Identities=56%  Similarity=0.797  Sum_probs=69.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             31488999999999999987248999999999975176222430489998876879999999974444210
Q gi|254780440|r    5 IPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEV   75 (158)
Q Consensus         5 ~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~i   75 (158)
                      +|||++||++|++||++|++++||+++++|++||++|||||||||++||++|+++++||.+|+.+|++|+|
T Consensus         1 ~~lT~eg~~~L~~EL~~L~~v~rp~i~~~i~~Ar~~GDlsENaeY~aAke~q~~le~RI~eLe~~L~~A~I   71 (71)
T pfam03449         1 NPITPEGYEKLQEELERLKNVERPEIIKAIAEAREHGDLSENAEYHAAKEEQREIEARIRELEDRLARAEI   71 (71)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999999987538999999999988599042067899999999999999999999961869


No 12 
>PRK01490 tig trigger factor; Provisional
Probab=91.53  E-value=1.3  Score=24.83  Aligned_cols=86  Identities=13%  Similarity=0.264  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEC--------CCCCEEEEEE-ECHHHCCCCCCEECCCCHH
Q ss_conf             768799999999744442104721013321113657999534--------7652359999-6310133458815013178
Q gi|254780440|r   56 QNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEK--------NSGDKKNYQI-VGDQEADVQSGLVSISSPI  126 (158)
Q Consensus        56 q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~--------~~~~~~~~~l-Vg~~e~d~~~~~IS~~SPl  126 (158)
                      ...++..|..|....+...-++.      .+..|..|++-..        +.+....|.+ +|+.         ++..-+
T Consensus       134 d~~Vd~~i~~l~~~~a~~~~~e~------~~~~gD~v~id~~~~~dg~~~~~~~~~~~~~~lg~~---------~~i~gf  198 (435)
T PRK01490        134 DEDVDEMLENLRKQFATLVPVER------PAENGDRVTIDFVGSIDGEEFEGGKAEDFSLELGSG---------RMIPGF  198 (435)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCH------HHCCCCEEEEEEEEEECCCCCCCCCCCCEEEEECCC---------CCCHHH
T ss_conf             89999999999975076556540------212698799998987668204677765069990588---------775559


Q ss_pred             HHHHCCCCCCCEEEEEC--CC--------C---EEEEEEEEEE
Q ss_conf             99872888887899982--89--------7---1999999989
Q gi|254780440|r  127 ARALIGKELGDIISVNA--PG--------G---EKTYEILQVL  156 (158)
Q Consensus       127 G~ALlG~~~Gd~V~v~~--p~--------G---~~~~~Il~I~  156 (158)
                      ..+|+|.++||++++.+  |.        |   ..+++|.+|.
T Consensus       199 ~~~LiG~k~Gd~~~~~v~fp~d~~~~~laGk~~~f~v~v~~I~  241 (435)
T PRK01490        199 EEQLVGMKAGEEKTIDVTFPEDYHAEDLAGKEATFKVTVKEVK  241 (435)
T ss_pred             HHHHCCCCCCCEEEEEECCCCCCCCHHHCCCCEEEEEEEEEEE
T ss_conf             9985468778621122037642220243488527999875530


No 13 
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=74.49  E-value=7.8  Score=19.88  Aligned_cols=34  Identities=24%  Similarity=0.338  Sum_probs=22.3

Q ss_pred             CCHHHHHHCCCCCCCEEE--EECCC--------C-E--EEEEEEEEE
Q ss_conf             317899872888887899--98289--------7-1--999999989
Q gi|254780440|r  123 SSPIARALIGKELGDIIS--VNAPG--------G-E--KTYEILQVL  156 (158)
Q Consensus       123 ~SPlG~ALlG~~~Gd~V~--v~~p~--------G-~--~~~~Il~I~  156 (158)
                      .--+-.+|+|.++||++.  +..|.        | .  ..++|.+|.
T Consensus       195 ipgFe~~LvG~k~Ge~k~i~vtFP~~y~a~~LaGK~a~F~V~vkeVk  241 (441)
T COG0544         195 IPGFEDQLVGMKAGEEKDIKVTFPEDYHAEELAGKEATFKVKVKEVK  241 (441)
T ss_pred             HHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHCCCCEEEEEEEEEEE
T ss_conf             44288641368579756898871665306673899638999999985


No 14 
>cd06213 oxygenase_e_transfer_subunit The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with  Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=70.62  E-value=9.5  Score=19.32  Aligned_cols=65  Identities=17%  Similarity=0.200  Sum_probs=42.2

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECHHHCCCCC-CEECC--CCHHHHHHCC-CCCCCEEEEECCCCEEEE
Q ss_conf             11365799953476523599996310133458-81501--3178998728-888878999828971999
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQS-GLVSI--SSPIARALIG-KELGDIISVNAPGGEKTY  150 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~-~~IS~--~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~  150 (158)
                      -..|-.|.+.-.+.+..+.|+|+.+...+..- -.|..  ...+...|.. .++||+|.+.-|.|...+
T Consensus        28 f~pGQ~v~l~~~g~~~~R~ySias~p~~~~~i~~~Vk~~~~G~~s~~l~~~l~~Gd~v~v~gP~G~f~l   96 (227)
T cd06213          28 YKAGQYAELTLPGLPAARSYSFANAPQGDGQLSFHIRKVPGGAFSGWLFGADRTGERLTVRGPFGDFWL   96 (227)
T ss_pred             CCCCEEEEEEECCCCCCCEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEECCCCCEEE
T ss_conf             199858999989907520345536899888899999986799427899843899989999747336483


No 15 
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=69.74  E-value=10  Score=19.20  Aligned_cols=79  Identities=28%  Similarity=0.331  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             9999999999999872489999999999751762224--30489998876879999999974444210472101332111
Q gi|254780440|r   10 KGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSEN--AEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIA   87 (158)
Q Consensus        10 ~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~EN--aeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V~   87 (158)
                      +-+.+++.+++.|+. +|-.++++|..+...|+-.+.  .+-..-+++...++..+.+++..|...- ..-..++.+.|.
T Consensus        35 ~~rr~l~~e~e~Lr~-erN~iSK~Ig~~kk~g~~~~~l~~~~~~lk~~i~~le~~~~~~~~~l~~~l-l~IPNi~~~~VP  112 (422)
T PRK05431         35 EERRELQTETEELQA-ERNALSKEIGQAKAKGEDAEELIAEVKELKEEIKALEAELKELEAELEELL-LSIPNLPHDSVP  112 (422)
T ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCCCCC
T ss_conf             999999999999999-999999999998748977999999999999999999999999999999999-848998886578


Q ss_pred             CCC
Q ss_conf             365
Q gi|254780440|r   88 FGA   90 (158)
Q Consensus        88 ~Gs   90 (158)
                      +|.
T Consensus       113 ~G~  115 (422)
T PRK05431        113 VGK  115 (422)
T ss_pred             CCC
T ss_conf             899


No 16 
>pfam02359 CDC48_N Cell division protein 48 (CDC48), N-terminal domain. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain.
Probab=68.84  E-value=10  Score=19.08  Aligned_cols=69  Identities=17%  Similarity=0.220  Sum_probs=51.5

Q ss_pred             HHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECHHHC-CCCCCEECCCCHHHHHHCCCCCCCEEEEEC
Q ss_conf             44421047210133211136579995347652359999631013-345881501317899872888887899982
Q gi|254780440|r   70 ITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEA-DVQSGLVSISSPIARALIGKELGDIISVNA  143 (158)
Q Consensus        70 L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~-d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~  143 (158)
                      ..+...++|..++.-.+.-|..|.+..    +..|.-+|.|... |...|.|.+..+. +.-+|-..||.|++..
T Consensus        14 g~~iarv~p~~m~~l~~~~GD~v~i~G----~r~t~a~v~~~~~~d~~~g~I~~d~~~-R~na~v~igd~V~V~~   83 (87)
T pfam02359        14 GRGIARLSPKDMDELGLFRGDIVEIKG----KRRTVAIVFPARPEDEGPGIIRMDGVQ-RKNAGVSIGDEVTVRP   83 (87)
T ss_pred             CCCEEEECHHHHHHCCCCCCCEEEEEE----CCEEEEEEECCCCCCCCCCEEEECHHH-HHHCCCCCCCEEEEEE
T ss_conf             887799699999985999999999981----744899997178242679879977788-8666988999899997


No 17 
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=68.67  E-value=7.1  Score=20.14  Aligned_cols=28  Identities=32%  Similarity=0.576  Sum_probs=22.6

Q ss_pred             CEECCCCHHHHHHCCCCCCCEEEEECCC
Q ss_conf             8150131789987288888789998289
Q gi|254780440|r  118 GLVSISSPIARALIGKELGDIISVNAPG  145 (158)
Q Consensus       118 ~~IS~~SPlG~ALlG~~~Gd~V~v~~p~  145 (158)
                      |.=++..+|=+||+|+.+|+..++.+|-
T Consensus        38 G~g~li~glE~al~g~~~Ge~~~V~IpP   65 (174)
T COG1047          38 GAGQLIPGLEEALLGKEVGEEFTVEIPP   65 (174)
T ss_pred             CCCCCCHHHHHHHHCCCCCCEEEEEECC
T ss_conf             6987206599987177789616898682


No 18 
>pfam11599 AviRa RRNA methyltransferase AviRa. This family of proteins represents the methyltransferase AviRa from Streptomyces viridochromogenes. This protein mediates the resistance to the antibiotic avilamycin. AviRa methylates a specific guanine base within the peptidyl-transferase loop of the 23S ribosomal RNA.
Probab=68.05  E-value=8.4  Score=19.67  Aligned_cols=86  Identities=16%  Similarity=0.266  Sum_probs=52.9

Q ss_pred             CCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             1488999999999999987-248999999999975176222430489998876879999999974444210472101332
Q gi|254780440|r    6 PVTSKGFDKIQQELRWRQQ-EERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD   84 (158)
Q Consensus         6 ~lT~~g~~~L~~El~~l~~-~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~   84 (158)
                      .+|++|+++-++||..+-. -.+|.-++..               ++|.+-.+.+.+.-..+-..+++|-|.|+.....-
T Consensus        99 LLt~~GL~~R~~eL~e~~~~f~k~s~~~aa---------------~aA~Rl~~~l~a~gg~~p~~~~~ADvfdp~~l~~~  163 (249)
T pfam11599        99 LLSKAGINAREDELKALSERFGKASHIDAA---------------HAADRIEELLTAEGGALPCAIKTADLFDGNALEAC  163 (249)
T ss_pred             HHCHHHHHHHHHHHHHHHHHHCCCHHHHHH---------------HHHHHHHHHHHCCCCCCCCHHHEECCCCCCHHHHH
T ss_conf             403201677899999999984882578899---------------88899999986038998612100023586036777


Q ss_pred             CCCCCCEEEEEECCCCCEEEEE
Q ss_conf             1113657999534765235999
Q gi|254780440|r   85 RIAFGATVSLVEKNSGDKKNYQ  106 (158)
Q Consensus        85 ~V~~Gs~V~l~d~~~~~~~~~~  106 (158)
                      ...++.-|.+.|+.-|+..+++
T Consensus       164 ~~g~~pDiVvTDlPYGe~t~We  185 (249)
T pfam11599       164 DAGFAPDIIITDLPYGEMTEWE  185 (249)
T ss_pred             HCCCCCCEEEECCCCCCEEEEC
T ss_conf             4378888688437877400223


No 19 
>PRK02195 V-type ATP synthase subunit D; Provisional
Probab=67.19  E-value=11  Score=18.87  Aligned_cols=69  Identities=17%  Similarity=0.287  Sum_probs=38.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99843148899999999999998------724899999999997517622243048999887687999999997444421
Q gi|254780440|r    1 MVDKIPVTSKGFDKIQQELRWRQ------QEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAE   74 (158)
Q Consensus         1 M~~k~~lT~~g~~~L~~El~~l~------~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~   74 (158)
                      ||-++-.|+--+.+++..|....      .-+|..+..++..+.+        ++...++....+...+......++.+-
T Consensus         1 mm~kv~pTr~eL~~lk~~Lk~a~rg~~lLk~Kr~~L~~e~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (201)
T PRK02195          1 MMSKVKLTKNSLRKQKQQLKMLERYLPTLKLKKAQLQAEVQRAKA--------EAAELELEREQLEERIYAFASLFSEPL   72 (201)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             976658749999999999999986434799999999999999999--------999999999999999999999855400


Q ss_pred             CCC
Q ss_conf             047
Q gi|254780440|r   75 VID   77 (158)
Q Consensus        75 iv~   77 (158)
                      .++
T Consensus        73 ~~~   75 (201)
T PRK02195         73 EFD   75 (201)
T ss_pred             HHH
T ss_conf             333


No 20 
>PRK04290 30S ribosomal protein S6e; Validated
Probab=62.93  E-value=11  Score=18.99  Aligned_cols=27  Identities=37%  Similarity=0.529  Sum_probs=18.5

Q ss_pred             EECCCCHHHHHHCCCCCCCEEEEECCC
Q ss_conf             150131789987288888789998289
Q gi|254780440|r  119 LVSISSPIARALIGKELGDIISVNAPG  145 (158)
Q Consensus       119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~  145 (158)
                      .+.+...-..+|+|++.||+|.-..-+
T Consensus        18 ~~ei~~~~~~~~~gkkIGdevdg~~lG   44 (115)
T PRK04290         18 QIEIDGAEANRLIGKKIGDEIDGSIVG   44 (115)
T ss_pred             EEEECCHHHHHHHCCCCCCEECCCEEC
T ss_conf             999784787433045011477531807


No 21 
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=57.49  E-value=17  Score=17.76  Aligned_cols=27  Identities=15%  Similarity=0.175  Sum_probs=17.3

Q ss_pred             CCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             288888789998289719999999897
Q gi|254780440|r  131 IGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus       131 lG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      --.++||.|.+....+.+.|+|.+++-
T Consensus        62 ~~l~~GD~I~v~~~~~~~~Y~V~~~~i   88 (127)
T cd06165          62 YKVKVGDKIYLTDKDNVYEYKVTSKKI   88 (127)
T ss_pred             HHCCCCCEEEEEECCCEEEEEEEEEEE
T ss_conf             568999999999899399999948999


No 22 
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=57.42  E-value=17  Score=17.75  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=11.0

Q ss_pred             CCHHHHHHCCCCCCCEEEEECCC
Q ss_conf             31789987288888789998289
Q gi|254780440|r  123 SSPIARALIGKELGDIISVNAPG  145 (158)
Q Consensus       123 ~SPlG~ALlG~~~Gd~V~v~~p~  145 (158)
                      ..-|=+||+|+++||.++|.+|.
T Consensus        42 ipglE~aL~G~~~Gd~~~vtl~p   64 (196)
T PRK10737         42 ISGLETALEGHEVGDKFDVAVGA   64 (196)
T ss_pred             CHHHHHHHCCCCCCCEEEEEECH
T ss_conf             67899985799999778999787


No 23 
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=56.14  E-value=18  Score=17.62  Aligned_cols=28  Identities=32%  Similarity=0.419  Sum_probs=16.3

Q ss_pred             HCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             7288888789998289719999999897
Q gi|254780440|r  130 LIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus       130 LlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      |--.+.||.|.+...++.+.|+|.+++.
T Consensus        62 L~~l~~GD~I~l~~~~~~y~Y~V~~~~i   89 (126)
T cd06166          62 LDEVEKGDEIKVTTKNGTYKYKITSIFV   89 (126)
T ss_pred             HHHCCCCCEEEEEECCEEEEEEEEEEEE
T ss_conf             5518589999999999899999977999


No 24 
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=55.88  E-value=12  Score=18.64  Aligned_cols=73  Identities=22%  Similarity=0.333  Sum_probs=50.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCC
Q ss_conf             22430489998876879999999974-444210472101332111365799953476523599996310133458
Q gi|254780440|r   44 SENAEYQAAKELQNLNEGRMAELENI-ITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQS  117 (158)
Q Consensus        44 ~ENaeY~aAke~q~~~~~ri~~L~~~-L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~  117 (158)
                      +||+.-|.-+..|..++++ +-|... +-.+.|-..-....+++++|-.|.+.|..-+..-.|+||..-|-+...
T Consensus        94 rEnqtthdfrqqQkiieaK-qSlk~~GiP~ykv~~~~epk~G~~Gl~iqvnY~Dd~a~~~P~yRivs~lEq~ve~  167 (222)
T COG5246          94 RENQTTHDFRQQQKIIEAK-QSLKRSGIPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEMPQYRIVSSLEQNVEE  167 (222)
T ss_pred             CCCCCHHHHHHHHHHHHHH-HHHHHCCCCCEEEEEEECCCCCCEEEEEEEECCCHHHCCCCCEEHHHHHHHCCHH
T ss_conf             3588404556677889998-8787549973367776637788400478972550221258614304466652010


No 25 
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=55.54  E-value=18  Score=17.56  Aligned_cols=26  Identities=35%  Similarity=0.510  Sum_probs=16.2

Q ss_pred             CCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             88888789998289719999999897
Q gi|254780440|r  132 GKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus       132 G~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      -.+.||.|.+...++.+.|+|.+++-
T Consensus        61 ~l~~GD~I~l~~~~~~y~Y~V~~~~v   86 (127)
T cd05828          61 ELEPGDIITLQTLGGTYTYRVTSTRI   86 (127)
T ss_pred             HCCCCCEEEEEECCEEEEEEEEEEEE
T ss_conf             57479999999788399999977999


No 26 
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=55.41  E-value=18  Score=17.54  Aligned_cols=36  Identities=25%  Similarity=0.252  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             0131789987288888789998289719999999897
Q gi|254780440|r  121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus       121 S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      ++.+|+. -|-..++||.|.+...++.+.|+|.+++-
T Consensus        55 ~~~~~F~-~L~~l~~GD~I~v~~~~~~~~Y~V~~~~i   90 (137)
T cd05830          55 TYGAPFN-DLDKLRPGDKIVVETADGWYTYVVRSSEI   90 (137)
T ss_pred             CCCCCCC-CHHCCCCCCEEEEEECCEEEEEEEEEEEE
T ss_conf             9775560-13538999999999999899999974999


No 27 
>pfam00970 FAD_binding_6 Oxidoreductase FAD-binding domain.
Probab=53.65  E-value=19  Score=17.36  Aligned_cols=65  Identities=20%  Similarity=0.244  Sum_probs=42.1

Q ss_pred             CCCCCEEEEEECCCC--CEEEEEEECHHHCC-CCCCEEC--CCCHHHHHHCCCCCCCEEEEECCCCEEEE
Q ss_conf             113657999534765--23599996310133-4588150--13178998728888878999828971999
Q gi|254780440|r   86 IAFGATVSLVEKNSG--DKKNYQIVGDQEAD-VQSGLVS--ISSPIARALIGKELGDIISVNAPGGEKTY  150 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~--~~~~~~lVg~~e~d-~~~~~IS--~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~  150 (158)
                      ...|..|.+.-...|  ....|+++.+...+ ...=.|-  ..-++-..|-..++||+|.+.-|-|...|
T Consensus        30 f~pGQ~v~l~~~~~g~~~~R~YS~~s~p~~~~~~e~~Vk~~~~G~~S~~l~~l~~Gd~v~i~gP~G~F~~   99 (99)
T pfam00970        30 LPPGQHIFLRLPIDGKLVVRAYSPASSPDDVGELELLVKVYPGGKMSQYLDSLKVGDTVEVKGPLGHFEY   99 (99)
T ss_pred             CCCCEEEEEEEEECCEEEEEEEECCCCCCCCCEEEEEEEEECCCCHHHHHHCCCCCCEEEEECCCEEEEC
T ss_conf             8996099999765998998772215665789859999999707966778752899999999843586679


No 28 
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=51.66  E-value=21  Score=17.16  Aligned_cols=38  Identities=26%  Similarity=0.302  Sum_probs=29.4

Q ss_pred             EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE
Q ss_conf             150131789987288888789998289719999999897
Q gi|254780440|r  119 LVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus       119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      .+|+.--+++. +|-|.||+|++..-+-+..-+|.+++-
T Consensus       598 ~VS~e~~~A~~-LglKLGDtvTf~v~gq~i~A~I~slR~  635 (829)
T COG3127         598 EVSMEEGEAKR-LGLKLGDTVTFMVLGQNITAKITSLRK  635 (829)
T ss_pred             CCCHHHHHHHH-HCCCCCCEEEEEECCCEEEEEECEEEE
T ss_conf             44020867987-097627779998426267765110223


No 29 
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=51.23  E-value=21  Score=17.12  Aligned_cols=29  Identities=24%  Similarity=0.350  Sum_probs=20.4

Q ss_pred             HCCCCCCCEEEEECCCCEEEEEEEEEEEC
Q ss_conf             72888887899982897199999998979
Q gi|254780440|r  130 LIGKELGDIISVNAPGGEKTYEILQVLWI  158 (158)
Q Consensus       130 LlG~~~Gd~V~v~~p~G~~~~~Il~I~yi  158 (158)
                      |--.+.||.|.+...++.+.|+|.+++.+
T Consensus        62 L~~l~~GD~i~i~~~~~~y~Y~V~~~~iv   90 (128)
T cd00004          62 LDNLKKGDKIYLTDGGKTYVYKVTSILTV   90 (128)
T ss_pred             HHHCCCCCEEEEEECCEEEEEEEEEEEEE
T ss_conf             54576899899999998999999889998


No 30 
>cd06210 MMO_FAD_NAD_binding Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water.
Probab=48.01  E-value=24  Score=16.81  Aligned_cols=64  Identities=14%  Similarity=0.215  Sum_probs=41.7

Q ss_pred             CCCCEEEEEECCCCCEEEEEEECHHHCCCC-CCEEC--CCCHHHHHHCC-CCCCCEEEEECCCCEEEE
Q ss_conf             136579995347652359999631013345-88150--13178998728-888878999828971999
Q gi|254780440|r   87 AFGATVSLVEKNSGDKKNYQIVGDQEADVQ-SGLVS--ISSPIARALIG-KELGDIISVNAPGGEKTY  150 (158)
Q Consensus        87 ~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~-~~~IS--~~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~  150 (158)
                      ..|--|++.-.+.+....|+|+++...+.. .=.|.  ....+...|.. .++||.|.+.-|.|...+
T Consensus        36 ~pGQ~v~l~~~g~~~~R~ySi~s~p~~~~~l~~~vk~~~~G~~S~~l~~~l~~Gd~v~v~gP~G~f~l  103 (236)
T cd06210          36 VPGQFVEIEIPGTDTRRSYSLANTPNWDGRLEFLIRLLPGGAFSTYLETRAKVGQRLNLRGPLGAFGL  103 (236)
T ss_pred             CCCCEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEEECCCCCCC
T ss_conf             89960899989988089887602799999899999998499467799855999999999706457501


No 31 
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345   Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene..
Probab=47.73  E-value=24  Score=16.78  Aligned_cols=21  Identities=0%  Similarity=0.208  Sum_probs=10.6

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECH
Q ss_conf             1136579995347652359999631
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGD  110 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~  110 (158)
                      +.+.-.+++.    ++..+|+||=|
T Consensus       393 A~~S~~~e~~----~~~v~FRviDP  413 (510)
T TIGR03007       393 AEVSKQMEVQ----DKAVSFRVIDP  413 (510)
T ss_pred             HHHHHHEEEE----CCCEEEEEECC
T ss_conf             5553303320----67024677567


No 32 
>cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain.  In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.
Probab=47.48  E-value=24  Score=16.75  Aligned_cols=64  Identities=16%  Similarity=0.248  Sum_probs=41.3

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECC--CCHHHHHHCCC-CCCCEEEEECCCCEEE
Q ss_conf             1136579995347652359999631013345881501--31789987288-8887899982897199
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSI--SSPIARALIGK-ELGDIISVNAPGGEKT  149 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~--~SPlG~ALlG~-~~Gd~V~v~~p~G~~~  149 (158)
                      -..|..|.+.-.+.+....|+|..+.+...-.-.|-.  .-+....|... ++||.|.+.-|-|.-.
T Consensus        31 f~pGQ~v~l~~~g~~~~R~ySias~p~~~~l~~~Ik~~~~G~~s~~l~~~~~~Gd~v~i~gP~G~f~   97 (228)
T cd06209          31 FLPGQYVNLQVPGTDETRSYSFSSAPGDPRLEFLIRLLPGGAMSSYLRDRAQPGDRLTLTGPLGSFY   97 (228)
T ss_pred             CCCCCEEEEEECCCCCEEEEEEECCCCCCEEEEEEEECCCCCHHHHHHHCCCCCCEEEEECCCCCCC
T ss_conf             4899759999899284689987008997989999999079956789985589999999970354742


No 33 
>COG3764 SrtA Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane]
Probab=46.84  E-value=25  Score=16.69  Aligned_cols=33  Identities=18%  Similarity=0.414  Sum_probs=27.0

Q ss_pred             CCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC
Q ss_conf             1317899872888887899982897199999998979
Q gi|254780440|r  122 ISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI  158 (158)
Q Consensus       122 ~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi  158 (158)
                      ..+||++    .++||.|-+..+++...|+|.+|.-|
T Consensus       128 ~F~~L~~----lk~GD~iyv~~~~~~~~Y~v~~~~~V  160 (210)
T COG3764         128 LFRPLGK----LKVGDKIYVTTKNETYVYKVTDISIV  160 (210)
T ss_pred             CCCCHHH----HCCCCEEEEEECCCEEEEEEEEEEEE
T ss_conf             5565556----03798899995795799999987885


No 34 
>pfam11160 DUF2945 Protein of unknown function (DUF2945). This family of proteins has no known function.
Probab=45.48  E-value=26  Score=16.56  Aligned_cols=22  Identities=32%  Similarity=0.407  Sum_probs=17.5

Q ss_pred             CCEEEEECCCCEEEEEEEEEEE
Q ss_conf             8789998289719999999897
Q gi|254780440|r  136 GDIISVNAPGGEKTYEILQVLW  157 (158)
Q Consensus       136 Gd~V~v~~p~G~~~~~Il~I~y  157 (158)
                      ||.|.|..+.|...=+|+++.+
T Consensus         1 GD~V~WnS~~g~~~G~V~~~~T   22 (62)
T pfam11160         1 GDHVRWNSEAGEVSGKIVKVHT   22 (62)
T ss_pred             CCCEEECCCCCEEEEEEEEEEC
T ss_conf             9822772899668689999983


No 35 
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=44.25  E-value=27  Score=16.44  Aligned_cols=130  Identities=13%  Similarity=0.195  Sum_probs=72.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             14889999999999999872489999999999751762224304899988768799999999744442104721013321
Q gi|254780440|r    6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDR   85 (158)
Q Consensus         6 ~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~   85 (158)
                      .+|++.|.+.-++....-.=+-.++...+.....  ..|+|-+|..|.    .+-.+|..|+...+.-.|+.....+.|+
T Consensus       169 ~is~e~Y~~~V~~~~~fL~Gk~~~~~~~L~~~M~--~aS~~l~FE~AA----~~RD~I~aL~~i~~~Q~v~~~~~~d~Dv  242 (519)
T PRK12306        169 NISSDEYLEQVKKAEEVLKGNIQELIEKLEEEMA--EKAKNQQFERAL----VIRDEINAIENLQERQNVERQKKYDEDI  242 (519)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH--HHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCCCCCCCCCCE
T ss_conf             6899999999999999981796899999999999--999744089999----9999999999997505111577655415


Q ss_pred             CCCC-----CEEEEEECCCCCEEEEEEECHHHC--------------------C-CCCCEECC----CCHHHHHHCCCCC
Q ss_conf             1136-----579995347652359999631013--------------------3-45881501----3178998728888
Q gi|254780440|r   86 IAFG-----ATVSLVEKNSGDKKNYQIVGDQEA--------------------D-VQSGLVSI----SSPIARALIGKEL  135 (158)
Q Consensus        86 V~~G-----s~V~l~d~~~~~~~~~~lVg~~e~--------------------d-~~~~~IS~----~SPlG~ALlG~~~  135 (158)
                      +++-     +.|.+...-.|.     |+|....                    . |..=.++.    ...+=...|..+.
T Consensus       243 i~~~~~~~~~~i~v~~vR~G~-----l~g~~~~~~~~~e~il~~fl~qyY~~~~~P~~Iil~~~~~~~~~~l~~~L~~~~  317 (519)
T PRK12306        243 INYIVKDGTVYLMVFNVLKGT-----LFDKKEFVFDYGENFFEEFLIQYYSENEPPSEIILSELPENLEEALLEYLSHKK  317 (519)
T ss_pred             EEEEECCCEEEEEEEEEECCE-----EECCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             789862882999999998999-----835752215764057999999997437998403425788766899999998860


Q ss_pred             CCEEEEECCCC
Q ss_conf             87899982897
Q gi|254780440|r  136 GDIISVNAPGG  146 (158)
Q Consensus       136 Gd~V~v~~p~G  146 (158)
                      |..|.+.+|..
T Consensus       318 ~~kv~i~~P~r  328 (519)
T PRK12306        318 GSKVKITVPKQ  328 (519)
T ss_pred             CCCEEEECCCC
T ss_conf             99569975896


No 36 
>PTZ00066 pyruvate kinase; Provisional
Probab=43.90  E-value=27  Score=16.40  Aligned_cols=87  Identities=21%  Similarity=0.268  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-----EEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCH-HHHHHCCC
Q ss_conf             9999999974444210472101332111365-----79995347652359999631013345881501317-89987288
Q gi|254780440|r   60 EGRMAELENIITRAEVIDISTMSGDRIAFGA-----TVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSP-IARALIGK  133 (158)
Q Consensus        60 ~~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs-----~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SP-lG~ALlG~  133 (158)
                      -..+++......+..+-=--+.++.+++.|.     .+.+   ..|+..  +|....+...+...|++..| |-+   ..
T Consensus        83 i~~iR~a~~~~~~~~v~Il~Dl~GPkIR~G~l~~~~~i~l---~~G~~v--~i~~~~~~~g~~~~I~v~~~~l~~---~v  154 (513)
T PTZ00066         83 LNNVREAQKSRPNANIGLMLDTKGPEIRTGFLKNHKPITL---KEGSTL--KITTDYTILGDETCISCSYKKLPQ---SV  154 (513)
T ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCEEEEEECCCCCEEEE---CCCCEE--EEECCCCCCCCCCEEEECCCCCHH---HC
T ss_conf             9999999986599966999988898258887489964785---389999--997488657987879725865775---67


Q ss_pred             CCCCEEEEECCCCEEEEEEEEEE
Q ss_conf             88878999828971999999989
Q gi|254780440|r  134 ELGDIISVNAPGGEKTYEILQVL  156 (158)
Q Consensus       134 ~~Gd~V~v~~p~G~~~~~Il~I~  156 (158)
                      ++||.+.+.  +|...++|+++.
T Consensus       155 ~~Gd~Ilid--DG~I~l~V~~v~  175 (513)
T PTZ00066        155 KVGNIILIA--DGSLSCEVLEVH  175 (513)
T ss_pred             CCCCEEEEE--CCEEEEEEEEEC
T ss_conf             889889997--997999999822


No 37 
>COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]
Probab=43.79  E-value=27  Score=16.39  Aligned_cols=65  Identities=18%  Similarity=0.235  Sum_probs=44.5

Q ss_pred             CCCCCCEEEEEECCC--CCEEEEEEECHHHCCCCCCEECCC----CHHHHHHC-CCCCCCEEEEECCCCEEEE
Q ss_conf             111365799953476--523599996310133458815013----17899872-8888878999828971999
Q gi|254780440|r   85 RIAFGATVSLVEKNS--GDKKNYQIVGDQEADVQSGLVSIS----SPIARALI-GKELGDIISVNAPGGEKTY  150 (158)
Q Consensus        85 ~V~~Gs~V~l~d~~~--~~~~~~~lVg~~e~d~~~~~IS~~----SPlG~ALl-G~~~Gd~V~v~~p~G~~~~  150 (158)
                      ....|.-|+|.-...  .....|+|+.+-..+ ..-.||+.    .++-.-|- ..++||++.+..|.|.-.+
T Consensus        34 ~f~pGQ~i~v~l~~~~~~~~R~YSl~s~p~~~-~~~~isVk~~~~G~~S~~Lh~~lk~Gd~l~v~~P~G~F~l  105 (266)
T COG1018          34 DFEPGQYITVGLPNGGEPLLRAYSLSSAPDED-SLYRISVKREDGGGGSNWLHDHLKVGDTLEVSAPAGDFVL  105 (266)
T ss_pred             CCCCCCEEEEEEECCCCEEEEEEEECCCCCCC-CEEEEEEEECCCCCCCHHHHHCCCCCCEEEEECCCCCCCC
T ss_conf             25799738998655994378888833799998-3499999973899746788845999999999668877636


No 38 
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is 
Probab=43.16  E-value=28  Score=16.33  Aligned_cols=29  Identities=21%  Similarity=0.252  Sum_probs=17.1

Q ss_pred             HHHCCCCCCCEEEEECCCCEEEEEEEEEE
Q ss_conf             98728888878999828971999999989
Q gi|254780440|r  128 RALIGKELGDIISVNAPGGEKTYEILQVL  156 (158)
Q Consensus       128 ~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~  156 (158)
                      ..|--.+.||.|.+...++.+.|+|.+++
T Consensus        62 ~~L~~l~~GD~I~l~~~~~~y~Y~V~~~~   90 (131)
T cd05827          62 TDLDKLKKGDKFYIHVLGETLAYQVDQIE   90 (131)
T ss_pred             CHHHCCCCCCEEEEEECCEEEEEEEEEEE
T ss_conf             10343878999999979909999998899


No 39 
>pfam06940 DUF1287 Domain of unknown function (DUF1287). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to pfam00877.
Probab=43.08  E-value=28  Score=16.32  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=15.1

Q ss_pred             CCCCCCEEEEECCCCEEEEEEEE
Q ss_conf             88888789998289719999999
Q gi|254780440|r  132 GKELGDIISVNAPGGEKTYEILQ  154 (158)
Q Consensus       132 G~~~Gd~V~v~~p~G~~~~~Il~  154 (158)
                      --+.||.|+|.+|+|..+.-|++
T Consensus       106 ~yqpGDIV~w~l~~~~~HIgIVs  128 (164)
T pfam06940       106 DYQPGDIVTWMLPGNLPHIGIVS  128 (164)
T ss_pred             HCCCCCEEEEECCCCCCEEEEEE
T ss_conf             66897879997799974589983


No 40 
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.39  E-value=29  Score=16.26  Aligned_cols=23  Identities=30%  Similarity=0.342  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99988768799999999744442
Q gi|254780440|r   51 AAKELQNLNEGRMAELENIITRA   73 (158)
Q Consensus        51 aAke~q~~~~~ri~~L~~~L~~A   73 (158)
                      -+|++...+++||.+|+.+|..+
T Consensus        70 rtR~kl~~Leari~~LEarl~~~   92 (103)
T COG2960          70 RTREKLAALEARIEELEARLASA   92 (103)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999999874246


No 41 
>pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Probab=41.65  E-value=30  Score=16.19  Aligned_cols=60  Identities=23%  Similarity=0.178  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999999999987248999999999975176222430489998876879999999974444
Q gi|254780440|r    9 SKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITR   72 (158)
Q Consensus         9 ~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~   72 (158)
                      +...++|+.|++.|+..-+.++.+--  |--.+|+  |-|=-.-|++++..+.+|.++..++..
T Consensus        79 r~e~e~L~~dve~L~~~L~~ei~k~~--a~~klDl--NleK~riree~~~~e~ki~e~~~kId~  138 (177)
T pfam07798        79 QAENEKLKNDLEKLKNRLRDEIDKVT--AGVRLDL--NLEKGRIREELAEQELKIKETDTKIDT  138 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999861--5257654--555207789998799999999989999


No 42 
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=41.06  E-value=30  Score=16.13  Aligned_cols=70  Identities=23%  Similarity=0.253  Sum_probs=45.6

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEE--CHH-HCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEE-EEEEEE
Q ss_conf             11365799953476523599996--310-1334588150131789987288888789998289719999-999897
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIV--GDQ-EADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYE-ILQVLW  157 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lV--g~~-e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~-Il~I~y  157 (158)
                      --||.. .+.....++.+++.|-  |-. +.+...-.++|.||+|.-......| ...+..|+|...-+ +++.+|
T Consensus        99 PYFGrI-Df~e~g~~~~eriYIGk~g~~de~~~~~lvvDWRaPIasLfYs~t~g-k~~y~~~~~~v~gel~~krk~  172 (747)
T COG3973          99 PYFGRI-DFREGGHGREERIYIGKFGLRDEVGGEHLVVDWRAPIASLFYSDTLG-KRRYKKPQIRVRGELVLKRKF  172 (747)
T ss_pred             CCEEEE-EEEECCCCCCEEEEEEECCCCCCCCCCEEEEECCCCCCCHHCCCCCC-CCCEECCCCEEEEEEEEEEEE
T ss_conf             730157-67745877603688730023456797237886567421000368877-632013661488788752220


No 43 
>COG3738 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.37  E-value=17  Score=17.67  Aligned_cols=31  Identities=19%  Similarity=0.312  Sum_probs=22.7

Q ss_pred             HHHHHHCCCCCCCEEEEECCCCEEEEEEEEE
Q ss_conf             7899872888887899982897199999998
Q gi|254780440|r  125 PIARALIGKELGDIISVNAPGGEKTYEILQV  155 (158)
Q Consensus       125 PlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I  155 (158)
                      |+-+..--.+.||.|+|.+++|.-..-|++-
T Consensus       133 p~~~~~s~y~aGDIvsWRLdngl~HiGv~sd  163 (200)
T COG3738         133 PLSKDPSDYQAGDIVSWRLDNGLAHIGVVSD  163 (200)
T ss_pred             CCCCCCCCCCCCCEEEEECCCCCCEEEEEEC
T ss_conf             9987800037876589872799743678633


No 44 
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=39.80  E-value=30  Score=16.12  Aligned_cols=30  Identities=7%  Similarity=0.148  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCEEEEEECCCCCEEEEEEECHHH
Q ss_conf             13321113657999534765235999963101
Q gi|254780440|r   81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQE  112 (158)
Q Consensus        81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e  112 (158)
                      -|...|-+|..++|.. . ....+|.+++..+
T Consensus        44 KpS~~VK~GD~l~i~~-~-~~~~~v~Vl~~~~   73 (100)
T COG1188          44 KPSKEVKVGDILTIRF-G-NKEFTVKVLALGE   73 (100)
T ss_pred             CCCCCCCCCCEEEEEE-C-CCEEEEEEEECCC
T ss_conf             6556147798999995-7-8189999973543


No 45 
>cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.
Probab=38.36  E-value=33  Score=15.86  Aligned_cols=64  Identities=14%  Similarity=0.247  Sum_probs=42.4

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECHHHCC-CCCCEE--CCCCHHHHHHCC-CCCCCEEEEECCCCEEEE
Q ss_conf             11365799953476523599996310133-458815--013178998728-888878999828971999
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGDQEAD-VQSGLV--SISSPIARALIG-KELGDIISVNAPGGEKTY  150 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d-~~~~~I--S~~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~  150 (158)
                      -..|-.|.+.- +.+....|+|+++...+ ...=.|  .....+...|+. .++||++.+.-|.|...+
T Consensus        26 f~pGQ~v~v~~-~~~~~R~ySi~s~p~~~~~l~l~ik~~~~G~~s~~l~~~l~~Gd~v~v~gP~G~f~l   93 (224)
T cd06189          26 FLAGQYLDLLL-DDGDKRPFSIASAPHEDGEIELHIRAVPGGSFSDYVFEELKENGLVRIEGPLGDFFL   93 (224)
T ss_pred             CCCCCEEEEEE-CCCCEEEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEECCCCCCCC
T ss_conf             78997489995-998789986165899998399999996798158899854999998999706757411


No 46 
>PRK09239 chorismate mutase; Provisional
Probab=37.85  E-value=34  Score=15.81  Aligned_cols=54  Identities=19%  Similarity=0.215  Sum_probs=34.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             9984314889999999999999872------48999999999975176222430489998876
Q gi|254780440|r    1 MVDKIPVTSKGFDKIQQELRWRQQE------ERPRIIKAISEARAYGDLSENAEYQAAKELQN   57 (158)
Q Consensus         1 M~~k~~lT~~g~~~L~~El~~l~~~------~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~   57 (158)
                      |++...=+++.+..|+.+++.+-..      +|-.++.+|..-....++   .-|+..|+++-
T Consensus         1 ~~~~~~~~~~~L~~lR~~ID~iD~~iv~LLa~R~~~~~~Ig~~K~~~~~---pv~dp~RE~~v   60 (104)
T PRK09239          1 MSDEQARAPAELAALRQSIDNIDAALIHMLAERFKCTQAVGVLKAEHGL---PPADPAREARQ   60 (104)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCHHHHHHH
T ss_conf             9847887689999999999999999999999999999999999987598---98888999999


No 47 
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand  is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=36.56  E-value=35  Score=15.68  Aligned_cols=33  Identities=15%  Similarity=0.192  Sum_probs=25.9

Q ss_pred             EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEE
Q ss_conf             150131789987288888789998289719999
Q gi|254780440|r  119 LVSISSPIARALIGKELGDIISVNAPGGEKTYE  151 (158)
Q Consensus       119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~  151 (158)
                      .|+-.+-|-..+-++++||+|++..-++-...+
T Consensus        38 ~v~~~~~l~~~i~~~~~Gd~V~l~v~R~gk~~~   70 (79)
T cd00986          38 PFKEAEELIDYIQSKKEGDTVKLKVKREEKELP   70 (79)
T ss_pred             ECCCHHHHHHHHHCCCCCCEEEEEEEECCEEEE
T ss_conf             957999999999659999989999999999999


No 48 
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=35.17  E-value=30  Score=16.13  Aligned_cols=26  Identities=27%  Similarity=0.600  Sum_probs=20.8

Q ss_pred             EECCCCHHHHHHCCCCCCCEEEEECCC
Q ss_conf             150131789987288888789998289
Q gi|254780440|r  119 LVSISSPIARALIGKELGDIISVNAPG  145 (158)
Q Consensus       119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~  145 (158)
                      +|+..-|++++ +|.+.||.|.+.--.
T Consensus        42 kI~~~DPva~~-lgak~GdvVkIvRkS   67 (80)
T COG2012          42 KIKASDPVAKA-LGAKPGDVVKIVRKS   67 (80)
T ss_pred             CCCCCCHHHHH-HCCCCCCEEEEEECC
T ss_conf             50246766777-067878679998638


No 49 
>TIGR01801 CM_A chorismate mutase; InterPro: IPR010954   This entry represents chorismate mutase (CM) domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some Gram-positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44 0dentity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the Gram-positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role..
Probab=34.33  E-value=38  Score=15.46  Aligned_cols=45  Identities=27%  Similarity=0.463  Sum_probs=31.0

Q ss_pred             HHHHHHHHHH-------HHHHHHHHHHHHHHHHHH-HHCCCCCCCCHHHHHHHHHHH
Q ss_conf             9999999999-------998724899999999997-517622243048999887687
Q gi|254780440|r   11 GFDKIQQELR-------WRQQEERPRIIKAISEAR-AYGDLSENAEYQAAKELQNLN   59 (158)
Q Consensus        11 g~~~L~~El~-------~l~~~~r~~~~~~i~~A~-~~GDl~ENaeY~aAke~q~~~   59 (158)
                      -++.|++|.+       .|.+ +|-++++.|+.|. ++|--   --|+-+||++.+.
T Consensus         6 ~le~lR~e~d~lN~qiL~Lis-~RGevv~~IG~aK~a~Gr~---n~yDP~RE~~~L~   58 (104)
T TIGR01801         6 ELEDLRAEVDELNRQILKLIS-KRGEVVKKIGKAKEAQGRV---NRYDPAREKEMLN   58 (104)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCC---CCCCCHHHHHHHH
T ss_conf             188899999998799999985-3118999975777617899---8889853799999


No 50 
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=34.31  E-value=39  Score=15.46  Aligned_cols=31  Identities=26%  Similarity=0.328  Sum_probs=17.5

Q ss_pred             CCCHHHHHHCCCCCCCEEEEECCCCEEEEEE
Q ss_conf             1317899872888887899982897199999
Q gi|254780440|r  122 ISSPIARALIGKELGDIISVNAPGGEKTYEI  152 (158)
Q Consensus       122 ~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I  152 (158)
                      ..+|--.+=+|-+-||.|.+..+.|.....+
T Consensus        36 ~i~p~dA~~lgi~~Gd~V~v~s~~G~~~~~~   66 (129)
T cd02782          36 RIHPDDAAALGLADGDKVRVTSAAGSVEAEV   66 (129)
T ss_pred             EECHHHHHHCCCCCCCEEEEECCCEEEEEEE
T ss_conf             9999999886998999999986984799999


No 51 
>cd06193 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hy
Probab=33.96  E-value=28  Score=16.36  Aligned_cols=61  Identities=23%  Similarity=0.377  Sum_probs=41.0

Q ss_pred             CCCCCEEEEEECCCC---------------------CEEEEEEECHHHCCCCCCEECC-------CCHHHHHHCCCCCCC
Q ss_conf             113657999534765---------------------2359999631013345881501-------317899872888887
Q gi|254780440|r   86 IAFGATVSLVEKNSG---------------------DKKNYQIVGDQEADVQSGLVSI-------SSPIARALIGKELGD  137 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~---------------------~~~~~~lVg~~e~d~~~~~IS~-------~SPlG~ALlG~~~Gd  137 (158)
                      -..|..|+|.....+                     ...+||+.   ..|+..+.+.+       ..|-+.=....++||
T Consensus        27 ~~~~~~vkl~~p~~~~~~~~~~~~~~~~~~~~~~~p~~R~YTvR---~~d~~~~~l~iDfvlH~~~Gpas~WA~~a~~GD  103 (235)
T cd06193          27 DGPDQHVKLLFPDPGQAPPVLPVLGRRRWPPEEPRPVMRTYTVR---RFDPEAGELDIDFVLHGDEGPASRWAASAQPGD  103 (235)
T ss_pred             CCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE---EECCCCCEEEEEEEECCCCCCHHHHHHHCCCCC
T ss_conf             99988799984799987777876664235787888878777401---177878979999996799985799998589999


Q ss_pred             EEEEECCCCEEE
Q ss_conf             899982897199
Q gi|254780440|r  138 IISVNAPGGEKT  149 (158)
Q Consensus       138 ~V~v~~p~G~~~  149 (158)
                      .+.+.-|+|...
T Consensus       104 ~i~i~gP~g~~~  115 (235)
T cd06193         104 TLGIAGPGGSFL  115 (235)
T ss_pred             EEEEECCCCCCC
T ss_conf             778886898878


No 52 
>PRK05802 hypothetical protein; Provisional
Probab=33.85  E-value=39  Score=15.41  Aligned_cols=66  Identities=18%  Similarity=0.312  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCEEEEEE-ECHHHCCCCCCEECC----CCHHHHHHCCCCCCCEEEEECC
Q ss_conf             7210133211136579995347652359999-631013345881501----3178998728888878999828
Q gi|254780440|r   77 DISTMSGDRIAFGATVSLVEKNSGDKKNYQI-VGDQEADVQSGLVSI----SSPIARALIGKELGDIISVNAP  144 (158)
Q Consensus        77 ~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~l-Vg~~e~d~~~~~IS~----~SPlG~ALlG~~~Gd~V~v~~p  144 (158)
                      -|.....+-+.+||.|=+++.++..  -|.. .+-.++|.+.+.|.+    .-|=-+.|...+.||.+.+.-|
T Consensus        87 vp~kLa~~L~~PGSfVFlR~~~~~~--yfd~PISIM~~d~~~~ii~vaiei~G~KTk~i~~~~~~~~i~iRGP  157 (328)
T PRK05802         87 VPHKLARDLVYPGSFVFLRNKNSNP--FFDVPISIMESDTEENIIKVAIEVRGIKTKKILNLNKGEEILIRGP  157 (328)
T ss_pred             CCHHHHHHHCCCCCEEEEECCCCCC--CCCCCEEEEECCCCCCEEEEEEEEECCCCHHHHHCCCCCEEEEECC
T ss_conf             8689999706897589985798887--5246548876155567599999971234030331246876999677


No 53 
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex  and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=32.62  E-value=41  Score=15.28  Aligned_cols=31  Identities=23%  Similarity=0.302  Sum_probs=15.6

Q ss_pred             CCCCHHHHHHCCCCCCCEEEEECCCCEEEEE
Q ss_conf             0131789987288888789998289719999
Q gi|254780440|r  121 SISSPIARALIGKELGDIISVNAPGGEKTYE  151 (158)
Q Consensus       121 S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~  151 (158)
                      -..+|--.+-+|-+.||.|.+..+.|.....
T Consensus        37 v~~~p~dA~~lgi~~Gd~V~v~s~~G~~~~~   67 (120)
T cd00508          37 VEIHPEDAARLGIKDGDLVRVSSRRGSVVVR   67 (120)
T ss_pred             EEECHHHHHHCCCCCCCEEEEECCCEEEEEE
T ss_conf             9999999988599999999998177389999


No 54 
>cd06183 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH.
Probab=32.37  E-value=41  Score=15.26  Aligned_cols=65  Identities=18%  Similarity=0.349  Sum_probs=41.9

Q ss_pred             CCCCCEEEEEECCCCC--EEEEEEECHHHC-CCCCCEE--CCCCHHHHHHCCCCCCCEEEEECCCCEEEE
Q ss_conf             1136579995347652--359999631013-3458815--013178998728888878999828971999
Q gi|254780440|r   86 IAFGATVSLVEKNSGD--KKNYQIVGDQEA-DVQSGLV--SISSPIARALIGKELGDIISVNAPGGEKTY  150 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~--~~~~~lVg~~e~-d~~~~~I--S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~  150 (158)
                      ...|-.|.+.-...|+  .+.|+++.+... +...-.|  -...++...|-..++||.+.+.-|.|...+
T Consensus        29 ~~~GQ~v~l~~~~~g~~~~R~YS~~s~~~~~~~~~~~Vk~~~~G~~s~~L~~~~~Gd~l~v~gP~G~f~~   98 (234)
T cd06183          29 LPVGQHVELKAPDDGEQVVRPYTPISPDDDKGYFDLLIKIYPGGKMSQYLHSLKPGDTVEIRGPFGKFEY   98 (234)
T ss_pred             CCCCEEEEEEEEECCEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCHHHHCCCCCCEEEEECCCCCEEE
T ss_conf             8999789998341994899767889779999989999999809997223532899999998778053676


No 55 
>PRK10465 hydrogenase 2-specific chaperone; Provisional
Probab=31.84  E-value=42  Score=15.20  Aligned_cols=83  Identities=11%  Similarity=0.099  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHH-HHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCC
Q ss_conf             87999999997-44442104721013321113657999534765235999963101334588150131789987288888
Q gi|254780440|r   58 LNEGRMAELEN-IITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELG  136 (158)
Q Consensus        58 ~~~~ri~~L~~-~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~G  136 (158)
                      ++++.-+++-+ ++..--++. ..++-..|+|-.+      + |. -.=.+|.||=.|.-.     .-.-++..-++++|
T Consensus        15 ~Lea~f~~I~~~~M~dLP~~N-paL~VeAvGF~~~------e-g~-wlGvliTPWfmnLv~-----lPg~~q~w~~~~~G   80 (159)
T PRK10465         15 LVQAAFEEIARRSMHDLPFLH-PSMPVYVSDFTLF------E-GQ-WTGCVLTPWMLSAVI-----FPGPDQLWPLRTVG   80 (159)
T ss_pred             HHHHHHHHHHHHHHCCCCCCC-CCCCEEEECCEEE------C-CE-EEEEEECHHHHHEEE-----CCCCCCCCCCCCCC
T ss_conf             999999999997743587458-8874676067898------7-87-899880432354254-----56886666667887


Q ss_pred             CEEEEECCCCEEEEEEEE
Q ss_conf             789998289719999999
Q gi|254780440|r  137 DIISVNAPGGEKTYEILQ  154 (158)
Q Consensus       137 d~V~v~~p~G~~~~~Il~  154 (158)
                      +.+.+..|.|.+.|.+-.
T Consensus        81 ~k~~~~lP~G~~~F~~~~   98 (159)
T PRK10465         81 EKLGLQLPYGTMTFTVGE   98 (159)
T ss_pred             CEEEEECCCCCEEEEECC
T ss_conf             667886477757887316


No 56 
>KOG3206 consensus
Probab=31.47  E-value=43  Score=15.16  Aligned_cols=97  Identities=23%  Similarity=0.367  Sum_probs=49.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99843148899999999999998724899999999997517622243048999887687999999997444421047210
Q gi|254780440|r    1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST   80 (158)
Q Consensus         1 M~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~   80 (158)
                      |.+|.-|+++.|.+-.+-...-+            .++-.|  +=|++-.    .|+..+++ ..+....+.+.      
T Consensus        94 ~veky~iSee~Y~qRtdSvr~~k------------k~~~~g--ryn~~~~----~q~ea~~~-~~~~e~~~~~~------  148 (234)
T KOG3206          94 IVEKYEISEEDYLQRTDSVRRFK------------KKHGYG--RYNAEEQ----AQAEAEAK-QDLAEERAQAT------  148 (234)
T ss_pred             CCEEEECCHHHHHHHHHHHHHHH------------HHHCCC--CCCHHHH----HHHHHHHH-HHHHHHHHHHC------
T ss_conf             30014427888866558999999------------985115--4341326----58988867-77999987300------


Q ss_pred             CCCCCCCCCCEEEEE-ECCCCCEEEEEEECHHHCCCCCC-E--ECCCCHHHHH
Q ss_conf             133211136579995-34765235999963101334588-1--5013178998
Q gi|254780440|r   81 MSGDRIAFGATVSLV-EKNSGDKKNYQIVGDQEADVQSG-L--VSISSPIARA  129 (158)
Q Consensus        81 ~~~~~V~~Gs~V~l~-d~~~~~~~~~~lVg~~e~d~~~~-~--IS~~SPlG~A  129 (158)
                           +.+|....+. .......-++.-|||.+  ...| +  |-+.-|+|+-
T Consensus       149 -----i~vG~rCeVtv~G~~~Rrg~vrYvG~~~--~k~G~wiGVeydEplGKn  194 (234)
T KOG3206         149 -----IAVGRRCEVTVPGQAPRRGTVRYVGPLE--FKPGYWIGVEYDEPLGKN  194 (234)
T ss_pred             -----CCCCCEEEEECCCCCCCCEEEEEECCCC--CCCCEEEEEECCCCCCCC
T ss_conf             -----5137806895389787514788832468--888428877547766667


No 57 
>pfam11344 DUF3146 Protein of unknown function (DUF3146). This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=31.14  E-value=18  Score=17.49  Aligned_cols=41  Identities=22%  Similarity=0.408  Sum_probs=26.5

Q ss_pred             CCCCCEECCCCHHHHHHCCCCCCC---EEEEEC-CCCEEEEEEEE
Q ss_conf             345881501317899872888887---899982-89719999999
Q gi|254780440|r  114 DVQSGLVSISSPIARALIGKELGD---IISVNA-PGGEKTYEILQ  154 (158)
Q Consensus       114 d~~~~~IS~~SPlG~ALlG~~~Gd---~V~v~~-p~G~~~~~Il~  154 (158)
                      ....|.+++.-|||+||+--..+-   .-.+++ |+|.+.|+|-+
T Consensus        35 ~F~~G~L~V~PsLGRALI~d~L~RFL~k~DY~LE~GgdY~Ftira   79 (80)
T pfam11344        35 HFRRGELLVEPSLGRALIKDALLRFLEKSDYQLEPGGDYSFTVRA   79 (80)
T ss_pred             EECCCEEEECCCCCHHHHHHHHHHHHHHCCEEECCCCCEEEEEEC
T ss_conf             976982998686027888879997886514060589947899965


No 58 
>pfam01191 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain. The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.
Probab=30.87  E-value=44  Score=15.10  Aligned_cols=29  Identities=24%  Similarity=0.471  Sum_probs=23.7

Q ss_pred             CEECCCCHHHHHHCCCCCCCEEEEECCCCE
Q ss_conf             815013178998728888878999828971
Q gi|254780440|r  118 GLVSISSPIARALIGKELGDIISVNAPGGE  147 (158)
Q Consensus       118 ~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~  147 (158)
                      =+|+..-|+++.+ |.+.||.+.+.-++.+
T Consensus        35 P~I~~~DPv~~~~-g~~~GdiikI~R~s~t   63 (74)
T pfam01191        35 PRILATDPVARYL-GLKPGDVVKITRKSET   63 (74)
T ss_pred             CEECCCCHHHHHH-CCCCCCEEEEEECCCC
T ss_conf             8163619988982-9999978999974887


No 59 
>pfam06152 Phage_min_cap2 Phage minor capsid protein 2. Family of related phage minor capsid proteins.
Probab=30.43  E-value=45  Score=15.05  Aligned_cols=14  Identities=21%  Similarity=0.347  Sum_probs=6.6

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             48899999999999
Q gi|254780440|r    7 VTSKGFDKIQQELR   20 (158)
Q Consensus         7 lT~~g~~~L~~El~   20 (158)
                      |||+-+.++-+.+.
T Consensus         3 LtPe~l~~~~~~vv   16 (361)
T pfam06152         3 LTPEQLDLLSQPVV   16 (361)
T ss_pred             CCHHHHHHCCHHHH
T ss_conf             98799987007899


No 60 
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=29.78  E-value=46  Score=14.98  Aligned_cols=28  Identities=21%  Similarity=0.493  Sum_probs=22.7

Q ss_pred             CEECCCCHHHHHHCCCCCCCEEEEECCCC
Q ss_conf             81501317899872888887899982897
Q gi|254780440|r  118 GLVSISSPIARALIGKELGDIISVNAPGG  146 (158)
Q Consensus       118 ~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G  146 (158)
                      =+|+..-|+++.+ |.+.||.|.+.-++.
T Consensus        38 P~I~~~DPva~~l-g~~~GdvvkI~R~S~   65 (79)
T PRK09570         38 PKIKASDPVVKAI-GAKPGDVVKIVRKSP   65 (79)
T ss_pred             CCCCCCCHHHHHH-CCCCCCEEEEEECCC
T ss_conf             9213519888984-999996899997577


No 61 
>COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]
Probab=29.47  E-value=29  Score=16.25  Aligned_cols=18  Identities=44%  Similarity=0.724  Sum_probs=10.7

Q ss_pred             CCHHHHHHCCCCCCCEEE
Q ss_conf             317899872888887899
Q gi|254780440|r  123 SSPIARALIGKELGDIIS  140 (158)
Q Consensus       123 ~SPlG~ALlG~~~Gd~V~  140 (158)
                      ..+-+..|+|++.||++.
T Consensus        22 ~~~~a~~ligkkIGd~~d   39 (120)
T COG2125          22 DEARARRLIGKKIGDEVD   39 (120)
T ss_pred             CHHHHHHHHHHEECCCCC
T ss_conf             646655443210044137


No 62 
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a  large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=29.34  E-value=47  Score=14.93  Aligned_cols=34  Identities=24%  Similarity=0.309  Sum_probs=23.6

Q ss_pred             EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEE
Q ss_conf             1501317899872888887899982897199999
Q gi|254780440|r  119 LVSISSPIARALIGKELGDIISVNAPGGEKTYEI  152 (158)
Q Consensus       119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I  152 (158)
                      -.-+.+|--.+-+|-+.||.|.+..+.|.....+
T Consensus        23 ~~v~~np~dA~~~Gi~~Gd~v~v~~~~g~~~~~~   56 (101)
T cd02775          23 PVVEINPEDAAALGIKDGDLVRVESRRGSVVLRA   56 (101)
T ss_pred             CEEEECHHHHHHCCCCCCCEEEEEECCEEEEEEE
T ss_conf             9899999999986998899999996985899999


No 63 
>pfam10781 DSRB Dextransucrase DSRB. DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose.
Probab=29.13  E-value=47  Score=14.91  Aligned_cols=23  Identities=30%  Similarity=0.468  Sum_probs=12.8

Q ss_pred             CCCCEEEEECCCCEE-EEEEEEEE
Q ss_conf             888789998289719-99999989
Q gi|254780440|r  134 ELGDIISVNAPGGEK-TYEILQVL  156 (158)
Q Consensus       134 ~~Gd~V~v~~p~G~~-~~~Il~I~  156 (158)
                      +++|.|++++-+|++ .=.|+.|+
T Consensus         2 ~vnD~VtVKTDG~~rReG~il~vE   25 (62)
T pfam10781         2 KVNDRVTVKTDGGPRREGVILAVE   25 (62)
T ss_pred             CCCCEEEEECCCCCCCCEEEEEEE
T ss_conf             335679995489755440699983


No 64 
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=28.87  E-value=43  Score=15.16  Aligned_cols=15  Identities=20%  Similarity=0.206  Sum_probs=6.6

Q ss_pred             CEEEEEEECHHHCCC
Q ss_conf             235999963101334
Q gi|254780440|r  101 DKKNYQIVGDQEADV  115 (158)
Q Consensus       101 ~~~~~~lVg~~e~d~  115 (158)
                      .....-||.|...-|
T Consensus        79 ~k~K~liv~peHLk~   93 (98)
T COG2139          79 NKEKTLIVRPEHLKP   93 (98)
T ss_pred             CCEEEEEECHHHCCC
T ss_conf             945899867788544


No 65 
>TIGR01076 sortase_fam sortase family protein; InterPro: IPR005754   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad .    This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan . Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported , .    Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope.  .
Probab=28.72  E-value=48  Score=14.87  Aligned_cols=31  Identities=16%  Similarity=0.184  Sum_probs=21.9

Q ss_pred             HHHCCCCCCCEEEEECCCCEEEEEEEEEEEC
Q ss_conf             9872888887899982897199999998979
Q gi|254780440|r  128 RALIGKELGDIISVNAPGGEKTYEILQVLWI  158 (158)
Q Consensus       128 ~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi  158 (158)
                      +.|=-.|+||.+-+..-.+...|+|.+|+-|
T Consensus        59 ~~L~~~K~GD~ly~~~~~e~~~Y~~~~~~~v   89 (140)
T TIGR01076        59 TNLDKLKKGDALYLKVGNEVLTYQVTSTKIV   89 (140)
T ss_pred             CCCCCCCCCCEEEEEECCCEEEEEEEEEEEE
T ss_conf             2221001375889984251898887888984


No 66 
>PRK10708 hypothetical protein; Provisional
Probab=28.64  E-value=48  Score=14.86  Aligned_cols=23  Identities=26%  Similarity=0.458  Sum_probs=10.7

Q ss_pred             CCCCEEEEECCCCEE-EEEEEEEE
Q ss_conf             888789998289719-99999989
Q gi|254780440|r  134 ELGDIISVNAPGGEK-TYEILQVL  156 (158)
Q Consensus       134 ~~Gd~V~v~~p~G~~-~~~Il~I~  156 (158)
                      +++|.|++++-+|++ .=.|+.|+
T Consensus         2 kvnd~VtVKTDG~~rR~G~ilavE   25 (62)
T PRK10708          2 KVNDRVTVKTDGGPRRPGVVLAVE   25 (62)
T ss_pred             CCCCEEEEECCCCCCCCCEEEEEE
T ss_conf             435549995489856664699983


No 67 
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=27.58  E-value=50  Score=14.74  Aligned_cols=135  Identities=17%  Similarity=0.247  Sum_probs=76.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             14889999999999999872489999999999751762224304899988768799999999744442104721013321
Q gi|254780440|r    6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDR   85 (158)
Q Consensus         6 ~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~   85 (158)
                      .+|++.|.+.-+++...-.=.-.++...+...+..  .|+|-+|..|.+    +-.+|..|+.....-.|+.+...+.|+
T Consensus       183 ~Is~~~Y~~~V~~~~~fL~G~~~~l~~~L~~~M~~--aS~~l~FE~Aa~----~RD~i~aL~~i~~~Q~v~~~~~~d~DV  256 (609)
T PRK00558        183 LVSKEEYAELVDEAKLFLQGKSDEVIKELEEKMEK--ASENLEFERAAR----LRDQIQALRRVQEKQKVSLADLEDADV  256 (609)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--HHHHHHHHHHHH----HHHHHHHHHHHHHCCEEECCCCCCCEE
T ss_conf             57999999999999999827949999999999999--997320667899----999999999986356532588765407


Q ss_pred             CCCC-----CEEEEEECCCCC---EEEEEEECHHHCC-------------------CCCCEECC----CCHHHHHHCCCC
Q ss_conf             1136-----579995347652---3599996310133-------------------45881501----317899872888
Q gi|254780440|r   86 IAFG-----ATVSLVEKNSGD---KKNYQIVGDQEAD-------------------VQSGLVSI----SSPIARALIGKE  134 (158)
Q Consensus        86 V~~G-----s~V~l~d~~~~~---~~~~~lVg~~e~d-------------------~~~~~IS~----~SPlG~ALlG~~  134 (158)
                      +++-     +.|.+...-.|.   ..+|.+=...+.+                   |..=.++.    ...+=...|..+
T Consensus       257 i~i~~~~~~~~i~v~~vR~G~i~g~~~~~~~~~~~~~~~eil~~fl~q~Y~~~~~~P~eIlv~~~~~~d~~~l~~~L~~~  336 (609)
T PRK00558        257 IAIAVDKGWACVQVFFIRGGKLLGRRSFFPKVPGDTELEEVLEAFIGQFYLDNRPIPKEILVPHELEIDKELLEEALSEK  336 (609)
T ss_pred             EEEEECCCEEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHH
T ss_conf             99997198589999998788996005677046677998999999999998417899976883576785689999999853


Q ss_pred             CCCEEEEECCCC
Q ss_conf             887899982897
Q gi|254780440|r  135 LGDIISVNAPGG  146 (158)
Q Consensus       135 ~Gd~V~v~~p~G  146 (158)
                      -|..|.+..|..
T Consensus       337 ~~~kv~i~~Pkr  348 (609)
T PRK00558        337 AGRKVKIRVPQR  348 (609)
T ss_pred             CCCCEEEECCCC
T ss_conf             599469961885


No 68 
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=27.34  E-value=50  Score=14.71  Aligned_cols=71  Identities=24%  Similarity=0.412  Sum_probs=47.1

Q ss_pred             HHHHHHHHHCCC------------CCCCCCCCCCCCCEEEEEECCCCCE-EEEEEECHHHCCCCCCEECCCCHHHHHHCC
Q ss_conf             997444421047------------2101332111365799953476523-599996310133458815013178998728
Q gi|254780440|r   66 LENIITRAEVID------------ISTMSGDRIAFGATVSLVEKNSGDK-KNYQIVGDQEADVQSGLVSISSPIARALIG  132 (158)
Q Consensus        66 L~~~L~~A~iv~------------~~~~~~~~V~~Gs~V~l~d~~~~~~-~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG  132 (158)
                      |..+|.+|.|.+            +.-.+..-+..+-.|.+.|..+|.. .||-|.|+.-+    |.|+.   =|.|---
T Consensus         5 l~aKiHratVT~A~L~Y~GSitID~dlldaagile~EkV~I~N~nNGaRf~TYvI~g~rGS----g~I~l---NGAAArl   77 (126)
T COG0853           5 LKAKIHRATVTEADLNYVGSITIDEDLLDAAGILENEKVDIVNVNNGARFSTYVIAGERGS----GVICL---NGAAARL   77 (126)
T ss_pred             HHHHHHEEEEEECCCCEEEEEEECHHHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCCCC----CEEEE---CHHHHHH
T ss_conf             4312102688502330477688899999653898776689998888837899998726878----67975---6698852


Q ss_pred             CCCCCEEEEEC
Q ss_conf             88887899982
Q gi|254780440|r  133 KELGDIISVNA  143 (158)
Q Consensus       133 ~~~Gd~V~v~~  143 (158)
                      .++||.|-+-.
T Consensus        78 ~~~GD~VII~s   88 (126)
T COG0853          78 VQVGDLVIIMS   88 (126)
T ss_pred             CCCCCEEEEEE
T ss_conf             68899899998


No 69 
>pfam01092 Ribosomal_S6e Ribosomal protein S6e.
Probab=27.32  E-value=50  Score=14.71  Aligned_cols=20  Identities=25%  Similarity=0.378  Sum_probs=12.9

Q ss_pred             HHHHHCCCCCCCEEEEECCC
Q ss_conf             89987288888789998289
Q gi|254780440|r  126 IARALIGKELGDIISVNAPG  145 (158)
Q Consensus       126 lG~ALlG~~~Gd~V~v~~p~  145 (158)
                      --++++|++.||+|.-..-+
T Consensus        23 ~~~~f~gkrIGdevdg~~lG   42 (127)
T pfam01092        23 RLRVFYEKRMGQEVDGDAVG   42 (127)
T ss_pred             HHHHHHCCCCCCEECHHCCC
T ss_conf             74343156021477502028


No 70 
>TIGR02160 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit; InterPro: IPR011884 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA .    .
Probab=26.70  E-value=42  Score=15.21  Aligned_cols=64  Identities=23%  Similarity=0.409  Sum_probs=37.8

Q ss_pred             CCCCCEEEEEECCCCCE--EEEEEE-CHHHCCCCCCE--E--CCCCHHHHHHCCCCCCCEEEEECCCCEEEE
Q ss_conf             11365799953476523--599996-31013345881--5--013178998728888878999828971999
Q gi|254780440|r   86 IAFGATVSLVEKNSGDK--KNYQIV-GDQEADVQSGL--V--SISSPIARALIGKELGDIISVNAPGGEKTY  150 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~--~~~~lV-g~~e~d~~~~~--I--S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~  150 (158)
                      -..|=.++|+-.=+|++  ++|.|+ ++....+.-+.  |  -.-|--+.- =|-|.||+++|-+|.|...+
T Consensus        33 F~pGQ~l~Lk~~~dG~e~RRSYSIC~~~~~~~~rvAvk~~~GG~FS~wa~d-~Gir~GdtlEVM~P~G~F~~  103 (371)
T TIGR02160        33 FEPGQHLTLKAEVDGEELRRSYSICDAPAPGEIRVAVKKIEGGLFSTWAND-EGIRAGDTLEVMAPQGRFTS  103 (371)
T ss_pred             CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEHHHHC-CCCCCCCEEEEECCCCCCCC
T ss_conf             688934554200077411302222167798963388997289711321111-87044887887167897788


No 71 
>KOG3129 consensus
Probab=26.24  E-value=53  Score=14.59  Aligned_cols=33  Identities=27%  Similarity=0.226  Sum_probs=21.8

Q ss_pred             EEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEE
Q ss_conf             99631013345881501317899872888887899
Q gi|254780440|r  106 QIVGDQEADVQSGLVSISSPIARALIGKELGDIIS  140 (158)
Q Consensus       106 ~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~  140 (158)
                      +..||.-+=..-+.|+..||-..|  |.++||.+.
T Consensus       132 ~~~gP~~~Fa~V~sV~~~SPA~~a--Gl~~gD~il  164 (231)
T KOG3129         132 TSLGPMRPFAVVDSVVPGSPADEA--GLCVGDEIL  164 (231)
T ss_pred             CCCCCCCCEEEEEECCCCCHHHHH--CCCCCCEEE
T ss_conf             005786524887522789834540--754376578


No 72 
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=25.77  E-value=54  Score=14.53  Aligned_cols=31  Identities=26%  Similarity=0.327  Sum_probs=16.5

Q ss_pred             CCCCHHHHHHCCCCCCCEEEEECCCCEEEEE
Q ss_conf             0131789987288888789998289719999
Q gi|254780440|r  121 SISSPIARALIGKELGDIISVNAPGGEKTYE  151 (158)
Q Consensus       121 S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~  151 (158)
                      -..||--.+-||-+.||.|++..++|...+-
T Consensus        31 ~~l~~~dA~~Lgl~~G~~v~v~~~~g~~~LP   61 (96)
T cd02788          31 ARLSPADAARLGLADGDLVEFSLGDGTLTLP   61 (96)
T ss_pred             EEECHHHHHHHCCCCCCEEEEEECCEEEEEE
T ss_conf             9999989998199999989999899689999


No 73 
>TIGR00875 talC transaldolase, putative; InterPro: IPR004731   Transaldolase (2.2.1.2 from EC) catalyzes the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. This enzyme, together with transketolase, provides a link between the glycolytic and pentose-phosphate pathways. Transaldolase is an enzyme of about 34 Kd whose sequence has been well conserved throughout evolution. A lysine has been implicated  in the catalytic mechanism of the enzyme; it acts as a nucleophilic group that attacks the carbonyl group of fructose-6-phosphate.   Transaldolase is evolutionary related  to a bacterial protein of about 20 Kd (known as talC in Escherichia coli), whose exact function is not yet known.; GO: 0005975 carbohydrate metabolic process.
Probab=25.47  E-value=39  Score=15.42  Aligned_cols=12  Identities=50%  Similarity=0.947  Sum_probs=5.3

Q ss_pred             CCCCCHHHHHHH
Q ss_conf             431488999999
Q gi|254780440|r    4 KIPVTSKGFDKI   15 (158)
Q Consensus         4 k~~lT~~g~~~L   15 (158)
                      |||||++|++..
T Consensus        86 KIP~T~~GLkAv   97 (216)
T TIGR00875        86 KIPMTSEGLKAV   97 (216)
T ss_pred             EECCCHHHHHHH
T ss_conf             614785379999


No 74 
>KOG3026 consensus
Probab=25.13  E-value=55  Score=14.46  Aligned_cols=34  Identities=24%  Similarity=0.248  Sum_probs=18.3

Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99751762224304899988768799999999744442
Q gi|254780440|r   36 EARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRA   73 (158)
Q Consensus        36 ~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A   73 (158)
                      +|+-+|| .+|.||.--++.+..+   |.--++.|..+
T Consensus        16 eaaL~~d-P~NeEllkLe~DLkEv---IsLTedLlqT~   49 (262)
T KOG3026          16 EAALQGD-PENEELLKLEKDLKEV---ISLTEDLLQTQ   49 (262)
T ss_pred             HHHHCCC-CCCHHHHHHHHHHHHH---HHHHHHHHHHH
T ss_conf             9997069-8538999999889999---99999998750


No 75 
>pfam06273 eIF-4B Plant specific eukaryotic initiation factor 4B. This family consists of several plant specific eukaryotic initiation factor 4B proteins.
Probab=24.42  E-value=44  Score=15.11  Aligned_cols=38  Identities=18%  Similarity=0.268  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEE
Q ss_conf             99999997444421047210133211136579995347652359
Q gi|254780440|r   61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKN  104 (158)
Q Consensus        61 ~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~  104 (158)
                      -.|.+.+..|.....    + -.|+|+||-....+ ..++--.+
T Consensus       341 e~i~~kEk~Le~L~r----~-lDdKvRFgqk~~eR-PgSgAgR~  378 (430)
T pfam06273       341 ELIRQKEKELERLTR----E-LDDKVRFGQKAVER-PGSGAGRT  378 (430)
T ss_pred             HHHHHHHHHHHHHHH----H-HCCCCCCCCCCCCC-CCCCCCCC
T ss_conf             998877888999998----7-33531235111448-77666753


No 76 
>cd06190 T4MO_e_transfer_like Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family.
Probab=24.21  E-value=57  Score=14.35  Aligned_cols=63  Identities=16%  Similarity=0.179  Sum_probs=40.3

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECHH-HCCCCCCEE--CCCCHHHHHHC-CCCCCCEEEEECCCCEE
Q ss_conf             11365799953476523599996310-133458815--01317899872-88888789998289719
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGDQ-EADVQSGLV--SISSPIARALI-GKELGDIISVNAPGGEK  148 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~~-e~d~~~~~I--S~~SPlG~ALl-G~~~Gd~V~v~~p~G~~  148 (158)
                      ...|-.|.+.-...+....|+|+.+. +.+.-.-.|  .....+..+|. ..++||.|.+.-|.|..
T Consensus        24 f~pGQ~v~l~i~~~~~~R~ySi~s~p~~~~~l~~~i~~~~~G~~S~~L~~~l~~Gd~v~v~gP~G~f   90 (232)
T cd06190          24 FLPGQYALLALPGVEGARAYSMANLANASGEWEFIIKRKPGGAASNALFDNLEPGDELELDGPYGLA   90 (232)
T ss_pred             CCCCEEEEEEECCCCEEEEEEECCCCCCCCEEEEEEEEEECCHHHHHHHHCCCCCCEEEEEECCCCC
T ss_conf             0898069999899012688886528999987999999943992688998648999999999545674


No 77 
>cd06215 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur pr
Probab=24.18  E-value=58  Score=14.34  Aligned_cols=64  Identities=22%  Similarity=0.267  Sum_probs=38.7

Q ss_pred             CCCCCEEEEEECCCCC--EEEEEEECH-HHCCCCCCEECC--CCHHHHHHC-CCCCCCEEEEECCCCEEE
Q ss_conf             1136579995347652--359999631-013345881501--317899872-888887899982897199
Q gi|254780440|r   86 IAFGATVSLVEKNSGD--KKNYQIVGD-QEADVQSGLVSI--SSPIARALI-GKELGDIISVNAPGGEKT  149 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~--~~~~~lVg~-~e~d~~~~~IS~--~SPlG~ALl-G~~~Gd~V~v~~p~G~~~  149 (158)
                      -..|-.|.+.-...|+  ...|+|+.. .+.+...=.|..  ...+-..|. ..++||.|.+.-|.|...
T Consensus        28 f~aGQ~v~l~~~~~g~~~~R~ySias~p~~~~~~~~~Vk~~~~G~~S~~l~~~l~~G~~v~v~gP~G~f~   97 (231)
T cd06215          28 YKPGQFLTLELEIDGETVYRAYTLSSSPSRPDSLSITVKRVPGGLVSNWLHDNLKVGDELWASGPAGEFT   97 (231)
T ss_pred             CCCCEEEEEEEEECCEEEEEEEECCCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEEECCCCCC
T ss_conf             5898779999766993787666335579999989999999559806789996188999999970344874


No 78 
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a  Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.59  E-value=59  Score=14.27  Aligned_cols=33  Identities=18%  Similarity=0.201  Sum_probs=21.7

Q ss_pred             ECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEE
Q ss_conf             501317899872888887899982897199999
Q gi|254780440|r  120 VSISSPIARALIGKELGDIISVNAPGGEKTYEI  152 (158)
Q Consensus       120 IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I  152 (158)
                      +-..+|--.+=+|-+.||.|.+..+.|.....+
T Consensus        36 ~v~i~p~dA~~lGi~~Gd~V~v~s~~G~i~~~a   68 (116)
T cd02790          36 YVEINPEDAKRLGIEDGEKVRVSSRRGSVEVRA   68 (116)
T ss_pred             EEEECHHHHHHCCCCCCCEEEEECCCEEEEEEE
T ss_conf             899899999885998899899987998999999


No 79 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=22.68  E-value=62  Score=14.16  Aligned_cols=32  Identities=31%  Similarity=0.505  Sum_probs=18.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             76222430489998876879999999974444
Q gi|254780440|r   41 GDLSENAEYQAAKELQNLNEGRMAELENIITR   72 (158)
Q Consensus        41 GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~   72 (158)
                      -.|.++++|..|++-...+...+..|+..+..
T Consensus       185 ~~lt~~Gd~~~A~evl~~l~~~~~~L~~~me~  216 (569)
T PRK04778        185 VELTESGDYVEAREVLDKLEEELAALEQIMEE  216 (569)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99986889899999999999999999999988


No 80 
>pfam11939 DUF3457 Protein of unknown function (DUF3457). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 162 to 197 amino acids in length. This protein has a conserved CSL sequence motif.
Probab=22.58  E-value=62  Score=14.15  Aligned_cols=44  Identities=14%  Similarity=0.209  Sum_probs=31.3

Q ss_pred             EEECHHHCCCCCCEECCCCH-HHHHHCCCCCCCEEEEECCCCEEEEEEEEE
Q ss_conf             99631013345881501317-899872888887899982897199999998
Q gi|254780440|r  106 QIVGDQEADVQSGLVSISSP-IARALIGKELGDIISVNAPGGEKTYEILQV  155 (158)
Q Consensus       106 ~lVg~~e~d~~~~~IS~~SP-lG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I  155 (158)
                      -+|.||=.|.-.      =| =+...-++++|+...+.+|.|.+.|.+-.+
T Consensus        48 vliTPWfmnLv~------lPg~~~~w~~~~~G~k~~~~lP~G~~eF~~~~~   92 (158)
T pfam11939        48 VLVTPWFMNLVL------LPGPDQDWSALPVGDKLALALPSGTYEFIVGEL   92 (158)
T ss_pred             EEECHHHHHHEE------CCCCCCCCCCCCCCCEEEEECCCCCEEEEEECC
T ss_conf             980445575502------448855666689886778763775279885247


No 81 
>KOG0534 consensus
Probab=22.55  E-value=62  Score=14.14  Aligned_cols=65  Identities=22%  Similarity=0.292  Sum_probs=41.4

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEE------CCCCHHHHHHCCCCCCCEEEEECCCCEEEEE
Q ss_conf             11365799953476523599996310133458815------0131789987288888789998289719999
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLV------SISSPIARALIGKELGDIISVNAPGGEKTYE  151 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~I------S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~  151 (158)
                      ...|..|.+.-.- +....++=-.|--.|...|.+      -..-|+.+-|-..+.||+|+|.-|-|...|.
T Consensus        82 lp~g~hv~~~~~i-~g~~vvRpYTPvs~~~~~g~~~l~VK~Y~~G~mS~~l~~LkiGd~ve~rGP~G~~~~~  152 (286)
T KOG0534          82 LPIGQHVVLKAPI-GGKLVVRPYTPVSLDDDKGYFDLVVKVYPKGKMSQHLDSLKIGDTVEFRGPIGEFKYD  152 (286)
T ss_pred             CCCCEEEEEEECC-CCCEEEEECCCCCCCCCCCEEEEEEEECCCCCCCHHHHCCCCCCEEEEECCCCCEEEC
T ss_conf             6552589999628-9868997068746713465089999952688653788659999989996684335767


No 82 
>TIGR01439 lp_hng_hel_AbrB transcriptional regulator, AbrB family; InterPro: IPR006339   This DNA-binding domain is found in proteins like AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. .
Probab=22.51  E-value=62  Score=14.14  Aligned_cols=33  Identities=30%  Similarity=0.441  Sum_probs=23.0

Q ss_pred             CCEECCCCHHHHHHCCCCCCCEEEEE-CCCCEEEE
Q ss_conf             88150131789987288888789998-28971999
Q gi|254780440|r  117 SGLVSISSPIARALIGKELGDIISVN-APGGEKTY  150 (158)
Q Consensus       117 ~~~IS~~SPlG~ALlG~~~Gd~V~v~-~p~G~~~~  150 (158)
                      +|.|.+=..+ +..||-+.||.+.+. ..+|...+
T Consensus         7 kG~i~IPK~i-R~~lgl~eGd~l~~~~~~d~~i~l   40 (44)
T TIGR01439         7 KGQIVIPKEI-REKLGLKEGDKLEVIRVEDGEIIL   40 (44)
T ss_pred             CCEEEECHHH-HHHCCCCCCCEEEEEEECCCEEEE
T ss_conf             7629927389-640699999878898827987989


No 83 
>pfam02403 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase.
Probab=22.25  E-value=63  Score=14.11  Aligned_cols=58  Identities=21%  Similarity=0.177  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999872489999999999751762224304899988768799999999744442
Q gi|254780440|r   10 KGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRA   73 (158)
Q Consensus        10 ~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A   73 (158)
                      .-+..+..+++.|.. +|-.+++.|+.+...|+     +-..-+++...+...|..++..+...
T Consensus        36 ~~~r~~~~~~e~L~~-~~N~~sk~ig~~~~~~~-----~~~~l~~~~~~lk~~i~~le~~~~~~   93 (108)
T pfam02403        36 EERRELQVELEELQA-ERNELSKEIGKAKKKKE-----DAEALIAEVKELKDELKALEAELREL   93 (108)
T ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999-98598999999875774-----16889999999999999999999999


No 84 
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.14  E-value=63  Score=14.09  Aligned_cols=26  Identities=27%  Similarity=0.408  Sum_probs=10.4

Q ss_pred             CCHHHHHHCCCCCCCEEEEECCCCEE
Q ss_conf             31789987288888789998289719
Q gi|254780440|r  123 SSPIARALIGKELGDIISVNAPGGEK  148 (158)
Q Consensus       123 ~SPlG~ALlG~~~Gd~V~v~~p~G~~  148 (158)
                      .+|--.+=+|-+-||.|.+..+.|..
T Consensus        34 inp~dA~~~Gi~dGd~V~v~s~~G~~   59 (123)
T cd02778          34 INPETAARLGIKDGDRVEVSSARGKV   59 (123)
T ss_pred             ECHHHHHHCCCCCCCEEEEECCCEEE
T ss_conf             99999998499999999998899689


No 85 
>KOG3227 consensus
Probab=21.12  E-value=66  Score=13.96  Aligned_cols=57  Identities=33%  Similarity=0.342  Sum_probs=39.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             431488999999999999987248999999999975176222430489998876879999999974444210
Q gi|254780440|r    4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEV   75 (158)
Q Consensus         4 k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~i   75 (158)
                      +--+|.+.-.|+.+|=.+|..        .|-+--..|-++|-+.|++.      |.+-+.+|- .|+.+.-
T Consensus        17 ~~~vt~~~IQk~LdEN~~LI~--------~I~e~Qn~Gk~~EC~qyq~~------LhrNL~YLA-~iAD~qp   73 (231)
T KOG3227          17 KGEVTSEQIQKMLDENKHLIQ--------CIVESQNKGKLSECAQYQAL------LHRNLVYLA-TIADSQP   73 (231)
T ss_pred             CCCCCHHHHHHHHHHHHHHHH--------HHHHHHCCCHHHHHHHHHHH------HHHHHHHHH-HHHHCCC
T ss_conf             776689999999975047999--------99986314307889999999------987489999-9861488


No 86 
>KOG0493 consensus
Probab=20.88  E-value=67  Score=13.93  Aligned_cols=29  Identities=10%  Similarity=0.438  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Q ss_conf             48899999999999---998724899999999
Q gi|254780440|r    7 VTSKGFDKIQQELR---WRQQEERPRIIKAIS   35 (158)
Q Consensus         7 lT~~g~~~L~~El~---~l~~~~r~~~~~~i~   35 (158)
                      .|.+.+.||+.|+.   +|...+|++++.++.
T Consensus       253 FtaeQL~RLK~EF~enRYlTEqRRQ~La~ELg  284 (342)
T KOG0493         253 FTAEQLQRLKAEFQENRYLTEQRRQELAQELG  284 (342)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             14999999999986603578999999998737


No 87 
>cd06212 monooxygenase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.
Probab=20.61  E-value=68  Score=13.89  Aligned_cols=65  Identities=14%  Similarity=0.231  Sum_probs=42.2

Q ss_pred             CCCCCEEEEEECCCCCEEEEEEECHH-HCCCCCCEECC--CCHHHHHHCC-CCCCCEEEEECCCCEEEE
Q ss_conf             11365799953476523599996310-13345881501--3178998728-888878999828971999
Q gi|254780440|r   86 IAFGATVSLVEKNSGDKKNYQIVGDQ-EADVQSGLVSI--SSPIARALIG-KELGDIISVNAPGGEKTY  150 (158)
Q Consensus        86 V~~Gs~V~l~d~~~~~~~~~~lVg~~-e~d~~~~~IS~--~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~  150 (158)
                      ...|-.|++.-.+.+....|+|..+. +.+.-.=.|..  ...+...|.. .++||.|.+.-|-|.-.+
T Consensus        30 f~~GQ~v~~~~~g~~~~R~ySi~s~p~~~~~~~l~Vk~~~~G~~s~~l~~~l~~Gd~v~v~gP~G~f~l   98 (232)
T cd06212          30 FFAGQYVDITVPGTEETRSFSMANTPADPGRLEFIIKKYPGGLFSSFLDDGLAVGDPVTVTGPYGTCTL   98 (232)
T ss_pred             CCCCEEEEEEECCCCCEEEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEECCCCCCEE
T ss_conf             189855999989988178997462799998899999997799558899855899989999737567510


No 88 
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=20.02  E-value=70  Score=13.81  Aligned_cols=31  Identities=26%  Similarity=0.369  Sum_probs=17.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6222430489998876879999999974444
Q gi|254780440|r   42 DLSENAEYQAAKELQNLNEGRMAELENIITR   72 (158)
Q Consensus        42 Dl~ENaeY~aAke~q~~~~~ri~~L~~~L~~   72 (158)
                      .|.++++|..|++-...++..+..|+..+..
T Consensus       182 ~lt~~Gd~~~A~e~l~~l~~~~~~L~~~me~  212 (559)
T pfam06160       182 ELTESGDYLEAREVLLKLEEETDALEQKMEE  212 (559)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9986899899999999999999999999998


Done!