Query         gi|254780939|ref|YP_003065352.1| type I signal peptidase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 248
No_of_seqs    132 out of 2445
Neff          6.6 
Searched_HMMs 39220
Date          Mon May 30 03:23:12 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780939.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10861 lsignal peptidase I;  100.0       0       0  484.1  17.0  223   11-247    58-323 (324)
  2 TIGR02227 sigpep_I_bact signal 100.0       0       0  385.7  14.4  195   16-224     1-203 (203)
  3 KOG0171 consensus              100.0 1.5E-31 3.7E-36  218.4  11.1  134   28-225    26-160 (176)
  4 pfam10502 Peptidase_S26 Peptid 100.0 1.7E-29 4.4E-34  205.4   9.5  107   82-220    19-137 (138)
  5 cd06530 S26_SPase_I The S26 Ty  99.9 7.3E-25 1.9E-29  176.3   7.5   85   36-216     1-85  (85)
  6 KOG1568 consensus               99.9 2.3E-23 5.9E-28  166.8   7.2  134   15-222     9-150 (174)
  7 PRK13884 conjugal transfer pep  99.8 3.9E-19   1E-23  140.2  12.2  109   83-220    49-176 (178)
  8 COG0681 LepB Signal peptidase   99.8 3.5E-19 9.1E-24  140.5  10.3   91   14-124     8-100 (166)
  9 TIGR02771 TraF_Ti conjugative   99.7 2.2E-17 5.5E-22  129.3   9.3  107   82-217    47-178 (183)
 10 PRK13838 conjugal transfer pil  99.7 1.3E-15 3.2E-20  118.2  11.7  105   83-220    49-172 (176)
 11 TIGR02754 sod_Ni_protease nick  99.6 1.6E-15   4E-20  117.6   6.9   89   38-217     1-89  (90)
 12 COG4959 TraF Type IV secretory  99.3 3.9E-12   1E-16   96.2   6.4  106   83-220    51-169 (173)
 13 cd06462 Peptidase_S24_S26 The   99.1 3.1E-10   8E-15   84.2   6.7   82   37-215     2-83  (84)
 14 TIGR02228 sigpep_I_arch signal  99.0 1.7E-09 4.5E-14   79.5   6.6   80   12-110     2-95  (175)
 15 pfam00717 Peptidase_S24 Peptid  98.7 1.2E-08 2.9E-13   74.4   4.7   56   39-118     1-56  (67)
 16 COG2932 Predicted transcriptio  98.0   9E-06 2.3E-10   56.1   5.4   57   37-117   125-181 (214)
 17 cd06529 S24_LexA-like Peptidas  97.8 4.4E-05 1.1E-09   51.8   5.7   56   37-117     2-57  (81)
 18 KOG3342 consensus               97.4 0.00015 3.7E-09   48.5   3.1   52   38-110    51-102 (180)
 19 PRK00215 LexA repressor; Valid  96.7  0.0033 8.4E-08   40.0   5.3   53   37-115   119-172 (204)
 20 COG0681 LepB Signal peptidase   96.3  0.0041 1.1E-07   39.4   3.3   28  101-128   138-165 (166)
 21 PRK10276 DNA polymerase V subu  96.2  0.0088 2.2E-07   37.3   4.9   45   38-107    54-99  (139)
 22 PHA00361 cI Repressor           96.2   0.011 2.8E-07   36.7   5.2   56   31-112    72-131 (165)
 23 PRK12423 LexA repressor; Provi  95.5   0.033 8.4E-07   33.7   5.2   54   38-117   117-171 (202)
 24 COG1974 LexA SOS-response tran  92.6    0.29 7.4E-06   27.8   5.1   47   38-108   115-162 (201)
 25 TIGR02896 spore_III_AF stage I  84.7     1.1 2.9E-05   24.1   3.4   31   11-47      1-31  (113)
 26 COG3602 Uncharacterized protei  64.2       4  0.0001   20.6   1.6   17   43-59     12-28  (134)
 27 COG1969 HyaC Ni,Fe-hydrogenase  64.2     6.4 0.00016   19.3   2.7   34   13-48     20-53  (227)
 28 pfam11101 DUF2884 Protein of u  63.8     4.9 0.00013   20.0   2.1   27  106-132    17-44  (229)
 29 pfam10000 DUF2241 Uncharacteri  60.3     5.2 0.00013   19.9   1.7   16   43-58     12-27  (72)
 30 TIGR01237 D1pyr5carbox2 delta-  55.9     5.7 0.00014   19.7   1.3   21   98-118   273-295 (518)
 31 pfam02836 Glyco_hydro_2_C Glyc  54.6     5.7 0.00015   19.6   1.1   28  184-211   252-279 (297)
 32 KOG1247 consensus               50.8     9.7 0.00025   18.2   1.8   41  203-246   250-291 (567)
 33 TIGR01718 Uridine-psphlse urid  49.4      14 0.00036   17.2   2.4   31   24-58     75-106 (248)
 34 PRK09919 hypothetical protein;  45.0      11 0.00027   17.9   1.3   24  109-132    39-62  (114)
 35 cd02776 MopB_CT_Nitrate-R-NarG  44.1      23  0.0006   15.8   2.9   36   84-124    25-62  (141)
 36 TIGR01704 MTA/SAH-Nsdase MTA/S  43.8      17 0.00044   16.6   2.2   42   20-62     52-96  (229)
 37 TIGR00185 rRNA_methyl_2 RNA me  43.3      24 0.00061   15.7   3.5  103   89-193     3-109 (161)
 38 PRK09525 lacZ beta-D-galactosi  42.5      12 0.00031   17.6   1.2   17  114-130   335-351 (1027)
 39 COG0361 InfA Translation initi  41.3      21 0.00054   16.1   2.3   13   49-61     47-59  (75)
 40 TIGR00915 2A0602 RND transport  41.3     8.4 0.00021   18.6   0.3   15   83-97    659-673 (1058)
 41 cd04438 DEP_dishevelled DEP (D  39.0      15 0.00038   17.0   1.3   13  179-191    72-84  (84)
 42 cd01287 FabA FabA, beta-hydrox  38.2      16 0.00041   16.8   1.3   26  104-129   112-137 (150)
 43 PRK10340 ebgA cryptic beta-D-g  37.1      16 0.00042   16.7   1.2   16  114-129   319-334 (1030)
 44 TIGR02390 RNA_pol_rpoA1 DNA-di  35.6      21 0.00054   16.0   1.6   34   82-117   430-467 (901)
 45 PRK08566 DNA-directed RNA poly  35.2      32 0.00082   14.9   3.0   33   83-117   410-446 (881)
 46 COG1097 RRP4 RNA-binding prote  34.2      33 0.00085   14.8   4.3   17   42-58    106-122 (239)
 47 TIGR02219 phage_NlpC_fam putat  33.4      22 0.00057   15.9   1.4   19   79-97     71-90  (135)
 48 pfam11057 Cortexin Cortexin of  32.2      25 0.00064   15.6   1.5   29   19-47     35-66  (81)
 49 PRK10838 spr putative outer me  30.1      18 0.00046   16.5   0.5   12   22-33     15-26  (188)
 50 TIGR02656 cyanin_plasto plasto  29.9      18 0.00045   16.5   0.4   21  106-126    18-38  (102)
 51 PRK10369 heme lyase subunit Nr  29.4      40   0.001   14.3   2.9   23  106-128   428-450 (552)
 52 pfam00623 RNA_pol_Rpb1_2 RNA p  28.9      41   0.001   14.2   2.2   34   82-117    91-128 (165)
 53 TIGR00575 dnlj DNA ligase, NAD  28.7      34 0.00087   14.7   1.7   12   41-52    345-356 (706)
 54 KOG2915 consensus               28.3      20 0.00051   16.2   0.4   21  104-124    48-70  (314)
 55 TIGR02730 carot_isom carotene   28.0      43  0.0011   14.1   2.2   25   42-67    200-224 (506)
 56 TIGR02823 oxido_YhdH putative   27.7      43  0.0011   14.1   3.0   21   43-63     72-92  (330)
 57 TIGR00110 ilvD dihydroxy-acid   27.6      28 0.00072   15.3   1.1   18   80-97    455-474 (601)
 58 KOG1618 consensus               27.6      35 0.00088   14.7   1.6   47  180-228   294-342 (389)
 59 TIGR03468 HpnG hopanoid-associ  27.0      44  0.0011   14.0   2.1   23   42-64     55-77  (212)
 60 cd00986 PDZ_LON_protease PDZ d  26.8      30 0.00076   15.1   1.1   42   85-129    25-69  (79)
 61 COG3250 LacZ Beta-galactosidas  26.7      31 0.00078   15.0   1.2   17  113-129   284-300 (808)
 62 TIGR02634 xylF D-xylose ABC tr  26.2      31  0.0008   15.0   1.1   13  180-192   116-128 (307)
 63 PRK05174 3-hydroxydecanoyl-(ac  25.1      39   0.001   14.4   1.5   13  117-129   143-155 (172)
 64 PRK10150 beta-D-glucuronidase;  25.1      35  0.0009   14.7   1.2   19  114-132   280-298 (605)
 65 PRK06714 S-adenosylhomocystein  24.9      48  0.0012   13.8   3.6   42   21-63     55-99  (236)
 66 TIGR01857 FGAM-synthase phosph  24.6      39   0.001   14.4   1.4   20   31-51    361-380 (1279)
 67 COG2949 SanA Uncharacterized m  23.6      47  0.0012   13.9   1.6   14  185-198    96-109 (235)
 68 PRK05584 5'-methylthioadenosin  23.4      47  0.0012   13.9   1.6   40   22-62     55-97  (230)
 69 pfam00877 NLPC_P60 NlpC/P60 fa  23.1      38 0.00098   14.4   1.1   16   80-95     46-61  (105)
 70 pfam01048 PNP_UDP_1 Phosphoryl  22.6      49  0.0013   13.7   1.6   22   41-62     78-99  (232)
 71 PRK02122 glucosamine-6-phospha  22.4      21 0.00053   16.1  -0.4   21  180-200   528-548 (660)
 72 COG4615 PvdE ABC-type sideroph  22.1      35  0.0009   14.7   0.7   46   84-133   345-391 (546)
 73 pfam05382 Amidase_5 Bacterioph  22.0      43  0.0011   14.1   1.1   13   84-96     75-87  (145)
 74 TIGR01285 nifN nitrogenase mol  21.2      46  0.0012   13.9   1.2   97   28-133   195-335 (451)
 75 pfam05257 CHAP CHAP domain. Th  21.1      57  0.0015   13.3   2.7   14   82-95     55-68  (119)
 76 TIGR00066 g_glut_trans gamma-g  20.6      36 0.00091   14.6   0.5   11   39-49    455-465 (583)
 77 TIGR01026 fliI_yscN ATPase Fli  20.1      60  0.0015   13.2   3.8   71   33-125    23-103 (455)
 78 cd03295 ABC_OpuCA_Osmoprotecti  20.1      37 0.00093   14.6   0.5   44   84-131    23-67  (242)

No 1  
>PRK10861 lsignal peptidase I; Provisional
Probab=100.00  E-value=0  Score=484.08  Aligned_cols=223  Identities=38%  Similarity=0.699  Sum_probs=170.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             03587899999999999988751689899878667764336988999840058766412211542222112555334704
Q gi|254780939|r   11 IFGSDTLKSILQALFFAILIRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDV   90 (248)
Q Consensus        11 ~f~~e~i~~l~~~i~i~~~ir~fv~~~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDI   90 (248)
                      -.+-|+.++++.++++++++|+|++|||+|||+||+|||++||+|||||++||+|.|.+..+.      +..++||||||
T Consensus        58 p~~~e~~~s~fpvi~~v~ilRsFl~EPF~IPSgSM~PTLlvGDfIlVnKf~YG~r~P~~~~~i------i~~~~PkRGDV  131 (324)
T PRK10861         58 PGWLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTL------IETGHPKRGDI  131 (324)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHEECEECCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCC------CCCCCCCCCCE
T ss_conf             615556677999999999999883237027864343423558889998120466777667512------45799988999


Q ss_pred             EEEECCCCCHHHEEEEEEEECHHHEEEC--CCCEEECCC-----------CCCCCCCCCCE-------------------
Q ss_conf             6640144200310000003042343200--773245353-----------12245446400-------------------
Q gi|254780939|r   91 VVFRYPKDPSIDYVKRVIGLPGDRISLE--KGIIYINGA-----------PVVRHMEGYFS-------------------  138 (248)
Q Consensus        91 VVF~~P~d~~~~yVKRvIGlPGDtV~i~--~~~l~INg~-----------~i~~~~~~~~~-------------------  138 (248)
                      |||++|.|++++|||||||+|||+|+++  |++++|+..           ++.+......+                   
T Consensus       132 VVF~yP~d~~~dYIKRvIGLPGD~I~y~~~~k~l~i~p~~~~~~~~~~~l~i~~~~~~~~d~~~~~~~~~~~~~~~~~~~  211 (324)
T PRK10861        132 VVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFE  211 (324)
T ss_pred             EEEECCCCCCCCEECCCCCCCCCEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99958999987644104556987797413565267613555451125642101343561345552102578622353101


Q ss_pred             EECC--CCCCEEEEEECCCCCCCCCCCEEEC---------CCCCCCCCCCEEECCCCEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             2214--7862012210221467850002212---------4557887453023244649997178877764453653026
Q gi|254780939|r  139 YHYK--EDWSSNVPIFQEKLSNGVLYNVLSQ---------DFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFV  207 (248)
Q Consensus       139 ~~~~--~~~~~~~~~~~e~l~~~~~~~~~~~---------~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~~~G~V  207 (248)
                      .+..  .........+.|++++ ..|.++..         ....++...++|+||+|||||||||||||.||||  ||||
T Consensus       212 ~p~~~~~~~~~~~~~~~e~l~~-~~h~il~~p~~~~~~~~~~~~~~~~~~~~~VP~g~YFmMGDNRDNS~DSRy--WGFV  288 (324)
T PRK10861        212 VPLNETKENGIRLSERKETLGD-VTHRILTVPIAQDQLGMYYQQPGQPLATWIVPPGQYFMMGDNRDNSADSRY--WGFV  288 (324)
T ss_pred             CCCCCCCCCCEEEEEEEEECCC-CCEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCEEEEECCCCCCCCCCC--EECC
T ss_conf             5655577664354235650487-320367525643334421135777665479689958984128888764574--6167


Q ss_pred             CHHHEEEEEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCC
Q ss_conf             0888253389999743788775435554567013342232
Q gi|254780939|r  208 PEENLVGRASFVLFSIGGDTPFSKVWLWIPNMRWDRLFKI  247 (248)
Q Consensus       208 p~~~IvGka~~i~~S~d~~~~~~~~~~~~~~iRw~R~f~~  247 (248)
                      |++||+|||++||||+|.+..     .|+.++||+|+++.
T Consensus       289 Pe~~IVGKA~~IWmS~d~~~~-----~~p~~iR~~RiG~i  323 (324)
T PRK10861        289 PEANLVGKATAIWMSFEKQEG-----EWPTGVRLSRIGGI  323 (324)
T ss_pred             CHHHCEEEEEEEEEECCCCCC-----CCCCCCCEEECCCC
T ss_conf             789945626899998148768-----78776624403267


No 2  
>TIGR02227 sigpep_I_bact signal peptidase I; InterPro: IPR000223   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   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.    This group of serine peptidases belong to MEROPS peptidase family S26 (signal peptidase I family, clan SF), subfamily S26A.   At least 3 eubacterial leader peptidases are known: murein prelipoprotein peptidase, which cleaves the leader peptide from a component of the bacterial outer membrane; type IV prepilin leader peptidase; and the serine-dependent leader peptidase 1, which has the more general role of cleaving the leader peptide from a variety of secreted proteins and proteins directed to the periplasm and periplasmic membrane . Leader peptidase 1 is similar to the eukaryotic signal peptidase, although the bacterial protein is monomeric, while the eukaryotic protein is multimeric .   Mitochondria contain a similar two-subunit serine protease that removes leader peptides from nuclear- and mitochondrial-encoded proteins, which localise in the inner mitochondrial space . The catalytic residues of a number of these peptides have been identified as a serine/lysine dyad .; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0016020 membrane.
Probab=100.00  E-value=0  Score=385.69  Aligned_cols=195  Identities=41%  Similarity=0.745  Sum_probs=160.6

Q ss_pred             HHHHHHHHHHHHHHHHHEEEEE-EEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             8999999999999887516898-998786677643369889998400587664122115422221125553347046640
Q gi|254780939|r   16 TLKSILQALFFAILIRTFLFQP-SVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFR   94 (248)
Q Consensus        16 ~i~~l~~~i~i~~~ir~fv~~~-f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~   94 (248)
                      ++.++++|+++++++|+|++++ +.|||+||+|||+.||+|||||++|+ | .++|++...+   +.+++|+|||||||+
T Consensus         1 ~~~~~~~~~~~~~~~r~f~~~~~~~v~g~SM~PTL~~gD~~lv~K~~y~-r-~~lp~~~~~~---~~~~~~~rgDivVF~   75 (203)
T TIGR02227         1 VILSILIAILLALLIRTFVFFPVYKVPGGSMEPTLKEGDRILVNKFAYG-R-LKLPFTHKLL---FKTSDPKRGDIVVFK   75 (203)
T ss_pred             CHHHHHHHHHHHHHHHHHHEEEEEEECCCCCCHHHCCCCEEEEEEECCC-E-EEEECCEEEE---EEECCCEECCEEEEE
T ss_conf             9555678999999986411478898088975532237988999981264-4-5630210003---560575004089995


Q ss_pred             CCCCCHH-HEEEEEEEECHHHEEECC-CCEEECC-CCCCCC--CCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEECCC
Q ss_conf             1442003-100000030423432007-7324535-312245--4464002214786201221022146785000221245
Q gi|254780939|r   95 YPKDPSI-DYVKRVIGLPGDRISLEK-GIIYING-APVVRH--MEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDF  169 (248)
Q Consensus        95 ~P~d~~~-~yVKRvIGlPGDtV~i~~-~~l~INg-~~i~~~--~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~  169 (248)
                      .|.+++. .|||||||+|||+|+++| |+||||| ++++++  +..........+......       .+ .+ +.....
T Consensus        76 ~~~~~~~~~yiKRviglPGD~v~~~~~g~ly~Ng~~~~~e~~~y~~~~~~~~~~~~~~~~~-------~~-~~-~~~~~~  146 (203)
T TIGR02227        76 APDDPDNRIYIKRVIGLPGDKVEIKDKGKLYINGLKKIDEPNEYLKPNKSLDTSEFNAATG-------RG-KH-VTNFAS  146 (203)
T ss_pred             CCCCCCCCEEEEEEEECCCCEEEEEECCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC-------CC-HH-HHHHHH
T ss_conf             3899889616789996588889998089069858601236765456544434555310220-------00-01-122211


Q ss_pred             CCCCCCCCEEECCCCEEEEEECCCCCCCCCCCC--CCCCCCHHHEEEEEEEEEEECC
Q ss_conf             578874530232446499971788777644536--5302608882533899997437
Q gi|254780939|r  170 LAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWV--EVGFVPEENLVGRASFVLFSIG  224 (248)
Q Consensus       170 ~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~--~~G~Vp~~~IvGka~~i~~S~d  224 (248)
                      .....+.++++||+||||||||||+||.|||++  .||+||+++|+|||.+++||++
T Consensus       147 ~~~~~~~~~~~VP~g~yFvLGDNR~~S~DSR~~~~~~G~v~~~~i~G~~~~~~~p~~  203 (203)
T TIGR02227       147 EEIITDYGPVTVPEGKYFVLGDNRDNSLDSRFWDDYFGFVPRDDIIGKVSFVFYPFD  203 (203)
T ss_pred             HHHHHCCCCEEECCCCEEEEECCCCCCCCCCCCCCEECCCCHHHEEEEEEEEEEECC
T ss_conf             110112587680798579870254466655357862546207786589999986069


No 3  
>KOG0171 consensus
Probab=99.97  E-value=1.5e-31  Score=218.44  Aligned_cols=134  Identities=31%  Similarity=0.528  Sum_probs=112.5

Q ss_pred             HHHHHEEEEEEEECCCCCCCCCCC-CCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEE
Q ss_conf             988751689899878667764336-9889998400587664122115422221125553347046640144200310000
Q gi|254780939|r   28 ILIRTFLFQPSVIPSGSMIPTLLV-GDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKR  106 (248)
Q Consensus        28 ~~ir~fv~~~f~Ips~SM~PTL~~-GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKR  106 (248)
                      -....|+++.-.+++.||+|||+. ||++++.|++|                  +++.||+||||||+.|.+++++++||
T Consensus        26 h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~------------------~f~~~~~gDIVi~~sP~~~~~~~cKR   87 (176)
T KOG0171          26 HVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSY------------------RFRKPQVGDIVIAKSPPDPKEHICKR   87 (176)
T ss_pred             HHHHHHHCCEEECCCCCCCCEECCCCCEEEHHHHHH------------------HHCCCCCCCEEEEECCCCCHHHHHHE
T ss_conf             999987422066258875753627986886335457------------------64589877789994899803422110


Q ss_pred             EEEECHHHEEECCCCEEECCCCCCCCCCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEE
Q ss_conf             00304234320077324535312245446400221478620122102214678500022124557887453023244649
Q gi|254780939|r  107 VIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHY  186 (248)
Q Consensus       107 vIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~y  186 (248)
                      +||+|||-+++.++.+.+|+.-  +                                          +...+..||+||.
T Consensus        88 Iva~eGD~v~v~~~~~~~n~~~--e------------------------------------------~~~~~i~VP~GhV  123 (176)
T KOG0171          88 IVAMEGDLVEVHDGPLVVNDLV--E------------------------------------------KFSTPIRVPEGHV  123 (176)
T ss_pred             EECCCCCEEEEECCCCCCCHHH--H------------------------------------------HCCCEEECCCCEE
T ss_conf             3214886289962774343113--2------------------------------------------0564046137518


Q ss_pred             EEEECCCCCCCCCCCCCCCCCCHHHEEEEEEEEEEECCC
Q ss_conf             997178877764453653026088825338999974378
Q gi|254780939|r  187 FMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVLFSIGG  225 (248)
Q Consensus       187 fvlGDNRdnS~DSR~~~~G~Vp~~~IvGka~~i~~S~d~  225 (248)
                      ||+||||.||.|||  .||++|..+|.||..+-+|....
T Consensus       124 fv~GDN~~nS~DSr--~yGplP~glI~gRvv~r~Wp~s~  160 (176)
T KOG0171         124 FVEGDNRNNSLDSR--NYGPLPMGLIQGRVVFRIWPPSR  160 (176)
T ss_pred             EEECCCCCCCCCCC--CCCCCCHHHEEEEEEEEECCCHH
T ss_conf             98658887766456--43777452433568888669311


No 4  
>pfam10502 Peptidase_S26 Peptidase S26. This is a family of serine endopeptidases which function in the processing of newly-synthesized secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes.
Probab=99.96  E-value=1.7e-29  Score=205.43  Aligned_cols=107  Identities=32%  Similarity=0.557  Sum_probs=84.0

Q ss_pred             CCCCCCCCEEEEECCCCC------------HHHEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEECCCCCCEEE
Q ss_conf             555334704664014420------------03100000030423432007732453531224544640022147862012
Q gi|254780939|r   82 NNQPRRGDVVVFRYPKDP------------SIDYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNV  149 (248)
Q Consensus        82 ~~~p~RGDIVVF~~P~d~------------~~~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~  149 (248)
                      ..+|+|||+|+|..|.+.            +..|||||+|+|||+|++++++++|||+++.+.....        .    
T Consensus        19 ~~~~~rGD~V~f~~P~~~~~~~~~rgyl~~g~~~iKrV~g~pGD~V~i~~~~v~INg~~~~~~~~~d--------~----   86 (138)
T pfam10502        19 LDRPEVGDLVAVCPPEPAAFFAAERGYLPRGVPLLKRVLALPGQRVCIRDGLVTIDGVPVSAALERD--------R----   86 (138)
T ss_pred             CCCCCCCCEEEEECCHHHHHHHHHCCCCCCCCCEEEEEEEECCCEEEEECCEEEECCEECCCEECCC--------C----
T ss_conf             8987428899997984887778766867789957889998099899998999988899953210337--------6----


Q ss_pred             EEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHEEEEEEEEE
Q ss_conf             21022146785000221245578874530232446499971788777644536530260888253389999
Q gi|254780939|r  150 PIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVL  220 (248)
Q Consensus       150 ~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~~~G~Vp~~~IvGka~~i~  220 (248)
                              .+....          ...+..+||+|+||||||||++|.||||  ||+||+++|+|||.-||
T Consensus        87 --------~g~~l~----------~~~~~~~vp~g~~fvlgdn~~~S~DSRy--~G~V~~~~I~G~a~pi~  137 (138)
T pfam10502        87 --------KGRPLP----------PWQGCRVLPEGELFLMSVTSPDSFDSRY--FGPVPASAIIGRARPVW  137 (138)
T ss_pred             --------CCCCCC----------CCCCCCEECCCEEEEECCCCCCCCCCCC--EEECCHHHEEEEEEEEE
T ss_conf             --------788577----------6678629189989997699998754541--81357799699999967


No 5  
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.91  E-value=7.3e-25  Score=176.30  Aligned_cols=85  Identities=58%  Similarity=1.046  Sum_probs=78.1

Q ss_pred             EEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHE
Q ss_conf             98998786677643369889998400587664122115422221125553347046640144200310000003042343
Q gi|254780939|r   36 QPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRI  115 (248)
Q Consensus        36 ~~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV  115 (248)
                      +++.|+|+||+|||..||.++++|+.|.                  ..++++||||+|++|.+++..+||||||      
T Consensus         1 ~~~~V~g~SM~Pt~~~Gd~v~v~~~~~~------------------~~~~~~GDivv~~~p~~~~~~~ikRVi~------   56 (85)
T cd06530           1 EPVVVPGGSMEPTLQPGDLVLVNKLSYG------------------FREPKRGDVVVFKSPGDPGKPIIKRVIG------   56 (85)
T ss_pred             CCEEECCCCCCCCCCCCCEEEEEECCCC------------------CCCCCCCCEEEEECCCCCCCEEEECCCE------
T ss_conf             9969568888060308989999961356------------------5777778699996799999759974327------


Q ss_pred             EECCCCEEECCCCCCCCCCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCC
Q ss_conf             20077324535312245446400221478620122102214678500022124557887453023244649997178877
Q gi|254780939|r  116 SLEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDK  195 (248)
Q Consensus       116 ~i~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdn  195 (248)
                                                                                            ||++||||+|
T Consensus        57 ----------------------------------------------------------------------~~~~GDN~~n   66 (85)
T cd06530          57 ----------------------------------------------------------------------YFVLGDNRNN   66 (85)
T ss_pred             ----------------------------------------------------------------------EEEEECCCCC
T ss_conf             ----------------------------------------------------------------------8987359676


Q ss_pred             CCCCCCCCCCCCCHHHEEEEE
Q ss_conf             764453653026088825338
Q gi|254780939|r  196 SKDSRWVEVGFVPEENLVGRA  216 (248)
Q Consensus       196 S~DSR~~~~G~Vp~~~IvGka  216 (248)
                      |.|||+  ||++|.++|+||+
T Consensus        67 s~Dsr~--~g~v~~~~i~Gkv   85 (85)
T cd06530          67 SLDSRY--WGPVPEDDIVGKV   85 (85)
T ss_pred             CCCCCC--CCCCCHHHEEEEC
T ss_conf             864571--4767789939959


No 6  
>KOG1568 consensus
Probab=99.89  E-value=2.3e-23  Score=166.83  Aligned_cols=134  Identities=33%  Similarity=0.509  Sum_probs=101.8

Q ss_pred             HHHHHHHHHHHHH--HHHHHEEEEEEEECCCCCCCCCCCC------CEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7899999999999--9887516898998786677643369------8899984005876641221154222211255533
Q gi|254780939|r   15 DTLKSILQALFFA--ILIRTFLFQPSVIPSGSMIPTLLVG------DYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPR   86 (248)
Q Consensus        15 e~i~~l~~~i~i~--~~ir~fv~~~f~Ips~SM~PTL~~G------D~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~   86 (248)
                      -+.++++.++.-.  +-+---+.-.-+|-+.||.|||..+      |+||+.|+.                  +......
T Consensus         9 ~~~ksl~~s~~~~v~~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~------------------v~n~~~~   70 (174)
T KOG1568           9 VFEKSLTGSLKWHVLLTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWN------------------VKNRKVS   70 (174)
T ss_pred             HHHHCEEEEEEEHEEEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEC------------------CCCCEEC
T ss_conf             9874003554401024562047787678547678751887665535489998503------------------3343034


Q ss_pred             CCCEEEEECCCCCHHHEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEE
Q ss_conf             47046640144200310000003042343200773245353122454464002214786201221022146785000221
Q gi|254780939|r   87 RGDVVVFRYPKDPSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLS  166 (248)
Q Consensus        87 RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~  166 (248)
                      |||||+|++|.|+.+.+||||+|+|||.+.-.+                                               
T Consensus        71 rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~-----------------------------------------------  103 (174)
T KOG1568          71 RGDIVVLKSPNDPDKVIIKRVAALEGDIMVTED-----------------------------------------------  103 (174)
T ss_pred             CCCEEEEECCCCHHHEEEEEEECCCCCEECCCC-----------------------------------------------
T ss_conf             687899958999215235515135664751588-----------------------------------------------


Q ss_pred             CCCCCCCCCCCEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHEEEEEEEEEEE
Q ss_conf             24557887453023244649997178877764453653026088825338999974
Q gi|254780939|r  167 QDFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVLFS  222 (248)
Q Consensus       167 ~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~~~G~Vp~~~IvGka~~i~~S  222 (248)
                             ..-.++.||+||+||.|||--+|.|||  .||+|+-..|+|||..|.|.
T Consensus       104 -------~k~~~v~vpkghcWVegDn~~hs~DSn--tFGPVS~gli~grai~ilwp  150 (174)
T KOG1568         104 -------EKEEPVVVPKGHCWVEGDNQKHSYDSN--TFGPVSTGLIVGRAIYILWP  150 (174)
T ss_pred             -------CCCCCEECCCCCEEEECCCCCCCCCCC--CCCCCCHHHEEEEEEEEECC
T ss_conf             -------877735468984789648755334467--54773342124258999748


No 7  
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.81  E-value=3.9e-19  Score=140.23  Aligned_cols=109  Identities=20%  Similarity=0.268  Sum_probs=79.3

Q ss_pred             CCCCCCCEEEEECCCCCH-------------------HHEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEECCC
Q ss_conf             553347046640144200-------------------3100000030423432007732453531224544640022147
Q gi|254780939|r   83 NQPRRGDVVVFRYPKDPS-------------------IDYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKE  143 (248)
Q Consensus        83 ~~p~RGDIVVF~~P~d~~-------------------~~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~~~  143 (248)
                      ..+++||.|+|-.|...-                   ...+|||+|+|||+|++.++.++|||+.+.....-..      
T Consensus        49 ~~~~~gd~V~~~pp~~~~~~~a~~RgYl~~G~cpgg~~pLiKrV~AlpGd~V~i~~~~V~InG~~lp~s~~~~~------  122 (178)
T PRK13884         49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVADDGVRVNGELLPLSKPIKA------  122 (178)
T ss_pred             CCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEECCCCEEEEECCEEEECCEECCCCCCCCC------
T ss_conf             87565888999479669999998758656788998864037888506998899869999999998666433334------


Q ss_pred             CCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHEEEEEEEEE
Q ss_conf             86201221022146785000221245578874530232446499971788777644536530260888253389999
Q gi|254780939|r  144 DWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVL  220 (248)
Q Consensus       144 ~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~~~G~Vp~~~IvGka~~i~  220 (248)
                      +            ..|..         .+.-+...+++++|+||+|+|++.+|.||||  ||+||+++|+|+|.=+|
T Consensus       123 D------------~~GRp---------Lp~~~~~~~~l~~~e~fll~~~~~~SfDSRY--FGPV~~s~I~G~a~Pl~  176 (178)
T PRK13884        123 D------------KAGRP---------LPRYQANSYTLGNSELLLMSDVSATSFDGRY--FGPINRSQIKTVIRPVI  176 (178)
T ss_pred             C------------CCCCC---------CCCCCCCCEECCCCEEEEECCCCCCCCCCCC--CCCCCHHHEEEEEEEEE
T ss_conf             5------------58995---------8854788458279969996699998765445--55465788069999706


No 8  
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.80  E-value=3.5e-19  Score=140.50  Aligned_cols=91  Identities=44%  Similarity=0.799  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHHHHHHH--HHEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             87899999999999988--7516898998786677643369889998400587664122115422221125553347046
Q gi|254780939|r   14 SDTLKSILQALFFAILI--RTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVV   91 (248)
Q Consensus        14 ~e~i~~l~~~i~i~~~i--r~fv~~~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIV   91 (248)
                      .++++.++.++++++++  +.|+++++.|||+||+|||+.||+|+|+|++|+..                  +++.+|++
T Consensus         8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~------------------~~~~~~~~   69 (166)
T COG0681           8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFG------------------KLKVPDII   69 (166)
T ss_pred             HHHHHHHHHHHHHHHHHHHEEEEEEEEEEECCCCCCCCCCCCEEEEECCCCCCC------------------CCCCCCEE
T ss_conf             999999999999999753204346889980898745677788999966556766------------------45654200


Q ss_pred             EEECCCCCHHHEEEEEEEECHHHEEECCCCEEE
Q ss_conf             640144200310000003042343200773245
Q gi|254780939|r   92 VFRYPKDPSIDYVKRVIGLPGDRISLEKGIIYI  124 (248)
Q Consensus        92 VF~~P~d~~~~yVKRvIGlPGDtV~i~~~~l~I  124 (248)
                        ..|......++||++|+|||++.++++.+++
T Consensus        70 --~~~~~~~~~~~kr~~~~~GD~i~~~~~~~~~  100 (166)
T COG0681          70 --VLPAVVEGDLIKRVIGLRGDIVVFKDDRLYV  100 (166)
T ss_pred             --CCCCCCCCCCCCCCCCCCCCEEEECCCCCCC
T ss_conf             --1442233404032467998889976876310


No 9  
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF; InterPro: IPR014139   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   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.    This entry contains the conjugative transfer signal peptidase (TraF), which belongs to MEROPS peptidase family S26, subfamily S26C (TraF signal peptidase, clan SF). It is found in operons that encode elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as LepB. This family is present in both Ti-type and I-type conjugative systems ..
Probab=99.73  E-value=2.2e-17  Score=129.26  Aligned_cols=107  Identities=34%  Similarity=0.576  Sum_probs=81.9

Q ss_pred             CCCCCCCCEEEEECC-CCCHH-------------------HEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEEC
Q ss_conf             555334704664014-42003-------------------1000000304234320077324535312245446400221
Q gi|254780939|r   82 NNQPRRGDVVVFRYP-KDPSI-------------------DYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHY  141 (248)
Q Consensus        82 ~~~p~RGDIVVF~~P-~d~~~-------------------~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~  141 (248)
                      -++++|||.|+|.+| +++..                   .++|||+|+|||+|+++.+.+.|||+.+........+   
T Consensus        47 ~~~v~~G~yV~fcpPe~~~~~~~A~~RGY~~~G~C~GGf~pl~K~v~~l~Gd~v~~~~~~v~iNg~~~~~~~~~~~D---  123 (183)
T TIGR02771        47 SKPVERGDYVVFCPPEDNAVFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGKLLPYSKPLATD---  123 (183)
T ss_pred             CCCCCCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHEEECCCCCEEEEECCEEEECCEECCCCCEEECC---
T ss_conf             26877787789835986678740545143357888986001202321278955886068888878677987311007---


Q ss_pred             CCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCC-C-EEECCCC--EEEEEECCCC-CCCCCCCCCCCCCCHHHEEEEE
Q ss_conf             47862012210221467850002212455788745-3-0232446--4999717887-7764453653026088825338
Q gi|254780939|r  142 KEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNI-S-EFLVPKG--HYFMMGDNRD-KSKDSRWVEVGFVPEENLVGRA  216 (248)
Q Consensus       142 ~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~-~-~~~VP~g--~yfvlGDNRd-nS~DSR~~~~G~Vp~~~IvGka  216 (248)
                                     +.|..        .   ..+ . +-++|+|  .+|+|-|... .|.||||..||+|++++|+|++
T Consensus       124 ---------------~~GR~--------l---~p~k~s~~~~p~G~~~~~~v~~~~~a~SFDSRYA~fG~i~~~q~~~~~  177 (183)
T TIGR02771       124 ---------------SEGRP--------L---PPLKASEGVVPPGEAEFLVVSDTSPATSFDSRYAEFGPISREQVIGRV  177 (183)
T ss_pred             ---------------CCCCC--------C---CCCCCCCCEECCCCCEEEEEECCCCCCCCCHHHHCCCCEECCCEEEEE
T ss_conf             ---------------88888--------8---765788853028862178985088987610011024772000505877


Q ss_pred             E
Q ss_conf             9
Q gi|254780939|r  217 S  217 (248)
Q Consensus       217 ~  217 (248)
                      .
T Consensus       178 ~  178 (183)
T TIGR02771       178 K  178 (183)
T ss_pred             E
T ss_conf             1


No 10 
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.67  E-value=1.3e-15  Score=118.17  Aligned_cols=105  Identities=28%  Similarity=0.432  Sum_probs=74.6

Q ss_pred             CCCCCCCEEEEECCCCCH-------------H------HEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEECCC
Q ss_conf             553347046640144200-------------3------100000030423432007732453531224544640022147
Q gi|254780939|r   83 NQPRRGDVVVFRYPKDPS-------------I------DYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKE  143 (248)
Q Consensus        83 ~~p~RGDIVVF~~P~d~~-------------~------~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~~~  143 (248)
                      +.+++||+|+|..|+..-             .      ..+|||+|+|||+|++.+ .+.|||+.+.......-+     
T Consensus        49 ~~~~~GdlV~vcpP~~~a~~~a~~RgYL~~G~Cpgg~~pLlKrV~Al~Gd~V~i~~-~V~Ing~~v~~s~~~~~D-----  122 (176)
T PRK13838         49 RPAAVGDLVFICPPDTAAFREARARGYLRSGLCPGGFAPLIKTVAAVAGQRVEIGD-SVSIDGRPVPSSSLARRD-----  122 (176)
T ss_pred             CCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCEEEECC-CEEECCEECCCCCCCCCC-----
T ss_conf             87644989998689479999998778753575888865202565146998899689-789989981235332547-----


Q ss_pred             CCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHEEEEEEEEE
Q ss_conf             86201221022146785000221245578874530232446499971788777644536530260888253389999
Q gi|254780939|r  144 DWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVL  220 (248)
Q Consensus       144 ~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~~~G~Vp~~~IvGka~~i~  220 (248)
                                   ..|...        .   ....-++|+|++|+|.|+.+ |.||||  ||+||+++|+|+|.=+|
T Consensus       123 -------------~~GrpL--------p---~~~~~~~~~g~~fL~~~~~~-SfDsRY--FGpv~~s~IiG~a~Pl~  172 (176)
T PRK13838        123 -------------GEGRPL--------L---PFPGGVVPPGHLFLHSSFAG-SYDSRY--FGPVPASGILGLARPVL  172 (176)
T ss_pred             -------------CCCCCC--------C---CCCCEECCCCEEEEECCCCC-CCCCCC--CCCCCHHHEEEEEEEEE
T ss_conf             -------------899806--------6---60881827986998579998-765555--14066778369999827


No 11 
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease; InterPro: IPR014124   Members of this protein family are predicted proteases that are encoded adjacent to the genes for a nickel-type superoxide dismutase (IPR014123 from INTERPRO). This family of predicted peptidases belong to MEROPS peptidase subfamily S26A (signal peptidase I), which have a Ser/Lys catalytic dyad..
Probab=99.61  E-value=1.6e-15  Score=117.58  Aligned_cols=89  Identities=39%  Similarity=0.564  Sum_probs=77.3

Q ss_pred             EEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHEEE
Q ss_conf             99878667764336988999840058766412211542222112555334704664014420031000000304234320
Q gi|254780939|r   38 SVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISL  117 (248)
Q Consensus        38 f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~i  117 (248)
                      .+|.+.||.|||..+|+|||+=+.|..                  +-++-|.|||..||..+....|||..|        
T Consensus         1 ~kV~G~SM~P~L~~~D~~~V~P~~~~~------------------r~~~~G~v~v~~HP~~p~~~~iKRL~~--------   54 (90)
T TIGR02754         1 LKVTGESMSPTLKPGDRILVRPLLKIA------------------RVPPIGEVVVVRHPLKPSLLIIKRLAA--------   54 (90)
T ss_pred             CEECCCCCCCCCCCCCEEEEEECCCCC------------------CCCCCCEEEEEECCCCCCEEEEEEEEE--------
T ss_conf             944332157613988869883011023------------------487788089985698997478986132--------


Q ss_pred             CCCCEEECCCCCCCCCCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCCCC
Q ss_conf             07732453531224544640022147862012210221467850002212455788745302324464999717887776
Q gi|254780939|r  118 EKGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKSK  197 (248)
Q Consensus       118 ~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~  197 (248)
                                                                                     +-+|-.++||||-+.|-
T Consensus        55 ---------------------------------------------------------------~~~nG~~~LGDnp~ASt   71 (90)
T TIGR02754        55 ---------------------------------------------------------------VDDNGLFLLGDNPKAST   71 (90)
T ss_pred             ---------------------------------------------------------------ECCCCCEEECCCCCCCC
T ss_conf             ---------------------------------------------------------------31788388567377876


Q ss_pred             CCCCCCCCCCCHHHEEEEEE
Q ss_conf             44536530260888253389
Q gi|254780939|r  198 DSRWVEVGFVPEENLVGRAS  217 (248)
Q Consensus       198 DSR~~~~G~Vp~~~IvGka~  217 (248)
                      |||  .||.||++.++|+|.
T Consensus        72 DSR--~~G~v~~~~L~G~v~   89 (90)
T TIGR02754        72 DSR--QLGPVPRELLLGKVL   89 (90)
T ss_pred             CCH--HHCCCCCHHEEEEEE
T ss_conf             712--105888202544785


No 12 
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.31  E-value=3.9e-12  Score=96.18  Aligned_cols=106  Identities=25%  Similarity=0.439  Sum_probs=78.7

Q ss_pred             CCC-CCCCEEEEECCCCC------------HHHEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEECCCCCCEEE
Q ss_conf             553-34704664014420------------03100000030423432007732453531224544640022147862012
Q gi|254780939|r   83 NQP-RRGDVVVFRYPKDP------------SIDYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNV  149 (248)
Q Consensus        83 ~~p-~RGDIVVF~~P~d~------------~~~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~  149 (248)
                      +.| ++||+|++.+|+.-            ....+||+.|+|||+|.+..+.+.|||+++.......       .     
T Consensus        51 ~~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D-------~-----  118 (173)
T COG4959          51 SAPVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVD-------R-----  118 (173)
T ss_pred             CCCCCCCCEEEECCCCHHHHHHHHCCCCCCCCHHHHHHHCCCCCCEEEECCEEEECCEEEEEECCCC-------C-----
T ss_conf             7875368889987970676767653766666278998751799827873361789899812340225-------6-----


Q ss_pred             EEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHEEEEEEEEE
Q ss_conf             21022146785000221245578874530232446499971788777644536530260888253389999
Q gi|254780939|r  150 PIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVL  220 (248)
Q Consensus       150 ~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS~DSR~~~~G~Vp~~~IvGka~~i~  220 (248)
                              .|.....+         +... .+-+++.|+|+|--..|.||||  ||+||.++|+|.|.=+|
T Consensus       119 --------~GR~lp~~---------~gcR-~l~~~el~lL~~~~~~SfDsRY--fGpipas~vig~aRPvw  169 (173)
T COG4959         119 --------VGRALPRW---------QGCR-YLAPSELLLLTDRSSTSFDSRY--FGPIPASQVIGVARPVW  169 (173)
T ss_pred             --------CCCCCCCC---------CCCC-EECCCEEEEEECCCCCCCCCCE--ECCCCHHHCCEEEEEEE
T ss_conf             --------67758763---------6872-5568727998456776554422--05667788101111100


No 13 
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=99.08  E-value=3.1e-10  Score=84.21  Aligned_cols=82  Identities=52%  Similarity=0.846  Sum_probs=65.4

Q ss_pred             EEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHEE
Q ss_conf             89987866776433698899984005876641221154222211255533470466401442003100000030423432
Q gi|254780939|r   37 PSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRIS  116 (248)
Q Consensus        37 ~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~  116 (248)
                      .++|.++||+||+..||.|+|++..                     .+++.||+++|+.+.  +..+|||++..++    
T Consensus         2 ~~~v~gdSM~P~i~~Gd~v~vd~~~---------------------~~~~~Gdiv~~~~~~--~~~~iKrl~~~~~----   54 (84)
T cd06462           2 ALRVEGDSMEPTIPDGDLVLVDKSS---------------------YEPKRGDIVVFRLPG--GELTVKRVIGLPG----   54 (84)
T ss_pred             EEEEECCCCCCHHHCCCEEEEECCC---------------------CCCCCCCEEEEEECC--CEEEEEEEEEECC----
T ss_conf             7996567771046489899997356---------------------657899699999789--9399999998889----


Q ss_pred             ECCCCEEECCCCCCCCCCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCCCEEECCCCEEEEEECCCCCC
Q ss_conf             00773245353122454464002214786201221022146785000221245578874530232446499971788777
Q gi|254780939|r  117 LEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKS  196 (248)
Q Consensus       117 i~~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~VP~g~yfvlGDNRdnS  196 (248)
                                                                                        ++++++.||| .++
T Consensus        55 ------------------------------------------------------------------~~~~~l~~dN-~~~   67 (84)
T cd06462          55 ------------------------------------------------------------------EGHYFLLGDN-PNS   67 (84)
T ss_pred             ------------------------------------------------------------------CCCEEEECCC-CCC
T ss_conf             ------------------------------------------------------------------9989997989-999


Q ss_pred             CCCCCCCCCCCCHHHEEEE
Q ss_conf             6445365302608882533
Q gi|254780939|r  197 KDSRWVEVGFVPEENLVGR  215 (248)
Q Consensus       197 ~DSR~~~~G~Vp~~~IvGk  215 (248)
                      .|++.  ++. +...++|+
T Consensus        68 ~~~~~--~~~-~~~~~~g~   83 (84)
T cd06462          68 PDSRI--DGP-PELDIVGV   83 (84)
T ss_pred             CCCCC--CCC-CCEEEEEE
T ss_conf             88124--899-97299998


No 14 
>TIGR02228 sigpep_I_arch signal peptidase I; InterPro: IPR001733   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   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.    This group of serine peptidases belong to MEROPS peptidase family S26 (signal peptidase I family, clan SF), subfamily S26B.   Eukaryotic microsomal signal peptidase is involved in the removal of signal peptides from secretory proteins as they pass into the endoplasmic reticulum lumen . The peptidase is more complex than its mitochondrial and bacterial counterparts, containing a number of subunits, ranging from two in the chicken oviduct peptidase, to five in the dog pancreas protein . They share sequence similarity with the bacterial leader peptidases (family S26A), although activity here is mediated by a serine/histidine dyad rather than a serine/lysine dyad . Archaeal signal peptidases also belong to this group. ; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0006508 proteolysis, 0016020 membrane.
Probab=98.96  E-value=1.7e-09  Score=79.51  Aligned_cols=80  Identities=29%  Similarity=0.414  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHEE------------EEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf             35878999999999999887516------------898998786677643369889998400587664122115422221
Q gi|254780939|r   12 FGSDTLKSILQALFFAILIRTFL------------FQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGR   79 (248)
Q Consensus        12 f~~e~i~~l~~~i~i~~~ir~fv------------~~~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~   79 (248)
                      .++|.+-.++++++++++.-.+.            +|.+.|-|+||||+++.||.+++.--                   
T Consensus         2 ~~~~~i~~~~~~ll~~~l~~~l~~~~~~~~p~V~GY~~kSVlSgSMEP~f~~Gd~~~~~~~-------------------   62 (175)
T TIGR02228         2 KISNVIYVILIILLVILLLVGLVSKASGPDPVVVGYQLKSVLSGSMEPTFNTGDLILVTGK-------------------   62 (175)
T ss_pred             CHHHHHHHHHHHHHHHHHHHEEEEEECCCCCEEEEEEEEEEEEEEECCEEECCEEEEEECC-------------------
T ss_conf             0233235578999998754315466528972798579898985543062521309998042-------------------


Q ss_pred             CCCCCCCCCCEEEEECCCCC--HHHEEEEEEEE
Q ss_conf             12555334704664014420--03100000030
Q gi|254780939|r   80 IFNNQPRRGDVVVFRYPKDP--SIDYVKRVIGL  110 (248)
Q Consensus        80 i~~~~p~RGDIVVF~~P~d~--~~~yVKRvIGl  110 (248)
                      ...++.|+||||+|+.+..+  +..-+-||+++
T Consensus        63 ~~~~~~~~GDvI~y~~~~~~WyG~~v~HRv~~~   95 (175)
T TIGR02228        63 VDPEDIQVGDVIVYKSEGKRWYGTPVIHRVIEI   95 (175)
T ss_pred             CCHHHCCCCCEEEEEECCCCCCCEEEEEEEEEE
T ss_conf             176663015679992469952353899999988


No 15 
>pfam00717 Peptidase_S24 Peptidase S24-like.
Probab=98.74  E-value=1.2e-08  Score=74.35  Aligned_cols=56  Identities=52%  Similarity=0.899  Sum_probs=47.0

Q ss_pred             EECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHEEEC
Q ss_conf             98786677643369889998400587664122115422221125553347046640144200310000003042343200
Q gi|254780939|r   39 VIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISLE  118 (248)
Q Consensus        39 ~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~i~  118 (248)
                      +|.++||+||++.||.|+|++-                      .++++||+|+|..+.++  .+|||+...+|+.+.+.
T Consensus         1 ~V~GdSM~p~i~~Gd~viv~~~----------------------~~~~~Gdivv~~~~~~~--~~iKrl~~~~~~~~l~~   56 (67)
T pfam00717         1 RVPGDSMEPTIPDGDLLLVDKT----------------------SEPKRGDIVVARLPGEE--AYVKRLIGLPGDIILLP   56 (67)
T ss_pred             CCCCCCCCCCCCCCCEEEEEEC----------------------CCCCCCCEEEEEECCCC--EEEEEEEEECCEEEEEE
T ss_conf             9717887557149999999834----------------------64546959999989995--69999996599299981


No 16 
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.04  E-value=9e-06  Score=56.14  Aligned_cols=57  Identities=33%  Similarity=0.442  Sum_probs=42.8

Q ss_pred             EEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHEE
Q ss_conf             89987866776433698899984005876641221154222211255533470466401442003100000030423432
Q gi|254780939|r   37 PSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRIS  116 (248)
Q Consensus        37 ~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~  116 (248)
                      ...|-++||+|++..||.+||+.                      .....+||.|++..  +++..||||+...||=.++
T Consensus       125 ~i~V~GDSMeP~~~~Gd~ilVd~----------------------~~~~~~gd~v~v~~--~g~~~~VK~l~~~~~~~~~  180 (214)
T COG2932         125 ALRVTGDSMEPTYEDGDTLLVDP----------------------GVNTRRGDRVYVET--DGGELYVKKLQREPGGLLR  180 (214)
T ss_pred             EEEEECCCCCCCCCCCCEEEEEC----------------------CCCEEECCEEEEEE--ECCEEEEEEEEEECCCEEE
T ss_conf             99996776663015999999978----------------------98425199999999--5994889999995798799


Q ss_pred             E
Q ss_conf             0
Q gi|254780939|r  117 L  117 (248)
Q Consensus       117 i  117 (248)
                      +
T Consensus       181 l  181 (214)
T COG2932         181 L  181 (214)
T ss_pred             E
T ss_conf             9


No 17 
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains:  an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=97.82  E-value=4.4e-05  Score=51.79  Aligned_cols=56  Identities=36%  Similarity=0.488  Sum_probs=43.9

Q ss_pred             EEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHEE
Q ss_conf             89987866776433698899984005876641221154222211255533470466401442003100000030423432
Q gi|254780939|r   37 PSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRIS  116 (248)
Q Consensus        37 ~f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~  116 (248)
                      ..+|.++||+|++..||.|+|++-                      .+++.||++++....   ..+|||+.-.+++.+.
T Consensus         2 ~l~v~GdSM~P~i~~Gd~vivd~~----------------------~~~~~g~i~vv~~~~---~~~iKrl~~~~~~~~~   56 (81)
T cd06529           2 ALRVKGDSMEPTIPDGDLVLVDPS----------------------DTPRDGDIVVARLDG---ELTVKRLQRRGGGRLR   56 (81)
T ss_pred             EEEEECCCCCCCCCCCCEEEEECC----------------------CCCCCCCEEEEEECC---CCEEEEEEECCCCEEE
T ss_conf             899967747714069999999377----------------------504799899999759---8069999991896399


Q ss_pred             E
Q ss_conf             0
Q gi|254780939|r  117 L  117 (248)
Q Consensus       117 i  117 (248)
                      +
T Consensus        57 L   57 (81)
T cd06529          57 L   57 (81)
T ss_pred             E
T ss_conf             9


No 18 
>KOG3342 consensus
Probab=97.36  E-value=0.00015  Score=48.54  Aligned_cols=52  Identities=37%  Similarity=0.542  Sum_probs=36.1

Q ss_pred             EEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEE
Q ss_conf             9987866776433698899984005876641221154222211255533470466401442003100000030
Q gi|254780939|r   38 SVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGL  110 (248)
Q Consensus        38 f~Ips~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGl  110 (248)
                      ..|-|+||||..+.||.+|.....                    ....+-||||||+-+. .....|-|||-+
T Consensus        51 VVVLSgSMePaF~RGDlLfL~N~~--------------------~~p~~vGdivVf~veg-R~IPiVHRviK~  102 (180)
T KOG3342          51 VVVLSGSMEPAFHRGDLLFLTNRN--------------------EDPIRVGDIVVFKVEG-REIPIVHRVIKQ  102 (180)
T ss_pred             EEEECCCCCCCCCCCCEEEEECCC--------------------CCCCEECCEEEEEECC-CCCCHHHHHHHH
T ss_conf             999738867551257489985588--------------------9964005489998889-247511788998


No 19 
>PRK00215 LexA repressor; Validated
Probab=96.74  E-value=0.0033  Score=40.00  Aligned_cols=53  Identities=34%  Similarity=0.384  Sum_probs=38.8

Q ss_pred             EEEECCCCC-CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHE
Q ss_conf             899878667-7643369889998400587664122115422221125553347046640144200310000003042343
Q gi|254780939|r   37 PSVIPSGSM-IPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRI  115 (248)
Q Consensus        37 ~f~Ips~SM-~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV  115 (248)
                      ..+|.++|| ++.++.||.++|.|-                      .+++-|||||...  +. ...+||.-- -|+.+
T Consensus       119 ~LrV~GdSMi~~~I~dGD~viV~~~----------------------~~~~~G~Ivva~i--~~-e~tlKr~~~-~~~~i  172 (204)
T PRK00215        119 LLRVRGDSMIDAGILDGDLVIVRKQ----------------------QTARNGQIVVALI--DD-EATVKRFRR-EGGHI  172 (204)
T ss_pred             EEEECCCCCCCCCCCCCCEEEEECC----------------------CCCCCCCEEEEEE--CC-CCEEEEEEE-ECCEE
T ss_conf             9996378766579899999999578----------------------9688996999997--37-758999999-79999


No 20 
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=96.27  E-value=0.0041  Score=39.40  Aligned_cols=28  Identities=57%  Similarity=0.934  Sum_probs=14.9

Q ss_pred             HHEEEEEEEECHHHEEECCCCEEECCCC
Q ss_conf             3100000030423432007732453531
Q gi|254780939|r  101 IDYVKRVIGLPGDRISLEKGIIYINGAP  128 (248)
Q Consensus       101 ~~yVKRvIGlPGDtV~i~~~~l~INg~~  128 (248)
                      ..++||++++|||.+...+..+++||++
T Consensus       138 ~~~~~~~~~~~gd~~~~~~~~~~~~g~~  165 (166)
T COG0681         138 KDYIKRVIGLPGDNILYTDDDLPINGKP  165 (166)
T ss_pred             CCCCEEEEECCCCCEEEECCCEEECCCC
T ss_conf             2332028971476357504534478810


No 21 
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=96.24  E-value=0.0088  Score=37.34  Aligned_cols=45  Identities=27%  Similarity=0.298  Sum_probs=36.3

Q ss_pred             EEECCCCC-CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEE
Q ss_conf             99878667-76433698899984005876641221154222211255533470466401442003100000
Q gi|254780939|r   38 SVIPSGSM-IPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRV  107 (248)
Q Consensus        38 f~Ips~SM-~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRv  107 (248)
                      .+|-++|| +..+..||.++|+|-                      .+|+.|||||..-  | +...|||.
T Consensus        54 lrV~GdSMi~agI~dGDiliVdr~----------------------~~~~~GdIVva~i--d-ge~tvKrl   99 (139)
T PRK10276         54 VKASGDSMIDAGISDGDLLIVDSS----------------------ITASHGDIVIAAV--D-GEFTVKKL   99 (139)
T ss_pred             EEEECCCCCCCCCCCCCEEEEEEC----------------------CCCCCCCEEEEEE--C-CEEEEEEE
T ss_conf             997268734488899899999405----------------------9877899999998--9-98899999


No 22 
>PHA00361 cI Repressor
Probab=96.20  E-value=0.011  Score=36.73  Aligned_cols=56  Identities=29%  Similarity=0.393  Sum_probs=39.7

Q ss_pred             HHEEEEEEEECCCCCCC----CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEE
Q ss_conf             75168989987866776----43369889998400587664122115422221125553347046640144200310000
Q gi|254780939|r   31 RTFLFQPSVIPSGSMIP----TLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKR  106 (248)
Q Consensus        31 r~fv~~~f~Ips~SM~P----TL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKR  106 (248)
                      ++|.   .+|.+.||+|    ++..||.|+|+.                      -.+|+-||+||-+-..+... -+||
T Consensus        72 ~~F~---L~V~GdSM~~p~g~~~~~Gd~iiVdp----------------------~~~~~~G~~VvA~~~~~~ea-T~K~  125 (165)
T PHA00361         72 RTFW---LEVEGDSMTAPTGLSFPEGDSILVDP----------------------EVEAEPGDLVIARLEGASEA-TFKK  125 (165)
T ss_pred             CEEE---EEEECCCCCCCCCCCCCCCCEEEECC----------------------CCCCCCCCEEEEEECCCCCE-EEEE
T ss_conf             8899---99966767887568738999999827----------------------87578899999996899834-8999


Q ss_pred             EEEECH
Q ss_conf             003042
Q gi|254780939|r  107 VIGLPG  112 (248)
Q Consensus       107 vIGlPG  112 (248)
                      .+--.|
T Consensus       126 l~~d~~  131 (165)
T PHA00361        126 LIIDGG  131 (165)
T ss_pred             EEEECC
T ss_conf             999599


No 23 
>PRK12423 LexA repressor; Provisional
Probab=95.47  E-value=0.033  Score=33.72  Aligned_cols=54  Identities=35%  Similarity=0.444  Sum_probs=38.1

Q ss_pred             EEECCCCCCC-CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEEEECHHHEE
Q ss_conf             9987866776-433698899984005876641221154222211255533470466401442003100000030423432
Q gi|254780939|r   38 SVIPSGSMIP-TLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRIS  116 (248)
Q Consensus        38 f~Ips~SM~P-TL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~  116 (248)
                      .+|-++||.. .++.||.|+|.|-                      ..++-|||||..-  |. ..-+||.- .-|+.+.
T Consensus       117 LrV~GdSMi~~gI~dGD~viV~~~----------------------~~~~~GdIVvA~i--dg-E~TlKr~~-~~~~~i~  170 (202)
T PRK12423        117 LQVQGDSMIDDGILDGDLVGVHRS----------------------PEARDGQIVVARL--DG-EVTIKRLE-RGADRIR  170 (202)
T ss_pred             EEECCCCCCCCCCCCCCEEEEECC----------------------CCCCCCCEEEEEE--CC-EEEEEEEE-EECCEEE
T ss_conf             998888654489689999999636----------------------8789996999998--99-28999999-9899999


Q ss_pred             E
Q ss_conf             0
Q gi|254780939|r  117 L  117 (248)
Q Consensus       117 i  117 (248)
                      .
T Consensus       171 L  171 (202)
T PRK12423        171 L  171 (202)
T ss_pred             E
T ss_conf             9


No 24 
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=92.56  E-value=0.29  Score=27.76  Aligned_cols=47  Identities=30%  Similarity=0.440  Sum_probs=31.2

Q ss_pred             EEECCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHEEEEEE
Q ss_conf             99878667764-336988999840058766412211542222112555334704664014420031000000
Q gi|254780939|r   38 SVIPSGSMIPT-LLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVI  108 (248)
Q Consensus        38 f~Ips~SM~PT-L~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p~RGDIVVF~~P~d~~~~yVKRvI  108 (248)
                      -+|.++||..- +..||.|+|.+                      ..+.+-|||||-.-..  ...=+||..
T Consensus       115 L~V~GdSM~~~gi~dGDlvvV~~----------------------~~~a~~GdiVvA~i~g--~e~TvKrl~  162 (201)
T COG1974         115 LRVSGDSMIDAGILDGDLVVVDP----------------------TEDAENGDIVVALIDG--EEATVKRLY  162 (201)
T ss_pred             EEECCCCCCCCCCCCCCEEEECC----------------------CCCCCCCCEEEEECCC--CCEEEEEEE
T ss_conf             99458850027788898999838----------------------8877799789998389--817899999


No 25 
>TIGR02896 spore_III_AF stage III sporulation protein AF; InterPro: IPR014245   This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved. .
Probab=84.72  E-value=1.1  Score=24.06  Aligned_cols=31  Identities=19%  Similarity=0.402  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHEEEEEEEECCCCCCC
Q ss_conf             0358789999999999998875168989987866776
Q gi|254780939|r   11 IFGSDTLKSILQALFFAILIRTFLFQPSVIPSGSMIP   47 (248)
Q Consensus        11 ~f~~e~i~~l~~~i~i~~~ir~fv~~~f~Ips~SM~P   47 (248)
                      .|..||+++++.+++++.++-..+      |+++|--
T Consensus         1 ~~L~~Wv~~i~~~~llat~~e~LL------P~~~lkK   31 (113)
T TIGR02896         1 EFLKEWVTNIIVLILLATILEMLL------PNSSLKK   31 (113)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHC------CCCCCCH
T ss_conf             938999999999999999999976------7998517


No 26 
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.25  E-value=4  Score=20.64  Aligned_cols=17  Identities=47%  Similarity=0.804  Sum_probs=15.0

Q ss_pred             CCCCCCCCCCCEEEEEC
Q ss_conf             66776433698899984
Q gi|254780939|r   43 GSMIPTLLVGDYIIVNK   59 (248)
Q Consensus        43 ~SM~PTL~~GD~i~VnK   59 (248)
                      .||.|-|+.||++|..-
T Consensus        12 ~smtPeL~~G~yVfcT~   28 (134)
T COG3602          12 ASMTPELLDGDYVFCTV   28 (134)
T ss_pred             HHCCCCCCCCCEEEEEE
T ss_conf             96591005896699984


No 27 
>COG1969 HyaC Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]
Probab=64.21  E-value=6.4  Score=19.32  Aligned_cols=34  Identities=15%  Similarity=0.097  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHEEEEEEEECCCCCCCC
Q ss_conf             587899999999999988751689899878667764
Q gi|254780939|r   13 GSDTLKSILQALFFAILIRTFLFQPSVIPSGSMIPT   48 (248)
Q Consensus        13 ~~e~i~~l~~~i~i~~~ir~fv~~~f~Ips~SM~PT   48 (248)
                      ++-|++++.++++++...  |+..||.-||.|=|+|
T Consensus        20 lwHWv~alsi~vL~~TGy--yIg~pf~~Pss~geat   53 (227)
T COG1969          20 LWHWVTALSIVVLIVTGY--YIGYPFLLPSSSGEAT   53 (227)
T ss_pred             HHHHHHHHHHHHHHHHCC--EECCCCCCCCCCCCHH
T ss_conf             899999999999998231--5525434777777201


No 28 
>pfam11101 DUF2884 Protein of unknown function (DUF2884). Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=63.84  E-value=4.9  Score=20.05  Aligned_cols=27  Identities=22%  Similarity=0.500  Sum_probs=22.7

Q ss_pred             EEEEECHHHEEE-CCCCEEECCCCCCCC
Q ss_conf             000304234320-077324535312245
Q gi|254780939|r  106 RVIGLPGDRISL-EKGIIYINGAPVVRH  132 (248)
Q Consensus       106 RvIGlPGDtV~i-~~~~l~INg~~i~~~  132 (248)
                      +|++-.|+++.| .+|.|||||+.+..+
T Consensus        17 ~i~~~~~~~~~I~~~g~L~v~G~~v~L~   44 (229)
T pfam11101        17 EVVDKSGPKYQIDEDGQLFVDGKWVTLS   44 (229)
T ss_pred             EEEECCCCEEEECCCCCEEECCEECCCC
T ss_conf             9997899658984999678999867799


No 29 
>pfam10000 DUF2241 Uncharacterized protein conserved in bacteria (DUF2241). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=60.28  E-value=5.2  Score=19.87  Aligned_cols=16  Identities=38%  Similarity=0.657  Sum_probs=14.9

Q ss_pred             CCCCCCCCCCCEEEEE
Q ss_conf             6677643369889998
Q gi|254780939|r   43 GSMIPTLLVGDYIIVN   58 (248)
Q Consensus        43 ~SM~PTL~~GD~i~Vn   58 (248)
                      .||.|.|..|+|+|++
T Consensus        12 ~~m~P~L~~~~yVF~t   27 (72)
T pfam10000        12 ASMSPELDDGEYVFCT   27 (72)
T ss_pred             HHCCCEECCCCEEEEE
T ss_conf             6599377899689999


No 30 
>TIGR01237 D1pyr5carbox2 delta-1-pyrroline-5-carboxylate dehydrogenase, putative; InterPro: IPR005932    The delta(1)-pyrroline-5-carboxylate synthetase (1.5.1.12 from EC) a mitochondrial inner membrane, ATP- and NADPH-dependent, bifunctional enzyme, catalyzes the reduction of glutamate to delta1-pyrroline-5-carboxylate, a critical step in the de novo biosynthesis of proline and ornithine. It is the rate-limiting enzyme in proline biosynthesis and is subject to feedback inhibition by proline.  1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH     This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase.; GO: 0003842 1-pyrroline-5-carboxylate dehydrogenase activity, 0006561 proline biosynthetic process.
Probab=55.87  E-value=5.7  Score=19.65  Aligned_cols=21  Identities=33%  Similarity=0.645  Sum_probs=16.3

Q ss_pred             CCHHHEEEEEEE-ECH-HHEEEC
Q ss_conf             200310000003-042-343200
Q gi|254780939|r   98 DPSIDYVKRVIG-LPG-DRISLE  118 (248)
Q Consensus        98 d~~~~yVKRvIG-lPG-DtV~i~  118 (248)
                      +|++.++||||+ |.| |+|-++
T Consensus       273 QPGQkhlKRVIaEmGGKd~~iVD  295 (518)
T TIGR01237       273 QPGQKHLKRVIAEMGGKDAVIVD  295 (518)
T ss_pred             CCCCCEEEEEEEEECCCCEEEEC
T ss_conf             98850241133320788507875


No 31 
>pfam02836 Glyco_hydro_2_C Glycosyl hydrolases family 2, TIM barrel domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.
Probab=54.64  E-value=5.7  Score=19.64  Aligned_cols=28  Identities=25%  Similarity=0.361  Sum_probs=13.3

Q ss_pred             CEEEEEECCCCCCCCCCCCCCCCCCHHH
Q ss_conf             6499971788777644536530260888
Q gi|254780939|r  184 GHYFMMGDNRDKSKDSRWVEVGFVPEEN  211 (248)
Q Consensus       184 g~yfvlGDNRdnS~DSR~~~~G~Vp~~~  211 (248)
                      .+++-.||-.+.-.|.++..-|.|-.++
T Consensus       252 ~~~w~g~Df~~~~~d~~~~~nGlv~~dR  279 (297)
T pfam02836       252 ELYAYGGDFGDRPSDYRFCGNGLFFADR  279 (297)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             7999682118999988736585789999


No 32 
>KOG1247 consensus
Probab=50.85  E-value=9.7  Score=18.19  Aligned_cols=41  Identities=20%  Similarity=0.379  Sum_probs=27.8

Q ss_pred             CCC-CCCHHHEEEEEEEEEEECCCCCCCCCCCCCCCCCCHHHCCC
Q ss_conf             530-26088825338999974378877543555456701334223
Q gi|254780939|r  203 EVG-FVPEENLVGRASFVLFSIGGDTPFSKVWLWIPNMRWDRLFK  246 (248)
Q Consensus       203 ~~G-~Vp~~~IvGka~~i~~S~d~~~~~~~~~~~~~~iRw~R~f~  246 (248)
                      .|| +||-+.-.+|+..+||  |...++.+..+... --|++.+|
T Consensus       250 kWGtpVPle~fk~KVfYVWF--DA~IGYlsit~~yt-~ew~kWwk  291 (567)
T KOG1247         250 KWGTPVPLEKFKDKVFYVWF--DAPIGYLSITKNYT-DEWEKWWK  291 (567)
T ss_pred             CCCCCCCHHHHCCCEEEEEE--CCCCEEEEEEHHHH-HHHHHHHC
T ss_conf             56887674551662799997--37513788506666-78999846


No 33 
>TIGR01718 Uridine-psphlse uridine phosphorylase; InterPro: IPR010058   This entry represents a family of bacterial and archaeal uridine phosphorylases unrelated to the mammalian enzymes of the same name. The Escherichia coli , Salmonella  and Klebsiella  genes have been characterised. Sequences from Clostridium, Streptomyces, Treponema, Aeropyrum and Pyrobaculum are also included in this family, but it does not include related sequences from Halobacterium, which are more distantly related and represent enzymes with a slightly different substrate specificity. Also distantly related is a clade of archaeal sequences which are related to the DeoD family of inosine phosphorylases (IPR004402 from INTERPRO) as they are to these uridine phosphorylases. This clade includes a characterised protein from Sulfolobus solfataricus which has been miss-named as a methylthioadenosine phosphorylase, but which acts on inosine and guanosine - it is unclear whether uridine has been evaluated as a substrate .; GO: 0004850 uridine phosphorylase activity, 0009166 nucleotide catabolic process, 0005737 cytoplasm.
Probab=49.40  E-value=14  Score=17.19  Aligned_cols=31  Identities=26%  Similarity=0.511  Sum_probs=25.9

Q ss_pred             HHHHHHHHHEEEEEEEEC-CCCCCCCCCCCCEEEEE
Q ss_conf             999998875168989987-86677643369889998
Q gi|254780939|r   24 LFFAILIRTFLFQPSVIP-SGSMIPTLLVGDYIIVN   58 (248)
Q Consensus        24 i~i~~~ir~fv~~~f~Ip-s~SM~PTL~~GD~i~Vn   58 (248)
                      =++.+.++||+    ||= ||.|.|-++.||.|+..
T Consensus        75 EL~~lGa~TFi----RvGTtGa~qphI~~Gdv~i~t  106 (248)
T TIGR01718        75 ELLYLGADTFI----RVGTTGALQPHIKVGDVVIAT  106 (248)
T ss_pred             HHHHHCCCEEE----EECCCCCCCCCCCCCCEEEEE
T ss_conf             99973401255----422666532322004145552


No 34 
>PRK09919 hypothetical protein; Provisional
Probab=44.97  E-value=11  Score=17.91  Aligned_cols=24  Identities=21%  Similarity=0.102  Sum_probs=19.8

Q ss_pred             EECHHHEEECCCCEEECCCCCCCC
Q ss_conf             304234320077324535312245
Q gi|254780939|r  109 GLPGDRISLEKGIIYINGAPVVRH  132 (248)
Q Consensus       109 GlPGDtV~i~~~~l~INg~~i~~~  132 (248)
                      =.|||.+...+..+.|||++..-+
T Consensus        39 L~pG~~i~~~~~gvliN~k~~~it   62 (114)
T PRK09919         39 LPPGSIFTPVKSGILLNDKEYPIT   62 (114)
T ss_pred             ECCCCEEEECCCEEEECCCEEEEE
T ss_conf             089988897488389889386678


No 35 
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=44.13  E-value=23  Score=15.78  Aligned_cols=36  Identities=28%  Similarity=0.425  Sum_probs=22.7

Q ss_pred             CCCCCCEEEEECCCCCHHHEEEEEEEECHHHEEECC--CCEEE
Q ss_conf             533470466401442003100000030423432007--73245
Q gi|254780939|r   84 QPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISLEK--GIIYI  124 (248)
Q Consensus        84 ~p~RGDIVVF~~P~d~~~~yVKRvIGlPGDtV~i~~--~~l~I  124 (248)
                      +-+||.-+|.-+|+|-...=||     -||.|++-|  |.+..
T Consensus        25 ~L~rg~P~vwinp~DA~~~GI~-----DgD~Vev~N~~G~v~a   62 (141)
T cd02776          25 RLQRGGPVVWMNPKDAAELGIK-----DNDWVEVFNDNGVVVA   62 (141)
T ss_pred             HCCCCCCEEEECHHHHHHCCCC-----CCCEEEEECCCCEEEE
T ss_conf             5001897799999999886998-----8999999848925999


No 36 
>TIGR01704 MTA/SAH-Nsdase MTA/SAH nucleosidase; InterPro: IPR010049   This entry represents the enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase which acts on its two substrates at the same active site. This enzyme is involved in the recycling of the components of S-adenosylmethionine after it has donated one of its two non-ribose sulphur ligands to an acceptor. In the case of 5'-methylthioadenosine this represents the first step of the methionine salvage pathway in bacteria , ,]. This enzyme is widely distributed in bacteria. ; GO: 0008782 adenosylhomocysteine nucleosidase activity, 0008930 methylthioadenosine nucleosidase activity, 0009164 nucleoside catabolic process, 0019509 methionine salvage.
Probab=43.83  E-value=17  Score=16.63  Aligned_cols=42  Identities=29%  Similarity=0.503  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHEEEEEEEECCC---CCCCCCCCCCEEEEECCCC
Q ss_conf             999999999887516898998786---6776433698899984005
Q gi|254780939|r   20 ILQALFFAILIRTFLFQPSVIPSG---SMIPTLLVGDYIIVNKFSY   62 (248)
Q Consensus        20 l~~~i~i~~~ir~fv~~~f~Ips~---SM~PTL~~GD~i~VnK~~Y   62 (248)
                      +-.|+-..||+--+= --|.|.||   -+.|||..||.++-+...|
T Consensus        52 V~AA~~~TLLL~~~K-PD~~INTGSAGGl~~TL~VGD~V~S~~~R~   96 (229)
T TIGR01704        52 VAAALSATLLLDRYK-PDVVINTGSAGGLAHTLKVGDVVVSDDVRY   96 (229)
T ss_pred             HHHHHHHHHHHHCCC-CCEEEECCCCCCCCCCCCCCCEEEECCCEE
T ss_conf             899988888875079-976985887544233132056787167402


No 37 
>TIGR00185 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 2; InterPro: IPR004440 The RNA methyltransferase, TrmH family, group 2 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification.; GO: 0008173 RNA methyltransferase activity, 0009451 RNA modification.
Probab=43.31  E-value=24  Score=15.70  Aligned_cols=103  Identities=13%  Similarity=0.104  Sum_probs=49.4

Q ss_pred             CEEEEECCCCCHHHEEEEEEEECHHHEEEC-CCCEEECCCCCCCCCCCCCEEECCCCCCEEEEEECCCCCCCC-CCCEEE
Q ss_conf             046640144200310000003042343200-773245353122454464002214786201221022146785-000221
Q gi|254780939|r   89 DVVVFRYPKDPSIDYVKRVIGLPGDRISLE-KGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGV-LYNVLS  166 (248)
Q Consensus        89 DIVVF~~P~d~~~~yVKRvIGlPGDtV~i~-~~~l~INg~~i~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~-~~~~~~  166 (248)
                      +||.|.+.-.+.+-=|=|..|-=|=++++. -=....|+|.+.|.-..+++...-..=..-... -|....++ ..-.+.
T Consensus         3 ~iVLy~PeIP~NTGNI~R~Caat~~~LHLi~PlGF~~~DK~L~RAGLdyw~fv~~~~H~s~E~f-le~~~~~~~nlf~lT   81 (161)
T TIGR00185         3 NIVLYEPEIPPNTGNIVRTCAATGTRLHLIKPLGFELDDKRLKRAGLDYWEFVQLFYHKSWEEF-LEAEKPQKGNLFLLT   81 (161)
T ss_pred             EEEEECCCCCCCCCHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCCCCEEEEECCCHHHH-HHHCCCCCEEEEEEE
T ss_conf             5774078897884112010111586245660578620781423147874452323562556888-863389971688884


Q ss_pred             CCC--CCCCCCCCEEECCCCEEEEEECCC
Q ss_conf             245--578874530232446499971788
Q gi|254780939|r  167 QDF--LAPSSNISEFLVPKGHYFMMGDNR  193 (248)
Q Consensus       167 ~~~--~~~~~~~~~~~VP~g~yfvlGDNR  193 (248)
                      ...  ..+.. .-.|+-.+.+|||+|.--
T Consensus        82 ~~G~~t~~~~-~~~~~~~d~~yl~fG~ET  109 (161)
T TIGR00185        82 KKGDKTPDHI-SVTYQDGDELYLVFGQET  109 (161)
T ss_pred             ECCCCCCCCE-EEEECCCCCEEEEECCCC
T ss_conf             0388774504-665437861699836877


No 38 
>PRK09525 lacZ beta-D-galactosidase; Reviewed
Probab=42.48  E-value=12  Score=17.57  Aligned_cols=17  Identities=29%  Similarity=0.927  Sum_probs=11.0

Q ss_pred             HEEECCCCEEECCCCCC
Q ss_conf             43200773245353122
Q gi|254780939|r  114 RISLEKGIIYINGAPVV  130 (248)
Q Consensus       114 tV~i~~~~l~INg~~i~  130 (248)
                      +|+++|+.++|||+++.
T Consensus       335 ~iei~~~~l~vNG~~i~  351 (1027)
T PRK09525        335 KVEIENGLLKLNGKPLL  351 (1027)
T ss_pred             EEEEECCEEEECCCEEE
T ss_conf             99997999999996899


No 39 
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=41.34  E-value=21  Score=16.05  Aligned_cols=13  Identities=31%  Similarity=0.537  Sum_probs=6.0

Q ss_pred             CCCCCEEEEECCC
Q ss_conf             3369889998400
Q gi|254780939|r   49 LLVGDYIIVNKFS   61 (248)
Q Consensus        49 L~~GD~i~VnK~~   61 (248)
                      +..||.|+|.-+.
T Consensus        47 I~~GD~V~Ve~~~   59 (75)
T COG0361          47 ILPGDVVLVELSP   59 (75)
T ss_pred             ECCCCEEEEEECC
T ss_conf             5799999997456


No 40 
>TIGR00915 2A0602 RND transporter, hydrophobe/amphiphile efflux-1 (HAE1) family; InterPro: IPR004764   Hydrophobe/amphiphile efflux-1 HAE1 is involved in toxin production and resistance processes.; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane.
Probab=41.34  E-value=8.4  Score=18.57  Aligned_cols=15  Identities=27%  Similarity=0.359  Sum_probs=10.5

Q ss_pred             CCCCCCCEEEEECCC
Q ss_conf             553347046640144
Q gi|254780939|r   83 NQPRRGDVVVFRYPK   97 (248)
Q Consensus        83 ~~p~RGDIVVF~~P~   97 (248)
                      ++.|-+-|+-|.+|.
T Consensus       659 G~ikdA~v~a~~pPa  673 (1058)
T TIGR00915       659 GQIKDAMVIAFVPPA  673 (1058)
T ss_pred             CCCCCCEEECCCCCC
T ss_conf             768763174046864


No 41 
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins.  Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=38.98  E-value=15  Score=16.98  Aligned_cols=13  Identities=23%  Similarity=0.680  Sum_probs=11.2

Q ss_pred             EECCCCEEEEEEC
Q ss_conf             2324464999717
Q gi|254780939|r  179 FLVPKGHYFMMGD  191 (248)
Q Consensus       179 ~~VP~g~yfvlGD  191 (248)
                      .++-+++|||+||
T Consensus        72 ~~F~e~cYyvfgd   84 (84)
T cd04438          72 ITFSEQCYYVFGD   84 (84)
T ss_pred             CCCCCCEEEEECC
T ss_conf             4424451686079


No 42 
>cd01287 FabA FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA structure is a homodimer with two independent active sites located at the dimer interface.  Each active site is tunnel-shaped and completely inaccessible to solvent.  No metal ions or cofactors are required for ligand binding or catalysis.
Probab=38.23  E-value=16  Score=16.78  Aligned_cols=26  Identities=12%  Similarity=0.201  Sum_probs=15.0

Q ss_pred             EEEEEEECHHHEEECCCCEEECCCCC
Q ss_conf             00000304234320077324535312
Q gi|254780939|r  104 VKRVIGLPGDRISLEKGIIYINGAPV  129 (248)
Q Consensus       104 VKRvIGlPGDtV~i~~~~l~INg~~i  129 (248)
                      ||||....+..+-+-|+.++++|+.+
T Consensus       112 I~~v~~~~~~~~~iADg~l~vDGk~I  137 (150)
T cd01287         112 IKEVGRDGPRPYIIADASLWVDGLRI  137 (150)
T ss_pred             EEEEEECCCCEEEEEEEEEEECCEEE
T ss_conf             99998049958999999999899899


No 43 
>PRK10340 ebgA cryptic beta-D-galactosidase subunit alpha; Reviewed
Probab=37.14  E-value=16  Score=16.73  Aligned_cols=16  Identities=31%  Similarity=0.517  Sum_probs=8.8

Q ss_pred             HEEECCCCEEECCCCC
Q ss_conf             4320077324535312
Q gi|254780939|r  114 RISLEKGIIYINGAPV  129 (248)
Q Consensus       114 tV~i~~~~l~INg~~i  129 (248)
                      +|++++++++|||+++
T Consensus       319 ~iei~~~~~llNGkpi  334 (1030)
T PRK10340        319 DIKVRDGLFLINNRYV  334 (1030)
T ss_pred             EEEEECCEEEECCCEE
T ss_conf             9999899999889788


No 44 
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=35.64  E-value=21  Score=16.03  Aligned_cols=34  Identities=32%  Similarity=0.608  Sum_probs=24.4

Q ss_pred             CCCCCCCCEEEEECCCCCHHH----EEEEEEEECHHHEEE
Q ss_conf             555334704664014420031----000000304234320
Q gi|254780939|r   82 NNQPRRGDVVVFRYPKDPSID----YVKRVIGLPGDRISL  117 (248)
Q Consensus        82 ~~~p~RGDIVVF~~P~d~~~~----yVKRvIGlPGDtV~i  117 (248)
                      .++-.-||||.||  .+|+.|    +==+|-=|||-|.+.
T Consensus       430 ERHL~dGDiVLFN--RQPSLHRmSmMgH~VkVLPgkTFRL  467 (901)
T TIGR02390       430 ERHLIDGDIVLFN--RQPSLHRMSMMGHKVKVLPGKTFRL  467 (901)
T ss_pred             EEEECCCCEEEEC--CCCCHHHHHHCCCEEEECCCCCCCC
T ss_conf             9871268887665--8864202101144546788885213


No 45 
>PRK08566 DNA-directed RNA polymerase subunit alpha; Validated
Probab=35.18  E-value=32  Score=14.90  Aligned_cols=33  Identities=36%  Similarity=0.669  Sum_probs=17.9

Q ss_pred             CCCCCCCEEEEECCCCCHHH----EEEEEEEECHHHEEE
Q ss_conf             55334704664014420031----000000304234320
Q gi|254780939|r   83 NQPRRGDVVVFRYPKDPSID----YVKRVIGLPGDRISL  117 (248)
Q Consensus        83 ~~p~RGDIVVF~~P~d~~~~----yVKRvIGlPGDtV~i  117 (248)
                      ++...||+|+|+  .+|..|    .-=|+.=+||-|+++
T Consensus       410 Rhl~dgD~Vl~N--RqPTLHr~sima~~v~v~~gktirl  446 (881)
T PRK08566        410 RHLIDGDIVLFN--RQPSLHRMSIMAHRVRVLPGKTFRL  446 (881)
T ss_pred             EEEECCCEEEEC--CCCHHHHHCCCCEEEEEEECCEEEE
T ss_conf             564359667752--7733544200010379974345775


No 46 
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=34.25  E-value=33  Score=14.81  Aligned_cols=17  Identities=29%  Similarity=0.479  Sum_probs=8.3

Q ss_pred             CCCCCCCCCCCCEEEEE
Q ss_conf             86677643369889998
Q gi|254780939|r   42 SGSMIPTLLVGDYIIVN   58 (248)
Q Consensus        42 s~SM~PTL~~GD~i~Vn   58 (248)
                      +..|.|.|..||.|.+-
T Consensus       106 ~~~~r~~l~vGD~v~Ak  122 (239)
T COG1097         106 EKDLRPFLNVGDLVYAK  122 (239)
T ss_pred             CCCCCCCCCCCCEEEEE
T ss_conf             23452226768789999


No 47 
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family; InterPro: IPR011929    Members of this family show sequence similarity to members of the NlpC/P60 family, described by Anantharaman and Aravind . The NlpC/P60 family includes a number of characterised bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes..
Probab=33.43  E-value=22  Score=15.92  Aligned_cols=19  Identities=21%  Similarity=0.497  Sum_probs=14.5

Q ss_pred             CCC-CCCCCCCCEEEEECCC
Q ss_conf             112-5553347046640144
Q gi|254780939|r   79 RIF-NNQPRRGDVVVFRYPK   97 (248)
Q Consensus        79 ~i~-~~~p~RGDIVVF~~P~   97 (248)
                      +++ ..++|.||+.||+.-.
T Consensus        71 ~~pG~~~~qpGDlLlFRw~~   90 (135)
T TIGR02219        71 AVPGLEAAQPGDLLLFRWRP   90 (135)
T ss_pred             CCCCCCCCCCCCEEEECCCC
T ss_conf             57888878887667771552


No 48 
>pfam11057 Cortexin Cortexin of kidney. In the middle of cortexin protein there is a single membrane-spanning domain which indicates that this protein may be a membrane protein involved in intracellular or extracellular signalling of the kidney or brain, since it is expressed specifically in the kidneys and brain only. The protein is highly conserved among species. Cortexin is also thought to be important to neurons of both the developing and adult cerebral cortex.
Probab=32.16  E-value=25  Score=15.57  Aligned_cols=29  Identities=24%  Similarity=0.522  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHE--EEEEEE-ECCCCCCC
Q ss_conf             999999999988751--689899-87866776
Q gi|254780939|r   19 SILQALFFAILIRTF--LFQPSV-IPSGSMIP   47 (248)
Q Consensus        19 ~l~~~i~i~~~ir~f--v~~~f~-Ips~SM~P   47 (248)
                      .++.+++.++++|.|  +++||. .|++|-+.
T Consensus        35 ~ll~ifL~~livRCfrillDPYssmPsStW~d   66 (81)
T pfam11057        35 GLLLIFLGLLIVRCFRILLDPYSSMPASSWTD   66 (81)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHCCCCCCHHHH
T ss_conf             99999999999999999808110388530344


No 49 
>PRK10838 spr putative outer membrane lipoprotein; Provisional
Probab=30.12  E-value=18  Score=16.51  Aligned_cols=12  Identities=25%  Similarity=0.409  Sum_probs=4.5

Q ss_pred             HHHHHHHHHHHE
Q ss_conf             999999988751
Q gi|254780939|r   22 QALFFAILIRTF   33 (248)
Q Consensus        22 ~~i~i~~~ir~f   33 (248)
                      .+++++.++..+
T Consensus        15 ~~~~~~~~l~ac   26 (188)
T PRK10838         15 PAIAVAVLLSAC   26 (188)
T ss_pred             HHHHHHHHHHHH
T ss_conf             799999988863


No 50 
>TIGR02656 cyanin_plasto plastocyanin; InterPro: IPR002387   Blue or 'type-1' copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm , . The most well known members of this class of proteins are the plant chloroplastic plastocyanins, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. Plastocyanin participates in electron transfer between the cytochrome b6f complex and photosystem I. Many cyanobacteria and eukaryotic algae can synthesise both plastocyanin and its functional analog cytochrome c6, depending on bioavailabilities of copper and iron, respectively .  Plastocyanin participates in electron transfer between P700 and the cytochrome b/f complex in photosystem I. ; GO: 0005507 copper ion binding, 0009055 electron carrier activity, 0006118 electron transport.
Probab=29.90  E-value=18  Score=16.55  Aligned_cols=21  Identities=10%  Similarity=0.044  Sum_probs=14.4

Q ss_pred             EEEEECHHHEEECCCCEEECC
Q ss_conf             000304234320077324535
Q gi|254780939|r  106 RVIGLPGDRISLEKGIIYING  126 (248)
Q Consensus       106 RvIGlPGDtV~i~~~~l~INg  126 (248)
                      .+=--|||||++.|++++=++
T Consensus        18 ~~~i~aGDtV~f~NNK~~PHN   38 (102)
T TIGR02656        18 KISIAAGDTVKFVNNKGGPHN   38 (102)
T ss_pred             CEEECCCCEEEEEECCCCCCC
T ss_conf             104688981788437889976


No 51 
>PRK10369 heme lyase subunit NrfE; Provisional
Probab=29.36  E-value=40  Score=14.30  Aligned_cols=23  Identities=13%  Similarity=0.154  Sum_probs=16.1

Q ss_pred             EEEEECHHHEEECCCCEEECCCC
Q ss_conf             00030423432007732453531
Q gi|254780939|r  106 RVIGLPGDRISLEKGIIYINGAP  128 (248)
Q Consensus       106 RvIGlPGDtV~i~~~~l~INg~~  128 (248)
                      -+.-.|||++++.+-++..++-+
T Consensus       428 ~~~L~~Ges~~i~~y~i~f~~i~  450 (552)
T PRK10369        428 SLNLQPGQQVTLAGYTFRFERLD  450 (552)
T ss_pred             EEECCCCCEEEECCEEEEECCCE
T ss_conf             46507998599888899991248


No 52 
>pfam00623 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Probab=28.88  E-value=41  Score=14.24  Aligned_cols=34  Identities=29%  Similarity=0.471  Sum_probs=22.1

Q ss_pred             CCCCCCCCEEEEECCCCCHHH----EEEEEEEECHHHEEE
Q ss_conf             555334704664014420031----000000304234320
Q gi|254780939|r   82 NNQPRRGDVVVFRYPKDPSID----YVKRVIGLPGDRISL  117 (248)
Q Consensus        82 ~~~p~RGDIVVF~~P~d~~~~----yVKRvIGlPGDtV~i  117 (248)
                      .+..+.||+|+|+  .+|..+    .--|+.-++|.|+++
T Consensus        91 ~R~l~dGD~Vl~N--RqPTLHr~si~a~~v~i~~~~tirl  128 (165)
T pfam00623        91 LRHVIDGDVVLLN--RQPTLHRMSIMAHRPRVLEGKTIRL  128 (165)
T ss_pred             HHHHHCCCEEEEE--CCCCCCCCEEEEEEEEEECCCEEEE
T ss_conf             6576479889992--7852251420366889968970587


No 53 
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC).   This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=28.68  E-value=34  Score=14.74  Aligned_cols=12  Identities=25%  Similarity=0.706  Sum_probs=6.2

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             786677643369
Q gi|254780939|r   41 PSGSMIPTLLVG   52 (248)
Q Consensus        41 ps~SM~PTL~~G   52 (248)
                      |.+-|||=-+.|
T Consensus       345 PvA~LePV~vaG  356 (706)
T TIGR00575       345 PVAKLEPVFVAG  356 (706)
T ss_pred             CEEEECCEEECC
T ss_conf             036756558720


No 54 
>KOG2915 consensus
Probab=28.25  E-value=20  Score=16.19  Aligned_cols=21  Identities=33%  Similarity=0.850  Sum_probs=11.6

Q ss_pred             EEEEEEEC-HHHEEECCC-CEEE
Q ss_conf             00000304-234320077-3245
Q gi|254780939|r  104 VKRVIGLP-GDRISLEKG-IIYI  124 (248)
Q Consensus       104 VKRvIGlP-GDtV~i~~~-~l~I  124 (248)
                      .+-+||.| |..|+...| .+|+
T Consensus        48 h~~iIGK~~G~~v~sskG~~vyl   70 (314)
T KOG2915          48 HSDIIGKPYGSKVASSKGKFVYL   70 (314)
T ss_pred             HHHEECCCCCCEEEECCCCEEEE
T ss_conf             01111577553465337847999


No 55 
>TIGR02730 carot_isom carotene isomerase; InterPro: IPR014101   Members of this family, including sll0033 (crtH) of Synechocystis sp. (strain PCC 6803), catalyse a cis-trans isomerization of carotenes to the all-trans lycopene, a reaction that can also occur non-enzymatically in light through photoisomerization..
Probab=27.96  E-value=43  Score=14.14  Aligned_cols=25  Identities=12%  Similarity=0.224  Sum_probs=12.0

Q ss_pred             CCCCCCCCCCCCEEEEECCCCCCCCC
Q ss_conf             86677643369889998400587664
Q gi|254780939|r   42 SGSMIPTLLVGDYIIVNKFSYGYSKY   67 (248)
Q Consensus        42 s~SM~PTL~~GD~i~VnK~~YG~~~~   67 (248)
                      -..|-|-+..| +||-+++.=|+..|
T Consensus       200 pA~~TPMINAg-MVfsDRH~GGiNYP  224 (506)
T TIGR02730       200 PADQTPMINAG-MVFSDRHYGGINYP  224 (506)
T ss_pred             CCCCCCCCCCH-HHHCCCCCCCCCCC
T ss_conf             10258740011-21003455763389


No 56 
>TIGR02823 oxido_YhdH putative quinone oxidoreductase, YhdH/YhfP family; InterPro: IPR014188   This entry represents a subfamily of the alcohol dehydrogenase, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This entry includes YhdH from Escherichia coli and YhfP from Bacillus subtilis both of which bind NADPH or NAD, but not zinc. Both proteins have been studied crystallographically for insight into function. .
Probab=27.72  E-value=43  Score=14.12  Aligned_cols=21  Identities=33%  Similarity=0.521  Sum_probs=16.2

Q ss_pred             CCCCCCCCCCCEEEEECCCCC
Q ss_conf             667764336988999840058
Q gi|254780939|r   43 GSMIPTLLVGDYIIVNKFSYG   63 (248)
Q Consensus        43 ~SM~PTL~~GD~i~VnK~~YG   63 (248)
                      .|=.|....||.|+|+=|=-|
T Consensus        72 ~S~dp~F~~GD~VivTGyglG   92 (330)
T TIGR02823        72 SSEDPRFRPGDEVIVTGYGLG   92 (330)
T ss_pred             ECCCCCCCCCCEEEEEEECCC
T ss_conf             448877578871899740245


No 57 
>TIGR00110 ilvD dihydroxy-acid dehydratase; InterPro: IPR004404   Two dehydratases, dihydroxy-acid dehydratase (gene ilvD or ILV3) and 6-phosphogluconate dehydratase (gene edd) have been shown to be evolutionary related . Dihydroxy-acid dehydratase catalyzes the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyzes the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. Another protein containing this signature is the Escherichia coli hypothetical protein yjhG. The N-terminal part of the proteins contains a cysteine that could be involved in the binding of a 2Fe-2S iron-sulphur cluster .   This family represents dihydroxy-acid dehydratase (DAD). It contains a catalytically essential [4Fe-4S] cluster and catalyses the fourth step in valine and isoleucine biosynthesis.; GO: 0004160 dihydroxy-acid dehydratase activity, 0009082 branched chain family amino acid biosynthetic process.
Probab=27.62  E-value=28  Score=15.28  Aligned_cols=18  Identities=44%  Similarity=0.781  Sum_probs=14.6

Q ss_pred             CCCCCCCCCC--EEEEECCC
Q ss_conf             1255533470--46640144
Q gi|254780939|r   80 IFNNQPRRGD--VVVFRYPK   97 (248)
Q Consensus        80 i~~~~p~RGD--IVVF~~P~   97 (248)
                      |..+++++||  |||.+|..
T Consensus       455 Il~Gki~~GDktVVVIRYEG  474 (601)
T TIGR00110       455 ILGGKIKEGDKTVVVIRYEG  474 (601)
T ss_pred             HHCCEEEECCCEEEEEEECC
T ss_conf             75790431681689997048


No 58 
>KOG1618 consensus
Probab=27.59  E-value=35  Score=14.71  Aligned_cols=47  Identities=30%  Similarity=0.327  Sum_probs=33.4

Q ss_pred             ECCCCEEEEEECCCCCCCCCCC--CCCCCCCHHHEEEEEEEEEEECCCCCC
Q ss_conf             3244649997178877764453--653026088825338999974378877
Q gi|254780939|r  180 LVPKGHYFMMGDNRDKSKDSRW--VEVGFVPEENLVGRASFVLFSIGGDTP  228 (248)
Q Consensus       180 ~VP~g~yfvlGDNRdnS~DSR~--~~~G~Vp~~~IvGka~~i~~S~d~~~~  228 (248)
                      .=|..+.+|+|||-..  |=|-  ..-++-|+.++.|.|-.-|.|+=-.++
T Consensus       294 ~~~~k~lymvGDNP~s--Dv~GA~lf~~yap~~~~g~~~~~~w~SILV~TG  342 (389)
T KOG1618         294 AAPIKKLYMVGDNPMS--DVRGANLFHQYAPELGAGGSANYGWISILVRTG  342 (389)
T ss_pred             CCCCCEEEEECCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEE
T ss_conf             6775256664688754--433330002346332544334777168998530


No 59 
>TIGR03468 HpnG hopanoid-associated phosphorylase. The sequences in this family are members of the pfam01048 family of phosphorylases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene is adjacent to the genes PhnA-E and squalene-hopene cyclase (which would be HpnF) in Zymomonas mobilis and their association with hopene biosynthesis has been noted in the literature. Extending the gene symbol sequence, we suggest the symbol HpnG for the product of this gene. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species.
Probab=27.00  E-value=44  Score=14.04  Aligned_cols=23  Identities=22%  Similarity=0.410  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             86677643369889998400587
Q gi|254780939|r   42 SGSMIPTLLVGDYIIVNKFSYGY   64 (248)
Q Consensus        42 s~SM~PTL~~GD~i~VnK~~YG~   64 (248)
                      .|++.|.|..||.|+.+++.|..
T Consensus        55 AGgL~p~L~~GDvVv~~~V~~~~   77 (212)
T TIGR03468        55 AGALDPALQPGDLVVPEEVRADG   77 (212)
T ss_pred             CCCCCCCCCCCCEEEEEEEECCC
T ss_conf             04678889767899975675278


No 60 
>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=26.79  E-value=30  Score=15.11  Aligned_cols=42  Identities=14%  Similarity=0.267  Sum_probs=24.1

Q ss_pred             CCCCCEEEEEC--CCCCHHHEEEEEEEE-CHHHEEECCCCEEECCCCC
Q ss_conf             33470466401--442003100000030-4234320077324535312
Q gi|254780939|r   85 PRRGDVVVFRY--PKDPSIDYVKRVIGL-PGDRISLEKGIIYINGAPV  129 (248)
Q Consensus        85 p~RGDIVVF~~--P~d~~~~yVKRvIGl-PGDtV~i~~~~l~INg~~i  129 (248)
                      .|.||+|+=-.  |-.....+++++-+. |||+|.+.   +..||++.
T Consensus        25 Lk~GDvI~~vdGk~v~~~~~l~~~i~~~~~Gd~V~l~---v~R~gk~~   69 (79)
T cd00986          25 LKAGDHIIAVDGKPFKEAEELIDYIQSKKEGDTVKLK---VKREEKEL   69 (79)
T ss_pred             CCCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEE---EEECCEEE
T ss_conf             7789999999998957999999999659999989999---99999999


No 61 
>COG3250 LacZ Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]
Probab=26.66  E-value=31  Score=15.04  Aligned_cols=17  Identities=35%  Similarity=0.872  Sum_probs=14.4

Q ss_pred             HHEEECCCCEEECCCCC
Q ss_conf             34320077324535312
Q gi|254780939|r  113 DRISLEKGIIYINGAPV  129 (248)
Q Consensus       113 DtV~i~~~~l~INg~~i  129 (248)
                      =+|+++++.++|||+++
T Consensus       284 R~iei~~~~~~iNGkpv  300 (808)
T COG3250         284 RTVEIKDGLLLINGKPV  300 (808)
T ss_pred             EEEEEECCEEEECCEEE
T ss_conf             79999768289988689


No 62 
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein; InterPro: IPR013456   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry represents the D-xylose ABC transporter substrate-binding protein which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter..
Probab=26.19  E-value=31  Score=14.98  Aligned_cols=13  Identities=46%  Similarity=1.165  Sum_probs=10.3

Q ss_pred             ECCCCEEEEEECC
Q ss_conf             3244649997178
Q gi|254780939|r  180 LVPKGHYFMMGDN  192 (248)
Q Consensus       180 ~VP~g~yfvlGDN  192 (248)
                      ..|+|.||+||=-
T Consensus       116 ~~P~GnY~l~~Gs  128 (307)
T TIGR02634       116 AAPKGNYFLLGGS  128 (307)
T ss_pred             CCCCCCEEEEECC
T ss_conf             1678757884177


No 63 
>PRK05174 3-hydroxydecanoyl-(acyl carrier protein) dehydratase; Validated
Probab=25.14  E-value=39  Score=14.36  Aligned_cols=13  Identities=15%  Similarity=0.644  Sum_probs=5.7

Q ss_pred             ECCCCEEECCCCC
Q ss_conf             0077324535312
Q gi|254780939|r  117 LEKGIIYINGAPV  129 (248)
Q Consensus       117 i~~~~l~INg~~i  129 (248)
                      +-|+.++++|+.|
T Consensus       143 iADg~l~vDg~~I  155 (172)
T PRK05174        143 IADGRVLVDGEEI  155 (172)
T ss_pred             EEEEEEEECCEEE
T ss_conf             9989999899899


No 64 
>PRK10150 beta-D-glucuronidase; Provisional
Probab=25.08  E-value=35  Score=14.66  Aligned_cols=19  Identities=21%  Similarity=0.380  Sum_probs=14.0

Q ss_pred             HEEECCCCEEECCCCCCCC
Q ss_conf             4320077324535312245
Q gi|254780939|r  114 RISLEKGIIYINGAPVVRH  132 (248)
Q Consensus       114 tV~i~~~~l~INg~~i~~~  132 (248)
                      +|+++++++++||+++...
T Consensus       280 ~i~~~~~~f~LNGkpi~Lr  298 (605)
T PRK10150        280 SVAVKGGQFLINHKPFYFK  298 (605)
T ss_pred             EEEECCCEEEECCCEEEEE
T ss_conf             9998599799899389973


No 65 
>PRK06714 S-adenosylhomocysteine nucleosidase; Validated
Probab=24.88  E-value=48  Score=13.79  Aligned_cols=42  Identities=17%  Similarity=0.146  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHEEEEEEEE---CCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             99999999887516898998---78667764336988999840058
Q gi|254780939|r   21 LQALFFAILIRTFLFQPSVI---PSGSMIPTLLVGDYIIVNKFSYG   63 (248)
Q Consensus        21 ~~~i~i~~~ir~fv~~~f~I---ps~SM~PTL~~GD~i~VnK~~YG   63 (248)
                      -.|+...+++..|=.+ ..|   ..|++.|.|..||.|+.+++.|.
T Consensus        55 nAA~~t~~LI~~F~~d-~IIntGvAGgl~~~l~igDvVIa~~~~~h   99 (236)
T PRK06714         55 SCASCVQLLISEFQPD-ELFMTGICGSLSNKVKNGHIVVALNAIQH   99 (236)
T ss_pred             HHHHHHHHHHHHCCCC-EEEECCCCCCCCCCCCCCCEEEECEEEEC
T ss_conf             9999999999844999-99987863235898805889998725873


No 66 
>TIGR01857 FGAM-synthase phosphoribosylformylglycinamidine synthase; InterPro: IPR010141   This entry represents a single-molecule form of phosphoribosylformylglycinamidine synthase, also called FGAM synthase, an enzyme of purine de novo biosynthesis, which represent a second clade of the enzymes found in Clostridia, Bifidobacteria and Streptococcus species. This enzyme performs the fourth step in IMP biosynthesis (the precursor of all purines) from PRPP..
Probab=24.63  E-value=39  Score=14.36  Aligned_cols=20  Identities=30%  Similarity=0.644  Sum_probs=17.6

Q ss_pred             HHEEEEEEEECCCCCCCCCCC
Q ss_conf             751689899878667764336
Q gi|254780939|r   31 RTFLFQPSVIPSGSMIPTLLV   51 (248)
Q Consensus        31 r~fv~~~f~Ips~SM~PTL~~   51 (248)
                      |+||.|+-|| |||=.||--+
T Consensus       361 RSYVYQAmRv-tGaadpt~~v  380 (1279)
T TIGR01857       361 RSYVYQAMRV-TGAADPTVPV  380 (1279)
T ss_pred             HHHEEEEEEE-ECCCCCCCCH
T ss_conf             0030110011-0577885540


No 67 
>COG2949 SanA Uncharacterized membrane protein [Function unknown]
Probab=23.64  E-value=47  Score=13.89  Aligned_cols=14  Identities=29%  Similarity=0.389  Sum_probs=5.5

Q ss_pred             EEEEEECCCCCCCC
Q ss_conf             49997178877764
Q gi|254780939|r  185 HYFMMGDNRDKSKD  198 (248)
Q Consensus       185 ~yfvlGDNRdnS~D  198 (248)
                      +.++-|||+.+|.|
T Consensus        96 ~LLlSGDN~~~sYn  109 (235)
T COG2949          96 YLLLSGDNATVSYN  109 (235)
T ss_pred             EEEEECCCCCCCCC
T ss_conf             99981687753465


No 68 
>PRK05584 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated
Probab=23.44  E-value=47  Score=13.87  Aligned_cols=40  Identities=30%  Similarity=0.452  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHEE---EEEEEECCCCCCCCCCCCCEEEEECCCC
Q ss_conf             9999999887516---8989987866776433698899984005
Q gi|254780939|r   22 QALFFAILIRTFL---FQPSVIPSGSMIPTLLVGDYIIVNKFSY   62 (248)
Q Consensus        22 ~~i~i~~~ir~fv---~~~f~Ips~SM~PTL~~GD~i~VnK~~Y   62 (248)
                      .++....++..|=   +=..- -.|++.|.|..||.++.+++.|
T Consensus        55 AA~~~~~li~~f~p~~ii~~G-~AGgl~~~l~iGDvvia~~~~~   97 (230)
T PRK05584         55 AALTATILIEHFKVDAVINTG-VAGGLAPGLKVGDVVVADELVQ   97 (230)
T ss_pred             HHHHHHHHHHHCCCCEEEEEC-CCCCCCCCCCCCEEEEECEEEE
T ss_conf             999999999737998999942-4334688984780999765797


No 69 
>pfam00877 NLPC_P60 NlpC/P60 family. The function of this domain is unknown. It is found in several lipoproteins.
Probab=23.14  E-value=38  Score=14.42  Aligned_cols=16  Identities=44%  Similarity=0.794  Sum_probs=12.2

Q ss_pred             CCCCCCCCCCEEEEEC
Q ss_conf             1255533470466401
Q gi|254780939|r   80 IFNNQPRRGDVVVFRY   95 (248)
Q Consensus        80 i~~~~p~RGDIVVF~~   95 (248)
                      +..+++|.||+|.|..
T Consensus        46 v~~~~~~~GDLvFf~~   61 (105)
T pfam00877        46 IPKSEPQRGDLVFFGT   61 (105)
T ss_pred             CCHHHCCCCCEEEECC
T ss_conf             4789989878899778


No 70 
>pfam01048 PNP_UDP_1 Phosphorylase superfamily. Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Probab=22.62  E-value=49  Score=13.75  Aligned_cols=22  Identities=27%  Similarity=0.425  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCCCCEEEEECCCC
Q ss_conf             7866776433698899984005
Q gi|254780939|r   41 PSGSMIPTLLVGDYIIVNKFSY   62 (248)
Q Consensus        41 ps~SM~PTL~~GD~i~VnK~~Y   62 (248)
                      ..|||.|.+..||.++.+++.+
T Consensus        78 ~aG~l~~~~~~Gdvvi~~~~i~   99 (232)
T pfam01048        78 TAGGLNPDLKPGDLVIPTDAIN   99 (232)
T ss_pred             CCCCCCCCCCCCCEEEEHHHHH
T ss_conf             6455787899998996437752


No 71 
>PRK02122 glucosamine-6-phosphate deaminase-like protein; Validated
Probab=22.44  E-value=21  Score=16.08  Aligned_cols=21  Identities=24%  Similarity=0.336  Sum_probs=15.1

Q ss_pred             ECCCCEEEEEECCCCCCCCCC
Q ss_conf             324464999717887776445
Q gi|254780939|r  180 LVPKGHYFMMGDNRDKSKDSR  200 (248)
Q Consensus       180 ~VP~g~yfvlGDNRdnS~DSR  200 (248)
                      .|.+.+.|+.||=-|-.---|
T Consensus       528 ~vkPhqIyaAGDlaDPhgThr  548 (660)
T PRK02122        528 EIKPHQIFVAGDLADPHGTHR  548 (660)
T ss_pred             HCCCCEEEECCCCCCCCCCCH
T ss_conf             559777987366679876259


No 72 
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=22.13  E-value=35  Score=14.67  Aligned_cols=46  Identities=22%  Similarity=0.308  Sum_probs=30.0

Q ss_pred             CCCCCCEEEEECC-CCCHHHEEEEEEEECHHHEEECCCCEEECCCCCCCCC
Q ss_conf             5334704664014-4200310000003042343200773245353122454
Q gi|254780939|r   84 QPRRGDVVVFRYP-KDPSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRHM  133 (248)
Q Consensus        84 ~p~RGDIVVF~~P-~d~~~~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~  133 (248)
                      +++|||+|-..-. ..++..++|=..|+-    +=+.|.+++||+++..+.
T Consensus       345 ~ikrGelvFliG~NGsGKST~~~LLtGL~----~PqsG~I~ldg~pV~~e~  391 (546)
T COG4615         345 TIKRGELVFLIGGNGSGKSTLAMLLTGLY----QPQSGEILLDGKPVSAEQ  391 (546)
T ss_pred             EEECCCEEEEECCCCCCHHHHHHHHHHCC----CCCCCCEEECCCCCCCCC
T ss_conf             87337389998889963889999997066----888882667893488447


No 73 
>pfam05382 Amidase_5 Bacteriophage peptidoglycan hydrolase. At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 has been shown to be a N-acetylmuramoyl-L-alanine amidase. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids. This family appears to be related to pfam00877.
Probab=21.96  E-value=43  Score=14.14  Aligned_cols=13  Identities=23%  Similarity=0.657  Sum_probs=10.2

Q ss_pred             CCCCCCEEEEECC
Q ss_conf             5334704664014
Q gi|254780939|r   84 QPRRGDVVVFRYP   96 (248)
Q Consensus        84 ~p~RGDIVVF~~P   96 (248)
                      ++||||||+.=.+
T Consensus        75 ~~q~GDI~IwG~~   87 (145)
T pfam05382        75 NAKRGDIFIWGKR   87 (145)
T ss_pred             CCCCCCEEEEECC
T ss_conf             7776889999268


No 74 
>TIGR01285 nifN nitrogenase molybdenum-iron cofactor biosynthesis protein NifN; InterPro: IPR005975    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I.; GO: 0005515 protein binding, 0006461 protein complex assembly, 0009399 nitrogen fixation.
Probab=21.19  E-value=46  Score=13.95  Aligned_cols=97  Identities=20%  Similarity=0.314  Sum_probs=55.4

Q ss_pred             HHHHHEEEEEEEEC--CCCCCCCCCCCCEEEEECCCCCCCCC----CCCCC-------------CCCCCCCCCCCCCCCC
Q ss_conf             98875168989987--86677643369889998400587664----12211-------------5422221125553347
Q gi|254780939|r   28 ILIRTFLFQPSVIP--SGSMIPTLLVGDYIIVNKFSYGYSKY----SFPFS-------------YNLFNGRIFNNQPRRG   88 (248)
Q Consensus        28 ~~ir~fv~~~f~Ip--s~SM~PTL~~GD~i~VnK~~YG~~~~----~~p~~-------------~~~~~~~i~~~~p~RG   88 (248)
                      =.|+.|=++|..+|  |.||..+|-.||+   +-.++|...-    ++|-+             ...+..|      -+.
T Consensus       195 ~~vEaFGL~P~~LPDLS~SLDGHLa~dd~---s~~T~GGT~l~~i~~~g~s~~tlaIGe~mr~aA~~l~~R------~g~  265 (451)
T TIGR01285       195 DMVEAFGLKPVVLPDLSRSLDGHLADDDF---SPITLGGTTLEDIRELGQSAVTLAIGESMRAAAELLKDR------CGV  265 (451)
T ss_pred             HHHHHCCCCCEECCCHHCCCCCCCCCCCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------CCC
T ss_conf             99986089722402110024650087870---056789973599987368874688777654446752212------177


Q ss_pred             CEEEEECCCC-CHH-HEEEEEEEECHHH----------E-------------EECCCCEEECCCCCCCCC
Q ss_conf             0466401442-003-1000000304234----------3-------------200773245353122454
Q gi|254780939|r   89 DVVVFRYPKD-PSI-DYVKRVIGLPGDR----------I-------------SLEKGIIYINGAPVVRHM  133 (248)
Q Consensus        89 DIVVF~~P~d-~~~-~yVKRvIGlPGDt----------V-------------~i~~~~l~INg~~i~~~~  133 (248)
                      ...||-+=.. +.. .||.+...+-|..          |             .+-|.+.|.||+++.-.-
T Consensus       266 ~y~vF~~L~GLeavD~F~~~L~~~SG~~CdhhfPfvP~vP~~~~RqR~QL~DA~LD~HF~~gG~k~AiAa  335 (451)
T TIGR01285       266 PYEVFPSLMGLEAVDAFVSVLSKISGSRCDHHFPFVPAVPERFERQRAQLQDAMLDTHFFLGGKKVAIAA  335 (451)
T ss_pred             CCHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEC
T ss_conf             4001012244689999999999984432156789889886334520788999999887741310232016


No 75 
>pfam05257 CHAP CHAP domain. This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of the bifunctional Escherichia coli GSP synthetase/GSP amidase, where is functions as a glutathionylspermidine amidase EC:3.5.1.78. This domain is found to be the catalytic domain of PlyCA.
Probab=21.11  E-value=57  Score=13.33  Aligned_cols=14  Identities=36%  Similarity=0.674  Sum_probs=11.6

Q ss_pred             CCCCCCCCEEEEEC
Q ss_conf             55533470466401
Q gi|254780939|r   82 NNQPRRGDVVVFRY   95 (248)
Q Consensus        82 ~~~p~RGDIVVF~~   95 (248)
                      ...|+.|||+||..
T Consensus        55 ~~~P~~G~i~v~~~   68 (119)
T pfam05257        55 GFTPKVGDIAVFDS   68 (119)
T ss_pred             CCCCCCCEEEEECC
T ss_conf             98999988999878


No 76 
>TIGR00066 g_glut_trans gamma-glutamyltransferase; InterPro: IPR000101   Gamma-glutamyltranspeptidase (2.3.2.2 from EC) (GGT)  catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate). GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification . In prokaryotes and eukaryotes, it is an enzyme that consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. The active site of GGT is known to be located in the light subunit. The sequences of mammalian and bacterial GGT show a number of regions of high similarity . Pseudomonas cephalosporin acylases (3.5.1 from EC) that convert 7-beta-(4-carboxybutanamido)-cephalosporanic acid (GL-7ACA) into 7-aminocephalosporanic acid (7ACA) and glutaric acid are evolutionary related to GGT and also show some GGT activity . Like GGT, these GL-7ACA acylases, are also composed of two subunits.   As an autocatalytic peptidase GGT belongs to MEROPS peptidase family T3 (gamma-glutamyltransferase family, clan PB(T)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. The type example is gamma-glutamyltransferase 1 from Escherichia coli. ; GO: 0003840 gamma-glutamyltransferase activity.
Probab=20.56  E-value=36  Score=14.62  Aligned_cols=11  Identities=45%  Similarity=0.619  Sum_probs=4.4

Q ss_pred             EECCCCCCCCC
Q ss_conf             98786677643
Q gi|254780939|r   39 VIPSGSMIPTL   49 (248)
Q Consensus        39 ~Ips~SM~PTL   49 (248)
                      +=|.+||.||+
T Consensus       455 KRplSsm~PTI  465 (583)
T TIGR00066       455 KRPLSSMAPTI  465 (583)
T ss_pred             CCCCCCCCCEE
T ss_conf             87510047312


No 77 
>TIGR01026 fliI_yscN ATPase FliI/YscN family; InterPro: IPR005714    Proteins in this entry show extensive homology to the ATP synthase F1 beta subunit, and are involved in type III protein secretion. They fall into the two separate functional groups outlined below.   The first group, exemplified by the Salmonella typhimurium FliI protein (P26465 from SWISSPROT), is needed for flagellar assembly. Most structural components of the bacterial flagellum are translocated through the central channel of the growing flagellar structure by the type III flagellar protein-export apparatus in an ATPase-driven manner, to be assembled at the growing end. FliI is the ATPase that couples ATP hydrolysis to the translocation reaction , .   The second group couples ATP hydrolysis to protein translocation in non-flagellar type III secretion systems. Often these systems are involved in virulence and pathogenicity. YscN (P40290 from SWISSPROT) from pathogenic Yersinia species, for example, energises the injection of antihost factors directly into eukaryotic cells, thus overcoming host defences .; GO: 0016887 ATPase activity, 0009058 biosynthetic process, 0015031 protein transport, 0005737 cytoplasm.
Probab=20.05  E-value=60  Score=13.19  Aligned_cols=71  Identities=20%  Similarity=0.283  Sum_probs=44.8

Q ss_pred             EEEEEEEECC---CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCEEEEECCCCCHHHEEEEE
Q ss_conf             1689899878---6677643369889998400587664122115422221125553--3470466401442003100000
Q gi|254780939|r   33 FLFQPSVIPS---GSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQP--RRGDVVVFRYPKDPSIDYVKRV  107 (248)
Q Consensus        33 fv~~~f~Ips---~SM~PTL~~GD~i~VnK~~YG~~~~~~p~~~~~~~~~i~~~~p--~RGDIVVF~~P~d~~~~yVKRv  107 (248)
                      ++.+--.|-+   .|.-|....||...+.+-                     ..+.  =+++||.|+-+.=--.-| .-+
T Consensus        23 ~~G~v~~v~Gl~~ea~gp~~~vG~~c~I~~~---------------------g~~~~~~~~EVVGf~~~~v~LmPy-~~~   80 (455)
T TIGR01026        23 RVGRVTKVKGLLIEAVGPQASVGDLCLIERK---------------------GSEGKEVVAEVVGFNGEKVLLMPY-EEV   80 (455)
T ss_pred             EEEEEEEEEEEEEEEECCCCCCCCEEEEEEE---------------------CCCCCEEEEEEEEEECCEEEECCC-CCC
T ss_conf             5789999852689852477667777899973---------------------789877999988520675675236-544


Q ss_pred             EEE-CHHHEEECC----CCEEEC
Q ss_conf             030-423432007----732453
Q gi|254780939|r  108 IGL-PGDRISLEK----GIIYIN  125 (248)
Q Consensus       108 IGl-PGDtV~i~~----~~l~IN  125 (248)
                      -|+ ||++|...|    ..|.++
T Consensus        81 ~G~~~G~~V~~~~isae~~L~~~  103 (455)
T TIGR01026        81 EGVEPGSKVLAKNISAEEGLSIK  103 (455)
T ss_pred             CCCCCCCEEEEECCCCCCCCCCC
T ss_conf             43353452332043300254557


No 78 
>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment.  ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=20.05  E-value=37  Score=14.56  Aligned_cols=44  Identities=23%  Similarity=0.396  Sum_probs=26.3

Q ss_pred             CCCCCCEEEEECCCCC-HHHEEEEEEEECHHHEEECCCCEEECCCCCCC
Q ss_conf             5334704664014420-03100000030423432007732453531224
Q gi|254780939|r   84 QPRRGDVVVFRYPKDP-SIDYVKRVIGLPGDRISLEKGIIYINGAPVVR  131 (248)
Q Consensus        84 ~p~RGDIVVF~~P~d~-~~~yVKRvIGlPGDtV~i~~~~l~INg~~i~~  131 (248)
                      +.++|+++++--|..- +....+=+.|+    .....|.+.+||+.+..
T Consensus        23 ~i~~Ge~~~ilGpSG~GKSTllr~i~gl----~~p~~G~I~i~g~~i~~   67 (242)
T cd03295          23 EIAKGEFLVLIGPSGSGKTTTMKMINRL----IEPTSGEIFIDGEDIRE   67 (242)
T ss_pred             EECCCCEEEEECCCCCHHHHHHHHHHCC----CCCCCEEEEECCEECCC
T ss_conf             8869989999999995699999999759----99981599999999999


Done!