Query         gi|254780310|ref|YP_003064723.1| hypothetical protein CLIBASIA_00975 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 119
No_of_seqs    116 out of 730
Neff          7.9 
Searched_HMMs 39220
Date          Sun May 29 15:45:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780310.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11595 gluconate periplasmic  99.9 8.1E-24 2.1E-28  152.3   8.3   99   18-117     2-102 (227)
  2 COG1040 ComFC Predicted amidop  99.6 8.8E-17 2.2E-21  113.4   4.2  101   14-117     5-106 (225)
  3 TIGR00201 comF comF family pro  99.3   1E-12 2.6E-17   90.8   3.1   82   24-119     1-82  (207)
  4 TIGR00143 hypF [NiFe] hydrogen  91.0    0.27   7E-06   27.5   3.6   71   18-100   120-212 (799)
  5 pfam04981 NMD3 NMD3 family. Th  85.2    0.46 1.2E-05   26.3   1.6   36   24-59      1-44  (237)
  6 COG1499 NMD3 NMD protein affec  74.8     2.1 5.3E-05   22.7   2.1   37   23-59      8-52  (355)
  7 PRK11788 hypothetical protein;  73.1     3.2 8.2E-05   21.6   2.7   44    5-48    338-383 (389)
  8 pfam09889 DUF2116 Uncharacteri  68.0     2.2 5.7E-05   22.5   1.0   24   22-45      4-28  (59)
  9 TIGR00599 rad18 DNA repair pro  67.7     3.7 9.5E-05   21.3   2.1   59   23-100    29-93  (421)
 10 KOG2041 consensus               64.6     2.8 7.2E-05   21.9   1.0   45   23-72   1119-1165(1189)
 11 pfam10764 Gin Inhibitor of sig  64.4     3.6 9.1E-05   21.4   1.4   27   23-49      1-32  (46)
 12 pfam03660 PHF5 PHF5-like prote  61.8       4  0.0001   21.1   1.3   50   22-74     27-79  (105)
 13 PRK11032 hypothetical protein;  59.5     2.2 5.7E-05   22.5  -0.3   33   28-60    117-152 (160)
 14 pfam07295 DUF1451 Protein of u  57.4     7.5 0.00019   19.6   2.1   48   13-60     92-142 (148)
 15 pfam07191 DUF1407 Protein of u  56.9     1.3 3.4E-05   23.7  -1.8   38   23-62      3-42  (70)
 16 PRK05580 primosome assembly pr  55.9     2.8 7.1E-05   22.0  -0.3   43   24-71    407-452 (699)
 17 KOG0978 consensus               55.4     2.5 6.5E-05   22.2  -0.6   40   23-62    645-690 (698)
 18 COG4068 Uncharacterized protei  55.0     4.9 0.00013   20.6   0.8   18   23-40     10-27  (64)
 19 pfam10977 DUF2797 Protein of u  54.8     6.6 0.00017   19.9   1.4   25   23-47     13-39  (233)
 20 KOG4080 consensus               53.2     6.1 0.00015   20.1   1.0   26   22-48     94-119 (176)
 21 pfam04423 Rad50_zn_hook Rad50   52.7      14 0.00035   18.1   2.8   30    3-34      4-33  (54)
 22 TIGR00575 dnlj DNA ligase, NAD  50.8     9.6 0.00024   19.0   1.7   16   18-33    408-423 (706)
 23 TIGR00269 TIGR00269 conserved   49.8     8.4 0.00021   19.3   1.3   19   51-69     82-100 (106)
 24 PRK00420 hypothetical protein;  48.8      15 0.00039   17.9   2.5   37    5-42      4-43  (107)
 25 COG2888 Predicted Zn-ribbon RN  45.9     3.7 9.5E-05   21.3  -1.0   24   20-43      8-35  (61)
 26 pfam10217 DUF2039 Uncharacteri  45.6     4.7 0.00012   20.7  -0.5   34   21-59     55-90  (92)
 27 pfam04216 FdhE Protein involve  43.5      26 0.00066   16.6   3.0   56    4-60    139-215 (283)
 28 COG2956 Predicted N-acetylgluc  41.8      21 0.00053   17.1   2.3   42    5-46    338-381 (389)
 29 COG5432 RAD18 RING-finger-cont  40.6      13 0.00034   18.2   1.2   37   23-60     27-69  (391)
 30 KOG4265 consensus               39.7      11 0.00027   18.8   0.5   41   21-62    290-337 (349)
 31 pfam10571 UPF0547 Uncharacteri  39.1       9 0.00023   19.1   0.1   22   38-60      3-24  (26)
 32 PRK08359 transcription factor;  38.4      15 0.00039   17.9   1.2   26   21-46      6-41  (175)
 33 PRK10410 hypothetical protein;  38.3      20  0.0005   17.3   1.8   73    8-98      9-95  (114)
 34 COG0068 HypF Hydrogenase matur  38.1      29 0.00074   16.3   2.6   12   34-45    100-111 (750)
 35 COG2995 PqiA Uncharacterized p  37.9      13 0.00034   18.2   0.8   27   34-60    219-245 (418)
 36 KOG1512 consensus               37.5      15 0.00037   18.0   1.0   55   23-81    316-372 (381)
 37 pfam06906 DUF1272 Protein of u  37.4      25 0.00062   16.7   2.1   37   21-60      5-51  (57)
 38 pfam10083 DUF2321 Uncharacteri  36.5      12 0.00032   18.4   0.5   11   50-60     68-78  (158)
 39 pfam03854 zf-P11 P-11 zinc fin  36.0      13 0.00033   18.2   0.6   32   30-62     15-47  (50)
 40 cd00350 rubredoxin_like Rubred  35.0      21 0.00053   17.2   1.4   25   23-60      3-27  (33)
 41 KOG3002 consensus               34.3      25 0.00063   16.7   1.7   35   23-61     50-91  (299)
 42 pfam08772 NOB1_Zn_bind Nin one  33.8      13 0.00032   18.3   0.2   23   37-59     11-33  (73)
 43 KOG2660 consensus               33.7      23 0.00058   16.9   1.5   65   17-96     11-82  (331)
 44 KOG1813 consensus               32.7      28 0.00072   16.4   1.8   44   17-61    237-286 (313)
 45 pfam05810 NinF NinF protein. T  31.7      25 0.00063   16.7   1.4   22   24-45     20-42  (58)
 46 COG1198 PriA Primosomal protei  31.2     9.2 0.00024   19.1  -0.9   36   22-59    445-484 (730)
 47 PRK08620 DNA topoisomerase III  30.5      46  0.0012   15.2   3.2   58    4-61    580-659 (726)
 48 COG1592 Rubrerythrin [Energy p  29.8      45  0.0011   15.3   2.4   38    9-60    119-159 (166)
 49 pfam10146 zf-C4H2 Zinc finger-  29.1     9.5 0.00024   19.0  -1.1   21   37-58    186-206 (220)
 50 COG1439 Predicted nucleic acid  29.1      14 0.00035   18.1  -0.3   23   37-60    141-163 (177)
 51 TIGR00354 polC DNA polymerase   28.8      15 0.00038   18.0  -0.2   43   22-69    680-722 (1173)
 52 COG1997 RPL43A Ribosomal prote  27.1      53  0.0013   14.9   2.4   25    3-30     20-44  (89)
 53 TIGR00570 cdk7 CDK-activating   26.7      34 0.00086   16.0   1.4   39   22-61      9-62  (322)
 54 pfam05290 Baculo_IE-1 Baculovi  26.6      54  0.0014   14.8   2.9   45   18-62     75-133 (141)
 55 PRK01343 zinc-binding protein;  26.0      33 0.00085   16.0   1.2   12   21-32      9-20  (56)
 56 TIGR01405 polC_Gram_pos DNA po  25.5      26 0.00066   16.6   0.6   29   34-63    716-757 (1264)
 57 COG1645 Uncharacterized Zn-fin  24.9      23 0.00058   16.9   0.2   23   21-43     28-52  (131)
 58 KOG1842 consensus               24.7      15 0.00039   17.9  -0.7   11   36-46    205-215 (505)
 59 KOG2613 consensus               23.5      46  0.0012   15.2   1.6   71   24-100    17-90  (502)
 60 TIGR02688 TIGR02688 conserved   23.2      62  0.0016   14.5   2.2   19    5-23    417-435 (470)
 61 COG1644 RPB10 DNA-directed RNA  23.0      22 0.00057   17.0  -0.1   15   19-33      2-16  (63)
 62 PRK07220 DNA topoisomerase I;   23.0      59  0.0015   14.6   2.0   83   23-105   591-711 (740)
 63 TIGR01054 rgy reverse gyrase;   23.0      13 0.00034   18.2  -1.3   31   16-46      2-36  (1843)
 64 pfam08274 PhnA_Zn_Ribbon PhnA   22.8      29 0.00074   16.3   0.4   24   22-45      3-29  (30)
 65 COG5175 MOT2 Transcriptional r  22.7      32 0.00081   16.1   0.6   41   23-63     16-66  (480)
 66 COG0199 RpsN Ribosomal protein  22.7      31 0.00079   16.2   0.6   24   23-46     23-48  (61)
 67 COG1110 Reverse gyrase [DNA re  21.7      26 0.00066   16.6  -0.0   31   16-46      3-37  (1187)
 68 PRK04023 DNA polymerase II lar  21.7      25 0.00065   16.7  -0.1   52   19-75    631-682 (1128)
 69 pfam11290 DUF3090 Protein of u  21.2      45  0.0012   15.3   1.1   13   50-62    154-166 (171)
 70 COG5220 TFB3 Cdk activating ki  21.1      41   0.001   15.5   0.9   37   22-58     11-61  (314)
 71 PRK03564 formate dehydrogenase  20.5      72  0.0018   14.1   5.7   56    4-60    160-236 (307)
 72 cd00162 RING RING-finger (Real  20.4      54  0.0014   14.8   1.4   37   23-59      1-44  (45)
 73 COG4306 Uncharacterized protei  20.1      46  0.0012   15.2   1.0   10   51-60     69-78  (160)

No 1  
>PRK11595 gluconate periplasmic binding protein; Provisional
Probab=99.90  E-value=8.1e-24  Score=152.33  Aligned_cols=99  Identities=17%  Similarity=0.237  Sum_probs=89.4

Q ss_pred             HHCCCCCCCCCCCCC-CCCEECHHHHHHCCCCCCCCCCCCCCCCCCCC-CCHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             857874710375156-57702888995086767862012444653347-6089851678435301200021279999999
Q gi|254780310|r   18 CIYPSICPIYSRIIN-LRFCLCGHCWSKIHFITATEHILKNNKDNIDK-DPLKSMQKDLPLTQIRSVTLYCDMSCVLVRL   95 (119)
Q Consensus        18 ~lfP~~C~~C~~~~~-~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~-~C~~C~~~~~~f~~~~a~~~Y~~~~r~lI~~   95 (119)
                      ++||++|++|+..+. ++..||.+|+++++++ ++.|++||.|..... .|++|...+|+|++.+++|.|+++++++||+
T Consensus         2 L~~P~~C~~C~~~l~~~~~~lC~~C~~~l~~~-~~~C~~Cg~p~~~~~~~C~~C~~~~p~~~~~~a~~~Y~~~~~~lI~~   80 (227)
T PRK11595          2 LTVPGLCWLCRMPLALSHWGICSVCSRALRTL-PTLCPQCGLPATHTHLPCGRCLQKPPPWQRLVFVSDYAPPLSGLIHQ   80 (227)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC-CCCCCCCCCCCCCCCCCCHHHHCCCCCHHHEEHHHHCCHHHHHHHHH
T ss_conf             66898471369961138784466676008766-67575136967656777779881996566620343037799999999


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             7447876699999999999974
Q gi|254780310|r   96 LKYHDRTDLAIMMAQWMFRVLE  117 (119)
Q Consensus        96 ~Ky~~~~~la~~la~~m~r~~~  117 (119)
                      |||+|+.+++..||++|+..++
T Consensus        81 ~Ky~~~~~l~~~la~~l~~~~~  102 (227)
T PRK11595         81 LKFSRRSELASALARLLLLEVL  102 (227)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHH
T ss_conf             8738867899999999999999


No 2  
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=99.65  E-value=8.8e-17  Score=113.36  Aligned_cols=101  Identities=20%  Similarity=0.274  Sum_probs=93.2

Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCCCCC-CCCHHHHCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             99998578747103751565770288899508676786201244465334-76089851678435301200021279999
Q gi|254780310|r   14 ELFHCIYPSICPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKDNID-KDPLKSMQKDLPLTQIRSVTLYCDMSCVL   92 (119)
Q Consensus        14 ~ll~~lfP~~C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~-~~C~~C~~~~~~f~~~~a~~~Y~~~~r~l   92 (119)
                      .. ..++|+.|..|...+..+ .+|..|++.++++.. .|+.||.+.... ..|+.|...+++|++.++++.|+++++++
T Consensus         5 ~~-~~~~~~~~~~~~~~l~~~-~~C~~C~~~~~~~~~-~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~l~~~   81 (225)
T COG1040           5 LC-RLLLPPRCWLCLLLLFFP-GLCSGCQADLPLIGN-LCPLCGLPLSSHACRCGECLAKPPPFERLRSLGSYNGPLREL   81 (225)
T ss_pred             HH-CCCCCCCHHHHHHHCCCC-CCCHHHHHHHHHHHH-HHHHHHCCCCCCCCCCHHHHCCCCCCCCEEEEEEECHHHHHH
T ss_conf             52-546662019887653689-869455423467762-757875514443344888853588530258888731999999


Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             9997447876699999999999974
Q gi|254780310|r   93 VRLLKYHDRTDLAIMMAQWMFRVLE  117 (119)
Q Consensus        93 I~~~Ky~~~~~la~~la~~m~r~~~  117 (119)
                      |+++||+++..++..||.||++++.
T Consensus        82 i~~~Kf~~~~~l~~~la~~l~~~~~  106 (225)
T COG1040          82 ISQLKFQGDLDLAKLLARLLAKALD  106 (225)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9986526717789999999999865


No 3  
>TIGR00201 comF comF family protein; InterPro: IPR005222   Proteins in this family are found in bacterial species which posses systems for natural transformation with exogenous DNA (eg Bacillus subtilis, Haemophilus influenzae), and also species without these systems (eg Escherichia coli). Competence protein F has been shown to be important for the uptake of exogenous DNA in naturally competent bacteria, though the precise role of this protein is not yet known , . GntX is a periplasmic gluconate binding protein thought to be part of a high-affinity gluconate transport system ..
Probab=99.30  E-value=1e-12  Score=90.81  Aligned_cols=82  Identities=17%  Similarity=0.286  Sum_probs=71.9

Q ss_pred             CCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
Q ss_conf             71037515657702888995086767862012444653347608985167843530120002127999999974478766
Q gi|254780310|r   24 CPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKDNIDKDPLKSMQKDLPLTQIRSVTLYCDMSCVLVRLLKYHDRTD  103 (119)
Q Consensus        24 C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~~C~~C~~~~~~f~~~~a~~~Y~~~~r~lI~~~Ky~~~~~  103 (119)
                      |++||+.+.+...+|.+|......+              ...|+.|+..+|+|++.+.++.|.+++..+|++|||.++.+
T Consensus         1 C~~C~k~~~S~~a~C~~C~~~~t~~--------------~~~CG~~L~~~P~W~~l~~v~~Y~~~l~~li~~fKf~~~~~   66 (207)
T TIGR00201         1 CSLCGKRIKSSKALCDQCGSERTLF--------------RDSCGLCLKQNPSWDKLVSVFEYKEPLKELISRFKFDAQAE   66 (207)
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHH--------------HCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCHHH
T ss_conf             9888887300776246666246664--------------11023013787581303777605434789999733450368


Q ss_pred             HHHHHHHHHHHHHHCC
Q ss_conf             9999999999997429
Q gi|254780310|r  104 LAIMMAQWMFRVLEKI  119 (119)
Q Consensus       104 la~~la~~m~r~~~~i  119 (119)
                      ++..|+..++.++.+|
T Consensus        67 I~~~L~~~l~~~~~~~   82 (207)
T TIGR00201        67 IARALASLLALTVSKA   82 (207)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             9999889999998603


No 4  
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421   The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif.   The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate .   The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction .   The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear.   Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=91.03  E-value=0.27  Score=27.54  Aligned_cols=71  Identities=20%  Similarity=0.122  Sum_probs=41.7

Q ss_pred             HHCCC-CCCCCCCC---C---C--------CCCEECHHHHHHCCCC-------CCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf             85787-47103751---5---6--------5770288899508676-------786201244465334760898516784
Q gi|254780310|r   18 CIYPS-ICPIYSRI---I---N--------LRFCLCGHCWSKIHFI-------TATEHILKNNKDNIDKDPLKSMQKDLP   75 (119)
Q Consensus        18 ~lfP~-~C~~C~~~---~---~--------~~~~lC~~C~~~l~~i-------~~~~C~~Cg~~~~~~~~C~~C~~~~~~   75 (119)
                      ++||= .|.-||-.   +   +        .+.+||++|.++-.-.       .+..||+||-.+....           
T Consensus       120 Y~YPF~~CT~CGPRfTi~~aLPYDRe~T~m~~FpLC~~C~~EY~dP~DRRFHAQ~~aCP~CGP~L~f~~-----------  188 (799)
T TIGR00143       120 YLYPFISCTDCGPRFTIIEALPYDRENTSMADFPLCPDCEKEYKDPLDRRFHAQAIACPRCGPKLEFVS-----------  188 (799)
T ss_pred             CCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEECCCCCCCCCCCCCEEC-----------
T ss_conf             127432435567525676427888874334578988468997078876304644627733578653021-----------


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHCC
Q ss_conf             3530120002127999999974478
Q gi|254780310|r   76 LTQIRSVTLYCDMSCVLVRLLKYHD  100 (119)
Q Consensus        76 f~~~~a~~~Y~~~~r~lI~~~Ky~~  100 (119)
                       +.......-+++++..|.++|-++
T Consensus       189 -~~~~vIae~~~al~~a~~~L~~G~  212 (799)
T TIGR00143       189 -RGGEVIAEKDDALKEAAKLLKKGK  212 (799)
T ss_pred             -CCCEEEECCCHHHHHHHHHHCCCC
T ss_conf             -687167527736899999840797


No 5  
>pfam04981 NMD3 NMD3 family. The NMD3 protein is involved in nonsense mediated mRNA decay. This amino terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway.
Probab=85.15  E-value=0.46  Score=26.30  Aligned_cols=36  Identities=25%  Similarity=0.253  Sum_probs=24.6

Q ss_pred             CCCCCCCCCC-CCEECHHHHHHCCCCCC-------CCCCCCCCC
Q ss_conf             7103751565-77028889950867678-------620124446
Q gi|254780310|r   24 CPIYSRIINL-RFCLCGHCWSKIHFITA-------TEHILKNNK   59 (119)
Q Consensus        24 C~~C~~~~~~-~~~lC~~C~~~l~~i~~-------~~C~~Cg~~   59 (119)
                      |+.||.+.+. ...+|.+|..+-..+..       ..|+.||.-
T Consensus         1 C~~CG~~~~~~~~~mC~~C~~~~~~i~~ip~~~~v~~C~~Cg~~   44 (237)
T pfam04981         1 CPRCGRPIEPLIDGLCPDCYRERVDITEIPEELTVVVCRDCGRY   44 (237)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHCCCCEEECCCEEEEEECCCCCCE
T ss_conf             98579989977356666787105765998985899999999879


No 6  
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=74.84  E-value=2.1  Score=22.66  Aligned_cols=37  Identities=22%  Similarity=0.348  Sum_probs=25.1

Q ss_pred             CCCCCCCCCC-CCCEECHHHHHHCCC-CC------CCCCCCCCCC
Q ss_conf             4710375156-577028889950867-67------8620124446
Q gi|254780310|r   23 ICPIYSRIIN-LRFCLCGHCWSKIHF-IT------ATEHILKNNK   59 (119)
Q Consensus        23 ~C~~C~~~~~-~~~~lC~~C~~~l~~-i~------~~~C~~Cg~~   59 (119)
                      .|+.||+..+ ....+|.+|.-+-.. +.      --+|..||..
T Consensus         8 ~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~   52 (355)
T COG1499           8 LCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAY   52 (355)
T ss_pred             EECCCCCCCCHHHHCCCHHHHHCCCCCCCCCCCEEEEECCCCCCC
T ss_conf             715688968645505467787504622038873578987767870


No 7  
>PRK11788 hypothetical protein; Provisional
Probab=73.06  E-value=3.2  Score=21.62  Aligned_cols=44  Identities=16%  Similarity=0.336  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECHHH--HHHCCCC
Q ss_conf             9999999999999857874710375156577028889--9508676
Q gi|254780310|r    5 IQTVKSIIIELFHCIYPSICPIYSRIINLRFCLCGHC--WSKIHFI   48 (119)
Q Consensus         5 ~~~ik~~~~~ll~~lfP~~C~~C~~~~~~~~~lC~~C--~~~l~~i   48 (119)
                      ++.++.++.+.+.--..=+|--||=....-.+-|+.|  |..+.++
T Consensus       338 l~~l~~~v~~~~~~~~~Y~C~~CGF~~~~~~WqCPsC~~W~Si~P~  383 (389)
T PRK11788        338 LELLRDLVGEQLKRKPRYRCRNCGFTARTLYWHCPSCKAWETIKPI  383 (389)
T ss_pred             HHHHHHHHHHHHHCCCCEECCCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf             9999999999971799976999999888314579099986784898


No 8  
>pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=67.99  E-value=2.2  Score=22.51  Aligned_cols=24  Identities=17%  Similarity=0.408  Sum_probs=14.8

Q ss_pred             CCCCCCCCCCCCCCEECHH-HHHHC
Q ss_conf             7471037515657702888-99508
Q gi|254780310|r   22 SICPIYSRIINLRFCLCGH-CWSKI   45 (119)
Q Consensus        22 ~~C~~C~~~~~~~~~lC~~-C~~~l   45 (119)
                      .+|++||..++.+..+|++ |..++
T Consensus         4 kHC~vCG~~Ipp~e~fCS~kC~~~~   28 (59)
T pfam09889         4 KHCIVCGTAIPPDESFCSEKCQEEY   28 (59)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             5356579978943223148899999


No 9  
>TIGR00599 rad18 DNA repair protein rad18; InterPro: IPR004580    During DNA replication, lesion bypass is an important cellular response to unrepaired damage in the genome. In the yeast Saccharomyces cerevisiae, Rad6 and Rad18 are required for both the error-free and error-prone lesion bypass mechanisms. The RAD18 gene encodes a RING-finger protein with single-stranded DNA binding activity that interacts with the ubiquitin-conjugating enzyme RAD6. ; GO: 0003684 damaged DNA binding, 0006281 DNA repair, 0005634 nucleus.
Probab=67.72  E-value=3.7  Score=21.27  Aligned_cols=59  Identities=15%  Similarity=0.154  Sum_probs=36.1

Q ss_pred             CCCCCCCCCC-----C-CCEECHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             4710375156-----5-770288899508676786201244465334760898516784353012000212799999997
Q gi|254780310|r   23 ICPIYSRIIN-----L-RFCLCGHCWSKIHFITATEHILKNNKDNIDKDPLKSMQKDLPLTQIRSVTLYCDMSCVLVRLL   96 (119)
Q Consensus        23 ~C~~C~~~~~-----~-~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~~C~~C~~~~~~f~~~~a~~~Y~~~~r~lI~~~   96 (119)
                      ||.+|.....     + .+-+|.-|.+.- +-+++-||.|-.++-.                  +-.+-+-.++++|-.|
T Consensus        29 RC~iCkdFf~~P~lTsC~HTFCSLCIR~~-L~~~p~CP~Cr~~~qE------------------s~LR~n~~l~E~vesF   89 (421)
T TIGR00599        29 RCHICKDFFDAPVLTSCSHTFCSLCIRRC-LSEEPKCPLCRAEDQE------------------SKLRKNWVLEEIVESF   89 (421)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCHHHHHHH-HCCCCCCCCCCCCHHH------------------HHHHHHHHHHHHHHHH
T ss_conf             35676898468830488632003688776-1478888736770456------------------6667889999999888


Q ss_pred             HHCC
Q ss_conf             4478
Q gi|254780310|r   97 KYHD  100 (119)
Q Consensus        97 Ky~~  100 (119)
                      |--.
T Consensus        90 k~~R   93 (421)
T TIGR00599        90 KNLR   93 (421)
T ss_pred             HHHH
T ss_conf             7466


No 10 
>KOG2041 consensus
Probab=64.64  E-value=2.8  Score=21.94  Aligned_cols=45  Identities=13%  Similarity=0.130  Sum_probs=32.9

Q ss_pred             CCCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCCCCCC--CCHHHHCC
Q ss_conf             471037515657702888995086767862012444653347--60898516
Q gi|254780310|r   23 ICPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKDNIDK--DPLKSMQK   72 (119)
Q Consensus        23 ~C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~--~C~~C~~~   72 (119)
                      .|..||..++....-|++|..++|     .|..-|.|.+...  .|..|...
T Consensus      1119 dc~~cg~~i~~~~~~c~ec~~kfP-----~CiasG~pIt~~~fWlC~~CkH~ 1165 (1189)
T KOG2041        1119 DCSVCGAKIDPYDLQCSECQTKFP-----VCIASGRPITDNIFWLCPRCKHR 1165 (1189)
T ss_pred             EEEECCCCCCCCCCCCHHHCCCCC-----EEECCCCCCCCCEEEECCCCCCC
T ss_conf             243048847966777733337676-----36505975355538974633355


No 11 
>pfam10764 Gin Inhibitor of sigma-G Gin. Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB.
Probab=64.36  E-value=3.6  Score=21.36  Aligned_cols=27  Identities=22%  Similarity=0.314  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCC-----CCEECHHHHHHCCCCC
Q ss_conf             47103751565-----7702888995086767
Q gi|254780310|r   23 ICPIYSRIINL-----RFCLCGHCWSKIHFIT   49 (119)
Q Consensus        23 ~C~~C~~~~~~-----~~~lC~~C~~~l~~i~   49 (119)
                      .|++|+++...     +..||.+|.++|.-++
T Consensus         1 ~CiIC~~~k~~GI~i~~~fIC~~CE~~iv~t~   32 (46)
T pfam10764         1 KCIICEKPKNEGIHLYGKFICTECEKKLINTE   32 (46)
T ss_pred             CEEECCCCCCCCEEEECCCCHHHHHHHHHCCC
T ss_conf             93868983888789978791578899884289


No 12 
>pfam03660 PHF5 PHF5-like protein. This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse, may act as a chromatin-associated protein. The S. pombe ini1 gene is essential, required for splicing. It is localized in the nucleus, but not detected in the nucleolus and can be complemented by human ini1.
Probab=61.76  E-value=4  Score=21.06  Aligned_cols=50  Identities=14%  Similarity=0.260  Sum_probs=34.2

Q ss_pred             CCCCCCCCCCCC--CCEECHHHHHHCCCCCCCCCCCCCCCCCCC-CCCHHHHCCCC
Q ss_conf             747103751565--770288899508676786201244465334-76089851678
Q gi|254780310|r   22 SICPIYSRIINL--RFCLCGHCWSKIHFITATEHILKNNKDNID-KDPLKSMQKDL   74 (119)
Q Consensus        22 ~~C~~C~~~~~~--~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~-~~C~~C~~~~~   74 (119)
                      .+|++|+..+..  ...||.+|--.   .....|..||.+...+ .+|.+|...+.
T Consensus        27 GkCpiCDS~Vrp~~~vrICdeCs~G---~~~~rCIiCg~~g~sdAYYC~eC~~lEK   79 (105)
T pfam03660        27 GKCPICDSYVRPTTKVRICDECSFG---SLGNKCIICGSPGVSDAYYCWECVRLEK   79 (105)
T ss_pred             CCCCCCCCCCCCCCEEEECCCCCCC---CCCCCEEEECCCCCCCCHHHHHHHHHHC
T ss_conf             8466454645765447898878888---7798569808988760210688886312


No 13 
>PRK11032 hypothetical protein; Provisional
Probab=59.49  E-value=2.2  Score=22.48  Aligned_cols=33  Identities=15%  Similarity=0.331  Sum_probs=24.5

Q ss_pred             CCCCCCCCEECHHHHHHCCCCCC---CCCCCCCCCC
Q ss_conf             75156577028889950867678---6201244465
Q gi|254780310|r   28 SRIINLRFCLCGHCWSKIHFITA---TEHILKNNKD   60 (119)
Q Consensus        28 ~~~~~~~~~lC~~C~~~l~~i~~---~~C~~Cg~~~   60 (119)
                      |..++.+..+|..|-.++.+.++   |.|+.||...
T Consensus       117 GEivg~G~LvC~~Cg~~~~~~~~~~ippCp~Cg~~~  152 (160)
T PRK11032        117 GEVVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQ  152 (160)
T ss_pred             CEEEECCEEEHHHCCCEEEEECCCCCCCCCCCCCCE
T ss_conf             605325566574289877874687798887799976


No 14 
>pfam07295 DUF1451 Protein of unknown function (DUF1451). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=57.43  E-value=7.5  Score=19.59  Aligned_cols=48  Identities=17%  Similarity=0.203  Sum_probs=30.7

Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCEECHHHHHHCCCCCC---CCCCCCCCCC
Q ss_conf             99999857874710375156577028889950867678---6201244465
Q gi|254780310|r   13 IELFHCIYPSICPIYSRIINLRFCLCGHCWSKIHFITA---TEHILKNNKD   60 (119)
Q Consensus        13 ~~ll~~lfP~~C~~C~~~~~~~~~lC~~C~~~l~~i~~---~~C~~Cg~~~   60 (119)
                      ..+.+=+=..-.---|..++.+..+|..|-.++.+..+   |.|+.||...
T Consensus        92 ~el~~dl~h~g~Y~sGEvvg~G~LvC~~Cg~~~~~~~p~~ip~Cp~Cg~~~  142 (148)
T pfam07295        92 HELFQDLEHHGVYQSGEIVGLGTLVCENCGHMLTFYHPSVIPPCPKCGHTE  142 (148)
T ss_pred             HHHHHHHHCCCEEECCCEEECCEEEECCCCCEEEEECCCCCCCCCCCCCCE
T ss_conf             999987541572424605416457723689878874687688987799982


No 15 
>pfam07191 DUF1407 Protein of unknown function (DUF1407). This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains.
Probab=56.95  E-value=1.3  Score=23.72  Aligned_cols=38  Identities=13%  Similarity=0.230  Sum_probs=26.6

Q ss_pred             CCCCCCCCCC--CCCEECHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             4710375156--577028889950867678620124446533
Q gi|254780310|r   23 ICPIYSRIIN--LRFCLCGHCWSKIHFITATEHILKNNKDNI   62 (119)
Q Consensus        23 ~C~~C~~~~~--~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~   62 (119)
                      .|+.|+..++  ++..-|..|.+.+..  ..+||.|+.++..
T Consensus         3 ~CP~C~~~l~~~~~~~~C~~C~~~~~~--~a~CP~C~~~Lq~   42 (70)
T pfam07191         3 ICPQCQQELEWKGGHYHCDQCQKDFKK--QALCPDCHQELEV   42 (70)
T ss_pred             CCCCCCCCCEECCCCEECHHHCCEEEE--EEECCCCCCHHHH
T ss_conf             288899952433997797033010147--8989762437899


No 16 
>PRK05580 primosome assembly protein PriA; Validated
Probab=55.88  E-value=2.8  Score=21.97  Aligned_cols=43  Identities=12%  Similarity=0.169  Sum_probs=18.9

Q ss_pred             CCCCCCCCCCCCEECHHHHHHCCCCC---CCCCCCCCCCCCCCCCCHHHHC
Q ss_conf             71037515657702888995086767---8620124446533476089851
Q gi|254780310|r   24 CPIYSRIINLRFCLCGHCWSKIHFIT---ATEHILKNNKDNIDKDPLKSMQ   71 (119)
Q Consensus        24 C~~C~~~~~~~~~lC~~C~~~l~~i~---~~~C~~Cg~~~~~~~~C~~C~~   71 (119)
                      |.-||..     .-|+.|-..|.+..   ...|..||........|..|-.
T Consensus       407 C~~Cg~~-----~~C~~C~~~L~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cgs  452 (699)
T PRK05580        407 CRDCGWV-----ARCPHCDGPLTLHRAGRRLRCHHCGYQEPIPRACPECGS  452 (699)
T ss_pred             CHHCCCE-----EECCCCCCEEEECCCCCCEECCCCCCCCCCCCCCCCCCC
T ss_conf             4531994-----565678986342068983322646883657554656799


No 17 
>KOG0978 consensus
Probab=55.43  E-value=2.5  Score=22.19  Aligned_cols=40  Identities=13%  Similarity=0.134  Sum_probs=28.9

Q ss_pred             CCCCCCCC-----CC-CCCEECHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             47103751-----56-577028889950867678620124446533
Q gi|254780310|r   23 ICPIYSRI-----IN-LRFCLCGHCWSKIHFITATEHILKNNKDNI   62 (119)
Q Consensus        23 ~C~~C~~~-----~~-~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~   62 (119)
                      .|++|...     +. =.+.+|..|....--+...-||.|+.+++.
T Consensus       645 kCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga  690 (698)
T KOG0978         645 KCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA  690 (698)
T ss_pred             ECCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             2877667556689983206888998888998854879998888785


No 18 
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=54.96  E-value=4.9  Score=20.58  Aligned_cols=18  Identities=17%  Similarity=0.385  Sum_probs=9.1

Q ss_pred             CCCCCCCCCCCCCEECHH
Q ss_conf             471037515657702888
Q gi|254780310|r   23 ICPIYSRIINLRFCLCGH   40 (119)
Q Consensus        23 ~C~~C~~~~~~~~~lC~~   40 (119)
                      +|++||..++.+..+|++
T Consensus        10 HC~VCg~aIp~de~~CSe   27 (64)
T COG4068          10 HCVVCGKAIPPDEQVCSE   27 (64)
T ss_pred             CCCCCCCCCCCCCCHHHH
T ss_conf             566058868974036889


No 19 
>pfam10977 DUF2797 Protein of unknown function (DUF2797). This family of proteins has no known function.
Probab=54.76  E-value=6.6  Score=19.90  Aligned_cols=25  Identities=24%  Similarity=0.376  Sum_probs=19.8

Q ss_pred             CCCCCCCCCC--CCCEECHHHHHHCCC
Q ss_conf             4710375156--577028889950867
Q gi|254780310|r   23 ICPIYSRIIN--LRFCLCGHCWSKIHF   47 (119)
Q Consensus        23 ~C~~C~~~~~--~~~~lC~~C~~~l~~   47 (119)
                      .|+.||+.+.  -....|..|+.+++.
T Consensus        13 ~C~~CG~~t~ksf~qG~C~~Cf~~~p~   39 (233)
T pfam10977        13 GCLNCGRKTKKSFSQGYCYPCFSKLAQ   39 (233)
T ss_pred             EEECCCCCCCCCCCCCCCHHHHHCCCC
T ss_conf             741168867656668578777522703


No 20 
>KOG4080 consensus
Probab=53.19  E-value=6.1  Score=20.09  Aligned_cols=26  Identities=31%  Similarity=0.691  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCCCCEECHHHHHHCCCC
Q ss_conf             747103751565770288899508676
Q gi|254780310|r   22 SICPIYSRIINLRFCLCGHCWSKIHFI   48 (119)
Q Consensus        22 ~~C~~C~~~~~~~~~lC~~C~~~l~~i   48 (119)
                      .+|+.||..- ..+.||..|..++...
T Consensus        94 ~~CP~CGh~k-~a~~LC~~Cy~kV~ke  119 (176)
T KOG4080          94 NTCPACGHIK-PAHTLCDYCYAKVHKE  119 (176)
T ss_pred             CCCCCCCCCC-CCCCCHHHHHHHHHHH
T ss_conf             4375457644-1452079999999999


No 21 
>pfam04423 Rad50_zn_hook Rad50 zinc hook motif. The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.
Probab=52.67  E-value=14  Score=18.13  Aligned_cols=30  Identities=20%  Similarity=0.339  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             89999999999999985787471037515657
Q gi|254780310|r    3 AIIQTVKSIIIELFHCIYPSICPIYSRIINLR   34 (119)
Q Consensus         3 ~~~~~ik~~~~~ll~~lfP~~C~~C~~~~~~~   34 (119)
                      +-..-.+..+..+.+-  ...|++||+.++.+
T Consensus         4 ~~~~~~~k~i~~l~~~--~~~CPvC~r~l~~e   33 (54)
T pfam04423         4 SETEEYNKAIEELKEA--KGCCPVCGRPLDEE   33 (54)
T ss_pred             HHHHHHHHHHHHHHHH--CCCCCCCCCCCCHH
T ss_conf             3789999999999984--58777669976678


No 22 
>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=50.77  E-value=9.6  Score=19.00  Aligned_cols=16  Identities=19%  Similarity=0.451  Sum_probs=12.5

Q ss_pred             HHCCCCCCCCCCCCCC
Q ss_conf             8578747103751565
Q gi|254780310|r   18 CIYPSICPIYSRIINL   33 (119)
Q Consensus        18 ~lfP~~C~~C~~~~~~   33 (119)
                      +.||.+||.|+..+..
T Consensus       408 ~~~P~~CP~C~s~lv~  423 (706)
T TIGR00575       408 IKFPTHCPSCGSPLVR  423 (706)
T ss_pred             EECCCCCCCCCCEEEC
T ss_conf             3428718888833111


No 23 
>TIGR00269 TIGR00269 conserved hypothetical protein TIGR00269; InterPro: IPR000541 The following uncharacterised proteins have been shown to share regions of similarities, yeast chromosome VII hypothetical protein YGL211w; Dictyostelium discoideum (Slime mold) protein veg136; and Methanococcus jannaschii hypothetical proteins MJ1157 and MJ1478..
Probab=49.79  E-value=8.4  Score=19.31  Aligned_cols=19  Identities=5%  Similarity=-0.279  Sum_probs=9.1

Q ss_pred             CCCCCCCCCCCCCCCCHHH
Q ss_conf             6201244465334760898
Q gi|254780310|r   51 TEHILKNNKDNIDKDPLKS   69 (119)
Q Consensus        51 ~~C~~Cg~~~~~~~~C~~C   69 (119)
                      ..|.+||.|-+-+..|..|
T Consensus        82 ~~C~~CGeP~SPG~~CkaC  100 (106)
T TIGR00269        82 RRCERCGEPASPGKICKAC  100 (106)
T ss_pred             CCCCCCCCCCCCCCHHHHH
T ss_conf             5000147888875443666


No 24 
>PRK00420 hypothetical protein; Validated
Probab=48.76  E-value=15  Score=17.88  Aligned_cols=37  Identities=8%  Similarity=0.158  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCC---CCCEECHHHH
Q ss_conf             9999999999999857874710375156---5770288899
Q gi|254780310|r    5 IQTVKSIIIELFHCIYPSICPIYSRIIN---LRFCLCGHCW   42 (119)
Q Consensus         5 ~~~ik~~~~~ll~~lfP~~C~~C~~~~~---~~~~lC~~C~   42 (119)
                      ++.+-..+.+... ..+.+|+.||.++-   ++..+|+.|-
T Consensus         4 vK~~a~ll~~Ga~-ml~~~C~~Cg~plf~~k~G~~~Cp~cg   43 (107)
T PRK00420          4 VKKAAELLRSGAK-MLDKHCPVCGLPLFELKDGEVVCPNHG   43 (107)
T ss_pred             HHHHHHHHHHHHH-HHHHHCCCCCCCEEECCCCCEECCCCC
T ss_conf             9999999995777-635137657984057489877689898


No 25 
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.89  E-value=3.7  Score=21.27  Aligned_cols=24  Identities=25%  Similarity=0.462  Sum_probs=15.2

Q ss_pred             CCCCCCCCCCCCC-CCC---EECHHHHH
Q ss_conf             7874710375156-577---02888995
Q gi|254780310|r   20 YPSICPIYSRIIN-LRF---CLCGHCWS   43 (119)
Q Consensus        20 fP~~C~~C~~~~~-~~~---~lC~~C~~   43 (119)
                      .|+.|..||..+. .+.   +.|+.|-+
T Consensus         8 ~~~~CtSCg~~i~p~e~~v~F~CPnCGe   35 (61)
T COG2888           8 DPPVCTSCGREIAPGETAVKFPCPNCGE   35 (61)
T ss_pred             CCCEECCCCCEECCCCCEEEEECCCCCC
T ss_conf             8852123787704687500864899982


No 26 
>pfam10217 DUF2039 Uncharacterized conserved protein (DUF2039). This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=45.63  E-value=4.7  Score=20.72  Aligned_cols=34  Identities=12%  Similarity=0.326  Sum_probs=15.5

Q ss_pred             CCCCCCCCC-CCC-CCCEECHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             874710375-156-577028889950867678620124446
Q gi|254780310|r   21 PSICPIYSR-IIN-LRFCLCGHCWSKIHFITATEHILKNNK   59 (119)
Q Consensus        21 P~~C~~C~~-~~~-~~~~lC~~C~~~l~~i~~~~C~~Cg~~   59 (119)
                      |..|.-|+. -+. +=..||.+|..++.     .|..|+.|
T Consensus        55 p~kC~kC~qktVk~AYH~iC~~Ca~~~~-----~CaKC~k~   90 (92)
T pfam10217        55 PKKCNKCQQKTVRHAYHHICDDCAKELK-----VCAKCQKP   90 (92)
T ss_pred             CCCCHHCCCCHHHHHHHHHHHHHHHHHH-----HCCCCCCC
T ss_conf             7402221113699999998899998754-----37366999


No 27 
>pfam04216 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase.
Probab=43.55  E-value=26  Score=16.60  Aligned_cols=56  Identities=14%  Similarity=0.339  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHC-----C-----CCCCCCCCC-C-----CC-----CCEECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999999999999857-----8-----747103751-5-----65-----770288899508676786201244465
Q gi|254780310|r    4 IIQTVKSIIIELFHCIY-----P-----SICPIYSRI-I-----NL-----RFCLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus         4 ~~~~ik~~~~~ll~~lf-----P-----~~C~~C~~~-~-----~~-----~~~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      +...+.-.+..+...+.     |     ..|++||.. +     ..     ....|.-|..+.++ ....|+.||...
T Consensus       139 i~AaLqv~~a~~A~~l~~~~~~~~~~~~~~CPvCGs~P~~s~~~~~~~~G~Ryl~Cs~C~teW~~-~R~~C~~Cg~~~  215 (283)
T pfam04216       139 LWAALQLYWAQLAQQLDARALPEAGWQRGLCPVCGSAPVASVIRGGGAQGLRYLHCSLCETEWHF-VRVKCTNCGSTK  215 (283)
T ss_pred             HHHHHHHHHHHHHHCCCCHHCCCCCCCCCCCCCCCCCCHHHEEECCCCCCCEEEECCCCCCCCCC-CCCCCCCCCCCC
T ss_conf             99999999999996288010377776589699999810001131378788368865888783242-265479999999


No 28 
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=41.80  E-value=21  Score=17.11  Aligned_cols=42  Identities=14%  Similarity=0.354  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECHHH--HHHCC
Q ss_conf             9999999999999857874710375156577028889--95086
Q gi|254780310|r    5 IQTVKSIIIELFHCIYPSICPIYSRIINLRFCLCGHC--WSKIH   46 (119)
Q Consensus         5 ~~~ik~~~~~ll~~lfP~~C~~C~~~~~~~~~lC~~C--~~~l~   46 (119)
                      +..+++++.+-+.-..+=+|--||=....-.+=|++|  |..+.
T Consensus       338 L~~lr~mvgeql~~~~~YRC~~CGF~a~~l~W~CPsC~~W~Tik  381 (389)
T COG2956         338 LDLLRDMVGEQLRRKPRYRCQNCGFTAHTLYWHCPSCRAWETIK  381 (389)
T ss_pred             HHHHHHHHHHHHHHCCCCEECCCCCCHHEEEEECCCCCCCCCCC
T ss_conf             99999999999731677210016863101354188756522417


No 29 
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=40.58  E-value=13  Score=18.23  Aligned_cols=37  Identities=19%  Similarity=0.287  Sum_probs=26.7

Q ss_pred             CCCCCCCCCC------CCCEECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             4710375156------5770288899508676786201244465
Q gi|254780310|r   23 ICPIYSRIIN------LRFCLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus        23 ~C~~C~~~~~------~~~~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      +|.+|+..+.      =++.+|.-|... +.-+.|.||.|..+.
T Consensus        27 rC~IC~~~i~ip~~TtCgHtFCslCIR~-hL~~qp~CP~Cr~~~   69 (391)
T COG5432          27 RCRICDCRISIPCETTCGHTFCSLCIRR-HLGTQPFCPVCREDP   69 (391)
T ss_pred             HHHHHHHEEECCEECCCCCCHHHHHHHH-HHCCCCCCCCCCCCH
T ss_conf             7654011040412225665065889998-726799985102657


No 30 
>KOG4265 consensus
Probab=39.69  E-value=11  Score=18.77  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=27.5

Q ss_pred             CCCCCCCCCCCC-------CCCEECHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             874710375156-------577028889950867678620124446533
Q gi|254780310|r   21 PSICPIYSRIIN-------LRFCLCGHCWSKIHFITATEHILKNNKDNI   62 (119)
Q Consensus        21 P~~C~~C~~~~~-------~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~   62 (119)
                      +..|++|-...-       ..--+|.+|...|.+ ...-||.|..|...
T Consensus       290 gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~  337 (349)
T KOG4265         290 GKECVICLSESRDTVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE  337 (349)
T ss_pred             CCEEEEEECCCCCEEEECCHHHEHHHHHHHHHHH-HHCCCCCCCCCHHH
T ss_conf             8705997458865388504221301758999987-61599712364475


No 31 
>pfam10571 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif.
Probab=39.05  E-value=9  Score=19.14  Aligned_cols=22  Identities=14%  Similarity=0.190  Sum_probs=11.8

Q ss_pred             CHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             88899508676786201244465
Q gi|254780310|r   38 CGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus        38 C~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      |++|.+.++ +....|+.||..+
T Consensus         3 CP~C~~~vp-~~~~~Cp~CG~~F   24 (26)
T pfam10571         3 CPECGAEVP-LAAKICPHCGYEF   24 (26)
T ss_pred             CCCCCCCCC-HHCCCCCCCCCCC
T ss_conf             875548364-0034477888555


No 32 
>PRK08359 transcription factor; Validated
Probab=38.36  E-value=15  Score=17.89  Aligned_cols=26  Identities=27%  Similarity=0.673  Sum_probs=18.2

Q ss_pred             CCCCCCCCCCCCCC----------CEECHHHHHHCC
Q ss_conf             87471037515657----------702888995086
Q gi|254780310|r   21 PSICPIYSRIINLR----------FCLCGHCWSKIH   46 (119)
Q Consensus        21 P~~C~~C~~~~~~~----------~~lC~~C~~~l~   46 (119)
                      |..|=+||..+...          -.+|.+|..++-
T Consensus         6 ~~yCEiCG~~i~g~~~~v~ieGael~VC~~C~~K~g   41 (175)
T PRK08359          6 PKYCELCGREIRGPGHRIRIEGAELLVCDDCYRKYG   41 (175)
T ss_pred             CCEEECCCCCCCCCCEEEEECCEEEHHHHHHHHHHC
T ss_conf             865447998034880699989988725767899868


No 33 
>PRK10410 hypothetical protein; Provisional
Probab=38.27  E-value=20  Score=17.26  Aligned_cols=73  Identities=10%  Similarity=0.069  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCEECHHHHHHCCC-----------CCCCCCCCCCCCCCCCCCCHHHHCCCCCH
Q ss_conf             9999999999857874710375156577028889950867-----------67862012444653347608985167843
Q gi|254780310|r    8 VKSIIIELFHCIYPSICPIYSRIINLRFCLCGHCWSKIHF-----------ITATEHILKNNKDNIDKDPLKSMQKDLPL   76 (119)
Q Consensus         8 ik~~~~~ll~~lfP~~C~~C~~~~~~~~~lC~~C~~~l~~-----------i~~~~C~~Cg~~~~~~~~C~~C~~~~~~f   76 (119)
                      =+.++..++.+       .|..-.. ...||++|.+-+.+           .+-|+|..|-      ..|.    .+...
T Consensus         9 E~~ti~~MI~l-------YC~~~H~-~~~lC~eC~~L~~YA~~Rl~~Cp~ge~Kp~C~~C~------iHCY----~p~~r   70 (114)
T PRK10410          9 EKKTIKKMIRL-------YCKKHHQ-ASALCPECEELLEYAQKRLDKCPFGEEKPTCKQCP------VHCY----KPAKR   70 (114)
T ss_pred             HHHHHHHHHHH-------HHHHCCC-CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC------CCCC----CHHHH
T ss_conf             99999999999-------9982688-88888999999999999996399999998888899------7779----98999


Q ss_pred             HHHHHHHCCCHH---HHHHHHHHHH
Q ss_conf             530120002127---9999999744
Q gi|254780310|r   77 TQIRSVTLYCDM---SCVLVRLLKY   98 (119)
Q Consensus        77 ~~~~a~~~Y~~~---~r~lI~~~Ky   98 (119)
                      .+.+.+..|.|+   .++-|..+++
T Consensus        71 ~~ir~VMr~sGPRMl~~hPi~ai~H   95 (114)
T PRK10410         71 EKIKQIMRWSGPRMLWRHPILAVRH   95 (114)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             9999999861740888679999999


No 34 
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=38.12  E-value=29  Score=16.32  Aligned_cols=12  Identities=25%  Similarity=0.664  Sum_probs=5.3

Q ss_pred             CCEECHHHHHHC
Q ss_conf             770288899508
Q gi|254780310|r   34 RFCLCGHCWSKI   45 (119)
Q Consensus        34 ~~~lC~~C~~~l   45 (119)
                      +..+|++|..++
T Consensus       100 D~a~C~~Cl~Ei  111 (750)
T COG0068         100 DAATCEDCLEEI  111 (750)
T ss_pred             CHHHHHHHHHHH
T ss_conf             502149999985


No 35 
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=37.87  E-value=13  Score=18.20  Aligned_cols=27  Identities=11%  Similarity=-0.001  Sum_probs=18.3

Q ss_pred             CCEECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             770288899508676786201244465
Q gi|254780310|r   34 RFCLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus        34 ~~~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      ....|..|....+.-.++.|+|||.+.
T Consensus       219 ~~~~C~~C~~~~~~~~~~~CpRC~~~L  245 (418)
T COG2995         219 GLRSCLCCHYILPHDAEPRCPRCGSKL  245 (418)
T ss_pred             CCEECCCCCCCCCHHHCCCCCCCCCHH
T ss_conf             213536343447875578888778802


No 36 
>KOG1512 consensus
Probab=37.47  E-value=15  Score=17.98  Aligned_cols=55  Identities=16%  Similarity=0.097  Sum_probs=33.0

Q ss_pred             CCCCCCCCCC-CCCEECHHHHHHCCCCCCCCCCCCCCCCCCCCCCH-HHHCCCCCHHHHHH
Q ss_conf             4710375156-57702888995086767862012444653347608-98516784353012
Q gi|254780310|r   23 ICPIYSRIIN-LRFCLCGHCWSKIHFITATEHILKNNKDNIDKDPL-KSMQKDLPLTQIRS   81 (119)
Q Consensus        23 ~C~~C~~~~~-~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~~C~-~C~~~~~~f~~~~a   81 (119)
                      .|.+|+++.. .+..+|.-|-...+    .+|.--+.--.+...|+ .|....+++.+-.+
T Consensus       316 lC~IC~~P~~E~E~~FCD~CDRG~H----T~CVGL~~lP~G~WICD~~C~~~~~~t~R~~s  372 (381)
T KOG1512         316 LCRICLGPVIESEHLFCDVCDRGPH----TLCVGLQDLPRGEWICDMRCREATLNTTRQSS  372 (381)
T ss_pred             HHHHCCCCCCHHHEEEEECCCCCCC----EEEEECCCCCCCCEEECCHHHHHCCCCCHHHH
T ss_conf             1121388543012244200057662----35532264788766602377875689853666


No 37 
>pfam06906 DUF1272 Protein of unknown function (DUF1272). This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=37.36  E-value=25  Score=16.73  Aligned_cols=37  Identities=11%  Similarity=0.059  Sum_probs=24.6

Q ss_pred             CCCCCCCCCCCCCCC----------EECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             874710375156577----------0288899508676786201244465
Q gi|254780310|r   21 PSICPIYSRIINLRF----------CLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus        21 P~~C~~C~~~~~~~~----------~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      -+.|--|++.+..+.          -+|.+|...+-   ...|+.||-.+
T Consensus         5 rpnCE~C~~dLppds~~A~ICsfECTFC~~C~~~~l---~~~CPNCgGel   51 (57)
T pfam06906         5 RPNCECCDRDLPPDSPDARICSFECTFCADCAETRL---HGVCPNCGGEL   51 (57)
T ss_pred             CCCCCCCCCCCCCCCCCCEEEEEECEECHHHHHHHH---CCCCCCCCCCC
T ss_conf             668655699899998887788785612678997886---68484998812


No 38 
>pfam10083 DUF2321 Uncharacterized protein conserved in bacteria (DUF2321). Members of this family of hypothetical bacterial proteins have no known function.
Probab=36.46  E-value=12  Score=18.37  Aligned_cols=11  Identities=0%  Similarity=-0.423  Sum_probs=5.4

Q ss_pred             CCCCCCCCCCC
Q ss_conf             86201244465
Q gi|254780310|r   50 ATEHILKNNKD   60 (119)
Q Consensus        50 ~~~C~~Cg~~~   60 (119)
                      +.+|..||.|+
T Consensus        68 PsyC~nCG~py   78 (158)
T pfam10083        68 PSYCHNCGKPF   78 (158)
T ss_pred             CHHHHHCCCCC
T ss_conf             54687479988


No 39 
>pfam03854 zf-P11 P-11 zinc finger.
Probab=36.00  E-value=13  Score=18.24  Aligned_cols=32  Identities=9%  Similarity=0.159  Sum_probs=23.9

Q ss_pred             CCC-CCCEECHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             156-577028889950867678620124446533
Q gi|254780310|r   30 IIN-LRFCLCGHCWSKIHFITATEHILKNNKDNI   62 (119)
Q Consensus        30 ~~~-~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~   62 (119)
                      .+. +++.||-.|...|-- ...+|+.|+.|+..
T Consensus        15 Li~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LPt   47 (50)
T pfam03854        15 LVTCSDHYLCLRCLQLLLS-VSERCPICKKPLPT   47 (50)
T ss_pred             EEEECCHHHHHHHHHHHHC-CCCCCCCCCCCCCC
T ss_conf             2213420449999999973-05677624675765


No 40 
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer.  Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain.  Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=35.03  E-value=21  Score=17.15  Aligned_cols=25  Identities=12%  Similarity=0.157  Sum_probs=14.6

Q ss_pred             CCCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             47103751565770288899508676786201244465
Q gi|254780310|r   23 ICPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus        23 ~C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      .|.+||-....+.             .+-.||.||.+.
T Consensus         3 ~C~vCGyi~~~~~-------------~p~~CP~Cg~~k   27 (33)
T cd00350           3 VCPVCGYIYDGEE-------------APWVCPVCGAPK   27 (33)
T ss_pred             CCCCCCCEEECCC-------------CCCCCCCCCCCH
T ss_conf             8886998875786-------------987287889978


No 41 
>KOG3002 consensus
Probab=34.25  E-value=25  Score=16.72  Aligned_cols=35  Identities=14%  Similarity=0.248  Sum_probs=24.6

Q ss_pred             CCCCCCCCCC-------CCCEECHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             4710375156-------57702888995086767862012444653
Q gi|254780310|r   23 ICPIYSRIIN-------LRFCLCGHCWSKIHFITATEHILKNNKDN   61 (119)
Q Consensus        23 ~C~~C~~~~~-------~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~   61 (119)
                      .|++|...+.       +++.+|.+|..++.    ..||.|..+.+
T Consensus        50 eCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~----~~CP~Cr~~~g   91 (299)
T KOG3002          50 DCPVCFNPLSPPIFQCDNGHLACSSCRTKVS----NKCPTCRLPIG   91 (299)
T ss_pred             CCCHHHCCCCCCCEECCCCCEEHHHHHHHHC----CCCCCCCCCCC
T ss_conf             6950316476653724888675654334540----55986545565


No 42 
>pfam08772 NOB1_Zn_bind Nin one binding (NOB1) Zn-ribbon like. This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1.
Probab=33.84  E-value=13  Score=18.32  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=15.8

Q ss_pred             ECHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             28889950867678620124446
Q gi|254780310|r   37 LCGHCWSKIHFITATEHILKNNK   59 (119)
Q Consensus        37 lC~~C~~~l~~i~~~~C~~Cg~~   59 (119)
                      .|..|+.-.+-.+..+|+.||..
T Consensus        11 rC~aCf~~t~~~~k~FCpkCGn~   33 (73)
T pfam08772        11 RCHACFKTTPDMTKQFCPKCGNA   33 (73)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCC
T ss_conf             54232348489766127536999


No 43 
>KOG2660 consensus
Probab=33.73  E-value=23  Score=16.90  Aligned_cols=65  Identities=11%  Similarity=-0.030  Sum_probs=34.0

Q ss_pred             HHHCCCCCCCCCCCCCC-CC------EECHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHHCCCHHH
Q ss_conf             98578747103751565-77------028889950867678620124446533476089851678435301200021279
Q gi|254780310|r   17 HCIYPSICPIYSRIINL-RF------CLCGHCWSKIHFITATEHILKNNKDNIDKDPLKSMQKDLPLTQIRSVTLYCDMS   89 (119)
Q Consensus        17 ~~lfP~~C~~C~~~~~~-~~------~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~~C~~C~~~~~~f~~~~a~~~Y~~~~   89 (119)
                      ++-.=-.|.+|++.+-. ..      .+|.+|.-+- +....+|+.|+.-......          ...    -.++..+
T Consensus        11 ~~n~~itC~LC~GYliDATTI~eCLHTFCkSCIvk~-l~~~~~CP~C~i~ih~t~p----------l~n----i~~Drtl   75 (331)
T KOG2660          11 ELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKY-LEESKYCPTCDIVIHKTHP----------LLN----IRSDRTL   75 (331)
T ss_pred             HCCCCEECCCCCCEEECCHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCEECCCCCC----------CCC----CCCCHHH
T ss_conf             136410203154644443018999998889999999-9861678766325267554----------124----7700489


Q ss_pred             HHHHHHH
Q ss_conf             9999997
Q gi|254780310|r   90 CVLVRLL   96 (119)
Q Consensus        90 r~lI~~~   96 (119)
                      |++|.+|
T Consensus        76 qdiVyKL   82 (331)
T KOG2660          76 QDIVYKL   82 (331)
T ss_pred             HHHHHHH
T ss_conf             9999997


No 44 
>KOG1813 consensus
Probab=32.70  E-value=28  Score=16.38  Aligned_cols=44  Identities=14%  Similarity=0.264  Sum_probs=30.1

Q ss_pred             HHHCCCCCCCCCCCCC------CCCEECHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             9857874710375156------57702888995086767862012444653
Q gi|254780310|r   17 HCIYPSICPIYSRIIN------LRFCLCGHCWSKIHFITATEHILKNNKDN   61 (119)
Q Consensus        17 ~~lfP~~C~~C~~~~~------~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~   61 (119)
                      ..++|-.|.+|++...      -.+.+|..|..+ ++...+.|..|+....
T Consensus       237 ~~~~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~-~~qk~~~c~vC~~~t~  286 (313)
T KOG1813         237 IELLPFKCFICRKYFYRPVVTKCGHYFCEVCALK-PYQKGEKCYVCSQQTH  286 (313)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCCEEEHHHHCC-CCCCCCCCEECCCCCC
T ss_conf             4347754341034334644332786455122034-2036983334160104


No 45 
>pfam05810 NinF NinF protein. This family consists of several bacteriophage NinF proteins as well as related sequences from E. coli.
Probab=31.69  E-value=25  Score=16.70  Aligned_cols=22  Identities=14%  Similarity=0.463  Sum_probs=17.3

Q ss_pred             CCCCCCCCC-CCCEECHHHHHHC
Q ss_conf             710375156-5770288899508
Q gi|254780310|r   24 CPIYSRIIN-LRFCLCGHCWSKI   45 (119)
Q Consensus        24 C~~C~~~~~-~~~~lC~~C~~~l   45 (119)
                      |..|++.+. .+..+|.+|-.++
T Consensus        20 CA~C~kqL~~~Ev~~C~eC~~E~   42 (58)
T pfam05810        20 CAGCGKQLHPDEVHVCEECVAEA   42 (58)
T ss_pred             HHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             81714135704887899999999


No 46 
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=31.16  E-value=9.2  Score=19.08  Aligned_cols=36  Identities=11%  Similarity=0.101  Sum_probs=17.8

Q ss_pred             CCCCCCCCCCC----CCCEECHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             74710375156----577028889950867678620124446
Q gi|254780310|r   22 SICPIYSRIIN----LRFCLCGHCWSKIHFITATEHILKNNK   59 (119)
Q Consensus        22 ~~C~~C~~~~~----~~~~lC~~C~~~l~~i~~~~C~~Cg~~   59 (119)
                      ..|+-|+..+.    .....|..|-.+-+  .+..|+.||..
T Consensus       445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~--~p~~Cp~Cgs~  484 (730)
T COG1198         445 AECPNCDSPLTLHKATGQLRCHYCGYQEP--IPQSCPECGSE  484 (730)
T ss_pred             CCCCCCCCCEEEECCCCEEEECCCCCCCC--CCCCCCCCCCC
T ss_conf             24899995127864798067077999899--88779899997


No 47 
>PRK08620 DNA topoisomerase III; Provisional
Probab=30.48  E-value=46  Score=15.21  Aligned_cols=58  Identities=17%  Similarity=0.273  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHH------C------CCCCCCCCCCCC-----CC-CEECHH--HH--HHCCCCCCCCCCCCCCCCC
Q ss_conf             9999999999999985------7------874710375156-----57-702888--99--5086767862012444653
Q gi|254780310|r    4 IIQTVKSIIIELFHCI------Y------PSICPIYSRIIN-----LR-FCLCGH--CW--SKIHFITATEHILKNNKDN   61 (119)
Q Consensus         4 ~~~~ik~~~~~ll~~l------f------P~~C~~C~~~~~-----~~-~~lC~~--C~--~~l~~i~~~~C~~Cg~~~~   61 (119)
                      +++.++..+.++++-+      |      -..|+-||..+-     .+ ...|++  |.  ..+...++..||.||....
T Consensus       580 fi~~~~~~~~~~v~~~k~~~~~~~~~~~t~~~Cp~Cg~~m~~~~gr~Gkf~~C~~peC~~~k~~~~~~~~~Cp~C~~~~~  659 (726)
T PRK08620        580 FINEMKNYTKKVVNEIKNSDKKYKHDNLTGTKCPDCGKFMLEVKGKNGKMLVCQDRECGHRKNVSRKTNARCPNCKKKLE  659 (726)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCEEE
T ss_conf             99999999999999997401442457778985642683211685898755746899899977710212894999998568


No 48 
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=29.80  E-value=45  Score=15.28  Aligned_cols=38  Identities=8%  Similarity=0.149  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHCCC---CCCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99999999985787---47103751565770288899508676786201244465
Q gi|254780310|r    9 KSIIIELFHCIYPS---ICPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus         9 k~~~~~ll~~lfP~---~C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      ..+++.+|+.+.-.   +|++||-....+              .+-.||.||.|.
T Consensus       119 ~~~~~~~Le~~~~~~~~vC~vCGy~~~ge--------------~P~~CPiCga~k  159 (166)
T COG1592         119 AEMFRGLLERLEEGKVWVCPVCGYTHEGE--------------APEVCPICGAPK  159 (166)
T ss_pred             HHHHHHHHHHHHCCCEEECCCCCCCCCCC--------------CCCCCCCCCCHH
T ss_conf             99999999866038778768788812689--------------987699999818


No 49 
>pfam10146 zf-C4H2 Zinc finger-containing protein. This is a family of proteins which appears to have a highly conserved zinc finger domain at the C terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members are annotated as being tumour-associated antigen HCA127 in humans but this could not confirmed.
Probab=29.14  E-value=9.5  Score=19.01  Aligned_cols=21  Identities=29%  Similarity=0.414  Sum_probs=15.7

Q ss_pred             ECHHHHHHCCCCCCCCCCCCCC
Q ss_conf             2888995086767862012444
Q gi|254780310|r   37 LCGHCWSKIHFITATEHILKNN   58 (119)
Q Consensus        37 lC~~C~~~l~~i~~~~C~~Cg~   58 (119)
                      .|.+|..+++. +.|.|+.|-.
T Consensus       186 ~ClSChQQIHR-NAPICPlCKA  206 (220)
T pfam10146       186 VCLSCHQQIHR-NAPICPLCKA  206 (220)
T ss_pred             HHHHHHHHHHC-CCCCCCCCCC
T ss_conf             66618988855-7977742334


No 50 
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=29.09  E-value=14  Score=18.14  Aligned_cols=23  Identities=9%  Similarity=-0.026  Sum_probs=14.1

Q ss_pred             ECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             288899508676786201244465
Q gi|254780310|r   37 LCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus        37 lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      .|..|...++ .+..+|+.||.+.
T Consensus       141 rC~GC~~~f~-~~~~~Cp~CG~~~  163 (177)
T COG1439         141 RCHGCKRIFP-EPKDFCPICGSPL  163 (177)
T ss_pred             EEECCCEECC-CCCCCCCCCCCCE
T ss_conf             9845752508-9888077899911


No 51 
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=28.82  E-value=15  Score=17.96  Aligned_cols=43  Identities=14%  Similarity=0.148  Sum_probs=22.7

Q ss_pred             CCCCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             747103751565770288899508676786201244465334760898
Q gi|254780310|r   22 SICPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKDNIDKDPLKS   69 (119)
Q Consensus        22 ~~C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~~C~~C   69 (119)
                      .+||-||..  +-..+|+.|=+....  ..+||.|....+. ..|..|
T Consensus       680 ~~CP~Cgk~--s~~~~Cp~CG~~te~--~~~gPsCrmknts-svCesC  722 (1173)
T TIGR00354       680 AKCPSCGKE--SLYRVCPVCGEKTEL--DEYGPSCRMKNTS-SVCESC  722 (1173)
T ss_pred             CCCCCCCCC--CEEEECCCCCCEEEE--CCCCCCCCCCCCC-CHHHCC
T ss_conf             218876640--000145778854544--5778853003542-022105


No 52 
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=27.08  E-value=53  Score=14.90  Aligned_cols=25  Identities=24%  Similarity=0.416  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             8999999999999998578747103751
Q gi|254780310|r    3 AIIQTVKSIIIELFHCIYPSICPIYSRI   30 (119)
Q Consensus         3 ~~~~~ik~~~~~ll~~lfP~~C~~C~~~   30 (119)
                      ++.+.++.+-...-+   +..|+.|++.
T Consensus        20 ~~Rrrv~~ie~~~~~---~~~Cp~C~~~   44 (89)
T COG1997          20 KLRRRVKEIEAQQRA---KHVCPFCGRT   44 (89)
T ss_pred             HHHHHHHHHHHHHHC---CCCCCCCCCC
T ss_conf             899999999999854---7769978974


No 53 
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1; InterPro: IPR004575   MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle . CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 .    The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus.
Probab=26.68  E-value=34  Score=15.97  Aligned_cols=39  Identities=15%  Similarity=0.293  Sum_probs=26.1

Q ss_pred             CCCCCCCC--C-------CCC---CCEECHHHHHHCCCCCC-CCCC--CCCCCCC
Q ss_conf             74710375--1-------565---77028889950867678-6201--2444653
Q gi|254780310|r   22 SICPIYSR--I-------INL---RFCLCGHCWSKIHFITA-TEHI--LKNNKDN   61 (119)
Q Consensus        22 ~~C~~C~~--~-------~~~---~~~lC~~C~~~l~~i~~-~~C~--~Cg~~~~   61 (119)
                      ..||.|..  .       +-+   ++-||.+|-.-| |+.+ ..||  -|+.|+.
T Consensus         9 d~CPrCKTtkYrnPslKLlVNPvCGHtLCESCVdlL-F~~Gsg~CPyk~C~~pLR   62 (322)
T TIGR00570         9 DACPRCKTTKYRNPSLKLLVNPVCGHTLCESCVDLL-FVRGSGSCPYKECDTPLR   62 (322)
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCCCHHHHHHH-HHCCCCCCCCCCCCCCCC
T ss_conf             788887766666886422227866560104478888-734888888546787443


No 54 
>pfam05290 Baculo_IE-1 Baculovirus immediate-early protein (IE-0). The Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is thought to play a central role in stimulating early viral transcription. IE-1 has been demonstrated to activate several early viral gene promoters and to negatively regulate the promoters of two other AcMNPV regulatory genes, ie-0 and ie-2. It is thought that that IE-1 negatively regulates the expression of certain genes by binding directly, or as part of a complex, to promoter regions containing a specific IE-1-binding motif (5'-ACBYGTAA-3') near their mRNA start sites.
Probab=26.58  E-value=54  Score=14.82  Aligned_cols=45  Identities=11%  Similarity=0.210  Sum_probs=28.6

Q ss_pred             HHCCC--CCCCCCCCCCCCC----------EECHHHHHHCCCC--CCCCCCCCCCCCCC
Q ss_conf             85787--4710375156577----------0288899508676--78620124446533
Q gi|254780310|r   18 CIYPS--ICPIYSRIINLRF----------CLCGHCWSKIHFI--TATEHILKNNKDNI   62 (119)
Q Consensus        18 ~lfP~--~C~~C~~~~~~~~----------~lC~~C~~~l~~i--~~~~C~~Cg~~~~~   62 (119)
                      |+=|+  .|-+|......++          .+|..|..+|...  ..|.||.|...+..
T Consensus        75 F~d~~lYeCnIC~etS~e~~FLKPnECCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs  133 (141)
T pfam05290        75 FLEPKLYQCNICQDTSAEEHFLKPNECCGYKICNLCYANLWKFCTVYPVCPVCKTSFKS  133 (141)
T ss_pred             CCCCCCEEECCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             04887146037534330120379633424059999999999874558778866676567


No 55 
>PRK01343 zinc-binding protein; Provisional
Probab=26.02  E-value=33  Score=15.99  Aligned_cols=12  Identities=17%  Similarity=0.346  Sum_probs=7.7

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             874710375156
Q gi|254780310|r   21 PSICPIYSRIIN   32 (119)
Q Consensus        21 P~~C~~C~~~~~   32 (119)
                      ++.|++|++...
T Consensus         9 ~~~CPiC~k~~~   20 (56)
T PRK01343          9 TRPCPECGKPST   20 (56)
T ss_pred             CCCCCCCCCCCC
T ss_conf             998988899774


No 56 
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308   These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=25.47  E-value=26  Score=16.61  Aligned_cols=29  Identities=21%  Similarity=0.272  Sum_probs=16.2

Q ss_pred             CCEECHHHHHHCCCCC-----------CCCCCCCC--CCCCCC
Q ss_conf             7702888995086767-----------86201244--465334
Q gi|254780310|r   34 RFCLCGHCWSKIHFIT-----------ATEHILKN--NKDNID   63 (119)
Q Consensus        34 ~~~lC~~C~~~l~~i~-----------~~~C~~Cg--~~~~~~   63 (119)
                      .+.+|+.|.. .+|++           +--||+||  .|+..+
T Consensus       716 PHY~Cp~Cky-~Ef~~D~~~~~GfDLp~K~CP~Cgak~pl~kD  757 (1264)
T TIGR01405       716 PHYLCPNCKY-SEFVTDGSVGSGFDLPDKDCPKCGAKAPLKKD  757 (1264)
T ss_pred             CCCCCCCCCE-EEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             8750878735-53003787788776857888888877763457


No 57 
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.93  E-value=23  Score=16.90  Aligned_cols=23  Identities=17%  Similarity=0.271  Sum_probs=15.0

Q ss_pred             CCCCCCCCCCCC--CCCEECHHHHH
Q ss_conf             874710375156--57702888995
Q gi|254780310|r   21 PSICPIYSRIIN--LRFCLCGHCWS   43 (119)
Q Consensus        21 P~~C~~C~~~~~--~~~~lC~~C~~   43 (119)
                      =-+|+.||.++=  .+..+|+.|..
T Consensus        28 ~~hCp~Cg~PLF~KdG~v~CPvC~~   52 (131)
T COG1645          28 AKHCPKCGTPLFRKDGEVFCPVCGY   52 (131)
T ss_pred             HHHCCCCCCCCEEECCEEECCCCCC
T ss_conf             7448655883163089587777776


No 58 
>KOG1842 consensus
Probab=24.66  E-value=15  Score=17.86  Aligned_cols=11  Identities=27%  Similarity=0.682  Sum_probs=7.0

Q ss_pred             EECHHHHHHCC
Q ss_conf             02888995086
Q gi|254780310|r   36 CLCGHCWSKIH   46 (119)
Q Consensus        36 ~lC~~C~~~l~   46 (119)
                      .+|.+|...++
T Consensus       205 VmC~~C~k~iS  215 (505)
T KOG1842         205 VMCRDCSKFIS  215 (505)
T ss_pred             HHHHHHHHHCC
T ss_conf             77888887468


No 59 
>KOG2613 consensus
Probab=23.46  E-value=46  Score=15.19  Aligned_cols=71  Identities=17%  Similarity=0.061  Sum_probs=35.7

Q ss_pred             CCCCCCCCCC-CCEECHHHHHHCCCCCCCCCCCCCCCC-CCCCCCHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHHCC
Q ss_conf             7103751565-770288899508676786201244465-334760898516-7843530120002127999999974478
Q gi|254780310|r   24 CPIYSRIINL-RFCLCGHCWSKIHFITATEHILKNNKD-NIDKDPLKSMQK-DLPLTQIRSVTLYCDMSCVLVRLLKYHD  100 (119)
Q Consensus        24 C~~C~~~~~~-~~~lC~~C~~~l~~i~~~~C~~Cg~~~-~~~~~C~~C~~~-~~~f~~~~a~~~Y~~~~r~lI~~~Ky~~  100 (119)
                      |--||-++++ ..-.|.+|...-.-|+..      .|- .....|..|-+- .||=.+.++.+.-.+-+.-.+.++|--+
T Consensus        17 CCeCGvpi~Pn~anMC~~Clrs~VDITeg------ipr~~~i~~Cr~CeRYlqPP~~Wi~a~leSrELLaiclkklK~L~   90 (502)
T KOG2613          17 CCECGVPIEPNPANMCVDCLRSEVDITEG------IPRQATISFCRECERYLQPPKTWIRAELESRELLAICLKKLKGLN   90 (502)
T ss_pred             EECCCCCCCCCHHHHHHHHHHEEEEHHCC------CCCHHHHHHCCCCCEECCCCHHHHHHHHCCHHHHHHHHHHHCCCC
T ss_conf             94379867986678899876403015038------850001000216610047937776211111789999998615766


No 60 
>TIGR02688 TIGR02688 conserved hypothetical protein TIGR02688; InterPro: IPR014061   Members of this entry are uncharacterised proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families IPR004815 from INTERPRO (ATP-dependent protease La) or IPR003111 from INTERPRO (ATP-dependent protease La (LON) domain). The proteins in this entry are encoded by genes repeatedly found downstream of another gene that encodes an uncharacterised protein of about 880 amino acids in length (see IPR014060 from INTERPRO)..
Probab=23.19  E-value=62  Score=14.48  Aligned_cols=19  Identities=21%  Similarity=0.509  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHHCCCC
Q ss_conf             9999999999999857874
Q gi|254780310|r    5 IQTVKSIIIELFHCIYPSI   23 (119)
Q Consensus         5 ~~~ik~~~~~ll~~lfP~~   23 (119)
                      .++||.+.+.++.+|||..
T Consensus       417 ~~avk~~~SGl~KlLFPh~  435 (470)
T TIGR02688       417 VKAVKKLFSGLLKLLFPHG  435 (470)
T ss_pred             HHHHHHHHHHHHHHHCCCC
T ss_conf             6789999877766416898


No 61 
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=23.05  E-value=22  Score=16.96  Aligned_cols=15  Identities=27%  Similarity=0.481  Sum_probs=12.1

Q ss_pred             HCCCCCCCCCCCCCC
Q ss_conf             578747103751565
Q gi|254780310|r   19 IYPSICPIYSRIINL   33 (119)
Q Consensus        19 lfP~~C~~C~~~~~~   33 (119)
                      ++|-+|..||+.+++
T Consensus         2 iiPiRCFsCGkvi~~   16 (63)
T COG1644           2 IIPVRCFSCGKVIGH   16 (63)
T ss_pred             CCCEEEECCCCCHHH
T ss_conf             885375238878788


No 62 
>PRK07220 DNA topoisomerase I; Validated
Probab=23.00  E-value=59  Score=14.62  Aligned_cols=83  Identities=10%  Similarity=-0.017  Sum_probs=45.0

Q ss_pred             CCCCCCCCCC-----CC-C-EECH---HHHHHCCCC-------CCCCCCCCCCCCC---------CCCCCHHHHCCC---
Q ss_conf             4710375156-----57-7-0288---899508676-------7862012444653---------347608985167---
Q gi|254780310|r   23 ICPIYSRIIN-----LR-F-CLCG---HCWSKIHFI-------TATEHILKNNKDN---------IDKDPLKSMQKD---   73 (119)
Q Consensus        23 ~C~~C~~~~~-----~~-~-~lC~---~C~~~l~~i-------~~~~C~~Cg~~~~---------~~~~C~~C~~~~---   73 (119)
                      .|+.||..+-     .+ . .=|.   +|...+|.-       ++-.|+.||.+.-         ....|..|.-..   
T Consensus       591 ~CP~Cg~~l~~r~~k~g~~FigCs~YP~C~~t~pLp~~g~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~cp~c~~~~~~~  670 (740)
T PRK07220        591 KCSLCGSELMVRRSKRGSRFIGCSGYPNCTFSLPLPKSGQIIVTDKVCEAHGLHHIKIINGGKRPWDLGCPQCNFIEWQK  670 (740)
T ss_pred             CCCCCCCCCEEEECCCCCEEEECCCCCCCCCCEECCCCCCEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCHHHHC
T ss_conf             78889960047745879978858989999985226999846347886877998379998089875767899877601301


Q ss_pred             ---------CCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHH
Q ss_conf             ---------84353012000212799999997447876699
Q gi|254780310|r   74 ---------LPLTQIRSVTLYCDMSCVLVRLLKYHDRTDLA  105 (119)
Q Consensus        74 ---------~~f~~~~a~~~Y~~~~r~lI~~~Ky~~~~~la  105 (119)
                               |.-...-+.-.-+|......-+++-++-..+.
T Consensus       671 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  711 (740)
T PRK07220        671 TQKEEQAQQPKKEKPKSIKDIEGVGKATAGKLEEAGITTVE  711 (740)
T ss_pred             HHHHHHHCCCCCCCCCHHHCCCCCCHHHHHHHHHCCCCCHH
T ss_conf             12455431544568520121556588999999976887599


No 63 
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=22.95  E-value=13  Score=18.19  Aligned_cols=31  Identities=19%  Similarity=0.450  Sum_probs=22.2

Q ss_pred             HHHHCCCCCCCCCCCCCCCC---E-ECHHHHHHCC
Q ss_conf             99857874710375156577---0-2888995086
Q gi|254780310|r   16 FHCIYPSICPIYSRIINLRF---C-LCGHCWSKIH   46 (119)
Q Consensus        16 l~~lfP~~C~~C~~~~~~~~---~-lC~~C~~~l~   46 (119)
                      +..||-.-|+.||+.++++.   + -|+.|..+.+
T Consensus         2 ~~~vy~~lCPNCGG~i~~eRL~kGLPC~kCLP~~~   36 (1843)
T TIGR01054         2 IPAVYKELCPNCGGEISSERLEKGLPCEKCLPEEP   36 (1843)
T ss_pred             CHHHHHCCCCCCCCCCCHHHHHCCCCCCCCCCCCC
T ss_conf             40046348898989877898735788864578767


No 64 
>pfam08274 PhnA_Zn_Ribbon PhnA Zinc-Ribbon.
Probab=22.81  E-value=29  Score=16.31  Aligned_cols=24  Identities=17%  Similarity=0.472  Sum_probs=14.4

Q ss_pred             CCCCCCCCCC---CCCCEECHHHHHHC
Q ss_conf             7471037515---65770288899508
Q gi|254780310|r   22 SICPIYSRII---NLRFCLCGHCWSKI   45 (119)
Q Consensus        22 ~~C~~C~~~~---~~~~~lC~~C~~~l   45 (119)
                      +.|+.|+...   ..+..+|++|-.+.
T Consensus         3 P~Cp~C~seytY~d~~~~vCpeC~hEw   29 (30)
T pfam08274         3 PKCPLCNSEYTYEDGALLVCPECAHEW   29 (30)
T ss_pred             CCCCCCCCCCEECCCCEEECCCCCCCC
T ss_conf             878878981247479997997545656


No 65 
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=22.72  E-value=32  Score=16.11  Aligned_cols=41  Identities=15%  Similarity=0.332  Sum_probs=25.4

Q ss_pred             CCCCCCCCCC--C--------CCEECHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             4710375156--5--------770288899508676786201244465334
Q gi|254780310|r   23 ICPIYSRIIN--L--------RFCLCGHCWSKIHFITATEHILKNNKDNID   63 (119)
Q Consensus        23 ~C~~C~~~~~--~--------~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~   63 (119)
                      .|++|=.++.  .        +..+|.-||..+...-...|+.|.+..+.+
T Consensus        16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHCCCC
T ss_conf             474115643245677565776218999999888765058883765423434


No 66 
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=22.67  E-value=31  Score=16.16  Aligned_cols=24  Identities=25%  Similarity=0.580  Sum_probs=12.9

Q ss_pred             CCCCCCCCCC--CCCEECHHHHHHCC
Q ss_conf             4710375156--57702888995086
Q gi|254780310|r   23 ICPIYSRIIN--LRFCLCGHCWSKIH   46 (119)
Q Consensus        23 ~C~~C~~~~~--~~~~lC~~C~~~l~   46 (119)
                      +|..||++-+  ....||--|+.++-
T Consensus        23 RC~~cGRprgv~Rkf~lcR~cfRE~A   48 (61)
T COG0199          23 RCRRCGRPRGVIRKFGLCRICFRELA   48 (61)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             13036997323355543799999986


No 67 
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=21.73  E-value=26  Score=16.60  Aligned_cols=31  Identities=29%  Similarity=0.447  Sum_probs=20.7

Q ss_pred             HHHHCCCCCCCCCCCCCCCC---EE-CHHHHHHCC
Q ss_conf             99857874710375156577---02-888995086
Q gi|254780310|r   16 FHCIYPSICPIYSRIINLRF---CL-CGHCWSKIH   46 (119)
Q Consensus        16 l~~lfP~~C~~C~~~~~~~~---~l-C~~C~~~l~   46 (119)
                      ...+|-..|+.||..++++.   .+ |..|..+-+
T Consensus         3 ~~~iY~~~CpNCGG~isseRL~~glpCe~CLp~~~   37 (1187)
T COG1110           3 PNAIYGSSCPNCGGDISSERLEKGLPCERCLPEDT   37 (1187)
T ss_pred             CHHHHHCCCCCCCCCCCHHHHHCCCCCHHCCCCCC
T ss_conf             46566256998899675778745998332068864


No 68 
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.66  E-value=25  Score=16.65  Aligned_cols=52  Identities=10%  Similarity=0.077  Sum_probs=28.5

Q ss_pred             HCCCCCCCCCCCCCCCCEECHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCC
Q ss_conf             578747103751565770288899508676786201244465334760898516784
Q gi|254780310|r   19 IYPSICPIYSRIINLRFCLCGHCWSKIHFITATEHILKNNKDNIDKDPLKSMQKDLP   75 (119)
Q Consensus        19 lfP~~C~~C~~~~~~~~~lC~~C~~~l~~i~~~~C~~Cg~~~~~~~~C~~C~~~~~~   75 (119)
                      +..++|+-||...  -...|+.|-..-.  ....|+.||.... ...|..|......
T Consensus       631 vg~R~Cp~Cg~eT--~~~~C~~CG~~T~--~~~~c~~C~~~~~-~~~c~~c~~~~~~  682 (1128)
T PRK04023        631 VGNRKCPSCGKET--FYRRCPFCGTHTE--PVYRCPRCGIEVD-EEVCPKCGREPTG  682 (1128)
T ss_pred             EEEEECCCCCCCC--CCCCCCCCCCCCC--CCCCCCCCCCCCC-CCCCCCCCCCCCC
T ss_conf             8202889999835--7557877799665--4324776666556-6535445776777


No 69 
>pfam11290 DUF3090 Protein of unknown function (DUF3090). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.20  E-value=45  Score=15.26  Aligned_cols=13  Identities=8%  Similarity=-0.192  Sum_probs=8.2

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             8620124446533
Q gi|254780310|r   50 ATEHILKNNKDNI   62 (119)
Q Consensus        50 ~~~C~~Cg~~~~~   62 (119)
                      .|.|+.||.|.+-
T Consensus       154 Rp~Cp~Cg~Pidp  166 (171)
T pfam11290       154 RPPCPLCGQPLDP  166 (171)
T ss_pred             CCCCCCCCCCCCC
T ss_conf             9999988997699


No 70 
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=21.07  E-value=41  Score=15.51  Aligned_cols=37  Identities=16%  Similarity=0.333  Sum_probs=22.7

Q ss_pred             CCCCCCCC--CCCCCC----------EECHHHHHHCCCCCCCCCC--CCCC
Q ss_conf             74710375--156577----------0288899508676786201--2444
Q gi|254780310|r   22 SICPIYSR--IINLRF----------CLCGHCWSKIHFITATEHI--LKNN   58 (119)
Q Consensus        22 ~~C~~C~~--~~~~~~----------~lC~~C~~~l~~i~~~~C~--~Cg~   58 (119)
                      .+|++|..  .+..+-          -+|.+|...+--..+..||  -||.
T Consensus        11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220          11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             CCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH
T ss_conf             248854445414888479978999999999999998627988899843789


No 71 
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.54  E-value=72  Score=14.14  Aligned_cols=56  Identities=14%  Similarity=0.214  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHHHCCC----------CCCCCCC-CC-------CCCC---EECHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             9999999999999985787----------4710375-15-------6577---0288899508676786201244465
Q gi|254780310|r    4 IIQTVKSIIIELFHCIYPS----------ICPIYSR-II-------NLRF---CLCGHCWSKIHFITATEHILKNNKD   60 (119)
Q Consensus         4 ~~~~ik~~~~~ll~~lfP~----------~C~~C~~-~~-------~~~~---~lC~~C~~~l~~i~~~~C~~Cg~~~   60 (119)
                      |.-++...+.++...|=+.          .|++||. ++       +.++   ..|.-|..+.++. ...|..|+...
T Consensus       160 i~AALqv~wa~lA~~l~~~~~~~~~~~~~~CPvCGs~Pvasvv~~g~~~G~RyL~CslC~teW~~~-R~~C~~C~~~~  236 (307)
T PRK03564        160 IWAALSLYWAQMAQLIPGKARAEYGEQRQYCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV-RVKCSNCEQSG  236 (307)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCCCCCCCCC-CCCCCCCCCCC
T ss_conf             999999999999854895224787777885998898751455750687870688648777740213-53468888988


No 72 
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=20.39  E-value=54  Score=14.85  Aligned_cols=37  Identities=19%  Similarity=0.238  Sum_probs=21.7

Q ss_pred             CCCCCCCCCCC-------CCEECHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             47103751565-------77028889950867678620124446
Q gi|254780310|r   23 ICPIYSRIINL-------RFCLCGHCWSKIHFITATEHILKNNK   59 (119)
Q Consensus        23 ~C~~C~~~~~~-------~~~lC~~C~~~l~~i~~~~C~~Cg~~   59 (119)
                      .|.+|......       ++.+|..|..++.......|+.|..+
T Consensus         1 ~C~iC~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~   44 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP   44 (45)
T ss_pred             CCCCCCHHHCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf             98408803278118818999106899999994791868382880


No 73 
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.13  E-value=46  Score=15.22  Aligned_cols=10  Identities=0%  Similarity=-0.403  Sum_probs=4.9

Q ss_pred             CCCCCCCCCC
Q ss_conf             6201244465
Q gi|254780310|r   51 TEHILKNNKD   60 (119)
Q Consensus        51 ~~C~~Cg~~~   60 (119)
                      .+|..||.++
T Consensus        69 sfchncgs~f   78 (160)
T COG4306          69 SFCHNCGSRF   78 (160)
T ss_pred             CHHHCCCCCC
T ss_conf             0654179988


Done!