Query         gi|254780128|ref|YP_003064541.1| VRR-NUC domain-containing protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs    109 out of 449
Neff          6.0 
Searched_HMMs 39220
Date          Sun May 22 11:54:33 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780128.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam08774 VRR_NUC VRR-NUC doma  99.6 4.4E-16 1.1E-20  119.2   7.3   81    9-89      1-96  (96)
  2 KOG2143 consensus               98.8   2E-08   5E-13   73.0   6.1   52   36-87    793-845 (854)
  3 cd00523 archeal_HJR Holliday j  97.6  0.0011 2.8E-08   44.2  10.4   77    9-86      3-85  (123)
  4 pfam01870 Hjc Archaeal hollida  97.6   0.001 2.5E-08   44.5   9.8   72   14-86      2-79  (93)
  5 COG1591 Holliday junction reso  97.0   0.012   3E-07   38.0   9.6   76   10-86      5-86  (137)
  6 pfam02021 UPF0102 Uncharacteri  94.3    0.45 1.1E-05   28.4   8.4   60   15-75      3-70  (94)
  7 PHA01753 Holliday junction res  94.1     0.5 1.3E-05   28.1   8.4   63   12-75      8-75  (121)
  8 COG2810 Predicted type IV rest  93.5    0.77   2E-05   27.0   8.3   78    8-86     20-104 (284)
  9 PRK12497 hypothetical protein;  93.2    0.57 1.5E-05   27.8   7.3   62   13-75     11-80  (118)
 10 cd00221 Vsr Very Short Patch R  92.9    0.93 2.4E-05   26.5   8.0   75   11-88     17-113 (115)
 11 pfam03838 RecU Recombination p  91.9     1.3 3.4E-05   25.6   8.4   75   11-86      7-109 (167)
 12 pfam10107 Endonuc_Holl Endonuc  91.6    0.72 1.8E-05   27.2   6.2   48   39-86     97-151 (153)
 13 COG0792 Predicted endonuclease  88.9     2.4 6.2E-05   24.0   7.5   66    9-75      3-76  (114)
 14 COG4741 Predicted secreted end  88.9     1.7 4.5E-05   24.9   6.3   48   39-86    113-167 (175)
 15 pfam08722 TnsA_N TnsA endonucl  88.7     1.2   3E-05   25.9   5.3   48   39-86     29-80  (81)
 16 PRK04247 hypothetical protein;  88.6     2.6 6.5E-05   23.9   6.9   90    9-98    128-226 (250)
 17 PRK03298 hypothetical protein;  86.8     3.3 8.3E-05   23.2   8.1   89    9-97    103-200 (224)
 18 pfam01939 DUF91 Protein of unk  86.6     3.4 8.6E-05   23.2   6.8   90    9-98    104-203 (228)
 19 TIGR00632 vsr DNA mismatch end  85.5    0.57 1.5E-05   27.8   2.2   78   10-88     39-142 (143)
 20 pfam03852 Vsr DNA mismatch end  83.4     3.2   8E-05   23.3   5.2   44   11-56     20-63  (75)
 21 pfam06319 DUF1052 Protein of u  83.3     2.9 7.5E-05   23.5   5.0   56    9-64     19-74  (158)
 22 PRK02234 recU Holliday junctio  76.6       8  0.0002   20.9   8.5   77    9-86     30-135 (199)
 23 COG1637 Predicted nuclease of   76.5       8  0.0002   20.9   6.3   89    9-97    129-226 (253)
 24 cd01037 Restriction_endonuclea  76.2     8.2 0.00021   20.8   6.9   70   14-86      2-79  (80)
 25 pfam08378 NERD Nuclease-relate  75.3     3.6 9.1E-05   23.0   3.4   84   13-99      6-98  (123)
 26 PRK09225 threonine synthase; V  73.9     5.8 0.00015   21.7   4.2   41   60-100   165-206 (465)
 27 cd01560 Thr-synth_2 Threonine   73.2     5.5 0.00014   21.9   3.9   41   60-100   164-205 (460)
 28 pfam07711 RabGGT_insert Rab ge  72.1     5.9 0.00015   21.7   3.9   45   24-69     11-55  (102)
 29 pfam09520 RE_MjaII MjaII restr  72.0     7.9  0.0002   20.9   4.5   27   40-68    144-170 (252)
 30 PRK13731 conjugal transfer sur  68.1      13 0.00032   19.7   6.1   54   39-94     38-93  (243)
 31 pfam05818 TraT Enterobacterial  65.9      13 0.00034   19.6   4.6   45   48-94     19-63  (215)
 32 TIGR00252 TIGR00252 conserved   63.6     7.4 0.00019   21.1   2.9   48   13-60     22-70  (141)
 33 pfam05116 S6PP Sucrose-6F-phos  61.7      17 0.00043   18.9   6.7   43    7-54     18-73  (247)
 34 cd02410 archeal_CPSF_KH The ar  59.6      18 0.00046   18.8   4.3   62   34-96     62-130 (145)
 35 COG3727 Vsr DNA G:T-mismatch r  58.8      19 0.00048   18.6   7.6   76   10-87     20-116 (150)
 36 pfam06555 consensus             58.1      19 0.00049   18.6   4.3   13   18-30      3-15  (200)
 37 cd01473 vWA_CTRP CTRP for  CS   53.9      23 0.00058   18.1   5.8   68   34-101   102-189 (192)
 38 COG0610 Type I site-specific r  53.6      19 0.00049   18.6   3.7   37   37-74    123-162 (962)
 39 pfam03460 NIR_SIR_ferr Nitrite  52.4      24 0.00061   18.0   6.5   52   48-100     4-66  (67)
 40 pfam10313 DUF2415 Uncharacteri  50.9      25 0.00065   17.8   4.0   30   28-59      4-34  (43)
 41 pfam04313 HSDR_N Type I restri  48.9      19 0.00048   18.6   3.0   23   37-60     17-40  (90)
 42 COG2894 MinD Septum formation   44.8      32  0.0008   17.3   4.0   34   60-93     93-127 (272)
 43 COG1139 Uncharacterized conser  44.3      32 0.00082   17.2   4.8   37   64-100    63-99  (459)
 44 TIGR00260 thrC threonine synth  44.1      17 0.00043   18.9   2.2   41   60-100   115-156 (423)
 45 cd01471 vWA_micronemal_protein  43.4      33 0.00085   17.1   5.7   42   34-85    102-143 (186)
 46 PRK03379 vitamin B12-transport  42.7      34 0.00087   17.1   5.1   32   69-100    90-123 (265)
 47 COG4073 Uncharacterized protei  42.0      35 0.00089   17.0   6.0   79   11-99     68-160 (198)
 48 COG3331 PrfA Penicillin-bindin  41.8      35  0.0009   17.0   8.7   75   11-86     11-113 (177)
 49 PRK09534 btuF corrinoid ABC tr  40.2      37 0.00095   16.8   5.5   33   68-100   130-165 (364)
 50 TIGR02258 2_5_ligase 2'-5' RNA  40.1      37 0.00095   16.8   5.1   63   15-81     54-119 (189)
 51 PRK00453 rpsF 30S ribosomal pr  39.9      38 0.00096   16.8   4.9   57   13-69     21-77  (95)
 52 TIGR00348 hsdR type I site-spe  38.8      35  0.0009   17.0   3.1   26   37-63    133-162 (813)
 53 cd00114 LIGANc NAD+ dependent   37.6      41   0.001   16.6   6.3   48   53-100   214-265 (307)
 54 TIGR03675 arCOG00543 arCOG0178  37.1      42  0.0011   16.5   4.5   54   34-88     79-132 (630)
 55 PRK01395 V-type ATP synthase s  36.9      42  0.0011   16.5   3.6   28   73-100    16-43  (104)
 56 pfam09572 RE_XamI XamI restric  36.5      43  0.0011   16.5   7.8   57    9-65    120-201 (251)
 57 pfam06616 BsuBI_PstI_RE BsuBI/  36.0      43  0.0011   16.4   8.4   63   37-99    212-279 (306)
 58 pfam06250 DUF1016 Protein of u  35.6      44  0.0011   16.4   4.0   57    9-65    182-249 (320)
 59 PRK09566 nirA ferredoxin-nitri  35.5      44  0.0011   16.4   7.0   50   52-101    65-126 (513)
 60 TIGR00075 hypD hydrogenase exp  35.3      40   0.001   16.7   2.9   57   38-97     74-141 (384)
 61 pfam08011 DUF1703 Protein of u  31.2      52  0.0013   15.9   8.8   70   10-80      2-73  (101)
 62 PRK10361 DNA recombination pro  30.9      52  0.0013   15.9   3.0   26   36-61    236-261 (475)
 63 TIGR02349 DnaJ_bact chaperone   30.9      53  0.0013   15.9   3.8   40   38-78    343-385 (386)
 64 PRK10976 putative sugar phosph  30.1      54  0.0014   15.8   6.5   44    6-54     17-71  (266)
 65 COG1540 Uncharacterized protei  29.8      47  0.0012   16.2   2.6   29   15-48     46-74  (252)
 66 pfam04720 DUF506 Protein of un  29.5      54  0.0014   15.9   2.8   73   12-98     87-184 (218)
 67 pfam08652 RAI1 RAI1 like. RAI1  28.8      57  0.0015   15.7   3.0   25   49-73     13-37  (68)
 68 pfam08608 Wyosine_form Wyosine  28.6      25 0.00063   17.9   1.0   26   50-75      2-33  (62)
 69 pfam04471 Mrr_cat Restriction   28.5      58  0.0015   15.7   8.3   66   19-85      2-69  (98)
 70 PRK10513 sugar phosphatase; Pr  27.4      61  0.0015   15.6   7.1   44    6-54     18-75  (270)
 71 TIGR01942 pcnB poly(A) polymer  26.6      60  0.0015   15.6   2.6   26   62-87     12-37  (448)
 72 COG1553 DsrE Uncharacterized c  26.5      59  0.0015   15.6   2.6   54   44-97     37-90  (126)
 73 pfam03190 DUF255 Protein of un  26.5      48  0.0012   16.2   2.1   54    7-60     53-123 (163)
 74 COG0498 ThrC Threonine synthas  26.3      63  0.0016   15.4   4.0   42   57-100   154-195 (411)
 75 PRK09567 nirA ferredoxin-nitri  25.0      67  0.0017   15.3   8.1   25   52-76    113-137 (591)
 76 cd01143 YvrC Periplasmic bindi  24.9      67  0.0017   15.3   3.9   30   70-99     73-105 (195)
 77 COG1782 Predicted metal-depend  24.9      68  0.0017   15.3   3.8   77   11-88     47-138 (637)
 78 TIGR02291 rimK_rel_E_lig alpha  24.5      69  0.0017   15.2   2.7   62    7-68    108-188 (320)
 79 TIGR02502 type_III_YscX type I  24.3      24 0.00061   18.0   0.2   17   37-53     24-40  (126)
 80 TIGR02717 AcCoA-syn-alpha acet  24.1      70  0.0018   15.2   2.9   26   12-40    110-135 (457)
 81 TIGR02249 integrase_gron integ  23.7      57  0.0014   15.7   2.1   23    5-27    238-260 (320)
 82 pfam01250 Ribosomal_S6 Ribosom  23.1      73  0.0019   15.1   4.3   60    9-68     13-75  (92)
 83 cd03008 TryX_like_RdCVF Trypar  23.1      73  0.0019   15.1   4.3   39   15-53     77-126 (146)
 84 pfam08282 Hydrolase_3 haloacid  23.1      73  0.0019   15.1   5.9   73    7-84     14-100 (254)
 85 TIGR03081 metmalonyl_epim meth  22.8      74  0.0019   15.0   6.2   85   11-101     9-93  (128)
 86 pfam09588 YqaJ YqaJ-like viral  22.7      74  0.0019   15.0   4.9   50   13-63     56-113 (141)
 87 cd01472 vWA_collagen von Wille  22.2      76  0.0019   14.9   4.1   56   33-100    96-151 (164)
 88 PRK10767 chaperone protein Dna  22.1      76  0.0019   14.9   4.0   46   38-85    308-355 (376)
 89 PRK07810 O-succinylhomoserine   22.1      77   0.002   14.9   2.8   85   17-102   282-405 (406)
 90 pfam02646 RmuC RmuC family. Th  21.9      77   0.002   14.9   2.9   27   35-61     98-124 (301)
 91 pfam04555 XhoI Restriction end  21.7      78   0.002   14.9   2.7   23   39-62     61-84  (196)
 92 KOG2364 consensus               21.7      78   0.002   14.9   4.9   54   10-65    232-286 (433)
 93 TIGR00678 holB DNA polymerase   20.5      51  0.0013   16.0   1.3   51   39-90     62-130 (216)

No 1  
>pfam08774 VRR_NUC VRR-NUC domain.
Probab=99.64  E-value=4.4e-16  Score=119.19  Aligned_cols=81  Identities=37%  Similarity=0.491  Sum_probs=72.9

Q ss_pred             CCHHHHHHHHHHHHHHCC-CEEEEEECC------------C-CCCCCEEEEECCCCC-EEEEEEECCCCCCCHHHHHHHH
Q ss_conf             899999999999999789-899998118------------8-898743999906982-9999997689886889999999
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKLD-CWVRKASFV------------G-RRGCPDRLIITPNGG-LWWIEVKKPTGRLSHQQMSEIE   73 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~G-~~~~K~~~~------------g-~~GvPDli~~~~~g~-~~fIEvK~~~gkls~~Q~~~~~   73 (103)
                      ++|..+|..+...+++.| +.+.+..+.            | +.|+|||+++.|.|+ +.|||||+|+|++|++|+.|++
T Consensus         1 ~~e~~~e~~~~~~~~k~g~~~~~~~~~~~~~~~~~~~~~~g~~~G~PDli~~~~~~~~~~~iEvK~p~~~~~~~Q~~~~~   80 (96)
T pfam08774         1 MREGRIEVALVEALKKLGYPLPRKNWGKKGAEALGKYFRYGLRKGVPDLILFLPPGKRFLLVEVKGPGDKLSPEQRAWLD   80 (96)
T ss_pred             CCCCEEEHHHHHHHHHHCCCCCCCCCCCCCHHHHCCHHHCCCCCCCCCEEEEECCCCEEEEEEEECCCCCCCHHHHHHHH
T ss_conf             97640000999999982898876553543867731044157879998789981599869999987899998989999999


Q ss_pred             HHHHCCCEEEEECCHH
Q ss_conf             9997898899985989
Q gi|254780128|r   74 ELRRRGQRVKVLVSME   89 (103)
Q Consensus        74 ~l~~~G~~~~Vv~s~e   89 (103)
                      .|++.|+.++||+|.|
T Consensus        81 ~l~~~g~~v~V~~~~~   96 (96)
T pfam08774        81 RLARSGFKVAVCDSVE   96 (96)
T ss_pred             HHHHCCCEEEEEECCC
T ss_conf             9997799499960769


No 2  
>KOG2143 consensus
Probab=98.75  E-value=2e-08  Score=72.95  Aligned_cols=52  Identities=35%  Similarity=0.440  Sum_probs=47.6

Q ss_pred             CCCCCCEEEEECC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf             8898743999906-982999999768988688999999999978988999859
Q gi|254780128|r   36 GRRGCPDRLIITP-NGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVS   87 (103)
Q Consensus        36 g~~GvPDli~~~~-~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s   87 (103)
                      .+.|+|||.++.| .+++.++|||.|++|+|..|+.|+..|.+-|+.|.||.-
T Consensus       793 srsG~PDL~lWNp~~k~fklvEVKgpnDRLSekQr~WLalL~dsg~~VEVChV  845 (854)
T KOG2143         793 SRSGFPDLTLWNPETKRFKLVEVKGPNDRLSEKQRLWLALLADSGIRVEVCHV  845 (854)
T ss_pred             CCCCCCCEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             13799844323577761789983488651028999999999857887799885


No 3  
>cd00523 archeal_HJR Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
Probab=97.62  E-value=0.0011  Score=44.20  Aligned_cols=77  Identities=26%  Similarity=0.275  Sum_probs=59.3

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCCC---CCHHHHHHHHHH-HHCCCEE
Q ss_conf             8999999999999997898999981188--898743999906982999999768988---688999999999-9789889
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTGR---LSHQQMSEIEEL-RRRGQRV   82 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l-~~~G~~~   82 (103)
                      .+=+..|+.|+..+...|+.|.+..+.|  .+..||++.. ++++++.||||+..+.   ++..|..-+..+ +.-|+..
T Consensus         3 rkG~~~EReL~~~l~~~GfavvR~~gSG~~~~~~pDiiA~-~~~~~~~iEvKst~~~~iYi~~e~ve~L~~Fa~~fG~~p   81 (123)
T cd00523           3 RKGSRAERELVKILEEKGFAVVRAPGSGGGPRPLPDIVAG-NGGTYLAIEVKSTKKDKIYIKKEQVEKLVEFARRFGGEP   81 (123)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCEEEECHHHHHHHHHHHHHCCCEE
T ss_conf             5503799999999986593499834678887889988975-698599999996269808984999999999999749938


Q ss_pred             EEEC
Q ss_conf             9985
Q gi|254780128|r   83 KVLV   86 (103)
Q Consensus        83 ~Vv~   86 (103)
                      +|+-
T Consensus        82 ~iav   85 (123)
T cd00523          82 YLAV   85 (123)
T ss_pred             EEEE
T ss_conf             9999


No 4  
>pfam01870 Hjc Archaeal holliday junction resolvase (hjc). This family of archaebacterial proteins are holliday junction resolvases (hjc gene). The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar.
Probab=97.59  E-value=0.001  Score=44.48  Aligned_cols=72  Identities=28%  Similarity=0.261  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCC---CCCHHHHHHHHHH-HHCCCEEEEEC
Q ss_conf             99999999997898999981188--89874399990698299999976898---8688999999999-97898899985
Q gi|254780128|r   14 VEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTG---RLSHQQMSEIEEL-RRRGQRVKVLV   86 (103)
Q Consensus        14 ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~g---kls~~Q~~~~~~l-~~~G~~~~Vv~   86 (103)
                      .|+.+++.+...|+.+.+..+.|  ..+.||++.. .++.++.||||+..+   .++..|..-+..+ +..|...+++.
T Consensus         2 ~ERel~~~l~~~gFavvR~~gSG~~~~~~pDiiA~-~g~~~~~iEvKst~~~kiyl~~eqve~L~~f~~~fg~~p~iav   79 (93)
T pfam01870         2 YERELVKILEERGFAVVRAAGSGGAVKPLPDIIAG-NGGVYLVIEVKSRKKDKIYLKKEQVEKLVEFARRFGGEPFLAV   79 (93)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             07999999986891699956789988899988985-6987999999961698188789999999999997399699999


No 5  
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=96.97  E-value=0.012  Score=37.98  Aligned_cols=76  Identities=28%  Similarity=0.282  Sum_probs=56.9

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCC-C--CCHHHHHHH-HHHHHCCCEEE
Q ss_conf             999999999999997898999981188--89874399990698299999976898-8--688999999-99997898899
Q gi|254780128|r   10 TEKDVEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTG-R--LSHQQMSEI-EELRRRGQRVK   83 (103)
Q Consensus        10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~g-k--ls~~Q~~~~-~~l~~~G~~~~   83 (103)
                      +=+..|+.|++.+...|+-+.+.-+.|  .+=+||++. ..+|.++-||||+..+ +  +.+.|..-+ +..+..|+..+
T Consensus         5 kG~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA-~~g~~~l~iE~K~~~~~kiYl~~e~ve~L~~FA~~fGg~p~   83 (137)
T COG1591           5 KGSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVA-GNGGVYLAIEVKSRRETKIYLDKEQVEKLVEFARRFGGEPY   83 (137)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEE-CCCCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCCEE
T ss_conf             33268899999998648549983467899999987885-28978999999861588478759999999999997199568


Q ss_pred             EEC
Q ss_conf             985
Q gi|254780128|r   84 VLV   86 (103)
Q Consensus        84 Vv~   86 (103)
                      +.-
T Consensus        84 iav   86 (137)
T COG1591          84 IAV   86 (137)
T ss_pred             EEE
T ss_conf             999


No 6  
>pfam02021 UPF0102 Uncharacterized protein family UPF0102. The function of this family is unknown.
Probab=94.33  E-value=0.45  Score=28.44  Aligned_cols=60  Identities=15%  Similarity=0.176  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf             999999999789899998118889874399990698299999976898--------8688999999999
Q gi|254780128|r   15 EKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--------RLSHQQMSEIEEL   75 (103)
Q Consensus        15 e~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l   75 (103)
                      |..-..+|.+.|+....-..-.+.|==||+.. .++..+|||||+-.+        .+++.|...+.+.
T Consensus         3 E~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~-~~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~a   70 (94)
T pfam02021         3 EALAARWLESKGLIILERNWRSRTGEIDIIAR-DDRTIVFVEVKTRSGENYGPAAEAVTPRKQKKIIRT   70 (94)
T ss_pred             HHHHHHHHHHCCCEEEEEEECCCCCCEEEEEE-ECCEEEEEEEEEEECCCCCCHHHHCCHHHHHHHHHH
T ss_conf             99999999987999987783268983769998-299999999997106997496692999999999999


No 7  
>PHA01753 Holliday junction resolvase
Probab=94.14  E-value=0.5  Score=28.15  Aligned_cols=63  Identities=17%  Similarity=0.185  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEE-CC-CCCCCCEEEEECCCCCEEEEEEECCCCC---CCHHHHHHHHHH
Q ss_conf             9999999999997898999981-18-8898743999906982999999768988---688999999999
Q gi|254780128|r   12 KDVEKRLVTGAKKLDCWVRKAS-FV-GRRGCPDRLIITPNGGLWWIEVKKPTGR---LSHQQMSEIEEL   75 (103)
Q Consensus        12 ~~ie~~l~~~lk~~G~~~~K~~-~~-g~~GvPDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l   75 (103)
                      ...|..++..++..|-.+.+.- |+ +.+-+||++.. +++.++.||||+...+   ....|..-+-++
T Consensus         8 k~~Er~lv~~L~~~GF~avRiPaSgs~~~plPDIiA~-k~n~~laiEvKST~~~~I~Vd~~QI~KL~eF   75 (121)
T PHA01753          8 KYYEYKTLEILESNGFKALRIPVSGTGKQALPDIIAT-KNNTIYPIEVKSTSKDVVTVDKFQIEKLFRF   75 (121)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCEEEECHHHHHHHHHH
T ss_conf             3669999999986791179811578999989857873-6978999998503342699718999999999


No 8  
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=93.48  E-value=0.77  Score=27.03  Aligned_cols=78  Identities=17%  Similarity=0.181  Sum_probs=58.1

Q ss_pred             CCCHHHHHHHHHHHH-HHCCCEEEEE--ECC---CCCCCCEEEEECCCCCE-EEEEEECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             889999999999999-9789899998--118---88987439999069829-9999976898868899999999997898
Q gi|254780128|r    8 YQTEKDVEKRLVTGA-KKLDCWVRKA--SFV---GRRGCPDRLIITPNGGL-WWIEVKKPTGRLSHQQMSEIEELRRRGQ   80 (103)
Q Consensus         8 ~~~E~~ie~~l~~~l-k~~G~~~~K~--~~~---g~~GvPDli~~~~~g~~-~fIEvK~~~gkls~~Q~~~~~~l~~~G~   80 (103)
                      ..+|..+.+.++.-. .++||-....  +-|   +.-|.||..++. ||++ .|+|-|.-.--+-..|..-....-+.|.
T Consensus        20 ~~nEa~vrq~lIlp~L~slGwdi~nPkEV~PEe~t~~GraDyalik-d~kvfafieak~ls~~~akd~qq~~~Yav~~Gv   98 (284)
T COG2810          20 SRNEAAVRQHLILPFLSSLGWDIDNPKEVRPEEKTEEGRADYALIK-DGKVFAFIEAKNLSVNPAKDVQQLAKYAVDKGV   98 (284)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEE-CCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             9618888899889999970777899020586424555765448885-693899872113475726899999999885283


Q ss_pred             EEEEEC
Q ss_conf             899985
Q gi|254780128|r   81 RVKVLV   86 (103)
Q Consensus        81 ~~~Vv~   86 (103)
                      .+.+|.
T Consensus        99 ~~~iVt  104 (284)
T COG2810          99 EVGIVT  104 (284)
T ss_pred             EEEEEE
T ss_conf             799996


No 9  
>PRK12497 hypothetical protein; Reviewed
Probab=93.18  E-value=0.57  Score=27.80  Aligned_cols=62  Identities=16%  Similarity=0.111  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf             99999999999789899998118889874399990698299999976898--------8688999999999
Q gi|254780128|r   13 DVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--------RLSHQQMSEIEEL   75 (103)
Q Consensus        13 ~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l   75 (103)
                      .-|.....+|++.|+.+..--.-.+.|==|||.. .++..+|||||+-.+        .+++.|...+.+.
T Consensus        11 ~gE~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~-~~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~a   80 (118)
T PRK12497         11 AGEDLAARYLESKGLRILARNFRCRFGEIDLIAR-DGDTLVFVEVKTRRSDLFGGAAEAVTPRKQRRIRRA   80 (118)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEE-ECCEEEEEEEECCCCCCCCCHHHHCCHHHHHHHHHH
T ss_conf             9999999999987999999850048995058999-699999999821557898897895999999999999


No 10 
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=92.91  E-value=0.93  Score=26.51  Aligned_cols=75  Identities=15%  Similarity=0.107  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEE--------ECCCCCCCHHHHHHH----------
Q ss_conf             99999999999997898999981188898743999906982999999--------768988688999999----------
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEV--------KKPTGRLSHQQMSEI----------   72 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEv--------K~~~gkls~~Q~~~~----------   72 (103)
                      ..+.|..+.+.|.+.|..+ ......-+|-||+ ++.+-...+||-=        .. ...|..+...|.          
T Consensus        17 ~TkpE~~vrk~L~~~G~Ry-r~~~k~lpG~PDi-v~~~~k~aIFvdGCFWHgh~~~~-~~~pk~n~~fW~~Ki~~N~~RD   93 (115)
T cd00221          17 DTKPERAVRSALWELGYRF-RKQDKDLPGKPDI-VVPGYRLAIFVDGCFWHGHPCHK-RKPPPKNTEFWLEKIERNVERD   93 (115)
T ss_pred             CCHHHHHHHHHHHHCCCEE-EECCCCCCCCCCE-EECCCCEEEEECCEEECCCCCCC-CCCCCCCHHHHHHHHHHHHHHH
T ss_conf             9869999999999889989-9668877999999-73576289993240433888757-8889853899999999999989


Q ss_pred             ----HHHHHCCCEEEEECCH
Q ss_conf             ----9999789889998598
Q gi|254780128|r   73 ----EELRRRGQRVKVLVSM   88 (103)
Q Consensus        73 ----~~l~~~G~~~~Vv~s~   88 (103)
                          +.|.++|..+.+++.-
T Consensus        94 ~~~~~~L~~~GW~v~~vWEc  113 (115)
T cd00221          94 RRVQAALERLGWRVLRVWEC  113 (115)
T ss_pred             HHHHHHHHHCCCEEEEEEEC
T ss_conf             99999999889989999830


No 11 
>pfam03838 RecU Recombination protein U.
Probab=91.88  E-value=1.3  Score=25.58  Aligned_cols=75  Identities=12%  Similarity=0.146  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEE---------ECC------------CCCCCCEEEEECCCCCEEEEEEECCCC-------
Q ss_conf             9999999999999789899998---------118------------889874399990698299999976898-------
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRKA---------SFV------------GRRGCPDRLIITPNGGLWWIEVKKPTG-------   62 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K~---------~~~------------g~~GvPDli~~~~~g~~~fIEvK~~~g-------   62 (103)
                      |..|....--+..+.=+.+.|-         ..|            ..+.-+|....+ .|+++..|.|...+       
T Consensus         7 E~~IN~tn~~Y~~~~~A~I~KkptPi~ivkv~~~~r~~a~I~~ayf~~kSt~DY~Gvy-~G~~i~FEAKeT~nkt~Fpl~   85 (167)
T pfam03838         7 EELINETNQYYLANGIAVIHKKPTPIQIVKVDYPKRSAAVIKEAYFKQKSTTDYNGVY-KGRYIDFEAKETKNKTSFPLK   85 (167)
T ss_pred             HHHHHHHHHHHHHCCEEEEEEECCCEEEEECCCCCCCCCEEEEEEECCCCCCCCCEEE-CCEEEEEECCCCCCCCCCCHH
T ss_conf             9999999999987797999970788179943786555334677887357767733167-789999982243566745724


Q ss_pred             CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             868899999999997898899985
Q gi|254780128|r   63 RLSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        63 kls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                      ...++|...++.+.++|+.++++=
T Consensus        86 Ni~~HQi~~L~~~~~~gGiaF~ii  109 (167)
T pfam03838        86 NIHEHQIEHLKQVLKQGGICFVII  109 (167)
T ss_pred             HCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf             556999999999998899799999


No 12 
>pfam10107 Endonuc_Holl Endonuclease related to archaeal Holliday junction resolvase. This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=91.63  E-value=0.72  Score=27.20  Aligned_cols=48  Identities=21%  Similarity=0.371  Sum_probs=36.2

Q ss_pred             CCC-EEEEEC-----CCCCEEEEEEECCC-CCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             874-399990-----69829999997689-8868899999999997898899985
Q gi|254780128|r   39 GCP-DRLIIT-----PNGGLWWIEVKKPT-GRLSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        39 GvP-Dli~~~-----~~g~~~fIEvK~~~-gkls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                      |-| |.+++-     ..-.+.|+|||+.+ .+||..|+...+.+++--..+..++
T Consensus        97 G~PIDyIvFdgl~~~~~~~IvfiEVKsGksa~Lt~~qr~IrdaIe~g~V~w~~ir  151 (153)
T pfam10107        97 GTPVDYIVFDGLSEGEIREIVFVEVKTGKSARLTEREKAVREAIEAGRVRFETIR  151 (153)
T ss_pred             CCCEEEEEECCCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCEEEEEEE
T ss_conf             8980489974878787444999996458642458778999999985976899986


No 13 
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=88.94  E-value=2.4  Score=24.01  Aligned_cols=66  Identities=12%  Similarity=0.065  Sum_probs=44.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf             899999999999999789899998118889874399990698299999976898--------8688999999999
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--------RLSHQQMSEIEEL   75 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l   75 (103)
                      +....-|..-...|++.|...+.-..-.+-|==|||.- .++.++|||||+-.+        .+++.....+.+.
T Consensus         3 ~~G~~~E~~A~~~L~~~G~~iL~rN~r~r~GEIDlIa~-~~~~ivFVEVK~R~~~~~g~a~~aV~~~K~~ki~~a   76 (114)
T COG0792           3 QLGAAGEDLAARFLESKGLRILARNWRCRYGEIDLIAR-DGDTVVFVEVKYRRNDLYGGAAEAVTPRKQRKLRRA   76 (114)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCEEEEEE-CCCEEEEEEEEEECCCCCCCHHHHCCHHHHHHHHHH
T ss_conf             04778999999999976930255530378874689996-599899999974126776666774899999999999


No 14 
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=88.91  E-value=1.7  Score=24.87  Aligned_cols=48  Identities=21%  Similarity=0.391  Sum_probs=37.0

Q ss_pred             CCC-EEEEEC--CCCC---EEEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             874-399990--6982---999999768-98868899999999997898899985
Q gi|254780128|r   39 GCP-DRLIIT--PNGG---LWWIEVKKP-TGRLSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        39 GvP-Dli~~~--~~g~---~~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                      |-| |++++-  .+|.   .+|+|+|+. ++++|..-+..++.+++--..+.+..
T Consensus       113 GTPvD~iVFdGLs~G~i~~IvFvEVKtGkt~~LseREk~Vr~ai~~~rVs~ei~~  167 (175)
T COG4741         113 GTPVDFIVFDGLSEGNIESIVFVEVKTGKTSSLSEREKAVRDAIENGRVSWEIYH  167 (175)
T ss_pred             CCCCEEEEECCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEE
T ss_conf             7971289873777686107999998328767721889999999961813799885


No 15 
>pfam08722 TnsA_N TnsA endonuclease N terminal. The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The N terminal domain of TnsA is catalytic.
Probab=88.67  E-value=1.2  Score=25.89  Aligned_cols=48  Identities=21%  Similarity=0.157  Sum_probs=32.6

Q ss_pred             CCCEEEEECCCCCEEEEEEECCCCC----CCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             8743999906982999999768988----68899999999997898899985
Q gi|254780128|r   39 GCPDRLIITPNGGLWWIEVKKPTGR----LSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        39 GvPDli~~~~~g~~~fIEvK~~~gk----ls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                      =.||.++.+.||...++|+|....=    ..+.-..-.+..+..|....|+.
T Consensus        29 yTpDflv~~~dg~~~~~eVK~~~~l~~~~~~~K~~~~r~~~~~~g~~~~i~T   80 (81)
T pfam08722        29 YTPDFLVTYKDGKPEAVEVKYSEDLEDERTLEKFEIERRYAEERGIPFRIVT   80 (81)
T ss_pred             ECCCEEEEEECCCEEEEEEEHHHHHCCHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             9988999996793999997447563377789999999999998498599970


No 16 
>PRK04247 hypothetical protein; Provisional
Probab=88.60  E-value=2.6  Score=23.87  Aligned_cols=90  Identities=20%  Similarity=0.207  Sum_probs=61.7

Q ss_pred             CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCC-CHHH-HHHHHHHHHCCC-E--
Q ss_conf             89999999999999978--989999811888987439999069829999997689886-8899-999999997898-8--
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRL-SHQQ-MSEIEELRRRGQ-R--   81 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkl-s~~Q-~~~~~~l~~~G~-~--   81 (103)
                      ..|+++|..+......+  |.....-..+...|.-|+++--.+|+.+-||+|+-++.+ --.| ..+.+.|++... .  
T Consensus       128 G~Ea~l~~llae~p~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~V~VEvKR~ra~idaV~QL~RYve~l~~~~~~~VR  207 (250)
T PRK04247        128 GSEADMVDAILENPDLIEEGFRPVAREYETPAGIIDILGRDKEGNLVVLELKRRRAGLSAVSQLKRYVEAYREELGAKVR  207 (250)
T ss_pred             EEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCE
T ss_conf             31999999998590532589889988873598846489987998999999971337814799999999998763699821


Q ss_pred             -EEEECC-HHHHHHHHHHH
Q ss_conf             -999859-89999999999
Q gi|254780128|r   82 -VKVLVS-MEEVDNFLEEL   98 (103)
Q Consensus        82 -~~Vv~s-~edv~~~l~~l   98 (103)
                       ++++-+ .++++.++++.
T Consensus       208 GIlvAp~It~~Ar~Ll~dr  226 (250)
T PRK04247        208 GILVAPSITERARRLLEKE  226 (250)
T ss_pred             EEEECCCCCHHHHHHHHHC
T ss_conf             9999885898799999975


No 17 
>PRK03298 hypothetical protein; Provisional
Probab=86.83  E-value=3.3  Score=23.22  Aligned_cols=89  Identities=16%  Similarity=0.120  Sum_probs=60.2

Q ss_pred             CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHH-HHHHHHHHHCCCE----
Q ss_conf             89999999999999978--9899998118889874399990698299999976898868899-9999999978988----
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQ-MSEIEELRRRGQR----   81 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q-~~~~~~l~~~G~~----   81 (103)
                      -.|+++|..+...-..+  |.....-..+...|.-|+++--.+|..+-||+|+.++----.| ..+.+.|++....    
T Consensus       103 G~Eadl~~llae~P~~ie~Gf~~v~rE~~T~~G~VDll~~D~~G~~V~VEiKRra~idaV~QL~RYve~l~rd~~~~~VR  182 (224)
T PRK03298        103 GVEAHLQELLAEHIELLGEGYTLVRREYMTAIGPVDLLCRDADGATVAVEIKRRGEIDGVEQLTRYLELLNRDPLLAPVR  182 (224)
T ss_pred             ECHHHHHHHHHHCCHHHCCCCEEEEEEECCCCCCEEEEEECCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             01999999987592421589898778731798835389987999999999983068108999999999985575888514


Q ss_pred             -EEEECC-HHHHHHHHHH
Q ss_conf             -999859-8999999999
Q gi|254780128|r   82 -VKVLVS-MEEVDNFLEE   97 (103)
Q Consensus        82 -~~Vv~s-~edv~~~l~~   97 (103)
                       .+++-+ .++++.++++
T Consensus       183 GIlvAp~It~~Ar~Ll~d  200 (224)
T PRK03298        183 GVFAAQQIKPQARTLATD  200 (224)
T ss_pred             EEEECCCCCHHHHHHHHH
T ss_conf             999987478879999997


No 18 
>pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.
Probab=86.63  E-value=3.4  Score=23.16  Aligned_cols=90  Identities=19%  Similarity=0.215  Sum_probs=61.9

Q ss_pred             CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCC-CHHH-HHHHHHHHHCC--CE-
Q ss_conf             89999999999999978--989999811888987439999069829999997689886-8899-99999999789--88-
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRL-SHQQ-MSEIEELRRRG--QR-   81 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkl-s~~Q-~~~~~~l~~~G--~~-   81 (103)
                      ..|++++..+...-..+  |.....-..+...|.-|+++--.+|+.+-||+|+-.+.+ .-.| ..+.+.|++.-  .. 
T Consensus       104 G~Eadl~~~l~~~P~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~VvVEvKRr~a~idaV~QL~RYve~l~rd~~~~~V  183 (228)
T pfam01939       104 GSEAEMAALIFEHPQLIEEGFKPVRREYQIAHGIVDILGKDEDGNIVILELKRRKADLHAVSQLKRYVDSLKEDYVEAKV  183 (228)
T ss_pred             EEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             31999999998591532489899988852588736689987999999999974037820799999999998655488860


Q ss_pred             --EEEECC-HHHHHHHHHHH
Q ss_conf             --999859-89999999999
Q gi|254780128|r   82 --VKVLVS-MEEVDNFLEEL   98 (103)
Q Consensus        82 --~~Vv~s-~edv~~~l~~l   98 (103)
                        ++|+-+ -++++.++++.
T Consensus       184 RGIlvAp~It~~Ar~Ll~d~  203 (228)
T pfam01939       184 RGVLVAPSITEGAKKLLEEE  203 (228)
T ss_pred             EEEEECCCCCHHHHHHHHHC
T ss_conf             39999985898899999975


No 19 
>TIGR00632 vsr DNA mismatch endonuclease Vsr; InterPro: IPR004603   This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology . ; GO: 0004519 endonuclease activity, 0006298 mismatch repair.
Probab=85.53  E-value=0.57  Score=27.81  Aligned_cols=78  Identities=18%  Similarity=0.062  Sum_probs=51.3

Q ss_pred             CHHHHHHHHHHHHHHCCCEEE----EEECCCCCCCCEEEEECCCCCEEEE--------EEECCCCCCCHHHHHHHH----
Q ss_conf             999999999999997898999----9811888987439999069829999--------997689886889999999----
Q gi|254780128|r   10 TEKDVEKRLVTGAKKLDCWVR----KASFVGRRGCPDRLIITPNGGLWWI--------EVKKPTGRLSHQQMSEIE----   73 (103)
Q Consensus        10 ~E~~ie~~l~~~lk~~G~~~~----K~~~~g~~GvPDli~~~~~g~~~fI--------EvK~~~gkls~~Q~~~~~----   73 (103)
                      +..++|..|...|-++|..+.    +=..-|-+|-||+. +..---++||        .+-.-+-.|..+...|+.    
T Consensus        39 ~~T~pE~~l~s~L~~lGlryRkdfl~~~~~G~~g~PD~v-f~~~k~~iFidGCFWHg~~C~~~~~~p~s~~~fW~~Ki~~  117 (143)
T TIGR00632        39 KGTKPEKALASLLFALGLRYRKDFLLRDKDGLPGTPDIV-FKEYKVVIFIDGCFWHGHDCDILGKVPKSRKDFWSPKIEK  117 (143)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE-ECCCEEEEEECCCEECCCCCCCCCCCCCCCHHCCHHHHHH
T ss_conf             798178999999999889988898752368985467544-3473588860273005876740147886642303688874


Q ss_pred             ----------HHHHCCCEEEEECCH
Q ss_conf             ----------999789889998598
Q gi|254780128|r   74 ----------ELRRRGQRVKVLVSM   88 (103)
Q Consensus        74 ----------~l~~~G~~~~Vv~s~   88 (103)
                                .|.+.|..|.+|+.-
T Consensus       118 N~~RD~~~~~~L~~~GWrv~~vW~~  142 (143)
T TIGR00632       118 NVERDRRVNDALAEEGWRVLRVWEC  142 (143)
T ss_pred             HHHCCCCHHHHHHHCCCEEEEEECC
T ss_conf             2530311789998459989896137


No 20 
>pfam03852 Vsr DNA mismatch endonuclease Vsr.
Probab=83.40  E-value=3.2  Score=23.32  Aligned_cols=44  Identities=20%  Similarity=0.093  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEE
Q ss_conf             9999999999999789899998118889874399990698299999
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIE   56 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIE   56 (103)
                      ..+.|..+.+.|.+.|..+.+ ....-+|-|| |++.+....+||.
T Consensus        20 ~TkpE~~vr~~L~~~G~ryr~-~~~~lpG~PD-iv~~~~k~aIFvd   63 (75)
T pfam03852        20 GTKPELALRSLLFGLGLRYRK-NDKSLPGKPD-IVFPKYKLAVFIH   63 (75)
T ss_pred             CCHHHHHHHHHHHHCCCEEEE-CCCCCCCCCC-EEECCCCEEEEEE
T ss_conf             976999999999988988997-3787899999-9766877899941


No 21 
>pfam06319 DUF1052 Protein of unknown function (DUF1052). This family consists of several bacterial proteins of unknown function.
Probab=83.32  E-value=2.9  Score=23.51  Aligned_cols=56  Identities=18%  Similarity=0.274  Sum_probs=43.3

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCC
Q ss_conf             89999999999999978989999811888987439999069829999997689886
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRL   64 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkl   64 (103)
                      .+-..|.+-+.+.+..+|..++.-.++..--=-|++.+-++|.++-||+|+...-.
T Consensus        19 eta~~i~RGv~Rll~~~g~a~l~E~~L~~GrRaDl~al~~kGei~IVEiKSs~aDF   74 (158)
T pfam06319        19 ETALAVRRGVQRLLMELGHAVLPELPLASGRRADLIALSPKGEIWIVEIKSSIEDF   74 (158)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECCCCCEEEEEEECCHHHH
T ss_conf             88999999999999977996335663799977779988799959999983678884


No 22 
>PRK02234 recU Holliday junction-specific endonuclease; Reviewed
Probab=76.58  E-value=8  Score=20.89  Aligned_cols=77  Identities=14%  Similarity=0.153  Sum_probs=57.3

Q ss_pred             CC-HHHHHHHHHHHHHHCCCEEEEE---------ECCC------------CCCCCEEEEECCCCCEEEEEEECCCC----
Q ss_conf             89-9999999999999789899998---------1188------------89874399990698299999976898----
Q gi|254780128|r    9 QT-EKDVEKRLVTGAKKLDCWVRKA---------SFVG------------RRGCPDRLIITPNGGLWWIEVKKPTG----   62 (103)
Q Consensus         9 ~~-E~~ie~~l~~~lk~~G~~~~K~---------~~~g------------~~GvPDli~~~~~g~~~fIEvK~~~g----   62 (103)
                      |+ |..|.....-++..-=+++.|-         ..|.            .+--.|....+ .|+++-.|.|...+    
T Consensus        30 M~LE~~IN~tN~yY~~~~iAvIhKkPTPIqivkVdypkRs~a~I~eAyf~~~STtDY~Gvy-kG~yIdFEAKET~nktsF  108 (199)
T PRK02234         30 MSLEKDINETNDYYLSNGIAVIHKKPTPIQIVKVDYPKRSKAVIKEAYFRQASTTDYNGVY-KGKYIDFEAKETKNKTSF  108 (199)
T ss_pred             CHHHHHHHHHHHHHHHCCEEEEEECCCCEEEEECCCCCCCCCHHHHHEECCCCCCCCCCEE-CCEEEEEECCCCCCCCCC
T ss_conf             0599999999999987797899835888069961554433001001023577877743256-788988875455787744


Q ss_pred             ---CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             ---868899999999997898899985
Q gi|254780128|r   63 ---RLSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        63 ---kls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                         ...++|...++.+.++|+.++++=
T Consensus       109 pl~Nih~HQi~hl~~~~~qgGI~F~iI  135 (199)
T PRK02234        109 PLKNFHEHQIEHMKQVLAQGGICFVII  135 (199)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             723403899999999997799799999


No 23 
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=76.49  E-value=8  Score=20.87  Aligned_cols=89  Identities=22%  Similarity=0.233  Sum_probs=58.1

Q ss_pred             CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHCCCE---
Q ss_conf             89999999999999978--98999981188898743999906982999999768988688-99-9999999978988---
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSH-QQ-MSEIEELRRRGQR---   81 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~G~~---   81 (103)
                      .+|.++++.+..--.-+  |-...--..+...|.-|++..-.+|++.-||+|+-++.++. .| +.+.+.++.....   
T Consensus       129 g~E~~m~~~I~e~P~lleeG~~~v~~E~~t~~G~vDilg~De~G~~viiElKR~ka~~~Av~QL~RYv~~l~~~~~~~VR  208 (253)
T COG1637         129 GSEADMQELIAENPQLLEEGFRPVAREYQTAIGKVDILGRDERGNIVIIELKRRKAGLSAVSQLKRYVELLREDTGDKVR  208 (253)
T ss_pred             CHHHHHHHHHHHCHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCEEE
T ss_conf             40999987876594667575433126521374256799886899999999942547710899999999970534686078


Q ss_pred             -EEEEC-CHHHHHHHHHH
Q ss_conf             -99985-98999999999
Q gi|254780128|r   82 -VKVLV-SMEEVDNFLEE   97 (103)
Q Consensus        82 -~~Vv~-s~edv~~~l~~   97 (103)
                       ..|+. --+++..++++
T Consensus       209 GiLvAp~it~~a~~ll~~  226 (253)
T COG1637         209 GILVAPSITEQARRLLED  226 (253)
T ss_pred             EEEECCCCCHHHHHHHHH
T ss_conf             999866440889999997


No 24 
>cd01037 Restriction_endonuclease_like Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI
Probab=76.19  E-value=8.2  Score=20.82  Aligned_cols=70  Identities=19%  Similarity=0.067  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHCCCEEEEEECC--CCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHH------HHHHHHHHCCCEEEEE
Q ss_conf             9999999999789899998118--8898743999906982999999768988688999------9999999789889998
Q gi|254780128|r   14 VEKRLVTGAKKLDCWVRKASFV--GRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM------SEIEELRRRGQRVKVL   85 (103)
Q Consensus        14 ie~~l~~~lk~~G~~~~K~~~~--g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~------~~~~~l~~~G~~~~Vv   85 (103)
                      .|..+...+.+.+....++...  ..++.||. ++.  ..-+.||+|.........+.      .....+...|..+.++
T Consensus         2 ~E~~l~~~l~~~~~~~~~~~~~~~~~~~~pDf-~~~--~~~l~iE~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   78 (80)
T cd01037           2 AERLLWKLLRAKGLAVRRFRRQVPIGSYIPDF-VCP--SAKLVIELKGTFHDGLLRKLRTSEKQERIAFLEADGKKVLRF   78 (80)
T ss_pred             HHHHHHHHHHHCCCCCCEEEECCCCCCEEEEE-ECC--CCCEEEEECCCHHCCCHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             79999999985587887057137507887757-725--448799914512153135554411778999999889989974


Q ss_pred             C
Q ss_conf             5
Q gi|254780128|r   86 V   86 (103)
Q Consensus        86 ~   86 (103)
                      .
T Consensus        79 ~   79 (80)
T cd01037          79 W   79 (80)
T ss_pred             C
T ss_conf             3


No 25 
>pfam08378 NERD Nuclease-related domain. The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.
Probab=75.29  E-value=3.6  Score=22.98  Aligned_cols=84  Identities=23%  Similarity=0.298  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHC-----CCEEEEE-ECC---CCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEE
Q ss_conf             9999999999978-----9899998-118---889874399990698299999976898868899999999997898899
Q gi|254780128|r   13 DVEKRLVTGAKKL-----DCWVRKA-SFV---GRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVK   83 (103)
Q Consensus        13 ~ie~~l~~~lk~~-----G~~~~K~-~~~---g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~   83 (103)
                      .-|+.+-.++++.     ++.++.- .-+   |...==|.+++.|+| ++-||+|.-.|....++..|..  ...+....
T Consensus         6 ~gE~~v~~~L~~~~~~~~~~~vl~n~~l~~~~~~~~eID~lvi~~~g-i~vvE~K~~~G~i~~~~~~W~~--~~~~~~~~   82 (123)
T pfam08378         6 EGEKLVARALKKLLPDDYEYFVLHNLRLPTHGGSTTEIDHLVISPDG-IFVIEVKNYKGTIIADGGKWTQ--TIGGRKEE   82 (123)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEEECEEECCCCCCEEEEEEEEECCCE-EEEEEECCCCEEEEECCCEEEE--EECCCEEE
T ss_conf             99999999999637888988999543962699978897799994891-9999946862489962763999--86995588


Q ss_pred             EECCHHHHHHHHHHHH
Q ss_conf             9859899999999998
Q gi|254780128|r   84 VLVSMEEVDNFLEELA   99 (103)
Q Consensus        84 Vv~s~edv~~~l~~l~   99 (103)
                      +-.-+.|+..-...+.
T Consensus        83 ~~nPi~Q~~~~~~~l~   98 (123)
T pfam08378        83 FKNPLLQAYRHAKLLR   98 (123)
T ss_pred             CCCHHHHHHHHHHHHH
T ss_conf             6899999999999999


No 26 
>PRK09225 threonine synthase; Validated
Probab=73.90  E-value=5.8  Score=21.74  Aligned_cols=41  Identities=15%  Similarity=0.283  Sum_probs=32.3

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHHH
Q ss_conf             89886889999999999789889998-598999999999986
Q gi|254780128|r   60 PTGRLSHQQMSEIEELRRRGQRVKVL-VSMEEVDNFLEELAC  100 (103)
Q Consensus        60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~edv~~~l~~l~~  100 (103)
                      |.|+.|+-|+..+.-..+.+..+.-| -++||++.++.++-.
T Consensus       165 P~g~vS~iQ~~QMtt~~~~NV~~i~v~G~FDDcQ~lVK~~f~  206 (465)
T PRK09225        165 PKGKVSPVQEKQMTTLQGDNIHVVAVEGDFDDCQALVKAAFN  206 (465)
T ss_pred             CCCCCCHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             799999779998622179977999846876789999999971


No 27 
>cd01560 Thr-synth_2 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins.
Probab=73.20  E-value=5.5  Score=21.86  Aligned_cols=41  Identities=17%  Similarity=0.289  Sum_probs=31.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHHH
Q ss_conf             89886889999999999789889998-598999999999986
Q gi|254780128|r   60 PTGRLSHQQMSEIEELRRRGQRVKVL-VSMEEVDNFLEELAC  100 (103)
Q Consensus        60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~edv~~~l~~l~~  100 (103)
                      |.|+.|+-|+..+.-..+.+..+.-| =++||++.++.++-.
T Consensus       164 P~g~vS~iQ~~QMtT~~~~NV~~iav~G~FDDcQ~~VK~~f~  205 (460)
T cd01560         164 PKGGVSPIQELQMTTLPADNVHVVAVEGDFDDCQSLVKALFA  205 (460)
T ss_pred             CCCCCCHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
T ss_conf             888899889998625478977999964880888999999960


No 28 
>pfam07711 RabGGT_insert Rab geranylgeranyl transferase alpha-subunit, insert domain. Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. This domain is inserted between pfam01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP.
Probab=72.13  E-value=5.9  Score=21.67  Aligned_cols=45  Identities=20%  Similarity=0.163  Sum_probs=37.2

Q ss_pred             HCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHH
Q ss_conf             7898999981188898743999906982999999768988688999
Q gi|254780128|r   24 KLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM   69 (103)
Q Consensus        24 ~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~   69 (103)
                      ..++...-|..|-..|.-+|++.. ||...++|-.+|.|+.++.|.
T Consensus        11 ~e~~lsv~FSrpv~v~~~~L~Lv~-Dg~p~~veWrt~~~r~r~s~v   55 (102)
T pfam07711        11 DEGCVSVAFSRPVLVGMVGLLLVL-DGQPQAVEWRTAHPRLRHSPV   55 (102)
T ss_pred             CCCEEEEEECCEEEECCCEEEEEE-CCCCEEEEEECCCCCCCCCCE
T ss_conf             678499996141540332689996-798079997689997675827


No 29 
>pfam09520 RE_MjaII MjaII restriction endonuclease. This family includes the MjaII (recognizes GGNCC but the cleavage site is unknown) restriction endonuclease.
Probab=71.96  E-value=7.9  Score=20.90  Aligned_cols=27  Identities=22%  Similarity=0.418  Sum_probs=22.1

Q ss_pred             CCEEEEECCCCCEEEEEEECCCCCCCHHH
Q ss_conf             74399990698299999976898868899
Q gi|254780128|r   40 CPDRLIITPNGGLWWIEVKKPTGRLSHQQ   68 (103)
Q Consensus        40 vPDli~~~~~g~~~fIEvK~~~gkls~~Q   68 (103)
                      +.|+.+-.+||.-+|+|+|+|  +|+..|
T Consensus       144 v~Dlyi~~kdg~e~~feIKT~--KPNkgq  170 (252)
T pfam09520       144 VADLYVQRKDGRELYFEIKSP--KPNKGQ  170 (252)
T ss_pred             EEEEEEECCCCCEEEEEECCC--CCCHHH
T ss_conf             778999827995899983577--998377


No 30 
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=68.15  E-value=13  Score=19.68  Aligned_cols=54  Identities=13%  Similarity=0.304  Sum_probs=40.3

Q ss_pred             CCCEEEEECC-CCCEEEEEEECCCCC-CCHHHHHHHHHHHHCCCEEEEECCHHHHHHH
Q ss_conf             8743999906-982999999768988-6889999999999789889998598999999
Q gi|254780128|r   39 GCPDRLIITP-NGGLWWIEVKKPTGR-LSHQQMSEIEELRRRGQRVKVLVSMEEVDNF   94 (103)
Q Consensus        39 GvPDli~~~~-~g~~~fIEvK~~~gk-ls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~   94 (103)
                      -..|=|.+-| ..+.+||.+|...++ .+..|......|...|+  .|+++|+++.=+
T Consensus        38 kMS~TIfLdP~s~ktVyv~vrNTS~~~~~~l~~~i~~~L~akGY--~iv~~P~~A~Y~   93 (243)
T PRK13731         38 QMSETIWLEPASERTVFLQIKNTSDKDMSGLQGKIADAVKAKGY--QVVTSPDKAYYW   93 (243)
T ss_pred             EECCCEEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCE--EEECCHHHCEEE
T ss_conf             00043886685455799998517877245678999999985890--986786576077


No 31 
>pfam05818 TraT Enterobacterial TraT complement resistance protein. The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings.
Probab=65.95  E-value=13  Score=19.55  Aligned_cols=45  Identities=13%  Similarity=0.307  Sum_probs=35.5

Q ss_pred             CCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHH
Q ss_conf             69829999997689886889999999999789889998598999999
Q gi|254780128|r   48 PNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNF   94 (103)
Q Consensus        48 ~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~   94 (103)
                      |+.+.+||.+|...++-=..|......|...|+  .|+++++++.=+
T Consensus        19 ~~~ktVyv~vrNTSd~~i~l~~~i~~~L~akGY--~iv~~P~~A~Y~   63 (215)
T pfam05818        19 PEQRTVYLSIRNTSDKNVNLEQKLISALQAKGY--KVVDDPDKAHYW   63 (215)
T ss_pred             CCCCEEEEEEECCCCCCCCCHHHHHHHHHHCCC--EEECCHHHCEEE
T ss_conf             003779999853887766733899999984893--886796577077


No 32 
>TIGR00252 TIGR00252 conserved hypothetical protein TIGR00252; InterPro: IPR003509 The function of this family is unknown. Members include several bacterial hypothetical proteins..
Probab=63.63  E-value=7.4  Score=21.08  Aligned_cols=48  Identities=15%  Similarity=0.116  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCE-EEEEEECC
Q ss_conf             9999999999978989999811888987439999069829-99999768
Q gi|254780128|r   13 DVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGL-WWIEVKKP   60 (103)
Q Consensus        13 ~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~-~fIEvK~~   60 (103)
                      -.|......|+.-|+...--....+-|==|||.-.||++. +|||||.=
T Consensus        22 a~E~~ar~wLE~kGl~fiaa~~~~~~GEiDLI~~fPd~~~i~FVEVr~R   70 (141)
T TIGR00252        22 AFESQARAWLEQKGLKFIAANVNSKWGEIDLIMRFPDKKTIVFVEVRTR   70 (141)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEECCCCCCCEEEEEEEECC
T ss_conf             1799999987733157667530689981221111899726888875105


No 33 
>pfam05116 S6PP Sucrose-6F-phosphate phosphohydrolase. This family consists of Sucrose-6F-phosphate phosphohydrolase proteins found in plants and cyanobacteria. Sucrose-6(F)-phosphate phosphohydrolase catalyses the final step in the pathway of sucrose biosynthesis.
Probab=61.66  E-value=17  Score=18.93  Aligned_cols=43  Identities=21%  Similarity=0.243  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CC--CEEEEECCCCCEEE
Q ss_conf             48899999999999999789899998118889-----------87--43999906982999
Q gi|254780128|r    7 HYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GC--PDRLIITPNGGLWW   54 (103)
Q Consensus         7 h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------Gv--PDli~~~~~g~~~f   54 (103)
                      +..++..  .+.++.+++.|..+.  .+.||+           |+  ||.+++. +|...+
T Consensus        18 ~~i~~~~--~~al~~l~~~Gi~vv--iaTGR~~~~~~~~~~~l~l~~p~~~I~~-nG~~I~   73 (247)
T pfam05116        18 NEALARL--NQLLEAQYRPDSLLV--FATGRSLDSAKELLKEKPLPTPDVLITS-VGTEIY   73 (247)
T ss_pred             CCCCHHH--HHHHHHHHHCCCEEE--EECCCCHHHHHHHHHHCCCCCCCEEEEC-CCEEEE
T ss_conf             9588999--999999995898899--9889999999999997598999989975-975999


No 34 
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH).  The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold.  The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.  In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=59.60  E-value=18  Score=18.76  Aligned_cols=62  Identities=23%  Similarity=0.253  Sum_probs=42.1

Q ss_pred             CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCH-------HHHHHHHH
Q ss_conf             1888987439999069829999997689886889999999999789889998598-------99999999
Q gi|254780128|r   34 FVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM-------EEVDNFLE   96 (103)
Q Consensus        34 ~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~-------edv~~~l~   96 (103)
                      -|-.+|+-| +.+-++-.=+.||++.|+--.........+-..+.|+...|++++       +++++++.
T Consensus        62 vPeeA~i~~-i~FD~~~gEV~Iea~kPg~viGk~g~~l~eI~~~tGW~p~v~RtPpi~S~ti~~IR~~l~  130 (145)
T cd02410          62 VPEEAGITD-IYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPPIQSRTVKSIRRFLR  130 (145)
T ss_pred             CCCCCCCEE-EEECCCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             896468446-897488857999977977797276167999999739815788659996178999999999


No 35 
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=58.80  E-value=19  Score=18.63  Aligned_cols=76  Identities=21%  Similarity=0.268  Sum_probs=46.5

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEE--------E---ECCCCC-------CCH---HH
Q ss_conf             99999999999999789899998118889874399990698299999--------9---768988-------688---99
Q gi|254780128|r   10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIE--------V---KKPTGR-------LSH---QQ   68 (103)
Q Consensus        10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIE--------v---K~~~gk-------ls~---~Q   68 (103)
                      ++..+|..+...+-..|-.+.. ...+-+|-||+ ++-.---++|+-        +   |.|+.+       ++.   .-
T Consensus        20 ~dTkpE~~lr~~L~~~G~rfR~-~~~~lpGkPDi-Vl~~y~~viFvHGCFWh~H~c~~a~vPksnt~fWleKi~kNveRD   97 (150)
T COG3727          20 RDTKPEKRLRSLLTGQGLRFRV-QDKDLPGKPDI-VLPKYRCVIFVHGCFWHGHHCYLAKVPKSNTEFWLEKIGKNVERD   97 (150)
T ss_pred             CCCCHHHHHHHHHHHCCEEEEE-CCCCCCCCCCE-EECCCEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             4766899999998536627885-37889999988-523733899985100257744445688742388999986666654


Q ss_pred             HHHHHHHHHCCCEEEEECC
Q ss_conf             9999999978988999859
Q gi|254780128|r   69 MSEIEELRRRGQRVKVLVS   87 (103)
Q Consensus        69 ~~~~~~l~~~G~~~~Vv~s   87 (103)
                      +.-+.+|++.|+.+-||+-
T Consensus        98 ~r~~~~L~~~GwrvlvVWE  116 (150)
T COG3727          98 ERDIKRLQQLGWRVLVVWE  116 (150)
T ss_pred             HHHHHHHHHCCCEEEEEEE
T ss_conf             8999999975975999986


No 36 
>pfam06555 consensus
Probab=58.14  E-value=19  Score=18.59  Aligned_cols=13  Identities=15%  Similarity=-0.048  Sum_probs=5.3

Q ss_pred             HHHHHHHCCCEEE
Q ss_conf             9999997898999
Q gi|254780128|r   18 LVTGAKKLDCWVR   30 (103)
Q Consensus        18 l~~~lk~~G~~~~   30 (103)
                      +++.+++.|.-++
T Consensus         3 ~i~~L~~~~f~~~   15 (200)
T pfam06555         3 TVENLEKNNFEAY   15 (200)
T ss_pred             HHHHHHHCCCEEE
T ss_conf             7999997898799


No 37 
>cd01473 vWA_CTRP CTRP for  CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60  amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=53.92  E-value=23  Score=18.14  Aligned_cols=68  Identities=9%  Similarity=0.068  Sum_probs=38.3

Q ss_pred             CCCCCCCCEEEEECCCCCE-----------------EEEEEEC-CCCCCCHHHHHHHHHH--HHCCCEEEEECCHHHHHH
Q ss_conf             1888987439999069829-----------------9999976-8988688999999999--978988999859899999
Q gi|254780128|r   34 FVGRRGCPDRLIITPNGGL-----------------WWIEVKK-PTGRLSHQQMSEIEEL--RRRGQRVKVLVSMEEVDN   93 (103)
Q Consensus        34 ~~g~~GvPDli~~~~~g~~-----------------~fIEvK~-~~gkls~~Q~~~~~~l--~~~G~~~~Vv~s~edv~~   93 (103)
                      .+.|+|+|.+++..-||+-                 -.|++-+ .-|.....|...+.-.  .+..|..+...+++.+..
T Consensus       102 ~g~R~~vpkv~IvlTDG~s~~~~~~~~~~~a~~lr~~gV~i~avGVg~~~~~eL~~iag~~~~~~~c~~~~~~~fd~l~~  181 (192)
T cd01473         102 GNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLAGCDINNDNCPNVIKTEWNNLNG  181 (192)
T ss_pred             CCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHCCCCCCCCCCEEEECCHHHHHH
T ss_conf             78888997499999569988731678999999999879789999806379999999869998899775799479789999


Q ss_pred             HHHHHHHH
Q ss_conf             99999863
Q gi|254780128|r   94 FLEELACT  101 (103)
Q Consensus        94 ~l~~l~~t  101 (103)
                      +++++...
T Consensus       182 i~~~l~~~  189 (192)
T cd01473         182 ISKFLTDK  189 (192)
T ss_pred             HHHHHHHH
T ss_conf             99999997


No 38 
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=53.58  E-value=19  Score=18.58  Aligned_cols=37  Identities=30%  Similarity=0.427  Sum_probs=26.5

Q ss_pred             CCCCCEEEEECCCCC-EEEEEEECCCCCCCH--HHHHHHHH
Q ss_conf             898743999906982-999999768988688--99999999
Q gi|254780128|r   37 RRGCPDRLIITPNGG-LWWIEVKKPTGRLSH--QQMSEIEE   74 (103)
Q Consensus        37 ~~GvPDli~~~~~g~-~~fIEvK~~~gkls~--~Q~~~~~~   74 (103)
                      ..=.||+.++. +|- .+.||+|+|......  +|...-+.
T Consensus       123 ~~~rpDvvlfI-NGiPlv~iElK~~~~~~~~a~~Qi~~Y~~  162 (962)
T COG0610         123 RKRRPDVVLFI-NGLPLVTIELKNPGVENNEAFNQIKRYQK  162 (962)
T ss_pred             CCCCCCEEEEE-CCCEEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             88787569998-68656877506875356999999988610


No 39 
>pfam03460 NIR_SIR_ferr Nitrite/Sulfite reductase ferredoxin-like half domain. Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidized anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.
Probab=52.39  E-value=24  Score=17.99  Aligned_cols=52  Identities=29%  Similarity=0.592  Sum_probs=38.5

Q ss_pred             CCCCEEEEEEECCCCCCCHHHHHHHHHHH-HCC-CEEEEE---------CCHHHHHHHHHHHHH
Q ss_conf             69829999997689886889999999999-789-889998---------598999999999986
Q gi|254780128|r   48 PNGGLWWIEVKKPTGRLSHQQMSEIEELR-RRG-QRVKVL---------VSMEEVDNFLEELAC  100 (103)
Q Consensus        48 ~~g~~~fIEvK~~~gkls~~Q~~~~~~l~-~~G-~~~~Vv---------~s~edv~~~l~~l~~  100 (103)
                      ++| .+++-++.|.|++++.|...+..+. +.| ....+.         -..+++.+++++|..
T Consensus         4 ~~g-~~~vri~~p~G~lt~~ql~~la~ia~~yg~g~i~lT~rq~i~l~~i~~~~~~~v~~~L~~   66 (67)
T pfam03460         4 KDG-DYMVRVRVPGGRLTAEQLRALADIAEKYGDGEIRLTTRQNLELHGVPEEDLPELLEELAE   66 (67)
T ss_pred             CCC-CEEEEEECCCCEECHHHHHHHHHHHHHHCCCCEEECCCCCEEECCCCHHHHHHHHHHHHC
T ss_conf             678-689999618908489999999999998379958787987579679898999999999970


No 40 
>pfam10313 DUF2415 Uncharacterized protein domain (DUF2415). This is a short, 30 residue domain, from a family of proteins conserved in fungi. The function is unknown. There is a characteristic DLL sequence motif.
Probab=50.88  E-value=25  Score=17.85  Aligned_cols=30  Identities=27%  Similarity=0.298  Sum_probs=23.5

Q ss_pred             EEEEEECCCCCCCCEEEEECC-CCCEEEEEEEC
Q ss_conf             999981188898743999906-98299999976
Q gi|254780128|r   28 WVRKASFVGRRGCPDRLIITP-NGGLWWIEVKK   59 (103)
Q Consensus        28 ~~~K~~~~g~~GvPDli~~~~-~g~~~fIEvK~   59 (103)
                      +|.||..  .+|.+||+++.. .|++.-+.+++
T Consensus         4 R~~kFSp--~~~~~DLLv~sE~~Grvhv~DlR~   34 (43)
T pfam10313         4 RVCKFSP--ENGLNDLLVISEHVGRVHVADLRT   34 (43)
T ss_pred             EEEEECC--CCCCCCEEEEEECCCEEEEEECCC
T ss_conf             7999669--899763799991687388999000


No 41 
>pfam04313 HSDR_N Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
Probab=48.87  E-value=19  Score=18.60  Aligned_cols=23  Identities=35%  Similarity=0.527  Sum_probs=17.3

Q ss_pred             CCCCCEEEEECCCCC-EEEEEEECC
Q ss_conf             898743999906982-999999768
Q gi|254780128|r   37 RRGCPDRLIITPNGG-LWWIEVKKP   60 (103)
Q Consensus        37 ~~GvPDli~~~~~g~-~~fIEvK~~   60 (103)
                      +..-||++++. +|- .+.||+|++
T Consensus        17 ~~~r~Divlfi-NGlPl~~iE~K~~   40 (90)
T pfam04313        17 QKRRPDYVLFV-NGLPLAVIELKRT   40 (90)
T ss_pred             CCCCCCEEEEE-CCCEEEEEEECCC
T ss_conf             06656699998-8969999997588


No 42 
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=44.81  E-value=32  Score=17.27  Aligned_cols=34  Identities=12%  Similarity=0.181  Sum_probs=27.6

Q ss_pred             CCCCCCHHHH-HHHHHHHHCCCEEEEECCHHHHHH
Q ss_conf             8988688999-999999978988999859899999
Q gi|254780128|r   60 PTGRLSHQQM-SEIEELRRRGQRVKVLVSMEEVDN   93 (103)
Q Consensus        60 ~~gkls~~Q~-~~~~~l~~~G~~~~Vv~s~edv~~   93 (103)
                      .++-++|+|. ..++.|+..+|.+.+|+|+..+++
T Consensus        93 dKdalt~E~v~~vv~eL~~~~fDyIi~DsPAGIE~  127 (272)
T COG2894          93 DKDALTPEGVKKVVNELKAMDFDYIIIDSPAGIEQ  127 (272)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCEEEECCCCHHHH
T ss_conf             72227999999999999766998899648406778


No 43 
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=44.31  E-value=32  Score=17.22  Aligned_cols=37  Identities=19%  Similarity=0.222  Sum_probs=28.2

Q ss_pred             CCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf             6889999999999789889998598999999999986
Q gi|254780128|r   64 LSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC  100 (103)
Q Consensus        64 ls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l~~  100 (103)
                      |...=....+.+.+.|+.++.+.+.||+.+++.++--
T Consensus        63 Ld~~l~~~~~~v~~~Gg~vy~A~~aedA~~ii~~iv~   99 (459)
T COG1139          63 LDEYLEQLEENVTRNGGHVYFAKDAEDAREIIGEIVG   99 (459)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
T ss_conf             8999999999999719879983788999999999975


No 44 
>TIGR00260 thrC threonine synthase; InterPro: IPR004450   Threonine synthase () is involved in threonine biosynthesis. It catalyses the conversion of O-phospho-L-homoserine and water into L-threonine and orthophosphate, using pyridoxal phosphate as a cofactor. The pyridoxal-phosphate binding site is a Lys (K) residue. The enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes .; GO: 0004795 threonine synthase activity, 0009088 threonine biosynthetic process.
Probab=44.12  E-value=17  Score=18.92  Aligned_cols=41  Identities=17%  Similarity=0.363  Sum_probs=34.5

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHHHH
Q ss_conf             898868899999999997898899985-98999999999986
Q gi|254780128|r   60 PTGRLSHQQMSEIEELRRRGQRVKVLV-SMEEVDNFLEELAC  100 (103)
Q Consensus        60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv~-s~edv~~~l~~l~~  100 (103)
                      |.|+++|.|..-+-.--..|..+.=|+ ++||+.+++.++-.
T Consensus       115 P~Gki~p~Q~~Kl~~~~~~n~~v~~i~G~FDda~~~v~~~~~  156 (423)
T TIGR00260       115 PAGKISPLQLGKLAQALIYNAKVIAIDGNFDDAQRLVKELFE  156 (423)
T ss_pred             CCCCCCHHHCCCEEEEECCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf             288533302153013323783899982787999999999861


No 45 
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=43.43  E-value=33  Score=17.14  Aligned_cols=42  Identities=29%  Similarity=0.411  Sum_probs=27.9

Q ss_pred             CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf             1888987439999069829999997689886889999999999789889998
Q gi|254780128|r   34 FVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVL   85 (103)
Q Consensus        34 ~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv   85 (103)
                      .++|+++|.++++.-||+.        .+...+.  ...+.|++.|...+++
T Consensus       102 ~g~R~~vpkv~illTDG~s--------~d~~~~~--~~a~~Lr~~GV~ifav  143 (186)
T cd01471         102 RGNRENAPQLVIIMTDGIP--------DSKFRTL--KEARKLRERGVIIAVL  143 (186)
T ss_pred             CCCCCCCCEEEEEEECCCC--------CCCCHHH--HHHHHHHHCCCEEEEE
T ss_conf             6889999859999906987--------7852589--9999999889999999


No 46 
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=42.70  E-value=34  Score=17.07  Aligned_cols=32  Identities=25%  Similarity=0.404  Sum_probs=24.0

Q ss_pred             HHHHHHHHHCCCEEEEE--CCHHHHHHHHHHHHH
Q ss_conf             99999999789889998--598999999999986
Q gi|254780128|r   69 MSEIEELRRRGQRVKVL--VSMEEVDNFLEELAC  100 (103)
Q Consensus        69 ~~~~~~l~~~G~~~~Vv--~s~edv~~~l~~l~~  100 (103)
                      ...+++|+++|..+++.  .|+||+.+-++.+..
T Consensus        90 ~~~~~~L~~~GI~v~~~~~~sl~di~~~i~~lG~  123 (265)
T PRK03379         90 ERQVDQLASLGIKVMWVDATSIEQIADALRQLAP  123 (265)
T ss_pred             HHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHH
T ss_conf             8999999816975883599999999999999998


No 47 
>COG4073 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.05  E-value=35  Score=17.01  Aligned_cols=79  Identities=18%  Similarity=0.195  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHHHCCCEEE------------EEECCCCC-CCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             99999999999997898999------------98118889-874399990698299999976898868899999999997
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVR------------KASFVGRR-GCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRR   77 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~------------K~~~~g~~-GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~   77 (103)
                      ++..-..+.+.++++.--+|            |.++++++ |||-|+.+- .| ++.       |.+||.|+..+-. .+
T Consensus        68 ~s~~G~~ilr~vek~rP~vY~ElH~Yr~eny~KLt~~~Rs~gVP~lidl~-ag-VLl-------gSVSP~irkr~~~-e~  137 (198)
T COG4073          68 RSEVGARILRVVEKLRPDVYVELHCYRPENYRKLTAERRSGGVPPLIDLG-AG-VLL-------GSVSPRIRKRIFK-ED  137 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHCCCCCCCCCCCEEEEC-CC-EEE-------EECCHHHHHHHCC-CC
T ss_conf             54120799999997297618997634876787752554358999606605-77-588-------4058899877453-10


Q ss_pred             CCCEEEE-ECCHHHHHHHHHHHH
Q ss_conf             8988999-859899999999998
Q gi|254780128|r   78 RGQRVKV-LVSMEEVDNFLEELA   99 (103)
Q Consensus        78 ~G~~~~V-v~s~edv~~~l~~l~   99 (103)
                      .--...| +++.+.+.+++.++.
T Consensus       138 lclT~Eip~~~s~~s~d~v~eiL  160 (198)
T COG4073         138 LCLTLEIPRRGSDRSLDVVSEIL  160 (198)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHH
T ss_conf             37999804789806899999999


No 48 
>COG3331 PrfA Penicillin-binding protein-related factor A, putative recombinase [General function prediction only]
Probab=41.80  E-value=35  Score=16.99  Aligned_cols=75  Identities=16%  Similarity=0.180  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHHHHCCCEEEE---------EECCCC------------CCCCEEEEECCCCCEEEEEEECCCCC------
Q ss_conf             999999999999978989999---------811888------------98743999906982999999768988------
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRK---------ASFVGR------------RGCPDRLIITPNGGLWWIEVKKPTGR------   63 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K---------~~~~g~------------~GvPDli~~~~~g~~~fIEvK~~~gk------   63 (103)
                      |+.|+.-+.-++.+--.+..|         +..|-+            +---|-...++ |.++-.|.|..+++      
T Consensus        11 E~~In~T~~~y~~~~~a~i~Kk~tPVqiv~v~yp~rs~a~i~eayf~~kSttDY~GvYk-G~yidFEaKeTknktsFpl~   89 (177)
T COG3331          11 EADINKTNDYYLAHDIAVIHKKPTPVQIVNVDYPKRSGAVIKEAYFRQKSTTDYYGVYK-GYYIDFEAKETKNKTSFPLK   89 (177)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECCCCCEEEEECCCCCCCCHHHHHHCCCCCCCEEEEEEC-CEEEEEEECCCCCCCCCCHH
T ss_conf             99999899887635736886047662378704720032011233405788630456850-27975560013566647345


Q ss_pred             -CCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             -68899999999997898899985
Q gi|254780128|r   64 -LSHQQMSEIEELRRRGQRVKVLV   86 (103)
Q Consensus        64 -ls~~Q~~~~~~l~~~G~~~~Vv~   86 (103)
                       ..|+|...+....+.|+.+++.-
T Consensus        90 ni~~HQi~hlk~v~~q~Gi~Flli  113 (177)
T COG3331          90 NIHPHQIEHLKNVLQQGGISFLLI  113 (177)
T ss_pred             HCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf             438889999999985698389999


No 49 
>PRK09534 btuF corrinoid ABC transporter substrate-binding protein; Reviewed
Probab=40.23  E-value=37  Score=16.84  Aligned_cols=33  Identities=18%  Similarity=0.189  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHCCCEEEEEC---CHHHHHHHHHHHHH
Q ss_conf             9999999997898899985---98999999999986
Q gi|254780128|r   68 QMSEIEELRRRGQRVKVLV---SMEEVDNFLEELAC  100 (103)
Q Consensus        68 Q~~~~~~l~~~G~~~~Vv~---s~edv~~~l~~l~~  100 (103)
                      +...++.|+++|..++++.   |+|++.+-|+.|..
T Consensus       130 ~~~~v~~L~~~GI~V~v~~~a~SiddV~~~I~~iG~  165 (364)
T PRK09534        130 RNDTVTRLRSAGITVFQFRAATSIDGVVEKTATIGR  165 (364)
T ss_pred             CHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             567899999769969991898899999999999999


No 50 
>TIGR02258 2_5_ligase 2'-5' RNA ligase; InterPro: IPR004175 Members of this entry are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known . They belong to the 2H phosphoeseterase superfamily . They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.; GO: 0008664 2'-5'-RNA ligase activity, 0016070 RNA metabolic process.
Probab=40.07  E-value=37  Score=16.82  Aligned_cols=63  Identities=14%  Similarity=0.108  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHCCCEE--EEEECCCCCCCCEEEEECCCCCEEEEEEECCCC-CCCHHHHHHHHHHHHCCCE
Q ss_conf             999999999789899--998118889874399990698299999976898-8688999999999978988
Q gi|254780128|r   15 EKRLVTGAKKLDCWV--RKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG-RLSHQQMSEIEELRRRGQR   81 (103)
Q Consensus        15 e~~l~~~lk~~G~~~--~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g-kls~~Q~~~~~~l~~~G~~   81 (103)
                      -..|..++.+...--  +.+.-.|--.+|+    ..+.|++|+.|+.+.+ .|+..|...-+.+.++|+.
T Consensus        54 ~~~l~~~L~~~~~~~~~F~l~l~g~G~F~~----~~~pRvlWaGv~~~~~~~L~~L~~~~~~~l~~~G~~  119 (189)
T TIGR02258        54 VEELEDALAKIAEPPEPFTLKLEGVGVFGN----PKSPRVLWAGVEESEEKELTQLQEELERALAKAGFS  119 (189)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEEECCCCC----CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             999999888750389973478752102788----888768998438996157899999999999964888


No 51 
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=39.91  E-value=38  Score=16.81  Aligned_cols=57  Identities=12%  Similarity=0.049  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHH
Q ss_conf             999999999997898999981188898743999906982999999768988688999
Q gi|254780128|r   13 DVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM   69 (103)
Q Consensus        13 ~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~   69 (103)
                      .+.+++.+.+.+.|+.+.+....|.+-.+=-|-=...|.++++.+..+...+++..+
T Consensus        21 ~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~   77 (95)
T PRK00453         21 ALVERYKGVITKNGGEIHKVEDWGRRRLAYPINKLRKGHYVLLNFEADPAAIAELER   77 (95)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECCCCEEEEEEEEEEECHHHHHHHHH
T ss_conf             999999999997998899985021200442306675899999999989889999999


No 52 
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473   There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below:    Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA.    Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.   This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.
Probab=38.81  E-value=35  Score=16.97  Aligned_cols=26  Identities=35%  Similarity=0.353  Sum_probs=20.5

Q ss_pred             CCC---CCEEEEECCCCCE-EEEEEECCCCC
Q ss_conf             898---7439999069829-99999768988
Q gi|254780128|r   37 RRG---CPDRLIITPNGGL-WWIEVKKPTGR   63 (103)
Q Consensus        37 ~~G---vPDli~~~~~g~~-~fIEvK~~~gk   63 (103)
                      ..|   .||+.++. +|-. +-||+|.|=++
T Consensus       133 ~~~kfRrpD~~lfv-NGiPLv~iElKkp~~~  162 (813)
T TIGR00348       133 ENIKFRRPDVTLFV-NGIPLVIIELKKPLKE  162 (813)
T ss_pred             CCCCEECCCEEEEE-CCCEEEEEECCCCCCC
T ss_conf             88866457047875-2211253230686663


No 53 
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=37.64  E-value=41  Score=16.59  Aligned_cols=48  Identities=21%  Similarity=0.303  Sum_probs=34.3

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHHH
Q ss_conf             999997689886889999999999789889----998598999999999986
Q gi|254780128|r   53 WWIEVKKPTGRLSHQQMSEIEELRRRGQRV----KVLVSMEEVDNFLEELAC  100 (103)
Q Consensus        53 ~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~----~Vv~s~edv~~~l~~l~~  100 (103)
                      +.-++=.+.+..-..|...+..|+..|+.+    .++.+.+++.++++++..
T Consensus       214 ~~y~~~~~~~~~~~t~~e~l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~~  265 (307)
T cd00114         214 FIYGLGEAEGLGPKTQSEALAFLKEWGFPVSPETRLCKNIEEVLAFYDEIEA  265 (307)
T ss_pred             EEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHH
T ss_conf             8998552578886778999999997799668861897999999999999997


No 54 
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=37.11  E-value=42  Score=16.54  Aligned_cols=54  Identities=20%  Similarity=0.135  Sum_probs=36.0

Q ss_pred             CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCH
Q ss_conf             1888987439999069829999997689886889999999999789889998598
Q gi|254780128|r   34 FVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM   88 (103)
Q Consensus        34 ~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~   88 (103)
                      -|-.+|+-| +.+-++-.-+.||+|.|+--.-.......+-..+.|+...|++++
T Consensus        79 vp~~a~i~~-~~fd~~~~ev~i~~~kpg~~~g~~g~~~~~i~~~~gw~~~v~r~p  132 (630)
T TIGR03675        79 VPEEAGITD-IYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP  132 (630)
T ss_pred             CCCCCCCEE-EEECCCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECC
T ss_conf             895358415-897489727999977963676475167999999749746888659


No 55 
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=36.85  E-value=42  Score=16.51  Aligned_cols=28  Identities=25%  Similarity=0.258  Sum_probs=16.6

Q ss_pred             HHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf             9999789889998598999999999986
Q gi|254780128|r   73 EELRRRGQRVKVLVSMEEVDNFLEELAC  100 (103)
Q Consensus        73 ~~l~~~G~~~~Vv~s~edv~~~l~~l~~  100 (103)
                      --++..|..++.+.+.|++.+.|++|..
T Consensus        16 lgF~~lG~dvfpv~~~eEa~~~l~~La~   43 (104)
T PRK01395         16 LPFKALGFDVFPVIEEQEARNTLRKLAM   43 (104)
T ss_pred             HHHHHCCEEEEECCCHHHHHHHHHHHHH
T ss_conf             8888658047854887999999999986


No 56 
>pfam09572 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
Probab=36.52  E-value=43  Score=16.48  Aligned_cols=57  Identities=12%  Similarity=0.012  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEE------EE--------------CCCCCCC-CEEEEECCCCC----EEEEEEECCCCC
Q ss_conf             89999999999999978989999------81--------------1888987-43999906982----999999768988
Q gi|254780128|r    9 QTEKDVEKRLVTGAKKLDCWVRK------AS--------------FVGRRGC-PDRLIITPNGG----LWWIEVKKPTGR   63 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~~G~~~~K------~~--------------~~g~~Gv-PDli~~~~~g~----~~fIEvK~~~gk   63 (103)
                      -.|.+-+.++..++.+.|..-..      +.              -+++--+ -|.++...|++    ..+||+|+.++-
T Consensus       120 aqErRQl~~I~~~L~A~Gy~k~~~~~~~~~~~m~Pgt~sFr~nv~vG~~~~i~vD~Vi~~~d~r~~~lp~~iEaKss~d~  199 (251)
T pfam09572       120 AQERRQLAAIKSWLEARGYTQLATGAALPVNSMPPGTFSFRRNVPVGKRVNIPVDAVVRPHDGRSGKLPMLIEAKSSGDF  199 (251)
T ss_pred             HHHHHHHHHHHHHHHHCCCEECCCCCCCCHHHCCCCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCC
T ss_conf             67788899999999966965646778874533498762466723347744665667985047766775546774225675


Q ss_pred             CC
Q ss_conf             68
Q gi|254780128|r   64 LS   65 (103)
Q Consensus        64 ls   65 (103)
                      .+
T Consensus       200 TN  201 (251)
T pfam09572       200 TN  201 (251)
T ss_pred             CC
T ss_conf             56


No 57 
>pfam06616 BsuBI_PstI_RE BsuBI/PstI restriction endonuclease C-terminus. This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognize the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system.
Probab=36.00  E-value=43  Score=16.43  Aligned_cols=63  Identities=19%  Similarity=0.227  Sum_probs=44.3

Q ss_pred             CCCCCEEEEECCCCCE-EEEEEECCCCCCCHHHHHHHHHHHH--CCCEEEEE--CCHHHHHHHHHHHH
Q ss_conf             8987439999069829-9999976898868899999999997--89889998--59899999999998
Q gi|254780128|r   37 RRGCPDRLIITPNGGL-WWIEVKKPTGRLSHQQMSEIEELRR--RGQRVKVL--VSMEEVDNFLEELA   99 (103)
Q Consensus        37 ~~GvPDli~~~~~g~~-~fIEvK~~~gkls~~Q~~~~~~l~~--~G~~~~Vv--~s~edv~~~l~~l~   99 (103)
                      +.-.||+++...+..+ +|||.=+..|-+++.-+..+.+|-.  ....++|-  -+....++++.+|.
T Consensus       212 h~klPDvVl~d~~~~wL~liEaVtS~GPv~~~R~~eL~~l~~~~~~~lvfVTAF~dR~~fkk~~~eiA  279 (306)
T pfam06616       212 HGKLPDIVLYDLGKKWLVLVEVVASDGPVDGKRHEELAKLFADAPAGLVFVTAFPDRSAFKKYLAEIA  279 (306)
T ss_pred             CCCCCCEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHC
T ss_conf             56899789984689969999997377998989999999998538888699995589899999988732


No 58 
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=35.56  E-value=44  Score=16.39  Aligned_cols=57  Identities=21%  Similarity=0.156  Sum_probs=40.8

Q ss_pred             CCHHHHHHHHHHHHHH----CC-CEEE-----EEECCCCCCCCEEEEECCC-CCEEEEEEECCCCCCC
Q ss_conf             8999999999999997----89-8999-----9811888987439999069-8299999976898868
Q gi|254780128|r    9 QTEKDVEKRLVTGAKK----LD-CWVR-----KASFVGRRGCPDRLIITPN-GGLWWIEVKKPTGRLS   65 (103)
Q Consensus         9 ~~E~~ie~~l~~~lk~----~G-~~~~-----K~~~~g~~GvPDli~~~~~-g~~~fIEvK~~~gkls   65 (103)
                      ..|+++|+.+++.+++    +| |.++     ++..++..=..||+..... ..++-||+|+.+=+|.
T Consensus       182 ~~E~dLE~ali~~i~~FLLELG~GFaFvgrQ~ri~v~~~dfyiDLlFYh~~L~c~V~IELK~g~f~pe  249 (320)
T pfam06250       182 YSEKDLEKALINHLEKFLLELGAGFAFVGRQKRIQVDDEDFYIDLLFYHRKLRCLVAVDLKIGKFKPE  249 (320)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEHHHHHHHHHCCCEEEEEECCCCCCHH
T ss_conf             48899999999999999998189816754557888779323404766634114136776415876778


No 59 
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=35.53  E-value=44  Score=16.39  Aligned_cols=50  Identities=20%  Similarity=0.415  Sum_probs=33.1

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHH-HCC--CEEEEE-C--------CHHHHHHHHHHHHHH
Q ss_conf             9999997689886889999999999-789--889998-5--------989999999999863
Q gi|254780128|r   52 LWWIEVKKPTGRLSHQQMSEIEELR-RRG--QRVKVL-V--------SMEEVDNFLEELACT  101 (103)
Q Consensus        52 ~~fIEvK~~~gkls~~Q~~~~~~l~-~~G--~~~~Vv-~--------s~edv~~~l~~l~~t  101 (103)
                      .|++=+|-|+|.+|+.|...+..+. +.|  +...+. +        ..+|+.++++.|.+.
T Consensus        65 ~FMlRvriPgG~lt~~Q~r~la~ia~~yg~~G~~~iTTRQniQlh~I~~~d~~~i~~~L~~v  126 (513)
T PRK09566         65 KFMLRLRVPNGILTSQQLRVLASIVQRYGEDGSADITTRQNLQLRGILLEDLPEILNRLKAV  126 (513)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHCCCCHHHHHHHHHHHHHC
T ss_conf             46889667897559999999999999868998599973711211587778899999999986


No 60 
>TIGR00075 hypD hydrogenase expression/formation protein HypD; InterPro: IPR002780   HypD is involved in the hyp operon which is needed for the activity of the three hydrogenase isoenzymes in Escherichia coli. HypD is one of the genes needed for formation of these enzymes . This protein has been found in Gram-negative and Gram-positive bacteria and Archaea. HypD contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into HypD resulted in Rhizobium leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas .; GO: 0046872 metal ion binding.
Probab=35.35  E-value=40  Score=16.67  Aligned_cols=57  Identities=23%  Similarity=0.321  Sum_probs=35.8

Q ss_pred             CCCCEEEEECCCCCE-EEEEE--------ECCCC--CCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHH
Q ss_conf             987439999069829-99999--------76898--86889999999999789889998598999999999
Q gi|254780128|r   38 RGCPDRLIITPNGGL-WWIEV--------KKPTG--RLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEE   97 (103)
Q Consensus        38 ~GvPDli~~~~~g~~-~fIEv--------K~~~g--kls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~   97 (103)
                      +|+|=  +..|+.+. --+|+        =+-||  |+ |-|..=+-..++.|+.+.+|||+-|+.++=.+
T Consensus        74 PGCPV--Cv~P~~~ID~a~~LA~~~~~i~~tfGDM~RV-PGs~~SL~~~ra~G~DvRIVYS~~dal~iA~~  141 (384)
T TIGR00075        74 PGCPV--CVTPMEEIDEAIELAEKPEVIITTFGDMLRV-PGSGGSLLQARAEGADVRIVYSPMDALKIAKE  141 (384)
T ss_pred             CCCCE--EECCHHHHHHHHHHHCCCCEEEEECCCCCCC-CCCCCCHHHHHHCCCCEEEEECHHHHHHHHHH
T ss_conf             44881--3557378999999863798599822211117-98854478997558867998087899999986


No 61 
>pfam08011 DUF1703 Protein of unknown function (DUF1703). This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus.
Probab=31.16  E-value=52  Score=15.95  Aligned_cols=70  Identities=11%  Similarity=0.015  Sum_probs=39.0

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--CCCHHHHHHHHHHHHCCC
Q ss_conf             99999999999999789899998118889874399990698299999976898--868899999999997898
Q gi|254780128|r   10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--RLSHQQMSEIEELRRRGQ   80 (103)
Q Consensus        10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--kls~~Q~~~~~~l~~~G~   80 (103)
                      .|+-.+.-+-..+..+| ...+.......|-+|+++...++..+-+|+|..+.  .+......=++++++.++
T Consensus         2 ~E~~Y~~~~~~~~~~~~-y~v~se~es~~GR~Di~l~p~~~~~~IiE~K~~~~~~~~~~~~~~Al~QI~~k~Y   73 (101)
T pfam08011         2 DEGYYASVFYAYFASLG-YEVISEDETNKGRIDLTLKPTYTYIYIFEFKYIKVKDSDKEIAEEALEQIKEYGY   73 (101)
T ss_pred             CCHHHHHHHHHHHHHCC-CEEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             64008999999999889-7999814569994649999748819999999638643101568999999997674


No 62 
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=30.88  E-value=52  Score=15.93  Aligned_cols=26  Identities=27%  Similarity=0.285  Sum_probs=22.2

Q ss_pred             CCCCCCEEEEECCCCCEEEEEEECCC
Q ss_conf             88987439999069829999997689
Q gi|254780128|r   36 GRRGCPDRLIITPNGGLWWIEVKKPT   61 (103)
Q Consensus        36 g~~GvPDli~~~~~g~~~fIEvK~~~   61 (103)
                      |.+--||.+|-+|+|+-+-|.-|.|-
T Consensus       236 g~r~rPDvIV~LP~~k~iVIDSKvsL  261 (475)
T PRK10361        236 RSRMQPDVIVRLPQGKDVVIDAKMTL  261 (475)
T ss_pred             CCCCCCCEEEECCCCCEEEEECCCCC
T ss_conf             88228976898789975888627884


No 63 
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.   Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.  DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately.    This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=30.88  E-value=53  Score=15.92  Aligned_cols=40  Identities=30%  Similarity=0.395  Sum_probs=29.3

Q ss_pred             CCCCEEEEEC--CCCC-EEEEEEECCCCCCCHHHHHHHHHHHHC
Q ss_conf             9874399990--6982-999999768988688999999999978
Q gi|254780128|r   38 RGCPDRLIIT--PNGG-LWWIEVKKPTGRLSHQQMSEIEELRRR   78 (103)
Q Consensus        38 ~GvPDli~~~--~~g~-~~fIEvK~~~gkls~~Q~~~~~~l~~~   78 (103)
                      .|+|++---.  ..|. ++=|.|-+|+. ||+.|+.-+++|.+.
T Consensus       343 kG~p~~~~~~Fk~~GDl~v~V~v~~P~~-Ls~~q~~lLe~l~~~  385 (386)
T TIGR02349       343 KGVPRLRGSNFKGRGDLLVTVKVETPKN-LSKEQKELLEELAEA  385 (386)
T ss_pred             CCCCCCCCCCCCCCCCEEEEEEEEECCC-CCHHHHHHHHHHHHC
T ss_conf             7501468876763366699999985898-788899999999732


No 64 
>PRK10976 putative sugar phosphatase; Provisional
Probab=30.10  E-value=54  Score=15.84  Aligned_cols=44  Identities=16%  Similarity=0.040  Sum_probs=25.5

Q ss_pred             ECCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CCCEEEEECCCCCEEE
Q ss_conf             048899999999999999789899998118889-----------8743999906982999
Q gi|254780128|r    6 FHYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GCPDRLIITPNGGLWW   54 (103)
Q Consensus         6 ~h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------GvPDli~~~~~g~~~f   54 (103)
                      -|..++..  ...++.+++.|..+.  .+.||+           |+++.+++. +|...+
T Consensus        17 ~~~is~~~--~~ai~~l~~~Gi~~v--iATGR~~~~~~~~~~~l~~~~~~I~~-NGa~i~   71 (266)
T PRK10976         17 DHTLSPYA--KETLKLLTARGIHFV--FATGRHHVDVGQIRDNLEIKSYMITS-NGARVH   71 (266)
T ss_pred             CCCCCHHH--HHHHHHHHHCCCEEE--EECCCCHHHHHHHHHHCCCCCEEEEC-CCEEEE
T ss_conf             79719999--999999997899999--99799979999999973997418962-877999


No 65 
>COG1540 Uncharacterized proteins, homologs of lactam utilization protein B [General function prediction only]
Probab=29.76  E-value=47  Score=16.22  Aligned_cols=29  Identities=24%  Similarity=0.182  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECC
Q ss_conf             9999999997898999981188898743999906
Q gi|254780128|r   15 EKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITP   48 (103)
Q Consensus        15 e~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~   48 (103)
                      =++.++..+..|..+     +-++|+|||..+-.
T Consensus        46 M~rtV~lA~e~gV~I-----GAHPgyPDl~gFGR   74 (252)
T COG1540          46 MRRTVRLAKENGVAI-----GAHPGYPDLVGFGR   74 (252)
T ss_pred             HHHHHHHHHHCCCEE-----CCCCCCCCCCCCCC
T ss_conf             999999999849766-----35899863235674


No 66 
>pfam04720 DUF506 Protein of unknown function (DUF506). Family of uncharacterized plant proteins.
Probab=29.50  E-value=54  Score=15.87  Aligned_cols=73  Identities=16%  Similarity=0.208  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHCCCEEE----EEECCCCCCCCEEEEECCCCCEEEEEEECCC---------------------CCCCH
Q ss_conf             9999999999997898999----9811888987439999069829999997689---------------------88688
Q gi|254780128|r   12 KDVEKRLVTGAKKLDCWVR----KASFVGRRGCPDRLIITPNGGLWWIEVKKPT---------------------GRLSH   66 (103)
Q Consensus        12 ~~ie~~l~~~lk~~G~~~~----K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~---------------------gkls~   66 (103)
                      +.+.+.++..|+..|.-+-    ||.+  ..++|       .|.+-||+|-.++                     .||++
T Consensus        87 s~lrr~v~~~Lr~~GydAaiCkSkW~~--s~~~p-------~G~yeYiDVv~~~~~~~~~~R~iVd~dFrs~FEiARpt~  157 (218)
T pfam04720        87 SCLRRKVMSLLRELGYDAAICKSKWES--SGKVP-------AGEYEYIDVVDGGESKKQEVRLIVDLDFRSEFEIARPTE  157 (218)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCC--CCCCC-------CCCCEEEEEEECCCCCCCCEEEEEECCCHHHEEEECCCH
T ss_conf             899999999998669884133330678--89978-------976148999822788887505999456557523436858


Q ss_pred             HHHHHHHHHHHCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999999997898899985989999999999
Q gi|254780128|r   67 QQMSEIEELRRRGQRVKVLVSMEEVDNFLEEL   98 (103)
Q Consensus        67 ~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l   98 (103)
                      .=..-+..|    -.++|- +.|...+++.-+
T Consensus       158 ~Y~~ll~~L----P~vfVG-~~~rL~~iv~im  184 (218)
T pfam04720       158 EYKRILQSL----PRVFVG-KVERLKQLVRIM  184 (218)
T ss_pred             HHHHHHHHC----CCEEEE-CHHHHHHHHHHH
T ss_conf             999999969----984772-799999999999


No 67 
>pfam08652 RAI1 RAI1 like. RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z and binds to a nuclear exoribonuclease. It is required for 5.8S rRNA processing.
Probab=28.77  E-value=57  Score=15.70  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=17.2

Q ss_pred             CCCEEEEEEECCCCCCCHHHHHHHH
Q ss_conf             9829999997689886889999999
Q gi|254780128|r   49 NGGLWWIEVKKPTGRLSHQQMSEIE   73 (103)
Q Consensus        49 ~g~~~fIEvK~~~gkls~~Q~~~~~   73 (103)
                      ++-..|||+|+...-.++.|....+
T Consensus        13 ~~~~~yVELKTs~~~~~~~~~~~F~   37 (68)
T pfam08652        13 DNLSHYVELKTSREIQNPRQVRNFE   37 (68)
T ss_pred             CCCCCEEEEEEEECCCCHHHHHHHH
T ss_conf             9966089986641228877999999


No 68 
>pfam08608 Wyosine_form Wyosine base formation. Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Probab=28.61  E-value=25  Score=17.90  Aligned_cols=26  Identities=31%  Similarity=0.387  Sum_probs=15.8

Q ss_pred             CCEEEEEEECCC--C----CCCHHHHHHHHHH
Q ss_conf             829999997689--8----8688999999999
Q gi|254780128|r   50 GGLWWIEVKKPT--G----RLSHQQMSEIEEL   75 (103)
Q Consensus        50 g~~~fIEvK~~~--g----kls~~Q~~~~~~l   75 (103)
                      +...|||+|++.  |    +++..-.-+++++
T Consensus         2 a~P~fVEvKay~~~G~S~~rLt~~nmp~heeV   33 (62)
T pfam08608         2 AEPDFVELKAYMHVGYSRNRLTMGNMPAHEEV   33 (62)
T ss_pred             CCCCEEEEEEEEEECCCCCCCCHHHCCCHHHH
T ss_conf             99998988318986158887771339988999


No 69 
>pfam04471 Mrr_cat Restriction endonuclease. Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA.
Probab=28.54  E-value=58  Score=15.68  Aligned_cols=66  Identities=15%  Similarity=0.135  Sum_probs=41.3

Q ss_pred             HHHHHHCCCEEEEEECC-CCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHH-HHHHHHCCCEEEEE
Q ss_conf             99999789899998118-889874399990698299999976898868899999-99999789889998
Q gi|254780128|r   19 VTGAKKLDCWVRKASFV-GRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSE-IEELRRRGQRVKVL   85 (103)
Q Consensus        19 ~~~lk~~G~~~~K~~~~-g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~-~~~l~~~G~~~~Vv   85 (103)
                      .+-++++|+.-.+.+.. +--|+ |++...+++.-..|++|.-.+.+....... ...+...++.-.++
T Consensus         2 ~~ll~~~G~~~v~~t~~~~D~Gi-Dvia~~~~~~~~~VQ~K~~~~~vg~~~v~~l~~~~~~~~~~~~i~   69 (98)
T pfam04471         2 AELLEALGYREVELTGKSGDGGI-DVVATTSDGERIVVQAKRYRSTVGRPVIQELLGAKAGYGADKGVV   69 (98)
T ss_pred             HHHHHHCCCCEEEECCCCCCCCE-EEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEE
T ss_conf             68897679988997889898845-899993799899999998789899899999960277618987999


No 70 
>PRK10513 sugar phosphatase; Provisional
Probab=27.43  E-value=61  Score=15.56  Aligned_cols=44  Identities=25%  Similarity=0.164  Sum_probs=22.4

Q ss_pred             ECCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CC--C-EEEEECCCCCEEE
Q ss_conf             048899999999999999789899998118889-----------87--4-3999906982999
Q gi|254780128|r    6 FHYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GC--P-DRLIITPNGGLWW   54 (103)
Q Consensus         6 ~h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------Gv--P-Dli~~~~~g~~~f   54 (103)
                      -|-.++..+  ..++.+++.|..+.  .+.||+           |+  | |.+++. +|...+
T Consensus        18 ~~~i~~~~~--~ai~~l~~~Gi~~~--iaTGR~~~~~~~~~~~l~~~~~~~~~I~~-NGa~i~   75 (270)
T PRK10513         18 DHTISPAVK--NAIAAARAKGVNVV--LTTGRPYAGVHRYLKELHMEQPGDYCITY-NGALVQ   75 (270)
T ss_pred             CCCCCHHHH--HHHHHHHHCCCEEE--EECCCCHHHHHHHHHHHCCCCCCCEEEEC-CCEEEE
T ss_conf             796899999--99999997899999--99799868789999983888899889985-985999


No 71 
>TIGR01942 pcnB poly(A) polymerase; InterPro: IPR010206   This entry describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell , . This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well . Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase.; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0006378 mRNA polyadenylation.
Probab=26.55  E-value=60  Score=15.56  Aligned_cols=26  Identities=12%  Similarity=0.310  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf             88688999999999978988999859
Q gi|254780128|r   62 GRLSHQQMSEIEELRRRGQRVKVLVS   87 (103)
Q Consensus        62 gkls~~Q~~~~~~l~~~G~~~~Vv~s   87 (103)
                      ..+|.+=...+++|+.+||.+|||=+
T Consensus        12 ~~~S~~A~~Vv~rL~~AGyqAY~VGG   37 (448)
T TIGR01942        12 QSFSAHALNVVRRLKKAGYQAYIVGG   37 (448)
T ss_pred             HHHHHHHHHHHHHHHHCCEEEEEECC
T ss_conf             77649999999987007823767231


No 72 
>COG1553 DsrE Uncharacterized conserved protein involved in intracellular sulfur reduction [Inorganic ion transport and metabolism]
Probab=26.54  E-value=59  Score=15.61  Aligned_cols=54  Identities=22%  Similarity=0.144  Sum_probs=37.4

Q ss_pred             EEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHH
Q ss_conf             999069829999997689886889999999999789889998598999999999
Q gi|254780128|r   44 LIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEE   97 (103)
Q Consensus        44 i~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~   97 (103)
                      +.++.||-...--.-.|..-=-+++..|.+-+.++|..+.+|-...+.+.++++
T Consensus        37 iFly~DgV~~~~~~~~Pa~dEf~l~~~~~~l~~~~gv~v~~C~~ca~~RGv~~~   90 (126)
T COG1553          37 LFLYQDGVHNGNKGQKPASDEFNLIQAWLELLTEQGVPVKLCVACALRRGVTEE   90 (126)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEHHHHHHCCCCCC
T ss_conf             998601000243576986333524999999999759807660987873486641


No 73 
>pfam03190 DUF255 Protein of unknown function, DUF255.
Probab=26.51  E-value=48  Score=16.17  Aligned_cols=54  Identities=20%  Similarity=0.247  Sum_probs=34.4

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEEEEC-----------------CCCCCCCEEEEECCCCCEEEEEEECC
Q ss_conf             4889999999999999978989999811-----------------88898743999906982999999768
Q gi|254780128|r    7 HYQTEKDVEKRLVTGAKKLDCWVRKASF-----------------VGRRGCPDRLIITPNGGLWWIEVKKP   60 (103)
Q Consensus         7 h~~~E~~ie~~l~~~lk~~G~~~~K~~~-----------------~g~~GvPDli~~~~~g~~~fIEvK~~   60 (103)
                      |.|-+..+++.-+..+=...-...|+..                 .|..|+|=-+++.|||+.+|.=.=-|
T Consensus        53 hvM~~esF~d~~vA~~lN~~Fv~VkVDree~PdiD~~Ym~~~q~~~g~gGWPL~vfltPdg~Pf~~gTY~P  123 (163)
T pfam03190        53 HVMAHESFEDPEVAAILNEHFVPIKVDREERPDIDAIYMTAVQALTGSGGWPLTVFLTPDGKPFFGGTYFP  123 (163)
T ss_pred             HHHHHHHCCCHHHHHHHHHHEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEEEEEECC
T ss_conf             99998734899999999742033340632375578999999999707899751246879997468876269


No 74 
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=26.31  E-value=63  Score=15.43  Aligned_cols=42  Identities=19%  Similarity=0.343  Sum_probs=30.9

Q ss_pred             EECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf             97689886889999999999789889998598999999999986
Q gi|254780128|r   57 VKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC  100 (103)
Q Consensus        57 vK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l~~  100 (103)
                      +=-|.|+.++.|...+.-+.+  ....|--++||+.+++.++..
T Consensus       154 Vl~P~g~vs~~k~~q~~~~ga--~~i~v~G~fDda~~~vk~~~~  195 (411)
T COG0498         154 VLYPKGKVSPGKLAQMLTLGA--HVIAVDGNFDDAQELVKEAAN  195 (411)
T ss_pred             EEECCCCCCHHHHHHHHHCCC--EEEEECCCHHHHHHHHHHHHH
T ss_conf             994598788788999975388--899975968999999999996


No 75 
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=25.03  E-value=67  Score=15.29  Aligned_cols=25  Identities=24%  Similarity=0.514  Sum_probs=12.4

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             9999997689886889999999999
Q gi|254780128|r   52 LWWIEVKKPTGRLSHQQMSEIEELR   76 (103)
Q Consensus        52 ~~fIEvK~~~gkls~~Q~~~~~~l~   76 (103)
                      .+++=+|-|+|.+++.|...+..+.
T Consensus       113 ~FMlRiRiPgG~lt~~Q~r~la~iA  137 (591)
T PRK09567        113 SYMCRLRIPNGILTHWQLAGLADLA  137 (591)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             0489953689635999999999999


No 76 
>cd01143 YvrC Periplasmic binding protein YvrC.  These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=24.93  E-value=67  Score=15.28  Aligned_cols=30  Identities=30%  Similarity=0.446  Sum_probs=21.4

Q ss_pred             HHHHHHHHCCCEEEEEC---CHHHHHHHHHHHH
Q ss_conf             99999997898899985---9899999999998
Q gi|254780128|r   70 SEIEELRRRGQRVKVLV---SMEEVDNFLEELA   99 (103)
Q Consensus        70 ~~~~~l~~~G~~~~Vv~---s~edv~~~l~~l~   99 (103)
                      ...+.|++.|..+.++.   +++++.+.+..+.
T Consensus        73 ~~~~~L~~~gi~v~~~~~~~~~~~~~~~i~~lg  105 (195)
T cd01143          73 ELLEKLKDAGIPVVVLPAASSLDEIYDQIELIG  105 (195)
T ss_pred             HHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHH
T ss_conf             799998641885999758999999999999999


No 77 
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=24.87  E-value=68  Score=15.27  Aligned_cols=77  Identities=23%  Similarity=0.189  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHHHHC-----CCEEEE----------EECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             999999999999978-----989999----------81188898743999906982999999768988688999999999
Q gi|254780128|r   11 EKDVEKRLVTGAKKL-----DCWVRK----------ASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEEL   75 (103)
Q Consensus        11 E~~ie~~l~~~lk~~-----G~~~~K----------~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l   75 (103)
                      ..++-+.+.+.+++.     .-.+++          -+-|-.+|+-| +.+-++-.=+.||.|.|+=..-..-....+-.
T Consensus        47 ~~dlik~lAk~lrKRI~iR~dPsvl~~~e~A~~~I~eivP~ea~i~~-i~Fd~~tGEViIea~KPGlvigk~g~~~reI~  125 (637)
T COG1782          47 DGDLIKDLAKDLRKRIIIRPDPSVLKPPEEARKIILEIVPEEAGITD-IYFDDDTGEVIIEAKKPGLVIGKGGSTLREIT  125 (637)
T ss_pred             CHHHHHHHHHHHHHCEEECCCCHHCCCHHHHHHHHHHHCCCCCCCEE-EEECCCCCEEEEEECCCCEEEECCCHHHHHHH
T ss_conf             31699999999863268436902218989999999974862137036-78618874499995589558824721799999


Q ss_pred             HHCCCEEEEECCH
Q ss_conf             9789889998598
Q gi|254780128|r   76 RRRGQRVKVLVSM   88 (103)
Q Consensus        76 ~~~G~~~~Vv~s~   88 (103)
                      ++.|+...|++.+
T Consensus       126 ~~tgW~p~ivR~P  138 (637)
T COG1782         126 AETGWAPKIVRTP  138 (637)
T ss_pred             HHHCCCCEEEECC
T ss_conf             9748753056369


No 78 
>TIGR02291 rimK_rel_E_lig alpha-L-glutamate ligase homolog; InterPro: IPR011758   Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (IPR004666 from INTERPRO), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown..
Probab=24.53  E-value=69  Score=15.23  Aligned_cols=62  Identities=19%  Similarity=0.187  Sum_probs=40.1

Q ss_pred             CCCCHHHHHHHHHHHH---HHCCCEE---E-----E----EECCCCCCCCEEEEECCCCCEE--EEEEEC--CCCCCCHH
Q ss_conf             4889999999999999---9789899---9-----9----8118889874399990698299--999976--89886889
Q gi|254780128|r    7 HYQTEKDVEKRLVTGA---KKLDCWV---R-----K----ASFVGRRGCPDRLIITPNGGLW--WIEVKK--PTGRLSHQ   67 (103)
Q Consensus         7 h~~~E~~ie~~l~~~l---k~~G~~~---~-----K----~~~~g~~GvPDli~~~~~g~~~--fIEvK~--~~gkls~~   67 (103)
                      ..++|.+||.++=..|   -++||.-   +     |    |.+-+-.||||+=++.-.|-.+  ++=+-|  .+||-+=+
T Consensus       108 ~~i~~eeiE~hvSniL~GLySLGG~~D~AliEyrvkfDp~F~~~SYeGVPDiRiIVf~GyPVmaM~RlpTr~SdGKANLH  187 (320)
T TIGR02291       108 ALISKEEIERHVSNILAGLYSLGGKRDRALIEYRVKFDPLFESVSYEGVPDIRIIVFKGYPVMAMLRLPTRASDGKANLH  187 (320)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEECCCCHHHHCCCCCCCCCCCCCCC
T ss_conf             10154567788888887776507997736885320105344771113458726896418610210027656788830212


Q ss_pred             H
Q ss_conf             9
Q gi|254780128|r   68 Q   68 (103)
Q Consensus        68 Q   68 (103)
                      |
T Consensus       188 Q  188 (320)
T TIGR02291       188 Q  188 (320)
T ss_pred             C
T ss_conf             4


No 79 
>TIGR02502 type_III_YscX type III secretion protein, YscX family; InterPro: IPR012672   Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery ..
Probab=24.27  E-value=24  Score=18.00  Aligned_cols=17  Identities=24%  Similarity=0.477  Sum_probs=15.0

Q ss_pred             CCCCCEEEEECCCCCEE
Q ss_conf             89874399990698299
Q gi|254780128|r   37 RRGCPDRLIITPNGGLW   53 (103)
Q Consensus        37 ~~GvPDli~~~~~g~~~   53 (103)
                      ..++||+..+.|||+.+
T Consensus        24 ~~~LP~Ry~L~PDG~~V   40 (126)
T TIGR02502        24 DTDLPERYALLPDGQPV   40 (126)
T ss_pred             CCCCCCCCCCCCCCCCH
T ss_conf             89876112688767862


No 80 
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain; InterPro: IPR014089   This group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which they have been characterised , , . In most species this protein is bifunctional, existing as fused alpha-beta domains. In Pyrococcus and related species, however, the domains exist as separate polypeptides. This entry represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. One of these (along with its beta-domain partner) was characterised as ACS-II showing specificity for phenylacetyl-CoA . This entry excludes non-ACS-I paralogs. .
Probab=24.13  E-value=70  Score=15.18  Aligned_cols=26  Identities=23%  Similarity=0.192  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCCCC
Q ss_conf             99999999999978989999811888987
Q gi|254780128|r   12 KDVEKRLVTGAKKLDCWVRKASFVGRRGC   40 (103)
Q Consensus        12 ~~ie~~l~~~lk~~G~~~~K~~~~g~~Gv   40 (103)
                      .++|++|+.-++++|.+.   ..||+-|+
T Consensus       110 ~~LE~~l~~~a~kYg~Rl---~GPNclG~  135 (457)
T TIGR02717       110 AELEQKLVEIARKYGMRL---LGPNCLGI  135 (457)
T ss_pred             HHHHHHHHHHHHHCCCEE---ECCCEEEE
T ss_conf             999999999997678817---76736225


No 81 
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946    Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=23.73  E-value=57  Score=15.73  Aligned_cols=23  Identities=13%  Similarity=0.206  Sum_probs=19.2

Q ss_pred             EECCCCHHHHHHHHHHHHHHCCC
Q ss_conf             10488999999999999997898
Q gi|254780128|r    5 SFHYQTEKDVEKRLVTGAKKLDC   27 (103)
Q Consensus         5 ~~h~~~E~~ie~~l~~~lk~~G~   27 (103)
                      .+|=|+|+.||+.+.+++...|-
T Consensus       238 ~RHH~~e~~~QRav~~Av~~AGI  260 (320)
T TIGR02249       238 RRHHIDEKTIQRAVRRAVERAGI  260 (320)
T ss_pred             EEEECCCCHHHHHHHHHHHHCCC
T ss_conf             00106700432899999995789


No 82 
>pfam01250 Ribosomal_S6 Ribosomal protein S6.
Probab=23.13  E-value=73  Score=15.07  Aligned_cols=60  Identities=12%  Similarity=0.052  Sum_probs=38.6

Q ss_pred             CCHHH---HHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHH
Q ss_conf             89999---9999999999789899998118889874399990698299999976898868899
Q gi|254780128|r    9 QTEKD---VEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQ   68 (103)
Q Consensus         9 ~~E~~---ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q   68 (103)
                      .+|.+   +...+.+.+++.||.+.+....|.+-.+=-|-=...|.++++.+.++...++...
T Consensus        13 l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~   75 (92)
T pfam01250        13 LSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAELE   75 (92)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCEEEEEEEEEEECHHHHHHHH
T ss_conf             998999999999999998789889998513100033043778899999999999988999999


No 83 
>cd03008 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors. RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity.
Probab=23.12  E-value=73  Score=15.06  Aligned_cols=39  Identities=13%  Similarity=0.178  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHCC--CEEEEEEC---------CCCCCCCEEEEECCCCCEE
Q ss_conf             999999999789--89999811---------8889874399990698299
Q gi|254780128|r   15 EKRLVTGAKKLD--CWVRKASF---------VGRRGCPDRLIITPNGGLW   53 (103)
Q Consensus        15 e~~l~~~lk~~G--~~~~K~~~---------~g~~GvPDli~~~~~g~~~   53 (103)
                      +.....+.+.+.  |.++.|..         .+-+|+|-|+++-++|.++
T Consensus        77 e~~f~~y~~~MP~~WlAlPf~d~~~~~L~~~f~V~gIPtLVil~~dG~vi  126 (146)
T cd03008          77 EQQQESFLKDMPKKWLFLPFEDEFRRELEAQFSVEELPTVVVLKPDGDVL  126 (146)
T ss_pred             HHHHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCCCCCEEEEECCCCCEE
T ss_conf             99999999977987266576968999999985998788899998999897


No 84 
>pfam08282 Hydrolase_3 haloacid dehalogenase-like hydrolase. This family contains haloacid dehalogenase-like hydrolase enzymes.
Probab=23.06  E-value=73  Score=15.06  Aligned_cols=73  Identities=19%  Similarity=0.180  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CCCEEEEECCCCCEEEEEEEC--CCCCCCHHHH-HHH
Q ss_conf             48899999999999999789899998118889-----------874399990698299999976--8988688999-999
Q gi|254780128|r    7 HYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GCPDRLIITPNGGLWWIEVKK--PTGRLSHQQM-SEI   72 (103)
Q Consensus         7 h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------GvPDli~~~~~g~~~fIEvK~--~~gkls~~Q~-~~~   72 (103)
                      |..++..+  +.++++++.|..+.  .+.||+           |+++-+++. +|...+..=..  -...+++.+. ..+
T Consensus        14 ~~i~~~~~--~ai~~l~~~G~~~~--iaTGR~~~~~~~~~~~l~~~~~~I~~-NGa~i~~~~~~~l~~~~i~~~~~~~i~   88 (254)
T pfam08282        14 KKISERTK--EAIKKLQEKGIKVV--IATGRPYRGALPVLEELGLDLPVICF-NGAYIYDENGKILYKNPISKEDVKEII   88 (254)
T ss_pred             CCCCHHHH--HHHHHHHHCCCEEE--EECCCCHHHHHHHHHHCCCCCCEEEC-CCCEEEECCCEEEEEECCCHHHHHHHH
T ss_conf             93899999--99999998899999--99498799999999980999759977-971999689869999349999999999


Q ss_pred             HHHHHCCCEEEE
Q ss_conf             999978988999
Q gi|254780128|r   73 EELRRRGQRVKV   84 (103)
Q Consensus        73 ~~l~~~G~~~~V   84 (103)
                      +.+++.+....+
T Consensus        89 ~~~~~~~~~~~~  100 (254)
T pfam08282        89 EYLKENNLSILL  100 (254)
T ss_pred             HHHHHCCCEEEE
T ss_conf             999986986999


No 85 
>TIGR03081 metmalonyl_epim methylmalonyl-CoA epimerase. Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer.
Probab=22.80  E-value=74  Score=15.03  Aligned_cols=85  Identities=19%  Similarity=0.232  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHH
Q ss_conf             99999999999997898999981188898743999906982999999768988688999999999978988999859899
Q gi|254780128|r   11 EKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEE   90 (103)
Q Consensus        11 E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~ed   90 (103)
                      =+++++.+.-+.+.+|..+..-......|+=  +++...|. ..+|+=.|.+.-+|... +++  +..++..++|..++|
T Consensus         9 V~Dld~a~~fy~~~lG~~~~~~~~~~~~~~~--~~~~~~g~-~~ieL~~~~~~~~~~~~-~l~--~~g~G~~Hiaf~V~D   82 (128)
T TIGR03081         9 VPDLEEAAKLYEDVLGAHVSHIEEVPEQGVK--VVFIALGN-TKVELLEPLGEDSPIAK-FLE--KNGGGIHHIAIEVDD   82 (128)
T ss_pred             CCCHHHHHHHHHHHHCCCEEECCCCCCCCEE--EEEEECCC-CCEEEEEECCCCCCHHH-HCC--CCCCCCEEEEEECCC
T ss_conf             0999999999999709956531115667959--99994689-71788630578985344-111--469985699998799


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999863
Q gi|254780128|r   91 VDNFLEELACT  101 (103)
Q Consensus        91 v~~~l~~l~~t  101 (103)
                      +++.++.+.+.
T Consensus        83 i~~~~~~l~~~   93 (128)
T TIGR03081        83 IEAALETLKEK   93 (128)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999999988


No 86 
>pfam09588 YqaJ YqaJ-like viral recombinase domain. This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Probab=22.69  E-value=74  Score=15.01  Aligned_cols=50  Identities=22%  Similarity=0.298  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHH-HCCCEEEEE----ECC---CCCCCCEEEEECCCCCEEEEEEECCCCC
Q ss_conf             99999999999-789899998----118---8898743999906982999999768988
Q gi|254780128|r   13 DVEKRLVTGAK-KLDCWVRKA----SFV---GRRGCPDRLIITPNGGLWWIEVKKPTGR   63 (103)
Q Consensus        13 ~ie~~l~~~lk-~~G~~~~K~----~~~---g~~GvPDli~~~~~g~~~fIEvK~~~gk   63 (103)
                      ..|..+..... ..|..+...    ..+   ...+-||-++..+++. ..+|+|.|..+
T Consensus        56 ~~E~~a~~~~~~~~g~~v~~~~~~~~~~~~~~~~aSpDg~~~~~~~~-~~lEiK~~~~~  113 (141)
T pfam09588        56 ELEPLARAEYEERTGIKVREVGGLLQHPEDPFLGASPDGLVVDGDGG-GILEIKTPFET  113 (141)
T ss_pred             HHHHHHHHHHHHHHCCEEEEECEEEECCCCCEEEECCCEEECCCCCC-EEEEEECCCHH
T ss_conf             40399999999997998985033896378882677288744048876-37998468627


No 87 
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins.  This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via  the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=22.16  E-value=76  Score=14.95  Aligned_cols=56  Identities=20%  Similarity=0.275  Sum_probs=34.2

Q ss_pred             ECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf             11888987439999069829999997689886889999999999789889998598999999999986
Q gi|254780128|r   33 SFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC  100 (103)
Q Consensus        33 ~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l~~  100 (103)
                      ..+.++|+|-.+++.-||+.            +..-..-...+++.|..++++==-+.-.+-|+.|-+
T Consensus        96 ~~~~r~~~~kvvvllTDG~s------------~~~~~~~a~~lr~~Gi~v~~VGig~~~~~~L~~iAs  151 (164)
T cd01472          96 ASGSREGVPKVLVVITDGKS------------QDDVEEPAVELKQAGIEVFAVGVKNADEEELKQIAS  151 (164)
T ss_pred             CCCCCCCCEEEEEEEECCCC------------CCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHC
T ss_conf             57876785159999837998------------640889999999889889999788479999999967


No 88 
>PRK10767 chaperone protein DnaJ; Provisional
Probab=22.13  E-value=76  Score=14.94  Aligned_cols=46  Identities=22%  Similarity=0.269  Sum_probs=28.7

Q ss_pred             CCCCEEEEECCCCC-EEEEEEECCCCCCCHHHHHHHHHHHH-CCCEEEEE
Q ss_conf             98743999906982-99999976898868899999999997-89889998
Q gi|254780128|r   38 RGCPDRLIITPNGG-LWWIEVKKPTGRLSHQQMSEIEELRR-RGQRVKVL   85 (103)
Q Consensus        38 ~GvPDli~~~~~g~-~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~~~~Vv   85 (103)
                      .|+|+.=- -..|. ++-+.|+-|+ +||+.|+.-+++|++ .|-.....
T Consensus       308 ~Gmp~~~~-~~~GDl~V~~~V~~P~-~Ls~~Qk~ll~el~~~~~~~~~~~  355 (376)
T PRK10767        308 KGVKSVRG-GAQGDLLCRVVVETPV-GLNEKQKQLLQELQESFGGPTGEK  355 (376)
T ss_pred             CCCCCCCC-CCCCCEEEEEEEECCC-CCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             89898997-9977889999998999-999999999999999746766676


No 89 
>PRK07810 O-succinylhomoserine sulfhydrylase; Provisional
Probab=22.10  E-value=77  Score=14.94  Aligned_cols=85  Identities=18%  Similarity=0.259  Sum_probs=46.1

Q ss_pred             HHHHHHHHCCCEEEEEECCCCCCCCEEEEECC----CCCEEEEEEECCCCCCCHHHHHHHHHH-----------------
Q ss_conf             99999997898999981188898743999906----982999999768988688999999999-----------------
Q gi|254780128|r   17 RLVTGAKKLDCWVRKASFVGRRGCPDRLIITP----NGGLWWIEVKKPTGRLSHQQMSEIEEL-----------------   75 (103)
Q Consensus        17 ~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~----~g~~~fIEvK~~~gkls~~Q~~~~~~l-----------------   75 (103)
                      ++...|+.+- .+-++..||-+..|+--+..+    .|..+.+|+|.........=..+++.|                 
T Consensus       282 ~vA~~L~~hp-~V~~V~yPgL~shp~h~la~r~~~g~G~~~sf~l~~~~~~~~~~~~~~~~~l~l~~~a~slGg~~SLi~  360 (406)
T PRK07810        282 RIAEFLEGHP-AVRWVRYPYLPSHPQYDLAKRQMSGGGTVVTFELDAPEDAAKQRAFEVLDKLRLIDISNNLGDAKSLIT  360 (406)
T ss_pred             HHHHHHHHCC-CCCEEECCCCCCCCCHHHHHHHCCCCCCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEECCCCCCEEEE
T ss_conf             9999997399-813798057877817789984478998632899803617889999999982872435335676660466


Q ss_pred             ---------------HHCCC---EEEEECCHHHHHHHHHHHHHHC
Q ss_conf             ---------------97898---8999859899999999998630
Q gi|254780128|r   76 ---------------RRRGQ---RVKVLVSMEEVDNFLEELACTL  102 (103)
Q Consensus        76 ---------------~~~G~---~~~Vv~s~edv~~~l~~l~~t~  102 (103)
                                     +..|.   .+.+.=+.||++.++++|++.|
T Consensus       361 ~Pas~th~~~~~e~r~~~Gi~~~liRlSVGlEd~~DLi~DL~qAL  405 (406)
T PRK07810        361 HPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDLIADLDRAL  405 (406)
T ss_pred             CCCCCCCCCCCHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
T ss_conf             775356510799899866979495999932199999999999754


No 90 
>pfam02646 RmuC RmuC family. This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures.
Probab=21.87  E-value=77  Score=14.91  Aligned_cols=27  Identities=41%  Similarity=0.460  Sum_probs=22.5

Q ss_pred             CCCCCCCEEEEECCCCCEEEEEEECCC
Q ss_conf             888987439999069829999997689
Q gi|254780128|r   35 VGRRGCPDRLIITPNGGLWWIEVKKPT   61 (103)
Q Consensus        35 ~g~~GvPDli~~~~~g~~~fIEvK~~~   61 (103)
                      .+..-.||.++-+|+++.+-|..|.|-
T Consensus        98 ~~~~~rpD~vi~lP~~~~i~IDSK~pl  124 (301)
T pfam02646        98 EGGRLRPDFAIRLPGGKLLVIDAKFPL  124 (301)
T ss_pred             CCCCCCCEEEEECCCCCEEEEEHHHHH
T ss_conf             899837618898689986777521148


No 91 
>pfam04555 XhoI Restriction endonuclease XhoI. This family consists of type II restriction enzymes (EC:3.1.21.4) that recognize the double-stranded sequence CTCGAG and cleave after C-1.
Probab=21.72  E-value=78  Score=14.89  Aligned_cols=23  Identities=30%  Similarity=0.332  Sum_probs=16.6

Q ss_pred             CCCEEEEECCCCCE-EEEEEECCCC
Q ss_conf             87439999069829-9999976898
Q gi|254780128|r   39 GCPDRLIITPNGGL-WWIEVKKPTG   62 (103)
Q Consensus        39 GvPDli~~~~~g~~-~fIEvK~~~g   62 (103)
                      --=||++... |.. ..||+|+..|
T Consensus        61 K~WDllVv~~-g~LvAaiElKSqvG   84 (196)
T pfam04555        61 KLWDLLVVQK-GVLIAAVELKSQVG   84 (196)
T ss_pred             CCCCEEEEEC-CEEEEEEEECCCCC
T ss_conf             6521799988-93889987300038


No 92 
>KOG2364 consensus
Probab=21.67  E-value=78  Score=14.89  Aligned_cols=54  Identities=22%  Similarity=0.249  Sum_probs=39.5

Q ss_pred             CHHHHHHHHHHHHHHC-CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCC
Q ss_conf             9999999999999978-9899998118889874399990698299999976898868
Q gi|254780128|r   10 TEKDVEKRLVTGAKKL-DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLS   65 (103)
Q Consensus        10 ~E~~ie~~l~~~lk~~-G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls   65 (103)
                      .|..++..+++.++.. +.--..|++.||--+-=++  +-.||.|-+|+|.|+-..-
T Consensus       232 ~enSveE~i~dhl~~~F~a~d~~F~sSGREDvDVRm--LG~GRPFvlEl~N~rr~~~  286 (433)
T KOG2364         232 KENSVEEDIKDHLKEFFSADDVVFISSGREDVDVRM--LGTGRPFVLELKNPRRNLG  286 (433)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEE--CCCCCCEEEECCCCCCCCH
T ss_conf             455488999999986437001465147875301475--0589835998578541213


No 93 
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622   DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.
Probab=20.48  E-value=51  Score=16.01  Aligned_cols=51  Identities=16%  Similarity=0.182  Sum_probs=31.8

Q ss_pred             CCCEEEEECCCCCEEE-------------EEEECCC-----CCCCHHHHHHHHHHHHCCCEEEEECCHHH
Q ss_conf             8743999906982999-------------9997689-----88688999999999978988999859899
Q gi|254780128|r   39 GCPDRLIITPNGGLWW-------------IEVKKPT-----GRLSHQQMSEIEELRRRGQRVKVLVSMEE   90 (103)
Q Consensus        39 GvPDli~~~~~g~~~f-------------IEvK~~~-----gkls~~Q~~~~~~l~~~G~~~~Vv~s~ed   90 (103)
                      -.||+..+.|+|..--             .. +++.     +..+..+......=..-|+.|+|++..|.
T Consensus        62 ~HPD~~~~~P~~~~~~~~~de~~~~~~g~a~-~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~  130 (216)
T TIGR00678        62 NHPDLHRLEPEGQSKSLTADEAAEGEEGSAK-RRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAER  130 (216)
T ss_pred             CCCCEEEEEEECCCCCCCHHHHHHHHCCCCC-CCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHH
T ss_conf             9982378742347777776458976256421-13678787278999999986064214751799767323


Done!