Query         gi|254781194|ref|YP_003065607.1| hypothetical protein CLIBASIA_05505 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 98
No_of_seqs    107 out of 430
Neff          6.2 
Searched_HMMs 39220
Date          Mon May 30 05:57:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781194.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  99.7   1E-16 2.7E-21  119.9   7.4   81    6-86      1-96  (96)
  2 KOG2143 consensus               98.9 4.6E-09 1.2E-13   75.1   6.2   51   34-84    794-845 (854)
  3 pfam01870 Hjc Archaeal hollida  97.6  0.0014 3.5E-08   42.9  10.2   72   11-83      2-79  (93)
  4 cd00523 archeal_HJR Holliday j  97.4  0.0024 6.2E-08   41.5  10.2   76    7-83      4-85  (123)
  5 COG1591 Holliday junction reso  96.6   0.035 8.9E-07   34.7   9.6   76    7-83      5-86  (137)
  6 PHA01753 Holliday junction res  93.4    0.36 9.2E-06   28.7   6.5   64    9-73      8-76  (121)
  7 COG2810 Predicted type IV rest  92.9    0.95 2.4E-05   26.3   8.2   77    8-84     23-105 (284)
  8 pfam03838 RecU Recombination p  92.5     1.1 2.8E-05   25.9   9.3   77    7-84      6-110 (167)
  9 cd00221 Vsr Very Short Patch R  92.5    0.81 2.1E-05   26.7   7.3   76    7-84     16-112 (115)
 10 pfam10107 Endonuc_Holl Endonuc  92.1    0.58 1.5E-05   27.5   6.2   48   36-83     97-151 (153)
 11 pfam02021 UPF0102 Uncharacteri  91.3     1.5 3.9E-05   25.1   8.4   60   12-72      3-70  (94)
 12 pfam08722 TnsA_N TnsA endonucl  90.4    0.74 1.9E-05   26.9   5.3   48   36-83     29-80  (81)
 13 COG4741 Predicted secreted end  89.6    0.74 1.9E-05   26.9   4.8   48   36-83    113-167 (175)
 14 TIGR00632 vsr DNA mismatch end  89.3    0.23 5.8E-06   29.9   1.9   84    1-85     32-142 (143)
 15 PRK12497 hypothetical protein;  89.1     2.3 5.9E-05   24.0   8.8   61   10-71     11-79  (118)
 16 PRK04247 hypothetical protein;  88.4     2.3 5.8E-05   24.0   6.6   90    5-94    127-225 (250)
 17 PRK03298 hypothetical protein;  87.8     2.8 7.2E-05   23.5   8.2   88    6-94    103-200 (224)
 18 pfam01939 DUF91 Protein of unk  86.6     3.1   8E-05   23.2   6.4   90    5-94    103-202 (228)
 19 pfam03852 Vsr DNA mismatch end  83.1     2.7 6.9E-05   23.6   4.8   44    7-52     19-62  (75)
 20 COG3727 Vsr DNA G:T-mismatch r  83.0     4.9 0.00012   22.1   7.0   80    2-84     15-116 (150)
 21 COG1637 Predicted nuclease of   77.4     7.5 0.00019   21.0   5.9   90    5-94    128-226 (253)
 22 pfam07711 RabGGT_insert Rab ge  77.2     3.8 9.7E-05   22.7   3.9   45   21-66     11-55  (102)
 23 PRK02234 recU Holliday junctio  76.2     8.1 0.00021   20.8   8.8   77    6-83     31-135 (199)
 24 cd01037 Restriction_endonuclea  75.1     8.7 0.00022   20.6   6.8   70   11-83      2-79  (80)
 25 PRK09225 threonine synthase; V  74.9     5.1 0.00013   22.0   4.1   40   56-95    164-204 (465)
 26 cd01560 Thr-synth_2 Threonine   74.6     4.6 0.00012   22.2   3.8   40   56-95    163-203 (460)
 27 COG0792 Predicted endonuclease  74.2     9.2 0.00023   20.5   6.3   52    7-59      4-55  (114)
 28 pfam06319 DUF1052 Protein of u  74.0     9.3 0.00024   20.5   6.7   54    8-61     21-74  (158)
 29 TIGR00252 TIGR00252 conserved   73.1     3.3 8.4E-05   23.1   2.7   48   10-57     22-70  (141)
 30 pfam08378 NERD Nuclease-relate  73.0     2.4 6.2E-05   23.9   2.1   88    4-95      4-97  (123)
 31 pfam06250 DUF1016 Protein of u  66.3     9.7 0.00025   20.3   4.0   59    4-62    180-249 (320)
 32 pfam09520 RE_MjaII MjaII restr  64.3      13 0.00034   19.6   4.3   22   37-58    144-165 (252)
 33 PRK13731 conjugal transfer sur  63.0      16  0.0004   19.1   6.0   53   36-90     38-92  (243)
 34 TIGR00260 thrC threonine synth  62.9     5.3 0.00013   21.9   2.1   41   56-96    114-155 (423)
 35 cd02410 archeal_CPSF_KH The ar  57.2      20 0.00051   18.5   5.8   84    9-95     25-132 (145)
 36 pfam03460 NIR_SIR_ferr Nitrite  55.1      22 0.00055   18.3   6.2   52   45-97      4-66  (67)
 37 pfam06555 consensus             54.6      22 0.00057   18.2   4.2   12   15-26      3-14  (200)
 38 pfam05818 TraT Enterobacterial  54.1      23 0.00058   18.2   4.5   52   38-91      9-63  (215)
 39 PRK03379 vitamin B12-transport  53.6      23 0.00059   18.1   5.2   30   66-95     90-121 (265)
 40 pfam08011 DUF1703 Protein of u  53.4      23 0.00059   18.1   8.8   70    8-78      3-74  (101)
 41 COG1139 Uncharacterized conser  53.1      23  0.0006   18.1   4.6   37   60-96     62-98  (459)
 42 pfam06616 BsuBI_PstI_RE BsuBI/  53.0      24  0.0006   18.1   7.5   63   34-96    212-279 (306)
 43 cd00114 LIGANc NAD+ dependent   52.8      24 0.00061   18.1   6.1   48   49-96    213-264 (307)
 44 TIGR02291 rimK_rel_E_lig alpha  52.5      14 0.00037   19.3   2.9   60    4-65    108-188 (320)
 45 COG0610 Type I site-specific r  50.5      25 0.00064   17.9   3.9   35   35-70    124-161 (962)
 46 KOG2364 consensus               49.3      27 0.00069   17.7   5.0   59    6-66    231-290 (433)
 47 pfam04313 HSDR_N Type I restri  47.6      20 0.00051   18.5   3.0   23   34-57     17-40  (90)
 48 pfam05116 S6PP Sucrose-6F-phos  47.3      29 0.00074   17.5   7.0   35   14-51     26-73  (247)
 49 pfam04471 Mrr_cat Restriction   46.7      30 0.00076   17.5   8.1   77   16-93      2-84  (98)
 50 PRK01395 V-type ATP synthase s  45.4      27 0.00068   17.8   3.3   27   70-96     16-42  (104)
 51 PRK09534 btuF corrinoid ABC tr  44.6      32 0.00082   17.3   5.1   30   66-95    131-163 (364)
 52 pfam09588 YqaJ YqaJ-like viral  42.1      35  0.0009   17.1   3.6   50   10-60     56-113 (141)
 53 PRK10767 chaperone protein Dna  41.7      36 0.00091   17.0   6.4   60   35-95    308-374 (376)
 54 PRK00453 rpsF 30S ribosomal pr  40.6      37 0.00094   16.9   4.7   56   10-65     21-76  (95)
 55 pfam09564 RE_NgoBV NgoBV restr  40.6      37 0.00095   16.9   4.7   61   10-73     46-112 (194)
 56 pfam10313 DUF2415 Uncharacteri  38.1      41   0.001   16.7   4.2   30   25-56      4-34  (43)
 57 PRK09566 nirA ferredoxin-nitri  36.5      43  0.0011   16.5   6.8   48   49-96     65-124 (513)
 58 TIGR01213 TIGR01213 conserved   36.4      43  0.0011   16.5   3.9   62   19-83    254-317 (450)
 59 PRK08058 DNA polymerase III su  35.2      35 0.00089   17.1   2.6   50   36-96     76-135 (329)
 60 PRK09567 nirA ferredoxin-nitri  33.7      48  0.0012   16.3   7.9   26   49-74    113-138 (591)
 61 TIGR00348 hsdR type I site-spe  33.5      48  0.0012   16.3   4.0   26   34-60    133-162 (813)
 62 PRK10361 DNA recombination pro  33.3      48  0.0012   16.3   3.1   25   33-57    236-260 (475)
 63 COG1258 Predicted pseudouridyl  31.1      53  0.0014   16.0   5.7   81    8-92    190-275 (398)
 64 TIGR00678 holB DNA polymerase   29.0      53  0.0013   16.0   2.7   60   36-96     62-144 (216)
 65 COG0498 ThrC Threonine synthas  28.6      59  0.0015   15.8   3.9   41   53-96    153-194 (411)
 66 TIGR02349 DnaJ_bact chaperone   27.5      61  0.0016   15.6   4.9   40   35-75    343-385 (386)
 67 COG5321 Uncharacterized protei  27.4      56  0.0014   15.9   2.6   43   13-57     26-70  (164)
 68 smart00532 LIGANc Ligase N fam  25.4      67  0.0017   15.4   6.0   34   63-96    231-268 (441)
 69 cd01473 vWA_CTRP CTRP for  CS   24.7      69  0.0018   15.3   5.9   66   31-96    102-187 (192)
 70 pfam01250 Ribosomal_S6 Ribosom  23.8      72  0.0018   15.2   4.1   59    6-64     13-74  (92)
 71 TIGR00963 secA preprotein tran  23.7      72  0.0018   15.2   4.0   53   23-84     58-111 (904)
 72 COG3331 PrfA Penicillin-bindin  23.4      73  0.0019   15.2   9.1   77    6-83      9-113 (177)
 73 TIGR02502 type_III_YscX type I  23.2      25 0.00064   17.9   0.2   17   34-50     24-40  (126)
 74 pfam06241 DUF1012 Protein of u  23.1      61  0.0016   15.6   2.1   18   34-51    111-130 (208)
 75 pfam08608 Wyosine_form Wyosine  22.6      36 0.00093   17.0   0.9   26   47-72      2-33  (62)
 76 TIGR02258 2_5_ligase 2'-5' RNA  22.3      77   0.002   15.0   5.3   63   13-79     55-121 (189)
 77 TIGR03081 metmalonyl_epim meth  22.2      78   0.002   15.0   5.8   85    6-96      7-91  (128)
 78 TIGR03675 arCOG00543 arCOG0178  22.1      78   0.002   15.0   6.1   84    8-94     41-148 (630)
 79 pfam09521 RE_NgoPII NgoPII res  21.9      79   0.002   15.0   2.6   40    8-57     49-88  (263)
 80 pfam04720 DUF506 Protein of un  21.8      79   0.002   15.0   2.8   73    9-95     87-184 (218)
 81 cd03008 TryX_like_RdCVF Trypar  20.9      83  0.0021   14.9   4.4   39   12-50     77-126 (146)
 82 pfam09491 RE_AlwI AlwI restric  20.3      85  0.0022   14.8   6.3   54   30-86    333-396 (429)

No 1  
>pfam08774 VRR_NUC VRR-NUC domain.
Probab=99.68  E-value=1e-16  Score=119.92  Aligned_cols=81  Identities=32%  Similarity=0.371  Sum_probs=72.5

Q ss_pred             CCHHHHHHHHHHHHHHCC-CEEEEEECC-------------CCCCCCCEEEEECCCC-EEEEEEECCCCCCCHHHHHHHH
Q ss_conf             059999999999999789-889997148-------------9887662799915991-9999972789886989999999
Q gi|254781194|r    6 LSEAKLEKRLVKGSKKLD-CLVFKTQFI-------------NQRGCPDRLIITPNGA-HFWVEMKTSRGRLSNAQKRVIA   70 (98)
Q Consensus         6 m~E~~ie~~i~~~~k~~g-~~~~k~~~~-------------g~~G~PDli~~~~~g~-~~fIEvK~~~gkls~~Q~~~~~   70 (98)
                      |+|..+|..+...+++.| +..++..+.             +..|+|||+++.|.|+ +.|||||+|++++|++|+.|++
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             9997898699983989
Q gi|254781194|r   71 TLLLYHQKVQVLSSTE   86 (98)
Q Consensus        71 ~l~~~G~~~~Vv~s~e   86 (98)
                      .|+++|+.++||+|.+
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=98.87  E-value=4.6e-09  Score=75.06  Aligned_cols=51  Identities=29%  Similarity=0.323  Sum_probs=47.9

Q ss_pred             CCCCCCEEEEEC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf             887662799915-991999997278988698999999999978986999839
Q gi|254781194|r   34 QRGCPDRLIITP-NGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLSS   84 (98)
Q Consensus        34 ~~G~PDli~~~~-~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s   84 (98)
                      ++|+|||.++.| .+++.++|||.|++|||..|+.|+..|.+.|..|.||.-
T Consensus       794 rsG~PDL~lWNp~~k~fklvEVKgpnDRLSekQr~WLalL~dsg~~VEVChV  845 (854)
T KOG2143         794 RSGFPDLTLWNPETKRFKLVEVKGPNDRLSEKQRLWLALLADSGIRVEVCHV  845 (854)
T ss_pred             CCCCCCEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             3799844323577761789983488651028999999999857887799885


No 3  
>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=97.56  E-value=0.0014  Score=42.94  Aligned_cols=72  Identities=17%  Similarity=0.173  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCC---CCCHHHHHHHHHHH-HCCCEEEEEC
Q ss_conf             99999999997898899971489--88766279991599199999727898---86989999999999-7898699983
Q gi|254781194|r   11 LEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRG---RLSNAQKRVIATLL-LYHQKVQVLS   83 (98)
Q Consensus        11 ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~g---kls~~Q~~~~~~l~-~~G~~~~Vv~   83 (98)
                      .|+.++..+...|..+.....+|  +.+.||++... ++.++.||||...+   .++..|..-+..+. ..|+..+++.
T Consensus         2 ~ERel~~~l~~~gFavvR~~gSG~~~~~~pDiiA~~-g~~~~~iEvKst~~~kiyl~~eqve~L~~f~~~fg~~p~iav   79 (93)
T pfam01870         2 YERELVKILEERGFAVVRAAGSGGAVKPLPDIIAGN-GGVYLVIEVKSRKKDKIYLKKEQVEKLVEFARRFGGEPFLAV   79 (93)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             079999999868916999567899888999889856-987999999961698188789999999999997399699999


No 4  
>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=97.45  E-value=0.0024  Score=41.47  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=58.3

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCCC---CCHHHHHHHHHHH-HCCCEEE
Q ss_conf             599999999999997898899971489--887662799915991999997278988---6989999999999-7898699
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRGR---LSNAQKRVIATLL-LYHQKVQ   80 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l~-~~G~~~~   80 (98)
                      +=+..|+.|+..+...|+-+....++|  ++..||++... +++++.||||...+.   ++..|..-+..+. ..|+..+
T Consensus         4 kG~~~EReL~~~l~~~GfavvR~~gSG~~~~~~pDiiA~~-~~~~~~iEvKst~~~~iYi~~e~ve~L~~Fa~~fG~~p~   82 (123)
T cd00523           4 KGSRAERELVKILEEKGFAVVRAPGSGGGPRPLPDIVAGN-GGTYLAIEVKSTKKDKIYIKKEQVEKLVEFARRFGGEPY   82 (123)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCEEEECHHHHHHHHHHHHHCCCEEE
T ss_conf             5037999999999865934998346788878899889756-985999999962698089849999999999997499389


Q ss_pred             EEC
Q ss_conf             983
Q gi|254781194|r   81 VLS   83 (98)
Q Consensus        81 Vv~   83 (98)
                      |+-
T Consensus        83 iav   85 (123)
T cd00523          83 LAV   85 (123)
T ss_pred             EEE
T ss_conf             999


No 5  
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=96.59  E-value=0.035  Score=34.69  Aligned_cols=76  Identities=17%  Similarity=0.225  Sum_probs=57.1

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCC-CC--CCHHHHHHHHHH-HHCCCEEE
Q ss_conf             599999999999997898899971489--8876627999159919999972789-88--698999999999-97898699
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSR-GR--LSNAQKRVIATL-LLYHQKVQ   80 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~-gk--ls~~Q~~~~~~l-~~~G~~~~   80 (98)
                      +=+..|+.|+..++..|+-+....+.|  .+=+||++... +|.++.||||+.. ++  +.+.|..-+-.+ +..|+..+
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 KGSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGN-GGVYLAIEVKSRRETKIYLDKEQVEKLVEFARRFGGEPY   83 (137)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEECC-CCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCCEE
T ss_conf             3326889999999864854998346789999998788528-978999999861588478759999999999997199568


Q ss_pred             EEC
Q ss_conf             983
Q gi|254781194|r   81 VLS   83 (98)
Q Consensus        81 Vv~   83 (98)
                      +.-
T Consensus        84 iav   86 (137)
T COG1591          84 IAV   86 (137)
T ss_pred             EEE
T ss_conf             999


No 6  
>PHA01753 Holliday junction resolvase
Probab=93.40  E-value=0.36  Score=28.73  Aligned_cols=64  Identities=11%  Similarity=0.132  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCCC---CCHHHHHHHHHHH
Q ss_conf             9999999999997898899971489--887662799915991999997278988---6989999999999
Q gi|254781194|r    9 AKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRGR---LSNAQKRVIATLL   73 (98)
Q Consensus         9 ~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l~   73 (98)
                      ...|..++..++..|--+....++|  .+-.||++... ++.++.||+|+...+   ....|..-+-++.
T Consensus         8 k~~Er~lv~~L~~~GF~avRiPaSgs~~~plPDIiA~k-~n~~laiEvKST~~~~I~Vd~~QI~KL~eF~   76 (121)
T PHA01753          8 KYYEYKTLEILESNGFKALRIPVSGTGKQALPDIIATK-NNTIYPIEVKSTSKDVVTVDKFQIEKLFRFC   76 (121)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCEEEECHHHHHHHHHHH
T ss_conf             36699999999867911798115789999898578736-9789999985033426997189999999999


No 7  
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=92.93  E-value=0.95  Score=26.25  Aligned_cols=77  Identities=13%  Similarity=0.101  Sum_probs=55.4

Q ss_pred             HHHHHHHHH-HHHHHCCCEEEEE--ECC---CCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEE
Q ss_conf             999999999-9999789889997--148---9887662799915991999997278988698999999999978986999
Q gi|254781194|r    8 EAKLEKRLV-KGSKKLDCLVFKT--QFI---NQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQV   81 (98)
Q Consensus         8 E~~ie~~i~-~~~k~~g~~~~k~--~~~---g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~V   81 (98)
                      |.-+.+.|+ ..+.+.||-....  +-|   +--|.||..++..++-|.|+|-|.-.-.+...|..-....-+.|..+.+
T Consensus        23 Ea~vrq~lIlp~L~slGwdi~nPkEV~PEe~t~~GraDyalikd~kvfafieak~ls~~~akd~qq~~~Yav~~Gv~~~i  102 (284)
T COG2810          23 EAAVRQHLILPFLSSLGWDIDNPKEVRPEEKTEEGRADYALIKDGKVFAFIEAKNLSVNPAKDVQQLAKYAVDKGVEVGI  102 (284)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             88888998899999707778990205864245557654488856938998721134757268999999998852837999


Q ss_pred             ECC
Q ss_conf             839
Q gi|254781194|r   82 LSS   84 (98)
Q Consensus        82 v~s   84 (98)
                      |.+
T Consensus       103 Vtn  105 (284)
T COG2810         103 VTN  105 (284)
T ss_pred             EEC
T ss_conf             967


No 8  
>pfam03838 RecU Recombination protein U.
Probab=92.51  E-value=1.1  Score=25.91  Aligned_cols=77  Identities=13%  Similarity=0.016  Sum_probs=58.3

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECC---------------------CCCCCCCEEEEECCCCEEEEEEECCC-------
Q ss_conf             59999999999999789889997148---------------------98876627999159919999972789-------
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFI---------------------NQRGCPDRLIITPNGAHFWVEMKTSR-------   58 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~---------------------g~~G~PDli~~~~~g~~~fIEvK~~~-------   58 (98)
                      .|..|.....-+..+.=+...|..+|                     -++.-+|...++ .|+++..|.|.-.       
T Consensus         6 lE~~IN~tn~~Y~~~~~A~I~KkptPi~ivkv~~~~r~~a~I~~ayf~~kSt~DY~Gvy-~G~~i~FEAKeT~nkt~Fpl   84 (167)
T pfam03838         6 LEELINETNQYYLANGIAVIHKKPTPIQIVKVDYPKRSAAVIKEAYFKQKSTTDYNGVY-KGRYIDFEAKETKNKTSFPL   84 (167)
T ss_pred             HHHHHHHHHHHHHHCCEEEEEEECCCEEEEECCCCCCCCCEEEEEEECCCCCCCCCEEE-CCEEEEEECCCCCCCCCCCH
T ss_conf             99999999999987797999970788179943786555334677887357767733167-78999998224356674572


Q ss_pred             CCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf             88698999999999978986999839
Q gi|254781194|r   59 GRLSNAQKRVIATLLLYHQKVQVLSS   84 (98)
Q Consensus        59 gkls~~Q~~~~~~l~~~G~~~~Vv~s   84 (98)
                      ....++|...++++..+|+.++++=.
T Consensus        85 ~Ni~~HQi~~L~~~~~~gGiaF~ii~  110 (167)
T pfam03838        85 KNIHEHQIEHLKQVLKQGGICFVIIR  110 (167)
T ss_pred             HHCCHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             45569999999999988997999999


No 9  
>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=92.48  E-value=0.81  Score=26.67  Aligned_cols=76  Identities=16%  Similarity=0.072  Sum_probs=46.7

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEE----CC---CCCCCHHHHHHH----------
Q ss_conf             5999999999999978988999714898876627999159919999972----78---988698999999----------
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMK----TS---RGRLSNAQKRVI----------   69 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK----~~---~gkls~~Q~~~~----------   69 (98)
                      +.+..|..+.+.|.+.|.++. .....-+|-||+. +.+-..++||-==    -|   ...|..|...|.          
T Consensus        16 k~TkpE~~vrk~L~~~G~Ryr-~~~k~lpG~PDiv-~~~~k~aIFvdGCFWHgh~~~~~~~pk~n~~fW~~Ki~~N~~RD   93 (115)
T cd00221          16 KDTKPERAVRSALWELGYRFR-KQDKDLPGKPDIV-VPGYRLAIFVDGCFWHGHPCHKRKPPPKNTEFWLEKIERNVERD   93 (115)
T ss_pred             CCCHHHHHHHHHHHHCCCEEE-ECCCCCCCCCCEE-ECCCCEEEEECCEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             998699999999998899899-6688779999997-35762899932404338887578889853899999999999989


Q ss_pred             ----HHHHHCCCEEEEECC
Q ss_conf             ----999978986999839
Q gi|254781194|r   70 ----ATLLLYHQKVQVLSS   84 (98)
Q Consensus        70 ----~~l~~~G~~~~Vv~s   84 (98)
                          +.|.++|+.+.+++.
T Consensus        94 ~~~~~~L~~~GW~v~~vWE  112 (115)
T cd00221          94 RRVQAALERLGWRVLRVWE  112 (115)
T ss_pred             HHHHHHHHHCCCEEEEEEE
T ss_conf             9999999988998999983


No 10 
>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=92.12  E-value=0.58  Score=27.52  Aligned_cols=48  Identities=23%  Similarity=0.362  Sum_probs=36.3

Q ss_pred             CCC-CEEEEEC-----CCCEEEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             766-2799915-----991999997278-98869899999999997898699983
Q gi|254781194|r   36 GCP-DRLIITP-----NGAHFWVEMKTS-RGRLSNAQKRVIATLLLYHQKVQVLS   83 (98)
Q Consensus        36 G~P-Dli~~~~-----~g~~~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~   83 (98)
                      |-| |+++|..     ...+.|+|+|+. ..+||..|+...+.+++--..+..++
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 11 
>pfam02021 UPF0102 Uncharacterized protein family UPF0102. The function of this family is unknown.
Probab=91.27  E-value=1.5  Score=25.08  Aligned_cols=60  Identities=15%  Similarity=0.225  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf             999999999789889997148988766279991599199999727898--------8698999999999
Q gi|254781194|r   12 EKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG--------RLSNAQKRVIATL   72 (98)
Q Consensus        12 e~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l   72 (98)
                      |..-..+|.+.|+....--.-.+.|==||+.. .++...|||||+-.+        .+++.|...+.+.
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 12 
>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=90.36  E-value=0.74  Score=26.90  Aligned_cols=48  Identities=19%  Similarity=0.056  Sum_probs=32.6

Q ss_pred             CCCCEEEEECCCCEEEEEEECCCC----CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             766279991599199999727898----869899999999997898699983
Q gi|254781194|r   36 GCPDRLIITPNGAHFWVEMKTSRG----RLSNAQKRVIATLLLYHQKVQVLS   83 (98)
Q Consensus        36 G~PDli~~~~~g~~~fIEvK~~~g----kls~~Q~~~~~~l~~~G~~~~Vv~   83 (98)
                      =.||+++...+|...++|+|....    +....-..-....+..|....++.
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 13 
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=89.62  E-value=0.74  Score=26.89  Aligned_cols=48  Identities=25%  Similarity=0.350  Sum_probs=37.1

Q ss_pred             CCC-CEEEEEC--CCCE---EEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             766-2799915--9919---99997278-98869899999999997898699983
Q gi|254781194|r   36 GCP-DRLIITP--NGAH---FWVEMKTS-RGRLSNAQKRVIATLLLYHQKVQVLS   83 (98)
Q Consensus        36 G~P-Dli~~~~--~g~~---~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~   83 (98)
                      |-| |+++|..  +|..   +|||+|+. ++++|..-+...+.+.+.-..+.+.+
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 14 
>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=89.26  E-value=0.23  Score=29.90  Aligned_cols=84  Identities=13%  Similarity=-0.037  Sum_probs=56.0

Q ss_pred             CCCH-HCCHHHHHHHHHHHHHHCCCEEE----EEECCCCCCCCCEEEEECCCCEEEE--------EEECCCCCCCHHHHH
Q ss_conf             9501-20599999999999997898899----9714898876627999159919999--------972789886989999
Q gi|254781194|r    1 MRTD-YLSEAKLEKRLVKGSKKLDCLVF----KTQFINQRGCPDRLIITPNGAHFWV--------EMKTSRGRLSNAQKR   67 (98)
Q Consensus         1 ~~~~-~m~E~~ie~~i~~~~k~~g~~~~----k~~~~g~~G~PDli~~~~~g~~~fI--------EvK~~~gkls~~Q~~   67 (98)
                      |+.. .-+...+|+.|..+|-++|-.+.    +-...|-.|-||+.+ ..-.-++||        .+-.-+-.|..+...
T Consensus        32 M~a~s~~~~T~pE~~l~s~L~~lGlryRkdfl~~~~~G~~g~PD~vf-~~~k~~iFidGCFWHg~~C~~~~~~p~s~~~f  110 (143)
T TIGR00632        32 MQAVSRSKGTKPEKALASLLFALGLRYRKDFLLRDKDGLPGTPDIVF-KEYKVVIFIDGCFWHGHDCDILGKVPKSRKDF  110 (143)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE-CCCEEEEEECCCEECCCCCCCCCCCCCCCHHC
T ss_conf             88764157981789999999998899888987523689854675443-47358886027300587674014788664230


Q ss_pred             HHHH--------------HHHCCCEEEEECCH
Q ss_conf             9999--------------99789869998398
Q gi|254781194|r   68 VIAT--------------LLLYHQKVQVLSST   85 (98)
Q Consensus        68 ~~~~--------------l~~~G~~~~Vv~s~   85 (98)
                      |+.+              |.+.|+.|++|+.-
T Consensus       111 W~~Ki~~N~~RD~~~~~~L~~~GWrv~~vW~~  142 (143)
T TIGR00632       111 WSPKIEKNVERDRRVNDALAEEGWRVLRVWEC  142 (143)
T ss_pred             CHHHHHHHHHCCCCHHHHHHHCCCEEEEEECC
T ss_conf             36888742530311789998459989896137


No 15 
>PRK12497 hypothetical protein; Reviewed
Probab=89.10  E-value=2.3  Score=23.99  Aligned_cols=61  Identities=18%  Similarity=0.165  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC--------CCCHHHHHHHHH
Q ss_conf             99999999999789889997148988766279991599199999727898--------869899999999
Q gi|254781194|r   10 KLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG--------RLSNAQKRVIAT   71 (98)
Q Consensus        10 ~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~   71 (98)
                      .=|.....+|++.|+..+.--.-.+.|==|||... ++...|||||+-.+        .+++.|...+.+
T Consensus        11 ~gE~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~~-~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~   79 (118)
T PRK12497         11 AGEDLAARYLESKGLRILARNFRCRFGEIDLIARD-GDTLVFVEVKTRRSDLFGGAAEAVTPRKQRRIRR   79 (118)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEEE-CCEEEEEEEECCCCCCCCCHHHHCCHHHHHHHHH
T ss_conf             99999999999879999998500489950589996-9999999982155789889789599999999999


No 16 
>PRK04247 hypothetical protein; Provisional
Probab=88.41  E-value=2.3  Score=24.03  Aligned_cols=90  Identities=23%  Similarity=0.224  Sum_probs=60.4

Q ss_pred             HCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHC-CCE-
Q ss_conf             205999999999999978--98899971489887662799915991999997278988698-99-9999999978-986-
Q gi|254781194|r    5 YLSEAKLEKRLVKGSKKL--DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSN-AQ-KRVIATLLLY-HQK-   78 (98)
Q Consensus         5 ~m~E~~ie~~i~~~~k~~--g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~-G~~-   78 (98)
                      ...|+++|..|.+.....  |.....--.+...|.=|++.-..+|....||+|+-++-+.. .| .++.+.|++- +.+ 
T Consensus       127 ~G~Ea~l~~llae~p~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~V~VEvKR~ra~idaV~QL~RYve~l~~~~~~~V  206 (250)
T PRK04247        127 TGSEADMVDAILENPDLIEEGFRPVAREYETPAGIIDILGRDKEGNLVVLELKRRRAGLSAVSQLKRYVEAYREELGAKV  206 (250)
T ss_pred             EEEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             73199999999859053258988998887359884648998799899999997133781479999999999876369982


Q ss_pred             --EEEECC-HHHHHHHHHH
Q ss_conf             --999839-8999999998
Q gi|254781194|r   79 --VQVLSS-TEEVDGFLRM   94 (98)
Q Consensus        79 --~~Vv~s-~e~v~~~i~~   94 (98)
                        ++++-+ .++++.++++
T Consensus       207 RGIlvAp~It~~Ar~Ll~d  225 (250)
T PRK04247        207 RGILVAPSITERARRLLEK  225 (250)
T ss_pred             EEEEECCCCCHHHHHHHHH
T ss_conf             1999988589879999997


No 17 
>PRK03298 hypothetical protein; Provisional
Probab=87.81  E-value=2.8  Score=23.49  Aligned_cols=88  Identities=22%  Similarity=0.226  Sum_probs=58.0

Q ss_pred             CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHCCC----
Q ss_conf             05999999999999978--98899971489887662799915991999997278988698-99-999999997898----
Q gi|254781194|r    6 LSEAKLEKRLVKGSKKL--DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSN-AQ-KRVIATLLLYHQ----   77 (98)
Q Consensus         6 m~E~~ie~~i~~~~k~~--g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~G~----   77 (98)
                      ..|+++|..|.+.-...  |.....--.+...|.=|++.-..+|....||+|+ ++-+.. .| ..+.+.|++-..    
T Consensus       103 G~Eadl~~llae~P~~ie~Gf~~v~rE~~T~~G~VDll~~D~~G~~V~VEiKR-ra~idaV~QL~RYve~l~rd~~~~~V  181 (224)
T PRK03298        103 GVEAHLQELLAEHIELLGEGYTLVRREYMTAIGPVDLLCRDADGATVAVEIKR-RGEIDGVEQLTRYLELLNRDPLLAPV  181 (224)
T ss_pred             ECHHHHHHHHHHCCHHHCCCCEEEEEEECCCCCCEEEEEECCCCCEEEEEEEE-CCCHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             01999999987592421589898778731798835389987999999999983-06810899999999998557588851


Q ss_pred             -EEEEECC-HHHHHHHHHH
Q ss_conf             -6999839-8999999998
Q gi|254781194|r   78 -KVQVLSS-TEEVDGFLRM   94 (98)
Q Consensus        78 -~~~Vv~s-~e~v~~~i~~   94 (98)
                       -.+++-| .++++.++++
T Consensus       182 RGIlvAp~It~~Ar~Ll~d  200 (224)
T PRK03298        182 RGVFAAQQIKPQARTLATD  200 (224)
T ss_pred             EEEEECCCCCHHHHHHHHH
T ss_conf             4999987478879999997


No 18 
>pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.
Probab=86.59  E-value=3.1  Score=23.22  Aligned_cols=90  Identities=23%  Similarity=0.240  Sum_probs=60.9

Q ss_pred             HCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHC--CCE
Q ss_conf             205999999999999978--98899971489887662799915991999997278988698-99-9999999978--986
Q gi|254781194|r    5 YLSEAKLEKRLVKGSKKL--DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSN-AQ-KRVIATLLLY--HQK   78 (98)
Q Consensus         5 ~m~E~~ie~~i~~~~k~~--g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~--G~~   78 (98)
                      ...|+++|..|.+.-...  |.....--.+...|.=|++.-..+|....||+|+-.+-+.. .| ..+.+.|++-  ..+
T Consensus       103 ~G~Eadl~~~l~~~P~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~VvVEvKRr~a~idaV~QL~RYve~l~rd~~~~~  182 (228)
T pfam01939       103 TGSEAEMAALIFEHPQLIEEGFKPVRREYQIAHGIVDILGKDEDGNIVILELKRRKADLHAVSQLKRYVDSLKEDYVEAK  182 (228)
T ss_pred             EEEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             73199999999859153248989998885258873668998799999999997403782079999999999865548886


Q ss_pred             ---EEEECC-HHHHHHHHHH
Q ss_conf             ---999839-8999999998
Q gi|254781194|r   79 ---VQVLSS-TEEVDGFLRM   94 (98)
Q Consensus        79 ---~~Vv~s-~e~v~~~i~~   94 (98)
                         ++|+-| .++++.++++
T Consensus       183 VRGIlvAp~It~~Ar~Ll~d  202 (228)
T pfam01939       183 VRGVLVAPSITEGAKKLLEE  202 (228)
T ss_pred             CEEEEECCCCCHHHHHHHHH
T ss_conf             03999998589889999997


No 19 
>pfam03852 Vsr DNA mismatch endonuclease Vsr.
Probab=83.14  E-value=2.7  Score=23.61  Aligned_cols=44  Identities=18%  Similarity=0.035  Sum_probs=31.3

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEE
Q ss_conf             5999999999999978988999714898876627999159919999
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWV   52 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fI   52 (98)
                      +....|..+.+.+.+.|-++.+ ....-+|-||+ ++.+-.-++||
T Consensus        19 k~TkpE~~vr~~L~~~G~ryr~-~~~~lpG~PDi-v~~~~k~aIFv   62 (75)
T pfam03852        19 KGTKPELALRSLLFGLGLRYRK-NDKSLPGKPDI-VFPKYKLAVFI   62 (75)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEE-CCCCCCCCCCE-EECCCCEEEEE
T ss_conf             9976999999999988988997-37878999999-76687789994


No 20 
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=82.98  E-value=4.9  Score=22.10  Aligned_cols=80  Identities=23%  Similarity=0.175  Sum_probs=49.4

Q ss_pred             CCHHCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCC-EEEEE--------E---ECCCCC-------CC
Q ss_conf             50120599999999999997898899971489887662799915991-99999--------7---278988-------69
Q gi|254781194|r    2 RTDYLSEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGA-HFWVE--------M---KTSRGR-------LS   62 (98)
Q Consensus         2 ~~~~m~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~-~~fIE--------v---K~~~gk-------ls   62 (98)
                      +.-.-++..+|..+...+-..|-.+.. .--.-+|-||+.+  |+-+ ++|+-        +   |.|+.+       .+
T Consensus        15 ~rIrs~dTkpE~~lr~~L~~~G~rfR~-~~~~lpGkPDiVl--~~y~~viFvHGCFWh~H~c~~a~vPksnt~fWleKi~   91 (150)
T COG3727          15 RRIRSRDTKPEKRLRSLLTGQGLRFRV-QDKDLPGKPDIVL--PKYRCVIFVHGCFWHGHHCYLAKVPKSNTEFWLEKIG   91 (150)
T ss_pred             HHHHCCCCCHHHHHHHHHHHCCEEEEE-CCCCCCCCCCEEE--CCCEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             998814766899999998536627885-3788999998852--3733899985100257744445688742388999986


Q ss_pred             HH---HHHHHHHHHHCCCEEEEECC
Q ss_conf             89---99999999978986999839
Q gi|254781194|r   63 NA---QKRVIATLLLYHQKVQVLSS   84 (98)
Q Consensus        63 ~~---Q~~~~~~l~~~G~~~~Vv~s   84 (98)
                      .|   -+.-+.+|+.+|+.+-||+-
T Consensus        92 kNveRD~r~~~~L~~~GwrvlvVWE  116 (150)
T COG3727          92 KNVERDERDIKRLQQLGWRVLVVWE  116 (150)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             6666548999999975975999986


No 21 
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=77.39  E-value=7.5  Score=21.00  Aligned_cols=90  Identities=23%  Similarity=0.205  Sum_probs=58.8

Q ss_pred             HCCHHHHHHHHHHHHHHCCCEEEEE--ECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHH-H-HHHHHHHHHCCCE--
Q ss_conf             2059999999999999789889997--14898876627999159919999972789886989-9-9999999978986--
Q gi|254781194|r    5 YLSEAKLEKRLVKGSKKLDCLVFKT--QFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNA-Q-KRVIATLLLYHQK--   78 (98)
Q Consensus         5 ~m~E~~ie~~i~~~~k~~g~~~~k~--~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~-Q-~~~~~~l~~~G~~--   78 (98)
                      .++|.++++.|...-.-++-...-+  -.+...|.-|++....+|++..||+|+-++.+++. | +...+.+++-...  
T Consensus       128 ~g~E~~m~~~I~e~P~lleeG~~~v~~E~~t~~G~vDilg~De~G~~viiElKR~ka~~~Av~QL~RYv~~l~~~~~~~V  207 (253)
T COG1637         128 DGSEADMQELIAENPQLLEEGFRPVAREYQTAIGKVDILGRDERGNIVIIELKRRKAGLSAVSQLKRYVELLREDTGDKV  207 (253)
T ss_pred             CCHHHHHHHHHHHCHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCEE
T ss_conf             04099998787659466757543312652137425679988689999999994254771089999999997053468607


Q ss_pred             --EEEECC-HHHHHHHHHH
Q ss_conf             --999839-8999999998
Q gi|254781194|r   79 --VQVLSS-TEEVDGFLRM   94 (98)
Q Consensus        79 --~~Vv~s-~e~v~~~i~~   94 (98)
                        ..|+.| .+++..++++
T Consensus       208 RGiLvAp~it~~a~~ll~~  226 (253)
T COG1637         208 RGILVAPSITEQARRLLED  226 (253)
T ss_pred             EEEEECCCCCHHHHHHHHH
T ss_conf             8999866440889999997


No 22 
>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=77.20  E-value=3.8  Score=22.74  Aligned_cols=45  Identities=20%  Similarity=0.210  Sum_probs=36.9

Q ss_pred             HCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHH
Q ss_conf             7898899971489887662799915991999997278988698999
Q gi|254781194|r   21 KLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQK   66 (98)
Q Consensus        21 ~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~   66 (98)
                      ..++...-|.-|-..|.-+|++.. ||...++|-.+|.++.++.|.
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 23 
>PRK02234 recU Holliday junction-specific endonuclease; Reviewed
Probab=76.19  E-value=8.1  Score=20.80  Aligned_cols=77  Identities=13%  Similarity=-0.000  Sum_probs=59.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEEEECC---------C------------CCCCCCEEEEECCCCEEEEEEECCCC-----
Q ss_conf             059999999999999789889997148---------9------------88766279991599199999727898-----
Q gi|254781194|r    6 LSEAKLEKRLVKGSKKLDCLVFKTQFI---------N------------QRGCPDRLIITPNGAHFWVEMKTSRG-----   59 (98)
Q Consensus         6 m~E~~ie~~i~~~~k~~g~~~~k~~~~---------g------------~~G~PDli~~~~~g~~~fIEvK~~~g-----   59 (98)
                      -.|.+|.....-++..-=+++.|-.+|         -            ++--.|...++. |+++..|.|.-.+     
T Consensus        31 ~LE~~IN~tN~yY~~~~iAvIhKkPTPIqivkVdypkRs~a~I~eAyf~~~STtDY~Gvyk-G~yIdFEAKET~nktsFp  109 (199)
T PRK02234         31 SLEKDINETNDYYLSNGIAVIHKKPTPIQIVKVDYPKRSKAVIKEAYFRQASTTDYNGVYK-GKYIDFEAKETKNKTSFP  109 (199)
T ss_pred             HHHHHHHHHHHHHHHCCEEEEEECCCCEEEEECCCCCCCCCHHHHHEECCCCCCCCCCEEC-CEEEEEECCCCCCCCCCC
T ss_conf             5999999999999877978998358880699615544330010010235778777432567-889888754557877447


Q ss_pred             --CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             --869899999999997898699983
Q gi|254781194|r   60 --RLSNAQKRVIATLLLYHQKVQVLS   83 (98)
Q Consensus        60 --kls~~Q~~~~~~l~~~G~~~~Vv~   83 (98)
                        ...++|...++++...|+.+|++=
T Consensus       110 l~Nih~HQi~hl~~~~~qgGI~F~iI  135 (199)
T PRK02234        110 LKNFHEHQIEHMKQVLAQGGICFVII  135 (199)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             23403899999999997799799999


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=75.14  E-value=8.7  Score=20.63  Aligned_cols=70  Identities=21%  Similarity=0.043  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHCCCEEEEEE--CCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHH------HHHHHHHHCCCEEEEE
Q ss_conf             99999999997898899971--489887662799915991999997278988698999------9999999789869998
Q gi|254781194|r   11 LEKRLVKGSKKLDCLVFKTQ--FINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQK------RVIATLLLYHQKVQVL   82 (98)
Q Consensus        11 ie~~i~~~~k~~g~~~~k~~--~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~------~~~~~l~~~G~~~~Vv   82 (98)
                      .|..+...+.+.+....++.  .+..++.||.. + + ...+.||+|.........+.      .....+...|..+.++
T Consensus         2 ~E~~l~~~l~~~~~~~~~~~~~~~~~~~~pDf~-~-~-~~~l~iE~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   78 (80)
T cd01037           2 AERLLWKLLRAKGLAVRRFRRQVPIGSYIPDFV-C-P-SAKLVIELKGTFHDGLLRKLRTSEKQERIAFLEADGKKVLRF   78 (80)
T ss_pred             HHHHHHHHHHHCCCCCCEEEECCCCCCEEEEEE-C-C-CCCEEEEECCCHHCCCHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             799999999855878870571375078877577-2-5-448799914512153135554411778999999889989974


Q ss_pred             C
Q ss_conf             3
Q gi|254781194|r   83 S   83 (98)
Q Consensus        83 ~   83 (98)
                      .
T Consensus        79 ~   79 (80)
T cd01037          79 W   79 (80)
T ss_pred             C
T ss_conf             3


No 25 
>PRK09225 threonine synthase; Validated
Probab=74.85  E-value=5.1  Score=22.00  Aligned_cols=40  Identities=15%  Similarity=0.278  Sum_probs=30.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHH
Q ss_conf             7898869899999999997898699983-989999999986
Q gi|254781194|r   56 TSRGRLSNAQKRVIATLLLYHQKVQVLS-STEEVDGFLRML   95 (98)
Q Consensus        56 ~~~gkls~~Q~~~~~~l~~~G~~~~Vv~-s~e~v~~~i~~l   95 (98)
                      -|.|+.|+-|+.++.....-...+.-|+ ++||++.+++.+
T Consensus       164 yP~g~vS~iQ~~QMtt~~~~NV~~i~v~G~FDDcQ~lVK~~  204 (465)
T PRK09225        164 YPKGKVSPVQEKQMTTLQGDNIHVVAVEGDFDDCQALVKAA  204 (465)
T ss_pred             ECCCCCCHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHHH
T ss_conf             07999997799986221799779998468767899999999


No 26 
>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=74.65  E-value=4.6  Score=22.22  Aligned_cols=40  Identities=18%  Similarity=0.268  Sum_probs=30.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHH
Q ss_conf             789886989999999999789869998-3989999999986
Q gi|254781194|r   56 TSRGRLSNAQKRVIATLLLYHQKVQVL-SSTEEVDGFLRML   95 (98)
Q Consensus        56 ~~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~e~v~~~i~~l   95 (98)
                      -|.|+.|+-|+.++.........+.-| -++||++.+++.+
T Consensus       163 yP~g~vS~iQ~~QMtT~~~~NV~~iav~G~FDDcQ~~VK~~  203 (460)
T cd01560         163 YPKGGVSPIQELQMTTLPADNVHVVAVEGDFDDCQSLVKAL  203 (460)
T ss_pred             CCCCCCCHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
T ss_conf             48888998899986254789779999648808889999999


No 27 
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=74.16  E-value=9.2  Score=20.49  Aligned_cols=52  Identities=15%  Similarity=0.072  Sum_probs=36.7

Q ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC
Q ss_conf             59999999999999789889997148988766279991599199999727898
Q gi|254781194|r    7 SEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG   59 (98)
Q Consensus         7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g   59 (98)
                      ....-|..-..+|++.|...+.--.-.+-|==|||.- .++...|||||+-.+
T Consensus         4 ~G~~~E~~A~~~L~~~G~~iL~rN~r~r~GEIDlIa~-~~~~ivFVEVK~R~~   55 (114)
T COG0792           4 LGAAGEDLAARFLESKGLRILARNWRCRYGEIDLIAR-DGDTVVFVEVKYRRN   55 (114)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCEEEEEE-CCCEEEEEEEEEECC
T ss_conf             4778999999999976930255530378874689996-599899999974126


No 28 
>pfam06319 DUF1052 Protein of unknown function (DUF1052). This family consists of several bacterial proteins of unknown function.
Probab=74.00  E-value=9.3  Score=20.46  Aligned_cols=54  Identities=17%  Similarity=0.228  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCC
Q ss_conf             999999999999978988999714898876627999159919999972789886
Q gi|254781194|r    8 EAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRL   61 (98)
Q Consensus         8 E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkl   61 (98)
                      -..|.+.+...+..+|..++.-.++..--=-|++.+-+.|.++.||+|....-.
T Consensus        21 a~~i~RGv~Rll~~~g~a~l~E~~L~~GrRaDl~al~~kGei~IVEiKSs~aDF   74 (158)
T pfam06319        21 ALAVRRGVQRLLMELGHAVLPELPLASGRRADLIALSPKGEIWIVEIKSSIEDF   74 (158)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECCCCCEEEEEEECCHHHH
T ss_conf             999999999999977996335663799977779988799959999983678884


No 29 
>TIGR00252 TIGR00252 conserved hypothetical protein TIGR00252; InterPro: IPR003509 The function of this family is unknown. Members include several bacterial hypothetical proteins..
Probab=73.09  E-value=3.3  Score=23.10  Aligned_cols=48  Identities=15%  Similarity=0.167  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCE-EEEEEECC
Q ss_conf             9999999999978988999714898876627999159919-99997278
Q gi|254781194|r   10 KLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAH-FWVEMKTS   57 (98)
Q Consensus        10 ~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~-~fIEvK~~   57 (98)
                      -.|......|+..|+...---.-.+-|==|||.-.||++. .|||||.=
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 30 
>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=72.99  E-value=2.4  Score=23.85  Aligned_cols=88  Identities=16%  Similarity=0.214  Sum_probs=47.0

Q ss_pred             HHCCHHHHHHHHHHHHHH-CCCEEEEEE-CC---CCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCE
Q ss_conf             120599999999999997-898899971-48---9887662799915991999997278988698999999999978986
Q gi|254781194|r    4 DYLSEAKLEKRLVKGSKK-LDCLVFKTQ-FI---NQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQK   78 (98)
Q Consensus         4 ~~m~E~~ie~~i~~~~k~-~g~~~~k~~-~~---g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~   78 (98)
                      ++.-|..+-..|...+.. .++.++.-. -+   |+..-=|.+++.|+| ++.||+|.-.|........|..   ..+..
T Consensus         4 G~~gE~~v~~~L~~~~~~~~~~~vl~n~~l~~~~~~~~eID~lvi~~~g-i~vvE~K~~~G~i~~~~~~W~~---~~~~~   79 (123)
T pfam08378         4 GAEGEKLVARALKKLLPDDYEYFVLHNLRLPTHGGSTTEIDHLVISPDG-IFVIEVKNYKGTIIADGGKWTQ---TIGGR   79 (123)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEECEEECCCCCCEEEEEEEEECCCE-EEEEEECCCCEEEEECCCEEEE---EECCC
T ss_conf             7999999999999637888988999543962699978897799994891-9999946862489962763999---86995


Q ss_pred             EEEEC-CHHHHHHHHHHH
Q ss_conf             99983-989999999986
Q gi|254781194|r   79 VQVLS-STEEVDGFLRML   95 (98)
Q Consensus        79 ~~Vv~-s~e~v~~~i~~l   95 (98)
                      ..... -+.|+..-...|
T Consensus        80 ~~~~~nPi~Q~~~~~~~l   97 (123)
T pfam08378        80 KEEFKNPLLQAYRHAKLL   97 (123)
T ss_pred             EEECCCHHHHHHHHHHHH
T ss_conf             588689999999999999


No 31 
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=66.25  E-value=9.7  Score=20.35  Aligned_cols=59  Identities=24%  Similarity=0.236  Sum_probs=41.9

Q ss_pred             HHCCHHHHHHHHHHHHHHC-----CCEEE-----EEECCCCCCCCCEEEEEC-CCCEEEEEEECCCCCCC
Q ss_conf             1205999999999999978-----98899-----971489887662799915-99199999727898869
Q gi|254781194|r    4 DYLSEAKLEKRLVKGSKKL-----DCLVF-----KTQFINQRGCPDRLIITP-NGAHFWVEMKTSRGRLS   62 (98)
Q Consensus         4 ~~m~E~~ie~~i~~~~k~~-----g~~~~-----k~~~~g~~G~PDli~~~~-~g~~~fIEvK~~~gkls   62 (98)
                      +...|+++|+.|++.+.+.     .|.+|     ++...|.-=+.||+.+.- =..++.||+|+..=++.
T Consensus       180 ~~~~E~dLE~ali~~i~~FLLELG~GFaFvgrQ~ri~v~~~dfyiDLlFYh~~L~c~V~IELK~g~f~pe  249 (320)
T pfam06250       180 DLYSEKDLEKALINHLEKFLLELGAGFAFVGRQKRIQVDDEDFYIDLLFYHRKLRCLVAVDLKIGKFKPE  249 (320)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEHHHHHHHHHCCCEEEEEECCCCCCHH
T ss_conf             6648899999999999999998189816754557888779323404766634114136776415876778


No 32 
>pfam09520 RE_MjaII MjaII restriction endonuclease. This family includes the MjaII (recognizes GGNCC but the cleavage site is unknown) restriction endonuclease.
Probab=64.32  E-value=13  Score=19.56  Aligned_cols=22  Identities=18%  Similarity=0.484  Sum_probs=19.0

Q ss_pred             CCCEEEEECCCCEEEEEEECCC
Q ss_conf             6627999159919999972789
Q gi|254781194|r   37 CPDRLIITPNGAHFWVEMKTSR   58 (98)
Q Consensus        37 ~PDli~~~~~g~~~fIEvK~~~   58 (98)
                      +.|+.+..+||.-+|+|+|+|+
T Consensus       144 v~Dlyi~~kdg~e~~feIKT~K  165 (252)
T pfam09520       144 VADLYVQRKDGRELYFEIKSPK  165 (252)
T ss_pred             EEEEEEECCCCCEEEEEECCCC
T ss_conf             7789998279958999835779


No 33 
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=63.04  E-value=16  Score=19.09  Aligned_cols=53  Identities=11%  Similarity=0.206  Sum_probs=40.1

Q ss_pred             CCCCEEEEEC-CCCEEEEEEECCCCCCC-HHHHHHHHHHHHCCCEEEEECCHHHHHH
Q ss_conf             7662799915-99199999727898869-8999999999978986999839899999
Q gi|254781194|r   36 GCPDRLIITP-NGAHFWVEMKTSRGRLS-NAQKRVIATLLLYHQKVQVLSSTEEVDG   90 (98)
Q Consensus        36 G~PDli~~~~-~g~~~fIEvK~~~gkls-~~Q~~~~~~l~~~G~~~~Vv~s~e~v~~   90 (98)
                      -..|=|.+.| ..+..||.+|.-.++.. ..|......|...|  +-|+++++++.=
T Consensus        38 kMS~TIfLdP~s~ktVyv~vrNTS~~~~~~l~~~i~~~L~akG--Y~iv~~P~~A~Y   92 (243)
T PRK13731         38 QMSETIWLEPASERTVFLQIKNTSDKDMSGLQGKIADAVKAKG--YQVVTSPDKAYY   92 (243)
T ss_pred             EECCCEEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCC--EEEECCHHHCEE
T ss_conf             0004388668545579999851787724567899999998589--098678657607


No 34 
>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=62.90  E-value=5.3  Score=21.89  Aligned_cols=41  Identities=22%  Similarity=0.362  Sum_probs=36.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHHH
Q ss_conf             7898869899999999997898699983-9899999999862
Q gi|254781194|r   56 TSRGRLSNAQKRVIATLLLYHQKVQVLS-STEEVDGFLRMLE   96 (98)
Q Consensus        56 ~~~gkls~~Q~~~~~~l~~~G~~~~Vv~-s~e~v~~~i~~l~   96 (98)
                      -|.||.+|.|+..+-+--..|..+.-++ ++||++++++.+.
T Consensus       114 ~P~Gki~p~Q~~Kl~~~~~~n~~v~~i~G~FDda~~~v~~~~  155 (423)
T TIGR00260       114 YPAGKISPLQLGKLAQALIYNAKVIAIDGNFDDAQRLVKELF  155 (423)
T ss_pred             ECCCCCCHHHCCCEEEEECCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             328853330215301332378389998278799999999986


No 35 
>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=57.24  E-value=20  Score=18.49  Aligned_cols=84  Identities=15%  Similarity=0.184  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHHHCCCEEEEE-----------------ECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             999999999999789889997-----------------148988766279991599199999727898869899999999
Q gi|254781194|r    9 AKLEKRLVKGSKKLDCLVFKT-----------------QFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIAT   71 (98)
Q Consensus         9 ~~ie~~i~~~~k~~g~~~~k~-----------------~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~   71 (98)
                      .++=++|.+.+|+.  .+.+.                 .-|--+|+-| +.|.|+-.=..||++.|+--.........+-
T Consensus        25 ~~li~~iAk~ikKR--IviRpdpsil~~~e~a~~~I~~ivPeeA~i~~-i~FD~~~gEV~Iea~kPg~viGk~g~~l~eI  101 (145)
T cd02410          25 GDLVKDLAKDLRKR--IVIRPDPSVLKPPEEAIKIILEIVPEEAGITD-IYFDDDTGEVIIEAEKPGLVIGKGGSTLREI  101 (145)
T ss_pred             CHHHHHHHHHHHCE--EEECCCHHHCCCHHHHHHHHHHHCCCCCCCEE-EEECCCCCEEEEEECCCEEEECCCCHHHHHH
T ss_conf             40999999987202--79738803418999999999985896468446-8974888579999779777972761679999


Q ss_pred             HHHCCCEEEEECC-------HHHHHHHHHHH
Q ss_conf             9978986999839-------89999999986
Q gi|254781194|r   72 LLLYHQKVQVLSS-------TEEVDGFLRML   95 (98)
Q Consensus        72 l~~~G~~~~Vv~s-------~e~v~~~i~~l   95 (98)
                      ....||..-|+++       ++++++++...
T Consensus       102 ~~~tGW~p~v~RtPpi~S~ti~~IR~~l~~~  132 (145)
T cd02410         102 TRETGWAPKVVRTPPIQSRTVKSIRRFLRRE  132 (145)
T ss_pred             HHHHCCEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             9973981578865999617899999999980


No 36 
>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=55.14  E-value=22  Score=18.29  Aligned_cols=52  Identities=23%  Similarity=0.453  Sum_probs=38.4

Q ss_pred             CCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CC-CEEEEE--------C-CHHHHHHHHHHHHC
Q ss_conf             599199999727898869899999999997-89-869998--------3-98999999998623
Q gi|254781194|r   45 PNGAHFWVEMKTSRGRLSNAQKRVIATLLL-YH-QKVQVL--------S-STEEVDGFLRMLEC   97 (98)
Q Consensus        45 ~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G-~~~~Vv--------~-s~e~v~~~i~~l~~   97 (98)
                      ++| .+++-++.|+|++++.|...+..+.+ .| ....+.        + ..+++.+++++|+-
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 37 
>pfam06555 consensus
Probab=54.62  E-value=22  Score=18.23  Aligned_cols=12  Identities=17%  Similarity=0.050  Sum_probs=4.8

Q ss_pred             HHHHHHHCCCEE
Q ss_conf             999999789889
Q gi|254781194|r   15 LVKGSKKLDCLV   26 (98)
Q Consensus        15 i~~~~k~~g~~~   26 (98)
                      +++.+++.|--+
T Consensus         3 ~i~~L~~~~f~~   14 (200)
T pfam06555         3 TVENLEKNNFEA   14 (200)
T ss_pred             HHHHHHHCCCEE
T ss_conf             799999789879


No 38 
>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=54.12  E-value=23  Score=18.19  Aligned_cols=52  Identities=10%  Similarity=0.326  Sum_probs=38.4

Q ss_pred             CCEEEEEC---CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHH
Q ss_conf             62799915---9919999972789886989999999999789869998398999999
Q gi|254781194|r   38 PDRLIITP---NGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLSSTEEVDGF   91 (98)
Q Consensus        38 PDli~~~~---~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~e~v~~~   91 (98)
                      .+=|.+.|   +.+..||.+|...++--..+......|...|  +-|+++++++.=+
T Consensus         9 S~TIfLdPV~~~~ktVyv~vrNTSd~~i~l~~~i~~~L~akG--Y~iv~~P~~A~Y~   63 (215)
T pfam05818         9 SQTIFLDPVAPEQRTVYLSIRNTSDKNVNLEQKLISALQAKG--YKVVDDPDKAHYW   63 (215)
T ss_pred             ECCEEECCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHCC--CEEECCHHHCEEE
T ss_conf             032886788800377999985388776673389999998489--3886796577077


No 39 
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=53.57  E-value=23  Score=18.13  Aligned_cols=30  Identities=30%  Similarity=0.325  Sum_probs=21.1

Q ss_pred             HHHHHHHHHCCCEEEEEC--CHHHHHHHHHHH
Q ss_conf             999999997898699983--989999999986
Q gi|254781194|r   66 KRVIATLLLYHQKVQVLS--STEEVDGFLRML   95 (98)
Q Consensus        66 ~~~~~~l~~~G~~~~Vv~--s~e~v~~~i~~l   95 (98)
                      ...+++|+.+|.++++.+  |++++.+-|+.+
T Consensus        90 ~~~~~~L~~~GI~v~~~~~~sl~di~~~i~~l  121 (265)
T PRK03379         90 ERQVDQLASLGIKVMWVDATSIEQIADALRQL  121 (265)
T ss_pred             HHHHHHHHHCCCEEEECCCCCHHHHHHHHHHH
T ss_conf             89999998169758835999999999999999


No 40 
>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=53.42  E-value=23  Score=18.12  Aligned_cols=70  Identities=10%  Similarity=-0.001  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC--CCCHHHHHHHHHHHHCCCE
Q ss_conf             9999999999999789889997148988766279991599199999727898--8698999999999978986
Q gi|254781194|r    8 EAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG--RLSNAQKRVIATLLLYHQK   78 (98)
Q Consensus         8 E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g--kls~~Q~~~~~~l~~~G~~   78 (98)
                      |.-++.-+-..+...|.. .+.-.-...|-+|+++...++..+.+|+|..+.  .+......=++++++.++.
T Consensus         3 E~~Y~~~~~~~~~~~~y~-v~se~es~~GR~Di~l~p~~~~~~IiE~K~~~~~~~~~~~~~~Al~QI~~k~Y~   74 (101)
T pfam08011         3 EGYYASVFYAYFASLGYE-VISEDETNKGRIDLTLKPTYTYIYIFEFKYIKVKDSDKEIAEEALEQIKEYGYA   74 (101)
T ss_pred             CHHHHHHHHHHHHHCCCE-EEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCH
T ss_conf             400899999999988979-998145699946499997488199999996386431015689999999976740


No 41 
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=53.11  E-value=23  Score=18.09  Aligned_cols=37  Identities=8%  Similarity=0.075  Sum_probs=28.0

Q ss_pred             CCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHH
Q ss_conf             8698999999999978986999839899999999862
Q gi|254781194|r   60 RLSNAQKRVIATLLLYHQKVQVLSSTEEVDGFLRMLE   96 (98)
Q Consensus        60 kls~~Q~~~~~~l~~~G~~~~Vv~s~e~v~~~i~~l~   96 (98)
                      +|...-....+.+...|+.++.+.+.||+.++|.++.
T Consensus        62 nLd~~l~~~~~~v~~~Gg~vy~A~~aedA~~ii~~iv   98 (459)
T COG1139          62 NLDEYLEQLEENVTRNGGHVYFAKDAEDAREIIGEIV   98 (459)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHH
T ss_conf             2899999999999971987998378899999999997


No 42 
>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=52.98  E-value=24  Score=18.08  Aligned_cols=63  Identities=17%  Similarity=0.220  Sum_probs=44.4

Q ss_pred             CCCCCCEEEEECCCCE-EEEEEECCCCCCCHHHHHHHHHHHHC--CCEEEEEC--CHHHHHHHHHHHH
Q ss_conf             8876627999159919-99997278988698999999999978--98699983--9899999999862
Q gi|254781194|r   34 QRGCPDRLIITPNGAH-FWVEMKTSRGRLSNAQKRVIATLLLY--HQKVQVLS--STEEVDGFLRMLE   96 (98)
Q Consensus        34 ~~G~PDli~~~~~g~~-~fIEvK~~~gkls~~Q~~~~~~l~~~--G~~~~Vv~--s~e~v~~~i~~l~   96 (98)
                      +.-.||+++...+..+ +|||.=+..|-.++.-+..+.+|-..  ...+||--  +....++++.+|+
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 43 
>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=52.80  E-value=24  Score=18.06  Aligned_cols=48  Identities=23%  Similarity=0.257  Sum_probs=34.4

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHH
Q ss_conf             9999972789886989999999999789869----99839899999999862
Q gi|254781194|r   49 HFWVEMKTSRGRLSNAQKRVIATLLLYHQKV----QVLSSTEEVDGFLRMLE   96 (98)
Q Consensus        49 ~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~----~Vv~s~e~v~~~i~~l~   96 (98)
                      +++-++=.+.+..-..|...+..|+.+|+++    .++.+.+++.++++.+.
T Consensus       213 f~~y~~~~~~~~~~~t~~e~l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~  264 (307)
T cd00114         213 FFIYGLGEAEGLGPKTQSEALAFLKEWGFPVSPETRLCKNIEEVLAFYDEIE  264 (307)
T ss_pred             EEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHHH
T ss_conf             7899855257888677899999999779966886189799999999999999


No 44 
>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=52.48  E-value=14  Score=19.32  Aligned_cols=60  Identities=22%  Similarity=0.315  Sum_probs=37.0

Q ss_pred             HHCCHHHHHHHHHHHH---HHCCCE--------------EEEEECCCCCCCCCEEEEECCCCEEE--EEE--ECCCCCCC
Q ss_conf             1205999999999999---978988--------------99971489887662799915991999--997--27898869
Q gi|254781194|r    4 DYLSEAKLEKRLVKGS---KKLDCL--------------VFKTQFINQRGCPDRLIITPNGAHFW--VEM--KTSRGRLS   62 (98)
Q Consensus         4 ~~m~E~~ie~~i~~~~---k~~g~~--------------~~k~~~~g~~G~PDli~~~~~g~~~f--IEv--K~~~gkls   62 (98)
                      ..++|.+||.++=..|   -++||.              +|+..|+  .||||+=++.=.|-.+.  +=+  ...+||..
T Consensus       108 ~~i~~eeiE~hvSniL~GLySLGG~~D~AliEyrvkfDp~F~~~SY--eGVPDiRiIVf~GyPVmaM~RlpTr~SdGKAN  185 (320)
T TIGR02291       108 ALISKEEIERHVSNILAGLYSLGGKRDRALIEYRVKFDPLFESVSY--EGVPDIRIIVFKGYPVMAMLRLPTRASDGKAN  185 (320)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCC--CCCCCEEEEEECCCCHHHHCCCCCCCCCCCCC
T ss_conf             1015456778888888777650799773688532010534477111--34587268964186102100276567888302


Q ss_pred             HHH
Q ss_conf             899
Q gi|254781194|r   63 NAQ   65 (98)
Q Consensus        63 ~~Q   65 (98)
                      -+|
T Consensus       186 LHQ  188 (320)
T TIGR02291       186 LHQ  188 (320)
T ss_pred             CCC
T ss_conf             124


No 45 
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=50.50  E-value=25  Score=17.92  Aligned_cols=35  Identities=20%  Similarity=0.269  Sum_probs=25.3

Q ss_pred             CCCCCEEEEECCCCE-EEEEEECCCCCCCH--HHHHHHH
Q ss_conf             876627999159919-99997278988698--9999999
Q gi|254781194|r   35 RGCPDRLIITPNGAH-FWVEMKTSRGRLSN--AQKRVIA   70 (98)
Q Consensus        35 ~G~PDli~~~~~g~~-~fIEvK~~~gkls~--~Q~~~~~   70 (98)
                      .=.||+.++. +|-+ +.||+|+|......  +|....+
T Consensus       124 ~~rpDvvlfI-NGiPlv~iElK~~~~~~~~a~~Qi~~Y~  161 (962)
T COG0610         124 KRRPDVVLFI-NGLPLVTIELKNPGVENNEAFNQIKRYQ  161 (962)
T ss_pred             CCCCCEEEEE-CCCEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             8787569998-6865687750687535699999998861


No 46 
>KOG2364 consensus
Probab=49.30  E-value=27  Score=17.73  Aligned_cols=59  Identities=20%  Similarity=0.191  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHHHHHHHC-CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHH
Q ss_conf             05999999999999978-98899971489887662799915991999997278988698999
Q gi|254781194|r    6 LSEAKLEKRLVKGSKKL-DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQK   66 (98)
Q Consensus         6 m~E~~ie~~i~~~~k~~-g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~   66 (98)
                      ..|.-++..|++.++.. +.--..|.+.|+--+-=++  +..||.+.+|+++|+...--.|.
T Consensus       231 l~enSveE~i~dhl~~~F~a~d~~F~sSGREDvDVRm--LG~GRPFvlEl~N~rr~~~~~q~  290 (433)
T KOG2364         231 LKENSVEEDIKDHLKEFFSADDVVFISSGREDVDVRM--LGTGRPFVLELKNPRRNLGFEQL  290 (433)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEE--CCCCCCEEEECCCCCCCCHHHHH
T ss_conf             4455488999999986437001465147875301475--05898359985785412137776


No 47 
>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=47.61  E-value=20  Score=18.50  Aligned_cols=23  Identities=30%  Similarity=0.515  Sum_probs=17.8

Q ss_pred             CCCCCCEEEEECCCCE-EEEEEECC
Q ss_conf             8876627999159919-99997278
Q gi|254781194|r   34 QRGCPDRLIITPNGAH-FWVEMKTS   57 (98)
Q Consensus        34 ~~G~PDli~~~~~g~~-~fIEvK~~   57 (98)
                      +..-||+.++. +|-+ .+||+|++
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 48 
>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=47.26  E-value=29  Score=17.54  Aligned_cols=35  Identities=23%  Similarity=0.394  Sum_probs=17.0

Q ss_pred             HHHHHHHHCCCEEEEEECCCCC-----------C--CCCEEEEECCCCEEE
Q ss_conf             9999999789889997148988-----------7--662799915991999
Q gi|254781194|r   14 RLVKGSKKLDCLVFKTQFINQR-----------G--CPDRLIITPNGAHFW   51 (98)
Q Consensus        14 ~i~~~~k~~g~~~~k~~~~g~~-----------G--~PDli~~~~~g~~~f   51 (98)
                      +..+.+++.|..+.=  +.||+           |  .||.+++. +|...+
T Consensus        26 ~al~~l~~~Gi~vvi--aTGR~~~~~~~~~~~l~l~~p~~~I~~-nG~~I~   73 (247)
T pfam05116        26 QLLEAQYRPDSLLVF--ATGRSLDSAKELLKEKPLPTPDVLITS-VGTEIY   73 (247)
T ss_pred             HHHHHHHHCCCEEEE--ECCCCHHHHHHHHHHCCCCCCCEEEEC-CCEEEE
T ss_conf             999999958988999--889999999999997598999989975-975999


No 49 
>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=46.66  E-value=30  Score=17.48  Aligned_cols=77  Identities=17%  Similarity=0.132  Sum_probs=45.0

Q ss_pred             HHHHHHCCCEE-EEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHH-HHHHHHHCCCEEEEE--CC--HHHHH
Q ss_conf             99999789889-99714898876627999159919999972789886989999-999999789869998--39--89999
Q gi|254781194|r   16 VKGSKKLDCLV-FKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKR-VIATLLLYHQKVQVL--SS--TEEVD   89 (98)
Q Consensus        16 ~~~~k~~g~~~-~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~-~~~~l~~~G~~~~Vv--~s--~e~v~   89 (98)
                      .+.+++.|+.- ......|--|+ |++...+++.-+.|++|.-++........ ++..+...++.-.++  .|  .+++.
T Consensus         2 ~~ll~~~G~~~v~~t~~~~D~Gi-Dvia~~~~~~~~~VQ~K~~~~~vg~~~v~~l~~~~~~~~~~~~i~vTt~~fT~~A~   80 (98)
T pfam04471         2 AELLEALGYREVELTGKSGDGGI-DVVATTSDGERIVVQAKRYRSTVGRPVIQELLGAKAGYGADKGVVVTTSGFTSAAR   80 (98)
T ss_pred             HHHHHHCCCCEEEECCCCCCCCE-EEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHH
T ss_conf             68897679988997889898845-89999379989999999878989989999996027761898799998774398899


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254781194|r   90 GFLR   93 (98)
Q Consensus        90 ~~i~   93 (98)
                      ++-+
T Consensus        81 ~~A~   84 (98)
T pfam04471        81 ELAE   84 (98)
T ss_pred             HHHH
T ss_conf             9997


No 50 
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=45.38  E-value=27  Score=17.78  Aligned_cols=27  Identities=19%  Similarity=0.099  Sum_probs=16.2

Q ss_pred             HHHHHCCCEEEEECCHHHHHHHHHHHH
Q ss_conf             999978986999839899999999862
Q gi|254781194|r   70 ATLLLYHQKVQVLSSTEEVDGFLRMLE   96 (98)
Q Consensus        70 ~~l~~~G~~~~Vv~s~e~v~~~i~~l~   96 (98)
                      --++..|..+|-+.+.|++.+.|+.|+
T Consensus        16 lgF~~lG~dvfpv~~~eEa~~~l~~La   42 (104)
T PRK01395         16 LPFKALGFDVFPVIEEQEARNTLRKLA   42 (104)
T ss_pred             HHHHHCCEEEEECCCHHHHHHHHHHHH
T ss_conf             888865804785488799999999998


No 51 
>PRK09534 btuF corrinoid ABC transporter substrate-binding protein; Reviewed
Probab=44.57  E-value=32  Score=17.29  Aligned_cols=30  Identities=13%  Similarity=-0.002  Sum_probs=23.7

Q ss_pred             HHHHHHHHHCCCEEEEEC---CHHHHHHHHHHH
Q ss_conf             999999997898699983---989999999986
Q gi|254781194|r   66 KRVIATLLLYHQKVQVLS---STEEVDGFLRML   95 (98)
Q Consensus        66 ~~~~~~l~~~G~~~~Vv~---s~e~v~~~i~~l   95 (98)
                      ...+++|+++|..++++.   |+|++-+-|+.|
T Consensus       131 ~~~v~~L~~~GI~V~v~~~a~SiddV~~~I~~i  163 (364)
T PRK09534        131 NDTVTRLRSAGITVFQFRAATSIDGVVEKTATI  163 (364)
T ss_pred             HHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf             678999997699699918988999999999999


No 52 
>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=42.10  E-value=35  Score=17.06  Aligned_cols=50  Identities=22%  Similarity=0.185  Sum_probs=28.6

Q ss_pred             HHHHHHHHHH-HHCCCEEEEE----EC---CCCCCCCCEEEEECCCCEEEEEEECCCCC
Q ss_conf             9999999999-9789889997----14---89887662799915991999997278988
Q gi|254781194|r   10 KLEKRLVKGS-KKLDCLVFKT----QF---INQRGCPDRLIITPNGAHFWVEMKTSRGR   60 (98)
Q Consensus        10 ~ie~~i~~~~-k~~g~~~~k~----~~---~g~~G~PDli~~~~~g~~~fIEvK~~~gk   60 (98)
                      ..|..+.... +..|..+...    ..   +...+-||-++..+++. ..+|+|.|..+
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 53 
>PRK10767 chaperone protein DnaJ; Provisional
Probab=41.73  E-value=36  Score=17.03  Aligned_cols=60  Identities=18%  Similarity=0.139  Sum_probs=35.2

Q ss_pred             CCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CCCEEEEECC------HHHHHHHHHHH
Q ss_conf             8766279991599199999727898869899999999997-8986999839------89999999986
Q gi|254781194|r   35 RGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLL-YHQKVQVLSS------TEEVDGFLRML   95 (98)
Q Consensus        35 ~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~~~~Vv~s------~e~v~~~i~~l   95 (98)
                      .|+|+.=--..+-.++-+.|+-|. +||+.|+..+++|++ .|-......+      ++-+.++.++|
T Consensus       308 ~Gmp~~~~~~~GDl~V~~~V~~P~-~Ls~~Qk~ll~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  374 (376)
T PRK10767        308 KGVKSVRGGAQGDLLCRVVVETPV-GLNEKQKQLLQELQESFGGPTGEKNSPRSKSFFDGVKKFFDDL  374 (376)
T ss_pred             CCCCCCCCCCCCCEEEEEEEECCC-CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             898989979977889999998999-9999999999999997467666767854478899999998751


No 54 
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=40.64  E-value=37  Score=16.93  Aligned_cols=56  Identities=11%  Similarity=0.050  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHH
Q ss_conf             99999999999789889997148988766279991599199999727898869899
Q gi|254781194|r   10 KLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQ   65 (98)
Q Consensus        10 ~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q   65 (98)
                      .+.+.+.+.+.+.||.+.+....|.+-.+=-|-=...|.++++.+..+...++...
T Consensus        21 ~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~   76 (95)
T PRK00453         21 ALVERYKGVITKNGGEIHKVEDWGRRRLAYPINKLRKGHYVLLNFEADPAAIAELE   76 (95)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECCCCEEEEEEEEEEECHHHHHHHH
T ss_conf             99999999999799889998502120044230667589999999998988999999


No 55 
>pfam09564 RE_NgoBV NgoBV restriction endonuclease. This family includes the NgoBV (recognizes GGNNCC but cleavage site is unknown) restriction endonuclease.
Probab=40.59  E-value=37  Score=16.92  Aligned_cols=61  Identities=13%  Similarity=0.046  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHCCCEEEEEE-CCCCCCCCCEEEEECCCCEEEEEEECCCC--CCCHHH---HHHHHHHH
Q ss_conf             999999999997898899971-48988766279991599199999727898--869899---99999999
Q gi|254781194|r   10 KLEKRLVKGSKKLDCLVFKTQ-FINQRGCPDRLIITPNGAHFWVEMKTSRG--RLSNAQ---KRVIATLL   73 (98)
Q Consensus        10 ~ie~~i~~~~k~~g~~~~k~~-~~g~~G~PDli~~~~~g~~~fIEvK~~~g--kls~~Q---~~~~~~l~   73 (98)
                      .||..+..++.+..   .+|. ++|++-.||+++=..+..--.+|+|+-+.  .|+=.-   +.+.+.+.
T Consensus        46 iiQ~WL~~~L~~~~---I~f~~~~nTQ~pPDf~Ln~~~~~e~llEIK~Fn~~~sP~FDIA~f~ay~~~l~  112 (194)
T pfam09564        46 IIQEWLGGWLRKRE---IEFDVSTNTQMPPDFFLNKKDRSRELLEVKAFNRNACPGFDIADFKMYSDEIF  112 (194)
T ss_pred             HHHHHHHHHHHHCC---EEECCCCCCCCCCCEEECCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHH
T ss_conf             99999999876445---55148999878985465567675550888764278998642677999999885


No 56 
>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=38.06  E-value=41  Score=16.69  Aligned_cols=30  Identities=27%  Similarity=0.269  Sum_probs=23.2

Q ss_pred             EEEEEECCCCCCCCCEEEEEC-CCCEEEEEEEC
Q ss_conf             899971489887662799915-99199999727
Q gi|254781194|r   25 LVFKTQFINQRGCPDRLIITP-NGAHFWVEMKT   56 (98)
Q Consensus        25 ~~~k~~~~g~~G~PDli~~~~-~g~~~fIEvK~   56 (98)
                      ++.||...  +|.+||+++-. .|++-.+.+++
T Consensus         4 R~~kFSp~--~~~~DLLv~sE~~Grvhv~DlR~   34 (43)
T pfam10313         4 RVCKFSPE--NGLNDLLVISEHVGRVHVADLRT   34 (43)
T ss_pred             EEEEECCC--CCCCCEEEEEECCCEEEEEECCC
T ss_conf             79996698--99763799991687388999000


No 57 
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=36.49  E-value=43  Score=16.54  Aligned_cols=48  Identities=23%  Similarity=0.457  Sum_probs=33.8

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHH-CC--CEEEEEC---------CHHHHHHHHHHHH
Q ss_conf             99999727898869899999999997-89--8699983---------9899999999862
Q gi|254781194|r   49 HFWVEMKTSRGRLSNAQKRVIATLLL-YH--QKVQVLS---------STEEVDGFLRMLE   96 (98)
Q Consensus        49 ~~fIEvK~~~gkls~~Q~~~~~~l~~-~G--~~~~Vv~---------s~e~v~~~i~~l~   96 (98)
                      ++.+=+|-|+|.+|+.|...+..+.+ .|  +...+..         ..+++-++++.|+
T Consensus        65 ~FMlRvriPgG~lt~~Q~r~la~ia~~yg~~G~~~iTTRQniQlh~I~~~d~~~i~~~L~  124 (513)
T PRK09566         65 KFMLRLRVPNGILTSQQLRVLASIVQRYGEDGSADITTRQNLQLRGILLEDLPEILNRLK  124 (513)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHCCCCHHHHHHHHHHHH
T ss_conf             468896678975599999999999998689985999737112115877788999999999


No 58 
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912    The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.  .
Probab=36.38  E-value=43  Score=16.53  Aligned_cols=62  Identities=19%  Similarity=0.124  Sum_probs=43.0

Q ss_pred             HHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CCCE-EEEEC
Q ss_conf             99789889997148988766279991599199999727898869899999999997-8986-99983
Q gi|254781194|r   19 SKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLL-YHQK-VQVLS   83 (98)
Q Consensus        19 ~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~~-~~Vv~   83 (98)
                      ++..||.-..|+..||==+==+  ++-+||.|-||+|.|+.|--+.-. ..+++++ +.+. |.|..
T Consensus       254 ~~~~~G~~~~fHGaGREDvDvR--MLG~GRPFVlEv~~Pr~R~~dl~~-l~~eiN~~a~GkGVEv~~  317 (450)
T TIGR01213       254 LKATGGTDAVFHGAGREDVDVR--MLGTGRPFVLEVKEPRKRKIDLDE-LEEEINKGASGKGVEVLG  317 (450)
T ss_pred             HHHCCCEEEEEEECCCCCEEEE--CCCCCCCEEEEECCCCCCCCCHHH-HHHHHCCCCCCCEEEEEE
T ss_conf             6422880699962566400010--178888359972588658888789-999954678853489973


No 59 
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=35.17  E-value=35  Score=17.09  Aligned_cols=50  Identities=22%  Similarity=0.484  Sum_probs=30.4

Q ss_pred             CCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHH-HHH----HCCCEEEEECCHH-----HHHHHHHHHH
Q ss_conf             76627999159919999972789886989999999-999----7898699983989-----9999999862
Q gi|254781194|r   36 GCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIA-TLL----LYHQKVQVLSSTE-----EVDGFLRMLE   96 (98)
Q Consensus        36 G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~-~l~----~~G~~~~Vv~s~e-----~v~~~i~~l~   96 (98)
                      -.||++.+.|+|..           ....|.+-+. .+.    ..++.++|++..|     -++.+|+-|+
T Consensus        76 ~HPD~~~i~p~~~~-----------i~idqiR~L~~~~~~~p~~g~~KV~II~~Ae~m~~~AaNALLKtLE  135 (329)
T PRK08058         76 NHPDVHLVAPDGQS-----------IKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLE  135 (329)
T ss_pred             CCCCEEEECCCCCC-----------CCHHHHHHHHHHHCCCCCCCCCEEEEEECHHHHCHHHHHHHHHHHH
T ss_conf             99976774566140-----------7799999999996438757886799973477629999999999864


No 60 
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=33.66  E-value=48  Score=16.26  Aligned_cols=26  Identities=19%  Similarity=0.231  Sum_probs=13.8

Q ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             99999727898869899999999997
Q gi|254781194|r   49 HFWVEMKTSRGRLSNAQKRVIATLLL   74 (98)
Q Consensus        49 ~~fIEvK~~~gkls~~Q~~~~~~l~~   74 (98)
                      .+.+=+|-|+|.+|+.|...+..+.+
T Consensus       113 ~FMlRiRiPgG~lt~~Q~r~la~iA~  138 (591)
T PRK09567        113 SYMCRLRIPNGILTHWQLAGLADLAD  138 (591)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             04899536896359999999999999


No 61 
>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=33.52  E-value=48  Score=16.25  Aligned_cols=26  Identities=23%  Similarity=0.325  Sum_probs=20.8

Q ss_pred             CCC---CCCEEEEECCCCE-EEEEEECCCCC
Q ss_conf             887---6627999159919-99997278988
Q gi|254781194|r   34 QRG---CPDRLIITPNGAH-FWVEMKTSRGR   60 (98)
Q Consensus        34 ~~G---~PDli~~~~~g~~-~fIEvK~~~gk   60 (98)
                      ..|   .||++++. ||-+ .-||+|.|=++
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 62 
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=33.35  E-value=48  Score=16.28  Aligned_cols=25  Identities=24%  Similarity=0.446  Sum_probs=21.7

Q ss_pred             CCCCCCCEEEEECCCCEEEEEEECC
Q ss_conf             9887662799915991999997278
Q gi|254781194|r   33 NQRGCPDRLIITPNGAHFWVEMKTS   57 (98)
Q Consensus        33 g~~G~PDli~~~~~g~~~fIEvK~~   57 (98)
                      |.+--||.+|-+|+|+.+.|--|.|
T Consensus       236 g~r~rPDvIV~LP~~k~iVIDSKvs  260 (475)
T PRK10361        236 RSRMQPDVIVRLPQGKDVVIDAKMT  260 (475)
T ss_pred             CCCCCCCEEEECCCCCEEEEECCCC
T ss_conf             8822897689878997588862788


No 63 
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=31.07  E-value=53  Score=16.01  Aligned_cols=81  Identities=20%  Similarity=0.188  Sum_probs=50.2

Q ss_pred             HHHHHHHHHH-HHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEEC---
Q ss_conf             9999999999-999789889997148988766279991599199999727898869899999999997898699983---
Q gi|254781194|r    8 EAKLEKRLVK-GSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLS---   83 (98)
Q Consensus         8 E~~ie~~i~~-~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~---   83 (98)
                      ..-++.-|.. ..+..|+.-.+|+..|+--+-=+|  +.+|+.+-+|+|.|..|--+. ......++.-| .|.|.+   
T Consensus       190 ~~sve~~i~~~~~~~f~g~~~~fhgAGREDvDvRM--LG~GRPfVlEvk~Pr~R~~dl-~~l~~~in~~~-~vev~~l~f  265 (398)
T COG1258         190 PESVEELIKQPIKEAFGGLDAKFHGAGREDVDVRM--LGTGRPFVLEVKEPRRRNVDL-DELEEEINRGG-KVEVFDLEF  265 (398)
T ss_pred             CCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCEEE--ECCCCCEEEEECCCCCCCCCH-HHHHHHHCCCC-CEEEEEEEE
T ss_conf             44199998789998606850699716877663466--058983699923742256886-78899763588-589998774


Q ss_pred             -CHHHHHHHH
Q ss_conf             -989999999
Q gi|254781194|r   84 -STEEVDGFL   92 (98)
Q Consensus        84 -s~e~v~~~i   92 (98)
                       +.++++.+-
T Consensus       266 ~~~e~v~~ik  275 (398)
T COG1258         266 VGREEVEEIK  275 (398)
T ss_pred             CCHHHHHHHH
T ss_conf             4799999987


No 64 
>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=29.03  E-value=53  Score=16.04  Aligned_cols=60  Identities=17%  Similarity=0.252  Sum_probs=36.2

Q ss_pred             CCCCEEEEECCCCEEE-------------EEEECC-----CCCCCHHHHHHHHHHHHCCCEEEEECCHHH-----HHHHH
Q ss_conf             7662799915991999-------------997278-----988698999999999978986999839899-----99999
Q gi|254781194|r   36 GCPDRLIITPNGAHFW-------------VEMKTS-----RGRLSNAQKRVIATLLLYHQKVQVLSSTEE-----VDGFL   92 (98)
Q Consensus        36 G~PDli~~~~~g~~~f-------------IEvK~~-----~gkls~~Q~~~~~~l~~~G~~~~Vv~s~e~-----v~~~i   92 (98)
                      -.||+..+.|+|..--             .. +++     -+..+..+......=...|+.|+|++..|.     ++.+|
T Consensus        62 ~HPD~~~~~P~~~~~~~~~de~~~~~~g~a~-~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~mn~~AANALL  140 (216)
T TIGR00678        62 NHPDLHRLEPEGQSKSLTADEAAEGEEGSAK-RRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAERMNEAAANALL  140 (216)
T ss_pred             CCCCEEEEEEECCCCCCCHHHHHHHHCCCCC-CCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHH
T ss_conf             9982378742347777776458976256421-136787872789999999860642147517997673232589898651


Q ss_pred             HHHH
Q ss_conf             9862
Q gi|254781194|r   93 RMLE   96 (98)
Q Consensus        93 ~~l~   96 (98)
                      +-||
T Consensus       141 KtLE  144 (216)
T TIGR00678       141 KTLE  144 (216)
T ss_pred             HHEE
T ss_conf             0101


No 65 
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=28.57  E-value=59  Score=15.75  Aligned_cols=41  Identities=12%  Similarity=0.182  Sum_probs=28.1

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHH
Q ss_conf             972789886989999999999789869998-39899999999862
Q gi|254781194|r   53 EMKTSRGRLSNAQKRVIATLLLYHQKVQVL-SSTEEVDGFLRMLE   96 (98)
Q Consensus        53 EvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~e~v~~~i~~l~   96 (98)
                      -+=-|.|+.++.|+.++..+.   ..+.-+ -++||++++++++.
T Consensus       153 ~Vl~P~g~vs~~k~~q~~~~g---a~~i~v~G~fDda~~~vk~~~  194 (411)
T COG0498         153 FVLYPKGKVSPGKLAQMLTLG---AHVIAVDGNFDDAQELVKEAA  194 (411)
T ss_pred             EEEECCCCCCHHHHHHHHHCC---CEEEEECCCHHHHHHHHHHHH
T ss_conf             999459878878899997538---889997596899999999999


No 66 
>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=27.52  E-value=61  Score=15.64  Aligned_cols=40  Identities=23%  Similarity=0.226  Sum_probs=28.9

Q ss_pred             CCCCCEEEE---ECCCCEEEEEEECCCCCCCHHHHHHHHHHHHC
Q ss_conf             876627999---15991999997278988698999999999978
Q gi|254781194|r   35 RGCPDRLII---TPNGAHFWVEMKTSRGRLSNAQKRVIATLLLY   75 (98)
Q Consensus        35 ~G~PDli~~---~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~   75 (98)
                      .|+|++---   ..+-.++-|.|-.|+. ||..|+.-+++|...
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 67 
>COG5321 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.38  E-value=56  Score=15.87  Aligned_cols=43  Identities=16%  Similarity=0.275  Sum_probs=27.9

Q ss_pred             HHHHHHHHHCCCEEEEEE--CCCCCCCCCEEEEECCCCEEEEEEECC
Q ss_conf             999999997898899971--489887662799915991999997278
Q gi|254781194|r   13 KRLVKGSKKLDCLVFKTQ--FINQRGCPDRLIITPNGAHFWVEMKTS   57 (98)
Q Consensus        13 ~~i~~~~k~~g~~~~k~~--~~g~~G~PDli~~~~~g~~~fIEvK~~   57 (98)
                      +.+..-+-..|.-++--.  ..|+  -.|||.+-|.|..+.||+|+.
T Consensus        26 RGvqrLl~~mg~a~LpEltLasGR--RADLials~kGeiwIiEiKss   70 (164)
T COG5321          26 RGVQRLLMAMGHAVLPELTLASGR--RADLIALSPKGEIWIIEIKSS   70 (164)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCC--CCCEEEECCCCCEEEEEEECC
T ss_conf             869999998234547433146786--200025557785899996234


No 68 
>smart00532 LIGANc Ligase N family.
Probab=25.42  E-value=67  Score=15.41  Aligned_cols=34  Identities=18%  Similarity=0.163  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHH
Q ss_conf             89999999999789869----99839899999999862
Q gi|254781194|r   63 NAQKRVIATLLLYHQKV----QVLSSTEEVDGFLRMLE   96 (98)
Q Consensus        63 ~~Q~~~~~~l~~~G~~~----~Vv~s~e~v~~~i~~l~   96 (98)
                      ..|...++.|+..|+++    .++.+.+++.++++.+.
T Consensus       231 ~t~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~  268 (441)
T smart00532      231 KTQSEALKWLKELGFPVSPHTRLCKNADEVIEYYEEWE  268 (441)
T ss_pred             CCHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             68999999999779924876199689999999999999


No 69 
>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=24.74  E-value=69  Score=15.34  Aligned_cols=66  Identities=12%  Similarity=0.140  Sum_probs=37.0

Q ss_pred             CCCCCCCCCEEEEECCCCE-----------------EEEEEECC-CCCCCHHHHHHHHHH--HHCCCEEEEECCHHHHHH
Q ss_conf             4898876627999159919-----------------99997278-988698999999999--978986999839899999
Q gi|254781194|r   31 FINQRGCPDRLIITPNGAH-----------------FWVEMKTS-RGRLSNAQKRVIATL--LLYHQKVQVLSSTEEVDG   90 (98)
Q Consensus        31 ~~g~~G~PDli~~~~~g~~-----------------~fIEvK~~-~gkls~~Q~~~~~~l--~~~G~~~~Vv~s~e~v~~   90 (98)
                      .+.++|+|.+++..-||+.                 ..|++-+= -|.....|...+.-.  ....|+.+...+++.+..
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             HHHHHH
Q ss_conf             999862
Q gi|254781194|r   91 FLRMLE   96 (98)
Q Consensus        91 ~i~~l~   96 (98)
                      +++.|.
T Consensus       182 i~~~l~  187 (192)
T cd01473         182 ISKFLT  187 (192)
T ss_pred             HHHHHH
T ss_conf             999999


No 70 
>pfam01250 Ribosomal_S6 Ribosomal protein S6.
Probab=23.85  E-value=72  Score=15.23  Aligned_cols=59  Identities=15%  Similarity=0.105  Sum_probs=39.0

Q ss_pred             CCHHH---HHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHH
Q ss_conf             05999---999999999978988999714898876627999159919999972789886989
Q gi|254781194|r    6 LSEAK---LEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNA   64 (98)
Q Consensus         6 m~E~~---ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~   64 (98)
                      +.|.+   +.+.+.+.+.+.||.+.+....|.+-.+=-|-=...|.++++.+..+...+...
T Consensus        13 l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el   74 (92)
T pfam01250        13 LSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAEL   74 (92)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCEEEEEEEEEEECHHHHHHH
T ss_conf             99899999999999999878988999851310003304377889999999999998899999


No 71 
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185   Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.     The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion .   SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae  as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=23.69  E-value=72  Score=15.21  Aligned_cols=53  Identities=21%  Similarity=0.235  Sum_probs=39.1

Q ss_pred             CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf             98899971489887662799915991999997278-988698999999999978986999839
Q gi|254781194|r   23 DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTS-RGRLSNAQKRVIATLLLYHQKVQVLSS   84 (98)
Q Consensus        23 g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~s   84 (98)
                      |=+.|++.-.|-      ++++ +|.  ..||||+ |..|++-.-..+..|..-|.++--|+.
T Consensus        58 G~r~fDVQliGg------~~LH-~G~--IAEMkTGEGKTL~AtLpaYLNAL~GkGVHvVTVNd  111 (904)
T TIGR00963        58 GLRPFDVQLIGG------IVLH-KGK--IAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVND  111 (904)
T ss_pred             CCCCHHHHHHHH------HHHC-CCC--EEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECC
T ss_conf             785618999999------9980-896--67831488628999999998765179627996350


No 72 
>COG3331 PrfA Penicillin-binding protein-related factor A, putative recombinase [General function prediction only]
Probab=23.40  E-value=73  Score=15.18  Aligned_cols=77  Identities=14%  Similarity=0.035  Sum_probs=58.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEEEECC---------CC------------CCCCCEEEEECCCCEEEEEEECCCCC----
Q ss_conf             059999999999999789889997148---------98------------87662799915991999997278988----
Q gi|254781194|r    6 LSEAKLEKRLVKGSKKLDCLVFKTQFI---------NQ------------RGCPDRLIITPNGAHFWVEMKTSRGR----   60 (98)
Q Consensus         6 m~E~~ie~~i~~~~k~~g~~~~k~~~~---------g~------------~G~PDli~~~~~g~~~fIEvK~~~gk----   60 (98)
                      ..|++|++.+.-++.+--.+..|-.+|         -+            +---|...++. |.++-.|.|..+++    
T Consensus         9 ~lE~~In~T~~~y~~~~~a~i~Kk~tPVqiv~v~yp~rs~a~i~eayf~~kSttDY~GvYk-G~yidFEaKeTknktsFp   87 (177)
T COG3331           9 SLEADINKTNDYYLAHDIAVIHKKPTPVQIVNVDYPKRSGAVIKEAYFRQKSTTDYYGVYK-GYYIDFEAKETKNKTSFP   87 (177)
T ss_pred             CHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEECCCCCCCCHHHHHHCCCCCCCEEEEEEC-CEEEEEEECCCCCCCCCC
T ss_conf             3899999899887635736886047662378704720032011233405788630456850-279755600135666473


Q ss_pred             ---CCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             ---69899999999997898699983
Q gi|254781194|r   61 ---LSNAQKRVIATLLLYHQKVQVLS   83 (98)
Q Consensus        61 ---ls~~Q~~~~~~l~~~G~~~~Vv~   83 (98)
                         ..++|...+..+...|+.+++.-
T Consensus        88 l~ni~~HQi~hlk~v~~q~Gi~Flli  113 (177)
T COG3331          88 LKNIHPHQIEHLKNVLQQGGISFLLI  113 (177)
T ss_pred             HHHCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf             45438889999999985698389999


No 73 
>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=23.24  E-value=25  Score=17.93  Aligned_cols=17  Identities=24%  Similarity=0.593  Sum_probs=15.0

Q ss_pred             CCCCCCEEEEECCCCEE
Q ss_conf             88766279991599199
Q gi|254781194|r   34 QRGCPDRLIITPNGAHF   50 (98)
Q Consensus        34 ~~G~PDli~~~~~g~~~   50 (98)
                      ..++||+..+.|||+.+
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 74 
>pfam06241 DUF1012 Protein of unknown function (DUF1012). Family of uncharacterized proteins found in both eukaryotes and bacteria.
Probab=23.09  E-value=61  Score=15.65  Aligned_cols=18  Identities=11%  Similarity=0.263  Sum_probs=14.3

Q ss_pred             CCCCCCEEEE--ECCCCEEE
Q ss_conf             8876627999--15991999
Q gi|254781194|r   34 QRGCPDRLII--TPNGAHFW   51 (98)
Q Consensus        34 ~~G~PDli~~--~~~g~~~f   51 (98)
                      ++|+||..+|  +++|+..|
T Consensus       111 Rrgf~e~VVCGl~rnGki~F  130 (208)
T pfam06241       111 RLGFQEVVVCGILRDGKVNF  130 (208)
T ss_pred             HHCCCCEEEEEEECCCCCCC
T ss_conf             72688607997751896230


No 75 
>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=22.58  E-value=36  Score=16.97  Aligned_cols=26  Identities=23%  Similarity=0.279  Sum_probs=14.6

Q ss_pred             CCEEEEEEECCC--C----CCCHHHHHHHHHH
Q ss_conf             919999972789--8----8698999999999
Q gi|254781194|r   47 GAHFWVEMKTSR--G----RLSNAQKRVIATL   72 (98)
Q Consensus        47 g~~~fIEvK~~~--g----kls~~Q~~~~~~l   72 (98)
                      +...|||+|++.  |    +++..-.-+|+++
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 76 
>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=22.26  E-value=77  Score=15.05  Aligned_cols=63  Identities=13%  Similarity=0.101  Sum_probs=44.1

Q ss_pred             HHHHHHHHHCCCEE--EEEECCCCCCCCCEEEEECCCCEEEEEEECCCC-CCCHHHHHHHHHHHHCCCE-E
Q ss_conf             99999999789889--997148988766279991599199999727898-8698999999999978986-9
Q gi|254781194|r   13 KRLVKGSKKLDCLV--FKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG-RLSNAQKRVIATLLLYHQK-V   79 (98)
Q Consensus        13 ~~i~~~~k~~g~~~--~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g-kls~~Q~~~~~~l~~~G~~-~   79 (98)
                      ..|.+++.+..---  |.+.--|--.||+.    .+-|++|+.++.+.+ .|+..|....+.+..+|+. .
T Consensus        55 ~~l~~~L~~~~~~~~~F~l~l~g~G~F~~~----~~pRvlWaGv~~~~~~~L~~L~~~~~~~l~~~G~~~~  121 (189)
T TIGR02258        55 EELEDALAKIAEPPEPFTLKLEGVGVFGNP----KSPRVLWAGVEESEEKELTQLQEELERALAKAGFSRK  121 (189)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEEECCCCCC----CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             999998887503899734787521027888----8876899843899615789999999999996488889


No 77 
>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=22.25  E-value=78  Score=15.04  Aligned_cols=85  Identities=15%  Similarity=0.153  Sum_probs=48.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCH
Q ss_conf             05999999999999978988999714898876627999159919999972789886989999999999789869998398
Q gi|254781194|r    6 LSEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLSST   85 (98)
Q Consensus         6 m~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~   85 (98)
                      +.=+++++.+.-|.+.+|..+.........|+=  +++.+.|. ..+|+=.|.+.-++... +++.  .-++..++|..+
T Consensus         7 i~V~Dld~a~~fy~~~lG~~~~~~~~~~~~~~~--~~~~~~g~-~~ieL~~~~~~~~~~~~-~l~~--~g~G~~Hiaf~V   80 (128)
T TIGR03081         7 IAVPDLEEAAKLYEDVLGAHVSHIEEVPEQGVK--VVFIALGN-TKVELLEPLGEDSPIAK-FLEK--NGGGIHHIAIEV   80 (128)
T ss_pred             EECCCHHHHHHHHHHHHCCCEEECCCCCCCCEE--EEEEECCC-CCEEEEEECCCCCCHHH-HCCC--CCCCCEEEEEEC
T ss_conf             980999999999999709956531115667959--99994689-71788630578985344-1114--699856999987


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999862
Q gi|254781194|r   86 EEVDGFLRMLE   96 (98)
Q Consensus        86 e~v~~~i~~l~   96 (98)
                      ++++..++.|+
T Consensus        81 ~Di~~~~~~l~   91 (128)
T TIGR03081        81 DDIEAALETLK   91 (128)
T ss_pred             CCHHHHHHHHH
T ss_conf             99999999999


No 78 
>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=22.10  E-value=78  Score=15.03  Aligned_cols=84  Identities=14%  Similarity=0.164  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEE-----------------ECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHH
Q ss_conf             9999999999999789889997-----------------14898876627999159919999972789886989999999
Q gi|254781194|r    8 EAKLEKRLVKGSKKLDCLVFKT-----------------QFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIA   70 (98)
Q Consensus         8 E~~ie~~i~~~~k~~g~~~~k~-----------------~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~   70 (98)
                      ..++-++|.+.+|+.  .+.+.                 .-|-.+|+-|+ .|.++-.-..||.|.|+--.-.......+
T Consensus        41 ~~~~i~~~a~~~kkr--i~ir~d~~~~~~~~~a~~~i~~~vp~~a~i~~~-~fd~~~~ev~i~~~kpg~~~g~~g~~~~~  117 (630)
T TIGR03675        41 DDDLVKELAKKLRKR--IVIRPDPSVLLPPEEAIEKIKEIVPEEAGITDI-YFDDVTGEVIIEAEKPGLVIGKGGSTLRE  117 (630)
T ss_pred             CCHHHHHHHHHHCCE--EEECCCCHHCCCHHHHHHHHHHHCCCCCCCEEE-EECCCCCEEEEEECCCEEEECCCCHHHHH
T ss_conf             741999999986043--898279033189999999999758953584158-97489727999977963676475167999


Q ss_pred             HHHHCCCEEEEECC-------HHHHHHHHHH
Q ss_conf             99978986999839-------8999999998
Q gi|254781194|r   71 TLLLYHQKVQVLSS-------TEEVDGFLRM   94 (98)
Q Consensus        71 ~l~~~G~~~~Vv~s-------~e~v~~~i~~   94 (98)
                      -....||..-|+++       ++++++++..
T Consensus       118 i~~~~gw~~~v~r~p~~~s~~~~~ir~~~~~  148 (630)
T TIGR03675       118 ITAETGWTPKVVRTPPIESKTIKNIREYLRS  148 (630)
T ss_pred             HHHHHCCEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             9997497468886599970789999999997


No 79 
>pfam09521 RE_NgoPII NgoPII restriction endonuclease. This family includes the NgoPII (recognizes and cleaves GG^CC) restriction endonuclease.
Probab=21.88  E-value=79  Score=15.00  Aligned_cols=40  Identities=33%  Similarity=0.302  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECC
Q ss_conf             99999999999997898899971489887662799915991999997278
Q gi|254781194|r    8 EAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTS   57 (98)
Q Consensus         8 E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~   57 (98)
                      +++.+++...+-+...+      .++..-.||+|+  .+|.  .||+|.-
T Consensus        49 ~~d~~~r~~~~~~~fsy------~Gn~nnpPD~il--k~Gd--aiEvKKi   88 (263)
T pfam09521        49 ENDEEKKDEIYSEVFSY------LGNQNNPPDMIL--KNGD--AVEVKKI   88 (263)
T ss_pred             HHHHHHHHHHHHHHHEE------CCCCCCCCHHHE--ECCC--EEEEEEE
T ss_conf             22188999998877231------267799942320--0787--2567772


No 80 
>pfam04720 DUF506 Protein of unknown function (DUF506). Family of uncharacterized plant proteins.
Probab=21.81  E-value=79  Score=14.99  Aligned_cols=73  Identities=16%  Similarity=0.294  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHCCCEEE----EEECCCCCCCCCEEEEECCCCEEEEEEECC---------------------CCCCCH
Q ss_conf             9999999999997898899----971489887662799915991999997278---------------------988698
Q gi|254781194|r    9 AKLEKRLVKGSKKLDCLVF----KTQFINQRGCPDRLIITPNGAHFWVEMKTS---------------------RGRLSN   63 (98)
Q Consensus         9 ~~ie~~i~~~~k~~g~~~~----k~~~~g~~G~PDli~~~~~g~~~fIEvK~~---------------------~gkls~   63 (98)
                      +.+.+.++..|+..|.-+-    ||...  .++|       .|.+-||+|-.+                     -.|+|+
T Consensus        87 s~lrr~v~~~Lr~~GydAaiCkSkW~~s--~~~p-------~G~yeYiDVv~~~~~~~~~~R~iVd~dFrs~FEiARpt~  157 (218)
T pfam04720        87 SCLRRKVMSLLRELGYDAAICKSKWESS--GKVP-------AGEYEYIDVVDGGESKKQEVRLIVDLDFRSEFEIARPTE  157 (218)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCC--CCCC-------CCCCEEEEEEECCCCCCCCEEEEEECCCHHHEEEECCCH
T ss_conf             8999999999986698841333306788--9978-------976148999822788887505999456557523436858


Q ss_pred             HHHHHHHHHHHCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999999997898699983989999999986
Q gi|254781194|r   64 AQKRVIATLLLYHQKVQVLSSTEEVDGFLRML   95 (98)
Q Consensus        64 ~Q~~~~~~l~~~G~~~~Vv~s~e~v~~~i~~l   95 (98)
                      .=+..++.|    -.+| |-+.|...++|+-+
T Consensus       158 ~Y~~ll~~L----P~vf-VG~~~rL~~iv~im  184 (218)
T pfam04720       158 EYKRILQSL----PRVF-VGKVERLKQLVRIM  184 (218)
T ss_pred             HHHHHHHHC----CCEE-EECHHHHHHHHHHH
T ss_conf             999999969----9847-72799999999999


No 81 
>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=20.85  E-value=83  Score=14.87  Aligned_cols=39  Identities=15%  Similarity=0.251  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHCC--CEEEEEEC---------CCCCCCCCEEEEECCCCEE
Q ss_conf             999999999789--88999714---------8988766279991599199
Q gi|254781194|r   12 EKRLVKGSKKLD--CLVFKTQF---------INQRGCPDRLIITPNGAHF   50 (98)
Q Consensus        12 e~~i~~~~k~~g--~~~~k~~~---------~g~~G~PDli~~~~~g~~~   50 (98)
                      |.....+.+...  |+++.+..         .+-+|+|-|+++.|+|.++
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 82 
>pfam09491 RE_AlwI AlwI restriction endonuclease. This family includes the AlwI (recognizes GGATC), Bsp6I (recognizes GC^NGC), BstNBI (recognizes GASTC), PleI(recognizes GAGTC) and MlyI (recognizes GAGTC) restriction endonucleases.
Probab=20.32  E-value=85  Score=14.81  Aligned_cols=54  Identities=13%  Similarity=0.078  Sum_probs=34.2

Q ss_pred             ECCCCCCCCCEEEEECCCCEEEEEEECCCCC------CCHHHHHHHHHHHHCC----CEEEEECCHH
Q ss_conf             1489887662799915991999997278988------6989999999999789----8699983989
Q gi|254781194|r   30 QFINQRGCPDRLIITPNGAHFWVEMKTSRGR------LSNAQKRVIATLLLYH----QKVQVLSSTE   86 (98)
Q Consensus        30 ~~~g~~G~PDli~~~~~g~~~fIEvK~~~gk------ls~~Q~~~~~~l~~~G----~~~~Vv~s~e   86 (98)
                      ++||  |.||+++.+.+ ..+.||++...|+      -.|-+++.-+.-...+    +..+|+-+++
T Consensus       333 ~A~g--~~~DI~~~~~d-~~~iiEvTl~~~~~Q~~~E~~pv~rHl~~~~~~~~~~~~y~lFiAp~I~  396 (429)
T pfam09491       333 TAGG--NKPDIEIEYDD-FSLLIEVTLSKGSTQSNMEGEPVSRHLKELKKKYPNKNVYGLFIAPKIH  396 (429)
T ss_pred             CCCC--CCCCEEEEECC-EEEEEEEEEECCCHHHHHCCCCHHHHHHHHHHHCCCCCEEEEEECCCCC
T ss_conf             7899--99888999578-1799999860673587706896789999999847998505999735205


Done!