Query gi|254780128|ref|YP_003064541.1| VRR-NUC domain-containing protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs 109 out of 449
Neff 6.0
Searched_HMMs 39220
Date Sun May 22 11:54:33 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780128.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam08774 VRR_NUC VRR-NUC doma 99.6 4.4E-16 1.1E-20 119.2 7.3 81 9-89 1-96 (96)
2 KOG2143 consensus 98.8 2E-08 5E-13 73.0 6.1 52 36-87 793-845 (854)
3 cd00523 archeal_HJR Holliday j 97.6 0.0011 2.8E-08 44.2 10.4 77 9-86 3-85 (123)
4 pfam01870 Hjc Archaeal hollida 97.6 0.001 2.5E-08 44.5 9.8 72 14-86 2-79 (93)
5 COG1591 Holliday junction reso 97.0 0.012 3E-07 38.0 9.6 76 10-86 5-86 (137)
6 pfam02021 UPF0102 Uncharacteri 94.3 0.45 1.1E-05 28.4 8.4 60 15-75 3-70 (94)
7 PHA01753 Holliday junction res 94.1 0.5 1.3E-05 28.1 8.4 63 12-75 8-75 (121)
8 COG2810 Predicted type IV rest 93.5 0.77 2E-05 27.0 8.3 78 8-86 20-104 (284)
9 PRK12497 hypothetical protein; 93.2 0.57 1.5E-05 27.8 7.3 62 13-75 11-80 (118)
10 cd00221 Vsr Very Short Patch R 92.9 0.93 2.4E-05 26.5 8.0 75 11-88 17-113 (115)
11 pfam03838 RecU Recombination p 91.9 1.3 3.4E-05 25.6 8.4 75 11-86 7-109 (167)
12 pfam10107 Endonuc_Holl Endonuc 91.6 0.72 1.8E-05 27.2 6.2 48 39-86 97-151 (153)
13 COG0792 Predicted endonuclease 88.9 2.4 6.2E-05 24.0 7.5 66 9-75 3-76 (114)
14 COG4741 Predicted secreted end 88.9 1.7 4.5E-05 24.9 6.3 48 39-86 113-167 (175)
15 pfam08722 TnsA_N TnsA endonucl 88.7 1.2 3E-05 25.9 5.3 48 39-86 29-80 (81)
16 PRK04247 hypothetical protein; 88.6 2.6 6.5E-05 23.9 6.9 90 9-98 128-226 (250)
17 PRK03298 hypothetical protein; 86.8 3.3 8.3E-05 23.2 8.1 89 9-97 103-200 (224)
18 pfam01939 DUF91 Protein of unk 86.6 3.4 8.6E-05 23.2 6.8 90 9-98 104-203 (228)
19 TIGR00632 vsr DNA mismatch end 85.5 0.57 1.5E-05 27.8 2.2 78 10-88 39-142 (143)
20 pfam03852 Vsr DNA mismatch end 83.4 3.2 8E-05 23.3 5.2 44 11-56 20-63 (75)
21 pfam06319 DUF1052 Protein of u 83.3 2.9 7.5E-05 23.5 5.0 56 9-64 19-74 (158)
22 PRK02234 recU Holliday junctio 76.6 8 0.0002 20.9 8.5 77 9-86 30-135 (199)
23 COG1637 Predicted nuclease of 76.5 8 0.0002 20.9 6.3 89 9-97 129-226 (253)
24 cd01037 Restriction_endonuclea 76.2 8.2 0.00021 20.8 6.9 70 14-86 2-79 (80)
25 pfam08378 NERD Nuclease-relate 75.3 3.6 9.1E-05 23.0 3.4 84 13-99 6-98 (123)
26 PRK09225 threonine synthase; V 73.9 5.8 0.00015 21.7 4.2 41 60-100 165-206 (465)
27 cd01560 Thr-synth_2 Threonine 73.2 5.5 0.00014 21.9 3.9 41 60-100 164-205 (460)
28 pfam07711 RabGGT_insert Rab ge 72.1 5.9 0.00015 21.7 3.9 45 24-69 11-55 (102)
29 pfam09520 RE_MjaII MjaII restr 72.0 7.9 0.0002 20.9 4.5 27 40-68 144-170 (252)
30 PRK13731 conjugal transfer sur 68.1 13 0.00032 19.7 6.1 54 39-94 38-93 (243)
31 pfam05818 TraT Enterobacterial 65.9 13 0.00034 19.6 4.6 45 48-94 19-63 (215)
32 TIGR00252 TIGR00252 conserved 63.6 7.4 0.00019 21.1 2.9 48 13-60 22-70 (141)
33 pfam05116 S6PP Sucrose-6F-phos 61.7 17 0.00043 18.9 6.7 43 7-54 18-73 (247)
34 cd02410 archeal_CPSF_KH The ar 59.6 18 0.00046 18.8 4.3 62 34-96 62-130 (145)
35 COG3727 Vsr DNA G:T-mismatch r 58.8 19 0.00048 18.6 7.6 76 10-87 20-116 (150)
36 pfam06555 consensus 58.1 19 0.00049 18.6 4.3 13 18-30 3-15 (200)
37 cd01473 vWA_CTRP CTRP for CS 53.9 23 0.00058 18.1 5.8 68 34-101 102-189 (192)
38 COG0610 Type I site-specific r 53.6 19 0.00049 18.6 3.7 37 37-74 123-162 (962)
39 pfam03460 NIR_SIR_ferr Nitrite 52.4 24 0.00061 18.0 6.5 52 48-100 4-66 (67)
40 pfam10313 DUF2415 Uncharacteri 50.9 25 0.00065 17.8 4.0 30 28-59 4-34 (43)
41 pfam04313 HSDR_N Type I restri 48.9 19 0.00048 18.6 3.0 23 37-60 17-40 (90)
42 COG2894 MinD Septum formation 44.8 32 0.0008 17.3 4.0 34 60-93 93-127 (272)
43 COG1139 Uncharacterized conser 44.3 32 0.00082 17.2 4.8 37 64-100 63-99 (459)
44 TIGR00260 thrC threonine synth 44.1 17 0.00043 18.9 2.2 41 60-100 115-156 (423)
45 cd01471 vWA_micronemal_protein 43.4 33 0.00085 17.1 5.7 42 34-85 102-143 (186)
46 PRK03379 vitamin B12-transport 42.7 34 0.00087 17.1 5.1 32 69-100 90-123 (265)
47 COG4073 Uncharacterized protei 42.0 35 0.00089 17.0 6.0 79 11-99 68-160 (198)
48 COG3331 PrfA Penicillin-bindin 41.8 35 0.0009 17.0 8.7 75 11-86 11-113 (177)
49 PRK09534 btuF corrinoid ABC tr 40.2 37 0.00095 16.8 5.5 33 68-100 130-165 (364)
50 TIGR02258 2_5_ligase 2'-5' RNA 40.1 37 0.00095 16.8 5.1 63 15-81 54-119 (189)
51 PRK00453 rpsF 30S ribosomal pr 39.9 38 0.00096 16.8 4.9 57 13-69 21-77 (95)
52 TIGR00348 hsdR type I site-spe 38.8 35 0.0009 17.0 3.1 26 37-63 133-162 (813)
53 cd00114 LIGANc NAD+ dependent 37.6 41 0.001 16.6 6.3 48 53-100 214-265 (307)
54 TIGR03675 arCOG00543 arCOG0178 37.1 42 0.0011 16.5 4.5 54 34-88 79-132 (630)
55 PRK01395 V-type ATP synthase s 36.9 42 0.0011 16.5 3.6 28 73-100 16-43 (104)
56 pfam09572 RE_XamI XamI restric 36.5 43 0.0011 16.5 7.8 57 9-65 120-201 (251)
57 pfam06616 BsuBI_PstI_RE BsuBI/ 36.0 43 0.0011 16.4 8.4 63 37-99 212-279 (306)
58 pfam06250 DUF1016 Protein of u 35.6 44 0.0011 16.4 4.0 57 9-65 182-249 (320)
59 PRK09566 nirA ferredoxin-nitri 35.5 44 0.0011 16.4 7.0 50 52-101 65-126 (513)
60 TIGR00075 hypD hydrogenase exp 35.3 40 0.001 16.7 2.9 57 38-97 74-141 (384)
61 pfam08011 DUF1703 Protein of u 31.2 52 0.0013 15.9 8.8 70 10-80 2-73 (101)
62 PRK10361 DNA recombination pro 30.9 52 0.0013 15.9 3.0 26 36-61 236-261 (475)
63 TIGR02349 DnaJ_bact chaperone 30.9 53 0.0013 15.9 3.8 40 38-78 343-385 (386)
64 PRK10976 putative sugar phosph 30.1 54 0.0014 15.8 6.5 44 6-54 17-71 (266)
65 COG1540 Uncharacterized protei 29.8 47 0.0012 16.2 2.6 29 15-48 46-74 (252)
66 pfam04720 DUF506 Protein of un 29.5 54 0.0014 15.9 2.8 73 12-98 87-184 (218)
67 pfam08652 RAI1 RAI1 like. RAI1 28.8 57 0.0015 15.7 3.0 25 49-73 13-37 (68)
68 pfam08608 Wyosine_form Wyosine 28.6 25 0.00063 17.9 1.0 26 50-75 2-33 (62)
69 pfam04471 Mrr_cat Restriction 28.5 58 0.0015 15.7 8.3 66 19-85 2-69 (98)
70 PRK10513 sugar phosphatase; Pr 27.4 61 0.0015 15.6 7.1 44 6-54 18-75 (270)
71 TIGR01942 pcnB poly(A) polymer 26.6 60 0.0015 15.6 2.6 26 62-87 12-37 (448)
72 COG1553 DsrE Uncharacterized c 26.5 59 0.0015 15.6 2.6 54 44-97 37-90 (126)
73 pfam03190 DUF255 Protein of un 26.5 48 0.0012 16.2 2.1 54 7-60 53-123 (163)
74 COG0498 ThrC Threonine synthas 26.3 63 0.0016 15.4 4.0 42 57-100 154-195 (411)
75 PRK09567 nirA ferredoxin-nitri 25.0 67 0.0017 15.3 8.1 25 52-76 113-137 (591)
76 cd01143 YvrC Periplasmic bindi 24.9 67 0.0017 15.3 3.9 30 70-99 73-105 (195)
77 COG1782 Predicted metal-depend 24.9 68 0.0017 15.3 3.8 77 11-88 47-138 (637)
78 TIGR02291 rimK_rel_E_lig alpha 24.5 69 0.0017 15.2 2.7 62 7-68 108-188 (320)
79 TIGR02502 type_III_YscX type I 24.3 24 0.00061 18.0 0.2 17 37-53 24-40 (126)
80 TIGR02717 AcCoA-syn-alpha acet 24.1 70 0.0018 15.2 2.9 26 12-40 110-135 (457)
81 TIGR02249 integrase_gron integ 23.7 57 0.0014 15.7 2.1 23 5-27 238-260 (320)
82 pfam01250 Ribosomal_S6 Ribosom 23.1 73 0.0019 15.1 4.3 60 9-68 13-75 (92)
83 cd03008 TryX_like_RdCVF Trypar 23.1 73 0.0019 15.1 4.3 39 15-53 77-126 (146)
84 pfam08282 Hydrolase_3 haloacid 23.1 73 0.0019 15.1 5.9 73 7-84 14-100 (254)
85 TIGR03081 metmalonyl_epim meth 22.8 74 0.0019 15.0 6.2 85 11-101 9-93 (128)
86 pfam09588 YqaJ YqaJ-like viral 22.7 74 0.0019 15.0 4.9 50 13-63 56-113 (141)
87 cd01472 vWA_collagen von Wille 22.2 76 0.0019 14.9 4.1 56 33-100 96-151 (164)
88 PRK10767 chaperone protein Dna 22.1 76 0.0019 14.9 4.0 46 38-85 308-355 (376)
89 PRK07810 O-succinylhomoserine 22.1 77 0.002 14.9 2.8 85 17-102 282-405 (406)
90 pfam02646 RmuC RmuC family. Th 21.9 77 0.002 14.9 2.9 27 35-61 98-124 (301)
91 pfam04555 XhoI Restriction end 21.7 78 0.002 14.9 2.7 23 39-62 61-84 (196)
92 KOG2364 consensus 21.7 78 0.002 14.9 4.9 54 10-65 232-286 (433)
93 TIGR00678 holB DNA polymerase 20.5 51 0.0013 16.0 1.3 51 39-90 62-130 (216)
No 1
>pfam08774 VRR_NUC VRR-NUC domain.
Probab=99.64 E-value=4.4e-16 Score=119.19 Aligned_cols=81 Identities=37% Similarity=0.491 Sum_probs=72.9
Q ss_pred CCHHHHHHHHHHHHHHCC-CEEEEEECC------------C-CCCCCEEEEECCCCC-EEEEEEECCCCCCCHHHHHHHH
Q ss_conf 899999999999999789-899998118------------8-898743999906982-9999997689886889999999
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKLD-CWVRKASFV------------G-RRGCPDRLIITPNGG-LWWIEVKKPTGRLSHQQMSEIE 73 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~G-~~~~K~~~~------------g-~~GvPDli~~~~~g~-~~fIEvK~~~gkls~~Q~~~~~ 73 (103)
++|..+|..+...+++.| +.+.+..+. | +.|+|||+++.|.|+ +.|||||+|+|++|++|+.|++
T Consensus 1 ~~e~~~e~~~~~~~~k~g~~~~~~~~~~~~~~~~~~~~~~g~~~G~PDli~~~~~~~~~~~iEvK~p~~~~~~~Q~~~~~ 80 (96)
T pfam08774 1 MREGRIEVALVEALKKLGYPLPRKNWGKKGAEALGKYFRYGLRKGVPDLILFLPPGKRFLLVEVKGPGDKLSPEQRAWLD 80 (96)
T ss_pred CCCCEEEHHHHHHHHHHCCCCCCCCCCCCCHHHHCCHHHCCCCCCCCCEEEEECCCCEEEEEEEECCCCCCCHHHHHHHH
T ss_conf 97640000999999982898876553543867731044157879998789981599869999987899998989999999
Q ss_pred HHHHCCCEEEEECCHH
Q ss_conf 9997898899985989
Q gi|254780128|r 74 ELRRRGQRVKVLVSME 89 (103)
Q Consensus 74 ~l~~~G~~~~Vv~s~e 89 (103)
.|++.|+.++||+|.|
T Consensus 81 ~l~~~g~~v~V~~~~~ 96 (96)
T pfam08774 81 RLARSGFKVAVCDSVE 96 (96)
T ss_pred HHHHCCCEEEEEECCC
T ss_conf 9997799499960769
No 2
>KOG2143 consensus
Probab=98.75 E-value=2e-08 Score=72.95 Aligned_cols=52 Identities=35% Similarity=0.440 Sum_probs=47.6
Q ss_pred CCCCCCEEEEECC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf 8898743999906-982999999768988688999999999978988999859
Q gi|254780128|r 36 GRRGCPDRLIITP-NGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVS 87 (103)
Q Consensus 36 g~~GvPDli~~~~-~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s 87 (103)
.+.|+|||.++.| .+++.++|||.|++|+|..|+.|+..|.+-|+.|.||.-
T Consensus 793 srsG~PDL~lWNp~~k~fklvEVKgpnDRLSekQr~WLalL~dsg~~VEVChV 845 (854)
T KOG2143 793 SRSGFPDLTLWNPETKRFKLVEVKGPNDRLSEKQRLWLALLADSGIRVEVCHV 845 (854)
T ss_pred CCCCCCCEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 13799844323577761789983488651028999999999857887799885
No 3
>cd00523 archeal_HJR Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
Probab=97.62 E-value=0.0011 Score=44.20 Aligned_cols=77 Identities=26% Similarity=0.275 Sum_probs=59.3
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCCC---CCHHHHHHHHHH-HHCCCEE
Q ss_conf 8999999999999997898999981188--898743999906982999999768988---688999999999-9789889
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTGR---LSHQQMSEIEEL-RRRGQRV 82 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l-~~~G~~~ 82 (103)
.+=+..|+.|+..+...|+.|.+..+.| .+..||++.. ++++++.||||+..+. ++..|..-+..+ +.-|+..
T Consensus 3 rkG~~~EReL~~~l~~~GfavvR~~gSG~~~~~~pDiiA~-~~~~~~~iEvKst~~~~iYi~~e~ve~L~~Fa~~fG~~p 81 (123)
T cd00523 3 RKGSRAERELVKILEEKGFAVVRAPGSGGGPRPLPDIVAG-NGGTYLAIEVKSTKKDKIYIKKEQVEKLVEFARRFGGEP 81 (123)
T ss_pred CCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCEEEECHHHHHHHHHHHHHCCCEE
T ss_conf 5503799999999986593499834678887889988975-698599999996269808984999999999999749938
Q ss_pred EEEC
Q ss_conf 9985
Q gi|254780128|r 83 KVLV 86 (103)
Q Consensus 83 ~Vv~ 86 (103)
+|+-
T Consensus 82 ~iav 85 (123)
T cd00523 82 YLAV 85 (123)
T ss_pred EEEE
T ss_conf 9999
No 4
>pfam01870 Hjc Archaeal holliday junction resolvase (hjc). This family of archaebacterial proteins are holliday junction resolvases (hjc gene). The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar.
Probab=97.59 E-value=0.001 Score=44.48 Aligned_cols=72 Identities=28% Similarity=0.261 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCC---CCCHHHHHHHHHH-HHCCCEEEEEC
Q ss_conf 99999999997898999981188--89874399990698299999976898---8688999999999-97898899985
Q gi|254780128|r 14 VEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTG---RLSHQQMSEIEEL-RRRGQRVKVLV 86 (103)
Q Consensus 14 ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~g---kls~~Q~~~~~~l-~~~G~~~~Vv~ 86 (103)
.|+.+++.+...|+.+.+..+.| ..+.||++.. .++.++.||||+..+ .++..|..-+..+ +..|...+++.
T Consensus 2 ~ERel~~~l~~~gFavvR~~gSG~~~~~~pDiiA~-~g~~~~~iEvKst~~~kiyl~~eqve~L~~f~~~fg~~p~iav 79 (93)
T pfam01870 2 YERELVKILEERGFAVVRAAGSGGAVKPLPDIIAG-NGGVYLVIEVKSRKKDKIYLKKEQVEKLVEFARRFGGEPFLAV 79 (93)
T ss_pred HHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 07999999986891699956789988899988985-6987999999961698188789999999999997399699999
No 5
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=96.97 E-value=0.012 Score=37.98 Aligned_cols=76 Identities=28% Similarity=0.282 Sum_probs=56.9
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCEEEEECCCCCEEEEEEECCCC-C--CCHHHHHHH-HHHHHCCCEEE
Q ss_conf 999999999999997898999981188--89874399990698299999976898-8--688999999-99997898899
Q gi|254780128|r 10 TEKDVEKRLVTGAKKLDCWVRKASFVG--RRGCPDRLIITPNGGLWWIEVKKPTG-R--LSHQQMSEI-EELRRRGQRVK 83 (103)
Q Consensus 10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g--~~GvPDli~~~~~g~~~fIEvK~~~g-k--ls~~Q~~~~-~~l~~~G~~~~ 83 (103)
+=+..|+.|++.+...|+-+.+.-+.| .+=+||++. ..+|.++-||||+..+ + +.+.|..-+ +..+..|+..+
T Consensus 5 kG~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA-~~g~~~l~iE~K~~~~~kiYl~~e~ve~L~~FA~~fGg~p~ 83 (137)
T COG1591 5 KGSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVA-GNGGVYLAIEVKSRRETKIYLDKEQVEKLVEFARRFGGEPY 83 (137)
T ss_pred CCCHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEE-CCCCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCCEE
T ss_conf 33268899999998648549983467899999987885-28978999999861588478759999999999997199568
Q ss_pred EEC
Q ss_conf 985
Q gi|254780128|r 84 VLV 86 (103)
Q Consensus 84 Vv~ 86 (103)
+.-
T Consensus 84 iav 86 (137)
T COG1591 84 IAV 86 (137)
T ss_pred EEE
T ss_conf 999
No 6
>pfam02021 UPF0102 Uncharacterized protein family UPF0102. The function of this family is unknown.
Probab=94.33 E-value=0.45 Score=28.44 Aligned_cols=60 Identities=15% Similarity=0.176 Sum_probs=42.6
Q ss_pred HHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf 999999999789899998118889874399990698299999976898--------8688999999999
Q gi|254780128|r 15 EKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--------RLSHQQMSEIEEL 75 (103)
Q Consensus 15 e~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l 75 (103)
|..-..+|.+.|+....-..-.+.|==||+.. .++..+|||||+-.+ .+++.|...+.+.
T Consensus 3 E~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~-~~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~a 70 (94)
T pfam02021 3 EALAARWLESKGLIILERNWRSRTGEIDIIAR-DDRTIVFVEVKTRSGENYGPAAEAVTPRKQKKIIRT 70 (94)
T ss_pred HHHHHHHHHHCCCEEEEEEECCCCCCEEEEEE-ECCEEEEEEEEEEECCCCCCHHHHCCHHHHHHHHHH
T ss_conf 99999999987999987783268983769998-299999999997106997496692999999999999
No 7
>PHA01753 Holliday junction resolvase
Probab=94.14 E-value=0.5 Score=28.15 Aligned_cols=63 Identities=17% Similarity=0.185 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHCCCEEEEEE-CC-CCCCCCEEEEECCCCCEEEEEEECCCCC---CCHHHHHHHHHH
Q ss_conf 9999999999997898999981-18-8898743999906982999999768988---688999999999
Q gi|254780128|r 12 KDVEKRLVTGAKKLDCWVRKAS-FV-GRRGCPDRLIITPNGGLWWIEVKKPTGR---LSHQQMSEIEEL 75 (103)
Q Consensus 12 ~~ie~~l~~~lk~~G~~~~K~~-~~-g~~GvPDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l 75 (103)
...|..++..++..|-.+.+.- |+ +.+-+||++.. +++.++.||||+...+ ....|..-+-++
T Consensus 8 k~~Er~lv~~L~~~GF~avRiPaSgs~~~plPDIiA~-k~n~~laiEvKST~~~~I~Vd~~QI~KL~eF 75 (121)
T PHA01753 8 KYYEYKTLEILESNGFKALRIPVSGTGKQALPDIIAT-KNNTIYPIEVKSTSKDVVTVDKFQIEKLFRF 75 (121)
T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEE-CCCEEEEEEEEECCCCEEEECHHHHHHHHHH
T ss_conf 3669999999986791179811578999989857873-6978999998503342699718999999999
No 8
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=93.48 E-value=0.77 Score=27.03 Aligned_cols=78 Identities=17% Similarity=0.181 Sum_probs=58.1
Q ss_pred CCCHHHHHHHHHHHH-HHCCCEEEEE--ECC---CCCCCCEEEEECCCCCE-EEEEEECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf 889999999999999-9789899998--118---88987439999069829-9999976898868899999999997898
Q gi|254780128|r 8 YQTEKDVEKRLVTGA-KKLDCWVRKA--SFV---GRRGCPDRLIITPNGGL-WWIEVKKPTGRLSHQQMSEIEELRRRGQ 80 (103)
Q Consensus 8 ~~~E~~ie~~l~~~l-k~~G~~~~K~--~~~---g~~GvPDli~~~~~g~~-~fIEvK~~~gkls~~Q~~~~~~l~~~G~ 80 (103)
..+|..+.+.++.-. .++||-.... +-| +.-|.||..++. ||++ .|+|-|.-.--+-..|..-....-+.|.
T Consensus 20 ~~nEa~vrq~lIlp~L~slGwdi~nPkEV~PEe~t~~GraDyalik-d~kvfafieak~ls~~~akd~qq~~~Yav~~Gv 98 (284)
T COG2810 20 SRNEAAVRQHLILPFLSSLGWDIDNPKEVRPEEKTEEGRADYALIK-DGKVFAFIEAKNLSVNPAKDVQQLAKYAVDKGV 98 (284)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEE-CCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf 9618888899889999970777899020586424555765448885-693899872113475726899999999885283
Q ss_pred EEEEEC
Q ss_conf 899985
Q gi|254780128|r 81 RVKVLV 86 (103)
Q Consensus 81 ~~~Vv~ 86 (103)
.+.+|.
T Consensus 99 ~~~iVt 104 (284)
T COG2810 99 EVGIVT 104 (284)
T ss_pred EEEEEE
T ss_conf 799996
No 9
>PRK12497 hypothetical protein; Reviewed
Probab=93.18 E-value=0.57 Score=27.80 Aligned_cols=62 Identities=16% Similarity=0.111 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf 99999999999789899998118889874399990698299999976898--------8688999999999
Q gi|254780128|r 13 DVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--------RLSHQQMSEIEEL 75 (103)
Q Consensus 13 ~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l 75 (103)
.-|.....+|++.|+.+..--.-.+.|==|||.. .++..+|||||+-.+ .+++.|...+.+.
T Consensus 11 ~gE~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~-~~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~a 80 (118)
T PRK12497 11 AGEDLAARYLESKGLRILARNFRCRFGEIDLIAR-DGDTLVFVEVKTRRSDLFGGAAEAVTPRKQRRIRRA 80 (118)
T ss_pred HHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEE-ECCEEEEEEEECCCCCCCCCHHHHCCHHHHHHHHHH
T ss_conf 9999999999987999999850048995058999-699999999821557898897895999999999999
No 10
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=92.91 E-value=0.93 Score=26.51 Aligned_cols=75 Identities=15% Similarity=0.107 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEE--------ECCCCCCCHHHHHHH----------
Q ss_conf 99999999999997898999981188898743999906982999999--------768988688999999----------
Q gi|254780128|r 11 EKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEV--------KKPTGRLSHQQMSEI---------- 72 (103)
Q Consensus 11 E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEv--------K~~~gkls~~Q~~~~---------- 72 (103)
..+.|..+.+.|.+.|..+ ......-+|-||+ ++.+-...+||-= .. ...|..+...|.
T Consensus 17 ~TkpE~~vrk~L~~~G~Ry-r~~~k~lpG~PDi-v~~~~k~aIFvdGCFWHgh~~~~-~~~pk~n~~fW~~Ki~~N~~RD 93 (115)
T cd00221 17 DTKPERAVRSALWELGYRF-RKQDKDLPGKPDI-VVPGYRLAIFVDGCFWHGHPCHK-RKPPPKNTEFWLEKIERNVERD 93 (115)
T ss_pred CCHHHHHHHHHHHHCCCEE-EECCCCCCCCCCE-EECCCCEEEEECCEEECCCCCCC-CCCCCCCHHHHHHHHHHHHHHH
T ss_conf 9869999999999889989-9668877999999-73576289993240433888757-8889853899999999999989
Q ss_pred ----HHHHHCCCEEEEECCH
Q ss_conf ----9999789889998598
Q gi|254780128|r 73 ----EELRRRGQRVKVLVSM 88 (103)
Q Consensus 73 ----~~l~~~G~~~~Vv~s~ 88 (103)
+.|.++|..+.+++.-
T Consensus 94 ~~~~~~L~~~GW~v~~vWEc 113 (115)
T cd00221 94 RRVQAALERLGWRVLRVWEC 113 (115)
T ss_pred HHHHHHHHHCCCEEEEEEEC
T ss_conf 99999999889989999830
No 11
>pfam03838 RecU Recombination protein U.
Probab=91.88 E-value=1.3 Score=25.58 Aligned_cols=75 Identities=12% Similarity=0.146 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHCCCEEEEE---------ECC------------CCCCCCEEEEECCCCCEEEEEEECCCC-------
Q ss_conf 9999999999999789899998---------118------------889874399990698299999976898-------
Q gi|254780128|r 11 EKDVEKRLVTGAKKLDCWVRKA---------SFV------------GRRGCPDRLIITPNGGLWWIEVKKPTG------- 62 (103)
Q Consensus 11 E~~ie~~l~~~lk~~G~~~~K~---------~~~------------g~~GvPDli~~~~~g~~~fIEvK~~~g------- 62 (103)
|..|....--+..+.=+.+.|- ..| ..+.-+|....+ .|+++..|.|...+
T Consensus 7 E~~IN~tn~~Y~~~~~A~I~KkptPi~ivkv~~~~r~~a~I~~ayf~~kSt~DY~Gvy-~G~~i~FEAKeT~nkt~Fpl~ 85 (167)
T pfam03838 7 EELINETNQYYLANGIAVIHKKPTPIQIVKVDYPKRSAAVIKEAYFKQKSTTDYNGVY-KGRYIDFEAKETKNKTSFPLK 85 (167)
T ss_pred HHHHHHHHHHHHHCCEEEEEEECCCEEEEECCCCCCCCCEEEEEEECCCCCCCCCEEE-CCEEEEEECCCCCCCCCCCHH
T ss_conf 9999999999987797999970788179943786555334677887357767733167-789999982243566745724
Q ss_pred CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 868899999999997898899985
Q gi|254780128|r 63 RLSHQQMSEIEELRRRGQRVKVLV 86 (103)
Q Consensus 63 kls~~Q~~~~~~l~~~G~~~~Vv~ 86 (103)
...++|...++.+.++|+.++++=
T Consensus 86 Ni~~HQi~~L~~~~~~gGiaF~ii 109 (167)
T pfam03838 86 NIHEHQIEHLKQVLKQGGICFVII 109 (167)
T ss_pred HCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf 556999999999998899799999
No 12
>pfam10107 Endonuc_Holl Endonuclease related to archaeal Holliday junction resolvase. This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=91.63 E-value=0.72 Score=27.20 Aligned_cols=48 Identities=21% Similarity=0.371 Sum_probs=36.2
Q ss_pred CCC-EEEEEC-----CCCCEEEEEEECCC-CCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 874-399990-----69829999997689-8868899999999997898899985
Q gi|254780128|r 39 GCP-DRLIIT-----PNGGLWWIEVKKPT-GRLSHQQMSEIEELRRRGQRVKVLV 86 (103)
Q Consensus 39 GvP-Dli~~~-----~~g~~~fIEvK~~~-gkls~~Q~~~~~~l~~~G~~~~Vv~ 86 (103)
|-| |.+++- ..-.+.|+|||+.+ .+||..|+...+.+++--..+..++
T Consensus 97 G~PIDyIvFdgl~~~~~~~IvfiEVKsGksa~Lt~~qr~IrdaIe~g~V~w~~ir 151 (153)
T pfam10107 97 GTPVDYIVFDGLSEGEIREIVFVEVKTGKSARLTEREKAVREAIEAGRVRFETIR 151 (153)
T ss_pred CCCEEEEEECCCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCEEEEEEE
T ss_conf 8980489974878787444999996458642458778999999985976899986
No 13
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=88.94 E-value=2.4 Score=24.01 Aligned_cols=66 Identities=12% Similarity=0.065 Sum_probs=44.9
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf 899999999999999789899998118889874399990698299999976898--------8688999999999
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--------RLSHQQMSEIEEL 75 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l 75 (103)
+....-|..-...|++.|...+.-..-.+-|==|||.- .++.++|||||+-.+ .+++.....+.+.
T Consensus 3 ~~G~~~E~~A~~~L~~~G~~iL~rN~r~r~GEIDlIa~-~~~~ivFVEVK~R~~~~~g~a~~aV~~~K~~ki~~a 76 (114)
T COG0792 3 QLGAAGEDLAARFLESKGLRILARNWRCRYGEIDLIAR-DGDTVVFVEVKYRRNDLYGGAAEAVTPRKQRKLRRA 76 (114)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCEEEEEE-CCCEEEEEEEEEECCCCCCCHHHHCCHHHHHHHHHH
T ss_conf 04778999999999976930255530378874689996-599899999974126776666774899999999999
No 14
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=88.91 E-value=1.7 Score=24.87 Aligned_cols=48 Identities=21% Similarity=0.391 Sum_probs=37.0
Q ss_pred CCC-EEEEEC--CCCC---EEEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 874-399990--6982---999999768-98868899999999997898899985
Q gi|254780128|r 39 GCP-DRLIIT--PNGG---LWWIEVKKP-TGRLSHQQMSEIEELRRRGQRVKVLV 86 (103)
Q Consensus 39 GvP-Dli~~~--~~g~---~~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~ 86 (103)
|-| |++++- .+|. .+|+|+|+. ++++|..-+..++.+++--..+.+..
T Consensus 113 GTPvD~iVFdGLs~G~i~~IvFvEVKtGkt~~LseREk~Vr~ai~~~rVs~ei~~ 167 (175)
T COG4741 113 GTPVDFIVFDGLSEGNIESIVFVEVKTGKTSSLSEREKAVRDAIENGRVSWEIYH 167 (175)
T ss_pred CCCCEEEEECCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEE
T ss_conf 7971289873777686107999998328767721889999999961813799885
No 15
>pfam08722 TnsA_N TnsA endonuclease N terminal. The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The N terminal domain of TnsA is catalytic.
Probab=88.67 E-value=1.2 Score=25.89 Aligned_cols=48 Identities=21% Similarity=0.157 Sum_probs=32.6
Q ss_pred CCCEEEEECCCCCEEEEEEECCCCC----CCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 8743999906982999999768988----68899999999997898899985
Q gi|254780128|r 39 GCPDRLIITPNGGLWWIEVKKPTGR----LSHQQMSEIEELRRRGQRVKVLV 86 (103)
Q Consensus 39 GvPDli~~~~~g~~~fIEvK~~~gk----ls~~Q~~~~~~l~~~G~~~~Vv~ 86 (103)
=.||.++.+.||...++|+|....= ..+.-..-.+..+..|....|+.
T Consensus 29 yTpDflv~~~dg~~~~~eVK~~~~l~~~~~~~K~~~~r~~~~~~g~~~~i~T 80 (81)
T pfam08722 29 YTPDFLVTYKDGKPEAVEVKYSEDLEDERTLEKFEIERRYAEERGIPFRIVT 80 (81)
T ss_pred ECCCEEEEEECCCEEEEEEEHHHHHCCHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 9988999996793999997447563377789999999999998498599970
No 16
>PRK04247 hypothetical protein; Provisional
Probab=88.60 E-value=2.6 Score=23.87 Aligned_cols=90 Identities=20% Similarity=0.207 Sum_probs=61.7
Q ss_pred CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCC-CHHH-HHHHHHHHHCCC-E--
Q ss_conf 89999999999999978--989999811888987439999069829999997689886-8899-999999997898-8--
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRL-SHQQ-MSEIEELRRRGQ-R-- 81 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkl-s~~Q-~~~~~~l~~~G~-~-- 81 (103)
..|+++|..+......+ |.....-..+...|.-|+++--.+|+.+-||+|+-++.+ --.| ..+.+.|++... .
T Consensus 128 G~Ea~l~~llae~p~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~V~VEvKR~ra~idaV~QL~RYve~l~~~~~~~VR 207 (250)
T PRK04247 128 GSEADMVDAILENPDLIEEGFRPVAREYETPAGIIDILGRDKEGNLVVLELKRRRAGLSAVSQLKRYVEAYREELGAKVR 207 (250)
T ss_pred EEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCE
T ss_conf 31999999998590532589889988873598846489987998999999971337814799999999998763699821
Q ss_pred -EEEECC-HHHHHHHHHHH
Q ss_conf -999859-89999999999
Q gi|254780128|r 82 -VKVLVS-MEEVDNFLEEL 98 (103)
Q Consensus 82 -~~Vv~s-~edv~~~l~~l 98 (103)
++++-+ .++++.++++.
T Consensus 208 GIlvAp~It~~Ar~Ll~dr 226 (250)
T PRK04247 208 GILVAPSITERARRLLEKE 226 (250)
T ss_pred EEEECCCCCHHHHHHHHHC
T ss_conf 9999885898799999975
No 17
>PRK03298 hypothetical protein; Provisional
Probab=86.83 E-value=3.3 Score=23.22 Aligned_cols=89 Identities=16% Similarity=0.120 Sum_probs=60.2
Q ss_pred CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHH-HHHHHHHHHCCCE----
Q ss_conf 89999999999999978--9899998118889874399990698299999976898868899-9999999978988----
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQ-MSEIEELRRRGQR---- 81 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q-~~~~~~l~~~G~~---- 81 (103)
-.|+++|..+...-..+ |.....-..+...|.-|+++--.+|..+-||+|+.++----.| ..+.+.|++....
T Consensus 103 G~Eadl~~llae~P~~ie~Gf~~v~rE~~T~~G~VDll~~D~~G~~V~VEiKRra~idaV~QL~RYve~l~rd~~~~~VR 182 (224)
T PRK03298 103 GVEAHLQELLAEHIELLGEGYTLVRREYMTAIGPVDLLCRDADGATVAVEIKRRGEIDGVEQLTRYLELLNRDPLLAPVR 182 (224)
T ss_pred ECHHHHHHHHHHCCHHHCCCCEEEEEEECCCCCCEEEEEECCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCEE
T ss_conf 01999999987592421589898778731798835389987999999999983068108999999999985575888514
Q ss_pred -EEEECC-HHHHHHHHHH
Q ss_conf -999859-8999999999
Q gi|254780128|r 82 -VKVLVS-MEEVDNFLEE 97 (103)
Q Consensus 82 -~~Vv~s-~edv~~~l~~ 97 (103)
.+++-+ .++++.++++
T Consensus 183 GIlvAp~It~~Ar~Ll~d 200 (224)
T PRK03298 183 GVFAAQQIKPQARTLATD 200 (224)
T ss_pred EEEECCCCCHHHHHHHHH
T ss_conf 999987478879999997
No 18
>pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.
Probab=86.63 E-value=3.4 Score=23.16 Aligned_cols=90 Identities=19% Similarity=0.215 Sum_probs=61.9
Q ss_pred CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCC-CHHH-HHHHHHHHHCC--CE-
Q ss_conf 89999999999999978--989999811888987439999069829999997689886-8899-99999999789--88-
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRL-SHQQ-MSEIEELRRRG--QR- 81 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkl-s~~Q-~~~~~~l~~~G--~~- 81 (103)
..|++++..+...-..+ |.....-..+...|.-|+++--.+|+.+-||+|+-.+.+ .-.| ..+.+.|++.- ..
T Consensus 104 G~Eadl~~~l~~~P~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~VvVEvKRr~a~idaV~QL~RYve~l~rd~~~~~V 183 (228)
T pfam01939 104 GSEAEMAALIFEHPQLIEEGFKPVRREYQIAHGIVDILGKDEDGNIVILELKRRKADLHAVSQLKRYVDSLKEDYVEAKV 183 (228)
T ss_pred EEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 31999999998591532489899988852588736689987999999999974037820799999999998655488860
Q ss_pred --EEEECC-HHHHHHHHHHH
Q ss_conf --999859-89999999999
Q gi|254780128|r 82 --VKVLVS-MEEVDNFLEEL 98 (103)
Q Consensus 82 --~~Vv~s-~edv~~~l~~l 98 (103)
++|+-+ -++++.++++.
T Consensus 184 RGIlvAp~It~~Ar~Ll~d~ 203 (228)
T pfam01939 184 RGVLVAPSITEGAKKLLEEE 203 (228)
T ss_pred EEEEECCCCCHHHHHHHHHC
T ss_conf 39999985898899999975
No 19
>TIGR00632 vsr DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology . ; GO: 0004519 endonuclease activity, 0006298 mismatch repair.
Probab=85.53 E-value=0.57 Score=27.81 Aligned_cols=78 Identities=18% Similarity=0.062 Sum_probs=51.3
Q ss_pred CHHHHHHHHHHHHHHCCCEEE----EEECCCCCCCCEEEEECCCCCEEEE--------EEECCCCCCCHHHHHHHH----
Q ss_conf 999999999999997898999----9811888987439999069829999--------997689886889999999----
Q gi|254780128|r 10 TEKDVEKRLVTGAKKLDCWVR----KASFVGRRGCPDRLIITPNGGLWWI--------EVKKPTGRLSHQQMSEIE---- 73 (103)
Q Consensus 10 ~E~~ie~~l~~~lk~~G~~~~----K~~~~g~~GvPDli~~~~~g~~~fI--------EvK~~~gkls~~Q~~~~~---- 73 (103)
+..++|..|...|-++|..+. +=..-|-+|-||+. +..---++|| .+-.-+-.|..+...|+.
T Consensus 39 ~~T~pE~~l~s~L~~lGlryRkdfl~~~~~G~~g~PD~v-f~~~k~~iFidGCFWHg~~C~~~~~~p~s~~~fW~~Ki~~ 117 (143)
T TIGR00632 39 KGTKPEKALASLLFALGLRYRKDFLLRDKDGLPGTPDIV-FKEYKVVIFIDGCFWHGHDCDILGKVPKSRKDFWSPKIEK 117 (143)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE-ECCCEEEEEECCCEECCCCCCCCCCCCCCCHHCCHHHHHH
T ss_conf 798178999999999889988898752368985467544-3473588860273005876740147886642303688874
Q ss_pred ----------HHHHCCCEEEEECCH
Q ss_conf ----------999789889998598
Q gi|254780128|r 74 ----------ELRRRGQRVKVLVSM 88 (103)
Q Consensus 74 ----------~l~~~G~~~~Vv~s~ 88 (103)
.|.+.|..|.+|+.-
T Consensus 118 N~~RD~~~~~~L~~~GWrv~~vW~~ 142 (143)
T TIGR00632 118 NVERDRRVNDALAEEGWRVLRVWEC 142 (143)
T ss_pred HHHCCCCHHHHHHHCCCEEEEEECC
T ss_conf 2530311789998459989896137
No 20
>pfam03852 Vsr DNA mismatch endonuclease Vsr.
Probab=83.40 E-value=3.2 Score=23.32 Aligned_cols=44 Identities=20% Similarity=0.093 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEE
Q ss_conf 9999999999999789899998118889874399990698299999
Q gi|254780128|r 11 EKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIE 56 (103)
Q Consensus 11 E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIE 56 (103)
..+.|..+.+.|.+.|..+.+ ....-+|-|| |++.+....+||.
T Consensus 20 ~TkpE~~vr~~L~~~G~ryr~-~~~~lpG~PD-iv~~~~k~aIFvd 63 (75)
T pfam03852 20 GTKPELALRSLLFGLGLRYRK-NDKSLPGKPD-IVFPKYKLAVFIH 63 (75)
T ss_pred CCHHHHHHHHHHHHCCCEEEE-CCCCCCCCCC-EEECCCCEEEEEE
T ss_conf 976999999999988988997-3787899999-9766877899941
No 21
>pfam06319 DUF1052 Protein of unknown function (DUF1052). This family consists of several bacterial proteins of unknown function.
Probab=83.32 E-value=2.9 Score=23.51 Aligned_cols=56 Identities=18% Similarity=0.274 Sum_probs=43.3
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCC
Q ss_conf 89999999999999978989999811888987439999069829999997689886
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRL 64 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkl 64 (103)
.+-..|.+-+.+.+..+|..++.-.++..--=-|++.+-++|.++-||+|+...-.
T Consensus 19 eta~~i~RGv~Rll~~~g~a~l~E~~L~~GrRaDl~al~~kGei~IVEiKSs~aDF 74 (158)
T pfam06319 19 ETALAVRRGVQRLLMELGHAVLPELPLASGRRADLIALSPKGEIWIVEIKSSIEDF 74 (158)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECCCCCEEEEEEECCHHHH
T ss_conf 88999999999999977996335663799977779988799959999983678884
No 22
>PRK02234 recU Holliday junction-specific endonuclease; Reviewed
Probab=76.58 E-value=8 Score=20.89 Aligned_cols=77 Identities=14% Similarity=0.153 Sum_probs=57.3
Q ss_pred CC-HHHHHHHHHHHHHHCCCEEEEE---------ECCC------------CCCCCEEEEECCCCCEEEEEEECCCC----
Q ss_conf 89-9999999999999789899998---------1188------------89874399990698299999976898----
Q gi|254780128|r 9 QT-EKDVEKRLVTGAKKLDCWVRKA---------SFVG------------RRGCPDRLIITPNGGLWWIEVKKPTG---- 62 (103)
Q Consensus 9 ~~-E~~ie~~l~~~lk~~G~~~~K~---------~~~g------------~~GvPDli~~~~~g~~~fIEvK~~~g---- 62 (103)
|+ |..|.....-++..-=+++.|- ..|. .+--.|....+ .|+++-.|.|...+
T Consensus 30 M~LE~~IN~tN~yY~~~~iAvIhKkPTPIqivkVdypkRs~a~I~eAyf~~~STtDY~Gvy-kG~yIdFEAKET~nktsF 108 (199)
T PRK02234 30 MSLEKDINETNDYYLSNGIAVIHKKPTPIQIVKVDYPKRSKAVIKEAYFRQASTTDYNGVY-KGKYIDFEAKETKNKTSF 108 (199)
T ss_pred CHHHHHHHHHHHHHHHCCEEEEEECCCCEEEEECCCCCCCCCHHHHHEECCCCCCCCCCEE-CCEEEEEECCCCCCCCCC
T ss_conf 0599999999999987797899835888069961554433001001023577877743256-788988875455787744
Q ss_pred ---CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf ---868899999999997898899985
Q gi|254780128|r 63 ---RLSHQQMSEIEELRRRGQRVKVLV 86 (103)
Q Consensus 63 ---kls~~Q~~~~~~l~~~G~~~~Vv~ 86 (103)
...++|...++.+.++|+.++++=
T Consensus 109 pl~Nih~HQi~hl~~~~~qgGI~F~iI 135 (199)
T PRK02234 109 PLKNFHEHQIEHMKQVLAQGGICFVII 135 (199)
T ss_pred CHHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 723403899999999997799799999
No 23
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=76.49 E-value=8 Score=20.87 Aligned_cols=89 Identities=22% Similarity=0.233 Sum_probs=58.1
Q ss_pred CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHCCCE---
Q ss_conf 89999999999999978--98999981188898743999906982999999768988688-99-9999999978988---
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKL--DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSH-QQ-MSEIEELRRRGQR--- 81 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~--G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~G~~--- 81 (103)
.+|.++++.+..--.-+ |-...--..+...|.-|++..-.+|++.-||+|+-++.++. .| +.+.+.++.....
T Consensus 129 g~E~~m~~~I~e~P~lleeG~~~v~~E~~t~~G~vDilg~De~G~~viiElKR~ka~~~Av~QL~RYv~~l~~~~~~~VR 208 (253)
T COG1637 129 GSEADMQELIAENPQLLEEGFRPVAREYQTAIGKVDILGRDERGNIVIIELKRRKAGLSAVSQLKRYVELLREDTGDKVR 208 (253)
T ss_pred CHHHHHHHHHHHCHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCEEE
T ss_conf 40999987876594667575433126521374256799886899999999942547710899999999970534686078
Q ss_pred -EEEEC-CHHHHHHHHHH
Q ss_conf -99985-98999999999
Q gi|254780128|r 82 -VKVLV-SMEEVDNFLEE 97 (103)
Q Consensus 82 -~~Vv~-s~edv~~~l~~ 97 (103)
..|+. --+++..++++
T Consensus 209 GiLvAp~it~~a~~ll~~ 226 (253)
T COG1637 209 GILVAPSITEQARRLLED 226 (253)
T ss_pred EEEECCCCCHHHHHHHHH
T ss_conf 999866440889999997
No 24
>cd01037 Restriction_endonuclease_like Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI
Probab=76.19 E-value=8.2 Score=20.82 Aligned_cols=70 Identities=19% Similarity=0.067 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHCCCEEEEEECC--CCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHH------HHHHHHHHCCCEEEEE
Q ss_conf 9999999999789899998118--8898743999906982999999768988688999------9999999789889998
Q gi|254780128|r 14 VEKRLVTGAKKLDCWVRKASFV--GRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM------SEIEELRRRGQRVKVL 85 (103)
Q Consensus 14 ie~~l~~~lk~~G~~~~K~~~~--g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~------~~~~~l~~~G~~~~Vv 85 (103)
.|..+...+.+.+....++... ..++.||. ++. ..-+.||+|.........+. .....+...|..+.++
T Consensus 2 ~E~~l~~~l~~~~~~~~~~~~~~~~~~~~pDf-~~~--~~~l~iE~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 78 (80)
T cd01037 2 AERLLWKLLRAKGLAVRRFRRQVPIGSYIPDF-VCP--SAKLVIELKGTFHDGLLRKLRTSEKQERIAFLEADGKKVLRF 78 (80)
T ss_pred HHHHHHHHHHHCCCCCCEEEECCCCCCEEEEE-ECC--CCCEEEEECCCHHCCCHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 79999999985587887057137507887757-725--448799914512153135554411778999999889989974
Q ss_pred C
Q ss_conf 5
Q gi|254780128|r 86 V 86 (103)
Q Consensus 86 ~ 86 (103)
.
T Consensus 79 ~ 79 (80)
T cd01037 79 W 79 (80)
T ss_pred C
T ss_conf 3
No 25
>pfam08378 NERD Nuclease-related domain. The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.
Probab=75.29 E-value=3.6 Score=22.98 Aligned_cols=84 Identities=23% Similarity=0.298 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHC-----CCEEEEE-ECC---CCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEE
Q ss_conf 9999999999978-----9899998-118---889874399990698299999976898868899999999997898899
Q gi|254780128|r 13 DVEKRLVTGAKKL-----DCWVRKA-SFV---GRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVK 83 (103)
Q Consensus 13 ~ie~~l~~~lk~~-----G~~~~K~-~~~---g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~ 83 (103)
.-|+.+-.++++. ++.++.- .-+ |...==|.+++.|+| ++-||+|.-.|....++..|.. ...+....
T Consensus 6 ~gE~~v~~~L~~~~~~~~~~~vl~n~~l~~~~~~~~eID~lvi~~~g-i~vvE~K~~~G~i~~~~~~W~~--~~~~~~~~ 82 (123)
T pfam08378 6 EGEKLVARALKKLLPDDYEYFVLHNLRLPTHGGSTTEIDHLVISPDG-IFVIEVKNYKGTIIADGGKWTQ--TIGGRKEE 82 (123)
T ss_pred HHHHHHHHHHHHHCCCCCCEEEEECEEECCCCCCEEEEEEEEECCCE-EEEEEECCCCEEEEECCCEEEE--EECCCEEE
T ss_conf 99999999999637888988999543962699978897799994891-9999946862489962763999--86995588
Q ss_pred EECCHHHHHHHHHHHH
Q ss_conf 9859899999999998
Q gi|254780128|r 84 VLVSMEEVDNFLEELA 99 (103)
Q Consensus 84 Vv~s~edv~~~l~~l~ 99 (103)
+-.-+.|+..-...+.
T Consensus 83 ~~nPi~Q~~~~~~~l~ 98 (123)
T pfam08378 83 FKNPLLQAYRHAKLLR 98 (123)
T ss_pred CCCHHHHHHHHHHHHH
T ss_conf 6899999999999999
No 26
>PRK09225 threonine synthase; Validated
Probab=73.90 E-value=5.8 Score=21.74 Aligned_cols=41 Identities=15% Similarity=0.283 Sum_probs=32.3
Q ss_pred CCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHHH
Q ss_conf 89886889999999999789889998-598999999999986
Q gi|254780128|r 60 PTGRLSHQQMSEIEELRRRGQRVKVL-VSMEEVDNFLEELAC 100 (103)
Q Consensus 60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~edv~~~l~~l~~ 100 (103)
|.|+.|+-|+..+.-..+.+..+.-| -++||++.++.++-.
T Consensus 165 P~g~vS~iQ~~QMtt~~~~NV~~i~v~G~FDDcQ~lVK~~f~ 206 (465)
T PRK09225 165 PKGKVSPVQEKQMTTLQGDNIHVVAVEGDFDDCQALVKAAFN 206 (465)
T ss_pred CCCCCCHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 799999779998622179977999846876789999999971
No 27
>cd01560 Thr-synth_2 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins.
Probab=73.20 E-value=5.5 Score=21.86 Aligned_cols=41 Identities=17% Similarity=0.289 Sum_probs=31.9
Q ss_pred CCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHHH
Q ss_conf 89886889999999999789889998-598999999999986
Q gi|254780128|r 60 PTGRLSHQQMSEIEELRRRGQRVKVL-VSMEEVDNFLEELAC 100 (103)
Q Consensus 60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~edv~~~l~~l~~ 100 (103)
|.|+.|+-|+..+.-..+.+..+.-| =++||++.++.++-.
T Consensus 164 P~g~vS~iQ~~QMtT~~~~NV~~iav~G~FDDcQ~~VK~~f~ 205 (460)
T cd01560 164 PKGGVSPIQELQMTTLPADNVHVVAVEGDFDDCQSLVKALFA 205 (460)
T ss_pred CCCCCCHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
T ss_conf 888899889998625478977999964880888999999960
No 28
>pfam07711 RabGGT_insert Rab geranylgeranyl transferase alpha-subunit, insert domain. Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. This domain is inserted between pfam01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP.
Probab=72.13 E-value=5.9 Score=21.67 Aligned_cols=45 Identities=20% Similarity=0.163 Sum_probs=37.2
Q ss_pred HCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHH
Q ss_conf 7898999981188898743999906982999999768988688999
Q gi|254780128|r 24 KLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM 69 (103)
Q Consensus 24 ~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~ 69 (103)
..++...-|..|-..|.-+|++.. ||...++|-.+|.|+.++.|.
T Consensus 11 ~e~~lsv~FSrpv~v~~~~L~Lv~-Dg~p~~veWrt~~~r~r~s~v 55 (102)
T pfam07711 11 DEGCVSVAFSRPVLVGMVGLLLVL-DGQPQAVEWRTAHPRLRHSPV 55 (102)
T ss_pred CCCEEEEEECCEEEECCCEEEEEE-CCCCEEEEEECCCCCCCCCCE
T ss_conf 678499996141540332689996-798079997689997675827
No 29
>pfam09520 RE_MjaII MjaII restriction endonuclease. This family includes the MjaII (recognizes GGNCC but the cleavage site is unknown) restriction endonuclease.
Probab=71.96 E-value=7.9 Score=20.90 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=22.1
Q ss_pred CCEEEEECCCCCEEEEEEECCCCCCCHHH
Q ss_conf 74399990698299999976898868899
Q gi|254780128|r 40 CPDRLIITPNGGLWWIEVKKPTGRLSHQQ 68 (103)
Q Consensus 40 vPDli~~~~~g~~~fIEvK~~~gkls~~Q 68 (103)
+.|+.+-.+||.-+|+|+|+| +|+..|
T Consensus 144 v~Dlyi~~kdg~e~~feIKT~--KPNkgq 170 (252)
T pfam09520 144 VADLYVQRKDGRELYFEIKSP--KPNKGQ 170 (252)
T ss_pred EEEEEEECCCCCEEEEEECCC--CCCHHH
T ss_conf 778999827995899983577--998377
No 30
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=68.15 E-value=13 Score=19.68 Aligned_cols=54 Identities=13% Similarity=0.304 Sum_probs=40.3
Q ss_pred CCCEEEEECC-CCCEEEEEEECCCCC-CCHHHHHHHHHHHHCCCEEEEECCHHHHHHH
Q ss_conf 8743999906-982999999768988-6889999999999789889998598999999
Q gi|254780128|r 39 GCPDRLIITP-NGGLWWIEVKKPTGR-LSHQQMSEIEELRRRGQRVKVLVSMEEVDNF 94 (103)
Q Consensus 39 GvPDli~~~~-~g~~~fIEvK~~~gk-ls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~ 94 (103)
-..|=|.+-| ..+.+||.+|...++ .+..|......|...|+ .|+++|+++.=+
T Consensus 38 kMS~TIfLdP~s~ktVyv~vrNTS~~~~~~l~~~i~~~L~akGY--~iv~~P~~A~Y~ 93 (243)
T PRK13731 38 QMSETIWLEPASERTVFLQIKNTSDKDMSGLQGKIADAVKAKGY--QVVTSPDKAYYW 93 (243)
T ss_pred EECCCEEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCE--EEECCHHHCEEE
T ss_conf 00043886685455799998517877245678999999985890--986786576077
No 31
>pfam05818 TraT Enterobacterial TraT complement resistance protein. The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings.
Probab=65.95 E-value=13 Score=19.55 Aligned_cols=45 Identities=13% Similarity=0.307 Sum_probs=35.5
Q ss_pred CCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHH
Q ss_conf 69829999997689886889999999999789889998598999999
Q gi|254780128|r 48 PNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNF 94 (103)
Q Consensus 48 ~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~ 94 (103)
|+.+.+||.+|...++-=..|......|...|+ .|+++++++.=+
T Consensus 19 ~~~ktVyv~vrNTSd~~i~l~~~i~~~L~akGY--~iv~~P~~A~Y~ 63 (215)
T pfam05818 19 PEQRTVYLSIRNTSDKNVNLEQKLISALQAKGY--KVVDDPDKAHYW 63 (215)
T ss_pred CCCCEEEEEEECCCCCCCCCHHHHHHHHHHCCC--EEECCHHHCEEE
T ss_conf 003779999853887766733899999984893--886796577077
No 32
>TIGR00252 TIGR00252 conserved hypothetical protein TIGR00252; InterPro: IPR003509 The function of this family is unknown. Members include several bacterial hypothetical proteins..
Probab=63.63 E-value=7.4 Score=21.08 Aligned_cols=48 Identities=15% Similarity=0.116 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCE-EEEEEECC
Q ss_conf 9999999999978989999811888987439999069829-99999768
Q gi|254780128|r 13 DVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGL-WWIEVKKP 60 (103)
Q Consensus 13 ~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~-~fIEvK~~ 60 (103)
-.|......|+.-|+...--....+-|==|||.-.||++. +|||||.=
T Consensus 22 a~E~~ar~wLE~kGl~fiaa~~~~~~GEiDLI~~fPd~~~i~FVEVr~R 70 (141)
T TIGR00252 22 AFESQARAWLEQKGLKFIAANVNSKWGEIDLIMRFPDKKTIVFVEVRTR 70 (141)
T ss_pred HHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEECCCCCCCEEEEEEEECC
T ss_conf 1799999987733157667530689981221111899726888875105
No 33
>pfam05116 S6PP Sucrose-6F-phosphate phosphohydrolase. This family consists of Sucrose-6F-phosphate phosphohydrolase proteins found in plants and cyanobacteria. Sucrose-6(F)-phosphate phosphohydrolase catalyses the final step in the pathway of sucrose biosynthesis.
Probab=61.66 E-value=17 Score=18.93 Aligned_cols=43 Identities=21% Similarity=0.243 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CC--CEEEEECCCCCEEE
Q ss_conf 48899999999999999789899998118889-----------87--43999906982999
Q gi|254780128|r 7 HYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GC--PDRLIITPNGGLWW 54 (103)
Q Consensus 7 h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------Gv--PDli~~~~~g~~~f 54 (103)
+..++.. .+.++.+++.|..+. .+.||+ |+ ||.+++. +|...+
T Consensus 18 ~~i~~~~--~~al~~l~~~Gi~vv--iaTGR~~~~~~~~~~~l~l~~p~~~I~~-nG~~I~ 73 (247)
T pfam05116 18 NEALARL--NQLLEAQYRPDSLLV--FATGRSLDSAKELLKEKPLPTPDVLITS-VGTEIY 73 (247)
T ss_pred CCCCHHH--HHHHHHHHHCCCEEE--EECCCCHHHHHHHHHHCCCCCCCEEEEC-CCEEEE
T ss_conf 9588999--999999995898899--9889999999999997598999989975-975999
No 34
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=59.60 E-value=18 Score=18.76 Aligned_cols=62 Identities=23% Similarity=0.253 Sum_probs=42.1
Q ss_pred CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCH-------HHHHHHHH
Q ss_conf 1888987439999069829999997689886889999999999789889998598-------99999999
Q gi|254780128|r 34 FVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM-------EEVDNFLE 96 (103)
Q Consensus 34 ~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~-------edv~~~l~ 96 (103)
-|-.+|+-| +.+-++-.=+.||++.|+--.........+-..+.|+...|++++ +++++++.
T Consensus 62 vPeeA~i~~-i~FD~~~gEV~Iea~kPg~viGk~g~~l~eI~~~tGW~p~v~RtPpi~S~ti~~IR~~l~ 130 (145)
T cd02410 62 VPEEAGITD-IYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPPIQSRTVKSIRRFLR 130 (145)
T ss_pred CCCCCCCEE-EEECCCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHH
T ss_conf 896468446-897488857999977977797276167999999739815788659996178999999999
No 35
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=58.80 E-value=19 Score=18.63 Aligned_cols=76 Identities=21% Similarity=0.268 Sum_probs=46.5
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEE--------E---ECCCCC-------CCH---HH
Q ss_conf 99999999999999789899998118889874399990698299999--------9---768988-------688---99
Q gi|254780128|r 10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIE--------V---KKPTGR-------LSH---QQ 68 (103)
Q Consensus 10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIE--------v---K~~~gk-------ls~---~Q 68 (103)
++..+|..+...+-..|-.+.. ...+-+|-||+ ++-.---++|+- + |.|+.+ ++. .-
T Consensus 20 ~dTkpE~~lr~~L~~~G~rfR~-~~~~lpGkPDi-Vl~~y~~viFvHGCFWh~H~c~~a~vPksnt~fWleKi~kNveRD 97 (150)
T COG3727 20 RDTKPEKRLRSLLTGQGLRFRV-QDKDLPGKPDI-VLPKYRCVIFVHGCFWHGHHCYLAKVPKSNTEFWLEKIGKNVERD 97 (150)
T ss_pred CCCCHHHHHHHHHHHCCEEEEE-CCCCCCCCCCE-EECCCEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 4766899999998536627885-37889999988-523733899985100257744445688742388999986666654
Q ss_pred HHHHHHHHHCCCEEEEECC
Q ss_conf 9999999978988999859
Q gi|254780128|r 69 MSEIEELRRRGQRVKVLVS 87 (103)
Q Consensus 69 ~~~~~~l~~~G~~~~Vv~s 87 (103)
+.-+.+|++.|+.+-||+-
T Consensus 98 ~r~~~~L~~~GwrvlvVWE 116 (150)
T COG3727 98 ERDIKRLQQLGWRVLVVWE 116 (150)
T ss_pred HHHHHHHHHCCCEEEEEEE
T ss_conf 8999999975975999986
No 36
>pfam06555 consensus
Probab=58.14 E-value=19 Score=18.59 Aligned_cols=13 Identities=15% Similarity=-0.048 Sum_probs=5.3
Q ss_pred HHHHHHHCCCEEE
Q ss_conf 9999997898999
Q gi|254780128|r 18 LVTGAKKLDCWVR 30 (103)
Q Consensus 18 l~~~lk~~G~~~~ 30 (103)
+++.+++.|.-++
T Consensus 3 ~i~~L~~~~f~~~ 15 (200)
T pfam06555 3 TVENLEKNNFEAY 15 (200)
T ss_pred HHHHHHHCCCEEE
T ss_conf 7999997898799
No 37
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=53.92 E-value=23 Score=18.14 Aligned_cols=68 Identities=9% Similarity=0.068 Sum_probs=38.3
Q ss_pred CCCCCCCCEEEEECCCCCE-----------------EEEEEEC-CCCCCCHHHHHHHHHH--HHCCCEEEEECCHHHHHH
Q ss_conf 1888987439999069829-----------------9999976-8988688999999999--978988999859899999
Q gi|254780128|r 34 FVGRRGCPDRLIITPNGGL-----------------WWIEVKK-PTGRLSHQQMSEIEEL--RRRGQRVKVLVSMEEVDN 93 (103)
Q Consensus 34 ~~g~~GvPDli~~~~~g~~-----------------~fIEvK~-~~gkls~~Q~~~~~~l--~~~G~~~~Vv~s~edv~~ 93 (103)
.+.|+|+|.+++..-||+- -.|++-+ .-|.....|...+.-. .+..|..+...+++.+..
T Consensus 102 ~g~R~~vpkv~IvlTDG~s~~~~~~~~~~~a~~lr~~gV~i~avGVg~~~~~eL~~iag~~~~~~~c~~~~~~~fd~l~~ 181 (192)
T cd01473 102 GNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLAGCDINNDNCPNVIKTEWNNLNG 181 (192)
T ss_pred CCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHCCCCCCCCCCEEEECCHHHHHH
T ss_conf 78888997499999569988731678999999999879789999806379999999869998899775799479789999
Q ss_pred HHHHHHHH
Q ss_conf 99999863
Q gi|254780128|r 94 FLEELACT 101 (103)
Q Consensus 94 ~l~~l~~t 101 (103)
+++++...
T Consensus 182 i~~~l~~~ 189 (192)
T cd01473 182 ISKFLTDK 189 (192)
T ss_pred HHHHHHHH
T ss_conf 99999997
No 38
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=53.58 E-value=19 Score=18.58 Aligned_cols=37 Identities=30% Similarity=0.427 Sum_probs=26.5
Q ss_pred CCCCCEEEEECCCCC-EEEEEEECCCCCCCH--HHHHHHHH
Q ss_conf 898743999906982-999999768988688--99999999
Q gi|254780128|r 37 RRGCPDRLIITPNGG-LWWIEVKKPTGRLSH--QQMSEIEE 74 (103)
Q Consensus 37 ~~GvPDli~~~~~g~-~~fIEvK~~~gkls~--~Q~~~~~~ 74 (103)
..=.||+.++. +|- .+.||+|+|...... +|...-+.
T Consensus 123 ~~~rpDvvlfI-NGiPlv~iElK~~~~~~~~a~~Qi~~Y~~ 162 (962)
T COG0610 123 RKRRPDVVLFI-NGLPLVTIELKNPGVENNEAFNQIKRYQK 162 (962)
T ss_pred CCCCCCEEEEE-CCCEEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 88787569998-68656877506875356999999988610
No 39
>pfam03460 NIR_SIR_ferr Nitrite/Sulfite reductase ferredoxin-like half domain. Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidized anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.
Probab=52.39 E-value=24 Score=17.99 Aligned_cols=52 Identities=29% Similarity=0.592 Sum_probs=38.5
Q ss_pred CCCCEEEEEEECCCCCCCHHHHHHHHHHH-HCC-CEEEEE---------CCHHHHHHHHHHHHH
Q ss_conf 69829999997689886889999999999-789-889998---------598999999999986
Q gi|254780128|r 48 PNGGLWWIEVKKPTGRLSHQQMSEIEELR-RRG-QRVKVL---------VSMEEVDNFLEELAC 100 (103)
Q Consensus 48 ~~g~~~fIEvK~~~gkls~~Q~~~~~~l~-~~G-~~~~Vv---------~s~edv~~~l~~l~~ 100 (103)
++| .+++-++.|.|++++.|...+..+. +.| ....+. -..+++.+++++|..
T Consensus 4 ~~g-~~~vri~~p~G~lt~~ql~~la~ia~~yg~g~i~lT~rq~i~l~~i~~~~~~~v~~~L~~ 66 (67)
T pfam03460 4 KDG-DYMVRVRVPGGRLTAEQLRALADIAEKYGDGEIRLTTRQNLELHGVPEEDLPELLEELAE 66 (67)
T ss_pred CCC-CEEEEEECCCCEECHHHHHHHHHHHHHHCCCCEEECCCCCEEECCCCHHHHHHHHHHHHC
T ss_conf 678-689999618908489999999999998379958787987579679898999999999970
No 40
>pfam10313 DUF2415 Uncharacterized protein domain (DUF2415). This is a short, 30 residue domain, from a family of proteins conserved in fungi. The function is unknown. There is a characteristic DLL sequence motif.
Probab=50.88 E-value=25 Score=17.85 Aligned_cols=30 Identities=27% Similarity=0.298 Sum_probs=23.5
Q ss_pred EEEEEECCCCCCCCEEEEECC-CCCEEEEEEEC
Q ss_conf 999981188898743999906-98299999976
Q gi|254780128|r 28 WVRKASFVGRRGCPDRLIITP-NGGLWWIEVKK 59 (103)
Q Consensus 28 ~~~K~~~~g~~GvPDli~~~~-~g~~~fIEvK~ 59 (103)
+|.||.. .+|.+||+++.. .|++.-+.+++
T Consensus 4 R~~kFSp--~~~~~DLLv~sE~~Grvhv~DlR~ 34 (43)
T pfam10313 4 RVCKFSP--ENGLNDLLVISEHVGRVHVADLRT 34 (43)
T ss_pred EEEEECC--CCCCCCEEEEEECCCEEEEEECCC
T ss_conf 7999669--899763799991687388999000
No 41
>pfam04313 HSDR_N Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
Probab=48.87 E-value=19 Score=18.60 Aligned_cols=23 Identities=35% Similarity=0.527 Sum_probs=17.3
Q ss_pred CCCCCEEEEECCCCC-EEEEEEECC
Q ss_conf 898743999906982-999999768
Q gi|254780128|r 37 RRGCPDRLIITPNGG-LWWIEVKKP 60 (103)
Q Consensus 37 ~~GvPDli~~~~~g~-~~fIEvK~~ 60 (103)
+..-||++++. +|- .+.||+|++
T Consensus 17 ~~~r~Divlfi-NGlPl~~iE~K~~ 40 (90)
T pfam04313 17 QKRRPDYVLFV-NGLPLAVIELKRT 40 (90)
T ss_pred CCCCCCEEEEE-CCCEEEEEEECCC
T ss_conf 06656699998-8969999997588
No 42
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=44.81 E-value=32 Score=17.27 Aligned_cols=34 Identities=12% Similarity=0.181 Sum_probs=27.6
Q ss_pred CCCCCCHHHH-HHHHHHHHCCCEEEEECCHHHHHH
Q ss_conf 8988688999-999999978988999859899999
Q gi|254780128|r 60 PTGRLSHQQM-SEIEELRRRGQRVKVLVSMEEVDN 93 (103)
Q Consensus 60 ~~gkls~~Q~-~~~~~l~~~G~~~~Vv~s~edv~~ 93 (103)
.++-++|+|. ..++.|+..+|.+.+|+|+..+++
T Consensus 93 dKdalt~E~v~~vv~eL~~~~fDyIi~DsPAGIE~ 127 (272)
T COG2894 93 DKDALTPEGVKKVVNELKAMDFDYIIIDSPAGIEQ 127 (272)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCEEEECCCCHHHH
T ss_conf 72227999999999999766998899648406778
No 43
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=44.31 E-value=32 Score=17.22 Aligned_cols=37 Identities=19% Similarity=0.222 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf 6889999999999789889998598999999999986
Q gi|254780128|r 64 LSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC 100 (103)
Q Consensus 64 ls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l~~ 100 (103)
|...=....+.+.+.|+.++.+.+.||+.+++.++--
T Consensus 63 Ld~~l~~~~~~v~~~Gg~vy~A~~aedA~~ii~~iv~ 99 (459)
T COG1139 63 LDEYLEQLEENVTRNGGHVYFAKDAEDAREIIGEIVG 99 (459)
T ss_pred HHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
T ss_conf 8999999999999719879983788999999999975
No 44
>TIGR00260 thrC threonine synthase; InterPro: IPR004450 Threonine synthase () is involved in threonine biosynthesis. It catalyses the conversion of O-phospho-L-homoserine and water into L-threonine and orthophosphate, using pyridoxal phosphate as a cofactor. The pyridoxal-phosphate binding site is a Lys (K) residue. The enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes .; GO: 0004795 threonine synthase activity, 0009088 threonine biosynthetic process.
Probab=44.12 E-value=17 Score=18.92 Aligned_cols=41 Identities=17% Similarity=0.363 Sum_probs=34.5
Q ss_pred CCCCCCHHHHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHHHH
Q ss_conf 898868899999999997898899985-98999999999986
Q gi|254780128|r 60 PTGRLSHQQMSEIEELRRRGQRVKVLV-SMEEVDNFLEELAC 100 (103)
Q Consensus 60 ~~gkls~~Q~~~~~~l~~~G~~~~Vv~-s~edv~~~l~~l~~ 100 (103)
|.|+++|.|..-+-.--..|..+.=|+ ++||+.+++.++-.
T Consensus 115 P~Gki~p~Q~~Kl~~~~~~n~~v~~i~G~FDda~~~v~~~~~ 156 (423)
T TIGR00260 115 PAGKISPLQLGKLAQALIYNAKVIAIDGNFDDAQRLVKELFE 156 (423)
T ss_pred CCCCCCHHHCCCEEEEECCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf 288533302153013323783899982787999999999861
No 45
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=43.43 E-value=33 Score=17.14 Aligned_cols=42 Identities=29% Similarity=0.411 Sum_probs=27.9
Q ss_pred CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf 1888987439999069829999997689886889999999999789889998
Q gi|254780128|r 34 FVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVL 85 (103)
Q Consensus 34 ~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv 85 (103)
.++|+++|.++++.-||+. .+...+. ...+.|++.|...+++
T Consensus 102 ~g~R~~vpkv~illTDG~s--------~d~~~~~--~~a~~Lr~~GV~ifav 143 (186)
T cd01471 102 RGNRENAPQLVIIMTDGIP--------DSKFRTL--KEARKLRERGVIIAVL 143 (186)
T ss_pred CCCCCCCCEEEEEEECCCC--------CCCCHHH--HHHHHHHHCCCEEEEE
T ss_conf 6889999859999906987--------7852589--9999999889999999
No 46
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=42.70 E-value=34 Score=17.07 Aligned_cols=32 Identities=25% Similarity=0.404 Sum_probs=24.0
Q ss_pred HHHHHHHHHCCCEEEEE--CCHHHHHHHHHHHHH
Q ss_conf 99999999789889998--598999999999986
Q gi|254780128|r 69 MSEIEELRRRGQRVKVL--VSMEEVDNFLEELAC 100 (103)
Q Consensus 69 ~~~~~~l~~~G~~~~Vv--~s~edv~~~l~~l~~ 100 (103)
...+++|+++|..+++. .|+||+.+-++.+..
T Consensus 90 ~~~~~~L~~~GI~v~~~~~~sl~di~~~i~~lG~ 123 (265)
T PRK03379 90 ERQVDQLASLGIKVMWVDATSIEQIADALRQLAP 123 (265)
T ss_pred HHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHH
T ss_conf 8999999816975883599999999999999998
No 47
>COG4073 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.05 E-value=35 Score=17.01 Aligned_cols=79 Identities=18% Similarity=0.195 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHCCCEEE------------EEECCCCC-CCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf 99999999999997898999------------98118889-874399990698299999976898868899999999997
Q gi|254780128|r 11 EKDVEKRLVTGAKKLDCWVR------------KASFVGRR-GCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRR 77 (103)
Q Consensus 11 E~~ie~~l~~~lk~~G~~~~------------K~~~~g~~-GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~ 77 (103)
++..-..+.+.++++.--+| |.++++++ |||-|+.+- .| ++. |.+||.|+..+-. .+
T Consensus 68 ~s~~G~~ilr~vek~rP~vY~ElH~Yr~eny~KLt~~~Rs~gVP~lidl~-ag-VLl-------gSVSP~irkr~~~-e~ 137 (198)
T COG4073 68 RSEVGARILRVVEKLRPDVYVELHCYRPENYRKLTAERRSGGVPPLIDLG-AG-VLL-------GSVSPRIRKRIFK-ED 137 (198)
T ss_pred CCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHCCCCCCCCCCCEEEEC-CC-EEE-------EECCHHHHHHHCC-CC
T ss_conf 54120799999997297618997634876787752554358999606605-77-588-------4058899877453-10
Q ss_pred CCCEEEE-ECCHHHHHHHHHHHH
Q ss_conf 8988999-859899999999998
Q gi|254780128|r 78 RGQRVKV-LVSMEEVDNFLEELA 99 (103)
Q Consensus 78 ~G~~~~V-v~s~edv~~~l~~l~ 99 (103)
.--...| +++.+.+.+++.++.
T Consensus 138 lclT~Eip~~~s~~s~d~v~eiL 160 (198)
T COG4073 138 LCLTLEIPRRGSDRSLDVVSEIL 160 (198)
T ss_pred EEEEEEECCCCCHHHHHHHHHHH
T ss_conf 37999804789806899999999
No 48
>COG3331 PrfA Penicillin-binding protein-related factor A, putative recombinase [General function prediction only]
Probab=41.80 E-value=35 Score=16.99 Aligned_cols=75 Identities=16% Similarity=0.180 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHCCCEEEE---------EECCCC------------CCCCEEEEECCCCCEEEEEEECCCCC------
Q ss_conf 999999999999978989999---------811888------------98743999906982999999768988------
Q gi|254780128|r 11 EKDVEKRLVTGAKKLDCWVRK---------ASFVGR------------RGCPDRLIITPNGGLWWIEVKKPTGR------ 63 (103)
Q Consensus 11 E~~ie~~l~~~lk~~G~~~~K---------~~~~g~------------~GvPDli~~~~~g~~~fIEvK~~~gk------ 63 (103)
|+.|+.-+.-++.+--.+..| +..|-+ +---|-...++ |.++-.|.|..+++
T Consensus 11 E~~In~T~~~y~~~~~a~i~Kk~tPVqiv~v~yp~rs~a~i~eayf~~kSttDY~GvYk-G~yidFEaKeTknktsFpl~ 89 (177)
T COG3331 11 EADINKTNDYYLAHDIAVIHKKPTPVQIVNVDYPKRSGAVIKEAYFRQKSTTDYYGVYK-GYYIDFEAKETKNKTSFPLK 89 (177)
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCCCEEEEECCCCCCCCHHHHHHCCCCCCCEEEEEEC-CEEEEEEECCCCCCCCCCHH
T ss_conf 99999899887635736886047662378704720032011233405788630456850-27975560013566647345
Q ss_pred -CCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf -68899999999997898899985
Q gi|254780128|r 64 -LSHQQMSEIEELRRRGQRVKVLV 86 (103)
Q Consensus 64 -ls~~Q~~~~~~l~~~G~~~~Vv~ 86 (103)
..|+|...+....+.|+.+++.-
T Consensus 90 ni~~HQi~hlk~v~~q~Gi~Flli 113 (177)
T COG3331 90 NIHPHQIEHLKNVLQQGGISFLLI 113 (177)
T ss_pred HCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf 438889999999985698389999
No 49
>PRK09534 btuF corrinoid ABC transporter substrate-binding protein; Reviewed
Probab=40.23 E-value=37 Score=16.84 Aligned_cols=33 Identities=18% Similarity=0.189 Sum_probs=25.1
Q ss_pred HHHHHHHHHHCCCEEEEEC---CHHHHHHHHHHHHH
Q ss_conf 9999999997898899985---98999999999986
Q gi|254780128|r 68 QMSEIEELRRRGQRVKVLV---SMEEVDNFLEELAC 100 (103)
Q Consensus 68 Q~~~~~~l~~~G~~~~Vv~---s~edv~~~l~~l~~ 100 (103)
+...++.|+++|..++++. |+|++.+-|+.|..
T Consensus 130 ~~~~v~~L~~~GI~V~v~~~a~SiddV~~~I~~iG~ 165 (364)
T PRK09534 130 RNDTVTRLRSAGITVFQFRAATSIDGVVEKTATIGR 165 (364)
T ss_pred CHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 567899999769969991898899999999999999
No 50
>TIGR02258 2_5_ligase 2'-5' RNA ligase; InterPro: IPR004175 Members of this entry are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known . They belong to the 2H phosphoeseterase superfamily . They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.; GO: 0008664 2'-5'-RNA ligase activity, 0016070 RNA metabolic process.
Probab=40.07 E-value=37 Score=16.82 Aligned_cols=63 Identities=14% Similarity=0.108 Sum_probs=47.9
Q ss_pred HHHHHHHHHHCCCEE--EEEECCCCCCCCEEEEECCCCCEEEEEEECCCC-CCCHHHHHHHHHHHHCCCE
Q ss_conf 999999999789899--998118889874399990698299999976898-8688999999999978988
Q gi|254780128|r 15 EKRLVTGAKKLDCWV--RKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG-RLSHQQMSEIEELRRRGQR 81 (103)
Q Consensus 15 e~~l~~~lk~~G~~~--~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g-kls~~Q~~~~~~l~~~G~~ 81 (103)
-..|..++.+...-- +.+.-.|--.+|+ ..+.|++|+.|+.+.+ .|+..|...-+.+.++|+.
T Consensus 54 ~~~l~~~L~~~~~~~~~F~l~l~g~G~F~~----~~~pRvlWaGv~~~~~~~L~~L~~~~~~~l~~~G~~ 119 (189)
T TIGR02258 54 VEELEDALAKIAEPPEPFTLKLEGVGVFGN----PKSPRVLWAGVEESEEKELTQLQEELERALAKAGFS 119 (189)
T ss_pred HHHHHHHHHHHHCCCCCCEEEEEEECCCCC----CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 999999888750389973478752102788----888768998438996157899999999999964888
No 51
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=39.91 E-value=38 Score=16.81 Aligned_cols=57 Identities=12% Similarity=0.049 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHH
Q ss_conf 999999999997898999981188898743999906982999999768988688999
Q gi|254780128|r 13 DVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM 69 (103)
Q Consensus 13 ~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~ 69 (103)
.+.+++.+.+.+.|+.+.+....|.+-.+=-|-=...|.++++.+..+...+++..+
T Consensus 21 ~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~ 77 (95)
T PRK00453 21 ALVERYKGVITKNGGEIHKVEDWGRRRLAYPINKLRKGHYVLLNFEADPAAIAELER 77 (95)
T ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECCCCEEEEEEEEEEECHHHHHHHHH
T ss_conf 999999999997998899985021200442306675899999999989889999999
No 52
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.
Probab=38.81 E-value=35 Score=16.97 Aligned_cols=26 Identities=35% Similarity=0.353 Sum_probs=20.5
Q ss_pred CCC---CCEEEEECCCCCE-EEEEEECCCCC
Q ss_conf 898---7439999069829-99999768988
Q gi|254780128|r 37 RRG---CPDRLIITPNGGL-WWIEVKKPTGR 63 (103)
Q Consensus 37 ~~G---vPDli~~~~~g~~-~fIEvK~~~gk 63 (103)
..| .||+.++. +|-. +-||+|.|=++
T Consensus 133 ~~~kfRrpD~~lfv-NGiPLv~iElKkp~~~ 162 (813)
T TIGR00348 133 ENIKFRRPDVTLFV-NGIPLVIIELKKPLKE 162 (813)
T ss_pred CCCCEECCCEEEEE-CCCEEEEEECCCCCCC
T ss_conf 88866457047875-2211253230686663
No 53
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=37.64 E-value=41 Score=16.59 Aligned_cols=48 Identities=21% Similarity=0.303 Sum_probs=34.3
Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHHH
Q ss_conf 999997689886889999999999789889----998598999999999986
Q gi|254780128|r 53 WWIEVKKPTGRLSHQQMSEIEELRRRGQRV----KVLVSMEEVDNFLEELAC 100 (103)
Q Consensus 53 ~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~----~Vv~s~edv~~~l~~l~~ 100 (103)
+.-++=.+.+..-..|...+..|+..|+.+ .++.+.+++.++++++..
T Consensus 214 ~~y~~~~~~~~~~~t~~e~l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~~ 265 (307)
T cd00114 214 FIYGLGEAEGLGPKTQSEALAFLKEWGFPVSPETRLCKNIEEVLAFYDEIEA 265 (307)
T ss_pred EEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHH
T ss_conf 8998552578886778999999997799668861897999999999999997
No 54
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=37.11 E-value=42 Score=16.54 Aligned_cols=54 Identities=20% Similarity=0.135 Sum_probs=36.0
Q ss_pred CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCH
Q ss_conf 1888987439999069829999997689886889999999999789889998598
Q gi|254780128|r 34 FVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM 88 (103)
Q Consensus 34 ~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~ 88 (103)
-|-.+|+-| +.+-++-.-+.||+|.|+--.-.......+-..+.|+...|++++
T Consensus 79 vp~~a~i~~-~~fd~~~~ev~i~~~kpg~~~g~~g~~~~~i~~~~gw~~~v~r~p 132 (630)
T TIGR03675 79 VPEEAGITD-IYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CCCCCCCEE-EEECCCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECC
T ss_conf 895358415-897489727999977963676475167999999749746888659
No 55
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=36.85 E-value=42 Score=16.51 Aligned_cols=28 Identities=25% Similarity=0.258 Sum_probs=16.6
Q ss_pred HHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf 9999789889998598999999999986
Q gi|254780128|r 73 EELRRRGQRVKVLVSMEEVDNFLEELAC 100 (103)
Q Consensus 73 ~~l~~~G~~~~Vv~s~edv~~~l~~l~~ 100 (103)
--++..|..++.+.+.|++.+.|++|..
T Consensus 16 lgF~~lG~dvfpv~~~eEa~~~l~~La~ 43 (104)
T PRK01395 16 LPFKALGFDVFPVIEEQEARNTLRKLAM 43 (104)
T ss_pred HHHHHCCEEEEECCCHHHHHHHHHHHHH
T ss_conf 8888658047854887999999999986
No 56
>pfam09572 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
Probab=36.52 E-value=43 Score=16.48 Aligned_cols=57 Identities=12% Similarity=0.012 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEE------EE--------------CCCCCCC-CEEEEECCCCC----EEEEEEECCCCC
Q ss_conf 89999999999999978989999------81--------------1888987-43999906982----999999768988
Q gi|254780128|r 9 QTEKDVEKRLVTGAKKLDCWVRK------AS--------------FVGRRGC-PDRLIITPNGG----LWWIEVKKPTGR 63 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~~G~~~~K------~~--------------~~g~~Gv-PDli~~~~~g~----~~fIEvK~~~gk 63 (103)
-.|.+-+.++..++.+.|..-.. +. -+++--+ -|.++...|++ ..+||+|+.++-
T Consensus 120 aqErRQl~~I~~~L~A~Gy~k~~~~~~~~~~~m~Pgt~sFr~nv~vG~~~~i~vD~Vi~~~d~r~~~lp~~iEaKss~d~ 199 (251)
T pfam09572 120 AQERRQLAAIKSWLEARGYTQLATGAALPVNSMPPGTFSFRRNVPVGKRVNIPVDAVVRPHDGRSGKLPMLIEAKSSGDF 199 (251)
T ss_pred HHHHHHHHHHHHHHHHCCCEECCCCCCCCHHHCCCCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCC
T ss_conf 67788899999999966965646778874533498762466723347744665667985047766775546774225675
Q ss_pred CC
Q ss_conf 68
Q gi|254780128|r 64 LS 65 (103)
Q Consensus 64 ls 65 (103)
.+
T Consensus 200 TN 201 (251)
T pfam09572 200 TN 201 (251)
T ss_pred CC
T ss_conf 56
No 57
>pfam06616 BsuBI_PstI_RE BsuBI/PstI restriction endonuclease C-terminus. This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognize the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system.
Probab=36.00 E-value=43 Score=16.43 Aligned_cols=63 Identities=19% Similarity=0.227 Sum_probs=44.3
Q ss_pred CCCCCEEEEECCCCCE-EEEEEECCCCCCCHHHHHHHHHHHH--CCCEEEEE--CCHHHHHHHHHHHH
Q ss_conf 8987439999069829-9999976898868899999999997--89889998--59899999999998
Q gi|254780128|r 37 RRGCPDRLIITPNGGL-WWIEVKKPTGRLSHQQMSEIEELRR--RGQRVKVL--VSMEEVDNFLEELA 99 (103)
Q Consensus 37 ~~GvPDli~~~~~g~~-~fIEvK~~~gkls~~Q~~~~~~l~~--~G~~~~Vv--~s~edv~~~l~~l~ 99 (103)
+.-.||+++...+..+ +|||.=+..|-+++.-+..+.+|-. ....++|- -+....++++.+|.
T Consensus 212 h~klPDvVl~d~~~~wL~liEaVtS~GPv~~~R~~eL~~l~~~~~~~lvfVTAF~dR~~fkk~~~eiA 279 (306)
T pfam06616 212 HGKLPDIVLYDLGKKWLVLVEVVASDGPVDGKRHEELAKLFADAPAGLVFVTAFPDRSAFKKYLAEIA 279 (306)
T ss_pred CCCCCCEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHC
T ss_conf 56899789984689969999997377998989999999998538888699995589899999988732
No 58
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=35.56 E-value=44 Score=16.39 Aligned_cols=57 Identities=21% Similarity=0.156 Sum_probs=40.8
Q ss_pred CCHHHHHHHHHHHHHH----CC-CEEE-----EEECCCCCCCCEEEEECCC-CCEEEEEEECCCCCCC
Q ss_conf 8999999999999997----89-8999-----9811888987439999069-8299999976898868
Q gi|254780128|r 9 QTEKDVEKRLVTGAKK----LD-CWVR-----KASFVGRRGCPDRLIITPN-GGLWWIEVKKPTGRLS 65 (103)
Q Consensus 9 ~~E~~ie~~l~~~lk~----~G-~~~~-----K~~~~g~~GvPDli~~~~~-g~~~fIEvK~~~gkls 65 (103)
..|+++|+.+++.+++ +| |.++ ++..++..=..||+..... ..++-||+|+.+=+|.
T Consensus 182 ~~E~dLE~ali~~i~~FLLELG~GFaFvgrQ~ri~v~~~dfyiDLlFYh~~L~c~V~IELK~g~f~pe 249 (320)
T pfam06250 182 YSEKDLEKALINHLEKFLLELGAGFAFVGRQKRIQVDDEDFYIDLLFYHRKLRCLVAVDLKIGKFKPE 249 (320)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEHHHHHHHHHCCCEEEEEECCCCCCHH
T ss_conf 48899999999999999998189816754557888779323404766634114136776415876778
No 59
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=35.53 E-value=44 Score=16.39 Aligned_cols=50 Identities=20% Similarity=0.415 Sum_probs=33.1
Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHH-HCC--CEEEEE-C--------CHHHHHHHHHHHHHH
Q ss_conf 9999997689886889999999999-789--889998-5--------989999999999863
Q gi|254780128|r 52 LWWIEVKKPTGRLSHQQMSEIEELR-RRG--QRVKVL-V--------SMEEVDNFLEELACT 101 (103)
Q Consensus 52 ~~fIEvK~~~gkls~~Q~~~~~~l~-~~G--~~~~Vv-~--------s~edv~~~l~~l~~t 101 (103)
.|++=+|-|+|.+|+.|...+..+. +.| +...+. + ..+|+.++++.|.+.
T Consensus 65 ~FMlRvriPgG~lt~~Q~r~la~ia~~yg~~G~~~iTTRQniQlh~I~~~d~~~i~~~L~~v 126 (513)
T PRK09566 65 KFMLRLRVPNGILTSQQLRVLASIVQRYGEDGSADITTRQNLQLRGILLEDLPEILNRLKAV 126 (513)
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHCCCCHHHHHHHHHHHHHC
T ss_conf 46889667897559999999999999868998599973711211587778899999999986
No 60
>TIGR00075 hypD hydrogenase expression/formation protein HypD; InterPro: IPR002780 HypD is involved in the hyp operon which is needed for the activity of the three hydrogenase isoenzymes in Escherichia coli. HypD is one of the genes needed for formation of these enzymes . This protein has been found in Gram-negative and Gram-positive bacteria and Archaea. HypD contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into HypD resulted in Rhizobium leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas .; GO: 0046872 metal ion binding.
Probab=35.35 E-value=40 Score=16.67 Aligned_cols=57 Identities=23% Similarity=0.321 Sum_probs=35.8
Q ss_pred CCCCEEEEECCCCCE-EEEEE--------ECCCC--CCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHH
Q ss_conf 987439999069829-99999--------76898--86889999999999789889998598999999999
Q gi|254780128|r 38 RGCPDRLIITPNGGL-WWIEV--------KKPTG--RLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEE 97 (103)
Q Consensus 38 ~GvPDli~~~~~g~~-~fIEv--------K~~~g--kls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~ 97 (103)
+|+|= +..|+.+. --+|+ =+-|| |+ |-|..=+-..++.|+.+.+|||+-|+.++=.+
T Consensus 74 PGCPV--Cv~P~~~ID~a~~LA~~~~~i~~tfGDM~RV-PGs~~SL~~~ra~G~DvRIVYS~~dal~iA~~ 141 (384)
T TIGR00075 74 PGCPV--CVTPMEEIDEAIELAEKPEVIITTFGDMLRV-PGSGGSLLQARAEGADVRIVYSPMDALKIAKE 141 (384)
T ss_pred CCCCE--EECCHHHHHHHHHHHCCCCEEEEECCCCCCC-CCCCCCHHHHHHCCCCEEEEECHHHHHHHHHH
T ss_conf 44881--3557378999999863798599822211117-98854478997558867998087899999986
No 61
>pfam08011 DUF1703 Protein of unknown function (DUF1703). This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus.
Probab=31.16 E-value=52 Score=15.95 Aligned_cols=70 Identities=11% Similarity=0.015 Sum_probs=39.0
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCC--CCCHHHHHHHHHHHHCCC
Q ss_conf 99999999999999789899998118889874399990698299999976898--868899999999997898
Q gi|254780128|r 10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG--RLSHQQMSEIEELRRRGQ 80 (103)
Q Consensus 10 ~E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~g--kls~~Q~~~~~~l~~~G~ 80 (103)
.|+-.+.-+-..+..+| ...+.......|-+|+++...++..+-+|+|..+. .+......=++++++.++
T Consensus 2 ~E~~Y~~~~~~~~~~~~-y~v~se~es~~GR~Di~l~p~~~~~~IiE~K~~~~~~~~~~~~~~Al~QI~~k~Y 73 (101)
T pfam08011 2 DEGYYASVFYAYFASLG-YEVISEDETNKGRIDLTLKPTYTYIYIFEFKYIKVKDSDKEIAEEALEQIKEYGY 73 (101)
T ss_pred CCHHHHHHHHHHHHHCC-CEEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCC
T ss_conf 64008999999999889-7999814569994649999748819999999638643101568999999997674
No 62
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=30.88 E-value=52 Score=15.93 Aligned_cols=26 Identities=27% Similarity=0.285 Sum_probs=22.2
Q ss_pred CCCCCCEEEEECCCCCEEEEEEECCC
Q ss_conf 88987439999069829999997689
Q gi|254780128|r 36 GRRGCPDRLIITPNGGLWWIEVKKPT 61 (103)
Q Consensus 36 g~~GvPDli~~~~~g~~~fIEvK~~~ 61 (103)
|.+--||.+|-+|+|+-+-|.-|.|-
T Consensus 236 g~r~rPDvIV~LP~~k~iVIDSKvsL 261 (475)
T PRK10361 236 RSRMQPDVIVRLPQGKDVVIDAKMTL 261 (475)
T ss_pred CCCCCCCEEEECCCCCEEEEECCCCC
T ss_conf 88228976898789975888627884
No 63
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=30.88 E-value=53 Score=15.92 Aligned_cols=40 Identities=30% Similarity=0.395 Sum_probs=29.3
Q ss_pred CCCCEEEEEC--CCCC-EEEEEEECCCCCCCHHHHHHHHHHHHC
Q ss_conf 9874399990--6982-999999768988688999999999978
Q gi|254780128|r 38 RGCPDRLIIT--PNGG-LWWIEVKKPTGRLSHQQMSEIEELRRR 78 (103)
Q Consensus 38 ~GvPDli~~~--~~g~-~~fIEvK~~~gkls~~Q~~~~~~l~~~ 78 (103)
.|+|++---. ..|. ++=|.|-+|+. ||+.|+.-+++|.+.
T Consensus 343 kG~p~~~~~~Fk~~GDl~v~V~v~~P~~-Ls~~q~~lLe~l~~~ 385 (386)
T TIGR02349 343 KGVPRLRGSNFKGRGDLLVTVKVETPKN-LSKEQKELLEELAEA 385 (386)
T ss_pred CCCCCCCCCCCCCCCCEEEEEEEEECCC-CCHHHHHHHHHHHHC
T ss_conf 7501468876763366699999985898-788899999999732
No 64
>PRK10976 putative sugar phosphatase; Provisional
Probab=30.10 E-value=54 Score=15.84 Aligned_cols=44 Identities=16% Similarity=0.040 Sum_probs=25.5
Q ss_pred ECCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CCCEEEEECCCCCEEE
Q ss_conf 048899999999999999789899998118889-----------8743999906982999
Q gi|254780128|r 6 FHYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GCPDRLIITPNGGLWW 54 (103)
Q Consensus 6 ~h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------GvPDli~~~~~g~~~f 54 (103)
-|..++.. ...++.+++.|..+. .+.||+ |+++.+++. +|...+
T Consensus 17 ~~~is~~~--~~ai~~l~~~Gi~~v--iATGR~~~~~~~~~~~l~~~~~~I~~-NGa~i~ 71 (266)
T PRK10976 17 DHTLSPYA--KETLKLLTARGIHFV--FATGRHHVDVGQIRDNLEIKSYMITS-NGARVH 71 (266)
T ss_pred CCCCCHHH--HHHHHHHHHCCCEEE--EECCCCHHHHHHHHHHCCCCCEEEEC-CCEEEE
T ss_conf 79719999--999999997899999--99799979999999973997418962-877999
No 65
>COG1540 Uncharacterized proteins, homologs of lactam utilization protein B [General function prediction only]
Probab=29.76 E-value=47 Score=16.22 Aligned_cols=29 Identities=24% Similarity=0.182 Sum_probs=18.9
Q ss_pred HHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECC
Q ss_conf 9999999997898999981188898743999906
Q gi|254780128|r 15 EKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITP 48 (103)
Q Consensus 15 e~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~ 48 (103)
=++.++..+..|..+ +-++|+|||..+-.
T Consensus 46 M~rtV~lA~e~gV~I-----GAHPgyPDl~gFGR 74 (252)
T COG1540 46 MRRTVRLAKENGVAI-----GAHPGYPDLVGFGR 74 (252)
T ss_pred HHHHHHHHHHCCCEE-----CCCCCCCCCCCCCC
T ss_conf 999999999849766-----35899863235674
No 66
>pfam04720 DUF506 Protein of unknown function (DUF506). Family of uncharacterized plant proteins.
Probab=29.50 E-value=54 Score=15.87 Aligned_cols=73 Identities=16% Similarity=0.208 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHCCCEEE----EEECCCCCCCCEEEEECCCCCEEEEEEECCC---------------------CCCCH
Q ss_conf 9999999999997898999----9811888987439999069829999997689---------------------88688
Q gi|254780128|r 12 KDVEKRLVTGAKKLDCWVR----KASFVGRRGCPDRLIITPNGGLWWIEVKKPT---------------------GRLSH 66 (103)
Q Consensus 12 ~~ie~~l~~~lk~~G~~~~----K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~---------------------gkls~ 66 (103)
+.+.+.++..|+..|.-+- ||.+ ..++| .|.+-||+|-.++ .||++
T Consensus 87 s~lrr~v~~~Lr~~GydAaiCkSkW~~--s~~~p-------~G~yeYiDVv~~~~~~~~~~R~iVd~dFrs~FEiARpt~ 157 (218)
T pfam04720 87 SCLRRKVMSLLRELGYDAAICKSKWES--SGKVP-------AGEYEYIDVVDGGESKKQEVRLIVDLDFRSEFEIARPTE 157 (218)
T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCC--CCCCC-------CCCCEEEEEEECCCCCCCCEEEEEECCCHHHEEEECCCH
T ss_conf 899999999998669884133330678--89978-------976148999822788887505999456557523436858
Q ss_pred HHHHHHHHHHHCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999999997898899985989999999999
Q gi|254780128|r 67 QQMSEIEELRRRGQRVKVLVSMEEVDNFLEEL 98 (103)
Q Consensus 67 ~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l 98 (103)
.=..-+..| -.++|- +.|...+++.-+
T Consensus 158 ~Y~~ll~~L----P~vfVG-~~~rL~~iv~im 184 (218)
T pfam04720 158 EYKRILQSL----PRVFVG-KVERLKQLVRIM 184 (218)
T ss_pred HHHHHHHHC----CCEEEE-CHHHHHHHHHHH
T ss_conf 999999969----984772-799999999999
No 67
>pfam08652 RAI1 RAI1 like. RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z and binds to a nuclear exoribonuclease. It is required for 5.8S rRNA processing.
Probab=28.77 E-value=57 Score=15.70 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=17.2
Q ss_pred CCCEEEEEEECCCCCCCHHHHHHHH
Q ss_conf 9829999997689886889999999
Q gi|254780128|r 49 NGGLWWIEVKKPTGRLSHQQMSEIE 73 (103)
Q Consensus 49 ~g~~~fIEvK~~~gkls~~Q~~~~~ 73 (103)
++-..|||+|+...-.++.|....+
T Consensus 13 ~~~~~yVELKTs~~~~~~~~~~~F~ 37 (68)
T pfam08652 13 DNLSHYVELKTSREIQNPRQVRNFE 37 (68)
T ss_pred CCCCCEEEEEEEECCCCHHHHHHHH
T ss_conf 9966089986641228877999999
No 68
>pfam08608 Wyosine_form Wyosine base formation. Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Probab=28.61 E-value=25 Score=17.90 Aligned_cols=26 Identities=31% Similarity=0.387 Sum_probs=15.8
Q ss_pred CCEEEEEEECCC--C----CCCHHHHHHHHHH
Q ss_conf 829999997689--8----8688999999999
Q gi|254780128|r 50 GGLWWIEVKKPT--G----RLSHQQMSEIEEL 75 (103)
Q Consensus 50 g~~~fIEvK~~~--g----kls~~Q~~~~~~l 75 (103)
+...|||+|++. | +++..-.-+++++
T Consensus 2 a~P~fVEvKay~~~G~S~~rLt~~nmp~heeV 33 (62)
T pfam08608 2 AEPDFVELKAYMHVGYSRNRLTMGNMPAHEEV 33 (62)
T ss_pred CCCCEEEEEEEEEECCCCCCCCHHHCCCHHHH
T ss_conf 99998988318986158887771339988999
No 69
>pfam04471 Mrr_cat Restriction endonuclease. Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA.
Probab=28.54 E-value=58 Score=15.68 Aligned_cols=66 Identities=15% Similarity=0.135 Sum_probs=41.3
Q ss_pred HHHHHHCCCEEEEEECC-CCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHH-HHHHHHCCCEEEEE
Q ss_conf 99999789899998118-889874399990698299999976898868899999-99999789889998
Q gi|254780128|r 19 VTGAKKLDCWVRKASFV-GRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSE-IEELRRRGQRVKVL 85 (103)
Q Consensus 19 ~~~lk~~G~~~~K~~~~-g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~-~~~l~~~G~~~~Vv 85 (103)
.+-++++|+.-.+.+.. +--|+ |++...+++.-..|++|.-.+.+....... ...+...++.-.++
T Consensus 2 ~~ll~~~G~~~v~~t~~~~D~Gi-Dvia~~~~~~~~~VQ~K~~~~~vg~~~v~~l~~~~~~~~~~~~i~ 69 (98)
T pfam04471 2 AELLEALGYREVELTGKSGDGGI-DVVATTSDGERIVVQAKRYRSTVGRPVIQELLGAKAGYGADKGVV 69 (98)
T ss_pred HHHHHHCCCCEEEECCCCCCCCE-EEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEE
T ss_conf 68897679988997889898845-899993799899999998789899899999960277618987999
No 70
>PRK10513 sugar phosphatase; Provisional
Probab=27.43 E-value=61 Score=15.56 Aligned_cols=44 Identities=25% Similarity=0.164 Sum_probs=22.4
Q ss_pred ECCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CC--C-EEEEECCCCCEEE
Q ss_conf 048899999999999999789899998118889-----------87--4-3999906982999
Q gi|254780128|r 6 FHYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GC--P-DRLIITPNGGLWW 54 (103)
Q Consensus 6 ~h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------Gv--P-Dli~~~~~g~~~f 54 (103)
-|-.++..+ ..++.+++.|..+. .+.||+ |+ | |.+++. +|...+
T Consensus 18 ~~~i~~~~~--~ai~~l~~~Gi~~~--iaTGR~~~~~~~~~~~l~~~~~~~~~I~~-NGa~i~ 75 (270)
T PRK10513 18 DHTISPAVK--NAIAAARAKGVNVV--LTTGRPYAGVHRYLKELHMEQPGDYCITY-NGALVQ 75 (270)
T ss_pred CCCCCHHHH--HHHHHHHHCCCEEE--EECCCCHHHHHHHHHHHCCCCCCCEEEEC-CCEEEE
T ss_conf 796899999--99999997899999--99799868789999983888899889985-985999
No 71
>TIGR01942 pcnB poly(A) polymerase; InterPro: IPR010206 This entry describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell , . This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well . Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase.; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0006378 mRNA polyadenylation.
Probab=26.55 E-value=60 Score=15.56 Aligned_cols=26 Identities=12% Similarity=0.310 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf 88688999999999978988999859
Q gi|254780128|r 62 GRLSHQQMSEIEELRRRGQRVKVLVS 87 (103)
Q Consensus 62 gkls~~Q~~~~~~l~~~G~~~~Vv~s 87 (103)
..+|.+=...+++|+.+||.+|||=+
T Consensus 12 ~~~S~~A~~Vv~rL~~AGyqAY~VGG 37 (448)
T TIGR01942 12 QSFSAHALNVVRRLKKAGYQAYIVGG 37 (448)
T ss_pred HHHHHHHHHHHHHHHHCCEEEEEECC
T ss_conf 77649999999987007823767231
No 72
>COG1553 DsrE Uncharacterized conserved protein involved in intracellular sulfur reduction [Inorganic ion transport and metabolism]
Probab=26.54 E-value=59 Score=15.61 Aligned_cols=54 Identities=22% Similarity=0.144 Sum_probs=37.4
Q ss_pred EEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHH
Q ss_conf 999069829999997689886889999999999789889998598999999999
Q gi|254780128|r 44 LIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEE 97 (103)
Q Consensus 44 i~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~ 97 (103)
+.++.||-...--.-.|..-=-+++..|.+-+.++|..+.+|-...+.+.++++
T Consensus 37 iFly~DgV~~~~~~~~Pa~dEf~l~~~~~~l~~~~gv~v~~C~~ca~~RGv~~~ 90 (126)
T COG1553 37 LFLYQDGVHNGNKGQKPASDEFNLIQAWLELLTEQGVPVKLCVACALRRGVTEE 90 (126)
T ss_pred EEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEHHHHHHCCCCCC
T ss_conf 998601000243576986333524999999999759807660987873486641
No 73
>pfam03190 DUF255 Protein of unknown function, DUF255.
Probab=26.51 E-value=48 Score=16.17 Aligned_cols=54 Identities=20% Similarity=0.247 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHHHCCCEEEEEEC-----------------CCCCCCCEEEEECCCCCEEEEEEECC
Q ss_conf 4889999999999999978989999811-----------------88898743999906982999999768
Q gi|254780128|r 7 HYQTEKDVEKRLVTGAKKLDCWVRKASF-----------------VGRRGCPDRLIITPNGGLWWIEVKKP 60 (103)
Q Consensus 7 h~~~E~~ie~~l~~~lk~~G~~~~K~~~-----------------~g~~GvPDli~~~~~g~~~fIEvK~~ 60 (103)
|.|-+..+++.-+..+=...-...|+.. .|..|+|=-+++.|||+.+|.=.=-|
T Consensus 53 hvM~~esF~d~~vA~~lN~~Fv~VkVDree~PdiD~~Ym~~~q~~~g~gGWPL~vfltPdg~Pf~~gTY~P 123 (163)
T pfam03190 53 HVMAHESFEDPEVAAILNEHFVPIKVDREERPDIDAIYMTAVQALTGSGGWPLTVFLTPDGKPFFGGTYFP 123 (163)
T ss_pred HHHHHHHCCCHHHHHHHHHHEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCEEEEEEECC
T ss_conf 99998734899999999742033340632375578999999999707899751246879997468876269
No 74
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=26.31 E-value=63 Score=15.43 Aligned_cols=42 Identities=19% Similarity=0.343 Sum_probs=30.9
Q ss_pred EECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf 97689886889999999999789889998598999999999986
Q gi|254780128|r 57 VKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC 100 (103)
Q Consensus 57 vK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l~~ 100 (103)
+=-|.|+.++.|...+.-+.+ ....|--++||+.+++.++..
T Consensus 154 Vl~P~g~vs~~k~~q~~~~ga--~~i~v~G~fDda~~~vk~~~~ 195 (411)
T COG0498 154 VLYPKGKVSPGKLAQMLTLGA--HVIAVDGNFDDAQELVKEAAN 195 (411)
T ss_pred EEECCCCCCHHHHHHHHHCCC--EEEEECCCHHHHHHHHHHHHH
T ss_conf 994598788788999975388--899975968999999999996
No 75
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=25.03 E-value=67 Score=15.29 Aligned_cols=25 Identities=24% Similarity=0.514 Sum_probs=12.4
Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf 9999997689886889999999999
Q gi|254780128|r 52 LWWIEVKKPTGRLSHQQMSEIEELR 76 (103)
Q Consensus 52 ~~fIEvK~~~gkls~~Q~~~~~~l~ 76 (103)
.+++=+|-|+|.+++.|...+..+.
T Consensus 113 ~FMlRiRiPgG~lt~~Q~r~la~iA 137 (591)
T PRK09567 113 SYMCRLRIPNGILTHWQLAGLADLA 137 (591)
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf 0489953689635999999999999
No 76
>cd01143 YvrC Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=24.93 E-value=67 Score=15.28 Aligned_cols=30 Identities=30% Similarity=0.446 Sum_probs=21.4
Q ss_pred HHHHHHHHCCCEEEEEC---CHHHHHHHHHHHH
Q ss_conf 99999997898899985---9899999999998
Q gi|254780128|r 70 SEIEELRRRGQRVKVLV---SMEEVDNFLEELA 99 (103)
Q Consensus 70 ~~~~~l~~~G~~~~Vv~---s~edv~~~l~~l~ 99 (103)
...+.|++.|..+.++. +++++.+.+..+.
T Consensus 73 ~~~~~L~~~gi~v~~~~~~~~~~~~~~~i~~lg 105 (195)
T cd01143 73 ELLEKLKDAGIPVVVLPAASSLDEIYDQIELIG 105 (195)
T ss_pred HHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHH
T ss_conf 799998641885999758999999999999999
No 77
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=24.87 E-value=68 Score=15.27 Aligned_cols=77 Identities=23% Similarity=0.189 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHC-----CCEEEE----------EECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf 999999999999978-----989999----------81188898743999906982999999768988688999999999
Q gi|254780128|r 11 EKDVEKRLVTGAKKL-----DCWVRK----------ASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEEL 75 (103)
Q Consensus 11 E~~ie~~l~~~lk~~-----G~~~~K----------~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l 75 (103)
..++-+.+.+.+++. .-.+++ -+-|-.+|+-| +.+-++-.=+.||.|.|+=..-..-....+-.
T Consensus 47 ~~dlik~lAk~lrKRI~iR~dPsvl~~~e~A~~~I~eivP~ea~i~~-i~Fd~~tGEViIea~KPGlvigk~g~~~reI~ 125 (637)
T COG1782 47 DGDLIKDLAKDLRKRIIIRPDPSVLKPPEEARKIILEIVPEEAGITD-IYFDDDTGEVIIEAKKPGLVIGKGGSTLREIT 125 (637)
T ss_pred CHHHHHHHHHHHHHCEEECCCCHHCCCHHHHHHHHHHHCCCCCCCEE-EEECCCCCEEEEEECCCCEEEECCCHHHHHHH
T ss_conf 31699999999863268436902218989999999974862137036-78618874499995589558824721799999
Q ss_pred HHCCCEEEEECCH
Q ss_conf 9789889998598
Q gi|254780128|r 76 RRRGQRVKVLVSM 88 (103)
Q Consensus 76 ~~~G~~~~Vv~s~ 88 (103)
++.|+...|++.+
T Consensus 126 ~~tgW~p~ivR~P 138 (637)
T COG1782 126 AETGWAPKIVRTP 138 (637)
T ss_pred HHHCCCCEEEECC
T ss_conf 9748753056369
No 78
>TIGR02291 rimK_rel_E_lig alpha-L-glutamate ligase homolog; InterPro: IPR011758 Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (IPR004666 from INTERPRO), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown..
Probab=24.53 E-value=69 Score=15.23 Aligned_cols=62 Identities=19% Similarity=0.187 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHH---HHCCCEE---E-----E----EECCCCCCCCEEEEECCCCCEE--EEEEEC--CCCCCCHH
Q ss_conf 4889999999999999---9789899---9-----9----8118889874399990698299--999976--89886889
Q gi|254780128|r 7 HYQTEKDVEKRLVTGA---KKLDCWV---R-----K----ASFVGRRGCPDRLIITPNGGLW--WIEVKK--PTGRLSHQ 67 (103)
Q Consensus 7 h~~~E~~ie~~l~~~l---k~~G~~~---~-----K----~~~~g~~GvPDli~~~~~g~~~--fIEvK~--~~gkls~~ 67 (103)
..++|.+||.++=..| -++||.- + | |.+-+-.||||+=++.-.|-.+ ++=+-| .+||-+=+
T Consensus 108 ~~i~~eeiE~hvSniL~GLySLGG~~D~AliEyrvkfDp~F~~~SYeGVPDiRiIVf~GyPVmaM~RlpTr~SdGKANLH 187 (320)
T TIGR02291 108 ALISKEEIERHVSNILAGLYSLGGKRDRALIEYRVKFDPLFESVSYEGVPDIRIIVFKGYPVMAMLRLPTRASDGKANLH 187 (320)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEECCCCHHHHCCCCCCCCCCCCCCC
T ss_conf 10154567788888887776507997736885320105344771113458726896418610210027656788830212
Q ss_pred H
Q ss_conf 9
Q gi|254780128|r 68 Q 68 (103)
Q Consensus 68 Q 68 (103)
|
T Consensus 188 Q 188 (320)
T TIGR02291 188 Q 188 (320)
T ss_pred C
T ss_conf 4
No 79
>TIGR02502 type_III_YscX type III secretion protein, YscX family; InterPro: IPR012672 Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery ..
Probab=24.27 E-value=24 Score=18.00 Aligned_cols=17 Identities=24% Similarity=0.477 Sum_probs=15.0
Q ss_pred CCCCCEEEEECCCCCEE
Q ss_conf 89874399990698299
Q gi|254780128|r 37 RRGCPDRLIITPNGGLW 53 (103)
Q Consensus 37 ~~GvPDli~~~~~g~~~ 53 (103)
..++||+..+.|||+.+
T Consensus 24 ~~~LP~Ry~L~PDG~~V 40 (126)
T TIGR02502 24 DTDLPERYALLPDGQPV 40 (126)
T ss_pred CCCCCCCCCCCCCCCCH
T ss_conf 89876112688767862
No 80
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain; InterPro: IPR014089 This group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which they have been characterised , , . In most species this protein is bifunctional, existing as fused alpha-beta domains. In Pyrococcus and related species, however, the domains exist as separate polypeptides. This entry represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. One of these (along with its beta-domain partner) was characterised as ACS-II showing specificity for phenylacetyl-CoA . This entry excludes non-ACS-I paralogs. .
Probab=24.13 E-value=70 Score=15.18 Aligned_cols=26 Identities=23% Similarity=0.192 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCCC
Q ss_conf 99999999999978989999811888987
Q gi|254780128|r 12 KDVEKRLVTGAKKLDCWVRKASFVGRRGC 40 (103)
Q Consensus 12 ~~ie~~l~~~lk~~G~~~~K~~~~g~~Gv 40 (103)
.++|++|+.-++++|.+. ..||+-|+
T Consensus 110 ~~LE~~l~~~a~kYg~Rl---~GPNclG~ 135 (457)
T TIGR02717 110 AELEQKLVEIARKYGMRL---LGPNCLGI 135 (457)
T ss_pred HHHHHHHHHHHHHCCCEE---ECCCEEEE
T ss_conf 999999999997678817---76736225
No 81
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946 Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=23.73 E-value=57 Score=15.73 Aligned_cols=23 Identities=13% Similarity=0.206 Sum_probs=19.2
Q ss_pred EECCCCHHHHHHHHHHHHHHCCC
Q ss_conf 10488999999999999997898
Q gi|254780128|r 5 SFHYQTEKDVEKRLVTGAKKLDC 27 (103)
Q Consensus 5 ~~h~~~E~~ie~~l~~~lk~~G~ 27 (103)
.+|=|+|+.||+.+.+++...|-
T Consensus 238 ~RHH~~e~~~QRav~~Av~~AGI 260 (320)
T TIGR02249 238 RRHHIDEKTIQRAVRRAVERAGI 260 (320)
T ss_pred EEEECCCCHHHHHHHHHHHHCCC
T ss_conf 00106700432899999995789
No 82
>pfam01250 Ribosomal_S6 Ribosomal protein S6.
Probab=23.13 E-value=73 Score=15.07 Aligned_cols=60 Identities=12% Similarity=0.052 Sum_probs=38.6
Q ss_pred CCHHH---HHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHH
Q ss_conf 89999---9999999999789899998118889874399990698299999976898868899
Q gi|254780128|r 9 QTEKD---VEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQ 68 (103)
Q Consensus 9 ~~E~~---ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q 68 (103)
.+|.+ +...+.+.+++.||.+.+....|.+-.+=-|-=...|.++++.+.++...++...
T Consensus 13 l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~ 75 (92)
T pfam01250 13 LSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAELE 75 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCEEEEEEEEEEECHHHHHHHH
T ss_conf 998999999999999998789889998513100033043778899999999999988999999
No 83
>cd03008 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors. RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity.
Probab=23.12 E-value=73 Score=15.06 Aligned_cols=39 Identities=13% Similarity=0.178 Sum_probs=27.0
Q ss_pred HHHHHHHHHHCC--CEEEEEEC---------CCCCCCCEEEEECCCCCEE
Q ss_conf 999999999789--89999811---------8889874399990698299
Q gi|254780128|r 15 EKRLVTGAKKLD--CWVRKASF---------VGRRGCPDRLIITPNGGLW 53 (103)
Q Consensus 15 e~~l~~~lk~~G--~~~~K~~~---------~g~~GvPDli~~~~~g~~~ 53 (103)
+.....+.+.+. |.++.|.. .+-+|+|-|+++-++|.++
T Consensus 77 e~~f~~y~~~MP~~WlAlPf~d~~~~~L~~~f~V~gIPtLVil~~dG~vi 126 (146)
T cd03008 77 EQQQESFLKDMPKKWLFLPFEDEFRRELEAQFSVEELPTVVVLKPDGDVL 126 (146)
T ss_pred HHHHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCCCCCEEEEECCCCCEE
T ss_conf 99999999977987266576968999999985998788899998999897
No 84
>pfam08282 Hydrolase_3 haloacid dehalogenase-like hydrolase. This family contains haloacid dehalogenase-like hydrolase enzymes.
Probab=23.06 E-value=73 Score=15.06 Aligned_cols=73 Identities=19% Similarity=0.180 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHHHCCCEEEEEECCCCC-----------CCCEEEEECCCCCEEEEEEEC--CCCCCCHHHH-HHH
Q ss_conf 48899999999999999789899998118889-----------874399990698299999976--8988688999-999
Q gi|254780128|r 7 HYQTEKDVEKRLVTGAKKLDCWVRKASFVGRR-----------GCPDRLIITPNGGLWWIEVKK--PTGRLSHQQM-SEI 72 (103)
Q Consensus 7 h~~~E~~ie~~l~~~lk~~G~~~~K~~~~g~~-----------GvPDli~~~~~g~~~fIEvK~--~~gkls~~Q~-~~~ 72 (103)
|..++..+ +.++++++.|..+. .+.||+ |+++-+++. +|...+..=.. -...+++.+. ..+
T Consensus 14 ~~i~~~~~--~ai~~l~~~G~~~~--iaTGR~~~~~~~~~~~l~~~~~~I~~-NGa~i~~~~~~~l~~~~i~~~~~~~i~ 88 (254)
T pfam08282 14 KKISERTK--EAIKKLQEKGIKVV--IATGRPYRGALPVLEELGLDLPVICF-NGAYIYDENGKILYKNPISKEDVKEII 88 (254)
T ss_pred CCCCHHHH--HHHHHHHHCCCEEE--EECCCCHHHHHHHHHHCCCCCCEEEC-CCCEEEECCCEEEEEECCCHHHHHHHH
T ss_conf 93899999--99999998899999--99498799999999980999759977-971999689869999349999999999
Q ss_pred HHHHHCCCEEEE
Q ss_conf 999978988999
Q gi|254780128|r 73 EELRRRGQRVKV 84 (103)
Q Consensus 73 ~~l~~~G~~~~V 84 (103)
+.+++.+....+
T Consensus 89 ~~~~~~~~~~~~ 100 (254)
T pfam08282 89 EYLKENNLSILL 100 (254)
T ss_pred HHHHHCCCEEEE
T ss_conf 999986986999
No 85
>TIGR03081 metmalonyl_epim methylmalonyl-CoA epimerase. Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer.
Probab=22.80 E-value=74 Score=15.03 Aligned_cols=85 Identities=19% Similarity=0.232 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHH
Q ss_conf 99999999999997898999981188898743999906982999999768988688999999999978988999859899
Q gi|254780128|r 11 EKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEE 90 (103)
Q Consensus 11 E~~ie~~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~ed 90 (103)
=+++++.+.-+.+.+|..+..-......|+= +++...|. ..+|+=.|.+.-+|... +++ +..++..++|..++|
T Consensus 9 V~Dld~a~~fy~~~lG~~~~~~~~~~~~~~~--~~~~~~g~-~~ieL~~~~~~~~~~~~-~l~--~~g~G~~Hiaf~V~D 82 (128)
T TIGR03081 9 VPDLEEAAKLYEDVLGAHVSHIEEVPEQGVK--VVFIALGN-TKVELLEPLGEDSPIAK-FLE--KNGGGIHHIAIEVDD 82 (128)
T ss_pred CCCHHHHHHHHHHHHCCCEEECCCCCCCCEE--EEEEECCC-CCEEEEEECCCCCCHHH-HCC--CCCCCCEEEEEECCC
T ss_conf 0999999999999709956531115667959--99994689-71788630578985344-111--469985699998799
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999863
Q gi|254780128|r 91 VDNFLEELACT 101 (103)
Q Consensus 91 v~~~l~~l~~t 101 (103)
+++.++.+.+.
T Consensus 83 i~~~~~~l~~~ 93 (128)
T TIGR03081 83 IEAALETLKEK 93 (128)
T ss_pred HHHHHHHHHHC
T ss_conf 99999999988
No 86
>pfam09588 YqaJ YqaJ-like viral recombinase domain. This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Probab=22.69 E-value=74 Score=15.01 Aligned_cols=50 Identities=22% Similarity=0.298 Sum_probs=29.5
Q ss_pred HHHHHHHHHHH-HCCCEEEEE----ECC---CCCCCCEEEEECCCCCEEEEEEECCCCC
Q ss_conf 99999999999-789899998----118---8898743999906982999999768988
Q gi|254780128|r 13 DVEKRLVTGAK-KLDCWVRKA----SFV---GRRGCPDRLIITPNGGLWWIEVKKPTGR 63 (103)
Q Consensus 13 ~ie~~l~~~lk-~~G~~~~K~----~~~---g~~GvPDli~~~~~g~~~fIEvK~~~gk 63 (103)
..|..+..... ..|..+... ..+ ...+-||-++..+++. ..+|+|.|..+
T Consensus 56 ~~E~~a~~~~~~~~g~~v~~~~~~~~~~~~~~~~aSpDg~~~~~~~~-~~lEiK~~~~~ 113 (141)
T pfam09588 56 ELEPLARAEYEERTGIKVREVGGLLQHPEDPFLGASPDGLVVDGDGG-GILEIKTPFET 113 (141)
T ss_pred HHHHHHHHHHHHHHCCEEEEECEEEECCCCCEEEECCCEEECCCCCC-EEEEEECCCHH
T ss_conf 40399999999997998985033896378882677288744048876-37998468627
No 87
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=22.16 E-value=76 Score=14.95 Aligned_cols=56 Identities=20% Similarity=0.275 Sum_probs=34.2
Q ss_pred ECCCCCCCCEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHH
Q ss_conf 11888987439999069829999997689886889999999999789889998598999999999986
Q gi|254780128|r 33 SFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC 100 (103)
Q Consensus 33 ~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~edv~~~l~~l~~ 100 (103)
..+.++|+|-.+++.-||+. +..-..-...+++.|..++++==-+.-.+-|+.|-+
T Consensus 96 ~~~~r~~~~kvvvllTDG~s------------~~~~~~~a~~lr~~Gi~v~~VGig~~~~~~L~~iAs 151 (164)
T cd01472 96 ASGSREGVPKVLVVITDGKS------------QDDVEEPAVELKQAGIEVFAVGVKNADEEELKQIAS 151 (164)
T ss_pred CCCCCCCCEEEEEEEECCCC------------CCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHC
T ss_conf 57876785159999837998------------640889999999889889999788479999999967
No 88
>PRK10767 chaperone protein DnaJ; Provisional
Probab=22.13 E-value=76 Score=14.94 Aligned_cols=46 Identities=22% Similarity=0.269 Sum_probs=28.7
Q ss_pred CCCCEEEEECCCCC-EEEEEEECCCCCCCHHHHHHHHHHHH-CCCEEEEE
Q ss_conf 98743999906982-99999976898868899999999997-89889998
Q gi|254780128|r 38 RGCPDRLIITPNGG-LWWIEVKKPTGRLSHQQMSEIEELRR-RGQRVKVL 85 (103)
Q Consensus 38 ~GvPDli~~~~~g~-~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~~~~Vv 85 (103)
.|+|+.=- -..|. ++-+.|+-|+ +||+.|+.-+++|++ .|-.....
T Consensus 308 ~Gmp~~~~-~~~GDl~V~~~V~~P~-~Ls~~Qk~ll~el~~~~~~~~~~~ 355 (376)
T PRK10767 308 KGVKSVRG-GAQGDLLCRVVVETPV-GLNEKQKQLLQELQESFGGPTGEK 355 (376)
T ss_pred CCCCCCCC-CCCCCEEEEEEEECCC-CCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf 89898997-9977889999998999-999999999999999746766676
No 89
>PRK07810 O-succinylhomoserine sulfhydrylase; Provisional
Probab=22.10 E-value=77 Score=14.94 Aligned_cols=85 Identities=18% Similarity=0.259 Sum_probs=46.1
Q ss_pred HHHHHHHHCCCEEEEEECCCCCCCCEEEEECC----CCCEEEEEEECCCCCCCHHHHHHHHHH-----------------
Q ss_conf 99999997898999981188898743999906----982999999768988688999999999-----------------
Q gi|254780128|r 17 RLVTGAKKLDCWVRKASFVGRRGCPDRLIITP----NGGLWWIEVKKPTGRLSHQQMSEIEEL----------------- 75 (103)
Q Consensus 17 ~l~~~lk~~G~~~~K~~~~g~~GvPDli~~~~----~g~~~fIEvK~~~gkls~~Q~~~~~~l----------------- 75 (103)
++...|+.+- .+-++..||-+..|+--+..+ .|..+.+|+|.........=..+++.|
T Consensus 282 ~vA~~L~~hp-~V~~V~yPgL~shp~h~la~r~~~g~G~~~sf~l~~~~~~~~~~~~~~~~~l~l~~~a~slGg~~SLi~ 360 (406)
T PRK07810 282 RIAEFLEGHP-AVRWVRYPYLPSHPQYDLAKRQMSGGGTVVTFELDAPEDAAKQRAFEVLDKLRLIDISNNLGDAKSLIT 360 (406)
T ss_pred HHHHHHHHCC-CCCEEECCCCCCCCCHHHHHHHCCCCCCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEECCCCCCEEEE
T ss_conf 9999997399-813798057877817789984478998632899803617889999999982872435335676660466
Q ss_pred ---------------HHCCC---EEEEECCHHHHHHHHHHHHHHC
Q ss_conf ---------------97898---8999859899999999998630
Q gi|254780128|r 76 ---------------RRRGQ---RVKVLVSMEEVDNFLEELACTL 102 (103)
Q Consensus 76 ---------------~~~G~---~~~Vv~s~edv~~~l~~l~~t~ 102 (103)
+..|. .+.+.=+.||++.++++|++.|
T Consensus 361 ~Pas~th~~~~~e~r~~~Gi~~~liRlSVGlEd~~DLi~DL~qAL 405 (406)
T PRK07810 361 HPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDLIADLDRAL 405 (406)
T ss_pred CCCCCCCCCCCHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
T ss_conf 775356510799899866979495999932199999999999754
No 90
>pfam02646 RmuC RmuC family. This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures.
Probab=21.87 E-value=77 Score=14.91 Aligned_cols=27 Identities=41% Similarity=0.460 Sum_probs=22.5
Q ss_pred CCCCCCCEEEEECCCCCEEEEEEECCC
Q ss_conf 888987439999069829999997689
Q gi|254780128|r 35 VGRRGCPDRLIITPNGGLWWIEVKKPT 61 (103)
Q Consensus 35 ~g~~GvPDli~~~~~g~~~fIEvK~~~ 61 (103)
.+..-.||.++-+|+++.+-|..|.|-
T Consensus 98 ~~~~~rpD~vi~lP~~~~i~IDSK~pl 124 (301)
T pfam02646 98 EGGRLRPDFAIRLPGGKLLVIDAKFPL 124 (301)
T ss_pred CCCCCCCEEEEECCCCCEEEEEHHHHH
T ss_conf 899837618898689986777521148
No 91
>pfam04555 XhoI Restriction endonuclease XhoI. This family consists of type II restriction enzymes (EC:3.1.21.4) that recognize the double-stranded sequence CTCGAG and cleave after C-1.
Probab=21.72 E-value=78 Score=14.89 Aligned_cols=23 Identities=30% Similarity=0.332 Sum_probs=16.6
Q ss_pred CCCEEEEECCCCCE-EEEEEECCCC
Q ss_conf 87439999069829-9999976898
Q gi|254780128|r 39 GCPDRLIITPNGGL-WWIEVKKPTG 62 (103)
Q Consensus 39 GvPDli~~~~~g~~-~fIEvK~~~g 62 (103)
--=||++... |.. ..||+|+..|
T Consensus 61 K~WDllVv~~-g~LvAaiElKSqvG 84 (196)
T pfam04555 61 KLWDLLVVQK-GVLIAAVELKSQVG 84 (196)
T ss_pred CCCCEEEEEC-CEEEEEEEECCCCC
T ss_conf 6521799988-93889987300038
No 92
>KOG2364 consensus
Probab=21.67 E-value=78 Score=14.89 Aligned_cols=54 Identities=22% Similarity=0.249 Sum_probs=39.5
Q ss_pred CHHHHHHHHHHHHHHC-CCEEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCC
Q ss_conf 9999999999999978-9899998118889874399990698299999976898868
Q gi|254780128|r 10 TEKDVEKRLVTGAKKL-DCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLS 65 (103)
Q Consensus 10 ~E~~ie~~l~~~lk~~-G~~~~K~~~~g~~GvPDli~~~~~g~~~fIEvK~~~gkls 65 (103)
.|..++..+++.++.. +.--..|++.||--+-=++ +-.||.|-+|+|.|+-..-
T Consensus 232 ~enSveE~i~dhl~~~F~a~d~~F~sSGREDvDVRm--LG~GRPFvlEl~N~rr~~~ 286 (433)
T KOG2364 232 KENSVEEDIKDHLKEFFSADDVVFISSGREDVDVRM--LGTGRPFVLELKNPRRNLG 286 (433)
T ss_pred CCCCHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEE--CCCCCCEEEECCCCCCCCH
T ss_conf 455488999999986437001465147875301475--0589835998578541213
No 93
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622 DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.
Probab=20.48 E-value=51 Score=16.01 Aligned_cols=51 Identities=16% Similarity=0.182 Sum_probs=31.8
Q ss_pred CCCEEEEECCCCCEEE-------------EEEECCC-----CCCCHHHHHHHHHHHHCCCEEEEECCHHH
Q ss_conf 8743999906982999-------------9997689-----88688999999999978988999859899
Q gi|254780128|r 39 GCPDRLIITPNGGLWW-------------IEVKKPT-----GRLSHQQMSEIEELRRRGQRVKVLVSMEE 90 (103)
Q Consensus 39 GvPDli~~~~~g~~~f-------------IEvK~~~-----gkls~~Q~~~~~~l~~~G~~~~Vv~s~ed 90 (103)
-.||+..+.|+|..-- .. +++. +..+..+......=..-|+.|+|++..|.
T Consensus 62 ~HPD~~~~~P~~~~~~~~~de~~~~~~g~a~-~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~ 130 (216)
T TIGR00678 62 NHPDLHRLEPEGQSKSLTADEAAEGEEGSAK-RRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAER 130 (216)
T ss_pred CCCCEEEEEEECCCCCCCHHHHHHHHCCCCC-CCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHH
T ss_conf 9982378742347777776458976256421-13678787278999999986064214751799767323
Done!