Query 000431
Match_columns 1515
No_of_seqs 310 out of 1976
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 08:25:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000431.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000431hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15628 RRM_DME: RRM in Demet 100.0 2.9E-67 6.3E-72 497.7 8.3 103 1399-1501 1-103 (103)
2 COG0177 Nth Predicted EndoIII- 100.0 5.5E-39 1.2E-43 341.2 16.4 182 962-1176 28-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 1.2E-37 2.6E-42 330.5 17.0 180 963-1175 29-208 (211)
4 TIGR01084 mutY A/G-specific ad 100.0 9.5E-34 2.1E-38 311.1 18.7 194 963-1188 26-219 (275)
5 PRK10880 adenine DNA glycosyla 100.0 8.8E-34 1.9E-38 320.0 17.8 185 963-1176 30-214 (350)
6 TIGR01083 nth endonuclease III 100.0 2.5E-32 5.5E-37 284.1 16.7 166 963-1161 26-191 (191)
7 PRK13910 DNA glycosylase MutY; 100.0 5.5E-32 1.2E-36 299.1 18.2 171 972-1177 1-173 (289)
8 COG2231 Uncharacterized protei 100.0 2.9E-31 6.3E-36 279.9 15.7 182 966-1174 33-214 (215)
9 PRK13913 3-methyladenine DNA g 100.0 4.5E-30 9.7E-35 274.7 16.8 183 963-1156 30-216 (218)
10 KOG1921 Endonuclease III [Repl 100.0 1.3E-28 2.7E-33 264.6 13.2 180 963-1173 78-260 (286)
11 COG1194 MutY A/G-specific DNA 99.9 1.1E-27 2.5E-32 268.4 14.6 183 963-1177 34-220 (342)
12 smart00478 ENDO3c endonuclease 99.9 5.7E-25 1.2E-29 218.3 17.0 148 972-1151 1-148 (149)
13 cd00056 ENDO3c endonuclease II 99.9 3.3E-24 7.1E-29 214.4 15.4 156 966-1150 3-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 1.3E-21 2.8E-26 208.8 13.3 139 961-1118 35-185 (208)
15 KOG2457 A/G-specific adenine D 99.8 1.7E-21 3.8E-26 218.8 9.1 182 966-1176 128-311 (555)
16 TIGR00588 ogg 8-oxoguanine DNA 99.8 2.3E-19 5E-24 200.5 15.4 134 963-1100 119-264 (310)
17 COG0122 AlkA 3-methyladenine D 99.7 7.7E-18 1.7E-22 186.9 12.9 150 963-1118 105-260 (285)
18 TIGR03252 uncharacterized HhH- 99.7 2.3E-17 5E-22 172.9 10.3 112 962-1078 17-135 (177)
19 PRK10308 3-methyl-adenine DNA 99.7 4.3E-16 9.4E-21 172.8 13.6 141 963-1118 113-262 (283)
20 PF00730 HhH-GPD: HhH-GPD supe 99.6 6.2E-15 1.3E-19 139.6 8.4 107 968-1118 1-107 (108)
21 KOG2875 8-oxoguanine DNA glyco 99.6 7.5E-15 1.6E-19 161.6 9.9 127 967-1097 121-258 (323)
22 KOG1918 3-methyladenine DNA gl 99.5 4E-14 8.7E-19 152.0 7.4 150 963-1118 75-227 (254)
23 COG1059 Thermostable 8-oxoguan 98.8 1.5E-08 3.2E-13 108.0 10.7 122 964-1103 40-166 (210)
24 PF15629 Perm-CXXC: Permuted s 98.8 2.4E-09 5.3E-14 85.5 1.3 31 1366-1396 1-32 (32)
25 PF00633 HHH: Helix-hairpin-he 96.8 0.00079 1.7E-08 53.7 2.4 25 1051-1077 6-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 95.7 0.0044 9.6E-08 44.3 0.9 17 1154-1170 1-17 (17)
27 PF09674 DUF2400: Protein of u 94.8 0.02 4.4E-07 64.0 3.3 54 1024-1103 143-196 (232)
28 smart00525 FES FES domain. iro 94.8 0.014 3E-07 44.7 1.2 23 1153-1175 1-23 (26)
29 TIGR02757 conserved hypothetic 93.6 0.054 1.2E-06 60.7 3.3 52 1025-1103 142-193 (229)
30 PRK10353 3-methyl-adenine DNA 85.3 5.3 0.00011 44.2 9.8 65 970-1038 38-104 (187)
31 smart00278 HhH1 Helix-hairpin- 84.9 0.67 1.5E-05 35.7 2.1 20 1059-1078 2-21 (26)
32 PF12826 HHH_2: Helix-hairpin- 84.4 1.4 3E-05 40.3 4.2 40 1032-1077 15-54 (64)
33 PF03352 Adenine_glyco: Methyl 83.3 2.5 5.4E-05 46.3 6.3 69 970-1042 33-106 (179)
34 PRK13901 ruvA Holliday junctio 76.8 7.6 0.00016 43.2 7.4 65 995-1080 59-129 (196)
35 PF14716 HHH_8: Helix-hairpin- 76.6 9.9 0.00022 35.1 7.0 58 1010-1077 9-66 (68)
36 TIGR00426 competence protein C 75.7 5 0.00011 36.7 4.8 58 1003-1077 9-66 (69)
37 TIGR00624 tag DNA-3-methyladen 75.2 22 0.00047 39.3 10.2 68 967-1038 34-103 (179)
38 PF09171 DUF1886: Domain of un 73.2 7.9 0.00017 44.5 6.6 133 1010-1156 77-232 (246)
39 COG2818 Tag 3-methyladenine DN 72.7 14 0.0003 41.2 8.0 64 976-1043 45-113 (188)
40 TIGR00608 radc DNA repair prot 69.8 7.8 0.00017 43.5 5.5 61 1006-1075 13-77 (218)
41 PRK00024 hypothetical protein; 69.3 7.5 0.00016 43.6 5.3 61 1006-1075 23-83 (224)
42 PF14520 HHH_5: Helix-hairpin- 67.3 13 0.00029 33.3 5.4 33 1041-1077 25-57 (60)
43 PRK02515 psbU photosystem II c 64.6 9.6 0.00021 40.4 4.6 52 1003-1076 54-105 (132)
44 PRK14606 ruvA Holliday junctio 64.5 22 0.00047 39.2 7.5 22 1057-1078 107-128 (188)
45 PRK00076 recR recombination pr 63.8 6.4 0.00014 43.8 3.4 28 1053-1080 6-33 (196)
46 PRK13844 recombination protein 63.3 6.7 0.00014 43.9 3.4 28 1053-1080 10-37 (200)
47 TIGR00615 recR recombination p 62.9 6.9 0.00015 43.6 3.4 27 1053-1079 6-32 (195)
48 PF14490 HHH_4: Helix-hairpin- 57.8 16 0.00035 35.6 4.6 57 1008-1076 7-64 (94)
49 PRK14605 ruvA Holliday junctio 56.8 32 0.0007 38.0 7.2 65 995-1076 60-126 (194)
50 PF14520 HHH_5: Helix-hairpin- 56.5 8.9 0.00019 34.4 2.4 26 1056-1081 3-28 (60)
51 COG0632 RuvA Holliday junction 56.1 8.2 0.00018 43.1 2.6 22 1057-1078 107-128 (201)
52 COG0353 RecR Recombinational D 55.2 11 0.00023 42.3 3.2 27 1054-1080 8-34 (198)
53 PRK14602 ruvA Holliday junctio 55.1 14 0.00031 41.0 4.2 21 1057-1077 108-128 (203)
54 PRK00116 ruvA Holliday junctio 54.9 20 0.00044 39.2 5.3 21 1057-1077 107-127 (192)
55 PRK14973 DNA topoisomerase I; 54.8 23 0.00049 47.3 6.6 98 996-1100 821-919 (936)
56 TIGR00575 dnlj DNA ligase, NAD 52.7 38 0.00081 43.7 7.8 31 1000-1033 456-486 (652)
57 TIGR00084 ruvA Holliday juncti 52.7 19 0.0004 39.7 4.6 66 995-1077 59-126 (191)
58 PRK14600 ruvA Holliday junctio 51.5 33 0.00071 37.9 6.2 20 1057-1077 107-126 (186)
59 COG2003 RadC DNA repair protei 51.1 29 0.00064 39.6 5.9 60 1006-1074 23-82 (224)
60 PRK14603 ruvA Holliday junctio 50.9 20 0.00044 39.7 4.5 21 1057-1077 106-126 (197)
61 PRK14601 ruvA Holliday junctio 49.8 13 0.00027 41.0 2.7 24 1057-1080 107-130 (183)
62 TIGR01259 comE comEA protein. 49.7 34 0.00074 35.2 5.6 58 1002-1077 60-117 (120)
63 PRK14604 ruvA Holliday junctio 49.2 22 0.00049 39.4 4.5 22 1057-1078 107-128 (195)
64 smart00483 POLXc DNA polymeras 49.0 23 0.00049 41.9 4.8 51 1019-1074 54-105 (334)
65 COG1555 ComEA DNA uptake prote 48.0 29 0.00062 37.1 4.9 54 1004-1075 91-144 (149)
66 PF11731 Cdd1: Pathogenicity l 47.3 17 0.00037 36.5 3.0 26 1056-1081 10-35 (93)
67 PF02371 Transposase_20: Trans 46.9 14 0.00031 35.4 2.3 42 1058-1102 2-43 (87)
68 PRK07945 hypothetical protein; 43.4 35 0.00076 40.3 5.2 61 1010-1077 8-68 (335)
69 PRK07956 ligA NAD-dependent DN 43.1 91 0.002 40.5 9.1 20 1058-1077 543-562 (665)
70 cd04370 BAH BAH, or Bromo Adja 41.0 13 0.00027 35.9 1.0 64 1419-1493 59-122 (123)
71 smart00483 POLXc DNA polymeras 40.6 58 0.0012 38.6 6.4 56 1011-1077 12-67 (334)
72 PRK14351 ligA NAD-dependent DN 38.4 1.2E+02 0.0026 39.7 9.1 28 1000-1030 486-513 (689)
73 PRK00116 ruvA Holliday junctio 37.1 27 0.00059 38.3 2.9 20 1057-1076 72-91 (192)
74 PF03568 Peptidase_C50: Peptid 36.8 32 0.00069 41.3 3.6 36 582-623 62-98 (383)
75 TIGR00084 ruvA Holliday juncti 35.5 30 0.00065 38.2 2.9 22 1055-1076 69-90 (191)
76 PF12836 HHH_3: Helix-hairpin- 33.4 39 0.00085 31.0 2.8 21 1057-1077 13-33 (65)
77 PF12836 HHH_3: Helix-hairpin- 33.1 68 0.0015 29.5 4.3 52 1005-1074 9-60 (65)
78 PRK14605 ruvA Holliday junctio 32.9 34 0.00074 37.8 2.8 23 1055-1077 70-92 (194)
79 cd00141 NT_POLXc Nucleotidyltr 32.3 75 0.0016 37.3 5.6 19 1059-1077 46-64 (307)
80 PF14229 DUF4332: Domain of un 31.4 1.4E+02 0.003 30.9 6.6 60 996-1080 14-75 (122)
81 TIGR01259 comE comEA protein. 31.4 41 0.0009 34.6 2.9 21 1057-1077 67-87 (120)
82 PRK14350 ligA NAD-dependent DN 31.2 72 0.0016 41.5 5.6 22 1057-1078 540-561 (669)
83 COG1555 ComEA DNA uptake prote 30.8 39 0.00085 36.1 2.7 22 1057-1078 96-117 (149)
84 PF10391 DNA_pol_lambd_f: Fing 28.9 45 0.00097 30.2 2.4 20 1058-1077 2-21 (52)
85 cd00141 NT_POLXc Nucleotidyltr 28.5 47 0.001 38.8 3.1 50 1020-1075 52-102 (307)
86 PF11798 IMS_HHH: IMS family H 27.9 42 0.0009 27.5 1.8 15 1060-1074 13-27 (32)
87 TIGR01083 nth endonuclease III 27.8 27 0.00059 37.8 1.0 55 601-655 2-56 (191)
88 PRK13482 DNA integrity scannin 27.5 78 0.0017 38.5 4.7 39 1030-1074 297-335 (352)
89 PF05559 DUF763: Protein of un 26.6 1.6E+02 0.0035 35.5 6.9 22 1057-1078 268-289 (319)
90 COG1796 POL4 DNA polymerase IV 23.3 1.5E+02 0.0032 35.9 5.8 58 1010-1077 13-72 (326)
91 smart00279 HhH2 Helix-hairpin- 22.3 58 0.0013 27.5 1.7 16 1060-1075 18-33 (36)
92 TIGR01448 recD_rel helicase, p 22.2 3.3E+02 0.0071 35.8 9.1 56 1009-1076 143-199 (720)
93 COG0272 Lig NAD-dependent DNA 21.8 1.5E+02 0.0033 38.8 5.9 57 1011-1077 506-562 (667)
94 PRK08097 ligB NAD-dependent DN 21.4 2.6E+02 0.0056 36.1 7.7 30 1044-1077 510-539 (562)
95 cd00080 HhH2_motif Helix-hairp 21.0 46 0.00099 31.6 1.0 20 1058-1077 22-41 (75)
96 PRK13901 ruvA Holliday junctio 20.5 80 0.0017 35.5 2.9 22 1055-1076 69-90 (196)
97 TIGR00426 competence protein C 20.5 96 0.0021 28.5 2.9 21 1057-1077 15-36 (69)
98 PRK14600 ruvA Holliday junctio 20.3 78 0.0017 35.1 2.7 22 1055-1076 70-91 (186)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=2.9e-67 Score=497.67 Aligned_cols=103 Identities=67% Similarity=1.197 Sum_probs=102.1
Q ss_pred eeEEeecccccCCCCCCCccceeeeeeeeccCCCCCCcccchhhhhcccceEEEecCChhhhhcccCHHHHHHHHhccce
Q 000431 1399 GTILIPCRTANRGRFPLNGTYFQVNEVFADHETSHHPINVPRHTIANLRREIVCFGSSATTLFNALDMRQIQEYFWRGFV 1478 (1515)
Q Consensus 1399 GTiLIPCRTAMRGsFPLNGTYFQvNEVFADh~SS~nPI~VpR~~IwnL~Rr~VYFGTSV~SIfkGlt~eeIq~cFwkG~V 1478 (1515)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
T Consensus 1 gtiLiPCrtAmrg~FPLnGTYFQ~nEVFaD~~Ss~~Pi~vpr~~iw~L~rr~vYfGtsv~SIfrGls~~eIq~cF~~G~V 80 (103)
T PF15628_consen 1 GTILIPCRTAMRGSFPLNGTYFQVNEVFADHESSRNPIDVPRELIWNLPRRIVYFGTSVSSIFRGLSREEIQQCFWKGFV 80 (103)
T ss_pred CceEeeehhhhCCccccCceEEEEEEEEeccccccCCeeccHHHhhcCCceEEEecCcHHHHhcccCHHHHHHHHhcCcE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeccccccCCCcccccccccCC
Q 000431 1479 CVRGFDRRYRCPRPLVNRLHCSP 1501 (1515)
Q Consensus 1479 CVRgFDr~TR~PrPL~~rlH~~~ 1501 (1515)
|||||||+||+||||++|||+++
T Consensus 81 CVR~FDr~Tr~PrpL~~rLH~~~ 103 (103)
T PF15628_consen 81 CVRGFDRKTRAPRPLCARLHFPA 103 (103)
T ss_pred EEeecccccCCCcchhhhccCCC
Confidence 99999999999999999999985
No 2
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.5e-39 Score=341.19 Aligned_cols=182 Identities=30% Similarity=0.434 Sum_probs=170.7
Q ss_pred CccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 000431 962 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 1041 (1515)
Q Consensus 962 k~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~G 1041 (1515)
.+..-+|..||+|||.=+.+.++..+|.+ .++||++|+.+++++|+++|+.+|||++||++|+++++.|+++||
T Consensus 28 ~pf~lLva~iLSaqttD~~vn~at~~Lf~------~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~ 101 (211)
T COG0177 28 DPFELLVAVILSAQTTDEVVNKATPALFK------RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFG 101 (211)
T ss_pred CcHHHHHHHHHhccCchHHHHHHHHHHHH------HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcC
Confidence 36667899999999999999999999974 567999999999999999999999999999999999999999999
Q ss_pred CCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchh
Q 000431 1042 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 1121 (1515)
Q Consensus 1042 GiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E 1121 (1515)
| .+|.+ +++|++|||||+|||++||.++||.|+|+|||||.||++||||++ ..+|++++..|++++|
T Consensus 102 g-------~vP~~--~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP--- 168 (211)
T COG0177 102 G-------EVPDT--REELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIP--- 168 (211)
T ss_pred C-------CCCch--HHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC---
Confidence 8 78888 999999999999999999999999999999999999999999998 5799999999999998
Q ss_pred hhhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhhh
Q 000431 1122 KIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1176 (1515)
Q Consensus 1122 ~IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYass 1176 (1515)
+++|. .+|.+||.|||.+|++++|+|+.||+++.|+++...
T Consensus 169 ---~~~~~-----------~~h~~lI~~GR~iC~ar~P~C~~C~l~~~C~~~~~~ 209 (211)
T COG0177 169 ---KELWT-----------DLHHWLILHGRYICKARKPRCEECPLADLCPSAGKT 209 (211)
T ss_pred ---HHHHH-----------HHHHHHHHhhhhhccCCCCCcCcccchhhCchhccc
Confidence 55664 999999999999999999999999999999998764
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1.2e-37 Score=330.51 Aligned_cols=180 Identities=21% Similarity=0.213 Sum_probs=164.1
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
+..-+|++||+|||+|.++.+++.+|.. .+|||++|++++.++|+++|+++|||++||++|+++|+.+.++||+
T Consensus 29 p~e~lvs~iLsq~t~~~~v~~~~~~L~~------~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~ 102 (211)
T PRK10702 29 PFELLIAVLLSAQATDVSVNKATAKLYP------VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG 102 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHHH------HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC
Confidence 4555889999999999999999999963 5899999999999999999999999999999999999999998887
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1122 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~ 1122 (1515)
.+|.+ +++|++|||||+|||+|||+|+||+++||||+||.||+.|+||.+. .++++++..++..+|
T Consensus 103 -------~~p~~--~~~Ll~lpGVG~ktA~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~-~~~~~~~~~l~~~lp---- 168 (211)
T PRK10702 103 -------EVPED--RAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPG-KNVEQVEEKLLKVVP---- 168 (211)
T ss_pred -------CCCch--HHHHhcCCcccHHHHHHHHHHHcCCCcccccchHHHHHHHhCCCCC-CCHHHHHHHHHHhCC----
Confidence 46655 8999999999999999999999999999999999999999999875 578999999988887
Q ss_pred hhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhh
Q 000431 1123 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFAS 1175 (1515)
Q Consensus 1123 IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYas 1175 (1515)
++.| .++|++||+||+.+|++++|+|+.|||++.|+||.+
T Consensus 169 --~~~~-----------~~~~~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 169 --AEFK-----------VDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred --chHH-----------HHHHHHHHHHhHHHcCCCCCCCCCCcChhhcCcccc
Confidence 3334 389999999999999999999999999999998654
No 4
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=100.00 E-value=9.5e-34 Score=311.11 Aligned_cols=194 Identities=19% Similarity=0.209 Sum_probs=163.4
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
+....|++||+|||+|++|.+++.+|.+ .+||+++|++++.++|.++|+++|||+ ||++|+++|+.|.++||+
T Consensus 26 py~vlvseIL~QQT~v~~v~~~~~rl~~------~fpt~~~La~a~~eeL~~~~~~lG~y~-RAr~L~~~A~~i~~~~~g 98 (275)
T TIGR01084 26 PYRVWLSEVMLQQTQVATVIPYFERFLE------RFPTVQALANAPQDEVLKLWEGLGYYA-RARNLHKAAQEVVEEFGG 98 (275)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHH------hCCCHHHHHCcCHHHHHHHHHHCCcHH-HHHHHHHHHHHHHHHcCC
Confidence 4455789999999999999999999974 589999999999999999999999995 999999999999999987
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1122 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~ 1122 (1515)
.+|.+ +++|++|||||+|||+|||+|+||+++++||+||.||+.|++.+....++.+++..+..+.. +
T Consensus 99 -------~~p~~--~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~--~- 166 (275)
T TIGR01084 99 -------EFPQD--FEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAE--S- 166 (275)
T ss_pred -------CCcHH--HHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHH--H-
Confidence 46755 89999999999999999999999999999999999999999766554556666665433221 0
Q ss_pred hhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhhhcccccccCCCCC
Q 000431 1123 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAVASARFALPGPS 1188 (1515)
Q Consensus 1123 IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYass~asaRlaLp~pe 1188 (1515)
.++...+..||++||+||+.+|++++|+|+.|||+..|.+|.... ...+|...
T Consensus 167 ----------~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~---~~~~p~~~ 219 (275)
T TIGR01084 167 ----------LLPKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGT---WEEYPVKK 219 (275)
T ss_pred ----------HCChhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCC---HhhcCCCC
Confidence 112345679999999999999999999999999999999998753 23455443
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=8.8e-34 Score=320.03 Aligned_cols=185 Identities=18% Similarity=0.198 Sum_probs=159.6
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
+..-.|++||+|||+|++|..++.+|.+ .|||+++|++|+.++|.++|+++|||+ ||++|+++|+.|+++|||
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~------~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g 102 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMA------RFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGG 102 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHH------HCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCC
Confidence 3445789999999999999999999974 689999999999999999999999997 999999999999999987
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1122 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~ 1122 (1515)
.+|.+ +++|++|||||+|||+|||+|+||+++++||+||.||+.|++.+.....+.++++.+.++..
T Consensus 103 -------~~p~~--~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~---- 169 (350)
T PRK10880 103 -------EFPET--FEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSE---- 169 (350)
T ss_pred -------Cchhh--HHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHH----
Confidence 46655 89999999999999999999999999999999999999998554433455666665543321
Q ss_pred hhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhhh
Q 000431 1123 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1176 (1515)
Q Consensus 1123 IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYass 1176 (1515)
. .++...+.+||++||+||+.+|++++|+|..|||+..|.+|+..
T Consensus 170 ---~------l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~ 214 (350)
T PRK10880 170 ---Q------VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANH 214 (350)
T ss_pred ---H------hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcC
Confidence 1 11235667999999999999999999999999999999999876
No 6
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.98 E-value=2.5e-32 Score=284.07 Aligned_cols=166 Identities=27% Similarity=0.250 Sum_probs=150.5
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
+...+|++||+|||+|+++.+++.+|.+ .+|||++|+.++.++|+++|+++||+++||++|+++|+.+.+++|+
T Consensus 26 pf~~Li~~ILsqqt~~~~~~~~~~~l~~------~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~ 99 (191)
T TIGR01083 26 PFELLVATILSAQATDKSVNKATKKLFE------VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG 99 (191)
T ss_pred HHHHHHHHHHHhhCcHHHHHHHHHHHHH------HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCC
Confidence 4566889999999999999999999974 5899999999999999999999999999999999999999998876
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1122 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~ 1122 (1515)
.+|. ++++|++|||||+|||+|||+|+|++++||||+||.|++.|+||... .++++++..++.++|
T Consensus 100 -------~~~~--~~~~L~~l~GIG~ktA~~ill~~~~~~~~~vD~~v~Ri~~r~g~~~~-~~~~~~~~~l~~~~p---- 165 (191)
T TIGR01083 100 -------EVPE--DREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSKG-KDPDKVEEELLKLIP---- 165 (191)
T ss_pred -------CCch--HHHHHHhCCCCcHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCC-CCHHHHHHHHHHHCC----
Confidence 3443 48999999999999999999999999999999999999999999865 578999999988887
Q ss_pred hhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCC
Q 000431 1123 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNC 1161 (1515)
Q Consensus 1123 IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnC 1161 (1515)
.. .+.+||++||+||+.+|++++|+|
T Consensus 166 --~~-----------~~~~~h~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 166 --RE-----------FWTKLHHWLILHGRYTCKARKPLC 191 (191)
T ss_pred --ch-----------hHHHHHHHHHHHhHHhcCCCCCCC
Confidence 22 245999999999999999999999
No 7
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.98 E-value=5.5e-32 Score=299.11 Aligned_cols=171 Identities=22% Similarity=0.315 Sum_probs=148.3
Q ss_pred ecccccHHHHHH-HHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhc
Q 000431 972 NTVQQDWDLLRR-IYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN 1050 (1515)
Q Consensus 972 LsQQTSWdnVrk-a~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~ 1050 (1515)
|.|||..++|.. +|.+|.+ .|||+++|++|++++|.++|+++|||+ ||++|+++|+.|.++|+| .
T Consensus 1 mlQQT~v~~v~~~yy~rf~~------~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g-------~ 66 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLE------AFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHS-------Q 66 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHH------HCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCC-------C
Confidence 579999999975 9999974 699999999999999999999999996 999999999999999887 5
Q ss_pred CCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhc-CCCCCCCChHHHHHHHHhhCCchhhhhhhhhc
Q 000431 1051 VPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRL-GWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWP 1129 (1515)
Q Consensus 1051 VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RL-GLVp~k~sPEeLEk~LeeL~P~~E~IqKeLW~ 1129 (1515)
+|.+ +++|++|||||+|||++||+|+||+++++||+||.||+.|+ |+... ..+.+++.....++|
T Consensus 67 ~P~~--~~~L~~LpGIG~kTA~aIl~~af~~~~~~VD~nV~RVl~Rl~g~~~~-~~~~~l~~~~~~~l~----------- 132 (289)
T PRK13910 67 LPND--YQSLLKLPGIGAYTANAILCFGFREKSACVDANIKRVLLRLFGLDPN-IHAKDLQIKANDFLN----------- 132 (289)
T ss_pred CChh--HHHHHhCCCCCHHHHHHHHHHHCCCCcCcccHHHHHHHHHHhcCCCC-ccHHHHHHHHHHhCC-----------
Confidence 7776 89999999999999999999999999999999999999997 77542 344444433333333
Q ss_pred ccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhhhc
Q 000431 1130 RLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAV 1177 (1515)
Q Consensus 1130 RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYass~ 1177 (1515)
...++.+|++||+||+.+|++ +|+|+.|||++.|.+|....
T Consensus 133 ------~~~~~~~nqaLm~~Ga~iC~~-~P~C~~CPl~~~C~~~~~~~ 173 (289)
T PRK13910 133 ------LNESFNHNQALIDLGALICSP-KPKCAICPLNPYCLGKNNPE 173 (289)
T ss_pred ------ccchHHHHHHHHHHhHHHcCC-CCCCCCCcChhhhhhhhcCC
Confidence 234579999999999999999 79999999999999998754
No 8
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.97 E-value=2.9e-31 Score=279.92 Aligned_cols=182 Identities=24% Similarity=0.427 Sum_probs=161.4
Q ss_pred cceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCCh
Q 000431 966 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDL 1045 (1515)
Q Consensus 966 ~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDL 1045 (1515)
-++|+||+|+|+|++|.+++++|+. .+..++++|..++.++|+++||+.|||++||+||+++...+...|.++
T Consensus 33 iiigAILtQNT~WknvekAlenLk~-----~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~-- 105 (215)
T COG2231 33 IIIGAILTQNTSWKNVEKALENLKN-----EGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL-- 105 (215)
T ss_pred HHHHHHHhccccHHHHHHHHHHHHH-----cccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh--
Confidence 4779999999999999999999975 567789999999999999999999999999999999999998876542
Q ss_pred hhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhhhhh
Q 000431 1046 EWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQM 1125 (1515)
Q Consensus 1046 E~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~IqK 1125 (1515)
+ .+-...+|++|++|+|||..|||.||+|+|++|+|+||.+.+|++.|||.+..+ +|+++++.+++-+|.
T Consensus 106 ~---~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k-~ydeik~~fe~~l~~------ 175 (215)
T COG2231 106 E---SFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEK-KYDEIKELFEENLPE------ 175 (215)
T ss_pred h---ccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHHHHHHHHhcccccc-cHHHHHHHHHhcchh------
Confidence 2 333444799999999999999999999999999999999999999999999765 899999888776651
Q ss_pred hhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhh
Q 000431 1126 YLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFA 1174 (1515)
Q Consensus 1126 eLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYa 1174 (1515)
+...+.+||.+|+.|||.+|+. +|.|+.|||...|.++.
T Consensus 176 ---------~~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 176 ---------NLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred ---------HHHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 2335789999999999999987 59999999999999874
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.97 E-value=4.5e-30 Score=274.71 Aligned_cols=183 Identities=15% Similarity=0.176 Sum_probs=148.8
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhccc-CCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSH-DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 1041 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~-e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~G 1041 (1515)
+...+|++||+|||+|++|.+++.+|++++. +...+++|++|+.++.++|+++|+++||+++||++|+++|+.+.+++|
T Consensus 30 ~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g 109 (218)
T PRK13913 30 KFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFG 109 (218)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcC
Confidence 3456899999999999999999999975321 112467999999999999999999999999999999999999999987
Q ss_pred CCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchh
Q 000431 1042 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 1121 (1515)
Q Consensus 1042 GiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E 1121 (1515)
++ +.+. ..+++++|++|||||+|||++||+|+|++|+|+||+|+.||+.|+||.. .+|++++..++..++ +
T Consensus 110 ~~--~~~~---~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~y~~~~~~~~~~l~--~ 180 (218)
T PRK13913 110 SF--ENFK---QEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQ--E 180 (218)
T ss_pred Cc--hhcc---CchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CCHHHHHHHHHHhhh--h
Confidence 63 3332 2356999999999999999999999999999999999999999999976 479999988887653 1
Q ss_pred hhhhhhhcccccC---ChhhHHHHHHHHHHHhHHhccC
Q 000431 1122 KIQMYLWPRLCYL---DQKTLYELHYQMITFGKIFCKK 1156 (1515)
Q Consensus 1122 ~IqKeLW~RL~~~---D~e~l~ELH~lLIdFGR~ICtA 1156 (1515)
.+.+ +... -.. +...+.+||.+|++||+.+|.-
T Consensus 181 ~~~~-~~~~-~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 181 NLNS-ALAL-YENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred hhhh-hhcc-ccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 1110 0000 011 2357899999999999999964
No 10
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.95 E-value=1.3e-28 Score=264.61 Aligned_cols=180 Identities=26% Similarity=0.388 Sum_probs=165.2
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
....+++.+|+-||.-+....++.||++ .+.+|+++|+++++..|.++|.++|||++||.||+..|+.+.++|+|
T Consensus 78 RfqvLv~lmLSSQTKDevt~~Am~rL~~-----~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~g 152 (286)
T KOG1921|consen 78 RFQVLVGLMLSSQTKDEVTAAAMLRLKE-----YGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDG 152 (286)
T ss_pred hHHHHHHHHHhcchHHHHHHHHHHHHHH-----hcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCC
Confidence 3344779999999997777889999986 45789999999999999999999999999999999999999999998
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCe-eeecchHHHHHHHhcCCCCCC-CChHHHHHHHHhhCCch
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRLGWVPLQ-PLPGDLHIHLLKEYPVM 1120 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrp-vFPVDTHV~RIL~RLGLVp~k-~sPEeLEk~LeeL~P~~ 1120 (1515)
++|++ .+.|++|||||+|+|..+|..|+|.- .+-||+||+||++||||++.+ .+|++++..|+.++|
T Consensus 153 -------DIP~~--v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktkspE~TR~aLq~wLP-- 221 (286)
T KOG1921|consen 153 -------DIPDT--VEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDTKTKSPEQTRVALQQWLP-- 221 (286)
T ss_pred -------CCchh--HHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhcccccccCCHHHHHHHHHHhCc--
Confidence 79988 89999999999999999999999985 899999999999999999854 459999999999998
Q ss_pred hhhhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCC-cccchhh
Q 000431 1121 DKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPL-RGECKHF 1173 (1515)
Q Consensus 1121 E~IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPL-r~~C~yY 1173 (1515)
+.+|. ++|.+|+.||+.||++++|+|+.|.+ ++.|+..
T Consensus 222 ----k~lW~-----------eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss 260 (286)
T KOG1921|consen 222 ----KSLWV-----------EINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSS 260 (286)
T ss_pred ----HHHHh-----------hhhceeecccceeeecCCCCccccccCcccCchh
Confidence 77785 99999999999999999999999999 6999973
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.95 E-value=1.1e-27 Score=268.45 Aligned_cols=183 Identities=20% Similarity=0.262 Sum_probs=156.7
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
+=+-.|.+||.|||..+.|..+|.++.+ .|||+++||+|+.+||..+|.++|||. ||++|+.+|+.|+++|||
T Consensus 34 PY~VwvSEiMLQQT~v~~Vi~yy~~fl~------rfPti~~LA~A~~~evl~~W~gLGYys-RArnL~~~A~~v~~~~~G 106 (342)
T COG1194 34 PYRVWVSEIMLQQTQVATVIPYYERFLE------RFPTIKALAAAPEDEVLKAWEGLGYYS-RARNLHKAAQEVVERHGG 106 (342)
T ss_pred cceehhHHHHhhhccHhhhhhhHHHHHH------hCCCHHHHhcCCHHHHHHHHHhcChHH-HHHHHHHHHHHHHHHcCC
Confidence 3344679999999999999999999974 799999999999999999999999776 999999999999999999
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCC----hHHHHHHHHhhCC
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPL----PGDLHIHLLKEYP 1118 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~s----PEeLEk~LeeL~P 1118 (1515)
.+|.+ .+.|.+|||||+|||.+||.|+|+++...||+||.||+.|+.-+..... ...+...++.++.
T Consensus 107 -------~~P~~--~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ll~ 177 (342)
T COG1194 107 -------EFPDD--EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLT 177 (342)
T ss_pred -------CCCCC--HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHHhcC
Confidence 69988 7999999999999999999999999999999999999999955443222 2233333333221
Q ss_pred chhhhhhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhhhc
Q 000431 1119 VMDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAV 1177 (1515)
Q Consensus 1119 ~~E~IqKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYass~ 1177 (1515)
....+.+|+++||++|+.||++++|+|..|||+..|..|..+.
T Consensus 178 ----------------p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~ 220 (342)
T COG1194 178 ----------------PDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGT 220 (342)
T ss_pred ----------------CCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCC
Confidence 1222789999999999999999999999999999999998864
No 12
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.93 E-value=5.7e-25 Score=218.29 Aligned_cols=148 Identities=30% Similarity=0.345 Sum_probs=133.8
Q ss_pred ecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcC
Q 000431 972 NTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNV 1051 (1515)
Q Consensus 972 LsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~V 1051 (1515)
|+|||+|+++.+++.+|.+ .+++|++|+.++.++|.++|+++||+++||++|+++++.+.+.+++ .+
T Consensus 1 l~qq~~~~~a~~~~~~l~~------~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~-------~~ 67 (149)
T smart00478 1 LSQQTSDEAVNKATERLFE------KFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG-------EV 67 (149)
T ss_pred CCCcccHHHHHHHHHHHHH------HCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-------Cc
Confidence 5899999999999999975 4789999999999999999999999999999999999999998765 23
Q ss_pred CchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhhhhhhhhccc
Q 000431 1052 PPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRL 1131 (1515)
Q Consensus 1052 P~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~IqKeLW~RL 1131 (1515)
+ +.+++|++|||||+|||+|||+|+|+++++|||+||.|++.|+|+++..+++++++.+++.++| ..
T Consensus 68 ~--~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p------~~----- 134 (149)
T smart00478 68 P--DDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP------KE----- 134 (149)
T ss_pred c--HHHHHHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCC------HH-----
Confidence 4 3589999999999999999999999999999999999999999999877789999999998887 22
Q ss_pred ccCChhhHHHHHHHHHHHhH
Q 000431 1132 CYLDQKTLYELHYQMITFGK 1151 (1515)
Q Consensus 1132 ~~~D~e~l~ELH~lLIdFGR 1151 (1515)
.++.||++++.||+
T Consensus 135 ------~~~~~~~~~l~~g~ 148 (149)
T smart00478 135 ------DWRELNLLLIDFGR 148 (149)
T ss_pred ------HHHHHHHHHHHHcC
Confidence 34589999999997
No 13
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.91 E-value=3.3e-24 Score=214.35 Aligned_cols=156 Identities=29% Similarity=0.359 Sum_probs=137.0
Q ss_pred cceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCCh
Q 000431 966 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDL 1045 (1515)
Q Consensus 966 ~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDL 1045 (1515)
.++.+||.||++++++.+++.+|.++ .+ |||++|+.++.++|.+++.++| ++.||++|+++++.+.+++++...
T Consensus 3 ~Li~~il~q~~s~~~a~~~~~~l~~~----~g-pt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~ 76 (158)
T cd00056 3 VLVSEILSQQTTDKAVNKAYERLFER----YG-PTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVL 76 (158)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHH----hC-CCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccC
Confidence 35788999999999999999999752 12 9999999999999999999999 788999999999999998876322
Q ss_pred hhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhhhhh
Q 000431 1046 EWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQM 1125 (1515)
Q Consensus 1046 E~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~IqK 1125 (1515)
+.+++++.|++|||||+|||+|||+|+++.++||||+|+.|++.|+|+++..+++++++..+..+.|
T Consensus 77 ------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~------- 143 (158)
T cd00056 77 ------DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP------- 143 (158)
T ss_pred ------CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCC-------
Confidence 6677899999999999999999999999988999999999999999997666788999988888775
Q ss_pred hhhcccccCChhhHHHHHHHHHHHh
Q 000431 1126 YLWPRLCYLDQKTLYELHYQMITFG 1150 (1515)
Q Consensus 1126 eLW~RL~~~D~e~l~ELH~lLIdFG 1150 (1515)
......+|++||+||
T Consensus 144 ----------~~~~~~~~~~l~~~g 158 (158)
T cd00056 144 ----------KPYWGEANQALMDLG 158 (158)
T ss_pred ----------HHHHHHHHHHHHHcC
Confidence 123458999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.86 E-value=1.3e-21 Score=208.81 Aligned_cols=139 Identities=16% Similarity=0.025 Sum_probs=116.6
Q ss_pred CCccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcC--ChHHHHHHHHHHHHHH--
Q 000431 961 TKKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERG--QQNIIAGRIKEFLNRL-- 1036 (1515)
Q Consensus 961 ~k~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lG--FynqKAkyIk~LAr~I-- 1036 (1515)
..+...++.+||+|||+|.++.+++.+|. ++.+ .++.++|+++|+++| |+++||++|+++++.+
T Consensus 35 ~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-----------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~ 102 (208)
T PRK01229 35 EDLFSELSFCILTANSSAEGGIKAQKEIG-----------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGK 102 (208)
T ss_pred CChHHHHHHHHhcCcCcHHHHHHHHHhcC-----------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHH
Confidence 44667789999999999999999999995 2456 899999999999995 9999999999999874
Q ss_pred -HHHhCCCChhhhhcCCchHHHHHHH-cCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCC------CCChHH
Q 000431 1037 -VELHGSIDLEWLRNVPPDKVKEYLL-DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPL------QPLPGD 1108 (1515)
Q Consensus 1037 -ve~~GGiDLE~Lr~VP~DEAREeLL-SLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~------k~sPEe 1108 (1515)
.+.+. ...+..++|++|+ +|||||+|||++||++.+.+++|+||+||.|++.|+||++. ..+|.+
T Consensus 103 l~~~~~-------~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~ 175 (208)
T PRK01229 103 LKEIIK-------ADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLE 175 (208)
T ss_pred HHHHHh-------ccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHH
Confidence 33320 1223456799999 99999999999999766569999999999999999999975 257999
Q ss_pred HHHHHHhhCC
Q 000431 1109 LHIHLLKEYP 1118 (1515)
Q Consensus 1109 LEk~LeeL~P 1118 (1515)
++..|.++.+
T Consensus 176 ~E~~l~~~~~ 185 (208)
T PRK01229 176 IEEILREIAE 185 (208)
T ss_pred HHHHHHHHHH
Confidence 9998887664
No 15
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.84 E-value=1.7e-21 Score=218.84 Aligned_cols=182 Identities=16% Similarity=0.219 Sum_probs=155.9
Q ss_pred cceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCH-HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCC
Q 000431 966 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADE-SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSID 1044 (1515)
Q Consensus 966 ~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~-EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiD 1044 (1515)
..|..||.|||....|.+.|.+..+ ..||..+|+.|+. +++..+|.++|||. |+++|++-|+.+++.++|
T Consensus 128 VwVSEiMLQQTrV~TV~~YYt~WMq------kwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~g-- 198 (555)
T KOG2457|consen 128 VWVSEIMLQQTRVQTVMKYYTRWMQ------KWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTEG-- 198 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------hCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCCC--
Confidence 3578999999999999999999874 7899999999998 88999999999997 999999999999999988
Q ss_pred hhhhhcCCchHHHHHHHc-CCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhhh
Q 000431 1045 LEWLRNVPPDKVKEYLLD-IEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKI 1123 (1515)
Q Consensus 1045 LE~Lr~VP~DEAREeLLS-LpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~I 1123 (1515)
.+|.. -+.|.+ |||||+|||.+|+.++|+.+.-+||.||.|++.|.--+....+..+.-..++++.
T Consensus 199 -----e~Prt--a~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~~wkLA------ 265 (555)
T KOG2457|consen 199 -----EFPRT--ASSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQSSWKLA------ 265 (555)
T ss_pred -----CCCCh--HHHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHHHHHHH------
Confidence 68876 356665 9999999999999999999999999999999999755544444444443333322
Q ss_pred hhhhhcccccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhhhhh
Q 000431 1124 QMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1176 (1515)
Q Consensus 1124 qKeLW~RL~~~D~e~l~ELH~lLIdFGR~ICtARkPnCdaCPLr~~C~yYass 1176 (1515)
-..+|...+++||+++|++|+.+||+.+|.|..||+...|+.|...
T Consensus 266 -------~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q~~ 311 (555)
T KOG2457|consen 266 -------AQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQLS 311 (555)
T ss_pred -------HHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHhHh
Confidence 1245778899999999999999999999999999999999999853
No 16
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=99.81 E-value=2.3e-19 Score=200.50 Aligned_cols=134 Identities=22% Similarity=0.261 Sum_probs=115.4
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhc-ccC--------CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHH
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEER-SHD--------KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFL 1033 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrER-g~e--------~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LA 1033 (1515)
+...++.+|++||+++.++.+++++|.++ +.. ...||+|++|+.++.++ .|+.+||.. ||++|+++|
T Consensus 119 ~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g~-Ra~~I~~~A 194 (310)
T TIGR00588 119 PFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLGY-RARYIRETA 194 (310)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCHH-HHHHHHHHH
Confidence 44557899999999999999999999654 211 23589999999976553 478899954 899999999
Q ss_pred HHHHHHhCCC-ChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCe-eeecchHHHHHHHhc-CCC
Q 000431 1034 NRLVELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRL-GWV 1100 (1515)
Q Consensus 1034 r~Ive~~GGi-DLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrp-vFPVDTHV~RIL~RL-GLV 1100 (1515)
+.+.+++++. +|+.|..++.++++++|++|||||+|||+|||+|+|+++ +||||+||+|++.|+ |+.
T Consensus 195 ~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~ 264 (310)
T TIGR00588 195 RALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWH 264 (310)
T ss_pred HHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhccc
Confidence 9999987664 788888999999999999999999999999999999997 899999999999998 553
No 17
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.74 E-value=7.7e-18 Score=186.93 Aligned_cols=150 Identities=19% Similarity=0.197 Sum_probs=122.8
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccC----CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHD----KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVE 1038 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e----~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive 1038 (1515)
+...++.+|+.||.|.+.+.+++++|.+...+ ...||+|++|+.++++.| +.+|++..||+||+++|+++.+
T Consensus 105 ~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l----~~~g~s~~Ka~yi~~~A~~~~~ 180 (285)
T COG0122 105 PFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEAL----RRCGLSGRKAEYIISLARAAAE 180 (285)
T ss_pred HHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHH----HHhCCcHHHHHHHHHHHHHHHc
Confidence 45568899999999999999999999654211 123899999999999975 6889999999999999999987
Q ss_pred HhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCe-eeec-chHHHHHHHhcCCCCCCCChHHHHHHHHhh
Q 000431 1039 LHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPV-DVNVGRIAVRLGWVPLQPLPGDLHIHLLKE 1116 (1515)
Q Consensus 1039 ~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrp-vFPV-DTHV~RIL~RLGLVp~k~sPEeLEk~LeeL 1116 (1515)
|.+|++.+..++.++++++|++|+|||+|||+|||+|++|++ +||+ |.+++|.+.+++..+...+...+....+.+
T Consensus 181 --g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w 258 (285)
T COG0122 181 --GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERW 258 (285)
T ss_pred --CCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCchHHHHHHHHhcc
Confidence 568999999999999999999999999999999999999986 9995 788888888887333333332334444444
Q ss_pred CC
Q 000431 1117 YP 1118 (1515)
Q Consensus 1117 ~P 1118 (1515)
-|
T Consensus 259 ~p 260 (285)
T COG0122 259 GP 260 (285)
T ss_pred cC
Confidence 44
No 18
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=99.71 E-value=2.3e-17 Score=172.86 Aligned_cols=112 Identities=15% Similarity=0.069 Sum_probs=98.7
Q ss_pred CccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhc----CChHHHHHHHHHHHHHHH
Q 000431 962 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKER----GQQNIIAGRIKEFLNRLV 1037 (1515)
Q Consensus 962 k~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~l----GFynqKAkyIk~LAr~Iv 1037 (1515)
.+...+|++||+|||+|++|.+++.+|..+ .+.+||++|+.++.++|+++|++. |||++||++|+++++.|+
T Consensus 17 ~pFelLVa~ILSQqTtd~nv~kA~~~L~~~----~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~ii 92 (177)
T TIGR03252 17 DPFALLTGMLLDQQVPMERAFAGPHKIARR----MGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVV 92 (177)
T ss_pred ChHHHHHHHHHhccCcHHHHHHHHHHHHHH----hCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHH
Confidence 356778999999999999999999999532 345899999999999999999876 999999999999999999
Q ss_pred HHhCCCChhhhhc---CCchHHHHHHHcCCCCCHHHHHHHHHHh
Q 000431 1038 ELHGSIDLEWLRN---VPPDKVKEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1038 e~~GGiDLE~Lr~---VP~DEAREeLLSLpGIGpKTADcILLFa 1078 (1515)
++||| +++.|.. .+..+++++|++|||||+|||++||.+.
T Consensus 93 e~y~G-~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l 135 (177)
T TIGR03252 93 DTYDG-DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALL 135 (177)
T ss_pred HHhCC-ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 99987 7777765 3456789999999999999999999863
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.66 E-value=4.3e-16 Score=172.79 Aligned_cols=141 Identities=14% Similarity=0.075 Sum_probs=115.7
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhc-ccC------CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHH
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEER-SHD------KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNR 1035 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrER-g~e------~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~ 1035 (1515)
+...++.+|+.||.+...+.++..++.++ +.. ...||+|++|++++.++| +.+||+++||++|+++|+.
T Consensus 113 ~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL----~~~Gl~~~Ra~~L~~lA~~ 188 (283)
T PRK10308 113 AFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQAL----KALGMPLKRAEALIHLANA 188 (283)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHH----HHCCCCHHHHHHHHHHHHH
Confidence 44557899999999999999999988654 332 246899999999999986 5789999999999999999
Q ss_pred HHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCe-ee-ecchHHHHHHHhcCCCCCCCChHHHHHHH
Q 000431 1036 LVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AF-PVDVNVGRIAVRLGWVPLQPLPGDLHIHL 1113 (1515)
Q Consensus 1036 Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrp-vF-PVDTHV~RIL~RLGLVp~k~sPEeLEk~L 1113 (1515)
+.+ |.++++... +.+++++.|++|||||+|||+||++|+||++ +| +.|.+++|.+ + ..++++++...
T Consensus 189 i~~--g~l~l~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~----~~~~~~~~~~a 257 (283)
T PRK10308 189 ALE--GTLPLTIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P----GMTPAQIRRYA 257 (283)
T ss_pred HHc--CCCCccccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c----cCCHHHHHHHH
Confidence 987 667776543 4578899999999999999999999999996 77 6799999854 1 23567777777
Q ss_pred HhhCC
Q 000431 1114 LKEYP 1118 (1515)
Q Consensus 1114 eeL~P 1118 (1515)
+.+-|
T Consensus 258 ~~w~P 262 (283)
T PRK10308 258 ERWKP 262 (283)
T ss_pred HhcCC
Confidence 76666
No 20
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=99.56 E-value=6.2e-15 Score=139.59 Aligned_cols=107 Identities=25% Similarity=0.241 Sum_probs=92.4
Q ss_pred eeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhh
Q 000431 968 KNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEW 1047 (1515)
Q Consensus 968 VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~ 1047 (1515)
|.+||+||++++++.+++.+|.++ +++|||++|+.+++++|.++|+++||++.||++|+++++.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~----~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~---------- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFER----YGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL---------- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHH----HSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH----------
T ss_pred CeeeecCcCcHHHHHHHHHHHHHH----hcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh----------
Confidence 467999999999999999999753 459999999999999999999999999999999999999887
Q ss_pred hhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCC
Q 000431 1048 LRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYP 1118 (1515)
Q Consensus 1048 Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P 1118 (1515)
+...+++|+|+|+.|++.|+|+++..+++++++..+++.+|
T Consensus 67 ------------------------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~ 107 (108)
T PF00730_consen 67 ------------------------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWP 107 (108)
T ss_dssp ------------------------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGT
T ss_pred ------------------------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCc
Confidence 22225899999999999999999877789999988877654
No 21
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.56 E-value=7.5e-15 Score=161.63 Aligned_cols=127 Identities=23% Similarity=0.259 Sum_probs=110.4
Q ss_pred ceeeeecccccHHHHHHHHHhhhhc-c--------cCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHH
Q 000431 967 KKNSDNTVQQDWDLLRRIYSTGEER-S--------HDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLV 1037 (1515)
Q Consensus 967 ~VgAILsQQTSWdnVrka~~RLrER-g--------~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Iv 1037 (1515)
++..|+++|.+...+.++.++|... + .+..+||+.++|+. .++++-||.+||.. ||+||...|++|+
T Consensus 121 lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGY-RAkYI~~ta~~l~ 196 (323)
T KOG2875|consen 121 LFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGY-RAKYISATARALQ 196 (323)
T ss_pred HHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcch-hHHHHHHHHHHHH
Confidence 5678999999999999999877432 1 23468999999986 66777889999988 9999999999999
Q ss_pred HHhCC-CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCe-eeecchHHHHHHHhc
Q 000431 1038 ELHGS-IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRL 1097 (1515)
Q Consensus 1038 e~~GG-iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrp-vFPVDTHV~RIL~RL 1097 (1515)
++.|+ -.|..|++++.++|++.|+.|||||+|+||||+++++++. ++|||+||.||+.-+
T Consensus 197 ~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y 258 (323)
T KOG2875|consen 197 EKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDY 258 (323)
T ss_pred HhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcc
Confidence 99988 3566777889999999999999999999999999999986 999999999999944
No 22
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.48 E-value=4e-14 Score=152.02 Aligned_cols=150 Identities=17% Similarity=0.146 Sum_probs=123.6
Q ss_pred ccccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000431 963 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1042 (1515)
Q Consensus 963 ~k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GG 1042 (1515)
+.-+++.+|+.||.+-+++..+++||.........+++|+.+..++.++| +.|||+.+|+-||+.+|.+..+.+ -
T Consensus 75 Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~l----rkcG~S~rK~~yLh~lA~~~~ng~-I 149 (254)
T KOG1918|consen 75 PFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEEL----RKCGFSKRKASYLHSLAEAYTNGY-I 149 (254)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHHH----HHhCcchhhHHHHHHHHHHHhcCC-C
Confidence 45568899999999999999999999654333478999999999999985 789999999999999999988753 3
Q ss_pred CChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCe-eeecch-HHHHHHHhc-CCCCCCCChHHHHHHHHhhCC
Q 000431 1043 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDV-NVGRIAVRL-GWVPLQPLPGDLHIHLLKEYP 1118 (1515)
Q Consensus 1043 iDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrp-vFPVDT-HV~RIL~RL-GLVp~k~sPEeLEk~LeeL~P 1118 (1515)
...+.+.+++.+++.+.|+.++|||+||+.|+|.|+|+|+ ++|+|. -|++-+..| |+-+ .+.+.+++++-+..-|
T Consensus 150 ~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~-~p~~~evekl~e~~kp 227 (254)
T KOG1918|consen 150 PSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP-LPLPKEVEKLCEKCKP 227 (254)
T ss_pred CchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCC-CCchHHHHHHhhhccc
Confidence 4667778899999999999999999999999999999997 999965 555555555 5544 3567777777666665
No 23
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.83 E-value=1.5e-08 Score=108.01 Aligned_cols=122 Identities=20% Similarity=0.154 Sum_probs=98.3
Q ss_pred cccceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcC--ChHHHHHHHHHHHHHHHHHhC
Q 000431 964 TTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERG--QQNIIAGRIKEFLNRLVELHG 1041 (1515)
Q Consensus 964 k~~~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lG--FynqKAkyIk~LAr~Ive~~G 1041 (1515)
.+.+.=.||+.|+++....++.+.+. +.+..++.+||++.|+.+| |++.||+||..+-+.+-
T Consensus 40 f~ELsFCILTANsSA~~~~~~q~~lG------------~gfly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~---- 103 (210)
T COG1059 40 FKELSFCILTANSSATMGLRAQNELG------------DGFLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFD---- 103 (210)
T ss_pred HHHHHHHhccccchHHHHHHHHHHhc------------cccccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHH----
Confidence 34455678999999999999999885 3455678999999999996 89999999999655542
Q ss_pred CCChhhhhcCCchH--HHHHHH-cCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCC
Q 000431 1042 SIDLEWLRNVPPDK--VKEYLL-DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 1103 (1515)
Q Consensus 1042 GiDLE~Lr~VP~DE--AREeLL-SLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k 1103 (1515)
++..+-..+..+ +|++|+ .|+|||.|-|+++|....-..+.++|.|+.|.+.|+|++...
T Consensus 104 --~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~ 166 (210)
T COG1059 104 --DLKIIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDEN 166 (210)
T ss_pred --HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccC
Confidence 234444444333 899999 999999999999998865577889999999999999998653
No 24
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=98.76 E-value=2.4e-09 Score=85.47 Aligned_cols=31 Identities=55% Similarity=1.114 Sum_probs=29.8
Q ss_pred CCcccCCcCC-CccCCcccccCccccccccce
Q 000431 1366 PQYRCNSKDS-KLCNSEICYSCNSVCERNAGI 1396 (1515)
Q Consensus 1366 p~~~c~s~~~-~lc~~~~c~~C~s~rE~~~~~ 1396 (1515)
|+++|+|+++ +||+++|||+||||||+++|+
T Consensus 1 Pe~~C~sqe~gkLC~~~tCfsCNsiREa~sQ~ 32 (32)
T PF15629_consen 1 PERRCNSQESGKLCDEETCFSCNSIREANSQT 32 (32)
T ss_pred CcccccccccccccCCccccccccHhHHhccC
Confidence 7999999999 999999999999999999986
No 25
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=96.83 E-value=0.00079 Score=53.74 Aligned_cols=25 Identities=24% Similarity=0.542 Sum_probs=21.0
Q ss_pred CCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1051 VPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1051 VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
+|.+ +++|++|||||+|||++|+.|
T Consensus 6 ~pas--~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 6 IPAS--IEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HTSS--HHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCC--HHHHHhCCCcCHHHHHHHHhC
Confidence 4555 799999999999999999976
No 26
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=95.68 E-value=0.0044 Score=44.32 Aligned_cols=17 Identities=47% Similarity=1.302 Sum_probs=11.6
Q ss_pred ccCCCCCCCCCCCcccc
Q 000431 1154 CKKRSPNCGACPLRGEC 1170 (1515)
Q Consensus 1154 CtARkPnCdaCPLr~~C 1170 (1515)
|++++|+|+.|||++.|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999988
No 27
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=94.84 E-value=0.02 Score=63.95 Aligned_cols=54 Identities=24% Similarity=0.462 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCC
Q 000431 1024 IIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 1103 (1515)
Q Consensus 1024 qKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k 1103 (1515)
.=+|+|.-+++|++.+..++|+.-+..+++.++ .+|+||||.||+.+||++..+
T Consensus 143 SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps~L--------------------------iiPLDtHv~~var~LGL~~rk 196 (232)
T PF09674_consen 143 SACKRLNMFLRWMVRKDSPVDFGLWSSIDPSDL--------------------------IIPLDTHVFRVARKLGLLKRK 196 (232)
T ss_pred cHHHHHHHHHHhhccCCCCCCCcCCCCCCHHHc--------------------------cccchHhHHHHHHHcCCccCC
Confidence 357899999999998765688888888887642 689999999999999999754
No 28
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=94.75 E-value=0.014 Score=44.71 Aligned_cols=23 Identities=35% Similarity=1.083 Sum_probs=20.5
Q ss_pred hccCCCCCCCCCCCcccchhhhh
Q 000431 1153 FCKKRSPNCGACPLRGECKHFAS 1175 (1515)
Q Consensus 1153 ICtARkPnCdaCPLr~~C~yYas 1175 (1515)
+|++++|+|+.|||+..|++|..
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~~ 23 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYXX 23 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhhc
Confidence 69999999999999999997543
No 29
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=93.57 E-value=0.054 Score=60.66 Aligned_cols=52 Identities=25% Similarity=0.425 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCCC
Q 000431 1025 IAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 1103 (1515)
Q Consensus 1025 KAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~k 1103 (1515)
=+|+|--+++|++.+- ++||.-+..+++.+ -++|+||||.||+.+||+...+
T Consensus 142 a~KR~nMFLRWMVR~d-~VD~GlW~~i~ps~--------------------------LiiPLDtH~~rvar~LgL~~Rk 193 (229)
T TIGR02757 142 PLKRLNMFLRWMIRKD-EVDLGIWESFKPSD--------------------------LILPLDTHVFRIAKKLKLLKRK 193 (229)
T ss_pred hHHHHHHHHHhhccCC-CCCCcCCCCCCHHH--------------------------ceeechHhHHHHHHHhCCcccC
Confidence 3488889999999854 48888777787764 2789999999999999998753
No 30
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=85.29 E-value=5.3 Score=44.17 Aligned_cols=65 Identities=9% Similarity=0.069 Sum_probs=48.9
Q ss_pred eeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCCh--HHHHHHHHHHHHHHHH
Q 000431 970 SDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQ--NIIAGRIKEFLNRLVE 1038 (1515)
Q Consensus 970 AILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFy--nqKAkyIk~LAr~Ive 1038 (1515)
+++--=.+|..|.+-...+++ ....++++.||..++++|+.++..-|.- +.|.+.+++=|+.+.+
T Consensus 38 e~~QAGLSW~tIL~Kre~fr~----aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~ 104 (187)
T PRK10353 38 EGQQAGLSWITVLKKRENYRA----CFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ 104 (187)
T ss_pred HHhcccccHHHHHHHHHHHHH----HHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHH
Confidence 333344689999988887764 4677899999999999999999999984 4455566665666543
No 31
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=84.95 E-value=0.67 Score=35.68 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=17.5
Q ss_pred HHHcCCCCCHHHHHHHHHHh
Q 000431 1059 YLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1059 eLLSLpGIGpKTADcILLFa 1078 (1515)
.|++|+|||+|+|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998753
No 32
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=84.39 E-value=1.4 Score=40.34 Aligned_cols=40 Identities=30% Similarity=0.318 Sum_probs=28.6
Q ss_pred HHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1032 FLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1032 LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
.|+.|.+.|| +++.|...+ .++|.+++|||+++|+.|..|
T Consensus 15 ~ak~L~~~f~--sl~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFG--SLEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCS--CHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcC--CHHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 4566777776 477777653 568999999999999999776
No 33
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=83.34 E-value=2.5 Score=46.30 Aligned_cols=69 Identities=16% Similarity=0.188 Sum_probs=48.3
Q ss_pred eeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHH---HhCC
Q 000431 970 SDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQ--QNIIAGRIKEFLNRLVE---LHGS 1042 (1515)
Q Consensus 970 AILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGF--ynqKAkyIk~LAr~Ive---~~GG 1042 (1515)
.+.--=.+|..|.+-...+++ ....++++.|+..++++|++++..-|+ ++.|.+.+..=|+.+++ +||+
T Consensus 33 e~fQaGLsW~~Il~Kr~~~r~----aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~gs 106 (179)
T PF03352_consen 33 EGFQAGLSWSTILKKREAFRE----AFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFGS 106 (179)
T ss_dssp HHHTTTS-HHHHHHTHHHHHH----HTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS-
T ss_pred HHHHhhCCHHHHHHHHHHHHH----HHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcCC
Confidence 344344689999887777754 356679999999999999999999888 56677777777777654 4554
No 34
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.80 E-value=7.6 Score=43.22 Aligned_cols=65 Identities=18% Similarity=0.155 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHH------HHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCH
Q 000431 995 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIK------EFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 1068 (1515)
Q Consensus 995 ~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk------~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGp 1068 (1515)
.+||.+.++. +-...+|.--|-.-+.|-.|. +++.+|.. .| .+.|.++||||+
T Consensus 59 LYGF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--------------~D--~~~L~~vpGIGk 117 (196)
T PRK13901 59 LFGFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--------------ED--IELISKVKGIGN 117 (196)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCH
Confidence 5788877763 223344544566665665555 33333432 23 578999999999
Q ss_pred HHHHHHHHHhcC
Q 000431 1069 KSVECVRLLSLQ 1080 (1515)
Q Consensus 1069 KTADcILLFaLg 1080 (1515)
|||+-|++---+
T Consensus 118 KtAeRIIlELkd 129 (196)
T PRK13901 118 KMAGKIFLKLRG 129 (196)
T ss_pred HHHHHHHHHHHH
Confidence 999988755333
No 35
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=76.57 E-value=9.9 Score=35.07 Aligned_cols=58 Identities=17% Similarity=0.193 Sum_probs=37.3
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1010 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1010 EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
+++.++..-.|-..-|+....+++..|.. +. .+-....+.|.+|||||.++|..|--|
T Consensus 9 ~~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~---------~~i~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 9 EELADLYELQGGDPFRARAYRRAAAAIKA-LP---------YPITSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHHTSTSHHHHHHHHHHHHHHHH-SS---------S-HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHhhCCcHHHHHHHHHHHHHHh-CC---------HhHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence 44555555564344488888888888865 22 122222225999999999999988543
No 36
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=75.65 E-value=5 Score=36.70 Aligned_cols=58 Identities=24% Similarity=0.249 Sum_probs=36.2
Q ss_pred HHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1003 AVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1003 ALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
+|=.|+.++|..++..+|. .+|+.|.+.- ..+|++ .+ .++|..++|||.++|+-|+.+
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R----~~~g~~---------~s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSYR----EEYGPF---------KT--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHHH----HHcCCc---------CC--HHHHHcCCCCCHHHHHHHHhh
Confidence 3445777777665444554 4444443321 124543 12 578999999999999998765
No 37
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.17 E-value=22 Score=39.32 Aligned_cols=68 Identities=7% Similarity=0.032 Sum_probs=50.6
Q ss_pred ceeeeecccccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHH--HHHHHHHHHHHHH
Q 000431 967 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNII--AGRIKEFLNRLVE 1038 (1515)
Q Consensus 967 ~VgAILsQQTSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynqK--AkyIk~LAr~Ive 1038 (1515)
++-.++--=.+|..+.+-...+++ ....++++.||..++++|++++..-|.-+.| .+.+++=|+.+.+
T Consensus 34 L~Le~fQAGLSW~tIL~Kr~~fr~----aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 34 MSLEGFQAGLSWITVLRKRENYRR----AFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HHHHHHhCcCCHHHHHHhHHHHHH----HHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 433444444689999988888864 4577899999999999999999999986555 4456665666665
No 38
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=73.21 E-value=7.9 Score=44.45 Aligned_cols=133 Identities=13% Similarity=0.084 Sum_probs=73.5
Q ss_pred HHHHHHHHhc----CChHHHHHHHHHHHHHHHHHhCCCChhhhhc--CCchHHHHHHHcCCCCC--H-------HHHHHH
Q 000431 1010 SEIADAIKER----GQQNIIAGRIKEFLNRLVELHGSIDLEWLRN--VPPDKVKEYLLDIEGLG--L-------KSVECV 1074 (1515)
Q Consensus 1010 EELeelIR~l----GFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~--VP~DEAREeLLSLpGIG--p-------KTADcI 1074 (1515)
+++.+.|... -+.++|.++|.++...+.. +.+..... -+-..+++.|..+=|-. . |++...
T Consensus 77 ~~~~~FL~~s~~n~r~~~~KikRl~k~~~~~~~----l~l~~~~~~y~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya 152 (246)
T PF09171_consen 77 EAFIEFLSNSKYNRRLLEQKIKRLRKFCPFLEN----LSLQDNPLYYEDLEELWRELAKILNSKPESKTIVFAVKMFGYA 152 (246)
T ss_dssp HHHHHHCCC-TTS-TTHHHHHHHHHHHCCHHHT----T-HHHHHHHHCTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHH
T ss_pred HHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHH----hhhhhhhhhhhhHHHHHHHHHHHhCCCCccchhhHHHHHHHHH
Confidence 3444455432 3567799999888766533 21211111 22345566676654433 2 333344
Q ss_pred HHHhcCC--e-----eeecchHHHHHHHhcCCCCCCCChHHHHHHHHhhCCchhhhhhhhhcccccCChhhHHHHHHHHH
Q 000431 1075 RLLSLQH--I-----AFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLDQKTLYELHYQMI 1147 (1515)
Q Consensus 1075 LLFaLgr--p-----vFPVDTHV~RIL~RLGLVp~k~sPEeLEk~LeeL~P~~E~IqKeLW~RL~~~D~e~l~ELH~lLI 1147 (1515)
+..+||. + -+|||.||.++..++|++.. .++ .. . .. +......|..++....-.+.+++..||
T Consensus 153 ~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~--~~~---~~-~-~~---~~~v~~~W~~Va~~sgIpplhLDs~lW 222 (246)
T PF09171_consen 153 CRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIEC--ERE---EM-M-RT---REEVQKAWREVAKESGIPPLHLDSLLW 222 (246)
T ss_dssp HHHHCTS-----TTS-----HHHHHHHHCTTS-SS---HH---HH-H-CT---CCHHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHhcCCCCCCcccCCCCccHHHHHHHHHhccccc--cHH---hh-h-cc---HHHHHHHHHHHHhhcCCCchhhhhHHH
Confidence 4445564 2 68999999999999999864 222 11 1 12 223345788777767778899999999
Q ss_pred -HHhHHhccC
Q 000431 1148 -TFGKIFCKK 1156 (1515)
Q Consensus 1148 -dFGR~ICtA 1156 (1515)
-+|+..+..
T Consensus 223 ~l~G~~~~~~ 232 (246)
T PF09171_consen 223 PLLGRARDVK 232 (246)
T ss_dssp HHHCCHHCCT
T ss_pred Hhcccchhhh
Confidence 999988765
No 39
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=72.68 E-value=14 Score=41.16 Aligned_cols=64 Identities=14% Similarity=0.143 Sum_probs=47.9
Q ss_pred ccHHHHHHHHHhhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHH--HHHHHHHHHHHHH---HHhCCC
Q 000431 976 QDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNI--IAGRIKEFLNRLV---ELHGSI 1043 (1515)
Q Consensus 976 TSWdnVrka~~RLrERg~e~~dfPTpEALAeAd~EELeelIR~lGFynq--KAkyIk~LAr~Iv---e~~GGi 1043 (1515)
.+|..|.+-.+++++ ....++|+.||..++++++.++...|.-+. |.+.+++=|+.+. ++||++
T Consensus 45 LSW~tVL~KRe~fre----aF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 45 LSWLTVLKKREAFRE----AFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred chHHHHHHhHHHHHH----HHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 589999988888865 345679999999999999999999998655 4445555555543 466653
No 40
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.79 E-value=7.8 Score=43.49 Aligned_cols=61 Identities=25% Similarity=0.428 Sum_probs=44.5
Q ss_pred cCCHHHHHHHHHhcCChHHHHH-HHHHHHHHHHHHh---CCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHH
Q 000431 1006 CADESEIADAIKERGQQNIIAG-RIKEFLNRLVELH---GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1075 (1515)
Q Consensus 1006 eAd~EELeelIR~lGFynqKAk-yIk~LAr~Ive~~---GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcIL 1075 (1515)
.++..||.++|=..|..+ + -...+|+.+.+.| |+ |..|...+. ++|.+++|||+..|..++
T Consensus 13 ~Lsd~ELLailL~~g~~~---~~~~~~lA~~ll~~f~~~g~--l~~l~~a~~----~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 13 ALSDYELLAIILRTGTPK---GLDVLSLSKRLLDVFGRQDS--LGHLLSAPP----EELSSVPGIGEAKAIQLK 77 (218)
T ss_pred cCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccCC--HHHHHhCCH----HHHHhCcCCcHHHHHHHH
Confidence 446677777766666644 3 4568899999988 64 777777764 579999999997776654
No 41
>PRK00024 hypothetical protein; Reviewed
Probab=69.33 E-value=7.5 Score=43.59 Aligned_cols=61 Identities=20% Similarity=0.341 Sum_probs=44.2
Q ss_pred cCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHH
Q 000431 1006 CADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1075 (1515)
Q Consensus 1006 eAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcIL 1075 (1515)
.++..||.++|=..|..+ +-.+.+|+.+.++||+ |..+...+. ++|.+++|||+..|..++
T Consensus 23 ~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgs--L~~l~~as~----~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 23 ALSDAELLAILLRTGTKG---KSVLDLARELLQRFGS--LRGLLDASL----EELQSIKGIGPAKAAQLK 83 (224)
T ss_pred cCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCC--HHHHHhCCH----HHHhhccCccHHHHHHHH
Confidence 446677777665666543 3455789999988875 677777664 579999999999886654
No 42
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=67.27 E-value=13 Score=33.29 Aligned_cols=33 Identities=36% Similarity=0.370 Sum_probs=24.6
Q ss_pred CCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1041 GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1041 GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
|-.+++.|...+ .+.|..++|||+++|+-+...
T Consensus 25 G~~t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 25 GIKTLEDLANAD----PEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp TCSSHHHHHTSH----HHHHHTSTTSSHHHHHHHHHH
T ss_pred CCCcHHHHHcCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 334577777653 457999999999999987643
No 43
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=64.56 E-value=9.6 Score=40.38 Aligned_cols=52 Identities=17% Similarity=0.234 Sum_probs=33.8
Q ss_pred HHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHH
Q 000431 1003 AVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRL 1076 (1515)
Q Consensus 1003 ALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILL 1076 (1515)
+|-.|+.+++.. --|++-.+|+.|. ++|.+ .+ .+.|++++|||+++.+.+--
T Consensus 54 diN~A~~~el~~---lpGigP~~A~~IV--------~nGpf---------~s--veDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 54 DLNNSSVRAFRQ---FPGMYPTLAGKIV--------KNAPY---------DS--VEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred cCCccCHHHHHH---CCCCCHHHHHHHH--------HCCCC---------CC--HHHHHcCCCCCHHHHHHHHH
Confidence 455667776644 3677777777665 25553 12 57888899999887766543
No 44
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.47 E-value=22 Score=39.24 Aligned_cols=22 Identities=23% Similarity=0.237 Sum_probs=18.9
Q ss_pred HHHHHcCCCCCHHHHHHHHHHh
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFa 1078 (1515)
.+.|.++||||+|||+-|.+--
T Consensus 107 ~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 107 VEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHHhhCCCCCHHHHHHHHHHH
Confidence 5789999999999999887543
No 45
>PRK00076 recR recombination protein RecR; Reviewed
Probab=63.76 E-value=6.4 Score=43.79 Aligned_cols=28 Identities=32% Similarity=0.401 Sum_probs=22.2
Q ss_pred chHHHHHHHcCCCCCHHHHHHHHHHhcC
Q 000431 1053 PDKVKEYLLDIEGLGLKSVECVRLLSLQ 1080 (1515)
Q Consensus 1053 ~DEAREeLLSLpGIGpKTADcILLFaLg 1080 (1515)
-+++++.|.+|||||+|||.=+.++-+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~ 33 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQ 33 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3577899999999999999766655443
No 46
>PRK13844 recombination protein RecR; Provisional
Probab=63.34 E-value=6.7 Score=43.85 Aligned_cols=28 Identities=29% Similarity=0.278 Sum_probs=22.5
Q ss_pred chHHHHHHHcCCCCCHHHHHHHHHHhcC
Q 000431 1053 PDKVKEYLLDIEGLGLKSVECVRLLSLQ 1080 (1515)
Q Consensus 1053 ~DEAREeLLSLpGIGpKTADcILLFaLg 1080 (1515)
-+++++.|.+|||||+|+|.=+.++-+.
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~ 37 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLD 37 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3678899999999999999766665443
No 47
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.88 E-value=6.9 Score=43.55 Aligned_cols=27 Identities=30% Similarity=0.361 Sum_probs=21.7
Q ss_pred chHHHHHHHcCCCCCHHHHHHHHHHhc
Q 000431 1053 PDKVKEYLLDIEGLGLKSVECVRLLSL 1079 (1515)
Q Consensus 1053 ~DEAREeLLSLpGIGpKTADcILLFaL 1079 (1515)
-+++++.|.+|||||+|||.=+.++-+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll 32 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLL 32 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence 357789999999999999976655544
No 48
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=57.84 E-value=16 Score=35.60 Aligned_cols=57 Identities=25% Similarity=0.423 Sum_probs=36.7
Q ss_pred CHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHc-CCCCCHHHHHHHHH
Q 000431 1008 DESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLD-IEGLGLKSVECVRL 1076 (1515)
Q Consensus 1008 d~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLS-LpGIGpKTADcILL 1076 (1515)
...++...|...|+... ++..|.+.||.-.++.|++=|.. |+. +.|||-++||-|.+
T Consensus 7 ~~~~~~~~L~~~gl~~~-------~a~kl~~~yg~~ai~~l~~nPY~-----L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPK-------LAMKLYKKYGDDAIEILKENPYR-----LIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HH-------HHHHHHHHH-TTHHHHHHH-STC-----CCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHH-------HHHHHHHHHhHHHHHHHHHChHH-----HHHHccCCCHHHHHHHHH
Confidence 34567778889999873 45556666777556666666654 565 99999999988744
No 49
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.76 E-value=32 Score=38.02 Aligned_cols=65 Identities=20% Similarity=0.189 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhh-hcC-CchHHHHHHHcCCCCCHHHHH
Q 000431 995 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWL-RNV-PPDKVKEYLLDIEGLGLKSVE 1072 (1515)
Q Consensus 995 ~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~L-r~V-P~DEAREeLLSLpGIGpKTAD 1072 (1515)
.+||.+.++- +-...+|.--|.....|..|.+ .+ +.+.| ..+ ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs-------~~---~~~~l~~aI~~~D--~~~L~~vpGIGkKtAe 122 (194)
T PRK14605 60 LFGFATTEEL-----SLFETLIDVSGIGPKLGLAMLS-------AM---NAEALASAIISGN--AELLSTIPGIGKKTAS 122 (194)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHH-------hC---CHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 5788877652 2233344444665544444433 22 22221 112 223 5789999999999999
Q ss_pred HHHH
Q 000431 1073 CVRL 1076 (1515)
Q Consensus 1073 cILL 1076 (1515)
-|++
T Consensus 123 rIil 126 (194)
T PRK14605 123 RIVL 126 (194)
T ss_pred HHHH
Confidence 8653
No 50
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=56.49 E-value=8.9 Score=34.37 Aligned_cols=26 Identities=31% Similarity=0.386 Sum_probs=21.5
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHhcCC
Q 000431 1056 VKEYLLDIEGLGLKSVECVRLLSLQH 1081 (1515)
Q Consensus 1056 AREeLLSLpGIGpKTADcILLFaLgr 1081 (1515)
+.+.|++|+|||+++|..+.-.+++-
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t 28 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKT 28 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSS
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCc
Confidence 46789999999999998887776654
No 51
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=56.15 E-value=8.2 Score=43.10 Aligned_cols=22 Identities=32% Similarity=0.357 Sum_probs=19.2
Q ss_pred HHHHHcCCCCCHHHHHHHHHHh
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFa 1078 (1515)
...|.++||||+|||+-+++--
T Consensus 107 ~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHHHH
Confidence 6899999999999999887653
No 52
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=55.16 E-value=11 Score=42.30 Aligned_cols=27 Identities=30% Similarity=0.426 Sum_probs=21.2
Q ss_pred hHHHHHHHcCCCCCHHHHHHHHHHhcC
Q 000431 1054 DKVKEYLLDIEGLGLKSVECVRLLSLQ 1080 (1515)
Q Consensus 1054 DEAREeLLSLpGIGpKTADcILLFaLg 1080 (1515)
+.+++.|..|||||+|+|.=+..+.++
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHc
Confidence 567899999999999999665554443
No 53
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.11 E-value=14 Score=41.01 Aligned_cols=21 Identities=24% Similarity=0.351 Sum_probs=18.5
Q ss_pred HHHHHcCCCCCHHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLF 1077 (1515)
.+.|.++||||+|||+-|++-
T Consensus 108 ~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 108 VAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 578999999999999988754
No 54
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=54.91 E-value=20 Score=39.21 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=18.5
Q ss_pred HHHHHcCCCCCHHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLF 1077 (1515)
.+.|.++||||+|+|+.|+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 468999999999999999855
No 55
>PRK14973 DNA topoisomerase I; Provisional
Probab=54.78 E-value=23 Score=47.32 Aligned_cols=98 Identities=16% Similarity=0.099 Sum_probs=59.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHH
Q 000431 996 MDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN-RLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1074 (1515)
Q Consensus 996 ~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr-~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcI 1074 (1515)
.||-++++++.|++++|+. -.|+.--.+..+...+. .+.. -+-+.......+..+.+|++|+|||++|++-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~---~~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLAL---KTGISPETICRHAKLVCEKLGR----PVPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhc---CCCCChhhHHHHHHHHHHHhcC----CCchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 4777999999999999854 47888666666655444 3332 12222222222333566999999999999665
Q ss_pred HHHhcCCeeeecchHHHHHHHhcCCC
Q 000431 1075 RLLSLQHIAFPVDVNVGRIAVRLGWV 1100 (1515)
Q Consensus 1075 LLFaLgrpvFPVDTHV~RIL~RLGLV 1100 (1515)
-.-+.-.+.-.+-....+++.+-|+.
T Consensus 894 ~~ag~~~~e~l~~~d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSADPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccCCHHHHhhhcCCC
Confidence 44444333222222556666665653
No 56
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=52.72 E-value=38 Score=43.67 Aligned_cols=31 Identities=6% Similarity=0.097 Sum_probs=17.3
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHH
Q 000431 1000 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFL 1033 (1515)
Q Consensus 1000 TpEALAeAd~EELeelIR~lGFynqKAkyIk~LA 1033 (1515)
++++|..+..++|.++ -||....|..|.+..
T Consensus 456 ~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~I 486 (652)
T TIGR00575 456 SVADLYALKKEDLLEL---EGFGEKSAQNLLNAI 486 (652)
T ss_pred CHHHHHhcCHHHHhhc---cCccHHHHHHHHHHH
Confidence 5677777776665432 355555555554433
No 57
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=52.70 E-value=19 Score=39.72 Aligned_cols=66 Identities=21% Similarity=0.160 Sum_probs=39.7
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhc-CC-chHHHHHHHcCCCCCHHHHH
Q 000431 995 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN-VP-PDKVKEYLLDIEGLGLKSVE 1072 (1515)
Q Consensus 995 ~~dfPTpEALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~-VP-~DEAREeLLSLpGIGpKTAD 1072 (1515)
.++|.|.++- +-...+++--|....+|..|... ++.+.|.. +- .| ...|.++||||+|||+
T Consensus 59 LyGF~~~~Er-----~lF~~L~~V~GIGpK~Al~iL~~----------~~~~el~~aI~~~d--~~~L~~ipGiGkKtAe 121 (191)
T TIGR00084 59 LFGFNTLEER-----ELFKELIKVNGVGPKLALAILSN----------MSPEEFVYAIETEE--VKALVKIPGVGKKTAE 121 (191)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHhc----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 5788877652 22344555567777666665332 22222221 11 12 4679999999999999
Q ss_pred HHHHH
Q 000431 1073 CVRLL 1077 (1515)
Q Consensus 1073 cILLF 1077 (1515)
-|++-
T Consensus 122 rIile 126 (191)
T TIGR00084 122 RLLLE 126 (191)
T ss_pred HHHHH
Confidence 99843
No 58
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.52 E-value=33 Score=37.90 Aligned_cols=20 Identities=25% Similarity=0.371 Sum_probs=17.1
Q ss_pred HHHHHcCCCCCHHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLF 1077 (1515)
.+.| ++||||+|||+-|++-
T Consensus 107 ~~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 107 KAAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred Hhhe-ECCCCcHHHHHHHHHH
Confidence 4678 9999999999988754
No 59
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=51.14 E-value=29 Score=39.60 Aligned_cols=60 Identities=20% Similarity=0.325 Sum_probs=44.2
Q ss_pred cCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHH
Q 000431 1006 CADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1074 (1515)
Q Consensus 1006 eAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcI 1074 (1515)
.++..||.+++=..|- |-+-...+|+.+...||+ |..|...+ .++|.+++|||..-|--+
T Consensus 23 ~Lsd~ELLailLrtG~---~~~~~~~la~~lL~~fg~--L~~l~~a~----~~el~~v~GiG~aka~~l 82 (224)
T COG2003 23 ALSDAELLAILLRTGT---KGESVLDLAKELLQEFGS--LAELLKAS----VEELSSVKGIGLAKAIQI 82 (224)
T ss_pred hcchHHHHHHHHhcCC---CCCCHHHHHHHHHHHccc--HHHHHhCC----HHHHhhCCCccHHHHHHH
Confidence 4466777777766676 345667899999999987 66776665 468999999997655433
No 60
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.86 E-value=20 Score=39.69 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=18.3
Q ss_pred HHHHHcCCCCCHHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLF 1077 (1515)
...|.++||||+|||+-|++-
T Consensus 106 ~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 578999999999999988744
No 61
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.80 E-value=13 Score=40.99 Aligned_cols=24 Identities=21% Similarity=0.236 Sum_probs=19.8
Q ss_pred HHHHHcCCCCCHHHHHHHHHHhcC
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLSLQ 1080 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFaLg 1080 (1515)
.+.|.++||||+|||+-|++---+
T Consensus 107 ~~~L~~vpGIGkKtAeRIilELkd 130 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAELSD 130 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 578999999999999988755333
No 62
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=49.67 E-value=34 Score=35.17 Aligned_cols=58 Identities=22% Similarity=0.284 Sum_probs=37.4
Q ss_pred HHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1002 EAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1002 EALAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
-+|-.|+.++|..+ -|....+|+.|.+.-. .+|.+ .+ .++|..++|||+++++-+.-|
T Consensus 60 iniNtA~~~eL~~l---pGIG~~~A~~Ii~~R~----~~g~f---------~s--~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 60 VNINAASLEELQAL---PGIGPAKAKAIIEYRE----ENGAF---------KS--VDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred EeCCcCCHHHHhcC---CCCCHHHHHHHHHHHH----hcCCc---------CC--HHHHHcCCCCCHHHHHHHHhc
Confidence 34556677776442 4555567766655332 23442 12 578999999999999888654
No 63
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.19 E-value=22 Score=39.36 Aligned_cols=22 Identities=27% Similarity=0.333 Sum_probs=18.9
Q ss_pred HHHHHcCCCCCHHHHHHHHHHh
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFa 1078 (1515)
.+.|.++||||+|||+-|++--
T Consensus 107 ~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 107 VARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHHhhCCCCCHHHHHHHHHHH
Confidence 5789999999999999887543
No 64
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=48.97 E-value=23 Score=41.91 Aligned_cols=51 Identities=20% Similarity=0.220 Sum_probs=31.0
Q ss_pred cCChHHHHHHHHHHHHHHHHHhCCCC-hhhhhcCCchHHHHHHHcCCCCCHHHHHHH
Q 000431 1019 RGQQNIIAGRIKEFLNRLVELHGSID-LEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1074 (1515)
Q Consensus 1019 lGFynqKAkyIk~LAr~Ive~~GGiD-LE~Lr~VP~DEAREeLLSLpGIGpKTADcI 1074 (1515)
-|....-|..|.++++ .|.+. +.....-+.-.+..+|++|+|||+|||..+
T Consensus 54 pgIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 54 PGIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CCccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 3555545555555432 35554 222223334456899999999999999655
No 65
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=48.02 E-value=29 Score=37.08 Aligned_cols=54 Identities=24% Similarity=0.411 Sum_probs=36.1
Q ss_pred HHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHH
Q 000431 1004 VRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1075 (1515)
Q Consensus 1004 LAeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcIL 1075 (1515)
|=.|+.+|| ..|.++|- .||+.|.+-- +++|.| .+ .+.|...+|||+++.+-+.
T Consensus 91 iNtAs~eeL-~~lpgIG~--~kA~aIi~yR----e~~G~f---------~s--v~dL~~v~GiG~~~~ekl~ 144 (149)
T COG1555 91 INTASAEEL-QALPGIGP--KKAQAIIDYR----EENGPF---------KS--VDDLAKVKGIGPKTLEKLK 144 (149)
T ss_pred ccccCHHHH-HHCCCCCH--HHHHHHHHHH----HHcCCC---------Cc--HHHHHhccCCCHHHHHHHH
Confidence 456778887 55555664 4777666532 455643 12 6789999999999987654
No 66
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=47.26 E-value=17 Score=36.52 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=21.4
Q ss_pred HHHHHHcCCCCCHHHHHHHHHHhcCC
Q 000431 1056 VKEYLLDIEGLGLKSVECVRLLSLQH 1081 (1515)
Q Consensus 1056 AREeLLSLpGIGpKTADcILLFaLgr 1081 (1515)
....|+.|||||+.+|.-+.++++..
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCC
Confidence 46789999999999998887666654
No 67
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=46.89 E-value=14 Score=35.37 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=29.9
Q ss_pred HHHHcCCCCCHHHHHHHHHHhcCCeeeecchHHHHHHHhcCCCCC
Q 000431 1058 EYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPL 1102 (1515)
Q Consensus 1058 EeLLSLpGIGpKTADcILLFaLgrpvFPVDTHV~RIL~RLGLVp~ 1102 (1515)
+.|++|||||+-||..++....+...|+= ...+..-+|+.+.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~---~~~l~~~~Gl~P~ 43 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKS---AKQLASYAGLAPR 43 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhccc---chhhhhccccccc
Confidence 46889999999999999888744445653 3444455687764
No 68
>PRK07945 hypothetical protein; Provisional
Probab=43.41 E-value=35 Score=40.34 Aligned_cols=61 Identities=11% Similarity=0.110 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1010 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1010 EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
++++.+|.-.|=..=|++..+++|+.|.. ++-+.+..+... ..|.+|||||.-||..|.-+
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~----~~~~~~~~~~~~---g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA----LDAAERARRARA---GSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh----cChhHHHHHHhc---CCcccCCCcCHHHHHHHHHH
Confidence 45666666666544488888898888764 221112222111 16899999999999988655
No 69
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=43.10 E-value=91 Score=40.47 Aligned_cols=20 Identities=25% Similarity=0.365 Sum_probs=13.7
Q ss_pred HHHHcCCCCCHHHHHHHHHH
Q 000431 1058 EYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1058 EeLLSLpGIGpKTADcILLF 1077 (1515)
++|.+++|||+++|..|..|
T Consensus 543 eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 543 EELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred HHHhccCCcCHHHHHHHHHH
Confidence 45677777777777776555
No 70
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=40.99 E-value=13 Score=35.91 Aligned_cols=64 Identities=17% Similarity=0.216 Sum_probs=44.7
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhhcccceEEEecCChhhhhcccCHHHHHHHHhccceEeeccccccCCCccc
Q 000431 1419 YFQVNEVFADHETSHHPINVPRHTIANLRREIVCFGSSATTLFNALDMRQIQEYFWRGFVCVRGFDRRYRCPRPL 1493 (1515)
Q Consensus 1419 YFQvNEVFADh~SS~nPI~VpR~~IwnL~Rr~VYFGTSV~SIfkGlt~eeIq~cFwkG~VCVRgFDr~TR~PrPL 1493 (1515)
+|.-||||+-+....+||. .=+.++.|.+-........ ....-...-|+|=++||+.++.-|+|
T Consensus 59 ~~~~~Elf~s~~~~~i~v~------~I~gkc~V~~~~~~~~~~~-----~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 59 FALRRELFLSDHLDEIPVE------SIIGKCKVLFVSEFEGLKQ-----RPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred ccccceeEEecCccccCHH------HhccccEEEechHhhcccc-----ccccCCCCeEEEEEEECcCcceEEeC
Confidence 7999999998888877775 3355777777664433321 00112457899999999998877665
No 71
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=40.62 E-value=58 Score=38.64 Aligned_cols=56 Identities=13% Similarity=0.147 Sum_probs=36.8
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1011 EIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1011 ELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
++++++.-.|-...|+.+..+++..|.. +. .++ +. .+.|.+|||||.++|+.|--+
T Consensus 12 ~la~l~el~gen~~k~~ay~~Aa~~i~~-l~-~~i--------~~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 12 ILAENYEVFGENKRKCSYFRKAASVLKS-LP-FPI--------NS-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHHh-CC-CCC--------CC-HHHHhcCCCccHHHHHHHHHH
Confidence 4445555466555577778787777754 22 111 22 247899999999999998644
No 72
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=38.43 E-value=1.2e+02 Score=39.73 Aligned_cols=28 Identities=11% Similarity=0.099 Sum_probs=16.4
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHH
Q 000431 1000 DWEAVRCADESEIADAIKERGQQNIIAGRIK 1030 (1515)
Q Consensus 1000 TpEALAeAd~EELeelIR~lGFynqKAkyIk 1030 (1515)
++.+|..+..++|..+ -||...+|..|.
T Consensus 486 ~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll 513 (689)
T PRK14351 486 SLADLYDLTVADLAEL---EGWGETSAENLL 513 (689)
T ss_pred CHHHHHHcCHHHHhcC---cCcchhHHHHHH
Confidence 6777777777665332 366555555443
No 73
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=37.09 E-value=27 Score=38.25 Aligned_cols=20 Identities=20% Similarity=0.303 Sum_probs=17.0
Q ss_pred HHHHHcCCCCCHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRL 1076 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILL 1076 (1515)
...|+.++|||+|||..+|.
T Consensus 72 f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 46788999999999988854
No 74
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=36.83 E-value=32 Score=41.26 Aligned_cols=36 Identities=36% Similarity=0.924 Sum_probs=30.7
Q ss_pred CCchhhHHHHHHHHHHHhhhHHHHHHHHHh-hccCcccccCCC
Q 000431 582 TSNEDMEKWWQKEREVFEGRIQSFTARMHL-ILGDRRFKPWKG 623 (1515)
Q Consensus 582 G~D~~k~kwWeeER~VF~gRvdSFIArMhl-vqGDRRFSpWKG 623 (1515)
.+.++|.+||+ +|.-...|...++..|-- ..| +|||
T Consensus 62 ~t~~~kk~WW~-~R~~LD~rL~~LL~~iE~~wLG-----~wkg 98 (383)
T PF03568_consen 62 KTKEDKKKWWK-ERKALDSRLKDLLENIENSWLG-----GWKG 98 (383)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH-----HHhh
Confidence 37889999997 588899999999999987 554 8997
No 75
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=35.47 E-value=30 Score=38.16 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.5
Q ss_pred HHHHHHHcCCCCCHHHHHHHHH
Q 000431 1055 KVKEYLLDIEGLGLKSVECVRL 1076 (1515)
Q Consensus 1055 EAREeLLSLpGIGpKTADcILL 1076 (1515)
++-..|++++|||+|+|-.+|.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 4567899999999999988854
No 76
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=33.38 E-value=39 Score=30.99 Aligned_cols=21 Identities=24% Similarity=0.352 Sum_probs=17.1
Q ss_pred HHHHHcCCCCCHHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLF 1077 (1515)
.++|.++||||++.|..|+.+
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHH
Confidence 578999999999999999876
No 77
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=33.10 E-value=68 Score=29.46 Aligned_cols=52 Identities=25% Similarity=0.307 Sum_probs=29.2
Q ss_pred HcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHH
Q 000431 1005 RCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1074 (1515)
Q Consensus 1005 AeAd~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcI 1074 (1515)
-.|+.++|..+ -|+....|+.|.+.-+ .+|++ . + .++|..++|||+++.+-+
T Consensus 9 N~as~~eL~~l---pgi~~~~A~~Iv~~R~----~~G~f-------~--s--~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 9 NTASAEELQAL---PGIGPKQAKAIVEYRE----KNGPF-------K--S--LEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTS-HHHHHTS---TT--HHHHHHHHHHHH----HH-S--------S--S--GGGGGGSTT--HHHHHHH
T ss_pred ccCCHHHHHHc---CCCCHHHHHHHHHHHH----hCcCC-------C--C--HHHHhhCCCCCHHHHHHH
Confidence 35666765322 3888878887776432 34653 1 1 467999999999998765
No 78
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.87 E-value=34 Score=37.80 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=19.7
Q ss_pred HHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1055 KVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1055 EAREeLLSLpGIGpKTADcILLF 1077 (1515)
++-..|++++|||+|+|-.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh
Confidence 45678999999999999998873
No 79
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=32.33 E-value=75 Score=37.26 Aligned_cols=19 Identities=21% Similarity=0.291 Sum_probs=11.0
Q ss_pred HHHcCCCCCHHHHHHHHHH
Q 000431 1059 YLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1059 eLLSLpGIGpKTADcILLF 1077 (1515)
++.+|||||+++|+.|--+
T Consensus 46 ~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HhcCCCCccHHHHHHHHHH
Confidence 4456666666666665433
No 80
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=31.38 E-value=1.4e+02 Score=30.94 Aligned_cols=60 Identities=15% Similarity=0.106 Sum_probs=38.7
Q ss_pred CCCCCHHHHHcCCHHHHHH--HHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHH
Q 000431 996 MDSVDWEAVRCADESEIAD--AIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVEC 1073 (1515)
Q Consensus 996 ~dfPTpEALAeAd~EELee--lIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADc 1073 (1515)
.|--|+++|++++...+.. +....|.. ...+.++ ..+..|..++|||+..|..
T Consensus 14 ~GI~t~~~Ll~~~~~~~~r~~La~~~~i~----------------------~~~l~~w---~~~AdL~ri~gi~~~~a~L 68 (122)
T PF14229_consen 14 AGIKTTGDLLEAGDTPLGRKALAKKLGIS----------------------ERNLLKW---VNQADLMRIPGIGPQYAEL 68 (122)
T ss_pred cCCCcHHHHHHcCCCHHHHHHHHHhcCCC----------------------HHHHHHH---HhHHHhhhcCCCCHHHHHH
Confidence 4666889988888777655 44444443 2222222 1156788999999999877
Q ss_pred HHHHhcC
Q 000431 1074 VRLLSLQ 1080 (1515)
Q Consensus 1074 ILLFaLg 1080 (1515)
++--++.
T Consensus 69 L~~AGv~ 75 (122)
T PF14229_consen 69 LEHAGVD 75 (122)
T ss_pred HHHhCcC
Confidence 6655554
No 81
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=31.37 E-value=41 Score=34.55 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=19.2
Q ss_pred HHHHHcCCCCCHHHHHHHHHH
Q 000431 1057 KEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLF 1077 (1515)
.+.|..|||||++.|..|+.+
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 578999999999999999877
No 82
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=31.22 E-value=72 Score=41.46 Aligned_cols=22 Identities=27% Similarity=0.209 Sum_probs=19.5
Q ss_pred HHHHHcCCCCCHHHHHHHHHHh
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFa 1078 (1515)
.+.|++|+|||+++|..|..|-
T Consensus 540 ~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHHH
Confidence 4689999999999999998873
No 83
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=30.76 E-value=39 Score=36.09 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=19.4
Q ss_pred HHHHHcCCCCCHHHHHHHHHHh
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFa 1078 (1515)
.++|..|||||++.|..|.-+-
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 4678999999999999998774
No 84
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=28.93 E-value=45 Score=30.24 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=14.4
Q ss_pred HHHHcCCCCCHHHHHHHHHH
Q 000431 1058 EYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1058 EeLLSLpGIGpKTADcILLF 1077 (1515)
+.|++|.|||+.||.-....
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~ 21 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAK 21 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHT
T ss_pred cchhhcccccHHHHHHHHHh
Confidence 57899999999999776443
No 85
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=28.51 E-value=47 Score=38.84 Aligned_cols=50 Identities=32% Similarity=0.396 Sum_probs=30.9
Q ss_pred CChHHHHHHHHHHHHHHHHHhCCC-ChhhhhcCCchHHHHHHHcCCCCCHHHHHHHH
Q 000431 1020 GQQNIIAGRIKEFLNRLVELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1075 (1515)
Q Consensus 1020 GFynqKAkyIk~LAr~Ive~~GGi-DLE~Lr~VP~DEAREeLLSLpGIGpKTADcIL 1075 (1515)
|....-|..|.++.+ .|.+ .|+.|+.- .-....+|++|+|||++||..+.
T Consensus 52 giG~~ia~kI~E~~~-----tG~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 52 GIGKKIAEKIEEILE-----TGKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CccHHHHHHHHHHHH-----cCCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH
Confidence 555556666655543 1432 23444432 23447899999999999996654
No 86
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=27.86 E-value=42 Score=27.55 Aligned_cols=15 Identities=20% Similarity=0.373 Sum_probs=11.1
Q ss_pred HHcCCCCCHHHHHHH
Q 000431 1060 LLDIEGLGLKSVECV 1074 (1515)
Q Consensus 1060 LLSLpGIGpKTADcI 1074 (1515)
+..|+|||++|+.-+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 347899999999763
No 87
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=27.81 E-value=27 Score=37.84 Aligned_cols=55 Identities=15% Similarity=0.139 Sum_probs=42.2
Q ss_pred hHHHHHHHHHhhccCcccccCCCccccceeeeeeecccccccchhHHhhhhhccC
Q 000431 601 RIQSFTARMHLILGDRRFKPWKGSVVDSVVGVYLTQNVSDNLSSSAYMSLAARFP 655 (1515)
Q Consensus 601 RvdSFIArMhlvqGDRRFSpWKGSVVDSVVGVFLTQNVSDHLSSSAFMSLAAkFP 655 (1515)
+++....+|----|+.+-.-|...-...+|+..|+||.++.-...||-.|.++||
T Consensus 2 ~~~~i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~p 56 (191)
T TIGR01083 2 KAQEILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLFEVYP 56 (191)
T ss_pred hHHHHHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHCC
Confidence 3445555555555655434455677899999999999999999999999999998
No 88
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=27.48 E-value=78 Score=38.45 Aligned_cols=39 Identities=31% Similarity=0.422 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHH
Q 000431 1030 KEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1074 (1515)
Q Consensus 1030 k~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcI 1074 (1515)
+.+|+.+++.||+ |..+...+ .++|..++|||++.|..|
T Consensus 297 k~iAk~Ll~~FGS--L~~Il~As----~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 297 SAVIENLVEHFGS--LQGLLAAS----IEDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHHHHHcCC--HHHHHcCC----HHHHhhCCCcCHHHHHHH
Confidence 3578889999985 67676654 467999999999999764
No 89
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=26.57 E-value=1.6e+02 Score=35.54 Aligned_cols=22 Identities=32% Similarity=0.484 Sum_probs=19.1
Q ss_pred HHHHHcCCCCCHHHHHHHHHHh
Q 000431 1057 KEYLLDIEGLGLKSVECVRLLS 1078 (1515)
Q Consensus 1057 REeLLSLpGIGpKTADcILLFa 1078 (1515)
.++|+.++|||++|..++.+.+
T Consensus 268 feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 268 FEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred HHHHHhcCCCCHHHHHHHHHHH
Confidence 6899999999999998876653
No 90
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=23.31 E-value=1.5e+02 Score=35.93 Aligned_cols=58 Identities=22% Similarity=0.345 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHH--HHHcCCCCCHHHHHHHHHH
Q 000431 1010 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKE--YLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1010 EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEARE--eLLSLpGIGpKTADcILLF 1077 (1515)
++++.++.-.|=..-|+..-+.+|+.|... .-|+ +++.+ .++.|||||+.+|+.|.-|
T Consensus 13 e~iA~~me~~Gen~fk~~aYr~Aa~sle~~--~e~~--------~ei~e~~~~t~l~gIGk~ia~~I~e~ 72 (326)
T COG1796 13 ERIADYMELEGENPFKIRAYRKAAQSLENL--TEDL--------EEIEERGRLTELPGIGKGIAEKISEY 72 (326)
T ss_pred HHHHHHHHhcCCCccchHHHHHHHHhhhhc--ccch--------HHHHhhcccCCCCCccHHHHHHHHHH
Confidence 344455555564433777777777777542 1233 33333 4899999999999999766
No 91
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=22.34 E-value=58 Score=27.53 Aligned_cols=16 Identities=19% Similarity=0.364 Sum_probs=13.0
Q ss_pred HHcCCCCCHHHHHHHH
Q 000431 1060 LLDIEGLGLKSVECVR 1075 (1515)
Q Consensus 1060 LLSLpGIGpKTADcIL 1075 (1515)
+-.+||||+|||--+|
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 3578999999997665
No 92
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=22.20 E-value=3.3e+02 Score=35.81 Aligned_cols=56 Identities=16% Similarity=0.279 Sum_probs=36.6
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHH-cCCCCCHHHHHHHHH
Q 000431 1009 ESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLL-DIEGLGLKSVECVRL 1076 (1515)
Q Consensus 1009 ~EELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLL-SLpGIGpKTADcILL 1076 (1515)
..++...|...|+.... +.+|.+.||.-.++.|..=|.. |+ .++|||-++||.|..
T Consensus 143 ~~~~~~~L~~~gi~~~~-------a~ki~~~yg~~~~~~i~~nPY~-----L~~~i~gigF~~aD~iA~ 199 (720)
T TIGR01448 143 ERRLLAGLQGLGIGIKL-------AQRIYKFYQADTLDRVEKDPYL-----LAEDVKGIGFLTADQLAQ 199 (720)
T ss_pred HHHHHHHHHHcCCCHHH-------HHHHHHHHhHHHHHHHHhCchh-----hhhhcCCCCHHHHHHHHH
Confidence 45566677777887644 4444445665445566655543 44 699999999998754
No 93
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=21.78 E-value=1.5e+02 Score=38.77 Aligned_cols=57 Identities=21% Similarity=0.243 Sum_probs=37.7
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1011 EIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1011 ELeelIR~lGFynqKAkyIk~LAr~Ive~~GGiDLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
.|..+|-.+|....-... |+.+...||. ++.|...+ .++|.+|+|||.+.|..|.-|
T Consensus 506 ~l~r~l~aLGIr~VG~~~----Ak~La~~f~s--l~~l~~a~----~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 506 PLARFLYALGIRHVGETT----AKSLARHFGT--LEALLAAS----EEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred CHHHHHHHcCCchhhHHH----HHHHHHHhhh--HHHHHhcC----HHHHhhccchhHHHHHHHHHH
Confidence 345556667765543333 3334444543 67777665 457899999999999999776
No 94
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=21.35 E-value=2.6e+02 Score=36.09 Aligned_cols=30 Identities=10% Similarity=0.138 Sum_probs=22.7
Q ss_pred ChhhhhcCCchHHHHHHHcCCCCCHHHHHHHHHH
Q 000431 1044 DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1044 DLE~Lr~VP~DEAREeLLSLpGIGpKTADcILLF 1077 (1515)
+++.|.... .+.|.+|+|||+++|+.|..|
T Consensus 510 ~i~~l~~a~----~e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 510 SWQQLLSRS----EQQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred CHHHHHcCC----HHHHhcCCCchHHHHHHHHHH
Confidence 355555433 357999999999999999877
No 95
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=21.04 E-value=46 Score=31.62 Aligned_cols=20 Identities=15% Similarity=0.204 Sum_probs=15.9
Q ss_pred HHHHcCCCCCHHHHHHHHHH
Q 000431 1058 EYLLDIEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1058 EeLLSLpGIGpKTADcILLF 1077 (1515)
+.+-.+||||+|||.-++.-
T Consensus 22 D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred ccCCCCCcccHHHHHHHHHH
Confidence 46778999999999776643
No 96
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.45 E-value=80 Score=35.48 Aligned_cols=22 Identities=27% Similarity=0.404 Sum_probs=18.8
Q ss_pred HHHHHHHcCCCCCHHHHHHHHH
Q 000431 1055 KVKEYLLDIEGLGLKSVECVRL 1076 (1515)
Q Consensus 1055 EAREeLLSLpGIGpKTADcILL 1076 (1515)
++-+.|+++.|||||+|=.||.
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4567899999999999988874
No 97
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=20.45 E-value=96 Score=28.50 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=18.2
Q ss_pred HHHHHc-CCCCCHHHHHHHHHH
Q 000431 1057 KEYLLD-IEGLGLKSVECVRLL 1077 (1515)
Q Consensus 1057 REeLLS-LpGIGpKTADcILLF 1077 (1515)
.+.|.. ++|||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999998876
No 98
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.33 E-value=78 Score=35.06 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=18.7
Q ss_pred HHHHHHHcCCCCCHHHHHHHHH
Q 000431 1055 KVKEYLLDIEGLGLKSVECVRL 1076 (1515)
Q Consensus 1055 EAREeLLSLpGIGpKTADcILL 1076 (1515)
++-+.|+++.|||+|+|=.||.
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4467889999999999988876
Done!