Query 000414
Match_columns 1541
No_of_seqs 303 out of 1979
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 07:47:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000414.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000414hhsearch_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 3.7E-67 7.9E-72 497.5 8.3 103 1425-1527 1-103 (103)
2 COG0177 Nth Predicted EndoIII- 100.0 4.5E-39 9.8E-44 342.0 16.5 183 987-1202 27-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 1.3E-37 2.7E-42 330.5 16.7 180 989-1201 29-208 (211)
4 TIGR01084 mutY A/G-specific ad 100.0 1.6E-33 3.6E-38 309.3 18.2 185 989-1202 26-210 (275)
5 PRK10880 adenine DNA glycosyla 100.0 1.1E-33 2.3E-38 319.5 16.2 185 989-1202 30-214 (350)
6 TIGR01083 nth endonuclease III 100.0 2.1E-32 4.7E-37 284.7 15.9 166 989-1187 26-191 (191)
7 PRK13910 DNA glycosylase MutY; 100.0 1.5E-31 3.2E-36 295.9 17.9 171 998-1203 1-173 (289)
8 COG2231 Uncharacterized protei 100.0 2.6E-31 5.7E-36 280.5 15.9 182 992-1200 33-214 (215)
9 PRK13913 3-methyladenine DNA g 100.0 3.2E-30 7E-35 275.9 16.3 184 989-1182 30-216 (218)
10 KOG1921 Endonuclease III [Repl 100.0 3.7E-29 8.1E-34 268.9 13.2 181 989-1200 78-261 (286)
11 COG1194 MutY A/G-specific DNA 99.9 2.5E-27 5.3E-32 266.0 14.7 183 989-1203 34-220 (342)
12 smart00478 ENDO3c endonuclease 99.9 1.2E-24 2.6E-29 216.0 16.7 148 998-1177 1-148 (149)
13 cd00056 ENDO3c endonuclease II 99.9 5.5E-24 1.2E-28 212.8 15.3 156 992-1176 3-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 1.6E-21 3.5E-26 208.2 13.5 140 986-1144 34-185 (208)
15 KOG2457 A/G-specific adenine D 99.8 2E-20 4.4E-25 210.5 8.9 183 990-1202 126-311 (555)
16 TIGR00588 ogg 8-oxoguanine DNA 99.8 3.4E-19 7.3E-24 199.3 15.6 134 989-1126 119-264 (310)
17 COG0122 AlkA 3-methyladenine D 99.7 1.1E-17 2.4E-22 185.8 13.5 161 989-1155 105-271 (285)
18 TIGR03252 uncharacterized HhH- 99.7 2.1E-17 4.5E-22 173.4 10.4 112 988-1104 17-135 (177)
19 PRK10308 3-methyl-adenine DNA 99.6 7.7E-16 1.7E-20 170.9 13.2 151 989-1154 113-272 (283)
20 PF00730 HhH-GPD: HhH-GPD supe 99.5 1.4E-14 2.9E-19 137.3 8.9 107 994-1144 1-107 (108)
21 KOG2875 8-oxoguanine DNA glyco 99.5 2E-14 4.3E-19 158.5 10.8 127 993-1123 121-258 (323)
22 KOG1918 3-methyladenine DNA gl 99.5 5.1E-14 1.1E-18 151.4 7.2 161 989-1155 75-238 (254)
23 COG1059 Thermostable 8-oxoguan 98.8 2.7E-08 5.8E-13 106.2 10.8 122 990-1129 40-166 (210)
24 PF15629 Perm-CXXC: Permuted s 98.8 2.4E-09 5.3E-14 85.6 1.3 31 1392-1422 1-32 (32)
25 PF00633 HHH: Helix-hairpin-he 96.8 0.00084 1.8E-08 53.7 2.4 25 1077-1103 6-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 95.6 0.0047 1E-07 44.3 0.8 17 1180-1196 1-17 (17)
27 smart00525 FES FES domain. iro 94.6 0.016 3.4E-07 44.5 1.2 23 1179-1201 1-23 (26)
28 PF09674 DUF2400: Protein of u 94.3 0.031 6.8E-07 62.5 3.1 54 1050-1129 143-196 (232)
29 TIGR02757 conserved hypothetic 92.5 0.091 2E-06 58.9 3.2 52 1051-1129 142-193 (229)
30 PF12826 HHH_2: Helix-hairpin- 85.4 1.2 2.6E-05 40.8 4.2 40 1058-1103 15-54 (64)
31 smart00278 HhH1 Helix-hairpin- 84.8 0.67 1.5E-05 35.7 2.0 20 1085-1104 2-21 (26)
32 PRK10353 3-methyl-adenine DNA 84.3 6.2 0.00013 43.7 9.8 68 993-1064 35-104 (187)
33 PF03352 Adenine_glyco: Methyl 84.0 2.4 5.3E-05 46.4 6.5 72 993-1068 30-106 (179)
34 PF14716 HHH_8: Helix-hairpin- 77.8 8.8 0.00019 35.5 7.0 58 1036-1103 9-66 (68)
35 PRK13901 ruvA Holliday junctio 76.5 7.5 0.00016 43.3 7.3 62 1021-1103 59-126 (196)
36 TIGR00426 competence protein C 76.2 4.7 0.0001 36.9 4.8 58 1029-1103 9-66 (69)
37 TIGR00624 tag DNA-3-methyladen 75.2 4.9 0.00011 44.2 5.4 68 993-1064 34-103 (179)
38 PF09171 DUF1886: Domain of un 72.4 11 0.00025 43.3 7.6 122 1047-1182 92-232 (246)
39 TIGR00608 radc DNA repair prot 70.2 7.3 0.00016 43.7 5.4 63 1031-1102 12-78 (218)
40 PF14520 HHH_5: Helix-hairpin- 69.8 11 0.00024 33.9 5.4 31 1069-1103 27-57 (60)
41 PRK00024 hypothetical protein; 69.1 7.5 0.00016 43.6 5.2 63 1031-1102 22-84 (224)
42 COG2818 Tag 3-methyladenine DN 67.5 25 0.00055 39.3 8.6 66 1000-1069 43-113 (188)
43 PRK00076 recR recombination pr 65.0 5.9 0.00013 44.1 3.4 28 1079-1106 6-33 (196)
44 PRK02515 psbU photosystem II c 64.9 9.1 0.0002 40.6 4.5 53 1029-1103 54-106 (132)
45 PRK13844 recombination protein 64.3 6.2 0.00014 44.1 3.4 28 1079-1106 10-37 (200)
46 TIGR00615 recR recombination p 64.2 6.3 0.00014 43.9 3.4 28 1079-1106 6-33 (195)
47 PRK14606 ruvA Holliday junctio 63.5 23 0.00049 39.2 7.4 62 1021-1103 60-127 (188)
48 TIGR00575 dnlj DNA ligase, NAD 62.0 34 0.00074 44.0 9.6 32 1026-1060 456-487 (652)
49 PF14490 HHH_4: Helix-hairpin- 58.9 16 0.00035 35.6 4.8 57 1034-1102 7-64 (94)
50 COG0353 RecR Recombinational D 57.5 9.3 0.0002 42.8 3.2 27 1080-1106 8-34 (198)
51 PRK14973 DNA topoisomerase I; 55.9 20 0.00043 47.9 6.3 98 1022-1126 821-919 (936)
52 PRK14602 ruvA Holliday junctio 54.7 14 0.00031 41.0 4.1 21 1083-1103 108-128 (203)
53 PRK00116 ruvA Holliday junctio 54.6 20 0.00044 39.3 5.2 21 1083-1103 107-127 (192)
54 PRK14601 ruvA Holliday junctio 54.5 15 0.00032 40.5 4.1 24 1083-1106 107-130 (183)
55 PRK14605 ruvA Holliday junctio 54.3 36 0.00078 37.7 7.0 65 1021-1102 60-126 (194)
56 PRK07956 ligA NAD-dependent DN 52.6 49 0.0011 42.8 8.8 20 1084-1103 543-562 (665)
57 COG0632 RuvA Holliday junction 52.6 12 0.00027 41.8 3.3 22 1083-1104 107-128 (201)
58 COG2003 RadC DNA repair protei 51.0 29 0.00063 39.7 5.8 61 1031-1100 22-82 (224)
59 PRK14603 ruvA Holliday junctio 50.7 18 0.00039 40.1 4.1 21 1083-1103 106-126 (197)
60 smart00483 POLXc DNA polymeras 49.8 21 0.00046 42.2 4.7 52 1045-1101 54-106 (334)
61 PRK14604 ruvA Holliday junctio 48.6 23 0.00049 39.3 4.5 21 1083-1103 107-127 (195)
62 TIGR01259 comE comEA protein. 47.7 27 0.00059 35.9 4.6 58 1028-1103 60-117 (120)
63 PF11731 Cdd1: Pathogenicity l 47.1 18 0.00038 36.5 3.0 28 1081-1108 9-36 (93)
64 PRK07945 hypothetical protein; 46.1 30 0.00065 40.9 5.2 61 1036-1103 8-68 (335)
65 PF02371 Transposase_20: Trans 45.9 15 0.00033 35.2 2.4 42 1084-1128 2-43 (87)
66 PRK14600 ruvA Holliday junctio 43.1 26 0.00056 38.7 3.8 20 1083-1103 107-126 (186)
67 PRK14351 ligA NAD-dependent DN 42.0 1E+02 0.0022 40.3 9.3 29 1026-1057 486-514 (689)
68 TIGR00084 ruvA Holliday juncti 41.0 23 0.00049 39.1 3.0 66 1021-1103 59-126 (191)
69 cd04370 BAH BAH, or Bromo Adja 40.9 13 0.00028 35.9 1.0 64 1445-1519 59-122 (123)
70 PF14520 HHH_5: Helix-hairpin- 40.6 49 0.0011 29.8 4.6 36 1022-1060 24-59 (60)
71 COG1555 ComEA DNA uptake prote 39.4 46 0.001 35.6 4.9 55 1030-1102 91-145 (149)
72 PF14229 DUF4332: Domain of un 38.5 3.2E+02 0.0069 28.4 10.5 61 1022-1107 14-76 (122)
73 PF03568 Peptidase_C50: Peptid 37.1 31 0.00068 41.3 3.6 36 608-649 62-98 (383)
74 smart00483 POLXc DNA polymeras 36.8 81 0.0018 37.5 6.8 56 1037-1103 12-67 (334)
75 PRK00116 ruvA Holliday junctio 36.4 28 0.00061 38.2 2.8 20 1083-1102 72-91 (192)
76 PRK14350 ligA NAD-dependent DN 36.0 52 0.0011 42.7 5.5 22 1083-1104 540-561 (669)
77 PF12836 HHH_3: Helix-hairpin- 35.3 35 0.00076 31.4 2.8 21 1083-1103 13-33 (65)
78 TIGR00084 ruvA Holliday juncti 35.0 31 0.00066 38.1 2.8 22 1081-1102 69-90 (191)
79 PF12836 HHH_3: Helix-hairpin- 33.4 44 0.00095 30.7 3.2 53 1030-1100 8-60 (65)
80 cd00141 NT_POLXc Nucleotidyltr 32.9 48 0.001 38.8 4.1 50 1046-1101 52-102 (307)
81 TIGR01259 comE comEA protein. 32.2 39 0.00084 34.8 2.9 21 1083-1103 67-87 (120)
82 COG1555 ComEA DNA uptake prote 32.2 35 0.00076 36.5 2.7 28 1076-1104 90-117 (149)
83 PRK14605 ruvA Holliday junctio 31.9 36 0.00078 37.7 2.8 23 1081-1103 70-92 (194)
84 cd00141 NT_POLXc Nucleotidyltr 30.7 95 0.0021 36.5 6.0 57 1036-1103 8-64 (307)
85 PF05559 DUF763: Protein of un 29.7 1.3E+02 0.0028 36.4 6.8 22 1083-1104 268-289 (319)
86 PRK13482 DNA integrity scannin 27.5 84 0.0018 38.2 5.0 39 1056-1100 297-335 (352)
87 TIGR01083 nth endonuclease III 27.4 28 0.00061 37.8 1.0 55 627-681 2-56 (191)
88 PF11798 IMS_HHH: IMS family H 26.9 46 0.001 27.3 1.9 15 1086-1100 13-27 (32)
89 COG0272 Lig NAD-dependent DNA 26.8 1E+02 0.0022 40.2 5.8 64 1030-1103 499-562 (667)
90 PF10391 DNA_pol_lambd_f: Fing 24.9 58 0.0013 29.6 2.3 20 1084-1103 2-21 (52)
91 smart00279 HhH2 Helix-hairpin- 22.0 59 0.0013 27.5 1.7 16 1086-1101 18-33 (36)
92 COG1796 POL4 DNA polymerase IV 21.5 1.7E+02 0.0036 35.5 5.8 57 1037-1103 14-72 (326)
93 PRK14973 DNA topoisomerase I; 21.1 4E+02 0.0086 36.4 9.7 62 1022-1106 763-824 (936)
94 TIGR00426 competence protein C 21.0 90 0.0019 28.7 2.8 21 1083-1103 15-36 (69)
95 cd00080 HhH2_motif Helix-hairp 20.9 50 0.0011 31.4 1.3 20 1084-1103 22-41 (75)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=3.7e-67 Score=497.54 Aligned_cols=103 Identities=67% Similarity=1.197 Sum_probs=102.1
Q ss_pred eeEEeecccccCCCCCCCccceeeeeeeeccCCCCCCcccchhhhhcccceEEEecCChhhhhcccCHHHHHHHHhccce
Q 000414 1425 GTILIPCRTANRGRFPLNGTYFQVNEVFADHETSHHPINVPRHTIANLRREIVCFGSSATTLFNALDMRQIQEYFWRGFV 1504 (1541)
Q Consensus 1425 GTiLIPCRTAMRGsFPLNGTYFQvNEVFADh~SS~nPI~VpR~~IwnL~Rr~VYFGTSV~SIfkGlt~eeIq~cFwkG~V 1504 (1541)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
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 000414 1505 CVRGFDRRYRCPRPLVNRLHCSP 1527 (1541)
Q Consensus 1505 CVRgFDr~TR~PrPL~~rlH~~~ 1527 (1541)
|||||||+||+||||++|||+++
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=4.5e-39 Score=342.03 Aligned_cols=183 Identities=30% Similarity=0.431 Sum_probs=171.2
Q ss_pred CCcccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHh
Q 000414 987 TKKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELH 1066 (1541)
Q Consensus 987 ~k~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdh 1066 (1541)
..+...+|+.||+||+.-+.+.++..+|.+ .++||++|+.+++++|+++|+.+|||++||++|+++++.|+++|
T Consensus 27 ~~pf~lLva~iLSaqttD~~vn~at~~Lf~------~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~ 100 (211)
T COG0177 27 KDPFELLVAVILSAQTTDEVVNKATPALFK------RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKF 100 (211)
T ss_pred CCcHHHHHHHHHhccCchHHHHHHHHHHHH------HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHc
Confidence 346777899999999999999999999963 56799999999999999999999999999999999999999999
Q ss_pred CCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCch
Q 000414 1067 GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVM 1146 (1541)
Q Consensus 1067 GGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~ 1146 (1541)
|| .+|.+ +++|++|||||+|||++||.++||.|+|+|||||.||++||||++ ..+|++++..|++++|
T Consensus 101 ~g-------~vP~~--~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP-- 168 (211)
T COG0177 101 GG-------EVPDT--REELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIP-- 168 (211)
T ss_pred CC-------CCCch--HHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC--
Confidence 99 78888 999999999999999999999999999999999999999999998 5799999999999987
Q ss_pred hhHhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHhh
Q 000414 1147 DKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1202 (1541)
Q Consensus 1147 e~IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYasa 1202 (1541)
+++|. .+|.+||.|||.+|++++|+|+.|||++.|+++...
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 999999999999999999999999999999998753
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1.3e-37 Score=330.53 Aligned_cols=180 Identities=21% Similarity=0.210 Sum_probs=164.8
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
+...+|++||+|||+|.++.+++.+|. ..+|+|++|+++++++|+++|+++|||++||++|+++|+++.++||+
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 PFELLIAVLLSAQATDVSVNKATAKLY------PVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG 102 (211)
T ss_pred hHHHHHHHHHHhhcCHHHHHHHHHHHH------HHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC
Confidence 566789999999999999999999996 36899999999999999999999999999999999999999998887
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1148 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~ 1148 (1541)
.+|.+ +++|++|||||+|||+|||+|+||+++||||+||.||+.|+||.+. .++++++..+++.+|
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 8999999999999999999999999999999999999999999864 578999999988877
Q ss_pred HhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHh
Q 000414 1149 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFAS 1201 (1541)
Q Consensus 1149 IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYas 1201 (1541)
++.| .++|.+||+||+.+|++++|+|+.|||++.|+||.+
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 3344 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=1.6e-33 Score=309.34 Aligned_cols=185 Identities=19% Similarity=0.222 Sum_probs=161.1
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
+-..+|++||.|||+|++|..++.+|.+ .+||+++|+++++++|.++|+++|||+ ||++|+++|+.|.++||+
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 5667899999999999999999999973 589999999999999999999999995 999999999999999988
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1148 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~ 1148 (1541)
.+|.+ +++|++|||||+|||+|||+|+|+++.++||+||.||+.|++.+....+++++++.+..+.. +
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 46765 89999999999999999999999999999999999999999766554566666666433221 0
Q ss_pred HhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHhh
Q 000414 1149 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1202 (1541)
Q Consensus 1149 IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYasa 1202 (1541)
.++...++.||++||+||+.+|++++|+|+.|||+..|.+|..+
T Consensus 167 ----------~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~ 210 (275)
T TIGR01084 167 ----------LLPKADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQG 210 (275)
T ss_pred ----------HCChhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcC
Confidence 12334567999999999999999999999999999999999875
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=1.1e-33 Score=319.47 Aligned_cols=185 Identities=18% Similarity=0.198 Sum_probs=160.8
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
+-...|++||.|||+|++|..++.+|.+ .|||+++|++|++++|.++|+++|||+ ||++|+++|+.|+++|||
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 5567899999999999999999999974 689999999999999999999999997 999999999999999987
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1148 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~ 1148 (1541)
.+|.+ +++|++|||||+|||+|||+|+||+++++||+||.||+.|++.+.....+.++++.+.++..
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 HhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHhh
Q 000414 1149 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1202 (1541)
Q Consensus 1149 IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYasa 1202 (1541)
. .++...+++||++||+||+.+|++++|+|..|||+..|.+|+..
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 12345678999999999999999999999999999999999875
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=2.1e-32 Score=284.71 Aligned_cols=166 Identities=27% Similarity=0.249 Sum_probs=151.0
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
+...++++||+|||+|+++.+++.+|.+ .+|||++|+.++.++|+++|+++||+++||++|+++|+++.+++++
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 5667899999999999999999999963 5899999999999999999999999999999999999999998876
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhh
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDK 1148 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~ 1148 (1541)
.+|. ++++|++|||||+|||+|||+|+|++++||||+||.||+.|+||+.. .++++++..++.++|.
T Consensus 100 -------~~~~--~~~~L~~l~GIG~ktA~~ill~~~~~~~~~vD~~v~Ri~~r~g~~~~-~~~~~~~~~l~~~~p~--- 166 (191)
T TIGR01083 100 -------EVPE--DREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSKG-KDPDKVEEELLKLIPR--- 166 (191)
T ss_pred -------CCch--HHHHHHhCCCCcHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCC-CCHHHHHHHHHHHCCc---
Confidence 3443 48999999999999999999999999999999999999999999865 5799999999888872
Q ss_pred HhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCC
Q 000414 1149 IQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNC 1187 (1541)
Q Consensus 1149 IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~C 1187 (1541)
. .+.+||.+||+||+.+|++++|+|
T Consensus 167 ---~-----------~~~~~h~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 167 ---E-----------FWTKLHHWLILHGRYTCKARKPLC 191 (191)
T ss_pred ---h-----------hHHHHHHHHHHHhHHhcCCCCCCC
Confidence 2 246999999999999999999999
No 7
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.97 E-value=1.5e-31 Score=295.86 Aligned_cols=171 Identities=22% Similarity=0.304 Sum_probs=147.8
Q ss_pred ecccccHHHHHH-HHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhc
Q 000414 998 NTVQQDWDLLRR-IYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN 1076 (1541)
Q Consensus 998 LsQQTSWdnVrk-a~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~ 1076 (1541)
+.|||..++|.. .|.++. ..|||+++|++|+++||+++|+++|||+ ||++|+++|+.|.++|+| .
T Consensus 1 mlQQT~v~~v~~~yy~rf~------~~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g-------~ 66 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFL------EAFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHS-------Q 66 (289)
T ss_pred CCCCCcHHHhHHHHHHHHH------HHCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCC-------C
Confidence 469999999975 999996 3789999999999999999999999996 999999999999999887 5
Q ss_pred CCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhc-CCCCCCCChHHHHHHHHhhCCchhhHhhhhhh
Q 000414 1077 VPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRL-GWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWP 1155 (1541)
Q Consensus 1077 VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RL-GLVp~k~dPEEIEk~LeeL~P~~e~IqK~LW~ 1155 (1541)
+|.+ +++|++|||||+|||++||+|+||+++++||+||.||+.|+ |+... ..+.+++.....++|
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 77543 344444433333332
Q ss_pred hcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHhhh
Q 000414 1156 RLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAV 1203 (1541)
Q Consensus 1156 RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYasa~ 1203 (1541)
...++.+|++||+||+.+|++ +|+|+.|||++.|.+|..+.
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 345679999999999999999 79999999999999998754
No 8
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.97 E-value=2.6e-31 Score=280.49 Aligned_cols=182 Identities=25% Similarity=0.429 Sum_probs=161.9
Q ss_pred ccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCCh
Q 000414 992 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDL 1071 (1541)
Q Consensus 992 ~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDL 1071 (1541)
.++|+||+|||+|++|.+++++|+. ++..++++|..++.++|+++||+.|||++||+||+++...+.+.+.+ +
T Consensus 33 iiigAILtQNT~WknvekAlenLk~-----~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~--~ 105 (215)
T COG2231 33 IIIGAILTQNTSWKNVEKALENLKN-----EGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFIN--L 105 (215)
T ss_pred HHHHHHHhccccHHHHHHHHHHHHH-----cccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhh--h
Confidence 5789999999999999999999975 67788999999999999999999999999999999999999887654 2
Q ss_pred hhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhhHhh
Q 000414 1072 EWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQM 1151 (1541)
Q Consensus 1072 E~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~IqK 1151 (1541)
+ .+-+..+|++|++|+|||..|||.||+|+|++|+|+||.+.+|++.|+|.+..+ +++++++.+++-+| +
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-KYDEIKELFEENLP------E 175 (215)
T ss_pred h---ccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHHHHHHHHhcccccc-cHHHHHHHHHhcch------h
Confidence 2 344445799999999999999999999999999999999999999999998764 89999998887665 1
Q ss_pred hhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHH
Q 000414 1152 YLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFA 1200 (1541)
Q Consensus 1152 ~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYa 1200 (1541)
+...+.+||.+|+.|||.+|++ +|.|+.|||...|.++.
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 59999999999999864
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.97 E-value=3.2e-30 Score=275.94 Aligned_cols=184 Identities=15% Similarity=0.177 Sum_probs=149.6
Q ss_pred cccccccceecccccHHHHHHHHHHhhhccc-CCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSH-DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 1067 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~-e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhG 1067 (1541)
+...+|++||+|||+|++|.+++.+|.+++. +..++++|++|++++.++|+++|+++||+++||++|+++|+++.+++|
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 4567899999999999999999999964321 112567999999999999999999999999999999999999999987
Q ss_pred CCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchh
Q 000414 1068 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 1147 (1541)
Q Consensus 1068 GIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e 1147 (1541)
++ +.+ ...+++++|++|||||+|||++||+|+|++|+|+||+|++||+.|+||.. .+|++++..++..++ +
T Consensus 110 ~~--~~~---~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~y~~~~~~~~~~l~--~ 180 (218)
T PRK13913 110 SF--ENF---KQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQ--E 180 (218)
T ss_pred Cc--hhc---cCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CCHHHHHHHHHHhhh--h
Confidence 63 333 22356899999999999999999999999999999999999999999975 479999998887653 1
Q ss_pred hHhhhhhhhcc-cC-ChhhHHHHHHHHHHHhHHhccC
Q 000414 1148 KIQMYLWPRLC-YL-DQKTLYELHYQMITFGKIFCKK 1182 (1541)
Q Consensus 1148 ~IqK~LW~RL~-~l-D~edl~ELH~lLIdFGK~ICta 1182 (1541)
.+.+ +...-. .. +...+.+||.+|++|||.+|.-
T Consensus 181 ~~~~-~~~~~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 181 NLNS-ALALYENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred hhhh-hhccccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 1110 000000 00 2367899999999999999964
No 10
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.96 E-value=3.7e-29 Score=268.88 Aligned_cols=181 Identities=26% Similarity=0.381 Sum_probs=166.4
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
...++++.+|+-||.-+....++.||++ .+.+++++|+++++..|.++|.++|||++||.||+..|+.+.++|+|
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 4445789999999998888889999976 55799999999999999999999999999999999999999999998
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCc-eeecchHHHHHHhhcCCCCCC-CChHHHHHHHHhhCCch
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRLGWVPLQ-PLPGDLHIHLLKEYPVM 1146 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrp-aFPVDTHV~RIL~RLGLVp~k-~dPEEIEk~LeeL~P~~ 1146 (1541)
++|++ .+.|++|||||+|+|..+|..|+|.- .+.||+||+||++||||++.. .+||+++..|+.++|
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 359999999999988
Q ss_pred hhHhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCC-cccchhHH
Q 000414 1147 DKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPL-RGECKHFA 1200 (1541)
Q Consensus 1147 e~IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPL-R~~C~yYa 1200 (1541)
+.+|. ++|.+|+.||+.||++++|+|+.|.+ ++.|+..-
T Consensus 222 ----k~lW~-----------eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~ 261 (286)
T KOG1921|consen 222 ----KSLWV-----------EINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSF 261 (286)
T ss_pred ----HHHHh-----------hhhceeecccceeeecCCCCccccccCcccCchhh
Confidence 77775 99999999999999999999999999 69999743
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.95 E-value=2.5e-27 Score=265.96 Aligned_cols=183 Identities=20% Similarity=0.262 Sum_probs=157.9
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
+=++.|..|+.|||..+.|...|.++.+ .|||+++||+|+.+||..+|.++|||. ||++|+.+|+.|+++|||
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 6667899999999999999999999963 799999999999999999999999876 999999999999999999
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCC----hHHHHHHHHhhCC
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPL----PGDLHIHLLKEYP 1144 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~d----PEEIEk~LeeL~P 1144 (1541)
.+|++ .+.|.+|||||++||.+||.|+|+++...||+||.||+.|+.-+..... ...++..++.++.
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 69998 7999999999999999999999999999999999999999954433222 2223333333221
Q ss_pred chhhHhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHhhh
Q 000414 1145 VMDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAV 1203 (1541)
Q Consensus 1145 ~~e~IqK~LW~RL~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYasa~ 1203 (1541)
....+.+|+++||++|+.||++++|+|..|||+..|..|..+.
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 1223789999999999999999999999999999999998864
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=99.92 E-value=1.2e-24 Score=216.00 Aligned_cols=148 Identities=30% Similarity=0.345 Sum_probs=133.8
Q ss_pred ecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcC
Q 000414 998 NTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNV 1077 (1541)
Q Consensus 998 LsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~V 1077 (1541)
|+||++|+++.+++.+|.+ .+++|++|+.++.++|.++|+++||+++||++|+++++.+.+.+++ .+
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 5799999999999999974 4789999999999999999999999999999999999999988765 24
Q ss_pred CchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhhHhhhhhhhc
Q 000414 1078 PPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRL 1157 (1541)
Q Consensus 1078 PdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~IqK~LW~RL 1157 (1541)
+ +.+++|++|||||+|||+|||+|+|+++++|||+||.|++.|+|+++..+++++++.+++.++| ..
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 12
Q ss_pred ccCChhhHHHHHHHHHHHhH
Q 000414 1158 CYLDQKTLYELHYQMITFGK 1177 (1541)
Q Consensus 1158 ~~lD~edl~ELH~lLIdFGK 1177 (1541)
.++.||.+++.||+
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=5.5e-24 Score=212.77 Aligned_cols=156 Identities=29% Similarity=0.359 Sum_probs=137.3
Q ss_pred ccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCCh
Q 000414 992 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDL 1071 (1541)
Q Consensus 992 ~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDL 1071 (1541)
.++.+||.||++++++.+++.+|.++ .+ |||++|+.++.++|.+++.+.| ++.||++|+++++.+.+.+++...
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 46789999999999999999999742 12 9999999999999999999999 788999999999999998876322
Q ss_pred hhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhhHhh
Q 000414 1072 EWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQM 1151 (1541)
Q Consensus 1072 E~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~IqK 1151 (1541)
+.++++++|++|||||+|||+|||+|+++.++||||+|+.|++.|+|++...+++++++..++.+.|
T Consensus 77 ------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~------- 143 (158)
T cd00056 77 ------DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP------- 143 (158)
T ss_pred ------CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCC-------
Confidence 6677899999999999999999999999988999999999999999997666789999998888775
Q ss_pred hhhhhcccCChhhHHHHHHHHHHHh
Q 000414 1152 YLWPRLCYLDQKTLYELHYQMITFG 1176 (1541)
Q Consensus 1152 ~LW~RL~~lD~edl~ELH~lLIdFG 1176 (1541)
......+|++||+||
T Consensus 144 ----------~~~~~~~~~~l~~~g 158 (158)
T cd00056 144 ----------KPYWGEANQALMDLG 158 (158)
T ss_pred ----------HHHHHHHHHHHHHcC
Confidence 122458999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.86 E-value=1.6e-21 Score=208.21 Aligned_cols=140 Identities=16% Similarity=0.018 Sum_probs=117.6
Q ss_pred cCCcccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcC--ChHHHHHHHHHHHHHH-
Q 000414 986 RTKKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERG--QQNIIAGRIKEFLNRL- 1062 (1541)
Q Consensus 986 ~~k~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lG--f~nqKAkrIkeLAr~I- 1062 (1541)
...+...+|++||+|||+|.++.+++.+|. ++.+ .++.++|+++|+++| |+++||++|+++++++
T Consensus 34 ~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-----------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~ 101 (208)
T PRK01229 34 EEDLFSELSFCILTANSSAEGGIKAQKEIG-----------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYG 101 (208)
T ss_pred cCChHHHHHHHHhcCcCcHHHHHHHHHhcC-----------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHH
Confidence 344677899999999999999999999994 2456 899999999999995 9999999999999874
Q ss_pred --HHHhCCCChhhhhcCCchHHHHHHh-cCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCC------CChH
Q 000414 1063 --VELHGSIDLEWLRNVPPDKVKEYLL-DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ------PLPG 1133 (1541)
Q Consensus 1063 --vEdhGGIDLE~Lr~VPdDEAREeLL-SLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k------~dPE 1133 (1541)
.+.+. ...+..++|++|+ +|||||+|||++||++.+.+++|+||+||.|++.|+|+++.. .+|.
T Consensus 102 ~l~~~~~-------~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~ 174 (208)
T PRK01229 102 KLKEIIK-------ADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYL 174 (208)
T ss_pred HHHHHHh-------ccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHH
Confidence 33320 1223456799999 999999999999997665599999999999999999999752 5799
Q ss_pred HHHHHHHhhCC
Q 000414 1134 DLHIHLLKEYP 1144 (1541)
Q Consensus 1134 EIEk~LeeL~P 1144 (1541)
+++..|.++.+
T Consensus 175 ~~E~~l~~~~~ 185 (208)
T PRK01229 175 EIEEILREIAE 185 (208)
T ss_pred HHHHHHHHHHH
Confidence 99999887653
No 15
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.81 E-value=2e-20 Score=210.53 Aligned_cols=183 Identities=16% Similarity=0.239 Sum_probs=154.6
Q ss_pred ccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCH-HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 990 TTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADE-SEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 990 kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~Ade-EELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
-.+.|..|+.|||....|.+.|.+..+ ..||..+++.|+. +++..+|.++|||+ |+++|++-|+.+++.++|
T Consensus 126 YeVwVSEiMLQQTrV~TV~~YYt~WMq------kwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~g 198 (555)
T KOG2457|consen 126 YEVWVSEIMLQQTRVQTVMKYYTRWMQ------KWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTEG 198 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH------hCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCCC
Confidence 345689999999999999999999863 7899999999998 88999999999998 999999999999999988
Q ss_pred CChhhhhcCCchHHHHHHhc-CCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchh
Q 000414 1069 IDLEWLRNVPPDKVKEYLLD-IEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 1147 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLS-LPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e 1147 (1541)
.+|.. -+.|.+ +||||+|||.+|+.+||+++.=+||.||.|++.|.--+....+..+.-..
T Consensus 199 -------e~Prt--a~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~--------- 260 (555)
T KOG2457|consen 199 -------EFPRT--ASSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQS--------- 260 (555)
T ss_pred -------CCCCh--HHHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHH---------
Confidence 68876 355665 99999999999999999999999999999999997444433333333222
Q ss_pred hHhhhhhhhc-ccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCcccchhHHhh
Q 000414 1148 KIQMYLWPRL-CYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 1202 (1541)
Q Consensus 1148 ~IqK~LW~RL-~~lD~edl~ELH~lLIdFGK~ICtaRkP~CnaCPLR~~C~yYasa 1202 (1541)
+|... -..|..++++||+++|++|+..|++.+|.|..||+...|++|...
T Consensus 261 -----~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q~~ 311 (555)
T KOG2457|consen 261 -----SWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQLS 311 (555)
T ss_pred -----HHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHhHh
Confidence 23321 135778899999999999999999999999999999999998854
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=99.80 E-value=3.4e-19 Score=199.26 Aligned_cols=134 Identities=22% Similarity=0.254 Sum_probs=115.4
Q ss_pred cccccccceecccccHHHHHHHHHHhhhccc-C--------CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHH
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSH-D--------KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFL 1059 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~-e--------~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLA 1059 (1541)
+...++.+|++||+++.++.+++.+|.++.. . ...||+|++|+.++.++ .|+.+||. .||++|+++|
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---HLRKLGLG-YRARYIRETA 194 (310)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH-HHHHHHHHHH
Confidence 4456889999999999999999999965421 1 23589999999976553 57889995 4899999999
Q ss_pred HHHHHHhCCC-ChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCc-eeecchHHHHHHhhc-CCC
Q 000414 1060 NRLVELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRL-GWV 1126 (1541)
Q Consensus 1060 r~IvEdhGGI-DLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrp-aFPVDTHV~RIL~RL-GLV 1126 (1541)
+.+.+++++. +++.|..++.++++++|++|||||+|||+|||+|+|+++ +||||+||+|++.|+ |+.
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 653
No 17
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.74 E-value=1.1e-17 Score=185.82 Aligned_cols=161 Identities=20% Similarity=0.230 Sum_probs=129.4
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccC----CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHD----KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVE 1064 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e----~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvE 1064 (1541)
+...++.+|+.||.+.+.+.+++++|.+...+ ...||+|++|+.++++.+ +.+|++..||+||+.+|+++.+
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 44558899999999999999999999654221 123899999999999876 5789999999999999999987
Q ss_pred HhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCc-eeec-chHHHHHHhhcCCCCCCCChHHHHHHHHhh
Q 000414 1065 LHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPV-DVNVGRIAVRLGWVPLQPLPGDLHIHLLKE 1142 (1541)
Q Consensus 1065 dhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrp-aFPV-DTHV~RIL~RLGLVp~k~dPEEIEk~LeeL 1142 (1541)
|.+|++.+..+++++++++|++|+|||+|||+|||+|++|++ +||+ |.+++|.+.+++..+...+...++...+.+
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 557999999999999999999999999999999999999986 8995 777888888887333333333356666666
Q ss_pred CCchhhHhhhhhh
Q 000414 1143 YPVMDKIQMYLWP 1155 (1541)
Q Consensus 1143 ~P~~e~IqK~LW~ 1155 (1541)
-|+....+-|+|.
T Consensus 259 ~p~rs~A~~yLw~ 271 (285)
T COG0122 259 GPYRSYAALYLWR 271 (285)
T ss_pred cCHHHHHHHHHHH
Confidence 6654444445553
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=2.1e-17 Score=173.37 Aligned_cols=112 Identities=15% Similarity=0.069 Sum_probs=99.2
Q ss_pred CcccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhc----CChHHHHHHHHHHHHHHH
Q 000414 988 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKER----GQQNIIAGRIKEFLNRLV 1063 (1541)
Q Consensus 988 k~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~l----Gf~nqKAkrIkeLAr~Iv 1063 (1541)
.+...+|++||+|||+|+++.+++.+|..+ .+.+||++|++++.++|+++|++. |||++||++|++++++|+
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 367789999999999999999999999432 455899999999999999999876 999999999999999999
Q ss_pred HHhCCCChhhhhc---CCchHHHHHHhcCCCCcHHHHHHHHHHh
Q 000414 1064 ELHGSIDLEWLRN---VPPDKVKEYLLDIEGLGLKSVECVRLLS 1104 (1541)
Q Consensus 1064 EdhGGIDLE~Lr~---VPdDEAREeLLSLPGIGpKTADcILLFA 1104 (1541)
++|+| +++.|.. .+..+++++|++|||||+|||++||.+.
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 7777766 3455789999999999999999999863
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.65 E-value=7.7e-16 Score=170.89 Aligned_cols=151 Identities=14% Similarity=0.091 Sum_probs=120.0
Q ss_pred cccccccceecccccHHHHHHHHHHhhhc-ccC------CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHH
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEER-SHD------KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNR 1061 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER-~~e------~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~ 1061 (1541)
+...++.+|+.||.+...+.++..++.++ +.. ...||+|++|++++.++| +.+||+++||++|+++|+.
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 44457899999999999999999988654 322 246899999999999986 5789999999999999999
Q ss_pred HHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCc-ee-ecchHHHHHHhhcCCCCCCCChHHHHHHH
Q 000414 1062 LVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AF-PVDVNVGRIAVRLGWVPLQPLPGDLHIHL 1139 (1541)
Q Consensus 1062 IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrp-aF-PVDTHV~RIL~RLGLVp~k~dPEEIEk~L 1139 (1541)
+.+ |.++++.+. +.+++++.|++|||||+|||+||++|+||++ +| +.|.+++|.+ + ..++++++...
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 667766543 4577899999999999999999999999996 77 7799998854 1 23677888888
Q ss_pred HhhCCchhhHhhhhh
Q 000414 1140 LKEYPVMDKIQMYLW 1154 (1541)
Q Consensus 1140 eeL~P~~e~IqK~LW 1154 (1541)
+.+-|+-....-++|
T Consensus 258 ~~w~P~rsya~~~LW 272 (283)
T PRK10308 258 ERWKPWRSYALLHIW 272 (283)
T ss_pred HhcCCHHHHHHHHHH
Confidence 777774333333444
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=99.54 E-value=1.4e-14 Score=137.33 Aligned_cols=107 Identities=25% Similarity=0.241 Sum_probs=92.5
Q ss_pred ccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhh
Q 000414 994 KNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEW 1073 (1541)
Q Consensus 994 VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~ 1073 (1541)
|++||.||++++++.+++.+|.++ +|+|||++|+.+++++|.++|+++||++.||++|+++|+.+.
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 468999999999999999999752 469999999999999999999999999999999999999887
Q ss_pred hhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCC
Q 000414 1074 LRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYP 1144 (1541)
Q Consensus 1074 Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P 1144 (1541)
+...+++++|+|+.|++.|+|+++..++++++++.+++.+|
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 22235899999999999999999887789999988876553
No 21
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.54 E-value=2e-14 Score=158.50 Aligned_cols=127 Identities=23% Similarity=0.259 Sum_probs=110.8
Q ss_pred cccceecccccHHHHHHHHHHhhhc---------ccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHH
Q 000414 993 KKNSDNTVQQDWDLLRRIYSTGEER---------SHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLV 1063 (1541)
Q Consensus 993 ~VgAILsQQTSWdnVrka~aRLrER---------~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~Iv 1063 (1541)
+...|.++|.+..++-++.++|..- +-+..+||+.++|+. .++++-||.+||.. ||+||...|++|.
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 5688999999999999999987432 233468999999987 66778889999977 9999999999999
Q ss_pred HHhCC-CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCc-eeecchHHHHHHhhc
Q 000414 1064 ELHGS-IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRL 1123 (1541)
Q Consensus 1064 EdhGG-IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrp-aFPVDTHV~RIL~RL 1123 (1541)
++.|+ -.|..|+.++.+++++.|..|||||+|+||||+++++++. ++|||+||.||+.-+
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 3566677889999999999999999999999999999986 999999999999944
No 22
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.47 E-value=5.1e-14 Score=151.35 Aligned_cols=161 Identities=18% Similarity=0.168 Sum_probs=132.7
Q ss_pred cccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 000414 989 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 1068 (1541)
Q Consensus 989 ~kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGG 1068 (1541)
|.-.++.+|+.||.+-.++..+++||.........+|+|+.+..++.++| +.|||+.+||-||+.+|++..+.+ =
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 45568899999999999999999999543333478999999999999986 778999999999999999998754 2
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCc-eeecchH-HHHHHhhc-CCCCCCCChHHHHHHHHhhCCc
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVN-VGRIAVRL-GWVPLQPLPGDLHIHLLKEYPV 1145 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrp-aFPVDTH-V~RIL~RL-GLVp~k~dPEEIEk~LeeL~P~ 1145 (1541)
...+...+++.+++++.|+.++|||+|||.|+|.|+++|+ ++|+|.- |++-+..| |+-+ .+.+.+++++.+..-|+
T Consensus 150 ~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~-~p~~~evekl~e~~kpy 228 (254)
T KOG1918|consen 150 PSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP-LPLPKEVEKLCEKCKPY 228 (254)
T ss_pred CchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCC-CCchHHHHHHhhhccch
Confidence 3667788899999999999999999999999999999997 8999655 66666666 5543 46788888888888776
Q ss_pred hhhHhhhhhh
Q 000414 1146 MDKIQMYLWP 1155 (1541)
Q Consensus 1146 ~e~IqK~LW~ 1155 (1541)
-.....|+|.
T Consensus 229 RtvaawYlWk 238 (254)
T KOG1918|consen 229 RTVAAWYLWK 238 (254)
T ss_pred HHHHHHHHHh
Confidence 5544556664
No 23
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.79 E-value=2.7e-08 Score=106.24 Aligned_cols=122 Identities=20% Similarity=0.154 Sum_probs=99.4
Q ss_pred ccccccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcC--ChHHHHHHHHHHHHHHHHHhC
Q 000414 990 TTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERG--QQNIIAGRIKEFLNRLVELHG 1067 (1541)
Q Consensus 990 kk~~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lG--f~nqKAkrIkeLAr~IvEdhG 1067 (1541)
.+.+.=.||+.|+++....++.+.+. +.+..++.+||++.|+.+| |+++||+||..+-+.+-
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 34456689999999999999999885 3466779999999999996 78999999999765543
Q ss_pred CCChhhhhcCCchH--HHHHHh-cCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCC
Q 000414 1068 SIDLEWLRNVPPDK--VKEYLL-DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 1129 (1541)
Q Consensus 1068 GIDLE~Lr~VPdDE--AREeLL-SLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k 1129 (1541)
++..+-..+..+ +|++|+ .++|||.|-|+++|....-....++|.|+.|.+.|+|.+...
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 234444444332 899999 999999999999998866578889999999999999998654
No 24
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=98.76 E-value=2.4e-09 Score=85.61 Aligned_cols=31 Identities=55% Similarity=1.114 Sum_probs=29.8
Q ss_pred CCcccCCcCC-CccCCcccccCccccccccce
Q 000414 1392 PQYRCNSKDS-KLCNSEICYSCNSVCERNAGI 1422 (1541)
Q Consensus 1392 p~~~c~s~~~-~lc~~~~c~sC~s~rE~~~~~ 1422 (1541)
|+++|+|+++ +||+++|||+||||||+++|+
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=96.80 E-value=0.00084 Score=53.65 Aligned_cols=25 Identities=24% Similarity=0.542 Sum_probs=20.9
Q ss_pred CCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1077 VPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1077 VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
+|.+ +++|++|||||+|||+.|+.|
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=95.61 E-value=0.0047 Score=44.29 Aligned_cols=17 Identities=47% Similarity=1.302 Sum_probs=11.6
Q ss_pred ccCCCCCCCCCCCcccc
Q 000414 1180 CKKRSPNCGACPLRGEC 1196 (1541)
Q Consensus 1180 CtaRkP~CnaCPLR~~C 1196 (1541)
|++++|+|+.|||++.|
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
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=94.59 E-value=0.016 Score=44.46 Aligned_cols=23 Identities=35% Similarity=1.083 Sum_probs=20.5
Q ss_pred hccCCCCCCCCCCCcccchhHHh
Q 000414 1179 FCKKRSPNCGACPLRGECKHFAS 1201 (1541)
Q Consensus 1179 ICtaRkP~CnaCPLR~~C~yYas 1201 (1541)
+|++++|+|+.|||+..|.+|..
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~~ 23 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYXX 23 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhhc
Confidence 69999999999999999997543
No 28
>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=94.26 E-value=0.031 Score=62.52 Aligned_cols=54 Identities=24% Similarity=0.462 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCC
Q 000414 1050 IIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 1129 (1541)
Q Consensus 1050 qKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k 1129 (1541)
.-+|+|..+++|++.+..++|+.--..+++.++ .+|+||||.||+.+||++..+
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 367899999999998755688876666776643 589999999999999999754
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=92.54 E-value=0.091 Score=58.92 Aligned_cols=52 Identities=25% Similarity=0.417 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCCC
Q 000414 1051 IAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 1129 (1541)
Q Consensus 1051 KAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~k 1129 (1541)
-+|+|-.+++|++.+ .++|+.--..+++.++ ++|+||||.||+.+||++..+
T Consensus 142 a~KR~nMFLRWMVR~-d~VD~GlW~~i~ps~L--------------------------iiPLDtH~~rvar~LgL~~Rk 193 (229)
T TIGR02757 142 PLKRLNMFLRWMIRK-DEVDLGIWESFKPSDL--------------------------ILPLDTHVFRIAKKLKLLKRK 193 (229)
T ss_pred hHHHHHHHHHhhccC-CCCCCcCCCCCCHHHc--------------------------eeechHhHHHHHHHhCCcccC
Confidence 358999999999985 3478776666766542 689999999999999998753
No 30
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=85.42 E-value=1.2 Score=40.80 Aligned_cols=40 Identities=30% Similarity=0.318 Sum_probs=28.6
Q ss_pred HHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1058 FLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1058 LAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
.|+.|.+.|| +++.|...+ .++|.+++|||+++|+.|..|
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 4566677776 477777654 568999999999999999876
No 31
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=84.80 E-value=0.67 Score=35.75 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=17.5
Q ss_pred HHhcCCCCcHHHHHHHHHHh
Q 000414 1085 YLLDIEGLGLKSVECVRLLS 1104 (1541)
Q Consensus 1085 eLLSLPGIGpKTADcILLFA 1104 (1541)
.|++++|||+|+|+.++.+.
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
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=84.31 E-value=6.2 Score=43.69 Aligned_cols=68 Identities=9% Similarity=0.042 Sum_probs=51.7
Q ss_pred cccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHH
Q 000414 993 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQ--QNIIAGRIKEFLNRLVE 1064 (1541)
Q Consensus 993 ~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf--~nqKAkrIkeLAr~IvE 1064 (1541)
++-.+.--=.+|..+.+-...+++ ....++++.||..++++|+.++..-|+ ++.|.+.++.=|+.+.+
T Consensus 35 L~Le~~QAGLSW~tIL~Kre~fr~----aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~ 104 (187)
T PRK10353 35 ICLEGQQAGLSWITVLKKRENYRA----CFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ 104 (187)
T ss_pred HHHHHhcccccHHHHHHHHHHHHH----HHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHH
Confidence 333344445689999998888864 467799999999999999999999998 45566677776666554
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=83.97 E-value=2.4 Score=46.40 Aligned_cols=72 Identities=15% Similarity=0.157 Sum_probs=51.1
Q ss_pred cccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHH---HhC
Q 000414 993 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQ--QNIIAGRIKEFLNRLVE---LHG 1067 (1541)
Q Consensus 993 ~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf--~nqKAkrIkeLAr~IvE---dhG 1067 (1541)
++-.+.--=.+|..|.+-...+++ ....++++.||..++++|++++..-|+ ++.|.+.+..=|+.+.+ +||
T Consensus 30 L~Le~fQaGLsW~~Il~Kr~~~r~----aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~g 105 (179)
T PF03352_consen 30 LTLEGFQAGLSWSTILKKREAFRE----AFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFG 105 (179)
T ss_dssp HHHHHHTTTS-HHHHHHTHHHHHH----HTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHhhCCHHHHHHHHHHHHH----HHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcC
Confidence 333444445689999987777754 356789999999999999999999998 67788888888877654 455
Q ss_pred C
Q 000414 1068 S 1068 (1541)
Q Consensus 1068 G 1068 (1541)
+
T Consensus 106 s 106 (179)
T PF03352_consen 106 S 106 (179)
T ss_dssp -
T ss_pred C
Confidence 4
No 34
>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=77.76 E-value=8.8 Score=35.46 Aligned_cols=58 Identities=17% Similarity=0.188 Sum_probs=38.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1036 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1036 EELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
+++.++..-.|=..-|+...+.++..|.. ++. +-....+.|.+|||||.++|..|--|
T Consensus 9 ~~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~~---------~i~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 9 EELADLYELQGGDPFRARAYRRAAAAIKA-LPY---------PITSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHHTSTSHHHHHHHHHHHHHHHH-SSS----------HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHhhCCcHHHHHHHHHHHHHHh-CCH---------hHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence 44555555664444588888888888876 221 22222225999999999999988543
No 35
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.50 E-value=7.5 Score=43.28 Aligned_cols=62 Identities=19% Similarity=0.192 Sum_probs=41.3
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHH------HHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcH
Q 000414 1021 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIK------EFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 1094 (1541)
Q Consensus 1021 ~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIk------eLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGp 1094 (1541)
.+||.+.++.. -.+.+|.--|.-.+.|-.|. +++++|.. .| .+.|.++||||+
T Consensus 59 LYGF~t~~Er~-----lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--------------~D--~~~L~~vpGIGk 117 (196)
T PRK13901 59 LFGFLNSSERE-----VFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--------------ED--IELISKVKGIGN 117 (196)
T ss_pred eeCCCCHHHHH-----HHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCH
Confidence 57888877632 23445555677666666665 34444433 12 578999999999
Q ss_pred HHHHHHHHH
Q 000414 1095 KSVECVRLL 1103 (1541)
Q Consensus 1095 KTADcILLF 1103 (1541)
|||+-|++-
T Consensus 118 KtAeRIIlE 126 (196)
T PRK13901 118 KMAGKIFLK 126 (196)
T ss_pred HHHHHHHHH
Confidence 999988754
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=76.17 E-value=4.7 Score=36.92 Aligned_cols=58 Identities=24% Similarity=0.249 Sum_probs=36.1
Q ss_pred HHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1029 AVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1029 ALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
+|-.|+.++|..++..+|. .+|+.|.+.- ..+|++ . + .++|..++|||.++|+-|+.+
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R----~~~g~~--------~-s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSYR----EEYGPF--------K-T--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHHH----HHcCCc--------C-C--HHHHHcCCCCCHHHHHHHHhh
Confidence 3455777777665444444 3444333321 124543 1 2 578999999999999998766
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=75.20 E-value=4.9 Score=44.16 Aligned_cols=68 Identities=7% Similarity=0.034 Sum_probs=51.7
Q ss_pred cccceecccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHH--HHHHHHHHHHHHHH
Q 000414 993 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNI--IAGRIKEFLNRLVE 1064 (1541)
Q Consensus 993 ~VgAILsQQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nq--KAkrIkeLAr~IvE 1064 (1541)
++-.+.--=.+|..+.+-...+++ ....++++.||..++++|++++..-|.-+. |.+.++.=|+.+.+
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 433444445689999998888864 467799999999999999999999998554 45557776777665
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=72.45 E-value=11 Score=43.26 Aligned_cols=122 Identities=14% Similarity=0.097 Sum_probs=70.5
Q ss_pred ChHHHHHHHHHHHHHHHHHhCCCChhhhhc--CCchHHHHHHhcCCCCc--H-------HHHHHHHHHhcCC--c-----
Q 000414 1047 QQNIIAGRIKEFLNRLVELHGSIDLEWLRN--VPPDKVKEYLLDIEGLG--L-------KSVECVRLLSLQH--I----- 1108 (1541)
Q Consensus 1047 f~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~--VPdDEAREeLLSLPGIG--p-------KTADcILLFAfgr--p----- 1108 (1541)
+.++|.++|+++...+.+ +.+..+.. -+-..+++.|..+=|-. . |++...+..+||. +
T Consensus 92 ~~~~KikRl~k~~~~~~~----l~l~~~~~~y~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya~r~~~g~~~~~p~~I 167 (246)
T PF09171_consen 92 LLEQKIKRLRKFCPFLEN----LSLQDNPLYYEDLEELWRELAKILNSKPESKTIVFAVKMFGYACRIAFGEFRPYPEEI 167 (246)
T ss_dssp THHHHHHHHHHHCCHHHT----T-HHHHHHHHCTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHCTS-----TTS
T ss_pred HHHHHHHHHHHHHHHHHH----hhhhhhhhhhhhHHHHHHHHHHHhCCCCccchhhHHHHHHHHHHHHhcCCCCCCcccC
Confidence 567799999988776543 22221111 23345566776654433 2 3444445555565 2
Q ss_pred eeecchHHHHHHhhcCCCCCCCChHHHHHHHHhhCCchhhHhhhhhhhcccCChhhHHHHHHHHH-HHhHHhccC
Q 000414 1109 AFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLDQKTLYELHYQMI-TFGKIFCKK 1182 (1541)
Q Consensus 1109 aFPVDTHV~RIL~RLGLVp~k~dPEEIEk~LeeL~P~~e~IqK~LW~RL~~lD~edl~ELH~lLI-dFGK~ICta 1182 (1541)
-+|||.||.++..++|++.. .++. . . .. +......|..++..+...+.+++..|| -+|+..+..
T Consensus 168 pIPvD~Rva~~T~~sGi~~~--~~~~---~-~-~~---~~~v~~~W~~Va~~sgIpplhLDs~lW~l~G~~~~~~ 232 (246)
T PF09171_consen 168 PIPVDYRVAKLTKRSGIIEC--EREE---M-M-RT---REEVQKAWREVAKESGIPPLHLDSLLWPLLGRARDVK 232 (246)
T ss_dssp -----HHHHHHHHCTTS-SS---HHH---H-H-CT---CCHHHHHHHHHHHHHT--HHHHHHHHHHHHCCHHCCT
T ss_pred CCCccHHHHHHHHHhccccc--cHHh---h-h-cc---HHHHHHHHHHHHhhcCCCchhhhhHHHHhcccchhhh
Confidence 68999999999999999763 2221 1 1 12 123345798887777788899999999 999988765
No 39
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.17 E-value=7.3 Score=43.71 Aligned_cols=63 Identities=24% Similarity=0.410 Sum_probs=46.3
Q ss_pred HcCCHHHHHHHHHhcCChHHHHH-HHHHHHHHHHHHh---CCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHH
Q 000414 1031 RCADESEIADAIKERGQQNIIAG-RIKEFLNRLVELH---GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRL 1102 (1541)
Q Consensus 1031 A~AdeEELeeLIR~lGf~nqKAk-rIkeLAr~IvEdh---GGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILL 1102 (1541)
..++..||.++|=..|..+ + -...+|+.|.+.| |+ |..|...+. ++|.+++|||+..|..+++
T Consensus 12 ~~Lsd~ELLailL~~g~~~---~~~~~~lA~~ll~~f~~~g~--l~~l~~a~~----~eL~~i~GiG~aka~~l~a 78 (218)
T TIGR00608 12 EALSDYELLAIILRTGTPK---GLDVLSLSKRLLDVFGRQDS--LGHLLSAPP----EELSSVPGIGEAKAIQLKA 78 (218)
T ss_pred ccCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccCC--HHHHHhCCH----HHHHhCcCCcHHHHHHHHH
Confidence 3456777777776777744 3 5668899999887 64 777877764 5799999999977766643
No 40
>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=69.79 E-value=11 Score=33.85 Aligned_cols=31 Identities=35% Similarity=0.342 Sum_probs=24.1
Q ss_pred CChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1069 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1069 IDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
-+++.|...+ .+.|..++|||+++|+-+...
T Consensus 27 ~t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 27 KTLEDLANAD----PEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp SSHHHHHTSH----HHHHHTSTTSSHHHHHHHHHH
T ss_pred CcHHHHHcCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 3677777664 467999999999999988654
No 41
>PRK00024 hypothetical protein; Reviewed
Probab=69.11 E-value=7.5 Score=43.63 Aligned_cols=63 Identities=19% Similarity=0.321 Sum_probs=45.8
Q ss_pred HcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHH
Q 000414 1031 RCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRL 1102 (1541)
Q Consensus 1031 A~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILL 1102 (1541)
..++..||.++|=..|..+ +-.+.+|+.|.+.||+ |..+...+. ++|.+++|||+..|..+++
T Consensus 22 ~~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgs--L~~l~~as~----~eL~~i~GIG~akA~~L~a 84 (224)
T PRK00024 22 AALSDAELLAILLRTGTKG---KSVLDLARELLQRFGS--LRGLLDASL----EELQSIKGIGPAKAAQLKA 84 (224)
T ss_pred ccCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCC--HHHHHhCCH----HHHhhccCccHHHHHHHHH
Confidence 4556677777776667644 3455788899988875 677777664 5799999999998866643
No 42
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=67.47 E-value=25 Score=39.26 Aligned_cols=66 Identities=14% Similarity=0.134 Sum_probs=49.9
Q ss_pred ccccHHHHHHHHHHhhhcccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHH--HHHHHHHHHHHHH---HHhCCC
Q 000414 1000 VQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNI--IAGRIKEFLNRLV---ELHGSI 1069 (1541)
Q Consensus 1000 QQTSWdnVrka~aRLrER~~e~~gfPTPEALA~AdeEELeeLIR~lGf~nq--KAkrIkeLAr~Iv---EdhGGI 1069 (1541)
-=.+|..|.+-.+++++ ....++++.||..++++++.++...|.-+. |.+.++.-|+++. ++||++
T Consensus 43 AGLSW~tVL~KRe~fre----aF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 43 AGLSWLTVLKKREAFRE----AFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred ccchHHHHHHhHHHHHH----HHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 34589999998888864 345689999999999999999999998544 5555666666544 466663
No 43
>PRK00076 recR recombination protein RecR; Reviewed
Probab=65.02 E-value=5.9 Score=44.12 Aligned_cols=28 Identities=32% Similarity=0.401 Sum_probs=22.5
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcC
Q 000414 1079 PDKVKEYLLDIEGLGLKSVECVRLLSLQ 1106 (1541)
Q Consensus 1079 dDEAREeLLSLPGIGpKTADcILLFAfg 1106 (1541)
-+++++.|.+|||||+|||.=+.++-+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~ 33 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQ 33 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3577899999999999999776666443
No 44
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=64.93 E-value=9.1 Score=40.59 Aligned_cols=53 Identities=17% Similarity=0.211 Sum_probs=34.7
Q ss_pred HHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1029 AVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1029 ALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
+|-.|+.+++.. --|++..+|+.|. .+|.+ .+ .++|+.++|||+++.+.+--+
T Consensus 54 diN~A~~~el~~---lpGigP~~A~~IV--------~nGpf---------~s--veDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 54 DLNNSSVRAFRQ---FPGMYPTLAGKIV--------KNAPY---------DS--VEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cCCccCHHHHHH---CCCCCHHHHHHHH--------HCCCC---------CC--HHHHHcCCCCCHHHHHHHHHh
Confidence 456677777644 3677777776666 25553 12 578889999998877665433
No 45
>PRK13844 recombination protein RecR; Provisional
Probab=64.28 E-value=6.2 Score=44.11 Aligned_cols=28 Identities=29% Similarity=0.278 Sum_probs=22.7
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcC
Q 000414 1079 PDKVKEYLLDIEGLGLKSVECVRLLSLQ 1106 (1541)
Q Consensus 1079 dDEAREeLLSLPGIGpKTADcILLFAfg 1106 (1541)
-+++++.|.+|||||+|+|.=+..+-+.
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~ 37 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLD 37 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3678899999999999999877666443
No 46
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.24 E-value=6.3 Score=43.90 Aligned_cols=28 Identities=29% Similarity=0.366 Sum_probs=22.4
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcC
Q 000414 1079 PDKVKEYLLDIEGLGLKSVECVRLLSLQ 1106 (1541)
Q Consensus 1079 dDEAREeLLSLPGIGpKTADcILLFAfg 1106 (1541)
-+++++.|.+|||||+|||.=+.++-+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3578899999999999999776665443
No 47
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=63.49 E-value=23 Score=39.16 Aligned_cols=62 Identities=15% Similarity=0.059 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHH------HHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcH
Q 000414 1021 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKE------FLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 1094 (1541)
Q Consensus 1021 ~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIke------LAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGp 1094 (1541)
.+||.+.++- +-...+|.--|--.+.|-.|.. ++++|.. .| .+.|.++||||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~--------------~D--~~~L~~vpGIGk 118 (188)
T PRK14606 60 LYGFSNERKK-----ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS--------------QD--VEGLSKLPGISK 118 (188)
T ss_pred eeCCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCH
Confidence 5788777652 1233344445665555544442 2233322 12 578999999999
Q ss_pred HHHHHHHHH
Q 000414 1095 KSVECVRLL 1103 (1541)
Q Consensus 1095 KTADcILLF 1103 (1541)
|||+-|.+-
T Consensus 119 KtAerIilE 127 (188)
T PRK14606 119 KTAERIVME 127 (188)
T ss_pred HHHHHHHHH
Confidence 999988754
No 48
>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=61.99 E-value=34 Score=44.04 Aligned_cols=32 Identities=6% Similarity=0.103 Sum_probs=18.0
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Q 000414 1026 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN 1060 (1541)
Q Consensus 1026 TPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr 1060 (1541)
++++|..+..++|.++ -||....|..|.+..+
T Consensus 456 ~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 456 SVADLYALKKEDLLEL---EGFGEKSAQNLLNAIE 487 (652)
T ss_pred CHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHH
Confidence 6667777766665432 3565555555544433
No 49
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=58.85 E-value=16 Score=35.65 Aligned_cols=57 Identities=25% Similarity=0.423 Sum_probs=36.8
Q ss_pred CHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhc-CCCCcHHHHHHHHH
Q 000414 1034 DESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLD-IEGLGLKSVECVRL 1102 (1541)
Q Consensus 1034 deEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLS-LPGIGpKTADcILL 1102 (1541)
...++...|...|++.. .+.+|.+.||.-.++.|+.=|.. |+. +.|||-++||-|..
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 34567778889999874 45555566777566666666654 565 99999999988743
No 50
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=57.48 E-value=9.3 Score=42.80 Aligned_cols=27 Identities=30% Similarity=0.426 Sum_probs=21.6
Q ss_pred hHHHHHHhcCCCCcHHHHHHHHHHhcC
Q 000414 1080 DKVKEYLLDIEGLGLKSVECVRLLSLQ 1106 (1541)
Q Consensus 1080 DEAREeLLSLPGIGpKTADcILLFAfg 1106 (1541)
+++++.|..|||||+|+|.=+..+.+.
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHc
Confidence 578999999999999999766555443
No 51
>PRK14973 DNA topoisomerase I; Provisional
Probab=55.87 E-value=20 Score=47.89 Aligned_cols=98 Identities=16% Similarity=0.093 Sum_probs=59.9
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHH
Q 000414 1022 MDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN-RLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1100 (1541)
Q Consensus 1022 ~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr-~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcI 1100 (1541)
.||-++++++.|++++|+.+ .|+..-.+..+...+. .+.. -+-+....-..+..+.+|++++|||++|++-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGR----PVPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcC----CCchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 47779999999999998544 7888766666655554 4433 11222222222333566999999999999765
Q ss_pred HHHhcCCceeecchHHHHHHhhcCCC
Q 000414 1101 RLLSLQHIAFPVDVNVGRIAVRLGWV 1126 (1541)
Q Consensus 1101 LLFAfgrpaFPVDTHV~RIL~RLGLV 1126 (1541)
-.-+.-...-.+-.-..+++.+-|+.
T Consensus 894 ~~ag~~~~e~l~~~d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSADPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccCCHHHHhhhcCCC
Confidence 44444433222222455666665653
No 52
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=54.73 E-value=14 Score=41.02 Aligned_cols=21 Identities=24% Similarity=0.351 Sum_probs=18.5
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.+.|.++||||+|||+-|++-
T Consensus 108 ~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 108 VAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 578999999999999988754
No 53
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=54.60 E-value=20 Score=39.27 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=18.5
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.+.|.++||||+|+|+.|+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 468999999999999999855
No 54
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=54.47 E-value=15 Score=40.53 Aligned_cols=24 Identities=21% Similarity=0.236 Sum_probs=19.7
Q ss_pred HHHHhcCCCCcHHHHHHHHHHhcC
Q 000414 1083 KEYLLDIEGLGLKSVECVRLLSLQ 1106 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLFAfg 1106 (1541)
.+.|.++||||+|||+-|++---+
T Consensus 107 ~~~L~~vpGIGkKtAeRIilELkd 130 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAELSD 130 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 578999999999999988755333
No 55
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=54.32 E-value=36 Score=37.71 Aligned_cols=65 Identities=20% Similarity=0.189 Sum_probs=37.9
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhh-hcC-CchHHHHHHhcCCCCcHHHHH
Q 000414 1021 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWL-RNV-PPDKVKEYLLDIEGLGLKSVE 1098 (1541)
Q Consensus 1021 ~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~L-r~V-PdDEAREeLLSLPGIGpKTAD 1098 (1541)
.+||.+.++- +-...+|.--|...+.|..|.. .+ +.+.| ..+ ..| .+.|.++||||+|||+
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 5788877752 2233445445666645544443 22 22222 112 223 5789999999999999
Q ss_pred HHHH
Q 000414 1099 CVRL 1102 (1541)
Q Consensus 1099 cILL 1102 (1541)
-|++
T Consensus 123 rIil 126 (194)
T PRK14605 123 RIVL 126 (194)
T ss_pred HHHH
Confidence 8653
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=52.62 E-value=49 Score=42.80 Aligned_cols=20 Identities=25% Similarity=0.365 Sum_probs=14.3
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 000414 1084 EYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1084 EeLLSLPGIGpKTADcILLF 1103 (1541)
++|.+++|||+++|..|..|
T Consensus 543 eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 543 EELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred HHHhccCCcCHHHHHHHHHH
Confidence 46777777777777777655
No 57
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=52.61 E-value=12 Score=41.76 Aligned_cols=22 Identities=32% Similarity=0.357 Sum_probs=19.1
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 000414 1083 KEYLLDIEGLGLKSVECVRLLS 1104 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLFA 1104 (1541)
.+.|.++||||.|||+-+++--
T Consensus 107 ~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHHHH
Confidence 6899999999999999887653
No 58
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=51.05 E-value=29 Score=39.68 Aligned_cols=61 Identities=20% Similarity=0.322 Sum_probs=45.8
Q ss_pred HcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHH
Q 000414 1031 RCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1100 (1541)
Q Consensus 1031 A~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcI 1100 (1541)
..++..||.+++=..|- |-+-...+|+.+...||+ |..|...+ .++|.+++|||..-|--+
T Consensus 22 ~~Lsd~ELLailLrtG~---~~~~~~~la~~lL~~fg~--L~~l~~a~----~~el~~v~GiG~aka~~l 82 (224)
T COG2003 22 EALSDAELLAILLRTGT---KGESVLDLAKELLQEFGS--LAELLKAS----VEELSSVKGIGLAKAIQI 82 (224)
T ss_pred hhcchHHHHHHHHhcCC---CCCCHHHHHHHHHHHccc--HHHHHhCC----HHHHhhCCCccHHHHHHH
Confidence 44566788888877777 345667899999999987 66776665 468999999997655443
No 59
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.68 E-value=18 Score=40.09 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=18.3
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.+.|.++||||+|||+-|++-
T Consensus 106 ~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 578999999999999988743
No 60
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=49.83 E-value=21 Score=42.18 Aligned_cols=52 Identities=19% Similarity=0.204 Sum_probs=32.3
Q ss_pred cCChHHHHHHHHHHHHHHHHHhCCCC-hhhhhcCCchHHHHHHhcCCCCcHHHHHHHH
Q 000414 1045 RGQQNIIAGRIKEFLNRLVELHGSID-LEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1101 (1541)
Q Consensus 1045 lGf~nqKAkrIkeLAr~IvEdhGGID-LE~Lr~VPdDEAREeLLSLPGIGpKTADcIL 1101 (1541)
-|....-|..|.++.+ .|.+. +..+..-+...+..+|++|+|||+|||..+.
T Consensus 54 pgIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~ 106 (334)
T smart00483 54 PGIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWY 106 (334)
T ss_pred CCccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHH
Confidence 4665555655655532 35544 2322233344568999999999999996653
No 61
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.57 E-value=23 Score=39.34 Aligned_cols=21 Identities=29% Similarity=0.382 Sum_probs=18.5
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.+.|.++||||+|||+-|++-
T Consensus 107 ~~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 107 VARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 578999999999999988754
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=47.68 E-value=27 Score=35.86 Aligned_cols=58 Identities=22% Similarity=0.284 Sum_probs=38.1
Q ss_pred HHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1028 EAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1028 EALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
-+|-.|+.++|..+ -|....+|+.|.+.-. .+|.+ .+ .++|..++|||+++++-|.-|
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 45666777776443 4666667766655432 24442 12 578999999999999988655
No 63
>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=47.13 E-value=18 Score=36.51 Aligned_cols=28 Identities=29% Similarity=0.337 Sum_probs=22.6
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHHhcCCc
Q 000414 1081 KVKEYLLDIEGLGLKSVECVRLLSLQHI 1108 (1541)
Q Consensus 1081 EAREeLLSLPGIGpKTADcILLFAfgrp 1108 (1541)
.....|..|||||+.+|.-+.++++..+
T Consensus 9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s~ 36 (93)
T PF11731_consen 9 AGLSDLTDIPNIGKATAEDLRLLGIRSP 36 (93)
T ss_pred HHHHHHhcCCCccHHHHHHHHHcCCCCH
Confidence 3467899999999999998877766553
No 64
>PRK07945 hypothetical protein; Provisional
Probab=46.14 E-value=30 Score=40.90 Aligned_cols=61 Identities=11% Similarity=0.110 Sum_probs=40.1
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1036 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1036 EELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
++++.+|.-.|=..=|++..+++|+.|.. ++-+.+..+... ..|.+|||||.-||..|.-+
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 45666676677554588888899888864 211112222111 16899999999999988765
No 65
>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=45.85 E-value=15 Score=35.19 Aligned_cols=42 Identities=21% Similarity=0.233 Sum_probs=30.1
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCceeecchHHHHHHhhcCCCCC
Q 000414 1084 EYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPL 1128 (1541)
Q Consensus 1084 EeLLSLPGIGpKTADcILLFAfgrpaFPVDTHV~RIL~RLGLVp~ 1128 (1541)
+.|++|||||+-||..++....+...|. +...+..-+|+.+.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~---~~~~l~~~~Gl~P~ 43 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFK---SAKQLASYAGLAPR 43 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcc---cchhhhhccccccc
Confidence 4688999999999999998875444554 33444555688764
No 66
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.08 E-value=26 Score=38.74 Aligned_cols=20 Identities=25% Similarity=0.371 Sum_probs=17.1
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.+.| ++||||+|||+-|++-
T Consensus 107 ~~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 107 KAAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred Hhhe-ECCCCcHHHHHHHHHH
Confidence 3678 9999999999988754
No 67
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=42.01 E-value=1e+02 Score=40.27 Aligned_cols=29 Identities=10% Similarity=0.095 Sum_probs=16.4
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHH
Q 000414 1026 DWEAVRCADESEIADAIKERGQQNIIAGRIKE 1057 (1541)
Q Consensus 1026 TPEALA~AdeEELeeLIR~lGf~nqKAkrIke 1057 (1541)
++.+|..+..++|..+ -||...+|..|.+
T Consensus 486 ~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~ 514 (689)
T PRK14351 486 SLADLYDLTVADLAEL---EGWGETSAENLLA 514 (689)
T ss_pred CHHHHHHcCHHHHhcC---cCcchhHHHHHHH
Confidence 6677777776654332 3665555554433
No 68
>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=40.99 E-value=23 Score=39.13 Aligned_cols=66 Identities=21% Similarity=0.160 Sum_probs=40.1
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhc-CC-chHHHHHHhcCCCCcHHHHH
Q 000414 1021 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN-VP-PDKVKEYLLDIEGLGLKSVE 1098 (1541)
Q Consensus 1021 ~~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~-VP-dDEAREeLLSLPGIGpKTAD 1098 (1541)
.+||.|.++- +-...+|+--|.-.++|..|... ++.+.|.. +- .| ...|.++||||+|||+
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 4788877652 22344555567777667666322 22222221 11 12 3679999999999999
Q ss_pred HHHHH
Q 000414 1099 CVRLL 1103 (1541)
Q Consensus 1099 cILLF 1103 (1541)
-|++-
T Consensus 122 rIile 126 (191)
T TIGR00084 122 RLLLE 126 (191)
T ss_pred HHHHH
Confidence 99843
No 69
>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=40.85 E-value=13 Score=35.91 Aligned_cols=64 Identities=17% Similarity=0.216 Sum_probs=44.7
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhhcccceEEEecCChhhhhcccCHHHHHHHHhccceEeeccccccCCCccc
Q 000414 1445 YFQVNEVFADHETSHHPINVPRHTIANLRREIVCFGSSATTLFNALDMRQIQEYFWRGFVCVRGFDRRYRCPRPL 1519 (1541)
Q Consensus 1445 YFQvNEVFADh~SS~nPI~VpR~~IwnL~Rr~VYFGTSV~SIfkGlt~eeIq~cFwkG~VCVRgFDr~TR~PrPL 1519 (1541)
+|.-||||+-+....+||. .=..++.|.+-........ ....-...-|+|=++||+.++.-|+|
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 70
>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=40.65 E-value=49 Score=29.75 Aligned_cols=36 Identities=25% Similarity=0.197 Sum_probs=29.5
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Q 000414 1022 MDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN 1060 (1541)
Q Consensus 1022 ~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr 1060 (1541)
.|+.|+++|+.++.++|.+ --|+...+|..|++.++
T Consensus 24 ~G~~t~~~l~~a~~~~L~~---i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 24 AGIKTLEDLANADPEELAE---IPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp TTCSSHHHHHTSHHHHHHT---STTSSHHHHHHHHHHHH
T ss_pred cCCCcHHHHHcCCHHHHhc---CCCCCHHHHHHHHHHHh
Confidence 4678999999999998755 36888889999888765
No 71
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=39.41 E-value=46 Score=35.62 Aligned_cols=55 Identities=24% Similarity=0.379 Sum_probs=35.4
Q ss_pred HHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHH
Q 000414 1030 VRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRL 1102 (1541)
Q Consensus 1030 LA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILL 1102 (1541)
|-.|+.+|| ..|-++|- .||+.|.+-- +.+|.| .+ .+.|...+|||+++.+-+.-
T Consensus 91 iNtAs~eeL-~~lpgIG~--~kA~aIi~yR----e~~G~f---------~s--v~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 91 INTASAEEL-QALPGIGP--KKAQAIIDYR----EENGPF---------KS--VDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred ccccCHHHH-HHCCCCCH--HHHHHHHHHH----HHcCCC---------Cc--HHHHHhccCCCHHHHHHHHh
Confidence 556777777 44444554 4676666542 345543 12 57899999999999876543
No 72
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=38.55 E-value=3.2e+02 Score=28.38 Aligned_cols=61 Identities=15% Similarity=0.103 Sum_probs=39.9
Q ss_pred CCCCCHHHHHcCCHHHHHH--HHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHH
Q 000414 1022 MDSVDWEAVRCADESEIAD--AIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVEC 1099 (1541)
Q Consensus 1022 ~gfPTPEALA~AdeEELee--LIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADc 1099 (1541)
.|.-|+++|.++....+.. +....|.. ...+..+ ..+..|..++|||+..|..
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 5667889988888776654 44444443 3322222 1156788999999999987
Q ss_pred HHHHhcCC
Q 000414 1100 VRLLSLQH 1107 (1541)
Q Consensus 1100 ILLFAfgr 1107 (1541)
++--++.-
T Consensus 69 L~~AGv~T 76 (122)
T PF14229_consen 69 LEHAGVDT 76 (122)
T ss_pred HHHhCcCc
Confidence 77666544
No 73
>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=37.10 E-value=31 Score=41.34 Aligned_cols=36 Identities=36% Similarity=0.924 Sum_probs=30.7
Q ss_pred CCchhhHHHHHHHHHHHhhhHHHHHHHHHh-hccCcccccCCC
Q 000414 608 TSNEDMEKWWQKEREVFEGRIQSFTARMHL-ILGDRRFKPWKG 649 (1541)
Q Consensus 608 G~D~~kekwWeeER~VF~gRvdSFIArMHl-vqGDRRFSpWKG 649 (1541)
.+.++|.+||+ +|.-...|...++..|-- ..| +|||
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 74
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=36.80 E-value=81 Score=37.46 Aligned_cols=56 Identities=13% Similarity=0.147 Sum_probs=37.3
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1037 EIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1037 ELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
+|.+++.-.|-...|+.+.++++..|.. ++ .++ +. .+.|.+|||||.++|+-|--+
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 4445555556555577778788877765 22 121 22 247899999999999998754
No 75
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=36.35 E-value=28 Score=38.19 Aligned_cols=20 Identities=20% Similarity=0.303 Sum_probs=17.2
Q ss_pred HHHHhcCCCCcHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRL 1102 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILL 1102 (1541)
...|+.+||||+|+|..+|.
T Consensus 72 f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 56788999999999988864
No 76
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=36.03 E-value=52 Score=42.68 Aligned_cols=22 Identities=27% Similarity=0.209 Sum_probs=19.6
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 000414 1083 KEYLLDIEGLGLKSVECVRLLS 1104 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLFA 1104 (1541)
.++|++|+|||+++|..|..|-
T Consensus 540 ~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHHH
Confidence 4689999999999999998883
No 77
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=35.28 E-value=35 Score=31.36 Aligned_cols=21 Identities=24% Similarity=0.352 Sum_probs=17.3
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.++|.++||||.+.|..|+.+
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 578999999999999999877
No 78
>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=34.99 E-value=31 Score=38.14 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.8
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 000414 1081 KVKEYLLDIEGLGLKSVECVRL 1102 (1541)
Q Consensus 1081 EAREeLLSLPGIGpKTADcILL 1102 (1541)
++-..|++++|||+|+|-.||.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 4577899999999999988854
No 79
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=33.43 E-value=44 Score=30.72 Aligned_cols=53 Identities=26% Similarity=0.344 Sum_probs=29.7
Q ss_pred HHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHH
Q 000414 1030 VRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1100 (1541)
Q Consensus 1030 LA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcI 1100 (1541)
|-.|+.++|..+ -|+....|+.|.+.- +.+|++ . + .++|..++|||+++.+-+
T Consensus 8 iN~as~~eL~~l---pgi~~~~A~~Iv~~R----~~~G~f--------~-s--~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQAL---PGIGPKQAKAIVEYR----EKNGPF--------K-S--LEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTS---TT--HHHHHHHHHHH----HHH-S---------S-S--GGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHc---CCCCHHHHHHHHHHH----HhCcCC--------C-C--HHHHhhCCCCCHHHHHHH
Confidence 345666665322 388887887777653 234553 1 2 468999999999998765
No 80
>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=32.92 E-value=48 Score=38.84 Aligned_cols=50 Identities=32% Similarity=0.396 Sum_probs=31.7
Q ss_pred CChHHHHHHHHHHHHHHHHHhCCC-ChhhhhcCCchHHHHHHhcCCCCcHHHHHHHH
Q 000414 1046 GQQNIIAGRIKEFLNRLVELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1101 (1541)
Q Consensus 1046 Gf~nqKAkrIkeLAr~IvEdhGGI-DLE~Lr~VPdDEAREeLLSLPGIGpKTADcIL 1101 (1541)
|.-..-|..|.++.+ .|.+ .++.|+.- ......+|++|+|||+++|..+.
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 555556666666543 1332 23444432 23447899999999999997664
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=32.25 E-value=39 Score=34.81 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=19.3
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 000414 1083 KEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLF 1103 (1541)
.+.|..|||||++.|..|+.+
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 578999999999999999877
No 82
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=32.19 E-value=35 Score=36.50 Aligned_cols=28 Identities=21% Similarity=0.318 Sum_probs=22.2
Q ss_pred cCCchHHHHHHhcCCCCcHHHHHHHHHHh
Q 000414 1076 NVPPDKVKEYLLDIEGLGLKSVECVRLLS 1104 (1541)
Q Consensus 1076 ~VPdDEAREeLLSLPGIGpKTADcILLFA 1104 (1541)
+++... -++|..|||||++.|..|..+-
T Consensus 90 NiNtAs-~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 90 NINTAS-AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred cccccC-HHHHHHCCCCCHHHHHHHHHHH
Confidence 445444 4788999999999999998873
No 83
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.93 E-value=36 Score=37.69 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=20.0
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1081 KVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1081 EAREeLLSLPGIGpKTADcILLF 1103 (1541)
++-+.|++++|||+|+|-.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh
Confidence 45678999999999999999874
No 84
>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=30.69 E-value=95 Score=36.47 Aligned_cols=57 Identities=19% Similarity=0.208 Sum_probs=36.7
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1036 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1036 EELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
++|+.++.-.|=..-|++..+.+|..|.. .. . +-+. .+++.+|||||.++|+.|--+
T Consensus 8 ~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~-l~-~--------~i~~-~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 8 EELADLLELLGGNPFRVRAYRKAARALES-LP-E--------PIES-LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HHHHHHHHhccCCcchHHHHHHHHHHHHh-CC-c--------ccCC-HHHhcCCCCccHHHHHHHHHH
Confidence 34445555554333377777788888765 22 1 1122 346799999999999999765
No 85
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=29.66 E-value=1.3e+02 Score=36.37 Aligned_cols=22 Identities=32% Similarity=0.484 Sum_probs=19.1
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 000414 1083 KEYLLDIEGLGLKSVECVRLLS 1104 (1541)
Q Consensus 1083 REeLLSLPGIGpKTADcILLFA 1104 (1541)
.++|+.++|||++|..++.+.+
T Consensus 268 feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 268 FEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred HHHHHhcCCCCHHHHHHHHHHH
Confidence 6899999999999998876653
No 86
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=27.51 E-value=84 Score=38.20 Aligned_cols=39 Identities=31% Similarity=0.422 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHH
Q 000414 1056 KEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 1100 (1541)
Q Consensus 1056 keLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcI 1100 (1541)
+.+|+.+++.||+ |..+...+ .++|..++|||++.|..|
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 3678889999985 67776655 468999999999999774
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=27.41 E-value=28 Score=37.79 Aligned_cols=55 Identities=15% Similarity=0.139 Sum_probs=42.3
Q ss_pred hHHHHHHHHHhhccCcccccCCCccccceeeeeeecccccccchhHHhhhhhccC
Q 000414 627 RIQSFTARMHLILGDRRFKPWKGSVVDSVVGVYLTQNVSDNLSSSAYMSLAARFP 681 (1541)
Q Consensus 627 RvdSFIArMHlvqGDRRFSpWKGSVVDSVVGVFLTQNVSDHLSSSAFMSLAAkFP 681 (1541)
+++....+|----|+.+-.-|...-...+|+..|+||.++.-...||-.|.++||
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
>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=26.85 E-value=46 Score=27.34 Aligned_cols=15 Identities=20% Similarity=0.373 Sum_probs=11.1
Q ss_pred HhcCCCCcHHHHHHH
Q 000414 1086 LLDIEGLGLKSVECV 1100 (1541)
Q Consensus 1086 LLSLPGIGpKTADcI 1100 (1541)
+..++|||++|+.-+
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 89
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=26.78 E-value=1e+02 Score=40.20 Aligned_cols=64 Identities=19% Similarity=0.242 Sum_probs=40.7
Q ss_pred HHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 000414 1030 VRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1030 LA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcILLF 1103 (1541)
|..+-.-.+..+|-.+|....-...-+.+ ...|+. ++.|...+ .++|.+++|||.+.|..|..|
T Consensus 499 Ie~sK~~~l~r~l~aLGIr~VG~~~Ak~L----a~~f~s--l~~l~~a~----~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 499 IEKSKKQPLARFLYALGIRHVGETTAKSL----ARHFGT--LEALLAAS----EEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred HHHhccCCHHHHHHHcCCchhhHHHHHHH----HHHhhh--HHHHHhcC----HHHHhhccchhHHHHHHHHHH
Confidence 33334444555666677655444333333 334443 67776665 357889999999999999877
No 90
>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=24.91 E-value=58 Score=29.59 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=14.4
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 000414 1084 EYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1084 EeLLSLPGIGpKTADcILLF 1103 (1541)
+.|..|.|||+.||.-....
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 57899999999999876443
No 91
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=21.96 E-value=59 Score=27.53 Aligned_cols=16 Identities=19% Similarity=0.364 Sum_probs=13.2
Q ss_pred HhcCCCCcHHHHHHHH
Q 000414 1086 LLDIEGLGLKSVECVR 1101 (1541)
Q Consensus 1086 LLSLPGIGpKTADcIL 1101 (1541)
+-.+||||+|||--+|
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 4578999999997765
No 92
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=21.48 E-value=1.7e+02 Score=35.49 Aligned_cols=57 Identities=23% Similarity=0.350 Sum_probs=37.2
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHH--HhcCCCCcHHHHHHHHHH
Q 000414 1037 EIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEY--LLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1037 ELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREe--LLSLPGIGpKTADcILLF 1103 (1541)
++...+.-.|=..-|+..-+.+|+.|... .-|+ +++.+. |+.|||||+.+|+.|--|
T Consensus 14 ~iA~~me~~Gen~fk~~aYr~Aa~sle~~--~e~~--------~ei~e~~~~t~l~gIGk~ia~~I~e~ 72 (326)
T COG1796 14 RIADYMELEGENPFKIRAYRKAAQSLENL--TEDL--------EEIEERGRLTELPGIGKGIAEKISEY 72 (326)
T ss_pred HHHHHHHhcCCCccchHHHHHHHHhhhhc--ccch--------HHHHhhcccCCCCCccHHHHHHHHHH
Confidence 44444444554434777777777777652 2233 333344 899999999999999766
No 93
>PRK14973 DNA topoisomerase I; Provisional
Probab=21.14 E-value=4e+02 Score=36.40 Aligned_cols=62 Identities=18% Similarity=0.113 Sum_probs=44.7
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhcCCchHHHHHHhcCCCCcHHHHHHHH
Q 000414 1022 MDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1101 (1541)
Q Consensus 1022 ~gfPTPEALA~AdeEELeeLIR~lGf~nqKAkrIkeLAr~IvEdhGGIDLE~Lr~VPdDEAREeLLSLPGIGpKTADcIL 1101 (1541)
.|..+.++|+.|++..| +..|++..+++.+.+.|+-++. +.|++++||=..+|+.+.
T Consensus 763 ~~~~~~~~~~~~~~~~~----~~~~~sE~~~~~~~~~a~~~~~-------------------~~~~~~~gv~~~~~~~~~ 819 (936)
T PRK14973 763 SGINDIAALARADPADL----KKAGLSEAEAASLLAEAKSLCN-------------------ISRLKEIGVPAVSLKKYQ 819 (936)
T ss_pred cCcchHHHHhhCCHHHH----HHcCCCHHHHHHHHHHHHHHHH-------------------HHhhcccCCCHHHHHHHH
Confidence 46679999999999875 7789999999999888865542 236666666666666554
Q ss_pred HHhcC
Q 000414 1102 LLSLQ 1106 (1541)
Q Consensus 1102 LFAfg 1106 (1541)
..+|.
T Consensus 820 ~~G~~ 824 (936)
T PRK14973 820 EAGFD 824 (936)
T ss_pred HhcCC
Confidence 44443
No 94
>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=20.98 E-value=90 Score=28.74 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=18.3
Q ss_pred HHHHhc-CCCCcHHHHHHHHHH
Q 000414 1083 KEYLLD-IEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1083 REeLLS-LPGIGpKTADcILLF 1103 (1541)
.+.|.. +||||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999999877
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=20.93 E-value=50 Score=31.37 Aligned_cols=20 Identities=15% Similarity=0.204 Sum_probs=16.1
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 000414 1084 EYLLDIEGLGLKSVECVRLL 1103 (1541)
Q Consensus 1084 EeLLSLPGIGpKTADcILLF 1103 (1541)
+.+-.+||||+|||.-++.-
T Consensus 22 D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred ccCCCCCcccHHHHHHHHHH
Confidence 46778999999999877643
Done!