Query 021493
Match_columns 311
No_of_seqs 271 out of 1804
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 03:24:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2875 8-oxoguanine DNA glyco 100.0 4.6E-68 1E-72 480.1 21.7 276 33-311 3-283 (323)
2 TIGR00588 ogg 8-oxoguanine DNA 100.0 1.9E-61 4.1E-66 457.2 29.4 274 35-310 2-286 (310)
3 PRK10308 3-methyl-adenine DNA 100.0 6.1E-38 1.3E-42 293.3 26.4 220 66-310 31-261 (283)
4 COG0122 AlkA 3-methyladenine D 100.0 9.8E-39 2.1E-43 298.5 20.0 195 98-310 61-259 (285)
5 TIGR01083 nth endonuclease III 100.0 2.8E-29 6E-34 222.6 14.8 137 128-290 5-148 (191)
6 PRK10702 endonuclease III; Pro 100.0 2.8E-29 6.1E-34 225.6 14.5 136 129-290 9-151 (211)
7 COG0177 Nth Predicted EndoIII- 100.0 3.3E-28 7.1E-33 216.9 14.2 138 128-291 8-152 (211)
8 cd00056 ENDO3c endonuclease II 100.0 1.1E-27 2.3E-32 205.4 13.6 137 148-310 1-142 (158)
9 PF07934 OGG_N: 8-oxoguanine D 99.9 3.7E-28 7.9E-33 199.2 9.0 111 40-151 1-117 (117)
10 PRK13913 3-methyladenine DNA g 99.9 7E-27 1.5E-31 210.4 17.4 146 142-310 25-175 (218)
11 KOG1918 3-methyladenine DNA gl 99.9 3.6E-27 7.8E-32 207.8 13.1 174 121-310 48-226 (254)
12 TIGR01084 mutY A/G-specific ad 99.9 4.2E-26 9.2E-31 212.5 14.4 121 144-290 23-147 (275)
13 PRK10880 adenine DNA glycosyla 99.9 2.4E-24 5.2E-29 206.5 14.1 120 144-289 27-150 (350)
14 smart00478 ENDO3c endonuclease 99.9 7.3E-24 1.6E-28 180.0 14.0 125 156-309 1-130 (149)
15 PRK01229 N-glycosylase/DNA lya 99.9 7.6E-24 1.7E-28 189.3 14.6 154 128-310 16-181 (208)
16 PRK13910 DNA glycosylase MutY; 99.9 3.8E-21 8.3E-26 180.1 12.5 107 156-288 1-112 (289)
17 TIGR03252 uncharacterized HhH- 99.8 2.2E-18 4.7E-23 149.9 12.7 124 144-286 15-151 (177)
18 COG2231 Uncharacterized protei 99.8 9E-18 2E-22 147.7 16.0 140 143-310 26-170 (215)
19 KOG1921 Endonuclease III [Repl 99.8 7.9E-18 1.7E-22 151.1 14.8 122 147-292 78-204 (286)
20 COG1194 MutY A/G-specific DNA 99.8 1.2E-18 2.5E-23 164.8 9.8 139 145-309 32-175 (342)
21 PF00730 HhH-GPD: HhH-GPD supe 99.7 6.6E-16 1.4E-20 124.1 11.4 98 152-309 1-106 (108)
22 COG1059 Thermostable 8-oxoguan 99.3 1.2E-11 2.7E-16 107.5 12.2 143 144-311 36-184 (210)
23 KOG2457 A/G-specific adenine D 99.2 5.1E-11 1.1E-15 113.4 9.2 117 145-287 123-245 (555)
24 PF00633 HHH: Helix-hairpin-he 98.0 7E-06 1.5E-10 51.2 2.7 23 244-266 8-30 (30)
25 PF06029 AlkA_N: AlkA N-termin 97.4 0.00035 7.5E-09 57.3 5.5 76 66-144 31-113 (116)
26 smart00278 HhH1 Helix-hairpin- 95.6 0.0068 1.5E-07 36.3 1.5 20 248-267 2-21 (26)
27 PRK13901 ruvA Holliday junctio 94.9 0.038 8.3E-07 49.4 4.5 68 186-266 58-126 (196)
28 PF12826 HHH_2: Helix-hairpin- 94.7 0.063 1.4E-06 39.2 4.6 40 219-266 15-54 (64)
29 PRK14601 ruvA Holliday junctio 94.6 0.049 1.1E-06 48.2 4.5 68 186-266 59-127 (183)
30 PRK14606 ruvA Holliday junctio 94.4 0.057 1.2E-06 48.0 4.5 69 185-266 58-127 (188)
31 TIGR00084 ruvA Holliday juncti 93.8 0.085 1.8E-06 46.9 4.4 67 185-265 57-125 (191)
32 PRK14602 ruvA Holliday junctio 93.5 0.091 2E-06 47.2 4.2 67 186-265 60-127 (203)
33 COG0632 RuvA Holliday junction 93.2 0.069 1.5E-06 47.9 2.8 54 207-271 79-132 (201)
34 PRK14600 ruvA Holliday junctio 93.0 0.11 2.3E-06 46.1 3.8 66 186-265 59-125 (186)
35 PF09674 DUF2400: Protein of u 92.9 0.12 2.6E-06 47.4 4.0 37 273-311 176-212 (232)
36 PRK14603 ruvA Holliday junctio 92.5 0.094 2E-06 46.9 2.7 23 243-265 103-125 (197)
37 PRK14605 ruvA Holliday junctio 92.2 0.17 3.8E-06 45.1 4.0 67 185-264 58-125 (194)
38 PRK14604 ruvA Holliday junctio 92.2 0.11 2.4E-06 46.5 2.7 24 243-266 104-127 (195)
39 TIGR02757 conserved hypothetic 92.1 0.15 3.3E-06 46.6 3.6 37 273-311 173-209 (229)
40 PF14716 HHH_8: Helix-hairpin- 90.8 0.54 1.2E-05 34.5 4.8 45 208-264 20-64 (68)
41 PF14520 HHH_5: Helix-hairpin- 90.5 0.43 9.3E-06 34.1 3.9 32 230-265 25-56 (60)
42 PRK00076 recR recombination pr 90.5 0.2 4.3E-06 44.8 2.6 33 241-273 5-37 (196)
43 TIGR00615 recR recombination p 90.3 0.22 4.8E-06 44.5 2.7 33 241-273 5-37 (195)
44 COG0353 RecR Recombinational D 90.2 0.22 4.7E-06 44.4 2.5 32 241-272 6-37 (198)
45 PRK13844 recombination protein 89.9 0.28 6.1E-06 43.9 3.0 32 241-272 9-40 (200)
46 TIGR00624 tag DNA-3-methyladen 88.8 13 0.00028 32.9 12.5 125 125-265 7-164 (179)
47 PRK02515 psbU photosystem II c 88.7 0.97 2.1E-05 37.8 5.2 50 195-265 54-105 (132)
48 PF03118 RNA_pol_A_CTD: Bacter 88.3 0.6 1.3E-05 34.3 3.3 47 205-264 15-61 (66)
49 smart00483 POLXc DNA polymeras 87.6 0.79 1.7E-05 44.2 4.7 56 203-265 49-107 (334)
50 TIGR00608 radc DNA repair prot 86.6 0.76 1.7E-05 41.8 3.7 64 200-270 15-84 (218)
51 PF11731 Cdd1: Pathogenicity l 86.3 0.79 1.7E-05 36.1 3.1 30 243-272 8-37 (93)
52 PRK10353 3-methyl-adenine DNA 86.0 16 0.00035 32.4 11.6 132 124-269 7-170 (187)
53 PF14520 HHH_5: Helix-hairpin- 85.5 2.5 5.3E-05 30.1 5.2 32 190-221 26-59 (60)
54 TIGR01259 comE comEA protein. 84.7 1.5 3.3E-05 36.0 4.3 57 192-265 58-116 (120)
55 PF12836 HHH_3: Helix-hairpin- 84.6 1.5 3.3E-05 31.8 3.8 51 196-263 8-60 (65)
56 PRK00024 hypothetical protein; 84.1 1.7 3.6E-05 39.7 4.7 56 200-263 25-82 (224)
57 TIGR00575 dnlj DNA ligase, NAD 83.4 4 8.8E-05 43.0 7.8 72 192-267 456-550 (652)
58 PF02371 Transposase_20: Trans 83.2 1 2.2E-05 34.7 2.5 35 247-282 2-36 (87)
59 TIGR00084 ruvA Holliday juncti 82.7 1 2.2E-05 40.0 2.7 24 241-264 66-89 (191)
60 COG1948 MUS81 ERCC4-type nucle 82.7 21 0.00046 33.2 11.3 125 148-278 75-213 (254)
61 PRK14605 ruvA Holliday junctio 82.6 1 2.2E-05 40.1 2.7 25 241-265 67-91 (194)
62 KOG2841 Structure-specific end 82.5 3.6 7.8E-05 37.8 6.1 60 145-222 187-249 (254)
63 cd00141 NT_POLXc Nucleotidyltr 82.1 1.8 3.9E-05 41.2 4.3 54 208-270 52-106 (307)
64 PRK07956 ligA NAD-dependent DN 82.1 4.5 9.9E-05 42.7 7.6 72 191-266 468-562 (665)
65 PF10391 DNA_pol_lambd_f: Fing 81.0 1.4 3.1E-05 30.9 2.3 24 247-270 2-25 (52)
66 PF11798 IMS_HHH: IMS family H 79.7 1.2 2.6E-05 28.0 1.4 15 249-263 13-27 (32)
67 PRK00116 ruvA Holliday junctio 79.5 1.7 3.7E-05 38.6 3.0 21 246-266 107-127 (192)
68 PRK14350 ligA NAD-dependent DN 79.2 7.7 0.00017 41.0 8.1 23 245-267 539-561 (669)
69 TIGR00426 competence protein C 79.1 2.8 6E-05 30.6 3.5 55 195-266 9-66 (69)
70 PRK00116 ruvA Holliday junctio 78.9 1.7 3.6E-05 38.7 2.7 22 243-264 69-90 (192)
71 COG1555 ComEA DNA uptake prote 77.7 3.8 8.2E-05 35.0 4.4 50 197-263 92-143 (149)
72 PF03352 Adenine_glyco: Methyl 77.6 14 0.0003 32.6 8.0 128 125-265 3-162 (179)
73 PRK14973 DNA topoisomerase I; 75.1 9.9 0.00022 41.8 7.8 93 189-288 822-917 (936)
74 PRK13901 ruvA Holliday junctio 74.8 2.5 5.5E-05 37.8 2.7 25 241-265 66-90 (196)
75 PRK14601 ruvA Holliday junctio 74.7 2.5 5.5E-05 37.4 2.6 25 241-265 67-91 (183)
76 PRK14351 ligA NAD-dependent DN 74.6 19 0.00041 38.3 9.5 68 191-266 485-579 (689)
77 PRK08609 hypothetical protein; 74.2 3.4 7.4E-05 42.8 3.8 31 233-264 75-105 (570)
78 PRK14600 ruvA Holliday junctio 74.2 2.6 5.7E-05 37.3 2.6 25 241-265 67-91 (186)
79 PF12836 HHH_3: Helix-hairpin- 73.8 3.3 7.2E-05 30.0 2.7 23 245-267 12-34 (65)
80 PRK14606 ruvA Holliday junctio 73.0 2.9 6.4E-05 37.1 2.7 25 241-265 67-91 (188)
81 PRK14603 ruvA Holliday junctio 72.1 3.2 6.9E-05 37.1 2.7 25 241-265 66-90 (197)
82 PRK14604 ruvA Holliday junctio 71.7 3.3 7.1E-05 37.0 2.6 25 241-265 67-91 (195)
83 smart00279 HhH2 Helix-hairpin- 71.4 2.9 6.4E-05 26.9 1.7 16 249-264 18-33 (36)
84 TIGR01259 comE comEA protein. 70.5 3.9 8.5E-05 33.5 2.7 23 245-267 66-88 (120)
85 PRK14602 ruvA Holliday junctio 70.4 3.7 7.9E-05 36.9 2.7 25 241-265 68-92 (203)
86 PRK08097 ligB NAD-dependent DN 70.4 14 0.00031 38.3 7.2 72 191-266 448-539 (562)
87 PRK07945 hypothetical protein; 69.8 5.5 0.00012 38.4 3.9 49 207-266 17-68 (335)
88 smart00483 POLXc DNA polymeras 68.8 6.8 0.00015 37.8 4.3 43 211-266 25-67 (334)
89 PRK13482 DNA integrity scannin 68.5 13 0.00028 36.3 6.1 39 187-225 304-344 (352)
90 COG1555 ComEA DNA uptake prote 68.1 4.1 8.8E-05 34.8 2.4 23 246-268 96-118 (149)
91 COG2003 RadC DNA repair protei 67.9 6.2 0.00013 36.0 3.6 55 200-262 25-81 (224)
92 COG1415 Uncharacterized conser 67.2 9.9 0.00021 36.9 4.9 25 243-267 274-298 (373)
93 COG1796 POL4 DNA polymerase IV 67.2 8.8 0.00019 36.8 4.6 49 207-267 22-73 (326)
94 PRK07758 hypothetical protein; 66.8 10 0.00022 30.0 4.1 31 230-264 54-84 (95)
95 PRK02515 psbU photosystem II c 66.3 4.6 0.0001 33.8 2.2 20 246-265 60-79 (132)
96 cd00141 NT_POLXc Nucleotidyltr 65.3 8.9 0.00019 36.5 4.3 46 209-267 20-65 (307)
97 cd00080 HhH2_motif Helix-hairp 64.4 3.7 8E-05 30.8 1.2 23 247-270 22-44 (75)
98 COG0632 RuvA Holliday junction 64.0 5 0.00011 36.0 2.2 25 241-265 67-91 (201)
99 PF00416 Ribosomal_S13: Riboso 62.1 7.4 0.00016 31.2 2.7 24 244-267 12-35 (107)
100 PRK13482 DNA integrity scannin 60.5 13 0.00029 36.2 4.6 38 218-263 298-335 (352)
101 TIGR01448 recD_rel helicase, p 57.7 98 0.0021 33.1 10.9 20 249-269 182-202 (720)
102 KOG2534 DNA polymerase IV (fam 56.2 27 0.00058 33.7 5.6 74 233-308 83-160 (353)
103 TIGR00426 competence protein C 53.0 12 0.00026 27.2 2.3 21 246-266 15-36 (69)
104 COG2818 Tag 3-methyladenine DN 52.3 56 0.0012 29.1 6.7 76 138-225 22-105 (188)
105 PF01367 5_3_exonuc: 5'-3' exo 52.2 3.6 7.8E-05 32.9 -0.7 26 248-274 19-44 (101)
106 PRK08609 hypothetical protein; 51.8 19 0.00042 37.3 4.4 44 210-266 24-67 (570)
107 PF12826 HHH_2: Helix-hairpin- 51.0 17 0.00036 26.2 2.8 32 188-219 21-54 (64)
108 PF14490 HHH_4: Helix-hairpin- 47.8 25 0.00055 27.2 3.5 19 248-266 46-65 (94)
109 PF05559 DUF763: Protein of un 46.4 23 0.0005 34.0 3.6 32 243-274 265-299 (319)
110 PLN03132 NADH dehydrogenase (u 46.4 11 0.00024 38.1 1.6 18 15-32 13-30 (461)
111 PRK00024 hypothetical protein; 46.3 56 0.0012 29.7 6.0 31 190-220 54-86 (224)
112 CHL00137 rps13 ribosomal prote 44.3 13 0.00028 30.7 1.4 22 245-266 15-36 (122)
113 COG4277 Predicted DNA-binding 43.4 17 0.00036 34.9 2.2 22 245-266 328-349 (404)
114 PF09597 IGR: IGR protein moti 42.9 36 0.00079 24.3 3.3 37 188-224 17-55 (57)
115 TIGR01448 recD_rel helicase, p 41.3 40 0.00086 36.1 4.9 24 241-264 76-101 (720)
116 PF13592 HTH_33: Winged helix- 39.2 24 0.00051 25.0 2.0 55 256-310 3-57 (60)
117 COG0099 RpsM Ribosomal protein 38.9 19 0.00041 29.7 1.6 23 245-267 15-37 (121)
118 TIGR00608 radc DNA repair prot 38.6 95 0.0021 28.1 6.3 30 191-220 49-80 (218)
119 PRK05179 rpsM 30S ribosomal pr 38.5 18 0.00039 29.9 1.4 22 245-266 15-36 (122)
120 KOG2534 DNA polymerase IV (fam 38.2 37 0.00081 32.7 3.6 43 211-266 33-75 (353)
121 COG1948 MUS81 ERCC4-type nucle 36.7 44 0.00096 31.1 3.8 28 234-265 205-232 (254)
122 PTZ00134 40S ribosomal protein 36.0 20 0.00044 30.8 1.4 23 244-266 27-49 (154)
123 PF09999 DUF2240: Uncharacteri 35.5 95 0.0021 26.4 5.4 36 144-179 83-120 (144)
124 TIGR03629 arch_S13P archaeal r 35.2 20 0.00044 30.4 1.3 22 245-266 19-40 (144)
125 TIGR01954 nusA_Cterm_rpt trans 34.8 89 0.0019 20.6 4.3 33 190-222 14-48 (50)
126 TIGR03631 bact_S13 30S ribosom 34.8 21 0.00044 29.1 1.2 22 245-266 13-34 (113)
127 PRK14976 5'-3' exonuclease; Pr 34.6 23 0.00049 33.4 1.6 25 248-273 192-216 (281)
128 PF11549 Sec31: Protein transp 33.6 7.4 0.00016 26.9 -1.3 28 19-46 2-34 (51)
129 PRK04053 rps13p 30S ribosomal 33.5 23 0.00049 30.3 1.3 23 244-266 22-44 (149)
130 PRK12766 50S ribosomal protein 33.4 24 0.00053 32.4 1.5 23 247-269 3-25 (232)
131 COG1623 Predicted nucleic-acid 33.0 52 0.0011 31.4 3.7 33 187-219 310-344 (349)
132 COG3168 PilP Tfp pilus assembl 32.7 1.1E+02 0.0024 26.5 5.3 36 48-83 98-141 (170)
133 PF11239 DUF3040: Protein of u 32.6 72 0.0016 24.1 3.8 22 116-137 11-32 (82)
134 PRK09482 flap endonuclease-lik 32.1 27 0.00059 32.5 1.7 24 248-272 183-206 (256)
135 PF09171 DUF1886: Domain of un 32.1 14 0.00031 34.2 -0.2 148 121-291 14-186 (246)
136 PRK11511 DNA-binding transcrip 31.9 2.3E+02 0.005 22.9 7.1 37 156-204 2-42 (127)
137 PF14579 HHH_6: Helix-hairpin- 31.0 36 0.00078 26.1 2.0 21 245-265 25-45 (90)
138 smart00475 53EXOc 5'-3' exonuc 31.0 30 0.00064 32.2 1.7 24 248-272 187-210 (259)
139 cd00008 53EXOc 5'-3' exonuclea 30.5 31 0.00067 31.6 1.7 25 247-272 183-207 (240)
140 TIGR00596 rad1 DNA repair prot 29.8 41 0.00088 36.6 2.7 26 241-266 751-776 (814)
141 TIGR00375 conserved hypothetic 29.0 1.1E+02 0.0023 30.3 5.3 50 145-208 296-346 (374)
142 PF07647 SAM_2: SAM domain (St 28.3 1.4E+02 0.003 20.9 4.6 21 190-210 30-50 (66)
143 COG0272 Lig NAD-dependent DNA 27.8 1.2E+02 0.0027 32.1 5.7 29 234-266 534-562 (667)
144 PRK00558 uvrC excinuclease ABC 27.7 96 0.0021 32.5 5.0 28 234-265 566-593 (598)
145 KOG0739 AAA+-type ATPase [Post 27.4 94 0.002 30.2 4.4 62 246-308 254-330 (439)
146 PF11731 Cdd1: Pathogenicity l 27.3 1.2E+02 0.0025 24.0 4.2 26 230-255 32-57 (93)
147 COG0177 Nth Predicted EndoIII- 26.6 4.7E+02 0.01 23.7 8.6 111 145-275 69-189 (211)
148 PF12482 DUF3701: Phage integr 26.3 68 0.0015 25.4 2.8 23 247-269 50-72 (96)
149 PRK05182 DNA-directed RNA poly 26.1 99 0.0021 29.6 4.4 48 204-264 251-298 (310)
150 PF14475 Mso1_Sec1_bdg: Sec1-b 25.9 36 0.00079 22.7 1.0 15 275-289 17-31 (41)
151 PF14635 HHH_7: Helix-hairpin- 25.3 49 0.0011 26.6 1.8 38 207-260 56-94 (104)
152 KOG2675 Adenylate cyclase-asso 25.0 50 0.0011 33.2 2.1 46 138-198 419-465 (480)
153 TIGR02027 rpoA DNA-directed RN 24.8 1.1E+02 0.0023 29.1 4.4 48 204-264 237-284 (297)
154 KOG1945 Protein phosphatase 1 24.8 37 0.00081 33.1 1.2 13 13-25 37-49 (377)
155 TIGR00575 dnlj DNA ligase, NAD 23.2 1.1E+02 0.0023 32.5 4.4 28 233-264 456-483 (652)
156 TIGR02236 recomb_radA DNA repa 23.0 2.3E+02 0.0049 26.5 6.2 34 190-223 20-55 (310)
157 PRK14351 ligA NAD-dependent DN 22.4 4.2E+02 0.009 28.4 8.5 33 186-218 544-578 (689)
158 PF11372 DUF3173: Domain of un 22.3 3.1E+02 0.0067 19.8 5.6 28 199-226 4-32 (59)
159 PRK10371 DNA-binding transcrip 22.1 4.4E+02 0.0096 24.6 8.0 55 238-308 241-295 (302)
160 PF06568 DUF1127: Domain of un 22.0 63 0.0014 21.0 1.6 19 192-210 16-34 (40)
161 PRK00254 ski2-like helicase; P 21.7 1.2E+02 0.0027 32.1 4.6 20 247-266 678-697 (720)
162 COG1379 PHP family phosphoeste 21.6 1.4E+02 0.0031 29.1 4.4 37 143-179 301-338 (403)
163 COG3743 Uncharacterized conser 21.5 43 0.00093 28.1 0.8 17 247-263 67-83 (133)
164 COG0258 Exo 5'-3' exonuclease 21.4 44 0.00095 31.7 1.0 20 249-269 200-219 (310)
165 PRK14973 DNA topoisomerase I; 21.3 3.2E+02 0.007 30.3 7.7 109 192-305 767-893 (936)
166 COG1152 CdhA CO dehydrogenase/ 21.1 3.5E+02 0.0076 28.6 7.3 125 139-271 88-216 (772)
No 1
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=100.00 E-value=4.6e-68 Score=480.12 Aligned_cols=276 Identities=46% Similarity=0.871 Sum_probs=252.3
Q ss_pred CCCCCcccccCCCCCCCcCcccCCCCCcCceeeCCCceEEeeCCeEEEEEEecCCcEEEEEcCCCC--hHHHHHHHHHhh
Q 021493 33 NKPSKWTPLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHTSPS--EPAAKSALLDFL 110 (311)
Q Consensus 33 ~~~~~w~~l~~~~~~~~L~~tl~~GQ~Frw~~~~~~~~~gv~~~~~v~l~q~~~~~l~~~~~~~~~--~~~~~~~l~~yf 110 (311)
+.+..|.+|+++.++++|+.||.+||+|||++.+.+.|+||+++.+|.++|+++.-+.|.+.++.+ .++..+.|++||
T Consensus 3 ~t~~~w~~i~~~~sEl~L~~tL~sGQsFRWr~~~~~~ysG~lg~~v~~L~Q~ee~~~~y~~~~s~~~p~~del~~i~~yf 82 (323)
T KOG2875|consen 3 STPALWASIPCSRSELDLELTLPSGQSFRWREQSPAHYSGVLGDQVWTLTQTEEQCTVYRGDKSASRPTPDELEAISKYF 82 (323)
T ss_pred CccccceeccCCHHHcchhhhccCCceeeeecCCcccccceeccEEEEEEecCCceEEEEeecCCCCCChHHHHHHHHHH
Confidence 445679999999999999999999999999999989999999999999999876545566655422 334455899999
Q ss_pred cCCCCHHHHHHHHhccChhHHHHHHHhcCCccCCCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCcccccccccc
Q 021493 111 NMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHE 189 (311)
Q Consensus 111 ~Ld~dl~~~~~~l~~~D~~l~~~~~~~~GlR~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~ 189 (311)
+||++|..+|.+|...|+.|.+++. .|+|+++|||||||++||||+||||++|++|+++|| .||..++.++|..||.
T Consensus 83 ~ldv~L~~l~~~W~~~D~~F~~la~--qgvRlLrQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~ 160 (323)
T KOG2875|consen 83 QLDVTLAQLYHHWGSVDDHFQELAQ--QGVRLLRQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHG 160 (323)
T ss_pred hheeeHHHHHHHhCcCChHHHHHHH--hhhHHHhcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCccccc
Confidence 9999999999999999999999998 899999999999999999999999999999999999 8999999999999999
Q ss_pred CCCHHHHh-cCCHHHHHHcCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhc
Q 021493 190 FPSLERLS-LVSEVELRNAGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 268 (311)
Q Consensus 190 FPtpe~La-~~~~e~Lr~~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l 268 (311)
|||.++|+ ...+++||++|||||||||..+|++|.++.+ |.-||..|++++++|++++|+.+||||+|||||||||+|
T Consensus 161 FPsl~~L~g~~~Ea~LR~~gfGYRAkYI~~ta~~l~~~~g-~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l 239 (323)
T KOG2875|consen 161 FPSLQALAGPEVEAELRKLGFGYRAKYISATARALQEKQG-GLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSL 239 (323)
T ss_pred CccHHHhcCcHhHHHHHHcCcchhHHHHHHHHHHHHHhcc-cchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhc
Confidence 99999999 5678999999999999999999999999865 567999999999999999999999999999999999999
Q ss_pred CCCCccccchHHHHHHHHcCCCcccCCC-CCHHHHHHHHHHhhC
Q 021493 269 DQHHAIPVDTHVWKIATRYLLPELAGVR-LTPKLCSRVAEAFCE 311 (311)
Q Consensus 269 ~~~d~fPVDt~v~Ri~~r~~~~~~~~~~-~t~k~y~~i~~~~~~ 311 (311)
+...++|||+||+|+++.++++...++. +++|.|.+++.+|++
T Consensus 240 ~~~~~VPVDvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~~ 283 (323)
T KOG2875|consen 240 DKLSAVPVDVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFRS 283 (323)
T ss_pred CCCCcccchhhHHHHhhcccCCCccccccCCcchhHHHHHHHHH
Confidence 9999999999999999977777666544 999999999988863
No 2
>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=100.00 E-value=1.9e-61 Score=457.22 Aligned_cols=274 Identities=38% Similarity=0.726 Sum_probs=241.8
Q ss_pred CCCcccccCCCCCCCcCcccCCCCCcCce-eeCCCceEE--eeCCe-EEEEEEecCCcEEEEEcC-C-CChHHHHHHHHH
Q 021493 35 PSKWTPLNLTQSELSLPLTFPTGQTFRWK-KTGPLQYTG--PIGPH-LISLKHLQNGDVCYHIHT-S-PSEPAAKSALLD 108 (311)
Q Consensus 35 ~~~w~~l~~~~~~~~L~~tl~~GQ~Frw~-~~~~~~~~g--v~~~~-~v~l~q~~~~~l~~~~~~-~-~~~~~~~~~l~~ 108 (311)
.++|.+|.++.++|||+.||+|||||||+ +.++|.|.+ ++++. ++.++|.++. +.+..+. . ...+.+.+.|++
T Consensus 2 ~~~w~~~~~~~~~~~l~~tl~~GQ~Frw~~~~~~~~y~~~~~~~~~~~~~~~q~~~~-~~~~~~~~~~~~~~~~~~~ir~ 80 (310)
T TIGR00588 2 GHRWASIPIPRSELRLDLVLRSGQSFRWRWEESPAHWSGLLVIADQPVWTLTQTEEQ-LLCTVYRGDKPTQDELETKLEK 80 (310)
T ss_pred CCcccccCCchhcccHHHHcCCCceecCceeCCCCeEEEEEEECCeeEEEEEEcCCc-eEEEEecCCCccHHHHHHHHHH
Confidence 46899999999999999999999999998 777889999 88887 8889987543 3333332 2 124567899999
Q ss_pred hhcCCCCHHHHHHHHhccChhHHHHHHHhcCCccCCCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCcccccccc
Q 021493 109 FLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEF 187 (311)
Q Consensus 109 yf~Ld~dl~~~~~~l~~~D~~l~~~~~~~~GlR~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~ 187 (311)
||+||.|++.+++.|...||.|+++++.++|+|++++||||+||++|||||+|+++|.+++++|+ .||+++...++..+
T Consensus 81 ~f~Ld~d~~~i~~~~~~~D~~l~~~~~~~~GlRi~~~d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~ 160 (310)
T TIGR00588 81 YFQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQDPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTY 160 (310)
T ss_pred HhcCCCCHHHHHHHHhhcCHHHHHHHHhCCCCCCCCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCccc
Confidence 99999999999999977899999999999999999999999999999999999999999999999 89998877777789
Q ss_pred ccCCCHHHHhcCC-HHHHHHcCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 188 HEFPSLERLSLVS-EVELRNAGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 188 ~~FPtpe~La~~~-~e~Lr~~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
+.||||++|++++ +++||.||+||||+||+++|+++.++++ +..+++.|.++++++++++|++|||||+|||||||||
T Consensus 161 ~~FPtp~~La~~~~e~~Lr~~G~g~Ra~~I~~~A~~i~~~~~-~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 161 HGFPSLHALTGPEAEAHLRKLGLGYRARYIRETARALLEEQG-GRAWLQQIRGASYEDAREALCELPGVGPKVADCICLM 239 (310)
T ss_pred ccCCCHHHHhCCChHHHHHHcCCHHHHHHHHHHHHHHHhccC-CchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH
Confidence 9999999999875 5689999999999999999999998543 4557889999999999999999999999999999999
Q ss_pred hcCCCCccccchHHHHHHHHcCCCcc---cCCCCCHHHHHHHHHHhh
Q 021493 267 SLDQHHAIPVDTHVWKIATRYLLPEL---AGVRLTPKLCSRVAEAFC 310 (311)
Q Consensus 267 ~l~~~d~fPVDt~v~Ri~~r~~~~~~---~~~~~t~k~y~~i~~~~~ 310 (311)
+|+++++||||+||+|+++++|.... ..+.++++.|+++.+.++
T Consensus 240 ~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~ 286 (310)
T TIGR00588 240 GLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFR 286 (310)
T ss_pred hCCCCCceeecHHHHHHHHHHhcccccccccccCChhHHHHHHHHHH
Confidence 99999999999999999999874321 234578999999998765
No 3
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=6.1e-38 Score=293.29 Aligned_cols=220 Identities=18% Similarity=0.189 Sum_probs=183.1
Q ss_pred CCCceEEeeC----CeEEEEEEecCC-cEEEEEcCCC--ChHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHHHHHhc
Q 021493 66 GPLQYTGPIG----PHLISLKHLQNG-DVCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLA 138 (311)
Q Consensus 66 ~~~~~~gv~~----~~~v~l~q~~~~-~l~~~~~~~~--~~~~~~~~l~~yf~Ld~dl~~~~~~l~~~D~~l~~~~~~~~ 138 (311)
+++.|...+. ..++.|++.++. .+.+++..+. ....+...+++|||||.|++.|+..+ ..+++.++
T Consensus 31 ~~~~y~R~~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L-------~~~~~~~~ 103 (283)
T PRK10308 31 AEGYYARSLAVGEHRGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGAL-------GKLGAARP 103 (283)
T ss_pred ECCEEEEEEEECCccEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHH-------HHHHHhCC
Confidence 3456665442 567888886543 3566665532 23468899999999999999998655 56899999
Q ss_pred CCccC-CCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHHHHHHcCCch-HHHH
Q 021493 139 GARVL-RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGY-RAKY 215 (311)
Q Consensus 139 GlR~l-~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~Glg~-RA~~ 215 (311)
|+|++ .+||||++|++||+||+|+++|.++..+|+ +||+++.+ +..++.||||++|+++++++|++||+++ ||+|
T Consensus 104 GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~--~~~~~~FPtpe~La~~~~~eL~~~Gl~~~Ra~~ 181 (283)
T PRK10308 104 GLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDD--FPEYVCFPTPERLAAADPQALKALGMPLKRAEA 181 (283)
T ss_pred CCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccC--CCCccCCCCHHHHHcCCHHHHHHCCCCHHHHHH
Confidence 99998 599999999999999999999999999999 89998743 2347899999999999999999999985 9999
Q ss_pred HHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccc-cchHHHHHHHHcCCCcccC
Q 021493 216 ITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIP-VDTHVWKIATRYLLPELAG 294 (311)
Q Consensus 216 I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fP-VDt~v~Ri~~r~~~~~~~~ 294 (311)
|+++|+++.+ |.++++.. .+.++++++|++|||||+|||+||+||+||++|+|| .|+|++|.+ +
T Consensus 182 L~~lA~~i~~----g~l~l~~~--~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~------ 246 (283)
T PRK10308 182 LIHLANAALE----GTLPLTIP--GDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P------ 246 (283)
T ss_pred HHHHHHHHHc----CCCCcccc--CCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c------
Confidence 9999999998 66776653 367899999999999999999999999999999995 599998744 1
Q ss_pred CCCCHHHHHHHHHHhh
Q 021493 295 VRLTPKLCSRVAEAFC 310 (311)
Q Consensus 295 ~~~t~k~y~~i~~~~~ 310 (311)
..++++..++++.|+
T Consensus 247 -~~~~~~~~~~a~~w~ 261 (283)
T PRK10308 247 -GMTPAQIRRYAERWK 261 (283)
T ss_pred -cCCHHHHHHHHHhcC
Confidence 247788888888875
No 4
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.8e-39 Score=298.52 Aligned_cols=195 Identities=26% Similarity=0.391 Sum_probs=175.1
Q ss_pred ChHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHHHHHhcCCcc-CCCCHHHHHHHHHHhccccHHHHHHHHHHHH-hh
Q 021493 98 SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARV-LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SL 175 (311)
Q Consensus 98 ~~~~~~~~l~~yf~Ld~dl~~~~~~l~~~D~~l~~~~~~~~GlR~-l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~ 175 (311)
..+++...+.++|+||.++..+++.+. .++.... +|+|+ +.+||||+||++|||||+|+++|.+++++|+ .|
T Consensus 61 ~~~~~~~~~~~~~~lD~~l~~i~~~~~-~~~~~~~-----~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~ 134 (285)
T COG0122 61 VAEDIEAALRRLFDLDPDLAPIIDALG-PLPLLRA-----PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLY 134 (285)
T ss_pred hhHHHHHHHHHHHhcCCcHHHHHHhcC-ccccccc-----cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHh
Confidence 346788999999999999999998886 5555444 66664 5799999999999999999999999999999 89
Q ss_pred CCCCccccccccccCCCHHHHhcCCHHHHHHcCCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCc
Q 021493 176 GSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPG 254 (311)
Q Consensus 176 G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~G 254 (311)
|+.+. .+|.|||||+|++++++.|+.||++ +||+||+++|+++.+ |.+++..+..++++++++.|++|+|
T Consensus 135 g~~~~-----~~~~fptpe~l~~~~~~~l~~~g~s~~Ka~yi~~~A~~~~~----g~~~~~~l~~~~~e~a~e~L~~i~G 205 (285)
T COG0122 135 GNALE-----IYHSFPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAE----GELDLSELKPLSDEEAIEELTALKG 205 (285)
T ss_pred CCccc-----cccCCCCHHHHHhcCHHHHHHhCCcHHHHHHHHHHHHHHHc----CCccHHHhccCCHHHHHHHHHcCCC
Confidence 98873 6899999999999999999999985 899999999999998 7899999999999999999999999
Q ss_pred cchHHHHHHHHHhcCCCCcccc-chHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 021493 255 VGPKVAACIALFSLDQHHAIPV-DTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 310 (311)
Q Consensus 255 IG~ktAd~vlLf~l~~~d~fPV-Dt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~~ 310 (311)
||||||+|+|||+||++|+||+ |.++++.++++| . ..+..+.+...++++.|+
T Consensus 206 IG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~-~--~~~~~~~~~~~~~~e~w~ 259 (285)
T COG0122 206 IGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLY-R--LPTRPTEKEVRELAERWG 259 (285)
T ss_pred cCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHh-c--CCCCchHHHHHHHHhccc
Confidence 9999999999999999999996 778899999988 2 346788888999999886
No 5
>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=99.96 E-value=2.8e-29 Score=222.59 Aligned_cols=137 Identities=26% Similarity=0.372 Sum_probs=119.2
Q ss_pred hhHHHHHHHhcCCc--cCCCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHH-
Q 021493 128 CRFAELAKYLAGAR--VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL- 204 (311)
Q Consensus 128 ~~l~~~~~~~~GlR--~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~L- 204 (311)
+.+.++.+.+++.+ ...+||||+||++|||||++++++.++..+|. ..||||++|+++++++|
T Consensus 5 ~i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~--------------~~~pt~~~l~~~~~~~L~ 70 (191)
T TIGR01083 5 EILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLF--------------EVYPTPQALAQAGLEELE 70 (191)
T ss_pred HHHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHH--------------HHCCCHHHHHcCCHHHHH
Confidence 34566667777765 34589999999999999999999999998873 46899999999999998
Q ss_pred ---HHcCCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHH
Q 021493 205 ---RNAGFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHV 280 (311)
Q Consensus 205 ---r~~Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v 280 (311)
+.+||. .||+||+++|+.+.++++| +.++.+++|+++||||+|||+|||+|+++++ +||||+||
T Consensus 71 ~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~-----------~~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v 138 (191)
T TIGR01083 71 EYIKSIGLYRNKAKNIIALCRILVERYGG-----------EVPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHV 138 (191)
T ss_pred HHHHhcCChHHHHHHHHHHHHHHHHHcCC-----------CCchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhH
Confidence 778986 5999999999999987654 3456899999999999999999999999984 69999999
Q ss_pred HHHHHHcCCC
Q 021493 281 WKIATRYLLP 290 (311)
Q Consensus 281 ~Ri~~r~~~~ 290 (311)
+|+++|+|+.
T Consensus 139 ~Ri~~r~g~~ 148 (191)
T TIGR01083 139 FRVSNRLGLS 148 (191)
T ss_pred HHHHHHcCCC
Confidence 9999999875
No 6
>PRK10702 endonuclease III; Provisional
Probab=99.96 E-value=2.8e-29 Score=225.64 Aligned_cols=136 Identities=22% Similarity=0.313 Sum_probs=117.1
Q ss_pred hHHHHHHHhcC--CccCCCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHH
Q 021493 129 RFAELAKYLAG--ARVLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN 206 (311)
Q Consensus 129 ~l~~~~~~~~G--lR~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~ 206 (311)
.+..+.+.++. .....+||||+||++|||||+++.++.+++.+| +..||||++|+++++++|++
T Consensus 9 i~~~l~~~~~~~~~~~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L--------------~~~~pt~e~l~~a~~~~l~~ 74 (211)
T PRK10702 9 ILTRLRDNNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKL--------------YPVANTPAAMLELGVEGVKT 74 (211)
T ss_pred HHHHHHHHCCCCCCCCCCCChHHHHHHHHHHhhcCHHHHHHHHHHH--------------HHHcCCHHHHHCCCHHHHHH
Confidence 34445555553 234569999999999999999999999999887 35789999999999999865
Q ss_pred ----cCCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHH
Q 021493 207 ----AGFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVW 281 (311)
Q Consensus 207 ----~Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~ 281 (311)
+||. .||++|+++|+.+.++++| +.++.+++|++|||||+|||+|||+|++++ ++||||+||+
T Consensus 75 ~i~~~G~y~~kA~~l~~~a~~i~~~~~~-----------~~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v~ 142 (211)
T PRK10702 75 YIKTIGLYNSKAENVIKTCRILLEQHNG-----------EVPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIF 142 (211)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHcCC-----------CCCchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchHH
Confidence 6775 4999999999999987765 456789999999999999999999999999 7999999999
Q ss_pred HHHHHcCCC
Q 021493 282 KIATRYLLP 290 (311)
Q Consensus 282 Ri~~r~~~~ 290 (311)
|++.|+|+.
T Consensus 143 Rv~~r~g~~ 151 (211)
T PRK10702 143 RVCNRTQFA 151 (211)
T ss_pred HHHHHhCCC
Confidence 999999874
No 7
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.96 E-value=3.3e-28 Score=216.94 Aligned_cols=138 Identities=30% Similarity=0.444 Sum_probs=122.0
Q ss_pred hhHHHHHHHhcCCcc-C-CCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHH-
Q 021493 128 CRFAELAKYLAGARV-L-RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL- 204 (311)
Q Consensus 128 ~~l~~~~~~~~GlR~-l-~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~L- 204 (311)
..+..+.+.++..+. + ..|||+.||+.|||||++.+++.++..+| |..|||||+|+++++++|
T Consensus 8 ~i~~~l~~~~p~~~~~l~~~~pf~lLva~iLSaqttD~~vn~at~~L--------------f~~~~t~e~l~~a~~~~l~ 73 (211)
T COG0177 8 EILDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPAL--------------FKRYPTPEDLLNADEEELE 73 (211)
T ss_pred HHHHHHHHHCCCCCCccCcCCcHHHHHHHHHhccCchHHHHHHHHHH--------------HHHcCCHHHHHcCCHHHHH
Confidence 345556666776653 3 48999999999999999999999999887 456789999999999887
Q ss_pred ---HHcCCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHH
Q 021493 205 ---RNAGFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHV 280 (311)
Q Consensus 205 ---r~~Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v 280 (311)
+.+||. .||++|+++|+.|.++++| ..++.+++|++|||||+|||++||.+++|.+ +|||||||
T Consensus 74 ~~I~~iGlyr~KAk~I~~~~~~l~e~~~g-----------~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDTHV 141 (211)
T COG0177 74 ELIKSIGLYRNKAKNIKELARILLEKFGG-----------EVPDTREELLSLPGVGRKTANVVLSFAFGIP-AIAVDTHV 141 (211)
T ss_pred HHHHhcCCcHHHHHHHHHHHHHHHHHcCC-----------CCCchHHHHHhCCCcchHHHHHHHHhhcCCC-cccccchH
Confidence 568997 4999999999999999987 6788999999999999999999999999996 99999999
Q ss_pred HHHHHHcCCCc
Q 021493 281 WKIATRYLLPE 291 (311)
Q Consensus 281 ~Ri~~r~~~~~ 291 (311)
.|+++|+++..
T Consensus 142 ~Rvs~R~gl~~ 152 (211)
T COG0177 142 HRVSNRLGLVP 152 (211)
T ss_pred HHHHHHhCCCC
Confidence 99999999864
No 8
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.95 E-value=1.1e-27 Score=205.35 Aligned_cols=137 Identities=31% Similarity=0.415 Sum_probs=119.3
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHHHHHHcCCc----hHHHHHHHHHHH
Q 021493 148 VECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFG----YRAKYITGTVDV 222 (311)
Q Consensus 148 fe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~Glg----~RA~~I~~~A~~ 222 (311)
||+|+++||+||+++++|.+++++|+ +|| |||++|+++++++|++|+.+ +||++|+++|+.
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g--------------pt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~~ 66 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG--------------PTPEALAAADEEELRELIRSLGYRRKAKYLKELARA 66 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC--------------CCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHHH
Confidence 79999999999999999999999998 555 89999999999999998765 699999999999
Q ss_pred HHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCCCCHHHH
Q 021493 223 LQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLC 302 (311)
Q Consensus 223 i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y 302 (311)
+.+++.+ +.. +.+++++.|++|||||+|||+|+++|+++ .++||+|+|+.|+++++|+. ....+.+.+
T Consensus 67 ~~~~~~~----~~~----~~~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pvD~~v~r~~~~~~~~---~~~~~~~~~ 134 (158)
T cd00056 67 IVEGFGG----LVL----DDPDAREELLALPGVGRKTANVVLLFALG-PDAFPVDTHVRRVLKRLGLI---PKKKTPEEL 134 (158)
T ss_pred HHHHcCC----ccC----CCcccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCccchhHHHHHHHhCCC---CCCCCHHHH
Confidence 9986543 211 67899999999999999999999999999 79999999999999999863 234567777
Q ss_pred HHHHHHhh
Q 021493 303 SRVAEAFC 310 (311)
Q Consensus 303 ~~i~~~~~ 310 (311)
.++.+.|.
T Consensus 135 ~~~~~~~~ 142 (158)
T cd00056 135 EELLEELL 142 (158)
T ss_pred HHHHHHHC
Confidence 77766653
No 9
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=99.95 E-value=3.7e-28 Score=199.16 Aligned_cols=111 Identities=32% Similarity=0.594 Sum_probs=86.3
Q ss_pred cccCCCCCCCcCcccCCCCCcCceeeCCCceEEeeCCeEEEEEEecCCcEEEEEcC------CCChHHHHHHHHHhhcCC
Q 021493 40 PLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHT------SPSEPAAKSALLDFLNMG 113 (311)
Q Consensus 40 ~l~~~~~~~~L~~tl~~GQ~Frw~~~~~~~~~gv~~~~~v~l~q~~~~~l~~~~~~------~~~~~~~~~~l~~yf~Ld 113 (311)
+|++++++|||+.||+|||||||++.+++.|+||+++++|.|+|.+ +.+.+.+.. ..+.++..+.|++||+||
T Consensus 1 ~l~~~~~~~~L~~tL~sGQ~FrW~~~~~~~~~gv~~~~~~~l~q~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~YF~Ld 79 (117)
T PF07934_consen 1 KLPIPKEEFNLDKTLFSGQSFRWRKIDDGEWSGVIGDRVVQLRQDD-DNLLYRCLSSAEPSNSSSEEDIEEFLRDYFDLD 79 (117)
T ss_dssp EEE-STTT--HHHHCCTTS-SSEEEECTTEEEEEETTEEEEEEEET-TEEEEECE--TTS---S-HHHHHHCHHHHTTTT
T ss_pred CCcCCHHHcCHHHHhcccCcccCEEeCCCeEEEEcCCeEEEEEECC-CEEEEEEecCCCcccccchhhHHHHHHHHhcCC
Confidence 4788899999999999999999999988779999999999999975 456665543 123567889999999999
Q ss_pred CCHHHHHHHHhccChhHHHHHHHhcCCccCCCCHHHHH
Q 021493 114 ISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECL 151 (311)
Q Consensus 114 ~dl~~~~~~l~~~D~~l~~~~~~~~GlR~l~~dpfe~L 151 (311)
.||+++|+.|++.|+.|+.+++.+.|+|+++|||||||
T Consensus 80 ~dl~~l~~~~~~~D~~l~~~~~~~~GlRiLrQdp~E~L 117 (117)
T PF07934_consen 80 VDLEKLYEDWSKKDPRLAKAIDKYRGLRILRQDPFETL 117 (117)
T ss_dssp S-HHHHHHHHCCHSHHHHHHHHCTTT-------HHHHH
T ss_pred ccHHHHHHHHhhhCHHHHHHHhcCCCcEEECCChhhhC
Confidence 99999999999889999999999999999999999997
No 10
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.95 E-value=7e-27 Score=210.45 Aligned_cols=146 Identities=14% Similarity=0.144 Sum_probs=119.6
Q ss_pred cCCCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHHc----CCc-hHHHHH
Q 021493 142 VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA----GFG-YRAKYI 216 (311)
Q Consensus 142 ~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~----Glg-~RA~~I 216 (311)
....+|||.||++|++||++++++.+++.+|..-|.-. -..+|||+.|+++++++|+++ ||. .||+||
T Consensus 25 Wp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~-------~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~L 97 (218)
T PRK13913 25 WPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILE-------NDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRL 97 (218)
T ss_pred CcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccc-------cccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHH
Confidence 45689999999999999999999999999996321100 025799999999999998776 997 499999
Q ss_pred HHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCC
Q 021493 217 TGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVR 296 (311)
Q Consensus 217 ~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~ 296 (311)
+++|+.+.++++| ++ .+..++++++|+++||||+|||||||+|++++ ++||||+|++|++.|+|+..
T Consensus 98 k~la~~i~~~~g~----~~---~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~r-p~fvVDty~~Rv~~RlG~~~----- 164 (218)
T PRK13913 98 IDLSENILKDFGS----FE---NFKQEVTREWLLDQKGIGKESADAILCYVCAK-EVMVVDKYSYLFLKKLGIEI----- 164 (218)
T ss_pred HHHHHHHHHHcCC----ch---hccCchHHHHHHcCCCccHHHHHHHHHHHcCC-CccccchhHHHHHHHcCCCC-----
Confidence 9999999987643 32 23346789999999999999999999999999 68999999999999998742
Q ss_pred CCHHHHHHHHHHhh
Q 021493 297 LTPKLCSRVAEAFC 310 (311)
Q Consensus 297 ~t~k~y~~i~~~~~ 310 (311)
+.|.++.+.|.
T Consensus 165 ---~~y~~~~~~~~ 175 (218)
T PRK13913 165 ---EDYDELQHFFE 175 (218)
T ss_pred ---CCHHHHHHHHH
Confidence 13666666553
No 11
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.95 E-value=3.6e-27 Score=207.80 Aligned_cols=174 Identities=20% Similarity=0.273 Sum_probs=151.7
Q ss_pred HHHhccChhHHHHHHHhcCCccC-CCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhc
Q 021493 121 EGFSASDCRFAELAKYLAGARVL-RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSL 198 (311)
Q Consensus 121 ~~l~~~D~~l~~~~~~~~GlR~l-~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~ 198 (311)
.++...||.|.+++.-+..++.- .|.||+.|+++|+|||.+.++|..+++|++ .||.. +.||+|+.+..
T Consensus 48 ~hl~~kd~~L~~lv~~~~p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~---------~~~~~pe~i~~ 118 (254)
T KOG1918|consen 48 SHLDEKDPSLVKLVGNHEPLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGA---------EKFPTPEFIDP 118 (254)
T ss_pred HhhhhcchHHHHHhcCCCCCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---------cCCCCchhcCc
Confidence 45556788888888877766654 599999999999999999999999999998 67742 57999999999
Q ss_pred CCHHHHHHcCCc-hHHHHHHHHHHHHHHhcCCC-ccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCcccc
Q 021493 199 VSEVELRNAGFG-YRAKYITGTVDVLQSKHSGG-AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPV 276 (311)
Q Consensus 199 ~~~e~Lr~~Glg-~RA~~I~~~A~~i~~~~~gg-~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPV 276 (311)
++.++||.|||+ .||.||+.+|++..+ | ......+.+|+.+++.+.|+.++|||+||++|+++|+|+|+|++|+
T Consensus 119 ~~~~~lrkcG~S~rK~~yLh~lA~~~~n----g~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~ 194 (254)
T KOG1918|consen 119 LDCEELRKCGFSKRKASYLHSLAEAYTN----GYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPA 194 (254)
T ss_pred CCHHHHHHhCcchhhHHHHHHHHHHHhc----CCCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCc
Confidence 999999999997 699999999999998 4 6678888899999999999999999999999999999999999999
Q ss_pred c-hHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 021493 277 D-THVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 310 (311)
Q Consensus 277 D-t~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~~ 310 (311)
| ..|++-++.++.. ..-+.+++.+++.+.|+
T Consensus 195 dDlgir~g~k~l~gl---~~~p~~~evekl~e~~k 226 (254)
T KOG1918|consen 195 DDLGIRNGVKKLLGL---KPLPLPKEVEKLCEKCK 226 (254)
T ss_pred hhhhHHHHHHHHhCC---CCCCchHHHHHHhhhcc
Confidence 5 5788888887532 23467888888888875
No 12
>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=99.94 E-value=4.2e-26 Score=212.47 Aligned_cols=121 Identities=20% Similarity=0.370 Sum_probs=108.3
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHH----HHcCCchHHHHHHHH
Q 021493 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL----RNAGFGYRAKYITGT 219 (311)
Q Consensus 144 ~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~L----r~~Glg~RA~~I~~~ 219 (311)
.+|||++||++|++||++++++...+.+|. ..||||++|+++++++| +.+|+..||++|+++
T Consensus 23 ~~dpy~vlvseIL~QQT~v~~v~~~~~rl~--------------~~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~~~ 88 (275)
T TIGR01084 23 NKTPYRVWLSEVMLQQTQVATVIPYFERFL--------------ERFPTVQALANAPQDEVLKLWEGLGYYARARNLHKA 88 (275)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHH--------------HhCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHHHH
Confidence 489999999999999999999999999884 46899999999999999 677876699999999
Q ss_pred HHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCC
Q 021493 220 VDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLP 290 (311)
Q Consensus 220 A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~ 290 (311)
|+.+.++++| ..++.+++|++|||||+|||+||++|+|++. .++||+||+|++.|+|..
T Consensus 89 A~~i~~~~~g-----------~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~-~~~vD~~v~RVl~Rl~~~ 147 (275)
T TIGR01084 89 AQEVVEEFGG-----------EFPQDFEDLAALPGVGRYTAGAILSFALNKP-YPILDGNVKRVLSRLFAV 147 (275)
T ss_pred HHHHHHHcCC-----------CCcHHHHHHHhCCCCCHHHHHHHHHHHCCCC-CCcchHhHHHHHHHHccC
Confidence 9999998765 3346799999999999999999999999996 456999999999998753
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.91 E-value=2.4e-24 Score=206.45 Aligned_cols=120 Identities=23% Similarity=0.421 Sum_probs=106.8
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHHc--CCch--HHHHHHHH
Q 021493 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA--GFGY--RAKYITGT 219 (311)
Q Consensus 144 ~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~--Glg~--RA~~I~~~ 219 (311)
..|||+.+|+.|++||++++++...+++|. ..|||+++|+++++++|..+ |+|| ||++|+++
T Consensus 27 ~~dpy~ilVseILlQQT~v~~v~~~~~rl~--------------~~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~~~ 92 (350)
T PRK10880 27 DKTPYKVWLSEVMLQQTQVATVIPYFERFM--------------ARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKA 92 (350)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHH--------------HHCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHHHH
Confidence 479999999999999999999999999884 36899999999999999762 5554 99999999
Q ss_pred HHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCC
Q 021493 220 VDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLL 289 (311)
Q Consensus 220 A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~ 289 (311)
|+.+.++++| ..++.+++|++|||||+|||+|||+|++++ .+++||+||+|++.|+|.
T Consensus 93 A~~i~~~~~g-----------~~p~~~~~L~~LpGIG~~TA~aIl~~af~~-~~~iVD~nV~RV~~Rl~~ 150 (350)
T PRK10880 93 AQQVATLHGG-----------EFPETFEEVAALPGVGRSTAGAILSLSLGK-HFPILDGNVKRVLARCYA 150 (350)
T ss_pred HHHHHHHhCC-----------CchhhHHHHhcCCCccHHHHHHHHHHHCCC-CeecccHHHHHHHHHHhc
Confidence 9999988776 456889999999999999999999999999 455579999999999864
No 14
>smart00478 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=7.3e-24 Score=180.03 Aligned_cols=125 Identities=34% Similarity=0.510 Sum_probs=105.7
Q ss_pred HhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHH----HHcCCc-hHHHHHHHHHHHHHHhcCCC
Q 021493 156 CSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL----RNAGFG-YRAKYITGTVDVLQSKHSGG 230 (311)
Q Consensus 156 lsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~L----r~~Glg-~RA~~I~~~A~~i~~~~~gg 230 (311)
||||++++++.+++++|. ..||||++|+++++++| +++|++ .||++|+++|+.+.++++|
T Consensus 1 l~qq~~~~~a~~~~~~l~--------------~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~- 65 (149)
T smart00478 1 LSQQTSDEAVNKATERLF--------------EKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG- 65 (149)
T ss_pred CCCcccHHHHHHHHHHHH--------------HHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-
Confidence 589999999999999996 24789999999999888 778997 5999999999999986654
Q ss_pred ccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHh
Q 021493 231 AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAF 309 (311)
Q Consensus 231 ~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~ 309 (311)
+.++.++.|++|||||+|||+||++|++++ +++|||+|+.|+++++|+.+ ...+.+...++.+.|
T Consensus 66 ----------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~---~~~~~~~~~~~~~~~ 130 (149)
T smart00478 66 ----------EVPDDREELLKLPGVGRKTANAVLSFALGK-PFIPVDTHVLRIAKRLGLVD---KKSTPEEVEKLLEKL 130 (149)
T ss_pred ----------CccHHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccchHHHHHHHHhCCCC---CCCCHHHHHHHHHHH
Confidence 234689999999999999999999999999 89999999999999998643 234455565555554
No 15
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.91 E-value=7.6e-24 Score=189.29 Aligned_cols=154 Identities=23% Similarity=0.163 Sum_probs=119.0
Q ss_pred hhHHHHHHHhcCCc--cCCCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHH-
Q 021493 128 CRFAELAKYLAGAR--VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL- 204 (311)
Q Consensus 128 ~~l~~~~~~~~GlR--~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~L- 204 (311)
+.+.+.++.|..+- .-..|||+.|+.+|||||++...+.++..+|. ++.+ ++++++|
T Consensus 16 ~~~~~r~~ef~~~~~~~~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-------------------~~~l-~~~~eeL~ 75 (208)
T PRK01229 16 DRVEERIEEFKLLGEKGDEEDLFSELSFCILTANSSAEGGIKAQKEIG-------------------DGFL-YLSEEELE 75 (208)
T ss_pred HHHHHHHHHHHHhhhccccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-------------------HHHc-CCCHHHHH
Confidence 34455555555442 24589999999999999999999999999872 2333 4555544
Q ss_pred ---HHcC--Cc-hHHHHHHHHHHHHHHhcCCCccchhhh--hCCCHHHHHHHhh-cCCccchHHHHHHHHHhcCCCCccc
Q 021493 205 ---RNAG--FG-YRAKYITGTVDVLQSKHSGGAEWLLSL--RKLDLQEAIDALC-TLPGVGPKVAACIALFSLDQHHAIP 275 (311)
Q Consensus 205 ---r~~G--lg-~RA~~I~~~A~~i~~~~~gg~~~l~~L--~~~~~~e~~~~L~-~l~GIG~ktAd~vlLf~l~~~d~fP 275 (311)
|.+| |. .||++|+++++.+. .+..+ ...+.++++++|+ ++||||+|||+|||+.... .++|+
T Consensus 76 ~~Ir~~Gygf~~~KAk~I~~~~~~~~--------~l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~-~~~~i 146 (208)
T PRK01229 76 EKLKEVGHRFYNKRAEYIVEARKLYG--------KLKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGY-EDLAI 146 (208)
T ss_pred HHHHHhhcccHHHHHHHHHHHHHHHH--------HHHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccC-CCeee
Confidence 6776 64 49999999998751 12222 2457789999999 9999999999999975544 68999
Q ss_pred cchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 021493 276 VDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 310 (311)
Q Consensus 276 VDt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~~ 310 (311)
||+|+.|+++|+|+.+...+++|++.|.++.+.|+
T Consensus 147 VDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~ 181 (208)
T PRK01229 147 LDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILR 181 (208)
T ss_pred eeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHH
Confidence 99999999999998765455889999999998875
No 16
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.85 E-value=3.8e-21 Score=180.06 Aligned_cols=107 Identities=22% Similarity=0.395 Sum_probs=90.8
Q ss_pred HhccccHHHHHH-HHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHH----cCCchHHHHHHHHHHHHHHhcCCC
Q 021493 156 CSSNNNIARITK-MVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN----AGFGYRAKYITGTVDVLQSKHSGG 230 (311)
Q Consensus 156 lsQq~~i~~a~~-~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~----~Glg~RA~~I~~~A~~i~~~~~gg 230 (311)
++|||.+.++.. ..+++ +..|||+++|+++++++|.+ +|+..||++|+++|+.+.++++|
T Consensus 1 mlQQT~v~~v~~~yy~rf--------------~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g- 65 (289)
T PRK13910 1 MSQQTQINTVVERFYSPF--------------LEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHS- 65 (289)
T ss_pred CCCCCcHHHhHHHHHHHH--------------HHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCC-
Confidence 479999888864 66665 35799999999999999955 45434999999999999988765
Q ss_pred ccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcC
Q 021493 231 AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 288 (311)
Q Consensus 231 ~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~ 288 (311)
..++.+++|++|||||+|||+|||+|++++ .++|||+||+|++.|++
T Consensus 66 ----------~~P~~~~~L~~LpGIG~kTA~aIl~~af~~-~~~~VD~nV~RVl~Rl~ 112 (289)
T PRK13910 66 ----------QLPNDYQSLLKLPGIGAYTANAILCFGFRE-KSACVDANIKRVLLRLF 112 (289)
T ss_pred ----------CCChhHHHHHhCCCCCHHHHHHHHHHHCCC-CcCcccHHHHHHHHHHh
Confidence 234468999999999999999999999998 57799999999999974
No 17
>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=99.78 E-value=2.2e-18 Score=149.90 Aligned_cols=124 Identities=19% Similarity=0.218 Sum_probs=100.3
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHHHHHH----c----CCc-hHH
Q 021493 144 RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN----A----GFG-YRA 213 (311)
Q Consensus 144 ~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~----~----Glg-~RA 213 (311)
..+|||.||.+|||||++.+++.+++.+|. ++|. +||+.|++++.++|.. . ||. .||
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~-------------~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KA 81 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGS-------------LDAEDIAKYDPQAFVALFSERPAVHRFPGSMA 81 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC-------------CCHHHHHcCCHHHHHHHHhcCccccCchHHHH
Confidence 479999999999999999999999999995 5552 5899999999988843 3 765 499
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhhC---CCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHH
Q 021493 214 KYITGTVDVLQSKHSGGAEWLLSLRK---LDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 286 (311)
Q Consensus 214 ~~I~~~A~~i~~~~~gg~~~l~~L~~---~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r 286 (311)
++|+++|+.|.++++| +++.|.. .+..+++++|++|||||+|||+|||.+. ++ -|-|-.--+|-+.-
T Consensus 82 k~Lk~~a~~iie~y~G---~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l-~~--~~~~~~~~~~~~~~ 151 (177)
T TIGR03252 82 KRVQALAQYVVDTYDG---DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALL-GK--QLGVTPEGWREAAG 151 (177)
T ss_pred HHHHHHHHHHHHHhCC---ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHH-HH--HhCCCCcchHHhcc
Confidence 9999999999999987 6777766 4567889999999999999999999965 44 24453333444443
No 18
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.77 E-value=9e-18 Score=147.65 Aligned_cols=140 Identities=22% Similarity=0.302 Sum_probs=114.2
Q ss_pred CCCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHH----HHcCCc-hHHHHHH
Q 021493 143 LRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL----RNAGFG-YRAKYIT 217 (311)
Q Consensus 143 l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~L----r~~Glg-~RA~~I~ 217 (311)
+..+-.|.++++||.||++++.+.+++++|...|. -+++.|..++.++| |+.||. .||++|+
T Consensus 26 p~~~~~EiiigAILtQNT~WknvekAlenLk~~~~-------------~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk 92 (215)
T COG2231 26 PADNKDEIIIGAILTQNTSWKNVEKALENLKNEGI-------------LNLKKILKLDEEELAELIRPSGFYNQKAKRLK 92 (215)
T ss_pred CCCCchhHHHHHHHhccccHHHHHHHHHHHHHccc-------------CCHHHHhcCCHHHHHHHHhccchHHHHHHHHH
Confidence 44555699999999999999999999999985442 15899999998887 556986 4999999
Q ss_pred HHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCCC
Q 021493 218 GTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRL 297 (311)
Q Consensus 218 ~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~~ 297 (311)
++++.+...+ ..+........|++|++++|||+-|||.|||+++++ ++|+||...+|++.|+|....
T Consensus 93 ~l~k~l~~~~-------~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~r-p~FVvD~Yt~R~l~rlg~i~~----- 159 (215)
T COG2231 93 ALSKNLAKFF-------INLESFKSEVLREELLSIKGIGKETADSILLYALDR-PVFVVDKYTRRLLSRLGGIEE----- 159 (215)
T ss_pred HHHHHHHHHh-------hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcC-cccchhHHHHHHHHHhccccc-----
Confidence 9988888743 233333445589999999999999999999999998 799999999999999985432
Q ss_pred CHHHHHHHHHHhh
Q 021493 298 TPKLCSRVAEAFC 310 (311)
Q Consensus 298 t~k~y~~i~~~~~ 310 (311)
+.|+++.+.|.
T Consensus 160 --k~ydeik~~fe 170 (215)
T COG2231 160 --KKYDEIKELFE 170 (215)
T ss_pred --ccHHHHHHHHH
Confidence 35777777664
No 19
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.77 E-value=7.9e-18 Score=151.06 Aligned_cols=122 Identities=30% Similarity=0.446 Sum_probs=111.2
Q ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHH----cCCc-hHHHHHHHHHH
Q 021493 147 PVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN----AGFG-YRAKYITGTVD 221 (311)
Q Consensus 147 pfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~----~Glg-~RA~~I~~~A~ 221 (311)
-|..|++.+||+|+.......++.||.+||. -|+|.+.++++..|.+ .||. .||+||+.+|+
T Consensus 78 RfqvLv~lmLSSQTKDevt~~Am~rL~~~~g-------------LT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~ 144 (286)
T KOG1921|consen 78 RFQVLVGLMLSSQTKDEVTAAAMLRLKEYGG-------------LTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAK 144 (286)
T ss_pred hHHHHHHHHHhcchHHHHHHHHHHHHHHhcC-------------CCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHH
Confidence 4999999999999999999999999987761 2899999999888865 5886 59999999999
Q ss_pred HHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcc
Q 021493 222 VLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPEL 292 (311)
Q Consensus 222 ~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~ 292 (311)
.+.++|+| +.+...+.|++|||||||.|..+|-.+.|+...+-|||||+|+++|++|.+.
T Consensus 145 IL~d~f~g-----------DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ 204 (286)
T KOG1921|consen 145 ILQDKFDG-----------DIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDT 204 (286)
T ss_pred HHHHHhCC-----------CCchhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhccccc
Confidence 99999987 6788899999999999999999999999999999999999999999998753
No 20
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.77 E-value=1.2e-18 Score=164.77 Aligned_cols=139 Identities=24% Similarity=0.449 Sum_probs=117.7
Q ss_pred CCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHH--cCCch--HHHHHHHHH
Q 021493 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN--AGFGY--RAKYITGTV 220 (311)
Q Consensus 145 ~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~--~Glg~--RA~~I~~~A 220 (311)
.+||..+||.|+.||+.++++.....++ ...|||+++||+++++++.. .|+|| ||++++.+|
T Consensus 32 ~~PY~VwvSEiMLQQT~v~~Vi~yy~~f--------------l~rfPti~~LA~A~~~evl~~W~gLGYysRArnL~~~A 97 (342)
T COG1194 32 KDPYRVWVSEIMLQQTQVATVIPYYERF--------------LERFPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAA 97 (342)
T ss_pred CCcceehhHHHHhhhccHhhhhhhHHHH--------------HHhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHH
Confidence 6899999999999999999998877765 35799999999999888755 37764 999999999
Q ss_pred HHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCC-cccCCCCCH
Q 021493 221 DVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLP-ELAGVRLTP 299 (311)
Q Consensus 221 ~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~-~~~~~~~t~ 299 (311)
+.+.++++| ..++..+.|.+|||||++||..|+.|++++...+ ||++|.|++.|++.. ...++..+.
T Consensus 98 ~~v~~~~~G-----------~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~~-lDgNV~RVl~R~f~i~~~~~~~~~~ 165 (342)
T COG1194 98 QEVVERHGG-----------EFPDDEEELAALPGVGPYTAGAILSFAFNQPEPV-LDGNVKRVLSRLFAISGDIGKPKTK 165 (342)
T ss_pred HHHHHHcCC-----------CCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCCce-eecchheeehhhhcccccccccchh
Confidence 999999987 4455678899999999999999999999995544 799999999998643 334556788
Q ss_pred HHHHHHHHHh
Q 021493 300 KLCSRVAEAF 309 (311)
Q Consensus 300 k~y~~i~~~~ 309 (311)
+.+.++++.+
T Consensus 166 ~~~~~~~~~l 175 (342)
T COG1194 166 KELWELAEQL 175 (342)
T ss_pred HHHHHHHHHh
Confidence 8898888763
No 21
>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=99.67 E-value=6.6e-16 Score=124.10 Aligned_cols=98 Identities=30% Similarity=0.365 Sum_probs=79.5
Q ss_pred HHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHHHHHHc----CCc-hHHHHHHHHHHHHHH
Q 021493 152 LQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA----GFG-YRAKYITGTVDVLQS 225 (311)
Q Consensus 152 i~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~----Glg-~RA~~I~~~A~~i~~ 225 (311)
|++||+||++++++.+++++|+ .|| ||||++|+++++++|+++ ||+ +||+||+++|+.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g-------------~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYG-------------FPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHS-------------CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH-
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhc-------------CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh-
Confidence 6899999999999999999998 777 899999999999999887 998 79999999999875
Q ss_pred hcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCC-ccccchHHHHHHHHcCCCcccCCCCCHHHHHH
Q 021493 226 KHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH-AIPVDTHVWKIATRYLLPELAGVRLTPKLCSR 304 (311)
Q Consensus 226 ~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d-~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y~~ 304 (311)
|+.+ ++|+|+|+.|++.++|+... ..+.+...+
T Consensus 67 -------------------------------------------~~~d~~~~~D~~v~r~~~r~~~~~~---~~~~~~~~~ 100 (108)
T PF00730_consen 67 -------------------------------------------GRPDPFPPVDTHVRRVLQRLGGIPE---KKTKEETEK 100 (108)
T ss_dssp -------------------------------------------C-SSSS-TTSHHHHHHHHHHTSSSS---STTHHHHHH
T ss_pred -------------------------------------------hcccceecCcHHHHHHHHHHcCCCC---CCCHHHHHH
Confidence 7777 77899999999999986432 244444444
Q ss_pred HH-HHh
Q 021493 305 VA-EAF 309 (311)
Q Consensus 305 i~-~~~ 309 (311)
.. +.|
T Consensus 101 ~~~e~~ 106 (108)
T PF00730_consen 101 KLEELW 106 (108)
T ss_dssp HHHHHG
T ss_pred HHHhhC
Confidence 33 555
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.34 E-value=1.2e-11 Score=107.51 Aligned_cols=143 Identities=24% Similarity=0.299 Sum_probs=111.4
Q ss_pred CCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHHcCCch---HHHHHHHHH
Q 021493 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGY---RAKYITGTV 220 (311)
Q Consensus 144 ~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~Glg~---RA~~I~~~A 220 (311)
..+.|..|..+|+..|+|...+.++.+.| |+ | .+|. +.|+| .+.|+.+|..| ||+||+.+-
T Consensus 36 ~e~lf~ELsFCILTANsSA~~~~~~q~~l---G~------g-fly~--~~eEL----~e~Lk~~g~Rf~n~raeyIVeaR 99 (210)
T COG1059 36 KEDLFKELSFCILTANSSATMGLRAQNEL---GD------G-FLYL--SEEEL----REKLKEVGYRFYNVRAEYIVEAR 99 (210)
T ss_pred HHHHHHHHHHHhccccchHHHHHHHHHHh---cc------c-cccC--CHHHH----HHHHHHhcchhcccchHHHHHHH
Confidence 36789999999999999999999988876 21 1 1222 66666 35578898753 999999987
Q ss_pred HHHHHhcCCCccchhhhhCCCH--HHHHHHhh-cCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCCC
Q 021493 221 DVLQSKHSGGAEWLLSLRKLDL--QEAIDALC-TLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRL 297 (311)
Q Consensus 221 ~~i~~~~~gg~~~l~~L~~~~~--~e~~~~L~-~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~~ 297 (311)
+.+.+ +..+-+.+. ..+|+.|. +++|||.|-|..+|- ..|..|..-+|.||.|.+.++|.....++++
T Consensus 100 ~~~~~--------lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLR-NVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~ 170 (210)
T COG1059 100 EKFDD--------LKIIVKADENEKVARELLVENIKGIGYKEASHFLR-NVGFEDLAILDRHILRWLVRYGLIDENPKTL 170 (210)
T ss_pred HHHHH--------HHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHH-hcChhHHHHHHHHHHHHHHHhcccccCcccc
Confidence 77643 444444442 33899999 899999999999965 5577676667999999999998776667899
Q ss_pred CHHHHHHHHHHhhC
Q 021493 298 TPKLCSRVAEAFCE 311 (311)
Q Consensus 298 t~k~y~~i~~~~~~ 311 (311)
|+|.|.++.+.+++
T Consensus 171 t~K~YLe~E~ilr~ 184 (210)
T COG1059 171 TRKLYLEIEEILRS 184 (210)
T ss_pred cHHHHHHHHHHHHH
Confidence 99999999988763
No 23
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.20 E-value=5.1e-11 Score=113.44 Aligned_cols=117 Identities=24% Similarity=0.402 Sum_probs=96.3
Q ss_pred CCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCH-HHHHH--cCCch--HHHHHHHH
Q 021493 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSE-VELRN--AGFGY--RAKYITGT 219 (311)
Q Consensus 145 ~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~-e~Lr~--~Glg~--RA~~I~~~ 219 (311)
+..||.+||.|+.||+.+..+.+-+.+ .+..+||..+++.++. +++.+ .|+|| |+++|...
T Consensus 123 rRaYeVwVSEiMLQQTrV~TV~~YYt~--------------WMqkwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~eg 188 (555)
T KOG2457|consen 123 RRAYEVWVSEIMLQQTRVQTVMKYYTR--------------WMQKWPTLYDLAQASLEKEVNELWAGLGYYRRARRLLEG 188 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHhCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 357999999999999998887665443 2457899999999985 66665 47774 99999999
Q ss_pred HHHHHHhcCCCccchhhhhCCCHHHHHHHhhc-CCccchHHHHHHHHHhcCCCCccccchHHHHHHHHc
Q 021493 220 VDVLQSKHSGGAEWLLSLRKLDLQEAIDALCT-LPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRY 287 (311)
Q Consensus 220 A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~-l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~ 287 (311)
|+++++..+| ..+..-+.|++ +||||++||..|+..+++....+ ||-+|.|++.|.
T Consensus 189 a~~vv~~~~g-----------e~Prta~~l~kgvpGVG~YTAGAiaSIAf~q~tGi-VDGNVirvlsRa 245 (555)
T KOG2457|consen 189 AKMVVAGTEG-----------EFPRTASSLMKGVPGVGQYTAGAIASIAFNQVTGI-VDGNVIRVLSRA 245 (555)
T ss_pred HHHHHHhCCC-----------CCCChHHHHHhhCCCCCccchhhhhhhhhcCcccc-cccchHHHhHHh
Confidence 9999986654 33445667777 99999999999999999997776 999999999884
No 24
>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=97.95 E-value=7e-06 Score=51.24 Aligned_cols=23 Identities=48% Similarity=0.869 Sum_probs=19.5
Q ss_pred HHHHHhhcCCccchHHHHHHHHH
Q 021493 244 EAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 244 e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
..+++|+++||||+|||+.|+.|
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHhC
Confidence 35789999999999999999875
No 25
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=97.37 E-value=0.00035 Score=57.34 Aligned_cols=76 Identities=16% Similarity=0.192 Sum_probs=48.1
Q ss_pred CCCceEEeeC----CeEEEEEEecC-CcEEEEEcCCC--ChHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHHHHHhc
Q 021493 66 GPLQYTGPIG----PHLISLKHLQN-GDVCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLA 138 (311)
Q Consensus 66 ~~~~~~gv~~----~~~v~l~q~~~-~~l~~~~~~~~--~~~~~~~~l~~yf~Ld~dl~~~~~~l~~~D~~l~~~~~~~~ 138 (311)
+++.|...+. ..+++++..++ +.+.+++..+. ....+...|+++||||.|.+.|.+.+ ||.++.+....+
T Consensus 31 ~~~~Y~Rt~~l~~~~g~v~v~~~~~~~~l~v~~~~~~~~~l~~~~~rvRrlfDLdaDp~~I~~~L---dp~l~p~~~~~p 107 (116)
T PF06029_consen 31 DDGSYRRTFRLGGGPGWVSVRHDPEKNHLRVTLSLSDLRDLPAVIARVRRLFDLDADPQAIEAHL---DPLLAPLVAARP 107 (116)
T ss_dssp ESSEEEEEEEETTEEEEEEEEEETTTTEEEEEE-GGGGGGHHHHHHHHHHHTTTT--HHHHHHHH-------GGGGTS-T
T ss_pred eCCeEEEEEEeCCeEEEEEEEEcCCCCEEEEEEEcccHHHHHHHHHHHHHHhCCCCCHHHHHHHH---hhcccccccCCC
Confidence 3456665543 35788887653 45777776533 35678899999999999999999999 899999999999
Q ss_pred CCccCC
Q 021493 139 GARVLR 144 (311)
Q Consensus 139 GlR~l~ 144 (311)
|+|++.
T Consensus 108 GLRlPG 113 (116)
T PF06029_consen 108 GLRLPG 113 (116)
T ss_dssp T-----
T ss_pred CCcCCC
Confidence 999874
No 26
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=95.61 E-value=0.0068 Score=36.26 Aligned_cols=20 Identities=40% Similarity=0.617 Sum_probs=17.5
Q ss_pred HhhcCCccchHHHHHHHHHh
Q 021493 248 ALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 248 ~L~~l~GIG~ktAd~vlLf~ 267 (311)
.|+++||||+|+|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 68899999999999998644
No 27
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.85 E-value=0.038 Score=49.38 Aligned_cols=68 Identities=25% Similarity=0.234 Sum_probs=40.0
Q ss_pred ccccCCCHHHHhcCCHHHHHH-cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 186 EFHEFPSLERLSLVSEVELRN-AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 186 ~~~~FPtpe~La~~~~e~Lr~-~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
.+|.|.|.++..- -+.|-. -|+|.|. |-.+.+ .++.+.|...-..+..+.|+++||||+|||+-++
T Consensus 58 ~LYGF~t~~Er~l--F~~LisVsGIGPK~------ALaILs-----~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 58 KLFGFLNSSEREV--FEELIGVDGIGPRA------ALRVLS-----GIKYNEFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred eeeCCCCHHHHHH--HHHHhCcCCcCHHH------HHHHHc-----CCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3577877776521 223333 3888762 233332 1223333333233356799999999999999998
Q ss_pred HH
Q 021493 265 LF 266 (311)
Q Consensus 265 Lf 266 (311)
+=
T Consensus 125 lE 126 (196)
T PRK13901 125 LK 126 (196)
T ss_pred HH
Confidence 53
No 28
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=94.73 E-value=0.063 Score=39.17 Aligned_cols=40 Identities=33% Similarity=0.577 Sum_probs=27.1
Q ss_pred HHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 219 TVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 219 ~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.|+.+.++++ +++.|...+. ++|.+++|||+++|+.|.-|
T Consensus 15 ~ak~L~~~f~----sl~~l~~a~~----e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFG----SLEALMNASV----EELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCS----CHHHHCC--H----HHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcC----CHHHHHHcCH----HHHhccCCcCHHHHHHHHHH
Confidence 3556666554 5788877654 57999999999999998755
No 29
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.57 E-value=0.049 Score=48.20 Aligned_cols=68 Identities=22% Similarity=0.169 Sum_probs=40.7
Q ss_pred ccccCCCHHHHhcCCHHHHHH-cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 186 EFHEFPSLERLSLVSEVELRN-AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 186 ~~~~FPtpe~La~~~~e~Lr~-~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
..|.|-|.++-.- -+.|.. -|+|.|. |-.+.+ .++.+.+...-..+..+.|+++||||+|||+-++
T Consensus 59 ~LyGF~~~~Er~l--F~~Li~VsGIGpK~------Al~ILs-----~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 59 KLYGFLDKDEQKM--FEMLLKVNGIGANT------AMAVCS-----SLDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred eeeCCCCHHHHHH--HHHHhccCCccHHH------HHHHHc-----CCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 4577877776521 223333 3888773 333332 1233333333333456789999999999999998
Q ss_pred HH
Q 021493 265 LF 266 (311)
Q Consensus 265 Lf 266 (311)
+=
T Consensus 126 lE 127 (183)
T PRK14601 126 AE 127 (183)
T ss_pred HH
Confidence 53
No 30
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.42 E-value=0.057 Score=47.97 Aligned_cols=69 Identities=20% Similarity=0.266 Sum_probs=40.4
Q ss_pred cccccCCCHHHHhcCCHHHHHH-cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHH
Q 021493 185 FEFHEFPSLERLSLVSEVELRN-AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 263 (311)
Q Consensus 185 ~~~~~FPtpe~La~~~~e~Lr~-~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~v 263 (311)
..+|.|.|.++..- -+.|.. -|+|.|. |-.+.+ .++.+.+...=..+..+.|+++||||+|||+-+
T Consensus 58 ~~LyGF~~~~Er~l--F~~Li~V~GIGpK~------AL~iLs-----~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 58 ITLYGFSNERKKEL--FLSLTKVSRLGPKT------ALKIIS-----NEDAETLVTMIASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred ceeeCCCCHHHHHH--HHHHhccCCccHHH------HHHHHc-----CCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 34577877766521 222333 3888763 333332 122333333323334678999999999999999
Q ss_pred HHH
Q 021493 264 ALF 266 (311)
Q Consensus 264 lLf 266 (311)
++=
T Consensus 125 ilE 127 (188)
T PRK14606 125 VME 127 (188)
T ss_pred HHH
Confidence 853
No 31
>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=93.77 E-value=0.085 Score=46.94 Aligned_cols=67 Identities=30% Similarity=0.279 Sum_probs=38.7
Q ss_pred cccccCCCHHHHhcCCHHHHHH-cCCchH-HHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHH
Q 021493 185 FEFHEFPSLERLSLVSEVELRN-AGFGYR-AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAAC 262 (311)
Q Consensus 185 ~~~~~FPtpe~La~~~~e~Lr~-~Glg~R-A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~ 262 (311)
..+|.|.|.++..- -..|.. -|+|.| |..|.+. .+.+.|...=..+..+.|.++||||+|||+-
T Consensus 57 ~~LyGF~~~~Er~l--F~~L~~V~GIGpK~Al~iL~~------------~~~~el~~aI~~~d~~~L~~ipGiGkKtAer 122 (191)
T TIGR00084 57 ELLFGFNTLEEREL--FKELIKVNGVGPKLALAILSN------------MSPEEFVYAIETEEVKALVKIPGVGKKTAER 122 (191)
T ss_pred ceeeCCCCHHHHHH--HHHHhCCCCCCHHHHHHHHhc------------CCHHHHHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 34678888776521 223333 488875 5444221 1233332221222346799999999999999
Q ss_pred HHH
Q 021493 263 IAL 265 (311)
Q Consensus 263 vlL 265 (311)
|++
T Consensus 123 Iil 125 (191)
T TIGR00084 123 LLL 125 (191)
T ss_pred HHH
Confidence 984
No 32
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.55 E-value=0.091 Score=47.22 Aligned_cols=67 Identities=25% Similarity=0.312 Sum_probs=38.2
Q ss_pred ccccCCCHHHHhcCCHHHHHH-cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 186 EFHEFPSLERLSLVSEVELRN-AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 186 ~~~~FPtpe~La~~~~e~Lr~-~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
.+|.|-|.++..- -+.|.. -|+|.|. |-.+.+. ++.+.|...=.....+.|+++||||+|||+-++
T Consensus 60 ~LyGF~~~~Er~l--F~~Li~V~GIGpK~------Al~iLs~-----~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 60 ELFGFATWDERQT--FIVLISISKVGAKT------ALAILSQ-----FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred eeeCCCCHHHHHH--HHHHhCCCCcCHHH------HHHHHhh-----CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 3567777766521 223333 3788762 3333321 122222222223346789999999999999998
Q ss_pred H
Q 021493 265 L 265 (311)
Q Consensus 265 L 265 (311)
+
T Consensus 127 l 127 (203)
T PRK14602 127 L 127 (203)
T ss_pred H
Confidence 4
No 33
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=93.23 E-value=0.069 Score=47.94 Aligned_cols=54 Identities=26% Similarity=0.254 Sum_probs=35.9
Q ss_pred cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCC
Q 021493 207 AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQH 271 (311)
Q Consensus 207 ~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~ 271 (311)
-|+|.|. |-++.+ .++.+.|...=..+..+.|+++||||+|||+-+++==-++.
T Consensus 79 nGIGpK~------ALaiLs-----~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~ 132 (201)
T COG0632 79 NGIGPKL------ALAILS-----NLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKL 132 (201)
T ss_pred CCccHHH------HHHHHc-----CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhh
Confidence 4778773 344443 23455554444445678999999999999999987554443
No 34
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.05 E-value=0.11 Score=46.14 Aligned_cols=66 Identities=23% Similarity=0.196 Sum_probs=37.6
Q ss_pred ccccCCCHHHHhcCCHHHHHH-cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 186 EFHEFPSLERLSLVSEVELRN-AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 186 ~~~~FPtpe~La~~~~e~Lr~-~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
.+|.|-|.++..- -+.|.+ -|+|.|. |-.+.+. ++.+.|...=..+..+.| ++||||+|||+-++
T Consensus 59 ~LyGF~~~~Er~l--F~~LisV~GIGpK~------Al~iLs~-----~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 59 QLYGFLNREEQDC--LRMLVKVSGVNYKT------AMSILSK-----LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRII 124 (186)
T ss_pred eeeCCCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcc-----CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHH
Confidence 3577877776521 223333 3888763 3333321 123333322222234788 99999999999998
Q ss_pred H
Q 021493 265 L 265 (311)
Q Consensus 265 L 265 (311)
+
T Consensus 125 l 125 (186)
T PRK14600 125 T 125 (186)
T ss_pred H
Confidence 5
No 35
>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=92.91 E-value=0.12 Score=47.44 Aligned_cols=37 Identities=32% Similarity=0.414 Sum_probs=32.0
Q ss_pred ccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhhC
Q 021493 273 AIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFCE 311 (311)
Q Consensus 273 ~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~~~ 311 (311)
++|+||||.|+++++|+. ..++.+-|.-.|+.+.+++
T Consensus 176 iiPLDtHv~~var~LGL~--~rk~~d~k~A~elT~~lr~ 212 (232)
T PF09674_consen 176 IIPLDTHVFRVARKLGLL--KRKSADWKAARELTEALRE 212 (232)
T ss_pred cccchHhHHHHHHHcCCc--cCCCccHHHHHHHHHHHHh
Confidence 589999999999999975 3577888999999998874
No 36
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.53 E-value=0.094 Score=46.93 Aligned_cols=23 Identities=39% Similarity=0.495 Sum_probs=19.5
Q ss_pred HHHHHHhhcCCccchHHHHHHHH
Q 021493 243 QEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 243 ~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
.+..+.|+++||||+|||+-+++
T Consensus 103 ~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 103 EGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHH
Confidence 33567899999999999999974
No 37
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.20 E-value=0.17 Score=45.08 Aligned_cols=67 Identities=27% Similarity=0.334 Sum_probs=36.9
Q ss_pred cccccCCCHHHHhcCCHHHHHH-cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHH
Q 021493 185 FEFHEFPSLERLSLVSEVELRN-AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 263 (311)
Q Consensus 185 ~~~~~FPtpe~La~~~~e~Lr~-~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~v 263 (311)
..+|.|-+.++-.- -..|.. -|+|.| +|..|.+.+ +.+.|...=..+..+.|+++||||+|||+-+
T Consensus 58 ~~LyGF~~~~Er~l--F~~Li~V~GIGpK------~Al~ILs~~-----~~~~l~~aI~~~D~~~L~~vpGIGkKtAerI 124 (194)
T PRK14605 58 LSLFGFATTEELSL--FETLIDVSGIGPK------LGLAMLSAM-----NAEALASAIISGNAELLSTIPGIGKKTASRI 124 (194)
T ss_pred ceeeCCCCHHHHHH--HHHHhCCCCCCHH------HHHHHHHhC-----CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 34577777766521 222333 388875 233344321 1222211111234567999999999999996
Q ss_pred H
Q 021493 264 A 264 (311)
Q Consensus 264 l 264 (311)
+
T Consensus 125 i 125 (194)
T PRK14605 125 V 125 (194)
T ss_pred H
Confidence 5
No 38
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.20 E-value=0.11 Score=46.45 Aligned_cols=24 Identities=33% Similarity=0.516 Sum_probs=20.0
Q ss_pred HHHHHHhhcCCccchHHHHHHHHH
Q 021493 243 QEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 243 ~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.+..+.|+++||||+|||+-+++=
T Consensus 104 ~~D~~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 104 GGDVARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHHH
Confidence 334678999999999999999853
No 39
>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=92.12 E-value=0.15 Score=46.58 Aligned_cols=37 Identities=32% Similarity=0.467 Sum_probs=31.2
Q ss_pred ccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhhC
Q 021493 273 AIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFCE 311 (311)
Q Consensus 273 ~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~~~ 311 (311)
++|+|||+.|+++++|+. ..|..+-|.-.|+.+.+++
T Consensus 173 iiPLDtH~~rvar~LgL~--~Rk~~d~kaa~ElT~~Lr~ 209 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKLL--KRKSYDLKAAIEITEALRE 209 (229)
T ss_pred eeechHhHHHHHHHhCCc--ccCchhHHHHHHHHHHHHh
Confidence 579999999999999975 3567778889999988874
No 40
>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=90.81 E-value=0.54 Score=34.53 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=32.1
Q ss_pred CCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 208 GFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 208 Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
|-.+|++.-.++|..|.+-+ . +.....+.|.+|||||+++|.-|-
T Consensus 20 ~~~~r~~aY~~Aa~~i~~l~----~--------~i~~~~~~~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 20 GDPFRARAYRRAAAAIKALP----Y--------PITSGEEDLKKLPGIGKSIAKKID 64 (68)
T ss_dssp TSHHHHHHHHHHHHHHHHSS----S---------HHSHHHHHCTSTTTTHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHhCC----H--------hHhhHHHHHhhCCCCCHHHHHHHH
Confidence 44589999999999988621 1 222221259999999999998774
No 41
>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=90.55 E-value=0.43 Score=34.05 Aligned_cols=32 Identities=34% Similarity=0.488 Sum_probs=23.9
Q ss_pred CccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 230 GAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 230 g~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
|-.+++.|...+ .++|.+++|||+++|+-+.-
T Consensus 25 G~~t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 25 GIKTLEDLANAD----PEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp TCSSHHHHHTSH----HHHHHTSTTSSHHHHHHHHH
T ss_pred CCCcHHHHHcCC----HHHHhcCCCCCHHHHHHHHH
Confidence 344677776653 35699999999999998754
No 42
>PRK00076 recR recombination protein RecR; Reviewed
Probab=90.55 E-value=0.2 Score=44.82 Aligned_cols=33 Identities=36% Similarity=0.656 Sum_probs=28.6
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHHHhcCCCCc
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQHHA 273 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~ 273 (311)
+.+++.+.|.+|||||+|+|.=++++-+.+.+.
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~~~ 37 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQRDRE 37 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHH
Confidence 367899999999999999999999999876443
No 43
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.26 E-value=0.22 Score=44.46 Aligned_cols=33 Identities=33% Similarity=0.612 Sum_probs=28.4
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHHHhcCCCCc
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQHHA 273 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~ 273 (311)
+.+++.+.|.+|||||+|+|.=++++-+...+.
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~~ 37 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPS 37 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHH
Confidence 367899999999999999999999988876443
No 44
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=90.20 E-value=0.22 Score=44.37 Aligned_cols=32 Identities=44% Similarity=0.694 Sum_probs=27.7
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHHHhcCCCC
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQHH 272 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d 272 (311)
..+.+++.|.++||||+|+|.=++.+-+.+.+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~~~ 37 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQRDR 37 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHccCH
Confidence 45778999999999999999999988887743
No 45
>PRK13844 recombination protein RecR; Provisional
Probab=89.88 E-value=0.28 Score=43.94 Aligned_cols=32 Identities=31% Similarity=0.572 Sum_probs=28.2
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHHHhcCCCC
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQHH 272 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d 272 (311)
..+++.+.|.+|||||+|+|.=++++-+...+
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~~ 40 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALYLLDKSP 40 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 46789999999999999999999999987643
No 46
>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=88.76 E-value=13 Score=32.86 Aligned_cols=125 Identities=8% Similarity=0.063 Sum_probs=81.4
Q ss_pred ccChhHHHHHHHhcCCccCC-CCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHH
Q 021493 125 ASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEV 202 (311)
Q Consensus 125 ~~D~~l~~~~~~~~GlR~l~-~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e 202 (311)
..||.+..-...-=|..+-. +..||.|+-.+...-.|+..|.+-...+. .|. .| +|+.+|..+++
T Consensus 7 ~~~~l~~~YHD~eWG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~------------~F-d~~~VA~~~e~ 73 (179)
T TIGR00624 7 SVDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFS------------GF-DIVKVARMTDA 73 (179)
T ss_pred CCChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHc------------CC-CHHHHhCCCHH
Confidence 34444433333333666553 78899999999999999999998888886 443 23 79999999999
Q ss_pred HHHHc----CCc-h--HHHHHHHHHHHHHHhcCCCccchhhh--------------------hCCC--HHHHHHHhhc--
Q 021493 203 ELRNA----GFG-Y--RAKYITGTVDVLQSKHSGGAEWLLSL--------------------RKLD--LQEAIDALCT-- 251 (311)
Q Consensus 203 ~Lr~~----Glg-~--RA~~I~~~A~~i~~~~~gg~~~l~~L--------------------~~~~--~~e~~~~L~~-- 251 (311)
++..+ |+= . |.+.++.-|+++.+-... ++... ...+ .+.+-+.|.+
T Consensus 74 ~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~i~~e---sf~~ylW~fv~~~Pi~~~~~~~~~~p~~t~~S~~lskdLKkrG 150 (179)
T TIGR00624 74 DVERLLQDDGIIRNRGKIEATIANARAALQLEQN---DLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESKAMSKELKKRG 150 (179)
T ss_pred HHHHHhcCccchhhHHHHHHHHHHHHHHHHHHHc---cHHHHHHhccCCCCccCCccccccCCCCCHHHHHHHHHHHHcC
Confidence 88653 542 2 566688888887752211 22211 1111 3445556654
Q ss_pred CCccchHHHHHHHH
Q 021493 252 LPGVGPKVAACIAL 265 (311)
Q Consensus 252 l~GIG~ktAd~vlL 265 (311)
++=|||-++-.+|.
T Consensus 151 fkFvGpt~~ysfmq 164 (179)
T TIGR00624 151 FRFVGPTICYALMQ 164 (179)
T ss_pred CeecChHHHHHHHH
Confidence 78888888877765
No 47
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=88.72 E-value=0.97 Score=37.79 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=35.6
Q ss_pred HHhcCCHHHHHHc-CCch-HHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 195 RLSLVSEVELRNA-GFGY-RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 195 ~La~~~~e~Lr~~-Glg~-RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
+|-.++.++|+.+ |+|. +|+.|+. +| ++ ...++|.++||||+++.+.+--
T Consensus 54 diN~A~~~el~~lpGigP~~A~~IV~---------nG-----------pf-~sveDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 54 DLNNSSVRAFRQFPGMYPTLAGKIVK---------NA-----------PY-DSVEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred cCCccCHHHHHHCCCCCHHHHHHHHH---------CC-----------CC-CCHHHHHcCCCCCHHHHHHHHH
Confidence 5566788888875 8885 8877772 22 11 1367899999999998876643
No 48
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=88.29 E-value=0.6 Score=34.32 Aligned_cols=47 Identities=21% Similarity=0.201 Sum_probs=32.5
Q ss_pred HHcCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 205 RNAGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 205 r~~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
..+|++.||.....-+ |.-++..|..++. +.|++++|+|+++.+-|.
T Consensus 15 ~~L~LS~Ra~n~L~~~---------~I~tv~dL~~~s~----~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 15 EDLGLSVRAYNCLKRA---------GIHTVGDLVKYSE----EDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp GGSTSBHHHHHHHHCT---------T--BHHHHHCS-H----HHHHTSTTSHHHHHHHHH
T ss_pred HHhCCCHHHHHHHHHh---------CCcCHHHHHhCCH----HHHHhCCCCCHhHHHHHH
Confidence 4589998875543322 5557777777765 579999999999998763
No 49
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=87.63 E-value=0.79 Score=44.22 Aligned_cols=56 Identities=25% Similarity=0.411 Sum_probs=37.3
Q ss_pred HHHHc-CCchH-HHHHHHHHHHHHHhcCCCccc-hhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 203 ELRNA-GFGYR-AKYITGTVDVLQSKHSGGAEW-LLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 203 ~Lr~~-Glg~R-A~~I~~~A~~i~~~~~gg~~~-l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
+|.++ |+|.+ |+-|.++ +.. |.+. +.....-+.+.+..+|++++|||||+|.-+--
T Consensus 49 ~l~~lpgIG~~ia~kI~Ei---l~t----G~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~ 107 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEI---IET----GKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR 107 (334)
T ss_pred HHhcCCCccHHHHHHHHHH---HHh----CcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH
Confidence 45553 77764 3333332 222 6655 45555567888999999999999999977644
No 50
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.62 E-value=0.76 Score=41.76 Aligned_cols=64 Identities=22% Similarity=0.176 Sum_probs=42.4
Q ss_pred CHHHHHH--cCCchHHH-HHHHHHHHHHHhcC--CCccchhhhhCCCHHHHHHHhhcCCccchHHH-HHHHHHhcCC
Q 021493 200 SEVELRN--AGFGYRAK-YITGTVDVLQSKHS--GGAEWLLSLRKLDLQEAIDALCTLPGVGPKVA-ACIALFSLDQ 270 (311)
Q Consensus 200 ~~e~Lr~--~Glg~RA~-~I~~~A~~i~~~~~--gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktA-d~vlLf~l~~ 270 (311)
+..||=+ ++.|.+-+ -...+|+.+.+++. | +|..+.+.+.+ +|++++|||+..| ...+.+-+++
T Consensus 15 sd~ELLailL~~g~~~~~~~~~lA~~ll~~f~~~g---~l~~l~~a~~~----eL~~i~GiG~aka~~l~a~~El~r 84 (218)
T TIGR00608 15 SDYELLAIILRTGTPKGLDVLSLSKRLLDVFGRQD---SLGHLLSAPPE----ELSSVPGIGEAKAIQLKAAVELAK 84 (218)
T ss_pred CHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhcccC---CHHHHHhCCHH----HHHhCcCCcHHHHHHHHHHHHHHH
Confidence 4444544 56665556 78899999998762 2 47777777654 5889999999554 4444554543
No 51
>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=86.27 E-value=0.79 Score=36.13 Aligned_cols=30 Identities=17% Similarity=0.408 Sum_probs=25.3
Q ss_pred HHHHHHhhcCCccchHHHHHHHHHhcCCCC
Q 021493 243 QEAIDALCTLPGVGPKVAACIALFSLDQHH 272 (311)
Q Consensus 243 ~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d 272 (311)
.+....|+.|||||+.+|.-..+.|....+
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~ 37 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRSPA 37 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCCHH
Confidence 456789999999999999999988876643
No 52
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=85.95 E-value=16 Score=32.43 Aligned_cols=132 Identities=11% Similarity=0.069 Sum_probs=84.3
Q ss_pred hccChhHHHHHHHhcCCccCC-CCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCH
Q 021493 124 SASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSE 201 (311)
Q Consensus 124 ~~~D~~l~~~~~~~~GlR~l~-~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~ 201 (311)
+..||.+..-...-=|..+-. +..||.|+-.....-.|+..|.+-...+. .|. .| +|+.+|..++
T Consensus 7 ~~~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~------------~F-d~~~VA~~~e 73 (187)
T PRK10353 7 VSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFH------------QF-DPVKVAAMQE 73 (187)
T ss_pred CCCChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHc------------CC-CHHHHhCCCH
Confidence 334554444333333666654 78899999999999999999999888886 443 23 7999999999
Q ss_pred HHHHHc----CCc---hHHHHHHHHHHHHHHh-cCCCcc--ch----------------hhhhCCCH--HHHHHHhhc--
Q 021493 202 VELRNA----GFG---YRAKYITGTVDVLQSK-HSGGAE--WL----------------LSLRKLDL--QEAIDALCT-- 251 (311)
Q Consensus 202 e~Lr~~----Glg---~RA~~I~~~A~~i~~~-~~gg~~--~l----------------~~L~~~~~--~e~~~~L~~-- 251 (311)
+++..+ |+= .|.+.++.-|+++.+- .++|.+ .+ ..+...+. +.+-+.|.+
T Consensus 74 ~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gSf~~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~~lskdLKkrG 153 (187)
T PRK10353 74 EDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQVTQATTLSEIPTSTPASDALSKALKKRG 153 (187)
T ss_pred HHHHHHhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCCHHHHHhhccCCCcccCCccchhcCCCCCHHHHHHHHHHHHcC
Confidence 888653 542 2667788878877641 112221 11 01111111 245556664
Q ss_pred CCccchHHHHHHHHHhcC
Q 021493 252 LPGVGPKVAACIALFSLD 269 (311)
Q Consensus 252 l~GIG~ktAd~vlLf~l~ 269 (311)
++=|||-|+-.+|. +.|
T Consensus 154 FkFvGpt~~ysfmq-A~G 170 (187)
T PRK10353 154 FKFVGTTICYSFMQ-ACG 170 (187)
T ss_pred CcccCcHHHHHHHH-HHC
Confidence 88899999888765 334
No 53
>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=85.48 E-value=2.5 Score=30.05 Aligned_cols=32 Identities=28% Similarity=0.339 Sum_probs=27.1
Q ss_pred CCCHHHHhcCCHHHHHHc-CCch-HHHHHHHHHH
Q 021493 190 FPSLERLSLVSEVELRNA-GFGY-RAKYITGTVD 221 (311)
Q Consensus 190 FPtpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~ 221 (311)
|.|+++|+.+++++|..+ |+|. +|+.|++.++
T Consensus 26 ~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 26 IKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 569999999999999886 9995 7888887665
No 54
>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=84.66 E-value=1.5 Score=35.98 Aligned_cols=57 Identities=26% Similarity=0.369 Sum_probs=39.1
Q ss_pred CHHHHhcCCHHHHHHc-CCch-HHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 192 SLERLSLVSEVELRNA-GFGY-RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 192 tpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
.+-.|-.++.++|..+ |+|. +|+.|++--+. + | . + ...++|..++|||+++++-+.-
T Consensus 58 ~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~----~-g-~--f---------~s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 58 AAVNINAASLEELQALPGIGPAKAKAIIEYREE----N-G-A--F---------KSVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh----c-C-C--c---------CCHHHHHcCCCCCHHHHHHHHh
Confidence 3445666788888775 8885 88877764432 1 2 1 1 2357889999999999987754
No 55
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=84.62 E-value=1.5 Score=31.78 Aligned_cols=51 Identities=29% Similarity=0.460 Sum_probs=31.0
Q ss_pred HhcCCHHHHHHc-CCch-HHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHH
Q 021493 196 LSLVSEVELRNA-GFGY-RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 263 (311)
Q Consensus 196 La~~~~e~Lr~~-Glg~-RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~v 263 (311)
|-.++.++|..+ |++. .|+.|++.-+.. |+ +. ..++|..++|||+++.+-+
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~~-----G~---f~---------s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREKN-----GP---FK---------SLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHHH------S----S---------SGGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHhC-----cC---CC---------CHHHHhhCCCCCHHHHHHH
Confidence 345788899887 9985 788887654433 11 11 2557899999999998755
No 56
>PRK00024 hypothetical protein; Reviewed
Probab=84.14 E-value=1.7 Score=39.66 Aligned_cols=56 Identities=27% Similarity=0.344 Sum_probs=39.9
Q ss_pred CHHHHHH--cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHH
Q 021493 200 SEVELRN--AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 263 (311)
Q Consensus 200 ~~e~Lr~--~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~v 263 (311)
+..||=+ ++.|.+-+-...+|+.+.++++ ++..+...+.+ +|++++|||+..|..+
T Consensus 25 sd~ELLa~lL~~g~~~~~~~~LA~~LL~~fg----sL~~l~~as~~----eL~~i~GIG~akA~~L 82 (224)
T PRK00024 25 SDAELLAILLRTGTKGKSVLDLARELLQRFG----SLRGLLDASLE----ELQSIKGIGPAKAAQL 82 (224)
T ss_pred CHHHHHHHHHcCCCCCCCHHHHHHHHHHHcC----CHHHHHhCCHH----HHhhccCccHHHHHHH
Confidence 4444444 5666666677889999988775 37777776654 5889999999888544
No 57
>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=83.37 E-value=4 Score=42.99 Aligned_cols=72 Identities=29% Similarity=0.431 Sum_probs=45.8
Q ss_pred CHHHHhcCCHHHHHHc-CCch-HHHHHHHHHHHHHHhc----------CC-Ccc----------chhhhhCCCHHHHHHH
Q 021493 192 SLERLSLVSEVELRNA-GFGY-RAKYITGTVDVLQSKH----------SG-GAE----------WLLSLRKLDLQEAIDA 248 (311)
Q Consensus 192 tpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~~i~~~~----------~g-g~~----------~l~~L~~~~~~e~~~~ 248 (311)
++++|..+..++|..+ |+|. .|..|.+..+.-.... .| |.- +++.|.+.+ .++
T Consensus 456 ~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~sl~~l~~As----~ee 531 (652)
T TIGR00575 456 SVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAAS----LEE 531 (652)
T ss_pred CHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhCCHHHHHhCC----HHH
Confidence 7888888888888876 8885 5666665554322100 00 110 233333333 347
Q ss_pred hhcCCccchHHHHHHHHHh
Q 021493 249 LCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 249 L~~l~GIG~ktAd~vlLf~ 267 (311)
|.+++|||+++|..|.-|-
T Consensus 532 L~~i~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 532 LLSVEGVGPKVAESIVNFF 550 (652)
T ss_pred HhcCCCcCHHHHHHHHHHH
Confidence 9999999999999997763
No 58
>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=83.21 E-value=1 Score=34.66 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=27.1
Q ss_pred HHhhcCCccchHHHHHHHHHhcCCCCccccchHHHH
Q 021493 247 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWK 282 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~R 282 (311)
+.|+++||||+-+|..++..- +..+-|+-..++..
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~~~~~l~~ 36 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFKSAKQLAS 36 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhcccchhhhh
Confidence 468999999999999888766 66677876555543
No 59
>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=82.74 E-value=1 Score=40.03 Aligned_cols=24 Identities=38% Similarity=0.596 Sum_probs=20.7
Q ss_pred CHHHHHHHhhcCCccchHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
...+....|++++|||||+|-.+|
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL 89 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAIL 89 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHH
Confidence 446789999999999999998773
No 60
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=82.67 E-value=21 Score=33.23 Aligned_cols=125 Identities=17% Similarity=0.141 Sum_probs=70.3
Q ss_pred HHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCcccccc-ccccCC--CHHHHhcCCHHHHHHcCCc--h------HHHH
Q 021493 148 VECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGF-EFHEFP--SLERLSLVSEVELRNAGFG--Y------RAKY 215 (311)
Q Consensus 148 fe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~-~~~~FP--tpe~La~~~~e~Lr~~Glg--~------RA~~ 215 (311)
..-+++.|+.- +.....++|+ .|-.++--+.|. .++..+ .|+++..+-....-..|+. + =|..
T Consensus 75 ~~Dfv~Si~dg-----RlfeQ~~rL~~~y~rpvliVegd~~~~~~~~i~~~av~~al~s~~vdfg~~vi~t~~~~~Ta~~ 149 (254)
T COG1948 75 ISDFVSSIIDG-----RLFEQAKRLKKSYERPVLIVEGDDSFSRRPKIHPNAVRGALASLAVDFGLPVIWTRSPEETAEL 149 (254)
T ss_pred HHHHHHHHhcc-----hHHHHHHHHHhcCCccEEEEEcccccccccccCHHHHHHHHHHHHhhcCceEEEeCCHHHHHHH
Confidence 45566666544 5555667787 454554333344 444444 6777765433322334553 1 3788
Q ss_pred HHHHHHHHHHhcCCCccchhhhh-CCCHHHHHH-HhhcCCccchHHHHHHHHHhcCCCCccccch
Q 021493 216 ITGTVDVLQSKHSGGAEWLLSLR-KLDLQEAID-ALCTLPGVGPKVAACIALFSLDQHHAIPVDT 278 (311)
Q Consensus 216 I~~~A~~i~~~~~gg~~~l~~L~-~~~~~e~~~-~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt 278 (311)
|..+|+....+... ........ ..++.+... .|.++||||++.|.-++..-...-+++-++.
T Consensus 150 i~~la~req~e~~r-~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~ 213 (254)
T COG1948 150 IHELARREQEERKR-SVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASE 213 (254)
T ss_pred HHHHHHHHHHhccc-cccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH
Confidence 88899888743211 11122222 245666554 5668999999999988754434445554544
No 61
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.62 E-value=1 Score=40.11 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=22.0
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+..+.|++++|||||+|-.|+-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 4467899999999999999999876
No 62
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=82.51 E-value=3.6 Score=37.80 Aligned_cols=60 Identities=30% Similarity=0.401 Sum_probs=42.6
Q ss_pred CCHHHHHHHHHHhcc-ccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHHc-CCch-HHHHHHHHHH
Q 021493 145 QDPVECLLQFLCSSN-NNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA-GFGY-RAKYITGTVD 221 (311)
Q Consensus 145 ~dpfe~Li~~IlsQq-~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~ 221 (311)
.|+...+..|+++-. ++-.-|. .....|++.+++..+|+++|..| |+|. ||+.|++.-.
T Consensus 187 ~d~ls~~~~~Lt~i~~VnKtda~------------------~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~ 248 (254)
T KOG2841|consen 187 RDLLSSLLGFLTTIPGVNKTDAQ------------------LLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLH 248 (254)
T ss_pred ccHHHHHHHHHHhCCCCCcccHH------------------HHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHh
Confidence 666677777776654 1211121 12467899999999999999987 9995 9999987654
Q ss_pred H
Q 021493 222 V 222 (311)
Q Consensus 222 ~ 222 (311)
+
T Consensus 249 ~ 249 (254)
T KOG2841|consen 249 Q 249 (254)
T ss_pred c
Confidence 3
No 63
>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=82.15 E-value=1.8 Score=41.23 Aligned_cols=54 Identities=31% Similarity=0.424 Sum_probs=35.7
Q ss_pred CCch-HHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCC
Q 021493 208 GFGY-RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQ 270 (311)
Q Consensus 208 Glg~-RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~ 270 (311)
|+|. -|+.|.++.+ . |..-.++.|..- .+....+|++++|||||+|.-+- .+|-
T Consensus 52 giG~~ia~kI~E~~~---t---G~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~--~lGi 106 (307)
T cd00141 52 GIGKKIAEKIEEILE---T---GKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY--ELGI 106 (307)
T ss_pred CccHHHHHHHHHHHH---c---CCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH--HcCC
Confidence 7775 3444444332 2 222245556554 78899999999999999998776 4553
No 64
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=82.14 E-value=4.5 Score=42.71 Aligned_cols=72 Identities=25% Similarity=0.345 Sum_probs=45.2
Q ss_pred CCHHHHhcCCHHHHHHc-CCch-HHHHHHHHHHHHHHhc----------CC-Ccc----------chhhhhCCCHHHHHH
Q 021493 191 PSLERLSLVSEVELRNA-GFGY-RAKYITGTVDVLQSKH----------SG-GAE----------WLLSLRKLDLQEAID 247 (311)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~~i~~~~----------~g-g~~----------~l~~L~~~~~~e~~~ 247 (311)
-++++|..+..++|..+ |||. .|..|.+..+...+.. .+ |+- +++.|.+.+ .+
T Consensus 468 ~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As----~e 543 (665)
T PRK07956 468 HDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAAS----EE 543 (665)
T ss_pred CCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCC----HH
Confidence 48888888888888876 8885 5666655443322100 00 111 233333333 35
Q ss_pred HhhcCCccchHHHHHHHHH
Q 021493 248 ALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 248 ~L~~l~GIG~ktAd~vlLf 266 (311)
+|.+++|||+++|..|.-|
T Consensus 544 eL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 544 ELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred HHhccCCcCHHHHHHHHHH
Confidence 7999999999999999765
No 65
>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=81.04 E-value=1.4 Score=30.89 Aligned_cols=24 Identities=25% Similarity=0.256 Sum_probs=17.1
Q ss_pred HHhhcCCccchHHHHHHHHHhcCC
Q 021493 247 DALCTLPGVGPKVAACIALFSLDQ 270 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf~l~~ 270 (311)
+.++++.|||+.||.-..-.|+.-
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~rt 25 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGIRT 25 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT--S
T ss_pred cchhhcccccHHHHHHHHHhCCCC
Confidence 578999999999999988766544
No 66
>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=79.70 E-value=1.2 Score=27.95 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=11.4
Q ss_pred hhcCCccchHHHHHH
Q 021493 249 LCTLPGVGPKVAACI 263 (311)
Q Consensus 249 L~~l~GIG~ktAd~v 263 (311)
+..++|||++|+.-.
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 457999999999863
No 67
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.54 E-value=1.7 Score=38.56 Aligned_cols=21 Identities=43% Similarity=0.672 Sum_probs=18.3
Q ss_pred HHHhhcCCccchHHHHHHHHH
Q 021493 246 IDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 246 ~~~L~~l~GIG~ktAd~vlLf 266 (311)
.+.|.++||||+|+|+-|+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 457999999999999999854
No 68
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=79.21 E-value=7.7 Score=41.03 Aligned_cols=23 Identities=30% Similarity=0.391 Sum_probs=19.2
Q ss_pred HHHHhhcCCccchHHHHHHHHHh
Q 021493 245 AIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
..++|++++|||+++|..+.-|-
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 34579999999999999997653
No 69
>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=79.11 E-value=2.8 Score=30.58 Aligned_cols=55 Identities=18% Similarity=0.342 Sum_probs=35.3
Q ss_pred HHhcCCHHHHHH--cCCch-HHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 195 RLSLVSEVELRN--AGFGY-RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 195 ~La~~~~e~Lr~--~Glg~-RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.|-.++.++|.. -|+|. +|+.|++--.. +++ + +..++|.+++|||.++|+-+.-+
T Consensus 9 nvNta~~~~L~~~ipgig~~~a~~Il~~R~~----~g~----~---------~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGLKKAEAIVSYREE----YGP----F---------KTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCHHHHHHHHHHHHH----cCC----c---------CCHHHHHcCCCCCHHHHHHHHhh
Confidence 344467778877 48886 66555543221 111 1 14678899999999999988754
No 70
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=78.91 E-value=1.7 Score=38.65 Aligned_cols=22 Identities=41% Similarity=0.662 Sum_probs=18.9
Q ss_pred HHHHHHhhcCCccchHHHHHHH
Q 021493 243 QEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 243 ~e~~~~L~~l~GIG~ktAd~vl 264 (311)
.+....|..+||||||+|..++
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il 90 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAIL 90 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHH
Confidence 4557799999999999999885
No 71
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=77.71 E-value=3.8 Score=35.01 Aligned_cols=50 Identities=28% Similarity=0.473 Sum_probs=34.6
Q ss_pred hcCCHHHHHHc-CCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHH
Q 021493 197 SLVSEVELRNA-GFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 263 (311)
Q Consensus 197 a~~~~e~Lr~~-Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~v 263 (311)
-.++.++|+.+ |+| .+|+.|++--+. + | .+ ...+.|...+|||+++.+-.
T Consensus 92 NtAs~eeL~~lpgIG~~kA~aIi~yRe~----~-G---~f---------~sv~dL~~v~GiG~~~~ekl 143 (149)
T COG1555 92 NTASAEELQALPGIGPKKAQAIIDYREE----N-G---PF---------KSVDDLAKVKGIGPKTLEKL 143 (149)
T ss_pred cccCHHHHHHCCCCCHHHHHHHHHHHHH----c-C---CC---------CcHHHHHhccCCCHHHHHHH
Confidence 34678899776 788 588887754322 2 1 11 24678999999999998754
No 72
>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=77.58 E-value=14 Score=32.64 Aligned_cols=128 Identities=15% Similarity=0.124 Sum_probs=74.9
Q ss_pred ccChhHHHHHHHhcCCccCC-CCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHH
Q 021493 125 ASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEV 202 (311)
Q Consensus 125 ~~D~~l~~~~~~~~GlR~l~-~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e 202 (311)
..+|.+..-...-=|..+.. +..||.|+-.+...-.|+..+.+-...+. .|- .| +|+.+|..+++
T Consensus 3 ~~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~------------~F-d~~~vA~~~e~ 69 (179)
T PF03352_consen 3 NSDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFA------------GF-DPEKVAKMDEE 69 (179)
T ss_dssp TSSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTG------------GG-HHHHHHT--HH
T ss_pred CCChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH------------CC-CHHHHHcCCHH
Confidence 34555555444444666654 67899999999999999999998888886 432 22 79999999999
Q ss_pred HHHHc----CCc---hHHHHHHHHHHHHHHhc-CCCcc--chh-------------hhhCCC-----HHHHHHHhh--cC
Q 021493 203 ELRNA----GFG---YRAKYITGTVDVLQSKH-SGGAE--WLL-------------SLRKLD-----LQEAIDALC--TL 252 (311)
Q Consensus 203 ~Lr~~----Glg---~RA~~I~~~A~~i~~~~-~gg~~--~l~-------------~L~~~~-----~~e~~~~L~--~l 252 (311)
++..+ |+= .|.+.++.-|+++.+-. .+|.+ .+. ...+++ .+.+.+.|. .+
T Consensus 70 ~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF 149 (179)
T PF03352_consen 70 DIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFGSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGF 149 (179)
T ss_dssp HHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT-
T ss_pred HHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcCCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcc
Confidence 98663 441 37888888888876411 11111 011 011111 234455555 37
Q ss_pred CccchHHHHHHHH
Q 021493 253 PGVGPKVAACIAL 265 (311)
Q Consensus 253 ~GIG~ktAd~vlL 265 (311)
+=|||-|+..+|.
T Consensus 150 ~FvGpt~vysflq 162 (179)
T PF03352_consen 150 KFVGPTTVYSFLQ 162 (179)
T ss_dssp -S--HHHHHHHHH
T ss_pred eeECHHHHHHHHH
Confidence 8899999888865
No 73
>PRK14973 DNA topoisomerase I; Provisional
Probab=75.13 E-value=9.9 Score=41.80 Aligned_cols=93 Identities=16% Similarity=0.087 Sum_probs=57.9
Q ss_pred cCCCHHHHhcCCHHHHHH-cCCc-hHHHHHHHHHH-HHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 189 EFPSLERLSLVSEVELRN-AGFG-YRAKYITGTVD-VLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 189 ~FPtpe~La~~~~e~Lr~-~Glg-~RA~~I~~~A~-~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
.|-++++++.+++++|.. .|++ -.+..+...|. .+.. .+-+.......+.-+.+|++++|||++|++-.-.
T Consensus 822 G~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ 895 (936)
T PRK14973 822 GFDTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGR------PVPEKISKAAFERGRAELLSVPGLGETTLEKLYL 895 (936)
T ss_pred cCCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcC------CCchhhhhhhhcccchhhhhccCCCHHHHHHHHH
Confidence 588999999999999977 5887 36666654444 3332 1222222333444555699999999999987666
Q ss_pred HhcCCCCccccchHHHHHHHHcC
Q 021493 266 FSLDQHHAIPVDTHVWKIATRYL 288 (311)
Q Consensus 266 f~l~~~d~fPVDt~v~Ri~~r~~ 288 (311)
-|.-..+.+-.+ -+.+++..-+
T Consensus 896 ag~~~~e~l~~~-d~~~la~~~~ 917 (936)
T PRK14973 896 AGVYDGDLLVSA-DPKKLAKVTG 917 (936)
T ss_pred cCCCCHHHhccC-CHHHHhhhcC
Confidence 555443333222 3344444434
No 74
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.80 E-value=2.5 Score=37.80 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=21.5
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+..+.|+++.|||||+|=.||-
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 4467899999999999999988863
No 75
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.69 E-value=2.5 Score=37.36 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=21.5
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+.++.|+++.|||||+|=.||-
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 4467899999999999999988864
No 76
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=74.59 E-value=19 Score=38.33 Aligned_cols=68 Identities=26% Similarity=0.355 Sum_probs=43.4
Q ss_pred CCHHHHhcCCHHHHHHc-CCch-HHHHHHHHHH-------------------------HHHHhcCCCccchhhhhCCCHH
Q 021493 191 PSLERLSLVSEVELRNA-GFGY-RAKYITGTVD-------------------------VLQSKHSGGAEWLLSLRKLDLQ 243 (311)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~-------------------------~i~~~~~gg~~~l~~L~~~~~~ 243 (311)
-++.+|-.+..++|..+ |||. .|..|.+..+ .+..+++ +++.|.+.+
T Consensus 485 ~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~----si~~L~~As-- 558 (689)
T PRK14351 485 ESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFG----TFEAIMDAD-- 558 (689)
T ss_pred CCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHhC----CHHHHHhCC--
Confidence 37788888888888765 7875 5555544332 1222221 244444443
Q ss_pred HHHHHhhcCCccchHHHHHHHHH
Q 021493 244 EAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 244 e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.++|.+++|||+++|..|.-|
T Consensus 559 --~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 559 --EEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred --HHHHhccCCcCHHHHHHHHHH
Confidence 356899999999999998765
No 77
>PRK08609 hypothetical protein; Provisional
Probab=74.20 E-value=3.4 Score=42.79 Aligned_cols=31 Identities=35% Similarity=0.494 Sum_probs=23.0
Q ss_pred chhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 233 WLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 233 ~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
-++.|+. ..++...+|+++||||||+|.-+-
T Consensus 75 ~le~l~~-~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 75 VLQELKK-EVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred HHHHHHh-hCcHHHHHHhcCCCCCHHHHHHHH
Confidence 4666665 345566689999999999997653
No 78
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.19 E-value=2.6 Score=37.34 Aligned_cols=25 Identities=28% Similarity=0.360 Sum_probs=21.5
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+..+.|+++.|||||+|=.+|-
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3457899999999999999988875
No 79
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=73.79 E-value=3.3 Score=29.99 Aligned_cols=23 Identities=39% Similarity=0.741 Sum_probs=17.3
Q ss_pred HHHHhhcCCccchHHHHHHHHHh
Q 021493 245 AIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
..++|.++||||++.|..|+-+-
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHH
Confidence 46789999999999999998654
No 80
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.03 E-value=2.9 Score=37.07 Aligned_cols=25 Identities=28% Similarity=0.310 Sum_probs=21.6
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+.++.|+++.|||||+|=.+|-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 4567899999999999999988863
No 81
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.10 E-value=3.2 Score=37.13 Aligned_cols=25 Identities=36% Similarity=0.533 Sum_probs=21.6
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+.++.|+++.|||||+|=.+|-
T Consensus 66 ~Er~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 66 DSLELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3467899999999999999988875
No 82
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.66 E-value=3.3 Score=37.02 Aligned_cols=25 Identities=28% Similarity=0.441 Sum_probs=21.7
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+.++.|+++.|||||+|=.+|-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 4467899999999999999988875
No 83
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=71.42 E-value=2.9 Score=26.95 Aligned_cols=16 Identities=31% Similarity=0.561 Sum_probs=13.0
Q ss_pred hhcCCccchHHHHHHH
Q 021493 249 LCTLPGVGPKVAACIA 264 (311)
Q Consensus 249 L~~l~GIG~ktAd~vl 264 (311)
+-.+||||+|+|--++
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 3578999999997664
No 84
>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=70.55 E-value=3.9 Score=33.54 Aligned_cols=23 Identities=35% Similarity=0.725 Sum_probs=19.7
Q ss_pred HHHHhhcCCccchHHHHHHHHHh
Q 021493 245 AIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
..++|+++||||++.|.-|+-+=
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Confidence 36688999999999999998763
No 85
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.40 E-value=3.7 Score=36.90 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=21.8
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+.++.|+++.|||||+|=.+|-
T Consensus 68 ~Er~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 68 DERQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHh
Confidence 4467899999999999999988875
No 86
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=70.36 E-value=14 Score=38.26 Aligned_cols=72 Identities=19% Similarity=0.220 Sum_probs=45.0
Q ss_pred CCHHHHhcCCHHHHHHc-CCch-HHHHHHHHHHHHHHh------------cCC------CccchhhhhCCCHHHHHHHhh
Q 021493 191 PSLERLSLVSEVELRNA-GFGY-RAKYITGTVDVLQSK------------HSG------GAEWLLSLRKLDLQEAIDALC 250 (311)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A~~i~~~------------~~g------g~~~l~~L~~~~~~e~~~~L~ 250 (311)
-++.+|-.++.++|..+ |||. .|+.|.+..+.-.+. +=| .--+++.|...+ .++|+
T Consensus 448 ~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~l~~a~----~e~l~ 523 (562)
T PRK08097 448 EHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDRSWQQLLSRS----EQQWQ 523 (562)
T ss_pred CCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcCCHHHHHcCC----HHHHh
Confidence 57888888888888776 7875 566665543321110 000 001244444433 35799
Q ss_pred cCCccchHHHHHHHHH
Q 021493 251 TLPGVGPKVAACIALF 266 (311)
Q Consensus 251 ~l~GIG~ktAd~vlLf 266 (311)
+++|||+++|+.+.-|
T Consensus 524 ~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 524 QLPGIGEGRARQLIAF 539 (562)
T ss_pred cCCCchHHHHHHHHHH
Confidence 9999999999999776
No 87
>PRK07945 hypothetical protein; Provisional
Probab=69.83 E-value=5.5 Score=38.43 Aligned_cols=49 Identities=31% Similarity=0.437 Sum_probs=33.7
Q ss_pred cCC-chHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHH--HhhcCCccchHHHHHHHHH
Q 021493 207 AGF-GYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAID--ALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 207 ~Gl-g~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~--~L~~l~GIG~ktAd~vlLf 266 (311)
.|- .||++.-.++|+.+..- ..+ . .++..+ .|++|||||.-+|..|.=+
T Consensus 17 ~~~n~frv~ayr~aa~~~~~~----~~~--~-----~~~~~~~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 17 ARADTYRVRAFRRAADVVEAL----DAA--E-----RARRARAGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred cCCChhhHHHHHHHHHHHHhc----Chh--H-----HHHHHhcCCcccCCCcCHHHHHHHHHH
Confidence 344 48999999999998751 111 0 222222 6999999999999988644
No 88
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=68.76 E-value=6.8 Score=37.78 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 211 YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 211 ~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
+|+++..++|+.|.... .+++. .++|.+|||||+++|+-|-=+
T Consensus 25 ~k~~ay~~Aa~~i~~l~----~~i~~---------~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 25 RKCSYFRKAASVLKSLP----FPINS---------MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHHHHHHHhCC----CCCCC---------HHHHhcCCCccHHHHHHHHHH
Confidence 68888888898887621 12222 237889999999999988733
No 89
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=68.54 E-value=13 Score=36.30 Aligned_cols=39 Identities=31% Similarity=0.394 Sum_probs=33.8
Q ss_pred cccCCCHHHHhcCCHHHHHHc-CCc-hHHHHHHHHHHHHHH
Q 021493 187 FHEFPSLERLSLVSEVELRNA-GFG-YRAKYITGTVDVLQS 225 (311)
Q Consensus 187 ~~~FPtpe~La~~~~e~Lr~~-Glg-~RA~~I~~~A~~i~~ 225 (311)
...|.+.+.+.+++.++|..+ |+| .||+.|.+..+.+.+
T Consensus 304 l~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 304 VEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAE 344 (352)
T ss_pred HHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHH
Confidence 456779999999999999886 898 599999999988876
No 90
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=68.13 E-value=4.1 Score=34.82 Aligned_cols=23 Identities=39% Similarity=0.654 Sum_probs=19.4
Q ss_pred HHHhhcCCccchHHHHHHHHHhc
Q 021493 246 IDALCTLPGVGPKVAACIALFSL 268 (311)
Q Consensus 246 ~~~L~~l~GIG~ktAd~vlLf~l 268 (311)
.++|..+||||++.|..|.-+--
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yRe 118 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYRE 118 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Confidence 45669999999999999987763
No 91
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=67.89 E-value=6.2 Score=36.03 Aligned_cols=55 Identities=22% Similarity=0.291 Sum_probs=38.7
Q ss_pred CHHHHHH--cCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHH
Q 021493 200 SEVELRN--AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAAC 262 (311)
Q Consensus 200 ~~e~Lr~--~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~ 262 (311)
+..||=+ ++-|.|-+..+.+|+.+.+++++ |..|.+.+ .++|++++|||+-.|--
T Consensus 25 sd~ELLailLrtG~~~~~~~~la~~lL~~fg~----L~~l~~a~----~~el~~v~GiG~aka~~ 81 (224)
T COG2003 25 SDAELLAILLRTGTKGESVLDLAKELLQEFGS----LAELLKAS----VEELSSVKGIGLAKAIQ 81 (224)
T ss_pred chHHHHHHHHhcCCCCCCHHHHHHHHHHHccc----HHHHHhCC----HHHHhhCCCccHHHHHH
Confidence 3444544 35556677888999999998864 77776665 45799999999655443
No 92
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=67.22 E-value=9.9 Score=36.90 Aligned_cols=25 Identities=28% Similarity=0.679 Sum_probs=20.7
Q ss_pred HHHHHHhhcCCccchHHHHHHHHHh
Q 021493 243 QEAIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 243 ~e~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
.+..++|+-+|||||+|+-...|.+
T Consensus 274 p~Df~elLl~~GiGpstvRALalVA 298 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVA 298 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHH
Confidence 3467889999999999998887754
No 93
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=67.21 E-value=8.8 Score=36.84 Aligned_cols=49 Identities=24% Similarity=0.417 Sum_probs=36.6
Q ss_pred cCCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHH--hhcCCccchHHHHHHHHHh
Q 021493 207 AGFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDA--LCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 207 ~Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~--L~~l~GIG~ktAd~vlLf~ 267 (311)
.|-. +|++.-..+|+.+.+. +-+++++.+. ++.|||||+.+|+.|.-+-
T Consensus 22 ~Gen~fk~~aYr~Aa~sle~~------------~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 22 EGENPFKIRAYRKAAQSLENL------------TEDLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred cCCCccchHHHHHHHHhhhhc------------ccchHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 3543 7888888888888752 1256666666 9999999999999987543
No 94
>PRK07758 hypothetical protein; Provisional
Probab=66.79 E-value=10 Score=30.02 Aligned_cols=31 Identities=23% Similarity=0.334 Sum_probs=23.9
Q ss_pred CccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 230 GAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 230 g~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
|.-.+++|..++. ++|++++|+|+|+.+-|-
T Consensus 54 GI~TL~dLv~~te----~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 54 GIHTVEELSKYSE----KEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCCcHHHHHcCCH----HHHHHccCCCHHHHHHHH
Confidence 5556777777654 578999999999988763
No 95
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=66.26 E-value=4.6 Score=33.80 Aligned_cols=20 Identities=30% Similarity=0.507 Sum_probs=17.4
Q ss_pred HHHhhcCCccchHHHHHHHH
Q 021493 246 IDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 246 ~~~L~~l~GIG~ktAd~vlL 265 (311)
.++|+++|||||..|.-|.-
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45688899999999999984
No 96
>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=65.27 E-value=8.9 Score=36.53 Aligned_cols=46 Identities=26% Similarity=0.335 Sum_probs=32.7
Q ss_pred CchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHh
Q 021493 209 FGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 209 lg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
-.||++.-..+|..+.+- ...+.. .+++.+|||||+++|+.|-=+-
T Consensus 20 ~~~r~~aY~~Aa~~l~~l----~~~i~~---------~~~~~~ipgiG~~ia~kI~E~~ 65 (307)
T cd00141 20 NPFRVRAYRKAARALESL----PEPIES---------LEEAKKLPGIGKKIAEKIEEIL 65 (307)
T ss_pred CcchHHHHHHHHHHHHhC----CcccCC---------HHHhcCCCCccHHHHHHHHHHH
Confidence 457998888889888752 112221 2366999999999999987543
No 97
>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=64.37 E-value=3.7 Score=30.75 Aligned_cols=23 Identities=30% Similarity=0.550 Sum_probs=17.6
Q ss_pred HHhhcCCccchHHHHHHHHHhcCC
Q 021493 247 DALCTLPGVGPKVAACIALFSLDQ 270 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf~l~~ 270 (311)
+.+..+||||+|+|.-++. -++.
T Consensus 22 D~i~gv~giG~k~A~~ll~-~~~~ 44 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLK-EYGS 44 (75)
T ss_pred ccCCCCCcccHHHHHHHHH-HhCC
Confidence 4566899999999998864 3444
No 98
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=63.97 E-value=5 Score=36.04 Aligned_cols=25 Identities=32% Similarity=0.533 Sum_probs=21.3
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+.+..|+++.|||||+|=.||-
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs 91 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILS 91 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHc
Confidence 4467899999999999999987764
No 99
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=62.12 E-value=7.4 Score=31.20 Aligned_cols=24 Identities=25% Similarity=0.181 Sum_probs=20.3
Q ss_pred HHHHHhhcCCccchHHHHHHHHHh
Q 021493 244 EAIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 244 e~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
.+.-.|++|.|||+.+|..||...
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~l 35 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKL 35 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHT
T ss_pred chHhHHhhhhccCHHHHHHHHHHc
Confidence 367789999999999999987643
No 100
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=60.55 E-value=13 Score=36.15 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHH
Q 021493 218 GTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 263 (311)
Q Consensus 218 ~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~v 263 (311)
.+|+.+.++|+ +|..+-+.+. ++|.+++|||++.|..|
T Consensus 298 ~iAk~Ll~~FG----SL~~Il~As~----eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 298 AVIENLVEHFG----SLQGLLAASI----EDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHHHHcC----CHHHHHcCCH----HHHhhCCCcCHHHHHHH
Confidence 56788888885 4777766664 46999999999999873
No 101
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=57.74 E-value=98 Score=33.13 Aligned_cols=20 Identities=30% Similarity=0.355 Sum_probs=16.0
Q ss_pred hh-cCCccchHHHHHHHHHhcC
Q 021493 249 LC-TLPGVGPKVAACIALFSLD 269 (311)
Q Consensus 249 L~-~l~GIG~ktAd~vlLf~l~ 269 (311)
|+ .++|||-++||.+... +|
T Consensus 182 L~~~i~gigF~~aD~iA~~-~g 202 (720)
T TIGR01448 182 LAEDVKGIGFLTADQLAQA-LG 202 (720)
T ss_pred hhhhcCCCCHHHHHHHHHH-cC
Confidence 44 5899999999999764 44
No 102
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=56.23 E-value=27 Score=33.69 Aligned_cols=74 Identities=18% Similarity=0.149 Sum_probs=50.7
Q ss_pred chhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCcccc--c--hHHHHHHHHcCCCcccCCCCCHHHHHHHHHH
Q 021493 233 WLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPV--D--THVWKIATRYLLPELAGVRLTPKLCSRVAEA 308 (311)
Q Consensus 233 ~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPV--D--t~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~ 308 (311)
-++.+++-+.....+.++++-|||.++|+..-..|+.-.+.+-= | |+-.++--.+|-. --+.++..+..++.+.
T Consensus 83 ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk~~~kft~qqk~Gl~yy~D--f~~~v~ReE~~~i~~~ 160 (353)
T KOG2534|consen 83 ELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYED--FLKRVTREEATAIQQT 160 (353)
T ss_pred hHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHHH--HhhhccHHHHHHHHHH
Confidence 45555665677889999999999999999999999875554431 2 3444555555521 2367888887776653
No 103
>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=53.01 E-value=12 Score=27.20 Aligned_cols=21 Identities=33% Similarity=0.493 Sum_probs=17.7
Q ss_pred HHHhhc-CCccchHHHHHHHHH
Q 021493 246 IDALCT-LPGVGPKVAACIALF 266 (311)
Q Consensus 246 ~~~L~~-l~GIG~ktAd~vlLf 266 (311)
.+.|.. +||||+++|..++-+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 347777 999999999999876
No 104
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=52.30 E-value=56 Score=29.06 Aligned_cols=76 Identities=17% Similarity=0.170 Sum_probs=57.0
Q ss_pred cCCccCC-CCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhcCCHHHHHH----cCCc-h
Q 021493 138 AGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN----AGFG-Y 211 (311)
Q Consensus 138 ~GlR~l~-~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~----~Glg-~ 211 (311)
-|.++.. +..||.|+-.+...-.|+..+.+=.+...+ -|+.| +|+.+|..+++++.. .|+= .
T Consensus 22 WG~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~fre-----------aF~~F-d~~kVA~~~~~dverLl~d~gIIR~ 89 (188)
T COG2818 22 WGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFRE-----------AFHGF-DPEKVAAMTEEDVERLLADAGIIRN 89 (188)
T ss_pred cCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHH-----------HHhcC-CHHHHHcCCHHHHHHHHhCcchhhh
Confidence 3777765 688999999999999999999887777751 13444 899999999888855 4663 3
Q ss_pred --HHHHHHHHHHHHHH
Q 021493 212 --RAKYITGTVDVLQS 225 (311)
Q Consensus 212 --RA~~I~~~A~~i~~ 225 (311)
|.+.++.-|+++.+
T Consensus 90 r~KI~A~i~NA~~~l~ 105 (188)
T COG2818 90 RGKIKATINNARAVLE 105 (188)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 66677777777654
No 105
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=52.16 E-value=3.6 Score=32.87 Aligned_cols=26 Identities=31% Similarity=0.507 Sum_probs=15.4
Q ss_pred HhhcCCccchHHHHHHHHHhcCCCCcc
Q 021493 248 ALCTLPGVGPKVAACIALFSLDQHHAI 274 (311)
Q Consensus 248 ~L~~l~GIG~ktAd~vlLf~l~~~d~f 274 (311)
-+-.+||||+|||.-.+- -+|..+.+
T Consensus 19 NIPGV~GIG~KtA~~LL~-~ygsle~i 44 (101)
T PF01367_consen 19 NIPGVPGIGPKTAAKLLQ-EYGSLENI 44 (101)
T ss_dssp TB---TTSTCHCCCCCHH-HHTSCHCC
T ss_pred CCCCCCCCCHHHHHHHHH-HcCCHHHH
Confidence 345789999999986653 44544444
No 106
>PRK08609 hypothetical protein; Provisional
Probab=51.77 E-value=19 Score=37.30 Aligned_cols=44 Identities=23% Similarity=0.385 Sum_probs=32.4
Q ss_pred chHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 210 GYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 210 g~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.||++.-.++|+.+.+.. .++ .+ ..+|.+|||||+.+|+.|-=+
T Consensus 24 ~fr~~aYr~Aa~~i~~l~----~~i--------~~-~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 24 PFKISAFRKAAQALELDE----RSL--------SE-IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred cHHHHHHHHHHHHHHhCc----hhh--------hh-hhhhccCCCcCHHHHHHHHHH
Confidence 489999999999887621 112 21 247999999999999988644
No 107
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=51.02 E-value=17 Score=26.25 Aligned_cols=32 Identities=38% Similarity=0.312 Sum_probs=21.9
Q ss_pred ccCCCHHHHhcCCHHHHHHc-CCch-HHHHHHHH
Q 021493 188 HEFPSLERLSLVSEVELRNA-GFGY-RAKYITGT 219 (311)
Q Consensus 188 ~~FPtpe~La~~~~e~Lr~~-Glg~-RA~~I~~~ 219 (311)
..|.+.+.|.+++.++|..+ |+|. .|+.|.+.
T Consensus 21 ~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 21 KHFGSLEALMNASVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred HHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence 46789999999999999886 8886 66666543
No 108
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=47.81 E-value=25 Score=27.22 Aligned_cols=19 Identities=42% Similarity=0.464 Sum_probs=16.3
Q ss_pred Hhhc-CCccchHHHHHHHHH
Q 021493 248 ALCT-LPGVGPKVAACIALF 266 (311)
Q Consensus 248 ~L~~-l~GIG~ktAd~vlLf 266 (311)
.|+. +.|||-++||-+.+.
T Consensus 46 ~L~~~i~gi~F~~aD~iA~~ 65 (94)
T PF14490_consen 46 RLIEDIDGIGFKTADKIALK 65 (94)
T ss_dssp CCCB-SSSSBHHHHHHHHHT
T ss_pred HHHHHccCCCHHHHHHHHHH
Confidence 4666 999999999999874
No 109
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=46.44 E-value=23 Score=33.99 Aligned_cols=32 Identities=22% Similarity=0.404 Sum_probs=24.8
Q ss_pred HHHHHHhhcCCccchHHHHHHHHHh---cCCCCcc
Q 021493 243 QEAIDALCTLPGVGPKVAACIALFS---LDQHHAI 274 (311)
Q Consensus 243 ~e~~~~L~~l~GIG~ktAd~vlLf~---l~~~d~f 274 (311)
.+-.++|+.++||||+|.....|.+ +|-+..|
T Consensus 265 p~~feeLL~~~GvGp~TlRALaLvaelIyg~p~s~ 299 (319)
T PF05559_consen 265 PSDFEELLLIKGVGPSTLRALALVAELIYGVPPSF 299 (319)
T ss_pred ccCHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCc
Confidence 3457899999999999999998877 4444333
No 110
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=46.39 E-value=11 Score=38.06 Aligned_cols=18 Identities=50% Similarity=0.995 Sum_probs=11.1
Q ss_pred CCCCCCCCCCCCcccccc
Q 021493 15 RLTPQPPPTPPNPQTLTT 32 (311)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~ 32 (311)
..||||||+||.|.+-|+
T Consensus 13 ~~~~~~~~~~~~~~~~~~ 30 (461)
T PLN03132 13 AATPQPPPPPPPPEKTHF 30 (461)
T ss_pred cCCCCCcccCCCCcccCC
Confidence 457777776666655443
No 111
>PRK00024 hypothetical protein; Reviewed
Probab=46.28 E-value=56 Score=29.72 Aligned_cols=31 Identities=32% Similarity=0.384 Sum_probs=23.2
Q ss_pred CCCHHHHhcCCHHHHHHc-CCch-HHHHHHHHH
Q 021493 190 FPSLERLSLVSEVELRNA-GFGY-RAKYITGTV 220 (311)
Q Consensus 190 FPtpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A 220 (311)
|.+...+.+++.++|+.. |+|. ||..|..+.
T Consensus 54 fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~ 86 (224)
T PRK00024 54 FGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL 86 (224)
T ss_pred cCCHHHHHhCCHHHHhhccCccHHHHHHHHHHH
Confidence 447899999999999885 8884 666554443
No 112
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=44.25 E-value=13 Score=30.73 Aligned_cols=22 Identities=27% Similarity=0.096 Sum_probs=19.0
Q ss_pred HHHHhhcCCccchHHHHHHHHH
Q 021493 245 AIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf 266 (311)
+.-.|+.|.|||+.+|..||-.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~ 36 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEK 36 (122)
T ss_pred eeeeecccccccHHHHHHHHHH
Confidence 5567999999999999999864
No 113
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=43.35 E-value=17 Score=34.92 Aligned_cols=22 Identities=32% Similarity=0.498 Sum_probs=19.2
Q ss_pred HHHHhhcCCccchHHHHHHHHH
Q 021493 245 AIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf 266 (311)
-.++|+.+||||.|+|.-|++.
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred CHHHhcccCCCChHHHHHHHHH
Confidence 4789999999999999988764
No 114
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=42.87 E-value=36 Score=24.34 Aligned_cols=37 Identities=27% Similarity=0.387 Sum_probs=30.0
Q ss_pred ccCCC-HHHHhcCCHHHHHHcCCchH-HHHHHHHHHHHH
Q 021493 188 HEFPS-LERLSLVSEVELRNAGFGYR-AKYITGTVDVLQ 224 (311)
Q Consensus 188 ~~FPt-pe~La~~~~e~Lr~~Glg~R-A~~I~~~A~~i~ 224 (311)
-.|++ +++|-..+-.+|++.|+.-| -+||....+.+.
T Consensus 17 ~kf~~~w~~lf~~~s~~LK~~GIp~r~RryiL~~~ek~r 55 (57)
T PF09597_consen 17 EKFESDWEKLFTTSSKQLKELGIPVRQRRYILRWREKYR 55 (57)
T ss_pred HHHHHHHHHHHhcCHHHHHHCCCCHHHHHHHHHHHHHHh
Confidence 35788 99999999999999999743 478888777664
No 115
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=41.34 E-value=40 Score=36.06 Aligned_cols=24 Identities=29% Similarity=0.445 Sum_probs=15.5
Q ss_pred CHHHHHHHhhc--CCccchHHHHHHH
Q 021493 241 DLQEAIDALCT--LPGVGPKVAACIA 264 (311)
Q Consensus 241 ~~~e~~~~L~~--l~GIG~ktAd~vl 264 (311)
+.+.+...|.+ +||||+++|.-+.
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv 101 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIV 101 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHH
Confidence 34455666654 7777777777664
No 116
>PF13592 HTH_33: Winged helix-turn helix
Probab=39.16 E-value=24 Score=25.01 Aligned_cols=55 Identities=18% Similarity=0.123 Sum_probs=31.4
Q ss_pred chHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 021493 256 GPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 310 (311)
Q Consensus 256 G~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~~~ 310 (311)
|.||+.-|.-+--..+.+-=-..+|.+++.++|+.-.......++.=.+..+.|.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~kp~~~~~k~d~~~q~~f~ 57 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQKPRPRPPKADEEAQEAFK 57 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccccCCCCcccCCHHHHHHHH
Confidence 3455555554443333322246789999999987644444444555555555554
No 117
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=38.93 E-value=19 Score=29.72 Aligned_cols=23 Identities=26% Similarity=0.268 Sum_probs=18.9
Q ss_pred HHHHhhcCCccchHHHHHHHHHh
Q 021493 245 AIDALCTLPGVGPKVAACIALFS 267 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf~ 267 (311)
+.=.|+.|.|||..+|..||--+
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~ 37 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKA 37 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHc
Confidence 34479999999999999998643
No 118
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.62 E-value=95 Score=28.15 Aligned_cols=30 Identities=30% Similarity=0.355 Sum_probs=23.5
Q ss_pred CCHHHHhcCCHHHHHHc-CCch-HHHHHHHHH
Q 021493 191 PSLERLSLVSEVELRNA-GFGY-RAKYITGTV 220 (311)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~-RA~~I~~~A 220 (311)
.+...|.+++.++|+.. |+|. ||..|..+.
T Consensus 49 g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~ 80 (218)
T TIGR00608 49 DSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV 80 (218)
T ss_pred CCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHH
Confidence 47899999999999885 8984 776665543
No 119
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=38.52 E-value=18 Score=29.88 Aligned_cols=22 Identities=27% Similarity=0.228 Sum_probs=18.9
Q ss_pred HHHHhhcCCccchHHHHHHHHH
Q 021493 245 AIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf 266 (311)
+.-.|+.|.|||+.+|..||-.
T Consensus 15 v~~aL~~I~GIG~~~a~~i~~~ 36 (122)
T PRK05179 15 VVIALTYIYGIGRTRAKEILAA 36 (122)
T ss_pred EEeeecccccccHHHHHHHHHH
Confidence 4557899999999999999864
No 120
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=38.18 E-value=37 Score=32.72 Aligned_cols=43 Identities=30% Similarity=0.318 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 211 YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 211 ~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.|+..-..+|..+.+-+- . -...+++.+|||||+|+|.-|--+
T Consensus 33 ~r~~~y~~Aasvlk~~p~----~---------I~S~~ea~~lP~iG~kia~ki~Ei 75 (353)
T KOG2534|consen 33 DRARAYRRAASVLKSLPF----P---------ITSGEEAEKLPGIGPKIAEKIQEI 75 (353)
T ss_pred HHHHHHHHHHHHHHhCCC----C---------cccHHHhcCCCCCCHHHHHHHHHH
Confidence 488777777877765110 1 123567788999999999988644
No 121
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=36.66 E-value=44 Score=31.14 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=21.3
Q ss_pred hhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 234 LLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 234 l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
...+...+. ++|+.++|||.+.|.-|--
T Consensus 205 ~~~~~tas~----~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 205 VEDVLTASE----EELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHHHhhcCH----HHHHHhcCccHHHHHHHHH
Confidence 444444444 7999999999999998753
No 122
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=36.04 E-value=20 Score=30.82 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=19.1
Q ss_pred HHHHHhhcCCccchHHHHHHHHH
Q 021493 244 EAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 244 e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.+.-.|+.|.|||+.+|..||--
T Consensus 27 ~v~~aLt~I~GIG~~~A~~I~~~ 49 (154)
T PTZ00134 27 KVPYALTAIKGIGRRFAYLVCKK 49 (154)
T ss_pred EEEEeecccccccHHHHHHHHHH
Confidence 35568999999999999988753
No 123
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=35.47 E-value=95 Score=26.44 Aligned_cols=36 Identities=22% Similarity=0.466 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHh-ccccHHHHHHHHHHHH-hhCCCC
Q 021493 144 RQDPVECLLQFLCS-SNNNIARITKMVDFLA-SLGSHL 179 (311)
Q Consensus 144 ~~dpfe~Li~~Ils-Qq~~i~~a~~~~~~L~-~~G~~~ 179 (311)
.+++||.++..|.+ ...+-+.+...++++. +||..+
T Consensus 83 e~~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~l 120 (144)
T PF09999_consen 83 ERDPFERILDYIAAKTGIEKQEVVAEINELQEELGGLL 120 (144)
T ss_pred cccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccC
Confidence 48999999999999 6689999999999987 788655
No 124
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=35.17 E-value=20 Score=30.45 Aligned_cols=22 Identities=32% Similarity=0.350 Sum_probs=18.4
Q ss_pred HHHHhhcCCccchHHHHHHHHH
Q 021493 245 AIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf 266 (311)
+.-.|+.|.|||+..|..||--
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~~ 40 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIARK 40 (144)
T ss_pred EEEeecceeccCHHHHHHHHHH
Confidence 4557899999999999988753
No 125
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=34.81 E-value=89 Score=20.61 Aligned_cols=33 Identities=30% Similarity=0.375 Sum_probs=26.7
Q ss_pred CCCHHHHhcCCHHHHHH-cCCch-HHHHHHHHHHH
Q 021493 190 FPSLERLSLVSEVELRN-AGFGY-RAKYITGTVDV 222 (311)
Q Consensus 190 FPtpe~La~~~~e~Lr~-~Glg~-RA~~I~~~A~~ 222 (311)
|=|.+.++.+++++|.. .|++. ++..|+..|+.
T Consensus 14 ~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 14 FTTVEDLAYVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred CCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 44899999999999977 58874 88888877763
No 126
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=34.75 E-value=21 Score=29.11 Aligned_cols=22 Identities=27% Similarity=0.101 Sum_probs=18.7
Q ss_pred HHHHhhcCCccchHHHHHHHHH
Q 021493 245 AIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlLf 266 (311)
+.-.|+.|.|||+.+|..||-.
T Consensus 13 v~~aL~~i~GIG~~~a~~i~~~ 34 (113)
T TIGR03631 13 VEIALTYIYGIGRTRARKILEK 34 (113)
T ss_pred EeeeeeeeecccHHHHHHHHHH
Confidence 4557899999999999988854
No 127
>PRK14976 5'-3' exonuclease; Provisional
Probab=34.64 E-value=23 Score=33.37 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=17.7
Q ss_pred HhhcCCccchHHHHHHHHHhcCCCCc
Q 021493 248 ALCTLPGVGPKVAACIALFSLDQHHA 273 (311)
Q Consensus 248 ~L~~l~GIG~ktAd~vlLf~l~~~d~ 273 (311)
-+-.+||||+|||.-++ -.+|..+.
T Consensus 192 nipGVpGIG~KtA~~LL-~~~gsle~ 216 (281)
T PRK14976 192 NIKGVKGIGPKTAIKLL-NKYGNIEN 216 (281)
T ss_pred CCCCCCcccHHHHHHHH-HHcCCHHH
Confidence 45679999999999775 34454443
No 128
>PF11549 Sec31: Protein transport protein SEC31; InterPro: IPR021614 Sec31 is involved in COPII coat formation as it forms through the sequential binding of three cytoplasmic proteins: Sar1, Sec23/24 and Sec13/31. Sec13/31 is recruited by the pre-budding complex and polymerisation of Sec13/31 occurs to form an octahedral cage that is the outer shell of the COPII coat []. Sec13/31 is a hetero-tetramer which is organised as a linear array of alpha-solenoid and beta-propeller domains to form a rod in which twenty-four copies assemble to form the COPII cub-octahedron []. ; PDB: 2QTV_D.
Probab=33.65 E-value=7.4 Score=26.95 Aligned_cols=28 Identities=36% Similarity=0.750 Sum_probs=5.0
Q ss_pred CCCCCCCCccc-----cccCCCCCcccccCCCC
Q 021493 19 QPPPTPPNPQT-----LTTNKPSKWTPLNLTQS 46 (311)
Q Consensus 19 ~~~~~~~~~~~-----~~~~~~~~w~~l~~~~~ 46 (311)
.|||+++||.. |...-..+|.+|++.-.
T Consensus 2 ~~~p~~~~~~SGQ~PhlNkkaNdGWNDLpl~vk 34 (51)
T PF11549_consen 2 PPPPPPPNVYSGQTPHLNKKANDGWNDLPLKVK 34 (51)
T ss_dssp -----------SSS-TT-HHHHS-TT---S---
T ss_pred CCCCcccccccCcCCcccccccCcccccchhhh
Confidence 45556666532 33334558888887643
No 129
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=33.48 E-value=23 Score=30.35 Aligned_cols=23 Identities=30% Similarity=0.326 Sum_probs=19.1
Q ss_pred HHHHHhhcCCccchHHHHHHHHH
Q 021493 244 EAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 244 e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
.+.-.|+.|.|||+.+|..||--
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~~ 44 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIARK 44 (149)
T ss_pred EEeeeccccccccHHHHHHHHHH
Confidence 35568999999999999998753
No 130
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=33.39 E-value=24 Score=32.38 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=0.0
Q ss_pred HHhhcCCccchHHHHHHHHHhcC
Q 021493 247 DALCTLPGVGPKVAACIALFSLD 269 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf~l~ 269 (311)
+.|..|+|||+++|...+-.|++
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~ 25 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFE 25 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCC
No 131
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=32.99 E-value=52 Score=31.42 Aligned_cols=33 Identities=27% Similarity=0.401 Sum_probs=27.5
Q ss_pred cccCCCHHHHhcCCHHHHHHc-CCc-hHHHHHHHH
Q 021493 187 FHEFPSLERLSLVSEVELRNA-GFG-YRAKYITGT 219 (311)
Q Consensus 187 ~~~FPtpe~La~~~~e~Lr~~-Glg-~RA~~I~~~ 219 (311)
...|-+..+|.+++.++|.+. |.| .||+.|++-
T Consensus 310 V~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~G 344 (349)
T COG1623 310 VRAFGTLDGILEASAEDLDAVEGIGEARARAIKEG 344 (349)
T ss_pred HHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHh
Confidence 457889999999999999886 788 599888753
No 132
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=32.66 E-value=1.1e+02 Score=26.49 Aligned_cols=36 Identities=19% Similarity=0.158 Sum_probs=25.7
Q ss_pred CCcCcccCCCCC-cCceeeC-------CCceEEeeCCeEEEEEE
Q 021493 48 LSLPLTFPTGQT-FRWKKTG-------PLQYTGPIGPHLISLKH 83 (311)
Q Consensus 48 ~~L~~tl~~GQ~-Frw~~~~-------~~~~~gv~~~~~v~l~q 83 (311)
|.|--|+.+||. |..-+.. -|.|.|..+++|+.|..
T Consensus 98 ~rlvGtm~~g~~~~A~i~~~~~v~~V~vG~YlGqN~GrV~rI~d 141 (170)
T COG3168 98 FRLVGTLKSGQGVSALIEAPGGVYRVRVGQYLGQNYGRVVRITD 141 (170)
T ss_pred eeeEEEecCCCceEEEEEcCCceEEEeeccEeeccCceEEEecC
Confidence 555568889887 5555443 35788888899998873
No 133
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=32.61 E-value=72 Score=24.09 Aligned_cols=22 Identities=32% Similarity=0.276 Sum_probs=18.4
Q ss_pred HHHHHHHHhccChhHHHHHHHh
Q 021493 116 LGELWEGFSASDCRFAELAKYL 137 (311)
Q Consensus 116 l~~~~~~l~~~D~~l~~~~~~~ 137 (311)
++++.+++...||.|....+..
T Consensus 11 L~eiEr~L~~~DP~fa~~l~~~ 32 (82)
T PF11239_consen 11 LEEIERQLRADDPRFAARLRSG 32 (82)
T ss_pred HHHHHHHHHhcCcHHHHHhccC
Confidence 5788899999999998877763
No 134
>PRK09482 flap endonuclease-like protein; Provisional
Probab=32.11 E-value=27 Score=32.54 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=16.8
Q ss_pred HhhcCCccchHHHHHHHHHhcCCCC
Q 021493 248 ALCTLPGVGPKVAACIALFSLDQHH 272 (311)
Q Consensus 248 ~L~~l~GIG~ktAd~vlLf~l~~~d 272 (311)
-+-.+||||||||--++- -+|..+
T Consensus 183 nIpGVpGIG~KtA~~LL~-~~gsle 206 (256)
T PRK09482 183 KIPGVAGIGPKSAAELLN-QFRSLE 206 (256)
T ss_pred CCCCCCCcChHHHHHHHH-HhCCHH
Confidence 455789999999987653 444433
No 135
>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=32.08 E-value=14 Score=34.18 Aligned_cols=148 Identities=16% Similarity=0.088 Sum_probs=69.4
Q ss_pred HHHhccChhHHHHHHHhcCCccCCCCHHH--HHHHHHHhccccHHHHHHHHHHHHhh-CCCCccccccccccCCCHHHHh
Q 021493 121 EGFSASDCRFAELAKYLAGARVLRQDPVE--CLLQFLCSSNNNIARITKMVDFLASL-GSHLGNVEGFEFHEFPSLERLS 197 (311)
Q Consensus 121 ~~l~~~D~~l~~~~~~~~GlR~l~~dpfe--~Li~~IlsQq~~i~~a~~~~~~L~~~-G~~~~~~~~~~~~~FPtpe~La 197 (311)
..+.+.||.+..+..-...+ ...+|- +++.++.|=|.+.+. ..-|..+++| ...- .. ..++++.
T Consensus 14 ~~iEe~DpQy~av~~L~~~~---g~~~~~~Lvi~NaLvSYqLs~kG-Ee~W~~Fs~yfs~~~--~~-------~~~~~~~ 80 (246)
T PF09171_consen 14 RYIEERDPQYKAVKNLVESY---GEELFAKLVIANALVSYQLSGKG-EEYWWEFSEYFSKRP--IE-------DICEAFI 80 (246)
T ss_dssp HHHHCCSHHHHHHHHHHCCC----HHHHHHHHHHHHHT-SS-TT-H-HHHHHHHHHHHCTS----S-------SHHHHHH
T ss_pred HHHHHhChHHHHHHHHHHHc---CchHHHHHHHHHHHHHHhcCCch-HHHHHHHHHHHhcCC--ch-------hHHHHHH
Confidence 44555688776665544433 223332 344566666666554 4455555532 2110 00 0122221
Q ss_pred cCCHHHHHH-----cCCchHHHHHHHHHHHHHHhcCCCccchhhhhC--CCHHHHHHHhhcCCccc---------hHHHH
Q 021493 198 LVSEVELRN-----AGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRK--LDLQEAIDALCTLPGVG---------PKVAA 261 (311)
Q Consensus 198 ~~~~e~Lr~-----~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~--~~~~e~~~~L~~l~GIG---------~ktAd 261 (311)
+ =|.. .+...|.++|.++...+.+ +++..... -+.++.++.|..+=|-. -|.+.
T Consensus 81 ~----FL~~s~~n~r~~~~KikRl~k~~~~~~~------l~l~~~~~~y~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~ 150 (246)
T PF09171_consen 81 E----FLSNSKYNRRLLEQKIKRLRKFCPFLEN------LSLQDNPLYYEDLEELWRELAKILNSKPESKTIVFAVKMFG 150 (246)
T ss_dssp H----HCCC-TTS-TTHHHHHHHHHHHCCHHHT------T-HHHHHHHHCTHHHHHHHHHHHHTS-TTSHHHHHHHHHHH
T ss_pred H----HHhhCcchHHHHHHHHHHHHHHHHHHHH------hhhhhhhhhhhhHHHHHHHHHHHhCCCCccchhhHHHHHHH
Confidence 1 1111 1222477777776655433 12232222 45677777777655554 24555
Q ss_pred HHHHHhcCCC------CccccchHHHHHHHHcCCCc
Q 021493 262 CIALFSLDQH------HAIPVDTHVWKIATRYLLPE 291 (311)
Q Consensus 262 ~vlLf~l~~~------d~fPVDt~v~Ri~~r~~~~~ 291 (311)
+.+..++|.. --+|||.|+.++..+.|+.+
T Consensus 151 Ya~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~ 186 (246)
T PF09171_consen 151 YACRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIE 186 (246)
T ss_dssp HHHHHHCTS-----TTS-----HHHHHHHHCTTS-S
T ss_pred HHHHHhcCCCCCCcccCCCCccHHHHHHHHHhcccc
Confidence 6666665541 13578999999999988743
No 136
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.90 E-value=2.3e+02 Score=22.88 Aligned_cols=37 Identities=30% Similarity=0.400 Sum_probs=24.1
Q ss_pred HhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhc---CCHHHH
Q 021493 156 CSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSL---VSEVEL 204 (311)
Q Consensus 156 lsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~---~~~e~L 204 (311)
+.+++....+.++++.+. .+.++ ++.++||+ +++..|
T Consensus 2 ~~~~~~~~~i~~~~~~I~~~~~~~------------~sl~~lA~~~g~S~~~l 42 (127)
T PRK11511 2 SRRNTDAITIHSILDWIEDNLESP------------LSLEKVSERSGYSKWHL 42 (127)
T ss_pred CcccccHHHHHHHHHHHHHhcCCC------------CCHHHHHHHHCcCHHHH
Confidence 567788888888888886 44432 36777764 344444
No 137
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=31.05 E-value=36 Score=26.10 Aligned_cols=21 Identities=29% Similarity=0.322 Sum_probs=15.8
Q ss_pred HHHHhhcCCccchHHHHHHHH
Q 021493 245 AIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 245 ~~~~L~~l~GIG~ktAd~vlL 265 (311)
++=-|..|+|||..+|+.|+-
T Consensus 25 Ir~gl~~Ikglg~~~a~~I~~ 45 (90)
T PF14579_consen 25 IRLGLSAIKGLGEEVAEKIVE 45 (90)
T ss_dssp EE-BGGGSTTS-HHHHHHHHH
T ss_pred EeehHhhcCCCCHHHHHHHHH
Confidence 344588999999999998874
No 138
>smart00475 53EXOc 5'-3' exonuclease.
Probab=31.05 E-value=30 Score=32.20 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=17.1
Q ss_pred HhhcCCccchHHHHHHHHHhcCCCC
Q 021493 248 ALCTLPGVGPKVAACIALFSLDQHH 272 (311)
Q Consensus 248 ~L~~l~GIG~ktAd~vlLf~l~~~d 272 (311)
-+-.+||||+|||.-++- -+|..+
T Consensus 187 nipGV~GIG~KtA~~Ll~-~ygsle 210 (259)
T smart00475 187 NIPGVPGIGEKTAAKLLK-EFGSLE 210 (259)
T ss_pred CCCCCCCCCHHHHHHHHH-HhCCHH
Confidence 466789999999987753 444433
No 139
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=30.53 E-value=31 Score=31.57 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=17.3
Q ss_pred HHhhcCCccchHHHHHHHHHhcCCCC
Q 021493 247 DALCTLPGVGPKVAACIALFSLDQHH 272 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf~l~~~d 272 (311)
+-+-.+||||||+|.-++ --+|..+
T Consensus 183 DnipGv~GiG~ktA~~Ll-~~~gsle 207 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLL-KEYGSLE 207 (240)
T ss_pred cCCCCCCccCHHHHHHHH-HHhCCHH
Confidence 356688999999997654 3445433
No 140
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=29.81 E-value=41 Score=36.58 Aligned_cols=26 Identities=27% Similarity=0.119 Sum_probs=22.7
Q ss_pred CHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 241 DLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 241 ~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
..+++.+.|.+|||||++.|..+|--
T Consensus 751 ~~~~~q~~L~~lPgI~~~~a~~ll~~ 776 (814)
T TIGR00596 751 FNDGPQDFLLKLPGVTKKNYRNLRKK 776 (814)
T ss_pred ccHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 45678899999999999999999864
No 141
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=29.05 E-value=1.1e+02 Score=30.26 Aligned_cols=50 Identities=12% Similarity=0.110 Sum_probs=42.1
Q ss_pred CCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHHHHHHcC
Q 021493 145 QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAG 208 (311)
Q Consensus 145 ~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~G 208 (311)
+=|.+.+++.+.......+.+...+++|. +||.. .+-|.+++.++|+...
T Consensus 296 ~iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~E--------------~~iL~~~~~eel~~~~ 346 (374)
T TIGR00375 296 LIPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGTE--------------IAVLHEAAEEDLARVV 346 (374)
T ss_pred eCCHHHHHhhhcCCCCccHHHHHHHHHHHHHhccH--------------HHHHhcCCHHHHHHHH
Confidence 66889999999998889999999999998 89864 4677888888887654
No 142
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=28.27 E-value=1.4e+02 Score=20.86 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=17.5
Q ss_pred CCCHHHHhcCCHHHHHHcCCc
Q 021493 190 FPSLERLSLVSEVELRNAGFG 210 (311)
Q Consensus 190 FPtpe~La~~~~e~Lr~~Glg 210 (311)
+-..+.|+.+++++|+++|+.
T Consensus 30 i~g~~~L~~l~~~~L~~lGI~ 50 (66)
T PF07647_consen 30 IDGLEDLLQLTEEDLKELGIT 50 (66)
T ss_dssp CSHHHHHTTSCHHHHHHTTTT
T ss_pred CcHHHHHhhCCHHHHHHcCCC
Confidence 334488999999999999995
No 143
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=27.78 E-value=1.2e+02 Score=32.07 Aligned_cols=29 Identities=34% Similarity=0.532 Sum_probs=21.3
Q ss_pred hhhhhCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 021493 234 LLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 234 l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf 266 (311)
++.|...+ .++|.+++|||.++|..|.-|
T Consensus 534 l~~l~~a~----~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 534 LEALLAAS----EEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred HHHHHhcC----HHHHhhccchhHHHHHHHHHH
Confidence 45554444 456778999999999998654
No 144
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=27.65 E-value=96 Score=32.48 Aligned_cols=28 Identities=25% Similarity=0.523 Sum_probs=16.4
Q ss_pred hhhhhCCCHHHHHHHhhcCCccchHHHHHHHH
Q 021493 234 LLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265 (311)
Q Consensus 234 l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlL 265 (311)
++.+.+.+. ++|.+++|||+++|..+.-
T Consensus 566 ~~~i~~As~----eeL~~v~Gig~~~A~~I~~ 593 (598)
T PRK00558 566 LKAIKEASV----EELAKVPGISKKLAEAIYE 593 (598)
T ss_pred HHHHHhCCH----HHHhhcCCcCHHHHHHHHH
Confidence 444444443 3466777777777776654
No 145
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=27.37 E-value=94 Score=30.20 Aligned_cols=62 Identities=21% Similarity=0.260 Sum_probs=45.3
Q ss_pred HHHhhcCCccc--------------hHHHHHHHHHhcCCCCcccc-chHHHHHHHHcCCCcccCCCCCHHHHHHHHHH
Q 021493 246 IDALCTLPGVG--------------PKVAACIALFSLDQHHAIPV-DTHVWKIATRYLLPELAGVRLTPKLCSRVAEA 308 (311)
Q Consensus 246 ~~~L~~l~GIG--------------~ktAd~vlLf~l~~~d~fPV-Dt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~ 308 (311)
-+.|.+..||| ||+-|...-+-|.+.-.+|+ +.|.+..+-++.+.. ....+|..+|.+++..
T Consensus 254 TEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG~-tp~~LT~~d~~eL~~k 330 (439)
T KOG0739|consen 254 TEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGD-TPHVLTEQDFKELARK 330 (439)
T ss_pred HHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceeccCCcHHHhhhhheeccCC-CccccchhhHHHHHhh
Confidence 35788999999 68888777777777667776 677776666654422 3457899999998864
No 146
>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=27.30 E-value=1.2e+02 Score=23.97 Aligned_cols=26 Identities=31% Similarity=0.469 Sum_probs=22.5
Q ss_pred CccchhhhhCCCHHHHHHHhhcCCcc
Q 021493 230 GAEWLLSLRKLDLQEAIDALCTLPGV 255 (311)
Q Consensus 230 g~~~l~~L~~~~~~e~~~~L~~l~GI 255 (311)
|.-++++|...+.++..+.|+.+.|.
T Consensus 32 Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 32 GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 56678889999999999999999873
No 147
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=26.58 E-value=4.7e+02 Score=23.71 Aligned_cols=111 Identities=15% Similarity=0.099 Sum_probs=67.8
Q ss_pred CCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCccccccccccCCCHHHHhcCCHHHHHHcCCchHHHHHHHHHHHH
Q 021493 145 QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRAKYITGTVDVL 223 (311)
Q Consensus 145 ~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~~~~~~~~~~FPtpe~La~~~~e~Lr~~Glg~RA~~I~~~A~~i 223 (311)
.+-.+.+|+.|=--++..+++..+.+.|. .||..+.. +-++|..+ -|+|.|..+++-.- .+
T Consensus 69 ~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~----------~~~eL~~L-------PGVGrKTAnvVL~~-a~ 130 (211)
T COG0177 69 EEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPD----------TREELLSL-------PGVGRKTANVVLSF-AF 130 (211)
T ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCc----------hHHHHHhC-------CCcchHHHHHHHHh-hc
Confidence 44456677766666788888888888888 78875521 23333322 38888865554221 11
Q ss_pred HHhcCCCccc--hhh------h-hCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccc
Q 021493 224 QSKHSGGAEW--LLS------L-RKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIP 275 (311)
Q Consensus 224 ~~~~~gg~~~--l~~------L-~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fP 275 (311)
-. + +=..| ... | ...+++++.++|+++=.=..|.--...|..+||.-+-|
T Consensus 131 g~-p-~i~VDTHV~Rvs~R~gl~~~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~iC~a 189 (211)
T COG0177 131 GI-P-AIAVDTHVHRVSNRLGLVPGKTPEEVEEALMKLIPKELWTDLHHWLILHGRYICKA 189 (211)
T ss_pred CC-C-cccccchHHHHHHHhCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhhhhccC
Confidence 00 0 00000 000 1 14578888899998777888888888888888865544
No 148
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=26.31 E-value=68 Score=25.43 Aligned_cols=23 Identities=22% Similarity=0.251 Sum_probs=18.8
Q ss_pred HHhhcCCccchHHHHHHHHHhcC
Q 021493 247 DALCTLPGVGPKVAACIALFSLD 269 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf~l~ 269 (311)
..-.++||||.+-|..|..|=-.
T Consensus 50 ~Wwr~vpglG~~~A~~I~awLa~ 72 (96)
T PF12482_consen 50 RWWRAVPGLGAAGARRIEAWLAA 72 (96)
T ss_pred hHHHhCcccchHHHHHHHHHHHH
Confidence 46778999999999999876533
No 149
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=26.06 E-value=99 Score=29.60 Aligned_cols=48 Identities=15% Similarity=0.111 Sum_probs=33.5
Q ss_pred HHHcCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 204 LRNAGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 204 Lr~~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
+..++++-|+....+-| |...+..|-+++. ++|++++|+|+|+.+-|.
T Consensus 251 I~~L~LS~R~~n~Lk~~---------~I~ti~dL~~~~~----~~l~~~~n~G~ksl~ei~ 298 (310)
T PRK05182 251 IEELELSVRSYNCLKRA---------GINTIGDLVQRTE----EELLKTRNLGKKSLEEIK 298 (310)
T ss_pred HHHhccchHHHHHHHHc---------CCcCHHHHHhCCH----HHHhcCCCCChhhHHHHH
Confidence 45578888875544332 4446666666654 469999999999988764
No 150
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=25.91 E-value=36 Score=22.73 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=12.9
Q ss_pred ccchHHHHHHHHcCC
Q 021493 275 PVDTHVWKIATRYLL 289 (311)
Q Consensus 275 PVDt~v~Ri~~r~~~ 289 (311)
+-||||.|++..+|.
T Consensus 17 eddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 17 EDDTHVHRVLRKYYT 31 (41)
T ss_pred cchhHHHHHHHHHHH
Confidence 458999999999984
No 151
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=25.32 E-value=49 Score=26.60 Aligned_cols=38 Identities=32% Similarity=0.407 Sum_probs=22.2
Q ss_pred cCCc-hHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHH
Q 021493 207 AGFG-YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVA 260 (311)
Q Consensus 207 ~Glg-~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktA 260 (311)
||+| +||..+++..+.. ||. =+.|++|...-.+|++|-
T Consensus 56 ~GLGPRKA~~Ll~~l~~~-----g~~-----------l~~R~~Lv~~~~~g~~Vf 94 (104)
T PF14635_consen 56 CGLGPRKAQALLKALKQN-----GGR-----------LENRSQLVTKCLMGPKVF 94 (104)
T ss_dssp TT--HHHHHHHHHHHHHC------S---------------TTHHHHTTSS-HHHH
T ss_pred cCCChHHHHHHHHHHHHc-----CCc-----------cccHHHHHhcCCCCCeEE
Confidence 7999 5899988866632 222 235778888788898764
No 152
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=25.01 E-value=50 Score=33.15 Aligned_cols=46 Identities=28% Similarity=0.419 Sum_probs=26.4
Q ss_pred cCCcc-CCCCHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCccccccccccCCCHHHHhc
Q 021493 138 AGARV-LRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSL 198 (311)
Q Consensus 138 ~GlR~-l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~~~G~~~~~~~~~~~~~FPtpe~La~ 198 (311)
.|+.+ |..|-.+|=|.+=+|.-.|+..- .-.+..|.-||=||++..
T Consensus 419 dGc~iYLSk~sL~~eIvtsKSsemNi~vp---------------~~~dgDy~EfpvPEQfkt 465 (480)
T KOG2675|consen 419 DGCHIYLSKDSLDCEIVTSKSSEMNINVP---------------TNEDGDYVEFPVPEQFKT 465 (480)
T ss_pred CCeeEEeccccccceEEeecccceeEecc---------------cCCCCCcccccChHHHhh
Confidence 36665 45666666555555554443221 113456788999999854
No 153
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=24.85 E-value=1.1e+02 Score=29.13 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=33.8
Q ss_pred HHHcCCchHHHHHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 204 LRNAGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 204 Lr~~Glg~RA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
+..++++-||..-.+-| |...+..|-.++. ++|++++|+|+|+.+-|-
T Consensus 237 I~~L~LSvR~~n~Lk~~---------~I~ti~dL~~~~~----~~l~~~~n~G~ksl~ei~ 284 (297)
T TIGR02027 237 IEELDLSVRSYNCLKRA---------GIHTLGELVSKSE----EELLKIKNFGKKSLTEIK 284 (297)
T ss_pred HHHhCccHHHHhHHHHc---------CCcCHHHHHhCCH----HHHhhCCCCChhhHHHHH
Confidence 56688988876544332 4446666666654 469999999999988764
No 154
>KOG1945 consensus Protein phosphatase 1 binding protein spinophilin/neurabin II [Signal transduction mechanisms]
Probab=24.84 E-value=37 Score=33.08 Aligned_cols=13 Identities=62% Similarity=1.180 Sum_probs=8.8
Q ss_pred CCCCCCCCCCCCC
Q 021493 13 RPRLTPQPPPTPP 25 (311)
Q Consensus 13 ~~~~~~~~~~~~~ 25 (311)
-||+.|||||+||
T Consensus 37 ~p~~q~~ppp~~p 49 (377)
T KOG1945|consen 37 SPRLQRQPPPPLP 49 (377)
T ss_pred CcccCCCCCCCCC
Confidence 4678887776654
No 155
>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=23.19 E-value=1.1e+02 Score=32.49 Aligned_cols=28 Identities=29% Similarity=0.326 Sum_probs=19.1
Q ss_pred chhhhhCCCHHHHHHHhhcCCccchHHHHHHH
Q 021493 233 WLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264 (311)
Q Consensus 233 ~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vl 264 (311)
++.+|..+. .+.|.+++|+|.|+|+-++
T Consensus 456 ~~~Dl~~L~----~~~L~~L~GfG~Ksa~nIl 483 (652)
T TIGR00575 456 SVADLYALK----KEDLLELEGFGEKSAQNLL 483 (652)
T ss_pred CHHHHHhcC----HHHHhhccCccHHHHHHHH
Confidence 455555444 3478888999999988663
No 156
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=23.05 E-value=2.3e+02 Score=26.52 Aligned_cols=34 Identities=24% Similarity=0.318 Sum_probs=27.6
Q ss_pred CCCHHHHhcCCHHHHHH-cCCch-HHHHHHHHHHHH
Q 021493 190 FPSLERLSLVSEVELRN-AGFGY-RAKYITGTVDVL 223 (311)
Q Consensus 190 FPtpe~La~~~~e~Lr~-~Glg~-RA~~I~~~A~~i 223 (311)
|-|.++|+.+++++|.. +|++. +|..|.+.|...
T Consensus 20 i~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~ 55 (310)
T TIGR02236 20 YDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKA 55 (310)
T ss_pred CCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHH
Confidence 55899999999999966 69875 788888877643
No 157
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.39 E-value=4.2e+02 Score=28.40 Aligned_cols=33 Identities=27% Similarity=0.252 Sum_probs=26.1
Q ss_pred ccccCCCHHHHhcCCHHHHHHc-CCch-HHHHHHH
Q 021493 186 EFHEFPSLERLSLVSEVELRNA-GFGY-RAKYITG 218 (311)
Q Consensus 186 ~~~~FPtpe~La~~~~e~Lr~~-Glg~-RA~~I~~ 218 (311)
....|.+.++|.+++.++|..+ |+|. .|..|.+
T Consensus 544 L~~~F~si~~L~~As~eeL~~i~GIG~k~A~sI~~ 578 (689)
T PRK14351 544 LAREFGTFEAIMDADEEALRAVDDVGPTVAEEIRE 578 (689)
T ss_pred HHHHhCCHHHHHhCCHHHHhccCCcCHHHHHHHHH
Confidence 3457889999999999999886 8886 6666654
No 158
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=22.31 E-value=3.1e+02 Score=19.79 Aligned_cols=28 Identities=25% Similarity=0.342 Sum_probs=22.6
Q ss_pred CCHHHHHHcCCc-hHHHHHHHHHHHHHHh
Q 021493 199 VSEVELRNAGFG-YRAKYITGTVDVLQSK 226 (311)
Q Consensus 199 ~~~e~Lr~~Glg-~RA~~I~~~A~~i~~~ 226 (311)
++-++|-++||+ +-|+.|++-|+.+.=+
T Consensus 4 v~k~dLi~lGf~~~tA~~IIrqAK~~lV~ 32 (59)
T PF11372_consen 4 VTKKDLIELGFSESTARDIIRQAKALLVQ 32 (59)
T ss_pred cCHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 456788889998 6999999999887543
No 159
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=22.09 E-value=4.4e+02 Score=24.57 Aligned_cols=55 Identities=5% Similarity=0.216 Sum_probs=30.5
Q ss_pred hCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHH
Q 021493 238 RKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEA 308 (311)
Q Consensus 238 ~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~~~~~~t~k~y~~i~~~ 308 (311)
...-.+.|.+.|.. . +..+.+.-.-.|++. =.|..|..++++ ..||.+|++..+.
T Consensus 241 ~~~Rl~~A~~lL~~-~--~~si~eIA~~~Gf~~------~s~F~r~Fk~~~-------G~tP~~yr~~~~~ 295 (302)
T PRK10371 241 TAMRINHVRALLSD-T--DKSILDIALTAGFRS------SSRFYSTFGKYV-------GMSPQQYRKLSQQ 295 (302)
T ss_pred HHHHHHHHHHHHhc-C--CCCHHHHHHHcCCCC------HHHHHHHHHHHH-------CcCHHHHHHHhhc
Confidence 33444556666554 1 223333333333333 247778888876 3788899876553
No 160
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=22.05 E-value=63 Score=21.02 Aligned_cols=19 Identities=21% Similarity=0.371 Sum_probs=16.9
Q ss_pred CHHHHhcCCHHHHHHcCCc
Q 021493 192 SLERLSLVSEVELRNAGFG 210 (311)
Q Consensus 192 tpe~La~~~~e~Lr~~Glg 210 (311)
+-.+|+.+++.+|+.+|+.
T Consensus 16 tr~~L~~Lsd~~L~DIGl~ 34 (40)
T PF06568_consen 16 TRRELAELSDRQLADIGLT 34 (40)
T ss_pred HHHHHccCCHHHHHHcCCC
Confidence 5678999999999999985
No 161
>PRK00254 ski2-like helicase; Provisional
Probab=21.75 E-value=1.2e+02 Score=32.13 Aligned_cols=20 Identities=25% Similarity=0.416 Sum_probs=14.1
Q ss_pred HHhhcCCccchHHHHHHHHH
Q 021493 247 DALCTLPGVGPKVAACIALF 266 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~vlLf 266 (311)
++|.+++|||+++|.-|.-+
T Consensus 678 ~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 678 SELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred HHHhcCCCCCHHHHHHHHHH
Confidence 45677778888888777554
No 162
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=21.57 E-value=1.4e+02 Score=29.06 Aligned_cols=37 Identities=11% Similarity=0.254 Sum_probs=31.6
Q ss_pred CCCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCC
Q 021493 143 LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHL 179 (311)
Q Consensus 143 l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~ 179 (311)
+++=|...+++--+.-.+..+.+.++|++|. +||..+
T Consensus 301 lhliPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGtEi 338 (403)
T COG1379 301 LHLIPLAEIISMALGKGITTKAVKRTWERLVRAFGTEI 338 (403)
T ss_pred eecccHHHHHHHHhccceechhHHHHHHHHHHHhcchh
Confidence 3567888888888888899999999999998 899754
No 163
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=21.48 E-value=43 Score=28.11 Aligned_cols=17 Identities=35% Similarity=0.827 Sum_probs=14.9
Q ss_pred HHhhcCCccchHHHHHH
Q 021493 247 DALCTLPGVGPKVAACI 263 (311)
Q Consensus 247 ~~L~~l~GIG~ktAd~v 263 (311)
+.|+.|.||||+.+...
T Consensus 67 DDLt~I~GIGPk~e~~L 83 (133)
T COG3743 67 DDLTRISGIGPKLEKVL 83 (133)
T ss_pred ccchhhcccCHHHHHHH
Confidence 78999999999998753
No 164
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=21.36 E-value=44 Score=31.67 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=14.5
Q ss_pred hhcCCccchHHHHHHHHHhcC
Q 021493 249 LCTLPGVGPKVAACIALFSLD 269 (311)
Q Consensus 249 L~~l~GIG~ktAd~vlLf~l~ 269 (311)
+-.++|||+|||--++ ..+|
T Consensus 200 ipGV~GIG~ktA~~Ll-~~~g 219 (310)
T COG0258 200 IPGVKGIGPKTALKLL-QEYG 219 (310)
T ss_pred CCCCCCcCHHHHHHHH-HHhC
Confidence 3449999999998764 3444
No 165
>PRK14973 DNA topoisomerase I; Provisional
Probab=21.29 E-value=3.2e+02 Score=30.34 Aligned_cols=109 Identities=17% Similarity=0.152 Sum_probs=63.5
Q ss_pred CHHHHhcCCHHHHHHcCCc-hHHHHHHHHHHHHHHh-----c-----------CCCccchhhhhCCCHHHHHHHhhcCCc
Q 021493 192 SLERLSLVSEVELRNAGFG-YRAKYITGTVDVLQSK-----H-----------SGGAEWLLSLRKLDLQEAIDALCTLPG 254 (311)
Q Consensus 192 tpe~La~~~~e~Lr~~Glg-~RA~~I~~~A~~i~~~-----~-----------~gg~~~l~~L~~~~~~e~~~~L~~l~G 254 (311)
+.++|+.+++..|+..|++ -|++.+..-|+.+... . .+|--+++++... .-++|..++|
T Consensus 767 ~~~~~~~~~~~~~~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a----~p~~La~~~g 842 (936)
T PRK14973 767 DIAALARADPADLKKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSV----HPAYLALKTG 842 (936)
T ss_pred hHHHHhhCCHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhc----CHHHHhcCCC
Confidence 7889999999999999998 5888888888543321 0 1122222222222 2458999999
Q ss_pred cchHHHHHHHHHhcCCCCccccchHHHHHHHHcCCCcc-cCCCCCHHHHHHH
Q 021493 255 VGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPEL-AGVRLTPKLCSRV 305 (311)
Q Consensus 255 IG~ktAd~vlLf~l~~~d~fPVDt~v~Ri~~r~~~~~~-~~~~~t~k~y~~i 305 (311)
|.+-|+.-....+..+ -+.|..+-+.+....-+-.+. .-+.+.++..+.+
T Consensus 843 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 843 ISPETICRHAKLVCEK-LGRPVPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred CChhhHHHHHHHHHHH-hcCCCchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 9988887664444312 245665555443333332211 1234555555444
No 166
>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]
Probab=21.11 E-value=3.5e+02 Score=28.56 Aligned_cols=125 Identities=16% Similarity=0.205 Sum_probs=79.7
Q ss_pred CCccCCCCHHHHHHHHHHhccccHHHHHHHHHHHH-hhCCCCc-cccccccccCCCHHHHhcCCHHHHHHc--CCchHHH
Q 021493 139 GARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLG-NVEGFEFHEFPSLERLSLVSEVELRNA--GFGYRAK 214 (311)
Q Consensus 139 GlR~l~~dpfe~Li~~IlsQq~~i~~a~~~~~~L~-~~G~~~~-~~~~~~~~~FPtpe~La~~~~e~Lr~~--Glg~RA~ 214 (311)
|+-+..|..=+.++.++++...+...++.++.-|. .+|+.+. +..+..--.-|-.+.+...++..|-.+ ++.|--+
T Consensus 88 Gid~~~~~aR~v~l~c~iGta~ha~haRHLv~hlie~~Ged~pidlG~e~~v~aPi~~t~~G~kPktlgdle~~l~y~Ee 167 (772)
T COG1152 88 GIDMAGQTAREVFLACCIGTACHAAHARHLVDHLIETFGEDLPIDLGSEVNVEAPIIETVTGIKPKTLGDLEAALEYAEE 167 (772)
T ss_pred ccchhhhhhheehhhhhhhhhhhhhhHHHHHHHHHHHhCccCccCCCcccccccchhhhhhCCCccchHHHHHHHHHHHH
Confidence 45556688888999999999999999999999998 8998442 111111223466777777776666543 5667666
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhCCCHHHHHHHhhcCCccchHHHHHHHHHhcCCC
Q 021493 215 YITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQH 271 (311)
Q Consensus 215 ~I~~~A~~i~~~~~gg~~~l~~L~~~~~~e~~~~L~~l~GIG~ktAd~vlLf~l~~~ 271 (311)
-|..+...++....|..+| ++.--=..-.+--+|.-+||..-+-+++.+
T Consensus 168 qlt~~ls~~h~gqE~~~~d--------yeSkAlhaG~~d~l~~EiaDiaqi~a~~~p 216 (772)
T COG1152 168 QLTQLLSAVHTGQEGSLLD--------YESKALHAGMIDHLGMEIADIAQIVAYDFP 216 (772)
T ss_pred HHHHHHHHHhccCcccccc--------hhHHHhhhhhhhHHHHHHHHHHHHHhhcCC
Confidence 6666666666533332222 322222233455578888887776666643
Done!