Query 020295
Match_columns 328
No_of_seqs 259 out of 1792
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 08:36:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020295.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020295hhsearch_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 3.7E-66 8E-71 477.0 21.8 275 33-327 3-282 (323)
2 TIGR00588 ogg 8-oxoguanine DNA 100.0 1.5E-58 3.2E-63 443.8 28.7 274 35-327 2-286 (310)
3 PRK10308 3-methyl-adenine DNA 100.0 1.8E-35 3.8E-40 280.9 26.1 220 67-327 32-261 (283)
4 COG0122 AlkA 3-methyladenine D 100.0 1.1E-35 2.5E-40 282.2 19.9 196 98-327 61-259 (285)
5 COG0177 Nth Predicted EndoIII- 100.0 8.1E-31 1.7E-35 237.8 13.7 143 128-308 8-152 (211)
6 PRK10702 endonuclease III; Pro 100.0 1.2E-30 2.7E-35 238.1 15.0 142 129-308 9-152 (211)
7 TIGR01083 nth endonuclease III 100.0 6.6E-30 1.4E-34 229.8 15.3 143 128-308 5-149 (191)
8 PRK13913 3-methyladenine DNA g 100.0 2E-29 4.4E-34 230.7 16.4 151 142-327 25-175 (218)
9 cd00056 ENDO3c endonuclease II 99.9 8.4E-27 1.8E-31 202.3 14.3 141 148-327 1-142 (158)
10 PF07934 OGG_N: 8-oxoguanine D 99.9 3E-27 6.4E-32 196.6 9.5 111 40-151 1-117 (117)
11 PRK01229 N-glycosylase/DNA lya 99.9 4.8E-26 1E-30 207.0 15.3 159 129-328 17-182 (208)
12 TIGR01084 mutY A/G-specific ad 99.9 1.4E-25 3.1E-30 212.2 14.8 125 144-307 23-147 (275)
13 KOG1918 3-methyladenine DNA gl 99.9 4.8E-25 1E-29 198.4 13.0 176 121-327 48-226 (254)
14 PRK10880 adenine DNA glycosyla 99.9 1E-24 2.2E-29 212.4 14.8 125 144-307 27-151 (350)
15 smart00478 ENDO3c endonuclease 99.9 6.4E-24 1.4E-28 182.7 14.1 130 156-326 1-130 (149)
16 KOG1921 Endonuclease III [Repl 99.9 1.3E-22 2.9E-27 185.3 15.0 131 145-311 76-206 (286)
17 COG2231 Uncharacterized protei 99.9 2.3E-21 5.1E-26 173.6 16.8 146 142-327 25-170 (215)
18 PRK13910 DNA glycosylase MutY; 99.9 3.4E-21 7.3E-26 183.4 13.0 111 156-305 1-112 (289)
19 TIGR03252 uncharacterized HhH- 99.8 2.1E-20 4.5E-25 165.5 13.4 129 144-303 15-151 (177)
20 COG1194 MutY A/G-specific DNA 99.7 1.4E-17 2.9E-22 160.4 10.1 141 145-326 32-175 (342)
21 PF00730 HhH-GPD: HhH-GPD supe 99.7 7.4E-16 1.6E-20 125.5 12.0 103 152-326 1-106 (108)
22 COG1059 Thermostable 8-oxoguan 99.5 6.7E-14 1.5E-18 124.1 10.3 144 144-328 36-184 (210)
23 KOG2457 A/G-specific adenine D 99.0 1E-09 2.2E-14 106.7 9.2 119 145-304 123-245 (555)
24 PF00633 HHH: Helix-hairpin-he 97.9 1.4E-05 2.9E-10 51.2 2.8 24 260-283 7-30 (30)
25 PF06029 AlkA_N: AlkA N-termin 96.8 0.0026 5.7E-08 53.1 5.4 75 67-144 32-113 (116)
26 TIGR02757 conserved hypothetic 95.6 0.64 1.4E-05 43.4 15.1 37 290-328 173-209 (229)
27 smart00278 HhH1 Helix-hairpin- 95.2 0.012 2.6E-07 36.0 1.6 20 265-284 2-21 (26)
28 PF09674 DUF2400: Protein of u 95.1 1.6 3.4E-05 40.9 16.3 37 290-328 176-212 (232)
29 PF12826 HHH_2: Helix-hairpin- 94.8 0.061 1.3E-06 40.0 4.8 41 235-283 14-54 (64)
30 TIGR00624 tag DNA-3-methyladen 92.7 3.7 8E-05 36.9 13.2 135 125-286 7-167 (179)
31 PRK10353 3-methyl-adenine DNA 92.3 3.8 8.2E-05 37.1 12.7 139 124-286 7-170 (187)
32 COG0632 RuvA Holliday junction 90.7 0.19 4E-06 46.0 2.7 40 250-289 94-133 (201)
33 PRK14601 ruvA Holliday junctio 90.7 0.18 4E-06 45.4 2.5 28 260-287 104-131 (183)
34 PRK13901 ruvA Holliday junctio 90.6 0.19 4E-06 45.9 2.6 28 260-287 103-130 (196)
35 PRK14606 ruvA Holliday junctio 90.1 0.22 4.7E-06 45.1 2.6 28 260-287 104-131 (188)
36 PF14520 HHH_5: Helix-hairpin- 89.6 0.58 1.3E-05 34.0 4.0 32 247-282 25-56 (60)
37 PRK14603 ruvA Holliday junctio 89.6 0.26 5.5E-06 44.9 2.6 23 260-282 103-125 (197)
38 PF03352 Adenine_glyco: Methyl 89.1 2.7 5.8E-05 37.8 8.7 139 125-287 3-166 (179)
39 PRK14602 ruvA Holliday junctio 88.8 0.29 6.2E-06 44.8 2.4 23 261-283 106-128 (203)
40 PRK14604 ruvA Holliday junctio 88.8 0.31 6.7E-06 44.3 2.6 28 260-287 104-131 (195)
41 smart00483 POLXc DNA polymeras 88.2 0.75 1.6E-05 45.1 5.0 39 247-287 71-110 (334)
42 PRK00076 recR recombination pr 88.2 0.42 9.2E-06 43.6 3.0 31 258-288 5-35 (196)
43 TIGR00615 recR recombination p 87.8 0.47 1E-05 43.2 3.0 30 259-288 6-35 (195)
44 PRK13844 recombination protein 87.6 0.48 1E-05 43.3 3.0 31 258-288 9-39 (200)
45 COG0353 RecR Recombinational D 87.3 0.5 1.1E-05 43.0 2.9 30 258-287 6-35 (198)
46 PRK00024 hypothetical protein; 87.1 1.7 3.6E-05 40.3 6.4 43 230-280 40-82 (224)
47 TIGR00084 ruvA Holliday juncti 87.1 0.44 9.6E-06 43.1 2.4 21 263-283 106-126 (191)
48 PF14716 HHH_8: Helix-hairpin- 86.9 1.5 3.3E-05 32.7 4.9 41 229-281 24-64 (68)
49 PRK14605 ruvA Holliday junctio 86.3 0.46 1E-05 43.1 2.1 21 262-282 106-126 (194)
50 PRK14600 ruvA Holliday junctio 86.0 0.46 1E-05 42.9 1.9 21 262-283 106-126 (186)
51 PRK07956 ligA NAD-dependent DN 85.4 1.5 3.2E-05 47.0 5.7 83 191-283 468-562 (665)
52 PF11731 Cdd1: Pathogenicity l 85.2 1.1 2.3E-05 36.2 3.5 28 260-287 8-35 (93)
53 PF14520 HHH_5: Helix-hairpin- 85.1 0.96 2.1E-05 32.8 2.9 25 262-286 3-27 (60)
54 TIGR00608 radc DNA repair prot 85.0 1.2 2.6E-05 41.2 4.2 49 232-287 33-84 (218)
55 PF02371 Transposase_20: Trans 82.9 1 2.3E-05 35.2 2.5 37 264-301 2-38 (87)
56 PRK00116 ruvA Holliday junctio 82.5 1.4 3.1E-05 39.7 3.6 22 262-283 106-127 (192)
57 cd00141 NT_POLXc Nucleotidyltr 82.0 2.7 5.9E-05 40.6 5.5 36 249-287 71-106 (307)
58 TIGR00575 dnlj DNA ligase, NAD 81.9 4.6 0.0001 43.2 7.6 83 191-283 455-549 (652)
59 PF10391 DNA_pol_lambd_f: Fing 79.9 1.7 3.7E-05 31.2 2.5 24 263-286 1-24 (52)
60 PF11798 IMS_HHH: IMS family H 78.7 1.4 3E-05 28.3 1.6 15 266-280 13-27 (32)
61 KOG2841 Structure-specific end 78.4 1.6 3.4E-05 40.9 2.5 37 187-239 212-249 (254)
62 TIGR00084 ruvA Holliday juncti 77.5 2 4.3E-05 38.9 2.8 24 258-281 66-89 (191)
63 PRK14350 ligA NAD-dependent DN 77.5 3.5 7.5E-05 44.3 5.0 22 262-283 539-560 (669)
64 PRK14605 ruvA Holliday junctio 77.3 2 4.4E-05 39.0 2.8 28 258-286 67-94 (194)
65 PRK14973 DNA topoisomerase I; 76.3 14 0.00031 41.2 9.5 96 189-306 822-918 (936)
66 PF12836 HHH_3: Helix-hairpin- 76.3 5 0.00011 29.6 4.2 51 197-280 9-60 (65)
67 PRK00116 ruvA Holliday junctio 75.9 2.3 5.1E-05 38.3 2.8 23 260-282 69-91 (192)
68 PF09171 DUF1886: Domain of un 75.6 1.1 2.5E-05 42.1 0.7 78 225-308 92-186 (246)
69 COG2003 RadC DNA repair protei 75.1 5.9 0.00013 36.9 5.2 40 230-277 40-79 (224)
70 PRK02515 psbU photosystem II c 74.3 3.9 8.5E-05 35.0 3.6 50 196-282 55-105 (132)
71 TIGR01259 comE comEA protein. 74.0 6.1 0.00013 33.0 4.6 58 193-283 59-117 (120)
72 PRK14351 ligA NAD-dependent DN 73.8 11 0.00025 40.6 7.8 81 191-283 485-579 (689)
73 PF12836 HHH_3: Helix-hairpin- 73.0 3.6 7.9E-05 30.4 2.8 22 262-283 12-33 (65)
74 PRK08609 hypothetical protein; 72.9 5.7 0.00012 41.8 5.2 32 249-281 74-105 (570)
75 COG2818 Tag 3-methyladenine DN 72.8 19 0.00041 32.7 7.7 79 137-242 21-105 (188)
76 COG1948 MUS81 ERCC4-type nucle 72.6 47 0.001 31.6 10.7 133 148-295 75-213 (254)
77 TIGR01259 comE comEA protein. 70.1 4.2 9.1E-05 34.0 2.8 22 262-283 66-87 (120)
78 PF00416 Ribosomal_S13: Riboso 70.1 17 0.00037 29.6 6.4 26 261-287 12-37 (107)
79 COG1555 ComEA DNA uptake prote 69.0 3.9 8.5E-05 35.6 2.5 23 263-285 96-118 (149)
80 smart00279 HhH2 Helix-hairpin- 67.5 4.1 8.9E-05 26.9 1.8 16 266-281 18-33 (36)
81 PRK02515 psbU photosystem II c 66.4 4.7 0.0001 34.5 2.4 20 263-282 60-79 (132)
82 PRK13901 ruvA Holliday junctio 66.3 5.2 0.00011 36.5 2.8 25 258-282 66-90 (196)
83 PRK14601 ruvA Holliday junctio 65.8 5.3 0.00012 36.0 2.8 25 258-282 67-91 (183)
84 PRK14600 ruvA Holliday junctio 65.3 5.5 0.00012 36.0 2.7 24 259-282 68-91 (186)
85 PRK14606 ruvA Holliday junctio 63.6 6.2 0.00013 35.7 2.8 25 258-282 67-91 (188)
86 PRK08097 ligB NAD-dependent DN 62.8 25 0.00055 37.1 7.4 29 251-283 511-539 (562)
87 PTZ00134 40S ribosomal protein 62.8 14 0.0003 32.5 4.7 26 260-286 26-51 (154)
88 PRK14603 ruvA Holliday junctio 62.6 6.6 0.00014 35.7 2.8 25 258-282 66-90 (197)
89 PRK14604 ruvA Holliday junctio 62.2 6.7 0.00014 35.7 2.7 25 258-282 67-91 (195)
90 PRK14602 ruvA Holliday junctio 61.3 7.2 0.00016 35.6 2.8 25 258-282 68-92 (203)
91 COG1415 Uncharacterized conser 59.8 17 0.00036 36.1 5.1 25 260-284 274-298 (373)
92 PRK04053 rps13p 30S ribosomal 59.6 16 0.00035 31.9 4.5 25 261-286 22-46 (149)
93 cd00080 HhH2_motif Helix-hairp 58.9 5.4 0.00012 30.5 1.3 22 265-287 23-44 (75)
94 PRK13482 DNA integrity scannin 58.7 16 0.00034 36.4 4.8 38 235-280 298-335 (352)
95 TIGR03629 arch_S13P archaeal r 57.1 16 0.00034 31.7 4.0 25 261-286 18-42 (144)
96 COG1796 POL4 DNA polymerase IV 57.0 18 0.00038 35.5 4.7 42 230-283 29-72 (326)
97 PF03118 RNA_pol_A_CTD: Bacter 56.8 19 0.00041 26.9 3.9 31 247-281 31-61 (66)
98 smart00483 POLXc DNA polymeras 54.3 18 0.0004 35.4 4.5 42 229-283 26-67 (334)
99 COG1555 ComEA DNA uptake prote 53.9 18 0.00039 31.4 3.9 51 198-281 93-144 (149)
100 PRK07758 hypothetical protein; 53.2 24 0.00052 28.6 4.2 31 247-281 54-84 (95)
101 TIGR00426 competence protein C 52.3 15 0.00032 27.2 2.7 21 263-283 15-36 (69)
102 cd00141 NT_POLXc Nucleotidyltr 51.8 19 0.0004 34.9 4.0 41 230-283 24-64 (307)
103 TIGR00426 competence protein C 50.6 16 0.00034 27.1 2.6 22 262-283 45-66 (69)
104 COG0632 RuvA Holliday junction 49.7 14 0.0003 33.9 2.6 25 258-282 67-91 (201)
105 TIGR01448 recD_rel helicase, p 49.6 24 0.00053 38.2 4.9 29 258-287 76-106 (720)
106 KOG2534 DNA polymerase IV (fam 48.8 32 0.0007 33.8 5.0 74 250-325 83-160 (353)
107 PRK07945 hypothetical protein; 46.5 26 0.00056 34.3 4.2 43 230-283 24-68 (335)
108 CHL00137 rps13 ribosomal prote 44.9 12 0.00025 31.7 1.3 26 261-287 14-39 (122)
109 PF01367 5_3_exonuc: 5'-3' exo 44.1 5 0.00011 32.7 -1.0 25 266-291 20-44 (101)
110 COG1948 MUS81 ERCC4-type nucle 40.8 36 0.00078 32.4 4.0 40 236-283 194-233 (254)
111 PLN03132 NADH dehydrogenase (u 40.2 16 0.00034 37.7 1.6 18 15-32 13-30 (461)
112 PF13592 HTH_33: Winged helix- 39.5 20 0.00044 25.9 1.7 54 274-327 4-57 (60)
113 PRK14973 DNA topoisomerase I; 39.3 76 0.0016 35.7 6.8 71 192-282 767-853 (936)
114 PF05559 DUF763: Protein of un 38.3 36 0.00078 33.4 3.6 25 260-284 265-289 (319)
115 COG0099 RpsM Ribosomal protein 38.2 20 0.00044 30.2 1.7 21 262-282 15-35 (121)
116 PF09597 IGR: IGR protein moti 38.0 37 0.0008 24.9 2.8 37 189-241 18-55 (57)
117 PRK05179 rpsM 30S ribosomal pr 37.9 19 0.00041 30.4 1.5 26 261-287 14-39 (122)
118 PF14635 HHH_7: Helix-hairpin- 37.9 16 0.00035 30.0 1.0 39 207-277 56-94 (104)
119 PF09862 DUF2089: Protein of u 37.8 30 0.00064 28.9 2.6 49 206-266 58-112 (113)
120 PRK13482 DNA integrity scannin 36.3 72 0.0016 31.8 5.4 40 187-242 304-344 (352)
121 PRK08609 hypothetical protein; 35.3 51 0.0011 34.8 4.5 41 230-283 27-67 (570)
122 TIGR03631 bact_S13 30S ribosom 35.1 20 0.00044 29.7 1.2 26 261-287 12-37 (113)
123 COG4277 Predicted DNA-binding 35.0 27 0.0006 34.2 2.2 21 262-282 328-348 (404)
124 PRK12766 50S ribosomal protein 34.2 25 0.00054 33.0 1.7 23 265-287 4-26 (232)
125 KOG2534 DNA polymerase IV (fam 32.1 30 0.00065 34.0 2.0 22 262-283 54-75 (353)
126 PRK14976 5'-3' exonuclease; Pr 31.9 28 0.00061 33.3 1.8 25 265-290 192-216 (281)
127 COG1379 PHP family phosphoeste 29.6 1.3E+02 0.0029 29.8 5.9 49 143-205 301-350 (403)
128 smart00475 53EXOc 5'-3' exonuc 29.1 35 0.00075 32.3 1.9 22 265-287 187-208 (259)
129 PRK09482 flap endonuclease-lik 28.9 34 0.00073 32.5 1.7 22 265-287 183-204 (256)
130 cd00008 53EXOc 5'-3' exonuclea 28.5 36 0.00078 31.6 1.8 22 265-287 184-205 (240)
131 PRK00558 uvrC excinuclease ABC 28.2 91 0.002 33.2 5.0 24 262-285 541-564 (598)
132 PRK00024 hypothetical protein; 28.1 1.4E+02 0.003 27.6 5.6 22 190-211 54-76 (224)
133 PF14579 HHH_6: Helix-hairpin- 28.0 45 0.00097 26.1 2.1 21 262-282 25-45 (90)
134 KOG0739 AAA+-type ATPase [Post 26.5 94 0.002 30.8 4.3 62 263-325 254-330 (439)
135 TIGR00596 rad1 DNA repair prot 26.5 52 0.0011 36.4 2.9 28 258-286 751-778 (814)
136 COG1152 CdhA CO dehydrogenase/ 26.0 1.4E+02 0.0031 31.9 5.7 127 139-290 88-218 (772)
137 COG0272 Lig NAD-dependent DNA 25.4 1.2E+02 0.0026 32.7 5.2 29 251-283 534-562 (667)
138 PF11239 DUF3040: Protein of u 25.1 1.2E+02 0.0025 23.4 3.9 22 116-137 11-32 (82)
139 PHA00368 internal virion prote 24.9 8.3E+02 0.018 28.2 11.4 100 46-155 770-872 (1315)
140 PRK13280 N-glycosylase/DNA lya 23.7 3.5E+02 0.0076 26.0 7.5 79 225-309 102-197 (269)
141 PF14475 Mso1_Sec1_bdg: Sec1-b 22.9 44 0.00096 22.9 1.0 15 292-306 17-31 (41)
142 COG3017 LolB Outer membrane li 22.4 3.3E+02 0.0071 25.2 6.8 62 60-124 71-138 (206)
143 PRK12766 50S ribosomal protein 22.0 1.6E+02 0.0035 27.7 4.8 35 250-289 26-60 (232)
144 TIGR00375 conserved hypothetic 21.9 1.1E+02 0.0025 30.6 4.0 50 144-207 295-345 (374)
145 COG3743 Uncharacterized conser 21.7 43 0.00093 28.7 0.9 18 264-281 67-84 (133)
146 TIGR00608 radc DNA repair prot 21.7 2.4E+02 0.0052 26.0 5.9 21 191-211 49-70 (218)
147 PF14490 HHH_4: Helix-hairpin- 21.6 1.6E+02 0.0036 23.0 4.2 21 265-286 46-67 (94)
148 PF12482 DUF3701: Phage integr 21.4 97 0.0021 25.1 2.9 21 264-284 50-70 (96)
149 PF09999 DUF2240: Uncharacteri 20.7 2.5E+02 0.0054 24.4 5.4 36 144-179 83-120 (144)
150 PRK14036 citrate synthase; Pro 20.5 8.6E+02 0.019 24.3 11.1 17 228-244 267-283 (377)
151 PRK14670 uvrC excinuclease ABC 20.4 1.4E+02 0.0031 31.7 4.6 19 263-281 513-531 (574)
No 1
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=100.00 E-value=3.7e-66 Score=477.00 Aligned_cols=275 Identities=45% Similarity=0.872 Sum_probs=255.1
Q ss_pred CCCCCcccccCCCCCCCcCcccCCCCcccceecCCceEEEeECCeEEEEEEecCCcEEEEEcCCC--ChHHHHHHHHHhh
Q 020295 33 NKPSKWTPLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHTSP--SEPAAKSALLDFL 110 (328)
Q Consensus 33 ~~~~~w~~l~~~~~~~~L~~tl~~GQ~Frw~~~~~~~~~g~~g~~~i~l~q~~~~~l~~~~~~~~--~~~~~~~~l~~~f 110 (328)
+++..|.+|+++.+|++|+.||++||+|||++.+...|+|++|+.+|.++|+++.-+.|++.++. ..++..+.+++||
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 45667999999999999999999999999999999999999999999999987664667777652 2345556899999
Q ss_pred cCCCCHHHHHHHHhccChhHHHHHHHhcCCccCCCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCccccccccc
Q 020295 111 NMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHE 189 (328)
Q Consensus 111 ~Ld~dl~~~~~~~~~~D~~l~~l~~~~~G~R~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~ 189 (328)
+||++|..+|++|...|+.|.+++. .|+|+++|||||||++||||+||||++|++|+++|| .||.++.+++|..||.
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 799999999999999999999999999999999999 8999999999999999
Q ss_pred CCCHHHHh-cCCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhc
Q 020295 190 FPSLERLS-LVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCT 268 (328)
Q Consensus 190 fPtpe~La-~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~ 268 (328)
|||.++|+ ...+++||.+||||| |+||.++|+++.++.+ |..||..|+++++++++++|+.
T Consensus 161 FPsl~~L~g~~~Ea~LR~~gfGYR-----------------AkYI~~ta~~l~~~~g-~~~wLqsl~~~~yeear~~L~~ 222 (323)
T KOG2875|consen 161 FPSLQALAGPEVEAELRKLGFGYR-----------------AKYISATARALQEKQG-GLAWLQSLRKSSYEEAREALCS 222 (323)
T ss_pred CccHHHhcCcHhHHHHHHcCcchh-----------------HHHHHHHHHHHHHhcc-cchHHHHHhcccHHHHHHHHhc
Confidence 99999999 456899999999999 9999999999999865 5789999999999999999999
Q ss_pred CCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHcCCCcccCCC-CCHHHHHHHHHHhh
Q 020295 269 LPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVR-LTPKLCSRVAEAFC 327 (328)
Q Consensus 269 l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~~~~~~~~~-lt~k~y~~i~e~~~ 327 (328)
+||||+||||||||++|+.+.++|||+||+|+++.+++++..+++ +|++.|.+++++|+
T Consensus 223 lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~ 282 (323)
T KOG2875|consen 223 LPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFR 282 (323)
T ss_pred CCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcccCCCccccccCCcchhHHHHHHHH
Confidence 999999999999999999999999999999999988788877766 99999999998886
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=1.5e-58 Score=443.82 Aligned_cols=274 Identities=38% Similarity=0.726 Sum_probs=241.3
Q ss_pred CCCcccccCCCCCCCcCcccCCCCcccce-ecCCceEEE--eECCe-EEEEEEecCCcEEEEEcC-C-CChHHHHHHHHH
Q 020295 35 PSKWTPLNLTQSELSLPLTFPTGQTFRWK-KTGPLQYTG--PIGPH-LISLKHLQNGDVCYHIHT-S-PSEPAAKSALLD 108 (328)
Q Consensus 35 ~~~w~~l~~~~~~~~L~~tl~~GQ~Frw~-~~~~~~~~g--~~g~~-~i~l~q~~~~~l~~~~~~-~-~~~~~~~~~l~~ 108 (328)
.++|.+|.++.++|||+.||.|||||||+ +.+++.|.+ +++++ ++.++|.++. +.+.++. . ...+.+.+.+++
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 36899999999999999999999999998 788889999 77877 8888987543 3333332 2 234567889999
Q ss_pred hhcCCCCHHHHHHHHhccChhHHHHHHHhcCCccCCCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCccccccc
Q 020295 109 FLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEF 187 (328)
Q Consensus 109 ~f~Ld~dl~~~~~~~~~~D~~l~~l~~~~~G~R~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~ 187 (328)
||+||.|++.+++.|...||.|+++++.++|+|++++||||+||++|||||+|+++|.+++++|+ .||+++.+.+|..+
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 99999999999999977899999999999999999999999999999999999999999999998 89998877778889
Q ss_pred ccCCCHHHHhcCC-HHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHh
Q 020295 188 HEFPSLERLSLVS-EVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDAL 266 (328)
Q Consensus 188 ~~fPtpe~La~~~-~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L 266 (328)
+.||||++|+..+ +++||.+|+||| |+||+++|+.+.++++ +..+++.|+.+++++++++|
T Consensus 161 ~~FPtp~~La~~~~e~~Lr~~G~g~R-----------------a~~I~~~A~~i~~~~~-~~~~l~~l~~~~~~~~~~~L 222 (310)
T TIGR00588 161 HGFPSLHALTGPEAEAHLRKLGLGYR-----------------ARYIRETARALLEEQG-GRAWLQQIRGASYEDAREAL 222 (310)
T ss_pred ccCCCHHHHhCCChHHHHHHcCCHHH-----------------HHHHHHHHHHHHhccC-CchhHHhhccCChHHHHHHH
Confidence 9999999999875 568999999988 9999999999998653 45688899999999999999
Q ss_pred hcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHcCCCcc---cCCCCCHHHHHHHHHHhh
Q 020295 267 CTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPEL---AGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 267 ~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~~~~~---~~~~lt~k~y~~i~e~~~ 327 (328)
++|||||+|||+|||||+++++++||||+||+|+++++|.... ..+.++++.|.++.++++
T Consensus 223 ~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~ 286 (310)
T TIGR00588 223 CELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFR 286 (310)
T ss_pred HhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccccccCChhHHHHHHHHHH
Confidence 9999999999999999999999999999999999999875321 234578999999988765
No 3
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=1.8e-35 Score=280.86 Aligned_cols=220 Identities=17% Similarity=0.184 Sum_probs=180.9
Q ss_pred CceEEEeE----CCeEEEEEEecCC-cEEEEEcCCC--ChHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHHHHHhcC
Q 020295 67 PLQYTGPI----GPHLISLKHLQNG-DVCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAG 139 (328)
Q Consensus 67 ~~~~~g~~----g~~~i~l~q~~~~-~l~~~~~~~~--~~~~~~~~l~~~f~Ld~dl~~~~~~~~~~D~~l~~l~~~~~G 139 (328)
++.|.-.+ +..++.|++.++. .+.+++..+. ....+.+.++++||||.|++.+++.+ ..+++..+|
T Consensus 32 ~~~y~R~~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L-------~~~~~~~~G 104 (283)
T PRK10308 32 EGYYARSLAVGEHRGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGAL-------GKLGAARPG 104 (283)
T ss_pred CCEEEEEEEECCccEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHH-------HHHHHhCCC
Confidence 34555443 4667888886543 2555555432 23457899999999999999998655 578999999
Q ss_pred CccC-CCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCcc
Q 020295 140 ARVL-RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQS 217 (328)
Q Consensus 140 ~R~l-~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~ 217 (328)
+|++ .+||||++|++||+||+|+..+.++..+|+ .||+++.+ +..++.||||++|+++++++|++||++++
T Consensus 105 lR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~--~~~~~~FPtpe~La~~~~~eL~~~Gl~~~----- 177 (283)
T PRK10308 105 LRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDD--FPEYVCFPTPERLAAADPQALKALGMPLK----- 177 (283)
T ss_pred CcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccC--CCCccCCCCHHHHHcCCHHHHHHCCCCHH-----
Confidence 9997 599999999999999999999999999998 89998743 23478999999999999999999999754
Q ss_pred chhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccc-cchH
Q 020295 218 SLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIP-VDTH 296 (328)
Q Consensus 218 ~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~P-VDth 296 (328)
||+||+++|+.+.+ |.++++.. .+.++++++|++|||||+|||+||++|++|++|+|| .|.|
T Consensus 178 -----------Ra~~L~~lA~~i~~----g~l~l~~~--~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~ 240 (283)
T PRK10308 178 -----------RAEALIHLANAALE----GTLPLTIP--GDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYL 240 (283)
T ss_pred -----------HHHHHHHHHHHHHc----CCCCcccc--CCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHH
Confidence 89999999999987 56666543 467899999999999999999999999999999995 5999
Q ss_pred HHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 020295 297 VWKIATRYLLPELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 297 v~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~ 327 (328)
++|.+ . ..++++..++++.|+
T Consensus 241 l~~~~---~-------~~~~~~~~~~a~~w~ 261 (283)
T PRK10308 241 IKQRF---P-------GMTPAQIRRYAERWK 261 (283)
T ss_pred HHHhc---c-------cCCHHHHHHHHHhcC
Confidence 98743 1 247888898888885
No 4
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-35 Score=282.20 Aligned_cols=196 Identities=26% Similarity=0.379 Sum_probs=173.6
Q ss_pred ChHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHHHHHhcCCc-cCCCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hh
Q 020295 98 SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGAR-VLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SL 175 (328)
Q Consensus 98 ~~~~~~~~l~~~f~Ld~dl~~~~~~~~~~D~~l~~l~~~~~G~R-~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~ 175 (328)
..+++...+.++|+||.++..+++.+. .++.... +|+| .+.+||||+||++|||||+|+++|.+++++|+ .|
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 346778999999999999999998886 5665544 6666 45899999999999999999999999999998 79
Q ss_pred CCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhh
Q 020295 176 GSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLR 255 (328)
Q Consensus 176 G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~ 255 (328)
|+.+. .+|.|||||+|++++++.|+.||+.- .||+||+++|+++.+ |++++..+.
T Consensus 135 g~~~~-----~~~~fptpe~l~~~~~~~l~~~g~s~----------------~Ka~yi~~~A~~~~~----g~~~~~~l~ 189 (285)
T COG0122 135 GNALE-----IYHSFPTPEQLAAADEEALRRCGLSG----------------RKAEYIISLARAAAE----GELDLSELK 189 (285)
T ss_pred CCccc-----cccCCCCHHHHHhcCHHHHHHhCCcH----------------HHHHHHHHHHHHHHc----CCccHHHhc
Confidence 98763 68999999999999999999998843 479999999999997 778999999
Q ss_pred CCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccc-chHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 020295 256 KLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPV-DTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 256 ~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PV-Dthv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~ 327 (328)
.++++++++.|++|+|||||||+|+|||++|++|+||+ |.++++.++++|. .++..+++...+++|.|.
T Consensus 190 ~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~---~~~~~~~~~~~~~~e~w~ 259 (285)
T COG0122 190 PLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYR---LPTRPTEKEVRELAERWG 259 (285)
T ss_pred cCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhc---CCCCchHHHHHHHHhccc
Confidence 99999999999999999999999999999999999996 7788888999882 246778888899999886
No 5
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.97 E-value=8.1e-31 Score=237.84 Aligned_cols=143 Identities=29% Similarity=0.403 Sum_probs=127.4
Q ss_pred hhHHHHHHHhcCCcc-CC-CCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHH
Q 020295 128 CRFAELAKYLAGARV-LR-QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELR 205 (328)
Q Consensus 128 ~~l~~l~~~~~G~R~-l~-~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr 205 (328)
..+..+.+.++..+. ++ .|||+.||+.|||||++..++.++..+|- ..|||||+|+++++++|.
T Consensus 8 ~i~~~l~~~~p~~~~~l~~~~pf~lLva~iLSaqttD~~vn~at~~Lf--------------~~~~t~e~l~~a~~~~l~ 73 (211)
T COG0177 8 EILDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPALF--------------KRYPTPEDLLNADEEELE 73 (211)
T ss_pred HHHHHHHHHCCCCCCccCcCCcHHHHHHHHHhccCchHHHHHHHHHHH--------------HHcCCHHHHHcCCHHHHH
Confidence 345555666666553 44 89999999999999999999999988773 457899999999999998
Q ss_pred hcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhC
Q 020295 206 NAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 285 (328)
Q Consensus 206 ~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~l 285 (328)
+ +|+++||+++||++|+++|+.+.++|+| +.++.+++|++|||||+|||++||.+++
T Consensus 74 ~------------~I~~iGlyr~KAk~I~~~~~~l~e~~~g-----------~vP~~~~eL~~LPGVGrKTAnvVL~~a~ 130 (211)
T COG0177 74 E------------LIKSIGLYRNKAKNIKELARILLEKFGG-----------EVPDTREELLSLPGVGRKTANVVLSFAF 130 (211)
T ss_pred H------------HHHhcCCcHHHHHHHHHHHHHHHHHcCC-----------CCCchHHHHHhCCCcchHHHHHHHHhhc
Confidence 7 4889999999999999999999999987 6789999999999999999999999999
Q ss_pred CCCCccccchHHHHHHHHcCCCc
Q 020295 286 DQHHAIPVDTHVWKIATRYLLPE 308 (328)
Q Consensus 286 g~~d~~PVDthv~Ri~~rl~~~~ 308 (328)
|.+ +|||||||+|+++|+++..
T Consensus 131 g~p-~i~VDTHV~Rvs~R~gl~~ 152 (211)
T COG0177 131 GIP-AIAVDTHVHRVSNRLGLVP 152 (211)
T ss_pred CCC-cccccchHHHHHHHhCCCC
Confidence 995 9999999999999999875
No 6
>PRK10702 endonuclease III; Provisional
Probab=99.97 E-value=1.2e-30 Score=238.12 Aligned_cols=142 Identities=20% Similarity=0.260 Sum_probs=123.3
Q ss_pred hHHHHHHHhcCC--ccCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHh
Q 020295 129 RFAELAKYLAGA--RVLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN 206 (328)
Q Consensus 129 ~l~~l~~~~~G~--R~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~ 206 (328)
.+..+.+.++.. ....+||||+||++|||||+++.++.+++.+|. ..||||++|+++++++|++
T Consensus 9 i~~~l~~~~~~~~~~~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~--------------~~~pt~e~l~~a~~~~l~~ 74 (211)
T PRK10702 9 ILTRLRDNNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLY--------------PVANTPAAMLELGVEGVKT 74 (211)
T ss_pred HHHHHHHHCCCCCCCCCCCChHHHHHHHHHHhhcCHHHHHHHHHHHH--------------HHcCCHHHHHCCCHHHHHH
Confidence 344455555532 344699999999999999999999999998773 4689999999999999988
Q ss_pred cCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 207 AGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 207 ~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
+ |+++||+++||++|+++|+.+.++++| +.++++++|++|||||+|||+|||+|+++
T Consensus 75 ~------------i~~~G~y~~kA~~l~~~a~~i~~~~~~-----------~~p~~~~~Ll~lpGVG~ktA~~ill~a~~ 131 (211)
T PRK10702 75 Y------------IKTIGLYNSKAENVIKTCRILLEQHNG-----------EVPEDRAALEALPGVGRKTANVVLNTAFG 131 (211)
T ss_pred H------------HHHcCCHHHHHHHHHHHHHHHHHHcCC-----------CCCchHHHHhcCCcccHHHHHHHHHHHcC
Confidence 4 778888899999999999999988765 45788999999999999999999999999
Q ss_pred CCCccccchHHHHHHHHcCCCc
Q 020295 287 QHHAIPVDTHVWKIATRYLLPE 308 (328)
Q Consensus 287 ~~d~~PVDthv~Ri~~rl~~~~ 308 (328)
+ ++||||+||+|+++|+|+..
T Consensus 132 ~-~~~~VDt~v~Rv~~r~g~~~ 152 (211)
T PRK10702 132 W-PTIAVDTHIFRVCNRTQFAP 152 (211)
T ss_pred C-CcccccchHHHHHHHhCCCC
Confidence 9 89999999999999998753
No 7
>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=99.97 E-value=6.6e-30 Score=229.76 Aligned_cols=143 Identities=25% Similarity=0.334 Sum_probs=122.8
Q ss_pred hhHHHHHHHhcCCc--cCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHH
Q 020295 128 CRFAELAKYLAGAR--VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELR 205 (328)
Q Consensus 128 ~~l~~l~~~~~G~R--~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr 205 (328)
+.+.++.+.+++.+ ...+||||+||++|||||++++++..++.+|. ..||||++|+++++++|.
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 34556667777665 34589999999999999999999999998875 358999999999999997
Q ss_pred hcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhC
Q 020295 206 NAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 285 (328)
Q Consensus 206 ~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~l 285 (328)
++ |+++||+++||+||+++|+.+.++++| +.++++++|+++||||+|||+|||+|++
T Consensus 71 ~~------------ir~~G~~~~Ka~~i~~~a~~i~~~~~~-----------~~~~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 71 EY------------IKSIGLYRNKAKNIIALCRILVERYGG-----------EVPEDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred HH------------HHhcCChHHHHHHHHHHHHHHHHHcCC-----------CCchHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 63 566777789999999999999987754 3456899999999999999999999999
Q ss_pred CCCCccccchHHHHHHHHcCCCc
Q 020295 286 DQHHAIPVDTHVWKIATRYLLPE 308 (328)
Q Consensus 286 g~~d~~PVDthv~Ri~~rl~~~~ 308 (328)
++ +.||||+||+|+++|+|+.+
T Consensus 128 ~~-~~~~vD~~v~Ri~~r~g~~~ 149 (191)
T TIGR01083 128 GI-PAIAVDTHVFRVSNRLGLSK 149 (191)
T ss_pred CC-CccccchhHHHHHHHcCCCC
Confidence 98 57999999999999998753
No 8
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.96 E-value=2e-29 Score=230.67 Aligned_cols=151 Identities=13% Similarity=0.112 Sum_probs=126.2
Q ss_pred cCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhh
Q 020295 142 VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLF 221 (328)
Q Consensus 142 ~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~ 221 (328)
-...+|||+||++||+|||+++++..++.+|..-|.- . -..||||+.|+++++++|+++ |+
T Consensus 25 Wp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~----~---~~~~~t~e~L~~a~~eeL~~~------------Ir 85 (218)
T PRK13913 25 WPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFIL----E---NDDEINLKKIAYIEFSKLAEC------------VR 85 (218)
T ss_pred CcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhccc----c---cccCCCHHHHHcCCHHHHHHH------------HH
Confidence 4578999999999999999999999999999732210 0 024789999999999999885 88
Q ss_pred hhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHH
Q 020295 222 SVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIA 301 (328)
Q Consensus 222 ~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~ 301 (328)
++||+++||+||+++|+.+.++++| ++ .+..++++++|+++||||+|||||||+|++++ ++||||+|++|++
T Consensus 86 p~Gf~~~KA~~Lk~la~~i~~~~g~----~~---~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~r-p~fvVDty~~Rv~ 157 (218)
T PRK13913 86 PSGFYNQKAKRLIDLSENILKDFGS----FE---NFKQEVTREWLLDQKGIGKESADAILCYVCAK-EVMVVDKYSYLFL 157 (218)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHcCC----ch---hccCchHHHHHHcCCCccHHHHHHHHHHHcCC-CccccchhHHHHH
Confidence 9999999999999999999987743 22 23446899999999999999999999999999 8999999999999
Q ss_pred HHcCCCcccCCCCCHHHHHHHHHHhh
Q 020295 302 TRYLLPELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 302 ~rl~~~~~~~~~lt~k~y~~i~e~~~ 327 (328)
+|+|+.. +.|+++.+.|.
T Consensus 158 ~RlG~~~--------~~y~~~~~~~~ 175 (218)
T PRK13913 158 KKLGIEI--------EDYDELQHFFE 175 (218)
T ss_pred HHcCCCC--------CCHHHHHHHHH
Confidence 9998742 13666666653
No 9
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.94 E-value=8.4e-27 Score=202.27 Aligned_cols=141 Identities=30% Similarity=0.401 Sum_probs=121.2
Q ss_pred HHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcc
Q 020295 148 VECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRS 226 (328)
Q Consensus 148 fe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~ 226 (328)
||+|+++||+||++++++..++++|+ .|| |||++|+.+++++|++++.+ +| +
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g--------------pt~~~l~~~~~~~l~~~~~~------------~G-~ 53 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG--------------PTPEALAAADEEELRELIRS------------LG-Y 53 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC--------------CCHHHHHCCCHHHHHHHHHh------------cC-h
Confidence 79999999999999999999999998 565 89999999999999997653 34 3
Q ss_pred hHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHcCC
Q 020295 227 FKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLL 306 (328)
Q Consensus 227 ~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~~ 306 (328)
+.||++|+++|+.+.+++.+ +.. +.+++++.|++|||||+|||+|+++|+++ .++||||+|+.|+++++|+
T Consensus 54 ~~kA~~i~~~a~~~~~~~~~----~~~----~~~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pvD~~v~r~~~~~~~ 124 (158)
T cd00056 54 RRKAKYLKELARAIVEGFGG----LVL----DDPDAREELLALPGVGRKTANVVLLFALG-PDAFPVDTHVRRVLKRLGL 124 (158)
T ss_pred HHHHHHHHHHHHHHHHHcCC----ccC----CCcccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCccchhHHHHHHHhCC
Confidence 47999999999999987653 111 67899999999999999999999999999 7999999999999999986
Q ss_pred CcccCCCCCHHHHHHHHHHhh
Q 020295 307 PELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 307 ~~~~~~~lt~k~y~~i~e~~~ 327 (328)
. ....+.+.+.++.+.|.
T Consensus 125 ~---~~~~~~~~~~~~~~~~~ 142 (158)
T cd00056 125 I---PKKKTPEELEELLEELL 142 (158)
T ss_pred C---CCCCCHHHHHHHHHHHC
Confidence 3 23457777777777664
No 10
>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=99.94 E-value=3e-27 Score=196.56 Aligned_cols=111 Identities=32% Similarity=0.594 Sum_probs=86.8
Q ss_pred cccCCCCCCCcCcccCCCCcccceecCCceEEEeECCeEEEEEEecCCcEEEEEcC------CCChHHHHHHHHHhhcCC
Q 020295 40 PLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHT------SPSEPAAKSALLDFLNMG 113 (328)
Q Consensus 40 ~l~~~~~~~~L~~tl~~GQ~Frw~~~~~~~~~g~~g~~~i~l~q~~~~~l~~~~~~------~~~~~~~~~~l~~~f~Ld 113 (328)
+|++++++|||+.||+|||||||++.+++.|+||+|+++|.|+|.+ +.+.|.+.. ..+..+..+.+++||+||
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 4788899999999999999999999988889999999999999975 566665543 124567889999999999
Q ss_pred CCHHHHHHHHhccChhHHHHHHHhcCCccCCCCHHHHH
Q 020295 114 ISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECL 151 (328)
Q Consensus 114 ~dl~~~~~~~~~~D~~l~~l~~~~~G~R~l~~dpfe~L 151 (328)
.||+++|+.|++.|+.|+++++.+.|+|+++|||||||
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 11
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.94 E-value=4.8e-26 Score=206.96 Aligned_cols=159 Identities=23% Similarity=0.140 Sum_probs=125.3
Q ss_pred hHHHHHHHhcCCc--cCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHh
Q 020295 129 RFAELAKYLAGAR--VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN 206 (328)
Q Consensus 129 ~l~~l~~~~~G~R--~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~ 206 (328)
.+.+.++.|..+- .-..|||+.||++|||||+++..+.++..+|. ++.+ .+++++|++
T Consensus 17 ~~~~r~~ef~~~~~~~~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-------------------~~~l-~~~~eeL~~ 76 (208)
T PRK01229 17 RVEERIEEFKLLGEKGDEEDLFSELSFCILTANSSAEGGIKAQKEIG-------------------DGFL-YLSEEELEE 76 (208)
T ss_pred HHHHHHHHHHHhhhccccCChHHHHHHHHhcCcCcHHHHHHHHHhcC-------------------HHHc-CCCHHHHHH
Confidence 3334444444332 24589999999999999999999999998773 3445 678888877
Q ss_pred cCCCCCCCCccchhhhhh--cchHHHHHHHHHHHHHHHhcCCCchhhhhh--hCCCHHHHHHHhh-cCCCccHHHHHHHH
Q 020295 207 AGFGYRSAPQSSLLFSVR--RSFKQAKYITGTVDVLQSKHSGGAEWLLSL--RKLDLQEAIDALC-TLPGVGPKVAACIA 281 (328)
Q Consensus 207 ~Glg~R~~~~~~li~~v~--~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L--~~~~~~ea~~~L~-~l~GIG~ktAd~vl 281 (328)
+ |+++| |+++||+||+++++.+. .+..+ ...+.++++++|+ ++||||+|||+|||
T Consensus 77 ~------------Ir~~Gygf~~~KAk~I~~~~~~~~--------~l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 77 K------------LKEVGHRFYNKRAEYIVEARKLYG--------KLKEIIKADKDQFEAREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred H------------HHHhhcccHHHHHHHHHHHHHHHH--------HHHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHH
Confidence 3 77774 99999999999998741 01222 2457799999999 99999999999999
Q ss_pred HHhCCCCCccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhhC
Q 020295 282 LFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFCE 328 (328)
Q Consensus 282 lf~lg~~d~~PVDthv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~~ 328 (328)
+.... .++|+||+||+|+++|+|+.+...+++|++.|.++.+.|++
T Consensus 137 ~~~~~-~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~ 182 (208)
T PRK01229 137 RNVGY-EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILRE 182 (208)
T ss_pred HHccC-CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHH
Confidence 75545 58999999999999999987655568999999999988753
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=99.93 E-value=1.4e-25 Score=212.20 Aligned_cols=125 Identities=18% Similarity=0.309 Sum_probs=108.0
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhh
Q 020295 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSV 223 (328)
Q Consensus 144 ~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v 223 (328)
.+|||++||++|++|||+++++...+.+|. ..|||+++|+++++++|.++ ++++
T Consensus 23 ~~dpy~vlvseIL~QQT~v~~v~~~~~rl~--------------~~fpt~~~La~a~~eeL~~~------------~~~l 76 (275)
T TIGR01084 23 NKTPYRVWLSEVMLQQTQVATVIPYFERFL--------------ERFPTVQALANAPQDEVLKL------------WEGL 76 (275)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHH--------------HhCCCHHHHHCcCHHHHHHH------------HHHC
Confidence 489999999999999999999999998875 35899999999999999652 2333
Q ss_pred hcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHH
Q 020295 224 RRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 303 (328)
Q Consensus 224 ~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~r 303 (328)
||+ +||++|+++|+.|.++++| ..++.+++|++|||||+|||+|||+|+|++ +.++||+||+|+++|
T Consensus 77 G~y-~RAr~L~~~A~~i~~~~~g-----------~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~-~~~~vD~~v~RVl~R 143 (275)
T TIGR01084 77 GYY-ARARNLHKAAQEVVEEFGG-----------EFPQDFEDLAALPGVGRYTAGAILSFALNK-PYPILDGNVKRVLSR 143 (275)
T ss_pred CcH-HHHHHHHHHHHHHHHHcCC-----------CCcHHHHHHHhCCCCCHHHHHHHHHHHCCC-CCCcchHhHHHHHHH
Confidence 444 4899999999999998765 345679999999999999999999999999 467799999999999
Q ss_pred cCCC
Q 020295 304 YLLP 307 (328)
Q Consensus 304 l~~~ 307 (328)
+|..
T Consensus 144 l~~~ 147 (275)
T TIGR01084 144 LFAV 147 (275)
T ss_pred HccC
Confidence 8754
No 13
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.92 E-value=4.8e-25 Score=198.41 Aligned_cols=176 Identities=19% Similarity=0.254 Sum_probs=151.4
Q ss_pred HHHhccChhHHHHHHHhcCCccC-CCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhc
Q 020295 121 EGFSASDCRFAELAKYLAGARVL-RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSL 198 (328)
Q Consensus 121 ~~~~~~D~~l~~l~~~~~G~R~l-~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~ 198 (328)
+++...|+.+.+++..+..++.- .|.||+.|+++|+|||.+.+++.++++|++ .||.- +.||+||.+..
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 34556788888888887766664 599999999999999999999999999998 67642 57999999999
Q ss_pred CCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHH
Q 020295 199 VSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAA 278 (328)
Q Consensus 199 ~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd 278 (328)
++.++||.|||+-| |+.||+.+|++..+. -......+.+|+.++..+.|+.++|||+||++
T Consensus 119 ~~~~~lrkcG~S~r----------------K~~yLh~lA~~~~ng---~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~ 179 (254)
T KOG1918|consen 119 LDCEELRKCGFSKR----------------KASYLHSLAEAYTNG---YIPSKSGIEKMSEEELIERLTNVKGIGRWTVE 179 (254)
T ss_pred CCHHHHHHhCcchh----------------hHHHHHHHHHHHhcC---CCCchHHHhhcCHHHHHHHHHhccCccceeee
Confidence 99999999999877 899999999999872 26678888899999999999999999999999
Q ss_pred HHHHHhCCCCCccccc-hHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 020295 279 CIALFSLDQHHAIPVD-THVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 279 ~vllf~lg~~d~~PVD-thv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~ 327 (328)
++|+|+|+|+|++|+| ..|++-.+.++.. ...+.+++.+++.+.|+
T Consensus 180 MflIfsL~R~DVmp~dDlgir~g~k~l~gl---~~~p~~~evekl~e~~k 226 (254)
T KOG1918|consen 180 MFLIFSLHRPDVMPADDLGIRNGVKKLLGL---KPLPLPKEVEKLCEKCK 226 (254)
T ss_pred eeeeeccCCCcccCchhhhHHHHHHHHhCC---CCCCchHHHHHHhhhcc
Confidence 9999999999999995 4688888887532 22467788888888775
No 14
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.92 E-value=1e-24 Score=212.38 Aligned_cols=125 Identities=19% Similarity=0.309 Sum_probs=109.6
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhh
Q 020295 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSV 223 (328)
Q Consensus 144 ~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v 223 (328)
..|||+++|+.|++|||+++++...+++|. ..|||+++|+++++++|..+ |+++
T Consensus 27 ~~dpy~ilVseILlQQT~v~~v~~~~~rl~--------------~~fPt~~~La~a~~eel~~~------------~~gl 80 (350)
T PRK10880 27 DKTPYKVWLSEVMLQQTQVATVIPYFERFM--------------ARFPTVTDLANAPLDEVLHL------------WTGL 80 (350)
T ss_pred CCCHHHHHHHHHHHhhccHHHHHHHHHHHH--------------HHCcCHHHHHCcCHHHHHHH------------HHcC
Confidence 479999999999999999999999999885 35899999999999999873 3344
Q ss_pred hcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHH
Q 020295 224 RRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 303 (328)
Q Consensus 224 ~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~r 303 (328)
||++ ||++|+++|+.+.++++| ..++.+++|++|||||+|||+|||+|+|++ .+++||+||+|+++|
T Consensus 81 Gyy~-RAr~L~~~A~~i~~~~~g-----------~~p~~~~~L~~LpGIG~~TA~aIl~~af~~-~~~iVD~nV~RV~~R 147 (350)
T PRK10880 81 GYYA-RARNLHKAAQQVATLHGG-----------EFPETFEEVAALPGVGRSTAGAILSLSLGK-HFPILDGNVKRVLAR 147 (350)
T ss_pred ChHH-HHHHHHHHHHHHHHHhCC-----------CchhhHHHHhcCCCccHHHHHHHHHHHCCC-CeecccHHHHHHHHH
Confidence 4553 899999999999998876 457889999999999999999999999999 566789999999999
Q ss_pred cCCC
Q 020295 304 YLLP 307 (328)
Q Consensus 304 l~~~ 307 (328)
++..
T Consensus 148 l~~i 151 (350)
T PRK10880 148 CYAV 151 (350)
T ss_pred Hhcc
Confidence 8643
No 15
>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=6.4e-24 Score=182.67 Aligned_cols=130 Identities=30% Similarity=0.448 Sum_probs=107.5
Q ss_pred HhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHH
Q 020295 156 CSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITG 235 (328)
Q Consensus 156 lsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~ 235 (328)
|+||++++++..++.+|.. .||||++|+++++++|.++ |+++||+++||+||++
T Consensus 1 l~qq~~~~~a~~~~~~l~~--------------~~~~~~~l~~~~~~eL~~~------------l~~~g~~~~ka~~i~~ 54 (149)
T smart00478 1 LSQQTSDEAVNKATERLFE--------------KFPTPEDLAAADEEELEEL------------IRPLGFYRRKAKYLIE 54 (149)
T ss_pred CCCcccHHHHHHHHHHHHH--------------HCCCHHHHHCCCHHHHHHH------------HHHcCChHHHHHHHHH
Confidence 5899999999999999972 3679999999999998552 3344555689999999
Q ss_pred HHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHcCCCcccCCCCC
Q 020295 236 TVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLT 315 (328)
Q Consensus 236 ~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~~~~~~~~~lt 315 (328)
+|+.+.++++| +.++.++.|++|||||+|||+|||+|++++ +++|||+|+.|+++++|+.+ ...+
T Consensus 55 ~a~~~~~~~~~-----------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~---~~~~ 119 (149)
T smart00478 55 LARILVEEYGG-----------EVPDDREELLKLPGVGRKTANAVLSFALGK-PFIPVDTHVLRIAKRLGLVD---KKST 119 (149)
T ss_pred HHHHHHHHHCC-----------CccHHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccchHHHHHHHHhCCCC---CCCC
Confidence 99999887654 235789999999999999999999999999 99999999999999998653 3345
Q ss_pred HHHHHHHHHHh
Q 020295 316 PKLCSRVAEAF 326 (328)
Q Consensus 316 ~k~y~~i~e~~ 326 (328)
.+...++.+.|
T Consensus 120 ~~~~~~~~~~~ 130 (149)
T smart00478 120 PEEVEKLLEKL 130 (149)
T ss_pred HHHHHHHHHHH
Confidence 66666666655
No 16
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.89 E-value=1.3e-22 Score=185.29 Aligned_cols=131 Identities=28% Similarity=0.418 Sum_probs=120.9
Q ss_pred CCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhhh
Q 020295 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVR 224 (328)
Q Consensus 145 ~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~ 224 (328)
..-|+.|++.+||+|+.......+|.||.+||. -|+|.+.++++..|.+ ||.+||
T Consensus 76 ~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~g-------------LT~e~v~~~de~~l~~------------LI~~Vg 130 (286)
T KOG1921|consen 76 ERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGG-------------LTLEAVLKIDEPTLNE------------LIYPVG 130 (286)
T ss_pred hHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcC-------------CCHHHHhccChHhHHh------------hhhhcc
Confidence 457999999999999999999999999997772 2899999999988876 599999
Q ss_pred cchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHc
Q 020295 225 RSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRY 304 (328)
Q Consensus 225 ~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl 304 (328)
||++||+||+.+|+.+.++|+| |.+...+.|++|||||||.|..+|-.++|+...+.|||||+||++|+
T Consensus 131 Fy~rKA~ylkkta~IL~d~f~g-----------DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrl 199 (286)
T KOG1921|consen 131 FYTRKAKYLKKTAKILQDKFDG-----------DIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRL 199 (286)
T ss_pred chHHHHHHHHHHHHHHHHHhCC-----------CCchhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHh
Confidence 9999999999999999999988 78899999999999999999999999999999999999999999999
Q ss_pred CCCcccC
Q 020295 305 LLPELAG 311 (328)
Q Consensus 305 ~~~~~~~ 311 (328)
+|...+.
T Consensus 200 gWv~~kt 206 (286)
T KOG1921|consen 200 GWVDTKT 206 (286)
T ss_pred ccccccc
Confidence 9987433
No 17
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.87 E-value=2.3e-21 Score=173.60 Aligned_cols=146 Identities=19% Similarity=0.218 Sum_probs=123.5
Q ss_pred cCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhh
Q 020295 142 VLRQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLF 221 (328)
Q Consensus 142 ~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~ 221 (328)
.+.++-.|.++++||.|||+++++.+++++|+..|. -++++|..+++++|.++ |+
T Consensus 25 Wp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~-------------~~l~~I~~~~~~~L~el------------Ir 79 (215)
T COG2231 25 WPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGI-------------LNLKKILKLDEEELAEL------------IR 79 (215)
T ss_pred CCCCCchhHHHHHHHhccccHHHHHHHHHHHHHccc-------------CCHHHHhcCCHHHHHHH------------Hh
Confidence 344566699999999999999999999999986542 15899999999999884 89
Q ss_pred hhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHH
Q 020295 222 SVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIA 301 (328)
Q Consensus 222 ~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~ 301 (328)
|.|||++||++|+++...+...+.+ +.+......+++|++|+|||+.|||.||+|++++ ++|+||.+.+|++
T Consensus 80 psGFYnqKa~rLk~l~k~l~~~~~~-------~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~r-p~FVvD~Yt~R~l 151 (215)
T COG2231 80 PSGFYNQKAKRLKALSKNLAKFFIN-------LESFKSEVLREELLSIKGIGKETADSILLYALDR-PVFVVDKYTRRLL 151 (215)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhhh-------hhccchHHHHHHHHccCCcchhhHHHHHHHHhcC-cccchhHHHHHHH
Confidence 9999999999999999888875432 3333455589999999999999999999999999 8999999999999
Q ss_pred HHcCCCcccCCCCCHHHHHHHHHHhh
Q 020295 302 TRYLLPELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 302 ~rl~~~~~~~~~lt~k~y~~i~e~~~ 327 (328)
.|+|.... +.|+++.+.|.
T Consensus 152 ~rlg~i~~-------k~ydeik~~fe 170 (215)
T COG2231 152 SRLGGIEE-------KKYDEIKELFE 170 (215)
T ss_pred HHhccccc-------ccHHHHHHHHH
Confidence 99986532 35888877765
No 18
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.86 E-value=3.4e-21 Score=183.37 Aligned_cols=111 Identities=20% Similarity=0.325 Sum_probs=93.5
Q ss_pred HhcccCHHHHHH-HHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHH
Q 020295 156 CSSNNNIARITK-MVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYIT 234 (328)
Q Consensus 156 lsQn~si~~a~~-~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~ 234 (328)
++|||.+.++.. .++++. ..|||+++|+++++++|.++ |+++||+ +||++|+
T Consensus 1 mlQQT~v~~v~~~yy~rf~--------------~~fPt~e~La~a~~~el~~~------------~~glGyy-~RAr~L~ 53 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFL--------------EAFPTLKDLANAPLEEVLLL------------WRGLGYY-SRAKNLK 53 (289)
T ss_pred CCCCCcHHHhHHHHHHHHH--------------HHCCCHHHHHCCCHHHHHHH------------HHcCCcH-HHHHHHH
Confidence 479999888864 666553 56999999999999999873 4445555 4899999
Q ss_pred HHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHcC
Q 020295 235 GTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305 (328)
Q Consensus 235 ~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~ 305 (328)
++|+.+.++++| ..+..+++|++|||||+|||+|||+|+|++ +++|||+||+|++.|++
T Consensus 54 ~~A~~i~~~~~g-----------~~P~~~~~L~~LpGIG~kTA~aIl~~af~~-~~~~VD~nV~RVl~Rl~ 112 (289)
T PRK13910 54 KSAEICVKEHHS-----------QLPNDYQSLLKLPGIGAYTANAILCFGFRE-KSACVDANIKRVLLRLF 112 (289)
T ss_pred HHHHHHHHHhCC-----------CCChhHHHHHhCCCCCHHHHHHHHHHHCCC-CcCcccHHHHHHHHHHh
Confidence 999999998865 234568999999999999999999999998 67899999999999974
No 19
>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=99.84 E-value=2.1e-20 Score=165.53 Aligned_cols=129 Identities=19% Similarity=0.205 Sum_probs=106.1
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhh
Q 020295 144 RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFS 222 (328)
Q Consensus 144 ~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~ 222 (328)
..+|||.||++|||||++++++.+++.+|. ++|. +||+.|++++.++|.++ |++
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~-------------~tp~~La~a~~eeL~~l------------I~~ 69 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGS-------------LDAEDIAKYDPQAFVAL------------FSE 69 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC-------------CCHHHHHcCCHHHHHHH------------Hhc
Confidence 479999999999999999999999999996 5652 58999999999999874 655
Q ss_pred h----hcchHHHHHHHHHHHHHHHhcCCCchhhhhhhC---CCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccch
Q 020295 223 V----RRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRK---LDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDT 295 (328)
Q Consensus 223 v----~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~---~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDt 295 (328)
+ ||+++||++|+++|+.+.++|+| +++.|.. .+..+++++|++|||||+|||+|||.+ |++ -|-|-.
T Consensus 70 ~pal~Gfy~~KAk~Lk~~a~~iie~y~G---~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~-l~~--~~~~~~ 143 (177)
T TIGR03252 70 RPAVHRFPGSMAKRVQALAQYVVDTYDG---DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLAL-LGK--QLGVTP 143 (177)
T ss_pred CccccCchHHHHHHHHHHHHHHHHHhCC---ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHH-HHH--HhCCCC
Confidence 4 99999999999999999999987 5666655 466788999999999999999999995 554 345533
Q ss_pred HHHHHHHH
Q 020295 296 HVWKIATR 303 (328)
Q Consensus 296 hv~Ri~~r 303 (328)
--||-+.-
T Consensus 144 ~~~~~~~~ 151 (177)
T TIGR03252 144 EGWREAAG 151 (177)
T ss_pred cchHHhcc
Confidence 33444433
No 20
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.72 E-value=1.4e-17 Score=160.37 Aligned_cols=141 Identities=23% Similarity=0.406 Sum_probs=119.8
Q ss_pred CCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHh--cCCCCCCCCccchhhh
Q 020295 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRN--AGFGYRSAPQSSLLFS 222 (328)
Q Consensus 145 ~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~--~Glg~R~~~~~~li~~ 222 (328)
.+||.++||.|+.|||.++.+...+.++. ..|||+++||+++++++.. .|+||.
T Consensus 32 ~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl--------------~rfPti~~LA~A~~~evl~~W~gLGYy---------- 87 (342)
T COG1194 32 KDPYRVWVSEIMLQQTQVATVIPYYERFL--------------ERFPTIKALAAAPEDEVLKAWEGLGYY---------- 87 (342)
T ss_pred CCcceehhHHHHhhhccHhhhhhhHHHHH--------------HhCCCHHHHhcCCHHHHHHHHHhcChH----------
Confidence 67999999999999999999988776653 4699999999999888866 589976
Q ss_pred hhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHHH
Q 020295 223 VRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIAT 302 (328)
Q Consensus 223 v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~ 302 (328)
+||+.++++|+.+.++|+| ..++..+.|.+|||||++||..|+.|++++ ..-.||++|.|++.
T Consensus 88 -----sRArnL~~~A~~v~~~~~G-----------~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~-~~~~lDgNV~RVl~ 150 (342)
T COG1194 88 -----SRARNLHKAAQEVVERHGG-----------EFPDDEEELAALPGVGPYTAGAILSFAFNQ-PEPVLDGNVKRVLS 150 (342)
T ss_pred -----HHHHHHHHHHHHHHHHcCC-----------CCCCCHHHHHhCCCCcHHHHHHHHHHHhCC-CCceeecchheeeh
Confidence 6899999999999999987 456667888899999999999999999998 44456999999999
Q ss_pred HcCCCc-ccCCCCCHHHHHHHHHHh
Q 020295 303 RYLLPE-LAGVRLTPKLCSRVAEAF 326 (328)
Q Consensus 303 rl~~~~-~~~~~lt~k~y~~i~e~~ 326 (328)
|++..+ ..++.-+.+.+.++++.+
T Consensus 151 R~f~i~~~~~~~~~~~~~~~~~~~l 175 (342)
T COG1194 151 RLFAISGDIGKPKTKKELWELAEQL 175 (342)
T ss_pred hhhcccccccccchhHHHHHHHHHh
Confidence 986443 345567888898888764
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=7.4e-16 Score=125.47 Aligned_cols=103 Identities=27% Similarity=0.301 Sum_probs=82.4
Q ss_pred HHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcchHHH
Q 020295 152 LQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQA 230 (328)
Q Consensus 152 is~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA 230 (328)
|++||+||++++++.+++.+|. .|| ||||++|+++++++|+++ |+++||++.||
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g-------------~pt~~~l~~~~~~el~~~------------i~~~G~~~~ka 55 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYG-------------FPTPEALAEASEEELREL------------IRPLGFSRRKA 55 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHS-------------CSSHHHHHCSHHHHHHHH------------HTTSTSHHHHH
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhc-------------CCCHHHHHhCCHHHHHHH------------hhccCCCHHHH
Confidence 6899999999999999999998 777 899999999999999986 55566777899
Q ss_pred HHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCC-ccccchHHHHHHHHcCCCcc
Q 020295 231 KYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH-AIPVDTHVWKIATRYLLPEL 309 (328)
Q Consensus 231 ~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d-~~PVDthv~Ri~~rl~~~~~ 309 (328)
+||+++|+.+. |+.+ ++|+|+|++|++.++|+...
T Consensus 56 ~~i~~~a~~~~--------------------------------------------~~~d~~~~~D~~v~r~~~r~~~~~~ 91 (108)
T PF00730_consen 56 KYIIELARAIL--------------------------------------------GRPDPFPPVDTHVRRVLQRLGGIPE 91 (108)
T ss_dssp HHHHHHHHHHH--------------------------------------------C-SSSS-TTSHHHHHHHHHHTSSSS
T ss_pred HHHHHHHHHhh--------------------------------------------hcccceecCcHHHHHHHHHHcCCCC
Confidence 99999999874 7766 78899999999999986542
Q ss_pred cCCCCCHHHHHHHH-HHh
Q 020295 310 AGVRLTPKLCSRVA-EAF 326 (328)
Q Consensus 310 ~~~~lt~k~y~~i~-e~~ 326 (328)
..+++...+.. +.|
T Consensus 92 ---~~~~~~~~~~~~e~~ 106 (108)
T PF00730_consen 92 ---KKTKEETEKKLEELW 106 (108)
T ss_dssp ---STTHHHHHHHHHHHG
T ss_pred ---CCCHHHHHHHHHhhC
Confidence 24555554444 555
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.52 E-value=6.7e-14 Score=124.07 Aligned_cols=144 Identities=25% Similarity=0.284 Sum_probs=112.7
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCHHHHHhc--CCCCCCCCccchhh
Q 020295 144 RQDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA--GFGYRSAPQSSLLF 221 (328)
Q Consensus 144 ~~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~--Glg~R~~~~~~li~ 221 (328)
..+.|..|.-||+.+|++...+.++.+.| |+ | +.-++.|||++. -+|||
T Consensus 36 ~e~lf~ELsFCILTANsSA~~~~~~q~~l---G~------g-----------fly~~~eEL~e~Lk~~g~R--------- 86 (210)
T COG1059 36 KEDLFKELSFCILTANSSATMGLRAQNEL---GD------G-----------FLYLSEEELREKLKEVGYR--------- 86 (210)
T ss_pred HHHHHHHHHHHhccccchHHHHHHHHHHh---cc------c-----------cccCCHHHHHHHHHHhcch---------
Confidence 47899999999999999998888877655 31 1 112345555441 23578
Q ss_pred hhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCH--HHHHHHhh-cCCCccHHHHHHHHHHhCCCCCccccchHHH
Q 020295 222 SVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDL--QEAIDALC-TLPGVGPKVAACIALFSLDQHHAIPVDTHVW 298 (328)
Q Consensus 222 ~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~--~ea~~~L~-~l~GIG~ktAd~vllf~lg~~d~~PVDthv~ 298 (328)
|++.||+||+.+-+.+- ++..+-..+. ..+++.|. .++|||.|-|+.+|. ..|..|+..+|.||.
T Consensus 87 ---f~n~raeyIVeaR~~~~--------~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLR-NVG~~D~AIlDrHIl 154 (210)
T COG1059 87 ---FYNVRAEYIVEAREKFD--------DLKIIVKADENEKVARELLVENIKGIGYKEASHFLR-NVGFEDLAILDRHIL 154 (210)
T ss_pred ---hcccchHHHHHHHHHHH--------HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHH-hcChhHHHHHHHHHH
Confidence 99999999999887764 2344444443 33999999 999999999999976 888888888999999
Q ss_pred HHHHHcCCCcccCCCCCHHHHHHHHHHhhC
Q 020295 299 KIATRYLLPELAGVRLTPKLCSRVAEAFCE 328 (328)
Q Consensus 299 Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~~ 328 (328)
|.+.+++.....++++|+|.|.++.+.+++
T Consensus 155 r~l~r~g~i~e~~kt~t~K~YLe~E~ilr~ 184 (210)
T COG1059 155 RWLVRYGLIDENPKTLTRKLYLEIEEILRS 184 (210)
T ss_pred HHHHHhcccccCcccccHHHHHHHHHHHHH
Confidence 999999887777789999999999988864
No 23
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.02 E-value=1e-09 Score=106.71 Aligned_cols=119 Identities=22% Similarity=0.359 Sum_probs=95.7
Q ss_pred CCHHHHHHHHHHhcccCHHHHHHHHHHHHhhCCCCCcccccccccCCCHHHHhcCCH-HHHHh--cCCCCCCCCccchhh
Q 020295 145 QDPVECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSE-VELRN--AGFGYRSAPQSSLLF 221 (328)
Q Consensus 145 ~dpfe~Lis~IlsQn~si~~a~~~~~~L~~~G~~~~~~~g~~~~~fPtpe~La~~~~-e~Lr~--~Glg~R~~~~~~li~ 221 (328)
+..||++|+.|+.||+.+..+.+-+.+ ....+||..+++.++- +++.+ +|+||-
T Consensus 123 rRaYeVwVSEiMLQQTrV~TV~~YYt~--------------WMqkwPTl~dla~Asl~~eVn~lWaGlGyY--------- 179 (555)
T KOG2457|consen 123 RRAYEVWVSEIMLQQTRVQTVMKYYTR--------------WMQKWPTLYDLAQASLEKEVNELWAGLGYY--------- 179 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHhCchHHHHHHHHHHHHHHHHHhhhhHH---------
Confidence 357999999999999987776653322 2457899999999985 56655 588864
Q ss_pred hhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhc-CCCccHHHHHHHHHHhCCCCCccccchHHHHH
Q 020295 222 SVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCT-LPGVGPKVAACIALFSLDQHHAIPVDTHVWKI 300 (328)
Q Consensus 222 ~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~-l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri 300 (328)
++++++.+.|+++.+..+| ..+..-+.|++ +||||++||..|+..+|+. ..=.||-+|.|+
T Consensus 180 ------~R~rrL~ega~~vv~~~~g-----------e~Prta~~l~kgvpGVG~YTAGAiaSIAf~q-~tGiVDGNVirv 241 (555)
T KOG2457|consen 180 ------RRARRLLEGAKMVVAGTEG-----------EFPRTASSLMKGVPGVGQYTAGAIASIAFNQ-VTGIVDGNVIRV 241 (555)
T ss_pred ------HHHHHHHHHHHHHHHhCCC-----------CCCChHHHHHhhCCCCCccchhhhhhhhhcC-cccccccchHHH
Confidence 5799999999999987655 34556667776 9999999999999999998 444689999999
Q ss_pred HHHc
Q 020295 301 ATRY 304 (328)
Q Consensus 301 ~~rl 304 (328)
+.|.
T Consensus 242 lsRa 245 (555)
T KOG2457|consen 242 LSRA 245 (555)
T ss_pred hHHh
Confidence 9885
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=97.85 E-value=1.4e-05 Score=51.17 Aligned_cols=24 Identities=46% Similarity=0.830 Sum_probs=20.1
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHH
Q 020295 260 QEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
+..+++|+++||||+|||+.|+.|
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHhC
Confidence 445789999999999999999875
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=96.78 E-value=0.0026 Score=53.12 Aligned_cols=75 Identities=17% Similarity=0.228 Sum_probs=46.6
Q ss_pred CceEEEeE--C--CeEEEEEEecC-CcEEEEEcCCC--ChHHHHHHHHHhhcCCCCHHHHHHHHhccChhHHHHHHHhcC
Q 020295 67 PLQYTGPI--G--PHLISLKHLQN-GDVCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAG 139 (328)
Q Consensus 67 ~~~~~g~~--g--~~~i~l~q~~~-~~l~~~~~~~~--~~~~~~~~l~~~f~Ld~dl~~~~~~~~~~D~~l~~l~~~~~G 139 (328)
++.|.-.+ + ..+++++..+. +.+.+++..+. ..+.+...++++||||.|...+.+.+ ||.++.+....+|
T Consensus 32 ~~~Y~Rt~~l~~~~g~v~v~~~~~~~~l~v~~~~~~~~~l~~~~~rvRrlfDLdaDp~~I~~~L---dp~l~p~~~~~pG 108 (116)
T PF06029_consen 32 DGSYRRTFRLGGGPGWVSVRHDPEKNHLRVTLSLSDLRDLPAVIARVRRLFDLDADPQAIEAHL---DPLLAPLVAARPG 108 (116)
T ss_dssp SSEEEEEEEETTEEEEEEEEEETTTTEEEEEE-GGGGGGHHHHHHHHHHHTTTT--HHHHHHHH-------GGGGTS-TT
T ss_pred CCeEEEEEEeCCeEEEEEEEEcCCCCEEEEEEEcccHHHHHHHHHHHHHHhCCCCCHHHHHHHH---hhcccccccCCCC
Confidence 44555443 2 45788888763 45777776533 34678899999999999999999999 8999999999999
Q ss_pred CccCC
Q 020295 140 ARVLR 144 (328)
Q Consensus 140 ~R~l~ 144 (328)
+|++.
T Consensus 109 LRlPG 113 (116)
T PF06029_consen 109 LRLPG 113 (116)
T ss_dssp -----
T ss_pred CcCCC
Confidence 99864
No 26
>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=95.60 E-value=0.64 Score=43.39 Aligned_cols=37 Identities=32% Similarity=0.481 Sum_probs=29.9
Q ss_pred ccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhhC
Q 020295 290 AIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFCE 328 (328)
Q Consensus 290 ~~PVDthv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~~ 328 (328)
++|+||||.|+++++|+.. .++-+-|...|+.+.+++
T Consensus 173 iiPLDtH~~rvar~LgL~~--Rk~~d~kaa~ElT~~Lr~ 209 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKLLK--RKSYDLKAAIEITEALRE 209 (229)
T ss_pred eeechHhHHHHHHHhCCcc--cCchhHHHHHHHHHHHHh
Confidence 4799999999999999764 456667888888888764
No 27
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=95.20 E-value=0.012 Score=36.04 Aligned_cols=20 Identities=40% Similarity=0.617 Sum_probs=17.4
Q ss_pred HhhcCCCccHHHHHHHHHHh
Q 020295 265 ALCTLPGVGPKVAACIALFS 284 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~ 284 (328)
.|++++|||+|+|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998643
No 28
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=95.14 E-value=1.6 Score=40.85 Aligned_cols=37 Identities=32% Similarity=0.428 Sum_probs=31.0
Q ss_pred ccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhhC
Q 020295 290 AIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFCE 328 (328)
Q Consensus 290 ~~PVDthv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~~ 328 (328)
++|+||||.|+++++|+.. .++-+-+.-.|+.+.+++
T Consensus 176 iiPLDtHv~~var~LGL~~--rk~~d~k~A~elT~~lr~ 212 (232)
T PF09674_consen 176 IIPLDTHVFRVARKLGLLK--RKSADWKAARELTEALRE 212 (232)
T ss_pred cccchHhHHHHHHHcCCcc--CCCccHHHHHHHHHHHHh
Confidence 4799999999999999864 566778888999888864
No 29
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=94.80 E-value=0.061 Score=40.03 Aligned_cols=41 Identities=32% Similarity=0.565 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 235 GTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 235 ~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
..|+.+.++|+ +++.+...+ .++|.+++|||+++|+.|.-|
T Consensus 14 ~~ak~L~~~f~----sl~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 14 KTAKLLAKHFG----SLEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHHCCS----CHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHHcC----CHHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 44566677664 477777665 457999999999999998765
No 30
>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=92.72 E-value=3.7 Score=36.94 Aligned_cols=135 Identities=7% Similarity=0.026 Sum_probs=89.5
Q ss_pred ccChhHHHHHHHhcCCccCC-CCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHH
Q 020295 125 ASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEV 202 (328)
Q Consensus 125 ~~D~~l~~l~~~~~G~R~l~-~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e 202 (328)
..||.+..-.+.--|..+-. +..||.|+-.+..+-.|+..|.+-...+. .|.. | +|+.+|..+++
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 SVDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSG------------F-DIVKVARMTDA 73 (179)
T ss_pred CCChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcC------------C-CHHHHhCCCHH
Confidence 34555544444444666643 78999999999999999999999888886 4532 1 79999999999
Q ss_pred HHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhh--------------------hCCC--HH
Q 020295 203 ELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSL--------------------RKLD--LQ 260 (328)
Q Consensus 203 ~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L--------------------~~~~--~~ 260 (328)
++..+--.. .+|+ ++.|.+.+++-|+++.+-... ++... ...+ ..
T Consensus 74 ~ie~L~~d~------~IIR----nr~KI~Avi~NA~~~l~i~~e---sf~~ylW~fv~~~Pi~~~~~~~~~~p~~t~~S~ 140 (179)
T TIGR00624 74 DVERLLQDD------GIIR----NRGKIEATIANARAALQLEQN---DLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESK 140 (179)
T ss_pred HHHHHhcCc------cchh----hHHHHHHHHHHHHHHHHHHHc---cHHHHHHhccCCCCccCCccccccCCCCCHHHH
Confidence 987742211 1333 457899999999888753211 22211 1111 34
Q ss_pred HHHHHhh--cCCCccHHHHHHHHHHhCC
Q 020295 261 EAIDALC--TLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 261 ea~~~L~--~l~GIG~ktAd~vllf~lg 286 (328)
.+-+.|. .++=|||-++..+|. +.|
T Consensus 141 ~lskdLKkrGfkFvGpt~~ysfmq-A~G 167 (179)
T TIGR00624 141 AMSKELKKRGFRFVGPTICYALMQ-ATG 167 (179)
T ss_pred HHHHHHHHcCCeecChHHHHHHHH-HHC
Confidence 4555665 478889988887765 555
No 31
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=92.26 E-value=3.8 Score=37.13 Aligned_cols=139 Identities=9% Similarity=0.033 Sum_probs=91.2
Q ss_pred hccChhHHHHHHHhcCCccCC-CCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCH
Q 020295 124 SASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSE 201 (328)
Q Consensus 124 ~~~D~~l~~l~~~~~G~R~l~-~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~ 201 (328)
...||.+..-.+.--|..+-. +..||.|+-....+-.|+..|.+-...++ .|.. | +|+.+|..++
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 VSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQ------------F-DPVKVAAMQE 73 (187)
T ss_pred CCCChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcC------------C-CHHHHhCCCH
Confidence 345565555455445666644 78999999999999999999999888887 4532 1 7899999999
Q ss_pred HHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhc-CCCch--hh----------------hhhhCCCH--H
Q 020295 202 VELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKH-SGGAE--WL----------------LSLRKLDL--Q 260 (328)
Q Consensus 202 e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~-~gg~~--~l----------------~~L~~~~~--~ 260 (328)
+++..+=-.. .+|+ ++.|.+.+++-|+.+.+-. .+|.+ .+ ..+...+. +
T Consensus 74 ~die~Ll~d~------~IIR----nr~KI~Avi~NA~~~l~i~~e~gSf~~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~ 143 (187)
T PRK10353 74 EDVERLVQDA------GIIR----HRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQVTQATTLSEIPTSTPASD 143 (187)
T ss_pred HHHHHHhcCc------hhHH----hHHHHHHHHHHHHHHHHHHHhcCCHHHHHhhccCCCcccCCccchhcCCCCCHHHH
Confidence 9987742111 1333 4689999999888876421 12221 11 11112222 2
Q ss_pred HHHHHhh--cCCCccHHHHHHHHHHhCC
Q 020295 261 EAIDALC--TLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 261 ea~~~L~--~l~GIG~ktAd~vllf~lg 286 (328)
.+-+.|. .++=|||-|+..+|. +.|
T Consensus 144 ~lskdLKkrGFkFvGpt~~ysfmq-A~G 170 (187)
T PRK10353 144 ALSKALKKRGFKFVGTTICYSFMQ-ACG 170 (187)
T ss_pred HHHHHHHHcCCcccCcHHHHHHHH-HHC
Confidence 4556665 488899999888776 555
No 32
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=90.75 E-value=0.19 Score=46.03 Aligned_cols=40 Identities=28% Similarity=0.262 Sum_probs=28.9
Q ss_pred hhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCC
Q 020295 250 WLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH 289 (328)
Q Consensus 250 ~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d 289 (328)
+.+.|...=..+..+.|+++||||.|||+-+++-=-++..
T Consensus 94 ~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~~ 133 (201)
T COG0632 94 DPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKLA 133 (201)
T ss_pred CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhhh
Confidence 4455554444556789999999999999999885555533
No 33
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.65 E-value=0.18 Score=45.38 Aligned_cols=28 Identities=32% Similarity=0.361 Sum_probs=21.9
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+..+.|+++||||+|||+-+++==-++
T Consensus 104 ~~D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 104 LGDESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 3456789999999999999998643333
No 34
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.62 E-value=0.19 Score=45.85 Aligned_cols=28 Identities=29% Similarity=0.412 Sum_probs=21.7
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+..+.|+++||||+|||+-+++==-++
T Consensus 103 ~~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 103 REDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 3446799999999999999998643333
No 35
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.14 E-value=0.22 Score=45.07 Aligned_cols=28 Identities=29% Similarity=0.498 Sum_probs=21.6
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+..+.|+++||||+|||+-+++==-++
T Consensus 104 ~~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 104 SQDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 3346789999999999999998643333
No 36
>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=89.59 E-value=0.58 Score=34.02 Aligned_cols=32 Identities=34% Similarity=0.488 Sum_probs=23.9
Q ss_pred CchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 247 GAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 247 g~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
|-.++++|...+ .+.|.+++|||+++|+-+..
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 35699999999999987764
No 37
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.57 E-value=0.26 Score=44.93 Aligned_cols=23 Identities=39% Similarity=0.495 Sum_probs=19.7
Q ss_pred HHHHHHhhcCCCccHHHHHHHHH
Q 020295 260 QEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vll 282 (328)
....+.|+++||||+|||+-+++
T Consensus 103 ~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 103 EGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHH
Confidence 34467899999999999999885
No 38
>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=89.13 E-value=2.7 Score=37.85 Aligned_cols=139 Identities=12% Similarity=0.100 Sum_probs=82.1
Q ss_pred ccChhHHHHHHHhcCCccCC-CCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHH
Q 020295 125 ASDCRFAELAKYLAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEV 202 (328)
Q Consensus 125 ~~D~~l~~l~~~~~G~R~l~-~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e 202 (328)
..||.+..-.+.--|..+.. +..||.|+-.+...-.|+..|.+-...+. .|-. | +|+.++..+++
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 NSDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAG------------F-DPEKVAKMDEE 69 (179)
T ss_dssp TSSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGG------------G-HHHHHHT--HH
T ss_pred CCChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHC------------C-CHHHHHcCCHH
Confidence 45666666666656776654 67999999999999999999998888776 3321 1 78999999999
Q ss_pred HHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHH---hcCCCchhhh----------------hhhCCC--HHH
Q 020295 203 ELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQS---KHSGGAEWLL----------------SLRKLD--LQE 261 (328)
Q Consensus 203 ~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~---~~~gg~~~l~----------------~L~~~~--~~e 261 (328)
++.++--..+ +|+ ++.|.+.++..|+.+.+ ++++=.-.+. .+...+ .+.
T Consensus 70 ~ie~l~~d~~------iIR----nr~KI~Avi~NA~~~l~i~~e~gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~ 139 (179)
T PF03352_consen 70 DIERLMQDPG------IIR----NRRKIRAVINNARAILKIQEEFGSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEA 139 (179)
T ss_dssp HHHHHTTSTT------SS------HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHH
T ss_pred HHHHHhcCcc------hhh----hHHHHHHHHHHHHHHHHHHHhcCCHHHHHHhcCCCcCccccccccccCcCccHHHHH
Confidence 9987522222 343 45899999999988763 2221000011 111111 234
Q ss_pred HHHHhh--cCCCccHHHHHHHHHHhCCC
Q 020295 262 AIDALC--TLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 262 a~~~L~--~l~GIG~ktAd~vllf~lg~ 287 (328)
..+.|. .++=|||-|+..+|. +.|-
T Consensus 140 isk~lkk~GF~FvGpt~vysflq-A~G~ 166 (179)
T PF03352_consen 140 ISKDLKKRGFKFVGPTTVYSFLQ-AIGM 166 (179)
T ss_dssp HHHHHHHTT--S--HHHHHHHHH-HTTS
T ss_pred HHHHHHhCcceeECHHHHHHHHH-HhCC
Confidence 455555 478899999988876 5553
No 39
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.83 E-value=0.29 Score=44.78 Aligned_cols=23 Identities=39% Similarity=0.517 Sum_probs=19.6
Q ss_pred HHHHHhhcCCCccHHHHHHHHHH
Q 020295 261 EAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf 283 (328)
...+.|+++||||+|||+-+++=
T Consensus 106 ~D~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 106 EDVAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred CCHHHHhcCCCcCHHHHHHHHHH
Confidence 34678999999999999999853
No 40
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.82 E-value=0.31 Score=44.32 Aligned_cols=28 Identities=29% Similarity=0.412 Sum_probs=21.7
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+..+.|+++||||+|||+-+++==-++
T Consensus 104 ~~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 104 GGDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred hCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 3446789999999999999988743333
No 41
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=88.20 E-value=0.75 Score=45.07 Aligned_cols=39 Identities=23% Similarity=0.284 Sum_probs=29.9
Q ss_pred Cchh-hhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 247 GAEW-LLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 247 g~~~-l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
|.+. +.....-+.+.+..+|++++|||||+|.-+-- +|-
T Consensus 71 G~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~--lGi 110 (334)
T smart00483 71 GKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR--KGI 110 (334)
T ss_pred CcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH--hCC
Confidence 5655 55555667899999999999999999976644 553
No 42
>PRK00076 recR recombination protein RecR; Reviewed
Probab=88.18 E-value=0.42 Score=43.56 Aligned_cols=31 Identities=39% Similarity=0.692 Sum_probs=27.2
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIALFSLDQH 288 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~ 288 (328)
+.+++.+.|.+|||||+|+|.=+.++-+.+.
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~ 35 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQRD 35 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 3578899999999999999999999888763
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=87.82 E-value=0.47 Score=43.23 Aligned_cols=30 Identities=37% Similarity=0.680 Sum_probs=26.7
Q ss_pred HHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 020295 259 LQEAIDALCTLPGVGPKVAACIALFSLDQH 288 (328)
Q Consensus 259 ~~ea~~~L~~l~GIG~ktAd~vllf~lg~~ 288 (328)
.+++.+.|.+|||||+|+|.=++++-+...
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~ 35 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKRD 35 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 578899999999999999999998888763
No 44
>PRK13844 recombination protein RecR; Provisional
Probab=87.61 E-value=0.48 Score=43.31 Aligned_cols=31 Identities=32% Similarity=0.603 Sum_probs=27.2
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIALFSLDQH 288 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~ 288 (328)
..+++.+.|.+|||||+|+|.=++++-+...
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~ 39 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALYLLDKS 39 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 3578899999999999999999999888763
No 45
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=87.35 E-value=0.5 Score=43.00 Aligned_cols=30 Identities=47% Similarity=0.729 Sum_probs=26.5
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
..+.+++.|.++||||+|+|.=++.+-+.+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~ 35 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR 35 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence 357789999999999999999998888876
No 46
>PRK00024 hypothetical protein; Reviewed
Probab=87.14 E-value=1.7 Score=40.33 Aligned_cols=43 Identities=26% Similarity=0.382 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHH
Q 020295 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 280 (328)
Q Consensus 230 A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~v 280 (328)
-+-...+|+.+.++|++ +..+...+. ++|++++|||+..|..+
T Consensus 40 ~~~~~~LA~~LL~~fgs----L~~l~~as~----~eL~~i~GIG~akA~~L 82 (224)
T PRK00024 40 GKSVLDLARELLQRFGS----LRGLLDASL----EELQSIKGIGPAKAAQL 82 (224)
T ss_pred CCCHHHHHHHHHHHcCC----HHHHHhCCH----HHHhhccCccHHHHHHH
Confidence 45566888888887753 676666664 46889999999887544
No 47
>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=87.08 E-value=0.44 Score=43.13 Aligned_cols=21 Identities=43% Similarity=0.661 Sum_probs=18.2
Q ss_pred HHHhhcCCCccHHHHHHHHHH
Q 020295 263 IDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 263 ~~~L~~l~GIG~ktAd~vllf 283 (328)
.+.|.++||||+|||+-|++-
T Consensus 106 ~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 106 VKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 467999999999999999853
No 48
>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=86.94 E-value=1.5 Score=32.75 Aligned_cols=41 Identities=20% Similarity=0.326 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHH
Q 020295 229 QAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 281 (328)
Q Consensus 229 KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vl 281 (328)
|+..-.++|..|.+. .. +.....+.|.+|||||+++|.-|-
T Consensus 24 r~~aY~~Aa~~i~~l-~~-----------~i~~~~~~~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 24 RARAYRRAAAAIKAL-PY-----------PITSGEEDLKKLPGIGKSIAKKID 64 (68)
T ss_dssp HHHHHHHHHHHHHHS-SS------------HHSHHHHHCTSTTTTHHHHHHHH
T ss_pred HHHHHHHHHHHHHhC-CH-----------hHhhHHHHHhhCCCCCHHHHHHHH
Confidence 377777888887652 11 222221259999999999998774
No 49
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.31 E-value=0.46 Score=43.11 Aligned_cols=21 Identities=43% Similarity=0.725 Sum_probs=17.8
Q ss_pred HHHHhhcCCCccHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vll 282 (328)
..+.|+++||||+|||+-+++
T Consensus 106 D~~~L~~vpGIGkKtAerIil 126 (194)
T PRK14605 106 NAELLSTIPGIGKKTASRIVL 126 (194)
T ss_pred CHHHHHhCCCCCHHHHHHHHH
Confidence 456799999999999999653
No 50
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.00 E-value=0.46 Score=42.91 Aligned_cols=21 Identities=29% Similarity=0.322 Sum_probs=17.8
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..+.| ++||||+|||+-+++=
T Consensus 106 D~~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 106 DKAAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred CHhhe-ECCCCcHHHHHHHHHH
Confidence 34688 9999999999999864
No 51
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=85.44 E-value=1.5 Score=47.05 Aligned_cols=83 Identities=24% Similarity=0.360 Sum_probs=50.7
Q ss_pred CCHHHHhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHH--HHHH---------HHHHHHHHhcCCCchhhhhhhCCC
Q 020295 191 PSLERLSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQA--KYIT---------GTVDVLQSKHSGGAEWLLSLRKLD 258 (328)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA--~~I~---------~~A~~i~~~~~gg~~~l~~L~~~~ 258 (328)
-++++|..+..++|..+ |||-+ -..+|+..+-..+... ++|. ..|+.+.++|+ +++.+...+
T Consensus 468 ~~i~DL~~L~~~~L~~l~gfG~K--sa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~----sl~~l~~As 541 (665)
T PRK07956 468 HDPADLFKLTAEDLLGLEGFGEK--SAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFG----SLEALRAAS 541 (665)
T ss_pred CCHHHHHhcCHHHHhcCcCcchH--HHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcC----CHHHHHhCC
Confidence 48888888888888875 77754 1134444443322211 2222 13334444442 355555544
Q ss_pred HHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 259 LQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 259 ~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
.++|.+++|||+++|..|.-|
T Consensus 542 ----~eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 542 ----EEELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred ----HHHHhccCCcCHHHHHHHHHH
Confidence 357999999999999999776
No 52
>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=85.23 E-value=1.1 Score=36.17 Aligned_cols=28 Identities=18% Similarity=0.459 Sum_probs=23.8
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+....|+.|||||+.+|.-+.+.|+..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCC
Confidence 4567899999999999999888777765
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=85.09 E-value=0.96 Score=32.85 Aligned_cols=25 Identities=32% Similarity=0.585 Sum_probs=20.4
Q ss_pred HHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 262 AIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
+.+.|++++|||+++|.-+.-.++.
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~ 27 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIK 27 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCS
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCC
Confidence 5678999999999999877765444
No 54
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.02 E-value=1.2 Score=41.25 Aligned_cols=49 Identities=18% Similarity=0.181 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHhcC--CCchhhhhhhCCCHHHHHHHhhcCCCccHH-HHHHHHHHhCCC
Q 020295 232 YITGTVDVLQSKHS--GGAEWLLSLRKLDLQEAIDALCTLPGVGPK-VAACIALFSLDQ 287 (328)
Q Consensus 232 ~I~~~A~~i~~~~~--gg~~~l~~L~~~~~~ea~~~L~~l~GIG~k-tAd~vllf~lg~ 287 (328)
-...+|+.+.++|. | +|..+...+. ++|++++|||+. .+...+.+-+++
T Consensus 33 ~~~~lA~~ll~~f~~~g---~l~~l~~a~~----~eL~~i~GiG~aka~~l~a~~El~r 84 (218)
T TIGR00608 33 DVLSLSKRLLDVFGRQD---SLGHLLSAPP----EELSSVPGIGEAKAIQLKAAVELAK 84 (218)
T ss_pred CHHHHHHHHHHHhcccC---CHHHHHhCCH----HHHHhCcCCcHHHHHHHHHHHHHHH
Confidence 67789999988772 2 3777766664 468899999994 445555555543
No 55
>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=82.91 E-value=1 Score=35.18 Aligned_cols=37 Identities=22% Similarity=0.327 Sum_probs=28.0
Q ss_pred HHhhcCCCccHHHHHHHHHHhCCCCCccccchHHHHHH
Q 020295 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIA 301 (328)
Q Consensus 264 ~~L~~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~ 301 (328)
+.|+++||||+-+|..++... +..+-|+-..++...+
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~~~~~l~~~~ 38 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFKSAKQLASYA 38 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhcccchhhhhcc
Confidence 468999999999999888865 6667787666654433
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=82.48 E-value=1.4 Score=39.70 Aligned_cols=22 Identities=41% Similarity=0.637 Sum_probs=18.8
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..+.|.++||||+|+|+-++..
T Consensus 106 d~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 106 DVKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred CHHHHHhCCCCCHHHHHHHHHH
Confidence 3557999999999999999864
No 57
>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=81.96 E-value=2.7 Score=40.65 Aligned_cols=36 Identities=33% Similarity=0.413 Sum_probs=28.0
Q ss_pred hhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 249 EWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 249 ~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
-.++.|..- .+....+|++++|||||+|.-+- .+|.
T Consensus 71 ~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~--~lGi 106 (307)
T cd00141 71 RKLEELRED-VPPGLLLLLRVPGVGPKTARKLY--ELGI 106 (307)
T ss_pred HHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH--HcCC
Confidence 346666655 78899999999999999998766 5554
No 58
>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=81.85 E-value=4.6 Score=43.25 Aligned_cols=83 Identities=28% Similarity=0.422 Sum_probs=47.2
Q ss_pred CCHHHHhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHH--HHHH---------HHHHHHHHhcCCCchhhhhhhCCC
Q 020295 191 PSLERLSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQA--KYIT---------GTVDVLQSKHSGGAEWLLSLRKLD 258 (328)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA--~~I~---------~~A~~i~~~~~gg~~~l~~L~~~~ 258 (328)
-++++|..+..++|.++ |+|-. -..+|+..+-..+... ++|. ..|+.+.++|+ +++.|...+
T Consensus 455 ~~~~Dl~~L~~~~L~~L~GfG~K--sa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~----sl~~l~~As 528 (652)
T TIGR00575 455 RSVADLYALKKEDLLELEGFGEK--SAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFG----TLDKLKAAS 528 (652)
T ss_pred CCHHHHHhcCHHHHhhccCccHH--HHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhC----CHHHHHhCC
Confidence 37888888888888875 77643 1123333332111110 1111 12333444432 355555544
Q ss_pred HHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 259 LQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 259 ~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
.++|.+++|||+++|..|.-|
T Consensus 529 ----~eeL~~i~GIG~~~A~~I~~f 549 (652)
T TIGR00575 529 ----LEELLSVEGVGPKVAESIVNF 549 (652)
T ss_pred ----HHHHhcCCCcCHHHHHHHHHH
Confidence 347999999999999999876
No 59
>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=79.90 E-value=1.7 Score=31.18 Aligned_cols=24 Identities=25% Similarity=0.295 Sum_probs=16.6
Q ss_pred HHHhhcCCCccHHHHHHHHHHhCC
Q 020295 263 IDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 263 ~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
++.++++.|||+.||.-..-.++.
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--
T ss_pred CcchhhcccccHHHHHHHHHhCCC
Confidence 357899999999999987765554
No 60
>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=78.73 E-value=1.4 Score=28.34 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=11.5
Q ss_pred hhcCCCccHHHHHHH
Q 020295 266 LCTLPGVGPKVAACI 280 (328)
Q Consensus 266 L~~l~GIG~ktAd~v 280 (328)
+..++|||++|+.-.
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 467999999999863
No 61
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=78.41 E-value=1.6 Score=40.90 Aligned_cols=37 Identities=32% Similarity=0.449 Sum_probs=31.5
Q ss_pred cccCCCHHHHhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHHHHHHHHHHH
Q 020295 187 FHEFPSLERLSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQAKYITGTVDV 239 (328)
Q Consensus 187 ~~~fPtpe~La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~ 239 (328)
...|++.+++..+++++|..| |+|.+ ||+.|++..++
T Consensus 212 L~~FgsLq~~~~AS~~ele~~~G~G~~----------------kak~l~~~l~~ 249 (254)
T KOG2841|consen 212 LQKFGSLQQISNASEGELEQCPGLGPA----------------KAKRLHKFLHQ 249 (254)
T ss_pred HHhcccHHHHHhcCHhHHHhCcCcCHH----------------HHHHHHHHHhc
Confidence 356889999999999999996 89876 89999987654
No 62
>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=77.54 E-value=2 Score=38.88 Aligned_cols=24 Identities=38% Similarity=0.596 Sum_probs=20.3
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIA 281 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vl 281 (328)
...+....|++++|||||+|-.+|
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL 89 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAIL 89 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHH
Confidence 345788899999999999997774
No 63
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=77.49 E-value=3.5 Score=44.31 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=19.2
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..++|++++|||+++|..+.-|
T Consensus 539 ~~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHH
Confidence 3467999999999999999876
No 64
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.31 E-value=2 Score=38.95 Aligned_cols=28 Identities=18% Similarity=0.485 Sum_probs=23.2
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
...+..+.|++++|||||+|-.|+- .++
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs-~~~ 94 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLS-AMN 94 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHH-hCC
Confidence 3457888999999999999998887 454
No 65
>PRK14973 DNA topoisomerase I; Provisional
Probab=76.32 E-value=14 Score=41.24 Aligned_cols=96 Identities=17% Similarity=0.170 Sum_probs=55.3
Q ss_pred cCCCHHHHhcCCHHHHHh-cCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhh
Q 020295 189 EFPSLERLSLVSEVELRN-AGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALC 267 (328)
Q Consensus 189 ~fPtpe~La~~~~e~Lr~-~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~ 267 (328)
.|-++++++.+++++|.. -|++ -..|.+.+..+.++. +..+-+.......+..+.+|.
T Consensus 822 G~~~~~d~~~a~p~~La~~~g~~-------------------~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~el~ 880 (936)
T PRK14973 822 GFDTPEDFCSVHPAYLALKTGIS-------------------PETICRHAKLVCEKL--GRPVPEKISKAAFERGRAELL 880 (936)
T ss_pred cCCCHHHHHhcCHHHHhcCCCCC-------------------hhhHHHHHHHHHHHh--cCCCchhhhhhhhcccchhhh
Confidence 588999999999999987 4774 344444433333111 112222222333444556699
Q ss_pred cCCCccHHHHHHHHHHhCCCCCccccchHHHHHHHHcCC
Q 020295 268 TLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLL 306 (328)
Q Consensus 268 ~l~GIG~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~~ 306 (328)
+++|||++|++-.-.-|.-..+.+-.+ -..+++..-++
T Consensus 881 ~vkg~ge~t~~~l~~ag~~~~e~l~~~-d~~~la~~~~i 918 (936)
T PRK14973 881 SVPGLGETTLEKLYLAGVYDGDLLVSA-DPKKLAKVTGI 918 (936)
T ss_pred hccCCCHHHHHHHHHcCCCCHHHhccC-CHHHHhhhcCC
Confidence 999999999976665444433333222 24444544444
No 66
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=76.26 E-value=5 Score=29.64 Aligned_cols=51 Identities=31% Similarity=0.461 Sum_probs=29.0
Q ss_pred hcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHH
Q 020295 197 SLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPK 275 (328)
Q Consensus 197 a~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~k 275 (328)
-.++.++|..+ |+|.. .|+.|++--+.. |+-. ..++|..++|||++
T Consensus 9 N~as~~eL~~lpgi~~~----------------~A~~Iv~~R~~~-----G~f~------------s~~dL~~v~gi~~~ 55 (65)
T PF12836_consen 9 NTASAEELQALPGIGPK----------------QAKAIVEYREKN-----GPFK------------SLEDLKEVPGIGPK 55 (65)
T ss_dssp TTS-HHHHHTSTT--HH----------------HHHHHHHHHHHH------S-S------------SGGGGGGSTT--HH
T ss_pred ccCCHHHHHHcCCCCHH----------------HHHHHHHHHHhC-----cCCC------------CHHHHhhCCCCCHH
Confidence 35678889887 88743 566666544332 2111 24588999999999
Q ss_pred HHHHH
Q 020295 276 VAACI 280 (328)
Q Consensus 276 tAd~v 280 (328)
+.+-+
T Consensus 56 ~~~~l 60 (65)
T PF12836_consen 56 TYEKL 60 (65)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 98755
No 67
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=75.85 E-value=2.3 Score=38.32 Aligned_cols=23 Identities=39% Similarity=0.603 Sum_probs=19.0
Q ss_pred HHHHHHhhcCCCccHHHHHHHHH
Q 020295 260 QEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vll 282 (328)
.+....|..+||||||+|..++-
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHH
Confidence 34577899999999999988854
No 68
>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=75.59 E-value=1.1 Score=42.14 Aligned_cols=78 Identities=21% Similarity=0.145 Sum_probs=49.3
Q ss_pred cchHHHHHHHHHHHHHHHhcCCCchhhhhhhC--CCHHHHHHHhhcCCCcc---------HHHHHHHHHHhCCCC-----
Q 020295 225 RSFKQAKYITGTVDVLQSKHSGGAEWLLSLRK--LDLQEAIDALCTLPGVG---------PKVAACIALFSLDQH----- 288 (328)
Q Consensus 225 ~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~--~~~~ea~~~L~~l~GIG---------~ktAd~vllf~lg~~----- 288 (328)
+.++|.++|.++...+.+ +++.+... -+.+..++.|..+-|-. -|.+.+.+..++|..
T Consensus 92 ~~~~KikRl~k~~~~~~~------l~l~~~~~~y~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya~r~~~g~~~~~p~ 165 (246)
T PF09171_consen 92 LLEQKIKRLRKFCPFLEN------LSLQDNPLYYEDLEELWRELAKILNSKPESKTIVFAVKMFGYACRIAFGEFRPYPE 165 (246)
T ss_dssp THHHHHHHHHHHCCHHHT------T-HHHHHHHHCTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHCTS-----T
T ss_pred HHHHHHHHHHHHHHHHHH------hhhhhhhhhhhhHHHHHHHHHHHhCCCCccchhhHHHHHHHHHHHHhcCCCCCCcc
Confidence 567899999988776543 23333332 56778888888766655 366677777776651
Q ss_pred Cc-cccchHHHHHHHHcCCCc
Q 020295 289 HA-IPVDTHVWKIATRYLLPE 308 (328)
Q Consensus 289 d~-~PVDthv~Ri~~rl~~~~ 308 (328)
++ +|||.||.++..+.|+.+
T Consensus 166 ~IpIPvD~Rva~~T~~sGi~~ 186 (246)
T PF09171_consen 166 EIPIPVDYRVAKLTKRSGIIE 186 (246)
T ss_dssp TS-----HHHHHHHHCTTS-S
T ss_pred cCCCCccHHHHHHHHHhcccc
Confidence 11 578999999999988754
No 69
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=75.12 E-value=5.9 Score=36.88 Aligned_cols=40 Identities=20% Similarity=0.316 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHH
Q 020295 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVA 277 (328)
Q Consensus 230 A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktA 277 (328)
-+-.+.+|+.+.++|++ |..|.+.+ .++|++++|||+-.|
T Consensus 40 ~~~~~~la~~lL~~fg~----L~~l~~a~----~~el~~v~GiG~aka 79 (224)
T COG2003 40 GESVLDLAKELLQEFGS----LAELLKAS----VEELSSVKGIGLAKA 79 (224)
T ss_pred CCCHHHHHHHHHHHccc----HHHHHhCC----HHHHhhCCCccHHHH
Confidence 45677999999998864 66666555 568999999996554
No 70
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=74.26 E-value=3.9 Score=34.96 Aligned_cols=50 Identities=18% Similarity=0.259 Sum_probs=33.9
Q ss_pred HhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccH
Q 020295 196 LSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGP 274 (328)
Q Consensus 196 La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ 274 (328)
|-.++.++|+.+ |+|. .||+.|+. +| . + ...++|.++||||+
T Consensus 55 iN~A~~~el~~lpGigP----------------~~A~~IV~---------nG-p--f---------~sveDL~~V~GIge 97 (132)
T PRK02515 55 LNNSSVRAFRQFPGMYP----------------TLAGKIVK---------NA-P--Y---------DSVEDVLNLPGLSE 97 (132)
T ss_pred CCccCHHHHHHCCCCCH----------------HHHHHHHH---------CC-C--C---------CCHHHHHcCCCCCH
Confidence 455678888874 7754 47887772 12 1 1 23568899999999
Q ss_pred HHHHHHHH
Q 020295 275 KVAACIAL 282 (328)
Q Consensus 275 ktAd~vll 282 (328)
++.+.+--
T Consensus 98 kqk~~l~k 105 (132)
T PRK02515 98 RQKELLEA 105 (132)
T ss_pred HHHHHHHH
Confidence 98776654
No 71
>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=73.98 E-value=6.1 Score=33.02 Aligned_cols=58 Identities=24% Similarity=0.365 Sum_probs=36.4
Q ss_pred HHHHhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCC
Q 020295 193 LERLSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPG 271 (328)
Q Consensus 193 pe~La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~G 271 (328)
+-+|-.++.++|..+ |+|.. +|+.|++--.. + |. + ...++|.+++|
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~----------------~A~~Ii~~R~~----~-g~---f---------~s~eeL~~V~G 105 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPA----------------KAKAIIEYREE----N-GA---F---------KSVDDLTKVSG 105 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHH----------------HHHHHHHHHHh----c-CC---c---------CCHHHHHcCCC
Confidence 334556778888774 77742 56666543322 1 21 1 23578899999
Q ss_pred ccHHHHHHHHHH
Q 020295 272 VGPKVAACIALF 283 (328)
Q Consensus 272 IG~ktAd~vllf 283 (328)
||+++++-+.-|
T Consensus 106 Ig~k~~~~i~~~ 117 (120)
T TIGR01259 106 IGEKSLEKLKDY 117 (120)
T ss_pred CCHHHHHHHHhc
Confidence 999999877543
No 72
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=73.80 E-value=11 Score=40.56 Aligned_cols=81 Identities=25% Similarity=0.338 Sum_probs=47.3
Q ss_pred CCHHHHhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHH----HHHH---------HHHHHHHHhcCCCchhhhhhhC
Q 020295 191 PSLERLSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQA----KYIT---------GTVDVLQSKHSGGAEWLLSLRK 256 (328)
Q Consensus 191 Ptpe~La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA----~~I~---------~~A~~i~~~~~gg~~~l~~L~~ 256 (328)
-++.+|-.+..++|..+ |+|.. ...+|+..+- .+|. ++|. ..|+.+..+|+ +++.|..
T Consensus 485 ~~~~Dl~~L~~~~L~~l~g~g~K--sa~~Ll~~Ie--~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~----si~~L~~ 556 (689)
T PRK14351 485 ESLADLYDLTVADLAELEGWGET--SAENLLAELE--ASREPPLADFLVALGIPEVGPTTARNLAREFG----TFEAIMD 556 (689)
T ss_pred CCHHHHHHcCHHHHhcCcCcchh--HHHHHHHHHH--HHccCCHHHHHHHcCCCCcCHHHHHHHHHHhC----CHHHHHh
Confidence 47788888888888765 77754 1123333331 0110 1111 23344444443 2555655
Q ss_pred CCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 257 LDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 257 ~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
.+ .++|.+++|||+++|+.|.-|
T Consensus 557 As----~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 557 AD----EEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred CC----HHHHhccCCcCHHHHHHHHHH
Confidence 54 356899999999999998765
No 73
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=73.02 E-value=3.6 Score=30.38 Aligned_cols=22 Identities=41% Similarity=0.777 Sum_probs=16.9
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..++|.++||||++.|..|+-+
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHH
Confidence 4668999999999999999876
No 74
>PRK08609 hypothetical protein; Provisional
Probab=72.90 E-value=5.7 Score=41.82 Aligned_cols=32 Identities=34% Similarity=0.481 Sum_probs=23.8
Q ss_pred hhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHH
Q 020295 249 EWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 281 (328)
Q Consensus 249 ~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vl 281 (328)
--++.|+. +.++...+|+++||||||+|.-+-
T Consensus 74 ~~le~l~~-~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 74 SVLQELKK-EVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred HHHHHHHh-hCcHHHHHHhcCCCCCHHHHHHHH
Confidence 34667776 356566689999999999997553
No 75
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=72.77 E-value=19 Score=32.69 Aligned_cols=79 Identities=15% Similarity=0.142 Sum_probs=60.7
Q ss_pred hcCCccCC-CCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHHhc----CCC
Q 020295 137 LAGARVLR-QDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA----GFG 210 (328)
Q Consensus 137 ~~G~R~l~-~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~----Glg 210 (328)
--|.++.. +..||.|+-.+..+-.|+..|-+-.+... .| +.| +|+.+|..+++++..+ |+
T Consensus 21 eWG~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF------------~~F-d~~kVA~~~~~dverLl~d~gI- 86 (188)
T COG2818 21 EWGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAF------------HGF-DPEKVAAMTEEDVERLLADAGI- 86 (188)
T ss_pred ccCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHH------------hcC-CHHHHHcCCHHHHHHHHhCcch-
Confidence 34777765 57999999999999999999988887776 32 222 7999999999888663 54
Q ss_pred CCCCCccchhhhhhcchHHHHHHHHHHHHHHH
Q 020295 211 YRSAPQSSLLFSVRRSFKQAKYITGTVDVLQS 242 (328)
Q Consensus 211 ~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~ 242 (328)
-| ++.|.+.++..|+++.+
T Consensus 87 IR-------------~r~KI~A~i~NA~~~l~ 105 (188)
T COG2818 87 IR-------------NRGKIKATINNARAVLE 105 (188)
T ss_pred hh-------------hHHHHHHHHHHHHHHHH
Confidence 33 55789999988888653
No 76
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=72.63 E-value=47 Score=31.60 Aligned_cols=133 Identities=15% Similarity=0.119 Sum_probs=66.7
Q ss_pred HHHHHHHHHhcccCHHHHHHHHHHHHhhC-CCCCccccc-ccccCC--CHHHHhcCCHHHHHhcCCCCCCCCccchhhhh
Q 020295 148 VECLLQFLCSSNNNIARITKMVDFLASLG-SHLGNVEGF-EFHEFP--SLERLSLVSEVELRNAGFGYRSAPQSSLLFSV 223 (328)
Q Consensus 148 fe~Lis~IlsQn~si~~a~~~~~~L~~~G-~~~~~~~g~-~~~~fP--tpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v 223 (328)
..-+|++|+.- +......+|+++| .++--+.|. .+...+ .|+++..+-....-..|+ + +|+.-
T Consensus 75 ~~Dfv~Si~dg-----RlfeQ~~rL~~~y~rpvliVegd~~~~~~~~i~~~av~~al~s~~vdfg~--~------vi~t~ 141 (254)
T COG1948 75 ISDFVSSIIDG-----RLFEQAKRLKKSYERPVLIVEGDDSFSRRPKIHPNAVRGALASLAVDFGL--P------VIWTR 141 (254)
T ss_pred HHHHHHHHhcc-----hHHHHHHHHHhcCCccEEEEEcccccccccccCHHHHHHHHHHHHhhcCc--e------EEEeC
Confidence 45566666654 4444456677433 333223333 344433 566665432222222333 2 11111
Q ss_pred hcchHHHHHHHHHHHHHHHhcCCCchhhhhhh-CCCHHHHHH-HhhcCCCccHHHHHHHHHHhCCCCCccccch
Q 020295 224 RRSFKQAKYITGTVDVLQSKHSGGAEWLLSLR-KLDLQEAID-ALCTLPGVGPKVAACIALFSLDQHHAIPVDT 295 (328)
Q Consensus 224 ~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~-~~~~~ea~~-~L~~l~GIG~ktAd~vllf~lg~~d~~PVDt 295 (328)
=...-|..|+.+|+....+-.. ........ ..++.+... .|.++||||++.|.-++..-...-+++=++.
T Consensus 142 -~~~~Ta~~i~~la~req~e~~r-~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~ 213 (254)
T COG1948 142 -SPEETAELIHELARREQEERKR-SVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASE 213 (254)
T ss_pred -CHHHHHHHHHHHHHHHHHhccc-cccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH
Confidence 0123578888888887742111 11111111 245555544 4558999999999988764333334444444
No 77
>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=70.09 E-value=4.2 Score=34.00 Aligned_cols=22 Identities=36% Similarity=0.761 Sum_probs=19.3
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..++|+++||||++.|.-|+-+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 3568899999999999999876
No 78
>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=70.09 E-value=17 Score=29.64 Aligned_cols=26 Identities=27% Similarity=0.222 Sum_probs=21.3
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 261 EAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+.-.|++|.|||+.+|..||.. +|-
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~-lgi 37 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKK-LGI 37 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHH-TTS
T ss_pred chHhHHhhhhccCHHHHHHHHHH-cCC
Confidence 36778999999999999988773 554
No 79
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=68.99 E-value=3.9 Score=35.57 Aligned_cols=23 Identities=39% Similarity=0.654 Sum_probs=19.3
Q ss_pred HHHhhcCCCccHHHHHHHHHHhC
Q 020295 263 IDALCTLPGVGPKVAACIALFSL 285 (328)
Q Consensus 263 ~~~L~~l~GIG~ktAd~vllf~l 285 (328)
.++|..+||||++.|..|.-+--
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yRe 118 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYRE 118 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Confidence 45669999999999999988753
No 80
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=67.48 E-value=4.1 Score=26.93 Aligned_cols=16 Identities=31% Similarity=0.561 Sum_probs=12.9
Q ss_pred hhcCCCccHHHHHHHH
Q 020295 266 LCTLPGVGPKVAACIA 281 (328)
Q Consensus 266 L~~l~GIG~ktAd~vl 281 (328)
+-.+||||+|+|--++
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 3578999999997654
No 81
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=66.38 E-value=4.7 Score=34.49 Aligned_cols=20 Identities=30% Similarity=0.507 Sum_probs=17.4
Q ss_pred HHHhhcCCCccHHHHHHHHH
Q 020295 263 IDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 263 ~~~L~~l~GIG~ktAd~vll 282 (328)
.++|+++|||||..|..|.-
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45688999999999999984
No 82
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.30 E-value=5.2 Score=36.51 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=21.3
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
..-+..+.|+++.|||||+|=.||.
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3456888999999999999988874
No 83
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.79 E-value=5.3 Score=35.99 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=21.3
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
...+..+.|+++.|||||+|=.||.
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 4467889999999999999988874
No 84
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.25 E-value=5.5 Score=35.98 Aligned_cols=24 Identities=29% Similarity=0.337 Sum_probs=20.8
Q ss_pred HHHHHHHhhcCCCccHHHHHHHHH
Q 020295 259 LQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 259 ~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
.-+..+.|+++.|||||+|=.+|.
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHc
Confidence 456888999999999999988876
No 85
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=63.61 E-value=6.2 Score=35.66 Aligned_cols=25 Identities=28% Similarity=0.310 Sum_probs=21.2
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
...+..+.|+++.|||||+|=.+|.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 4467889999999999999988774
No 86
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=62.83 E-value=25 Score=37.07 Aligned_cols=29 Identities=24% Similarity=0.282 Sum_probs=22.5
Q ss_pred hhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 251 LLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 251 l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
++.|...+. ++|++++|||+++|+.+.-|
T Consensus 511 i~~l~~a~~----e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 511 WQQLLSRSE----QQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHHHcCCH----HHHhcCCCchHHHHHHHHHH
Confidence 455544443 57999999999999999876
No 87
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=62.78 E-value=14 Score=32.51 Aligned_cols=26 Identities=19% Similarity=0.303 Sum_probs=20.4
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
..+.-.|+.|.|||+.+|..||- .+|
T Consensus 26 K~v~~aLt~I~GIG~~~A~~I~~-~lg 51 (154)
T PTZ00134 26 RKVPYALTAIKGIGRRFAYLVCK-KAG 51 (154)
T ss_pred CEEEEeecccccccHHHHHHHHH-HcC
Confidence 34556899999999999998876 344
No 88
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.57 E-value=6.6 Score=35.73 Aligned_cols=25 Identities=36% Similarity=0.533 Sum_probs=21.3
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
...+..+.|+++.|||||+|=.+|.
T Consensus 66 ~Er~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 66 DSLELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3456788999999999999988876
No 89
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.21 E-value=6.7 Score=35.67 Aligned_cols=25 Identities=28% Similarity=0.441 Sum_probs=21.3
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
...+....|+++.|||||+|=.+|.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3456888999999999999988875
No 90
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.26 E-value=7.2 Score=35.63 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=21.4
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
...+....|+++.|||||+|=.+|.
T Consensus 68 ~Er~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 68 DERQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHh
Confidence 3456888999999999999988876
No 91
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=59.77 E-value=17 Score=36.09 Aligned_cols=25 Identities=28% Similarity=0.679 Sum_probs=19.8
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHh
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFS 284 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~ 284 (328)
++..++|.-+|||||+|+-...+.+
T Consensus 274 p~Df~elLl~~GiGpstvRALalVA 298 (373)
T COG1415 274 PDDFEELLLVPGIGPSTVRALALVA 298 (373)
T ss_pred cccHHHHHhccCCCHHHHHHHHHHH
Confidence 4457788899999999988776643
No 92
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=59.61 E-value=16 Score=31.93 Aligned_cols=25 Identities=32% Similarity=0.400 Sum_probs=19.8
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 261 EAIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
.+.-.|+.|.|||+.+|..||- -+|
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~-~lg 46 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIAR-KLG 46 (149)
T ss_pred EEeeeccccccccHHHHHHHHH-HcC
Confidence 3556899999999999998865 344
No 93
>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=58.87 E-value=5.4 Score=30.45 Aligned_cols=22 Identities=27% Similarity=0.504 Sum_probs=17.1
Q ss_pred HhhcCCCccHHHHHHHHHHhCCC
Q 020295 265 ALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+..+||||+|+|.-++. -++.
T Consensus 23 ~i~gv~giG~k~A~~ll~-~~~~ 44 (75)
T cd00080 23 NIPGVPGIGPKTALKLLK-EYGS 44 (75)
T ss_pred cCCCCCcccHHHHHHHHH-HhCC
Confidence 566899999999988875 3443
No 94
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=58.74 E-value=16 Score=36.39 Aligned_cols=38 Identities=24% Similarity=0.338 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHH
Q 020295 235 GTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACI 280 (328)
Q Consensus 235 ~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~v 280 (328)
.+|+.+.++|++ |..+-+.+ .++|.+++|||++.|..|
T Consensus 298 ~iAk~Ll~~FGS----L~~Il~As----~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 298 AVIENLVEHFGS----LQGLLAAS----IEDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHHHHcCC----HHHHHcCC----HHHHhhCCCcCHHHHHHH
Confidence 678888888864 77766655 456999999999999873
No 95
>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=57.12 E-value=16 Score=31.74 Aligned_cols=25 Identities=32% Similarity=0.401 Sum_probs=19.5
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 261 EAIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
.+.-.|+.|.|||++.|..||- -+|
T Consensus 18 ~v~~aLt~I~GIG~~~a~~I~~-~lg 42 (144)
T TIGR03629 18 PVEYALTGIKGIGRRFARAIAR-KLG 42 (144)
T ss_pred EEEEeecceeccCHHHHHHHHH-HcC
Confidence 3455789999999999998865 344
No 96
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=57.00 E-value=18 Score=35.51 Aligned_cols=42 Identities=26% Similarity=0.417 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHH--hhcCCCccHHHHHHHHHH
Q 020295 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDA--LCTLPGVGPKVAACIALF 283 (328)
Q Consensus 230 A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~--L~~l~GIG~ktAd~vllf 283 (328)
+..-..+|+.+.+. +-+.+++.+. ++.|||||+.+|+.|.-|
T Consensus 29 ~~aYr~Aa~sle~~------------~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~ 72 (326)
T COG1796 29 IRAYRKAAQSLENL------------TEDLEEIEERGRLTELPGIGKGIAEKISEY 72 (326)
T ss_pred hHHHHHHHHhhhhc------------ccchHHHHhhcccCCCCCccHHHHHHHHHH
Confidence 66666777777541 1256666666 999999999999998765
No 97
>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=56.82 E-value=19 Score=26.89 Aligned_cols=31 Identities=23% Similarity=0.204 Sum_probs=22.3
Q ss_pred CchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHH
Q 020295 247 GAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 281 (328)
Q Consensus 247 g~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vl 281 (328)
|.-.+.+|..++. +.|++++|+|+++.+-|.
T Consensus 31 ~I~tv~dL~~~s~----~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 31 GIHTVGDLVKYSE----EDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp T--BHHHHHCS-H----HHHHTSTTSHHHHHHHHH
T ss_pred CCcCHHHHHhCCH----HHHHhCCCCCHhHHHHHH
Confidence 4556777777754 579999999999998663
No 98
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=54.27 E-value=18 Score=35.40 Aligned_cols=42 Identities=29% Similarity=0.384 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 229 QAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 229 KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
|+.+..++|..|... . .++.. .++|.+|||||.++|+-|-=+
T Consensus 26 k~~ay~~Aa~~i~~l-~---~~i~~---------~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 26 KCSYFRKAASVLKSL-P---FPINS---------MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHHHHHHhC-C---CCCCC---------HHHHhcCCCccHHHHHHHHHH
Confidence 577788888877652 1 12221 237889999999999987643
No 99
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=53.91 E-value=18 Score=31.45 Aligned_cols=51 Identities=27% Similarity=0.460 Sum_probs=33.6
Q ss_pred cCCHHHHHhc-CCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHH
Q 020295 198 LVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKV 276 (328)
Q Consensus 198 ~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~kt 276 (328)
.++.++|+.+ |+|- .||+.|++-- ++++ . + ...+.|...+|||+++
T Consensus 93 tAs~eeL~~lpgIG~----------------~kA~aIi~yR----e~~G--~--f---------~sv~dL~~v~GiG~~~ 139 (149)
T COG1555 93 TASAEELQALPGIGP----------------KKAQAIIDYR----EENG--P--F---------KSVDDLAKVKGIGPKT 139 (149)
T ss_pred ccCHHHHHHCCCCCH----------------HHHHHHHHHH----HHcC--C--C---------CcHHHHHhccCCCHHH
Confidence 4678889775 6773 4677776433 3222 1 1 2466899999999999
Q ss_pred HHHHH
Q 020295 277 AACIA 281 (328)
Q Consensus 277 Ad~vl 281 (328)
-+-..
T Consensus 140 ~ekl~ 144 (149)
T COG1555 140 LEKLK 144 (149)
T ss_pred HHHHH
Confidence 87543
No 100
>PRK07758 hypothetical protein; Provisional
Probab=53.22 E-value=24 Score=28.57 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=23.3
Q ss_pred CchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHH
Q 020295 247 GAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 281 (328)
Q Consensus 247 g~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vl 281 (328)
|.-.+.+|..++ .++|.+|+|+|+|+.+-|-
T Consensus 54 GI~TL~dLv~~t----e~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 54 GIHTVEELSKYS----EKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCCcHHHHHcCC----HHHHHHccCCCHHHHHHHH
Confidence 455677776665 4579999999999988653
No 101
>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=52.25 E-value=15 Score=27.23 Aligned_cols=21 Identities=33% Similarity=0.493 Sum_probs=17.7
Q ss_pred HHHhhc-CCCccHHHHHHHHHH
Q 020295 263 IDALCT-LPGVGPKVAACIALF 283 (328)
Q Consensus 263 ~~~L~~-l~GIG~ktAd~vllf 283 (328)
.+.|.. +||||+++|..++-+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 347777 999999999998876
No 102
>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=51.82 E-value=19 Score=34.90 Aligned_cols=41 Identities=24% Similarity=0.343 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 230 A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
+....++|..+.+- . ..+. ..+++.+|||||+++|+.|-=+
T Consensus 24 ~~aY~~Aa~~l~~l-~---~~i~---------~~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 24 VRAYRKAARALESL-P---EPIE---------SLEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HHHHHHHHHHHHhC-C---cccC---------CHHHhcCCCCccHHHHHHHHHH
Confidence 77777888777641 1 1222 1236699999999999988655
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=50.63 E-value=16 Score=27.06 Aligned_cols=22 Identities=18% Similarity=0.398 Sum_probs=18.7
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..++|.+++|||.++|+-+.-+
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4668899999999999988765
No 104
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=49.73 E-value=14 Score=33.87 Aligned_cols=25 Identities=32% Similarity=0.533 Sum_probs=20.9
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
+..+....|+++.|||||+|=.||.
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs 91 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILS 91 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHc
Confidence 3456788999999999999977765
No 105
>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=49.64 E-value=24 Score=38.22 Aligned_cols=29 Identities=24% Similarity=0.406 Sum_probs=18.4
Q ss_pred CHHHHHHHhhc--CCCccHHHHHHHHHHhCCC
Q 020295 258 DLQEAIDALCT--LPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 258 ~~~ea~~~L~~--l~GIG~ktAd~vllf~lg~ 287 (328)
+.+.+...|.+ +||||+++|.-+.- .||.
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~-~fg~ 106 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVK-TFGE 106 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHH-HhCH
Confidence 44566666664 78888888876653 3443
No 106
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=48.80 E-value=32 Score=33.80 Aligned_cols=74 Identities=16% Similarity=0.153 Sum_probs=50.0
Q ss_pred hhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccc--ch--HHHHHHHHcCCCcccCCCCCHHHHHHHHHH
Q 020295 250 WLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPV--DT--HVWKIATRYLLPELAGVRLTPKLCSRVAEA 325 (328)
Q Consensus 250 ~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~~PV--Dt--hv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~ 325 (328)
-++..++-+.....+.++++-|||.++|+..-..++.-.+.+-= |. +..++--.+|- + =-+++|..+..++.+.
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 ELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYE-D-FLKRVTREEATAIQQT 160 (353)
T ss_pred hHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHH-H-HhhhccHHHHHHHHHH
Confidence 46666666778889999999999999999999988875444431 22 23333333442 1 1367888887777654
No 107
>PRK07945 hypothetical protein; Provisional
Probab=46.49 E-value=26 Score=34.34 Aligned_cols=43 Identities=28% Similarity=0.417 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHH--HhhcCCCccHHHHHHHHHH
Q 020295 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAID--ALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 230 A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~--~L~~l~GIG~ktAd~vllf 283 (328)
++...++|+.|... ..+ . .++... .|++|||||.-+|..|.=+
T Consensus 24 v~ayr~aa~~~~~~----~~~--~-----~~~~~~~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 24 VRAFRRAADVVEAL----DAA--E-----RARRARAGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred HHHHHHHHHHHHhc----Chh--H-----HHHHHhcCCcccCCCcCHHHHHHHHHH
Confidence 78888888887641 111 0 122222 6999999999999987654
No 108
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=44.95 E-value=12 Score=31.65 Aligned_cols=26 Identities=23% Similarity=0.075 Sum_probs=20.8
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 261 EAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+.-.|+.|.|||+.+|..||-. +|-
T Consensus 14 ~v~~aLt~i~GIG~~~A~~ic~~-lgi 39 (122)
T CHL00137 14 RIEYALTYIYGIGLTSAKEILEK-ANI 39 (122)
T ss_pred EeeeeecccccccHHHHHHHHHH-cCc
Confidence 34567899999999999988874 554
No 109
>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=44.14 E-value=5 Score=32.73 Aligned_cols=25 Identities=32% Similarity=0.531 Sum_probs=15.0
Q ss_pred hhcCCCccHHHHHHHHHHhCCCCCcc
Q 020295 266 LCTLPGVGPKVAACIALFSLDQHHAI 291 (328)
Q Consensus 266 L~~l~GIG~ktAd~vllf~lg~~d~~ 291 (328)
+-.+||||+|||.-++- -+|-.+.+
T Consensus 20 IPGV~GIG~KtA~~LL~-~ygsle~i 44 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQ-EYGSLENI 44 (101)
T ss_dssp B---TTSTCHCCCCCHH-HHTSCHCC
T ss_pred CCCCCCCCHHHHHHHHH-HcCCHHHH
Confidence 45689999999976655 45544443
No 110
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=40.85 E-value=36 Score=32.37 Aligned_cols=40 Identities=23% Similarity=0.263 Sum_probs=27.4
Q ss_pred HHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 236 TVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 236 ~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
.|..+..+|++ +..+...+. ++|+.++|||.+.|.-|--|
T Consensus 194 ~a~~ll~~fgS----~~~~~tas~----~eL~~v~gig~k~A~~I~~~ 233 (254)
T COG1948 194 LAERLLKKFGS----VEDVLTASE----EELMKVKGIGEKKAREIYRF 233 (254)
T ss_pred HHHHHHHHhcC----HHHHhhcCH----HHHHHhcCccHHHHHHHHHH
Confidence 44555555543 444444444 79999999999999877543
No 111
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=40.18 E-value=16 Score=37.67 Aligned_cols=18 Identities=50% Similarity=0.995 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCCcccccc
Q 020295 15 RLTPQPPPTPPNPQTLTT 32 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~ 32 (328)
..||||||+||.|.+-|+
T Consensus 13 ~~~~~~~~~~~~~~~~~~ 30 (461)
T PLN03132 13 AATPQPPPPPPPPEKTHF 30 (461)
T ss_pred cCCCCCcccCCCCcccCC
Confidence 357777766665555443
No 112
>PF13592 HTH_33: Winged helix-turn helix
Probab=39.45 E-value=20 Score=25.93 Aligned_cols=54 Identities=17% Similarity=0.084 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhCCCCCccccchHHHHHHHHcCCCcccCCCCCHHHHHHHHHHhh
Q 020295 274 PKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFC 327 (328)
Q Consensus 274 ~ktAd~vllf~lg~~d~~PVDthv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~~~ 327 (328)
.||+.-|.-+--..+.+---..+|.+++.++|+.-..+....++.=.+..+.|.
T Consensus 4 ~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~kp~~~~~k~d~~~q~~f~ 57 (60)
T PF13592_consen 4 RWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQKPRPRPPKADEEAQEAFK 57 (60)
T ss_pred cccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccccCCCCcccCCHHHHHHHH
Confidence 344444444333222222236789999999998655554444444455555554
No 113
>PRK14973 DNA topoisomerase I; Provisional
Probab=39.30 E-value=76 Score=35.68 Aligned_cols=71 Identities=17% Similarity=0.220 Sum_probs=43.5
Q ss_pred CHHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHH----------------HhcCCCchhhhhhh
Q 020295 192 SLERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQ----------------SKHSGGAEWLLSLR 255 (328)
Q Consensus 192 tpe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~----------------~~~~gg~~~l~~L~ 255 (328)
+..+|+.+++..|+..|++ ++ +++.+.+-|+.+. .-|.+|--+++++.
T Consensus 767 ~~~~~~~~~~~~~~~~~~s--E~--------------~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~ 830 (936)
T PRK14973 767 DIAALARADPADLKKAGLS--EA--------------EAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFC 830 (936)
T ss_pred hHHHHhhCCHHHHHHcCCC--HH--------------HHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHH
Confidence 6788999999999999886 22 3444443332111 11223555555554
Q ss_pred CCCHHHHHHHhhcCCCccHHHHHHHHH
Q 020295 256 KLDLQEAIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 256 ~~~~~ea~~~L~~l~GIG~ktAd~vll 282 (328)
..+ -++|..++||.+-|+.-...
T Consensus 831 ~a~----p~~La~~~g~~~~~~~~~~~ 853 (936)
T PRK14973 831 SVH----PAYLALKTGISPETICRHAK 853 (936)
T ss_pred hcC----HHHHhcCCCCChhhHHHHHH
Confidence 443 45899999999888755433
No 114
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=38.26 E-value=36 Score=33.36 Aligned_cols=25 Identities=28% Similarity=0.537 Sum_probs=21.2
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHh
Q 020295 260 QEAIDALCTLPGVGPKVAACIALFS 284 (328)
Q Consensus 260 ~ea~~~L~~l~GIG~ktAd~vllf~ 284 (328)
++..++|+.++||||+|.....|.+
T Consensus 265 p~~feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 265 PSDFEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred ccCHHHHHhcCCCCHHHHHHHHHHH
Confidence 4557899999999999998887765
No 115
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=38.20 E-value=20 Score=30.22 Aligned_cols=21 Identities=29% Similarity=0.328 Sum_probs=18.2
Q ss_pred HHHHhhcCCCccHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vll 282 (328)
+.=.|+.|.|||..+|..||-
T Consensus 15 v~iALt~IyGIG~~~a~~I~~ 35 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICK 35 (121)
T ss_pred EeehhhhhccccHHHHHHHHH
Confidence 344789999999999999987
No 116
>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=37.97 E-value=37 Score=24.92 Aligned_cols=37 Identities=30% Similarity=0.408 Sum_probs=29.8
Q ss_pred cCCC-HHHHhcCCHHHHHhcCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHH
Q 020295 189 EFPS-LERLSLVSEVELRNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQ 241 (328)
Q Consensus 189 ~fPt-pe~La~~~~e~Lr~~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~ 241 (328)
.|++ +++|..++-.+|++.|+.-| --+||....+.+.
T Consensus 18 kf~~~w~~lf~~~s~~LK~~GIp~r----------------~RryiL~~~ek~r 55 (57)
T PF09597_consen 18 KFESDWEKLFTTSSKQLKELGIPVR----------------QRRYILRWREKYR 55 (57)
T ss_pred HHHHHHHHHHhcCHHHHHHCCCCHH----------------HHHHHHHHHHHHh
Confidence 5788 99999999999999999654 3578888776654
No 117
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=37.95 E-value=19 Score=30.36 Aligned_cols=26 Identities=23% Similarity=0.160 Sum_probs=20.6
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 261 EAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+.-.|+.|.|||+.+|..||-. +|-
T Consensus 14 ~v~~aL~~I~GIG~~~a~~i~~~-lgi 39 (122)
T PRK05179 14 RVVIALTYIYGIGRTRAKEILAA-AGI 39 (122)
T ss_pred EEEeeecccccccHHHHHHHHHH-hCc
Confidence 34567899999999999988774 553
No 118
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=37.89 E-value=16 Score=30.02 Aligned_cols=39 Identities=33% Similarity=0.416 Sum_probs=23.9
Q ss_pred cCCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHH
Q 020295 207 AGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVA 277 (328)
Q Consensus 207 ~Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktA 277 (328)
||+|.| ||..+++..+.. ||. =+.|++|.+.-.+|++|-
T Consensus 56 ~GLGPR----------------KA~~Ll~~l~~~-----g~~-----------l~~R~~Lv~~~~~g~~Vf 94 (104)
T PF14635_consen 56 CGLGPR----------------KAQALLKALKQN-----GGR-----------LENRSQLVTKCLMGPKVF 94 (104)
T ss_dssp TT--HH----------------HHHHHHHHHHHC------S---------------TTHHHHTTSS-HHHH
T ss_pred cCCChH----------------HHHHHHHHHHHc-----CCc-----------cccHHHHHhcCCCCCeEE
Confidence 799988 899998876631 222 235778888888999875
No 119
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=37.85 E-value=30 Score=28.92 Aligned_cols=49 Identities=16% Similarity=0.270 Sum_probs=30.4
Q ss_pred hcCCCCC--CCCccchhhhhhc----chHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHh
Q 020295 206 NAGFGYR--SAPQSSLLFSVRR----SFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDAL 266 (328)
Q Consensus 206 ~~Glg~R--~~~~~~li~~v~~----~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L 266 (328)
.+|++|- .+++..+|..+|| .........++.+++.+ |++ +.++|.+.|
T Consensus 58 ~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~----GeI--------s~eeA~~~L 112 (113)
T PF09862_consen 58 ELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEK----GEI--------SVEEALEIL 112 (113)
T ss_pred HHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHc----CCC--------CHHHHHHHh
Confidence 4799884 3566788888888 22233444455555553 444 667777766
No 120
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=36.25 E-value=72 Score=31.78 Aligned_cols=40 Identities=28% Similarity=0.330 Sum_probs=32.7
Q ss_pred cccCCCHHHHhcCCHHHHHhc-CCCCCCCCccchhhhhhcchHHHHHHHHHHHHHHH
Q 020295 187 FHEFPSLERLSLVSEVELRNA-GFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQS 242 (328)
Q Consensus 187 ~~~fPtpe~La~~~~e~Lr~~-Glg~R~~~~~~li~~v~~~~~KA~~I~~~A~~i~~ 242 (328)
...|.+.+.+.+++.++|.+. |+|- .||+.|.+.++.+.+
T Consensus 304 l~~FGSL~~Il~As~eeL~~VeGIGe----------------~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 304 VEHFGSLQGLLAASIEDLDEVEGIGE----------------VRARAIREGLSRLAE 344 (352)
T ss_pred HHHcCCHHHHHcCCHHHHhhCCCcCH----------------HHHHHHHHHHHHHHH
Confidence 346789999999999999885 8874 479999988888765
No 121
>PRK08609 hypothetical protein; Provisional
Probab=35.25 E-value=51 Score=34.77 Aligned_cols=41 Identities=24% Similarity=0.359 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 230 AKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 230 A~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
+..-.++|+.|.+. ..++ .+ ..+|.+|||||..+|+.|-=+
T Consensus 27 ~~aYr~Aa~~i~~l----~~~i--------~~-~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 27 ISAFRKAAQALELD----ERSL--------SE-IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHHHHHHHhC----chhh--------hh-hhhhccCCCcCHHHHHHHHHH
Confidence 77777888877652 1112 21 247899999999999987654
No 122
>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=35.14 E-value=20 Score=29.72 Aligned_cols=26 Identities=23% Similarity=0.052 Sum_probs=20.3
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCCC
Q 020295 261 EAIDALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 261 ea~~~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.+.-.|++|.|||+.+|..||-. +|-
T Consensus 12 ~v~~aL~~i~GIG~~~a~~i~~~-lgi 37 (113)
T TIGR03631 12 RVEIALTYIYGIGRTRARKILEK-AGI 37 (113)
T ss_pred EEeeeeeeeecccHHHHHHHHHH-hCc
Confidence 34557899999999999988764 543
No 123
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=34.96 E-value=27 Score=34.21 Aligned_cols=21 Identities=33% Similarity=0.556 Sum_probs=18.3
Q ss_pred HHHHhhcCCCccHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vll 282 (328)
-.++|+.+||||+|+|.-|++
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~ 348 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVM 348 (404)
T ss_pred CHHHhcccCCCChHHHHHHHH
Confidence 468999999999999987766
No 124
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=34.17 E-value=25 Score=32.98 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=17.3
Q ss_pred HhhcCCCccHHHHHHHHHHhCCC
Q 020295 265 ALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
.|..|+|||++.|..++-.||+-
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~S 26 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFES 26 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCC
Confidence 57778888888888777765664
No 125
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=32.14 E-value=30 Score=34.02 Aligned_cols=22 Identities=36% Similarity=0.585 Sum_probs=17.7
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf 283 (328)
..+++.+|||||+|+|..|--+
T Consensus 54 S~~ea~~lP~iG~kia~ki~Ei 75 (353)
T KOG2534|consen 54 SGEEAEKLPGIGPKIAEKIQEI 75 (353)
T ss_pred cHHHhcCCCCCCHHHHHHHHHH
Confidence 3567788999999999887554
No 126
>PRK14976 5'-3' exonuclease; Provisional
Probab=31.88 E-value=28 Score=33.30 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=17.7
Q ss_pred HhhcCCCccHHHHHHHHHHhCCCCCc
Q 020295 265 ALCTLPGVGPKVAACIALFSLDQHHA 290 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~lg~~d~ 290 (328)
-+-.+||||+|||.-++- .+|..+.
T Consensus 192 nipGVpGIG~KtA~~LL~-~~gsle~ 216 (281)
T PRK14976 192 NIKGVKGIGPKTAIKLLN-KYGNIEN 216 (281)
T ss_pred CCCCCCcccHHHHHHHHH-HcCCHHH
Confidence 455789999999987764 5554333
No 127
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=29.63 E-value=1.3e+02 Score=29.82 Aligned_cols=49 Identities=14% Similarity=0.205 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHH
Q 020295 143 LRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELR 205 (328)
Q Consensus 143 l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr 205 (328)
+++=|...+++--+.-....+.+..++++|. .||+.+ +.|.+++.|+|.
T Consensus 301 lhliPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGtEi--------------~vLi~a~~e~La 350 (403)
T COG1379 301 LHLIPLAEIISMALGKGITTKAVKRTWERLVRAFGTEI--------------DVLIDAPIEELA 350 (403)
T ss_pred eecccHHHHHHHHhccceechhHHHHHHHHHHHhcchh--------------hhHhcCCHHHHh
Confidence 4577888888888888889999999999998 899865 456666666653
No 128
>smart00475 53EXOc 5'-3' exonuclease.
Probab=29.10 E-value=35 Score=32.31 Aligned_cols=22 Identities=27% Similarity=0.466 Sum_probs=16.4
Q ss_pred HhhcCCCccHHHHHHHHHHhCCC
Q 020295 265 ALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
-+-.+||||+|||.-++- -+|-
T Consensus 187 nipGV~GIG~KtA~~Ll~-~ygs 208 (259)
T smart00475 187 NIPGVPGIGEKTAAKLLK-EFGS 208 (259)
T ss_pred CCCCCCCCCHHHHHHHHH-HhCC
Confidence 356789999999987664 4554
No 129
>PRK09482 flap endonuclease-like protein; Provisional
Probab=28.89 E-value=34 Score=32.48 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=16.2
Q ss_pred HhhcCCCccHHHHHHHHHHhCCC
Q 020295 265 ALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
-+-.+||||+|||--++- -+|-
T Consensus 183 nIpGVpGIG~KtA~~LL~-~~gs 204 (256)
T PRK09482 183 KIPGVAGIGPKSAAELLN-QFRS 204 (256)
T ss_pred CCCCCCCcChHHHHHHHH-HhCC
Confidence 345689999999987654 4554
No 130
>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=28.46 E-value=36 Score=31.64 Aligned_cols=22 Identities=27% Similarity=0.436 Sum_probs=16.2
Q ss_pred HhhcCCCccHHHHHHHHHHhCCC
Q 020295 265 ALCTLPGVGPKVAACIALFSLDQ 287 (328)
Q Consensus 265 ~L~~l~GIG~ktAd~vllf~lg~ 287 (328)
-+-.+||||||+|.-++- -+|.
T Consensus 184 nipGv~GiG~ktA~~Ll~-~~gs 205 (240)
T cd00008 184 NIPGVPGIGEKTAAKLLK-EYGS 205 (240)
T ss_pred CCCCCCccCHHHHHHHHH-HhCC
Confidence 456789999999976654 4554
No 131
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=28.21 E-value=91 Score=33.20 Aligned_cols=24 Identities=29% Similarity=0.405 Sum_probs=13.7
Q ss_pred HHHHhhcCCCccHHHHHHHHHHhC
Q 020295 262 AIDALCTLPGVGPKVAACIALFSL 285 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vllf~l 285 (328)
....|..|||||++++..++-.--
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~~Fg 564 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLKHFG 564 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHHHcC
Confidence 345566666666666665554433
No 132
>PRK00024 hypothetical protein; Reviewed
Probab=28.07 E-value=1.4e+02 Score=27.65 Aligned_cols=22 Identities=41% Similarity=0.413 Sum_probs=17.7
Q ss_pred CCCHHHHhcCCHHHHHh-cCCCC
Q 020295 190 FPSLERLSLVSEVELRN-AGFGY 211 (328)
Q Consensus 190 fPtpe~La~~~~e~Lr~-~Glg~ 211 (328)
|.+...+..++.++|+. .|+|-
T Consensus 54 fgsL~~l~~as~~eL~~i~GIG~ 76 (224)
T PRK00024 54 FGSLRGLLDASLEELQSIKGIGP 76 (224)
T ss_pred cCCHHHHHhCCHHHHhhccCccH
Confidence 33688999999999988 48874
No 133
>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=28.04 E-value=45 Score=26.06 Aligned_cols=21 Identities=29% Similarity=0.322 Sum_probs=15.4
Q ss_pred HHHHhhcCCCccHHHHHHHHH
Q 020295 262 AIDALCTLPGVGPKVAACIAL 282 (328)
Q Consensus 262 a~~~L~~l~GIG~ktAd~vll 282 (328)
++==|..|+|||..+|+.|+-
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 344588999999999997765
No 134
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=26.46 E-value=94 Score=30.83 Aligned_cols=62 Identities=21% Similarity=0.224 Sum_probs=44.8
Q ss_pred HHHhhcCCCcc--------------HHHHHHHHHHhCCCCCcccc-chHHHHHHHHcCCCcccCCCCCHHHHHHHHHH
Q 020295 263 IDALCTLPGVG--------------PKVAACIALFSLDQHHAIPV-DTHVWKIATRYLLPELAGVRLTPKLCSRVAEA 325 (328)
Q Consensus 263 ~~~L~~l~GIG--------------~ktAd~vllf~lg~~d~~PV-Dthv~Ri~~rl~~~~~~~~~lt~k~y~~i~e~ 325 (328)
-+.|.+..||| ||+-|.....-|.+.-.+|+ +.|.+..+-++.+. .....+|..++.+++..
T Consensus 254 TEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG-~tp~~LT~~d~~eL~~k 330 (439)
T KOG0739|consen 254 TEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLG-DTPHVLTEQDFKELARK 330 (439)
T ss_pred HHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceeccCCcHHHhhhhheeccC-CCccccchhhHHHHHhh
Confidence 35678999999 67777777777777566777 67776666665432 23567999999998864
No 135
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=26.45 E-value=52 Score=36.37 Aligned_cols=28 Identities=25% Similarity=0.138 Sum_probs=23.6
Q ss_pred CHHHHHHHhhcCCCccHHHHHHHHHHhCC
Q 020295 258 DLQEAIDALCTLPGVGPKVAACIALFSLD 286 (328)
Q Consensus 258 ~~~ea~~~L~~l~GIG~ktAd~vllf~lg 286 (328)
..+++.+.|.+|||||++.|..+|-. ++
T Consensus 751 ~~~~~q~~L~~lPgI~~~~a~~ll~~-f~ 778 (814)
T TIGR00596 751 FNDGPQDFLLKLPGVTKKNYRNLRKK-VK 778 (814)
T ss_pred ccHHHHHHHHHCCCCCHHHHHHHHHH-cC
Confidence 45677889999999999999999874 55
No 136
>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]
Probab=25.96 E-value=1.4e+02 Score=31.92 Aligned_cols=127 Identities=18% Similarity=0.247 Sum_probs=78.5
Q ss_pred CCccCCCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCC-cccccccccCCCHHHHhcCCHHHHHhc--CCCCCCC
Q 020295 139 GARVLRQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLG-NVEGFEFHEFPSLERLSLVSEVELRNA--GFGYRSA 214 (328)
Q Consensus 139 G~R~l~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~-~~~g~~~~~fPtpe~La~~~~e~Lr~~--Glg~R~~ 214 (328)
|+.+..|.-=+.++.++++...+...++.++.-|. .+|+.+. +..+..--..|-.+.+...++..|-++ ++.|-
T Consensus 88 Gid~~~~~aR~v~l~c~iGta~ha~haRHLv~hlie~~Ged~pidlG~e~~v~aPi~~t~~G~kPktlgdle~~l~y~-- 165 (772)
T COG1152 88 GIDMAGQTAREVFLACCIGTACHAAHARHLVDHLIETFGEDLPIDLGSEVNVEAPIIETVTGIKPKTLGDLEAALEYA-- 165 (772)
T ss_pred ccchhhhhhheehhhhhhhhhhhhhhHHHHHHHHHHHhCccCccCCCcccccccchhhhhhCCCccchHHHHHHHHHH--
Confidence 45555677888999999999999999999999997 8998542 222122223456666666655444332 33333
Q ss_pred CccchhhhhhcchHHHHHHHHHHHHHHHhcCCCchhhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCCc
Q 020295 215 PQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHA 290 (328)
Q Consensus 215 ~~~~li~~v~~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d~ 290 (328)
-+.|..+...++. |.+-++ ++++.-.-..-.+.-+|..+||..-+.+++.+.+
T Consensus 166 ---------------Eeqlt~~ls~~h~---gqE~~~-----~dyeSkAlhaG~~d~l~~EiaDiaqi~a~~~pk~ 218 (772)
T COG1152 166 ---------------EEQLTQLLSAVHT---GQEGSL-----LDYESKALHAGMIDHLGMEIADIAQIVAYDFPKG 218 (772)
T ss_pred ---------------HHHHHHHHHHHhc---cCcccc-----cchhHHHhhhhhhhHHHHHHHHHHHHHhhcCCCC
Confidence 3445555555554 322222 2455444444567778999999877777765433
No 137
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=25.44 E-value=1.2e+02 Score=32.74 Aligned_cols=29 Identities=34% Similarity=0.532 Sum_probs=22.3
Q ss_pred hhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHH
Q 020295 251 LLSLRKLDLQEAIDALCTLPGVGPKVAACIALF 283 (328)
Q Consensus 251 l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf 283 (328)
++.|...+ .++|.+++|||.++|..|.-|
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 55555544 457788999999999998875
No 138
>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=25.13 E-value=1.2e+02 Score=23.43 Aligned_cols=22 Identities=32% Similarity=0.276 Sum_probs=18.1
Q ss_pred HHHHHHHHhccChhHHHHHHHh
Q 020295 116 LGELWEGFSASDCRFAELAKYL 137 (328)
Q Consensus 116 l~~~~~~~~~~D~~l~~l~~~~ 137 (328)
|+++.+++...||.|+...+..
T Consensus 11 L~eiEr~L~~~DP~fa~~l~~~ 32 (82)
T PF11239_consen 11 LEEIERQLRADDPRFAARLRSG 32 (82)
T ss_pred HHHHHHHHHhcCcHHHHHhccC
Confidence 5788889999999998877663
No 139
>PHA00368 internal virion protein D
Probab=24.87 E-value=8.3e+02 Score=28.22 Aligned_cols=100 Identities=20% Similarity=0.241 Sum_probs=48.1
Q ss_pred CCCCcCcccCCCCcccceecCCceEEEeE--CCeEEEEEEecCCcEEEEEcCCCChHHHHHHHHHhhcCCCCHHHHHHHH
Q 020295 46 SELSLPLTFPTGQTFRWKKTGPLQYTGPI--GPHLISLKHLQNGDVCYHIHTSPSEPAAKSALLDFLNMGISLGELWEGF 123 (328)
Q Consensus 46 ~~~~L~~tl~~GQ~Frw~~~~~~~~~g~~--g~~~i~l~q~~~~~l~~~~~~~~~~~~~~~~l~~~f~Ld~dl~~~~~~~ 123 (328)
.+-|++.+|+.||+|.-+..-+....-++ .++-| +|+|.+-.-+.....+.+..+...=.--.+-.. .
T Consensus 770 FDSD~~v~lpdG~~FSVNdLR~~Dm~~impaYdRRv------nGDiaIMg~tGktT~~lkdei~~l~~~~~~~g~----~ 839 (1315)
T PHA00368 770 FDSDMSVTLPDGQTFSVNDLRDFDMKRIMPAYDRRV------NGDIAIMGGTGKTTKELKDEILALDKKAEGDGK----L 839 (1315)
T ss_pred cccCCceeCCCCCccccchhhhhhhhhhhhhhcccc------CCceeeecCCCccHHHHHHHHHHHHhhccCCCc----c
Confidence 45688899999999987755321111111 12111 566655433333444444333322110000000 1
Q ss_pred hccChhHHHHHHHhcCC-ccCCCCHHHHHHHHH
Q 020295 124 SASDCRFAELAKYLAGA-RVLRQDPVECLLQFL 155 (328)
Q Consensus 124 ~~~D~~l~~l~~~~~G~-R~l~~dpfe~Lis~I 155 (328)
+..-..|...++-+.|. |--.++-|++.++++
T Consensus 840 k~eV~aL~dtvKiLTGRARRn~d~af~t~~Rsl 872 (1315)
T PHA00368 840 KGEVEALKDTVKILTGRARRNPDTAFETALRSL 872 (1315)
T ss_pred chhHHHHHHHHHHHhcccccCcchHHHHHHHHH
Confidence 11123445555555553 333478888888776
No 140
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=23.72 E-value=3.5e+02 Score=25.99 Aligned_cols=79 Identities=25% Similarity=0.215 Sum_probs=52.1
Q ss_pred cchHHHHHHHHHHHHHHHhcCCCchhhhhhhC--CCHHHHHHHhhcCCCcc---------HHHHHHHHHHhCCCC-----
Q 020295 225 RSFKQAKYITGTVDVLQSKHSGGAEWLLSLRK--LDLQEAIDALCTLPGVG---------PKVAACIALFSLDQH----- 288 (328)
Q Consensus 225 ~~~~KA~~I~~~A~~i~~~~~gg~~~l~~L~~--~~~~ea~~~L~~l~GIG---------~ktAd~vllf~lg~~----- 288 (328)
+.++|.++|.+++..+.+ +++.++.. -+.+++++.|..+=|-- -|.+.+.+..+++..
T Consensus 102 l~e~KikRi~r~~~fl~~------L~l~~~~~~y~~l~~l~~~La~~L~s~~~~KTiVFAvKM~~Ya~r~~~~~~~p~p~ 175 (269)
T PRK13280 102 LLEQKIKRIEKVEPFLES------LTLLDLPLYYEDLEELLEQLAKILGAKKESKTVVFAVKMFGYACRAAFGEFRPYPM 175 (269)
T ss_pred HHHHHHHHHHHHHHHhhh------hccchhhhhHhhHHHHHHHHHHHhCCCCCcceeeeHHHHHHHHHHHhccccCCCCc
Confidence 446788999888765432 23333332 45677888887766654 477777777666542
Q ss_pred Cc-cccchHHHHHHHHcCCCcc
Q 020295 289 HA-IPVDTHVWKIATRYLLPEL 309 (328)
Q Consensus 289 d~-~PVDthv~Ri~~rl~~~~~ 309 (328)
++ +|||..|..+....++.+.
T Consensus 176 ~IpIPvD~Ria~~T~~sglv~~ 197 (269)
T PRK13280 176 EIPIPVDYRIAKLTKCSGLVEG 197 (269)
T ss_pred CCCCcccHHHHHHHHHhccccC
Confidence 22 5889999999888776543
No 141
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=22.92 E-value=44 Score=22.93 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=13.0
Q ss_pred ccchHHHHHHHHcCC
Q 020295 292 PVDTHVWKIATRYLL 306 (328)
Q Consensus 292 PVDthv~Ri~~rl~~ 306 (328)
+-||||+|++..+|-
T Consensus 17 eddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 17 EDDTHVHRVLRKYYT 31 (41)
T ss_pred cchhHHHHHHHHHHH
Confidence 458999999999984
No 142
>COG3017 LolB Outer membrane lipoprotein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]
Probab=22.38 E-value=3.3e+02 Score=25.17 Aligned_cols=62 Identities=19% Similarity=0.343 Sum_probs=43.2
Q ss_pred ccceecCCceEEEe----ECCeEEEEEEecCCcEEEEEcCCC--ChHHHHHHHHHhhcCCCCHHHHHHHHh
Q 020295 60 FRWKKTGPLQYTGP----IGPHLISLKHLQNGDVCYHIHTSP--SEPAAKSALLDFLNMGISLGELWEGFS 124 (328)
Q Consensus 60 Frw~~~~~~~~~g~----~g~~~i~l~q~~~~~l~~~~~~~~--~~~~~~~~l~~~f~Ld~dl~~~~~~~~ 124 (328)
|-|.+.+ ..|.-. +|..+..|.+..++ ...+..... ..+++++.+.+..+++..++.+. .|-
T Consensus 71 F~Wqq~p-~~y~L~Ls~pLg~t~l~L~~~~~g-a~led~~g~~y~ae~ae~Ll~el~G~~lPl~~L~-~Wi 138 (206)
T COG3017 71 FFWQQQP-DRYRLLLSNPLGSTLLELSQDRGG-ARLEDNKGQRYQAEDAEELLQELTGMDLPLESLR-DWI 138 (206)
T ss_pred EEEEEcC-CcEEEEEeccCCcceEEEEecCCc-eEEEeCCCCeeeccCHHHHHHHhhCCcccHHHHH-HHH
Confidence 6788884 456654 48888889887654 444444333 35678889999999999998763 443
No 143
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=21.97 E-value=1.6e+02 Score=27.67 Aligned_cols=35 Identities=23% Similarity=0.255 Sum_probs=25.4
Q ss_pred hhhhhhCCCHHHHHHHhhcCCCccHHHHHHHHHHhCCCCC
Q 020295 250 WLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH 289 (328)
Q Consensus 250 ~l~~L~~~~~~ea~~~L~~l~GIG~ktAd~vllf~lg~~d 289 (328)
+++.+...+ .++|.+++|||.++|+-|.-+ ++..+
T Consensus 26 Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~-l~~~~ 60 (232)
T PRK12766 26 SVEDVRAAD----QSELAEVDGIGNALAARIKAD-VGGLE 60 (232)
T ss_pred CHHHHHhCC----HHHHHHccCCCHHHHHHHHHH-hcccc
Confidence 455555444 567899999999999999775 54433
No 144
>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=21.86 E-value=1.1e+02 Score=30.62 Aligned_cols=50 Identities=12% Similarity=0.136 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHH-hhCCCCCcccccccccCCCHHHHhcCCHHHHHhc
Q 020295 144 RQDPVECLLQFLCSSNNNIARITKMVDFLA-SLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA 207 (328)
Q Consensus 144 ~~dpfe~Lis~IlsQn~si~~a~~~~~~L~-~~G~~~~~~~g~~~~~fPtpe~La~~~~e~Lr~~ 207 (328)
.+=|++.+++.+.......+.+...+++|. +||..+ +-|.+++.|+|+..
T Consensus 295 ~~iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~E~--------------~iL~~~~~eel~~~ 345 (374)
T TIGR00375 295 HLIPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGTEI--------------AVLHEAAEEDLARV 345 (374)
T ss_pred eeCCHHHHHhhhcCCCCccHHHHHHHHHHHHHhccHH--------------HHHhcCCHHHHHHH
Confidence 366899999999998888999999999997 899753 66888888888653
No 145
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=21.73 E-value=43 Score=28.74 Aligned_cols=18 Identities=33% Similarity=0.776 Sum_probs=15.3
Q ss_pred HHhhcCCCccHHHHHHHH
Q 020295 264 DALCTLPGVGPKVAACIA 281 (328)
Q Consensus 264 ~~L~~l~GIG~ktAd~vl 281 (328)
+.|+.|.||||+.+...-
T Consensus 67 DDLt~I~GIGPk~e~~Ln 84 (133)
T COG3743 67 DDLTRISGIGPKLEKVLN 84 (133)
T ss_pred ccchhhcccCHHHHHHHH
Confidence 689999999999987543
No 146
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.67 E-value=2.4e+02 Score=26.03 Aligned_cols=21 Identities=33% Similarity=0.371 Sum_probs=17.4
Q ss_pred CCHHHHhcCCHHHHHh-cCCCC
Q 020295 191 PSLERLSLVSEVELRN-AGFGY 211 (328)
Q Consensus 191 Ptpe~La~~~~e~Lr~-~Glg~ 211 (328)
.+...|..++.++|.. -|+|-
T Consensus 49 g~l~~l~~a~~~eL~~i~GiG~ 70 (218)
T TIGR00608 49 DSLGHLLSAPPEELSSVPGIGE 70 (218)
T ss_pred CCHHHHHhCCHHHHHhCcCCcH
Confidence 3688999999999988 48874
No 147
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=21.60 E-value=1.6e+02 Score=23.03 Aligned_cols=21 Identities=43% Similarity=0.485 Sum_probs=17.0
Q ss_pred Hhhc-CCCccHHHHHHHHHHhCC
Q 020295 265 ALCT-LPGVGPKVAACIALFSLD 286 (328)
Q Consensus 265 ~L~~-l~GIG~ktAd~vllf~lg 286 (328)
.|+. +.|||-++||-+.+- +|
T Consensus 46 ~L~~~i~gi~F~~aD~iA~~-~g 67 (94)
T PF14490_consen 46 RLIEDIDGIGFKTADKIALK-LG 67 (94)
T ss_dssp CCCB-SSSSBHHHHHHHHHT-TT
T ss_pred HHHHHccCCCHHHHHHHHHH-cC
Confidence 3555 999999999999883 54
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=21.40 E-value=97 Score=25.08 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=17.8
Q ss_pred HHhhcCCCccHHHHHHHHHHh
Q 020295 264 DALCTLPGVGPKVAACIALFS 284 (328)
Q Consensus 264 ~~L~~l~GIG~ktAd~vllf~ 284 (328)
.+-.++||||.+-|..|..|-
T Consensus 50 ~Wwr~vpglG~~~A~~I~awL 70 (96)
T PF12482_consen 50 RWWRAVPGLGAAGARRIEAWL 70 (96)
T ss_pred hHHHhCcccchHHHHHHHHHH
Confidence 366789999999999998873
No 149
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=20.65 E-value=2.5e+02 Score=24.40 Aligned_cols=36 Identities=22% Similarity=0.466 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHh-cccCHHHHHHHHHHHH-hhCCCC
Q 020295 144 RQDPVECLLQFLCS-SNNNIARITKMVDFLA-SLGSHL 179 (328)
Q Consensus 144 ~~dpfe~Lis~Ils-Qn~si~~a~~~~~~L~-~~G~~~ 179 (328)
.+++|+.++..|.+ ...+-..+...++.+. +||..+
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 6788888889999987 787544
No 150
>PRK14036 citrate synthase; Provisional
Probab=20.50 E-value=8.6e+02 Score=24.30 Aligned_cols=17 Identities=12% Similarity=0.180 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHhc
Q 020295 228 KQAKYITGTVDVLQSKH 244 (328)
Q Consensus 228 ~KA~~I~~~A~~i~~~~ 244 (328)
-|++.++++++.+.++.
T Consensus 267 PRa~~L~~~~~~l~~~~ 283 (377)
T PRK14036 267 PRATILQKLAEELFARF 283 (377)
T ss_pred ccHHHHHHHHHHHHHhc
Confidence 37899999998886543
No 151
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=20.37 E-value=1.4e+02 Score=31.66 Aligned_cols=19 Identities=26% Similarity=0.260 Sum_probs=10.5
Q ss_pred HHHhhcCCCccHHHHHHHH
Q 020295 263 IDALCTLPGVGPKVAACIA 281 (328)
Q Consensus 263 ~~~L~~l~GIG~ktAd~vl 281 (328)
...|..|||||++.....|
T Consensus 513 ~s~L~~I~GiG~kr~~~LL 531 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKIL 531 (574)
T ss_pred ccccccCCCCCHHHHHHHH
Confidence 3455566666666555444
Done!