Query 039703
Match_columns 284
No_of_seqs 176 out of 1520
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 12:21:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039703.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039703hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1918 3-methyladenine DNA gl 100.0 1.9E-48 4E-53 340.9 16.6 209 61-269 35-245 (254)
2 COG0122 AlkA 3-methyladenine D 100.0 9.5E-48 2.1E-52 355.9 19.8 203 66-268 62-277 (285)
3 PRK10308 3-methyl-adenine DNA 100.0 7.9E-45 1.7E-49 336.3 21.3 201 55-271 74-282 (283)
4 TIGR00588 ogg 8-oxoguanine DNA 100.0 1E-43 2.2E-48 332.8 21.8 211 55-268 74-308 (310)
5 cd00056 ENDO3c endonuclease II 100.0 1E-32 2.2E-37 233.7 14.9 152 102-263 1-157 (158)
6 KOG2875 8-oxoguanine DNA glyco 100.0 6.8E-32 1.5E-36 244.0 13.0 203 55-262 74-298 (323)
7 TIGR01083 nth endonuclease III 100.0 2.6E-30 5.7E-35 226.7 19.5 168 81-263 5-177 (191)
8 COG0177 Nth Predicted EndoIII- 100.0 2.9E-28 6.3E-33 215.8 19.7 170 80-264 7-181 (211)
9 PRK13913 3-methyladenine DNA g 100.0 4.2E-28 9.1E-33 216.6 17.7 153 89-248 18-176 (218)
10 smart00478 ENDO3c endonuclease 100.0 5.4E-28 1.2E-32 203.0 16.1 140 110-263 1-147 (149)
11 PRK10702 endonuclease III; Pro 100.0 2.5E-27 5.5E-32 211.1 19.1 167 81-262 8-179 (211)
12 TIGR01084 mutY A/G-specific ad 99.9 1.3E-25 2.8E-30 207.3 19.7 155 83-252 6-170 (275)
13 PRK10880 adenine DNA glycosyla 99.9 3.5E-23 7.6E-28 196.7 19.1 155 83-252 10-174 (350)
14 PRK01229 N-glycosylase/DNA lya 99.9 2E-21 4.3E-26 172.5 18.1 165 83-265 18-203 (208)
15 COG2231 Uncharacterized protei 99.8 6.5E-20 1.4E-24 160.4 15.4 158 81-248 10-171 (215)
16 PRK13910 DNA glycosylase MutY; 99.8 4.6E-20 9.9E-25 171.3 15.3 133 110-257 1-138 (289)
17 KOG1921 Endonuclease III [Repl 99.8 7.5E-19 1.6E-23 157.0 17.3 179 66-257 38-227 (286)
18 PF00730 HhH-GPD: HhH-GPD supe 99.8 3.9E-19 8.4E-24 141.4 12.2 103 106-251 1-108 (108)
19 TIGR03252 uncharacterized HhH- 99.8 1.3E-18 2.7E-23 150.5 13.1 129 98-233 15-155 (177)
20 COG1194 MutY A/G-specific DNA 99.7 4.2E-17 9.2E-22 153.2 14.3 166 85-268 17-194 (342)
21 KOG2457 A/G-specific adenine D 98.7 4.9E-08 1.1E-12 93.0 10.0 124 100-238 124-253 (555)
22 COG1059 Thermostable 8-oxoguan 98.5 3.2E-06 6.9E-11 73.8 12.3 150 97-263 35-203 (210)
23 PF00633 HHH: Helix-hairpin-he 97.8 2.2E-05 4.8E-10 48.9 2.9 22 187-208 9-30 (30)
24 PF07934 OGG_N: 8-oxoguanine D 97.7 2.1E-05 4.5E-10 63.6 2.4 50 55-105 68-117 (117)
25 smart00278 HhH1 Helix-hairpin- 95.4 0.013 2.9E-07 34.9 2.2 20 190-209 2-21 (26)
26 PRK13901 ruvA Holliday junctio 95.0 0.051 1.1E-06 48.2 5.7 42 153-208 79-126 (196)
27 PF06029 AlkA_N: AlkA N-termin 94.6 0.0079 1.7E-07 49.0 -0.6 41 55-98 74-114 (116)
28 PRK10353 3-methyl-adenine DNA 94.4 1.3 2.8E-05 39.1 13.0 128 78-208 8-168 (187)
29 PF03352 Adenine_glyco: Methyl 94.4 0.53 1.2E-05 41.2 10.5 128 78-208 3-163 (179)
30 PF14520 HHH_5: Helix-hairpin- 94.2 0.13 2.7E-06 36.6 5.1 45 153-207 12-56 (60)
31 TIGR00624 tag DNA-3-methyladen 93.9 1.9 4.2E-05 37.7 12.9 126 78-207 7-164 (179)
32 PF12826 HHH_2: Helix-hairpin- 93.2 0.19 4.1E-06 36.4 4.7 40 165-208 15-54 (64)
33 PRK14601 ruvA Holliday junctio 93.1 0.087 1.9E-06 46.3 3.2 48 153-208 80-127 (183)
34 PRK02515 psbU photosystem II c 92.8 0.25 5.5E-06 41.0 5.4 52 140-208 54-106 (132)
35 PRK14606 ruvA Holliday junctio 92.8 0.1 2.2E-06 46.0 3.2 42 153-208 80-127 (188)
36 PRK14603 ruvA Holliday junctio 92.2 0.13 2.8E-06 45.6 3.2 41 153-207 79-125 (197)
37 TIGR00084 ruvA Holliday juncti 92.0 0.14 3.1E-06 45.1 3.2 48 153-208 79-126 (191)
38 PRK14604 ruvA Holliday junctio 91.9 0.15 3.3E-06 45.2 3.2 48 153-208 80-127 (195)
39 PRK14605 ruvA Holliday junctio 91.9 0.35 7.6E-06 42.7 5.5 46 153-206 80-125 (194)
40 PRK14602 ruvA Holliday junctio 91.7 0.17 3.7E-06 45.1 3.3 42 153-208 81-128 (203)
41 TIGR00615 recR recombination p 91.7 0.19 4E-06 44.6 3.5 31 184-214 6-36 (195)
42 PRK00076 recR recombination pr 91.6 0.18 4E-06 44.7 3.4 31 184-214 6-36 (196)
43 PRK13844 recombination protein 91.5 0.19 4.1E-06 44.7 3.5 31 184-214 10-40 (200)
44 COG0632 RuvA Holliday junction 91.2 0.2 4.3E-06 44.7 3.3 52 153-212 80-131 (201)
45 TIGR00575 dnlj DNA ligase, NAD 91.0 1.2 2.6E-05 46.4 9.2 68 137-208 456-549 (652)
46 smart00483 POLXc DNA polymeras 90.8 0.6 1.3E-05 44.6 6.3 58 147-207 48-107 (334)
47 PRK14600 ruvA Holliday junctio 90.4 0.21 4.6E-06 43.9 2.6 47 153-208 80-126 (186)
48 COG0353 RecR Recombinational D 90.2 0.27 5.9E-06 43.5 3.2 30 184-213 7-36 (198)
49 PRK07956 ligA NAD-dependent DN 90.2 1.5 3.3E-05 45.8 9.1 30 175-208 533-562 (665)
50 PF12836 HHH_3: Helix-hairpin- 89.9 0.55 1.2E-05 33.9 4.1 52 141-205 8-60 (65)
51 cd00141 NT_POLXc Nucleotidyltr 89.5 1.3 2.9E-05 41.7 7.5 60 148-213 46-107 (307)
52 TIGR01259 comE comEA protein. 88.9 1.1 2.5E-05 36.4 5.7 57 139-208 60-117 (120)
53 PF11731 Cdd1: Pathogenicity l 88.4 0.49 1.1E-05 37.1 3.1 61 185-263 8-69 (93)
54 PF14520 HHH_5: Helix-hairpin- 87.4 1.8 3.9E-05 30.6 5.3 42 122-167 17-59 (60)
55 PRK08609 hypothetical protein; 87.3 1.4 3.1E-05 45.1 6.5 55 148-206 49-105 (570)
56 COG1555 ComEA DNA uptake prote 87.2 1.6 3.6E-05 36.9 5.8 54 141-207 91-145 (149)
57 PRK14973 DNA topoisomerase I; 87.0 2.3 5E-05 46.1 8.1 84 135-220 823-908 (936)
58 PF02371 Transposase_20: Trans 86.9 0.52 1.1E-05 36.0 2.4 41 189-235 2-42 (87)
59 PRK08097 ligB NAD-dependent DN 86.3 4.6 9.9E-05 41.4 9.5 69 136-208 448-539 (562)
60 PRK14350 ligA NAD-dependent DN 86.0 3 6.5E-05 43.6 8.1 21 188-208 540-560 (669)
61 PRK13482 DNA integrity scannin 85.5 1.8 4E-05 41.7 5.8 48 121-173 298-346 (352)
62 TIGR00084 ruvA Holliday juncti 83.4 1 2.2E-05 39.7 2.9 24 183-206 66-89 (191)
63 PRK14351 ligA NAD-dependent DN 82.6 6.4 0.00014 41.4 8.8 30 175-208 550-579 (689)
64 PF10391 DNA_pol_lambd_f: Fing 82.1 1.3 2.9E-05 30.9 2.5 24 188-211 1-24 (52)
65 PF14716 HHH_8: Helix-hairpin- 82.1 4.6 0.0001 29.3 5.6 44 154-206 20-64 (68)
66 PRK00116 ruvA Holliday junctio 81.8 1.5 3.3E-05 38.5 3.4 48 153-208 80-127 (192)
67 PRK14605 ruvA Holliday junctio 81.7 1.3 2.7E-05 39.2 2.9 25 183-207 67-91 (194)
68 PRK00024 hypothetical protein; 81.6 3.9 8.4E-05 36.9 6.0 82 105-192 29-114 (224)
69 PF03118 RNA_pol_A_CTD: Bacter 81.6 3.1 6.6E-05 30.4 4.4 53 140-206 8-61 (66)
70 PRK00116 ruvA Holliday junctio 79.3 1.7 3.7E-05 38.2 2.9 23 185-207 69-91 (192)
71 COG1379 PHP family phosphoeste 76.8 8.5 0.00019 36.9 6.8 50 98-151 302-351 (403)
72 PRK00024 hypothetical protein; 76.4 3.9 8.4E-05 36.9 4.3 58 144-206 24-83 (224)
73 TIGR00608 radc DNA repair prot 76.1 7.6 0.00016 35.0 6.1 82 105-192 19-108 (218)
74 TIGR00426 competence protein C 75.4 13 0.00028 26.8 6.2 55 141-208 10-66 (69)
75 TIGR00608 radc DNA repair prot 75.3 4 8.6E-05 36.8 4.1 63 144-211 14-83 (218)
76 PF12836 HHH_3: Helix-hairpin- 74.6 3.3 7.2E-05 29.8 2.8 23 187-209 12-34 (65)
77 KOG2841 Structure-specific end 74.1 5 0.00011 36.7 4.4 34 135-168 215-249 (254)
78 smart00279 HhH2 Helix-hairpin- 73.9 2.5 5.4E-05 27.2 1.8 16 191-206 18-33 (36)
79 PF12826 HHH_2: Helix-hairpin- 73.8 5.9 0.00013 28.4 4.0 41 121-166 14-55 (64)
80 COG2818 Tag 3-methyladenine DN 72.7 18 0.0004 31.9 7.4 89 80-171 11-105 (188)
81 PRK14600 ruvA Holliday junctio 72.5 3.3 7E-05 36.5 2.8 24 184-207 68-91 (186)
82 PRK14601 ruvA Holliday junctio 72.4 3.3 7.2E-05 36.3 2.8 25 183-207 67-91 (183)
83 PRK13901 ruvA Holliday junctio 72.0 3.5 7.6E-05 36.6 2.9 25 183-207 66-90 (196)
84 PF11798 IMS_HHH: IMS family H 71.3 3 6.4E-05 26.1 1.6 15 191-205 13-27 (32)
85 PRK14606 ruvA Holliday junctio 71.1 3.7 8.1E-05 36.1 2.8 25 182-206 66-90 (188)
86 PRK14604 ruvA Holliday junctio 70.9 3.7 8E-05 36.4 2.8 25 183-207 67-91 (195)
87 PRK14603 ruvA Holliday junctio 70.7 3.8 8.2E-05 36.3 2.8 25 183-207 66-90 (197)
88 TIGR00375 conserved hypothetic 69.0 9.2 0.0002 37.3 5.3 68 99-176 296-363 (374)
89 PRK14602 ruvA Holliday junctio 69.0 4.4 9.5E-05 36.1 2.8 25 183-207 68-92 (203)
90 TIGR01259 comE comEA protein. 68.2 5.2 0.00011 32.5 2.9 23 187-209 66-88 (120)
91 PF09597 IGR: IGR protein moti 67.8 18 0.00038 25.9 5.2 37 136-172 20-57 (57)
92 cd00080 HhH2_motif Helix-hairp 66.0 3.4 7.3E-05 30.8 1.3 23 190-213 23-45 (75)
93 KOG2534 DNA polymerase IV (fam 65.6 15 0.00034 35.1 5.8 64 147-213 56-121 (353)
94 COG1555 ComEA DNA uptake prote 65.2 6 0.00013 33.5 2.8 23 187-209 95-117 (149)
95 TIGR01954 nusA_Cterm_rpt trans 63.8 33 0.00071 22.6 5.8 42 123-168 6-48 (50)
96 PRK02515 psbU photosystem II c 63.8 6.1 0.00013 32.9 2.5 21 187-207 59-79 (132)
97 PRK07758 hypothetical protein; 63.6 9.4 0.0002 30.1 3.4 32 171-206 53-84 (95)
98 PRK14973 DNA topoisomerase I; 62.6 38 0.00082 37.0 8.9 71 136-210 766-856 (936)
99 COG0272 Lig NAD-dependent DNA 59.4 42 0.00092 35.2 8.2 46 175-233 533-578 (667)
100 smart00483 POLXc DNA polymeras 59.3 23 0.00049 33.8 5.9 46 152-206 20-65 (334)
101 PF00416 Ribosomal_S13: Riboso 58.0 9.9 0.00022 30.2 2.8 24 186-209 12-35 (107)
102 PRK12766 50S ribosomal protein 57.9 27 0.00058 31.9 5.7 53 152-215 9-61 (232)
103 COG0632 RuvA Holliday junction 57.3 7.9 0.00017 34.5 2.3 25 183-207 67-91 (201)
104 PF14635 HHH_7: Helix-hairpin- 57.2 10 0.00022 30.4 2.6 39 152-202 56-94 (104)
105 PRK07945 hypothetical protein; 55.3 21 0.00046 34.0 5.0 50 152-208 17-68 (335)
106 TIGR00426 competence protein C 49.0 17 0.00036 26.2 2.5 21 188-208 15-36 (69)
107 COG1948 MUS81 ERCC4-type nucle 48.6 44 0.00096 30.9 5.7 62 159-220 147-213 (254)
108 TIGR01448 recD_rel helicase, p 48.4 70 0.0015 33.8 7.9 18 193-211 185-202 (720)
109 PRK13482 DNA integrity scannin 47.6 27 0.00059 33.8 4.3 38 163-204 297-334 (352)
110 PF01367 5_3_exonuc: 5'-3' exo 47.4 3.9 8.4E-05 32.5 -1.2 18 191-208 20-37 (101)
111 COG1796 POL4 DNA polymerase IV 46.9 27 0.00058 33.4 4.1 16 191-206 55-70 (326)
112 PRK14666 uvrC excinuclease ABC 46.8 43 0.00093 35.4 5.9 41 123-168 650-691 (694)
113 TIGR01448 recD_rel helicase, p 46.3 29 0.00063 36.6 4.7 23 184-206 77-101 (720)
114 PF11731 Cdd1: Pathogenicity l 46.1 40 0.00088 26.4 4.4 26 172-197 32-57 (93)
115 cd00141 NT_POLXc Nucleotidyltr 45.8 28 0.0006 32.8 4.1 42 158-208 23-64 (307)
116 COG2003 RadC DNA repair protei 45.1 63 0.0014 29.4 6.0 83 105-193 29-115 (224)
117 PRK12766 50S ribosomal protein 45.0 52 0.0011 30.1 5.5 43 123-169 16-59 (232)
118 COG1623 Predicted nucleic-acid 43.9 32 0.00069 32.7 4.0 39 121-164 304-343 (349)
119 PF06738 DUF1212: Protein of u 43.4 63 0.0014 27.7 5.7 89 108-201 4-105 (193)
120 COG4277 Predicted DNA-binding 42.9 18 0.00039 34.6 2.3 22 187-208 328-349 (404)
121 PRK14667 uvrC excinuclease ABC 42.4 45 0.00097 34.4 5.2 31 135-165 534-564 (567)
122 PRK00254 ski2-like helicase; P 41.8 47 0.001 34.9 5.5 23 191-213 647-669 (720)
123 CHL00137 rps13 ribosomal prote 40.1 16 0.00034 30.0 1.3 23 187-209 15-37 (122)
124 PF05559 DUF763: Protein of un 39.7 54 0.0012 31.3 4.9 24 186-209 266-289 (319)
125 PRK05179 rpsM 30S ribosomal pr 39.7 15 0.00033 30.1 1.2 23 187-209 15-37 (122)
126 PRK14976 5'-3' exonuclease; Pr 38.5 19 0.00042 33.5 1.8 22 191-213 193-214 (281)
127 TIGR02757 conserved hypothetic 37.2 36 0.00079 31.0 3.3 22 215-238 173-194 (229)
128 PRK09482 flap endonuclease-lik 36.5 23 0.00049 32.8 1.9 22 191-213 184-205 (256)
129 smart00475 53EXOc 5'-3' exonuc 36.4 22 0.00047 32.8 1.8 17 191-207 188-204 (259)
130 PRK12337 2-phosphoglycerate ki 36.0 3.2E+02 0.0069 27.7 9.9 117 98-230 176-297 (475)
131 PTZ00134 40S ribosomal protein 36.0 19 0.0004 30.9 1.2 23 187-209 28-50 (154)
132 cd00008 53EXOc 5'-3' exonuclea 35.5 24 0.00052 31.9 1.9 23 190-213 184-206 (240)
133 COG1948 MUS81 ERCC4-type nucle 34.6 91 0.002 28.9 5.5 46 121-171 193-239 (254)
134 COG0099 RpsM Ribosomal protein 34.5 27 0.00058 28.7 1.8 23 187-209 15-37 (121)
135 COG2003 RadC DNA repair protei 33.6 54 0.0012 29.8 3.8 41 159-203 40-80 (224)
136 COG0177 Nth Predicted EndoIII- 33.4 1.3E+02 0.0029 27.0 6.2 122 82-213 50-185 (211)
137 TIGR03629 arch_S13P archaeal r 32.9 21 0.00047 30.1 1.0 22 187-208 19-40 (144)
138 TIGR03631 bact_S13 30S ribosom 32.7 21 0.00046 28.8 0.9 23 187-209 13-35 (113)
139 PF05361 PP1_inhibitor: PKC-ac 32.5 35 0.00077 28.9 2.2 66 122-201 55-121 (144)
140 PRK04053 rps13p 30S ribosomal 32.3 26 0.00056 29.8 1.4 22 187-208 23-44 (149)
141 PF11239 DUF3040: Protein of u 32.2 91 0.002 23.4 4.3 25 68-92 10-34 (82)
142 TIGR01083 nth endonuclease III 32.0 2.1E+02 0.0045 24.7 7.2 83 119-205 3-86 (191)
143 TIGR02238 recomb_DMC1 meiotic 31.9 1.2E+02 0.0026 28.6 6.1 47 122-172 13-60 (313)
144 PRK13766 Hef nuclease; Provisi 31.4 1E+02 0.0023 32.4 6.1 40 123-167 728-768 (773)
145 PTZ00035 Rad51 protein; Provis 30.5 1.2E+02 0.0026 29.0 5.8 46 122-171 35-81 (337)
146 PRK14671 uvrC excinuclease ABC 30.0 85 0.0018 32.7 5.0 32 184-216 564-595 (621)
147 PF12482 DUF3701: Phage integr 29.8 59 0.0013 25.6 3.0 26 189-214 50-75 (96)
148 PLN03187 meiotic recombination 29.8 1.3E+02 0.0028 29.0 5.9 47 121-171 42-89 (344)
149 PF09674 DUF2400: Protein of u 29.6 63 0.0014 29.5 3.5 21 215-237 176-196 (232)
150 PRK14672 uvrC excinuclease ABC 29.4 1E+02 0.0022 32.6 5.5 37 135-171 628-665 (691)
151 TIGR02509 type_III_yopR type I 28.3 1.3E+02 0.0029 25.0 4.9 66 104-172 15-93 (131)
152 PF14579 HHH_6: Helix-hairpin- 28.1 47 0.001 25.2 2.1 21 187-207 25-45 (90)
153 PRK07956 ligA NAD-dependent DN 27.5 1E+02 0.0022 32.4 5.1 28 175-206 469-496 (665)
154 PRK04301 radA DNA repair and r 27.3 1.7E+02 0.0038 27.2 6.3 45 122-170 18-63 (317)
155 KOG1936 Histidyl-tRNA syntheta 27.2 4.3E+02 0.0092 26.7 8.9 51 149-209 225-275 (518)
156 COG1179 Dinucleotide-utilizing 27.1 60 0.0013 30.1 2.9 66 192-257 36-104 (263)
157 PF04282 DUF438: Family of unk 27.0 1.2E+02 0.0026 22.6 4.0 56 115-174 11-66 (71)
158 TIGR00575 dnlj DNA ligase, NAD 26.3 97 0.0021 32.5 4.7 27 175-205 456-482 (652)
159 PRK10702 endonuclease III; Pro 26.1 3E+02 0.0065 24.4 7.3 74 117-193 4-78 (211)
160 PRK14670 uvrC excinuclease ABC 26.1 1.4E+02 0.0031 30.8 5.8 32 135-166 534-566 (574)
161 PF07647 SAM_2: SAM domain (St 26.0 2.2E+02 0.0048 19.6 5.3 22 136-157 30-52 (66)
162 PRK00558 uvrC excinuclease ABC 25.2 1.1E+02 0.0025 31.6 5.0 20 187-206 541-560 (598)
163 TIGR02236 recomb_radA DNA repa 24.5 2.2E+02 0.0048 26.3 6.4 46 121-170 10-56 (310)
164 PRK14668 uvrC excinuclease ABC 24.5 1.4E+02 0.0029 31.0 5.3 36 124-164 539-575 (577)
165 COG1415 Uncharacterized conser 24.4 59 0.0013 31.5 2.5 24 186-209 275-298 (373)
166 TIGR00596 rad1 DNA repair prot 24.3 65 0.0014 34.7 3.0 28 183-211 751-778 (814)
167 KOG2534 DNA polymerase IV (fam 24.1 1.2E+02 0.0027 29.1 4.5 21 188-208 55-75 (353)
168 PRK08609 hypothetical protein; 23.4 1.4E+02 0.0031 30.7 5.2 41 158-207 26-66 (570)
169 PF14475 Mso1_Sec1_bdg: Sec1-b 22.9 61 0.0013 21.6 1.6 18 217-234 16-33 (41)
170 PF06568 DUF1127: Domain of un 22.8 71 0.0015 20.7 1.9 21 137-157 16-36 (40)
171 PRK00558 uvrC excinuclease ABC 22.5 1.6E+02 0.0035 30.5 5.4 39 122-165 555-594 (598)
172 PF14229 DUF4332: Domain of un 22.4 84 0.0018 25.4 2.7 24 188-211 52-75 (122)
173 COG3743 Uncharacterized conser 21.8 1.1E+02 0.0023 25.7 3.2 18 189-206 67-84 (133)
174 PRK00254 ski2-like helicase; P 21.2 1.5E+02 0.0032 31.2 4.9 33 135-167 666-699 (720)
175 COG1152 CdhA CO dehydrogenase/ 21.1 2.8E+02 0.0061 29.1 6.6 111 99-214 94-217 (772)
176 KOG3109 Haloacid dehalogenase- 20.6 92 0.002 28.5 2.8 78 118-201 37-119 (244)
177 PF09999 DUF2240: Uncharacteri 20.4 2.9E+02 0.0062 23.4 5.6 41 98-140 83-124 (144)
No 1
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=100.00 E-value=1.9e-48 Score=340.89 Aligned_cols=209 Identities=47% Similarity=0.829 Sum_probs=198.4
Q ss_pred CCCCCchhHHHHHHHHHhcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCC-CCCCCHH
Q 039703 61 KPLTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNG-EDNILPD 139 (284)
Q Consensus 61 ~~l~l~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~-~~~p~Pe 139 (284)
..++.....+.+++||...||.|..++.-+.++++...+.||+.|+++|++||++.++|+.|++||+..||+ ..||+|+
T Consensus 35 ~~~s~~~k~e~al~hl~~kd~~L~~lv~~~~p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe 114 (254)
T KOG1918|consen 35 YILSHEEKAEIALSHLDEKDPSLVKLVGNHEPLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPE 114 (254)
T ss_pred cccccHHHHHHHHHhhhhcchHHHHHhcCCCCCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCch
Confidence 347777889999999999999999999999988888889999999999999999999999999999999998 6799999
Q ss_pred HHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcCC-CChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccc
Q 039703 140 AVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGI-LSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPV 218 (284)
Q Consensus 140 ~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~-l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv 218 (284)
.+..++.++||.||||.||+.||+.+|+++.+|. .+.+.+.+|+.|++++.|+.++|||+||++|+|+|+|+|+||||+
T Consensus 115 ~i~~~~~~~lrkcG~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~ 194 (254)
T KOG1918|consen 115 FIDPLDCEELRKCGFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPA 194 (254)
T ss_pred hcCcCCHHHHHHhCcchhhHHHHHHHHHHHhcCCCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCc
Confidence 9999999999999999999999999999999994 578888899999999999999999999999999999999999999
Q ss_pred cChHHHHHHHHHhCCCCCCCHHHHHHHHHhcCChhHHHHHHHHHhhhhcCC
Q 039703 219 GDLGVRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGSWYMWRLMEAKGV 269 (284)
Q Consensus 219 ~D~~v~r~~~rly~~~~~~~~~~~~~~~e~~~Pyrs~a~~yLw~~~~~~~~ 269 (284)
+|++|+++++.+||+...+.+.+++++++.|.|||+.++||||+..+.+..
T Consensus 195 dDlgir~g~k~l~gl~~~p~~~evekl~e~~kpyRtvaawYlWki~~~~~~ 245 (254)
T KOG1918|consen 195 DDLGIRNGVKKLLGLKPLPLPKEVEKLCEKCKPYRTVAAWYLWKIIKLDIT 245 (254)
T ss_pred hhhhHHHHHHHHhCCCCCCchHHHHHHhhhccchHHHHHHHHHhhhhhhcc
Confidence 999999999999999999999999999999999999999999999887653
No 2
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.5e-48 Score=355.88 Aligned_cols=203 Identities=36% Similarity=0.647 Sum_probs=179.0
Q ss_pred chhHHHHHHHHHhcCchHHHHHHHcC--------CCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCC---
Q 039703 66 KGEVDIALRHLRDKDPLLATLIDAHR--------PPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGED--- 134 (284)
Q Consensus 66 ~~d~~~~~~~l~~~Dp~l~~li~~~~--------g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~--- 134 (284)
..++..+++++...|+.+..+++..+ |.+.+...||||+||++|++||+|+++|.++++||+..||+..
T Consensus 62 ~~~~~~~~~~~~~lD~~l~~i~~~~~~~~~~~~~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~ 141 (285)
T COG0122 62 AEDIEAALRRLFDLDPDLAPIIDALGPLPLLRAPGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIY 141 (285)
T ss_pred hHHHHHHHHHHHhcCCcHHHHHHhcCccccccccCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccc
Confidence 34444455555555555555555554 4444446899999999999999999999999999999999764
Q ss_pred --CCCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 039703 135 --NILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHK 212 (284)
Q Consensus 135 --~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r 212 (284)
||+|++|++++++.|+.||++.+|++||+++|+++.+|.++++.+..++++++++.|++|+|||+|||+|+|||+||+
T Consensus 142 ~~fptpe~l~~~~~~~l~~~g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr 221 (285)
T COG0122 142 HSFPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGR 221 (285)
T ss_pred cCCCCHHHHHhcCHHHHHHhCCcHHHHHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccChHHHHHHHHHhCCCCCCCHHHHHHHHHhcCChhHHHHHHHHHhhhhcC
Q 039703 213 PDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGSWYMWRLMEAKG 268 (284)
Q Consensus 213 ~dvfPv~D~~v~r~~~rly~~~~~~~~~~~~~~~e~~~Pyrs~a~~yLw~~~~~~~ 268 (284)
+|+||++|++++++++++|+.+..++...++.+.|.|+||+|||++|||++++...
T Consensus 222 ~dvfP~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w~p~rs~A~~yLw~~~~~~~ 277 (285)
T COG0122 222 PDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERWGPYRSYAALYLWRYARATT 277 (285)
T ss_pred CCCCChHHHHHHHHHHHHhcCCCCchHHHHHHHHhcccCHHHHHHHHHHHhhhccc
Confidence 99999999999999999996666667677899999999999999999999987653
No 3
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=7.9e-45 Score=336.34 Aligned_cols=201 Identities=21% Similarity=0.297 Sum_probs=181.9
Q ss_pred CcccccCCCCCchhHHHHHHHHHhcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCC
Q 039703 55 NSPKIFKPLTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGED 134 (284)
Q Consensus 55 ~~p~~~~~l~l~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~ 134 (284)
...+++++|+||.|++.+.++| +.+++.++|+|+++..|+||++|++||+||+|+.++.++..||+++||++.
T Consensus 74 ~~~~vrr~fdLd~d~~~i~~~L-------~~~~~~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l 146 (283)
T PRK10308 74 CLAKMSRLFDLQCNPQIVNGAL-------GKLGAARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERL 146 (283)
T ss_pred HHHHHHHHcCCCCCHHHHHHHH-------HHHHHhCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccc
Confidence 4566889999999999998755 578999999999988999999999999999999999999999999999743
Q ss_pred --------CCCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 135 --------NILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 135 --------~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
||+|++|+++++++|++|||+++|++||+++|+.+.+|.++++.. .+.+++++.|++|||||+|||+||+
T Consensus 147 ~~~~~~~~FPtpe~La~~~~~eL~~~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~--~~~~~~~~~L~~LpGIGpwTA~~vl 224 (283)
T PRK10308 147 DDFPEYVCFPTPERLAAADPQALKALGMPLKRAEALIHLANAALEGTLPLTIP--GDVEQAMKTLQTFPGIGRWTANYFA 224 (283)
T ss_pred cCCCCccCCCCHHHHHcCCHHHHHHCCCCHHHHHHHHHHHHHHHcCCCCcccc--CCHHHHHHHHhcCCCcCHHHHHHHH
Confidence 799999999999999999999999999999999999999987653 4678999999999999999999999
Q ss_pred HHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHHHHHHHHhcCChhHHHHHHHHHhhhhcCCch
Q 039703 207 IFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGSWYMWRLMEAKGVLP 271 (284)
Q Consensus 207 lf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~~~~~~e~~~Pyrs~a~~yLw~~~~~~~~~~ 271 (284)
||+||++|+||.+|+||+|.+ .+ .++++++++++.|+|||+|+++|||+.....+.++
T Consensus 225 lr~lg~~D~fp~~D~~l~~~~---~~----~~~~~~~~~a~~w~P~rsya~~~LW~~~~~~~~~~ 282 (283)
T PRK10308 225 LRGWQAKDVFLPDDYLIKQRF---PG----MTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDED 282 (283)
T ss_pred HHhCCCCCCCCcccHHHHHhc---cc----CCHHHHHHHHHhcCCHHHHHHHHHHHcCCccCCCC
Confidence 999999999999999999854 22 36788999999999999999999999866555444
No 4
>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=1e-43 Score=332.84 Aligned_cols=211 Identities=17% Similarity=0.207 Sum_probs=188.1
Q ss_pred CcccccCCCCCchhHHHHHHHHHhcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCC-
Q 039703 55 NSPKIFKPLTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGE- 133 (284)
Q Consensus 55 ~~p~~~~~l~l~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~- 133 (284)
...+++++|+||.|++.+++++...||.|+.++++++|+|+++. +|||+||++|||||+|+++|.+++++|+++||..
T Consensus 74 ~~~~ir~~f~Ld~d~~~i~~~~~~~D~~l~~~~~~~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~ 152 (310)
T TIGR00588 74 LETKLEKYFQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGPRL 152 (310)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHhhcCHHHHHHHHhCCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCc
Confidence 34568899999999999999987899999999999999999876 9999999999999999999999999999999943
Q ss_pred ---------CCCCHHHHhcCCH-HHHHhcCCChHHHHHHHHHHHHHHcCCC---ChhHhhcCChHHHHHHhhcCCCccHH
Q 039703 134 ---------DNILPDAVLAVSP-QQLREIGVSYRKASYLRDLAEKYTDGIL---SDESIVEMDDVTMFKMLTSVKGIGAW 200 (284)
Q Consensus 134 ---------~~p~Pe~la~~~~-e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l---~l~~l~~~~~ee~~~~L~~l~GIGpw 200 (284)
.||+|++|+..+. ++|+.|||++| |+||+.+|+.+.+|.. +++.|..++++++++.|++|||||+|
T Consensus 153 ~~~~g~~~~~FPtp~~La~~~~e~~Lr~~G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~ 231 (310)
T TIGR00588 153 ITLDGVTYHGFPSLHALTGPEAEAHLRKLGLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPK 231 (310)
T ss_pred ccCCCcccccCCCHHHHhCCChHHHHHHcCCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHH
Confidence 2899999998765 58999999875 9999999999999653 56778899999999999999999999
Q ss_pred HHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCC---------CCHHHHHHH-HHhcCChhHHHHHHHHHhhhhcC
Q 039703 201 SVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKEL---------PGALKMEEV-CEKWKPYRSVGSWYMWRLMEAKG 268 (284)
Q Consensus 201 TA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~---------~~~~~~~~~-~e~~~Pyrs~a~~yLw~~~~~~~ 268 (284)
||+||+||+|+++|+||+ |+||+|+++++|+.... .++++++++ .+.|+||+|||+.|||.+.+..+
T Consensus 232 tAd~vll~~l~~~d~~Pv-D~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~~~~g~~ag~aq~~lf~~~~~~~ 308 (310)
T TIGR00588 232 VADCICLMGLDKPQAVPV-DVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSLWGPYAGWAQAVLFSADLRQG 308 (310)
T ss_pred HHHHHHHHhCCCCCceee-cHHHHHHHHHHhcccccccccccCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhhcc
Confidence 999999999999999999 99999999999987431 234556664 56899999999999999987654
No 5
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=100.00 E-value=1e-32 Score=233.71 Aligned_cols=152 Identities=31% Similarity=0.429 Sum_probs=142.1
Q ss_pred HHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCC---hHHHHHHHHHHHHHHcCCCChhH
Q 039703 102 FLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVS---YRKASYLRDLAEKYTDGILSDES 178 (284)
Q Consensus 102 fe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~---~rKA~~I~~lA~~i~~g~l~l~~ 178 (284)
||+||++||+||++++++..++.+|++.|| |+|++|+.++.++|++||.+ ++||++|+++|+.+.++..++..
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g----pt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~ 76 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG----PTPEALAAADEEELRELIRSLGYRRKAKYLKELARAIVEGFGGLVL 76 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC----CCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCccC
Confidence 799999999999999999999999999998 89999999999999998887 88999999999999998765543
Q ss_pred hhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHHHHHHHHhcC--ChhHHH
Q 039703 179 IVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWK--PYRSVG 256 (284)
Q Consensus 179 l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~~~~~~e~~~--Pyrs~a 256 (284)
+++++++.|++|||||+|||+|+++|+++ +++||+ |+|++|+++++++.+..++++++..+++.|. ||++++
T Consensus 77 ----~~~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pv-D~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (158)
T cd00056 77 ----DDPDAREELLALPGVGRKTANVVLLFALG-PDAFPV-DTHVRRVLKRLGLIPKKKTPEELEELLEELLPKPYWGEA 150 (158)
T ss_pred ----CCcccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCcc-chhHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHH
Confidence 77899999999999999999999999999 899999 9999999999988777788999999999998 899999
Q ss_pred HHHHHHh
Q 039703 257 SWYMWRL 263 (284)
Q Consensus 257 ~~yLw~~ 263 (284)
.+|||.+
T Consensus 151 ~~~l~~~ 157 (158)
T cd00056 151 NQALMDL 157 (158)
T ss_pred HHHHHHc
Confidence 9999985
No 6
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.97 E-value=6.8e-32 Score=243.98 Aligned_cols=203 Identities=17% Similarity=0.156 Sum_probs=175.1
Q ss_pred CcccccCCCCCchhHHHHHHHHHhcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCC
Q 039703 55 NSPKIFKPLTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGED 134 (284)
Q Consensus 55 ~~p~~~~~l~l~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~ 134 (284)
..--|+.||.+|.++...+.++...|+.++.+.. .|.|+. +++|||+|+++|||||.+++++..|.++|+..||...
T Consensus 74 el~~i~~yf~ldv~L~~l~~~W~~~D~~F~~la~--qgvRlL-rQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i 150 (323)
T KOG2875|consen 74 ELEAISKYFQLDVTLAQLYHHWGSVDDHFQELAQ--QGVRLL-RQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRI 150 (323)
T ss_pred HHHHHHHHHhheeeHHHHHHHhCcCChHHHHHHH--hhhHHH-hcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcce
Confidence 3334889999999999999999999999999986 577875 5899999999999999999999999999999999652
Q ss_pred ----------CCCHHHHhc-CCHHHHHhcCCChHHHHHHHHHHHHHHcCCC---ChhHhhcCChHHHHHHhhcCCCccHH
Q 039703 135 ----------NILPDAVLA-VSPQQLREIGVSYRKASYLRDLAEKYTDGIL---SDESIVEMDDVTMFKMLTSVKGIGAW 200 (284)
Q Consensus 135 ----------~p~Pe~la~-~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l---~l~~l~~~~~ee~~~~L~~l~GIGpw 200 (284)
||+.+.|.. ..+++||++||+|| |+||...|+++++..- .+..|+.+++||++++|+.+||||+|
T Consensus 151 ~~~dg~~~h~FPsl~~L~g~~~Ea~LR~~gfGYR-AkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~K 229 (323)
T KOG2875|consen 151 IQLDGVDYHGFPSLQALAGPEVEAELRKLGFGYR-AKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPK 229 (323)
T ss_pred EeecCcccccCccHHHhcCcHhHHHHHHcCcchh-HHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcch
Confidence 799999884 45678999999999 9999999999998433 47788899999999999999999999
Q ss_pred HHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCC--C--CC---HHHHHH-HHHhcCChhHHHHHHHHH
Q 039703 201 SVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE--L--PG---ALKMEE-VCEKWKPYRSVGSWYMWR 262 (284)
Q Consensus 201 TA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~--~--~~---~~~~~~-~~e~~~Pyrs~a~~yLw~ 262 (284)
+|+||++++|+...++|| |+||.|+.+.++..+. . .+ +.++.. +.+.|++|+|||+.+|+.
T Consensus 230 VADCI~Lm~l~~~~~VPV-DvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~~~~G~YAGwAQ~~lfs 298 (323)
T KOG2875|consen 230 VADCICLMSLDKLSAVPV-DVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFRSLWGEYAGWAQAVLFS 298 (323)
T ss_pred HhhhhhhhhcCCCCcccc-hhhHHHHhhcccCCCccccccCCcchhHHHHHHHHHHhcccccchhheeec
Confidence 999999999999999999 9999999995433221 1 12 234444 568999999999999985
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=2.6e-30 Score=226.72 Aligned_cols=168 Identities=21% Similarity=0.233 Sum_probs=145.8
Q ss_pred chHHHHHHHcCCCCC-CCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcCCC
Q 039703 81 PLLATLIDAHRPPTF-ESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGVS 155 (284)
Q Consensus 81 p~l~~li~~~~g~r~-~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~Gl~ 155 (284)
.++..+.+.|++.+. ....|||+.||++||+||++++++.+++.+|.+.| |+|++|++++.++| +++||+
T Consensus 5 ~i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~-----pt~~~l~~~~~~~L~~~ir~~G~~ 79 (191)
T TIGR01083 5 EILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLFEVY-----PTPQALAQAGLEELEEYIKSIGLY 79 (191)
T ss_pred HHHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHC-----CCHHHHHcCCHHHHHHHHHhcCCh
Confidence 467778888987653 23479999999999999999999999999999876 79999999999997 789999
Q ss_pred hHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCC
Q 039703 156 YRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE 235 (284)
Q Consensus 156 ~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~ 235 (284)
++||++|+++|+.+.++.- .+.++.++.|++|||||+|||+|||+|++++++ ||+ |+|++|++.|+ |+..
T Consensus 80 ~~Ka~~i~~~a~~i~~~~~-------~~~~~~~~~L~~l~GIG~ktA~~ill~~~~~~~-~~v-D~~v~Ri~~r~-g~~~ 149 (191)
T TIGR01083 80 RNKAKNIIALCRILVERYG-------GEVPEDREELVKLPGVGRKTANVVLNVAFGIPA-IAV-DTHVFRVSNRL-GLSK 149 (191)
T ss_pred HHHHHHHHHHHHHHHHHcC-------CCCchHHHHHHhCCCCcHHHHHHHHHHHcCCCc-ccc-chhHHHHHHHc-CCCC
Confidence 9999999999999987421 123457999999999999999999999999985 899 99999999998 5555
Q ss_pred CCCHHHHHHHHHhcCChhHHHHHHHHHh
Q 039703 236 LPGALKMEEVCEKWKPYRSVGSWYMWRL 263 (284)
Q Consensus 236 ~~~~~~~~~~~e~~~Pyrs~a~~yLw~~ 263 (284)
..+++++++..+.|.|+..|..+|+|..
T Consensus 150 ~~~~~~~~~~l~~~~p~~~~~~~h~~li 177 (191)
T TIGR01083 150 GKDPDKVEEELLKLIPREFWTKLHHWLI 177 (191)
T ss_pred CCCHHHHHHHHHHHCCchhHHHHHHHHH
Confidence 5678889999999999999998888853
No 8
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.96 E-value=2.9e-28 Score=215.79 Aligned_cols=170 Identities=21% Similarity=0.269 Sum_probs=149.7
Q ss_pred CchHHHHHHHcCCCCCCC-CCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcCC
Q 039703 80 DPLLATLIDAHRPPTFES-SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGV 154 (284)
Q Consensus 80 Dp~l~~li~~~~g~r~~~-~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~Gl 154 (284)
+.++..+.+.+|.+.... ..+||+.||.+|||||++++.+..++.+|++.| ++|++++.+++++| +.+||
T Consensus 7 ~~i~~~l~~~~p~~~~~l~~~~pf~lLva~iLSaqttD~~vn~at~~Lf~~~-----~t~e~l~~a~~~~l~~~I~~iGl 81 (211)
T COG0177 7 LEILDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPALFKRY-----PTPEDLLNADEEELEELIKSIGL 81 (211)
T ss_pred HHHHHHHHHHCCCCCCccCcCCcHHHHHHHHHhccCchHHHHHHHHHHHHHc-----CCHHHHHcCCHHHHHHHHHhcCC
Confidence 345777788888876653 489999999999999999999999999999999 59999999999876 57899
Q ss_pred ChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCC
Q 039703 155 SYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLK 234 (284)
Q Consensus 155 ~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~ 234 (284)
+++||++|+.+++.+.+..- .+.++.+++|++|||||+|||++||.++||.| +||| |+||.|+..|+ |+.
T Consensus 82 yr~KAk~I~~~~~~l~e~~~-------g~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~V-DTHV~Rvs~R~-gl~ 151 (211)
T COG0177 82 YRNKAKNIKELARILLEKFG-------GEVPDTREELLSLPGVGRKTANVVLSFAFGIP-AIAV-DTHVHRVSNRL-GLV 151 (211)
T ss_pred cHHHHHHHHHHHHHHHHHcC-------CCCCchHHHHHhCCCcchHHHHHHHHhhcCCC-cccc-cchHHHHHHHh-CCC
Confidence 99999999999999998321 13345899999999999999999999999999 9999 99999999999 887
Q ss_pred CCCCHHHHHHHHHhcCChhHHHHHHHHHhh
Q 039703 235 ELPGALKMEEVCEKWKPYRSVGSWYMWRLM 264 (284)
Q Consensus 235 ~~~~~~~~~~~~e~~~Pyrs~a~~yLw~~~ 264 (284)
...+++++++-...+-|..-|-.++.|...
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~h~~lI~ 181 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDLHHWLIL 181 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 778999999999999998888888887653
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.96 E-value=4.2e-28 Score=216.62 Aligned_cols=153 Identities=23% Similarity=0.234 Sum_probs=129.5
Q ss_pred HcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhC--CCCCCCHHHHhcCCHHHHHhc----CCChHHHHHH
Q 039703 89 AHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFN--GEDNILPDAVLAVSPQQLREI----GVSYRKASYL 162 (284)
Q Consensus 89 ~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G--~~~~p~Pe~la~~~~e~Lr~~----Gl~~rKA~~I 162 (284)
.+++..|+...+||+.||++||+||++++++.+++.+|.+++. +..+++|+.|++++.++|+++ ||+++||++|
T Consensus 18 ~~~~~~WWp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~L 97 (218)
T PRK13913 18 KNAPAWWWPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRL 97 (218)
T ss_pred hcCCCCCCcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHH
Confidence 4555556667899999999999999999999999999998742 223579999999999998766 9999999999
Q ss_pred HHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHHH
Q 039703 163 RDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKM 242 (284)
Q Consensus 163 ~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~~ 242 (284)
+++|+.+.++..+++. +..++.+++|++|||||+|||++||+|++++| +||| |+|++|++.|+ |+.. .+++++
T Consensus 98 k~la~~i~~~~g~~~~---~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp-~fvV-Dty~~Rv~~Rl-G~~~-~~y~~~ 170 (218)
T PRK13913 98 IDLSENILKDFGSFEN---FKQEVTREWLLDQKGIGKESADAILCYVCAKE-VMVV-DKYSYLFLKKL-GIEI-EDYDEL 170 (218)
T ss_pred HHHHHHHHHHcCCchh---ccCchHHHHHHcCCCccHHHHHHHHHHHcCCC-cccc-chhHHHHHHHc-CCCC-CCHHHH
Confidence 9999999885444433 33457899999999999999999999999998 7999 99999999998 8853 467888
Q ss_pred HHHHHh
Q 039703 243 EEVCEK 248 (284)
Q Consensus 243 ~~~~e~ 248 (284)
+.+.+.
T Consensus 171 ~~~~~~ 176 (218)
T PRK13913 171 QHFFEK 176 (218)
T ss_pred HHHHHH
Confidence 777664
No 10
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.96 E-value=5.4e-28 Score=203.04 Aligned_cols=140 Identities=24% Similarity=0.272 Sum_probs=125.6
Q ss_pred HhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcCCChHHHHHHHHHHHHHHcCCCChhHhhcCChH
Q 039703 110 LYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDV 185 (284)
Q Consensus 110 lsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~e 185 (284)
|+||++++.+..++.+|++.| ++|++|+++++++| ++||++++|+++|+++|+.+.+... .+.+
T Consensus 1 l~qq~~~~~a~~~~~~l~~~~-----~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~-------~~~~ 68 (149)
T smart00478 1 LSQQTSDEAVNKATERLFEKF-----PTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYG-------GEVP 68 (149)
T ss_pred CCCcccHHHHHHHHHHHHHHC-----CCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHC-------CCcc
Confidence 589999999999999999998 58999999999987 7899999999999999999987321 1224
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHHHHHHHHhcCC---hhHHHHHHHHH
Q 039703 186 TMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKP---YRSVGSWYMWR 262 (284)
Q Consensus 186 e~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~~~~~~e~~~P---yrs~a~~yLw~ 262 (284)
+.++.|++|||||+|||+||++|++++ +++|+ |+|++|+++++|..+..+++++++.+++.|.| |++++.+|+|+
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~-D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~ 146 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALGK-PFIPV-DTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPKEDWRELNLLLIDF 146 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCcc-chHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence 678999999999999999999999999 67777 99999999999888777778999999999999 99999999998
Q ss_pred h
Q 039703 263 L 263 (284)
Q Consensus 263 ~ 263 (284)
.
T Consensus 147 g 147 (149)
T smart00478 147 G 147 (149)
T ss_pred c
Confidence 4
No 11
>PRK10702 endonuclease III; Provisional
Probab=99.95 E-value=2.5e-27 Score=211.07 Aligned_cols=167 Identities=17% Similarity=0.157 Sum_probs=138.5
Q ss_pred chHHHHHHHcCCC-CCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHH----hcCCC
Q 039703 81 PLLATLIDAHRPP-TFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLR----EIGVS 155 (284)
Q Consensus 81 p~l~~li~~~~g~-r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr----~~Gl~ 155 (284)
.++..+.+.||.. .+...++|||+||.+|||||+++..+..++.+|...| |+|++|+++++++|+ .+||+
T Consensus 8 ~i~~~l~~~~~~~~~~~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~-----pt~e~l~~a~~~~l~~~i~~~G~y 82 (211)
T PRK10702 8 EILTRLRDNNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVA-----NTPAAMLELGVEGVKTYIKTIGLY 82 (211)
T ss_pred HHHHHHHHHCCCCCCCCCCCChHHHHHHHHHHhhcCHHHHHHHHHHHHHHc-----CCHHHHHCCCHHHHHHHHHHcCCH
Confidence 3566777888753 3445789999999999999999999999999999876 799999999999876 57999
Q ss_pred hHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCC
Q 039703 156 YRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE 235 (284)
Q Consensus 156 ~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~ 235 (284)
++||++|+++|+.+.+.. +.+.++.+++|++|||||+|||++||+|+|+++ +||| |+||+|++.|++ +..
T Consensus 83 ~~kA~~l~~~a~~i~~~~-------~~~~p~~~~~Ll~lpGVG~ktA~~ill~a~~~~-~~~V-Dt~v~Rv~~r~g-~~~ 152 (211)
T PRK10702 83 NSKAENVIKTCRILLEQH-------NGEVPEDRAALEALPGVGRKTANVVLNTAFGWP-TIAV-DTHIFRVCNRTQ-FAP 152 (211)
T ss_pred HHHHHHHHHHHHHHHHHc-------CCCCCchHHHHhcCCcccHHHHHHHHHHHcCCC-cccc-cchHHHHHHHhC-CCC
Confidence 999999999999998631 123356899999999999999999999999996 8999 999999999994 444
Q ss_pred CCCHHHHHHHHHhcCChhHHHHHHHHH
Q 039703 236 LPGALKMEEVCEKWKPYRSVGSWYMWR 262 (284)
Q Consensus 236 ~~~~~~~~~~~e~~~Pyrs~a~~yLw~ 262 (284)
..+++++++..+..-|-.-+..++.|.
T Consensus 153 ~~~~~~~~~~l~~~lp~~~~~~~~~~l 179 (211)
T PRK10702 153 GKNVEQVEEKLLKVVPAEFKVDCHHWL 179 (211)
T ss_pred CCCHHHHHHHHHHhCCchHHHHHHHHH
Confidence 457778877766666766665555553
No 12
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.94 E-value=1.3e-25 Score=207.32 Aligned_cols=155 Identities=20% Similarity=0.341 Sum_probs=128.8
Q ss_pred HHHHHHHcC--CCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcCCCh
Q 039703 83 LATLIDAHR--PPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGVSY 156 (284)
Q Consensus 83 l~~li~~~~--g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~Gl~~ 156 (284)
|-.+++.++ .++|+...|||+.||+.||+||++++++..++.||.++| |+|++|+++++++| +.+|++
T Consensus 6 l~~w~~~~~r~~lpWr~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~~f-----pt~~~La~a~~eeL~~~~~~lG~y- 79 (275)
T TIGR01084 6 LLSWYDKYGRKTLPWRQNKTPYRVWLSEVMLQQTQVATVIPYFERFLERF-----PTVQALANAPQDEVLKLWEGLGYY- 79 (275)
T ss_pred HHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-----CCHHHHHCcCHHHHHHHHHHCCcH-
Confidence 444555555 378888899999999999999999999999999999986 89999999999998 789998
Q ss_pred HHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCC
Q 039703 157 RKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKEL 236 (284)
Q Consensus 157 rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~ 236 (284)
+||++|+++|+.+.+... ...++.+++|++|||||+|||+||++|+|++++ +++ |+||+|+++|+|+....
T Consensus 80 ~RAr~L~~~A~~i~~~~~-------g~~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~-~~v-D~~v~RVl~Rl~~~~~~ 150 (275)
T TIGR01084 80 ARARNLHKAAQEVVEEFG-------GEFPQDFEDLAALPGVGRYTAGAILSFALNKPY-PIL-DGNVKRVLSRLFAVEGW 150 (275)
T ss_pred HHHHHHHHHHHHHHHHcC-------CCCcHHHHHHHhCCCCCHHHHHHHHHHHCCCCC-Ccc-hHhHHHHHHHHccCcCC
Confidence 579999999999987211 112346899999999999999999999999995 456 99999999999998766
Q ss_pred CCHHHHHH----HHHhcCCh
Q 039703 237 PGALKMEE----VCEKWKPY 252 (284)
Q Consensus 237 ~~~~~~~~----~~e~~~Py 252 (284)
++++++++ +++.+-|.
T Consensus 151 ~~~~~~~~~l~~~~~~~lp~ 170 (275)
T TIGR01084 151 PGKKKVENRLWTLAESLLPK 170 (275)
T ss_pred CCHHHHHHHHHHHHHHHCCh
Confidence 65544443 46777664
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.91 E-value=3.5e-23 Score=196.66 Aligned_cols=155 Identities=17% Similarity=0.241 Sum_probs=125.6
Q ss_pred HHHHHHHcC--CCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHH----hcCCCh
Q 039703 83 LATLIDAHR--PPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLR----EIGVSY 156 (284)
Q Consensus 83 l~~li~~~~--g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr----~~Gl~~ 156 (284)
|-.+.+.++ .++|+...|||+.+|+.|++||++++++...+.||.++| |++++|+++++++|. .+|++
T Consensus 10 ll~W~~~~~r~~lpWr~~~dpy~ilVseILlQQT~v~~v~~~~~rl~~~f-----Pt~~~La~a~~eel~~~~~glGyy- 83 (350)
T PRK10880 10 VLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARF-----PTVTDLANAPLDEVLHLWTGLGYY- 83 (350)
T ss_pred HHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHHC-----cCHHHHHCcCHHHHHHHHHcCChH-
Confidence 344555655 457877889999999999999999999999999999987 899999999999986 47886
Q ss_pred HHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCC
Q 039703 157 RKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKEL 236 (284)
Q Consensus 157 rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~ 236 (284)
+||++|+.+|+.+.+.. +...++.+++|++|||||+|||++||+|+|+++ +++| |+||+|++.|+|+....
T Consensus 84 ~RAr~L~~~A~~i~~~~-------~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~~-~~iV-D~nV~RV~~Rl~~i~~~ 154 (350)
T PRK10880 84 ARARNLHKAAQQVATLH-------GGEFPETFEEVAALPGVGRSTAGAILSLSLGKH-FPIL-DGNVKRVLARCYAVSGW 154 (350)
T ss_pred HHHHHHHHHHHHHHHHh-------CCCchhhHHHHhcCCCccHHHHHHHHHHHCCCC-eecc-cHHHHHHHHHHhcccCC
Confidence 48999999999997631 112246899999999999999999999999996 4445 99999999999998755
Q ss_pred CCHHHH----HHHHHhcCCh
Q 039703 237 PGALKM----EEVCEKWKPY 252 (284)
Q Consensus 237 ~~~~~~----~~~~e~~~Py 252 (284)
+++++. .++.+.+-|-
T Consensus 155 ~~~~~~~~~l~~~~~~l~p~ 174 (350)
T PRK10880 155 PGKKEVENRLWQLSEQVTPA 174 (350)
T ss_pred CChHHHHHHHHHHHHHhCCh
Confidence 544443 3445555553
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.88 E-value=2e-21 Score=172.47 Aligned_cols=165 Identities=20% Similarity=0.261 Sum_probs=126.3
Q ss_pred HHHHHHHcCCC-CCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcC--CC
Q 039703 83 LATLIDAHRPP-TFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIG--VS 155 (284)
Q Consensus 83 l~~li~~~~g~-r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~G--l~ 155 (284)
+.+-++.|-.+ .+....+||+.||.+||+||+++..+.++..+|.. +.+ .++.++| +++| |+
T Consensus 18 ~~~r~~ef~~~~~~~~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~~----------~~l-~~~~eeL~~~Ir~~Gygf~ 86 (208)
T PRK01229 18 VEERIEEFKLLGEKGDEEDLFSELSFCILTANSSAEGGIKAQKEIGD----------GFL-YLSEEELEEKLKEVGHRFY 86 (208)
T ss_pred HHHHHHHHHHhhhccccCChHHHHHHHHhcCcCcHHHHHHHHHhcCH----------HHc-CCCHHHHHHHHHHhhcccH
Confidence 33334444332 33356799999999999999999999999999942 233 5666654 5675 99
Q ss_pred hHHHHHHHHHHHHHHcCCCChhHhh--cCChHHHHHHhh-cCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhC
Q 039703 156 YRKASYLRDLAEKYTDGILSDESIV--EMDDVTMFKMLT-SVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYG 232 (284)
Q Consensus 156 ~rKA~~I~~lA~~i~~g~l~l~~l~--~~~~ee~~~~L~-~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~ 232 (284)
++||++|+++++.+ |.+ ..+. ..+.++++++|+ +|||||++||++||+.... .++|+| |+|++|++.|+ |
T Consensus 87 ~~KAk~I~~~~~~~--~~l--~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~-~~~~iV-DtHv~Ri~~Rl-G 159 (208)
T PRK01229 87 NKRAEYIVEARKLY--GKL--KEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGY-EDLAIL-DRHILRFLKRY-G 159 (208)
T ss_pred HHHHHHHHHHHHHH--HHH--HHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccC-CCeeee-eHHHHHHHHHh-C
Confidence 99999999999986 322 2232 556789999999 9999999999999975544 569999 99999999999 5
Q ss_pred CCCC-------CCHHHH----HHHHHhcCChhHHHHHHHHHhhh
Q 039703 233 LKEL-------PGALKM----EEVCEKWKPYRSVGSWYMWRLME 265 (284)
Q Consensus 233 ~~~~-------~~~~~~----~~~~e~~~Pyrs~a~~yLw~~~~ 265 (284)
+... .++.++ ..++..++=+.|..-+|||..+.
T Consensus 160 ~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~~~~~Ldl~~w~~~~ 203 (208)
T PRK01229 160 LIEEIPKTLSKKRYLEIEEILREIAEELGISLGELDLYIWYKET 203 (208)
T ss_pred CCcccccccCcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 5332 355554 45678888899999999998654
No 15
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.84 E-value=6.5e-20 Score=160.39 Aligned_cols=158 Identities=21% Similarity=0.257 Sum_probs=133.6
Q ss_pred chHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcCCCh
Q 039703 81 PLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGVSY 156 (284)
Q Consensus 81 p~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~Gl~~ 156 (284)
.++..+...+|...|+...+-+|.+|++||.||++|+++.+.+++|....- ..++.|..++.++| ++.||++
T Consensus 10 ~iy~~L~~~yg~q~WWp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~----~~l~~I~~~~~~~L~elIrpsGFYn 85 (215)
T COG2231 10 KIYKELLRLYGDQGWWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGI----LNLKKILKLDEEELAELIRPSGFYN 85 (215)
T ss_pred HHHHHHHHHcCCccCCCCCCchhHHHHHHHhccccHHHHHHHHHHHHHccc----CCHHHHhcCCHHHHHHHHhccchHH
Confidence 357778888888888877888899999999999999999999999998742 67999999999886 4679999
Q ss_pred HHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCC
Q 039703 157 RKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKEL 236 (284)
Q Consensus 157 rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~ 236 (284)
+|+++|+++...+...-.+++.+. ....+++|++|+|||+-|||.+|++++++| +|+| |..-+|.+.|+++....
T Consensus 86 qKa~rLk~l~k~l~~~~~~~~~~~---~~~~R~~LL~iKGIG~ETaDsILlYa~~rp-~FVv-D~Yt~R~l~rlg~i~~k 160 (215)
T COG2231 86 QKAKRLKALSKNLAKFFINLESFK---SEVLREELLSIKGIGKETADSILLYALDRP-VFVV-DKYTRRLLSRLGGIEEK 160 (215)
T ss_pred HHHHHHHHHHHHHHHHhhhhhccc---hHHHHHHHHccCCcchhhHHHHHHHHhcCc-ccch-hHHHHHHHHHhcccccc
Confidence 999999888888887555554442 334899999999999999999999999998 8999 99999999999665543
Q ss_pred CCHHHHHHHHHh
Q 039703 237 PGALKMEEVCEK 248 (284)
Q Consensus 237 ~~~~~~~~~~e~ 248 (284)
+++++.++.+.
T Consensus 161 -~ydeik~~fe~ 171 (215)
T COG2231 161 -KYDEIKELFEE 171 (215)
T ss_pred -cHHHHHHHHHh
Confidence 77888777654
No 16
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.84 E-value=4.6e-20 Score=171.32 Aligned_cols=133 Identities=18% Similarity=0.280 Sum_probs=110.3
Q ss_pred HhcccCHHHHH-HHHHHHHHHhCCCCCCCHHHHhcCCHHHH----HhcCCChHHHHHHHHHHHHHHcCCCChhHhhcCCh
Q 039703 110 LYQQLAYKAAK-SIYTRFVALFNGEDNILPDAVLAVSPQQL----REIGVSYRKASYLRDLAEKYTDGILSDESIVEMDD 184 (284)
Q Consensus 110 lsQq~s~~~a~-~i~~rL~~~~G~~~~p~Pe~la~~~~e~L----r~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ 184 (284)
+.||+.+.++. ..++||.++| |++++|+++++++| +.+|++ +||++|+.+|+.+.++.. ..++
T Consensus 1 mlQQT~v~~v~~~yy~rf~~~f-----Pt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~-----g~~P- 68 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLEAF-----PTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHH-----SQLP- 68 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHHHC-----CCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhC-----CCCC-
Confidence 47999999986 4999999998 79999999999998 457886 579999999999986321 1122
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHHHHHHHHhcCChhHHHH
Q 039703 185 VTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGS 257 (284)
Q Consensus 185 ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~~~~~~e~~~Pyrs~a~ 257 (284)
+.+++|++|||||+|||++||+|+|+++ ++|| |+||+|++.|+||.....+.+++..+.+.+.|...+..
T Consensus 69 -~~~~~L~~LpGIG~kTA~aIl~~af~~~-~~~V-D~nV~RVl~Rl~g~~~~~~~~~l~~~~~~~l~~~~~~~ 138 (289)
T PRK13910 69 -NDYQSLLKLPGIGAYTANAILCFGFREK-SACV-DANIKRVLLRLFGLDPNIHAKDLQIKANDFLNLNESFN 138 (289)
T ss_pred -hhHHHHHhCCCCCHHHHHHHHHHHCCCC-cCcc-cHHHHHHHHHHhcCCCCccHHHHHHHHHHhCCccchHH
Confidence 3589999999999999999999999998 5788 99999999999999876677777777777776544433
No 17
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.82 E-value=7.5e-19 Score=157.02 Aligned_cols=179 Identities=20% Similarity=0.200 Sum_probs=143.5
Q ss_pred chhHHHHHHHHHhcCchHHHHHHHcCCCCCCC-----CCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHH
Q 039703 66 KGEVDIALRHLRDKDPLLATLIDAHRPPTFES-----SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDA 140 (284)
Q Consensus 66 ~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~-----~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~ 140 (284)
+.+|.+.++.+...-...-.=++..|+-+... ...-|..|+..+||.|+.++.....+.||.+..| .+++.
T Consensus 38 pe~w~~~y~~ir~mR~k~~APVD~mGc~~~~~~~~~pk~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~g----LT~e~ 113 (286)
T KOG1921|consen 38 PENWLEVYERIRKMRSKIVAPVDTMGCSRIPSLKADPKERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGG----LTLEA 113 (286)
T ss_pred CccHHHHHHHHHHHhhcccCCccccccccCccccCChhhHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcC----CCHHH
Confidence 35677777776433222233345555544332 2356999999999999999999999999999876 89999
Q ss_pred HhcCCHHHHH----hcCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcc
Q 039703 141 VLAVSPQQLR----EIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVL 216 (284)
Q Consensus 141 la~~~~e~Lr----~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvf 216 (284)
++++++.+|. .+||+.|||.||+.+|+.+.+.. +.|..+.++.|++||||||+.|..+|..+++.-..+
T Consensus 114 v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f-------~gDIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI 186 (286)
T KOG1921|consen 114 VLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKF-------DGDIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGI 186 (286)
T ss_pred HhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHh-------CCCCchhHHHHhcCCCCchHHHHHHHHHHhccceeE
Confidence 9999987764 57999999999999999998742 123345799999999999999999999999999999
Q ss_pred cccChHHHHHHHHHhCCCCCC--CHHHHHHHHHhcCChhHHHH
Q 039703 217 PVGDLGVRKGLQVLYGLKELP--GALKMEEVCEKWKPYRSVGS 257 (284)
Q Consensus 217 Pv~D~~v~r~~~rly~~~~~~--~~~~~~~~~e~~~Pyrs~a~ 257 (284)
.| |+||+|+..++ |+-+.. ++++++.-.+.|.|..-|..
T Consensus 187 ~V-DtHVHRi~nrl-gWv~~ktkspE~TR~aLq~wLPk~lW~e 227 (286)
T KOG1921|consen 187 CV-DTHVHRICNRL-GWVDTKTKSPEQTRVALQQWLPKSLWVE 227 (286)
T ss_pred Ee-ehHHHHHHHHh-cccccccCCHHHHHHHHHHhCcHHHHhh
Confidence 99 99999999999 554444 48999999999999876644
No 18
>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=99.81 E-value=3.9e-19 Score=141.36 Aligned_cols=103 Identities=38% Similarity=0.542 Sum_probs=91.5
Q ss_pred HHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc----CCChHHHHHHHHHHHHHHcCCCChhHhhc
Q 039703 106 AKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI----GVSYRKASYLRDLAEKYTDGILSDESIVE 181 (284)
Q Consensus 106 i~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~----Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~ 181 (284)
|++||+||++++++.+++.+|+++|| ||+|++|+++++++|+++ ||+++||+||+++|+.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g---~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~----------- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYG---FPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL----------- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHS---CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH-----------
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhc---CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh-----------
Confidence 68999999999999999999999999 799999999999999887 999999999999999987
Q ss_pred CChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHHHHHHH-HhcCC
Q 039703 182 MDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALKMEEVC-EKWKP 251 (284)
Q Consensus 182 ~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~~~~~~-e~~~P 251 (284)
|++|++++.|+|++|+++++|+....++++++++.. +.|.|
T Consensus 67 -----------------------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~p 108 (108)
T PF00730_consen 67 -----------------------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWPP 108 (108)
T ss_dssp -----------------------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGTT
T ss_pred -----------------------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCcC
Confidence 888856666999999999999998777888887776 78776
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=99.79 E-value=1.3e-18 Score=150.46 Aligned_cols=129 Identities=21% Similarity=0.242 Sum_probs=105.0
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHH----hc----CCChHHHHHHHHHHHHH
Q 039703 98 SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLR----EI----GVSYRKASYLRDLAEKY 169 (284)
Q Consensus 98 ~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr----~~----Gl~~rKA~~I~~lA~~i 169 (284)
..+||+.||.+|||||++++++.+++.+|.+.+|. ++|+.|+.++.++|. ++ ||+++||++|+++++.+
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~---~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~i 91 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGS---LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYV 91 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC---CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999988875 799999999998864 34 99999999999999999
Q ss_pred HcC-CCChhHhhc---CChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCC
Q 039703 170 TDG-ILSDESIVE---MDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGL 233 (284)
Q Consensus 170 ~~g-~l~l~~l~~---~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~ 233 (284)
.+. .-+++.|.. .+..++++.|++|||||++||+|||.+. ++. |-|.|-+-+.... -||.
T Consensus 92 ie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l-~~~--~~~~~~~~~~~~~-~~~~ 155 (177)
T TIGR03252 92 VDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALL-GKQ--LGVTPEGWREAAG-PYGE 155 (177)
T ss_pred HHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHH-HHH--hCCCCcchHHhcc-ccCC
Confidence 862 235566655 5667889999999999999999999964 443 4555666555433 3354
No 20
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.73 E-value=4.2e-17 Score=153.17 Aligned_cols=166 Identities=20% Similarity=0.342 Sum_probs=135.7
Q ss_pred HHHHHcC-CCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHh--cCCC-hHHHH
Q 039703 85 TLIDAHR-PPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLRE--IGVS-YRKAS 160 (284)
Q Consensus 85 ~li~~~~-g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~--~Gl~-~rKA~ 160 (284)
..+++++ .++|+...+||..+|+.|+.||+.++.+...+.+|.++| |++++|++++.+++.. .|++ |+||+
T Consensus 17 ~Wy~~~~R~LPWR~~~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rf-----Pti~~LA~A~~~evl~~W~gLGYysRAr 91 (342)
T COG1194 17 DWYDKNGRDLPWRETKDPYRVWVSEIMLQQTQVATVIPYYERFLERF-----PTIKALAAAPEDEVLKAWEGLGYYSRAR 91 (342)
T ss_pred HHHHHhCCcCCCCCCCCcceehhHHHHhhhccHhhhhhhHHHHHHhC-----CCHHHHhcCCHHHHHHHHHhcChHHHHH
Confidence 3444443 577877889999999999999999999999999999998 8999999999988653 2444 67799
Q ss_pred HHHHHHHHHHc---CCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCC
Q 039703 161 YLRDLAEKYTD---GILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELP 237 (284)
Q Consensus 161 ~I~~lA~~i~~---g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~ 237 (284)
.|+..|+.+.+ |.++. ..+.|.+|||||++||..|+.|+++++ +|+-|.+|+|++.|+|+.+..+
T Consensus 92 nL~~~A~~v~~~~~G~~P~----------~~~~l~~LpGiG~yTa~Ail~~a~~~~--~~~lDgNV~RVl~R~f~i~~~~ 159 (342)
T COG1194 92 NLHKAAQEVVERHGGEFPD----------DEEELAALPGVGPYTAGAILSFAFNQP--EPVLDGNVKRVLSRLFAISGDI 159 (342)
T ss_pred HHHHHHHHHHHHcCCCCCC----------CHHHHHhCCCCcHHHHHHHHHHHhCCC--Cceeecchheeehhhhcccccc
Confidence 99999999987 44432 467788899999999999999999998 5777999999999999987643
Q ss_pred ----CHHHHHHHHHh-cCChhHHHHHHHHHhhhhcC
Q 039703 238 ----GALKMEEVCEK-WKPYRSVGSWYMWRLMEAKG 268 (284)
Q Consensus 238 ----~~~~~~~~~e~-~~Pyrs~a~~yLw~~~~~~~ 268 (284)
+.+++..+++. ..|-+. ...|-|.+++-+.
T Consensus 160 ~~~~~~~~~~~~~~~ll~p~~~-~~~fnqammdlGA 194 (342)
T COG1194 160 GKPKTKKELWELAEQLLTPDRR-PGDFNQAMMDLGA 194 (342)
T ss_pred cccchhHHHHHHHHHhcCCCCC-hHHHHHHHHHhhh
Confidence 35677888887 456665 5667777777654
No 21
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=98.75 E-value=4.9e-08 Score=92.97 Aligned_cols=124 Identities=18% Similarity=0.198 Sum_probs=97.9
Q ss_pred CHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHH-HHH----hcCCChHHHHHHHHHHHHHHcCCC
Q 039703 100 SPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQ-QLR----EIGVSYRKASYLRDLAEKYTDGIL 174 (284)
Q Consensus 100 ~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e-~Lr----~~Gl~~rKA~~I~~lA~~i~~g~l 174 (284)
..||.+|+.|+-||+.+....+-|.+..+.+ |+..+++.++.+ +.. .+|++ +++++|+.-|+.+++|.-
T Consensus 124 RaYeVwVSEiMLQQTrV~TV~~YYt~WMqkw-----PTl~dla~Asl~~eVn~lWaGlGyY-~R~rrL~ega~~vv~~~~ 197 (555)
T KOG2457|consen 124 RAYEVWVSEIMLQQTRVQTVMKYYTRWMQKW-----PTLYDLAQASLEKEVNELWAGLGYY-RRARRLLEGAKMVVAGTE 197 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-----chHHHHHHHHHHHHHHHHHhhhhHH-HHHHHHHHHHHHHHHhCC
Confidence 5799999999999999999999999999987 788899888763 333 45555 459999999999998532
Q ss_pred ChhHhhcCChHHHHHHhhc-CCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCC
Q 039703 175 SDESIVEMDDVTMFKMLTS-VKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPG 238 (284)
Q Consensus 175 ~l~~l~~~~~ee~~~~L~~-l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~ 238 (284)
. ++| ..-+.|++ |||||++||..|+-.+|+.+.. -| |-+|.|++.|.......++
T Consensus 198 g-----e~P--rta~~l~kgvpGVG~YTAGAiaSIAf~q~tG-iV-DGNVirvlsRalAIhsDcS 253 (555)
T KOG2457|consen 198 G-----EFP--RTASSLMKGVPGVGQYTAGAIASIAFNQVTG-IV-DGNVIRVLSRALAIHSDCS 253 (555)
T ss_pred C-----CCC--ChHHHHHhhCCCCCccchhhhhhhhhcCccc-cc-ccchHHHhHHhHhhcCCcc
Confidence 1 122 13455655 9999999999999999999854 34 9999999999877655443
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.45 E-value=3.2e-06 Score=73.77 Aligned_cols=150 Identities=19% Similarity=0.215 Sum_probs=112.8
Q ss_pred CCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHH----HHhc--CCChHHHHHHHHHHHHHH
Q 039703 97 SSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQ----LREI--GVSYRKASYLRDLAEKYT 170 (284)
Q Consensus 97 ~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~----Lr~~--Gl~~rKA~~I~~lA~~i~ 170 (284)
...+.|.-|+-+||..|.|...+.++.+.|-+-|. .++.|+ |+.+ .|.++||+||...=+.+-
T Consensus 35 ~~e~lf~ELsFCILTANsSA~~~~~~q~~lG~gfl-----------y~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~ 103 (210)
T COG1059 35 TKEDLFKELSFCILTANSSATMGLRAQNELGDGFL-----------YLSEEELREKLKEVGYRFYNVRAEYIVEAREKFD 103 (210)
T ss_pred cHHHHHHHHHHHhccccchHHHHHHHHHHhccccc-----------cCCHHHHHHHHHHhcchhcccchHHHHHHHHHHH
Confidence 34588999999999999999988887776653332 234444 5567 588999999998777664
Q ss_pred cCCCChhHhhcCChHH--HHHHhh-cCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCC---CH-----
Q 039703 171 DGILSDESIVEMDDVT--MFKMLT-SVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELP---GA----- 239 (284)
Q Consensus 171 ~g~l~l~~l~~~~~ee--~~~~L~-~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~---~~----- 239 (284)
++..+..++..+ .++.|. .|+|||-+-|.-+| +-.|..|+--+ |.||.|-+.+.+-.+..+ ++
T Consensus 104 ----~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFL-RNVG~~D~AIl-DrHIlr~l~r~g~i~e~~kt~t~K~YLe 177 (210)
T COG1059 104 ----DLKIIVKADENEKVARELLVENIKGIGYKEASHFL-RNVGFEDLAIL-DRHILRWLVRYGLIDENPKTLTRKLYLE 177 (210)
T ss_pred ----HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHH-HhcChhHHHHH-HHHHHHHHHHhcccccCcccccHHHHHH
Confidence 334455555433 788888 99999999999887 45677887666 999999999996665443 22
Q ss_pred --HHHHHHHHhcCChhHHHHHHHHHh
Q 039703 240 --LKMEEVCEKWKPYRSVGSWYMWRL 263 (284)
Q Consensus 240 --~~~~~~~e~~~Pyrs~a~~yLw~~ 263 (284)
+.++.+++.++---|...+|+|..
T Consensus 178 ~E~ilr~iae~~g~s~gelDL~IWY~ 203 (210)
T COG1059 178 IEEILRSIAEEVGISLGELDLYIWYK 203 (210)
T ss_pred HHHHHHHHHHHhCCCcchhHHHHHHH
Confidence 346778888888888999999974
No 23
>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=97.78 E-value=2.2e-05 Score=48.90 Aligned_cols=22 Identities=23% Similarity=0.435 Sum_probs=19.1
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf 208 (284)
.+++|++|||||++||+.|+.|
T Consensus 9 s~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 9 SIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SHHHHHTSTT-SHHHHHHHHHH
T ss_pred CHHHHHhCCCcCHHHHHHHHhC
Confidence 5789999999999999999875
No 24
>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=97.70 E-value=2.1e-05 Score=63.63 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.8
Q ss_pred CcccccCCCCCchhHHHHHHHHHhcCchHHHHHHHcCCCCCCCCCCHHHHH
Q 039703 55 NSPKIFKPLTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESSRSPFLSL 105 (284)
Q Consensus 55 ~~p~~~~~l~l~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~~~~pfe~L 105 (284)
....+++||+|+.|++++++.+...|+.|+.+++.++|+|+ ..+||||+|
T Consensus 68 ~~~~l~~YF~Ld~dl~~l~~~~~~~D~~l~~~~~~~~GlRi-LrQdp~E~L 117 (117)
T PF07934_consen 68 IEEFLRDYFDLDVDLEKLYEDWSKKDPRLAKAIDKYRGLRI-LRQDPFETL 117 (117)
T ss_dssp HHHCHHHHTTTTS-HHHHHHHHCCHSHHHHHHHHCTTT--------HHHHH
T ss_pred HHHHHHHHhcCCccHHHHHHHHhhhCHHHHHHHhcCCCcEE-ECCChhhhC
Confidence 45668899999999999999998889999999999999999 479999997
No 25
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=95.41 E-value=0.013 Score=34.89 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=17.4
Q ss_pred HhhcCCCccHHHHHHHHHHh
Q 039703 190 MLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 190 ~L~~l~GIGpwTA~~vllf~ 209 (284)
.|++|+|||+|+|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999998644
No 26
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.00 E-value=0.051 Score=48.25 Aligned_cols=42 Identities=19% Similarity=0.306 Sum_probs=33.0
Q ss_pred CCChHHHHHHH------HHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLR------DLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~------~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.+.|-.|. .+++++.++ ..+.|+++||||++||+-+.+=
T Consensus 79 GIGPK~ALaILs~~~~~el~~aI~~~--------------D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 79 GIGPRAALRVLSGIKYNEFRDAIDRE--------------DIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CcCHHHHHHHHcCCCHHHHHHHHHhC--------------CHHHHhhCCCCCHHHHHHHHHH
Confidence 89998777776 455566554 3688999999999999988854
No 27
>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=94.55 E-value=0.0079 Score=48.98 Aligned_cols=41 Identities=22% Similarity=0.340 Sum_probs=25.3
Q ss_pred CcccccCCCCCchhHHHHHHHHHhcCchHHHHHHHcCCCCCCCC
Q 039703 55 NSPKIFKPLTFKGEVDIALRHLRDKDPLLATLIDAHRPPTFESS 98 (284)
Q Consensus 55 ~~p~~~~~l~l~~d~~~~~~~l~~~Dp~l~~li~~~~g~r~~~~ 98 (284)
...+|+|+|+||.|++.+.++| ||.++.++...+|+|+++.
T Consensus 74 ~~~rvRrlfDLdaDp~~I~~~L---dp~l~p~~~~~pGLRlPG~ 114 (116)
T PF06029_consen 74 VIARVRRLFDLDADPQAIEAHL---DPLLAPLVAARPGLRLPGA 114 (116)
T ss_dssp HHHHHHHHTTTT--HHHHHHHH-------GGGGTS-TT------
T ss_pred HHHHHHHHhCCCCCHHHHHHHH---hhcccccccCCCCCcCCCc
Confidence 3456889999999999999999 9999999999999999764
No 28
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=94.44 E-value=1.3 Score=39.08 Aligned_cols=128 Identities=19% Similarity=0.168 Sum_probs=93.2
Q ss_pred hcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc----C
Q 039703 78 DKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI----G 153 (284)
Q Consensus 78 ~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~----G 153 (284)
..||.+..-.+.--|.+.......||.|+=.+...-+|+..+.+=...|.+.|.+ .+|+.++..+++++..+ |
T Consensus 8 ~~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~---Fd~~~VA~~~e~die~Ll~d~~ 84 (187)
T PRK10353 8 SQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQ---FDPVKVAAMQEEDVERLVQDAG 84 (187)
T ss_pred CCChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcC---CCHHHHhCCCHHHHHHHhcCch
Confidence 4677777666666666666677899999999999999999999999999999975 78999999999887543 5
Q ss_pred C--ChHHHHHHHHHHHHHHc---CCCChhHhh-----------------cCC-----hHHHHHHh--hcCCCccHHHHHH
Q 039703 154 V--SYRKASYLRDLAEKYTD---GILSDESIV-----------------EMD-----DVTMFKML--TSVKGIGAWSVHM 204 (284)
Q Consensus 154 l--~~rKA~~I~~lA~~i~~---g~l~l~~l~-----------------~~~-----~ee~~~~L--~~l~GIGpwTA~~ 204 (284)
+ .++|.+.+++=|+.+.+ ...+++.+- +.| .+.+-+.| .+++=|||-|+..
T Consensus 85 IIRnr~KI~Avi~NA~~~l~i~~e~gSf~~ylW~fv~~~p~~~~~~~~~~~P~~t~~S~~lskdLKkrGFkFvGpt~~ys 164 (187)
T PRK10353 85 IIRHRGKIQAIIGNARAYLQMEQNGEPFADFVWSFVNHQPQVTQATTLSEIPTSTPASDALSKALKKRGFKFVGTTICYS 164 (187)
T ss_pred hHHhHHHHHHHHHHHHHHHHHHHhcCCHHHHHhhccCCCcccCCccchhcCCCCCHHHHHHHHHHHHcCCcccCcHHHHH
Confidence 5 56788888887777664 112333221 111 23455666 3578889988888
Q ss_pred HHHH
Q 039703 205 FMIF 208 (284)
Q Consensus 205 vllf 208 (284)
+|.-
T Consensus 165 fmqA 168 (187)
T PRK10353 165 FMQA 168 (187)
T ss_pred HHHH
Confidence 7753
No 29
>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=94.41 E-value=0.53 Score=41.22 Aligned_cols=128 Identities=19% Similarity=0.217 Sum_probs=86.2
Q ss_pred hcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc----C
Q 039703 78 DKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI----G 153 (284)
Q Consensus 78 ~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~----G 153 (284)
..||.+..-.+..-|.+.......||.|+-.+...-+|+..+.+-...|.+.|-+ .+|+.++..+++++.++ |
T Consensus 3 ~~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~---Fd~~~vA~~~e~~ie~l~~d~~ 79 (179)
T PF03352_consen 3 NSDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAG---FDPEKVAKMDEEDIERLMQDPG 79 (179)
T ss_dssp TSSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGG---GHHHHHHT--HHHHHHHTTSTT
T ss_pred CCChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHC---CCHHHHHcCCHHHHHHHhcCcc
Confidence 4577777777777676665667899999999999999999999999999999864 68999999999988653 5
Q ss_pred C--ChHHHHHHHHHHHHHHc---CCCChhHh-h----------------cCC-----hHHHHHHh--hcCCCccHHHHHH
Q 039703 154 V--SYRKASYLRDLAEKYTD---GILSDESI-V----------------EMD-----DVTMFKML--TSVKGIGAWSVHM 204 (284)
Q Consensus 154 l--~~rKA~~I~~lA~~i~~---g~l~l~~l-~----------------~~~-----~ee~~~~L--~~l~GIGpwTA~~ 204 (284)
+ .++|.+.+++=|+.+.+ ...++..+ . +++ .+.+-+.| .+++=|||-|+..
T Consensus 80 iIRnr~KI~Avi~NA~~~l~i~~e~gsF~~ylw~f~~~~~i~~~~~~~~~~p~~t~~s~~isk~lkk~GF~FvGpt~vys 159 (179)
T PF03352_consen 80 IIRNRRKIRAVINNARAILKIQEEFGSFSDYLWSFVNGKPIVNHWRSPEDVPASTPLSEAISKDLKKRGFKFVGPTTVYS 159 (179)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHCTTTS-EE---SSGGGS-S--HHHHHHHHHHHHTT--S--HHHHHH
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHhcCCHHHHHHhcCCCcCccccccccccCcCccHHHHHHHHHHHhCcceeECHHHHHH
Confidence 5 67788888888887765 11233322 1 111 34555666 3678899999988
Q ss_pred HHHH
Q 039703 205 FMIF 208 (284)
Q Consensus 205 vllf 208 (284)
+|.-
T Consensus 160 flqA 163 (179)
T PF03352_consen 160 FLQA 163 (179)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 8853
No 30
>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=94.18 E-value=0.13 Score=36.58 Aligned_cols=45 Identities=24% Similarity=0.395 Sum_probs=31.2
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
|++...+..|.+ .|.-+++++...+ .+.|..++|||+.+|+-+.-
T Consensus 12 Gig~~~a~~L~~------~G~~t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 12 GIGPKRAEKLYE------AGIKTLEDLANAD----PEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp TCHHHHHHHHHH------TTCSSHHHHHTSH----HHHHHTSTTSSHHHHHHHHH
T ss_pred CCCHHHHHHHHh------cCCCcHHHHHcCC----HHHHhcCCCCCHHHHHHHHH
Confidence 677664444433 2666788887664 35688999999999987753
No 31
>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=93.87 E-value=1.9 Score=37.75 Aligned_cols=126 Identities=14% Similarity=0.102 Sum_probs=91.0
Q ss_pred hcCchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc----C
Q 039703 78 DKDPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI----G 153 (284)
Q Consensus 78 ~~Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~----G 153 (284)
..||.+..-.+.--|.+.......||.|+-.+...-+|+..+.+=...|.+.|.+ .+|+.++..+++++..+ |
T Consensus 7 ~~~~l~~~YHD~eWG~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~---Fd~~~VA~~~e~~ie~L~~d~~ 83 (179)
T TIGR00624 7 SVDPLYRAYHDNEWGVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSG---FDIVKVARMTDADVERLLQDDG 83 (179)
T ss_pred CCChHHHHhhhccCCCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcC---CCHHHHhCCCHHHHHHHhcCcc
Confidence 4567666666666666666677899999999999999999999999999999975 78999999999887543 4
Q ss_pred C--ChHHHHHHHHHHHHHHc--CCCChhHhh-----cCC-----------------hHHHHHHh--hcCCCccHHHHHHH
Q 039703 154 V--SYRKASYLRDLAEKYTD--GILSDESIV-----EMD-----------------DVTMFKML--TSVKGIGAWSVHMF 205 (284)
Q Consensus 154 l--~~rKA~~I~~lA~~i~~--g~l~l~~l~-----~~~-----------------~ee~~~~L--~~l~GIGpwTA~~v 205 (284)
+ .++|.+.+++=|+.+.+ .+ +++..- .-| .+.+-+.| .+++=|||-|+..+
T Consensus 84 IIRnr~KI~Avi~NA~~~l~i~~e-sf~~ylW~fv~~~Pi~~~~~~~~~~p~~t~~S~~lskdLKkrGfkFvGpt~~ysf 162 (179)
T TIGR00624 84 IIRNRGKIEATIANARAALQLEQN-DLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESKAMSKELKKRGFRFVGPTICYAL 162 (179)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHc-cHHHHHHhccCCCCccCCccccccCCCCCHHHHHHHHHHHHcCCeecChHHHHHH
Confidence 3 35577778777777764 12 444321 001 34455566 35778888888777
Q ss_pred HH
Q 039703 206 MI 207 (284)
Q Consensus 206 ll 207 (284)
|.
T Consensus 163 mq 164 (179)
T TIGR00624 163 MQ 164 (179)
T ss_pred HH
Confidence 75
No 32
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=93.23 E-value=0.19 Score=36.39 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=26.8
Q ss_pred HHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 165 LAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 165 lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
.|+.+.+.--+++.+...+ .++|.+++|||+.+|+.+.-|
T Consensus 15 ~ak~L~~~f~sl~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFGSLEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCSCHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 3444455445788887664 467899999999999998866
No 33
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.11 E-value=0.087 Score=46.27 Aligned_cols=48 Identities=21% Similarity=0.165 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.+.|-.|.+ .++.+.+..+=..+..+.|+++||||+|||+-+++=
T Consensus 80 GIGpK~Al~ILs--------~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 80 GIGANTAMAVCS--------SLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred CccHHHHHHHHc--------CCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHH
Confidence 888886655542 122222222212224688999999999999988854
No 34
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=92.83 E-value=0.25 Score=41.04 Aligned_cols=52 Identities=10% Similarity=0.111 Sum_probs=39.9
Q ss_pred HHhcCCHHHHHhc-CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 140 AVLAVSPQQLREI-GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 140 ~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
+|-.++.++|+.+ |++..+|+.|. .+|... .++.|..++|||+++.+.+-=+
T Consensus 54 diN~A~~~el~~lpGigP~~A~~IV------~nGpf~-----------sveDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 54 DLNNSSVRAFRQFPGMYPTLAGKIV------KNAPYD-----------SVEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cCCccCHHHHHHCCCCCHHHHHHHH------HCCCCC-----------CHHHHHcCCCCCHHHHHHHHHh
Confidence 4556778888876 99999999888 266542 3678889999999988776643
No 35
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.77 E-value=0.1 Score=45.99 Aligned_cols=42 Identities=12% Similarity=0.099 Sum_probs=30.7
Q ss_pred CCChHHHHHHHH------HHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRD------LAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~------lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.+.|-.|.+ +++++.+| ..+.|+++||||++||+-+.+=
T Consensus 80 GIGpK~AL~iLs~~~~~el~~aI~~~--------------D~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 80 RLGPKTALKIISNEDAETLVTMIASQ--------------DVEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred CccHHHHHHHHcCCCHHHHHHHHHhC--------------CHHHHhhCCCCCHHHHHHHHHH
Confidence 888886666542 34444443 4688999999999999988853
No 36
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.21 E-value=0.13 Score=45.63 Aligned_cols=41 Identities=29% Similarity=0.359 Sum_probs=29.9
Q ss_pred CCChHHHHHHHH------HHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 153 GVSYRKASYLRD------LAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 153 Gl~~rKA~~I~~------lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
|++.+.|-.|.+ +++++.+| ..+.|+++||||++||+-+++
T Consensus 79 GIGpK~AL~iLs~~~~~~l~~aI~~~--------------D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 79 GVGPKLALALLSALPPALLARALLEG--------------DARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred CcCHHHHHHHHcCCCHHHHHHHHHhC--------------CHHHHhhCCCCCHHHHHHHHH
Confidence 888886655543 34444433 468899999999999998884
No 37
>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=92.00 E-value=0.14 Score=45.13 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=31.4
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.++|..|.+ .++.+++...=.++....|.++||||++||+-+++-
T Consensus 79 GIGpK~Al~iL~--------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 79 GVGPKLALAILS--------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCHHHHHHHHh--------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 999998877632 223333332111123467899999999999999843
No 38
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.87 E-value=0.15 Score=45.18 Aligned_cols=48 Identities=19% Similarity=0.104 Sum_probs=30.3
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.+.|-.|.+. ++.+.+...=..+..+.|+.+||||++||+-+++=
T Consensus 80 GIGpK~Al~iLs~--------~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 80 GVGPKAALNLLSS--------GTPDELQLAIAGGDVARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred CcCHHHHHHHHcC--------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHH
Confidence 8888866655431 12222222111224688999999999999988753
No 39
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.86 E-value=0.35 Score=42.74 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=29.0
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
|++.+.|..|.+. ++.+.+...=..+..+.|+++||||++||+-++
T Consensus 80 GIGpK~Al~ILs~--------~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 80 GIGPKLGLAMLSA--------MNAEALASAIISGNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred CCCHHHHHHHHHh--------CCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 8888877666552 122222111111235779999999999999855
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.68 E-value=0.17 Score=45.09 Aligned_cols=42 Identities=21% Similarity=0.222 Sum_probs=30.1
Q ss_pred CCChHHHHHHHH------HHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRD------LAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~------lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.+.|-.|.+ +++++.+| ..+.|+++||||++||+-+++=
T Consensus 81 GIGpK~Al~iLs~~~~~~l~~aI~~~--------------D~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 81 KVGAKTALAILSQFRPDDLRRLVAEE--------------DVAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred CcCHHHHHHHHhhCCHHHHHHHHHhC--------------CHHHHhcCCCcCHHHHHHHHHH
Confidence 888886665544 23344333 3688999999999999988843
No 41
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.65 E-value=0.19 Score=44.64 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=27.7
Q ss_pred hHHHHHHhhcCCCccHHHHHHHHHHhCCCCC
Q 039703 184 DVTMFKMLTSVKGIGAWSVHMFMIFSLHKPD 214 (284)
Q Consensus 184 ~ee~~~~L~~l~GIGpwTA~~vllf~l~r~d 214 (284)
.+++++.|..|||||++||+-+.++-+..++
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~ 36 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKRDP 36 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 5789999999999999999999998887764
No 42
>PRK00076 recR recombination protein RecR; Reviewed
Probab=91.63 E-value=0.18 Score=44.72 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=27.7
Q ss_pred hHHHHHHhhcCCCccHHHHHHHHHHhCCCCC
Q 039703 184 DVTMFKMLTSVKGIGAWSVHMFMIFSLHKPD 214 (284)
Q Consensus 184 ~ee~~~~L~~l~GIGpwTA~~vllf~l~r~d 214 (284)
.+++++.|..|||||++||+-+.++-+.+++
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~~ 36 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQRDR 36 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 4779999999999999999999999887764
No 43
>PRK13844 recombination protein RecR; Provisional
Probab=91.54 E-value=0.19 Score=44.73 Aligned_cols=31 Identities=19% Similarity=0.260 Sum_probs=27.9
Q ss_pred hHHHHHHhhcCCCccHHHHHHHHHHhCCCCC
Q 039703 184 DVTMFKMLTSVKGIGAWSVHMFMIFSLHKPD 214 (284)
Q Consensus 184 ~ee~~~~L~~l~GIGpwTA~~vllf~l~r~d 214 (284)
.+++++.|..|||||++||+-+.++-+..++
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~~ 40 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLDKSP 40 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 5789999999999999999999999887764
No 44
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=91.23 E-value=0.2 Score=44.65 Aligned_cols=52 Identities=19% Similarity=0.197 Sum_probs=33.4
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHK 212 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r 212 (284)
|++.+=|-.| .+ .++.+.|.+.=..+..+.|+++||||++||+-+++---++
T Consensus 80 GIGpK~ALai-------Ls-~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K 131 (201)
T COG0632 80 GIGPKLALAI-------LS-NLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGK 131 (201)
T ss_pred CccHHHHHHH-------Hc-CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhh
Confidence 8887744333 32 2344444443334457899999999999999887654333
No 45
>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=91.02 E-value=1.2 Score=46.41 Aligned_cols=68 Identities=21% Similarity=0.273 Sum_probs=38.4
Q ss_pred CHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHHHHcC-------------------------CCChhHhhcCChHHHHHH
Q 039703 137 LPDAVLAVSPQQLREI-GVSYRKASYLRDLAEKYTDG-------------------------ILSDESIVEMDDVTMFKM 190 (284)
Q Consensus 137 ~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~g-------------------------~l~l~~l~~~~~ee~~~~ 190 (284)
++++|..+..++|..+ ||+..++..|.+..+.-... .-+++.|...+ .++
T Consensus 456 ~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~sl~~l~~As----~ee 531 (652)
T TIGR00575 456 SVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAAS----LEE 531 (652)
T ss_pred CHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhCCHHHHHhCC----HHH
Confidence 5555555565566555 55655555554443322110 01344444433 246
Q ss_pred hhcCCCccHHHHHHHHHH
Q 039703 191 LTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 191 L~~l~GIGpwTA~~vllf 208 (284)
|.+++|||+++|+.+.-|
T Consensus 532 L~~i~GIG~~~A~~I~~f 549 (652)
T TIGR00575 532 LLSVEGVGPKVAESIVNF 549 (652)
T ss_pred HhcCCCcCHHHHHHHHHH
Confidence 788888888888888776
No 46
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=90.81 E-value=0.6 Score=44.58 Aligned_cols=58 Identities=19% Similarity=0.273 Sum_probs=40.3
Q ss_pred HHHHhc-CCChHHHHHHHHHHHHHHcCCCC-hhHhhcCChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 147 QQLREI-GVSYRKASYLRDLAEKYTDGILS-DESIVEMDDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 147 e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l~-l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
++|.++ |++..=++-| .+.+..|.+. +.....-+....+..|++|+||||+||..+--
T Consensus 48 ~~l~~lpgIG~~ia~kI---~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~ 107 (334)
T smart00483 48 KDLKGLPGIGDKIKKKI---EEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR 107 (334)
T ss_pred HHHhcCCCccHHHHHHH---HHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH
Confidence 356664 7886644433 3445568876 44444556778999999999999999976643
No 47
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.39 E-value=0.21 Score=43.92 Aligned_cols=47 Identities=23% Similarity=0.255 Sum_probs=28.8
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.+.|-.|.+. ++.+.+..+=..+..+.| ++||||++||+-+++=
T Consensus 80 GIGpK~Al~iLs~--------~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 80 GVNYKTAMSILSK--------LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred CcCHHHHHHHHcc--------CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHH
Confidence 8888866655441 122222211111234788 9999999999988843
No 48
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=90.25 E-value=0.27 Score=43.54 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=26.8
Q ss_pred hHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 039703 184 DVTMFKMLTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 184 ~ee~~~~L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
.+.+++.|..|||||+++|.-+..+-+.+.
T Consensus 7 i~~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 7 IEKLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 467899999999999999999998888775
No 49
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=90.19 E-value=1.5 Score=45.79 Aligned_cols=30 Identities=23% Similarity=0.319 Sum_probs=21.8
Q ss_pred ChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 175 SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 175 ~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
+++.+...+ .++|.+++|||+.+|+.+.-|
T Consensus 533 sl~~l~~As----~eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 533 SLEALRAAS----EEELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred CHHHHHhCC----HHHHhccCCcCHHHHHHHHHH
Confidence 344454443 356899999999999998776
No 50
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=89.94 E-value=0.55 Score=33.91 Aligned_cols=52 Identities=23% Similarity=0.400 Sum_probs=33.0
Q ss_pred HhcCCHHHHHhc-CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHH
Q 039703 141 VLAVSPQQLREI-GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMF 205 (284)
Q Consensus 141 la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~v 205 (284)
|-.++.++|..+ |++...|+.|...=+.. |.+. .+++|..++|||+.+.+-+
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~~--G~f~-----------s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREKN--GPFK-----------SLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHHH---S-S-----------SGGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHhC--cCCC-----------CHHHHhhCCCCCHHHHHHH
Confidence 456788999998 99999888877655443 5441 2466789999999998765
No 51
>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=89.54 E-value=1.3 Score=41.67 Aligned_cols=60 Identities=18% Similarity=0.280 Sum_probs=40.0
Q ss_pred HHHhc-CCChHHHHHHHHHHHHHHcCCC-ChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 039703 148 QLREI-GVSYRKASYLRDLAEKYTDGIL-SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 148 ~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l-~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
++..+ |++..-+..|..+ +..|.+ .++.+..- ....+..|++|+||||+||.-+- .+|--
T Consensus 46 ~~~~ipgiG~~ia~kI~E~---~~tG~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~--~lGi~ 107 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEI---LETGKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY--ELGIR 107 (307)
T ss_pred HhcCCCCccHHHHHHHHHH---HHcCCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH--HcCCC
Confidence 34444 7887656555554 445766 34444433 67789999999999999998766 44443
No 52
>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=88.87 E-value=1.1 Score=36.44 Aligned_cols=57 Identities=26% Similarity=0.371 Sum_probs=40.8
Q ss_pred HHHhcCCHHHHHhc-CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 139 DAVLAVSPQQLREI-GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 139 e~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
-+|-.++.++|..+ |++..+|+.|..-=.. +|.+ ..+++|..++|||+++++-+.-+
T Consensus 60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f-----------~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 60 VNINAASLEELQALPGIGPAKAKAIIEYREE--NGAF-----------KSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCCc-----------CCHHHHHcCCCCCHHHHHHHHhc
Confidence 34566788888875 8999888877665443 3432 13577889999999999877643
No 53
>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=88.45 E-value=0.49 Score=37.13 Aligned_cols=61 Identities=18% Similarity=0.250 Sum_probs=40.3
Q ss_pred HHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCCCCCHHH-HHHHHHhcCChhHHHHHHHHHh
Q 039703 185 VTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKELPGALK-MEEVCEKWKPYRSVGSWYMWRL 263 (284)
Q Consensus 185 ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~~~~~~~-~~~~~e~~~Pyrs~a~~yLw~~ 263 (284)
.+....|+.|||||+.+|+.+...|+..++ |+ -|. +|.+ .+++++.-+-+---+++|.|++
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~-----~L---------~g~----dP~~Ly~~lc~~~G~~~DpCvldvfr~ 69 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRSPA-----DL---------KGR----DPEELYERLCALTGQRHDPCVLDVFRC 69 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCCHH-----HH---------hCC----CHHHHHHHHHHHcCCcCCcHHHHHHHH
Confidence 457889999999999999999887776542 22 121 3333 3555665555555566666654
No 54
>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=87.45 E-value=1.8 Score=30.57 Aligned_cols=42 Identities=17% Similarity=0.242 Sum_probs=34.0
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHH
Q 039703 122 IYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAE 167 (284)
Q Consensus 122 i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~ 167 (284)
...+|.+. | +.++++|+.+++++|..+ |++.++++.|..-++
T Consensus 17 ~a~~L~~~-G---~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 17 RAEKLYEA-G---IKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHHT-T---CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred HHHHHHhc-C---CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 34556655 5 468999999999999987 999999999887665
No 55
>PRK08609 hypothetical protein; Provisional
Probab=87.33 E-value=1.4 Score=45.10 Aligned_cols=55 Identities=13% Similarity=0.174 Sum_probs=34.8
Q ss_pred HHHhc-CCChHHHHHHHHHHHHHHcCCC-ChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 148 QLREI-GVSYRKASYLRDLAEKYTDGIL-SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 148 ~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l-~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
+|.++ |++..=|+ .+.+.+..|.+ -++.|.. +..+.+..|++|+||||+||..+-
T Consensus 49 ~l~~ipgIG~~ia~---kI~Eil~tG~~~~le~l~~-~~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 49 DFTKLKGIGKGTAE---VIQEYRETGESSVLQELKK-EVPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred hhccCCCcCHHHHH---HHHHHHHhCChHHHHHHHh-hCcHHHHHHhcCCCCCHHHHHHHH
Confidence 45443 77766333 34445556766 3555654 344456689999999999996543
No 56
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=87.17 E-value=1.6 Score=36.95 Aligned_cols=54 Identities=26% Similarity=0.404 Sum_probs=39.3
Q ss_pred HhcCCHHHHHhc-CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 141 VLAVSPQQLREI-GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 141 la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
|-.++.|+|+.+ |+|..||+.|.+-=+ ..|.+. .++.|..++|||+.+.+-..-
T Consensus 91 iNtAs~eeL~~lpgIG~~kA~aIi~yRe--~~G~f~-----------sv~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 91 INTASAEELQALPGIGPKKAQAIIDYRE--ENGPFK-----------SVDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred ccccCHHHHHHCCCCCHHHHHHHHHHHH--HcCCCC-----------cHHHHHhccCCCHHHHHHHHh
Confidence 345788899876 799999998866433 345331 367888999999999886553
No 57
>PRK14973 DNA topoisomerase I; Provisional
Probab=86.99 E-value=2.3 Score=46.14 Aligned_cols=84 Identities=21% Similarity=0.162 Sum_probs=55.4
Q ss_pred CCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHH-HHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCC
Q 039703 135 NILPDAVLAVSPQQLREI-GVSYRKASYLRDLAE-KYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHK 212 (284)
Q Consensus 135 ~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~-~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r 212 (284)
|-+|++++.+++++|... |++.--+..+...|. .... -+.+.......++-..+|++|+|||+.|++-.-.-|.-.
T Consensus 823 ~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ag~~~ 900 (936)
T PRK14973 823 FDTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGR--PVPEKISKAAFERGRAELLSVPGLGETTLEKLYLAGVYD 900 (936)
T ss_pred CCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcC--CCchhhhhhhhcccchhhhhccCCCHHHHHHHHHcCCCC
Confidence 689999999999999874 999775555544444 3221 122222233334445559999999999998777666655
Q ss_pred CCcccccC
Q 039703 213 PDVLPVGD 220 (284)
Q Consensus 213 ~dvfPv~D 220 (284)
.+.+-..|
T Consensus 901 ~e~l~~~d 908 (936)
T PRK14973 901 GDLLVSAD 908 (936)
T ss_pred HHHhccCC
Confidence 55444434
No 58
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=86.93 E-value=0.52 Score=35.97 Aligned_cols=41 Identities=24% Similarity=0.300 Sum_probs=31.6
Q ss_pred HHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCCCC
Q 039703 189 KMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGLKE 235 (284)
Q Consensus 189 ~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~~~ 235 (284)
+.|++|||||+-||..++... ++++.|+- .+.+..+.|+..
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~~-----~~~l~~~~Gl~P 42 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFKS-----AKQLASYAGLAP 42 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhccc-----chhhhhcccccc
Confidence 468999999999999998775 78888886 344566667653
No 59
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=86.33 E-value=4.6 Score=41.44 Aligned_cols=69 Identities=19% Similarity=0.181 Sum_probs=44.9
Q ss_pred CCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHHHHc----------------------CCCChhHhhcCChHHHHHHhh
Q 039703 136 ILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEKYTD----------------------GILSDESIVEMDDVTMFKMLT 192 (284)
Q Consensus 136 p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~----------------------g~l~l~~l~~~~~ee~~~~L~ 192 (284)
-++.+|-.++.++|..+ ||+.+++..|.+-.+.-.+ ..-+++.|.+.+ .+.|+
T Consensus 448 ~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~l~~a~----~e~l~ 523 (562)
T PRK08097 448 EHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDRSWQQLLSRS----EQQWQ 523 (562)
T ss_pred CCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcCCHHHHHcCC----HHHHh
Confidence 46777777777777766 7777777766554432211 112344454443 35689
Q ss_pred cCCCccHHHHHHHHHH
Q 039703 193 SVKGIGAWSVHMFMIF 208 (284)
Q Consensus 193 ~l~GIGpwTA~~vllf 208 (284)
+|+|||+.+|+.+.-|
T Consensus 524 ~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 524 QLPGIGEGRARQLIAF 539 (562)
T ss_pred cCCCchHHHHHHHHHH
Confidence 9999999999998877
No 60
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=86.04 E-value=3 Score=43.63 Aligned_cols=21 Identities=24% Similarity=0.259 Sum_probs=18.3
Q ss_pred HHHhhcCCCccHHHHHHHHHH
Q 039703 188 FKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 188 ~~~L~~l~GIGpwTA~~vllf 208 (284)
.+.|++|+|||+.+|+.+.-|
T Consensus 540 ~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHH
Confidence 457999999999999998877
No 61
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=85.47 E-value=1.8 Score=41.73 Aligned_cols=48 Identities=21% Similarity=0.339 Sum_probs=42.4
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHHHHcCC
Q 039703 121 SIYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEKYTDGI 173 (284)
Q Consensus 121 ~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~ 173 (284)
.+.++|+++|| +.+.|+.++.++|..+ |++..||+.|++..+.+.+..
T Consensus 298 ~iAk~Ll~~FG-----SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e~~ 346 (352)
T PRK13482 298 AVIENLVEHFG-----SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAEQS 346 (352)
T ss_pred HHHHHHHHHcC-----CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 56788999998 6889999999999987 999999999999999988653
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=83.41 E-value=1 Score=39.71 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=20.7
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
..-+++..|++++||||++|-.+|
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL 89 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAIL 89 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHH
Confidence 446789999999999999997773
No 63
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=82.63 E-value=6.4 Score=41.40 Aligned_cols=30 Identities=23% Similarity=0.303 Sum_probs=20.5
Q ss_pred ChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 175 SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 175 ~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
+++.|...+ .++|.+++|||+.+|+.+.-|
T Consensus 550 si~~L~~As----~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 550 TFEAIMDAD----EEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred CHHHHHhCC----HHHHhccCCcCHHHHHHHHHH
Confidence 345554443 345788889999988888765
No 64
>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=82.15 E-value=1.3 Score=30.86 Aligned_cols=24 Identities=17% Similarity=0.411 Sum_probs=16.9
Q ss_pred HHHhhcCCCccHHHHHHHHHHhCC
Q 039703 188 FKMLTSVKGIGAWSVHMFMIFSLH 211 (284)
Q Consensus 188 ~~~L~~l~GIGpwTA~~vllf~l~ 211 (284)
++.+++|.|||+.||....-.|+.
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 467899999999999988776654
No 65
>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=82.13 E-value=4.6 Score=29.28 Aligned_cols=44 Identities=18% Similarity=-0.007 Sum_probs=30.0
Q ss_pred CChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHH-HhhcCCCccHHHHHHHH
Q 039703 154 VSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFK-MLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 154 l~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~-~L~~l~GIGpwTA~~vl 206 (284)
-..-|+..-...+..+..-..++.. . + .|.+|||||+.++.-|-
T Consensus 20 ~~~~r~~aY~~Aa~~i~~l~~~i~~--------~-~~~~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 20 GDPFRARAYRRAAAAIKALPYPITS--------G-EEDLKKLPGIGKSIAKKID 64 (68)
T ss_dssp TSHHHHHHHHHHHHHHHHSSS-HHS--------H-HHHHCTSTTTTHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHhCCHhHhh--------H-HHHHhhCCCCCHHHHHHHH
Confidence 3344577777888887764333321 2 3 59999999999998775
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=81.78 E-value=1.5 Score=38.53 Aligned_cols=48 Identities=29% Similarity=0.251 Sum_probs=29.4
Q ss_pred CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 153 GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 153 Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|++.++|..|.+. +..+.+.+.=.++..+.|.++||||+++|+.++..
T Consensus 80 GIGpk~A~~il~~--------fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 80 GVGPKLALAILSG--------LSPEELVQAIANGDVKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred CCCHHHHHHHHHh--------CCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 8888877766432 11111110001123567899999999999999854
No 67
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.71 E-value=1.3 Score=39.22 Aligned_cols=25 Identities=24% Similarity=0.469 Sum_probs=22.2
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
..-++++.|.+++||||++|-.+|-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 4467899999999999999999886
No 68
>PRK00024 hypothetical protein; Reviewed
Probab=81.61 E-value=3.9 Score=36.94 Aligned_cols=82 Identities=21% Similarity=0.229 Sum_probs=54.6
Q ss_pred HHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHH---HHHHHHcCCCChhHhh
Q 039703 105 LAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRD---LAEKYTDGILSDESIV 180 (284)
Q Consensus 105 Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~---lA~~i~~g~l~l~~l~ 180 (284)
|+..+|+.-+.-+.+..+-++|.+.|| +...+..+++++|..+ |++..||..|.. +++++........ -.
T Consensus 29 LLa~lL~~g~~~~~~~~LA~~LL~~fg-----sL~~l~~as~~eL~~i~GIG~akA~~L~a~~El~~R~~~~~~~~~-~~ 102 (224)
T PRK00024 29 LLAILLRTGTKGKSVLDLARELLQRFG-----SLRGLLDASLEELQSIKGIGPAKAAQLKAALELARRILAERLRER-EV 102 (224)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHcC-----CHHHHHhCCHHHHhhccCccHHHHHHHHHHHHHHHHHHhchhccC-CC
Confidence 555666666666677778888888987 5788999999999986 999998876644 4445544322110 01
Q ss_pred cCChHHHHHHhh
Q 039703 181 EMDDVTMFKMLT 192 (284)
Q Consensus 181 ~~~~ee~~~~L~ 192 (284)
-.+.+++.+.|.
T Consensus 103 i~~~~~~~~~l~ 114 (224)
T PRK00024 103 LLSPEDVADYLM 114 (224)
T ss_pred CCCHHHHHHHHH
Confidence 134566666664
No 69
>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=81.56 E-value=3.1 Score=30.36 Aligned_cols=53 Identities=23% Similarity=0.330 Sum_probs=33.7
Q ss_pred HHhcCCHHHHHhcCCChHHHHHHHHHHHHHHc-CCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 140 AVLAVSPQQLREIGVSYRKASYLRDLAEKYTD-GILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 140 ~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~-g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
.+...+. ..+|||.| + ...+.. |--++.+|..++. +.|..++|+|+++.+-|.
T Consensus 8 ~~~~~~I---~~L~LS~R-a------~n~L~~~~I~tv~dL~~~s~----~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 8 ELLDTPI---EDLGLSVR-A------YNCLKRAGIHTVGDLVKYSE----EDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp HHHCSBG---GGSTSBHH-H------HHHHHCTT--BHHHHHCS-H----HHHHTSTTSHHHHHHHHH
T ss_pred HHhcCcH---HHhCCCHH-H------HHHHHHhCCcCHHHHHhCCH----HHHHhCCCCCHhHHHHHH
Confidence 3444443 44599987 2 222222 4457888888765 579999999999998654
No 70
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.29 E-value=1.7 Score=38.16 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=19.3
Q ss_pred HHHHHHhhcCCCccHHHHHHHHH
Q 039703 185 VTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 185 ee~~~~L~~l~GIGpwTA~~vll 207 (284)
.+.+..|..+|||||++|..++-
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHH
Confidence 34578899999999999988863
No 71
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=76.79 E-value=8.5 Score=36.95 Aligned_cols=50 Identities=20% Similarity=0.280 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHh
Q 039703 98 SRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLRE 151 (284)
Q Consensus 98 ~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~ 151 (284)
..=|..-++...++--+..+.+.++|++|++.||. ..+.|.+++.|+|..
T Consensus 302 hliPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGt----Ei~vLi~a~~e~La~ 351 (403)
T COG1379 302 HLIPLAEIISMALGKGITTKAVKRTWERLVRAFGT----EIDVLIDAPIEELAR 351 (403)
T ss_pred ecccHHHHHHHHhccceechhHHHHHHHHHHHhcc----hhhhHhcCCHHHHhh
Confidence 34678888888889999999999999999999994 556677888888854
No 72
>PRK00024 hypothetical protein; Reviewed
Probab=76.36 E-value=3.9 Score=36.95 Aligned_cols=58 Identities=21% Similarity=0.246 Sum_probs=37.8
Q ss_pred CCHHHHHh--cCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 144 VSPQQLRE--IGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 144 ~~~e~Lr~--~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
++..||-+ +|.+.+ -+-...+|+.+.+..-++..+..++. ++|++++|||+..|..++
T Consensus 24 Lsd~ELLa~lL~~g~~-~~~~~~LA~~LL~~fgsL~~l~~as~----~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 24 LSDAELLAILLRTGTK-GKSVLDLARELLQRFGSLRGLLDASL----EELQSIKGIGPAKAAQLK 83 (224)
T ss_pred CCHHHHHHHHHcCCCC-CCCHHHHHHHHHHHcCCHHHHHhCCH----HHHhhccCccHHHHHHHH
Confidence 34444444 343333 34667788888875447778877764 558899999998885543
No 73
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.06 E-value=7.6 Score=34.98 Aligned_cols=82 Identities=21% Similarity=0.293 Sum_probs=53.0
Q ss_pred HHHHHHhcccCHH-HHHHHHHHHHHHh---CCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHH---HHHHHcCCCCh
Q 039703 105 LAKSILYQQLAYK-AAKSIYTRFVALF---NGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDL---AEKYTDGILSD 176 (284)
Q Consensus 105 Li~~IlsQq~s~~-~a~~i~~rL~~~~---G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~l---A~~i~~g~l~l 176 (284)
|+..+|+.-+..+ .+..+-++|.+.| | +...+..+++++|..+ |++..||..|..+ ++++.......
T Consensus 19 LLailL~~g~~~~~~~~~lA~~ll~~f~~~g-----~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~El~rR~~~~~~~~ 93 (218)
T TIGR00608 19 LLAIILRTGTPKGLDVLSLSKRLLDVFGRQD-----SLGHLLSAPPEELSSVPGIGEAKAIQLKAAVELAKRYAKSRMLE 93 (218)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHHhcccC-----CHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHHHHHHHHhhhhcc
Confidence 4455666666555 6667778888888 6 5778999999999986 9999888877554 44454332211
Q ss_pred hHhhcCChHHHHHHhh
Q 039703 177 ESIVEMDDVTMFKMLT 192 (284)
Q Consensus 177 ~~l~~~~~ee~~~~L~ 192 (284)
. ..-.+.+++.+.|.
T Consensus 94 ~-~~l~s~~~v~~~l~ 108 (218)
T TIGR00608 94 R-PVIRSPEAAAEFLH 108 (218)
T ss_pred C-CCCCCHHHHHHHHH
Confidence 0 01134566666663
No 74
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=75.39 E-value=13 Score=26.79 Aligned_cols=55 Identities=24% Similarity=0.349 Sum_probs=36.7
Q ss_pred HhcCCHHHHHh-c-CCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 141 VLAVSPQQLRE-I-GVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 141 la~~~~e~Lr~-~-Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|-.++.++|.. + |++..+++.|.+-=. ..|.+ + ..++|..++|||..+++-+.-+
T Consensus 10 vNta~~~~L~~~ipgig~~~a~~Il~~R~--~~g~~--~---------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 10 INTATAEELQRAMNGVGLKKAEAIVSYRE--EYGPF--K---------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CcCCCHHHHHhHCCCCCHHHHHHHHHHHH--HcCCc--C---------CHHHHHcCCCCCHHHHHHHHhh
Confidence 44567788887 3 899876655544221 12222 1 3577789999999999988765
No 75
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.35 E-value=4 Score=36.80 Aligned_cols=63 Identities=19% Similarity=0.168 Sum_probs=39.7
Q ss_pred CCHHHHHh--cCCChHHHH-HHHHHHHHHHcCC---CChhHhhcCChHHHHHHhhcCCCccHHHHHHHH-HHhCC
Q 039703 144 VSPQQLRE--IGVSYRKAS-YLRDLAEKYTDGI---LSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM-IFSLH 211 (284)
Q Consensus 144 ~~~e~Lr~--~Gl~~rKA~-~I~~lA~~i~~g~---l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl-lf~l~ 211 (284)
++..||-+ ++.+.+ -+ -...+|+.+.+.. -++..+.+++. ++|++++|||+-.|-.++ ++-++
T Consensus 14 Lsd~ELLailL~~g~~-~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~----~eL~~i~GiG~aka~~l~a~~El~ 83 (218)
T TIGR00608 14 LSDYELLAIILRTGTP-KGLDVLSLSKRLLDVFGRQDSLGHLLSAPP----EELSSVPGIGEAKAIQLKAAVELA 83 (218)
T ss_pred CCHHHHHHHHHhCCCC-CCCCHHHHHHHHHHHhcccCCHHHHHhCCH----HHHHhCcCCcHHHHHHHHHHHHHH
Confidence 34445544 344433 23 6778888888753 47888877765 567899999996665544 44343
No 76
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=74.59 E-value=3.3 Score=29.76 Aligned_cols=23 Identities=17% Similarity=0.303 Sum_probs=17.3
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
..++|.++||||++.|+.++-+-
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHH
Confidence 46789999999999999888654
No 77
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=74.06 E-value=5 Score=36.69 Aligned_cols=34 Identities=18% Similarity=0.136 Sum_probs=30.0
Q ss_pred CCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHH
Q 039703 135 NILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEK 168 (284)
Q Consensus 135 ~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~ 168 (284)
|.+.++|..++.++|..| |+|.+||+.|++....
T Consensus 215 FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 215 FGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred cccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhc
Confidence 568999999999999998 9999999999886543
No 78
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=73.94 E-value=2.5 Score=27.19 Aligned_cols=16 Identities=31% Similarity=0.563 Sum_probs=13.1
Q ss_pred hhcCCCccHHHHHHHH
Q 039703 191 LTSVKGIGAWSVHMFM 206 (284)
Q Consensus 191 L~~l~GIGpwTA~~vl 206 (284)
+..+||||++||.-++
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 3489999999997665
No 79
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=73.85 E-value=5.9 Score=28.45 Aligned_cols=41 Identities=17% Similarity=0.252 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHH
Q 039703 121 SIYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLA 166 (284)
Q Consensus 121 ~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA 166 (284)
+.-++|.+.|| +.+.|..++.|+|..+ |++...|+.|.+.-
T Consensus 14 ~~ak~L~~~f~-----sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 14 KTAKLLAKHFG-----SLEALMNASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp HHHHHHHHCCS-----CHHHHCC--HHHHCTSTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHcC-----CHHHHHHcCHHHHhccCCcCHHHHHHHHHHH
Confidence 34567778886 7899999999999987 99999887776643
No 80
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=72.73 E-value=18 Score=31.89 Aligned_cols=89 Identities=18% Similarity=0.219 Sum_probs=68.2
Q ss_pred CchHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHh----cCCC
Q 039703 80 DPLLATLIDAHRPPTFESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLRE----IGVS 155 (284)
Q Consensus 80 Dp~l~~li~~~~g~r~~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~----~Gl~ 155 (284)
||.+..-.+.--|.+.......||.|+=-+...-+||..+.+=.+.+.+.|-+ .+|+.++..+++++.. .|+=
T Consensus 11 ~ply~~YHD~eWG~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~---Fd~~kVA~~~~~dverLl~d~gII 87 (188)
T COG2818 11 DPLYLAYHDTEWGVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAFHG---FDPEKVAAMTEEDVERLLADAGII 87 (188)
T ss_pred CchhhcccccccCCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhc---CCHHHHHcCCHHHHHHHHhCcchh
Confidence 55555555555566666666899999999999999999999999999999854 6899999999988754 3654
Q ss_pred --hHHHHHHHHHHHHHHc
Q 039703 156 --YRKASYLRDLAEKYTD 171 (284)
Q Consensus 156 --~rKA~~I~~lA~~i~~ 171 (284)
+.|.+.++.=|+++.+
T Consensus 88 R~r~KI~A~i~NA~~~l~ 105 (188)
T COG2818 88 RNRGKIKATINNARAVLE 105 (188)
T ss_pred hhHHHHHHHHHHHHHHHH
Confidence 4467777777777664
No 81
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.45 E-value=3.3 Score=36.46 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=21.2
Q ss_pred hHHHHHHhhcCCCccHHHHHHHHH
Q 039703 184 DVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 184 ~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
.-++++.|.++.||||++|=.+|-
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHc
Confidence 457899999999999999988875
No 82
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.45 E-value=3.3 Score=36.33 Aligned_cols=25 Identities=40% Similarity=0.571 Sum_probs=21.5
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
..-++++.|.++.||||++|=.+|-
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 4467899999999999999988773
No 83
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.01 E-value=3.5 Score=36.63 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=21.6
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
..-++++.|.++.||||++|=.+|-
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 4467899999999999999988873
No 84
>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=71.32 E-value=3 Score=26.05 Aligned_cols=15 Identities=20% Similarity=0.344 Sum_probs=11.5
Q ss_pred hhcCCCccHHHHHHH
Q 039703 191 LTSVKGIGAWSVHMF 205 (284)
Q Consensus 191 L~~l~GIGpwTA~~v 205 (284)
+..++|||++|++-+
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 368999999999864
No 85
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.11 E-value=3.7 Score=36.11 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=21.6
Q ss_pred CChHHHHHHhhcCCCccHHHHHHHH
Q 039703 182 MDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 182 ~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
...-++++.|+++.||||++|=.+|
T Consensus 66 ~~Er~lF~~Li~V~GIGpK~AL~iL 90 (188)
T PRK14606 66 ERKKELFLSLTKVSRLGPKTALKII 90 (188)
T ss_pred HHHHHHHHHHhccCCccHHHHHHHH
Confidence 3456799999999999999998877
No 86
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.90 E-value=3.7 Score=36.37 Aligned_cols=25 Identities=20% Similarity=0.440 Sum_probs=21.8
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
..-+++..|.++.||||++|=.+|-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3467899999999999999988875
No 87
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.73 E-value=3.8 Score=36.33 Aligned_cols=25 Identities=24% Similarity=0.518 Sum_probs=21.7
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
..-++++.|+++.||||++|=.+|-
T Consensus 66 ~Er~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 66 DSLELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3457899999999999999988875
No 88
>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=69.03 E-value=9.2 Score=37.31 Aligned_cols=68 Identities=15% Similarity=0.147 Sum_probs=51.6
Q ss_pred CCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcCCCCh
Q 039703 99 RSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSD 176 (284)
Q Consensus 99 ~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l~l 176 (284)
.=|++-++..+++--...+.+..+|++|+++|| +..+-|.+++.|+|+.+. . .|-.....+.+|.+..
T Consensus 296 ~iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG----~E~~iL~~~~~eel~~~~--~----~~a~~I~~~R~G~v~~ 363 (374)
T TIGR00375 296 LIPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFG----TEIAVLHEAAEEDLARVV--P----KVAALIVKFRSGKLEL 363 (374)
T ss_pred eCCHHHHHhhhcCCCCccHHHHHHHHHHHHHhc----cHHHHHhcCCHHHHHHHH--H----HHHHHHHHHHCCCEEE
Confidence 357889999999988999999999999999999 456677899999997753 2 2333334455676644
No 89
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.98 E-value=4.4 Score=36.09 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=21.6
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
..-+++..|+++.||||++|=.+|-
T Consensus 68 ~Er~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 68 DERQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHh
Confidence 3467899999999999999988775
No 90
>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=68.17 E-value=5.2 Score=32.55 Aligned_cols=23 Identities=17% Similarity=0.375 Sum_probs=19.9
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
..+.|++|||||+..|.-++-+-
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Confidence 46788999999999999998763
No 91
>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=67.81 E-value=18 Score=25.86 Aligned_cols=37 Identities=30% Similarity=0.540 Sum_probs=32.4
Q ss_pred CC-HHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcC
Q 039703 136 IL-PDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDG 172 (284)
Q Consensus 136 p~-Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g 172 (284)
.+ +++|...+-.+|++.|++.+--+||....+.+..|
T Consensus 20 ~~~w~~lf~~~s~~LK~~GIp~r~RryiL~~~ek~r~G 57 (57)
T PF09597_consen 20 ESDWEKLFTTSSKQLKELGIPVRQRRYILRWREKYRQG 57 (57)
T ss_pred HHHHHHHHhcCHHHHHHCCCCHHHHHHHHHHHHHHhCc
Confidence 45 88999999999999999988889999999888764
No 92
>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=66.05 E-value=3.4 Score=30.77 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=17.1
Q ss_pred HhhcCCCccHHHHHHHHHHhCCCC
Q 039703 190 MLTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 190 ~L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
.+..|||||++||.-++.- ++..
T Consensus 23 ~i~gv~giG~k~A~~ll~~-~~~~ 45 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKE-YGSL 45 (75)
T ss_pred cCCCCCcccHHHHHHHHHH-hCCH
Confidence 3558999999999888743 4433
No 93
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=65.62 E-value=15 Score=35.05 Aligned_cols=64 Identities=14% Similarity=0.315 Sum_probs=43.8
Q ss_pred HHHHhc-CCChHHHHHHHHHHHHHHcCCC-ChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 039703 147 QQLREI-GVSYRKASYLRDLAEKYTDGIL-SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 147 e~Lr~~-Gl~~rKA~~I~~lA~~i~~g~l-~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
+++..+ |++.+-++-|+.++ ..|.+ -++++.+-+....++.+++|-|||.+||+..-.-||.-.
T Consensus 56 ~ea~~lP~iG~kia~ki~Eil---etG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTl 121 (353)
T KOG2534|consen 56 EEAEKLPGIGPKIAEKIQEIL---ETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTL 121 (353)
T ss_pred HHhcCCCCCCHHHHHHHHHHH---HcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHH
Confidence 444443 66666455444433 34665 355565556778899999999999999998887777543
No 94
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=65.22 E-value=6 Score=33.52 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=19.2
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
..++|..|||||++.|..|.-+.
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHH
Confidence 34556999999999999998776
No 95
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=63.83 E-value=33 Score=22.64 Aligned_cols=42 Identities=19% Similarity=0.101 Sum_probs=32.9
Q ss_pred HHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHH
Q 039703 123 YTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEK 168 (284)
Q Consensus 123 ~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~ 168 (284)
..+|.+. | +-+.++++.+++++|..+ |++..++..|+.-|+.
T Consensus 6 ~~~L~~~-G---~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 6 AQLLVEE-G---FTTVEDLAYVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred HHHHHHc-C---CCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 3444443 5 578999999999999874 9999889988887764
No 96
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=63.81 E-value=6.1 Score=32.93 Aligned_cols=21 Identities=5% Similarity=-0.001 Sum_probs=18.0
Q ss_pred HHHHhhcCCCccHHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vll 207 (284)
..++|.++|||||..|..|.-
T Consensus 59 ~~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHH
Confidence 356688999999999999994
No 97
>PRK07758 hypothetical protein; Provisional
Probab=63.59 E-value=9.4 Score=30.08 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=25.5
Q ss_pred cCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 171 DGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 171 ~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
.|.-++++|..++. ++|++|+|+|+++.+-+-
T Consensus 53 AGI~TL~dLv~~te----~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 53 HGIHTVEELSKYSE----KEILKLHGMGPASLPKLR 84 (95)
T ss_pred cCCCcHHHHHcCCH----HHHHHccCCCHHHHHHHH
Confidence 36667888888765 678899999999998764
No 98
>PRK14973 DNA topoisomerase I; Provisional
Probab=62.59 E-value=38 Score=37.02 Aligned_cols=71 Identities=18% Similarity=0.172 Sum_probs=51.9
Q ss_pred CCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHc--------------------CCCChhHhhcCChHHHHHHhhcCC
Q 039703 136 ILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTD--------------------GILSDESIVEMDDVTMFKMLTSVK 195 (284)
Q Consensus 136 p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~--------------------g~l~l~~l~~~~~ee~~~~L~~l~ 195 (284)
.+..+|+.+++++|+..|+|-.+++.+..-|+.+++ |--+++++...+ -+.|.+++
T Consensus 766 ~~~~~~~~~~~~~~~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~----p~~La~~~ 841 (936)
T PRK14973 766 NDIAALARADPADLKKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVH----PAYLALKT 841 (936)
T ss_pred chHHHHhhCCHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcC----HHHHhcCC
Confidence 567788999999999999999999999888853331 333444444333 46789999
Q ss_pred CccHHHHHHHHHHhC
Q 039703 196 GIGAWSVHMFMIFSL 210 (284)
Q Consensus 196 GIGpwTA~~vllf~l 210 (284)
||.+-|+.-....+.
T Consensus 842 g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 842 GISPETICRHAKLVC 856 (936)
T ss_pred CCChhhHHHHHHHHH
Confidence 999999976644443
No 99
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=59.40 E-value=42 Score=35.16 Aligned_cols=46 Identities=20% Similarity=0.263 Sum_probs=30.8
Q ss_pred ChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHHhCC
Q 039703 175 SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVLYGL 233 (284)
Q Consensus 175 ~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rly~~ 233 (284)
+++.|...+ .+.|.+|+|||...|.-+.-| |. +.+.+..+.+|...
T Consensus 533 sl~~l~~a~----~e~l~~i~giG~~vA~si~~f-f~--------~~~~~~li~~L~~~ 578 (667)
T COG0272 533 TLEALLAAS----EEELASIPGIGEVVARSIIEF-FA--------NEENRELIDELLAA 578 (667)
T ss_pred hHHHHHhcC----HHHHhhccchhHHHHHHHHHH-Hc--------CHHHHHHHHHHHHc
Confidence 466665554 456777999999999988876 32 34555666666443
No 100
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=59.33 E-value=23 Score=33.82 Aligned_cols=46 Identities=28% Similarity=0.297 Sum_probs=33.9
Q ss_pred cCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 152 IGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 152 ~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
.|-...|..+....|+.+..-..+++. .+.|..|||||+.+|+-|-
T Consensus 20 ~gen~~k~~ay~~Aa~~i~~l~~~i~~---------~~~l~~lpgIG~~ia~kI~ 65 (334)
T smart00483 20 FGENKRKCSYFRKAASVLKSLPFPINS---------MKDLKGLPGIGDKIKKKIE 65 (334)
T ss_pred hcccHHHHHHHHHHHHHHHhCCCCCCC---------HHHHhcCCCccHHHHHHHH
Confidence 455556788888888888764444432 2478899999999999776
No 101
>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=58.03 E-value=9.9 Score=30.22 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=20.8
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHh
Q 039703 186 TMFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 186 e~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
.+.-.|++|.|||+.+|..++...
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~l 35 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKL 35 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHT
T ss_pred chHhHHhhhhccCHHHHHHHHHHc
Confidence 378899999999999999988654
No 102
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=57.91 E-value=27 Score=31.93 Aligned_cols=53 Identities=30% Similarity=0.277 Sum_probs=38.6
Q ss_pred cCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCc
Q 039703 152 IGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDV 215 (284)
Q Consensus 152 ~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dv 215 (284)
-|+|..+++.|.. .|.-+++.+...+ .+.|..++|||..+|+-|.-+ |+.+++
T Consensus 9 pGIG~krakkLl~------~GF~Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~-l~~~~~ 61 (232)
T PRK12766 9 SGVGPSKAEALRE------AGFESVEDVRAAD----QSELAEVDGIGNALAARIKAD-VGGLEV 61 (232)
T ss_pred CCcCHHHHHHHHH------cCCCCHHHHHhCC----HHHHHHccCCCHHHHHHHHHH-hccccc
Confidence 3788776665532 3556777777654 567799999999999999876 566655
No 103
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=57.29 E-value=7.9 Score=34.54 Aligned_cols=25 Identities=28% Similarity=0.532 Sum_probs=21.0
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
+.-+++..|.++-||||++|=.+|-
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs 91 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILS 91 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHc
Confidence 3457899999999999999977764
No 104
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=57.19 E-value=10 Score=30.40 Aligned_cols=39 Identities=23% Similarity=0.155 Sum_probs=23.1
Q ss_pred cCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHH
Q 039703 152 IGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSV 202 (284)
Q Consensus 152 ~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA 202 (284)
||||.|||.+|....+.. .|.+. -++.|...-.+|+.+-
T Consensus 56 ~GLGPRKA~~Ll~~l~~~-g~~l~-----------~R~~Lv~~~~~g~~Vf 94 (104)
T PF14635_consen 56 CGLGPRKAQALLKALKQN-GGRLE-----------NRSQLVTKCLMGPKVF 94 (104)
T ss_dssp TT--HHHHHHHHHHHHHC--S---------------TTHHHHTTSS-HHHH
T ss_pred cCCChHHHHHHHHHHHHc-CCccc-----------cHHHHHhcCCCCCeEE
Confidence 799999999999887741 23442 4566666678888653
No 105
>PRK07945 hypothetical protein; Provisional
Probab=55.27 E-value=21 Score=34.03 Aligned_cols=50 Identities=16% Similarity=0.071 Sum_probs=32.4
Q ss_pred cCCChHHHHHHHHHHHHHHcCCCC-hhHhhcCChHHHHH-HhhcCCCccHHHHHHHHHH
Q 039703 152 IGVSYRKASYLRDLAEKYTDGILS-DESIVEMDDVTMFK-MLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 152 ~Gl~~rKA~~I~~lA~~i~~g~l~-l~~l~~~~~ee~~~-~L~~l~GIGpwTA~~vllf 208 (284)
.|=..-|.+.-++.|+.+..-.-+ ++.+. .+ .|++|||||+-+|..|.=+
T Consensus 17 ~~~n~frv~ayr~aa~~~~~~~~~~~~~~~-------~~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 17 ARADTYRVRAFRRAADVVEALDAAERARRA-------RAGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred cCCChhhHHHHHHHHHHHHhcChhHHHHHH-------hcCCcccCCCcCHHHHHHHHHH
Confidence 354444688888888888653222 22221 11 6889999999999877633
No 106
>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=49.04 E-value=17 Score=26.16 Aligned_cols=21 Identities=14% Similarity=0.327 Sum_probs=17.6
Q ss_pred HHHhhc-CCCccHHHHHHHHHH
Q 039703 188 FKMLTS-VKGIGAWSVHMFMIF 208 (284)
Q Consensus 188 ~~~L~~-l~GIGpwTA~~vllf 208 (284)
.+.|.. +||||+.+|..++-+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 456777 999999999998866
No 107
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=48.60 E-value=44 Score=30.94 Aligned_cols=62 Identities=18% Similarity=0.200 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHc---CCCChhHhh-cCChHHH-HHHhhcCCCccHHHHHHHHHHhCCCCCcccccC
Q 039703 159 ASYLRDLAEKYTD---GILSDESIV-EMDDVTM-FKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGD 220 (284)
Q Consensus 159 A~~I~~lA~~i~~---g~l~l~~l~-~~~~ee~-~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D 220 (284)
+..|+.+|+..+. ..+...... ..+..+. ...|.++||||+..|.-++..-..-.+++=++.
T Consensus 147 a~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~ 213 (254)
T COG1948 147 AELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASE 213 (254)
T ss_pred HHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH
Confidence 7889999999883 222222121 2344444 455699999999999988865555556776643
No 108
>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=48.38 E-value=70 Score=33.85 Aligned_cols=18 Identities=33% Similarity=0.409 Sum_probs=14.8
Q ss_pred cCCCccHHHHHHHHHHhCC
Q 039703 193 SVKGIGAWSVHMFMIFSLH 211 (284)
Q Consensus 193 ~l~GIGpwTA~~vllf~l~ 211 (284)
.++|||-++||-+... +|
T Consensus 185 ~i~gigF~~aD~iA~~-~g 202 (720)
T TIGR01448 185 DVKGIGFLTADQLAQA-LG 202 (720)
T ss_pred hcCCCCHHHHHHHHHH-cC
Confidence 5899999999998754 44
No 109
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=47.57 E-value=27 Score=33.82 Aligned_cols=38 Identities=18% Similarity=0.264 Sum_probs=26.3
Q ss_pred HHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHH
Q 039703 163 RDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHM 204 (284)
Q Consensus 163 ~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~ 204 (284)
+.+|+.+.+..-++..+.+.+ .++|..++|||+..|..
T Consensus 297 k~iAk~Ll~~FGSL~~Il~As----~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 297 SAVIENLVEHFGSLQGLLAAS----IEDLDEVEGIGEVRARA 334 (352)
T ss_pred HHHHHHHHHHcCCHHHHHcCC----HHHHhhCCCcCHHHHHH
Confidence 346677776655677776555 35578888888888876
No 110
>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=47.37 E-value=3.9 Score=32.48 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=12.1
Q ss_pred hhcCCCccHHHHHHHHHH
Q 039703 191 LTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 191 L~~l~GIGpwTA~~vllf 208 (284)
+-.+||||++||.-++-.
T Consensus 20 IPGV~GIG~KtA~~LL~~ 37 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQE 37 (101)
T ss_dssp B---TTSTCHCCCCCHHH
T ss_pred CCCCCCCCHHHHHHHHHH
Confidence 458999999999776654
No 111
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=46.86 E-value=27 Score=33.42 Aligned_cols=16 Identities=31% Similarity=0.368 Sum_probs=9.1
Q ss_pred hhcCCCccHHHHHHHH
Q 039703 191 LTSVKGIGAWSVHMFM 206 (284)
Q Consensus 191 L~~l~GIGpwTA~~vl 206 (284)
++.|||||+-+|+.+.
T Consensus 55 ~t~l~gIGk~ia~~I~ 70 (326)
T COG1796 55 LTELPGIGKGIAEKIS 70 (326)
T ss_pred cCCCCCccHHHHHHHH
Confidence 5556666666555544
No 112
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=46.83 E-value=43 Score=35.37 Aligned_cols=41 Identities=17% Similarity=0.203 Sum_probs=33.5
Q ss_pred HHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHH
Q 039703 123 YTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEK 168 (284)
Q Consensus 123 ~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~ 168 (284)
..+|.+.|| +.+.|..++.++|..+ |++..+|+.|....+.
T Consensus 650 ~k~LL~~FG-----Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~ 691 (694)
T PRK14666 650 ARLLWERFG-----SLQAMAAAGEEGLAAVPGIGPARAAALHEHLKT 691 (694)
T ss_pred HHHHHHHhC-----CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHH
Confidence 456677776 7899999999999987 9999988888776544
No 113
>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=46.33 E-value=29 Score=36.65 Aligned_cols=23 Identities=22% Similarity=0.378 Sum_probs=14.6
Q ss_pred hHHHHHHhhc--CCCccHHHHHHHH
Q 039703 184 DVTMFKMLTS--VKGIGAWSVHMFM 206 (284)
Q Consensus 184 ~ee~~~~L~~--l~GIGpwTA~~vl 206 (284)
.+.++..|.+ +||||++||.-+.
T Consensus 77 ~~~i~~yL~s~~~~GIG~~~A~~iv 101 (720)
T TIGR01448 77 KEGIVAYLSSRSIKGVGKKLAQRIV 101 (720)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHH
Confidence 3456666654 7777777776554
No 114
>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=46.13 E-value=40 Score=26.42 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=22.9
Q ss_pred CCCChhHhhcCChHHHHHHhhcCCCc
Q 039703 172 GILSDESIVEMDDVTMFKMLTSVKGI 197 (284)
Q Consensus 172 g~l~l~~l~~~~~ee~~~~L~~l~GI 197 (284)
|.-++++|...+.+++.+.|..+.|.
T Consensus 32 Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 32 GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 66688899999999999999999874
No 115
>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=45.84 E-value=28 Score=32.80 Aligned_cols=42 Identities=17% Similarity=0.075 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHH
Q 039703 158 KASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 158 KA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf 208 (284)
|+..-...|+.+..-..++.. ..++++|||||+.+|+.|-=+
T Consensus 23 r~~aY~~Aa~~l~~l~~~i~~---------~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 23 RVRAYRKAARALESLPEPIES---------LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred hHHHHHHHHHHHHhCCcccCC---------HHHhcCCCCccHHHHHHHHHH
Confidence 477777778877764444322 235689999999999987744
No 116
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=45.06 E-value=63 Score=29.38 Aligned_cols=83 Identities=16% Similarity=0.203 Sum_probs=56.2
Q ss_pred HHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHH---HHHcCCCChhHhh
Q 039703 105 LAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAE---KYTDGILSDESIV 180 (284)
Q Consensus 105 Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~---~i~~g~l~l~~l~ 180 (284)
|+..+|.--+.-..+..+-++|...|| +...|..++.++|..+ |+|..|+-.|+.+.+ .+....+.. ...
T Consensus 29 LLailLrtG~~~~~~~~la~~lL~~fg-----~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~~R~~~~~~~~-~~~ 102 (224)
T COG2003 29 LLAILLRTGTKGESVLDLAKELLQEFG-----SLAELLKASVEELSSVKGIGLAKAIQIKAAIELGKRILAERLRE-GVV 102 (224)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHcc-----cHHHHHhCCHHHHhhCCCccHHHHHHHHHHHHHHHHHHHHHhcc-CCc
Confidence 445556666666777788889999998 4778899999999876 899888877766554 333322210 111
Q ss_pred cCChHHHHHHhhc
Q 039703 181 EMDDVTMFKMLTS 193 (284)
Q Consensus 181 ~~~~ee~~~~L~~ 193 (284)
-.+++++.+.|..
T Consensus 103 i~sp~~~~~~l~~ 115 (224)
T COG2003 103 ITSPEAVAEYLRA 115 (224)
T ss_pred cCCHHHHHHHHHH
Confidence 2467778888873
No 117
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=44.98 E-value=52 Score=30.09 Aligned_cols=43 Identities=14% Similarity=0.096 Sum_probs=34.1
Q ss_pred HHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHHH
Q 039703 123 YTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEKY 169 (284)
Q Consensus 123 ~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i 169 (284)
..+|.+. | |-+.+.|..++.++|..+ |++..+|.-|......+
T Consensus 16 akkLl~~-G---F~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~ 59 (232)
T PRK12766 16 AEALREA-G---FESVEDVRAADQSELAEVDGIGNALAARIKADVGGL 59 (232)
T ss_pred HHHHHHc-C---CCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccc
Confidence 3455555 2 348999999999999997 99999999998876644
No 118
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=43.91 E-value=32 Score=32.66 Aligned_cols=39 Identities=23% Similarity=0.459 Sum_probs=32.8
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHH
Q 039703 121 SIYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRD 164 (284)
Q Consensus 121 ~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~ 164 (284)
.+.++++..|| +...|++++.|+|.++ |++..+|+.|++
T Consensus 304 ~iv~nlV~~F~-----~l~~il~As~edL~~VeGIGe~rAr~i~~ 343 (349)
T COG1623 304 AIVENLVRAFG-----TLDGILEASAEDLDAVEGIGEARARAIKE 343 (349)
T ss_pred HHHHHHHHHHh-----hHHHHHHhcHhHHhhhcchhHHHHHHHHH
Confidence 45678888887 6788999999999987 899888888875
No 119
>PF06738 DUF1212: Protein of unknown function (DUF1212); InterPro: IPR010619 This entry represents a predicted domain found within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. Some of these sequences are predicted to be membrane proteins.
Probab=43.35 E-value=63 Score=27.70 Aligned_cols=89 Identities=15% Similarity=0.215 Sum_probs=60.4
Q ss_pred HHHhcccCHHHHHHHHHHHHHHhCCC---CCCCHHHHh-cCCHH--------HHHhcCCChHHHHHHHHHHHHHHcCCCC
Q 039703 108 SILYQQLAYKAAKSIYTRFVALFNGE---DNILPDAVL-AVSPQ--------QLREIGVSYRKASYLRDLAEKYTDGILS 175 (284)
Q Consensus 108 ~IlsQq~s~~~a~~i~~rL~~~~G~~---~~p~Pe~la-~~~~e--------~Lr~~Gl~~rKA~~I~~lA~~i~~g~l~ 175 (284)
.++.--.....+.....|+.+.||-+ .+.+|..|. ..+.+ ....-++.-.|...+.++++.+.+|.++
T Consensus 4 ~Ll~~Ga~~~rve~~~~ria~~~G~~~~~~~v~~t~i~is~~~~~~~~t~~~~v~~~~~nl~~l~~v~~l~~~~~~~~~~ 83 (193)
T PF06738_consen 4 ALLESGAETYRVEDTMQRIARALGLEDVEVFVTPTGIFISFDDDGEPRTRVRRVPPRGVNLDKLAAVNRLSRRIVAGQLS 83 (193)
T ss_pred HHHHhCCcHHHHHHHHHHHHHHcCCCeeEEEEecCEEEEEEecCCcceEEEEEeCCCCcCHHHHHHHHHHHHHHhcCCCC
Confidence 45555667778888999999999965 244444321 22111 1235588888999999999999999998
Q ss_pred hhHhhcCChHHHHHHhhcCC-CccHHH
Q 039703 176 DESIVEMDDVTMFKMLTSVK-GIGAWS 201 (284)
Q Consensus 176 l~~l~~~~~ee~~~~L~~l~-GIGpwT 201 (284)
+++. .+-++++..-| ..++|.
T Consensus 84 ~~ea-----~~~L~~I~~~~~~y~~~~ 105 (193)
T PF06738_consen 84 LEEA-----IERLDEIDREPPRYPPWL 105 (193)
T ss_pred HHHH-----HHHHHHHhhCCCCCCHHH
Confidence 8655 23455555555 777774
No 120
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=42.86 E-value=18 Score=34.58 Aligned_cols=22 Identities=32% Similarity=0.412 Sum_probs=18.3
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf 208 (284)
-.++|+.+||||+++|.-|++.
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred CHHHhcccCCCChHHHHHHHHH
Confidence 4678999999999999877653
No 121
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=42.41 E-value=45 Score=34.40 Aligned_cols=31 Identities=10% Similarity=0.142 Sum_probs=26.6
Q ss_pred CCCHHHHhcCCHHHHHhcCCChHHHHHHHHH
Q 039703 135 NILPDAVLAVSPQQLREIGVSYRKASYLRDL 165 (284)
Q Consensus 135 ~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~l 165 (284)
|-+.+.|..++.|||..+|++...|+.|...
T Consensus 534 Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~ 564 (567)
T PRK14667 534 FKTLYDFLKADDEELKKLGIPPSVKQEVKKY 564 (567)
T ss_pred hCCHHHHHhCCHHHHHHcCCCHHHHHHHHHH
Confidence 4488999999999999999999988887653
No 122
>PRK00254 ski2-like helicase; Provisional
Probab=41.77 E-value=47 Score=34.88 Aligned_cols=23 Identities=13% Similarity=0.066 Sum_probs=14.5
Q ss_pred hhcCCCccHHHHHHHHHHhCCCC
Q 039703 191 LTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 191 L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
|.+|||||+..+.-.+-.|++-.
T Consensus 647 L~~ipgig~~~~~~l~~~g~~s~ 669 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGFRSI 669 (720)
T ss_pred hhcCCCCCHHHHHHHHHccCCCH
Confidence 45667777777666666655544
No 123
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=40.10 E-value=16 Score=30.04 Aligned_cols=23 Identities=26% Similarity=0.200 Sum_probs=19.7
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.-.|+.|.|||+.+|..++-..
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~l 37 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKA 37 (122)
T ss_pred eeeeecccccccHHHHHHHHHHc
Confidence 56678999999999999988653
No 124
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=39.74 E-value=54 Score=31.34 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=20.1
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHh
Q 039703 186 TMFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 186 e~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.+++|+.++||||.|.....|.+
T Consensus 266 ~~feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 266 SDFEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred cCHHHHHhcCCCCHHHHHHHHHHH
Confidence 357889999999999998877655
No 125
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=39.67 E-value=15 Score=30.07 Aligned_cols=23 Identities=22% Similarity=0.261 Sum_probs=19.5
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.-.|+.|.|||+.+|..++-..
T Consensus 15 v~~aL~~I~GIG~~~a~~i~~~l 37 (122)
T PRK05179 15 VVIALTYIYGIGRTRAKEILAAA 37 (122)
T ss_pred EEeeecccccccHHHHHHHHHHh
Confidence 56678999999999999988653
No 126
>PRK14976 5'-3' exonuclease; Provisional
Probab=38.53 E-value=19 Score=33.52 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=16.2
Q ss_pred hhcCCCccHHHHHHHHHHhCCCC
Q 039703 191 LTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 191 L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
+-++||||++||.-++- -+|..
T Consensus 193 ipGVpGIG~KtA~~LL~-~~gsl 214 (281)
T PRK14976 193 IKGVKGIGPKTAIKLLN-KYGNI 214 (281)
T ss_pred CCCCCcccHHHHHHHHH-HcCCH
Confidence 44799999999987774 34443
No 127
>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=37.22 E-value=36 Score=30.99 Aligned_cols=22 Identities=27% Similarity=0.291 Sum_probs=18.2
Q ss_pred cccccChHHHHHHHHHhCCCCCCC
Q 039703 215 VLPVGDLGVRKGLQVLYGLKELPG 238 (284)
Q Consensus 215 vfPv~D~~v~r~~~rly~~~~~~~ 238 (284)
++|+ |+|+.|+..++ |+-.+.+
T Consensus 173 iiPL-DtH~~rvar~L-gL~~Rk~ 194 (229)
T TIGR02757 173 ILPL-DTHVFRIAKKL-KLLKRKS 194 (229)
T ss_pred eeec-hHhHHHHHHHh-CCcccCc
Confidence 6899 99999999888 8866554
No 128
>PRK09482 flap endonuclease-like protein; Provisional
Probab=36.47 E-value=23 Score=32.79 Aligned_cols=22 Identities=23% Similarity=0.299 Sum_probs=16.1
Q ss_pred hhcCCCccHHHHHHHHHHhCCCC
Q 039703 191 LTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 191 L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
+.++|||||+||--++-- +|..
T Consensus 184 IpGVpGIG~KtA~~LL~~-~gsl 205 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQ-FRSL 205 (256)
T ss_pred CCCCCCcChHHHHHHHHH-hCCH
Confidence 448999999999877643 4433
No 129
>smart00475 53EXOc 5'-3' exonuclease.
Probab=36.42 E-value=22 Score=32.80 Aligned_cols=17 Identities=24% Similarity=0.431 Sum_probs=14.2
Q ss_pred hhcCCCccHHHHHHHHH
Q 039703 191 LTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 191 L~~l~GIGpwTA~~vll 207 (284)
+.++|||||+||.-++-
T Consensus 188 ipGV~GIG~KtA~~Ll~ 204 (259)
T smart00475 188 IPGVPGIGEKTAAKLLK 204 (259)
T ss_pred CCCCCCCCHHHHHHHHH
Confidence 45899999999987764
No 130
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=36.04 E-value=3.2e+02 Score=27.72 Aligned_cols=117 Identities=19% Similarity=0.216 Sum_probs=69.6
Q ss_pred CCCHHHH--HHHHHHhcccCHHHHHHHHHHHHHHh---CCCCCCCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcC
Q 039703 98 SRSPFLS--LAKSILYQQLAYKAAKSIYTRFVALF---NGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDG 172 (284)
Q Consensus 98 ~~~pfe~--Li~~IlsQq~s~~~a~~i~~rL~~~~---G~~~~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g 172 (284)
.+.||.. |.+.++.+.+....|..+...|.+.+ |.. ..+.+.+...-.+.|.. .++..-+.++ .+++.+...
T Consensus 176 ~~~PFSkGiLaRsLi~aDV~~~~A~~Ia~~Lk~~L~~kg~~-~~~ra~VR~~V~~~L~~-~l~~~~a~~y-~la~~i~~~ 252 (475)
T PRK12337 176 PRVPFSKGILAQSLMAAGLAPDVARRLARETERDLRRSGDR-VVRRDQLRRKVEALLLE-EAGEEVARRY-RLLRSIRRP 252 (475)
T ss_pred CCCCCchhHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccc-cccHHHHHHHHHHHHHh-hhhhhHHHHH-HHHHHhhcc
Confidence 4588988 99999999999999999999998776 321 12333333222222222 1111112222 344444331
Q ss_pred CCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcccccChHHHHHHHHH
Q 039703 173 ILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVLPVGDLGVRKGLQVL 230 (284)
Q Consensus 173 ~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~v~r~~~rl 230 (284)
.-+ .+=.+.+++|+|.-|...-|...++-..++.. |. ++.++..+
T Consensus 253 k~p-----------~vil~~G~~G~GKSt~a~~LA~~lg~~~ii~t-D~-iR~~lr~~ 297 (475)
T PRK12337 253 PRP-----------LHVLIGGVSGVGKSVLASALAYRLGITRIVST-DA-VREVLRAM 297 (475)
T ss_pred CCC-----------eEEEEECCCCCCHHHHHHHHHHHcCCcEEeeh-hH-HHHHHHhh
Confidence 100 12245789999999999988888887555565 64 34444444
No 131
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=36.02 E-value=19 Score=30.86 Aligned_cols=23 Identities=26% Similarity=0.244 Sum_probs=19.4
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.-.|+.|.|||+.+|..|+-..
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~l 50 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKA 50 (154)
T ss_pred EEEeecccccccHHHHHHHHHHc
Confidence 56678999999999999888543
No 132
>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=35.47 E-value=24 Score=31.94 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=16.1
Q ss_pred HhhcCCCccHHHHHHHHHHhCCCC
Q 039703 190 MLTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 190 ~L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
-+.++|||||+||.-++- -+|..
T Consensus 184 nipGv~GiG~ktA~~Ll~-~~gsl 206 (240)
T cd00008 184 NIPGVPGIGEKTAAKLLK-EYGSL 206 (240)
T ss_pred CCCCCCccCHHHHHHHHH-HhCCH
Confidence 345899999999966653 34433
No 133
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=34.65 E-value=91 Score=28.91 Aligned_cols=46 Identities=20% Similarity=0.276 Sum_probs=37.3
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCCHHHHHh-cCCChHHHHHHHHHHHHHHc
Q 039703 121 SIYTRFVALFNGEDNILPDAVLAVSPQQLRE-IGVSYRKASYLRDLAEKYTD 171 (284)
Q Consensus 121 ~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~-~Gl~~rKA~~I~~lA~~i~~ 171 (284)
....+|...|| +.+.+..++.++|.. -|.|..||..|..+-+..-+
T Consensus 193 ~~a~~ll~~fg-----S~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~~ 239 (254)
T COG1948 193 KLAERLLKKFG-----SVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEYK 239 (254)
T ss_pred HHHHHHHHHhc-----CHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhchhh
Confidence 44567777777 788999999999875 59999999999998876544
No 134
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=34.47 E-value=27 Score=28.74 Aligned_cols=23 Identities=22% Similarity=0.202 Sum_probs=19.4
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.=.|+.|.|||.-+|..|+--+
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~ 37 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKA 37 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHc
Confidence 44578999999999999998654
No 135
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=33.63 E-value=54 Score=29.81 Aligned_cols=41 Identities=27% Similarity=0.289 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHH
Q 039703 159 ASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVH 203 (284)
Q Consensus 159 A~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~ 203 (284)
-.-...+|+.+.+.--++..|..++ .++|++++|||+-.+-
T Consensus 40 ~~~~~~la~~lL~~fg~L~~l~~a~----~~el~~v~GiG~aka~ 80 (224)
T COG2003 40 GESVLDLAKELLQEFGSLAELLKAS----VEELSSVKGIGLAKAI 80 (224)
T ss_pred CCCHHHHHHHHHHHcccHHHHHhCC----HHHHhhCCCccHHHHH
Confidence 3577889999998655677776664 5789999999976553
No 136
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=33.41 E-value=1.3e+02 Score=27.03 Aligned_cols=122 Identities=18% Similarity=0.175 Sum_probs=73.8
Q ss_pred hHHHHHHHcCCCC-C-CCCCCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHH
Q 039703 82 LLATLIDAHRPPT-F-ESSRSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRK 158 (284)
Q Consensus 82 ~l~~li~~~~g~r-~-~~~~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rK 158 (284)
....|.+.++-+. + .-..+-.+.+|+.|=-=+...+....+-+.|++.||+++ |++ -++|.++ |+|+.-
T Consensus 50 at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~v---P~~-----~~eL~~LPGVGrKT 121 (211)
T COG0177 50 ATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEV---PDT-----REELLSLPGVGRKT 121 (211)
T ss_pred HHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCC---Cch-----HHHHHhCCCcchHH
Confidence 4455666665321 1 123466777888777777778888888999999999743 332 3445554 777653
Q ss_pred HHHHHHHHHHHH----c-------CCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCC
Q 039703 159 ASYLRDLAEKYT----D-------GILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKP 213 (284)
Q Consensus 159 A~~I~~lA~~i~----~-------g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~ 213 (284)
|.-+...|-..- | .++.+. ...+++++.++|+.+=.=.-|+---.+|..+||.
T Consensus 122 AnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~--~~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~ 185 (211)
T COG0177 122 ANVVLSFAFGIPAIAVDTHVHRVSNRLGLV--PGKTPEEVEEALMKLIPKELWTDLHHWLILHGRY 185 (211)
T ss_pred HHHHHHhhcCCCcccccchHHHHHHHhCCC--CCCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhhh
Confidence 433333322111 1 011111 1356788888888877777888777777777775
No 137
>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=32.94 E-value=21 Score=30.10 Aligned_cols=22 Identities=27% Similarity=0.228 Sum_probs=18.6
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf 208 (284)
+.-.|+.|.|||+.+|..++-.
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~~ 40 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIARK 40 (144)
T ss_pred EEEeecceeccCHHHHHHHHHH
Confidence 5567899999999999988754
No 138
>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=32.67 E-value=21 Score=28.83 Aligned_cols=23 Identities=22% Similarity=0.170 Sum_probs=19.4
Q ss_pred HHHHhhcCCCccHHHHHHHHHHh
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.-.|+.|.|||+.+|..++-..
T Consensus 13 v~~aL~~i~GIG~~~a~~i~~~l 35 (113)
T TIGR03631 13 VEIALTYIYGIGRTRARKILEKA 35 (113)
T ss_pred EeeeeeeeecccHHHHHHHHHHh
Confidence 56678999999999999888553
No 139
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=32.47 E-value=35 Score=28.87 Aligned_cols=66 Identities=15% Similarity=0.352 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHH-hhcCCCccHH
Q 039703 122 IYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKM-LTSVKGIGAW 200 (284)
Q Consensus 122 i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~-L~~l~GIGpw 200 (284)
|...|.++|.......|+ +++.++|-.+--.-.|+++|+.+...+-+ +.++.+.+ |..++|+..-
T Consensus 55 Id~qL~eLy~~~e~~~p~---EIDIDeLLDl~sdeeR~~~LqelL~~C~~-----------ptE~FI~ELL~kLkgL~k~ 120 (144)
T PF05361_consen 55 IDEQLQELYDCQEDEMPE---EIDIDELLDLESDEERRRKLQELLQDCPK-----------PTEDFIQELLSKLKGLRKL 120 (144)
T ss_dssp HHHHHHHCSSSSSTTS-S---SSHHHHHHCTSSTTHHHHHHHHHHTTCSS-----------TTHHHHHHHHHHCTTT---
T ss_pred HHHHHHHHhcCCCCCCCC---cccHHHHhcCCchHHHHHHHHHHHhhcCC-----------CHHHHHHHHHHHHHhhhcC
Confidence 456788888755433333 56677777666666788888877654322 23444444 4778888765
Q ss_pred H
Q 039703 201 S 201 (284)
Q Consensus 201 T 201 (284)
+
T Consensus 121 s 121 (144)
T PF05361_consen 121 S 121 (144)
T ss_dssp -
T ss_pred C
Confidence 4
No 140
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=32.31 E-value=26 Score=29.82 Aligned_cols=22 Identities=27% Similarity=0.293 Sum_probs=18.9
Q ss_pred HHHHhhcCCCccHHHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vllf 208 (284)
+.-.|+.|.|||+.+|..++-.
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~~ 44 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIARK 44 (149)
T ss_pred EeeeccccccccHHHHHHHHHH
Confidence 5678899999999999988754
No 141
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=32.23 E-value=91 Score=23.35 Aligned_cols=25 Identities=32% Similarity=0.545 Sum_probs=20.0
Q ss_pred hHHHHHHHHHhcCchHHHHHHHcCC
Q 039703 68 EVDIALRHLRDKDPLLATLIDAHRP 92 (284)
Q Consensus 68 d~~~~~~~l~~~Dp~l~~li~~~~g 92 (284)
-++++.++|...||.|+.-....+.
T Consensus 10 ~L~eiEr~L~~~DP~fa~~l~~~~~ 34 (82)
T PF11239_consen 10 RLEEIERQLRADDPRFAARLRSGRP 34 (82)
T ss_pred HHHHHHHHHHhcCcHHHHHhccCCC
Confidence 4788889999999999988876433
No 142
>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=31.95 E-value=2.1e+02 Score=24.73 Aligned_cols=83 Identities=11% Similarity=0.061 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCC-hHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCc
Q 039703 119 AKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVS-YRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGI 197 (284)
Q Consensus 119 a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~-~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GI 197 (284)
+..++++|.+.||...-+.+ ..=.-+.|-++=|+ +...+.+..+...+.+...+.+.+.+++.+++.+.|..+ |.
T Consensus 3 ~~~i~~~l~~~~~~~~~~~~---~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~pt~~~l~~~~~~~L~~~ir~~-G~ 78 (191)
T TIGR01083 3 AQEILERLRKNYPHPTTELD---YNNPFELLVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSI-GL 78 (191)
T ss_pred HHHHHHHHHHHCCCCCcccC---CCCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHhc-CC
Confidence 46789999999985310000 00112333332222 223445555555555555688999999988887766554 55
Q ss_pred cHHHHHHH
Q 039703 198 GAWSVHMF 205 (284)
Q Consensus 198 GpwTA~~v 205 (284)
-..-|+.+
T Consensus 79 ~~~Ka~~i 86 (191)
T TIGR01083 79 YRNKAKNI 86 (191)
T ss_pred hHHHHHHH
Confidence 44444444
No 143
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=31.89 E-value=1.2e+02 Score=28.61 Aligned_cols=47 Identities=15% Similarity=0.172 Sum_probs=38.2
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCCHHHHHh-cCCChHHHHHHHHHHHHHHcC
Q 039703 122 IYTRFVALFNGEDNILPDAVLAVSPQQLRE-IGVSYRKASYLRDLAEKYTDG 172 (284)
Q Consensus 122 i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~-~Gl~~rKA~~I~~lA~~i~~g 172 (284)
..++|.+. | +.|.++++.+++.+|.. +|++..|+.-|+..|......
T Consensus 13 ~~~~L~~~-g---~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 13 DIKKLKSA-G---ICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHc-C---CCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhhhcc
Confidence 45556555 4 47899999999999965 899999999999999888764
No 144
>PRK13766 Hef nuclease; Provisional
Probab=31.40 E-value=1e+02 Score=32.37 Aligned_cols=40 Identities=23% Similarity=0.437 Sum_probs=32.0
Q ss_pred HHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHH
Q 039703 123 YTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDLAE 167 (284)
Q Consensus 123 ~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~ 167 (284)
..+|.+.|| +++.+..++.++|..+ |++..+++.|..+.+
T Consensus 728 a~~Ll~~fg-----s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 728 ARNLLEHFG-----SVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HHHHHHHcC-----CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 456666776 7889999999999998 999888888876543
No 145
>PTZ00035 Rad51 protein; Provisional
Probab=30.49 E-value=1.2e+02 Score=28.96 Aligned_cols=46 Identities=15% Similarity=0.152 Sum_probs=37.8
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCCHHHHHh-cCCChHHHHHHHHHHHHHHc
Q 039703 122 IYTRFVALFNGEDNILPDAVLAVSPQQLRE-IGVSYRKASYLRDLAEKYTD 171 (284)
Q Consensus 122 i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~-~Gl~~rKA~~I~~lA~~i~~ 171 (284)
..++|.+. | +.|.++|+.+++.+|.. +|++..|+.-|+..|+.+..
T Consensus 35 ~~~kL~~~-g---~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 35 DIKKLKEA-G---ICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred HHHHHHHc-C---CCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHhcc
Confidence 44556554 5 47899999999999965 89999999999999998875
No 146
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=30.04 E-value=85 Score=32.73 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=23.3
Q ss_pred hHHHHHHhhcCCCccHHHHHHHHHHhCCCCCcc
Q 039703 184 DVTMFKMLTSVKGIGAWSVHMFMIFSLHKPDVL 216 (284)
Q Consensus 184 ~ee~~~~L~~l~GIGpwTA~~vllf~l~r~dvf 216 (284)
.......|.+|+|||++++..++- .||-.+.+
T Consensus 564 k~~~~s~L~~I~GIG~k~a~~Ll~-~Fgs~~~i 595 (621)
T PRK14671 564 KRTLQTELTDIAGIGEKTAEKLLE-HFGSVEKV 595 (621)
T ss_pred HHHhhhhhhcCCCcCHHHHHHHHH-HcCCHHHH
Confidence 355678899999999999996664 46544333
No 147
>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=29.82 E-value=59 Score=25.61 Aligned_cols=26 Identities=19% Similarity=0.316 Sum_probs=20.9
Q ss_pred HHhhcCCCccHHHHHHHHHHhCCCCC
Q 039703 189 KMLTSVKGIGAWSVHMFMIFSLHKPD 214 (284)
Q Consensus 189 ~~L~~l~GIGpwTA~~vllf~l~r~d 214 (284)
.+-.+|||||+.-|..|..|--.+++
T Consensus 50 ~Wwr~vpglG~~~A~~I~awLa~h~~ 75 (96)
T PF12482_consen 50 RWWRAVPGLGAAGARRIEAWLAAHPA 75 (96)
T ss_pred hHHHhCcccchHHHHHHHHHHHHhHH
Confidence 55679999999999999988655543
No 148
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=29.78 E-value=1.3e+02 Score=28.96 Aligned_cols=47 Identities=15% Similarity=0.128 Sum_probs=38.2
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCCHHHHH-hcCCChHHHHHHHHHHHHHHc
Q 039703 121 SIYTRFVALFNGEDNILPDAVLAVSPQQLR-EIGVSYRKASYLRDLAEKYTD 171 (284)
Q Consensus 121 ~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr-~~Gl~~rKA~~I~~lA~~i~~ 171 (284)
...++|.+. | +.+.++|+.+++.+|. .+|++..|+.-|...|+.+..
T Consensus 42 ~~~~kL~~~-g---~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 42 GDVKKLQDA-G---IYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred HHHHHHHHc-C---CCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHhhc
Confidence 345666655 5 5789999999999985 479999999999998888765
No 149
>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=29.63 E-value=63 Score=29.48 Aligned_cols=21 Identities=29% Similarity=0.420 Sum_probs=17.0
Q ss_pred cccccChHHHHHHHHHhCCCCCC
Q 039703 215 VLPVGDLGVRKGLQVLYGLKELP 237 (284)
Q Consensus 215 vfPv~D~~v~r~~~rly~~~~~~ 237 (284)
++|+ |+||.|+..++ |+-...
T Consensus 176 iiPL-DtHv~~var~L-GL~~rk 196 (232)
T PF09674_consen 176 IIPL-DTHVFRVARKL-GLLKRK 196 (232)
T ss_pred cccc-hHhHHHHHHHc-CCccCC
Confidence 5899 99999998888 775543
No 150
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=29.41 E-value=1e+02 Score=32.57 Aligned_cols=37 Identities=14% Similarity=0.108 Sum_probs=31.6
Q ss_pred CCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHHHHHc
Q 039703 135 NILPDAVLAVSPQQLREI-GVSYRKASYLRDLAEKYTD 171 (284)
Q Consensus 135 ~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~~i~~ 171 (284)
|-+.+.|..++.++|..+ |++...|+.|...|..-..
T Consensus 628 FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~ 665 (691)
T PRK14672 628 FGSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTT 665 (691)
T ss_pred hcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccc
Confidence 458899999999999987 9999999999998876443
No 151
>TIGR02509 type_III_yopR type III secretion effector, YopR family. Members of this family are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yops protein is unusual in that it is released to extracellularly rather than injected directly into the target cell as are most Yops.
Probab=28.29 E-value=1.3e+02 Score=24.97 Aligned_cols=66 Identities=17% Similarity=0.132 Sum_probs=40.3
Q ss_pred HHHHHHHhcccCH--------HHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHh-----cCCChHHHHHHHHHHHHHH
Q 039703 104 SLAKSILYQQLAY--------KAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLRE-----IGVSYRKASYLRDLAEKYT 170 (284)
Q Consensus 104 ~Li~~IlsQq~s~--------~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~-----~Gl~~rKA~~I~~lA~~i~ 170 (284)
.++|.+..|-.+. .-...+.++|..+||+...+ ....+|-.|||+ .-++.+|-..|..+-..+.
T Consensus 15 e~lWq~~~q~~~~~~~~~~~~~L~~pv~e~Ll~~F~g~~l~---v~p~~D~~ELrA~lref~Plg~q~E~~Ll~~l~~lK 91 (131)
T TIGR02509 15 ELLWQQYQQGKPAAGTADLVPELLSPVKERLLGRFGGQQLP---VVPPIDRLELRAMLRQFDPLGRQQEAALLQLLGKLK 91 (131)
T ss_pred HHHHHHHHccCCCcchhHHHHHHHHHHHHHHHHHhcccccC---CCCccchHHHHHHHHHhCccchHHHHHHHHHHHHcc
Confidence 3445555554442 33344567888889875211 112345556664 4788999999988888876
Q ss_pred cC
Q 039703 171 DG 172 (284)
Q Consensus 171 ~g 172 (284)
..
T Consensus 92 ~~ 93 (131)
T TIGR02509 92 SL 93 (131)
T ss_pred CC
Confidence 53
No 152
>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=28.08 E-value=47 Score=25.22 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=15.7
Q ss_pred HHHHhhcCCCccHHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vll 207 (284)
++=-|..|+|||..+|+.++-
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 455688999999999987764
No 153
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=27.47 E-value=1e+02 Score=32.38 Aligned_cols=28 Identities=14% Similarity=0.311 Sum_probs=18.6
Q ss_pred ChhHhhcCChHHHHHHhhcCCCccHHHHHHHH
Q 039703 175 SDESIVEMDDVTMFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 175 ~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vl 206 (284)
++.+|..+. .+.|.+++|+|.++++-++
T Consensus 469 ~i~DL~~L~----~~~L~~l~gfG~Ksa~~ll 496 (665)
T PRK07956 469 DPADLFKLT----AEDLLGLEGFGEKSAQNLL 496 (665)
T ss_pred CHHHHHhcC----HHHHhcCcCcchHHHHHHH
Confidence 455555444 2358888899998887653
No 154
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=27.33 E-value=1.7e+02 Score=27.24 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=35.0
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCCHHHHHh-cCCChHHHHHHHHHHHHHH
Q 039703 122 IYTRFVALFNGEDNILPDAVLAVSPQQLRE-IGVSYRKASYLRDLAEKYT 170 (284)
Q Consensus 122 i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~-~Gl~~rKA~~I~~lA~~i~ 170 (284)
+.++|.+. | +-+.++|+.+++++|.. +|++..++..|...++...
T Consensus 18 ~a~~L~~~-G---i~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 18 TAEKLREA-G---YDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAA 63 (317)
T ss_pred HHHHHHHc-C---CCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhh
Confidence 34455544 5 47899999999999954 6999999999998887643
No 155
>KOG1936 consensus Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.20 E-value=4.3e+02 Score=26.74 Aligned_cols=51 Identities=14% Similarity=0.037 Sum_probs=38.6
Q ss_pred HHhcCCChHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHh
Q 039703 149 LREIGVSYRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 149 Lr~~Gl~~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
|.-||++..|-++|... .++|..++.|++.+++.--+|+-+-+|+-+.-+.
T Consensus 225 f~v~GVp~~~frtICSs----------IDKLdK~pwedVkkEmv~eKGlsee~ad~igeyv 275 (518)
T KOG1936|consen 225 FAVCGVPEDKFRTICSS----------IDKLDKMPWEDVKKEMVFEKGLSEEAADRIGEYV 275 (518)
T ss_pred HHHhCCCHHHhhhHHHh----------hhhhhcCCHHHHHHHHHHhcCCCHHHHHHHHHHh
Confidence 34577777766666553 3456678999999999999999999998776554
No 156
>COG1179 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]
Probab=27.06 E-value=60 Score=30.12 Aligned_cols=66 Identities=18% Similarity=0.355 Sum_probs=40.9
Q ss_pred hcCCCccHHHHHHHHHHhCCCCCcccccChH---HHHHHHHHhCCCCCCCHHHHHHHHHhcCChhHHHH
Q 039703 192 TSVKGIGAWSVHMFMIFSLHKPDVLPVGDLG---VRKGLQVLYGLKELPGALKMEEVCEKWKPYRSVGS 257 (284)
Q Consensus 192 ~~l~GIGpwTA~~vllf~l~r~dvfPv~D~~---v~r~~~rly~~~~~~~~~~~~~~~e~~~Pyrs~a~ 257 (284)
..+=|||.|++++..=-|.|+.-++-.||+- +-|.+.-+.+.-..++.+.|.+.....-||.-+-.
T Consensus 36 vGiGGVGSw~veALaRsGig~itlID~D~v~vTN~NRQi~A~~~~iGk~Kv~vm~eri~~InP~c~V~~ 104 (263)
T COG1179 36 VGIGGVGSWAVEALARSGIGRITLIDMDDVCVTNTNRQIHALLGDIGKPKVEVMKERIKQINPECEVTA 104 (263)
T ss_pred EecCchhHHHHHHHHHcCCCeEEEEecccccccccchhhHhhhhhcccHHHHHHHHHHHhhCCCceEee
Confidence 4688999999999998899987666655543 33444444333233344455555555566654433
No 157
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=27.01 E-value=1.2e+02 Score=22.58 Aligned_cols=56 Identities=18% Similarity=0.280 Sum_probs=39.5
Q ss_pred CHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCChHHHHHHHHHHHHHHcCCC
Q 039703 115 AYKAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRDLAEKYTDGIL 174 (284)
Q Consensus 115 s~~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~lA~~i~~g~l 174 (284)
.......+.++|.+.|++ .+|..|..+. .+|-.=|++......+.++=..+-.|.+
T Consensus 11 ~G~~~e~vk~~F~~~~~~---Vs~~EI~~~E-q~Li~eG~~~eeiq~LCdvH~~lf~~~i 66 (71)
T PF04282_consen 11 EGEDPEEVKEEFKKLFSD---VSASEISAAE-QELIQEGMPVEEIQKLCDVHAALFKGSI 66 (71)
T ss_pred CCCCHHHHHHHHHHHHCC---CCHHHHHHHH-HHHHHcCCCHHHHHHHhHHHHHHHHHHH
Confidence 334445667788888875 7888887663 4555579999988888887766665543
No 158
>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=26.26 E-value=97 Score=32.47 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=18.6
Q ss_pred ChhHhhcCChHHHHHHhhcCCCccHHHHHHH
Q 039703 175 SDESIVEMDDVTMFKMLTSVKGIGAWSVHMF 205 (284)
Q Consensus 175 ~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~v 205 (284)
++.+|..+. .+.|.+|+|+|.++|+-+
T Consensus 456 ~~~Dl~~L~----~~~L~~L~GfG~Ksa~nI 482 (652)
T TIGR00575 456 SVADLYALK----KEDLLELEGFGEKSAQNL 482 (652)
T ss_pred CHHHHHhcC----HHHHhhccCccHHHHHHH
Confidence 455555444 346778899999998765
No 159
>PRK10702 endonuclease III; Provisional
Probab=26.10 E-value=3e+02 Score=24.44 Aligned_cols=74 Identities=9% Similarity=-0.007 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCC-hHHHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhc
Q 039703 117 KAAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVS-YRKASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTS 193 (284)
Q Consensus 117 ~~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~-~rKA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~ 193 (284)
..+..++++|.+.||... +... ..-+-+.|-+.=|+ +.+...+......+.....+.+.|.+++.+++.+.+..
T Consensus 4 ~~~~~i~~~l~~~~~~~~-~~~~--~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~pt~e~l~~a~~~~l~~~i~~ 78 (211)
T PRK10702 4 AKRLEILTRLRDNNPHPT-TELN--FSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKT 78 (211)
T ss_pred HHHHHHHHHHHHHCCCCC-CCCC--CCChHHHHHHHHHHhhcCHHHHHHHHHHHHHHcCCHHHHHCCCHHHHHHHHHH
Confidence 356789999999998521 1100 01112334443344 23455666666666666668899999998888776654
No 160
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=26.07 E-value=1.4e+02 Score=30.79 Aligned_cols=32 Identities=13% Similarity=0.179 Sum_probs=27.0
Q ss_pred CCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHH
Q 039703 135 NILPDAVLAVSPQQLREI-GVSYRKASYLRDLA 166 (284)
Q Consensus 135 ~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA 166 (284)
|-+.+.|..++.|||..+ |++...|+.|....
T Consensus 534 Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l 566 (574)
T PRK14670 534 LGTYKDILLLNEDEIAEKMKINIKMAKKIKKFA 566 (574)
T ss_pred hCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 348899999999999998 99998888876654
No 161
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=25.99 E-value=2.2e+02 Score=19.57 Aligned_cols=22 Identities=23% Similarity=0.493 Sum_probs=18.6
Q ss_pred CCH-HHHhcCCHHHHHhcCCChH
Q 039703 136 ILP-DAVLAVSPQQLREIGVSYR 157 (284)
Q Consensus 136 p~P-e~la~~~~e~Lr~~Gl~~r 157 (284)
.+- +.|..++.++|+.+|+...
T Consensus 30 i~g~~~L~~l~~~~L~~lGI~~~ 52 (66)
T PF07647_consen 30 IDGLEDLLQLTEEDLKELGITNL 52 (66)
T ss_dssp CSHHHHHTTSCHHHHHHTTTTHH
T ss_pred CcHHHHHhhCCHHHHHHcCCCCH
Confidence 555 8899999999999999754
No 162
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=25.20 E-value=1.1e+02 Score=31.58 Aligned_cols=20 Identities=20% Similarity=0.393 Sum_probs=11.3
Q ss_pred HHHHhhcCCCccHHHHHHHH
Q 039703 187 MFKMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 187 ~~~~L~~l~GIGpwTA~~vl 206 (284)
..-.|..|||||+.++..++
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll 560 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALL 560 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHH
Confidence 34555666666666666444
No 163
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=24.52 E-value=2.2e+02 Score=26.30 Aligned_cols=46 Identities=22% Similarity=0.225 Sum_probs=35.2
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCCHHHHHh-cCCChHHHHHHHHHHHHHH
Q 039703 121 SIYTRFVALFNGEDNILPDAVLAVSPQQLRE-IGVSYRKASYLRDLAEKYT 170 (284)
Q Consensus 121 ~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~-~Gl~~rKA~~I~~lA~~i~ 170 (284)
.+.++|.+. | +-+.++|+.+++++|.. +|++..++..|...++...
T Consensus 10 ~~~~~L~~~-G---i~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~ 56 (310)
T TIGR02236 10 ATAEKLREA-G---YDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAA 56 (310)
T ss_pred HHHHHHHHc-C---CCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHh
Confidence 344556555 4 46899999999999975 6999888999988887443
No 164
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=24.47 E-value=1.4e+02 Score=30.99 Aligned_cols=36 Identities=28% Similarity=0.489 Sum_probs=28.5
Q ss_pred HHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHH
Q 039703 124 TRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRD 164 (284)
Q Consensus 124 ~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~ 164 (284)
.+|.+.|| +++.|..++.++|..+ |++...|+.|..
T Consensus 539 ~~LL~~FG-----S~~~I~~As~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 539 KRLLRRFG-----SVEGVREASVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred HHHHHHcC-----CHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 34555555 8999999999999998 999887777653
No 165
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=24.38 E-value=59 Score=31.53 Aligned_cols=24 Identities=29% Similarity=0.430 Sum_probs=19.5
Q ss_pred HHHHHhhcCCCccHHHHHHHHHHh
Q 039703 186 TMFKMLTSVKGIGAWSVHMFMIFS 209 (284)
Q Consensus 186 e~~~~L~~l~GIGpwTA~~vllf~ 209 (284)
+.+++|.-+|||||.|+....+.+
T Consensus 275 ~Df~elLl~~GiGpstvRALalVA 298 (373)
T COG1415 275 DDFEELLLVPGIGPSTVRALALVA 298 (373)
T ss_pred ccHHHHHhccCCCHHHHHHHHHHH
Confidence 467888999999999998776543
No 166
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=24.26 E-value=65 Score=34.73 Aligned_cols=28 Identities=7% Similarity=-0.057 Sum_probs=23.3
Q ss_pred ChHHHHHHhhcCCCccHHHHHHHHHHhCC
Q 039703 183 DDVTMFKMLTSVKGIGAWSVHMFMIFSLH 211 (284)
Q Consensus 183 ~~ee~~~~L~~l~GIGpwTA~~vllf~l~ 211 (284)
...+.++.|.+|||||+..|..+|-. |+
T Consensus 751 ~~~~~q~~L~~lPgI~~~~a~~ll~~-f~ 778 (814)
T TIGR00596 751 FNDGPQDFLLKLPGVTKKNYRNLRKK-VK 778 (814)
T ss_pred ccHHHHHHHHHCCCCCHHHHHHHHHH-cC
Confidence 45577888999999999999999875 44
No 167
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=24.13 E-value=1.2e+02 Score=29.14 Aligned_cols=21 Identities=14% Similarity=0.060 Sum_probs=17.4
Q ss_pred HHHhhcCCCccHHHHHHHHHH
Q 039703 188 FKMLTSVKGIGAWSVHMFMIF 208 (284)
Q Consensus 188 ~~~L~~l~GIGpwTA~~vllf 208 (284)
.+++..|||||+++|+.|--+
T Consensus 55 ~~ea~~lP~iG~kia~ki~Ei 75 (353)
T KOG2534|consen 55 GEEAEKLPGIGPKIAEKIQEI 75 (353)
T ss_pred HHHhcCCCCCCHHHHHHHHHH
Confidence 567778999999999987644
No 168
>PRK08609 hypothetical protein; Provisional
Probab=23.42 E-value=1.4e+02 Score=30.66 Aligned_cols=41 Identities=24% Similarity=0.194 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHH
Q 039703 158 KASYLRDLAEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMI 207 (284)
Q Consensus 158 KA~~I~~lA~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vll 207 (284)
|+..-+..|+.+..-.-++.. +..|..|||||+.+|+.|-=
T Consensus 26 r~~aYr~Aa~~i~~l~~~i~~---------~~~l~~ipgIG~~ia~kI~E 66 (570)
T PRK08609 26 KISAFRKAAQALELDERSLSE---------IDDFTKLKGIGKGTAEVIQE 66 (570)
T ss_pred HHHHHHHHHHHHHhCchhhhh---------hhhhccCCCcCHHHHHHHHH
Confidence 477777777777653323221 24789999999999987753
No 169
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=22.94 E-value=61 Score=21.64 Aligned_cols=18 Identities=28% Similarity=0.272 Sum_probs=14.6
Q ss_pred cccChHHHHHHHHHhCCC
Q 039703 217 PVGDLGVRKGLQVLYGLK 234 (284)
Q Consensus 217 Pv~D~~v~r~~~rly~~~ 234 (284)
-.+|++|+|++.++|...
T Consensus 16 teddT~v~r~l~~yY~~k 33 (41)
T PF14475_consen 16 TEDDTHVHRVLRKYYTEK 33 (41)
T ss_pred CcchhHHHHHHHHHHHHc
Confidence 346999999999998653
No 170
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=22.78 E-value=71 Score=20.69 Aligned_cols=21 Identities=24% Similarity=0.376 Sum_probs=17.6
Q ss_pred CHHHHhcCCHHHHHhcCCChH
Q 039703 137 LPDAVLAVSPQQLREIGVSYR 157 (284)
Q Consensus 137 ~Pe~la~~~~e~Lr~~Gl~~r 157 (284)
+-.+|..++..+|+.+|++..
T Consensus 16 tr~~L~~Lsd~~L~DIGl~R~ 36 (40)
T PF06568_consen 16 TRRELAELSDRQLADIGLTRS 36 (40)
T ss_pred HHHHHccCCHHHHHHcCCCHH
Confidence 445788999999999999865
No 171
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=22.46 E-value=1.6e+02 Score=30.54 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=31.8
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCCHHHHHhc-CCChHHHHHHHHH
Q 039703 122 IYTRFVALFNGEDNILPDAVLAVSPQQLREI-GVSYRKASYLRDL 165 (284)
Q Consensus 122 i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~l 165 (284)
...+|.+.|| +++.|..++.++|..+ |++...|+.|...
T Consensus 555 ~~k~Ll~~Fg-----S~~~i~~As~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 555 RRKALLKHFG-----SLKAIKEASVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred HHHHHHHHcC-----CHHHHHhCCHHHHhhcCCcCHHHHHHHHHH
Confidence 3457778886 7899999999999998 9999888777553
No 172
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=22.37 E-value=84 Score=25.45 Aligned_cols=24 Identities=17% Similarity=0.196 Sum_probs=0.0
Q ss_pred HHHhhcCCCccHHHHHHHHHHhCC
Q 039703 188 FKMLTSVKGIGAWSVHMFMIFSLH 211 (284)
Q Consensus 188 ~~~L~~l~GIGpwTA~~vllf~l~ 211 (284)
+..|+.|+|||+..|..++--|+.
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHHhCcC
No 173
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=21.80 E-value=1.1e+02 Score=25.71 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=15.3
Q ss_pred HHhhcCCCccHHHHHHHH
Q 039703 189 KMLTSVKGIGAWSVHMFM 206 (284)
Q Consensus 189 ~~L~~l~GIGpwTA~~vl 206 (284)
+.|+.|.||||+....+-
T Consensus 67 DDLt~I~GIGPk~e~~Ln 84 (133)
T COG3743 67 DDLTRISGIGPKLEKVLN 84 (133)
T ss_pred ccchhhcccCHHHHHHHH
Confidence 689999999999887644
No 174
>PRK00254 ski2-like helicase; Provisional
Probab=21.21 E-value=1.5e+02 Score=31.21 Aligned_cols=33 Identities=9% Similarity=0.139 Sum_probs=28.9
Q ss_pred CCCHHHHhcCCHHHHHhc-CCChHHHHHHHHHHH
Q 039703 135 NILPDAVLAVSPQQLREI-GVSYRKASYLRDLAE 167 (284)
Q Consensus 135 ~p~Pe~la~~~~e~Lr~~-Gl~~rKA~~I~~lA~ 167 (284)
|-++++|..++.++|..+ |++.+.|+-|....+
T Consensus 666 ~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 666 FRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred CCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 568999999999999998 999998988887755
No 175
>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]
Probab=21.15 E-value=2.8e+02 Score=29.07 Aligned_cols=111 Identities=12% Similarity=0.152 Sum_probs=76.9
Q ss_pred CCHHHHHHHHHHhcccCHHHHHHHHHHHHHHhCCCC-----------CCCHHHHhcCCHHHHHhc--CCChHHHHHHHHH
Q 039703 99 RSPFLSLAKSILYQQLAYKAAKSIYTRFVALFNGED-----------NILPDAVLAVSPQQLREI--GVSYRKASYLRDL 165 (284)
Q Consensus 99 ~~pfe~Li~~IlsQq~s~~~a~~i~~rL~~~~G~~~-----------~p~Pe~la~~~~e~Lr~~--Gl~~rKA~~I~~l 165 (284)
+..=+.++..+++.-.....++.+..-|++.||+.. -|..+.+..+.+..|-.+ +|.|- -+-|..+
T Consensus 94 ~~aR~v~l~c~iGta~ha~haRHLv~hlie~~Ged~pidlG~e~~v~aPi~~t~~G~kPktlgdle~~l~y~-Eeqlt~~ 172 (772)
T COG1152 94 QTAREVFLACCIGTACHAAHARHLVDHLIETFGEDLPIDLGSEVNVEAPIIETVTGIKPKTLGDLEAALEYA-EEQLTQL 172 (772)
T ss_pred hhhheehhhhhhhhhhhhhhHHHHHHHHHHHhCccCccCCCcccccccchhhhhhCCCccchHHHHHHHHHH-HHHHHHH
Confidence 456677888889999999999999999999999732 134455666666655432 66666 5566677
Q ss_pred HHHHHcCCCChhHhhcCChHHHHHHhhcCCCccHHHHHHHHHHhCCCCC
Q 039703 166 AEKYTDGILSDESIVEMDDVTMFKMLTSVKGIGAWSVHMFMIFSLHKPD 214 (284)
Q Consensus 166 A~~i~~g~l~l~~l~~~~~ee~~~~L~~l~GIGpwTA~~vllf~l~r~d 214 (284)
...+..|.-. ...|+|.--=..-.|--+|.-.|+..-+-++..|.
T Consensus 173 ls~~h~gqE~----~~~dyeSkAlhaG~~d~l~~EiaDiaqi~a~~~pk 217 (772)
T COG1152 173 LSAVHTGQEG----SLLDYESKALHAGMIDHLGMEIADIAQIVAYDFPK 217 (772)
T ss_pred HHHHhccCcc----cccchhHHHhhhhhhhHHHHHHHHHHHHHhhcCCC
Confidence 7777766421 11455554455567778899999998888887653
No 176
>KOG3109 consensus Haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=20.62 E-value=92 Score=28.51 Aligned_cols=78 Identities=17% Similarity=0.248 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHhCCCCCCCHHHHhcCCHHHHHhcCCChHHHHHHHH---HH--HHHHcCCCChhHhhcCChHHHHHHhh
Q 039703 118 AAKSIYTRFVALFNGEDNILPDAVLAVSPQQLREIGVSYRKASYLRD---LA--EKYTDGILSDESIVEMDDVTMFKMLT 192 (284)
Q Consensus 118 ~a~~i~~rL~~~~G~~~~p~Pe~la~~~~e~Lr~~Gl~~rKA~~I~~---lA--~~i~~g~l~l~~l~~~~~ee~~~~L~ 192 (284)
-...|.+=|++.+| ...+....+-.+.-+..|+..+=-.++.. .- ..++.|.++++.| -|+..+++.|.
T Consensus 37 ~~~nI~~f~~eklg----i~~e~a~~L~~~~yk~YG~t~aGL~~~~~~~d~deY~~~V~~~LPlq~L--kPD~~LRnlLL 110 (244)
T KOG3109|consen 37 MRNNIQEFFVEKLG----ISEEEAEELRESLYKEYGLTMAGLKAVGYIFDADEYHRFVHGRLPLQDL--KPDPVLRNLLL 110 (244)
T ss_pred HHHHHHHHHHHHhC----CChhhhHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHhhccCcHhhc--CCCHHHHHHHH
Confidence 33445667888888 33333222223333445555442222211 11 1345688888875 47788999999
Q ss_pred cCCCccHHH
Q 039703 193 SVKGIGAWS 201 (284)
Q Consensus 193 ~l~GIGpwT 201 (284)
++|-.+.|.
T Consensus 111 ~l~~r~k~~ 119 (244)
T KOG3109|consen 111 SLKKRRKWI 119 (244)
T ss_pred hCccccEEE
Confidence 999998553
No 177
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=20.42 E-value=2.9e+02 Score=23.37 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHh-cccCHHHHHHHHHHHHHHhCCCCCCCHHH
Q 039703 98 SRSPFLSLAKSILY-QQLAYKAAKSIYTRFVALFNGEDNILPDA 140 (284)
Q Consensus 98 ~~~pfe~Li~~Ils-Qq~s~~~a~~i~~rL~~~~G~~~~p~Pe~ 140 (284)
..++|+-++..|.+ -..+-+.+-..++++.+.||+ ..+++.
T Consensus 83 e~~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~--~l~~e~ 124 (144)
T PF09999_consen 83 ERDPFERILDYIAAKTGIEKQEVVAEINELQEELGG--LLDPEA 124 (144)
T ss_pred cccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc--cCCHHH
Confidence 47999999999999 678889999999999999985 256654
Done!