Query 017612
Match_columns 368
No_of_seqs 219 out of 591
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:07:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017612.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017612hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2841 Structure-specific end 100.0 4.9E-46 1.1E-50 348.9 15.8 187 69-276 7-253 (254)
2 COG5241 RAD10 Nucleotide excis 99.9 3.3E-25 7.1E-30 203.5 2.4 136 137-275 32-224 (224)
3 TIGR00597 rad10 DNA repair pro 99.8 8.4E-21 1.8E-25 161.8 4.6 44 139-182 1-44 (112)
4 PF03834 Rad10: Binding domain 99.8 1.9E-19 4.1E-24 142.2 4.0 44 139-182 1-45 (69)
5 COG1948 MUS81 ERCC4-type nucle 99.5 2.5E-14 5.4E-19 136.6 9.4 108 165-276 128-240 (254)
6 PF12826 HHH_2: Helix-hairpin- 99.5 3.3E-14 7.1E-19 109.1 5.6 60 215-275 1-60 (64)
7 PRK13766 Hef nuclease; Provisi 99.3 7E-11 1.5E-15 124.4 15.1 140 136-275 560-772 (773)
8 PRK14670 uvrC excinuclease ABC 99.1 6.1E-11 1.3E-15 124.1 6.3 88 171-273 479-569 (574)
9 PRK14667 uvrC excinuclease ABC 99.1 1.9E-10 4.1E-15 120.3 6.4 88 170-271 476-566 (567)
10 PF14520 HHH_5: Helix-hairpin- 99.0 3.9E-10 8.5E-15 84.8 5.3 56 216-271 3-59 (60)
11 TIGR00596 rad1 DNA repair prot 99.0 7.9E-10 1.7E-14 119.7 8.4 97 177-275 706-813 (814)
12 PRK14669 uvrC excinuclease ABC 99.0 7E-10 1.5E-14 117.2 7.3 91 171-276 515-608 (624)
13 PRK14666 uvrC excinuclease ABC 99.0 7.5E-10 1.6E-14 118.0 7.2 79 183-274 615-693 (694)
14 PRK00558 uvrC excinuclease ABC 99.0 7.1E-10 1.5E-14 116.4 6.6 90 170-272 505-597 (598)
15 PRK14672 uvrC excinuclease ABC 98.9 2.3E-09 5.1E-14 114.2 7.0 90 170-272 570-662 (691)
16 COG0322 UvrC Nuclease subunit 98.8 4.2E-09 9.1E-14 110.6 6.5 86 171-270 493-581 (581)
17 PRK14668 uvrC excinuclease ABC 98.8 8E-09 1.7E-13 108.4 7.8 86 170-270 489-577 (577)
18 PRK13482 DNA integrity scannin 98.8 1E-08 2.2E-13 102.3 6.1 59 216-274 285-343 (352)
19 TIGR00575 dnlj DNA ligase, NAD 98.8 6.7E-09 1.4E-13 110.1 5.2 65 211-276 492-556 (652)
20 PRK00116 ruvA Holliday junctio 98.7 2.2E-08 4.7E-13 91.4 7.0 83 177-275 45-133 (192)
21 PRK12766 50S ribosomal protein 98.7 2.8E-08 6E-13 94.5 6.0 53 219-271 4-57 (232)
22 PRK07956 ligA NAD-dependent DN 98.7 1.8E-08 3.9E-13 107.2 4.6 63 212-275 506-568 (665)
23 COG0272 Lig NAD-dependent DNA 98.6 2.2E-08 4.8E-13 106.4 4.9 85 190-276 481-569 (667)
24 PRK14351 ligA NAD-dependent DN 98.6 3E-08 6.5E-13 106.0 5.6 64 210-274 521-584 (689)
25 PRK14671 uvrC excinuclease ABC 98.6 8.1E-08 1.8E-12 101.6 8.1 87 170-271 531-620 (621)
26 PRK14350 ligA NAD-dependent DN 98.4 3.1E-07 6.7E-12 98.1 4.8 64 210-274 495-565 (669)
27 PRK08097 ligB NAD-dependent DN 98.2 6.9E-07 1.5E-11 93.9 3.7 62 210-275 484-545 (562)
28 PRK00254 ski2-like helicase; P 98.0 7.3E-06 1.6E-10 87.1 6.3 55 219-273 646-701 (720)
29 TIGR00194 uvrC excinuclease AB 97.9 8.9E-06 1.9E-10 85.7 4.6 68 171-251 504-574 (574)
30 PF00633 HHH: Helix-hairpin-he 97.9 1.5E-05 3.3E-10 54.0 4.1 30 240-269 1-30 (30)
31 TIGR00426 competence protein C 97.8 2.7E-05 5.8E-10 59.9 4.9 48 219-271 17-68 (69)
32 COG1623 Predicted nucleic-acid 97.8 2.1E-05 4.7E-10 77.8 4.7 55 217-271 292-346 (349)
33 TIGR01259 comE comEA protein. 97.8 2.6E-05 5.7E-10 66.9 4.1 53 217-271 67-119 (120)
34 KOG0442 Structure-specific end 97.7 0.0001 2.2E-09 80.7 8.7 94 183-277 777-879 (892)
35 PRK14605 ruvA Holliday junctio 97.6 0.00014 3E-09 67.2 6.0 60 216-275 71-133 (194)
36 PRK14602 ruvA Holliday junctio 97.6 0.00016 3.4E-09 67.3 6.3 60 216-275 72-134 (203)
37 PRK13901 ruvA Holliday junctio 97.4 0.00022 4.9E-09 66.5 5.7 59 216-275 70-132 (196)
38 PRK14606 ruvA Holliday junctio 97.4 0.00024 5.1E-09 65.6 5.5 59 216-275 71-133 (188)
39 PRK14604 ruvA Holliday junctio 97.4 0.0003 6.6E-09 65.2 5.5 58 217-275 72-133 (195)
40 PRK14601 ruvA Holliday junctio 97.4 0.00031 6.8E-09 64.7 5.6 58 216-274 71-132 (183)
41 PRK00024 hypothetical protein; 97.3 0.00033 7.2E-09 65.9 5.6 50 222-271 37-87 (224)
42 TIGR00084 ruvA Holliday juncti 97.3 0.00041 8.9E-09 63.9 6.0 58 217-275 71-132 (191)
43 PRK14600 ruvA Holliday junctio 97.3 0.00032 7E-09 64.7 5.0 58 216-275 71-132 (186)
44 COG2003 RadC DNA repair protei 97.3 0.00048 1E-08 65.8 6.2 52 220-271 35-87 (224)
45 PRK14603 ruvA Holliday junctio 97.3 0.00044 9.5E-09 64.2 5.6 59 216-275 70-132 (197)
46 TIGR00608 radc DNA repair prot 97.2 0.00049 1.1E-08 64.8 5.1 50 222-271 27-81 (218)
47 COG0632 RuvA Holliday junction 97.1 0.001 2.2E-08 62.4 6.3 59 218-277 73-135 (201)
48 TIGR02236 recomb_radA DNA repa 97.0 0.0015 3.3E-08 62.4 6.1 52 220-271 1-53 (310)
49 PRK04301 radA DNA repair and r 96.6 0.0032 7E-08 60.8 5.6 54 219-272 7-61 (317)
50 PRK02515 psbU photosystem II c 95.9 0.014 3E-07 52.1 5.3 50 217-272 60-109 (132)
51 cd00141 NT_POLXc Nucleotidyltr 95.5 0.045 9.8E-07 53.6 7.4 49 219-267 46-102 (307)
52 COG1555 ComEA DNA uptake prote 95.4 0.03 6.5E-07 50.1 5.5 48 218-270 97-147 (149)
53 PRK02515 psbU photosystem II c 95.4 0.015 3.3E-07 51.8 3.6 47 226-276 39-85 (132)
54 COG1796 POL4 DNA polymerase IV 95.2 0.024 5.2E-07 56.9 4.7 58 214-271 47-114 (326)
55 TIGR01448 recD_rel helicase, p 95.2 0.036 7.7E-07 60.2 6.3 56 216-272 80-139 (720)
56 PRK07956 ligA NAD-dependent DN 95.2 0.046 1E-06 59.1 7.0 51 222-272 449-501 (665)
57 TIGR00575 dnlj DNA ligase, NAD 95.2 0.042 9.2E-07 59.2 6.6 51 222-272 436-488 (652)
58 PF12836 HHH_3: Helix-hairpin- 95.1 0.024 5.1E-07 43.6 3.4 51 218-270 14-64 (65)
59 TIGR01954 nusA_Cterm_rpt trans 95.0 0.075 1.6E-06 37.8 5.6 46 227-272 2-48 (50)
60 PRK01172 ski2-like helicase; P 95.0 0.032 7E-07 59.1 5.2 53 219-271 613-666 (674)
61 smart00483 POLXc DNA polymeras 94.8 0.052 1.1E-06 53.8 5.8 52 219-271 49-109 (334)
62 cd00080 HhH2_motif Helix-hairp 94.3 0.042 9.2E-07 43.6 3.0 30 220-249 24-53 (75)
63 PRK08609 hypothetical protein; 94.1 0.083 1.8E-06 56.0 5.6 52 219-270 49-108 (570)
64 TIGR01259 comE comEA protein. 94.0 0.056 1.2E-06 46.5 3.4 31 242-272 60-90 (120)
65 PF03118 RNA_pol_A_CTD: Bacter 93.8 0.1 2.2E-06 40.8 4.3 43 229-271 21-65 (66)
66 PRK14351 ligA NAD-dependent DN 93.6 0.15 3.2E-06 55.6 6.6 60 213-272 453-518 (689)
67 cd00008 53EXOc 5'-3' exonuclea 93.5 0.099 2.1E-06 49.4 4.4 30 219-248 184-213 (240)
68 PRK02362 ski2-like helicase; P 93.4 0.13 2.7E-06 55.5 5.5 51 219-271 653-704 (737)
69 smart00278 HhH1 Helix-hairpin- 93.3 0.07 1.5E-06 34.5 2.2 21 250-270 1-21 (26)
70 COG1555 ComEA DNA uptake prote 93.2 0.056 1.2E-06 48.4 2.3 37 239-275 86-124 (149)
71 PRK09482 flap endonuclease-lik 93.2 0.11 2.4E-06 50.4 4.4 29 219-247 183-211 (256)
72 PRK08609 hypothetical protein; 92.8 0.12 2.6E-06 54.8 4.4 53 219-271 89-144 (570)
73 TIGR02238 recomb_DMC1 meiotic 92.7 0.21 4.5E-06 49.3 5.6 50 224-273 7-57 (313)
74 smart00475 53EXOc 5'-3' exonuc 92.7 0.13 2.8E-06 49.6 4.0 29 219-247 187-215 (259)
75 PF12836 HHH_3: Helix-hairpin- 92.5 0.12 2.6E-06 39.7 2.9 31 245-275 9-41 (65)
76 PRK14976 5'-3' exonuclease; Pr 92.4 0.15 3.2E-06 49.7 4.2 28 219-246 192-219 (281)
77 PTZ00035 Rad51 protein; Provis 92.4 0.22 4.7E-06 49.6 5.3 49 224-272 29-78 (337)
78 PRK08097 ligB NAD-dependent DN 92.0 0.29 6.3E-06 52.4 5.9 59 214-272 417-481 (562)
79 PF01367 5_3_exonuc: 5'-3' exo 91.8 0.0099 2.1E-07 50.3 -4.2 28 219-246 19-46 (101)
80 PLN03187 meiotic recombination 91.5 0.32 7E-06 48.9 5.4 48 224-271 37-85 (344)
81 PF00730 HhH-GPD: HhH-GPD supe 90.8 0.22 4.7E-06 40.4 2.9 43 230-272 17-64 (108)
82 PRK07758 hypothetical protein; 89.9 0.62 1.4E-05 39.7 4.9 49 224-272 40-89 (95)
83 TIGR03252 uncharacterized HhH- 89.1 0.71 1.5E-05 43.0 5.1 49 231-279 88-144 (177)
84 TIGR00593 pola DNA polymerase 88.7 0.54 1.2E-05 52.7 4.8 29 219-247 186-214 (887)
85 PRK14350 ligA NAD-dependent DN 88.4 0.68 1.5E-05 50.5 5.2 51 222-272 440-492 (669)
86 PRK03980 flap endonuclease-1; 88.1 0.52 1.1E-05 46.3 3.7 27 220-246 191-217 (292)
87 PRK10736 hypothetical protein; 88.1 0.71 1.5E-05 47.3 4.8 47 218-268 8-54 (374)
88 PLN03186 DNA repair protein RA 87.8 0.92 2E-05 45.6 5.3 48 224-271 34-82 (342)
89 TIGR00426 competence protein C 87.6 0.46 9.9E-06 36.5 2.4 29 243-271 9-38 (69)
90 COG0258 Exo 5'-3' exonuclease 87.6 0.61 1.3E-05 45.4 3.9 50 219-275 199-248 (310)
91 PRK10702 endonuclease III; Pro 87.0 0.63 1.4E-05 43.7 3.5 37 231-270 93-129 (211)
92 PF14716 HHH_8: Helix-hairpin- 86.5 0.7 1.5E-05 35.7 2.9 20 251-270 48-67 (68)
93 PRK13913 3-methyladenine DNA g 86.5 0.95 2.1E-05 43.1 4.4 46 230-275 100-147 (218)
94 PF14520 HHH_5: Helix-hairpin- 86.3 0.53 1.2E-05 35.3 2.1 22 250-271 5-27 (60)
95 COG0177 Nth Predicted EndoIII- 86.2 0.88 1.9E-05 43.4 4.0 45 229-276 91-136 (211)
96 PRK05755 DNA polymerase I; Pro 84.8 0.76 1.6E-05 51.0 3.3 29 219-247 188-216 (880)
97 PRK00116 ruvA Holliday junctio 84.6 1.2 2.5E-05 41.1 3.9 42 228-272 54-95 (192)
98 cd00128 XPG Xeroderma pigmento 84.4 0.93 2E-05 44.1 3.3 52 220-273 225-276 (316)
99 PRK14973 DNA topoisomerase I; 83.9 1.5 3.3E-05 49.6 5.2 52 220-271 879-931 (936)
100 smart00279 HhH2 Helix-hairpin- 83.9 0.69 1.5E-05 32.5 1.6 28 241-268 7-34 (36)
101 smart00611 SEC63 Domain of unk 83.7 1.8 4E-05 41.2 4.9 54 219-272 152-206 (312)
102 TIGR03674 fen_arch flap struct 83.2 1 2.3E-05 44.9 3.2 27 221-247 239-265 (338)
103 TIGR02239 recomb_RAD51 DNA rep 83.2 1.9 4.1E-05 42.6 5.0 47 225-271 8-55 (316)
104 PF11731 Cdd1: Pathogenicity l 83.1 2.4 5.1E-05 36.0 4.8 38 215-252 9-47 (93)
105 PTZ00217 flap endonuclease-1; 82.7 1.2 2.5E-05 45.7 3.3 28 220-247 237-264 (393)
106 cd00080 HhH2_motif Helix-hairp 82.4 0.93 2E-05 36.0 2.0 36 237-272 9-44 (75)
107 PF02371 Transposase_20: Trans 80.5 1.3 2.7E-05 35.7 2.2 38 219-258 3-40 (87)
108 PRK10702 endonuclease III; Pro 80.4 3.6 7.8E-05 38.7 5.5 61 211-272 28-95 (211)
109 smart00478 ENDO3c endonuclease 80.0 2.3 4.9E-05 36.5 3.8 45 225-269 43-91 (149)
110 COG0272 Lig NAD-dependent DNA 80.0 2.7 5.8E-05 46.2 5.1 53 219-272 447-501 (667)
111 PRK10880 adenine DNA glycosyla 78.7 2.6 5.6E-05 42.8 4.2 29 246-274 105-134 (350)
112 COG1796 POL4 DNA polymerase IV 78.5 4.3 9.4E-05 41.2 5.7 57 217-274 93-152 (326)
113 smart00279 HhH2 Helix-hairpin- 77.0 2.1 4.7E-05 30.1 2.2 20 219-238 17-36 (36)
114 PRK14973 DNA topoisomerase I; 76.5 6.9 0.00015 44.5 7.2 52 220-271 804-856 (936)
115 PRK13910 DNA glycosylase MutY; 76.2 3.2 6.9E-05 41.1 4.0 28 246-273 68-96 (289)
116 PF10391 DNA_pol_lambd_f: Fing 74.7 2.9 6.3E-05 31.6 2.6 19 250-268 2-20 (52)
117 PHA00439 exonuclease 73.1 3.2 7E-05 41.3 3.2 78 234-333 172-251 (286)
118 TIGR01084 mutY A/G-specific ad 72.1 4.3 9.3E-05 39.7 3.7 24 246-269 101-124 (275)
119 cd01702 PolY_Pol_eta DNA Polym 71.7 5.5 0.00012 40.0 4.5 52 219-272 183-238 (359)
120 PF00633 HHH: Helix-hairpin-he 71.1 4.3 9.3E-05 27.6 2.5 19 218-236 11-29 (30)
121 PRK01229 N-glycosylase/DNA lya 70.4 5.7 0.00012 37.7 4.0 55 214-268 72-137 (208)
122 TIGR01083 nth endonuclease III 70.4 5.3 0.00012 36.4 3.7 24 247-270 103-126 (191)
123 PRK13910 DNA glycosylase MutY; 70.4 5.2 0.00011 39.6 3.9 40 232-271 16-57 (289)
124 COG2231 Uncharacterized protei 70.3 11 0.00023 36.5 5.8 81 183-270 45-135 (215)
125 smart00478 ENDO3c endonuclease 70.0 10 0.00022 32.5 5.2 42 230-271 13-57 (149)
126 COG1948 MUS81 ERCC4-type nucle 69.0 19 0.00041 35.6 7.3 135 137-272 26-204 (254)
127 PRK09482 flap endonuclease-lik 68.1 3.5 7.6E-05 40.2 2.2 43 230-272 155-204 (256)
128 smart00278 HhH1 Helix-hairpin- 67.2 5.3 0.00012 25.7 2.2 20 219-238 2-21 (26)
129 TIGR01083 nth endonuclease III 66.3 11 0.00024 34.3 4.9 40 232-271 49-91 (191)
130 PRK10308 3-methyl-adenine DNA 65.9 12 0.00027 36.6 5.5 34 237-271 154-187 (283)
131 PF11798 IMS_HHH: IMS family H 64.6 6 0.00013 27.0 2.2 18 251-268 12-29 (32)
132 PRK14976 5'-3' exonuclease; Pr 63.8 4.5 9.7E-05 39.6 2.0 41 231-271 165-212 (281)
133 KOG2093 Translesion DNA polyme 62.8 7.7 0.00017 44.2 3.7 80 189-272 520-602 (1016)
134 smart00475 53EXOc 5'-3' exonuc 62.6 5.4 0.00012 38.6 2.3 35 237-271 173-207 (259)
135 cd00008 53EXOc 5'-3' exonuclea 62.6 5.1 0.00011 38.0 2.1 32 240-271 173-204 (240)
136 cd00056 ENDO3c endonuclease II 62.5 9.2 0.0002 33.0 3.5 25 247-271 80-104 (158)
137 TIGR00084 ruvA Holliday juncti 62.1 5.7 0.00012 36.9 2.3 23 250-272 72-94 (191)
138 PRK05179 rpsM 30S ribosomal pr 61.9 6.3 0.00014 34.5 2.4 51 215-274 14-64 (122)
139 COG4277 Predicted DNA-binding 61.6 5.5 0.00012 40.9 2.2 47 224-270 304-350 (404)
140 KOG1921 Endonuclease III [Repl 61.5 7.1 0.00015 38.9 2.9 38 228-268 140-177 (286)
141 PF00416 Ribosomal_S13: Riboso 61.5 8.7 0.00019 32.4 3.1 48 216-272 13-60 (107)
142 PRK00076 recR recombination pr 61.1 7.2 0.00016 36.9 2.8 46 213-271 6-51 (196)
143 PF14229 DUF4332: Domain of un 60.8 17 0.00037 31.3 4.8 20 249-268 52-71 (122)
144 PRK05182 DNA-directed RNA poly 60.5 9.1 0.0002 38.2 3.5 44 229-272 258-303 (310)
145 PF14842 FliG_N: FliG N-termin 59.8 3 6.5E-05 35.1 0.0 73 183-272 20-100 (108)
146 PRK04053 rps13p 30S ribosomal 59.7 7.5 0.00016 35.3 2.5 52 215-275 22-73 (149)
147 PRK12766 50S ribosomal protein 59.6 5.6 0.00012 38.7 1.8 26 249-274 2-28 (232)
148 TIGR00615 recR recombination p 59.4 8.1 0.00018 36.6 2.8 25 213-237 6-30 (195)
149 TIGR02027 rpoA DNA-directed RN 58.9 9.8 0.00021 37.7 3.4 44 229-272 244-289 (297)
150 cd00141 NT_POLXc Nucleotidyltr 58.6 8.7 0.00019 37.9 3.0 26 247-272 42-67 (307)
151 PRK03352 DNA polymerase IV; Va 58.2 14 0.00031 36.1 4.4 51 219-271 178-229 (346)
152 PF11731 Cdd1: Pathogenicity l 57.7 9.8 0.00021 32.3 2.7 25 244-268 6-30 (93)
153 COG0055 AtpD F0F1-type ATP syn 57.2 6 0.00013 41.6 1.7 48 229-276 364-412 (468)
154 cd00056 ENDO3c endonuclease II 56.8 11 0.00024 32.5 3.0 42 230-272 21-66 (158)
155 PRK07945 hypothetical protein; 56.7 14 0.00031 36.8 4.1 51 219-272 50-102 (335)
156 TIGR03252 uncharacterized HhH- 56.6 28 0.0006 32.6 5.7 60 211-271 17-89 (177)
157 PF02889 Sec63: Sec63 Brl doma 56.3 18 0.00038 34.5 4.6 60 218-277 148-209 (314)
158 PRK14605 ruvA Holliday junctio 56.2 9.1 0.0002 35.6 2.6 25 250-274 73-97 (194)
159 smart00483 POLXc DNA polymeras 56.2 10 0.00022 37.9 3.0 25 250-274 48-72 (334)
160 PRK13844 recombination protein 55.2 10 0.00022 36.1 2.8 47 212-271 9-55 (200)
161 PRK03348 DNA polymerase IV; Pr 55.0 23 0.0005 36.7 5.5 106 219-346 181-287 (454)
162 COG0353 RecR Recombinational D 54.9 8.2 0.00018 36.9 2.0 17 250-266 12-28 (198)
163 TIGR00596 rad1 DNA repair prot 53.9 57 0.0012 36.9 8.6 42 138-179 586-630 (814)
164 PF10391 DNA_pol_lambd_f: Fing 53.8 16 0.00034 27.7 3.0 29 218-246 2-31 (52)
165 KOG1350 F0F1-type ATP synthase 53.8 10 0.00022 39.4 2.7 48 229-276 414-462 (521)
166 PTZ00134 40S ribosomal protein 52.8 16 0.00035 33.4 3.5 50 215-273 27-76 (154)
167 COG0258 Exo 5'-3' exonuclease 52.1 12 0.00026 36.6 2.7 34 238-271 186-219 (310)
168 PF05559 DUF763: Protein of un 51.3 30 0.00065 35.3 5.4 34 242-275 261-294 (319)
169 TIGR00588 ogg 8-oxoguanine DNA 51.3 16 0.00035 36.2 3.5 39 231-269 194-239 (310)
170 TIGR03631 bact_S13 30S ribosom 51.3 12 0.00026 32.4 2.3 50 215-273 12-61 (113)
171 PRK03858 DNA polymerase IV; Va 51.3 22 0.00047 35.4 4.5 51 219-271 174-225 (396)
172 PF14579 HHH_6: Helix-hairpin- 51.0 28 0.00061 28.1 4.3 46 216-268 25-75 (90)
173 PRK14671 uvrC excinuclease ABC 50.7 18 0.00038 39.5 4.0 45 228-272 547-591 (621)
174 TIGR03491 RecB family nuclease 50.3 23 0.0005 36.6 4.6 51 218-268 207-258 (457)
175 COG0177 Nth Predicted EndoIII- 50.0 24 0.00052 33.8 4.3 51 225-276 46-102 (211)
176 COG0632 RuvA Holliday junction 49.5 12 0.00026 35.5 2.2 21 217-237 107-127 (201)
177 cd01703 PolY_Pol_iota DNA Poly 49.4 28 0.0006 35.4 4.9 53 219-273 173-241 (379)
178 PRK10880 adenine DNA glycosyla 48.9 20 0.00044 36.5 3.9 41 231-271 52-94 (350)
179 cd01701 PolY_Rev1 DNA polymera 47.4 26 0.00056 35.5 4.4 52 219-272 223-277 (404)
180 PF00570 HRDC: HRDC domain Blo 46.9 23 0.00049 26.4 3.0 27 243-269 37-63 (68)
181 PRK14606 ruvA Holliday junctio 46.7 15 0.00032 34.2 2.3 21 217-237 107-127 (188)
182 KOG2534 DNA polymerase IV (fam 46.3 17 0.00036 37.4 2.8 27 248-274 54-80 (353)
183 KOG2875 8-oxoguanine DNA glyco 45.8 23 0.00051 35.9 3.7 40 228-267 189-235 (323)
184 PRK14601 ruvA Holliday junctio 45.4 16 0.00034 34.0 2.3 21 217-237 107-127 (183)
185 PRK00076 recR recombination pr 45.3 21 0.00046 33.8 3.2 21 250-270 11-31 (196)
186 KOG2534 DNA polymerase IV (fam 44.9 26 0.00057 36.0 3.9 49 219-268 57-115 (353)
187 PF12826 HHH_2: Helix-hairpin- 43.4 25 0.00053 27.0 2.7 28 217-244 34-61 (64)
188 PRK01216 DNA polymerase IV; Va 43.3 41 0.00088 33.8 5.0 51 219-271 179-230 (351)
189 CHL00137 rps13 ribosomal prote 43.0 19 0.00042 31.6 2.4 49 215-272 14-62 (122)
190 PRK14602 ruvA Holliday junctio 42.6 19 0.00042 33.8 2.4 21 217-237 108-128 (203)
191 PRK07945 hypothetical protein; 42.5 32 0.0007 34.3 4.2 23 251-273 50-72 (335)
192 PF14229 DUF4332: Domain of un 42.5 32 0.0007 29.7 3.6 36 219-254 54-90 (122)
193 TIGR00615 recR recombination p 42.2 24 0.00052 33.5 3.0 17 250-266 11-27 (195)
194 PRK13844 recombination protein 41.9 26 0.00056 33.4 3.2 21 250-270 15-35 (200)
195 PF14635 HHH_7: Helix-hairpin- 41.9 20 0.00044 30.9 2.3 23 250-272 50-72 (104)
196 CHL00013 rpoA RNA polymerase a 41.7 24 0.00051 35.8 3.0 39 237-275 282-320 (327)
197 PRK13901 ruvA Holliday junctio 41.6 19 0.00042 34.0 2.3 21 217-237 106-126 (196)
198 PF14490 HHH_4: Helix-hairpin- 40.9 39 0.00085 27.6 3.7 57 214-271 9-67 (94)
199 PF01367 5_3_exonuc: 5'-3' exo 40.7 0.95 2.1E-05 38.4 -5.9 31 242-272 10-40 (101)
200 PRK14603 ruvA Holliday junctio 40.1 22 0.00047 33.4 2.3 21 217-237 106-126 (197)
201 PRK14604 ruvA Holliday junctio 39.9 22 0.00047 33.3 2.3 22 217-238 107-128 (195)
202 TIGR01084 mutY A/G-specific ad 39.8 40 0.00086 33.1 4.2 41 231-271 48-90 (275)
203 COG0099 RpsM Ribosomal protein 39.8 22 0.00048 31.7 2.2 50 214-272 13-62 (121)
204 PF12482 DUF3701: Phage integr 39.8 20 0.00044 30.5 2.0 22 251-272 51-72 (96)
205 PRK13913 3-methyladenine DNA g 39.8 27 0.00058 33.4 2.9 33 239-271 67-102 (218)
206 COG1936 Predicted nucleotide k 39.3 20 0.00043 33.9 1.9 23 219-241 4-26 (180)
207 PRK14669 uvrC excinuclease ABC 37.9 26 0.00057 38.4 2.9 24 249-272 551-574 (624)
208 COG0122 AlkA 3-methyladenine D 37.8 51 0.0011 32.5 4.7 21 215-235 195-215 (285)
209 TIGR00194 uvrC excinuclease AB 37.7 26 0.00055 38.0 2.8 24 249-272 540-563 (574)
210 COG1491 Predicted RNA-binding 37.1 70 0.0015 30.8 5.2 53 215-274 127-187 (202)
211 TIGR00593 pola DNA polymerase 37.1 21 0.00045 40.5 2.0 42 230-271 158-206 (887)
212 PRK10308 3-methyl-adenine DNA 36.8 28 0.00061 34.2 2.7 45 225-269 173-226 (283)
213 PF02371 Transposase_20: Trans 36.5 42 0.00091 26.9 3.2 24 250-273 2-25 (87)
214 PRK05755 DNA polymerase I; Pro 36.3 22 0.00048 39.8 2.1 32 240-271 177-208 (880)
215 COG0353 RecR Recombinational D 35.8 38 0.00082 32.5 3.3 49 211-272 5-53 (198)
216 TIGR03629 arch_S13P archaeal r 34.9 42 0.00091 30.3 3.3 49 215-272 18-66 (144)
217 PRK14670 uvrC excinuclease ABC 34.8 27 0.00059 37.9 2.4 25 248-272 512-536 (574)
218 PRK09202 nusA transcription el 34.5 78 0.0017 33.6 5.6 59 218-276 356-415 (470)
219 PF00416 Ribosomal_S13: Riboso 34.0 38 0.00082 28.6 2.7 23 250-272 15-37 (107)
220 TIGR01448 recD_rel helicase, p 32.4 51 0.0011 36.4 4.0 48 225-272 154-203 (720)
221 PRK14667 uvrC excinuclease ABC 32.2 32 0.00069 37.3 2.4 24 249-272 513-536 (567)
222 PRK01810 DNA polymerase IV; Va 31.3 64 0.0014 32.4 4.2 51 219-272 180-231 (407)
223 cd01700 PolY_Pol_V_umuC umuC s 30.7 69 0.0015 31.4 4.3 50 219-271 177-227 (344)
224 TIGR00600 rad2 DNA excision re 30.3 45 0.00097 38.8 3.3 26 221-246 869-896 (1034)
225 PRK02406 DNA polymerase IV; Va 30.2 76 0.0016 31.1 4.5 51 219-272 169-220 (343)
226 PRK02794 DNA polymerase IV; Pr 29.8 69 0.0015 32.5 4.2 51 219-272 210-261 (419)
227 COG0758 Smf Predicted Rossmann 29.8 70 0.0015 32.8 4.2 48 218-266 10-57 (350)
228 KOG2379 Endonuclease MUS81 [Re 29.4 1.2E+02 0.0027 32.8 6.1 57 215-271 427-498 (501)
229 COG4969 PilA Tfp pilus assembl 29.4 16 0.00034 32.1 -0.4 15 56-70 24-38 (125)
230 PRK14600 ruvA Holliday junctio 28.9 37 0.0008 31.7 1.9 22 250-271 73-94 (186)
231 PRK14668 uvrC excinuclease ABC 28.8 41 0.0009 36.5 2.6 26 249-274 524-549 (577)
232 PRK14552 C/D box methylation g 28.1 59 0.0013 34.0 3.4 47 219-272 265-311 (414)
233 COG1204 Superfamily II helicas 27.7 72 0.0016 35.8 4.2 60 217-276 674-735 (766)
234 PRK14133 DNA polymerase IV; Pr 27.7 89 0.0019 30.7 4.5 50 219-271 174-224 (347)
235 KOG2518 5'-3' exonuclease [Rep 26.7 56 0.0012 35.6 3.0 27 219-245 226-252 (556)
236 PRK00558 uvrC excinuclease ABC 26.7 47 0.001 36.1 2.5 24 249-272 542-565 (598)
237 COG0122 AlkA 3-methyladenine D 25.8 97 0.0021 30.6 4.3 30 240-269 184-217 (285)
238 PRK03103 DNA polymerase IV; Re 25.6 96 0.0021 31.2 4.4 51 219-272 182-233 (409)
239 PRK14672 uvrC excinuclease ABC 25.6 49 0.0011 36.9 2.5 23 250-272 608-630 (691)
240 PRK11057 ATP-dependent DNA hel 25.5 56 0.0012 35.0 2.8 32 239-270 561-595 (607)
241 COG3743 Uncharacterized conser 25.2 41 0.00088 30.5 1.5 20 250-269 67-86 (133)
242 PF09597 IGR: IGR protein moti 25.2 74 0.0016 24.8 2.7 40 225-267 7-47 (57)
243 PF04919 DUF655: Protein of un 24.8 1E+02 0.0022 29.3 4.0 53 217-273 115-172 (181)
244 COG1194 MutY A/G-specific DNA 24.7 89 0.0019 32.2 3.9 102 157-274 24-138 (342)
245 KOG2519 5'-3' exonuclease [Rep 24.2 75 0.0016 33.9 3.4 25 222-246 233-257 (449)
246 PRK14666 uvrC excinuclease ABC 24.0 91 0.002 34.9 4.1 24 248-271 635-658 (694)
247 COG1194 MutY A/G-specific DNA 23.7 1E+02 0.0022 31.9 4.1 40 231-270 56-97 (342)
248 KOG3311 Ribosomal protein S18 23.4 31 0.00066 31.9 0.3 46 214-271 24-69 (152)
249 cd03586 PolY_Pol_IV_kappa DNA 23.3 1.2E+02 0.0027 29.1 4.5 50 219-271 172-222 (334)
250 PF14579 HHH_6: Helix-hairpin- 22.5 90 0.002 25.2 2.9 24 252-275 29-53 (90)
251 COG3743 Uncharacterized conser 22.2 59 0.0013 29.5 1.9 51 218-268 67-118 (133)
252 COG0389 DinP Nucleotidyltransf 21.8 1.2E+02 0.0027 30.4 4.2 56 210-270 170-226 (354)
253 PHA00439 exonuclease 21.6 71 0.0015 32.0 2.5 29 218-247 188-219 (286)
254 TIGR03674 fen_arch flap struct 20.4 61 0.0013 32.5 1.8 29 241-271 229-257 (338)
255 TIGR00375 conserved hypothetic 20.2 65 0.0014 33.3 2.0 41 231-274 320-361 (374)
No 1
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=100.00 E-value=4.9e-46 Score=348.93 Aligned_cols=187 Identities=42% Similarity=0.681 Sum_probs=162.5
Q ss_pred CCCCCCCccCCccHHHHhhhhhcccccCCCCCCCCCCCCCCCCCCcCCCCCcccCCCcccCCccccCCCCCeEEEcCCcc
Q 017612 69 TNPPQNLFTPSQSFSQAFSFIKSSEFYNPPPPPPANPPTTSQNPTLSQGGEQNVGTASASASSSQSIQSRNAILVSQRQK 148 (368)
Q Consensus 69 ~~~~~~~~~~s~~f~~~f~~~k~~~~y~~p~~~~~~~~~~~~~~t~~~~~~~~~~~p~~~~~~~~~~~~~~~IlVS~rQr 148 (368)
...|+++++||+.+.+++.+++.-..+..- ..+ ....+|.-+ ..+...+++|+||+|||
T Consensus 7 ~s~~~~~~s~s~~~~~~~~~v~~p~~~~~~-----------~~p-------~~s~~P~~~---g~~~~~~~~Ilvn~rQk 65 (254)
T KOG2841|consen 7 KSFPDSLGSPSLEIDAKKLFVQAPARIASN-----------PIP-------MNSQPPDGS---GPVTVPGGHILVNPRQK 65 (254)
T ss_pred cccCccccCcchHHHHhhhhccCcHhHhcC-----------CCc-------ccCCCCCCC---CCCCCCCceEEeccccc
Confidence 446899999999999999999921000000 000 011112111 23456789999999999
Q ss_pred CChhHHhhhccceEee-ecccceEeccceeeeeec---------------------------------------------
Q 017612 149 GNPLLKYIRNVRWAFA-DVVCDYLVGQNSCALYLS--------------------------------------------- 182 (368)
Q Consensus 149 GNPLLk~IrnVpwefa-DIvpDY~Ig~ttcILFLS--------------------------------------------- 182 (368)
|||||+|||||+|+|+ ||.|||++|+++||||||
T Consensus 66 GNplLk~vrnv~w~f~ddi~PDf~lg~~~cvLyLSl~yH~l~pdYi~~Ri~~l~k~yk~~VLl~~vd~~e~~~~l~el~k 145 (254)
T KOG2841|consen 66 GNPLLKHVRNVKWEFGDDIIPDFVLGRGCCVLYLSLKYHKLHPDYIYRRIRKLGKNYKLRVLLVHVDMEEPYKPLLELTK 145 (254)
T ss_pred cChHHHHHhcCCeEecCCCCcceEecCceEEEEeehHhhhcCcHHHHHHHHHhcccccceEEEEEecCcchHHHHHHHHH
Confidence 9999999999999999 799999999999999999
Q ss_pred --------------hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612 183 --------------LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDAS 248 (368)
Q Consensus 183 --------------~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS 248 (368)
.||||+|||+|+.||+++++.|+++.++||.++++.+||+||||||+||..||.+||||++|++||
T Consensus 146 ~~~l~~~Tl~lA~s~EeaaryIE~~k~~ek~p~dli~~~~~~d~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS 225 (254)
T KOG2841|consen 146 TCDLNDVTLVLAWSMEEAARYIETYKEYEKKPIDLIMERKDRDLLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNAS 225 (254)
T ss_pred HHHhhceeeeeeccHHHHHHHHHHHHHhhcCCchhhhhcccccHHHHHHHHHHhCCCCCcccHHHHHHhcccHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 249 MEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
.+||++|+|+|+.||++|+++||+||..
T Consensus 226 ~~ele~~~G~G~~kak~l~~~l~~pf~~ 253 (254)
T KOG2841|consen 226 EGELEQCPGLGPAKAKRLHKFLHQPFLS 253 (254)
T ss_pred HhHHHhCcCcCHHHHHHHHHHHhccccC
Confidence 9999999999999999999999999974
No 2
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=99.90 E-value=3.3e-25 Score=203.46 Aligned_cols=136 Identities=27% Similarity=0.332 Sum_probs=129.8
Q ss_pred CCCeEEEcCCccCChhHHhhhccceEeee-cccceEeccceeeeeec---------------------------------
Q 017612 137 SRNAILVSQRQKGNPLLKYIRNVRWAFAD-VVCDYLVGQNSCALYLS--------------------------------- 182 (368)
Q Consensus 137 ~~~~IlVS~rQrGNPLLk~IrnVpwefaD-IvpDY~Ig~ttcILFLS--------------------------------- 182 (368)
....|.||++|+|||+|-|.+|++|+|.+ |+|||.++...|-||||
T Consensus 32 ~s~~I~vsplQkgnp~l~~~~N~~w~y~~~i~Pd~~~~s~~~~lflslrfhs~~Peyi~~riSklKsYk~r~LL~hvd~~ 111 (224)
T COG5241 32 QSLEIDVSPLQKGNPQLSRRINSNWVYNAFIKPDEWTDSKATDLFLSLRFHSTRPEYIVLRISKLKSYKERPLLNHVDST 111 (224)
T ss_pred eeeEEecChhhcCCCcccccccCcceeccccCcchhhcchHHHHHHHHhhhcCCCceEEEeeeccccccccceeeeeccc
Confidence 35699999999999999999999999998 99999999999999999
Q ss_pred -----------------------hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcC
Q 017612 183 -----------------------LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFG 239 (368)
Q Consensus 183 -----------------------~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FG 239 (368)
.|||+|||++|+.++......||++...|+ + .+.|+.|++|||.|+..+|..||
T Consensus 112 N~~asIqElv~Tt~inti~l~~svee~sry~~t~~~~~~~s~~iir~~~s~d~-s--~~fl~~i~~Vnksds~~~L~d~g 188 (224)
T COG5241 112 NWRASIQELVSTTGINTIYLDYSVEERSRYFLTLTYHKLYSDYIIRRMQSLDR-S--NEFLILIFIVNKSDSEDTLNDIG 188 (224)
T ss_pred cHHHHHHHHHHhcccceeehhhhhhHHHHHHHHhHHHhhcCHHHHHhcCCCcc-c--ccceEEEEeeccccHHHHHHHHH
Confidence 899999999999999999999999888887 2 67899999999999999999999
Q ss_pred CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 240 SLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+|+....||.+|+..+.|+|..||.++.++++.||.
T Consensus 189 ~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~pFm 224 (224)
T COG5241 189 KLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLPFM 224 (224)
T ss_pred HHHHHhccchhHHHHHHccCHHHHHHHHHHhcccCC
Confidence 999999999999999999999999999999999994
No 3
>TIGR00597 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.82 E-value=8.4e-21 Score=161.85 Aligned_cols=44 Identities=64% Similarity=1.158 Sum_probs=43.0
Q ss_pred CeEEEcCCccCChhHHhhhccceEeeecccceEeccceeeeeec
Q 017612 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLS 182 (368)
Q Consensus 139 ~~IlVS~rQrGNPLLk~IrnVpwefaDIvpDY~Ig~ttcILFLS 182 (368)
++|+||+||||||||+|||+|+|+|+||+|||++|+++||||||
T Consensus 1 ~~ilvs~~QkgNPlL~~i~nv~wey~di~~Dy~~g~~~~vLFLS 44 (112)
T TIGR00597 1 NSILVNPRQKGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLS 44 (112)
T ss_pred CcEEeCccccCChHHHHHhcCCeEecCcCCCEEEcCccEEEEEE
Confidence 47999999999999999999999999999999999999999999
No 4
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA inter-strand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [].; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus; PDB: 2JNW_A 2JPD_A 2A1I_A.
Probab=99.77 E-value=1.9e-19 Score=142.21 Aligned_cols=44 Identities=64% Similarity=1.146 Sum_probs=35.1
Q ss_pred CeEEEcCCccCChhHHhhhccceEe-eecccceEeccceeeeeec
Q 017612 139 NAILVSQRQKGNPLLKYIRNVRWAF-ADVVCDYLVGQNSCALYLS 182 (368)
Q Consensus 139 ~~IlVS~rQrGNPLLk~IrnVpwef-aDIvpDY~Ig~ttcILFLS 182 (368)
++|+||++|||||||++|++||||| +||+|||+||+++||||||
T Consensus 1 ~~I~vn~~QkGNplL~~i~nv~we~~~~i~~Dy~vg~~~~vLFLS 45 (69)
T PF03834_consen 1 NSILVNPRQKGNPLLKHIRNVPWEYDSDIVPDYVVGSTTCVLFLS 45 (69)
T ss_dssp SSEEE-GGGTT-CHHHH--SS-EEE----SSSEEEETTEEEEEEE
T ss_pred CcEEECchhcCChHHHHHhcCCeEecCCCCCCEEECCeEEEEEEe
Confidence 4799999999999999999999999 8999999999999999999
No 5
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=99.53 E-value=2.5e-14 Score=136.63 Aligned_cols=108 Identities=21% Similarity=0.328 Sum_probs=96.8
Q ss_pred ecccceEeccceeeeeec-hhhHHHHHHHHHHhhc---CCcchhcc-cccccHHHHHHHhhccCCCCCHHHHHHHHHhcC
Q 017612 165 DVVCDYLVGQNSCALYLS-LEECGRYLETIKVYEN---KPADLIQG-QMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFG 239 (368)
Q Consensus 165 DIvpDY~Ig~ttcILFLS-~EEAArYIEt~K~~E~---K~~d~Ire-k~e~dy~srL~saLTsIpgVnKTDA~~LLs~FG 239 (368)
.+..||.+ .|+|.+ .+|++.+|..|++.++ +.....+. +...++.+++.+.|.+|||||...|.+||.+||
T Consensus 128 s~~vdfg~----~vi~t~~~~~Ta~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fg 203 (254)
T COG1948 128 SLAVDFGL----PVIWTRSPEETAELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFG 203 (254)
T ss_pred HHHhhcCc----eEEEeCCHHHHHHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhc
Confidence 46788987 799996 9999999999999988 43333444 444789999999999999999999999999999
Q ss_pred CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 240 SLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
|++++++||.+||..+.|||+++|.+|+++|..+|..
T Consensus 204 S~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~~~ 240 (254)
T COG1948 204 SVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEYKL 240 (254)
T ss_pred CHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhchhhh
Confidence 9999999999999999999999999999999999984
No 6
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=99.49 E-value=3.3e-14 Score=109.08 Aligned_cols=60 Identities=35% Similarity=0.658 Sum_probs=50.0
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
|++.+| +|||||.+.|+.|+++|||+++|++|+.|||..|+|||++.|+.|+++|+.+-+
T Consensus 1 R~l~aL-GI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n 60 (64)
T PF12826_consen 1 RFLFAL-GIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPEN 60 (64)
T ss_dssp HHHHHC-TSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHH
T ss_pred CeeeeC-CCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHh
Confidence 577888 899999999999999999999999999999999999999999999999998754
No 7
>PRK13766 Hef nuclease; Provisional
Probab=99.27 E-value=7e-11 Score=124.36 Aligned_cols=140 Identities=21% Similarity=0.286 Sum_probs=112.8
Q ss_pred CCCCeEEEcCCccCChhHHhh--hccceEeeec-ccceEeccceeeeeec------------------------------
Q 017612 136 QSRNAILVSQRQKGNPLLKYI--RNVRWAFADV-VCDYLVGQNSCALYLS------------------------------ 182 (368)
Q Consensus 136 ~~~~~IlVS~rQrGNPLLk~I--rnVpwefaDI-vpDY~Ig~ttcILFLS------------------------------ 182 (368)
...-.|+|-.|-....|..+| .+|+++...+ +-||+++...||=-=|
T Consensus 560 ~~~~~i~vD~RE~~~~~~~~l~~~g~~~~~~~L~~gDy~~~~~~~vERK~~~Dl~~s~~~~r~~~q~~~l~~~~~~~~ll 639 (773)
T PRK13766 560 PEGPKIIVDSRELRSNVARHLKRLGAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYERPVLI 639 (773)
T ss_pred CCCcEEEEeCCCccchhhHHHHhCCCEEEEEecCCCCEEccCCeEEEeCcHHHHHHHhhcCcHHHHHHHHHhcCCCcEEE
Confidence 344578999886555566665 3588888776 7899999888881000
Q ss_pred ------------------------------------hhhHHHHHHHHHHhhcCCc----chhcccccccHHHHHHHhhcc
Q 017612 183 ------------------------------------LEECGRYLETIKVYENKPA----DLIQGQMDTDYLSRLTHALTS 222 (368)
Q Consensus 183 ------------------------------------~EEAArYIEt~K~~E~K~~----d~Irek~e~dy~srL~saLTs 222 (368)
.+|+|.||+.|+.+++..+ ....++...+..++....|.+
T Consensus 640 iE~~~~~~~~~~~~~i~~~l~~l~~~~~~~ii~~~~~~eta~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~ 719 (773)
T PRK13766 640 IEGDLYTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEKREVSVHGEKKAMTLKEQQEYIVES 719 (773)
T ss_pred EEcCchhhcccCHHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHHHHhhccccCCCCcccccCCCCCCHHHHHHHHHhc
Confidence 8999999999999886332 233445555555666668999
Q ss_pred CCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 223 VRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 223 IpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
|||||...+.+|+++|||+++|++|+.++|..|+|||+++|++|+++|+.+|.
T Consensus 720 ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~~~ 772 (773)
T PRK13766 720 LPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSEYK 772 (773)
T ss_pred CCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999999999999999999999999885
No 8
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=99.12 E-value=6.1e-11 Score=124.06 Aligned_cols=88 Identities=11% Similarity=0.159 Sum_probs=74.3
Q ss_pred Eeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 171 LVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 171 ~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
.+..++.+|+| . .+||+||-.+|++.-. .+ +.+.|..|||||++..+.||+||||+++|.+|
T Consensus 479 ~l~~~s~~l~lLq~iRDEaHRFAit~hRk~R-------~k--------~~s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 479 KLPKGNPALRILQNVRDEAHRKANGFNKKLR-------EN--------IKLNYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred ecCCCCHHHHHHHHHHHHHHHHHHHHHHHhh-------cc--------cccccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 34455555533 3 9999999999998641 11 34689999999999999999999999999999
Q ss_pred CHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 248 SMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 248 S~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
|.|||+.|||||++.|+.|+++|+..
T Consensus 544 s~eeL~~v~gi~~~~A~~I~~~l~~~ 569 (574)
T PRK14670 544 NEDEIAEKMKINIKMAKKIKKFAEKQ 569 (574)
T ss_pred CHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence 99999999999999999999999754
No 9
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=99.06 E-value=1.9e-10 Score=120.28 Aligned_cols=88 Identities=14% Similarity=0.167 Sum_probs=74.4
Q ss_pred eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
+.+..++.+|+|= .+||+||-.+|++.-. . ...+.+.|..|+|||++..+.||+||||+++|.+
T Consensus 476 ~~l~~~s~~l~lLq~irDEaHRFAi~~hR~~r---------~----k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~ 542 (567)
T PRK14667 476 IPLKENPILYKVFGLIRDEAHRFALSYNRKLR---------E----KEGLKDILDKIKGIGEVKKEIIYRNFKTLYDFLK 542 (567)
T ss_pred eeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh---------h----cccccCccccCCCCCHHHHHHHHHHhCCHHHHHh
Confidence 4555555555443 9999999999998631 1 1224678999999999999999999999999999
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
||.|||+.| |||++.|+.|++.|+
T Consensus 543 As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 543 ADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred CCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 999999999 999999999999986
No 10
>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=99.02 E-value=3.9e-10 Score=84.79 Aligned_cols=56 Identities=23% Similarity=0.422 Sum_probs=52.5
Q ss_pred HHHhhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 216 LTHALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
+...|..|+|||++++.+|++. |+|+++|.+++.++|..|+|||+++|++|.+.++
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 3456779999999999999999 9999999999999999999999999999999875
No 11
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=99.00 E-value=7.9e-10 Score=119.70 Aligned_cols=97 Identities=20% Similarity=0.256 Sum_probs=77.1
Q ss_pred eeeeec-hhhHHHHHHHHHHhhcCCc----chhcc-----cccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 177 CALYLS-LEECGRYLETIKVYENKPA----DLIQG-----QMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 177 cILFLS-~EEAArYIEt~K~~E~K~~----d~Ire-----k~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
.|||.+ ++|+|.+|..||..++.+. ..++. .....+.......|.+|||||...|.+||.+|||+++|++
T Consensus 706 ~IiwS~s~~~TA~i~~~Lk~~e~epd~~~~v~i~~~~~~~~k~~~~~~~~q~~L~~lPgI~~~~a~~ll~~f~si~~l~~ 785 (814)
T TIGR00596 706 RIIWSSSPYATAEIFEELKLGKEEPDPATAAALGSDENTTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAK 785 (814)
T ss_pred eEEecCCHHHHHHHHHHHHhcCCCCCcccceecCcccccccccccccHHHHHHHHHCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 577776 9999999999999987542 22331 1111233333445779999999999999999999999999
Q ss_pred CCHHhhhcCCCCC-HHHHHHHHHHhccccc
Q 017612 247 ASMEDLARCPGIG-ERKVKRLYDTFHEPFK 275 (368)
Q Consensus 247 AS~EELa~VPGIG-~kKA~rI~e~F~ePF~ 275 (368)
||.+||..+ || +++|++||++||.++.
T Consensus 786 as~eeL~~~--iG~~~~A~~i~~fl~~~~~ 813 (814)
T TIGR00596 786 LSQNELNEL--IGDEEAAKRLYDFLRTEKL 813 (814)
T ss_pred CCHHHHHHH--hCCHHHHHHHHHHhccccC
Confidence 999999996 88 9999999999998753
No 12
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=98.99 E-value=7e-10 Score=117.20 Aligned_cols=91 Identities=22% Similarity=0.249 Sum_probs=76.5
Q ss_pred Eeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 171 LVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 171 ~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
.+..++.+|+| . .+||+||-.+|++.- +. ...+.+.|.+|||||++.++.||+||||+++|.+|
T Consensus 515 ~l~~~s~~l~lLq~iRDEaHRFAIt~hRk~---------R~----k~~~~S~L~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 515 VLDRFSPVLHLVQSIRDEAHRFAITFHRKR---------RE----TRDRTSELLEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred ecCCCCHHHHHHHHHHHHHHHHHHHHhHHH---------hh----HHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 34445555533 2 999999999998863 11 33467899999999999999999999999999999
Q ss_pred CHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 248 SMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 248 S~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
|.+||+.| ||.++|++|+++|+.+|-.
T Consensus 582 s~eeL~~v--i~~k~A~~I~~~l~~~~~~ 608 (624)
T PRK14669 582 TETQLAAV--VGRAAAEAIIAHFTTEEAA 608 (624)
T ss_pred CHHHHHHH--hCHHHHHHHHHHhcCcCCC
Confidence 99999999 9999999999999987763
No 13
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=98.98 E-value=7.5e-10 Score=118.02 Aligned_cols=79 Identities=25% Similarity=0.309 Sum_probs=71.7
Q ss_pred hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHH
Q 017612 183 LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERK 262 (368)
Q Consensus 183 ~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kK 262 (368)
.+||+||-.+|++.-. . ...+.+.|..|+|||++.+++||++|||+++|..|+.+||+.|+|||+++
T Consensus 615 RDEaHRfAi~~hR~~r---------~----k~~~~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~ 681 (694)
T PRK14666 615 RDTVHDYAIGRHRRAR---------A----GAALTGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPAR 681 (694)
T ss_pred HHHHHHHHHHHHHHHH---------H----hhhhHhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHH
Confidence 9999999999998641 1 23457899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccc
Q 017612 263 VKRLYDTFHEPF 274 (368)
Q Consensus 263 A~rI~e~F~ePF 274 (368)
|++|++.|+.-|
T Consensus 682 Ae~I~~~L~~~~ 693 (694)
T PRK14666 682 AAALHEHLKTLF 693 (694)
T ss_pred HHHHHHHHHHhh
Confidence 999999998766
No 14
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=98.97 E-value=7.1e-10 Score=116.37 Aligned_cols=90 Identities=32% Similarity=0.514 Sum_probs=75.5
Q ss_pred eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
+.+..++.+|+|= .+||+||-.+|++.- +. ...+...|+.|||||+..++.||++|||+++|..
T Consensus 505 ~~l~~~~~~l~llq~irDEaHRFAi~~hR~~---------R~----k~~~~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~ 571 (598)
T PRK00558 505 IILPPDSPALYLLQRIRDEAHRFAITFHRKK---------RS----KARLTSALDDIPGIGPKRRKALLKHFGSLKAIKE 571 (598)
T ss_pred EecCCCCHHHHHHHHHHHHhhhhhhhhhccc---------cc----cchhhhhHhhCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 4455555555443 999999999998853 11 1225678999999999999999999999999999
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
|+.+||..|+|||++.|+.|+++|+.
T Consensus 572 As~eeL~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 572 ASVEELAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred CCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence 99999999999999999999999975
No 15
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=98.89 E-value=2.3e-09 Score=114.21 Aligned_cols=90 Identities=18% Similarity=0.194 Sum_probs=74.7
Q ss_pred eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
+.+.....+|++= .+||+||-.+|++.-. . ...+.+.|..|+|||++....||+||||+++|..
T Consensus 570 ~~L~~~s~~l~lLq~iRDEaHRFAIt~hR~~R---------~----k~~~~s~L~~IpGiG~kr~~~LL~~FgS~~~i~~ 636 (691)
T PRK14672 570 LVLDRRNPALHMLQRIRDEAHRFAITRNRHLR---------T----KKELVLSFERLPHVGKVRAHRLLAHFGSFRSLQS 636 (691)
T ss_pred eecCCCCHHHHHHHHHHHHHHHHHHHHHHHHh---------h----hhhcccccccCCCCCHHHHHHHHHHhcCHHHHHh
Confidence 4444555555332 9999999999988631 1 2335678999999999999999999999999999
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
||.+||+.|+|||.+.|+.|+.+...
T Consensus 637 As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 637 ATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 99999999999999999999998753
No 16
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=98.83 E-value=4.2e-09 Score=110.64 Aligned_cols=86 Identities=29% Similarity=0.417 Sum_probs=72.6
Q ss_pred Eeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 171 LVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 171 ~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
.+.+.+.+||+= .+||+||-.++++-. + ....+.+.|..|+|||++..+.||+||||+++|..|
T Consensus 493 ~l~~~~p~l~~lq~irDEaHrfAi~~hR~~---------R----~k~~~~s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~A 559 (581)
T COG0322 493 DLPPNSPALYLLQRIRDEAHRFAITYHRKK---------R----SKAMLQSSLDDIPGIGPKRRKALLKHFGSLKGIKSA 559 (581)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHHH---------h----hhhhhcCccccCCCcCHHHHHHHHHHhhCHHHHHhc
Confidence 334444444443 999999999998853 1 245578899999999999999999999999999999
Q ss_pred CHHhhhcCCCCCHHHHHHHHHHh
Q 017612 248 SMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 248 S~EELa~VPGIG~kKA~rI~e~F 270 (368)
|.+||+.| ||+.+.|++|++.|
T Consensus 560 s~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 560 SVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred CHHHHHHc-CCCHHHHHHHHhhC
Confidence 99999999 99999999999865
No 17
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=98.81 E-value=8e-09 Score=108.37 Aligned_cols=86 Identities=24% Similarity=0.368 Sum_probs=72.1
Q ss_pred eEeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 170 YLVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 170 Y~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
+.+..++.+|+| . .+||+||-.+|++.-. ..+...|+.|+|||+..++.||++|||+++|..
T Consensus 489 ~~l~~~~~~l~lL~~irDEaHRFAi~~hR~~r---------------~~~~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~ 553 (577)
T PRK14668 489 YDWPDDAPQLHLLQRVRDEAHRFAVQYHQTLR---------------DDVSTVLDDVPGVGPETRKRLLRRFGSVEGVRE 553 (577)
T ss_pred eecCCCCHHHHHHHHHHHHHHHHHhhHHHHHH---------------HHHHhHHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 334445544433 3 9999999999998631 125689999999999999999999999999999
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
||.+||..+||||.+.|+.|++++
T Consensus 554 As~eeL~~vpGi~~~~A~~I~~~~ 577 (577)
T PRK14668 554 ASVEDLRDVPGVGEKTAETIRERL 577 (577)
T ss_pred CCHHHHHhCCCCCHHHHHHHHHhC
Confidence 999999999999999999998764
No 18
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=98.76 E-value=1e-08 Score=102.35 Aligned_cols=59 Identities=25% Similarity=0.388 Sum_probs=54.8
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
-.-+|++||+|++..|++|+++|||+++|++|+.+||..|+|||+++|+.|++.+.+-.
T Consensus 285 GyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~ 343 (352)
T PRK13482 285 GYRLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLA 343 (352)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHH
Confidence 34589999999999999999999999999999999999999999999999999987543
No 19
>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=98.76 E-value=6.7e-09 Score=110.14 Aligned_cols=65 Identities=32% Similarity=0.589 Sum_probs=60.7
Q ss_pred cHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 211 dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
..+.+++.+| +|||||++.|+.|+++|||+++|.+|+.++|..|+|||+++|++|+++|+.++..
T Consensus 492 ~~l~r~L~aL-gIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~~~ 556 (652)
T TIGR00575 492 KPLARLLFAL-GIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNNR 556 (652)
T ss_pred CcHHHHHhhc-cCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhhHH
Confidence 3457889999 8999999999999999999999999999999999999999999999999998753
No 20
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=98.73 E-value=2.2e-08 Score=91.38 Aligned_cols=83 Identities=20% Similarity=0.293 Sum_probs=67.7
Q ss_pred eeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCC---HHHHHcCCHH
Q 017612 177 CALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGS---LSHIMDASME 250 (368)
Q Consensus 177 cILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGS---Lk~I~~AS~E 250 (368)
+.||+- .||+.++ ..|+..+ ...+...|..|+|||++.|..||++||. .+.|.+++.+
T Consensus 45 ~~l~~~~~~rd~~~~l-~gF~~~~---------------ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~ 108 (192)
T PRK00116 45 VKLYTHLVVREDAILL-YGFLTKE---------------ERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVK 108 (192)
T ss_pred EEEEEEEEEechhHHH-cCcCCHH---------------HHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHH
Confidence 445554 8888887 5554322 1123456778999999999999999999 9999999999
Q ss_pred hhhcCCCCCHHHHHHHHHHhccccc
Q 017612 251 DLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 251 ELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+|..|||||+++|++|+..|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 9999999999999999999987764
No 21
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=98.68 E-value=2.8e-08 Score=94.50 Aligned_cols=53 Identities=23% Similarity=0.361 Sum_probs=51.6
Q ss_pred hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|..|+|||+.++..|+++ |+|+++|..|+.++|..|+|||.++|++|++.|+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 5789999999999999999 9999999999999999999999999999999997
No 22
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=98.66 E-value=1.8e-08 Score=107.15 Aligned_cols=63 Identities=32% Similarity=0.442 Sum_probs=59.4
Q ss_pred HHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 212 y~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
.+.+++.+| +|||||++.|+.|+++|+|+++|.+|+.+||..|+|||+++|+.|+++|+.+..
T Consensus 506 ~l~R~l~al-gi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~ 568 (665)
T PRK07956 506 SLARFLYAL-GIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEEN 568 (665)
T ss_pred CHHHhhHhh-hccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhhH
Confidence 457899999 899999999999999999999999999999999999999999999999998763
No 23
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=98.65 E-value=2.2e-08 Score=106.42 Aligned_cols=85 Identities=32% Similarity=0.493 Sum_probs=70.0
Q ss_pred HHHHHHhhcCCcch----hcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHH
Q 017612 190 LETIKVYENKPADL----IQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKR 265 (368)
Q Consensus 190 IEt~K~~E~K~~d~----Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~r 265 (368)
|..+..+..+.... |...+ +..+++++.+| +||+||.+.|+.|..+|||+++|+.|+.++|..|+|||++.|++
T Consensus 481 l~~l~~~~~ks~~nLl~aIe~sK-~~~l~r~l~aL-GIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~s 558 (667)
T COG0272 481 LLSLEGFGEKSAENLLNAIEKSK-KQPLARFLYAL-GIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARS 558 (667)
T ss_pred HhhccchhhhHHHHHHHHHHHhc-cCCHHHHHHHc-CCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHH
Confidence 33444444455433 33322 34579999999 99999999999999999999999999999999999999999999
Q ss_pred HHHHhcccccc
Q 017612 266 LYDTFHEPFKR 276 (368)
Q Consensus 266 I~e~F~ePF~~ 276 (368)
|.++|+.+.+.
T Consensus 559 i~~ff~~~~~~ 569 (667)
T COG0272 559 IIEFFANEENR 569 (667)
T ss_pred HHHHHcCHHHH
Confidence 99999988764
No 24
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=98.63 E-value=3e-08 Score=105.97 Aligned_cols=64 Identities=25% Similarity=0.353 Sum_probs=60.2
Q ss_pred ccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 210 TDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 210 ~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
...+.+++.+| +|||||++.|+.|+.+|||+++|.+|+.++|..|+|||++.|+.|+++|+.+.
T Consensus 521 ~~~l~r~l~AL-gIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 521 EPPLADFLVAL-GIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFFDSER 584 (689)
T ss_pred cCCHHHHHHHc-CCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhH
Confidence 34578999999 89999999999999999999999999999999999999999999999998875
No 25
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=98.62 E-value=8.1e-08 Score=101.60 Aligned_cols=87 Identities=25% Similarity=0.375 Sum_probs=72.2
Q ss_pred eEeccceeeeeec---hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 170 YLVGQNSCALYLS---LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 170 Y~Ig~ttcILFLS---~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
+.+..+..+|+|- .||++||-.+|++.. +. ...+.+.|.+|+|||++.+..||++|||+++|.+
T Consensus 531 ~~L~~~~~~l~ll~~iRDEaHrfAi~yhr~~---------r~----k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 531 FNLPKTSPALKLLQQLRDEAHRFAITYHRKL---------RS----KRTLQTELTDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred eecCCCCcceEEEEEEehHHHHHHHHhChhh---------HH----HHHhhhhhhcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 4454555555443 999999999987753 11 2335678899999999999999999999999999
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
|+.++|..| ||++.|++|+++|+
T Consensus 598 As~eeL~~v--ig~k~A~~I~~~~~ 620 (621)
T PRK14671 598 ASLEELAAV--AGPKTAETIYRYYH 620 (621)
T ss_pred CCHHHHHHH--hCHHHHHHHHHHhC
Confidence 999999999 99999999999986
No 26
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=98.37 E-value=3.1e-07 Score=98.08 Aligned_cols=64 Identities=17% Similarity=0.398 Sum_probs=59.2
Q ss_pred ccHHHHHHHhhccCCCCCHHHHHHHH-HhcCCHHHHHc------CCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 210 TDYLSRLTHALTSVRSVNKTDVVTLG-STFGSLSHIMD------ASMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 210 ~dy~srL~saLTsIpgVnKTDA~~LL-s~FGSLk~I~~------AS~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
...+.+++.+| +||+||.+.|+.|+ .+|++++++++ ++.++|..|+|||++.|.+|+++|+.+.
T Consensus 495 ~~~l~r~l~AL-GI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~~~ 565 (669)
T PRK14350 495 KRPFSKLLLSM-GIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKI 565 (669)
T ss_pred CCCHHHHHHHc-CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcCHH
Confidence 34578999999 79999999999999 99999999987 6899999999999999999999998875
No 27
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=98.23 E-value=6.9e-07 Score=93.92 Aligned_cols=62 Identities=21% Similarity=0.268 Sum_probs=56.3
Q ss_pred ccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 210 TDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 210 ~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
...+++++.+| +||+||++.|+. +|+++++|++|+.|+|..|+|||+++|+.|+++|+.+..
T Consensus 484 ~~~l~r~l~aL-GI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~~~a~si~~~f~~~~~ 545 (562)
T PRK08097 484 QQPFSRWLKAL-GIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPEV 545 (562)
T ss_pred CCCHHHHHHHc-CCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchHHHHHHHHHHHcCHHH
Confidence 34578999999 899999987775 999999999999999999999999999999999987653
No 28
>PRK00254 ski2-like helicase; Provisional
Probab=98.02 E-value=7.3e-06 Score=87.06 Aligned_cols=55 Identities=20% Similarity=0.389 Sum_probs=52.2
Q ss_pred hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
.|..|||||+..+++|+++ |+|+++|+.|+.+||..|+|||+++|+.|++.++..
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence 5668999999999999999 999999999999999999999999999999999844
No 29
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=97.92 E-value=8.9e-06 Score=85.74 Aligned_cols=68 Identities=29% Similarity=0.349 Sum_probs=54.1
Q ss_pred Eeccceeeeee-c--hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 171 LVGQNSCALYL-S--LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 171 ~Ig~ttcILFL-S--~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
.+..++.+|+| . .+||+||-.+|++.- +. ...+.+.|..|||||++..+.||+||||+++|..|
T Consensus 504 ~l~~~s~~l~lLq~irDEaHRFAi~~hR~~---------r~----k~~~~S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 504 NIDLNSPALQLLQHIRDEAHRFAISFHRKK---------RL----KASLQSPLLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred ecCCCCHHHHHHHHHHHHHHHHHHHHHHHH---------HH----HHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 34444444433 2 999999999999863 11 34467899999999999999999999999999999
Q ss_pred CHHh
Q 017612 248 SMED 251 (368)
Q Consensus 248 S~EE 251 (368)
|.||
T Consensus 571 s~ee 574 (574)
T TIGR00194 571 SVEE 574 (574)
T ss_pred CccC
Confidence 9875
No 30
>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=97.91 E-value=1.5e-05 Score=53.98 Aligned_cols=30 Identities=33% Similarity=0.626 Sum_probs=26.7
Q ss_pred CHHHHHcCCHHhhhcCCCCCHHHHHHHHHH
Q 017612 240 SLSHIMDASMEDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~ 269 (368)
++..++.++.|||..+||||+++|..|+.+
T Consensus 1 ~~~g~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 1 SLDGLIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 578899999999999999999999999864
No 31
>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=97.84 E-value=2.7e-05 Score=59.89 Aligned_cols=48 Identities=25% Similarity=0.458 Sum_probs=42.9
Q ss_pred hhcc-CCCCCHHHHHHHHHh---cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTS-VRSVNKTDVVTLGST---FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTs-IpgVnKTDA~~LLs~---FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|.. ++|||...|++|+.+ ||.++ +.+||..|+|||++++++|+.++.
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~-----s~~dL~~v~gi~~~~~~~i~~~~~ 68 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFK-----TVEDLKQVPGIGNSLVEKNLAVIT 68 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcC-----CHHHHHcCCCCCHHHHHHHHhhcc
Confidence 5556 999999999999999 88776 889999999999999999998763
No 32
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=97.80 E-value=2.1e-05 Score=77.78 Aligned_cols=55 Identities=29% Similarity=0.445 Sum_probs=52.3
Q ss_pred HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.-.|..||.+-+..+.+|...||++.+|..||.|||..|.|||+.+|+.|++.+.
T Consensus 292 YR~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~ 346 (349)
T COG1623 292 YRLLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLS 346 (349)
T ss_pred hHHHhcCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence 4478899999999999999999999999999999999999999999999999875
No 33
>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=97.76 E-value=2.6e-05 Score=66.88 Aligned_cols=53 Identities=19% Similarity=0.270 Sum_probs=45.3
Q ss_pred HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
...|..|||||...|.+|+.+|.. +..-+|.+||..|+|||++++++|+++|.
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f~s~eeL~~V~GIg~k~~~~i~~~l~ 119 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEYREE--NGAFKSVDDLTKVSGIGEKSLEKLKDYAT 119 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHh--cCCcCCHHHHHcCCCCCHHHHHHHHhceE
Confidence 456778999999999999999954 22347899999999999999999998863
No 34
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=97.72 E-value=0.0001 Score=80.71 Aligned_cols=94 Identities=26% Similarity=0.328 Sum_probs=78.7
Q ss_pred hhhHHHHHHHHHHhhcCCc--chhcc-c------ccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhh
Q 017612 183 LEECGRYLETIKVYENKPA--DLIQG-Q------MDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLA 253 (368)
Q Consensus 183 ~EEAArYIEt~K~~E~K~~--d~Ire-k------~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa 253 (368)
+..+|.+++.+|.-+..+. ..|.- . ....|.+.....|-.+|||...+..+|+.+|+|++++.+.|.++|+
T Consensus 777 p~~Ta~if~eLKl~~~epD~~~Ai~lg~~~~~~~~~~~~n~~~~~fll~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~ 856 (892)
T KOG0442|consen 777 PLATAEIFEELKLSEPEPDPARAISLGTDEEGNSESESYNSSALDFLLSLPGVSYINYRNLRHKFKSLKELANSSQEELS 856 (892)
T ss_pred hhHHHHHHHHHhhcCCCCCcchheeecccccccccccccCchHHHHHhcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHH
Confidence 8999999999999988773 22221 1 1234667778888899999999999999999999999999999999
Q ss_pred cCCCCCHHHHHHHHHHhccccccc
Q 017612 254 RCPGIGERKVKRLYDTFHEPFKRV 277 (368)
Q Consensus 254 ~VPGIG~kKA~rI~e~F~ePF~~~ 277 (368)
..-|. ...|+.||++||..|...
T Consensus 857 el~~~-~~~a~~LYdFi~~~~~~~ 879 (892)
T KOG0442|consen 857 ELLGV-HENAKLLYDFIHTEFADQ 879 (892)
T ss_pred HHhcc-hHHHHHHHHHHHHhhhhh
Confidence 99554 999999999999888643
No 35
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.56 E-value=0.00014 Score=67.16 Aligned_cols=60 Identities=20% Similarity=0.323 Sum_probs=49.1
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHH---HHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLS---HIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk---~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+-..|.+|+|||++.|..+|++|+-=+ .|.+-+.+.|.+|||||+|+|++|.--|...+.
T Consensus 71 lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~Ki~ 133 (194)
T PRK14605 71 LFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDKIA 133 (194)
T ss_pred HHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 345667999999999999999997433 455778899999999999999997766666653
No 36
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.55 E-value=0.00016 Score=67.32 Aligned_cols=60 Identities=18% Similarity=0.325 Sum_probs=50.9
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCH---HHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSL---SHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSL---k~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+-..|.+|.|||++.|..+|.+|+.- ..|.+-+...|.++||||+|+|++|.--|+..+.
T Consensus 72 lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK~~ 134 (203)
T PRK14602 72 TFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYKLK 134 (203)
T ss_pred HHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHhhc
Confidence 34566799999999999999997554 4566668999999999999999999988888774
No 37
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.43 E-value=0.00022 Score=66.53 Aligned_cols=59 Identities=14% Similarity=0.292 Sum_probs=49.2
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+-..|.+|.|||++.|..+|+.| ++++|+. -+...|.++||||+|.|+||.--|...+.
T Consensus 70 lF~~LisVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdKl~ 132 (196)
T PRK13901 70 VFEELIGVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKLV 132 (196)
T ss_pred HHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence 34456689999999999999987 5555554 47889999999999999999988877764
No 38
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.42 E-value=0.00024 Score=65.56 Aligned_cols=59 Identities=20% Similarity=0.380 Sum_probs=49.6
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+-..|.+|.|||++.|..+|.+| +.++++. -+...|.++||||+|.|++|.--|...+.
T Consensus 71 lF~~Li~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK~~ 133 (188)
T PRK14606 71 LFLSLTKVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDEFE 133 (188)
T ss_pred HHHHHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence 44566799999999999999987 5665554 47889999999999999999988887764
No 39
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.36 E-value=0.0003 Score=65.20 Aligned_cols=58 Identities=24% Similarity=0.324 Sum_probs=49.2
Q ss_pred HHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
-..|.+|.|||++.|..+|+.| +.++|+.| +...|.++||||+|.|+||.--|+..+.
T Consensus 72 F~~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~~ 133 (195)
T PRK14604 72 FELLIGVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGKID 133 (195)
T ss_pred HHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhc
Confidence 4456689999999999999985 66666544 7888999999999999999988888774
No 40
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.35 E-value=0.00031 Score=64.70 Aligned_cols=58 Identities=19% Similarity=0.379 Sum_probs=48.9
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
+-..|.++.|||++.|..+|..| +.+++..| +...|.++||||+|.|+||.--|...+
T Consensus 71 lF~~Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 71 MFEMLLKVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred HHHHHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 34566789999999999999996 66666554 778899999999999999998887776
No 41
>PRK00024 hypothetical protein; Reviewed
Probab=97.34 E-value=0.00033 Score=65.90 Aligned_cols=50 Identities=30% Similarity=0.424 Sum_probs=42.9
Q ss_pred cCCCCC-HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 222 SVRSVN-KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 222 sIpgVn-KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
++++-. +.-|..||++||++.+|++|+.+||..|+|||+.||..|..++.
T Consensus 37 g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~E 87 (224)
T PRK00024 37 GTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALE 87 (224)
T ss_pred CCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHHH
Confidence 345544 34788999999999999999999999999999999999977765
No 42
>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=97.33 E-value=0.00041 Score=63.92 Aligned_cols=58 Identities=19% Similarity=0.332 Sum_probs=46.8
Q ss_pred HHhhccCCCCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
-..|.+|+|||++.|..||..|+ ++++.. -+...|..+||||+|+|++|.--|...+.
T Consensus 71 F~~L~~V~GIGpK~Al~iL~~~~-~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~~ 132 (191)
T TIGR00084 71 FKELIKVNGVGPKLALAILSNMS-PEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKLK 132 (191)
T ss_pred HHHHhCCCCCCHHHHHHHHhcCC-HHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhhc
Confidence 34556999999999999999874 555554 45678999999999999999977766653
No 43
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.30 E-value=0.00032 Score=64.65 Aligned_cols=58 Identities=21% Similarity=0.349 Sum_probs=48.3
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+-..|.++.|||++.|..+|++| ++++++.| +..-| ++||||+|.|+||.--|+..+.
T Consensus 71 lF~~LisV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~K~~ 132 (186)
T PRK14600 71 CLRMLVKVSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYKVS 132 (186)
T ss_pred HHHHHhCcCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHHHhh
Confidence 34466699999999999999996 66666544 77889 9999999999999988887774
No 44
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=97.29 E-value=0.00048 Score=65.75 Aligned_cols=52 Identities=27% Similarity=0.372 Sum_probs=45.2
Q ss_pred hccCCCCC-HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 220 LTSVRSVN-KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 220 LTsIpgVn-KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|+++|-. ..-|+.||.+|||+.+++.|+.++|+.++|||..||-.|..++.
T Consensus 35 rtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~E 87 (224)
T COG2003 35 RTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIE 87 (224)
T ss_pred hcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHHHH
Confidence 35677666 45688999999999999999999999999999999999877764
No 45
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=97.27 E-value=0.00044 Score=64.17 Aligned_cols=59 Identities=17% Similarity=0.224 Sum_probs=49.0
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHH----cCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIM----DASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~----~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
+-..|.++.|||++.|..+|+.| +.++++ +-+..-|.++||||+|+|++|.--|...+.
T Consensus 70 lF~~L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~~ 132 (197)
T PRK14603 70 LFELLLGVSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASGVGKKLAERIALELKGKVP 132 (197)
T ss_pred HHHHHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhh
Confidence 34466689999999999999986 555544 558889999999999999999988887764
No 46
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.20 E-value=0.00049 Score=64.78 Aligned_cols=50 Identities=30% Similarity=0.412 Sum_probs=43.1
Q ss_pred cCCCC-C-HHHHHHHHHhc---CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 222 SVRSV-N-KTDVVTLGSTF---GSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 222 sIpgV-n-KTDA~~LLs~F---GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
++++- + ..-|+.||++| |++.+++.|+.+||..|+|||+.||..|..++.
T Consensus 27 g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~E 81 (218)
T TIGR00608 27 GTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81 (218)
T ss_pred CCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHH
Confidence 45555 3 35788999999 999999999999999999999999999977764
No 47
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=97.11 E-value=0.001 Score=62.41 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=49.4
Q ss_pred HhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhhcCCCCCHHHHHHHHHHhccccccc
Q 017612 218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLARCPGIGERKVKRLYDTFHEPFKRV 277 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa~VPGIG~kKA~rI~e~F~ePF~~~ 277 (368)
..|.++.|||++.|..||+.+ ++.+|+.| +..-|.++||||+|.|++|.--+...|...
T Consensus 73 ~~LisVnGIGpK~ALaiLs~~-~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~~~~ 135 (201)
T COG0632 73 RLLISVNGIGPKLALAILSNL-DPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKLAAF 135 (201)
T ss_pred HHHHccCCccHHHHHHHHcCC-CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhhhhh
Confidence 455589999999999999984 56665544 778899999999999999999998888754
No 48
>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=96.95 E-value=0.0015 Score=62.37 Aligned_cols=52 Identities=19% Similarity=0.315 Sum_probs=49.2
Q ss_pred hccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 220 LTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
|..|+|||+..+.+|.+. |.|+++|..++.++|..+.|+++..|+.|++...
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 457899999999999999 9999999999999999999999999999998876
No 49
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=96.62 E-value=0.0032 Score=60.79 Aligned_cols=54 Identities=22% Similarity=0.386 Sum_probs=50.7
Q ss_pred hhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|..+||||+..+..|.+. |.|+++|..++.++|..+.|+++++|+.|++..+.
T Consensus 7 ~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred cHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 4678999999999999998 99999999999999999999999999999988765
No 50
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=95.94 E-value=0.014 Score=52.08 Aligned_cols=50 Identities=20% Similarity=0.281 Sum_probs=36.4
Q ss_pred HHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 217 THALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
...|..+||||++.|++++.+ |-++ +.|||.+|+|||+++.+.|.+....
T Consensus 60 ~~el~~lpGigP~~A~~IV~n-Gpf~-----sveDL~~V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVKN-APYD-----SVEDVLNLPGLSERQKELLEANLDN 109 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHHC-CCCC-----CHHHHHcCCCCCHHHHHHHHHhhcc
Confidence 345667899999999999963 2222 3478888999999887777766543
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=95.47 E-value=0.045 Score=53.59 Aligned_cols=49 Identities=20% Similarity=0.421 Sum_probs=37.3
Q ss_pred hhccCCCCCHHHHHHHHH--hcCCHHHHHcCC------HHhhhcCCCCCHHHHHHHH
Q 017612 219 ALTSVRSVNKTDVVTLGS--TFGSLSHIMDAS------MEDLARCPGIGERKVKRLY 267 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs--~FGSLk~I~~AS------~EELa~VPGIG~kKA~rI~ 267 (368)
.++.|||||+..|..+-+ .=|++..+-..- .-+|.+|+|||+++|++|+
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 447999999998876644 126666555332 3489999999999999999
No 52
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.43 E-value=0.03 Score=50.11 Aligned_cols=48 Identities=23% Similarity=0.435 Sum_probs=38.1
Q ss_pred HhhccCCCCCHHHHHHHHHh---cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 218 HALTSVRSVNKTDVVTLGST---FGSLSHIMDASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~---FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
+-|..+||||+..|..|+.+ +|-+ .+.+||.+|+|||+++.+++...+
T Consensus 97 eeL~~lpgIG~~kA~aIi~yRe~~G~f-----~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 97 EELQALPGIGPKKAQAIIDYREENGPF-----KSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHcCCC-----CcHHHHHhccCCCHHHHHHHHhhc
Confidence 34478999999999999874 2211 456899999999999999998875
No 53
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=95.42 E-value=0.015 Score=51.81 Aligned_cols=47 Identities=21% Similarity=0.448 Sum_probs=40.8
Q ss_pred CCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 226 VNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 226 VnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
+|..|++ |. .+|.-=+|=+|+.+||..+||||+++|++|.+ |.||..
T Consensus 39 ~N~~d~k-l~-~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~--nGpf~s 85 (132)
T PRK02515 39 QNVADAK-LG-EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVK--NAPYDS 85 (132)
T ss_pred cChhhHH-HH-hcCCcccCCccCHHHHHHCCCCCHHHHHHHHH--CCCCCC
Confidence 5888855 34 78999999999999999999999999999995 778874
No 54
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=95.23 E-value=0.024 Score=56.92 Aligned_cols=58 Identities=21% Similarity=0.442 Sum_probs=46.4
Q ss_pred HHHHHh--hccCCCCCHHHHHHHHH--hcCCHHHHHc------CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 214 SRLTHA--LTSVRSVNKTDVVTLGS--TFGSLSHIMD------ASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 214 srL~sa--LTsIpgVnKTDA~~LLs--~FGSLk~I~~------AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
+.+.+. +|.|||||+..|..|.. ..|+++-+.. ...++|..+||+|++|..++|+.|.
T Consensus 47 ~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elg 114 (326)
T COG1796 47 EEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELG 114 (326)
T ss_pred HHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHC
Confidence 446666 99999999999988865 4566554443 3567999999999999999999995
No 55
>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=95.22 E-value=0.036 Score=60.17 Aligned_cols=56 Identities=23% Similarity=0.456 Sum_probs=45.0
Q ss_pred HHHhhcc--CCCCCHHHHHHHHHhcCC--HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 216 LTHALTS--VRSVNKTDVVTLGSTFGS--LSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 216 L~saLTs--IpgVnKTDA~~LLs~FGS--Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+...|.+ |+|||++.|++|.++||. ++.| .-..+.|..|+|||+++++.|++.+..
T Consensus 80 i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i-~~~~~~L~~v~gi~~~~~~~i~~~~~~ 139 (720)
T TIGR01448 80 IVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVL-DDDPEKLLEVPGISKANLEKFVSQWSQ 139 (720)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHH-HhCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 4445543 999999999999999994 4444 445889999999999999999887754
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.17 E-value=0.046 Score=59.14 Aligned_cols=51 Identities=18% Similarity=0.288 Sum_probs=47.4
Q ss_pred cCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 222 SVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 222 sIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|+|+|++.+..|.++- .++.+|..+..++|..++|||+++|++|++.+..
T Consensus 449 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~ 501 (665)
T PRK07956 449 DIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEK 501 (665)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHH
Confidence 69999999999999874 5999999999999999999999999999999974
No 57
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=95.16 E-value=0.042 Score=59.25 Aligned_cols=51 Identities=18% Similarity=0.309 Sum_probs=46.9
Q ss_pred cCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 222 SVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 222 sIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|+|+|++.+..|.+.- .++.+|..+..++|..++|||+++|++|++.+..
T Consensus 436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~ 488 (652)
T TIGR00575 436 DIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEK 488 (652)
T ss_pred CCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHH
Confidence 59999999999999864 5999999999999999999999999999999974
No 58
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=95.11 E-value=0.024 Score=43.57 Aligned_cols=51 Identities=20% Similarity=0.277 Sum_probs=33.6
Q ss_pred HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
+-|..+||||...|.+|+++=. ... .=.|.+||..|+|||+.+.++|..++
T Consensus 14 ~eL~~lpgi~~~~A~~Iv~~R~-~~G-~f~s~~dL~~v~gi~~~~~~~l~~~l 64 (65)
T PF12836_consen 14 EELQALPGIGPKQAKAIVEYRE-KNG-PFKSLEDLKEVPGIGPKTYEKLKPYL 64 (65)
T ss_dssp HHHHTSTT--HHHHHHHHHHHH-HH--S-SSGGGGGGSTT--HHHHHHHCCCE
T ss_pred HHHHHcCCCCHHHHHHHHHHHH-hCc-CCCCHHHHhhCCCCCHHHHHHHHhhc
Confidence 4566899999999999997511 000 11356899999999999999987654
No 59
>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=95.04 E-value=0.075 Score=37.83 Aligned_cols=46 Identities=15% Similarity=0.256 Sum_probs=38.9
Q ss_pred CHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 227 NKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 227 nKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
....+..|.. -|.|+++|..++.++|..++||++.+|..|....++
T Consensus 2 ~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 2 DEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred CHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 3455666665 699999999999999999999999999999877653
No 60
>PRK01172 ski2-like helicase; Provisional
Probab=94.99 E-value=0.032 Score=59.09 Aligned_cols=53 Identities=15% Similarity=0.218 Sum_probs=48.9
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|-.|||||+..|++|.+ -|.|+.+|+.++.++|..|.|+|++.|+.|.+.++
T Consensus 613 ~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~ 666 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred hhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence 455899999999999998 69999999999999999999999999999998754
No 61
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=94.84 E-value=0.052 Score=53.82 Aligned_cols=52 Identities=12% Similarity=0.258 Sum_probs=39.8
Q ss_pred hhccCCCCCHHHHHHHHH--hcCCHHHH---HcCC----HHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS--TFGSLSHI---MDAS----MEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs--~FGSLk~I---~~AS----~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|+.|||||+.-|..+-+ .=|++..+ .... .-+|.+|+|||+++|++|++ +.
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~-lG 109 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR-KG 109 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH-hC
Confidence 467999999998877653 33887633 3332 45899999999999999998 64
No 62
>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=94.28 E-value=0.042 Score=43.58 Aligned_cols=30 Identities=17% Similarity=0.368 Sum_probs=27.1
Q ss_pred hccCCCCCHHHHHHHHHhcCCHHHHHcCCH
Q 017612 220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASM 249 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS~ 249 (368)
+.+|||||++.|..|+..||++++|+.+-.
T Consensus 24 i~gv~giG~k~A~~ll~~~~~~~~~~~~~~ 53 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYGSLENLLENLD 53 (75)
T ss_pred CCCCCcccHHHHHHHHHHhCCHHHHHHHHH
Confidence 568999999999999999999999997643
No 63
>PRK08609 hypothetical protein; Provisional
Probab=94.06 E-value=0.083 Score=55.98 Aligned_cols=52 Identities=21% Similarity=0.468 Sum_probs=30.3
Q ss_pred hhccCCCCCHHHHHHHHH--hcCCHHHHHcC------CHHhhhcCCCCCHHHHHHHHHHh
Q 017612 219 ALTSVRSVNKTDVVTLGS--TFGSLSHIMDA------SMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs--~FGSLk~I~~A------S~EELa~VPGIG~kKA~rI~e~F 270 (368)
.|+.|||||+.-|..+-+ .=|++..+-.. ..-+|.+|||||+++|++||+-+
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~l 108 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKEL 108 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHh
Confidence 466777777776654433 12444333321 24467777777777777777654
No 64
>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=93.98 E-value=0.056 Score=46.52 Aligned_cols=31 Identities=39% Similarity=0.543 Sum_probs=27.8
Q ss_pred HHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 242 SHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 242 k~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
=+|=.|+.++|..+||||+++|++|.+++..
T Consensus 60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 60 VNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 3566899999999999999999999999954
No 65
>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=93.80 E-value=0.1 Score=40.84 Aligned_cols=43 Identities=12% Similarity=0.254 Sum_probs=34.3
Q ss_pred HHHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 229 TDVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 229 TDA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
..+.+.|. .+.|+.+|+..+.++|..++|||++-+..|.+.++
T Consensus 21 ~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 21 VRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence 44555555 46699999999999999999999999999999875
No 66
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=93.61 E-value=0.15 Score=55.63 Aligned_cols=60 Identities=22% Similarity=0.321 Sum_probs=50.4
Q ss_pred HHHHHHhhc----cCCCCCHHHHHHHHHhc--CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 213 LSRLTHALT----SVRSVNKTDVVTLGSTF--GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 213 ~srL~saLT----sIpgVnKTDA~~LLs~F--GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
..++.++.+ .|+|+|++.+..|.+.- .++.+|..+..++|..++|||+++|++|++.+..
T Consensus 453 ~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~ 518 (689)
T PRK14351 453 ERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEA 518 (689)
T ss_pred HHHHHHHhcccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHH
Confidence 344444442 69999999999999874 5999999999999999999999999999999863
No 67
>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=93.47 E-value=0.099 Score=49.41 Aligned_cols=30 Identities=20% Similarity=0.384 Sum_probs=27.1
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcCC
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDAS 248 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS 248 (368)
-+.+|||||++.|..||++|||+++|+.+-
T Consensus 184 nipGv~GiG~ktA~~Ll~~~gsle~i~~~~ 213 (240)
T cd00008 184 NIPGVPGIGEKTAAKLLKEYGSLEGILENL 213 (240)
T ss_pred CCCCCCccCHHHHHHHHHHhCCHHHHHHhH
Confidence 567899999999999999999999999653
No 68
>PRK02362 ski2-like helicase; Provisional
Probab=93.36 E-value=0.13 Score=55.54 Aligned_cols=51 Identities=16% Similarity=0.212 Sum_probs=47.2
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|..|||||+..|++|.+ -|.|+.+|+.++.++|..+ ||++.|++|++.++
T Consensus 653 ~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~ 704 (737)
T PRK02362 653 DLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQAG 704 (737)
T ss_pred HHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence 455899999999999987 4889999999999999999 99999999999987
No 69
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=93.33 E-value=0.07 Score=34.48 Aligned_cols=21 Identities=29% Similarity=0.782 Sum_probs=18.0
Q ss_pred HhhhcCCCCCHHHHHHHHHHh
Q 017612 250 EDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F 270 (368)
++|..|+|||+++|++|.+..
T Consensus 1 ~~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 1 EELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred ChhhhCCCCCHHHHHHHHHhc
Confidence 368899999999999998754
No 70
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=93.23 E-value=0.056 Score=48.36 Aligned_cols=37 Identities=41% Similarity=0.593 Sum_probs=29.7
Q ss_pred CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc--ccc
Q 017612 239 GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE--PFK 275 (368)
Q Consensus 239 GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e--PF~ 275 (368)
...=+|=.||.+||..+||||+++|++|.++-.+ +|.
T Consensus 86 ~~~vNiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~ 124 (149)
T COG1555 86 EKKVNINTASAEELQALPGIGPKKAQAIIDYREENGPFK 124 (149)
T ss_pred cccccccccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCC
Confidence 3344566899999999999999999999887643 565
No 71
>PRK09482 flap endonuclease-like protein; Provisional
Probab=93.18 E-value=0.11 Score=50.36 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=26.4
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
-+.+|||||++.|..||+.|||+++|+..
T Consensus 183 nIpGVpGIG~KtA~~LL~~~gsle~i~~~ 211 (256)
T PRK09482 183 KIPGVAGIGPKSAAELLNQFRSLENIYES 211 (256)
T ss_pred CCCCCCCcChHHHHHHHHHhCCHHHHHHh
Confidence 45689999999999999999999999954
No 72
>PRK08609 hypothetical protein; Provisional
Probab=92.84 E-value=0.12 Score=54.79 Aligned_cols=53 Identities=9% Similarity=0.231 Sum_probs=45.5
Q ss_pred hhccCCCCCHHHHHHHHH--hcCCHHHHHcCCHH-hhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS--TFGSLSHIMDASME-DLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs--~FGSLk~I~~AS~E-ELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|+.|+|||++.|.+|-. .+.|+++|..|-.+ .|..++|||++.++.|.+.+.
T Consensus 89 ~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~ 144 (570)
T PRK08609 89 PLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVK 144 (570)
T ss_pred HHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHH
Confidence 455899999999999997 56799999988754 599999999999999977764
No 73
>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=92.72 E-value=0.21 Score=49.30 Aligned_cols=50 Identities=18% Similarity=0.355 Sum_probs=46.0
Q ss_pred CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
.|||..++.+|-+. |.|+++|..++..||..+.||+..+|++|.+....-
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI 57 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence 47999999999985 999999999999999999999999999999877653
No 74
>smart00475 53EXOc 5'-3' exonuclease.
Probab=92.67 E-value=0.13 Score=49.59 Aligned_cols=29 Identities=24% Similarity=0.472 Sum_probs=26.4
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
-+.+|||||++.|..||.+|||+++|+.+
T Consensus 187 nipGV~GIG~KtA~~Ll~~ygsle~i~~~ 215 (259)
T smart00475 187 NIPGVPGIGEKTAAKLLKEFGSLENILEN 215 (259)
T ss_pred CCCCCCCCCHHHHHHHHHHhCCHHHHHHH
Confidence 46789999999999999999999999854
No 75
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=92.49 E-value=0.12 Score=39.66 Aligned_cols=31 Identities=39% Similarity=0.620 Sum_probs=22.2
Q ss_pred HcCCHHhhhcCCCCCHHHHHHHHHHhc--cccc
Q 017612 245 MDASMEDLARCPGIGERKVKRLYDTFH--EPFK 275 (368)
Q Consensus 245 ~~AS~EELa~VPGIG~kKA~rI~e~F~--ePF~ 275 (368)
=.|+.+||..+||||++.|++|.++=. .+|.
T Consensus 9 N~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~ 41 (65)
T PF12836_consen 9 NTASAEELQALPGIGPKQAKAIVEYREKNGPFK 41 (65)
T ss_dssp TTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-S
T ss_pred ccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCC
Confidence 368999999999999999999987753 3565
No 76
>PRK14976 5'-3' exonuclease; Provisional
Probab=92.45 E-value=0.15 Score=49.69 Aligned_cols=28 Identities=14% Similarity=0.474 Sum_probs=25.7
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
-+.+|||||++.|..||+.|||+++|+.
T Consensus 192 nipGVpGIG~KtA~~LL~~~gsle~i~~ 219 (281)
T PRK14976 192 NIKGVKGIGPKTAIKLLNKYGNIENIYE 219 (281)
T ss_pred CCCCCCcccHHHHHHHHHHcCCHHHHHH
Confidence 4568999999999999999999999984
No 77
>PTZ00035 Rad51 protein; Provisional
Probab=92.43 E-value=0.22 Score=49.58 Aligned_cols=49 Identities=22% Similarity=0.392 Sum_probs=45.4
Q ss_pred CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+|||..++.+|-+. |.|+++|+.++..||..+.||+..+|++|.+....
T Consensus 29 ~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~ 78 (337)
T PTZ00035 29 AGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASK 78 (337)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 78999999999985 99999999999999999999999999999876654
No 78
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=91.98 E-value=0.29 Score=52.43 Aligned_cols=59 Identities=25% Similarity=0.413 Sum_probs=50.6
Q ss_pred HHHHHhhc----cCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 214 SRLTHALT----SVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 214 srL~saLT----sIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.++.++.+ .|.|+|.+.+..|.+. ..++.+|...+.++|..++|||+++|++|++.+..
T Consensus 417 ~~i~hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~ 481 (562)
T PRK08097 417 ARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNL 481 (562)
T ss_pred HHhHhhhcccccCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHH
Confidence 34555432 4999999999999974 58999999999999999999999999999999863
No 79
>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=91.79 E-value=0.0099 Score=50.30 Aligned_cols=28 Identities=21% Similarity=0.414 Sum_probs=23.3
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
-+-+|+|||.+.|..||++||||++|+.
T Consensus 19 NIPGV~GIG~KtA~~LL~~ygsle~i~~ 46 (101)
T PF01367_consen 19 NIPGVPGIGPKTAAKLLQEYGSLENILA 46 (101)
T ss_dssp TB---TTSTCHCCCCCHHHHTSCHCCCC
T ss_pred CCCCCCCCCHHHHHHHHHHcCCHHHHHH
Confidence 3568999999999999999999999996
No 80
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=91.53 E-value=0.32 Score=48.90 Aligned_cols=48 Identities=21% Similarity=0.344 Sum_probs=44.2
Q ss_pred CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|||..++.+|.+. |.|+++|+.++..||..+.||++.+|.+|.+...
T Consensus 37 ~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~ 85 (344)
T PLN03187 37 QGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAE 85 (344)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 58999999999985 9999999999999999999999999999876544
No 81
>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=90.81 E-value=0.22 Score=40.39 Aligned_cols=43 Identities=23% Similarity=0.275 Sum_probs=37.2
Q ss_pred HHHHHHHhcC--CHHHHHcCCHHhhhcC---CCCCHHHHHHHHHHhcc
Q 017612 230 DVVTLGSTFG--SLSHIMDASMEDLARC---PGIGERKVKRLYDTFHE 272 (368)
Q Consensus 230 DA~~LLs~FG--SLk~I~~AS~EELa~V---PGIG~kKA~rI~e~F~e 272 (368)
--.+|.++|| +.+.|..++.+||..+ -|++..||+.|.++.+.
T Consensus 17 ~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~ 64 (108)
T PF00730_consen 17 IYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARA 64 (108)
T ss_dssp HHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHH
Confidence 3467888887 9999999999999877 89999999999988754
No 82
>PRK07758 hypothetical protein; Provisional
Probab=89.94 E-value=0.62 Score=39.70 Aligned_cols=49 Identities=12% Similarity=0.241 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHH-HhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 224 RSVNKTDVVTLG-STFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 224 pgVnKTDA~~LL-s~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
++++..-...|. ..+.+|.+|+.-+.+||.++.|||++-.+.|.+.|.+
T Consensus 40 ~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 40 SLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred ccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence 455555555553 3689999999999999999999999999999999865
No 83
>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=89.11 E-value=0.71 Score=42.98 Aligned_cols=49 Identities=14% Similarity=0.262 Sum_probs=36.6
Q ss_pred HHHHHHhcC-CHHHHHcC----C---HHhhhcCCCCCHHHHHHHHHHhcccccccCC
Q 017612 231 VVTLGSTFG-SLSHIMDA----S---MEDLARCPGIGERKVKRLYDTFHEPFKRVVS 279 (368)
Q Consensus 231 A~~LLs~FG-SLk~I~~A----S---~EELa~VPGIG~kKA~rI~e~F~ePF~~~~~ 279 (368)
++.|+++|+ .+..|... + .++|..+||||++.|.-+..+|...|.-.+.
T Consensus 88 a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~~~~~~ 144 (177)
T TIGR03252 88 AQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQLGVTPE 144 (177)
T ss_pred HHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHhCCCCc
Confidence 344455555 56777651 2 3789999999999999999999999975444
No 84
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.73 E-value=0.54 Score=52.68 Aligned_cols=29 Identities=24% Similarity=0.480 Sum_probs=26.1
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
-+.+|||||++.|..||.+|||+++|+..
T Consensus 186 nIpGVpGIG~KtA~kLL~~ygsle~i~~~ 214 (887)
T TIGR00593 186 NIPGVKGIGEKTAAKLLQEFGSLENIYEN 214 (887)
T ss_pred CCCCCCCcCHHHHHHHHHHcCCHHHHHHH
Confidence 45679999999999999999999999853
No 85
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.41 E-value=0.68 Score=50.55 Aligned_cols=51 Identities=10% Similarity=0.218 Sum_probs=46.2
Q ss_pred cCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 222 SVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 222 sIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|.|+|......|+++ ..++.+|+..+.++|..++|||++.|++|++.+..
T Consensus 440 dI~GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie~ 492 (669)
T PRK14350 440 NIVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSIEA 492 (669)
T ss_pred cccCcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHHHH
Confidence 5999999999999964 47888999999999999999999999999999863
No 86
>PRK03980 flap endonuclease-1; Provisional
Probab=88.15 E-value=0.52 Score=46.34 Aligned_cols=27 Identities=11% Similarity=0.357 Sum_probs=25.2
Q ss_pred hccCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 220 LTSVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
..+|+|||.+.|..|++.||||++|+.
T Consensus 191 ~~GI~GIG~ktA~kLi~~~~sle~i~~ 217 (292)
T PRK03980 191 NPGIKGIGPKTALKLIKKHGDLEKVLE 217 (292)
T ss_pred CCCCCCccHHHHHHHHHHCCCHHHHHH
Confidence 348999999999999999999999997
No 87
>PRK10736 hypothetical protein; Provisional
Probab=88.06 E-value=0.71 Score=47.26 Aligned_cols=47 Identities=19% Similarity=0.220 Sum_probs=40.7
Q ss_pred HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
-.|..++|||.....+|+.+||+.+ .++.++|..+ |++++.+..+.+
T Consensus 8 l~L~~~~giG~~~~~~L~~~~~~~~---~~~~~~l~~~-g~~~~~~~~~~~ 54 (374)
T PRK10736 8 LRLMSVSSLYGDKMVRIAHRLLAQS---QIDAVVLQAT-GLTLRQAQQFLQ 54 (374)
T ss_pred HHHHhCCCCCHHHHHHHHHHhcChh---hCCHHHHHHc-CCCHHHHHHHhc
Confidence 3778899999999999999999999 4788999887 999988877643
No 88
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=87.83 E-value=0.92 Score=45.56 Aligned_cols=48 Identities=21% Similarity=0.360 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 224 RSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 224 pgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.||+..|+.+|-++ |.|+++|+.++..+|..+-||...+|+++.+...
T Consensus 34 ~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~ 82 (342)
T PLN03186 34 SGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAAS 82 (342)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 58999999999885 9999999999999999999999999987776553
No 89
>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=87.61 E-value=0.46 Score=36.48 Aligned_cols=29 Identities=28% Similarity=0.424 Sum_probs=25.6
Q ss_pred HHHcCCHHhhhc-CCCCCHHHHHHHHHHhc
Q 017612 243 HIMDASMEDLAR-CPGIGERKVKRLYDTFH 271 (368)
Q Consensus 243 ~I~~AS~EELa~-VPGIG~kKA~rI~e~F~ 271 (368)
+|=.|+.++|.. +||||++.|++|.+...
T Consensus 9 nvNta~~~~L~~~ipgig~~~a~~Il~~R~ 38 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGLKKAEAIVSYRE 38 (69)
T ss_pred ECcCCCHHHHHhHCCCCCHHHHHHHHHHHH
Confidence 455689999999 99999999999999974
No 90
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=87.59 E-value=0.61 Score=45.41 Aligned_cols=50 Identities=16% Similarity=0.303 Sum_probs=35.6
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
-+.+|+|||++.|..||..|||++.|...-. .++.+-...+.+....-|.
T Consensus 199 nipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~-------~~~~~~~~~l~~~~~~afl 248 (310)
T COG0258 199 NIPGVKGIGPKTALKLLQEYGSLEGLYENLD-------IIKKKTREKLLEDKEKAFL 248 (310)
T ss_pred CCCCCCCcCHHHHHHHHHHhCCHHHHHHhhh-------hhcchhhHHHHHHHHHHhc
Confidence 3557999999999999999999999985432 3444555555555544444
No 91
>PRK10702 endonuclease III; Provisional
Probab=87.01 E-value=0.63 Score=43.69 Aligned_cols=37 Identities=16% Similarity=0.242 Sum_probs=26.3
Q ss_pred HHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 231 VVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 231 A~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
|+.+++.||. -.-.+.++|..+||||++.|.-|.-+.
T Consensus 93 a~~i~~~~~~---~~p~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 93 CRILLEQHNG---EVPEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred HHHHHHHcCC---CCCchHHHHhcCCcccHHHHHHHHHHH
Confidence 3344455543 234578999999999999999987543
No 92
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=86.51 E-value=0.7 Score=35.74 Aligned_cols=20 Identities=35% Similarity=0.722 Sum_probs=18.4
Q ss_pred hhhcCCCCCHHHHHHHHHHh
Q 017612 251 DLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 251 ELa~VPGIG~kKA~rI~e~F 270 (368)
+|..+||||++.|.+|.+++
T Consensus 48 ~~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHH
Confidence 49999999999999999886
No 93
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=86.51 E-value=0.95 Score=43.09 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=33.9
Q ss_pred HHHHHHHhcCCHHHHH-cCCHHhhhcCCCCCHHHHHHHHH-Hhccccc
Q 017612 230 DVVTLGSTFGSLSHIM-DASMEDLARCPGIGERKVKRLYD-TFHEPFK 275 (368)
Q Consensus 230 DA~~LLs~FGSLk~I~-~AS~EELa~VPGIG~kKA~rI~e-~F~ePF~ 275 (368)
-|..+++.||++..+. ....++|..+||||++.|..|.- +|++|..
T Consensus 100 la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~f 147 (218)
T PRK13913 100 LSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVCAKEVM 147 (218)
T ss_pred HHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHcCCCcc
Confidence 3445667788876654 34678999999999999999876 5555543
No 94
>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=86.31 E-value=0.53 Score=35.33 Aligned_cols=22 Identities=36% Similarity=0.898 Sum_probs=19.9
Q ss_pred HhhhcCCCCCHHHHHHHHHH-hc
Q 017612 250 EDLARCPGIGERKVKRLYDT-FH 271 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~-F~ 271 (368)
++|..|+|||++.|++|++. |.
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~G~~ 27 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEAGIK 27 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHTTCS
T ss_pred HhhccCCCCCHHHHHHHHhcCCC
Confidence 68999999999999999998 54
No 95
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=86.18 E-value=0.88 Score=43.39 Aligned_cols=45 Identities=22% Similarity=0.327 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHH-hcccccc
Q 017612 229 TDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDT-FHEPFKR 276 (368)
Q Consensus 229 TDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~-F~ePF~~ 276 (368)
.-++.|+++||+ -+-.+.+||..+||+|.|.|.-+... |..|-..
T Consensus 91 ~~~~~l~e~~~g---~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~ 136 (211)
T COG0177 91 ELARILLEKFGG---EVPDTREELLSLPGVGRKTANVVLSFAFGIPAIA 136 (211)
T ss_pred HHHHHHHHHcCC---CCCchHHHHHhCCCcchHHHHHHHHhhcCCCccc
Confidence 344556777777 34556789999999999999998876 6666443
No 96
>PRK05755 DNA polymerase I; Provisional
Probab=84.81 E-value=0.76 Score=51.00 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=26.3
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
-+-+|||||++.|..||++|||+++|+.+
T Consensus 188 nipGv~GiG~ktA~~Ll~~~gsle~i~~~ 216 (880)
T PRK05755 188 NIPGVPGIGEKTAAKLLQEYGSLEGLYEN 216 (880)
T ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHh
Confidence 46789999999999999999999999944
No 97
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=84.57 E-value=1.2 Score=41.09 Aligned_cols=42 Identities=14% Similarity=0.185 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 228 KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 228 KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+.++.+| =.|.+.++--. ...|..|+|||+++|.+|.+.|..
T Consensus 54 rd~~~~l-~gF~~~~ek~~--f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 54 REDAILL-YGFLTKEEREL--FRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred echhHHH-cCcCCHHHHHH--HHHHhcCCCCCHHHHHHHHHhCCH
Confidence 3455555 44555554333 678999999999999999999974
No 98
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=84.42 E-value=0.93 Score=44.07 Aligned_cols=52 Identities=15% Similarity=0.321 Sum_probs=34.2
Q ss_pred hccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 220 LTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
+.+|+|||.+.|..|++.||+++.++..=...+..+| ..-.-..++++|..|
T Consensus 225 ~~gv~giG~k~A~~li~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~f~~p 276 (316)
T cd00128 225 TEGIPGIGPVTALKLIKKYGDIEKDIERLKKKLYRSP--EDFPLKEAREFFLNP 276 (316)
T ss_pred CCCCCCccHHHHHHHHHHcCChHHHHHHHHHhCccCC--CcCChHHHHHHHcCC
Confidence 4589999999999999999998777644333333433 112234556666533
No 99
>PRK14973 DNA topoisomerase I; Provisional
Probab=83.92 E-value=1.5 Score=49.55 Aligned_cols=52 Identities=25% Similarity=0.264 Sum_probs=47.1
Q ss_pred hccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 220 LTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
|..|+|||.+.+..|-. -.-+++.+.+|+.++|+.+.|||.++++.|+..+.
T Consensus 879 l~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~ 931 (936)
T PRK14973 879 LLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK 931 (936)
T ss_pred hhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence 77999999999977755 68899999999999999999999999999998774
No 100
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=83.88 E-value=0.69 Score=32.53 Aligned_cols=28 Identities=14% Similarity=0.360 Sum_probs=15.0
Q ss_pred HHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 241 LSHIMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 241 Lk~I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
+..|+.-..+.+..|||||+++|.+|.+
T Consensus 7 ~~~L~GD~~dni~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 7 YAILVGDYSDNIPGVKGIGPKTALKLLR 34 (36)
T ss_pred HHHHhCcCCCCCCCCCcccHHHHHHHHH
Confidence 3444443333455666666666666554
No 101
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=83.68 E-value=1.8 Score=41.21 Aligned_cols=54 Identities=15% Similarity=0.228 Sum_probs=48.8
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|-++|+||+..++.|-. ...++.+|+..+.+++..+-|+++..++.|+++++.
T Consensus 152 ~L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~ 206 (312)
T smart00611 152 PLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSR 206 (312)
T ss_pred ccccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 566899999999999987 468999999999999999999999999999998864
No 102
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=83.22 E-value=1 Score=44.86 Aligned_cols=27 Identities=19% Similarity=0.395 Sum_probs=25.6
Q ss_pred ccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 221 TSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 221 TsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
.+|+|||.+.|..|++.|||+++|+..
T Consensus 239 ~Gv~GIG~ktA~kli~~~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHh
Confidence 699999999999999999999999875
No 103
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=83.22 E-value=1.9 Score=42.55 Aligned_cols=47 Identities=17% Similarity=0.291 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 225 SVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 225 gVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
||+..++..|-+ .|.|+++|+.++..||.++-||...+++.+...+.
T Consensus 8 ~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~ 55 (316)
T TIGR02239 8 GITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAA 55 (316)
T ss_pred CCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 699999999987 79999999999999999999999999999887554
No 104
>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=83.07 E-value=2.4 Score=35.96 Aligned_cols=38 Identities=18% Similarity=0.171 Sum_probs=33.2
Q ss_pred HHHHhhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhh
Q 017612 215 RLTHALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDL 252 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EEL 252 (368)
.....|+.||+||+..|+-|.. =+.++++|...+.++|
T Consensus 9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~L 47 (93)
T PF11731_consen 9 AGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGRDPEEL 47 (93)
T ss_pred HHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCCCHHHH
Confidence 3567889999999999999987 6889999999998765
No 105
>PTZ00217 flap endonuclease-1; Provisional
Probab=82.70 E-value=1.2 Score=45.70 Aligned_cols=28 Identities=11% Similarity=0.315 Sum_probs=25.5
Q ss_pred hccCCCCCHHHHHHHHHhcCCHHHHHcC
Q 017612 220 LTSVRSVNKTDVVTLGSTFGSLSHIMDA 247 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs~FGSLk~I~~A 247 (368)
+.+|+|||.+.|..|++.||++++|+..
T Consensus 237 ~pgi~GIG~ktA~~Li~~~gsle~il~~ 264 (393)
T PTZ00217 237 CDTIKGIGPKTAYKLIKKYKSIEEILEH 264 (393)
T ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHH
Confidence 4589999999999999999999999853
No 106
>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=82.39 E-value=0.93 Score=35.98 Aligned_cols=36 Identities=19% Similarity=0.481 Sum_probs=28.5
Q ss_pred hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|-.+..++.-+.+-+..|||||+++|.+|..-+..
T Consensus 9 q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~ 44 (75)
T cd00080 9 QFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGS 44 (75)
T ss_pred HHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCC
Confidence 455566667766778899999999999999988753
No 107
>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=80.54 E-value=1.3 Score=35.66 Aligned_cols=38 Identities=29% Similarity=0.434 Sum_probs=19.2
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCC
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGI 258 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGI 258 (368)
.|.+|||||...|..|+..+|.++..-++ .+|...-|+
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~rF~~~--~~l~~~~Gl 40 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDISRFKSA--KQLASYAGL 40 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCchhcccc--hhhhhcccc
Confidence 34555666666666666555555443322 344444443
No 108
>PRK10702 endonuclease III; Provisional
Probab=80.41 E-value=3.6 Score=38.68 Aligned_cols=61 Identities=18% Similarity=0.206 Sum_probs=43.5
Q ss_pred cHHHHHHHhh----ccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcC-C--CCCHHHHHHHHHHhcc
Q 017612 211 DYLSRLTHAL----TSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARC-P--GIGERKVKRLYDTFHE 272 (368)
Q Consensus 211 dy~srL~saL----TsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~V-P--GIG~kKA~rI~e~F~e 272 (368)
++.+.++.++ |+++.|++. ...|...|.+++.|.+|+.+||..+ . |+-..||++|++..+.
T Consensus 28 ~p~e~lvs~iLsq~t~~~~v~~~-~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~ 95 (211)
T PRK10702 28 SPFELLIAVLLSAQATDVSVNKA-TAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRI 95 (211)
T ss_pred ChHHHHHHHHHHhhcCHHHHHHH-HHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4445554433 455555544 4577789999999999999999874 3 5557899998877764
No 109
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=80.04 E-value=2.3 Score=36.48 Aligned_cols=45 Identities=16% Similarity=0.215 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHhcCCHHHHHc----CCHHhhhcCCCCCHHHHHHHHHH
Q 017612 225 SVNKTDVVTLGSTFGSLSHIMD----ASMEDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 225 gVnKTDA~~LLs~FGSLk~I~~----AS~EELa~VPGIG~kKA~rI~e~ 269 (368)
|.....|+.|.+--..+.+-.+ ...++|..++|||++.|..+.-+
T Consensus 43 g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 43 GFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred CChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence 5556666666654433333222 24567777888888887776544
No 110
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=79.98 E-value=2.7 Score=46.20 Aligned_cols=53 Identities=19% Similarity=0.355 Sum_probs=48.8
Q ss_pred hhccCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+| .|.|+|.+-...|.++ +.++.+|+..+.++|..++|+|+++|++|++.++.
T Consensus 447 Am-dI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~aIe~ 501 (667)
T COG0272 447 AL-DIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNAIEK 501 (667)
T ss_pred cc-CCCCcCHHHHHHHHHcCccCCHHHHHhCCHHHHhhccchhhhHHHHHHHHHHH
Confidence 45 5999999999999985 89999999999999999999999999999999964
No 111
>PRK10880 adenine DNA glycosylase; Provisional
Probab=78.65 E-value=2.6 Score=42.78 Aligned_cols=29 Identities=21% Similarity=0.528 Sum_probs=24.1
Q ss_pred cCCHHhhhcCCCCCHHHHHHHHH-Hhcccc
Q 017612 246 DASMEDLARCPGIGERKVKRLYD-TFHEPF 274 (368)
Q Consensus 246 ~AS~EELa~VPGIG~kKA~rI~e-~F~ePF 274 (368)
..+.++|..+||||++.|..|.. +|+.++
T Consensus 105 p~~~~~L~~LpGIG~~TA~aIl~~af~~~~ 134 (350)
T PRK10880 105 PETFEEVAALPGVGRSTAGAILSLSLGKHF 134 (350)
T ss_pred hhhHHHHhcCCCccHHHHHHHHHHHCCCCe
Confidence 35679999999999999999987 566554
No 112
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=78.54 E-value=4.3 Score=41.22 Aligned_cols=57 Identities=14% Similarity=0.239 Sum_probs=45.4
Q ss_pred HHhhccCCCCCHHHHHHHHHhc--CCHHHHHcCCH-HhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 217 THALTSVRSVNKTDVVTLGSTF--GSLSHIMDASM-EDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~F--GSLk~I~~AS~-EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
+..| .+||+|++....|.+.+ .+++.+..|-. ..+..++|+|++.+..|++....-+
T Consensus 93 ~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~ 152 (326)
T COG1796 93 EPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAE 152 (326)
T ss_pred HHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHh
Confidence 4444 89999999999999987 56777766643 4689999999999999998875433
No 113
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=76.99 E-value=2.1 Score=30.05 Aligned_cols=20 Identities=15% Similarity=0.348 Sum_probs=17.7
Q ss_pred hhccCCCCCHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGSTF 238 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~F 238 (368)
-+.+|||||.+.|..||++|
T Consensus 17 ni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 17 NIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CCCCCCcccHHHHHHHHHhC
Confidence 34689999999999999987
No 114
>PRK14973 DNA topoisomerase I; Provisional
Probab=76.51 E-value=6.9 Score=44.53 Aligned_cols=52 Identities=13% Similarity=0.059 Sum_probs=45.9
Q ss_pred hccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 220 LTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 220 LTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
|-.++||...-+++|.++ |.++++++.|+.++|+.++||++-.+.++.....
T Consensus 804 ~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 804 RLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGISPETICRHAKLVC 856 (936)
T ss_pred hhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHH
Confidence 557899999999999985 9999999999999999999999888887755443
No 115
>PRK13910 DNA glycosylase MutY; Provisional
Probab=76.18 E-value=3.2 Score=41.09 Aligned_cols=28 Identities=25% Similarity=0.440 Sum_probs=22.8
Q ss_pred cCCHHhhhcCCCCCHHHHHHHHHH-hccc
Q 017612 246 DASMEDLARCPGIGERKVKRLYDT-FHEP 273 (368)
Q Consensus 246 ~AS~EELa~VPGIG~kKA~rI~e~-F~eP 273 (368)
-.+.++|..+||||++.|..|..+ |+.+
T Consensus 68 P~~~~~L~~LpGIG~kTA~aIl~~af~~~ 96 (289)
T PRK13910 68 PNDYQSLLKLPGIGAYTANAILCFGFREK 96 (289)
T ss_pred ChhHHHHHhCCCCCHHHHHHHHHHHCCCC
Confidence 457899999999999999999763 4443
No 116
>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=74.66 E-value=2.9 Score=31.63 Aligned_cols=19 Identities=16% Similarity=0.415 Sum_probs=15.3
Q ss_pred HhhhcCCCCCHHHHHHHHH
Q 017612 250 EDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e 268 (368)
..+..|-|||+++|+++++
T Consensus 2 ~~f~~I~GVG~~tA~~w~~ 20 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYA 20 (52)
T ss_dssp HHHHTSTT--HHHHHHHHH
T ss_pred cchhhcccccHHHHHHHHH
Confidence 5689999999999999987
No 117
>PHA00439 exonuclease
Probab=73.08 E-value=3.2 Score=41.26 Aligned_cols=78 Identities=19% Similarity=0.272 Sum_probs=50.6
Q ss_pred HHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccccCCCCCCCCCCCCccccCCCCccchhhccccchHHHH
Q 017612 234 LGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIPETPSQKDVERSSVNEVTEVEKDTEDVNK 313 (368)
Q Consensus 234 LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 (368)
....|..++.|+.-+.+.+-.||||| ++|..|.+ +||.-..-. .+=-++.+ ..+...+
T Consensus 172 ~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~---~~~~~~~~~-----------~~~~sg~~-------~~~~~~~ 229 (286)
T PHA00439 172 TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLE---NPYIFEQVE-----------KVLKSGKR-------KGQTVTK 229 (286)
T ss_pred cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHh---Cccccchhh-----------HHhhcccc-------cccchhh
Confidence 36778889999999999999999999 99998765 455432210 00011111 1233457
Q ss_pred hhhccchh--hHHHHHHHHHHH
Q 017612 314 RRKKETES--TVKSALSAAFAK 333 (368)
Q Consensus 314 ~~~~~~~~--~~~~~~~~~~~~ 333 (368)
+||+.|+. ++=-++-++|||
T Consensus 230 ~~k~~~~~~~~~w~~~v~~~~k 251 (286)
T PHA00439 230 WKKRAPEPEETLWDCIVTLGAK 251 (286)
T ss_pred hhccCCCccccHHHHHHHHHHH
Confidence 77776664 766666667765
No 118
>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=72.14 E-value=4.3 Score=39.75 Aligned_cols=24 Identities=29% Similarity=0.499 Sum_probs=20.8
Q ss_pred cCCHHhhhcCCCCCHHHHHHHHHH
Q 017612 246 DASMEDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 246 ~AS~EELa~VPGIG~kKA~rI~e~ 269 (368)
..+.++|..+||||++.|..|.-+
T Consensus 101 p~~~~~L~~LpGIG~~TA~~Il~~ 124 (275)
T TIGR01084 101 PQDFEDLAALPGVGRYTAGAILSF 124 (275)
T ss_pred cHHHHHHHhCCCCCHHHHHHHHHH
Confidence 456899999999999999998764
No 119
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=71.71 E-value=5.5 Score=39.99 Aligned_cols=52 Identities=19% Similarity=0.233 Sum_probs=43.7
Q ss_pred hhccCCCCCHHHHHHHHHhc--CCHHHHHcC--CHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGSTF--GSLSHIMDA--SMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~F--GSLk~I~~A--S~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-|..++|||+..+..||..+ .|+.+|... +.++|... +|.+.++.|++.++.
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~--fG~~~g~~l~~~a~G 238 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEH--FGEKLGEWLYNLLRG 238 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHH--HHHHHHHHHHHHhCC
Confidence 56778999998888887755 588999999 99999987 888889999888754
No 120
>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=71.13 E-value=4.3 Score=27.56 Aligned_cols=19 Identities=11% Similarity=0.130 Sum_probs=15.4
Q ss_pred HhhccCCCCCHHHHHHHHH
Q 017612 218 HALTSVRSVNKTDVVTLGS 236 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs 236 (368)
+-|..+||||+..|..++.
T Consensus 11 eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 11 EELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHTSTT-SHHHHHHHHH
T ss_pred HHHHhCCCcCHHHHHHHHh
Confidence 4566999999999999986
No 121
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=70.42 E-value=5.7 Score=37.71 Aligned_cols=55 Identities=20% Similarity=0.277 Sum_probs=37.2
Q ss_pred HHHHHhhccCC-CCCHHHHHHHHH---hcCCHHHHH------cCCHHhhh-cCCCCCHHHHHHHHH
Q 017612 214 SRLTHALTSVR-SVNKTDVVTLGS---TFGSLSHIM------DASMEDLA-RCPGIGERKVKRLYD 268 (368)
Q Consensus 214 srL~saLTsIp-gVnKTDA~~LLs---~FGSLk~I~------~AS~EELa-~VPGIG~kKA~rI~e 268 (368)
+.+..+|-.+- |.-+..|+.|.. .||.+.++. ....++|. .+||||++.|.-|..
T Consensus 72 eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~ 137 (208)
T PRK01229 72 EELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLR 137 (208)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHH
Confidence 44555553332 355788876654 446677665 23467899 999999999999983
No 122
>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=70.41 E-value=5.3 Score=36.38 Aligned_cols=24 Identities=21% Similarity=0.530 Sum_probs=20.1
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
...++|..+||||++.|.-|.-+.
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHH
Confidence 357899999999999999987443
No 123
>PRK13910 DNA glycosylase MutY; Provisional
Probab=70.39 E-value=5.2 Score=39.59 Aligned_cols=40 Identities=20% Similarity=0.355 Sum_probs=34.2
Q ss_pred HHHHHhcCCHHHHHcCCHHhhhcC-CCCC-HHHHHHHHHHhc
Q 017612 232 VTLGSTFGSLSHIMDASMEDLARC-PGIG-ERKVKRLYDTFH 271 (368)
Q Consensus 232 ~~LLs~FGSLk~I~~AS~EELa~V-PGIG-~kKA~rI~e~F~ 271 (368)
.+++++|.++++|..|+.+||..+ .|+| -.+|++|+++..
T Consensus 16 ~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~ 57 (289)
T PRK13910 16 SPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAE 57 (289)
T ss_pred HHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 688899999999999999998774 7888 567999888765
No 124
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=70.33 E-value=11 Score=36.52 Aligned_cols=81 Identities=17% Similarity=0.145 Sum_probs=53.8
Q ss_pred hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCC--HHHHHHH-------HHhcCCHHHHHcCC-HHhh
Q 017612 183 LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVN--KTDVVTL-------GSTFGSLSHIMDAS-MEDL 252 (368)
Q Consensus 183 ~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVn--KTDA~~L-------Ls~FGSLk~I~~AS-~EEL 252 (368)
.+-+.+-|+.++.........|..- ..+.|.++ |+..| ++.|.+| +.+|.+++.+-.-. .++|
T Consensus 45 WknvekAlenLk~~~~~~l~~I~~~----~~~~L~el---IrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R~~L 117 (215)
T COG2231 45 WKNVEKALENLKNEGILNLKKILKL----DEEELAEL---IRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLREEL 117 (215)
T ss_pred HHHHHHHHHHHHHcccCCHHHHhcC----CHHHHHHH---HhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHHHHH
Confidence 6777777888887654443222221 12333333 33444 5555554 88898888887664 8999
Q ss_pred hcCCCCCHHHHHHHHHHh
Q 017612 253 ARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 253 a~VPGIG~kKA~rI~e~F 270 (368)
..|.|||+-.|..|.=+.
T Consensus 118 L~iKGIG~ETaDsILlYa 135 (215)
T COG2231 118 LSIKGIGKETADSILLYA 135 (215)
T ss_pred HccCCcchhhHHHHHHHH
Confidence 999999999999997654
No 125
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=70.01 E-value=10 Score=32.51 Aligned_cols=42 Identities=24% Similarity=0.223 Sum_probs=32.0
Q ss_pred HHHHHHHhcCCHHHHHcCCHHhhhcC---CCCCHHHHHHHHHHhc
Q 017612 230 DVVTLGSTFGSLSHIMDASMEDLARC---PGIGERKVKRLYDTFH 271 (368)
Q Consensus 230 DA~~LLs~FGSLk~I~~AS~EELa~V---PGIG~kKA~rI~e~F~ 271 (368)
-..+|.++|++.++|..++.+||..+ =|+...||+.|++..+
T Consensus 13 ~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~ 57 (149)
T smart00478 13 ATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELAR 57 (149)
T ss_pred HHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence 34567788999999999999888442 2778889988877664
No 126
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=69.02 E-value=19 Score=35.57 Aligned_cols=135 Identities=16% Similarity=0.233 Sum_probs=77.5
Q ss_pred CCCeEEEcCCccCChhHHhhhc--cceEeeec-ccceEeccceeeeeec-------------hhhHHHHHHHHHHh----
Q 017612 137 SRNAILVSQRQKGNPLLKYIRN--VRWAFADV-VCDYLVGQNSCALYLS-------------LEECGRYLETIKVY---- 196 (368)
Q Consensus 137 ~~~~IlVS~rQrGNPLLk~Irn--VpwefaDI-vpDY~Ig~ttcILFLS-------------~EEAArYIEt~K~~---- 196 (368)
..-.|+|-.|-.-+++..+|+. |..+...+ +-||+++..+||=-=| ++.|.++-..|.+-
T Consensus 26 ~~~~viVD~RE~rs~v~~~L~~~gv~v~~~~LevGDYvvs~~v~VERKs~~Dfv~Si~dgRlfeQ~~rL~~~y~rpvliV 105 (254)
T COG1948 26 FEVVVIVDSRELRSEVPRLLKRLGVKVEVRTLEVGDYVVSDDVIVERKSISDFVSSIIDGRLFEQAKRLKKSYERPVLIV 105 (254)
T ss_pred cceEEEEecchhcccchHHHHhCCCeEEEEecccccEEeecCeeEEeccHHHHHHHHhcchHHHHHHHHHhcCCccEEEE
Confidence 4558999999999999887754 88888886 7999999999885333 66666655443321
Q ss_pred hcCCcchhccc-cc-ccHHHHHHHhh-----ccCCCCCHHHHHHHHHhcCCHHHH-----------Hc-CCH-----Hhh
Q 017612 197 ENKPADLIQGQ-MD-TDYLSRLTHAL-----TSVRSVNKTDVVTLGSTFGSLSHI-----------MD-ASM-----EDL 252 (368)
Q Consensus 197 E~K~~d~Irek-~e-~dy~srL~saL-----TsIpgVnKTDA~~LLs~FGSLk~I-----------~~-AS~-----EEL 252 (368)
|-- ....+.. .. ..+...+...+ .=|..=++.+...|+..-....+. .. -+. .=|
T Consensus 106 egd-~~~~~~~~i~~~av~~al~s~~vdfg~~vi~t~~~~~Ta~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il 184 (254)
T COG1948 106 EGD-DSFSRRPKIHPNAVRGALASLAVDFGLPVIWTRSPEETAELIHELARREQEERKRSVNPHGKKKAKTLKELQLYIL 184 (254)
T ss_pred Ecc-cccccccccCHHHHHHHHHHHHhhcCceEEEeCCHHHHHHHHHHHHHHHHHhccccccccccccccchHHHHHHHH
Confidence 000 0111111 11 22223332221 112223455555444433222220 00 111 237
Q ss_pred hcCCCCCHHHHHHHHHHhcc
Q 017612 253 ARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 253 a~VPGIG~kKA~rI~e~F~e 272 (368)
..+||||.+.|+++++.|..
T Consensus 185 ~s~pgig~~~a~~ll~~fgS 204 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFGS 204 (254)
T ss_pred HcCCCccHHHHHHHHHHhcC
Confidence 89999999999999999954
No 127
>PRK09482 flap endonuclease-like protein; Provisional
Probab=68.09 E-value=3.5 Score=40.19 Aligned_cols=43 Identities=21% Similarity=0.398 Sum_probs=33.8
Q ss_pred HHHHHHHhcC-------CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 230 DVVTLGSTFG-------SLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 230 DA~~LLs~FG-------SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+...+.++|| .+..|+.-+.+-+-.|||||+++|.+|.+-+..
T Consensus 155 ~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gs 204 (256)
T PRK09482 155 DAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRS 204 (256)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCC
Confidence 3444556666 356788888899999999999999999988753
No 128
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=67.17 E-value=5.3 Score=25.67 Aligned_cols=20 Identities=10% Similarity=0.111 Sum_probs=17.0
Q ss_pred hhccCCCCCHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGSTF 238 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~F 238 (368)
.|..|+|||++.|.+|+.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 35689999999999999754
No 129
>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=66.28 E-value=11 Score=34.31 Aligned_cols=40 Identities=18% Similarity=0.243 Sum_probs=33.0
Q ss_pred HHHHHhcCCHHHHHcCCHHhhhcC---CCCCHHHHHHHHHHhc
Q 017612 232 VTLGSTFGSLSHIMDASMEDLARC---PGIGERKVKRLYDTFH 271 (368)
Q Consensus 232 ~~LLs~FGSLk~I~~AS~EELa~V---PGIG~kKA~rI~e~F~ 271 (368)
.+|...|.+++.|..++.+||..+ -|+-..||+.|++..+
T Consensus 49 ~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~ 91 (191)
T TIGR01083 49 KKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCR 91 (191)
T ss_pred HHHHHHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Confidence 457889999999999999998543 3777889999987765
No 130
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=65.85 E-value=12 Score=36.57 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=29.9
Q ss_pred hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|-+.+.|..++.++|..| |++..||+.|++.-+
T Consensus 154 ~FPtpe~La~~~~~eL~~~-Gl~~~Ra~~L~~lA~ 187 (283)
T PRK10308 154 CFPTPERLAAADPQALKAL-GMPLKRAEALIHLAN 187 (283)
T ss_pred CCCCHHHHHcCCHHHHHHC-CCCHHHHHHHHHHHH
Confidence 3557999999999999999 999999999987764
No 131
>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=64.62 E-value=6 Score=26.98 Aligned_cols=18 Identities=28% Similarity=0.532 Sum_probs=13.2
Q ss_pred hhhcCCCCCHHHHHHHHH
Q 017612 251 DLARCPGIGERKVKRLYD 268 (368)
Q Consensus 251 ELa~VPGIG~kKA~rI~e 268 (368)
.+.+++|||++.+++|.+
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 577888888888888753
No 132
>PRK14976 5'-3' exonuclease; Provisional
Probab=63.81 E-value=4.5 Score=39.57 Aligned_cols=41 Identities=15% Similarity=0.374 Sum_probs=30.9
Q ss_pred HHHHHHhcC-------CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 231 VVTLGSTFG-------SLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 231 A~~LLs~FG-------SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
...+.++|| .++.|+.-+.+.+-.|||||+++|.+|.+-+.
T Consensus 165 ~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 165 TNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred HHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcC
Confidence 344555566 45566666788999999999999999987663
No 133
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=62.77 E-value=7.7 Score=44.21 Aligned_cols=80 Identities=15% Similarity=0.268 Sum_probs=56.2
Q ss_pred HHHHHHHhhcCCc-chhcc-cccccHHHHHHHhhccCCCCCHHHHHHHHHhc-CCHHHHHcCCHHhhhcCCCCCHHHHHH
Q 017612 189 YLETIKVYENKPA-DLIQG-QMDTDYLSRLTHALTSVRSVNKTDVVTLGSTF-GSLSHIMDASMEDLARCPGIGERKVKR 265 (368)
Q Consensus 189 YIEt~K~~E~K~~-d~Ire-k~e~dy~srL~saLTsIpgVnKTDA~~LLs~F-GSLk~I~~AS~EELa~VPGIG~kKA~r 265 (368)
+|..|+.+..||. .++.. ..-.+|.+.+ -|+.+||||-..-.+|...| .+.-+|...+.++|..+ +|++.++.
T Consensus 520 LLARlATr~AKP~Gq~~l~a~~veeFis~~--~v~~LPGVG~sm~~kL~s~~i~tCgdLq~~T~~kl~k~--~G~Klgq~ 595 (1016)
T KOG2093|consen 520 LLARLATRVAKPNGQFYLSAEKVEEFISQL--KVDDLPGVGSSMKSKLVSQFIQTCGDLQLITLIKLRKV--FGPKLGQK 595 (1016)
T ss_pred HHHHHHHhhcCCCceeeecHHHHHHHhhhc--ccccCCCccHHHHHHHHHhccchhHHHHHHHHHHHHhh--hcccHHHH
Confidence 5666777777775 22222 2223454444 67889999999999998877 34455666778888888 99999999
Q ss_pred HHHHhcc
Q 017612 266 LYDTFHE 272 (368)
Q Consensus 266 I~e~F~e 272 (368)
||...+.
T Consensus 596 i~~~CrG 602 (1016)
T KOG2093|consen 596 IYRGCRG 602 (1016)
T ss_pred HHHhcCC
Confidence 9887753
No 134
>smart00475 53EXOc 5'-3' exonuclease.
Probab=62.63 E-value=5.4 Score=38.60 Aligned_cols=35 Identities=26% Similarity=0.521 Sum_probs=28.4
Q ss_pred hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.|-.+..|+.-+.+-+-.|||||+++|..|.+-+.
T Consensus 173 q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 173 QIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred HHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhC
Confidence 33456677776778899999999999999998774
No 135
>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=62.62 E-value=5.1 Score=37.98 Aligned_cols=32 Identities=25% Similarity=0.586 Sum_probs=27.1
Q ss_pred CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 240 SLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.+..|+.-+.+-+..|||||+++|.+|.+-+.
T Consensus 173 d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 173 DYKALMGDSSDNIPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred HHHHHcCCcccCCCCCCccCHHHHHHHHHHhC
Confidence 56677777788999999999999999988763
No 136
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=62.55 E-value=9.2 Score=33.00 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=20.8
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
...++|..++|||++.|..+.-+..
T Consensus 80 ~~~~~L~~l~GIG~~tA~~~l~~~~ 104 (158)
T cd00056 80 DAREELLALPGVGRKTANVVLLFAL 104 (158)
T ss_pred ccHHHHHcCCCCCHHHHHHHHHHHC
Confidence 3467899999999999999887653
No 137
>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=62.13 E-value=5.7 Score=36.89 Aligned_cols=23 Identities=13% Similarity=0.398 Sum_probs=20.2
Q ss_pred HhhhcCCCCCHHHHHHHHHHhcc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.+|..|+|||+++|.+|...+.-
T Consensus 72 ~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred HHHhCCCCCCHHHHHHHHhcCCH
Confidence 57999999999999999887754
No 138
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=61.86 E-value=6.3 Score=34.53 Aligned_cols=51 Identities=14% Similarity=0.333 Sum_probs=35.4
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
.+..+|+.|.|||...|..|+..+| .+.-..+.-+.+.-...|.+++..+|
T Consensus 14 ~v~~aL~~I~GIG~~~a~~i~~~lg---------i~~~~~~~~L~~~qi~~l~~~i~~~~ 64 (122)
T PRK05179 14 RVVIALTYIYGIGRTRAKEILAAAG---------IDPDTRVKDLTDEELDKIREEIDKNY 64 (122)
T ss_pred EEEeeecccccccHHHHHHHHHHhC---------cCcccccccCCHHHHHHHHHHHHhhc
Confidence 3567999999999999999999987 22333444455555566666665543
No 139
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=61.60 E-value=5.5 Score=40.86 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 224 RSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 224 pgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
+.|.++.+-.|-+.=-=.=+|-.|+.++|..|||||.+-|++|...=
T Consensus 304 ~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~R 350 (404)
T COG4277 304 PDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMTR 350 (404)
T ss_pred CCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHHh
Confidence 35677777776533222346778999999999999999999997653
No 140
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=61.50 E-value=7.1 Score=38.88 Aligned_cols=38 Identities=24% Similarity=0.396 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 228 KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 228 KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
|..|+-|..+|++ =+-++.+||..+||||+|.|--...
T Consensus 140 kkta~IL~d~f~g---DIP~~v~dLlsLPGVGPKMa~L~m~ 177 (286)
T KOG1921|consen 140 KKTAKILQDKFDG---DIPDTVEDLLSLPGVGPKMAHLTMQ 177 (286)
T ss_pred HHHHHHHHHHhCC---CCchhHHHHhcCCCCchHHHHHHHH
Confidence 5667777888876 2456789999999999999865433
No 141
>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=61.48 E-value=8.7 Score=32.45 Aligned_cols=48 Identities=10% Similarity=0.272 Sum_probs=32.8
Q ss_pred HHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 216 LTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+..+|+.|.|||+..|..|+..+|= +.-..+--+.+....+|.+.+..
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lgi---------~~~~~~~~Ls~~~i~~l~~~i~~ 60 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLGI---------NPNKKVGDLSDEQIDKLRKIIEK 60 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTTS----------SSSBTTTSTHHHHHHHHHHHHT
T ss_pred hHhHHhhhhccCHHHHHHHHHHcCC---------ChhhhcccCCHHHHHHHHHHHHH
Confidence 6778899999999999998888762 22234444555666666666655
No 142
>PRK00076 recR recombination protein RecR; Reviewed
Probab=61.12 E-value=7.2 Score=36.92 Aligned_cols=46 Identities=17% Similarity=0.114 Sum_probs=30.1
Q ss_pred HHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 213 ~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.+.|++.|..+||||++.|++|.-+ =|..=+.-+...|+.|.++..
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~-------------ll~~~~~~~~~la~~i~~~~~ 51 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFH-------------LLQRDREDVLRLAQALEEAKE 51 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH-------------HHcCCHHHHHHHHHHHHHHHH
Confidence 5667777877888888888887765 244445555556666655553
No 143
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=60.76 E-value=17 Score=31.33 Aligned_cols=20 Identities=40% Similarity=0.586 Sum_probs=15.2
Q ss_pred HHhhhcCCCCCHHHHHHHHH
Q 017612 249 MEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e 268 (368)
..+|..|+|||+..|.-|..
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~ 71 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEH 71 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHH
Confidence 46788888888888877654
No 144
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=60.47 E-value=9.1 Score=38.17 Aligned_cols=44 Identities=9% Similarity=0.288 Sum_probs=37.8
Q ss_pred HHHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 229 TDVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 229 TDA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
..+.+-|+ ...++.+++.-+.+||.+++|||++-.+.|.+.|++
T Consensus 258 ~R~~n~Lk~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~ 303 (310)
T PRK05182 258 VRSYNCLKRAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAE 303 (310)
T ss_pred hHHHHHHHHcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence 34555555 466999999999999999999999999999999975
No 145
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=59.82 E-value=3 Score=35.07 Aligned_cols=73 Identities=19% Similarity=0.313 Sum_probs=38.8
Q ss_pred hhhHHHHHHHHHHhhcCCcchhcccccccHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHH----HHcCCHHh----hhc
Q 017612 183 LEECGRYLETIKVYENKPADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSH----IMDASMED----LAR 254 (368)
Q Consensus 183 ~EEAArYIEt~K~~E~K~~d~Irek~e~dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~----I~~AS~EE----La~ 254 (368)
.+.|++.+..|... -..++...+..+..|.+.++..+|..|..... +.....+- |.+
T Consensus 20 ee~Aa~vlk~l~~~---------------ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~~~~~~~~~~~gg~~~~~~lL~~ 84 (108)
T PF14842_consen 20 EEAAAEVLKHLDEE---------------EIERISREMAKLGSVSPEEVEEVLEEFYDEIRAQGGIVSGGRDFARRLLEK 84 (108)
T ss_dssp HHHHHHHHHHS-HH---------------HHHHHHHHHHT-----HHHHHHHHHHHHHHHHHTT---S-HHHHHHH-HHH
T ss_pred HHHHHHHHccCCHH---------------HHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHccccccChHHHHHHHHHH
Confidence 56666666655443 36788899999999999999999999988222 22222222 444
Q ss_pred CCCCCHHHHHHHHHHhcc
Q 017612 255 CPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 255 VPGIG~kKA~rI~e~F~e 272 (368)
. +|+.+|+.|++-+..
T Consensus 85 a--lg~~~a~~il~~~~~ 100 (108)
T PF14842_consen 85 A--LGEEKAKEILDRLEQ 100 (108)
T ss_dssp H--S---HHHHH------
T ss_pred H--CCHHHHHHHHHHHhc
Confidence 4 899999999887754
No 146
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=59.68 E-value=7.5 Score=35.31 Aligned_cols=52 Identities=12% Similarity=0.385 Sum_probs=43.9
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
.+..+|+.|.|||...|..||...| .+.-..+.-+.+....+|.+++..+|.
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~~lg---------i~~~~~~~~Lt~~qi~~l~~~i~~~~~ 73 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIARKLG---------LDPNAKLGYLSDEEIEKIEEALEDPAE 73 (149)
T ss_pred EEeeeccccccccHHHHHHHHHHcC---------cCCCCccCcCCHHHHHHHHHHHHhhcc
Confidence 3567999999999999999999987 445567777888999999999988775
No 147
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=59.63 E-value=5.6 Score=38.73 Aligned_cols=26 Identities=27% Similarity=0.434 Sum_probs=22.0
Q ss_pred HHhhhcCCCCCHHHHHHHHHH-hcccc
Q 017612 249 MEDLARCPGIGERKVKRLYDT-FHEPF 274 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~-F~ePF 274 (368)
.++|..|+|||++++++|++. |..--
T Consensus 2 ~~~L~~IpGIG~krakkLl~~GF~Sve 28 (232)
T PRK12766 2 PEELEDISGVGPSKAEALREAGFESVE 28 (232)
T ss_pred ccccccCCCcCHHHHHHHHHcCCCCHH
Confidence 357999999999999999999 76533
No 148
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.41 E-value=8.1 Score=36.62 Aligned_cols=25 Identities=16% Similarity=0.287 Sum_probs=16.5
Q ss_pred HHHHHHhhccCCCCCHHHHHHHHHh
Q 017612 213 LSRLTHALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 213 ~srL~saLTsIpgVnKTDA~~LLs~ 237 (368)
.+.|++.|..+||||++.|++|.-|
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFH 30 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 4566666666777777777666654
No 149
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=58.90 E-value=9.8 Score=37.68 Aligned_cols=44 Identities=14% Similarity=0.263 Sum_probs=37.8
Q ss_pred HHHHHHHH--hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 229 TDVVTLGS--TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 229 TDA~~LLs--~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.++.+-|+ ...++.+++..+.+||.+++|+|++-.+.|++.|.+
T Consensus 244 vR~~n~Lk~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~~ 289 (297)
T TIGR02027 244 VRSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAE 289 (297)
T ss_pred HHHHhHHHHcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHHHH
Confidence 34455554 567999999999999999999999999999999976
No 150
>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=58.61 E-value=8.7 Score=37.86 Aligned_cols=26 Identities=23% Similarity=0.590 Sum_probs=22.7
Q ss_pred CCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 247 ASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 247 AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
++.+++..+||||++.|++|.+++..
T Consensus 42 ~~~~~~~~ipgiG~~ia~kI~E~~~t 67 (307)
T cd00141 42 ESLEEAKKLPGIGKKIAEKIEEILET 67 (307)
T ss_pred CCHHHhcCCCCccHHHHHHHHHHHHc
Confidence 44567899999999999999999976
No 151
>PRK03352 DNA polymerase IV; Validated
Probab=58.18 E-value=14 Score=36.10 Aligned_cols=51 Identities=14% Similarity=0.134 Sum_probs=43.2
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|..++|||+..+..|.. -+.++.+|...+.++|... +|...++.|++..+
T Consensus 178 pl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~--fG~~~~~~l~~~a~ 229 (346)
T PRK03352 178 PTDALWGVGPKTAKRLAALGITTVADLAAADPAELAAT--FGPTTGPWLLLLAR 229 (346)
T ss_pred CHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHH--hChHHHHHHHHHhC
Confidence 466789999999998765 4669999999999999999 88878888888854
No 152
>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=57.74 E-value=9.8 Score=32.28 Aligned_cols=25 Identities=28% Similarity=0.449 Sum_probs=20.8
Q ss_pred HHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 244 IMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 244 I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
+..+...+|..+||||+..|+-|+.
T Consensus 6 ~~~~~~~~L~~iP~IG~a~a~DL~~ 30 (93)
T PF11731_consen 6 VKRAGLSDLTDIPNIGKATAEDLRL 30 (93)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHHH
Confidence 3445667999999999999999974
No 153
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=57.20 E-value=6 Score=41.61 Aligned_cols=48 Identities=15% Similarity=0.335 Sum_probs=42.0
Q ss_pred HHHHHHHHhcCCHHHHHcC-CHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 229 TDVVTLGSTFGSLSHIMDA-SMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 229 TDA~~LLs~FGSLk~I~~A-S~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
..++.+|.+|+.|++|+.. -.+||+.-.-+=-.+|++|..+|.+||.-
T Consensus 364 ~~vq~iLqrYkeLqDIIaILGmdELseedk~~V~rArki~~FlSQpF~v 412 (468)
T COG0055 364 REVQSILQRYKELQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFFV 412 (468)
T ss_pred HHHHHHHHHHHHHHHHHHHhCchhcChhHHHHHHHHHHHHHHhcCcchh
Confidence 5678999999999999865 67888888888889999999999999964
No 154
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=56.83 E-value=11 Score=32.52 Aligned_cols=42 Identities=19% Similarity=0.110 Sum_probs=33.9
Q ss_pred HHHHHHHhc-CCHHHHHcCCHHhhhcCCCCC---HHHHHHHHHHhcc
Q 017612 230 DVVTLGSTF-GSLSHIMDASMEDLARCPGIG---ERKVKRLYDTFHE 272 (368)
Q Consensus 230 DA~~LLs~F-GSLk~I~~AS~EELa~VPGIG---~kKA~rI~e~F~e 272 (368)
-..+|..+| -|.+.|..++.++|..| |.+ ..||+.|+++.+.
T Consensus 21 ~~~~l~~~~gpt~~~l~~~~~~~l~~~-~~~~G~~~kA~~i~~~a~~ 66 (158)
T cd00056 21 AYERLFERYGPTPEALAAADEEELREL-IRSLGYRRKAKYLKELARA 66 (158)
T ss_pred HHHHHHHHhCCCHHHHHCCCHHHHHHH-HHhcChHHHHHHHHHHHHH
Confidence 346777888 59999999999999987 334 7999999888754
No 155
>PRK07945 hypothetical protein; Provisional
Probab=56.68 E-value=14 Score=36.83 Aligned_cols=51 Identities=16% Similarity=0.177 Sum_probs=33.9
Q ss_pred hhccCCCCCHHHHHHHHHh--cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGST--FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~--FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.|+.|||||+..|..|.+- =|++..+-..- ++..-. | |+..+.+|+-=+|.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~-~~~~~~-~-g~~l~~~~~~D~H~ 102 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGRVPDYLAELR-ADAEPL-G-GGALRAALRGDLHT 102 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcCCHHHHHHHH-HhhcCC-c-cHHHHHHHhhhccc
Confidence 5899999999998877652 36655443221 222222 7 99999999885553
No 156
>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=56.60 E-value=28 Score=32.65 Aligned_cols=60 Identities=15% Similarity=0.110 Sum_probs=42.1
Q ss_pred cHHHHHHHhhccCCCCCHHHHH----HHHHhcC--CHHHHHcCCHHhhhcCC-------CCCHHHHHHHHHHhc
Q 017612 211 DYLSRLTHALTSVRSVNKTDVV----TLGSTFG--SLSHIMDASMEDLARCP-------GIGERKVKRLYDTFH 271 (368)
Q Consensus 211 dy~srL~saLTsIpgVnKTDA~----~LLs~FG--SLk~I~~AS~EELa~VP-------GIG~kKA~rI~e~F~ 271 (368)
+..+.++.++-+- ...-..+. +|...+| +.+.|..|+.+||..+= |+-..||++|+++..
T Consensus 17 ~pFelLVa~ILSQ-qTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~ 89 (177)
T TIGR03252 17 DPFALLTGMLLDQ-QVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQ 89 (177)
T ss_pred ChHHHHHHHHHhc-cCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHH
Confidence 3455565555332 34555554 6656664 89999999999987764 777899999988765
No 157
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=56.34 E-value=18 Score=34.46 Aligned_cols=60 Identities=15% Similarity=0.149 Sum_probs=43.7
Q ss_pred HhhccCCCCCHHHHHHHHHhc-CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc-ccccc
Q 017612 218 HALTSVRSVNKTDVVTLGSTF-GSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE-PFKRV 277 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~F-GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e-PF~~~ 277 (368)
+.|-.+|+||...+..|..+= .++++|+..+.++|..+=+..+..+..|.++++. |....
T Consensus 148 ~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~P~~~i 209 (314)
T PF02889_consen 148 SPLLQLPHIGEESLKKLEKRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRIPRLEI 209 (314)
T ss_dssp -GGGGSTT--HHHHHHHHHTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS--EEE
T ss_pred ChhhcCCCCCHHHHHHHhccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHCCCEEE
Confidence 467799999999999988852 5999999999999999977778999999999875 44443
No 158
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.24 E-value=9.1 Score=35.64 Aligned_cols=25 Identities=20% Similarity=0.296 Sum_probs=21.9
Q ss_pred HhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
+.|..|+|||++.|.+|.+.|....
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~~~~~ 97 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAMNAEA 97 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhCCHHH
Confidence 5799999999999999999987544
No 159
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=56.17 E-value=10 Score=37.91 Aligned_cols=25 Identities=28% Similarity=0.506 Sum_probs=22.0
Q ss_pred HhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
++|..+||||+..|++|.+++..--
T Consensus 48 ~~l~~lpgIG~~ia~kI~Eil~tG~ 72 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEIIETGK 72 (334)
T ss_pred HHHhcCCCccHHHHHHHHHHHHhCc
Confidence 5899999999999999999997543
No 160
>PRK13844 recombination protein RecR; Provisional
Probab=55.22 E-value=10 Score=36.08 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=30.6
Q ss_pred HHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 212 YLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 212 y~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
..+.|++.|..+||||++.|++|.-+ =|..=++-....|+.|.++.+
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~-------------lL~~~~~~~~~la~~i~~~~~ 55 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALY-------------LLDKSPETAIAIANSLLDATA 55 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHH-------------HHcCCHHHHHHHHHHHHHHHH
Confidence 35778888888888888888888766 244444445555555555443
No 161
>PRK03348 DNA polymerase IV; Provisional
Probab=55.02 E-value=23 Score=36.66 Aligned_cols=106 Identities=9% Similarity=0.082 Sum_probs=67.1
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccccCCCCCCCCCCCCccccCCCC
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPPIPETPSQKDVERSS 297 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~~~~s~~~~~~~~~~~~~~~~~ 297 (368)
-|..|+|||+.....|.. -..++.+|...+.++|... +|...+..|++..+.--. +++.+... +.+
T Consensus 181 Pv~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~~--fG~~~g~~L~~~a~G~d~-----~pv~~~~~------~ks 247 (454)
T PRK03348 181 PVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVANL--LGATVGPALHRLARGIDD-----RPVAERAE------AKQ 247 (454)
T ss_pred CccccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHH--HCHHHHHHHHHHHcCCCC-----CCcccCCC------Cce
Confidence 567899999998888755 4569999999999999999 898889999887643322 12211111 111
Q ss_pred ccchhhccccchHHHHhhhccchhhHHHHHHHHHHHHHHHhhcccCCcc
Q 017612 298 VNEVTEVEKDTEDVNKRRKKETESTVKSALSAAFAKYADKIGKKKNRSS 346 (368)
Q Consensus 298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 346 (368)
. .....-..+ -..-..+.-+|.........|+++++....
T Consensus 248 i---s~e~tf~~~------i~~~~~l~~~L~~L~~~l~~rL~~~g~~~r 287 (454)
T PRK03348 248 I---SAESTFAVD------LTTRAQLREAIERIAEHAHRRLLKDGRGAR 287 (454)
T ss_pred E---EEEEECCCC------CCCHHHHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 0 000000000 011234667778888888888887776554
No 162
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=54.91 E-value=8.2 Score=36.87 Aligned_cols=17 Identities=35% Similarity=0.856 Sum_probs=14.0
Q ss_pred HhhhcCCCCCHHHHHHH
Q 017612 250 EDLARCPGIGERKVKRL 266 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI 266 (368)
+.|.++||||+|.|+||
T Consensus 12 ~~l~kLPGvG~KsA~R~ 28 (198)
T COG0353 12 DALKKLPGVGPKSAQRL 28 (198)
T ss_pred HHHhhCCCCChhHHHHH
Confidence 67888888888888887
No 163
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=53.88 E-value=57 Score=36.89 Aligned_cols=42 Identities=21% Similarity=0.385 Sum_probs=32.0
Q ss_pred CCeEEEcCCccCChhHHhh--hccceEeeec-ccceEeccceeee
Q 017612 138 RNAILVSQRQKGNPLLKYI--RNVRWAFADV-VCDYLVGQNSCAL 179 (368)
Q Consensus 138 ~~~IlVS~rQrGNPLLk~I--rnVpwefaDI-vpDY~Ig~ttcIL 179 (368)
.-.|+|-.|-....|-.+| +++..+...+ +.||+|++..||=
T Consensus 586 ~~~IiVD~REfrS~lp~~L~~~G~~v~p~tL~VGDYilS~~i~VE 630 (814)
T TIGR00596 586 QPKVIVDMREFRSSLPSLLHRRGIRVIPCMLTVGDYILTPDICVE 630 (814)
T ss_pred CceEEEecCcccchhHHHHHHCCCEEEEEecCcccEEecCCeEEE
Confidence 4489999888666664444 4577777776 7899999999994
No 164
>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=53.84 E-value=16 Score=27.72 Aligned_cols=29 Identities=10% Similarity=0.125 Sum_probs=21.1
Q ss_pred HhhccCCCCCHHHHHHHHH-hcCCHHHHHc
Q 017612 218 HALTSVRSVNKTDVVTLGS-TFGSLSHIMD 246 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs-~FGSLk~I~~ 246 (368)
..|++|-|||++.|+.+.. -|.||++|..
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred cchhhcccccHHHHHHHHHhCCCCHHHHhh
Confidence 3577999999999999998 5899999953
No 165
>KOG1350 consensus F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=53.78 E-value=10 Score=39.45 Aligned_cols=48 Identities=17% Similarity=0.328 Sum_probs=42.2
Q ss_pred HHHHHHHHhcCCHHHHHcC-CHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 229 TDVVTLGSTFGSLSHIMDA-SMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 229 TDA~~LLs~FGSLk~I~~A-S~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
.-++..|..|+||++|+.. -++||+.-.-+--..|++|.++|.+||.-
T Consensus 414 ~~Vqk~LQ~YKsLQDIIAILGmDELSEeDkLTV~RARKiqRFLSQPF~V 462 (521)
T KOG1350|consen 414 RGVQKTLQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQV 462 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHhCchhhchhhhhhHHHHHHHHHHHcCchhh
Confidence 3467899999999999864 68899999999999999999999999963
No 166
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=52.85 E-value=16 Score=33.42 Aligned_cols=50 Identities=12% Similarity=0.323 Sum_probs=40.7
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
.+..+|+.|.|||...|..||..+| .+.-..+--+.+.-+.+|.+++..+
T Consensus 27 ~v~~aLt~I~GIG~~~A~~I~~~lg---------i~~~~~~~~Lt~~qi~~l~~~i~~~ 76 (154)
T PTZ00134 27 KVPYALTAIKGIGRRFAYLVCKKAG---------IDVTKRAGELTAEEIEKIVEIIANP 76 (154)
T ss_pred EEEEeecccccccHHHHHHHHHHcC---------cCcCCCcccCCHHHHHHHHHHHhcc
Confidence 3566999999999999999999988 3444566667788888999999765
No 167
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=52.13 E-value=12 Score=36.61 Aligned_cols=34 Identities=18% Similarity=0.407 Sum_probs=28.3
Q ss_pred cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 238 FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 238 FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
|-.+..|+.-+.+-+-.|+|||+++|..|..-+.
T Consensus 186 liD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 186 LIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhC
Confidence 3456777777788999999999999999987765
No 168
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=51.31 E-value=30 Score=35.29 Aligned_cols=34 Identities=15% Similarity=0.168 Sum_probs=24.9
Q ss_pred HHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 242 SHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 242 k~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
.+.--.+.|||..++|||+++.+.|.=+-.--|.
T Consensus 261 ~e~~p~~feeLL~~~GvGp~TlRALaLvaelIyg 294 (319)
T PF05559_consen 261 YERQPSDFEELLLIKGVGPSTLRALALVAELIYG 294 (319)
T ss_pred hhCCccCHHHHHhcCCCCHHHHHHHHHHHHHHcC
Confidence 3334456789999999999999998655444443
No 169
>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=51.30 E-value=16 Score=36.19 Aligned_cols=39 Identities=28% Similarity=0.349 Sum_probs=26.8
Q ss_pred HHHHHHhcCC---HHHHHcCC----HHhhhcCCCCCHHHHHHHHHH
Q 017612 231 VVTLGSTFGS---LSHIMDAS----MEDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 231 A~~LLs~FGS---Lk~I~~AS----~EELa~VPGIG~kKA~rI~e~ 269 (368)
|+.+++.++. ++.|...+ .++|..+||||++.|.-|.-+
T Consensus 194 A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 194 ARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLM 239 (310)
T ss_pred HHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH
Confidence 4445555543 34554444 578999999999999988644
No 170
>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=51.28 E-value=12 Score=32.40 Aligned_cols=50 Identities=16% Similarity=0.240 Sum_probs=33.1
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
.+..+|+.|.|||...|..|+..+|= +.-..+--+.+.-..+|.+++..+
T Consensus 12 ~v~~aL~~i~GIG~~~a~~i~~~lgi---------~~~~~~~~L~~~qi~~l~~~l~~~ 61 (113)
T TIGR03631 12 RVEIALTYIYGIGRTRARKILEKAGI---------DPDKRVKDLTEEELNAIREEIEAK 61 (113)
T ss_pred EEeeeeeeeecccHHHHHHHHHHhCc---------CcccccccCCHHHHHHHHHHHHhc
Confidence 35679999999999999999999873 222333334444555555555443
No 171
>PRK03858 DNA polymerase IV; Validated
Probab=51.25 E-value=22 Score=35.45 Aligned_cols=51 Identities=12% Similarity=0.193 Sum_probs=43.7
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|+.++|||+..+.+|-+ -..|+.+|.+.+.+.|... +|...++.|++..+
T Consensus 174 pl~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~--fG~~~~~~l~~~a~ 225 (396)
T PRK03858 174 PVRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVSL--LGPAAGRHLHALAH 225 (396)
T ss_pred ChhhcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHH--hCcHHHHHHHHHhC
Confidence 566789999999999866 4669999999999999998 88888999988764
No 172
>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=51.01 E-value=28 Score=28.13 Aligned_cols=46 Identities=17% Similarity=0.374 Sum_probs=31.6
Q ss_pred HHHhhccCCCCCHHHHHHHHH-----hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 216 LTHALTSVRSVNKTDVVTLGS-----TFGSLSHIMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 216 L~saLTsIpgVnKTDA~~LLs-----~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
+.-.|..|+|||...|+.|++ .|.|+.+++... ++|.....+.|..
T Consensus 25 Ir~gl~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~-------~~i~~~~le~Li~ 75 (90)
T PF14579_consen 25 IRLGLSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL-------PKINKRQLEALIK 75 (90)
T ss_dssp EE-BGGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS--------TS-HHHHHHHHH
T ss_pred EeehHhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH-------hcCCHHHHHHHHH
Confidence 345789999999999999996 578888876544 2777777776654
No 173
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=50.66 E-value=18 Score=39.50 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 228 KTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 228 KTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
+.+|.++.-.|+=-..--..-...|..|+|||+++|+.|.+.|..
T Consensus 547 RDEaHrfAi~yhr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs 591 (621)
T PRK14671 547 RDEAHRFAITYHRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFGS 591 (621)
T ss_pred ehHHHHHHHHhChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcCC
Confidence 456777776666655555555678999999999999999999964
No 174
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=50.34 E-value=23 Score=36.59 Aligned_cols=51 Identities=18% Similarity=0.171 Sum_probs=43.8
Q ss_pred HhhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 218 HALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
.-|+-++||+...+..|-+ -+-|+++|..++..+|..++|+|..++.+|+.
T Consensus 207 ~~lslv~gi~~~~~~~L~~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~ 258 (457)
T TIGR03491 207 GHLSLVPGIGPSRYRLLQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQ 258 (457)
T ss_pred CCeeecCCCCHHHHHHHHHcCCCcHHHHhcCCccccccccccCHHHHHHHHH
Confidence 3566799999999999966 58899999999988899999999988888653
No 175
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=49.98 E-value=24 Score=33.83 Aligned_cols=51 Identities=24% Similarity=0.336 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHhcCCHHHHHcCCHHhhh---cCCCCCHHHHHHHHHHhc---ccccc
Q 017612 225 SVNKTDVVTLGSTFGSLSHIMDASMEDLA---RCPGIGERKVKRLYDTFH---EPFKR 276 (368)
Q Consensus 225 gVnKTDA~~LLs~FGSLk~I~~AS~EELa---~VPGIG~kKA~rI~e~F~---ePF~~ 276 (368)
.+|+. ...|.+.|++.++|.+|+.++|. .--|+-..||++|.+..+ +.|..
T Consensus 46 ~vn~a-t~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g 102 (211)
T COG0177 46 VVNKA-TPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG 102 (211)
T ss_pred HHHHH-HHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC
Confidence 34443 47899999999999999988755 456999999999977654 45654
No 176
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=49.55 E-value=12 Score=35.53 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=18.4
Q ss_pred HHhhccCCCCCHHHHHHHHHh
Q 017612 217 THALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~ 237 (368)
...|+.+|||||+.|++|+-.
T Consensus 107 ~~~L~k~PGIGkKtAerivle 127 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVLE 127 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHHH
Confidence 458999999999999999764
No 177
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=49.42 E-value=28 Score=35.42 Aligned_cols=53 Identities=13% Similarity=0.235 Sum_probs=43.4
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCC---------------HHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDAS---------------MEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS---------------~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
-|..|+|||+..+.+|.. -..++.++...+ .+.|... +|+..+.+|++..+.-
T Consensus 173 pv~~l~GiG~~~~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~--fG~~~g~~l~~~a~G~ 241 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKE--FGEGIGQRIWKLLFGR 241 (379)
T ss_pred CccccCCcCHHHHHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHH--HCHHHHHHHHHHHCCC
Confidence 577899999999998887 345788898888 7788877 8988899998888643
No 178
>PRK10880 adenine DNA glycosylase; Provisional
Probab=48.86 E-value=20 Score=36.46 Aligned_cols=41 Identities=12% Similarity=0.358 Sum_probs=32.8
Q ss_pred HHHHHHhcCCHHHHHcCCHHhhhc-CCCCCH-HHHHHHHHHhc
Q 017612 231 VVTLGSTFGSLSHIMDASMEDLAR-CPGIGE-RKVKRLYDTFH 271 (368)
Q Consensus 231 A~~LLs~FGSLk~I~~AS~EELa~-VPGIG~-kKA~rI~e~F~ 271 (368)
-.+|+++|.++++|..|+.+||.. +.|+|= .||+.|+++..
T Consensus 52 ~~rl~~~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~~~A~ 94 (350)
T PRK10880 52 FERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQ 94 (350)
T ss_pred HHHHHHHCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHHHHHH
Confidence 467899999999999999999876 356664 47888887754
No 179
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=47.44 E-value=26 Score=35.53 Aligned_cols=52 Identities=17% Similarity=0.180 Sum_probs=43.9
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCC--HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDAS--MEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS--~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-|+.|+|||+..+..|.. -..|+.++.+.+ .+.|... +|.+.+..|++..+.
T Consensus 223 Pv~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~~~~~~L~~~--fG~~~g~~L~~~a~G 277 (404)
T cd01701 223 KVGDLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQKV--LGPKTGEKLYDYCRG 277 (404)
T ss_pred CHhHhCCCCHHHHHHHHHcCCcchHHHHhCcccHHHHHHH--HCHHHHHHHHHHhCC
Confidence 566789999999999887 456999999998 9999998 888889998887753
No 180
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=46.89 E-value=23 Score=26.44 Aligned_cols=27 Identities=37% Similarity=0.703 Sum_probs=19.9
Q ss_pred HHHcCCHHhhhcCCCCCHHHHHHHHHH
Q 017612 243 HIMDASMEDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 243 ~I~~AS~EELa~VPGIG~kKA~rI~e~ 269 (368)
...-.|.++|..|+|+|+.++++--+.
T Consensus 37 ~~~P~s~~~L~~i~g~~~~~~~~~g~~ 63 (68)
T PF00570_consen 37 KRLPTSIEELLQIPGMGKRKVRKYGDE 63 (68)
T ss_dssp HH--SSHHHHHTSTTCGHHHHHHCHHH
T ss_pred HhCCCCHHHHHHccCCCHHHHHHHHHH
Confidence 334568999999999999998864443
No 181
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.72 E-value=15 Score=34.25 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=18.5
Q ss_pred HHhhccCCCCCHHHHHHHHHh
Q 017612 217 THALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~ 237 (368)
...|+.+|||||+.|++|+-.
T Consensus 107 ~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 107 VEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 458999999999999999855
No 182
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=46.34 E-value=17 Score=37.38 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=24.1
Q ss_pred CHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 248 SMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 248 S~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
|.+|+..+||||++.|+.|.+++..--
T Consensus 54 S~~ea~~lP~iG~kia~ki~EiletG~ 80 (353)
T KOG2534|consen 54 SGEEAEKLPGIGPKIAEKIQEILETGV 80 (353)
T ss_pred cHHHhcCCCCCCHHHHHHHHHHHHcCC
Confidence 789999999999999999999996543
No 183
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=45.83 E-value=23 Score=35.91 Aligned_cols=40 Identities=23% Similarity=0.393 Sum_probs=33.9
Q ss_pred HHHHHHHHHhcCC---HHHHHcCCHH----hhhcCCCCCHHHHHHHH
Q 017612 228 KTDVVTLGSTFGS---LSHIMDASME----DLARCPGIGERKVKRLY 267 (368)
Q Consensus 228 KTDA~~LLs~FGS---Lk~I~~AS~E----ELa~VPGIG~kKA~rI~ 267 (368)
-..|+.|++..|- +..|..++.| .|..+||||+|.|.=|.
T Consensus 189 ~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 189 SATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCIC 235 (323)
T ss_pred HHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhh
Confidence 3568899999999 8889888765 59999999999999664
No 184
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.35 E-value=16 Score=34.04 Aligned_cols=21 Identities=10% Similarity=0.128 Sum_probs=18.4
Q ss_pred HHhhccCCCCCHHHHHHHHHh
Q 017612 217 THALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~ 237 (368)
...|+.+||||++.|++|+-.
T Consensus 107 ~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 458999999999999999855
No 185
>PRK00076 recR recombination protein RecR; Reviewed
Probab=45.29 E-value=21 Score=33.84 Aligned_cols=21 Identities=38% Similarity=0.640 Sum_probs=18.4
Q ss_pred HhhhcCCCCCHHHHHHHHHHh
Q 017612 250 EDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F 270 (368)
+.|.++||||+|.|+||.-++
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~l 31 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHL 31 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHH
Confidence 689999999999999995554
No 186
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=44.92 E-value=26 Score=36.02 Aligned_cols=49 Identities=12% Similarity=0.233 Sum_probs=34.9
Q ss_pred hhccCCCCCHHHHHHH---HHhcCCHHHHHcCC-------HHhhhcCCCCCHHHHHHHHH
Q 017612 219 ALTSVRSVNKTDVVTL---GSTFGSLSHIMDAS-------MEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 219 aLTsIpgVnKTDA~~L---Ls~FGSLk~I~~AS-------~EELa~VPGIG~kKA~rI~e 268 (368)
-+.+|||||++.|..+ |++ |.++++-... ..=+.+|-|||.+.|++++.
T Consensus 57 ea~~lP~iG~kia~ki~Eilet-G~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~ 115 (353)
T KOG2534|consen 57 EAEKLPGIGPKIAEKIQEILET-GVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYR 115 (353)
T ss_pred HhcCCCCCCHHHHHHHHHHHHc-CCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHH
Confidence 4557999999988765 443 5555544332 23467899999999999875
No 187
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=43.44 E-value=25 Score=27.03 Aligned_cols=28 Identities=7% Similarity=0.108 Sum_probs=20.9
Q ss_pred HHhhccCCCCCHHHHHHHHHhcCCHHHH
Q 017612 217 THALTSVRSVNKTDVVTLGSTFGSLSHI 244 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~FGSLk~I 244 (368)
.+.|+.|+|||++.|..|.+.|..-++.
T Consensus 34 ~e~L~~i~gIG~~~A~si~~ff~~~~n~ 61 (64)
T PF12826_consen 34 VEELSAIPGIGPKIAQSIYEFFQDPENR 61 (64)
T ss_dssp HHHHCTSTT--HHHHHHHHHHHH-HHHH
T ss_pred HHHHhccCCcCHHHHHHHHHHHCCHHhh
Confidence 3468899999999999999999876653
No 188
>PRK01216 DNA polymerase IV; Validated
Probab=43.31 E-value=41 Score=33.83 Aligned_cols=51 Identities=18% Similarity=0.319 Sum_probs=42.4
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|..++|||+..+..|-. -+.|+.+|.+.+.++|... +|+..+..|++..+
T Consensus 179 Pi~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~r--fG~~~~~~L~~~a~ 230 (351)
T PRK01216 179 DIADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKGI--IGEAKAKYLFSLAR 230 (351)
T ss_pred CcccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHH--HCHHHHHHHHHHhC
Confidence 466789999888877765 4679999999999999998 88888888888663
No 189
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=43.04 E-value=19 Score=31.57 Aligned_cols=49 Identities=16% Similarity=0.240 Sum_probs=32.2
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.+..+|+.|.|||...|..|+...| .+.-..+.-+.+....+|.+++..
T Consensus 14 ~v~~aLt~i~GIG~~~A~~ic~~lg---------i~~~~~~~~Lt~~qi~~l~~~i~~ 62 (122)
T CHL00137 14 RIEYALTYIYGIGLTSAKEILEKAN---------IDPDIRTKDLTDEQISALREIIEE 62 (122)
T ss_pred EeeeeecccccccHHHHHHHHHHcC---------cCcCcCcccCCHHHHHHHHHHHHH
Confidence 3567999999999999999999877 222233333444445555555543
No 190
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.57 E-value=19 Score=33.80 Aligned_cols=21 Identities=24% Similarity=0.192 Sum_probs=18.6
Q ss_pred HHhhccCCCCCHHHHHHHHHh
Q 017612 217 THALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~ 237 (368)
...|+.|||||++.|++|+-.
T Consensus 108 ~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 108 VAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 458999999999999999865
No 191
>PRK07945 hypothetical protein; Provisional
Probab=42.53 E-value=32 Score=34.31 Aligned_cols=23 Identities=26% Similarity=0.485 Sum_probs=21.2
Q ss_pred hhhcCCCCCHHHHHHHHHHhccc
Q 017612 251 DLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 251 ELa~VPGIG~kKA~rI~e~F~eP 273 (368)
+|..+||||+..|..|.+++..-
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg 72 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGR 72 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcC
Confidence 89999999999999999998764
No 192
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=42.48 E-value=32 Score=29.67 Aligned_cols=36 Identities=8% Similarity=0.169 Sum_probs=31.2
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLAR 254 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~ 254 (368)
-|..|+|||..+|..|.+ -+.|+++|..++.++|..
T Consensus 54 dL~ri~gi~~~~a~LL~~AGv~Tv~~LA~~~p~~L~~ 90 (122)
T PF14229_consen 54 DLMRIPGIGPQYAELLEHAGVDTVEELAQRNPQNLHQ 90 (122)
T ss_pred HhhhcCCCCHHHHHHHHHhCcCcHHHHHhCCHHHHHH
Confidence 455899999999999887 688999999999988764
No 193
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.18 E-value=24 Score=33.50 Aligned_cols=17 Identities=47% Similarity=0.907 Sum_probs=16.2
Q ss_pred HhhhcCCCCCHHHHHHH
Q 017612 250 EDLARCPGIGERKVKRL 266 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI 266 (368)
+.|.++||||+|.|+||
T Consensus 11 ~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 11 ESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHCCCCCHHHHHHH
Confidence 68999999999999999
No 194
>PRK13844 recombination protein RecR; Provisional
Probab=41.93 E-value=26 Score=33.44 Aligned_cols=21 Identities=33% Similarity=0.523 Sum_probs=18.2
Q ss_pred HhhhcCCCCCHHHHHHHHHHh
Q 017612 250 EDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F 270 (368)
+.|..+||||+|.|+||--++
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~l 35 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYL 35 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHH
Confidence 689999999999999995444
No 195
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=41.86 E-value=20 Score=30.86 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=18.4
Q ss_pred HhhhcCCCCCHHHHHHHHHHhcc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.-|.=|.|+||+||..|.+.+..
T Consensus 50 ~~LqfV~GLGPRKA~~Ll~~l~~ 72 (104)
T PF14635_consen 50 NLLQFVCGLGPRKAQALLKALKQ 72 (104)
T ss_dssp GGGGGSTT--HHHHHHHHHHHHH
T ss_pred hhHhHhcCCChHHHHHHHHHHHH
Confidence 35788999999999999999984
No 196
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=41.68 E-value=24 Score=35.76 Aligned_cols=39 Identities=21% Similarity=0.458 Sum_probs=35.3
Q ss_pred hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccccc
Q 017612 237 TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275 (368)
Q Consensus 237 ~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~ 275 (368)
...++.+++.-|++||.+++.+|++-++.|.+.|+..|.
T Consensus 282 ~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L~~~~g 320 (327)
T CHL00013 282 NIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQKRFG 320 (327)
T ss_pred CccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHHHHHhC
Confidence 567999999999999999999999999999999976443
No 197
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.65 E-value=19 Score=34.03 Aligned_cols=21 Identities=5% Similarity=0.056 Sum_probs=18.3
Q ss_pred HHhhccCCCCCHHHHHHHHHh
Q 017612 217 THALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~ 237 (368)
...|+.+||||++.|++|+-.
T Consensus 106 ~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 106 IELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 458999999999999999854
No 198
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=40.93 E-value=39 Score=27.58 Aligned_cols=57 Identities=16% Similarity=0.191 Sum_probs=38.6
Q ss_pred HHHHHhhccCCCCCHHHHHHHHHhcCCH-HHHHcCCHHhhhc-CCCCCHHHHHHHHHHhc
Q 017612 214 SRLTHALTSVRSVNKTDVVTLGSTFGSL-SHIMDASMEDLAR-CPGIGERKVKRLYDTFH 271 (368)
Q Consensus 214 srL~saLTsIpgVnKTDA~~LLs~FGSL-k~I~~AS~EELa~-VPGIG~kKA~rI~e~F~ 271 (368)
..+...|... ||+...|.+|.++||.- -+++..+.=.|.. |.|||=++|.+|-.-+.
T Consensus 9 ~~~~~~L~~~-gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 9 RELMAFLQEY-GLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHHHHHHT-T--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcC
Confidence 3445555433 99999999999999972 2344445556776 99999999999988763
No 199
>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=40.70 E-value=0.95 Score=38.43 Aligned_cols=31 Identities=19% Similarity=0.533 Sum_probs=21.7
Q ss_pred HHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 242 SHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 242 k~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
..|+.-+.+.+-.|||||+|+|..|.+-|..
T Consensus 10 ~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygs 40 (101)
T PF01367_consen 10 KALVGDSSDNIPGVPGIGPKTAAKLLQEYGS 40 (101)
T ss_dssp CCCC-CCCCTB---TTSTCHCCCCCHHHHTS
T ss_pred HHHcCCcccCCCCCCCCCHHHHHHHHHHcCC
Confidence 3445556678889999999999999998863
No 200
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.13 E-value=22 Score=33.37 Aligned_cols=21 Identities=24% Similarity=0.180 Sum_probs=18.6
Q ss_pred HHhhccCCCCCHHHHHHHHHh
Q 017612 217 THALTSVRSVNKTDVVTLGST 237 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~ 237 (368)
...|+.+||||++.|++|+-.
T Consensus 106 ~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 458999999999999999865
No 201
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.92 E-value=22 Score=33.34 Aligned_cols=22 Identities=14% Similarity=0.154 Sum_probs=19.1
Q ss_pred HHhhccCCCCCHHHHHHHHHhc
Q 017612 217 THALTSVRSVNKTDVVTLGSTF 238 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs~F 238 (368)
...|+.+||||++.|++|+-..
T Consensus 107 ~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 107 VARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHHhhCCCCCHHHHHHHHHHH
Confidence 4589999999999999998763
No 202
>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=39.83 E-value=40 Score=33.14 Aligned_cols=41 Identities=12% Similarity=0.301 Sum_probs=31.4
Q ss_pred HHHHHHhcCCHHHHHcCCHHhhhcC-CCCCH-HHHHHHHHHhc
Q 017612 231 VVTLGSTFGSLSHIMDASMEDLARC-PGIGE-RKVKRLYDTFH 271 (368)
Q Consensus 231 A~~LLs~FGSLk~I~~AS~EELa~V-PGIG~-kKA~rI~e~F~ 271 (368)
-.+|+++|-++++|.+|+.+||..+ .|+|= .+|+.|+++..
T Consensus 48 ~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~~~A~ 90 (275)
T TIGR01084 48 FERFLERFPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQ 90 (275)
T ss_pred HHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3678899999999999999999543 34443 57888877754
No 203
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=39.81 E-value=22 Score=31.71 Aligned_cols=50 Identities=20% Similarity=0.343 Sum_probs=32.6
Q ss_pred HHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 214 SRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 214 srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.++..+||.|.|||++.|..++..-| .+.=..+-.+.+--..+|.+++..
T Consensus 13 K~v~iALt~IyGIG~~~a~~I~~~~g---------i~~~~r~~eLteeei~~ir~~i~~ 62 (121)
T COG0099 13 KRVVIALTYIYGIGRRRAKEICKKAG---------IDPDKRVGELTEEEIERLRDAIQN 62 (121)
T ss_pred ceEeehhhhhccccHHHHHHHHHHcC---------CCHhHhhccCCHHHHHHHHHHHHh
Confidence 34677999999999999999998755 222233333444444555555554
No 204
>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=39.80 E-value=20 Score=30.48 Aligned_cols=22 Identities=18% Similarity=0.302 Sum_probs=19.2
Q ss_pred hhhcCCCCCHHHHHHHHHHhcc
Q 017612 251 DLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 251 ELa~VPGIG~kKA~rI~e~F~e 272 (368)
=-..|||||..+|++|-.+|..
T Consensus 51 Wwr~vpglG~~~A~~I~awLa~ 72 (96)
T PF12482_consen 51 WWRAVPGLGAAGARRIEAWLAA 72 (96)
T ss_pred HHHhCcccchHHHHHHHHHHHH
Confidence 3578999999999999999964
No 205
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=39.76 E-value=27 Score=33.44 Aligned_cols=33 Identities=33% Similarity=0.440 Sum_probs=29.0
Q ss_pred CCHHHHHcCCHHhhhcC---CCCCHHHHHHHHHHhc
Q 017612 239 GSLSHIMDASMEDLARC---PGIGERKVKRLYDTFH 271 (368)
Q Consensus 239 GSLk~I~~AS~EELa~V---PGIG~kKA~rI~e~F~ 271 (368)
.++++|+.++.++|..+ -|+-..||++|+++..
T Consensus 67 ~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~ 102 (218)
T PRK13913 67 INLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSE 102 (218)
T ss_pred CCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 38999999999999888 6999999999987654
No 206
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=39.31 E-value=20 Score=33.89 Aligned_cols=23 Identities=35% Similarity=0.356 Sum_probs=20.0
Q ss_pred hhccCCCCCHHHHHHHHHhcCCH
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSL 241 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSL 241 (368)
++|+.||+|||.+-.+|+.+|--
T Consensus 4 ~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 4 AITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred EEeCCCCCchHHHHHHHHHhCCc
Confidence 68999999999999999976643
No 207
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=37.87 E-value=26 Score=38.36 Aligned_cols=24 Identities=33% Similarity=0.704 Sum_probs=21.6
Q ss_pred HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 249 MEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
...|..|||||++++++|++.|..
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~~FgS 574 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLKHFGS 574 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCC
Confidence 468999999999999999999964
No 208
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.82 E-value=51 Score=32.53 Aligned_cols=21 Identities=10% Similarity=0.099 Sum_probs=11.2
Q ss_pred HHHHhhccCCCCCHHHHHHHH
Q 017612 215 RLTHALTSVRSVNKTDVVTLG 235 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LL 235 (368)
.+.+.|++|+|||+-.|.-+|
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~l 215 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFL 215 (285)
T ss_pred HHHHHHHcCCCcCHHHHHHHH
Confidence 345555556666655555443
No 209
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=37.74 E-value=26 Score=37.98 Aligned_cols=24 Identities=33% Similarity=0.720 Sum_probs=21.5
Q ss_pred HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 249 MEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
...|..|||||+++.+.|++.|..
T Consensus 540 ~S~Ld~I~GIG~kr~~~LL~~Fgs 563 (574)
T TIGR00194 540 QSPLLKIPGVGEKRVQKLLKYFGS 563 (574)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCC
Confidence 357999999999999999999964
No 210
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=37.11 E-value=70 Score=30.80 Aligned_cols=53 Identities=19% Similarity=0.297 Sum_probs=41.9
Q ss_pred HHHHhhccCCCCCHHHHHHHHH-----hcCCHHHHHcCCHHhhhcCCCC---CHHHHHHHHHHhcccc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGS-----TFGSLSHIMDASMEDLARCPGI---GERKVKRLYDTFHEPF 274 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs-----~FGSLk~I~~AS~EELa~VPGI---G~kKA~rI~e~F~ePF 274 (368)
.-++.|.-+||||++....||. -|-|+++|. ..|+|+ -+-.|++|.+-+..++
T Consensus 127 ~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~-------~Rv~~~~~p~~~I~~RIl~El~~~~ 187 (202)
T COG1491 127 LRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIK-------ERVKGLHDPAKMIAERILDELKDED 187 (202)
T ss_pred HHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHH-------HHhcCCCCHHHHHHHHHHHHhcCCC
Confidence 3467888889999999999997 499999887 345555 4667899988887775
No 211
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.05 E-value=21 Score=40.54 Aligned_cols=42 Identities=21% Similarity=0.449 Sum_probs=31.4
Q ss_pred HHHHHHHhcC-------CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 230 DVVTLGSTFG-------SLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 230 DA~~LLs~FG-------SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
|....+++|| .+..|+.-+.+-+-.|||||+|+|.+|..-+.
T Consensus 158 ~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~yg 206 (887)
T TIGR00593 158 TPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFG 206 (887)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcC
Confidence 3444556666 46677777788999999999999999976543
No 212
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=36.75 E-value=28 Score=34.16 Aligned_cols=45 Identities=20% Similarity=0.269 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHh---c--CCHHHHH----cCCHHhhhcCCCCCHHHHHHHHHH
Q 017612 225 SVNKTDVVTLGST---F--GSLSHIM----DASMEDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 225 gVnKTDA~~LLs~---F--GSLk~I~----~AS~EELa~VPGIG~kKA~rI~e~ 269 (368)
|++...|+.|..- + |.+.--. .+..++|..+||||++.|.-|.-.
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHH
Confidence 7777666665442 2 3221111 112578999999999999987643
No 213
>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=36.45 E-value=42 Score=26.90 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=20.7
Q ss_pred HhhhcCCCCCHHHHHHHHHHhccc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
+-|..|||||+..|-.|...+..+
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~ 25 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDI 25 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCc
Confidence 458899999999999999999544
No 214
>PRK05755 DNA polymerase I; Provisional
Probab=36.27 E-value=22 Score=39.77 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=26.9
Q ss_pred CHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 240 SLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 240 SLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
.+..|+.-+.+-+-.|||||+++|..|.+-|.
T Consensus 177 d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 177 DYLALMGDSSDNIPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred HHHHHhCCccCCCCCCCCccHHHHHHHHHHcC
Confidence 56777777788999999999999999976554
No 215
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=35.85 E-value=38 Score=32.49 Aligned_cols=49 Identities=20% Similarity=0.291 Sum_probs=37.0
Q ss_pred cHHHHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 211 DYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 211 dy~srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.+.++|++.|..+||||++-|.+|.=| ++.-+.+++. ..|++|.++...
T Consensus 5 ~~i~~LI~~l~kLPGvG~KsA~R~Afh------LL~~~~~~~~-------~la~al~~a~~~ 53 (198)
T COG0353 5 PPIEKLIDALKKLPGVGPKSAQRLAFH------LLQRDREDVE-------RLAKALLEAKEN 53 (198)
T ss_pred HHHHHHHHHHhhCCCCChhHHHHHHHH------HHccCHHHHH-------HHHHHHHHHHhc
Confidence 478999999999999999999999876 4555555543 346666666543
No 216
>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=34.86 E-value=42 Score=30.33 Aligned_cols=49 Identities=12% Similarity=0.307 Sum_probs=38.8
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
.+..+|+.|.|||+..|..|+...| .+.-..+.-+.+.....|.+++..
T Consensus 18 ~v~~aLt~I~GIG~~~a~~I~~~lg---------i~~~~~~~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 18 PVEYALTGIKGIGRRFARAIARKLG---------VDPNAKLGYLDDEEIEKLEEAVEN 66 (144)
T ss_pred EEEEeecceeccCHHHHHHHHHHcC---------cCCCCCcccCCHHHHHHHHHHHHh
Confidence 3567999999999999999999887 344556666777778888888865
No 217
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=34.81 E-value=27 Score=37.87 Aligned_cols=25 Identities=24% Similarity=0.478 Sum_probs=21.9
Q ss_pred CHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 248 SMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 248 S~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
....|..|||||+++.+.|++.|..
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs 536 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGT 536 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCC
Confidence 3458999999999999999999954
No 218
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=34.48 E-value=78 Score=33.64 Aligned_cols=59 Identities=19% Similarity=0.279 Sum_probs=50.2
Q ss_pred HhhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 218 HALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
..+....+|...-+..|.. -|.++++|..++.++|..++|+.+..+..|.+.....+..
T Consensus 356 ~~f~~~~~ide~~~~~l~~~g~~~~e~~~~~~~~el~~i~~~~ee~~~~l~~~~~~~~~~ 415 (470)
T PRK09202 356 DLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDEETVEELRERAKEALET 415 (470)
T ss_pred HHHhhhccccHHHHHHHHHcCcccHHHHhcCCHHHHhhccCCCHHHHHHHHHHHHHHhhh
Confidence 3445667888888888877 6999999999999999999999999999999888765553
No 219
>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=34.03 E-value=38 Score=28.60 Aligned_cols=23 Identities=30% Similarity=0.453 Sum_probs=20.5
Q ss_pred HhhhcCCCCCHHHHHHHHHHhcc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-.|..|.|||..+|..|.+.+.-
T Consensus 15 ~aLt~IyGIG~~~A~~Ic~~lgi 37 (107)
T PF00416_consen 15 IALTKIYGIGRRKAKQICKKLGI 37 (107)
T ss_dssp HHHTTSTTBCHHHHHHHHHHTTS
T ss_pred hHHhhhhccCHHHHHHHHHHcCC
Confidence 36899999999999999999963
No 220
>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=32.35 E-value=51 Score=36.39 Aligned_cols=48 Identities=13% Similarity=0.040 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHhcCCH-HHHHcCCHHhhh-cCCCCCHHHHHHHHHHhcc
Q 017612 225 SVNKTDVVTLGSTFGSL-SHIMDASMEDLA-RCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 225 gVnKTDA~~LLs~FGSL-k~I~~AS~EELa-~VPGIG~kKA~rI~e~F~e 272 (368)
||+..-|.+|.++||.- -+++.++.=.|. .++|||=++|.+|...|..
T Consensus 154 gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~ 203 (720)
T TIGR01448 154 GIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGI 203 (720)
T ss_pred CCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCC
Confidence 66666777777777642 235555666666 5888998888888776653
No 221
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=32.18 E-value=32 Score=37.27 Aligned_cols=24 Identities=33% Similarity=0.551 Sum_probs=21.5
Q ss_pred HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 249 MEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
...|..|||||+++.+.|++.|..
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~Fgs 536 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNFKT 536 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHhCC
Confidence 357999999999999999999964
No 222
>PRK01810 DNA polymerase IV; Validated
Probab=31.26 E-value=64 Score=32.42 Aligned_cols=51 Identities=12% Similarity=0.143 Sum_probs=41.2
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-|+.++|||+..+..|.. -..++.+|..++.++|... +|. ....+++..+.
T Consensus 180 pv~~l~giG~~~~~~L~~~Gi~tigdL~~~~~~~L~~r--fG~-~g~~l~~~a~G 231 (407)
T PRK01810 180 PVGEMHGIGEKTAEKLKDIGIQTIGDLAKADEHILRAK--LGI-NGVRLQRRANG 231 (407)
T ss_pred CHhhcCCcCHHHHHHHHHcCCCcHHHHHhCCHHHHHHH--HhH-HHHHHHHHhcC
Confidence 456789999999988755 3679999999999999998 775 57778877753
No 223
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=30.71 E-value=69 Score=31.39 Aligned_cols=50 Identities=14% Similarity=0.209 Sum_probs=40.0
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|..++|||+.....|-. -+.++.+|.+.+.++|... +|. ....+++..+
T Consensus 177 pl~~l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L~~r--fG~-~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLLRKK--FGV-VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHHHHHHHHHcCCCcHHHHhcCCHHHHHHH--HHH-HHHHHHHHhC
Confidence 466789999999998765 4679999999999999998 775 4666766664
No 224
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.34 E-value=45 Score=38.82 Aligned_cols=26 Identities=12% Similarity=0.303 Sum_probs=22.6
Q ss_pred ccCCCCCHHHHHHHHHhcC--CHHHHHc
Q 017612 221 TSVRSVNKTDVVTLGSTFG--SLSHIMD 246 (368)
Q Consensus 221 TsIpgVnKTDA~~LLs~FG--SLk~I~~ 246 (368)
.+|+|||.+.|..|++.|| +++.|+.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~~ 896 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLLK 896 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHHH
Confidence 5899999999999999999 4777663
No 225
>PRK02406 DNA polymerase IV; Validated
Probab=30.16 E-value=76 Score=31.08 Aligned_cols=51 Identities=18% Similarity=0.297 Sum_probs=40.6
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-|+.++|||+..+..|-. -+.|+.+|...+.++|... +|. ....+++..+.
T Consensus 169 pi~~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~--fG~-~~~~l~~~a~G 220 (343)
T PRK02406 169 PVEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELIRH--FGK-FGRRLYERARG 220 (343)
T ss_pred CcchhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHH--HhH-HHHHHHHHhCC
Confidence 567789999999888754 3679999999999999998 675 56667776643
No 226
>PRK02794 DNA polymerase IV; Provisional
Probab=29.81 E-value=69 Score=32.54 Aligned_cols=51 Identities=18% Similarity=0.236 Sum_probs=41.9
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-|+.++|||+..+..|-. -..|+.+|.+.+.++|... +|. .+..+++..+.
T Consensus 210 Pl~~L~GiG~~~~~~L~~~GI~tigdL~~l~~~~L~~r--fG~-~g~~l~~~a~G 261 (419)
T PRK02794 210 PVGIIWGVGPATAARLARDGIRTIGDLQRADEADLMRR--FGS-MGLRLWRLARG 261 (419)
T ss_pred ChhhhCCCCHHHHHHHHHhccchHHHHhhCCHHHHHHH--HhH-HHHHHHHHhCC
Confidence 567789999999998865 4569999999999999998 776 57778877753
No 227
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=29.80 E-value=70 Score=32.84 Aligned_cols=48 Identities=19% Similarity=0.318 Sum_probs=43.7
Q ss_pred HhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHH
Q 017612 218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRL 266 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI 266 (368)
-.|..+++++...-..|+.+||+.+.+......+|..+ |.....+.++
T Consensus 10 l~L~~~~~l~~~~~~~ll~~~~~~~~~~~~~~~~l~~~-g~~~~~~~~~ 57 (350)
T COG0758 10 LKLSSTNNLGPLNLLLLLKHFGNKESILKIPLPQLEIE-GLSSRRLLAE 57 (350)
T ss_pred HHHhhCCCCChHHHHHHHHhcCCHhhhhhccHHHHHHh-ccchHHHHhh
Confidence 46778999999999999999999999999999999999 9988888864
No 228
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=29.41 E-value=1.2e+02 Score=32.77 Aligned_cols=57 Identities=18% Similarity=0.365 Sum_probs=41.0
Q ss_pred HHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcC----CHHhhh--cC---------CCCCHHHHHHHHHHhc
Q 017612 215 RLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDA----SMEDLA--RC---------PGIGERKVKRLYDTFH 271 (368)
Q Consensus 215 rL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~A----S~EELa--~V---------PGIG~kKA~rI~e~F~ 271 (368)
-+...|=.|+||+...|..|+++|.|+..|+.| +.+++. .+ .-||++....|+.+|.
T Consensus 427 vf~~qLMqvkg~S~erAiAI~d~YpTl~sLl~AY~~s~~~k~~~l~ln~~~~~~~~rn~~~~Ls~~l~~~F~ 498 (501)
T KOG2379|consen 427 VFARQLMQVKGMSLERAIAIADRYPTLRSLLSAYEVSADDKLRLLLLNPIKCGPGSRNIGPALSAKLYEFFL 498 (501)
T ss_pred HHHHHHHhccCccHHHHHHHHHhccCHHHHHHHHhccCcHHHHhccccccccccccccccHHHHHHHHHhhh
Confidence 334456689999999999999999999999976 222222 11 1267777878888774
No 229
>COG4969 PilA Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=29.36 E-value=16 Score=32.07 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=13.2
Q ss_pred EEeccchHHHhhcCC
Q 017612 56 IITIPSYQEVINATN 70 (368)
Q Consensus 56 ~~~~~~~~~~~~~~~ 70 (368)
-|.||+||+++..++
T Consensus 24 aIaiP~YQ~y~~k~~ 38 (125)
T COG4969 24 AIAIPLYQNYVARAQ 38 (125)
T ss_pred HhhhhHHHHHHHHHH
Confidence 389999999999876
No 230
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.89 E-value=37 Score=31.66 Aligned_cols=22 Identities=9% Similarity=0.280 Sum_probs=19.5
Q ss_pred HhhhcCCCCCHHHHHHHHHHhc
Q 017612 250 EDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~ 271 (368)
+.|..|.|||++.|-+|...+.
T Consensus 73 ~~LisV~GIGpK~Al~iLs~~~ 94 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSILSKLT 94 (186)
T ss_pred HHHhCcCCcCHHHHHHHHccCC
Confidence 5789999999999999988764
No 231
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=28.78 E-value=41 Score=36.45 Aligned_cols=26 Identities=31% Similarity=0.417 Sum_probs=22.7
Q ss_pred HHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 249 MEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
.-.|..|||||++++++|++.|...-
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~FGS~~ 549 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRFGSVE 549 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHcCCHH
Confidence 46799999999999999999997543
No 232
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=28.05 E-value=59 Score=34.00 Aligned_cols=47 Identities=21% Similarity=0.304 Sum_probs=35.5
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-|+.| ||...|.+|+.+-|+|.++.......++- +|..|| +...|..
T Consensus 265 NLtaL--VG~~lAArLIa~AGsL~~Lak~PastIqi---LGAeKa--lf~~l~t 311 (414)
T PRK14552 265 NLTAL--VGPSLGARLISLAGGLEELAKMPASTIQV---LGAEKA--LFRHLRT 311 (414)
T ss_pred HHHHH--HhhHHHHHHHHHhCCHHHHhhCCchHHHH---hchhhH--HHHHhcc
Confidence 46666 99999999999999998876665544433 799998 5555643
No 233
>COG1204 Superfamily II helicase [General function prediction only]
Probab=27.73 E-value=72 Score=35.80 Aligned_cols=60 Identities=23% Similarity=0.311 Sum_probs=53.0
Q ss_pred HHhhccCCCCCHHHHHHHHH-hcCCHHHHH-cCCHHhhhcCCCCCHHHHHHHHHHhcccccc
Q 017612 217 THALTSVRSVNKTDVVTLGS-TFGSLSHIM-DASMEDLARCPGIGERKVKRLYDTFHEPFKR 276 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs-~FGSLk~I~-~AS~EELa~VPGIG~kKA~rI~e~F~ePF~~ 276 (368)
...|..|+++|...|+.|-. .|.+++++. .+...++..+.|+|.+.+..|.+.+......
T Consensus 674 ~~~l~~i~~~grvrar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ 735 (766)
T COG1204 674 LLELVEIRGVGRVRARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILESLGRDVLL 735 (766)
T ss_pred hcccccccccchhHHHHHHHhhhccHHHHHhhcChhhhhhhhhhHHHHHHHHHHHhhhhhhc
Confidence 34566899999999999877 689999999 8999999999999999999999999877654
No 234
>PRK14133 DNA polymerase IV; Provisional
Probab=27.68 E-value=89 Score=30.71 Aligned_cols=50 Identities=18% Similarity=0.317 Sum_probs=40.7
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|..++|||+..+..|-+ -+.++.+|.+.+.++|... +|. ....+++..+
T Consensus 174 pv~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~r--fG~-~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEY--FGK-FGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHHHHHHHHcCCccHHHHhhCCHHHHHHH--HhH-HHHHHHHHhC
Confidence 567789999999988765 4679999999999999999 775 5677777664
No 235
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=26.71 E-value=56 Score=35.61 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=25.4
Q ss_pred hhccCCCCCHHHHHHHHHhcCCHHHHH
Q 017612 219 ALTSVRSVNKTDVVTLGSTFGSLSHIM 245 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs~FGSLk~I~ 245 (368)
-|.+|||||-..|.+|+.+|.+++.++
T Consensus 226 Yl~slpGvGl~tA~k~l~k~~~~d~vi 252 (556)
T KOG2518|consen 226 YLSSLPGVGLATAHKLLSKYNTPDRVI 252 (556)
T ss_pred ccccCccccHHHHHHHHHhcCcHHHHH
Confidence 477899999999999999999999997
No 236
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=26.71 E-value=47 Score=36.07 Aligned_cols=24 Identities=33% Similarity=0.582 Sum_probs=21.7
Q ss_pred HHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 249 MEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 249 ~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
...|..|||||++++++|.+.|..
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~FgS 565 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFGS 565 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcCC
Confidence 357899999999999999999975
No 237
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.75 E-value=97 Score=30.63 Aligned_cols=30 Identities=27% Similarity=0.275 Sum_probs=24.1
Q ss_pred CHHHHHcCCH----HhhhcCCCCCHHHHHHHHHH
Q 017612 240 SLSHIMDASM----EDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 240 SLk~I~~AS~----EELa~VPGIG~kKA~rI~e~ 269 (368)
++..+...+. |.|..++|||+..|+-+.-+
T Consensus 184 ~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 184 DLSELKPLSDEEAIEELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred cHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHH
Confidence 6677777664 67999999999999987644
No 238
>PRK03103 DNA polymerase IV; Reviewed
Probab=25.65 E-value=96 Score=31.22 Aligned_cols=51 Identities=14% Similarity=0.186 Sum_probs=41.0
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhcc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~e 272 (368)
-++.++|||+..+..|-. .+.|+.+|...+.++|... +|. .+..+++.++.
T Consensus 182 pi~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~~~--fG~-~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLKKR--WGI-NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHHHH--HCH-HHHHHHHHhcC
Confidence 456789999998888754 4559999999999999998 675 57888887764
No 239
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=25.56 E-value=49 Score=36.93 Aligned_cols=23 Identities=26% Similarity=0.512 Sum_probs=20.9
Q ss_pred HhhhcCCCCCHHHHHHHHHHhcc
Q 017612 250 EDLARCPGIGERKVKRLYDTFHE 272 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~F~e 272 (368)
..|..|||||+++.+.|++.|..
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS 630 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGS 630 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcC
Confidence 57899999999999999999964
No 240
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=25.54 E-value=56 Score=34.99 Aligned_cols=32 Identities=22% Similarity=0.545 Sum_probs=24.3
Q ss_pred CCHHHHHcC---CHHhhhcCCCCCHHHHHHHHHHh
Q 017612 239 GSLSHIMDA---SMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 239 GSLk~I~~A---S~EELa~VPGIG~kKA~rI~e~F 270 (368)
++|.+|... +.++|..|+|||++|+++--+.|
T Consensus 561 ~tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~ 595 (607)
T PRK11057 561 ATLIEMAEQMPITASEMLSVNGVGQRKLERFGKPF 595 (607)
T ss_pred HHHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHH
Confidence 356666644 89999999999999998754433
No 241
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=25.24 E-value=41 Score=30.52 Aligned_cols=20 Identities=40% Similarity=0.611 Sum_probs=17.6
Q ss_pred HhhhcCCCCCHHHHHHHHHH
Q 017612 250 EDLARCPGIGERKVKRLYDT 269 (368)
Q Consensus 250 EELa~VPGIG~kKA~rI~e~ 269 (368)
+||..|.|||++.+..|.+.
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 79999999999999988764
No 242
>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=25.22 E-value=74 Score=24.85 Aligned_cols=40 Identities=18% Similarity=0.292 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHhcCC-HHHHHcCCHHhhhcCCCCCHHHHHHHH
Q 017612 225 SVNKTDVVTLGSTFGS-LSHIMDASMEDLARCPGIGERKVKRLY 267 (368)
Q Consensus 225 gVnKTDA~~LLs~FGS-Lk~I~~AS~EELa~VPGIG~kKA~rI~ 267 (368)
.||+. +...++.|.+ +++++.++-.+|... || +.+.++..
T Consensus 7 ~IGR~-~~~~~~kf~~~w~~lf~~~s~~LK~~-GI-p~r~Rryi 47 (57)
T PF09597_consen 7 LIGRG-CEEHAEKFESDWEKLFTTSSKQLKEL-GI-PVRQRRYI 47 (57)
T ss_pred HHccc-HHHHHHHHHHHHHHHHhcCHHHHHHC-CC-CHHHHHHH
Confidence 34543 4778889999 999999999999887 99 55555543
No 243
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=24.77 E-value=1e+02 Score=29.25 Aligned_cols=53 Identities=15% Similarity=0.218 Sum_probs=32.5
Q ss_pred HHhhccCCCCCHHHHHHHHH-----hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhccc
Q 017612 217 THALTSVRSVNKTDVVTLGS-----TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEP 273 (368)
Q Consensus 217 ~saLTsIpgVnKTDA~~LLs-----~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~eP 273 (368)
++.|.=+|||||+....+|. -|.|+++|-+ -+..+...=+..|+||.+=+..+
T Consensus 115 lH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~----Rv~gl~~p~~~i~~RIl~EL~~~ 172 (181)
T PF04919_consen 115 LHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE----RVKGLHDPVKLIVERILEELQGE 172 (181)
T ss_dssp SBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH----HSTT---HHHHHHHHHHHHHH-T
T ss_pred HHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH----HhccCCCHHHHHHHHHHHHHcCC
Confidence 46777889999999999997 5999999872 22223333456788888877654
No 244
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.72 E-value=89 Score=32.24 Aligned_cols=102 Identities=14% Similarity=0.244 Sum_probs=63.4
Q ss_pred hccceEeeecccceEeccceeeeeec-----hhhHHHHHHHHHHhhcCCc--chhcccccccHHHHHHHhhccCCCCC-H
Q 017612 157 RNVRWAFADVVCDYLVGQNSCALYLS-----LEECGRYLETIKVYENKPA--DLIQGQMDTDYLSRLTHALTSVRSVN-K 228 (368)
Q Consensus 157 rnVpwefaDIvpDY~Ig~ttcILFLS-----~EEAArYIEt~K~~E~K~~--d~Irek~e~dy~srL~saLTsIpgVn-K 228 (368)
|..||....- | | -+++| .--++..|..|.++-++=+ ..+-... ..++|.-..|+| -
T Consensus 24 R~LPWR~~~~-P-Y-------~VwvSEiMLQQT~v~~Vi~yy~~fl~rfPti~~LA~A~-------~~evl~~W~gLGYy 87 (342)
T COG1194 24 RDLPWRETKD-P-Y-------RVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAP-------EDEVLKAWEGLGYY 87 (342)
T ss_pred CcCCCCCCCC-c-c-------eehhHHHHhhhccHhhhhhhHHHHHHhCCCHHHHhcCC-------HHHHHHHHHhcChH
Confidence 3577776532 2 3 23445 5556777887877744333 2222222 123444455899 8
Q ss_pred HHHHHHHHhcCCHHH----HHcCCHHhhhcCCCCCHHHHHHHHHH-hcccc
Q 017612 229 TDVVTLGSTFGSLSH----IMDASMEDLARCPGIGERKVKRLYDT-FHEPF 274 (368)
Q Consensus 229 TDA~~LLs~FGSLk~----I~~AS~EELa~VPGIG~kKA~rI~e~-F~ePF 274 (368)
..|++|-+-=.-+.+ ++--+.++|..+||||.-.|..|..+ |+.++
T Consensus 88 sRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~ 138 (342)
T COG1194 88 SRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQPE 138 (342)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCC
Confidence 888888765333322 33447899999999999999999775 55555
No 245
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=24.24 E-value=75 Score=33.92 Aligned_cols=25 Identities=16% Similarity=0.470 Sum_probs=24.1
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHc
Q 017612 222 SVRSVNKTDVVTLGSTFGSLSHIMD 246 (368)
Q Consensus 222 sIpgVnKTDA~~LLs~FGSLk~I~~ 246 (368)
+|+|||+..|..|++.+|++++|+.
T Consensus 233 ~I~Gig~~~al~lir~~~~i~~ile 257 (449)
T KOG2519|consen 233 TIRGIGPKKALKLIRQHGDIENILE 257 (449)
T ss_pred cccccChHHHHHHHHHhcCHHHHhh
Confidence 4999999999999999999999998
No 246
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=24.01 E-value=91 Score=34.94 Aligned_cols=24 Identities=29% Similarity=0.559 Sum_probs=21.9
Q ss_pred CHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 248 SMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 248 S~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-..+|..|||||++++++|++.|.
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhC
Confidence 357899999999999999999996
No 247
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.74 E-value=1e+02 Score=31.86 Aligned_cols=40 Identities=15% Similarity=0.272 Sum_probs=24.7
Q ss_pred HHHHHHhcCCHHHHHcCCHHh-hhcCCCCC-HHHHHHHHHHh
Q 017612 231 VVTLGSTFGSLSHIMDASMED-LARCPGIG-ERKVKRLYDTF 270 (368)
Q Consensus 231 A~~LLs~FGSLk~I~~AS~EE-La~VPGIG-~kKA~rI~e~F 270 (368)
=.+-+++|-+++.+.+|+.+| |..-.|+| ..+|++|++.-
T Consensus 56 y~~fl~rfPti~~LA~A~~~evl~~W~gLGYysRArnL~~~A 97 (342)
T COG1194 56 YERFLERFPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAA 97 (342)
T ss_pred HHHHHHhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHH
Confidence 355666677777777776655 44556677 66666665543
No 248
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=23.41 E-value=31 Score=31.91 Aligned_cols=46 Identities=17% Similarity=0.257 Sum_probs=36.8
Q ss_pred HHHHHhhccCCCCCHHHHHHHHHhcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 214 SRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 214 srL~saLTsIpgVnKTDA~~LLs~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
..+..+|++|.|||+..|...+++-+ |....|+|+.++..|...+.
T Consensus 24 ~~V~fAl~~i~Gig~~~A~~ic~K~~------------~~~~~r~gelt~~qi~~i~~ 69 (152)
T KOG3311|consen 24 RKVTFALTSIKGIGRRYAEIVCKKAD------------LDLTKRAGELTEEQILRILQ 69 (152)
T ss_pred ceeEEEEEEEeeechhhhhhhhhhcC------------cchhhhhccccHHHHHHHHH
Confidence 44667999999999999999999866 66777788888777766554
No 249
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=23.32 E-value=1.2e+02 Score=29.12 Aligned_cols=50 Identities=18% Similarity=0.340 Sum_probs=38.7
Q ss_pred hhccCCCCCHHHHHHHHH-hcCCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 219 ALTSVRSVNKTDVVTLGS-TFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 219 aLTsIpgVnKTDA~~LLs-~FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
-|+.++|||+..+..|.. -+.++.+|.+.+..+|... +| ..+..+++.++
T Consensus 172 pl~~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~--~g-~~~~~l~~~~~ 222 (334)
T cd03586 172 PVRKIPGVGKVTAEKLKELGIKTIGDLAKLDVELLKKL--FG-KSGRRLYELAR 222 (334)
T ss_pred CchhhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHHHHH--Hh-HHHHHHHHHhC
Confidence 456778999999887765 3779999999999999985 34 46677777664
No 250
>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=22.51 E-value=90 Score=25.20 Aligned_cols=24 Identities=29% Similarity=0.617 Sum_probs=18.6
Q ss_pred hhcCCCCCHHHHHHHHHHh-ccccc
Q 017612 252 LARCPGIGERKVKRLYDTF-HEPFK 275 (368)
Q Consensus 252 La~VPGIG~kKA~rI~e~F-~ePF~ 275 (368)
|..|.|||+..|++|.+.- +.||.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~ 53 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFK 53 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-S
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCC
Confidence 7899999999999998766 55665
No 251
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=22.23 E-value=59 Score=29.52 Aligned_cols=51 Identities=14% Similarity=0.042 Sum_probs=40.7
Q ss_pred HhhccCCCCCHHHHHHHHHh-cCCHHHHHcCCHHhhhcCCCCCHHHHHHHHH
Q 017612 218 HALTSVRSVNKTDVVTLGST-FGSLSHIMDASMEDLARCPGIGERKVKRLYD 268 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~-FGSLk~I~~AS~EELa~VPGIG~kKA~rI~e 268 (368)
+-|+-|.|||++....|-.+ -=++.+|...+.+|+..|.+.=..+.+..++
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l~f~GRi~RD 118 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELGIFTFAQIAAWTRADIAWIDDYLNFDGRIERD 118 (133)
T ss_pred ccchhhcccCHHHHHHHHHcCCccHHHHHhcCHHHHHHHHhhcCCcchhHHH
Confidence 46888999999998888764 3378999999999999888776666666655
No 252
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=21.85 E-value=1.2e+02 Score=30.38 Aligned_cols=56 Identities=18% Similarity=0.284 Sum_probs=44.2
Q ss_pred ccHHHHHHHhhccCCCCCHHHHHHHHHhc-CCHHHHHcCCHHhhhcCCCCCHHHHHHHHHHh
Q 017612 210 TDYLSRLTHALTSVRSVNKTDVVTLGSTF-GSLSHIMDASMEDLARCPGIGERKVKRLYDTF 270 (368)
Q Consensus 210 ~dy~srL~saLTsIpgVnKTDA~~LLs~F-GSLk~I~~AS~EELa~VPGIG~kKA~rI~e~F 270 (368)
.++...+ .++.++|||+..+..|-..- .++.++...+.+.|... +|... .+|+..-
T Consensus 170 ~~~l~~L--pv~~~~GvG~~~~~~l~~~Gi~ti~dl~~~~~~~L~~~--~g~~~-~~l~~~a 226 (354)
T COG0389 170 PALLWQL--PVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKKR--FGKLG-ERLYRLA 226 (354)
T ss_pred HHHHhcC--ChhhhCCCCHHHHHHHHHcCChhHHHHHhcCHHHHHHH--HhHhH-HHHHHHh
Confidence 3444444 55689999999998887764 78999999999999988 88888 8888743
No 253
>PHA00439 exonuclease
Probab=21.56 E-value=71 Score=32.03 Aligned_cols=29 Identities=3% Similarity=0.195 Sum_probs=22.9
Q ss_pred HhhccCCCCCHHHHHHHHHh---cCCHHHHHcC
Q 017612 218 HALTSVRSVNKTDVVTLGST---FGSLSHIMDA 247 (368)
Q Consensus 218 saLTsIpgVnKTDA~~LLs~---FGSLk~I~~A 247 (368)
+-+.+||||| +.|..||.+ |-.++.++.-
T Consensus 188 DNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 188 DGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred cCCCCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 3567999999 999999999 7666666644
No 254
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=20.39 E-value=61 Score=32.55 Aligned_cols=29 Identities=14% Similarity=0.258 Sum_probs=21.1
Q ss_pred HHHHHcCCHHhhhcCCCCCHHHHHHHHHHhc
Q 017612 241 LSHIMDASMEDLARCPGIGERKVKRLYDTFH 271 (368)
Q Consensus 241 Lk~I~~AS~EELa~VPGIG~kKA~rI~e~F~ 271 (368)
+.-|+..+ ....|+|||+++|-+|.+-+.
T Consensus 229 ~~iL~G~d--yn~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 229 IAILVGTD--YNEGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred HHHhcCCC--CCCCCCCccHHHHHHHHHHcC
Confidence 34444443 348999999999999987654
No 255
>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=20.20 E-value=65 Score=33.33 Aligned_cols=41 Identities=22% Similarity=0.267 Sum_probs=32.4
Q ss_pred HHHHHHhcCCHHHH-HcCCHHhhhcCCCCCHHHHHHHHHHhcccc
Q 017612 231 VVTLGSTFGSLSHI-MDASMEDLARCPGIGERKVKRLYDTFHEPF 274 (368)
Q Consensus 231 A~~LLs~FGSLk~I-~~AS~EELa~VPGIG~kKA~rI~e~F~ePF 274 (368)
-.+|+++||+==+| .++..|||+.+ + ++.|+.|..+=....
T Consensus 320 ~~~l~~~fG~E~~iL~~~~~eel~~~--~-~~~a~~I~~~R~G~v 361 (374)
T TIGR00375 320 WEKLKKAFGTEIAVLHEAAEEDLARV--V-PKVAALIVKFRSGKL 361 (374)
T ss_pred HHHHHHHhccHHHHHhcCCHHHHHHH--H-HHHHHHHHHHHCCCE
Confidence 56899999995554 58899999998 4 999999988765443
Done!