Query 039604
Match_columns 373
No_of_seqs 194 out of 1560
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 11:18:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1918 3-methyladenine DNA gl 100.0 3.4E-48 7.4E-53 357.7 17.0 225 110-334 25-251 (254)
2 COG0122 AlkA 3-methyladenine D 100.0 1.7E-44 3.6E-49 350.4 22.9 203 119-327 70-277 (285)
3 PRK10308 3-methyl-adenine DNA 100.0 1.7E-41 3.7E-46 329.2 22.1 191 118-324 78-276 (283)
4 TIGR00588 ogg 8-oxoguanine DNA 100.0 4.3E-41 9.3E-46 330.1 22.6 206 118-326 78-307 (310)
5 cd00056 ENDO3c endonuclease II 100.0 3.7E-31 8E-36 233.8 14.9 152 161-322 1-157 (158)
6 COG0177 Nth Predicted EndoIII- 100.0 2.2E-29 4.8E-34 234.5 19.4 192 139-361 7-208 (211)
7 TIGR01083 nth endonuclease III 100.0 3.5E-29 7.7E-34 229.8 19.6 168 140-322 5-177 (191)
8 KOG2875 8-oxoguanine DNA glyco 100.0 8.1E-29 1.7E-33 236.2 13.4 199 118-321 78-298 (323)
9 PRK10702 endonuclease III; Pro 100.0 1E-27 2.2E-32 224.0 18.1 190 141-358 9-205 (211)
10 PRK13913 3-methyladenine DNA g 99.9 5.4E-27 1.2E-31 220.1 17.8 153 148-307 18-176 (218)
11 smart00478 ENDO3c endonuclease 99.9 5.8E-27 1.2E-31 205.5 15.2 140 169-322 1-147 (149)
12 TIGR01084 mutY A/G-specific ad 99.9 7E-26 1.5E-30 219.3 19.8 191 142-360 6-208 (275)
13 PRK10880 adenine DNA glycosyla 99.9 6.2E-24 1.3E-28 211.8 19.4 188 142-360 10-212 (350)
14 PRK01229 N-glycosylase/DNA lya 99.9 5.7E-21 1.2E-25 178.2 17.9 165 142-324 18-203 (208)
15 PRK13910 DNA glycosylase MutY; 99.8 3.7E-20 8.1E-25 180.5 14.5 162 169-359 1-169 (289)
16 COG2231 Uncharacterized protei 99.8 2.9E-19 6.2E-24 164.9 15.3 158 140-307 10-171 (215)
17 KOG1921 Endonuclease III [Repl 99.8 2.6E-18 5.7E-23 162.0 15.6 208 124-360 37-261 (286)
18 PF00730 HhH-GPD: HhH-GPD supe 99.8 5.3E-18 1.2E-22 140.9 12.2 103 165-310 1-108 (108)
19 TIGR03252 uncharacterized HhH- 99.7 2E-17 4.4E-22 150.6 12.9 125 157-287 15-151 (177)
20 COG1194 MutY A/G-specific DNA 99.7 1.5E-15 3.2E-20 150.3 15.2 162 144-324 17-191 (342)
21 KOG2457 A/G-specific adenine D 98.8 4.4E-08 9.6E-13 98.3 12.6 162 159-349 124-298 (555)
22 COG1059 Thermostable 8-oxoguan 98.5 2E-06 4.4E-11 79.3 11.7 151 156-323 35-204 (210)
23 PF00633 HHH: Helix-hairpin-he 97.5 7.7E-05 1.7E-09 49.4 3.0 21 247-267 10-30 (30)
24 PF07934 OGG_N: 8-oxoguanine D 97.5 8E-05 1.7E-09 63.2 3.0 49 115-164 69-117 (117)
25 smart00278 HhH1 Helix-hairpin- 94.1 0.033 7.1E-07 35.3 1.8 20 249-268 2-21 (26)
26 PRK13901 ruvA Holliday junctio 91.4 0.4 8.7E-06 45.0 5.6 25 247-271 106-130 (196)
27 PF06029 AlkA_N: AlkA N-termin 90.3 0.084 1.8E-06 45.4 0.0 37 118-157 78-114 (116)
28 PF12826 HHH_2: Helix-hairpin- 90.3 0.57 1.2E-05 35.8 4.6 36 228-267 19-54 (64)
29 PRK14606 ruvA Holliday junctio 90.1 0.43 9.2E-06 44.4 4.5 22 247-268 107-128 (188)
30 PRK14601 ruvA Holliday junctio 89.8 0.46 1E-05 44.0 4.5 24 247-270 107-130 (183)
31 PRK14602 ruvA Holliday junctio 89.1 0.55 1.2E-05 44.1 4.5 21 247-267 108-128 (203)
32 PRK13844 recombination protein 89.1 0.35 7.7E-06 45.5 3.2 31 243-273 10-40 (200)
33 PRK00076 recR recombination pr 89.0 0.36 7.8E-06 45.3 3.1 31 243-273 6-36 (196)
34 PRK14603 ruvA Holliday junctio 88.9 0.59 1.3E-05 43.7 4.5 21 247-267 106-126 (197)
35 TIGR00624 tag DNA-3-methyladen 88.8 13 0.00028 34.5 13.1 74 153-229 23-102 (179)
36 TIGR00615 recR recombination p 88.7 0.46 9.9E-06 44.6 3.6 31 243-273 6-36 (195)
37 PRK14604 ruvA Holliday junctio 88.4 0.67 1.5E-05 43.3 4.5 22 247-268 107-128 (195)
38 PF14520 HHH_5: Helix-hairpin- 87.4 1.1 2.3E-05 33.6 4.3 32 231-266 25-56 (60)
39 COG0353 RecR Recombinational D 86.6 0.65 1.4E-05 43.6 3.3 30 243-272 7-36 (198)
40 PF14716 HHH_8: Helix-hairpin- 85.5 3.1 6.7E-05 32.0 6.1 46 211-265 18-64 (68)
41 COG0632 RuvA Holliday junction 85.3 1 2.2E-05 42.5 4.0 26 247-272 107-132 (201)
42 PRK14600 ruvA Holliday junctio 84.7 1.1 2.5E-05 41.5 3.9 20 247-267 107-126 (186)
43 PRK14605 ruvA Holliday junctio 83.4 2.4 5.2E-05 39.5 5.5 19 247-265 107-125 (194)
44 TIGR00084 ruvA Holliday juncti 83.0 1.8 3.8E-05 40.3 4.5 21 247-267 106-126 (191)
45 PF14520 HHH_5: Helix-hairpin- 83.0 1.1 2.4E-05 33.5 2.6 27 245-271 2-28 (60)
46 smart00483 POLXc DNA polymeras 82.5 2.3 4.9E-05 42.8 5.4 50 221-272 61-111 (334)
47 PF11731 Cdd1: Pathogenicity l 82.5 1.2 2.5E-05 37.2 2.7 61 244-322 8-69 (93)
48 PF12836 HHH_3: Helix-hairpin- 81.1 2.5 5.4E-05 32.3 4.0 52 200-264 8-60 (65)
49 TIGR00084 ruvA Holliday juncti 81.1 1.2 2.6E-05 41.4 2.6 27 239-265 63-89 (191)
50 PF02371 Transposase_20: Trans 80.6 1.4 3E-05 35.5 2.5 41 248-294 2-42 (87)
51 PRK14605 ruvA Holliday junctio 80.3 1.3 2.8E-05 41.3 2.6 28 239-266 64-91 (194)
52 cd00141 NT_POLXc Nucleotidyltr 80.2 5 0.00011 39.8 6.8 47 223-272 60-107 (307)
53 TIGR00575 dnlj DNA ligase, NAD 78.5 10 0.00022 41.8 9.0 29 196-224 456-485 (652)
54 PRK07956 ligA NAD-dependent DN 76.7 12 0.00026 41.3 8.9 20 248-267 543-562 (665)
55 PRK14973 DNA topoisomerase I; 76.4 8.8 0.00019 44.0 8.0 85 194-280 823-909 (936)
56 PRK10353 3-methyl-adenine DNA 76.3 20 0.00044 33.5 9.1 89 138-229 9-103 (187)
57 TIGR00608 radc DNA repair prot 74.7 2.7 5.7E-05 40.0 2.9 52 215-270 27-83 (218)
58 PF10391 DNA_pol_lambd_f: Fing 74.4 2.8 6.1E-05 31.1 2.4 24 247-270 1-24 (52)
59 PRK02515 psbU photosystem II c 73.9 7.5 0.00016 34.4 5.3 50 199-265 54-104 (132)
60 PRK14601 ruvA Holliday junctio 73.6 2.6 5.6E-05 39.1 2.5 28 239-266 64-91 (183)
61 PRK14606 ruvA Holliday junctio 73.5 2.7 5.8E-05 39.1 2.6 28 239-266 64-91 (188)
62 PRK00116 ruvA Holliday junctio 72.8 3.5 7.6E-05 38.2 3.2 22 244-265 69-90 (192)
63 PRK13901 ruvA Holliday junctio 72.5 2.9 6.2E-05 39.3 2.6 28 239-266 63-90 (196)
64 PRK14350 ligA NAD-dependent DN 72.3 13 0.00028 41.1 7.8 21 247-267 540-560 (669)
65 PRK14603 ruvA Holliday junctio 72.2 2.3 5E-05 39.8 1.8 27 240-266 64-90 (197)
66 PF03352 Adenine_glyco: Methyl 71.8 15 0.00032 34.1 7.0 89 138-229 4-98 (179)
67 PRK14604 ruvA Holliday junctio 71.1 3.1 6.7E-05 38.9 2.4 28 239-266 64-91 (195)
68 PRK14600 ruvA Holliday junctio 69.7 3.5 7.5E-05 38.3 2.4 26 241-266 66-91 (186)
69 PF09597 IGR: IGR protein moti 69.1 8.4 0.00018 29.3 3.9 37 195-231 20-57 (57)
70 PRK13482 DNA integrity scannin 68.5 10 0.00022 38.7 5.7 48 180-232 298-346 (352)
71 PRK14602 ruvA Holliday junctio 68.2 4 8.6E-05 38.4 2.5 27 240-266 66-92 (203)
72 PRK00116 ruvA Holliday junctio 67.2 14 0.00029 34.3 5.8 21 247-267 107-127 (192)
73 PF11798 IMS_HHH: IMS family H 67.0 3.9 8.5E-05 27.2 1.6 15 250-264 13-27 (32)
74 PRK00024 hypothetical protein; 65.7 16 0.00035 34.8 6.2 59 163-226 28-87 (224)
75 smart00483 POLXc DNA polymeras 64.8 14 0.0003 37.2 5.8 46 211-265 20-65 (334)
76 PRK00024 hypothetical protein; 64.7 8.6 0.00019 36.6 4.1 47 215-265 37-83 (224)
77 PRK14973 DNA topoisomerase I; 64.1 73 0.0016 36.8 11.9 67 195-265 766-852 (936)
78 PRK08609 hypothetical protein; 63.8 17 0.00037 39.3 6.6 42 223-265 63-105 (570)
79 PF03118 RNA_pol_A_CTD: Bacter 63.7 9.8 0.00021 29.4 3.5 31 231-265 31-61 (66)
80 PRK08097 ligB NAD-dependent DN 63.3 24 0.00053 38.2 7.6 68 196-267 449-539 (562)
81 PRK07945 hypothetical protein; 62.9 12 0.00025 37.7 4.9 53 208-266 14-67 (335)
82 TIGR01259 comE comEA protein. 62.9 19 0.00042 30.9 5.6 57 198-267 60-117 (120)
83 PRK07758 hypothetical protein; 62.3 15 0.00032 30.9 4.5 31 231-265 54-84 (95)
84 PF12836 HHH_3: Helix-hairpin- 62.0 8.4 0.00018 29.3 2.9 22 247-268 13-34 (65)
85 smart00279 HhH2 Helix-hairpin- 60.3 6.5 0.00014 27.0 1.8 18 248-265 16-33 (36)
86 TIGR00426 competence protein C 59.8 13 0.00027 28.5 3.5 54 200-267 10-66 (69)
87 PRK14351 ligA NAD-dependent DN 59.2 42 0.00091 37.3 8.7 29 235-267 551-579 (689)
88 COG0632 RuvA Holliday junction 58.6 5.1 0.00011 37.8 1.3 25 242-266 67-91 (201)
89 TIGR00608 radc DNA repair prot 57.2 29 0.00062 33.1 6.1 58 164-226 19-81 (218)
90 COG1555 ComEA DNA uptake prote 56.9 25 0.00054 31.5 5.4 53 201-266 92-145 (149)
91 TIGR01259 comE comEA protein. 55.4 12 0.00025 32.3 3.0 22 247-268 67-88 (120)
92 cd00080 HhH2_motif Helix-hairp 53.4 7 0.00015 30.8 1.1 22 248-270 22-43 (75)
93 TIGR01448 recD_rel helicase, p 52.2 27 0.00059 38.8 5.9 73 242-321 76-150 (720)
94 COG1555 ComEA DNA uptake prote 51.2 14 0.00029 33.2 2.8 28 240-268 90-117 (149)
95 KOG2534 DNA polymerase IV (fam 47.7 40 0.00087 34.2 5.7 44 228-271 76-120 (353)
96 PRK02515 psbU photosystem II c 46.0 18 0.00038 32.1 2.6 20 247-266 60-79 (132)
97 TIGR01448 recD_rel helicase, p 46.0 57 0.0012 36.3 7.2 20 250-270 183-202 (720)
98 cd00141 NT_POLXc Nucleotidyltr 45.6 29 0.00063 34.5 4.4 47 212-267 18-64 (307)
99 COG1948 MUS81 ERCC4-type nucle 44.9 80 0.0017 31.0 7.1 84 218-309 147-235 (254)
100 COG1379 PHP family phosphoeste 44.5 77 0.0017 32.5 7.1 49 158-210 303-351 (403)
101 PF00416 Ribosomal_S13: Riboso 44.2 21 0.00045 30.0 2.7 22 246-267 13-34 (107)
102 COG1796 POL4 DNA polymerase IV 43.1 32 0.0007 34.8 4.2 48 212-267 23-72 (326)
103 COG2818 Tag 3-methyladenine DN 43.0 1.1E+02 0.0024 28.8 7.4 76 151-229 23-104 (188)
104 COG2003 RadC DNA repair protei 38.8 28 0.00062 33.5 3.0 56 201-261 22-79 (224)
105 PRK12766 50S ribosomal protein 38.1 74 0.0016 30.8 5.7 52 212-274 10-61 (232)
106 PF12826 HHH_2: Helix-hairpin- 37.7 55 0.0012 24.8 3.9 39 181-224 15-54 (64)
107 PRK08609 hypothetical protein; 37.3 52 0.0011 35.6 5.1 46 211-265 20-65 (570)
108 TIGR00375 conserved hypothetic 36.8 67 0.0015 33.2 5.5 67 159-235 297-363 (374)
109 COG0177 Nth Predicted EndoIII- 36.5 2.1E+02 0.0046 27.3 8.4 104 159-272 70-185 (211)
110 PF01367 5_3_exonuc: 5'-3' exo 35.7 8.7 0.00019 32.4 -0.9 20 248-267 18-37 (101)
111 TIGR00426 competence protein C 35.4 41 0.0009 25.5 2.9 21 247-267 15-36 (69)
112 PRK13482 DNA integrity scannin 34.6 54 0.0012 33.6 4.3 37 223-263 298-334 (352)
113 TIGR02757 conserved hypothetic 34.3 47 0.001 32.0 3.7 31 274-306 173-205 (229)
114 PF14475 Mso1_Sec1_bdg: Sec1-b 33.3 30 0.00065 24.7 1.7 16 276-291 16-31 (41)
115 PF05559 DUF763: Protein of un 33.2 76 0.0016 32.1 5.1 22 247-268 268-289 (319)
116 PRK14667 uvrC excinuclease ABC 31.3 70 0.0015 34.8 4.8 29 196-224 536-564 (567)
117 PF09674 DUF2400: Protein of u 31.2 49 0.0011 31.9 3.3 60 218-306 145-208 (232)
118 KOG2841 Structure-specific end 30.9 73 0.0016 31.1 4.3 32 195-226 216-248 (254)
119 PF14229 DUF4332: Domain of un 29.8 2.8E+02 0.0061 23.7 7.5 24 247-270 52-75 (122)
120 PRK14666 uvrC excinuclease ABC 28.8 1.1E+02 0.0024 34.2 5.9 32 196-227 659-691 (694)
121 TIGR01954 nusA_Cterm_rpt trans 28.6 1.8E+02 0.0038 20.2 5.1 36 228-267 10-45 (50)
122 PRK05179 rpsM 30S ribosomal pr 28.5 32 0.0007 29.9 1.4 22 246-267 15-36 (122)
123 COG4277 Predicted DNA-binding 28.5 41 0.00088 34.2 2.3 20 247-266 329-348 (404)
124 CHL00137 rps13 ribosomal prote 28.4 33 0.00072 29.8 1.5 22 246-267 15-36 (122)
125 PRK12337 2-phosphoglycerate ki 27.9 4.1E+02 0.0089 28.5 9.7 154 120-289 130-297 (475)
126 TIGR01954 nusA_Cterm_rpt trans 27.6 2.1E+02 0.0046 19.8 5.7 34 194-227 14-48 (50)
127 KOG2534 DNA polymerase IV (fam 27.6 89 0.0019 31.9 4.5 43 216-267 33-75 (353)
128 PRK12766 50S ribosomal protein 26.5 1.3E+02 0.0029 29.1 5.3 42 182-228 16-59 (232)
129 COG1415 Uncharacterized conser 26.5 56 0.0012 33.5 2.9 22 247-268 277-298 (373)
130 PF00536 SAM_1: SAM domain (St 26.4 79 0.0017 23.2 3.1 21 227-247 23-43 (64)
131 PRK14976 5'-3' exonuclease; Pr 26.3 40 0.00086 33.2 1.8 23 248-271 191-213 (281)
132 PTZ00134 40S ribosomal protein 25.5 39 0.00085 30.7 1.4 22 246-267 28-49 (154)
133 PRK00254 ski2-like helicase; P 25.2 1.3E+02 0.0029 33.2 5.8 24 249-272 646-669 (720)
134 smart00475 53EXOc 5'-3' exonuc 24.8 46 0.00099 32.4 1.9 22 248-270 186-207 (259)
135 PF06568 DUF1127: Domain of un 24.6 53 0.0012 22.8 1.7 21 196-216 16-36 (40)
136 PRK09482 flap endonuclease-lik 24.5 46 0.001 32.5 1.9 22 248-270 182-203 (256)
137 COG1179 Dinucleotide-utilizing 24.5 63 0.0014 31.8 2.7 69 250-318 35-106 (263)
138 cd00008 53EXOc 5'-3' exonuclea 24.3 47 0.001 31.7 1.9 22 248-270 183-204 (240)
139 TIGR03629 arch_S13P archaeal r 24.1 42 0.0009 30.1 1.3 21 246-266 19-39 (144)
140 PF11239 DUF3040: Protein of u 23.6 1.5E+02 0.0033 23.5 4.4 26 127-152 10-35 (82)
141 PRK04053 rps13p 30S ribosomal 23.4 48 0.001 29.9 1.6 21 246-266 23-43 (149)
142 TIGR03631 bact_S13 30S ribosom 23.0 43 0.00094 28.7 1.2 22 246-267 13-34 (113)
143 COG0272 Lig NAD-dependent DNA 21.7 1.7E+02 0.0037 32.6 5.6 66 209-291 512-577 (667)
144 TIGR00575 dnlj DNA ligase, NAD 21.6 1.2E+02 0.0027 33.4 4.6 31 231-265 452-483 (652)
145 PRK14672 uvrC excinuclease ABC 21.5 1.5E+02 0.0031 33.3 5.1 36 194-229 628-664 (691)
146 COG0099 RpsM Ribosomal protein 21.1 63 0.0014 28.3 1.8 21 247-267 16-36 (121)
147 PRK14671 uvrC excinuclease ABC 20.6 1.5E+02 0.0032 32.6 5.0 30 242-272 563-592 (621)
148 PF11731 Cdd1: Pathogenicity l 20.5 1.4E+02 0.003 24.9 3.7 26 231-256 32-57 (93)
No 1
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=100.00 E-value=3.4e-48 Score=357.71 Aligned_cols=225 Identities=47% Similarity=0.788 Sum_probs=210.2
Q ss_pred hhcchhhhhcCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHh
Q 039604 110 QTLTVPRIIARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALC 189 (373)
Q Consensus 110 r~~~~~~~~~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~ 189 (373)
|.+.+...-+.+++.....+..+.||.+.||.|..++..+.++++...+.||+.|+++|++||++.++|++|+.||+..|
T Consensus 25 r~~~v~~~~~~~~s~~~k~e~al~hl~~kd~~L~~lv~~~~p~~~~~~q~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~ 104 (254)
T KOG1918|consen 25 RPLEVILPEKYILSHEEKAEIALSHLDEKDPSLVKLVGNHEPLTFKETQTPFERLIRAILSQQLSGKAANSIYNRFVSLC 104 (254)
T ss_pred CCcccccccccccccHHHHHHHHHhhhhcchHHHHHhcCCCCCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 55666666667888889999999999999999999999999899988999999999999999999999999999999999
Q ss_pred CC-CCCCCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHHcCC-CCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 190 GG-EAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGI-LSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 190 G~-~~~ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~~G~-l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
|+ ..|++|+.+..++.++|+.||||++|+.||+.+|+++.+|- .+.+.+.+|+.|++++.|+.++|||+||++|+|+|
T Consensus 105 ~g~~~~~~pe~i~~~~~~~lrkcG~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIf 184 (254)
T KOG1918|consen 105 GGAEKFPTPEFIDPLDCEELRKCGFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIF 184 (254)
T ss_pred CCCcCCCCchhcCcCCHHHHHHhCcchhhHHHHHHHHHHHhcCCCCchHHHhhcCHHHHHHHHHhccCccceeeeeeeee
Confidence 98 56899999999999999999999999999999999999994 57778899999999999999999999999999999
Q ss_pred hCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCCchHHHHHHHHHhhhhcCCCCchhh
Q 039604 268 SLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYLWRFVEAKGAPSSAAA 334 (373)
Q Consensus 268 ~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyrg~a~~yLW~~~~~~~~~~~~~~ 334 (373)
+|+|+||||++|++|+++++.+||+...+.+++|+++++.|+|||+++.||||+.++.+.-++...+
T Consensus 185 sL~R~DVmp~dDlgir~g~k~l~gl~~~p~~~evekl~e~~kpyRtvaawYlWki~~~~~~~k~~~~ 251 (254)
T KOG1918|consen 185 SLHRPDVMPADDLGIRNGVKKLLGLKPLPLPKEVEKLCEKCKPYRTVAAWYLWKIIKLDITEKCSET 251 (254)
T ss_pred ccCCCcccCchhhhHHHHHHHHhCCCCCCchHHHHHHhhhccchHHHHHHHHHhhhhhhccCCCccc
Confidence 9999999999999999999999999999999999999999999999999999999988776655543
No 2
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.7e-44 Score=350.45 Aligned_cols=203 Identities=36% Similarity=0.650 Sum_probs=177.6
Q ss_pred cCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCC-----
Q 039604 119 ARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEA----- 193 (373)
Q Consensus 119 ~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~----- 193 (373)
.++|++|.++..+++++- .++.+.. ++++.....|+||+||++|++||+|+++|.++++||+..||+..
T Consensus 70 ~~~~~lD~~l~~i~~~~~-~~~~~~~-----~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~ 143 (285)
T COG0122 70 RRLFDLDPDLAPIIDALG-PLPLLRA-----PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHS 143 (285)
T ss_pred HHHHhcCCcHHHHHHhcC-ccccccc-----cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccC
Confidence 345555555555554443 3333322 34444456899999999999999999999999999999999764
Q ss_pred CCCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCC
Q 039604 194 GVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPD 273 (373)
Q Consensus 194 ~ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpD 273 (373)
||+|++|+.++++.|+.||++++|++||+.+|+++.+|++++..+..|+++++++.|++|+|||||||+|+|||+|||+|
T Consensus 144 fptpe~l~~~~~~~l~~~g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~d 223 (285)
T COG0122 144 FPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPD 223 (285)
T ss_pred CCCHHHHHhcCHHHHHHhCCcHHHHHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCCchHHHHHHHHHhhhhcC
Q 039604 274 VLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYLWRFVEAKG 327 (373)
Q Consensus 274 vfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyrg~a~~yLW~~~~~~~ 327 (373)
+||++|++++++++++|+.+..++.+.++++.|.|+||+|||++|||++++...
T Consensus 224 vfP~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w~p~rs~A~~yLw~~~~~~~ 277 (285)
T COG0122 224 VFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERWGPYRSYAALYLWRYARATT 277 (285)
T ss_pred CCChHHHHHHHHHHHHhcCCCCchHHHHHHHHhcccCHHHHHHHHHHHhhhccc
Confidence 999999999999999997666777778899999999999999999999976433
No 3
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=1.7e-41 Score=329.17 Aligned_cols=191 Identities=23% Similarity=0.335 Sum_probs=175.4
Q ss_pred hcCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCC----
Q 039604 118 IARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEA---- 193 (373)
Q Consensus 118 ~~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~---- 193 (373)
+.++||||.|++.+++.| +.+++.++|+|+....|+||++|++||+||+|+++|.+++.+|+++||...
T Consensus 78 vrr~fdLd~d~~~i~~~L-------~~~~~~~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~ 150 (283)
T PRK10308 78 MSRLFDLQCNPQIVNGAL-------GKLGAARPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFP 150 (283)
T ss_pred HHHHcCCCCCHHHHHHHH-------HHHHHhCCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCC
Confidence 668999999999998765 568999999999989999999999999999999999999999999999742
Q ss_pred ----CCCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhC
Q 039604 194 ----GVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSL 269 (373)
Q Consensus 194 ----~ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~l 269 (373)
||+|++|+++++++|++|||+++|++||+++|+++.+|.++++.. .+.+++++.|++|||||||||+||+||+|
T Consensus 151 ~~~~FPtpe~La~~~~~eL~~~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~--~~~~~~~~~L~~LpGIGpwTA~~vllr~l 228 (283)
T PRK10308 151 EYVCFPTPERLAAADPQALKALGMPLKRAEALIHLANAALEGTLPLTIP--GDVEQAMKTLQTFPGIGRWTANYFALRGW 228 (283)
T ss_pred CccCCCCHHHHHcCCHHHHHHCCCCHHHHHHHHHHHHHHHcCCCCcccc--CCHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence 799999999999999999999999999999999999999987653 46789999999999999999999999999
Q ss_pred CCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCCchHHHHHHHHHhhh
Q 039604 270 HRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYLWRFVE 324 (373)
Q Consensus 270 grpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyrg~a~~yLW~~~~ 324 (373)
|++|+||.+|+||+|.+ .+ .++++++++.+.|+|||+|+++|||+...
T Consensus 229 g~~D~fp~~D~~l~~~~---~~----~~~~~~~~~a~~w~P~rsya~~~LW~~~~ 276 (283)
T PRK10308 229 QAKDVFLPDDYLIKQRF---PG----MTPAQIRRYAERWKPWRSYALLHIWYTEG 276 (283)
T ss_pred CCCCCCCcccHHHHHhc---cc----CCHHHHHHHHHhcCCHHHHHHHHHHHcCC
Confidence 99999999999999855 22 36789999999999999999999999854
No 4
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=100.00 E-value=4.3e-41 Score=330.05 Aligned_cols=206 Identities=16% Similarity=0.199 Sum_probs=184.7
Q ss_pred hcCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCC-----
Q 039604 118 IARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGE----- 192 (373)
Q Consensus 118 ~~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~----- 192 (373)
+.+||+||.|++.+++++...||.|+.+++.++|+|+.+. +|||+||++|||||+|+++|.+++.+|+++||..
T Consensus 78 ir~~f~Ld~d~~~i~~~~~~~D~~l~~~~~~~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~ 156 (310)
T TIGR00588 78 LEKYFQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGPRLITLD 156 (310)
T ss_pred HHHHhcCCCCHHHHHHHHhhcCHHHHHHHHhCCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCC
Confidence 6789999999999999987789999999999999999877 9999999999999999999999999999999943
Q ss_pred -----CCCCHHHHhcCCh-HHHHhcCCChhHHHHHHHHHHHHHcCCC---CchhhhCCChHHHHHHHhcCCCCCHHHHHH
Q 039604 193 -----AGVVPETVLALTP-QQLRQIGVSGRKASYLHDLARKYQNGIL---SDSAIVNMDDKSLFTMLTMVNGIGSWSVHM 263 (373)
Q Consensus 193 -----~~ptPe~La~l~~-eeLr~~Gls~~KA~yI~~lA~~i~~G~l---~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~ 263 (373)
.||+|++|+..+. ++|+.||| ++||+||+++|+++.+|.. +++.|.+++++++++.|++|||||+|||+|
T Consensus 157 g~~~~~FPtp~~La~~~~e~~Lr~~G~-g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~ 235 (310)
T TIGR00588 157 GVTYHGFPSLHALTGPEAEAHLRKLGL-GYRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADC 235 (310)
T ss_pred CcccccCCCHHHHhCCChHHHHHHcCC-HHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHH
Confidence 2799999998764 58999999 7899999999999998653 567788999999999999999999999999
Q ss_pred HHHHhCCCCCccCCCCHHHHHHHHHHhcCCCC---------CCHHHHHHH-HhhcCCchHHHHHHHHHhhhhc
Q 039604 264 FMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL---------PRPSQMDQL-CEKWRPYRSVASWYLWRFVEAK 326 (373)
Q Consensus 264 vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~---------~~~~e~~~l-~e~w~Pyrg~a~~yLW~~~~~~ 326 (373)
||||+|+++|+||+ |+||+|+++++||.... .+.+++.++ .+.|+||+|||+.|||++.+..
T Consensus 236 vll~~l~~~d~~Pv-D~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~~~~g~~ag~aq~~lf~~~~~~ 307 (310)
T TIGR00588 236 ICLMGLDKPQAVPV-DVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSLWGPYAGWAQAVLFSADLRQ 307 (310)
T ss_pred HHHHhCCCCCceee-cHHHHHHHHHHhcccccccccccCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhhc
Confidence 99999999999999 99999999999987431 234466664 5689999999999999997754
No 5
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.97 E-value=3.7e-31 Score=233.85 Aligned_cols=152 Identities=31% Similarity=0.441 Sum_probs=141.6
Q ss_pred HHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHhcCCC---hhHHHHHHHHHHHHHcCCCCchh
Q 039604 161 FLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQIGVS---GRKASYLHDLARKYQNGILSDSA 237 (373)
Q Consensus 161 fE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~Gls---~~KA~yI~~lA~~i~~G~l~L~~ 237 (373)
||+||++||+||+++++|..++.+|++.|| |+|+.|+.++.++|+.||.+ ++||++|+++|+.+.++..++..
T Consensus 1 ~e~Li~~il~q~~s~~~a~~~~~~l~~~~g----pt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~ 76 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNKAYERLFERYG----PTPEALAAADEEELRELIRSLGYRRKAKYLKELARAIVEGFGGLVL 76 (158)
T ss_pred CHHHHHHHHHhcccHHHHHHHHHHHHHHhC----CCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCccC
Confidence 799999999999999999999999999998 79999999999999988877 89999999999999987765443
Q ss_pred hhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcC--CchHHH
Q 039604 238 IVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWR--PYRSVA 315 (373)
Q Consensus 238 L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~--Pyrg~a 315 (373)
+++++++.|++|||||+|||+|+++|+++ .++||+ |+|++|+++++++....++++++.++++.|. ||++++
T Consensus 77 ----~~~~~~~~L~~l~GIG~~tA~~~l~~~~~-~~~~pv-D~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (158)
T cd00056 77 ----DDPDAREELLALPGVGRKTANVVLLFALG-PDAFPV-DTHVRRVLKRLGLIPKKKTPEELEELLEELLPKPYWGEA 150 (158)
T ss_pred ----CCcccHHHHHcCCCCCHHHHHHHHHHHCC-CCCCcc-chhHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHH
Confidence 77889999999999999999999999999 899999 9999999999987677788999999999998 999999
Q ss_pred HHHHHHh
Q 039604 316 SWYLWRF 322 (373)
Q Consensus 316 ~~yLW~~ 322 (373)
.+|||++
T Consensus 151 ~~~l~~~ 157 (158)
T cd00056 151 NQALMDL 157 (158)
T ss_pred HHHHHHc
Confidence 9999985
No 6
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.97 E-value=2.2e-29 Score=234.48 Aligned_cols=192 Identities=20% Similarity=0.264 Sum_probs=171.3
Q ss_pred ChHHHHHHHhCCCCCcCC-CCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCC
Q 039604 139 DRQLASLIDIHPPPTFDS-FHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGV 213 (373)
Q Consensus 139 Dp~La~li~~~gg~r~~~-~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gl 213 (373)
...+..+.+.++...... +.|||+.||.+|||||++++.++.++.+|.+.|+ +|++|+.+++++| +.+||
T Consensus 7 ~~i~~~l~~~~p~~~~~l~~~~pf~lLva~iLSaqttD~~vn~at~~Lf~~~~-----t~e~l~~a~~~~l~~~I~~iGl 81 (211)
T COG0177 7 LEILDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPALFKRYP-----TPEDLLNADEEELEELIKSIGL 81 (211)
T ss_pred HHHHHHHHHHCCCCCCccCcCCcHHHHHHHHHhccCchHHHHHHHHHHHHHcC-----CHHHHHcCCHHHHHHHHHhcCC
Confidence 345667778888776653 4899999999999999999999999999999985 8999999999876 57999
Q ss_pred ChhHHHHHHHHHHHHHc---CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHh
Q 039604 214 SGRKASYLHDLARKYQN---GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLY 290 (373)
Q Consensus 214 s~~KA~yI~~lA~~i~~---G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rly 290 (373)
+++||++|+.+|+.+.+ |++ ...+++|++|||||+|||++||.++||.+ +||| |+||+|+.+|+
T Consensus 82 yr~KAk~I~~~~~~l~e~~~g~v----------P~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~V-DTHV~Rvs~R~- 148 (211)
T COG0177 82 YRNKAKNIKELARILLEKFGGEV----------PDTREELLSLPGVGRKTANVVLSFAFGIP-AIAV-DTHVHRVSNRL- 148 (211)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCC----------CchHHHHHhCCCcchHHHHHHHHhhcCCC-cccc-cchHHHHHHHh-
Confidence 99999999999999996 443 34589999999999999999999999999 9999 99999999999
Q ss_pred cCCCCCCHHHHHHHHhhcCCchHHHHHHHHHhhhhcCCCCchhhhhhccCC--CCchhhhhhhhHHHHhhhhh
Q 039604 291 SLEELPRPSQMDQLCEKWRPYRSVASWYLWRFVEAKGAPSSAAAVAAGAAL--PQPQQEEQQQPQLLDQINSL 361 (373)
Q Consensus 291 gl~~~~~~~e~~~l~e~w~Pyrg~a~~yLW~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 361 (373)
|+....++.++++-...|-|..-|..+|.|- +.+|+.. .+.++|+.|.+..+||....
T Consensus 149 gl~~~~~p~~ve~~L~~~iP~~~~~~~h~~l-------------I~~GR~iC~ar~P~C~~C~l~~~C~~~~~ 208 (211)
T COG0177 149 GLVPGKTPEEVEEALMKLIPKELWTDLHHWL-------------ILHGRYICKARKPRCEECPLADLCPSAGK 208 (211)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHHHHHH-------------HHhhhhhccCCCCCcCcccchhhCchhcc
Confidence 9888889999999999999999999999997 4789985 78999999999999997654
No 7
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.97 E-value=3.5e-29 Score=229.79 Aligned_cols=168 Identities=19% Similarity=0.236 Sum_probs=145.1
Q ss_pred hHHHHHHHhCCCCCc-CCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCCC
Q 039604 140 RQLASLIDIHPPPTF-DSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGVS 214 (373)
Q Consensus 140 p~La~li~~~gg~r~-~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gls 214 (373)
.++..+.+.|++... ....|||+.||++||+||++++++.+++.+|.+.| ++|++|+.++.++| +.+||+
T Consensus 5 ~i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~-----pt~~~l~~~~~~~L~~~ir~~G~~ 79 (191)
T TIGR01083 5 EILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLFEVY-----PTPQALAQAGLEELEEYIKSIGLY 79 (191)
T ss_pred HHHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHC-----CCHHHHHcCCHHHHHHHHHhcCCh
Confidence 456677888886643 33579999999999999999999999999998876 68999999999997 789999
Q ss_pred hhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCC
Q 039604 215 GRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEE 294 (373)
Q Consensus 215 ~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~ 294 (373)
++||+||+++|+++.++. + .+.++.++.|++|||||+|||+|||+|+|++++ ||+ |+||+|+++|+ |+..
T Consensus 80 ~~Ka~~i~~~a~~i~~~~-~------~~~~~~~~~L~~l~GIG~ktA~~ill~~~~~~~-~~v-D~~v~Ri~~r~-g~~~ 149 (191)
T TIGR01083 80 RNKAKNIIALCRILVERY-G------GEVPEDREELVKLPGVGRKTANVVLNVAFGIPA-IAV-DTHVFRVSNRL-GLSK 149 (191)
T ss_pred HHHHHHHHHHHHHHHHHc-C------CCCchHHHHHHhCCCCcHHHHHHHHHHHcCCCc-ccc-chhHHHHHHHc-CCCC
Confidence 999999999999998642 1 122356899999999999999999999999985 999 99999999998 6665
Q ss_pred CCCHHHHHHHHhhcCCchHHHHHHHHHh
Q 039604 295 LPRPSQMDQLCEKWRPYRSVASWYLWRF 322 (373)
Q Consensus 295 ~~~~~e~~~l~e~w~Pyrg~a~~yLW~~ 322 (373)
..++++++++.+.|.|+..+..+|+|-.
T Consensus 150 ~~~~~~~~~~l~~~~p~~~~~~~h~~li 177 (191)
T TIGR01083 150 GKDPDKVEEELLKLIPREFWTKLHHWLI 177 (191)
T ss_pred CCCHHHHHHHHHHHCCchhHHHHHHHHH
Confidence 5678899999999999999999998853
No 8
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.96 E-value=8.1e-29 Score=236.15 Aligned_cols=199 Identities=18% Similarity=0.226 Sum_probs=172.0
Q ss_pred hcCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCC----
Q 039604 118 IARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEA---- 193 (373)
Q Consensus 118 ~~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~---- 193 (373)
+..||.+|.++...++++...|+.+.++.. .|.|+ .+++|||+|+++|||+|++++.+..|.++|+..||...
T Consensus 78 i~~yf~ldv~L~~l~~~W~~~D~~F~~la~--qgvRl-LrQdP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~d 154 (323)
T KOG2875|consen 78 ISKYFQLDVTLAQLYHHWGSVDDHFQELAQ--QGVRL-LRQDPIECLFSFICSSNNNIARITGMVERFCQAFGPRIIQLD 154 (323)
T ss_pred HHHHHhheeeHHHHHHHhCcCChHHHHHHH--hhhHH-HhcCcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeec
Confidence 668999999999999999999999999887 46666 57899999999999999999999999999999999753
Q ss_pred ------CCCHHHHh-cCChHHHHhcCCChhHHHHHHHHHHHHHc--CC-CCchhhhCCChHHHHHHHhcCCCCCHHHHHH
Q 039604 194 ------GVVPETVL-ALTPQQLRQIGVSGRKASYLHDLARKYQN--GI-LSDSAIVNMDDKSLFTMLTMVNGIGSWSVHM 263 (373)
Q Consensus 194 ------~ptPe~La-~l~~eeLr~~Gls~~KA~yI~~lA~~i~~--G~-l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~ 263 (373)
||+.+.|. ...+++||.+|| +|||+||...|+++.+ |. -.|..|+++++||+++.|+.+||||+|+|+|
T Consensus 155 g~~~h~FPsl~~L~g~~~Ea~LR~~gf-GYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADC 233 (323)
T KOG2875|consen 155 GVDYHGFPSLQALAGPEVEAELRKLGF-GYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADC 233 (323)
T ss_pred CcccccCccHHHhcCcHhHHHHHHcCc-chhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhh
Confidence 78888887 456788999999 9999999999999997 33 3477888999999999999999999999999
Q ss_pred HHHHhCCCCCccCCCCHHHHHHHHHHhc--CCCC--CCH---HHHHH-HHhhcCCchHHHHHHHHH
Q 039604 264 FMIFSLHRPDVLPINDLGVRKGVQLLYS--LEEL--PRP---SQMDQ-LCEKWRPYRSVASWYLWR 321 (373)
Q Consensus 264 vLLf~lgrpDvfPv~D~~VrR~l~rlyg--l~~~--~~~---~e~~~-l~e~w~Pyrg~a~~yLW~ 321 (373)
|++++|+...++|| |+||.|+.+.++. +... .++ .++.. +.+.|++|+|||+.+++.
T Consensus 234 I~Lm~l~~~~~VPV-DvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~~~~G~YAGwAQ~~lfs 298 (323)
T KOG2875|consen 234 ICLMSLDKLSAVPV-DVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFRSLWGEYAGWAQAVLFS 298 (323)
T ss_pred hhhhhcCCCCcccc-hhhHHHHhhcccCCCccccccCCcchhHHHHHHHHHHhcccccchhheeec
Confidence 99999999999999 9999999994432 2111 122 24444 567999999999999995
No 9
>PRK10702 endonuclease III; Provisional
Probab=99.96 E-value=1e-27 Score=224.04 Aligned_cols=190 Identities=16% Similarity=0.157 Sum_probs=156.7
Q ss_pred HHHHHHHhCCC-CCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHH----hcCCCh
Q 039604 141 QLASLIDIHPP-PTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLR----QIGVSG 215 (373)
Q Consensus 141 ~La~li~~~gg-~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr----~~Gls~ 215 (373)
++..+.+.|+. ..+....+|||.||.+|||||+++.++.+++.+|...| ++|++|++++.++|+ .+||++
T Consensus 9 i~~~l~~~~~~~~~~~~~~~p~e~lvs~iLsq~t~~~~v~~~~~~L~~~~-----pt~e~l~~a~~~~l~~~i~~~G~y~ 83 (211)
T PRK10702 9 ILTRLRDNNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVA-----NTPAAMLELGVEGVKTYIKTIGLYN 83 (211)
T ss_pred HHHHHHHHCCCCCCCCCCCChHHHHHHHHHHhhcCHHHHHHHHHHHHHHc-----CCHHHHHCCCHHHHHHHHHHcCCHH
Confidence 45667778875 34556889999999999999999999999999998776 689999999999875 589999
Q ss_pred hHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCC
Q 039604 216 RKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL 295 (373)
Q Consensus 216 ~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~ 295 (373)
+||++|+++|+.+.+.. +.+..+.+++|++|||||+|||++||+|+|+++ +||| |+||+|+++|+ |+...
T Consensus 84 ~kA~~l~~~a~~i~~~~-------~~~~p~~~~~Ll~lpGVG~ktA~~ill~a~~~~-~~~V-Dt~v~Rv~~r~-g~~~~ 153 (211)
T PRK10702 84 SKAENVIKTCRILLEQH-------NGEVPEDRAALEALPGVGRKTANVVLNTAFGWP-TIAV-DTHIFRVCNRT-QFAPG 153 (211)
T ss_pred HHHHHHHHHHHHHHHHc-------CCCCCchHHHHhcCCcccHHHHHHHHHHHcCCC-cccc-cchHHHHHHHh-CCCCC
Confidence 99999999999998521 112345689999999999999999999999996 7999 99999999999 55555
Q ss_pred CCHHHHHHHHhhcCCchHHHHHHHHHhhhhcCCCCchhhhhhccCC--CCchhhhhhhhHHHHhh
Q 039604 296 PRPSQMDQLCEKWRPYRSVASWYLWRFVEAKGAPSSAAAVAAGAAL--PQPQQEEQQQPQLLDQI 358 (373)
Q Consensus 296 ~~~~e~~~l~e~w~Pyrg~a~~yLW~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 358 (373)
.+++++++..+..-|..-+..+|.|- |.+|... ...++|++|.++-+|+.
T Consensus 154 ~~~~~~~~~l~~~lp~~~~~~~~~~l-------------i~~Gr~~C~~~~P~C~~Cpl~~~C~~ 205 (211)
T PRK10702 154 KNVEQVEEKLLKVVPAEFKVDCHHWL-------------ILHGRYTCIARKPRCGSCIIEDLCEY 205 (211)
T ss_pred CCHHHHHHHHHHhCCchHHHHHHHHH-------------HHHhHHHcCCCCCCCCCCcChhhcCc
Confidence 57778888777677776666666664 4577774 56899999999998874
No 10
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.95 E-value=5.4e-27 Score=220.07 Aligned_cols=153 Identities=18% Similarity=0.162 Sum_probs=130.0
Q ss_pred hCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhC--CCCCCCHHHHhcCChHHHHhc----CCChhHHHHH
Q 039604 148 IHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCG--GEAGVVPETVLALTPQQLRQI----GVSGRKASYL 221 (373)
Q Consensus 148 ~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G--~~~~ptPe~La~l~~eeLr~~----Gls~~KA~yI 221 (373)
.+++..|+...++||.||.+||+||++++++.+++.+|.+++. +..+++|+.|++++.++|+++ ||+++||+||
T Consensus 18 ~~~~~~WWp~~~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~L 97 (218)
T PRK13913 18 KNAPAWWWPNALKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRL 97 (218)
T ss_pred hcCCCCCCcCcCHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHH
Confidence 5666678889999999999999999999999999999988742 122468999999999998765 9999999999
Q ss_pred HHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHH
Q 039604 222 HDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQM 301 (373)
Q Consensus 222 ~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~ 301 (373)
+++|+.+.++..+++ .+..++.+++|++|||||+|||++||+|+|+++ +|+| |+|++|+++|+ |+.. .++.++
T Consensus 98 k~la~~i~~~~g~~~---~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp-~fvV-Dty~~Rv~~Rl-G~~~-~~y~~~ 170 (218)
T PRK13913 98 IDLSENILKDFGSFE---NFKQEVTREWLLDQKGIGKESADAILCYVCAKE-VMVV-DKYSYLFLKKL-GIEI-EDYDEL 170 (218)
T ss_pred HHHHHHHHHHcCCch---hccCchHHHHHHcCCCccHHHHHHHHHHHcCCC-cccc-chhHHHHHHHc-CCCC-CCHHHH
Confidence 999999987433333 333456889999999999999999999999998 7999 99999999998 8864 467888
Q ss_pred HHHHhh
Q 039604 302 DQLCEK 307 (373)
Q Consensus 302 ~~l~e~ 307 (373)
+++.+.
T Consensus 171 ~~~~~~ 176 (218)
T PRK13913 171 QHFFEK 176 (218)
T ss_pred HHHHHH
Confidence 887664
No 11
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.95 E-value=5.8e-27 Score=205.46 Aligned_cols=140 Identities=24% Similarity=0.299 Sum_probs=124.7
Q ss_pred HhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCChH
Q 039604 169 LYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDK 244 (373)
Q Consensus 169 LsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~e 244 (373)
|+||++++++.+++.+|++.|| +|++|+.+++++| +.||++++|++||+++|+.+.+.. +.+.+
T Consensus 1 l~qq~~~~~a~~~~~~l~~~~~-----~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~-------~~~~~ 68 (149)
T smart00478 1 LSQQTSDEAVNKATERLFEKFP-----TPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEY-------GGEVP 68 (149)
T ss_pred CCCcccHHHHHHHHHHHHHHCC-----CHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH-------CCCcc
Confidence 5899999999999999999985 8999999999987 789999999999999999988631 11123
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCC---chHHHHHHHHH
Q 039604 245 SLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRP---YRSVASWYLWR 321 (373)
Q Consensus 245 e~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~P---yrg~a~~yLW~ 321 (373)
+.++.|++|||||+|||+|||+|++++ +++|+ |+||+|+++++|+.+..+++++++++++.|.| |++++++|+|+
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~-D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~ 146 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALGK-PFIPV-DTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPKEDWRELNLLLIDF 146 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCcc-chHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence 568999999999999999999999999 67777 99999999999877766778999999999999 99999999998
Q ss_pred h
Q 039604 322 F 322 (373)
Q Consensus 322 ~ 322 (373)
-
T Consensus 147 g 147 (149)
T smart00478 147 G 147 (149)
T ss_pred c
Confidence 4
No 12
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.94 E-value=7e-26 Score=219.33 Aligned_cols=191 Identities=17% Similarity=0.250 Sum_probs=151.9
Q ss_pred HHHHHHhCCC--CCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCCCh
Q 039604 142 LASLIDIHPP--PTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGVSG 215 (373)
Q Consensus 142 La~li~~~gg--~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gls~ 215 (373)
|-.+.+.++. ++|+...|||+.||++||+||++++++..++.+|.++| |+|++|+++++++| +.+|++
T Consensus 6 l~~w~~~~~r~~lpWr~~~dpy~vlvseIL~QQT~v~~v~~~~~rl~~~f-----pt~~~La~a~~eeL~~~~~~lG~y- 79 (275)
T TIGR01084 6 LLSWYDKYGRKTLPWRQNKTPYRVWLSEVMLQQTQVATVIPYFERFLERF-----PTVQALANAPQDEVLKLWEGLGYY- 79 (275)
T ss_pred HHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-----CCHHHHHCcCHHHHHHHHHHCCcH-
Confidence 4466666664 88988999999999999999999999999999999886 69999999999998 789997
Q ss_pred hHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCC
Q 039604 216 RKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL 295 (373)
Q Consensus 216 ~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~ 295 (373)
+||++|+++|+.+.+... ..++ +.++.|++|||||+|||+|||+|+|++++ +++ |+||+|+++|+||++..
T Consensus 80 ~RAr~L~~~A~~i~~~~~-----g~~p--~~~~~L~~LpGIG~~TA~~Il~~a~~~~~-~~v-D~~v~RVl~Rl~~~~~~ 150 (275)
T TIGR01084 80 ARARNLHKAAQEVVEEFG-----GEFP--QDFEDLAALPGVGRYTAGAILSFALNKPY-PIL-DGNVKRVLSRLFAVEGW 150 (275)
T ss_pred HHHHHHHHHHHHHHHHcC-----CCCc--HHHHHHHhCCCCCHHHHHHHHHHHCCCCC-Ccc-hHhHHHHHHHHccCcCC
Confidence 699999999999986210 0122 34899999999999999999999999995 456 99999999999998766
Q ss_pred CCHHHHHH----HHhhcCCchHHHHHHHHHhhhhcCCCCchhhhhhccCC--CCchhhhhhhhHHHHhhhh
Q 039604 296 PRPSQMDQ----LCEKWRPYRSVASWYLWRFVEAKGAPSSAAAVAAGAAL--PQPQQEEQQQPQLLDQINS 360 (373)
Q Consensus 296 ~~~~e~~~----l~e~w~Pyrg~a~~yLW~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 360 (373)
++.+++++ +++.+-|..-+..++ ..-|.+|... ...++|..|.++-+|+...
T Consensus 151 ~~~~~~~~~l~~~~~~~lp~~~~~~~n-------------~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~ 208 (275)
T TIGR01084 151 PGKKKVENRLWTLAESLLPKADPEAFN-------------QALMDLGAMICTRKKPKCDLCPLQDFCLAYQ 208 (275)
T ss_pred CCHHHHHHHHHHHHHHHCChhhHHHHH-------------HHHHHHhHHHcCCCCCCCCCCCChhhCHHHH
Confidence 65554444 367777653322222 1235567774 5689999998888887543
No 13
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.92 E-value=6.2e-24 Score=211.79 Aligned_cols=188 Identities=18% Similarity=0.214 Sum_probs=148.5
Q ss_pred HHHHHHhCC--CCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHH----hcCCCh
Q 039604 142 LASLIDIHP--PPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLR----QIGVSG 215 (373)
Q Consensus 142 La~li~~~g--g~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr----~~Gls~ 215 (373)
|-.+.+.++ .++|+...|||+.+|++||+||++++++..++.||.++| |++++|++++.++|. .+|++
T Consensus 10 ll~W~~~~~r~~lpWr~~~dpy~ilVseILlQQT~v~~v~~~~~rl~~~f-----Pt~~~La~a~~eel~~~~~glGyy- 83 (350)
T PRK10880 10 VLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARF-----PTVTDLANAPLDEVLHLWTGLGYY- 83 (350)
T ss_pred HHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhhccHHHHHHHHHHHHHHC-----cCHHHHHCcCHHHHHHHHHcCChH-
Confidence 445666766 467888899999999999999999999999999999986 689999999999976 58997
Q ss_pred hHHHHHHHHHHHHHc---CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcC
Q 039604 216 RKASYLHDLARKYQN---GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSL 292 (373)
Q Consensus 216 ~KA~yI~~lA~~i~~---G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl 292 (373)
+||++|+++|+.+.+ |.+ ++.++.|++|||||+|||++||+|+|+++ +++| |+||+|+++|+||+
T Consensus 84 ~RAr~L~~~A~~i~~~~~g~~----------p~~~~~L~~LpGIG~~TA~aIl~~af~~~-~~iV-D~nV~RV~~Rl~~i 151 (350)
T PRK10880 84 ARARNLHKAAQQVATLHGGEF----------PETFEEVAALPGVGRSTAGAILSLSLGKH-FPIL-DGNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHHhCCCc----------hhhHHHHhcCCCccHHHHHHHHHHHCCCC-eecc-cHHHHHHHHHHhcc
Confidence 499999999999964 332 35689999999999999999999999996 4445 99999999999998
Q ss_pred CCCCCHHHHH----HHHhhcCCchHHHHHHHHHhhhhcCCCCchhhhhhccCC--CCchhhhhhhhHHHHhhhh
Q 039604 293 EELPRPSQMD----QLCEKWRPYRSVASWYLWRFVEAKGAPSSAAAVAAGAAL--PQPQQEEQQQPQLLDQINS 360 (373)
Q Consensus 293 ~~~~~~~e~~----~l~e~w~Pyrg~a~~yLW~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 360 (373)
...++.++.+ ++.+.+-|-.-+..++ ..=|.+|... ...++|+.|.++-+|+...
T Consensus 152 ~~~~~~~~~~~~l~~~~~~l~p~~~~~~~n-------------qalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~ 212 (350)
T PRK10880 152 SGWPGKKEVENRLWQLSEQVTPAVGVERFN-------------QAMMDLGAMVCTRSKPKCELCPLQNGCIAYA 212 (350)
T ss_pred cCCCChHHHHHHHHHHHHHhCChhHHHHHH-------------HHHHHhhHHhccCCCCCCCCCccHhhhHHHH
Confidence 7655544443 3445555543222222 1235567774 6789999999999887643
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.87 E-value=5.7e-21 Score=178.24 Aligned_cols=165 Identities=18% Similarity=0.218 Sum_probs=126.6
Q ss_pred HHHHHHhCCC-CCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcC--CC
Q 039604 142 LASLIDIHPP-PTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIG--VS 214 (373)
Q Consensus 142 La~li~~~gg-~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~G--ls 214 (373)
+.+-++.|-. ..+....+||+.||.+||+||+++.++.++..+|. ++.+ .++.++| +.+| |+
T Consensus 18 ~~~r~~ef~~~~~~~~~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~----------~~~l-~~~~eeL~~~Ir~~Gygf~ 86 (208)
T PRK01229 18 VEERIEEFKLLGEKGDEEDLFSELSFCILTANSSAEGGIKAQKEIG----------DGFL-YLSEEELEEKLKEVGHRFY 86 (208)
T ss_pred HHHHHHHHHHhhhccccCChHHHHHHHHhcCcCcHHHHHHHHHhcC----------HHHc-CCCHHHHHHHHHHhhcccH
Confidence 3344444432 23336779999999999999999999999999983 2334 5666654 5675 99
Q ss_pred hhHHHHHHHHHHHHHcCCCCchhhh--CCChHHHHHHHh-cCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhc
Q 039604 215 GRKASYLHDLARKYQNGILSDSAIV--NMDDKSLFTMLT-MVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYS 291 (373)
Q Consensus 215 ~~KA~yI~~lA~~i~~G~l~L~~L~--~~~~ee~~~~L~-sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlyg 291 (373)
++||++|+++++.+ |.+ ..+. ..+.++++++|+ ++||||+|||++||+.... .++|+| |+||+|++.|+ |
T Consensus 87 ~~KAk~I~~~~~~~--~~l--~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~-~~~~iV-DtHv~Ri~~Rl-G 159 (208)
T PRK01229 87 NKRAEYIVEARKLY--GKL--KEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGY-EDLAIL-DRHILRFLKRY-G 159 (208)
T ss_pred HHHHHHHHHHHHHH--HHH--HHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccC-CCeeee-eHHHHHHHHHh-C
Confidence 99999999999986 322 2232 556678999999 9999999999999975544 568999 99999999999 7
Q ss_pred CCCC-------CCHHH----HHHHHhhcCCchHHHHHHHHHhhh
Q 039604 292 LEEL-------PRPSQ----MDQLCEKWRPYRSVASWYLWRFVE 324 (373)
Q Consensus 292 l~~~-------~~~~e----~~~l~e~w~Pyrg~a~~yLW~~~~ 324 (373)
+... .++.+ +.+++..++=+.|..-+|+|+...
T Consensus 160 ~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~~~~~Ldl~~w~~~~ 203 (208)
T PRK01229 160 LIEEIPKTLSKKRYLEIEEILREIAEELGISLGELDLYIWYKET 203 (208)
T ss_pred CCcccccccCcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 6442 34554 455678889999999999999754
No 15
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.83 E-value=3.7e-20 Score=180.53 Aligned_cols=162 Identities=12% Similarity=0.172 Sum_probs=126.1
Q ss_pred HhhccCHHHHH-HHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCCh
Q 039604 169 LYQQLAFKAGT-SIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDD 243 (373)
Q Consensus 169 LsQQ~S~~aA~-~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ 243 (373)
+.|||.+..+. ..+.||.++| |++++|+++++++| +.+||+ +||++|+++|+.+.++.. ..++.
T Consensus 1 mlQQT~v~~v~~~yy~rf~~~f-----Pt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~-----g~~P~ 69 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLEAF-----PTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHH-----SQLPN 69 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHHHC-----CCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhC-----CCCCh
Confidence 47999999886 4999999998 58999999999997 569997 599999999999985210 12222
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCCchHHHHHHHHHhh
Q 039604 244 KSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYLWRFV 323 (373)
Q Consensus 244 ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyrg~a~~yLW~~~ 323 (373)
.++.|++|||||+|||++||+|+|+++ +++| |+||+|++.|+||+......+++..+.+.|.|...+..++..-
T Consensus 70 --~~~~L~~LpGIG~kTA~aIl~~af~~~-~~~V-D~nV~RVl~Rl~g~~~~~~~~~l~~~~~~~l~~~~~~~~nqaL-- 143 (289)
T PRK13910 70 --DYQSLLKLPGIGAYTANAILCFGFREK-SACV-DANIKRVLLRLFGLDPNIHAKDLQIKANDFLNLNESFNHNQAL-- 143 (289)
T ss_pred --hHHHHHhCCCCCHHHHHHHHHHHCCCC-cCcc-cHHHHHHHHHHhcCCCCccHHHHHHHHHHhCCccchHHHHHHH--
Confidence 379999999999999999999999998 4788 9999999999999987666677777777777654333332221
Q ss_pred hhcCCCCchhhhhhccCC--CCchhhhhhhhHHHHhhh
Q 039604 324 EAKGAPSSAAAVAAGAAL--PQPQQEEQQQPQLLDQIN 359 (373)
Q Consensus 324 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 359 (373)
|.+|... . .++|+.|-++-+|...
T Consensus 144 -----------m~~Ga~iC~~-~P~C~~CPl~~~C~~~ 169 (289)
T PRK13910 144 -----------IDLGALICSP-KPKCAICPLNPYCLGK 169 (289)
T ss_pred -----------HHHhHHHcCC-CCCCCCCcChhhhhhh
Confidence 2345553 4 5788888888777654
No 16
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.82 E-value=2.9e-19 Score=164.93 Aligned_cols=158 Identities=19% Similarity=0.250 Sum_probs=132.8
Q ss_pred hHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCCCh
Q 039604 140 RQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGVSG 215 (373)
Q Consensus 140 p~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gls~ 215 (373)
.++..+.+.||...||...+-+|.+|.+||.|+++|+++.+.+++|....- ..+..|..++.++| ++.||++
T Consensus 10 ~iy~~L~~~yg~q~WWp~~~~~EiiigAILtQNT~WknvekAlenLk~~~~----~~l~~I~~~~~~~L~elIrpsGFYn 85 (215)
T COG2231 10 KIYKELLRLYGDQGWWPADNKDEIIIGAILTQNTSWKNVEKALENLKNEGI----LNLKKILKLDEEELAELIRPSGFYN 85 (215)
T ss_pred HHHHHHHHHcCCccCCCCCCchhHHHHHHHhccccHHHHHHHHHHHHHccc----CCHHHHhcCCHHHHHHHHhccchHH
Confidence 346677888999989999999999999999999999999999999987742 57999999998876 5689999
Q ss_pred hHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCC
Q 039604 216 RKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL 295 (373)
Q Consensus 216 ~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~ 295 (373)
+||++|+++...+...-.+++ ......++++|.+|+|||+-|||.+|+++++++ +|+| |..-+|.+.|+.+....
T Consensus 86 qKa~rLk~l~k~l~~~~~~~~---~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp-~FVv-D~Yt~R~l~rlg~i~~k 160 (215)
T COG2231 86 QKAKRLKALSKNLAKFFINLE---SFKSEVLREELLSIKGIGKETADSILLYALDRP-VFVV-DKYTRRLLSRLGGIEEK 160 (215)
T ss_pred HHHHHHHHHHHHHHHHhhhhh---ccchHHHHHHHHccCCcchhhHHHHHHHHhcCc-ccch-hHHHHHHHHHhcccccc
Confidence 999999777777765433433 333344799999999999999999999999998 7999 99999999999665544
Q ss_pred CCHHHHHHHHhh
Q 039604 296 PRPSQMDQLCEK 307 (373)
Q Consensus 296 ~~~~e~~~l~e~ 307 (373)
+..++.++.+.
T Consensus 161 -~ydeik~~fe~ 171 (215)
T COG2231 161 -KYDEIKELFEE 171 (215)
T ss_pred -cHHHHHHHHHh
Confidence 78888887764
No 17
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.79 E-value=2.6e-18 Score=161.96 Aligned_cols=208 Identities=19% Similarity=0.216 Sum_probs=163.9
Q ss_pred CchhHHHHHHHHHhhChHHHHHHHhCCCCCcC-----CCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHH
Q 039604 124 SEGEVEAAIRHLRNADRQLASLIDIHPPPTFD-----SFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPE 198 (373)
Q Consensus 124 ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~-----~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe 198 (373)
...+|.+.|..++......-.=++.+|.-+.. ...--|..||..+||.|+.+.....++.||.+.+| .+++
T Consensus 37 ppe~w~~~y~~ir~mR~k~~APVD~mGc~~~~~~~~~pk~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~g----LT~e 112 (286)
T KOG1921|consen 37 PPENWLEVYERIRKMRSKIVAPVDTMGCSRIPSLKADPKERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGG----LTLE 112 (286)
T ss_pred CCccHHHHHHHHHHHhhcccCCccccccccCccccCChhhHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcC----CCHH
Confidence 34467777777765443333445666654433 22357999999999999999999999999999976 7999
Q ss_pred HHhcCChHHH----HhcCCChhHHHHHHHHHHHHHc---CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCC
Q 039604 199 TVLALTPQQL----RQIGVSGRKASYLHDLARKYQN---GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHR 271 (373)
Q Consensus 199 ~La~l~~eeL----r~~Gls~~KA~yI~~lA~~i~~---G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgr 271 (373)
.|+++++..| ..+||+.+||.||+.+|+.+.+ |.|+ ..++.|++|||||||.|+.+|..++|+
T Consensus 113 ~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP----------~~v~dLlsLPGVGPKMa~L~m~~AWn~ 182 (286)
T KOG1921|consen 113 AVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIP----------DTVEDLLSLPGVGPKMAHLTMQVAWNK 182 (286)
T ss_pred HHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCc----------hhHHHHhcCCCCchHHHHHHHHHHhcc
Confidence 9999998665 4689999999999999999986 3443 348999999999999999999999999
Q ss_pred CCccCCCCHHHHHHHHHHhcCCCCC--CHHHHHHHHhhcCCchHHHHHHHHHhhhhcCCCCchhhhhhccC--CCCchhh
Q 039604 272 PDVLPINDLGVRKGVQLLYSLEELP--RPSQMDQLCEKWRPYRSVASWYLWRFVEAKGAPSSAAAVAAGAA--LPQPQQE 347 (373)
Q Consensus 272 pDvfPv~D~~VrR~l~rlygl~~~~--~~~e~~~l~e~w~Pyrg~a~~yLW~~~~~~~~~~~~~~~~~~~~--~~~~~~~ 347 (373)
-..+.| |+||+|+.+|+ |+-+.. ++++.+.-.+.|.|.. +|.- .|-+-|.-|.. ++..++|
T Consensus 183 i~GI~V-DtHVHRi~nrl-gWv~~ktkspE~TR~aLq~wLPk~------lW~e-------IN~lLVGFGQ~iC~p~~prC 247 (286)
T KOG1921|consen 183 IVGICV-DTHVHRICNRL-GWVDTKTKSPEQTRVALQQWLPKS------LWVE-------INHLLVGFGQTICTPRRPRC 247 (286)
T ss_pred ceeEEe-ehHHHHHHHHh-cccccccCCHHHHHHHHHHhCcHH------HHhh-------hhceeecccceeeecCCCCc
Confidence 999999 99999999999 775544 4889999999999976 4543 23334444655 3668899
Q ss_pred hhhhh-HHHHhhhh
Q 039604 348 EQQQP-QLLDQINS 360 (373)
Q Consensus 348 ~~~~~-~~~~~~~~ 360 (373)
.-|.. +.+||+..
T Consensus 248 ~~C~~~~~~Cpss~ 261 (286)
T KOG1921|consen 248 GLCLLSRDLCPSSF 261 (286)
T ss_pred cccccCcccCchhh
Confidence 77777 89999843
No 18
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=99.76 E-value=5.3e-18 Score=140.89 Aligned_cols=103 Identities=36% Similarity=0.533 Sum_probs=91.2
Q ss_pred HHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHhc----CCChhHHHHHHHHHHHHHcCCCCchhhhC
Q 039604 165 TRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQI----GVSGRKASYLHDLARKYQNGILSDSAIVN 240 (373)
Q Consensus 165 V~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~----Gls~~KA~yI~~lA~~i~~G~l~L~~L~~ 240 (373)
|++||+||++++++.+++.+|+++|| ||+|++|+.+++++|+++ ||+++||+||+++|+.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~~g---~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~----------- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFERYG---FPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL----------- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHHHS---CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH-----------
T ss_pred CeeeecCcCcHHHHHHHHHHHHHHhc---CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh-----------
Confidence 68999999999999999999999999 699999999999999887 999999999999999987
Q ss_pred CChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHH-hhcCC
Q 039604 241 MDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLC-EKWRP 310 (373)
Q Consensus 241 ~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~-e~w~P 310 (373)
|++|.+++.|+|++|++.++|+....++++++++.. +.|.|
T Consensus 67 -----------------------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~p 108 (108)
T PF00730_consen 67 -----------------------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWPP 108 (108)
T ss_dssp -----------------------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGTT
T ss_pred -----------------------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCcC
Confidence 888856666999999999999988777888888876 78876
No 19
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=99.74 E-value=2e-17 Score=150.60 Aligned_cols=125 Identities=22% Similarity=0.273 Sum_probs=103.1
Q ss_pred CCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHH----hc----CCChhHHHHHHHHHHHH
Q 039604 157 FHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLR----QI----GVSGRKASYLHDLARKY 228 (373)
Q Consensus 157 ~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr----~~----Gls~~KA~yI~~lA~~i 228 (373)
..+|||.||.+||+||++++++.+++.+|.+.+|. ++|+.|+.++.++|. .+ ||+++||++|+++|+.+
T Consensus 15 ~~~pFelLVa~ILSQqTtd~nv~kA~~~L~~~~g~---~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~i 91 (177)
T TIGR03252 15 SSDPFALLTGMLLDQQVPMERAFAGPHKIARRMGS---LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYV 91 (177)
T ss_pred cCChHHHHHHHHHhccCcHHHHHHHHHHHHHHhCC---CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHH
Confidence 45899999999999999999999999999888875 689999999998864 34 99999999999999999
Q ss_pred Hc-CCCCchhhhC---CChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHH
Q 039604 229 QN-GILSDSAIVN---MDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQ 287 (373)
Q Consensus 229 ~~-G~l~L~~L~~---~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~ 287 (373)
.+ ..-+++.|.. -+..++++.|++|||||++||+|||.+ |++. |-|-|-+-|....
T Consensus 92 ie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~-l~~~--~~~~~~~~~~~~~ 151 (177)
T TIGR03252 92 VDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLAL-LGKQ--LGVTPEGWREAAG 151 (177)
T ss_pred HHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHH-HHHH--hCCCCcchHHhcc
Confidence 74 2224555555 456788999999999999999999985 5654 6666766665543
No 20
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.66 E-value=1.5e-15 Score=150.27 Aligned_cols=162 Identities=18% Similarity=0.305 Sum_probs=132.3
Q ss_pred HHHHhCC-CCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHH----HhcCCChhHH
Q 039604 144 SLIDIHP-PPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQL----RQIGVSGRKA 218 (373)
Q Consensus 144 ~li~~~g-g~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeL----r~~Gls~~KA 218 (373)
.+.++++ .++|+...+||..+|+.|+.||+.++.+...+.+|.++| |++++|++++.+++ ..+|+ ..||
T Consensus 17 ~Wy~~~~R~LPWR~~~~PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rf-----Pti~~LA~A~~~evl~~W~gLGY-ysRA 90 (342)
T COG1194 17 DWYDKNGRDLPWRETKDPYRVWVSEIMLQQTQVATVIPYYERFLERF-----PTIKALAAAPEDEVLKAWEGLGY-YSRA 90 (342)
T ss_pred HHHHHhCCcCCCCCCCCcceehhHHHHhhhccHhhhhhhHHHHHHhC-----CCHHHHhcCCHHHHHHHHHhcCh-HHHH
Confidence 5555555 577878889999999999999999999999999999998 68999999998875 35885 7899
Q ss_pred HHHHHHHHHHHc---CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCC
Q 039604 219 SYLHDLARKYQN---GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL 295 (373)
Q Consensus 219 ~yI~~lA~~i~~---G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~ 295 (373)
+.|+..|+.+.+ |.++-+ .+.|.+|||||++||..||.|+|+++ +|+-|.+|+|++.|+|+.+..
T Consensus 91 rnL~~~A~~v~~~~~G~~P~~----------~~~l~~LpGiG~yTa~Ail~~a~~~~--~~~lDgNV~RVl~R~f~i~~~ 158 (342)
T COG1194 91 RNLHKAAQEVVERHGGEFPDD----------EEELAALPGVGPYTAGAILSFAFNQP--EPVLDGNVKRVLSRLFAISGD 158 (342)
T ss_pred HHHHHHHHHHHHHcCCCCCCC----------HHHHHhCCCCcHHHHHHHHHHHhCCC--Cceeecchheeehhhhccccc
Confidence 999999999985 555432 57788899999999999999999997 577799999999999998764
Q ss_pred C----CHHHHHHHHhh-cCCchHHHHHHHHHhhh
Q 039604 296 P----RPSQMDQLCEK-WRPYRSVASWYLWRFVE 324 (373)
Q Consensus 296 ~----~~~e~~~l~e~-w~Pyrg~a~~yLW~~~~ 324 (373)
. ..+++..+++. .-|-+. ...|-|..++
T Consensus 159 ~~~~~~~~~~~~~~~~ll~p~~~-~~~fnqammd 191 (342)
T COG1194 159 IGKPKTKKELWELAEQLLTPDRR-PGDFNQAMMD 191 (342)
T ss_pred ccccchhHHHHHHHHHhcCCCCC-hHHHHHHHHH
Confidence 3 35677778877 445554 4445555543
No 21
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=98.81 E-value=4.4e-08 Score=98.31 Aligned_cols=162 Identities=17% Similarity=0.187 Sum_probs=121.0
Q ss_pred CHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChH-H----HHhcCCChhHHHHHHHHHHHHHcCCC
Q 039604 159 TPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQ-Q----LRQIGVSGRKASYLHDLARKYQNGIL 233 (373)
Q Consensus 159 dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~e-e----Lr~~Gls~~KA~yI~~lA~~i~~G~l 233 (373)
..||.+|+.|+.||+.+.-..+-|.+..+.+ ||..+++.++.+ + +..+|+ -+|++.|+.-|+++..|.-
T Consensus 124 RaYeVwVSEiMLQQTrV~TV~~YYt~WMqkw-----PTl~dla~Asl~~eVn~lWaGlGy-Y~R~rrL~ega~~vv~~~~ 197 (555)
T KOG2457|consen 124 RAYEVWVSEIMLQQTRVQTVMKYYTRWMQKW-----PTLYDLAQASLEKEVNELWAGLGY-YRRARRLLEGAKMVVAGTE 197 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-----chHHHHHHHHHHHHHHHHHhhhhH-HHHHHHHHHHHHHHHHhCC
Confidence 4899999999999999999999999999987 578888877763 2 346888 5779999999999986321
Q ss_pred CchhhhCCChHHHHHHHhc-CCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCCch
Q 039604 234 SDSAIVNMDDKSLFTMLTM-VNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYR 312 (373)
Q Consensus 234 ~L~~L~~~~~ee~~~~L~s-LpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyr 312 (373)
. .++. .-+.|+. +||||++||..|+..+|+.+.. .| |-+|.|++.|...+... +-.
T Consensus 198 g-----e~Pr--ta~~l~kgvpGVG~YTAGAiaSIAf~q~tG-iV-DGNVirvlsRalAIhsD--------------cSk 254 (555)
T KOG2457|consen 198 G-----EFPR--TASSLMKGVPGVGQYTAGAIASIAFNQVTG-IV-DGNVIRVLSRALAIHSD--------------CSK 254 (555)
T ss_pred C-----CCCC--hHHHHHhhCCCCCccchhhhhhhhhcCccc-cc-ccchHHHhHHhHhhcCC--------------cch
Confidence 1 1222 2355555 9999999999999999998754 34 99999999998766543 345
Q ss_pred HHHHHHHHHhhhhcCCCCc-----hhhhhhccCC--CCchhhhh
Q 039604 313 SVASWYLWRFVEAKGAPSS-----AAAVAAGAAL--PQPQQEEQ 349 (373)
Q Consensus 313 g~a~~yLW~~~~~~~~~~~-----~~~~~~~~~~--~~~~~~~~ 349 (373)
|.+..-+|.....-.+|.- +..|.-|.-+ +|.+.|-+
T Consensus 255 gk~~q~~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~ 298 (555)
T KOG2457|consen 255 GKFFQSSWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSS 298 (555)
T ss_pred hhHHHHHHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCC
Confidence 6677778877665555442 2444446654 88888844
No 22
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.46 E-value=2e-06 Score=79.29 Aligned_cols=151 Identities=18% Similarity=0.254 Sum_probs=113.7
Q ss_pred CCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHH----HHhc--CCChhHHHHHHHHHHHHH
Q 039604 156 SFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQ----LRQI--GVSGRKASYLHDLARKYQ 229 (373)
Q Consensus 156 ~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~ee----Lr~~--Gls~~KA~yI~~lA~~i~ 229 (373)
...+.|.-|+-+||..|.|...+.++...| |+. +..++.|+ |+.+ .|++.||+||...=+.+-
T Consensus 35 ~~e~lf~ELsFCILTANsSA~~~~~~q~~l----G~g-------fly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~ 103 (210)
T COG1059 35 TKEDLFKELSFCILTANSSATMGLRAQNEL----GDG-------FLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFD 103 (210)
T ss_pred cHHHHHHHHHHHhccccchHHHHHHHHHHh----ccc-------cccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHH
Confidence 345789999999999999999998887776 432 23334444 5567 588999999998777665
Q ss_pred cCCCCchhhhCCChHH--HHHHHh-cCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCC---CH-----
Q 039604 230 NGILSDSAIVNMDDKS--LFTMLT-MVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELP---RP----- 298 (373)
Q Consensus 230 ~G~l~L~~L~~~~~ee--~~~~L~-sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~---~~----- 298 (373)
++..+.+++..+ +++.|. .++|||-|-|.-+| +.-|..|+-.+ |.||.|.+.+++-....+ ++
T Consensus 104 ----~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFL-RNVG~~D~AIl-DrHIlr~l~r~g~i~e~~kt~t~K~YLe 177 (210)
T COG1059 104 ----DLKIIVKADENEKVARELLVENIKGIGYKEASHFL-RNVGFEDLAIL-DRHILRWLVRYGLIDENPKTLTRKLYLE 177 (210)
T ss_pred ----HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHH-HhcChhHHHHH-HHHHHHHHHHhcccccCcccccHHHHHH
Confidence 334455555433 788888 99999999999996 67788886555 999999999985444432 22
Q ss_pred --HHHHHHHhhcCCchHHHHHHHHHhh
Q 039604 299 --SQMDQLCEKWRPYRSVASWYLWRFV 323 (373)
Q Consensus 299 --~e~~~l~e~w~Pyrg~a~~yLW~~~ 323 (373)
+.++.+++.++---|..-+|+|+..
T Consensus 178 ~E~ilr~iae~~g~s~gelDL~IWY~e 204 (210)
T COG1059 178 IEEILRSIAEEVGISLGELDLYIWYKE 204 (210)
T ss_pred HHHHHHHHHHHhCCCcchhHHHHHHHH
Confidence 3567788888888899999999863
No 23
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=97.55 E-value=7.7e-05 Score=49.43 Aligned_cols=21 Identities=24% Similarity=0.430 Sum_probs=18.5
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
+++|++|||||++||+.|+.|
T Consensus 10 ~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 10 IEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHHHHTSTT-SHHHHHHHHHH
T ss_pred HHHHHhCCCcCHHHHHHHHhC
Confidence 689999999999999999875
No 24
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=97.47 E-value=8e-05 Score=63.22 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=37.6
Q ss_pred hhhhcCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCCCCHHHHH
Q 039604 115 PRIIARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSFHTPFLAL 164 (373)
Q Consensus 115 ~~~~~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~~dpfE~L 164 (373)
...+.+||+||.|++.+++.+.+.|+.|+.+++.+.|+|+ .++||||+|
T Consensus 69 ~~~l~~YF~Ld~dl~~l~~~~~~~D~~l~~~~~~~~GlRi-LrQdp~E~L 117 (117)
T PF07934_consen 69 EEFLRDYFDLDVDLEKLYEDWSKKDPRLAKAIDKYRGLRI-LRQDPFETL 117 (117)
T ss_dssp HHCHHHHTTTTS-HHHHHHHHCCHSHHHHHHHHCTTT--------HHHHH
T ss_pred HHHHHHHhcCCccHHHHHHHHhhhCHHHHHHHhcCCCcEE-ECCChhhhC
Confidence 3447789999999999999998889999999999999999 799999987
No 25
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=94.15 E-value=0.033 Score=35.34 Aligned_cols=20 Identities=25% Similarity=0.267 Sum_probs=17.4
Q ss_pred HHhcCCCCCHHHHHHHHHHh
Q 039604 249 MLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 249 ~L~sLpGIGpwTA~~vLLf~ 268 (373)
.|+.++|||+|+|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998643
No 26
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.41 E-value=0.4 Score=45.00 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=20.4
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhCCC
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFSLHR 271 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~lgr 271 (373)
.+.|+++||||+|||+-+++---++
T Consensus 106 ~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 106 IELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 5889999999999999998643333
No 27
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=90.31 E-value=0.084 Score=45.39 Aligned_cols=37 Identities=24% Similarity=0.343 Sum_probs=22.6
Q ss_pred hcCCCCCchhHHHHHHHHHhhChHHHHHHHhCCCCCcCCC
Q 039604 118 IARPLSSEGEVEAAIRHLRNADRQLASLIDIHPPPTFDSF 157 (373)
Q Consensus 118 ~~r~l~ld~Dl~~~~~~L~~~Dp~La~li~~~gg~r~~~~ 157 (373)
+.|+||||.|.+.+.++| ||.++.++...+|+|+++.
T Consensus 78 vRrlfDLdaDp~~I~~~L---dp~l~p~~~~~pGLRlPG~ 114 (116)
T PF06029_consen 78 VRRLFDLDADPQAIEAHL---DPLLAPLVAARPGLRLPGA 114 (116)
T ss_dssp HHHHTTTT--HHHHHHHH-------GGGGTS-TT------
T ss_pred HHHHhCCCCCHHHHHHHH---hhcccccccCCCCCcCCCc
Confidence 568999999999999999 9999999999999998754
No 28
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=90.27 E-value=0.57 Score=35.85 Aligned_cols=36 Identities=22% Similarity=0.251 Sum_probs=23.8
Q ss_pred HHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 228 YQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 228 i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
+.+.--+++.|.+.+ .++|.+++|||+.+|+.+.-|
T Consensus 19 L~~~f~sl~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 19 LAKHFGSLEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHCCSCHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHcCCHHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 333334677787765 467899999999999998765
No 29
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.08 E-value=0.43 Score=44.40 Aligned_cols=22 Identities=14% Similarity=0.131 Sum_probs=19.2
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
.+.|+++||||+|||+-+++--
T Consensus 107 ~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 107 VEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHHhhCCCCCHHHHHHHHHHH
Confidence 5889999999999999998543
No 30
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.82 E-value=0.46 Score=44.04 Aligned_cols=24 Identities=25% Similarity=0.206 Sum_probs=20.0
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhCC
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
.+.|+++||||+|||+-+++---+
T Consensus 107 ~~~L~~vpGIGkKtAeRIilELkd 130 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAELSD 130 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 588999999999999999854333
No 31
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.11 E-value=0.55 Score=44.13 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=18.7
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.+.|+++||||+|||+-+++-
T Consensus 108 ~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 108 VAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 588999999999999998854
No 32
>PRK13844 recombination protein RecR; Provisional
Probab=89.06 E-value=0.35 Score=45.50 Aligned_cols=31 Identities=16% Similarity=0.246 Sum_probs=27.6
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHHhCCCCC
Q 039604 243 DKSLFTMLTMVNGIGSWSVHMFMIFSLHRPD 273 (373)
Q Consensus 243 ~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpD 273 (373)
-+++++.|..|||||+|||.-+.++-|..++
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~~ 40 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLDKSP 40 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 5788999999999999999999999887653
No 33
>PRK00076 recR recombination protein RecR; Reviewed
Probab=88.98 E-value=0.36 Score=45.33 Aligned_cols=31 Identities=26% Similarity=0.323 Sum_probs=27.5
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHHhCCCCC
Q 039604 243 DKSLFTMLTMVNGIGSWSVHMFMIFSLHRPD 273 (373)
Q Consensus 243 ~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpD 273 (373)
.+++++.|..|||||+|||.-+.++-+.+++
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~~ 36 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQRDR 36 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 4778999999999999999999998887654
No 34
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.86 E-value=0.59 Score=43.75 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=18.6
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.+.|+++||||+|||+-+++-
T Consensus 106 ~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 588999999999999998743
No 35
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.76 E-value=13 Score=34.51 Aligned_cols=74 Identities=12% Similarity=-0.005 Sum_probs=58.3
Q ss_pred CcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHh------cCCChhHHHHHHHHHH
Q 039604 153 TFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQ------IGVSGRKASYLHDLAR 226 (373)
Q Consensus 153 r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~------~Gls~~KA~yI~~lA~ 226 (373)
+.......||.|+-.+...-+||..+.+=...|.++|.+ .+|+.++..+++++.. +--.+.|.+.+.+=|+
T Consensus 23 p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~~---Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~ 99 (179)
T TIGR00624 23 PLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFSG---FDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANAR 99 (179)
T ss_pred cCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHcC---CCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHH
Confidence 333456799999999999999999999999999999975 5899999999988753 3334566666777666
Q ss_pred HHH
Q 039604 227 KYQ 229 (373)
Q Consensus 227 ~i~ 229 (373)
++.
T Consensus 100 ~~l 102 (179)
T TIGR00624 100 AAL 102 (179)
T ss_pred HHH
Confidence 665
No 36
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.69 E-value=0.46 Score=44.62 Aligned_cols=31 Identities=26% Similarity=0.296 Sum_probs=27.4
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHHhCCCCC
Q 039604 243 DKSLFTMLTMVNGIGSWSVHMFMIFSLHRPD 273 (373)
Q Consensus 243 ~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpD 273 (373)
-+++++.|..|||||+|||.-+.++-+..++
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~ 36 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKRDP 36 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcCCH
Confidence 4788999999999999999999988887653
No 37
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.35 E-value=0.67 Score=43.34 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=19.2
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
.+.|+.+||||+|||+-+++--
T Consensus 107 ~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 107 VARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHHhhCCCCCHHHHHHHHHHH
Confidence 5889999999999999988543
No 38
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=87.45 E-value=1.1 Score=33.63 Aligned_cols=32 Identities=25% Similarity=0.355 Sum_probs=24.8
Q ss_pred CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 231 GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 231 G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
|--++++|...+. +.|..++|||+++|+-+.-
T Consensus 25 G~~t~~~l~~a~~----~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 25 GIKTLEDLANADP----EELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp TCSSHHHHHTSHH----HHHHTSTTSSHHHHHHHHH
T ss_pred CCCcHHHHHcCCH----HHHhcCCCCCHHHHHHHHH
Confidence 5567777877743 5689999999999987753
No 39
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=86.57 E-value=0.65 Score=43.59 Aligned_cols=30 Identities=23% Similarity=0.331 Sum_probs=26.5
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 243 DKSLFTMLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 243 ~ee~~~~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
.+.+++.|..|||||+|+|.-+..+-+.+.
T Consensus 7 i~~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 7 IEKLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 467899999999999999999998888764
No 40
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=85.54 E-value=3.1 Score=32.05 Aligned_cols=46 Identities=15% Similarity=-0.003 Sum_probs=34.2
Q ss_pred cCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHH-HHhcCCCCCHHHHHHHH
Q 039604 211 IGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFT-MLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 211 ~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~-~L~sLpGIGpwTA~~vL 265 (373)
-|-..+|+..-++.+..+.+-..++. .+ + .|..|||||+.+|..|-
T Consensus 18 ~~~~~~r~~aY~~Aa~~i~~l~~~i~---~~------~~~~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 18 QGGDPFRARAYRRAAAAIKALPYPIT---SG------EEDLKKLPGIGKSIAKKID 64 (68)
T ss_dssp TSTSHHHHHHHHHHHHHHHHSSS-HH---SH------HHHHCTSTTTTHHHHHHHH
T ss_pred hhCCcHHHHHHHHHHHHHHhCCHhHh---hH------HHHHhhCCCCCHHHHHHHH
Confidence 33558899999999999887443332 22 3 59999999999998874
No 41
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=85.35 E-value=1 Score=42.47 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=21.3
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
.+.|+++||||+|||+-+++---++.
T Consensus 107 ~~~L~k~PGIGkKtAerivleLk~K~ 132 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVLELKGKL 132 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHHHHhhhh
Confidence 68899999999999998887554443
No 42
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.74 E-value=1.1 Score=41.54 Aligned_cols=20 Identities=30% Similarity=0.331 Sum_probs=17.4
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.+.| ++||||+|||+-+++-
T Consensus 107 ~~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 107 KAAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred Hhhe-ECCCCcHHHHHHHHHH
Confidence 4788 9999999999999854
No 43
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.38 E-value=2.4 Score=39.53 Aligned_cols=19 Identities=21% Similarity=0.415 Sum_probs=17.1
Q ss_pred HHHHhcCCCCCHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vL 265 (373)
.+.|+++||||+|||+-++
T Consensus 107 ~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 107 AELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHHHhCCCCCHHHHHHHH
Confidence 5789999999999999965
No 44
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=83.04 E-value=1.8 Score=40.35 Aligned_cols=21 Identities=14% Similarity=0.338 Sum_probs=18.3
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.+.|+++||||+|||+-+++-
T Consensus 106 ~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 106 VKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 477999999999999999854
No 45
>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=82.99 E-value=1.1 Score=33.51 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=22.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHhCCC
Q 039604 245 SLFTMLTMVNGIGSWSVHMFMIFSLHR 271 (373)
Q Consensus 245 e~~~~L~sLpGIGpwTA~~vLLf~lgr 271 (373)
++++.|++|+|||+++|..+.-.|+.-
T Consensus 2 ~~~~~L~~I~Gig~~~a~~L~~~G~~t 28 (60)
T PF14520_consen 2 GVFDDLLSIPGIGPKRAEKLYEAGIKT 28 (60)
T ss_dssp HHHHHHHTSTTCHHHHHHHHHHTTCSS
T ss_pred HHHHhhccCCCCCHHHHHHHHhcCCCc
Confidence 357899999999999999887665553
No 46
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=82.52 E-value=2.3 Score=42.80 Aligned_cols=50 Identities=16% Similarity=0.121 Sum_probs=35.6
Q ss_pred HHHHHHHHHcCCCC-chhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 221 LHDLARKYQNGILS-DSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 221 I~~lA~~i~~G~l~-L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
-..+.+.+..|.+. +.....-+....+..|++|+||||++|..+-- +|-.
T Consensus 61 a~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~--lGi~ 111 (334)
T smart00483 61 KKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR--KGIR 111 (334)
T ss_pred HHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH--hCCC
Confidence 33444555678887 55555556677899999999999999977643 6543
No 47
>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=82.46 E-value=1.2 Score=37.20 Aligned_cols=61 Identities=18% Similarity=0.333 Sum_probs=41.6
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHH-HHHHhhcCCchHHHHHHHHHh
Q 039604 244 KSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQM-DQLCEKWRPYRSVASWYLWRF 322 (373)
Q Consensus 244 ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~-~~l~e~w~Pyrg~a~~yLW~~ 322 (373)
.+....|+.|||||+.+|..+...|+..++ | |-|. ++.+| +++++.-+-+---..+|.|+.
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~-----~---------L~g~----dP~~Ly~~lc~~~G~~~DpCvldvfr~ 69 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRSPA-----D---------LKGR----DPEELYERLCALTGQRHDPCVLDVFRC 69 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCCHH-----H---------HhCC----CHHHHHHHHHHHcCCcCCcHHHHHHHH
Confidence 456789999999999999998877665432 2 2222 34444 556666666666777787765
No 48
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=81.10 E-value=2.5 Score=32.26 Aligned_cols=52 Identities=21% Similarity=0.380 Sum_probs=32.5
Q ss_pred HhcCChHHHHhc-CCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHH
Q 039604 200 VLALTPQQLRQI-GVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMF 264 (373)
Q Consensus 200 La~l~~eeLr~~-Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~v 264 (373)
|-.++.++|..+ |++...|+.|.+.=+. .|.+. -+++|..++|||+.+.+-+
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~--~G~f~-----------s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREK--NGPFK-----------SLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHH--H-S-S-----------SGGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHh--CcCCC-----------CHHHHhhCCCCCHHHHHHH
Confidence 346788999998 9988888877664433 25542 1578999999999988755
No 49
>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=81.10 E-value=1.2 Score=41.44 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=22.5
Q ss_pred hCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 239 VNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 239 ~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
.+....+++..|++++||||++|-.+|
T Consensus 63 ~~~~Er~lF~~L~~V~GIGpK~Al~iL 89 (191)
T TIGR00084 63 NTLEERELFKELIKVNGVGPKLALAIL 89 (191)
T ss_pred CCHHHHHHHHHHhCCCCCCHHHHHHHH
Confidence 344566889999999999999998874
No 50
>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=80.64 E-value=1.4 Score=35.53 Aligned_cols=41 Identities=17% Similarity=0.174 Sum_probs=30.9
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCC
Q 039604 248 TMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEE 294 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~ 294 (373)
+.|++|||||+-||..++... +.++.|+- . +.+..+.|+..
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~~-~----~~l~~~~Gl~P 42 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFKS-A----KQLASYAGLAP 42 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhccc-c----hhhhhcccccc
Confidence 468999999999999998765 77777876 3 34455557654
No 51
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.34 E-value=1.3 Score=41.31 Aligned_cols=28 Identities=29% Similarity=0.349 Sum_probs=23.8
Q ss_pred hCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 239 VNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 239 ~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
.+....++++.|++++||||++|-.+|.
T Consensus 64 ~~~~Er~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 64 ATTEELSLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred CCHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 3445668899999999999999999985
No 52
>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=80.24 E-value=5 Score=39.83 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=32.1
Q ss_pred HHHHHHHcCCCC-chhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 223 DLARKYQNGILS-DSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 223 ~lA~~i~~G~l~-L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
.+.+.+..|.+. ++.|..- ....+..|+.|+||||++|.-+- .+|--
T Consensus 60 kI~E~~~tG~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~--~lGi~ 107 (307)
T cd00141 60 KIEEILETGKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY--ELGIR 107 (307)
T ss_pred HHHHHHHcCCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH--HcCCC
Confidence 344445567763 3444443 56678999999999999998776 55543
No 53
>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=78.46 E-value=10 Score=41.76 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=16.5
Q ss_pred CHHHHhcCChHHHHhc-CCChhHHHHHHHH
Q 039604 196 VPETVLALTPQQLRQI-GVSGRKASYLHDL 224 (373)
Q Consensus 196 tPe~La~l~~eeLr~~-Gls~~KA~yI~~l 224 (373)
++.+|..+..++|..+ |+...++..|.+.
T Consensus 456 ~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~ 485 (652)
T TIGR00575 456 SVADLYALKKEDLLELEGFGEKSAQNLLNA 485 (652)
T ss_pred CHHHHHhcCHHHHhhccCccHHHHHHHHHH
Confidence 5667777777666654 5544444444433
No 54
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=76.74 E-value=12 Score=41.35 Aligned_cols=20 Identities=25% Similarity=0.431 Sum_probs=16.9
Q ss_pred HHHhcCCCCCHHHHHHHHHH
Q 039604 248 TMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf 267 (373)
+.|.+++|||+++|+.+.-|
T Consensus 543 eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 543 EELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred HHHhccCCcCHHHHHHHHHH
Confidence 56889999999999988765
No 55
>PRK14973 DNA topoisomerase I; Provisional
Probab=76.36 E-value=8.8 Score=43.99 Aligned_cols=85 Identities=19% Similarity=0.143 Sum_probs=54.0
Q ss_pred CCCHHHHhcCChHHHHh-cCCChhHHHHHHHHHH-HHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCC
Q 039604 194 GVVPETVLALTPQQLRQ-IGVSGRKASYLHDLAR-KYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHR 271 (373)
Q Consensus 194 ~ptPe~La~l~~eeLr~-~Gls~~KA~yI~~lA~-~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgr 271 (373)
|-++++++.+++++|.. -|++.--+..+...|. .+.. -+-......-.++-..+|.+++|||+.|++-.-.-|.-.
T Consensus 823 ~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ag~~~ 900 (936)
T PRK14973 823 FDTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGR--PVPEKISKAAFERGRAELLSVPGLGETTLEKLYLAGVYD 900 (936)
T ss_pred CCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcC--CCchhhhhhhhcccchhhhhccCCCHHHHHHHHHcCCCC
Confidence 56899999999999986 6888766666655554 3221 111112222223334559999999999998777666655
Q ss_pred CCccCCCCH
Q 039604 272 PDVLPINDL 280 (373)
Q Consensus 272 pDvfPv~D~ 280 (373)
.+.+-..|+
T Consensus 901 ~e~l~~~d~ 909 (936)
T PRK14973 901 GDLLVSADP 909 (936)
T ss_pred HHHhccCCH
Confidence 554444343
No 56
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=76.30 E-value=20 Score=33.49 Aligned_cols=89 Identities=15% Similarity=0.056 Sum_probs=64.3
Q ss_pred hChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHh----cCC
Q 039604 138 ADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQ----IGV 213 (373)
Q Consensus 138 ~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~----~Gl 213 (373)
.||++..--+.-=|.+.......||.|+-.+...-+||..+.+=...|.++|.+ .+|+.++..+++++.. -|+
T Consensus 9 ~~~l~~~YHD~eWG~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~~---Fd~~~VA~~~e~die~Ll~d~~I 85 (187)
T PRK10353 9 QDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQ---FDPVKVAAMQEEDVERLVQDAGI 85 (187)
T ss_pred CChHHHHhhhccCCCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHcC---CCHHHHhCCCHHHHHHHhcCchh
Confidence 455443333322233334456799999999999999999999999999999975 5899999999988653 344
Q ss_pred --ChhHHHHHHHHHHHHH
Q 039604 214 --SGRKASYLHDLARKYQ 229 (373)
Q Consensus 214 --s~~KA~yI~~lA~~i~ 229 (373)
.+.|.+.+.+=|+++.
T Consensus 86 IRnr~KI~Avi~NA~~~l 103 (187)
T PRK10353 86 IRHRGKIQAIIGNARAYL 103 (187)
T ss_pred HHhHHHHHHHHHHHHHHH
Confidence 4667777777666665
No 57
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.70 E-value=2.7 Score=40.04 Aligned_cols=52 Identities=17% Similarity=0.181 Sum_probs=35.4
Q ss_pred hhHHH-HHHHHHHHHHcCC---CCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH-HHhCC
Q 039604 215 GRKAS-YLHDLARKYQNGI---LSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM-IFSLH 270 (373)
Q Consensus 215 ~~KA~-yI~~lA~~i~~G~---l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL-Lf~lg 270 (373)
+.|-+ ....+|+.+.+.- -++..+.+++. ++|++++|||+-.|-.++ .+-++
T Consensus 27 g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~----~eL~~i~GiG~aka~~l~a~~El~ 83 (218)
T TIGR00608 27 GTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPP----EELSSVPGIGEAKAIQLKAAVELA 83 (218)
T ss_pred CCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCH----HHHHhCcCCcHHHHHHHHHHHHHH
Confidence 33445 6778888888643 37888888875 568899999996655443 44333
No 58
>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=74.35 E-value=2.8 Score=31.15 Aligned_cols=24 Identities=13% Similarity=0.314 Sum_probs=16.9
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhCC
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
++.++.|.|||+.||....-.|+.
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--
T ss_pred CcchhhcccccHHHHHHHHHhCCC
Confidence 467999999999999988765553
No 59
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=73.88 E-value=7.5 Score=34.42 Aligned_cols=50 Identities=12% Similarity=0.109 Sum_probs=36.1
Q ss_pred HHhcCChHHHHh-cCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 199 TVLALTPQQLRQ-IGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 199 ~La~l~~eeLr~-~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
+|-.++.++|+. =|+...+|+.|. .+|... -.+.|..++|||+++.+.+-
T Consensus 54 diN~A~~~el~~lpGigP~~A~~IV------~nGpf~-----------sveDL~~V~GIgekqk~~l~ 104 (132)
T PRK02515 54 DLNNSSVRAFRQFPGMYPTLAGKIV------KNAPYD-----------SVEDVLNLPGLSERQKELLE 104 (132)
T ss_pred cCCccCHHHHHHCCCCCHHHHHHHH------HCCCCC-----------CHHHHHcCCCCCHHHHHHHH
Confidence 445567777776 377788888887 356542 26888999999998877765
No 60
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.58 E-value=2.6 Score=39.14 Aligned_cols=28 Identities=32% Similarity=0.546 Sum_probs=23.3
Q ss_pred hCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 239 VNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 239 ~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
.+....++++.|+++.||||++|=.+|.
T Consensus 64 ~~~~Er~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 64 LDKDEQKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred CCHHHHHHHHHHhccCCccHHHHHHHHc
Confidence 3445668899999999999999988874
No 61
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.50 E-value=2.7 Score=39.13 Aligned_cols=28 Identities=29% Similarity=0.328 Sum_probs=23.4
Q ss_pred hCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 239 VNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 239 ~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
.+....++++.|+++.||||++|=.+|.
T Consensus 64 ~~~~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 64 SNERKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred CCHHHHHHHHHHhccCCccHHHHHHHHc
Confidence 3445678899999999999999988873
No 62
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=72.78 E-value=3.5 Score=38.22 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=19.0
Q ss_pred HHHHHHHhcCCCCCHHHHHHHH
Q 039604 244 KSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 244 ee~~~~L~sLpGIGpwTA~~vL 265 (373)
.+++..|..++||||++|..++
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il 90 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAIL 90 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHH
Confidence 3457889999999999999886
No 63
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.46 E-value=2.9 Score=39.32 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=23.4
Q ss_pred hCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 239 VNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 239 ~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
......++++.|+++.||||++|=.+|.
T Consensus 63 ~t~~Er~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 63 LNSSEREVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred CCHHHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3445668899999999999999988873
No 64
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=72.32 E-value=13 Score=41.14 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=18.2
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.+.|++++|||+.+|+.+.-|
T Consensus 540 ~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHH
Confidence 357999999999999999866
No 65
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.16 E-value=2.3 Score=39.83 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=23.1
Q ss_pred CCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 240 NMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 240 ~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
+....++++.|+++.||||++|=.+|.
T Consensus 64 ~~~Er~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 64 DEDSLELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred CHHHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 444567899999999999999988875
No 66
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=71.84 E-value=15 Score=34.13 Aligned_cols=89 Identities=18% Similarity=0.107 Sum_probs=61.3
Q ss_pred hChHHHHHHHhCCCCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHh------c
Q 039604 138 ADRQLASLIDIHPPPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQ------I 211 (373)
Q Consensus 138 ~Dp~La~li~~~gg~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~------~ 211 (373)
.||.+..--+..=|.+.......||.|+-.+...-+||..+.+=...|.++|-+ .+|+.|+..+++++.. +
T Consensus 4 ~~~~~~~YHD~eWG~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~~---Fd~~~vA~~~e~~ie~l~~d~~i 80 (179)
T PF03352_consen 4 SDPLYRAYHDEEWGRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFAG---FDPEKVAKMDEEDIERLMQDPGI 80 (179)
T ss_dssp SSHHHHHHHHHTTTSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTGG---GHHHHHHT--HHHHHHHTTSTTS
T ss_pred CChHHHHHhcccCCCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHC---CCHHHHHcCCHHHHHHHhcCcch
Confidence 345554444433233333445699999999999999999999999999999864 5799999999988753 3
Q ss_pred CCChhHHHHHHHHHHHHH
Q 039604 212 GVSGRKASYLHDLARKYQ 229 (373)
Q Consensus 212 Gls~~KA~yI~~lA~~i~ 229 (373)
--.+.|.+.+.+=|+++.
T Consensus 81 IRnr~KI~Avi~NA~~~l 98 (179)
T PF03352_consen 81 IRNRRKIRAVINNARAIL 98 (179)
T ss_dssp S--HHHHHHHHHHHHHHH
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 336788888887777776
No 67
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.15 E-value=3.1 Score=38.93 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=23.6
Q ss_pred hCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 239 VNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 239 ~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
.+....++++.|+++.||||++|=.+|.
T Consensus 64 ~~~~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 64 STPAQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred CCHHHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3445668899999999999999998885
No 68
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.70 E-value=3.5 Score=38.34 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=22.5
Q ss_pred CChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 241 MDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 241 ~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
-...++++.|+++.||||++|=.+|.
T Consensus 66 ~~Er~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 66 REEQDCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 34567899999999999999988875
No 69
>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=69.08 E-value=8.4 Score=29.34 Aligned_cols=37 Identities=24% Similarity=0.503 Sum_probs=32.7
Q ss_pred CC-HHHHhcCChHHHHhcCCChhHHHHHHHHHHHHHcC
Q 039604 195 VV-PETVLALTPQQLRQIGVSGRKASYLHDLARKYQNG 231 (373)
Q Consensus 195 pt-Pe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~~G 231 (373)
.+ ++.|...+-.+|+..|++-+-.+||....+.+..|
T Consensus 20 ~~~w~~lf~~~s~~LK~~GIp~r~RryiL~~~ek~r~G 57 (57)
T PF09597_consen 20 ESDWEKLFTTSSKQLKELGIPVRQRRYILRWREKYRQG 57 (57)
T ss_pred HHHHHHHHhcCHHHHHHCCCCHHHHHHHHHHHHHHhCc
Confidence 45 89999999999999999999899999999888765
No 70
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=68.52 E-value=10 Score=38.73 Aligned_cols=48 Identities=13% Similarity=0.265 Sum_probs=39.6
Q ss_pred HHHHHHHHHhCCCCCCCHHHHhcCChHHHHhc-CCChhHHHHHHHHHHHHHcCC
Q 039604 180 SIYTRFIALCGGEAGVVPETVLALTPQQLRQI-GVSGRKASYLHDLARKYQNGI 232 (373)
Q Consensus 180 ~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~~i~~G~ 232 (373)
.+.++|+++|| +...|++++.++|..+ |+...||+.|++.++.+.+..
T Consensus 298 ~iAk~Ll~~FG-----SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e~~ 346 (352)
T PRK13482 298 AVIENLVEHFG-----SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAEQS 346 (352)
T ss_pred HHHHHHHHHcC-----CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 44567777787 6899999999999885 788899999999999887643
No 71
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.17 E-value=4 Score=38.38 Aligned_cols=27 Identities=15% Similarity=0.368 Sum_probs=23.1
Q ss_pred CCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 240 NMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 240 ~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
+...-++++.|+++.||||++|=.+|.
T Consensus 66 ~~~Er~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 66 TWDERQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred CHHHHHHHHHHhCCCCcCHHHHHHHHh
Confidence 444567899999999999999988875
No 72
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=67.25 E-value=14 Score=34.31 Aligned_cols=21 Identities=29% Similarity=0.362 Sum_probs=18.3
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.+.|+.+||||+++|+.++..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 467999999999999999854
No 73
>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=67.01 E-value=3.9 Score=27.22 Aligned_cols=15 Identities=20% Similarity=0.319 Sum_probs=11.8
Q ss_pred HhcCCCCCHHHHHHH
Q 039604 250 LTMVNGIGSWSVHMF 264 (373)
Q Consensus 250 L~sLpGIGpwTA~~v 264 (373)
+..++|||++|+.-+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 578999999999864
No 74
>PRK00024 hypothetical protein; Reviewed
Probab=65.74 E-value=16 Score=34.76 Aligned_cols=59 Identities=19% Similarity=0.196 Sum_probs=43.4
Q ss_pred HHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHhc-CCChhHHHHHHHHHH
Q 039604 163 ALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQI-GVSGRKASYLHDLAR 226 (373)
Q Consensus 163 ~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~ 226 (373)
-|+..+|+.-+..+.+..+.++|.+.|| +...+..++.++|+.+ |+...||..|..+.+
T Consensus 28 ELLa~lL~~g~~~~~~~~LA~~LL~~fg-----sL~~l~~as~~eL~~i~GIG~akA~~L~a~~E 87 (224)
T PRK00024 28 ELLAILLRTGTKGKSVLDLARELLQRFG-----SLRGLLDASLEELQSIKGIGPAKAAQLKAALE 87 (224)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHcC-----CHHHHHhCCHHHHhhccCccHHHHHHHHHHHH
Confidence 3555566655555666677788888887 5889999999999874 887888877755543
No 75
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=64.79 E-value=14 Score=37.20 Aligned_cols=46 Identities=22% Similarity=0.229 Sum_probs=35.5
Q ss_pred cCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 211 IGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 211 ~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
.|-..+|+.+..+.|..+.+-..++.. .+.|..|||||+.+|+-|-
T Consensus 20 ~gen~~k~~ay~~Aa~~i~~l~~~i~~---------~~~l~~lpgIG~~ia~kI~ 65 (334)
T smart00483 20 FGENKRKCSYFRKAASVLKSLPFPINS---------MKDLKGLPGIGDKIKKKIE 65 (334)
T ss_pred hcccHHHHHHHHHHHHHHHhCCCCCCC---------HHHHhcCCCccHHHHHHHH
Confidence 466578899999999988875544432 2478999999999999776
No 76
>PRK00024 hypothetical protein; Reviewed
Probab=64.67 E-value=8.6 Score=36.62 Aligned_cols=47 Identities=23% Similarity=0.274 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 215 GRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 215 ~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
+.+-+-...+|+.+.+.--++..+.+++. ++|++++|||+..|..++
T Consensus 37 g~~~~~~~~LA~~LL~~fgsL~~l~~as~----~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 37 GTKGKSVLDLARELLQRFGSLRGLLDASL----EELQSIKGIGPAKAAQLK 83 (224)
T ss_pred CCCCCCHHHHHHHHHHHcCCHHHHHhCCH----HHHhhccCccHHHHHHHH
Confidence 44455667888888864346788888875 568899999999885553
No 77
>PRK14973 DNA topoisomerase I; Provisional
Probab=64.14 E-value=73 Score=36.78 Aligned_cols=67 Identities=16% Similarity=0.200 Sum_probs=51.0
Q ss_pred CCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHH--------------------cCCCCchhhhCCChHHHHHHHhcCC
Q 039604 195 VVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQ--------------------NGILSDSAIVNMDDKSLFTMLTMVN 254 (373)
Q Consensus 195 ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~--------------------~G~l~L~~L~~~~~ee~~~~L~sLp 254 (373)
.+..+|+.++++.|+..|+|..+++.+..-|+.+. .|--+++++...+ .++|..++
T Consensus 766 ~~~~~~~~~~~~~~~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~----p~~La~~~ 841 (936)
T PRK14973 766 NDIAALARADPADLKKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVH----PAYLALKT 841 (936)
T ss_pred chHHHHhhCCHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcC----HHHHhcCC
Confidence 35788899999999999999999999998884222 2444555555554 36799999
Q ss_pred CCCHHHHHHHH
Q 039604 255 GIGSWSVHMFM 265 (373)
Q Consensus 255 GIGpwTA~~vL 265 (373)
||.+-|+.-..
T Consensus 842 g~~~~~~~~~~ 852 (936)
T PRK14973 842 GISPETICRHA 852 (936)
T ss_pred CCChhhHHHHH
Confidence 99999987653
No 78
>PRK08609 hypothetical protein; Provisional
Probab=63.76 E-value=17 Score=39.27 Aligned_cols=42 Identities=12% Similarity=0.058 Sum_probs=27.9
Q ss_pred HHHHHHHcCCCC-chhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 223 DLARKYQNGILS-DSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 223 ~lA~~i~~G~l~-L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
.+.+.+..|.+. ++.|..- ..+.+..|++|+||||+||..+-
T Consensus 63 kI~Eil~tG~~~~le~l~~~-~p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 63 VIQEYRETGESSVLQELKKE-VPEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred HHHHHHHhCChHHHHHHHhh-CcHHHHHHhcCCCCCHHHHHHHH
Confidence 444555668763 4556543 33445689999999999997653
No 79
>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=63.70 E-value=9.8 Score=29.40 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=23.4
Q ss_pred CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 231 GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 231 G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
|--.+.+|..++. +.|..++|+|+++.+-+.
T Consensus 31 ~I~tv~dL~~~s~----~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 31 GIHTVGDLVKYSE----EDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp T--BHHHHHCS-H----HHHHTSTTSHHHHHHHHH
T ss_pred CCcCHHHHHhCCH----HHHHhCCCCCHhHHHHHH
Confidence 5557888888875 579999999999988653
No 80
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=63.31 E-value=24 Score=38.25 Aligned_cols=68 Identities=22% Similarity=0.241 Sum_probs=41.4
Q ss_pred CHHHHhcCChHHHHhc-CCChhHHHHHHHHHHHHHc----------------------CCCCchhhhCCChHHHHHHHhc
Q 039604 196 VPETVLALTPQQLRQI-GVSGRKASYLHDLARKYQN----------------------GILSDSAIVNMDDKSLFTMLTM 252 (373)
Q Consensus 196 tPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~~i~~----------------------G~l~L~~L~~~~~ee~~~~L~s 252 (373)
++.+|..++.++|..+ ||...++..|.+..+.-.+ ..-+++.|.+.+. +.|.+
T Consensus 449 ~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~l~~a~~----e~l~~ 524 (562)
T PRK08097 449 HLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDRSWQQLLSRSE----QQWQQ 524 (562)
T ss_pred CHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcCCHHHHHcCCH----HHHhc
Confidence 5777777777777665 5545555544433221111 1113444444443 56999
Q ss_pred CCCCCHHHHHHHHHH
Q 039604 253 VNGIGSWSVHMFMIF 267 (373)
Q Consensus 253 LpGIGpwTA~~vLLf 267 (373)
++|||+.+|+.+.-|
T Consensus 525 i~gIG~~~a~si~~~ 539 (562)
T PRK08097 525 LPGIGEGRARQLIAF 539 (562)
T ss_pred CCCchHHHHHHHHHH
Confidence 999999999999876
No 81
>PRK07945 hypothetical protein; Provisional
Probab=62.91 E-value=12 Score=37.73 Aligned_cols=53 Identities=13% Similarity=0.065 Sum_probs=36.7
Q ss_pred HHhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHH-HHhcCCCCCHHHHHHHHH
Q 039604 208 LRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFT-MLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 208 Lr~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~-~L~sLpGIGpwTA~~vLL 266 (373)
|.--|=..+|++.-++.|+.+..-.-+ .+..+. .+ .|++|||||.-+|..+.=
T Consensus 14 le~~~~n~frv~ayr~aa~~~~~~~~~--~~~~~~----~~g~l~~~~giG~~~a~~i~e 67 (335)
T PRK07945 14 LERARADTYRVRAFRRAADVVEALDAA--ERARRA----RAGSLTSLPGIGPKTAKVIAQ 67 (335)
T ss_pred HHHcCCChhhHHHHHHHHHHHHhcChh--HHHHHH----hcCCcccCCCcCHHHHHHHHH
Confidence 344577679999999999988753222 122221 11 699999999999997763
No 82
>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=62.88 E-value=19 Score=30.91 Aligned_cols=57 Identities=25% Similarity=0.328 Sum_probs=37.3
Q ss_pred HHHhcCChHHHHh-cCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 198 ETVLALTPQQLRQ-IGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 198 e~La~l~~eeLr~-~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
-+|-.++.++|.. -|+...+|+.|..--.. +|.+. -.++|..++|||+++++-+.-|
T Consensus 60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f~-----------s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 60 VNINAASLEELQALPGIGPAKAKAIIEYREE--NGAFK-----------SVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCCcC-----------CHHHHHcCCCCCHHHHHHHHhc
Confidence 3455677788876 36766777666553322 34321 2578899999999999877543
No 83
>PRK07758 hypothetical protein; Provisional
Probab=62.26 E-value=15 Score=30.89 Aligned_cols=31 Identities=16% Similarity=0.309 Sum_probs=25.5
Q ss_pred CCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 231 GILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 231 G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
|--.+++|..++. ++|.+|+|+|+++.+-+-
T Consensus 54 GI~TL~dLv~~te----~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 54 GIHTVEELSKYSE----KEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCCcHHHHHcCCH----HHHHHccCCCHHHHHHHH
Confidence 6667888888875 678999999999988754
No 84
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=61.99 E-value=8.4 Score=29.32 Aligned_cols=22 Identities=18% Similarity=0.288 Sum_probs=17.3
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
.++|.++||||++.|+.++-+-
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHH
Confidence 5789999999999999998654
No 85
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=60.32 E-value=6.5 Score=26.97 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=14.3
Q ss_pred HHHhcCCCCCHHHHHHHH
Q 039604 248 TMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vL 265 (373)
+.+..+||||++||.-++
T Consensus 16 dni~Gv~giG~ktA~~ll 33 (36)
T smart00279 16 DNIPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCCCcccHHHHHHHH
Confidence 345689999999998665
No 86
>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=59.81 E-value=13 Score=28.45 Aligned_cols=54 Identities=24% Similarity=0.257 Sum_probs=34.1
Q ss_pred HhcCChHHHHh--cCCChhHHHHHHHHHHHHH-cCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 200 VLALTPQQLRQ--IGVSGRKASYLHDLARKYQ-NGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 200 La~l~~eeLr~--~Gls~~KA~yI~~lA~~i~-~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
|-.++.++|.. -|++..+|+.|.+ +.. .|.+. -.++|..++|||.++++-++-+
T Consensus 10 vNta~~~~L~~~ipgig~~~a~~Il~---~R~~~g~~~-----------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 10 INTATAEELQRAMNGVGLKKAEAIVS---YREEYGPFK-----------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CcCCCHHHHHhHCCCCCHHHHHHHHH---HHHHcCCcC-----------CHHHHHcCCCCCHHHHHHHHhh
Confidence 34456777776 3676555544433 222 23221 2578899999999999988754
No 87
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=59.21 E-value=42 Score=37.31 Aligned_cols=29 Identities=24% Similarity=0.251 Sum_probs=19.4
Q ss_pred chhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 235 DSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 235 L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
++.|.+.+ .+.|.+++|||+++|+.+.-|
T Consensus 551 i~~L~~As----~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 551 FEAIMDAD----EEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred HHHHHhCC----HHHHhccCCcCHHHHHHHHHH
Confidence 34444443 245788888888888888655
No 88
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=58.56 E-value=5.1 Score=37.80 Aligned_cols=25 Identities=32% Similarity=0.569 Sum_probs=21.6
Q ss_pred ChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 242 DDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 242 ~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
...+++..|+++.||||++|=.+|.
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs 91 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILS 91 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHc
Confidence 3567899999999999999988873
No 89
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.15 E-value=29 Score=33.07 Aligned_cols=58 Identities=21% Similarity=0.246 Sum_probs=42.0
Q ss_pred HHHHHHhhccCHH-HHHHHHHHHHHHh---CCCCCCCHHHHhcCChHHHHhc-CCChhHHHHHHHHHH
Q 039604 164 LTRSILYQQLAFK-AGTSIYTRFIALC---GGEAGVVPETVLALTPQQLRQI-GVSGRKASYLHDLAR 226 (373)
Q Consensus 164 LV~aILsQQ~S~~-aA~~i~~rL~~~~---G~~~~ptPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~ 226 (373)
|+..+|+.-+..+ .+..+.++|.+.| | +...|..++.++|..+ |+...||..|+.+.+
T Consensus 19 LLailL~~g~~~~~~~~~lA~~ll~~f~~~g-----~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~E 81 (218)
T TIGR00608 19 LLAIILRTGTPKGLDVLSLSKRLLDVFGRQD-----SLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81 (218)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHHhcccC-----CHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHH
Confidence 4455565555555 5666777888888 6 5889999999999874 887788888766544
No 90
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=56.93 E-value=25 Score=31.49 Aligned_cols=53 Identities=23% Similarity=0.339 Sum_probs=37.0
Q ss_pred hcCChHHHHhc-CCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHH
Q 039604 201 LALTPQQLRQI-GVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 201 a~l~~eeLr~~-Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLL 266 (373)
-.++.++|+.+ |+...||+.|.+-= -.+|... .++.|..++|||+++.+-..-
T Consensus 92 NtAs~eeL~~lpgIG~~kA~aIi~yR--e~~G~f~-----------sv~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 92 NTASAEELQALPGIGPKKAQAIIDYR--EENGPFK-----------SVDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred cccCHHHHHHCCCCCHHHHHHHHHHH--HHcCCCC-----------cHHHHHhccCCCHHHHHHHHh
Confidence 45678888764 57778888876532 2345331 268899999999999886653
No 91
>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=55.41 E-value=12 Score=32.26 Aligned_cols=22 Identities=18% Similarity=0.363 Sum_probs=19.3
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
.+.|+.|||||++.|.-++-+-
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHHH
Confidence 5788999999999999998663
No 92
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=53.36 E-value=7 Score=30.82 Aligned_cols=22 Identities=18% Similarity=0.208 Sum_probs=17.5
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCC
Q 039604 248 TMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
+.+..+||||++||.-++. -++
T Consensus 22 D~i~gv~giG~k~A~~ll~-~~~ 43 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLK-EYG 43 (75)
T ss_pred ccCCCCCcccHHHHHHHHH-HhC
Confidence 5577899999999998874 344
No 93
>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=52.17 E-value=27 Score=38.80 Aligned_cols=73 Identities=7% Similarity=0.144 Sum_probs=43.8
Q ss_pred ChHHHHHHHhc--CCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCCCCHHHHHHHHhhcCCchHHHHHHH
Q 039604 242 DDKSLFTMLTM--VNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWYL 319 (373)
Q Consensus 242 ~~ee~~~~L~s--LpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyrg~a~~yL 319 (373)
+.+.++..|.+ +||||++||.-+. -.||. +.+- .-. .--.++.... ..+++..+.+.+.|.-++.....+.
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv-~~fg~-~~~~---~i~-~~~~~L~~v~-gi~~~~~~~i~~~~~~~~~~~~~~~ 148 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIV-KTFGE-AAFD---VLD-DDPEKLLEVP-GISKANLEKFVSQWSQQGDERRLLA 148 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHH-HHhCH-hHHH---HHH-hCHHHHhcCC-CCCHHHHHHHHHHHHHhHHHHHHHH
Confidence 55678888876 9999999999776 23443 2221 111 1122332221 2456777788888877776655555
Q ss_pred HH
Q 039604 320 WR 321 (373)
Q Consensus 320 W~ 321 (373)
|.
T Consensus 149 ~L 150 (720)
T TIGR01448 149 GL 150 (720)
T ss_pred HH
Confidence 54
No 94
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=51.20 E-value=14 Score=33.21 Aligned_cols=28 Identities=21% Similarity=0.353 Sum_probs=21.4
Q ss_pred CCChHHHHHHHhcCCCCCHHHHHHHHHHh
Q 039604 240 NMDDKSLFTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 240 ~~~~ee~~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
+.+... .++|..|||||++.|..|.-+.
T Consensus 90 NiNtAs-~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 90 NINTAS-AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred cccccC-HHHHHHCCCCCHHHHHHHHHHH
Confidence 334433 3667999999999999998765
No 95
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=47.74 E-value=40 Score=34.24 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=33.4
Q ss_pred HHcCCC-CchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCC
Q 039604 228 YQNGIL-SDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHR 271 (373)
Q Consensus 228 i~~G~l-~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgr 271 (373)
+..|.+ -++++.+-+....++.++++-|||.+||+..-.-||.-
T Consensus 76 letG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrT 120 (353)
T KOG2534|consen 76 LETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRT 120 (353)
T ss_pred HHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhH
Confidence 345766 34555555567789999999999999999988777753
No 96
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=46.04 E-value=18 Score=32.11 Aligned_cols=20 Identities=5% Similarity=-0.049 Sum_probs=17.5
Q ss_pred HHHHhcCCCCCHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLL 266 (373)
.++|.++|||||..|..|.-
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 46688999999999999984
No 97
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=46.03 E-value=57 Score=36.31 Aligned_cols=20 Identities=25% Similarity=0.240 Sum_probs=15.7
Q ss_pred HhcCCCCCHHHHHHHHHHhCC
Q 039604 250 LTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 250 L~sLpGIGpwTA~~vLLf~lg 270 (373)
+..++|||-++||-+... +|
T Consensus 183 ~~~i~gigF~~aD~iA~~-~g 202 (720)
T TIGR01448 183 AEDVKGIGFLTADQLAQA-LG 202 (720)
T ss_pred hhhcCCCCHHHHHHHHHH-cC
Confidence 346999999999998754 44
No 98
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=45.63 E-value=29 Score=34.46 Aligned_cols=47 Identities=13% Similarity=0.029 Sum_probs=34.8
Q ss_pred CCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 212 GVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 212 Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
|-..+|+..-++.|..+.+-..++.. .+.+..|||||+.+|+.+-=+
T Consensus 18 ~~~~~r~~aY~~Aa~~l~~l~~~i~~---------~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 18 GGNPFRVRAYRKAARALESLPEPIES---------LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred cCCcchHHHHHHHHHHHHhCCcccCC---------HHHhcCCCCccHHHHHHHHHH
Confidence 44468898889999988865444331 236699999999999987643
No 99
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=44.93 E-value=80 Score=30.99 Aligned_cols=84 Identities=20% Similarity=0.215 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHH---cCCCCchhhhC-CChHHHHHH-HhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcC
Q 039604 218 ASYLHDLARKYQ---NGILSDSAIVN-MDDKSLFTM-LTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSL 292 (373)
Q Consensus 218 A~yI~~lA~~i~---~G~l~L~~L~~-~~~ee~~~~-L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl 292 (373)
+..|+.+|+... ...+....... .++++.... |.+|||||+..|.-++..-.+--+++-+++ .-+.+..|.
T Consensus 147 a~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~----~eL~~v~gi 222 (254)
T COG1948 147 AELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASE----EELMKVKGI 222 (254)
T ss_pred HHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH----HHHHHhcCc
Q ss_pred CCCCCHHHHHHHHhhcC
Q 039604 293 EELPRPSQMDQLCEKWR 309 (373)
Q Consensus 293 ~~~~~~~e~~~l~e~w~ 309 (373)
+. +...++.+.|.
T Consensus 223 g~----k~A~~I~~~~~ 235 (254)
T COG1948 223 GE----KKAREIYRFLR 235 (254)
T ss_pred cH----HHHHHHHHHHh
No 100
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=44.48 E-value=77 Score=32.49 Aligned_cols=49 Identities=14% Similarity=0.225 Sum_probs=39.9
Q ss_pred CCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHh
Q 039604 158 HTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQ 210 (373)
Q Consensus 158 ~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~ 210 (373)
.=|...++.-.++--+..+...++|++|++.||. .-+.|..++.|+|..
T Consensus 303 liPLaeIi~~~~g~gi~tK~V~~~we~lv~~FGt----Ei~vLi~a~~e~La~ 351 (403)
T COG1379 303 LIPLAEIISMALGKGITTKAVKRTWERLVRAFGT----EIDVLIDAPIEELAR 351 (403)
T ss_pred cccHHHHHHHHhccceechhHHHHHHHHHHHhcc----hhhhHhcCCHHHHhh
Confidence 3477777877788889999999999999999996 356777888888844
No 101
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=44.17 E-value=21 Score=30.03 Aligned_cols=22 Identities=23% Similarity=0.354 Sum_probs=19.5
Q ss_pred HHHHHhcCCCCCHHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLLf 267 (373)
+.-.|+.|.|||+.+|..++..
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~ 34 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKK 34 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHH
T ss_pred hHhHHhhhhccCHHHHHHHHHH
Confidence 5788999999999999998754
No 102
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=43.15 E-value=32 Score=34.80 Aligned_cols=48 Identities=21% Similarity=0.138 Sum_probs=29.6
Q ss_pred CCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHH--HhcCCCCCHHHHHHHHHH
Q 039604 212 GVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTM--LTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 212 Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~--L~sLpGIGpwTA~~vLLf 267 (373)
|-...|+..-+..|+.+.+-.- +.+++.+. ++.|||||+-+|+.+.-|
T Consensus 23 Gen~fk~~aYr~Aa~sle~~~e--------~~~ei~e~~~~t~l~gIGk~ia~~I~e~ 72 (326)
T COG1796 23 GENPFKIRAYRKAAQSLENLTE--------DLEEIEERGRLTELPGIGKGIAEKISEY 72 (326)
T ss_pred CCCccchHHHHHHHHhhhhccc--------chHHHHhhcccCCCCCccHHHHHHHHHH
Confidence 4433677777777776664322 33445555 778888888888776533
No 103
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.03 E-value=1.1e+02 Score=28.80 Aligned_cols=76 Identities=18% Similarity=0.123 Sum_probs=56.6
Q ss_pred CCCcCCCCCHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHH----hcCCCh--hHHHHHHHH
Q 039604 151 PPTFDSFHTPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLR----QIGVSG--RKASYLHDL 224 (373)
Q Consensus 151 g~r~~~~~dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr----~~Gls~--~KA~yI~~l 224 (373)
|.+.......||.|+-.+--.-+||..+.+=.+.|.+.|-+ ..|+.|+..+++++. ..|+-+ .|.+.+.+=
T Consensus 23 G~p~~Dd~~LFE~l~Le~fQAGLSW~tVL~KRe~freaF~~---Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~N 99 (188)
T COG2818 23 GVPLHDDQRLFELLCLEGFQAGLSWLTVLKKREAFREAFHG---FDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINN 99 (188)
T ss_pred CCCCCChHHHHHHHHHHHHhccchHHHHHHhHHHHHHHHhc---CCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHH
Confidence 33444445689999999888889999998889999999854 589999999998865 345544 555566666
Q ss_pred HHHHH
Q 039604 225 ARKYQ 229 (373)
Q Consensus 225 A~~i~ 229 (373)
|+++.
T Consensus 100 A~~~l 104 (188)
T COG2818 100 ARAVL 104 (188)
T ss_pred HHHHH
Confidence 66665
No 104
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=38.77 E-value=28 Score=33.45 Aligned_cols=56 Identities=25% Similarity=0.299 Sum_probs=0.0
Q ss_pred hcCChHHHHh--cCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHH
Q 039604 201 LALTPQQLRQ--IGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSV 261 (373)
Q Consensus 201 a~l~~eeLr~--~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA 261 (373)
..++..||-+ ++- +.|-.....+|+.+.+.--+|..|...+ .++|++++|||+--|
T Consensus 22 ~~Lsd~ELLailLrt-G~~~~~~~~la~~lL~~fg~L~~l~~a~----~~el~~v~GiG~aka 79 (224)
T COG2003 22 EALSDAELLAILLRT-GTKGESVLDLAKELLQEFGSLAELLKAS----VEELSSVKGIGLAKA 79 (224)
T ss_pred hhcchHHHHHHHHhc-CCCCCCHHHHHHHHHHHcccHHHHHhCC----HHHHhhCCCccHHHH
No 105
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=38.15 E-value=74 Score=30.83 Aligned_cols=52 Identities=27% Similarity=0.256 Sum_probs=35.6
Q ss_pred CCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCc
Q 039604 212 GVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDV 274 (373)
Q Consensus 212 Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDv 274 (373)
|+...+++.|. ..|--+++.|...+ .+.|..++|||..+|+-+.-+ |+.+++
T Consensus 10 GIG~krakkLl------~~GF~Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~-l~~~~~ 61 (232)
T PRK12766 10 GVGPSKAEALR------EAGFESVEDVRAAD----QSELAEVDGIGNALAARIKAD-VGGLEV 61 (232)
T ss_pred CcCHHHHHHHH------HcCCCCHHHHHhCC----HHHHHHccCCCHHHHHHHHHH-hccccc
Confidence 45455554442 23455677777665 467899999999999999765 666654
No 106
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=37.69 E-value=55 Score=24.82 Aligned_cols=39 Identities=15% Similarity=0.255 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCCCCHHHHhcCChHHHHhc-CCChhHHHHHHHH
Q 039604 181 IYTRFIALCGGEAGVVPETVLALTPQQLRQI-GVSGRKASYLHDL 224 (373)
Q Consensus 181 i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~-Gls~~KA~yI~~l 224 (373)
..++|.++|| +.+.|..++.++|..+ |+....|+.|.+.
T Consensus 15 ~ak~L~~~f~-----sl~~l~~a~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFG-----SLEALMNASVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCS-----CHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcC-----CHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence 3456777776 7999999999999875 6766777766654
No 107
>PRK08609 hypothetical protein; Provisional
Probab=37.25 E-value=52 Score=35.61 Aligned_cols=46 Identities=22% Similarity=0.164 Sum_probs=34.4
Q ss_pred cCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 211 IGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 211 ~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
.|=..+|++.-++.|+.+.+-.-++. . +..|..|||||+.+|+.|-
T Consensus 20 ~g~n~fr~~aYr~Aa~~i~~l~~~i~---~------~~~l~~ipgIG~~ia~kI~ 65 (570)
T PRK08609 20 KGENPFKISAFRKAAQALELDERSLS---E------IDDFTKLKGIGKGTAEVIQ 65 (570)
T ss_pred cCCCcHHHHHHHHHHHHHHhCchhhh---h------hhhhccCCCcCHHHHHHHH
Confidence 45556899999999998876443332 1 2478999999999998765
No 108
>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=36.77 E-value=67 Score=33.17 Aligned_cols=67 Identities=15% Similarity=0.157 Sum_probs=49.9
Q ss_pred CHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHHcCCCCc
Q 039604 159 TPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSD 235 (373)
Q Consensus 159 dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~~G~l~L 235 (373)
=|++.++..+++--...+....+|++|+++||. -.+-|.+++.|+|+.+. .-|-.....+.+|++..
T Consensus 297 iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~----E~~iL~~~~~eel~~~~------~~~a~~I~~~R~G~v~~ 363 (374)
T TIGR00375 297 IPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGT----EIAVLHEAAEEDLARVV------PKVAALIVKFRSGKLEL 363 (374)
T ss_pred CCHHHHHhhhcCCCCccHHHHHHHHHHHHHhcc----HHHHHhcCCHHHHHHHH------HHHHHHHHHHHCCCEEE
Confidence 478899999999888999999999999999994 35677888999997653 22223333455676643
No 109
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=36.53 E-value=2.1e+02 Score=27.27 Aligned_cols=104 Identities=18% Similarity=0.091 Sum_probs=59.2
Q ss_pred CHHHHHHHHHHhhccCHHHHHHHHHHHHHHhCCCCCCCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHH---------
Q 039604 159 TPFLALTRSILYQQLAFKAGTSIYTRFIALCGGEAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQ--------- 229 (373)
Q Consensus 159 dpfE~LV~aILsQQ~S~~aA~~i~~rL~~~~G~~~~ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~--------- 229 (373)
+-.+.+|+.|=-=+...++...+.+.|++.||+.+.-+-+.|..++ |+ |+|..++.-.-.+-.
T Consensus 70 ~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LP-------GV-GrKTAnvVL~~a~g~p~i~VDTHV 141 (211)
T COG0177 70 EELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLP-------GV-GRKTANVVLSFAFGIPAIAVDTHV 141 (211)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCC-------Cc-chHHHHHHHHhhcCCCcccccchH
Confidence 4556666666555667778888889999999975422223333322 56 566555432111000
Q ss_pred ---cCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 230 ---NGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 230 ---~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
...+.+. ...+.+++.+.|+.+=.=.-|+---..|..+||.
T Consensus 142 ~Rvs~R~gl~--~~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~ 185 (211)
T COG0177 142 HRVSNRLGLV--PGKTPEEVEEALMKLIPKELWTDLHHWLILHGRY 185 (211)
T ss_pred HHHHHHhCCC--CCCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhhh
Confidence 0111111 1356677777777777777777666666667765
No 110
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=35.71 E-value=8.7 Score=32.35 Aligned_cols=20 Identities=20% Similarity=0.205 Sum_probs=13.1
Q ss_pred HHHhcCCCCCHHHHHHHHHH
Q 039604 248 TMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf 267 (373)
+-+-.+||||+|||.-++-.
T Consensus 18 DNIPGV~GIG~KtA~~LL~~ 37 (101)
T PF01367_consen 18 DNIPGVPGIGPKTAAKLLQE 37 (101)
T ss_dssp CTB---TTSTCHCCCCCHHH
T ss_pred cCCCCCCCCCHHHHHHHHHH
Confidence 44678999999999876643
No 111
>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=35.43 E-value=41 Score=25.55 Aligned_cols=21 Identities=19% Similarity=0.316 Sum_probs=17.8
Q ss_pred HHHHhc-CCCCCHHHHHHHHHH
Q 039604 247 FTMLTM-VNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~s-LpGIGpwTA~~vLLf 267 (373)
.+.|.. ++|||+.+|..++-+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 357777 999999999999866
No 112
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=34.56 E-value=54 Score=33.64 Aligned_cols=37 Identities=16% Similarity=0.124 Sum_probs=23.3
Q ss_pred HHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHH
Q 039604 223 DLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHM 263 (373)
Q Consensus 223 ~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~ 263 (373)
.+|+.+.+.--++..+.+.+. ++|..++|||+..|..
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~----eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASI----EDLDEVEGIGEVRARA 334 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCH----HHHhhCCCcCHHHHHH
Confidence 445555554445666666553 4577777888777776
No 113
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=34.26 E-value=47 Score=32.03 Aligned_cols=31 Identities=23% Similarity=0.225 Sum_probs=22.1
Q ss_pred ccCCCCHHHHHHHHHHhcCCCCCCH--HHHHHHHh
Q 039604 274 VLPINDLGVRKGVQLLYSLEELPRP--SQMDQLCE 306 (373)
Q Consensus 274 vfPv~D~~VrR~l~rlygl~~~~~~--~e~~~l~e 306 (373)
++|+ |+|+.|+..++ |+-.+.+. +.+.++.+
T Consensus 173 iiPL-DtH~~rvar~L-gL~~Rk~~d~kaa~ElT~ 205 (229)
T TIGR02757 173 ILPL-DTHVFRIAKKL-KLLKRKSYDLKAAIEITE 205 (229)
T ss_pred eeec-hHhHHHHHHHh-CCcccCchhHHHHHHHHH
Confidence 5799 99999999888 98776543 33444433
No 114
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=33.33 E-value=30 Score=24.74 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=13.3
Q ss_pred CCCCHHHHHHHHHHhc
Q 039604 276 PINDLGVRKGVQLLYS 291 (373)
Q Consensus 276 Pv~D~~VrR~l~rlyg 291 (373)
-.+|+||+|++.++|.
T Consensus 16 teddT~v~r~l~~yY~ 31 (41)
T PF14475_consen 16 TEDDTHVHRVLRKYYT 31 (41)
T ss_pred CcchhHHHHHHHHHHH
Confidence 3459999999999984
No 115
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=33.16 E-value=76 Score=32.15 Aligned_cols=22 Identities=18% Similarity=0.549 Sum_probs=19.4
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
+++|+.++||||.|.....|.+
T Consensus 268 feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 268 FEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred HHHHHhcCCCCHHHHHHHHHHH
Confidence 6899999999999998877765
No 116
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=31.26 E-value=70 Score=34.80 Aligned_cols=29 Identities=10% Similarity=0.206 Sum_probs=25.6
Q ss_pred CHHHHhcCChHHHHhcCCChhHHHHHHHH
Q 039604 196 VPETVLALTPQQLRQIGVSGRKASYLHDL 224 (373)
Q Consensus 196 tPe~La~l~~eeLr~~Gls~~KA~yI~~l 224 (373)
+.+.|.+++.|+|..+|++...|+.|++.
T Consensus 536 s~~~ik~As~eeL~~vgi~~~~A~~I~~~ 564 (567)
T PRK14667 536 TLYDFLKADDEELKKLGIPPSVKQEVKKY 564 (567)
T ss_pred CHHHHHhCCHHHHHHcCCCHHHHHHHHHH
Confidence 78999999999999999998888888654
No 117
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=31.25 E-value=49 Score=31.94 Aligned_cols=60 Identities=18% Similarity=0.171 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHH-cCC-CCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHHHhcCCCC
Q 039604 218 ASYLHDLARKYQ-NGI-LSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQLLYSLEEL 295 (373)
Q Consensus 218 A~yI~~lA~~i~-~G~-l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~rlygl~~~ 295 (373)
.|.+.-..+|++ ... +|+.-|...+..++ ++|+ |+||.|+..++ |+-.+
T Consensus 145 cKR~~MFLRWMVR~d~~VD~GlW~~i~ps~L---------------------------iiPL-DtHv~~var~L-GL~~r 195 (232)
T PF09674_consen 145 CKRLNMFLRWMVRKDSPVDFGLWSSIDPSDL---------------------------IIPL-DTHVFRVARKL-GLLKR 195 (232)
T ss_pred HHHHHHHHHhhccCCCCCCCcCCCCCCHHHc---------------------------cccc-hHhHHHHHHHc-CCccC
Confidence 455555566665 233 66665655554332 5799 99999999998 88654
Q ss_pred CC--HHHHHHHHh
Q 039604 296 PR--PSQMDQLCE 306 (373)
Q Consensus 296 ~~--~~e~~~l~e 306 (373)
.+ -+.+.++.+
T Consensus 196 k~~d~k~A~elT~ 208 (232)
T PF09674_consen 196 KSADWKAARELTE 208 (232)
T ss_pred CCccHHHHHHHHH
Confidence 32 334444444
No 118
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=30.88 E-value=73 Score=31.12 Aligned_cols=32 Identities=22% Similarity=0.259 Sum_probs=27.9
Q ss_pred CCHHHHhcCChHHHHhc-CCChhHHHHHHHHHH
Q 039604 195 VVPETVLALTPQQLRQI-GVSGRKASYLHDLAR 226 (373)
Q Consensus 195 ptPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~ 226 (373)
.+.+.|..++.++|..| |+...||+.|++...
T Consensus 216 gsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~ 248 (254)
T KOG2841|consen 216 GSLQQISNASEGELEQCPGLGPAKAKRLHKFLH 248 (254)
T ss_pred ccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHh
Confidence 47999999999999885 888999999998764
No 119
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=29.79 E-value=2.8e+02 Score=23.74 Aligned_cols=24 Identities=17% Similarity=0.187 Sum_probs=20.1
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhCC
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
+..|+.++|||+..|..++--|+.
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHHhCcC
Confidence 577889999999999988876653
No 120
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=28.84 E-value=1.1e+02 Score=34.17 Aligned_cols=32 Identities=19% Similarity=0.317 Sum_probs=26.6
Q ss_pred CHHHHhcCChHHHHhc-CCChhHHHHHHHHHHH
Q 039604 196 VPETVLALTPQQLRQI-GVSGRKASYLHDLARK 227 (373)
Q Consensus 196 tPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~~ 227 (373)
+.+.|..++.++|..+ |++..+|+.|++..+.
T Consensus 659 Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~ 691 (694)
T PRK14666 659 SLQAMAAAGEEGLAAVPGIGPARAAALHEHLKT 691 (694)
T ss_pred CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHH
Confidence 7899999999999987 8888888888776544
No 121
>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=28.59 E-value=1.8e+02 Score=20.20 Aligned_cols=36 Identities=8% Similarity=0.100 Sum_probs=27.1
Q ss_pred HHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 228 YQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 228 i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
..+|.-+++.+...+. +.|..++|++.-.|+-+..-
T Consensus 10 ~~~G~~s~e~la~~~~----~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 10 VEEGFTTVEDLAYVPI----DELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHcCCCCHHHHHccCH----HHHhcCCCCCHHHHHHHHHH
Confidence 3467778888888875 56678999998888776543
No 122
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=28.49 E-value=32 Score=29.88 Aligned_cols=22 Identities=23% Similarity=0.324 Sum_probs=18.7
Q ss_pred HHHHHhcCCCCCHHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLLf 267 (373)
+.-.|+.|.|||+.+|..++-.
T Consensus 15 v~~aL~~I~GIG~~~a~~i~~~ 36 (122)
T PRK05179 15 VVIALTYIYGIGRTRAKEILAA 36 (122)
T ss_pred EEeeecccccccHHHHHHHHHH
Confidence 4567899999999999998854
No 123
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=28.48 E-value=41 Score=34.16 Aligned_cols=20 Identities=30% Similarity=0.430 Sum_probs=17.5
Q ss_pred HHHHhcCCCCCHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLL 266 (373)
.++|+.+||||.++|.-|++
T Consensus 329 ~~~llRVPGiG~ksa~rIv~ 348 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVM 348 (404)
T ss_pred HHHhcccCCCChHHHHHHHH
Confidence 68899999999999987764
No 124
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=28.36 E-value=33 Score=29.83 Aligned_cols=22 Identities=27% Similarity=0.223 Sum_probs=18.8
Q ss_pred HHHHHhcCCCCCHHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLLf 267 (373)
+.-.|+.|.|||+.+|..++-.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~ 36 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEK 36 (122)
T ss_pred eeeeecccccccHHHHHHHHHH
Confidence 4567999999999999998854
No 125
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=27.90 E-value=4.1e+02 Score=28.48 Aligned_cols=154 Identities=15% Similarity=0.148 Sum_probs=84.3
Q ss_pred CCCCCchhHHHHHHHHHhh-ChHHHHHHHhCCC----CCc----CCCCCHHHH--HHHHHHhhccCHHHHHHHHHHHHHH
Q 039604 120 RPLSSEGEVEAAIRHLRNA-DRQLASLIDIHPP----PTF----DSFHTPFLA--LTRSILYQQLAFKAGTSIYTRFIAL 188 (373)
Q Consensus 120 r~l~ld~Dl~~~~~~L~~~-Dp~La~li~~~gg----~r~----~~~~dpfE~--LV~aILsQQ~S~~aA~~i~~rL~~~ 188 (373)
+.++.++--.-.+..|.+. ++.++.-....-. +-. ...+.||.. |.+.++...++...|..+...|.+.
T Consensus 130 ~~Is~~eL~~~v~~~l~~~~g~e~a~ry~~~~~~~~~~~v~~~~~~~~~PFSkGiLaRsLi~aDV~~~~A~~Ia~~Lk~~ 209 (475)
T PRK12337 130 REIGAKELEKRTARELAERYGEEARLRYRARQQNAGELFVEEAEGAPRVPFSKGILAQSLMAAGLAPDVARRLARETERD 209 (475)
T ss_pred cccCHHHHHHHHHHHHHHhcCHHHHHHHHHhcccchheeeeeCCCCCCCCCchhHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3455555445555566543 3555543322211 111 123578988 9999999999999999999999877
Q ss_pred h---CCCCCCCHHHHhcCChHHHHhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 189 C---GGEAGVVPETVLALTPQQLRQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 189 ~---G~~~~ptPe~La~l~~eeLr~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
+ |.. ..+.+.+...-.+.|.. .+...-++++ +++..+....- ..+-.+..++|+|.-|...-|
T Consensus 210 L~~kg~~-~~~ra~VR~~V~~~L~~-~l~~~~a~~y-~la~~i~~~k~-----------p~vil~~G~~G~GKSt~a~~L 275 (475)
T PRK12337 210 LRRSGDR-VVRRDQLRRKVEALLLE-EAGEEVARRY-RLLRSIRRPPR-----------PLHVLIGGVSGVGKSVLASAL 275 (475)
T ss_pred HHhcccc-cccHHHHHHHHHHHHHh-hhhhhHHHHH-HHHHHhhccCC-----------CeEEEEECCCCCCHHHHHHHH
Confidence 6 321 12334433222222322 1111112222 34443333110 013357889999999988888
Q ss_pred HHhCCCCCccCCCCHHHHHHHHHH
Q 039604 266 IFSLHRPDVLPINDLGVRKGVQLL 289 (373)
Q Consensus 266 Lf~lgrpDvfPv~D~~VrR~l~rl 289 (373)
...++-..++.. |. ++.++..+
T Consensus 276 A~~lg~~~ii~t-D~-iR~~lr~~ 297 (475)
T PRK12337 276 AYRLGITRIVST-DA-VREVLRAM 297 (475)
T ss_pred HHHcCCcEEeeh-hH-HHHHHHhh
Confidence 888876545455 65 34444433
No 126
>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=27.65 E-value=2.1e+02 Score=19.78 Aligned_cols=34 Identities=21% Similarity=0.126 Sum_probs=28.5
Q ss_pred CCCHHHHhcCChHHHHh-cCCChhHHHHHHHHHHH
Q 039604 194 GVVPETVLALTPQQLRQ-IGVSGRKASYLHDLARK 227 (373)
Q Consensus 194 ~ptPe~La~l~~eeLr~-~Gls~~KA~yI~~lA~~ 227 (373)
+-+.++++.+++++|.. .|++.-++..|+..|+.
T Consensus 14 ~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 14 FTTVEDLAYVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred CCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 46899999999999987 58988888888877763
No 127
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=27.64 E-value=89 Score=31.85 Aligned_cols=43 Identities=12% Similarity=-0.028 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHH
Q 039604 216 RKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 216 ~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf 267 (373)
.|+..-..+|..+.+=..+.. -.+++..|||||+++|+.+--|
T Consensus 33 ~r~~~y~~Aasvlk~~p~~I~---------S~~ea~~lP~iG~kia~ki~Ei 75 (353)
T KOG2534|consen 33 DRARAYRRAASVLKSLPFPIT---------SGEEAEKLPGIGPKIAEKIQEI 75 (353)
T ss_pred HHHHHHHHHHHHHHhCCCCcc---------cHHHhcCCCCCCHHHHHHHHHH
Confidence 344444555555554332221 2577889999999999988643
No 128
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=26.54 E-value=1.3e+02 Score=29.13 Aligned_cols=42 Identities=14% Similarity=0.110 Sum_probs=33.5
Q ss_pred HHHHHHH-hCCCCCCCHHHHhcCChHHHHhc-CCChhHHHHHHHHHHHH
Q 039604 182 YTRFIAL-CGGEAGVVPETVLALTPQQLRQI-GVSGRKASYLHDLARKY 228 (373)
Q Consensus 182 ~~rL~~~-~G~~~~ptPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~~i 228 (373)
.++|.+. || +.+.|..++.++|..+ |++..+|..|+.....+
T Consensus 16 akkLl~~GF~-----Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~ 59 (232)
T PRK12766 16 AEALREAGFE-----SVEDVRAADQSELAEVDGIGNALAARIKADVGGL 59 (232)
T ss_pred HHHHHHcCCC-----CHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccc
Confidence 3455555 54 7999999999999987 99999999998876644
No 129
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=26.50 E-value=56 Score=33.53 Aligned_cols=22 Identities=32% Similarity=0.566 Sum_probs=18.7
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q 039604 247 FTMLTMVNGIGSWSVHMFMIFS 268 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf~ 268 (373)
+++|.-+|||||.|+....+.+
T Consensus 277 f~elLl~~GiGpstvRALalVA 298 (373)
T COG1415 277 FEELLLVPGIGPSTVRALALVA 298 (373)
T ss_pred HHHHHhccCCCHHHHHHHHHHH
Confidence 6899999999999998776644
No 130
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=26.39 E-value=79 Score=23.23 Aligned_cols=21 Identities=5% Similarity=0.385 Sum_probs=12.8
Q ss_pred HHHcCCCCchhhhCCChHHHH
Q 039604 227 KYQNGILSDSAIVNMDDKSLF 247 (373)
Q Consensus 227 ~i~~G~l~L~~L~~~~~ee~~ 247 (373)
.|.+|.++.+.|..++.+++.
T Consensus 23 ~F~~~~i~g~~L~~lt~~dL~ 43 (64)
T PF00536_consen 23 NFEKNYIDGEDLLSLTEEDLE 43 (64)
T ss_dssp HHHHTTSSHHHHTTSCHHHHH
T ss_pred HHHcCCchHHHHHhcCHHHHH
Confidence 334466677777777666543
No 131
>PRK14976 5'-3' exonuclease; Provisional
Probab=26.29 E-value=40 Score=33.21 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=17.4
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Q 039604 248 TMLTMVNGIGSWSVHMFMIFSLHR 271 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf~lgr 271 (373)
+.+-.+||||+|||.-++ --+|-
T Consensus 191 DnipGVpGIG~KtA~~LL-~~~gs 213 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLL-NKYGN 213 (281)
T ss_pred CCCCCCCcccHHHHHHHH-HHcCC
Confidence 456789999999998876 34543
No 132
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=25.52 E-value=39 Score=30.67 Aligned_cols=22 Identities=23% Similarity=0.187 Sum_probs=18.5
Q ss_pred HHHHHhcCCCCCHHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLLf 267 (373)
+.-.|+.|.|||+.+|..++-.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~ 49 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKK 49 (154)
T ss_pred EEEeecccccccHHHHHHHHHH
Confidence 4567999999999999988743
No 133
>PRK00254 ski2-like helicase; Provisional
Probab=25.22 E-value=1.3e+02 Score=33.15 Aligned_cols=24 Identities=13% Similarity=0.012 Sum_probs=14.9
Q ss_pred HHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 249 MLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 249 ~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
.|.+|||||++.|.-++-.|++-.
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~ 669 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSI 669 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCH
Confidence 455666666666666666656543
No 134
>smart00475 53EXOc 5'-3' exonuclease.
Probab=24.79 E-value=46 Score=32.38 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=16.9
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCC
Q 039604 248 TMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
+.+..+||||++||.-++- -+|
T Consensus 186 DnipGV~GIG~KtA~~Ll~-~yg 207 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLK-EFG 207 (259)
T ss_pred cCCCCCCCCCHHHHHHHHH-HhC
Confidence 4568899999999987763 344
No 135
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=24.60 E-value=53 Score=22.77 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=17.3
Q ss_pred CHHHHhcCChHHHHhcCCChh
Q 039604 196 VPETVLALTPQQLRQIGVSGR 216 (373)
Q Consensus 196 tPe~La~l~~eeLr~~Gls~~ 216 (373)
+-..|..++..+|+.+|+++.
T Consensus 16 tr~~L~~Lsd~~L~DIGl~R~ 36 (40)
T PF06568_consen 16 TRRELAELSDRQLADIGLTRS 36 (40)
T ss_pred HHHHHccCCHHHHHHcCCCHH
Confidence 356788999999999999753
No 136
>PRK09482 flap endonuclease-like protein; Provisional
Probab=24.48 E-value=46 Score=32.50 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=16.9
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCC
Q 039604 248 TMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
+.+..+|||||+||--++- -+|
T Consensus 182 DnIpGVpGIG~KtA~~LL~-~~g 203 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLN-QFR 203 (256)
T ss_pred cCCCCCCCcChHHHHHHHH-HhC
Confidence 4567899999999988764 344
No 137
>COG1179 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]
Probab=24.46 E-value=63 Score=31.78 Aligned_cols=69 Identities=17% Similarity=0.330 Sum_probs=44.2
Q ss_pred HhcCCCCCHHHHHHHHHHhCCCCCccCCCCHH---HHHHHHHHhcCCCCCCHHHHHHHHhhcCCchHHHHHH
Q 039604 250 LTMVNGIGSWSVHMFMIFSLHRPDVLPINDLG---VRKGVQLLYSLEELPRPSQMDQLCEKWRPYRSVASWY 318 (373)
Q Consensus 250 L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~---VrR~l~rlygl~~~~~~~e~~~l~e~w~Pyrg~a~~y 318 (373)
...+=|||.|++++..=-|.|+..++=.+|+- +-|.+.-+.+--..+..+.|++.....-||.-+-..-
T Consensus 35 VvGiGGVGSw~veALaRsGig~itlID~D~v~vTN~NRQi~A~~~~iGk~Kv~vm~eri~~InP~c~V~~~~ 106 (263)
T COG1179 35 VVGIGGVGSWAVEALARSGIGRITLIDMDDVCVTNTNRQIHALLGDIGKPKVEVMKERIKQINPECEVTAIN 106 (263)
T ss_pred EEecCchhHHHHHHHHHcCCCeEEEEecccccccccchhhHhhhhhcccHHHHHHHHHHHhhCCCceEeehH
Confidence 46788999999999998899987655554443 3344433333223344456666666667777655544
No 138
>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=24.28 E-value=47 Score=31.70 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=16.6
Q ss_pred HHHhcCCCCCHHHHHHHHHHhCC
Q 039604 248 TMLTMVNGIGSWSVHMFMIFSLH 270 (373)
Q Consensus 248 ~~L~sLpGIGpwTA~~vLLf~lg 270 (373)
+.+..+|||||+||.-++ --+|
T Consensus 183 DnipGv~GiG~ktA~~Ll-~~~g 204 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLL-KEYG 204 (240)
T ss_pred cCCCCCCccCHHHHHHHH-HHhC
Confidence 456789999999997665 3344
No 139
>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=24.11 E-value=42 Score=30.09 Aligned_cols=21 Identities=24% Similarity=0.203 Sum_probs=17.8
Q ss_pred HHHHHhcCCCCCHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLL 266 (373)
+.-.|+.|.|||+.+|..++-
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~ 39 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIAR 39 (144)
T ss_pred EEEeecceeccCHHHHHHHHH
Confidence 355789999999999998864
No 140
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=23.59 E-value=1.5e+02 Score=23.50 Aligned_cols=26 Identities=27% Similarity=0.386 Sum_probs=20.1
Q ss_pred hHHHHHHHHHhhChHHHHHHHhCCCC
Q 039604 127 EVEAAIRHLRNADRQLASLIDIHPPP 152 (373)
Q Consensus 127 Dl~~~~~~L~~~Dp~La~li~~~gg~ 152 (373)
-++++.++|...||.+++-....+..
T Consensus 10 ~L~eiEr~L~~~DP~fa~~l~~~~~~ 35 (82)
T PF11239_consen 10 RLEEIERQLRADDPRFAARLRSGRPR 35 (82)
T ss_pred HHHHHHHHHHhcCcHHHHHhccCCCC
Confidence 35788889999999999888764333
No 141
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=23.37 E-value=48 Score=29.88 Aligned_cols=21 Identities=24% Similarity=0.272 Sum_probs=18.1
Q ss_pred HHHHHhcCCCCCHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMI 266 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLL 266 (373)
+.-.|+.|.|||+.+|..++-
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~ 43 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIAR 43 (149)
T ss_pred EeeeccccccccHHHHHHHHH
Confidence 456799999999999998864
No 142
>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=22.96 E-value=43 Score=28.69 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=18.5
Q ss_pred HHHHHhcCCCCCHHHHHHHHHH
Q 039604 246 LFTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 246 ~~~~L~sLpGIGpwTA~~vLLf 267 (373)
+.-.|+.|.|||..+|..++-.
T Consensus 13 v~~aL~~i~GIG~~~a~~i~~~ 34 (113)
T TIGR03631 13 VEIALTYIYGIGRTRARKILEK 34 (113)
T ss_pred EeeeeeeeecccHHHHHHHHHH
Confidence 4567899999999999988754
No 143
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=21.66 E-value=1.7e+02 Score=32.60 Aligned_cols=66 Identities=18% Similarity=0.292 Sum_probs=42.8
Q ss_pred HhcCCChhHHHHHHHHHHHHHcCCCCchhhhCCChHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCccCCCCHHHHHHHHH
Q 039604 209 RQIGVSGRKASYLHDLARKYQNGILSDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFMIFSLHRPDVLPINDLGVRKGVQL 288 (373)
Q Consensus 209 r~~Gls~~KA~yI~~lA~~i~~G~l~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrpDvfPv~D~~VrR~l~r 288 (373)
-++|+...-...-+.||+.|. +++.|...+. +.|.+++|||...|.-+.-| |. +-+.+..+.+
T Consensus 512 ~aLGIr~VG~~~Ak~La~~f~----sl~~l~~a~~----e~l~~i~giG~~vA~si~~f-f~--------~~~~~~li~~ 574 (667)
T COG0272 512 YALGIRHVGETTAKSLARHFG----TLEALLAASE----EELASIPGIGEVVARSIIEF-FA--------NEENRELIDE 574 (667)
T ss_pred HHcCCchhhHHHHHHHHHHhh----hHHHHHhcCH----HHHhhccchhHHHHHHHHHH-Hc--------CHHHHHHHHH
Confidence 345655444455555665543 3566666654 56788999999999999865 22 5666667776
Q ss_pred Hhc
Q 039604 289 LYS 291 (373)
Q Consensus 289 lyg 291 (373)
|..
T Consensus 575 L~~ 577 (667)
T COG0272 575 LLA 577 (667)
T ss_pred HHH
Confidence 643
No 144
>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=21.63 E-value=1.2e+02 Score=33.43 Aligned_cols=31 Identities=16% Similarity=0.242 Sum_probs=22.4
Q ss_pred CCC-CchhhhCCChHHHHHHHhcCCCCCHHHHHHHH
Q 039604 231 GIL-SDSAIVNMDDKSLFTMLTMVNGIGSWSVHMFM 265 (373)
Q Consensus 231 G~l-~L~~L~~~~~ee~~~~L~sLpGIGpwTA~~vL 265 (373)
|.+ ++.+|..+. .+.|.+|+|+|.++|+-++
T Consensus 452 g~I~~~~Dl~~L~----~~~L~~L~GfG~Ksa~nIl 483 (652)
T TIGR00575 452 KLVRSVADLYALK----KEDLLELEGFGEKSAQNLL 483 (652)
T ss_pred CCcCCHHHHHhcC----HHHHhhccCccHHHHHHHH
Confidence 443 556666665 3478899999999998764
No 145
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=21.45 E-value=1.5e+02 Score=33.26 Aligned_cols=36 Identities=14% Similarity=0.060 Sum_probs=30.7
Q ss_pred CCCHHHHhcCChHHHHhc-CCChhHHHHHHHHHHHHH
Q 039604 194 GVVPETVLALTPQQLRQI-GVSGRKASYLHDLARKYQ 229 (373)
Q Consensus 194 ~ptPe~La~l~~eeLr~~-Gls~~KA~yI~~lA~~i~ 229 (373)
|-+.+.|..++.++|..+ |++...|+.|+..|..-.
T Consensus 628 FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~ 664 (691)
T PRK14672 628 FGSFRSLQSATPQDIATAIHIPLTQAHTILHAATRST 664 (691)
T ss_pred hcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhccc
Confidence 347899999999999986 999999999999887543
No 146
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.07 E-value=63 Score=28.29 Aligned_cols=21 Identities=24% Similarity=0.246 Sum_probs=18.1
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q 039604 247 FTMLTMVNGIGSWSVHMFMIF 267 (373)
Q Consensus 247 ~~~L~sLpGIGpwTA~~vLLf 267 (373)
.=.|+.|.|||.-+|..|+--
T Consensus 16 ~iALt~IyGIG~~~a~~I~~~ 36 (121)
T COG0099 16 VIALTYIYGIGRRRAKEICKK 36 (121)
T ss_pred eehhhhhccccHHHHHHHHHH
Confidence 446999999999999999854
No 147
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=20.60 E-value=1.5e+02 Score=32.65 Aligned_cols=30 Identities=23% Similarity=0.304 Sum_probs=22.6
Q ss_pred ChHHHHHHHhcCCCCCHHHHHHHHHHhCCCC
Q 039604 242 DDKSLFTMLTMVNGIGSWSVHMFMIFSLHRP 272 (373)
Q Consensus 242 ~~ee~~~~L~sLpGIGpwTA~~vLLf~lgrp 272 (373)
....+...|..|+|||++++..++ -.||-.
T Consensus 563 ~k~~~~s~L~~I~GIG~k~a~~Ll-~~Fgs~ 592 (621)
T PRK14671 563 SKRTLQTELTDIAGIGEKTAEKLL-EHFGSV 592 (621)
T ss_pred HHHHhhhhhhcCCCcCHHHHHHHH-HHcCCH
Confidence 334567889999999999999765 456543
No 148
>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=20.47 E-value=1.4e+02 Score=24.94 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=21.3
Q ss_pred CCCCchhhhCCChHHHHHHHhcCCCC
Q 039604 231 GILSDSAIVNMDDKSLFTMLTMVNGI 256 (373)
Q Consensus 231 G~l~L~~L~~~~~ee~~~~L~sLpGI 256 (373)
|--++++|...+.+++.+.|+.+.|.
T Consensus 32 Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 32 GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 44467778899999999999999874
Done!