Query 041647
Match_columns 216
No_of_seqs 127 out of 299
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 09:18:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041647hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2841 Structure-specific end 99.7 5.3E-18 1.1E-22 148.5 4.1 62 2-107 192-253 (254)
2 PF12826 HHH_2: Helix-hairpin- 99.0 2.7E-10 5.9E-15 79.1 3.2 52 9-104 7-58 (64)
3 PF14520 HHH_5: Helix-hairpin- 98.6 3.3E-08 7.1E-13 66.9 2.7 56 3-102 3-59 (60)
4 PRK14670 uvrC excinuclease ABC 98.2 1.6E-06 3.4E-11 82.4 5.5 57 3-103 512-568 (574)
5 PRK13482 DNA integrity scannin 98.2 1.4E-06 3.1E-11 79.4 5.0 53 6-102 288-340 (352)
6 PRK12766 50S ribosomal protein 98.1 3.9E-06 8.3E-11 73.3 5.4 56 5-104 3-59 (232)
7 PRK13766 Hef nuclease; Provisi 98.1 3.7E-06 8E-11 78.3 5.2 58 6-107 716-773 (773)
8 PRK00558 uvrC excinuclease ABC 98.0 6.2E-06 1.3E-10 78.0 5.3 57 3-103 541-597 (598)
9 PRK14666 uvrC excinuclease ABC 98.0 6.7E-06 1.4E-10 80.4 4.2 59 3-105 635-693 (694)
10 COG1948 MUS81 ERCC4-type nucle 97.9 1E-05 2.2E-10 71.3 4.4 59 5-107 182-240 (254)
11 PRK14669 uvrC excinuclease ABC 97.9 1.3E-05 2.9E-10 76.9 4.4 59 3-107 550-608 (624)
12 TIGR00575 dnlj DNA ligase, NAD 97.7 4.4E-05 9.5E-10 73.2 5.3 36 71-106 520-555 (652)
13 PRK14672 uvrC excinuclease ABC 97.7 6.3E-05 1.4E-09 73.8 5.5 56 3-102 606-661 (691)
14 PF00633 HHH: Helix-hairpin-he 97.7 6.6E-05 1.4E-09 47.1 3.7 29 71-99 1-29 (30)
15 PRK00116 ruvA Holliday junctio 97.6 7.7E-05 1.7E-09 61.1 4.9 59 4-106 72-133 (192)
16 COG5241 RAD10 Nucleotide excis 97.6 4.6E-05 9.9E-10 66.8 2.8 59 4-106 166-224 (224)
17 PRK07956 ligA NAD-dependent DN 97.5 0.00012 2.6E-09 70.5 5.1 35 71-105 533-567 (665)
18 TIGR00596 rad1 DNA repair prot 97.5 9.4E-05 2E-09 73.0 4.1 56 5-106 757-813 (814)
19 PRK00254 ski2-like helicase; P 97.3 0.00032 6.9E-09 66.2 5.5 55 6-104 646-701 (720)
20 PRK14351 ligA NAD-dependent DN 97.3 0.00039 8.4E-09 67.6 5.3 35 71-105 550-584 (689)
21 COG0272 Lig NAD-dependent DNA 96.5 0.003 6.5E-08 62.3 4.5 37 71-107 533-569 (667)
22 TIGR00426 competence protein C 96.2 0.0052 1.1E-07 42.3 3.0 23 79-101 45-67 (69)
23 PRK14350 ligA NAD-dependent DN 96.1 0.0063 1.4E-07 59.3 4.2 35 71-105 525-565 (669)
24 COG1623 Predicted nucleic-acid 96.1 0.0061 1.3E-07 56.5 3.8 52 6-101 294-345 (349)
25 PRK00024 hypothetical protein; 96.0 0.0099 2.1E-07 50.3 4.6 32 71-102 56-87 (224)
26 TIGR00608 radc DNA repair prot 96.0 0.011 2.4E-07 50.3 4.6 32 71-102 50-81 (218)
27 PRK14605 ruvA Holliday junctio 95.9 0.014 3.1E-07 48.5 4.9 57 5-102 73-129 (194)
28 TIGR01259 comE comEA protein. 95.9 0.0094 2E-07 46.1 3.5 24 78-101 95-118 (120)
29 PRK14603 ruvA Holliday junctio 95.8 0.017 3.7E-07 48.3 5.2 60 5-105 72-131 (197)
30 PRK14601 ruvA Holliday junctio 95.8 0.017 3.7E-07 48.2 5.0 60 5-105 73-132 (183)
31 PRK14602 ruvA Holliday junctio 95.8 0.02 4.3E-07 48.1 5.3 61 5-106 74-134 (203)
32 PRK13901 ruvA Holliday junctio 95.7 0.018 4E-07 48.9 5.0 61 5-106 72-132 (196)
33 TIGR00084 ruvA Holliday juncti 95.6 0.025 5.4E-07 47.0 5.3 60 5-105 72-131 (191)
34 PRK14600 ruvA Holliday junctio 95.5 0.025 5.5E-07 47.2 4.8 59 5-105 73-131 (186)
35 PRK08097 ligB NAD-dependent DN 95.4 0.017 3.6E-07 55.6 4.1 35 71-105 510-544 (562)
36 PRK14606 ruvA Holliday junctio 95.4 0.03 6.5E-07 46.7 5.1 60 5-105 73-132 (188)
37 TIGR01259 comE comEA protein. 95.2 0.021 4.5E-07 44.3 3.3 33 74-106 61-95 (120)
38 PRK14604 ruvA Holliday junctio 95.1 0.044 9.5E-07 45.9 5.1 61 5-106 73-133 (195)
39 TIGR02236 recomb_radA DNA repa 94.7 0.067 1.5E-06 45.1 5.3 52 7-102 1-53 (310)
40 COG2003 RadC DNA repair protei 94.4 0.061 1.3E-06 47.2 4.5 31 71-101 56-86 (224)
41 PRK02515 psbU photosystem II c 94.4 0.026 5.7E-07 46.4 2.1 33 74-108 54-86 (132)
42 COG0632 RuvA Holliday junction 94.0 0.24 5.1E-06 42.4 7.1 63 5-108 73-135 (201)
43 smart00278 HhH1 Helix-hairpin- 93.2 0.075 1.6E-06 31.5 2.1 21 81-101 1-21 (26)
44 PF03118 RNA_pol_A_CTD: Bacter 92.9 0.1 2.2E-06 37.0 2.7 33 71-103 34-66 (66)
45 PRK04301 radA DNA repair and r 92.9 0.16 3.5E-06 43.5 4.4 54 6-103 7-61 (317)
46 PRK14667 uvrC excinuclease ABC 92.4 0.13 2.8E-06 49.5 3.6 37 62-102 530-566 (567)
47 COG1555 ComEA DNA uptake prote 91.5 0.12 2.6E-06 41.7 2.0 36 73-108 89-126 (149)
48 PF12836 HHH_3: Helix-hairpin- 91.5 0.19 4.2E-06 34.7 2.7 33 76-108 9-43 (65)
49 TIGR00426 competence protein C 91.1 0.29 6.3E-06 33.7 3.3 32 75-106 10-44 (69)
50 TIGR01448 recD_rel helicase, p 90.9 0.27 5.9E-06 47.8 4.0 54 6-102 83-138 (720)
51 KOG0442 Structure-specific end 90.3 0.21 4.6E-06 51.2 2.8 60 5-109 821-880 (892)
52 TIGR01954 nusA_Cterm_rpt trans 89.6 0.54 1.2E-05 29.8 3.4 31 71-101 16-46 (50)
53 PRK14668 uvrC excinuclease ABC 87.6 0.57 1.2E-05 45.2 3.6 31 71-101 547-577 (577)
54 PRK08609 hypothetical protein; 87.3 0.94 2E-05 43.0 4.8 23 80-102 87-109 (570)
55 PF14520 HHH_5: Helix-hairpin- 87.3 0.45 9.7E-06 32.1 1.9 20 81-100 5-24 (60)
56 PRK01172 ski2-like helicase; P 82.5 1.7 3.6E-05 41.0 4.0 32 71-102 635-666 (674)
57 smart00483 POLXc DNA polymeras 81.7 1.1 2.4E-05 39.8 2.4 22 80-102 88-109 (334)
58 PF00570 HRDC: HRDC domain Blo 79.9 2.1 4.6E-05 28.5 2.8 31 71-101 34-64 (68)
59 PRK07956 ligA NAD-dependent DN 79.9 3.6 7.9E-05 40.3 5.4 32 71-102 469-500 (665)
60 PRK09482 flap endonuclease-lik 79.4 3.7 8.1E-05 36.1 4.9 32 71-102 172-203 (256)
61 PRK02362 ski2-like helicase; P 79.2 4.7 0.0001 38.7 5.9 30 71-102 675-704 (737)
62 COG0322 UvrC Nuclease subunit 79.2 1.8 4E-05 42.2 3.2 30 71-101 552-581 (581)
63 PRK02515 psbU photosystem II c 79.1 2.2 4.8E-05 35.3 3.2 24 78-101 84-107 (132)
64 PF14229 DUF4332: Domain of un 78.9 4.2 9.1E-05 31.5 4.5 30 71-100 42-72 (122)
65 TIGR00575 dnlj DNA ligase, NAD 78.0 4.4 9.5E-05 39.6 5.3 32 71-102 456-487 (652)
66 PF10391 DNA_pol_lambd_f: Fing 77.9 2.1 4.5E-05 29.7 2.3 20 81-100 2-21 (52)
67 smart00279 HhH2 Helix-hairpin- 76.5 2.9 6.2E-05 27.0 2.5 31 71-101 6-36 (36)
68 PTZ00035 Rad51 protein; Provis 76.0 4.9 0.00011 35.8 4.7 32 71-102 46-77 (337)
69 TIGR02238 recomb_DMC1 meiotic 75.9 5.2 0.00011 35.4 4.8 33 71-103 24-56 (313)
70 smart00475 53EXOc 5'-3' exonuc 75.8 5.8 0.00013 34.3 5.0 32 71-102 176-207 (259)
71 COG1555 ComEA DNA uptake prote 74.6 2.5 5.5E-05 34.2 2.3 24 78-101 124-147 (149)
72 PF12836 HHH_3: Helix-hairpin- 74.3 2.9 6.2E-05 28.9 2.2 22 78-99 41-62 (65)
73 cd00141 NT_POLXc Nucleotidyltr 74.1 2.5 5.3E-05 37.1 2.3 20 79-98 83-102 (307)
74 smart00478 ENDO3c endonuclease 74.0 6 0.00013 29.9 4.1 21 79-99 70-90 (149)
75 PRK07758 hypothetical protein; 73.7 4.2 9.1E-05 32.1 3.3 33 71-103 57-89 (95)
76 PRK14671 uvrC excinuclease ABC 73.5 2.9 6.2E-05 40.8 2.8 30 71-102 591-620 (621)
77 TIGR01083 nth endonuclease III 73.2 9.9 0.00021 30.8 5.4 76 18-102 7-91 (191)
78 PLN03187 meiotic recombination 73.1 6.3 0.00014 35.8 4.7 31 71-101 54-84 (344)
79 PRK10702 endonuclease III; Pro 72.6 7 0.00015 33.0 4.6 27 78-104 106-133 (211)
80 PF00730 HhH-GPD: HhH-GPD supe 71.5 4.1 9E-05 29.1 2.6 46 56-102 15-63 (108)
81 PRK14976 5'-3' exonuclease; Pr 71.1 8 0.00017 33.9 4.8 32 71-102 181-212 (281)
82 PRK00116 ruvA Holliday junctio 69.5 4.1 8.9E-05 33.6 2.5 23 80-102 72-94 (192)
83 cd00008 53EXOc 5'-3' exonuclea 69.4 9.7 0.00021 32.2 4.8 32 71-102 173-204 (240)
84 PRK14351 ligA NAD-dependent DN 69.4 9 0.00019 38.0 5.2 32 71-102 486-517 (689)
85 PRK08609 hypothetical protein; 68.3 6.8 0.00015 37.4 4.0 27 71-97 112-139 (570)
86 PRK10702 endonuclease III; Pro 67.8 8.8 0.00019 32.4 4.2 74 19-102 11-94 (211)
87 PRK12766 50S ribosomal protein 66.1 4 8.6E-05 36.3 1.9 23 80-102 2-25 (232)
88 cd00080 HhH2_motif Helix-hairp 66.0 6 0.00013 28.3 2.5 30 73-102 14-43 (75)
89 PF14635 HHH_7: Helix-hairpin- 65.4 5 0.00011 31.5 2.2 30 82-111 51-80 (104)
90 TIGR00588 ogg 8-oxoguanine DNA 64.4 18 0.00039 32.0 5.7 24 80-103 219-243 (310)
91 cd01702 PolY_Pol_eta DNA Polym 64.3 27 0.00059 31.3 6.8 30 71-102 206-237 (359)
92 PRK05182 DNA-directed RNA poly 63.5 8.3 0.00018 34.5 3.4 33 71-103 271-303 (310)
93 cd00056 ENDO3c endonuclease II 62.5 16 0.00035 27.8 4.4 24 77-100 79-102 (158)
94 TIGR03252 uncharacterized HhH- 62.2 24 0.00052 30.1 5.8 85 20-108 42-142 (177)
95 PRK14350 ligA NAD-dependent DN 60.9 9 0.0002 37.9 3.5 32 71-102 460-491 (669)
96 TIGR00615 recR recombination p 60.0 8.2 0.00018 33.3 2.7 27 72-102 6-33 (195)
97 PF14716 HHH_8: Helix-hairpin- 59.4 12 0.00025 26.1 2.9 19 82-100 48-66 (68)
98 TIGR02027 rpoA DNA-directed RN 59.3 10 0.00022 33.7 3.3 33 71-103 257-289 (297)
99 smart00341 HRDC Helicase and R 57.4 15 0.00032 24.9 3.1 30 72-101 38-67 (81)
100 PLN03186 DNA repair protein RA 55.8 21 0.00046 32.2 4.7 31 71-101 51-81 (342)
101 PRK08097 ligB NAD-dependent DN 55.8 13 0.00027 36.4 3.5 33 71-103 449-481 (562)
102 PF02371 Transposase_20: Trans 54.6 8.5 0.00019 27.6 1.6 29 5-36 2-30 (87)
103 PRK14973 DNA topoisomerase I; 54.1 18 0.0004 37.2 4.4 32 70-101 899-930 (936)
104 COG0122 AlkA 3-methyladenine D 53.7 43 0.00093 29.7 6.2 102 19-142 128-240 (285)
105 PRK13844 recombination protein 53.5 12 0.00026 32.5 2.6 25 71-99 9-33 (200)
106 PRK05755 DNA polymerase I; Pro 53.2 23 0.0005 35.2 4.9 32 71-102 177-208 (880)
107 PRK03858 DNA polymerase IV; Va 52.8 71 0.0015 28.1 7.3 30 71-102 196-225 (396)
108 PRK10308 3-methyl-adenine DNA 52.6 16 0.00036 32.0 3.4 31 71-102 157-187 (283)
109 PRK00076 recR recombination pr 51.6 9.9 0.00022 32.7 1.8 21 81-101 11-31 (196)
110 TIGR01083 nth endonuclease III 51.5 26 0.00056 28.4 4.1 22 78-99 103-124 (191)
111 COG0177 Nth Predicted EndoIII- 50.9 15 0.00033 31.9 2.8 32 77-108 105-137 (211)
112 TIGR00985 3a0801s04tom mitocho 50.8 15 0.00033 30.5 2.8 23 36-58 18-40 (148)
113 COG1796 POL4 DNA polymerase IV 50.6 11 0.00024 35.2 2.1 25 78-102 90-114 (326)
114 TIGR00593 pola DNA polymerase 50.4 25 0.00054 35.9 4.7 32 71-102 175-206 (887)
115 PRK14669 uvrC excinuclease ABC 47.2 16 0.00034 36.0 2.7 22 81-102 552-573 (624)
116 TIGR03252 uncharacterized HhH- 47.2 28 0.00062 29.6 3.9 40 70-109 50-99 (177)
117 TIGR00084 ruvA Holliday juncti 47.2 15 0.00032 30.7 2.2 22 81-102 72-93 (191)
118 PRK14668 uvrC excinuclease ABC 46.2 14 0.0003 35.9 2.1 23 81-103 525-547 (577)
119 PF12826 HHH_2: Helix-hairpin- 44.8 15 0.00032 25.5 1.6 18 85-102 7-24 (64)
120 COG0353 RecR Recombinational D 43.5 16 0.00034 32.1 1.8 24 71-98 6-29 (198)
121 TIGR00194 uvrC excinuclease AB 42.3 18 0.0004 35.1 2.3 22 81-102 541-562 (574)
122 PRK14670 uvrC excinuclease ABC 41.6 19 0.00042 35.1 2.3 22 81-102 514-535 (574)
123 PF00416 Ribosomal_S13: Riboso 40.8 17 0.00036 27.6 1.4 28 2-29 12-39 (107)
124 PRK14667 uvrC excinuclease ABC 40.1 22 0.00049 34.6 2.5 22 81-102 514-535 (567)
125 PRK13913 3-methyladenine DNA g 40.1 53 0.0011 28.4 4.5 31 71-101 68-101 (218)
126 PRK14666 uvrC excinuclease ABC 38.7 28 0.0006 35.2 2.9 23 80-102 636-658 (694)
127 COG0258 Exo 5'-3' exonuclease 38.4 30 0.00065 30.0 2.8 33 70-102 187-219 (310)
128 cd00008 53EXOc 5'-3' exonuclea 38.3 33 0.00071 29.0 2.9 23 4-26 182-204 (240)
129 COG4277 Predicted DNA-binding 37.6 23 0.00049 34.0 2.0 25 76-100 325-349 (404)
130 cd01701 PolY_Rev1 DNA polymera 36.9 1.7E+02 0.0036 26.4 7.3 30 71-102 245-276 (404)
131 PRK03352 DNA polymerase IV; Va 36.1 1.3E+02 0.0028 26.0 6.3 30 71-102 200-229 (346)
132 PRK01810 DNA polymerase IV; Va 34.6 1.7E+02 0.0037 26.0 6.9 29 71-102 202-230 (407)
133 PF11798 IMS_HHH: IMS family H 34.4 37 0.0008 21.2 2.0 18 82-99 12-29 (32)
134 COG0272 Lig NAD-dependent DNA 34.1 35 0.00076 34.5 2.9 33 71-103 469-501 (667)
135 cd00080 HhH2_motif Helix-hairp 33.9 43 0.00093 23.9 2.6 22 5-26 22-43 (75)
136 PRK11057 ATP-dependent DNA hel 33.9 47 0.001 31.5 3.5 31 71-101 562-595 (607)
137 PRK14672 uvrC excinuclease ABC 33.3 31 0.00067 35.0 2.3 22 81-102 608-629 (691)
138 PRK10880 adenine DNA glycosyla 33.3 39 0.00086 31.0 2.8 30 78-107 106-136 (350)
139 PRK03609 umuC DNA polymerase V 33.1 1.8E+02 0.0039 26.2 6.9 73 71-146 202-275 (422)
140 COG0177 Nth Predicted EndoIII- 33.1 84 0.0018 27.4 4.7 73 28-109 26-104 (211)
141 PRK13913 3-methyladenine DNA g 33.0 45 0.00098 28.8 3.0 31 78-108 118-149 (218)
142 PRK03348 DNA polymerase IV; Pr 32.8 2.2E+02 0.0047 26.5 7.5 38 71-110 203-241 (454)
143 PRK10308 3-methyl-adenine DNA 32.6 64 0.0014 28.4 3.9 22 78-99 204-225 (283)
144 PRK02362 ski2-like helicase; P 32.4 70 0.0015 30.9 4.4 21 79-99 650-670 (737)
145 PF13542 HTH_Tnp_ISL3: Helix-t 31.9 55 0.0012 20.7 2.6 28 74-101 23-51 (52)
146 PRK07945 hypothetical protein; 31.8 1.4E+02 0.0031 26.6 6.0 45 53-102 25-70 (335)
147 TIGR03674 fen_arch flap struct 31.4 98 0.0021 27.8 4.9 22 81-102 236-257 (338)
148 PRK00558 uvrC excinuclease ABC 31.2 35 0.00077 33.1 2.3 23 81-103 543-565 (598)
149 PRK10736 hypothetical protein; 31.2 36 0.00079 31.7 2.3 23 82-104 9-31 (374)
150 PTZ00134 40S ribosomal protein 31.2 49 0.0011 27.6 2.8 38 2-39 27-71 (154)
151 TIGR03631 bact_S13 30S ribosom 31.0 49 0.0011 25.9 2.7 37 2-38 12-55 (113)
152 smart00611 SEC63 Domain of unk 30.7 88 0.0019 26.3 4.3 38 71-108 174-212 (312)
153 PRK00254 ski2-like helicase; P 30.6 28 0.00061 33.5 1.5 26 81-106 645-671 (720)
154 PRK05179 rpsM 30S ribosomal pr 30.3 53 0.0012 26.1 2.8 37 3-39 15-58 (122)
155 PRK09482 flap endonuclease-lik 30.1 47 0.001 29.3 2.7 22 5-26 182-203 (256)
156 cd00141 NT_POLXc Nucleotidyltr 29.4 53 0.0011 28.9 2.9 25 78-102 42-66 (307)
157 PRK01229 N-glycosylase/DNA lya 29.3 46 0.001 28.7 2.4 30 77-106 114-145 (208)
158 PRK14605 ruvA Holliday junctio 29.2 47 0.001 27.8 2.5 24 81-104 73-96 (194)
159 PF12482 DUF3701: Phage integr 28.9 41 0.00089 26.2 1.9 19 84-102 53-71 (96)
160 PRK13910 DNA glycosylase MutY; 28.6 60 0.0013 29.1 3.1 29 78-106 69-98 (289)
161 PRK10736 hypothetical protein; 28.4 66 0.0014 30.0 3.5 21 6-26 9-29 (374)
162 smart00475 53EXOc 5'-3' exonuc 28.2 54 0.0012 28.5 2.7 22 5-26 186-207 (259)
163 PF11731 Cdd1: Pathogenicity l 27.8 59 0.0013 25.3 2.6 23 77-99 8-30 (93)
164 CHL00013 rpoA RNA polymerase a 27.8 58 0.0013 29.8 2.9 51 45-104 268-318 (327)
165 PF14261 DUF4351: Domain of un 26.9 1.1E+02 0.0023 21.6 3.6 39 32-84 2-40 (59)
166 cd00056 ENDO3c endonuclease II 26.8 88 0.0019 23.8 3.3 33 70-102 31-65 (158)
167 TIGR02236 recomb_radA DNA repa 26.7 47 0.001 28.2 2.0 20 83-102 1-21 (310)
168 PRK14133 DNA polymerase IV; Pr 26.2 3E+02 0.0065 23.9 6.9 29 71-102 196-224 (347)
169 PRK04053 rps13p 30S ribosomal 25.7 73 0.0016 26.4 2.9 38 2-39 22-66 (149)
170 COG4483 Uncharacterized protei 25.6 72 0.0016 24.3 2.6 13 16-28 5-17 (68)
171 PRK13980 NAD synthetase; Provi 25.2 2E+02 0.0044 24.4 5.6 79 7-107 159-251 (265)
172 cd03586 PolY_Pol_IV_kappa DNA 25.1 4.2E+02 0.0092 22.4 8.0 29 71-102 194-222 (334)
173 PRK01216 DNA polymerase IV; Va 25.0 4.1E+02 0.0088 23.9 7.7 29 71-101 201-229 (351)
174 TIGR02239 recomb_RAD51 DNA rep 24.9 66 0.0014 28.5 2.7 32 71-102 24-55 (316)
175 PRK13766 Hef nuclease; Provisi 24.3 57 0.0012 31.2 2.3 21 83-103 717-737 (773)
176 TIGR01448 recD_rel helicase, p 23.5 57 0.0012 32.2 2.2 42 68-111 73-114 (720)
177 PF00416 Ribosomal_S13: Riboso 23.4 76 0.0016 24.1 2.4 21 82-102 16-36 (107)
178 TIGR01084 mutY A/G-specific ad 23.3 69 0.0015 28.3 2.5 28 78-105 102-130 (275)
179 PRK14976 5'-3' exonuclease; Pr 23.2 78 0.0017 27.8 2.8 22 5-26 191-212 (281)
180 COG0322 UvrC Nuclease subunit 23.1 59 0.0013 32.1 2.2 21 82-102 531-551 (581)
181 CHL00137 rps13 ribosomal prote 22.7 93 0.002 24.8 2.9 35 3-37 15-56 (122)
182 KOG3449 60S acidic ribosomal p 22.1 2E+02 0.0044 23.6 4.7 54 12-91 17-70 (112)
183 TIGR03629 arch_S13P archaeal r 21.9 91 0.002 25.6 2.8 38 2-39 18-62 (144)
184 COG1948 MUS81 ERCC4-type nucle 21.8 70 0.0015 28.9 2.2 25 79-103 180-204 (254)
185 smart00483 POLXc DNA polymeras 21.5 90 0.0019 27.9 2.9 24 79-102 46-69 (334)
186 PRK14671 uvrC excinuclease ABC 21.4 67 0.0015 31.6 2.2 22 81-102 569-590 (621)
187 cd00424 PolY Y-family of DNA p 20.5 5E+02 0.011 22.5 7.1 72 71-146 196-269 (343)
188 PF02540 NAD_synthase: NAD syn 20.4 1.9E+02 0.0041 24.7 4.5 78 7-102 148-233 (242)
189 TIGR01389 recQ ATP-dependent D 20.2 1.2E+02 0.0026 28.4 3.5 31 71-101 551-584 (591)
No 1
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=99.71 E-value=5.3e-18 Score=148.52 Aligned_cols=62 Identities=40% Similarity=0.522 Sum_probs=59.9
Q ss_pred cccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHh
Q 041647 2 ALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASME 81 (216)
Q Consensus 2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~E 81 (216)
++.++||+|+||||||++.||.+|| ||++|.+||++
T Consensus 192 ~~~~~Lt~i~~VnKtda~~LL~~Fg--------------------------------------------sLq~~~~AS~~ 227 (254)
T KOG2841|consen 192 SLLGFLTTIPGVNKTDAQLLLQKFG--------------------------------------------SLQQISNASEG 227 (254)
T ss_pred HHHHHHHhCCCCCcccHHHHHHhcc--------------------------------------------cHHHHHhcCHh
Confidence 4678999999999999999999999 99999999999
Q ss_pred hhccCCCCcHHHHHHHHHHhcCCCCC
Q 041647 82 DLARCPGIVERKVKCLYDTFHEPFKP 107 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~fhePF~~ 107 (216)
||++|||+|++||++||++||+||.+
T Consensus 228 ele~~~G~G~~kak~l~~~l~~pf~~ 253 (254)
T KOG2841|consen 228 ELEQCPGLGPAKAKRLHKFLHQPFLS 253 (254)
T ss_pred HHHhCcCcCHHHHHHHHHHHhccccC
Confidence 99999999999999999999999986
No 2
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=99.00 E-value=2.7e-10 Score=79.11 Aligned_cols=52 Identities=31% Similarity=0.543 Sum_probs=43.9
Q ss_pred ccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhccCCC
Q 041647 9 SVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPG 88 (216)
Q Consensus 9 sV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~cPG 88 (216)
.|++|+++.+..|+..|| |++.|++|+.|||..+||
T Consensus 7 GI~~VG~~~ak~L~~~f~--------------------------------------------sl~~l~~a~~e~L~~i~g 42 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG--------------------------------------------SLEALMNASVEELSAIPG 42 (64)
T ss_dssp TSTT--HHHHHHHHHCCS--------------------------------------------CHHHHCC--HHHHCTSTT
T ss_pred CCCCccHHHHHHHHHHcC--------------------------------------------CHHHHHHcCHHHHhccCC
Confidence 689999999999999999 999999999999999999
Q ss_pred CcHHHHHHHHHHhcCC
Q 041647 89 IVERKVKCLYDTFHEP 104 (216)
Q Consensus 89 ig~~Kvk~L~d~fheP 104 (216)
||+..++.|++.|++|
T Consensus 43 IG~~~A~si~~ff~~~ 58 (64)
T PF12826_consen 43 IGPKIAQSIYEFFQDP 58 (64)
T ss_dssp --HHHHHHHHHHHH-H
T ss_pred cCHHHHHHHHHHHCCH
Confidence 9999999999999976
No 3
>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=98.58 E-value=3.3e-08 Score=66.94 Aligned_cols=56 Identities=21% Similarity=0.294 Sum_probs=51.3
Q ss_pred ccccccccCCcChhhHHHHHhh-cCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHh
Q 041647 3 LTHALTSVWSVNKTDVVNLGST-SGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASME 81 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlst-fG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~E 81 (216)
+...|.+|+||+++.+.+|.+. |+ |+++|.+++.+
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~--------------------------------------------t~~~l~~a~~~ 38 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIK--------------------------------------------TLEDLANADPE 38 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCS--------------------------------------------SHHHHHTSHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCC--------------------------------------------cHHHHHcCCHH
Confidence 3467889999999999999999 77 99999999999
Q ss_pred hhccCCCCcHHHHHHHHHHhc
Q 041647 82 DLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~fh 102 (216)
+|+.+||||++++++|.+.+.
T Consensus 39 ~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 39 ELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHTSTTSSHHHHHHHHHHHH
T ss_pred HHhcCCCCCHHHHHHHHHHHh
Confidence 999999999999999998764
No 4
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=98.23 E-value=1.6e-06 Score=82.42 Aligned_cols=57 Identities=11% Similarity=0.112 Sum_probs=54.5
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhh
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMED 82 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~Ed 82 (216)
+...|..|+||++.....|+.+|| |+++|..||.||
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fg--------------------------------------------s~~~I~~As~ee 547 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLG--------------------------------------------TYKDILLLNEDE 547 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhC--------------------------------------------CHHHHHhCCHHH
Confidence 457899999999999999999999 999999999999
Q ss_pred hccCCCCcHHHHHHHHHHhcC
Q 041647 83 LARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~fhe 103 (216)
|+.+|||+++.|+.|++.||.
T Consensus 548 L~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 548 IAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred HHhCCCCCHHHHHHHHHHHHH
Confidence 999999999999999999985
No 5
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=98.22 E-value=1.4e-06 Score=79.36 Aligned_cols=53 Identities=26% Similarity=0.372 Sum_probs=50.7
Q ss_pred cccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhcc
Q 041647 6 ALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLAR 85 (216)
Q Consensus 6 aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~ 85 (216)
.|++|++|+|..+.+|+.+|| ||++|++|+.|||..
T Consensus 288 iLs~IPrl~k~iAk~Ll~~FG--------------------------------------------SL~~Il~As~eeL~~ 323 (352)
T PRK13482 288 LLSKIPRLPSAVIENLVEHFG--------------------------------------------SLQGLLAASIEDLDE 323 (352)
T ss_pred HHhcCCCCCHHHHHHHHHHcC--------------------------------------------CHHHHHcCCHHHHhh
Confidence 588999999999999999999 999999999999999
Q ss_pred CCCCcHHHHHHHHHHhc
Q 041647 86 CPGIVERKVKCLYDTFH 102 (216)
Q Consensus 86 cPGig~~Kvk~L~d~fh 102 (216)
++|||+.+|+.+++.+.
T Consensus 324 VeGIGe~rA~~I~e~l~ 340 (352)
T PRK13482 324 VEGIGEVRARAIREGLS 340 (352)
T ss_pred CCCcCHHHHHHHHHHHH
Confidence 99999999999988775
No 6
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=98.13 E-value=3.9e-06 Score=73.32 Aligned_cols=56 Identities=16% Similarity=0.144 Sum_probs=53.2
Q ss_pred ccccccCCcChhhHHHHHhh-cCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhh
Q 041647 5 HALTSVWSVNKTDVVNLGST-SGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDL 83 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlst-fG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdL 83 (216)
+.|..|+||++.++..|+.+ || |++.|..||.++|
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~--------------------------------------------Sve~Ik~AS~eEL 38 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFE--------------------------------------------SVEDVRAADQSEL 38 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCC--------------------------------------------CHHHHHhCCHHHH
Confidence 46889999999999999999 99 9999999999999
Q ss_pred ccCCCCcHHHHHHHHHHhcCC
Q 041647 84 ARCPGIVERKVKCLYDTFHEP 104 (216)
Q Consensus 84 A~cPGig~~Kvk~L~d~fheP 104 (216)
+.+||||+.+|+.|++.|+++
T Consensus 39 ~~V~GIg~k~AekI~e~l~~~ 59 (232)
T PRK12766 39 AEVDGIGNALAARIKADVGGL 59 (232)
T ss_pred HHccCCCHHHHHHHHHHhccc
Confidence 999999999999999999944
No 7
>PRK13766 Hef nuclease; Provisional
Probab=98.11 E-value=3.7e-06 Score=78.28 Aligned_cols=58 Identities=28% Similarity=0.309 Sum_probs=55.4
Q ss_pred cccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhcc
Q 041647 6 ALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLAR 85 (216)
Q Consensus 6 aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~ 85 (216)
.|+.++||++..+..|+.+|| |+++|++++.++|..
T Consensus 716 ~L~~ipgig~~~a~~Ll~~fg--------------------------------------------s~~~i~~as~~~L~~ 751 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEHFG--------------------------------------------SVEAVMTASEEELME 751 (773)
T ss_pred HHhcCCCCCHHHHHHHHHHcC--------------------------------------------CHHHHHhCCHHHHHh
Confidence 588999999999999999999 999999999999999
Q ss_pred CCCCcHHHHHHHHHHhcCCCCC
Q 041647 86 CPGIVERKVKCLYDTFHEPFKP 107 (216)
Q Consensus 86 cPGig~~Kvk~L~d~fhePF~~ 107 (216)
+||||+++++.|++.|+.||.+
T Consensus 752 i~Gig~~~a~~i~~~~~~~~~~ 773 (773)
T PRK13766 752 VEGIGEKTAKRIREVVTSEYKE 773 (773)
T ss_pred CCCCCHHHHHHHHHHHhhhhcC
Confidence 9999999999999999999863
No 8
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=98.03 E-value=6.2e-06 Score=78.04 Aligned_cols=57 Identities=33% Similarity=0.526 Sum_probs=54.5
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhh
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMED 82 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~Ed 82 (216)
+...|+.|+||++..+..|+.+|| |++.|.+||.|+
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~~Fg--------------------------------------------S~~~i~~As~ee 576 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLKHFG--------------------------------------------SLKAIKEASVEE 576 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHHHcC--------------------------------------------CHHHHHhCCHHH
Confidence 457899999999999999999999 999999999999
Q ss_pred hccCCCCcHHHHHHHHHHhcC
Q 041647 83 LARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~fhe 103 (216)
|+.+||||+..++.|++.||.
T Consensus 577 L~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 577 LAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred HhhcCCcCHHHHHHHHHHhcc
Confidence 999999999999999999985
No 9
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=97.96 E-value=6.7e-06 Score=80.39 Aligned_cols=59 Identities=29% Similarity=0.320 Sum_probs=56.0
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhh
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMED 82 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~Ed 82 (216)
++..|..|+||++..+..|+.+|| |++.|..||.|+
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FG--------------------------------------------Sle~I~~AS~eE 670 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFG--------------------------------------------SLQAMAAAGEEG 670 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhC--------------------------------------------CHHHHHhcCHHH
Confidence 567899999999999999999999 999999999999
Q ss_pred hccCCCCcHHHHHHHHHHhcCCC
Q 041647 83 LARCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~fhePF 105 (216)
|+.++|||+++++.|++.||.=|
T Consensus 671 La~V~Gig~k~Ae~I~~~L~~~~ 693 (694)
T PRK14666 671 LAAVPGIGPARAAALHEHLKTLF 693 (694)
T ss_pred HHhcCCcCHHHHHHHHHHHHHhh
Confidence 99999999999999999998755
No 10
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=97.93 E-value=1e-05 Score=71.27 Aligned_cols=59 Identities=25% Similarity=0.341 Sum_probs=56.2
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+++||....+.+|+..|| |++.++.||+++|.
T Consensus 182 ~il~s~pgig~~~a~~ll~~fg--------------------------------------------S~~~~~tas~~eL~ 217 (254)
T COG1948 182 YILESIPGIGPKLAERLLKKFG--------------------------------------------SVEDVLTASEEELM 217 (254)
T ss_pred HHHHcCCCccHHHHHHHHHHhc--------------------------------------------CHHHHhhcCHHHHH
Confidence 4578999999999999999999 99999999999999
Q ss_pred cCCCCcHHHHHHHHHHhcCCCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPFKP 107 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF~~ 107 (216)
.+.|||++||+.||..|..||+.
T Consensus 218 ~v~gig~k~A~~I~~~~~t~~~~ 240 (254)
T COG1948 218 KVKGIGEKKAREIYRFLRTEYKL 240 (254)
T ss_pred HhcCccHHHHHHHHHHHhchhhh
Confidence 99999999999999999999983
No 11
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=97.87 E-value=1.3e-05 Score=76.90 Aligned_cols=59 Identities=20% Similarity=0.180 Sum_probs=55.5
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhh
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMED 82 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~Ed 82 (216)
+.+.|.+|+||++.....|+.+|| |++.|..||.|+
T Consensus 550 ~~S~L~~IpGIG~kr~~~LL~~Fg--------------------------------------------Si~~I~~As~ee 585 (624)
T PRK14669 550 RTSELLEIPGVGAKTVQRLLKHFG--------------------------------------------SLERVRAATETQ 585 (624)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcC--------------------------------------------CHHHHHhCCHHH
Confidence 457799999999999999999999 999999999999
Q ss_pred hccCCCCcHHHHHHHHHHhcCCCCC
Q 041647 83 LARCPGIVERKVKCLYDTFHEPFKP 107 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~fhePF~~ 107 (216)
|+.+ ||+++|+.|++.||.+|..
T Consensus 586 L~~v--i~~k~A~~I~~~l~~~~~~ 608 (624)
T PRK14669 586 LAAV--VGRAAAEAIIAHFTTEEAA 608 (624)
T ss_pred HHHH--hCHHHHHHHHHHhcCcCCC
Confidence 9999 9999999999999988853
No 12
>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=97.72 E-value=4.4e-05 Score=73.16 Aligned_cols=36 Identities=25% Similarity=0.505 Sum_probs=34.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFK 106 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF~ 106 (216)
|++.|++|+.|+|..+||||+.+++.|++.|+.|+.
T Consensus 520 sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~~ 555 (652)
T TIGR00575 520 TLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNN 555 (652)
T ss_pred CHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhhH
Confidence 899999999999999999999999999999999873
No 13
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=97.67 E-value=6.3e-05 Score=73.81 Aligned_cols=56 Identities=18% Similarity=0.171 Sum_probs=52.8
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhh
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMED 82 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~Ed 82 (216)
+...|..|+||++.....|+.+|| |++.|..||.||
T Consensus 606 ~~s~L~~IpGiG~kr~~~LL~~Fg--------------------------------------------S~~~i~~As~ee 641 (691)
T PRK14672 606 LVLSFERLPHVGKVRAHRLLAHFG--------------------------------------------SFRSLQSATPQD 641 (691)
T ss_pred cccccccCCCCCHHHHHHHHHHhc--------------------------------------------CHHHHHhCCHHH
Confidence 467899999999999999999999 999999999999
Q ss_pred hccCCCCcHHHHHHHHHHhc
Q 041647 83 LARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~fh 102 (216)
|+.+|||+.+.|+.|+..-.
T Consensus 642 l~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 642 IATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred HHhCCCCCHHHHHHHHHHhh
Confidence 99999999999999998754
No 14
>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=97.66 E-value=6.6e-05 Score=47.13 Aligned_cols=29 Identities=31% Similarity=0.572 Sum_probs=25.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHH
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d 99 (216)
|+..++.+|.|||..+||||+.+|..+++
T Consensus 1 ~~~g~~pas~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 1 SLDGLIPASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp SHHHHHTSSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCCCcCCCCHHHHHhCCCcCHHHHHHHHh
Confidence 46788999999999999999999999876
No 15
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.64 E-value=7.7e-05 Score=61.07 Aligned_cols=59 Identities=17% Similarity=0.238 Sum_probs=52.4
Q ss_pred cccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhc---HHHHHhCCH
Q 041647 4 THALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVS---LSHIMDASM 80 (216)
Q Consensus 4 t~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~S---L~~Im~AS~ 80 (216)
.+.|.+|+||++.-+..++++|| + .+.|.+++.
T Consensus 72 f~~L~~i~GIGpk~A~~il~~fg--------------------------------------------~~~l~~~i~~~d~ 107 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSGLS--------------------------------------------PEELVQAIANGDV 107 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHhCC--------------------------------------------HHHHHHHHHhCCH
Confidence 35688999999999999999999 3 566788999
Q ss_pred hhhccCCCCcHHHHHHHHHHhcCCCC
Q 041647 81 EDLARCPGIVERKVKCLYDTFHEPFK 106 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fhePF~ 106 (216)
+.|..+||||++++++|+..|++-+.
T Consensus 108 ~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 108 KALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 99999999999999999999997664
No 16
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=97.57 E-value=4.6e-05 Score=66.77 Aligned_cols=59 Identities=22% Similarity=0.246 Sum_probs=56.1
Q ss_pred cccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhh
Q 041647 4 THALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDL 83 (216)
Q Consensus 4 t~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdL 83 (216)
.+.|++|++|||.|+..+|+.|| +|....-||.+++
T Consensus 166 ~~fl~~i~~Vnksds~~~L~d~g--------------------------------------------~L~rf~gaSrdE~ 201 (224)
T COG5241 166 NEFLILIFIVNKSDSEDTLNDIG--------------------------------------------KLCRFNGASRDEF 201 (224)
T ss_pred ccceEEEEeeccccHHHHHHHHH--------------------------------------------HHHHHhccchhHH
Confidence 46799999999999999999999 8999999999999
Q ss_pred ccCCCCcHHHHHHHHHHhcCCCC
Q 041647 84 ARCPGIVERKVKCLYDTFHEPFK 106 (216)
Q Consensus 84 A~cPGig~~Kvk~L~d~fhePF~ 106 (216)
.++-|+|..||.+..+.+..||.
T Consensus 202 e~l~g~g~~ka~~~ieyln~pFm 224 (224)
T COG5241 202 ELLLGFGFEKAAKYIEYLNLPFM 224 (224)
T ss_pred HHHHccCHHHHHHHHHHhcccCC
Confidence 99999999999999999999994
No 17
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.52 E-value=0.00012 Score=70.51 Aligned_cols=35 Identities=29% Similarity=0.294 Sum_probs=33.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF 105 (216)
|+++|++|+.|+|..++|||+.+++.|++.|+.|.
T Consensus 533 sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~ 567 (665)
T PRK07956 533 SLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEE 567 (665)
T ss_pred CHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhh
Confidence 89999999999999999999999999999999775
No 18
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=97.49 E-value=9.4e-05 Score=73.01 Aligned_cols=56 Identities=25% Similarity=0.237 Sum_probs=52.2
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
+.|.+++||+...+.+|+.+|| |+++|++||.|+|.
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~--------------------------------------------si~~l~~as~eeL~ 792 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVK--------------------------------------------SIRELAKLSQNELN 792 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcC--------------------------------------------CHHHHHhCCHHHHH
Confidence 4578999999999999999999 99999999999999
Q ss_pred cCCCCc-HHHHHHHHHHhcCCCC
Q 041647 85 RCPGIV-ERKVKCLYDTFHEPFK 106 (216)
Q Consensus 85 ~cPGig-~~Kvk~L~d~fhePF~ 106 (216)
.+ || +.+|++||+.||.++.
T Consensus 793 ~~--iG~~~~A~~i~~fl~~~~~ 813 (814)
T TIGR00596 793 EL--IGDEEAAKRLYDFLRTEKL 813 (814)
T ss_pred HH--hCCHHHHHHHHHHhccccC
Confidence 94 88 9999999999998864
No 19
>PRK00254 ski2-like helicase; Provisional
Probab=97.34 E-value=0.00032 Score=66.15 Aligned_cols=55 Identities=16% Similarity=0.234 Sum_probs=50.6
Q ss_pred cccccCCcChhhHHHHHhh-cCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 6 ALTSVWSVNKTDVVNLGST-SGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 6 aLTsV~sVNKTDv~nLlst-fG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
.|..|+||++..+..|+.. |+ |+.+|+.|+.++|.
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~--------------------------------------------s~~~i~~a~~~el~ 681 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFR--------------------------------------------SIEDIVNAKPSELL 681 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCC--------------------------------------------CHHHHHhCCHHHHh
Confidence 3567899999999999998 88 99999999999999
Q ss_pred cCCCCcHHHHHHHHHHhcCC
Q 041647 85 RCPGIVERKVKCLYDTFHEP 104 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fheP 104 (216)
.|||||++.|+.+++.+|..
T Consensus 682 ~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 682 KVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred cCCCCCHHHHHHHHHHhccc
Confidence 99999999999999999955
No 20
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.26 E-value=0.00039 Score=67.56 Aligned_cols=35 Identities=20% Similarity=0.225 Sum_probs=33.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF 105 (216)
|+++|++|+.++|..++|||+..++.|++.|+.|-
T Consensus 550 si~~L~~As~eeL~~i~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 550 TFEAIMDADEEALRAVDDVGPTVAEEIREFFDSER 584 (689)
T ss_pred CHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhH
Confidence 99999999999999999999999999999999775
No 21
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=96.50 E-value=0.003 Score=62.26 Aligned_cols=37 Identities=30% Similarity=0.425 Sum_probs=34.9
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCCCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKP 107 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF~~ 107 (216)
|++.++.|+.|+|..+||||+..|+.|++.|++|...
T Consensus 533 sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~~~~~~ 569 (667)
T COG0272 533 TLEALLAASEEELASIPGIGEVVARSIIEFFANEENR 569 (667)
T ss_pred hHHHHHhcCHHHHhhccchhHHHHHHHHHHHcCHHHH
Confidence 8999999999999999999999999999999988654
No 22
>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=96.18 E-value=0.0052 Score=42.33 Aligned_cols=23 Identities=30% Similarity=0.429 Sum_probs=20.7
Q ss_pred CHhhhccCCCCcHHHHHHHHHHh
Q 041647 79 SMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~d~f 101 (216)
+.+||.++||||++++++|++..
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhhc
Confidence 77899999999999999998864
No 23
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.10 E-value=0.0063 Score=59.26 Aligned_cols=35 Identities=20% Similarity=0.367 Sum_probs=30.9
Q ss_pred cHHHHHh------CCHhhhccCCCCcHHHHHHHHHHhcCCC
Q 041647 71 SLSHIMD------ASMEDLARCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 71 SL~~Im~------AS~EdLA~cPGig~~Kvk~L~d~fhePF 105 (216)
+++++++ ++.|+|..++|||+..++.|++.|+.|.
T Consensus 525 ~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~~~ 565 (669)
T PRK14350 525 SFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKI 565 (669)
T ss_pred CHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcCHH
Confidence 6667765 6899999999999999999999999874
No 24
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=96.08 E-value=0.0061 Score=56.51 Aligned_cols=52 Identities=29% Similarity=0.356 Sum_probs=47.5
Q ss_pred cccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhcc
Q 041647 6 ALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLAR 85 (216)
Q Consensus 6 aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~ 85 (216)
.|..|+-+.+.++.||..+|| .|.+|..||.|||..
T Consensus 294 ~l~kIpRlp~~iv~nlV~~F~--------------------------------------------~l~~il~As~edL~~ 329 (349)
T COG1623 294 LLNKIPRLPFAIVENLVRAFG--------------------------------------------TLDGILEASAEDLDA 329 (349)
T ss_pred HHhcCcCccHHHHHHHHHHHh--------------------------------------------hHHHHHHhcHhHHhh
Confidence 466788889999999999999 999999999999999
Q ss_pred CCCCcHHHHHHHHHHh
Q 041647 86 CPGIVERKVKCLYDTF 101 (216)
Q Consensus 86 cPGig~~Kvk~L~d~f 101 (216)
+.|||+.+|+.+.+-+
T Consensus 330 VeGIGe~rAr~i~~Gl 345 (349)
T COG1623 330 VEGIGEARARAIKEGL 345 (349)
T ss_pred hcchhHHHHHHHHHhH
Confidence 9999999999998765
No 25
>PRK00024 hypothetical protein; Reviewed
Probab=96.04 E-value=0.0099 Score=50.30 Aligned_cols=32 Identities=34% Similarity=0.436 Sum_probs=29.7
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
||..+.+++.++|..++|||+.|+..|...+.
T Consensus 56 sL~~l~~as~~eL~~i~GIG~akA~~L~a~~E 87 (224)
T PRK00024 56 SLRGLLDASLEELQSIKGIGPAKAAQLKAALE 87 (224)
T ss_pred CHHHHHhCCHHHHhhccCccHHHHHHHHHHHH
Confidence 89999999999999999999999998877765
No 26
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.97 E-value=0.011 Score=50.26 Aligned_cols=32 Identities=38% Similarity=0.518 Sum_probs=29.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
||..+++|+.+||..++|||+.|+..|...+.
T Consensus 50 ~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~E 81 (218)
T TIGR00608 50 SLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81 (218)
T ss_pred CHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHH
Confidence 89999999999999999999999998877654
No 27
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.90 E-value=0.014 Score=48.51 Aligned_cols=57 Identities=21% Similarity=0.229 Sum_probs=45.1
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+|.||++.-+..++++|+ |++|. ..|.+-..+-|.
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~~----~~~l~-------------------------------------~aI~~~D~~~L~ 111 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAMN----AEALA-------------------------------------SAIISGNAELLS 111 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhCC----HHHHH-------------------------------------HHHHhCCHHHHH
Confidence 4578999999999999999998 44332 234567788999
Q ss_pred cCCCCcHHHHHHHHHHhc
Q 041647 85 RCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fh 102 (216)
++||||+++|++|.--+.
T Consensus 112 ~vpGIGkKtAerIilELk 129 (194)
T PRK14605 112 TIPGIGKKTASRIVLELK 129 (194)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 999999999999544433
No 28
>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=95.87 E-value=0.0094 Score=46.13 Aligned_cols=24 Identities=33% Similarity=0.484 Sum_probs=20.7
Q ss_pred CCHhhhccCCCCcHHHHHHHHHHh
Q 041647 78 ASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
+|.|||.++||||+.+++.|.+.+
T Consensus 95 ~s~eeL~~V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 95 KSVDDLTKVSGIGEKSLEKLKDYA 118 (120)
T ss_pred CCHHHHHcCCCCCHHHHHHHHhce
Confidence 577899999999999999988765
No 29
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.83 E-value=0.017 Score=48.31 Aligned_cols=60 Identities=18% Similarity=0.189 Sum_probs=49.0
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+|.||++.=+.+++++++ |++|.++ |.+.+..-|.
T Consensus 72 ~~L~~V~GIGpK~AL~iLs~~~----~~~l~~a-------------------------------------I~~~D~~~L~ 110 (197)
T PRK14603 72 ELLLGVSGVGPKLALALLSALP----PALLARA-------------------------------------LLEGDARLLT 110 (197)
T ss_pred HHHhCcCCcCHHHHHHHHcCCC----HHHHHHH-------------------------------------HHhCCHHHHh
Confidence 4578999999999999999987 6665544 4566778999
Q ss_pred cCCCCcHHHHHHHHHHhcCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF 105 (216)
++||||++.|++|.--+..-+
T Consensus 111 kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 111 SASGVGKKLAERIALELKGKV 131 (197)
T ss_pred hCCCCCHHHHHHHHHHHHHHh
Confidence 999999999999876666554
No 30
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.79 E-value=0.017 Score=48.23 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=49.0
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+|.||++.=+.++++++. |++|.++- ..-+..-|.
T Consensus 73 ~~Li~VsGIGpK~Al~ILs~~~----~~el~~aI-------------------------------------~~~D~~~L~ 111 (183)
T PRK14601 73 EMLLKVNGIGANTAMAVCSSLD----VNSFYKAL-------------------------------------SLGDESVLK 111 (183)
T ss_pred HHHhccCCccHHHHHHHHcCCC----HHHHHHHH-------------------------------------HhCCHHHHh
Confidence 4588999999999999999987 66665543 456678899
Q ss_pred cCCCCcHHHHHHHHHHhcCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF 105 (216)
++||||++.|++|.--+..-+
T Consensus 112 ~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 112 KVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred hCCCCCHHHHHHHHHHHHHHh
Confidence 999999999999877666555
No 31
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.78 E-value=0.02 Score=48.07 Aligned_cols=61 Identities=20% Similarity=0.316 Sum_probs=50.2
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+|.||++.=+.++|++++ |++|.+ .|++.+..-|.
T Consensus 74 ~~Li~V~GIGpK~Al~iLs~~~----~~~l~~-------------------------------------aI~~~D~~~L~ 112 (203)
T PRK14602 74 IVLISISKVGAKTALAILSQFR----PDDLRR-------------------------------------LVAEEDVAALT 112 (203)
T ss_pred HHHhCCCCcCHHHHHHHHhhCC----HHHHHH-------------------------------------HHHhCCHHHHh
Confidence 4578999999999999999998 555543 34667888999
Q ss_pred cCCCCcHHHHHHHHHHhcCCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPFK 106 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF~ 106 (216)
++||||++.|++|.--+..-+.
T Consensus 113 ~ipGIGkKtAerIilELkdK~~ 134 (203)
T PRK14602 113 RVSGIGKKTAQHIFLELKYKLK 134 (203)
T ss_pred cCCCcCHHHHHHHHHHHHHhhc
Confidence 9999999999999877776653
No 32
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.74 E-value=0.018 Score=48.92 Aligned_cols=61 Identities=13% Similarity=0.138 Sum_probs=49.5
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
.-|.+|.||++.=+.++++++. |++|.++ |.+-+..-|.
T Consensus 72 ~~LisVsGIGPK~ALaILs~~~----~~el~~a-------------------------------------I~~~D~~~L~ 110 (196)
T PRK13901 72 EELIGVDGIGPRAALRVLSGIK----YNEFRDA-------------------------------------IDREDIELIS 110 (196)
T ss_pred HHHhCcCCcCHHHHHHHHcCCC----HHHHHHH-------------------------------------HHhCCHHHHh
Confidence 4578999999999999999987 6665443 3466778999
Q ss_pred cCCCCcHHHHHHHHHHhcCCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPFK 106 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF~ 106 (216)
++||||++.|++|.--+..-+.
T Consensus 111 ~vpGIGkKtAeRIIlELkdKl~ 132 (196)
T PRK13901 111 KVKGIGNKMAGKIFLKLRGKLV 132 (196)
T ss_pred hCCCCCHHHHHHHHHHHHHhhc
Confidence 9999999999998877666553
No 33
>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=95.61 E-value=0.025 Score=46.96 Aligned_cols=60 Identities=20% Similarity=0.297 Sum_probs=46.8
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+|+||++.-+..++++++ +++|.++ |.+-...-|.
T Consensus 72 ~~L~~V~GIGpK~Al~iL~~~~----~~el~~a-------------------------------------I~~~d~~~L~ 110 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILSNMS----PEEFVYA-------------------------------------IETEEVKALV 110 (191)
T ss_pred HHHhCCCCCCHHHHHHHHhcCC----HHHHHHH-------------------------------------HHhCCHHHHH
Confidence 3578999999999999999887 4444333 3345678899
Q ss_pred cCCCCcHHHHHHHHHHhcCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF 105 (216)
++||||++++++|.-.+..-+
T Consensus 111 ~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 111 KIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred hCCCCCHHHHHHHHHHHHhhh
Confidence 999999999999986666554
No 34
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.46 E-value=0.025 Score=47.15 Aligned_cols=59 Identities=24% Similarity=0.301 Sum_probs=47.8
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
.-|.+|.||++.=+.+++++++ |++|.++- .+.+..-|
T Consensus 73 ~~LisV~GIGpK~Al~iLs~~~----~~~l~~aI-------------------------------------~~~D~~~L- 110 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSILSKLT----PEQLFSAI-------------------------------------VNEDKAAL- 110 (186)
T ss_pred HHHhCcCCcCHHHHHHHHccCC----HHHHHHHH-------------------------------------HcCCHhhe-
Confidence 4578999999999999999997 66655443 45566789
Q ss_pred cCCCCcHHHHHHHHHHhcCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF 105 (216)
++||||++.|++|.--+..-+
T Consensus 111 ~vpGIGkKtAerIilELk~K~ 131 (186)
T PRK14600 111 KVNGIGEKLINRIITELQYKV 131 (186)
T ss_pred ECCCCcHHHHHHHHHHHHHHh
Confidence 999999999999987777655
No 35
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.43 E-value=0.017 Score=55.64 Aligned_cols=35 Identities=23% Similarity=0.373 Sum_probs=33.0
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF 105 (216)
++++|++++.|+|..++|||+..++.|++.|+.|.
T Consensus 510 ~i~~l~~a~~e~l~~i~gIG~~~a~si~~~f~~~~ 544 (562)
T PRK08097 510 SWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPE 544 (562)
T ss_pred CHHHHHcCCHHHHhcCCCchHHHHHHHHHHHcCHH
Confidence 78999999999999999999999999999999764
No 36
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.42 E-value=0.03 Score=46.67 Aligned_cols=60 Identities=22% Similarity=0.371 Sum_probs=48.8
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
..|.+|.||++.=+.++++++. |++|-++ |.+-+..-|.
T Consensus 73 ~~Li~V~GIGpK~AL~iLs~~~----~~el~~a-------------------------------------I~~~D~~~L~ 111 (188)
T PRK14606 73 LSLTKVSRLGPKTALKIISNED----AETLVTM-------------------------------------IASQDVEGLS 111 (188)
T ss_pred HHHhccCCccHHHHHHHHcCCC----HHHHHHH-------------------------------------HHhCCHHHHh
Confidence 4578999999999999999987 5555443 4456778899
Q ss_pred cCCCCcHHHHHHHHHHhcCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPF 105 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF 105 (216)
++||||++.|++|.--+..-+
T Consensus 112 ~vpGIGkKtAerIilELkdK~ 132 (188)
T PRK14606 112 KLPGISKKTAERIVMELKDEF 132 (188)
T ss_pred hCCCCCHHHHHHHHHHHHHhh
Confidence 999999999999987777655
No 37
>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=95.23 E-value=0.021 Score=44.25 Aligned_cols=33 Identities=36% Similarity=0.493 Sum_probs=28.6
Q ss_pred HHHhCCHhhhccCCCCcHHHHHHHHHHhc--CCCC
Q 041647 74 HIMDASMEDLARCPGIVERKVKCLYDTFH--EPFK 106 (216)
Q Consensus 74 ~Im~AS~EdLA~cPGig~~Kvk~L~d~fh--ePF~ 106 (216)
+|=.|+.++|..+||||+.++++|.+.+. .||.
T Consensus 61 niNtA~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~ 95 (120)
T TIGR01259 61 NINAASLEELQALPGIGPAKAKAIIEYREENGAFK 95 (120)
T ss_pred eCCcCCHHHHhcCCCCCHHHHHHHHHHHHhcCCcC
Confidence 45679999999999999999999999995 5664
No 38
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.08 E-value=0.044 Score=45.94 Aligned_cols=61 Identities=26% Similarity=0.354 Sum_probs=49.3
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
.-|.+|.||++.=+.++|+++. |++|.++ |.+-+..-|.
T Consensus 73 ~~Li~V~GIGpK~Al~iLs~~~----~~el~~a-------------------------------------I~~~D~~~L~ 111 (195)
T PRK14604 73 ELLIGVSGVGPKAALNLLSSGT----PDELQLA-------------------------------------IAGGDVARLA 111 (195)
T ss_pred HHHhCcCCcCHHHHHHHHcCCC----HHHHHHH-------------------------------------HHhCCHHHHh
Confidence 4578999999999999999886 6655544 3456678899
Q ss_pred cCCCCcHHHHHHHHHHhcCCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPFK 106 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF~ 106 (216)
++||||++.|++|.--+..-+.
T Consensus 112 kvpGIGkKtAerIilELk~K~~ 133 (195)
T PRK14604 112 RVPGIGKKTAERIVLELKGKID 133 (195)
T ss_pred hCCCCCHHHHHHHHHHHHHHhc
Confidence 9999999999999877776653
No 39
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=94.69 E-value=0.067 Score=45.14 Aligned_cols=52 Identities=19% Similarity=0.204 Sum_probs=47.7
Q ss_pred ccccCCcChhhHHHHHhh-cCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhcc
Q 041647 7 LTSVWSVNKTDVVNLGST-SGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLAR 85 (216)
Q Consensus 7 LTsV~sVNKTDv~nLlst-fG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~ 85 (216)
|..++||++..+..|... |. |+++|..++.++|+.
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~--------------------------------------------ti~dl~~~~~~~L~~ 36 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYD--------------------------------------------TFEAIAVASPKELSE 36 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCC--------------------------------------------CHHHHHcCCHHHHHh
Confidence 467899999999999988 88 999999999999999
Q ss_pred CCCCcHHHHHHHHHHhc
Q 041647 86 CPGIVERKVKCLYDTFH 102 (216)
Q Consensus 86 cPGig~~Kvk~L~d~fh 102 (216)
.+|+++.+++.|+....
T Consensus 37 ~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 37 IAGISEGTAAKIIQAAR 53 (310)
T ss_pred ccCCCHHHHHHHHHHHH
Confidence 99999999999988775
No 40
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=94.39 E-value=0.061 Score=47.20 Aligned_cols=31 Identities=29% Similarity=0.381 Sum_probs=27.9
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
||..++.||.++|..++|||..|+-.|..++
T Consensus 56 ~L~~l~~a~~~el~~v~GiG~aka~~l~a~~ 86 (224)
T COG2003 56 SLAELLKASVEELSSVKGIGLAKAIQIKAAI 86 (224)
T ss_pred cHHHHHhCCHHHHhhCCCccHHHHHHHHHHH
Confidence 7999999999999999999999987776554
No 41
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.35 E-value=0.026 Score=46.39 Aligned_cols=33 Identities=15% Similarity=0.402 Sum_probs=28.9
Q ss_pred HHHhCCHhhhccCCCCcHHHHHHHHHHhcCCCCCC
Q 041647 74 HIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPV 108 (216)
Q Consensus 74 ~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF~~~ 108 (216)
+|=.|+.++|..+||||+.||++|.+ |-||+.+
T Consensus 54 diN~A~~~el~~lpGigP~~A~~IV~--nGpf~sv 86 (132)
T PRK02515 54 DLNNSSVRAFRQFPGMYPTLAGKIVK--NAPYDSV 86 (132)
T ss_pred cCCccCHHHHHHCCCCCHHHHHHHHH--CCCCCCH
Confidence 34578999999999999999999995 8899866
No 42
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=93.98 E-value=0.24 Score=42.43 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=47.6
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
.-|.+|.||++.-+-++++++. +++|-++ |...+..-|.
T Consensus 73 ~~LisVnGIGpK~ALaiLs~~~----~~~l~~a-------------------------------------I~~~d~~~L~ 111 (201)
T COG0632 73 RLLISVNGIGPKLALAILSNLD----PEELAQA-------------------------------------IANEDVKALS 111 (201)
T ss_pred HHHHccCCccHHHHHHHHcCCC----HHHHHHH-------------------------------------HHhcChHhhh
Confidence 3477889999999999998876 4444333 2345667899
Q ss_pred cCCCCcHHHHHHHHHHhcCCCCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPFKPV 108 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF~~~ 108 (216)
++||||.+-|++|.--+..-|...
T Consensus 112 k~PGIGkKtAerivleLk~K~~~~ 135 (201)
T COG0632 112 KIPGIGKKTAERIVLELKGKLAAF 135 (201)
T ss_pred cCCCCCHHHHHHHHHHHhhhhhhh
Confidence 999999999999988877666553
No 43
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=93.20 E-value=0.075 Score=31.47 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=18.4
Q ss_pred hhhccCCCCcHHHHHHHHHHh
Q 041647 81 EDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~f 101 (216)
++|..+||||++++++|++..
T Consensus 1 ~~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 1 EELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred ChhhhCCCCCHHHHHHHHHhc
Confidence 478899999999999999844
No 44
>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=92.89 E-value=0.1 Score=37.03 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=29.7
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
++.+++..|.+||.+++|||.+-+..|.+.++|
T Consensus 34 tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~e 66 (66)
T PF03118_consen 34 TVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLKE 66 (66)
T ss_dssp BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHHH
T ss_pred CHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHcC
Confidence 999999999999999999999999999988753
No 45
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=92.87 E-value=0.16 Score=43.48 Aligned_cols=54 Identities=20% Similarity=0.228 Sum_probs=47.7
Q ss_pred cccccCCcChhhHHHHHhh-cCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 6 ALTSVWSVNKTDVVNLGST-SGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 6 aLTsV~sVNKTDv~nLlst-fG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
-|+.++||++..+..|... |. |++++.+++.++|.
T Consensus 7 ~l~~l~gIg~~~a~~L~~~Gi~--------------------------------------------t~~dl~~~~~~~L~ 42 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREAGYD--------------------------------------------TVEAIAVASPKELS 42 (317)
T ss_pred cHhhcCCCCHHHHHHHHHcCCC--------------------------------------------CHHHHHcCCHHHHH
Confidence 4678999999888877765 55 99999999999999
Q ss_pred cCCCCcHHHHHHHHHHhcC
Q 041647 85 RCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhe 103 (216)
+..|+++.++..|++..++
T Consensus 43 ~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 43 EAAGIGESTAAKIIEAARE 61 (317)
T ss_pred HhcCCCHHHHHHHHHHHHH
Confidence 9999999999999988775
No 46
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=92.42 E-value=0.13 Score=49.51 Aligned_cols=37 Identities=16% Similarity=0.283 Sum_probs=32.9
Q ss_pred hhccccchhcHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 62 LFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 62 ~~~~~s~~~SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
|++.-. |+++|..||.|||+.+ ||+++.|+.||+.||
T Consensus 530 Ll~~Fg---s~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 530 IYRNFK---TLYDFLKADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred HHHHhC---CHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 444445 8999999999999999 999999999999986
No 47
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=91.50 E-value=0.12 Score=41.72 Aligned_cols=36 Identities=39% Similarity=0.549 Sum_probs=28.8
Q ss_pred HHHHhCCHhhhccCCCCcHHHHHHHHHHhc--CCCCCC
Q 041647 73 SHIMDASMEDLARCPGIVERKVKCLYDTFH--EPFKPV 108 (216)
Q Consensus 73 ~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh--ePF~~~ 108 (216)
=+|=.||.|||..+||||+.||+.|.+.=. -||..+
T Consensus 89 vNiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv 126 (149)
T COG1555 89 VNINTASAEELQALPGIGPKKAQAIIDYREENGPFKSV 126 (149)
T ss_pred ccccccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcH
Confidence 345679999999999999999999987653 466543
No 48
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=91.45 E-value=0.19 Score=34.70 Aligned_cols=33 Identities=33% Similarity=0.524 Sum_probs=22.3
Q ss_pred HhCCHhhhccCCCCcHHHHHHHHHHh--cCCCCCC
Q 041647 76 MDASMEDLARCPGIVERKVKCLYDTF--HEPFKPV 108 (216)
Q Consensus 76 m~AS~EdLA~cPGig~~Kvk~L~d~f--hePF~~~ 108 (216)
=.||.++|..+||||+..|+.|.+.= +-||...
T Consensus 9 N~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~ 43 (65)
T PF12836_consen 9 NTASAEELQALPGIGPKQAKAIVEYREKNGPFKSL 43 (65)
T ss_dssp TTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSG
T ss_pred ccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCH
Confidence 35899999999999999999997653 4677543
No 49
>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=91.11 E-value=0.29 Score=33.66 Aligned_cols=32 Identities=31% Similarity=0.430 Sum_probs=26.5
Q ss_pred HHhCCHhhhcc-CCCCcHHHHHHHHHHh--cCCCC
Q 041647 75 IMDASMEDLAR-CPGIVERKVKCLYDTF--HEPFK 106 (216)
Q Consensus 75 Im~AS~EdLA~-cPGig~~Kvk~L~d~f--hePF~ 106 (216)
|=.|+.++|.. +||||+.+++.|.+.. +.+|.
T Consensus 10 vNta~~~~L~~~ipgig~~~a~~Il~~R~~~g~~~ 44 (69)
T TIGR00426 10 INTATAEELQRAMNGVGLKKAEAIVSYREEYGPFK 44 (69)
T ss_pred CcCCCHHHHHhHCCCCCHHHHHHHHHHHHHcCCcC
Confidence 34589999999 9999999999999986 34554
No 50
>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=90.90 E-value=0.27 Score=47.75 Aligned_cols=54 Identities=22% Similarity=0.296 Sum_probs=37.9
Q ss_pred cccc--cCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhh
Q 041647 6 ALTS--VWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDL 83 (216)
Q Consensus 6 aLTs--V~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdL 83 (216)
.|.| ++||++.-+..|...||.- .++.| ...++.|
T Consensus 83 yL~s~~~~GIG~~~A~~iv~~fg~~------------------------------------------~~~~i-~~~~~~L 119 (720)
T TIGR01448 83 YLSSRSIKGVGKKLAQRIVKTFGEA------------------------------------------AFDVL-DDDPEKL 119 (720)
T ss_pred HHhcCCCCCcCHHHHHHHHHHhCHh------------------------------------------HHHHH-HhCHHHH
Confidence 4544 9999999999999999910 23333 3446777
Q ss_pred ccCCCCcHHHHHHHHHHhc
Q 041647 84 ARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 84 A~cPGig~~Kvk~L~d~fh 102 (216)
..+||||++|++.|++.+.
T Consensus 120 ~~v~gi~~~~~~~i~~~~~ 138 (720)
T TIGR01448 120 LEVPGISKANLEKFVSQWS 138 (720)
T ss_pred hcCCCCCHHHHHHHHHHHH
Confidence 7777777777777666553
No 51
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=90.27 E-value=0.21 Score=51.17 Aligned_cols=60 Identities=28% Similarity=0.342 Sum_probs=53.8
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
+.|-+++||+.++..+++..|+ |+.++..-|+++|+
T Consensus 821 ~fll~lPgVs~~n~~~l~~k~k--------------------------------------------s~~~La~sS~~el~ 856 (892)
T KOG0442|consen 821 DFLLSLPGVSYINYRNLRHKFK--------------------------------------------SLKELANSSQEELS 856 (892)
T ss_pred HHHhcCCCccHHHHHHHHHHhh--------------------------------------------HHHHHHhCcHHHHH
Confidence 4677899999999999999999 99999999999999
Q ss_pred cCCCCcHHHHHHHHHHhcCCCCCCC
Q 041647 85 RCPGIVERKVKCLYDTFHEPFKPVV 109 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fhePF~~~~ 109 (216)
..-|. ..+++.|||.||.-|....
T Consensus 857 el~~~-~~~a~~LYdFi~~~~~~~~ 880 (892)
T KOG0442|consen 857 ELLGV-HENAKLLYDFIHTEFADQE 880 (892)
T ss_pred HHhcc-hHHHHHHHHHHHHhhhhhh
Confidence 99777 9999999999997776543
No 52
>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=89.63 E-value=0.54 Score=29.84 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=28.3
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
|+.++..++.++|..++||++.++..|...-
T Consensus 16 s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a 46 (50)
T TIGR01954 16 TVEDLAYVPIDELLSIEGFDEETAKELINRA 46 (50)
T ss_pred CHHHHHccCHHHHhcCCCCCHHHHHHHHHHH
Confidence 8999999999999999999999999887543
No 53
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=87.63 E-value=0.57 Score=45.17 Aligned_cols=31 Identities=29% Similarity=0.551 Sum_probs=28.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
|+++|..||.++|+.+||||++.|+.|++.+
T Consensus 547 S~~~I~~As~eeL~~vpGi~~~~A~~I~~~~ 577 (577)
T PRK14668 547 SVEGVREASVEDLRDVPGVGEKTAETIRERL 577 (577)
T ss_pred CHHHHHhCCHHHHHhCCCCCHHHHHHHHHhC
Confidence 8899999999999999999999999998753
No 54
>PRK08609 hypothetical protein; Provisional
Probab=87.34 E-value=0.94 Score=43.03 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=19.4
Q ss_pred HhhhccCCCCcHHHHHHHHHHhc
Q 041647 80 MEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 80 ~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..+|.+|||||+++|++||+.+.
T Consensus 87 ~~~l~~i~GiGpk~a~~l~~~lG 109 (570)
T PRK08609 87 LLPLLKLPGLGGKKIAKLYKELG 109 (570)
T ss_pred HHHHhcCCCCCHHHHHHHHHHhC
Confidence 45678999999999999998765
No 55
>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=87.28 E-value=0.45 Score=32.12 Aligned_cols=20 Identities=35% Similarity=0.705 Sum_probs=18.8
Q ss_pred hhhccCCCCcHHHHHHHHHH
Q 041647 81 EDLARCPGIVERKVKCLYDT 100 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~ 100 (216)
++|..+||||+..++.|++.
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~ 24 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEA 24 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHT
T ss_pred HhhccCCCCCHHHHHHHHhc
Confidence 58899999999999999998
No 56
>PRK01172 ski2-like helicase; Provisional
Probab=82.49 E-value=1.7 Score=40.96 Aligned_cols=32 Identities=13% Similarity=0.218 Sum_probs=29.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
|+.+|++++.++|.++.|+|+++++.++....
T Consensus 635 ~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~ 666 (674)
T PRK01172 635 TVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred CHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence 89999999999999999999999999987643
No 57
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=81.69 E-value=1.1 Score=39.80 Aligned_cols=22 Identities=9% Similarity=0.105 Sum_probs=19.5
Q ss_pred HhhhccCCCCcHHHHHHHHHHhc
Q 041647 80 MEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 80 ~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
+-+|.+|||||++||+.||+ +.
T Consensus 88 l~~l~~i~GiGpk~a~~l~~-lG 109 (334)
T smart00483 88 LKLFTNVFGVGPKTAAKWYR-KG 109 (334)
T ss_pred HHHHHccCCcCHHHHHHHHH-hC
Confidence 46788999999999999999 55
No 58
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=79.89 E-value=2.1 Score=28.52 Aligned_cols=31 Identities=29% Similarity=0.502 Sum_probs=23.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
.+...+-.|.++|.+|+|+|+.|++..-+.|
T Consensus 34 ~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~i 64 (68)
T PF00570_consen 34 EIAKRLPTSIEELLQIPGMGKRKVRKYGDEI 64 (68)
T ss_dssp HHHHH--SSHHHHHTSTTCGHHHHHHCHHHH
T ss_pred HHHHhCCCCHHHHHHccCCCHHHHHHHHHHH
Confidence 4555556899999999999999999765544
No 59
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=79.89 E-value=3.6 Score=40.32 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=29.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|..+..++|..+||+|++++++|++.+.
T Consensus 469 ~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie 500 (665)
T PRK07956 469 DPADLFKLTAEDLLGLEGFGEKSAQNLLDAIE 500 (665)
T ss_pred CHHHHHhcCHHHHhcCcCcchHHHHHHHHHHH
Confidence 78889999999999999999999999999887
No 60
>PRK09482 flap endonuclease-like protein; Provisional
Probab=79.43 E-value=3.7 Score=36.08 Aligned_cols=32 Identities=16% Similarity=0.223 Sum_probs=27.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
.+..||--+-+.+-.|||||++.|..|...|.
T Consensus 172 D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 172 DYWGLAGISSSKIPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred HHHHHhCCCccCCCCCCCcChHHHHHHHHHhC
Confidence 44557777888999999999999999999886
No 61
>PRK02362 ski2-like helicase; Provisional
Probab=79.25 E-value=4.7 Score=38.74 Aligned_cols=30 Identities=10% Similarity=0.058 Sum_probs=29.0
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
|+.+|+.++.++|+.+ ||++.++.|++.+.
T Consensus 675 s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~ 704 (737)
T PRK02362 675 SRADLRAADKSVVLAI--LGEKIAENILEQAG 704 (737)
T ss_pred CHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence 8999999999999999 99999999999987
No 62
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=79.21 E-value=1.8 Score=42.20 Aligned_cols=30 Identities=37% Similarity=0.616 Sum_probs=28.3
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
|++.|..||.|||+.+ ||+...|+.+|+.|
T Consensus 552 s~~~i~~As~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 552 SLKGIKSASVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred CHHHHHhcCHHHHHHc-CCCHHHHHHHHhhC
Confidence 8999999999999999 99999999999865
No 63
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=79.13 E-value=2.2 Score=35.28 Aligned_cols=24 Identities=33% Similarity=0.535 Sum_probs=19.0
Q ss_pred CCHhhhccCCCCcHHHHHHHHHHh
Q 041647 78 ASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
.|.|||-++||||+++.+.|....
T Consensus 84 ~sveDL~~V~GIgekqk~~l~k~~ 107 (132)
T PRK02515 84 DSVEDVLNLPGLSERQKELLEANL 107 (132)
T ss_pred CCHHHHHcCCCCCHHHHHHHHHhh
Confidence 478999999999998776665543
No 64
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=78.91 E-value=4.2 Score=31.53 Aligned_cols=30 Identities=27% Similarity=0.379 Sum_probs=23.3
Q ss_pred cHHHHHh-CCHhhhccCCCCcHHHHHHHHHH
Q 041647 71 SLSHIMD-ASMEDLARCPGIVERKVKCLYDT 100 (216)
Q Consensus 71 SL~~Im~-AS~EdLA~cPGig~~Kvk~L~d~ 100 (216)
+.+.|.. ..+-||.++||||+.-+.-|...
T Consensus 42 ~~~~l~~w~~~AdL~ri~gi~~~~a~LL~~A 72 (122)
T PF14229_consen 42 SERNLLKWVNQADLMRIPGIGPQYAELLEHA 72 (122)
T ss_pred CHHHHHHHHhHHHhhhcCCCCHHHHHHHHHh
Confidence 4555544 56789999999999999988753
No 65
>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=77.98 E-value=4.4 Score=39.63 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=28.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|.....++|..+||+|++++++|++.+.
T Consensus 456 ~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 456 SVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred CHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 78888888889999999999999999998887
No 66
>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=77.95 E-value=2.1 Score=29.67 Aligned_cols=20 Identities=10% Similarity=0.140 Sum_probs=15.8
Q ss_pred hhhccCCCCcHHHHHHHHHH
Q 041647 81 EDLARCPGIVERKVKCLYDT 100 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~ 100 (216)
..+.+|-|+|+.+|+.+|+.
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~ 21 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAK 21 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHT
T ss_pred cchhhcccccHHHHHHHHHh
Confidence 56789999999999999984
No 67
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=76.47 E-value=2.9 Score=27.03 Aligned_cols=31 Identities=13% Similarity=0.239 Sum_probs=22.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
.+.-|+--+.+.+..+||||+++|..|...|
T Consensus 6 ~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 6 DYAILVGDYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred HHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence 3444455445667899999999999987654
No 68
>PTZ00035 Rad51 protein; Provisional
Probab=76.03 E-value=4.9 Score=35.81 Aligned_cols=32 Identities=25% Similarity=0.350 Sum_probs=29.2
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
|+++|..++.++|+++-||++.||+.|...-.
T Consensus 46 t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~ 77 (337)
T PTZ00035 46 TVESVAYATKKDLCNIKGISEAKVEKIKEAAS 77 (337)
T ss_pred cHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986544
No 69
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=75.91 E-value=5.2 Score=35.40 Aligned_cols=33 Identities=15% Similarity=0.303 Sum_probs=30.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
|++++..++.+||.++-||.+.||+.+.+...+
T Consensus 24 t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~ 56 (313)
T TIGR02238 24 TVNGVIMTTRRALCKIKGLSEAKVDKIKEAASK 56 (313)
T ss_pred cHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 899999999999999999999999999887653
No 70
>smart00475 53EXOc 5'-3' exonuclease.
Probab=75.80 E-value=5.8 Score=34.34 Aligned_cols=32 Identities=25% Similarity=0.446 Sum_probs=25.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
.+..|+-=+-+.+-.|||||+++|..|...|.
T Consensus 176 d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 176 DYKALMGDSSDNIPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred HHHHHhCCcccCCCCCCCCCHHHHHHHHHHhC
Confidence 33445665667899999999999999998775
No 71
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=74.58 E-value=2.5 Score=34.18 Aligned_cols=24 Identities=33% Similarity=0.484 Sum_probs=21.4
Q ss_pred CCHhhhccCCCCcHHHHHHHHHHh
Q 041647 78 ASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
.|.|||++++|||+.++++|.+.+
T Consensus 124 ~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 124 KSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred CcHHHHHhccCCCHHHHHHHHhhc
Confidence 478999999999999999998764
No 72
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=74.27 E-value=2.9 Score=28.87 Aligned_cols=22 Identities=36% Similarity=0.495 Sum_probs=17.2
Q ss_pred CCHhhhccCCCCcHHHHHHHHH
Q 041647 78 ASMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d 99 (216)
.|.+||..++||++.+.+.|..
T Consensus 41 ~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 41 KSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp SSGGGGGGSTT--HHHHHHHCC
T ss_pred CCHHHHhhCCCCCHHHHHHHHh
Confidence 4779999999999999998854
No 73
>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=74.07 E-value=2.5 Score=37.12 Aligned_cols=20 Identities=30% Similarity=0.534 Sum_probs=17.8
Q ss_pred CHhhhccCCCCcHHHHHHHH
Q 041647 79 SMEDLARCPGIVERKVKCLY 98 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~ 98 (216)
.+.+|.+|||||+++|+.||
T Consensus 83 ~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 83 GLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred HHHHHHcCCCCCHHHHHHHH
Confidence 34578899999999999999
No 74
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=74.02 E-value=6 Score=29.91 Aligned_cols=21 Identities=19% Similarity=0.477 Sum_probs=17.7
Q ss_pred CHhhhccCCCCcHHHHHHHHH
Q 041647 79 SMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~d 99 (216)
..++|..+||||+.-|.++.-
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~ 90 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLS 90 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHH
Confidence 578899999999999988643
No 75
>PRK07758 hypothetical protein; Provisional
Probab=73.71 E-value=4.2 Score=32.10 Aligned_cols=33 Identities=12% Similarity=0.223 Sum_probs=31.1
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
++.++..-+.+||.++.|||++-.+.|.+.+.|
T Consensus 57 TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 57 TVEELSKYSEKEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred cHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999999888765
No 76
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=73.52 E-value=2.9 Score=40.77 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=27.5
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
|+++|++||.|+|+.+ ||++.|++|++.||
T Consensus 591 s~~~i~~As~eeL~~v--ig~k~A~~I~~~~~ 620 (621)
T PRK14671 591 SVEKVAKASLEELAAV--AGPKTAETIYRYYH 620 (621)
T ss_pred CHHHHHhCCHHHHHHH--hCHHHHHHHHHHhC
Confidence 7889999999999998 99999999999886
No 77
>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=73.19 E-value=9.9 Score=30.82 Aligned_cols=76 Identities=21% Similarity=0.299 Sum_probs=45.1
Q ss_pred HHHHHhhcCCC------CChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhcc---CCC
Q 041647 18 VVNLGSTSGIH------NDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLAR---CPG 88 (216)
Q Consensus 18 v~nLlstfG~~------~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~---cPG 88 (216)
+..|...||-. .||-+.+ +..++..+-+.+.-.+--..||..-. +.+.|.+++.+||.. .-|
T Consensus 7 ~~~l~~~~~~~~~~~~~~dpf~~L------i~~ILsqqt~~~~~~~~~~~l~~~~p---t~~~l~~~~~~~L~~~ir~~G 77 (191)
T TIGR01083 7 LERLRKNYPHPTTELDYNNPFELL------VATILSAQATDKSVNKATKKLFEVYP---TPQALAQAGLEELEEYIKSIG 77 (191)
T ss_pred HHHHHHHCCCCCcccCCCCHHHHH------HHHHHHhhCcHHHHHHHHHHHHHHCC---CHHHHHcCCHHHHHHHHHhcC
Confidence 34577788732 3554433 33334444333333333333454332 789999999999954 458
Q ss_pred CcHHHHHHHHHHhc
Q 041647 89 IVERKVKCLYDTFH 102 (216)
Q Consensus 89 ig~~Kvk~L~d~fh 102 (216)
+..+|++.|.+...
T Consensus 78 ~~~~Ka~~i~~~a~ 91 (191)
T TIGR01083 78 LYRNKAKNIIALCR 91 (191)
T ss_pred ChHHHHHHHHHHHH
Confidence 88899999986643
No 78
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=73.13 E-value=6.3 Score=35.76 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=28.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
|+++|..++.++|+++-||.+.||..|.+.-
T Consensus 54 tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a 84 (344)
T PLN03187 54 TCNGLMMHTKKNLTGIKGLSEAKVDKICEAA 84 (344)
T ss_pred cHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 8999999999999999999999999987643
No 79
>PRK10702 endonuclease III; Provisional
Probab=72.56 E-value=7 Score=33.00 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=22.1
Q ss_pred CCHhhhccCCCCcHHHHHHHH-HHhcCC
Q 041647 78 ASMEDLARCPGIVERKVKCLY-DTFHEP 104 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~-d~fheP 104 (216)
.++++|-.+||||+.-|.++. -.|+.|
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~~~~ 133 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAFGWP 133 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHcCCC
Confidence 578999999999999999975 345555
No 80
>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=71.48 E-value=4.1 Score=29.10 Aligned_cols=46 Identities=22% Similarity=0.262 Sum_probs=34.2
Q ss_pred hhhhhhhhccccchhcHHHHHhCCHhhhccC---CCCcHHHHHHHHHHhc
Q 041647 56 QRQNNLLFKTQSAPVSLSHIMDASMEDLARC---PGIVERKVKCLYDTFH 102 (216)
Q Consensus 56 ~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~c---PGig~~Kvk~L~d~fh 102 (216)
.+..+.|++.-. ..+.+.|.+++.|+|..| =|++.+|++.|.+.-.
T Consensus 15 ~~~~~~l~~~~g-~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~ 63 (108)
T PF00730_consen 15 RKIYRRLFERYG-FPTPEALAEASEEELRELIRPLGFSRRKAKYIIELAR 63 (108)
T ss_dssp HHHHHHHHHHHS-CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhc-CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHH
Confidence 344444554422 348999999999999887 8999999999987654
No 81
>PRK14976 5'-3' exonuclease; Provisional
Probab=71.14 E-value=8 Score=33.88 Aligned_cols=32 Identities=13% Similarity=0.259 Sum_probs=26.3
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
-+.-|+-=+-+.+..|||||++.|..|...|.
T Consensus 181 d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 181 DYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred HHHHHhCCccCCCCCCCcccHHHHHHHHHHcC
Confidence 34456776778999999999999999998774
No 82
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=69.47 E-value=4.1 Score=33.56 Aligned_cols=23 Identities=9% Similarity=0.153 Sum_probs=21.0
Q ss_pred HhhhccCCCCcHHHHHHHHHHhc
Q 041647 80 MEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 80 ~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
-..|..+||||+++|+.|.+.|.
T Consensus 72 f~~L~~i~GIGpk~A~~il~~fg 94 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSGLS 94 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHhCC
Confidence 46788999999999999999998
No 83
>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=69.40 E-value=9.7 Score=32.17 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=25.8
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
.+.-|+-=+-+.+..|||||++.|..|...|.
T Consensus 173 d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 173 DYKALMGDSSDNIPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred HHHHHcCCcccCCCCCCccCHHHHHHHHHHhC
Confidence 44455666678899999999999999998864
No 84
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=69.36 E-value=9 Score=38.01 Aligned_cols=32 Identities=28% Similarity=0.386 Sum_probs=26.0
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|.....++|..++|+|++++++|++.+.
T Consensus 486 ~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie 517 (689)
T PRK14351 486 SLADLYDLTVADLAELEGWGETSAENLLAELE 517 (689)
T ss_pred CHHHHHHcCHHHHhcCcCcchhHHHHHHHHHH
Confidence 67777888888888888888888888888776
No 85
>PRK08609 hypothetical protein; Provisional
Probab=68.29 E-value=6.8 Score=37.40 Aligned_cols=27 Identities=7% Similarity=0.148 Sum_probs=21.4
Q ss_pred cHHHHHhCCHh-hhccCCCCcHHHHHHH
Q 041647 71 SLSHIMDASME-DLARCPGIVERKVKCL 97 (216)
Q Consensus 71 SL~~Im~AS~E-dLA~cPGig~~Kvk~L 97 (216)
|++++..|-.+ .|...||+|++..+.|
T Consensus 112 tl~~L~~a~~~~~~~~~~gfg~k~~~~i 139 (570)
T PRK08609 112 DKESLKEACENGKVQALAGFGKKTEEKI 139 (570)
T ss_pred CHHHHHHHHHhCChhhccCcchhHHHHH
Confidence 78888876654 4889999999987776
No 86
>PRK10702 endonuclease III; Provisional
Probab=67.83 E-value=8.8 Score=32.40 Aligned_cols=74 Identities=16% Similarity=0.224 Sum_probs=45.6
Q ss_pred HHHHhhcCC------CCChHHHHHHHHHHHHhhhhhcc-chhhhhhhhhhhhccccchhcHHHHHhCCHhhhccC---CC
Q 041647 19 VNLGSTSGI------HNDPEQLLRARVSLVLYLNTKRR-SAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARC---PG 88 (216)
Q Consensus 19 ~nLlstfG~------~~dpeql~~~~~~l~~~l~t~rr-~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~c---PG 88 (216)
..|..+||. +.||-+++-+.+ +--+|+.. ..+.+. .||+.-. +.+.|.+|+.|||..+ -|
T Consensus 11 ~~l~~~~~~~~~~~~~~~p~e~lvs~i---Lsq~t~~~~v~~~~~----~L~~~~p---t~e~l~~a~~~~l~~~i~~~G 80 (211)
T PRK10702 11 TRLRDNNPHPTTELNFSSPFELLIAVL---LSAQATDVSVNKATA----KLYPVAN---TPAAMLELGVEGVKTYIKTIG 80 (211)
T ss_pred HHHHHHCCCCCCCCCCCChHHHHHHHH---HHhhcCHHHHHHHHH----HHHHHcC---CHHHHHCCCHHHHHHHHHHcC
Confidence 356677874 346655543322 22233332 333333 3454433 7899999999999874 56
Q ss_pred CcHHHHHHHHHHhc
Q 041647 89 IVERKVKCLYDTFH 102 (216)
Q Consensus 89 ig~~Kvk~L~d~fh 102 (216)
+-.+|++.|++..+
T Consensus 81 ~y~~kA~~l~~~a~ 94 (211)
T PRK10702 81 LYNSKAENVIKTCR 94 (211)
T ss_pred CHHHHHHHHHHHHH
Confidence 66899999887766
No 87
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=66.15 E-value=4 Score=36.31 Aligned_cols=23 Identities=26% Similarity=0.443 Sum_probs=20.5
Q ss_pred HhhhccCCCCcHHHHHHHHHH-hc
Q 041647 80 MEDLARCPGIVERKVKCLYDT-FH 102 (216)
Q Consensus 80 ~EdLA~cPGig~~Kvk~L~d~-fh 102 (216)
.++|..+||||+.+++.|++. |.
T Consensus 2 ~~~L~~IpGIG~krakkLl~~GF~ 25 (232)
T PRK12766 2 PEELEDISGVGPSKAEALREAGFE 25 (232)
T ss_pred ccccccCCCcCHHHHHHHHHcCCC
Confidence 357889999999999999999 76
No 88
>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=65.99 E-value=6 Score=28.29 Aligned_cols=30 Identities=13% Similarity=0.327 Sum_probs=23.4
Q ss_pred HHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 73 SHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 73 ~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
.-++.-+-+-+..+||||+++|..|...|.
T Consensus 14 ~~L~GD~~D~i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 14 AILVGDKSDNIPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred HHHcCCccccCCCCCcccHHHHHHHHHHhC
Confidence 334454566788999999999999988765
No 89
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=65.43 E-value=5 Score=31.54 Aligned_cols=30 Identities=20% Similarity=0.179 Sum_probs=18.4
Q ss_pred hhccCCCCcHHHHHHHHHHhcCCCCCCCCC
Q 041647 82 DLARCPGIVERKVKCLYDTFHEPFKPVVSR 111 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~fhePF~~~~sr 111 (216)
-|.=++|+|+|||..|...+..--....+|
T Consensus 51 ~LqfV~GLGPRKA~~Ll~~l~~~g~~l~~R 80 (104)
T PF14635_consen 51 LLQFVCGLGPRKAQALLKALKQNGGRLENR 80 (104)
T ss_dssp GGGGSTT--HHHHHHHHHHHHHC-S----T
T ss_pred hHhHhcCCChHHHHHHHHHHHHcCCccccH
Confidence 466799999999999999998433333344
No 90
>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=64.39 E-value=18 Score=32.00 Aligned_cols=24 Identities=21% Similarity=0.458 Sum_probs=19.3
Q ss_pred HhhhccCCCCcHHHHHHHHHH-hcC
Q 041647 80 MEDLARCPGIVERKVKCLYDT-FHE 103 (216)
Q Consensus 80 ~EdLA~cPGig~~Kvk~L~d~-fhe 103 (216)
.++|..+||||+.-|.|+.-. |..
T Consensus 219 ~~~L~~l~GIG~~tAd~vll~~l~~ 243 (310)
T TIGR00588 219 REALCELPGVGPKVADCICLMGLDK 243 (310)
T ss_pred HHHHHhCCCccHHHHHHHHHHhCCC
Confidence 688999999999999997533 443
No 91
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=64.33 E-value=27 Score=31.31 Aligned_cols=30 Identities=20% Similarity=0.244 Sum_probs=22.4
Q ss_pred cHHHHHhC--CHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDA--SMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~A--S~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|.+. +.++|.+. +|....+.||+..+
T Consensus 206 ti~dl~~~~~~~~~L~~~--fG~~~g~~l~~~a~ 237 (359)
T cd01702 206 TEGDVAGFRSSESDLQEH--FGEKLGEWLYNLLR 237 (359)
T ss_pred CHHHHHhccCCHHHHHHH--HHHHHHHHHHHHhC
Confidence 66777777 77777765 66667888888877
No 92
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=63.47 E-value=8.3 Score=34.54 Aligned_cols=33 Identities=9% Similarity=0.324 Sum_probs=31.3
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
++.+++.-|.+||.+++|+|++-.+.+.+.+++
T Consensus 271 ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~ 303 (310)
T PRK05182 271 TIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAE 303 (310)
T ss_pred CHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence 899999999999999999999999999998876
No 93
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=62.46 E-value=16 Score=27.78 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=19.9
Q ss_pred hCCHhhhccCCCCcHHHHHHHHHH
Q 041647 77 DASMEDLARCPGIVERKVKCLYDT 100 (216)
Q Consensus 77 ~AS~EdLA~cPGig~~Kvk~L~d~ 100 (216)
+...+.|..+||||+.-|.++.-.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHH
Confidence 345788999999999999987654
No 94
>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=62.25 E-value=24 Score=30.09 Aligned_cols=85 Identities=15% Similarity=0.217 Sum_probs=51.8
Q ss_pred HHHhhcCCCCChHHHHHHHHHHHHhhhhh-----c---cchhhhhhhhhhhhc-cccchhcHHHHHh----CC---Hhhh
Q 041647 20 NLGSTSGIHNDPEQLLRARVSLVLYLNTK-----R---RSAKSFQRQNNLLFK-TQSAPVSLSHIMD----AS---MEDL 83 (216)
Q Consensus 20 nLlstfG~~~dpeql~~~~~~l~~~l~t~-----r---r~a~~~~~~nn~~~~-~~s~~~SL~~Im~----AS---~EdL 83 (216)
+|-..+|. .||+.+.++...-+--+... + +.|+..+.--+.+.. -+. .++.|.+ -+ +++|
T Consensus 42 ~L~~~~g~-~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G---~v~~L~~~~~p~t~~lre~L 117 (177)
T TIGR03252 42 KIARRMGS-LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDG---DATAVWTEGDPDGKELLRRL 117 (177)
T ss_pred HHHHHhCC-CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCC---ChhhhhcccCCCcHHHHHHH
Confidence 44456664 68888877765433333322 1 344444443333332 222 4445543 12 4789
Q ss_pred ccCCCCcHHHHHHHHHHhcCCCCCC
Q 041647 84 ARCPGIVERKVKCLYDTFHEPFKPV 108 (216)
Q Consensus 84 A~cPGig~~Kvk~L~d~fhePF~~~ 108 (216)
-.+||||++.|.++..++-.-|+-.
T Consensus 118 l~LpGVG~KTAnvVL~~l~~~~~~~ 142 (177)
T TIGR03252 118 KALPGFGKQKAKIFLALLGKQLGVT 142 (177)
T ss_pred HcCCCCCHHHHHHHHHHHHHHhCCC
Confidence 9999999999999999998888754
No 95
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=60.88 E-value=9 Score=37.93 Aligned_cols=32 Identities=13% Similarity=0.264 Sum_probs=30.2
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|...+.++|+.++|+|++++++|++.+.
T Consensus 460 ~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie 491 (669)
T PRK14350 460 SEIDLYTFNFDRLINLKGFKDKRINNLKRSIE 491 (669)
T ss_pred CHHHHhhCCHHHHhhccCccHHHHHHHHHHHH
Confidence 77889999999999999999999999999887
No 96
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.00 E-value=8.2 Score=33.29 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=20.8
Q ss_pred HHHHHhCCHhhhccCCCCcHHHHHHH-HHHhc
Q 041647 72 LSHIMDASMEDLARCPGIVERKVKCL-YDTFH 102 (216)
Q Consensus 72 L~~Im~AS~EdLA~cPGig~~Kvk~L-~d~fh 102 (216)
+++++ +.|+++||||++-|++| |..+.
T Consensus 6 ~~~Li----~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 6 ISKLI----ESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHH----HHHHHCCCCCHHHHHHHHHHHHc
Confidence 45554 78999999999999998 44443
No 97
>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=59.38 E-value=12 Score=26.07 Aligned_cols=19 Identities=32% Similarity=0.455 Sum_probs=16.1
Q ss_pred hhccCCCCcHHHHHHHHHH
Q 041647 82 DLARCPGIVERKVKCLYDT 100 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~ 100 (216)
++..+||||+.-++.+-+.
T Consensus 48 ~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 4999999999988888554
No 98
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=59.33 E-value=10 Score=33.67 Aligned_cols=33 Identities=15% Similarity=0.309 Sum_probs=31.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
++.+++..|.+||.+++|+|++-.+.+.+.+.+
T Consensus 257 ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~~ 289 (297)
T TIGR02027 257 TLGELVSKSEEELLKIKNFGKKSLTEIKEKLAE 289 (297)
T ss_pred CHHHHHhCCHHHHhhCCCCChhhHHHHHHHHHH
Confidence 889999999999999999999999999998876
No 99
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=57.42 E-value=15 Score=24.92 Aligned_cols=30 Identities=13% Similarity=0.263 Sum_probs=22.1
Q ss_pred HHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 72 LSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 72 L~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
+....-.+.++|..++|+|+.|++.-.+.|
T Consensus 38 ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~ 67 (81)
T smart00341 38 MAAALPTNVSELLAIDGVGEEKARRYGKDL 67 (81)
T ss_pred HHHHCCCCHHHHhcCCCCCHHHHHHHHHHH
Confidence 333344689999999999999987655544
No 100
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=55.84 E-value=21 Score=32.25 Aligned_cols=31 Identities=26% Similarity=0.366 Sum_probs=28.0
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
|+++|..++..+|+++-||.+.|++.+....
T Consensus 51 T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~ 81 (342)
T PLN03186 51 TVESLAYAPKKDLLQIKGISEAKVEKILEAA 81 (342)
T ss_pred cHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 8999999999999999999999997776554
No 101
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=55.77 E-value=13 Score=36.44 Aligned_cols=33 Identities=27% Similarity=0.416 Sum_probs=30.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
++.+|...+.+||...+|+|++++++|++.+..
T Consensus 449 ~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~ 481 (562)
T PRK08097 449 HLFSWLALTPEQLANTPGIGKARAEQLWHQFNL 481 (562)
T ss_pred CHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHH
Confidence 788999999999999999999999999999873
No 102
>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=54.56 E-value=8.5 Score=27.64 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=23.9
Q ss_pred ccccccCCcChhhHHHHHhhcCCCCChHHHHH
Q 041647 5 HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLR 36 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~ 36 (216)
+.|++|+||+..-+..|+...| |++.|--
T Consensus 2 ~~l~sipGig~~~a~~llaeig---d~~rF~~ 30 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIG---DISRFKS 30 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHc---Cchhccc
Confidence 5689999999999999999998 5554443
No 103
>PRK14973 DNA topoisomerase I; Provisional
Probab=54.06 E-value=18 Score=37.16 Aligned_cols=32 Identities=25% Similarity=0.289 Sum_probs=28.7
Q ss_pred hcHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 70 VSLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 70 ~SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
++.+.+.++..++||+..||+..|++.|+...
T Consensus 899 ~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~ 930 (936)
T PRK14973 899 YDGDLLVSADPKKLAKVTGIDEKKLRNLQAYA 930 (936)
T ss_pred CCHHHhccCCHHHHhhhcCCCHHHHHHHHHHH
Confidence 38888899999999999999999999998754
No 104
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=53.75 E-value=43 Score=29.67 Aligned_cols=102 Identities=20% Similarity=0.141 Sum_probs=62.4
Q ss_pred HHHHhhcCC-------CCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCC----HhhhccCC
Q 041647 19 VNLGSTSGI-------HNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDAS----MEDLARCP 87 (216)
Q Consensus 19 ~nLlstfG~-------~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS----~EdLA~cP 87 (216)
..|.+.||- +-.||+|........--...++|.+.....--..+-.-+ +++..+...+ +|.|..++
T Consensus 128 ~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~~~g~s~~Ka~yi~~~A~~~~~g~---~~~~~l~~~~~e~a~e~L~~i~ 204 (285)
T COG0122 128 ARLVSLYGNALEIYHSFPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGE---LDLSELKPLSDEEAIEELTALK 204 (285)
T ss_pred HHHHHHhCCccccccCCCCHHHHHhcCHHHHHHhCCcHHHHHHHHHHHHHHHcCC---ccHHHhccCCHHHHHHHHHcCC
Confidence 456677773 779999999888766555555554444433222222222 3666666654 57789999
Q ss_pred CCcHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCcchhhHHHHHHHHH
Q 041647 88 GIVERKVKCLYDTFHEPFKPVVSRHPPIPETPSLKDVEPSSVNESALSAAFANYA 142 (216)
Q Consensus 88 Gig~~Kvk~L~d~fhePF~~~~sr~~~~p~t~~~k~~epssv~esalsaAfa~~a 142 (216)
|||+--|+++.-. - +...+-.++.+-.+-.|+..+-
T Consensus 205 GIG~WTAe~~llf-~------------------lgr~dvfP~~D~~lr~~~~~~~ 240 (285)
T COG0122 205 GIGPWTAEMFLLF-G------------------LGRPDVFPADDLGLRRAIKKLY 240 (285)
T ss_pred CcCHHHHHHHHHH-c------------------CCCCCCCChHHHHHHHHHHHHh
Confidence 9999999886532 1 1222334455667777766654
No 105
>PRK13844 recombination protein RecR; Provisional
Probab=53.51 E-value=12 Score=32.46 Aligned_cols=25 Identities=24% Similarity=0.347 Sum_probs=20.0
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHH
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d 99 (216)
+++++. +.|.+.||||++-|++|--
T Consensus 9 ~~~~LI----~~l~~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 9 KISAVI----ESLRKLPTIGKKSSQRLAL 33 (200)
T ss_pred HHHHHH----HHHHHCCCCCHHHHHHHHH
Confidence 455555 7899999999999999843
No 106
>PRK05755 DNA polymerase I; Provisional
Probab=53.25 E-value=23 Score=35.23 Aligned_cols=32 Identities=22% Similarity=0.407 Sum_probs=25.2
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
-+.-|+--+-+.+..|||||++.|..|...|.
T Consensus 177 d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 177 DYLALMGDSSDNIPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred HHHHHhCCccCCCCCCCCccHHHHHHHHHHcC
Confidence 44456666778899999999999998876654
No 107
>PRK03858 DNA polymerase IV; Validated
Probab=52.80 E-value=71 Score=28.10 Aligned_cols=30 Identities=10% Similarity=0.099 Sum_probs=22.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.++.+.+.+.|.+. +|....+.|++.-+
T Consensus 196 t~~dl~~l~~~~L~~~--fG~~~~~~l~~~a~ 225 (396)
T PRK03858 196 TVGDVAELPESALVSL--LGPAAGRHLHALAH 225 (396)
T ss_pred cHHHHhcCCHHHHHHH--hCcHHHHHHHHHhC
Confidence 7888888888888876 55566777887554
No 108
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=52.60 E-value=16 Score=32.00 Aligned_cols=31 Identities=13% Similarity=0.197 Sum_probs=27.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
+.+.|.+++.++|..| |++.+|++.|.+.-.
T Consensus 157 tpe~La~~~~~eL~~~-Gl~~~Ra~~L~~lA~ 187 (283)
T PRK10308 157 TPERLAAADPQALKAL-GMPLKRAEALIHLAN 187 (283)
T ss_pred CHHHHHcCCHHHHHHC-CCCHHHHHHHHHHHH
Confidence 7899999999999999 999999999887654
No 109
>PRK00076 recR recombination protein RecR; Reviewed
Probab=51.57 E-value=9.9 Score=32.69 Aligned_cols=21 Identities=29% Similarity=0.374 Sum_probs=17.7
Q ss_pred hhhccCCCCcHHHHHHHHHHh
Q 041647 81 EDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~f 101 (216)
+.|++.||||++-|++|--.+
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~l 31 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHL 31 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHH
Confidence 789999999999999984433
No 110
>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=51.50 E-value=26 Score=28.44 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=18.6
Q ss_pred CCHhhhccCCCCcHHHHHHHHH
Q 041647 78 ASMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d 99 (216)
...+.|..+||||+.-|.++.-
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLN 124 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHH
Confidence 3578999999999999998753
No 111
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=50.90 E-value=15 Score=31.94 Aligned_cols=32 Identities=22% Similarity=0.358 Sum_probs=24.5
Q ss_pred hCCHhhhccCCCCcHHHHHHHHHH-hcCCCCCC
Q 041647 77 DASMEDLARCPGIVERKVKCLYDT-FHEPFKPV 108 (216)
Q Consensus 77 ~AS~EdLA~cPGig~~Kvk~L~d~-fhePF~~~ 108 (216)
..++++|..+||+|.+-|...... |..|-++|
T Consensus 105 P~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~V 137 (211)
T COG0177 105 PDTREELLSLPGVGRKTANVVLSFAFGIPAIAV 137 (211)
T ss_pred CchHHHHHhCCCcchHHHHHHHHhhcCCCcccc
Confidence 357888999999998888877666 77775444
No 112
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=50.84 E-value=15 Score=30.48 Aligned_cols=23 Identities=26% Similarity=0.574 Sum_probs=19.7
Q ss_pred HHHHHHHHhhhhhccchhhhhhh
Q 041647 36 RARVSLVLYLNTKRRSAKSFQRQ 58 (216)
Q Consensus 36 ~~~~~l~~~l~t~rr~a~~~~~~ 58 (216)
.+-++.|.|+-.|||+.|.|.+.
T Consensus 18 ~~flgYciYFD~KRR~dPdFRkk 40 (148)
T TIGR00985 18 AAFLGYAIYFDYKRRNDPDFRKK 40 (148)
T ss_pred HHHHHHHHhhhhhhccCHHHHHH
Confidence 55667899999999999999864
No 113
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=50.64 E-value=11 Score=35.17 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=22.0
Q ss_pred CCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 78 ASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
...++|-.+||+|++|...||+.|-
T Consensus 90 ~gl~~Ll~v~GlGpkKi~~Ly~elg 114 (326)
T COG1796 90 EGLEPLLKVPGLGPKKIVSLYKELG 114 (326)
T ss_pred cchHHHhhCCCCCcHHHHHHHHHHC
Confidence 3467888999999999999999985
No 114
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.44 E-value=25 Score=35.85 Aligned_cols=32 Identities=22% Similarity=0.378 Sum_probs=24.8
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
.+..||--+-+.+-.|||||++.|..|...|.
T Consensus 175 D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~yg 206 (887)
T TIGR00593 175 DLKALVGDSSDNIPGVKGIGEKTAAKLLQEFG 206 (887)
T ss_pred HHHHHcCCcccCCCCCCCcCHHHHHHHHHHcC
Confidence 44456766778899999999999998876543
No 115
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=47.22 E-value=16 Score=36.04 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=20.0
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|..+||||+++++.|+..|.
T Consensus 552 S~L~~IpGIG~kr~~~LL~~Fg 573 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHFG 573 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHcC
Confidence 4678999999999999999996
No 116
>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=47.21 E-value=28 Score=29.64 Aligned_cols=40 Identities=5% Similarity=-0.020 Sum_probs=29.6
Q ss_pred hcHHHHHhCCHhhhccCC-------CCcHHHHHHHHHHhc---CCCCCCC
Q 041647 70 VSLSHIMDASMEDLARCP-------GIVERKVKCLYDTFH---EPFKPVV 109 (216)
Q Consensus 70 ~SL~~Im~AS~EdLA~cP-------Gig~~Kvk~L~d~fh---ePF~~~~ 109 (216)
.+...|..++.|+|+.+= |+-.+|+++|++.-. +-|...+
T Consensus 50 ~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G~v 99 (177)
T TIGR03252 50 LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDGDA 99 (177)
T ss_pred CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCCCh
Confidence 378899999999987642 677899999987654 4454443
No 117
>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=47.19 E-value=15 Score=30.70 Aligned_cols=22 Identities=9% Similarity=0.291 Sum_probs=19.5
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++|-.+||||+++|..|...+.
T Consensus 72 ~~L~~V~GIGpK~Al~iL~~~~ 93 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILSNMS 93 (191)
T ss_pred HHHhCCCCCCHHHHHHHHhcCC
Confidence 5788999999999999988765
No 118
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=46.22 E-value=14 Score=35.94 Aligned_cols=23 Identities=26% Similarity=0.330 Sum_probs=20.7
Q ss_pred hhhccCCCCcHHHHHHHHHHhcC
Q 041647 81 EDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
--|..+||||+++++.|++.|..
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS 547 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGS 547 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCC
Confidence 46789999999999999999974
No 119
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=44.81 E-value=15 Score=25.45 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=14.6
Q ss_pred cCCCCcHHHHHHHHHHhc
Q 041647 85 RCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 85 ~cPGig~~Kvk~L~d~fh 102 (216)
.+||+|+..++.|-+.|.
T Consensus 7 GI~~VG~~~ak~L~~~f~ 24 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG 24 (64)
T ss_dssp TSTT--HHHHHHHHHCCS
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 589999999999999887
No 120
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=43.46 E-value=16 Score=32.14 Aligned_cols=24 Identities=17% Similarity=0.473 Sum_probs=19.9
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHH
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLY 98 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~ 98 (216)
.+++++ +.|+++||+|++-|+++-
T Consensus 6 ~i~~LI----~~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 6 PIEKLI----DALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHHHHH----HHHhhCCCCChhHHHHHH
Confidence 566665 689999999999999983
No 121
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=42.35 E-value=18 Score=35.10 Aligned_cols=22 Identities=32% Similarity=0.564 Sum_probs=19.8
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|-.+||||+++.+.|+..|-
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHcC
Confidence 4678999999999999999985
No 122
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=41.62 E-value=19 Score=35.14 Aligned_cols=22 Identities=23% Similarity=0.360 Sum_probs=20.0
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|-.+||||+++.+.|+..|-
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fg 535 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLG 535 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhC
Confidence 3788999999999999999985
No 123
>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=40.78 E-value=17 Score=27.64 Aligned_cols=28 Identities=18% Similarity=0.370 Sum_probs=24.3
Q ss_pred cccccccccCCcChhhHHHHHhhcCCCC
Q 041647 2 ALTHALTSVWSVNKTDVVNLGSTSGIHN 29 (216)
Q Consensus 2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~ 29 (216)
.+.-+|+.|.||++.-+..++..+|+..
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lgi~~ 39 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLGINP 39 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTTS-S
T ss_pred chHhHHhhhhccCHHHHHHHHHHcCCCh
Confidence 3567899999999999999999999865
No 124
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=40.10 E-value=22 Score=34.59 Aligned_cols=22 Identities=32% Similarity=0.493 Sum_probs=19.8
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|-.+||||+++.+.|+..|.
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~Fg 535 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRNFK 535 (567)
T ss_pred CccccCCCCCHHHHHHHHHHhC
Confidence 4678999999999999999985
No 125
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=40.08 E-value=53 Score=28.36 Aligned_cols=31 Identities=32% Similarity=0.470 Sum_probs=27.1
Q ss_pred cHHHHHhCCHhhhccC---CCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARC---PGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~c---PGig~~Kvk~L~d~f 101 (216)
+.+.|.+++.++|+.| -|+-.+|+++|.+..
T Consensus 68 t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la 101 (218)
T PRK13913 68 NLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLS 101 (218)
T ss_pred CHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 7899999999998877 799999999988654
No 126
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=38.70 E-value=28 Score=35.25 Aligned_cols=23 Identities=26% Similarity=0.481 Sum_probs=21.0
Q ss_pred HhhhccCCCCcHHHHHHHHHHhc
Q 041647 80 MEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 80 ~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
...|..+||||+++++.|++.|.
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhC
Confidence 46889999999999999999986
No 127
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=38.40 E-value=30 Score=30.02 Aligned_cols=33 Identities=15% Similarity=0.321 Sum_probs=26.8
Q ss_pred hcHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 70 VSLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 70 ~SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
+-+..+|.-+-+.+..+||||+++|..|..-|-
T Consensus 187 iD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 187 IDLKALVGDSSDNIPGVKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhC
Confidence 455556666678888999999999999988876
No 128
>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=38.28 E-value=33 Score=29.05 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=20.2
Q ss_pred cccccccCCcChhhHHHHHhhcC
Q 041647 4 THALTSVWSVNKTDVVNLGSTSG 26 (216)
Q Consensus 4 t~aLTsV~sVNKTDv~nLlstfG 26 (216)
++-+..|+||++..+..|+..||
T Consensus 182 sDnipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 182 SDNIPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred ccCCCCCCccCHHHHHHHHHHhC
Confidence 34567899999999999999999
No 129
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=37.56 E-value=23 Score=34.02 Aligned_cols=25 Identities=28% Similarity=0.400 Sum_probs=22.3
Q ss_pred HhCCHhhhccCCCCcHHHHHHHHHH
Q 041647 76 MDASMEDLARCPGIVERKVKCLYDT 100 (216)
Q Consensus 76 m~AS~EdLA~cPGig~~Kvk~L~d~ 100 (216)
-.|+.++|-++||||.+-|+++..+
T Consensus 325 n~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 325 NKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred cccCHHHhcccCCCChHHHHHHHHH
Confidence 4689999999999999999999765
No 130
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=36.91 E-value=1.7e+02 Score=26.45 Aligned_cols=30 Identities=20% Similarity=0.201 Sum_probs=21.2
Q ss_pred cHHHHHhCC--HhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDAS--MEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS--~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.++.... .+.|.+. +|....+.||+..+
T Consensus 245 t~~dl~~~~~~~~~L~~~--fG~~~g~~L~~~a~ 276 (404)
T cd01701 245 TCGGLELRSKTKEKLQKV--LGPKTGEKLYDYCR 276 (404)
T ss_pred chHHHHhCcccHHHHHHH--HCHHHHHHHHHHhC
Confidence 666666666 7777765 56666888888776
No 131
>PRK03352 DNA polymerase IV; Validated
Probab=36.05 E-value=1.3e+02 Score=26.01 Aligned_cols=30 Identities=13% Similarity=0.050 Sum_probs=21.7
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|.+.+.++|++. +|....+.|++.-+
T Consensus 200 ti~dl~~l~~~~L~~~--fG~~~~~~l~~~a~ 229 (346)
T PRK03352 200 TVADLAAADPAELAAT--FGPTTGPWLLLLAR 229 (346)
T ss_pred cHHHHhcCCHHHHHHH--hChHHHHHHHHHhC
Confidence 7888888888888887 44445566777644
No 132
>PRK01810 DNA polymerase IV; Validated
Probab=34.63 E-value=1.7e+02 Score=26.01 Aligned_cols=29 Identities=14% Similarity=0.015 Sum_probs=22.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+|...+.++|.+.=| . ....+|+..+
T Consensus 202 tigdL~~~~~~~L~~rfG--~-~g~~l~~~a~ 230 (407)
T PRK01810 202 TIGDLAKADEHILRAKLG--I-NGVRLQRRAN 230 (407)
T ss_pred cHHHHHhCCHHHHHHHHh--H-HHHHHHHHhc
Confidence 788888889889887744 3 5777888777
No 133
>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=34.44 E-value=37 Score=21.16 Aligned_cols=18 Identities=22% Similarity=0.248 Sum_probs=14.5
Q ss_pred hhccCCCCcHHHHHHHHH
Q 041647 82 DLARCPGIVERKVKCLYD 99 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d 99 (216)
.+..++|||.+-+++|.+
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 678899999999998853
No 134
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=34.13 E-value=35 Score=34.55 Aligned_cols=33 Identities=18% Similarity=0.347 Sum_probs=31.1
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
+..+|...+.|||...+|+|++++++|++.++.
T Consensus 469 ~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~aIe~ 501 (667)
T COG0272 469 DIADLYTLTEEDLLSLEGFGEKSAENLLNAIEK 501 (667)
T ss_pred CHHHHHhCCHHHHhhccchhhhHHHHHHHHHHH
Confidence 788999999999999999999999999999983
No 135
>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=33.94 E-value=43 Score=23.90 Aligned_cols=22 Identities=14% Similarity=0.187 Sum_probs=20.0
Q ss_pred ccccccCCcChhhHHHHHhhcC
Q 041647 5 HALTSVWSVNKTDVVNLGSTSG 26 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG 26 (216)
+-+..|+||++.-+..|+..||
T Consensus 22 D~i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred ccCCCCCcccHHHHHHHHHHhC
Confidence 4567899999999999999999
No 136
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=33.92 E-value=47 Score=31.53 Aligned_cols=31 Identities=16% Similarity=0.371 Sum_probs=24.9
Q ss_pred cHHHHHh---CCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMD---ASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~---AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
+|.+|.. ++.++|.+++|+|++|+.+--+.|
T Consensus 562 tL~~ia~~~P~t~~~l~~i~Gvg~~K~~~yg~~~ 595 (607)
T PRK11057 562 TLIEMAEQMPITASEMLSVNGVGQRKLERFGKPF 595 (607)
T ss_pred HHHHHHHHCCCCHHHHcCCCCCCHHHHHHHHHHH
Confidence 6666665 499999999999999998765554
No 137
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=33.30 E-value=31 Score=34.99 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=19.7
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|-.+||||+++.+.|+..|-
T Consensus 608 s~L~~IpGiG~kr~~~LL~~Fg 629 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFG 629 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhc
Confidence 3577999999999999999985
No 138
>PRK10880 adenine DNA glycosylase; Provisional
Probab=33.26 E-value=39 Score=30.99 Aligned_cols=30 Identities=17% Similarity=0.386 Sum_probs=25.4
Q ss_pred CCHhhhccCCCCcHHHHHHHHH-HhcCCCCC
Q 041647 78 ASMEDLARCPGIVERKVKCLYD-TFHEPFKP 107 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d-~fhePF~~ 107 (216)
.+.++|..+||||+.-|.++.- .|+.||..
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~af~~~~~i 136 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLSLGKHFPI 136 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHHCCCCeec
Confidence 5679999999999999999875 78888754
No 139
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=33.15 E-value=1.8e+02 Score=26.22 Aligned_cols=73 Identities=11% Similarity=0.172 Sum_probs=35.1
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc-CCCCCCCCCCCCCCCCCCCCCCCCCCcchhhHHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH-EPFKPVVSRHPPIPETPSLKDVEPSSVNESALSAAFANYADKMG 146 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh-ePF~~~~sr~~~~p~t~~~k~~epssv~esalsaAfa~~a~~~~ 146 (216)
++.++.+.+.+.|.+.=|. ....+++..+ ..-.++....++...-.....-+..-.+...+..+...++++..
T Consensus 202 TigdL~~~~~~~L~~~fG~---~~~~l~~~a~G~~~~~~~~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~ 275 (422)
T PRK03609 202 TALDLADTNIRFIRKHFNV---VLERTVRELRGEPCLSLEEFAPTKQEIVCSRSFGERITDYESMRQAICSYAARAA 275 (422)
T ss_pred cHHHHhcCCHHHHHHHHCH---HHHHHHHHhCCCCCCCccccCCCCceEEEeeECCCCCCCHHHHHHHHHHHHHHHH
Confidence 7788888888888776453 3445555544 22111111111100000011112233355667777777776654
No 140
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=33.06 E-value=84 Score=27.41 Aligned_cols=73 Identities=23% Similarity=0.355 Sum_probs=49.9
Q ss_pred CCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc---cCCCCcHHHHHHHHHHhc--
Q 041647 28 HNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA---RCPGIVERKVKCLYDTFH-- 102 (216)
Q Consensus 28 ~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA---~cPGig~~Kvk~L~d~fh-- 102 (216)
+.||=+++-+-+ +..|-.-+.-.+.--.||+.-. +.+.+.+++.|+|+ +.-|+-.+||++|+.+-.
T Consensus 26 ~~~pf~lLva~i------LSaqttD~~vn~at~~Lf~~~~---t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l 96 (211)
T COG0177 26 FKDPFELLVAVI------LSAQTTDEVVNKATPALFKRYP---TPEDLLNADEEELEELIKSIGLYRNKAKNIKELARIL 96 (211)
T ss_pred cCCcHHHHHHHH------HhccCchHHHHHHHHHHHHHcC---CHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHH
Confidence 457777664433 3333333444444456788777 89999999988876 468999999999987654
Q ss_pred -CCCCCCC
Q 041647 103 -EPFKPVV 109 (216)
Q Consensus 103 -ePF~~~~ 109 (216)
|-|...+
T Consensus 97 ~e~~~g~v 104 (211)
T COG0177 97 LEKFGGEV 104 (211)
T ss_pred HHHcCCCC
Confidence 6676633
No 141
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=33.00 E-value=45 Score=28.77 Aligned_cols=31 Identities=16% Similarity=0.077 Sum_probs=25.0
Q ss_pred CCHhhhccCCCCcHHHHHHHHH-HhcCCCCCC
Q 041647 78 ASMEDLARCPGIVERKVKCLYD-TFHEPFKPV 108 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d-~fhePF~~~ 108 (216)
..+++|-.+||||+.-|.++.- .|+.|-.+|
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvV 149 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCAKEVMVV 149 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcCCCcccc
Confidence 4678999999999999998754 677776544
No 142
>PRK03348 DNA polymerase IV; Provisional
Probab=32.80 E-value=2.2e+02 Score=26.45 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=26.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc-CCCCCCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH-EPFKPVVS 110 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh-ePF~~~~s 110 (216)
++.+|.+.+.++|.+. +|......||+..+ ..-.++..
T Consensus 203 TigDLa~l~~~~L~~~--fG~~~g~~L~~~a~G~d~~pv~~ 241 (454)
T PRK03348 203 TIGDLAALSEAEVANL--LGATVGPALHRLARGIDDRPVAE 241 (454)
T ss_pred cHHHHhcCCHHHHHHH--HCHHHHHHHHHHHcCCCCCCccc
Confidence 7888899999999887 56666777887654 33334433
No 143
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=32.57 E-value=64 Score=28.36 Aligned_cols=22 Identities=23% Similarity=0.293 Sum_probs=18.4
Q ss_pred CCHhhhccCCCCcHHHHHHHHH
Q 041647 78 ASMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d 99 (216)
..+++|..+||||+.-|.++.-
T Consensus 204 ~~~~~L~~LpGIGpwTA~~vll 225 (283)
T PRK10308 204 QAMKTLQTFPGIGRWTANYFAL 225 (283)
T ss_pred HHHHHHhcCCCcCHHHHHHHHH
Confidence 3468999999999999998753
No 144
>PRK02362 ski2-like helicase; Provisional
Probab=32.41 E-value=70 Score=30.95 Aligned_cols=21 Identities=24% Similarity=0.441 Sum_probs=18.3
Q ss_pred CHhhhccCCCCcHHHHHHHHH
Q 041647 79 SMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~d 99 (216)
..-+|.++||||+..++.||+
T Consensus 650 ~~~~L~~ip~i~~~~a~~l~~ 670 (737)
T PRK02362 650 ELLDLVGLRGVGRVRARRLYN 670 (737)
T ss_pred HHHHHhCCCCCCHHHHHHHHH
Confidence 445788999999999999997
No 145
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=31.93 E-value=55 Score=20.68 Aligned_cols=28 Identities=25% Similarity=0.501 Sum_probs=23.5
Q ss_pred HHHhC-CHhhhccCCCCcHHHHHHHHHHh
Q 041647 74 HIMDA-SMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 74 ~Im~A-S~EdLA~cPGig~~Kvk~L~d~f 101 (216)
.+... |+.++|+.=|++..-|+++++.+
T Consensus 23 ~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 23 LLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34445 89999999999999999999864
No 146
>PRK07945 hypothetical protein; Provisional
Probab=31.80 E-value=1.4e+02 Score=26.63 Aligned_cols=45 Identities=18% Similarity=0.341 Sum_probs=27.5
Q ss_pred hhhhhhhhhhhccccchhc-HHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 53 KSFQRQNNLLFKTQSAPVS-LSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 53 ~~~~~~nn~~~~~~s~~~S-L~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|++--..+-.... + +..+...- +|..+||||+.-+..|.+...
T Consensus 25 ~ayr~aa~~~~~~~~---~~~~~~~~~g--~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 25 RAFRRAADVVEALDA---AERARRARAG--SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred HHHHHHHHHHHhcCh---hHHHHHHhcC--CcccCCCcCHHHHHHHHHHHh
Confidence 344444444444333 4 45554333 899999999998877766554
No 147
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=31.39 E-value=98 Score=27.80 Aligned_cols=22 Identities=14% Similarity=0.037 Sum_probs=17.6
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++-..+||||+++|-.|...|.
T Consensus 236 dyn~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 236 DYNEGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred CCCCCCCCccHHHHHHHHHHcC
Confidence 4458899999999998886654
No 148
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=31.20 E-value=35 Score=33.12 Aligned_cols=23 Identities=30% Similarity=0.489 Sum_probs=20.8
Q ss_pred hhhccCCCCcHHHHHHHHHHhcC
Q 041647 81 EDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
..|..+||||+++++.|+..|..
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~FgS 565 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKHFGS 565 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHcCC
Confidence 46789999999999999999975
No 149
>PRK10736 hypothetical protein; Provisional
Probab=31.18 E-value=36 Score=31.72 Aligned_cols=23 Identities=9% Similarity=0.086 Sum_probs=20.1
Q ss_pred hhccCCCCcHHHHHHHHHHhcCC
Q 041647 82 DLARCPGIVERKVKCLYDTFHEP 104 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~fheP 104 (216)
-|..+||||.++.++|++.|..+
T Consensus 9 ~L~~~~giG~~~~~~L~~~~~~~ 31 (374)
T PRK10736 9 RLMSVSSLYGDKMVRIAHRLLAQ 31 (374)
T ss_pred HHHhCCCCCHHHHHHHHHHhcCh
Confidence 46789999999999999998744
No 150
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=31.17 E-value=49 Score=27.61 Aligned_cols=38 Identities=16% Similarity=0.180 Sum_probs=31.4
Q ss_pred cccccccccCCcChhhHHHHHhhcCCCC-------ChHHHHHHHH
Q 041647 2 ALTHALTSVWSVNKTDVVNLGSTSGIHN-------DPEQLLRARV 39 (216)
Q Consensus 2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~-------dpeql~~~~~ 39 (216)
.+.-+||.|.||+..-+..++...|++. +++|+.+=..
T Consensus 27 ~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~ 71 (154)
T PTZ00134 27 KVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVE 71 (154)
T ss_pred EEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHH
Confidence 3567899999999999999999999964 6777765544
No 151
>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=31.01 E-value=49 Score=25.94 Aligned_cols=37 Identities=24% Similarity=0.360 Sum_probs=29.8
Q ss_pred cccccccccCCcChhhHHHHHhhcCCCC-------ChHHHHHHH
Q 041647 2 ALTHALTSVWSVNKTDVVNLGSTSGIHN-------DPEQLLRAR 38 (216)
Q Consensus 2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~-------dpeql~~~~ 38 (216)
.+.-+|+.|.||+..-+..++...|++. .++|+.+=.
T Consensus 12 ~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~ 55 (113)
T TIGR03631 12 RVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIR 55 (113)
T ss_pred EEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHH
Confidence 3567899999999999999999999864 566665433
No 152
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=30.74 E-value=88 Score=26.25 Aligned_cols=38 Identities=16% Similarity=0.317 Sum_probs=32.4
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc-CCCCCC
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH-EPFKPV 108 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh-ePF~~~ 108 (216)
|+.++.+.+.+++..+-|+++..++.+++..+ =|...+
T Consensus 174 s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v 212 (312)
T smart00611 174 SLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNI 212 (312)
T ss_pred CHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCccee
Confidence 89999999999999999999999999988876 455444
No 153
>PRK00254 ski2-like helicase; Provisional
Probab=30.65 E-value=28 Score=33.49 Aligned_cols=26 Identities=27% Similarity=0.471 Sum_probs=21.7
Q ss_pred hhhccCCCCcHHHHHHHHHH-hcCCCC
Q 041647 81 EDLARCPGIVERKVKCLYDT-FHEPFK 106 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~-fhePF~ 106 (216)
-.|..+||+|+.+++.||+. |...+.
T Consensus 645 ~~L~~ipgig~~~~~~l~~~g~~s~~~ 671 (720)
T PRK00254 645 LELMRLPMIGRKRARALYNAGFRSIED 671 (720)
T ss_pred hhhhcCCCCCHHHHHHHHHccCCCHHH
Confidence 35678999999999999999 876653
No 154
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=30.30 E-value=53 Score=26.12 Aligned_cols=37 Identities=24% Similarity=0.384 Sum_probs=30.0
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCC-------ChHHHHHHHH
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHN-------DPEQLLRARV 39 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~-------dpeql~~~~~ 39 (216)
+.-+|+.|.||+..-+..++..+|++. .++|+.+=..
T Consensus 15 v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~ 58 (122)
T PRK05179 15 VVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIRE 58 (122)
T ss_pred EEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHH
Confidence 567899999999999999999999864 5666654433
No 155
>PRK09482 flap endonuclease-like protein; Provisional
Probab=30.06 E-value=47 Score=29.33 Aligned_cols=22 Identities=9% Similarity=0.066 Sum_probs=19.3
Q ss_pred ccccccCCcChhhHHHHHhhcC
Q 041647 5 HALTSVWSVNKTDVVNLGSTSG 26 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG 26 (216)
+-+-.|+||++.-+..|+..||
T Consensus 182 DnIpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred cCCCCCCCcChHHHHHHHHHhC
Confidence 3456799999999999999999
No 156
>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=29.39 E-value=53 Score=28.93 Aligned_cols=25 Identities=20% Similarity=0.410 Sum_probs=21.4
Q ss_pred CCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 78 ASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.+++..+||||+.-++.|.+.+.
T Consensus 42 ~~~~~~~~ipgiG~~ia~kI~E~~~ 66 (307)
T cd00141 42 ESLEEAKKLPGIGKKIAEKIEEILE 66 (307)
T ss_pred CCHHHhcCCCCccHHHHHHHHHHHH
Confidence 5667889999999999999888776
No 157
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=29.28 E-value=46 Score=28.66 Aligned_cols=30 Identities=17% Similarity=0.062 Sum_probs=22.6
Q ss_pred hCCHhhhc-cCCCCcHHHHHHHH-HHhcCCCC
Q 041647 77 DASMEDLA-RCPGIVERKVKCLY-DTFHEPFK 106 (216)
Q Consensus 77 ~AS~EdLA-~cPGig~~Kvk~L~-d~fhePF~ 106 (216)
...+++|- .+||||++-|.++. ..+..|..
T Consensus 114 ~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~ 145 (208)
T PRK01229 114 FEAREFLVKNIKGIGYKEASHFLRNVGYEDLA 145 (208)
T ss_pred hHHHHHHHHcCCCCcHHHHHHHHHHccCCCee
Confidence 35678888 99999999999987 34335643
No 158
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.24 E-value=47 Score=27.78 Aligned_cols=24 Identities=17% Similarity=0.218 Sum_probs=21.0
Q ss_pred hhhccCCCCcHHHHHHHHHHhcCC
Q 041647 81 EDLARCPGIVERKVKCLYDTFHEP 104 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fheP 104 (216)
+.|-.++|||++.|..+.+.|...
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhCCHH
Confidence 568899999999999999998733
No 159
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=28.87 E-value=41 Score=26.19 Aligned_cols=19 Identities=11% Similarity=0.158 Sum_probs=16.7
Q ss_pred ccCCCCcHHHHHHHHHHhc
Q 041647 84 ARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 84 A~cPGig~~Kvk~L~d~fh 102 (216)
..+||||..|+++|-..|.
T Consensus 53 r~vpglG~~~A~~I~awLa 71 (96)
T PF12482_consen 53 RAVPGLGAAGARRIEAWLA 71 (96)
T ss_pred HhCcccchHHHHHHHHHHH
Confidence 4699999999999988775
No 160
>PRK13910 DNA glycosylase MutY; Provisional
Probab=28.55 E-value=60 Score=29.11 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=23.7
Q ss_pred CCHhhhccCCCCcHHHHHHHHH-HhcCCCC
Q 041647 78 ASMEDLARCPGIVERKVKCLYD-TFHEPFK 106 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d-~fhePF~ 106 (216)
.+.++|..+||||+.-|.++.- .|+.|..
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~ 98 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKSA 98 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC
Confidence 4689999999999999998765 5777654
No 161
>PRK10736 hypothetical protein; Provisional
Probab=28.39 E-value=66 Score=30.03 Aligned_cols=21 Identities=24% Similarity=0.142 Sum_probs=19.2
Q ss_pred cccccCCcChhhHHHHHhhcC
Q 041647 6 ALTSVWSVNKTDVVNLGSTSG 26 (216)
Q Consensus 6 aLTsV~sVNKTDv~nLlstfG 26 (216)
.|+.++||+......|+..||
T Consensus 9 ~L~~~~giG~~~~~~L~~~~~ 29 (374)
T PRK10736 9 RLMSVSSLYGDKMVRIAHRLL 29 (374)
T ss_pred HHHhCCCCCHHHHHHHHHHhc
Confidence 577899999999999999999
No 162
>smart00475 53EXOc 5'-3' exonuclease.
Probab=28.19 E-value=54 Score=28.46 Aligned_cols=22 Identities=14% Similarity=0.175 Sum_probs=19.6
Q ss_pred ccccccCCcChhhHHHHHhhcC
Q 041647 5 HALTSVWSVNKTDVVNLGSTSG 26 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG 26 (216)
+-+..|+||++.-+..|+..||
T Consensus 186 DnipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred cCCCCCCCCCHHHHHHHHHHhC
Confidence 4567899999999999999999
No 163
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=27.80 E-value=59 Score=25.31 Aligned_cols=23 Identities=26% Similarity=0.278 Sum_probs=19.3
Q ss_pred hCCHhhhccCCCCcHHHHHHHHH
Q 041647 77 DASMEDLARCPGIVERKVKCLYD 99 (216)
Q Consensus 77 ~AS~EdLA~cPGig~~Kvk~L~d 99 (216)
.....+|..+||||+.-++.|..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~ 30 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRL 30 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHH
Confidence 34557899999999999999875
No 164
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=27.77 E-value=58 Score=29.77 Aligned_cols=51 Identities=20% Similarity=0.312 Sum_probs=41.0
Q ss_pred hhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCC
Q 041647 45 LNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEP 104 (216)
Q Consensus 45 l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fheP 104 (216)
|.-+-|+.....|.|=. ++.+++.-|.+||-+++.+|.+-+..+.+.+++-
T Consensus 268 L~LSvRs~NcLk~a~I~---------ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L~~~ 318 (327)
T CHL00013 268 LELSVRAYNCLKRANIH---------TLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQKR 318 (327)
T ss_pred ccCchhhhhhhhhcCcc---------CHHHHHhcCHHHHhhhhccCHhHHHHHHHHHHHH
Confidence 33445555555665555 9999999999999999999999999999998763
No 165
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=26.94 E-value=1.1e+02 Score=21.57 Aligned_cols=39 Identities=28% Similarity=0.374 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhc
Q 041647 32 EQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLA 84 (216)
Q Consensus 32 eql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA 84 (216)
++..+|...+++-++++| |.+-++.+. ..|..+|.++|.
T Consensus 2 eG~qeg~~~lllRlL~rr-------------FG~lp~~~~-~~I~~l~~eqLE 40 (59)
T PF14261_consen 2 EGRQEGEARLLLRLLTRR-------------FGELPPEIQ-ERIQQLSLEQLE 40 (59)
T ss_pred hHHHHHHHHHHHHHHHHH-------------cCCCCHHHH-HHHHcCCHHHHH
Confidence 456678888998888887 344444433 566666666664
No 166
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=26.82 E-value=88 Score=23.76 Aligned_cols=33 Identities=21% Similarity=0.147 Sum_probs=25.7
Q ss_pred hcHHHHHhCCHhhhccCCCC--cHHHHHHHHHHhc
Q 041647 70 VSLSHIMDASMEDLARCPGI--VERKVKCLYDTFH 102 (216)
Q Consensus 70 ~SL~~Im~AS~EdLA~cPGi--g~~Kvk~L~d~fh 102 (216)
.|.+.|..++.++|..|=.- -.+|++.|.+...
T Consensus 31 pt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~ 65 (158)
T cd00056 31 PTPEALAAADEEELRELIRSLGYRRKAKYLKELAR 65 (158)
T ss_pred CCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHH
Confidence 48999999999999986321 2789999887654
No 167
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=26.71 E-value=47 Score=28.20 Aligned_cols=20 Identities=20% Similarity=0.413 Sum_probs=17.4
Q ss_pred hccCCCCcHHHHHHHHHH-hc
Q 041647 83 LARCPGIVERKVKCLYDT-FH 102 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~-fh 102 (216)
|..+||||+..++.|++. |+
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ 21 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYD 21 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCC
Confidence 467899999999999998 66
No 168
>PRK14133 DNA polymerase IV; Provisional
Probab=26.19 E-value=3e+02 Score=23.90 Aligned_cols=29 Identities=17% Similarity=0.230 Sum_probs=21.9
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.++.+.+.++|.+.=| . ....+|+..+
T Consensus 196 ti~dl~~l~~~~L~~rfG--~-~g~~l~~~a~ 224 (347)
T PRK14133 196 TIEDLLKLSREFLIEYFG--K-FGVEIYERIR 224 (347)
T ss_pred cHHHHhhCCHHHHHHHHh--H-HHHHHHHHhC
Confidence 788899999999988844 3 5666777665
No 169
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=25.70 E-value=73 Score=26.37 Aligned_cols=38 Identities=13% Similarity=0.251 Sum_probs=31.0
Q ss_pred cccccccccCCcChhhHHHHHhhcCCCC-------ChHHHHHHHH
Q 041647 2 ALTHALTSVWSVNKTDVVNLGSTSGIHN-------DPEQLLRARV 39 (216)
Q Consensus 2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~-------dpeql~~~~~ 39 (216)
.+.-+|+.|.||++.-+..++...|++. .++|+.+=..
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~ 66 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEE 66 (149)
T ss_pred EEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHH
Confidence 3567899999999999999999999965 5677665444
No 170
>COG4483 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.57 E-value=72 Score=24.29 Aligned_cols=13 Identities=38% Similarity=0.279 Sum_probs=11.4
Q ss_pred hhHHHHHhhcCCC
Q 041647 16 TDVVNLGSTSGIH 28 (216)
Q Consensus 16 TDv~nLlstfG~~ 28 (216)
-||+.||.+||+.
T Consensus 5 YDVqQlLK~~G~i 17 (68)
T COG4483 5 YDVQQLLKKFGII 17 (68)
T ss_pred HHHHHHHHHCCee
Confidence 4999999999983
No 171
>PRK13980 NAD synthetase; Provisional
Probab=25.23 E-value=2e+02 Score=24.41 Aligned_cols=79 Identities=24% Similarity=0.340 Sum_probs=45.4
Q ss_pred ccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccc-------hhcHHHHH---
Q 041647 7 LTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSA-------PVSLSHIM--- 76 (216)
Q Consensus 7 LTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~-------~~SL~~Im--- 76 (216)
|.=+.++.|++|..|....|+ |+.+..-.. +|- |+..|+. .--|..|+
T Consensus 159 l~Pl~~l~K~eV~~la~~lgi---p~~i~~k~p-----------sa~--------L~~~q~De~~lg~~Y~~lD~~l~~~ 216 (265)
T PRK13980 159 LNPIGDLYKTQVRELARHLGV---PEDIIEKPP-----------SAD--------LWEGQTDEGELGFSYETIDEILYLL 216 (265)
T ss_pred cccCCCCcHHHHHHHHHHHCc---hHHHhCCCC-----------CcC--------CCCCCCCHHHcCCCHHHHHHHHHHH
Confidence 344578999999999999994 332222111 111 1111210 11233333
Q ss_pred ---hCCHhhhccCCCCcHHHHHHHHHHhcC-CCCC
Q 041647 77 ---DASMEDLARCPGIVERKVKCLYDTFHE-PFKP 107 (216)
Q Consensus 77 ---~AS~EdLA~cPGig~~Kvk~L~d~fhe-PF~~ 107 (216)
..+.++++.--|+.+.+++.++..++. -||.
T Consensus 217 ~~~~~~~~~i~~~~~~~~~~~~~i~~~~~~~~~Kr 251 (265)
T PRK13980 217 FDKKMSREEILEELGVPEDLVDRVRRLVQRSQHKR 251 (265)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhcc
Confidence 245667766558889999998888773 4553
No 172
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=25.06 E-value=4.2e+02 Score=22.38 Aligned_cols=29 Identities=14% Similarity=0.230 Sum_probs=21.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++.++.+.+..+|.+.- ......+|+..+
T Consensus 194 ti~dl~~~~~~~L~~~~---g~~~~~l~~~~~ 222 (334)
T cd03586 194 TIGDLAKLDVELLKKLF---GKSGRRLYELAR 222 (334)
T ss_pred CHHHHHcCCHHHHHHHH---hHHHHHHHHHhC
Confidence 78888888988998843 345666777666
No 173
>PRK01216 DNA polymerase IV; Validated
Probab=24.97 E-value=4.1e+02 Score=23.95 Aligned_cols=29 Identities=24% Similarity=0.335 Sum_probs=22.6
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
++.++.+.+.++|.+. +|....+.|++..
T Consensus 201 TigdL~~~~~~~L~~r--fG~~~~~~L~~~a 229 (351)
T PRK01216 201 KLVDTLRIEFDELKGI--IGEAKAKYLFSLA 229 (351)
T ss_pred cHHHHhcCCHHHHHHH--HCHHHHHHHHHHh
Confidence 7888888888888886 6666677788844
No 174
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=24.88 E-value=66 Score=28.46 Aligned_cols=32 Identities=19% Similarity=0.219 Sum_probs=29.3
Q ss_pred cHHHHHhCCHhhhccCCCCcHHHHHHHHHHhc
Q 041647 71 SLSHIMDASMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 71 SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
|+++|..++.+||.++-||.+.+++.++....
T Consensus 24 t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~ 55 (316)
T TIGR02239 24 TVESVAYAPKKQLLEIKGISEAKADKILAEAA 55 (316)
T ss_pred cHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 89999999999999999999999998887544
No 175
>PRK13766 Hef nuclease; Provisional
Probab=24.30 E-value=57 Score=31.19 Aligned_cols=21 Identities=14% Similarity=0.259 Sum_probs=19.3
Q ss_pred hccCCCCcHHHHHHHHHHhcC
Q 041647 83 LARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 83 LA~cPGig~~Kvk~L~d~fhe 103 (216)
|..+||||+.++++|.+.|..
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs 737 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGS 737 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCC
Confidence 789999999999999999863
No 176
>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=23.52 E-value=57 Score=32.17 Aligned_cols=42 Identities=21% Similarity=0.217 Sum_probs=29.1
Q ss_pred chhcHHHHHhCCHhhhccCCCCcHHHHHHHHHHhcCCCCCCCCC
Q 041647 68 APVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSR 111 (216)
Q Consensus 68 ~~~SL~~Im~AS~EdLA~cPGig~~Kvk~L~d~fhePF~~~~sr 111 (216)
.|.+.+.|+.-=.. ..+||||++.|++|++.|.+....+...
T Consensus 73 ~p~~~~~i~~yL~s--~~~~GIG~~~A~~iv~~fg~~~~~~i~~ 114 (720)
T TIGR01448 73 APTSKEGIVAYLSS--RSIKGVGKKLAQRIVKTFGEAAFDVLDD 114 (720)
T ss_pred CCCCHHHHHHHHhc--CCCCCcCHHHHHHHHHHhCHhHHHHHHh
Confidence 34466666542111 2499999999999999999877665443
No 177
>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=23.37 E-value=76 Score=24.08 Aligned_cols=21 Identities=29% Similarity=0.363 Sum_probs=19.3
Q ss_pred hhccCCCCcHHHHHHHHHHhc
Q 041647 82 DLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~fh 102 (216)
.|..+.|||..+++.|.+.+-
T Consensus 16 aLt~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 16 ALTKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp HHTTSTTBCHHHHHHHHHHTT
T ss_pred HHhhhhccCHHHHHHHHHHcC
Confidence 578999999999999999886
No 178
>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=23.28 E-value=69 Score=28.27 Aligned_cols=28 Identities=25% Similarity=0.568 Sum_probs=21.8
Q ss_pred CCHhhhccCCCCcHHHHHHHHH-HhcCCC
Q 041647 78 ASMEDLARCPGIVERKVKCLYD-TFHEPF 105 (216)
Q Consensus 78 AS~EdLA~cPGig~~Kvk~L~d-~fhePF 105 (216)
.+.++|..+||||+.-|.++.- .|+.|.
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~a~~~~~ 130 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSFALNKPY 130 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHCCCCC
Confidence 4589999999999999988754 455553
No 179
>PRK14976 5'-3' exonuclease; Provisional
Probab=23.25 E-value=78 Score=27.82 Aligned_cols=22 Identities=14% Similarity=0.244 Sum_probs=19.6
Q ss_pred ccccccCCcChhhHHHHHhhcC
Q 041647 5 HALTSVWSVNKTDVVNLGSTSG 26 (216)
Q Consensus 5 ~aLTsV~sVNKTDv~nLlstfG 26 (216)
+-+-.|+||++.-+.+|+..||
T Consensus 191 DnipGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCCCCcccHHHHHHHHHHcC
Confidence 4466899999999999999999
No 180
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=23.09 E-value=59 Score=32.08 Aligned_cols=21 Identities=33% Similarity=0.542 Sum_probs=19.2
Q ss_pred hhccCCCCcHHHHHHHHHHhc
Q 041647 82 DLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 82 dLA~cPGig~~Kvk~L~d~fh 102 (216)
.|-.+||||+...+.|.+.|-
T Consensus 531 ~Ld~I~GiG~~r~~~LL~~Fg 551 (581)
T COG0322 531 SLDDIPGIGPKRRKALLKHFG 551 (581)
T ss_pred ccccCCCcCHHHHHHHHHHhh
Confidence 678899999999999999985
No 181
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=22.68 E-value=93 Score=24.81 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=28.8
Q ss_pred ccccccccCCcChhhHHHHHhhcCCCC-------ChHHHHHH
Q 041647 3 LTHALTSVWSVNKTDVVNLGSTSGIHN-------DPEQLLRA 37 (216)
Q Consensus 3 lt~aLTsV~sVNKTDv~nLlstfG~~~-------dpeql~~~ 37 (216)
+.-+||.|.||++.-+..++...|++. .++|+.+=
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l 56 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL 56 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHH
Confidence 556899999999999999999999865 56665543
No 182
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=22.11 E-value=2e+02 Score=23.59 Aligned_cols=54 Identities=20% Similarity=0.255 Sum_probs=41.7
Q ss_pred CcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhhccCCCCcH
Q 041647 12 SVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVE 91 (216)
Q Consensus 12 sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdLA~cPGig~ 91 (216)
+-+-.|...++..-|+-.|+|.+- .+++-|+ .+ ++.+||....|.|+.+|.=|.
T Consensus 17 ~psa~DikkIl~sVG~E~d~e~i~----~visel~-------------GK---------~i~ElIA~G~eklAsvpsGGa 70 (112)
T KOG3449|consen 17 SPSASDIKKILESVGAEIDDERIN----LVLSELK-------------GK---------DIEELIAAGREKLASVPSGGA 70 (112)
T ss_pred CCCHHHHHHHHHHhCcccCHHHHH----HHHHHhc-------------CC---------CHHHHHHHhHHHHhcCCCCCc
Confidence 446789999999999999988763 1222232 22 999999999999999998775
No 183
>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=21.89 E-value=91 Score=25.57 Aligned_cols=38 Identities=16% Similarity=0.247 Sum_probs=30.6
Q ss_pred cccccccccCCcChhhHHHHHhhcCCCC-------ChHHHHHHHH
Q 041647 2 ALTHALTSVWSVNKTDVVNLGSTSGIHN-------DPEQLLRARV 39 (216)
Q Consensus 2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~-------dpeql~~~~~ 39 (216)
.+.-||+.|.||++.-+..++...|++. .++|+.+=..
T Consensus 18 ~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~ 62 (144)
T TIGR03629 18 PVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEE 62 (144)
T ss_pred EEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHH
Confidence 3567899999999999999999999964 5666655443
No 184
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=21.77 E-value=70 Score=28.86 Aligned_cols=25 Identities=24% Similarity=0.317 Sum_probs=20.8
Q ss_pred CHhhhccCCCCcHHHHHHHHHHhcC
Q 041647 79 SMEDLARCPGIVERKVKCLYDTFHE 103 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~d~fhe 103 (216)
...=|..+||||...+++|++.|-.
T Consensus 180 q~~il~s~pgig~~~a~~ll~~fgS 204 (254)
T COG1948 180 QLYILESIPGIGPKLAERLLKKFGS 204 (254)
T ss_pred HHHHHHcCCCccHHHHHHHHHHhcC
Confidence 3345678999999999999999863
No 185
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=21.49 E-value=90 Score=27.92 Aligned_cols=24 Identities=33% Similarity=0.473 Sum_probs=19.5
Q ss_pred CHhhhccCCCCcHHHHHHHHHHhc
Q 041647 79 SMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
++++|..+||||+.-++.|.+.+.
T Consensus 46 ~~~~l~~lpgIG~~ia~kI~Eil~ 69 (334)
T smart00483 46 SMKDLKGLPGIGDKIKKKIEEIIE 69 (334)
T ss_pred CHHHHhcCCCccHHHHHHHHHHHH
Confidence 456899999999998888877655
No 186
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=21.44 E-value=67 Score=31.58 Aligned_cols=22 Identities=27% Similarity=0.460 Sum_probs=20.1
Q ss_pred hhhccCCCCcHHHHHHHHHHhc
Q 041647 81 EDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 81 EdLA~cPGig~~Kvk~L~d~fh 102 (216)
..|..+||||+++++.|...|.
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fg 590 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFG 590 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcC
Confidence 5678999999999999999996
No 187
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=20.45 E-value=5e+02 Score=22.51 Aligned_cols=72 Identities=14% Similarity=0.104 Sum_probs=33.2
Q ss_pred cHHHHHhCC-HhhhccCCCCcHHHHHHHHHHhc-CCCCCCCCCCCCCCCCCCCCCCCCCCcchhhHHHHHHHHHHHhc
Q 041647 71 SLSHIMDAS-MEDLARCPGIVERKVKCLYDTFH-EPFKPVVSRHPPIPETPSLKDVEPSSVNESALSAAFANYADKMG 146 (216)
Q Consensus 71 SL~~Im~AS-~EdLA~cPGig~~Kvk~L~d~fh-ePF~~~~sr~~~~p~t~~~k~~epssv~esalsaAfa~~a~~~~ 146 (216)
++.++.+.+ ...|.+.= ......||+..+ ....++...+++ +.-.....-+....+...+..++..++++..
T Consensus 196 ti~dl~~~~~~~~l~~~f---g~~~~~l~~~a~G~d~~~v~~~~~~-ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~ 269 (343)
T cd00424 196 PIGDLLAASPDALLALWG---GVSGERLWYALRGIDDEPLSPPRPR-KSFSHERVLPRDSRNAEDARPLLRLLLEKLA 269 (343)
T ss_pred cHHHHhcCCHHHHHHHHh---hHHHHHHHHHhCCcCCCCCCCCCCC-CceeeeEECCCCCCCHHHHHHHHHHHHHHHH
Confidence 566666666 45555432 245677777766 222222222211 1111112223333344556666666665554
No 188
>PF02540 NAD_synthase: NAD synthase; InterPro: IPR022310 NAD+ synthase (6.3.5.1 from EC) catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide and is induced by stress factors such as heat shock and glucose limitation. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP shows that the enzyme consists of a tight homodimer with alpha/beta subunit topology []. Catalyzes the synthesis of GMP from XMP. The protein is a homodimer, but in the archaea it is a heterodimer composed of a glutamine amidotransferase subunit (A) and a GMP-binding subunit (B). This entry contains the GMP-binding subunit (B). ; PDB: 2VXO_A 3UOW_B 3N05_A 2DPL_B 3A4I_A 3SEQ_D 3SZG_A 3SYT_A 3SDB_A 3SEZ_C ....
Probab=20.38 E-value=1.9e+02 Score=24.70 Aligned_cols=78 Identities=24% Similarity=0.294 Sum_probs=43.7
Q ss_pred ccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhh---hhhhccccchhcHHHHHh-----C
Q 041647 7 LTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQN---NLLFKTQSAPVSLSHIMD-----A 78 (216)
Q Consensus 7 LTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~n---n~~~~~~s~~~SL~~Im~-----A 78 (216)
+.=+.++.||+|..|....| =|+.+....- +|.-+.-|. -+-| +- --|..++. .
T Consensus 148 ~~Pi~~L~K~eV~~la~~l~---ip~~ii~k~P-----------sa~L~~gqtDE~elg~-~Y---~~lD~~l~~~~~~~ 209 (242)
T PF02540_consen 148 IAPIADLYKTEVRELARYLG---IPEEIIEKPP-----------SAGLWPGQTDEDELGF-SY---EELDAILRLIEEGL 209 (242)
T ss_dssp BETTTTS-HHHHHHHHHHTT---CGHHHHCS-------------BHHSSTT-BHHHHHTS-TH---HHHHHHHHHHTSST
T ss_pred ceeeCCcCHHHHHHHHHHHh---hHHHHhcCCC-----------CCCCCCCCCCHHHhCC-CH---HHHHHHHHHHHcCC
Confidence 34467899999999999999 3444332221 221111111 1100 00 12344443 5
Q ss_pred CHhhhccCCCCcHHHHHHHHHHhc
Q 041647 79 SMEDLARCPGIVERKVKCLYDTFH 102 (216)
Q Consensus 79 S~EdLA~cPGig~~Kvk~L~d~fh 102 (216)
+.++++..-|+.+..++++.....
T Consensus 210 ~~~~~~~~~~~~~~~~~~i~~~~~ 233 (242)
T PF02540_consen 210 SPEEIAEKLGVDPEVVERIERLHK 233 (242)
T ss_dssp THHHHHHTCTS-HHHHHHHHHHHH
T ss_pred CHHHHHHhcCCCHHHHHHHHHHHH
Confidence 778888888999999998887765
No 189
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=20.15 E-value=1.2e+02 Score=28.36 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=24.0
Q ss_pred cHHHHHh---CCHhhhccCCCCcHHHHHHHHHHh
Q 041647 71 SLSHIMD---ASMEDLARCPGIVERKVKCLYDTF 101 (216)
Q Consensus 71 SL~~Im~---AS~EdLA~cPGig~~Kvk~L~d~f 101 (216)
+|.+|.. .+.++|.+++|+|++|+++--+.|
T Consensus 551 ~L~~ia~~~P~~~~~l~~i~gv~~~k~~~~G~~~ 584 (591)
T TIGR01389 551 TLREMAEKRPATLNALLKIKGVGQNKLDRYGEAF 584 (591)
T ss_pred HHHHHHHHCCCCHHHHhCCCCCCHHHHHHHHHHH
Confidence 4566654 489999999999999997765544
Done!