Query 034973
Match_columns 77
No_of_seqs 97 out of 99
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 08:10:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2841 Structure-specific end 99.0 1.6E-10 3.4E-15 88.7 2.6 32 1-32 222-253 (254)
2 PF12826 HHH_2: Helix-hairpin- 98.0 6.2E-06 1.4E-10 50.0 2.5 30 1-30 30-59 (64)
3 PF00633 HHH: Helix-hairpin-he 97.8 1.3E-05 2.8E-10 43.6 2.2 23 2-24 7-29 (30)
4 PRK02515 psbU photosystem II c 97.3 0.00022 4.8E-09 50.6 3.0 30 2-33 57-86 (132)
5 PF14520 HHH_5: Helix-hairpin- 97.1 0.00032 6.9E-09 41.4 2.1 26 2-27 34-59 (60)
6 TIGR01259 comE comEA protein. 97.0 0.00089 1.9E-08 45.1 3.3 30 2-31 64-95 (120)
7 COG1555 ComEA DNA uptake prote 96.2 0.0037 8.1E-08 43.8 2.6 31 2-32 93-125 (149)
8 PF12836 HHH_3: Helix-hairpin- 96.2 0.005 1.1E-07 37.1 2.7 32 2-33 10-43 (65)
9 PRK13766 Hef nuclease; Provisi 96.2 0.0038 8.3E-08 51.0 2.6 30 2-31 743-772 (773)
10 smart00278 HhH1 Helix-hairpin- 96.0 0.0054 1.2E-07 31.5 2.0 21 6-26 1-21 (26)
11 PRK12766 50S ribosomal protein 95.7 0.015 3.3E-07 44.4 3.9 28 2-29 32-59 (232)
12 TIGR00426 competence protein C 95.6 0.017 3.6E-07 34.7 3.2 30 2-31 12-44 (69)
13 COG1948 MUS81 ERCC4-type nucle 95.0 0.016 3.5E-07 44.6 2.3 33 1-33 209-241 (254)
14 TIGR00575 dnlj DNA ligase, NAD 95.0 0.018 3.8E-07 48.4 2.5 31 2-32 526-556 (652)
15 COG5241 RAD10 Nucleotide excis 94.9 0.014 3.1E-07 44.5 1.7 30 2-31 195-224 (224)
16 PRK00116 ruvA Holliday junctio 94.8 0.022 4.7E-07 40.7 2.3 30 2-31 104-133 (192)
17 PRK13482 DNA integrity scannin 94.7 0.025 5.3E-07 45.3 2.6 30 1-30 314-343 (352)
18 PF14520 HHH_5: Helix-hairpin- 94.6 0.032 6.9E-07 32.8 2.4 22 6-27 5-27 (60)
19 smart00483 POLXc DNA polymeras 94.5 0.027 5.9E-07 43.3 2.3 22 5-27 88-109 (334)
20 PRK07956 ligA NAD-dependent DN 94.0 0.039 8.4E-07 46.5 2.5 30 2-31 539-568 (665)
21 TIGR00426 competence protein C 93.5 0.083 1.8E-06 31.6 2.6 23 4-26 45-67 (69)
22 PRK08609 hypothetical protein; 93.1 0.072 1.6E-06 43.8 2.5 23 5-27 87-109 (570)
23 PRK00254 ski2-like helicase; P 93.0 0.09 1.9E-06 43.5 2.9 28 2-29 674-701 (720)
24 PRK14666 uvrC excinuclease ABC 92.8 0.072 1.6E-06 45.9 2.1 29 2-30 665-693 (694)
25 PRK14670 uvrC excinuclease ABC 92.6 0.098 2.1E-06 43.8 2.7 28 2-29 542-569 (574)
26 PF10391 DNA_pol_lambd_f: Fing 92.6 0.13 2.8E-06 30.7 2.5 19 6-24 2-20 (52)
27 PF00570 HRDC: HRDC domain Blo 92.4 0.13 2.8E-06 30.0 2.3 24 3-26 41-64 (68)
28 PRK00558 uvrC excinuclease ABC 92.4 0.11 2.5E-06 43.2 2.8 27 2-28 571-597 (598)
29 PRK00024 hypothetical protein; 92.2 0.12 2.6E-06 38.1 2.4 28 1-28 61-88 (224)
30 cd00141 NT_POLXc Nucleotidyltr 92.2 0.11 2.4E-06 39.5 2.3 19 5-23 84-102 (307)
31 TIGR00608 radc DNA repair prot 92.1 0.13 2.8E-06 38.0 2.6 27 1-27 55-81 (218)
32 PF14635 HHH_7: Helix-hairpin- 92.0 0.12 2.6E-06 35.0 2.1 22 7-28 51-72 (104)
33 TIGR01259 comE comEA protein. 92.0 0.15 3.2E-06 34.3 2.5 24 3-26 95-118 (120)
34 PRK08097 ligB NAD-dependent DN 91.5 0.16 3.6E-06 42.5 2.8 32 1-32 515-546 (562)
35 PF03118 RNA_pol_A_CTD: Bacter 91.2 0.19 4.2E-06 30.8 2.2 27 2-28 40-66 (66)
36 smart00279 HhH2 Helix-hairpin- 91.2 0.18 3.8E-06 28.1 1.9 20 7-26 17-36 (36)
37 PRK00116 ruvA Holliday junctio 90.1 0.27 5.8E-06 35.2 2.5 23 6-28 73-95 (192)
38 PRK14351 ligA NAD-dependent DN 89.7 0.26 5.7E-06 42.0 2.5 29 2-30 556-584 (689)
39 PRK12766 50S ribosomal protein 89.3 0.24 5.1E-06 37.9 1.7 25 5-29 2-27 (232)
40 TIGR00615 recR recombination p 88.7 0.41 8.8E-06 35.6 2.6 23 5-27 10-33 (195)
41 PF12836 HHH_3: Helix-hairpin- 88.3 0.46 9.9E-06 28.5 2.2 21 3-23 41-61 (65)
42 COG0272 Lig NAD-dependent DNA 88.3 0.36 7.8E-06 41.7 2.4 33 1-33 538-570 (667)
43 PRK14350 ligA NAD-dependent DN 88.3 0.45 9.8E-06 40.5 2.9 28 3-30 538-565 (669)
44 cd00080 HhH2_motif Helix-hairp 88.0 0.38 8.2E-06 29.8 1.8 25 5-29 21-45 (75)
45 TIGR03252 uncharacterized HhH- 87.9 0.64 1.4E-05 34.1 3.2 59 5-68 114-172 (177)
46 COG1796 POL4 DNA polymerase IV 86.5 0.52 1.1E-05 37.8 2.2 23 5-27 92-114 (326)
47 PRK00076 recR recombination pr 86.4 0.51 1.1E-05 35.0 2.0 17 6-22 11-27 (196)
48 PRK14669 uvrC excinuclease ABC 85.9 0.56 1.2E-05 39.8 2.2 30 2-33 580-609 (624)
49 TIGR00084 ruvA Holliday juncti 85.8 0.71 1.5E-05 33.3 2.4 26 5-30 106-131 (191)
50 TIGR00596 rad1 DNA repair prot 85.6 0.51 1.1E-05 41.1 1.9 29 1-31 784-813 (814)
51 PRK14605 ruvA Holliday junctio 85.4 0.75 1.6E-05 33.3 2.4 27 4-30 106-132 (194)
52 PRK13901 ruvA Holliday junctio 85.3 0.76 1.6E-05 34.0 2.4 28 4-31 105-132 (196)
53 PRK14667 uvrC excinuclease ABC 84.9 0.79 1.7E-05 38.4 2.7 25 2-27 542-566 (567)
54 COG2003 RadC DNA repair protei 84.9 0.85 1.9E-05 34.7 2.6 26 2-27 62-87 (224)
55 COG0353 RecR Recombinational D 84.3 0.66 1.4E-05 35.0 1.8 18 5-22 11-28 (198)
56 PRK13844 recombination protein 84.3 0.72 1.6E-05 34.4 2.0 17 6-22 15-31 (200)
57 PRK14601 ruvA Holliday junctio 84.2 0.93 2E-05 32.9 2.4 26 5-30 107-132 (183)
58 smart00341 HRDC Helicase and R 84.2 1.4 3.1E-05 26.0 2.9 24 3-26 44-67 (81)
59 PRK14602 ruvA Holliday junctio 83.7 0.95 2.1E-05 33.0 2.3 29 3-31 106-134 (203)
60 TIGR00084 ruvA Holliday juncti 83.6 0.9 2E-05 32.8 2.2 23 6-28 72-94 (191)
61 TIGR01954 nusA_Cterm_rpt trans 83.4 1.7 3.7E-05 23.9 2.8 27 2-28 22-48 (50)
62 PRK14603 ruvA Holliday junctio 83.0 1.2 2.5E-05 32.5 2.6 27 4-30 105-131 (197)
63 PF14716 HHH_8: Helix-hairpin- 82.9 1.6 3.5E-05 26.3 2.8 23 4-26 44-67 (68)
64 PRK14606 ruvA Holliday junctio 82.2 1.2 2.7E-05 32.2 2.4 27 4-30 106-132 (188)
65 PRK14668 uvrC excinuclease ABC 81.8 1.1 2.3E-05 37.6 2.2 25 6-30 525-549 (577)
66 COG4277 Predicted DNA-binding 80.7 1.4 3E-05 36.2 2.5 24 2-25 326-349 (404)
67 PRK14668 uvrC excinuclease ABC 80.6 1.5 3.2E-05 36.8 2.6 25 2-26 553-577 (577)
68 PRK09482 flap endonuclease-lik 79.1 1.3 2.7E-05 33.8 1.7 25 4-28 180-204 (256)
69 cd00008 53EXOc 5'-3' exonuclea 78.6 1.4 3E-05 32.3 1.7 23 5-27 182-204 (240)
70 PRK07956 ligA NAD-dependent DN 78.0 1.8 3.8E-05 36.8 2.4 26 3-28 476-501 (665)
71 PRK14976 5'-3' exonuclease; Pr 77.2 1.5 3.2E-05 33.3 1.5 21 5-25 190-210 (281)
72 PRK14604 ruvA Holliday junctio 77.1 2.5 5.5E-05 30.8 2.7 28 4-31 106-133 (195)
73 PRK10702 endonuclease III; Pro 76.4 2.6 5.7E-05 30.8 2.6 27 3-29 106-133 (211)
74 PRK10736 hypothetical protein; 76.2 2.1 4.6E-05 34.3 2.3 24 7-30 9-32 (374)
75 smart00475 53EXOc 5'-3' exonuc 76.2 1.8 3.8E-05 32.5 1.7 23 5-27 185-207 (259)
76 PRK14350 ligA NAD-dependent DN 76.0 2.2 4.8E-05 36.5 2.4 25 4-28 468-492 (669)
77 PRK08097 ligB NAD-dependent DN 75.4 2.4 5.2E-05 35.7 2.5 25 4-28 457-481 (562)
78 TIGR00575 dnlj DNA ligase, NAD 75.4 2.3 5.1E-05 36.0 2.4 26 3-28 463-488 (652)
79 PRK10880 adenine DNA glycosyla 74.8 2.9 6.4E-05 33.0 2.7 29 3-31 106-135 (350)
80 PRK02515 psbU photosystem II c 74.2 3.3 7.2E-05 29.5 2.6 22 3-24 84-105 (132)
81 PRK14600 ruvA Holliday junctio 73.7 2.7 5.9E-05 30.5 2.1 26 4-30 106-131 (186)
82 PRK14672 uvrC excinuclease ABC 72.7 3.3 7.2E-05 36.0 2.7 26 2-27 636-661 (691)
83 COG1623 Predicted nucleic-acid 72.5 2.3 5E-05 34.5 1.7 27 1-27 320-346 (349)
84 PRK14605 ruvA Holliday junctio 72.3 3.5 7.6E-05 29.8 2.4 25 6-30 73-97 (194)
85 PRK14669 uvrC excinuclease ABC 71.8 3.4 7.3E-05 35.2 2.5 24 5-28 551-574 (624)
86 PF11798 IMS_HHH: IMS family H 71.7 3.5 7.5E-05 22.1 1.8 18 7-24 12-29 (32)
87 COG0177 Nth Predicted EndoIII- 70.9 3.9 8.5E-05 30.6 2.5 29 3-31 106-135 (211)
88 PRK00254 ski2-like helicase; P 70.6 2.8 6.2E-05 34.8 1.8 26 7-32 646-672 (720)
89 PRK14351 ligA NAD-dependent DN 70.4 3.3 7.2E-05 35.5 2.2 26 3-28 493-518 (689)
90 COG1555 ComEA DNA uptake prote 70.3 4.3 9.4E-05 28.4 2.4 24 3-26 124-147 (149)
91 PF12482 DUF3701: Phage integr 69.7 3.6 7.8E-05 27.6 1.8 19 9-27 53-71 (96)
92 TIGR00194 uvrC excinuclease AB 68.7 4.4 9.6E-05 34.0 2.6 23 6-28 541-563 (574)
93 PRK07758 hypothetical protein; 68.5 5 0.00011 27.2 2.3 26 3-28 64-89 (95)
94 PRK14666 uvrC excinuclease ABC 67.7 4 8.7E-05 35.5 2.2 24 5-28 636-659 (694)
95 PRK00558 uvrC excinuclease ABC 67.6 4 8.7E-05 34.2 2.1 24 5-28 542-565 (598)
96 COG0632 RuvA Holliday junction 67.4 4.9 0.00011 29.8 2.3 29 4-32 106-134 (201)
97 PRK13910 DNA glycosylase MutY; 66.7 6.4 0.00014 30.4 2.9 28 3-30 69-97 (289)
98 PRK14670 uvrC excinuclease ABC 66.4 4.3 9.3E-05 34.2 2.1 23 6-28 514-536 (574)
99 PRK13766 Hef nuclease; Provisi 66.3 4.7 0.0001 33.3 2.2 22 8-29 717-738 (773)
100 KOG1921 Endonuclease III [Repl 65.1 4.1 9E-05 32.4 1.6 19 2-20 155-173 (286)
101 TIGR01084 mutY A/G-specific ad 64.5 6.6 0.00014 29.9 2.6 28 3-30 102-130 (275)
102 PRK13913 3-methyladenine DNA g 63.8 7.1 0.00015 29.1 2.6 27 4-30 119-146 (218)
103 cd00056 ENDO3c endonuclease II 60.9 9.4 0.0002 25.2 2.6 22 3-24 80-101 (158)
104 PRK14667 uvrC excinuclease ABC 60.1 6.6 0.00014 33.0 2.1 23 6-28 514-536 (567)
105 cd00128 XPG Xeroderma pigmento 60.0 7 0.00015 29.2 2.0 20 9-28 226-245 (316)
106 PF02371 Transposase_20: Trans 60.0 13 0.00028 23.1 3.0 26 6-31 2-27 (87)
107 TIGR01448 recD_rel helicase, p 59.7 6.6 0.00014 33.3 2.0 25 10-34 88-112 (720)
108 cd00141 NT_POLXc Nucleotidyltr 59.6 9.6 0.00021 29.0 2.7 26 3-28 42-67 (307)
109 PRK02362 ski2-like helicase; P 59.4 7.1 0.00015 32.6 2.1 20 6-25 652-671 (737)
110 PRK10308 3-methyl-adenine DNA 59.2 9.3 0.0002 29.0 2.6 25 2-27 163-187 (283)
111 COG1491 Predicted RNA-binding 59.0 6.6 0.00014 29.9 1.7 30 2-31 126-156 (202)
112 PF00730 HhH-GPD: HhH-GPD supe 58.1 6.9 0.00015 24.3 1.5 28 3-30 36-66 (108)
113 PRK14672 uvrC excinuclease ABC 57.9 7.5 0.00016 34.0 2.1 24 6-29 608-631 (691)
114 COG0272 Lig NAD-dependent DNA 57.2 7.9 0.00017 33.7 2.1 26 3-28 476-501 (667)
115 PRK01229 N-glycosylase/DNA lya 56.8 11 0.00024 28.0 2.6 27 4-30 116-144 (208)
116 smart00478 ENDO3c endonuclease 56.4 12 0.00025 24.6 2.4 27 4-30 70-97 (149)
117 TIGR01083 nth endonuclease III 55.8 10 0.00022 26.7 2.1 27 4-30 104-131 (191)
118 PRK05755 DNA polymerase I; Pro 55.3 7.6 0.00016 33.5 1.7 21 5-25 186-206 (880)
119 PRK14671 uvrC excinuclease ABC 54.2 10 0.00022 32.1 2.2 24 6-29 569-592 (621)
120 TIGR02236 recomb_radA DNA repa 53.6 9.1 0.0002 28.2 1.7 20 8-27 1-21 (310)
121 PF11731 Cdd1: Pathogenicity l 53.1 10 0.00022 25.4 1.7 21 4-24 10-30 (93)
122 COG1948 MUS81 ERCC4-type nucle 52.9 12 0.00026 29.0 2.3 22 8-29 184-205 (254)
123 COG0258 Exo 5'-3' exonuclease 51.8 9.6 0.00021 28.7 1.6 22 5-26 197-218 (310)
124 KOG2534 DNA polymerase IV (fam 51.0 15 0.00032 30.1 2.6 30 4-33 54-83 (353)
125 TIGR00593 pola DNA polymerase 50.7 9.5 0.00021 33.6 1.6 20 5-24 184-203 (887)
126 PF01367 5_3_exonuc: 5'-3' exo 50.1 1.4 3E-05 29.4 -2.8 25 4-28 16-40 (101)
127 PF13821 DUF4187: Domain of un 50.1 11 0.00023 22.7 1.3 13 3-15 38-51 (55)
128 TIGR01448 recD_rel helicase, p 49.4 11 0.00024 32.0 1.8 25 4-28 115-139 (720)
129 PRK11057 ATP-dependent DNA hel 49.2 18 0.00039 29.8 2.9 24 3-26 572-595 (607)
130 PF04919 DUF655: Protein of un 49.1 14 0.00029 27.6 2.0 27 5-31 115-142 (181)
131 PRK03980 flap endonuclease-1; 48.7 14 0.0003 28.4 2.0 18 10-27 193-210 (292)
132 PF00416 Ribosomal_S13: Riboso 48.4 18 0.00039 23.7 2.3 23 7-29 16-38 (107)
133 PRK14671 uvrC excinuclease ABC 47.9 12 0.00026 31.7 1.8 24 2-27 597-620 (621)
134 smart00483 POLXc DNA polymeras 47.6 20 0.00044 27.7 2.8 27 3-29 45-71 (334)
135 PRK04301 radA DNA repair and r 46.3 19 0.0004 26.9 2.4 27 2-28 35-61 (317)
136 TIGR03674 fen_arch flap struct 45.3 17 0.00036 28.2 2.1 17 9-25 239-255 (338)
137 PRK01172 ski2-like helicase; P 45.3 14 0.0003 30.4 1.7 24 2-25 641-664 (674)
138 PTZ00217 flap endonuclease-1; 43.2 18 0.0004 28.8 2.1 18 9-26 238-255 (393)
139 PRK14602 ruvA Holliday junctio 43.2 22 0.00047 25.9 2.3 23 7-29 75-97 (203)
140 TIGR02236 recomb_radA DNA repa 42.4 25 0.00054 25.9 2.5 26 2-27 28-53 (310)
141 PF14229 DUF4332: Domain of un 41.7 24 0.00053 23.6 2.2 20 5-24 52-71 (122)
142 PRK05182 DNA-directed RNA poly 40.8 24 0.00051 27.4 2.3 27 2-28 277-303 (310)
143 PHA00439 exonuclease 40.5 16 0.00034 28.6 1.3 21 4-25 186-206 (286)
144 TIGR02027 rpoA DNA-directed RN 39.5 25 0.00054 27.1 2.2 27 2-28 263-289 (297)
145 PRK14604 ruvA Holliday junctio 39.4 22 0.00048 25.9 1.8 20 7-26 74-93 (195)
146 TIGR01389 recQ ATP-dependent D 39.2 32 0.0007 27.8 2.9 24 3-26 561-584 (591)
147 PF05559 DUF763: Protein of un 39.2 25 0.00055 28.2 2.2 22 4-25 267-288 (319)
148 COG1415 Uncharacterized conser 38.6 26 0.00057 28.9 2.3 22 4-25 276-297 (373)
149 COG1194 MutY A/G-specific DNA 37.5 35 0.00076 27.6 2.8 27 4-30 111-138 (342)
150 PRK14600 ruvA Holliday junctio 37.3 26 0.00056 25.4 1.9 21 7-27 74-94 (186)
151 PF09035 Tn916-Xis: Excisionas 37.1 23 0.0005 22.3 1.4 28 4-31 15-43 (67)
152 KOG1856 Transcription elongati 37.0 16 0.00036 34.2 1.0 22 7-28 807-828 (1299)
153 COG0322 UvrC Nuclease subunit 36.9 25 0.00055 29.9 2.0 22 7-28 531-552 (581)
154 TIGR00588 ogg 8-oxoguanine DNA 36.0 32 0.0007 26.4 2.3 25 5-29 219-244 (310)
155 PF04994 TfoX_C: TfoX C-termin 35.8 31 0.00067 21.8 1.9 20 6-25 3-22 (81)
156 TIGR00596 rad1 DNA repair prot 35.6 28 0.00061 30.7 2.1 22 6-27 757-778 (814)
157 PRK14603 ruvA Holliday junctio 35.4 28 0.00061 25.3 1.9 20 7-26 73-92 (197)
158 PRK12278 50S ribosomal protein 34.9 25 0.00055 26.5 1.6 29 4-32 156-184 (221)
159 PRK04301 radA DNA repair and r 34.9 29 0.00062 26.0 1.8 22 4-25 4-25 (317)
160 PRK13913 3-methyladenine DNA g 34.7 31 0.00068 25.7 2.0 26 2-27 74-102 (218)
161 PRK13901 ruvA Holliday junctio 34.2 31 0.00068 25.5 1.9 21 6-26 72-92 (196)
162 PRK10702 endonuclease III; Pro 33.9 33 0.00071 25.1 2.0 27 2-28 66-95 (211)
163 PRK01172 ski2-like helicase; P 33.3 31 0.00068 28.4 2.0 19 7-25 613-631 (674)
164 PRK14601 ruvA Holliday junctio 33.2 33 0.00071 24.9 1.9 22 6-27 73-94 (183)
165 PF14579 HHH_6: Helix-hairpin- 32.6 57 0.0012 20.3 2.7 25 8-32 29-54 (90)
166 PF02828 L27: L27 domain; Int 31.9 28 0.00061 20.1 1.1 29 5-33 9-37 (56)
167 COG3743 Uncharacterized conser 28.5 34 0.00075 24.5 1.3 19 6-24 67-85 (133)
168 PF02961 BAF: Barrier to autoi 28.1 49 0.0011 22.3 1.9 17 7-23 20-36 (89)
169 PF11372 DUF3173: Domain of un 27.3 65 0.0014 20.0 2.3 21 3-24 4-24 (59)
170 TIGR02238 recomb_DMC1 meiotic 26.9 54 0.0012 25.2 2.2 28 2-29 30-57 (313)
171 COG1031 Uncharacterized Fe-S o 25.4 54 0.0012 28.4 2.1 30 2-33 512-541 (560)
172 PHA02088 hypothetical protein 25.3 59 0.0013 23.1 2.0 22 6-27 71-92 (125)
173 PTZ00035 Rad51 protein; Provis 24.2 60 0.0013 25.1 2.0 27 2-28 52-78 (337)
174 PRK08609 hypothetical protein; 24.2 58 0.0013 27.1 2.0 25 4-28 46-70 (570)
175 COG2390 DeoR Transcriptional r 23.7 49 0.0011 26.0 1.5 32 2-33 269-305 (321)
176 PRK12311 rpsB 30S ribosomal pr 22.5 54 0.0012 26.0 1.5 23 4-26 261-283 (326)
177 smart00511 ORANGE Orange domai 22.0 79 0.0017 17.4 1.8 23 8-30 18-40 (45)
178 PLN03137 ATP-dependent DNA hel 21.7 87 0.0019 29.3 2.8 24 3-26 1070-1093(1195)
No 1
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=99.01 E-value=1.6e-10 Score=88.69 Aligned_cols=32 Identities=38% Similarity=0.613 Sum_probs=30.5
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhcccccc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHEPFKR 32 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF~k 32 (77)
++||+++|+.|||+||.||++||++||+||.+
T Consensus 222 ~~AS~~ele~~~G~G~~kak~l~~~l~~pf~~ 253 (254)
T KOG2841|consen 222 SNASEGELEQCPGLGPAKAKRLHKFLHQPFLS 253 (254)
T ss_pred HhcCHhHHHhCcCcCHHHHHHHHHHHhccccC
Confidence 47999999999999999999999999999975
No 2
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.96 E-value=6.2e-06 Score=50.04 Aligned_cols=30 Identities=37% Similarity=0.732 Sum_probs=23.2
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
++||.|+|+.+||||++.|+.+++.|++|=
T Consensus 30 ~~a~~e~L~~i~gIG~~~A~si~~ff~~~~ 59 (64)
T PF12826_consen 30 MNASVEELSAIPGIGPKIAQSIYEFFQDPE 59 (64)
T ss_dssp CC--HHHHCTSTT--HHHHHHHHHHHH-HH
T ss_pred HHcCHHHHhccCCcCHHHHHHHHHHHCCHH
Confidence 579999999999999999999999999874
No 3
>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=97.83 E-value=1.3e-05 Score=43.59 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=20.3
Q ss_pred CCChhHHhcCCCchHHHHHHHHH
Q 034973 2 DASMEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~ 24 (77)
.||.|||..+||+|+..|..+++
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHh
Confidence 58999999999999999999875
No 4
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=97.29 E-value=0.00022 Score=50.57 Aligned_cols=30 Identities=17% Similarity=0.397 Sum_probs=27.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
+|+.++|..+|||||++|++|.+ |-||...
T Consensus 57 ~A~~~el~~lpGigP~~A~~IV~--nGpf~sv 86 (132)
T PRK02515 57 NSSVRAFRQFPGMYPTLAGKIVK--NAPYDSV 86 (132)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHH--CCCCCCH
Confidence 58999999999999999999995 9999776
No 5
>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=97.14 E-value=0.00032 Score=41.45 Aligned_cols=26 Identities=31% Similarity=0.475 Sum_probs=22.8
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
+|+.++|..+||||+++|.+|.+.++
T Consensus 34 ~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 34 NADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp TSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 57789999999999999999998775
No 6
>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=96.97 E-value=0.00089 Score=45.07 Aligned_cols=30 Identities=37% Similarity=0.521 Sum_probs=26.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc--cccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH--EPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh--ePF~ 31 (77)
.||.++|..+||+|+.+|++|++-+. -||.
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~ 95 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREENGAFK 95 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHhcCCcC
Confidence 58999999999999999999999884 4664
No 7
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=96.25 E-value=0.0037 Score=43.76 Aligned_cols=31 Identities=39% Similarity=0.593 Sum_probs=25.1
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHh--cccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTF--HEPFKR 32 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~af--hePF~k 32 (77)
.||.|||..+||+|+.||+.|.+-- +=||..
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~s 125 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREENGPFKS 125 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCc
Confidence 5899999999999999999995533 346754
No 8
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=96.21 E-value=0.005 Score=37.07 Aligned_cols=32 Identities=34% Similarity=0.586 Sum_probs=21.9
Q ss_pred CCChhHHhcCCCchHHHHHHHHH--Hhccccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYD--TFHEPFKRV 33 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~--afhePF~k~ 33 (77)
.||.++|..+||||+..|++|.+ ..+-||...
T Consensus 10 ~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~ 43 (65)
T PF12836_consen 10 TASAEELQALPGIGPKQAKAIVEYREKNGPFKSL 43 (65)
T ss_dssp TS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSG
T ss_pred cCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCH
Confidence 58999999999999999999954 445677544
No 9
>PRK13766 Hef nuclease; Provisional
Probab=96.16 E-value=0.0038 Score=51.01 Aligned_cols=30 Identities=30% Similarity=0.415 Sum_probs=27.9
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
.|+.++|..|||+|+++|++|++.|+.||.
T Consensus 743 ~as~~~L~~i~Gig~~~a~~i~~~~~~~~~ 772 (773)
T PRK13766 743 TASEEELMEVEGIGEKTAKRIREVVTSEYK 772 (773)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHHHhhhhc
Confidence 588999999999999999999999999985
No 10
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=96.05 E-value=0.0054 Score=31.52 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=18.2
Q ss_pred hHHhcCCCchHHHHHHHHHHh
Q 034973 6 EDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~af 26 (77)
++|..+||||++.|.+|++..
T Consensus 1 ~~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 1 EELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred ChhhhCCCCCHHHHHHHHHhc
Confidence 478999999999999999743
No 11
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=95.69 E-value=0.015 Score=44.39 Aligned_cols=28 Identities=18% Similarity=0.102 Sum_probs=25.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afheP 29 (77)
.||.++|..+||||..+|.+|++.|+.+
T Consensus 32 ~AS~eEL~~V~GIg~k~AekI~e~l~~~ 59 (232)
T PRK12766 32 AADQSELAEVDGIGNALAARIKADVGGL 59 (232)
T ss_pred hCCHHHHHHccCCCHHHHHHHHHHhccc
Confidence 5899999999999999999999999843
No 12
>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=95.60 E-value=0.017 Score=34.67 Aligned_cols=30 Identities=27% Similarity=0.376 Sum_probs=25.0
Q ss_pred CCChhHHhc-CCCchHHHHHHHHHHh--ccccc
Q 034973 2 DASMEDLAG-CPGIVERKVKCLYDTF--HEPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~-CPG~G~~KarrL~~af--hePF~ 31 (77)
.|+.++|.. .||||+..|++|.+.. +.+|.
T Consensus 12 ta~~~~L~~~ipgig~~~a~~Il~~R~~~g~~~ 44 (69)
T TIGR00426 12 TATAEELQRAMNGVGLKKAEAIVSYREEYGPFK 44 (69)
T ss_pred CCCHHHHHhHCCCCCHHHHHHHHHHHHHcCCcC
Confidence 478999999 9999999999998876 33554
No 13
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=95.04 E-value=0.016 Score=44.57 Aligned_cols=33 Identities=30% Similarity=0.498 Sum_probs=30.4
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
++||.++|....|+|+.||++|+..|.+||...
T Consensus 209 ~tas~~eL~~v~gig~k~A~~I~~~~~t~~~~~ 241 (254)
T COG1948 209 LTASEEELMKVKGIGEKKAREIYRFLRTEYKLI 241 (254)
T ss_pred hhcCHHHHHHhcCccHHHHHHHHHHHhchhhhh
Confidence 479999999999999999999999999999743
No 14
>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=94.98 E-value=0.018 Score=48.38 Aligned_cols=31 Identities=29% Similarity=0.558 Sum_probs=28.8
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFKR 32 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~k 32 (77)
.||.++|..+||||++.|..|++.|+.|+..
T Consensus 526 ~As~eeL~~i~GIG~~~A~~I~~ff~~~~~~ 556 (652)
T TIGR00575 526 AASLEELLSVEGVGPKVAESIVNFFHDPNNR 556 (652)
T ss_pred hCCHHHHhcCCCcCHHHHHHHHHHHhhhhHH
Confidence 5899999999999999999999999999844
No 15
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=94.93 E-value=0.014 Score=44.54 Aligned_cols=30 Identities=20% Similarity=0.188 Sum_probs=28.2
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
.||.+++.++-|||+.||.++.+.++.||.
T Consensus 195 gaSrdE~e~l~g~g~~ka~~~ieyln~pFm 224 (224)
T COG5241 195 GASRDEFELLLGFGFEKAAKYIEYLNLPFM 224 (224)
T ss_pred ccchhHHHHHHccCHHHHHHHHHHhcccCC
Confidence 489999999999999999999999999994
No 16
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.83 E-value=0.022 Score=40.73 Aligned_cols=30 Identities=13% Similarity=0.347 Sum_probs=26.8
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
.++.++|..+||||+++|.+|+..|+.-+.
T Consensus 104 ~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 104 NGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 467889999999999999999999987664
No 17
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=94.74 E-value=0.025 Score=45.29 Aligned_cols=30 Identities=27% Similarity=0.395 Sum_probs=26.3
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
++||.++|..++|+|+.+|+.+.+.+..-.
T Consensus 314 l~As~eeL~~VeGIGe~rA~~I~e~l~Rl~ 343 (352)
T PRK13482 314 LAASIEDLDEVEGIGEVRARAIREGLSRLA 343 (352)
T ss_pred HcCCHHHHhhCCCcCHHHHHHHHHHHHHHH
Confidence 479999999999999999999988876543
No 18
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=94.65 E-value=0.032 Score=32.81 Aligned_cols=22 Identities=32% Similarity=0.675 Sum_probs=19.9
Q ss_pred hHHhcCCCchHHHHHHHHHH-hc
Q 034973 6 EDLAGCPGIVERKVKCLYDT-FH 27 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~a-fh 27 (77)
++|...||+|++.|++|++. |.
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~G~~ 27 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEAGIK 27 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHTTCS
T ss_pred HhhccCCCCCHHHHHHHHhcCCC
Confidence 68999999999999999998 54
No 19
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=94.49 E-value=0.027 Score=43.29 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=19.1
Q ss_pred hhHHhcCCCchHHHHHHHHHHhc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.-+|..|||+||+||++||+ +.
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 35789999999999999998 54
No 20
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.03 E-value=0.039 Score=46.53 Aligned_cols=30 Identities=27% Similarity=0.289 Sum_probs=27.9
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
.||.++|..+||||++.|..|++.|+.|..
T Consensus 539 ~As~eeL~~i~GIG~~~A~sI~~ff~~~~~ 568 (665)
T PRK07956 539 AASEEELAAVEGVGEVVAQSIVEFFAVEEN 568 (665)
T ss_pred hCCHHHHhccCCcCHHHHHHHHHHHhhhhH
Confidence 589999999999999999999999998873
No 21
>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=93.49 E-value=0.083 Score=31.62 Aligned_cols=23 Identities=30% Similarity=0.393 Sum_probs=20.8
Q ss_pred ChhHHhcCCCchHHHHHHHHHHh
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~af 26 (77)
+.++|..+||||.+++.+|++.+
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhhc
Confidence 67999999999999999998764
No 22
>PRK08609 hypothetical protein; Provisional
Probab=93.07 E-value=0.072 Score=43.79 Aligned_cols=23 Identities=26% Similarity=0.450 Sum_probs=20.0
Q ss_pred hhHHhcCCCchHHHHHHHHHHhc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.-+|..|||+||++|++||+.+.
T Consensus 87 ~~~l~~i~GiGpk~a~~l~~~lG 109 (570)
T PRK08609 87 LLPLLKLPGLGGKKIAKLYKELG 109 (570)
T ss_pred HHHHhcCCCCCHHHHHHHHHHhC
Confidence 45789999999999999998664
No 23
>PRK00254 ski2-like helicase; Provisional
Probab=93.01 E-value=0.09 Score=43.48 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=25.7
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afheP 29 (77)
.|+.++|..|||||++.|+.+++.++..
T Consensus 674 ~a~~~el~~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 674 NAKPSELLKVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred hCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence 6889999999999999999999999955
No 24
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=92.76 E-value=0.072 Score=45.87 Aligned_cols=29 Identities=31% Similarity=0.452 Sum_probs=24.9
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
.||.|+|+.+||||+++|+.|++.|+.-|
T Consensus 665 ~AS~eELa~V~Gig~k~Ae~I~~~L~~~~ 693 (694)
T PRK14666 665 AAGEEGLAAVPGIGPARAAALHEHLKTLF 693 (694)
T ss_pred hcCHHHHHhcCCcCHHHHHHHHHHHHHhh
Confidence 57888899999999999999999888766
No 25
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=92.59 E-value=0.098 Score=43.77 Aligned_cols=28 Identities=11% Similarity=-0.043 Sum_probs=25.6
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afheP 29 (77)
.||.|||+.+|||+.+.|+.|++.||.-
T Consensus 542 ~As~eeL~~v~gi~~~~A~~I~~~l~~~ 569 (574)
T PRK14670 542 LLNEDEIAEKMKINIKMAKKIKKFAEKQ 569 (574)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence 5999999999999999999999999753
No 26
>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=92.59 E-value=0.13 Score=30.75 Aligned_cols=19 Identities=16% Similarity=0.279 Sum_probs=15.3
Q ss_pred hHHhcCCCchHHHHHHHHH
Q 034973 6 EDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~ 24 (77)
..|..|.|+|+++|++||+
T Consensus 2 ~~f~~I~GVG~~tA~~w~~ 20 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYA 20 (52)
T ss_dssp HHHHTSTT--HHHHHHHHH
T ss_pred cchhhcccccHHHHHHHHH
Confidence 5688999999999999987
No 27
>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=92.44 E-value=0.13 Score=29.97 Aligned_cols=24 Identities=38% Similarity=0.552 Sum_probs=20.4
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
.|.++|..|+|||+.++++.-+.|
T Consensus 41 ~s~~~L~~i~g~~~~~~~~~g~~i 64 (68)
T PF00570_consen 41 TSIEELLQIPGMGKRKVRKYGDEI 64 (68)
T ss_dssp SSHHHHHTSTTCGHHHHHHCHHHH
T ss_pred CCHHHHHHccCCCHHHHHHHHHHH
Confidence 578999999999999999765554
No 28
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=92.43 E-value=0.11 Score=43.15 Aligned_cols=27 Identities=37% Similarity=0.795 Sum_probs=24.0
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.||.++|..+||||++.|..|++.||.
T Consensus 571 ~As~eeL~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 571 EASVEELAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred hCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence 588999999999999999999998875
No 29
>PRK00024 hypothetical protein; Reviewed
Probab=92.23 E-value=0.12 Score=38.09 Aligned_cols=28 Identities=32% Similarity=0.385 Sum_probs=24.4
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
++||.++|..++|+|+.||..|..++.-
T Consensus 61 ~~as~~eL~~i~GIG~akA~~L~a~~El 88 (224)
T PRK00024 61 LDASLEELQSIKGIGPAKAAQLKAALEL 88 (224)
T ss_pred HhCCHHHHhhccCccHHHHHHHHHHHHH
Confidence 3689999999999999999999777654
No 30
>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=92.22 E-value=0.11 Score=39.51 Aligned_cols=19 Identities=26% Similarity=0.455 Sum_probs=17.0
Q ss_pred hhHHhcCCCchHHHHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCLY 23 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~ 23 (77)
.-+|..|||+||++|++||
T Consensus 84 l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 84 LLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred HHHHHcCCCCCHHHHHHHH
Confidence 3478899999999999999
No 31
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.12 E-value=0.13 Score=38.00 Aligned_cols=27 Identities=33% Similarity=0.432 Sum_probs=23.6
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
+.|+.++|...+|+|+.||..|..++.
T Consensus 55 ~~a~~~eL~~i~GiG~aka~~l~a~~E 81 (218)
T TIGR00608 55 LSAPPEELSSVPGIGEAKAIQLKAAVE 81 (218)
T ss_pred HhCCHHHHHhCcCCcHHHHHHHHHHHH
Confidence 368999999999999999999977754
No 32
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=92.01 E-value=0.12 Score=35.02 Aligned_cols=22 Identities=23% Similarity=0.252 Sum_probs=17.6
Q ss_pred HHhcCCCchHHHHHHHHHHhcc
Q 034973 7 DLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afhe 28 (77)
-|.-.+||||+||..|.+.+.+
T Consensus 51 ~LqfV~GLGPRKA~~Ll~~l~~ 72 (104)
T PF14635_consen 51 LLQFVCGLGPRKAQALLKALKQ 72 (104)
T ss_dssp GGGGSTT--HHHHHHHHHHHHH
T ss_pred hHhHhcCCChHHHHHHHHHHHH
Confidence 4777899999999999999985
No 33
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=91.97 E-value=0.15 Score=34.34 Aligned_cols=24 Identities=33% Similarity=0.432 Sum_probs=21.5
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
+|.|||..+||||++++.+|.+.+
T Consensus 95 ~s~eeL~~V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 95 KSVDDLTKVSGIGEKSLEKLKDYA 118 (120)
T ss_pred CCHHHHHcCCCCCHHHHHHHHhce
Confidence 688999999999999999997754
No 34
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=91.52 E-value=0.16 Score=42.53 Aligned_cols=32 Identities=22% Similarity=0.333 Sum_probs=28.5
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhcccccc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHEPFKR 32 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF~k 32 (77)
+.|+.|+|...+|||++.|..|++.|+.|...
T Consensus 515 ~~a~~e~l~~i~gIG~~~a~si~~~f~~~~~~ 546 (562)
T PRK08097 515 LSRSEQQWQQLPGIGEGRARQLIAFLQHPEVK 546 (562)
T ss_pred HcCCHHHHhcCCCchHHHHHHHHHHHcCHHHH
Confidence 36899999999999999999999999987643
No 35
>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=91.18 E-value=0.19 Score=30.85 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=22.9
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
..|.++|..+||||.+-+..+.+++++
T Consensus 40 ~~s~~~L~~i~n~G~ksl~EI~~~L~e 66 (66)
T PF03118_consen 40 KYSEEDLLKIKNFGKKSLEEIKEKLKE 66 (66)
T ss_dssp CS-HHHHHTSTTSHHHHHHHHHHHHHH
T ss_pred hCCHHHHHhCCCCCHhHHHHHHHHHcC
Confidence 457899999999999999999988764
No 36
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=91.17 E-value=0.18 Score=28.13 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=16.2
Q ss_pred HHhcCCCchHHHHHHHHHHh
Q 034973 7 DLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~af 26 (77)
.+.-+||+|+++|.+|.+-|
T Consensus 17 ni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 17 NIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CCCCCCcccHHHHHHHHHhC
Confidence 34579999999999998643
No 37
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=90.14 E-value=0.27 Score=35.17 Aligned_cols=23 Identities=9% Similarity=0.131 Sum_probs=20.8
Q ss_pred hHHhcCCCchHHHHHHHHHHhcc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhe 28 (77)
..|...||+||+.|.+|.+.|..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCCH
Confidence 47889999999999999999884
No 38
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=89.65 E-value=0.26 Score=42.01 Aligned_cols=29 Identities=17% Similarity=0.155 Sum_probs=27.5
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
.||.++|..++|||++.|..|++.|+.|-
T Consensus 556 ~As~eeL~~i~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 556 DADEEALRAVDDVGPTVAEEIREFFDSER 584 (689)
T ss_pred hCCHHHHhccCCcCHHHHHHHHHHHhhhH
Confidence 58999999999999999999999999987
No 39
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=89.26 E-value=0.24 Score=37.94 Aligned_cols=25 Identities=24% Similarity=0.392 Sum_probs=21.5
Q ss_pred hhHHhcCCCchHHHHHHHHHH-hccc
Q 034973 5 MEDLAGCPGIVERKVKCLYDT-FHEP 29 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~a-fheP 29 (77)
.++|..+||+|+++++.|++. |..-
T Consensus 2 ~~~L~~IpGIG~krakkLl~~GF~Sv 27 (232)
T PRK12766 2 PEELEDISGVGPSKAEALREAGFESV 27 (232)
T ss_pred ccccccCCCcCHHHHHHHHHcCCCCH
Confidence 357899999999999999999 7654
No 40
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.69 E-value=0.41 Score=35.58 Aligned_cols=23 Identities=26% Similarity=0.508 Sum_probs=18.5
Q ss_pred hhHHhcCCCchHHHHHHH-HHHhc
Q 034973 5 MEDLAGCPGIVERKVKCL-YDTFH 27 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL-~~afh 27 (77)
.+.|+.+||+|++-|+|| |..+.
T Consensus 10 i~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 10 IESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHc
Confidence 367999999999999999 44443
No 41
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=88.32 E-value=0.46 Score=28.46 Aligned_cols=21 Identities=38% Similarity=0.510 Sum_probs=16.7
Q ss_pred CChhHHhcCCCchHHHHHHHH
Q 034973 3 ASMEDLAGCPGIVERKVKCLY 23 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~ 23 (77)
.|.+||..+||||+.+..+|.
T Consensus 41 ~s~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 41 KSLEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp SSGGGGGGSTT--HHHHHHHC
T ss_pred CCHHHHhhCCCCCHHHHHHHH
Confidence 378999999999999999884
No 42
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=88.26 E-value=0.36 Score=41.70 Aligned_cols=33 Identities=33% Similarity=0.442 Sum_probs=30.1
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
+.||.|+|..+||+|++-|+.+.+.|+.|..+.
T Consensus 538 ~~a~~e~l~~i~giG~~vA~si~~ff~~~~~~~ 570 (667)
T COG0272 538 LAASEEELASIPGIGEVVARSIIEFFANEENRE 570 (667)
T ss_pred HhcCHHHHhhccchhHHHHHHHHHHHcCHHHHH
Confidence 468999999999999999999999999998654
No 43
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.26 E-value=0.45 Score=40.54 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=26.4
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
|+.|+|...||||++.|..|++.|+.|.
T Consensus 538 ~~~e~l~~i~giG~~~a~si~~ff~~~~ 565 (669)
T PRK14350 538 FALSKLLKIKGIGEKIALNIIEAFNDKI 565 (669)
T ss_pred CCHHHHhhCCCccHHHHHHHHHHHcCHH
Confidence 6889999999999999999999999985
No 44
>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=88.01 E-value=0.38 Score=29.85 Aligned_cols=25 Identities=20% Similarity=0.422 Sum_probs=19.6
Q ss_pred hhHHhcCCCchHHHHHHHHHHhccc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afheP 29 (77)
.+-+..+||+|+++|.+|...|...
T Consensus 21 ~D~i~gv~giG~k~A~~ll~~~~~~ 45 (75)
T cd00080 21 SDNIPGVPGIGPKTALKLLKEYGSL 45 (75)
T ss_pred cccCCCCCcccHHHHHHHHHHhCCH
Confidence 3456789999999999998776543
No 45
>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=87.93 E-value=0.64 Score=34.09 Aligned_cols=59 Identities=20% Similarity=0.246 Sum_probs=40.1
Q ss_pred hhHHhcCCCchHHHHHHHHHHhccccccccCCCCCCCCCCCCCCCCCCCcchhhhhhhcHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHHPPIPETPSLKDVEPSSVNEVTKVKKDTEERK 68 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhePF~k~~s~r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 (77)
.++|..+||+|++.|.-+...|-.-|... +..=-..-++-.+|+|--.|.|+. |.|.+-
T Consensus 114 re~Ll~LpGVG~KTAnvVL~~l~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 172 (177)
T TIGR03252 114 LRRLKALPGFGKQKAKIFLALLGKQLGVT----PEGWREAAGPYGEPGSFRSVADIT-DPESLT 172 (177)
T ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHhCCC----CcchHHhccccCCCCcccchhhcC-CHHHHH
Confidence 47899999999999999999998888644 111111223445788888887764 344443
No 46
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=86.45 E-value=0.52 Score=37.78 Aligned_cols=23 Identities=30% Similarity=0.592 Sum_probs=21.0
Q ss_pred hhHHhcCCCchHHHHHHHHHHhc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afh 27 (77)
-++|...||+||+|..+||..|-
T Consensus 92 l~~Ll~v~GlGpkKi~~Ly~elg 114 (326)
T COG1796 92 LEPLLKVPGLGPKKIVSLYKELG 114 (326)
T ss_pred hHHHhhCCCCCcHHHHHHHHHHC
Confidence 46899999999999999999985
No 47
>PRK00076 recR recombination protein RecR; Reviewed
Probab=86.41 E-value=0.51 Score=35.01 Aligned_cols=17 Identities=35% Similarity=0.485 Sum_probs=16.0
Q ss_pred hHHhcCCCchHHHHHHH
Q 034973 6 EDLAGCPGIVERKVKCL 22 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL 22 (77)
+.|+.+||+|++-|+||
T Consensus 11 ~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 11 EALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHCCCCCHHHHHHH
Confidence 67999999999999999
No 48
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=85.88 E-value=0.56 Score=39.76 Aligned_cols=30 Identities=13% Similarity=0.127 Sum_probs=24.5
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
.||.|+|+.+ ||.+.|++|++.||.+|...
T Consensus 580 ~As~eeL~~v--i~~k~A~~I~~~l~~~~~~~ 609 (624)
T PRK14669 580 AATETQLAAV--VGRAAAEAIIAHFTTEEAAP 609 (624)
T ss_pred hCCHHHHHHH--hCHHHHHHHHHHhcCcCCCc
Confidence 5888888887 88888888888888888644
No 49
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=85.78 E-value=0.71 Score=33.33 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=21.1
Q ss_pred hhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
...|...||||++.|.||.-.|+.-+
T Consensus 106 ~~~L~~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 106 VKALVKIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHhhh
Confidence 46789999999999999986555544
No 50
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=85.55 E-value=0.51 Score=41.05 Aligned_cols=29 Identities=28% Similarity=0.211 Sum_probs=23.9
Q ss_pred CCCChhHHhcCCCch-HHHHHHHHHHhccccc
Q 034973 1 MDASMEDLAGCPGIV-ERKVKCLYDTFHEPFK 31 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G-~~KarrL~~afhePF~ 31 (77)
++||.++|.. ++| +.+|++||+.||.+|.
T Consensus 784 ~~as~eeL~~--~iG~~~~A~~i~~fl~~~~~ 813 (814)
T TIGR00596 784 AKLSQNELNE--LIGDEEAAKRLYDFLRTEKL 813 (814)
T ss_pred HhCCHHHHHH--HhCCHHHHHHHHHHhccccC
Confidence 4688888888 588 9999999999998853
No 51
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.43 E-value=0.75 Score=33.28 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=21.1
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
..+.|..+||+|++.|.||.--+..-+
T Consensus 106 D~~~L~~vpGIGkKtAerIilELk~Ki 132 (194)
T PRK14605 106 NAELLSTIPGIGKKTASRIVLELKDKI 132 (194)
T ss_pred CHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 456799999999999999765555544
No 52
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.30 E-value=0.76 Score=33.97 Aligned_cols=28 Identities=11% Similarity=0.192 Sum_probs=22.7
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
....|+.+||+|++.|+||.=-+..-+.
T Consensus 105 D~~~L~~vpGIGkKtAeRIIlELkdKl~ 132 (196)
T PRK13901 105 DIELISKVKGIGNKMAGKIFLKLRGKLV 132 (196)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence 4567999999999999999777666553
No 53
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=84.94 E-value=0.79 Score=38.38 Aligned_cols=25 Identities=20% Similarity=0.149 Sum_probs=20.6
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.||.|||+.+ |+|...|+.|++.||
T Consensus 542 ~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 542 KADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred hCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 5788888888 888888888888775
No 54
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=84.89 E-value=0.85 Score=34.74 Aligned_cols=26 Identities=27% Similarity=0.296 Sum_probs=22.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.||.++|+..||+|+.|+-.|..++.
T Consensus 62 ~a~~~el~~v~GiG~aka~~l~a~~E 87 (224)
T COG2003 62 KASVEELSSVKGIGLAKAIQIKAAIE 87 (224)
T ss_pred hCCHHHHhhCCCccHHHHHHHHHHHH
Confidence 68999999999999999888765554
No 55
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=84.34 E-value=0.66 Score=34.95 Aligned_cols=18 Identities=22% Similarity=0.475 Sum_probs=16.3
Q ss_pred hhHHhcCCCchHHHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCL 22 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL 22 (77)
.+.|+.+||+|++-|+||
T Consensus 11 I~~l~kLPGvG~KsA~R~ 28 (198)
T COG0353 11 IDALKKLPGVGPKSAQRL 28 (198)
T ss_pred HHHHhhCCCCChhHHHHH
Confidence 367999999999999998
No 56
>PRK13844 recombination protein RecR; Provisional
Probab=84.30 E-value=0.72 Score=34.43 Aligned_cols=17 Identities=29% Similarity=0.362 Sum_probs=15.9
Q ss_pred hHHhcCCCchHHHHHHH
Q 034973 6 EDLAGCPGIVERKVKCL 22 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL 22 (77)
+.|..+||+|++-|+||
T Consensus 15 ~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHCCCCCHHHHHHH
Confidence 67899999999999999
No 57
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.20 E-value=0.93 Score=32.90 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=21.3
Q ss_pred hhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
...|+.+||+|++-|+||.=-+..-+
T Consensus 107 ~~~L~~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 45689999999999999976666555
No 58
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=84.18 E-value=1.4 Score=26.03 Aligned_cols=24 Identities=17% Similarity=0.282 Sum_probs=19.5
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
.|.++|..|+|+|..++++....|
T Consensus 44 ~~~~~L~~i~g~~~~~~~~~g~~~ 67 (81)
T smart00341 44 TNVSELLAIDGVGEEKARRYGKDL 67 (81)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHHH
Confidence 378899999999999987765544
No 59
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.71 E-value=0.95 Score=33.01 Aligned_cols=29 Identities=14% Similarity=0.297 Sum_probs=23.7
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
.+...|...||+|++.|+||.=-++.-+.
T Consensus 106 ~D~~~L~~ipGIGkKtAerIilELkdK~~ 134 (203)
T PRK14602 106 EDVAALTRVSGIGKKTAQHIFLELKYKLK 134 (203)
T ss_pred CCHHHHhcCCCcCHHHHHHHHHHHHHhhc
Confidence 34567999999999999999877776663
No 60
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=83.65 E-value=0.9 Score=32.78 Aligned_cols=23 Identities=9% Similarity=0.216 Sum_probs=19.5
Q ss_pred hHHhcCCCchHHHHHHHHHHhcc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.+|...||+||++|..+.+++.-
T Consensus 72 ~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred HHHhCCCCCCHHHHHHHHhcCCH
Confidence 35889999999999999887654
No 61
>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=83.40 E-value=1.7 Score=23.88 Aligned_cols=27 Identities=19% Similarity=0.258 Sum_probs=23.1
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.++.++|...+||++.+|..|.....+
T Consensus 22 ~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 22 YVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred ccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 478899999999999999999876554
No 62
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.01 E-value=1.2 Score=32.48 Aligned_cols=27 Identities=7% Similarity=0.091 Sum_probs=22.1
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
....|+..||+|++.|+||.--|..-+
T Consensus 105 D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 105 DARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 456689999999999999976666655
No 63
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=82.91 E-value=1.6 Score=26.28 Aligned_cols=23 Identities=30% Similarity=0.355 Sum_probs=18.8
Q ss_pred ChhH-HhcCCCchHHHHHHHHHHh
Q 034973 4 SMED-LAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 4 S~E~-Ls~CPG~G~~KarrL~~af 26 (77)
|.++ |..+||+|+.=+.++.+.+
T Consensus 44 ~~~~~~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 44 SGEEDLKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp SHHHHHCTSTTTTHHHHHHHHHHH
T ss_pred hHHHHHhhCCCCCHHHHHHHHHHH
Confidence 4455 9999999999999887654
No 64
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.18 E-value=1.2 Score=32.18 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=22.2
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
....|+.+||+|++.|+||.--+..-+
T Consensus 106 D~~~L~~vpGIGkKtAerIilELkdK~ 132 (188)
T PRK14606 106 DVEGLSKLPGISKKTAERIVMELKDEF 132 (188)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 345689999999999999987776655
No 65
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=81.84 E-value=1.1 Score=37.63 Aligned_cols=25 Identities=24% Similarity=0.234 Sum_probs=21.8
Q ss_pred hHHhcCCCchHHHHHHHHHHhcccc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
-.|..+||+|++++++|++.|..+=
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~ 549 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVE 549 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHH
Confidence 4588999999999999999998653
No 66
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=80.66 E-value=1.4 Score=36.23 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=21.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHH
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~a 25 (77)
.|+.++|...||||.+-|+|+..+
T Consensus 326 ~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 326 KAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred ccCHHHhcccCCCChHHHHHHHHH
Confidence 478899999999999999999655
No 67
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=80.62 E-value=1.5 Score=36.81 Aligned_cols=25 Identities=32% Similarity=0.632 Sum_probs=22.5
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHh
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
.||.++|..+||+|++.|..|++.+
T Consensus 553 ~As~eeL~~vpGi~~~~A~~I~~~~ 577 (577)
T PRK14668 553 EASVEDLRDVPGVGEKTAETIRERL 577 (577)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHhC
Confidence 5899999999999999999998753
No 68
>PRK09482 flap endonuclease-like protein; Provisional
Probab=79.14 E-value=1.3 Score=33.76 Aligned_cols=25 Identities=24% Similarity=0.425 Sum_probs=20.0
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+.+-+--||||||+.|..|.+.|..
T Consensus 180 ~sDnIpGVpGIG~KtA~~LL~~~gs 204 (256)
T PRK09482 180 SSSKIPGVAGIGPKSAAELLNQFRS 204 (256)
T ss_pred CccCCCCCCCcChHHHHHHHHHhCC
Confidence 3456778999999999999876654
No 69
>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=78.57 E-value=1.4 Score=32.29 Aligned_cols=23 Identities=26% Similarity=0.573 Sum_probs=18.9
Q ss_pred hhHHhcCCCchHHHHHHHHHHhc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.+-+..||||||+.|..|..-|.
T Consensus 182 sDnipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 182 SDNIPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred ccCCCCCCccCHHHHHHHHHHhC
Confidence 35567899999999999987754
No 70
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=78.04 E-value=1.8 Score=36.81 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=22.9
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+..++|..+||||++++.+|++++..
T Consensus 476 L~~~~L~~l~gfG~Ksa~~ll~~Ie~ 501 (665)
T PRK07956 476 LTAEDLLGLEGFGEKSAQNLLDAIEK 501 (665)
T ss_pred cCHHHHhcCcCcchHHHHHHHHHHHH
Confidence 45788999999999999999998875
No 71
>PRK14976 5'-3' exonuclease; Provisional
Probab=77.23 E-value=1.5 Score=33.31 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=17.2
Q ss_pred hhHHhcCCCchHHHHHHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~a 25 (77)
.+.+--|||+||+.|..|.+-
T Consensus 190 sDnipGVpGIG~KtA~~LL~~ 210 (281)
T PRK14976 190 SDNIKGVKGIGPKTAIKLLNK 210 (281)
T ss_pred cCCCCCCCcccHHHHHHHHHH
Confidence 456778999999999999654
No 72
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.10 E-value=2.5 Score=30.77 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=23.1
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhccccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
....|+..||+|++-|+||.--++.-+.
T Consensus 106 D~~~L~kvpGIGkKtAerIilELk~K~~ 133 (195)
T PRK14604 106 DVARLARVPGIGKKTAERIVLELKGKID 133 (195)
T ss_pred CHHHHhhCCCCCHHHHHHHHHHHHHHhc
Confidence 3466899999999999999877777663
No 73
>PRK10702 endonuclease III; Provisional
Probab=76.39 E-value=2.6 Score=30.76 Aligned_cols=27 Identities=19% Similarity=0.383 Sum_probs=22.2
Q ss_pred CChhHHhcCCCchHHHHHHHH-HHhccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLY-DTFHEP 29 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~-~afheP 29 (77)
.+.++|..+||+|++=|.-+. -+|++|
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~~~~ 133 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAFGWP 133 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHcCCC
Confidence 468999999999999988764 667766
No 74
>PRK10736 hypothetical protein; Provisional
Probab=76.24 E-value=2.1 Score=34.33 Aligned_cols=24 Identities=8% Similarity=0.052 Sum_probs=20.6
Q ss_pred HHhcCCCchHHHHHHHHHHhcccc
Q 034973 7 DLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afhePF 30 (77)
.|..|||+|++..++|++.|..+=
T Consensus 9 ~L~~~~giG~~~~~~L~~~~~~~~ 32 (374)
T PRK10736 9 RLMSVSSLYGDKMVRIAHRLLAQS 32 (374)
T ss_pred HHHhCCCCCHHHHHHHHHHhcChh
Confidence 478899999999999999887554
No 75
>smart00475 53EXOc 5'-3' exonuclease.
Probab=76.16 E-value=1.8 Score=32.53 Aligned_cols=23 Identities=30% Similarity=0.601 Sum_probs=18.4
Q ss_pred hhHHhcCCCchHHHHHHHHHHhc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.+-+-.|||+||+.|..|..-|.
T Consensus 185 sDnipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 185 SDNIPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred ccCCCCCCCCCHHHHHHHHHHhC
Confidence 35577899999999999976554
No 76
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=75.95 E-value=2.2 Score=36.48 Aligned_cols=25 Identities=12% Similarity=0.361 Sum_probs=22.2
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+.++|..++|||+++|.+|++++..
T Consensus 468 ~~~~l~~l~g~geksa~nl~~~Ie~ 492 (669)
T PRK14350 468 NFDRLINLKGFKDKRINNLKRSIEA 492 (669)
T ss_pred CHHHHhhccCccHHHHHHHHHHHHH
Confidence 4689999999999999999998873
No 77
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=75.38 E-value=2.4 Score=35.74 Aligned_cols=25 Identities=32% Similarity=0.546 Sum_probs=22.1
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+.++|..++|||+++|.+|++++..
T Consensus 457 ~~~~l~~l~gfgeks~~nll~aIe~ 481 (562)
T PRK08097 457 TPEQLANTPGIGKARAEQLWHQFNL 481 (562)
T ss_pred CHHHHhcCcCccHHHHHHHHHHHHH
Confidence 4689999999999999999988764
No 78
>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=75.38 E-value=2.3 Score=35.96 Aligned_cols=26 Identities=23% Similarity=0.331 Sum_probs=22.2
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
...++|..+||||+++|.+|++.+..
T Consensus 463 L~~~~L~~L~GfG~Ksa~nIl~~Ie~ 488 (652)
T TIGR00575 463 LKKEDLLELEGFGEKSAQNLLNAIEK 488 (652)
T ss_pred cCHHHHhhccCccHHHHHHHHHHHHH
Confidence 45678999999999999999988875
No 79
>PRK10880 adenine DNA glycosylase; Provisional
Probab=74.81 E-value=2.9 Score=33.04 Aligned_cols=29 Identities=17% Similarity=0.441 Sum_probs=24.7
Q ss_pred CChhHHhcCCCchHHHHHHHHH-Hhccccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYD-TFHEPFK 31 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~-afhePF~ 31 (77)
.+.++|..+||+|+.-|.-+.. +|++||-
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~af~~~~~ 135 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLSLGKHFP 135 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHHCCCCee
Confidence 3578999999999999998865 8999883
No 80
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=74.21 E-value=3.3 Score=29.51 Aligned_cols=22 Identities=36% Similarity=0.548 Sum_probs=17.7
Q ss_pred CChhHHhcCCCchHHHHHHHHH
Q 034973 3 ASMEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~ 24 (77)
.|.|||...||||+++.+.|-+
T Consensus 84 ~sveDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 84 DSVEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred CCHHHHHcCCCCCHHHHHHHHH
Confidence 3789999999999987666543
No 81
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.69 E-value=2.7 Score=30.45 Aligned_cols=26 Identities=15% Similarity=0.207 Sum_probs=21.2
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
....| ..||+|++.|+||.--+..-+
T Consensus 106 D~~~L-~vpGIGkKtAerIilELk~K~ 131 (186)
T PRK14600 106 DKAAL-KVNGIGEKLINRIITELQYKV 131 (186)
T ss_pred CHhhe-ECCCCcHHHHHHHHHHHHHHh
Confidence 34568 899999999999987777665
No 82
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=72.66 E-value=3.3 Score=36.03 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=23.3
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.||.|||+.+||||.+.|..|+-+-.
T Consensus 636 ~As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 636 SATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 58999999999999999999987654
No 83
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=72.54 E-value=2.3 Score=34.53 Aligned_cols=27 Identities=30% Similarity=0.517 Sum_probs=24.1
Q ss_pred CCCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 1 MDASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 1 i~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
+.||.|||...-|||..+|+.+.+-+.
T Consensus 320 l~As~edL~~VeGIGe~rAr~i~~Gl~ 346 (349)
T COG1623 320 LEASAEDLDAVEGIGEARARAIKEGLS 346 (349)
T ss_pred HHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence 369999999999999999999987664
No 84
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.28 E-value=3.5 Score=29.82 Aligned_cols=25 Identities=16% Similarity=0.185 Sum_probs=21.5
Q ss_pred hHHhcCCCchHHHHHHHHHHhcccc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhePF 30 (77)
+.|...+|+||+.|..+.+.|.-..
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~~~~~ 97 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAMNAEA 97 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhCCHHH
Confidence 3578899999999999999887665
No 85
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=71.83 E-value=3.4 Score=35.15 Aligned_cols=24 Identities=25% Similarity=0.455 Sum_probs=20.9
Q ss_pred hhHHhcCCCchHHHHHHHHHHhcc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
...|..+||+|+++++.|+..|..
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~~FgS 574 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLKHFGS 574 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCC
Confidence 356889999999999999999864
No 86
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=71.74 E-value=3.5 Score=22.14 Aligned_cols=18 Identities=22% Similarity=0.178 Sum_probs=14.1
Q ss_pred HHhcCCCchHHHHHHHHH
Q 034973 7 DLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~ 24 (77)
.+..+||+|.+-+++|..
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 367899999999999863
No 87
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=70.93 E-value=3.9 Score=30.64 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=23.6
Q ss_pred CChhHHhcCCCchHHHHHHHHH-Hhccccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYD-TFHEPFK 31 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~-afhePF~ 31 (77)
.++++|..+||.|++-|.-.+. +|..|-.
T Consensus 106 ~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i 135 (211)
T COG0177 106 DTREELLSLPGVGRKTANVVLSFAFGIPAI 135 (211)
T ss_pred chHHHHHhCCCcchHHHHHHHHhhcCCCcc
Confidence 4689999999999999987655 4888853
No 88
>PRK00254 ski2-like helicase; Provisional
Probab=70.64 E-value=2.8 Score=34.81 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=22.7
Q ss_pred HHhcCCCchHHHHHHHHHH-hcccccc
Q 034973 7 DLAGCPGIVERKVKCLYDT-FHEPFKR 32 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~a-fhePF~k 32 (77)
.|..+||||+.+|++|++. |..++.-
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i 672 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDI 672 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHH
Confidence 4778999999999999999 9888843
No 89
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=70.43 E-value=3.3 Score=35.49 Aligned_cols=26 Identities=23% Similarity=0.267 Sum_probs=21.8
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.+.++|..+||||+++|.+|++.+..
T Consensus 493 L~~~~L~~l~g~g~Ksa~~Ll~~Ie~ 518 (689)
T PRK14351 493 LTVADLAELEGWGETSAENLLAELEA 518 (689)
T ss_pred cCHHHHhcCcCcchhHHHHHHHHHHH
Confidence 45678999999999999999888763
No 90
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=70.26 E-value=4.3 Score=28.39 Aligned_cols=24 Identities=33% Similarity=0.432 Sum_probs=20.8
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
.|.|||...+|||+..+.+|.+-+
T Consensus 124 ~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 124 KSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred CcHHHHHhccCCCHHHHHHHHhhc
Confidence 478999999999999999987643
No 91
>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=69.67 E-value=3.6 Score=27.55 Aligned_cols=19 Identities=11% Similarity=0.177 Sum_probs=15.7
Q ss_pred hcCCCchHHHHHHHHHHhc
Q 034973 9 AGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 9 s~CPG~G~~KarrL~~afh 27 (77)
..+||||+.+|++|..-|.
T Consensus 53 r~vpglG~~~A~~I~awLa 71 (96)
T PF12482_consen 53 RAVPGLGAAGARRIEAWLA 71 (96)
T ss_pred HhCcccchHHHHHHHHHHH
Confidence 3589999999999976653
No 92
>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=68.68 E-value=4.4 Score=33.99 Aligned_cols=23 Identities=30% Similarity=0.488 Sum_probs=20.4
Q ss_pred hHHhcCCCchHHHHHHHHHHhcc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhe 28 (77)
..|..+||+|+++.+.|++.|..
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~Fgs 563 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYFGS 563 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCC
Confidence 46889999999999999998864
No 93
>PRK07758 hypothetical protein; Provisional
Probab=68.53 E-value=5 Score=27.22 Aligned_cols=26 Identities=15% Similarity=0.160 Sum_probs=23.3
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
-|.+||....|||++-...|.+.+.+
T Consensus 64 ~te~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 64 YSEKEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred CCHHHHHHccCCCHHHHHHHHHHHHH
Confidence 47899999999999999999888765
No 94
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=67.72 E-value=4 Score=35.50 Aligned_cols=24 Identities=21% Similarity=0.385 Sum_probs=21.4
Q ss_pred hhHHhcCCCchHHHHHHHHHHhcc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
...|..+||+|++++++|++.|..
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FGS 659 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFGS 659 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhCC
Confidence 467999999999999999999873
No 95
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=67.62 E-value=4 Score=34.18 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=21.6
Q ss_pred hhHHhcCCCchHHHHHHHHHHhcc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
...|...||+|++++++|++.|..
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~FgS 565 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFGS 565 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcCC
Confidence 356889999999999999999987
No 96
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=67.40 E-value=4.9 Score=29.85 Aligned_cols=29 Identities=14% Similarity=0.274 Sum_probs=23.6
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcccccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPFKR 32 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF~k 32 (77)
...-|+..||+|.+-|+||.--+.--|..
T Consensus 106 d~~~L~k~PGIGkKtAerivleLk~K~~~ 134 (201)
T COG0632 106 DVKALSKIPGIGKKTAERIVLELKGKLAA 134 (201)
T ss_pred ChHhhhcCCCCCHHHHHHHHHHHhhhhhh
Confidence 34568999999999999998777766654
No 97
>PRK13910 DNA glycosylase MutY; Provisional
Probab=66.66 E-value=6.4 Score=30.39 Aligned_cols=28 Identities=21% Similarity=0.279 Sum_probs=23.3
Q ss_pred CChhHHhcCCCchHHHHHHHHH-Hhcccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYD-TFHEPF 30 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~-afhePF 30 (77)
.+.++|..+||+|+.-|.-+.. +|++|.
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~ 97 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKS 97 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCc
Confidence 4678999999999999888754 788876
No 98
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=66.41 E-value=4.3 Score=34.22 Aligned_cols=23 Identities=22% Similarity=0.289 Sum_probs=20.5
Q ss_pred hHHhcCCCchHHHHHHHHHHhcc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhe 28 (77)
..|...||+|+++.+.|++.|..
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fgs 536 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLGT 536 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhCC
Confidence 46889999999999999999864
No 99
>PRK13766 Hef nuclease; Provisional
Probab=66.31 E-value=4.7 Score=33.34 Aligned_cols=22 Identities=14% Similarity=0.229 Sum_probs=19.8
Q ss_pred HhcCCCchHHHHHHHHHHhccc
Q 034973 8 LAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 8 Ls~CPG~G~~KarrL~~afheP 29 (77)
|..+||+|++++++|++.|..+
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~ 738 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSV 738 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCH
Confidence 7899999999999999998753
No 100
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=65.06 E-value=4.1 Score=32.38 Aligned_cols=19 Identities=26% Similarity=0.485 Sum_probs=16.2
Q ss_pred CCChhHHhcCCCchHHHHH
Q 034973 2 DASMEDLAGCPGIVERKVK 20 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~Kar 20 (77)
-++.++|..+||+||+-|.
T Consensus 155 P~~v~dLlsLPGVGPKMa~ 173 (286)
T KOG1921|consen 155 PDTVEDLLSLPGVGPKMAH 173 (286)
T ss_pred chhHHHHhcCCCCchHHHH
Confidence 4688999999999998753
No 101
>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=64.50 E-value=6.6 Score=29.91 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=22.2
Q ss_pred CChhHHhcCCCchHHHHHHHH-HHhcccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLY-DTFHEPF 30 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~-~afhePF 30 (77)
.+.++|..+||+|+.-|.-+. -+|+.|.
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~a~~~~~ 130 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSFALNKPY 130 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHCCCCC
Confidence 457899999999999987764 4677765
No 102
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=63.78 E-value=7.1 Score=29.05 Aligned_cols=27 Identities=15% Similarity=0.094 Sum_probs=22.8
Q ss_pred ChhHHhcCCCchHHHHHHHH-HHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCLY-DTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~-~afhePF 30 (77)
..++|..+||+|+.-|.-+. -+|+.|.
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLlya~~rp~ 146 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCYVCAKEV 146 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHHHcCCCc
Confidence 46889999999999998875 4888886
No 103
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=60.88 E-value=9.4 Score=25.23 Aligned_cols=22 Identities=18% Similarity=0.351 Sum_probs=18.0
Q ss_pred CChhHHhcCCCchHHHHHHHHH
Q 034973 3 ASMEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~ 24 (77)
...+.|..+||+|+.-|.-+.-
T Consensus 80 ~~~~~L~~l~GIG~~tA~~~l~ 101 (158)
T cd00056 80 DAREELLALPGVGRKTANVVLL 101 (158)
T ss_pred ccHHHHHcCCCCCHHHHHHHHH
Confidence 3568899999999999887644
No 104
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=60.13 E-value=6.6 Score=33.03 Aligned_cols=23 Identities=30% Similarity=0.416 Sum_probs=20.3
Q ss_pred hHHhcCCCchHHHHHHHHHHhcc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhe 28 (77)
..|...||+|+++.+.|++.|..
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~Fgs 536 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRNFKT 536 (567)
T ss_pred CccccCCCCCHHHHHHHHHHhCC
Confidence 46889999999999999999864
No 105
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=60.00 E-value=7 Score=29.24 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=17.0
Q ss_pred hcCCCchHHHHHHHHHHhcc
Q 034973 9 AGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 9 s~CPG~G~~KarrL~~afhe 28 (77)
..+||||+++|-+|...+..
T Consensus 226 ~gv~giG~k~A~~li~~~~~ 245 (316)
T cd00128 226 EGIPGIGPVTALKLIKKYGD 245 (316)
T ss_pred CCCCCccHHHHHHHHHHcCC
Confidence 45799999999999888764
No 106
>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=59.95 E-value=13 Score=23.06 Aligned_cols=26 Identities=23% Similarity=0.233 Sum_probs=22.0
Q ss_pred hHHhcCCCchHHHHHHHHHHhccccc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHEPFK 31 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afhePF~ 31 (77)
+-|...||+|+.=|-.|...+..+-+
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchh
Confidence 45788999999999999999877643
No 107
>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=59.74 E-value=6.6 Score=33.35 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=21.8
Q ss_pred cCCCchHHHHHHHHHHhcccccccc
Q 034973 10 GCPGIVERKVKCLYDTFHEPFKRVV 34 (77)
Q Consensus 10 ~CPG~G~~KarrL~~afhePF~k~~ 34 (77)
..||+|++.|++|++.|.......+
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i 112 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVL 112 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHH
Confidence 4899999999999999998876553
No 108
>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=59.56 E-value=9.6 Score=29.02 Aligned_cols=26 Identities=19% Similarity=0.345 Sum_probs=22.4
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+|.+++..+||||+.-|..+.+.+..
T Consensus 42 ~~~~~~~~ipgiG~~ia~kI~E~~~t 67 (307)
T cd00141 42 ESLEEAKKLPGIGKKIAEKIEEILET 67 (307)
T ss_pred CCHHHhcCCCCccHHHHHHHHHHHHc
Confidence 46788999999999999999877765
No 109
>PRK02362 ski2-like helicase; Provisional
Probab=59.40 E-value=7.1 Score=32.62 Aligned_cols=20 Identities=30% Similarity=0.549 Sum_probs=17.4
Q ss_pred hHHhcCCCchHHHHHHHHHH
Q 034973 6 EDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~a 25 (77)
-+|..+||||+..|++||+.
T Consensus 652 ~~L~~ip~i~~~~a~~l~~~ 671 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYNA 671 (737)
T ss_pred HHHhCCCCCCHHHHHHHHHc
Confidence 46888999999999999873
No 110
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=59.23 E-value=9.3 Score=29.03 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=20.8
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.++.++|..| ||+.+||+.|.++-.
T Consensus 163 ~~~~~eL~~~-Gl~~~Ra~~L~~lA~ 187 (283)
T PRK10308 163 AADPQALKAL-GMPLKRAEALIHLAN 187 (283)
T ss_pred cCCHHHHHHC-CCCHHHHHHHHHHHH
Confidence 4678888888 999999999987654
No 111
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=59.03 E-value=6.6 Score=29.92 Aligned_cols=30 Identities=20% Similarity=0.423 Sum_probs=22.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHH-hccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDT-FHEPFK 31 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~a-fhePF~ 31 (77)
+.-..+|.++||+|.+....|.+- =..||-
T Consensus 126 t~RLH~LELLpGiGkK~m~~ILeERkkkpFe 156 (202)
T COG1491 126 TLRLHQLELLPGIGKKTMWAILEERKKKPFE 156 (202)
T ss_pred hHHHHHHHhcccccHHHHHHHHHHHhcCCCc
Confidence 334678999999999999888654 345663
No 112
>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=58.08 E-value=6.9 Score=24.28 Aligned_cols=28 Identities=29% Similarity=0.318 Sum_probs=20.8
Q ss_pred CChhHHhcC---CCchHHHHHHHHHHhcccc
Q 034973 3 ASMEDLAGC---PGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 3 AS~E~Ls~C---PG~G~~KarrL~~afhePF 30 (77)
++.++|..| =||+..||++|.++.+.=.
T Consensus 36 ~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 36 ASEEELRELIRPLGFSRRKAKYIIELARAIL 66 (108)
T ss_dssp SHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHhhccCCCHHHHHHHHHHHHHhh
Confidence 456666555 6999999999988765433
No 113
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=57.89 E-value=7.5 Score=33.96 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=20.6
Q ss_pred hHHhcCCCchHHHHHHHHHHhccc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afheP 29 (77)
..|..+||+|+++.+.|+..|..-
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~ 631 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSF 631 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCH
Confidence 457899999999999999988653
No 114
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=57.24 E-value=7.9 Score=33.75 Aligned_cols=26 Identities=23% Similarity=0.353 Sum_probs=23.5
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
-+.++|..++|||.++|++|++++++
T Consensus 476 Lt~~~l~~l~~~~~ks~~nLl~aIe~ 501 (667)
T COG0272 476 LTEEDLLSLEGFGEKSAENLLNAIEK 501 (667)
T ss_pred CCHHHHhhccchhhhHHHHHHHHHHH
Confidence 36799999999999999999999875
No 115
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=56.79 E-value=11 Score=27.96 Aligned_cols=27 Identities=19% Similarity=0.130 Sum_probs=21.5
Q ss_pred ChhHHh-cCCCchHHHHHHHH-HHhcccc
Q 034973 4 SMEDLA-GCPGIVERKVKCLY-DTFHEPF 30 (77)
Q Consensus 4 S~E~Ls-~CPG~G~~KarrL~-~afhePF 30 (77)
..++|. .+||+|++-|--+. ..+..|.
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~ 144 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFLRNVGYEDL 144 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHccCCCe
Confidence 467899 99999999999887 4544664
No 116
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=56.39 E-value=12 Score=24.65 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=20.1
Q ss_pred ChhHHhcCCCchHHHHHHH-HHHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCL-YDTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL-~~afhePF 30 (77)
..+.|..+||||+.-|.-+ .-+|+.+|
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~~~~~~ 97 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFALGKPF 97 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHHCCCCC
Confidence 4678999999999988765 44556554
No 117
>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=55.79 E-value=10 Score=26.67 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=20.4
Q ss_pred ChhHHhcCCCchHHHHHHHH-HHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCLY-DTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~-~afhePF 30 (77)
+.+.|..+||+|+.-|.-+. -+|+.|.
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~~~~~~ 131 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVAFGIPA 131 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHHcCCCc
Confidence 56889999999999988763 4455543
No 118
>PRK05755 DNA polymerase I; Provisional
Probab=55.26 E-value=7.6 Score=33.47 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=17.2
Q ss_pred hhHHhcCCCchHHHHHHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~a 25 (77)
.+-+-.|||||++.|..|.+-
T Consensus 186 sDnipGv~GiG~ktA~~Ll~~ 206 (880)
T PRK05755 186 SDNIPGVPGIGEKTAAKLLQE 206 (880)
T ss_pred cCCCCCCCCccHHHHHHHHHH
Confidence 456778999999999999654
No 119
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=54.21 E-value=10 Score=32.15 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=21.1
Q ss_pred hHHhcCCCchHHHHHHHHHHhccc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afheP 29 (77)
..|..+||+|+++++.|++.|...
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fgs~ 592 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFGSV 592 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcCCH
Confidence 468899999999999999999754
No 120
>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=53.61 E-value=9.1 Score=28.19 Aligned_cols=20 Identities=20% Similarity=0.419 Sum_probs=15.0
Q ss_pred HhcCCCchHHHHHHHHHH-hc
Q 034973 8 LAGCPGIVERKVKCLYDT-FH 27 (77)
Q Consensus 8 Ls~CPG~G~~KarrL~~a-fh 27 (77)
|..+||+|+..+++|++. |+
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ 21 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYD 21 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCC
Confidence 356788888888888776 44
No 121
>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=53.12 E-value=10 Score=25.38 Aligned_cols=21 Identities=24% Similarity=0.278 Sum_probs=17.7
Q ss_pred ChhHHhcCCCchHHHHHHHHH
Q 034973 4 SMEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~ 24 (77)
...+|..+||+|+.=|+-|..
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~ 30 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRL 30 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHH
Confidence 356899999999999998853
No 122
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=52.91 E-value=12 Score=29.02 Aligned_cols=22 Identities=27% Similarity=0.395 Sum_probs=19.4
Q ss_pred HhcCCCchHHHHHHHHHHhccc
Q 034973 8 LAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 8 Ls~CPG~G~~KarrL~~afheP 29 (77)
|...||+|+..|.+|++.|...
T Consensus 184 l~s~pgig~~~a~~ll~~fgS~ 205 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFGSV 205 (254)
T ss_pred HHcCCCccHHHHHHHHHHhcCH
Confidence 6789999999999999988654
No 123
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=51.83 E-value=9.6 Score=28.65 Aligned_cols=22 Identities=18% Similarity=0.415 Sum_probs=16.8
Q ss_pred hhHHhcCCCchHHHHHHHHHHh
Q 034973 5 MEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~af 26 (77)
.+-+--+||+||++|..|..-|
T Consensus 197 sDnipGV~GIG~ktA~~Ll~~~ 218 (310)
T COG0258 197 SDNIPGVKGIGPKTALKLLQEY 218 (310)
T ss_pred ccCCCCCCCcCHHHHHHHHHHh
Confidence 3455668999999999995544
No 124
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=51.03 E-value=15 Score=30.13 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=24.7
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
|.+|+..+||||++-|+.+-+.+..--++.
T Consensus 54 S~~ea~~lP~iG~kia~ki~EiletG~l~e 83 (353)
T KOG2534|consen 54 SGEEAEKLPGIGPKIAEKIQEILETGVLRE 83 (353)
T ss_pred cHHHhcCCCCCCHHHHHHHHHHHHcCCchh
Confidence 789999999999999999988776655443
No 125
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.67 E-value=9.5 Score=33.60 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=16.4
Q ss_pred hhHHhcCCCchHHHHHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~ 24 (77)
.+-+-.||||||+.|..|..
T Consensus 184 sDnIpGVpGIG~KtA~kLL~ 203 (887)
T TIGR00593 184 SDNIPGVKGIGEKTAAKLLQ 203 (887)
T ss_pred ccCCCCCCCcCHHHHHHHHH
Confidence 45567799999999999854
No 126
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=50.14 E-value=1.4 Score=29.37 Aligned_cols=25 Identities=24% Similarity=0.510 Sum_probs=17.4
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+.+.+--+||+|++.|..|..-|..
T Consensus 16 ~sDNIPGV~GIG~KtA~~LL~~ygs 40 (101)
T PF01367_consen 16 SSDNIPGVPGIGPKTAAKLLQEYGS 40 (101)
T ss_dssp CCCTB---TTSTCHCCCCCHHHHTS
T ss_pred cccCCCCCCCCCHHHHHHHHHHcCC
Confidence 3455667899999999999887763
No 127
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=50.08 E-value=11 Score=22.75 Aligned_cols=13 Identities=46% Similarity=0.856 Sum_probs=10.2
Q ss_pred CChhHH-hcCCCch
Q 034973 3 ASMEDL-AGCPGIV 15 (77)
Q Consensus 3 AS~E~L-s~CPG~G 15 (77)
.|.++| ..|||+-
T Consensus 38 ~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 38 DDEEDLERNCPGPT 51 (55)
T ss_pred CCHHHHHhCCCCCC
Confidence 367788 8999974
No 128
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=49.36 E-value=11 Score=31.99 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=21.5
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.++.|..+||||++|+..|.+.+.+
T Consensus 115 ~~~~L~~v~gi~~~~~~~i~~~~~~ 139 (720)
T TIGR01448 115 DPEKLLEVPGISKANLEKFVSQWSQ 139 (720)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 4678999999999999999887754
No 129
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=49.20 E-value=18 Score=29.75 Aligned_cols=24 Identities=17% Similarity=0.368 Sum_probs=19.9
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
+|.++|..++|+|++|+.+.-..|
T Consensus 572 ~t~~~l~~i~Gvg~~K~~~yg~~~ 595 (607)
T PRK11057 572 ITASEMLSVNGVGQRKLERFGKPF 595 (607)
T ss_pred CCHHHHcCCCCCCHHHHHHHHHHH
Confidence 488999999999999998764444
No 130
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=49.05 E-value=14 Score=27.59 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=16.9
Q ss_pred hhHHhcCCCchHHHHHHHHHH-hccccc
Q 034973 5 MEDLAGCPGIVERKVKCLYDT-FHEPFK 31 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~a-fhePF~ 31 (77)
...|.++||||.+-...+.+. =.+||.
T Consensus 115 lH~LeLLPGIGKK~m~~ILeERkkkpFe 142 (181)
T PF04919_consen 115 LHSLELLPGIGKKTMWKILEERKKKPFE 142 (181)
T ss_dssp SBGGGGSTT--HHHHHHHHHHHHHS---
T ss_pred HHHHhhcccccHHHHHHHHHHHccCCCC
Confidence 568999999999998888654 345663
No 131
>PRK03980 flap endonuclease-1; Provisional
Probab=48.70 E-value=14 Score=28.37 Aligned_cols=18 Identities=22% Similarity=0.226 Sum_probs=15.0
Q ss_pred cCCCchHHHHHHHHHHhc
Q 034973 10 GCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 10 ~CPG~G~~KarrL~~afh 27 (77)
..||+|+++|-+|...+.
T Consensus 193 GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred CCCCccHHHHHHHHHHCC
Confidence 468999999999976665
No 132
>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=48.36 E-value=18 Score=23.70 Aligned_cols=23 Identities=26% Similarity=0.225 Sum_probs=19.4
Q ss_pred HHhcCCCchHHHHHHHHHHhccc
Q 034973 7 DLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afheP 29 (77)
.|....|||+.+|..|.+.+.-.
T Consensus 16 aLt~IyGIG~~~A~~Ic~~lgi~ 38 (107)
T PF00416_consen 16 ALTKIYGIGRRKAKQICKKLGIN 38 (107)
T ss_dssp HHTTSTTBCHHHHHHHHHHTTS-
T ss_pred HHhhhhccCHHHHHHHHHHcCCC
Confidence 58899999999999999887543
No 133
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=47.95 E-value=12 Score=31.69 Aligned_cols=24 Identities=29% Similarity=0.551 Sum_probs=22.3
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.||.++|+.+ ||++.|.+|++.|+
T Consensus 597 ~As~eeL~~v--ig~k~A~~I~~~~~ 620 (621)
T PRK14671 597 KASLEELAAV--AGPKTAETIYRYYH 620 (621)
T ss_pred hCCHHHHHHH--hCHHHHHHHHHHhC
Confidence 6899999999 99999999999986
No 134
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=47.63 E-value=20 Score=27.66 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=21.7
Q ss_pred CChhHHhcCCCchHHHHHHHHHHhccc
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~afheP 29 (77)
++.++|..+||||+.=|.++.+.+..-
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG 71 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETG 71 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhC
Confidence 456789999999999988887766543
No 135
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=46.27 E-value=19 Score=26.94 Aligned_cols=27 Identities=26% Similarity=0.289 Sum_probs=23.6
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.++.++|...+|+++.+|..|++..+.
T Consensus 35 ~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 35 VASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred cCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 478899999999999999999988765
No 136
>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=45.33 E-value=17 Score=28.20 Aligned_cols=17 Identities=24% Similarity=0.286 Sum_probs=14.4
Q ss_pred hcCCCchHHHHHHHHHH
Q 034973 9 AGCPGIVERKVKCLYDT 25 (77)
Q Consensus 9 s~CPG~G~~KarrL~~a 25 (77)
..+||+|+++|-.|...
T Consensus 239 ~Gv~GIG~ktA~kli~~ 255 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE 255 (338)
T ss_pred CCCCCccHHHHHHHHHH
Confidence 56899999999999754
No 137
>PRK01172 ski2-like helicase; Provisional
Probab=45.31 E-value=14 Score=30.40 Aligned_cols=24 Identities=13% Similarity=0.184 Sum_probs=14.1
Q ss_pred CCChhHHhcCCCchHHHHHHHHHH
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~a 25 (77)
.++.++|..+.|||+++|+.+++.
T Consensus 641 ~~~~~~~~~i~~~~~~~~~~i~~~ 664 (674)
T PRK01172 641 RSSPERIKKIYGFSDTLANAIVNR 664 (674)
T ss_pred hCCHHHHHHHhccCHHHHHHHHHH
Confidence 345556666666666666665554
No 138
>PTZ00217 flap endonuclease-1; Provisional
Probab=43.23 E-value=18 Score=28.83 Aligned_cols=18 Identities=17% Similarity=0.200 Sum_probs=14.4
Q ss_pred hcCCCchHHHHHHHHHHh
Q 034973 9 AGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 9 s~CPG~G~~KarrL~~af 26 (77)
-.+||||+++|-.|...+
T Consensus 238 pgi~GIG~ktA~~Li~~~ 255 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKKY 255 (393)
T ss_pred CCCCCccHHHHHHHHHHc
Confidence 458999999999996543
No 139
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.18 E-value=22 Score=25.94 Aligned_cols=23 Identities=9% Similarity=0.143 Sum_probs=19.0
Q ss_pred HHhcCCCchHHHHHHHHHHhccc
Q 034973 7 DLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afheP 29 (77)
.|....|+||+.|-.+.+++.-.
T Consensus 75 ~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 75 VLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHhCCCCcCHHHHHHHHhhCCHH
Confidence 47889999999999998876433
No 140
>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=42.40 E-value=25 Score=25.89 Aligned_cols=26 Identities=23% Similarity=0.230 Sum_probs=23.7
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afh 27 (77)
.|+.++|...+|+++.+|..|+....
T Consensus 28 ~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 28 VASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred cCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 57899999999999999999998876
No 141
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=41.65 E-value=24 Score=23.57 Aligned_cols=20 Identities=30% Similarity=0.338 Sum_probs=16.7
Q ss_pred hhHHhcCCCchHHHHHHHHH
Q 034973 5 MEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~ 24 (77)
+-||..+||||+.-|.=|..
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~ 71 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEH 71 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHH
Confidence 46899999999999887744
No 142
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=40.85 E-value=24 Score=27.41 Aligned_cols=27 Identities=11% Similarity=0.232 Sum_probs=24.2
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.-|.+||..++|||++-...+.+.|++
T Consensus 277 ~~~~~~l~~~~n~G~ksl~ei~~~L~~ 303 (310)
T PRK05182 277 QRTEEELLKTRNLGKKSLEEIKEKLAE 303 (310)
T ss_pred hCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence 347899999999999999999998876
No 143
>PHA00439 exonuclease
Probab=40.46 E-value=16 Score=28.61 Aligned_cols=21 Identities=19% Similarity=0.428 Sum_probs=16.7
Q ss_pred ChhHHhcCCCchHHHHHHHHHH
Q 034973 4 SMEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~a 25 (77)
+.+.+--||||| +.|..|++-
T Consensus 186 sSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 186 STDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred cccCCCCCCCcC-HHHHHHHhC
Confidence 446677899999 999988654
No 144
>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=39.52 E-value=25 Score=27.10 Aligned_cols=27 Identities=15% Similarity=0.198 Sum_probs=24.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.-|++||..++|||++-..-+.+.|.+
T Consensus 263 ~~~~~~l~~~~n~G~ksl~ei~~~l~~ 289 (297)
T TIGR02027 263 SKSEEELLKIKNFGKKSLTEIKEKLAE 289 (297)
T ss_pred hCCHHHHhhCCCCChhhHHHHHHHHHH
Confidence 358899999999999999999999887
No 145
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.39 E-value=22 Score=25.89 Aligned_cols=20 Identities=20% Similarity=0.192 Sum_probs=17.7
Q ss_pred HHhcCCCchHHHHHHHHHHh
Q 034973 7 DLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~af 26 (77)
.|....|+||+.|-.+.+++
T Consensus 74 ~Li~V~GIGpK~Al~iLs~~ 93 (195)
T PRK14604 74 LLIGVSGVGPKAALNLLSSG 93 (195)
T ss_pred HHhCcCCcCHHHHHHHHcCC
Confidence 57889999999999998876
No 146
>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=39.19 E-value=32 Score=27.82 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=19.7
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
.|.++|..++|+|++|+++.-+.|
T Consensus 561 ~~~~~l~~i~gv~~~k~~~~G~~~ 584 (591)
T TIGR01389 561 ATLNALLKIKGVGQNKLDRYGEAF 584 (591)
T ss_pred CCHHHHhCCCCCCHHHHHHHHHHH
Confidence 478999999999999997764433
No 147
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=39.15 E-value=25 Score=28.24 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=18.7
Q ss_pred ChhHHhcCCCchHHHHHHHHHH
Q 034973 4 SMEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~a 25 (77)
+-|+|.+.+|+||+.+|.|.=+
T Consensus 267 ~feeLL~~~GvGp~TlRALaLv 288 (319)
T PF05559_consen 267 DFEELLLIKGVGPSTLRALALV 288 (319)
T ss_pred CHHHHHhcCCCCHHHHHHHHHH
Confidence 4689999999999999998433
No 148
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=38.57 E-value=26 Score=28.88 Aligned_cols=22 Identities=32% Similarity=0.388 Sum_probs=18.8
Q ss_pred ChhHHhcCCCchHHHHHHHHHH
Q 034973 4 SMEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~a 25 (77)
.-++|.+.|||||.-+|.|.=+
T Consensus 276 Df~elLl~~GiGpstvRALalV 297 (373)
T COG1415 276 DFEELLLVPGIGPSTVRALALV 297 (373)
T ss_pred cHHHHHhccCCCHHHHHHHHHH
Confidence 4688999999999999999543
No 149
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.45 E-value=35 Score=27.56 Aligned_cols=27 Identities=26% Similarity=0.397 Sum_probs=22.8
Q ss_pred ChhHHhcCCCchHHHHHHH-HHHhcccc
Q 034973 4 SMEDLAGCPGIVERKVKCL-YDTFHEPF 30 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL-~~afhePF 30 (77)
+.++|..+||+|+--|..+ .=+|++|+
T Consensus 111 ~~~~l~~LpGiG~yTa~Ail~~a~~~~~ 138 (342)
T COG1194 111 DEEELAALPGVGPYTAGAILSFAFNQPE 138 (342)
T ss_pred CHHHHHhCCCCcHHHHHHHHHHHhCCCC
Confidence 5789999999999887765 56788888
No 150
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.26 E-value=26 Score=25.38 Aligned_cols=21 Identities=10% Similarity=0.191 Sum_probs=17.8
Q ss_pred HHhcCCCchHHHHHHHHHHhc
Q 034973 7 DLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afh 27 (77)
.|....|+||+.|-.+.+++.
T Consensus 74 ~LisV~GIGpK~Al~iLs~~~ 94 (186)
T PRK14600 74 MLVKVSGVNYKTAMSILSKLT 94 (186)
T ss_pred HHhCcCCcCHHHHHHHHccCC
Confidence 478899999999999987653
No 151
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=37.14 E-value=23 Score=22.26 Aligned_cols=28 Identities=32% Similarity=0.432 Sum_probs=19.7
Q ss_pred ChhHHhcCCCchHHHHHHHH-HHhccccc
Q 034973 4 SMEDLAGCPGIVERKVKCLY-DTFHEPFK 31 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~-~afhePF~ 31 (77)
|.++-+.--|||.+|.++|. +.=..||.
T Consensus 15 Ti~EAa~Y~gIG~~klr~l~~~~~~~~f~ 43 (67)
T PF09035_consen 15 TIEEAAEYFGIGEKKLRELAEENPDCPFV 43 (67)
T ss_dssp EHHHHHHHT-S-HHHHHHHHHH-TT-SSE
T ss_pred CHHHHHHHhCccHHHHHHHHHhCCCCCEE
Confidence 45677778899999999999 77788884
No 152
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=37.03 E-value=16 Score=34.19 Aligned_cols=22 Identities=23% Similarity=0.220 Sum_probs=17.7
Q ss_pred HHhcCCCchHHHHHHHHHHhcc
Q 034973 7 DLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afhe 28 (77)
=|.-.+||||+||..|.+.+.+
T Consensus 807 lLqyI~GlGpRKa~~lLKsl~~ 828 (1299)
T KOG1856|consen 807 LLQYICGLGPRKATSLLKSLKR 828 (1299)
T ss_pred hHHHhcCCCcccHHHHHHHHHH
Confidence 3778999999999988766543
No 153
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=36.85 E-value=25 Score=29.89 Aligned_cols=22 Identities=32% Similarity=0.526 Sum_probs=19.5
Q ss_pred HHhcCCCchHHHHHHHHHHhcc
Q 034973 7 DLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~afhe 28 (77)
.|...||+|++..++|+.-|..
T Consensus 531 ~Ld~I~GiG~~r~~~LL~~Fgs 552 (581)
T COG0322 531 SLDDIPGIGPKRRKALLKHFGS 552 (581)
T ss_pred ccccCCCcCHHHHHHHHHHhhC
Confidence 5778999999999999998864
No 154
>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=35.98 E-value=32 Score=26.35 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=20.2
Q ss_pred hhHHhcCCCchHHHHHHH-HHHhccc
Q 034973 5 MEDLAGCPGIVERKVKCL-YDTFHEP 29 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL-~~afheP 29 (77)
.++|..+||+|+.-|..+ .-+|+.|
T Consensus 219 ~~~L~~l~GIG~~tAd~vll~~l~~~ 244 (310)
T TIGR00588 219 REALCELPGVGPKVADCICLMGLDKP 244 (310)
T ss_pred HHHHHhCCCccHHHHHHHHHHhCCCC
Confidence 578999999999998876 4566665
No 155
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=35.75 E-value=31 Score=21.84 Aligned_cols=20 Identities=20% Similarity=0.268 Sum_probs=13.6
Q ss_pred hHHhcCCCchHHHHHHHHHH
Q 034973 6 EDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~a 25 (77)
.+|..+|+||++=.+.|.++
T Consensus 3 ~~l~~LpNig~~~e~~L~~v 22 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV 22 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT
T ss_pred cchhhCCCCCHHHHHHHHHc
Confidence 57899999999999888653
No 156
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=35.64 E-value=28 Score=30.66 Aligned_cols=22 Identities=18% Similarity=0.360 Sum_probs=19.0
Q ss_pred hHHhcCCCchHHHHHHHHHHhc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afh 27 (77)
+-|..+||+|++-|++|+.-|.
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~ 778 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVK 778 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcC
Confidence 4488999999999999998754
No 157
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.41 E-value=28 Score=25.30 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=17.2
Q ss_pred HHhcCCCchHHHHHHHHHHh
Q 034973 7 DLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~af 26 (77)
.|....|+||+.|-.+.+++
T Consensus 73 ~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 73 LLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred HHhCcCCcCHHHHHHHHcCC
Confidence 57889999999999997764
No 158
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=34.86 E-value=25 Score=26.54 Aligned_cols=29 Identities=21% Similarity=0.233 Sum_probs=24.5
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcccccc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHEPFKR 32 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhePF~k 32 (77)
..+||..+.|+||.-+.+|.++=-..|--
T Consensus 156 ~aDDL~~I~GIGp~~a~~L~eaGi~tfaQ 184 (221)
T PRK12278 156 GADDLTKITGVGPALAKKLNEAGVTTFAQ 184 (221)
T ss_pred CcchheeccccChHHHHHHHHcCCCCHHH
Confidence 35899999999999999998877666643
No 159
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=34.86 E-value=29 Score=25.95 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=18.5
Q ss_pred ChhHHhcCCCchHHHHHHHHHH
Q 034973 4 SMEDLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~a 25 (77)
.+-.|..+||+|+.-+.+|.+.
T Consensus 4 ~~~~l~~l~gIg~~~a~~L~~~ 25 (317)
T PRK04301 4 KEKDLEDLPGVGPATAEKLREA 25 (317)
T ss_pred ccccHhhcCCCCHHHHHHHHHc
Confidence 3457899999999999999665
No 160
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=34.75 E-value=31 Score=25.67 Aligned_cols=26 Identities=31% Similarity=0.436 Sum_probs=19.2
Q ss_pred CCChhHHhcC---CCchHHHHHHHHHHhc
Q 034973 2 DASMEDLAGC---PGIVERKVKCLYDTFH 27 (77)
Q Consensus 2 ~AS~E~Ls~C---PG~G~~KarrL~~afh 27 (77)
.|+.++|..| -||-.+||++|.+...
T Consensus 74 ~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~ 102 (218)
T PRK13913 74 YIEFSKLAECVRPSGFYNQKAKRLIDLSE 102 (218)
T ss_pred cCCHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 3566666655 6999999999976543
No 161
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.22 E-value=31 Score=25.51 Aligned_cols=21 Identities=29% Similarity=0.390 Sum_probs=17.6
Q ss_pred hHHhcCCCchHHHHHHHHHHh
Q 034973 6 EDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~af 26 (77)
+.|....|+||+.|-.+..++
T Consensus 72 ~~LisVsGIGPK~ALaILs~~ 92 (196)
T PRK13901 72 EELIGVDGIGPRAALRVLSGI 92 (196)
T ss_pred HHHhCcCCcCHHHHHHHHcCC
Confidence 357889999999999998764
No 162
>PRK10702 endonuclease III; Provisional
Probab=33.93 E-value=33 Score=25.07 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=21.7
Q ss_pred CCChhHHhcC---CCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGC---PGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~C---PG~G~~KarrL~~afhe 28 (77)
.|+.++|..| -||-.+||++|+++.+.
T Consensus 66 ~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~ 95 (211)
T PRK10702 66 ELGVEGVKTYIKTIGLYNSKAENVIKTCRI 95 (211)
T ss_pred CCCHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 5778888764 68889999999887775
No 163
>PRK01172 ski2-like helicase; Provisional
Probab=33.27 E-value=31 Score=28.36 Aligned_cols=19 Identities=32% Similarity=0.499 Sum_probs=17.0
Q ss_pred HHhcCCCchHHHHHHHHHH
Q 034973 7 DLAGCPGIVERKVKCLYDT 25 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~~a 25 (77)
.|..+||||..-|++|+++
T Consensus 613 ~L~~ip~~~~~~a~~l~~~ 631 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDA 631 (674)
T ss_pred hhcCCCCCCHHHHHHHHHc
Confidence 4778999999999999975
No 164
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.23 E-value=33 Score=24.90 Aligned_cols=22 Identities=18% Similarity=0.214 Sum_probs=18.0
Q ss_pred hHHhcCCCchHHHHHHHHHHhc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afh 27 (77)
+.|....|+||+.|-.+..++.
T Consensus 73 ~~Li~VsGIGpK~Al~ILs~~~ 94 (183)
T PRK14601 73 EMLLKVNGIGANTAMAVCSSLD 94 (183)
T ss_pred HHHhccCCccHHHHHHHHcCCC
Confidence 3478899999999999977653
No 165
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=32.64 E-value=57 Score=20.30 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=18.8
Q ss_pred HhcCCCchHHHHHHHHHHh-cccccc
Q 034973 8 LAGCPGIVERKVKCLYDTF-HEPFKR 32 (77)
Q Consensus 8 Ls~CPG~G~~KarrL~~af-hePF~k 32 (77)
|..+.|+|+.-|++|.+.- +.||..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s 54 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKS 54 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SS
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCC
Confidence 7789999999999997765 677753
No 166
>PF02828 L27: L27 domain; InterPro: IPR014775 The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein.; PDB: 1ZL8_B 1VA8_A 3LRA_A 3UIT_A 1Y74_D 1RSO_B.
Probab=31.91 E-value=28 Score=20.12 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=23.7
Q ss_pred hhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 5 MEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 5 ~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
-++|..+.+.-..++.-|...|..||.+.
T Consensus 9 L~~L~~~~~~~~~~~~eL~~lL~~p~~~a 37 (56)
T PF02828_consen 9 LEELQSLSSASQEDAQELQQLLQSPHFQA 37 (56)
T ss_dssp HHHHHHHTSSTHHHHHHHHHHHHSHHHHH
T ss_pred HHHHHhccCCChHHHHHHHHHHcCHHHHH
Confidence 36677777777899999999999999654
No 167
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=28.52 E-value=34 Score=24.48 Aligned_cols=19 Identities=32% Similarity=0.428 Sum_probs=17.4
Q ss_pred hHHhcCCCchHHHHHHHHH
Q 034973 6 EDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~ 24 (77)
+||.++-||||+-.+.|.+
T Consensus 67 DDLt~I~GIGPk~e~~Ln~ 85 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNE 85 (133)
T ss_pred ccchhhcccCHHHHHHHHH
Confidence 7999999999999999865
No 168
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=28.14 E-value=49 Score=22.26 Aligned_cols=17 Identities=24% Similarity=0.030 Sum_probs=12.4
Q ss_pred HHhcCCCchHHHHHHHH
Q 034973 7 DLAGCPGIVERKVKCLY 23 (77)
Q Consensus 7 ~Ls~CPG~G~~KarrL~ 23 (77)
....+||||+.=++||-
T Consensus 20 ~V~~laGIG~~lg~~L~ 36 (89)
T PF02961_consen 20 PVTELAGIGPVLGKRLE 36 (89)
T ss_dssp BGGGSTT--HHHHHHHH
T ss_pred CccccCCcCHHHHHHHH
Confidence 35679999999999993
No 169
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=27.28 E-value=65 Score=20.04 Aligned_cols=21 Identities=19% Similarity=0.295 Sum_probs=17.8
Q ss_pred CChhHHhcCCCchHHHHHHHHH
Q 034973 3 ASMEDLAGCPGIVERKVKCLYD 24 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~ 24 (77)
.+.+||-.+ ||++..|+++..
T Consensus 4 v~k~dLi~l-Gf~~~tA~~IIr 24 (59)
T PF11372_consen 4 VTKKDLIEL-GFSESTARDIIR 24 (59)
T ss_pred cCHHHHHHc-CCCHHHHHHHHH
Confidence 467899999 999999999843
No 170
>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=26.93 E-value=54 Score=25.15 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=24.4
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEP 29 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afheP 29 (77)
.|++.+|...-||...||.++.++..+-
T Consensus 30 ~~~~~~L~~~~gls~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 30 MTTRRALCKIKGLSEAKVDKIKEAASKI 57 (313)
T ss_pred hCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence 5789999999999999999998876653
No 171
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=25.44 E-value=54 Score=28.39 Aligned_cols=30 Identities=30% Similarity=0.521 Sum_probs=24.6
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~ 33 (77)
.||++.|..+||+|-+.++.++. ..||...
T Consensus 512 ~~s~~vl~~ipgig~~~~~~I~~--~Rp~~s~ 541 (560)
T COG1031 512 SASKDVLRAIPGIGKKTLRKILA--ERPFKSS 541 (560)
T ss_pred cccHHHHHhcccchhhhHHHHHh--cCCccch
Confidence 47899999999999999998864 5677544
No 172
>PHA02088 hypothetical protein
Probab=25.31 E-value=59 Score=23.07 Aligned_cols=22 Identities=23% Similarity=0.366 Sum_probs=17.2
Q ss_pred hHHhcCCCchHHHHHHHHHHhc
Q 034973 6 EDLAGCPGIVERKVKCLYDTFH 27 (77)
Q Consensus 6 E~Ls~CPG~G~~KarrL~~afh 27 (77)
-+++.|-|||=+|+.+.+.-.+
T Consensus 71 ~~f~~ckgi~frk~yk~l~~ir 92 (125)
T PHA02088 71 AIFSECKGINFRKAYKMLEQIR 92 (125)
T ss_pred cchhhccCccHHHHHHHHHHHh
Confidence 4688999999999877765543
No 173
>PTZ00035 Rad51 protein; Provisional
Probab=24.25 E-value=60 Score=25.13 Aligned_cols=27 Identities=30% Similarity=0.361 Sum_probs=23.1
Q ss_pred CCChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 2 DASMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 2 ~AS~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
.+++.+|+..-||...||..|..+..+
T Consensus 52 ~~~~~~L~~~~gis~~~~~~i~~~~~~ 78 (337)
T PTZ00035 52 YATKKDLCNIKGISEAKVEKIKEAASK 78 (337)
T ss_pred hCCHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 578999999999999999999866544
No 174
>PRK08609 hypothetical protein; Provisional
Probab=24.15 E-value=58 Score=27.08 Aligned_cols=25 Identities=12% Similarity=0.234 Sum_probs=19.7
Q ss_pred ChhHHhcCCCchHHHHHHHHHHhcc
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTFHE 28 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~afhe 28 (77)
+..+|..+||||+.=|+++-+.+.+
T Consensus 46 ~~~~l~~ipgIG~~ia~kI~Eil~t 70 (570)
T PRK08609 46 EIDDFTKLKGIGKGTAEVIQEYRET 70 (570)
T ss_pred hhhhhccCCCcCHHHHHHHHHHHHh
Confidence 4568899999999988877666654
No 175
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=23.71 E-value=49 Score=26.02 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=27.4
Q ss_pred CCChhHHhcCC---Cc--hHHHHHHHHHHhccccccc
Q 034973 2 DASMEDLAGCP---GI--VERKVKCLYDTFHEPFKRV 33 (77)
Q Consensus 2 ~AS~E~Ls~CP---G~--G~~KarrL~~afhePF~k~ 33 (77)
..+.++|..|| |+ |+.|+.-|..++.-.|...
T Consensus 269 gl~L~~l~~ip~vI~vAgG~~K~~AI~aaL~gg~~n~ 305 (321)
T COG2390 269 GLSLDDLRQIPKVIAVAGGESKAEAILAALRGGYINV 305 (321)
T ss_pred cCCHHHHhcCCcEEEEeCCcccHHHHHHHHhCCCCCE
Confidence 45789999999 44 9999999999999888765
No 176
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=22.50 E-value=54 Score=26.02 Aligned_cols=23 Identities=26% Similarity=0.206 Sum_probs=19.9
Q ss_pred ChhHHhcCCCchHHHHHHHHHHh
Q 034973 4 SMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 4 S~E~Ls~CPG~G~~KarrL~~af 26 (77)
..+||...-|+||..++.|.+.=
T Consensus 261 ~~DdL~~I~GiGp~~e~~L~~~G 283 (326)
T PRK12311 261 APDDLKKLTGVSPQIEKKLNDLG 283 (326)
T ss_pred CchhhhhhccCChhhhhhhhhcC
Confidence 45899999999999999997653
No 177
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=21.96 E-value=79 Score=17.45 Aligned_cols=23 Identities=17% Similarity=0.210 Sum_probs=18.9
Q ss_pred HhcCCCchHHHHHHHHHHhcccc
Q 034973 8 LAGCPGIVERKVKCLYDTFHEPF 30 (77)
Q Consensus 8 Ls~CPG~G~~KarrL~~afhePF 30 (77)
|+.+||+.+.--.+|++-|....
T Consensus 18 Ls~~~~~~~~~~~~Ll~HL~~~~ 40 (45)
T smart00511 18 LSQLPGTDPDVRARLLSHLQTHL 40 (45)
T ss_pred HhcCCCCChHHHHHHHHHHHHHH
Confidence 77899999988889988887654
No 178
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=21.67 E-value=87 Score=29.34 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=19.7
Q ss_pred CChhHHhcCCCchHHHHHHHHHHh
Q 034973 3 ASMEDLAGCPGIVERKVKCLYDTF 26 (77)
Q Consensus 3 AS~E~Ls~CPG~G~~KarrL~~af 26 (77)
.+.++|..++|+|++|+.+.-..|
T Consensus 1070 ~T~~eLl~I~GVG~~KlekYG~~f 1093 (1195)
T PLN03137 1070 RTKEELLEINGLGKAKVSKYGDRL 1093 (1195)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHH
Confidence 378999999999999998764444
Done!