Query 035374
Match_columns 66
No_of_seqs 124 out of 1068
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 02:33:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09482 flap endonuclease-lik 99.9 8.5E-25 1.8E-29 151.8 7.2 62 3-65 153-214 (256)
2 smart00475 53EXOc 5'-3' exonuc 99.9 1.8E-24 3.9E-29 149.7 7.3 62 3-65 157-218 (259)
3 PRK14976 5'-3' exonuclease; Pr 99.9 3.2E-24 6.9E-29 149.9 7.3 63 2-65 161-223 (281)
4 cd00008 53EXOc 5'-3' exonuclea 99.9 1.8E-23 3.9E-28 142.7 7.2 62 3-65 154-215 (240)
5 cd00080 HhH2_motif Helix-hairp 99.9 1E-23 2.2E-28 123.1 4.9 52 12-64 2-53 (75)
6 PF01367 5_3_exonuc: 5'-3' exo 99.9 1.3E-25 2.7E-30 138.2 -3.8 51 16-66 1-51 (101)
7 TIGR00593 pola DNA polymerase 99.9 2E-22 4.4E-27 157.1 7.4 63 3-66 156-218 (887)
8 PRK05755 DNA polymerase I; Pro 99.8 1.7E-21 3.7E-26 150.9 7.5 62 3-65 158-219 (880)
9 COG0258 Exo 5'-3' exonuclease 99.8 6.9E-21 1.5E-25 133.4 7.4 61 4-64 169-229 (310)
10 smart00279 HhH2 Helix-hairpin- 99.8 1.3E-19 2.9E-24 93.6 4.2 36 18-53 1-36 (36)
11 PTZ00217 flap endonuclease-1; 99.8 8.4E-19 1.8E-23 127.4 7.0 60 3-65 208-267 (393)
12 PRK03980 flap endonuclease-1; 99.8 1.2E-18 2.6E-23 122.5 7.1 58 3-63 162-219 (292)
13 TIGR03674 fen_arch flap struct 99.7 4.2E-18 9E-23 121.4 7.3 59 3-64 209-267 (338)
14 cd00128 XPG Xeroderma pigmento 99.7 9.7E-18 2.1E-22 117.3 6.9 59 2-63 195-253 (316)
15 PHA00439 exonuclease 99.5 4.2E-15 9.2E-20 105.0 3.8 45 17-62 172-219 (286)
16 TIGR00600 rad2 DNA excision re 99.4 6.8E-13 1.5E-17 105.5 6.8 55 3-60 839-895 (1034)
17 KOG2519 5'-3' exonuclease [Rep 99.3 1.3E-11 2.8E-16 91.5 6.2 57 2-61 201-257 (449)
18 PHA02567 rnh RnaseH; Provision 98.6 3.5E-08 7.5E-13 70.6 3.9 35 4-40 173-207 (304)
19 KOG2518 5'-3' exonuclease [Rep 98.5 1.3E-07 2.9E-12 71.7 5.0 44 16-61 210-253 (556)
20 KOG2520 5'-3' exonuclease [Rep 98.3 1E-06 2.2E-11 69.5 5.9 50 2-54 532-581 (815)
21 PF12826 HHH_2: Helix-hairpin- 98.2 9.4E-07 2E-11 49.9 2.0 25 37-61 7-31 (64)
22 PRK14667 uvrC excinuclease ABC 97.7 2.2E-05 4.7E-10 60.0 2.7 29 34-62 515-543 (567)
23 TIGR00194 uvrC excinuclease AB 97.7 3.2E-05 7E-10 59.1 3.1 30 34-63 542-571 (574)
24 PRK14670 uvrC excinuclease ABC 97.6 4.3E-05 9.4E-10 58.5 3.1 30 33-62 514-543 (574)
25 PRK14669 uvrC excinuclease ABC 97.6 4.3E-05 9.3E-10 59.0 2.8 29 34-62 553-581 (624)
26 PRK14672 uvrC excinuclease ABC 97.4 0.00016 3.4E-09 56.6 3.4 29 34-62 609-637 (691)
27 PF14520 HHH_5: Helix-hairpin- 97.3 0.00023 4.9E-09 39.2 2.8 27 36-62 8-35 (60)
28 PRK14671 uvrC excinuclease ABC 97.2 0.00027 5.9E-09 54.5 3.2 29 34-62 570-598 (621)
29 TIGR00084 ruvA Holliday juncti 97.1 0.00097 2.1E-08 44.7 4.7 43 10-61 57-99 (191)
30 PRK00558 uvrC excinuclease ABC 97.1 0.00038 8.2E-09 53.4 2.7 29 34-62 544-572 (598)
31 PRK14668 uvrC excinuclease ABC 97.1 0.00039 8.4E-09 53.3 2.8 30 33-62 525-554 (577)
32 PRK12766 50S ribosomal protein 97.1 0.00057 1.2E-08 47.6 3.3 29 34-62 4-33 (232)
33 PF00633 HHH: Helix-hairpin-he 97.1 0.00014 3E-09 35.9 0.2 20 32-51 10-29 (30)
34 COG0322 UvrC Nuclease subunit 97.1 0.00061 1.3E-08 52.4 3.7 48 12-63 513-560 (581)
35 PRK00116 ruvA Holliday junctio 97.0 0.0006 1.3E-08 45.5 2.9 25 37-61 77-104 (192)
36 PRK14666 uvrC excinuclease ABC 97.0 0.00054 1.2E-08 53.7 2.6 29 34-62 638-666 (694)
37 PRK14601 ruvA Holliday junctio 97.0 0.0012 2.5E-08 44.3 3.9 42 9-52 86-127 (183)
38 PF10391 DNA_pol_lambd_f: Fing 96.9 0.0014 3E-08 35.9 3.4 26 36-61 5-31 (52)
39 PRK14605 ruvA Holliday junctio 96.9 0.0025 5.4E-08 42.8 4.9 44 9-61 57-100 (194)
40 PRK14602 ruvA Holliday junctio 96.9 0.0024 5.2E-08 43.2 4.9 41 11-60 60-100 (203)
41 PRK14600 ruvA Holliday junctio 96.9 0.0021 4.6E-08 43.1 4.4 34 16-52 93-126 (186)
42 PRK13901 ruvA Holliday junctio 96.7 0.0022 4.8E-08 43.5 3.8 40 11-52 87-126 (196)
43 PRK14602 ruvA Holliday junctio 96.7 0.0018 3.9E-08 43.8 3.4 43 9-53 87-129 (203)
44 smart00278 HhH1 Helix-hairpin- 96.7 0.0014 3E-08 30.9 1.8 18 35-52 3-20 (26)
45 PRK14601 ruvA Holliday junctio 96.7 0.0035 7.6E-08 42.0 4.3 48 7-63 55-102 (183)
46 PRK13901 ruvA Holliday junctio 96.6 0.0038 8.3E-08 42.4 4.4 48 7-63 54-101 (196)
47 PRK14604 ruvA Holliday junctio 96.6 0.0037 8.1E-08 42.1 4.3 19 34-52 109-127 (195)
48 PRK14604 ruvA Holliday junctio 96.6 0.0029 6.2E-08 42.7 3.5 48 7-63 55-102 (195)
49 PRK14606 ruvA Holliday junctio 96.6 0.0044 9.5E-08 41.6 4.3 35 16-52 93-127 (188)
50 PRK14606 ruvA Holliday junctio 96.6 0.003 6.6E-08 42.3 3.5 48 7-63 55-102 (188)
51 PRK14600 ruvA Holliday junctio 96.6 0.0051 1.1E-07 41.2 4.6 49 6-63 54-102 (186)
52 PRK14603 ruvA Holliday junctio 96.6 0.0045 9.7E-08 41.7 4.3 36 16-53 92-127 (197)
53 PRK14603 ruvA Holliday junctio 96.5 0.0031 6.8E-08 42.5 3.4 48 7-63 54-101 (197)
54 PF00867 XPG_I: XPG I-region; 96.5 0.0029 6.2E-08 37.6 2.6 28 2-30 66-93 (94)
55 TIGR00575 dnlj DNA ligase, NAD 96.4 0.003 6.6E-08 49.0 3.0 26 37-62 502-527 (652)
56 COG1948 MUS81 ERCC4-type nucle 96.3 0.0044 9.4E-08 43.7 3.1 27 36-62 185-211 (254)
57 PRK14351 ligA NAD-dependent DN 96.2 0.0049 1.1E-07 48.3 3.3 26 37-62 532-557 (689)
58 PRK13482 DNA integrity scannin 96.1 0.017 3.6E-07 42.4 5.3 58 5-62 242-316 (352)
59 COG0632 RuvA Holliday junction 96.0 0.017 3.6E-07 39.4 4.9 47 6-61 54-100 (201)
60 PF02371 Transposase_20: Trans 96.0 0.0062 1.3E-07 35.7 2.3 27 34-60 3-29 (87)
61 TIGR01259 comE comEA protein. 95.9 0.0081 1.8E-07 37.5 2.7 26 35-60 70-101 (120)
62 TIGR00084 ruvA Holliday juncti 95.9 0.013 2.9E-07 39.2 3.9 47 4-52 80-126 (191)
63 TIGR00596 rad1 DNA repair prot 95.8 0.0076 1.6E-07 48.0 2.8 29 34-62 758-786 (814)
64 PRK07956 ligA NAD-dependent DN 95.7 0.01 2.2E-07 46.3 2.9 26 37-62 515-540 (665)
65 PRK13766 Hef nuclease; Provisi 95.6 0.012 2.6E-07 45.4 3.3 28 35-62 717-744 (773)
66 COG0632 RuvA Holliday junction 95.6 0.027 5.9E-07 38.4 4.4 44 9-54 86-129 (201)
67 PRK14605 ruvA Holliday junctio 95.4 0.017 3.8E-07 38.7 3.1 35 16-52 93-127 (194)
68 PRK02515 psbU photosystem II c 95.4 0.016 3.5E-07 37.4 2.7 26 36-61 64-91 (132)
69 smart00483 POLXc DNA polymeras 95.1 0.024 5.2E-07 40.6 3.1 29 35-63 91-120 (334)
70 PF12826 HHH_2: Helix-hairpin- 94.9 0.004 8.7E-08 34.9 -1.0 33 26-58 28-60 (64)
71 PF11798 IMS_HHH: IMS family H 94.8 0.019 4.1E-07 28.3 1.5 16 34-49 12-27 (32)
72 PRK08609 hypothetical protein; 94.6 0.041 8.8E-07 42.1 3.4 28 36-63 91-120 (570)
73 cd00141 NT_POLXc Nucleotidyltr 94.6 0.043 9.3E-07 38.9 3.3 27 36-62 88-115 (307)
74 PF14520 HHH_5: Helix-hairpin- 94.3 0.016 3.4E-07 31.7 0.4 22 32-53 37-58 (60)
75 COG0272 Lig NAD-dependent DNA 94.2 0.035 7.6E-07 43.7 2.3 27 36-62 514-540 (667)
76 COG1555 ComEA DNA uptake prote 94.1 0.053 1.2E-06 35.1 2.8 25 36-60 100-130 (149)
77 TIGR00426 competence protein C 94.1 0.078 1.7E-06 29.6 3.1 15 38-52 22-36 (69)
78 PRK00254 ski2-like helicase; P 93.6 0.057 1.2E-06 41.8 2.5 29 34-62 646-675 (720)
79 TIGR02236 recomb_radA DNA repa 93.5 0.089 1.9E-06 36.6 3.1 26 36-61 2-28 (310)
80 TIGR01448 recD_rel helicase, p 93.2 0.079 1.7E-06 41.5 2.8 37 17-61 76-114 (720)
81 COG0177 Nth Predicted EndoIII- 92.7 0.24 5.3E-06 34.0 4.2 20 36-55 112-132 (211)
82 KOG2841 Structure-specific end 92.4 0.1 2.3E-06 36.8 2.2 29 35-63 197-225 (254)
83 PRK00116 ruvA Holliday junctio 90.9 0.31 6.6E-06 32.5 3.1 23 33-55 108-130 (192)
84 COG0353 RecR Recombinational D 90.9 0.07 1.5E-06 36.5 0.0 17 34-50 13-29 (198)
85 TIGR03252 uncharacterized HhH- 90.4 0.16 3.5E-06 34.1 1.5 22 34-55 116-137 (177)
86 PRK00076 recR recombination pr 90.3 0.18 3.9E-06 34.3 1.6 18 35-52 13-30 (196)
87 TIGR00615 recR recombination p 90.3 0.18 3.9E-06 34.3 1.6 18 34-51 12-29 (195)
88 PRK13844 recombination protein 89.6 0.22 4.8E-06 34.1 1.6 19 34-52 16-34 (200)
89 PRK14350 ligA NAD-dependent DN 89.5 0.39 8.4E-06 37.8 3.1 25 37-61 506-531 (669)
90 PF13052 DUF3913: Protein of u 89.2 0.21 4.6E-06 27.5 1.1 29 27-58 14-42 (57)
91 PRK04301 radA DNA repair and r 88.9 0.36 7.9E-06 33.8 2.4 28 34-61 7-35 (317)
92 PF14716 HHH_8: Helix-hairpin- 88.9 0.36 7.9E-06 27.0 1.9 15 35-49 49-63 (68)
93 PF04919 DUF655: Protein of un 88.3 0.63 1.4E-05 31.5 3.1 45 17-61 97-149 (181)
94 PRK10702 endonuclease III; Pro 88.0 0.83 1.8E-05 31.0 3.6 19 34-52 110-128 (211)
95 KOG2841 Structure-specific end 88.0 0.54 1.2E-05 33.3 2.7 42 5-54 207-248 (254)
96 PF11731 Cdd1: Pathogenicity l 87.9 0.58 1.3E-05 28.5 2.5 26 35-60 14-40 (93)
97 PRK13910 DNA glycosylase MutY; 87.8 1 2.3E-05 32.0 4.1 19 33-51 72-90 (289)
98 PRK01229 N-glycosylase/DNA lya 87.8 0.45 9.8E-06 32.5 2.2 18 37-54 123-140 (208)
99 cd00056 ENDO3c endonuclease II 86.9 0.48 1E-05 29.7 1.8 18 35-52 85-102 (158)
100 PRK13482 DNA integrity scannin 86.7 0.4 8.7E-06 35.3 1.5 35 7-49 301-335 (352)
101 PRK13913 3-methyladenine DNA g 86.2 0.53 1.1E-05 32.3 1.9 17 35-51 123-139 (218)
102 PF00416 Ribosomal_S13: Riboso 85.9 0.72 1.6E-05 28.1 2.2 19 36-54 18-36 (107)
103 TIGR01084 mutY A/G-specific ad 85.8 1.6 3.6E-05 30.7 4.2 18 34-51 106-123 (275)
104 PF12836 HHH_3: Helix-hairpin- 85.7 1.5 3.3E-05 24.2 3.3 15 34-48 45-59 (65)
105 COG1491 Predicted RNA-binding 84.9 1.2 2.5E-05 30.7 3.0 44 18-61 112-163 (202)
106 PF14579 HHH_6: Helix-hairpin- 84.8 1.3 2.8E-05 25.9 2.9 28 35-62 29-61 (90)
107 smart00478 ENDO3c endonuclease 84.6 0.75 1.6E-05 28.6 1.9 19 34-52 73-91 (149)
108 PF14490 HHH_4: Helix-hairpin- 84.1 5.6 0.00012 23.4 5.4 46 8-54 13-67 (94)
109 TIGR01083 nth endonuclease III 84.0 0.74 1.6E-05 30.3 1.7 19 34-52 107-125 (191)
110 PRK10880 adenine DNA glycosyla 83.5 2.2 4.8E-05 31.2 4.1 22 33-54 109-131 (350)
111 PRK10736 hypothetical protein; 83.4 1.1 2.4E-05 33.1 2.5 22 37-58 12-33 (374)
112 PF14229 DUF4332: Domain of un 82.4 4.9 0.00011 24.9 4.9 47 8-60 34-81 (122)
113 PTZ00134 40S ribosomal protein 82.2 2.1 4.5E-05 28.2 3.3 36 19-54 9-51 (154)
114 KOG1921 Endonuclease III [Repl 80.6 2.7 5.8E-05 30.2 3.6 17 36-52 162-178 (286)
115 COG1194 MutY A/G-specific DNA 80.1 3 6.5E-05 30.7 3.8 35 7-52 98-132 (342)
116 PRK12766 50S ribosomal protein 79.6 0.5 1.1E-05 33.1 -0.3 35 24-58 27-61 (232)
117 PF04760 IF2_N: Translation in 76.9 3.7 8E-05 21.7 2.7 51 1-54 1-52 (54)
118 KOG2534 DNA polymerase IV (fam 76.7 1.8 4E-05 31.9 1.8 29 36-64 100-129 (353)
119 COG1796 POL4 DNA polymerase IV 76.4 6.7 0.00015 28.8 4.6 44 20-63 80-125 (326)
120 COG1555 ComEA DNA uptake prote 75.8 5 0.00011 25.9 3.6 47 5-52 95-146 (149)
121 COG1936 Predicted nucleotide k 75.7 2.3 5.1E-05 28.8 2.0 20 35-54 5-24 (180)
122 PRK10308 3-methyl-adenine DNA 75.5 2.1 4.5E-05 30.2 1.8 24 34-57 208-232 (283)
123 COG3743 Uncharacterized conser 74.7 2.1 4.5E-05 27.8 1.5 21 33-54 67-87 (133)
124 PF14635 HHH_7: Helix-hairpin- 73.9 3 6.6E-05 25.7 2.1 20 35-54 52-71 (104)
125 PRK08097 ligB NAD-dependent DN 73.5 3.8 8.2E-05 31.9 2.9 34 24-57 511-544 (562)
126 PRK07956 ligA NAD-dependent DN 73.5 1.9 4.2E-05 33.9 1.4 32 26-57 536-567 (665)
127 PRK00024 hypothetical protein; 73.1 2.5 5.3E-05 28.9 1.7 15 35-49 68-82 (224)
128 PRK14180 bifunctional 5,10-met 73.0 2.8 6.1E-05 29.9 2.0 19 34-52 253-272 (282)
129 TIGR03631 bact_S13 30S ribosom 72.7 3 6.5E-05 25.9 1.8 20 35-54 17-36 (113)
130 PRK05179 rpsM 30S ribosomal pr 72.5 3.4 7.3E-05 26.0 2.1 20 35-54 19-38 (122)
131 TIGR00588 ogg 8-oxoguanine DNA 72.3 2.7 5.8E-05 29.9 1.8 17 36-52 223-239 (310)
132 PF12482 DUF3701: Phage integr 72.2 5.5 0.00012 24.3 2.9 47 11-59 30-76 (96)
133 CHL00137 rps13 ribosomal prote 71.7 3.6 7.8E-05 25.9 2.1 19 36-54 20-38 (122)
134 TIGR00575 dnlj DNA ligase, NAD 71.2 2.2 4.8E-05 33.4 1.3 26 32-57 529-554 (652)
135 PRK08097 ligB NAD-dependent DN 71.2 3.2 7E-05 32.2 2.1 22 37-61 495-516 (562)
136 PRK14175 bifunctional 5,10-met 70.8 4.3 9.4E-05 28.9 2.5 19 34-52 254-273 (286)
137 COG1948 MUS81 ERCC4-type nucle 70.0 4.4 9.6E-05 28.7 2.4 31 33-63 214-244 (254)
138 PRK14973 DNA topoisomerase I; 69.8 7.8 0.00017 31.8 4.0 59 3-62 831-907 (936)
139 cd01702 PolY_Pol_eta DNA Polym 69.3 3.9 8.5E-05 29.5 2.1 28 34-61 183-212 (359)
140 PF02961 BAF: Barrier to autoi 69.1 5.6 0.00012 24.1 2.4 23 28-52 16-38 (89)
141 PRK14350 ligA NAD-dependent DN 68.8 5.9 0.00013 31.4 3.1 25 33-57 541-565 (669)
142 TIGR00608 radc DNA repair prot 68.1 3.7 8.1E-05 28.1 1.7 20 33-52 60-79 (218)
143 COG4277 Predicted DNA-binding 68.1 3.5 7.5E-05 30.7 1.6 17 36-52 333-349 (404)
144 COG0122 AlkA 3-methyladenine D 67.7 3.9 8.5E-05 29.0 1.8 18 35-52 200-217 (285)
145 TIGR03629 arch_S13P archaeal r 67.1 4.8 0.0001 26.1 2.0 19 36-54 24-42 (144)
146 COG2019 AdkA Archaeal adenylat 66.1 4.4 9.6E-05 27.6 1.7 18 35-52 9-26 (189)
147 PRK14666 uvrC excinuclease ABC 65.9 3.3 7.1E-05 33.1 1.2 24 32-55 668-691 (694)
148 PRK04053 rps13p 30S ribosomal 65.5 5.8 0.00013 25.9 2.1 36 19-54 4-46 (149)
149 PRK02362 ski2-like helicase; P 63.8 8.3 0.00018 30.2 3.0 27 35-61 654-681 (737)
150 PRK14351 ligA NAD-dependent DN 63.7 4.4 9.6E-05 32.1 1.5 27 31-57 558-584 (689)
151 PRK00558 uvrC excinuclease ABC 62.7 8.5 0.00018 29.9 2.9 40 7-54 557-596 (598)
152 COG1031 Uncharacterized Fe-S o 60.5 4.1 8.8E-05 31.7 0.8 30 33-62 516-547 (560)
153 KOG2379 Endonuclease MUS81 [Re 59.4 12 0.00025 29.0 3.1 29 35-63 432-460 (501)
154 PF12244 DUF3606: Protein of u 58.7 16 0.00034 20.0 2.8 27 4-31 21-47 (57)
155 COG1415 Uncharacterized conser 58.4 16 0.00035 27.3 3.6 38 3-52 260-299 (373)
156 COG2003 RadC DNA repair protei 58.3 8.4 0.00018 26.9 2.0 17 33-49 66-82 (224)
157 TIGR01448 recD_rel helicase, p 57.7 12 0.00027 29.5 3.1 26 32-57 116-141 (720)
158 PF00165 HTH_AraC: Bacterial r 56.6 12 0.00026 18.5 2.0 19 4-23 9-27 (42)
159 COG1796 POL4 DNA polymerase IV 55.7 14 0.00031 27.1 2.9 20 34-53 129-148 (326)
160 PRK14178 bifunctional 5,10-met 55.6 13 0.00029 26.5 2.7 19 34-52 247-266 (279)
161 PRK00254 ski2-like helicase; P 55.4 5 0.00011 31.3 0.6 24 32-55 677-700 (720)
162 PRK14189 bifunctional 5,10-met 55.3 9.8 0.00021 27.2 2.0 18 35-52 255-273 (285)
163 PRK07373 DNA polymerase III su 54.0 19 0.00041 27.2 3.4 29 35-63 116-150 (449)
164 COG5241 RAD10 Nucleotide excis 53.6 11 0.00023 26.2 1.9 30 23-52 189-218 (224)
165 COG0272 Lig NAD-dependent DNA 52.9 11 0.00025 30.1 2.2 38 20-57 530-567 (667)
166 PRK07945 hypothetical protein; 52.0 11 0.00023 27.1 1.7 18 34-51 50-67 (335)
167 cd07321 Extradiol_Dioxygenase_ 51.8 23 0.0005 20.4 2.9 17 5-22 25-41 (77)
168 PRK01172 ski2-like helicase; P 51.5 15 0.00033 28.3 2.7 29 34-62 613-642 (674)
169 PF03118 RNA_pol_A_CTD: Bacter 51.4 15 0.00032 20.5 2.0 20 33-52 44-63 (66)
170 PF07726 AAA_3: ATPase family 51.2 7.8 0.00017 24.9 0.9 19 35-53 4-22 (131)
171 COG1623 Predicted nucleic-acid 50.0 19 0.0004 26.6 2.8 28 35-62 295-322 (349)
172 COG0099 RpsM Ribosomal protein 49.5 14 0.0003 23.6 1.8 18 37-54 21-38 (121)
173 PRK08609 hypothetical protein; 49.3 21 0.00046 27.5 3.1 20 33-52 123-142 (570)
174 PF09293 RNaseH_C: T4 RNase H, 48.2 8.7 0.00019 24.5 0.7 26 17-42 2-27 (122)
175 COG0190 FolD 5,10-methylene-te 48.0 18 0.00039 26.0 2.4 19 34-52 252-271 (283)
176 PF12844 HTH_19: Helix-turn-he 47.5 11 0.00024 19.8 1.1 48 4-62 13-61 (64)
177 PRK14181 bifunctional 5,10-met 47.0 17 0.00038 26.0 2.2 19 34-52 258-277 (287)
178 PRK14194 bifunctional 5,10-met 46.9 15 0.00033 26.4 1.9 19 34-52 258-277 (301)
179 PF13238 AAA_18: AAA domain; P 46.0 15 0.00032 21.1 1.5 19 35-53 3-21 (129)
180 smart00153 VHP Villin headpiec 45.4 27 0.00059 17.5 2.2 19 4-23 2-20 (36)
181 PF00570 HRDC: HRDC domain Blo 45.3 13 0.00028 19.9 1.1 32 17-48 28-59 (68)
182 TIGR01954 nusA_Cterm_rpt trans 44.9 9.3 0.0002 19.3 0.4 27 26-52 19-45 (50)
183 PF02209 VHP: Villin headpiece 44.1 26 0.00057 17.6 2.0 20 4-24 2-21 (36)
184 PF02742 Fe_dep_repr_C: Iron d 43.7 15 0.00033 20.4 1.2 19 42-60 4-22 (71)
185 cd01703 PolY_Pol_iota DNA Poly 43.5 19 0.00041 26.3 2.0 26 34-59 173-199 (379)
186 PF01798 Nop: Putative snoRNA 43.4 23 0.0005 23.0 2.2 20 41-60 38-57 (150)
187 TIGR00041 DTMP_kinase thymidyl 42.9 21 0.00045 22.6 1.9 19 35-53 8-26 (195)
188 PF13207 AAA_17: AAA domain; P 42.3 18 0.00039 20.9 1.5 19 35-53 4-22 (121)
189 PRK01184 hypothetical protein; 42.3 27 0.00059 22.0 2.4 20 35-54 6-25 (184)
190 COG0685 MetF 5,10-methylenetet 42.0 32 0.00068 24.3 2.9 51 5-56 175-225 (291)
191 PF01476 LysM: LysM domain; I 41.7 39 0.00084 16.3 2.5 20 5-25 8-27 (44)
192 PRK05672 dnaE2 error-prone DNA 41.4 35 0.00075 28.5 3.3 28 35-62 818-850 (1046)
193 PF13411 MerR_1: MerR HTH fami 41.1 36 0.00077 18.0 2.5 24 4-29 1-24 (69)
194 PRK13973 thymidylate kinase; P 40.7 23 0.00049 23.3 1.9 19 35-53 8-26 (213)
195 PRK14670 uvrC excinuclease ABC 40.4 20 0.00043 28.0 1.8 24 31-54 544-567 (574)
196 COG3547 Transposase and inacti 39.5 31 0.00067 23.3 2.4 27 35-61 190-219 (303)
197 cd04761 HTH_MerR-SF Helix-Turn 39.3 48 0.001 16.2 2.7 24 4-29 1-24 (49)
198 COG2012 RPB5 DNA-directed RNA 39.0 14 0.00031 22.0 0.6 19 6-25 26-44 (80)
199 smart00422 HTH_MERR helix_turn 38.7 46 0.001 17.5 2.7 22 4-26 1-22 (70)
200 PRK07758 hypothetical protein; 38.6 17 0.00037 22.2 1.0 30 23-52 57-86 (95)
201 PF04255 DUF433: Protein of un 38.3 54 0.0012 17.4 2.9 21 4-24 32-52 (56)
202 cd07922 CarBa CarBa is the A s 38.3 49 0.0011 19.5 2.9 17 5-22 26-42 (81)
203 PF05559 DUF763: Protein of un 38.0 44 0.00096 24.5 3.2 30 11-52 259-290 (319)
204 PF00004 AAA: ATPase family as 38.0 38 0.00082 19.4 2.4 19 36-54 4-22 (132)
205 PF07037 DUF1323: Putative tra 37.7 71 0.0015 20.4 3.7 36 4-40 1-36 (122)
206 PF04994 TfoX_C: TfoX C-termin 37.3 31 0.00066 20.0 1.9 28 33-60 3-31 (81)
207 TIGR01405 polC_Gram_pos DNA po 36.9 41 0.00089 28.6 3.2 27 35-61 1152-1183(1213)
208 PRK08306 dipicolinate synthase 36.5 43 0.00093 23.5 2.8 25 35-61 262-287 (296)
209 PTZ00205 DNA polymerase kappa; 35.9 22 0.00048 27.9 1.4 26 34-60 310-337 (571)
210 PF11762 Arabinose_Iso_C: L-ar 35.6 29 0.00063 22.0 1.7 17 13-30 94-110 (115)
211 PRK00448 polC DNA polymerase I 35.0 46 0.00099 28.9 3.2 27 35-61 1375-1406(1437)
212 TIGR03643 conserved hypothetic 35.0 57 0.0012 19.1 2.7 19 5-24 15-33 (72)
213 PF13276 HTH_21: HTH-like doma 34.5 38 0.00082 17.9 1.9 15 40-54 37-51 (60)
214 PRK12278 50S ribosomal protein 33.9 27 0.00059 24.2 1.5 21 32-52 157-177 (221)
215 PRK13766 Hef nuclease; Provisi 33.7 17 0.00036 28.4 0.4 22 33-54 747-768 (773)
216 COG0125 Tmk Thymidylate kinase 33.6 34 0.00074 23.1 1.9 19 35-53 8-26 (208)
217 PF13604 AAA_30: AAA domain; P 33.1 53 0.0011 21.4 2.7 37 16-52 2-40 (196)
218 PF10985 DUF2805: Protein of u 32.8 64 0.0014 18.9 2.7 19 5-24 14-32 (73)
219 cd08305 Pyrin Pyrin: a protein 32.6 98 0.0021 17.5 4.1 40 15-57 7-51 (73)
220 PF14270 DUF4358: Domain of un 32.5 29 0.00063 20.6 1.3 28 1-29 12-39 (106)
221 COG2231 Uncharacterized protei 32.4 30 0.00066 24.1 1.5 16 36-51 118-133 (215)
222 cd01672 TMPK Thymidine monopho 32.1 38 0.00083 20.9 1.9 19 35-53 5-23 (200)
223 PRK03858 DNA polymerase IV; Va 32.1 33 0.00072 24.6 1.7 26 34-60 174-201 (396)
224 PRK13975 thymidylate kinase; P 31.8 39 0.00084 21.3 1.9 19 35-53 7-25 (196)
225 PRK10917 ATP-dependent DNA hel 31.7 31 0.00068 27.0 1.6 27 34-61 10-38 (681)
226 cd01673 dNK Deoxyribonucleosid 31.6 39 0.00085 21.3 1.9 19 35-53 4-22 (193)
227 PF01527 HTH_Tnp_1: Transposas 31.6 56 0.0012 17.5 2.3 23 5-28 25-47 (76)
228 PF08671 SinI: Anti-repressor 31.5 70 0.0015 15.5 2.4 15 11-26 13-27 (30)
229 PLN02924 thymidylate kinase 31.4 39 0.00085 22.7 1.9 19 35-53 21-39 (220)
230 PRK12311 rpsB 30S ribosomal pr 31.2 25 0.00054 25.7 1.0 21 32-52 262-282 (326)
231 cd07923 Gallate_dioxygenase_C 31.1 44 0.00095 20.4 1.9 17 5-22 27-43 (94)
232 PRK14552 C/D box methylation g 31.1 44 0.00096 25.1 2.3 32 27-60 258-289 (414)
233 PRK06369 nac nascent polypepti 30.8 55 0.0012 20.6 2.4 22 38-59 2-24 (115)
234 KOG2875 8-oxoguanine DNA glyco 30.7 22 0.00049 26.0 0.7 39 6-49 192-234 (323)
235 PF07746 LigA: Aromatic-ring-o 30.6 28 0.0006 20.7 1.0 17 5-22 20-36 (88)
236 smart00341 HRDC Helicase and R 30.5 69 0.0015 17.4 2.6 31 18-48 32-62 (81)
237 PRK13976 thymidylate kinase; P 30.4 42 0.00091 22.4 1.9 19 35-53 5-23 (209)
238 TIGR00180 parB_part ParB-like 30.4 70 0.0015 20.8 2.9 55 4-59 121-178 (187)
239 PHA03134 thymidine kinase; Pro 30.3 39 0.00084 24.9 1.9 23 33-55 16-38 (340)
240 PRK07279 dnaE DNA polymerase I 30.2 51 0.0011 27.7 2.7 29 35-63 752-782 (1034)
241 TIGR01764 excise DNA binding d 29.9 73 0.0016 15.2 2.9 22 4-26 2-23 (49)
242 cd01104 HTH_MlrA-CarA Helix-Tu 29.8 86 0.0019 16.4 2.8 25 4-29 1-25 (68)
243 TIGR02054 MerD mercuric resist 29.8 76 0.0016 19.7 2.9 25 1-26 1-25 (120)
244 PF10668 Phage_terminase: Phag 29.7 85 0.0018 17.5 2.8 22 4-26 23-44 (60)
245 PRK02406 DNA polymerase IV; Va 29.2 43 0.00094 23.5 1.9 27 34-61 169-197 (343)
246 PRK05673 dnaE DNA polymerase I 28.9 70 0.0015 27.0 3.3 28 35-62 822-855 (1135)
247 TIGR00594 polc DNA-directed DN 28.9 73 0.0016 26.6 3.4 28 35-62 826-859 (1022)
248 PRK06826 dnaE DNA polymerase I 28.9 71 0.0015 27.1 3.3 29 35-63 826-860 (1151)
249 PF13518 HTH_28: Helix-turn-he 28.8 83 0.0018 15.5 2.9 21 5-26 14-34 (52)
250 TIGR01359 UMP_CMP_kin_fam UMP- 28.7 61 0.0013 20.2 2.4 19 36-54 5-24 (183)
251 PRK14182 bifunctional 5,10-met 28.5 48 0.001 23.7 2.0 19 34-52 253-272 (282)
252 PHA03135 thymidine kinase; Pro 28.5 43 0.00093 24.7 1.8 21 34-54 14-34 (343)
253 PF12833 HTH_18: Helix-turn-he 28.3 60 0.0013 17.6 2.1 12 9-21 67-78 (81)
254 cd04764 HTH_MlrA-like_sg1 Heli 28.1 88 0.0019 16.6 2.7 22 4-26 1-22 (67)
255 PRK03348 DNA polymerase IV; Pr 28.1 50 0.0011 24.6 2.1 26 34-60 181-208 (454)
256 PF02223 Thymidylate_kin: Thym 28.0 41 0.00089 21.2 1.5 19 35-53 1-19 (186)
257 PRK06920 dnaE DNA polymerase I 28.0 74 0.0016 26.9 3.2 28 35-62 804-836 (1107)
258 PF12668 DUF3791: Protein of u 27.8 82 0.0018 17.0 2.5 21 40-60 16-36 (62)
259 PF03564 DUF1759: Protein of u 27.7 50 0.0011 20.1 1.8 38 25-62 36-76 (145)
260 PRK13749 transcriptional regul 27.4 89 0.0019 19.5 2.9 25 1-26 1-25 (121)
261 PRK07374 dnaE DNA polymerase I 27.3 79 0.0017 26.9 3.3 29 35-63 837-871 (1170)
262 cd01701 PolY_Rev1 DNA polymera 27.3 46 0.00099 24.3 1.8 27 34-60 223-250 (404)
263 PRK09570 rpoH DNA-directed RNA 27.2 18 0.0004 21.3 -0.2 22 6-30 23-44 (79)
264 PF09012 FeoC: FeoC like trans 27.1 94 0.002 16.9 2.7 26 3-29 14-42 (69)
265 PRK05472 redox-sensing transcr 26.8 1.2E+02 0.0026 19.9 3.7 35 3-43 32-66 (213)
266 PF06056 Terminase_5: Putative 26.4 1.2E+02 0.0026 16.5 3.9 43 4-49 14-56 (58)
267 COG2361 Uncharacterized conser 26.2 1.7E+02 0.0037 18.5 4.0 41 6-52 57-97 (117)
268 PF10213 MRP-S28: Mitochondria 26.2 95 0.0021 19.5 2.9 24 11-35 36-59 (127)
269 PRK03352 DNA polymerase IV; Va 26.2 45 0.00097 23.5 1.5 27 34-61 178-206 (346)
270 PF14117 DUF4287: Domain of un 26.1 93 0.002 17.3 2.5 23 6-29 6-28 (61)
271 PRK04040 adenylate kinase; Pro 26.1 61 0.0013 21.1 2.1 19 35-53 7-25 (188)
272 PF02777 Sod_Fe_C: Iron/mangan 26.0 89 0.0019 18.4 2.7 21 43-63 5-25 (106)
273 PF04218 CENP-B_N: CENP-B N-te 25.8 68 0.0015 16.9 1.9 19 6-25 25-43 (53)
274 cd04763 HTH_MlrA-like Helix-Tu 25.7 1.1E+02 0.0024 16.2 2.8 25 4-29 1-25 (68)
275 PF04539 Sigma70_r3: Sigma-70 25.6 1.2E+02 0.0027 16.4 3.5 24 5-29 22-45 (78)
276 COG5051 RPL36A Ribosomal prote 25.3 55 0.0012 20.0 1.6 24 41-64 64-88 (97)
277 cd04762 HTH_MerR-trunc Helix-T 25.2 90 0.0019 14.7 2.9 24 4-29 1-24 (49)
278 PF14501 HATPase_c_5: GHKL dom 24.9 73 0.0016 18.2 2.1 19 37-55 64-82 (100)
279 PRK12373 NADH dehydrogenase su 24.7 45 0.00097 25.1 1.4 24 29-52 319-342 (400)
280 PRK05898 dnaE DNA polymerase I 24.5 96 0.0021 26.0 3.3 28 34-61 753-785 (971)
281 cd07921 PCA_45_Doxase_A_like S 24.4 67 0.0015 20.0 1.9 17 5-22 35-51 (106)
282 PRK07135 dnaE DNA polymerase I 24.2 1.1E+02 0.0024 25.6 3.5 29 35-63 755-789 (973)
283 PF12728 HTH_17: Helix-turn-he 24.2 1.1E+02 0.0024 15.3 2.9 33 4-43 2-34 (51)
284 PRK10265 chaperone-modulator p 23.8 1.1E+02 0.0024 18.2 2.8 24 2-26 6-29 (101)
285 PRK10014 DNA-binding transcrip 23.8 2.4E+02 0.0051 19.0 4.9 37 4-51 7-43 (342)
286 PF06971 Put_DNA-bind_N: Putat 23.6 1.1E+02 0.0025 16.2 2.5 19 3-22 28-46 (50)
287 PF14129 DUF4296: Domain of un 23.5 84 0.0018 18.0 2.2 17 7-24 40-56 (87)
288 PRK06762 hypothetical protein; 23.5 69 0.0015 19.7 1.9 19 35-53 7-25 (166)
289 cd00424 PolY Y-family of DNA p 23.4 60 0.0013 22.9 1.8 27 34-61 174-202 (343)
290 PRK13502 transcriptional activ 23.3 85 0.0019 21.0 2.4 18 7-25 261-278 (282)
291 PF05626 DUF790: Protein of un 23.2 1.1E+02 0.0024 22.8 3.1 45 6-54 107-151 (379)
292 PF02682 AHS1: Allophanate hyd 23.1 1.2E+02 0.0026 20.3 3.1 21 5-26 101-121 (202)
293 PRK14625 hypothetical protein; 23.0 80 0.0017 19.5 2.1 16 26-41 92-107 (109)
294 PRK12339 2-phosphoglycerate ki 23.0 81 0.0018 20.9 2.2 19 35-53 8-26 (197)
295 cd01106 HTH_TipAL-Mta Helix-Tu 23.0 1.1E+02 0.0025 17.8 2.7 24 4-29 1-24 (103)
296 COG0714 MoxR-like ATPases [Gen 22.9 1.1E+02 0.0024 21.3 3.1 28 25-53 39-66 (329)
297 PRK03839 putative kinase; Prov 22.7 85 0.0019 19.6 2.2 19 35-53 5-23 (180)
298 PF07541 EIF_2_alpha: Eukaryot 22.6 95 0.0021 18.9 2.4 19 43-61 4-22 (114)
299 PF06599 DUF1139: Protein of u 22.5 1.2E+02 0.0027 22.1 3.2 44 11-56 179-222 (309)
300 PRK14133 DNA polymerase IV; Pr 22.3 77 0.0017 22.3 2.1 27 34-61 174-202 (347)
301 cd00592 HTH_MerR-like Helix-Tu 22.3 1.2E+02 0.0026 17.3 2.7 22 4-26 1-22 (100)
302 PF14894 Lsm_C: Lsm C-terminal 22.3 51 0.0011 18.8 1.0 18 36-53 39-58 (64)
303 KOG3218 RNA polymerase, 25-kDa 22.2 63 0.0014 22.4 1.6 54 4-59 37-97 (208)
304 PF13086 AAA_11: AAA domain; P 22.0 1.1E+02 0.0025 19.0 2.7 38 16-53 2-41 (236)
305 PRK08356 hypothetical protein; 22.0 95 0.0021 19.9 2.4 20 35-54 10-29 (195)
306 PRK01216 DNA polymerase IV; Va 22.0 63 0.0014 23.3 1.7 26 34-60 179-206 (351)
307 PF10108 DNA_pol_B_exo2: Predi 21.7 2.8E+02 0.006 19.0 5.2 52 4-61 102-153 (209)
308 PRK00625 shikimate kinase; Pro 21.7 91 0.002 20.1 2.2 19 35-53 5-23 (173)
309 cd01080 NAD_bind_m-THF_DH_Cycl 21.5 97 0.0021 20.1 2.4 20 34-53 143-163 (168)
310 PF11697 DUF3293: Protein of u 21.4 90 0.002 17.6 1.9 18 38-55 53-70 (73)
311 TIGR03759 conj_TIGR03759 integ 21.4 2.3E+02 0.005 19.5 4.2 40 7-49 6-45 (200)
312 PRK10219 DNA-binding transcrip 21.3 93 0.002 17.9 2.1 14 8-22 91-104 (107)
313 PRK02794 DNA polymerase IV; Pr 21.2 68 0.0015 23.4 1.7 26 34-60 210-237 (419)
314 smart00546 CUE Domain that may 21.1 1.3E+02 0.0027 14.8 3.0 25 39-63 14-39 (43)
315 PRK03609 umuC DNA polymerase V 20.9 59 0.0013 23.7 1.4 26 34-60 180-207 (422)
316 TIGR00264 alpha-NAC-related pr 20.9 76 0.0016 20.1 1.7 18 35-54 2-22 (116)
317 PRK14955 DNA polymerase III su 20.9 89 0.0019 22.7 2.3 19 35-53 43-61 (397)
318 cd02021 GntK Gluconate kinase 20.8 98 0.0021 18.6 2.2 19 35-53 4-22 (150)
319 PF10979 DUF2786: Protein of u 20.8 85 0.0019 16.2 1.6 14 41-54 26-39 (43)
320 PF11372 DUF3173: Domain of un 20.8 94 0.002 17.4 1.9 14 40-53 13-26 (59)
321 KOG2457 A/G-specific adenine D 20.6 41 0.00089 26.0 0.5 21 36-56 209-230 (555)
322 COG2442 Uncharacterized conser 20.6 1.6E+02 0.0035 17.1 2.9 26 4-29 44-69 (79)
323 PRK14667 uvrC excinuclease ABC 20.4 46 0.001 26.0 0.7 30 24-54 537-566 (567)
324 cd01105 HTH_GlnR-like Helix-Tu 20.3 1.4E+02 0.0031 17.0 2.7 22 4-26 2-23 (88)
325 PF10397 ADSL_C: Adenylosuccin 20.2 78 0.0017 17.9 1.5 15 39-53 16-30 (81)
326 PF13274 DUF4065: Protein of u 20.2 1.4E+02 0.0031 16.8 2.7 21 6-26 79-99 (108)
327 PRK07933 thymidylate kinase; V 20.1 83 0.0018 20.8 1.8 19 35-53 5-23 (213)
328 COG0680 HyaD Ni,Fe-hydrogenase 20.1 87 0.0019 20.3 1.9 18 39-56 17-34 (160)
329 cd01700 PolY_Pol_V_umuC umuC s 20.1 67 0.0014 22.6 1.4 26 34-60 177-204 (344)
No 1
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.91 E-value=8.5e-25 Score=151.82 Aligned_cols=62 Identities=29% Similarity=0.479 Sum_probs=59.4
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE 65 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~ 65 (66)
.++.++|.++|| ++|+|++||++|+||+|||||||||||||||.+||++|||+++|++++++
T Consensus 153 ~~~~~~v~~~~G-v~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~ 214 (256)
T PRK09482 153 WLDAPFIEQEFG-VEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDA 214 (256)
T ss_pred cCCHHHHHHHhC-CCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHH
Confidence 479999999998 99999999999999999999999999999999999999999999998765
No 2
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.91 E-value=1.8e-24 Score=149.69 Aligned_cols=62 Identities=42% Similarity=0.739 Sum_probs=59.6
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE 65 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~ 65 (66)
.++.++|.++|| ++|+||+||++|+||+|||||||||||||||.+||++|||++++++++++
T Consensus 157 ~~~~~~v~~~~G-v~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~ 218 (259)
T smart00475 157 LYTPENVIEKYG-LTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDK 218 (259)
T ss_pred EEcHHHHHHHhC-cCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHH
Confidence 589999999998 99999999999999999999999999999999999999999999998765
No 3
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.90 E-value=3.2e-24 Score=149.87 Aligned_cols=63 Identities=37% Similarity=0.644 Sum_probs=59.8
Q ss_pred ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374 2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE 65 (66)
Q Consensus 2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~ 65 (66)
..++++.|.++|| ++|+||+|+++|+||+|||||||||||||||.+||++|||++++++++++
T Consensus 161 ~~~~~~~v~~~~g-v~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~ 223 (281)
T PRK14976 161 FILNTNNFFELYG-IEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDK 223 (281)
T ss_pred EEEcHHHHHHHhC-cCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHH
Confidence 3589999999998 99999999999999999999999999999999999999999999988765
No 4
>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=99.89 E-value=1.8e-23 Score=142.74 Aligned_cols=62 Identities=39% Similarity=0.686 Sum_probs=59.1
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE 65 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~ 65 (66)
.++.+.|.++|| ++|+||+|+++|+||+|||+|||||||||||.+||++|||++++++++++
T Consensus 154 ~i~~~~v~~~~g-~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~ 215 (240)
T cd00008 154 LVTEENVIEKYG-VTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDK 215 (240)
T ss_pred EEeHHHHHHHhC-cCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHH
Confidence 578999999998 99999999999999999999999999999999999999999999988764
No 5
>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=99.89 E-value=1e-23 Score=123.14 Aligned_cols=52 Identities=50% Similarity=0.845 Sum_probs=49.5
Q ss_pred HhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374 12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS 64 (66)
Q Consensus 12 ~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~ 64 (66)
+|| ++|+||+|+|+|+||++||+|||||||+|+|.+||++|+++++++++++
T Consensus 2 ~~g-~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~ 53 (75)
T cd00080 2 KLG-LTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLD 53 (75)
T ss_pred CCC-cCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHH
Confidence 577 9999999999999999999999999999999999999999999998764
No 6
>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=99.89 E-value=1.3e-25 Score=138.22 Aligned_cols=51 Identities=41% Similarity=0.697 Sum_probs=42.2
Q ss_pred CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhccC
Q 035374 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM 66 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~~ 66 (66)
++|+|++||++|+||+|||||||||||||||.+||++|||+++|+++++++
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~ 51 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEI 51 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhc
Confidence 589999999999999999999999999999999999999999999887753
No 7
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.87 E-value=2e-22 Score=157.13 Aligned_cols=63 Identities=43% Similarity=0.727 Sum_probs=60.1
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhccC
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSEM 66 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~~ 66 (66)
.++.++|.++|| ++|+||+||++|+||+|||||||||||||||.+||++|||+++|+++++++
T Consensus 156 ~~~~~~v~~~~G-v~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i 218 (887)
T TIGR00593 156 EITPEYVVEKYG-VTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQI 218 (887)
T ss_pred EEcHHHHHHHhC-CCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 589999999998 999999999999999999999999999999999999999999999988753
No 8
>PRK05755 DNA polymerase I; Provisional
Probab=99.85 E-value=1.7e-21 Score=150.95 Aligned_cols=62 Identities=40% Similarity=0.737 Sum_probs=59.4
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE 65 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~ 65 (66)
.++.+.|.++|| ++|+||+|+++|+||+|||||||||||||||.+||++|||+++|++++++
T Consensus 158 ~~~~~~v~~~~g-~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~ 219 (880)
T PRK05755 158 ELDPEEVVEKYG-VTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDE 219 (880)
T ss_pred EEcHHHHHHHHC-cCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHH
Confidence 588999999998 99999999999999999999999999999999999999999999988764
No 9
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.84 E-value=6.9e-21 Score=133.37 Aligned_cols=61 Identities=39% Similarity=0.712 Sum_probs=57.3
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS 64 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~ 64 (66)
++.+.+.++|.+++|+|++|+++|+||+|||+|||||||||||.+||++||+++.++++++
T Consensus 169 ~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~ 229 (310)
T COG0258 169 LDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLD 229 (310)
T ss_pred CCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhh
Confidence 6889999999339999999999999999999999999999999999999999999998764
No 10
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.79 E-value=1.3e-19 Score=93.61 Aligned_cols=36 Identities=53% Similarity=0.932 Sum_probs=35.0
Q ss_pred hhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374 18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 18 p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f 53 (66)
|+||+|+++|+||.+||+|||||||+|+|.+||++|
T Consensus 1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence 689999999999999999999999999999999987
No 11
>PTZ00217 flap endonuclease-1; Provisional
Probab=99.77 E-value=8.4e-19 Score=127.36 Aligned_cols=60 Identities=27% Similarity=0.442 Sum_probs=56.6
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhcc
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFSE 65 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~~ 65 (66)
.++.+.+++.+| ++|+||+|+|+|+| +||+|||||||||||.+||++|+|+++++++++.
T Consensus 208 ~~~~~~v~~~~g-l~~~q~id~~iL~G--~Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~~ 267 (393)
T PTZ00217 208 EINLSTVLEELG-LSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDK 267 (393)
T ss_pred EEEHHHHHHHhC-CCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHh
Confidence 588999999998 99999999999999 6999999999999999999999999999987653
No 12
>PRK03980 flap endonuclease-1; Provisional
Probab=99.76 E-value=1.2e-18 Score=122.51 Aligned_cols=58 Identities=34% Similarity=0.554 Sum_probs=54.9
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
.++.+.+++++| ++|+||+|+|+|+| +||+|||||||||||.+|+++|+|+++++++.
T Consensus 162 ~~~~~~vl~~lg-l~~~q~id~~iL~G--~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~ 219 (292)
T PRK03980 162 LIELEEVLKELG-ITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDLEKVLEER 219 (292)
T ss_pred eeeHHHHHHHhC-CCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHCCCHHHHHHhc
Confidence 588999999998 99999999999999 69999999999999999999999999999753
No 13
>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=99.74 E-value=4.2e-18 Score=121.39 Aligned_cols=59 Identities=31% Similarity=0.478 Sum_probs=54.4
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhhc
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECFS 64 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~~ 64 (66)
.++.+++++++| ++|+||+|+|+|+|| |+.|||||||||||.+|+++|+|+++++++++
T Consensus 209 ~~~~~~v~~~lg-l~~~q~id~~iL~G~--dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~ 267 (338)
T TIGR03674 209 LIELEEVLSELG-ITREQLIDIAILVGT--DYNEGVKGIGPKTALKLIKEHGDLEKVLKARG 267 (338)
T ss_pred eeeHHHHHHHhC-CCHHHHHHHHHhcCC--CCCCCCCCccHHHHHHHHHHcCCHHHHHHhhc
Confidence 378999999998 999999999999998 44499999999999999999999999998754
No 14
>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=99.73 E-value=9.7e-18 Score=117.34 Aligned_cols=59 Identities=31% Similarity=0.613 Sum_probs=54.4
Q ss_pred ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
..++.+.+.+++| ++|+||+|+|+|+| +||+|||||||+|||.+|+++|+|++++++++
T Consensus 195 ~~~~~~~~~~~lg-l~~~q~id~~~L~G--~Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l 253 (316)
T cd00128 195 EEIDLEKILKELG-LTREKLIDLAILLG--CDYTEGIPGIGPVTALKLIKKYGDIEKDIERL 253 (316)
T ss_pred EEEEHHHHHHHcC-CCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHcCChHHHHHHH
Confidence 3588999999998 99999999999999 69999999999999999999999988877654
No 15
>PHA00439 exonuclease
Probab=99.54 E-value=4.2e-15 Score=104.96 Aligned_cols=45 Identities=18% Similarity=0.324 Sum_probs=41.3
Q ss_pred ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH---hCCHHHHHhh
Q 035374 17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK---FGMLVFNVEC 62 (66)
Q Consensus 17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~---fgsl~~i~~~ 62 (66)
.|+||+|+++|+||+||||||||||| |||.+||++ |..+++.+++
T Consensus 172 ~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 172 TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 58999999999999999999999999 999999999 7777777755
No 16
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.39 E-value=6.8e-13 Score=105.53 Aligned_cols=55 Identities=22% Similarity=0.448 Sum_probs=50.5
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
+|+.+++++.+| ++++||+++|+|+| +||.+||||||||+|.+||++|+ +++.++
T Consensus 839 ~~~~~~i~~~lg-lt~~qli~laiL~G--~DY~~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 839 YYQYVDIHNQLG-LDRNKLINLAYLLG--SDYTEGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred EeeHHHHHHHhC-CCHHHHHHHHHeeC--CCCCCCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 578899999998 99999999999999 59999999999999999999999 466655
No 17
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.25 E-value=1.3e-11 Score=91.54 Aligned_cols=57 Identities=30% Similarity=0.534 Sum_probs=54.6
Q ss_pred ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
.+|+.+.+++.++ ++.++|+|+|+|+|+ ||.++|.|||+++|.+|+++|++++++++
T Consensus 201 ~e~~~~~il~~l~-l~~~~fidL~lLlGC--DYc~~I~Gig~~~al~lir~~~~i~~ile 257 (449)
T KOG2519|consen 201 SEYDMSRILEGLG-LSRESFIDLCLLLGC--DYCPTIRGIGPKKALKLIRQHGDIENILE 257 (449)
T ss_pred EEeeHHHHHHHhc-ccHHHHHHHHHHhcC--cccccccccChHHHHHHHHHhcCHHHHhh
Confidence 5789999999999 999999999999995 99999999999999999999999999987
No 18
>PHA02567 rnh RnaseH; Provisional
Probab=98.63 E-value=3.5e-08 Score=70.55 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=31.7
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEG 40 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~G 40 (66)
++.++|.++|| .|+|++||++|+||+||||||||-
T Consensus 173 ~~~~~V~~k~G--~P~q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 173 MQKKWVKPKYG--SPEKDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred CCHHHHHHHhC--CHHHHHHHHHhCCcccCCcCCCCC
Confidence 46688999998 499999999999999999999975
No 19
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=98.54 E-value=1.3e-07 Score=71.69 Aligned_cols=44 Identities=20% Similarity=0.317 Sum_probs=40.8
Q ss_pred CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
++-++|.++|+|.|| ||++||||||-+||.+++.+|.+.+.++.
T Consensus 210 ~~~ekfr~mciLSGC--DYl~slpGvGl~tA~k~l~k~~~~d~vi~ 253 (556)
T KOG2518|consen 210 FTEEKFRRMCILSGC--DYLSSLPGVGLATAHKLLSKYNTPDRVII 253 (556)
T ss_pred cCHHHHHHHHHhcCC--cccccCccccHHHHHHHHHhcCcHHHHHH
Confidence 568899999999995 99999999999999999999999998763
No 20
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=98.35 E-value=1e-06 Score=69.52 Aligned_cols=50 Identities=26% Similarity=0.674 Sum_probs=47.5
Q ss_pred ceeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 2 ASFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
..|..+.+.++|+ +++..+|.++.|+| +||..||+||||++|..+|.+|+
T Consensus 532 e~y~~~di~kel~-l~R~~lI~lA~LlG--sDYt~Gl~giGpV~AlEil~Efp 581 (815)
T KOG2520|consen 532 EKYQLDDIEKELG-LDRPNLISLAQLLG--SDYTEGLKGIGPVSALEILAEFP 581 (815)
T ss_pred eeeehHHHHHHHc-cCchhhHHHHHhcc--cccccCCCcccchHHHHHHHHcC
Confidence 3578899999998 99999999999999 69999999999999999999999
No 21
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=98.19 E-value=9.4e-07 Score=49.87 Aligned_cols=25 Identities=32% Similarity=0.545 Sum_probs=21.6
Q ss_pred CCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 37 GVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
||||||+++|..|.++|+|++++.+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~ 31 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMN 31 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Confidence 7899999999999999999999875
No 22
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=97.73 E-value=2.2e-05 Score=60.01 Aligned_cols=29 Identities=21% Similarity=0.359 Sum_probs=25.8
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
-+.+||||||||..+||++|||+++|.++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 45567999999999999999999999864
No 23
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=97.69 E-value=3.2e-05 Score=59.08 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=26.1
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
-+.+||||||||..+||++|||+++|.++.
T Consensus 542 ~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~As 571 (574)
T TIGR00194 542 PLLKIPGVGEKRVQKLLKYFGSLKGIKKAS 571 (574)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 345669999999999999999999998753
No 24
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=97.64 E-value=4.3e-05 Score=58.48 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=26.7
Q ss_pred CCCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 33 DNIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
.-+..||||||||..+||+.|||+++|.++
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A 543 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLGTYKDILLL 543 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 356778999999999999999999999864
No 25
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=97.61 E-value=4.3e-05 Score=59.00 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=25.9
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
-+.+||||||||+.+||++|||+++|.++
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 45677999999999999999999999864
No 26
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=97.39 E-value=0.00016 Score=56.61 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=25.5
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
-+..|||||+||+.+||+.|||+++|.++
T Consensus 609 ~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred ccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 34566999999999999999999999864
No 27
>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=97.34 E-value=0.00023 Score=39.22 Aligned_cols=27 Identities=26% Similarity=0.253 Sum_probs=24.0
Q ss_pred CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374 36 PGVEGIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
..||||||++|.+|... |.|++++...
T Consensus 8 ~~I~Gig~~~a~~L~~~G~~t~~~l~~a 35 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYEAGIKTLEDLANA 35 (60)
T ss_dssp HTSTTCHHHHHHHHHHTTCSSHHHHHTS
T ss_pred ccCCCCCHHHHHHHHhcCCCcHHHHHcC
Confidence 46799999999999999 9999999753
No 28
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=97.24 E-value=0.00027 Score=54.51 Aligned_cols=29 Identities=24% Similarity=0.492 Sum_probs=25.5
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
-+.+|||||+|+|..|++.|||++++.++
T Consensus 570 ~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~A 598 (621)
T PRK14671 570 ELTDIAGIGEKTAEKLLEHFGSVEKVAKA 598 (621)
T ss_pred hhhcCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 45678999999999999999999998753
No 29
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=97.14 E-value=0.00097 Score=44.68 Aligned_cols=43 Identities=16% Similarity=0.102 Sum_probs=25.7
Q ss_pred HHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 10 ARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 10 ~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
..-||+.+++.---|..|++ |+|||||+|..+|..+ +++++.+
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~--------V~GIGpK~Al~iL~~~-~~~el~~ 99 (191)
T TIGR00084 57 ELLFGFNTLEERELFKELIK--------VNGVGPKLALAILSNM-SPEEFVY 99 (191)
T ss_pred ceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHhcC-CHHHHHH
Confidence 34566566666555565543 4677777777777665 4555544
No 30
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.10 E-value=0.00038 Score=53.41 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=25.8
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
-+.+|||||++++.+|++.|||++++.++
T Consensus 544 ~L~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 544 ALDDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred hHhhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 45678999999999999999999999864
No 31
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=97.10 E-value=0.00039 Score=53.31 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=26.8
Q ss_pred CCCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 33 DNIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
.-+..|||||++++.+||++|||+++|.++
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~A 554 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREA 554 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 456778999999999999999999999864
No 32
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.10 E-value=0.00057 Score=47.59 Aligned_cols=29 Identities=17% Similarity=0.252 Sum_probs=25.7
Q ss_pred CCCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
.+..|||||++++.+|++. |+|+++|..+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 4667899999999999999 9999999754
No 33
>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=97.10 E-value=0.00014 Score=35.90 Aligned_cols=20 Identities=20% Similarity=0.419 Sum_probs=14.8
Q ss_pred CCCCCCCCCccHHHHHHHHH
Q 035374 32 ADNIPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~ 51 (66)
.+.+..+||||+|+|..++.
T Consensus 10 ~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 10 IEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHHTSTT-SHHHHHHHHH
T ss_pred HHHHHhCCCcCHHHHHHHHh
Confidence 34455789999999998874
No 34
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=97.08 E-value=0.00061 Score=52.42 Aligned_cols=48 Identities=19% Similarity=0.277 Sum_probs=34.2
Q ss_pred HhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 12 ~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
+|. ++-..=.--+...-.+.| .||||||||..+||+.|||+++|.++.
T Consensus 513 rfA-i~~hR~~R~k~~~~s~Ld---~I~GiG~~r~~~LL~~Fgs~~~i~~As 560 (581)
T COG0322 513 RFA-ITYHRKKRSKAMLQSSLD---DIPGIGPKRRKALLKHFGSLKGIKSAS 560 (581)
T ss_pred HHH-HHHHHHHhhhhhhcCccc---cCCCcCHHHHHHHHHHhhCHHHHHhcC
Confidence 344 444444445565554444 559999999999999999999998643
No 35
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.03 E-value=0.0006 Score=45.45 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=20.3
Q ss_pred CCCCccHHHHHHHHHHhCC---HHHHHh
Q 035374 37 GVEGIGDVRAVQLITKFGM---LVFNVE 61 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgs---l~~i~~ 61 (66)
.|||||||+|.++++.|++ .+.+.+
T Consensus 77 ~i~GIGpk~A~~il~~fg~~~l~~~i~~ 104 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSPEELVQAIAN 104 (192)
T ss_pred cCCCCCHHHHHHHHHhCCHHHHHHHHHh
Confidence 3699999999999999987 444443
No 36
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=96.98 E-value=0.00054 Score=53.71 Aligned_cols=29 Identities=34% Similarity=0.464 Sum_probs=26.0
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
.+..|||||+|++.+|+++|||++++.++
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~A 666 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAA 666 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhc
Confidence 45677999999999999999999999864
No 37
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.97 E-value=0.0012 Score=44.30 Aligned_cols=42 Identities=24% Similarity=0.332 Sum_probs=26.9
Q ss_pred HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
-+.-...++|+++... +..|| ...+..+||||+|||.+++-+
T Consensus 86 Al~ILs~~~~~el~~a-I~~~D-~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 86 AMAVCSSLDVNSFYKA-LSLGD-ESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred HHHHHcCCCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHH
Confidence 3344444677777742 33455 457778888888888888754
No 38
>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=96.94 E-value=0.0014 Score=35.95 Aligned_cols=26 Identities=23% Similarity=0.216 Sum_probs=19.2
Q ss_pred CCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374 36 PGVEGIGDVRAVQLITK-FGMLVFNVE 61 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~ 61 (66)
.+|.||||+||.++..+ |.|++++..
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence 36799999999999998 789999865
No 39
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.89 E-value=0.0025 Score=42.80 Aligned_cols=44 Identities=14% Similarity=0.191 Sum_probs=30.5
Q ss_pred HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
-..-||+.+++.---|..|++ |+|||||+|..+|..|+ .+++.+
T Consensus 57 ~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~ILs~~~-~~~l~~ 100 (194)
T PRK14605 57 ALSLFGFATTEELSLFETLID--------VSGIGPKLGLAMLSAMN-AEALAS 100 (194)
T ss_pred CceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHHhCC-HHHHHH
Confidence 345577777777777777754 58888888888888874 445433
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.89 E-value=0.0024 Score=43.18 Aligned_cols=41 Identities=15% Similarity=0.173 Sum_probs=20.0
Q ss_pred HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHH
Q 035374 11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNV 60 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~ 60 (66)
.-||+.+.++-.-|..|++ |.|||||+|..+|..+ +.+++.
T Consensus 60 ~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~iLs~~-~~~~l~ 100 (203)
T PRK14602 60 ELFGFATWDERQTFIVLIS--------ISKVGAKTALAILSQF-RPDDLR 100 (203)
T ss_pred eeeCCCCHHHHHHHHHHhC--------CCCcCHHHHHHHHhhC-CHHHHH
Confidence 3355445554444444433 3555555555555554 333333
No 41
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.86 E-value=0.0021 Score=43.06 Aligned_cols=34 Identities=35% Similarity=0.546 Sum_probs=15.5
Q ss_pred CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
++|+++.+.-+ -||. ..+ .+||||+|+|.+++-+
T Consensus 93 ~~~~~l~~aI~-~~D~-~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 93 LTPEQLFSAIV-NEDK-AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred CCHHHHHHHHH-cCCH-hhe-ECCCCcHHHHHHHHHH
Confidence 34444443222 3442 344 5555555555555544
No 42
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.74 E-value=0.0022 Score=43.50 Aligned_cols=40 Identities=30% Similarity=0.361 Sum_probs=24.8
Q ss_pred HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
.-...++|+++... +.-|| ...+..+||||+|||.+++-+
T Consensus 87 aILs~~~~~el~~a-I~~~D-~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 87 RVLSGIKYNEFRDA-IDRED-IELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred HHHcCCCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHH
Confidence 33433567777643 23455 446677788888888877754
No 43
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.74 E-value=0.0018 Score=43.81 Aligned_cols=43 Identities=16% Similarity=0.308 Sum_probs=30.9
Q ss_pred HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374 9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f 53 (66)
-+.-...++|+++... +.-|| ...+..+||||+|||.+++-+.
T Consensus 87 Al~iLs~~~~~~l~~a-I~~~D-~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 87 ALAILSQFRPDDLRRL-VAEED-VAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred HHHHHhhCCHHHHHHH-HHhCC-HHHHhcCCCcCHHHHHHHHHHH
Confidence 3344444688888842 33555 6688999999999999998654
No 44
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=96.68 E-value=0.0014 Score=30.88 Aligned_cols=18 Identities=28% Similarity=0.445 Sum_probs=15.6
Q ss_pred CCCCCCccHHHHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~ 52 (66)
+..|||||+|+|.++++.
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 457899999999999974
No 45
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.67 E-value=0.0035 Score=41.98 Aligned_cols=48 Identities=23% Similarity=0.252 Sum_probs=37.0
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
|+-..-||+.+++.---|..|++ |.|||||+|..+|..+ +++++.++.
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li~--------VsGIGpK~Al~ILs~~-~~~el~~aI 102 (183)
T PRK14601 55 EDSNKLYGFLDKDEQKMFEMLLK--------VNGIGANTAMAVCSSL-DVNSFYKAL 102 (183)
T ss_pred cCCceeeCCCCHHHHHHHHHHhc--------cCCccHHHHHHHHcCC-CHHHHHHHH
Confidence 33445688888888888888754 5899999999999996 677776543
No 46
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.64 E-value=0.0038 Score=42.37 Aligned_cols=48 Identities=25% Similarity=0.330 Sum_probs=36.8
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
|+-..-||+.+.+.---|..|++ |.|||||+|..+|..+ +++++.++.
T Consensus 54 ED~~~LYGF~t~~Er~lF~~Lis--------VsGIGPK~ALaILs~~-~~~el~~aI 101 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEELIG--------VDGIGPRAALRVLSGI-KYNEFRDAI 101 (196)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHH
Confidence 33446688888888888888764 5899999999999997 666666543
No 47
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.63 E-value=0.0037 Score=42.11 Aligned_cols=19 Identities=26% Similarity=0.508 Sum_probs=9.8
Q ss_pred CCCCCCCccHHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+..+||||+|||.+++-+
T Consensus 109 ~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 109 RLARVPGIGKKTAERIVLE 127 (195)
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 4445555555555555544
No 48
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.58 E-value=0.0029 Score=42.68 Aligned_cols=48 Identities=27% Similarity=0.225 Sum_probs=36.6
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
|+-..-||+.+.+.---|..|++ |.|||||+|..+|..+ +++++.+++
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~iLs~~-~~~el~~aI 102 (195)
T PRK14604 55 EDALTLYGFSTPAQRQLFELLIG--------VSGVGPKAALNLLSSG-TPDELQLAI 102 (195)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHH
Confidence 34445688788887777777754 5899999999999986 677776544
No 49
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.57 E-value=0.0044 Score=41.56 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=17.1
Q ss_pred CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
++|+++.+. +..|| ...+..+||||+|||.+++-+
T Consensus 93 ~~~~el~~a-I~~~D-~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 93 EDAETLVTM-IASQD-VEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred CCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHH
Confidence 455555432 22343 334555555555555555544
No 50
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.56 E-value=0.003 Score=42.33 Aligned_cols=48 Identities=21% Similarity=0.136 Sum_probs=36.8
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
|+-..-||+.+.++---|..|++ |.|||||+|..+|..+ +++++.+++
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~AL~iLs~~-~~~el~~aI 102 (188)
T PRK14606 55 QDGITLYGFSNERKKELFLSLTK--------VSRLGPKTALKIISNE-DAETLVTMI 102 (188)
T ss_pred cCCceeeCCCCHHHHHHHHHHhc--------cCCccHHHHHHHHcCC-CHHHHHHHH
Confidence 34456688778888877888754 5899999999999986 677776543
No 51
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.55 E-value=0.0051 Score=41.21 Aligned_cols=49 Identities=18% Similarity=0.220 Sum_probs=38.1
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
.|+-..-||+.+++.---|..|++ |.|||||+|..+|..+ +++++.+++
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Lis--------V~GIGpK~Al~iLs~~-~~~~l~~aI 102 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRMLVK--------VSGVNYKTAMSILSKL-TPEQLFSAI 102 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHccC-CHHHHHHHH
Confidence 344556789888888888888754 5899999999999997 677776544
No 52
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.55 E-value=0.0045 Score=41.74 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=18.1
Q ss_pred CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f 53 (66)
++|+++... +.-|| ...+..+||||+|+|.+++-+.
T Consensus 92 ~~~~~l~~a-I~~~D-~~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 92 LPPALLARA-LLEGD-ARLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred CCHHHHHHH-HHhCC-HHHHhhCCCCCHHHHHHHHHHH
Confidence 455555532 22344 3345555666666666665443
No 53
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.54 E-value=0.0031 Score=42.51 Aligned_cols=48 Identities=23% Similarity=0.292 Sum_probs=35.8
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
|+-..-||+.+.+.-.-|..|++ |.|||||+|..+|..+ +++++.+++
T Consensus 54 Ed~~~LyGF~~~~Er~lF~~L~~--------V~GIGpK~AL~iLs~~-~~~~l~~aI 101 (197)
T PRK14603 54 EDALSLYGFPDEDSLELFELLLG--------VSGVGPKLALALLSAL-PPALLARAL 101 (197)
T ss_pred cCCceeeCcCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHH
Confidence 33445688777777777777754 5899999999999996 677776543
No 54
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave 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. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=96.46 E-value=0.0029 Score=37.61 Aligned_cols=28 Identities=29% Similarity=0.570 Sum_probs=25.5
Q ss_pred ceeCHHHHHHHhCCCChhHHHHHHHhhCC
Q 035374 2 ASFGMEDFARKYGELKPSQFVDVISLVGD 30 (66)
Q Consensus 2 ~~~~~~~v~~~~g~i~p~q~~d~~~L~Gd 30 (66)
..++.+.+.+.++ ++++||+++++|+|+
T Consensus 66 ~~~~~~~i~~~l~-l~~~~fi~~~iL~G~ 93 (94)
T PF00867_consen 66 EVIDLDDILKELG-LTREQFIDLCILCGC 93 (94)
T ss_dssp EEEEHHHHHHHHT-TSHHHHHHHHHHHHE
T ss_pred EEEEHHHHHHHcC-CCHHHHHHHheecCC
Confidence 3678899999998 999999999999995
No 55
>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=96.39 E-value=0.003 Score=49.00 Aligned_cols=26 Identities=31% Similarity=0.465 Sum_probs=23.8
Q ss_pred CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 37 GVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
||||||+++|..|+++|+|++++.++
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~~A 527 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLKAA 527 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence 67999999999999999999998754
No 56
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=96.29 E-value=0.0044 Score=43.69 Aligned_cols=27 Identities=30% Similarity=0.431 Sum_probs=24.3
Q ss_pred CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 36 PGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
.++||||++.|..|+++|||+++++.+
T Consensus 185 ~s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred HcCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 456899999999999999999999865
No 57
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.22 E-value=0.0049 Score=48.28 Aligned_cols=26 Identities=23% Similarity=0.454 Sum_probs=23.7
Q ss_pred CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 37 GVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
||||||+++|.+|++.|+|++++.++
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~A 557 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMDA 557 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence 57999999999999999999998753
No 58
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=96.07 E-value=0.017 Score=42.43 Aligned_cols=58 Identities=19% Similarity=0.319 Sum_probs=43.4
Q ss_pred CHHHHHHHhCCCChhHHHHHH---HhhCCCC-----CC---------CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 5 GMEDFARKYGELKPSQFVDVI---SLVGDKA-----DN---------IPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~---~L~Gd~~-----D~---------i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
+.+++.+++..++.+++.|.. .++|=+. |. +..||+++++.|.+|+++|||+.+++++
T Consensus 242 ~~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~A 316 (352)
T PRK13482 242 DPEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAA 316 (352)
T ss_pred CHHHHHHHHHhCCHHHhcCHHHHHHHhCCCCCCcccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcC
Confidence 356777777778888887764 4566211 11 2357999999999999999999999864
No 59
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=96.04 E-value=0.017 Score=39.39 Aligned_cols=47 Identities=23% Similarity=0.198 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
.|+...-||+.+.+.=..|..|.. |.|||||+|..+|..+ +++++.+
T Consensus 54 REd~~~LyGF~~~~ER~lF~~Lis--------VnGIGpK~ALaiLs~~-~~~~l~~ 100 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRLLIS--------VNGIGPKLALAILSNL-DPEELAQ 100 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHHHHc--------cCCccHHHHHHHHcCC-CHHHHHH
Confidence 344455566545544444444433 3466666666666553 4444443
No 60
>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=95.99 E-value=0.0062 Score=35.69 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=23.0
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~ 60 (66)
-+..|||||+.+|..|+.+.++++.+-
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~rF~ 29 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDISRFK 29 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCchhcc
Confidence 356889999999999999999887653
No 61
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=95.91 E-value=0.0081 Score=37.51 Aligned_cols=26 Identities=19% Similarity=0.188 Sum_probs=20.8
Q ss_pred CCCCCCccHHHHHHHHHHh------CCHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITKF------GMLVFNV 60 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f------gsl~~i~ 60 (66)
+..+||||+++|.++++.+ .|++++.
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~ 101 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLT 101 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHH
Confidence 4567999999999999984 6677664
No 62
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=95.90 E-value=0.013 Score=39.19 Aligned_cols=47 Identities=19% Similarity=0.350 Sum_probs=32.6
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
+++.....-.+..+++++.+... -+| ...+..+||||+|||.+++-+
T Consensus 80 IGpK~Al~iL~~~~~~el~~aI~-~~d-~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 80 VGPKLALAILSNMSPEEFVYAIE-TEE-VKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCHHHHHHHHhcCCHHHHHHHHH-hCC-HHHHHhCCCCCHHHHHHHHHH
Confidence 34444555566467888874332 466 447889999999999999854
No 63
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=95.82 E-value=0.0076 Score=48.02 Aligned_cols=29 Identities=10% Similarity=-0.020 Sum_probs=25.5
Q ss_pred CCCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
++-++||||++.|..||++|+|++++.++
T Consensus 758 ~L~~lPgI~~~~a~~ll~~f~si~~l~~a 786 (814)
T TIGR00596 758 FLLKLPGVTKKNYRNLRKKVKSIRELAKL 786 (814)
T ss_pred HHHHCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 34568999999999999999999999863
No 64
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.66 E-value=0.01 Score=46.27 Aligned_cols=26 Identities=27% Similarity=0.391 Sum_probs=23.7
Q ss_pred CCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 37 GVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
||||||+++|..|+++|+|++++.++
T Consensus 515 gi~~IG~~~ak~L~~~f~sl~~l~~A 540 (665)
T PRK07956 515 GIRHVGEKAAKALARHFGSLEALRAA 540 (665)
T ss_pred hccCcCHHHHHHHHHHcCCHHHHHhC
Confidence 68999999999999999999998753
No 65
>PRK13766 Hef nuclease; Provisional
Probab=95.64 E-value=0.012 Score=45.37 Aligned_cols=28 Identities=21% Similarity=0.389 Sum_probs=24.7
Q ss_pred CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
+.++||||+++|.+|+++|||+++++++
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4567999999999999999999998753
No 66
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=95.55 E-value=0.027 Score=38.37 Aligned_cols=44 Identities=18% Similarity=0.369 Sum_probs=31.6
Q ss_pred HHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 9 FARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 9 v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
-+.-...++++.+.+.-+ .+| ...+-.+||||+|+|.+++-+-.
T Consensus 86 ALaiLs~~~~~~l~~aI~-~~d-~~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 86 ALAILSNLDPEELAQAIA-NED-VKALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred HHHHHcCCCHHHHHHHHH-hcC-hHhhhcCCCCCHHHHHHHHHHHh
Confidence 334444467888885433 555 55889999999999999987643
No 67
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.42 E-value=0.017 Score=38.72 Aligned_cols=35 Identities=17% Similarity=0.446 Sum_probs=25.1
Q ss_pred CChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
++|++|+.. +..+| ...+..|||||+|||.+++-+
T Consensus 93 ~~~~~l~~a-I~~~D-~~~L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 93 MNAEALASA-IISGN-AELLSTIPGIGKKTASRIVLE 127 (194)
T ss_pred CCHHHHHHH-HHhCC-HHHHHhCCCCCHHHHHHHHHH
Confidence 567777642 22566 447889999999999996543
No 68
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=95.41 E-value=0.016 Score=37.41 Aligned_cols=26 Identities=8% Similarity=0.092 Sum_probs=22.3
Q ss_pred CCCCCccHHHHHHHHHH--hCCHHHHHh
Q 035374 36 PGVEGIGDVRAVQLITK--FGMLVFNVE 61 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~--fgsl~~i~~ 61 (66)
..+|||||++|.++++. |.|+|++++
T Consensus 64 ~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 64 RQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred HHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 45799999999999984 889998874
No 69
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=95.10 E-value=0.024 Score=40.64 Aligned_cols=29 Identities=21% Similarity=0.109 Sum_probs=22.8
Q ss_pred CCCCCCccHHHHHHHHHH-hCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITK-FGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~~ 63 (66)
+-.|||||||||.+|.+. +.|++++.++.
T Consensus 91 l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKWYRKGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHHHHhCCCCHHHHHhcc
Confidence 346799999999999993 24889887654
No 70
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=94.90 E-value=0.004 Score=34.88 Aligned_cols=33 Identities=18% Similarity=0.252 Sum_probs=21.9
Q ss_pred HhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHH
Q 035374 26 SLVGDKADNIPGVEGIGDVRAVQLITKFGMLVF 58 (66)
Q Consensus 26 ~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~ 58 (66)
.+.--+.+.+..||||||++|..+.+-|.+.++
T Consensus 28 ~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n 60 (64)
T PF12826_consen 28 ALMNASVEELSAIPGIGPKIAQSIYEFFQDPEN 60 (64)
T ss_dssp HHCC--HHHHCTSTT--HHHHHHHHHHHH-HHH
T ss_pred HHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHh
Confidence 344444566788999999999999999877654
No 71
>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=94.84 E-value=0.019 Score=28.34 Aligned_cols=16 Identities=38% Similarity=0.395 Sum_probs=12.7
Q ss_pred CCCCCCCccHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQL 49 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~L 49 (66)
.+..++|||+|++.+|
T Consensus 12 pi~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL 27 (32)
T ss_dssp BGGGSTTS-HHHHHHH
T ss_pred CHHhhCCccHHHHHHH
Confidence 4667899999999985
No 72
>PRK08609 hypothetical protein; Provisional
Probab=94.61 E-value=0.041 Score=42.08 Aligned_cols=28 Identities=14% Similarity=0.096 Sum_probs=22.8
Q ss_pred CCCCCccHHHHHHHHHHh--CCHHHHHhhh
Q 035374 36 PGVEGIGDVRAVQLITKF--GMLVFNVECF 63 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~f--gsl~~i~~~~ 63 (66)
-.|||||||+|.+|.++. .|++++.+++
T Consensus 91 ~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~ 120 (570)
T PRK08609 91 LKLPGLGGKKIAKLYKELGVVDKESLKEAC 120 (570)
T ss_pred hcCCCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 468999999999999865 5888887654
No 73
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=94.57 E-value=0.043 Score=38.90 Aligned_cols=27 Identities=22% Similarity=0.126 Sum_probs=21.5
Q ss_pred CCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374 36 PGVEGIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
-+|||||||+|.+|... +.|++++..+
T Consensus 88 ~~i~GiGpk~a~~l~~lGi~sl~dL~~a 115 (307)
T cd00141 88 LRVPGVGPKTARKLYELGIRTLEDLRKA 115 (307)
T ss_pred HcCCCCCHHHHHHHHHcCCCCHHHHHHH
Confidence 36899999999999932 5588888765
No 74
>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=94.26 E-value=0.016 Score=31.72 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=18.4
Q ss_pred CCCCCCCCCccHHHHHHHHHHh
Q 035374 32 ADNIPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~f 53 (66)
.+.+..|||||+++|.+|+...
T Consensus 37 ~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 37 PEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHHHTSTTSSHHHHHHHHHHH
T ss_pred HHHHhcCCCCCHHHHHHHHHHH
Confidence 3567788999999999999864
No 75
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=94.20 E-value=0.035 Score=43.66 Aligned_cols=27 Identities=26% Similarity=0.436 Sum_probs=24.7
Q ss_pred CCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 36 PGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
-|||.||+++|..|-+.|+|+++++++
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a 540 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAA 540 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhc
Confidence 478999999999999999999999864
No 76
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=94.14 E-value=0.053 Score=35.14 Aligned_cols=25 Identities=24% Similarity=0.295 Sum_probs=19.2
Q ss_pred CCCCCccHHHHHHHHH------HhCCHHHHH
Q 035374 36 PGVEGIGDVRAVQLIT------KFGMLVFNV 60 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~------~fgsl~~i~ 60 (66)
..+||||+|+|.+++. .|.|++++.
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~ 130 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLA 130 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence 4568999999999887 356777765
No 77
>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=94.10 E-value=0.078 Score=29.57 Aligned_cols=15 Identities=20% Similarity=0.477 Sum_probs=11.8
Q ss_pred CCCccHHHHHHHHHH
Q 035374 38 VEGIGDVRAVQLITK 52 (66)
Q Consensus 38 i~GiG~K~A~~Ll~~ 52 (66)
+||||+++|.++++.
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 577888888888877
No 78
>PRK00254 ski2-like helicase; Provisional
Probab=93.60 E-value=0.057 Score=41.81 Aligned_cols=29 Identities=24% Similarity=0.209 Sum_probs=25.8
Q ss_pred CCCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
.+..|||+|+++|.+|++. |+|++++.++
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 4558899999999999999 9999999764
No 79
>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=93.49 E-value=0.089 Score=36.57 Aligned_cols=26 Identities=15% Similarity=0.224 Sum_probs=23.6
Q ss_pred CCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374 36 PGVEGIGDVRAVQLITK-FGMLVFNVE 61 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~ 61 (66)
..+||||++++.+|.+. |.|++++..
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~ 28 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAV 28 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 46799999999999999 999999875
No 80
>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=93.23 E-value=0.079 Score=41.53 Aligned_cols=37 Identities=19% Similarity=0.377 Sum_probs=25.2
Q ss_pred ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCC--HHHHHh
Q 035374 17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGM--LVFNVE 61 (66)
Q Consensus 17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgs--l~~i~~ 61 (66)
+.+.++.|.. |.. +||||||+|.++++.||. ++.+.+
T Consensus 76 ~~~~i~~yL~-----s~~---~~GIG~~~A~~iv~~fg~~~~~~i~~ 114 (720)
T TIGR01448 76 SKEGIVAYLS-----SRS---IKGVGKKLAQRIVKTFGEAAFDVLDD 114 (720)
T ss_pred CHHHHHHHHh-----cCC---CCCcCHHHHHHHHHHhCHhHHHHHHh
Confidence 3456666644 223 589999999999999984 444443
No 81
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=92.68 E-value=0.24 Score=34.03 Aligned_cols=20 Identities=25% Similarity=0.519 Sum_probs=16.2
Q ss_pred CCCCCccHHHHHHHHHH-hCC
Q 035374 36 PGVEGIGDVRAVQLITK-FGM 55 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgs 55 (66)
..+||||+|||.-.|.. ||-
T Consensus 112 ~~LPGVGrKTAnvVL~~a~g~ 132 (211)
T COG0177 112 LSLPGVGRKTANVVLSFAFGI 132 (211)
T ss_pred HhCCCcchHHHHHHHHhhcCC
Confidence 45699999999998887 553
No 82
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=92.38 E-value=0.1 Score=36.82 Aligned_cols=29 Identities=24% Similarity=0.357 Sum_probs=25.7
Q ss_pred CCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
+..||||+..-|..||.+|||++++..+.
T Consensus 197 Lt~i~~VnKtda~~LL~~FgsLq~~~~AS 225 (254)
T KOG2841|consen 197 LTTIPGVNKTDAQLLLQKFGSLQQISNAS 225 (254)
T ss_pred HHhCCCCCcccHHHHHHhcccHHHHHhcC
Confidence 55689999999999999999999998643
No 83
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=90.92 E-value=0.31 Score=32.45 Aligned_cols=23 Identities=22% Similarity=0.384 Sum_probs=19.4
Q ss_pred CCCCCCCCccHHHHHHHHHHhCC
Q 035374 33 DNIPGVEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fgs 55 (66)
..+..+||||+|+|.+++.++..
T Consensus 108 ~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 108 KALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHH
Confidence 35778999999999999988753
No 84
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=90.88 E-value=0.07 Score=36.52 Aligned_cols=17 Identities=24% Similarity=0.421 Sum_probs=13.6
Q ss_pred CCCCCCCccHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLI 50 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll 50 (66)
.+..+||||||+|.++-
T Consensus 13 ~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 13 ALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHhhCCCCChhHHHHHH
Confidence 45667999999998863
No 85
>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=90.43 E-value=0.16 Score=34.07 Aligned_cols=22 Identities=18% Similarity=0.448 Sum_probs=18.4
Q ss_pred CCCCCCCccHHHHHHHHHHhCC
Q 035374 34 NIPGVEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fgs 55 (66)
.+-.+||||+|||--+|..+++
T Consensus 116 ~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 116 RLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HHHcCCCCCHHHHHHHHHHHHH
Confidence 4678899999999998887664
No 86
>PRK00076 recR recombination protein RecR; Reviewed
Probab=90.33 E-value=0.18 Score=34.33 Aligned_cols=18 Identities=28% Similarity=0.385 Sum_probs=14.4
Q ss_pred CCCCCCccHHHHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~ 52 (66)
+..+||||+|+|.++--.
T Consensus 13 l~~LPGIG~KsA~Rla~~ 30 (196)
T PRK00076 13 LRKLPGIGPKSAQRLAFH 30 (196)
T ss_pred HHHCCCCCHHHHHHHHHH
Confidence 456799999999987544
No 87
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.31 E-value=0.18 Score=34.32 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=14.3
Q ss_pred CCCCCCCccHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~ 51 (66)
.+..+||||+|+|.++--
T Consensus 12 ~l~~LPGIG~KsA~RlA~ 29 (195)
T TIGR00615 12 SLKKLPGIGPKSAQRLAF 29 (195)
T ss_pred HHHHCCCCCHHHHHHHHH
Confidence 355679999999998843
No 88
>PRK13844 recombination protein RecR; Provisional
Probab=89.65 E-value=0.22 Score=34.05 Aligned_cols=19 Identities=16% Similarity=0.212 Sum_probs=14.9
Q ss_pred CCCCCCCccHHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+..+||||+|+|.++--.
T Consensus 16 ~l~~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 16 SLRKLPTIGKKSSQRLALY 34 (200)
T ss_pred HHHHCCCCCHHHHHHHHHH
Confidence 3556799999999987544
No 89
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=89.50 E-value=0.39 Score=37.81 Aligned_cols=25 Identities=16% Similarity=0.299 Sum_probs=22.3
Q ss_pred CCCCccHHHHHHHH-HHhCCHHHHHh
Q 035374 37 GVEGIGDVRAVQLI-TKFGMLVFNVE 61 (66)
Q Consensus 37 gi~GiG~K~A~~Ll-~~fgsl~~i~~ 61 (66)
|||+||+++|..|. +.|++++++.+
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 57999999999999 89999998864
No 90
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=89.17 E-value=0.21 Score=27.50 Aligned_cols=29 Identities=24% Similarity=0.444 Sum_probs=20.9
Q ss_pred hhCCCCCCCCCCCCccHHHHHHHHHHhCCHHH
Q 035374 27 LVGDKADNIPGVEGIGDVRAVQLITKFGMLVF 58 (66)
Q Consensus 27 L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~ 58 (66)
|+|- +||+|.||.||+|. ++|+.-.++.+
T Consensus 14 llgi-wdnvptiprigekv--eilktirtvtd 42 (57)
T PF13052_consen 14 LLGI-WDNVPTIPRIGEKV--EILKTIRTVTD 42 (57)
T ss_pred hhhh-hccCCCccccchhh--hHHhhhheeee
Confidence 4564 89999999999985 45665555443
No 91
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=88.89 E-value=0.36 Score=33.84 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=24.4
Q ss_pred CCCCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITK-FGMLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~ 61 (66)
.+..+||||+++|.+|.+. |.|++++.+
T Consensus 7 ~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~ 35 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREAGYDTVEAIAV 35 (317)
T ss_pred cHhhcCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 4567899999999999999 899999865
No 92
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=88.86 E-value=0.36 Score=26.97 Aligned_cols=15 Identities=27% Similarity=0.483 Sum_probs=13.4
Q ss_pred CCCCCCccHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQL 49 (66)
Q Consensus 35 i~gi~GiG~K~A~~L 49 (66)
+.++||||+++|.++
T Consensus 49 ~~~l~gIG~~ia~kI 63 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKI 63 (68)
T ss_dssp HCTSTTTTHHHHHHH
T ss_pred HhhCCCCCHHHHHHH
Confidence 578899999999887
No 93
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=88.32 E-value=0.63 Score=31.49 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=25.9
Q ss_pred ChhHHHHHHHhhCCCCCCC---CCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374 17 KPSQFVDVISLVGDKADNI---PGVEGIGDVRAVQLITK-----FGMLVFNVE 61 (66)
Q Consensus 17 ~p~q~~d~~~L~Gd~~D~i---~gi~GiG~K~A~~Ll~~-----fgsl~~i~~ 61 (66)
+.+.|++|---+|-.+..+ .=+||||.|+.+++|.+ |.|.++|-+
T Consensus 97 ~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 97 NEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp THHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred ChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 5678899887777433332 23699999999999975 888887754
No 94
>PRK10702 endonuclease III; Provisional
Probab=87.99 E-value=0.83 Score=30.95 Aligned_cols=19 Identities=16% Similarity=0.384 Sum_probs=14.8
Q ss_pred CCCCCCCccHHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+-.+||||+|||--++--
T Consensus 110 ~Ll~lpGVG~ktA~~ill~ 128 (211)
T PRK10702 110 ALEALPGVGRKTANVVLNT 128 (211)
T ss_pred HHhcCCcccHHHHHHHHHH
Confidence 3446899999999887643
No 95
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=87.98 E-value=0.54 Score=33.30 Aligned_cols=42 Identities=14% Similarity=0.302 Sum_probs=30.6
Q ss_pred CHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
|...++.+|| + ++.+.+-+...+..+||+||..|.+|.+-|.
T Consensus 207 da~~LL~~Fg--s------Lq~~~~AS~~ele~~~G~G~~kak~l~~~l~ 248 (254)
T KOG2841|consen 207 DAQLLLQKFG--S------LQQISNASEGELEQCPGLGPAKAKRLHKFLH 248 (254)
T ss_pred cHHHHHHhcc--c------HHHHHhcCHhHHHhCcCcCHHHHHHHHHHHh
Confidence 4445556665 3 4455566667789999999999999988764
No 96
>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=87.90 E-value=0.58 Score=28.48 Aligned_cols=26 Identities=15% Similarity=0.051 Sum_probs=20.1
Q ss_pred CCCCCCccHHHHHHHHHH-hCCHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITK-FGMLVFNV 60 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~ 60 (66)
+..|||||+++|..|..= +.|++++.
T Consensus 14 L~~iP~IG~a~a~DL~~LGi~s~~~L~ 40 (93)
T PF11731_consen 14 LTDIPNIGKATAEDLRLLGIRSPADLK 40 (93)
T ss_pred HhcCCCccHHHHHHHHHcCCCCHHHHh
Confidence 456799999999999864 55676664
No 97
>PRK13910 DNA glycosylase MutY; Provisional
Probab=87.79 E-value=1 Score=32.03 Aligned_cols=19 Identities=21% Similarity=0.408 Sum_probs=15.3
Q ss_pred CCCCCCCCccHHHHHHHHH
Q 035374 33 DNIPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~ 51 (66)
+.+-.+||||+|||-.++.
T Consensus 72 ~~L~~LpGIG~kTA~aIl~ 90 (289)
T PRK13910 72 QSLLKLPGIGAYTANAILC 90 (289)
T ss_pred HHHHhCCCCCHHHHHHHHH
Confidence 3455679999999998876
No 98
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=87.76 E-value=0.45 Score=32.51 Aligned_cols=18 Identities=28% Similarity=0.602 Sum_probs=15.0
Q ss_pred CCCCccHHHHHHHHHHhC
Q 035374 37 GVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fg 54 (66)
.+||||+|||--+|...+
T Consensus 123 ~lpGIG~KTAd~vL~~~~ 140 (208)
T PRK01229 123 NIKGIGYKEASHFLRNVG 140 (208)
T ss_pred cCCCCcHHHHHHHHHHcc
Confidence 789999999999995433
No 99
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=86.94 E-value=0.48 Score=29.68 Aligned_cols=18 Identities=17% Similarity=0.281 Sum_probs=14.9
Q ss_pred CCCCCCccHHHHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~ 52 (66)
+..+||||+|+|.-++.-
T Consensus 85 L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 85 LLALPGVGRKTANVVLLF 102 (158)
T ss_pred HHcCCCCCHHHHHHHHHH
Confidence 358899999999987764
No 100
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=86.67 E-value=0.4 Score=35.29 Aligned_cols=35 Identities=31% Similarity=0.676 Sum_probs=26.6
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHH
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQL 49 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~L 49 (66)
+++.++|| .++.++.-+.+.+..|+|||+++|..+
T Consensus 301 k~Ll~~FG--------SL~~Il~As~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 301 ENLVEHFG--------SLQGLLAASIEDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHcC--------CHHHHHcCCHHHHhhCCCcCHHHHHHH
Confidence 45566666 556667766778889999999999984
No 101
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=86.24 E-value=0.53 Score=32.33 Aligned_cols=17 Identities=24% Similarity=0.399 Sum_probs=14.6
Q ss_pred CCCCCCccHHHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~ 51 (66)
+-.+||||++||--+|-
T Consensus 123 Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 123 LLDQKGIGKESADAILC 139 (218)
T ss_pred HHcCCCccHHHHHHHHH
Confidence 55789999999988775
No 102
>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=85.87 E-value=0.72 Score=28.09 Aligned_cols=19 Identities=37% Similarity=0.597 Sum_probs=16.7
Q ss_pred CCCCCccHHHHHHHHHHhC
Q 035374 36 PGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~fg 54 (66)
..|.|||+++|..+.++.|
T Consensus 18 t~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 18 TKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp TTSTTBCHHHHHHHHHHTT
T ss_pred hhhhccCHHHHHHHHHHcC
Confidence 4579999999999999875
No 103
>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=85.76 E-value=1.6 Score=30.70 Aligned_cols=18 Identities=17% Similarity=0.516 Sum_probs=14.3
Q ss_pred CCCCCCCccHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~ 51 (66)
.+-.+||||+|||.-++.
T Consensus 106 ~L~~LpGIG~~TA~~Il~ 123 (275)
T TIGR01084 106 DLAALPGVGRYTAGAILS 123 (275)
T ss_pred HHHhCCCCCHHHHHHHHH
Confidence 445679999999987665
No 104
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=85.69 E-value=1.5 Score=24.18 Aligned_cols=15 Identities=27% Similarity=0.412 Sum_probs=5.9
Q ss_pred CCCCCCCccHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQ 48 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~ 48 (66)
.+..|+|||+++..+
T Consensus 45 dL~~v~gi~~~~~~~ 59 (65)
T PF12836_consen 45 DLKEVPGIGPKTYEK 59 (65)
T ss_dssp GGGGSTT--HHHHHH
T ss_pred HHhhCCCCCHHHHHH
Confidence 334445555554443
No 105
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=84.87 E-value=1.2 Score=30.66 Aligned_cols=44 Identities=16% Similarity=0.177 Sum_probs=28.5
Q ss_pred hhHHHHHHHhhCCCCC---CCCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374 18 PSQFVDVISLVGDKAD---NIPGVEGIGDVRAVQLITK-----FGMLVFNVE 61 (66)
Q Consensus 18 p~q~~d~~~L~Gd~~D---~i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~ 61 (66)
.+.|++|.-=++-.+- .+.=+||||.|+.+.+|.+ |.|.+++.+
T Consensus 112 E~rFV~fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 112 EDRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred hhHHHHHhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 3456665544442211 1234699999999999975 788887754
No 106
>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=84.79 E-value=1.3 Score=25.88 Aligned_cols=28 Identities=18% Similarity=0.399 Sum_probs=21.1
Q ss_pred CCCCCCccHHHHHHHHHH-----hCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITK-----FGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~~ 62 (66)
+..|+|||++.|.+++++ |.|+++++..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R 61 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR 61 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH
Confidence 457899999999999964 6788887754
No 107
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=84.62 E-value=0.75 Score=28.59 Aligned_cols=19 Identities=16% Similarity=0.326 Sum_probs=14.4
Q ss_pred CCCCCCCccHHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+..+||||+|+|.-++..
T Consensus 73 ~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 73 ELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred HHHcCCCCcHHHHHHHHHH
Confidence 3457899999999766544
No 108
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=84.08 E-value=5.6 Score=23.37 Aligned_cols=46 Identities=28% Similarity=0.486 Sum_probs=30.0
Q ss_pred HHHHHhCCCChhHHHHHHHhhC---------CCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 8 DFARKYGELKPSQFVDVISLVG---------DKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 8 ~v~~~~g~i~p~q~~d~~~L~G---------d~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
.++.+|| +++..-.-+...-| ++..-+..|+|||-|+|-++-+++|
T Consensus 13 ~~L~~~g-l~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 13 AFLQEYG-LSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHHTT---HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHHcC-CCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcC
Confidence 4567777 88776555544444 5555555689999999999999986
No 109
>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=83.97 E-value=0.74 Score=30.29 Aligned_cols=19 Identities=16% Similarity=0.323 Sum_probs=15.4
Q ss_pred CCCCCCCccHHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+..+||||+|+|.-++..
T Consensus 107 ~L~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 107 ELVKLPGVGRKTANVVLNV 125 (191)
T ss_pred HHHhCCCCcHHHHHHHHHH
Confidence 4558899999999887754
No 110
>PRK10880 adenine DNA glycosylase; Provisional
Probab=83.52 E-value=2.2 Score=31.18 Aligned_cols=22 Identities=18% Similarity=0.581 Sum_probs=16.5
Q ss_pred CCCCCCCCccHHHHHHHHH-HhC
Q 035374 33 DNIPGVEGIGDVRAVQLIT-KFG 54 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~-~fg 54 (66)
+.+-.+||||+|||-.++. .|+
T Consensus 109 ~~L~~LpGIG~~TA~aIl~~af~ 131 (350)
T PRK10880 109 EEVAALPGVGRSTAGAILSLSLG 131 (350)
T ss_pred HHHhcCCCccHHHHHHHHHHHCC
Confidence 3455679999999998876 344
No 111
>PRK10736 hypothetical protein; Provisional
Probab=83.37 E-value=1.1 Score=33.13 Aligned_cols=22 Identities=9% Similarity=0.054 Sum_probs=19.6
Q ss_pred CCCCccHHHHHHHHHHhCCHHH
Q 035374 37 GVEGIGDVRAVQLITKFGMLVF 58 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgsl~~ 58 (66)
.+||||+++..+|++.|++.++
T Consensus 12 ~~~giG~~~~~~L~~~~~~~~~ 33 (374)
T PRK10736 12 SVSSLYGDKMVRIAHRLLAQSQ 33 (374)
T ss_pred hCCCCCHHHHHHHHHHhcChhh
Confidence 3599999999999999999874
No 112
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=82.45 E-value=4.9 Score=24.94 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=36.8
Q ss_pred HHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH-hCCHHHHH
Q 035374 8 DFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK-FGMLVFNV 60 (66)
Q Consensus 8 ~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~-fgsl~~i~ 60 (66)
...++.+ ++...+..+..+. |- -.|||||+..|.-|++. +.|++++-
T Consensus 34 ~La~~~~-i~~~~l~~w~~~A----dL-~ri~gi~~~~a~LL~~AGv~Tv~~LA 81 (122)
T PF14229_consen 34 ALAKKLG-ISERNLLKWVNQA----DL-MRIPGIGPQYAELLEHAGVDTVEELA 81 (122)
T ss_pred HHHHhcC-CCHHHHHHHHhHH----Hh-hhcCCCCHHHHHHHHHhCcCcHHHHH
Confidence 4667777 9999999887763 33 37899999999988887 56777764
No 113
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=82.21 E-value=2.1 Score=28.17 Aligned_cols=36 Identities=22% Similarity=0.477 Sum_probs=28.2
Q ss_pred hHHHHHHHhhCCCCCC-------CCCCCCccHHHHHHHHHHhC
Q 035374 19 SQFVDVISLVGDKADN-------IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 19 ~q~~d~~~L~Gd~~D~-------i~gi~GiG~K~A~~Ll~~fg 54 (66)
++|-.+.-++|...|+ +..|.|||..+|..++++.|
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 5777777788865544 34579999999999999975
No 114
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=80.63 E-value=2.7 Score=30.20 Aligned_cols=17 Identities=18% Similarity=0.196 Sum_probs=14.4
Q ss_pred CCCCCccHHHHHHHHHH
Q 035374 36 PGVEGIGDVRAVQLITK 52 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~ 52 (66)
-++||||||-|.-.|+.
T Consensus 162 lsLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 162 LSLPGVGPKMAHLTMQV 178 (286)
T ss_pred hcCCCCchHHHHHHHHH
Confidence 36799999999988875
No 115
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=80.13 E-value=3 Score=30.72 Aligned_cols=35 Identities=14% Similarity=0.302 Sum_probs=26.2
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
..+.++|+|.-|+..-+++. +||||+-||..++.-
T Consensus 98 ~~v~~~~~G~~P~~~~~l~~-----------LpGiG~yTa~Ail~~ 132 (342)
T COG1194 98 QEVVERHGGEFPDDEEELAA-----------LPGVGPYTAGAILSF 132 (342)
T ss_pred HHHHHHcCCCCCCCHHHHHh-----------CCCCcHHHHHHHHHH
Confidence 45667777777777666654 489999999998864
No 116
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=79.60 E-value=0.5 Score=33.06 Aligned_cols=35 Identities=23% Similarity=0.380 Sum_probs=26.4
Q ss_pred HHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHH
Q 035374 24 VISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVF 58 (66)
Q Consensus 24 ~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~ 58 (66)
+..+..-+-+.+-.|||||+++|.++++.++.++.
T Consensus 27 ve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 27 VEDVRAADQSELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred HHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc
Confidence 34444444556778899999999999999987653
No 117
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=76.92 E-value=3.7 Score=21.68 Aligned_cols=51 Identities=14% Similarity=0.269 Sum_probs=32.6
Q ss_pred CceeCHHHHHHHhCCCChhHHHHHHHh-hCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 1 MASFGMEDFARKYGELKPSQFVDVISL-VGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 1 ~~~~~~~~v~~~~g~i~p~q~~d~~~L-~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
|..+...++.+++| +++.+++..+.- .|-. ...--..+.+-.|..+..+|+
T Consensus 1 m~~i~V~elAk~l~-v~~~~ii~~l~~~~Gi~--~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 1 MEKIRVSELAKELG-VPSKEIIKKLFKELGIM--VKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp --EE-TTHHHHHHS-SSHHHHHHHH-HHHTS-----SSSS-EETTGGGHHHHHH-
T ss_pred CCceEHHHHHHHHC-cCHHHHHHHHHHhCCcC--cCCCCCcCCHHHHHHHHHHhC
Confidence 45567788999998 999999998855 7853 112225677777777777764
No 118
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=76.65 E-value=1.8 Score=31.91 Aligned_cols=29 Identities=17% Similarity=0.067 Sum_probs=23.5
Q ss_pred CCCCCccHHHHHHHHHH-hCCHHHHHhhhc
Q 035374 36 PGVEGIGDVRAVQLITK-FGMLVFNVECFS 64 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgsl~~i~~~~~ 64 (66)
..|-|||.|+|.+..++ |.|++++.++.+
T Consensus 100 tnifGvG~ktA~~Wy~~GfrTled~Rk~~~ 129 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKWYREGFRTLEDVRKKPD 129 (353)
T ss_pred HHHhccCHHHHHHHHHhhhhHHHHHHhCHH
Confidence 34689999999999988 889998875443
No 119
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=76.37 E-value=6.7 Score=28.80 Aligned_cols=44 Identities=20% Similarity=0.257 Sum_probs=23.4
Q ss_pred HHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC--CHHHHHhhh
Q 035374 20 QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG--MLVFNVECF 63 (66)
Q Consensus 20 q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~~~ 63 (66)
.+.+++--++-....+-.+||+|||+-..|-++++ +++++.+++
T Consensus 80 ~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~ 125 (326)
T COG1796 80 KLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIKDLEELQEAL 125 (326)
T ss_pred HHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHH
Confidence 34444444443344444667777766666666653 455554433
No 120
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=75.82 E-value=5 Score=25.89 Aligned_cols=47 Identities=21% Similarity=0.356 Sum_probs=33.9
Q ss_pred CHHHHHHHhCCCChh---HHHHHHHhhC--CCCCCCCCCCCccHHHHHHHHHH
Q 035374 5 GMEDFARKYGELKPS---QFVDVISLVG--DKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~---q~~d~~~L~G--d~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
+.+++ +.+.|+-|. .+++|.-=-| .+.|.+..|+|||+++-.++...
T Consensus 95 s~eeL-~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 95 SAEEL-QALPGIGPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred CHHHH-HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHHhh
Confidence 45555 444446664 6777776666 66788899999999999887654
No 121
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=75.70 E-value=2.3 Score=28.75 Aligned_cols=20 Identities=30% Similarity=0.747 Sum_probs=17.3
Q ss_pred CCCCCCccHHHHHHHHHHhC
Q 035374 35 IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fg 54 (66)
|.|-||+|.-|+.++|++++
T Consensus 5 ITGTPGvGKTT~~~~L~~lg 24 (180)
T COG1936 5 ITGTPGVGKTTVCKLLRELG 24 (180)
T ss_pred EeCCCCCchHHHHHHHHHhC
Confidence 45779999999999999765
No 122
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=75.51 E-value=2.1 Score=30.20 Aligned_cols=24 Identities=17% Similarity=0.155 Sum_probs=16.7
Q ss_pred CCCCCCCccHHHHHHHH-HHhCCHH
Q 035374 34 NIPGVEGIGDVRAVQLI-TKFGMLV 57 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll-~~fgsl~ 57 (66)
.+-.+||||+|||.-++ .-++..+
T Consensus 208 ~L~~LpGIGpwTA~~vllr~lg~~D 232 (283)
T PRK10308 208 TLQTFPGIGRWTANYFALRGWQAKD 232 (283)
T ss_pred HHhcCCCcCHHHHHHHHHHhCCCCC
Confidence 35678999999996655 4455443
No 123
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=74.68 E-value=2.1 Score=27.75 Aligned_cols=21 Identities=29% Similarity=0.569 Sum_probs=16.6
Q ss_pred CCCCCCCCccHHHHHHHHHHhC
Q 035374 33 DNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
|++.-|.|||||.+..| +..|
T Consensus 67 DDLt~I~GIGPk~e~~L-n~~G 87 (133)
T COG3743 67 DDLTRISGIGPKLEKVL-NELG 87 (133)
T ss_pred ccchhhcccCHHHHHHH-HHcC
Confidence 88999999999987655 4444
No 124
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=73.87 E-value=3 Score=25.74 Aligned_cols=20 Identities=25% Similarity=0.366 Sum_probs=14.6
Q ss_pred CCCCCCccHHHHHHHHHHhC
Q 035374 35 IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fg 54 (66)
++=|.|+||.+|..|++...
T Consensus 52 LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 52 LQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp GGGSTT--HHHHHHHHHHHH
T ss_pred HhHhcCCChHHHHHHHHHHH
Confidence 44569999999999998864
No 125
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=73.54 E-value=3.8 Score=31.87 Aligned_cols=34 Identities=26% Similarity=0.264 Sum_probs=24.5
Q ss_pred HHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 24 VISLVGDKADNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 24 ~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
+..|.-.+.+.+..|+|||+++|..+.+-|.+.+
T Consensus 511 i~~l~~a~~e~l~~i~gIG~~~a~si~~~f~~~~ 544 (562)
T PRK08097 511 WQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPE 544 (562)
T ss_pred HHHHHcCCHHHHhcCCCchHHHHHHHHHHHcCHH
Confidence 3344444445677889999999999999987643
No 126
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=73.53 E-value=1.9 Score=33.87 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=24.3
Q ss_pred HhhCCCCCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 26 SLVGDKADNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 26 ~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
.+.--+.+.+..|+|||+++|..+..-|.+.+
T Consensus 536 ~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~ 567 (665)
T PRK07956 536 ALRAASEEELAAVEGVGEVVAQSIVEFFAVEE 567 (665)
T ss_pred HHHhCCHHHHhccCCcCHHHHHHHHHHHhhhh
Confidence 33333445678899999999999999997643
No 127
>PRK00024 hypothetical protein; Reviewed
Probab=73.15 E-value=2.5 Score=28.91 Aligned_cols=15 Identities=40% Similarity=0.795 Sum_probs=7.5
Q ss_pred CCCCCCccHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQL 49 (66)
Q Consensus 35 i~gi~GiG~K~A~~L 49 (66)
+..|+|||+.+|..|
T Consensus 68 L~~i~GIG~akA~~L 82 (224)
T PRK00024 68 LQSIKGIGPAKAAQL 82 (224)
T ss_pred HhhccCccHHHHHHH
Confidence 334455555555444
No 128
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=73.05 E-value=2.8 Score=29.90 Aligned_cols=19 Identities=26% Similarity=0.504 Sum_probs=16.5
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
++..|| ||||-|...|++.
T Consensus 253 ~iTPVPGGVGp~T~a~L~~N 272 (282)
T PRK14180 253 AITPVPGGVGPMTITELLYN 272 (282)
T ss_pred EeccCCCChhHHHHHHHHHH
Confidence 566778 9999999999987
No 129
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=72.66 E-value=3 Score=25.91 Aligned_cols=20 Identities=35% Similarity=0.597 Sum_probs=17.3
Q ss_pred CCCCCCccHHHHHHHHHHhC
Q 035374 35 IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fg 54 (66)
+..|.|||..+|..+..+.|
T Consensus 17 L~~i~GIG~~~a~~i~~~lg 36 (113)
T TIGR03631 17 LTYIYGIGRTRARKILEKAG 36 (113)
T ss_pred eeeeecccHHHHHHHHHHhC
Confidence 34679999999999999976
No 130
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=72.50 E-value=3.4 Score=26.04 Aligned_cols=20 Identities=30% Similarity=0.557 Sum_probs=17.2
Q ss_pred CCCCCCccHHHHHHHHHHhC
Q 035374 35 IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fg 54 (66)
+..|.|||+.+|..++.+.|
T Consensus 19 L~~I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 19 LTYIYGIGRTRAKEILAAAG 38 (122)
T ss_pred ecccccccHHHHHHHHHHhC
Confidence 34679999999999999975
No 131
>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=72.30 E-value=2.7 Score=29.94 Aligned_cols=17 Identities=18% Similarity=0.108 Sum_probs=13.3
Q ss_pred CCCCCccHHHHHHHHHH
Q 035374 36 PGVEGIGDVRAVQLITK 52 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~ 52 (66)
-.+||||||||--++-.
T Consensus 223 ~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 223 CELPGVGPKVADCICLM 239 (310)
T ss_pred HhCCCccHHHHHHHHHH
Confidence 45899999999876543
No 132
>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=72.22 E-value=5.5 Score=24.30 Aligned_cols=47 Identities=19% Similarity=0.146 Sum_probs=33.5
Q ss_pred HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHH
Q 035374 11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFN 59 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i 59 (66)
..-|--|-..++++....|-.. ...|||+|+++|..+..=|..-...
T Consensus 30 ~aaGi~TL~dL~~~i~~rg~~W--wr~vpglG~~~A~~I~awLa~h~~~ 76 (96)
T PF12482_consen 30 AAAGIRTLADLVDRINRRGGRW--WRAVPGLGAAGARRIEAWLAAHPAL 76 (96)
T ss_pred HHcCCchHHHHHHHHHHccchH--HHhCcccchHHHHHHHHHHHHhHHH
Confidence 3444345678888998888433 5789999999999987766544333
No 133
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=71.66 E-value=3.6 Score=25.92 Aligned_cols=19 Identities=26% Similarity=0.330 Sum_probs=16.6
Q ss_pred CCCCCccHHHHHHHHHHhC
Q 035374 36 PGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~fg 54 (66)
..|.|||+++|.++.++.|
T Consensus 20 t~i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 20 TYIYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccccHHHHHHHHHHcC
Confidence 4579999999999999865
No 134
>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=71.23 E-value=2.2 Score=33.42 Aligned_cols=26 Identities=23% Similarity=0.310 Sum_probs=21.7
Q ss_pred CCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 32 ADNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
.+.+..|+|||+++|..+.+-|.+.+
T Consensus 529 ~eeL~~i~GIG~~~A~~I~~ff~~~~ 554 (652)
T TIGR00575 529 LEELLSVEGVGPKVAESIVNFFHDPN 554 (652)
T ss_pred HHHHhcCCCcCHHHHHHHHHHHhhhh
Confidence 34577889999999999999997744
No 135
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=71.22 E-value=3.2 Score=32.23 Aligned_cols=22 Identities=5% Similarity=-0.227 Sum_probs=13.4
Q ss_pred CCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 37 GVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
|||+||+++|.. .|++++++.+
T Consensus 495 GI~~vG~~~ak~---~~~~i~~l~~ 516 (562)
T PRK08097 495 GIPLPQAALNAL---DDRSWQQLLS 516 (562)
T ss_pred CCccHHHHHHHH---hcCCHHHHHc
Confidence 456667765554 6666666653
No 136
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=70.82 E-value=4.3 Score=28.94 Aligned_cols=19 Identities=21% Similarity=0.464 Sum_probs=15.6
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
++..|| |+||.|...|+++
T Consensus 254 ~iTPVPGGVGp~T~a~L~~n 273 (286)
T PRK14175 254 AITPVPGGVGPLTITMVLNN 273 (286)
T ss_pred CcCCCCCCCHHHHHHHHHHH
Confidence 456665 6999999999987
No 137
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=69.96 E-value=4.4 Score=28.70 Aligned_cols=31 Identities=19% Similarity=0.308 Sum_probs=25.0
Q ss_pred CCCCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 33 DNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
.-+..++|||+|+|..+-+-|.+..+..+..
T Consensus 214 ~eL~~v~gig~k~A~~I~~~~~t~~~~~~~~ 244 (254)
T COG1948 214 EELMKVKGIGEKKAREIYRFLRTEYKLIEAL 244 (254)
T ss_pred HHHHHhcCccHHHHHHHHHHHhchhhhhccc
Confidence 4456789999999999999999987765443
No 138
>PRK14973 DNA topoisomerase I; Provisional
Probab=69.75 E-value=7.8 Score=31.82 Aligned_cols=59 Identities=20% Similarity=0.202 Sum_probs=43.2
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhC-C---------------CC-CCCCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVG-D---------------KA-DNIPGVEGIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~G-d---------------~~-D~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
..+++.+....| ++++.......+++ + .. -.+..|+|+||+|..+|-+. +-+.+.+.++
T Consensus 831 ~a~p~~La~~~g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ag~~~~e~l~~~ 907 (936)
T PRK14973 831 SVHPAYLALKTG-ISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGETTLEKLYLAGVYDGDLLVSA 907 (936)
T ss_pred hcCHHHHhcCCC-CChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCHHHHHHHHHcCCCCHHHhccC
Confidence 356778888887 99999999988888 2 11 11567899999999777655 4567766643
No 139
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=69.35 E-value=3.9 Score=29.54 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=21.7
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~ 61 (66)
.+..+||||++++.++++++| ++.++.+
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~ 212 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAG 212 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHh
Confidence 456789999999999998876 5555543
No 140
>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=69.08 E-value=5.6 Score=24.15 Aligned_cols=23 Identities=30% Similarity=0.538 Sum_probs=14.9
Q ss_pred hCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 28 VGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 28 ~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
+|+ -.+.-+|||||+.+.+|-.+
T Consensus 16 MGe--K~V~~laGIG~~lg~~L~~~ 38 (89)
T PF02961_consen 16 MGE--KPVTELAGIGPVLGKRLEEK 38 (89)
T ss_dssp -TT---BGGGSTT--HHHHHHHHHT
T ss_pred cCC--CCccccCCcCHHHHHHHHHC
Confidence 676 33667899999998888766
No 141
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=68.83 E-value=5.9 Score=31.37 Aligned_cols=25 Identities=24% Similarity=0.500 Sum_probs=21.3
Q ss_pred CCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 33 DNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
+.+..|+|||+++|..+..-|.+.+
T Consensus 541 e~l~~i~giG~~~a~si~~ff~~~~ 565 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFNDKI 565 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHcCHH
Confidence 3567899999999999999997754
No 142
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.15 E-value=3.7 Score=28.05 Aligned_cols=20 Identities=35% Similarity=0.718 Sum_probs=12.4
Q ss_pred CCCCCCCCccHHHHHHHHHH
Q 035374 33 DNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~ 52 (66)
+.+..|+|||+.+|..|+.-
T Consensus 60 ~eL~~i~GiG~aka~~l~a~ 79 (218)
T TIGR00608 60 EELSSVPGIGEAKAIQLKAA 79 (218)
T ss_pred HHHHhCcCCcHHHHHHHHHH
Confidence 34556677777777666543
No 143
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=68.06 E-value=3.5 Score=30.68 Aligned_cols=17 Identities=29% Similarity=0.380 Sum_probs=14.4
Q ss_pred CCCCCccHHHHHHHHHH
Q 035374 36 PGVEGIGDVRAVQLITK 52 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~ 52 (66)
-.|||||+|+|..++-.
T Consensus 333 lRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 333 LRVPGIGVKSARRIVMT 349 (404)
T ss_pred cccCCCChHHHHHHHHH
Confidence 36899999999998754
No 144
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=67.65 E-value=3.9 Score=28.96 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=14.1
Q ss_pred CCCCCCccHHHHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~ 52 (66)
+..++|||++||.-+|-.
T Consensus 200 L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 200 LTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHcCCCcCHHHHHHHHHH
Confidence 345899999999877654
No 145
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=67.12 E-value=4.8 Score=26.08 Aligned_cols=19 Identities=37% Similarity=0.641 Sum_probs=16.6
Q ss_pred CCCCCccHHHHHHHHHHhC
Q 035374 36 PGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~fg 54 (66)
..|.|||+++|..++++.|
T Consensus 24 t~I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 24 TGIKGIGRRFARAIARKLG 42 (144)
T ss_pred cceeccCHHHHHHHHHHcC
Confidence 4579999999999999875
No 146
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=66.09 E-value=4.4 Score=27.64 Aligned_cols=18 Identities=33% Similarity=0.695 Sum_probs=15.3
Q ss_pred CCCCCCccHHHHHHHHHH
Q 035374 35 IPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~ 52 (66)
+.||||+|..|..+...+
T Consensus 9 itGVpGvGKTTVl~~~~~ 26 (189)
T COG2019 9 ITGVPGVGKTTVLKIALK 26 (189)
T ss_pred EEcCCCCChHHHHHHHHH
Confidence 568999999999887766
No 147
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=65.91 E-value=3.3 Score=33.08 Aligned_cols=24 Identities=29% Similarity=0.498 Sum_probs=19.7
Q ss_pred CCCCCCCCCccHHHHHHHHHHhCC
Q 035374 32 ADNIPGVEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~fgs 55 (66)
.+.+..|+|||+++|.++++.+..
T Consensus 668 ~eELa~V~Gig~k~Ae~I~~~L~~ 691 (694)
T PRK14666 668 EEGLAAVPGIGPARAAALHEHLKT 691 (694)
T ss_pred HHHHHhcCCcCHHHHHHHHHHHHH
Confidence 456788899999999999887643
No 148
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=65.49 E-value=5.8 Score=25.87 Aligned_cols=36 Identities=28% Similarity=0.617 Sum_probs=26.2
Q ss_pred hHHHHHHHhhCCCCCC-------CCCCCCccHHHHHHHHHHhC
Q 035374 19 SQFVDVISLVGDKADN-------IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 19 ~q~~d~~~L~Gd~~D~-------i~gi~GiG~K~A~~Ll~~fg 54 (66)
++|-++--++|...++ +..|.|||+++|.+++++.|
T Consensus 4 ~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 4 EEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred hhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcC
Confidence 4556666677754443 34578999999999999875
No 149
>PRK02362 ski2-like helicase; Provisional
Probab=63.81 E-value=8.3 Score=30.16 Aligned_cols=27 Identities=26% Similarity=0.327 Sum_probs=22.0
Q ss_pred CCCCCCccHHHHHHHHHH-hCCHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITK-FGMLVFNVE 61 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-fgsl~~i~~ 61 (66)
+-.|||+|+++|.+|.+. +.|++++.+
T Consensus 654 L~~ip~i~~~~a~~l~~~gi~s~~dl~~ 681 (737)
T PRK02362 654 LVGLRGVGRVRARRLYNAGIESRADLRA 681 (737)
T ss_pred HhCCCCCCHHHHHHHHHcCCCCHHHHHh
Confidence 346899999999999875 568888874
No 150
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=63.70 E-value=4.4 Score=32.12 Aligned_cols=27 Identities=15% Similarity=0.232 Sum_probs=22.4
Q ss_pred CCCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 31 KADNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 31 ~~D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
+.+.+..|+|||+++|..+.+-|.+.+
T Consensus 558 s~eeL~~i~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 558 DEEALRAVDDVGPTVAEEIREFFDSER 584 (689)
T ss_pred CHHHHhccCCcCHHHHHHHHHHHhhhH
Confidence 345677899999999999999987765
No 151
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=62.68 E-value=8.5 Score=29.93 Aligned_cols=40 Identities=13% Similarity=0.292 Sum_probs=28.1
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
..+++.|| +.+.+.+ -+.+.+..+||||++.|..+.+-|.
T Consensus 557 k~Ll~~Fg--S~~~i~~------As~eeL~~v~Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 557 KALLKHFG--SLKAIKE------ASVEELAKVPGISKKLAEAIYEALH 596 (598)
T ss_pred HHHHHHcC--CHHHHHh------CCHHHHhhcCCcCHHHHHHHHHHhc
Confidence 45667776 5555543 2234567889999999999988765
No 152
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=60.45 E-value=4.1 Score=31.70 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=24.9
Q ss_pred CCCCCCCCccHHHHHHHHHH--hCCHHHHHhh
Q 035374 33 DNIPGVEGIGDVRAVQLITK--FGMLVFNVEC 62 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~--fgsl~~i~~~ 62 (66)
+-+..|||||.|++.+++.+ |.|.+++++.
T Consensus 516 ~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~~ 547 (560)
T COG1031 516 DVLRAIPGIGKKTLRKILAERPFKSSEEFLKL 547 (560)
T ss_pred HHHHhcccchhhhHHHHHhcCCccchHHHHhc
Confidence 34677899999999999988 7789888753
No 153
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=59.37 E-value=12 Score=29.03 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=25.4
Q ss_pred CCCCCCccHHHHHHHHHHhCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
+..||||+.-+|..+..+|.|+-.++.+.
T Consensus 432 LMqvkg~S~erAiAI~d~YpTl~sLl~AY 460 (501)
T KOG2379|consen 432 LMQVKGMSLERAIAIADRYPTLRSLLSAY 460 (501)
T ss_pred HHhccCccHHHHHHHHHhccCHHHHHHHH
Confidence 34689999999999999999999988754
No 154
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=58.69 E-value=16 Score=19.96 Aligned_cols=27 Identities=19% Similarity=0.589 Sum_probs=21.8
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDK 31 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~ 31 (66)
+....+.++|| +|++|+...-.-+|.+
T Consensus 21 ~ev~ywa~~~g-vt~~~L~~AV~~vG~~ 47 (57)
T PF12244_consen 21 YEVRYWAKRFG-VTEEQLREAVRAVGNS 47 (57)
T ss_pred HHHHHHHHHHC-cCHHHHHHHHHHHCcC
Confidence 34567889998 9999999888888853
No 155
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=58.38 E-value=16 Score=27.29 Aligned_cols=38 Identities=26% Similarity=0.539 Sum_probs=26.0
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHH--HHHHH
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAV--QLITK 52 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~--~Ll~~ 52 (66)
.++...+..-|. .+|+.|-++.. +|||||+|.. .|+.+
T Consensus 260 ~i~~~~l~~~ye-~~p~Df~elLl-----------~~GiGpstvRALalVAE 299 (373)
T COG1415 260 RLNWRRLRRLYE-LNPDDFEELLL-----------VPGIGPSTVRALALVAE 299 (373)
T ss_pred cCcHHHHHhhhh-cCcccHHHHHh-----------ccCCCHHHHHHHHHHHH
Confidence 456666777776 88887776654 3899998754 44544
No 156
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=58.29 E-value=8.4 Score=26.87 Aligned_cols=17 Identities=35% Similarity=0.761 Sum_probs=8.1
Q ss_pred CCCCCCCCccHHHHHHH
Q 035374 33 DNIPGVEGIGDVRAVQL 49 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~L 49 (66)
..+-.+||||+..|.++
T Consensus 66 ~el~~v~GiG~aka~~l 82 (224)
T COG2003 66 EELSSVKGIGLAKAIQI 82 (224)
T ss_pred HHHhhCCCccHHHHHHH
Confidence 33444555555544443
No 157
>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=57.67 E-value=12 Score=29.50 Aligned_cols=26 Identities=12% Similarity=0.295 Sum_probs=20.7
Q ss_pred CCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 32 ADNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
-+.+..|||||+|++..+.+.+....
T Consensus 116 ~~~L~~v~gi~~~~~~~i~~~~~~~~ 141 (720)
T TIGR01448 116 PEKLLEVPGISKANLEKFVSQWSQQG 141 (720)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHHhH
Confidence 34677899999999999999886443
No 158
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=56.56 E-value=12 Score=18.48 Aligned_cols=19 Identities=37% Similarity=0.660 Sum_probs=9.2
Q ss_pred eCHHHHHHHhCCCChhHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVD 23 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d 23 (66)
++.+++.+..| +++..|..
T Consensus 9 ~~l~~iA~~~g-~S~~~f~r 27 (42)
T PF00165_consen 9 LTLEDIAEQAG-FSPSYFSR 27 (42)
T ss_dssp --HHHHHHHHT-S-HHHHHH
T ss_pred CCHHHHHHHHC-CCHHHHHH
Confidence 44556666665 56655543
No 159
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=55.68 E-value=14 Score=27.12 Aligned_cols=20 Identities=20% Similarity=0.574 Sum_probs=17.7
Q ss_pred CCCCCCCccHHHHHHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~f 53 (66)
.+.+++|.|+|++.++++.-
T Consensus 129 ~~~~l~GfG~kse~~il~~i 148 (326)
T COG1796 129 KIRGLRGFGKKSEAKILENI 148 (326)
T ss_pred CccccCCccchhHHHHHHHH
Confidence 67889999999999999863
No 160
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=55.63 E-value=13 Score=26.46 Aligned_cols=19 Identities=26% Similarity=0.503 Sum_probs=15.5
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
++..+| |+||.|...|+++
T Consensus 247 ~iTPVPGGVGp~T~a~L~~N 266 (279)
T PRK14178 247 AITPVPGGVGPMTIATLMEN 266 (279)
T ss_pred CcCCCCCCCHHHHHHHHHHH
Confidence 456665 6999999999987
No 161
>PRK00254 ski2-like helicase; Provisional
Probab=55.42 E-value=5 Score=31.28 Aligned_cols=24 Identities=25% Similarity=0.457 Sum_probs=20.1
Q ss_pred CCCCCCCCCccHHHHHHHHHHhCC
Q 035374 32 ADNIPGVEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~fgs 55 (66)
.+.+..+||||+|+|.++.+.+++
T Consensus 677 ~~el~~~~gi~~~~a~~i~~~~~~ 700 (720)
T PRK00254 677 PSELLKVEGIGAKIVEGIFKHLGV 700 (720)
T ss_pred HHHHhcCCCCCHHHHHHHHHHhcc
Confidence 466778999999999999888763
No 162
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=55.28 E-value=9.8 Score=27.16 Aligned_cols=18 Identities=28% Similarity=0.523 Sum_probs=14.7
Q ss_pred CCCCC-CccHHHHHHHHHH
Q 035374 35 IPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 35 i~gi~-GiG~K~A~~Ll~~ 52 (66)
+..+| ||||-|..-|+++
T Consensus 255 iTPVPGGVGp~T~a~Ll~N 273 (285)
T PRK14189 255 ITPVPGGVGPMTITMLLVN 273 (285)
T ss_pred ecCCCCCchHHHHHHHHHH
Confidence 44455 8999999999987
No 163
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=54.03 E-value=19 Score=27.17 Aligned_cols=29 Identities=14% Similarity=0.237 Sum_probs=23.9
Q ss_pred CCCCCCccHHHHHHHHHH------hCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITK------FGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~------fgsl~~i~~~~ 63 (66)
+-.|+|||+..+.+++++ |.|+.+++..+
T Consensus 116 L~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rv 150 (449)
T PRK07373 116 LSAVRNLGEGAIESILKAREEGGEFKSLADFCDRV 150 (449)
T ss_pred chhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHh
Confidence 567899999999999863 88898887644
No 164
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=53.58 E-value=11 Score=26.21 Aligned_cols=30 Identities=20% Similarity=0.264 Sum_probs=21.3
Q ss_pred HHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 23 DVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 23 d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+|...|-+.|...-+.|.|+..|.+.++-
T Consensus 189 ~L~rf~gaSrdE~e~l~g~g~~ka~~~iey 218 (224)
T COG5241 189 KLCRFNGASRDEFELLLGFGFEKAAKYIEY 218 (224)
T ss_pred HHHHHhccchhHHHHHHccCHHHHHHHHHH
Confidence 456667777777777777777777777653
No 165
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=52.88 E-value=11 Score=30.05 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=29.3
Q ss_pred HHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHH
Q 035374 20 QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLV 57 (66)
Q Consensus 20 q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~ 57 (66)
+|-.+..|.--+.+.+..|||||++.|..+..=|...+
T Consensus 530 ~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~~~~ 567 (667)
T COG0272 530 HFGTLEALLAASEEELASIPGIGEVVARSIIEFFANEE 567 (667)
T ss_pred HhhhHHHHHhcCHHHHhhccchhHHHHHHHHHHHcCHH
Confidence 44455566655567778899999999999999998754
No 166
>PRK07945 hypothetical protein; Provisional
Probab=51.96 E-value=11 Score=27.13 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=14.7
Q ss_pred CCCCCCCccHHHHHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~ 51 (66)
.+..|||||+.+|.++-.
T Consensus 50 ~l~~~~giG~~~a~~i~e 67 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQ 67 (335)
T ss_pred CcccCCCcCHHHHHHHHH
Confidence 567899999999987643
No 167
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=51.78 E-value=23 Score=20.38 Aligned_cols=17 Identities=29% Similarity=0.497 Sum_probs=14.8
Q ss_pred CHHHHHHHhCCCChhHHH
Q 035374 5 GMEDFARKYGELKPSQFV 22 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~ 22 (66)
|++.+.++|+ +|++|.-
T Consensus 25 dp~a~~~~~~-Lt~eE~~ 41 (77)
T cd07321 25 DPEAVLAEYG-LTPEEKA 41 (77)
T ss_pred CHHHHHHHcC-CCHHHHH
Confidence 6788999998 9999876
No 168
>PRK01172 ski2-like helicase; Provisional
Probab=51.51 E-value=15 Score=28.25 Aligned_cols=29 Identities=21% Similarity=0.233 Sum_probs=24.1
Q ss_pred CCCCCCCccHHHHHHHHHH-hCCHHHHHhh
Q 035374 34 NIPGVEGIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
.+..|||+|..+|.+|.+. +.|++++.+.
T Consensus 613 ~L~~ip~~~~~~a~~l~~~g~~~~~di~~~ 642 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDAGFKTVDDIARS 642 (674)
T ss_pred hhcCCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 3457899999999999997 7889888753
No 169
>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=51.39 E-value=15 Score=20.49 Aligned_cols=20 Identities=10% Similarity=0.295 Sum_probs=15.7
Q ss_pred CCCCCCCCccHHHHHHHHHH
Q 035374 33 DNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~ 52 (66)
+.+-.+||+|+|+..++.+.
T Consensus 44 ~~L~~i~n~G~ksl~EI~~~ 63 (66)
T PF03118_consen 44 EDLLKIKNFGKKSLEEIKEK 63 (66)
T ss_dssp HHHHTSTTSHHHHHHHHHHH
T ss_pred HHHHhCCCCCHhHHHHHHHH
Confidence 45667899999999887654
No 170
>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model. AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.
Probab=51.21 E-value=7.8 Score=24.90 Aligned_cols=19 Identities=21% Similarity=0.543 Sum_probs=13.4
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|+||+|+-+..+.|.+-
T Consensus 4 leg~PG~GKT~la~~lA~~ 22 (131)
T PF07726_consen 4 LEGVPGVGKTTLAKALARS 22 (131)
T ss_dssp EES---HHHHHHHHHHHHH
T ss_pred eECCCccHHHHHHHHHHHH
Confidence 4688999999999988874
No 171
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=50.03 E-value=19 Score=26.63 Aligned_cols=28 Identities=18% Similarity=0.171 Sum_probs=23.3
Q ss_pred CCCCCCccHHHHHHHHHHhCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITKFGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fgsl~~i~~~ 62 (66)
+..||-+-.+-+.++++.|+++.+++++
T Consensus 295 l~kIpRlp~~iv~nlV~~F~~l~~il~A 322 (349)
T COG1623 295 LNKIPRLPFAIVENLVRAFGTLDGILEA 322 (349)
T ss_pred HhcCcCccHHHHHHHHHHHhhHHHHHHh
Confidence 3457788889999999999999999864
No 172
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=49.46 E-value=14 Score=23.59 Aligned_cols=18 Identities=39% Similarity=0.514 Sum_probs=16.0
Q ss_pred CCCCccHHHHHHHHHHhC
Q 035374 37 GVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fg 54 (66)
.|.|||..+|.+++++-+
T Consensus 21 ~IyGIG~~~a~~I~~~~g 38 (121)
T COG0099 21 YIYGIGRRRAKEICKKAG 38 (121)
T ss_pred hhccccHHHHHHHHHHcC
Confidence 479999999999999865
No 173
>PRK08609 hypothetical protein; Provisional
Probab=49.31 E-value=21 Score=27.49 Aligned_cols=20 Identities=10% Similarity=0.395 Sum_probs=16.4
Q ss_pred CCCCCCCCccHHHHHHHHHH
Q 035374 33 DNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~ 52 (66)
..+..+||+|+|++.++++-
T Consensus 123 ~~~~~~~gfg~k~~~~il~~ 142 (570)
T PRK08609 123 GKVQALAGFGKKTEEKILEA 142 (570)
T ss_pred CChhhccCcchhHHHHHHHH
Confidence 46778999999999998543
No 174
>PF09293 RNaseH_C: T4 RNase H, C terminal; 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: 1TFR_A 3H8S_A 2IHN_A 3H7I_A 3H8W_A 3H8J_A.
Probab=48.23 E-value=8.7 Score=24.53 Aligned_cols=26 Identities=19% Similarity=0.263 Sum_probs=19.1
Q ss_pred ChhHHHHHHHhhCCCCCCCCCCCCcc
Q 035374 17 KPSQFVDVISLVGDKADNIPGVEGIG 42 (66)
Q Consensus 17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG 42 (66)
+|+.=.-++++-||.+|++++|.--+
T Consensus 2 s~~~d~~~KiiKGDkkDgVa~Ik~r~ 27 (122)
T PF09293_consen 2 SPEMDLMTKIIKGDKKDGVASIKVRS 27 (122)
T ss_dssp HHHHHHHHHHHHEBGGGTBE-TTS-T
T ss_pred ChhHHHHHHHHcCCccCCcCceeecc
Confidence 45666667999999999999886544
No 175
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]
Probab=48.03 E-value=18 Score=26.04 Aligned_cols=19 Identities=26% Similarity=0.506 Sum_probs=16.6
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
.+..|| ||||-|..-||+.
T Consensus 252 ~iTPVPGGVGPmTvamLl~N 271 (283)
T COG0190 252 AITPVPGGVGPMTVAMLLEN 271 (283)
T ss_pred ccCCCCCccCHHHHHHHHHH
Confidence 566788 9999999999987
No 176
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=47.54 E-value=11 Score=19.84 Aligned_cols=48 Identities=17% Similarity=0.128 Sum_probs=28.3
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC-CHHHHHhh
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG-MLVFNVEC 62 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg-sl~~i~~~ 62 (66)
++.+++.+..| +++.++. ...-|. .-+.+.++.++...|+ +++.++..
T Consensus 13 lt~~~~a~~~~-i~~~~i~--~~e~g~--------~~~~~~~l~~i~~~~~v~~~~l~~~ 61 (64)
T PF12844_consen 13 LTQKDLAEKLG-ISRSTIS--KIENGK--------RKPSVSTLKKIAEALGVSLDELFDG 61 (64)
T ss_dssp --HHHHHHHHT-S-HHHHH--HHHTTS--------S--BHHHHHHHHHHHTS-HHHHCCC
T ss_pred CCHHHHHHHHC-cCHHHHH--HHHCCC--------cCCCHHHHHHHHHHhCCCHHHHhcc
Confidence 45566777776 7777666 344553 2344788889988888 46666543
No 177
>PRK14181 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=47.01 E-value=17 Score=26.00 Aligned_cols=19 Identities=26% Similarity=0.499 Sum_probs=16.5
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
++..|| ||||-|...|+++
T Consensus 258 ~iTPVPGGVGp~T~a~L~~N 277 (287)
T PRK14181 258 AITPVPGGVGPMTVAMLMRN 277 (287)
T ss_pred cccCCCCchHHHHHHHHHHH
Confidence 466778 9999999999987
No 178
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=46.89 E-value=15 Score=26.43 Aligned_cols=19 Identities=26% Similarity=0.461 Sum_probs=16.0
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
++..|| ||||-|...|++.
T Consensus 258 ~iTPVPGGVGp~Tva~L~~N 277 (301)
T PRK14194 258 AITPVPGGVGPMTIAFLMKN 277 (301)
T ss_pred eecCCCCchhHHHHHHHHHH
Confidence 355677 9999999999987
No 179
>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C ....
Probab=45.99 E-value=15 Score=21.13 Aligned_cols=19 Identities=21% Similarity=0.434 Sum_probs=16.6
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
|-|.||.|.-|..+.|.+.
T Consensus 3 i~G~~GsGKtTia~~L~~~ 21 (129)
T PF13238_consen 3 ISGIPGSGKTTIAKELAER 21 (129)
T ss_dssp EEESTTSSHHHHHHHHHHH
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4588999999999999886
No 180
>smart00153 VHP Villin headpiece domain.
Probab=45.36 E-value=27 Score=17.52 Aligned_cols=19 Identities=26% Similarity=0.621 Sum_probs=15.4
Q ss_pred eCHHHHHHHhCCCChhHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVD 23 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d 23 (66)
++.+++.+-|| +++++|-.
T Consensus 2 LsdeeF~~vfg-msr~eF~~ 20 (36)
T smart00153 2 LSDEDFEEVFG-MTREEFYK 20 (36)
T ss_pred CCHHHHHHHHC-CCHHHHHh
Confidence 46788999998 99988754
No 181
>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=45.32 E-value=13 Score=19.87 Aligned_cols=32 Identities=6% Similarity=0.291 Sum_probs=22.7
Q ss_pred ChhHHHHHHHhhCCCCCCCCCCCCccHHHHHH
Q 035374 17 KPSQFVDVISLVGDKADNIPGVEGIGDVRAVQ 48 (66)
Q Consensus 17 ~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~ 48 (66)
+.+.+.++....=.+.+.+..|+|+|+..+.+
T Consensus 28 ~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~ 59 (68)
T PF00570_consen 28 SDEALLEIAKRLPTSIEELLQIPGMGKRKVRK 59 (68)
T ss_dssp -HHHHHHHHHH--SSHHHHHTSTTCGHHHHHH
T ss_pred CHHHHHHHHHhCCCCHHHHHHccCCCHHHHHH
Confidence 33467777777777788888999999987764
No 182
>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=44.85 E-value=9.3 Score=19.30 Aligned_cols=27 Identities=26% Similarity=0.389 Sum_probs=18.7
Q ss_pred HhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 26 SLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 26 ~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+...+.+.+-.++|+++.+|.+++..
T Consensus 19 ~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 19 DLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 334444455566789999999998765
No 183
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=44.09 E-value=26 Score=17.64 Aligned_cols=20 Identities=25% Similarity=0.659 Sum_probs=14.7
Q ss_pred eCHHHHHHHhCCCChhHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDV 24 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~ 24 (66)
++.+++.+-|| +++++|..+
T Consensus 2 Lsd~dF~~vFg-m~~~eF~~l 21 (36)
T PF02209_consen 2 LSDEDFEKVFG-MSREEFYKL 21 (36)
T ss_dssp S-HHHHHHHHS-S-HHHHHHS
T ss_pred cCHHHHHHHHC-CCHHHHHHC
Confidence 46789999998 999988643
No 184
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=43.72 E-value=15 Score=20.36 Aligned_cols=19 Identities=16% Similarity=0.184 Sum_probs=17.3
Q ss_pred cHHHHHHHHHHhCCHHHHH
Q 035374 42 GDVRAVQLITKFGMLVFNV 60 (66)
Q Consensus 42 G~K~A~~Ll~~fgsl~~i~ 60 (66)
|.+.|..++++|.-++.++
T Consensus 4 G~~~A~~i~~rH~~le~fl 22 (71)
T PF02742_consen 4 GREIAERILRRHRILEEFL 22 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7889999999999999887
No 185
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=43.47 E-value=19 Score=26.33 Aligned_cols=26 Identities=19% Similarity=0.139 Sum_probs=18.0
Q ss_pred CCCCCCCccHHHHHHHHHHh-CCHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKF-GMLVFN 59 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~f-gsl~~i 59 (66)
-+..+||||++++.+|-+-. .++.++
T Consensus 173 pv~~l~GiG~~~~~kL~~~GI~tigdl 199 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAHGISSVRDL 199 (379)
T ss_pred CccccCCcCHHHHHHHHHcCCCcHHHH
Confidence 45678999999998887641 234444
No 186
>PF01798 Nop: Putative snoRNA binding domain; InterPro: IPR002687 This domain is present in various pre-mRNA processing ribonucleoproteins. The function of the domain is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Proteins have been implicated in an expanding variety of functions during pre-mRNA splicing. Molecular cloning has identified genes encoding spliceosomal proteins that potentially act as novel RNA helicases, GTPases, or protein isomerases. Novel protein-protein and protein-RNA interactions that are required for functional spliceosome formation have also been described. Finally, growing evidence suggests that proteins may contribute directly to the spliceosome's active sites [].; PDB: 3GQX_B 3GQU_A 3NVM_A 3NMU_B 2NNW_C 3NVI_A 3NVK_A 2OZB_E 3SIU_B 3SIV_H ....
Probab=43.38 E-value=23 Score=22.97 Aligned_cols=20 Identities=30% Similarity=0.305 Sum_probs=17.2
Q ss_pred ccHHHHHHHHHHhCCHHHHH
Q 035374 41 IGDVRAVQLITKFGMLVFNV 60 (66)
Q Consensus 41 iG~K~A~~Ll~~fgsl~~i~ 60 (66)
+|+..|.+||..-|+++++-
T Consensus 38 vG~~vaA~Li~~aGgL~~La 57 (150)
T PF01798_consen 38 VGSSVAARLISHAGGLENLA 57 (150)
T ss_dssp HHHHHHHHHHHHHTSHHHHH
T ss_pred HCcHHHHHHHHHcccHHHHH
Confidence 45679999999999999875
No 187
>TIGR00041 DTMP_kinase thymidylate kinase. Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
Probab=42.94 E-value=21 Score=22.57 Aligned_cols=19 Identities=32% Similarity=0.725 Sum_probs=16.7
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|++|.|.-|..++|++.
T Consensus 8 ieG~~GsGKsT~~~~L~~~ 26 (195)
T TIGR00041 8 IEGIDGAGKTTQANLLKKL 26 (195)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5789999999999999875
No 188
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=42.32 E-value=18 Score=20.91 Aligned_cols=19 Identities=21% Similarity=0.324 Sum_probs=16.1
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
|-|.||.|.-|..+.|++.
T Consensus 4 I~G~~gsGKST~a~~La~~ 22 (121)
T PF13207_consen 4 ISGPPGSGKSTLAKELAER 22 (121)
T ss_dssp EEESTTSSHHHHHHHHHHH
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4578999999999998883
No 189
>PRK01184 hypothetical protein; Provisional
Probab=42.28 E-value=27 Score=21.97 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=17.1
Q ss_pred CCCCCCccHHHHHHHHHHhC
Q 035374 35 IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fg 54 (66)
+-|.||-|.-|..+++++++
T Consensus 6 l~G~~GsGKsT~a~~~~~~g 25 (184)
T PRK01184 6 VVGMPGSGKGEFSKIAREMG 25 (184)
T ss_pred EECCCCCCHHHHHHHHHHcC
Confidence 45779999999999988885
No 190
>COG0685 MetF 5,10-methylenetetrahydrofolate reductase [Amino acid transport and metabolism]
Probab=41.98 E-value=32 Score=24.32 Aligned_cols=51 Identities=22% Similarity=0.316 Sum_probs=40.0
Q ss_pred CHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCH
Q 035374 5 GMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl 56 (66)
..+.+..|+- .+.++|..|+--+-+..-++|=+|||-|.+..+-+.+|.++
T Consensus 175 GAd~~iTQ~~-fd~e~~~~~~~~~~~~g~~~pI~~Gimpi~~~~~~~~~~~~ 225 (291)
T COG0685 175 GADFFITQFF-FDVEAFERFAERVRAAGIDIPIIPGIMPVTNFKQLLRFASL 225 (291)
T ss_pred chHHHHHHHc-cCHHHHHHHHHHHHhcCCCCCeeecccccccHHHHHHHHHh
Confidence 4567788887 89999999877775433478889999999998888887654
No 191
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=41.67 E-value=39 Score=16.29 Aligned_cols=20 Identities=15% Similarity=0.496 Sum_probs=14.6
Q ss_pred CHHHHHHHhCCCChhHHHHHH
Q 035374 5 GMEDFARKYGELKPSQFVDVI 25 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~ 25 (66)
+...+.++|+ ++.+++..+-
T Consensus 8 tl~~IA~~~~-~~~~~l~~~N 27 (44)
T PF01476_consen 8 TLWSIAKRYG-ISVDELMELN 27 (44)
T ss_dssp -HHHHHHHTT-S-HHHHHHHC
T ss_pred cHHHHHhhhh-hhHhHHHHhc
Confidence 3567889998 9999988765
No 192
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=41.36 E-value=35 Score=28.50 Aligned_cols=28 Identities=18% Similarity=0.249 Sum_probs=23.6
Q ss_pred CCCCCCccHHHHHHHHHH-----hCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITK-----FGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~~ 62 (66)
+..|+|||+..|..++++ |.|+++++..
T Consensus 818 l~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R 850 (1046)
T PRK05672 818 LRLVRGLGEEAAERIVAARARGPFTSVEDLARR 850 (1046)
T ss_pred hhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHH
Confidence 557899999999999985 8899888753
No 193
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.12 E-value=36 Score=18.04 Aligned_cols=24 Identities=21% Similarity=0.414 Sum_probs=19.3
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|+..++.+.+| ++++.+.-|.- .|
T Consensus 1 yti~eva~~~g-vs~~tlr~y~~-~g 24 (69)
T PF13411_consen 1 YTIKEVAKLLG-VSPSTLRYYER-EG 24 (69)
T ss_dssp EEHHHHHHHTT-TTHHHHHHHHH-TT
T ss_pred CcHHHHHHHHC-cCHHHHHHHHH-hc
Confidence 56788999998 99999887755 44
No 194
>PRK13973 thymidylate kinase; Provisional
Probab=40.69 E-value=23 Score=23.34 Aligned_cols=19 Identities=26% Similarity=0.508 Sum_probs=17.1
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|++|-|.-|-.++|.++
T Consensus 8 iEG~dGsGKtTq~~~l~~~ 26 (213)
T PRK13973 8 FEGGEGAGKSTQIRLLAER 26 (213)
T ss_pred EEcCCCCCHHHHHHHHHHH
Confidence 5799999999999999886
No 195
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=40.45 E-value=20 Score=28.01 Aligned_cols=24 Identities=17% Similarity=-0.013 Sum_probs=19.9
Q ss_pred CCCCCCCCCCccHHHHHHHHHHhC
Q 035374 31 KADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 31 ~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
+.+.+..||||+++.|.++.+.|.
T Consensus 544 s~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 544 NEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred CHHHHHhCCCCCHHHHHHHHHHHH
Confidence 345677889999999999988874
No 196
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.51 E-value=31 Score=23.29 Aligned_cols=27 Identities=19% Similarity=0.357 Sum_probs=21.1
Q ss_pred CCCCCCccHHHHHHHH---HHhCCHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLI---TKFGMLVFNVE 61 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll---~~fgsl~~i~~ 61 (66)
+..+||+|+.+|..+. ..|.+..++-.
T Consensus 190 l~~~pgig~~~a~~i~~~~~~f~~~~~~~~ 219 (303)
T COG3547 190 LASIPGIGELTAAAIADDVGRFPSARQLAA 219 (303)
T ss_pred HHhCCCccHHHHHHHHHHhccCCcHHHHHH
Confidence 4568999999999998 66777766543
No 197
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.32 E-value=48 Score=16.18 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=18.2
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|+..++.+.+| +++..+..+ .--|
T Consensus 1 ~~~~e~a~~~g-v~~~tlr~~-~~~g 24 (49)
T cd04761 1 YTIGELAKLTG-VSPSTLRYY-ERIG 24 (49)
T ss_pred CcHHHHHHHHC-cCHHHHHHH-HHCC
Confidence 46788999998 999988755 3345
No 198
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=38.98 E-value=14 Score=22.01 Aligned_cols=19 Identities=16% Similarity=0.506 Sum_probs=16.0
Q ss_pred HHHHHHHhCCCChhHHHHHH
Q 035374 6 MEDFARKYGELKPSQFVDVI 25 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~ 25 (66)
.+.++++|+ +.|+|++.++
T Consensus 26 ~~~vLk~l~-i~~~qLPkI~ 44 (80)
T COG2012 26 AKEVLKELG-IEPEQLPKIK 44 (80)
T ss_pred HHHHHHHhC-CCHHHCCccc
Confidence 467899998 9999999554
No 199
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=38.73 E-value=46 Score=17.54 Aligned_cols=22 Identities=9% Similarity=0.138 Sum_probs=18.2
Q ss_pred eCHHHHHHHhCCCChhHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|+..++.+.+| ++++.+..|..
T Consensus 1 ~s~~eva~~~g-vs~~tlr~~~~ 22 (70)
T smart00422 1 YTIGEVAKLAG-VSVRTLRYYER 22 (70)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHH
Confidence 56788999998 99999887744
No 200
>PRK07758 hypothetical protein; Provisional
Probab=38.61 E-value=17 Score=22.24 Aligned_cols=30 Identities=20% Similarity=0.213 Sum_probs=21.0
Q ss_pred HHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 23 DVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 23 d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
.+.-|+.-+-+.+-.++|+|+|+-.+|..+
T Consensus 57 TL~dLv~~te~ELl~iknlGkKSL~EIkek 86 (95)
T PRK07758 57 TVEELSKYSEKEILKLHGMGPASLPKLRKA 86 (95)
T ss_pred cHHHHHcCCHHHHHHccCCCHHHHHHHHHH
Confidence 334455555567778899999998887554
No 201
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=38.32 E-value=54 Score=17.43 Aligned_cols=21 Identities=19% Similarity=0.205 Sum_probs=11.9
Q ss_pred eCHHHHHHHhCCCChhHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDV 24 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~ 24 (66)
.+++++.++|..++++|+.+-
T Consensus 32 ~s~eeI~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 32 ESPEEIAEDYPSLTLEDIRAA 52 (56)
T ss_dssp --HHHHHHHSTT--HHHHHHH
T ss_pred CCHHHHHHHCCCCCHHHHHHH
Confidence 356777777766777777643
No 202
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=38.28 E-value=49 Score=19.47 Aligned_cols=17 Identities=24% Similarity=0.448 Sum_probs=14.0
Q ss_pred CHHHHHHHhCCCChhHHH
Q 035374 5 GMEDFARKYGELKPSQFV 22 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~ 22 (66)
|++.+.++|| +|+++..
T Consensus 26 DPea~~~~~g-Lt~eE~~ 42 (81)
T cd07922 26 DPSAVFEEYG-LTPAERA 42 (81)
T ss_pred CHHHHHHHcC-CCHHHHH
Confidence 6788889998 9998765
No 203
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=38.00 E-value=44 Score=24.52 Aligned_cols=30 Identities=23% Similarity=0.598 Sum_probs=17.6
Q ss_pred HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHH--HHHHH
Q 035374 11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAV--QLITK 52 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~--~Ll~~ 52 (66)
.-|. .+|+.|-++.. ++||||+|.. .|+.+
T Consensus 259 ~~~e-~~p~~feeLL~-----------~~GvGp~TlRALaLvae 290 (319)
T PF05559_consen 259 KAYE-RQPSDFEELLL-----------IKGVGPSTLRALALVAE 290 (319)
T ss_pred HHhh-CCccCHHHHHh-----------cCCCCHHHHHHHHHHHH
Confidence 3343 56665555433 4899999754 44444
No 204
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=37.98 E-value=38 Score=19.42 Aligned_cols=19 Identities=16% Similarity=0.368 Sum_probs=15.8
Q ss_pred CCCCCccHHHHHHHHHHhC
Q 035374 36 PGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~fg 54 (66)
-|.||.|..+..+.+.+.-
T Consensus 4 ~G~~G~GKT~l~~~la~~l 22 (132)
T PF00004_consen 4 HGPPGTGKTTLARALAQYL 22 (132)
T ss_dssp ESSTTSSHHHHHHHHHHHT
T ss_pred ECcCCCCeeHHHHHHHhhc
Confidence 4779999999999888763
No 205
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=37.72 E-value=71 Score=20.42 Aligned_cols=36 Identities=25% Similarity=0.338 Sum_probs=26.3
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEG 40 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~G 40 (66)
|+++++.+..| ++..-+--+--=-|=.+..+|||+|
T Consensus 1 MT~eELA~~tG-~srQTINrWvRkegW~T~p~pGVkG 36 (122)
T PF07037_consen 1 MTPEELAELTG-YSRQTINRWVRKEGWKTEPKPGVKG 36 (122)
T ss_pred CCHHHHHHHhC-ccHHHHHHHHHhcCceeccCCcccc
Confidence 57888999998 8877666665566655667777766
No 206
>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=37.30 E-value=31 Score=20.00 Aligned_cols=28 Identities=11% Similarity=0.032 Sum_probs=15.0
Q ss_pred CCCCCCCCccHHHHHHHHHH-hCCHHHHH
Q 035374 33 DNIPGVEGIGDVRAVQLITK-FGMLVFNV 60 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~-fgsl~~i~ 60 (66)
..+..+|+||++....|-+- -.|++++.
T Consensus 3 ~~l~~LpNig~~~e~~L~~vGI~t~~~L~ 31 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVGIHTVEDLR 31 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT--SHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHcCCCCHHHHH
Confidence 34667799999988777554 13555543
No 207
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=36.87 E-value=41 Score=28.62 Aligned_cols=27 Identities=15% Similarity=0.159 Sum_probs=22.7
Q ss_pred CCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITK-----FGMLVFNVE 61 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~ 61 (66)
+..|+|+|+..|..+++. |.|++++..
T Consensus 1152 l~aI~glg~~~a~~Iv~~R~~g~F~s~~Df~~ 1183 (1213)
T TIGR01405 1152 FNAIPGLGENVANSIVEARNEKPFLSKEDLKK 1183 (1213)
T ss_pred hhhcCCCCHHHHHHHHHHHhhCCCCCHHHHHH
Confidence 457899999999999974 889888864
No 208
>PRK08306 dipicolinate synthase subunit A; Reviewed
Probab=36.49 E-value=43 Score=23.48 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=18.7
Q ss_pred CCCCC-CccHHHHHHHHHHhCCHHHHHh
Q 035374 35 IPGVE-GIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 35 i~gi~-GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
.+|+| +++|++|.+++.+ ++.+++.
T Consensus 262 ~~~lpg~vap~ta~~~~~~--~i~~~l~ 287 (296)
T PRK08306 262 APGLPGKVAPKTAGQILAN--VLSQLLA 287 (296)
T ss_pred ECCCCccCCHHHHHHHHHH--HHHHHHH
Confidence 37778 5779999999987 5555553
No 209
>PTZ00205 DNA polymerase kappa; Provisional
Probab=35.92 E-value=22 Score=27.89 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=18.4
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
.+..+||||++++.+| +++| ++.++.
T Consensus 310 pV~ki~GIG~~t~~~L-~~~GI~TigDLa 337 (571)
T PTZ00205 310 GLRSVPGVGKVTEALL-KGLGITTLSDIY 337 (571)
T ss_pred CcceeCCcCHHHHHHH-HHcCCCcHHHHh
Confidence 5678899999999766 5554 444443
No 210
>PF11762 Arabinose_Iso_C: L-arabinose isomerase C-terminal domain; InterPro: IPR024664 The Escherichia coli araBAD operon consists of three genes encoding three enzymes that convert L-arabinose to D-xylulose-5 phosphate. L-arabinose isomerase (AraA) 5.3.1.4 from EC catalyses the conversion of L-arabinose to L-ribulose as the first step in the pathway of L-arabinose utilization as a carbon source []. This entry represents a C-terminal non-catalytic domain in L-arabinose isomerase.; PDB: 4F2D_A 2AJT_C 2HXG_C.
Probab=35.58 E-value=29 Score=21.97 Aligned_cols=17 Identities=18% Similarity=0.270 Sum_probs=12.6
Q ss_pred hCCCChhHHHHHHHhhCC
Q 035374 13 YGELKPSQFVDVISLVGD 30 (66)
Q Consensus 13 ~g~i~p~q~~d~~~L~Gd 30 (66)
++ ++.+|+.||+-++|-
T Consensus 94 ~~-~t~e~~~d~A~~~gi 110 (115)
T PF11762_consen 94 TA-VTAEQLEDFAEMAGI 110 (115)
T ss_dssp SS---HHHHHHHHHHTT-
T ss_pred cc-CCHHHHHHHHHHhCC
Confidence 45 899999999999984
No 211
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=35.03 E-value=46 Score=28.89 Aligned_cols=27 Identities=15% Similarity=0.145 Sum_probs=23.0
Q ss_pred CCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITK-----FGMLVFNVE 61 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~ 61 (66)
+..|+|+|+..|..+++. |.|++++..
T Consensus 1375 l~~I~glG~~~a~~Iv~~R~~g~F~s~~Df~~ 1406 (1437)
T PRK00448 1375 FNALPGLGENVAKSIVEAREEGEFLSKEDLRK 1406 (1437)
T ss_pred chhcCCCCHHHHHHHHHHHhcCCCCCHHHHHH
Confidence 447899999999999985 899988874
No 212
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=34.98 E-value=57 Score=19.06 Aligned_cols=19 Identities=16% Similarity=0.525 Sum_probs=15.3
Q ss_pred CHHHHHHHhCCCChhHHHHH
Q 035374 5 GMEDFARKYGELKPSQFVDV 24 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~ 24 (66)
..+.+..+|| ++..+++.+
T Consensus 15 pFeaI~~~fG-L~E~eVi~l 33 (72)
T TIGR03643 15 PFEAIEQQFG-LSEKEVIKL 33 (72)
T ss_pred CHHHHHHHHC-CCHHHHHHH
Confidence 4678889998 999888754
No 213
>PF13276 HTH_21: HTH-like domain
Probab=34.50 E-value=38 Score=17.85 Aligned_cols=15 Identities=20% Similarity=0.457 Sum_probs=13.5
Q ss_pred CccHHHHHHHHHHhC
Q 035374 40 GIGDVRAVQLITKFG 54 (66)
Q Consensus 40 GiG~K~A~~Ll~~fg 54 (66)
-||.|++..|+++.|
T Consensus 37 ~v~~krV~RlM~~~g 51 (60)
T PF13276_consen 37 RVSRKRVRRLMREMG 51 (60)
T ss_pred cccHHHHHHHHHHcC
Confidence 589999999999975
No 214
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=33.92 E-value=27 Score=24.18 Aligned_cols=21 Identities=29% Similarity=0.485 Sum_probs=18.1
Q ss_pred CCCCCCCCCccHHHHHHHHHH
Q 035374 32 ADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
.|.+..|+||||+.+.+|-.-
T Consensus 157 aDDL~~I~GIGp~~a~~L~ea 177 (221)
T PRK12278 157 ADDLTKITGVGPALAKKLNEA 177 (221)
T ss_pred cchheeccccChHHHHHHHHc
Confidence 588899999999999988654
No 215
>PRK13766 Hef nuclease; Provisional
Probab=33.66 E-value=17 Score=28.36 Aligned_cols=22 Identities=27% Similarity=0.425 Sum_probs=17.0
Q ss_pred CCCCCCCCccHHHHHHHHHHhC
Q 035374 33 DNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
+.+..+||+|+++|..+.+-+.
T Consensus 747 ~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 747 EELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HHHHhCCCCCHHHHHHHHHHHh
Confidence 4566789999999999866543
No 216
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=33.60 E-value=34 Score=23.12 Aligned_cols=19 Identities=26% Similarity=0.616 Sum_probs=17.1
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|+.|-|.-|..++|+++
T Consensus 8 iEGiDGaGKTT~~~~L~~~ 26 (208)
T COG0125 8 IEGIDGAGKTTQAELLKER 26 (208)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 6799999999999999875
No 217
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=33.06 E-value=53 Score=21.41 Aligned_cols=37 Identities=22% Similarity=0.422 Sum_probs=26.8
Q ss_pred CChhHHHHHHHhh--CCCCCCCCCCCCccHHHHHHHHHH
Q 035374 16 LKPSQFVDVISLV--GDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 16 i~p~q~~d~~~L~--Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
++++|..-+..++ ++..--+.|.||-|..++.+.+.+
T Consensus 2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~ 40 (196)
T PF13604_consen 2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAE 40 (196)
T ss_dssp S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHH
Confidence 6788888887765 333445779999999998886654
No 218
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=32.77 E-value=64 Score=18.88 Aligned_cols=19 Identities=21% Similarity=0.581 Sum_probs=14.9
Q ss_pred CHHHHHHHhCCCChhHHHHH
Q 035374 5 GMEDFARKYGELKPSQFVDV 24 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~ 24 (66)
..+.+..+|| ++..+++.+
T Consensus 14 pFeaI~~qfG-l~E~eVi~l 32 (73)
T PF10985_consen 14 PFEAIERQFG-LSEKEVIKL 32 (73)
T ss_pred CHHHHHHHHC-CCHHHHHHH
Confidence 4678888998 888888754
No 219
>cd08305 Pyrin Pyrin: a protein-protein interaction domain. The Pyrin domain (or PYD), also called DAPIN or PAAD, is a subfamily of the Death Domain (DD) superfamily and it functions in several signaling pathways. The Pyrin domain is found at the N-terminus of a variety of proteins and serves as a linker that recruits other domains into signaling complexes. Pyrin-containing proteins include NALPs, ASC (Apoptosis-associated speck-like protein containing a CARD), and the interferon-inducible p200 (IFI-200) family of proteins which includes the human IFI-16, myeloid cell nuclear differentiation antigen (MNDA) and absent in melanoma (AIM) 2. NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR (leucine-rich repeats), a central nucleotide-binding site (NBS) domain or NACHT (for neuronal apoptosis inhibitor protein, CIITA, HET-E and TP1), and an N-terminal protein-protein interaction domain, which is a Pyrin domain in the case
Probab=32.56 E-value=98 Score=17.47 Aligned_cols=40 Identities=15% Similarity=0.093 Sum_probs=30.8
Q ss_pred CCChhHHHHHHHhhCCCCCCCCCCCCccH-----HHHHHHHHHhCCHH
Q 035374 15 ELKPSQFVDVISLVGDKADNIPGVEGIGD-----VRAVQLITKFGMLV 57 (66)
Q Consensus 15 ~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~-----K~A~~Ll~~fgsl~ 57 (66)
.++.++|-.|+.++.+. .+.+|+... ..|..|.+.|+.-.
T Consensus 7 ~L~~~efk~FK~~L~~~---~~~~~~~~~~~a~~~la~lL~~~y~~~~ 51 (73)
T cd08305 7 NITDEELKRFKSLLAND---LFLETKAQLEYTRIQIADLMEQKFGAVS 51 (73)
T ss_pred HcCHHHHHHHHHHHHhc---CCCCCcccccccHHHHHHHHHHHcChhH
Confidence 37899999999999973 567787776 66677788887643
No 220
>PF14270 DUF4358: Domain of unknown function (DUF4358)
Probab=32.51 E-value=29 Score=20.56 Aligned_cols=28 Identities=18% Similarity=0.474 Sum_probs=23.3
Q ss_pred CceeCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 1 MASFGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 1 ~~~~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|..++.+.+...|| ++++.+-++.+-..
T Consensus 12 ~~~~d~~~l~~~yg-i~~~~~~~~~~~~s 39 (106)
T PF14270_consen 12 MKEFDDDMLKKLYG-IDSDDYEDYVIYMS 39 (106)
T ss_pred cccccHHHHHHHhC-CCHHHhceEEEEec
Confidence 45678899999998 99999999876554
No 221
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=32.37 E-value=30 Score=24.08 Aligned_cols=16 Identities=25% Similarity=0.459 Sum_probs=12.4
Q ss_pred CCCCCccHHHHHHHHH
Q 035374 36 PGVEGIGDVRAVQLIT 51 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~ 51 (66)
-+|+|||+-||-.+|-
T Consensus 118 L~iKGIG~ETaDsILl 133 (215)
T COG2231 118 LSIKGIGKETADSILL 133 (215)
T ss_pred HccCCcchhhHHHHHH
Confidence 4679999999976653
No 222
>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
Probab=32.14 E-value=38 Score=20.89 Aligned_cols=19 Identities=21% Similarity=0.608 Sum_probs=16.3
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|++|.|.-|-.+.|.+.
T Consensus 5 ieG~~GsGKtT~~~~L~~~ 23 (200)
T cd01672 5 FEGIDGAGKTTLIELLAER 23 (200)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5688999999999998764
No 223
>PRK03858 DNA polymerase IV; Validated
Probab=32.07 E-value=33 Score=24.57 Aligned_cols=26 Identities=23% Similarity=0.281 Sum_probs=18.4
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
.+..+||||++++.+| +++| ++.++.
T Consensus 174 pl~~l~Gig~~~~~~L-~~~Gi~t~~dl~ 201 (396)
T PRK03858 174 PVRRLWGVGPVTAAKL-RAHGITTVGDVA 201 (396)
T ss_pred ChhhcCCCCHHHHHHH-HHhCCCcHHHHh
Confidence 4567799999999887 4554 555554
No 224
>PRK13975 thymidylate kinase; Provisional
Probab=31.81 E-value=39 Score=21.30 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=16.5
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|++|.|.-|-.++|++.
T Consensus 7 ieG~~GsGKtT~~~~L~~~ 25 (196)
T PRK13975 7 FEGIDGSGKTTQAKLLAEK 25 (196)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5789999999999998874
No 225
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=31.72 E-value=31 Score=26.96 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=19.5
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~ 61 (66)
.+..++|||||+|..| ++.| |+.+++.
T Consensus 10 ~~~~l~gvg~~~~~~l-~~lgi~t~~dll~ 38 (681)
T PRK10917 10 PLTSLKGVGPKTAEKL-AKLGIHTVQDLLL 38 (681)
T ss_pred ChhhcCCCCHHHHHHH-HHcCCCCHHHHhh
Confidence 4566799999998776 4554 6777664
No 226
>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
Probab=31.61 E-value=39 Score=21.33 Aligned_cols=19 Identities=16% Similarity=0.319 Sum_probs=16.8
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|++|.|.-|..+.|+++
T Consensus 4 ieG~~GsGKSTl~~~L~~~ 22 (193)
T cd01673 4 VEGNIGAGKSTLAKELAEH 22 (193)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5688999999999999985
No 227
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. 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; PDB: 2JN6_A 2RN7_A.
Probab=31.57 E-value=56 Score=17.53 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCChhHHHHHHHhh
Q 035374 5 GMEDFARKYGELKPSQFVDVISLV 28 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~~L~ 28 (66)
+...+..+|| |+|.+|..+..-.
T Consensus 25 sv~~va~~~g-i~~~~l~~W~~~~ 47 (76)
T PF01527_consen 25 SVSEVAREYG-ISPSTLYNWRKQY 47 (76)
T ss_dssp HHHHHHHHHT-S-HHHHHHHHHHH
T ss_pred ceEeeecccc-cccccccHHHHHH
Confidence 4567889998 9999998886654
No 228
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=31.48 E-value=70 Score=15.47 Aligned_cols=15 Identities=13% Similarity=0.419 Sum_probs=9.7
Q ss_pred HHhCCCChhHHHHHHH
Q 035374 11 RKYGELKPSQFVDVIS 26 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~ 26 (66)
.+.| ++.+++..|..
T Consensus 13 ~~~G-ls~eeir~FL~ 27 (30)
T PF08671_consen 13 KESG-LSKEEIREFLE 27 (30)
T ss_dssp HHTT---HHHHHHHHH
T ss_pred HHcC-CCHHHHHHHHH
Confidence 5666 99999888754
No 229
>PLN02924 thymidylate kinase
Probab=31.42 E-value=39 Score=22.72 Aligned_cols=19 Identities=16% Similarity=0.420 Sum_probs=16.8
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|++|-|..|-.++|+++
T Consensus 21 iEGiDGsGKsTq~~~L~~~ 39 (220)
T PLN02924 21 LEGLDRSGKSTQCAKLVSF 39 (220)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5789999999999999875
No 230
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=31.22 E-value=25 Score=25.66 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=17.5
Q ss_pred CCCCCCCCCccHHHHHHHHHH
Q 035374 32 ADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 32 ~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
.|.+.-|.||||+.+.+|=.-
T Consensus 262 ~DdL~~I~GiGp~~e~~L~~~ 282 (326)
T PRK12311 262 PDDLKKLTGVSPQIEKKLNDL 282 (326)
T ss_pred chhhhhhccCChhhhhhhhhc
Confidence 589999999999998877443
No 231
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=31.12 E-value=44 Score=20.36 Aligned_cols=17 Identities=18% Similarity=0.165 Sum_probs=14.6
Q ss_pred CHHHHHHHhCCCChhHHH
Q 035374 5 GMEDFARKYGELKPSQFV 22 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~ 22 (66)
|++.+.++|+ +|++|-.
T Consensus 27 D~ea~~~e~g-Lt~Ee~~ 43 (94)
T cd07923 27 DPEALFDEAG-LTEEERT 43 (94)
T ss_pred CHHHHHHHcC-CCHHHHH
Confidence 6788999998 9999765
No 232
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=31.05 E-value=44 Score=25.07 Aligned_cols=32 Identities=22% Similarity=0.266 Sum_probs=25.9
Q ss_pred hhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHH
Q 035374 27 LVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNV 60 (66)
Q Consensus 27 L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~ 60 (66)
.+-....|+..+ ||+.+|.+||.+-|++.++-
T Consensus 258 ~M~~iAPNLtaL--VG~~lAArLIa~AGsL~~La 289 (414)
T PRK14552 258 VMKEVAPNLTAL--VGPSLGARLISLAGGLEELA 289 (414)
T ss_pred HHHhhccHHHHH--HhhHHHHHHHHHhCCHHHHh
Confidence 344434578788 99999999999999999875
No 233
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=30.80 E-value=55 Score=20.60 Aligned_cols=22 Identities=14% Similarity=0.240 Sum_probs=17.3
Q ss_pred CCCccHHHHHHHHHHhC-CHHHH
Q 035374 38 VEGIGDVRAVQLITKFG-MLVFN 59 (66)
Q Consensus 38 i~GiG~K~A~~Ll~~fg-sl~~i 59 (66)
-.|+.||.+.+++++.| ..+++
T Consensus 2 ~~~~nprk~rkmmkkmGik~e~i 24 (115)
T PRK06369 2 MGGMNPRKMKQMMKQMGIDVEEL 24 (115)
T ss_pred CCCCCHHHHHHHHHHcCCcchhc
Confidence 36899999999999987 34444
No 234
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=30.73 E-value=22 Score=26.02 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=22.5
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhCC----CCCCCCCCCCccHHHHHHH
Q 035374 6 MEDFARKYGELKPSQFVDVISLVGD----KADNIPGVEGIGDVRAVQL 49 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~Gd----~~D~i~gi~GiG~K~A~~L 49 (66)
.+.+.++.|+ ...++.|.+. .-+.+-.+||||+|.|-=+
T Consensus 192 a~~l~~~~g~-----~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI 234 (323)
T KOG2875|consen 192 ARALQEKQGG-----LAWLQSLRKSSYEEAREALCSLPGVGPKVADCI 234 (323)
T ss_pred HHHHHHhccc-----chHHHHHhcccHHHHHHHHhcCCCCcchHhhhh
Confidence 3455666663 4444555551 1123446799999998643
No 235
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=30.65 E-value=28 Score=20.75 Aligned_cols=17 Identities=24% Similarity=0.413 Sum_probs=12.1
Q ss_pred CHHHHHHHhCCCChhHHH
Q 035374 5 GMEDFARKYGELKPSQFV 22 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~ 22 (66)
|++.+.++|| +|++|-.
T Consensus 20 D~~a~~~~~~-Lt~eer~ 36 (88)
T PF07746_consen 20 DPEAYLDEYG-LTEEERQ 36 (88)
T ss_dssp -HHHHHHCCT---HHHHH
T ss_pred CHHHHHHHcC-CCHHHHH
Confidence 6788999998 9999875
No 236
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=30.49 E-value=69 Score=17.39 Aligned_cols=31 Identities=10% Similarity=0.397 Sum_probs=21.7
Q ss_pred hhHHHHHHHhhCCCCCCCCCCCCccHHHHHH
Q 035374 18 PSQFVDVISLVGDKADNIPGVEGIGDVRAVQ 48 (66)
Q Consensus 18 p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~ 48 (66)
.+.+.+++...-.+.+.+-.++|+|++...+
T Consensus 32 ~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~ 62 (81)
T smart00341 32 DETLIKMAAALPTNVSELLAIDGVGEEKARR 62 (81)
T ss_pred HHHHHHHHHHCCCCHHHHhcCCCCCHHHHHH
Confidence 3566777766666566677889999876543
No 237
>PRK13976 thymidylate kinase; Provisional
Probab=30.44 E-value=42 Score=22.37 Aligned_cols=19 Identities=21% Similarity=0.677 Sum_probs=16.7
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|+.|-|.-|-.++|.++
T Consensus 5 ~EGiDGsGKsTq~~~L~~~ 23 (209)
T PRK13976 5 FEGIDGSGKTTQSRLLAEY 23 (209)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5799999999999998875
No 238
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=30.39 E-value=70 Score=20.75 Aligned_cols=55 Identities=18% Similarity=0.250 Sum_probs=39.4
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCC---CCCCCCCCCccHHHHHHHHHHhCCHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDK---ADNIPGVEGIGDVRAVQLITKFGMLVFN 59 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~---~D~i~gi~GiG~K~A~~Ll~~fgsl~~i 59 (66)
++.+++.+.+| +++..+..+..|.--+ -+-++..||....+..++++.+..-++.
T Consensus 121 ~s~~~iA~~lg-~s~~~V~r~l~l~~lp~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 (187)
T TIGR00180 121 MTQEDLAKKIG-KSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLALKKKPKL 178 (187)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHHHHcCCHHHHHHHHhccCCCcHHHHHHHHcCCCchHH
Confidence 46678889998 8988777777765421 1234455789999999999998775543
No 239
>PHA03134 thymidine kinase; Provisional
Probab=30.33 E-value=39 Score=24.94 Aligned_cols=23 Identities=17% Similarity=0.263 Sum_probs=19.6
Q ss_pred CCCCCCCCccHHHHHHHHHHhCC
Q 035374 33 DNIPGVEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 33 D~i~gi~GiG~K~A~~Ll~~fgs 55 (66)
-|+.|.-|||+-|..+.|...++
T Consensus 16 vYlDG~~GvGKTT~~~~l~~~~~ 38 (340)
T PHA03134 16 IYLDGAYGIGKSTTGRVMASAAS 38 (340)
T ss_pred EEEeCCCcCCHHHHHHHHHHhcc
Confidence 37889999999999999997543
No 240
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=30.19 E-value=51 Score=27.68 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=24.4
Q ss_pred CCCCCCccHHHHHHHHHH--hCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITK--FGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~--fgsl~~i~~~~ 63 (66)
+..|+|||+..+..++++ |.|+.+++..+
T Consensus 752 L~aIkgvg~~~~~~I~~~R~f~s~~Df~~R~ 782 (1034)
T PRK07279 752 LKNIKGLPRDLAYWIIENRPFSSIEDFLTRL 782 (1034)
T ss_pred hhhcCCCCHHHHHHHHHCCCCCCHHHHHHhc
Confidence 457899999999999986 89998887543
No 241
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=29.90 E-value=73 Score=15.17 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.1
Q ss_pred eCHHHHHHHhCCCChhHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
++.+++.+.+| +++..+-.+..
T Consensus 2 lt~~e~a~~lg-is~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLG-VSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHC-CCHHHHHHHHH
Confidence 67889999998 99998877653
No 242
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=29.82 E-value=86 Score=16.43 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=19.8
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|+..++.+.+| +++..+.-|.--.|
T Consensus 1 ~s~~eva~~~g-vs~~tlr~w~~~~g 25 (68)
T cd01104 1 YTIGAVARLTG-VSPDTLRAWERRYG 25 (68)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHHhCC
Confidence 46789999998 99999997765334
No 243
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=29.78 E-value=76 Score=19.67 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=22.0
Q ss_pred CceeCHHHHHHHhCCCChhHHHHHHH
Q 035374 1 MASFGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 1 ~~~~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|..|+..++.+.+| ++++.+..|--
T Consensus 1 m~~~tI~elA~~~g-vs~~tlR~Ye~ 25 (120)
T TIGR02054 1 MNAYTISRLAEDAG-VSVHVVRDYLL 25 (120)
T ss_pred CCCCcHHHHHHHHC-cCHHHHHHHHH
Confidence 66789999999998 99999998855
No 244
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=29.69 E-value=85 Score=17.49 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=18.2
Q ss_pred eCHHHHHHHhCCCChhHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
+.+.++.+++| +++.++..++.
T Consensus 23 i~lkdIA~~Lg-vs~~tIr~WK~ 44 (60)
T PF10668_consen 23 IKLKDIAEKLG-VSESTIRKWKS 44 (60)
T ss_pred ccHHHHHHHHC-CCHHHHHHHhh
Confidence 56788999998 99999887765
No 245
>PRK02406 DNA polymerase IV; Validated
Probab=29.21 E-value=43 Score=23.54 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=19.5
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~ 61 (66)
.+.-+||||++++.+| +++| ++.++.+
T Consensus 169 pi~~l~giG~~~~~~L-~~~Gi~ti~dl~~ 197 (343)
T PRK02406 169 PVEKIPGVGKVTAEKL-HALGIYTCADLQK 197 (343)
T ss_pred CcchhcCCCHHHHHHH-HHcCCCcHHHHHh
Confidence 4667899999999986 5544 5666653
No 246
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=28.93 E-value=70 Score=27.03 Aligned_cols=28 Identities=14% Similarity=0.260 Sum_probs=23.0
Q ss_pred CCCCCCccHHHHHHHHHH------hCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITK------FGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~------fgsl~~i~~~ 62 (66)
+..|+|||+..|..++++ |.|+++++..
T Consensus 822 L~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R 855 (1135)
T PRK05673 822 LGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCAR 855 (1135)
T ss_pred hhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Confidence 557899999999999963 8888888754
No 247
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.89 E-value=73 Score=26.55 Aligned_cols=28 Identities=18% Similarity=0.374 Sum_probs=23.0
Q ss_pred CCCCCCccHHHHHHHHHH------hCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITK------FGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~------fgsl~~i~~~ 62 (66)
+..|+|||+..|.+++++ |.|+.+++..
T Consensus 826 l~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R 859 (1022)
T TIGR00594 826 LGAIKGVGESVVKSIIEERNKNGPFKSLFDFINR 859 (1022)
T ss_pred hhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Confidence 457899999999999962 8888888754
No 248
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=28.89 E-value=71 Score=27.09 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=23.6
Q ss_pred CCCCCCccHHHHHHHHHH------hCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITK------FGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~------fgsl~~i~~~~ 63 (66)
+..|+|||+..|..++++ |.|+++++...
T Consensus 826 L~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~ 860 (1151)
T PRK06826 826 LAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERV 860 (1151)
T ss_pred hhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 457899999999999963 88888887543
No 249
>PF13518 HTH_28: Helix-turn-helix domain
Probab=28.76 E-value=83 Score=15.47 Aligned_cols=21 Identities=24% Similarity=0.485 Sum_probs=14.0
Q ss_pred CHHHHHHHhCCCChhHHHHHHH
Q 035374 5 GMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
+...+.++|| +++.++-.+..
T Consensus 14 s~~~~a~~~g-is~~tv~~w~~ 34 (52)
T PF13518_consen 14 SVREIAREFG-ISRSTVYRWIK 34 (52)
T ss_pred CHHHHHHHHC-CCHhHHHHHHH
Confidence 4566777777 77777665543
No 250
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=28.70 E-value=61 Score=20.16 Aligned_cols=19 Identities=26% Similarity=0.504 Sum_probs=13.7
Q ss_pred CCCCCccHHHHHH-HHHHhC
Q 035374 36 PGVEGIGDVRAVQ-LITKFG 54 (66)
Q Consensus 36 ~gi~GiG~K~A~~-Ll~~fg 54 (66)
-|.||-|.-|..+ |.++++
T Consensus 5 ~G~pGsGKst~a~~la~~~~ 24 (183)
T TIGR01359 5 LGGPGSGKGTQCAKIVENFG 24 (183)
T ss_pred ECCCCCCHHHHHHHHHHHcC
Confidence 4779999999644 445565
No 251
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=28.54 E-value=48 Score=23.70 Aligned_cols=19 Identities=26% Similarity=0.496 Sum_probs=15.2
Q ss_pred CCCCCC-CccHHHHHHHHHH
Q 035374 34 NIPGVE-GIGDVRAVQLITK 52 (66)
Q Consensus 34 ~i~gi~-GiG~K~A~~Ll~~ 52 (66)
++..|| ||||-|...|+++
T Consensus 253 ~iTPVPGGVGp~T~a~L~~N 272 (282)
T PRK14182 253 AITPVPGGVGPMTRAMLLVN 272 (282)
T ss_pred EecCCCCCChHHHHHHHHHH
Confidence 344555 8999999999987
No 252
>PHA03135 thymidine kinase; Provisional
Probab=28.52 E-value=43 Score=24.75 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=18.9
Q ss_pred CCCCCCCccHHHHHHHHHHhC
Q 035374 34 NIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg 54 (66)
++.|.-|+|+-|..+.+++.+
T Consensus 14 YlDG~~GvGKTT~~~~l~~~~ 34 (343)
T PHA03135 14 YLDGPFGIGKTSMLNEMPDHS 34 (343)
T ss_pred EEECCCCCCHHHHHHHHHHhc
Confidence 678999999999999999864
No 253
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=28.30 E-value=60 Score=17.61 Aligned_cols=12 Identities=42% Similarity=1.121 Sum_probs=5.1
Q ss_pred HHHHhCCCChhHH
Q 035374 9 FARKYGELKPSQF 21 (66)
Q Consensus 9 v~~~~g~i~p~q~ 21 (66)
+.+.+| ++|.++
T Consensus 67 fk~~~g-~tP~~~ 78 (81)
T PF12833_consen 67 FKRYFG-MTPSEY 78 (81)
T ss_dssp HHHHHS-S-HHHH
T ss_pred HHHHHC-cCHHHH
Confidence 344444 555544
No 254
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=28.14 E-value=88 Score=16.57 Aligned_cols=22 Identities=14% Similarity=0.330 Sum_probs=18.1
Q ss_pred eCHHHHHHHhCCCChhHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|+..++.+.+| +++..+.-|..
T Consensus 1 ~~i~evA~~~g-vs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIG-VKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHH
Confidence 46788999998 99999987754
No 255
>PRK03348 DNA polymerase IV; Provisional
Probab=28.06 E-value=50 Score=24.63 Aligned_cols=26 Identities=23% Similarity=0.304 Sum_probs=18.9
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
-+..+||||++++.+| +++| ++.++.
T Consensus 181 Pv~~L~GIG~~t~~~L-~~lGI~TigDLa 208 (454)
T PRK03348 181 PVRRLWGIGPVTEEKL-HRLGIETIGDLA 208 (454)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHh
Confidence 4667899999999887 5554 555554
No 256
>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2.7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....
Probab=28.02 E-value=41 Score=21.17 Aligned_cols=19 Identities=21% Similarity=0.620 Sum_probs=16.2
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
++|+.|-|.-|..++|.+.
T Consensus 1 ~EGiDGsGKtT~~~~L~~~ 19 (186)
T PF02223_consen 1 FEGIDGSGKTTQIRLLAEA 19 (186)
T ss_dssp EEESTTSSHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHH
Confidence 4689999999999998874
No 257
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=28.01 E-value=74 Score=26.92 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=23.3
Q ss_pred CCCCCCccHHHHHHHHHH-----hCCHHHHHhh
Q 035374 35 IPGVEGIGDVRAVQLITK-----FGMLVFNVEC 62 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~~ 62 (66)
+..|+|||+..+..++++ |.|+.+++..
T Consensus 804 L~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R 836 (1107)
T PRK06920 804 LLSIRNIGMATVTALYEEREKKMFEDLFEFCLR 836 (1107)
T ss_pred hhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHH
Confidence 557899999999999975 8888887753
No 258
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=27.77 E-value=82 Score=17.01 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=13.3
Q ss_pred CccHHHHHHHHHHhCCHHHHH
Q 035374 40 GIGDVRAVQLITKFGMLVFNV 60 (66)
Q Consensus 40 GiG~K~A~~Ll~~fgsl~~i~ 60 (66)
|+-++.|.+++++++.++-|.
T Consensus 16 ~~s~~ea~~~~~~~~~~~~i~ 36 (62)
T PF12668_consen 16 NISGEEAYNYFKRSGVIDYII 36 (62)
T ss_pred CcCHHHHHHHHHHcCcHHHHH
Confidence 555666777777777666443
No 259
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=27.66 E-value=50 Score=20.07 Aligned_cols=38 Identities=18% Similarity=0.233 Sum_probs=26.4
Q ss_pred HHhhCCCCCCCCCCC--CccHHHHHHHHHH-hCCHHHHHhh
Q 035374 25 ISLVGDKADNIPGVE--GIGDVRAVQLITK-FGMLVFNVEC 62 (66)
Q Consensus 25 ~~L~Gd~~D~i~gi~--GiG~K~A~~Ll~~-fgsl~~i~~~ 62 (66)
.+|.|...+-|.+++ +-+-..|.+.|++ ||+...+.++
T Consensus 36 ~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~ 76 (145)
T PF03564_consen 36 SCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRIIQA 76 (145)
T ss_pred HHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHHHH
Confidence 568888777776654 4455777777765 9998776643
No 260
>PRK13749 transcriptional regulator MerD; Provisional
Probab=27.36 E-value=89 Score=19.48 Aligned_cols=25 Identities=16% Similarity=0.262 Sum_probs=21.8
Q ss_pred CceeCHHHHHHHhCCCChhHHHHHHH
Q 035374 1 MASFGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 1 ~~~~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|..|+..++.+.+| +++..+..|--
T Consensus 1 M~~~tIgelA~~~g-vS~~tiR~YE~ 25 (121)
T PRK13749 1 MSAYTVSRLALDAG-VSVHIVRDYLL 25 (121)
T ss_pred CCCCcHHHHHHHHC-CCHHHHHHHHH
Confidence 66789999999998 99999998844
No 261
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=27.28 E-value=79 Score=26.90 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=23.4
Q ss_pred CCCCCCccHHHHHHHHHH------hCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLITK------FGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~------fgsl~~i~~~~ 63 (66)
+..|+|||+..|..++++ |.|+++++...
T Consensus 837 L~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~ 871 (1170)
T PRK07374 837 LSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRL 871 (1170)
T ss_pred hhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 557899999999999953 88888887543
No 262
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=27.27 E-value=46 Score=24.26 Aligned_cols=27 Identities=19% Similarity=0.199 Sum_probs=18.6
Q ss_pred CCCCCCCccHHHHHHHHHHh-CCHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKF-GMLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~f-gsl~~i~ 60 (66)
.+.-+||||++++.+|-+-. .++.++.
T Consensus 223 Pv~~l~GIG~~~~~~L~~~Gi~t~~dl~ 250 (404)
T cd01701 223 KVGDLPGVGSSLAEKLVKLFGDTCGGLE 250 (404)
T ss_pred CHhHhCCCCHHHHHHHHHcCCcchHHHH
Confidence 45677999999988887652 2454443
No 263
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=27.19 E-value=18 Score=21.33 Aligned_cols=22 Identities=27% Similarity=0.546 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhCC
Q 035374 6 MEDFARKYGELKPSQFVDVISLVGD 30 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~Gd 30 (66)
.+.++++|+ +.++|++ +++.-|
T Consensus 23 ~~~lL~~y~-i~~~qLP--~I~~~D 44 (79)
T PRK09570 23 AKKLLKEYG-IKPEQLP--KIKASD 44 (79)
T ss_pred HHHHHHHcC-CCHHHCC--ceeccC
Confidence 357889998 9999998 455444
No 264
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=27.14 E-value=94 Score=16.85 Aligned_cols=26 Identities=19% Similarity=0.493 Sum_probs=17.2
Q ss_pred eeCHHHHHHHhCCCChhHHHH---HHHhhC
Q 035374 3 SFGMEDFARKYGELKPSQFVD---VISLVG 29 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d---~~~L~G 29 (66)
.++..++..+|+ ++|+.+-. .+.-.|
T Consensus 14 ~~S~~eLa~~~~-~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 14 RVSLAELAREFG-ISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp SEEHHHHHHHTT---HHHHHHHHHHHHCCT
T ss_pred CcCHHHHHHHHC-cCHHHHHHHHHHHHHCC
Confidence 467889999998 99986554 455555
No 265
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=26.82 E-value=1.2e+02 Score=19.89 Aligned_cols=35 Identities=23% Similarity=0.442 Sum_probs=26.1
Q ss_pred eeCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccH
Q 035374 3 SFGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGD 43 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~ 43 (66)
.++.+++.+.+| ++|.++..-...+|. .|.||+|-
T Consensus 32 ~vs~~~L~~~~~-v~~~tirrDl~~l~~-----~G~~~~gy 66 (213)
T PRK05472 32 RVSSKELAEALG-VDSAQIRKDLSYFGE-----FGKRGVGY 66 (213)
T ss_pred EEeHHHHHHHhC-cCHHHHHHHHHHHHh-----cCCCCCCe
Confidence 456788999998 999998776666663 46678773
No 266
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=26.44 E-value=1.2e+02 Score=16.45 Aligned_cols=43 Identities=14% Similarity=0.220 Sum_probs=26.7
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQL 49 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~L 49 (66)
+...++.+++| +++..+-.++.--+ .|...++..+-...+..|
T Consensus 14 ~~~~eIA~~Lg-~~~~TV~~W~~r~~--W~~~~~~~rve~~~~~Rl 56 (58)
T PF06056_consen 14 WSIKEIAEELG-VPRSTVYSWKDRYK--WDELLPIERVEEAIERRL 56 (58)
T ss_pred CCHHHHHHHHC-CChHHHHHHHHhhC--ccccCchhhHHHHHHHHh
Confidence 56677888887 88777666666544 455555555544444443
No 267
>COG2361 Uncharacterized conserved protein [Function unknown]
Probab=26.20 E-value=1.7e+02 Score=18.49 Aligned_cols=41 Identities=12% Similarity=0.092 Sum_probs=33.3
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHH
Q 035374 6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
++++.++|..++..+++.+.-.+=. +| +|+-++..+..++.
T Consensus 57 p~~~re~~p~vPW~~magmRd~liH--~Y----fgvd~~~VW~~v~~ 97 (117)
T COG2361 57 PKSFREKYPEVPWKEMAGMRDKLIH--GY----FGVDLKIVWDTVKT 97 (117)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHh--hc----cCCCHHHHHHHHHh
Confidence 5678899988888888888776553 34 69999999999887
No 268
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 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 [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=26.19 E-value=95 Score=19.54 Aligned_cols=24 Identities=21% Similarity=0.209 Sum_probs=19.5
Q ss_pred HHhCCCChhHHHHHHHhhCCCCCCC
Q 035374 11 RKYGELKPSQFVDVISLVGDKADNI 35 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~L~Gd~~D~i 35 (66)
..++ +++.|..-+..|+|...|--
T Consensus 36 ~dL~-L~~~a~~Kl~~LaG~Ryd~~ 59 (127)
T PF10213_consen 36 SDLG-LSEKARHKLKLLAGPRYDPE 59 (127)
T ss_pred HhcC-CCHHHHHHHHHHhhcccCCC
Confidence 3457 99999999999999877643
No 269
>PRK03352 DNA polymerase IV; Validated
Probab=26.17 E-value=45 Score=23.48 Aligned_cols=27 Identities=19% Similarity=0.229 Sum_probs=19.4
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~ 61 (66)
.+.-+||||++++.+| +++| ++.++.+
T Consensus 178 pl~~l~gig~~~~~~L-~~~Gi~ti~dl~~ 206 (346)
T PRK03352 178 PTDALWGVGPKTAKRL-AALGITTVADLAA 206 (346)
T ss_pred CHHHcCCCCHHHHHHH-HHcCCccHHHHhc
Confidence 4667899999999986 5554 5666643
No 270
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=26.08 E-value=93 Score=17.35 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhC
Q 035374 6 MEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
.+++.+++| -++++|.++..=.|
T Consensus 6 ~~~Ie~kTG-k~~~~W~~~~~~~~ 28 (61)
T PF14117_consen 6 LPNIEKKTG-KTLDEWLALAREGG 28 (61)
T ss_pred HhHhHHHHC-cCHHHHHHHHHHhC
Confidence 467899998 99999998876554
No 271
>PRK04040 adenylate kinase; Provisional
Probab=26.07 E-value=61 Score=21.13 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=15.2
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|+||.|..|..+.|.+.
T Consensus 7 v~G~pG~GKtt~~~~l~~~ 25 (188)
T PRK04040 7 VTGVPGVGKTTVLNKALEK 25 (188)
T ss_pred EEeCCCCCHHHHHHHHHHH
Confidence 4588999999988877553
No 272
>PF02777 Sod_Fe_C: Iron/manganese superoxide dismutases, C-terminal domain Note: SCOP classifies the two domains separately.; InterPro: IPR019832 Superoxide dismutases (SODs) (1.15.1.1 from EC) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [, , ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers. The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) []. This entry represents the C-terminal domain of Manganese/iron superoxide dismutase. ; GO: 0004784 superoxide dismutase activity, 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 1KKC_Y 2GOJ_B 1UES_C 1UER_C 1QNN_A 1MY6_A 1MA1_F 1P7G_Q 3EVK_D 2GPC_A ....
Probab=26.00 E-value=89 Score=18.44 Aligned_cols=21 Identities=14% Similarity=0.031 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhCCHHHHHhhh
Q 035374 43 DVRAVQLITKFGMLVFNVECF 63 (66)
Q Consensus 43 ~K~A~~Ll~~fgsl~~i~~~~ 63 (66)
.+.+..|=+.|||++++.+..
T Consensus 5 g~l~~~I~~~FGS~d~fk~~f 25 (106)
T PF02777_consen 5 GKLKKAIEEDFGSFDNFKAEF 25 (106)
T ss_dssp HHHHHHHHHHHSSHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHH
Confidence 567788888999999887543
No 273
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=25.83 E-value=68 Score=16.89 Aligned_cols=19 Identities=26% Similarity=0.578 Sum_probs=11.3
Q ss_pred HHHHHHHhCCCChhHHHHHH
Q 035374 6 MEDFARKYGELKPSQFVDVI 25 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~ 25 (66)
..++.++|| +++.++.++.
T Consensus 25 ~~~ia~~fg-v~~sTv~~I~ 43 (53)
T PF04218_consen 25 KRDIAREFG-VSRSTVSTIL 43 (53)
T ss_dssp HHHHHHHHT---CCHHHHHH
T ss_pred HHHHHHHhC-CCHHHHHHHH
Confidence 356777777 7777776653
No 274
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=25.66 E-value=1.1e+02 Score=16.23 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=19.4
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|+..++.+..| +++..+..|.--.|
T Consensus 1 ~~i~e~A~~~g-Vs~~tlr~ye~~~g 25 (68)
T cd04763 1 YTIGEVALLTG-IKPHVLRAWEREFG 25 (68)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHHhcC
Confidence 46788999998 99999987754334
No 275
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=25.61 E-value=1.2e+02 Score=16.36 Aligned_cols=24 Identities=13% Similarity=0.268 Sum_probs=19.5
Q ss_pred CHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 5 GMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
+.+++.+.+| ++++++..+.....
T Consensus 22 t~eEiA~~lg-is~~~v~~~l~~~~ 45 (78)
T PF04539_consen 22 TDEEIAEELG-ISVEEVRELLQASR 45 (78)
T ss_dssp BHHHHHHHHT-S-HHHHHHHHHHHS
T ss_pred CHHHHHHHHc-ccHHHHHHHHHhCC
Confidence 5688999998 99999998887665
No 276
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=25.31 E-value=55 Score=20.02 Aligned_cols=24 Identities=29% Similarity=0.212 Sum_probs=16.4
Q ss_pred ccHHHHHHHHHH-hCCHHHHHhhhc
Q 035374 41 IGDVRAVQLITK-FGMLVFNVECFS 64 (66)
Q Consensus 41 iG~K~A~~Ll~~-fgsl~~i~~~~~ 64 (66)
=+.|+|.+|+++ .||........+
T Consensus 64 s~~krArKlakKRLGs~kRAkaKvE 88 (97)
T COG5051 64 SQDKRARKLAKKRLGSLKRAKAKVE 88 (97)
T ss_pred cccHHHHHHHHHHhhhHHHHHHHHH
Confidence 356899999887 677766554433
No 277
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=25.22 E-value=90 Score=14.66 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=18.5
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|+..++.+.+| +++..+..+.. .|
T Consensus 1 ~s~~e~a~~lg-vs~~tl~~~~~-~g 24 (49)
T cd04762 1 LTTKEAAELLG-VSPSTLRRWVK-EG 24 (49)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHH-cC
Confidence 46788999998 99988876654 45
No 278
>PF14501 HATPase_c_5: GHKL domain
Probab=24.89 E-value=73 Score=18.18 Aligned_cols=19 Identities=21% Similarity=0.324 Sum_probs=16.6
Q ss_pred CCCCccHHHHHHHHHHhCC
Q 035374 37 GVEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 37 gi~GiG~K~A~~Ll~~fgs 55 (66)
.-.|+|-+...+++++|+.
T Consensus 64 ~~~G~GL~~v~~i~~~y~g 82 (100)
T PF14501_consen 64 KGHGIGLKNVKKILEKYNG 82 (100)
T ss_pred CCCCcCHHHHHHHHHHCCC
Confidence 4479999999999999975
No 279
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=24.66 E-value=45 Score=25.15 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCCccHHHHHHHHHH
Q 035374 29 GDKADNIPGVEGIGDVRAVQLITK 52 (66)
Q Consensus 29 Gd~~D~i~gi~GiG~K~A~~Ll~~ 52 (66)
+...|.+..|.|||||.+.+|-.-
T Consensus 319 ~g~aDDLk~I~GIGpk~e~~Ln~~ 342 (400)
T PRK12373 319 PGGADDLKLISGVGPKIEATLNEL 342 (400)
T ss_pred CCCchhhhhccCCChHHHHHHHhc
Confidence 344788999999999999887543
No 280
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=24.47 E-value=96 Score=26.00 Aligned_cols=28 Identities=14% Similarity=0.358 Sum_probs=21.9
Q ss_pred CCCCCCCccHHHHHHHHHH-----hCCHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITK-----FGMLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~-----fgsl~~i~~ 61 (66)
.+..|+|||+..|..++++ |.|+.+++.
T Consensus 753 gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~ 785 (971)
T PRK05898 753 GFNTIKGFGDELLKKIKSALQNKTFSDFISYID 785 (971)
T ss_pred cchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHH
Confidence 3567899999999999974 777766653
No 281
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=24.35 E-value=67 Score=19.98 Aligned_cols=17 Identities=29% Similarity=0.458 Sum_probs=14.6
Q ss_pred CHHHHHHHhCCCChhHHH
Q 035374 5 GMEDFARKYGELKPSQFV 22 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~ 22 (66)
|++.+.++|+ +|++|--
T Consensus 35 D~eAy~~~~g-LTeEe~~ 51 (106)
T cd07921 35 DEEAYCDKFG-LTEEQKQ 51 (106)
T ss_pred CHHHHHHHcC-CCHHHHH
Confidence 6788999998 9999765
No 282
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=24.24 E-value=1.1e+02 Score=25.63 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=23.5
Q ss_pred CCCCCCccHHHHHHHHH------HhCCHHHHHhhh
Q 035374 35 IPGVEGIGDVRAVQLIT------KFGMLVFNVECF 63 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~------~fgsl~~i~~~~ 63 (66)
+..|+|||...|..+++ .|.|+++++...
T Consensus 755 L~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~ 789 (973)
T PRK07135 755 LIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRL 789 (973)
T ss_pred ccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhc
Confidence 55789999999999995 388888887543
No 283
>PF12728 HTH_17: Helix-turn-helix domain
Probab=24.20 E-value=1.1e+02 Score=15.28 Aligned_cols=33 Identities=24% Similarity=0.347 Sum_probs=23.3
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccH
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGD 43 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~ 43 (66)
++.+++.+.+| +++..+-.+.. . ..+|.+ ++|.
T Consensus 2 lt~~e~a~~l~-is~~tv~~~~~-~----g~i~~~-~~g~ 34 (51)
T PF12728_consen 2 LTVKEAAELLG-ISRSTVYRWIR-Q----GKIPPF-KIGR 34 (51)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHH-c----CCCCeE-EeCC
Confidence 67899999998 99998776653 2 356555 2544
No 284
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=23.80 E-value=1.1e+02 Score=18.19 Aligned_cols=24 Identities=13% Similarity=0.495 Sum_probs=20.1
Q ss_pred ceeCHHHHHHHhCCCChhHHHHHHH
Q 035374 2 ASFGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 2 ~~~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
+.++.+++.+.+| ++|+.+.++-.
T Consensus 6 ~~lt~~Elc~~~g-i~~~~l~eLve 29 (101)
T PRK10265 6 VTFTITEFCLHTG-VSEEELNEIVG 29 (101)
T ss_pred EEeeHHHHHHHHC-cCHHHHHHHHH
Confidence 4688999999998 99998887754
No 285
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=23.80 E-value=2.4e+02 Score=19.01 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=28.5
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLIT 51 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~ 51 (66)
.+..++.++.| +++.-.. .+|-|. ++|.++|..++++
T Consensus 7 ~Ti~dIA~~ag-VS~~TVS--r~Ln~~--------~~vs~~tr~~V~~ 43 (342)
T PRK10014 7 ITIHDVALAAG-VSVSTVS--LVLSGK--------GRISTATGERVNQ 43 (342)
T ss_pred CcHHHHHHHhC-CCHHHHH--HHHCCC--------CCCCHHHHHHHHH
Confidence 57889999998 9998887 445442 5789999888754
No 286
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.56 E-value=1.1e+02 Score=16.22 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=13.6
Q ss_pred eeCHHHHHHHhCCCChhHHH
Q 035374 3 SFGMEDFARKYGELKPSQFV 22 (66)
Q Consensus 3 ~~~~~~v~~~~g~i~p~q~~ 22 (66)
.+..+++.+..| ++|.|+.
T Consensus 28 ~vSS~~La~~~g-i~~~qVR 46 (50)
T PF06971_consen 28 RVSSQELAEALG-ITPAQVR 46 (50)
T ss_dssp EE-HHHHHHHHT-S-HHHHH
T ss_pred eECHHHHHHHHC-CCHHHhc
Confidence 456778888898 9999875
No 287
>PF14129 DUF4296: Domain of unknown function (DUF4296)
Probab=23.52 E-value=84 Score=18.04 Aligned_cols=17 Identities=29% Similarity=0.569 Sum_probs=14.0
Q ss_pred HHHHHHhCCCChhHHHHH
Q 035374 7 EDFARKYGELKPSQFVDV 24 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~ 24 (66)
..|.++|| +++.||..=
T Consensus 40 ~~I~kKy~-Ids~~f~~S 56 (87)
T PF14129_consen 40 QYIFKKYG-IDSAQFDSS 56 (87)
T ss_pred HHHHHHcC-CCHHHHHHH
Confidence 56889998 999998753
No 288
>PRK06762 hypothetical protein; Provisional
Probab=23.48 E-value=69 Score=19.65 Aligned_cols=19 Identities=21% Similarity=0.342 Sum_probs=15.3
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|.||-|+.|..+.|.+.
T Consensus 7 i~G~~GsGKST~A~~L~~~ 25 (166)
T PRK06762 7 IRGNSGSGKTTIAKQLQER 25 (166)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4578999999988888654
No 289
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=23.38 E-value=60 Score=22.85 Aligned_cols=27 Identities=26% Similarity=0.306 Sum_probs=19.0
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~ 61 (66)
.+..++|||++++.+|- ++| ++.++.+
T Consensus 174 pi~~l~giG~~~~~~L~-~~Gi~ti~dl~~ 202 (343)
T cd00424 174 PLTDLPGIGAVTAKRLE-AVGINPIGDLLA 202 (343)
T ss_pred ChhhcCCCCHHHHHHHH-HcCCCcHHHHhc
Confidence 45668999999999874 554 5555543
No 290
>PRK13502 transcriptional activator RhaR; Provisional
Probab=23.27 E-value=85 Score=20.97 Aligned_cols=18 Identities=33% Similarity=0.571 Sum_probs=14.1
Q ss_pred HHHHHHhCCCChhHHHHHH
Q 035374 7 EDFARKYGELKPSQFVDVI 25 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~ 25 (66)
+.|.+.+| +||.||...+
T Consensus 261 r~FKk~~G-~tP~~yRk~~ 278 (282)
T PRK13502 261 VVFTRETG-MTPSQWRHLS 278 (282)
T ss_pred HHHHHHHC-cCHHHHHHHh
Confidence 56778888 9999997654
No 291
>PF05626 DUF790: Protein of unknown function (DUF790); InterPro: IPR008508 This family consists of several hypothetical bacterial and archaeal proteins whose functions have not been experimentally verified. Computational analysis of sequence, predicted structure and genomic context suggests that these proteins may be endonucleases involved in either restriction-modification and/or DNA excision repair [].
Probab=23.16 E-value=1.1e+02 Score=22.81 Aligned_cols=45 Identities=18% Similarity=0.350 Sum_probs=32.3
Q ss_pred HHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 6 MEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
++.+.++++ ++|+++. .+|-+|-.+| .-+-..=+-++..|+++|.
T Consensus 107 L~~vA~~L~-v~~~e~e--~~LyaDlee~-~~L~~~~~~~p~~Ll~rYN 151 (379)
T PF05626_consen 107 LEEVAEELG-VSPEEVE--RALYADLEEN-QILVEFPAPTPEELLRRYN 151 (379)
T ss_pred HHHHHHHcC-CCHHHHH--HHHhhcChhc-ceeccCCCCCHHHHHHHHh
Confidence 467889998 9999998 7788875544 2233334557788999984
No 292
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=23.09 E-value=1.2e+02 Score=20.32 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=17.2
Q ss_pred CHHHHHHHhCCCChhHHHHHHH
Q 035374 5 GMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 5 ~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|++.+.+..| ++++++++...
T Consensus 101 DL~~vA~~~g-ls~~evi~~H~ 121 (202)
T PF02682_consen 101 DLEEVAEHNG-LSVEEVIRLHS 121 (202)
T ss_dssp THHHHHHHHT-S-HHHHHHHHH
T ss_pred CHHHHHHHhC-cCHHHHHHHHH
Confidence 5889999998 99999997754
No 293
>PRK14625 hypothetical protein; Provisional
Probab=23.04 E-value=80 Score=19.51 Aligned_cols=16 Identities=25% Similarity=0.439 Sum_probs=9.8
Q ss_pred HhhCCCCCCCCCCCCc
Q 035374 26 SLVGDKADNIPGVEGI 41 (66)
Q Consensus 26 ~L~Gd~~D~i~gi~Gi 41 (66)
.+.|--.+++||.||+
T Consensus 92 ~~tgg~~~~lPG~~~~ 107 (109)
T PRK14625 92 EAAGPMAGLMGGLPGM 107 (109)
T ss_pred HHhcCCCCCCCCCCCC
Confidence 3445322368999986
No 294
>PRK12339 2-phosphoglycerate kinase; Provisional
Probab=23.03 E-value=81 Score=20.86 Aligned_cols=19 Identities=26% Similarity=0.572 Sum_probs=15.0
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|+||.|.-|..+.|.+.
T Consensus 8 i~G~~G~GKst~a~~l~~~ 26 (197)
T PRK12339 8 IGGIPGVGKTSISGYIARH 26 (197)
T ss_pred EECCCCCCHHHHHHHHHHh
Confidence 3578999999988877654
No 295
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=22.98 E-value=1.1e+02 Score=17.76 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=18.9
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
|+..++.+.+| +++..+..|.- .|
T Consensus 1 ~ti~eva~~~g-vs~~tlR~ye~-~G 24 (103)
T cd01106 1 YTVGEVAKLTG-VSVRTLHYYDE-IG 24 (103)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHH-CC
Confidence 46788999998 99999986644 45
No 296
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=22.95 E-value=1.1e+02 Score=21.35 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=21.8
Q ss_pred HHhhCCCCCCCCCCCCccHHHHHHHHHHh
Q 035374 25 ISLVGDKADNIPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 25 ~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~f 53 (66)
+.+.|-.. -+.|.||+|+-+..+.+.+.
T Consensus 39 a~~~~~~v-ll~G~PG~gKT~la~~lA~~ 66 (329)
T COG0714 39 ALLAGGHV-LLEGPPGVGKTLLARALARA 66 (329)
T ss_pred HHHcCCCE-EEECCCCccHHHHHHHHHHH
Confidence 45566544 68899999999988888774
No 297
>PRK03839 putative kinase; Provisional
Probab=22.73 E-value=85 Score=19.61 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=15.6
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|.||.|.-|..+.|.+-
T Consensus 5 l~G~pGsGKsT~~~~La~~ 23 (180)
T PRK03839 5 ITGTPGVGKTTVSKLLAEK 23 (180)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4578999999999888773
No 298
>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....
Probab=22.59 E-value=95 Score=18.94 Aligned_cols=19 Identities=26% Similarity=0.265 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhCCHHHHHh
Q 035374 43 DVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 43 ~K~A~~Ll~~fgsl~~i~~ 61 (66)
.+.++.|.++||++.+.+.
T Consensus 4 ~~i~w~l~~~yg~~y~aFe 22 (114)
T PF07541_consen 4 EKIGWPLYKKYGSLYDAFE 22 (114)
T ss_dssp HHTHHHHHHHCSSHHHHHH
T ss_pred HHHHHHHHHHhCcHHHHHH
Confidence 4678899999999877665
No 299
>PF06599 DUF1139: Protein of unknown function (DUF1139); InterPro: IPR009519 This family consists of several hypothetical Fijivirus proteins of unknown function.
Probab=22.49 E-value=1.2e+02 Score=22.06 Aligned_cols=44 Identities=27% Similarity=0.550 Sum_probs=37.2
Q ss_pred HHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCH
Q 035374 11 RKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56 (66)
Q Consensus 11 ~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl 56 (66)
+.|. +.+.|+-.+--++|++. -.|||-=||.|.-...+..|+=.
T Consensus 179 Raf~-lk~~q~~~vsqiL~~sL-~f~giNlIgK~smipm~~n~si~ 222 (309)
T PF06599_consen 179 RAFD-LKPNQFEQVSQILSNSL-FFPGINLIGKKSMIPMFTNHSIP 222 (309)
T ss_pred eecc-cchhHHHHHHHHhhcCe-eecCcchhchhhhhHHHhccChH
Confidence 4577 89999999999999854 77999999999999999887543
No 300
>PRK14133 DNA polymerase IV; Provisional
Probab=22.34 E-value=77 Score=22.35 Aligned_cols=27 Identities=26% Similarity=0.377 Sum_probs=19.1
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHHh
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNVE 61 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~~ 61 (66)
.+.-++|||++++.+| +++| ++.++.+
T Consensus 174 pv~~l~gig~~~~~~L-~~~Gi~ti~dl~~ 202 (347)
T PRK14133 174 PISKVHGIGKKSVEKL-NNIGIYTIEDLLK 202 (347)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhh
Confidence 4567799999999986 5554 5555543
No 301
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.34 E-value=1.2e+02 Score=17.26 Aligned_cols=22 Identities=9% Similarity=0.178 Sum_probs=18.1
Q ss_pred eCHHHHHHHhCCCChhHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|+..++.+.+| +++..+..|.-
T Consensus 1 ~~~~eva~~~g-i~~~tlr~~~~ 22 (100)
T cd00592 1 YTIGEVAKLLG-VSVRTLRYYEE 22 (100)
T ss_pred CCHHHHHHHHC-cCHHHHHHHHH
Confidence 46788999998 99998887754
No 302
>PF14894 Lsm_C: Lsm C-terminal; PDB: 1M5Q_1.
Probab=22.29 E-value=51 Score=18.82 Aligned_cols=18 Identities=39% Similarity=0.739 Sum_probs=11.1
Q ss_pred CCCCCccHH--HHHHHHHHh
Q 035374 36 PGVEGIGDV--RAVQLITKF 53 (66)
Q Consensus 36 ~gi~GiG~K--~A~~Ll~~f 53 (66)
.||.|-||- |+..|.++|
T Consensus 39 ~GVEGsGPlAerv~~ly~ey 58 (64)
T PF14894_consen 39 NGVEGSGPLAERVYDLYNEY 58 (64)
T ss_dssp TEEE--SHHHHHHHHHHHHH
T ss_pred cccccCChHHHHHHHHHHHH
Confidence 488999984 566666665
No 303
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=22.16 E-value=63 Score=22.41 Aligned_cols=54 Identities=20% Similarity=0.279 Sum_probs=35.1
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhh---CCCCCC----CCCCCCccHHHHHHHHHHhCCHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLV---GDKADN----IPGVEGIGDVRAVQLITKFGMLVFN 59 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~---Gd~~D~----i~gi~GiG~K~A~~Ll~~fgsl~~i 59 (66)
++++.|.+.|| -.+-+--++-.++ -|++|. .|+=|-||-|+-..+..+..+ +++
T Consensus 37 ltLe~F~~~yg-~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~k~~~~~~~~-~ni 97 (208)
T KOG3218|consen 37 LTLEEFKARYG-DKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTMKTYVIQMQS-ENI 97 (208)
T ss_pred hhHHHHHHHhc-cCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHHHHHHHHHHh-cCc
Confidence 56788888898 5533333333332 333332 377799999999999988877 554
No 304
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=22.02 E-value=1.1e+02 Score=18.97 Aligned_cols=38 Identities=24% Similarity=0.335 Sum_probs=25.5
Q ss_pred CChhHHHHHHHhhCCCC-CCCCCCCCccHHH-HHHHHHHh
Q 035374 16 LKPSQFVDVISLVGDKA-DNIPGVEGIGDVR-AVQLITKF 53 (66)
Q Consensus 16 i~p~q~~d~~~L~Gd~~-D~i~gi~GiG~K~-A~~Ll~~f 53 (66)
++++|..-+...+.... --|-|-||-|.-+ ...++...
T Consensus 2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~ 41 (236)
T PF13086_consen 2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQL 41 (236)
T ss_dssp --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHh
Confidence 57888888888777543 5678999999984 55555554
No 305
>PRK08356 hypothetical protein; Provisional
Probab=21.98 E-value=95 Score=19.91 Aligned_cols=20 Identities=15% Similarity=0.321 Sum_probs=16.7
Q ss_pred CCCCCCccHHHHHHHHHHhC
Q 035374 35 IPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~fg 54 (66)
+-|-||-|.-|..+.|++++
T Consensus 10 ~~G~~gsGK~t~a~~l~~~g 29 (195)
T PRK08356 10 VVGKIAAGKTTVAKFFEEKG 29 (195)
T ss_pred EECCCCCCHHHHHHHHHHCC
Confidence 34679999999999998864
No 306
>PRK01216 DNA polymerase IV; Validated
Probab=21.95 E-value=63 Score=23.31 Aligned_cols=26 Identities=42% Similarity=0.714 Sum_probs=18.5
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
.+.-+||||++++.+| +++| ++.++.
T Consensus 179 Pi~~l~giG~~~~~~L-~~~Gi~TigdL~ 206 (351)
T PRK01216 179 DIADIPGIGDITAEKL-KKLGVNKLVDTL 206 (351)
T ss_pred CcccccCCCHHHHHHH-HHcCCCcHHHHh
Confidence 4667899999998766 4544 566654
No 307
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=21.69 E-value=2.8e+02 Score=19.00 Aligned_cols=52 Identities=23% Similarity=0.403 Sum_probs=35.1
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHHHHHhCCHHHHHh
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVE 61 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fgsl~~i~~ 61 (66)
+|+-++...||.-..-.+-.+|.++| |||=.||--....++..+ |.+++|.+
T Consensus 102 ~DLmd~l~~~g~~~~~sLd~la~~lg-----iPgK~~idGs~V~~~y~~-g~i~~I~~ 153 (209)
T PF10108_consen 102 LDLMDLLSFYGAKARTSLDELAALLG-----IPGKDDIDGSQVAELYQE-GDIDEIRE 153 (209)
T ss_pred ccHHHHHhccCccccCCHHHHHHHcC-----CCCCCCCCHHHHHHHHHc-CCHHHHHH
Confidence 45566667776344567888899988 577677744445555555 88888864
No 308
>PRK00625 shikimate kinase; Provisional
Probab=21.66 E-value=91 Score=20.14 Aligned_cols=19 Identities=21% Similarity=0.436 Sum_probs=15.2
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|.||.|.-|..+.|.+.
T Consensus 5 LiG~pGsGKTT~~k~La~~ 23 (173)
T PRK00625 5 LCGLPTVGKTSFGKALAKF 23 (173)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 3478999999988888663
No 309
>cd01080 NAD_bind_m-THF_DH_Cyclohyd NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well a
Probab=21.54 E-value=97 Score=20.10 Aligned_cols=20 Identities=25% Similarity=0.438 Sum_probs=15.2
Q ss_pred CCCCC-CCccHHHHHHHHHHh
Q 035374 34 NIPGV-EGIGDVRAVQLITKF 53 (66)
Q Consensus 34 ~i~gi-~GiG~K~A~~Ll~~f 53 (66)
+++++ -|+||.|+..|+++.
T Consensus 143 ~~~~~pggvgp~t~a~l~~n~ 163 (168)
T cd01080 143 AITPVPGGVGPMTVAMLMKNT 163 (168)
T ss_pred CcCCCCCcChHHHHHHHHHHH
Confidence 34444 479999999999874
No 310
>PF11697 DUF3293: Protein of unknown function (DUF3293); InterPro: IPR021710 This bacterial family of proteins has no known function.
Probab=21.41 E-value=90 Score=17.56 Aligned_cols=18 Identities=44% Similarity=0.492 Sum_probs=15.7
Q ss_pred CCCccHHHHHHHHHHhCC
Q 035374 38 VEGIGDVRAVQLITKFGM 55 (66)
Q Consensus 38 i~GiG~K~A~~Ll~~fgs 55 (66)
|+||.+..|..|-++|+-
T Consensus 53 V~~i~~~~A~~Lg~~f~Q 70 (73)
T PF11697_consen 53 VLGISLEEAIALGRKFGQ 70 (73)
T ss_pred EcCCCHHHHHHHHHHhCc
Confidence 579999999999999973
No 311
>TIGR03759 conj_TIGR03759 integrating conjugative element protein, PFL_4693 family. Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown.
Probab=21.38 E-value=2.3e+02 Score=19.51 Aligned_cols=40 Identities=15% Similarity=0.331 Sum_probs=27.7
Q ss_pred HHHHHHhCCCChhHHHHHHHhhCCCCCCCCCCCCccHHHHHHH
Q 035374 7 EDFARKYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQL 49 (66)
Q Consensus 7 ~~v~~~~g~i~p~q~~d~~~L~Gd~~D~i~gi~GiG~K~A~~L 49 (66)
+.-.+.+| ++++.+.-|.-|+--+. .+= =||+-|-||+-+
T Consensus 6 ~~~A~~WG-Lt~~Ew~RY~~LmqG~r-G~~-SPgLdPLtaLGI 45 (200)
T TIGR03759 6 KQRAKEWG-LTEDEWQRYQQLMQGPR-GVY-SPGLDPLTALGI 45 (200)
T ss_pred HHHHHHcC-CCHHHHHHHHHHhcCCc-cCc-CCCCChhhhhcc
Confidence 44567898 99999999999875322 111 177888887644
No 312
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=21.33 E-value=93 Score=17.91 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=8.0
Q ss_pred HHHHHhCCCChhHHH
Q 035374 8 DFARKYGELKPSQFV 22 (66)
Q Consensus 8 ~v~~~~g~i~p~q~~ 22 (66)
.+.+.+| ++|.+|.
T Consensus 91 ~Fk~~~G-~tP~~~r 104 (107)
T PRK10219 91 VFRRQFD-RTPSDYR 104 (107)
T ss_pred HHHHHHC-cCHHHHH
Confidence 3445555 6776664
No 313
>PRK02794 DNA polymerase IV; Provisional
Probab=21.20 E-value=68 Score=23.39 Aligned_cols=26 Identities=19% Similarity=0.178 Sum_probs=18.8
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
.+..+||||++++.+| +++| ++.++.
T Consensus 210 Pl~~L~GiG~~~~~~L-~~~GI~tigdL~ 237 (419)
T PRK02794 210 PVGIIWGVGPATAARL-ARDGIRTIGDLQ 237 (419)
T ss_pred ChhhhCCCCHHHHHHH-HHhccchHHHHh
Confidence 4567799999999988 4544 555554
No 314
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=21.14 E-value=1.3e+02 Score=14.84 Aligned_cols=25 Identities=4% Similarity=0.090 Sum_probs=19.0
Q ss_pred CCccHHHHHHHHHH-hCCHHHHHhhh
Q 035374 39 EGIGDVRAVQLITK-FGMLVFNVECF 63 (66)
Q Consensus 39 ~GiG~K~A~~Ll~~-fgsl~~i~~~~ 63 (66)
|.+++..+...|++ -|+++..++.+
T Consensus 14 P~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 14 PNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 78889899888885 46788776654
No 315
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=20.93 E-value=59 Score=23.71 Aligned_cols=26 Identities=19% Similarity=0.225 Sum_probs=18.5
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
-+..++|||++++.+| +++| |+-++.
T Consensus 180 Pv~~l~GiG~~~~~~L-~~lGi~TigdL~ 207 (422)
T PRK03609 180 PVEEVWGVGRRISKKL-NAMGIKTALDLA 207 (422)
T ss_pred ChhhcCCccHHHHHHH-HHcCCCcHHHHh
Confidence 4567899999999888 4443 555554
No 316
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=20.92 E-value=76 Score=20.05 Aligned_cols=18 Identities=17% Similarity=0.565 Sum_probs=14.4
Q ss_pred CCCCCCccHH---HHHHHHHHhC
Q 035374 35 IPGVEGIGDV---RAVQLITKFG 54 (66)
Q Consensus 35 i~gi~GiG~K---~A~~Ll~~fg 54 (66)
+|| |+-|+ ...+++++.|
T Consensus 2 ~pg--~~nPr~~~~mkkmMk~MG 22 (116)
T TIGR00264 2 FPG--KMNPKMLKQMQKMMKQMG 22 (116)
T ss_pred CCC--CCCcccHHHHHHHHHHcC
Confidence 355 68888 8999999987
No 317
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.89 E-value=89 Score=22.66 Aligned_cols=19 Identities=26% Similarity=0.616 Sum_probs=16.1
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|-||+|..++..++.+.
T Consensus 43 f~Gp~G~GKtt~A~~~a~~ 61 (397)
T PRK14955 43 FSGLRGVGKTTAARVFAKA 61 (397)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4578999999999988873
No 318
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=20.84 E-value=98 Score=18.57 Aligned_cols=19 Identities=21% Similarity=0.354 Sum_probs=15.5
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+-|.||.|+.|-.+.|.+.
T Consensus 4 l~G~~GsGKST~a~~l~~~ 22 (150)
T cd02021 4 VMGVSGSGKSTVGKALAER 22 (150)
T ss_pred EEcCCCCCHHHHHHHHHhh
Confidence 3478999999988888774
No 319
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=20.81 E-value=85 Score=16.17 Aligned_cols=14 Identities=29% Similarity=0.546 Sum_probs=10.5
Q ss_pred ccHHHHHHHHHHhC
Q 035374 41 IGDVRAVQLITKFG 54 (66)
Q Consensus 41 iG~K~A~~Ll~~fg 54 (66)
.--.+|.+|+.+|+
T Consensus 26 ~A~~kAq~Lm~ky~ 39 (43)
T PF10979_consen 26 AALAKAQRLMAKYG 39 (43)
T ss_pred HHHHHHHHHHHHhC
Confidence 34468889999886
No 320
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.76 E-value=94 Score=17.36 Aligned_cols=14 Identities=21% Similarity=0.397 Sum_probs=11.9
Q ss_pred CccHHHHHHHHHHh
Q 035374 40 GIGDVRAVQLITKF 53 (66)
Q Consensus 40 GiG~K~A~~Ll~~f 53 (66)
|.++.+|.+++++-
T Consensus 13 Gf~~~tA~~IIrqA 26 (59)
T PF11372_consen 13 GFSESTARDIIRQA 26 (59)
T ss_pred CCCHHHHHHHHHHH
Confidence 78899999998874
No 321
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=20.65 E-value=41 Score=26.00 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=15.1
Q ss_pred CCCCCccHHHHHHHHHH-hCCH
Q 035374 36 PGVEGIGDVRAVQLITK-FGML 56 (66)
Q Consensus 36 ~gi~GiG~K~A~~Ll~~-fgsl 56 (66)
.||||||+-||=.+..= |+..
T Consensus 209 kgvpGVG~YTAGAiaSIAf~q~ 230 (555)
T KOG2457|consen 209 KGVPGVGQYTAGAIASIAFNQV 230 (555)
T ss_pred hhCCCCCccchhhhhhhhhcCc
Confidence 46999999999777653 4433
No 322
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=20.57 E-value=1.6e+02 Score=17.09 Aligned_cols=26 Identities=12% Similarity=0.243 Sum_probs=18.8
Q ss_pred eCHHHHHHHhCCCChhHHHHHHHhhC
Q 035374 4 FGMEDFARKYGELKPSQFVDVISLVG 29 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~L~G 29 (66)
.+.+++++.|..++.+|+.+-.....
T Consensus 44 ~s~eeil~dyp~Lt~~dI~aal~ya~ 69 (79)
T COG2442 44 ESIEEILADYPDLTLEDIRAALRYAA 69 (79)
T ss_pred CCHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 45678888887788888877655443
No 323
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=20.44 E-value=46 Score=25.97 Aligned_cols=30 Identities=7% Similarity=0.179 Sum_probs=21.9
Q ss_pred HHHhhCCCCCCCCCCCCccHHHHHHHHHHhC
Q 035374 24 VISLVGDKADNIPGVEGIGDVRAVQLITKFG 54 (66)
Q Consensus 24 ~~~L~Gd~~D~i~gi~GiG~K~A~~Ll~~fg 54 (66)
+..+..-+.+.+..| ||+++.|.++.+.|.
T Consensus 537 ~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 537 LYDFLKADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred HHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 344444445667788 999999999988764
No 324
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.29 E-value=1.4e+02 Score=17.01 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=18.6
Q ss_pred eCHHHHHHHhCCCChhHHHHHHH
Q 035374 4 FGMEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 4 ~~~~~v~~~~g~i~p~q~~d~~~ 26 (66)
|+..++.+.+| +++.++.-|-.
T Consensus 2 ~ti~evA~~~g-vs~~tLR~ye~ 23 (88)
T cd01105 2 IGIGEVSKLTG-VSPRQLRYWEE 23 (88)
T ss_pred cCHHHHHHHHC-cCHHHHHHHHH
Confidence 67889999998 99999887744
No 325
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=20.21 E-value=78 Score=17.86 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.4
Q ss_pred CCccHHHHHHHHHHh
Q 035374 39 EGIGDVRAVQLITKF 53 (66)
Q Consensus 39 ~GiG~K~A~~Ll~~f 53 (66)
.|+|...|++++++.
T Consensus 16 ~G~gR~~Ah~lv~~~ 30 (81)
T PF10397_consen 16 KGLGRQEAHELVQEA 30 (81)
T ss_dssp TTH-HHHHHHHHHHH
T ss_pred HccCHHHHHHHHHHH
Confidence 589999999999985
No 326
>PF13274 DUF4065: Protein of unknown function (DUF4065)
Probab=20.20 E-value=1.4e+02 Score=16.82 Aligned_cols=21 Identities=14% Similarity=0.445 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCChhHHHHHHH
Q 035374 6 MEDFARKYGELKPSQFVDVIS 26 (66)
Q Consensus 6 ~~~v~~~~g~i~p~q~~d~~~ 26 (66)
.+.|.++|+..++.++.++-.
T Consensus 79 i~~V~~~~~~~s~~~L~~~sH 99 (108)
T PF13274_consen 79 IDEVINKYGDKSAWELSELSH 99 (108)
T ss_pred HHHHHHHHcCCCHHHHHHHHc
Confidence 366778888788888877643
No 327
>PRK07933 thymidylate kinase; Validated
Probab=20.12 E-value=83 Score=20.84 Aligned_cols=19 Identities=26% Similarity=0.459 Sum_probs=15.8
Q ss_pred CCCCCCccHHHHHHHHHHh
Q 035374 35 IPGVEGIGDVRAVQLITKF 53 (66)
Q Consensus 35 i~gi~GiG~K~A~~Ll~~f 53 (66)
+.|+.|.|..|-.++|.++
T Consensus 5 iEG~dGsGKST~~~~L~~~ 23 (213)
T PRK07933 5 IEGVDGAGKRTLTEALRAA 23 (213)
T ss_pred EEcCCCCCHHHHHHHHHHH
Confidence 5788999999988888774
No 328
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=20.10 E-value=87 Score=20.34 Aligned_cols=18 Identities=22% Similarity=0.298 Sum_probs=15.3
Q ss_pred CCccHHHHHHHHHHhCCH
Q 035374 39 EGIGDVRAVQLITKFGML 56 (66)
Q Consensus 39 ~GiG~K~A~~Ll~~fgsl 56 (66)
.|+|.+.|.+|-+++...
T Consensus 17 DG~Gv~vae~L~~~~~~~ 34 (160)
T COG0680 17 DGFGVRVAEKLKKRYKPP 34 (160)
T ss_pred CcccHHHHHHHHHhcCCC
Confidence 699999999999988643
No 329
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=20.09 E-value=67 Score=22.59 Aligned_cols=26 Identities=27% Similarity=0.213 Sum_probs=18.8
Q ss_pred CCCCCCCccHHHHHHHHHHhC--CHHHHH
Q 035374 34 NIPGVEGIGDVRAVQLITKFG--MLVFNV 60 (66)
Q Consensus 34 ~i~gi~GiG~K~A~~Ll~~fg--sl~~i~ 60 (66)
.+.-+||||++++.+| +++| ++.++.
T Consensus 177 pl~~l~gig~~~~~~L-~~~Gi~ti~dL~ 204 (344)
T cd01700 177 PVGDVWGIGRRTAKKL-NAMGIHTAGDLA 204 (344)
T ss_pred ChhhcCccCHHHHHHH-HHcCCCcHHHHh
Confidence 4567799999999886 5554 566554
Done!