Query 033150
Match_columns 126
No_of_seqs 107 out of 968
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 10:26:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033150hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0099 RpsM Ribosomal protein 99.9 2.2E-27 4.7E-32 174.9 5.0 78 47-124 1-80 (121)
2 CHL00137 rps13 ribosomal prote 99.9 1.4E-25 2.9E-30 165.3 5.6 78 47-124 1-80 (122)
3 PRK05179 rpsM 30S ribosomal pr 99.9 1.9E-25 4.1E-30 164.5 5.6 77 47-123 1-79 (122)
4 TIGR03629 arch_S13P archaeal r 99.9 4E-25 8.7E-30 166.8 6.2 79 45-123 3-104 (144)
5 PRK04053 rps13p 30S ribosomal 99.9 3.1E-25 6.7E-30 168.4 3.9 79 46-124 8-110 (149)
6 PTZ00134 40S ribosomal protein 99.9 1.5E-24 3.2E-29 165.5 4.9 80 45-124 12-115 (154)
7 TIGR03631 bact_S13 30S ribosom 99.9 1.2E-23 2.5E-28 153.2 5.3 75 49-123 1-77 (113)
8 PF00416 Ribosomal_S13: Riboso 99.9 5.1E-24 1.1E-28 152.6 2.0 75 49-123 1-77 (107)
9 KOG3311 Ribosomal protein S18 99.6 4.6E-16 1E-20 118.7 2.4 71 33-107 2-73 (152)
10 PRK01103 formamidopyrimidine/5 96.0 0.0072 1.6E-07 49.3 3.5 51 57-107 154-208 (274)
11 PF06831 H2TH: Formamidopyrimi 96.0 0.0081 1.7E-07 41.9 3.3 50 58-107 23-76 (92)
12 PRK14810 formamidopyrimidine-D 94.7 0.051 1.1E-06 44.4 4.5 51 57-107 153-207 (272)
13 PRK14811 formamidopyrimidine-D 94.1 0.084 1.8E-06 43.2 4.6 49 57-105 142-194 (269)
14 PRK10445 endonuclease VIII; Pr 93.7 0.11 2.5E-06 42.2 4.6 50 58-107 151-204 (263)
15 PRK13945 formamidopyrimidine-D 93.6 0.11 2.4E-06 42.6 4.3 51 57-107 163-217 (282)
16 TIGR00577 fpg formamidopyrimid 93.3 0.14 3E-06 41.9 4.4 50 58-107 155-208 (272)
17 PF00633 HHH: Helix-hairpin-he 93.2 0.055 1.2E-06 30.9 1.5 18 64-81 12-29 (30)
18 PF11798 IMS_HHH: IMS family H 92.2 0.081 1.8E-06 30.4 1.3 21 64-85 12-32 (32)
19 PF05833 FbpA: Fibronectin-bin 92.2 0.03 6.6E-07 47.7 -0.8 50 58-107 186-237 (455)
20 PRK04184 DNA topoisomerase VI 91.8 0.26 5.6E-06 44.5 4.6 43 66-108 264-307 (535)
21 PF10391 DNA_pol_lambd_f: Fing 90.1 0.19 4.1E-06 32.0 1.5 36 65-101 4-44 (52)
22 PRK02515 psbU photosystem II c 90.0 0.26 5.6E-06 37.3 2.5 62 50-111 48-113 (132)
23 COG3743 Uncharacterized conser 88.6 0.4 8.7E-06 36.3 2.6 43 63-106 67-110 (133)
24 COG0266 Nei Formamidopyrimidin 87.9 0.83 1.8E-05 38.2 4.3 52 56-107 153-208 (273)
25 smart00278 HhH1 Helix-hairpin- 87.2 0.46 9.9E-06 25.7 1.6 19 64-82 2-20 (26)
26 PF14520 HHH_5: Helix-hairpin- 87.1 0.12 2.6E-06 32.8 -0.9 38 62-100 4-42 (60)
27 PRK14606 ruvA Holliday junctio 86.3 0.41 8.8E-06 37.5 1.5 19 64-82 109-127 (188)
28 TIGR00275 flavoprotein, HI0933 85.9 0.91 2E-05 38.4 3.5 48 59-108 284-332 (400)
29 PF14579 HHH_6: Helix-hairpin- 85.3 0.85 1.9E-05 31.1 2.6 46 58-103 22-75 (90)
30 PRK14601 ruvA Holliday junctio 85.1 0.5 1.1E-05 37.0 1.5 17 64-80 109-125 (183)
31 PRK14603 ruvA Holliday junctio 84.8 0.52 1.1E-05 37.1 1.5 19 64-82 108-126 (197)
32 PRK14604 ruvA Holliday junctio 84.7 0.53 1.2E-05 37.1 1.5 21 63-83 108-128 (195)
33 PRK14602 ruvA Holliday junctio 83.7 0.63 1.4E-05 36.8 1.5 17 64-80 110-126 (203)
34 PF12826 HHH_2: Helix-hairpin- 83.6 0.24 5.3E-06 32.1 -0.7 18 67-84 7-24 (64)
35 COG0632 RuvA Holliday junction 83.1 0.73 1.6E-05 36.8 1.7 22 63-84 108-129 (201)
36 PRK13901 ruvA Holliday junctio 83.1 0.68 1.5E-05 36.8 1.5 18 64-81 108-125 (196)
37 TIGR01052 top6b DNA topoisomer 82.9 1.8 3.9E-05 38.8 4.2 42 66-107 255-300 (488)
38 PRK00274 ksgA 16S ribosomal RN 82.6 0.69 1.5E-05 37.3 1.4 49 58-107 221-270 (272)
39 PRK14600 ruvA Holliday junctio 80.5 1.1 2.4E-05 35.0 1.9 19 63-82 108-126 (186)
40 PRK00116 ruvA Holliday junctio 79.7 0.82 1.8E-05 35.5 0.8 57 51-107 61-130 (192)
41 PRK14605 ruvA Holliday junctio 78.3 1.2 2.6E-05 34.9 1.4 17 64-80 109-125 (194)
42 PF14520 HHH_5: Helix-hairpin- 77.4 1.8 3.8E-05 27.3 1.7 20 64-83 39-58 (60)
43 PF11731 Cdd1: Pathogenicity l 76.6 2.6 5.7E-05 30.0 2.6 36 63-99 12-48 (93)
44 PF03486 HI0933_like: HI0933-l 76.4 1.6 3.6E-05 37.7 1.8 50 57-108 289-340 (409)
45 cd00080 HhH2_motif Helix-hairp 74.4 2.6 5.6E-05 28.1 2.0 20 65-84 24-43 (75)
46 COG0030 KsgA Dimethyladenosine 73.7 1.5 3.2E-05 36.3 0.8 46 57-107 210-256 (259)
47 TIGR03252 uncharacterized HhH- 73.4 1.9 4.2E-05 33.9 1.4 29 56-84 108-136 (177)
48 TIGR00755 ksgA dimethyladenosi 72.0 1.7 3.7E-05 34.4 0.8 49 54-104 203-252 (253)
49 PF14716 HHH_8: Helix-hairpin- 71.8 2.6 5.7E-05 27.3 1.5 19 64-82 48-66 (68)
50 PF12836 HHH_3: Helix-hairpin- 71.7 2 4.4E-05 27.7 1.0 43 62-104 13-63 (65)
51 smart00483 POLXc DNA polymeras 71.6 2.6 5.6E-05 35.4 1.8 38 63-101 89-132 (334)
52 TIGR00084 ruvA Holliday juncti 70.9 2.5 5.4E-05 33.1 1.5 18 63-80 107-124 (191)
53 PRK14605 ruvA Holliday junctio 70.3 0.99 2.1E-05 35.4 -0.9 71 16-86 20-96 (194)
54 PF00398 RrnaAD: Ribosomal RNA 69.9 1.4 3E-05 35.3 -0.1 52 54-107 210-262 (262)
55 PF02371 Transposase_20: Trans 69.7 3.7 8.1E-05 27.7 2.0 20 64-83 3-22 (87)
56 smart00279 HhH2 Helix-hairpin- 69.4 3.9 8.5E-05 24.0 1.8 17 66-82 19-35 (36)
57 cd00141 NT_POLXc Nucleotidyltr 68.0 3.4 7.5E-05 34.3 1.8 22 64-86 86-107 (307)
58 PRK08609 hypothetical protein; 67.5 3.8 8.2E-05 37.0 2.1 23 64-86 89-111 (570)
59 cd00056 ENDO3c endonuclease II 67.0 3.2 6.9E-05 30.2 1.3 24 58-81 78-101 (158)
60 smart00478 ENDO3c endonuclease 66.9 3.3 7.1E-05 29.9 1.3 23 61-83 70-92 (149)
61 COG1389 DNA topoisomerase VI, 66.9 6.4 0.00014 35.8 3.4 42 67-108 265-311 (538)
62 COG1293 Predicted RNA-binding 66.1 7.1 0.00015 35.3 3.6 46 62-107 189-235 (564)
63 TIGR01259 comE comEA protein. 65.7 5.5 0.00012 28.9 2.3 32 54-85 59-90 (120)
64 PRK14606 ruvA Holliday junctio 65.4 1.2 2.6E-05 34.9 -1.3 76 10-86 13-96 (188)
65 PF14794 DUF4479: Domain of un 64.0 5.7 0.00012 26.9 2.0 16 92-107 47-62 (73)
66 PF02042 RWP-RK: RWP-RK domain 62.1 8.2 0.00018 24.7 2.3 20 67-86 23-42 (52)
67 TIGR00426 competence protein C 62.0 9.2 0.0002 24.5 2.7 43 63-105 16-67 (69)
68 PRK14601 ruvA Holliday junctio 60.8 1.7 3.8E-05 34.0 -1.1 75 11-86 14-96 (183)
69 TIGR01083 nth endonuclease III 60.2 4.8 0.0001 30.9 1.2 20 62-81 105-124 (191)
70 cd02020 CMPK Cytidine monophos 59.3 17 0.00037 25.1 3.8 40 63-102 2-42 (147)
71 PRK10702 endonuclease III; Pro 59.3 5.1 0.00011 31.7 1.3 21 61-81 107-127 (211)
72 PRK00116 ruvA Holliday junctio 58.3 6 0.00013 30.7 1.5 23 64-86 109-131 (192)
73 PRK12311 rpsB 30S ribosomal pr 58.1 6.1 0.00013 33.7 1.6 44 62-106 262-306 (326)
74 TIGR01448 recD_rel helicase, p 57.4 14 0.00031 34.2 4.0 39 67-105 88-137 (720)
75 PRK14602 ruvA Holliday junctio 56.4 2.4 5.3E-05 33.5 -1.0 70 17-86 22-97 (203)
76 TIGR00084 ruvA Holliday juncti 56.4 1.4 3E-05 34.5 -2.4 69 16-85 20-94 (191)
77 PRK12766 50S ribosomal protein 55.7 8.7 0.00019 31.6 2.1 37 64-101 4-41 (232)
78 COG0258 Exo 5'-3' exonuclease 54.6 11 0.00023 31.1 2.4 19 68-86 203-221 (310)
79 PRK00076 recR recombination pr 54.4 15 0.00032 29.4 3.1 40 61-107 9-48 (196)
80 PRK14603 ruvA Holliday junctio 53.9 2.3 4.9E-05 33.6 -1.6 70 16-86 20-95 (197)
81 TIGR00615 recR recombination p 53.6 16 0.00034 29.2 3.1 40 61-107 9-48 (195)
82 PF14490 HHH_4: Helix-hairpin- 52.1 7 0.00015 26.8 0.8 24 63-86 45-69 (94)
83 PRK07373 DNA polymerase III su 51.4 14 0.0003 32.7 2.8 25 58-82 109-133 (449)
84 COG2081 Predicted flavoprotein 50.3 21 0.00045 31.7 3.6 50 57-108 284-333 (408)
85 PRK14600 ruvA Holliday junctio 50.2 2.5 5.5E-05 33.1 -1.8 38 49-86 59-96 (186)
86 TIGR01084 mutY A/G-specific ad 50.0 8.9 0.00019 31.7 1.3 25 54-81 99-123 (275)
87 PRK13901 ruvA Holliday junctio 49.9 3.1 6.8E-05 33.1 -1.4 71 15-86 19-95 (196)
88 PRK13844 recombination protein 49.5 20 0.00042 28.8 3.1 40 61-107 13-52 (200)
89 PF14635 HHH_7: Helix-hairpin- 49.1 14 0.0003 26.7 2.0 26 59-84 46-71 (104)
90 PF11338 DUF3140: Protein of u 48.3 26 0.00057 25.0 3.3 34 71-107 35-68 (92)
91 TIGR00588 ogg 8-oxoguanine DNA 48.2 9.6 0.00021 31.8 1.2 22 61-82 218-239 (310)
92 PRK13913 3-methyladenine DNA g 47.8 10 0.00022 30.4 1.3 21 61-81 119-139 (218)
93 COG0353 RecR Recombinational D 47.6 21 0.00045 28.8 3.0 40 61-107 10-49 (198)
94 PRK00558 uvrC excinuclease ABC 46.8 16 0.00035 33.3 2.6 44 57-101 537-580 (598)
95 PF14842 FliG_N: FliG N-termin 46.8 5.2 0.00011 28.3 -0.5 36 72-107 7-44 (108)
96 PF09883 DUF2110: Uncharacteri 46.8 14 0.0003 30.4 1.9 63 58-120 96-175 (225)
97 COG1936 Predicted nucleotide k 46.2 21 0.00046 28.3 2.8 25 62-86 2-26 (180)
98 cd00008 53EXOc 5'-3' exonuclea 46.1 15 0.00033 29.3 2.0 20 65-84 185-204 (240)
99 PRK10308 3-methyl-adenine DNA 46.0 11 0.00025 31.0 1.4 22 61-82 205-226 (283)
100 cd01104 HTH_MlrA-CarA Helix-Tu 45.8 51 0.0011 20.3 4.1 42 65-106 6-52 (68)
101 PRK10880 adenine DNA glycosyla 45.3 11 0.00023 32.4 1.1 21 61-81 107-127 (350)
102 smart00475 53EXOc 5'-3' exonuc 45.0 16 0.00035 29.7 2.1 20 65-84 188-207 (259)
103 PRK01229 N-glycosylase/DNA lya 44.9 14 0.00031 29.5 1.7 26 60-85 115-141 (208)
104 PRK14604 ruvA Holliday junctio 44.7 3.8 8.2E-05 32.3 -1.6 71 15-85 19-95 (195)
105 PRK14671 uvrC excinuclease ABC 44.5 18 0.00039 33.3 2.5 49 52-101 558-606 (621)
106 PRK12278 50S ribosomal protein 43.8 20 0.00043 29.1 2.4 43 63-106 158-201 (221)
107 cd01702 PolY_Pol_eta DNA Polym 43.8 17 0.00038 30.7 2.1 37 64-100 183-222 (359)
108 KOG1014 17 beta-hydroxysteroid 43.8 30 0.00065 29.6 3.5 42 68-111 58-100 (312)
109 PRK13910 DNA glycosylase MutY; 43.7 12 0.00025 31.4 1.0 25 54-81 66-90 (289)
110 PF01367 5_3_exonuc: 5'-3' exo 43.6 3.1 6.8E-05 29.7 -2.0 19 66-84 21-39 (101)
111 PRK14976 5'-3' exonuclease; Pr 43.5 17 0.00036 30.0 1.9 19 66-84 194-212 (281)
112 PRK09482 flap endonuclease-lik 43.1 18 0.00038 29.8 2.0 19 66-84 185-203 (256)
113 COG0122 AlkA 3-methyladenine D 42.0 14 0.00031 30.6 1.3 21 60-80 195-215 (285)
114 PF06514 PsbU: Photosystem II 41.4 17 0.00036 26.1 1.4 58 52-109 12-73 (93)
115 PRK07945 hypothetical protein; 39.0 21 0.00045 30.0 1.9 50 64-121 50-99 (335)
116 PLN02200 adenylate kinase fami 37.9 41 0.00089 26.7 3.3 42 53-94 36-78 (234)
117 COG0632 RuvA Holliday junction 36.9 1.9 4.1E-05 34.5 -4.5 43 44-86 54-96 (201)
118 cd00128 XPG Xeroderma pigmento 36.8 25 0.00054 28.8 2.0 18 67-84 227-244 (316)
119 PRK14667 uvrC excinuclease ABC 36.5 24 0.00053 32.2 2.0 43 58-101 509-551 (567)
120 PF06819 Arc_PepC: Archaeal Pe 36.2 36 0.00078 25.0 2.5 26 90-115 84-109 (110)
121 PRK14666 uvrC excinuclease ABC 35.6 24 0.00052 33.2 1.8 40 61-101 635-674 (694)
122 PF13613 HTH_Tnp_4: Helix-turn 33.9 30 0.00065 21.2 1.6 20 64-83 24-43 (53)
123 PRK03980 flap endonuclease-1; 33.7 29 0.00063 28.8 1.9 18 67-84 193-210 (292)
124 COG1555 ComEA DNA uptake prote 33.7 47 0.001 25.0 2.9 42 64-105 98-147 (149)
125 PRK14670 uvrC excinuclease ABC 33.3 29 0.00063 31.8 2.0 40 61-101 512-551 (574)
126 PF04760 IF2_N: Translation in 33.3 23 0.0005 21.7 1.0 43 64-106 8-52 (54)
127 PF00034 Cytochrom_C: Cytochro 33.2 48 0.001 20.3 2.5 17 92-108 74-90 (91)
128 PRK02406 DNA polymerase IV; Va 32.7 40 0.00088 27.7 2.6 38 63-101 168-206 (343)
129 PF05291 Bystin: Bystin; Inte 32.7 32 0.0007 29.3 2.0 30 91-120 257-289 (301)
130 PRK12373 NADH dehydrogenase su 32.6 34 0.00073 30.2 2.2 43 63-106 323-366 (400)
131 PTZ00338 dimethyladenosine tra 32.0 40 0.00086 27.9 2.4 35 74-108 255-289 (294)
132 PF09397 Ftsk_gamma: Ftsk gamm 31.6 28 0.00061 23.0 1.2 20 64-83 25-44 (65)
133 PRK07194 fliG flagellar motor 31.6 39 0.00085 28.4 2.4 36 72-107 9-46 (334)
134 COG0177 Nth Predicted EndoIII- 31.3 26 0.00057 28.2 1.2 30 54-86 103-133 (211)
135 TIGR00194 uvrC excinuclease AB 31.2 31 0.00068 31.5 1.8 24 61-84 539-562 (574)
136 PF14213 DUF4325: Domain of un 31.0 1.3E+02 0.0029 19.4 4.4 54 54-107 13-74 (74)
137 TIGR03674 fen_arch flap struct 30.6 35 0.00075 28.8 1.9 19 66-84 239-257 (338)
138 PRK14529 adenylate kinase; Pro 30.6 87 0.0019 25.0 4.1 46 62-107 2-55 (223)
139 PRK05898 dnaE DNA polymerase I 30.5 47 0.001 32.5 2.9 45 58-102 747-801 (971)
140 PF06483 ChiC: Chitinase C; I 30.5 1.3E+02 0.0028 24.0 5.0 53 12-64 93-155 (180)
141 COG1536 FliG Flagellar motor s 29.9 34 0.00073 29.4 1.7 49 72-120 13-64 (339)
142 PRK06253 O-phosphoseryl-tRNA s 28.6 96 0.0021 28.5 4.4 34 69-108 105-138 (529)
143 PRK08118 topology modulation p 28.6 1.4E+02 0.0031 22.1 4.8 53 63-115 4-69 (167)
144 TIGR00608 radc DNA repair prot 28.2 37 0.00081 27.1 1.6 23 64-86 61-83 (218)
145 PRK14668 uvrC excinuclease ABC 27.6 36 0.00078 31.1 1.6 40 61-101 523-562 (577)
146 PF11460 DUF3007: Protein of u 27.4 35 0.00076 24.9 1.2 21 87-107 84-104 (104)
147 PRK13766 Hef nuclease; Provisi 27.2 65 0.0014 29.4 3.2 22 63-84 715-736 (773)
148 PRK14669 uvrC excinuclease ABC 27.2 40 0.00087 31.2 1.8 40 61-101 550-589 (624)
149 PRK03858 DNA polymerase IV; Va 27.2 58 0.0013 27.3 2.7 36 64-100 174-210 (396)
150 TIGR02236 recomb_radA DNA repa 27.0 54 0.0012 26.5 2.4 36 65-101 1-37 (310)
151 PF10415 FumaraseC_C: Fumarase 26.9 58 0.0013 20.6 2.1 33 71-103 9-48 (55)
152 PF13442 Cytochrome_CBB3: Cyto 26.9 63 0.0014 20.0 2.2 15 91-105 53-67 (67)
153 PF04273 DUF442: Putative phos 26.8 82 0.0018 22.5 3.0 32 76-107 49-84 (110)
154 COG3760 Uncharacterized conser 26.7 23 0.0005 27.7 0.2 11 16-26 40-50 (164)
155 PTZ00217 flap endonuclease-1; 26.7 45 0.00098 28.9 2.0 18 67-84 239-256 (393)
156 PRK03352 DNA polymerase IV; Va 26.6 59 0.0013 26.8 2.6 37 64-101 178-215 (346)
157 TIGR00575 dnlj DNA ligase, NAD 26.2 41 0.00088 31.1 1.7 36 66-101 435-471 (652)
158 PRK07956 ligA NAD-dependent DN 25.8 36 0.00078 31.6 1.3 36 66-101 448-484 (665)
159 PRK00024 hypothetical protein; 25.8 44 0.00095 26.7 1.6 23 64-86 67-89 (224)
160 TIGR00575 dnlj DNA ligase, NAD 25.8 43 0.00094 31.0 1.8 23 61-84 497-519 (652)
161 PRK05672 dnaE2 error-prone DNA 25.5 59 0.0013 31.9 2.7 45 58-103 811-863 (1046)
162 PRK02362 ski2-like helicase; P 25.3 53 0.0012 30.2 2.3 37 64-101 653-690 (737)
163 PRK03609 umuC DNA polymerase V 25.2 64 0.0014 27.6 2.6 37 64-101 180-217 (422)
164 PRK14672 uvrC excinuclease ABC 25.1 45 0.00098 31.5 1.8 42 59-101 604-645 (691)
165 PF03118 RNA_pol_A_CTD: Bacter 25.0 42 0.0009 21.9 1.1 20 64-83 45-64 (66)
166 PF14229 DUF4332: Domain of un 24.7 1.1E+02 0.0024 22.0 3.5 42 65-107 55-97 (122)
167 PF06207 DUF1002: Protein of u 24.5 1.4E+02 0.0029 24.3 4.2 15 93-107 192-206 (225)
168 TIGR01359 UMP_CMP_kin_fam UMP- 24.3 1.2E+02 0.0027 21.9 3.7 31 63-93 2-33 (183)
169 PRK05673 dnaE DNA polymerase I 23.9 62 0.0013 32.0 2.5 45 58-102 815-870 (1135)
170 TIGR00594 polc DNA-directed DN 23.7 63 0.0014 31.5 2.5 46 58-103 819-875 (1022)
171 PRK04301 radA DNA repair and r 23.6 67 0.0015 26.3 2.4 39 62-101 5-44 (317)
172 PRK03348 DNA polymerase IV; Pr 23.5 76 0.0016 27.7 2.8 38 64-102 181-219 (454)
173 PF03965 Penicillinase_R: Peni 23.3 71 0.0015 22.2 2.2 51 57-107 57-115 (115)
174 PRK07279 dnaE DNA polymerase I 23.3 63 0.0014 31.8 2.4 25 58-82 745-769 (1034)
175 PF09827 CRISPR_Cas2: CRISPR a 23.1 84 0.0018 20.3 2.4 35 73-107 16-53 (78)
176 PF13276 HTH_21: HTH-like doma 23.0 26 0.00056 21.7 -0.1 31 56-86 21-53 (60)
177 TIGR00207 fliG flagellar motor 22.9 73 0.0016 26.9 2.5 36 72-107 11-48 (338)
178 cd01700 PolY_Pol_V_umuC umuC s 22.6 79 0.0017 26.0 2.6 36 64-100 177-213 (344)
179 PF06897 DUF1269: Protein of u 22.5 38 0.00082 24.1 0.6 55 69-123 38-96 (102)
180 PRK07135 dnaE DNA polymerase I 22.5 71 0.0015 31.2 2.6 45 58-102 748-803 (973)
181 cd00141 NT_POLXc Nucleotidyltr 22.4 48 0.001 27.5 1.3 23 64-86 46-68 (307)
182 KOG2534 DNA polymerase IV (fam 22.1 68 0.0015 28.0 2.2 48 65-112 58-107 (353)
183 smart00843 Ftsk_gamma This dom 22.1 54 0.0012 21.7 1.3 20 64-83 24-43 (63)
184 PF00288 GHMP_kinases_N: GHMP 22.0 94 0.002 19.4 2.3 44 65-108 8-51 (67)
185 PRK01172 ski2-like helicase; P 21.9 71 0.0015 28.9 2.4 37 64-101 613-650 (674)
186 TIGR01573 cas2 CRISPR-associat 21.8 1.5E+02 0.0033 20.2 3.6 34 74-107 19-57 (95)
187 PRK07374 dnaE DNA polymerase I 21.7 76 0.0016 31.6 2.6 45 58-102 830-885 (1170)
188 TIGR01764 excise DNA binding d 21.4 79 0.0017 17.7 1.8 21 66-86 8-28 (49)
189 PRK14133 DNA polymerase IV; Pr 21.3 93 0.002 25.7 2.8 37 64-101 174-211 (347)
190 TIGR02698 CopY_TcrY copper tra 21.3 90 0.002 22.6 2.4 51 57-107 58-116 (130)
191 PRK00254 ski2-like helicase; P 21.3 56 0.0012 30.0 1.6 36 65-101 647-683 (720)
192 PHA02564 V virion protein; Pro 21.1 2.1E+02 0.0044 21.7 4.4 32 75-107 87-119 (141)
193 COG1796 POL4 DNA polymerase IV 20.8 70 0.0015 27.6 2.0 21 64-84 54-74 (326)
194 TIGR00470 sepS O-phosphoseryl- 20.5 1.6E+02 0.0035 27.1 4.3 33 69-108 105-137 (533)
195 PRK01810 DNA polymerase IV; Va 20.4 89 0.0019 26.4 2.5 37 64-101 180-217 (407)
196 cd03586 PolY_Pol_IV_kappa DNA 20.3 93 0.002 25.1 2.5 37 64-101 172-209 (334)
197 PRK05755 DNA polymerase I; Pro 20.2 68 0.0015 30.4 2.0 20 65-84 189-208 (880)
198 PRK03103 DNA polymerase IV; Re 20.2 92 0.002 26.3 2.6 37 64-101 182-219 (409)
199 PRK14896 ksgA 16S ribosomal RN 20.2 72 0.0016 25.3 1.8 50 55-106 201-255 (258)
No 1
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.2e-27 Score=174.91 Aligned_cols=78 Identities=38% Similarity=0.684 Sum_probs=75.9
Q ss_pred EEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh-hccccccchhhhcccccc
Q 033150 47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS-KYMIEGDLVIIPYFFVRG 124 (126)
Q Consensus 47 MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~-~~~Ie~dLrR~i~~nI~~ 124 (126)
|+||+|+|||++|+|.+|||+|||||+++|..||+++||+ +++++||||||+++|+++|+ .|+||+||++++++||+.
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkR 80 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKR 80 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999 99999999999999999999 599999999999999973
No 2
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=99.92 E-value=1.4e-25 Score=165.34 Aligned_cols=78 Identities=37% Similarity=0.718 Sum_probs=75.6
Q ss_pred EEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh-ccccccchhhhcccccc
Q 033150 47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEGDLVIIPYFFVRG 124 (126)
Q Consensus 47 MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~-~~Ie~dLrR~i~~nI~~ 124 (126)
|+||+|+|+|++|+|.+|||+|||||+++|.+||+++||| +.++++||++|+++|+++|++ |.||+||++++++||+.
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r 80 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEENYQVEGDLRRFESLNIKR 80 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999 999999999999999999985 99999999999999963
No 3
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=99.92 E-value=1.9e-25 Score=164.49 Aligned_cols=77 Identities=44% Similarity=0.749 Sum_probs=75.5
Q ss_pred EEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh-ccccccchhhhccccc
Q 033150 47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEGDLVIIPYFFVR 123 (126)
Q Consensus 47 MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~-~~Ie~dLrR~i~~nI~ 123 (126)
|+||+|+|+|++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|+++|++ |.+|+||++++++||+
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~ 79 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIK 79 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999 999999999999999999997 9999999999999986
No 4
>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=99.91 E-value=4e-25 Score=166.84 Aligned_cols=79 Identities=27% Similarity=0.386 Sum_probs=76.5
Q ss_pred eeEEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh----------------
Q 033150 45 IQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK---------------- 107 (126)
Q Consensus 45 ~~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~---------------- 107 (126)
+||+||+|+|||++|+|.+||++|||||+++|.+||+++||| ++++++||++|+++|+++|++
T Consensus 3 ~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~Nr~~d~ 82 (144)
T TIGR03629 3 KYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLLNRRKDY 82 (144)
T ss_pred ceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHhhccccc
Confidence 499999999999999999999999999999999999999999 999999999999999999985
Q ss_pred ------ccccccchhhhccccc
Q 033150 108 ------YMIEGDLVIIPYFFVR 123 (126)
Q Consensus 108 ------~~Ie~dLrR~i~~nI~ 123 (126)
|.||+||++++++||+
T Consensus 83 ~tg~~~~~ie~dL~~~~~~dI~ 104 (144)
T TIGR03629 83 ETGEDLHLIGSDLDMTVREDIN 104 (144)
T ss_pred ccCccceEehHHHHHHHHHHHH
Confidence 6799999999999996
No 5
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=99.91 E-value=3.1e-25 Score=168.40 Aligned_cols=79 Identities=28% Similarity=0.442 Sum_probs=76.1
Q ss_pred eEEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh------------------
Q 033150 46 QCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS------------------ 106 (126)
Q Consensus 46 ~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~------------------ 106 (126)
||+||+|+|||++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|+++|+
T Consensus 8 ~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~Nr~~d~ 87 (149)
T PRK04053 8 YIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLNRRKDY 87 (149)
T ss_pred hhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhcccccc
Confidence 99999999999999999999999999999999999999999 99999999999999999996
Q ss_pred -----hccccccchhhhcccccc
Q 033150 107 -----KYMIEGDLVIIPYFFVRG 124 (126)
Q Consensus 107 -----~~~Ie~dLrR~i~~nI~~ 124 (126)
+|.||+|||+++++||+.
T Consensus 88 ~tg~~~~~ie~dLr~~~~~~I~r 110 (149)
T PRK04053 88 ETGEDLHLIGSDLILTVREDINR 110 (149)
T ss_pred ccCccceEehHHHHHHHHHHHHH
Confidence 367999999999999963
No 6
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=99.90 E-value=1.5e-24 Score=165.52 Aligned_cols=80 Identities=16% Similarity=0.245 Sum_probs=76.0
Q ss_pred eeEEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh---cc-----------
Q 033150 45 IQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK---YM----------- 109 (126)
Q Consensus 45 ~~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~---~~----------- 109 (126)
+||+||+|+|+|++|+|.+||++|||||+++|.+||+++||| ++++++||++|+++|+++|++ |.
T Consensus 12 ~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~nr~kd 91 (154)
T PTZ00134 12 QHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFLNRQRD 91 (154)
T ss_pred hhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHhhcccc
Confidence 399999999999999999999999999999999999999999 999999999999999999986 53
Q ss_pred ---------ccccchhhhcccccc
Q 033150 110 ---------IEGDLVIIPYFFVRG 124 (126)
Q Consensus 110 ---------Ie~dLrR~i~~nI~~ 124 (126)
||+||++++++||+.
T Consensus 92 ~~tG~d~h~i~~dL~~~~~~dI~R 115 (154)
T PTZ00134 92 PKDGKNSHLTSNMLDTKLREDLER 115 (154)
T ss_pred ccccchhhhhHHHHHHHHHHHHHH
Confidence 699999999999963
No 7
>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=99.89 E-value=1.2e-23 Score=153.15 Aligned_cols=75 Identities=49% Similarity=0.814 Sum_probs=72.9
Q ss_pred EecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh-ccccccchhhhccccc
Q 033150 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEGDLVIIPYFFVR 123 (126)
Q Consensus 49 rIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~-~~Ie~dLrR~i~~nI~ 123 (126)
||+|+|+|++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|+++|++ |.||+||++.+++||+
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~ 77 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIK 77 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999 999999999999999999975 9999999999999996
No 8
>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=99.88 E-value=5.1e-24 Score=152.63 Aligned_cols=75 Identities=35% Similarity=0.494 Sum_probs=71.5
Q ss_pred EecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh-ccccccchhhhccccc
Q 033150 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEGDLVIIPYFFVR 123 (126)
Q Consensus 49 rIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~-~~Ie~dLrR~i~~nI~ 123 (126)
||+|++||++|+|.+||++|||||+++|.+||+++||+ +.++++|+++|+++|+++|++ |.+|+||++++.+||+
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~~~~i~~~L~~~~~~~i~ 77 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEKNHLIENDLKRQVRENIK 77 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHTHSTCHHHHHHHHHHHHH
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHHhccccchHHHHHHHHHH
Confidence 79999999999999999999999999999999999999 999999999999999999998 9999999999999986
No 9
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.59 E-value=4.6e-16 Score=118.66 Aligned_cols=71 Identities=15% Similarity=0.386 Sum_probs=67.3
Q ss_pred ccccCCCCCcceeeEEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 33 PVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 33 ~~~~~~~~~~~~~~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
|+.-+++|+ +|+||++++++++++|.|||+.|||||+..|..+|+++|++ ..++++|+++|++.+.+++++
T Consensus 2 sl~~~~~~q----~i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d 73 (152)
T KOG3311|consen 2 SLVIPEAFQ----HILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILND 73 (152)
T ss_pred ceecchhHH----HHHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcC
Confidence 456677888 99999999999999999999999999999999999999999 999999999999999999984
No 10
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=95.99 E-value=0.0072 Score=49.25 Aligned_cols=51 Identities=20% Similarity=0.292 Sum_probs=46.4
Q ss_pred CCeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 57 NNKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 57 ~nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+++|.-+| +.+-|||--.|.+||-++||| ..++++||++|++.|-+.+.+
T Consensus 154 ~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~ 208 (274)
T PRK01103 154 KKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA 208 (274)
T ss_pred CCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 567888999 889999999999999999999 889999999999999777754
No 11
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=95.98 E-value=0.0081 Score=41.91 Aligned_cols=50 Identities=26% Similarity=0.470 Sum_probs=40.0
Q ss_pred CeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 58 NKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 58 nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
+++|..+| +.+-|||--.+.+||-++||+ ..++++|+++|+.+|-+.+..
T Consensus 23 ~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~ 76 (92)
T PF06831_consen 23 RRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKR 76 (92)
T ss_dssp CSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHH
T ss_pred cchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 55666666 568899999999999999999 889999999999998777654
No 12
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=94.72 E-value=0.051 Score=44.45 Aligned_cols=51 Identities=24% Similarity=0.445 Sum_probs=43.2
Q ss_pred CCeEEEEeecc---ccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 57 NNKRIEYSLQY---IHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 57 ~nK~V~~ALt~---IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+.+|..+|-. |-|||--.|.+||-++||| ..++++||++|+..|-+.+.+
T Consensus 153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~ 207 (272)
T PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE 207 (272)
T ss_pred CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence 45667777744 4999999999999999999 899999999999999775543
No 13
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=94.13 E-value=0.084 Score=43.17 Aligned_cols=49 Identities=14% Similarity=0.230 Sum_probs=42.3
Q ss_pred CCeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHH
Q 033150 57 NNKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEV 105 (126)
Q Consensus 57 ~nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I 105 (126)
.+++|.-+| +-|-|||--.|.+||-.+||| ..++++||++|++.|-+.+
T Consensus 142 ~~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i 194 (269)
T PRK14811 142 TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAI 194 (269)
T ss_pred cCCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHH
Confidence 366777777 568899999999999999999 8899999999999984444
No 14
>PRK10445 endonuclease VIII; Provisional
Probab=93.68 E-value=0.11 Score=42.19 Aligned_cols=50 Identities=20% Similarity=0.343 Sum_probs=42.7
Q ss_pred CeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 58 NKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 58 nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
+++|..+| +-+-|||--.|.+||-++||| ..++++||++|+++|-+.+.+
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 204 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLD 204 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence 55666666 457799999999999999999 888999999999999777754
No 15
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=93.56 E-value=0.11 Score=42.61 Aligned_cols=51 Identities=16% Similarity=0.355 Sum_probs=43.3
Q ss_pred CCeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 57 NNKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 57 ~nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+++|.-+| +-|-|||--.|.+||-.+||| ..++++||++|++.|-+.+.+
T Consensus 163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~ 217 (282)
T PRK13945 163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE 217 (282)
T ss_pred CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 355666677 568899999999999999999 889999999998888776654
No 16
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.26 E-value=0.14 Score=41.86 Aligned_cols=50 Identities=18% Similarity=0.452 Sum_probs=42.4
Q ss_pred CeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 58 NKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 58 nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
+++|..+| +-+-|||--.|.+||-..+|| ..++++||++|+++|-+.+.+
T Consensus 155 ~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 208 (272)
T TIGR00577 155 KRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE 208 (272)
T ss_pred CCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence 45566666 556799999999999999999 889999999999999777654
No 17
>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=93.21 E-value=0.055 Score=30.88 Aligned_cols=18 Identities=33% Similarity=0.512 Sum_probs=15.0
Q ss_pred eeccccccCHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILV 81 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~ 81 (126)
.|.++.|||+++|..|+.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 478999999999999975
No 18
>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=92.25 E-value=0.081 Score=30.40 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=15.4
Q ss_pred eeccccccCHHHHHHHHHHhCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKM 85 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI 85 (126)
.+++++|||+.++.+ ++++||
T Consensus 12 pi~~~~GIG~kt~~k-L~~~GI 32 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKK-LNKLGI 32 (32)
T ss_dssp BGGGSTTS-HHHHHH-HHCTT-
T ss_pred CHHhhCCccHHHHHH-HHHccC
Confidence 578999999999988 455554
No 19
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=92.19 E-value=0.03 Score=47.69 Aligned_cols=50 Identities=24% Similarity=0.384 Sum_probs=38.1
Q ss_pred CeEEEEeecccc-ccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 58 NKRIEYSLQYIH-GVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 58 nK~V~~ALt~Iy-GIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
...+..+|...+ |+|+..|..+|.++|++ +.++.+++++++..|.+.+.+
T Consensus 186 ~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~~ 237 (455)
T PF05833_consen 186 EKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIRE 237 (455)
T ss_dssp G-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHHH
T ss_pred cccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHHH
Confidence 456677787777 99999999999999999 889999999999988777765
No 20
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=91.83 E-value=0.26 Score=44.52 Aligned_cols=43 Identities=30% Similarity=0.471 Sum_probs=39.7
Q ss_pred ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhhc
Q 033150 66 QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~~ 108 (126)
..+-.||..+|.+||+.+|++ +++.++|+++|+.+|-+.+.++
T Consensus 264 ~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 264 EEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred HhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 456789999999999999999 9999999999999999999874
No 21
>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=90.05 E-value=0.19 Score=32.01 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=21.8
Q ss_pred eccccccCHHHHHHHHHHhCCCc---cc--cCCCCHHHHHHH
Q 033150 65 LQYIHGVGRTRARQILVDLKMEN---KI--TKDMSEEELITI 101 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~~---~k--v~~LteeQI~~L 101 (126)
++.|||||+.+|.+..+ .|+.+ .+ -..||+.|.--|
T Consensus 4 f~~I~GVG~~tA~~w~~-~G~rtl~Dl~~~~~~Lt~~Q~iGl 44 (52)
T PF10391_consen 4 FTGIWGVGPKTARKWYA-KGIRTLEDLRKSKSKLTWQQQIGL 44 (52)
T ss_dssp HHTSTT--HHHHHHHHH-TT--SHHHHHHGGCGS-HHHHHHH
T ss_pred hhhcccccHHHHHHHHH-hCCCCHHHHhhhhccCCHHHHHHH
Confidence 68999999999999998 78761 11 136776665443
No 22
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=90.03 E-value=0.26 Score=37.29 Aligned_cols=62 Identities=15% Similarity=0.150 Sum_probs=48.0
Q ss_pred ecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCCc----cccCCCCHHHHHHHHHHHhhcccc
Q 033150 50 VGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMEN----KITKDMSEEELITIRDEVSKYMIE 111 (126)
Q Consensus 50 Ilgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~~----~kv~~LteeQI~~L~~~I~~~~Ie 111 (126)
-.+..++-|..=...|+++.|||+++|.+|++.-.+.+ ..+..+++.|.+.+++..+++++.
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV~ 113 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDNFTVT 113 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcceeeC
Confidence 34566666666677899999999999999997444441 347899999999999999886543
No 23
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=88.56 E-value=0.4 Score=36.34 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=37.8
Q ss_pred EeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh
Q 033150 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~ 106 (126)
-=||.|.|||+.... .++.+||- ..-+-.+|..++..+.++++
T Consensus 67 DDLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 67 DDLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred ccchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 459999999998875 56889999 88899999999999999886
No 24
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=87.91 E-value=0.83 Score=38.17 Aligned_cols=52 Identities=23% Similarity=0.423 Sum_probs=43.2
Q ss_pred CCCeEEEEee---ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 56 PNNKRIEYSL---QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 56 p~nK~V~~AL---t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
..+++|.-+| +-|-|||--.|.++|-++||+ .+..++|+++|+..|.+.+..
T Consensus 153 ~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~ 208 (273)
T COG0266 153 KKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKD 208 (273)
T ss_pred cCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHH
Confidence 3455566666 557899999999999999999 888999999998888777654
No 25
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=87.15 E-value=0.46 Score=25.68 Aligned_cols=19 Identities=32% Similarity=0.490 Sum_probs=16.4
Q ss_pred eeccccccCHHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~k 82 (126)
.|..+.|||+++|..|++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3678999999999999863
No 26
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=87.07 E-value=0.12 Score=32.80 Aligned_cols=38 Identities=24% Similarity=0.260 Sum_probs=26.1
Q ss_pred EEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHH
Q 033150 62 EYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELIT 100 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~ 100 (126)
+..|..|.|||+..|..+.+. |+. -.-+-..+.+++..
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~-G~~t~~~l~~a~~~~L~~ 42 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEA-GIKTLEDLANADPEELAE 42 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHT-TCSSHHHHHTSHHHHHHT
T ss_pred HHhhccCCCCCHHHHHHHHhc-CCCcHHHHHcCCHHHHhc
Confidence 346889999999999999877 777 33344444444433
No 27
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.26 E-value=0.41 Score=37.55 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=12.9
Q ss_pred eeccccccCHHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~k 82 (126)
+|+++.|||+++|.+||-.
T Consensus 109 ~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 109 GLSKLPGISKKTAERIVME 127 (188)
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 5667777777777777733
No 28
>TIGR00275 flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
Probab=85.90 E-value=0.91 Score=38.37 Aligned_cols=48 Identities=15% Similarity=0.280 Sum_probs=39.6
Q ss_pred eEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhhc
Q 033150 59 KRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 59 K~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~~ 108 (126)
+.+...|+.+ +-++++..+|+.+||+ ++++++|+++|+++|.+.+.+|
T Consensus 284 ~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~~ 332 (400)
T TIGR00275 284 KTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKNW 332 (400)
T ss_pred hhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhCC
Confidence 3444444432 7899999999999999 9999999999999999999874
No 29
>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=85.29 E-value=0.85 Score=31.14 Aligned_cols=46 Identities=20% Similarity=0.360 Sum_probs=30.3
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHhC---CCc-----cccCCCCHHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDLK---MEN-----KITKDMSEEELITIRD 103 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~klG---I~~-----~kv~~LteeQI~~L~~ 103 (126)
+..|+++|+.|.|||...|.+|.+.-. +.+ .++..++..+++.|.+
T Consensus 22 ~~~Ir~gl~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~~~i~~~~le~Li~ 75 (90)
T PF14579_consen 22 NNAIRLGLSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRLPKINKRQLEALIK 75 (90)
T ss_dssp -TEEE-BGGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS-TS-HHHHHHHHH
T ss_pred CCEEeehHhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHHhcCCHHHHHHHHH
Confidence 368999999999999999999997772 221 1222677777776654
No 30
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.06 E-value=0.5 Score=37.01 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=10.2
Q ss_pred eeccccccCHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQIL 80 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC 80 (126)
+|+++.|||+++|.+|+
T Consensus 109 ~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 109 VLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 45566666666666665
No 31
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.84 E-value=0.52 Score=37.15 Aligned_cols=19 Identities=32% Similarity=0.489 Sum_probs=15.2
Q ss_pred eeccccccCHHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~k 82 (126)
+|+++.|||+++|.+||-.
T Consensus 108 ~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 108 LLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 6788888888888888833
No 32
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.73 E-value=0.53 Score=37.09 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=15.9
Q ss_pred EeeccccccCHHHHHHHHHHh
Q 033150 63 YSLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~kl 83 (126)
.+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 367888888888888888443
No 33
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.75 E-value=0.63 Score=36.82 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=13.0
Q ss_pred eeccccccCHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQIL 80 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC 80 (126)
+|+++.|||+++|.+|+
T Consensus 110 ~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 110 ALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHhcCCCcCHHHHHHHH
Confidence 57777777777777777
No 34
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=83.59 E-value=0.24 Score=32.10 Aligned_cols=18 Identities=28% Similarity=0.381 Sum_probs=14.8
Q ss_pred cccccCHHHHHHHHHHhC
Q 033150 67 YIHGVGRTRARQILVDLK 84 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klG 84 (126)
.|+|||..+|+.+++.+|
T Consensus 7 GI~~VG~~~ak~L~~~f~ 24 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG 24 (64)
T ss_dssp TSTT--HHHHHHHHHCCS
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 589999999999999988
No 35
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=83.14 E-value=0.73 Score=36.81 Aligned_cols=22 Identities=36% Similarity=0.677 Sum_probs=18.0
Q ss_pred EeeccccccCHHHHHHHHHHhC
Q 033150 63 YSLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klG 84 (126)
.+|+++.|||+++|.+||-.|.
T Consensus 108 ~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHHh
Confidence 4789999999999999995543
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.07 E-value=0.68 Score=36.82 Aligned_cols=18 Identities=22% Similarity=0.523 Sum_probs=11.9
Q ss_pred eeccccccCHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILV 81 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~ 81 (126)
+|+++.|||+++|.+|+-
T Consensus 108 ~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 108 LISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHhhCCCCCHHHHHHHHH
Confidence 566667777777776663
No 37
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=82.94 E-value=1.8 Score=38.79 Aligned_cols=42 Identities=14% Similarity=0.325 Sum_probs=37.6
Q ss_pred ccccccCHHHHHHHHHHhCCC----ccccCCCCHHHHHHHHHHHhh
Q 033150 66 QYIHGVGRTRARQILVDLKME----NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klGI~----~~kv~~LteeQI~~L~~~I~~ 107 (126)
..+-.||..+|.+||+.+|++ +++.++|+++|+.+|.+.+.+
T Consensus 255 ~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~ 300 (488)
T TIGR01052 255 SEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE 300 (488)
T ss_pred HhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh
Confidence 556789999999999999998 566899999999999999976
No 38
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=82.65 E-value=0.69 Score=37.29 Aligned_cols=49 Identities=16% Similarity=0.386 Sum_probs=39.0
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
+|++..+|.++++. +..+.++++.+|++ +.+..+|+.+|..+|.+.+++
T Consensus 221 rk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 221 RKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 45566677666552 34567889999999 999999999999999988865
No 39
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.48 E-value=1.1 Score=35.05 Aligned_cols=19 Identities=21% Similarity=0.531 Sum_probs=14.3
Q ss_pred EeeccccccCHHHHHHHHHH
Q 033150 63 YSLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~k 82 (126)
.+| +++|||+++|.+||-.
T Consensus 108 ~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHH
Confidence 467 7888888888888843
No 40
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.65 E-value=0.82 Score=35.55 Aligned_cols=57 Identities=21% Similarity=0.166 Sum_probs=38.8
Q ss_pred cCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC--c-----------cccCCCCHHHHHHHHHHHhh
Q 033150 51 GGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME--N-----------KITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 51 lgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~--~-----------~kv~~LteeQI~~L~~~I~~ 107 (126)
.|..-...|.+..-|..|.|||+++|..|++.+|.+ . .++.-+++...++|...+.+
T Consensus 61 ~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 61 YGFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred cCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 444433445566688999999999999999999963 1 12344566666666666653
No 41
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.30 E-value=1.2 Score=34.93 Aligned_cols=17 Identities=35% Similarity=0.618 Sum_probs=9.9
Q ss_pred eeccccccCHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQIL 80 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC 80 (126)
+|+++.|||+++|.+|+
T Consensus 109 ~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 109 LLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHhCCCCCHHHHHHHH
Confidence 35566666666666644
No 42
>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=77.38 E-value=1.8 Score=27.33 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=17.7
Q ss_pred eeccccccCHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl 83 (126)
.|..+.|||+.+|..|++.+
T Consensus 39 ~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 39 ELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHTSTTSSHHHHHHHHHHH
T ss_pred HHhcCCCCCHHHHHHHHHHH
Confidence 38899999999999999765
No 43
>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=76.59 E-value=2.6 Score=30.01 Aligned_cols=36 Identities=25% Similarity=0.258 Sum_probs=26.6
Q ss_pred EeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHH
Q 033150 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELI 99 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~ 99 (126)
..|+.|.|||+.+|.-+- .+||+ -.-+..-+.+++.
T Consensus 12 ~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly 48 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELY 48 (93)
T ss_pred HHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHH
Confidence 358999999999999887 99999 4444444455543
No 44
>PF03486 HI0933_like: HI0933-like protein; InterPro: IPR004792 This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases.; PDB: 2I0Z_A 3V76_A 2GQF_A.
Probab=76.43 E-value=1.6 Score=37.66 Aligned_cols=50 Identities=12% Similarity=0.254 Sum_probs=40.4
Q ss_pred CCeEEEEeeccccccCHHHHHHHHHHhCC-C-ccccCCCCHHHHHHHHHHHhhc
Q 033150 57 NNKRIEYSLQYIHGVGRTRARQILVDLKM-E-NKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 57 ~nK~V~~ALt~IyGIG~~~A~~IC~klGI-~-~~kv~~LteeQI~~L~~~I~~~ 108 (126)
+++.+...|..+ +-++.+..+|+..+| + ++++.+++++++.+|.+.+.++
T Consensus 289 ~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~~ 340 (409)
T PF03486_consen 289 PKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKRF 340 (409)
T ss_dssp TTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHCE
T ss_pred HhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHhC
Confidence 445555556655 789999999999999 8 8999999999999999999873
No 45
>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=74.38 E-value=2.6 Score=28.13 Aligned_cols=20 Identities=20% Similarity=0.406 Sum_probs=17.5
Q ss_pred eccccccCHHHHHHHHHHhC
Q 033150 65 LQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klG 84 (126)
+..|.|||+.+|.++.++.|
T Consensus 24 i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC
Confidence 34689999999999999877
No 46
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=73.67 E-value=1.5 Score=36.32 Aligned_cols=46 Identities=15% Similarity=0.395 Sum_probs=41.0
Q ss_pred CCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 57 NNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 57 ~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+|.++.+|+..++ ..++|+.+|++ +.+..+|+.+|+-+|.+.+..
T Consensus 210 RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 210 RRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 46788888888888 88999999999 899999999999999998864
No 47
>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=73.36 E-value=1.9 Score=33.89 Aligned_cols=29 Identities=28% Similarity=0.492 Sum_probs=24.2
Q ss_pred CCCeEEEEeeccccccCHHHHHHHHHHhC
Q 033150 56 PNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 56 p~nK~V~~ALt~IyGIG~~~A~~IC~klG 84 (126)
|+...++.-|..+.|||+.+|..++.-||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 66666667899999999999999987665
No 48
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=72.02 E-value=1.7 Score=34.35 Aligned_cols=49 Identities=12% Similarity=0.281 Sum_probs=38.2
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHH
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDE 104 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~ 104 (126)
.--.+|++..+|..+++- ..+..+++.+|++ +++..+||.+|+.+|.+.
T Consensus 203 F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 203 FSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 344567777788776542 3556788999999 999999999999998765
No 49
>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=71.78 E-value=2.6 Score=27.34 Aligned_cols=19 Identities=26% Similarity=0.433 Sum_probs=16.5
Q ss_pred eeccccccCHHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~k 82 (126)
++++|+|||++++.+|-.-
T Consensus 48 ~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 5899999999999998643
No 50
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=71.68 E-value=2 Score=27.66 Aligned_cols=43 Identities=16% Similarity=0.209 Sum_probs=27.8
Q ss_pred EEeeccccccCHHHHHHHHHHh----CCC----ccccCCCCHHHHHHHHHH
Q 033150 62 EYSLQYIHGVGRTRARQILVDL----KME----NKITKDMSEEELITIRDE 104 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~kl----GI~----~~kv~~LteeQI~~L~~~ 104 (126)
...|..++|||+..|..|.+.= ++. =..+..++++.+++|..+
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~~ 63 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKPY 63 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCCC
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHhh
Confidence 3458899999999999999765 443 234677888888887543
No 51
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=71.60 E-value=2.6 Score=35.45 Aligned_cols=38 Identities=11% Similarity=0.220 Sum_probs=27.4
Q ss_pred EeeccccccCHHHHHHHHHHhCCCc--ccc----CCCCHHHHHHH
Q 033150 63 YSLQYIHGVGRTRARQILVDLKMEN--KIT----KDMSEEELITI 101 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klGI~~--~kv----~~LteeQI~~L 101 (126)
..|++|+|||+++|.++-+ +||.+ .-. ..|+.+|+.-|
T Consensus 89 ~~l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~~~~l~~~q~~gl 132 (334)
T smart00483 89 KLFTNVFGVGPKTAAKWYR-KGIRTLEELKKNKELKLTKQQKAGL 132 (334)
T ss_pred HHHHccCCcCHHHHHHHHH-hCCCCHHHHHhcccccCCHHHHHHH
Confidence 4568999999999999988 99982 111 24776664433
No 52
>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=70.94 E-value=2.5 Score=33.05 Aligned_cols=18 Identities=39% Similarity=0.604 Sum_probs=15.3
Q ss_pred EeeccccccCHHHHHHHH
Q 033150 63 YSLQYIHGVGRTRARQIL 80 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC 80 (126)
-+|++++|||+++|.+|+
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 357889999999999998
No 53
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.34 E-value=0.99 Score=35.42 Aligned_cols=71 Identities=13% Similarity=0.069 Sum_probs=48.1
Q ss_pred eecCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC
Q 033150 16 ICNGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
-|||=---++.|.+....+-..-.-..+-.|+ ..+.|..-...+.++.-|.++.|||+++|..|+..++.+
T Consensus 20 ~~~GvGY~v~~s~~~~~~l~~~g~~~~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 20 NVSGVGFRCYMPATSPALIGGLGQRVRVFTHLHVREDALSLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred EECCEEEEEEeCHHHHHhcccCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 35665555566655554332111111122233 467888888999999999999999999999999988755
No 54
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=69.90 E-value=1.4 Score=35.25 Aligned_cols=52 Identities=15% Similarity=0.255 Sum_probs=42.4
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
..-.+|++..+|.++++ ......+.+.+||+ +.++.+|+.+|..+|-+++++
T Consensus 210 F~~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~k 262 (262)
T PF00398_consen 210 FSQRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLNK 262 (262)
T ss_dssp HTTTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHHH
T ss_pred HhCcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhhC
Confidence 44578889999988764 33456777779999 999999999999999998864
No 55
>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=69.71 E-value=3.7 Score=27.70 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=18.3
Q ss_pred eeccccccCHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl 83 (126)
-|++|+|||+.+|..|...+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 37899999999999999888
No 56
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=69.45 E-value=3.9 Score=24.00 Aligned_cols=17 Identities=24% Similarity=0.472 Sum_probs=15.0
Q ss_pred ccccccCHHHHHHHHHH
Q 033150 66 QYIHGVGRTRARQILVD 82 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~k 82 (126)
..|.|||+.+|.++.++
T Consensus 19 ~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCcccHHHHHHHHHh
Confidence 57899999999999875
No 57
>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=68.01 E-value=3.4 Score=34.27 Aligned_cols=22 Identities=32% Similarity=0.546 Sum_probs=20.2
Q ss_pred eeccccccCHHHHHHHHHHhCCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
-|++|+|||+++|.++- .+|+.
T Consensus 86 ~l~~i~GiGpk~a~~l~-~lGi~ 107 (307)
T cd00141 86 LLLRVPGVGPKTARKLY-ELGIR 107 (307)
T ss_pred HHHcCCCCCHHHHHHHH-HcCCC
Confidence 46799999999999999 99998
No 58
>PRK08609 hypothetical protein; Provisional
Probab=67.50 E-value=3.8 Score=36.96 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=21.4
Q ss_pred eeccccccCHHHHHHHHHHhCCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.|++|+|||+++|.++-+.+||.
T Consensus 89 ~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 89 PLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHhcCCCCCHHHHHHHHHHhCCC
Confidence 57899999999999999999995
No 59
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=66.98 E-value=3.2 Score=30.21 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=20.8
Q ss_pred CeEEEEeeccccccCHHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~ 81 (126)
...+...|++++|||+.+|..++-
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~ 101 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLL 101 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHH
Confidence 355788899999999999999885
No 60
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=66.94 E-value=3.3 Score=29.94 Aligned_cols=23 Identities=30% Similarity=0.294 Sum_probs=19.1
Q ss_pred EEEeeccccccCHHHHHHHHHHh
Q 033150 61 IEYSLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~kl 83 (126)
....|.+++|||+.+|..+|-..
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 45678899999999999888653
No 61
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=66.89 E-value=6.4 Score=35.76 Aligned_cols=42 Identities=17% Similarity=0.308 Sum_probs=37.3
Q ss_pred cccccCHHHHHHHHHHhCCC-ccccCCCC----HHHHHHHHHHHhhc
Q 033150 67 YIHGVGRTRARQILVDLKME-NKITKDMS----EEELITIRDEVSKY 108 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klGI~-~~kv~~Lt----eeQI~~L~~~I~~~ 108 (126)
.+--||..+|..+|+.+|++ +++..+|+ .++..+|.+.+.+|
T Consensus 265 ef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 265 EFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred HHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 44568999999999999999 99999999 99999999998764
No 62
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=66.06 E-value=7.1 Score=35.33 Aligned_cols=46 Identities=24% Similarity=0.359 Sum_probs=39.7
Q ss_pred EEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 62 EYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
...|..+.|+|.-.|..+|-+.|++ .....++.++.+..+...+++
T Consensus 189 ~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~ 235 (564)
T COG1293 189 VRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE 235 (564)
T ss_pred HHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence 3446778899999999999999999 777899999999999876643
No 63
>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=65.74 E-value=5.5 Score=28.89 Aligned_cols=32 Identities=22% Similarity=0.252 Sum_probs=25.2
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHHHHhCC
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI 85 (126)
.++-|..-.-.|..+.|||+.+|.+|.+.-.-
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 34455555667899999999999999988743
No 64
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.39 E-value=1.2 Score=34.92 Aligned_cols=76 Identities=16% Similarity=0.110 Sum_probs=52.2
Q ss_pred Ccceeeee--cCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHH
Q 033150 10 APALSVIC--NGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 10 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~ 81 (126)
.|-.-||+ ||=--..+.+.+....+ ..-....+..|+ ..+.|..=...+.++.-|.++-|||+++|..|+.
T Consensus 13 ~~~~vvie~~~GvGY~v~~~~~~~~~l-~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 13 SGNVLLVETKSGVVFEIVCDVQTSEEV-EEGGECFLHTFLSVSQDGITLYGFSNERKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred cCCEEEEEeCCcEEEEEEeCHHHHHHc-CCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHc
Confidence 44555664 57666667776666655 211222233333 3678888888999999999999999999999997
Q ss_pred HhCCC
Q 033150 82 DLKME 86 (126)
Q Consensus 82 klGI~ 86 (126)
.+..+
T Consensus 92 ~~~~~ 96 (188)
T PRK14606 92 NEDAE 96 (188)
T ss_pred CCCHH
Confidence 76544
No 65
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=64.05 E-value=5.7 Score=26.86 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=12.5
Q ss_pred CCCHHHHHHHHHHHhh
Q 033150 92 DMSEEELITIRDEVSK 107 (126)
Q Consensus 92 ~LteeQI~~L~~~I~~ 107 (126)
.||++|++.|.+.|.+
T Consensus 47 ~Lt~eqv~~LN~~l~~ 62 (73)
T PF14794_consen 47 FLTEEQVAKLNQALQK 62 (73)
T ss_dssp ---HHHHHHHHHHHHH
T ss_pred EcCHHHHHHHHHHHHH
Confidence 6899999999999987
No 66
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=62.13 E-value=8.2 Score=24.72 Aligned_cols=20 Identities=20% Similarity=0.097 Sum_probs=18.0
Q ss_pred cccccCHHHHHHHHHHhCCC
Q 033150 67 YIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klGI~ 86 (126)
+--||+.+.-+++|.++||.
T Consensus 23 ~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 23 KELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred HHhCCCHHHHHHHHHHcCCC
Confidence 34699999999999999998
No 67
>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=62.00 E-value=9.2 Score=24.52 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=29.5
Q ss_pred Eeecc-ccccCHHHHHHHHHH---hC-CCc----cccCCCCHHHHHHHHHHH
Q 033150 63 YSLQY-IHGVGRTRARQILVD---LK-MEN----KITKDMSEEELITIRDEV 105 (126)
Q Consensus 63 ~ALt~-IyGIG~~~A~~IC~k---lG-I~~----~kv~~LteeQI~~L~~~I 105 (126)
-.|.. +.|||...|.+|++. .| +.+ .++.-++++-.++|..+|
T Consensus 16 ~~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 16 EELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred HHHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHHHHHHHhhc
Confidence 35777 999999999999988 44 431 224556666666665553
No 68
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.80 E-value=1.7 Score=33.99 Aligned_cols=75 Identities=16% Similarity=0.247 Sum_probs=51.4
Q ss_pred cceeee--ecCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHHH
Q 033150 11 PALSVI--CNGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 11 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~k 82 (126)
|-.-|| +||=---++.+.+....+ ....-..+..|+ ..+.|..-...+.++.-|.++-|||+++|..|+..
T Consensus 14 ~~~vvid~v~GVGY~v~i~~~~~~~l-~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 14 PTFIVLKTASGVSYGIFISLFCSAKI-QKGEKHELFITQIIKEDSNKLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred CCEEEEEcCCCEEEEEEecHHHHHHc-CCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcC
Confidence 444566 377666667766655544 211111233333 46788888889999999999999999999999976
Q ss_pred hCCC
Q 033150 83 LKME 86 (126)
Q Consensus 83 lGI~ 86 (126)
+..+
T Consensus 93 ~~~~ 96 (183)
T PRK14601 93 LDVN 96 (183)
T ss_pred CCHH
Confidence 6543
No 69
>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=60.22 E-value=4.8 Score=30.88 Aligned_cols=20 Identities=35% Similarity=0.456 Sum_probs=17.7
Q ss_pred EEeeccccccCHHHHHHHHH
Q 033150 62 EYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~ 81 (126)
...|.+++|||+.+|..+|-
T Consensus 105 ~~~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 105 REELVKLPGVGRKTANVVLN 124 (191)
T ss_pred HHHHHhCCCCcHHHHHHHHH
Confidence 56799999999999999884
No 70
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=59.30 E-value=17 Score=25.12 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=29.3
Q ss_pred EeeccccccCHHH-HHHHHHHhCCCccccCCCCHHHHHHHH
Q 033150 63 YSLQYIHGVGRTR-ARQILVDLKMENKITKDMSEEELITIR 102 (126)
Q Consensus 63 ~ALt~IyGIG~~~-A~~IC~klGI~~~kv~~LteeQI~~L~ 102 (126)
+++...+|-|+++ |..+.+++|+...-.+.+.++++....
T Consensus 2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~~i~~e~~~~~~ 42 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTGGIRTEEVGKLA 42 (147)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCceeccccCCHHHHHHHH
Confidence 5678889999998 888999999873333466666655543
No 71
>PRK10702 endonuclease III; Provisional
Probab=59.30 E-value=5.1 Score=31.74 Aligned_cols=21 Identities=33% Similarity=0.446 Sum_probs=18.2
Q ss_pred EEEeeccccccCHHHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~ 81 (126)
..-.|.+++|||+++|..|+-
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill 127 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLN 127 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHH
Confidence 357899999999999999873
No 72
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=58.28 E-value=6 Score=30.73 Aligned_cols=23 Identities=30% Similarity=0.637 Sum_probs=19.9
Q ss_pred eeccccccCHHHHHHHHHHhCCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.|+++.|||+++|.+|+..+.=.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHH
Confidence 58999999999999999877533
No 73
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=58.09 E-value=6.1 Score=33.71 Aligned_cols=44 Identities=18% Similarity=0.222 Sum_probs=37.1
Q ss_pred EEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh
Q 033150 62 EYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~ 106 (126)
.--|+.|.|||+.... .|+.+||. ..-+-.+|++++..+...+.
T Consensus 262 ~DdL~~I~GiGp~~e~-~L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 262 PDDLKKLTGVSPQIEK-KLNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred chhhhhhccCChhhhh-hhhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 3558999999998765 57899999 88899999999998877764
No 74
>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=57.42 E-value=14 Score=34.19 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=27.5
Q ss_pred cccccCHHHHHHHHHHhCCC-ccc----------cCCCCHHHHHHHHHHH
Q 033150 67 YIHGVGRTRARQILVDLKME-NKI----------TKDMSEEELITIRDEV 105 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klGI~-~~k----------v~~LteeQI~~L~~~I 105 (126)
.|+|||+.+|.+|.+.+|.+ -.. +.-++++..+.|.+.+
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~ 137 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQW 137 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHH
Confidence 49999999999999999977 222 2345555555555444
No 75
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.40 E-value=2.4 Score=33.47 Aligned_cols=70 Identities=14% Similarity=0.118 Sum_probs=49.2
Q ss_pred ecCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC
Q 033150 17 CNGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
|||=---++.+.++...+-..-....+..|+ ..+.|..=...+.++.-|..+-|||+++|..|+..++.+
T Consensus 22 v~GvGY~v~i~~~~~~~l~~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 22 PGGVGYEVFLPAHTLARLPEKGGQVSFFVHTVVREDALELFGFATWDERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred eCCEEEEEEcCHHHHHHhccCCCeEEEEEEEEEecCcceeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 6776666666666555442111222233333 467888888889999999999999999999999987754
No 76
>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=56.37 E-value=1.4 Score=34.51 Aligned_cols=69 Identities=17% Similarity=0.208 Sum_probs=46.1
Q ss_pred eecCccCCcccccceecccccCCCCCccee------eEEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCC
Q 033150 16 ICNGHNNNLLTNASLSFPVSKQPQYPGLSI------QCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (126)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI 85 (126)
-|||=---++.|.+....+-.+ .-..+.. .-..+.|..=...+.++.-|.++.|||+++|..|+..++.
T Consensus 20 ~v~GvGY~v~v~~~~~~~l~~g-~~v~l~t~~~vred~~~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 20 EVNGVGYELQVPMTCAYELNLE-QKAQVFTHLVVREDAELLFGFNTLEERELFKELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred EECCEEEEEEecHHHHHhcCCC-CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence 3555555555555555544111 1111222 2256788888889999999999999999999999876665
No 77
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=55.74 E-value=8.7 Score=31.56 Aligned_cols=37 Identities=24% Similarity=0.371 Sum_probs=26.7
Q ss_pred eeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
.|..|.|||+.++..+.+. |+. -..+..-|.++|.++
T Consensus 4 ~L~~IpGIG~krakkLl~~-GF~Sve~Ik~AS~eEL~~V 41 (232)
T PRK12766 4 ELEDISGVGPSKAEALREA-GFESVEDVRAADQSELAEV 41 (232)
T ss_pred ccccCCCcCHHHHHHHHHc-CCCCHHHHHhCCHHHHHHc
Confidence 5788899999999888765 676 444566666666665
No 78
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=54.56 E-value=11 Score=31.12 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=17.6
Q ss_pred ccccCHHHHHHHHHHhCCC
Q 033150 68 IHGVGRTRARQILVDLKME 86 (126)
Q Consensus 68 IyGIG~~~A~~IC~klGI~ 86 (126)
|.|||+.+|.++.++.|.-
T Consensus 203 V~GIG~ktA~~Ll~~~gs~ 221 (310)
T COG0258 203 VKGIGPKTALKLLQEYGSL 221 (310)
T ss_pred CCCcCHHHHHHHHHHhCCH
Confidence 9999999999999999944
No 79
>PRK00076 recR recombination protein RecR; Reviewed
Probab=54.40 E-value=15 Score=29.36 Aligned_cols=40 Identities=15% Similarity=0.380 Sum_probs=29.4
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhh
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~ 107 (126)
+..+|.+++|||+++|.++.-.+ =+..++++..|.+.|.+
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~l-------l~~~~~~~~~la~~i~~ 48 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHL-------LQRDREDVLRLAQALEE 48 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHH-------HcCCHHHHHHHHHHHHH
Confidence 34578999999999999998554 23357777777777754
No 80
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.89 E-value=2.3 Score=33.56 Aligned_cols=70 Identities=17% Similarity=0.096 Sum_probs=47.6
Q ss_pred eecCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC
Q 033150 16 ICNGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
-|||=---.+.|.+....+ ..-+-..+..|+ ..+.|..=...+.++.-|.++-|||+++|..|+..++.+
T Consensus 20 ~~~GvGY~V~vs~~~~~~l-~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~~~ 95 (197)
T PRK14603 20 LAGGVGLEVQCPAPTLARL-VEGQEAELHTRLVVREDALSLYGFPDEDSLELFELLLGVSGVGPKLALALLSALPPA 95 (197)
T ss_pred EECCEEEEEEcCHHHHHHc-CCCCeEEEEEEEEEccCCceeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 3566555566666555544 211222233333 367888888889999999999999999999999876643
No 81
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.58 E-value=16 Score=29.22 Aligned_cols=40 Identities=18% Similarity=0.338 Sum_probs=29.0
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhh
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~ 107 (126)
+.-+|.++.|||+++|.++.-.+ =+..++++..|.+.|.+
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~l-------l~~~~~~~~~la~ai~~ 48 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHL-------LKRDPSEVLRLAQALLE 48 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHH-------HcCCHHHHHHHHHHHHH
Confidence 34578999999999999997443 23456777777777654
No 82
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=52.14 E-value=7 Score=26.84 Aligned_cols=24 Identities=38% Similarity=0.585 Sum_probs=18.3
Q ss_pred Eeecc-ccccCHHHHHHHHHHhCCC
Q 033150 63 YSLQY-IHGVGRTRARQILVDLKME 86 (126)
Q Consensus 63 ~ALt~-IyGIG~~~A~~IC~klGI~ 86 (126)
+-|.. |.|||-.+|-+|..++|++
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~ 69 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIE 69 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCC
Confidence 44544 8999999999999999987
No 83
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=51.43 E-value=14 Score=32.68 Aligned_cols=25 Identities=20% Similarity=0.401 Sum_probs=22.3
Q ss_pred CeEEEEeeccccccCHHHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~k 82 (126)
++.|+++|..|+|||...+..|.+.
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~e 133 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKA 133 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHH
Confidence 4579999999999999999999863
No 84
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=50.27 E-value=21 Score=31.66 Aligned_cols=50 Identities=12% Similarity=0.179 Sum_probs=42.4
Q ss_pred CCeEEEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhhc
Q 033150 57 NNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 57 ~nK~V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~~ 108 (126)
++|.+..+|.. .++++.+..++.+.||.+....+|++.|+++|.+.|..+
T Consensus 284 ~~kslkn~L~~--~lp~rlv~~~l~~~~i~~~~~~~ls~~~~~~l~~~ik~~ 333 (408)
T COG2081 284 PKKSLKNALAK--LLPKRLVEFLLERAGIPDEPLAQLSPKELAQLAAALKAW 333 (408)
T ss_pred hhhHHHHHHHH--HhhhHHHHHHHHhccCCCcchhhcCHHHHHHHHHHHhcC
Confidence 45666666655 478899999999999988889999999999999999873
No 85
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.24 E-value=2.5 Score=33.10 Aligned_cols=38 Identities=24% Similarity=0.185 Sum_probs=33.2
Q ss_pred EecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC
Q 033150 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 49 rIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.+.|..-+..+.++.-|.++-|||+++|..|+..++.+
T Consensus 59 ~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 47888888899999999999999999999999876644
No 86
>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=49.99 E-value=8.9 Score=31.66 Aligned_cols=25 Identities=40% Similarity=0.530 Sum_probs=20.4
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHHH
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC~ 81 (126)
.+|.+ .-.|.++.|||+.+|..||.
T Consensus 99 ~~p~~---~~~L~~LpGIG~~TA~~Il~ 123 (275)
T TIGR01084 99 EFPQD---FEDLAALPGVGRYTAGAILS 123 (275)
T ss_pred CCcHH---HHHHHhCCCCCHHHHHHHHH
Confidence 45544 56899999999999999885
No 87
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.86 E-value=3.1 Score=33.09 Aligned_cols=71 Identities=13% Similarity=0.144 Sum_probs=47.1
Q ss_pred eeecCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC
Q 033150 15 VICNGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
+-|||=---++.|++....+ ....-..+..|+ ..+.|..-...+.++.-|.++-|||+++|..|+..+..+
T Consensus 19 idv~GVGY~v~vs~~~~~~l-~~g~~v~l~t~~~vrED~~~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 19 IMATPFEFELLVSSFCLAEL-RLLEDVEILTYLHTREDELKLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred EEeCCEEEEEEecHHHHHhc-CCCCcEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 33556555555665555444 111111233333 467888888899999999999999999999999766543
No 88
>PRK13844 recombination protein RecR; Provisional
Probab=49.47 E-value=20 Score=28.80 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=29.3
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhh
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~ 107 (126)
+.-+|.+++|||+++|.++.-.+ =+..+++++.|.+.|.+
T Consensus 13 LI~~l~~LPGIG~KsA~Rla~~l-------L~~~~~~~~~la~~i~~ 52 (200)
T PRK13844 13 VIESLRKLPTIGKKSSQRLALYL-------LDKSPETAIAIANSLLD 52 (200)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHH-------HcCCHHHHHHHHHHHHH
Confidence 34578999999999999988543 23456777777777654
No 89
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=49.07 E-value=14 Score=26.71 Aligned_cols=26 Identities=31% Similarity=0.580 Sum_probs=19.7
Q ss_pred eEEEEeeccccccCHHHHHHHHHHhC
Q 033150 59 KRIEYSLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 59 K~V~~ALt~IyGIG~~~A~~IC~klG 84 (126)
......|+++-|.|+++|..+.+.+.
T Consensus 46 ~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 46 PHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred hHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 33456789999999999999998775
No 90
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=48.34 E-value=26 Score=24.99 Aligned_cols=34 Identities=26% Similarity=0.456 Sum_probs=29.9
Q ss_pred cCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhh
Q 033150 71 VGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 71 IG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~ 107 (126)
+|.....+|++.|+ ++-.+||+++++..+++++-
T Consensus 35 ~Gh~sGRrIv~IL~---K~k~dltddD~~hMrkVV~y 68 (92)
T PF11338_consen 35 VGHESGRRIVEILR---KRKTDLTDDDYEHMRKVVGY 68 (92)
T ss_pred cCcchhhHHHHHHh---cCcccCCHHHHHHHHHHHHH
Confidence 68888899998888 67799999999999999874
No 91
>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=48.21 E-value=9.6 Score=31.76 Aligned_cols=22 Identities=27% Similarity=0.205 Sum_probs=19.1
Q ss_pred EEEeeccccccCHHHHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~k 82 (126)
+.-.|+.++|||+.+|..||-.
T Consensus 218 ~~~~L~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 218 AREALCELPGVGPKVADCICLM 239 (310)
T ss_pred HHHHHHhCCCccHHHHHHHHHH
Confidence 5678999999999999998843
No 92
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=47.78 E-value=10 Score=30.44 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=17.7
Q ss_pred EEEeeccccccCHHHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~ 81 (126)
.+-.|.+++|||+.+|..|+-
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILC 139 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHH
Confidence 446699999999999988774
No 93
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=47.58 E-value=21 Score=28.77 Aligned_cols=40 Identities=18% Similarity=0.313 Sum_probs=30.4
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhh
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~ 107 (126)
+..+|.++.|||++.|.++.--| -+.+++++.+|.+.+.+
T Consensus 10 LI~~l~kLPGvG~KsA~R~AfhL-------L~~~~~~~~~la~al~~ 49 (198)
T COG0353 10 LIDALKKLPGVGPKSAQRLAFHL-------LQRDREDVERLAKALLE 49 (198)
T ss_pred HHHHHhhCCCCChhHHHHHHHHH-------HccCHHHHHHHHHHHHH
Confidence 44578999999999999998554 34567788888777653
No 94
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=46.85 E-value=16 Score=33.29 Aligned_cols=44 Identities=30% Similarity=0.440 Sum_probs=31.3
Q ss_pred CCeEEEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 57 NNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 57 ~nK~V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
.++....+|..|.|||+.++..|++.+|= -..+.+-+.+++.++
T Consensus 537 ~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS-~~~i~~As~eeL~~v 580 (598)
T PRK00558 537 SKARLTSALDDIPGIGPKRRKALLKHFGS-LKAIKEASVEELAKV 580 (598)
T ss_pred ccchhhhhHhhCCCcCHHHHHHHHHHcCC-HHHHHhCCHHHHhhc
Confidence 34456789999999999999999999872 222344455665444
No 95
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=46.82 E-value=5.2 Score=28.29 Aligned_cols=36 Identities=33% Similarity=0.422 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHhCCC-ccc-cCCCCHHHHHHHHHHHhh
Q 033150 72 GRTRARQILVDLKME-NKI-TKDMSEEELITIRDEVSK 107 (126)
Q Consensus 72 G~~~A~~IC~klGI~-~~k-v~~LteeQI~~L~~~I~~ 107 (126)
|..+|..++-.+|-+ ..+ +++|+++++.+|...+.+
T Consensus 7 g~~KAAilLl~Lgee~Aa~vlk~l~~~ei~~i~~~ma~ 44 (108)
T PF14842_consen 7 GIQKAAILLLALGEEAAAEVLKHLDEEEIERISREMAK 44 (108)
T ss_dssp HHHHHHHHHHHS-HHHHHHHHHHS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHCHHHHHHHHccCCHHHHHHHHHHHHc
Confidence 456777788888888 555 488999999999998877
No 96
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=46.78 E-value=14 Score=30.36 Aligned_cols=63 Identities=8% Similarity=0.025 Sum_probs=46.0
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHhCCC-ccc------------cCCCCHHHHHHHHHHHhh----ccccccchhhhcc
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDLKME-NKI------------TKDMSEEELITIRDEVSK----YMIEGDLVIIPYF 120 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~klGI~-~~k------------v~~LteeQI~~L~~~I~~----~~Ie~dLrR~i~~ 120 (126)
.+.+++-=-.++|+|+....||.+++|+= +.. -..||++|+++|-+|... ..+.+--|.+++.
T Consensus 96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~~~drl~Vnsatr~ev~~ 175 (225)
T PF09883_consen 96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRDGTDRLNVNSATRSEVRA 175 (225)
T ss_pred cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhCCCCeEEEecccHHHHHH
Confidence 33444444677899999999999999986 554 246999999999999964 4555555555443
No 97
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=46.17 E-value=21 Score=28.33 Aligned_cols=25 Identities=24% Similarity=0.363 Sum_probs=22.8
Q ss_pred EEeeccccccCHHHHHHHHHHhCCC
Q 033150 62 EYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.+++|..+|.|+++....++++|+.
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 4789999999999999999999987
No 98
>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=46.08 E-value=15 Score=29.28 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=17.7
Q ss_pred eccccccCHHHHHHHHHHhC
Q 033150 65 LQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klG 84 (126)
+..|.|||+++|.++.++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34678999999999999987
No 99
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=46.05 E-value=11 Score=31.00 Aligned_cols=22 Identities=27% Similarity=0.318 Sum_probs=18.7
Q ss_pred EEEeeccccccCHHHHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~k 82 (126)
....|+.++|||+.+|..|+-.
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHH
Confidence 4568999999999999998844
No 100
>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=45.82 E-value=51 Score=20.33 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=33.3
Q ss_pred eccccccCHHHHHHHHHHhCCC-ccc----cCCCCHHHHHHHHHHHh
Q 033150 65 LQYIHGVGRTRARQILVDLKME-NKI----TKDMSEEELITIRDEVS 106 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~-~~k----v~~LteeQI~~L~~~I~ 106 (126)
+.+..||.+.+...-.++.|+. ..+ -...+++|+..|..+..
T Consensus 6 va~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~ 52 (68)
T cd01104 6 VARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRR 52 (68)
T ss_pred HHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHH
Confidence 3567899999999998888887 433 24789999999988875
No 101
>PRK10880 adenine DNA glycosylase; Provisional
Probab=45.30 E-value=11 Score=32.43 Aligned_cols=21 Identities=33% Similarity=0.396 Sum_probs=18.8
Q ss_pred EEEeeccccccCHHHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~ 81 (126)
....|.++.|||+.+|..||.
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~ 127 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILS 127 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHH
Confidence 347899999999999999996
No 102
>smart00475 53EXOc 5'-3' exonuclease.
Probab=45.05 E-value=16 Score=29.74 Aligned_cols=20 Identities=20% Similarity=0.488 Sum_probs=17.6
Q ss_pred eccccccCHHHHHHHHHHhC
Q 033150 65 LQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klG 84 (126)
+..+.|||+++|.+++++.|
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC
Confidence 34578999999999999988
No 103
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=44.87 E-value=14 Score=29.48 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=20.3
Q ss_pred EEEEeec-cccccCHHHHHHHHHHhCC
Q 033150 60 RIEYSLQ-YIHGVGRTRARQILVDLKM 85 (126)
Q Consensus 60 ~V~~ALt-~IyGIG~~~A~~IC~klGI 85 (126)
..+-.|. +++|||+.+|..++...|.
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~ 141 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGY 141 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccC
Confidence 4556677 9999999999999854443
No 104
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=44.71 E-value=3.8 Score=32.30 Aligned_cols=71 Identities=17% Similarity=0.092 Sum_probs=47.1
Q ss_pred eeecCccCCcccccceecccccCCCCCcceeeE------EEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCC
Q 033150 15 VICNGHNNNLLTNASLSFPVSKQPQYPGLSIQC------ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (126)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~M------vrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI 85 (126)
+-|||=---++.|.+....+-...+...+..|+ ..+.|..=...+.++.-|.++-|||+++|..|+..+..
T Consensus 19 ie~~GvGY~v~vs~~~~~~l~~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~ 95 (195)
T PRK14604 19 VETGGVGLLIYAPRSVLAAIGAIGDEVFLYTHLIVREDALTLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSGTP 95 (195)
T ss_pred EEECCEEEEEEeCHHHHHHhccCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCH
Confidence 336665555666655555442111222233333 45677777788889999999999999999999987643
No 105
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=44.50 E-value=18 Score=33.28 Aligned_cols=49 Identities=20% Similarity=0.329 Sum_probs=34.3
Q ss_pred CccCCCCeEEEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 52 GVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 52 gt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
+-..-.++.+.-.|..|.|||+.++..|.+.+| +-..+.+-+.++|.++
T Consensus 558 hr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~~~i~~As~eeL~~v 606 (621)
T PRK14671 558 HRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFG-SVEKVAKASLEELAAV 606 (621)
T ss_pred ChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcC-CHHHHHhCCHHHHHHH
Confidence 344445556677889999999999999999996 2122333467776655
No 106
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=43.82 E-value=20 Score=29.13 Aligned_cols=43 Identities=21% Similarity=0.346 Sum_probs=37.0
Q ss_pred EeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh
Q 033150 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~ 106 (126)
-.|+.|.|||+..+.. +..+|+. ...+-.++++++..+...++
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l~ 201 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKLS 201 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhccc
Confidence 4589999999998876 5789999 88899999999998887774
No 107
>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=43.77 E-value=17 Score=30.71 Aligned_cols=37 Identities=22% Similarity=0.320 Sum_probs=28.7
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCC--CHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDM--SEEELIT 100 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~L--teeQI~~ 100 (126)
-++.+.|||+.++.++.+.+||.+. -+-++ +.+++.+
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~ 222 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQE 222 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHH
Confidence 5789999999999999999999943 34555 6666654
No 108
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=43.76 E-value=30 Score=29.63 Aligned_cols=42 Identities=21% Similarity=0.459 Sum_probs=32.1
Q ss_pred ccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhh-cccc
Q 033150 68 IHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK-YMIE 111 (126)
Q Consensus 68 IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~-~~Ie 111 (126)
--|||+..|.++++ =|++--.++- |++-++++.++|++ |.+|
T Consensus 58 TDGIGKayA~eLAk-rG~nvvLIsR-t~~KL~~v~kEI~~~~~ve 100 (312)
T KOG1014|consen 58 TDGIGKAYARELAK-RGFNVVLISR-TQEKLEAVAKEIEEKYKVE 100 (312)
T ss_pred CCcchHHHHHHHHH-cCCEEEEEeC-CHHHHHHHHHHHHHHhCcE
Confidence 36999999999998 6777333322 78999999999975 7644
No 109
>PRK13910 DNA glycosylase MutY; Provisional
Probab=43.73 E-value=12 Score=31.37 Aligned_cols=25 Identities=36% Similarity=0.561 Sum_probs=20.8
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHHH
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQILV 81 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC~ 81 (126)
.+|.+ .-.|.++.|||+++|..|+.
T Consensus 66 ~~P~~---~~~L~~LpGIG~kTA~aIl~ 90 (289)
T PRK13910 66 QLPND---YQSLLKLPGIGAYTANAILC 90 (289)
T ss_pred CCChh---HHHHHhCCCCCHHHHHHHHH
Confidence 35554 57899999999999999985
No 110
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=43.63 E-value=3.1 Score=29.69 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=15.5
Q ss_pred ccccccCHHHHHHHHHHhC
Q 033150 66 QYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klG 84 (126)
-.+.|||+++|.+++++.|
T Consensus 21 PGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 21 PGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp ---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCHHHHHHHHHHcC
Confidence 4689999999999999998
No 111
>PRK14976 5'-3' exonuclease; Provisional
Probab=43.49 E-value=17 Score=30.03 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=17.1
Q ss_pred ccccccCHHHHHHHHHHhC
Q 033150 66 QYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klG 84 (126)
..+.|||+++|.+++++.|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999999988
No 112
>PRK09482 flap endonuclease-like protein; Provisional
Probab=43.14 E-value=18 Score=29.81 Aligned_cols=19 Identities=21% Similarity=0.476 Sum_probs=17.4
Q ss_pred ccccccCHHHHHHHHHHhC
Q 033150 66 QYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klG 84 (126)
..+.|||+++|.+++++.|
T Consensus 185 pGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCcChHHHHHHHHHhC
Confidence 4689999999999999988
No 113
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=42.02 E-value=14 Score=30.59 Aligned_cols=21 Identities=24% Similarity=0.289 Sum_probs=18.4
Q ss_pred EEEEeeccccccCHHHHHHHH
Q 033150 60 RIEYSLQYIHGVGRTRARQIL 80 (126)
Q Consensus 60 ~V~~ALt~IyGIG~~~A~~IC 80 (126)
.+.-.|++|.|||+-+|.-++
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~l 215 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFL 215 (285)
T ss_pred HHHHHHHcCCCcCHHHHHHHH
Confidence 366689999999999999887
No 114
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=41.44 E-value=17 Score=26.07 Aligned_cols=58 Identities=16% Similarity=0.164 Sum_probs=40.8
Q ss_pred CccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC--c--cccCCCCHHHHHHHHHHHhhcc
Q 033150 52 GVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME--N--KITKDMSEEELITIRDEVSKYM 109 (126)
Q Consensus 52 gt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~--~--~kv~~LteeQI~~L~~~I~~~~ 109 (126)
|..|+-|-.=..+.++..|.=++.|.+|+.-.=.+ . ..+..||+.|-+.|.+..++|+
T Consensus 12 G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~Ft 73 (93)
T PF06514_consen 12 GQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNFT 73 (93)
T ss_dssp CTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGEE
T ss_pred CCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccce
Confidence 34444455556788999999999999999877655 1 2367899999999999999864
No 115
>PRK07945 hypothetical protein; Provisional
Probab=39.00 E-value=21 Score=29.99 Aligned_cols=50 Identities=22% Similarity=0.192 Sum_probs=32.8
Q ss_pred eeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhhccccccchhhhccc
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFF 121 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~~~Ie~dLrR~i~~n 121 (126)
.|++|.|||+.+|.+|-+-+.= | +-+.+++|++.++--. +.+|.+.+.-|
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~t-----g--~~~~l~~l~~~~~~~~-g~~l~~~~~~D 99 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAG-----R--VPDYLAELRADAEPLG-GGALRAALRGD 99 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhc-----C--CHHHHHHHHHhhcCCc-cHHHHHHHhhh
Confidence 6999999999999999876542 2 2335566666554333 66666655544
No 116
>PLN02200 adenylate kinase family protein
Probab=37.88 E-value=41 Score=26.66 Aligned_cols=42 Identities=10% Similarity=0.064 Sum_probs=31.5
Q ss_pred ccCCCCeEEEEeeccccccCHHH-HHHHHHHhCCCccccCCCC
Q 033150 53 VEIPNNKRIEYSLQYIHGVGRTR-ARQILVDLKMENKITKDMS 94 (126)
Q Consensus 53 t~ip~nK~V~~ALt~IyGIG~~~-A~~IC~klGI~~~kv~~Lt 94 (126)
...+..++..+.+....|-|+++ |..|++++|+.....++|=
T Consensus 36 ~~~~~~~~~ii~I~G~PGSGKsT~a~~La~~~g~~his~gdll 78 (234)
T PLN02200 36 SSSKEKTPFITFVLGGPGSGKGTQCEKIVETFGFKHLSAGDLL 78 (234)
T ss_pred CCccCCCCEEEEEECCCCCCHHHHHHHHHHHhCCeEEEccHHH
Confidence 34444556888999999999998 5889999998755554443
No 117
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=36.88 E-value=1.9 Score=34.46 Aligned_cols=43 Identities=21% Similarity=0.224 Sum_probs=35.3
Q ss_pred eeeEEEecCccCCCCeEEEEeeccccccCHHHHHHHHHHhCCC
Q 033150 44 SIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 44 ~~~MvrIlgt~ip~nK~V~~ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
|-+...+.|..-...|.++.-|.++=|||+++|..|++.+..+
T Consensus 54 REd~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~ 96 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLDPE 96 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCHH
Confidence 3344567888888899999999999999999999999765533
No 118
>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=36.77 E-value=25 Score=28.85 Aligned_cols=18 Identities=22% Similarity=0.355 Sum_probs=16.9
Q ss_pred cccccCHHHHHHHHHHhC
Q 033150 67 YIHGVGRTRARQILVDLK 84 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klG 84 (126)
.|.|||+.+|.++.++.|
T Consensus 227 gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 227 GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 688999999999999988
No 119
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=36.47 E-value=24 Score=32.18 Aligned_cols=43 Identities=21% Similarity=0.280 Sum_probs=31.1
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
++...-.|..|.|||+.+...+++.+|= -..++.-|.+||.++
T Consensus 509 k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs-~~~ik~As~eeL~~v 551 (567)
T PRK14667 509 KEGLKDILDKIKGIGEVKKEIIYRNFKT-LYDFLKADDEELKKL 551 (567)
T ss_pred cccccCccccCCCCCHHHHHHHHHHhCC-HHHHHhCCHHHHHHc
Confidence 3445678899999999999999998873 223445566666554
No 120
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=36.22 E-value=36 Score=25.02 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=21.5
Q ss_pred cCCCCHHHHHHHHHHHhhccccccch
Q 033150 90 TKDMSEEELITIRDEVSKYMIEGDLV 115 (126)
Q Consensus 90 v~~LteeQI~~L~~~I~~~~Ie~dLr 115 (126)
.--||+|||+.|.+..++=.++++++
T Consensus 84 ~EGLs~E~IE~Lk~Lv~eGKi~nef~ 109 (110)
T PF06819_consen 84 AEGLSKEDIEKLKKLVEEGKIENEFN 109 (110)
T ss_pred ccCCCHHHHHHHHHHHHcCCCccccc
Confidence 46799999999999998767777663
No 121
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=35.55 E-value=24 Score=33.21 Aligned_cols=40 Identities=23% Similarity=0.326 Sum_probs=29.4
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
+.-.|..|.|||+.++..+.+.+| +-..+.+-+.++|.++
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FG-Sle~I~~AS~eELa~V 674 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFG-SLQAMAAAGEEGLAAV 674 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhC-CHHHHHhcCHHHHHhc
Confidence 456788999999999999999988 4333444556666544
No 122
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=33.93 E-value=30 Score=21.22 Aligned_cols=20 Identities=20% Similarity=0.499 Sum_probs=16.2
Q ss_pred eeccccccCHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl 83 (126)
-|...|||+++++.+++...
T Consensus 24 ~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 24 DLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred HHhhheeecHHHHHHHHHHH
Confidence 35678999999999998653
No 123
>PRK03980 flap endonuclease-1; Provisional
Probab=33.72 E-value=29 Score=28.84 Aligned_cols=18 Identities=22% Similarity=0.353 Sum_probs=16.8
Q ss_pred cccccCHHHHHHHHHHhC
Q 033150 67 YIHGVGRTRARQILVDLK 84 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klG 84 (126)
.|.|||+.+|.++.++.|
T Consensus 193 GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred CCCCccHHHHHHHHHHCC
Confidence 678999999999999988
No 124
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=33.69 E-value=47 Score=25.01 Aligned_cols=42 Identities=21% Similarity=0.348 Sum_probs=28.0
Q ss_pred eeccccccCHHHHHHHHHHh---C----CC-ccccCCCCHHHHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDL---K----ME-NKITKDMSEEELITIRDEV 105 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl---G----I~-~~kv~~LteeQI~~L~~~I 105 (126)
-|+.+.|||++.|..|.+.- | ++ -.++.-+-+.-++++...|
T Consensus 98 eL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 98 ELQALPGIGPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred HHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHHhhc
Confidence 35999999999999998654 2 22 2335555566666665543
No 125
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=33.34 E-value=29 Score=31.78 Aligned_cols=40 Identities=28% Similarity=0.395 Sum_probs=29.2
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
....|..|.|||+.+...+++.+|== ..+.+-|.+||.++
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs~-~~I~~As~eeL~~v 551 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGTY-KDILLLNEDEIAEK 551 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCCH-HHHHhCCHHHHHhC
Confidence 45688999999999999999988732 22444456666554
No 126
>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=33.31 E-value=23 Score=21.67 Aligned_cols=43 Identities=26% Similarity=0.278 Sum_probs=31.8
Q ss_pred eeccccccCHHHHHHHH-HHhCCC-ccccCCCCHHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQIL-VDLKME-NKITKDMSEEELITIRDEVS 106 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC-~klGI~-~~kv~~LteeQI~~L~~~I~ 106 (126)
-|.+-.|+-..--.+.| +.+|+. ...-..|++++...|.+.++
T Consensus 8 elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 8 ELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp HHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred HHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 35667788888888899 559999 77779999999998887653
No 127
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=33.20 E-value=48 Score=20.34 Aligned_cols=17 Identities=18% Similarity=0.276 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHHHhhc
Q 033150 92 DMSEEELITIRDEVSKY 108 (126)
Q Consensus 92 ~LteeQI~~L~~~I~~~ 108 (126)
.||++|+..|..+|..+
T Consensus 74 ~ls~~e~~~l~ayl~sl 90 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRSL 90 (91)
T ss_dssp TSSHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 79999999999999753
No 128
>PRK02406 DNA polymerase IV; Validated
Probab=32.70 E-value=40 Score=27.71 Aligned_cols=38 Identities=24% Similarity=0.288 Sum_probs=28.4
Q ss_pred EeeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHH
Q 033150 63 YSLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITI 101 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L 101 (126)
.-++.++|||+.++.++ +++||.+. -+-.++.+++.+.
T Consensus 168 lpi~~l~giG~~~~~~L-~~~Gi~ti~dl~~l~~~~L~~~ 206 (343)
T PRK02406 168 LPVEKIPGVGKVTAEKL-HALGIYTCADLQKYDLAELIRH 206 (343)
T ss_pred CCcchhcCCCHHHHHHH-HHcCCCcHHHHHhCCHHHHHHH
Confidence 35789999999999986 68999833 3566777776554
No 129
>PF05291 Bystin: Bystin; InterPro: IPR007955 Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy []. This family also includes the Saccharomyces cerevisiae protein ENP1. ENP1 is an essential protein in S. cerevisiae and is localised in the nucleus []. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective S. cerevisiae cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits [].
Probab=32.69 E-value=32 Score=29.31 Aligned_cols=30 Identities=17% Similarity=0.130 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHHHhh---ccccccchhhhcc
Q 033150 91 KDMSEEELITIRDEVSK---YMIEGDLVIIPYF 120 (126)
Q Consensus 91 ~~LteeQI~~L~~~I~~---~~Ie~dLrR~i~~ 120 (126)
.|+|++|-+.|.+.+.. +.|..|.||+...
T Consensus 257 ~di~~eqk~~L~~ll~~~~H~~ItpEIrreL~~ 289 (301)
T PF05291_consen 257 NDITEEQKEALLELLRKQKHPQITPEIRRELLA 289 (301)
T ss_pred HhCCHHHHHHHHHHHHhCCCCCCCHHHHHHHhc
Confidence 78999999999999974 7999999998753
No 130
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=32.59 E-value=34 Score=30.21 Aligned_cols=43 Identities=19% Similarity=0.159 Sum_probs=36.4
Q ss_pred EeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHh
Q 033150 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~ 106 (126)
--|+.|.|||+..+. .+..+||. ..-+-.++++++..+...+.
T Consensus 323 DDLk~I~GIGpk~e~-~Ln~~Gi~~f~QIA~wt~~eia~vd~~l~ 366 (400)
T PRK12373 323 DDLKLISGVGPKIEA-TLNELGIFTFDQVAAWKKAERAWVDGYLN 366 (400)
T ss_pred hhhhhccCCChHHHH-HHHhcCCCCHHHHhCCCHHHhHHhhhccc
Confidence 468999999998875 57899999 77899999999988877664
No 131
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=32.00 E-value=40 Score=27.90 Aligned_cols=35 Identities=17% Similarity=0.160 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhhc
Q 033150 74 TRARQILVDLKMENKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 74 ~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~~ 108 (126)
.....++..+|++..+..+|+-+|.-+|.+.+.+.
T Consensus 255 ~~~~~~l~~~~~~~~R~e~l~~~~f~~L~~~~~~~ 289 (294)
T PTZ00338 255 EFIAEILEDSGMFEKRSVKLDIDDFLKLLLAFNKK 289 (294)
T ss_pred HHHHHHHHHcCCcccChhhCCHHHHHHHHHHHHHc
Confidence 34456789999998899999999999999998763
No 132
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=31.64 E-value=28 Score=23.04 Aligned_cols=20 Identities=35% Similarity=0.414 Sum_probs=15.8
Q ss_pred eeccccccCHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl 83 (126)
.|++-++||+..|..|+++|
T Consensus 25 ~lQR~~rIGynrAariid~L 44 (65)
T PF09397_consen 25 LLQRKFRIGYNRAARIIDQL 44 (65)
T ss_dssp HHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHhCCCHHHHHHHHHHH
Confidence 37899999999999999876
No 133
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=31.61 E-value=39 Score=28.43 Aligned_cols=36 Identities=17% Similarity=0.352 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHhCCC-ccc-cCCCCHHHHHHHHHHHhh
Q 033150 72 GRTRARQILVDLKME-NKI-TKDMSEEELITIRDEVSK 107 (126)
Q Consensus 72 G~~~A~~IC~klGI~-~~k-v~~LteeQI~~L~~~I~~ 107 (126)
|..+|..++-.+|=+ ..+ +++|+++|+.+|...+.+
T Consensus 9 g~~KAAilll~LGee~aa~vl~~L~~~ei~~l~~~m~~ 46 (334)
T PRK07194 9 NLEQAAILLLSMGEEAAAMVMQQLSREEVQRLSQKMAR 46 (334)
T ss_pred hHHHHHHHHHHhCcHHHHHHHhcCCHHHHHHHHHHHHh
Confidence 667888899999988 555 499999999999998877
No 134
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=31.28 E-value=26 Score=28.23 Aligned_cols=30 Identities=30% Similarity=0.515 Sum_probs=22.2
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHHHH-hCCC
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQILVD-LKME 86 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC~k-lGI~ 86 (126)
.+|++. ..|.+..|||+++|+.++.. .|..
T Consensus 103 ~vP~~~---~eL~~LPGVGrKTAnvVL~~a~g~p 133 (211)
T COG0177 103 EVPDTR---EELLSLPGVGRKTANVVLSFAFGIP 133 (211)
T ss_pred CCCchH---HHHHhCCCcchHHHHHHHHhhcCCC
Confidence 455443 57899999999999988866 4443
No 135
>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=31.18 E-value=31 Score=31.48 Aligned_cols=24 Identities=29% Similarity=0.477 Sum_probs=20.9
Q ss_pred EEEeeccccccCHHHHHHHHHHhC
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klG 84 (126)
+.-.|..|.|||+.+...+++.+|
T Consensus 539 ~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 539 LQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcC
Confidence 345788999999999999999887
No 136
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=30.95 E-value=1.3e+02 Score=19.44 Aligned_cols=54 Identities=7% Similarity=0.137 Sum_probs=41.0
Q ss_pred cCCCCeEEEEeeccccccCHHHHHHHH----HHhCCC----ccccCCCCHHHHHHHHHHHhh
Q 033150 54 EIPNNKRIEYSLQYIHGVGRTRARQIL----VDLKME----NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 54 ~ip~nK~V~~ALt~IyGIG~~~A~~IC----~klGI~----~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+..+++|..-+..|.++|.+.+...- .+.|.+ ..++.+++++.-..|..++++
T Consensus 13 ~l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~~vi~n 74 (74)
T PF14213_consen 13 ALKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIKRVIEN 74 (74)
T ss_pred HHhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHHHHHhC
Confidence 455667799999999999999998765 445533 344688888888888887764
No 137
>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=30.62 E-value=35 Score=28.81 Aligned_cols=19 Identities=16% Similarity=0.387 Sum_probs=16.9
Q ss_pred ccccccCHHHHHHHHHHhC
Q 033150 66 QYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klG 84 (126)
..|.|||+.+|.++.++.|
T Consensus 239 ~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 4789999999999999865
No 138
>PRK14529 adenylate kinase; Provisional
Probab=30.55 E-value=87 Score=24.99 Aligned_cols=46 Identities=7% Similarity=0.141 Sum_probs=33.5
Q ss_pred EEeeccccccCHH-HHHHHHHHhCCCccccCCCCHHHH-------HHHHHHHhh
Q 033150 62 EYSLQYIHGVGRT-RARQILVDLKMENKITKDMSEEEL-------ITIRDEVSK 107 (126)
Q Consensus 62 ~~ALt~IyGIG~~-~A~~IC~klGI~~~kv~~LteeQI-------~~L~~~I~~ 107 (126)
.+.+-.-.|-|+. .|..|++++|+.....+++..+++ .++.+++++
T Consensus 2 ~I~l~G~PGsGK~T~a~~La~~~~~~~is~gdllr~~i~~~t~lg~~i~~~i~~ 55 (223)
T PRK14529 2 NILIFGPNGSGKGTQGALVKKKYDLAHIESGAIFREHIGGGTELGKKAKEYIDR 55 (223)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHCCCCcccchhhhhhccCCChHHHHHHHHHhc
Confidence 3566778899998 688999999998666677766654 345556654
No 139
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=30.51 E-value=47 Score=32.49 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=31.7
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHhC---CCc-------cccCCCCHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDLK---MEN-------KITKDMSEEELITIR 102 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~klG---I~~-------~kv~~LteeQI~~L~ 102 (126)
+..|+++|+.|+|||...+..|.+.-. +.+ .....++..+++.|.
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~r~~~~~i~k~~le~LI 801 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILI 801 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHHHhhhcCCCHHHHHHHH
Confidence 567999999999999999999986432 111 123456666666664
No 140
>PF06483 ChiC: Chitinase C; InterPro: IPR009470 This ~170 aa region is found at the C-terminal to the catalytic domain (IPR001223 from INTERPRO) found in members of glycoside hydrolase family 18.
Probab=30.50 E-value=1.3e+02 Score=23.96 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=41.0
Q ss_pred ceeeeecCcc---------CCcccccceecccccCCC-CCcceeeEEEecCccCCCCeEEEEe
Q 033150 12 ALSVICNGHN---------NNLLTNASLSFPVSKQPQ-YPGLSIQCARVGGVEIPNNKRIEYS 64 (126)
Q Consensus 12 ~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~-~~~~~~~MvrIlgt~ip~nK~V~~A 64 (126)
.+.||..||+ ++=|--.++..+..+..+ ....+.+|+|-+=+.=|.|=.|.+.
T Consensus 93 g~~vi~sght~~g~NiGGL~gdfHrvs~tlp~wqslapG~s~~~~~~YyLPiSgPsN~tv~~~ 155 (180)
T PF06483_consen 93 GLKVISSGHTAAGNNIGGLKGDFHRVSFTLPAWQSLAPGASVELDMVYYLPISGPSNFTVNIG 155 (180)
T ss_pred cEEEEecCCcccCCcccccCCceEEEEEECCCccccCCCCEEEEeEEEEeccCCCceEEEEEC
Confidence 3899999999 677777888877766644 3348899999998888888877643
No 141
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=29.92 E-value=34 Score=29.38 Aligned_cols=49 Identities=20% Similarity=0.207 Sum_probs=38.4
Q ss_pred CHHHHHHHHHHhCCC-cccc-CCCCHHHHHHHHHHHhh-ccccccchhhhcc
Q 033150 72 GRTRARQILVDLKME-NKIT-KDMSEEELITIRDEVSK-YMIEGDLVIIPYF 120 (126)
Q Consensus 72 G~~~A~~IC~klGI~-~~kv-~~LteeQI~~L~~~I~~-~~Ie~dLrR~i~~ 120 (126)
|...|..+|-.+|=+ ..++ +.|+++++..+...+.+ -.+..+.+..+..
T Consensus 13 ~~~KaAilLlslGe~~aa~vlk~l~~~eiq~l~~~~a~lk~v~~~~~~~il~ 64 (339)
T COG1536 13 GTEKAAILLLALGEEIAAEVLKHLSPEEIQRLSTEMATLKTVSPEEKEQVLE 64 (339)
T ss_pred HhHHHHHHHHHcCHHHHHHHHHhCCHHHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 567888999999998 6664 99999999999999987 4566666655543
No 142
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=28.64 E-value=96 Score=28.46 Aligned_cols=34 Identities=29% Similarity=0.461 Sum_probs=27.9
Q ss_pred cccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhhc
Q 033150 69 HGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 69 yGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~~ 108 (126)
-||+...-.+|-+.+|. ++++++++.|++++..|
T Consensus 105 vg~~~~~~~~i~~~~~~------~~~~~~~e~l~~~lh~y 138 (529)
T PRK06253 105 VGISDEKIEQIEEILGR------DLSEEKIESLREVLHSY 138 (529)
T ss_pred CCcCHHHHHHHHHHhCC------CCChhHHHHHHHHHHHh
Confidence 37888888888777765 78889999999999876
No 143
>PRK08118 topology modulation protein; Reviewed
Probab=28.57 E-value=1.4e+02 Score=22.07 Aligned_cols=53 Identities=28% Similarity=0.473 Sum_probs=33.8
Q ss_pred EeeccccccCHHH-HHHHHHHhCCC----cccc-----CCCCHHHHHHHHHH-Hhh--ccccccch
Q 033150 63 YSLQYIHGVGRTR-ARQILVDLKME----NKIT-----KDMSEEELITIRDE-VSK--YMIEGDLV 115 (126)
Q Consensus 63 ~ALt~IyGIG~~~-A~~IC~klGI~----~~kv-----~~LteeQI~~L~~~-I~~--~~Ie~dLr 115 (126)
+.+..--|-|+++ |++|++.+|+. +... ...+++++..+.+. +++ +.+||-..
T Consensus 4 I~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~~~~~~~~~~~~~~~wVidG~~~ 69 (167)
T PRK08118 4 IILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVPKEEQITVQNELVKEDEWIIDGNYG 69 (167)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcCCCHHHHHHHHHHHhcCCCEEEeCCcc
Confidence 4556677999987 89999999976 2122 24456666655444 443 67777443
No 144
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.21 E-value=37 Score=27.14 Aligned_cols=23 Identities=22% Similarity=0.486 Sum_probs=19.1
Q ss_pred eeccccccCHHHHHHHHHHhCCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.|++|.|||+..|.+|....-+.
T Consensus 61 eL~~i~GiG~aka~~l~a~~El~ 83 (218)
T TIGR00608 61 ELSSVPGIGEAKAIQLKAAVELA 83 (218)
T ss_pred HHHhCcCCcHHHHHHHHHHHHHH
Confidence 38899999999999998766655
No 145
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=27.61 E-value=36 Score=31.10 Aligned_cols=40 Identities=20% Similarity=0.318 Sum_probs=29.1
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
...+|+.|.|||+.++.++++.+|= -..+.+-+.+++.++
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS-~~~I~~As~eeL~~v 562 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGS-VEGVREASVEDLRDV 562 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCC-HHHHHhCCHHHHHhC
Confidence 4688999999999999999999862 223444455555444
No 146
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=27.42 E-value=35 Score=24.88 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=17.1
Q ss_pred ccccCCCCHHHHHHHHHHHhh
Q 033150 87 NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 87 ~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+|+.+||++|+++|.+.|++
T Consensus 84 qkRle~l~~eE~~~L~~eiee 104 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIEE 104 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhcC
Confidence 466889999999999888763
No 147
>PRK13766 Hef nuclease; Provisional
Probab=27.20 E-value=65 Score=29.44 Aligned_cols=22 Identities=27% Similarity=0.460 Sum_probs=20.0
Q ss_pred EeeccccccCHHHHHHHHHHhC
Q 033150 63 YSLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 63 ~ALt~IyGIG~~~A~~IC~klG 84 (126)
+.|+.|.|||+..|..|++.+|
T Consensus 715 ~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 715 YIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHhcCCCCCHHHHHHHHHHcC
Confidence 3589999999999999999987
No 148
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=27.19 E-value=40 Score=31.19 Aligned_cols=40 Identities=20% Similarity=0.281 Sum_probs=28.3
Q ss_pred EEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
..-.|..|.|||+.++..+++.+|= -..+..-|.+||.++
T Consensus 550 ~~S~L~~IpGIG~kr~~~LL~~FgS-i~~I~~As~eeL~~v 589 (624)
T PRK14669 550 RTSELLEIPGVGAKTVQRLLKHFGS-LERVRAATETQLAAV 589 (624)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcCC-HHHHHhCCHHHHHHH
Confidence 3456789999999999999998872 122344556666554
No 149
>PRK03858 DNA polymerase IV; Validated
Probab=27.16 E-value=58 Score=27.27 Aligned_cols=36 Identities=17% Similarity=0.330 Sum_probs=26.8
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELIT 100 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~ 100 (126)
-++.+.|||+.++.++ .++||.+. -+..++.+++.+
T Consensus 174 pl~~l~Gig~~~~~~L-~~~Gi~t~~dl~~l~~~~L~~ 210 (396)
T PRK03858 174 PVRRLWGVGPVTAAKL-RAHGITTVGDVAELPESALVS 210 (396)
T ss_pred ChhhcCCCCHHHHHHH-HHhCCCcHHHHhcCCHHHHHH
Confidence 4688899999999887 57899843 356667666654
No 150
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=26.99 E-value=54 Score=26.52 Aligned_cols=36 Identities=25% Similarity=0.315 Sum_probs=23.9
Q ss_pred eccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 65 LQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
|.++.|||+.++..+. +.||+ -.-+.+.+++++.++
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~ 37 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSEI 37 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHhc
Confidence 4678999999988765 56777 333555555555443
No 151
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=26.86 E-value=58 Score=20.61 Aligned_cols=33 Identities=24% Similarity=0.344 Sum_probs=21.4
Q ss_pred cCHHHHHHHHHHh---CCC-ccc---cCCCCHHHHHHHHH
Q 033150 71 VGRTRARQILVDL---KME-NKI---TKDMSEEELITIRD 103 (126)
Q Consensus 71 IG~~~A~~IC~kl---GI~-~~k---v~~LteeQI~~L~~ 103 (126)
||+..|.+|.+++ |.+ ..- .+-||++|++++-+
T Consensus 9 iGYe~aa~iAk~A~~~g~svre~v~~~g~lt~ee~d~ll~ 48 (55)
T PF10415_consen 9 IGYEKAAEIAKEALAEGRSVREVVLEEGLLTEEELDELLD 48 (55)
T ss_dssp HHHHHHHHHHHHHHHHT--HHHHHHHTTSS-HHHHHHHTS
T ss_pred hccHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHcC
Confidence 6888888888664 444 222 37799999998743
No 152
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=26.86 E-value=63 Score=19.97 Aligned_cols=15 Identities=20% Similarity=0.395 Sum_probs=13.2
Q ss_pred CCCCHHHHHHHHHHH
Q 033150 91 KDMSEEELITIRDEV 105 (126)
Q Consensus 91 ~~LteeQI~~L~~~I 105 (126)
+.||++|+..|..+|
T Consensus 53 ~~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 53 GQLSDEEIEALAAYI 67 (67)
T ss_dssp TTSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHC
Confidence 489999999998876
No 153
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=26.76 E-value=82 Score=22.48 Aligned_cols=32 Identities=13% Similarity=0.193 Sum_probs=22.7
Q ss_pred HHHHHHHhCCC--cccc--CCCCHHHHHHHHHHHhh
Q 033150 76 ARQILVDLKME--NKIT--KDMSEEELITIRDEVSK 107 (126)
Q Consensus 76 A~~IC~klGI~--~~kv--~~LteeQI~~L~~~I~~ 107 (126)
-.+.|+.+|+. +..+ ++++++++..+.+.++.
T Consensus 49 ~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~ 84 (110)
T PF04273_consen 49 EAAAAEALGLQYVHIPVDGGAITEEDVEAFADALES 84 (110)
T ss_dssp HHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHT
T ss_pred HHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHh
Confidence 35789999998 5554 89999999999999975
No 154
>COG3760 Uncharacterized conserved protein [Function unknown]
Probab=26.69 E-value=23 Score=27.71 Aligned_cols=11 Identities=45% Similarity=0.718 Sum_probs=9.5
Q ss_pred eecCccCCccc
Q 033150 16 ICNGHNNNLLT 26 (126)
Q Consensus 16 ~~~~~~~~~~~ 26 (126)
|.|||.||+|.
T Consensus 40 ipgghtKnLfL 50 (164)
T COG3760 40 IPGGHTKNLFL 50 (164)
T ss_pred cCCCccceeEe
Confidence 78999999973
No 155
>PTZ00217 flap endonuclease-1; Provisional
Probab=26.67 E-value=45 Score=28.91 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=16.4
Q ss_pred cccccCHHHHHHHHHHhC
Q 033150 67 YIHGVGRTRARQILVDLK 84 (126)
Q Consensus 67 ~IyGIG~~~A~~IC~klG 84 (126)
.|.|||+.+|.++.++.|
T Consensus 239 gi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 239 TIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 689999999999998866
No 156
>PRK03352 DNA polymerase IV; Validated
Probab=26.63 E-value=59 Score=26.76 Aligned_cols=37 Identities=19% Similarity=0.263 Sum_probs=27.5
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L 101 (126)
-+..+.|||+.++..+ +++||.+. -+-.++.+++.+.
T Consensus 178 pl~~l~gig~~~~~~L-~~~Gi~ti~dl~~l~~~~L~~~ 215 (346)
T PRK03352 178 PTDALWGVGPKTAKRL-AALGITTVADLAAADPAELAAT 215 (346)
T ss_pred CHHHcCCCCHHHHHHH-HHcCCccHHHHhcCCHHHHHHH
Confidence 4678899999999985 78999843 3566677776543
No 157
>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=26.16 E-value=41 Score=31.12 Aligned_cols=36 Identities=17% Similarity=0.249 Sum_probs=28.3
Q ss_pred ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 66 QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
-.|.|+|+.++.++.+..+|. -.-+..|+++++..|
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L 471 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLEL 471 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhc
Confidence 368999999999999999998 333447777777655
No 158
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=25.82 E-value=36 Score=31.59 Aligned_cols=36 Identities=17% Similarity=0.240 Sum_probs=28.7
Q ss_pred ccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 66 QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
-.|.|+|++++.++.+..+|. -.-+..|+++++..|
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l 484 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGL 484 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcC
Confidence 468999999999999999998 333447777777654
No 159
>PRK00024 hypothetical protein; Reviewed
Probab=25.81 E-value=44 Score=26.70 Aligned_cols=23 Identities=35% Similarity=0.599 Sum_probs=19.4
Q ss_pred eeccccccCHHHHHHHHHHhCCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.|++|.|||+..|.+|+...-+.
T Consensus 67 eL~~i~GIG~akA~~L~a~~El~ 89 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALELA 89 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHHH
Confidence 38899999999999998776665
No 160
>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=25.78 E-value=43 Score=30.95 Aligned_cols=23 Identities=22% Similarity=0.387 Sum_probs=18.2
Q ss_pred EEEeeccccccCHHHHHHHHHHhC
Q 033150 61 IEYSLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 61 V~~ALt~IyGIG~~~A~~IC~klG 84 (126)
+.+|| .|.|||+.+|+.+++.+|
T Consensus 497 ~L~aL-gIpgVG~~~ak~L~~~f~ 519 (652)
T TIGR00575 497 LLFAL-GIRHVGEVTAKNLAKHFG 519 (652)
T ss_pred HHhhc-cCCCcCHHHHHHHHHHhC
Confidence 44444 689999999999998887
No 161
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=25.52 E-value=59 Score=31.86 Aligned_cols=45 Identities=18% Similarity=0.393 Sum_probs=31.8
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHh--C----CC--ccccCCCCHHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDL--K----ME--NKITKDMSEEELITIRD 103 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~kl--G----I~--~~kv~~LteeQI~~L~~ 103 (126)
++.|+++|+.|+|||...+..|.+.= | +. -.+++ ++...++.|.+
T Consensus 811 ~~~I~~gl~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~~-~~~~~le~Li~ 863 (1046)
T PRK05672 811 GPAVRLGLRLVRGLGEEAAERIVAARARGPFTSVEDLARRAG-LDRRQLEALAD 863 (1046)
T ss_pred CCcEEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHhC-CCHHHHHHHHH
Confidence 46799999999999999999998643 2 11 12333 66666666643
No 162
>PRK02362 ski2-like helicase; Provisional
Probab=25.29 E-value=53 Score=30.19 Aligned_cols=37 Identities=27% Similarity=0.465 Sum_probs=29.5
Q ss_pred eeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
.|.+|.|||+..|.++- ++||. -.-+-.++++++.++
T Consensus 653 ~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~ 690 (737)
T PRK02362 653 DLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAI 690 (737)
T ss_pred HHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHH
Confidence 46789999999996666 59999 444558889998886
No 163
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=25.21 E-value=64 Score=27.55 Aligned_cols=37 Identities=14% Similarity=0.226 Sum_probs=28.0
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L 101 (126)
-+..++|||+.++..+ +++||.+. -+-+++.+.+.+.
T Consensus 180 Pv~~l~GiG~~~~~~L-~~lGi~TigdL~~~~~~~L~~~ 217 (422)
T PRK03609 180 PVEEVWGVGRRISKKL-NAMGIKTALDLADTNIRFIRKH 217 (422)
T ss_pred ChhhcCCccHHHHHHH-HHcCCCcHHHHhcCCHHHHHHH
Confidence 4588999999999888 67999943 3667777776544
No 164
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=25.07 E-value=45 Score=31.46 Aligned_cols=42 Identities=19% Similarity=0.348 Sum_probs=30.5
Q ss_pred eEEEEeeccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHH
Q 033150 59 KRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (126)
Q Consensus 59 K~V~~ALt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L 101 (126)
+...-.|..|.|||+.+...+++.+|== ..+..-|.+||.++
T Consensus 604 ~~~~s~L~~IpGiG~kr~~~LL~~FgS~-~~i~~As~eel~~v 645 (691)
T PRK14672 604 KELVLSFERLPHVGKVRAHRLLAHFGSF-RSLQSATPQDIATA 645 (691)
T ss_pred hhcccccccCCCCCHHHHHHHHHHhcCH-HHHHhCCHHHHHhC
Confidence 4456688999999999999999988732 22444456666554
No 165
>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=24.96 E-value=42 Score=21.88 Aligned_cols=20 Identities=25% Similarity=0.343 Sum_probs=17.3
Q ss_pred eeccccccCHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl 83 (126)
-|.+++|+|+.....|-+++
T Consensus 45 ~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 45 DLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp HHHTSTTSHHHHHHHHHHHH
T ss_pred HHHhCCCCCHhHHHHHHHHH
Confidence 47899999999999998765
No 166
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=24.75 E-value=1.1e+02 Score=22.00 Aligned_cols=42 Identities=17% Similarity=0.224 Sum_probs=31.3
Q ss_pred eccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 65 LQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
|..|.|||+..|. ++...||+ -..+.+.+.+++.+-...++.
T Consensus 55 L~ri~gi~~~~a~-LL~~AGv~Tv~~LA~~~p~~L~~~l~~~n~ 97 (122)
T PF14229_consen 55 LMRIPGIGPQYAE-LLEHAGVDTVEELAQRNPQNLHQKLGRLNR 97 (122)
T ss_pred hhhcCCCCHHHHH-HHHHhCcCcHHHHHhCCHHHHHHHHHHHHH
Confidence 4689999999986 55688999 555677778777766666653
No 167
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=24.45 E-value=1.4e+02 Score=24.28 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=10.5
Q ss_pred CCHHHHHHHHHHHhh
Q 033150 93 MSEEELITIRDEVSK 107 (126)
Q Consensus 93 LteeQI~~L~~~I~~ 107 (126)
||++|+.+|..++.+
T Consensus 192 ls~~q~~~i~~l~~~ 206 (225)
T PF06207_consen 192 LSDEQIQQIVNLMKK 206 (225)
T ss_pred CCHHHHHHHHHHHHH
Confidence 677777777777665
No 168
>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=24.28 E-value=1.2e+02 Score=21.90 Aligned_cols=31 Identities=13% Similarity=0.158 Sum_probs=23.1
Q ss_pred EeeccccccCHHH-HHHHHHHhCCCccccCCC
Q 033150 63 YSLQYIHGVGRTR-ARQILVDLKMENKITKDM 93 (126)
Q Consensus 63 ~ALt~IyGIG~~~-A~~IC~klGI~~~kv~~L 93 (126)
+.+....|-|+++ |..+++++|+....++++
T Consensus 2 i~i~G~pGsGKst~a~~la~~~~~~~is~~d~ 33 (183)
T TIGR01359 2 VFVLGGPGSGKGTQCAKIVENFGFTHLSAGDL 33 (183)
T ss_pred EEEECCCCCCHHHHHHHHHHHcCCeEEECChH
Confidence 3466778999998 699999999874444444
No 169
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=23.91 E-value=62 Score=32.01 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=32.0
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHh---C-CC-----cccc--CCCCHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDL---K-ME-----NKIT--KDMSEEELITIR 102 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~kl---G-I~-----~~kv--~~LteeQI~~L~ 102 (126)
+..|+++|..|+|||...+..|.+.= | +. -.++ +.++...++.|.
T Consensus 815 ~~~I~~gL~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li 870 (1135)
T PRK05673 815 DGDIRYGLGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKVNKRVLESLI 870 (1135)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccCCCCHHHHHHHH
Confidence 55799999999999999999998643 2 11 1222 456777766664
No 170
>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=23.66 E-value=63 Score=31.53 Aligned_cols=46 Identities=24% Similarity=0.402 Sum_probs=33.2
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHh---C-CC-----cccc--CCCCHHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDL---K-ME-----NKIT--KDMSEEELITIRD 103 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~kl---G-I~-----~~kv--~~LteeQI~~L~~ 103 (126)
++.|+++|+.|+|||...+..|.+.- | +. -.++ +.++..+++.|..
T Consensus 819 ~~~i~~gl~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R~~~~~~~~~~le~Li~ 875 (1022)
T TIGR00594 819 DKGIRYGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRVDFKKLNKKVLEALIK 875 (1022)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHHH
Confidence 45799999999999999999998643 2 11 1233 4577777777653
No 171
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=23.62 E-value=67 Score=26.25 Aligned_cols=39 Identities=23% Similarity=0.276 Sum_probs=26.7
Q ss_pred EEeeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 62 EYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 62 ~~ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
..-|..+.|||+..+..+ .+.||+ -.-+-+++++++.++
T Consensus 5 ~~~l~~l~gIg~~~a~~L-~~~Gi~t~~dl~~~~~~~L~~~ 44 (317)
T PRK04301 5 EKDLEDLPGVGPATAEKL-REAGYDTVEAIAVASPKELSEA 44 (317)
T ss_pred cccHhhcCCCCHHHHHHH-HHcCCCCHHHHHcCCHHHHHHh
Confidence 345789999999887765 567888 334555666666544
No 172
>PRK03348 DNA polymerase IV; Provisional
Probab=23.52 E-value=76 Score=27.71 Aligned_cols=38 Identities=18% Similarity=0.330 Sum_probs=29.2
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITIR 102 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L~ 102 (126)
-++.+.|||+.++.++ +++||.+. -+-.|+.+++.+.-
T Consensus 181 Pv~~L~GIG~~t~~~L-~~lGI~TigDLa~l~~~~L~~~f 219 (454)
T PRK03348 181 PVRRLWGIGPVTEEKL-HRLGIETIGDLAALSEAEVANLL 219 (454)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhcCCHHHHHHHH
Confidence 5688999999988876 78999944 36677787776653
No 173
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=23.32 E-value=71 Score=22.24 Aligned_cols=51 Identities=20% Similarity=0.137 Sum_probs=27.1
Q ss_pred CCeEEEEeeccccccCHHHHHHHHHHhC-CC-cc------ccCCCCHHHHHHHHHHHhh
Q 033150 57 NNKRIEYSLQYIHGVGRTRARQILVDLK-ME-NK------ITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 57 ~nK~V~~ALt~IyGIG~~~A~~IC~klG-I~-~~------kv~~LteeQI~~L~~~I~~ 107 (126)
+...++.++..---.=...+..+.+++- -+ .. .-.+||++|++.|++.|++
T Consensus 57 gr~~~Y~p~is~~e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~~ls~~el~~L~~li~e 115 (115)
T PF03965_consen 57 GRAYVYSPLISREEYLAQELRQFLDRLFDGSIPQLVAALVESEELSPEELEELRKLIDE 115 (115)
T ss_dssp TTCEEEEESSSHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-S-HHHHHHHHHHHH-
T ss_pred CCceEEEeCCcHHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcCCCCHHHHHHHHHHHcC
Confidence 4555666664433333344444444432 12 11 1247999999999999864
No 174
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=23.31 E-value=63 Score=31.78 Aligned_cols=25 Identities=36% Similarity=0.460 Sum_probs=22.6
Q ss_pred CeEEEEeeccccccCHHHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVD 82 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~k 82 (126)
++.|+++|..|+|||...+..|.+.
T Consensus 745 ~~~Ir~GL~aIkgvg~~~~~~I~~~ 769 (1034)
T PRK07279 745 NKKIYLGLKNIKGLPRDLAYWIIEN 769 (1034)
T ss_pred CCEEEeehhhcCCCCHHHHHHHHHC
Confidence 5579999999999999999999864
No 175
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=23.06 E-value=84 Score=20.31 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhCCC-cccc--CCCCHHHHHHHHHHHhh
Q 033150 73 RTRARQILVDLKME-NKIT--KDMSEEELITIRDEVSK 107 (126)
Q Consensus 73 ~~~A~~IC~klGI~-~~kv--~~LteeQI~~L~~~I~~ 107 (126)
+....++|+..|.. ...+ +++++.++..+.+.+++
T Consensus 16 ~~kv~k~L~~~g~~iQ~SVf~~~~~~~~~~~l~~~l~~ 53 (78)
T PF09827_consen 16 RNKVRKILKSYGTRIQYSVFEGNLTNAELRKLRRELEK 53 (78)
T ss_dssp HHHHHHHHHHTTEEEETTEEEEEE-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCccccceEEEEEcCHHHHHHHHHHHHh
Confidence 34567889999955 4443 99999999999999987
No 176
>PF13276 HTH_21: HTH-like domain
Probab=22.98 E-value=26 Score=21.70 Aligned_cols=31 Identities=26% Similarity=0.410 Sum_probs=25.3
Q ss_pred CCCeEEEEeeccccc--cCHHHHHHHHHHhCCC
Q 033150 56 PNNKRIEYSLQYIHG--VGRTRARQILVDLKME 86 (126)
Q Consensus 56 p~nK~V~~ALt~IyG--IG~~~A~~IC~klGI~ 86 (126)
.|-..+...|..-+| ||..+...|++.+||.
T Consensus 21 yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~ 53 (60)
T PF13276_consen 21 YGYRRIWAELRREGGIRVSRKRVRRLMREMGLR 53 (60)
T ss_pred eehhHHHHHHhccCcccccHHHHHHHHHHcCCc
Confidence 355667777877777 7999999999999997
No 177
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=22.88 E-value=73 Score=26.91 Aligned_cols=36 Identities=25% Similarity=0.476 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHhCCC-ccc-cCCCCHHHHHHHHHHHhh
Q 033150 72 GRTRARQILVDLKME-NKI-TKDMSEEELITIRDEVSK 107 (126)
Q Consensus 72 G~~~A~~IC~klGI~-~~k-v~~LteeQI~~L~~~I~~ 107 (126)
|..+|..++-.+|=+ ..+ ++.|+++|+.+|...+.+
T Consensus 11 g~qKAAilLl~lGee~aa~vlk~L~~~ei~~l~~~m~~ 48 (338)
T TIGR00207 11 GKQKAAILLISIGEDRSAEVFKHLSQEEIETLSAEIAN 48 (338)
T ss_pred hHhHHHHHHHHhCcHhHHHHHHcCCHHHHHHHHHHHHh
Confidence 557788888888888 555 499999999999888876
No 178
>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=22.58 E-value=79 Score=25.99 Aligned_cols=36 Identities=14% Similarity=0.272 Sum_probs=27.5
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELIT 100 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~ 100 (126)
-+..+.|||+.+...+ +++||.+. -+-.++.+++.+
T Consensus 177 pl~~l~gig~~~~~~L-~~~Gi~ti~dL~~~~~~~L~~ 213 (344)
T cd01700 177 PVGDVWGIGRRTAKKL-NAMGIHTAGDLAQADPDLLRK 213 (344)
T ss_pred ChhhcCccCHHHHHHH-HHcCCCcHHHHhcCCHHHHHH
Confidence 4678899999999875 78999843 366677777754
No 179
>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain two or more transmembrane segments.
Probab=22.54 E-value=38 Score=24.09 Aligned_cols=55 Identities=11% Similarity=0.050 Sum_probs=28.4
Q ss_pred cccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhhc---cccccchhhhccccc
Q 033150 69 HGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSKY---MIEGDLVIIPYFFVR 123 (126)
Q Consensus 69 yGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~~---~Ie~dLrR~i~~nI~ 123 (126)
+||.....+++-+++-=. ..-+=..++...+++.+.+++| .+..+|.++..+.+|
T Consensus 38 ~gI~d~~~~ev~~~L~~GssAl~~lv~~~~~d~v~~~l~~~gg~v~~t~ls~~~e~~L~ 96 (102)
T PF06897_consen 38 YGIDDEFIKEVGEALKPGSSALFLLVDEATEDKVDAALRKFGGKVLRTSLSEEDEDELQ 96 (102)
T ss_pred CCCCHHHHHHHHhhcCCCceEEEEEeccCCHHHHHHHHHhcCCEEEeccCCHHHHHHHH
Confidence 566666666666666655 3333333444555555555553 344555544444443
No 180
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=22.52 E-value=71 Score=31.21 Aligned_cols=45 Identities=18% Similarity=0.169 Sum_probs=32.5
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHh---C-C---C--cccc--CCCCHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDL---K-M---E--NKIT--KDMSEEELITIR 102 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~kl---G-I---~--~~kv--~~LteeQI~~L~ 102 (126)
++.|+++|+.|+|||...+..|.+.- | + . -.++ +.++...++.|.
T Consensus 748 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li 803 (973)
T PRK07135 748 NGKIFLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLI 803 (973)
T ss_pred CCEEEECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhccccCCCHHHHHHHH
Confidence 45799999999999999999998643 2 1 1 1233 467777777665
No 181
>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=22.38 E-value=48 Score=27.48 Aligned_cols=23 Identities=22% Similarity=0.297 Sum_probs=19.5
Q ss_pred eeccccccCHHHHHHHHHHhCCC
Q 033150 64 SLQYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~ 86 (126)
.+++|.|||+.+|.+|-+-+-=.
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG 68 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETG 68 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcC
Confidence 55899999999999999876644
No 182
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=22.12 E-value=68 Score=27.97 Aligned_cols=48 Identities=13% Similarity=0.105 Sum_probs=34.5
Q ss_pred eccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh-ccccc
Q 033150 65 LQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEG 112 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~-~~Ie~ 112 (126)
+.++.|||++.|..|=.-|.=. -..+.+...++..+.-+...+ |.|+.
T Consensus 58 a~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ 107 (353)
T KOG2534|consen 58 AEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGL 107 (353)
T ss_pred hcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCH
Confidence 5679999999999998887766 445566555566666666666 66554
No 183
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=22.11 E-value=54 Score=21.67 Aligned_cols=20 Identities=30% Similarity=0.360 Sum_probs=17.4
Q ss_pred eeccccccCHHHHHHHHHHh
Q 033150 64 SLQYIHGVGRTRARQILVDL 83 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~kl 83 (126)
.|++-+.||+..|..|+++|
T Consensus 24 ~lQR~~~IGynrAariid~l 43 (63)
T smart00843 24 LLQRRLRIGYNRAARLIDQL 43 (63)
T ss_pred HHHHHHhcchhHHHHHHHHH
Confidence 46888999999999999776
No 184
>PF00288 GHMP_kinases_N: GHMP kinases N terminal domain; InterPro: IPR006204 The galacto- (2.7.1.6 from EC), homoserine (2.7.1.39 from EC), mevalonate (2.7.1.36 from EC) and phosphomevalonate (2.7.4.2 from EC) kinases contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP [, ]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).; GO: 0005524 ATP binding, 0016301 kinase activity, 0016310 phosphorylation; PDB: 3F0N_B 1PIE_A 2AJ4_A 1K47_E 3GON_A 2R3V_C 3HUL_A 1KVK_A 2R42_A 3D4J_A ....
Probab=21.97 E-value=94 Score=19.37 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=32.9
Q ss_pred eccccccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhhc
Q 033150 65 LQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~~ 108 (126)
+-.=.|+|.+.|..++--..+....-.+++++|+.++....|++
T Consensus 8 iP~~~GLgSSaa~~~a~~~a~~~~~~~~~~~~~l~~~a~~~e~~ 51 (67)
T PF00288_consen 8 IPPGSGLGSSAALAVALAAALNKLFGLPLSKEELAKLAQEAERY 51 (67)
T ss_dssp STTTSSSSHHHHHHHHHHHHHHHHTTTSSBHHHHHHHHHHHHHH
T ss_pred CCCCCcccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHH
Confidence 33446999999998887777773333368999999998888853
No 185
>PRK01172 ski2-like helicase; Provisional
Probab=21.89 E-value=71 Score=28.89 Aligned_cols=37 Identities=35% Similarity=0.390 Sum_probs=29.6
Q ss_pred eeccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
.|.+|.|+|+..|.+ |.+.|+. -.-+-+++++++++|
T Consensus 613 ~L~~ip~~~~~~a~~-l~~~g~~~~~di~~~~~~~~~~i 650 (674)
T PRK01172 613 DLVLIPKVGRVRARR-LYDAGFKTVDDIARSSPERIKKI 650 (674)
T ss_pred hhcCCCCCCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHH
Confidence 467899999998865 7889999 555777888888776
No 186
>TIGR01573 cas2 CRISPR-associated endoribonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead.
Probab=21.78 E-value=1.5e+02 Score=20.25 Aligned_cols=34 Identities=9% Similarity=0.244 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCC--cccc--CCCCHHHHH-HHHHHHhh
Q 033150 74 TRARQILVDLKME--NKIT--KDMSEEELI-TIRDEVSK 107 (126)
Q Consensus 74 ~~A~~IC~klGI~--~~kv--~~LteeQI~-~L~~~I~~ 107 (126)
....++|++.|+. ...+ +++++.+.. .+.+.+++
T Consensus 19 ~kv~k~L~~~G~~rvQ~SVf~~~~~~~~~~~~l~~~l~~ 57 (95)
T TIGR01573 19 RKLRKLLEKYGLQRVQYSVFEGILEPNQLARKLIERLKR 57 (95)
T ss_pred HHHHHHHHHcchhheeccEEEEEcCHHHHHHHHHHHHHH
Confidence 4567889999944 4444 999999999 79999887
No 187
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=21.66 E-value=76 Score=31.61 Aligned_cols=45 Identities=16% Similarity=0.284 Sum_probs=31.7
Q ss_pred CeEEEEeeccccccCHHHHHHHHHHh---C-C----C-cccc--CCCCHHHHHHHH
Q 033150 58 NKRIEYSLQYIHGVGRTRARQILVDL---K-M----E-NKIT--KDMSEEELITIR 102 (126)
Q Consensus 58 nK~V~~ALt~IyGIG~~~A~~IC~kl---G-I----~-~~kv--~~LteeQI~~L~ 102 (126)
+..|+++|..|+|||...+..|.+.= | + | -.++ +.++...++.|.
T Consensus 830 ~~~Ir~GL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~LI 885 (1170)
T PRK07374 830 GNRILFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRLPSNVLNRRSLESLI 885 (1170)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccccCCHHHHHHHH
Confidence 45699999999999999999998543 3 1 1 1233 456677666664
No 188
>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=21.41 E-value=79 Score=17.66 Aligned_cols=21 Identities=10% Similarity=0.202 Sum_probs=14.5
Q ss_pred ccccccCHHHHHHHHHHhCCC
Q 033150 66 QYIHGVGRTRARQILVDLKME 86 (126)
Q Consensus 66 t~IyGIG~~~A~~IC~klGI~ 86 (126)
....||++.+....++.=.|.
T Consensus 8 a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 8 AEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHHCCCHHHHHHHHHcCCCC
Confidence 356677888877777665555
No 189
>PRK14133 DNA polymerase IV; Provisional
Probab=21.30 E-value=93 Score=25.66 Aligned_cols=37 Identities=19% Similarity=0.358 Sum_probs=27.9
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L 101 (126)
-+..++|||+.++..+ .++||.+. -+-.++.+++.+.
T Consensus 174 pv~~l~gig~~~~~~L-~~~Gi~ti~dl~~l~~~~L~~r 211 (347)
T PRK14133 174 PISKVHGIGKKSVEKL-NNIGIYTIEDLLKLSREFLIEY 211 (347)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhhCCHHHHHHH
Confidence 4678899999999985 68999943 3566777776554
No 190
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=21.30 E-value=90 Score=22.64 Aligned_cols=51 Identities=12% Similarity=0.165 Sum_probs=33.2
Q ss_pred CCeEEEEeeccccccCHHHHHHHHHHh-CCC-cc----c--cCCCCHHHHHHHHHHHhh
Q 033150 57 NNKRIEYSLQYIHGVGRTRARQILVDL-KME-NK----I--TKDMSEEELITIRDEVSK 107 (126)
Q Consensus 57 ~nK~V~~ALt~IyGIG~~~A~~IC~kl-GI~-~~----k--v~~LteeQI~~L~~~I~~ 107 (126)
+...++.++-.---.-...+..+.+++ |=+ .. - -.+||+++++.|+++|++
T Consensus 58 gr~~~Y~p~vs~ee~~~~~~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~li~~ 116 (130)
T TIGR02698 58 GRKFIYTALVSEDEAVENAAQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEKLLSE 116 (130)
T ss_pred CCcEEEEecCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHh
Confidence 555577776555555555566676655 111 11 1 268999999999999986
No 191
>PRK00254 ski2-like helicase; Provisional
Probab=21.26 E-value=56 Score=29.96 Aligned_cols=36 Identities=25% Similarity=0.349 Sum_probs=27.9
Q ss_pred eccccccCHHHHHHHHHHhCCC-ccccCCCCHHHHHHH
Q 033150 65 LQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klGI~-~~kv~~LteeQI~~L 101 (126)
|.+|.|||+.++.+ |.+.|+. -..+.+.+++|+..+
T Consensus 647 L~~ipgig~~~~~~-l~~~g~~s~~~i~~a~~~el~~~ 683 (720)
T PRK00254 647 LMRLPMIGRKRARA-LYNAGFRSIEDIVNAKPSELLKV 683 (720)
T ss_pred hhcCCCCCHHHHHH-HHHccCCCHHHHHhCCHHHHhcC
Confidence 66799999999988 5577788 555677777777765
No 192
>PHA02564 V virion protein; Provisional
Probab=21.10 E-value=2.1e+02 Score=21.74 Aligned_cols=32 Identities=6% Similarity=0.022 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCC-ccccCCCCHHHHHHHHHHHhh
Q 033150 75 RARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (126)
Q Consensus 75 ~A~~IC~klGI~-~~kv~~LteeQI~~L~~~I~~ 107 (126)
.+..+|+.+|++ +.++.-.++ .+..|.+.|.+
T Consensus 87 Yi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~ 119 (141)
T PHA02564 87 YATAVANAMGVPPQAGLHLDQD-TLAALVTAIIR 119 (141)
T ss_pred HHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHH
Confidence 478899999999 777764444 88888877744
No 193
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=20.76 E-value=70 Score=27.64 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=17.6
Q ss_pred eeccccccCHHHHHHHHHHhC
Q 033150 64 SLQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klG 84 (126)
++|.+.|||+.+|..|-.-+.
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l~ 74 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYLD 74 (326)
T ss_pred ccCCCCCccHHHHHHHHHHHH
Confidence 699999999999999875543
No 194
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.
Probab=20.45 E-value=1.6e+02 Score=27.10 Aligned_cols=33 Identities=24% Similarity=0.380 Sum_probs=26.6
Q ss_pred cccCHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHhhc
Q 033150 69 HGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY 108 (126)
Q Consensus 69 yGIG~~~A~~IC~klGI~~~kv~~LteeQI~~L~~~I~~~ 108 (126)
-||+...-.+|-+ +| .++++++.+.|++++..|
T Consensus 105 vgis~~~~~~i~~-~g------~~~~~~~~e~lr~~lh~y 137 (533)
T TIGR00470 105 VGLGNEKIEIIEN-LG------IDIDDEKKERLREVFHLY 137 (533)
T ss_pred cCcCHHHHHHHHH-hC------CCCChhHHHHHHHHHHHh
Confidence 3788888888876 66 467888999999999876
No 195
>PRK01810 DNA polymerase IV; Validated
Probab=20.44 E-value=89 Score=26.40 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=26.9
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L 101 (126)
-++.+.|||+.++..+ .++||.+. -+-.++.+++.+.
T Consensus 180 pv~~l~giG~~~~~~L-~~~Gi~tigdL~~~~~~~L~~r 217 (407)
T PRK01810 180 PVGEMHGIGEKTAEKL-KDIGIQTIGDLAKADEHILRAK 217 (407)
T ss_pred CHhhcCCcCHHHHHHH-HHcCCCcHHHHHhCCHHHHHHH
Confidence 4678899999999775 78999833 3566676666443
No 196
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=20.33 E-value=93 Score=25.14 Aligned_cols=37 Identities=22% Similarity=0.344 Sum_probs=28.2
Q ss_pred eeccccccCHHHHHHHHHHhCCCccc-cCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~k-v~~LteeQI~~L 101 (126)
-++.+.|||+.++..+ +++||.+.. +.+++..++.+.
T Consensus 172 pl~~l~gig~~~~~~L-~~~Gi~ti~dl~~~~~~~L~~~ 209 (334)
T cd03586 172 PVRKIPGVGKVTAEKL-KELGIKTIGDLAKLDVELLKKL 209 (334)
T ss_pred CchhhCCcCHHHHHHH-HHcCCcCHHHHHcCCHHHHHHH
Confidence 4588899999998875 788999443 667788777764
No 197
>PRK05755 DNA polymerase I; Provisional
Probab=20.25 E-value=68 Score=30.36 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=17.6
Q ss_pred eccccccCHHHHHHHHHHhC
Q 033150 65 LQYIHGVGRTRARQILVDLK 84 (126)
Q Consensus 65 Lt~IyGIG~~~A~~IC~klG 84 (126)
+..|.|||+++|.++.++.|
T Consensus 189 ipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 189 IPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred CCCCCCccHHHHHHHHHHcC
Confidence 34689999999999999987
No 198
>PRK03103 DNA polymerase IV; Reviewed
Probab=20.20 E-value=92 Score=26.32 Aligned_cols=37 Identities=14% Similarity=0.231 Sum_probs=26.9
Q ss_pred eeccccccCHHHHHHHHHHhCCCcc-ccCCCCHHHHHHH
Q 033150 64 SLQYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITI 101 (126)
Q Consensus 64 ALt~IyGIG~~~A~~IC~klGI~~~-kv~~LteeQI~~L 101 (126)
-++.+.|||+.++.++ +++||.+. -+-+++.+++.+.
T Consensus 182 pi~~l~gig~~~~~~L-~~~Gi~tigdl~~~~~~~L~~~ 219 (409)
T PRK03103 182 PVRKLFGVGSRMEKHL-RRMGIRTIGQLANTPLERLKKR 219 (409)
T ss_pred CHhhcCCccHHHHHHH-HHcCCCCHHHHhcCCHHHHHHH
Confidence 4678899999988885 68999833 3566677666444
No 199
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=20.20 E-value=72 Score=25.34 Aligned_cols=50 Identities=18% Similarity=0.208 Sum_probs=33.7
Q ss_pred CCCCeEEEEeecccc---ccCHHHHHHHHHHh-CCC-ccccCCCCHHHHHHHHHHHh
Q 033150 55 IPNNKRIEYSLQYIH---GVGRTRARQILVDL-KME-NKITKDMSEEELITIRDEVS 106 (126)
Q Consensus 55 ip~nK~V~~ALt~Iy---GIG~~~A~~IC~kl-GI~-~~kv~~LteeQI~~L~~~I~ 106 (126)
--.+|++..+|..++ +.|. ...+...+ +++ +.+..+||.+|+.+|.+.+.
T Consensus 201 ~~rrk~l~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~ 255 (258)
T PRK14896 201 QHRRKTLRNALKNSAHISGKED--IKAVVEALPEELLNKRVFQLSPEEIAELANLLY 255 (258)
T ss_pred ccccHHHHHHHhhhccccchhH--HHHHHHHcCCCCcCCCCccCCHHHHHHHHHHHH
Confidence 345567777776652 3221 13345556 455 88999999999999998875
Done!