Query 031757
Match_columns 153
No_of_seqs 109 out of 935
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 04:55:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031757.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031757hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0099 RpsM Ribosomal protein 100.0 1.1E-50 2.3E-55 304.8 10.1 119 31-149 1-121 (121)
2 CHL00137 rps13 ribosomal prote 100.0 3.1E-49 6.8E-54 298.6 11.5 119 31-149 1-121 (122)
3 PRK05179 rpsM 30S ribosomal pr 100.0 4.8E-49 1E-53 297.6 11.2 119 31-149 1-121 (122)
4 TIGR03629 arch_S13P archaeal r 100.0 9.9E-49 2.2E-53 303.2 11.5 121 23-149 1-144 (144)
5 PRK04053 rps13p 30S ribosomal 100.0 6.8E-49 1.5E-53 305.6 9.9 123 21-149 3-149 (149)
6 PTZ00134 40S ribosomal protein 100.0 8.9E-49 1.9E-53 306.3 10.3 129 15-149 2-154 (154)
7 TIGR03631 bact_S13 30S ribosom 100.0 2E-46 4.3E-51 280.0 10.2 110 33-142 1-112 (113)
8 PF00416 Ribosomal_S13: Riboso 100.0 8E-46 1.7E-50 273.2 5.2 105 33-137 1-107 (107)
9 KOG3311 Ribosomal protein S18 100.0 9.1E-38 2E-42 242.6 6.1 128 14-149 1-152 (152)
10 PF06831 H2TH: Formamidopyrimi 95.4 0.015 3.3E-07 41.7 3.0 50 41-90 22-75 (92)
11 PRK01103 formamidopyrimidine/5 94.6 0.043 9.4E-07 46.2 4.0 52 40-91 153-208 (274)
12 PRK14810 formamidopyrimidine-D 92.9 0.15 3.1E-06 43.1 4.2 51 40-90 152-206 (272)
13 PRK14811 formamidopyrimidine-D 92.5 0.16 3.5E-06 42.8 3.9 50 41-90 142-195 (269)
14 PRK10445 endonuclease VIII; Pr 91.9 0.21 4.5E-06 42.0 3.9 49 42-90 151-203 (263)
15 PF00633 HHH: Helix-hairpin-he 91.8 0.12 2.7E-06 30.0 1.7 19 47-65 11-29 (30)
16 PRK13945 formamidopyrimidine-D 90.7 0.38 8.3E-06 40.7 4.3 49 42-90 164-216 (282)
17 TIGR00577 fpg formamidopyrimid 90.5 0.4 8.7E-06 40.4 4.3 49 42-90 155-207 (272)
18 PRK02515 psbU photosystem II c 89.9 0.41 9E-06 37.1 3.5 61 35-95 49-113 (132)
19 PF05833 FbpA: Fibronectin-bin 89.1 0.071 1.5E-06 47.1 -1.4 50 41-90 185-236 (455)
20 KOG3311 Ribosomal protein S18 87.5 0.094 2E-06 41.4 -1.4 48 93-142 69-116 (152)
21 PF11798 IMS_HHH: IMS family H 87.3 0.4 8.7E-06 28.1 1.5 21 48-69 12-32 (32)
22 PRK04184 DNA topoisomerase VI 86.3 1.1 2.5E-05 41.6 4.6 49 44-92 257-307 (535)
23 PF14520 HHH_5: Helix-hairpin- 85.5 0.11 2.5E-06 33.8 -1.7 25 45-70 3-27 (60)
24 COG3743 Uncharacterized conser 84.6 0.83 1.8E-05 35.4 2.5 44 47-91 67-111 (133)
25 PF10391 DNA_pol_lambd_f: Fing 84.4 0.71 1.5E-05 30.0 1.8 36 48-84 3-43 (52)
26 smart00278 HhH1 Helix-hairpin- 81.9 1.2 2.6E-05 24.5 1.8 19 48-66 2-20 (26)
27 TIGR00275 flavoprotein, HI0933 80.7 1.2 2.6E-05 38.9 2.4 49 42-92 283-332 (400)
28 PF14579 HHH_6: Helix-hairpin- 79.8 2.2 4.7E-05 30.0 3.0 26 42-67 22-47 (90)
29 COG0266 Nei Formamidopyrimidin 79.4 2.7 5.8E-05 36.1 3.9 54 37-90 150-207 (273)
30 PRK14606 ruvA Holliday junctio 78.2 1.3 2.8E-05 35.7 1.6 18 48-65 109-126 (188)
31 PRK14601 ruvA Holliday junctio 76.5 1.6 3.4E-05 35.3 1.6 17 48-64 109-125 (183)
32 PF11731 Cdd1: Pathogenicity l 76.3 2.4 5.1E-05 31.0 2.4 37 46-83 11-48 (93)
33 PRK14604 ruvA Holliday junctio 76.1 1.6 3.5E-05 35.4 1.6 20 47-66 108-127 (195)
34 TIGR03252 uncharacterized HhH- 75.6 1.1 2.3E-05 36.3 0.4 29 40-68 108-136 (177)
35 PRK14603 ruvA Holliday junctio 75.5 1.7 3.7E-05 35.2 1.6 19 47-65 107-125 (197)
36 PRK14602 ruvA Holliday junctio 74.4 1.9 4.2E-05 35.1 1.7 17 48-64 110-126 (203)
37 PRK13901 ruvA Holliday junctio 74.1 1.9 4.2E-05 35.2 1.6 17 48-64 108-124 (196)
38 COG0632 RuvA Holliday junction 73.8 2.1 4.6E-05 35.1 1.8 21 47-67 108-128 (201)
39 PRK00116 ruvA Holliday junctio 72.9 0.73 1.6E-05 37.0 -1.1 47 24-70 50-96 (192)
40 TIGR01052 top6b DNA topoisomer 71.3 6.4 0.00014 36.3 4.4 49 43-91 247-300 (488)
41 PRK14605 ruvA Holliday junctio 70.2 1.5 3.3E-05 35.4 0.2 43 28-70 54-96 (194)
42 PF03486 HI0933_like: HI0933-l 70.0 5.1 0.00011 35.8 3.4 51 40-92 288-340 (409)
43 PRK14600 ruvA Holliday junctio 67.8 3.5 7.5E-05 33.2 1.8 18 47-65 108-125 (186)
44 PRK14605 ruvA Holliday junctio 65.9 3.6 7.8E-05 33.2 1.5 18 47-64 108-125 (194)
45 PF14520 HHH_5: Helix-hairpin- 64.7 5.2 0.00011 25.8 1.8 20 48-67 39-58 (60)
46 TIGR00084 ruvA Holliday juncti 64.5 1.5 3.2E-05 35.4 -1.0 43 26-68 51-93 (191)
47 PRK00274 ksgA 16S ribosomal RN 63.5 6.6 0.00014 32.7 2.7 49 42-91 221-270 (272)
48 PF14716 HHH_8: Helix-hairpin- 63.5 5.1 0.00011 26.7 1.7 19 48-66 48-66 (68)
49 cd00056 ENDO3c endonuclease II 63.1 3.7 8E-05 30.9 1.0 25 42-66 78-102 (158)
50 PF02371 Transposase_20: Trans 62.6 6.3 0.00014 27.3 2.1 20 48-67 3-22 (87)
51 PF12826 HHH_2: Helix-hairpin- 61.3 5 0.00011 26.6 1.3 18 51-68 7-24 (64)
52 TIGR00426 competence protein C 60.2 12 0.00027 24.6 3.1 47 42-88 11-66 (69)
53 cd00080 HhH2_motif Helix-hairp 59.5 8.1 0.00018 26.4 2.1 19 50-68 25-43 (75)
54 PRK14602 ruvA Holliday junctio 59.2 3.3 7.1E-05 33.7 0.1 45 26-70 53-97 (203)
55 smart00483 POLXc DNA polymeras 58.1 7.2 0.00016 33.8 2.1 40 45-85 87-132 (334)
56 COG0030 KsgA Dimethyladenosine 57.6 6.8 0.00015 33.3 1.8 46 41-91 210-256 (259)
57 smart00279 HhH2 Helix-hairpin- 57.1 9.7 0.00021 22.8 2.0 17 50-66 19-35 (36)
58 TIGR00084 ruvA Holliday juncti 56.7 7 0.00015 31.5 1.7 18 47-64 107-124 (191)
59 PRK14601 ruvA Holliday junctio 56.4 3 6.5E-05 33.6 -0.5 43 26-68 52-94 (183)
60 smart00478 ENDO3c endonuclease 56.4 7.2 0.00016 29.1 1.6 23 45-67 70-92 (149)
61 PRK14606 ruvA Holliday junctio 56.1 2.9 6.3E-05 33.7 -0.7 43 27-69 53-95 (188)
62 cd00141 NT_POLXc Nucleotidyltr 55.5 8.8 0.00019 32.9 2.2 40 46-86 84-129 (307)
63 PRK08609 hypothetical protein; 53.3 10 0.00022 35.3 2.4 24 47-70 88-111 (570)
64 PRK14603 ruvA Holliday junctio 52.9 3.6 7.7E-05 33.4 -0.6 41 28-68 53-93 (197)
65 PRK14600 ruvA Holliday junctio 52.6 4 8.6E-05 32.9 -0.4 40 31-70 57-96 (186)
66 PRK10702 endonuclease III; Pro 51.1 8.4 0.00018 31.4 1.3 23 45-67 107-129 (211)
67 TIGR01083 nth endonuclease III 51.0 9.3 0.0002 30.2 1.5 23 45-67 104-126 (191)
68 PRK07373 DNA polymerase III su 49.1 17 0.00038 33.0 3.1 60 28-87 87-165 (449)
69 TIGR00755 ksgA dimethyladenosi 48.5 13 0.00028 30.3 2.0 46 41-88 206-252 (253)
70 COG0632 RuvA Holliday junction 48.5 1.6 3.6E-05 35.7 -3.2 45 26-70 52-96 (201)
71 COG1389 DNA topoisomerase VI, 47.7 21 0.00045 33.4 3.3 43 50-92 264-311 (538)
72 PRK13901 ruvA Holliday junctio 47.2 5.3 0.00012 32.6 -0.4 41 29-69 54-94 (196)
73 PF00398 RrnaAD: Ribosomal RNA 46.8 11 0.00023 31.2 1.3 50 40-91 212-262 (262)
74 TIGR01259 comE comEA protein. 46.8 13 0.00028 27.7 1.6 32 38-69 59-90 (120)
75 COG0258 Exo 5'-3' exonuclease 46.5 46 0.001 28.3 5.2 18 52-69 203-220 (310)
76 TIGR01084 mutY A/G-specific ad 45.2 13 0.00028 31.6 1.6 22 46-67 104-125 (275)
77 PF12836 HHH_3: Helix-hairpin- 44.1 18 0.00039 23.8 1.9 48 40-87 7-62 (65)
78 PRK14604 ruvA Holliday junctio 43.5 6.3 0.00014 32.0 -0.5 40 28-67 54-93 (195)
79 PF04001 Vhr1: Transcription f 43.2 18 0.00038 26.5 1.8 59 59-126 8-67 (95)
80 COG1293 Predicted RNA-binding 43.2 22 0.00048 33.2 2.9 46 44-89 187-233 (564)
81 PRK12311 rpsB 30S ribosomal pr 42.7 15 0.00032 32.3 1.6 45 45-90 261-306 (326)
82 PRK14671 uvrC excinuclease ABC 42.5 6.2 0.00013 37.3 -0.8 61 24-85 543-606 (621)
83 PRK13913 3-methyladenine DNA g 42.4 16 0.00034 30.3 1.6 23 44-66 118-140 (218)
84 PRK00116 ruvA Holliday junctio 41.9 16 0.00035 29.2 1.6 22 48-69 109-130 (192)
85 PRK01229 N-glycosylase/DNA lya 41.6 19 0.00042 29.6 2.0 27 44-70 115-142 (208)
86 PRK10880 adenine DNA glycosyla 41.0 15 0.00032 32.5 1.4 22 45-66 107-128 (350)
87 PRK13910 DNA glycosylase MutY; 39.0 18 0.0004 31.1 1.6 21 46-66 71-91 (289)
88 TIGR01448 recD_rel helicase, p 39.0 60 0.0013 31.2 5.1 39 51-89 88-137 (720)
89 PRK12766 50S ribosomal protein 38.8 23 0.00049 29.9 2.1 22 48-70 4-25 (232)
90 PRK14666 uvrC excinuclease ABC 38.8 31 0.00068 33.4 3.2 59 44-109 634-692 (694)
91 TIGR00588 ogg 8-oxoguanine DNA 38.2 19 0.00041 31.0 1.5 23 44-66 217-239 (310)
92 PRK10308 3-methyl-adenine DNA 37.4 21 0.00046 30.3 1.7 22 45-66 205-226 (283)
93 TIGR00575 dnlj DNA ligase, NAD 37.0 29 0.00062 33.1 2.7 73 50-129 435-508 (652)
94 COG1936 Predicted nucleotide k 36.7 34 0.00074 27.8 2.7 25 46-70 2-26 (180)
95 TIGR00615 recR recombination p 36.4 34 0.00073 28.0 2.7 72 44-128 8-115 (195)
96 PF06514 PsbU: Photosystem II 36.3 27 0.00059 25.6 1.9 61 35-95 11-75 (93)
97 PF14490 HHH_4: Helix-hairpin- 36.0 21 0.00046 25.1 1.3 24 47-70 45-69 (94)
98 COG2081 Predicted flavoprotein 35.5 49 0.0011 30.1 3.8 50 40-91 283-332 (408)
99 COG0122 AlkA 3-methyladenine D 34.9 24 0.00051 30.2 1.6 25 42-66 193-217 (285)
100 COG0353 RecR Recombinational D 34.4 34 0.00075 28.2 2.4 67 44-123 9-108 (198)
101 COG0177 Nth Predicted EndoIII- 34.2 23 0.0005 29.3 1.4 25 46-70 108-133 (211)
102 PF02318 FYVE_2: FYVE-type zin 33.8 86 0.0019 23.0 4.3 17 75-91 1-17 (118)
103 PRK12278 50S ribosomal protein 32.1 38 0.00083 28.2 2.4 43 47-90 158-201 (221)
104 cd00008 53EXOc 5'-3' exonuclea 31.1 38 0.00082 27.9 2.2 20 49-68 185-204 (240)
105 PF02042 RWP-RK: RWP-RK domain 31.0 50 0.0011 21.5 2.3 19 52-70 24-42 (52)
106 PF09883 DUF2110: Uncharacteri 30.6 67 0.0015 27.0 3.5 66 42-107 96-178 (225)
107 PRK00558 uvrC excinuclease ABC 30.4 34 0.00074 32.2 2.0 46 39-85 535-580 (598)
108 cd01104 HTH_MlrA-CarA Helix-Tu 30.3 1.2E+02 0.0027 19.1 4.2 42 49-90 6-52 (68)
109 smart00475 53EXOc 5'-3' exonuc 30.0 40 0.00087 28.3 2.2 20 49-68 188-207 (259)
110 PRK07945 hypothetical protein; 29.9 35 0.00076 29.6 1.9 21 48-68 50-70 (335)
111 PRK07956 ligA NAD-dependent DN 29.8 46 0.00099 31.9 2.8 36 50-85 448-484 (665)
112 PF14635 HHH_7: Helix-hairpin- 29.8 44 0.00095 24.7 2.1 27 42-68 45-71 (104)
113 PF13035 DUF3896: Protein of u 29.5 79 0.0017 21.1 3.0 42 61-118 19-61 (61)
114 PRK14976 5'-3' exonuclease; Pr 28.3 43 0.00093 28.4 2.1 19 50-68 194-212 (281)
115 PF14794 DUF4479: Domain of un 28.2 50 0.0011 22.8 2.1 21 75-95 46-66 (73)
116 PF14842 FliG_N: FliG N-termin 28.2 42 0.0009 24.3 1.8 36 56-91 7-44 (108)
117 PRK00076 recR recombination pr 27.3 37 0.0008 27.8 1.5 66 45-123 9-107 (196)
118 PRK09482 flap endonuclease-lik 27.3 47 0.001 28.1 2.2 20 49-68 184-203 (256)
119 cd02020 CMPK Cytidine monophos 26.7 2.3E+02 0.005 19.9 6.6 42 47-88 2-44 (147)
120 PRK14667 uvrC excinuclease ABC 26.5 48 0.001 31.2 2.2 45 40-85 507-551 (567)
121 PHA02564 V virion protein; Pro 26.1 1.3E+02 0.0027 23.5 4.2 34 58-92 86-120 (141)
122 KOG1014 17 beta-hydroxysteroid 25.5 82 0.0018 27.7 3.4 39 51-91 57-95 (312)
123 PRK07279 dnaE DNA polymerase I 25.4 71 0.0015 32.4 3.3 46 42-87 745-797 (1034)
124 COG2231 Uncharacterized protei 25.1 26 0.00056 29.3 0.2 31 38-68 104-136 (215)
125 PHA03373 tegument protein; Pro 24.8 57 0.0012 27.7 2.2 58 55-113 103-162 (247)
126 PRK14670 uvrC excinuclease ABC 24.5 55 0.0012 30.9 2.3 40 45-85 512-551 (574)
127 PRK13844 recombination protein 24.1 46 0.001 27.4 1.5 38 45-89 13-50 (200)
128 PF01367 5_3_exonuc: 5'-3' exo 23.2 8.9 0.00019 28.1 -2.6 20 50-69 21-40 (101)
129 TIGR00194 uvrC excinuclease AB 23.0 58 0.0013 30.7 2.1 25 44-68 538-562 (574)
130 PRK05673 dnaE DNA polymerase I 22.8 81 0.0017 32.2 3.2 59 29-87 794-871 (1135)
131 PRK07374 dnaE DNA polymerase I 22.5 84 0.0018 32.2 3.2 58 30-87 810-886 (1170)
132 PF11338 DUF3140: Protein of u 22.4 1.1E+02 0.0024 22.3 3.1 35 54-91 34-68 (92)
133 PRK14529 adenylate kinase; Pro 22.1 3.3E+02 0.007 22.4 6.2 52 47-98 3-63 (223)
134 PRK07135 dnaE DNA polymerase I 22.1 79 0.0017 31.8 2.9 46 42-87 748-804 (973)
135 PF01698 FLO_LFY: Floricaula / 22.0 30 0.00065 31.3 0.0 71 49-120 54-131 (386)
136 cd00128 XPG Xeroderma pigmento 21.3 72 0.0016 27.0 2.2 18 51-68 227-244 (316)
137 PF13442 Cytochrome_CBB3: Cyto 21.2 90 0.002 19.8 2.2 16 74-89 52-67 (67)
138 TIGR00575 dnlj DNA ligase, NAD 21.2 47 0.001 31.7 1.1 39 45-85 497-535 (652)
139 PRK06826 dnaE DNA polymerase I 21.1 82 0.0018 32.2 2.8 46 42-87 819-875 (1151)
140 COG3415 Transposase and inacti 20.8 99 0.0021 23.9 2.7 78 48-127 26-115 (138)
141 PRK14668 uvrC excinuclease ABC 20.7 65 0.0014 30.4 1.9 40 45-85 523-562 (577)
142 PRK14669 uvrC excinuclease ABC 20.7 69 0.0015 30.5 2.1 41 44-85 549-589 (624)
143 PRK12373 NADH dehydrogenase su 20.6 75 0.0016 28.9 2.2 44 46-90 322-366 (400)
144 COG1796 POL4 DNA polymerase IV 20.6 69 0.0015 28.4 2.0 21 48-68 54-74 (326)
145 PRK03980 flap endonuclease-1; 20.5 75 0.0016 27.2 2.1 18 51-68 193-210 (292)
146 COG1555 ComEA DNA uptake prote 20.5 67 0.0015 24.9 1.7 26 42-67 92-117 (149)
147 cd01199 INT_Tn1545_C Tn1545-re 20.3 1.4E+02 0.003 22.2 3.4 16 77-92 2-17 (205)
148 PF01418 HTH_6: Helix-turn-hel 20.3 95 0.0021 20.8 2.3 23 48-70 39-61 (77)
149 PRK05898 dnaE DNA polymerase I 20.2 94 0.002 31.4 3.0 45 42-86 747-801 (971)
150 PF00034 Cytochrom_C: Cytochro 20.1 1E+02 0.0022 19.5 2.3 16 76-91 74-89 (91)
151 cd01702 PolY_Pol_eta DNA Polym 20.1 78 0.0017 27.6 2.2 37 48-84 183-222 (359)
152 PRK01172 ski2-like helicase; P 20.1 1.8E+02 0.004 27.2 4.8 39 47-86 612-651 (674)
No 1
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-50 Score=304.79 Aligned_cols=119 Identities=49% Similarity=0.813 Sum_probs=116.3
Q ss_pred eeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hccchHHHHHHHHHhHHH
Q 031757 31 GLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS-RYLTGEDLRRCIKNDVER 108 (153)
Q Consensus 31 ~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~-~~~i~~dL~~~~~~dI~r 108 (153)
|+||+|+|||++|.|.+|||+|||||.++|..||+++||| ++++++|||+|+++|.++++ .|++|+||++++++||+|
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 7999999999999999999999999999999999999999 77999999999999999999 799999999999999999
Q ss_pred HHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 109 LVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 109 L~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
|++|+||||+||.+|||||||||||||||+||.++||++||
T Consensus 81 l~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 81 LMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred HHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 99999999999999999999999999999999999988875
No 2
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=3.1e-49 Score=298.62 Aligned_cols=119 Identities=45% Similarity=0.776 Sum_probs=114.4
Q ss_pred eeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hccchHHHHHHHHHhHHH
Q 031757 31 GLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS-RYLTGEDLRRCIKNDVER 108 (153)
Q Consensus 31 ~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~-~~~i~~dL~~~~~~dI~r 108 (153)
|+||+|+|||++|+|++||++|||||+++|.+||+++||| +.++++||++|+++|.++|+ +|.+|+||++.+++||+|
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 6999999999999999999999999999999999999999 67899999999999999997 599999999999999999
Q ss_pred HHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 109 LVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 109 L~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
|++|+||||+||.+|||||||||||||||+|+....|..||
T Consensus 81 l~~I~sYRG~RH~~gLPVRGQRT~tNarT~k~~~~~~~~kk 121 (122)
T CHL00137 81 LMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGKK 121 (122)
T ss_pred HHHhCchhcccccCCCCCCCCcCCccccccCCCcccccccC
Confidence 99999999999999999999999999999999988887654
No 3
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=4.8e-49 Score=297.55 Aligned_cols=119 Identities=50% Similarity=0.862 Sum_probs=114.2
Q ss_pred eeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-ccchHHHHHHHHHhHHH
Q 031757 31 GLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR-YLTGEDLRRCIKNDVER 108 (153)
Q Consensus 31 ~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~-~~i~~dL~~~~~~dI~r 108 (153)
||||+|+|||++|+|.+||++|||||+++|.+||+++||| +.++++|+++|+++|.++|++ |.+|+||++.+++||+|
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r 80 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKR 80 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHH
Confidence 7999999999999999999999999999999999999999 678999999999999999986 99999999999999999
Q ss_pred HHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 109 LVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 109 L~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
|++|+||||+||.+|||||||||||||||+|+....+..||
T Consensus 81 l~~I~sYRG~RH~~gLPVRGQRT~TNart~k~~~~~~~~kk 121 (122)
T PRK05179 81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKK 121 (122)
T ss_pred HHHhcceeeeecccCCCCCCCcCCccccccCCccccccccC
Confidence 99999999999999999999999999999999888777554
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=100.00 E-value=9.9e-49 Score=303.19 Aligned_cols=121 Identities=36% Similarity=0.610 Sum_probs=116.7
Q ss_pred ccccceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh----------
Q 031757 23 SFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR---------- 91 (153)
Q Consensus 23 ~~~~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~---------- 91 (153)
+|||+ +||+|+|||++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|.++|++
T Consensus 1 ~~~~m----~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~ 76 (144)
T TIGR03629 1 EFKYI----VRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLL 76 (144)
T ss_pred Cccee----eeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHh
Confidence 47888 999999999999999999999999999999999999999 778999999999999999985
Q ss_pred ------------ccchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 92 ------------YLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 92 ------------~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
|.+|+||++++++||+||++|+||||+||.+||||||||||||||| +.++||.+||
T Consensus 77 Nr~~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRt--g~~~gv~~kk 144 (144)
T TIGR03629 77 NRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRR--GRTVGVSRKK 144 (144)
T ss_pred hcccccccCccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcC--CCccccccCC
Confidence 7899999999999999999999999999999999999999999998 8899999986
No 5
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=6.8e-49 Score=305.60 Aligned_cols=123 Identities=35% Similarity=0.568 Sum_probs=118.2
Q ss_pred CCccccceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh---------
Q 031757 21 TISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS--------- 90 (153)
Q Consensus 21 ~~~~~~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~--------- 90 (153)
.++|||+ +||+|+|||++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|.++|+
T Consensus 3 ~~~~~~m----~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~ 78 (149)
T PRK04053 3 EEEFKYI----VRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPS 78 (149)
T ss_pred hhhhhhh----HhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCch
Confidence 4579999 999999999999999999999999999999999999999 67899999999999999996
Q ss_pred --------------hccchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 91 --------------RYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 91 --------------~~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
.|+||+||++.+++||+||++|+||||+||.+||||||||||||||| +.++||.+||
T Consensus 79 w~~Nr~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRt--g~~~gv~~kk 149 (149)
T PRK04053 79 WMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRT--GGTVGVSRKK 149 (149)
T ss_pred hhhccccccccCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcC--CCccccccCC
Confidence 47899999999999999999999999999999999999999999998 8899999986
No 6
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=8.9e-49 Score=306.34 Aligned_cols=129 Identities=34% Similarity=0.507 Sum_probs=120.0
Q ss_pred eeeeccCCccccceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh--
Q 031757 15 SRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR-- 91 (153)
Q Consensus 15 ~~~~~~~~~~~~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~-- 91 (153)
++..+++++|||| +||+|+|||++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|.++|++
T Consensus 2 ~~~~~~~~~~~~m----vrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~ 77 (154)
T PTZ00134 2 SLTLEKADDFQHI----LRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPL 77 (154)
T ss_pred Cccccchhhhhhh----hhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccc
Confidence 3344444589999 999999999999999999999999999999999999999 678999999999999999975
Q ss_pred -c--------------------cchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 92 -Y--------------------LTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 92 -~--------------------~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
| ++|+||++.+++||+||++|+||||+||.+||||||||||||||| +.++||.+||
T Consensus 78 ~~~iP~w~~nr~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~--g~~~gv~~kk 154 (154)
T PTZ00134 78 QFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRR--GRTVGVSRKK 154 (154)
T ss_pred cCCCChhHhhccccccccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCcc--ccccceeccC
Confidence 4 579999999999999999999999999999999999999999998 8899999986
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=100.00 E-value=2e-46 Score=279.96 Aligned_cols=110 Identities=55% Similarity=0.928 Sum_probs=106.0
Q ss_pred EEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hccchHHHHHHHHHhHHHHH
Q 031757 33 RVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS-RYLTGEDLRRCIKNDVERLV 110 (153)
Q Consensus 33 rI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~-~~~i~~dL~~~~~~dI~rL~ 110 (153)
||+|+|||++|+|.+||++|||||.++|.+||+++||| +.++++|+++|+++|.++|+ .|.+|+||++.+++||+||+
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~rl~ 80 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLM 80 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999 67899999999999999996 59999999999999999999
Q ss_pred hhhhccCCccCCCCccCCccccccccCCCCcc
Q 031757 111 DIQCYRGIRHSQGLPCRGQRTSTNARTRKGKR 142 (153)
Q Consensus 111 ~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~ 142 (153)
+|+||||+||.+|||||||||||||||||+..
T Consensus 81 ~I~syRG~RH~~gLpVRGQRT~TNart~k~~~ 112 (113)
T TIGR03631 81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPR 112 (113)
T ss_pred HhcceeccccccCCCCCCCcCCccccccCCCC
Confidence 99999999999999999999999999998753
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=100.00 E-value=8e-46 Score=273.22 Aligned_cols=105 Identities=44% Similarity=0.761 Sum_probs=101.0
Q ss_pred EEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-ccchHHHHHHHHHhHHHHH
Q 031757 33 RVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR-YLTGEDLRRCIKNDVERLV 110 (153)
Q Consensus 33 rI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~-~~i~~dL~~~~~~dI~rL~ 110 (153)
||+|+|||++|+|.+||++|||||+++|.+||+++||| +.++++|+++|+++|.++|++ |.+++||++++++||+||+
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~~~~i~~~L~~~~~~~i~rl~ 80 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEKNHLIENDLKRQVRENIKRLK 80 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHTHSTCHHHHHHHHHHHHHHHH
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999 578999999999999999998 9999999999999999999
Q ss_pred hhhhccCCccCCCCccCCccccccccC
Q 031757 111 DIQCYRGIRHSQGLPCRGQRTSTNART 137 (153)
Q Consensus 111 ~I~sYRG~RH~~GLPVRGQRTrTNarT 137 (153)
+|+||||+||.+|||||||||||||||
T Consensus 81 ~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 81 KIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp HHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred HHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999986
No 9
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.1e-38 Score=242.61 Aligned_cols=128 Identities=35% Similarity=0.570 Sum_probs=118.4
Q ss_pred eeeeeccCCccccceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh--
Q 031757 14 VSRQLIQTISFHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS-- 90 (153)
Q Consensus 14 ~~~~~~~~~~~~~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~-- 90 (153)
||+.. ++.|||+ +||+|+++|++++|.|||++|||||..+|..+|+++||| .+++++|+++|++.+.++++
T Consensus 1 msl~~--~~~~q~i----~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~ 74 (152)
T KOG3311|consen 1 MSLVI--PEAFQHI----LRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDP 74 (152)
T ss_pred Cceec--chhHHHH----HHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCH
Confidence 45544 5559999 999999999999999999999999999999999999999 77999999999999998876
Q ss_pred ---------------------hccchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCCccccccccCCCCccccccCCC
Q 031757 91 ---------------------RYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKRVAIPGKK 149 (153)
Q Consensus 91 ---------------------~~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~~gv~~kk 149 (153)
.+++.+.|+...+++|+||++|.||||+||.||||||||||+|||+ |+++|||++||
T Consensus 75 ~~~~~~~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~--~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 75 RQYKIPDWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGR--RGKTVGVSGKK 152 (152)
T ss_pred HHhcCchHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCcccccccc--ccceeeecccC
Confidence 1567899999999999999999999999999999999999999995 69999999986
No 10
>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=95.43 E-value=0.015 Score=41.67 Aligned_cols=50 Identities=26% Similarity=0.391 Sum_probs=40.3
Q ss_pred CCceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHh
Q 031757 41 NDKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVS 90 (153)
Q Consensus 41 ~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~ 90 (153)
.+++|..+| +-+-|||.-++..+|-.+||+|. .+.+|+++|+..|-+.+.
T Consensus 22 ~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~ 75 (92)
T PF06831_consen 22 RRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIK 75 (92)
T ss_dssp CCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHH
T ss_pred CcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 467788788 67899999999999999999955 679999999999887663
No 11
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=94.61 E-value=0.043 Score=46.15 Aligned_cols=52 Identities=19% Similarity=0.282 Sum_probs=45.1
Q ss_pred CCCceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHhh
Q 031757 40 PNDKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVSR 91 (153)
Q Consensus 40 ~~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~~ 91 (153)
..+.+|..+| +-+-|||.-+|..||-.+||+|. ++++||++|++.|.+.+..
T Consensus 153 ~~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~ 208 (274)
T PRK01103 153 KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA 208 (274)
T ss_pred cCCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 3567888889 88999999999999999999955 6799999999999877643
No 12
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=92.92 E-value=0.15 Score=43.11 Aligned_cols=51 Identities=22% Similarity=0.399 Sum_probs=42.5
Q ss_pred CCCceeeeeccc---ccccCHHHHHHHHHHcCCCc-cccCCCCHHHHHHHHHHHh
Q 031757 40 PNDKRLETSLQH---VYGIGRSRAHQILCDLNIGN-KLTKELTGVELNSLREEVS 90 (153)
Q Consensus 40 ~~~k~i~~aLt~---I~GIG~~~A~~Ic~~lgi~~-~~~~~Ls~~qi~~L~~~l~ 90 (153)
..+.+|..+|-. |-|||.-+|..||-++|||+ ..+++||++|++.|.+.+.
T Consensus 152 ~~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~ 206 (272)
T PRK14810 152 GRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIG 206 (272)
T ss_pred cCCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence 345667777844 49999999999999999995 5789999999999988664
No 13
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=92.45 E-value=0.16 Score=42.79 Aligned_cols=50 Identities=20% Similarity=0.239 Sum_probs=42.8
Q ss_pred CCceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHh
Q 031757 41 NDKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVS 90 (153)
Q Consensus 41 ~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~ 90 (153)
.+.+|.-+| +-|-|||.-+|..||-.+||+|. ++++||++|++.|-+.+.
T Consensus 142 ~~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~ 195 (269)
T PRK14811 142 TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIR 195 (269)
T ss_pred cCCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHH
Confidence 366777777 66889999999999999999955 679999999999977663
No 14
>PRK10445 endonuclease VIII; Provisional
Probab=91.94 E-value=0.21 Score=41.96 Aligned_cols=49 Identities=18% Similarity=0.342 Sum_probs=40.7
Q ss_pred Cceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHh
Q 031757 42 DKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVS 90 (153)
Q Consensus 42 ~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~ 90 (153)
+++|..+| +-+-|||.-+|..||-.+||+|. .+++||++|++.|-+.+.
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~ 203 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALL 203 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHH
Confidence 44566666 45779999999999999999965 679999999999987664
No 15
>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=91.80 E-value=0.12 Score=30.03 Aligned_cols=19 Identities=37% Similarity=0.529 Sum_probs=15.6
Q ss_pred eecccccccCHHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQILC 65 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~ 65 (153)
..|.+++|||+.+|..|+.
T Consensus 11 eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 11 EELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHTSTT-SHHHHHHHHH
T ss_pred HHHHhCCCcCHHHHHHHHh
Confidence 3588999999999999974
No 16
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=90.65 E-value=0.38 Score=40.72 Aligned_cols=49 Identities=29% Similarity=0.374 Sum_probs=41.3
Q ss_pred Cceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHh
Q 031757 42 DKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVS 90 (153)
Q Consensus 42 ~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~ 90 (153)
..+|.-+| +-|-|||.-+|..||-.+||+|. .+++||++|++.|.+.+.
T Consensus 164 ~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 216 (282)
T PRK13945 164 TRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAII 216 (282)
T ss_pred CccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 45666666 56889999999999999999965 679999999999987663
No 17
>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=90.55 E-value=0.4 Score=40.38 Aligned_cols=49 Identities=27% Similarity=0.423 Sum_probs=40.5
Q ss_pred Cceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHh
Q 031757 42 DKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVS 90 (153)
Q Consensus 42 ~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~ 90 (153)
+.+|.-+| +-+-|||.-+|..||-.++|+|. ++++||++|++.|-+.+.
T Consensus 155 ~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 207 (272)
T TIGR00577 155 KRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIK 207 (272)
T ss_pred CCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHH
Confidence 44555555 55679999999999999999965 679999999999987663
No 18
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=89.92 E-value=0.41 Score=37.05 Aligned_cols=61 Identities=10% Similarity=0.064 Sum_probs=49.4
Q ss_pred ecccCCCCceeeeecccccccCHHHHHHHHHHcCCCc----cccCCCCHHHHHHHHHHHhhccch
Q 031757 35 GNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGN----KLTKELTGVELNSLREEVSRYLTG 95 (153)
Q Consensus 35 ~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~----~~~~~Ls~~qi~~L~~~l~~~~i~ 95 (153)
.+.-+|-|..-..+|..++|||+..|..|++.-.+.+ ..+..+++.|.+.+.++.+++.+.
T Consensus 49 ~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV~ 113 (132)
T PRK02515 49 FGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDNFTVT 113 (132)
T ss_pred cCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcceeeC
Confidence 4666777777788899999999999999997555652 246889999999999999887654
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=89.05 E-value=0.071 Score=47.11 Aligned_cols=50 Identities=32% Similarity=0.480 Sum_probs=37.0
Q ss_pred CCceeeeeccccc-ccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 031757 41 NDKRLETSLQHVY-GIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS 90 (153)
Q Consensus 41 ~~k~i~~aLt~I~-GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~ 90 (153)
+...+..+|...+ |+|+.+|..+|.++|++ +..+.++++++++.|.+.+.
T Consensus 185 ~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~ 236 (455)
T PF05833_consen 185 KEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIR 236 (455)
T ss_dssp CG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHH
T ss_pred CcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHH
Confidence 5677888886666 99999999999999999 66789999999988876654
No 20
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=87.51 E-value=0.094 Score=41.44 Aligned_cols=48 Identities=19% Similarity=0.008 Sum_probs=42.2
Q ss_pred cchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCCccccccccCCCCcc
Q 031757 93 LTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRGQRTSTNARTRKGKR 142 (153)
Q Consensus 93 ~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarTak~~~ 142 (153)
.+.+|.+.....|+..+.++.+|.|- .++||+.||.|+.|+.++|...
T Consensus 69 ~i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRlkk 116 (152)
T KOG3311|consen 69 QILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERLKK 116 (152)
T ss_pred HHhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHHhh
Confidence 35678888888999999999999999 9999999999999999877443
No 21
>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=87.27 E-value=0.4 Score=28.05 Aligned_cols=21 Identities=33% Similarity=0.713 Sum_probs=15.2
Q ss_pred ecccccccCHHHHHHHHHHcCC
Q 031757 48 SLQHVYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lgi 69 (153)
.+++++|||+.++.. ++++||
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 444543
No 22
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=86.26 E-value=1.1 Score=41.62 Aligned_cols=49 Identities=35% Similarity=0.455 Sum_probs=41.9
Q ss_pred eeeeec-ccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhc
Q 031757 44 RLETSL-QHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSRY 92 (153)
Q Consensus 44 ~i~~aL-t~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~~ 92 (153)
++.-=| ..+-.||..+|..||..+|++ ++...+|+++|++.|.+.+.++
T Consensus 257 ~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 257 TLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred CHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 344334 678899999999999999999 6678999999999999999863
No 23
>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=85.48 E-value=0.11 Score=33.83 Aligned_cols=25 Identities=28% Similarity=0.385 Sum_probs=21.4
Q ss_pred eeeecccccccCHHHHHHHHHHcCCC
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
++.+|.+|.|||+..|..+... |+.
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~-G~~ 27 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEA-GIK 27 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHT-TCS
T ss_pred HHHhhccCCCCCHHHHHHHHhc-CCC
Confidence 4567899999999999999877 777
No 24
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=84.64 E-value=0.83 Score=35.43 Aligned_cols=44 Identities=18% Similarity=0.237 Sum_probs=37.8
Q ss_pred eecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 031757 47 TSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
--||.|.|||+.... +++-+||- ...+-.+|..|++.+.++|+-
T Consensus 67 DDLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~f 111 (133)
T COG3743 67 DDLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLNF 111 (133)
T ss_pred ccchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcCC
Confidence 469999999998875 56789997 778899999999999998863
No 25
>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=84.44 E-value=0.71 Score=30.02 Aligned_cols=36 Identities=17% Similarity=0.204 Sum_probs=21.5
Q ss_pred ecccccccCHHHHHHHHHHcCCCc---cc--cCCCCHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQILCDLNIGN---KL--TKELTGVELNS 84 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lgi~~---~~--~~~Ls~~qi~~ 84 (153)
.|++|+|||+.+|..... .|+-+ .+ -..||..|.-=
T Consensus 3 ~f~~I~GVG~~tA~~w~~-~G~rtl~Dl~~~~~~Lt~~Q~iG 43 (52)
T PF10391_consen 3 LFTGIWGVGPKTARKWYA-KGIRTLEDLRKSKSKLTWQQQIG 43 (52)
T ss_dssp HHHTSTT--HHHHHHHHH-TT--SHHHHHHGGCGS-HHHHHH
T ss_pred chhhcccccHHHHHHHHH-hCCCCHHHHhhhhccCCHHHHHH
Confidence 368999999999999998 88852 11 13666665433
No 26
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=81.90 E-value=1.2 Score=24.52 Aligned_cols=19 Identities=42% Similarity=0.504 Sum_probs=16.4
Q ss_pred ecccccccCHHHHHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~ 66 (153)
.|..++|||+..|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3688999999999999863
No 27
>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=80.73 E-value=1.2 Score=38.92 Aligned_cols=49 Identities=18% Similarity=0.300 Sum_probs=40.4
Q ss_pred CceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhc
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSRY 92 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~~ 92 (153)
++.+...|..+ +-.+++..+|+.+||+ ++++++|+++|++.|.+.|..|
T Consensus 283 ~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~~ 332 (400)
T TIGR00275 283 KKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKNW 332 (400)
T ss_pred hhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhCC
Confidence 45555555533 7899999999999999 6788999999999999999764
No 28
>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=79.79 E-value=2.2 Score=29.98 Aligned_cols=26 Identities=19% Similarity=0.402 Sum_probs=21.3
Q ss_pred CceeeeecccccccCHHHHHHHHHHc
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
+..|+++|+.|+|||...|..|++.-
T Consensus 22 ~~~Ir~gl~~Ikglg~~~a~~I~~~R 47 (90)
T PF14579_consen 22 NNAIRLGLSAIKGLGEEVAEKIVEER 47 (90)
T ss_dssp -TEEE-BGGGSTTS-HHHHHHHHHHH
T ss_pred CCEEeehHhhcCCCCHHHHHHHHHhH
Confidence 46899999999999999999999766
No 29
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=79.43 E-value=2.7 Score=36.13 Aligned_cols=54 Identities=26% Similarity=0.357 Sum_probs=43.9
Q ss_pred ccCCCCceeeeec---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHh
Q 031757 37 TEIPNDKRLETSL---QHVYGIGRSRAHQILCDLNIGNK-LTKELTGVELNSLREEVS 90 (153)
Q Consensus 37 tnl~~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~-~~~~Ls~~qi~~L~~~l~ 90 (153)
.-...+++|.-+| +-+-|||.-+|..+|=++||+|. .+++|+.+|++.|.+.+.
T Consensus 150 ~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~ 207 (273)
T COG0266 150 KLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK 207 (273)
T ss_pred HHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHH
Confidence 3344556677777 66889999999999999999955 679999999888877663
No 30
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.23 E-value=1.3 Score=35.74 Aligned_cols=18 Identities=28% Similarity=0.495 Sum_probs=13.1
Q ss_pred ecccccccCHHHHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQILC 65 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~ 65 (153)
+|++++|||+.+|.+||-
T Consensus 109 ~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 109 GLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHhhCCCCCHHHHHHHHH
Confidence 567777777777777773
No 31
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.49 E-value=1.6 Score=35.25 Aligned_cols=17 Identities=41% Similarity=0.645 Sum_probs=10.7
Q ss_pred ecccccccCHHHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQIL 64 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic 64 (153)
+|++++|||+.+|.+|+
T Consensus 109 ~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 109 VLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 45666666666666666
No 32
>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=76.31 E-value=2.4 Score=30.96 Aligned_cols=37 Identities=24% Similarity=0.202 Sum_probs=26.8
Q ss_pred eeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHH
Q 031757 46 ETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELN 83 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~ 83 (153)
...|+.|+|||+.+|.-+. .+||+ ..-+..-+++++-
T Consensus 11 ~~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly 48 (93)
T PF11731_consen 11 LSDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELY 48 (93)
T ss_pred HHHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHH
Confidence 3468999999999999887 99998 4444333455443
No 33
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.11 E-value=1.6 Score=35.39 Aligned_cols=20 Identities=35% Similarity=0.604 Sum_probs=15.9
Q ss_pred eecccccccCHHHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~~ 66 (153)
.+|++++|||+++|.+|+-.
T Consensus 108 ~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 46888888888888888843
No 34
>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=75.56 E-value=1.1 Score=36.29 Aligned_cols=29 Identities=31% Similarity=0.512 Sum_probs=24.1
Q ss_pred CCCceeeeecccccccCHHHHHHHHHHcC
Q 031757 40 PNDKRLETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 40 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
++...++..|.+++|||+.+|..++.-||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 55666678899999999999999987655
No 35
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.45 E-value=1.7 Score=35.24 Aligned_cols=19 Identities=26% Similarity=0.391 Sum_probs=15.6
Q ss_pred eecccccccCHHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQILC 65 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~ 65 (153)
.+|++++|||+.+|.+||-
T Consensus 107 ~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 107 RLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 3688888888888888883
No 36
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.41 E-value=1.9 Score=35.08 Aligned_cols=17 Identities=41% Similarity=0.741 Sum_probs=14.0
Q ss_pred ecccccccCHHHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQIL 64 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic 64 (153)
+|++++|||+++|.+|+
T Consensus 110 ~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 110 ALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHhcCCCcCHHHHHHHH
Confidence 67888888888888887
No 37
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.07 E-value=1.9 Score=35.21 Aligned_cols=17 Identities=35% Similarity=0.534 Sum_probs=11.6
Q ss_pred ecccccccCHHHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQIL 64 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic 64 (153)
+|++++|||+.+|.+|+
T Consensus 108 ~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 108 LISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 56666777777777666
No 38
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=73.76 E-value=2.1 Score=35.09 Aligned_cols=21 Identities=33% Similarity=0.653 Sum_probs=17.4
Q ss_pred eecccccccCHHHHHHHHHHc
Q 031757 47 TSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~~l 67 (153)
.+|++++|||+.+|.+||-.|
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 478999999999999998544
No 39
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=72.92 E-value=0.73 Score=36.96 Aligned_cols=47 Identities=21% Similarity=0.176 Sum_probs=34.4
Q ss_pred cccceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC
Q 031757 24 FHGLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 24 ~~~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
+++++.--.|..|-.=...+.++..|..|+|||+.+|..|+..+|.+
T Consensus 50 ~~~~rd~~~~l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~ 96 (192)
T PRK00116 50 HLVVREDAILLYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPE 96 (192)
T ss_pred EEEEechhHHHcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHH
Confidence 34555444555666644455666688999999999999999999864
No 40
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=71.25 E-value=6.4 Score=36.34 Aligned_cols=49 Identities=24% Similarity=0.304 Sum_probs=40.6
Q ss_pred ceeeeec-ccccccCHHHHHHHHHHcCCC----ccccCCCCHHHHHHHHHHHhh
Q 031757 43 KRLETSL-QHVYGIGRSRAHQILCDLNIG----NKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 43 k~i~~aL-t~I~GIG~~~A~~Ic~~lgi~----~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
+++.-=| ..+-.||..+|..||..+|++ ++...+|+++|++.|.+.+.+
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~ 300 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE 300 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh
Confidence 3444344 678899999999999999998 446799999999999999875
No 41
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.22 E-value=1.5 Score=35.40 Aligned_cols=43 Identities=23% Similarity=0.257 Sum_probs=36.1
Q ss_pred eeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC
Q 031757 28 RVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 28 ~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
++--..++|-.=...+.++.-|.++.|||+.+|..|+..++.+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 54 REDALSLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 3334567888888999999999999999999999999877654
No 42
>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=69.95 E-value=5.1 Score=35.78 Aligned_cols=51 Identities=24% Similarity=0.307 Sum_probs=42.4
Q ss_pred CCCceeeeecccccccCHHHHHHHHHHcCC-C-ccccCCCCHHHHHHHHHHHhhc
Q 031757 40 PNDKRLETSLQHVYGIGRSRAHQILCDLNI-G-NKLTKELTGVELNSLREEVSRY 92 (153)
Q Consensus 40 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi-~-~~~~~~Ls~~qi~~L~~~l~~~ 92 (153)
.+++.+...|..+ +-++++..+|+.+++ + +.++.+|++++++.|.+.|..|
T Consensus 288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~~ 340 (409)
T PF03486_consen 288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKRF 340 (409)
T ss_dssp TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHCE
T ss_pred HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHhC
Confidence 4667777778776 899999999999999 7 6788999999999999999764
No 43
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.76 E-value=3.5 Score=33.24 Aligned_cols=18 Identities=33% Similarity=0.593 Sum_probs=13.6
Q ss_pred eecccccccCHHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQILC 65 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~ 65 (153)
.+| +++|||+.+|.+||-
T Consensus 108 ~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred hhe-ECCCCcHHHHHHHHH
Confidence 466 788888888888873
No 44
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.93 E-value=3.6 Score=33.21 Aligned_cols=18 Identities=33% Similarity=0.575 Sum_probs=16.2
Q ss_pred eecccccccCHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQIL 64 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic 64 (153)
.+|++++|||+.+|.+|+
T Consensus 108 ~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 468999999999999976
No 45
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=64.70 E-value=5.2 Score=25.85 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=17.8
Q ss_pred ecccccccCHHHHHHHHHHc
Q 031757 48 SLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~l 67 (153)
.|..++|||+..|..|+..+
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 48999999999999998764
No 46
>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=64.50 E-value=1.5 Score=35.40 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=33.7
Q ss_pred cceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcC
Q 031757 26 GLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 26 ~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
+.++--..++|-.=...+.++..|.++.|||+.+|..|+..++
T Consensus 51 ~vred~~~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~ 93 (191)
T TIGR00084 51 VVREDAELLFGFNTLEERELFKELIKVNGVGPKLALAILSNMS 93 (191)
T ss_pred EEecCCceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCC
Confidence 3344445778888888899999999999999999999965443
No 47
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=63.46 E-value=6.6 Score=32.66 Aligned_cols=49 Identities=20% Similarity=0.360 Sum_probs=36.4
Q ss_pred CceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
.|++..+|..+++. ...+..+++.+|++ +.++.+|+.+|...|.+.++.
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 34455566665442 24567789999999 779999999999999887754
No 48
>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=63.46 E-value=5.1 Score=26.67 Aligned_cols=19 Identities=37% Similarity=0.399 Sum_probs=16.6
Q ss_pred ecccccccCHHHHHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~ 66 (153)
+|+.++|||..+|..|-.-
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 6899999999999998654
No 49
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=63.08 E-value=3.7 Score=30.90 Aligned_cols=25 Identities=28% Similarity=0.368 Sum_probs=21.5
Q ss_pred CceeeeecccccccCHHHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
...+...|++++|||+.+|..++..
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHH
Confidence 3567888999999999999998864
No 50
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=62.57 E-value=6.3 Score=27.34 Aligned_cols=20 Identities=30% Similarity=0.507 Sum_probs=18.1
Q ss_pred ecccccccCHHHHHHHHHHc
Q 031757 48 SLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~l 67 (153)
-|++|+|||..+|..|+..+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 47899999999999999877
No 51
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=61.31 E-value=5 Score=26.58 Aligned_cols=18 Identities=17% Similarity=0.338 Sum_probs=15.0
Q ss_pred cccccCHHHHHHHHHHcC
Q 031757 51 HVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 51 ~I~GIG~~~A~~Ic~~lg 68 (153)
.|+|||...|..+++.+|
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 699999999999999888
No 52
>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=60.16 E-value=12 Score=24.59 Aligned_cols=47 Identities=15% Similarity=0.184 Sum_probs=30.2
Q ss_pred Cceeeeeccc-ccccCHHHHHHHHHH---cC-CCc----cccCCCCHHHHHHHHHH
Q 031757 42 DKRLETSLQH-VYGIGRSRAHQILCD---LN-IGN----KLTKELTGVELNSLREE 88 (153)
Q Consensus 42 ~k~i~~aLt~-I~GIG~~~A~~Ic~~---lg-i~~----~~~~~Ls~~qi~~L~~~ 88 (153)
|..-.-.|.. +.|||...|.+|+.. .| +.+ ..+..+++.-.++|..+
T Consensus 11 Nta~~~~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 11 NTATAEELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred cCCCHHHHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHHHHHHHhh
Confidence 3344446778 999999999999988 44 431 12344555555555544
No 53
>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=59.53 E-value=8.1 Score=26.39 Aligned_cols=19 Identities=32% Similarity=0.422 Sum_probs=16.8
Q ss_pred ccccccCHHHHHHHHHHcC
Q 031757 50 QHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~lg 68 (153)
..|+|||+.+|..++...|
T Consensus 25 ~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 25 PGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCcccHHHHHHHHHHhC
Confidence 4689999999999998866
No 54
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.24 E-value=3.3 Score=33.73 Aligned_cols=45 Identities=16% Similarity=0.141 Sum_probs=36.1
Q ss_pred cceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC
Q 031757 26 GLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 26 ~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
+.++--..++|-.=...+.++.-|.++.|||+.+|..|+..++.+
T Consensus 53 ~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 53 VVREDALELFGFATWDERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred EEecCcceeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 333444567888888889999999999999999999999766544
No 55
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=58.09 E-value=7.2 Score=33.83 Aligned_cols=40 Identities=20% Similarity=0.229 Sum_probs=29.4
Q ss_pred eeeecccccccCHHHHHHHHHHcCCCc--c--cc--CCCCHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIGN--K--LT--KELTGVELNSL 85 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~~--~--~~--~~Ls~~qi~~L 85 (153)
....|.+|+|||+.+|..+-+ +|+.+ . .. ..|+.+|+.-|
T Consensus 87 ~l~~l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~~~~l~~~q~~gl 132 (334)
T smart00483 87 SLKLFTNVFGVGPKTAAKWYR-KGIRTLEELKKNKELKLTKQQKAGL 132 (334)
T ss_pred HHHHHHccCCcCHHHHHHHHH-hCCCCHHHHHhcccccCCHHHHHHH
Confidence 345679999999999999999 99973 1 11 25777774444
No 56
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=57.64 E-value=6.8 Score=33.32 Aligned_cols=46 Identities=20% Similarity=0.363 Sum_probs=38.9
Q ss_pred CCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 031757 41 NDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 41 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
..|.+..+|...++ ...+|..+|+| +.++.+|+.+|+-.|.+.+..
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 35677778877777 88999999999 678999999999999988754
No 57
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=57.12 E-value=9.7 Score=22.78 Aligned_cols=17 Identities=35% Similarity=0.495 Sum_probs=15.0
Q ss_pred ccccccCHHHHHHHHHH
Q 031757 50 QHVYGIGRSRAHQILCD 66 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~ 66 (153)
..|+|||..+|..++++
T Consensus 19 ~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCcccHHHHHHHHHh
Confidence 57899999999999875
No 58
>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=56.71 E-value=7 Score=31.47 Aligned_cols=18 Identities=28% Similarity=0.636 Sum_probs=16.6
Q ss_pred eecccccccCHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQIL 64 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic 64 (153)
.+|++++|||+.+|.+|+
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 468899999999999999
No 59
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.44 E-value=3 Score=33.60 Aligned_cols=43 Identities=16% Similarity=0.211 Sum_probs=35.1
Q ss_pred cceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcC
Q 031757 26 GLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 26 ~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
+.++--..++|-.=...+.++.-|.++.|||+.+|..|+..+.
T Consensus 52 ~vrEd~~~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~~ 94 (183)
T PRK14601 52 IIKEDSNKLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSSLD 94 (183)
T ss_pred EEecCCceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC
Confidence 3344445778888889999999999999999999999985543
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=56.42 E-value=7.2 Score=29.07 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=19.5
Q ss_pred eeeecccccccCHHHHHHHHHHc
Q 031757 45 LETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
....|.+++|||+.+|..+|...
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 45678999999999999988764
No 61
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.07 E-value=2.9 Score=33.73 Aligned_cols=43 Identities=21% Similarity=0.247 Sum_probs=35.0
Q ss_pred ceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCC
Q 031757 27 LRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 27 i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 69 (153)
.++--..++|-.=...+.++.-|.++.|||+.+|..|+..+..
T Consensus 53 vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~~ 95 (188)
T PRK14606 53 VSQDGITLYGFSNERKKELFLSLTKVSRLGPKTALKIISNEDA 95 (188)
T ss_pred EecCCceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCH
Confidence 3444457788888889999999999999999999999865443
No 62
>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=55.48 E-value=8.8 Score=32.86 Aligned_cols=40 Identities=25% Similarity=0.286 Sum_probs=28.2
Q ss_pred eeecccccccCHHHHHHHHHHcCCCc--c--cc--CCCCHHHHHHHH
Q 031757 46 ETSLQHVYGIGRSRAHQILCDLNIGN--K--LT--KELTGVELNSLR 86 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~lgi~~--~--~~--~~Ls~~qi~~L~ 86 (153)
...|.+|+|||+.+|..+. .+|+.+ . .. ..+++.|+.-|.
T Consensus 84 l~~l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~g~k~~~~i~~gl~ 129 (307)
T cd00141 84 LLLLLRVPGVGPKTARKLY-ELGIRTLEDLRKAAGAKLEQNILIGLE 129 (307)
T ss_pred HHHHHcCCCCCHHHHHHHH-HcCCCCHHHHHHHhccccHHHHHHHHH
Confidence 3456899999999999999 999973 1 12 355555555544
No 63
>PRK08609 hypothetical protein; Provisional
Probab=53.28 E-value=10 Score=35.34 Aligned_cols=24 Identities=17% Similarity=0.354 Sum_probs=22.1
Q ss_pred eecccccccCHHHHHHHHHHcCCC
Q 031757 47 TSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
..|++|+|||+.+|..+-+.+||.
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Confidence 467899999999999999999996
No 64
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.90 E-value=3.6 Score=33.40 Aligned_cols=41 Identities=24% Similarity=0.196 Sum_probs=33.6
Q ss_pred eeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcC
Q 031757 28 RVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 28 ~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
++--..++|-.=...+.++.-|.++.|||+.+|..|+..++
T Consensus 53 rEd~~~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~ 93 (197)
T PRK14603 53 REDALSLYGFPDEDSLELFELLLGVSGVGPKLALALLSALP 93 (197)
T ss_pred ccCCceeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCC
Confidence 33345678888888999999999999999999999985443
No 65
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.55 E-value=4 Score=32.92 Aligned_cols=40 Identities=18% Similarity=0.078 Sum_probs=33.8
Q ss_pred eeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC
Q 031757 31 GLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 31 ~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
...++|-.=...+.++.-|.++.|||+.+|..|+..++.+
T Consensus 57 ~~~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 57 VTQLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred CceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 3457888888899999999999999999999999765443
No 66
>PRK10702 endonuclease III; Provisional
Probab=51.05 E-value=8.4 Score=31.44 Aligned_cols=23 Identities=26% Similarity=0.419 Sum_probs=19.5
Q ss_pred eeeecccccccCHHHHHHHHHHc
Q 031757 45 LETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
....|.+++|||+.+|..|+..+
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHHH
Confidence 46789999999999999998543
No 67
>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=50.96 E-value=9.3 Score=30.24 Aligned_cols=23 Identities=26% Similarity=0.328 Sum_probs=19.2
Q ss_pred eeeecccccccCHHHHHHHHHHc
Q 031757 45 LETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
....|.+++|||+.+|..+|...
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHH
Confidence 45679999999999999998543
No 68
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=49.13 E-value=17 Score=33.04 Aligned_cols=60 Identities=17% Similarity=0.230 Sum_probs=40.6
Q ss_pred eeeeeEEecccCCC--------CceeeeecccccccCHHHHHHHHHHc---C-CCc-----ccc--CCCCHHHHHHHHH
Q 031757 28 RVQGLRVGNTEIPN--------DKRLETSLQHVYGIGRSRAHQILCDL---N-IGN-----KLT--KELTGVELNSLRE 87 (153)
Q Consensus 28 ~~~~vrI~~tnl~~--------~k~i~~aLt~I~GIG~~~A~~Ic~~l---g-i~~-----~~~--~~Ls~~qi~~L~~ 87 (153)
+.|-+.|+..||+. +..|+++|..|+|||...+..|.+.= | +.+ .++ +.++...++.|..
T Consensus 87 r~~GI~VlpPdIN~S~~~Ftv~~~~IrfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rvd~~~vnkr~lE~LIk 165 (449)
T PRK07373 87 QKMGIEVEPPDINRSGKDFTPVGEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRVDLRVVNRRALETLIY 165 (449)
T ss_pred HHcCCeEeCCceeccCCccEEECCEEEEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHhCcccCCHHHHHHHHH
Confidence 34456666655442 34799999999999999999997532 3 221 233 4678887777764
No 69
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=48.52 E-value=13 Score=30.35 Aligned_cols=46 Identities=17% Similarity=0.291 Sum_probs=34.0
Q ss_pred CCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHH
Q 031757 41 NDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREE 88 (153)
Q Consensus 41 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~ 88 (153)
..|++..+|..+++- ..+..++..+|++ +.+..+|+.+|+..|.+.
T Consensus 206 rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 206 RRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred chHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 445566667665432 3456778889998 789999999999988764
No 70
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=48.50 E-value=1.6 Score=35.74 Aligned_cols=45 Identities=24% Similarity=0.200 Sum_probs=36.4
Q ss_pred cceeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCCC
Q 031757 26 GLRVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 26 ~i~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
+.++-...++|-.=...+.++..|.++-|||++.|.+|+..++.+
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~ 96 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLDPE 96 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCHH
Confidence 444445667888888899999999999999999999999655443
No 71
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=47.71 E-value=21 Score=33.39 Aligned_cols=43 Identities=26% Similarity=0.308 Sum_probs=37.1
Q ss_pred ccccccCHHHHHHHHHHcCCC-ccccCCCC----HHHHHHHHHHHhhc
Q 031757 50 QHVYGIGRSRAHQILCDLNIG-NKLTKELT----GVELNSLREEVSRY 92 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls----~~qi~~L~~~l~~~ 92 (153)
..+--||..+|..+|+.+|++ ++...+|+ .++.+.|.+.+.+|
T Consensus 264 sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 264 SEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred HHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 556679999999999999999 66778888 99999999988763
No 72
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.17 E-value=5.3 Score=32.65 Aligned_cols=41 Identities=20% Similarity=0.231 Sum_probs=33.9
Q ss_pred eeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHcCC
Q 031757 29 VQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 29 ~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 69 (153)
+--..++|-.=...+.++.-|.++.|||+..|..|+..+..
T Consensus 54 ED~~~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~~ 94 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGIKY 94 (196)
T ss_pred cCCceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCH
Confidence 33356788888899999999999999999999999865433
No 73
>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=46.84 E-value=11 Score=31.18 Aligned_cols=50 Identities=20% Similarity=0.294 Sum_probs=39.1
Q ss_pred CCCceeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 031757 40 PNDKRLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 40 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
...|++..+|..+++ ......+.+.+||+ +.++.+|+.+|..+|.+++++
T Consensus 212 ~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~k 262 (262)
T PF00398_consen 212 QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLNK 262 (262)
T ss_dssp TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHHH
T ss_pred CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhhC
Confidence 467788888887754 33456677779999 679999999999999988753
No 74
>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=46.82 E-value=13 Score=27.71 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=26.2
Q ss_pred cCCCCceeeeecccccccCHHHHHHHHHHcCC
Q 031757 38 EIPNDKRLETSLQHVYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 38 nl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 69 (153)
.++-|..-...|..++|||...|..|.....-
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 45566667778999999999999999988743
No 75
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=46.53 E-value=46 Score=28.25 Aligned_cols=18 Identities=33% Similarity=0.468 Sum_probs=16.9
Q ss_pred ccccCHHHHHHHHHHcCC
Q 031757 52 VYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 52 I~GIG~~~A~~Ic~~lgi 69 (153)
++|||+.+|..++...|.
T Consensus 203 V~GIG~ktA~~Ll~~~gs 220 (310)
T COG0258 203 VKGIGPKTALKLLQEYGS 220 (310)
T ss_pred CCCcCHHHHHHHHHHhCC
Confidence 999999999999999993
No 76
>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=45.21 E-value=13 Score=31.64 Aligned_cols=22 Identities=32% Similarity=0.309 Sum_probs=19.0
Q ss_pred eeecccccccCHHHHHHHHHHc
Q 031757 46 ETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
...|.+++|||+.+|..|+..+
T Consensus 104 ~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 104 FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 5679999999999999998643
No 77
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=44.10 E-value=18 Score=23.77 Aligned_cols=48 Identities=19% Similarity=0.167 Sum_probs=29.8
Q ss_pred CCCceeeeecccccccCHHHHHHHHHHc----CCCc----cccCCCCHHHHHHHHH
Q 031757 40 PNDKRLETSLQHVYGIGRSRAHQILCDL----NIGN----KLTKELTGVELNSLRE 87 (153)
Q Consensus 40 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~l----gi~~----~~~~~Ls~~qi~~L~~ 87 (153)
|-|..=...|..++|||...|..|.+.= ++.+ ..+..++++.+++|..
T Consensus 7 diN~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 7 DINTASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp ETTTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred cCccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 4455556678999999999999999655 4531 2456788887777654
No 78
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.55 E-value=6.3 Score=31.95 Aligned_cols=40 Identities=25% Similarity=0.295 Sum_probs=33.0
Q ss_pred eeeeeEEecccCCCCceeeeecccccccCHHHHHHHHHHc
Q 031757 28 RVQGLRVGNTEIPNDKRLETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 28 ~~~~vrI~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
++--..++|-.=...+.++.-|.++.|||+.+|..|+..+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~ 93 (195)
T PRK14604 54 REDALTLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSG 93 (195)
T ss_pred ecCCceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 3334567888888889999999999999999999998654
No 79
>PF04001 Vhr1: Transcription factor Vhr1; InterPro: IPR007147 This is a family of proteins of unknown function found in yeast.
Probab=43.25 E-value=18 Score=26.47 Aligned_cols=59 Identities=17% Similarity=0.302 Sum_probs=32.9
Q ss_pred HHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhccchHHHHHHHHHhHHHHHhhhhccCCccCCCCcc
Q 031757 59 RAHQILCDLNIG-NKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPC 126 (153)
Q Consensus 59 ~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPV 126 (153)
+.+.|-++|++. ..+-+.++.--++.|.. |.++.--..+..++|+..-.| +|-.+|+|+
T Consensus 8 ~Th~IR~~LnF~De~~WK~FSsRRLELId~----~~Ls~~KASEQd~~I~~iA~i-----LR~Ef~Yp~ 67 (95)
T PF04001_consen 8 TTHKIREQLNFHDERKWKRFSSRRLELIDK----FDLSSRKASEQDDNIRQIAEI-----LRTEFGYPE 67 (95)
T ss_pred hhHHHHHHhCCccHHHHHHHHHHHHHHHHH----cCcccchhhhhHHHHHHHHHH-----HHHHhCCCh
Confidence 456777888886 33446666555544433 333333334455556655555 666666664
No 80
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=43.15 E-value=22 Score=33.21 Aligned_cols=46 Identities=22% Similarity=0.351 Sum_probs=38.6
Q ss_pred eeeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHH
Q 031757 44 RLETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEV 89 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l 89 (153)
-+...|..+.|+|.-+|..+|-++|++ ...+.++.++++..+...+
T Consensus 187 ~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~ 233 (564)
T COG1293 187 DIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREAL 233 (564)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHH
Confidence 345667889999999999999999999 4457999999999987644
No 81
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=42.74 E-value=15 Score=32.29 Aligned_cols=45 Identities=22% Similarity=0.195 Sum_probs=37.7
Q ss_pred eeeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS 90 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~ 90 (153)
..--|+.|.|||+..+. .|..+|+. ...+-.++++++..+...+.
T Consensus 261 ~~DdL~~I~GiGp~~e~-~L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 261 APDDLKKLTGVSPQIEK-KLNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred CchhhhhhccCChhhhh-hhhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 34569999999998765 57889998 77889999999998888774
No 82
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=42.46 E-value=6.2 Score=37.35 Aligned_cols=61 Identities=21% Similarity=0.320 Sum_probs=42.8
Q ss_pred cccceeeeeEE---ecccCCCCceeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 24 FHGLRVQGLRV---GNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 24 ~~~i~~~~vrI---~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
.|+++..-.|. ++-..-..+.+.-.|..|.|||+..|..|++.+|=- ..+..-+.+++..+
T Consensus 543 l~~iRDEaHrfAi~yhr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~-~~i~~As~eeL~~v 606 (621)
T PRK14671 543 LQQLRDEAHRFAITYHRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFGSV-EKVAKASLEELAAV 606 (621)
T ss_pred EEEEehHHHHHHHHhChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcCCH-HHHHhCCHHHHHHH
Confidence 34555555566 677777778888889999999999999999999621 22223356666544
No 83
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=42.36 E-value=16 Score=30.27 Aligned_cols=23 Identities=35% Similarity=0.466 Sum_probs=19.0
Q ss_pred eeeeecccccccCHHHHHHHHHH
Q 031757 44 RLETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
.....|.+++|||+.+|..|+.-
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLly 140 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCY 140 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHH
Confidence 34567999999999999998753
No 84
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=41.92 E-value=16 Score=29.19 Aligned_cols=22 Identities=36% Similarity=0.578 Sum_probs=19.1
Q ss_pred ecccccccCHHHHHHHHHHcCC
Q 031757 48 SLQHVYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lgi 69 (153)
.|++++|||+.+|..|+..+.-
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHHH
Confidence 5899999999999999976653
No 85
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=41.65 E-value=19 Score=29.57 Aligned_cols=27 Identities=22% Similarity=0.327 Sum_probs=21.8
Q ss_pred eeeeecc-cccccCHHHHHHHHHHcCCC
Q 031757 44 RLETSLQ-HVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 44 ~i~~aLt-~I~GIG~~~A~~Ic~~lgi~ 70 (153)
..+..|. +++|||+.+|..|+...|..
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 5666788 99999999999999655553
No 86
>PRK10880 adenine DNA glycosylase; Provisional
Probab=41.05 E-value=15 Score=32.47 Aligned_cols=22 Identities=32% Similarity=0.339 Sum_probs=19.4
Q ss_pred eeeecccccccCHHHHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
....|.+++|||+.+|..||.-
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHHH
Confidence 4578999999999999999963
No 87
>PRK13910 DNA glycosylase MutY; Provisional
Probab=39.04 E-value=18 Score=31.05 Aligned_cols=21 Identities=43% Similarity=0.542 Sum_probs=18.9
Q ss_pred eeecccccccCHHHHHHHHHH
Q 031757 46 ETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
...|.+++|||+.+|..|+..
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 678999999999999999864
No 88
>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=38.97 E-value=60 Score=31.18 Aligned_cols=39 Identities=13% Similarity=0.245 Sum_probs=27.9
Q ss_pred cccccCHHHHHHHHHHcCCC-cc-------c---cCCCCHHHHHHHHHHH
Q 031757 51 HVYGIGRSRAHQILCDLNIG-NK-------L---TKELTGVELNSLREEV 89 (153)
Q Consensus 51 ~I~GIG~~~A~~Ic~~lgi~-~~-------~---~~~Ls~~qi~~L~~~l 89 (153)
.|+|||+.+|..|.+.+|.+ -. . +..+++...+.|.+.+
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 49999999999999999987 11 1 2346666666665433
No 89
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=38.83 E-value=23 Score=29.90 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=15.2
Q ss_pred ecccccccCHHHHHHHHHHcCCC
Q 031757 48 SLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
.|..|.|||+..+..+.+. ||.
T Consensus 4 ~L~~IpGIG~krakkLl~~-GF~ 25 (232)
T PRK12766 4 ELEDISGVGPSKAEALREA-GFE 25 (232)
T ss_pred ccccCCCcCHHHHHHHHHc-CCC
Confidence 4677778888777777654 555
No 90
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=38.83 E-value=31 Score=33.35 Aligned_cols=59 Identities=19% Similarity=0.206 Sum_probs=36.2
Q ss_pred eeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhhccchHHHHHHHHHhHHHH
Q 031757 44 RLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERL 109 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~~~i~~dL~~~~~~dI~rL 109 (153)
.+.-.|..|+|||+..+..+++.+| +-..+.+-+.+++.++. -++..+...+.+-++++
T Consensus 634 ~~~s~L~~IPGIGpkr~k~LL~~FG-Sle~I~~AS~eELa~V~------Gig~k~Ae~I~~~L~~~ 692 (694)
T PRK14666 634 ALTGELQRVEGIGPATARLLWERFG-SLQAMAAAGEEGLAAVP------GIGPARAAALHEHLKTL 692 (694)
T ss_pred hhHhHHhhCCCCCHHHHHHHHHHhC-CHHHHHhcCHHHHHhcC------CcCHHHHHHHHHHHHHh
Confidence 3456788999999999999999988 42333444555554431 13444444444444443
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=38.20 E-value=19 Score=30.99 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=20.1
Q ss_pred eeeeecccccccCHHHHHHHHHH
Q 031757 44 RLETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
.+...|+.++|||+.+|..||-.
T Consensus 217 ~~~~~L~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 217 DAREALCELPGVGPKVADCICLM 239 (310)
T ss_pred HHHHHHHhCCCccHHHHHHHHHH
Confidence 46788999999999999999865
No 92
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=37.38 E-value=21 Score=30.33 Aligned_cols=22 Identities=32% Similarity=0.306 Sum_probs=19.5
Q ss_pred eeeecccccccCHHHHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
+...|..++|||+.+|..|+-.
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHH
Confidence 5678999999999999998866
No 93
>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=36.98 E-value=29 Score=33.10 Aligned_cols=73 Identities=18% Similarity=0.203 Sum_probs=43.0
Q ss_pred ccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhccchHHHHHHHHHhHHHHHhhhhccCCccCCCCccCC
Q 031757 50 QHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCYRGIRHSQGLPCRG 128 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~GLPVRG 128 (153)
-+|.|+|+.++.++.+..++. ..-+-.|+.+++..|.. ++...-..+.+.|+.-+...-.| +-..+|+|--|
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~G------fG~Ksa~nIl~~Ie~sk~~~l~r-~L~aLgIpgVG 507 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEG------FGEKSAQNLLNAIEKSKEKPLAR-LLFALGIRHVG 507 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccC------ccHHHHHHHHHHHHHhccCcHHH-HHhhccCCCcC
Confidence 469999999999999999887 33334777776665532 23333334444444443322122 44555555555
Q ss_pred c
Q 031757 129 Q 129 (153)
Q Consensus 129 Q 129 (153)
.
T Consensus 508 ~ 508 (652)
T TIGR00575 508 E 508 (652)
T ss_pred H
Confidence 4
No 94
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=36.72 E-value=34 Score=27.82 Aligned_cols=25 Identities=16% Similarity=0.355 Sum_probs=22.8
Q ss_pred eeecccccccCHHHHHHHHHHcCCC
Q 031757 46 ETSLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
.+++|..+|.|++++...++.+|++
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 4688999999999999999999987
No 95
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.37 E-value=34 Score=28.05 Aligned_cols=72 Identities=26% Similarity=0.363 Sum_probs=47.4
Q ss_pred eeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh--------------------------------
Q 031757 44 RLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR-------------------------------- 91 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~-------------------------------- 91 (153)
.+..+|.+++|||++.|.++.--+= .-.+++.+.|.+.|..
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA~~ll-------~~~~~~~~~la~ai~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~ 80 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLAFHLL-------KRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV 80 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHH-------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCCCCCCCCCCCE
Confidence 3456789999999999999874432 2245566666555531
Q ss_pred -ccchHHHHHHHHHhHHHHHhhhhccCCccCCC---CccCC
Q 031757 92 -YLTGEDLRRCIKNDVERLVDIQCYRGIRHSQG---LPCRG 128 (153)
Q Consensus 92 -~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~G---LPVRG 128 (153)
-.||+. .|+.-+-+.+.|+|.=|-+| =|+-|
T Consensus 81 iCVVE~~------~Dv~aiE~~~~y~G~YhVL~G~iSPldg 115 (195)
T TIGR00615 81 ICVVEDP------KDVFALEKTKEFRGRYHVLGGHISPLDG 115 (195)
T ss_pred EEEECCH------HHHHHHHhhCccceEEEEccCccCccCC
Confidence 123332 35556777899999999987 45444
No 96
>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=36.27 E-value=27 Score=25.57 Aligned_cols=61 Identities=10% Similarity=0.062 Sum_probs=43.8
Q ss_pred ecccCCCCceeeeecccccccCHHHHHHHHHHcCCCc--c--ccCCCCHHHHHHHHHHHhhccch
Q 031757 35 GNTEIPNDKRLETSLQHVYGIGRSRAHQILCDLNIGN--K--LTKELTGVELNSLREEVSRYLTG 95 (153)
Q Consensus 35 ~~tnl~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~--~--~~~~Ls~~qi~~L~~~l~~~~i~ 95 (153)
+|..||-|-.-..+.++.+|.=+..|..|+.-.=.++ . .+-.||+.|-+.|.+..++|.+.
T Consensus 11 ~G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~Ftv~ 75 (93)
T PF06514_consen 11 LGQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNFTVT 75 (93)
T ss_dssp CCTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGEE--
T ss_pred cCCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccceec
Confidence 3456667777788999999999999999999887762 2 35789999999999999987654
No 97
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=35.98 E-value=21 Score=25.11 Aligned_cols=24 Identities=33% Similarity=0.394 Sum_probs=18.6
Q ss_pred eeccc-ccccCHHHHHHHHHHcCCC
Q 031757 47 TSLQH-VYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 47 ~aLt~-I~GIG~~~A~~Ic~~lgi~ 70 (153)
+.|.. |.|||..+|-.|..++|++
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 9999999999999999987
No 98
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=35.49 E-value=49 Score=30.13 Aligned_cols=50 Identities=18% Similarity=0.192 Sum_probs=42.1
Q ss_pred CCCceeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh
Q 031757 40 PNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 40 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
.+++.+..+|.. .++.+.+..++.+.||.+....+|++.|+++|.+.|..
T Consensus 283 ~~~kslkn~L~~--~lp~rlv~~~l~~~~i~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 283 NPKKSLKNALAK--LLPKRLVEFLLERAGIPDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred ChhhHHHHHHHH--HhhhHHHHHHHHhccCCCcchhhcCHHHHHHHHHHHhc
Confidence 456666666654 47899999999999997778899999999999999975
No 99
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.86 E-value=24 Score=30.19 Aligned_cols=25 Identities=28% Similarity=0.255 Sum_probs=20.7
Q ss_pred CceeeeecccccccCHHHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCD 66 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~ 66 (153)
...+.-.|++|+|||+-+|..++-.
T Consensus 193 ~e~a~e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 193 DEEAIEELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHHH
Confidence 3446778999999999999998854
No 100
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=34.37 E-value=34 Score=28.21 Aligned_cols=67 Identities=22% Similarity=0.366 Sum_probs=47.0
Q ss_pred eeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh--------------------------------
Q 031757 44 RLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR-------------------------------- 91 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~-------------------------------- 91 (153)
.+..+|.+.+|||++.|..+.--|- +.++++++.|.+.|..
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~AfhLL-------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~~ 81 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAFHLL-------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKSQ 81 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHHHHH-------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCce
Confidence 3557899999999999999985443 3456677777665531
Q ss_pred -ccchHHHHHHHHHhHHHHHhhhhccCCccCCC
Q 031757 92 -YLTGEDLRRCIKNDVERLVDIQCYRGIRHSQG 123 (153)
Q Consensus 92 -~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~G 123 (153)
-.+|. -.|+..+-+.+.|+|.=|-+|
T Consensus 82 icVVe~------p~Dv~a~E~~~~f~G~YhVL~ 108 (198)
T COG0353 82 LCVVEE------PKDVLALEKTGEFRGLYHVLG 108 (198)
T ss_pred EEEEcc------hHHHHHHHHhcccCeeEEEec
Confidence 01222 246667888899999999877
No 101
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=34.15 E-value=23 Score=29.29 Aligned_cols=25 Identities=28% Similarity=0.426 Sum_probs=20.5
Q ss_pred eeecccccccCHHHHHHHHHH-cCCC
Q 031757 46 ETSLQHVYGIGRSRAHQILCD-LNIG 70 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~-lgi~ 70 (153)
..+|.+.+|||+.+|+.++.. .|.+
T Consensus 108 ~~eL~~LPGVGrKTAnvVL~~a~g~p 133 (211)
T COG0177 108 REELLSLPGVGRKTANVVLSFAFGIP 133 (211)
T ss_pred HHHHHhCCCcchHHHHHHHHhhcCCC
Confidence 457899999999999999876 4444
No 102
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=33.78 E-value=86 Score=22.98 Aligned_cols=17 Identities=24% Similarity=0.235 Sum_probs=13.7
Q ss_pred CCCCHHHHHHHHHHHhh
Q 031757 75 KELTGVELNSLREEVSR 91 (153)
Q Consensus 75 ~~Ls~~qi~~L~~~l~~ 91 (153)
..||++|.+.|.++|..
T Consensus 1 s~Lt~eE~~~I~~Vl~R 17 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQR 17 (118)
T ss_dssp TTS-CHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 36999999999999975
No 103
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=32.11 E-value=38 Score=28.20 Aligned_cols=43 Identities=21% Similarity=0.377 Sum_probs=36.6
Q ss_pred eecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 031757 47 TSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS 90 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~ 90 (153)
-.|+.|.|||+..+.. +..+|+. ...+-.++++++..+...+.
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 4699999999998876 5678998 67889999999999988774
No 104
>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=31.05 E-value=38 Score=27.86 Aligned_cols=20 Identities=30% Similarity=0.488 Sum_probs=16.8
Q ss_pred cccccccCHHHHHHHHHHcC
Q 031757 49 LQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 49 Lt~I~GIG~~~A~~Ic~~lg 68 (153)
+..|+|||+.+|..++++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34679999999999998866
No 105
>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=30.97 E-value=50 Score=21.53 Aligned_cols=19 Identities=16% Similarity=0.156 Sum_probs=17.6
Q ss_pred ccccCHHHHHHHHHHcCCC
Q 031757 52 VYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 52 I~GIG~~~A~~Ic~~lgi~ 70 (153)
--||+...-+.+|.++||.
T Consensus 24 ~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 24 ELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred HhCCCHHHHHHHHHHcCCC
Confidence 4699999999999999998
No 106
>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=30.58 E-value=67 Score=27.03 Aligned_cols=66 Identities=12% Similarity=0.092 Sum_probs=46.3
Q ss_pred CceeeeecccccccCHHHHHHHHHHcCCC---c--cc--------cCCCCHHHHHHHHHHHhh----ccchHHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDLNIG---N--KL--------TKELTGVELNSLREEVSR----YLTGEDLRRCIKN 104 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~---~--~~--------~~~Ls~~qi~~L~~~l~~----~~i~~dL~~~~~~ 104 (153)
...+..-=-..+|+|.....+|..++|+= | .. -..||++|++.|-++... ..+.+.-+.+++.
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 44455555677899999999999999993 4 11 246999999999999874 3455555555554
Q ss_pred hHH
Q 031757 105 DVE 107 (153)
Q Consensus 105 dI~ 107 (153)
-++
T Consensus 176 aln 178 (225)
T PF09883_consen 176 ALN 178 (225)
T ss_pred HHH
Confidence 433
No 107
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=30.38 E-value=34 Score=32.20 Aligned_cols=46 Identities=28% Similarity=0.363 Sum_probs=31.8
Q ss_pred CCCCceeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 39 IPNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 39 l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
+-....+..+|..|+|||+..+..|++.+|= ...+.+-+.+++..+
T Consensus 535 ~R~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS-~~~i~~As~eeL~~v 580 (598)
T PRK00558 535 KRSKARLTSALDDIPGIGPKRRKALLKHFGS-LKAIKEASVEELAKV 580 (598)
T ss_pred ccccchhhhhHhhCCCcCHHHHHHHHHHcCC-HHHHHhCCHHHHhhc
Confidence 3445557789999999999999999998873 222333455555443
No 108
>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=30.31 E-value=1.2e+02 Score=19.07 Aligned_cols=42 Identities=7% Similarity=0.075 Sum_probs=31.9
Q ss_pred cccccccCHHHHHHHHHHcCCC-ccc----cCCCCHHHHHHHHHHHh
Q 031757 49 LQHVYGIGRSRAHQILCDLNIG-NKL----TKELTGVELNSLREEVS 90 (153)
Q Consensus 49 Lt~I~GIG~~~A~~Ic~~lgi~-~~~----~~~Ls~~qi~~L~~~l~ 90 (153)
+....||...+...-.+..|+. +.+ ....+++|+..|..+..
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 4567899999999988888886 333 24788999998887654
No 109
>smart00475 53EXOc 5'-3' exonuclease.
Probab=29.99 E-value=40 Score=28.28 Aligned_cols=20 Identities=30% Similarity=0.521 Sum_probs=16.3
Q ss_pred cccccccCHHHHHHHHHHcC
Q 031757 49 LQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 49 Lt~I~GIG~~~A~~Ic~~lg 68 (153)
+..++|||+.+|..++++.|
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC
Confidence 34578999999999998876
No 110
>PRK07945 hypothetical protein; Provisional
Probab=29.90 E-value=35 Score=29.56 Aligned_cols=21 Identities=38% Similarity=0.417 Sum_probs=18.5
Q ss_pred ecccccccCHHHHHHHHHHcC
Q 031757 48 SLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lg 68 (153)
.|++|+|||+.+|.+|-..+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 699999999999999987654
No 111
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=29.78 E-value=46 Score=31.85 Aligned_cols=36 Identities=22% Similarity=0.170 Sum_probs=27.6
Q ss_pred ccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHH
Q 031757 50 QHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSL 85 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L 85 (153)
-+|.|+|+.++.++.+..+|. ..-+-.|+.+++..|
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 479999999999999999997 333347777766554
No 112
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=29.75 E-value=44 Score=24.72 Aligned_cols=27 Identities=33% Similarity=0.517 Sum_probs=20.2
Q ss_pred CceeeeecccccccCHHHHHHHHHHcC
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
+......|+.+-|.|++.|..+.+.+.
T Consensus 45 ~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 45 HPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp -HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred ChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 444567789999999999999998775
No 113
>PF13035 DUF3896: Protein of unknown function (DUF3896)
Probab=29.45 E-value=79 Score=21.14 Aligned_cols=42 Identities=26% Similarity=0.468 Sum_probs=26.8
Q ss_pred HHHHHHcCCCccccCCCCHHHHHHHHHHHhhccchHHHHHHHHHhHHHHHhhhhc-cCC
Q 031757 61 HQILCDLNIGNKLTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQCY-RGI 118 (153)
Q Consensus 61 ~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~~~i~~dL~~~~~~dI~rL~~I~sY-RG~ 118 (153)
.++|++|. --.|++++-++|.-.|++|. -|-.|+.++.| ||+
T Consensus 19 q~lc~kls-----~~~ls~~er~qi~~eidnye-----------yilnlvemnhyergf 61 (61)
T PF13035_consen 19 QQLCKKLS-----SMHLSEKEREQIKLEIDNYE-----------YILNLVEMNHYERGF 61 (61)
T ss_pred HHHHHHHh-----hcccCHHHHHHHHhhhhhHH-----------HHHHHHHHhcccccC
Confidence 45666552 24678888888888777652 22346777777 553
No 114
>PRK14976 5'-3' exonuclease; Provisional
Probab=28.26 E-value=43 Score=28.45 Aligned_cols=19 Identities=32% Similarity=0.443 Sum_probs=16.6
Q ss_pred ccccccCHHHHHHHHHHcC
Q 031757 50 QHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~lg 68 (153)
..++|||+.+|..+++..|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999998876
No 115
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=28.22 E-value=50 Score=22.77 Aligned_cols=21 Identities=14% Similarity=0.058 Sum_probs=13.1
Q ss_pred CCCCHHHHHHHHHHHhhccch
Q 031757 75 KELTGVELNSLREEVSRYLTG 95 (153)
Q Consensus 75 ~~Ls~~qi~~L~~~l~~~~i~ 95 (153)
=.||++|++.|.+.|.+.=++
T Consensus 46 V~Lt~eqv~~LN~~l~~~Gf~ 66 (73)
T PF14794_consen 46 VFLTEEQVAKLNQALQKAGFD 66 (73)
T ss_dssp ----HHHHHHHHHHHHHTT--
T ss_pred EEcCHHHHHHHHHHHHHcCCC
Confidence 379999999999999874333
No 116
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=28.22 E-value=42 Score=24.30 Aligned_cols=36 Identities=22% Similarity=0.339 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHcCCC-cc-ccCCCCHHHHHHHHHHHhh
Q 031757 56 GRSRAHQILCDLNIG-NK-LTKELTGVELNSLREEVSR 91 (153)
Q Consensus 56 G~~~A~~Ic~~lgi~-~~-~~~~Ls~~qi~~L~~~l~~ 91 (153)
|...|..++..+|-+ .. -++.|+++|+++|...+.+
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 456777888888887 33 4589999999999988765
No 117
>PRK00076 recR recombination protein RecR; Reviewed
Probab=27.32 E-value=37 Score=27.79 Aligned_cols=66 Identities=23% Similarity=0.337 Sum_probs=44.2
Q ss_pred eeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh---------------------------------
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR--------------------------------- 91 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~--------------------------------- 91 (153)
+..+|.+++|||++.|.++.-.+= .-.+++.+.|.+.|..
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll-------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~i 81 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLL-------QRDREDVLRLAQALEEAKEKIKHCSVCGNLTEQDPCEICSDPRRDQSLI 81 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH-------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCcCCCCcCCCCCCCCCCCCEE
Confidence 456789999999999999885442 2245566666555531
Q ss_pred ccchHHHHHHHHHhHHHHHhhhhccCCccCCC
Q 031757 92 YLTGEDLRRCIKNDVERLVDIQCYRGIRHSQG 123 (153)
Q Consensus 92 ~~i~~dL~~~~~~dI~rL~~I~sYRG~RH~~G 123 (153)
-.||+. .|+.-+-+.+.|+|.=|-+|
T Consensus 82 cVVE~~------~Dv~aiE~s~~y~G~YhVL~ 107 (196)
T PRK00076 82 CVVESP------ADVLAIERTGEYRGLYHVLG 107 (196)
T ss_pred EEECCH------HHHHHHHhhCcCceEEEEec
Confidence 123332 35555667788999999887
No 118
>PRK09482 flap endonuclease-like protein; Provisional
Probab=27.31 E-value=47 Score=28.10 Aligned_cols=20 Identities=30% Similarity=0.503 Sum_probs=17.3
Q ss_pred cccccccCHHHHHHHHHHcC
Q 031757 49 LQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 49 Lt~I~GIG~~~A~~Ic~~lg 68 (153)
+..++|||+.+|..+++..|
T Consensus 184 IpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCCcChHHHHHHHHHhC
Confidence 35689999999999998877
No 119
>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=26.72 E-value=2.3e+02 Score=19.94 Aligned_cols=42 Identities=21% Similarity=0.216 Sum_probs=30.1
Q ss_pred eecccccccCHHH-HHHHHHHcCCCccccCCCCHHHHHHHHHH
Q 031757 47 TSLQHVYGIGRSR-AHQILCDLNIGNKLTKELTGVELNSLREE 88 (153)
Q Consensus 47 ~aLt~I~GIG~~~-A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~ 88 (153)
+++...+|-|.++ |..+++.+|+.---.+.+..+++....+.
T Consensus 2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~~i~~e~~~~~~~~ 44 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTGGIRTEEVGKLASE 44 (147)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCceeccccCCHHHHHHHHHH
Confidence 4677889999998 88899999987333346677766554443
No 120
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=26.49 E-value=48 Score=31.21 Aligned_cols=45 Identities=20% Similarity=0.225 Sum_probs=31.4
Q ss_pred CCCceeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 40 PNDKRLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 40 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
-.+......|..|+|||+....++++.+|== ..+..-|.+|+.++
T Consensus 507 r~k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~-~~ik~As~eeL~~v 551 (567)
T PRK14667 507 REKEGLKDILDKIKGIGEVKKEIIYRNFKTL-YDFLKADDEELKKL 551 (567)
T ss_pred hhcccccCccccCCCCCHHHHHHHHHHhCCH-HHHHhCCHHHHHHc
Confidence 3445566788999999999999999987732 22344455666554
No 121
>PHA02564 V virion protein; Provisional
Probab=26.13 E-value=1.3e+02 Score=23.47 Aligned_cols=34 Identities=12% Similarity=0.048 Sum_probs=24.9
Q ss_pred HHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhc
Q 031757 58 SRAHQILCDLNIG-NKLTKELTGVELNSLREEVSRY 92 (153)
Q Consensus 58 ~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~~~ 92 (153)
.++..||+.+|++ +..+.-.++ .+..|...|..|
T Consensus 86 aYi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~~ 120 (141)
T PHA02564 86 AYATAVANAMGVPPQAGLHLDQD-TLAALVTAIIRH 120 (141)
T ss_pred HHHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHHH
Confidence 4688999999999 555554444 788888877554
No 122
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=25.52 E-value=82 Score=27.72 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=29.5
Q ss_pred cccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh
Q 031757 51 HVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 51 ~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
.-.|||+.+|..+++ =|++--.++- |++.++++.++|+.
T Consensus 57 aTDGIGKayA~eLAk-rG~nvvLIsR-t~~KL~~v~kEI~~ 95 (312)
T KOG1014|consen 57 ATDGIGKAYARELAK-RGFNVVLISR-TQEKLEAVAKEIEE 95 (312)
T ss_pred CCCcchHHHHHHHHH-cCCEEEEEeC-CHHHHHHHHHHHHH
Confidence 458999999999998 6887333332 67888898887763
No 123
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=25.44 E-value=71 Score=32.37 Aligned_cols=46 Identities=17% Similarity=0.168 Sum_probs=33.0
Q ss_pred CceeeeecccccccCHHHHHHHHHHcCCCc-----ccc--CCCCHHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDLNIGN-----KLT--KELTGVELNSLRE 87 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~-----~~~--~~Ls~~qi~~L~~ 87 (153)
+..|+++|..|+|||...+..|.+.=-+.+ .++ +.++...++.|..
T Consensus 745 ~~~Ir~GL~aIkgvg~~~~~~I~~~R~f~s~~Df~~R~~~~~~~k~~le~LI~ 797 (1034)
T PRK07279 745 NKKIYLGLKNIKGLPRDLAYWIIENRPFSSIEDFLTRLPENYQKKEFLEPLIK 797 (1034)
T ss_pred CCEEEeehhhcCCCCHHHHHHHHHCCCCCCHHHHHHhcCcCCCCHHHHHHHHH
Confidence 457999999999999999999987433321 122 4467777776653
No 124
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=25.05 E-value=26 Score=29.29 Aligned_cols=31 Identities=26% Similarity=0.280 Sum_probs=23.5
Q ss_pred cCCCCcee--eeecccccccCHHHHHHHHHHcC
Q 031757 38 EIPNDKRL--ETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 38 nl~~~k~i--~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
++++.++. +--|-+|+|||+-+|..|+--+.
T Consensus 104 ~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~ 136 (215)
T COG2231 104 NLESFKSEVLREELLSIKGIGKETADSILLYAL 136 (215)
T ss_pred hhhccchHHHHHHHHccCCcchhhHHHHHHHHh
Confidence 45555555 67789999999999998875443
No 125
>PHA03373 tegument protein; Provisional
Probab=24.80 E-value=57 Score=27.70 Aligned_cols=58 Identities=28% Similarity=0.417 Sum_probs=40.3
Q ss_pred cCHHHHHHHHHHcCCC-cc-ccCCCCHHHHHHHHHHHhhccchHHHHHHHHHhHHHHHhhh
Q 031757 55 IGRSRAHQILCDLNIG-NK-LTKELTGVELNSLREEVSRYLTGEDLRRCIKNDVERLVDIQ 113 (153)
Q Consensus 55 IG~~~A~~Ic~~lgi~-~~-~~~~Ls~~qi~~L~~~l~~~~i~~dL~~~~~~dI~rL~~I~ 113 (153)
+--..|..|++.|+|= -+ .+|+++=.+-+.|+..+++|.+...- ..--+.|.+|+++-
T Consensus 103 vEc~KsqrIleaLDVvilKl~vGEFtmse~dsle~LL~KFStDQsT-LceveKi~~LVdmD 162 (247)
T PHA03373 103 VECMKSKRILEALDVVILKLLVGEFTMSETDSLNRLLEKFSTDQST-LCEVEKINRLVDMD 162 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccCcchHHHHHHHHhccchHH-HHHHHHHHHHHhcc
Confidence 4456889999999987 44 56999999999999999998765321 22223445555543
No 126
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=24.50 E-value=55 Score=30.87 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=28.9
Q ss_pred eeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
....|..|+|||+.....+++.+|== ..+..-|.+|+.++
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 45688999999999999999988742 22344455666554
No 127
>PRK13844 recombination protein RecR; Provisional
Probab=24.05 E-value=46 Score=27.39 Aligned_cols=38 Identities=13% Similarity=0.185 Sum_probs=26.3
Q ss_pred eeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEV 89 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l 89 (153)
+..+|.+.+|||++.|.++.--+= +-.+++.+.|.+.|
T Consensus 13 LI~~l~~LPGIG~KsA~Rla~~lL-------~~~~~~~~~la~~i 50 (200)
T PRK13844 13 VIESLRKLPTIGKKSSQRLALYLL-------DKSPETAIAIANSL 50 (200)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH-------cCCHHHHHHHHHHH
Confidence 456789999999999999874431 22455556665554
No 128
>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=23.18 E-value=8.9 Score=28.07 Aligned_cols=20 Identities=30% Similarity=0.396 Sum_probs=15.8
Q ss_pred ccccccCHHHHHHHHHHcCC
Q 031757 50 QHVYGIGRSRAHQILCDLNI 69 (153)
Q Consensus 50 t~I~GIG~~~A~~Ic~~lgi 69 (153)
-.++|||+.+|..++...|=
T Consensus 21 PGV~GIG~KtA~~LL~~ygs 40 (101)
T PF01367_consen 21 PGVPGIGPKTAAKLLQEYGS 40 (101)
T ss_dssp ---TTSTCHCCCCCHHHHTS
T ss_pred CCCCCCCHHHHHHHHHHcCC
Confidence 46899999999999999883
No 129
>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=22.97 E-value=58 Score=30.65 Aligned_cols=25 Identities=24% Similarity=0.511 Sum_probs=21.3
Q ss_pred eeeeecccccccCHHHHHHHHHHcC
Q 031757 44 RLETSLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~lg 68 (153)
.+.-.|..|+|||+.....+++.+|
T Consensus 538 ~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 538 SLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3445788999999999999998877
No 130
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=22.80 E-value=81 Score=32.19 Aligned_cols=59 Identities=19% Similarity=0.284 Sum_probs=39.6
Q ss_pred eeeeEEecccCCC--------CceeeeecccccccCHHHHHHHHHHc---C-CCc-----ccc--CCCCHHHHHHHHH
Q 031757 29 VQGLRVGNTEIPN--------DKRLETSLQHVYGIGRSRAHQILCDL---N-IGN-----KLT--KELTGVELNSLRE 87 (153)
Q Consensus 29 ~~~vrI~~tnl~~--------~k~i~~aLt~I~GIG~~~A~~Ic~~l---g-i~~-----~~~--~~Ls~~qi~~L~~ 87 (153)
.+-+.|+..||+. +..|.++|..|+|||...+..|.+.= | +.+ .++ ..++...++.|..
T Consensus 794 ~~gi~vl~pdin~S~~~f~~~~~~I~~gL~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li~ 871 (1135)
T PRK05673 794 RMGIKVLPPDVNESLYDFTVVDGDIRYGLGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKVNKRVLESLIK 871 (1135)
T ss_pred HCCCeEeCCceeccCCccEEECCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccCCCCHHHHHHHHH
Confidence 3345555555442 45799999999999999999998643 2 211 233 4577777777764
No 131
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=22.50 E-value=84 Score=32.21 Aligned_cols=58 Identities=21% Similarity=0.260 Sum_probs=38.9
Q ss_pred eeeEEecccCCC--------CceeeeecccccccCHHHHHHHHHHc---C-CCc-----ccc--CCCCHHHHHHHHH
Q 031757 30 QGLRVGNTEIPN--------DKRLETSLQHVYGIGRSRAHQILCDL---N-IGN-----KLT--KELTGVELNSLRE 87 (153)
Q Consensus 30 ~~vrI~~tnl~~--------~k~i~~aLt~I~GIG~~~A~~Ic~~l---g-i~~-----~~~--~~Ls~~qi~~L~~ 87 (153)
+-+.|+..||+. +..|.++|..|+|||...+..|.+.= | +.+ .++ +.++...++.|..
T Consensus 810 ~GI~vlpPdIN~S~~~f~~~~~~Ir~GL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~LI~ 886 (1170)
T PRK07374 810 MGIEVMPPDINRSGIDFTPKGNRILFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRLPSNVLNRRSLESLIH 886 (1170)
T ss_pred CCCEEeCCceecCCCCcEEECCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccccCCHHHHHHHHH
Confidence 335555555443 34699999999999999999998543 3 211 233 4577887777764
No 132
>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=22.41 E-value=1.1e+02 Score=22.26 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=28.5
Q ss_pred ccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh
Q 031757 54 GIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR 91 (153)
Q Consensus 54 GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~ 91 (153)
-+|......|+..|+ ++-.+||+++++.+.+++..
T Consensus 34 s~Gh~sGRrIv~IL~---K~k~dltddD~~hMrkVV~y 68 (92)
T PF11338_consen 34 SVGHESGRRIVEILR---KRKTDLTDDDYEHMRKVVGY 68 (92)
T ss_pred ccCcchhhHHHHHHh---cCcccCCHHHHHHHHHHHHH
Confidence 367778888888887 67789999999999887753
No 133
>PRK14529 adenylate kinase; Provisional
Probab=22.13 E-value=3.3e+02 Score=22.36 Aligned_cols=52 Identities=12% Similarity=0.196 Sum_probs=33.1
Q ss_pred eecccccccCHH-HHHHHHHHcCCCccccCCCCHHHH-------HHHHHHHhh-ccchHHH
Q 031757 47 TSLQHVYGIGRS-RAHQILCDLNIGNKLTKELTGVEL-------NSLREEVSR-YLTGEDL 98 (153)
Q Consensus 47 ~aLt~I~GIG~~-~A~~Ic~~lgi~~~~~~~Ls~~qi-------~~L~~~l~~-~~i~~dL 98 (153)
+.|-..+|-|+. .|..|++.+|+...-.++|..+++ ..+.+++++ -++..++
T Consensus 3 I~l~G~PGsGK~T~a~~La~~~~~~~is~gdllr~~i~~~t~lg~~i~~~i~~G~lvpdei 63 (223)
T PRK14529 3 ILIFGPNGSGKGTQGALVKKKYDLAHIESGAIFREHIGGGTELGKKAKEYIDRGDLVPDDI 63 (223)
T ss_pred EEEECCCCCCHHHHHHHHHHHHCCCCcccchhhhhhccCCChHHHHHHHHHhccCcchHHH
Confidence 456788999998 588899999997544455544443 344555543 3344443
No 134
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=22.07 E-value=79 Score=31.79 Aligned_cols=46 Identities=13% Similarity=0.170 Sum_probs=33.4
Q ss_pred CceeeeecccccccCHHHHHHHHHHc---C-CCc-----ccc--CCCCHHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDL---N-IGN-----KLT--KELTGVELNSLRE 87 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~l---g-i~~-----~~~--~~Ls~~qi~~L~~ 87 (153)
+..|.++|+.|+|||...+..|.+.- | +.+ .++ ..++...++.|..
T Consensus 748 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li~ 804 (973)
T PRK07135 748 NGKIFLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLIK 804 (973)
T ss_pred CCEEEECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhccccCCCHHHHHHHHH
Confidence 45799999999999999999998533 2 211 233 4678887777764
No 135
>PF01698 FLO_LFY: Floricaula / Leafy protein; InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2VY1_A 2VY2_A.
Probab=22.02 E-value=30 Score=31.27 Aligned_cols=71 Identities=24% Similarity=0.358 Sum_probs=0.0
Q ss_pred cccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh-----ccch--HHHHHHHHHhHHHHHhhhhccCCcc
Q 031757 49 LQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSLREEVSR-----YLTG--EDLRRCIKNDVERLVDIQCYRGIRH 120 (153)
Q Consensus 49 Lt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L~~~l~~-----~~i~--~dL~~~~~~dI~rL~~I~sYRG~RH 120 (153)
|=.=|||-..++..|. .|||--..+=+++|+|++.+.+.|.. .+++ -.++..++..-.||-.-...+..||
T Consensus 54 LF~~YGVRy~T~AKIa-ElGFTvsTLl~M~deELDdmM~sL~~ifRwdLLVGERYGIKAAvRAERRRl~e~~~~~rR~h 131 (386)
T PF01698_consen 54 LFQGYGVRYYTAAKIA-ELGFTVSTLLNMTDEELDDMMNSLSQIFRWDLLVGERYGIKAAVRAERRRLEEEEESRRRRH 131 (386)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred HHhhccccHHHHHHHH-HhcccHHHHhcccHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHhhcchhhhhhhc
Confidence 4456999999988876 58888444445688999999887764 3444 3678888888888887655566665
No 136
>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=21.34 E-value=72 Score=27.01 Aligned_cols=18 Identities=22% Similarity=0.361 Sum_probs=16.7
Q ss_pred cccccCHHHHHHHHHHcC
Q 031757 51 HVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 51 ~I~GIG~~~A~~Ic~~lg 68 (153)
.|+|||+.+|..+++..|
T Consensus 227 gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 227 GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 689999999999999987
No 137
>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=21.20 E-value=90 Score=19.81 Aligned_cols=16 Identities=19% Similarity=0.322 Sum_probs=13.7
Q ss_pred cCCCCHHHHHHHHHHH
Q 031757 74 TKELTGVELNSLREEV 89 (153)
Q Consensus 74 ~~~Ls~~qi~~L~~~l 89 (153)
.+.||++|+..|..+|
T Consensus 52 ~~~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 52 GGQLSDEEIEALAAYI 67 (67)
T ss_dssp TTTSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHC
Confidence 3589999999998876
No 138
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=21.20 E-value=47 Score=31.69 Aligned_cols=39 Identities=21% Similarity=0.135 Sum_probs=25.5
Q ss_pred eeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
+.+|| .|+|||...|..+++.++ +-..+...+.+++..+
T Consensus 497 ~L~aL-gIpgVG~~~ak~L~~~f~-sl~~l~~As~eeL~~i 535 (652)
T TIGR00575 497 LLFAL-GIRHVGEVTAKNLAKHFG-TLDKLKAASLEELLSV 535 (652)
T ss_pred HHhhc-cCCCcCHHHHHHHHHHhC-CHHHHHhCCHHHHhcC
Confidence 44455 799999999999999887 3122333455555444
No 139
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=21.08 E-value=82 Score=32.21 Aligned_cols=46 Identities=13% Similarity=0.239 Sum_probs=33.6
Q ss_pred CceeeeecccccccCHHHHHHHHHHc---C-CCc-----ccc--CCCCHHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDL---N-IGN-----KLT--KELTGVELNSLRE 87 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~l---g-i~~-----~~~--~~Ls~~qi~~L~~ 87 (153)
+..|.++|..|+|||...+..|.+.= | +.+ .++ +.++...++.|..
T Consensus 819 ~~~Ir~gL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~Li~ 875 (1151)
T PRK06826 819 GDKIRFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERVDTSQINKRAVESLIK 875 (1151)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHHH
Confidence 45799999999999999999998643 3 211 233 4578887777764
No 140
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.82 E-value=99 Score=23.90 Aligned_cols=78 Identities=18% Similarity=0.236 Sum_probs=50.0
Q ss_pred ecccccccCHHHHHHHHHHcC---CC--cc----ccCCCCHHHHHHHHHHHhhccchHHHHHHHHH-hHHHHH--hhhhc
Q 031757 48 SLQHVYGIGRSRAHQILCDLN---IG--NK----LTKELTGVELNSLREEVSRYLTGEDLRRCIKN-DVERLV--DIQCY 115 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lg---i~--~~----~~~~Ls~~qi~~L~~~l~~~~i~~dL~~~~~~-dI~rL~--~I~sY 115 (153)
...+++|+|.+++..-..+.. .+ +. +-..|+++|++.|.+.++... ..|+..... ..+.-+ ..+++
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~--wTl~~~~~~l~~e~gv~y~~~~v 103 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD--WTLKELVEELGLEFGVWYHASAV 103 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc--chHHHHHHHHhhhcCeEEeHHHH
Confidence 357889999999999998876 22 22 346999999999999987633 222221111 111222 22356
Q ss_pred cCCccCCCCccC
Q 031757 116 RGIRHSQGLPCR 127 (153)
Q Consensus 116 RG~RH~~GLPVR 127 (153)
+=+.|.+||+-.
T Consensus 104 ~~~l~~~Glsyk 115 (138)
T COG3415 104 RRLLHELGLSYK 115 (138)
T ss_pred HHHHHHcCCCcC
Confidence 667888888765
No 141
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=20.73 E-value=65 Score=30.35 Aligned_cols=40 Identities=20% Similarity=0.294 Sum_probs=28.2
Q ss_pred eeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 45 LETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 45 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
...+|..|+|||...+..+++.+|=- ..+.+-+.+++..+
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS~-~~I~~As~eeL~~v 562 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGSV-EGVREASVEDLRDV 562 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCCH-HHHHhCCHHHHHhC
Confidence 46789999999999999999988622 22334445555443
No 142
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=20.69 E-value=69 Score=30.54 Aligned_cols=41 Identities=15% Similarity=0.257 Sum_probs=28.7
Q ss_pred eeeeecccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 031757 44 RLETSLQHVYGIGRSRAHQILCDLNIGNKLTKELTGVELNSL 85 (153)
Q Consensus 44 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~~~~Ls~~qi~~L 85 (153)
.+...|.+|+|||+..+..+++.+|== ..+..-|.+|+.++
T Consensus 549 ~~~S~L~~IpGIG~kr~~~LL~~FgSi-~~I~~As~eeL~~v 589 (624)
T PRK14669 549 DRTSELLEIPGVGAKTVQRLLKHFGSL-ERVRAATETQLAAV 589 (624)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcCCH-HHHHhCCHHHHHHH
Confidence 345577899999999999999988731 12344456666554
No 143
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=20.65 E-value=75 Score=28.86 Aligned_cols=44 Identities=16% Similarity=0.134 Sum_probs=36.8
Q ss_pred eeecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 031757 46 ETSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLREEVS 90 (153)
Q Consensus 46 ~~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~~~l~ 90 (153)
.-.|+.|.|||+..+. .+..+||. ...+-.++++++..+...+.
T Consensus 322 aDDLk~I~GIGpk~e~-~Ln~~Gi~~f~QIA~wt~~eia~vd~~l~ 366 (400)
T PRK12373 322 ADDLKLISGVGPKIEA-TLNELGIFTFDQVAAWKKAERAWVDGYLN 366 (400)
T ss_pred chhhhhccCCChHHHH-HHHhcCCCCHHHHhCCCHHHhHHhhhccc
Confidence 3569999999998875 46789998 67888999999998888775
No 144
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=20.60 E-value=69 Score=28.36 Aligned_cols=21 Identities=33% Similarity=0.436 Sum_probs=17.5
Q ss_pred ecccccccCHHHHHHHHHHcC
Q 031757 48 SLQHVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lg 68 (153)
++|.++|||+.+|..|..-+.
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l~ 74 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYLD 74 (326)
T ss_pred ccCCCCCccHHHHHHHHHHHH
Confidence 599999999999998875443
No 145
>PRK03980 flap endonuclease-1; Provisional
Probab=20.55 E-value=75 Score=27.22 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=16.8
Q ss_pred cccccCHHHHHHHHHHcC
Q 031757 51 HVYGIGRSRAHQILCDLN 68 (153)
Q Consensus 51 ~I~GIG~~~A~~Ic~~lg 68 (153)
.|+|||+.+|..+++..|
T Consensus 193 GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred CCCCccHHHHHHHHHHCC
Confidence 688999999999999988
No 146
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=20.52 E-value=67 Score=24.85 Aligned_cols=26 Identities=27% Similarity=0.327 Sum_probs=19.8
Q ss_pred CceeeeecccccccCHHHHHHHHHHc
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDL 67 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~l 67 (153)
|..-...|..++|||+..|.+|..--
T Consensus 92 NtAs~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 92 NTASAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred cccCHHHHHHCCCCCHHHHHHHHHHH
Confidence 33344556999999999999998543
No 147
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=20.35 E-value=1.4e+02 Score=22.20 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=13.4
Q ss_pred CCHHHHHHHHHHHhhc
Q 031757 77 LTGVELNSLREEVSRY 92 (153)
Q Consensus 77 Ls~~qi~~L~~~l~~~ 92 (153)
||++|+..|.+.+..+
T Consensus 2 lt~ee~~~l~~~~~~~ 17 (205)
T cd01199 2 LEKNELKALLDVLNSY 17 (205)
T ss_pred CCHHHHHHHHHHHHhc
Confidence 7899999999988653
No 148
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=20.31 E-value=95 Score=20.84 Aligned_cols=23 Identities=17% Similarity=0.196 Sum_probs=17.9
Q ss_pred ecccccccCHHHHHHHHHHcCCC
Q 031757 48 SLQHVYGIGRSRAHQILCDLNIG 70 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lgi~ 70 (153)
.|...-|+.+.+...+|+++|++
T Consensus 39 elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 39 ELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHHHHcCCCHHHHHHHHHHhCCC
Confidence 34566788999999999999987
No 149
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=20.17 E-value=94 Score=31.35 Aligned_cols=45 Identities=11% Similarity=0.222 Sum_probs=31.4
Q ss_pred CceeeeecccccccCHHHHHHHHHHcC---CCc-----c--ccCCCCHHHHHHHH
Q 031757 42 DKRLETSLQHVYGIGRSRAHQILCDLN---IGN-----K--LTKELTGVELNSLR 86 (153)
Q Consensus 42 ~k~i~~aLt~I~GIG~~~A~~Ic~~lg---i~~-----~--~~~~Ls~~qi~~L~ 86 (153)
+..|+++|+.|+|||...+..|.+.-. +.+ . ....++...++.|.
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 457999999999999999999986332 111 0 12456666666665
No 150
>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=20.09 E-value=1e+02 Score=19.47 Aligned_cols=16 Identities=19% Similarity=0.204 Sum_probs=14.3
Q ss_pred CCCHHHHHHHHHHHhh
Q 031757 76 ELTGVELNSLREEVSR 91 (153)
Q Consensus 76 ~Ls~~qi~~L~~~l~~ 91 (153)
.||++|+..|..+|.+
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 7999999999999864
No 151
>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=20.09 E-value=78 Score=27.64 Aligned_cols=37 Identities=14% Similarity=0.279 Sum_probs=27.5
Q ss_pred ecccccccCHHHHHHHHHHcCCCcc-ccCCC--CHHHHHH
Q 031757 48 SLQHVYGIGRSRAHQILCDLNIGNK-LTKEL--TGVELNS 84 (153)
Q Consensus 48 aLt~I~GIG~~~A~~Ic~~lgi~~~-~~~~L--s~~qi~~ 84 (153)
.+..+.|||..++..++..+||... -+-.+ +.+++.+
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~ 222 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQE 222 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHH
Confidence 4689999999999999999999842 23344 5555543
No 152
>PRK01172 ski2-like helicase; Provisional
Probab=20.05 E-value=1.8e+02 Score=27.16 Aligned_cols=39 Identities=18% Similarity=0.207 Sum_probs=29.6
Q ss_pred eecccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHH
Q 031757 47 TSLQHVYGIGRSRAHQILCDLNIG-NKLTKELTGVELNSLR 86 (153)
Q Consensus 47 ~aLt~I~GIG~~~A~~Ic~~lgi~-~~~~~~Ls~~qi~~L~ 86 (153)
..|..|+|+|+..|.+ |...|+. ..-+-++++++++.|.
T Consensus 612 ~~L~~ip~~~~~~a~~-l~~~g~~~~~di~~~~~~~~~~i~ 651 (674)
T PRK01172 612 IDLVLIPKVGRVRARR-LYDAGFKTVDDIARSSPERIKKIY 651 (674)
T ss_pred HhhcCCCCCCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHHh
Confidence 3467899999998765 7889998 4456677888877763
Done!