Query 031812
Match_columns 152
No_of_seqs 120 out of 1028
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:41:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031812.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031812hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00134 40S ribosomal protein 100.0 1.6E-67 3.5E-72 407.4 11.6 152 1-152 1-154 (154)
2 PRK04053 rps13p 30S ribosomal 100.0 3.1E-66 6.6E-71 398.6 12.2 147 6-152 3-149 (149)
3 TIGR03629 arch_S13P archaeal r 100.0 1.4E-65 3.1E-70 393.1 11.3 144 8-152 1-144 (144)
4 COG0099 RpsM Ribosomal protein 100.0 2.3E-52 5.1E-57 309.4 8.3 119 12-152 1-121 (121)
5 KOG3311 Ribosomal protein S18 100.0 2.3E-51 4.9E-56 314.3 8.1 152 1-152 1-152 (152)
6 CHL00137 rps13 ribosomal prote 100.0 7.4E-49 1.6E-53 293.5 9.8 111 12-144 1-111 (122)
7 PRK05179 rpsM 30S ribosomal pr 100.0 9.6E-49 2.1E-53 292.8 10.2 111 12-144 1-111 (122)
8 TIGR03631 bact_S13 30S ribosom 100.0 4.1E-47 8.9E-52 280.7 10.3 111 14-146 1-111 (113)
9 PF00416 Ribosomal_S13: Riboso 100.0 2.5E-47 5.5E-52 278.8 3.8 107 14-142 1-107 (107)
10 PF06831 H2TH: Formamidopyrimi 97.1 0.00055 1.2E-08 48.7 3.1 51 22-72 22-75 (92)
11 PRK01103 formamidopyrimidine/5 96.9 0.0011 2.4E-08 55.3 4.3 53 21-73 153-208 (274)
12 PRK14810 formamidopyrimidine-D 96.2 0.0056 1.2E-07 51.2 3.8 52 22-73 153-207 (272)
13 PRK14811 formamidopyrimidine-D 96.1 0.0084 1.8E-07 50.1 4.5 51 22-72 142-195 (269)
14 PRK10445 endonuclease VIII; Pr 96.0 0.01 2.2E-07 49.4 4.4 51 23-73 151-204 (263)
15 PRK13945 formamidopyrimidine-D 95.9 0.01 2.2E-07 49.8 4.4 52 22-73 163-217 (282)
16 TIGR00577 fpg formamidopyrimid 95.9 0.01 2.3E-07 49.6 4.1 52 22-73 154-208 (272)
17 PRK04184 DNA topoisomerase VI 94.7 0.051 1.1E-06 49.9 4.9 49 26-74 259-307 (535)
18 PF00633 HHH: Helix-hairpin-he 93.6 0.038 8.3E-07 31.7 1.2 18 29-46 12-29 (30)
19 COG0266 Nei Formamidopyrimidin 93.2 0.1 2.3E-06 44.1 3.7 59 15-73 147-208 (273)
20 PF05833 FbpA: Fibronectin-bin 92.7 0.03 6.4E-07 49.2 -0.2 51 22-72 185-236 (455)
21 TIGR01052 top6b DNA topoisomer 92.6 0.19 4.1E-06 45.7 4.7 48 27-74 251-301 (488)
22 TIGR00275 flavoprotein, HI0933 90.6 0.15 3.3E-06 44.3 1.9 51 21-73 281-331 (400)
23 PF11798 IMS_HHH: IMS family H 89.1 0.21 4.5E-06 28.8 1.1 21 29-50 12-32 (32)
24 PF14520 HHH_5: Helix-hairpin- 88.4 0.04 8.6E-07 35.7 -2.6 35 27-62 4-38 (60)
25 PF10391 DNA_pol_lambd_f: Fing 87.2 0.33 7.2E-06 31.1 1.3 22 29-51 3-24 (52)
26 COG3743 Uncharacterized conser 86.6 0.46 1E-05 36.3 1.9 44 28-72 67-110 (133)
27 smart00278 HhH1 Helix-hairpin- 86.4 0.46 1E-05 25.8 1.4 19 29-47 2-20 (26)
28 PRK00274 ksgA 16S ribosomal RN 85.5 0.52 1.1E-05 39.0 1.9 62 9-73 209-270 (272)
29 PRK02515 psbU photosystem II c 85.2 0.42 9.2E-06 36.4 1.1 59 15-73 48-109 (132)
30 PRK14606 ruvA Holliday junctio 83.9 0.53 1.2E-05 37.6 1.2 21 28-48 108-128 (188)
31 KOG3311 Ribosomal protein S18 83.6 0.19 4.1E-06 39.2 -1.4 45 99-145 70-114 (152)
32 COG1389 DNA topoisomerase VI, 83.6 1.4 3E-05 40.3 3.8 48 27-74 260-311 (538)
33 PRK14601 ruvA Holliday junctio 83.0 0.61 1.3E-05 37.2 1.2 21 28-48 108-128 (183)
34 PRK14604 ruvA Holliday junctio 81.9 0.71 1.5E-05 37.1 1.2 21 28-48 108-128 (195)
35 PRK14603 ruvA Holliday junctio 81.8 0.72 1.6E-05 37.0 1.2 20 28-47 107-126 (197)
36 PRK13901 ruvA Holliday junctio 81.5 0.75 1.6E-05 37.2 1.2 21 28-48 107-127 (196)
37 COG0030 KsgA Dimethyladenosine 81.3 0.78 1.7E-05 38.6 1.3 48 21-73 209-256 (259)
38 COG0632 RuvA Holliday junction 81.0 0.87 1.9E-05 36.9 1.4 21 28-48 108-128 (201)
39 PRK14602 ruvA Holliday junctio 80.6 0.85 1.8E-05 36.8 1.2 20 28-47 109-128 (203)
40 TIGR03252 uncharacterized HhH- 80.2 0.55 1.2E-05 37.5 0.0 29 21-49 108-136 (177)
41 smart00279 HhH2 Helix-hairpin- 79.4 2.1 4.6E-05 25.3 2.4 34 7-47 2-35 (36)
42 PF14579 HHH_6: Helix-hairpin- 78.1 1.8 3.9E-05 30.1 2.2 27 23-49 22-48 (90)
43 PF03486 HI0933_like: HI0933-l 77.8 2 4.4E-05 38.0 2.9 51 21-73 288-339 (409)
44 PF09883 DUF2110: Uncharacteri 76.8 7.2 0.00016 32.2 5.6 52 23-74 96-159 (225)
45 PRK14600 ruvA Holliday junctio 76.5 1.6 3.4E-05 34.9 1.6 19 28-47 108-126 (186)
46 COG1293 Predicted RNA-binding 76.2 2.1 4.5E-05 39.5 2.6 50 25-74 187-236 (564)
47 TIGR00755 ksgA dimethyladenosi 76.0 1.6 3.4E-05 35.6 1.5 58 9-70 195-252 (253)
48 PF00398 RrnaAD: Ribosomal RNA 76.0 0.77 1.7E-05 37.7 -0.3 62 7-72 200-261 (262)
49 PF12826 HHH_2: Helix-hairpin- 75.8 1.4 3.1E-05 28.9 1.0 18 32-49 7-24 (64)
50 PF11731 Cdd1: Pathogenicity l 74.7 2 4.4E-05 30.8 1.7 36 28-64 12-47 (93)
51 PRK14605 ruvA Holliday junctio 73.7 1.7 3.6E-05 34.8 1.1 18 28-45 108-125 (194)
52 PF12836 HHH_3: Helix-hairpin- 73.4 1.3 2.8E-05 29.1 0.4 44 26-69 12-62 (65)
53 PF14520 HHH_5: Helix-hairpin- 72.4 2.4 5.2E-05 27.2 1.4 20 29-48 39-58 (60)
54 PF14716 HHH_8: Helix-hairpin- 72.4 2.1 4.6E-05 28.3 1.2 20 29-48 48-67 (68)
55 PRK14605 ruvA Holliday junctio 71.7 0.72 1.6E-05 36.9 -1.4 36 14-49 59-94 (194)
56 PF14490 HHH_4: Helix-hairpin- 71.2 2.3 5E-05 29.8 1.3 26 28-53 45-71 (94)
57 cd00080 HhH2_motif Helix-hairp 71.0 3 6.5E-05 28.2 1.7 38 5-49 6-43 (75)
58 PRK00116 ruvA Holliday junctio 70.7 2.6 5.5E-05 33.5 1.6 59 15-73 60-130 (192)
59 PF02042 RWP-RK: RWP-RK domain 70.0 4.2 9E-05 26.2 2.1 26 33-58 24-51 (52)
60 TIGR00426 competence protein C 69.9 2.3 5E-05 27.9 1.0 26 23-48 11-37 (69)
61 TIGR01259 comE comEA protein. 69.8 2 4.3E-05 31.7 0.7 31 20-50 60-90 (120)
62 PF02371 Transposase_20: Trans 69.6 3.3 7.1E-05 28.5 1.7 20 29-48 3-22 (87)
63 cd00056 ENDO3c endonuclease II 67.4 2.1 4.5E-05 32.1 0.4 25 23-47 78-102 (158)
64 PRK12278 50S ribosomal protein 66.4 4.6 0.0001 33.3 2.2 45 28-73 158-202 (221)
65 smart00483 POLXc DNA polymeras 65.9 3.7 8.1E-05 35.3 1.7 25 27-52 88-112 (334)
66 smart00478 ENDO3c endonuclease 65.9 3.2 6.9E-05 30.8 1.1 23 26-48 70-92 (149)
67 TIGR00084 ruvA Holliday juncti 65.5 3.3 7.2E-05 33.0 1.2 19 28-46 107-125 (191)
68 PF12826 HHH_2: Helix-hairpin- 63.9 4.3 9.3E-05 26.6 1.3 35 8-49 22-56 (64)
69 TIGR01084 mutY A/G-specific ad 63.4 3.2 7E-05 34.9 0.8 30 16-48 96-125 (275)
70 PRK14601 ruvA Holliday junctio 62.9 2.2 4.8E-05 34.0 -0.2 34 14-47 59-92 (183)
71 cd00141 NT_POLXc Nucleotidyltr 62.2 4.9 0.00011 34.1 1.7 24 28-52 85-108 (307)
72 PRK08609 hypothetical protein; 61.8 5.3 0.00011 36.9 2.0 24 28-51 88-111 (570)
73 TIGR00084 ruvA Holliday juncti 60.9 0.96 2.1E-05 36.1 -2.6 34 14-47 58-91 (191)
74 PRK10702 endonuclease III; Pro 60.8 4.8 0.0001 32.5 1.4 23 26-48 107-129 (211)
75 TIGR01083 nth endonuclease III 60.7 4.9 0.00011 31.6 1.4 23 26-48 104-126 (191)
76 PRK12311 rpsB 30S ribosomal pr 60.5 4.3 9.3E-05 35.2 1.1 45 27-72 262-306 (326)
77 PRK14603 ruvA Holliday junctio 60.0 2.7 5.8E-05 33.8 -0.2 35 14-48 58-92 (197)
78 PRK03980 flap endonuclease-1; 59.5 8.1 0.00017 32.8 2.6 35 6-49 176-210 (292)
79 PRK01229 N-glycosylase/DNA lya 58.3 6.4 0.00014 32.0 1.7 43 25-71 115-158 (208)
80 cd00128 XPG Xeroderma pigmento 56.6 9.8 0.00021 32.0 2.6 35 6-49 210-244 (316)
81 TIGR01448 recD_rel helicase, p 55.6 12 0.00027 35.4 3.3 41 32-72 88-138 (720)
82 PRK14602 ruvA Holliday junctio 55.3 2.2 4.8E-05 34.4 -1.5 36 14-49 60-95 (203)
83 PRK14606 ruvA Holliday junctio 55.2 1.7 3.6E-05 34.7 -2.1 35 14-48 59-93 (188)
84 PTZ00217 flap endonuclease-1; 54.6 11 0.00023 33.4 2.6 35 6-49 222-256 (393)
85 COG0353 RecR Recombinational D 54.6 12 0.00026 30.4 2.7 87 25-128 9-108 (198)
86 PRK00076 recR recombination pr 54.5 12 0.00025 30.3 2.6 86 26-128 9-107 (196)
87 PRK14600 ruvA Holliday junctio 53.8 1.9 4.2E-05 34.3 -2.0 35 14-48 59-93 (186)
88 TIGR00615 recR recombination p 53.6 7.9 0.00017 31.3 1.5 86 26-128 9-107 (195)
89 PRK12766 50S ribosomal protein 53.5 7.7 0.00017 32.3 1.4 19 29-47 4-22 (232)
90 PRK13913 3-methyladenine DNA g 52.6 7.1 0.00015 31.9 1.1 22 26-47 119-140 (218)
91 COG2081 Predicted flavoprotein 52.5 17 0.00036 32.7 3.5 50 21-73 283-332 (408)
92 PRK13901 ruvA Holliday junctio 52.3 2.1 4.5E-05 34.6 -2.1 35 14-48 58-92 (196)
93 COG0632 RuvA Holliday junction 52.2 1.7 3.7E-05 35.2 -2.5 38 12-49 57-94 (201)
94 PRK10880 adenine DNA glycosyla 52.2 7.3 0.00016 34.0 1.2 30 16-48 100-129 (350)
95 PRK13910 DNA glycosylase MutY; 51.5 7.6 0.00016 33.0 1.1 29 17-48 64-92 (289)
96 COG0258 Exo 5'-3' exonuclease 51.3 11 0.00024 31.8 2.1 33 7-49 184-219 (310)
97 PRK14667 uvrC excinuclease ABC 51.2 8.4 0.00018 35.8 1.4 44 22-67 508-551 (567)
98 PRK00116 ruvA Holliday junctio 50.5 8.3 0.00018 30.6 1.2 21 29-49 109-129 (192)
99 smart00475 53EXOc 5'-3' exonuc 49.5 15 0.00033 30.5 2.6 36 7-49 172-207 (259)
100 PRK13844 recombination protein 49.2 10 0.00022 30.9 1.5 86 26-128 13-111 (200)
101 cd01104 HTH_MlrA-CarA Helix-Tu 48.8 38 0.00083 21.4 4.0 43 30-72 6-52 (68)
102 PF01367 5_3_exonuc: 5'-3' exo 48.6 2.8 6.1E-05 30.3 -1.7 20 30-49 20-39 (101)
103 PRK14670 uvrC excinuclease ABC 48.0 9.5 0.00021 35.5 1.3 39 26-66 512-550 (574)
104 PRK00558 uvrC excinuclease ABC 46.3 15 0.00031 34.3 2.2 45 21-67 536-580 (598)
105 PHA02564 V virion protein; Pro 46.3 38 0.00082 26.0 4.2 33 40-73 87-119 (141)
106 PRK14976 5'-3' exonuclease; Pr 45.4 18 0.0004 30.4 2.5 19 31-49 194-212 (281)
107 PRK14669 uvrC excinuclease ABC 44.2 13 0.00029 34.9 1.6 41 25-67 549-589 (624)
108 TIGR00588 ogg 8-oxoguanine DNA 44.1 11 0.00024 32.1 1.0 29 25-53 217-245 (310)
109 PRK14604 ruvA Holliday junctio 44.1 3.2 7E-05 33.3 -2.1 35 14-48 59-93 (195)
110 TIGR03674 fen_arch flap struct 43.9 20 0.00043 30.9 2.5 35 6-49 223-257 (338)
111 COG2231 Uncharacterized protei 43.5 19 0.00041 29.6 2.2 36 18-53 103-140 (215)
112 PF11338 DUF3140: Protein of u 43.2 39 0.00084 24.3 3.5 34 35-72 34-67 (92)
113 KOG2518 5'-3' exonuclease [Rep 42.9 19 0.00041 33.4 2.4 60 5-73 211-277 (556)
114 cd00008 53EXOc 5'-3' exonuclea 42.7 16 0.00036 29.7 1.8 20 30-49 185-204 (240)
115 PF02318 FYVE_2: FYVE-type zin 40.6 37 0.0008 24.7 3.2 17 57-73 1-17 (118)
116 PRK09482 flap endonuclease-lik 39.4 20 0.00043 30.0 1.8 20 30-49 184-203 (256)
117 COG1936 Predicted nucleotide k 38.8 28 0.0006 27.9 2.5 25 27-51 2-26 (180)
118 COG1555 ComEA DNA uptake prote 37.9 27 0.00058 26.8 2.2 43 28-70 97-146 (149)
119 COG0122 AlkA 3-methyladenine D 37.7 17 0.00036 30.8 1.1 22 26-47 196-217 (285)
120 PRK07945 hypothetical protein; 37.7 20 0.00044 30.8 1.7 21 29-49 50-70 (335)
121 PRK12373 NADH dehydrogenase su 37.7 24 0.00053 31.5 2.2 45 28-73 323-367 (400)
122 PRK14668 uvrC excinuclease ABC 37.6 15 0.00032 34.2 0.9 39 26-66 523-561 (577)
123 PRK14671 uvrC excinuclease ABC 37.6 20 0.00044 33.6 1.7 49 17-67 558-606 (621)
124 PRK07373 DNA polymerase III su 37.0 26 0.00057 31.6 2.3 24 23-46 109-132 (449)
125 PRK10308 3-methyl-adenine DNA 35.3 27 0.00058 29.4 2.0 33 26-58 205-238 (283)
126 PRK14672 uvrC excinuclease ABC 35.2 18 0.0004 34.5 1.1 43 22-66 602-644 (691)
127 PRK13766 Hef nuclease; Provisi 34.9 23 0.0005 33.3 1.7 22 28-49 715-736 (773)
128 COG3415 Transposase and inacti 34.3 66 0.0014 24.6 3.8 45 29-73 26-78 (138)
129 KOG0650 WD40 repeat nucleolar 33.5 67 0.0014 30.6 4.3 42 56-104 147-188 (733)
130 KOG0494 Transcription factor C 33.3 22 0.00049 30.4 1.2 29 58-87 147-193 (332)
131 COG0177 Nth Predicted EndoIII- 31.3 55 0.0012 26.8 3.1 48 16-71 100-148 (211)
132 cd01702 PolY_Pol_eta DNA Polym 30.8 29 0.00063 30.1 1.5 37 29-65 183-221 (359)
133 cd00141 NT_POLXc Nucleotidyltr 30.5 19 0.00042 30.5 0.4 23 29-51 46-68 (307)
134 TIGR00600 rad2 DNA excision re 30.1 39 0.00085 33.8 2.4 35 7-50 854-888 (1034)
135 PRK05898 dnaE DNA polymerase I 29.8 90 0.002 31.1 4.8 25 23-47 747-771 (971)
136 COG2938 Uncharacterized conser 29.1 16 0.00034 26.3 -0.3 33 55-88 40-72 (94)
137 PTZ00338 dimethyladenosine tra 28.8 57 0.0012 27.6 2.9 33 40-73 256-288 (294)
138 PF14635 HHH_7: Helix-hairpin- 28.3 39 0.00086 24.6 1.6 42 8-49 27-71 (104)
139 PRK14896 ksgA 16S ribosomal RN 28.2 49 0.0011 27.0 2.4 63 9-73 192-256 (258)
140 smart00389 HOX Homeodomain. DN 28.2 40 0.00087 20.3 1.5 30 58-88 24-53 (56)
141 PF06514 PsbU: Photosystem II 27.7 51 0.0011 23.7 2.1 58 16-73 11-71 (93)
142 KOG2875 8-oxoguanine DNA glyco 27.6 23 0.00051 30.6 0.4 22 26-47 216-237 (323)
143 TIGR00194 uvrC excinuclease AB 27.2 36 0.00079 31.7 1.6 25 25-49 538-562 (574)
144 smart00483 POLXc DNA polymeras 27.2 31 0.00068 29.6 1.1 21 29-49 49-69 (334)
145 KOG2251 Homeobox transcription 27.1 47 0.001 27.6 2.0 31 59-90 44-92 (228)
146 PRK14666 uvrC excinuclease ABC 26.7 31 0.00068 33.0 1.1 25 25-49 634-658 (694)
147 PF13331 DUF4093: Domain of un 26.6 17 0.00036 25.6 -0.6 40 21-66 45-84 (87)
148 PF13442 Cytochrome_CBB3: Cyto 26.5 63 0.0014 20.3 2.2 14 58-71 54-67 (67)
149 PF04760 IF2_N: Translation in 26.0 30 0.00064 21.5 0.6 44 29-72 8-52 (54)
150 PF15614 WHIM3: WSTF, HB1, Itc 25.8 1.3E+02 0.0029 18.8 3.5 37 60-117 6-42 (46)
151 TIGR00608 radc DNA repair prot 25.8 28 0.00061 28.3 0.6 22 29-50 61-82 (218)
152 COG1948 MUS81 ERCC4-type nucle 25.8 48 0.001 27.9 1.9 38 27-66 181-218 (254)
153 TIGR00575 dnlj DNA ligase, NAD 25.6 35 0.00075 32.2 1.2 37 31-67 435-471 (652)
154 PF01698 FLO_LFY: Floricaula / 25.4 23 0.00051 31.5 0.0 77 31-125 55-131 (386)
155 COG1796 POL4 DNA polymerase IV 25.2 46 0.00099 29.1 1.7 21 29-49 54-74 (326)
156 TIGR02236 recomb_radA DNA repa 24.8 48 0.001 27.5 1.8 36 30-66 1-36 (310)
157 PRK04301 radA DNA repair and r 24.6 48 0.001 27.8 1.8 38 28-66 6-43 (317)
158 PF02879 PGM_PMM_II: Phosphogl 24.5 28 0.00062 24.1 0.3 41 10-50 5-46 (104)
159 COG0322 UvrC Nuclease subunit 23.8 46 0.001 31.2 1.6 43 23-67 525-567 (581)
160 PF00046 Homeobox: Homeobox do 22.3 37 0.0008 20.8 0.5 16 58-73 6-21 (57)
161 PF10500 SR-25: Nuclear RNA-sp 22.0 1.5E+02 0.0033 24.6 4.1 30 56-98 157-186 (225)
162 PRK08609 hypothetical protein; 21.8 31 0.00068 31.9 0.1 22 29-50 49-70 (570)
163 KOG2519 5'-3' exonuclease [Rep 21.8 92 0.002 28.4 3.0 34 7-49 217-250 (449)
164 PRK00024 hypothetical protein; 21.7 38 0.00082 27.6 0.6 22 29-50 67-88 (224)
165 TIGR03045 PS_II_C550 cytochrom 21.6 1.1E+02 0.0024 23.9 3.1 17 57-73 130-146 (159)
166 PF01418 HTH_6: Helix-turn-hel 21.6 72 0.0016 21.2 1.8 23 30-52 40-62 (77)
167 PF13613 HTH_Tnp_4: Helix-turn 21.5 56 0.0012 20.2 1.2 21 28-48 23-43 (53)
168 COG1636 Uncharacterized protei 21.1 1E+02 0.0022 25.2 2.8 81 48-148 118-198 (204)
169 PF14794 DUF4479: Domain of un 21.0 79 0.0017 21.5 1.9 16 58-73 47-62 (73)
170 PRK12766 50S ribosomal protein 20.4 64 0.0014 26.9 1.6 21 29-49 37-57 (232)
171 COG1059 Thermostable 8-oxoguan 20.3 57 0.0012 26.7 1.3 24 27-50 120-143 (210)
172 COG1194 MutY A/G-specific DNA 20.2 51 0.0011 29.0 1.1 36 9-47 97-132 (342)
173 KOG1921 Endonuclease III [Repl 20.1 41 0.00089 28.6 0.4 35 9-43 139-174 (286)
174 PF03118 RNA_pol_A_CTD: Bacter 20.1 57 0.0012 21.5 1.1 20 29-48 45-64 (66)
175 PRK07956 ligA NAD-dependent DN 20.1 44 0.00095 31.7 0.7 35 31-65 448-482 (665)
No 1
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=1.6e-67 Score=407.37 Aligned_cols=152 Identities=72% Similarity=1.162 Sum_probs=146.8
Q ss_pred CCCCC--ccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCcc
Q 031812 1 MSLVA--NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFK 78 (152)
Q Consensus 1 ~~~~~--~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ 78 (152)
|++.. +++|+||+||+|||||++|+|.+||++|||||+.+|.+||++|||||++++++||++|++.|.++|++|.+|.
T Consensus 1 ~~~~~~~~~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~ 80 (154)
T PTZ00134 1 MSLTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFK 80 (154)
T ss_pred CCccccchhhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCC
Confidence 44553 3589999999999999999999999999999999999999999999999999999999999999999988899
Q ss_pred CCcccccccCCcCCCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031812 79 IPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 79 ip~w~~nr~~d~~tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~~~gv~~~k 152 (152)
+|+||+|||+|++||+|.|+||+||++.+++||+||++|+||||+||++||||||||||||||||+++||++||
T Consensus 81 iP~w~~nr~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~~~gv~~kk 154 (154)
T PTZ00134 81 IPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK 154 (154)
T ss_pred CChhHhhccccccccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCccccccceeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=3.1e-66 Score=398.57 Aligned_cols=147 Identities=44% Similarity=0.804 Sum_probs=145.1
Q ss_pred ccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccc
Q 031812 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLN 85 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~n 85 (152)
+++|+||+||+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|++.|.++|++|..+.+|+||+|
T Consensus 3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~N 82 (149)
T PRK04053 3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLN 82 (149)
T ss_pred hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999989999999999
Q ss_pred ccCCcCCCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031812 86 RQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 86 r~~d~~tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~~~gv~~~k 152 (152)
|++|++||+|.|+||+||++.+++||+||++|+||||+||.+||||||||||||||||+++||+|||
T Consensus 83 r~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg~~~gv~~kk 149 (149)
T PRK04053 83 RRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTGGTVGVSRKK 149 (149)
T ss_pred cccccccCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999997
No 3
>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=1.4e-65 Score=393.08 Aligned_cols=144 Identities=49% Similarity=0.879 Sum_probs=142.0
Q ss_pred chhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccccc
Q 031812 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQ 87 (152)
Q Consensus 8 ~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~ 87 (152)
+|+||+||+|+|||++|+|.+||++|||||+++|.+||+++||||++++++||++|++.|.++|++ ..+.+|+||+||+
T Consensus 1 ~~~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~~Nr~ 79 (144)
T TIGR03629 1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWLLNRR 79 (144)
T ss_pred CcceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHHhhcc
Confidence 589999999999999999999999999999999999999999999999999999999999999998 6799999999999
Q ss_pred CCcCCCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031812 88 KDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 88 ~d~~tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~~~gv~~~k 152 (152)
+|++||+|.|+||+||++.+++||+||++|+||||+||.+||||||||||||||||+++||++||
T Consensus 80 ~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~~~gv~~kk 144 (144)
T TIGR03629 80 KDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGRTVGVSRKK 144 (144)
T ss_pred cccccCccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999997
No 4
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-52 Score=309.36 Aligned_cols=119 Identities=44% Similarity=0.705 Sum_probs=115.5
Q ss_pred hhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcC
Q 031812 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~ 91 (152)
|+||+|+|||++|.|.+|||+|||||.++|..||+++||||++++++|||+|+++|.++|++
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~------------------ 62 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN------------------ 62 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh------------------
Confidence 79999999999999999999999999999999999999999999999999999999999986
Q ss_pred CCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCC--ccceeeeccC
Q 031812 92 DGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR--GKTVGVSKKR 152 (152)
Q Consensus 92 tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart--~~~~gv~~~k 152 (152)
.|+||+||++++++||+||++|+||||+||.+|||||||||+||||| |.++||++||
T Consensus 63 ----~~~vegDLr~~v~~dIkRl~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 63 ----KYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred ----cCeehhHHHHHHHHHHHHHHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 25679999999999999999999999999999999999999999999 9999999987
No 5
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-51 Score=314.25 Aligned_cols=152 Identities=69% Similarity=1.142 Sum_probs=150.7
Q ss_pred CCCCCccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCC
Q 031812 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIP 80 (152)
Q Consensus 1 ~~~~~~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip 80 (152)
|||+.++.|+||+||||++++++++|.|||++|||||...|..+|+++||++.+++++|+++|++.+.+++++|..+.+|
T Consensus 1 msl~~~~~~q~i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~ 80 (152)
T KOG3311|consen 1 MSLVIPEAFQHILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIP 80 (152)
T ss_pred CceecchhHHHHHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcCCCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031812 81 DWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 81 ~w~~nr~~d~~tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~~~gv~~~k 152 (152)
.|++|+++|.++|+..|++.+.|+..++++|+|+++|.||||+||.+|||||||||+|||+.|++|||++||
T Consensus 81 ~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 81 DWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGRRGKTVGVSGKK 152 (152)
T ss_pred hHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccccccceeeecccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997
No 6
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=7.4e-49 Score=293.46 Aligned_cols=111 Identities=31% Similarity=0.499 Sum_probs=107.3
Q ss_pred hhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcC
Q 031812 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~ 91 (152)
|+||+|||||++|+|.+||++|||||+++|.+||+++||||++++++|+++|++.|.++|++ +|.
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~~------------- 65 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NYQ------------- 65 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hCc-------------
Confidence 79999999999999999999999999999999999999999999999999999999999986 343
Q ss_pred CCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCcc
Q 031812 92 DGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK 144 (152)
Q Consensus 92 tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~ 144 (152)
||+||++.+++||+||++|+||||+||.+|||||||||||||||++
T Consensus 66 -------i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~tNarT~k 111 (122)
T CHL00137 66 -------VEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRR 111 (122)
T ss_pred -------chHHHHHHHHHHHHHHHHhCchhcccccCCCCCCCCcCCccccccC
Confidence 5999999999999999999999999999999999999999999987
No 7
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=9.6e-49 Score=292.83 Aligned_cols=111 Identities=34% Similarity=0.529 Sum_probs=107.6
Q ss_pred hhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcC
Q 031812 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~ 91 (152)
||||+|||||++|+|.+||++|||||+++|.+||+++||||++++++|+++|++.|.++|+++ |
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~--~-------------- 64 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKN--Y-------------- 64 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhh--c--------------
Confidence 899999999999999999999999999999999999999999999999999999999999873 3
Q ss_pred CCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCcc
Q 031812 92 DGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK 144 (152)
Q Consensus 92 tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~ 144 (152)
.+|+||++++++||+||++|+||||+||++|||||||||||||||++
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~TNart~k 111 (122)
T PRK05179 65 ------KVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 111 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhcceeeeecccCCCCCCCcCCccccccC
Confidence 36999999999999999999999999999999999999999999997
No 8
>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=4.1e-47 Score=280.71 Aligned_cols=111 Identities=35% Similarity=0.519 Sum_probs=106.4
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcCCC
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg 93 (152)
||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++|+++|++.|.++|+++ |
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~--~---------------- 62 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAK--Y---------------- 62 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhc--C----------------
Confidence 7999999999999999999999999999999999999999999999999999999999873 3
Q ss_pred cceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCccce
Q 031812 94 RYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV 146 (152)
Q Consensus 94 ~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~~~ 146 (152)
.||+||++.+++||+||++|+||||+||++|||||||||||||||++..
T Consensus 63 ----~i~~~L~~~~~~dI~rl~~I~syRG~RH~~gLpVRGQRT~TNart~k~~ 111 (113)
T TIGR03631 63 ----KVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGP 111 (113)
T ss_pred ----cchHHHHHHHHHHHHHHHHhcceeccccccCCCCCCCcCCccccccCCC
Confidence 3699999999999999999999999999999999999999999999853
No 9
>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=2.5e-47 Score=278.78 Aligned_cols=107 Identities=45% Similarity=0.770 Sum_probs=101.7
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcCCC
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg 93 (152)
||+||+||++|+|.+||++|||||+++|.+||+++||+|++++++|+++|++.|.++|++
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~-------------------- 60 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK-------------------- 60 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--------------------
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--------------------
Confidence 799999999999999999999999999999999999999999999999999999999987
Q ss_pred cceeeehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCC
Q 031812 94 RYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR 142 (152)
Q Consensus 94 ~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart 142 (152)
.|++|+||++++++||+||++|+||||+||.+|||||||||||||||
T Consensus 61 --~~~i~~~L~~~~~~~i~rl~~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 61 --NHLIENDLKRQVRENIKRLKKIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp --HSTCHHHHHHHHHHHHHHHHHHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred --hccccchHHHHHHHHHHHHHHHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 24579999999999999999999999999999999999999999986
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=97.06 E-value=0.00055 Score=48.65 Aligned_cols=51 Identities=29% Similarity=0.389 Sum_probs=42.6
Q ss_pred CCeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 22 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
.+++|..+| +.+-|||...|..||-++||+|..++++|+++|+..|-+.+.
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 477887777 459999999999999999999999999999999999887764
No 11
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=96.92 E-value=0.0011 Score=55.32 Aligned_cols=53 Identities=30% Similarity=0.377 Sum_probs=48.4
Q ss_pred CCCeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 21 DGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
..++.|..+| +-+-|||.-.|..||-++||+|..++++||++|++.|-+.+.+
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 3567899999 8899999999999999999999999999999999999887754
No 12
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.17 E-value=0.0056 Score=51.21 Aligned_cols=52 Identities=25% Similarity=0.341 Sum_probs=45.2
Q ss_pred CCeEeeeeecc---ccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 22 GKQKIMFALTS---IKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aLt~---I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
.+..|..+|.. |-|||.-.|..||-++||+|..++++||++|++.|-+.+..
T Consensus 153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~ 207 (272)
T PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE 207 (272)
T ss_pred CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence 45667777755 49999999999999999999999999999999988886543
No 13
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.10 E-value=0.0084 Score=50.14 Aligned_cols=51 Identities=20% Similarity=0.229 Sum_probs=44.5
Q ss_pred CCeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 22 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
.+++|.-+| +-|-|||...|..||-.++|+|..++++||++|++.|-+.+.
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 367887777 448999999999999999999999999999999998866554
No 14
>PRK10445 endonuclease VIII; Provisional
Probab=95.97 E-value=0.01 Score=49.39 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=44.1
Q ss_pred CeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 23 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
+++|.-+| +-+-|||.-.|..||-.++|+|..++++||++|++.|-+.+.+
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 204 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLD 204 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence 55666666 3378999999999999999999999999999999999887754
No 15
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=95.95 E-value=0.01 Score=49.84 Aligned_cols=52 Identities=27% Similarity=0.355 Sum_probs=45.4
Q ss_pred CCeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
....|.-+| +-|-|||.-.|..||-.++|+|..++++||++|++.|-+.+..
T Consensus 163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~ 217 (282)
T PRK13945 163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE 217 (282)
T ss_pred CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 466777777 4489999999999999999999999999999999988877754
No 16
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.88 E-value=0.01 Score=49.55 Aligned_cols=52 Identities=31% Similarity=0.355 Sum_probs=45.5
Q ss_pred CCeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
.+..|..+| +-|-|||.-.|..||-+++|+|..++++||++|++.|-+.+.+
T Consensus 154 ~~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 208 (272)
T TIGR00577 154 SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE 208 (272)
T ss_pred CCCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence 456777777 4488999999999999999999999999999999999887754
No 17
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=94.67 E-value=0.051 Score=49.89 Aligned_cols=49 Identities=27% Similarity=0.405 Sum_probs=44.9
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCC
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANP 74 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~ 74 (152)
..|.-..+-.||..+|..||+.+|++++++..+|+++|+..|.+++.+.
T Consensus 259 ~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 259 KEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred HHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 3555577999999999999999999999999999999999999999874
No 18
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=93.58 E-value=0.038 Score=31.66 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=15.1
Q ss_pred eeccccccchhhHHHHHH
Q 031812 29 ALTSIKGIGRRLANIVCK 46 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~ 46 (152)
.|.+++|||+++|..|+.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 478999999999999975
No 19
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=93.18 E-value=0.1 Score=44.12 Aligned_cols=59 Identities=25% Similarity=0.368 Sum_probs=48.0
Q ss_pred hcCcccCCCeEeeeee---ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 15 VLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 15 i~~~~l~~~k~v~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
+...-...+++|.-+| +-|-|||...|..+|=++||+|...+++|+.+|+..|.+.+.+
T Consensus 147 l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~ 208 (273)
T COG0266 147 LAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKD 208 (273)
T ss_pred HHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHH
Confidence 3344445556677777 4489999999999999999999999999999998888777653
No 20
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=92.74 E-value=0.03 Score=49.24 Aligned_cols=51 Identities=29% Similarity=0.455 Sum_probs=36.0
Q ss_pred CCeEeeeeecccc-ccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 22 GKQKIMFALTSIK-GIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 22 ~~k~v~~aLt~I~-GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
+...+..+|...+ |+|+..|..+|.++|++++.++.+++++++..|.+.+.
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 4566666776655 99999999999999999999999999998766554443
No 21
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=92.57 E-value=0.19 Score=45.74 Aligned_cols=48 Identities=19% Similarity=0.347 Sum_probs=43.9
Q ss_pred eeeeccccccchhhHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhCC
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDQLMVVVANP 74 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~---~~~kv~~Ls~~qi~~L~~~i~~~ 74 (152)
.|.-..+-.||..+|..||..+|++ ++++..+|+++|++.|.+++.+.
T Consensus 251 ~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 301 (488)
T TIGR01052 251 SFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKEM 301 (488)
T ss_pred HHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHhc
Confidence 4555779999999999999999999 99999999999999999999873
No 22
>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=90.62 E-value=0.15 Score=44.25 Aligned_cols=51 Identities=24% Similarity=0.427 Sum_probs=43.9
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
.+++.+...|..+ +-.+.+..||+.+||++++++++|+++|++.|.+.|.+
T Consensus 281 ~~~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 281 NPKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred ChhhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 3366666666643 78899999999999999999999999999999999987
No 23
>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=89.06 E-value=0.21 Score=28.82 Aligned_cols=21 Identities=24% Similarity=0.488 Sum_probs=15.2
Q ss_pred eeccccccchhhHHHHHHHhCC
Q 031812 29 ALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
.+++++|||+.++..+ +++||
T Consensus 12 pi~~~~GIG~kt~~kL-~~~GI 32 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL-NKLGI 32 (32)
T ss_dssp BGGGSTTS-HHHHHHH-HCTT-
T ss_pred CHHhhCCccHHHHHHH-HHccC
Confidence 5789999999999984 44443
No 24
>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=88.36 E-value=0.04 Score=35.67 Aligned_cols=35 Identities=20% Similarity=0.249 Sum_probs=24.3
Q ss_pred eeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHH
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAA 62 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ 62 (152)
+.+|.+|.|||+..|..+.+. |+..-..+-..+.+
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~-G~~t~~~l~~a~~~ 38 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEA-GIKTLEDLANADPE 38 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHT-TCSSHHHHHTSHHH
T ss_pred HHhhccCCCCCHHHHHHHHhc-CCCcHHHHHcCCHH
Confidence 457889999999999999876 76643333333333
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=87.24 E-value=0.33 Score=31.11 Aligned_cols=22 Identities=23% Similarity=0.314 Sum_probs=15.6
Q ss_pred eeccccccchhhHHHHHHHhCCC
Q 031812 29 ALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi~ 51 (152)
.+++|+|||+.+|....+ .|+.
T Consensus 3 ~f~~I~GVG~~tA~~w~~-~G~r 24 (52)
T PF10391_consen 3 LFTGIWGVGPKTARKWYA-KGIR 24 (52)
T ss_dssp HHHTSTT--HHHHHHHHH-TT--
T ss_pred chhhcccccHHHHHHHHH-hCCC
Confidence 368999999999999987 6654
No 26
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=86.57 E-value=0.46 Score=36.29 Aligned_cols=44 Identities=18% Similarity=0.229 Sum_probs=39.2
Q ss_pred eeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
--||.|.|||+..+.. ++-+||--...+-.+|..++..+..+|+
T Consensus 67 DDLt~I~GIGPk~e~~-Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 67 DDLTRISGIGPKLEKV-LNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred ccchhhcccCHHHHHH-HHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 4699999999998765 5789999999999999999999999985
No 27
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=86.42 E-value=0.46 Score=25.83 Aligned_cols=19 Identities=26% Similarity=0.468 Sum_probs=16.5
Q ss_pred eeccccccchhhHHHHHHH
Q 031812 29 ALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~ 47 (152)
.|..++|||..+|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3678999999999999863
No 28
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=85.50 E-value=0.52 Score=38.98 Aligned_cols=62 Identities=21% Similarity=0.288 Sum_probs=45.3
Q ss_pred hhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
|..+++.+ .--..|.+..+|..+++. ...+..+++.+|++++.++.+|+.+|+..|-+.++.
T Consensus 209 ~~~~~~~~--F~~rrk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 209 FFRVVKAA--FAQRRKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHHHHHHH--HhchHHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 44444432 233466667777776542 245678899999999999999999999999988764
No 29
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=85.23 E-value=0.42 Score=36.45 Aligned_cols=59 Identities=20% Similarity=0.183 Sum_probs=44.8
Q ss_pred hcCcccCCCeEeeeeeccccccchhhHHHHHHHhC---CCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 15 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD---VDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 15 i~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg---i~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
-++..|+-|..=..+|+.++|||+..|.+|++.-. ++.-..+.-+++.|.+.|+++.++
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDN 109 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcc
Confidence 35666776766777899999999999999995322 222235777899999999998876
No 30
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.91 E-value=0.53 Score=37.58 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=18.2
Q ss_pred eeeccccccchhhHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.+|++++|||+++|.+||-.|
T Consensus 108 ~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 479999999999999999544
No 31
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=83.65 E-value=0.19 Score=39.19 Aligned_cols=45 Identities=13% Similarity=-0.073 Sum_probs=38.7
Q ss_pred ehhhHHHHHHHhHHHhHhhceeecccCCCCCccCCcCCcccCCCccc
Q 031812 99 VSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKT 145 (152)
Q Consensus 99 i~~dL~~~~~~~I~rl~~I~syRG~RH~~gLPVRGQRTrTNart~~~ 145 (152)
+.+|.+.+...++....++.+|.|- ..+||+.||.|+.|+.+.+.
T Consensus 70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRl 114 (152)
T KOG3311|consen 70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERL 114 (152)
T ss_pred HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHH
Confidence 3457777888899999999999999 99999999999999876643
No 32
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=83.59 E-value=1.4 Score=40.26 Aligned_cols=48 Identities=23% Similarity=0.351 Sum_probs=43.7
Q ss_pred eeeeccccccchhhHHHHHHHhCCCCCCcCCCCC----HHHHHHHHHHHhCC
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELS----AAELDQLMVVVANP 74 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls----~~qi~~L~~~i~~~ 74 (152)
.|....+--||..+|..+|+.+|++|++++.+|+ .+|.+.|.+++...
T Consensus 260 ~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 260 EFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred HHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 5556778899999999999999999999999999 99999999999873
No 33
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.01 E-value=0.61 Score=37.18 Aligned_cols=21 Identities=24% Similarity=0.371 Sum_probs=18.1
Q ss_pred eeeccccccchhhHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 479999999999999999443
No 34
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.95 E-value=0.71 Score=37.08 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=18.2
Q ss_pred eeeccccccchhhHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.+|++++|||+++|.+||-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 479999999999999999543
No 35
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.77 E-value=0.72 Score=37.05 Aligned_cols=20 Identities=35% Similarity=0.549 Sum_probs=17.6
Q ss_pred eeeccccccchhhHHHHHHH
Q 031812 28 FALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~ 47 (152)
.+|++++|||+++|.+||-.
T Consensus 107 ~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 47999999999999999943
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.49 E-value=0.75 Score=37.18 Aligned_cols=21 Identities=29% Similarity=0.501 Sum_probs=18.1
Q ss_pred eeeccccccchhhHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+|+-.|
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 479999999999999999443
No 37
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=81.33 E-value=0.78 Score=38.56 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=42.3
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
...|.+..+|+..++ ...+|+.+|++++.++.+|+.+|+-.|.+.+..
T Consensus 209 ~RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 209 QRRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hhhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 356777888888777 889999999999999999999999999998864
No 38
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=80.98 E-value=0.87 Score=36.93 Aligned_cols=21 Identities=33% Similarity=0.498 Sum_probs=18.2
Q ss_pred eeeccccccchhhHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+||-.|
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 479999999999999999543
No 39
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.59 E-value=0.85 Score=36.78 Aligned_cols=20 Identities=35% Similarity=0.554 Sum_probs=17.5
Q ss_pred eeeccccccchhhHHHHHHH
Q 031812 28 FALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~ 47 (152)
-+|++++|||+++|.+|+-.
T Consensus 109 ~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHhcCCCcCHHHHHHHHHH
Confidence 37999999999999999943
No 40
>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=80.24 E-value=0.55 Score=37.46 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=24.2
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
|+...+...|.+++|||+.+|..++.-||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 55556667899999999999999997765
No 41
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=79.44 E-value=2.1 Score=25.31 Aligned_cols=34 Identities=18% Similarity=0.354 Sum_probs=24.0
Q ss_pred cchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHH
Q 031812 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
++|-.+.=+.| |-.++ +..|+|||..+|..++++
T Consensus 2 ~q~~~~~~L~G-D~~dn------i~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 2 EQLIDYAILVG-DYSDN------IPGVKGIGPKTALKLLRE 35 (36)
T ss_pred HHHHHHHHHhC-cCCCC------CCCCCcccHHHHHHHHHh
Confidence 44556666667 44333 367899999999999865
No 42
>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=78.13 E-value=1.8 Score=30.05 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=21.6
Q ss_pred CeEeeeeeccccccchhhHHHHHHHhC
Q 031812 23 KQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 23 ~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
+..|.++|+.|+|||...|..|++.-.
T Consensus 22 ~~~Ir~gl~~Ikglg~~~a~~I~~~R~ 48 (90)
T PF14579_consen 22 NNAIRLGLSAIKGLGEEVAEKIVEERE 48 (90)
T ss_dssp -TEEE-BGGGSTTS-HHHHHHHHHHHH
T ss_pred CCEEeehHhhcCCCCHHHHHHHHHhHh
Confidence 478999999999999999999997653
No 43
>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=77.81 E-value=2 Score=37.96 Aligned_cols=51 Identities=27% Similarity=0.402 Sum_probs=44.0
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhCC-CCCCcCCCCCHHHHHHHHHHHhC
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKADV-DMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi-~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
.+++.+...|..+ +-.+.+..+|+.++| +++.++.+|+++++..|.+.|.+
T Consensus 288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 4567777777776 889999999999999 99999999999999999999987
No 44
>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=76.75 E-value=7.2 Score=32.24 Aligned_cols=52 Identities=10% Similarity=0.115 Sum_probs=41.9
Q ss_pred CeEeeeeeccccccchhhHHHHHHHhCCCCCCc------------CCCCCHHHHHHHHHHHhCC
Q 031812 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKR------------AGELSAAELDQLMVVVANP 74 (152)
Q Consensus 23 ~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k------------v~~Ls~~qi~~L~~~i~~~ 74 (152)
...+..-=-..+|+|+....+|.+++|+=++.+ -..||++|++.|-++...+
T Consensus 96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~~ 159 (225)
T PF09883_consen 96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRDG 159 (225)
T ss_pred cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhCC
Confidence 333334445578999999999999999998888 5579999999999998763
No 45
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.47 E-value=1.6 Score=34.88 Aligned_cols=19 Identities=37% Similarity=0.637 Sum_probs=16.5
Q ss_pred eeeccccccchhhHHHHHHH
Q 031812 28 FALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~ 47 (152)
.+| +++|||+++|.+||-.
T Consensus 108 ~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHH
Confidence 478 8999999999999944
No 46
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=76.25 E-value=2.1 Score=39.55 Aligned_cols=50 Identities=22% Similarity=0.292 Sum_probs=44.0
Q ss_pred EeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCC
Q 031812 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANP 74 (152)
Q Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~ 74 (152)
-+..+|..+.|+|.-.|..+|-++|+++...+.++.++++..+...+.++
T Consensus 187 ~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~~ 236 (564)
T COG1293 187 DIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEEL 236 (564)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHhh
Confidence 34567888999999999999999999999999999999999998876553
No 47
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=76.04 E-value=1.6 Score=35.55 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=42.4
Q ss_pred hhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHH
Q 031812 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVV 70 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~ 70 (152)
|.++++.+ .--..|.+..+|..+++- ..+..+++.+|+++++++.+|+.+|+..|.+.
T Consensus 195 ~~~~~~~~--F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 195 FEKLLKAA--FSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HHHHHHHH--HccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 55555542 234567777777776442 34567888899999999999999999998764
No 48
>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=76.00 E-value=0.77 Score=37.70 Aligned_cols=62 Identities=24% Similarity=0.311 Sum_probs=48.5
Q ss_pred cchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
+.|.++++.+=. -..|.+..+|..+++ ...+..+.+.+||+++.++.+|+.+|+..|-++|+
T Consensus 200 ~~~~~~~~~~F~--~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 200 DAFEYFVRQLFS--QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHHHHHHHHHHT--TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh--CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 357777766533 588889988888754 33346667779999999999999999999998875
No 49
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=75.78 E-value=1.4 Score=28.86 Aligned_cols=18 Identities=28% Similarity=0.589 Sum_probs=14.1
Q ss_pred cccccchhhHHHHHHHhC
Q 031812 32 SIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 32 ~I~GIG~~~A~~Ic~~lg 49 (152)
.|+|||..+|..+++.+|
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 689999999999998887
No 50
>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=74.72 E-value=2 Score=30.84 Aligned_cols=36 Identities=22% Similarity=0.168 Sum_probs=26.7
Q ss_pred eeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHH
Q 031812 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi 64 (152)
..|+.|+|||+++|.-+. .+||+.-..+..-+++++
T Consensus 12 ~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~L 47 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEEL 47 (93)
T ss_pred HHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHH
Confidence 458999999999999987 899987444444444444
No 51
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.70 E-value=1.7 Score=34.81 Aligned_cols=18 Identities=33% Similarity=0.567 Sum_probs=15.9
Q ss_pred eeeccccccchhhHHHHH
Q 031812 28 FALTSIKGIGRRLANIVC 45 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic 45 (152)
.+|++++|||+++|.+|+
T Consensus 108 ~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 368999999999999976
No 52
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=73.45 E-value=1.3 Score=29.05 Aligned_cols=44 Identities=16% Similarity=0.234 Sum_probs=27.8
Q ss_pred eeeeeccccccchhhHHHHHHHh-------CCCCCCcCCCCCHHHHHHHHH
Q 031812 26 IMFALTSIKGIGRRLANIVCKKA-------DVDMNKRAGELSAAELDQLMV 69 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~l-------gi~~~~kv~~Ls~~qi~~L~~ 69 (152)
=...|..++|||...|.+|.+.= .++.-..+..++++.+++|..
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 34568899999999999999664 344444666677777777654
No 53
>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=72.43 E-value=2.4 Score=27.16 Aligned_cols=20 Identities=35% Similarity=0.561 Sum_probs=17.7
Q ss_pred eeccccccchhhHHHHHHHh
Q 031812 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~l 48 (152)
.|..++|||+.+|..|++.+
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 48899999999999998765
No 54
>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=72.43 E-value=2.1 Score=28.25 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.4
Q ss_pred eeccccccchhhHHHHHHHh
Q 031812 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~l 48 (152)
++++|+|||.++|..|-+.+
T Consensus 48 ~~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHH
Confidence 68999999999999997644
No 55
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.68 E-value=0.72 Score=36.90 Aligned_cols=36 Identities=14% Similarity=0.276 Sum_probs=30.7
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.++|-.=...+.++.-|.++.|||+++|..|+..++
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~ 94 (194)
T PRK14605 59 SLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMN 94 (194)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCC
Confidence 566777777888888999999999999999997765
No 56
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=71.19 E-value=2.3 Score=29.80 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=20.6
Q ss_pred eeecc-ccccchhhHHHHHHHhCCCCC
Q 031812 28 FALTS-IKGIGRRLANIVCKKADVDMN 53 (152)
Q Consensus 28 ~aLt~-I~GIG~~~A~~Ic~~lgi~~~ 53 (152)
|.|.. |.|||..+|..|..++|++++
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 55655 999999999999999998864
No 57
>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=70.99 E-value=3 Score=28.22 Aligned_cols=38 Identities=21% Similarity=0.363 Sum_probs=27.6
Q ss_pred CccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 5 ~~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
++++|..+.=+.|-..|. +..|+|||+.+|..|+...|
T Consensus 6 ~~~q~~d~~~L~GD~~D~-------i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 6 TPEQFIDLAILVGDKSDN-------IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CHHHHHHHHHHcCCcccc-------CCCCCcccHHHHHHHHHHhC
Confidence 456777777777722222 34689999999999998866
No 58
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=70.69 E-value=2.6 Score=33.49 Aligned_cols=59 Identities=10% Similarity=0.226 Sum_probs=38.3
Q ss_pred hcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCC------------CcCCCCCHHHHHHHHHHHhC
Q 031812 15 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMN------------KRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 15 i~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~------------~kv~~Ls~~qi~~L~~~i~~ 73 (152)
+.|-.=...+.+...|..|+|||+.+|..|++.+|.+.- .++.-+++...++|...+.+
T Consensus 60 l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 60 LYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 355553334455568899999999999999999885221 12333555666666655544
No 59
>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=69.95 E-value=4.2 Score=26.20 Aligned_cols=26 Identities=8% Similarity=0.190 Sum_probs=20.1
Q ss_pred ccccchhhHHHHHHHhCCC--CCCcCCC
Q 031812 33 IKGIGRRLANIVCKKADVD--MNKRAGE 58 (152)
Q Consensus 33 I~GIG~~~A~~Ic~~lgi~--~~~kv~~ 58 (152)
--||+..+-+.+|+++||. |-.++.+
T Consensus 24 ~Lgv~~T~LKr~CR~~GI~RWP~Rkl~S 51 (52)
T PF02042_consen 24 ELGVSVTTLKRRCRRLGIPRWPYRKLKS 51 (52)
T ss_pred HhCCCHHHHHHHHHHcCCCCCCchhhcc
Confidence 4689999999999999997 4444433
No 60
>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=69.87 E-value=2.3 Score=27.91 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=20.2
Q ss_pred CeEeeeeecc-ccccchhhHHHHHHHh
Q 031812 23 KQKIMFALTS-IKGIGRRLANIVCKKA 48 (152)
Q Consensus 23 ~k~v~~aLt~-I~GIG~~~A~~Ic~~l 48 (152)
|..-...|.. +.|||...|.+|++.-
T Consensus 11 Nta~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 11 NTATAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred cCCCHHHHHhHCCCCCHHHHHHHHHHH
Confidence 3333446777 9999999999999884
No 61
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=69.81 E-value=2 Score=31.75 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=24.7
Q ss_pred cCCCeEeeeeeccccccchhhHHHHHHHhCC
Q 031812 20 VDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 20 l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
++-|..-...|..++|||+.+|.+|.+..+-
T Consensus 60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 60 VNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 4445555667899999999999999988753
No 62
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=69.59 E-value=3.3 Score=28.51 Aligned_cols=20 Identities=40% Similarity=0.423 Sum_probs=18.4
Q ss_pred eeccccccchhhHHHHHHHh
Q 031812 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~l 48 (152)
.|++|+|||..+|..|+..+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 47899999999999999887
No 63
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=67.41 E-value=2.1 Score=32.08 Aligned_cols=25 Identities=28% Similarity=0.383 Sum_probs=21.7
Q ss_pred CeEeeeeeccccccchhhHHHHHHH
Q 031812 23 KQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 23 ~k~v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
...+...|++++|||+.+|..++..
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHH
Confidence 3567888999999999999999875
No 64
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=66.37 E-value=4.6 Score=33.25 Aligned_cols=45 Identities=24% Similarity=0.319 Sum_probs=40.3
Q ss_pred eeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
-.|+.|.|||+..+..+ ..+|+.....+-.++++++..+...++-
T Consensus 158 DDL~~I~GIGp~~a~~L-~eaGi~tfaQIAa~t~a~ia~id~~l~~ 202 (221)
T PRK12278 158 DDLTKITGVGPALAKKL-NEAGVTTFAQIAALTDADIAKIDEKLSF 202 (221)
T ss_pred chheeccccChHHHHHH-HHcCCCCHHHhhCCChhhhhhhhhcccC
Confidence 56999999999999875 6899999999999999999999998854
No 65
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=65.93 E-value=3.7 Score=35.30 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=21.9
Q ss_pred eeeeccccccchhhHHHHHHHhCCCC
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~~ 52 (152)
...|++|+|||+++|..+.+ +||..
T Consensus 88 l~~l~~i~GiGpk~a~~l~~-lGi~t 112 (334)
T smart00483 88 LKLFTNVFGVGPKTAAKWYR-KGIRT 112 (334)
T ss_pred HHHHHccCCcCHHHHHHHHH-hCCCC
Confidence 45678999999999999999 99875
No 66
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=65.88 E-value=3.2 Score=30.80 Aligned_cols=23 Identities=35% Similarity=0.356 Sum_probs=19.4
Q ss_pred eeeeeccccccchhhHHHHHHHh
Q 031812 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
....|.+++|||+.+|..+|...
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 45668899999999999998764
No 67
>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=65.55 E-value=3.3 Score=33.00 Aligned_cols=19 Identities=32% Similarity=0.459 Sum_probs=16.8
Q ss_pred eeeccccccchhhHHHHHH
Q 031812 28 FALTSIKGIGRRLANIVCK 46 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~ 46 (152)
-+|++++|||+++|.+|+-
T Consensus 107 ~~L~~ipGiGkKtAerIil 125 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLLL 125 (191)
T ss_pred HHHHhCCCCCHHHHHHHHH
Confidence 4688999999999999983
No 68
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=63.93 E-value=4.3 Score=26.56 Aligned_cols=35 Identities=26% Similarity=0.513 Sum_probs=22.3
Q ss_pred chhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 8 ~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.|..+=.|...+.+ .|+.++|||+.+|..|.+.+.
T Consensus 22 ~f~sl~~l~~a~~e-------~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 22 HFGSLEALMNASVE-------ELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp CCSCHHHHCC--HH-------HHCTSTT--HHHHHHHHHHHH
T ss_pred HcCCHHHHHHcCHH-------HHhccCCcCHHHHHHHHHHHC
Confidence 35555555554443 689999999999999987664
No 69
>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=63.39 E-value=3.2 Score=34.92 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=23.1
Q ss_pred cCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 16 ~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.|-.+|.. ...|.+++|||+.+|..|+..+
T Consensus 96 ~~g~~p~~---~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 96 FGGEFPQD---FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred cCCCCcHH---HHHHHhCCCCCHHHHHHHHHHH
Confidence 34456643 5679999999999999998654
No 70
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.90 E-value=2.2 Score=33.98 Aligned_cols=34 Identities=26% Similarity=0.401 Sum_probs=28.3
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHH
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
.++|-.=...+.++.-|.++.|||+++|.+|+..
T Consensus 59 ~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 59 KLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred eeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcC
Confidence 5666666777888889999999999999999743
No 71
>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=62.25 E-value=4.9 Score=34.14 Aligned_cols=24 Identities=17% Similarity=0.373 Sum_probs=20.6
Q ss_pred eeeccccccchhhHHHHHHHhCCCC
Q 031812 28 FALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~~ 52 (152)
..|++|+|||+++|..+. .+|+..
T Consensus 85 ~~l~~i~GiGpk~a~~l~-~lGi~s 108 (307)
T cd00141 85 LLLLRVPGVGPKTARKLY-ELGIRT 108 (307)
T ss_pred HHHHcCCCCCHHHHHHHH-HcCCCC
Confidence 356789999999999999 899874
No 72
>PRK08609 hypothetical protein; Provisional
Probab=61.83 E-value=5.3 Score=36.89 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=21.5
Q ss_pred eeeccccccchhhHHHHHHHhCCC
Q 031812 28 FALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~ 51 (152)
..|++|+|||+++|.++.+.+||.
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Confidence 367899999999999999999984
No 73
>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=60.86 E-value=0.96 Score=36.09 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=27.9
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHH
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
.++|-.=...+.++..|.++.|||+++|..|+..
T Consensus 58 ~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 58 LLFGFNTLEERELFKELIKVNGVGPKLALAILSN 91 (191)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhc
Confidence 4666666777888889999999999999999543
No 74
>PRK10702 endonuclease III; Provisional
Probab=60.83 E-value=4.8 Score=32.52 Aligned_cols=23 Identities=39% Similarity=0.562 Sum_probs=19.2
Q ss_pred eeeeeccccccchhhHHHHHHHh
Q 031812 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
....|.+++|||+++|..|+..+
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHHH
Confidence 35779999999999999987543
No 75
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=60.66 E-value=4.9 Score=31.58 Aligned_cols=23 Identities=35% Similarity=0.465 Sum_probs=19.2
Q ss_pred eeeeeccccccchhhHHHHHHHh
Q 031812 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
....|++++|||+.+|..||...
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHH
Confidence 35679999999999999998544
No 76
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=60.48 E-value=4.3 Score=35.22 Aligned_cols=45 Identities=9% Similarity=0.083 Sum_probs=39.6
Q ss_pred eeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
.--|+.|.|||+..+.. |..+|+.....+..++++++..+...+.
T Consensus 262 ~DdL~~I~GiGp~~e~~-L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 262 PDDLKKLTGVSPQIEKK-LNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred chhhhhhccCChhhhhh-hhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 35699999999998765 6889999999999999999998888875
No 77
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.03 E-value=2.7 Score=33.77 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=28.7
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.++|-.=...+.++.-|.++.|||+++|.+|+..+
T Consensus 58 ~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 58 SLYGFPDEDSLELFELLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred eeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 45666667778888899999999999999997543
No 78
>PRK03980 flap endonuclease-1; Provisional
Probab=59.49 E-value=8.1 Score=32.80 Aligned_cols=35 Identities=31% Similarity=0.410 Sum_probs=28.1
Q ss_pred ccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.++|-.+.=++|+|-.+ .|+|||+.+|..+++..|
T Consensus 176 ~~q~id~~iL~G~Dy~~---------GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 176 REQLIDIAILVGTDYNP---------GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred HHHHHHHHHhcCCCCCC---------CCCCccHHHHHHHHHHCC
Confidence 35677888888865433 688999999999999887
No 79
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=58.26 E-value=6.4 Score=32.00 Aligned_cols=43 Identities=16% Similarity=0.116 Sum_probs=28.7
Q ss_pred Eeeeeec-cccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 031812 25 KIMFALT-SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (152)
Q Consensus 25 ~v~~aLt-~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i 71 (152)
.....|. +++|||+.+|..|+...|..|-.-+ |..+.++.+-+
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iV----DtHv~Ri~~Rl 158 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGYEDLAIL----DRHILRFLKRY 158 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccCCCeeee----eHHHHHHHHHh
Confidence 4455677 9999999999999965665443322 34555555544
No 80
>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=56.61 E-value=9.8 Score=32.05 Aligned_cols=35 Identities=26% Similarity=0.280 Sum_probs=28.2
Q ss_pred ccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.++|-.+.=++|+|--+ .|+|||+.+|..+++..|
T Consensus 210 ~~q~id~~~L~G~Dy~~---------gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 210 REKLIDLAILLGCDYTE---------GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred HHHHHHHHHhcCCCCCC---------CCCCccHHHHHHHHHHcC
Confidence 45677777888866544 589999999999999987
No 81
>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=55.59 E-value=12 Score=35.45 Aligned_cols=41 Identities=27% Similarity=0.405 Sum_probs=28.7
Q ss_pred cccccchhhHHHHHHHhCCCC--------C--CcCCCCCHHHHHHHHHHHh
Q 031812 32 SIKGIGRRLANIVCKKADVDM--------N--KRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 32 ~I~GIG~~~A~~Ic~~lgi~~--------~--~kv~~Ls~~qi~~L~~~i~ 72 (152)
.|+|||+.+|..|++.+|.+. . ..+.-|+++..+.|.+.+.
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~ 138 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWS 138 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 499999999999999998652 1 2334466666666665554
No 82
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.34 E-value=2.2 Score=34.38 Aligned_cols=36 Identities=14% Similarity=0.202 Sum_probs=29.7
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.++|-.=...+.++..|.++.|||+++|..|+..++
T Consensus 60 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~ 95 (203)
T PRK14602 60 ELFGFATWDERQTFIVLISISKVGAKTALAILSQFR 95 (203)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCC
Confidence 556666667778888899999999999999986654
No 83
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.16 E-value=1.7 Score=34.72 Aligned_cols=35 Identities=14% Similarity=0.311 Sum_probs=28.6
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.++|-.=...+.++..|.++.|||+++|.+|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~ 93 (188)
T PRK14606 59 TLYGFSNERKKELFLSLTKVSRLGPKTALKIISNE 93 (188)
T ss_pred eeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 45666666778888899999999999999997443
No 84
>PTZ00217 flap endonuclease-1; Provisional
Probab=54.64 E-value=11 Score=33.43 Aligned_cols=35 Identities=26% Similarity=0.332 Sum_probs=27.6
Q ss_pred ccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.++|-.+.=++|+|--+ .|+|||+.+|..|++..|
T Consensus 222 ~~q~id~~iL~G~Dy~p---------gi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 222 MDQFIDLCILCGCDYCD---------TIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred HHHHHHHHHHhCCCCCC---------CCCCccHHHHHHHHHHcC
Confidence 45677888888865433 689999999999998765
No 85
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=54.61 E-value=12 Score=30.41 Aligned_cols=87 Identities=23% Similarity=0.321 Sum_probs=55.8
Q ss_pred EeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-ccC------------CcccccccCCcC
Q 031812 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQ-FKI------------PDWFLNRQKDYK 91 (152)
Q Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~-~~i------------p~w~~nr~~d~~ 91 (152)
.+..+|.+.+|||++.|.++.--|- +.+++++..|.+.|.+... ... =.-+.+-++|..
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~AfhLL--------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~ 80 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAFHLL--------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKS 80 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHHHHH--------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCc
Confidence 3456899999999999999985543 3456777777666654211 110 012233444433
Q ss_pred CCcceeeehhhHHHHHHHhHHHhHhhceeecccCCCC
Q 031812 92 DGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 128 (152)
Q Consensus 92 tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~g 128 (152)
-.-+||. -.|+..+=+.+.|+|.=|..|
T Consensus 81 ---~icVVe~------p~Dv~a~E~~~~f~G~YhVL~ 108 (198)
T COG0353 81 ---QLCVVEE------PKDVLALEKTGEFRGLYHVLG 108 (198)
T ss_pred ---eEEEEcc------hHHHHHHHHhcccCeeEEEec
Confidence 3455655 357778888999999988876
No 86
>PRK00076 recR recombination protein RecR; Reviewed
Probab=54.51 E-value=12 Score=30.35 Aligned_cols=86 Identities=20% Similarity=0.287 Sum_probs=51.6
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-ccC-C-----------cccccccCCcCC
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQ-FKI-P-----------DWFLNRQKDYKD 92 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~-~~i-p-----------~w~~nr~~d~~t 92 (152)
+..+|.+++|||+++|.++.-.+=- -.++++..|.+.|.+-.+ ... + +-+.+-.+|
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll~--------~~~~~~~~la~~i~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd--- 77 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLLQ--------RDREDVLRLAQALEEAKEKIKHCSVCGNLTEQDPCEICSDPRRD--- 77 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHHHHHHcCCcCCCCCCcCCCCcCCCCCCCCCC---
Confidence 4467899999999999999865532 245666666666654211 110 0 011122222
Q ss_pred CcceeeehhhHHHHHHHhHHHhHhhceeecccCCCC
Q 031812 93 GRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 128 (152)
Q Consensus 93 g~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~g 128 (152)
..-.-+||+- .|+.-+=+.+.|+|+=|..|
T Consensus 78 ~~~icVVE~~------~Dv~aiE~s~~y~G~YhVL~ 107 (196)
T PRK00076 78 QSLICVVESP------ADVLAIERTGEYRGLYHVLG 107 (196)
T ss_pred CCEEEEECCH------HHHHHHHhhCcCceEEEEec
Confidence 1224466663 46666777888999888876
No 87
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.81 E-value=1.9 Score=34.35 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=29.5
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.++|-.=...+.++.-|.++.|||+++|.+|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~ 93 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKL 93 (186)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccC
Confidence 46777777788888999999999999999997543
No 88
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.57 E-value=7.9 Score=31.33 Aligned_cols=86 Identities=20% Similarity=0.290 Sum_probs=50.9
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-ccCCc------------ccccccCCcCC
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQ-FKIPD------------WFLNRQKDYKD 92 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~-~~ip~------------w~~nr~~d~~t 92 (152)
+..+|.+++|||+++|.++.-.+=- -.++++..|.+.|.+-.+ ...=+ -+.+-.+|
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~ll~--------~~~~~~~~la~ai~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd--- 77 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHLLK--------RDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRD--- 77 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCCCCCCCCC---
Confidence 4567899999999999999755432 345666666666554211 11000 11122222
Q ss_pred CcceeeehhhHHHHHHHhHHHhHhhceeecccCCCC
Q 031812 93 GRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 128 (152)
Q Consensus 93 g~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~g 128 (152)
..-.-+||+. .|+.-+=+.+.|+|+=|..|
T Consensus 78 ~~~iCVVE~~------~Dv~aiE~~~~y~G~YhVL~ 107 (195)
T TIGR00615 78 NSVICVVEDP------KDVFALEKTKEFRGRYHVLG 107 (195)
T ss_pred CCEEEEECCH------HHHHHHHhhCccceEEEEcc
Confidence 1124466663 46666777889999888876
No 89
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=53.52 E-value=7.7 Score=32.27 Aligned_cols=19 Identities=26% Similarity=0.431 Sum_probs=11.3
Q ss_pred eeccccccchhhHHHHHHH
Q 031812 29 ALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~ 47 (152)
.|..|.|||...+..+.+.
T Consensus 4 ~L~~IpGIG~krakkLl~~ 22 (232)
T PRK12766 4 ELEDISGVGPSKAEALREA 22 (232)
T ss_pred ccccCCCcCHHHHHHHHHc
Confidence 3556666666666666543
No 90
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=52.56 E-value=7.1 Score=31.92 Aligned_cols=22 Identities=27% Similarity=0.205 Sum_probs=18.1
Q ss_pred eeeeeccccccchhhHHHHHHH
Q 031812 26 IMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
....|.+++|||+.||..|+-.
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLly 140 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCY 140 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHH
Confidence 3456999999999999988754
No 91
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=52.54 E-value=17 Score=32.66 Aligned_cols=50 Identities=24% Similarity=0.352 Sum_probs=42.7
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
.+++.+..+|.. .++++.+..++++.|| |+....+|++.|+++|.+.|+.
T Consensus 283 ~~~kslkn~L~~--~lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 283 NPKKSLKNALAK--LLPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred ChhhHHHHHHHH--HhhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 345566666654 5788999999999999 9999999999999999999987
No 92
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.26 E-value=2.1 Score=34.62 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=28.7
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.++|-.=...+.++.-|.++.|||+++|.+|+..+
T Consensus 58 ~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~ 92 (196)
T PRK13901 58 KLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGI 92 (196)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 55666667778888899999999999999997443
No 93
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=52.17 E-value=1.7 Score=35.21 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=31.9
Q ss_pred hhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
...++|-.=...+.++..|.++-|||+++|.+|+.-++
T Consensus 57 ~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 57 AHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred HHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCC
Confidence 35677887788889999999999999999999985433
No 94
>PRK10880 adenine DNA glycosylase; Provisional
Probab=52.17 E-value=7.3 Score=34.04 Aligned_cols=30 Identities=13% Similarity=0.267 Sum_probs=23.0
Q ss_pred cCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 16 ~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.|-.+| .....|.+++|||+++|..||..+
T Consensus 100 ~~g~~p---~~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 100 HGGEFP---ETFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hCCCch---hhHHHHhcCCCccHHHHHHHHHHH
Confidence 344455 345789999999999999999643
No 95
>PRK13910 DNA glycosylase MutY; Provisional
Probab=51.46 E-value=7.6 Score=33.04 Aligned_cols=29 Identities=21% Similarity=0.273 Sum_probs=22.5
Q ss_pred CcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 17 ~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
+-.+|.+ ...|.+++|||+++|..|+..+
T Consensus 64 ~g~~P~~---~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 64 HSQLPND---YQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred CCCCChh---HHHHHhCCCCCHHHHHHHHHHH
Confidence 3345543 6789999999999999998643
No 96
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=51.34 E-value=11 Score=31.76 Aligned_cols=33 Identities=24% Similarity=0.462 Sum_probs=26.5
Q ss_pred cchhhhhhhcC--c-ccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 7 EDFQHILRVLN--T-NVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 7 ~~~~~~vri~~--~-~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
++|..+.=+.| + ++|| ++|||+.+|..+++..|
T Consensus 184 ~qliD~~~L~Gd~sDnipG----------V~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 184 EQLIDLKALVGDSSDNIPG----------VKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHHHHhCCcccCCCC----------CCCcCHHHHHHHHHHhC
Confidence 45677777778 3 3444 99999999999999998
No 97
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=51.22 E-value=8.4 Score=35.81 Aligned_cols=44 Identities=25% Similarity=0.258 Sum_probs=32.6
Q ss_pred CCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031812 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (152)
Q Consensus 22 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L 67 (152)
........|..|+|||+.+..++++.+| .-..+..-|.+||.++
T Consensus 508 ~k~~~~S~Ld~I~GiG~kr~~~Ll~~Fg--s~~~ik~As~eeL~~v 551 (567)
T PRK14667 508 EKEGLKDILDKIKGIGEVKKEIIYRNFK--TLYDFLKADDEELKKL 551 (567)
T ss_pred hcccccCccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHHc
Confidence 3445567899999999999999999988 3344555566666553
No 98
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=50.52 E-value=8.3 Score=30.56 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=18.7
Q ss_pred eeccccccchhhHHHHHHHhC
Q 031812 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.|+.++|||+++|.+|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 589999999999999997654
No 99
>smart00475 53EXOc 5'-3' exonuclease.
Probab=49.51 E-value=15 Score=30.54 Aligned_cols=36 Identities=19% Similarity=0.352 Sum_probs=24.0
Q ss_pred cchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
++|-.+.=+.|-.-|+ +..++|||+++|..++++.|
T Consensus 172 ~q~~d~~aL~GD~sDn-------ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 172 EQIIDYKALMGDSSDN-------IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred HHHHHHHHHhCCcccC-------CCCCCCCCHHHHHHHHHHhC
Confidence 3455555556621111 34589999999999998877
No 100
>PRK13844 recombination protein RecR; Provisional
Probab=49.23 E-value=10 Score=30.86 Aligned_cols=86 Identities=12% Similarity=0.083 Sum_probs=50.8
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-ccCCc------------ccccccCCcCC
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQ-FKIPD------------WFLNRQKDYKD 92 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~-~~ip~------------w~~nr~~d~~t 92 (152)
+..+|++.+|||+++|.++.-.+= +-.++++..|.+.|.+-.. ...=+ -+.+-.+|
T Consensus 13 LI~~l~~LPGIG~KsA~Rla~~lL--------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lte~~~C~IC~d~~Rd--- 81 (200)
T PRK13844 13 VIESLRKLPTIGKKSSQRLALYLL--------DKSPETAIAIANSLLDATANIKKCVYCQALTEDDVCNICSNTNRD--- 81 (200)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCCCCCCCCCCCCCC---
Confidence 446789999999999999975542 2345666666666654211 11000 11111111
Q ss_pred CcceeeehhhHHHHHHHhHHHhHhhceeecccCCCC
Q 031812 93 GRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 128 (152)
Q Consensus 93 g~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~g 128 (152)
..-.-+||+- .|+.-+=+.+.|+|+=|..|
T Consensus 82 ~~~iCVVE~~------~Dv~aiE~t~~y~G~YhVL~ 111 (200)
T PRK13844 82 DTKLCIIESM------LDMIAIEEAGIYRGKYFVLN 111 (200)
T ss_pred CCEEEEECCH------HHHHHHHhhCccceEEEEcc
Confidence 2224467663 46667778889999888764
No 101
>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=48.81 E-value=38 Score=21.35 Aligned_cols=43 Identities=12% Similarity=0.204 Sum_probs=32.1
Q ss_pred eccccccchhhHHHHHHHhCCCCCCcC----CCCCHHHHHHHHHHHh
Q 031812 30 LTSIKGIGRRLANIVCKKADVDMNKRA----GELSAAELDQLMVVVA 72 (152)
Q Consensus 30 Lt~I~GIG~~~A~~Ic~~lgi~~~~kv----~~Ls~~qi~~L~~~i~ 72 (152)
+....||...+...-.+..|+.+..+- ...+++++..|..+..
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 345789999999988887787654332 3678999988887764
No 102
>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=48.60 E-value=2.8 Score=30.32 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=15.6
Q ss_pred eccccccchhhHHHHHHHhC
Q 031812 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 Lt~I~GIG~~~A~~Ic~~lg 49 (152)
+-.++|||+++|..+++..|
T Consensus 20 IPGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp B---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCCHHHHHHHHHHcC
Confidence 34689999999999999987
No 103
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=47.99 E-value=9.5 Score=35.52 Aligned_cols=39 Identities=31% Similarity=0.365 Sum_probs=29.7
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
....|..|+|||+.+..++++.+| .-..+..-|.+||.+
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As~eeL~~ 550 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLG--TYKDILLLNEDEIAE 550 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHh
Confidence 556899999999999999999988 234455556666654
No 104
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=46.35 E-value=15 Score=34.34 Aligned_cols=45 Identities=29% Similarity=0.339 Sum_probs=32.0
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L 67 (152)
-....+..+|..|+|||..++..|++.+|= -..+.+-+.+|+..+
T Consensus 536 R~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~v 580 (598)
T PRK00558 536 RSKARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAKV 580 (598)
T ss_pred cccchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhhc
Confidence 344456789999999999999999999872 233444455555443
No 105
>PHA02564 V virion protein; Provisional
Probab=46.30 E-value=38 Score=26.04 Aligned_cols=33 Identities=15% Similarity=0.079 Sum_probs=26.8
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 40 LANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 40 ~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
.+..+|+.+|++|+.++.-..+ .+..|..+|..
T Consensus 87 Yi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~ 119 (141)
T PHA02564 87 YATAVANAMGVPPQAGLHLDQD-TLAALVTAIIR 119 (141)
T ss_pred HHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHH
Confidence 4788999999999999986555 78888777754
No 106
>PRK14976 5'-3' exonuclease; Provisional
Probab=45.36 E-value=18 Score=30.39 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=16.6
Q ss_pred ccccccchhhHHHHHHHhC
Q 031812 31 TSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 31 t~I~GIG~~~A~~Ic~~lg 49 (152)
-.++|||+++|..+++..|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999998776
No 107
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=44.20 E-value=13 Score=34.94 Aligned_cols=41 Identities=17% Similarity=0.221 Sum_probs=29.4
Q ss_pred EeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031812 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (152)
Q Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L 67 (152)
.+.-.|..|+|||+.++.++++.+| .-..+..-|.+||.++
T Consensus 549 ~~~S~L~~IpGIG~kr~~~LL~~Fg--Si~~I~~As~eeL~~v 589 (624)
T PRK14669 549 DRTSELLEIPGVGAKTVQRLLKHFG--SLERVRAATETQLAAV 589 (624)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHHH
Confidence 3456788999999999999999988 2233444555665443
No 108
>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=44.06 E-value=11 Score=32.08 Aligned_cols=29 Identities=21% Similarity=0.338 Sum_probs=22.5
Q ss_pred EeeeeeccccccchhhHHHHHHHhCCCCC
Q 031812 25 KIMFALTSIKGIGRRLANIVCKKADVDMN 53 (152)
Q Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~ 53 (152)
.+.-.|+.++|||+.+|..||-..-=.|+
T Consensus 217 ~~~~~L~~l~GIG~~tAd~vll~~l~~~d 245 (310)
T TIGR00588 217 DAREALCELPGVGPKVADCICLMGLDKPQ 245 (310)
T ss_pred HHHHHHHhCCCccHHHHHHHHHHhCCCCC
Confidence 35678899999999999999976443443
No 109
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=44.05 E-value=3.2 Score=33.28 Aligned_cols=35 Identities=11% Similarity=0.247 Sum_probs=27.9
Q ss_pred hhcCcccCCCeEeeeeeccccccchhhHHHHHHHh
Q 031812 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.++|-.=...+.++.-|.++.|||+++|..|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~ 93 (195)
T PRK14604 59 TLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSG 93 (195)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 45566666677788889999999999999997543
No 110
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=43.86 E-value=20 Score=30.94 Aligned_cols=35 Identities=26% Similarity=0.396 Sum_probs=26.7
Q ss_pred ccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.++|-.+.=+.|.+-. ..|+|||+.+|..+++..|
T Consensus 223 ~~q~id~~iL~G~dyn---------~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 223 REQLIDIAILVGTDYN---------EGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred HHHHHHHHHhcCCCCC---------CCCCCccHHHHHHHHHHcC
Confidence 4567777777887432 4789999999999998744
No 111
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=43.46 E-value=19 Score=29.63 Aligned_cols=36 Identities=28% Similarity=0.187 Sum_probs=26.6
Q ss_pred cccCCCeEe--eeeeccccccchhhHHHHHHHhCCCCC
Q 031812 18 TNVDGKQKI--MFALTSIKGIGRRLANIVCKKADVDMN 53 (152)
Q Consensus 18 ~~l~~~k~v--~~aLt~I~GIG~~~A~~Ic~~lgi~~~ 53 (152)
.++++.++. .--|.+|+|||+-+|.+|+-.+.=-|.
T Consensus 103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~ 140 (215)
T COG2231 103 INLESFKSEVLREELLSIKGIGKETADSILLYALDRPV 140 (215)
T ss_pred hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCcc
Confidence 355555555 667899999999999999877654443
No 112
>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=43.23 E-value=39 Score=24.28 Aligned_cols=34 Identities=18% Similarity=0.348 Sum_probs=29.9
Q ss_pred ccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 35 GIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 35 GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
-+|......|++.|+ ++-.+||+++++.+++++.
T Consensus 34 s~Gh~sGRrIv~IL~----K~k~dltddD~~hMrkVV~ 67 (92)
T PF11338_consen 34 SVGHESGRRIVEILR----KRKTDLTDDDYEHMRKVVG 67 (92)
T ss_pred ccCcchhhHHHHHHh----cCcccCCHHHHHHHHHHHH
Confidence 468888999999998 7778999999999999885
No 113
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=42.90 E-value=19 Score=33.44 Aligned_cols=60 Identities=13% Similarity=0.192 Sum_probs=41.6
Q ss_pred CccchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCC-------cCCCCCHHHHHHHHHHHhC
Q 031812 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNK-------RAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 5 ~~~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~-------kv~~Ls~~qi~~L~~~i~~ 73 (152)
..|.|++|.=+.|.|- |.++.|||..+|.++..+....... +--...++.++....+...
T Consensus 211 ~~ekfr~mciLSGCDY---------l~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~t 277 (556)
T KOG2518|consen 211 TEEKFRRMCILSGCDY---------LSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLT 277 (556)
T ss_pred CHHHHHHHHHhcCCcc---------cccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHh
Confidence 4578999999999985 6779999999999999876532111 1113456666666655543
No 114
>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=42.67 E-value=16 Score=29.74 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.0
Q ss_pred eccccccchhhHHHHHHHhC
Q 031812 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 Lt~I~GIG~~~A~~Ic~~lg 49 (152)
+..|+|||+++|..+++..|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 45679999999999998865
No 115
>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=40.61 E-value=37 Score=24.69 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHHHHHhC
Q 031812 57 GELSAAELDQLMVVVAN 73 (152)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (152)
+.||++|-+.|.++|..
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 46999999999999976
No 116
>PRK09482 flap endonuclease-like protein; Provisional
Probab=39.38 E-value=20 Score=30.03 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=17.2
Q ss_pred eccccccchhhHHHHHHHhC
Q 031812 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 Lt~I~GIG~~~A~~Ic~~lg 49 (152)
+..++|||+++|..+++..|
T Consensus 184 IpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCCcChHHHHHHHHHhC
Confidence 35689999999999998877
No 117
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=38.76 E-value=28 Score=27.94 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=21.9
Q ss_pred eeeeccccccchhhHHHHHHHhCCC
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~ 51 (152)
..|+|..+|+|++++...++.+|++
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 3689999999999999999888865
No 118
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=37.88 E-value=27 Score=26.78 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=26.8
Q ss_pred eeeccccccchhhHHHHHHHhCCC-CCC------cCCCCCHHHHHHHHHH
Q 031812 28 FALTSIKGIGRRLANIVCKKADVD-MNK------RAGELSAAELDQLMVV 70 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~-~~~------kv~~Ls~~qi~~L~~~ 70 (152)
.-|..++|||++.|.+|.+.-.-+ |.. ++.-+.+.-++++...
T Consensus 97 eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 97 EELQALPGIGPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHHhh
Confidence 446899999999999998654222 333 3333344555555544
No 119
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.74 E-value=17 Score=30.82 Aligned_cols=22 Identities=32% Similarity=0.362 Sum_probs=19.2
Q ss_pred eeeeeccccccchhhHHHHHHH
Q 031812 26 IMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
+.-.|++|+|||+-+|..++-.
T Consensus 196 a~e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 196 AIEELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHHHHHcCCCcCHHHHHHHHHH
Confidence 5567999999999999999855
No 120
>PRK07945 hypothetical protein; Provisional
Probab=37.69 E-value=20 Score=30.76 Aligned_cols=21 Identities=33% Similarity=0.623 Sum_probs=18.7
Q ss_pred eeccccccchhhHHHHHHHhC
Q 031812 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.|++|+|||..+|..|-+.+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 699999999999999987655
No 121
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=37.69 E-value=24 Score=31.55 Aligned_cols=45 Identities=13% Similarity=0.082 Sum_probs=39.8
Q ss_pred eeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
--|+.|.|||+..+.. +..+||.....+-.++++++..+...+.-
T Consensus 323 DDLk~I~GIGpk~e~~-Ln~~Gi~~f~QIA~wt~~eia~vd~~l~f 367 (400)
T PRK12373 323 DDLKLISGVGPKIEAT-LNELGIFTFDQVAAWKKAERAWVDGYLNF 367 (400)
T ss_pred hhhhhccCCChHHHHH-HHhcCCCCHHHHhCCCHHHhHHhhhcccC
Confidence 4689999999998876 57899999999999999999999888863
No 122
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=37.64 E-value=15 Score=34.22 Aligned_cols=39 Identities=15% Similarity=0.259 Sum_probs=29.6
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
...+|..|+|||..++..+++.+| .-..+.+.+.+|+..
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FG--S~~~I~~As~eeL~~ 561 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFG--SVEGVREASVEDLRD 561 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHh
Confidence 468999999999999999999987 233445556666644
No 123
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=37.60 E-value=20 Score=33.63 Aligned_cols=49 Identities=22% Similarity=0.377 Sum_probs=34.6
Q ss_pred CcccCCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031812 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (152)
Q Consensus 17 ~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L 67 (152)
+-..-..+.+.-.|..|.|||+.+|..|++.+| +. ..+..-+.++|.++
T Consensus 558 hr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~-~~i~~As~eeL~~v 606 (621)
T PRK14671 558 HRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFG-SV-EKVAKASLEELAAV 606 (621)
T ss_pred ChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcC-CH-HHHHhCCHHHHHHH
Confidence 444555566677889999999999999999996 11 23444466666554
No 124
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=36.99 E-value=26 Score=31.59 Aligned_cols=24 Identities=25% Similarity=0.578 Sum_probs=21.5
Q ss_pred CeEeeeeeccccccchhhHHHHHH
Q 031812 23 KQKIMFALTSIKGIGRRLANIVCK 46 (152)
Q Consensus 23 ~k~v~~aLt~I~GIG~~~A~~Ic~ 46 (152)
+..|.++|..|+|||...+.+|.+
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~ 132 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILK 132 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHH
Confidence 457999999999999999999975
No 125
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=35.26 E-value=27 Score=29.43 Aligned_cols=33 Identities=24% Similarity=0.253 Sum_probs=24.2
Q ss_pred eeeeeccccccchhhHHHHHHHhCCCCCCc-CCC
Q 031812 26 IMFALTSIKGIGRRLANIVCKKADVDMNKR-AGE 58 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k-v~~ 58 (152)
+...|+.|+|||+.+|..|+-+.==+|+.- .++
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D 238 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDD 238 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCccc
Confidence 356799999999999999987643355543 444
No 126
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=35.22 E-value=18 Score=34.52 Aligned_cols=43 Identities=7% Similarity=0.189 Sum_probs=31.4
Q ss_pred CCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 22 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
..+.+...|..|+|||+.....+++.+| .-..+..-|.+||..
T Consensus 602 ~k~~~~s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~ 644 (691)
T PRK14672 602 TKKELVLSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIAT 644 (691)
T ss_pred hhhhcccccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHh
Confidence 3445567899999999999999999988 233445555556544
No 127
>PRK13766 Hef nuclease; Provisional
Probab=34.87 E-value=23 Score=33.27 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=20.1
Q ss_pred eeeccccccchhhHHHHHHHhC
Q 031812 28 FALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
+.|..|.|||...|..|++.+|
T Consensus 715 ~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 715 YIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHhcCCCCCHHHHHHHHHHcC
Confidence 4689999999999999999887
No 128
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.31 E-value=66 Score=24.57 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=36.4
Q ss_pred eeccccccchhhHHHHHHHhC-----CCCC---CcCCCCCHHHHHHHHHHHhC
Q 031812 29 ALTSIKGIGRRLANIVCKKAD-----VDMN---KRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lg-----i~~~---~kv~~Ls~~qi~~L~~~i~~ 73 (152)
...+++|+|.+++..-..+.. +.+. -+...|+++|++.|.+.+..
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~ 78 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLRE 78 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhc
Confidence 356789999999999998865 3333 26778999999999999976
No 129
>KOG0650 consensus WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=33.46 E-value=67 Score=30.64 Aligned_cols=42 Identities=19% Similarity=0.434 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcCCCcceeeehhhHH
Q 031812 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALD 104 (152)
Q Consensus 56 v~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg~~~~~i~~dL~ 104 (152)
+.-...++++++...|+.| +.| ++.+|..||++..|...++.
T Consensus 147 ~kp~k~~~ld~fl~~iedp-----~~W--r~v~Dk~tG~dv~LTkEev~ 188 (733)
T KOG0650|consen 147 TKPAKGDELDSFLAKIEDP-----DYW--RKVKDKMTGKDVNLTKEEVK 188 (733)
T ss_pred cCCCccchHHHHHHhhcCc-----chh--ccccccCCCceeeecHHHHH
Confidence 4445567899999998875 456 89999999999988866653
No 130
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=33.33 E-value=22 Score=30.42 Aligned_cols=29 Identities=24% Similarity=0.538 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CCccccccc
Q 031812 58 ELSAAELDQLMVVVANPRQFK------------------IPDWFLNRQ 87 (152)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~------------------ip~w~~nr~ 87 (152)
-+|+.|++.|++.+++.. |. |..||-|||
T Consensus 147 iFT~~Qle~LEkaFkeaH-YPDv~Are~la~ktelpEDRIqVWfQNRR 193 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEAH-YPDVYAREMLADKTELPEDRIQVWFQNRR 193 (332)
T ss_pred hhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhccCchhhhhHHhhhhh
Confidence 478999999999887743 32 445999987
No 131
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=31.26 E-value=55 Score=26.76 Aligned_cols=48 Identities=19% Similarity=0.254 Sum_probs=30.9
Q ss_pred cCcccCCCeEeeeeeccccccchhhHHHHHHH-hCCCCCCcCCCCCHHHHHHHHHHH
Q 031812 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKK-ADVDMNKRAGELSAAELDQLMVVV 71 (152)
Q Consensus 16 ~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~-lgi~~~~kv~~Ls~~qi~~L~~~i 71 (152)
+|-.+|++ ..+|.+.+|||++||+-++.. +|.+ ...|.. .+.++.+-+
T Consensus 100 ~~g~vP~~---~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDT----HV~Rvs~R~ 148 (211)
T COG0177 100 FGGEVPDT---REELLSLPGVGRKTANVVLSFAFGIP-AIAVDT----HVHRVSNRL 148 (211)
T ss_pred cCCCCCch---HHHHHhCCCcchHHHHHHHHhhcCCC-cccccc----hHHHHHHHh
Confidence 34444443 357999999999999988876 4443 444443 555555544
No 132
>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=30.82 E-value=29 Score=30.07 Aligned_cols=37 Identities=22% Similarity=0.424 Sum_probs=27.3
Q ss_pred eeccccccchhhHHHHHHHhCCCCCCcCCCC--CHHHHH
Q 031812 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGEL--SAAELD 65 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~L--s~~qi~ 65 (152)
-+..+.|||..++..+++.+||..-.-+-.+ +.+++.
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 5789999999999999999999864333344 444443
No 133
>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=30.49 E-value=19 Score=30.53 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=19.8
Q ss_pred eeccccccchhhHHHHHHHhCCC
Q 031812 29 ALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi~ 51 (152)
.+++|+|||..+|..|.+.+.=.
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG 68 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETG 68 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcC
Confidence 56899999999999999887643
No 134
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.14 E-value=39 Score=33.79 Aligned_cols=35 Identities=11% Similarity=0.123 Sum_probs=28.3
Q ss_pred cchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhCC
Q 031812 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
++|-.+.-++|+|-.. .|+|||+.+|..|++..|=
T Consensus 854 ~qli~laiL~G~DY~~---------GI~GIGpktAl~li~~~~~ 888 (1034)
T TIGR00600 854 NKLINLAYLLGSDYTE---------GIPTVGPVSAMEILNEFPG 888 (1034)
T ss_pred HHHHHHHHeeCCCCCC---------CCCcccHHHHHHHHHHcCC
Confidence 5677777788877543 6999999999999999873
No 135
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=29.81 E-value=90 Score=31.13 Aligned_cols=25 Identities=36% Similarity=0.542 Sum_probs=22.4
Q ss_pred CeEeeeeeccccccchhhHHHHHHH
Q 031812 23 KQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 23 ~k~v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
+..|.++|+.|+|||...|..|.+.
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~ 771 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSA 771 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHH
Confidence 4579999999999999999999864
No 136
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=29.09 E-value=16 Score=26.33 Aligned_cols=33 Identities=18% Similarity=0.356 Sum_probs=26.3
Q ss_pred cCCCCCHHHHHHHHHHHhCCCCccCCcccccccC
Q 031812 55 RAGELSAAELDQLMVVVANPRQFKIPDWFLNRQK 88 (152)
Q Consensus 55 kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~ 88 (152)
...+||++|++.+..+|+.+. ..+=.|+.|+..
T Consensus 40 ~~~~lsd~el~~f~~LLe~~D-~dL~~Wi~g~~~ 72 (94)
T COG2938 40 EFDSLSDEELDEFERLLECED-NDLFNWIMGHGE 72 (94)
T ss_pred HHhhCCHHHHHHHHHHHcCCc-HHHHHHHhCCCC
Confidence 457899999999999998753 445568988876
No 137
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=28.79 E-value=57 Score=27.56 Aligned_cols=33 Identities=12% Similarity=0.229 Sum_probs=28.5
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 40 LANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 40 ~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
....+++.+|++ ..|..+|+-+|+-.|.+.+.+
T Consensus 256 ~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 256 FIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 344678999997 799999999999999999875
No 138
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=28.32 E-value=39 Score=24.62 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=30.6
Q ss_pred chhhhhhhcCcccCC---CeEeeeeeccccccchhhHHHHHHHhC
Q 031812 8 DFQHILRVLNTNVDG---KQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 8 ~~~~~vri~~~~l~~---~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.|-.+|--.|+||+. +.-....|+.+-|.|+++|..+.+.+.
T Consensus 27 ~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 27 AFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp HHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred HHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 466777778888863 555678899999999999999998765
No 139
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=28.23 E-value=49 Score=26.97 Aligned_cols=63 Identities=21% Similarity=0.269 Sum_probs=39.8
Q ss_pred hhhhhhhcCcccCCCeEeeeeeccccc-cchhhHHHHHHHh-CCCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 9 FQHILRVLNTNVDGKQKIMFALTSIKG-IGRRLANIVCKKA-DVDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aLt~I~G-IG~~~A~~Ic~~l-gi~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
|.++++.+ .--..|.+..+|..+.. .+......+...+ ++++++++.+||.+|+..|.+.+..
T Consensus 192 ~~~~~~~~--F~~rrk~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 192 FDDFVKAL--FQHRRKTLRNALKNSAHISGKEDIKAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHHHH--HccccHHHHHHHhhhccccchhHHHHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 45555432 23456777777766521 1211113345556 5668999999999999999998864
No 140
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=28.20 E-value=40 Score=20.31 Aligned_cols=30 Identities=23% Similarity=0.364 Sum_probs=16.3
Q ss_pred CCCHHHHHHHHHHHhCCCCccCCcccccccC
Q 031812 58 ELSAAELDQLMVVVANPRQFKIPDWFLNRQK 88 (152)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~ 88 (152)
..+.++++.|...+.-+ ...|-.||-|+|.
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR~ 53 (56)
T smart00389 24 YPSREEREELAAKLGLS-ERQVKVWFQNRRA 53 (56)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHhHHHHhh
Confidence 34566666666665432 2334557777653
No 141
>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=27.66 E-value=51 Score=23.73 Aligned_cols=58 Identities=21% Similarity=0.146 Sum_probs=42.9
Q ss_pred cCcccCCCeEeeeeeccccccchhhHHHHHHHhC---CCCCCcCCCCCHHHHHHHHHHHhC
Q 031812 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD---VDMNKRAGELSAAELDQLMVVVAN 73 (152)
Q Consensus 16 ~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg---i~~~~kv~~Ls~~qi~~L~~~i~~ 73 (152)
+|..||-|..-..+.+.++|.=+..|..|+.-.= ++.=..+..||+.|-+.|....++
T Consensus 11 ~G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~ 71 (93)
T PF06514_consen 11 LGQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDN 71 (93)
T ss_dssp CCTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGG
T ss_pred cCCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhcc
Confidence 4566666667778999999999999999997542 333446777999999999999986
No 142
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=27.56 E-value=23 Score=30.59 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=19.4
Q ss_pred eeeeeccccccchhhHHHHHHH
Q 031812 26 IMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 26 v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
+.-||+.++|||++.|.-||-.
T Consensus 216 ar~~L~~lpGVG~KVADCI~Lm 237 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCICLM 237 (323)
T ss_pred HHHHHhcCCCCcchHhhhhhhh
Confidence 5678999999999999999953
No 143
>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=27.21 E-value=36 Score=31.68 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=21.8
Q ss_pred EeeeeeccccccchhhHHHHHHHhC
Q 031812 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.+.-.|..|+|||+.+...+++.+|
T Consensus 538 ~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 538 SLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3456789999999999999998887
No 144
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=27.18 E-value=31 Score=29.63 Aligned_cols=21 Identities=19% Similarity=0.449 Sum_probs=19.1
Q ss_pred eeccccccchhhHHHHHHHhC
Q 031812 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.|+.|+|||..+|..|.+.+.
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~ 69 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIE 69 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHH
Confidence 588999999999999998876
No 145
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=27.13 E-value=47 Score=27.60 Aligned_cols=31 Identities=26% Similarity=0.563 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHHhCCCCcc------------------CCcccccccCCc
Q 031812 59 LSAAELDQLMVVVANPRQFK------------------IPDWFLNRQKDY 90 (152)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~------------------ip~w~~nr~~d~ 90 (152)
++-+|++.|+.++++ ..|. |-.||-|||++.
T Consensus 44 Ftr~QlevLe~LF~k-TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~ 92 (228)
T KOG2251|consen 44 FTRKQLEVLEALFAK-TQYPDVFMREELALKLNLPESRVQVWFKNRRAKC 92 (228)
T ss_pred ecHHHHHHHHHHHHh-hcCccHHHHHHHHHHhCCchhhhhhhhccccchh
Confidence 577888888888776 2232 344999998544
No 146
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=26.74 E-value=31 Score=33.00 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=22.0
Q ss_pred EeeeeeccccccchhhHHHHHHHhC
Q 031812 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 25 ~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.+.-.|..|+|||+..+..+++.+|
T Consensus 634 ~~~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 634 ALTGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred hhHhHHhhCCCCCHHHHHHHHHHhC
Confidence 3456788999999999999999988
No 147
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=26.59 E-value=17 Score=25.61 Aligned_cols=40 Identities=18% Similarity=0.196 Sum_probs=29.3
Q ss_pred CCCeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 21 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
++.+.-...|....|||+.-|+++.++|.. -.+|.+|+..
T Consensus 45 ~~s~~rR~~l~~~L~iGy~N~KqllkrLN~------f~it~~e~~~ 84 (87)
T PF13331_consen 45 PDSKERREKLGEYLGIGYGNAKQLLKRLNM------FGITREEFEE 84 (87)
T ss_pred ccHHHHHHHHHHHHCCCCCCHHHHHHHHHH------cCCCHHHHHH
Confidence 344666777888999999999999988763 2356666665
No 148
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=26.47 E-value=63 Score=20.35 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=12.7
Q ss_pred CCCHHHHHHHHHHH
Q 031812 58 ELSAAELDQLMVVV 71 (152)
Q Consensus 58 ~Ls~~qi~~L~~~i 71 (152)
.||++|+..|..+|
T Consensus 54 ~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 54 QLSDEEIEALAAYI 67 (67)
T ss_dssp TSTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHC
Confidence 79999999998876
No 149
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=26.02 E-value=30 Score=21.48 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=30.4
Q ss_pred eeccccccchhhHHHHH-HHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031812 29 ALTSIKGIGRRLANIVC-KKADVDMNKRAGELSAAELDQLMVVVA 72 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic-~~lgi~~~~kv~~Ls~~qi~~L~~~i~ 72 (152)
-|.+-.|+...--...| ..+|+.....-..|++++...|.+.+.
T Consensus 8 elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 8 ELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp HHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred HHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 35566778888888888 559999777778888898888887653
No 150
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=25.85 E-value=1.3e+02 Score=18.84 Aligned_cols=37 Identities=27% Similarity=0.372 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHhCCCCccCCcccccccCCcCCCcceeeehhhHHHHHHHhHHHhHhh
Q 031812 60 SAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKI 117 (152)
Q Consensus 60 s~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg~~~~~i~~dL~~~~~~~I~rl~~I 117 (152)
+++|++.|.++|++|. ++ =|..|+..+....+.+..|
T Consensus 6 ~~e~ld~L~~aL~~pr--G~-------------------RE~~L~~~L~~~~k~~~~~ 42 (46)
T PF15614_consen 6 DPEELDELLKALENPR--GK-------------------RESKLKKELDKHRKGPLEI 42 (46)
T ss_pred CHHHHHHHHHHHcCcc--cH-------------------hHHHHHHHHHHHhcchhhh
Confidence 5789999999986653 22 2677777666655444444
No 151
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.83 E-value=28 Score=28.33 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=17.6
Q ss_pred eeccccccchhhHHHHHHHhCC
Q 031812 29 ALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
.|++|+|||...|.+|.....+
T Consensus 61 eL~~i~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 61 ELSSVPGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHHhCcCCcHHHHHHHHHHHHH
Confidence 3889999999999888755444
No 152
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=25.83 E-value=48 Score=27.92 Aligned_cols=38 Identities=34% Similarity=0.399 Sum_probs=26.7
Q ss_pred eeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
.+-|.+|+|||...|..++..+|= -..+-..+++|+..
T Consensus 181 ~~il~s~pgig~~~a~~ll~~fgS--~~~~~tas~~eL~~ 218 (254)
T COG1948 181 LYILESIPGIGPKLAERLLKKFGS--VEDVLTASEEELMK 218 (254)
T ss_pred HHHHHcCCCccHHHHHHHHHHhcC--HHHHhhcCHHHHHH
Confidence 466789999999999999988772 23344445544443
No 153
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=25.60 E-value=35 Score=32.25 Aligned_cols=37 Identities=22% Similarity=0.274 Sum_probs=27.0
Q ss_pred ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031812 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (152)
Q Consensus 31 t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L 67 (152)
-.|.|+|+.++.++.+..+|..-.-+-.|+.+++..|
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L 471 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLEL 471 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhc
Confidence 3699999999999999888865444446665555443
No 154
>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=25.38 E-value=23 Score=31.51 Aligned_cols=77 Identities=19% Similarity=0.295 Sum_probs=0.0
Q ss_pred ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcCCCcceeeehhhHHHHHHHh
Q 031812 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (152)
Q Consensus 31 t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg~~~~~i~~dL~~~~~~~ 110 (152)
=.=|||-++|+..|. .||+--++-++ .+|+||+.+.+.|+..+- | |..=|+.+ -++..++..
T Consensus 55 F~~YGVRy~T~AKIa-ElGFTvsTLl~-M~deELDdmM~sL~~ifR-----w------dLLVGERY-----GIKAAvRAE 116 (386)
T PF01698_consen 55 FQGYGVRYYTAAKIA-ELGFTVSTLLN-MTDEELDDMMNSLSQIFR-----W------DLLVGERY-----GIKAAVRAE 116 (386)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HhhccccHHHHHHHH-HhcccHHHHhc-ccHHHHHHHHHHHHHHhh-----h------hhhhhhhh-----hHHHHHHHH
Confidence 345999999999986 58888776665 699999999998876321 1 22333333 345666666
Q ss_pred HHHhHhhceeecccC
Q 031812 111 LERLKKIRNHRGLRH 125 (152)
Q Consensus 111 I~rl~~I~syRG~RH 125 (152)
-.||-+-...+..||
T Consensus 117 RRRl~e~~~~~rR~h 131 (386)
T PF01698_consen 117 RRRLEEEEESRRRRH 131 (386)
T ss_dssp ---------------
T ss_pred HHHhhcchhhhhhhc
Confidence 666666544455554
No 155
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=25.21 E-value=46 Score=29.09 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=17.8
Q ss_pred eeccccccchhhHHHHHHHhC
Q 031812 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lg 49 (152)
++|.++|||+.+|..|-..+.
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l~ 74 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYLD 74 (326)
T ss_pred ccCCCCCccHHHHHHHHHHHH
Confidence 599999999999999876543
No 156
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=24.83 E-value=48 Score=27.54 Aligned_cols=36 Identities=25% Similarity=0.313 Sum_probs=23.3
Q ss_pred eccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 30 Lt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
|..++|||+.++..+. ..||..-..+...+++++..
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~ 36 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSE 36 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHh
Confidence 4578999999888875 56666544444455555443
No 157
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=24.63 E-value=48 Score=27.81 Aligned_cols=38 Identities=24% Similarity=0.316 Sum_probs=24.9
Q ss_pred eeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031812 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~ 66 (152)
..|..++|||+.+|..+ ...||..-.-+-.++++++.+
T Consensus 6 ~~l~~l~gIg~~~a~~L-~~~Gi~t~~dl~~~~~~~L~~ 43 (317)
T PRK04301 6 KDLEDLPGVGPATAEKL-REAGYDTVEAIAVASPKELSE 43 (317)
T ss_pred ccHhhcCCCCHHHHHHH-HHcCCCCHHHHHcCCHHHHHH
Confidence 45788999998888776 466776544444445544433
No 158
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=24.53 E-value=28 Score=24.06 Aligned_cols=41 Identities=10% Similarity=0.256 Sum_probs=30.4
Q ss_pred hhhhhhcC-cccCCCeEeeeeeccccccchhhHHHHHHHhCC
Q 031812 10 QHILRVLN-TNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 10 ~~~vri~~-~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
.++...++ ...-..+.+...+...+|.|...+..|++++|.
T Consensus 5 ~~l~~~~~~~~~~~~~~~kivvD~~~G~~~~~~~~ll~~lg~ 46 (104)
T PF02879_consen 5 ESLLSFIDILEAIKKSGLKIVVDCMNGAGSDILPRLLERLGC 46 (104)
T ss_dssp HHHHHTSCHHHHHHHTTCEEEEE-TTSTTHHHHHHHHHHTTC
T ss_pred HHHhhhccchhhcccCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence 34445555 444445566888999999999999999999997
No 159
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=23.75 E-value=46 Score=31.16 Aligned_cols=43 Identities=26% Similarity=0.277 Sum_probs=32.4
Q ss_pred CeEeeeeeccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031812 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (152)
Q Consensus 23 ~k~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~~L 67 (152)
...+...|-.|.|||+....++++.+| .-..+.+-|.+|+..+
T Consensus 525 k~~~~s~Ld~I~GiG~~r~~~LL~~Fg--s~~~i~~As~eel~~v 567 (581)
T COG0322 525 KAMLQSSLDDIPGIGPKRRKALLKHFG--SLKGIKSASVEELAKV 567 (581)
T ss_pred hhhhcCccccCCCcCHHHHHHHHHHhh--CHHHHHhcCHHHHHHc
Confidence 344567889999999999999999988 3344556666666654
No 160
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=22.32 E-value=37 Score=20.78 Aligned_cols=16 Identities=13% Similarity=0.169 Sum_probs=10.4
Q ss_pred CCCHHHHHHHHHHHhC
Q 031812 58 ELSAAELDQLMVVVAN 73 (152)
Q Consensus 58 ~Ls~~qi~~L~~~i~~ 73 (152)
.+|++|+..|.++.+.
T Consensus 6 ~~t~~q~~~L~~~f~~ 21 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQE 21 (57)
T ss_dssp SSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 3566777777776654
No 161
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=22.04 E-value=1.5e+02 Score=24.62 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcCCCcceee
Q 031812 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQV 98 (152)
Q Consensus 56 v~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg~~~~~ 98 (152)
..-+|.||++.-+.+|-. -=|++||....+
T Consensus 157 m~PmTkEEyearQSvIRr-------------VvDpETGRtRLI 186 (225)
T PF10500_consen 157 MAPMTKEEYEARQSVIRR-------------VVDPETGRTRLI 186 (225)
T ss_pred cCCCCHHHHHHHHhhhee-------------eecCCCCceeee
Confidence 445788888888888764 238999998754
No 162
>PRK08609 hypothetical protein; Provisional
Probab=21.84 E-value=31 Score=31.87 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=19.6
Q ss_pred eeccccccchhhHHHHHHHhCC
Q 031812 29 ALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
.|++|+|||..+|..|.+.+.=
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~t 70 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRET 70 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHh
Confidence 6899999999999999988763
No 163
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=21.80 E-value=92 Score=28.42 Aligned_cols=34 Identities=24% Similarity=0.353 Sum_probs=28.4
Q ss_pred cchhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHHhC
Q 031812 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~lg 49 (152)
++|-.+-=++|.|-.+. |.|||+..|..+.+..+
T Consensus 217 ~~fidL~lLlGCDYc~~---------I~Gig~~~al~lir~~~ 250 (449)
T KOG2519|consen 217 ESFIDLCLLLGCDYCPT---------IRGIGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHhcCccccc---------ccccChHHHHHHHHHhc
Confidence 45777777888887766 99999999999998888
No 164
>PRK00024 hypothetical protein; Reviewed
Probab=21.69 E-value=38 Score=27.57 Aligned_cols=22 Identities=36% Similarity=0.436 Sum_probs=17.9
Q ss_pred eeccccccchhhHHHHHHHhCC
Q 031812 29 ALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
.|.+|+|||+..|..|+....+
T Consensus 67 eL~~i~GIG~akA~~L~a~~El 88 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALEL 88 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHH
Confidence 4889999999999888755444
No 165
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=21.57 E-value=1.1e+02 Score=23.89 Aligned_cols=17 Identities=12% Similarity=0.128 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHHHHhC
Q 031812 57 GELSAAELDQLMVVVAN 73 (152)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (152)
..||++|+..|..+|..
T Consensus 130 ~~LsdeEL~avAaYIl~ 146 (159)
T TIGR03045 130 RNLTDEDLRLIAGHILV 146 (159)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 57999999999999976
No 166
>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=21.56 E-value=72 Score=21.19 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=16.7
Q ss_pred eccccccchhhHHHHHHHhCCCC
Q 031812 30 LTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 30 Lt~I~GIG~~~A~~Ic~~lgi~~ 52 (152)
|...-|+..++..++|+++|++.
T Consensus 40 lA~~~~vS~sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 40 LAEKAGVSPSTIVRFCKKLGFSG 62 (77)
T ss_dssp HHHHCTS-HHHHHHHHHHCTTTC
T ss_pred HHHHcCCCHHHHHHHHHHhCCCC
Confidence 44566888888888888888764
No 167
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=21.46 E-value=56 Score=20.21 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=16.7
Q ss_pred eeeccccccchhhHHHHHHHh
Q 031812 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aLt~I~GIG~~~A~~Ic~~l 48 (152)
.-|...+||+.+++..++..+
T Consensus 23 ~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 23 QDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred hHHhhheeecHHHHHHHHHHH
Confidence 346778999999999998653
No 168
>COG1636 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.15 E-value=1e+02 Score=25.23 Aligned_cols=81 Identities=14% Similarity=0.108 Sum_probs=50.8
Q ss_pred hCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccccccCCcCCCcceeeehhhHHHHHHHhHHHhHhhceeecccCCC
Q 031812 48 ADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYW 127 (152)
Q Consensus 48 lgi~~~~kv~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~~d~~tg~~~~~i~~dL~~~~~~~I~rl~~I~syRG~RH~~ 127 (152)
|+++|.+.+ .||..+-.-++++ +.++.|..|.||.--+ . +.+...-+..+==.+|=|+ ..
T Consensus 118 L~iSp~Kn~-----~qin~~G~~~~k~--y~V~yl~~dfrK~gg~----------~-r~~elske~~~YrQ~YCGC--vy 177 (204)
T COG1636 118 LLISPKKNM-----NQINEIGERAAKP--YGVVYLPSNFRKNGGY----------Q-RSIELSKEENIYRQEYCGC--VY 177 (204)
T ss_pred eecCcccCH-----HHHHHHhHHhhcc--cCceecCcccccccch----------H-HHHHHHHHHhHHHhhccch--hh
Confidence 445554433 4777777777775 8899999999865322 2 2222222222223467676 46
Q ss_pred CCccCCcCCcccCCCccceee
Q 031812 128 GLRVRGQHTKTTGRRGKTVGV 148 (152)
Q Consensus 128 gLPVRGQRTrTNart~~~~gv 148 (152)
+|.-.+|+-++++|....+|.
T Consensus 178 sl~~q~~~~~~~~r~~~~~~~ 198 (204)
T COG1636 178 SLKDQNEDRKEVNRQAIPFGK 198 (204)
T ss_pred hHhhhcchhhhhchhhhhHHh
Confidence 778888888888887776654
No 169
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=21.04 E-value=79 Score=21.45 Aligned_cols=16 Identities=13% Similarity=0.192 Sum_probs=12.4
Q ss_pred CCCHHHHHHHHHHHhC
Q 031812 58 ELSAAELDQLMVVVAN 73 (152)
Q Consensus 58 ~Ls~~qi~~L~~~i~~ 73 (152)
.||++|++.|.++|.+
T Consensus 47 ~Lt~eqv~~LN~~l~~ 62 (73)
T PF14794_consen 47 FLTEEQVAKLNQALQK 62 (73)
T ss_dssp ---HHHHHHHHHHHHH
T ss_pred EcCHHHHHHHHHHHHH
Confidence 4899999999999986
No 170
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=20.35 E-value=64 Score=26.87 Aligned_cols=21 Identities=29% Similarity=0.471 Sum_probs=19.1
Q ss_pred eeccccccchhhHHHHHHHhC
Q 031812 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~lg 49 (152)
.|..+.|||...|..|.+.++
T Consensus 37 EL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 37 ELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHHccCCCHHHHHHHHHHhc
Confidence 478999999999999999887
No 171
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.29 E-value=57 Score=26.71 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=20.5
Q ss_pred eeeeccccccchhhHHHHHHHhCC
Q 031812 27 MFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 27 ~~aLt~I~GIG~~~A~~Ic~~lgi 50 (152)
.+.+.+|+|||++-|.-.++-.|+
T Consensus 120 E~Lv~nikGiGyKEASHFLRNVG~ 143 (210)
T COG1059 120 ELLVENIKGIGYKEASHFLRNVGF 143 (210)
T ss_pred HHHHHHcccccHHHHHHHHHhcCh
Confidence 345569999999999999988886
No 172
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.24 E-value=51 Score=28.97 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=27.7
Q ss_pred hhhhhhhcCcccCCCeEeeeeeccccccchhhHHHHHHH
Q 031812 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aLt~I~GIG~~~A~~Ic~~ 47 (152)
.+.++.-.|-.+|++.. .|..++|||.++|.+|+.-
T Consensus 97 A~~v~~~~~G~~P~~~~---~l~~LpGiG~yTa~Ail~~ 132 (342)
T COG1194 97 AQEVVERHGGEFPDDEE---ELAALPGVGPYTAGAILSF 132 (342)
T ss_pred HHHHHHHcCCCCCCCHH---HHHhCCCCcHHHHHHHHHH
Confidence 45677777777887754 5667999999999999843
No 173
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=20.14 E-value=41 Score=28.64 Aligned_cols=35 Identities=23% Similarity=0.487 Sum_probs=25.6
Q ss_pred hhhhhhhcCcccCCCeEe-eeeeccccccchhhHHH
Q 031812 9 FQHILRVLNTNVDGKQKI-MFALTSIKGIGRRLANI 43 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v-~~aLt~I~GIG~~~A~~ 43 (152)
.+++++|+-.+.+++-+- .-.|-+.+|||+++|.-
T Consensus 139 lkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKMa~L 174 (286)
T KOG1921|consen 139 LKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHL 174 (286)
T ss_pred HHHHHHHHHHHhCCCCchhHHHHhcCCCCchHHHHH
Confidence 567788877766665544 34678899999999863
No 174
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=20.13 E-value=57 Score=21.48 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=16.8
Q ss_pred eeccccccchhhHHHHHHHh
Q 031812 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aLt~I~GIG~~~A~~Ic~~l 48 (152)
-|.+|+|+|......|.+.+
T Consensus 45 ~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 45 DLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp HHHTSTTSHHHHHHHHHHHH
T ss_pred HHHhCCCCCHhHHHHHHHHH
Confidence 47889999999999887664
No 175
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=20.12 E-value=44 Score=31.69 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=25.1
Q ss_pred ccccccchhhHHHHHHHhCCCCCCcCCCCCHHHHH
Q 031812 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (152)
Q Consensus 31 t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~qi~ 65 (152)
-.|.|+|+.++.++.+..+|..-.-+-.|+.+++.
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~ 482 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLL 482 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHh
Confidence 46999999999999999888753333344544443
Done!