Query psy8858
Match_columns 121
No_of_seqs 130 out of 937
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 21:09:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8858.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8858hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00137 rps13 ribosomal prote 100.0 4.9E-55 1.1E-59 307.8 11.6 121 1-121 1-122 (122)
2 COG0099 RpsM Ribosomal protein 100.0 4.3E-55 9.2E-60 304.5 10.1 120 1-120 1-121 (121)
3 PRK05179 rpsM 30S ribosomal pr 100.0 1.1E-54 2.5E-59 305.9 11.4 121 1-121 1-122 (122)
4 TIGR03631 bact_S13 30S ribosom 100.0 2.3E-51 4.9E-56 285.9 10.6 112 3-114 1-113 (113)
5 TIGR03629 arch_S13P archaeal r 100.0 1.1E-49 2.5E-54 287.3 11.2 118 1-120 5-144 (144)
6 PRK04053 rps13p 30S ribosomal 100.0 1.1E-49 2.4E-54 288.6 10.5 118 1-120 9-149 (149)
7 PF00416 Ribosomal_S13: Riboso 100.0 5.3E-50 1.2E-54 276.4 5.6 106 3-108 1-107 (107)
8 PTZ00134 40S ribosomal protein 100.0 7.2E-49 1.6E-53 285.5 10.4 118 1-120 14-154 (154)
9 KOG3311|consensus 100.0 1.7E-35 3.8E-40 213.1 6.1 118 1-120 12-152 (152)
10 PF06831 H2TH: Formamidopyrimi 97.7 3.6E-05 7.8E-10 51.6 3.3 50 12-61 23-75 (92)
11 PRK01103 formamidopyrimidine/5 97.4 0.00024 5.2E-09 55.9 4.2 51 11-61 154-207 (274)
12 PRK04184 DNA topoisomerase VI 97.3 0.00025 5.5E-09 60.9 4.3 53 12-64 256-308 (535)
13 PRK14810 formamidopyrimidine-D 97.0 0.00094 2E-08 52.6 4.4 51 11-61 153-206 (272)
14 PRK14811 formamidopyrimidine-D 96.9 0.0014 3.1E-08 51.6 4.7 50 12-61 143-195 (269)
15 PRK10445 endonuclease VIII; Pr 96.9 0.0015 3.4E-08 51.2 4.7 50 12-61 151-203 (263)
16 PRK13945 formamidopyrimidine-D 96.8 0.0017 3.7E-08 51.3 4.4 50 12-61 164-216 (282)
17 TIGR00577 fpg formamidopyrimid 96.8 0.0018 3.9E-08 51.0 4.4 50 12-61 155-207 (272)
18 TIGR01052 top6b DNA topoisomer 96.7 0.0023 4.9E-08 54.5 4.2 52 12-63 247-301 (488)
19 COG1389 DNA topoisomerase VI, 96.1 0.0045 9.9E-08 52.5 2.7 52 13-64 257-312 (538)
20 COG0266 Nei Formamidopyrimidin 95.5 0.022 4.8E-07 45.3 4.3 51 11-61 154-207 (273)
21 PF05833 FbpA: Fibronectin-bin 95.3 0.0067 1.4E-07 50.3 0.8 48 13-60 187-235 (455)
22 PF00633 HHH: Helix-hairpin-he 94.9 0.021 4.5E-07 30.7 1.9 18 18-35 12-29 (30)
23 TIGR00275 flavoprotein, HI0933 93.4 0.069 1.5E-06 43.8 2.8 50 13-64 284-333 (400)
24 KOG3311|consensus 93.3 0.019 4.1E-07 42.0 -0.5 47 65-113 70-116 (152)
25 PF11798 IMS_HHH: IMS family H 92.6 0.08 1.7E-06 28.7 1.5 20 18-38 12-31 (32)
26 PF10391 DNA_pol_lambd_f: Fing 91.5 0.15 3.2E-06 30.7 1.9 22 18-40 3-24 (52)
27 PRK00274 ksgA 16S ribosomal RN 91.3 0.19 4.1E-06 39.2 2.9 49 12-61 221-269 (272)
28 PF03486 HI0933_like: HI0933-l 91.2 0.3 6.5E-06 40.6 4.1 52 11-64 289-341 (409)
29 PF14520 HHH_5: Helix-hairpin- 91.0 0.035 7.7E-07 33.8 -1.2 26 15-41 3-28 (60)
30 smart00278 HhH1 Helix-hairpin- 90.1 0.27 5.8E-06 25.1 1.9 20 18-37 2-21 (26)
31 PRK02515 psbU photosystem II c 90.0 0.21 4.5E-06 35.8 1.9 62 6-67 50-114 (132)
32 COG0030 KsgA Dimethyladenosine 89.2 0.25 5.3E-06 39.1 1.9 46 11-61 210-255 (259)
33 TIGR00755 ksgA dimethyladenosi 87.6 0.43 9.3E-06 36.6 2.3 46 12-59 207-252 (253)
34 PRK14606 ruvA Holliday junctio 87.2 0.4 8.6E-06 36.0 1.8 22 17-38 108-129 (188)
35 COG3743 Uncharacterized conser 86.5 0.64 1.4E-05 33.3 2.5 43 18-61 68-110 (133)
36 PRK14601 ruvA Holliday junctio 86.5 0.46 1E-05 35.6 1.8 21 17-37 108-128 (183)
37 PRK13844 recombination protein 85.7 1.3 2.9E-05 33.7 4.0 72 15-94 13-111 (200)
38 PRK14603 ruvA Holliday junctio 85.7 0.53 1.1E-05 35.6 1.8 21 17-37 107-127 (197)
39 TIGR00615 recR recombination p 85.5 1.7 3.7E-05 33.0 4.5 77 15-99 9-115 (195)
40 PRK14604 ruvA Holliday junctio 85.5 0.55 1.2E-05 35.5 1.8 21 17-37 108-128 (195)
41 PRK13901 ruvA Holliday junctio 85.2 0.58 1.3E-05 35.6 1.8 21 17-37 107-127 (196)
42 TIGR03252 uncharacterized HhH- 84.7 0.39 8.5E-06 36.0 0.7 29 10-38 108-136 (177)
43 PRK14602 ruvA Holliday junctio 84.5 0.64 1.4E-05 35.3 1.8 21 17-37 109-129 (203)
44 PRK00076 recR recombination pr 84.5 1.9 4.2E-05 32.7 4.4 77 15-99 9-115 (196)
45 PF09883 DUF2110: Uncharacteri 84.5 1.6 3.5E-05 33.8 4.0 67 12-78 96-178 (225)
46 COG0632 RuvA Holliday junction 84.4 0.68 1.5E-05 35.3 1.9 21 17-37 108-128 (201)
47 COG0353 RecR Recombinational D 84.2 1.6 3.4E-05 33.3 3.8 78 14-99 9-116 (198)
48 PF00398 RrnaAD: Ribosomal RNA 83.9 0.62 1.3E-05 36.1 1.6 50 10-61 212-261 (262)
49 PF14579 HHH_6: Helix-hairpin- 83.8 1.2 2.6E-05 29.1 2.7 26 13-38 23-48 (90)
50 COG1293 Predicted RNA-binding 83.6 1.2 2.5E-05 38.8 3.2 46 15-60 188-233 (564)
51 PF14520 HHH_5: Helix-hairpin- 80.9 1.6 3.4E-05 26.4 2.2 20 18-37 39-58 (60)
52 PRK14605 ruvA Holliday junctio 80.4 0.55 1.2E-05 35.3 0.1 34 5-38 61-94 (194)
53 PRK14605 ruvA Holliday junctio 80.4 1.1 2.5E-05 33.6 1.8 18 18-35 109-126 (194)
54 PRK14600 ruvA Holliday junctio 80.0 1.2 2.6E-05 33.5 1.8 20 17-37 108-127 (186)
55 cd00141 NT_POLXc Nucleotidyltr 78.9 4.9 0.00011 32.1 5.1 24 17-41 85-108 (307)
56 cd00080 HhH2_motif Helix-hairp 78.6 1.8 3.9E-05 27.6 2.1 20 19-38 24-43 (75)
57 smart00279 HhH2 Helix-hairpin- 78.4 1.8 3.9E-05 24.0 1.8 17 20-36 19-35 (36)
58 PF02371 Transposase_20: Trans 77.8 2 4.4E-05 27.8 2.2 21 18-38 3-23 (87)
59 PF11731 Cdd1: Pathogenicity l 77.7 2.3 5.1E-05 28.6 2.5 37 17-54 12-48 (93)
60 PRK00116 ruvA Holliday junctio 77.3 1.8 3.9E-05 32.3 2.1 26 14-39 70-95 (192)
61 PF14716 HHH_8: Helix-hairpin- 77.0 1.9 4.1E-05 26.8 1.8 20 18-37 48-67 (68)
62 smart00483 POLXc DNA polymeras 75.0 2.3 5E-05 34.4 2.3 25 16-41 88-112 (334)
63 TIGR00426 competence protein C 74.3 2.5 5.3E-05 26.1 1.8 28 10-37 9-37 (69)
64 COG2081 Predicted flavoprotein 74.3 4.4 9.6E-05 34.1 3.8 50 12-64 285-334 (408)
65 PF02042 RWP-RK: RWP-RK domain 74.1 3.7 8E-05 24.8 2.5 26 22-47 24-51 (52)
66 cd00056 ENDO3c endonuclease II 74.1 2.2 4.8E-05 30.1 1.7 24 13-36 79-102 (158)
67 smart00478 ENDO3c endonuclease 73.9 2.2 4.8E-05 29.8 1.7 23 15-37 70-92 (149)
68 COG3415 Transposase and inacti 73.6 4.7 0.0001 29.0 3.3 86 18-106 26-122 (138)
69 TIGR00084 ruvA Holliday juncti 73.5 2.4 5.2E-05 31.8 1.9 20 17-36 107-126 (191)
70 PF12826 HHH_2: Helix-hairpin- 73.0 2 4.2E-05 26.5 1.1 18 21-38 7-24 (64)
71 PF12826 HHH_2: Helix-hairpin- 72.7 3.1 6.7E-05 25.6 2.0 21 18-38 36-56 (64)
72 PRK01229 N-glycosylase/DNA lya 72.7 3.2 6.8E-05 31.8 2.4 27 15-41 116-143 (208)
73 TIGR00084 ruvA Holliday juncti 72.4 0.76 1.7E-05 34.5 -1.0 33 4-36 59-91 (191)
74 PF12836 HHH_3: Helix-hairpin- 72.1 2.2 4.7E-05 26.3 1.2 47 11-57 8-61 (65)
75 PHA02564 V virion protein; Pro 71.9 9.9 0.00021 27.5 4.7 36 28-64 86-121 (141)
76 TIGR01259 comE comEA protein. 71.0 2.6 5.7E-05 29.3 1.5 31 9-39 60-90 (120)
77 PF14490 HHH_4: Helix-hairpin- 70.5 3 6.5E-05 27.5 1.6 23 20-42 49-71 (94)
78 PRK10702 endonuclease III; Pro 70.3 3.3 7.2E-05 31.5 2.0 23 15-37 107-129 (211)
79 TIGR01083 nth endonuclease III 70.3 3.5 7.5E-05 30.6 2.1 22 16-37 105-126 (191)
80 PRK08609 hypothetical protein; 70.1 3.6 7.9E-05 35.7 2.5 24 17-40 88-111 (570)
81 PRK14602 ruvA Holliday junctio 68.4 1.7 3.6E-05 33.0 0.0 35 4-38 61-95 (203)
82 COG0177 Nth Predicted EndoIII- 67.6 8.1 0.00018 29.7 3.7 40 17-60 109-148 (211)
83 PRK14601 ruvA Holliday junctio 67.1 1.4 3.1E-05 33.0 -0.5 34 4-37 60-93 (183)
84 PRK14600 ruvA Holliday junctio 67.0 1.5 3.2E-05 32.9 -0.5 35 4-38 60-94 (186)
85 PRK00116 ruvA Holliday junctio 66.5 14 0.00031 27.5 4.8 21 18-38 109-129 (192)
86 TIGR01448 recD_rel helicase, p 66.2 12 0.00026 33.4 5.0 40 21-60 88-137 (720)
87 PRK10308 3-methyl-adenine DNA 66.1 13 0.00028 29.5 4.7 33 15-47 205-238 (283)
88 PRK14606 ruvA Holliday junctio 66.0 1.5 3.2E-05 33.0 -0.7 34 4-37 60-93 (188)
89 TIGR01084 mutY A/G-specific ad 65.1 4.9 0.00011 31.8 2.1 22 16-37 104-125 (275)
90 PF04001 Vhr1: Transcription f 64.8 5.7 0.00012 26.7 2.0 60 29-97 8-67 (95)
91 PRK13901 ruvA Holliday junctio 64.1 1.8 3.9E-05 32.9 -0.5 34 4-37 59-92 (196)
92 PRK14603 ruvA Holliday junctio 63.8 1.8 3.9E-05 32.7 -0.6 34 4-37 59-92 (197)
93 PF13035 DUF3896: Protein of u 63.7 25 0.00055 21.5 4.5 43 30-89 18-61 (61)
94 PRK13913 3-methyladenine DNA g 63.5 7.8 0.00017 29.8 2.9 24 15-38 119-142 (218)
95 PRK12766 50S ribosomal protein 63.3 5.6 0.00012 31.1 2.0 38 18-56 4-41 (232)
96 PRK10880 adenine DNA glycosyla 63.1 4.9 0.00011 33.0 1.8 23 15-37 107-129 (350)
97 PRK13910 DNA glycosylase MutY; 62.7 5.1 0.00011 32.1 1.8 22 16-37 71-92 (289)
98 COG0258 Exo 5'-3' exonuclease 62.1 7.1 0.00015 31.0 2.5 17 22-38 203-219 (310)
99 cd01104 HTH_MlrA-CarA Helix-Tu 60.8 27 0.00058 20.8 4.5 42 19-60 6-51 (68)
100 PRK14604 ruvA Holliday junctio 57.7 2.6 5.7E-05 31.8 -0.6 34 4-37 60-93 (195)
101 TIGR00588 ogg 8-oxoguanine DNA 54.2 12 0.00026 30.0 2.7 43 15-60 218-260 (310)
102 smart00475 53EXOc 5'-3' exonuc 54.2 10 0.00022 29.7 2.1 20 19-38 188-207 (259)
103 COG2231 Uncharacterized protei 54.0 6.7 0.00015 30.3 1.1 42 8-49 104-147 (215)
104 PRK14667 uvrC excinuclease ABC 53.8 9.7 0.00021 33.3 2.1 43 12-56 509-551 (567)
105 cd00008 53EXOc 5'-3' exonuclea 53.7 10 0.00022 29.1 2.1 20 19-38 185-204 (240)
106 PF01367 5_3_exonuc: 5'-3' exo 53.2 1.4 3.1E-05 29.9 -2.4 19 20-38 21-39 (101)
107 PRK09482 flap endonuclease-lik 53.1 10 0.00022 29.8 2.1 19 20-38 185-203 (256)
108 PRK00558 uvrC excinuclease ABC 52.7 8.6 0.00019 33.7 1.7 42 12-55 538-579 (598)
109 COG0122 AlkA 3-methyladenine D 52.1 11 0.00023 30.1 2.0 32 14-45 195-226 (285)
110 PRK12311 rpsB 30S ribosomal pr 51.7 9.5 0.00021 31.1 1.7 44 17-61 263-306 (326)
111 cd01702 PolY_Pol_eta DNA Polym 51.1 13 0.00028 30.3 2.4 37 18-54 183-221 (359)
112 PRK14976 5'-3' exonuclease; Pr 50.6 12 0.00025 29.7 2.0 19 20-38 194-212 (281)
113 PRK14896 ksgA 16S ribosomal RN 49.5 21 0.00046 27.4 3.2 49 12-60 204-254 (258)
114 COG1555 ComEA DNA uptake prote 48.1 15 0.00032 26.5 2.1 23 15-37 95-117 (149)
115 PRK07373 DNA polymerase III su 48.0 17 0.00036 30.9 2.7 48 12-59 109-166 (449)
116 PRK05898 dnaE DNA polymerase I 47.6 38 0.00083 31.7 5.0 47 12-58 747-802 (971)
117 cd05124 AFK Actin-Fragmin Kina 46.8 68 0.0015 25.2 5.7 50 12-63 23-73 (238)
118 PRK14671 uvrC excinuclease ABC 46.3 16 0.00036 32.2 2.4 43 12-56 564-606 (621)
119 PRK14669 uvrC excinuclease ABC 46.2 17 0.00036 32.3 2.4 40 15-56 550-589 (624)
120 PF06514 PsbU: Photosystem II 46.2 13 0.00029 25.1 1.4 62 5-66 11-75 (93)
121 COG0632 RuvA Holliday junction 44.9 4.1 9E-05 31.0 -1.3 34 5-38 61-94 (201)
122 PTZ00338 dimethyladenosine tra 43.7 38 0.00082 26.9 3.9 34 29-63 256-289 (294)
123 PF11338 DUF3140: Protein of u 42.9 37 0.0008 22.9 3.2 33 24-60 34-66 (92)
124 PF00034 Cytochrom_C: Cytochro 42.8 27 0.00058 20.9 2.4 17 47-63 74-90 (91)
125 KOG0821|consensus 42.6 41 0.00088 26.8 3.8 39 28-66 270-308 (326)
126 cd08637 DNA_pol_A_pol_I_C Poly 42.0 52 0.0011 27.0 4.6 67 13-93 210-277 (377)
127 PRK14670 uvrC excinuclease ABC 42.0 20 0.00043 31.5 2.2 40 15-56 512-551 (574)
128 PF04760 IF2_N: Translation in 41.6 17 0.00037 21.2 1.3 44 17-60 7-51 (54)
129 PRK00033 clpS ATP-dependent Cl 41.6 30 0.00066 23.4 2.7 64 2-65 30-93 (100)
130 PRK12278 50S ribosomal protein 40.8 24 0.00052 27.3 2.3 43 17-60 158-200 (221)
131 COG1936 Predicted nucleotide k 40.5 26 0.00056 26.4 2.4 25 16-40 2-26 (180)
132 PRK07945 hypothetical protein; 40.3 20 0.00044 29.0 1.9 21 18-38 50-70 (335)
133 COG1059 Thermostable 8-oxoguan 40.0 15 0.00033 28.1 1.1 25 16-40 120-144 (210)
134 PF11328 DUF3130: Protein of u 39.5 51 0.0011 22.1 3.4 33 52-84 42-75 (90)
135 PRK06253 O-phosphoseryl-tRNA s 39.4 52 0.0011 28.8 4.3 35 23-64 105-139 (529)
136 TIGR00575 dnlj DNA ligase, NAD 39.0 24 0.00052 31.3 2.3 36 21-56 436-471 (652)
137 TIGR00194 uvrC excinuclease AB 38.4 23 0.00051 31.0 2.1 24 15-38 539-562 (574)
138 cd00128 XPG Xeroderma pigmento 37.6 24 0.00053 27.9 2.0 18 21-38 227-244 (316)
139 TIGR03045 PS_II_C550 cytochrom 37.3 42 0.00091 24.6 3.0 19 46-64 130-149 (159)
140 PF06207 DUF1002: Protein of u 37.1 91 0.002 24.1 5.0 26 31-63 182-207 (225)
141 PF14794 DUF4479: Domain of un 37.0 32 0.0007 21.9 2.1 21 45-65 45-65 (73)
142 PF13442 Cytochrome_CBB3: Cyto 36.8 35 0.00076 20.3 2.2 14 47-60 54-67 (67)
143 PF14635 HHH_7: Helix-hairpin- 36.7 32 0.00069 23.6 2.2 27 12-38 45-71 (104)
144 COG1908 FrhD Coenzyme F420-red 36.6 42 0.00091 23.9 2.8 35 29-63 82-117 (132)
145 cd01401 PncB_like Nicotinate p 36.6 59 0.0013 27.1 4.1 43 28-70 289-340 (377)
146 PF00542 Ribosomal_L12: Riboso 36.1 18 0.00039 22.7 0.8 43 15-60 16-58 (68)
147 PRK03980 flap endonuclease-1; 34.9 29 0.00062 27.7 2.0 18 21-38 193-210 (292)
148 PRK14666 uvrC excinuclease ABC 34.8 27 0.0006 31.4 2.0 24 15-38 635-658 (694)
149 cd00349 Ribosomal_L11 Ribosoma 34.7 1.1E+02 0.0024 21.5 4.8 51 27-77 65-121 (131)
150 PRK14668 uvrC excinuclease ABC 34.5 27 0.00058 30.7 1.9 40 15-56 523-562 (577)
151 PF03118 RNA_pol_A_CTD: Bacter 33.1 34 0.00075 21.1 1.8 20 18-37 45-64 (66)
152 PRK04301 radA DNA repair and r 32.9 41 0.0009 26.6 2.6 38 17-55 6-43 (317)
153 COG1194 MutY A/G-specific DNA 32.8 29 0.00062 28.7 1.7 19 18-36 114-132 (342)
154 TIGR02236 recomb_radA DNA repa 32.5 38 0.00081 26.6 2.3 37 19-56 1-37 (310)
155 TIGR03674 fen_arch flap struct 31.9 34 0.00073 27.8 2.0 19 20-38 239-257 (338)
156 PLN03072 60S ribosomal protein 31.6 88 0.0019 23.1 4.0 64 26-99 75-146 (166)
157 PRK00419 DNA primase small sub 31.4 35 0.00075 28.5 2.0 16 68-83 278-293 (376)
158 PRK07279 dnaE DNA polymerase I 31.2 48 0.001 31.2 3.0 47 12-58 745-797 (1034)
159 PF13613 HTH_Tnp_4: Helix-turn 30.8 45 0.00097 19.4 1.9 20 18-37 24-43 (53)
160 PRK13620 psbV cytochrome c-550 30.8 55 0.0012 25.3 2.8 24 37-60 167-197 (215)
161 PTZ00217 flap endonuclease-1; 30.6 37 0.00079 28.3 2.0 19 20-38 238-256 (393)
162 PF07700 HNOB: Heme NO binding 30.5 1.2E+02 0.0025 21.8 4.5 36 26-61 18-56 (171)
163 PRK06920 dnaE DNA polymerase I 30.5 65 0.0014 30.6 3.8 47 12-58 797-852 (1107)
164 PF04201 TPD52: Tumour protein 30.1 48 0.001 24.6 2.3 15 46-60 24-38 (162)
165 TIGR00608 radc DNA repair prot 30.1 29 0.00063 26.6 1.2 21 19-39 62-82 (218)
166 PF13331 DUF4093: Domain of un 30.0 13 0.00028 24.5 -0.6 26 13-38 48-73 (87)
167 KOG1014|consensus 29.9 68 0.0015 26.2 3.4 41 21-64 57-98 (312)
168 PRK05672 dnaE2 error-prone DNA 29.8 58 0.0013 30.7 3.3 46 12-58 811-863 (1046)
169 PRK02406 DNA polymerase IV; Va 29.6 47 0.001 26.5 2.4 36 18-54 169-204 (343)
170 TIGR00594 polc DNA-directed DN 29.5 51 0.0011 30.9 2.9 47 12-58 819-875 (1022)
171 TIGR00470 sepS O-phosphoseryl- 29.3 89 0.0019 27.3 4.1 34 23-64 105-138 (533)
172 PRK07956 ligA NAD-dependent DN 29.1 29 0.00063 30.9 1.2 35 20-54 448-482 (665)
173 PRK14672 uvrC excinuclease ABC 29.1 38 0.00082 30.5 1.9 42 13-56 604-645 (691)
174 PRK13766 Hef nuclease; Provisi 29.0 45 0.00097 29.6 2.4 37 16-54 714-750 (773)
175 PRK03352 DNA polymerase IV; Va 28.8 56 0.0012 26.0 2.7 36 18-54 178-213 (346)
176 PRK12373 NADH dehydrogenase su 28.7 46 0.001 28.0 2.3 43 18-61 324-366 (400)
177 cd01199 INT_Tn1545_C Tn1545-re 28.7 72 0.0016 22.4 3.1 15 48-62 2-16 (205)
178 PF13443 HTH_26: Cro/C1-type H 28.5 1E+02 0.0022 17.9 3.3 35 19-60 16-50 (63)
179 TIGR00630 uvra excinuclease AB 28.5 52 0.0011 30.6 2.8 31 28-58 320-350 (924)
180 smart00482 POLAc DNA polymeras 28.3 1.3E+02 0.0028 22.4 4.5 61 20-92 78-139 (206)
181 cd00141 NT_POLXc Nucleotidyltr 27.9 32 0.00069 27.5 1.2 23 18-40 46-68 (307)
182 PF13875 DUF4202: Domain of un 27.7 1.9E+02 0.0041 21.9 5.2 48 27-83 89-136 (185)
183 smart00483 POLXc DNA polymeras 27.5 44 0.00096 27.0 2.0 21 18-38 49-69 (334)
184 COG5485 Predicted ester cyclas 27.3 24 0.00051 25.2 0.3 12 92-103 89-100 (131)
185 PRK03858 DNA polymerase IV; Va 27.2 64 0.0014 26.2 2.9 36 18-54 174-209 (396)
186 PRK00024 hypothetical protein; 27.1 49 0.0011 25.3 2.0 22 18-39 67-88 (224)
187 PF01418 HTH_6: Helix-turn-hel 26.9 57 0.0012 20.4 2.0 22 19-40 40-61 (77)
188 PF10511 Cementoin: Trappin pr 26.9 30 0.00064 16.2 0.5 8 94-101 8-15 (17)
189 PF14261 DUF4351: Domain of un 26.8 62 0.0013 19.7 2.1 40 31-70 14-56 (59)
190 PF13276 HTH_21: HTH-like doma 26.6 40 0.00087 19.9 1.2 34 9-42 20-55 (60)
191 cd02020 CMPK Cytidine monophos 26.3 2E+02 0.0043 19.0 5.5 43 17-60 2-45 (147)
192 COG1948 MUS81 ERCC4-type nucle 26.1 54 0.0012 26.0 2.2 38 16-55 181-218 (254)
193 PRK05755 DNA polymerase I; Pro 26.0 47 0.001 30.4 2.0 20 19-38 189-208 (880)
194 PF14965 BRI3BP: Negative regu 25.7 1.3E+02 0.0028 22.7 4.0 32 28-59 48-79 (177)
195 PRK12766 50S ribosomal protein 25.7 60 0.0013 25.4 2.3 21 18-38 37-57 (232)
196 KOG2875|consensus 25.6 29 0.00062 28.2 0.5 22 15-36 216-237 (323)
197 PRK00349 uvrA excinuclease ABC 25.5 63 0.0014 30.1 2.7 30 28-57 322-351 (943)
198 KOG2534|consensus 25.3 1.4E+02 0.003 24.8 4.3 43 18-60 57-99 (353)
199 CHL00154 rpl29 ribosomal prote 25.2 1.2E+02 0.0027 18.9 3.3 42 45-86 9-62 (67)
200 TIGR00593 pola DNA polymerase 24.9 50 0.0011 30.5 2.0 19 20-38 188-206 (887)
201 smart00530 HTH_XRE Helix-turn- 24.9 83 0.0018 16.2 2.3 16 26-41 38-53 (56)
202 COG1796 POL4 DNA polymerase IV 24.9 55 0.0012 26.9 2.0 20 18-37 54-73 (326)
203 PRK03609 umuC DNA polymerase V 24.8 70 0.0015 26.4 2.7 36 18-54 180-215 (422)
204 KOG4302|consensus 24.7 2.7E+02 0.0059 25.1 6.4 36 28-63 188-238 (660)
205 smart00649 RL11 Ribosomal prot 24.6 2.1E+02 0.0045 20.2 4.8 52 26-77 64-121 (132)
206 PF02662 FlpD: Methyl-viologen 24.5 70 0.0015 22.1 2.3 35 29-63 81-116 (124)
207 PF00298 Ribosomal_L11: Riboso 24.4 1.9E+02 0.0041 18.1 4.1 49 28-76 4-58 (69)
208 PF08478 POTRA_1: POTRA domain 24.4 72 0.0016 18.9 2.1 34 21-54 7-40 (69)
209 PF14213 DUF4325: Domain of un 24.3 1.8E+02 0.0039 17.9 4.1 52 9-60 14-72 (74)
210 PRK02362 ski2-like helicase; P 24.1 64 0.0014 28.7 2.5 38 18-56 653-690 (737)
211 COG0080 RplK Ribosomal protein 24.1 2.4E+02 0.0051 20.5 4.9 63 27-99 72-140 (141)
212 TIGR03791 TTQ_mauG tryptophan 24.0 89 0.0019 25.0 3.1 26 38-63 253-278 (291)
213 CHL00133 psbV photosystem II c 24.0 86 0.0019 23.1 2.8 19 46-64 131-150 (163)
214 PF01595 DUF21: Domain of unkn 23.9 1.5E+02 0.0031 20.9 4.0 35 25-60 139-173 (183)
215 COG0322 UvrC Nuclease subunit 23.9 60 0.0013 28.6 2.2 41 14-56 527-567 (581)
216 PF01698 FLO_LFY: Floricaula / 23.9 26 0.00056 29.4 0.0 69 21-91 56-131 (386)
217 PRK01143 rpl11p 50S ribosomal 23.5 2.1E+02 0.0045 21.0 4.7 35 26-60 69-109 (163)
218 KOG1220|consensus 23.3 82 0.0018 28.0 2.9 33 9-41 242-274 (607)
219 TIGR01405 polC_Gram_pos DNA po 23.3 83 0.0018 30.2 3.1 25 13-37 1146-1170(1213)
220 TIGR00596 rad1 DNA repair prot 23.2 69 0.0015 29.4 2.5 38 15-55 756-793 (814)
221 PRK11235 bifunctional antitoxi 23.0 56 0.0012 21.3 1.5 16 28-43 14-29 (80)
222 PF15494 SRCR_2: Scavenger rec 23.0 78 0.0017 20.6 2.2 21 23-43 22-42 (98)
223 cd00093 HTH_XRE Helix-turn-hel 22.7 92 0.002 16.2 2.2 22 21-42 35-56 (58)
224 PF07957 DUF3294: Protein of u 22.2 3.1E+02 0.0068 21.2 5.6 74 12-94 124-212 (216)
225 PF09489 CbtB: Probable cobalt 22.0 35 0.00075 20.7 0.3 10 89-98 45-54 (54)
226 PRK07135 dnaE DNA polymerase I 21.9 99 0.0021 29.0 3.3 48 12-59 748-805 (973)
227 PF11460 DUF3007: Protein of u 21.9 52 0.0011 22.6 1.2 19 42-60 84-102 (104)
228 PRK05673 dnaE DNA polymerase I 21.9 75 0.0016 30.2 2.5 47 12-58 815-871 (1135)
229 TIGR02459 CbtB cobalt transpor 21.8 34 0.00074 21.3 0.2 10 89-98 51-60 (60)
230 PF02229 PC4: Transcriptional 21.8 34 0.00074 20.5 0.2 20 41-60 37-56 (56)
231 PRK07956 ligA NAD-dependent DN 21.7 46 0.001 29.7 1.1 39 15-56 510-548 (665)
232 cd01700 PolY_Pol_V_umuC umuC s 21.6 87 0.0019 24.9 2.6 36 18-54 177-212 (344)
233 TIGR02714 amido_AtzD_TrzD ring 21.5 1.8E+02 0.004 24.2 4.4 53 6-61 232-297 (366)
234 PF03677 UPF0137: Uncharacteri 21.4 1.3E+02 0.0029 23.6 3.5 26 43-68 32-57 (243)
235 PRK00140 rplK 50S ribosomal pr 21.2 1.8E+02 0.0039 20.8 3.9 48 26-73 72-125 (141)
236 PRK03348 DNA polymerase IV; Pr 21.2 87 0.0019 26.3 2.6 38 18-56 181-218 (454)
237 cd00424 PolY Y-family of DNA p 20.5 1E+02 0.0023 24.5 2.9 36 18-54 174-210 (343)
238 COG1131 CcmA ABC-type multidru 20.2 1.5E+02 0.0032 23.4 3.6 41 20-60 103-149 (293)
239 PRK13618 psbV cytochrome c-550 20.1 1.2E+02 0.0025 22.4 2.8 16 45-60 130-145 (163)
240 cd03586 PolY_Pol_IV_kappa DNA 20.0 1E+02 0.0022 24.2 2.6 37 18-55 172-208 (334)
No 1
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=4.9e-55 Score=307.78 Aligned_cols=121 Identities=51% Similarity=0.852 Sum_probs=118.1
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHH
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKR 79 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~r 79 (121)
||||+|+|||++|+|.+||++|||||+++|.+||+.+||||++++++|+++|+++|.++| ++|.+|+||++.+++||+|
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r 80 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEENYQVEGDLRRFESLNIKR 80 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999999999999999999 5799999999999999999
Q ss_pred HHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858 80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK 121 (121)
Q Consensus 80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~ 121 (121)
|++|+||||+||.+|||||||||||||||+|+++++++++++
T Consensus 81 l~~I~sYRG~RH~~gLPVRGQRT~tNarT~k~~~~~~~~kk~ 122 (122)
T CHL00137 81 LMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGKKK 122 (122)
T ss_pred HHHhCchhcccccCCCCCCCCcCCccccccCCCcccccccCC
Confidence 999999999999999999999999999999999999997664
No 2
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-55 Score=304.51 Aligned_cols=120 Identities=56% Similarity=1.053 Sum_probs=117.5
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-hcccchhhHHHHHHHHHH
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS-KFIIEGDLRREFSMNIKR 79 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~-~~~i~~~L~~~~~~~I~r 79 (121)
|+||+|+|||++|.|.+|||+|||||..+|.+||+++||||++++++|||+|+++|.++++ .|.+|+||++++++||+|
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkR 80 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKR 80 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999995 999999999999999999
Q ss_pred HHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858 80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120 (121)
Q Consensus 80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~ 120 (121)
|++|+||||+||.+|||||||||+|||||+|+++++++++|
T Consensus 81 l~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 81 LMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred HHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 99999999999999999999999999999999999987765
No 3
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=1.1e-54 Score=305.94 Aligned_cols=121 Identities=60% Similarity=1.047 Sum_probs=118.0
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-hcccchhhHHHHHHHHHH
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS-KFIIEGDLRREFSMNIKR 79 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~-~~~i~~~L~~~~~~~I~r 79 (121)
||||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++|+++|+++|.++|+ +|.+|+||++.+++||+|
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r 80 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKR 80 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999995 599999999999999999
Q ss_pred HHhhccccccccCCCCCcCCccccccccccCCCCcccccccC
Q psy8858 80 LIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLRK 121 (121)
Q Consensus 80 l~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~~ 121 (121)
|++|+||||+||.+|||||||||||||||+|+++++++++++
T Consensus 81 l~~I~sYRG~RH~~gLPVRGQRT~TNart~k~~~~~~~~kk~ 122 (122)
T PRK05179 81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK 122 (122)
T ss_pred HHHhcceeeeecccCCCCCCCcCCccccccCCccccccccCC
Confidence 999999999999999999999999999999999999987764
No 4
>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=2.3e-51 Score=285.87 Aligned_cols=112 Identities=63% Similarity=1.100 Sum_probs=109.1
Q ss_pred eeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHH
Q psy8858 3 RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKRLI 81 (121)
Q Consensus 3 ~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~rl~ 81 (121)
||+|+|+|++|+|.+||++|||||+.+|.+||+++||||++++++|+++|+++|.++| ++|.+|+||++.+++||+||+
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~rl~ 80 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLM 80 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence 6899999999999999999999999999999999999999999999999999999999 679999999999999999999
Q ss_pred hhccccccccCCCCCcCCccccccccccCCCCc
Q psy8858 82 DLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRR 114 (121)
Q Consensus 82 ~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~ 114 (121)
+|+||||+||.+|||||||||||||||+|+.++
T Consensus 81 ~I~syRG~RH~~gLpVRGQRT~TNart~k~~~~ 113 (113)
T TIGR03631 81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRK 113 (113)
T ss_pred HhcceeccccccCCCCCCCcCCccccccCCCCC
Confidence 999999999999999999999999999998753
No 5
>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=1.1e-49 Score=287.34 Aligned_cols=118 Identities=32% Similarity=0.537 Sum_probs=111.3
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh------------------
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK------------------ 62 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~------------------ 62 (121)
|+||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++||++|+++|.++|++
T Consensus 5 m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~Nr~~d~~t 84 (144)
T TIGR03629 5 IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLLNRRKDYET 84 (144)
T ss_pred eeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHhhccccccc
Confidence 89999999999999999999999999999999999999999999999999999999999964
Q ss_pred ----cccchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858 63 ----FIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120 (121)
Q Consensus 63 ----~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~ 120 (121)
|.+|+||++++++||+||++|+||||+||.+|||||||||||||||++ ..+|++||
T Consensus 85 g~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~--~~gv~~kk 144 (144)
T TIGR03629 85 GEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGR--TVGVSRKK 144 (144)
T ss_pred CccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCC--ccccccCC
Confidence 679999999999999999999999999999999999999999998864 45566654
No 6
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=1.1e-49 Score=288.62 Aligned_cols=118 Identities=33% Similarity=0.531 Sum_probs=111.0
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh-------------------
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS------------------- 61 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~------------------- 61 (121)
||||+|+|||++|+|.+||++|||||+++|.+||+.+||||++++++|+++|+++|.++|+
T Consensus 9 m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~Nr~~d~~ 88 (149)
T PRK04053 9 IVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLNRRKDYE 88 (149)
T ss_pred hHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhccccccc
Confidence 8999999999999999999999999999999999999999999999999999999999994
Q ss_pred ----hcccchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858 62 ----KFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120 (121)
Q Consensus 62 ----~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~ 120 (121)
++.+|+||++.+++||+||++|+||||+||.+|||||||||||||||. ++.+|+.+|
T Consensus 89 tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg--~~~gv~~kk 149 (149)
T PRK04053 89 TGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTG--GTVGVSRKK 149 (149)
T ss_pred cCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCC--CccccccCC
Confidence 467999999999999999999999999999999999999999999886 455566554
No 7
>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=5.3e-50 Score=276.38 Aligned_cols=106 Identities=58% Similarity=0.943 Sum_probs=102.2
Q ss_pred eeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh-cccchhhHHHHHHHHHHHH
Q psy8858 3 RIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK-FIIEGDLRREFSMNIKRLI 81 (121)
Q Consensus 3 ~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~-~~i~~~L~~~~~~~I~rl~ 81 (121)
||+|++||++|+|.+||++|||||+++|.+||+.+||+|++++++|+++|+++|.++|.+ |.+++||++.+.+||+||+
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~~~~i~~~L~~~~~~~i~rl~ 80 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEKNHLIENDLKRQVRENIKRLK 80 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHTHSTCHHHHHHHHHHHHHHHH
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHH
Confidence 799999999999999999999999999999999999999999999999999999999965 9999999999999999999
Q ss_pred hhccccccccCCCCCcCCccccccccc
Q psy8858 82 DLSCYRGIRHRKSLPCRGQRTRTNART 108 (121)
Q Consensus 82 ~i~~yRG~RH~~gLpVRGQRT~tNart 108 (121)
+|+||||+||.+|||||||||||||||
T Consensus 81 ~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 81 KIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp HHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred HHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999987
No 8
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=7.2e-49 Score=285.55 Aligned_cols=118 Identities=31% Similarity=0.494 Sum_probs=110.1
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh---cc-------------
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK---FI------------- 64 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~---~~------------- 64 (121)
||||+|+|||++|+|.+||++|||||+.+|.+||+++||||++++++|+++|+++|.++|++ |.
T Consensus 14 mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~nr~kd~~ 93 (154)
T PTZ00134 14 ILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFLNRQRDPK 93 (154)
T ss_pred hhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHhhcccccc
Confidence 89999999999999999999999999999999999999999999999999999999999954 53
Q ss_pred -------cchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858 65 -------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120 (121)
Q Consensus 65 -------i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~ 120 (121)
+|+||++.+++||+||++|+||||+||.+|||||||||||||||++ ..+|+++|
T Consensus 94 tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~--~~gv~~kk 154 (154)
T PTZ00134 94 DGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGR--TVGVSRKK 154 (154)
T ss_pred ccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCcccc--ccceeccC
Confidence 6999999999999999999999999999999999999999997764 45566554
No 9
>KOG3311|consensus
Probab=100.00 E-value=1.7e-35 Score=213.09 Aligned_cols=118 Identities=29% Similarity=0.568 Sum_probs=108.4
Q ss_pred CceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh---cc-------------
Q psy8858 1 MTRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK---FI------------- 64 (121)
Q Consensus 1 mv~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~---~~------------- 64 (121)
|++|+|++++++++|.|||++|||||...|..+|+++|||+.+++++|+++|++.+.+++++ |.
T Consensus 12 i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~~~~l~rq~~~~ 91 (152)
T KOG3311|consen 12 ILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIPDWFLNRQKDII 91 (152)
T ss_pred HHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCchHHHHhhcccc
Confidence 57899999999999999999999999999999999999999999999999999999999853 21
Q ss_pred -------cchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCCccccccc
Q psy8858 65 -------IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPRRAAQSLR 120 (121)
Q Consensus 65 -------i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~~~~~~~~ 120 (121)
+.+.++...+++|+||++|.||||+||.+|||||||||+||| ++++..+|++||
T Consensus 92 dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~--~~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 92 DGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNG--RRGKTVGVSGKK 152 (152)
T ss_pred cCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccc--cccceeeecccC
Confidence 356788999999999999999999999999999999999999 666677788775
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=97.71 E-value=3.6e-05 Score=51.58 Aligned_cols=50 Identities=30% Similarity=0.408 Sum_probs=41.5
Q ss_pred Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
+++|..+| +-+.|||...+.+||-.+||+|..++.+|+++|+..|.+.+.
T Consensus 23 ~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~ 75 (92)
T PF06831_consen 23 RRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIK 75 (92)
T ss_dssp CSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHH
T ss_pred cchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 45666666 679999999999999999999999999999999999988874
No 11
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=97.35 E-value=0.00024 Score=55.88 Aligned_cols=51 Identities=24% Similarity=0.288 Sum_probs=46.9
Q ss_pred CCeeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 11 NNQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 11 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
.+..|.-+| +-+.|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus 154 ~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~ 207 (274)
T PRK01103 154 KKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIK 207 (274)
T ss_pred CCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 456788888 889999999999999999999999999999999999998884
No 12
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=97.32 E-value=0.00025 Score=60.86 Aligned_cols=53 Identities=26% Similarity=0.333 Sum_probs=47.9
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
.....|+-.+|..||..+|.+||..+|++|++++.+|+++|++.|.++|+++.
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~ 308 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKYK 308 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhcc
Confidence 34456777899999999999999999999999999999999999999997764
No 13
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=97.02 E-value=0.00094 Score=52.62 Aligned_cols=51 Identities=22% Similarity=0.281 Sum_probs=44.3
Q ss_pred CCeeeeeehh---cccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 11 NNQHIIIGLT---AIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 11 ~~k~v~~aLt---~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
.+.+|.-+|- -|.|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus 153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~ 206 (272)
T PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIG 206 (272)
T ss_pred CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence 3455666664 35999999999999999999999999999999999999874
No 14
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.93 E-value=0.0014 Score=51.56 Aligned_cols=50 Identities=18% Similarity=0.218 Sum_probs=43.9
Q ss_pred Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
+.+|.-+| +-|-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus 143 ~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~ 195 (269)
T PRK14811 143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIR 195 (269)
T ss_pred CCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHH
Confidence 45566666 568999999999999999999999999999999999988773
No 15
>PRK10445 endonuclease VIII; Provisional
Probab=96.90 E-value=0.0015 Score=51.16 Aligned_cols=50 Identities=24% Similarity=0.302 Sum_probs=43.9
Q ss_pred Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
+++|.-+| +-+-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~ 203 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALL 203 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHH
Confidence 44555555 468899999999999999999999999999999999999884
No 16
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.82 E-value=0.0017 Score=51.35 Aligned_cols=50 Identities=30% Similarity=0.370 Sum_probs=43.8
Q ss_pred Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
..+|.-+| +-|-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.
T Consensus 164 ~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 216 (282)
T PRK13945 164 TRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAII 216 (282)
T ss_pred CccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 44555555 568999999999999999999999999999999999988873
No 17
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.80 E-value=0.0018 Score=50.96 Aligned_cols=50 Identities=24% Similarity=0.304 Sum_probs=43.8
Q ss_pred Ceeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 12 NQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 12 ~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
+.+|.-+| +-|-|||.-.|.+||-.++|+|..++.+||++|++.|.+.+.
T Consensus 155 ~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 207 (272)
T TIGR00577 155 KRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIK 207 (272)
T ss_pred CCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHH
Confidence 44555555 568899999999999999999999999999999999998884
No 18
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=96.66 E-value=0.0023 Score=54.52 Aligned_cols=52 Identities=23% Similarity=0.256 Sum_probs=46.6
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHHHHhhc
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKIS---TTKKIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~~l~~~ 63 (121)
.....|+-.+|..||..+|.+||..+|++ |++.+.+|+++|++.|.++|++.
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 301 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKEM 301 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHhc
Confidence 34456677899999999999999999999 99999999999999999999654
No 19
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=96.06 E-value=0.0045 Score=52.52 Aligned_cols=52 Identities=25% Similarity=0.282 Sum_probs=46.9
Q ss_pred eeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCC----HHHHHHHHHHHhhcc
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLN----DNELEKLREEISKFI 64 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls----~~qi~~L~~~l~~~~ 64 (121)
+.-.|...+|.-||..+|..+|+.+|++|++.+.+|+ ++|.+.|.+++++|.
T Consensus 257 tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~~ 312 (538)
T COG1389 257 TVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKMK 312 (538)
T ss_pred hHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhCc
Confidence 3345777899999999999999999999999999999 999999999997664
No 20
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.49 E-value=0.022 Score=45.30 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=43.9
Q ss_pred CCeeeeeeh---hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 11 NNQHIIIGL---TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 11 ~~k~v~~aL---t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
.+++|.-+| +-+-|||.-.|.++|-.+||+|....++|+++|+..|.+++.
T Consensus 154 ~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~ 207 (273)
T COG0266 154 KKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK 207 (273)
T ss_pred CccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHH
Confidence 344455555 568999999999999999999999999999999999888874
No 21
>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=95.26 E-value=0.0067 Score=50.27 Aligned_cols=48 Identities=33% Similarity=0.505 Sum_probs=35.7
Q ss_pred eeeeeeh-hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 13 QHIIIGL-TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 13 k~v~~aL-t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
..+.-+| ..+.|+|+..|..+|.++|++++..+.++++++++.|.+.+
T Consensus 187 ~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~ 235 (455)
T PF05833_consen 187 KTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAI 235 (455)
T ss_dssp -BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHH
T ss_pred ccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHH
Confidence 3444555 45569999999999999999999999999999999888877
No 22
>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=94.94 E-value=0.021 Score=30.72 Aligned_cols=18 Identities=33% Similarity=0.438 Sum_probs=15.2
Q ss_pred ehhcccccCHHHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICE 35 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~ 35 (121)
.|.+++|||+++|..|+.
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 578999999999999975
No 23
>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=93.39 E-value=0.069 Score=43.77 Aligned_cols=50 Identities=16% Similarity=0.205 Sum_probs=41.4
Q ss_pred eeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
+.+...|..+ +-...+..||+.+||++++++.+|+++|++.|.+.|++|.
T Consensus 284 ~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~~~ 333 (400)
T TIGR00275 284 KTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKNWP 333 (400)
T ss_pred hhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhCCE
Confidence 3444444432 7789999999999999999999999999999999997765
No 24
>KOG3311|consensus
Probab=93.32 E-value=0.019 Score=41.97 Aligned_cols=47 Identities=19% Similarity=0.024 Sum_probs=42.6
Q ss_pred cchhhHHHHHHHHHHHHhhccccccccCCCCCcCCccccccccccCCCC
Q psy8858 65 IEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRGQRTRTNARTRKGPR 113 (121)
Q Consensus 65 i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRGQRT~tNart~k~~~ 113 (121)
+.+|.+.+...|+..+.++.+|.|. ..+||+.||.|+.|+.++|.++
T Consensus 70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRlkk 116 (152)
T KOG3311|consen 70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERLKK 116 (152)
T ss_pred HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHHhh
Confidence 6678888899999999999999999 9999999999999999988554
No 25
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=92.63 E-value=0.08 Score=28.71 Aligned_cols=20 Identities=30% Similarity=0.566 Sum_probs=15.1
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.+++++|||+.++..+ +.+|
T Consensus 12 pi~~~~GIG~kt~~kL-~~~G 31 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL-NKLG 31 (32)
T ss_dssp BGGGSTTS-HHHHHHH-HCTT
T ss_pred CHHhhCCccHHHHHHH-HHcc
Confidence 5789999999999884 4444
No 26
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=91.53 E-value=0.15 Score=30.75 Aligned_cols=22 Identities=32% Similarity=0.498 Sum_probs=15.9
Q ss_pred ehhcccccCHHHHHHHHHHhCCC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKIS 40 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~ 40 (121)
.+++|+|||+.+|....+ .|+.
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 468999999999999997 7755
No 27
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=91.29 E-value=0.19 Score=39.20 Aligned_cols=49 Identities=14% Similarity=0.356 Sum_probs=37.4
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
.|.+..+|..+++. ...+..+++.+|++|+.++.+|+.+|+..|.+.+.
T Consensus 221 rk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~ 269 (272)
T PRK00274 221 RKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALA 269 (272)
T ss_pred HHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHH
Confidence 34445555555432 34567889999999999999999999999988874
No 28
>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=91.19 E-value=0.3 Score=40.64 Aligned_cols=52 Identities=17% Similarity=0.272 Sum_probs=43.0
Q ss_pred CCeeeeeehhcccccCHHHHHHHHHHhCC-CCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 11 NNQHIIIGLTAIYGIGRSRAKKICEVTKI-STTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi-~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
+++.+...|..+ +-...+..+|+.+++ +++.++.+++++++..|.+.|++|.
T Consensus 289 ~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~~~ 341 (409)
T PF03486_consen 289 PKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKRFP 341 (409)
T ss_dssp TTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHCEE
T ss_pred HhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHhCc
Confidence 455566666655 788999999999999 9999999999999999999997765
No 29
>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=90.98 E-value=0.035 Score=33.80 Aligned_cols=26 Identities=42% Similarity=0.571 Sum_probs=21.2
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCC
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKIST 41 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p 41 (121)
++-+|.+|.|||+..|..+.+. |+..
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~-G~~t 28 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEA-GIKT 28 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHT-TCSS
T ss_pred HHHhhccCCCCCHHHHHHHHhc-CCCc
Confidence 3457889999999999999877 7664
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.09 E-value=0.27 Score=25.11 Aligned_cols=20 Identities=40% Similarity=0.453 Sum_probs=16.9
Q ss_pred ehhcccccCHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (121)
.|.+++|||..+|..|+...
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 36799999999999998743
No 31
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=90.02 E-value=0.21 Score=35.77 Aligned_cols=62 Identities=18% Similarity=0.254 Sum_probs=44.3
Q ss_pred CccCCCCeeeeeehhcccccCHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHHHHhhcccch
Q psy8858 6 GINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKIS---TTKKIKDLNDNELEKLREEISKFIIEG 67 (121)
Q Consensus 6 ~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~~l~~~~i~~ 67 (121)
+.-++-|..-.-+|..++|||+.+|..|++--.+. .-..+.-+++.|.+.|.+...+|.+..
T Consensus 50 ~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV~~ 114 (132)
T PRK02515 50 GEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDNFTVTE 114 (132)
T ss_pred CCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcceeeCC
Confidence 44455556666678999999999999999632222 123466678888999988887776543
No 32
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=89.23 E-value=0.25 Score=39.06 Aligned_cols=46 Identities=15% Similarity=0.374 Sum_probs=39.6
Q ss_pred CCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 11 NNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
..|.+..+|+..++ ..++|..+|+|++.++.+|+.+|+-.|.+.+.
T Consensus 210 RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~ 255 (259)
T COG0030 210 RRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALK 255 (259)
T ss_pred hhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHh
Confidence 35666677777776 88999999999999999999999999999884
No 33
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=87.57 E-value=0.43 Score=36.64 Aligned_cols=46 Identities=13% Similarity=0.237 Sum_probs=35.1
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREE 59 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~ 59 (121)
.|.+..+|..+++- ..+..+++.+|+++++++.+|+.+|+..|.+.
T Consensus 207 rk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 207 RKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred hHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 45556666665432 34567888899999999999999999998765
No 34
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.18 E-value=0.4 Score=36.04 Aligned_cols=22 Identities=32% Similarity=0.465 Sum_probs=18.7
Q ss_pred eehhcccccCHHHHHHHHHHhC
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
-+|++++|||+++|.+||-.|-
T Consensus 108 ~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHHH
Confidence 3689999999999999996543
No 35
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=86.48 E-value=0.64 Score=33.32 Aligned_cols=43 Identities=23% Similarity=0.288 Sum_probs=38.4
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
-||.|.|||+.... .+..+||.....+-.+|..|+..+.++|.
T Consensus 68 DLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 68 DLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred cchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 58999999998765 67899999999999999999999999883
No 36
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.45 E-value=0.46 Score=35.61 Aligned_cols=21 Identities=33% Similarity=0.363 Sum_probs=18.1
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
-+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999554
No 37
>PRK13844 recombination protein RecR; Provisional
Probab=85.69 E-value=1.3 Score=33.73 Aligned_cols=72 Identities=15% Similarity=0.217 Sum_probs=48.6
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH----
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR---- 71 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~---- 71 (121)
+.-+|++++|||+++|..+.-.+= +.++++++.|.+.|.+.. |=+|-.|
T Consensus 13 LI~~l~~LPGIG~KsA~Rla~~lL--------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lte~~~C~IC~d~~Rd~~~ 84 (200)
T PRK13844 13 VIESLRKLPTIGKKSSQRLALYLL--------DKSPETAIAIANSLLDATANIKKCVYCQALTEDDVCNICSNTNRDDTK 84 (200)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCCCCCCCCCCCCCCCCE
Confidence 456789999999999999985542 345778888888873321 1011111
Q ss_pred ----HHHHHHHHHHhhccccccccCCC
Q psy8858 72 ----EFSMNIKRLIDLSCYRGIRHRKS 94 (121)
Q Consensus 72 ----~~~~~I~rl~~i~~yRG~RH~~g 94 (121)
+--.|+.-+-+.+.|+|.=|-+|
T Consensus 85 iCVVE~~~Dv~aiE~t~~y~G~YhVL~ 111 (200)
T PRK13844 85 LCIIESMLDMIAIEEAGIYRGKYFVLN 111 (200)
T ss_pred EEEECCHHHHHHHHhhCccceEEEEcc
Confidence 12346667778899999999875
No 38
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.67 E-value=0.53 Score=35.58 Aligned_cols=21 Identities=29% Similarity=0.316 Sum_probs=17.9
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
.+|++++|||+++|.+||-.|
T Consensus 107 ~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999443
No 39
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.52 E-value=1.7 Score=33.01 Aligned_cols=77 Identities=25% Similarity=0.295 Sum_probs=51.2
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH----
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR---- 71 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~---- 71 (121)
+..+|++++|||+++|..+.-.+= ..+++++..|.++|.+.. |=+|-.+
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~ll--------~~~~~~~~~la~ai~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~ 80 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHLL--------KRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV 80 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCCCCCCCCCCCE
Confidence 456789999999999999975443 335678888888773321 1011111
Q ss_pred ----HHHHHHHHHHhhccccccccCCC---CCcCC
Q psy8858 72 ----EFSMNIKRLIDLSCYRGIRHRKS---LPCRG 99 (121)
Q Consensus 72 ----~~~~~I~rl~~i~~yRG~RH~~g---LpVRG 99 (121)
+--.|+.-+-+.+.|+|.=|-+| -|.-|
T Consensus 81 iCVVE~~~Dv~aiE~~~~y~G~YhVL~G~iSPldg 115 (195)
T TIGR00615 81 ICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDG 115 (195)
T ss_pred EEEECCHHHHHHHHhhCccceEEEEccCccCccCC
Confidence 12346667778899999999987 55554
No 40
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.47 E-value=0.55 Score=35.47 Aligned_cols=21 Identities=29% Similarity=0.419 Sum_probs=18.2
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
.+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 468999999999999999554
No 41
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.18 E-value=0.58 Score=35.55 Aligned_cols=21 Identities=29% Similarity=0.249 Sum_probs=18.1
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
-+|++++|||.++|.+|+-.|
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999554
No 42
>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=84.74 E-value=0.39 Score=35.97 Aligned_cols=29 Identities=24% Similarity=0.492 Sum_probs=23.8
Q ss_pred CCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 10 PNNQHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 10 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
|+...+.-.|.+++|||+.+|..++..||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 44555567799999999999999998766
No 43
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.54 E-value=0.64 Score=35.26 Aligned_cols=21 Identities=33% Similarity=0.450 Sum_probs=17.8
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
-+|++++|||+++|.+|+-.|
T Consensus 109 ~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred HHHhcCCCcCHHHHHHHHHHH
Confidence 368999999999999999443
No 44
>PRK00076 recR recombination protein RecR; Reviewed
Probab=84.51 E-value=1.9 Score=32.74 Aligned_cols=77 Identities=23% Similarity=0.349 Sum_probs=50.9
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH----
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR---- 71 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~---- 71 (121)
+..+|++++|||+++|..+.-.+= ..+++++..|.+.|.+.. |=.|=.|
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll--------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~ 80 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLL--------QRDREDVLRLAQALEEAKEKIKHCSVCGNLTEQDPCEICSDPRRDQSL 80 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCcCCCCcCCCCCCCCCCCCE
Confidence 455789999999999999986543 335778888888773321 1001011
Q ss_pred ----HHHHHHHHHHhhccccccccCCC---CCcCC
Q psy8858 72 ----EFSMNIKRLIDLSCYRGIRHRKS---LPCRG 99 (121)
Q Consensus 72 ----~~~~~I~rl~~i~~yRG~RH~~g---LpVRG 99 (121)
+--.|+.-+-+.+.|+|.=|-+| -|.-|
T Consensus 81 icVVE~~~Dv~aiE~s~~y~G~YhVL~G~ispl~g 115 (196)
T PRK00076 81 ICVVESPADVLAIERTGEYRGLYHVLGGLLSPLDG 115 (196)
T ss_pred EEEECCHHHHHHHHhhCcCceEEEEecCCcCCCCC
Confidence 12346666778899999999987 45444
No 45
>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=84.50 E-value=1.6 Score=33.82 Aligned_cols=67 Identities=13% Similarity=0.184 Sum_probs=52.1
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcc------------cCCCCHHHHHHHHHHHhh----cccchhhHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKK------------IKDLNDNELEKLREEISK----FIIEGDLRREFSM 75 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~------------~~~Ls~~qi~~L~~~l~~----~~i~~~L~~~~~~ 75 (121)
...+..--..++|+|+....+|..++|+=++.+ ...|+++|++.|-++.+. ..+.+.-+.+++.
T Consensus 96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~~~drl~Vnsatr~ev~~ 175 (225)
T PF09883_consen 96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRDGTDRLNVNSATRSEVRA 175 (225)
T ss_pred cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhCCCCeEEEecccHHHHHH
Confidence 445555556788999999999999999999988 567999999999999943 4566666666665
Q ss_pred HHH
Q psy8858 76 NIK 78 (121)
Q Consensus 76 ~I~ 78 (121)
-++
T Consensus 176 aln 178 (225)
T PF09883_consen 176 ALN 178 (225)
T ss_pred HHH
Confidence 544
No 46
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=84.41 E-value=0.68 Score=35.29 Aligned_cols=21 Identities=33% Similarity=0.453 Sum_probs=18.4
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
-+|++++|||.++|.+||-.|
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 468999999999999999654
No 47
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=84.15 E-value=1.6 Score=33.31 Aligned_cols=78 Identities=22% Similarity=0.321 Sum_probs=53.6
Q ss_pred eeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc-------------------cchhhHH---
Q psy8858 14 HIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI-------------------IEGDLRR--- 71 (121)
Q Consensus 14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~-------------------i~~~L~~--- 71 (121)
.+..+|.+++|||+++|..+.--+- ..++++++.|.++|.+.. |=+|=.+
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 3556889999999999999985543 446788888888883321 1011111
Q ss_pred -----HHHHHHHHHHhhccccccccCCC---CCcCC
Q psy8858 72 -----EFSMNIKRLIDLSCYRGIRHRKS---LPCRG 99 (121)
Q Consensus 72 -----~~~~~I~rl~~i~~yRG~RH~~g---LpVRG 99 (121)
+--.|+..+-+.+.|+|.=|-.| -|.-|
T Consensus 81 ~icVVe~p~Dv~a~E~~~~f~G~YhVL~G~lspl~g 116 (198)
T COG0353 81 QLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDG 116 (198)
T ss_pred eEEEEcchHHHHHHHHhcccCeeEEEecCccCcccC
Confidence 12457778889999999999887 44444
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=83.94 E-value=0.62 Score=36.08 Aligned_cols=50 Identities=12% Similarity=0.258 Sum_probs=38.9
Q ss_pred CCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 10 PNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 10 ~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
...|.+..+|+.+++ ...+..+.+.+||+++.++.+|+.+|+..|.++|+
T Consensus 212 ~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 212 QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 345667777776643 34456777779999999999999999999998874
No 49
>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=83.82 E-value=1.2 Score=29.12 Aligned_cols=26 Identities=42% Similarity=0.626 Sum_probs=22.0
Q ss_pred eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
..|.++|+.|+|||...|..|++.-.
T Consensus 23 ~~Ir~gl~~Ikglg~~~a~~I~~~R~ 48 (90)
T PF14579_consen 23 NAIRLGLSAIKGLGEEVAEKIVEERE 48 (90)
T ss_dssp TEEE-BGGGSTTS-HHHHHHHHHHHH
T ss_pred CEEeehHhhcCCCCHHHHHHHHHhHh
Confidence 68999999999999999999998764
No 50
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=83.60 E-value=1.2 Score=38.76 Aligned_cols=46 Identities=26% Similarity=0.409 Sum_probs=41.1
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
+..++..+.|+|.-.|+++|.++|+++.....++.++++..+...+
T Consensus 188 ~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~ 233 (564)
T COG1293 188 IVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREAL 233 (564)
T ss_pred HHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHH
Confidence 3456778999999999999999999999999999999999997755
No 51
>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=80.88 E-value=1.6 Score=26.35 Aligned_cols=20 Identities=45% Similarity=0.604 Sum_probs=17.6
Q ss_pred ehhcccccCHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (121)
.|..++|||+.+|..|+..+
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 47889999999999999765
No 52
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.39 E-value=0.55 Score=35.34 Aligned_cols=34 Identities=15% Similarity=0.246 Sum_probs=21.4
Q ss_pred eCccCCCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 5 VGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 5 ~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
+|-.=...+.++..|.++.|||+++|..|+..++
T Consensus 61 yGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~ 94 (194)
T PRK14605 61 FGFATTEELSLFETLIDVSGIGPKLGLAMLSAMN 94 (194)
T ss_pred eCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCC
Confidence 3444444555666667777777777777776554
No 53
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.36 E-value=1.1 Score=33.63 Aligned_cols=18 Identities=39% Similarity=0.534 Sum_probs=16.0
Q ss_pred ehhcccccCHHHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICE 35 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~ 35 (121)
+|++++|||.++|..|+-
T Consensus 109 ~L~~vpGIGkKtAerIil 126 (194)
T PRK14605 109 LLSTIPGIGKKTASRIVL 126 (194)
T ss_pred HHHhCCCCCHHHHHHHHH
Confidence 589999999999999763
No 54
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.04 E-value=1.2 Score=33.46 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=16.8
Q ss_pred eehhcccccCHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~l 37 (121)
.+| +++|||.++|.+|+-.|
T Consensus 108 ~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHHH
Confidence 467 89999999999999544
No 55
>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=78.90 E-value=4.9 Score=32.12 Aligned_cols=24 Identities=29% Similarity=0.396 Sum_probs=20.7
Q ss_pred eehhcccccCHHHHHHHHHHhCCCC
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKIST 41 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~p 41 (121)
..|.+|+|||+++|..+. .+|+..
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 456899999999999999 899873
No 56
>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=78.56 E-value=1.8 Score=27.56 Aligned_cols=20 Identities=25% Similarity=0.346 Sum_probs=17.5
Q ss_pred hhcccccCHHHHHHHHHHhC
Q psy8858 19 LTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lG 38 (121)
+..++|||+.+|..++..+|
T Consensus 24 i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC
Confidence 34789999999999999876
No 57
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=78.35 E-value=1.8 Score=23.98 Aligned_cols=17 Identities=29% Similarity=0.415 Sum_probs=15.0
Q ss_pred hcccccCHHHHHHHHHH
Q psy8858 20 TAIYGIGRSRAKKICEV 36 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~ 36 (121)
..++|||..+|.+++++
T Consensus 19 ~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCcccHHHHHHHHHh
Confidence 57899999999999875
No 58
>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=77.83 E-value=2 Score=27.84 Aligned_cols=21 Identities=33% Similarity=0.290 Sum_probs=18.9
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.|++|+|||..+|..|+..+|
T Consensus 3 ~l~sipGig~~~a~~llaeig 23 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIG 23 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHc
Confidence 478999999999999998883
No 59
>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=77.75 E-value=2.3 Score=28.64 Aligned_cols=37 Identities=27% Similarity=0.369 Sum_probs=27.6
Q ss_pred eehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
..|+.|+|||+.+|.-+. .+||+.=..+..-+++++-
T Consensus 12 ~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly 48 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELY 48 (93)
T ss_pred HHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHH
Confidence 457999999999999987 8999864444444555544
No 60
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=77.34 E-value=1.8 Score=32.32 Aligned_cols=26 Identities=19% Similarity=0.155 Sum_probs=21.9
Q ss_pred eeeeehhcccccCHHHHHHHHHHhCC
Q psy8858 14 HIIIGLTAIYGIGRSRAKKICEVTKI 39 (121)
Q Consensus 14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi 39 (121)
.++..|.+|+|||+.+|..|++.+|.
T Consensus 70 ~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 70 ELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 34447789999999999999998885
No 61
>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=76.98 E-value=1.9 Score=26.77 Aligned_cols=20 Identities=50% Similarity=0.637 Sum_probs=17.1
Q ss_pred ehhcccccCHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (121)
++++++|||.++|..|-+.+
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 58999999999999986643
No 62
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=75.03 E-value=2.3 Score=34.42 Aligned_cols=25 Identities=28% Similarity=0.436 Sum_probs=21.9
Q ss_pred eeehhcccccCHHHHHHHHHHhCCCC
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVTKIST 41 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lGi~p 41 (121)
...|.+|+|||+++|..+.+ +|+..
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 45578999999999999999 99874
No 63
>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=74.32 E-value=2.5 Score=26.12 Aligned_cols=28 Identities=21% Similarity=0.262 Sum_probs=21.3
Q ss_pred CCCeeeeeehhc-ccccCHHHHHHHHHHh
Q psy8858 10 PNNQHIIIGLTA-IYGIGRSRAKKICEVT 37 (121)
Q Consensus 10 ~~~k~v~~aLt~-I~GIG~~~A~~Ic~~l 37 (121)
+=|..-.-.|.. +.|||...|..|++.-
T Consensus 9 nvNta~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred ECcCCCHHHHHhHCCCCCHHHHHHHHHHH
Confidence 334444446777 9999999999999884
No 64
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=74.31 E-value=4.4 Score=34.08 Aligned_cols=50 Identities=14% Similarity=0.210 Sum_probs=40.9
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
++.+..+|.. .++.+.+..++++.|| |+....+|++.|+++|.+.|+.+.
T Consensus 285 ~kslkn~L~~--~lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~~~ 334 (408)
T COG2081 285 KKSLKNALAK--LLPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKAWP 334 (408)
T ss_pred hhHHHHHHHH--HhhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhcCe
Confidence 3444444433 4678899999999999 999999999999999999997765
No 65
>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=74.14 E-value=3.7 Score=24.77 Aligned_cols=26 Identities=23% Similarity=0.405 Sum_probs=20.9
Q ss_pred ccccCHHHHHHHHHHhCCC--CCcccCC
Q psy8858 22 IYGIGRSRAKKICEVTKIS--TTKKIKD 47 (121)
Q Consensus 22 I~GIG~~~A~~Ic~~lGi~--p~~~~~~ 47 (121)
--||+.+.-+.+|.++||. |..++.+
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 4699999999999999997 5555544
No 66
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=74.07 E-value=2.2 Score=30.12 Aligned_cols=24 Identities=25% Similarity=0.274 Sum_probs=20.8
Q ss_pred eeeeeehhcccccCHHHHHHHHHH
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEV 36 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~ 36 (121)
..+...|++++|||+.+|..++..
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHH
Confidence 456778999999999999999875
No 67
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=73.89 E-value=2.2 Score=29.84 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=19.1
Q ss_pred eeeehhcccccCHHHHHHHHHHh
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
..-.|.+++|||+.+|..+|...
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 34567899999999999998775
No 68
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.62 E-value=4.7 Score=28.98 Aligned_cols=86 Identities=16% Similarity=0.197 Sum_probs=54.3
Q ss_pred ehhcccccCHHHHHHHHHHhC---CC--CC---cccCCCCHHHHHHHHHHHhhcccchhhHHHHHH-HHHHHH--hhccc
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK---IS--TT---KKIKDLNDNELEKLREEISKFIIEGDLRREFSM-NIKRLI--DLSCY 86 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG---i~--p~---~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~-~I~rl~--~i~~y 86 (121)
...+++|+|.+++..-..+.. .+ +. =++..|+++|.+.|.+.+..-. ..|+..... .-++-+ ...++
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~--wTl~~~~~~l~~e~gv~y~~~~v 103 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD--WTLKELVEELGLEFGVWYHASAV 103 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc--chHHHHHHHHhhhcCeEEeHHHH
Confidence 356889999999999998865 33 32 3788999999999999993222 333221111 111112 22356
Q ss_pred cccccCCCCCcCCccccccc
Q psy8858 87 RGIRHRKSLPCRGQRTRTNA 106 (121)
Q Consensus 87 RG~RH~~gLpVRGQRT~tNa 106 (121)
+=+-|..||+-. -+++|++
T Consensus 104 ~~~l~~~Glsyk-K~~~~~~ 122 (138)
T COG3415 104 RRLLHELGLSYK-KPRWTPA 122 (138)
T ss_pred HHHHHHcCCCcC-CCCCCcc
Confidence 667889999876 3444444
No 69
>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=73.49 E-value=2.4 Score=31.79 Aligned_cols=20 Identities=25% Similarity=0.413 Sum_probs=17.1
Q ss_pred eehhcccccCHHHHHHHHHH
Q psy8858 17 IGLTAIYGIGRSRAKKICEV 36 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~ 36 (121)
-+|++++|||.++|..|+-.
T Consensus 107 ~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred HHHHhCCCCCHHHHHHHHHH
Confidence 35789999999999999943
No 70
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=72.97 E-value=2 Score=26.51 Aligned_cols=18 Identities=28% Similarity=0.385 Sum_probs=15.0
Q ss_pred cccccCHHHHHHHHHHhC
Q psy8858 21 AIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lG 38 (121)
.|+|||..+|+.+++.+|
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 699999999999999988
No 71
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=72.73 E-value=3.1 Score=25.58 Aligned_cols=21 Identities=43% Similarity=0.517 Sum_probs=16.2
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.|+.++|||+.+|..|.+.+.
T Consensus 36 ~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 36 ELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp HHCTSTT--HHHHHHHHHHHH
T ss_pred HHhccCCcCHHHHHHHHHHHC
Confidence 578999999999999987664
No 72
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=72.69 E-value=3.2 Score=31.78 Aligned_cols=27 Identities=22% Similarity=0.121 Sum_probs=20.9
Q ss_pred eeeehh-cccccCHHHHHHHHHHhCCCC
Q psy8858 15 IIIGLT-AIYGIGRSRAKKICEVTKIST 41 (121)
Q Consensus 15 v~~aLt-~I~GIG~~~A~~Ic~~lGi~p 41 (121)
..-.|. +++|||+.+|..|+.-.|+.|
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL~~~~~~~ 143 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFLRNVGYED 143 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHccCCC
Confidence 344566 999999999999996566544
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=72.37 E-value=0.76 Score=34.50 Aligned_cols=33 Identities=21% Similarity=0.349 Sum_probs=25.7
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHH
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEV 36 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~ 36 (121)
++|-.=...+.++..|.++.|||+++|..|+..
T Consensus 59 LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 59 LFGFNTLEERELFKELIKVNGVGPKLALAILSN 91 (191)
T ss_pred eeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhc
Confidence 445555566778888999999999999999543
No 74
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=72.14 E-value=2.2 Score=26.27 Aligned_cols=47 Identities=30% Similarity=0.374 Sum_probs=26.8
Q ss_pred CCeeeeeehhcccccCHHHHHHHHHHh----CC---CCCcccCCCCHHHHHHHH
Q psy8858 11 NNQHIIIGLTAIYGIGRSRAKKICEVT----KI---STTKKIKDLNDNELEKLR 57 (121)
Q Consensus 11 ~~k~v~~aLt~I~GIG~~~A~~Ic~~l----Gi---~p~~~~~~Ls~~qi~~L~ 57 (121)
-|..=...|..++|||+..|..|.+.= ++ +.-..+..++++.++.|.
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHC
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHH
Confidence 344445568899999999999999654 22 223344455666666654
No 75
>PHA02564 V virion protein; Provisional
Probab=71.92 E-value=9.9 Score=27.46 Aligned_cols=36 Identities=14% Similarity=0.138 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 28 SRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
..+..||+.+|++|+..+.-..+ .+..|..+|..+.
T Consensus 86 aYi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~~E 121 (141)
T PHA02564 86 AYATAVANAMGVPPQAGLHLDQD-TLAALVTAIIRHE 121 (141)
T ss_pred HHHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHHHh
Confidence 35788999999999999886656 8889999884443
No 76
>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=71.00 E-value=2.6 Score=29.26 Aligned_cols=31 Identities=32% Similarity=0.375 Sum_probs=25.0
Q ss_pred CCCCeeeeeehhcccccCHHHHHHHHHHhCC
Q psy8858 9 IPNNQHIIIGLTAIYGIGRSRAKKICEVTKI 39 (121)
Q Consensus 9 ~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi 39 (121)
++-|..-.-.|..++|||+.+|..|.+..+-
T Consensus 60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 60 VNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 4455556667899999999999999998753
No 77
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=70.48 E-value=3 Score=27.49 Aligned_cols=23 Identities=35% Similarity=0.330 Sum_probs=15.7
Q ss_pred hcccccCHHHHHHHHHHhCCCCC
Q psy8858 20 TAIYGIGRSRAKKICEVTKISTT 42 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lGi~p~ 42 (121)
..|.|||..+|-.|...+|++++
T Consensus 49 ~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 49 EDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp B-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHccCCCHHHHHHHHHHcCCCCC
Confidence 44888888888888888887754
No 78
>PRK10702 endonuclease III; Provisional
Probab=70.31 E-value=3.3 Score=31.48 Aligned_cols=23 Identities=26% Similarity=0.364 Sum_probs=19.0
Q ss_pred eeeehhcccccCHHHHHHHHHHh
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
..-.|.+++|||+++|..|+..+
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHHH
Confidence 35678999999999999988543
No 79
>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=70.28 E-value=3.5 Score=30.55 Aligned_cols=22 Identities=27% Similarity=0.400 Sum_probs=18.7
Q ss_pred eeehhcccccCHHHHHHHHHHh
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
.-.|.+++|||+.+|..+|...
T Consensus 105 ~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 105 REELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHhCCCCcHHHHHHHHHHH
Confidence 4568999999999999999544
No 80
>PRK08609 hypothetical protein; Provisional
Probab=70.09 E-value=3.6 Score=35.70 Aligned_cols=24 Identities=17% Similarity=0.339 Sum_probs=21.8
Q ss_pred eehhcccccCHHHHHHHHHHhCCC
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKIS 40 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~ 40 (121)
+.|++|+|||+++|..+.+.+||.
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Confidence 467899999999999999999986
No 81
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.39 E-value=1.7 Score=32.98 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=27.2
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
++|-.=...+.++..|.++.|||+++|-.|+..++
T Consensus 61 LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~ 95 (203)
T PRK14602 61 LFGFATWDERQTFIVLISISKVGAKTALAILSQFR 95 (203)
T ss_pred eeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCC
Confidence 44544455667778889999999999999997654
No 82
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=67.57 E-value=8.1 Score=29.68 Aligned_cols=40 Identities=13% Similarity=0.236 Sum_probs=26.4
Q ss_pred eehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
.+|.+.+|||++||+-++..+---|...+.. .+.++..-+
T Consensus 109 ~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDT----HV~Rvs~R~ 148 (211)
T COG0177 109 EELLSLPGVGRKTANVVLSFAFGIPAIAVDT----HVHRVSNRL 148 (211)
T ss_pred HHHHhCCCcchHHHHHHHHhhcCCCcccccc----hHHHHHHHh
Confidence 5689999999999999887733333444432 444544444
No 83
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.09 E-value=1.4 Score=32.96 Aligned_cols=34 Identities=24% Similarity=0.393 Sum_probs=26.8
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHh
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
++|-.=...+.++..|.++.|||+++|-.|+..+
T Consensus 60 LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~ 93 (183)
T PRK14601 60 LYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSSL 93 (183)
T ss_pred eeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 4555555667778889999999999999998543
No 84
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.96 E-value=1.5 Score=32.90 Aligned_cols=35 Identities=17% Similarity=0.166 Sum_probs=27.8
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
++|-.=+..+.++..|.++.|||+++|-.|+..++
T Consensus 60 LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~ 94 (186)
T PRK14600 60 LYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKLT 94 (186)
T ss_pred eeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCC
Confidence 45555566777888899999999999999996543
No 85
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=66.51 E-value=14 Score=27.47 Aligned_cols=21 Identities=38% Similarity=0.539 Sum_probs=18.5
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.|++++|||..+|..|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 578999999999999997754
No 86
>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=66.19 E-value=12 Score=33.40 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=28.5
Q ss_pred cccccCHHHHHHHHHHhCCC--------CCc--ccCCCCHHHHHHHHHHH
Q psy8858 21 AIYGIGRSRAKKICEVTKIS--------TTK--KIKDLNDNELEKLREEI 60 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lGi~--------p~~--~~~~Ls~~qi~~L~~~l 60 (121)
.|+|||+.+|..|.+.+|.+ |+. .+.-++++.++.|.+.+
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~ 137 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQW 137 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHH
Confidence 49999999999999999966 221 23346666666666654
No 87
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=66.08 E-value=13 Score=29.45 Aligned_cols=33 Identities=21% Similarity=0.098 Sum_probs=25.5
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcc-cCC
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKK-IKD 47 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~-~~~ 47 (121)
+.-.|..++|||+.+|..|+-..-=+|+.- ++|
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D 238 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDD 238 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCccc
Confidence 456789999999999999997754466665 444
No 88
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.98 E-value=1.5 Score=32.96 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=26.7
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHh
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
++|-.=...+.++..|.++.|||+++|-.|+..+
T Consensus 60 LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~ 93 (188)
T PRK14606 60 LYGFSNERKKELFLSLTKVSRLGPKTALKIISNE 93 (188)
T ss_pred eeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 4455555667778889999999999999998544
No 89
>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=65.15 E-value=4.9 Score=31.83 Aligned_cols=22 Identities=32% Similarity=0.430 Sum_probs=18.8
Q ss_pred eeehhcccccCHHHHHHHHHHh
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
.-.|.+++|||+++|..|+..+
T Consensus 104 ~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 104 FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 4578999999999999998654
No 90
>PF04001 Vhr1: Transcription factor Vhr1; InterPro: IPR007147 This is a family of proteins of unknown function found in yeast.
Probab=64.79 E-value=5.7 Score=26.68 Aligned_cols=60 Identities=23% Similarity=0.346 Sum_probs=33.1
Q ss_pred HHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhhccccccccCCCCCc
Q psy8858 29 RAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97 (121)
Q Consensus 29 ~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpV 97 (121)
+.+.|-++|++..+..-+.+|.--++.| ..|.++.-=-.+...+|.....| +|-.+|+|+
T Consensus 8 ~Th~IR~~LnF~De~~WK~FSsRRLELI----d~~~Ls~~KASEQd~~I~~iA~i-----LR~Ef~Yp~ 67 (95)
T PF04001_consen 8 TTHKIREQLNFHDERKWKRFSSRRLELI----DKFDLSSRKASEQDDNIRQIAEI-----LRTEFGYPE 67 (95)
T ss_pred hhHHHHHHhCCccHHHHHHHHHHHHHHH----HHcCcccchhhhhHHHHHHHHHH-----HHHHhCCCh
Confidence 4566777777776666555555444433 23444333334455566665555 666666664
No 91
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.11 E-value=1.8 Score=32.87 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=26.7
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHh
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
++|-.=...+.++..|.++.|||+++|-.|+..+
T Consensus 59 LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~ 92 (196)
T PRK13901 59 LFGFLNSSEREVFEELIGVDGIGPRAALRVLSGI 92 (196)
T ss_pred eeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 4555555667778888999999999999999544
No 92
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=63.82 E-value=1.8 Score=32.72 Aligned_cols=34 Identities=15% Similarity=0.204 Sum_probs=26.4
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHh
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
++|-.=...+.++..|.++.|||+++|-.|+..+
T Consensus 59 LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 59 LYGFPDEDSLELFELLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred eeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 4455555667778888999999999999998543
No 93
>PF13035 DUF3896: Protein of unknown function (DUF3896)
Probab=63.66 E-value=25 Score=21.47 Aligned_cols=43 Identities=26% Similarity=0.577 Sum_probs=27.8
Q ss_pred HHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhhccc-ccc
Q psy8858 30 AKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCY-RGI 89 (121)
Q Consensus 30 A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl~~i~~y-RG~ 89 (121)
-.++|+++- --.|+++|-++|.-.|.+|. =|-.|++++.| ||+
T Consensus 18 kq~lc~kls------~~~ls~~er~qi~~eidnye-----------yilnlvemnhyergf 61 (61)
T PF13035_consen 18 KQQLCKKLS------SMHLSEKEREQIKLEIDNYE-----------YILNLVEMNHYERGF 61 (61)
T ss_pred HHHHHHHHh------hcccCHHHHHHHHhhhhhHH-----------HHHHHHHHhcccccC
Confidence 456777764 23577888888877775553 23347777777 554
No 94
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=63.45 E-value=7.8 Score=29.80 Aligned_cols=24 Identities=25% Similarity=0.095 Sum_probs=19.4
Q ss_pred eeeehhcccccCHHHHHHHHHHhC
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
..-.|.+++|||+.||..|+.-+-
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLlya~ 142 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCYVC 142 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHHHc
Confidence 445689999999999999886543
No 95
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=63.32 E-value=5.6 Score=31.08 Aligned_cols=38 Identities=24% Similarity=0.483 Sum_probs=22.3
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
.|..|.|||+.++..+++. ||..-..+..-+.++|..+
T Consensus 4 ~L~~IpGIG~krakkLl~~-GF~Sve~Ik~AS~eEL~~V 41 (232)
T PRK12766 4 ELEDISGVGPSKAEALREA-GFESVEDVRAADQSELAEV 41 (232)
T ss_pred ccccCCCcCHHHHHHHHHc-CCCCHHHHHhCCHHHHHHc
Confidence 4667777777777777654 5554444444455555444
No 96
>PRK10880 adenine DNA glycosylase; Provisional
Probab=63.06 E-value=4.9 Score=33.01 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=19.6
Q ss_pred eeeehhcccccCHHHHHHHHHHh
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
..-.|.+++|||+++|..||..+
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHHHH
Confidence 34678999999999999999753
No 97
>PRK13910 DNA glycosylase MutY; Provisional
Probab=62.73 E-value=5.1 Score=32.07 Aligned_cols=22 Identities=27% Similarity=0.238 Sum_probs=19.0
Q ss_pred eeehhcccccCHHHHHHHHHHh
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
.-.|.+++|||+++|..|+..+
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 5678999999999999998643
No 98
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=62.09 E-value=7.1 Score=31.03 Aligned_cols=17 Identities=29% Similarity=0.370 Sum_probs=16.7
Q ss_pred ccccCHHHHHHHHHHhC
Q psy8858 22 IYGIGRSRAKKICEVTK 38 (121)
Q Consensus 22 I~GIG~~~A~~Ic~~lG 38 (121)
++|||+.+|..++...|
T Consensus 203 V~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 203 VKGIGPKTALKLLQEYG 219 (310)
T ss_pred CCCcCHHHHHHHHHHhC
Confidence 99999999999999999
No 99
>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=60.82 E-value=27 Score=20.79 Aligned_cols=42 Identities=7% Similarity=0.159 Sum_probs=32.3
Q ss_pred hhcccccCHHHHHHHHHHhCCCCCcc----cCCCCHHHHHHHHHHH
Q psy8858 19 LTAIYGIGRSRAKKICEVTKISTTKK----IKDLNDNELEKLREEI 60 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lGi~p~~~----~~~Ls~~qi~~L~~~l 60 (121)
+.+..||...+...-.+..|+.+..+ -..++++|+..|..+.
T Consensus 6 va~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~ 51 (68)
T cd01104 6 VARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIR 51 (68)
T ss_pred HHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHH
Confidence 45678999999999888778765332 2477899999888877
No 100
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.73 E-value=2.6 Score=31.78 Aligned_cols=34 Identities=18% Similarity=0.369 Sum_probs=26.0
Q ss_pred eeCccCCCCeeeeeehhcccccCHHHHHHHHHHh
Q psy8858 4 IVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 4 i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
++|-.=...+.++..|.++.|||+++|-.|+..+
T Consensus 60 LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~ 93 (195)
T PRK14604 60 LYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSG 93 (195)
T ss_pred eeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 3444445566777788999999999999998543
No 101
>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=54.20 E-value=12 Score=29.97 Aligned_cols=43 Identities=16% Similarity=0.121 Sum_probs=29.9
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
+.-.|+.++|||+.+|..||-..-=.|+.-+- |--+.++.+.+
T Consensus 218 ~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv---D~~v~r~~~r~ 260 (310)
T TIGR00588 218 AREALCELPGVGPKVADCICLMGLDKPQAVPV---DVHVWRIANRD 260 (310)
T ss_pred HHHHHHhCCCccHHHHHHHHHHhCCCCCceee---cHHHHHHHHHH
Confidence 56778999999999999999776555555443 34454444433
No 102
>smart00475 53EXOc 5'-3' exonuclease.
Probab=54.19 E-value=10 Score=29.72 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=17.4
Q ss_pred hhcccccCHHHHHHHHHHhC
Q psy8858 19 LTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lG 38 (121)
+..++|||+++|..++++.|
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC
Confidence 34579999999999999988
No 103
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=54.04 E-value=6.7 Score=30.27 Aligned_cols=42 Identities=19% Similarity=0.145 Sum_probs=31.0
Q ss_pred cCCCCeee--eeehhcccccCHHHHHHHHHHhCCCCCcccCCCC
Q psy8858 8 NIPNNQHI--IIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLN 49 (121)
Q Consensus 8 ~~~~~k~v--~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls 49 (121)
++++.++. +--|-+|+|||+-||..|+--+.=-|.--+...|
T Consensus 104 ~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Yt 147 (215)
T COG2231 104 NLESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYT 147 (215)
T ss_pred hhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHH
Confidence 44555555 5678899999999999999888766665555444
No 104
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=53.84 E-value=9.7 Score=33.31 Aligned_cols=43 Identities=28% Similarity=0.291 Sum_probs=31.5
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
.......|.+|+|||+.+.+.+++.+|=- ..+..-|.+|+.++
T Consensus 509 k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~--~~ik~As~eeL~~v 551 (567)
T PRK14667 509 KEGLKDILDKIKGIGEVKKEIIYRNFKTL--YDFLKADDEELKKL 551 (567)
T ss_pred cccccCccccCCCCCHHHHHHHHHHhCCH--HHHHhCCHHHHHHc
Confidence 34456788999999999999999998832 34555566666544
No 105
>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=53.75 E-value=10 Score=29.15 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=17.3
Q ss_pred hhcccccCHHHHHHHHHHhC
Q psy8858 19 LTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lG 38 (121)
+..++|||+++|..+++..|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34679999999999999876
No 106
>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=53.15 E-value=1.4 Score=29.92 Aligned_cols=19 Identities=26% Similarity=0.354 Sum_probs=15.5
Q ss_pred hcccccCHHHHHHHHHHhC
Q psy8858 20 TAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lG 38 (121)
-.++|||+++|..+++.+|
T Consensus 21 PGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 21 PGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp ---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCHHHHHHHHHHcC
Confidence 4589999999999999998
No 107
>PRK09482 flap endonuclease-like protein; Provisional
Probab=53.15 E-value=10 Score=29.82 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=17.2
Q ss_pred hcccccCHHHHHHHHHHhC
Q psy8858 20 TAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lG 38 (121)
..++|||+++|..+++..|
T Consensus 185 pGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCcChHHHHHHHHHhC
Confidence 4689999999999999988
No 108
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=52.70 E-value=8.6 Score=33.71 Aligned_cols=42 Identities=31% Similarity=0.361 Sum_probs=30.2
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK 55 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~ 55 (121)
......+|..|.|||+.++..|++.+|= -..+.+-+.+|+..
T Consensus 538 k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~ 579 (598)
T PRK00558 538 KARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAK 579 (598)
T ss_pred cchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhh
Confidence 3446788999999999999999999883 22334445555543
No 109
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=52.15 E-value=11 Score=30.10 Aligned_cols=32 Identities=25% Similarity=0.066 Sum_probs=23.6
Q ss_pred eeeeehhcccccCHHHHHHHHHHhCCCCCccc
Q psy8858 14 HIIIGLTAIYGIGRSRAKKICEVTKISTTKKI 45 (121)
Q Consensus 14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~ 45 (121)
.+.-.|++|.|||+-+|..++-..-=.|+.-+
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP 226 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFLLFGLGRPDVFP 226 (285)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCC
Confidence 35667899999999999999866443344433
No 110
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=51.71 E-value=9.5 Score=31.14 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=38.2
Q ss_pred eehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
--|+.|.|||+..+. .|..+|+.....+-..+++++..+...+.
T Consensus 263 DdL~~I~GiGp~~e~-~L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 263 DDLKKLTGVSPQIEK-KLNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred hhhhhhccCChhhhh-hhhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 348999999998765 57899999999999999999998888774
No 111
>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=51.10 E-value=13 Score=30.34 Aligned_cols=37 Identities=19% Similarity=0.456 Sum_probs=28.4
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCC--CHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDL--NDNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~L--s~~qi~ 54 (121)
-+..++|||..++..+++.+||..-..+-.+ +.+++.
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 5689999999999999999999864444445 555554
No 112
>PRK14976 5'-3' exonuclease; Provisional
Probab=50.63 E-value=12 Score=29.73 Aligned_cols=19 Identities=26% Similarity=0.331 Sum_probs=17.0
Q ss_pred hcccccCHHHHHHHHHHhC
Q psy8858 20 TAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lG 38 (121)
..++|||+++|..++...|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999999887
No 113
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=49.48 E-value=21 Score=27.43 Aligned_cols=49 Identities=16% Similarity=0.220 Sum_probs=31.4
Q ss_pred Ceeeeeehhcccc-cCHHHHHHHHHHh-CCCCCcccCCCCHHHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYG-IGRSRAKKICEVT-KISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 12 ~k~v~~aLt~I~G-IG~~~A~~Ic~~l-Gi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
.|.+..+|..+.. .+......+...+ +++++.++.+||.+|+..|.+.+
T Consensus 204 rk~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~ 254 (258)
T PRK14896 204 RKTLRNALKNSAHISGKEDIKAVVEALPEELLNKRVFQLSPEEIAELANLL 254 (258)
T ss_pred cHHHHHHHhhhccccchhHHHHHHHHcCCCCcCCCCccCCHHHHHHHHHHH
Confidence 4555556655421 1111113344555 55689999999999999999887
No 114
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=48.06 E-value=15 Score=26.51 Aligned_cols=23 Identities=30% Similarity=0.391 Sum_probs=18.7
Q ss_pred eeeehhcccccCHHHHHHHHHHh
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
-.-.|..++|||+++|..|.+.-
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHH
Confidence 34456999999999999999654
No 115
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=47.98 E-value=17 Score=30.87 Aligned_cols=48 Identities=21% Similarity=0.346 Sum_probs=33.5
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCC-CC---------CcccCCCCHHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKI-ST---------TKKIKDLNDNELEKLREE 59 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi-~p---------~~~~~~Ls~~qi~~L~~~ 59 (121)
+..|.|+|..|+|||...+..|.+.=.- .| ....+.++...++.|..+
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rvd~~~vnkr~lE~LIka 166 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRVDLRVVNRRALETLIYC 166 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHhCcccCCHHHHHHHHHc
Confidence 4469999999999999999999864311 11 122345677777777663
No 116
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=47.61 E-value=38 Score=31.66 Aligned_cols=47 Identities=28% Similarity=0.309 Sum_probs=33.1
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCc---------ccCCCCHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTK---------KIKDLNDNELEKLRE 58 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~---------~~~~Ls~~qi~~L~~ 58 (121)
+..|.++|+.|+|||...+..|.+.-.-.|-. ....++...++.|..
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~r~~~~~i~k~~le~LI~ 802 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILIN 802 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHHHhhhcCCCHHHHHHHHH
Confidence 55799999999999999999998654322211 234456667766664
No 117
>cd05124 AFK Actin-Fragmin Kinase (AFK); catalytic domain. The AFK catalytic domain is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). AFK is found in slime molds, ciliates, and flowering plants. It catalyzes the transfer of the gamma-phosphoryl group from ATP specifically to threonine residues in the actin-fragmin complex. The phosphorylation sites are located at a minor contact site for DNase I and at an actin-actin contact site. Fragmin is an actin-binding protein that functions as a regulator of the microfilament system. It interferes with the growth of F-actin by severing actin filaments and capping their ends. The phosphorylation of the actin-fragmin complex inhibits its nucleation activity and results in calcium-dependent capping activity. Thus, AFK plays a role in regulating ac
Probab=46.81 E-value=68 Score=25.18 Aligned_cols=50 Identities=12% Similarity=0.232 Sum_probs=39.3
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCC-CCcccCCCCHHHHHHHHHHHhhc
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKIS-TTKKIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~-p~~~~~~Ls~~qi~~L~~~l~~~ 63 (121)
+.-|.-.-+.+ ..+..+.+++..||+. |.+++-+.++.|+..+.+.+...
T Consensus 23 ~a~ViK~s~ti--~~E~~~~~La~~LgVpiPq~rvi~~~~~E~~e~~~~L~~a 73 (238)
T cd05124 23 GAIVVKSSPNI--ASEYFLSKLAKILGLPIPQMRVLEWNSSEFTEMSENLLKA 73 (238)
T ss_pred cEEEEEcCccH--HHHHHHHHHHHHhCCCCCceeeeecCCHHHHHHHHHHHHH
Confidence 34444444556 7888999999999998 89999999889999888888444
No 118
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=46.31 E-value=16 Score=32.20 Aligned_cols=43 Identities=28% Similarity=0.341 Sum_probs=30.0
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
.+.+.-.|..|.|||+.+|..|++.+|=- ..+..-+.++|..+
T Consensus 564 k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~--~~i~~As~eeL~~v 606 (621)
T PRK14671 564 KRTLQTELTDIAGIGEKTAEKLLEHFGSV--EKVAKASLEELAAV 606 (621)
T ss_pred HHHhhhhhhcCCCcCHHHHHHHHHHcCCH--HHHHhCCHHHHHHH
Confidence 34456677899999999999999999721 23344466666543
No 119
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=46.25 E-value=17 Score=32.26 Aligned_cols=40 Identities=13% Similarity=0.253 Sum_probs=29.7
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
..-.|.+|+|||+.++..+++.+|=- ..+..-|.+||.++
T Consensus 550 ~~S~L~~IpGIG~kr~~~LL~~FgSi--~~I~~As~eeL~~v 589 (624)
T PRK14669 550 RTSELLEIPGVGAKTVQRLLKHFGSL--ERVRAATETQLAAV 589 (624)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcCCH--HHHHhCCHHHHHHH
Confidence 45568899999999999999998822 34555566666544
No 120
>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=46.23 E-value=13 Score=25.07 Aligned_cols=62 Identities=18% Similarity=0.214 Sum_probs=43.1
Q ss_pred eCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHHHHhhcccc
Q psy8858 5 VGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKIS---TTKKIKDLNDNELEKLREEISKFIIE 66 (121)
Q Consensus 5 ~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~~l~~~~i~ 66 (121)
+|..||-|..-..+.+++.|+=+..|..|+.-.=.+ .-..+..||+.|-+.|.+.+.+|.+.
T Consensus 11 ~G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~Ftv~ 75 (93)
T PF06514_consen 11 LGQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNFTVT 75 (93)
T ss_dssp CCTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGEE--
T ss_pred cCCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccceec
Confidence 345556666667788999999999999999875332 33456678999999999999888653
No 121
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=44.91 E-value=4.1 Score=31.03 Aligned_cols=34 Identities=21% Similarity=0.228 Sum_probs=25.7
Q ss_pred eCccCCCCeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 5 VGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 5 ~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
+|-.=..++.++..|.++-|||+++|-.|++.+.
T Consensus 61 yGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 61 YGFLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred cCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCC
Confidence 3444445666777889999999999999996443
No 122
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=43.70 E-value=38 Score=26.93 Aligned_cols=34 Identities=21% Similarity=0.133 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhc
Q psy8858 29 RAKKICEVTKISTTKKIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 29 ~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~ 63 (121)
....++..+|++ +.++.+|+.+|+-.|...+.+.
T Consensus 256 ~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~~ 289 (294)
T PTZ00338 256 FIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNKK 289 (294)
T ss_pred HHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHHc
Confidence 445678999997 7999999999999999988543
No 123
>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=42.90 E-value=37 Score=22.85 Aligned_cols=33 Identities=27% Similarity=0.662 Sum_probs=28.6
Q ss_pred ccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 24 GIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 24 GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
-+|......|+..|+ ++..+|++++++...+++
T Consensus 34 s~Gh~sGRrIv~IL~----K~k~dltddD~~hMrkVV 66 (92)
T PF11338_consen 34 SVGHESGRRIVEILR----KRKTDLTDDDYEHMRKVV 66 (92)
T ss_pred ccCcchhhHHHHHHh----cCcccCCHHHHHHHHHHH
Confidence 467888889999998 778999999999888877
No 124
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=42.75 E-value=27 Score=20.95 Aligned_cols=17 Identities=24% Similarity=0.374 Sum_probs=14.8
Q ss_pred CCCHHHHHHHHHHHhhc
Q psy8858 47 DLNDNELEKLREEISKF 63 (121)
Q Consensus 47 ~Ls~~qi~~L~~~l~~~ 63 (121)
.||++|+..|..+|.+.
T Consensus 74 ~ls~~e~~~l~ayl~sl 90 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRSL 90 (91)
T ss_dssp TSSHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 79999999999999653
No 125
>KOG0821|consensus
Probab=42.56 E-value=41 Score=26.83 Aligned_cols=39 Identities=18% Similarity=0.270 Sum_probs=33.7
Q ss_pred HHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcccc
Q psy8858 28 SRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIE 66 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i~ 66 (121)
-.+..+++++.|||..+.-.|+-||...|.+..+.+.++
T Consensus 270 E~~~~Ll~~~~idpT~r~~~L~iEQf~~LAE~Y~E~c~~ 308 (326)
T KOG0821|consen 270 ESTGRLLELADIDPTLRPRQLSIEQFKSLAEVYREMCDE 308 (326)
T ss_pred HHHHHHHHHhcCCCccCceeeeHHHHHHHHHHHHHHhcc
Confidence 357789999999999999999999999999988665554
No 126
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=42.00 E-value=52 Score=27.03 Aligned_cols=67 Identities=13% Similarity=0.180 Sum_probs=41.3
Q ss_pred eeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHHhhcccccccc
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKRLIDLSCYRGIRH 91 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH 91 (121)
|.+.|++ +||.|.. .+...+| +|.+|...+.+.+ ..|+--..+...+.+....---+.+.-|.|.
T Consensus 210 K~~~~g~--~YG~g~~---~la~~lg---------~s~~eA~~~~~~f~~~~p~v~~~~~~~~~~a~~~g~v~t~~GRrr 275 (377)
T cd08637 210 KAVNFGI--IYGISAF---GLSQQLG---------ISRKEAKEYIDRYFARYPGVKEYMEETVEEAREKGYVETLFGRRR 275 (377)
T ss_pred hHhhcch--hcCcchh---HHHHHcC---------CCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCcEEccCCCEE
Confidence 4555666 7888855 3455555 4567777766655 6676555566655555555455666666665
Q ss_pred CC
Q psy8858 92 RK 93 (121)
Q Consensus 92 ~~ 93 (121)
.+
T Consensus 276 ~~ 277 (377)
T cd08637 276 YI 277 (377)
T ss_pred eC
Confidence 43
No 127
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=41.96 E-value=20 Score=31.47 Aligned_cols=40 Identities=38% Similarity=0.467 Sum_probs=30.1
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
....|.+|+|||+.+.+.+++.+|=- ..+..-|.+|+.++
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs~--~~I~~As~eeL~~v 551 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGTY--KDILLLNEDEIAEK 551 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCCH--HHHHhCCHHHHHhC
Confidence 55688999999999999999998832 34555566666544
No 128
>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=41.65 E-value=17 Score=21.23 Aligned_cols=44 Identities=20% Similarity=0.180 Sum_probs=32.0
Q ss_pred eehhcccccCHHHHHHHH-HHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 17 IGLTAIYGIGRSRAKKIC-EVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic-~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
..|.+-.|+...-....| ..+|+.....-..|++++.+.|.+.+
T Consensus 7 ~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~ 51 (54)
T PF04760_consen 7 SELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEF 51 (54)
T ss_dssp THHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHh
Confidence 346677788888888899 55999977777888888888888766
No 129
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=41.56 E-value=30 Score=23.42 Aligned_cols=64 Identities=13% Similarity=0.123 Sum_probs=51.8
Q ss_pred ceeeCccCCCCeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhccc
Q psy8858 2 TRIVGINIPNNQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFII 65 (121)
Q Consensus 2 v~i~~~~~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i 65 (121)
|.++|=++..---|...|.+++|.....|.+|+...--....-++..+.+..+.....++.|.+
T Consensus 30 ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~~~~e~AE~~~~~l~~~~L 93 (100)
T PRK00033 30 VLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGVCTREVAETKVEQVHQHGL 93 (100)
T ss_pred EEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEEEcHHHHHHHHHHHHcCCC
Confidence 3455555655666778899999999999999999999888888999898888888888766654
No 130
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=40.85 E-value=24 Score=27.32 Aligned_cols=43 Identities=33% Similarity=0.478 Sum_probs=38.1
Q ss_pred eehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
-.|+.|.|||+..+.. +..+|+.....+-.++++++..+...+
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l 200 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKL 200 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhcc
Confidence 4589999999998876 568999999999999999999888887
No 131
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=40.53 E-value=26 Score=26.38 Aligned_cols=25 Identities=20% Similarity=0.361 Sum_probs=22.1
Q ss_pred eeehhcccccCHHHHHHHHHHhCCC
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVTKIS 40 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lGi~ 40 (121)
..++|..+|+|.+++...++.+|++
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 3678999999999999999988876
No 132
>PRK07945 hypothetical protein; Provisional
Probab=40.33 E-value=20 Score=28.95 Aligned_cols=21 Identities=38% Similarity=0.515 Sum_probs=18.5
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.|++|+|||..+|..|-+.+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 589999999999999987755
No 133
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=39.96 E-value=15 Score=28.13 Aligned_cols=25 Identities=20% Similarity=0.212 Sum_probs=21.7
Q ss_pred eeehhcccccCHHHHHHHHHHhCCC
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVTKIS 40 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lGi~ 40 (121)
.+.+.+|+|||++-|..++.-.|+.
T Consensus 120 E~Lv~nikGiGyKEASHFLRNVG~~ 144 (210)
T COG1059 120 ELLVENIKGIGYKEASHFLRNVGFE 144 (210)
T ss_pred HHHHHHcccccHHHHHHHHHhcChh
Confidence 4556799999999999999999974
No 134
>PF11328 DUF3130: Protein of unknown function (DUF3130; InterPro: IPR021477 This bacterial family of proteins has no known function.
Probab=39.48 E-value=51 Score=22.10 Aligned_cols=33 Identities=12% Similarity=0.282 Sum_probs=24.0
Q ss_pred HHHHHHHHH-hhcccchhhHHHHHHHHHHHHhhc
Q psy8858 52 ELEKLREEI-SKFIIEGDLRREFSMNIKRLIDLS 84 (121)
Q Consensus 52 qi~~L~~~l-~~~~i~~~L~~~~~~~I~rl~~i~ 84 (121)
-|..++++| .-..+-.++...+..|+.||++|+
T Consensus 42 sin~~r~Al~dLv~~Ve~fq~v~~~DA~RlkkmG 75 (90)
T PF11328_consen 42 SINQLRTALIDLVDVVENFQQVVKKDASRLKKMG 75 (90)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666 334456677888899999999886
No 135
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=39.39 E-value=52 Score=28.76 Aligned_cols=35 Identities=29% Similarity=0.518 Sum_probs=30.4
Q ss_pred cccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 23 YGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 23 ~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
-||+.....+|-..+|. +|++++++.|.+.|..|+
T Consensus 105 vg~~~~~~~~i~~~~~~-------~~~~~~~e~l~~~lh~yk 139 (529)
T PRK06253 105 VGISDEKIEQIEEILGR-------DLSEEKIESLREVLHSYK 139 (529)
T ss_pred CCcCHHHHHHHHHHhCC-------CCChhHHHHHHHHHHHhh
Confidence 38999999999998986 578999999999997775
No 136
>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=38.99 E-value=24 Score=31.35 Aligned_cols=36 Identities=19% Similarity=0.361 Sum_probs=26.7
Q ss_pred cccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 21 AIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
+|.|+|+.++.++.+..++..=..+-.|+.+++..|
T Consensus 436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L 471 (652)
T TIGR00575 436 DIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLEL 471 (652)
T ss_pred CCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhc
Confidence 689999999999999888864444446666655544
No 137
>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=38.39 E-value=23 Score=30.98 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=21.4
Q ss_pred eeeehhcccccCHHHHHHHHHHhC
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
+.-.|.+|+|||+.+.+.+++.+|
T Consensus 539 ~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 539 LQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcC
Confidence 456789999999999999999988
No 138
>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=37.64 E-value=24 Score=27.92 Aligned_cols=18 Identities=33% Similarity=0.338 Sum_probs=16.9
Q ss_pred cccccCHHHHHHHHHHhC
Q psy8858 21 AIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lG 38 (121)
.|+|||+.+|..+++..|
T Consensus 227 gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 227 GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 689999999999999988
No 139
>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=37.31 E-value=42 Score=24.64 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHH-hhcc
Q psy8858 46 KDLNDNELEKLREEI-SKFI 64 (121)
Q Consensus 46 ~~Ls~~qi~~L~~~l-~~~~ 64 (121)
..||++|+..|..+| .+..
T Consensus 130 ~~LsdeEL~avAaYIl~q~~ 149 (159)
T TIGR03045 130 RNLTDEDLRLIAGHILVQPK 149 (159)
T ss_pred CCCCHHHHHHHHHHHHHhcc
Confidence 579999999999998 4433
No 140
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=37.06 E-value=91 Score=24.12 Aligned_cols=26 Identities=15% Similarity=0.381 Sum_probs=16.0
Q ss_pred HHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhc
Q psy8858 31 KKICEVTKISTTKKIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 31 ~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~ 63 (121)
..+++.+||. ||++|+..|..+|.+|
T Consensus 182 ~~~~~~~~i~-------ls~~q~~~i~~l~~~~ 207 (225)
T PF06207_consen 182 NNVLNNYNIN-------LSDEQIQQIVNLMKKI 207 (225)
T ss_pred HHHHHHcCCC-------CCHHHHHHHHHHHHHH
Confidence 3444555544 7777777777777444
No 141
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=37.04 E-value=32 Score=21.94 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=12.6
Q ss_pred cCCCCHHHHHHHHHHHhhccc
Q psy8858 45 IKDLNDNELEKLREEISKFII 65 (121)
Q Consensus 45 ~~~Ls~~qi~~L~~~l~~~~i 65 (121)
.-.||+++++.|.++|..--.
T Consensus 45 ~V~Lt~eqv~~LN~~l~~~Gf 65 (73)
T PF14794_consen 45 QVFLTEEQVAKLNQALQKAGF 65 (73)
T ss_dssp -----HHHHHHHHHHHHHTT-
T ss_pred CEEcCHHHHHHHHHHHHHcCC
Confidence 457899999999999954333
No 142
>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=36.78 E-value=35 Score=20.28 Aligned_cols=14 Identities=43% Similarity=0.612 Sum_probs=12.6
Q ss_pred CCCHHHHHHHHHHH
Q psy8858 47 DLNDNELEKLREEI 60 (121)
Q Consensus 47 ~Ls~~qi~~L~~~l 60 (121)
.||++|+..|..+|
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 69999999999876
No 143
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=36.65 E-value=32 Score=23.55 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=19.7
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
+.-....|+.+-|.|+.+|..+.+.+.
T Consensus 45 ~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 45 HPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp -HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred ChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 334456789999999999999998775
No 144
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=36.65 E-value=42 Score=23.95 Aligned_cols=35 Identities=23% Similarity=0.303 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCCCc-ccCCCCHHHHHHHHHHHhhc
Q psy8858 29 RAKKICEVTKISTTK-KIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 29 ~A~~Ic~~lGi~p~~-~~~~Ls~~qi~~L~~~l~~~ 63 (121)
..+++++.+||.|.. +.-..|-+|.+++.+.+++|
T Consensus 82 ~lke~l~elgie~eRv~~~wiSa~E~ekf~e~~~ef 117 (132)
T COG1908 82 LLKELLKELGIEPERVRVLWISAAEGEKFAETINEF 117 (132)
T ss_pred HHHHHHHHhCCCcceEEEEEEehhhHHHHHHHHHHH
Confidence 356788999999854 55666889999999888544
No 145
>cd01401 PncB_like Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi.
Probab=36.64 E-value=59 Score=27.07 Aligned_cols=43 Identities=23% Similarity=0.187 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCCCCCcc----cCCCCHHHHHHHHHHHh-----hcccchhhH
Q psy8858 28 SRAKKICEVTKISTTKK----IKDLNDNELEKLREEIS-----KFIIEGDLR 70 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~----~~~Ls~~qi~~L~~~l~-----~~~i~~~L~ 70 (121)
..+....+++|++|..+ -++|+++.+..|.+..+ .|-|+..|-
T Consensus 289 ~k~r~~~~~~Gi~p~~K~iv~Sd~Lde~~i~~L~~~~~g~~~~~FGIGT~L~ 340 (377)
T cd01401 289 EKAIAHYEKLGIDPKTKTLVFSDGLDVEKALELYEYFKGRIKVSFGIGTNLT 340 (377)
T ss_pred HHHHHHHHHcCCCCCCcEEEEcCCCCHHHHHHHHHHHcCCcceeEecCccee
Confidence 34566678889988887 56889999988888764 455555443
No 146
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=36.10 E-value=18 Score=22.74 Aligned_cols=43 Identities=21% Similarity=0.403 Sum_probs=31.8
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
+.-++..+.|+|..-|+.+++.+ |..-...++.++-+.+.+.|
T Consensus 16 vIK~vR~~tgl~L~eAK~~vd~~---p~~ik~~v~keeAe~ik~~L 58 (68)
T PF00542_consen 16 VIKEVREITGLGLKEAKKLVDSL---PKVIKEGVSKEEAEEIKKKL 58 (68)
T ss_dssp HHHHHHHHC---HHHHHHHHCTT---TEEEEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHhCCcHHHHHHHHHhC---CHHHHcCCCHHHHHHHHHHH
Confidence 44567889999999999999888 66666678899999888877
No 147
>PRK03980 flap endonuclease-1; Provisional
Probab=34.87 E-value=29 Score=27.72 Aligned_cols=18 Identities=33% Similarity=0.407 Sum_probs=16.7
Q ss_pred cccccCHHHHHHHHHHhC
Q psy8858 21 AIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lG 38 (121)
.|+|||+.+|..+++..|
T Consensus 193 GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred CCCCccHHHHHHHHHHCC
Confidence 688999999999999988
No 148
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=34.82 E-value=27 Score=31.40 Aligned_cols=24 Identities=25% Similarity=0.293 Sum_probs=21.6
Q ss_pred eeeehhcccccCHHHHHHHHHHhC
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
+.-.|..|.|||+.++..+++.+|
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhC
Confidence 456788999999999999999988
No 149
>cd00349 Ribosomal_L11 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been im
Probab=34.66 E-value=1.1e+02 Score=21.55 Aligned_cols=51 Identities=6% Similarity=0.066 Sum_probs=37.4
Q ss_pred HHHHHHHHHHhCCCC------CcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHH
Q psy8858 27 RSRAKKICEVTKIST------TKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNI 77 (121)
Q Consensus 27 ~~~A~~Ic~~lGi~p------~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I 77 (121)
+.++..|.+.+|+.. ...++++|-+|+..|.+.-....-..+|+..+++=+
T Consensus 65 Pp~s~ll~ka~g~~kgs~~~~~~~~g~it~~~v~eIA~~K~~dl~~~~l~~~vk~v~ 121 (131)
T cd00349 65 PPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLPDLNAKTLKSAVKEIL 121 (131)
T ss_pred CCHHHHHHHHhCCCCCCCCCCCeeeeeecHHHHHHHHHHHHhhhcchhHHHHHHHHH
Confidence 778888888888875 446899999999999888744455556665554433
No 150
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=34.54 E-value=27 Score=30.66 Aligned_cols=40 Identities=13% Similarity=0.269 Sum_probs=29.4
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
...+|+.|+|||+.++..+++.+|= -..+.+-|.+|+..+
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS--~~~I~~As~eeL~~v 562 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGS--VEGVREASVEDLRDV 562 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCC--HHHHHhCCHHHHHhC
Confidence 4578999999999999999999872 233444555665443
No 151
>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=33.11 E-value=34 Score=21.14 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=16.9
Q ss_pred ehhcccccCHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (121)
-|.+|+|+|.....+|...+
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 47789999999999988765
No 152
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=32.92 E-value=41 Score=26.57 Aligned_cols=38 Identities=24% Similarity=0.333 Sum_probs=26.2
Q ss_pred eehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858 17 IGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK 55 (121)
Q Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~ 55 (121)
..|.+++|||+.+|..+ ...||..-..+-+++++++..
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 45789999999887765 467777655555555555543
No 153
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.81 E-value=29 Score=28.67 Aligned_cols=19 Identities=32% Similarity=0.403 Sum_probs=16.2
Q ss_pred ehhcccccCHHHHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEV 36 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~ 36 (121)
.|..+.|||.++|.+|+.-
T Consensus 114 ~l~~LpGiG~yTa~Ail~~ 132 (342)
T COG1194 114 ELAALPGVGPYTAGAILSF 132 (342)
T ss_pred HHHhCCCCcHHHHHHHHHH
Confidence 4677999999999999864
No 154
>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=32.55 E-value=38 Score=26.55 Aligned_cols=37 Identities=24% Similarity=0.342 Sum_probs=25.1
Q ss_pred hhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 19 LTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
|.+++|||+.++..+. ..||..-..+...+++++..+
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~ 37 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSEI 37 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHhc
Confidence 4678999999988765 567775555555566655443
No 155
>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=31.91 E-value=34 Score=27.77 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=16.7
Q ss_pred hcccccCHHHHHHHHHHhC
Q psy8858 20 TAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lG 38 (121)
..|+|||+.+|..+++..|
T Consensus 239 ~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 5789999999999998855
No 156
>PLN03072 60S ribosomal protein L12; Provisional
Probab=31.56 E-value=88 Score=23.15 Aligned_cols=64 Identities=11% Similarity=0.064 Sum_probs=42.3
Q ss_pred CHHHHHHHHHHhCCCCC--------cccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhhccccccccCCCCCc
Q psy8858 26 GRSRAKKICEVTKISTT--------KKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPC 97 (121)
Q Consensus 26 G~~~A~~Ic~~lGi~p~--------~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpV 97 (121)
-+.+|..|.+.+|+... ..+++||.+|+..|.+.-..-.-..+|+.. ++..-|--..+|+-|
T Consensus 75 ~Pp~s~LLkKa~g~~kgs~~~~~~~~~vG~it~~qv~eIA~~K~~dl~a~~l~~a----------vk~VlGTarSmGi~V 144 (166)
T PLN03072 75 VPSAAALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPRSMAKELAGT----------VKEILGTCVSVGCTV 144 (166)
T ss_pred CCCHHHHHHHHhCCCCCCCccCCCCeeeeeecHHHHHHHHHHHHHHhCcccHHHH----------HHHhHheeeeCeEEE
Confidence 58899999999999874 478999999999998876322233344432 233344555555555
Q ss_pred CC
Q psy8858 98 RG 99 (121)
Q Consensus 98 RG 99 (121)
-|
T Consensus 145 ~g 146 (166)
T PLN03072 145 DG 146 (166)
T ss_pred eC
Confidence 54
No 157
>PRK00419 DNA primase small subunit; Reviewed
Probab=31.40 E-value=35 Score=28.46 Aligned_cols=16 Identities=38% Similarity=0.659 Sum_probs=12.0
Q ss_pred hhHHHHHHHHHHHHhh
Q psy8858 68 DLRREFSMNIKRLIDL 83 (121)
Q Consensus 68 ~L~~~~~~~I~rl~~i 83 (121)
.++..|..||+||+.+
T Consensus 278 ~iDe~VT~DikRLiRl 293 (376)
T PRK00419 278 PIDEPVTIDIKRLIRL 293 (376)
T ss_pred cCCCCccccchhhhhC
Confidence 4667788899998754
No 158
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=31.21 E-value=48 Score=31.25 Aligned_cols=47 Identities=32% Similarity=0.285 Sum_probs=31.6
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCC------CCcccCCCCHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKIS------TTKKIKDLNDNELEKLRE 58 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~------p~~~~~~Ls~~qi~~L~~ 58 (121)
+..|.|+|..|+|||...+..|.+.=-+. .....+.++...++.|..
T Consensus 745 ~~~Ir~GL~aIkgvg~~~~~~I~~~R~f~s~~Df~~R~~~~~~~k~~le~LI~ 797 (1034)
T PRK07279 745 NKKIYLGLKNIKGLPRDLAYWIIENRPFSSIEDFLTRLPENYQKKEFLEPLIK 797 (1034)
T ss_pred CCEEEeehhhcCCCCHHHHHHHHHCCCCCCHHHHHHhcCcCCCCHHHHHHHHH
Confidence 55799999999999999999998642110 011223456666666654
No 159
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=30.80 E-value=45 Score=19.40 Aligned_cols=20 Identities=25% Similarity=0.348 Sum_probs=16.4
Q ss_pred ehhcccccCHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (121)
.|...+||+.+++..++...
T Consensus 24 ~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 24 DLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred HHhhheeecHHHHHHHHHHH
Confidence 45788999999999988653
No 160
>PRK13620 psbV cytochrome c-550; Provisional
Probab=30.76 E-value=55 Score=25.30 Aligned_cols=24 Identities=17% Similarity=0.523 Sum_probs=18.5
Q ss_pred hCCCCCcc-------cCCCCHHHHHHHHHHH
Q psy8858 37 TKISTTKK-------IKDLNDNELEKLREEI 60 (121)
Q Consensus 37 lGi~p~~~-------~~~Ls~~qi~~L~~~l 60 (121)
+.+||+.+ +.+|+|+|+..|..+|
T Consensus 167 ae~HPs~~s~d~mP~~r~LtdedL~aIa~~I 197 (215)
T PRK13620 167 SELHPSTKSTDIFPKMRNLTEDDLVAISGHI 197 (215)
T ss_pred hhcCccccccccccccCCCCHHHHHHHHHHH
Confidence 44555553 5679999999999987
No 161
>PTZ00217 flap endonuclease-1; Provisional
Probab=30.55 E-value=37 Score=28.30 Aligned_cols=19 Identities=37% Similarity=0.434 Sum_probs=16.7
Q ss_pred hcccccCHHHHHHHHHHhC
Q psy8858 20 TAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lG 38 (121)
..|.|||+.+|..+++..|
T Consensus 238 pgi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 3689999999999998866
No 162
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=30.51 E-value=1.2e+02 Score=21.79 Aligned_cols=36 Identities=22% Similarity=0.215 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHhCCC---CCcccCCCCHHHHHHHHHHHh
Q psy8858 26 GRSRAKKICEVTKIS---TTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 26 G~~~A~~Ic~~lGi~---p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
|...-.+|++++|++ .-...+..+|+++.+|.+++.
T Consensus 18 G~~~w~~i~~~~~~~~~~~f~~~~~Y~D~~~~~lv~a~a 56 (171)
T PF07700_consen 18 GEEVWDEILERAGLDSDGIFTSHGNYDDEETYKLVEAAA 56 (171)
T ss_dssp HHHHHHHHHHHTTSSTTSS--TTSBTTHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhCCCcCCccccccccCHHHHHHHHHHHH
Confidence 588899999999999 334788889999999999883
No 163
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=30.50 E-value=65 Score=30.59 Aligned_cols=47 Identities=19% Similarity=0.175 Sum_probs=33.1
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCc---------ccCCCCHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTK---------KIKDLNDNELEKLRE 58 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~---------~~~~Ls~~qi~~L~~ 58 (121)
+..|.++|..|+|||...+..|.+.=.-.|-. ..+.++...++.|..
T Consensus 797 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~~~~~~nk~~le~Li~ 852 (1107)
T PRK06920 797 GNAIRYSLLSIRNIGMATVTALYEEREKKMFEDLFEFCLRMPSKFVTERNLEAFVW 852 (1107)
T ss_pred CCeeEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHhccCCCHHHHHHHHH
Confidence 45799999999999999999998654212222 223466777776654
No 164
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=30.13 E-value=48 Score=24.56 Aligned_cols=15 Identities=40% Similarity=0.696 Sum_probs=11.1
Q ss_pred CCCCHHHHHHHHHHH
Q psy8858 46 KDLNDNELEKLREEI 60 (121)
Q Consensus 46 ~~Ls~~qi~~L~~~l 60 (121)
..|+++|-+.|...|
T Consensus 24 ~~LsEeE~eeLr~EL 38 (162)
T PF04201_consen 24 EGLSEEEREELRSEL 38 (162)
T ss_pred ccCCHHHHHHHHHHH
Confidence 578888777777766
No 165
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.10 E-value=29 Score=26.59 Aligned_cols=21 Identities=24% Similarity=0.539 Sum_probs=17.2
Q ss_pred hhcccccCHHHHHHHHHHhCC
Q psy8858 19 LTAIYGIGRSRAKKICEVTKI 39 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lGi 39 (121)
|++|+|||+..|.+|.....+
T Consensus 62 L~~i~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 62 LSSVPGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHhCcCCcHHHHHHHHHHHHH
Confidence 789999999999888765544
No 166
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=29.96 E-value=13 Score=24.54 Aligned_cols=26 Identities=23% Similarity=0.241 Sum_probs=16.5
Q ss_pred eeeeeehhcccccCHHHHHHHHHHhC
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~lG 38 (121)
+.-+..|....|||+.-+++++++|.
T Consensus 48 ~~rR~~l~~~L~iGy~N~KqllkrLN 73 (87)
T PF13331_consen 48 KERREKLGEYLGIGYGNAKQLLKRLN 73 (87)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHH
Confidence 33444556667777777777776665
No 167
>KOG1014|consensus
Probab=29.90 E-value=68 Score=26.17 Aligned_cols=41 Identities=24% Similarity=0.426 Sum_probs=31.9
Q ss_pred cccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcc
Q psy8858 21 AIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFI 64 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~ 64 (121)
.-.|||+..|.++++ =|++ --+-.=+++.++++.+.| ..+.
T Consensus 57 aTDGIGKayA~eLAk-rG~n--vvLIsRt~~KL~~v~kEI~~~~~ 98 (312)
T KOG1014|consen 57 ATDGIGKAYARELAK-RGFN--VVLISRTQEKLEAVAKEIEEKYK 98 (312)
T ss_pred CCCcchHHHHHHHHH-cCCE--EEEEeCCHHHHHHHHHHHHHHhC
Confidence 457999999999998 5766 444445889999999998 5554
No 168
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=29.80 E-value=58 Score=30.68 Aligned_cols=46 Identities=22% Similarity=0.443 Sum_probs=31.9
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCC-------cccCCCCHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTT-------KKIKDLNDNELEKLRE 58 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~-------~~~~~Ls~~qi~~L~~ 58 (121)
+..|.++|..|+|||...|..|.+.=.-.|- .++ +++...++.|..
T Consensus 811 ~~~I~~gl~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~-~~~~~~le~Li~ 863 (1046)
T PRK05672 811 GPAVRLGLRLVRGLGEEAAERIVAARARGPFTSVEDLARRA-GLDRRQLEALAD 863 (1046)
T ss_pred CCcEEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHh-CCCHHHHHHHHH
Confidence 4579999999999999999999875421121 122 256666666665
No 169
>PRK02406 DNA polymerase IV; Validated
Probab=29.62 E-value=47 Score=26.46 Aligned_cols=36 Identities=25% Similarity=0.352 Sum_probs=26.1
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
-++.++|||+.++..+ ..+||..=--+-.++.+++.
T Consensus 169 pi~~l~giG~~~~~~L-~~~Gi~ti~dl~~l~~~~L~ 204 (343)
T PRK02406 169 PVEKIPGVGKVTAEKL-HALGIYTCADLQKYDLAELI 204 (343)
T ss_pred CcchhcCCCHHHHHHH-HHcCCCcHHHHHhCCHHHHH
Confidence 4688999999999986 68898754445555555554
No 170
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.53 E-value=51 Score=30.91 Aligned_cols=47 Identities=36% Similarity=0.422 Sum_probs=33.4
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCC-CCC---------cccCCCCHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKI-STT---------KKIKDLNDNELEKLRE 58 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi-~p~---------~~~~~Ls~~qi~~L~~ 58 (121)
+..|.++|..|+|||...|..|.+.-.- .|- ...+.++...++.|..
T Consensus 819 ~~~i~~gl~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R~~~~~~~~~~le~Li~ 875 (1022)
T TIGR00594 819 DKGIRYGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRVDFKKLNKKVLEALIK 875 (1022)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHHH
Confidence 4579999999999999999999865321 121 1234567777777765
No 171
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.
Probab=29.33 E-value=89 Score=27.30 Aligned_cols=34 Identities=29% Similarity=0.517 Sum_probs=28.5
Q ss_pred cccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcc
Q psy8858 23 YGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFI 64 (121)
Q Consensus 23 ~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~ 64 (121)
-||+.....+|-+ +|. ++++++.+.|.+.|..|+
T Consensus 105 vgis~~~~~~i~~-~g~-------~~~~~~~e~lr~~lh~yk 138 (533)
T TIGR00470 105 VGLGNEKIEIIEN-LGI-------DIDDEKKERLREVFHLYK 138 (533)
T ss_pred cCcCHHHHHHHHH-hCC-------CCChhHHHHHHHHHHHhh
Confidence 3888999999888 774 578899999999997775
No 172
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=29.11 E-value=29 Score=30.91 Aligned_cols=35 Identities=20% Similarity=0.287 Sum_probs=25.2
Q ss_pred hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 20 TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
-+|.|+|+.++.++.+..++..=.-+-.|+.+++.
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 37899999999999999888643334455555544
No 173
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=29.10 E-value=38 Score=30.52 Aligned_cols=42 Identities=7% Similarity=0.280 Sum_probs=30.5
Q ss_pred eeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
+.....|.+|+|||+.....+++.+|=- ..+..-|.+||..+
T Consensus 604 ~~~~s~L~~IpGiG~kr~~~LL~~FgS~--~~i~~As~eel~~v 645 (691)
T PRK14672 604 KELVLSFERLPHVGKVRAHRLLAHFGSF--RSLQSATPQDIATA 645 (691)
T ss_pred hhcccccccCCCCCHHHHHHHHHHhcCH--HHHHhCCHHHHHhC
Confidence 3456788999999999999999998832 34445556666543
No 174
>PRK13766 Hef nuclease; Provisional
Probab=29.00 E-value=45 Score=29.56 Aligned_cols=37 Identities=14% Similarity=0.141 Sum_probs=25.9
Q ss_pred eeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
.+.|..|.|||...|..|++.+|- -..+-+.+.+++.
T Consensus 714 ~~~L~~ipgig~~~a~~Ll~~fgs--~~~i~~as~~~L~ 750 (773)
T PRK13766 714 EYIVESLPDVGPVLARNLLEHFGS--VEAVMTASEEELM 750 (773)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCC--HHHHHhCCHHHHH
Confidence 346899999999999999999872 2223344444443
No 175
>PRK03352 DNA polymerase IV; Validated
Probab=28.76 E-value=56 Score=26.05 Aligned_cols=36 Identities=25% Similarity=0.448 Sum_probs=26.3
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
-+..++|||+.++..+ ..+||..=..+-.++.+++.
T Consensus 178 pl~~l~gig~~~~~~L-~~~Gi~ti~dl~~l~~~~L~ 213 (346)
T PRK03352 178 PTDALWGVGPKTAKRL-AALGITTVADLAAADPAELA 213 (346)
T ss_pred CHHHcCCCCHHHHHHH-HHcCCccHHHHhcCCHHHHH
Confidence 3578899999999985 78999865555555665553
No 176
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=28.74 E-value=46 Score=28.04 Aligned_cols=43 Identities=16% Similarity=0.142 Sum_probs=37.7
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
-|+.|.|||+..+. .+..+||...-.+-..+++++..+...+.
T Consensus 324 DLk~I~GIGpk~e~-~Ln~~Gi~~f~QIA~wt~~eia~vd~~l~ 366 (400)
T PRK12373 324 DLKLISGVGPKIEA-TLNELGIFTFDQVAAWKKAERAWVDGYLN 366 (400)
T ss_pred hhhhccCCChHHHH-HHHhcCCCCHHHHhCCCHHHhHHhhhccc
Confidence 58999999998875 56889999999999999999998888774
No 177
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=28.68 E-value=72 Score=22.36 Aligned_cols=15 Identities=33% Similarity=0.534 Sum_probs=12.6
Q ss_pred CCHHHHHHHHHHHhh
Q psy8858 48 LNDNELEKLREEISK 62 (121)
Q Consensus 48 Ls~~qi~~L~~~l~~ 62 (121)
||++|+..|.+.+..
T Consensus 2 lt~ee~~~l~~~~~~ 16 (205)
T cd01199 2 LEKNELKALLDVLNS 16 (205)
T ss_pred CCHHHHHHHHHHHHh
Confidence 789999999998844
No 178
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.54 E-value=1e+02 Score=17.88 Aligned_cols=35 Identities=29% Similarity=0.365 Sum_probs=18.7
Q ss_pred hhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 19 LTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
|.+.-||.+.+...++. .++..++-+.+..|.++|
T Consensus 16 La~~~gis~~tl~~~~~-------~~~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 16 LARKTGISRSTLSRILN-------GKPSNPSLDTLEKIAKAL 50 (63)
T ss_dssp HHHHHT--HHHHHHHHT-------TT-----HHHHHHHHHHH
T ss_pred HHHHHCcCHHHHHHHHh-------cccccccHHHHHHHHHHc
Confidence 34445666666666663 335678888899888888
No 179
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.50 E-value=52 Score=30.56 Aligned_cols=31 Identities=16% Similarity=0.101 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCCCcccCCCCHHHHHHHHH
Q psy8858 28 SRAKKICEVTKISTTKKIKDLNDNELEKLRE 58 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~ 58 (121)
..-..+|+..|||.++++.+|+++|.+.|-.
T Consensus 320 ~~l~~~~~~~g~~~~~p~~~l~~~~~~~ll~ 350 (924)
T TIGR00630 320 QMLKSLAEHYGFDLDTPWKDLPEEVQKAVLY 350 (924)
T ss_pred HHHHHHHHHcCCCCCCChHHCCHHHHHHHhc
Confidence 3456689999999999999999999987753
No 180
>smart00482 POLAc DNA polymerase A domain.
Probab=28.31 E-value=1.3e+02 Score=22.38 Aligned_cols=61 Identities=20% Similarity=0.238 Sum_probs=34.0
Q ss_pred hcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHHhhccccccccC
Q psy8858 20 TAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI-SKFIIEGDLRREFSMNIKRLIDLSCYRGIRHR 92 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l-~~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~ 92 (121)
--+||.|. ..+.+.+| +|.+|...+.+.+ ..|+--..+...+.+....--.+.+.-|.|..
T Consensus 78 g~~YG~g~---~~la~~lg---------~s~~ea~~~~~~f~~~~p~v~~~~~~~~~~a~~~g~v~t~~Gr~r~ 139 (206)
T smart00482 78 GIIYGMGA---KGLAEQLG---------ISEAEAKELIKAYFARFPGVKRYIKRTLEEARRKGYVTTLFGRRRY 139 (206)
T ss_pred Hhhhccch---hHHHHHcC---------CCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHhCCEEEecCCCeee
Confidence 34678884 35555565 5677877776666 56665455555444443333334555555443
No 181
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=27.92 E-value=32 Score=27.46 Aligned_cols=23 Identities=30% Similarity=0.424 Sum_probs=19.6
Q ss_pred ehhcccccCHHHHHHHHHHhCCC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKIS 40 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~ 40 (121)
.+++++|||..+|..|.+.+.=.
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG 68 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETG 68 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcC
Confidence 56899999999999999887643
No 182
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=27.71 E-value=1.9e+02 Score=21.86 Aligned_cols=48 Identities=15% Similarity=0.168 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhh
Q psy8858 27 RSRAKKICEVTKISTTKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDL 83 (121)
Q Consensus 27 ~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl~~i 83 (121)
-..+..||..+|++ +++++.+..++.+-.+..|-.-++.+|.--|+.+
T Consensus 89 A~~~~~im~~~Gy~---------~~~i~rV~~lv~K~~lk~d~e~Q~LEDvacLVFL 136 (185)
T PF13875_consen 89 AAIAAEIMREAGYD---------EEEIDRVAALVRKEGLKRDPETQALEDVACLVFL 136 (185)
T ss_pred HHHHHHHHHHCCCC---------HHHHHHHHHHHHhccCCCCchHHHHHhhHHHHhH
Confidence 35678889888876 5777777777744444444444455555544444
No 183
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=27.51 E-value=44 Score=27.00 Aligned_cols=21 Identities=38% Similarity=0.529 Sum_probs=19.0
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.|++++|||...|..|.+.+.
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~ 69 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIE 69 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHH
Confidence 578999999999999998876
No 184
>COG5485 Predicted ester cyclase [General function prediction only]
Probab=27.29 E-value=24 Score=25.21 Aligned_cols=12 Identities=33% Similarity=0.603 Sum_probs=10.1
Q ss_pred CCCCCcCCcccc
Q psy8858 92 RKSLPCRGQRTR 103 (121)
Q Consensus 92 ~~gLpVRGQRT~ 103 (121)
-+|+||.|||.+
T Consensus 89 i~Gip~nGkrV~ 100 (131)
T COG5485 89 IMGIPPNGKRVR 100 (131)
T ss_pred EeccCCCCcEEE
Confidence 479999999965
No 185
>PRK03858 DNA polymerase IV; Validated
Probab=27.25 E-value=64 Score=26.20 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=25.4
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
-++.++|||..++..+ ..+||..-..+-.++.+++.
T Consensus 174 pl~~l~Gig~~~~~~L-~~~Gi~t~~dl~~l~~~~L~ 209 (396)
T PRK03858 174 PVRRLWGVGPVTAAKL-RAHGITTVGDVAELPESALV 209 (396)
T ss_pred ChhhcCCCCHHHHHHH-HHhCCCcHHHHhcCCHHHHH
Confidence 4578899999999887 56898864445555555443
No 186
>PRK00024 hypothetical protein; Reviewed
Probab=27.11 E-value=49 Score=25.33 Aligned_cols=22 Identities=27% Similarity=0.495 Sum_probs=17.9
Q ss_pred ehhcccccCHHHHHHHHHHhCC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKI 39 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi 39 (121)
.|.+|.|||+..|..|+....+
T Consensus 67 eL~~i~GIG~akA~~L~a~~El 88 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALEL 88 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHH
Confidence 4789999999999888765554
No 187
>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=26.93 E-value=57 Score=20.39 Aligned_cols=22 Identities=23% Similarity=0.372 Sum_probs=13.5
Q ss_pred hhcccccCHHHHHHHHHHhCCC
Q psy8858 19 LTAIYGIGRSRAKKICEVTKIS 40 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lGi~ 40 (121)
|.+--|+.+.+...+|+++|++
T Consensus 40 lA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 40 LAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHHHcCCCHHHHHHHHHHhCCC
Confidence 3444566777777777777765
No 188
>PF10511 Cementoin: Trappin protein transglutaminase binding domain; InterPro: IPR019541 Trappin-2,a protease inhibitor, has a unique N-terminal domain that enables it to become cross-linked to extracellular matrix proteins by transglutaminase []. This domain contains several repeated motifs (rpresented by this entry) with the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalysed cross-links. The whole domain is rich in glutamine and lysine, thus allowing and transglutaminase(s) to catalyse the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond []. Cementoin is associated with the WAP family, IPR008197 from INTERPRO, at the C terminus. ; PDB: 2REL_A.
Probab=26.93 E-value=30 Score=16.23 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=3.7
Q ss_pred CCCcCCcc
Q psy8858 94 SLPCRGQR 101 (121)
Q Consensus 94 gLpVRGQR 101 (121)
-+||.||-
T Consensus 8 ~~~vKGQd 15 (17)
T PF10511_consen 8 QVPVKGQD 15 (17)
T ss_dssp ---SSSSS
T ss_pred cccccCcC
Confidence 36888883
No 189
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=26.78 E-value=62 Score=19.66 Aligned_cols=40 Identities=25% Similarity=0.265 Sum_probs=27.8
Q ss_pred HHHHHHhCCCC---CcccCCCCHHHHHHHHHHHhhcccchhhH
Q psy8858 31 KKICEVTKIST---TKKIKDLNDNELEKLREEISKFIIEGDLR 70 (121)
Q Consensus 31 ~~Ic~~lGi~p---~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~ 70 (121)
..+-+++|--| ..++..|+.++++.|.+.+-.|.--.||.
T Consensus 14 RlL~rrFG~lp~~~~~~I~~l~~eqLE~l~e~ildf~~l~dL~ 56 (59)
T PF14261_consen 14 RLLTRRFGELPPEIQERIQQLSLEQLEALAEAILDFNSLEDLE 56 (59)
T ss_pred HHHHHHcCCCCHHHHHHHHcCCHHHHHHHHHHHhCCCCHHHHH
Confidence 34455666544 24788899999999999986666555654
No 190
>PF13276 HTH_21: HTH-like domain
Probab=26.60 E-value=40 Score=19.86 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=25.9
Q ss_pred CCCCeeeeeehhcccc--cCHHHHHHHHHHhCCCCC
Q psy8858 9 IPNNQHIIIGLTAIYG--IGRSRAKKICEVTKISTT 42 (121)
Q Consensus 9 ~~~~k~v~~aLt~I~G--IG~~~A~~Ic~~lGi~p~ 42 (121)
..|...|...|..-+| ||..+...|+..+||...
T Consensus 20 ~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 20 TYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred CeehhHHHHHHhccCcccccHHHHHHHHHHcCCccc
Confidence 3455667777877766 799999999999998754
No 191
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=26.31 E-value=2e+02 Score=19.01 Aligned_cols=43 Identities=23% Similarity=0.336 Sum_probs=29.4
Q ss_pred eehhcccccCHHH-HHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 17 IGLTAIYGIGRSR-AKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 17 ~aLt~I~GIG~~~-A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
+++...+|-|.++ |..+.+.+|+. -...+.+.++++....+..
T Consensus 2 I~i~G~~GsGKst~a~~la~~~~~~-~~~~~~i~~e~~~~~~~~~ 45 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLAKKLGLP-YLDTGGIRTEEVGKLASEV 45 (147)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCc-eeccccCCHHHHHHHHHHh
Confidence 4567789999998 77788889864 2334467777666554433
No 192
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=26.13 E-value=54 Score=25.95 Aligned_cols=38 Identities=24% Similarity=0.295 Sum_probs=27.3
Q ss_pred eeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858 16 IIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK 55 (121)
Q Consensus 16 ~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~ 55 (121)
.+.|.+|+|||...|..++..+|=- ..+-..+++++..
T Consensus 181 ~~il~s~pgig~~~a~~ll~~fgS~--~~~~tas~~eL~~ 218 (254)
T COG1948 181 LYILESIPGIGPKLAERLLKKFGSV--EDVLTASEEELMK 218 (254)
T ss_pred HHHHHcCCCccHHHHHHHHHHhcCH--HHHhhcCHHHHHH
Confidence 4557999999999999999998833 2344455555543
No 193
>PRK05755 DNA polymerase I; Provisional
Probab=26.03 E-value=47 Score=30.36 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=17.5
Q ss_pred hhcccccCHHHHHHHHHHhC
Q psy8858 19 LTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 19 Lt~I~GIG~~~A~~Ic~~lG 38 (121)
+..++|||+++|..+++..|
T Consensus 189 ipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 189 IPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred CCCCCCccHHHHHHHHHHcC
Confidence 35689999999999999877
No 194
>PF14965 BRI3BP: Negative regulator of p53/TP53
Probab=25.75 E-value=1.3e+02 Score=22.66 Aligned_cols=32 Identities=6% Similarity=-0.017 Sum_probs=27.6
Q ss_pred HHHHHHHHHhCCCCCcccCCCCHHHHHHHHHH
Q psy8858 28 SRAKKICEVTKISTTKKIKDLNDNELEKLREE 59 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~ 59 (121)
..+.++++.+|+|.+-....+|++++..+..+
T Consensus 48 ~i~~dlL~~~Gid~~~lt~~~SP~~V~~~llw 79 (177)
T PF14965_consen 48 RIWTDLLDVLGIDGSNLTHYFSPGGVQTVLLW 79 (177)
T ss_pred HHHHHHHHHhCccccccccccCHHHHHHHHHH
Confidence 35788999999999999999999999986554
No 195
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=25.66 E-value=60 Score=25.38 Aligned_cols=21 Identities=29% Similarity=0.357 Sum_probs=19.0
Q ss_pred ehhcccccCHHHHHHHHHHhC
Q psy8858 18 GLTAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lG 38 (121)
.|..+.|||...|..|...++
T Consensus 37 EL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 37 ELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHHccCCCHHHHHHHHHHhc
Confidence 478899999999999999987
No 196
>KOG2875|consensus
Probab=25.56 E-value=29 Score=28.23 Aligned_cols=22 Identities=27% Similarity=0.407 Sum_probs=19.2
Q ss_pred eeeehhcccccCHHHHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEV 36 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~ 36 (121)
+.-+|..++|||++.|.-||-.
T Consensus 216 ar~~L~~lpGVG~KVADCI~Lm 237 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCICLM 237 (323)
T ss_pred HHHHHhcCCCCcchHhhhhhhh
Confidence 5568999999999999999954
No 197
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=25.46 E-value=63 Score=30.10 Aligned_cols=30 Identities=17% Similarity=0.143 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCCCCcccCCCCHHHHHHHH
Q psy8858 28 SRAKKICEVTKISTTKKIKDLNDNELEKLR 57 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~ 57 (121)
..-..+|+..|||++++..+|+++|.+.|-
T Consensus 322 ~~l~~~~~~~g~~~~~p~~~l~~~~~~~ll 351 (943)
T PRK00349 322 QMLKSLAEHYGFDLDTPWKDLPEEVQDIIL 351 (943)
T ss_pred HHHHHHHHHcCCCCCCchHHCCHHHHHHHc
Confidence 456678999999999999999999987554
No 198
>KOG2534|consensus
Probab=25.30 E-value=1.4e+02 Score=24.79 Aligned_cols=43 Identities=19% Similarity=0.288 Sum_probs=28.9
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
.+..++|||++.|..|-+.+.=.--..+.+...+|..+..+.+
T Consensus 57 ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklF 99 (353)
T KOG2534|consen 57 EAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLF 99 (353)
T ss_pred HhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHH
Confidence 3567999999999999988875544444444444455555555
No 199
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=25.19 E-value=1.2e+02 Score=18.89 Aligned_cols=42 Identities=21% Similarity=0.169 Sum_probs=26.7
Q ss_pred cCCCCHHHHHHHHHHH-h-hcc---------cc-hhhHHHHHHHHHHHHhhccc
Q psy8858 45 IKDLNDNELEKLREEI-S-KFI---------IE-GDLRREFSMNIKRLIDLSCY 86 (121)
Q Consensus 45 ~~~Ls~~qi~~L~~~l-~-~~~---------i~-~~L~~~~~~~I~rl~~i~~y 86 (121)
+.+||.+|+..-...+ . -|. ++ ...-+.++.||.|+..+-+-
T Consensus 9 lr~ls~~eL~~~l~elk~elf~LRfq~atgql~n~~~ir~~RrdIARikTil~e 62 (67)
T CHL00154 9 IIDLTDSEISEEIIKTKKELFDLRLKKATRQNFKPHLFKHKKHRLAQLLTLLSS 62 (67)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHHHHHHH
Confidence 5677888877555554 1 122 22 24456799999999887554
No 200
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.92 E-value=50 Score=30.48 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=16.9
Q ss_pred hcccccCHHHHHHHHHHhC
Q psy8858 20 TAIYGIGRSRAKKICEVTK 38 (121)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lG 38 (121)
..++|||+++|..++...|
T Consensus 188 pGVpGIG~KtA~kLL~~yg 206 (887)
T TIGR00593 188 PGVKGIGEKTAAKLLQEFG 206 (887)
T ss_pred CCCCCcCHHHHHHHHHHcC
Confidence 4589999999999999877
No 201
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=24.89 E-value=83 Score=16.25 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=7.9
Q ss_pred CHHHHHHHHHHhCCCC
Q psy8858 26 GRSRAKKICEVTKIST 41 (121)
Q Consensus 26 G~~~A~~Ic~~lGi~p 41 (121)
...++..+|+.+|+++
T Consensus 38 ~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 38 SLETLKKLAKALGVSL 53 (56)
T ss_pred CHHHHHHHHHHhCCCh
Confidence 4444555555555443
No 202
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=24.87 E-value=55 Score=26.86 Aligned_cols=20 Identities=45% Similarity=0.587 Sum_probs=16.5
Q ss_pred ehhcccccCHHHHHHHHHHh
Q psy8858 18 GLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~l 37 (121)
++|.++|||+.+|..|..-+
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred ccCCCCCccHHHHHHHHHHH
Confidence 48899999999999887554
No 203
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=24.76 E-value=70 Score=26.41 Aligned_cols=36 Identities=25% Similarity=0.430 Sum_probs=26.2
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
-+..++|||..++..+ ..+||..=-.+-.++.+.+.
T Consensus 180 Pv~~l~GiG~~~~~~L-~~lGi~TigdL~~~~~~~L~ 215 (422)
T PRK03609 180 PVEEVWGVGRRISKKL-NAMGIKTALDLADTNIRFIR 215 (422)
T ss_pred ChhhcCCccHHHHHHH-HHcCCCcHHHHhcCCHHHHH
Confidence 3578999999999887 57999865555555655543
No 204
>KOG4302|consensus
Probab=24.74 E-value=2.7e+02 Score=25.13 Aligned_cols=36 Identities=19% Similarity=0.520 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCCCccc---------------CCCCHHHHHHHHHHHhhc
Q psy8858 28 SRAKKICEVTKISTTKKI---------------KDLNDNELEKLREEISKF 63 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~~~---------------~~Ls~~qi~~L~~~l~~~ 63 (121)
...+.+|..||+++...+ ..++++-+++|...+.+|
T Consensus 188 ~~I~~l~~~Lg~~~~~~vt~~~~sL~~~~~~~~~~is~etl~~L~~~v~~l 238 (660)
T KOG4302|consen 188 EEIKSLCSVLGLDFSMTVTDVEPSLVDHDGEQSRSISDETLDRLDKMVKKL 238 (660)
T ss_pred HHHHHHHHHhCCCcccchhhhhhhhhhccCcccccCCHHHHHHHHHHHHHH
Confidence 356789999999999777 456667777777666433
No 205
>smart00649 RL11 Ribosomal protein L11/L12.
Probab=24.64 E-value=2.1e+02 Score=20.19 Aligned_cols=52 Identities=10% Similarity=0.070 Sum_probs=35.8
Q ss_pred CHHHHHHHHHHhCCCCC------cccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHH
Q psy8858 26 GRSRAKKICEVTKISTT------KKIKDLNDNELEKLREEISKFIIEGDLRREFSMNI 77 (121)
Q Consensus 26 G~~~A~~Ic~~lGi~p~------~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I 77 (121)
-+.++..|.+.+|+... ..++++|-+|+..|.+.-..-....+|+..+++=+
T Consensus 64 ~P~~s~ll~k~~g~~kgs~~p~~~~~g~it~~~v~eIA~~K~~d~~~~~l~~~~k~V~ 121 (132)
T smart00649 64 TPPASFLLKKAAGIEKGSKKPGKKKVGNITLDQVYEIAKIKRPDLNAKDLEAAVKEIL 121 (132)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeeeeEEcHHHHHHHHHHHHHHhcchhHHHHHHHHH
Confidence 36678888899998843 45789999999988887733234455655444433
No 206
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=24.46 E-value=70 Score=22.13 Aligned_cols=35 Identities=23% Similarity=0.341 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCCCc-ccCCCCHHHHHHHHHHHhhc
Q psy8858 29 RAKKICEVTKISTTK-KIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 29 ~A~~Ic~~lGi~p~~-~~~~Ls~~qi~~L~~~l~~~ 63 (121)
.++++++.+||+|+. .+..++..+...+.+.++.|
T Consensus 81 ~~k~~L~~~Gi~~eRv~~~~~~~~~~~~fa~~~~~f 116 (124)
T PF02662_consen 81 RLKKLLEELGIEPERVRLYWISAPEGKRFAEIVNEF 116 (124)
T ss_pred HHHHHHHHcCCChhHeEEEEeCcccHHHHHHHHHHH
Confidence 456788889999654 66667778888888777433
No 207
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=24.40 E-value=1.9e+02 Score=18.08 Aligned_cols=49 Identities=8% Similarity=0.057 Sum_probs=34.3
Q ss_pred HHHHHHHHHhCCCC------CcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHH
Q psy8858 28 SRAKKICEVTKIST------TKKIKDLNDNELEKLREEISKFIIEGDLRREFSMN 76 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p------~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~ 76 (121)
.++..|.+.+|++. ...++++|-+|+..|.+.-..-....+|+..++.=
T Consensus 4 p~s~llkkaagi~kGs~~p~~~~vG~it~~~i~eIAk~K~~d~~~~~l~~~~k~v 58 (69)
T PF00298_consen 4 PTSWLLKKAAGIKKGSSKPGKEKVGTITLKQIYEIAKIKQKDLNAKSLESAVKSV 58 (69)
T ss_dssp THHHHHHHHHTTSSSSSSTTTSSSEEEEHHHHHHHHHHHTTTSSSSSHHHHHHHH
T ss_pred ChHHHHHHHhCCCCCCCCCCCceeeeecHHHHHHHHHHhhcccccCCHHHHHHHH
Confidence 35677888888852 24688999999999988874433556666554443
No 208
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=24.39 E-value=72 Score=18.87 Aligned_cols=34 Identities=18% Similarity=0.227 Sum_probs=25.5
Q ss_pred cccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 21 AIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
.|.|-......+|++.+++.+...+=.++.+++.
T Consensus 7 ~V~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 40 (69)
T PF08478_consen 7 EVSGNSYLSKEEILQALGIQKGKNLFSLDLKKIE 40 (69)
T ss_dssp EEES-SSS-HHHHHHHHCTTSTTTCCCSHHHHHH
T ss_pred EEECCCcCCHHHHHHHhCcCCCCeEEEECHHHHH
Confidence 4567778889999999999998877777666655
No 209
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=24.32 E-value=1.8e+02 Score=17.88 Aligned_cols=52 Identities=15% Similarity=0.241 Sum_probs=33.5
Q ss_pred CCCCeeeeeehhcccccCHHHHHHHHHHh----C---CCCCcccCCCCHHHHHHHHHHH
Q psy8858 9 IPNNQHIIIGLTAIYGIGRSRAKKICEVT----K---ISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 9 ~~~~k~v~~aLt~I~GIG~~~A~~Ic~~l----G---i~p~~~~~~Ls~~qi~~L~~~l 60 (121)
+..++.|..-+..+.+++.+++.+..-.+ | +.....+.+++++....|..++
T Consensus 14 l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~~vi 72 (74)
T PF14213_consen 14 LKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIKRVI 72 (74)
T ss_pred HhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHHHHH
Confidence 45566789999999999999999876543 2 2234445555555554444443
No 210
>PRK02362 ski2-like helicase; Provisional
Probab=24.10 E-value=64 Score=28.68 Aligned_cols=38 Identities=18% Similarity=0.470 Sum_probs=29.0
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
.|..|+|||+..|..+-+ +||..-..+-.++++++..+
T Consensus 653 ~L~~ip~i~~~~a~~l~~-~gi~s~~dl~~~~~~~l~~~ 690 (737)
T PRK02362 653 DLVGLRGVGRVRARRLYN-AGIESRADLRAADKSVVLAI 690 (737)
T ss_pred HHhCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHH
Confidence 467899999999977775 99887555556677776665
No 211
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=24.07 E-value=2.4e+02 Score=20.47 Aligned_cols=63 Identities=11% Similarity=0.132 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhCCCC------CcccCCCCHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhhccccccccCCCCCcCC
Q psy8858 27 RSRAKKICEVTKIST------TKKIKDLNDNELEKLREEISKFIIEGDLRREFSMNIKRLIDLSCYRGIRHRKSLPCRG 99 (121)
Q Consensus 27 ~~~A~~Ic~~lGi~p------~~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~~~~I~rl~~i~~yRG~RH~~gLpVRG 99 (121)
+..+..|.+.+|++. ...+++||.+|+..|.+.-..=....||+..+ +..-|--..+|+-|-|
T Consensus 72 PPas~LlkKa~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~K~~dl~a~~l~aA~----------k~I~GTa~SMGv~Veg 140 (141)
T COG0080 72 PPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMPDLNAKDLEAAV----------KEILGTARSMGVTVEG 140 (141)
T ss_pred CCHHHHHHHHhCCCCCCCCCCcceeeeeeHHHHHHHHHHhhhhhhhHHHHHHH----------HHHhhhhhhceEEeec
Confidence 456778888899874 36889999999998887653223344554332 3344555556655543
No 212
>TIGR03791 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain.
Probab=24.02 E-value=89 Score=24.95 Aligned_cols=26 Identities=31% Similarity=0.294 Sum_probs=20.0
Q ss_pred CCCCCcccCCCCHHHHHHHHHHHhhc
Q psy8858 38 KISTTKKIKDLNDNELEKLREEISKF 63 (121)
Q Consensus 38 Gi~p~~~~~~Ls~~qi~~L~~~l~~~ 63 (121)
++++....-.||++|++.|+.+|+.+
T Consensus 253 ~~~~~~~~~~Lt~~E~~dLvaFL~tL 278 (291)
T TIGR03791 253 SISAEMKPFELSEREREDLIAFIETL 278 (291)
T ss_pred ccccccccCCCCHHHHHHHHHHHHhc
Confidence 34455566699999999999999644
No 213
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=23.97 E-value=86 Score=23.13 Aligned_cols=19 Identities=21% Similarity=0.286 Sum_probs=15.8
Q ss_pred CCCCHHHHHHHHHHH-hhcc
Q psy8858 46 KDLNDNELEKLREEI-SKFI 64 (121)
Q Consensus 46 ~~Ls~~qi~~L~~~l-~~~~ 64 (121)
..||++|+..|..+| .+..
T Consensus 131 ~~LsdeEL~aVAaYIl~q~~ 150 (163)
T CHL00133 131 RSLTDEDLYAIAGHILLQPK 150 (163)
T ss_pred CCCCHHHHHHHHHHHHhccc
Confidence 579999999999998 4444
No 214
>PF01595 DUF21: Domain of unknown function DUF21; InterPro: IPR002550 This transmembrane region has no known function. Many of the sequences in this family are annotated as hemolysins, however this is due to a similarity to Q54318 from SWISSPROT that does not contain this domain. This domain is found in the N terminus of the proteins adjacent to two intracellular CBS domains (IPR000644 from INTERPRO).
Probab=23.93 E-value=1.5e+02 Score=20.89 Aligned_cols=35 Identities=23% Similarity=0.209 Sum_probs=28.8
Q ss_pred cCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHH
Q psy8858 25 IGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 25 IG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l 60 (121)
+....+..+++..|.++ ..-..+++||+..+.+.=
T Consensus 139 ~l~~i~~~~~~~~~~~~-~~~~~~s~eel~~lv~~~ 173 (183)
T PF01595_consen 139 LLSFISNKILKLFGIEN-EEDPAVSEEELRSLVEEG 173 (183)
T ss_pred HHHHHHHHHHHHhCCCc-cccCCCCHHHHHHHHHhH
Confidence 45667888899999998 778889999999888765
No 215
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=23.89 E-value=60 Score=28.64 Aligned_cols=41 Identities=32% Similarity=0.323 Sum_probs=30.0
Q ss_pred eeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 14 HIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 14 ~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
.+...|-.|.|||+...+.+++.+|=- ..+.+-|.+|+..+
T Consensus 527 ~~~s~Ld~I~GiG~~r~~~LL~~Fgs~--~~i~~As~eel~~v 567 (581)
T COG0322 527 MLQSSLDDIPGIGPKRRKALLKHFGSL--KGIKSASVEELAKV 567 (581)
T ss_pred hhcCccccCCCcCHHHHHHHHHHhhCH--HHHHhcCHHHHHHc
Confidence 355678899999999999999998832 34555566666544
No 216
>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=23.88 E-value=26 Score=29.36 Aligned_cols=69 Identities=22% Similarity=0.366 Sum_probs=0.0
Q ss_pred cccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHhh-c----ccc--hhhHHHHHHHHHHHHhhcccccccc
Q psy8858 21 AIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEISK-F----IIE--GDLRREFSMNIKRLIDLSCYRGIRH 91 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~~-~----~i~--~~L~~~~~~~I~rl~~i~~yRG~RH 91 (121)
.=|||=++|+..|. .+||.-++-+ +++|+||+.++..|.. | .++ .-++..++..-.||-+-...+..||
T Consensus 56 ~~YGVRy~T~AKIa-ElGFTvsTLl-~M~deELDdmM~sL~~ifRwdLLVGERYGIKAAvRAERRRl~e~~~~~rR~h 131 (386)
T PF01698_consen 56 QGYGVRYYTAAKIA-ELGFTVSTLL-NMTDEELDDMMNSLSQIFRWDLLVGERYGIKAAVRAERRRLEEEEESRRRRH 131 (386)
T ss_dssp ------------------------------------------------------------------------------
T ss_pred hhccccHHHHHHHH-HhcccHHHHh-cccHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHhhcchhhhhhhc
Confidence 45899999999886 6888876655 4699999998887732 2 232 2466667777777766544455555
No 217
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=23.48 E-value=2.1e+02 Score=21.05 Aligned_cols=35 Identities=11% Similarity=0.004 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHhCCCC------CcccCCCCHHHHHHHHHHH
Q psy8858 26 GRSRAKKICEVTKIST------TKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 26 G~~~A~~Ic~~lGi~p------~~~~~~Ls~~qi~~L~~~l 60 (121)
-+.++..|.+.+|+.. ...++++|.+|+..|.+..
T Consensus 69 ~Pp~s~ll~kaag~~kgs~~p~~~~vG~It~~qv~eIA~~K 109 (163)
T PRK01143 69 IPPTTALIKKELGIEKGSGEPGHEVVGNLSFEQVVKIAIMK 109 (163)
T ss_pred CCCHHHHHHHHhCCcCCCCCCCCceeeeecHHHHHHHHHHH
Confidence 4668888889999954 3467999999999998877
No 218
>KOG1220|consensus
Probab=23.34 E-value=82 Score=27.97 Aligned_cols=33 Identities=24% Similarity=0.089 Sum_probs=29.5
Q ss_pred CCCCeeeeeehhcccccCHHHHHHHHHHhCCCC
Q psy8858 9 IPNNQHIIIGLTAIYGIGRSRAKKICEVTKIST 41 (121)
Q Consensus 9 ~~~~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p 41 (121)
.++..++.|--+.+.|+|..+...+++.+|+++
T Consensus 242 ~n~~s~~~fVyta~hGvG~~F~~~al~~~~~~~ 274 (607)
T KOG1220|consen 242 ANPLSGLKFVYTAGHGVGGFFVKKALEKLGLDT 274 (607)
T ss_pred hccCCCceEEEecCCCccHHHHHHHHHHhCCCc
Confidence 346677899999999999999999999999987
No 219
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=23.30 E-value=83 Score=30.20 Aligned_cols=25 Identities=32% Similarity=0.466 Sum_probs=22.5
Q ss_pred eeeeeehhcccccCHHHHHHHHHHh
Q psy8858 13 QHIIIGLTAIYGIGRSRAKKICEVT 37 (121)
Q Consensus 13 k~v~~aLt~I~GIG~~~A~~Ic~~l 37 (121)
..|.+.|..|.|||...|..|.+.-
T Consensus 1146 ~~I~~~l~aI~glg~~~a~~Iv~~R 1170 (1213)
T TIGR01405 1146 NTLIPPFNAIPGLGENVANSIVEAR 1170 (1213)
T ss_pred CEEEeehhhcCCCCHHHHHHHHHHH
Confidence 4699999999999999999999764
No 220
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=23.22 E-value=69 Score=29.36 Aligned_cols=38 Identities=18% Similarity=0.357 Sum_probs=27.6
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK 55 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~ 55 (121)
..| |.+++|||+..|..|+..+| .=..+-++|.+|+..
T Consensus 756 q~~-L~~lPgI~~~~a~~ll~~f~--si~~l~~as~eeL~~ 793 (814)
T TIGR00596 756 QDF-LLKLPGVTKKNYRNLRKKVK--SIRELAKLSQNELNE 793 (814)
T ss_pred HHH-HHHCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHH
Confidence 455 77999999999999999866 223445556666654
No 221
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=22.99 E-value=56 Score=21.27 Aligned_cols=16 Identities=19% Similarity=0.297 Sum_probs=12.7
Q ss_pred HHHHHHHHHhCCCCCc
Q psy8858 28 SRAKKICEVTKISTTK 43 (121)
Q Consensus 28 ~~A~~Ic~~lGi~p~~ 43 (121)
..|..+|+.+|++++.
T Consensus 14 ~~A~~vl~~lGls~S~ 29 (80)
T PRK11235 14 ARAYAVLEKLGVTPSE 29 (80)
T ss_pred HHHHHHHHHhCCCHHH
Confidence 5688899999998643
No 222
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=22.96 E-value=78 Score=20.62 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=17.7
Q ss_pred cccCHHHHHHHHHHhCCCCCc
Q psy8858 23 YGIGRSRAKKICEVTKISTTK 43 (121)
Q Consensus 23 ~GIG~~~A~~Ic~~lGi~p~~ 43 (121)
.|+....|..+|..||+....
T Consensus 22 d~W~~~~s~~~C~qLGy~~~~ 42 (98)
T PF15494_consen 22 DNWNEALSKAACQQLGYSSSS 42 (98)
T ss_pred cccCHHHHHHHHHHhCCCCCC
Confidence 588999999999999996433
No 223
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=22.68 E-value=92 Score=16.21 Aligned_cols=22 Identities=9% Similarity=0.033 Sum_probs=16.4
Q ss_pred cccccCHHHHHHHHHHhCCCCC
Q psy8858 21 AIYGIGRSRAKKICEVTKISTT 42 (121)
Q Consensus 21 ~I~GIG~~~A~~Ic~~lGi~p~ 42 (121)
.-..++...+..+|+.+|+++.
T Consensus 35 g~~~~~~~~~~~i~~~~~~~~~ 56 (58)
T cd00093 35 GKRNPSLETLEKLAKALGVSLD 56 (58)
T ss_pred CCCCCCHHHHHHHHHHhCCChh
Confidence 3346778888888888887754
No 224
>PF07957 DUF3294: Protein of unknown function (DUF3294); InterPro: IPR012917 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of mitochondrial ribosomal proteins, which appears to be fungal specific [].
Probab=22.23 E-value=3.1e+02 Score=21.25 Aligned_cols=74 Identities=20% Similarity=0.310 Sum_probs=46.1
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh----hcc--------cchh---hHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKLREEIS----KFI--------IEGD---LRREFSMN 76 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~----~~~--------i~~~---L~~~~~~~ 76 (121)
.......|..|.-|......++|.-.++=|- + ++-+.|.++|. .+. ++.. +....-++
T Consensus 124 ~~~fP~TL~eF~~l~~~~l~~L~~FYellpp--~-----~e~e~~~~~Le~~~e~~~i~~~~d~~i~~~~k~~s~~eld~ 196 (216)
T PF07957_consen 124 DFLFPKTLKEFKNLDDVKLIKLAKFYELLPP--L-----KEQEEFEEFLEGKVEDFHINEESDEEIEKELKKYSKEELDE 196 (216)
T ss_pred cccChhhHHHHHhccHHHHHHHHHHHHhcCC--c-----ccHHHHHHHHhccccccccCCCChHHHHHHHHhcCHHHHHH
Confidence 4456677899999999999999999997653 2 23344445552 221 2222 22234445
Q ss_pred HHHHHhhccccccccCCC
Q psy8858 77 IKRLIDLSCYRGIRHRKS 94 (121)
Q Consensus 77 I~rl~~i~~yRG~RH~~g 94 (121)
| .-.+.-|=|+||++|
T Consensus 197 i--fdelARylGlr~RRg 212 (216)
T PF07957_consen 197 I--FDELARYLGLRSRRG 212 (216)
T ss_pred H--HHHHHHHhCchhccC
Confidence 5 346678889988865
No 225
>PF09489 CbtB: Probable cobalt transporter subunit (CbtB); InterPro: IPR012667 This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems []. Evidence for this assignment includes 1) prediction of a single transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a protein (CbtA) predicted to have five additional transmembrane segments.
Probab=21.98 E-value=35 Score=20.71 Aligned_cols=10 Identities=40% Similarity=1.039 Sum_probs=8.2
Q ss_pred cccCCCCCcC
Q psy8858 89 IRHRKSLPCR 98 (121)
Q Consensus 89 ~RH~~gLpVR 98 (121)
.||..|.|+.
T Consensus 45 ~RH~~gfPCH 54 (54)
T PF09489_consen 45 TRHAAGFPCH 54 (54)
T ss_pred hHHhcCCCCC
Confidence 6899999874
No 226
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=21.95 E-value=99 Score=29.03 Aligned_cols=48 Identities=27% Similarity=0.347 Sum_probs=33.7
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCC-CCC---------cccCCCCHHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKI-STT---------KKIKDLNDNELEKLREE 59 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi-~p~---------~~~~~Ls~~qi~~L~~~ 59 (121)
+..|.++|..|+|||...+..|.+.-.- .|- .....++...++.|..+
T Consensus 748 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li~a 805 (973)
T PRK07135 748 NGKIFLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLIKA 805 (973)
T ss_pred CCEEEECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhccccCCCHHHHHHHHHC
Confidence 4569999999999999999999864321 121 12245777777777653
No 227
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=21.94 E-value=52 Score=22.64 Aligned_cols=19 Identities=42% Similarity=0.730 Sum_probs=15.0
Q ss_pred CcccCCCCHHHHHHHHHHH
Q psy8858 42 TKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 42 ~~~~~~Ls~~qi~~L~~~l 60 (121)
.+++.+||++|+++|.+.+
T Consensus 84 qkRle~l~~eE~~~L~~ei 102 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEI 102 (104)
T ss_pred HHHHHhCCHHHHHHHHHHh
Confidence 4577889999998887765
No 228
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=21.89 E-value=75 Score=30.24 Aligned_cols=47 Identities=32% Similarity=0.449 Sum_probs=32.6
Q ss_pred CeeeeeehhcccccCHHHHHHHHHHhCC-CCCc---------ccCCCCHHHHHHHHH
Q psy8858 12 NQHIIIGLTAIYGIGRSRAKKICEVTKI-STTK---------KIKDLNDNELEKLRE 58 (121)
Q Consensus 12 ~k~v~~aLt~I~GIG~~~A~~Ic~~lGi-~p~~---------~~~~Ls~~qi~~L~~ 58 (121)
+..|.++|..|+|||...+..|.+.=.- .|-. ....++...++.|..
T Consensus 815 ~~~I~~gL~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li~ 871 (1135)
T PRK05673 815 DGDIRYGLGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKVNKRVLESLIK 871 (1135)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccCCCCHHHHHHHHH
Confidence 4579999999999999999999865421 1211 223466677776665
No 229
>TIGR02459 CbtB cobalt transporter subunit CbtB (proposed). This model represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of a single trans-membrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a protein (CbtA) predicted to have five additional trans-membrane segments.
Probab=21.83 E-value=34 Score=21.26 Aligned_cols=10 Identities=40% Similarity=1.075 Sum_probs=8.1
Q ss_pred cccCCCCCcC
Q psy8858 89 IRHRKSLPCR 98 (121)
Q Consensus 89 ~RH~~gLpVR 98 (121)
-||..|.|+.
T Consensus 51 ~RH~~gFPCH 60 (60)
T TIGR02459 51 TRHSAAFPCH 60 (60)
T ss_pred HHHhcCCCCC
Confidence 5888998874
No 230
>PF02229 PC4: Transcriptional Coactivator p15 (PC4); InterPro: IPR003173 p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain []. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.; GO: 0003677 DNA binding, 0003713 transcription coactivator activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3PM7_B 2LTD_A 2LTT_B 3OBH_B 2L3A_B 2PHE_B 1PCF_B 2C62_B.
Probab=21.75 E-value=34 Score=20.48 Aligned_cols=20 Identities=30% Similarity=0.403 Sum_probs=14.8
Q ss_pred CCcccCCCCHHHHHHHHHHH
Q psy8858 41 TTKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 41 p~~~~~~Ls~~qi~~L~~~l 60 (121)
|.++--+|+.+|+..|.++|
T Consensus 37 P~kKGIsL~~~q~~~l~~~l 56 (56)
T PF02229_consen 37 PTKKGISLTPEQWKELKEAL 56 (56)
T ss_dssp EEEEEEEE-HHHHHHHHHH-
T ss_pred CcCCEEEcCHHHHHHHHhhC
Confidence 56667789999999998875
No 231
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=21.65 E-value=46 Score=29.68 Aligned_cols=39 Identities=18% Similarity=0.320 Sum_probs=24.5
Q ss_pred eeeehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 15 IIIGLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 15 v~~aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
+.+|| .|.|||..+|+.|++.++= -..+.+.+.+++..+
T Consensus 510 ~l~al-gi~~IG~~~ak~L~~~f~s--l~~l~~As~eeL~~i 548 (665)
T PRK07956 510 FLYAL-GIRHVGEKAAKALARHFGS--LEALRAASEEELAAV 548 (665)
T ss_pred hhHhh-hccCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhcc
Confidence 33444 7899999999999987741 122344455555544
No 232
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=21.59 E-value=87 Score=24.91 Aligned_cols=36 Identities=28% Similarity=0.483 Sum_probs=26.9
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~ 54 (121)
-+..++|||..+...+ ..+||..--.+-.++.+++.
T Consensus 177 pl~~l~gig~~~~~~L-~~~Gi~ti~dL~~~~~~~L~ 212 (344)
T cd01700 177 PVGDVWGIGRRTAKKL-NAMGIHTAGDLAQADPDLLR 212 (344)
T ss_pred ChhhcCccCHHHHHHH-HHcCCCcHHHHhcCCHHHHH
Confidence 4578899999999875 68899865555566666654
No 233
>TIGR02714 amido_AtzD_TrzD ring-opening amidohydrolases. Members of this family are are ring-opening amidohydrolases, including cyanuric acid amidohydrolase (EC 3.5.2.15) (AtzD and TrzD) and barbiturase. Note that barbiturase does not act as defined for EC 3.5.2.1 (barbiturate + water = malonate + urea) but rather catalyzes the ring-opening of barbituric acid to ureidomalonic acid (see Soong, et al., PubMed:11485332).
Probab=21.49 E-value=1.8e+02 Score=24.21 Aligned_cols=53 Identities=21% Similarity=0.350 Sum_probs=34.9
Q ss_pred CccCCCCeeeeeehh----cccccCHHH---------HHHHHHHhCCCCCcccCCCCHHHHHHHHHHHh
Q psy8858 6 GINIPNNQHIIIGLT----AIYGIGRSR---------AKKICEVTKISTTKKIKDLNDNELEKLREEIS 61 (121)
Q Consensus 6 ~~~~~~~k~v~~aLt----~I~GIG~~~---------A~~Ic~~lGi~p~~~~~~Ls~~qi~~L~~~l~ 61 (121)
|+++..+.-|.++.. .=|-||... ....++.+|++.. ..++++|..+|.+.|-
T Consensus 232 GvEL~~~eiiv~Gns~~~~g~l~IgH~VM~DAiD~~~v~~al~~~Gl~~~---~~~~~~~~~rlv~Vfa 297 (366)
T TIGR02714 232 GIELDRNQIIVVGNSRGVGGRLVIGHSVMKDAIDQAGVRAAIRDAGLELP---ERPHSDDLDQLVNVFA 297 (366)
T ss_pred chhhccceEEEEecCCCCCCCeeecchhhhhhhhhHHHHHHHHHhCCCCC---CCCChHHHHHHHHHHh
Confidence 556666666666653 334455443 3456678898874 6677889888888883
No 234
>PF03677 UPF0137: Uncharacterised protein family (UPF0137); InterPro: IPR005350 This family of bacterial proteins includes a number of plasmid-encoded virulence proteins.
Probab=21.43 E-value=1.3e+02 Score=23.61 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=21.8
Q ss_pred cccCCCCHHHHHHHHHHHhhcccchh
Q psy8858 43 KKIKDLNDNELEKLREEISKFIIEGD 68 (121)
Q Consensus 43 ~~~~~Ls~~qi~~L~~~l~~~~i~~~ 68 (121)
.-..+|+++|-++|...+.+|.++.+
T Consensus 32 ~~~~~Ls~~E~~~le~Ll~~y~~~d~ 57 (243)
T PF03677_consen 32 FFSISLSSKEKQRLENLLEKYNFSDE 57 (243)
T ss_pred cccccCCHHHHHHHHHHHHhcCCccc
Confidence 55667999999999999988887665
No 235
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=21.19 E-value=1.8e+02 Score=20.82 Aligned_cols=48 Identities=8% Similarity=0.143 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHhCCCCC------cccCCCCHHHHHHHHHHHhhcccchhhHHHH
Q psy8858 26 GRSRAKKICEVTKISTT------KKIKDLNDNELEKLREEISKFIIEGDLRREF 73 (121)
Q Consensus 26 G~~~A~~Ic~~lGi~p~------~~~~~Ls~~qi~~L~~~l~~~~i~~~L~~~~ 73 (121)
-+.++..|.+.+|+... ..+++||-+|+..|.+.-..-....+|+..+
T Consensus 72 ~Pp~s~ll~k~~g~~~gs~~p~~~~vG~it~~~v~eIA~~K~~d~~~~~l~~~v 125 (141)
T PRK00140 72 TPPASVLLKKAAGIEKGSGEPNKEKVGKITRAQVREIAETKMPDLNAADIEAAM 125 (141)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeEEeeEcHHHHHHHHHHHHHhhCCCcHHHHH
Confidence 56788899999998863 4678999999999988763223344555433
No 236
>PRK03348 DNA polymerase IV; Provisional
Probab=21.19 E-value=87 Score=26.34 Aligned_cols=38 Identities=24% Similarity=0.437 Sum_probs=28.3
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEKL 56 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~L 56 (121)
-+..++|||..++..+ ..+||..=.-+-.|+.+++.+.
T Consensus 181 Pv~~L~GIG~~t~~~L-~~lGI~TigDLa~l~~~~L~~~ 218 (454)
T PRK03348 181 PVRRLWGIGPVTEEKL-HRLGIETIGDLAALSEAEVANL 218 (454)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhcCCHHHHHHH
Confidence 4578999999988876 7899986555666677666543
No 237
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=20.49 E-value=1e+02 Score=24.48 Aligned_cols=36 Identities=31% Similarity=0.398 Sum_probs=26.1
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCC-HHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLN-DNELE 54 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls-~~qi~ 54 (121)
-+..++|||..++..+ ..+||..--.+-.++ ...+.
T Consensus 174 pi~~l~giG~~~~~~L-~~~Gi~ti~dl~~~~~~~~l~ 210 (343)
T cd00424 174 PLTDLPGIGAVTAKRL-EAVGINPIGDLLAASPDALLA 210 (343)
T ss_pred ChhhcCCCCHHHHHHH-HHcCCCcHHHHhcCCHHHHHH
Confidence 3578999999999886 689998755555556 44443
No 238
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=20.17 E-value=1.5e+02 Score=23.37 Aligned_cols=41 Identities=20% Similarity=0.456 Sum_probs=33.4
Q ss_pred hcccccC----HHHHHHHHHHhCCCC--CcccCCCCHHHHHHHHHHH
Q psy8858 20 TAIYGIG----RSRAKKICEVTKIST--TKKIKDLNDNELEKLREEI 60 (121)
Q Consensus 20 t~I~GIG----~~~A~~Ic~~lGi~p--~~~~~~Ls~~qi~~L~~~l 60 (121)
.++||.. ...+..+++.+|++. +.++++||.-+-.++.=+.
T Consensus 103 ~~l~~~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ia~ 149 (293)
T COG1131 103 ARLYGLSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLSIAL 149 (293)
T ss_pred HHHhCCChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHHHHH
Confidence 5788876 567889999999998 7889999998877665544
No 239
>PRK13618 psbV cytochrome c-550; Provisional
Probab=20.13 E-value=1.2e+02 Score=22.42 Aligned_cols=16 Identities=31% Similarity=0.690 Sum_probs=14.7
Q ss_pred cCCCCHHHHHHHHHHH
Q psy8858 45 IKDLNDNELEKLREEI 60 (121)
Q Consensus 45 ~~~Ls~~qi~~L~~~l 60 (121)
+++||++|+..|..+|
T Consensus 130 ~~~Lsd~eL~ava~yl 145 (163)
T PRK13618 130 MRNLTDKDLEAIAGHI 145 (163)
T ss_pred CCCCCHHHHHHHHHHH
Confidence 5689999999999998
No 240
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=20.05 E-value=1e+02 Score=24.17 Aligned_cols=37 Identities=27% Similarity=0.388 Sum_probs=27.3
Q ss_pred ehhcccccCHHHHHHHHHHhCCCCCcccCCCCHHHHHH
Q psy8858 18 GLTAIYGIGRSRAKKICEVTKISTTKKIKDLNDNELEK 55 (121)
Q Consensus 18 aLt~I~GIG~~~A~~Ic~~lGi~p~~~~~~Ls~~qi~~ 55 (121)
-++.++|||..++..+ ..+||..=..+-.++.+++.+
T Consensus 172 pl~~l~gig~~~~~~L-~~~Gi~ti~dl~~~~~~~L~~ 208 (334)
T cd03586 172 PVRKIPGVGKVTAEKL-KELGIKTIGDLAKLDVELLKK 208 (334)
T ss_pred CchhhCCcCHHHHHHH-HHcCCcCHHHHHcCCHHHHHH
Confidence 4578899999998765 678988655566667766654
Done!