Query 031813
Match_columns 152
No_of_seqs 112 out of 1037
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 05:42:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031813.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031813hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00134 40S ribosomal protein 100.0 7E-65 1.5E-69 389.4 11.5 152 1-152 1-154 (154)
2 PRK04053 rps13p 30S ribosomal 100.0 7.6E-64 1.6E-68 382.1 10.6 147 6-152 3-149 (149)
3 TIGR03629 arch_S13P archaeal r 100.0 5.3E-63 1.1E-67 375.9 9.7 144 8-152 1-144 (144)
4 COG0099 RpsM Ribosomal protein 100.0 4E-51 8.6E-56 299.7 7.3 119 12-152 1-121 (121)
5 KOG3311 Ribosomal protein S18 100.0 2E-49 4.4E-54 300.5 6.5 152 1-152 1-152 (152)
6 PRK05179 rpsM 30S ribosomal pr 100.0 8.1E-48 1.8E-52 285.5 9.7 111 12-144 1-111 (122)
7 CHL00137 rps13 ribosomal prote 100.0 7.3E-48 1.6E-52 285.7 9.2 111 12-144 1-111 (122)
8 TIGR03631 bact_S13 30S ribosom 100.0 2E-46 4.4E-51 274.8 9.6 111 14-146 1-111 (113)
9 PF00416 Ribosomal_S13: Riboso 100.0 2.4E-46 5.3E-51 271.7 5.0 107 14-142 1-107 (107)
10 COG1389 DNA topoisomerase VI, 98.9 1.1E-09 2.4E-14 96.5 3.5 103 7-122 244-354 (538)
11 PRK04184 DNA topoisomerase VI 98.8 4.3E-09 9.4E-14 94.7 5.7 91 23-122 256-350 (535)
12 TIGR01052 top6b DNA topoisomer 98.8 6.1E-09 1.3E-13 92.9 5.6 102 8-122 236-344 (488)
13 PF06831 H2TH: Formamidopyrimi 97.4 0.0002 4.2E-09 50.6 3.5 52 22-73 22-76 (92)
14 PRK01103 formamidopyrimidine/5 97.2 0.00041 8.8E-09 57.6 4.6 53 21-73 153-208 (274)
15 PRK14810 formamidopyrimidine-D 96.6 0.003 6.5E-08 52.5 4.8 52 22-73 153-207 (272)
16 PRK14811 formamidopyrimidine-D 96.6 0.0032 6.9E-08 52.3 4.9 51 23-73 143-196 (269)
17 PRK10445 endonuclease VIII; Pr 96.6 0.0029 6.4E-08 52.3 4.5 51 23-73 151-204 (263)
18 PRK13945 formamidopyrimidine-D 96.5 0.0038 8.3E-08 52.1 4.6 52 22-73 163-217 (282)
19 TIGR00577 fpg formamidopyrimid 96.4 0.0041 8.9E-08 51.7 4.4 52 22-73 154-208 (272)
20 PRK14867 DNA topoisomerase VI 96.2 0.0066 1.4E-07 56.4 4.9 82 31-122 409-494 (659)
21 PRK14868 DNA topoisomerase VI 95.6 0.022 4.8E-07 53.8 5.6 54 60-122 482-539 (795)
22 COG0266 Nei Formamidopyrimidin 94.6 0.053 1.1E-06 45.5 4.5 59 15-73 147-208 (273)
23 PF00633 HHH: Helix-hairpin-he 94.2 0.041 9E-07 31.1 2.0 18 29-46 12-29 (30)
24 PF05833 FbpA: Fibronectin-bin 93.9 0.023 5E-07 49.7 1.0 51 22-72 185-236 (455)
25 TIGR00275 flavoprotein, HI0933 92.7 0.093 2E-06 45.4 2.8 51 21-73 281-331 (400)
26 PF11798 IMS_HHH: IMS family H 90.4 0.19 4.2E-06 28.6 1.6 22 28-50 11-32 (32)
27 PF14520 HHH_5: Helix-hairpin- 90.1 0.042 9E-07 35.3 -1.6 26 26-52 3-28 (60)
28 PRK00274 ksgA 16S ribosomal RN 89.1 0.43 9.3E-06 39.3 3.4 52 21-73 219-270 (272)
29 PF10391 DNA_pol_lambd_f: Fing 88.2 0.41 8.8E-06 30.4 2.1 22 29-51 3-24 (52)
30 smart00278 HhH1 Helix-hairpin- 87.8 0.49 1.1E-05 25.4 2.0 20 29-48 2-21 (26)
31 COG0030 KsgA Dimethyladenosine 87.6 0.44 9.6E-06 39.7 2.5 48 21-73 209-256 (259)
32 PRK02515 psbU photosystem II c 86.2 0.58 1.3E-05 35.3 2.2 59 15-73 48-109 (132)
33 PRK14606 ruvA Holliday junctio 85.9 0.5 1.1E-05 37.5 1.9 22 28-49 108-129 (188)
34 COG3743 Uncharacterized conser 85.7 0.58 1.3E-05 35.4 2.0 44 28-72 67-110 (133)
35 PF09239 Topo-VIb_trans: Topoi 85.4 0.35 7.6E-06 37.6 0.7 35 86-122 1-39 (160)
36 KOG3311 Ribosomal protein S18 85.3 0.14 3E-06 39.5 -1.5 46 99-146 70-115 (152)
37 PRK14601 ruvA Holliday junctio 85.1 0.57 1.2E-05 37.0 1.9 21 28-48 108-128 (183)
38 PF03486 HI0933_like: HI0933-l 84.5 1.5 3.2E-05 38.6 4.4 51 21-73 288-339 (409)
39 PRK14603 ruvA Holliday junctio 84.2 0.67 1.4E-05 37.0 1.9 21 28-48 107-127 (197)
40 PRK14604 ruvA Holliday junctio 83.9 0.69 1.5E-05 36.8 1.9 21 28-48 108-128 (195)
41 PRK13901 ruvA Holliday junctio 83.8 0.71 1.5E-05 37.0 1.9 21 28-48 107-127 (196)
42 TIGR00755 ksgA dimethyladenosi 83.6 1.1 2.4E-05 36.3 2.9 58 9-70 195-252 (253)
43 PF00398 RrnaAD: Ribosomal RNA 83.5 0.46 1E-05 38.8 0.7 62 7-72 200-261 (262)
44 COG0632 RuvA Holliday junction 83.2 0.79 1.7E-05 36.9 1.9 21 28-48 108-128 (201)
45 PRK14602 ruvA Holliday junctio 82.7 0.82 1.8E-05 36.6 1.9 21 28-48 109-129 (203)
46 TIGR03252 uncharacterized HhH- 82.2 0.74 1.6E-05 36.4 1.4 29 21-49 108-136 (177)
47 COG1293 Predicted RNA-binding 81.9 1.5 3.3E-05 40.2 3.5 51 23-73 185-235 (564)
48 smart00279 HhH2 Helix-hairpin- 78.8 2.4 5.3E-05 24.7 2.5 33 8-47 3-35 (36)
49 PRK14605 ruvA Holliday junctio 78.5 0.73 1.6E-05 36.6 0.3 36 14-49 59-94 (194)
50 PRK14600 ruvA Holliday junctio 78.2 1.4 3E-05 34.9 1.7 20 28-48 108-127 (186)
51 PF02042 RWP-RK: RWP-RK domain 77.6 2.5 5.5E-05 26.9 2.5 26 33-58 24-51 (52)
52 PRK14605 ruvA Holliday junctio 77.4 1.6 3.4E-05 34.7 1.8 19 28-46 108-126 (194)
53 PF14520 HHH_5: Helix-hairpin- 77.0 2.3 4.9E-05 27.0 2.2 20 29-48 39-58 (60)
54 PF09883 DUF2110: Uncharacteri 76.7 2.9 6.2E-05 34.2 3.2 51 23-73 96-158 (225)
55 PF14579 HHH_6: Helix-hairpin- 76.0 2.7 5.8E-05 29.0 2.5 27 23-49 22-48 (90)
56 PRK00116 ruvA Holliday junctio 74.5 1.3 2.9E-05 34.9 0.7 60 14-73 59-130 (192)
57 TIGR00426 competence protein C 74.5 2.7 5.9E-05 27.3 2.1 29 20-48 8-37 (69)
58 PF14716 HHH_8: Helix-hairpin- 73.5 2.6 5.7E-05 27.6 1.9 20 29-48 48-67 (68)
59 PF11731 Cdd1: Pathogenicity l 73.4 2.9 6.3E-05 29.7 2.2 37 28-65 12-48 (93)
60 PRK01229 N-glycosylase/DNA lya 72.9 13 0.00028 30.0 6.1 70 25-108 115-185 (208)
61 cd00080 HhH2_motif Helix-hairp 72.3 3.1 6.8E-05 27.9 2.1 37 6-49 7-43 (75)
62 PF02371 Transposase_20: Trans 71.9 3.3 7.2E-05 28.3 2.1 20 29-48 3-22 (87)
63 TIGR01259 comE comEA protein. 71.7 2.8 6.1E-05 30.7 1.9 32 19-50 59-90 (120)
64 PF12836 HHH_3: Helix-hairpin- 71.7 1.1 2.5E-05 29.0 -0.2 49 21-69 7-62 (65)
65 PF12826 HHH_2: Helix-hairpin- 71.1 2.5 5.4E-05 27.5 1.3 18 32-49 7-24 (64)
66 TIGR00084 ruvA Holliday juncti 69.4 3.3 7.2E-05 32.8 1.9 20 28-47 107-126 (191)
67 TIGR00084 ruvA Holliday juncti 68.2 1.2 2.5E-05 35.4 -0.9 35 13-47 57-91 (191)
68 cd00056 ENDO3c endonuclease II 67.8 3.1 6.7E-05 31.0 1.4 45 23-71 78-122 (158)
69 PF14490 HHH_4: Helix-hairpin- 67.2 3.9 8.4E-05 28.4 1.7 26 28-53 45-71 (94)
70 smart00478 ENDO3c endonuclease 67.0 3.9 8.5E-05 30.1 1.8 23 26-48 70-92 (149)
71 PRK12278 50S ribosomal protein 66.4 5 0.00011 32.8 2.4 45 28-73 158-202 (221)
72 smart00483 POLXc DNA polymeras 66.2 4.9 0.00011 34.4 2.4 26 26-52 87-112 (334)
73 TIGR00615 recR recombination p 66.1 3.2 6.9E-05 33.3 1.2 41 25-73 8-48 (195)
74 PF12826 HHH_2: Helix-hairpin- 66.0 4.9 0.00011 26.0 1.9 21 29-49 36-56 (64)
75 COG0353 RecR Recombinational D 65.7 2.8 6E-05 33.8 0.8 87 25-128 9-108 (198)
76 PRK14606 ruvA Holliday junctio 65.5 1.7 3.6E-05 34.5 -0.5 34 14-47 59-92 (188)
77 PRK14602 ruvA Holliday junctio 65.5 2.2 4.9E-05 34.1 0.2 37 13-49 59-95 (203)
78 COG0632 RuvA Holliday junction 65.1 1.4 3.1E-05 35.4 -1.0 38 12-49 57-94 (201)
79 PRK00076 recR recombination pr 64.8 3.4 7.4E-05 33.1 1.2 41 25-73 8-48 (196)
80 PRK14601 ruvA Holliday junctio 64.7 1.8 3.9E-05 34.2 -0.4 35 13-47 58-92 (183)
81 cd00141 NT_POLXc Nucleotidyltr 64.5 5.6 0.00012 33.5 2.5 25 27-52 84-108 (307)
82 PRK14600 ruvA Holliday junctio 64.1 1.9 4.2E-05 34.1 -0.3 35 14-48 59-93 (186)
83 PRK10702 endonuclease III; Pro 63.6 5.2 0.00011 32.1 2.0 23 26-48 107-129 (211)
84 PRK08609 hypothetical protein; 63.2 6.1 0.00013 36.2 2.6 25 28-52 88-112 (570)
85 TIGR01084 mutY A/G-specific ad 63.1 4.6 9.9E-05 33.8 1.7 29 17-48 97-125 (275)
86 TIGR01083 nth endonuclease III 62.8 5 0.00011 31.3 1.8 23 26-48 104-126 (191)
87 PRK13901 ruvA Holliday junctio 62.5 2.1 4.7E-05 34.2 -0.4 34 14-47 58-91 (196)
88 PRK14603 ruvA Holliday junctio 61.6 2.2 4.7E-05 34.0 -0.5 35 13-47 57-91 (197)
89 COG2081 Predicted flavoprotein 61.2 11 0.00024 33.5 3.8 50 21-73 283-332 (408)
90 PRK13844 recombination protein 61.1 4.4 9.6E-05 32.6 1.2 41 25-73 12-52 (200)
91 PRK12311 rpsB 30S ribosomal pr 61.0 4.6 0.0001 34.8 1.4 45 27-72 262-306 (326)
92 cd01104 HTH_MlrA-CarA Helix-Tu 59.9 28 0.00061 21.8 4.7 43 30-72 6-52 (68)
93 TIGR01448 recD_rel helicase, p 59.4 11 0.00024 35.6 3.6 42 32-73 88-139 (720)
94 COG0177 Nth Predicted EndoIII- 56.8 30 0.00064 28.1 5.3 40 27-71 108-148 (211)
95 PRK13910 DNA glycosylase MutY; 55.9 7.8 0.00017 32.7 1.9 22 27-48 71-92 (289)
96 PRK03980 flap endonuclease-1; 55.2 11 0.00025 31.7 2.8 34 7-49 177-210 (292)
97 COG2231 Uncharacterized protei 55.1 8.8 0.00019 31.2 2.0 37 18-54 103-141 (215)
98 PRK14604 ruvA Holliday junctio 55.0 3.3 7.1E-05 33.0 -0.5 34 14-47 59-92 (195)
99 PRK10880 adenine DNA glycosyla 55.0 8.1 0.00018 33.5 1.9 23 26-48 107-129 (350)
100 PRK13913 3-methyladenine DNA g 54.6 8.4 0.00018 31.3 1.8 23 26-48 119-141 (218)
101 PRK14667 uvrC excinuclease ABC 54.3 7.6 0.00016 35.8 1.7 44 22-67 508-551 (567)
102 PRK00116 ruvA Holliday junctio 54.0 9.1 0.0002 30.1 1.9 21 29-49 109-129 (192)
103 PRK12766 50S ribosomal protein 53.7 8.2 0.00018 31.8 1.6 20 30-49 38-57 (232)
104 cd00128 XPG Xeroderma pigmento 51.9 14 0.0003 30.9 2.8 34 7-49 211-244 (316)
105 COG0258 Exo 5'-3' exonuclease 51.6 13 0.00028 31.2 2.5 32 8-49 185-219 (310)
106 PRK14670 uvrC excinuclease ABC 51.4 8.5 0.00019 35.6 1.5 39 26-66 512-550 (574)
107 PRK10308 3-methyl-adenine DNA 51.3 32 0.0007 28.7 4.9 30 26-55 205-234 (283)
108 PTZ00217 flap endonuclease-1; 49.4 16 0.00034 32.2 2.8 34 7-49 223-256 (393)
109 COG3415 Transposase and inacti 49.2 38 0.00081 25.7 4.5 45 29-73 26-78 (138)
110 PRK00558 uvrC excinuclease ABC 48.9 16 0.00035 33.8 2.9 43 22-66 537-579 (598)
111 PRK14669 uvrC excinuclease ABC 48.8 12 0.00026 34.9 2.1 42 24-67 548-589 (624)
112 PHA02564 V virion protein; Pro 48.5 39 0.00085 25.7 4.5 34 39-73 86-119 (141)
113 PTZ00338 dimethyladenosine tra 47.9 28 0.00061 29.2 4.0 34 39-73 255-288 (294)
114 KOG2518 5'-3' exonuclease [Rep 47.2 16 0.00034 33.7 2.5 60 5-73 211-277 (556)
115 PF01698 FLO_LFY: Floricaula / 45.7 6.9 0.00015 34.5 0.0 77 32-126 56-132 (386)
116 TIGR00588 ogg 8-oxoguanine DNA 45.6 14 0.00029 31.4 1.8 44 25-71 217-260 (310)
117 PRK14668 uvrC excinuclease ABC 43.8 12 0.00026 34.6 1.3 39 26-66 523-561 (577)
118 cd00008 53EXOc 5'-3' exonuclea 43.4 18 0.00039 29.3 2.1 20 30-49 185-204 (240)
119 PRK09482 flap endonuclease-lik 43.4 18 0.00039 30.1 2.1 20 30-49 184-203 (256)
120 smart00475 53EXOc 5'-3' exonuc 42.7 19 0.0004 29.8 2.1 20 30-49 188-207 (259)
121 PRK14896 ksgA 16S ribosomal RN 42.6 36 0.00077 27.6 3.8 63 9-73 192-256 (258)
122 PF11338 DUF3140: Protein of u 42.6 35 0.00075 24.2 3.2 35 34-72 33-67 (92)
123 PRK14976 5'-3' exonuclease; Pr 41.5 20 0.00042 30.0 2.1 19 31-49 194-212 (281)
124 PF01367 5_3_exonuc: 5'-3' exo 41.0 2.9 6.4E-05 29.9 -2.5 19 31-49 21-39 (101)
125 TIGR03674 fen_arch flap struct 40.9 25 0.00054 30.1 2.7 57 7-74 224-283 (338)
126 KOG0494 Transcription factor C 39.4 14 0.00029 31.4 0.8 57 58-131 147-227 (332)
127 PF00542 Ribosomal_L12: Riboso 39.3 12 0.00026 24.9 0.4 45 26-73 16-60 (68)
128 cd01702 PolY_Pol_eta DNA Polym 39.2 21 0.00046 30.7 2.0 38 28-65 182-221 (359)
129 PRK13766 Hef nuclease; Provisi 39.1 24 0.00053 33.0 2.5 24 26-49 713-736 (773)
130 COG2938 Uncharacterized conser 38.8 28 0.00061 24.8 2.2 41 54-96 39-79 (94)
131 COG1948 MUS81 ERCC4-type nucle 38.8 23 0.0005 29.6 2.1 41 24-66 178-218 (254)
132 PF04760 IF2_N: Translation in 38.6 19 0.00041 22.2 1.2 44 29-72 8-52 (54)
133 PRK14672 uvrC excinuclease ABC 37.6 17 0.00038 34.4 1.3 43 22-66 602-644 (691)
134 PRK14671 uvrC excinuclease ABC 36.9 17 0.00037 33.9 1.1 50 16-67 557-606 (621)
135 COG0122 AlkA 3-methyladenine D 36.6 23 0.0005 29.7 1.8 30 25-54 195-224 (285)
136 COG1936 Predicted nucleotide k 36.5 31 0.00066 27.4 2.3 24 28-51 3-26 (180)
137 PRK12373 NADH dehydrogenase su 36.4 29 0.00064 30.8 2.5 45 28-73 323-367 (400)
138 PRK07945 hypothetical protein; 36.3 24 0.00053 30.1 1.9 21 29-49 50-70 (335)
139 PF06514 PsbU: Photosystem II 35.5 42 0.00091 23.9 2.7 58 16-73 11-71 (93)
140 PF02318 FYVE_2: FYVE-type zin 34.3 45 0.00097 24.1 2.8 17 57-73 1-17 (118)
141 PRK07373 DNA polymerase III su 33.5 34 0.00073 30.7 2.4 25 23-47 109-133 (449)
142 COG1059 Thermostable 8-oxoguan 32.7 25 0.00054 28.4 1.3 25 27-51 120-144 (210)
143 KOG2251 Homeobox transcription 30.9 36 0.00077 28.0 1.9 32 58-90 43-92 (228)
144 PF14635 HHH_7: Helix-hairpin- 30.9 15 0.00032 26.6 -0.2 42 8-49 27-71 (104)
145 PRK04301 radA DNA repair and r 30.8 40 0.00086 28.2 2.3 39 27-66 5-43 (317)
146 COG1555 ComEA DNA uptake prote 30.5 54 0.0012 24.9 2.8 22 27-48 96-117 (149)
147 PRK14666 uvrC excinuclease ABC 30.2 30 0.00065 32.9 1.6 39 25-65 634-672 (694)
148 TIGR00194 uvrC excinuclease AB 29.9 39 0.00085 31.3 2.3 26 24-49 537-562 (574)
149 PF13442 Cytochrome_CBB3: Cyto 29.7 51 0.0011 20.6 2.2 14 58-71 54-67 (67)
150 smart00483 POLXc DNA polymeras 28.9 34 0.00074 29.2 1.6 22 29-50 49-70 (334)
151 COG1636 Uncharacterized protei 28.6 43 0.00093 27.1 2.0 72 62-148 127-198 (204)
152 TIGR00600 rad2 DNA excision re 28.5 48 0.001 33.0 2.7 35 7-50 854-888 (1034)
153 cd00141 NT_POLXc Nucleotidyltr 28.3 24 0.00053 29.7 0.6 23 29-51 46-68 (307)
154 TIGR02236 recomb_radA DNA repa 27.7 42 0.00091 27.7 1.9 36 30-66 1-36 (310)
155 COG1131 CcmA ABC-type multidru 27.7 2.1E+02 0.0045 23.8 6.1 92 12-108 80-184 (293)
156 PF13276 HTH_21: HTH-like doma 27.7 50 0.0011 20.5 1.9 34 20-53 20-55 (60)
157 KOG1921 Endonuclease III [Repl 27.3 34 0.00073 28.8 1.3 38 8-45 138-176 (286)
158 PF03118 RNA_pol_A_CTD: Bacter 26.6 46 0.001 21.7 1.6 21 28-48 44-64 (66)
159 PF06207 DUF1002: Protein of u 26.6 1.5E+02 0.0033 24.2 4.9 27 42-75 182-208 (225)
160 PF01418 HTH_6: Helix-turn-hel 26.3 61 0.0013 21.4 2.2 24 29-52 39-62 (77)
161 TIGR00575 dnlj DNA ligase, NAD 26.3 30 0.00066 32.4 0.9 23 26-49 497-519 (652)
162 KOG0821 Predicted ribosomal RN 26.1 89 0.0019 26.3 3.5 35 39-73 270-304 (326)
163 TIGR00596 rad1 DNA repair prot 25.9 47 0.001 32.1 2.1 39 26-67 756-794 (814)
164 PF06394 Pepsin-I3: Pepsin inh 25.8 41 0.00089 23.0 1.3 21 53-73 34-54 (76)
165 COG0322 UvrC Nuclease subunit 25.7 47 0.001 30.9 2.0 43 23-67 525-567 (581)
166 COG1194 MutY A/G-specific DNA 25.4 46 0.00099 29.0 1.8 36 9-47 97-132 (342)
167 PF13331 DUF4093: Domain of un 24.8 23 0.00049 24.7 -0.1 40 21-66 45-84 (87)
168 PF13613 HTH_Tnp_4: Helix-turn 24.4 60 0.0013 19.9 1.8 21 28-48 23-43 (53)
169 PF15614 WHIM3: WSTF, HB1, Itc 24.3 1.5E+02 0.0031 18.4 3.4 37 60-117 6-42 (46)
170 KOG2875 8-oxoguanine DNA glyco 24.1 34 0.00073 29.3 0.7 22 26-47 216-237 (323)
171 PF14053 DUF4248: Domain of un 23.7 1.1E+02 0.0024 20.3 3.0 47 26-74 9-69 (69)
172 cd08334 DED_Caspase_8_10_repea 23.2 82 0.0018 21.5 2.4 62 57-121 13-82 (83)
173 COG1796 POL4 DNA polymerase IV 23.2 58 0.0012 28.2 1.9 21 29-49 54-74 (326)
174 PRK05898 dnaE DNA polymerase I 23.1 1.4E+02 0.003 29.6 4.7 26 23-48 747-772 (971)
175 KOG1647 Vacuolar H+-ATPase V1 23.1 48 0.001 27.4 1.4 23 99-121 187-209 (255)
176 smart00530 HTH_XRE Helix-turn- 23.0 71 0.0015 17.5 1.8 13 60-72 38-50 (56)
177 COG1111 MPH1 ERCC4-like helica 23.0 54 0.0012 30.2 1.8 85 23-124 161-249 (542)
178 TIGR00575 dnlj DNA ligase, NAD 22.8 46 0.001 31.2 1.4 33 32-64 436-468 (652)
179 PF10662 PduV-EutP: Ethanolami 22.8 76 0.0017 24.1 2.4 37 37-73 107-143 (143)
180 PRK02362 ski2-like helicase; P 22.6 61 0.0013 30.4 2.2 39 28-67 652-690 (737)
181 TIGR00608 radc DNA repair prot 22.4 46 0.001 26.9 1.2 21 30-50 62-82 (218)
182 PRK12766 50S ribosomal protein 22.3 74 0.0016 26.3 2.3 38 29-67 4-41 (232)
183 PRK07956 ligA NAD-dependent DN 22.1 41 0.00088 31.7 0.9 35 31-65 448-482 (665)
184 PF13443 HTH_26: Cro/C1-type H 22.0 1.6E+02 0.0034 18.0 3.4 37 29-72 15-51 (63)
185 PF00034 Cytochrom_C: Cytochro 21.9 86 0.0019 19.6 2.3 16 58-73 74-89 (91)
186 PF11460 DUF3007: Protein of u 21.8 45 0.00098 24.2 0.9 20 53-72 84-103 (104)
187 PRK03352 DNA polymerase IV; Va 21.3 80 0.0017 26.6 2.5 36 29-65 178-213 (346)
188 PRK13618 psbV cytochrome c-550 20.8 1.1E+02 0.0023 23.8 2.9 17 56-72 130-146 (163)
189 PF09079 Cdc6_C: CDC6, C termi 20.7 1.7E+02 0.0038 19.3 3.6 30 38-73 22-51 (85)
190 PRK08609 hypothetical protein; 20.7 38 0.00082 31.1 0.4 23 29-51 49-71 (570)
191 PF14794 DUF4479: Domain of un 20.5 83 0.0018 21.1 1.9 18 56-73 45-62 (73)
192 PF02879 PGM_PMM_II: Phosphogl 20.3 38 0.00083 23.2 0.2 40 11-50 6-46 (104)
193 PRK07956 ligA NAD-dependent DN 20.2 44 0.00096 31.4 0.7 23 26-49 510-532 (665)
194 PF07700 HNOB: Heme NO binding 20.2 1.5E+02 0.0032 22.4 3.5 37 37-73 18-57 (171)
195 KOG0202 Ca2+ transporting ATPa 20.0 1.4E+02 0.003 29.4 4.0 35 32-66 605-650 (972)
No 1
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=7e-65 Score=389.36 Aligned_cols=152 Identities=72% Similarity=1.163 Sum_probs=146.8
Q ss_pred CCCC--CccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCcc
Q 031813 1 MSLV--ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFK 78 (152)
Q Consensus 1 ~~~~--~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ 78 (152)
|+++ ++++|+|||||+|||||++|+|.+||++|||||..+|.+||++|||||++++++||++|++.|.++|++|.+|.
T Consensus 1 ~~~~~~~~~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~ 80 (154)
T PTZ00134 1 MSLTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFK 80 (154)
T ss_pred CCccccchhhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCC
Confidence 4455 33589999999999999999999999999999999999999999999999999999999999999999987899
Q ss_pred CCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813 79 IPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 79 ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k 152 (152)
+|+||+||++|+.||+|.|+||+||++.+++||+||++|+||||+||++||||||||||||||||+++||++||
T Consensus 81 iP~w~~nr~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~~~gv~~kk 154 (154)
T PTZ00134 81 IPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK 154 (154)
T ss_pred CChhHhhccccccccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCccccccceeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=7.6e-64 Score=382.12 Aligned_cols=147 Identities=44% Similarity=0.804 Sum_probs=144.9
Q ss_pred ccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccC
Q 031813 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLN 85 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~n 85 (152)
+++|++|+||+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++|+.+.+|+||+|
T Consensus 3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~N 82 (149)
T PRK04053 3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLN 82 (149)
T ss_pred hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999888999999999
Q ss_pred ccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813 86 RQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 86 r~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k 152 (152)
|++|+.||++.|+||+||++.+++||+||++|+||||+||.+||||||||||||||||+++||+|||
T Consensus 83 r~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg~~~gv~~kk 149 (149)
T PRK04053 83 RRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTGGTVGVSRKK 149 (149)
T ss_pred cccccccCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999997
No 3
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=100.00 E-value=5.3e-63 Score=375.85 Aligned_cols=144 Identities=49% Similarity=0.880 Sum_probs=141.8
Q ss_pred ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCcc
Q 031813 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQ 87 (152)
Q Consensus 8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~ 87 (152)
+|+||+||+|+|||++|+|.+||++|||||+.+|.+||+++|||+++++++||++|+++|.++|++ ..|.+|+||+||+
T Consensus 1 ~~~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~~Nr~ 79 (144)
T TIGR03629 1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWLLNRR 79 (144)
T ss_pred CcceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHHhhcc
Confidence 589999999999999999999999999999999999999999999999999999999999999998 6799999999999
Q ss_pred CCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813 88 KDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 88 ~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k 152 (152)
+|+.||++.|+||+||++.+++||+||++|+||||+||.+||||||||||||||||+++||++||
T Consensus 80 ~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~~~gv~~kk 144 (144)
T TIGR03629 80 KDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGRTVGVSRKK 144 (144)
T ss_pred cccccCccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999997
No 4
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-51 Score=299.67 Aligned_cols=119 Identities=44% Similarity=0.701 Sum_probs=115.1
Q ss_pred hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~ 91 (152)
|+||+|+|||++|.|.+|||+|||||..+|.+||+++||||++++++|||||+++|.+++++
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~------------------ 62 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN------------------ 62 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh------------------
Confidence 79999999999999999999999999999999999999999999999999999999999986
Q ss_pred CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCC--ccceeeeccC
Q 031813 92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR--GKTVGVSKKR 152 (152)
Q Consensus 92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart--~~~~gv~~~k 152 (152)
.|+||.||++++++||+||++|+||||+||..|||||||||+||||| |.++||.+||
T Consensus 63 ----~~~vegDLr~~v~~dIkRl~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 63 ----KYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred ----cCeehhHHHHHHHHHHHHHHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 23569999999999999999999999999999999999999999999 9999999987
No 5
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-49 Score=300.45 Aligned_cols=152 Identities=70% Similarity=1.140 Sum_probs=150.4
Q ss_pred CCCCCccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCC
Q 031813 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIP 80 (152)
Q Consensus 1 ~~~~~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip 80 (152)
|||+-++.||+|+||++++++++++|.|||++|||||...|..+|+++|+++.+++++|+++|++.+..++++|..|.+|
T Consensus 1 msl~~~~~~q~i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~ 80 (152)
T KOG3311|consen 1 MSLVIPEAFQHILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIP 80 (152)
T ss_pred CceecchhHHHHHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCc
Confidence 89999889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031813 81 DWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152 (152)
Q Consensus 81 ~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~gv~~~k 152 (152)
.|++|+++|..+|+..|++.++++..++++|+|++++.||||+||.+|||||||||+|||+.|++|||++||
T Consensus 81 ~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 81 DWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGRRGKTVGVSGKK 152 (152)
T ss_pred hHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccccccceeeecccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997
No 6
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=8.1e-48 Score=285.53 Aligned_cols=111 Identities=34% Similarity=0.527 Sum_probs=107.6
Q ss_pred hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~ 91 (152)
||||+|||||++|+|.+||++|||||..+|.+||+++||||++++++|+++|++.|.++|+++ |
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~--~-------------- 64 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKN--Y-------------- 64 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhh--c--------------
Confidence 899999999999999999999999999999999999999999999999999999999999873 3
Q ss_pred CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813 92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK 144 (152)
Q Consensus 92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~ 144 (152)
.+|+||++.+++||+||++|+||||+||++|||||||||||||||++
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~TNart~k 111 (122)
T PRK05179 65 ------KVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 111 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhcceeeeecccCCCCCCCcCCccccccC
Confidence 36999999999999999999999999999999999999999999998
No 7
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=7.3e-48 Score=285.74 Aligned_cols=111 Identities=31% Similarity=0.499 Sum_probs=107.4
Q ss_pred hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCC
Q 031813 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~ 91 (152)
||||+||+||++|+|.+||++|||||..+|.+||+++||||++++++||++|+++|.++|++ +|.
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~~------------- 65 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NYQ------------- 65 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hCc-------------
Confidence 79999999999999999999999999999999999999999999999999999999999986 353
Q ss_pred CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031813 92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK 144 (152)
Q Consensus 92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~ 144 (152)
+|+||++.+++||+||++|+||||+||.+|||||||||||||||++
T Consensus 66 -------i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~tNarT~k 111 (122)
T CHL00137 66 -------VEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRR 111 (122)
T ss_pred -------chHHHHHHHHHHHHHHHHhCchhcccccCCCCCCCCcCCccccccC
Confidence 5999999999999999999999999999999999999999999997
No 8
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=100.00 E-value=2e-46 Score=274.81 Aligned_cols=111 Identities=35% Similarity=0.519 Sum_probs=106.4
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCC
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg 93 (152)
||+|+|||++|+|.+||++|||||..+|.+||+++||||++++++|+++|++.|.++|+++ |
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~--~---------------- 62 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAK--Y---------------- 62 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhc--C----------------
Confidence 7999999999999999999999999999999999999999999999999999999999873 3
Q ss_pred chhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccce
Q 031813 94 KYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV 146 (152)
Q Consensus 94 ~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~ 146 (152)
.||+||++.+++||+||++|+||||+||++|||||||||||||||++..
T Consensus 63 ----~i~~~L~~~~~~dI~rl~~I~syRG~RH~~gLpVRGQRT~TNart~k~~ 111 (113)
T TIGR03631 63 ----KVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGP 111 (113)
T ss_pred ----cchHHHHHHHHHHHHHHHHhcceeccccccCCCCCCCcCCccccccCCC
Confidence 3699999999999999999999999999999999999999999999853
No 9
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=100.00 E-value=2.4e-46 Score=271.72 Aligned_cols=107 Identities=45% Similarity=0.768 Sum_probs=101.7
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCC
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg 93 (152)
||+||+||++|+|.+||++|||||+.+|.+||+++||+|+.++++|+++|+++|.++|++
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~-------------------- 60 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK-------------------- 60 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--------------------
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--------------------
Confidence 799999999999999999999999999999999999999999999999999999999987
Q ss_pred chhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCC
Q 031813 94 KYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR 142 (152)
Q Consensus 94 ~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart 142 (152)
.|++|+||++.+++||+||++|+||||+||.+|||||||||||||||
T Consensus 61 --~~~i~~~L~~~~~~~i~rl~~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 61 --NHLIENDLKRQVRENIKRLKKIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp --HSTCHHHHHHHHHHHHHHHHHHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred --hccccchHHHHHHHHHHHHHHHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 24579999999999999999999999999999999999999999986
No 10
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=98.88 E-value=1.1e-09 Score=96.49 Aligned_cols=103 Identities=19% Similarity=0.292 Sum_probs=89.0
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCC----HHHHHHHHHHHhCCCCccCCcc
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS----AAELDNLMVVVANPRQFKIPDW 82 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls----~~ei~~L~~~l~~~~~~~ip~w 82 (152)
+++..|++ .-+..+.-.|+..+|..||..+|..+|+.+|++|++.+.+|+ .+|..+|.+++.+ |.
T Consensus 244 ~~L~~M~~----~T~~~tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~---~~---- 312 (538)
T COG1389 244 DTLKKMAH----RTRRSTVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKK---MK---- 312 (538)
T ss_pred HHHHHHHH----HhhhhhHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHh---Cc----
Confidence 34555555 234455568889999999999999999999999999999999 9999999999987 53
Q ss_pred ccCccCCCCCCchhhhhhhhHHHHHHh----hhhhhhccceeec
Q 031813 83 FLNRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG 122 (152)
Q Consensus 83 ~~nr~~D~~sg~~~~lie~~L~~~~~~----~I~rl~~i~syRG 122 (152)
|+.|+.|++||++.++|+.+|+..++. .+.| +.+.|+|
T Consensus 313 fm~Pptd~LsPIGee~ie~gLk~~~~pefv~avTR--kPkvy~G 354 (538)
T COG1389 313 FMAPPTDGLSPIGEELIEKGLKSILNPEFVAAVTR--KPKVYRG 354 (538)
T ss_pred ccCCCccccCcccHHHHHHHHHHhcCchheeeecc--CccccCC
Confidence 366799999999999999999999977 6788 9999999
No 11
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=98.83 E-value=4.3e-09 Score=94.68 Aligned_cols=91 Identities=21% Similarity=0.329 Sum_probs=80.4
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhh
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNA 102 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~ 102 (152)
.....|+-.+|..||..+|..||+.+|+++++++.+|+++|+..|.+++.+ +++ +.|+.||+||++.++|+.+
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~---~~~----~~pp~~~lspige~~i~~g 328 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKK---YKF----MAPPTACLSPIGEELIEKG 328 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHh---ccC----cCCCCccCCCCCHHHHHHH
Confidence 455688889999999999999999999999999999999999999999997 543 4557789999999999999
Q ss_pred HHHHHHh----hhhhhhccceeec
Q 031813 103 LDMKLRD----DLERLKKIRNHRG 122 (152)
Q Consensus 103 L~~~~~~----~I~rl~~i~syRG 122 (152)
|+..++. .+.| +.+.|+|
T Consensus 329 l~~~~~p~f~~~~tr--~p~~y~g 350 (535)
T PRK04184 329 LKKILKPEFVAAVTR--KPKVYSG 350 (535)
T ss_pred HHHhcCccEEEEecc--CCcccCC
Confidence 9998877 4566 8888886
No 12
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=98.80 E-value=6.1e-09 Score=92.86 Aligned_cols=102 Identities=18% Similarity=0.275 Sum_probs=85.0
Q ss_pred ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCC---CCCCCCCCCHHHHHHHHHHHhCCCCccCCcccc
Q 031813 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVANPRQFKIPDWFL 84 (152)
Q Consensus 8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~---~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~ 84 (152)
+++.|++-.. ......|+..+|..||..+|..||+.+|++ +++++.+|+++|+..|.+++.+ .++ +
T Consensus 236 ~l~~m~~~t~----~~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~---~~~----~ 304 (488)
T TIGR01052 236 DLKSMARSTR----ASTLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE---MKF----M 304 (488)
T ss_pred HHHHHHHhcC----cccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh---cCC----C
Confidence 4455544332 245557888999999999999999999999 9999999999999999999987 332 4
Q ss_pred CccCCCCCCchhhhhhhhHHHHHHh----hhhhhhccceeec
Q 031813 85 NRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG 122 (152)
Q Consensus 85 nr~~D~~sg~~~~lie~~L~~~~~~----~I~rl~~i~syRG 122 (152)
.|+.||+||++.++|+.+|+..++. .+.| +.+.|+|
T Consensus 305 ~P~~~~lspige~~i~~gl~~~~~p~f~~~~tr--~p~~y~g 344 (488)
T TIGR01052 305 APPTDGLSPIGEENIEKGLKEILQPEFVGAVTR--SPKTYRG 344 (488)
T ss_pred CCCccccCCCCHHHHHHHHHHhcCccEEEEecc--CCccccC
Confidence 5688999999999999999998777 4667 8888987
No 13
>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=97.37 E-value=0.0002 Score=50.57 Aligned_cols=52 Identities=29% Similarity=0.376 Sum_probs=42.8
Q ss_pred CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+++|..+| +-|.|||...|.+||-++||+|..++++|+++|+..|-+.+..
T Consensus 22 ~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~ 76 (92)
T PF06831_consen 22 RRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKR 76 (92)
T ss_dssp CCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHH
T ss_pred CcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 467777666 4599999999999999999999999999999999998887754
No 14
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=97.24 E-value=0.00041 Score=57.61 Aligned_cols=53 Identities=30% Similarity=0.369 Sum_probs=48.6
Q ss_pred CCCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 21 DGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
..+..|.-+| +-+-|||...|.+||-++||+|..++++||++|++.|-+.+.+
T Consensus 153 ~~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~ 208 (274)
T PRK01103 153 KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA 208 (274)
T ss_pred cCCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 3567888889 8899999999999999999999999999999999999888765
No 15
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.65 E-value=0.003 Score=52.52 Aligned_cols=52 Identities=25% Similarity=0.337 Sum_probs=45.1
Q ss_pred CCeeheeehhc---ccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 22 GKQKIMFALTS---IKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aL~~---i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+.+|..+|.. |-|||...|.+||-++||+|..++++||++|++.|.+++.+
T Consensus 153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~ 207 (272)
T PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE 207 (272)
T ss_pred CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence 45667777755 49999999999999999999999999999999999887654
No 16
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.63 E-value=0.0032 Score=52.32 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=44.3
Q ss_pred Ceeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 23 ~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
+++|.-+| +-|-|||...|.+||-.++|+|..++++||++|++.|-+.+..
T Consensus 143 ~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 196 (269)
T PRK14811 143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIRE 196 (269)
T ss_pred CCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHHH
Confidence 66776666 3489999999999999999999999999999999998766653
No 17
>PRK10445 endonuclease VIII; Provisional
Probab=96.61 E-value=0.0029 Score=52.34 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=44.0
Q ss_pred Ceeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 23 ~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
+++|.-+| +-|-|||...|.+||-.++|+|..++++||++|++.|-+.+.+
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 204 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLD 204 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence 45665555 3388999999999999999999999999999999999888765
No 18
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.50 E-value=0.0038 Score=52.10 Aligned_cols=52 Identities=27% Similarity=0.347 Sum_probs=45.0
Q ss_pred CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
...+|.-+| +-|-|||...|.+||-.++|+|..++++||++|++.|.+.+..
T Consensus 163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~ 217 (282)
T PRK13945 163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE 217 (282)
T ss_pred CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 356666555 3489999999999999999999999999999999998887764
No 19
>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=96.45 E-value=0.0041 Score=51.67 Aligned_cols=52 Identities=31% Similarity=0.346 Sum_probs=45.2
Q ss_pred CCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 22 ~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+.+|.-+| +-|-|||...|.+||-.++|+|..++++||++|++.|-+.+.+
T Consensus 154 ~~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 208 (272)
T TIGR00577 154 SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE 208 (272)
T ss_pred CCCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence 456666666 4488999999999999999999999999999999999888765
No 20
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=96.22 E-value=0.0066 Score=56.40 Aligned_cols=82 Identities=13% Similarity=0.127 Sum_probs=61.0
Q ss_pred hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHh-
Q 031813 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD- 109 (152)
Q Consensus 31 ~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~- 109 (152)
..+-++-...+..+-+.+.=-+++.+.+|+++|+..|.+++.+ ..+ +.|+.||+||++..+|+.+| ..+++
T Consensus 409 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~a~~~---~~~----~aP~t~~LsPige~~i~~gl-~~~~pe 480 (659)
T PRK14867 409 KDKAMVSDEELEKYRKEIKDLLKKNPKEMTWKEAELIVNVLQD---MDF----MAPSTTGLRPIGAENIEKSL-ETLEPD 480 (659)
T ss_pred hhhhhhhhhhhhhhhhhhhhhccCChhhCCHHHHHHHHHHHHh---cCC----CCCCccccCCCCHHHHHHHH-HhcCcc
Confidence 3344444444444444332236889999999999999999987 332 45588999999999999999 88777
Q ss_pred ---hhhhhhccceeec
Q 031813 110 ---DLERLKKIRNHRG 122 (152)
Q Consensus 110 ---~I~rl~~i~syRG 122 (152)
.+.| +.+.|+|
T Consensus 481 f~~a~tR--~p~~y~g 494 (659)
T PRK14867 481 FLKTLTR--KPKTYKG 494 (659)
T ss_pred eEEEecc--CcccccC
Confidence 5677 8889987
No 21
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=95.63 E-value=0.022 Score=53.81 Aligned_cols=54 Identities=15% Similarity=0.216 Sum_probs=42.5
Q ss_pred CHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHh----hhhhhhccceeec
Q 031813 60 SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG 122 (152)
Q Consensus 60 s~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~----~I~rl~~i~syRG 122 (152)
+.++...|.+++.+ ..| +.|+.||+||++..+|+.+|+..++. .+.| +.+.|+|
T Consensus 482 ~~~~a~~L~~am~~---~~~----~aP~t~cLsPIgee~i~~Gl~k~~~peF~aa~TR--~p~vy~G 539 (795)
T PRK14868 482 DRDAASDLLEAMRE---TDI----IAPPTDCLSPISAELVEAGLRKEFDADFYAAATR--DAEVHGG 539 (795)
T ss_pred CHHHHHHHHHHHHh---cCC----CCCCccccCcCCHHHHHHHHHhhcCcceEEEecc--CCcccCC
Confidence 46677778888876 322 45688999999999999999998777 4566 7888876
No 22
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.64 E-value=0.053 Score=45.54 Aligned_cols=59 Identities=25% Similarity=0.361 Sum_probs=46.9
Q ss_pred hcCcccCCCeeheeeh---hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 15 VLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 15 i~~~~l~~~k~v~~aL---~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
+...-...++.|.-+| +-+-|||...|.++|-++||+|.+..++|+.+|+..|.+++..
T Consensus 147 l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~ 208 (273)
T COG0266 147 LAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKD 208 (273)
T ss_pred HHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHH
Confidence 3333344455565555 4489999999999999999999999999999998888777653
No 23
>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=94.17 E-value=0.041 Score=31.14 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=15.2
Q ss_pred ehhcccccCHHHHHHHHH
Q 031813 29 ALTSIKGIGRRLANIVCK 46 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~ 46 (152)
.|.+++|||+++|..|+.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 588999999999999975
No 24
>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=93.93 E-value=0.023 Score=49.74 Aligned_cols=51 Identities=29% Similarity=0.503 Sum_probs=35.0
Q ss_pred CCeeheeeh-hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 22 GKQKIMFAL-TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 22 ~~k~v~~aL-~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
+...+.-+| ..+.|+|+..|..+|.++|++++..+.+++++++..|.+.+.
T Consensus 185 ~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~ 236 (455)
T PF05833_consen 185 KEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIR 236 (455)
T ss_dssp CG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHH
T ss_pred CcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHH
Confidence 344454444 556699999999999999999999999999998776555543
No 25
>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=92.72 E-value=0.093 Score=45.40 Aligned_cols=51 Identities=24% Similarity=0.423 Sum_probs=44.4
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+++.+...|..+ +-.+.+..||+.+||++++++++|+++|++.|.+.|.+
T Consensus 281 ~~~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 281 NPKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred ChhhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 3466666666644 78999999999999999999999999999999999987
No 26
>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=90.39 E-value=0.19 Score=28.62 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=15.7
Q ss_pred eehhcccccCHHHHHHHHHHcCC
Q 031813 28 FALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi 50 (152)
..+++|.|||+.++..+ +++||
T Consensus 11 lpi~~~~GIG~kt~~kL-~~~GI 32 (32)
T PF11798_consen 11 LPIRKFWGIGKKTAKKL-NKLGI 32 (32)
T ss_dssp SBGGGSTTS-HHHHHHH-HCTT-
T ss_pred CCHHhhCCccHHHHHHH-HHccC
Confidence 36789999999999984 44443
No 27
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=90.07 E-value=0.042 Score=35.28 Aligned_cols=26 Identities=27% Similarity=0.404 Sum_probs=21.5
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~ 52 (152)
++..|.+|.|||+.+|..+.+. |+..
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 4567899999999999999876 7664
No 28
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=89.14 E-value=0.43 Score=39.28 Aligned_cols=52 Identities=23% Similarity=0.281 Sum_probs=41.4
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
-..|.+.-+|..+.+. ...+..+++.+|++++.++.+|+.+|+.+|.+.+..
T Consensus 219 ~rrk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 219 QRRKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred chHHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 3466677777776542 345678899999999999999999999999988764
No 29
>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=88.17 E-value=0.41 Score=30.39 Aligned_cols=22 Identities=23% Similarity=0.314 Sum_probs=15.9
Q ss_pred ehhcccccCHHHHHHHHHHcCCC
Q 031813 29 ALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~ 51 (152)
.+++|+|||+.+|....+ .|+.
T Consensus 3 ~f~~I~GVG~~tA~~w~~-~G~r 24 (52)
T PF10391_consen 3 LFTGIWGVGPKTARKWYA-KGIR 24 (52)
T ss_dssp HHHTSTT--HHHHHHHHH-TT--
T ss_pred chhhcccccHHHHHHHHH-hCCC
Confidence 478999999999999987 7754
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=87.79 E-value=0.49 Score=25.43 Aligned_cols=20 Identities=25% Similarity=0.434 Sum_probs=16.9
Q ss_pred ehhcccccCHHHHHHHHHHc
Q 031813 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~l 48 (152)
.|.++.|||..+|..|+...
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 36789999999999998643
No 31
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=87.57 E-value=0.44 Score=39.69 Aligned_cols=48 Identities=23% Similarity=0.295 Sum_probs=42.5
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
...|.+.-+|..+++ ...+|+.+|++++.++.+||.+|+-.|.+++..
T Consensus 209 ~RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 209 QRRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hhhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 346778888888777 899999999999999999999999999998864
No 32
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=86.16 E-value=0.58 Score=35.33 Aligned_cols=59 Identities=20% Similarity=0.161 Sum_probs=44.2
Q ss_pred hcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCC---CCCCCCCCCHHHHHHHHHHHhC
Q 031813 15 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 15 i~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~---~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
-.+.-||-|..-...|+.++|||+..|.+|++.-.+. .-..+..+++.|.+.|.+..++
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDN 109 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcc
Confidence 3566677677777789999999999999999632221 2235667899999999998876
No 33
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.89 E-value=0.5 Score=37.45 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=18.9
Q ss_pred eehhcccccCHHHHHHHHHHcC
Q 031813 28 FALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
-+|++++|||+++|.+||-.|.
T Consensus 108 ~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHHH
Confidence 4789999999999999996553
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=85.74 E-value=0.58 Score=35.36 Aligned_cols=44 Identities=18% Similarity=0.222 Sum_probs=39.3
Q ss_pred eehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
--|+.|.|||+..+.. +..+||-....+-.+|..|+..+..+|+
T Consensus 67 DDLt~I~GIGPk~e~~-Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 67 DDLTRISGIGPKLEKV-LNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred ccchhhcccCHHHHHH-HHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 4589999999998765 5789999999999999999999999985
No 35
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=85.37 E-value=0.35 Score=37.62 Aligned_cols=35 Identities=17% Similarity=0.208 Sum_probs=21.0
Q ss_pred ccCCCCCCchhhhhhhhHHHHHHhh----hhhhhccceeec
Q 031813 86 RQKDYKDGKYSQVVSNALDMKLRDD----LERLKKIRNHRG 122 (152)
Q Consensus 86 r~~D~~sg~~~~lie~~L~~~~~~~----I~rl~~i~syRG 122 (152)
|+.||+||++.++|+.+|+..++.+ ++| +.+.|+|
T Consensus 1 P~~~cLsPiGe~~i~~Gl~k~l~pefv~avtR--~p~vy~G 39 (160)
T PF09239_consen 1 PPTDCLSPIGEELIEKGLKKELNPEFVAAVTR--KPSVYSG 39 (160)
T ss_dssp --SCCS----HHHHHHHHHHHC--SEEEEEE-----EEETT
T ss_pred CCCcccCccCHHHHHHHHHHhcCccEEEEEcc--CCceecC
Confidence 4789999999999999999999884 566 7788876
No 36
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=85.34 E-value=0.14 Score=39.53 Aligned_cols=46 Identities=13% Similarity=-0.084 Sum_probs=39.0
Q ss_pred hhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCCCccce
Q 031813 99 VSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV 146 (152)
Q Consensus 99 ie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~ 146 (152)
+.+|.+.+..+++....++.+|.|- ..+||+.||.|+.|+.+.+.+
T Consensus 70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRlk 115 (152)
T KOG3311|consen 70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERLK 115 (152)
T ss_pred HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHHh
Confidence 4456677777899999999999999 999999999999998776543
No 37
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.13 E-value=0.57 Score=37.04 Aligned_cols=21 Identities=24% Similarity=0.371 Sum_probs=18.3
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 478999999999999999554
No 38
>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=84.51 E-value=1.5 Score=38.58 Aligned_cols=51 Identities=27% Similarity=0.394 Sum_probs=44.8
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcCC-CCCCCCCCCCHHHHHHHHHHHhC
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKADV-DMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi-~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+++.+...|..+ +-.+.+..+|+.+++ ++++++.+|+++++..|.+.|.+
T Consensus 288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 4577788888876 899999999999999 99999999999999999999987
No 39
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.15 E-value=0.67 Score=36.97 Aligned_cols=21 Identities=33% Similarity=0.504 Sum_probs=18.1
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.+|++++|||+++|.+||-.|
T Consensus 107 ~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 478999999999999999543
No 40
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.92 E-value=0.69 Score=36.85 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=18.4
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 479999999999999999554
No 41
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.75 E-value=0.71 Score=36.99 Aligned_cols=21 Identities=29% Similarity=0.501 Sum_probs=18.3
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+|+-.|
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 478999999999999999554
No 42
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=83.64 E-value=1.1 Score=36.29 Aligned_cols=58 Identities=17% Similarity=0.228 Sum_probs=42.8
Q ss_pred cchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHH
Q 031813 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVV 70 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~ 70 (152)
|.++++.+ ---..|.+.-+|..+.+- ..+..+++.+|+++++++.+||.+|+..|.+.
T Consensus 195 ~~~~~~~~--F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 195 FEKLLKAA--FSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HHHHHHHH--HccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 55555542 234567777778776442 34567888999999999999999999998765
No 43
>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=83.52 E-value=0.46 Score=38.83 Aligned_cols=62 Identities=24% Similarity=0.307 Sum_probs=48.7
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
+.|.++++.+=. -..|.+.-+|..+++ ...+..+.+.+||+++.++.+|+.+|+.+|-++|+
T Consensus 200 ~~~~~~~~~~F~--~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 200 DAFEYFVRQLFS--QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHHHHHHHHHHT--TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh--CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 356677765533 578888888887753 44456777789999999999999999999999875
No 44
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=83.24 E-value=0.79 Score=36.86 Aligned_cols=21 Identities=33% Similarity=0.498 Sum_probs=18.1
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+||-.|
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 478999999999999999654
No 45
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.75 E-value=0.82 Score=36.58 Aligned_cols=21 Identities=33% Similarity=0.509 Sum_probs=17.9
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
-+|++++|||+++|.+|+-.|
T Consensus 109 ~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred HHHhcCCCcCHHHHHHHHHHH
Confidence 468999999999999999443
No 46
>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=82.24 E-value=0.74 Score=36.38 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=24.3
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
++...+...|.+++|||+.+|.-+|..||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 55666667899999999999999987665
No 47
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=81.85 E-value=1.5 Score=40.18 Aligned_cols=51 Identities=22% Similarity=0.289 Sum_probs=45.1
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
..-+..++..+.|+|.-.|..+|-++|+++.....++.++++..+...+.+
T Consensus 185 ~~~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~ 235 (564)
T COG1293 185 GADIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE 235 (564)
T ss_pred chHHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence 344567788999999999999999999999999999999999999887654
No 48
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=78.78 E-value=2.4 Score=24.74 Aligned_cols=33 Identities=15% Similarity=0.329 Sum_probs=22.9
Q ss_pred ccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 8 ~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
+|-++.=|.| |-.+| ...+.|||..+|.+++++
T Consensus 3 q~~~~~~L~G-D~~dn------i~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 3 QLIDYAILVG-DYSDN------IPGVKGIGPKTALKLLRE 35 (36)
T ss_pred HHHHHHHHhC-cCCCC------CCCCCcccHHHHHHHHHh
Confidence 4555555666 44333 267899999999999875
No 49
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.53 E-value=0.73 Score=36.60 Aligned_cols=36 Identities=14% Similarity=0.276 Sum_probs=28.1
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
.++|-.=...+.++..|.++.|||+.+|..|+..++
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~ 94 (194)
T PRK14605 59 SLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMN 94 (194)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCC
Confidence 456666667777888888888888888888887655
No 50
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.19 E-value=1.4 Score=34.94 Aligned_cols=20 Identities=35% Similarity=0.586 Sum_probs=16.6
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.+| +++|||+++|.+||-.|
T Consensus 108 ~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHHH
Confidence 466 89999999999999543
No 51
>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=77.62 E-value=2.5 Score=26.89 Aligned_cols=26 Identities=8% Similarity=0.190 Sum_probs=20.5
Q ss_pred ccccCHHHHHHHHHHcCCC--CCCCCCC
Q 031813 33 IKGIGRRLANIVCKKADVD--MNKRAGE 58 (152)
Q Consensus 33 i~GIG~~~A~~Ic~~lgi~--~~~~~~~ 58 (152)
--||+..+-+.+|.++||. |..++.+
T Consensus 24 ~Lgv~~T~LKr~CR~~GI~RWP~Rkl~S 51 (52)
T PF02042_consen 24 ELGVSVTTLKRRCRRLGIPRWPYRKLKS 51 (52)
T ss_pred HhCCCHHHHHHHHHHcCCCCCCchhhcc
Confidence 3689999999999999997 4444443
No 52
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.38 E-value=1.6 Score=34.71 Aligned_cols=19 Identities=32% Similarity=0.501 Sum_probs=16.5
Q ss_pred eehhcccccCHHHHHHHHH
Q 031813 28 FALTSIKGIGRRLANIVCK 46 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~ 46 (152)
-+|++++|||+++|.+|+-
T Consensus 108 ~~L~~vpGIGkKtAerIil 126 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIVL 126 (194)
T ss_pred HHHHhCCCCCHHHHHHHHH
Confidence 3589999999999999773
No 53
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=76.98 E-value=2.3 Score=27.03 Aligned_cols=20 Identities=35% Similarity=0.561 Sum_probs=17.9
Q ss_pred ehhcccccCHHHHHHHHHHc
Q 031813 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~l 48 (152)
.|..++|||..+|..|++.+
T Consensus 39 ~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 39 ELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHTSTTSSHHHHHHHHHHH
T ss_pred HHhcCCCCCHHHHHHHHHHH
Confidence 48899999999999999865
No 54
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=76.67 E-value=2.9 Score=34.22 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=43.8
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcCCCCCCC------------CCCCCHHHHHHHHHHHhC
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKR------------AGELSAAELDNLMVVVAN 73 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~------------~~~Ls~~ei~~L~~~l~~ 73 (152)
...+..--..++|.|+....+|.+++|+=++.+ ...||++|+++|-++.+.
T Consensus 96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~ 158 (225)
T PF09883_consen 96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRD 158 (225)
T ss_pred cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhC
Confidence 555555566788999999999999999999988 567999999999999876
No 55
>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=75.99 E-value=2.7 Score=28.98 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=21.9
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcC
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
+..|.+.|+.|.|||...|..|++.-.
T Consensus 22 ~~~Ir~gl~~Ikglg~~~a~~I~~~R~ 48 (90)
T PF14579_consen 22 NNAIRLGLSAIKGLGEEVAEKIVEERE 48 (90)
T ss_dssp -TEEE-BGGGSTTS-HHHHHHHHHHHH
T ss_pred CCEEeehHhhcCCCCHHHHHHHHHhHh
Confidence 478999999999999999999997764
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=74.52 E-value=1.3 Score=34.88 Aligned_cols=60 Identities=10% Similarity=0.203 Sum_probs=38.3
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCC------------CCCCCCCHHHHHHHHHHHhC
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMN------------KRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~------------~~~~~Ls~~ei~~L~~~l~~ 73 (152)
|+.|-.=...+.+...|.+|+|||+.+|..|++.+|.+.- .++.-+++...++|...+..
T Consensus 59 ~l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 59 LLYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 3455553334455558899999999999999998885211 12333555666666655544
No 57
>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=74.47 E-value=2.7 Score=27.34 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=21.8
Q ss_pred cCCCeeheeehhc-ccccCHHHHHHHHHHc
Q 031813 20 VDGKQKIMFALTS-IKGIGRRLANIVCKKA 48 (152)
Q Consensus 20 l~~~k~v~~aL~~-i~GIG~~~A~~Ic~~l 48 (152)
|+=|..-.-.|.. +.|||...|.+|++.-
T Consensus 8 invNta~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 8 VNINTATAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred eECcCCCHHHHHhHCCCCCHHHHHHHHHHH
Confidence 3334444446777 9999999999999884
No 58
>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=73.52 E-value=2.6 Score=27.57 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.4
Q ss_pred ehhcccccCHHHHHHHHHHc
Q 031813 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~l 48 (152)
.+++++|||.++|..|-+.+
T Consensus 48 ~~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHH
Confidence 68999999999999997653
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=73.45 E-value=2.9 Score=29.73 Aligned_cols=37 Identities=22% Similarity=0.138 Sum_probs=28.1
Q ss_pred eehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHH
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~ 65 (152)
..|+.|+|||+++|.-+. .+||+.=..+..-+.+++-
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 468999999999999987 8999875544444555554
No 60
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=72.93 E-value=13 Score=29.96 Aligned_cols=70 Identities=13% Similarity=0.004 Sum_probs=45.1
Q ss_pred eheeehh-cccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhH
Q 031813 25 KIMFALT-SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNAL 103 (152)
Q Consensus 25 ~v~~aL~-~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L 103 (152)
.....|. +++|||+.+|..|+.-.|..|..- =|..+.++.+-+.= . . ...+-+|+.+..-+|..|
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~i----VDtHv~Ri~~RlG~---~------~-~~~~~lt~~~y~~~E~~l 180 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGYEDLAI----LDRHILRFLKRYGL---I------E-EIPKTLSKKRYLEIEEIL 180 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccCCCeee----eeHHHHHHHHHhCC---C------c-ccccccCcCCHHHHHHHH
Confidence 4455566 999999999999997666644322 34677777776531 0 0 012246667777788887
Q ss_pred HHHHH
Q 031813 104 DMKLR 108 (152)
Q Consensus 104 ~~~~~ 108 (152)
.....
T Consensus 181 ~~~~~ 185 (208)
T PRK01229 181 REIAE 185 (208)
T ss_pred HHHHH
Confidence 65544
No 61
>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=72.35 E-value=3.1 Score=27.88 Aligned_cols=37 Identities=22% Similarity=0.367 Sum_probs=26.2
Q ss_pred ccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 6 ~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
.++|..+.=+.|-..|. +..+.|||..+|..|+.+.|
T Consensus 7 ~~q~~d~~~L~GD~~D~-------i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 7 PEQFIDLAILVGDKSDN-------IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred HHHHHHHHHHcCCcccc-------CCCCCcccHHHHHHHHHHhC
Confidence 45677777777722221 23689999999999998866
No 62
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=71.89 E-value=3.3 Score=28.28 Aligned_cols=20 Identities=40% Similarity=0.423 Sum_probs=18.6
Q ss_pred ehhcccccCHHHHHHHHHHc
Q 031813 29 ALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~l 48 (152)
.|++|+|||..+|..|+..+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 58899999999999999888
No 63
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=71.69 E-value=2.8 Score=30.69 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=25.9
Q ss_pred ccCCCeeheeehhcccccCHHHHHHHHHHcCC
Q 031813 19 NVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 19 ~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi 50 (152)
-++-|..-...|..++|||..+|..|.+..+-
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 35556666678899999999999999998753
No 64
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=71.69 E-value=1.1 Score=29.04 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=29.3
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHc-------CCCCCCCCCCCCHHHHHHHHH
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKA-------DVDMNKRAGELSAAELDNLMV 69 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~l-------gi~~~~~~~~Ls~~ei~~L~~ 69 (152)
|-|..=...|..++|||...|.+|.+.= .++.-..+..++++.+++|..
T Consensus 7 diN~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 7 DINTASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp ETTTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred cCccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 3344445568899999999999999654 333334555567777776643
No 65
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=71.13 E-value=2.5 Score=27.47 Aligned_cols=18 Identities=28% Similarity=0.589 Sum_probs=14.9
Q ss_pred cccccCHHHHHHHHHHcC
Q 031813 32 SIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 32 ~i~GIG~~~A~~Ic~~lg 49 (152)
.|+|||..+|+.+++.+|
T Consensus 7 GI~~VG~~~ak~L~~~f~ 24 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG 24 (64)
T ss_dssp TSTT--HHHHHHHHHCCS
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 699999999999999888
No 66
>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=69.44 E-value=3.3 Score=32.77 Aligned_cols=20 Identities=30% Similarity=0.456 Sum_probs=17.2
Q ss_pred eehhcccccCHHHHHHHHHH
Q 031813 28 FALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~ 47 (152)
-+|++++|||.++|.+|+-.
T Consensus 107 ~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred HHHHhCCCCCHHHHHHHHHH
Confidence 45889999999999999944
No 67
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=68.16 E-value=1.2 Score=35.37 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=28.9
Q ss_pred hhhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 13 vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
+.++|-.=...+.++..|.++.|||+++|..|+..
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 57 ELLFGFNTLEERELFKELIKVNGVGPKLALAILSN 91 (191)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhc
Confidence 35667777778889999999999999999999543
No 68
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=67.76 E-value=3.1 Score=30.95 Aligned_cols=45 Identities=18% Similarity=0.234 Sum_probs=29.9
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHH
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l 71 (152)
...+...|++++|||+.+|..+|-.. ++++.-+- |.-+.++...+
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~~-~~~~~~pv---D~~v~r~~~~~ 122 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLFA-LGPDAFPV---DTHVRRVLKRL 122 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHHH-CCCCCCcc---chhHHHHHHHh
Confidence 35577889999999999999998753 33333222 45555555444
No 69
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=67.24 E-value=3.9 Score=28.43 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=19.8
Q ss_pred eehhc-ccccCHHHHHHHHHHcCCCCC
Q 031813 28 FALTS-IKGIGRRLANIVCKKADVDMN 53 (152)
Q Consensus 28 ~aL~~-i~GIG~~~A~~Ic~~lgi~~~ 53 (152)
|.|.. |.|||-.+|..|..++|++++
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 44544 999999999999999998763
No 70
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=66.98 E-value=3.9 Score=30.13 Aligned_cols=23 Identities=35% Similarity=0.356 Sum_probs=19.3
Q ss_pred heeehhcccccCHHHHHHHHHHc
Q 031813 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
....|.+++|||+.+|..+|...
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 45667899999999999998775
No 71
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=66.38 E-value=5 Score=32.78 Aligned_cols=45 Identities=24% Similarity=0.314 Sum_probs=40.1
Q ss_pred eehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
-.|+.|.|||+..+..+ ..+|+.....+-.++++++..+...+.-
T Consensus 158 DDL~~I~GIGp~~a~~L-~eaGi~tfaQIAa~t~a~ia~id~~l~~ 202 (221)
T PRK12278 158 DDLTKITGVGPALAKKL-NEAGVTTFAQIAALTDADIAKIDEKLSF 202 (221)
T ss_pred chheeccccChHHHHHH-HHcCCCCHHHhhCCChhhhhhhhhcccC
Confidence 45899999999998875 7899999999999999999999998853
No 72
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=66.16 E-value=4.9 Score=34.38 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=22.8
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~ 52 (152)
....|.+|+|||+.+|..+.+ +|+..
T Consensus 87 ~l~~l~~i~GiGpk~a~~l~~-lGi~t 112 (334)
T smart00483 87 SLKLFTNVFGVGPKTAAKWYR-KGIRT 112 (334)
T ss_pred HHHHHHccCCcCHHHHHHHHH-hCCCC
Confidence 356789999999999999998 99875
No 73
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=66.08 E-value=3.2 Score=33.28 Aligned_cols=41 Identities=20% Similarity=0.246 Sum_probs=29.7
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+..+|++++|||+++|.++.-.+= ...++++..|.++|.+
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA~~ll--------~~~~~~~~~la~ai~~ 48 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLAFHLL--------KRDPSEVLRLAQALLE 48 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHH
Confidence 4566899999999999999965442 2356677776666654
No 74
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=66.00 E-value=4.9 Score=26.04 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=16.4
Q ss_pred ehhcccccCHHHHHHHHHHcC
Q 031813 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lg 49 (152)
.|+.++|||+.+|..|.+.+.
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 689999999999999987654
No 75
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=65.66 E-value=2.8 Score=33.76 Aligned_cols=87 Identities=23% Similarity=0.315 Sum_probs=51.5
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCC-Ccc------------CCccccCccCCCC
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPR-QFK------------IPDWFLNRQKDYK 91 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~-~~~------------ip~w~~nr~~D~~ 91 (152)
.+..+|.+++|||+++|.++.--+- ..++++++.|.++|.+.. +.. .=....++++|..
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~AfhLL--------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~ 80 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAFHLL--------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKS 80 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHHHHH--------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCc
Confidence 4567899999999999999975543 346777777777765421 011 1112223444432
Q ss_pred CCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCC
Q 031813 92 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 128 (152)
Q Consensus 92 sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~g 128 (152)
-.-++|.- .|+..|=+.+.|+|.=|-.|
T Consensus 81 ---~icVVe~p------~Dv~a~E~~~~f~G~YhVL~ 108 (198)
T COG0353 81 ---QLCVVEEP------KDVLALEKTGEFRGLYHVLG 108 (198)
T ss_pred ---eEEEEcch------HHHHHHHHhcccCeeEEEec
Confidence 01122222 35556667788888877765
No 76
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.55 E-value=1.7 Score=34.47 Aligned_cols=34 Identities=15% Similarity=0.320 Sum_probs=28.9
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
.++|-.=...+.++..|.++.|||+++|..|+..
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~ 92 (188)
T PRK14606 59 TLYGFSNERKKELFLSLTKVSRLGPKTALKIISN 92 (188)
T ss_pred eeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcC
Confidence 5667777778889999999999999999999743
No 77
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.46 E-value=2.2 Score=34.08 Aligned_cols=37 Identities=16% Similarity=0.232 Sum_probs=30.7
Q ss_pred hhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 13 vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
+.++|-.=...+.++..|.++.|||+++|..|+..++
T Consensus 59 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~ 95 (203)
T PRK14602 59 LELFGFATWDERQTFIVLISISKVGAKTALAILSQFR 95 (203)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCC
Confidence 3566777777888899999999999999999986654
No 78
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=65.15 E-value=1.4 Score=35.42 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=32.2
Q ss_pred hhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 12 ~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
...++|-.=...+.++..|.++-|||+++|.+|+.-++
T Consensus 57 ~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 57 AHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred HHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCC
Confidence 36678888888899999999999999999999975433
No 79
>PRK00076 recR recombination protein RecR; Reviewed
Probab=64.78 E-value=3.4 Score=33.11 Aligned_cols=41 Identities=20% Similarity=0.245 Sum_probs=30.1
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+..+|.+++|||+++|.++.-.+= ...++++..|.++|.+
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla~~ll--------~~~~~~~~~la~~i~~ 48 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLAFHLL--------QRDREDVLRLAQALEE 48 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHH
Confidence 3556899999999999999976543 2356677777666654
No 80
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.69 E-value=1.8 Score=34.22 Aligned_cols=35 Identities=26% Similarity=0.361 Sum_probs=29.3
Q ss_pred hhhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 13 vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
+.++|-.=...+.++..|.++.|||+++|..|+..
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 58 NKLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred ceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcC
Confidence 35677777778889999999999999999999643
No 81
>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=64.53 E-value=5.6 Score=33.55 Aligned_cols=25 Identities=16% Similarity=0.396 Sum_probs=21.6
Q ss_pred eeehhcccccCHHHHHHHHHHcCCCC
Q 031813 27 MFALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~lgi~~ 52 (152)
...|.+|+|||+.+|..+. .+|+..
T Consensus 84 l~~l~~i~GiGpk~a~~l~-~lGi~s 108 (307)
T cd00141 84 LLLLLRVPGVGPKTARKLY-ELGIRT 108 (307)
T ss_pred HHHHHcCCCCCHHHHHHHH-HcCCCC
Confidence 4567899999999999999 899874
No 82
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.12 E-value=1.9 Score=34.06 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=29.9
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHHc
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.++|-.=...+.++..|.++.|||+++|..|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~ 93 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKL 93 (186)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccC
Confidence 56777777888899999999999999999997543
No 83
>PRK10702 endonuclease III; Provisional
Probab=63.56 E-value=5.2 Score=32.11 Aligned_cols=23 Identities=39% Similarity=0.562 Sum_probs=19.4
Q ss_pred heeehhcccccCHHHHHHHHHHc
Q 031813 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
..-.|.+++|||+++|..|+..+
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHHH
Confidence 45779999999999999998544
No 84
>PRK08609 hypothetical protein; Provisional
Probab=63.19 E-value=6.1 Score=36.24 Aligned_cols=25 Identities=20% Similarity=0.292 Sum_probs=22.1
Q ss_pred eehhcccccCHHHHHHHHHHcCCCC
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~ 52 (152)
..|++|+|||+++|..+.+.+||..
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~t 112 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVVD 112 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCCC
Confidence 4678999999999999999999853
No 85
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=63.13 E-value=4.6 Score=33.79 Aligned_cols=29 Identities=21% Similarity=0.290 Sum_probs=22.4
Q ss_pred CcccCCCeeheeehhcccccCHHHHHHHHHHc
Q 031813 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 17 ~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
|-.+|.. .-.|.+++|||..||..||..+
T Consensus 97 ~g~~p~~---~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 97 GGEFPQD---FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred CCCCcHH---HHHHHhCCCCCHHHHHHHHHHH
Confidence 4445543 5679999999999999998654
No 86
>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=62.84 E-value=5 Score=31.32 Aligned_cols=23 Identities=35% Similarity=0.465 Sum_probs=19.4
Q ss_pred heeehhcccccCHHHHHHHHHHc
Q 031813 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
....|.+++|||+.+|..||-..
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHH
Confidence 45679999999999999998544
No 87
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.49 E-value=2.1 Score=34.25 Aligned_cols=34 Identities=21% Similarity=0.298 Sum_probs=29.0
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
.++|-.=...+.++..|.++.|||+++|.+|+..
T Consensus 58 ~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~ 91 (196)
T PRK13901 58 KLFGFLNSSEREVFEELIGVDGIGPRAALRVLSG 91 (196)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcC
Confidence 5677777778889999999999999999999744
No 88
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.59 E-value=2.2 Score=34.01 Aligned_cols=35 Identities=17% Similarity=0.276 Sum_probs=29.3
Q ss_pred hhhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 13 vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
+.++|-.=...+.++..|.++.|||+++|.+|+..
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~ 91 (197)
T PRK14603 57 LSLYGFPDEDSLELFELLLGVSGVGPKLALALLSA 91 (197)
T ss_pred ceeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcC
Confidence 35677777778888999999999999999999744
No 89
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=61.18 E-value=11 Score=33.46 Aligned_cols=50 Identities=22% Similarity=0.339 Sum_probs=43.2
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+++.+.-+|.. .++.+.+..++++.|| ++....+||+.|+++|.+.|+.
T Consensus 283 ~~~kslkn~L~~--~lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 283 NPKKSLKNALAK--LLPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred ChhhHHHHHHHH--HhhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 445666666655 5788999999999999 9999999999999999999987
No 90
>PRK13844 recombination protein RecR; Provisional
Probab=61.14 E-value=4.4 Score=32.61 Aligned_cols=41 Identities=10% Similarity=0.108 Sum_probs=29.9
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.+..+|++++|||+++|.++.-.+= +..++++..|.++|.+
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla~~lL--------~~~~~~~~~la~~i~~ 52 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLALYLL--------DKSPETAIAIANSLLD 52 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHH
Confidence 3456899999999999999975542 3456677777666654
No 91
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=61.03 E-value=4.6 Score=34.75 Aligned_cols=45 Identities=9% Similarity=0.078 Sum_probs=39.6
Q ss_pred eeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
.--|+.|.|||+..+.. |..+|+..-..+..++++++..+.+.+.
T Consensus 262 ~DdL~~I~GiGp~~e~~-L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 262 PDDLKKLTGVSPQIEKK-LNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred chhhhhhccCChhhhhh-hhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 35689999999998765 6889999999999999999999888875
No 92
>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=59.87 E-value=28 Score=21.83 Aligned_cols=43 Identities=12% Similarity=0.188 Sum_probs=32.6
Q ss_pred hhcccccCHHHHHHHHHHcCCCCCCC-C---CCCCHHHHHHHHHHHh
Q 031813 30 LTSIKGIGRRLANIVCKKADVDMNKR-A---GELSAAELDNLMVVVA 72 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lgi~~~~~-~---~~Ls~~ei~~L~~~l~ 72 (152)
+.+..||...+...-.+..|+.+..+ . ...+++|+..|..+..
T Consensus 6 va~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~ 52 (68)
T cd01104 6 VARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRR 52 (68)
T ss_pred HHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHH
Confidence 45678999999999888878866433 2 3679999988887764
No 93
>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=59.39 E-value=11 Score=35.58 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=29.8
Q ss_pred cccccCHHHHHHHHHHcCCCC--------C--CCCCCCCHHHHHHHHHHHhC
Q 031813 32 SIKGIGRRLANIVCKKADVDM--------N--KRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 32 ~i~GIG~~~A~~Ic~~lgi~~--------~--~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.|+|||+.+|..|.+.+|.+. + ..+.-+++..++.|.+.+.+
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~ 139 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ 139 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 499999999999999988652 1 13344666766666665543
No 94
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=56.76 E-value=30 Score=28.08 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=28.4
Q ss_pred eeehhcccccCHHHHHHHHHH-cCCCCCCCCCCCCHHHHHHHHHHH
Q 031813 27 MFALTSIKGIGRRLANIVCKK-ADVDMNKRAGELSAAELDNLMVVV 71 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~-lgi~~~~~~~~Ls~~ei~~L~~~l 71 (152)
...|.+.+|||++||+-++.. +|.+ ...|-. .+.++.+-+
T Consensus 108 ~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDT----HV~Rvs~R~ 148 (211)
T COG0177 108 REELLSLPGVGRKTANVVLSFAFGIP-AIAVDT----HVHRVSNRL 148 (211)
T ss_pred HHHHHhCCCcchHHHHHHHHhhcCCC-cccccc----hHHHHHHHh
Confidence 457999999999999998877 4443 444433 666666654
No 95
>PRK13910 DNA glycosylase MutY; Provisional
Probab=55.90 E-value=7.8 Score=32.73 Aligned_cols=22 Identities=27% Similarity=0.277 Sum_probs=19.3
Q ss_pred eeehhcccccCHHHHHHHHHHc
Q 031813 27 MFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.-.|.+++|||++||..|+..+
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 6789999999999999998643
No 96
>PRK03980 flap endonuclease-1; Provisional
Probab=55.24 E-value=11 Score=31.65 Aligned_cols=34 Identities=32% Similarity=0.419 Sum_probs=26.6
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
++|-.+.=++|+|-.+ .|+|||..+|..++++.|
T Consensus 177 ~q~id~~iL~G~Dy~~---------GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 177 EQLIDIAILVGTDYNP---------GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred HHHHHHHHhcCCCCCC---------CCCCccHHHHHHHHHHCC
Confidence 4666777777754433 688999999999999987
No 97
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=55.15 E-value=8.8 Score=31.23 Aligned_cols=37 Identities=27% Similarity=0.152 Sum_probs=27.7
Q ss_pred cccCCCeeh--eeehhcccccCHHHHHHHHHHcCCCCCC
Q 031813 18 TNVDGKQKI--MFALTSIKGIGRRLANIVCKKADVDMNK 54 (152)
Q Consensus 18 ~~l~~~k~v--~~aL~~i~GIG~~~A~~Ic~~lgi~~~~ 54 (152)
.++++.++. .--|-+|.|||.-||..|+--+.=-|.-
T Consensus 103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~F 141 (215)
T COG2231 103 INLESFKSEVLREELLSIKGIGKETADSILLYALDRPVF 141 (215)
T ss_pred hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCccc
Confidence 355565655 6778999999999999998776644443
No 98
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.03 E-value=3.3 Score=32.99 Aligned_cols=34 Identities=12% Similarity=0.250 Sum_probs=28.4
Q ss_pred hhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 14 ri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
.++|-.=...+.++..|.++.|||+++|..|+..
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 59 TLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcC
Confidence 4566666677888899999999999999999754
No 99
>PRK10880 adenine DNA glycosylase; Provisional
Probab=55.01 E-value=8.1 Score=33.51 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=19.9
Q ss_pred heeehhcccccCHHHHHHHHHHc
Q 031813 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
..-.|.+++|||++||..||..+
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHHHH
Confidence 45789999999999999999754
No 100
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=54.61 E-value=8.4 Score=31.26 Aligned_cols=23 Identities=26% Similarity=0.198 Sum_probs=18.9
Q ss_pred heeehhcccccCHHHHHHHHHHc
Q 031813 26 IMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
..-.|.+++|||+.||..|+-.+
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLlya 141 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCYV 141 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHHH
Confidence 44669999999999999887543
No 101
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=54.30 E-value=7.6 Score=35.83 Aligned_cols=44 Identities=25% Similarity=0.257 Sum_probs=33.2
Q ss_pred CCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 22 ~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
....+...|..|+|||+.+.+++++.+|= -..+..-|.|||.++
T Consensus 508 ~k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs--~~~ik~As~eeL~~v 551 (567)
T PRK14667 508 EKEGLKDILDKIKGIGEVKKEIIYRNFKT--LYDFLKADDEELKKL 551 (567)
T ss_pred hcccccCccccCCCCCHHHHHHHHHHhCC--HHHHHhCCHHHHHHc
Confidence 34445678899999999999999999983 345556666777554
No 102
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=53.98 E-value=9.1 Score=30.12 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=18.7
Q ss_pred ehhcccccCHHHHHHHHHHcC
Q 031813 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lg 49 (152)
.|++++|||..+|..|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 589999999999999997764
No 103
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=53.71 E-value=8.2 Score=31.80 Aligned_cols=20 Identities=30% Similarity=0.494 Sum_probs=11.7
Q ss_pred hhcccccCHHHHHHHHHHcC
Q 031813 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lg 49 (152)
|..+.|||...|..|.+.++
T Consensus 38 L~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 38 LAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHccCCCHHHHHHHHHHhc
Confidence 45556666666666655554
No 104
>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=51.90 E-value=14 Score=30.92 Aligned_cols=34 Identities=26% Similarity=0.285 Sum_probs=26.6
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
++|-.+.=++|+|-.+ .|+|||..+|..++++.|
T Consensus 211 ~q~id~~~L~G~Dy~~---------gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 211 EKLIDLAILLGCDYTE---------GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred HHHHHHHHhcCCCCCC---------CCCCccHHHHHHHHHHcC
Confidence 4566666777755443 688999999999999987
No 105
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=51.58 E-value=13 Score=31.23 Aligned_cols=32 Identities=22% Similarity=0.439 Sum_probs=24.8
Q ss_pred ccchhhhhcC--c-ccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 8 DFQHILRVLN--T-NVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 8 ~~~~~vri~~--~-~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
++..+.=+.| + ++|| ++|||+.+|..++.+.|
T Consensus 185 qliD~~~L~Gd~sDnipG----------V~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 185 QLIDLKALVGDSSDNIPG----------VKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHHHhCCcccCCCC----------CCCcCHHHHHHHHHHhC
Confidence 4556666677 3 3344 99999999999999998
No 106
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=51.40 E-value=8.5 Score=35.57 Aligned_cols=39 Identities=31% Similarity=0.363 Sum_probs=30.4
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
....|..|+|||+.+.+.+++.+|= -..+..-|.+||.+
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs--~~~I~~As~eeL~~ 550 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGT--YKDILLLNEDEIAE 550 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCC--HHHHHhCCHHHHHh
Confidence 5568999999999999999999883 34555566666654
No 107
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=51.28 E-value=32 Score=28.73 Aligned_cols=30 Identities=27% Similarity=0.244 Sum_probs=23.4
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCCCCC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDMNKR 55 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~ 55 (152)
+...|..++|||+.+|..|+-..==+|+.-
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 456899999999999999987744455554
No 108
>PTZ00217 flap endonuclease-1; Provisional
Probab=49.44 E-value=16 Score=32.16 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=25.8
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcC
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
++|-.+.=+.|+|-. ..|.|||..+|..|+++.|
T Consensus 223 ~q~id~~iL~G~Dy~---------pgi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 223 DQFIDLCILCGCDYC---------DTIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred HHHHHHHHHhCCCCC---------CCCCCccHHHHHHHHHHcC
Confidence 456667777775433 2689999999999998865
No 109
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.23 E-value=38 Score=25.66 Aligned_cols=45 Identities=13% Similarity=0.128 Sum_probs=36.5
Q ss_pred ehhcccccCHHHHHHHHHHcC---C--CCC---CCCCCCCHHHHHHHHHHHhC
Q 031813 29 ALTSIKGIGRRLANIVCKKAD---V--DMN---KRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lg---i--~~~---~~~~~Ls~~ei~~L~~~l~~ 73 (152)
...+++|||.+|+..-..+.. . .+. -+++.|+++|++.|.+.+..
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~ 78 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLRE 78 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhc
Confidence 456789999999999998764 3 333 37889999999999999976
No 110
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=48.91 E-value=16 Score=33.83 Aligned_cols=43 Identities=30% Similarity=0.338 Sum_probs=31.6
Q ss_pred CCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 22 ~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
....+..+|..|.|||..++..|++.+|= -..+.+-+.+|+..
T Consensus 537 ~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~ 579 (598)
T PRK00558 537 SKARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAK 579 (598)
T ss_pred ccchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhh
Confidence 34456789999999999999999999883 23344455666544
No 111
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=48.78 E-value=12 Score=34.92 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=30.9
Q ss_pred eeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 24 k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
..+.-.|.+|+|||+.++.++++.+|= -..+..-|.+||.++
T Consensus 548 ~~~~S~L~~IpGIG~kr~~~LL~~FgS--i~~I~~As~eeL~~v 589 (624)
T PRK14669 548 RDRTSELLEIPGVGAKTVQRLLKHFGS--LERVRAATETQLAAV 589 (624)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHcCC--HHHHHhCCHHHHHHH
Confidence 344567889999999999999999982 234555566666553
No 112
>PHA02564 V virion protein; Provisional
Probab=48.47 E-value=39 Score=25.70 Aligned_cols=34 Identities=15% Similarity=0.070 Sum_probs=27.3
Q ss_pred HHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 39 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 39 ~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
..+..+|+.+|++|+.++.-..+ .+..|..+|..
T Consensus 86 aYi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~ 119 (141)
T PHA02564 86 AYATAVANAMGVPPQAGLHLDQD-TLAALVTAIIR 119 (141)
T ss_pred HHHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHH
Confidence 35788999999999999885545 88888888754
No 113
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=47.93 E-value=28 Score=29.19 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=29.4
Q ss_pred HHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 39 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 39 ~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
.....+++.+|++ +.|+.+|+-+|+-.|.+.+.+
T Consensus 255 ~~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 255 EFIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 3445678999997 799999999999999999976
No 114
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=47.17 E-value=16 Score=33.66 Aligned_cols=60 Identities=15% Similarity=0.209 Sum_probs=43.4
Q ss_pred CccccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCC-------CCCCCCHHHHHHHHHHHhC
Q 031813 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNK-------RAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 5 ~~~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~-------~~~~Ls~~ei~~L~~~l~~ 73 (152)
+.|.|++|.=+.|.|- |.++.|||..+|.++..+...-... +--...++.++....+..-
T Consensus 211 ~~ekfr~mciLSGCDY---------l~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~t 277 (556)
T KOG2518|consen 211 TEEKFRRMCILSGCDY---------LSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLT 277 (556)
T ss_pred CHHHHHHHHHhcCCcc---------cccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHh
Confidence 3568999999999985 6679999999999999876532111 1124567777777776654
No 115
>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=45.70 E-value=6.9 Score=34.49 Aligned_cols=77 Identities=19% Similarity=0.286 Sum_probs=0.0
Q ss_pred cccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHhhh
Q 031813 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDL 111 (152)
Q Consensus 32 ~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I 111 (152)
.=|||=++|+..|. .+|+--+.-++ ++|+||+.+.+.|... |- =|.+=|+-. +++..++..-
T Consensus 56 ~~YGVRy~T~AKIa-ElGFTvsTLl~-M~deELDdmM~sL~~i--fR---------wdLLVGERY-----GIKAAvRAER 117 (386)
T PF01698_consen 56 QGYGVRYYTAAKIA-ELGFTVSTLLN-MTDEELDDMMNSLSQI--FR---------WDLLVGERY-----GIKAAVRAER 117 (386)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhccccHHHHHHHH-HhcccHHHHhc-ccHHHHHHHHHHHHHH--hh---------hhhhhhhhh-----hHHHHHHHHH
Confidence 34899999999985 58887666555 8999999999998873 31 133333333 6677777777
Q ss_pred hhhhccceeecccCC
Q 031813 112 ERLKKIRNHRGLRHY 126 (152)
Q Consensus 112 ~rl~~i~syRG~RH~ 126 (152)
.||-.....+..||.
T Consensus 118 RRl~e~~~~~rR~hl 132 (386)
T PF01698_consen 118 RRLEEEEESRRRRHL 132 (386)
T ss_dssp ---------------
T ss_pred HHhhcchhhhhhhcc
Confidence 777775555566653
No 116
>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=45.64 E-value=14 Score=31.35 Aligned_cols=44 Identities=14% Similarity=0.123 Sum_probs=31.0
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHH
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l 71 (152)
.+.-.|+.++|||+.+|..||-..==.|+.-+. |--+.++.+-+
T Consensus 217 ~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv---D~~v~r~~~r~ 260 (310)
T TIGR00588 217 DAREALCELPGVGPKVADCICLMGLDKPQAVPV---DVHVWRIANRD 260 (310)
T ss_pred HHHHHHHhCCCccHHHHHHHHHHhCCCCCceee---cHHHHHHHHHH
Confidence 356788999999999999999775545554443 45666655543
No 117
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=43.80 E-value=12 Score=34.56 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=30.5
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
...+|+.|.|||..++..+++.+|= -..+.+-|.+|+..
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS--~~~I~~As~eeL~~ 561 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGS--VEGVREASVEDLRD 561 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCC--HHHHHhCCHHHHHh
Confidence 5689999999999999999999872 34455566666644
No 118
>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=43.44 E-value=18 Score=29.34 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.0
Q ss_pred hhcccccCHHHHHHHHHHcC
Q 031813 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lg 49 (152)
...++|||+.+|..++++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34679999999999998865
No 119
>PRK09482 flap endonuclease-like protein; Provisional
Probab=43.36 E-value=18 Score=30.07 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=17.4
Q ss_pred hhcccccCHHHHHHHHHHcC
Q 031813 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lg 49 (152)
...++|||+++|..++++.|
T Consensus 184 IpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCCcChHHHHHHHHHhC
Confidence 35689999999999998877
No 120
>smart00475 53EXOc 5'-3' exonuclease.
Probab=42.74 E-value=19 Score=29.78 Aligned_cols=20 Identities=25% Similarity=0.456 Sum_probs=17.3
Q ss_pred hhcccccCHHHHHHHHHHcC
Q 031813 30 LTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lg 49 (152)
+..++|||+.+|..++++.|
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC
Confidence 34579999999999999887
No 121
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=42.64 E-value=36 Score=27.61 Aligned_cols=63 Identities=21% Similarity=0.265 Sum_probs=40.2
Q ss_pred cchhhhhcCcccCCCeeheeehhcccc-cCHHHHHHHHHHc-CCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 9 FQHILRVLNTNVDGKQKIMFALTSIKG-IGRRLANIVCKKA-DVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aL~~i~G-IG~~~A~~Ic~~l-gi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
|.++++.+ .--..|.+.-+|..+.. .+......+...+ ++++++++.+||.+|+..|.+.+..
T Consensus 192 ~~~~~~~~--F~~rrk~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 192 FDDFVKAL--FQHRRKTLRNALKNSAHISGKEDIKAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHHHH--HccccHHHHHHHhhhccccchhHHHHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 44555432 23456777777777531 2221223345556 4567999999999999999998864
No 122
>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=42.58 E-value=35 Score=24.25 Aligned_cols=35 Identities=17% Similarity=0.350 Sum_probs=30.1
Q ss_pred cccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 34 KGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 34 ~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
--+|......|++.|+ ++..+||+++++-+.+++.
T Consensus 33 es~Gh~sGRrIv~IL~----K~k~dltddD~~hMrkVV~ 67 (92)
T PF11338_consen 33 ESVGHESGRRIVEILR----KRKTDLTDDDYEHMRKVVG 67 (92)
T ss_pred cccCcchhhHHHHHHh----cCcccCCHHHHHHHHHHHH
Confidence 3578888899999998 7789999999999988875
No 123
>PRK14976 5'-3' exonuclease; Provisional
Probab=41.54 E-value=20 Score=30.02 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=16.7
Q ss_pred hcccccCHHHHHHHHHHcC
Q 031813 31 TSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 31 ~~i~GIG~~~A~~Ic~~lg 49 (152)
-.++|||+++|..++++.|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999998877
No 124
>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=40.99 E-value=2.9 Score=29.94 Aligned_cols=19 Identities=21% Similarity=0.380 Sum_probs=15.3
Q ss_pred hcccccCHHHHHHHHHHcC
Q 031813 31 TSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 31 ~~i~GIG~~~A~~Ic~~lg 49 (152)
-.+.|||.++|..++.++|
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 4689999999999999987
No 125
>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=40.95 E-value=25 Score=30.12 Aligned_cols=57 Identities=21% Similarity=0.293 Sum_probs=33.7
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCC--CC-CCCCHHHHHHHHHHHhCC
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNK--RA-GELSAAELDNLMVVVANP 74 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~--~~-~~Ls~~ei~~L~~~l~~~ 74 (152)
++|-.+.=+.|++- + ..|.|||..+|..++++.|==.+. .+ ..+. ...++.+++.+|
T Consensus 224 ~q~id~~iL~G~dy--n-------~Gv~GIG~ktA~kli~~~gsie~il~~~~~~~~--~~~~~~~~f~~~ 283 (338)
T TIGR03674 224 EQLIDIAILVGTDY--N-------EGVKGIGPKTALKLIKEHGDLEKVLKARGEDIE--NYDEIREFFLNP 283 (338)
T ss_pred HHHHHHHHhcCCCC--C-------CCCCCccHHHHHHHHHHcCCHHHHHHhhcCCCC--CHHHHHHHhCCC
Confidence 45666666667632 2 479999999999999874410000 00 0122 236777777775
No 126
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=39.37 E-value=14 Score=31.37 Aligned_cols=57 Identities=18% Similarity=0.296 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CCccccCccCCCCCCchhhhhhhhHHHHHHh--hhhhhhcc
Q 031813 58 ELSAAELDNLMVVVANPRQFK------------------IPDWFLNRQKDYKDGKYSQVVSNALDMKLRD--DLERLKKI 117 (152)
Q Consensus 58 ~Ls~~ei~~L~~~l~~~~~~~------------------ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~--~I~rl~~i 117 (152)
-+|..|++.|++++++.+ |. |..||.|||.-|- +..+- +-.+ +
T Consensus 147 iFT~~Qle~LEkaFkeaH-YPDv~Are~la~ktelpEDRIqVWfQNRRAKWR-------------k~Ek~wg~sT~---m 209 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEAH-YPDVYAREMLADKTELPEDRIQVWFQNRRAKWR-------------KTEKRWGGSTI---M 209 (332)
T ss_pred hhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhccCchhhhhHHhhhhhHHhh-------------hhhhhcCcchh---h
Confidence 368999999999998754 43 5669999886442 11111 2222 2
Q ss_pred ceeec----ccCCCCCcc
Q 031813 118 RNHRG----LRHYWGLRV 131 (152)
Q Consensus 118 ~syRG----~RH~~gLpv 131 (152)
.+|-+ +||.+-||.
T Consensus 210 aeyglyGamvrhslplp~ 227 (332)
T KOG0494|consen 210 AEYGLYGAMVRHSLPLPD 227 (332)
T ss_pred hhhcccchhhcccCCchh
Confidence 34554 899999986
No 127
>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=39.29 E-value=12 Score=24.85 Aligned_cols=45 Identities=13% Similarity=0.192 Sum_probs=33.6
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
+.-.++.+.|+|..-|+.+++.+ |..-...++.++.+.|.+.|+.
T Consensus 16 vIK~vR~~tgl~L~eAK~~vd~~---p~~ik~~v~keeAe~ik~~Le~ 60 (68)
T PF00542_consen 16 VIKEVREITGLGLKEAKKLVDSL---PKVIKEGVSKEEAEEIKKKLEA 60 (68)
T ss_dssp HHHHHHHHC---HHHHHHHHCTT---TEEEEEEE-HHHHHHHHHHHHC
T ss_pred HHHHHHHHhCCcHHHHHHHHHhC---CHHHHcCCCHHHHHHHHHHHHH
Confidence 45677889999999999999888 4555556889999999998876
No 128
>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=39.21 E-value=21 Score=30.69 Aligned_cols=38 Identities=21% Similarity=0.430 Sum_probs=28.9
Q ss_pred eehhcccccCHHHHHHHHHHcCCCCCCCCCCC--CHHHHH
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGEL--SAAELD 65 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~L--s~~ei~ 65 (152)
.-+..+.|||..++..+++.+||..-..+-.+ +.+++.
T Consensus 182 lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 45789999999999999999999865444444 555444
No 129
>PRK13766 Hef nuclease; Provisional
Probab=39.08 E-value=24 Score=32.96 Aligned_cols=24 Identities=17% Similarity=0.241 Sum_probs=21.2
Q ss_pred heeehhcccccCHHHHHHHHHHcC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
..+.|..|.|||..+|..|++.+|
T Consensus 713 ~~~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 713 QEYIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcC
Confidence 344799999999999999999987
No 130
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=38.85 E-value=28 Score=24.79 Aligned_cols=41 Identities=20% Similarity=0.340 Sum_probs=29.2
Q ss_pred CCCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchh
Q 031813 54 KRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYS 96 (152)
Q Consensus 54 ~~~~~Ls~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~ 96 (152)
+...+||++|++.+..+|+.+. -.+-.|+.++.+ +.+..+.
T Consensus 39 ~~~~~lsd~el~~f~~LLe~~D-~dL~~Wi~g~~~-~~~~~~~ 79 (94)
T COG2938 39 KEFDSLSDEELDEFERLLECED-NDLFNWIMGHGE-PPDAELT 79 (94)
T ss_pred HHHhhCCHHHHHHHHHHHcCCc-HHHHHHHhCCCC-CCcHHHH
Confidence 3457899999999999998753 345578888776 4433333
No 131
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=38.83 E-value=23 Score=29.55 Aligned_cols=41 Identities=32% Similarity=0.346 Sum_probs=29.8
Q ss_pred eeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 24 k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
..-.+.|.+|+|||...|..+++.+|= -..+-..|++|+..
T Consensus 178 e~q~~il~s~pgig~~~a~~ll~~fgS--~~~~~tas~~eL~~ 218 (254)
T COG1948 178 ELQLYILESIPGIGPKLAERLLKKFGS--VEDVLTASEEELMK 218 (254)
T ss_pred HHHHHHHHcCCCccHHHHHHHHHHhcC--HHHHhhcCHHHHHH
Confidence 334678899999999999999998873 23444555555544
No 132
>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=38.57 E-value=19 Score=22.17 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=31.5
Q ss_pred ehhcccccCHHHHHHHH-HHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 29 ALTSIKGIGRRLANIVC-KKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic-~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
-|.+-.|+...-....| ..+|+.....-..|+++++..|.+.++
T Consensus 8 elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 8 ELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp HHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred HHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 45667788888888889 559999677778889999998888764
No 133
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=37.63 E-value=17 Score=34.39 Aligned_cols=43 Identities=7% Similarity=0.196 Sum_probs=31.8
Q ss_pred CCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 22 ~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
..+.+...|..|+|||+.....+++.+|= -..+..-|.+||..
T Consensus 602 ~k~~~~s~L~~IpGiG~kr~~~LL~~FgS--~~~i~~As~eel~~ 644 (691)
T PRK14672 602 TKKELVLSFERLPHVGKVRAHRLLAHFGS--FRSLQSATPQDIAT 644 (691)
T ss_pred hhhhcccccccCCCCCHHHHHHHHHHhcC--HHHHHhCCHHHHHh
Confidence 34455678999999999999999999883 34455556666644
No 134
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=36.93 E-value=17 Score=33.90 Aligned_cols=50 Identities=22% Similarity=0.329 Sum_probs=35.7
Q ss_pred cCcccCCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 16 ~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
.+-..-..+.+.-.|..|.|||+.+|..|++.+|=- ..+..-+.+||.++
T Consensus 557 yhr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~--~~i~~As~eeL~~v 606 (621)
T PRK14671 557 YHRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFGSV--EKVAKASLEELAAV 606 (621)
T ss_pred hChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcCCH--HHHHhCCHHHHHHH
Confidence 344455556677888999999999999999999621 33444566776654
No 135
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=36.63 E-value=23 Score=29.72 Aligned_cols=30 Identities=23% Similarity=0.180 Sum_probs=22.5
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCC
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNK 54 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~ 54 (152)
.+.-.|++|.|||+-||.-++-..-=.++.
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~llf~lgr~dv 224 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFLLFGLGRPDV 224 (285)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHcCCCCCC
Confidence 356679999999999999998664333444
No 136
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=36.54 E-value=31 Score=27.44 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=21.4
Q ss_pred eehhcccccCHHHHHHHHHHcCCC
Q 031813 28 FALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~ 51 (152)
.++|..+|+|++|+...++.+|++
T Consensus 3 I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 3 IAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred EEEeCCCCCchHHHHHHHHHhCCc
Confidence 578999999999999999988875
No 137
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=36.39 E-value=29 Score=30.78 Aligned_cols=45 Identities=13% Similarity=0.076 Sum_probs=39.7
Q ss_pred eehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
--|+.|.|||...+.. +..+||.....+-.++++++..+...+.-
T Consensus 323 DDLk~I~GIGpk~e~~-Ln~~Gi~~f~QIA~wt~~eia~vd~~l~f 367 (400)
T PRK12373 323 DDLKLISGVGPKIEAT-LNELGIFTFDQVAAWKKAERAWVDGYLNF 367 (400)
T ss_pred hhhhhccCCChHHHHH-HHhcCCCCHHHHhCCCHHHhHHhhhcccC
Confidence 4589999999998876 67899999999999999999999888863
No 138
>PRK07945 hypothetical protein; Provisional
Probab=36.27 E-value=24 Score=30.08 Aligned_cols=21 Identities=33% Similarity=0.623 Sum_probs=18.3
Q ss_pred ehhcccccCHHHHHHHHHHcC
Q 031813 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lg 49 (152)
.|++++|||..+|..|-+.+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 699999999999999987644
No 139
>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=35.52 E-value=42 Score=23.90 Aligned_cols=58 Identities=19% Similarity=0.100 Sum_probs=42.7
Q ss_pred cCcccCCCeeheeehhcccccCHHHHHHHHHHcCCC---CCCCCCCCCHHHHHHHHHHHhC
Q 031813 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 16 ~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~---~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
+|..||-|..-..+.+++.|.=+..|..|+.-+=.+ .=..+..||+.|-+.|...+++
T Consensus 11 ~G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~ 71 (93)
T PF06514_consen 11 LGQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDN 71 (93)
T ss_dssp CCTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGG
T ss_pred cCCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhcc
Confidence 456677777778899999999999999999765333 2335667899999999999987
No 140
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=34.27 E-value=45 Score=24.06 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHHHHHhC
Q 031813 57 GELSAAELDNLMVVVAN 73 (152)
Q Consensus 57 ~~Ls~~ei~~L~~~l~~ 73 (152)
+.||++|-+.|.++|..
T Consensus 1 s~Lt~eE~~~I~~Vl~R 17 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQR 17 (118)
T ss_dssp TTS-CHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 46999999999999976
No 141
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=33.49 E-value=34 Score=30.68 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=22.0
Q ss_pred CeeheeehhcccccCHHHHHHHHHH
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
+..|.|+|..|+|||...+.+|.+.
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~e 133 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKA 133 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHH
Confidence 3469999999999999999999764
No 142
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.72 E-value=25 Score=28.43 Aligned_cols=25 Identities=24% Similarity=0.403 Sum_probs=22.1
Q ss_pred eeehhcccccCHHHHHHHHHHcCCC
Q 031813 27 MFALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~lgi~ 51 (152)
.+.+.+|+|||+.-|.-++.-.|+.
T Consensus 120 E~Lv~nikGiGyKEASHFLRNVG~~ 144 (210)
T COG1059 120 ELLVENIKGIGYKEASHFLRNVGFE 144 (210)
T ss_pred HHHHHHcccccHHHHHHHHHhcChh
Confidence 5677799999999999999998874
No 143
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=30.94 E-value=36 Score=28.01 Aligned_cols=32 Identities=25% Similarity=0.540 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CCccccCccCCC
Q 031813 58 ELSAAELDNLMVVVANPRQFK------------------IPDWFLNRQKDY 90 (152)
Q Consensus 58 ~Ls~~ei~~L~~~l~~~~~~~------------------ip~w~~nr~~D~ 90 (152)
.++..|++.|++++++- .|. |-.||.|||+++
T Consensus 43 tFtr~QlevLe~LF~kT-qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~ 92 (228)
T KOG2251|consen 43 TFTRKQLEVLEALFAKT-QYPDVFMREELALKLNLPESRVQVWFKNRRAKC 92 (228)
T ss_pred eecHHHHHHHHHHHHhh-cCccHHHHHHHHHHhCCchhhhhhhhccccchh
Confidence 46788999998888762 232 455777877644
No 144
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=30.86 E-value=15 Score=26.58 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=30.3
Q ss_pred ccchhhhhcCcccCC---CeeheeehhcccccCHHHHHHHHHHcC
Q 031813 8 DFQHILRVLNTNVDG---KQKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 8 ~~~~~vri~~~~l~~---~k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
.|-.+|---|+||+. +.-....|+-+-|.|++.|..+.+.+.
T Consensus 27 ~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 27 AFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp HHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred HHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 355667777888763 556678899999999999999998765
No 145
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=30.82 E-value=40 Score=28.17 Aligned_cols=39 Identities=23% Similarity=0.284 Sum_probs=27.1
Q ss_pred eeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
...|.+++|||+.+|..+ ...||..-..+-.++++++.+
T Consensus 5 ~~~l~~l~gIg~~~a~~L-~~~Gi~t~~dl~~~~~~~L~~ 43 (317)
T PRK04301 5 EKDLEDLPGVGPATAEKL-REAGYDTVEAIAVASPKELSE 43 (317)
T ss_pred cccHhhcCCCCHHHHHHH-HHcCCCCHHHHHcCCHHHHHH
Confidence 346789999999888775 567777655555555555544
No 146
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=30.47 E-value=54 Score=24.91 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=18.0
Q ss_pred eeehhcccccCHHHHHHHHHHc
Q 031813 27 MFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 27 ~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.--|..++|||.+.|.+|.+.-
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 3445999999999999998653
No 147
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=30.15 E-value=30 Score=32.86 Aligned_cols=39 Identities=15% Similarity=0.220 Sum_probs=27.7
Q ss_pred eheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHH
Q 031813 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (152)
Q Consensus 25 ~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~ 65 (152)
.+.-.|..|.|||+.++..+++.+| .-..+.+-+.+||.
T Consensus 634 ~~~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa 672 (694)
T PRK14666 634 ALTGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLA 672 (694)
T ss_pred hhHhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHH
Confidence 3456789999999999999999988 22333334445543
No 148
>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=29.90 E-value=39 Score=31.25 Aligned_cols=26 Identities=19% Similarity=0.264 Sum_probs=22.4
Q ss_pred eeheeehhcccccCHHHHHHHHHHcC
Q 031813 24 QKIMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 24 k~v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
..+.-.|.+|+|||+.+...+++.+|
T Consensus 537 ~~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 537 ASLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 34456889999999999999999887
No 149
>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=29.68 E-value=51 Score=20.62 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=12.6
Q ss_pred CCCHHHHHHHHHHH
Q 031813 58 ELSAAELDNLMVVV 71 (152)
Q Consensus 58 ~Ls~~ei~~L~~~l 71 (152)
.||++|+..|.++|
T Consensus 54 ~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 54 QLSDEEIEALAAYI 67 (67)
T ss_dssp TSTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHC
Confidence 69999999999876
No 150
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=28.95 E-value=34 Score=29.22 Aligned_cols=22 Identities=18% Similarity=0.428 Sum_probs=19.5
Q ss_pred ehhcccccCHHHHHHHHHHcCC
Q 031813 29 ALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi 50 (152)
.|++++|||..+|..|.+.+.=
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~t 70 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIET 70 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHHh
Confidence 5889999999999999988763
No 151
>COG1636 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.55 E-value=43 Score=27.06 Aligned_cols=72 Identities=14% Similarity=0.171 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceeecccCCCCCccCCcCCcccCC
Q 031813 62 AELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGR 141 (152)
Q Consensus 62 ~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNar 141 (152)
.||+.+-.-++++ |+++.|..|.+|. ++-.+.+...-+...=-.+|=|+ ..+|.-.+|+-++++|
T Consensus 127 ~qin~~G~~~~k~--y~V~yl~~dfrK~-----------gg~~r~~elske~~~YrQ~YCGC--vysl~~q~~~~~~~~r 191 (204)
T COG1636 127 NQINEIGERAAKP--YGVVYLPSNFRKN-----------GGYQRSIELSKEENIYRQEYCGC--VYSLKDQNEDRKEVNR 191 (204)
T ss_pred HHHHHHhHHhhcc--cCceecCcccccc-----------cchHHHHHHHHHHhHHHhhccch--hhhHhhhcchhhhhch
Confidence 4777777778775 7888899888863 33333333322222223678776 4678888888899988
Q ss_pred Cccceee
Q 031813 142 RGKTVGV 148 (152)
Q Consensus 142 t~~~~gv 148 (152)
-...+|.
T Consensus 192 ~~~~~~~ 198 (204)
T COG1636 192 QAIPFGK 198 (204)
T ss_pred hhhhHHh
Confidence 8777664
No 152
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.47 E-value=48 Score=32.98 Aligned_cols=35 Identities=11% Similarity=0.123 Sum_probs=27.0
Q ss_pred cccchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHHcCC
Q 031813 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 7 ~~~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi 50 (152)
++|-.+.-++|+|-.. .|.|||..+|..|++..|=
T Consensus 854 ~qli~laiL~G~DY~~---------GI~GIGpktAl~li~~~~~ 888 (1034)
T TIGR00600 854 NKLINLAYLLGSDYTE---------GIPTVGPVSAMEILNEFPG 888 (1034)
T ss_pred HHHHHHHHeeCCCCCC---------CCCcccHHHHHHHHHHcCC
Confidence 4566666677766543 6999999999999999883
No 153
>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=28.34 E-value=24 Score=29.69 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=19.7
Q ss_pred ehhcccccCHHHHHHHHHHcCCC
Q 031813 29 ALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~ 51 (152)
.+++++|||..+|..|.+.+.-.
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG 68 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETG 68 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcC
Confidence 55899999999999999887643
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=27.68 E-value=42 Score=27.73 Aligned_cols=36 Identities=25% Similarity=0.305 Sum_probs=24.5
Q ss_pred hhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
+.+++|||..++..+. ..||..-..+...+.+++..
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~ 36 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSE 36 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHh
Confidence 4578999999988865 56776555555555555544
No 155
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=27.68 E-value=2.1e+02 Score=23.75 Aligned_cols=92 Identities=14% Similarity=0.111 Sum_probs=57.4
Q ss_pred hhhhcCcc-cCCCeeheeeh---hcccccC----HHHHHHHHHHcCCCC--CCCCCCCCHHHHHHHH---HHHhCCCCcc
Q 031813 12 ILRVLNTN-VDGKQKIMFAL---TSIKGIG----RRLANIVCKKADVDM--NKRAGELSAAELDNLM---VVVANPRQFK 78 (152)
Q Consensus 12 ~vri~~~~-l~~~k~v~~aL---~~i~GIG----~~~A~~Ic~~lgi~~--~~~~~~Ls~~ei~~L~---~~l~~~~~~~ 78 (152)
+-++.... +.+...+.-.| .++||.. ...+..+++.+|+.. ++++++||--+-.++. .++.+|
T Consensus 80 igy~~~~~~~~~~lT~~e~l~~~~~l~~~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ia~aL~~~P---- 155 (293)
T COG1131 80 IGYVPQEPSLYPELTVRENLEFFARLYGLSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLSIALALLHDP---- 155 (293)
T ss_pred eEEEccCCCCCccccHHHHHHHHHHHhCCChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHHHHHHHhcCC----
Confidence 44444433 45555554433 6788887 567889999999998 7889999988766554 333443
Q ss_pred CCccccCccCCCCCCchhhhhhhhHHHHHH
Q 031813 79 IPDWFLNRQKDYKDGKYSQVVSNALDMKLR 108 (152)
Q Consensus 79 ip~w~~nr~~D~~sg~~~~lie~~L~~~~~ 108 (152)
+-+++=.+...++|.....+-.-|+....
T Consensus 156 -~lliLDEPt~GLDp~~~~~~~~~l~~l~~ 184 (293)
T COG1131 156 -ELLILDEPTSGLDPESRREIWELLRELAK 184 (293)
T ss_pred -CEEEECCCCcCCCHHHHHHHHHHHHHHHh
Confidence 22444445556666666555555544333
No 156
>PF13276 HTH_21: HTH-like domain
Probab=27.68 E-value=50 Score=20.54 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=29.1
Q ss_pred cCCCeeheeehhcccc--cCHHHHHHHHHHcCCCCC
Q 031813 20 VDGKQKIMFALTSIKG--IGRRLANIVCKKADVDMN 53 (152)
Q Consensus 20 l~~~k~v~~aL~~i~G--IG~~~A~~Ic~~lgi~~~ 53 (152)
.-|...+...|..-+| ||..+...|+..+||...
T Consensus 20 ~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 20 TYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred CeehhHHHHHHhccCcccccHHHHHHHHHHcCCccc
Confidence 6678888889988876 799999999999999754
No 157
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=27.35 E-value=34 Score=28.82 Aligned_cols=38 Identities=21% Similarity=0.416 Sum_probs=28.8
Q ss_pred ccchhhhhcCcccCCCeeh-eeehhcccccCHHHHHHHH
Q 031813 8 DFQHILRVLNTNVDGKQKI-MFALTSIKGIGRRLANIVC 45 (152)
Q Consensus 8 ~~~~~vri~~~~l~~~k~v-~~aL~~i~GIG~~~A~~Ic 45 (152)
-++.+.+|+..+.+|.-+- .-.|-+.+|||+++|.-.+
T Consensus 138 ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKMa~L~m 176 (286)
T KOG1921|consen 138 YLKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHLTM 176 (286)
T ss_pred HHHHHHHHHHHHhCCCCchhHHHHhcCCCCchHHHHHHH
Confidence 3677888888777777665 3467889999999997544
No 158
>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=26.62 E-value=46 Score=21.70 Aligned_cols=21 Identities=24% Similarity=0.281 Sum_probs=17.5
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
.-|.+|+|+|..+...|.+.+
T Consensus 44 ~~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 44 EDLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp HHHHTSTTSHHHHHHHHHHHH
T ss_pred HHHHhCCCCCHhHHHHHHHHH
Confidence 357899999999999988764
No 159
>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=26.59 E-value=1.5e+02 Score=24.19 Aligned_cols=27 Identities=15% Similarity=0.331 Sum_probs=18.7
Q ss_pred HHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCC
Q 031813 42 NIVCKKADVDMNKRAGELSAAELDNLMVVVANPR 75 (152)
Q Consensus 42 ~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~ 75 (152)
..++..++|+ ||++|+..|.+++.+..
T Consensus 182 ~~~~~~~~i~-------ls~~q~~~i~~l~~~~~ 208 (225)
T PF06207_consen 182 NNVLNNYNIN-------LSDEQIQQIVNLMKKIQ 208 (225)
T ss_pred HHHHHHcCCC-------CCHHHHHHHHHHHHHHH
Confidence 3445556655 88888888888887743
No 160
>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=26.32 E-value=61 Score=21.37 Aligned_cols=24 Identities=21% Similarity=0.260 Sum_probs=16.9
Q ss_pred ehhcccccCHHHHHHHHHHcCCCC
Q 031813 29 ALTSIKGIGRRLANIVCKKADVDM 52 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~~ 52 (152)
.|.+--||+..+..++|+++|++.
T Consensus 39 elA~~~~vS~sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 39 ELAEKAGVSPSTIVRFCKKLGFSG 62 (77)
T ss_dssp HHHHHCTS-HHHHHHHHHHCTTTC
T ss_pred HHHHHcCCCHHHHHHHHHHhCCCC
Confidence 345566888888888888888763
No 161
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=26.26 E-value=30 Score=32.40 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=17.8
Q ss_pred heeehhcccccCHHHHHHHHHHcC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
+.+|| .|+|||..+|+.|++.++
T Consensus 497 ~L~aL-gIpgVG~~~ak~L~~~f~ 519 (652)
T TIGR00575 497 LLFAL-GIRHVGEVTAKNLAKHFG 519 (652)
T ss_pred HHhhc-cCCCcCHHHHHHHHHHhC
Confidence 33444 789999999999988876
No 162
>KOG0821 consensus Predicted ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=26.10 E-value=89 Score=26.30 Aligned_cols=35 Identities=23% Similarity=0.263 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 39 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 39 ~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
..+..+++++.|||..+.-.|+-||...|.+..++
T Consensus 270 E~~~~Ll~~~~idpT~r~~~L~iEQf~~LAE~Y~E 304 (326)
T KOG0821|consen 270 ESTGRLLELADIDPTLRPRQLSIEQFKSLAEVYRE 304 (326)
T ss_pred HHHHHHHHHhcCCCccCceeeeHHHHHHHHHHHHH
Confidence 45778999999999999999999999999998765
No 163
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=25.89 E-value=47 Score=32.09 Aligned_cols=39 Identities=26% Similarity=0.342 Sum_probs=28.9
Q ss_pred heeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
..+ |.+++|||...|..|++.+| .=..+-.+|.+|+..+
T Consensus 756 q~~-L~~lPgI~~~~a~~ll~~f~--si~~l~~as~eeL~~~ 794 (814)
T TIGR00596 756 QDF-LLKLPGVTKKNYRNLRKKVK--SIRELAKLSQNELNEL 794 (814)
T ss_pred HHH-HHHCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHHH
Confidence 355 77999999999999999866 3344555676666553
No 164
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=25.83 E-value=41 Score=23.01 Aligned_cols=21 Identities=24% Similarity=0.249 Sum_probs=15.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhC
Q 031813 53 NKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 53 ~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
...+.+||++|..+|..+-++
T Consensus 34 g~~~R~Lt~~E~~eL~~y~~~ 54 (76)
T PF06394_consen 34 GKYARDLTPDEQQELKTYQKK 54 (76)
T ss_dssp TCEEEE--HHHHHHHHHHHHH
T ss_pred CEeeccCCHHHHHHHHHHHHH
Confidence 456889999999999998765
No 165
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=25.66 E-value=47 Score=30.88 Aligned_cols=43 Identities=26% Similarity=0.274 Sum_probs=32.9
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
...+...|-.|.|||.....++++.+|= -..+.+-|.+|+..+
T Consensus 525 k~~~~s~Ld~I~GiG~~r~~~LL~~Fgs--~~~i~~As~eel~~v 567 (581)
T COG0322 525 KAMLQSSLDDIPGIGPKRRKALLKHFGS--LKGIKSASVEELAKV 567 (581)
T ss_pred hhhhcCccccCCCcCHHHHHHHHHHhhC--HHHHHhcCHHHHHHc
Confidence 3445677889999999999999999883 445666677777664
No 166
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.38 E-value=46 Score=28.99 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=27.2
Q ss_pred cchhhhhcCcccCCCeeheeehhcccccCHHHHHHHHHH
Q 031813 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 9 ~~~~vri~~~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
.+.++.-.|-.+|++.. .|..+.|||.+||.+|+.-
T Consensus 97 A~~v~~~~~G~~P~~~~---~l~~LpGiG~yTa~Ail~~ 132 (342)
T COG1194 97 AQEVVERHGGEFPDDEE---ELAALPGVGPYTAGAILSF 132 (342)
T ss_pred HHHHHHHcCCCCCCCHH---HHHhCCCCcHHHHHHHHHH
Confidence 35666777777777654 5666999999999999854
No 167
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=24.82 E-value=23 Score=24.66 Aligned_cols=40 Identities=18% Similarity=0.195 Sum_probs=30.0
Q ss_pred CCCeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q 031813 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (152)
Q Consensus 21 ~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~ 66 (152)
++.+.-...|...-|||+.-+++++++|..- .+|.+|+..
T Consensus 45 ~~s~~rR~~l~~~L~iGy~N~KqllkrLN~f------~it~~e~~~ 84 (87)
T PF13331_consen 45 PDSKERREKLGEYLGIGYGNAKQLLKRLNMF------GITREEFEE 84 (87)
T ss_pred ccHHHHHHHHHHHHCCCCCCHHHHHHHHHHc------CCCHHHHHH
Confidence 3446677888889999999999999887642 256677665
No 168
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=24.41 E-value=60 Score=19.89 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=17.0
Q ss_pred eehhcccccCHHHHHHHHHHc
Q 031813 28 FALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~l 48 (152)
..|...+||+.+++..++..+
T Consensus 23 ~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 23 QDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred hHHhhheeecHHHHHHHHHHH
Confidence 456778999999999998653
No 169
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=24.27 E-value=1.5e+02 Score=18.42 Aligned_cols=37 Identities=27% Similarity=0.364 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHHhCCCCccCCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhcc
Q 031813 60 SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKI 117 (152)
Q Consensus 60 s~~ei~~L~~~l~~~~~~~ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i 117 (152)
+++|++.|.++|.+|. ++ =|..|+..+....+.+..|
T Consensus 6 ~~e~ld~L~~aL~~pr--G~-------------------RE~~L~~~L~~~~k~~~~~ 42 (46)
T PF15614_consen 6 DPEELDELLKALENPR--GK-------------------RESKLKKELDKHRKGPLEI 42 (46)
T ss_pred CHHHHHHHHHHHcCcc--cH-------------------hHHHHHHHHHHHhcchhhh
Confidence 5789999999886542 22 2777777776655444333
No 170
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=24.10 E-value=34 Score=29.33 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=19.6
Q ss_pred heeehhcccccCHHHHHHHHHH
Q 031813 26 IMFALTSIKGIGRRLANIVCKK 47 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~ 47 (152)
+.-+|+.++|||++.|.-||-.
T Consensus 216 ar~~L~~lpGVG~KVADCI~Lm 237 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCICLM 237 (323)
T ss_pred HHHHHhcCCCCcchHhhhhhhh
Confidence 5678999999999999999964
No 171
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=23.75 E-value=1.1e+02 Score=20.32 Aligned_cols=47 Identities=6% Similarity=0.033 Sum_probs=32.9
Q ss_pred heeehhcccccCHHHHHHHH--------------HHcCCCCCCCCCCCCHHHHHHHHHHHhCC
Q 031813 26 IMFALTSIKGIGRRLANIVC--------------KKADVDMNKRAGELSAAELDNLMVVVANP 74 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic--------------~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~ 74 (152)
-+.|+..++++-...|..-+ ..+|.++.. ..||+.|+..|.+.+.+|
T Consensus 9 ~ELA~lYfP~~~~~sA~r~L~rwI~~~~~L~~~L~~~Gy~~~~--r~~TP~QV~lIv~~LGeP 69 (69)
T PF14053_consen 9 SELAQLYFPDLTPSSAVRKLRRWIRRNPELLEELEATGYHPRQ--RSFTPRQVRLIVRYLGEP 69 (69)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHCHHHHHHHHHcCCCCCC--EecCHHHHHHHHHHcCCC
Confidence 34566677777666665433 346776655 569999999999998763
No 172
>cd08334 DED_Caspase_8_10_repeat2 Death effector domain, repeat 2, of initator caspases 8 and 10. Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis, and they play partially redundant roles. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. They contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains foun
Probab=23.18 E-value=82 Score=21.51 Aligned_cols=62 Identities=13% Similarity=0.173 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHhCCC------Cc-c-CCccccCccCCCCCCchhhhhhhhHHHHHHhhhhhhhccceee
Q 031813 57 GELSAAELDNLMVVVANPR------QF-K-IPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHR 121 (152)
Q Consensus 57 ~~Ls~~ei~~L~~~l~~~~------~~-~-ip~w~~nr~~D~~sg~~~~lie~~L~~~~~~~I~rl~~i~syR 121 (152)
.+|++++++.+.-++...- +. . +..|..--..+.+++.|...++.-|... +.|.-+ +|..|+
T Consensus 13 e~Lt~~dl~~lKFLc~d~ip~~kle~~~s~ldlf~~Lek~~~l~~~nl~~L~elL~~i-r~dLl~--~I~~y~ 82 (83)
T cd08334 13 EDLTKENLDKLKFLLSSKLPRSKLEDNKTLLDVFVEMEKQGLLGEDNLDELKRILKSL-DKKLAK--KIEKYE 82 (83)
T ss_pred HhcCHHHHHHHHHHhHhhcchhhhhccCCHHHHHHHHHHcCCCCCccHHHHHHHHHHH-HHHHHH--HHHHHh
Confidence 3577888888777765310 00 0 0012223356678888888899988877 888776 555553
No 173
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=23.18 E-value=58 Score=28.22 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=17.6
Q ss_pred ehhcccccCHHHHHHHHHHcC
Q 031813 29 ALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lg 49 (152)
++|+++|||+.+|..|-+.+.
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l~ 74 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYLD 74 (326)
T ss_pred ccCCCCCccHHHHHHHHHHHH
Confidence 589999999999999876543
No 174
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=23.08 E-value=1.4e+02 Score=29.65 Aligned_cols=26 Identities=35% Similarity=0.506 Sum_probs=22.9
Q ss_pred CeeheeehhcccccCHHHHHHHHHHc
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKA 48 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~l 48 (152)
+..|.++|..|.|||...|..|.+.-
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R 772 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSAL 772 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHH
Confidence 45799999999999999999998643
No 175
>KOG1647 consensus Vacuolar H+-ATPase V1 sector, subunit D [Energy production and conversion]
Probab=23.05 E-value=48 Score=27.43 Aligned_cols=23 Identities=39% Similarity=0.577 Sum_probs=20.3
Q ss_pred hhhhHHHHHHhhhhhhhccceee
Q 031813 99 VSNALDMKLRDDLERLKKIRNHR 121 (152)
Q Consensus 99 ie~~L~~~~~~~I~rl~~i~syR 121 (152)
|.++|+..-++|.-||++|..++
T Consensus 187 I~sELdE~eRedF~RLKKiQ~~K 209 (255)
T KOG1647|consen 187 IVSELDELEREDFYRLKKIQAKK 209 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 68899999999999999997764
No 176
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.03 E-value=71 Score=17.48 Aligned_cols=13 Identities=23% Similarity=0.263 Sum_probs=7.2
Q ss_pred CHHHHHHHHHHHh
Q 031813 60 SAAELDNLMVVVA 72 (152)
Q Consensus 60 s~~ei~~L~~~l~ 72 (152)
+.+.+..|.+++.
T Consensus 38 ~~~~~~~i~~~~~ 50 (56)
T smart00530 38 SLETLKKLAKALG 50 (56)
T ss_pred CHHHHHHHHHHhC
Confidence 5555555555553
No 177
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=23.02 E-value=54 Score=30.21 Aligned_cols=85 Identities=14% Similarity=0.210 Sum_probs=61.2
Q ss_pred CeeheeehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhCCC----CccCCccccCccCCCCCCchhhh
Q 031813 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPR----QFKIPDWFLNRQKDYKDGKYSQV 98 (152)
Q Consensus 23 ~k~v~~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~~~----~~~ip~w~~nr~~D~~sg~~~~l 98 (152)
.++...|||.=+|=-......+|+-|||. +.-+..=.+.++.. ++..-. +..+|+|+- -
T Consensus 161 k~~~ilgLTASPGs~~ekI~eV~~nLgIe-~vevrTE~d~DV~~---Yv~~~kve~ikV~lp~e~~-------------~ 223 (542)
T COG1111 161 KNPLILGLTASPGSDLEKIQEVVENLGIE-KVEVRTEEDPDVRP---YVKKIKVEWIKVDLPEEIK-------------E 223 (542)
T ss_pred cCceEEEEecCCCCCHHHHHHHHHhCCcc-eEEEecCCCccHHH---hhccceeEEEeccCcHHHH-------------H
Confidence 44589999999999999999999999997 34444434444444 554310 122354444 3
Q ss_pred hhhhHHHHHHhhhhhhhccceeeccc
Q 031813 99 VSNALDMKLRDDLERLKKIRNHRGLR 124 (152)
Q Consensus 99 ie~~L~~~~~~~I~rl~~i~syRG~R 124 (152)
|-..|+..+++-.+.|++.+-|.+..
T Consensus 224 ir~~l~~~l~~~Lk~L~~~g~~~~~~ 249 (542)
T COG1111 224 IRDLLRDALKPRLKPLKELGVIESSS 249 (542)
T ss_pred HHHHHHHHHHHHHHHHHHcCceeccC
Confidence 77888888999999999999998876
No 178
>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=22.81 E-value=46 Score=31.22 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=23.5
Q ss_pred cccccCHHHHHHHHHHcCCCCCCCCCCCCHHHH
Q 031813 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (152)
Q Consensus 32 ~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei 64 (152)
+|.|+|+.++.++.+..++..-.-+-.|+.+++
T Consensus 436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L 468 (652)
T TIGR00575 436 DIEGLGDKVIEQLFEKKLVRSVADLYALKKEDL 468 (652)
T ss_pred CCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHH
Confidence 689999999999999888864333334444443
No 179
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=22.79 E-value=76 Score=24.06 Aligned_cols=37 Identities=14% Similarity=0.066 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 37 GRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 37 G~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
....|.+.++.+|+..=-.++.++.+-++.|.++|++
T Consensus 107 ~i~~a~~~L~~aG~~~if~vS~~~~eGi~eL~~~L~~ 143 (143)
T PF10662_consen 107 NIERAKKWLKNAGVKEIFEVSAVTGEGIEELKDYLEE 143 (143)
T ss_pred hHHHHHHHHHHcCCCCeEEEECCCCcCHHHHHHHHhC
Confidence 4456777888888888778888888888888888763
No 180
>PRK02362 ski2-like helicase; Provisional
Probab=22.65 E-value=61 Score=30.45 Aligned_cols=39 Identities=15% Similarity=0.288 Sum_probs=30.8
Q ss_pred eehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 28 ~aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
..|..++|||+..|..+.+ +||..-..+-.++++++..|
T Consensus 652 ~~L~~ip~i~~~~a~~l~~-~gi~s~~dl~~~~~~~l~~~ 690 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYN-AGIESRADLRAADKSVVLAI 690 (737)
T ss_pred HHHhCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHH
Confidence 4567899999999977665 99988666667777777776
No 181
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.42 E-value=46 Score=26.87 Aligned_cols=21 Identities=29% Similarity=0.408 Sum_probs=16.6
Q ss_pred hhcccccCHHHHHHHHHHcCC
Q 031813 30 LTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 30 L~~i~GIG~~~A~~Ic~~lgi 50 (152)
|++|.|||...|..|.....+
T Consensus 62 L~~i~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 62 LSSVPGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHhCcCCcHHHHHHHHHHHHH
Confidence 889999999999888654433
No 182
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=22.35 E-value=74 Score=26.27 Aligned_cols=38 Identities=18% Similarity=0.300 Sum_probs=26.7
Q ss_pred ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHH
Q 031813 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L 67 (152)
.|..|.|||..++..+++. |+..-..+..-|.+||..+
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 5789999999999999765 5555555544455555444
No 183
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.11 E-value=41 Score=31.67 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=25.2
Q ss_pred hcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHH
Q 031813 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (152)
Q Consensus 31 ~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~ 65 (152)
-+|.|+|+.++.++.+..+|..-.-+..|+.+++.
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~ 482 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLL 482 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHh
Confidence 46899999999999999888753334445554443
No 184
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.95 E-value=1.6e+02 Score=17.98 Aligned_cols=37 Identities=16% Similarity=0.245 Sum_probs=22.0
Q ss_pred ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHh
Q 031813 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~ 72 (152)
.|.+--||.+.+...++. .++..++-+.+..|..+|.
T Consensus 15 ~La~~~gis~~tl~~~~~-------~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 15 DLARKTGISRSTLSRILN-------GKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp HHHHHHT--HHHHHHHHT-------TT-----HHHHHHHHHHHT
T ss_pred HHHHHHCcCHHHHHHHHh-------cccccccHHHHHHHHHHcC
Confidence 345566788888777774 3356788899999999885
No 185
>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=21.91 E-value=86 Score=19.59 Aligned_cols=16 Identities=25% Similarity=0.333 Sum_probs=14.5
Q ss_pred CCCHHHHHHHHHHHhC
Q 031813 58 ELSAAELDNLMVVVAN 73 (152)
Q Consensus 58 ~Ls~~ei~~L~~~l~~ 73 (152)
.||++|+..|.++|..
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 7999999999999864
No 186
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=21.75 E-value=45 Score=24.22 Aligned_cols=20 Identities=40% Similarity=0.517 Sum_probs=15.7
Q ss_pred CCCCCCCCHHHHHHHHHHHh
Q 031813 53 NKRAGELSAAELDNLMVVVA 72 (152)
Q Consensus 53 ~~~~~~Ls~~ei~~L~~~l~ 72 (152)
.+|+.+||+||+++|.+-++
T Consensus 84 qkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhc
Confidence 35677899999998887764
No 187
>PRK03352 DNA polymerase IV; Validated
Probab=21.32 E-value=80 Score=26.56 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=27.2
Q ss_pred ehhcccccCHHHHHHHHHHcCCCCCCCCCCCCHHHHH
Q 031813 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~ 65 (152)
-+..+.|||..++..+ ..+||..=..+-.++.+++.
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 4678899999999985 78999875555555666654
No 188
>PRK13618 psbV cytochrome c-550; Provisional
Probab=20.77 E-value=1.1e+02 Score=23.85 Aligned_cols=17 Identities=12% Similarity=0.233 Sum_probs=14.7
Q ss_pred CCCCCHHHHHHHHHHHh
Q 031813 56 AGELSAAELDNLMVVVA 72 (152)
Q Consensus 56 ~~~Ls~~ei~~L~~~l~ 72 (152)
+++|||+|+..|..+|=
T Consensus 130 ~~~Lsd~eL~ava~yll 146 (163)
T PRK13618 130 MRNLTDKDLEAIAGHIL 146 (163)
T ss_pred CCCCCHHHHHHHHHHHH
Confidence 55799999999999874
No 189
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=20.73 E-value=1.7e+02 Score=19.26 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=21.4
Q ss_pred HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHHhC
Q 031813 38 RRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 38 ~~~A~~Ic~~lgi~~~~~~~~Ls~~ei~~L~~~l~~ 73 (152)
+.....||+..|++| |+..++..+..-|+.
T Consensus 22 y~~Y~~lc~~~~~~p------ls~~r~~~~l~eL~~ 51 (85)
T PF09079_consen 22 YEVYEELCESLGVDP------LSYRRFSDYLSELEM 51 (85)
T ss_dssp HHHHHHHHHHTTS----------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCC------CCHHHHHHHHHHHHh
Confidence 567789999999887 888888888877765
No 190
>PRK08609 hypothetical protein; Provisional
Probab=20.67 E-value=38 Score=31.12 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=19.9
Q ss_pred ehhcccccCHHHHHHHHHHcCCC
Q 031813 29 ALTSIKGIGRRLANIVCKKADVD 51 (152)
Q Consensus 29 aL~~i~GIG~~~A~~Ic~~lgi~ 51 (152)
.|++|+|||..+|..|.+.+.=.
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG 71 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETG 71 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhC
Confidence 68999999999999999887643
No 191
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=20.52 E-value=83 Score=21.14 Aligned_cols=18 Identities=11% Similarity=0.093 Sum_probs=12.4
Q ss_pred CCCCCHHHHHHHHHHHhC
Q 031813 56 AGELSAAELDNLMVVVAN 73 (152)
Q Consensus 56 ~~~Ls~~ei~~L~~~l~~ 73 (152)
.-.||+++++.|.++|.+
T Consensus 45 ~V~Lt~eqv~~LN~~l~~ 62 (73)
T PF14794_consen 45 QVFLTEEQVAKLNQALQK 62 (73)
T ss_dssp -----HHHHHHHHHHHHH
T ss_pred CEEcCHHHHHHHHHHHHH
Confidence 345999999999999987
No 192
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=20.25 E-value=38 Score=23.25 Aligned_cols=40 Identities=10% Similarity=0.248 Sum_probs=29.5
Q ss_pred hhhhhcC-cccCCCeeheeehhcccccCHHHHHHHHHHcCC
Q 031813 11 HILRVLN-TNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (152)
Q Consensus 11 ~~vri~~-~~l~~~k~v~~aL~~i~GIG~~~A~~Ic~~lgi 50 (152)
++...++ ...-....+...+...+|.|...+..|++++|.
T Consensus 6 ~l~~~~~~~~~~~~~~~kivvD~~~G~~~~~~~~ll~~lg~ 46 (104)
T PF02879_consen 6 SLLSFIDILEAIKKSGLKIVVDCMNGAGSDILPRLLERLGC 46 (104)
T ss_dssp HHHHTSCHHHHHHHTTCEEEEE-TTSTTHHHHHHHHHHTTC
T ss_pred HHhhhccchhhcccCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence 3444444 333345566888899999999999999999998
No 193
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=20.25 E-value=44 Score=31.43 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=17.0
Q ss_pred heeehhcccccCHHHHHHHHHHcC
Q 031813 26 IMFALTSIKGIGRRLANIVCKKAD 49 (152)
Q Consensus 26 v~~aL~~i~GIG~~~A~~Ic~~lg 49 (152)
+.+|| .|.|||..+|+.|++.++
T Consensus 510 ~l~al-gi~~IG~~~ak~L~~~f~ 532 (665)
T PRK07956 510 FLYAL-GIRHVGEKAAKALARHFG 532 (665)
T ss_pred hhHhh-hccCcCHHHHHHHHHHcC
Confidence 33444 688889988888888764
No 194
>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=20.15 E-value=1.5e+02 Score=22.45 Aligned_cols=37 Identities=19% Similarity=0.314 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHcCCCCC---CCCCCCCHHHHHHHHHHHhC
Q 031813 37 GRRLANIVCKKADVDMN---KRAGELSAAELDNLMVVVAN 73 (152)
Q Consensus 37 G~~~A~~Ic~~lgi~~~---~~~~~Ls~~ei~~L~~~l~~ 73 (152)
|..+-..|++++|+++. ...+..+|+++.+|.+++.+
T Consensus 18 G~~~w~~i~~~~~~~~~~~f~~~~~Y~D~~~~~lv~a~a~ 57 (171)
T PF07700_consen 18 GEEVWDEILERAGLDSDGIFTSHGNYDDEETYKLVEAAAE 57 (171)
T ss_dssp HHHHHHHHHHHTTSSTTSS--TTSBTTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhCCCcCCccccccccCHHHHHHHHHHHHH
Confidence 48889999999999933 36777899999999998876
No 195
>KOG0202 consensus Ca2+ transporting ATPase [Inorganic ion transport and metabolism]
Probab=20.03 E-value=1.4e+02 Score=29.43 Aligned_cols=35 Identities=23% Similarity=0.353 Sum_probs=25.9
Q ss_pred cccccCHHHHHHHHHHcCCCCCCC-----------CCCCCHHHHHH
Q 031813 32 SIKGIGRRLANIVCKKADVDMNKR-----------AGELSAAELDN 66 (152)
Q Consensus 32 ~i~GIG~~~A~~Ic~~lgi~~~~~-----------~~~Ls~~ei~~ 66 (152)
.|.|=...||.+||++.|+..... +-+|+++|++.
T Consensus 605 mITGD~~~TA~AI~r~iGi~~~~ed~~~~~~TG~efD~ls~~~~~~ 650 (972)
T KOG0202|consen 605 MITGDNKETAEAIAREIGIFSEDEDVSSMALTGSEFDDLSDEELDD 650 (972)
T ss_pred EEcCCCHHHHHHHHHHhCCCcCCccccccccchhhhhcCCHHHHHH
Confidence 467778999999999999876543 44566666654
Done!