Query 033487
Match_columns 118
No_of_seqs 103 out of 1019
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 02:50:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033487.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033487hhsearch_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 9.8E-46 2.1E-50 271.9 8.4 112 7-118 9-120 (154)
2 PRK04053 rps13p 30S ribosomal 100.0 9.7E-44 2.1E-48 260.2 8.6 114 5-118 2-115 (149)
3 TIGR03629 arch_S13P archaeal r 100.0 4.6E-43 1E-47 255.4 8.0 110 8-118 1-110 (144)
4 KOG3311 Ribosomal protein S18 100.0 3.1E-31 6.8E-36 193.4 4.3 118 1-118 1-118 (152)
5 COG0099 RpsM Ribosomal protein 100.0 1.4E-30 3E-35 184.0 6.2 85 12-118 1-85 (121)
6 CHL00137 rps13 ribosomal prote 100.0 8.6E-29 1.9E-33 176.1 6.6 85 12-118 1-85 (122)
7 PRK05179 rpsM 30S ribosomal pr 100.0 1.1E-28 2.5E-33 175.5 6.7 85 12-118 1-85 (122)
8 PF00416 Ribosomal_S13: Riboso 99.9 6.7E-27 1.4E-31 162.5 7.3 83 14-118 1-83 (107)
9 TIGR03631 bact_S13 30S ribosom 99.9 6.1E-27 1.3E-31 164.6 6.8 83 14-118 1-83 (113)
10 PF06831 H2TH: Formamidopyrimi 97.6 7.6E-05 1.6E-09 50.4 3.6 52 22-73 22-76 (92)
11 PRK04184 DNA topoisomerase VI 97.3 0.00035 7.6E-09 60.5 4.9 51 23-73 256-306 (535)
12 PRK01103 formamidopyrimidine/5 97.2 0.00044 9.5E-09 54.7 4.5 53 21-73 153-208 (274)
13 TIGR01052 top6b DNA topoisomer 97.0 0.0012 2.6E-08 56.6 4.8 51 23-73 247-300 (488)
14 PRK14810 formamidopyrimidine-D 96.8 0.0024 5.2E-08 50.6 4.9 52 21-72 152-206 (272)
15 PRK14811 formamidopyrimidine-D 96.7 0.0026 5.7E-08 50.4 4.5 50 22-71 142-194 (269)
16 PRK10445 endonuclease VIII; Pr 96.5 0.0039 8.5E-08 49.2 4.6 51 23-73 151-204 (263)
17 PRK13945 formamidopyrimidine-D 96.5 0.0044 9.4E-08 49.4 4.4 51 22-72 163-216 (282)
18 TIGR00577 fpg formamidopyrimid 96.4 0.0047 1E-07 48.9 4.1 52 22-73 154-208 (272)
19 COG1389 DNA topoisomerase VI, 96.2 0.0046 1E-07 53.1 3.5 53 21-73 254-310 (538)
20 PF05833 FbpA: Fibronectin-bin 95.7 0.0065 1.4E-07 50.5 2.1 51 22-72 185-236 (455)
21 COG0266 Nei Formamidopyrimidin 95.0 0.031 6.7E-07 44.9 3.9 58 15-72 147-207 (273)
22 TIGR00275 flavoprotein, HI0933 94.7 0.024 5.2E-07 46.7 2.7 51 21-73 281-331 (400)
23 PF00633 HHH: Helix-hairpin-he 94.6 0.02 4.3E-07 31.3 1.3 18 29-46 12-29 (30)
24 COG0030 KsgA Dimethyladenosine 93.2 0.09 1.9E-06 41.9 3.2 48 21-73 209-256 (259)
25 PF11798 IMS_HHH: IMS family H 93.0 0.056 1.2E-06 29.7 1.2 21 29-50 12-32 (32)
26 PRK00274 ksgA 16S ribosomal RN 92.8 0.15 3.3E-06 40.0 3.9 62 9-73 209-270 (272)
27 PF10391 DNA_pol_lambd_f: Fing 92.7 0.067 1.5E-06 32.7 1.4 22 29-51 3-24 (52)
28 PF14520 HHH_5: Helix-hairpin- 92.5 0.024 5.3E-07 34.8 -0.7 26 26-52 3-28 (60)
29 PRK02515 psbU photosystem II c 92.5 0.11 2.3E-06 37.7 2.5 58 16-73 49-109 (132)
30 TIGR00755 ksgA dimethyladenosi 90.8 0.3 6.6E-06 37.6 3.5 59 9-71 195-253 (253)
31 PF03486 HI0933_like: HI0933-l 90.6 0.47 1E-05 39.8 4.7 51 21-73 288-339 (409)
32 smart00278 HhH1 Helix-hairpin- 90.4 0.18 3.8E-06 26.2 1.3 20 29-48 2-21 (26)
33 TIGR03252 uncharacterized HhH- 88.2 0.32 6.9E-06 36.8 1.8 35 21-55 108-142 (177)
34 PF00398 RrnaAD: Ribosomal RNA 88.1 0.25 5.5E-06 38.4 1.3 61 8-72 201-261 (262)
35 PRK14606 ruvA Holliday junctio 87.6 0.33 7.2E-06 36.8 1.6 20 28-47 108-127 (188)
36 PRK14605 ruvA Holliday junctio 87.3 0.21 4.6E-06 37.9 0.4 39 13-51 58-96 (194)
37 PRK14601 ruvA Holliday junctio 87.2 0.36 7.9E-06 36.5 1.6 19 28-46 108-126 (183)
38 PF09883 DUF2110: Uncharacteri 86.7 2.6 5.7E-05 33.1 6.1 51 23-73 96-158 (225)
39 PRK14603 ruvA Holliday junctio 86.6 0.41 8.8E-06 36.5 1.6 18 28-45 107-124 (197)
40 PRK14604 ruvA Holliday junctio 86.5 0.42 9.1E-06 36.4 1.6 20 28-47 108-127 (195)
41 PRK13901 ruvA Holliday junctio 85.9 0.47 1E-05 36.4 1.6 19 28-46 107-125 (196)
42 PRK00116 ruvA Holliday junctio 85.4 0.34 7.3E-06 36.6 0.6 60 14-73 59-130 (192)
43 PRK14602 ruvA Holliday junctio 85.4 0.5 1.1E-05 36.1 1.6 18 28-45 109-126 (203)
44 COG1293 Predicted RNA-binding 85.2 1.1 2.4E-05 39.2 3.8 50 24-73 186-235 (564)
45 COG3743 Uncharacterized conser 85.2 0.57 1.2E-05 34.0 1.7 44 29-73 68-111 (133)
46 PF14579 HHH_6: Helix-hairpin- 84.9 0.54 1.2E-05 31.1 1.4 27 23-49 22-48 (90)
47 COG0632 RuvA Holliday junction 84.5 0.58 1.3E-05 36.0 1.6 19 28-46 108-126 (201)
48 PF14520 HHH_5: Helix-hairpin- 83.2 0.85 1.8E-05 27.8 1.7 20 29-48 39-58 (60)
49 TIGR00084 ruvA Holliday juncti 82.9 0.28 6.2E-06 37.1 -0.7 35 14-48 58-92 (191)
50 cd00080 HhH2_motif Helix-hairp 82.1 0.82 1.8E-05 29.5 1.4 34 7-49 8-43 (75)
51 PRK14605 ruvA Holliday junctio 81.5 0.92 2E-05 34.4 1.7 18 28-45 108-125 (194)
52 TIGR00426 competence protein C 81.3 1.5 3.3E-05 27.3 2.3 29 20-48 8-37 (69)
53 PRK14602 ruvA Holliday junctio 80.6 0.58 1.2E-05 35.8 0.3 61 13-73 59-131 (203)
54 PF12836 HHH_3: Helix-hairpin- 80.4 0.68 1.5E-05 28.8 0.5 48 22-69 8-62 (65)
55 PRK14606 ruvA Holliday junctio 80.2 0.49 1.1E-05 35.9 -0.3 37 13-49 58-94 (188)
56 PRK14600 ruvA Holliday junctio 80.2 0.5 1.1E-05 35.8 -0.2 35 14-48 59-93 (186)
57 PRK14601 ruvA Holliday junctio 80.1 0.5 1.1E-05 35.7 -0.2 36 13-48 58-93 (183)
58 PRK14600 ruvA Holliday junctio 80.1 0.93 2E-05 34.3 1.3 17 28-45 108-124 (186)
59 PF12826 HHH_2: Helix-hairpin- 79.5 0.85 1.8E-05 28.4 0.7 18 32-49 7-24 (64)
60 smart00279 HhH2 Helix-hairpin- 79.4 1.1 2.5E-05 25.2 1.2 32 9-47 4-35 (36)
61 PRK00076 recR recombination pr 79.2 2.6 5.5E-05 32.4 3.4 41 25-73 8-48 (196)
62 PRK13901 ruvA Holliday junctio 78.7 0.59 1.3E-05 35.8 -0.2 35 14-48 58-92 (196)
63 cd00056 ENDO3c endonuclease II 78.6 1.3 2.9E-05 31.4 1.6 45 23-71 78-122 (158)
64 TIGR01259 comE comEA protein. 78.5 1.6 3.4E-05 30.7 1.9 32 19-50 59-90 (120)
65 PRK14603 ruvA Holliday junctio 78.0 0.62 1.4E-05 35.5 -0.3 61 13-73 57-129 (197)
66 COG2081 Predicted flavoprotein 78.0 2.5 5.5E-05 35.8 3.3 50 21-73 283-332 (408)
67 KOG0843 Transcription factor E 77.9 2.9 6.3E-05 32.1 3.3 50 37-87 84-154 (197)
68 PF14716 HHH_8: Helix-hairpin- 77.8 1.5 3.3E-05 27.5 1.5 20 29-48 48-67 (68)
69 COG0353 RecR Recombinational D 77.6 3 6.4E-05 32.2 3.3 42 24-73 8-49 (198)
70 PF14490 HHH_4: Helix-hairpin- 77.5 1.3 2.7E-05 29.6 1.2 26 28-53 45-71 (94)
71 COG0632 RuvA Holliday junction 77.2 0.55 1.2E-05 36.1 -0.8 38 12-49 57-94 (201)
72 TIGR00615 recR recombination p 76.8 3.3 7.2E-05 31.8 3.4 42 24-73 7-48 (195)
73 smart00483 POLXc DNA polymeras 76.6 1.7 3.6E-05 35.5 1.8 26 26-52 87-112 (334)
74 PF02371 Transposase_20: Trans 75.8 1.8 3.9E-05 28.3 1.5 20 29-48 3-22 (87)
75 TIGR00084 ruvA Holliday juncti 75.1 1.9 4E-05 32.7 1.6 18 28-45 107-124 (191)
76 smart00478 ENDO3c endonuclease 74.3 1.7 3.7E-05 30.6 1.2 42 26-71 70-111 (149)
77 PRK01229 N-glycosylase/DNA lya 73.5 2.3 4.9E-05 32.8 1.8 43 25-71 115-158 (208)
78 PF11731 Cdd1: Pathogenicity l 73.5 2.8 6E-05 28.6 2.0 37 27-64 11-47 (93)
79 PRK14604 ruvA Holliday junctio 73.5 0.97 2.1E-05 34.4 -0.3 61 13-73 58-130 (195)
80 PF02042 RWP-RK: RWP-RK domain 73.0 2.9 6.3E-05 25.6 1.8 20 32-51 23-42 (52)
81 cd00141 NT_POLXc Nucleotidyltr 73.0 2.3 4.9E-05 34.3 1.7 26 26-52 83-108 (307)
82 PF06514 PsbU: Photosystem II 72.5 5.4 0.00012 27.3 3.2 58 16-73 11-71 (93)
83 PRK13844 recombination protein 72.2 5.1 0.00011 30.9 3.4 41 25-73 12-52 (200)
84 PRK08609 hypothetical protein; 71.5 2.7 5.9E-05 36.7 2.0 25 27-51 87-111 (570)
85 PRK10702 endonuclease III; Pro 70.8 2.2 4.7E-05 32.8 1.1 22 26-47 107-128 (211)
86 TIGR01083 nth endonuclease III 70.2 2.4 5.2E-05 31.6 1.2 22 26-47 104-125 (191)
87 PF01367 5_3_exonuc: 5'-3' exo 70.2 0.86 1.9E-05 31.4 -1.1 20 30-49 20-39 (101)
88 TIGR01084 mutY A/G-specific ad 68.5 2.8 6E-05 33.5 1.3 48 17-71 97-144 (275)
89 PRK12766 50S ribosomal protein 67.2 2.9 6.4E-05 32.9 1.2 38 29-67 4-41 (232)
90 COG0258 Exo 5'-3' exonuclease 66.7 4 8.7E-05 32.6 1.9 32 8-49 185-219 (310)
91 PRK03980 flap endonuclease-1; 66.6 3.5 7.6E-05 33.2 1.6 34 7-49 177-210 (292)
92 PRK14896 ksgA 16S ribosomal RN 65.5 13 0.00028 28.8 4.5 63 9-73 192-256 (258)
93 cd00128 XPG Xeroderma pigmento 65.3 3.4 7.5E-05 33.0 1.3 34 7-49 211-244 (316)
94 PHA02564 V virion protein; Pro 65.0 12 0.00027 27.3 4.0 32 41-73 88-119 (141)
95 cd01104 HTH_MlrA-CarA Helix-Tu 65.0 18 0.00039 21.7 4.3 43 30-72 6-52 (68)
96 PRK00116 ruvA Holliday junctio 64.9 4.2 9.2E-05 30.5 1.6 21 29-49 109-129 (192)
97 PTZ00338 dimethyladenosine tra 63.8 9.7 0.00021 30.5 3.6 33 40-73 256-288 (294)
98 KOG2518 5'-3' exonuclease [Rep 63.4 3.9 8.4E-05 35.9 1.3 37 5-50 211-247 (556)
99 TIGR01448 recD_rel helicase, p 63.3 7.6 0.00017 34.9 3.2 41 32-72 88-138 (720)
100 PF14635 HHH_7: Helix-hairpin- 63.2 5.4 0.00012 27.7 1.8 42 8-49 27-71 (104)
101 PRK07373 DNA polymerase III su 63.1 7.3 0.00016 33.3 2.9 47 23-69 109-165 (449)
102 PRK00558 uvrC excinuclease ABC 62.1 6.9 0.00015 34.5 2.6 44 22-67 537-580 (598)
103 PF11338 DUF3140: Protein of u 61.7 14 0.00031 25.2 3.6 35 34-72 33-67 (92)
104 KOG0844 Transcription factor E 61.6 5.3 0.00012 33.2 1.7 28 59-87 188-233 (408)
105 PF04760 IF2_N: Translation in 61.4 4.8 0.0001 23.9 1.1 45 28-72 7-52 (54)
106 smart00389 HOX Homeodomain. DN 61.0 7.2 0.00016 22.6 1.9 30 58-88 24-53 (56)
107 PRK13913 3-methyladenine DNA g 60.7 4.5 9.7E-05 31.4 1.1 24 25-48 118-141 (218)
108 PRK10880 adenine DNA glycosyla 60.6 5.3 0.00011 33.1 1.6 24 25-48 106-129 (350)
109 PRK13910 DNA glycosylase MutY; 60.5 5.5 0.00012 32.2 1.6 41 27-71 71-111 (289)
110 smart00475 53EXOc 5'-3' exonuc 60.5 5.1 0.00011 31.6 1.4 19 31-49 189-207 (259)
111 PRK09482 flap endonuclease-lik 60.3 5.4 0.00012 31.7 1.5 19 31-49 185-203 (256)
112 cd00008 53EXOc 5'-3' exonuclea 60.2 5.2 0.00011 31.0 1.4 20 30-49 185-204 (240)
113 PTZ00217 flap endonuclease-1; 59.8 5.5 0.00012 33.4 1.6 34 7-49 223-256 (393)
114 COG1059 Thermostable 8-oxoguan 59.7 5.9 0.00013 30.7 1.6 27 25-51 118-144 (210)
115 COG2231 Uncharacterized protei 59.2 8.6 0.00019 30.0 2.4 40 18-57 103-144 (215)
116 TIGR00588 ogg 8-oxoguanine DNA 58.8 5.6 0.00012 32.1 1.4 44 25-71 217-260 (310)
117 PRK07945 hypothetical protein; 58.5 19 0.00042 29.3 4.5 36 29-72 50-85 (335)
118 PRK14976 5'-3' exonuclease; Pr 58.0 5.9 0.00013 31.6 1.4 19 31-49 194-212 (281)
119 KOG0650 WD40 repeat nucleolar 57.6 17 0.00037 32.7 4.2 49 51-106 142-190 (733)
120 KOG2251 Homeobox transcription 57.0 7.9 0.00017 30.5 1.9 31 59-90 44-92 (228)
121 KOG3802 Transcription factor O 55.5 7.1 0.00015 33.1 1.5 28 60-88 320-347 (398)
122 COG0177 Nth Predicted EndoIII- 54.7 7.9 0.00017 30.0 1.6 21 27-47 108-128 (211)
123 PRK14669 uvrC excinuclease ABC 54.3 7.6 0.00016 34.6 1.6 41 24-66 548-588 (624)
124 PRK10308 3-methyl-adenine DNA 53.8 7.4 0.00016 31.1 1.4 29 26-54 205-233 (283)
125 PF13276 HTH_21: HTH-like doma 52.3 12 0.00026 22.4 1.9 35 20-54 20-56 (60)
126 PRK12278 50S ribosomal protein 52.1 11 0.00025 29.3 2.1 46 28-74 158-203 (221)
127 PRK12311 rpsB 30S ribosomal pr 51.8 8.2 0.00018 31.8 1.3 45 28-73 263-307 (326)
128 COG0122 AlkA 3-methyladenine D 51.3 6.6 0.00014 31.5 0.7 23 24-46 194-216 (285)
129 PRK13766 Hef nuclease; Provisi 51.0 13 0.00029 33.0 2.6 25 25-49 712-736 (773)
130 cd01702 PolY_Pol_eta DNA Polym 50.9 10 0.00022 31.2 1.7 37 29-65 183-221 (359)
131 TIGR02607 antidote_HigA addict 48.7 15 0.00032 22.7 1.9 29 58-91 44-72 (78)
132 COG1936 Predicted nucleotide k 48.5 10 0.00022 28.9 1.3 24 28-51 3-26 (180)
133 TIGR00194 uvrC excinuclease AB 48.1 9.2 0.0002 33.7 1.1 26 24-49 537-562 (574)
134 COG1555 ComEA DNA uptake prote 47.6 18 0.00039 26.3 2.5 44 28-71 97-147 (149)
135 PRK14667 uvrC excinuclease ABC 47.2 11 0.00024 33.2 1.5 43 23-67 509-551 (567)
136 PRK14670 uvrC excinuclease ABC 47.0 11 0.00024 33.2 1.5 40 26-67 512-551 (574)
137 PRK05898 dnaE DNA polymerase I 46.9 23 0.00051 33.3 3.6 47 23-69 747-802 (971)
138 PRK14668 uvrC excinuclease ABC 46.3 13 0.00028 32.8 1.7 40 26-67 523-562 (577)
139 PF01418 HTH_6: Helix-turn-hel 46.0 16 0.00034 23.2 1.7 23 29-51 39-61 (77)
140 PF13613 HTH_Tnp_4: Helix-turn 45.2 15 0.00031 21.8 1.4 21 28-48 23-43 (53)
141 KOG2875 8-oxoguanine DNA glyco 44.3 12 0.00025 30.8 1.1 20 26-45 216-235 (323)
142 PF00542 Ribosomal_L12: Riboso 44.3 14 0.00029 23.6 1.2 46 25-73 15-60 (68)
143 cd00086 homeodomain Homeodomai 44.2 6.6 0.00014 22.8 -0.3 30 58-88 24-53 (59)
144 TIGR03674 fen_arch flap struct 44.2 12 0.00027 30.5 1.3 19 31-49 239-257 (338)
145 TIGR03045 PS_II_C550 cytochrom 43.6 29 0.00063 25.7 3.1 17 57-73 130-146 (159)
146 PLN03072 60S ribosomal protein 43.1 45 0.00098 24.9 4.0 38 36-73 74-119 (166)
147 PRK00419 DNA primase small sub 42.3 14 0.00029 31.1 1.3 20 29-48 222-241 (376)
148 COG3415 Transposase and inacti 41.1 58 0.0013 23.6 4.2 45 29-73 26-78 (138)
149 PF00046 Homeobox: Homeobox do 41.0 6.1 0.00013 23.2 -0.8 29 59-88 25-53 (57)
150 TIGR02663 nifX nitrogen fixati 40.7 40 0.00087 23.1 3.3 47 34-85 70-117 (119)
151 PF13331 DUF4093: Domain of un 39.9 14 0.00029 24.7 0.7 41 21-67 45-85 (87)
152 cd00037 CLECT C-type lectin (C 39.4 90 0.002 19.1 4.7 50 35-89 9-58 (116)
153 PRK14671 uvrC excinuclease ABC 39.2 14 0.00029 33.0 0.8 50 16-67 557-606 (621)
154 COG0776 HimA Bacterial nucleoi 38.9 20 0.00043 24.4 1.4 60 40-100 7-74 (94)
155 TIGR02366 DHAK_reg probable di 38.3 19 0.00041 25.5 1.3 27 28-54 13-39 (176)
156 PF09397 Ftsk_gamma: Ftsk gamm 37.7 21 0.00045 22.6 1.3 27 23-49 19-45 (65)
157 KOG0494 Transcription factor C 37.6 20 0.00044 29.2 1.5 31 58-89 147-195 (332)
158 PRK14666 uvrC excinuclease ABC 37.4 17 0.00036 33.0 1.1 25 25-49 634-658 (694)
159 TIGR00608 radc DNA repair prot 37.2 16 0.00036 28.2 0.9 22 30-51 62-83 (218)
160 COG1131 CcmA ABC-type multidru 37.1 52 0.0011 26.1 3.8 60 12-71 80-149 (293)
161 smart00581 PSP proline-rich do 36.7 28 0.00062 21.5 1.8 31 53-88 3-33 (54)
162 CHL00154 rpl29 ribosomal prote 36.3 21 0.00046 22.7 1.2 51 56-117 9-59 (67)
163 TIGR00600 rad2 DNA excision re 36.2 20 0.00044 33.9 1.5 34 7-49 854-887 (1034)
164 PRK14672 uvrC excinuclease ABC 35.9 19 0.00042 32.6 1.3 43 23-67 603-645 (691)
165 PF13551 HTH_29: Winged helix- 35.5 92 0.002 20.0 4.3 46 28-73 16-72 (112)
166 TIGR00594 polc DNA-directed DN 35.2 26 0.00057 33.0 2.0 47 23-69 819-875 (1022)
167 PF10500 SR-25: Nuclear RNA-sp 34.9 77 0.0017 25.0 4.3 47 56-115 157-209 (225)
168 PF10662 PduV-EutP: Ethanolami 34.6 33 0.00072 24.9 2.1 37 37-73 107-143 (143)
169 PF03118 RNA_pol_A_CTD: Bacter 34.6 24 0.00051 22.1 1.2 21 28-48 44-64 (66)
170 cd00349 Ribosomal_L11 Ribosoma 34.1 92 0.002 22.2 4.3 38 36-73 62-106 (131)
171 smart00530 HTH_XRE Helix-turn- 34.0 34 0.00074 18.0 1.7 13 60-72 38-50 (56)
172 PRK00024 hypothetical protein; 33.4 20 0.00044 27.7 0.9 23 29-51 67-89 (224)
173 TIGR00575 dnlj DNA ligase, NAD 33.0 20 0.00044 32.0 1.0 23 26-49 497-519 (652)
174 PF12114 Period_C: Period prot 32.9 30 0.00066 26.5 1.8 40 79-118 94-133 (195)
175 PF13442 Cytochrome_CBB3: Cyto 32.9 44 0.00096 20.0 2.2 14 58-71 54-67 (67)
176 COG0080 RplK Ribosomal protein 32.3 1.2E+02 0.0026 22.2 4.7 49 38-109 72-126 (141)
177 PF04218 CENP-B_N: CENP-B N-te 32.3 28 0.00062 20.7 1.2 20 27-46 25-44 (53)
178 cd00093 HTH_XRE Helix-turn-hel 32.0 39 0.00084 17.9 1.7 14 58-71 38-51 (58)
179 KOG0488 Transcription factor B 31.7 23 0.0005 28.8 1.0 19 59-78 179-197 (309)
180 PRK05755 DNA polymerase I; Pro 31.5 25 0.00055 32.2 1.3 20 30-49 189-208 (880)
181 TIGR00593 pola DNA polymerase 31.4 26 0.00057 32.5 1.4 18 32-49 189-206 (887)
182 KOG0821 Predicted ribosomal RN 31.4 65 0.0014 26.0 3.4 35 39-73 270-304 (326)
183 PRK07956 ligA NAD-dependent DN 31.4 18 0.0004 32.4 0.4 34 32-65 449-482 (665)
184 PF13443 HTH_26: Cro/C1-type H 31.3 76 0.0017 18.6 3.1 37 29-72 15-51 (63)
185 TIGR00596 rad1 DNA repair prot 31.2 31 0.00067 31.8 1.8 39 26-67 756-794 (814)
186 PRK06920 dnaE DNA polymerase I 31.0 38 0.00081 32.4 2.3 46 23-68 797-851 (1107)
187 TIGR00677 fadh2_euk methylenet 30.9 22 0.00048 28.3 0.8 61 1-64 197-267 (281)
188 PRK07279 dnaE DNA polymerase I 30.4 45 0.00098 31.6 2.7 25 23-47 745-769 (1034)
189 TIGR00575 dnlj DNA ligase, NAD 30.4 23 0.0005 31.7 0.8 33 32-64 436-468 (652)
190 KOG1856 Transcription elongati 30.3 24 0.00051 34.0 0.9 44 8-51 783-829 (1299)
191 PF11174 DUF2970: Protein of u 30.1 9.7 0.00021 23.5 -1.1 20 84-103 19-38 (56)
192 PRK12277 50S ribosomal protein 29.8 47 0.001 22.3 2.0 44 28-73 34-77 (83)
193 PRK13622 psbV cytochrome c-550 29.8 66 0.0014 24.5 3.1 26 57-83 141-166 (180)
194 PRK10664 transcriptional regul 29.3 34 0.00074 22.6 1.4 58 40-98 6-71 (90)
195 smart00483 POLXc DNA polymeras 29.1 34 0.00073 27.9 1.6 23 29-51 49-71 (334)
196 PRK06266 transcription initiat 29.1 1.6E+02 0.0034 22.0 5.0 64 38-115 36-102 (178)
197 PF02879 PGM_PMM_II: Phosphogl 29.1 7.9 0.00017 25.6 -1.8 39 12-50 7-46 (104)
198 PRK03352 DNA polymerase IV; Va 29.1 42 0.00091 26.9 2.1 36 29-65 178-213 (346)
199 smart00843 Ftsk_gamma This dom 28.9 39 0.00085 21.4 1.5 26 24-49 19-44 (63)
200 CHL00133 psbV photosystem II c 28.8 70 0.0015 23.9 3.0 17 57-73 131-147 (163)
201 COG1948 MUS81 ERCC4-type nucle 28.5 35 0.00076 27.3 1.5 27 23-49 177-203 (254)
202 KOG0842 Transcription factor t 28.5 32 0.0007 28.2 1.3 9 79-87 197-205 (307)
203 PRK02406 DNA polymerase IV; Va 28.5 37 0.00081 27.1 1.7 36 29-65 169-204 (343)
204 COG1796 POL4 DNA polymerase IV 28.3 34 0.00074 28.4 1.4 20 29-48 54-73 (326)
205 PRK02362 ski2-like helicase; P 28.1 36 0.00077 30.4 1.6 39 28-67 652-690 (737)
206 COG1194 MutY A/G-specific DNA 27.7 38 0.00083 28.2 1.6 34 10-46 98-131 (342)
207 PF11460 DUF3007: Protein of u 27.7 32 0.0007 24.0 1.0 21 53-73 84-104 (104)
208 PRK05672 dnaE2 error-prone DNA 27.2 35 0.00075 32.3 1.4 26 23-48 811-836 (1046)
209 PF14053 DUF4248: Domain of un 26.9 1.6E+02 0.0035 18.7 4.2 47 25-73 8-68 (69)
210 PF00392 GntR: Bacterial regul 26.7 70 0.0015 19.2 2.4 29 20-48 19-48 (64)
211 PRK03858 DNA polymerase IV; Va 26.7 49 0.0011 27.0 2.1 35 29-64 174-208 (396)
212 PRK00919 GMP synthase subunit 26.5 1.3E+02 0.0028 24.4 4.5 50 50-106 154-203 (307)
213 PRK07956 ligA NAD-dependent DN 26.5 30 0.00066 31.0 0.9 23 26-49 510-532 (665)
214 cd00427 Ribosomal_L29_HIP Ribo 26.2 38 0.00083 20.5 1.1 51 56-117 3-53 (57)
215 KOG1647 Vacuolar H+-ATPase V1 26.2 54 0.0012 26.1 2.1 52 41-117 154-205 (255)
216 PRK03609 umuC DNA polymerase V 26.2 47 0.001 27.5 1.9 36 29-65 180-215 (422)
217 PF00440 TetR_N: Bacterial reg 25.9 37 0.0008 19.2 0.9 22 32-53 10-31 (47)
218 KOG2355 Predicted ABC-type tra 25.8 47 0.001 26.7 1.7 65 8-72 96-161 (291)
219 PF11198 DUF2857: Protein of u 25.7 1.2E+02 0.0027 22.5 4.0 44 29-72 92-136 (180)
220 TIGR02236 recomb_radA DNA repa 25.7 40 0.00087 26.5 1.4 34 30-64 1-34 (310)
221 cd01703 PolY_Pol_iota DNA Poly 25.6 27 0.00059 28.9 0.4 24 28-52 172-195 (379)
222 PRK12766 50S ribosomal protein 25.5 51 0.0011 26.1 1.9 21 29-49 37-57 (232)
223 PRK00254 ski2-like helicase; P 25.3 33 0.00071 30.6 0.9 39 28-67 645-683 (720)
224 TIGR00630 uvra excinuclease AB 25.3 62 0.0013 30.3 2.7 31 40-70 321-351 (924)
225 cd00141 NT_POLXc Nucleotidyltr 25.3 43 0.00092 26.9 1.5 24 29-52 46-69 (307)
226 PF00034 Cytochrom_C: Cytochro 25.2 72 0.0016 19.0 2.3 16 58-73 74-89 (91)
227 PRK00306 50S ribosomal protein 25.2 49 0.0011 20.6 1.5 51 56-117 6-56 (66)
228 PLN00131 hypothetical protein; 24.9 30 0.00065 26.3 0.5 49 39-87 156-216 (218)
229 COG2938 Uncharacterized conser 24.6 39 0.00084 23.1 1.0 33 55-88 40-72 (94)
230 TIGR01764 excise DNA binding d 24.5 46 0.001 18.1 1.1 16 32-47 9-24 (49)
231 PRK00140 rplK 50S ribosomal pr 24.4 1.4E+02 0.0031 21.5 4.0 37 37-73 72-114 (141)
232 PRK13620 psbV cytochrome c-550 24.3 85 0.0018 24.6 2.9 17 56-72 182-198 (215)
233 KOG3200 Uncharacterized conser 24.2 79 0.0017 24.5 2.6 33 56-91 18-52 (224)
234 PRK05673 dnaE DNA polymerase I 24.1 41 0.0009 32.1 1.3 26 23-48 815-840 (1135)
235 PRK12373 NADH dehydrogenase su 24.0 66 0.0014 27.4 2.4 46 28-74 323-368 (400)
236 PTZ00105 60S ribosomal protein 24.0 1.5E+02 0.0032 21.5 3.9 36 38-73 50-93 (140)
237 PF14794 DUF4479: Domain of un 23.9 66 0.0014 20.7 1.9 17 57-73 46-62 (73)
238 cd01401 PncB_like Nicotinate p 23.8 1.3E+02 0.0028 25.3 4.1 35 39-73 289-327 (377)
239 PF08478 POTRA_1: POTRA domain 23.8 1.2E+02 0.0025 18.1 3.0 38 32-72 7-44 (69)
240 TIGR02019 BchJ bacteriochlorop 23.7 2E+02 0.0043 21.9 4.8 44 28-73 12-58 (188)
241 cd02020 CMPK Cytidine monophos 23.6 1.2E+02 0.0026 20.2 3.3 36 28-64 2-38 (147)
242 PF00298 Ribosomal_L11: Riboso 23.6 1.8E+02 0.0038 18.4 3.9 36 38-73 3-44 (69)
243 COG1111 MPH1 ERCC4-like helica 23.6 35 0.00076 30.1 0.7 63 22-85 160-223 (542)
244 PF12844 HTH_19: Helix-turn-he 23.5 38 0.00082 20.0 0.7 20 34-53 37-56 (64)
245 PF14213 DUF4325: Domain of un 23.5 86 0.0019 19.6 2.4 54 19-72 13-73 (74)
246 COG0394 Wzb Protein-tyrosine-p 23.5 93 0.002 22.1 2.8 27 39-65 48-75 (139)
247 PRK11235 bifunctional antitoxi 23.3 40 0.00087 22.2 0.8 15 39-53 14-28 (80)
248 PF14229 DUF4332: Domain of un 23.3 37 0.0008 23.7 0.7 32 34-66 1-32 (122)
249 TIGR00334 5S_RNA_mat_M5 ribonu 23.3 38 0.00083 25.6 0.8 39 22-66 133-171 (174)
250 smart00649 RL11 Ribosomal prot 23.1 1.9E+02 0.0041 20.6 4.4 37 37-73 64-106 (132)
251 TIGR02836 spore_IV_A stage IV 23.1 1.5E+02 0.0033 26.0 4.4 89 23-118 180-277 (492)
252 PRK07374 dnaE DNA polymerase I 23.1 44 0.00096 32.1 1.3 47 23-69 830-886 (1170)
253 KOG2519 5'-3' exonuclease [Rep 23.1 71 0.0015 27.7 2.4 33 8-49 218-250 (449)
254 CHL00127 rpl11 ribosomal prote 23.1 2.1E+02 0.0046 20.7 4.6 37 37-73 72-114 (140)
255 PF02745 MCR_alpha_N: Methyl-c 22.9 45 0.00098 26.6 1.2 32 82-113 71-102 (267)
256 PRK00349 uvrA excinuclease ABC 22.8 73 0.0016 29.9 2.7 32 39-70 322-353 (943)
257 TIGR01448 recD_rel helicase, p 22.8 63 0.0014 29.1 2.2 40 31-71 184-223 (720)
258 COG0587 DnaE DNA polymerase II 22.5 49 0.0011 31.8 1.5 47 24-70 819-874 (1139)
259 PF04967 HTH_10: HTH DNA bindi 22.5 1.3E+02 0.0027 18.2 2.9 15 59-73 1-15 (53)
260 PF00288 GHMP_kinases_N: GHMP 22.4 65 0.0014 19.4 1.6 40 33-73 11-50 (67)
261 TIGR01405 polC_Gram_pos DNA po 22.1 51 0.0011 31.8 1.5 25 24-48 1146-1170(1213)
262 PRK15482 transcriptional regul 22.1 64 0.0014 25.0 1.9 24 29-52 39-62 (285)
263 COG0322 UvrC Nuclease subunit 22.0 43 0.00092 29.8 0.9 42 24-67 526-567 (581)
264 cd03067 PDI_b_PDIR_N PDIb fami 21.9 82 0.0018 22.2 2.2 32 28-59 42-81 (112)
265 PF07316 DUF1463: Protein of u 21.8 62 0.0013 23.5 1.6 47 1-47 42-93 (140)
266 TIGR03872 cytochrome_MoxG cyto 21.8 1.2E+02 0.0027 21.4 3.2 17 57-73 104-120 (133)
267 TIGR01632 L11_bact 50S ribosom 21.8 1.6E+02 0.0036 21.2 3.8 37 37-73 71-113 (140)
268 PRK00033 clpS ATP-dependent Cl 21.7 1.2E+02 0.0026 20.7 2.9 65 9-73 26-90 (100)
269 PF02617 ClpS: ATP-dependent C 21.6 21 0.00045 23.0 -0.8 65 9-73 5-69 (82)
270 KOG1014 17 beta-hydroxysteroid 21.4 74 0.0016 26.2 2.2 39 32-73 57-95 (312)
271 PF02037 SAP: SAP domain; Int 21.3 1.5E+02 0.0033 16.0 3.0 25 42-70 10-34 (35)
272 PRK08609 hypothetical protein; 21.2 56 0.0012 28.7 1.5 31 29-59 49-79 (570)
273 PRK06826 dnaE DNA polymerase I 21.1 52 0.0011 31.6 1.3 46 23-68 819-874 (1151)
274 KOG0492 Transcription factor M 21.0 68 0.0015 25.4 1.8 50 40-89 131-198 (246)
275 KOG3908 Queuine-tRNA ribosyltr 20.8 20 0.00044 29.8 -1.2 40 7-51 230-269 (396)
276 PRK01172 ski2-like helicase; P 20.8 60 0.0013 28.6 1.6 39 28-67 612-650 (674)
277 KOG2534 DNA polymerase IV (fam 20.8 1E+02 0.0023 25.7 2.9 48 30-79 58-105 (353)
278 smart00345 HTH_GNTR helix_turn 20.7 1E+02 0.0023 17.2 2.2 22 27-48 23-44 (60)
279 smart00550 Zalpha Z-DNA-bindin 20.6 67 0.0015 19.9 1.4 25 28-52 10-36 (68)
280 PRK07135 dnaE DNA polymerase I 20.5 51 0.0011 31.1 1.2 46 23-68 748-803 (973)
281 cd04761 HTH_MerR-SF Helix-Turn 20.5 1.5E+02 0.0032 16.2 2.8 38 31-68 7-47 (49)
282 PRK14133 DNA polymerase IV; Pr 20.4 70 0.0015 25.7 1.8 36 29-65 174-209 (347)
283 PRK03348 DNA polymerase IV; Pr 20.3 68 0.0015 27.2 1.8 37 29-66 181-217 (454)
284 smart00513 SAP Putative DNA-bi 20.3 1.6E+02 0.0034 15.7 2.8 11 41-51 9-19 (35)
285 PRK03103 DNA polymerase IV; Re 20.2 79 0.0017 26.0 2.1 35 29-64 182-216 (409)
286 COG2003 RadC DNA repair protei 20.2 66 0.0014 25.3 1.6 25 28-52 66-90 (224)
287 PRK08118 topology modulation p 20.2 1.9E+02 0.0042 20.7 4.0 43 29-71 5-56 (167)
288 cd08532 SAM_PNT-PDEF-like Ster 20.1 69 0.0015 20.8 1.4 33 45-81 1-33 (76)
289 PRK01810 DNA polymerase IV; Va 20.1 73 0.0016 26.2 1.9 35 29-64 180-214 (407)
290 COG1737 RpiR Transcriptional r 20.1 74 0.0016 25.0 1.9 24 29-52 41-64 (281)
291 PRK04301 radA DNA repair and r 20.0 80 0.0017 25.1 2.1 36 28-64 6-41 (317)
No 1
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=9.8e-46 Score=271.88 Aligned_cols=112 Identities=70% Similarity=1.126 Sum_probs=109.4
Q ss_pred cccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhcc
Q 033487 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNR 86 (118)
Q Consensus 7 ~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr 86 (118)
+||+||+||+||+||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|+++|++|.+|.+|+||+||
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~nr 88 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFLNR 88 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHhhc
Confidence 58999999999999999999999999999999999999999999999999999999999999999987678999999999
Q ss_pred ccccCCCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 87 QKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 87 ~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
|||++||++.|+||+||++.+++||+||++|+
T Consensus 89 ~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~ 120 (154)
T PTZ00134 89 QRDPKDGKNSHLTSNMLDTKLREDLERLKKIR 120 (154)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999986
No 2
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=9.7e-44 Score=260.18 Aligned_cols=114 Identities=39% Similarity=0.732 Sum_probs=110.7
Q ss_pred CccccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchh
Q 033487 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFL 84 (118)
Q Consensus 5 ~~~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~ 84 (118)
.+++|+||+||+||+||++|+|.+||++|||||+++|.+||+++||+|++++++||++|+++|.++|++|..+++|+||+
T Consensus 2 ~~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~ 81 (149)
T PRK04053 2 MEEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWML 81 (149)
T ss_pred chhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhh
Confidence 35789999999999999999999999999999999999999999999999999999999999999999877899999999
Q ss_pred ccccccCCCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 85 NRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 85 nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
|||+|++||++.|+||+||++.+++||+||++|+
T Consensus 82 Nr~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~ 115 (149)
T PRK04053 82 NRRKDYETGEDLHLIGSDLILTVREDINRMKKIR 115 (149)
T ss_pred ccccccccCccceEehHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999985
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=4.6e-43 Score=255.40 Aligned_cols=110 Identities=43% Similarity=0.809 Sum_probs=107.3
Q ss_pred ccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccc
Q 033487 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQ 87 (118)
Q Consensus 8 ~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~ 87 (118)
+|+||+||+|++||++|+|.+||++|||||+++|.+||+++||++++++++||++|+++|+++|++ ..|.+|+||+|||
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 589999999999999999999999999999999999999999999999999999999999999997 4689999999999
Q ss_pred cccCCCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 88 KDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 88 kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
||++||+|.|+||+||++++++||+||++|+
T Consensus 80 ~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~ 110 (144)
T TIGR03629 80 KDYETGEDLHLIGSDLDMTVREDINRMKKIR 110 (144)
T ss_pred cccccCccceEehHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999986
No 4
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.1e-31 Score=193.42 Aligned_cols=118 Identities=66% Similarity=1.073 Sum_probs=115.2
Q ss_pred CCCCCccccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCC
Q 033487 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIP 80 (118)
Q Consensus 1 ~~~~~~~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip 80 (118)
|+|+-.+.|+||+||+|++++++++|.|||+.|||||...|..+|+++||++.+++++|+++|+..+..++++|..+.+|
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 78998888999999999999999999999999999999999999999999999999999999999999999988889999
Q ss_pred cchhccccccCCCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 81 DWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 81 ~w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
.|++|||+|.+.|...|++++.|+..+++||+|+++|+
T Consensus 81 ~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~ 118 (152)
T KOG3311|consen 81 DWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIR 118 (152)
T ss_pred hHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhc
Confidence 99999999999999999999999999999999999985
No 5
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.4e-30 Score=183.95 Aligned_cols=85 Identities=39% Similarity=0.688 Sum_probs=82.7
Q ss_pred chhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccC
Q 033487 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (118)
Q Consensus 12 mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~ 91 (118)
|+||+|+|||++|+|.+|||+|||||.++|.+||+++||+|++++++||++|+++|+++|++ .|
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~--~~-------------- 64 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN--KY-------------- 64 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh--cC--------------
Confidence 89999999999999999999999999999999999999999999999999999999999996 46
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 92 DGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
+||+||++++++||+||++|+
T Consensus 65 ------~vegDLr~~v~~dIkRl~~i~ 85 (121)
T COG0099 65 ------LVEGDLRREVRMDIKRLMKIG 85 (121)
T ss_pred ------eehhHHHHHHHHHHHHHHHhh
Confidence 999999999999999999985
No 6
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=99.95 E-value=8.6e-29 Score=176.09 Aligned_cols=85 Identities=25% Similarity=0.420 Sum_probs=82.6
Q ss_pred chhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccC
Q 033487 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (118)
Q Consensus 12 mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~ 91 (118)
|+||+||++|++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++ +|
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~-------------- 64 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NY-------------- 64 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hC--------------
Confidence 89999999999999999999999999999999999999999999999999999999999986 57
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 92 DGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
.||+||++.+++||+||++|+
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~ 85 (122)
T CHL00137 65 ------QVEGDLRRFESLNIKRLMEIN 85 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhC
Confidence 799999999999999999986
No 7
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=99.95 E-value=1.1e-28 Score=175.46 Aligned_cols=85 Identities=26% Similarity=0.451 Sum_probs=82.6
Q ss_pred chhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccC
Q 033487 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (118)
Q Consensus 12 mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~ 91 (118)
||||+||++|++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++ +|
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~--~~-------------- 64 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDK--NY-------------- 64 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHh--hc--------------
Confidence 89999999999999999999999999999999999999999999999999999999999997 46
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 92 DGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
.||+||++++++||+||++|+
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~ 85 (122)
T PRK05179 65 ------KVEGDLRREVSMNIKRLMDIG 85 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhc
Confidence 799999999999999999986
No 8
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=99.94 E-value=6.7e-27 Score=162.51 Aligned_cols=83 Identities=41% Similarity=0.745 Sum_probs=78.5
Q ss_pred hhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCC
Q 033487 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (118)
Q Consensus 14 rI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg 93 (118)
||+||+||++|+|.+||++|||||+++|.+||+++||+|++++++||++|+++|.++|++ +|
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~--~~---------------- 62 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK--NH---------------- 62 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--HS----------------
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--hc----------------
Confidence 799999999999999999999999999999999999999999999999999999999997 46
Q ss_pred ccceeehhhHHHHHHHHHHHHHhCC
Q 033487 94 KYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 94 ~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
++++||++++++||+||++|+
T Consensus 63 ----~i~~~L~~~~~~~i~rl~~i~ 83 (107)
T PF00416_consen 63 ----LIENDLKRQVRENIKRLKKIK 83 (107)
T ss_dssp ----TCHHHHHHHHHHHHHHHHHHT
T ss_pred ----cccchHHHHHHHHHHHHHHHH
Confidence 899999999999999999985
No 9
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=99.94 E-value=6.1e-27 Score=164.62 Aligned_cols=83 Identities=28% Similarity=0.464 Sum_probs=80.3
Q ss_pred hhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCC
Q 033487 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (118)
Q Consensus 14 rI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg 93 (118)
||+|+++|++|+|.+||++|||||+.+|.+||+++||+|++++++||++|+++|.++|++ +|
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~--~~---------------- 62 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA--KY---------------- 62 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHh--cC----------------
Confidence 799999999999999999999999999999999999999999999999999999999987 46
Q ss_pred ccceeehhhHHHHHHHHHHHHHhCC
Q 033487 94 KYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 94 ~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
.||+||++.+++||+||++|+
T Consensus 63 ----~i~~~L~~~~~~dI~rl~~I~ 83 (113)
T TIGR03631 63 ----KVEGDLRREVSLNIKRLMDIG 83 (113)
T ss_pred ----cchHHHHHHHHHHHHHHHHhc
Confidence 799999999999999999985
No 10
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=97.60 E-value=7.6e-05 Score=50.43 Aligned_cols=52 Identities=29% Similarity=0.376 Sum_probs=44.6
Q ss_pred CCeehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+++|..+| +.+.|||.-.|.+||-.+||+|..++++|+++|+.+|.+.+..
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 578888888 6899999999999999999999999999999999999888763
No 11
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=97.30 E-value=0.00035 Score=60.48 Aligned_cols=51 Identities=25% Similarity=0.406 Sum_probs=47.0
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..-..|.-..|.+||..+|.+||+.+|+++++++++|+++|+.+|.+++.+
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~ 306 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKK 306 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHh
Confidence 344567778999999999999999999999999999999999999999996
No 12
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=97.24 E-value=0.00044 Score=54.74 Aligned_cols=53 Identities=30% Similarity=0.369 Sum_probs=48.6
Q ss_pred CCCeehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 21 DGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 21 ~~~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..+++|.-+| +-+-|||.-.|.+||-.+||+|.+++++||++|++.|.+.+.+
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 3568899999 8999999999999999999999999999999999998887764
No 13
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=96.96 E-value=0.0012 Score=56.63 Aligned_cols=51 Identities=18% Similarity=0.309 Sum_probs=46.5
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhC
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~---~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..-..|.-..|..||..+|.+||+.+|++ +++++++|+++|+.+|.+++.+
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~ 300 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE 300 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh
Confidence 34455777899999999999999999999 9999999999999999999997
No 14
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.77 E-value=0.0024 Score=50.63 Aligned_cols=52 Identities=25% Similarity=0.331 Sum_probs=45.0
Q ss_pred CCCeehhhhhhh---hcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 21 DGKQKIMFALTS---IKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 21 ~~~K~v~~aLt~---IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
..+.+|.-+|-. |-|||.-.|.+||-.+||+|.+++++||++|+++|.+++.
T Consensus 152 ~~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~ 206 (272)
T PRK14810 152 GRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIG 206 (272)
T ss_pred cCCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence 345678888854 4999999999999999999999999999999998887554
No 15
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.68 E-value=0.0026 Score=50.41 Aligned_cols=50 Identities=20% Similarity=0.229 Sum_probs=44.0
Q ss_pred CCeehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
.+++|.-+| +-|-|||.-.|.+||=.+||+|..++++||++|+++|.+++
T Consensus 142 ~~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i 194 (269)
T PRK14811 142 TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAI 194 (269)
T ss_pred cCCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHH
Confidence 367888888 57899999999999999999999999999999988884444
No 16
>PRK10445 endonuclease VIII; Provisional
Probab=96.53 E-value=0.0039 Score=49.20 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=45.3
Q ss_pred Ceehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 23 ~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
+++|.-+| +-+-|||.-.|.+||=.+||+|..++++||++|+++|.+.+.+
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 56777777 5688999999999999999999999999999999998877754
No 17
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.46 E-value=0.0044 Score=49.37 Aligned_cols=51 Identities=27% Similarity=0.348 Sum_probs=45.4
Q ss_pred CCeehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.+.+|.-+| +-|-|||.-.|.+||=.+||+|..++++||++|+++|.+.+.
T Consensus 163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 216 (282)
T PRK13945 163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAII 216 (282)
T ss_pred CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 466777777 578999999999999999999999999999999888877765
No 18
>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=96.37 E-value=0.0047 Score=48.92 Aligned_cols=52 Identities=31% Similarity=0.346 Sum_probs=46.3
Q ss_pred CCeehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+.+|.-+| +-+-|||.-.|.+||=.+||+|..++++||++|+++|.+.+.+
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 467777777 5788999999999999999999999999999999999887764
No 19
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=96.23 E-value=0.0046 Score=53.07 Aligned_cols=53 Identities=21% Similarity=0.296 Sum_probs=48.5
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCC----HHHHHHHHHHHhC
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS----AAELDNLMVVVAN 73 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls----~~qi~~L~~~i~~ 73 (118)
....--.|...+|..||..+|..+|+.+|++|+.++.+|+ +++.++|.+++.+
T Consensus 254 ~~~tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~ 310 (538)
T COG1389 254 RRSTVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKK 310 (538)
T ss_pred hhhhHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHh
Confidence 3455567888999999999999999999999999999999 9999999999986
No 20
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=95.68 E-value=0.0065 Score=50.54 Aligned_cols=51 Identities=29% Similarity=0.482 Sum_probs=35.8
Q ss_pred CCeehhhhhhhh-cccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 22 GKQKIMFALTSI-KGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 22 ~~K~v~~aLt~I-yGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
+...+.-+|... .|+|+..|..+|..+|+++++++.+++++++..|.+.+.
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 455666666554 599999999999999999999999999998776555543
No 21
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.02 E-value=0.031 Score=44.88 Aligned_cols=58 Identities=26% Similarity=0.354 Sum_probs=48.3
Q ss_pred hccccCCCCeehhhhh---hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 15 VLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 15 I~g~~i~~~K~v~~aL---t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
++..-...+++|.-+| +-+-|||.-.|.++|=.+||+|.+..++|+..|+..|.+++.
T Consensus 147 l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~ 207 (273)
T COG0266 147 LAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK 207 (273)
T ss_pred HHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHH
Confidence 3444445566677777 678999999999999999999999999999999888877765
No 22
>TIGR00275 flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
Probab=94.75 E-value=0.024 Score=46.67 Aligned_cols=51 Identities=24% Similarity=0.423 Sum_probs=45.3
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+++++...|+.+ +-.+.+..||+.+||++++++++|+++|+++|.+.+++
T Consensus 281 ~~~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 281 NPKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred ChhhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 3477777777754 78999999999999999999999999999999999986
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=94.63 E-value=0.02 Score=31.26 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=15.2
Q ss_pred hhhhhcccCcchHHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~ 46 (118)
-|.+++|||+.+|..|+.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 578999999999999975
No 24
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=93.24 E-value=0.09 Score=41.89 Aligned_cols=48 Identities=23% Similarity=0.295 Sum_probs=44.3
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
...|++..+|...++ ..++|+.+|++++.|+.+||-+|..+|.+++..
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 467889999999888 999999999999999999999999999999875
No 25
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=92.96 E-value=0.056 Score=29.73 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=15.4
Q ss_pred hhhhhcccCcchHHHHHHHhCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADV 50 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi 50 (118)
.+++++|||+.++.+ ++++||
T Consensus 12 pi~~~~GIG~kt~~k-L~~~GI 32 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKK-LNKLGI 32 (32)
T ss_dssp BGGGSTTS-HHHHHH-HHCTT-
T ss_pred CHHhhCCccHHHHHH-HHHccC
Confidence 578999999999988 455554
No 26
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=92.78 E-value=0.15 Score=39.98 Aligned_cols=62 Identities=21% Similarity=0.282 Sum_probs=46.9
Q ss_pred cccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 9 ~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
|.++++.+ .....|++.-+|..+++. ...+.++++.+|++++.|+.+|+.+|..+|.+.+..
T Consensus 209 ~~~~~~~~--F~~rrk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 209 FFRVVKAA--FAQRRKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHHHHHHH--HhchHHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 44444432 234567777788777552 345678899999999999999999999999998874
No 27
>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=92.66 E-value=0.067 Score=32.66 Aligned_cols=22 Identities=23% Similarity=0.314 Sum_probs=16.1
Q ss_pred hhhhhcccCcchHHHHHHHhCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.+++|+|||+.+|.+..+ .|+.
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 478999999999999998 7765
No 28
>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=92.55 E-value=0.024 Score=34.82 Aligned_cols=26 Identities=27% Similarity=0.404 Sum_probs=22.0
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCC
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
++-.|.+|.|||+.+|..+.+. |+..
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 5668899999999999999887 7774
No 29
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=92.49 E-value=0.11 Score=37.69 Aligned_cols=58 Identities=21% Similarity=0.175 Sum_probs=45.2
Q ss_pred ccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhC
Q 033487 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 16 ~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~---~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.|..|+-|..=...|+.+.|||+++|.+|++.-.+. .-..+..+++.|.+.+++..++
T Consensus 49 ~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 49 FGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDN 109 (132)
T ss_pred cCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcc
Confidence 466677677777789999999999999999643332 2345777899999999999875
No 30
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=90.78 E-value=0.3 Score=37.64 Aligned_cols=59 Identities=17% Similarity=0.235 Sum_probs=45.0
Q ss_pred cccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 9 ~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
|.++++.+ ..-..|++.-+|..+++- ..+..+++.+|+++++++.+||.+|...|.+++
T Consensus 195 ~~~~~~~~--F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~~ 253 (253)
T TIGR00755 195 FEKLLKAA--FSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANLL 253 (253)
T ss_pred HHHHHHHH--HccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHhC
Confidence 45555532 345678888888877542 356678999999999999999999999997753
No 31
>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=90.64 E-value=0.47 Score=39.76 Aligned_cols=51 Identities=27% Similarity=0.394 Sum_probs=45.2
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCC-CCCCcCCCCCHHHHHHHHHHHhC
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADV-DMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi-~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+++.+...|..+ +-++.+..+|+.+|+ ++++++.+|+++++.+|.+.+.+
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 4678888888877 889999999999999 99999999999999999999986
No 32
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.43 E-value=0.18 Score=26.17 Aligned_cols=20 Identities=25% Similarity=0.434 Sum_probs=17.0
Q ss_pred hhhhhcccCcchHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~l 48 (118)
.|..+.|||+++|..|+...
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 46799999999999998743
No 33
>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=88.16 E-value=0.32 Score=36.80 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=27.7
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCc
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKR 55 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r 55 (118)
|.+..+.-.|..++|||+++|.-+|..+|=-...+
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~~~~ 142 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQLGVT 142 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHhCCC
Confidence 66667778899999999999999998776443333
No 34
>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=88.07 E-value=0.25 Score=38.44 Aligned_cols=61 Identities=25% Similarity=0.284 Sum_probs=49.2
Q ss_pred ccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 8 ~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.|.++++.+= ....|++.-+|..+++ ...+..+.+.+||+++.++.+|+.+|..+|.++++
T Consensus 201 ~~~~~~~~~F--~~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 201 AFEYFVRQLF--SQRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHHHHHHHHH--TTTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHH--hCcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 4667776653 3688999999988764 33456777789999999999999999999999886
No 35
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.62 E-value=0.33 Score=36.77 Aligned_cols=20 Identities=20% Similarity=0.390 Sum_probs=17.0
Q ss_pred hhhhhhcccCcchHHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~ 47 (118)
-+|++++|||+++|.+||-.
T Consensus 108 ~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVME 127 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 46899999999999999933
No 36
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.27 E-value=0.21 Score=37.92 Aligned_cols=39 Identities=15% Similarity=0.313 Sum_probs=31.1
Q ss_pred hhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCC
Q 033487 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 13 vrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
..++|..-...+.++..|.++.|||+++|..|+..++.+
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 58 LSLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 356777777888888888999999999999988876544
No 37
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.18 E-value=0.36 Score=36.48 Aligned_cols=19 Identities=26% Similarity=0.410 Sum_probs=16.6
Q ss_pred hhhhhhcccCcchHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~ 46 (118)
-+|++++|||+++|.+||-
T Consensus 108 ~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 4689999999999999983
No 38
>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=86.69 E-value=2.6 Score=33.06 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=44.7
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCCCc------------CCCCCHHHHHHHHHHHhC
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKR------------AGELSAAELDNLMVVVAN 73 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r------------~~~Ls~~qi~~L~~~i~~ 73 (118)
...+..--..++|+|+....||.+.+|+=+.+. ...||++|+++|-.|.+.
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 555666667889999999999999999999988 567999999999999986
No 39
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.57 E-value=0.41 Score=36.49 Aligned_cols=18 Identities=39% Similarity=0.626 Sum_probs=16.3
Q ss_pred hhhhhhcccCcchHHHHH
Q 033487 28 FALTSIKGIGRRLANIVC 45 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (118)
.+|++++|||+++|.+||
T Consensus 107 ~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 107 RLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHhhCCCCCHHHHHHHH
Confidence 478999999999999998
No 40
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.46 E-value=0.42 Score=36.41 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=17.2
Q ss_pred hhhhhhcccCcchHHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~ 47 (118)
.+|++++|||+++|.+||-.
T Consensus 108 ~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 47899999999999999943
No 41
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.89 E-value=0.47 Score=36.39 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=16.2
Q ss_pred hhhhhhcccCcchHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~ 46 (118)
-+|++++|||+++|.+|+-
T Consensus 107 ~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 4688999999999999983
No 42
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=85.38 E-value=0.34 Score=36.55 Aligned_cols=60 Identities=10% Similarity=0.203 Sum_probs=42.5
Q ss_pred hhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCC------------CCcCCCCCHHHHHHHHHHHhC
Q 033487 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDM------------NKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 14 rI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~------------~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
|+.|..-...+.+...|..|.|||+++|..|++.+|.+. -.++.-+++...++|...+..
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 345666445556656889999999999999999988621 123555677777777777775
No 43
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.35 E-value=0.5 Score=36.14 Aligned_cols=18 Identities=39% Similarity=0.632 Sum_probs=16.1
Q ss_pred hhhhhhcccCcchHHHHH
Q 033487 28 FALTSIKGIGRRLANIVC 45 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (118)
-+|++++|||+++|.+||
T Consensus 109 ~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHhcCCCcCHHHHHHHH
Confidence 468999999999999998
No 44
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=85.21 E-value=1.1 Score=39.17 Aligned_cols=50 Identities=22% Similarity=0.302 Sum_probs=44.5
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.-+..++..+.|+|.-.|.++|-.+|+++.....++.++++..+...+++
T Consensus 186 ~~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~ 235 (564)
T COG1293 186 ADIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE 235 (564)
T ss_pred hHHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence 34567788999999999999999999999999999999999999887643
No 45
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=85.18 E-value=0.57 Score=33.99 Aligned_cols=44 Identities=20% Similarity=0.235 Sum_probs=38.9
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
=||.|.|||+..+. .+..+||-.--.+-.+|..++..+..+++-
T Consensus 68 DLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~f 111 (133)
T COG3743 68 DLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLNF 111 (133)
T ss_pred cchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcCC
Confidence 58999999998765 578899999889999999999999999963
No 46
>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=84.86 E-value=0.54 Score=31.06 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=22.1
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+..|.++|+.|+|||...|.+|++.-.
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 478999999999999999999998774
No 47
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=84.54 E-value=0.58 Score=36.01 Aligned_cols=19 Identities=37% Similarity=0.550 Sum_probs=15.1
Q ss_pred hhhhhhcccCcchHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~ 46 (118)
-+|++++|||+++|.+||-
T Consensus 108 ~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 108 KALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HhhhcCCCCCHHHHHHHHH
Confidence 4678888888888888883
No 48
>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=83.23 E-value=0.85 Score=27.80 Aligned_cols=20 Identities=35% Similarity=0.561 Sum_probs=17.9
Q ss_pred hhhhhcccCcchHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~l 48 (118)
.|..+.|||+.+|..|++.+
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 49
>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=82.85 E-value=0.28 Score=37.12 Aligned_cols=35 Identities=17% Similarity=0.322 Sum_probs=24.1
Q ss_pred hhccccCCCCeehhhhhhhhcccCcchHHHHHHHh
Q 033487 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 14 rI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
.++|..-...+.++..|.++.|||+++|..|+..+
T Consensus 58 ~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~ 92 (191)
T TIGR00084 58 LLFGFNTLEERELFKELIKVNGVGPKLALAILSNM 92 (191)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcC
Confidence 45666666667777777777777777777775443
No 50
>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=82.11 E-value=0.82 Score=29.45 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=25.5
Q ss_pred cccccchhhcc--ccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 7 EDFQHILRVLN--TNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 7 ~~~~~mvrI~g--~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
++|..+.=+.| +|- +..+.|||+++|.+++...|
T Consensus 8 ~q~~d~~~L~GD~~D~---------i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 8 EQFIDLAILVGDKSDN---------IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred HHHHHHHHHcCCcccc---------CCCCCcccHHHHHHHHHHhC
Confidence 55666666777 432 34689999999999998865
No 51
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.52 E-value=0.92 Score=34.40 Aligned_cols=18 Identities=33% Similarity=0.567 Sum_probs=16.0
Q ss_pred hhhhhhcccCcchHHHHH
Q 033487 28 FALTSIKGIGRRLANIVC 45 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (118)
-+|++++|||+++|.+||
T Consensus 108 ~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 468999999999999966
No 52
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=81.29 E-value=1.5 Score=27.34 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=22.3
Q ss_pred CCCCeehhhhhhh-hcccCcchHHHHHHHh
Q 033487 20 VDGKQKIMFALTS-IKGIGRRLANIVCKKA 48 (118)
Q Consensus 20 i~~~K~v~~aLt~-IyGIG~~~A~~Ic~~l 48 (118)
++=|..-.-.|.. +.|||...|.+|++.-
T Consensus 8 invNta~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 8 VNINTATAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred eECcCCCHHHHHhHCCCCCHHHHHHHHHHH
Confidence 3444444557777 9999999999999984
No 53
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.58 E-value=0.58 Score=35.80 Aligned_cols=61 Identities=13% Similarity=0.203 Sum_probs=46.4
Q ss_pred hhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCC------------CCCcCCCCCHHHHHHHHHHHhC
Q 033487 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD------------MNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 13 vrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~------------~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..++|..-...+.++..|.++.|||+++|..|+..++.+ .-+++.-+.+.--++|.-.++.
T Consensus 59 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 59 LELFGFATWDERQTFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence 357788888889999999999999999999999876543 2235555666666666666665
No 54
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=80.41 E-value=0.68 Score=28.85 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=30.3
Q ss_pred CCeehhhhhhhhcccCcchHHHHHHHh-------CCCCCCcCCCCCHHHHHHHHH
Q 033487 22 GKQKIMFALTSIKGIGRRLANIVCKKA-------DVDMNKRAGELSAAELDNLMV 69 (118)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~l-------gi~~~~r~~~Ls~~qi~~L~~ 69 (118)
-|..=.--|..++|||+..|.+|.+.= .++.-..+..++++.+++|..
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 344455668899999999999999765 334445566667777777654
No 55
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.23 E-value=0.49 Score=35.86 Aligned_cols=37 Identities=16% Similarity=0.362 Sum_probs=31.9
Q ss_pred hhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 13 vrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
..++|..-...+.++..|.++.|||+++|..|+..+.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~ 94 (188)
T PRK14606 58 ITLYGFSNERKKELFLSLTKVSRLGPKTALKIISNED 94 (188)
T ss_pred ceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC
Confidence 3567888888899999999999999999999996543
No 56
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.21 E-value=0.5 Score=35.75 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=26.0
Q ss_pred hhccccCCCCeehhhhhhhhcccCcchHHHHHHHh
Q 033487 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 14 rI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
.++|..-...+.++..|.++.|||+++|..|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~ 93 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKL 93 (186)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccC
Confidence 46677777777777778888888888888777654
No 57
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.15 E-value=0.5 Score=35.75 Aligned_cols=36 Identities=25% Similarity=0.340 Sum_probs=31.7
Q ss_pred hhhccccCCCCeehhhhhhhhcccCcchHHHHHHHh
Q 033487 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 13 vrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
+.++|..-...+.++..|.++.|||+++|..|+..+
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~ 93 (183)
T PRK14601 58 NKLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSSL 93 (183)
T ss_pred ceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 467888888899999999999999999999999654
No 58
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.14 E-value=0.93 Score=34.30 Aligned_cols=17 Identities=41% Similarity=0.686 Sum_probs=15.6
Q ss_pred hhhhhhcccCcchHHHHH
Q 033487 28 FALTSIKGIGRRLANIVC 45 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (118)
.+| +++|||+++|.+||
T Consensus 108 ~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 108 AAL-KVNGIGEKLINRII 124 (186)
T ss_pred hhe-ECCCCcHHHHHHHH
Confidence 467 89999999999999
No 59
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=79.49 E-value=0.85 Score=28.44 Aligned_cols=18 Identities=28% Similarity=0.589 Sum_probs=14.9
Q ss_pred hhcccCcchHHHHHHHhC
Q 033487 32 SIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lg 49 (118)
.|+|||..+|+.+++..|
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 60
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=79.44 E-value=1.1 Score=25.15 Aligned_cols=32 Identities=16% Similarity=0.329 Sum_probs=21.8
Q ss_pred cccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHH
Q 033487 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 9 ~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~ 47 (118)
|-++.=+.| |-.+| ...+.|||.++|.+++++
T Consensus 4 ~~~~~~L~G-D~~dn------i~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 4 LIDYAILVG-DYSDN------IPGVKGIGPKTALKLLRE 35 (36)
T ss_pred HHHHHHHhC-cCCCC------CCCCCcccHHHHHHHHHh
Confidence 444555556 33332 357899999999999875
No 61
>PRK00076 recR recombination protein RecR; Reviewed
Probab=79.20 E-value=2.6 Score=32.39 Aligned_cols=41 Identities=20% Similarity=0.234 Sum_probs=31.5
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+..+|+.++|||+++|.++.-.+=-. +++++..|.++|.+
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla~~ll~~--------~~~~~~~la~~i~~ 48 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLAFHLLQR--------DREDVLRLAQALEE 48 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHcC--------CHHHHHHHHHHHHH
Confidence 456789999999999999998655332 56777777777763
No 62
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.70 E-value=0.59 Score=35.82 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=31.3
Q ss_pred hhccccCCCCeehhhhhhhhcccCcchHHHHHHHh
Q 033487 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 14 rI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
.++|..-...+.++..|.++.|||+++|..|+..+
T Consensus 58 ~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~ 92 (196)
T PRK13901 58 KLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGI 92 (196)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 57888888899999999999999999999999654
No 63
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=78.56 E-value=1.3 Score=31.43 Aligned_cols=45 Identities=16% Similarity=0.214 Sum_probs=29.9
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
...+.-.|++++|||+.+|..+|-. +++++.-+- |-.+.++...+
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~-~~~~~~~pv---D~~v~r~~~~~ 122 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLF-ALGPDAFPV---DTHVRRVLKRL 122 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHH-HCCCCCCcc---chhHHHHHHHh
Confidence 3567888999999999999998864 333332222 45555555544
No 64
>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=78.54 E-value=1.6 Score=30.66 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=26.2
Q ss_pred cCCCCeehhhhhhhhcccCcchHHHHHHHhCC
Q 033487 19 NVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (118)
Q Consensus 19 ~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi 50 (118)
.++-|..-.-.|..++|||+.+|..|.+.-+-
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 45556666778899999999999999998753
No 65
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.04 E-value=0.62 Score=35.48 Aligned_cols=61 Identities=11% Similarity=0.170 Sum_probs=43.9
Q ss_pred hhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCC------------CCCcCCCCCHHHHHHHHHHHhC
Q 033487 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD------------MNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 13 vrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~------------~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..++|..-...+.++..|.++.|||+++|..|+..++.+ .-+++.-+.+.--++|.-.++.
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 57 LSLYGFPDEDSLELFELLLGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred ceeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 356788888889999999999999999999999765432 1234455555555566655654
No 66
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=78.02 E-value=2.5 Score=35.83 Aligned_cols=50 Identities=22% Similarity=0.339 Sum_probs=44.0
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.++|.+..+|.. .++.+.+..++++.|| ++....+||+.++++|.+.|+.
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 456777777765 4788999999999999 9999999999999999999986
No 67
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=77.88 E-value=2.9 Score=32.08 Aligned_cols=50 Identities=20% Similarity=0.251 Sum_probs=33.6
Q ss_pred CcchHHHHHHHhCCC--CCCcCC-CCCHHHHHHHHHHHhCCCCcc------------------CCcchhccc
Q 033487 37 GRRLANIVCKKADVD--MNKRAG-ELSAAELDNLMVVVANPRQFK------------------IPDWFLNRQ 87 (118)
Q Consensus 37 G~~~A~~Ic~~lgi~--~~~r~~-~Ls~~qi~~L~~~i~~~~~~~------------------ip~w~~nr~ 87 (118)
|...+..+.-.+.+. .-+|+. -.|.+|+.+|+.+++.. .|. |.-||-|||
T Consensus 84 ~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L~LsetQVkvWFQNRR 154 (197)
T KOG0843|consen 84 GKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSLSLSETQVKVWFQNRR 154 (197)
T ss_pred ccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHcCCChhHhhhhhhhhh
Confidence 444555555555555 334444 35999999999999975 343 677888887
No 68
>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=77.76 E-value=1.5 Score=27.47 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.1
Q ss_pred hhhhhcccCcchHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~l 48 (118)
+++.++|||.++|..|-+-+
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 68999999999999986543
No 69
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=77.64 E-value=3 Score=32.21 Aligned_cols=42 Identities=17% Similarity=0.285 Sum_probs=32.9
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..+..+|.+++|||++.|.++.=.+- +.+++++..|.+++.+
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL--------~~~~~~~~~la~al~~ 49 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLL--------QRDREDVERLAKALLE 49 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHH--------ccCHHHHHHHHHHHHH
Confidence 34667899999999999999985543 3477888888887763
No 70
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=77.47 E-value=1.3 Score=29.56 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=19.5
Q ss_pred hhhh-hhcccCcchHHHHHHHhCCCCC
Q 033487 28 FALT-SIKGIGRRLANIVCKKADVDMN 53 (118)
Q Consensus 28 ~aLt-~IyGIG~~~A~~Ic~~lgi~~~ 53 (118)
+.|. .|.|||-++|-+|..++|++++
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 3444 4999999999999999999864
No 71
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=77.20 E-value=0.55 Score=36.13 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=33.1
Q ss_pred chhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 12 mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
...++|..-...+.++-.|.++-|||+++|..||..+.
T Consensus 57 ~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 57 AHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred HHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCC
Confidence 35688888889999999999999999999999996543
No 72
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.82 E-value=3.3 Score=31.78 Aligned_cols=42 Identities=19% Similarity=0.219 Sum_probs=31.4
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..+..+|++++|||+++|.++.-.+=- -.++++..|.++|.+
T Consensus 7 ~~Li~~l~~LPGIG~KsA~RlA~~ll~--------~~~~~~~~la~ai~~ 48 (195)
T TIGR00615 7 SKLIESLKKLPGIGPKSAQRLAFHLLK--------RDPSEVLRLAQALLE 48 (195)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHHH
Confidence 346678999999999999999755432 356777777777763
No 73
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=76.58 E-value=1.7 Score=35.49 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=22.4
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCC
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
....|.+|+|||+++|..+-+ +||..
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 345678999999999999999 99974
No 74
>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=75.84 E-value=1.8 Score=28.31 Aligned_cols=20 Identities=40% Similarity=0.423 Sum_probs=18.2
Q ss_pred hhhhhcccCcchHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~l 48 (118)
.|+.|+|||..+|..|+..+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 47899999999999999888
No 75
>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=75.13 E-value=1.9 Score=32.67 Aligned_cols=18 Identities=33% Similarity=0.523 Sum_probs=16.4
Q ss_pred hhhhhhcccCcchHHHHH
Q 033487 28 FALTSIKGIGRRLANIVC 45 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (118)
-+|+.++|||+++|.+|+
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 457899999999999998
No 76
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=74.31 E-value=1.7 Score=30.60 Aligned_cols=42 Identities=19% Similarity=0.116 Sum_probs=26.8
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
..-.|..++|||+.+|..+|-.. ++...-+. |-.+.++...+
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~-~~~~~~~~---D~~v~r~~~rl 111 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA-LGKPFIPV---DTHVLRIAKRL 111 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH-CCCCCCcc---chHHHHHHHHh
Confidence 45667899999999999988764 33223333 33555544444
No 77
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=73.53 E-value=2.3 Score=32.83 Aligned_cols=43 Identities=16% Similarity=0.143 Sum_probs=29.6
Q ss_pred ehhhhhh-hhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 25 KIMFALT-SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 25 ~v~~aLt-~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
..+-.|. +++|||+++|..|+...|..|- -.=|-++.++.+-+
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~----~iVDtHv~Ri~~Rl 158 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGYEDL----AILDRHILRFLKRY 158 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccCCCe----eeeeHHHHHHHHHh
Confidence 4556666 9999999999999976666432 22345566655555
No 78
>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=73.52 E-value=2.8 Score=28.63 Aligned_cols=37 Identities=22% Similarity=0.188 Sum_probs=26.8
Q ss_pred hhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
-..|+.|+|||+++|.-+. .+||+.=.-+..-+.+++
T Consensus 11 ~~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~L 47 (93)
T PF11731_consen 11 LSDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEEL 47 (93)
T ss_pred HHHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHH
Confidence 3568999999999999887 899986443333344444
No 79
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.50 E-value=0.97 Score=34.42 Aligned_cols=61 Identities=11% Similarity=0.221 Sum_probs=42.6
Q ss_pred hhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCC------------CCCcCCCCCHHHHHHHHHHHhC
Q 033487 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD------------MNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 13 vrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~------------~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..++|..-...+.++.-|.++.|||+++|..|+..+..+ .-+++.-+...--++|.-.+..
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 58 LTLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred ceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 356777778888999999999999999999999765221 1234444555555555555554
No 80
>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=73.05 E-value=2.9 Score=25.58 Aligned_cols=20 Identities=10% Similarity=0.257 Sum_probs=17.8
Q ss_pred hhcccCcchHHHHHHHhCCC
Q 033487 32 SIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.--|||.++-+.+|..+||.
T Consensus 23 ~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 23 KELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred HHhCCCHHHHHHHHHHcCCC
Confidence 34699999999999999997
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=73.05 E-value=2.3 Score=34.28 Aligned_cols=26 Identities=15% Similarity=0.323 Sum_probs=21.8
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCC
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
...-|.+|+|||+++|.++- .+|+..
T Consensus 83 ~l~~l~~i~GiGpk~a~~l~-~lGi~s 108 (307)
T cd00141 83 GLLLLLRVPGVGPKTARKLY-ELGIRT 108 (307)
T ss_pred HHHHHHcCCCCCHHHHHHHH-HcCCCC
Confidence 34567899999999999999 899874
No 82
>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=72.48 E-value=5.4 Score=27.31 Aligned_cols=58 Identities=21% Similarity=0.145 Sum_probs=44.9
Q ss_pred ccccCCCCeehhhhhhhhcccCcchHHHHHHHh---CCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA---DVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 16 ~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~l---gi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
+|..|+-|..-..+.+++.|.=++.|..|+..+ .++.=..+..||+.|-+.|.+..++
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 456677777778899999999999999999876 3444566778999999999999986
No 83
>PRK13844 recombination protein RecR; Provisional
Probab=72.20 E-value=5.1 Score=30.91 Aligned_cols=41 Identities=10% Similarity=0.108 Sum_probs=31.2
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+.-+|+.++|||+++|.++.-.+= +-.++++..|.++|.+
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 4667899999999999999985542 2366777777777763
No 84
>PRK08609 hypothetical protein; Provisional
Probab=71.49 E-value=2.7 Score=36.68 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=22.2
Q ss_pred hhhhhhhcccCcchHHHHHHHhCCC
Q 033487 27 MFALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.+.|++|+|||+++|.++-+.+||.
T Consensus 87 ~~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 87 LLPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHHhcCCCCCHHHHHHHHHHhCCC
Confidence 3467899999999999999999985
No 85
>PRK10702 endonuclease III; Provisional
Probab=70.81 E-value=2.2 Score=32.77 Aligned_cols=22 Identities=36% Similarity=0.551 Sum_probs=18.6
Q ss_pred hhhhhhhhcccCcchHHHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~ 47 (118)
..-.|.+++|||+++|..|+-.
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~ 128 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNT 128 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHH
Confidence 4677999999999999988743
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=70.22 E-value=2.4 Score=31.61 Aligned_cols=22 Identities=32% Similarity=0.450 Sum_probs=18.7
Q ss_pred hhhhhhhhcccCcchHHHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~ 47 (118)
..-.|.+++|||+.+|..+|-.
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNV 125 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHH
Confidence 4567899999999999999843
No 87
>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=70.21 E-value=0.86 Score=31.36 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=15.7
Q ss_pred hhhhcccCcchHHHHHHHhC
Q 033487 30 LTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lg 49 (118)
...+.|||+++|..+++..|
T Consensus 20 IPGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp B---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCCHHHHHHHHHHcC
Confidence 34689999999999999988
No 88
>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=68.49 E-value=2.8 Score=33.48 Aligned_cols=48 Identities=13% Similarity=0.221 Sum_probs=29.5
Q ss_pred cccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 17 g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
|-.+|.+ .-.|.+++|||+.+|..||--+ ++-..- .-|..+.++..-+
T Consensus 97 ~g~~p~~---~~~L~~LpGIG~~TA~~Il~~a-~~~~~~---~vD~~v~RVl~Rl 144 (275)
T TIGR01084 97 GGEFPQD---FEDLAALPGVGRYTAGAILSFA-LNKPYP---ILDGNVKRVLSRL 144 (275)
T ss_pred CCCCcHH---HHHHHhCCCCCHHHHHHHHHHH-CCCCCC---cchHhHHHHHHHH
Confidence 3445543 5679999999999999998544 442222 2334454444443
No 89
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=67.23 E-value=2.9 Score=32.94 Aligned_cols=38 Identities=18% Similarity=0.300 Sum_probs=21.6
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
.|..|.|||+.++..+.+. ||..-..+..-|.++|..+
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 3566677777777666554 5555444444454554444
No 90
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=66.68 E-value=4 Score=32.63 Aligned_cols=32 Identities=19% Similarity=0.422 Sum_probs=24.9
Q ss_pred ccccchhhcc--cc-CCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 8 DFQHILRVLN--TN-VDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 8 ~~~~mvrI~g--~~-i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
++.++.=+.| +| +|| ++|||+++|.++++..|
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 4566666777 32 333 99999999999999999
No 91
>PRK03980 flap endonuclease-1; Provisional
Probab=66.59 E-value=3.5 Score=33.16 Aligned_cols=34 Identities=32% Similarity=0.419 Sum_probs=26.3
Q ss_pred cccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 7 ~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
++|-.+.=+.|+|-.. .|.|||+++|.++++..|
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 4566677777755432 688999999999999987
No 92
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=65.46 E-value=13 Score=28.80 Aligned_cols=63 Identities=19% Similarity=0.237 Sum_probs=42.3
Q ss_pred cccchhhccccCCCCeehhhhhhhhcc-cCcchHHHHHHHh-CCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 9 FQHILRVLNTNVDGKQKIMFALTSIKG-IGRRLANIVCKKA-DVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 9 ~~~mvrI~g~~i~~~K~v~~aLt~IyG-IG~~~A~~Ic~~l-gi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
|.++++. ..--..|++.-+|..+.. .+......+...+ ++++++|+.+||-+|...|.+.+..
T Consensus 192 ~~~~~~~--~F~~rrk~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 192 FDDFVKA--LFQHRRKTLRNALKNSAHISGKEDIKAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHHH--HHccccHHHHHHHhhhccccchhHHHHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 4444443 244567888888887631 2221223345556 5668999999999999999999875
No 93
>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=65.35 E-value=3.4 Score=32.96 Aligned_cols=34 Identities=26% Similarity=0.285 Sum_probs=26.5
Q ss_pred cccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 7 ~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
++|-.+.=+.|+|-.. .+.|||+++|.+++++.|
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 4566666677765533 688999999999999987
No 94
>PHA02564 V virion protein; Provisional
Probab=65.05 E-value=12 Score=27.26 Aligned_cols=32 Identities=16% Similarity=0.080 Sum_probs=27.7
Q ss_pred HHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 41 ANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 41 A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
+..+|+.+||+|+.++.-... .+.+|..+|-.
T Consensus 88 i~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~ 119 (141)
T PHA02564 88 ATAVANAMGVPPQAGLHLDQD-TLAALVTAIIR 119 (141)
T ss_pred HHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHH
Confidence 778999999999999987666 88899988864
No 95
>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=64.99 E-value=18 Score=21.73 Aligned_cols=43 Identities=12% Similarity=0.195 Sum_probs=33.4
Q ss_pred hhhhcccCcchHHHHHHHhCCCCCCcC----CCCCHHHHHHHHHHHh
Q 033487 30 LTSIKGIGRRLANIVCKKADVDMNKRA----GELSAAELDNLMVVVA 72 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lgi~~~~r~----~~Ls~~qi~~L~~~i~ 72 (118)
+....||...+...-.+..|+.+-.+- ...+++++..|..+..
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 467889999999999888788664332 3679999998887775
No 96
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=64.91 E-value=4.2 Score=30.55 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=18.4
Q ss_pred hhhhhcccCcchHHHHHHHhC
Q 033487 29 ALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lg 49 (118)
.|+.++|||+++|.+|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 588999999999999996654
No 97
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=63.79 E-value=9.7 Score=30.50 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=29.2
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 40 LANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 40 ~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
....+++.+|++ +.|+.+|+-+|.-+|.+++.+
T Consensus 256 ~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 256 FIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 445679999997 799999999999999999985
No 98
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=63.39 E-value=3.9 Score=35.93 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=32.4
Q ss_pred CccccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCC
Q 033487 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (118)
Q Consensus 5 ~~~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi 50 (118)
++|.|++|.=+.|+|- |..+.|||-.+|.++..+..-
T Consensus 211 ~~ekfr~mciLSGCDY---------l~slpGvGl~tA~k~l~k~~~ 247 (556)
T KOG2518|consen 211 TEEKFRRMCILSGCDY---------LSSLPGVGLATAHKLLSKYNT 247 (556)
T ss_pred CHHHHHHHHHhcCCcc---------cccCccccHHHHHHHHHhcCc
Confidence 5578999999999997 778999999999999987654
No 99
>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=63.26 E-value=7.6 Score=34.88 Aligned_cols=41 Identities=27% Similarity=0.368 Sum_probs=29.2
Q ss_pred hhcccCcchHHHHHHHhCCCC----------CCcCCCCCHHHHHHHHHHHh
Q 033487 32 SIKGIGRRLANIVCKKADVDM----------NKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~~----------~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.|+|||+.+|..|.+.+|.+. -..+.-|++...+.|.+.+.
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~ 138 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWS 138 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 499999999999999988661 12334566666666665554
No 100
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=63.16 E-value=5.4 Score=27.67 Aligned_cols=42 Identities=17% Similarity=0.336 Sum_probs=30.4
Q ss_pred ccccchhhccccCC---CCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 8 DFQHILRVLNTNVD---GKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 8 ~~~~mvrI~g~~i~---~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+|-.+|--.|+||+ .+......|+.+-|.|+++|..+.+.+.
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 45566667788875 4566778899999999999999998876
No 101
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=63.08 E-value=7.3 Score=33.26 Aligned_cols=47 Identities=17% Similarity=0.340 Sum_probs=32.1
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDNLMV 69 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi-~~---------~~r~~~Ls~~qi~~L~~ 69 (118)
++.|+|+|..|+|||...+.+|.+.=.- .| ....+.++...++.|..
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rvd~~~vnkr~lE~LIk 165 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRVDLRVVNRRALETLIY 165 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHhCcccCCHHHHHHHHH
Confidence 4569999999999999999999864321 11 12234566666666554
No 102
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=62.14 E-value=6.9 Score=34.55 Aligned_cols=44 Identities=30% Similarity=0.344 Sum_probs=31.5
Q ss_pred CCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
..+.+..+|..|.|||+.++..|++.+|= -..+.+-+.+++..+
T Consensus 537 ~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~v 580 (598)
T PRK00558 537 SKARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAKV 580 (598)
T ss_pred ccchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhhc
Confidence 34456789999999999999999998873 223344456665443
No 103
>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=61.67 E-value=14 Score=25.17 Aligned_cols=35 Identities=17% Similarity=0.350 Sum_probs=31.1
Q ss_pred cccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 34 KGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 34 yGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
--+|......|++.++ ++..+||++++...++++.
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 4578999999999998 7889999999999988886
No 104
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=61.61 E-value=5.3 Score=33.17 Aligned_cols=28 Identities=21% Similarity=0.461 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHHhCCCCcc------------------CCcchhccc
Q 033487 59 LSAAELDNLMVVVANPRQFK------------------IPDWFLNRQ 87 (118)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~------------------ip~w~~nr~ 87 (118)
+|.|||.+|++.+-. ++|. |..||-|||
T Consensus 188 FTReQIaRLEKEFyr-ENYVSRprRcELAAaLNLPEtTIKVWFQNRR 233 (408)
T KOG0844|consen 188 FTREQIARLEKEFYR-ENYVSRPRRCELAAALNLPETTIKVWFQNRR 233 (408)
T ss_pred hhHHHHHHHHHHHHH-hccccCchhhhHHHhhCCCcceeehhhhhch
Confidence 589999999987754 2453 567999998
No 105
>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=61.41 E-value=4.8 Score=23.91 Aligned_cols=45 Identities=11% Similarity=0.042 Sum_probs=34.2
Q ss_pred hhhhhhcccCcchHHHHH-HHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 28 FALTSIKGIGRRLANIVC-KKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic-~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.-|.+-.|+...-..+.| +.+|+.....-..|++++...|.+.+.
T Consensus 7 ~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 7 SELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp THHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred HHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 457788899999999999 669999777888899999999988775
No 106
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=60.99 E-value=7.2 Score=22.56 Aligned_cols=30 Identities=23% Similarity=0.355 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHhCCCCccCCcchhcccc
Q 033487 58 ELSAAELDNLMVVVANPRQFKIPDWFLNRQK 88 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~k 88 (118)
..+.+++..|...+.-+ ...|=.||-|||+
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR~ 53 (56)
T smart00389 24 YPSREEREELAAKLGLS-ERQVKVWFQNRRA 53 (56)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHhHHHHhh
Confidence 45667777777776542 2346678888875
No 107
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=60.69 E-value=4.5 Score=31.38 Aligned_cols=24 Identities=25% Similarity=0.166 Sum_probs=19.3
Q ss_pred ehhhhhhhhcccCcchHHHHHHHh
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
..+-.|.+++|||+.||..|+--+
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya 141 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYV 141 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHH
Confidence 455679999999999998877543
No 108
>PRK10880 adenine DNA glycosylase; Provisional
Probab=60.57 E-value=5.3 Score=33.10 Aligned_cols=24 Identities=17% Similarity=0.365 Sum_probs=20.3
Q ss_pred ehhhhhhhhcccCcchHHHHHHHh
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
...-.|.+++|||+.+|..||.-+
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHH
Confidence 345789999999999999999744
No 109
>PRK13910 DNA glycosylase MutY; Provisional
Probab=60.52 E-value=5.5 Score=32.16 Aligned_cols=41 Identities=17% Similarity=0.223 Sum_probs=27.4
Q ss_pred hhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
.-.|.+++|||+.+|..|+..+ ++-.. -.=|..+.++..-+
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~a-f~~~~---~~VD~nV~RVl~Rl 111 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCFG-FREKS---ACVDANIKRVLLRL 111 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH-CCCCc---CcccHHHHHHHHHH
Confidence 6789999999999999998633 44211 13445555555443
No 110
>smart00475 53EXOc 5'-3' exonuclease.
Probab=60.48 E-value=5.1 Score=31.60 Aligned_cols=19 Identities=26% Similarity=0.431 Sum_probs=16.8
Q ss_pred hhhcccCcchHHHHHHHhC
Q 033487 31 TSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 31 t~IyGIG~~~A~~Ic~~lg 49 (118)
..+.|||+++|.+++++.|
T Consensus 189 pGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCHHHHHHHHHHhC
Confidence 4578999999999999887
No 111
>PRK09482 flap endonuclease-like protein; Provisional
Probab=60.26 E-value=5.4 Score=31.67 Aligned_cols=19 Identities=21% Similarity=0.343 Sum_probs=16.9
Q ss_pred hhhcccCcchHHHHHHHhC
Q 033487 31 TSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 31 t~IyGIG~~~A~~Ic~~lg 49 (118)
..+.|||+++|.+++++.|
T Consensus 185 pGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCcChHHHHHHHHHhC
Confidence 4678999999999999877
No 112
>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=60.22 E-value=5.2 Score=30.99 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=16.9
Q ss_pred hhhhcccCcchHHHHHHHhC
Q 033487 30 LTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lg 49 (118)
...+.|||+++|.+++++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34578999999999999865
No 113
>PTZ00217 flap endonuclease-1; Provisional
Probab=59.81 E-value=5.5 Score=33.40 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=25.4
Q ss_pred cccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 7 ~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
++|-.+.-+.|+|-. ..|.|||+.+|.+++++.|
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 456666667775442 3689999999999998865
No 114
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=59.71 E-value=5.9 Score=30.68 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=23.4
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhCCC
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.-.+.+.+|+|||.+=|..++...|+.
T Consensus 118 aRE~Lv~nikGiGyKEASHFLRNVG~~ 144 (210)
T COG1059 118 ARELLVENIKGIGYKEASHFLRNVGFE 144 (210)
T ss_pred HHHHHHHHcccccHHHHHHHHHhcChh
Confidence 445677899999999999999999984
No 115
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=59.24 E-value=8.6 Score=30.03 Aligned_cols=40 Identities=25% Similarity=0.126 Sum_probs=28.9
Q ss_pred ccCCCCeeh--hhhhhhhcccCcchHHHHHHHhCCCCCCcCC
Q 033487 18 TNVDGKQKI--MFALTSIKGIGRRLANIVCKKADVDMNKRAG 57 (118)
Q Consensus 18 ~~i~~~K~v--~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~ 57 (118)
.++.+.++. +--|-+|+|||+-+|..|+-.+.=-|..-+.
T Consensus 103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD 144 (215)
T COG2231 103 INLESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVD 144 (215)
T ss_pred hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchh
Confidence 345555555 6778899999999999998777655554443
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=58.76 E-value=5.6 Score=32.12 Aligned_cols=44 Identities=14% Similarity=0.123 Sum_probs=28.4
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
.+.-.|+.++|||+.+|..||-..-=.|+.-+- |-.+.++.+.+
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 467788999999999999998554333333321 34444444443
No 117
>PRK07945 hypothetical protein; Provisional
Probab=58.53 E-value=19 Score=29.25 Aligned_cols=36 Identities=25% Similarity=0.336 Sum_probs=27.5
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.|+.|+|||..+|..|-+.+.=. +-+.+++|...++
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg--------~~~~l~~l~~~~~ 85 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGR--------VPDYLAELRADAE 85 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcC--------CHHHHHHHHHhhc
Confidence 58999999999999998876533 3356677776663
No 118
>PRK14976 5'-3' exonuclease; Provisional
Probab=57.96 E-value=5.9 Score=31.64 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=16.6
Q ss_pred hhhcccCcchHHHHHHHhC
Q 033487 31 TSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 31 t~IyGIG~~~A~~Ic~~lg 49 (118)
..+.|||+++|.++++..|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 3479999999999998876
No 119
>KOG0650 consensus WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=57.61 E-value=17 Score=32.75 Aligned_cols=49 Identities=22% Similarity=0.469 Sum_probs=38.0
Q ss_pred CCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHH
Q 033487 51 DMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMK 106 (118)
Q Consensus 51 ~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~ 106 (118)
+..+=++-...++++++.+.|+.| .| | ++.+|+.||++..+..-|+...
T Consensus 142 ~gkkI~kp~k~~~ld~fl~~iedp-~~----W--r~v~Dk~tG~dv~LTkEev~lI 190 (733)
T KOG0650|consen 142 DGKKITKPAKGDELDSFLAKIEDP-DY----W--RKVKDKMTGKDVNLTKEEVKLI 190 (733)
T ss_pred cccEecCCCccchHHHHHHhhcCc-ch----h--ccccccCCCceeeecHHHHHHH
Confidence 333445556779999999999985 24 6 9999999999999988877653
No 120
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=57.01 E-value=7.9 Score=30.45 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHhCCCCcc------------------CCcchhcccccc
Q 033487 59 LSAAELDNLMVVVANPRQFK------------------IPDWFLNRQKDY 90 (118)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~------------------ip~w~~nr~kd~ 90 (118)
.+.+|++.|++.+++- .|. |-.||-|||++.
T Consensus 44 Ftr~QlevLe~LF~kT-qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~ 92 (228)
T KOG2251|consen 44 FTRKQLEVLEALFAKT-QYPDVFMREELALKLNLPESRVQVWFKNRRAKC 92 (228)
T ss_pred ecHHHHHHHHHHHHhh-cCccHHHHHHHHHHhCCchhhhhhhhccccchh
Confidence 4788898888888752 232 567999999884
No 121
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=55.45 E-value=7.1 Score=33.10 Aligned_cols=28 Identities=18% Similarity=0.413 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHHhCCCCccCCcchhcccc
Q 033487 60 SAAELDNLMVVVANPRQFKIPDWFLNRQK 88 (118)
Q Consensus 60 s~~qi~~L~~~i~~~~~~~ip~w~~nr~k 88 (118)
|-+||..|.+-++= ++-.|-.||-|||.
T Consensus 320 t~qEIt~iA~~L~l-eKEVVRVWFCNRRQ 347 (398)
T KOG3802|consen 320 TSQEITHIAESLQL-EKEVVRVWFCNRRQ 347 (398)
T ss_pred CHHHHHHHHHHhcc-ccceEEEEeecccc
Confidence 67899999999972 25668999999985
No 122
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=54.70 E-value=7.9 Score=30.05 Aligned_cols=21 Identities=38% Similarity=0.507 Sum_probs=17.9
Q ss_pred hhhhhhhcccCcchHHHHHHH
Q 033487 27 MFALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~ 47 (118)
.-.|.+..|||++||.-++..
T Consensus 108 ~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 108 REELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHHHhCCCcchHHHHHHHHh
Confidence 457899999999999987766
No 123
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=54.28 E-value=7.6 Score=34.61 Aligned_cols=41 Identities=17% Similarity=0.221 Sum_probs=28.5
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~ 66 (118)
+...-.|..|.|||+.++..+++.+|= -..+..-|.+||.+
T Consensus 548 ~~~~S~L~~IpGIG~kr~~~LL~~FgS--i~~I~~As~eeL~~ 588 (624)
T PRK14669 548 RDRTSELLEIPGVGAKTVQRLLKHFGS--LERVRAATETQLAA 588 (624)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHcCC--HHHHHhCCHHHHHH
Confidence 344567889999999999999998872 12344445555543
No 124
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=53.81 E-value=7.4 Score=31.08 Aligned_cols=29 Identities=28% Similarity=0.289 Sum_probs=21.6
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCCCC
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDMNK 54 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~ 54 (118)
+.-.|..++|||+.+|..|+-..-=.|+.
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~ 233 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDV 233 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCC
Confidence 46789999999999999988543224444
No 125
>PF13276 HTH_21: HTH-like domain
Probab=52.29 E-value=12 Score=22.42 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=29.9
Q ss_pred CCCCeehhhhhhhhcc--cCcchHHHHHHHhCCCCCC
Q 033487 20 VDGKQKIMFALTSIKG--IGRRLANIVCKKADVDMNK 54 (118)
Q Consensus 20 i~~~K~v~~aLt~IyG--IG~~~A~~Ic~~lgi~~~~ 54 (118)
.-|...+...|..-+| ||.+++..|++..||....
T Consensus 20 ~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~~ 56 (60)
T PF13276_consen 20 TYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSKR 56 (60)
T ss_pred CeehhHHHHHHhccCcccccHHHHHHHHHHcCCcccC
Confidence 5678889999988877 7999999999999997654
No 126
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=52.10 E-value=11 Score=29.34 Aligned_cols=46 Identities=24% Similarity=0.279 Sum_probs=40.2
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANP 74 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~ 74 (118)
--|+.|.|||+..+.. +..+|+..--.+-.++++++..+...+.-+
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l~~~ 203 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKLSFK 203 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhcccCC
Confidence 4589999999998865 578999999999999999999999888643
No 127
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=51.76 E-value=8.2 Score=31.77 Aligned_cols=45 Identities=9% Similarity=0.076 Sum_probs=38.9
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
--|+.|.|||+..+. .|..+||..--.+..+|++++..+...+.-
T Consensus 263 DdL~~I~GiGp~~e~-~L~~~Gi~~f~QiA~~t~~~~a~vd~~l~f 307 (326)
T PRK12311 263 DDLKKLTGVSPQIEK-KLNDLGIFHFWQLAELDPDDAAKIGEELGL 307 (326)
T ss_pred hhhhhhccCChhhhh-hhhhcCCCCHHHhhCCChhhhhhhhhcccC
Confidence 558999999998765 578999999999999999999988887753
No 128
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.31 E-value=6.6 Score=31.52 Aligned_cols=23 Identities=30% Similarity=0.436 Sum_probs=19.5
Q ss_pred eehhhhhhhhcccCcchHHHHHH
Q 033487 24 QKIMFALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~ 46 (118)
..+.-.|+.|.|||+-+|.-+|-
T Consensus 194 e~a~e~L~~i~GIG~WTAe~~ll 216 (285)
T COG0122 194 EEAIEELTALKGIGPWTAEMFLL 216 (285)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHH
Confidence 44667899999999999999884
No 129
>PRK13766 Hef nuclease; Provisional
Probab=51.00 E-value=13 Score=33.01 Aligned_cols=25 Identities=16% Similarity=0.251 Sum_probs=21.5
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhC
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
...+.|+.|.|||+.+|..|++.+|
T Consensus 712 ~~~~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 712 QQEYIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3445789999999999999999887
No 130
>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=50.86 E-value=10 Score=31.19 Aligned_cols=37 Identities=22% Similarity=0.424 Sum_probs=27.1
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCC--CHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGEL--SAAELD 65 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~L--s~~qi~ 65 (118)
-++.+.|||++++.++++.+||..-.-+-.+ +..++.
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 4689999999999999999999854333333 444443
No 131
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=48.72 E-value=15 Score=22.72 Aligned_cols=29 Identities=24% Similarity=0.415 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHHHhCCCCccCCcchhccccccC
Q 033487 58 ELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 91 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~ 91 (118)
.++.+.+.+|.+++.- -|.|++++|+.++
T Consensus 44 ~~~~~~~~~l~~~l~v-----~~~~l~~~~~~~~ 72 (78)
T TIGR02607 44 GITADMALRLAKALGT-----SPEFWLNLQNAYD 72 (78)
T ss_pred CCCHHHHHHHHHHcCC-----CHHHHHHHHHHHH
Confidence 5678888888888752 3788888887643
No 132
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=48.53 E-value=10 Score=28.86 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=21.5
Q ss_pred hhhhhhcccCcchHHHHHHHhCCC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
+++|..+|+|++++...++.+|+.
T Consensus 3 I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 3 IAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred EEEeCCCCCchHHHHHHHHHhCCc
Confidence 578999999999999999988876
No 133
>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=48.06 E-value=9.2 Score=33.70 Aligned_cols=26 Identities=19% Similarity=0.264 Sum_probs=22.1
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhC
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+.+.-.|..|.|||+++...+++.+|
T Consensus 537 ~~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 537 ASLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 34456788999999999999999876
No 134
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=47.59 E-value=18 Score=26.29 Aligned_cols=44 Identities=16% Similarity=0.249 Sum_probs=27.1
Q ss_pred hhhhhhcccCcchHHHHHHHhCCC-CC------CcCCCCCHHHHHHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKKADVD-MN------KRAGELSAAELDNLMVVV 71 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~-~~------~r~~~Ls~~qi~~L~~~i 71 (118)
--|+.+.|||+++|.+|.+.-.-+ |- .++.-+.+.-++++...|
T Consensus 97 eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 97 EELQALPGIGPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHHhhc
Confidence 345999999999999999654222 22 333333445555555443
No 135
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=47.23 E-value=11 Score=33.21 Aligned_cols=43 Identities=26% Similarity=0.269 Sum_probs=31.4
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
.....-.|..|+|||+++..++++.+|= -..++.-|.+||.++
T Consensus 509 k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs--~~~ik~As~eeL~~v 551 (567)
T PRK14667 509 KEGLKDILDKIKGIGEVKKEIIYRNFKT--LYDFLKADDEELKKL 551 (567)
T ss_pred cccccCccccCCCCCHHHHHHHHHHhCC--HHHHHhCCHHHHHHc
Confidence 3445577899999999999999998773 234555566666554
No 136
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=46.99 E-value=11 Score=33.24 Aligned_cols=40 Identities=30% Similarity=0.336 Sum_probs=29.6
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
....|..|+|||+.+...+++.+|= -..+..-|.+||.++
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs--~~~I~~As~eeL~~v 551 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGT--YKDILLLNEDEIAEK 551 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCC--HHHHHhCCHHHHHhC
Confidence 4568889999999999999998773 234555566666544
No 137
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=46.94 E-value=23 Score=33.27 Aligned_cols=47 Identities=23% Similarity=0.343 Sum_probs=33.2
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCC---------CcCCCCCHHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMN---------KRAGELSAAELDNLMV 69 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~---------~r~~~Ls~~qi~~L~~ 69 (118)
+..|+++|+.|+|||...|..|.+.-.-.|- .....++...++.|.+
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~r~~~~~i~k~~le~LI~ 802 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILIN 802 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHHHhhhcCCCHHHHHHHHH
Confidence 5679999999999999999999865432221 1234567776666654
No 138
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=46.30 E-value=13 Score=32.85 Aligned_cols=40 Identities=15% Similarity=0.278 Sum_probs=29.8
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
...+|+.|.|||+.++.++++.+| .-..+.+-|.+++..+
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FG--S~~~I~~As~eeL~~v 562 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFG--SVEGVREASVEDLRDV 562 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhC
Confidence 568999999999999999999886 2234445566666443
No 139
>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=45.96 E-value=16 Score=23.23 Aligned_cols=23 Identities=22% Similarity=0.322 Sum_probs=16.3
Q ss_pred hhhhhcccCcchHHHHHHHhCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.|..--||.+.+..++|+++|++
T Consensus 39 elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 39 ELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHHHHcCCCHHHHHHHHHHhCCC
Confidence 35566778888888888888876
No 140
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=45.17 E-value=15 Score=21.79 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=17.5
Q ss_pred hhhhhhcccCcchHHHHHHHh
Q 033487 28 FALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~l 48 (118)
.-|...+||+.+++..++...
T Consensus 23 ~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 23 QDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred hHHhhheeecHHHHHHHHHHH
Confidence 457889999999999998654
No 141
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=44.32 E-value=12 Score=30.79 Aligned_cols=20 Identities=35% Similarity=0.698 Sum_probs=18.7
Q ss_pred hhhhhhhhcccCcchHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVC 45 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic 45 (118)
+.-+|..++|||++.|.-||
T Consensus 216 ar~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCIC 235 (323)
T ss_pred HHHHHhcCCCCcchHhhhhh
Confidence 67789999999999999999
No 142
>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=44.29 E-value=14 Score=23.56 Aligned_cols=46 Identities=15% Similarity=0.211 Sum_probs=34.9
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+.-.+..+.|+|-.-|+.+++.+ |..-...++.++-+.+.+.++.
T Consensus 15 ~vIK~vR~~tgl~L~eAK~~vd~~---p~~ik~~v~keeAe~ik~~Le~ 60 (68)
T PF00542_consen 15 KVIKEVREITGLGLKEAKKLVDSL---PKVIKEGVSKEEAEEIKKKLEA 60 (68)
T ss_dssp HHHHHHHHHC---HHHHHHHHCTT---TEEEEEEE-HHHHHHHHHHHHC
T ss_pred HHHHHHHHHhCCcHHHHHHHHHhC---CHHHHcCCCHHHHHHHHHHHHH
Confidence 345677899999999999999998 5555667899999999999986
No 143
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=44.20 E-value=6.6 Score=22.82 Aligned_cols=30 Identities=23% Similarity=0.319 Sum_probs=17.5
Q ss_pred CCCHHHHHHHHHHHhCCCCccCCcchhcccc
Q 033487 58 ELSAAELDNLMVVVANPRQFKIPDWFLNRQK 88 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~k 88 (118)
..+.+++..|...+.=+ ...|-.||-|||+
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR~ 53 (59)
T cd00086 24 YPSREEREELAKELGLT-ERQVKIWFQNRRA 53 (59)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHHHHHHHH
Confidence 34556666666665422 2335668888775
No 144
>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=44.19 E-value=12 Score=30.47 Aligned_cols=19 Identities=32% Similarity=0.457 Sum_probs=16.3
Q ss_pred hhhcccCcchHHHHHHHhC
Q 033487 31 TSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 31 t~IyGIG~~~A~~Ic~~lg 49 (118)
..|.|||+++|.++++..|
T Consensus 239 ~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 4789999999999998743
No 145
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=43.64 E-value=29 Score=25.74 Aligned_cols=17 Identities=12% Similarity=0.100 Sum_probs=15.5
Q ss_pred CCCCHHHHHHHHHHHhC
Q 033487 57 GELSAAELDNLMVVVAN 73 (118)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (118)
+.||++|+..|..+|-.
T Consensus 130 ~~LsdeEL~avAaYIl~ 146 (159)
T TIGR03045 130 RNLTDEDLRLIAGHILV 146 (159)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 57999999999999985
No 146
>PLN03072 60S ribosomal protein L12; Provisional
Probab=43.11 E-value=45 Score=24.94 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=32.3
Q ss_pred cCcchHHHHHHHhCCCCC--------CcCCCCCHHHHHHHHHHHhC
Q 033487 36 IGRRLANIVCKKADVDMN--------KRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 36 IG~~~A~~Ic~~lgi~~~--------~r~~~Ls~~qi~~L~~~i~~ 73 (118)
+-+.+|.-|.+.+|+... ..+++||-+|+..|.+.-..
T Consensus 74 v~Pp~s~LLkKa~g~~kgs~~~~~~~~~vG~it~~qv~eIA~~K~~ 119 (166)
T PLN03072 74 VVPSAAALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRP 119 (166)
T ss_pred eCCCHHHHHHHHhCCCCCCCccCCCCeeeeeecHHHHHHHHHHHHH
Confidence 368999999999999875 47899999999999987653
No 147
>PRK00419 DNA primase small subunit; Reviewed
Probab=42.32 E-value=14 Score=31.10 Aligned_cols=20 Identities=35% Similarity=0.471 Sum_probs=15.7
Q ss_pred hhhhhcccCcchHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~l 48 (118)
-|+.+.|||..+|+.+++..
T Consensus 222 ~l~~~~gi~~~~~~~~l~~~ 241 (376)
T PRK00419 222 RLEEFDGIGEGTAKKILKAA 241 (376)
T ss_pred hhhhhcccchhHHHHHHHHh
Confidence 46778899999888888653
No 148
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.07 E-value=58 Score=23.57 Aligned_cols=45 Identities=16% Similarity=0.168 Sum_probs=36.6
Q ss_pred hhhhhcccCcchHHHHHHHhC---CC--C---CCcCCCCCHHHHHHHHHHHhC
Q 033487 29 ALTSIKGIGRRLANIVCKKAD---VD--M---NKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lg---i~--~---~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..++.+|||.+++..-.++.. .+ + .=+++.|+++|++.|...++.
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 457889999999999997765 33 2 247889999999999999986
No 149
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=40.97 E-value=6.1 Score=23.18 Aligned_cols=29 Identities=24% Similarity=0.468 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHhCCCCccCCcchhcccc
Q 033487 59 LSAAELDNLMVVVANPRQFKIPDWFLNRQK 88 (118)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~k 88 (118)
.+.++.+.|...+.=+ ...|-.||.|||.
T Consensus 25 p~~~~~~~la~~l~l~-~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 25 PSKEEREELAKELGLT-ERQVKNWFQNRRR 53 (57)
T ss_dssp CHHHHHHHHHHHHTSS-HHHHHHHHHHHHH
T ss_pred cccccccccccccccc-ccccccCHHHhHH
Confidence 3445555555555421 1234567777663
No 150
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=40.68 E-value=40 Score=23.06 Aligned_cols=47 Identities=21% Similarity=0.248 Sum_probs=31.6
Q ss_pred cccCcchHHHHHHHhCCCCCCcC-CCCCHHHHHHHHHHHhCCCCccCCcchhc
Q 033487 34 KGIGRRLANIVCKKADVDMNKRA-GELSAAELDNLMVVVANPRQFKIPDWFLN 85 (118)
Q Consensus 34 yGIG~~~A~~Ic~~lgi~~~~r~-~~Ls~~qi~~L~~~i~~~~~~~ip~w~~n 85 (118)
.|||+. |...+..+||.+-... ..-=++-+++|...+.. ..|+||.+
T Consensus 70 ~~IG~~-a~~~L~~~gI~~~~~~~~~~v~eal~~l~~~~~~----~~~~w~~~ 117 (119)
T TIGR02663 70 LAIGGP-AAAKVVAAKIHPIKVNEPESISELLERLQKMLKG----NPPPWLRK 117 (119)
T ss_pred hhcCcc-HHHHHHHcCCeeEecCCCccHHHHHHHHHHHHcC----CCCHHHHh
Confidence 468875 4556677999985422 22346677788888864 46999975
No 151
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=39.92 E-value=14 Score=24.72 Aligned_cols=41 Identities=17% Similarity=0.181 Sum_probs=31.7
Q ss_pred CCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
++.+.-+..|....|||+.-|+++.++++.- .+|.+|++..
T Consensus 45 ~~s~~rR~~l~~~L~iGy~N~KqllkrLN~f------~it~~e~~~a 85 (87)
T PF13331_consen 45 PDSKERREKLGEYLGIGYGNAKQLLKRLNMF------GITREEFEEA 85 (87)
T ss_pred ccHHHHHHHHHHHHCCCCCCHHHHHHHHHHc------CCCHHHHHHH
Confidence 4557888889999999999999999988743 3466666543
No 152
>cd00037 CLECT C-type lectin (CTL)/C-type lectin-like (CTLD) domain. CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initia
Probab=39.43 E-value=90 Score=19.07 Aligned_cols=50 Identities=16% Similarity=0.111 Sum_probs=36.9
Q ss_pred ccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccc
Q 033487 35 GIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKD 89 (118)
Q Consensus 35 GIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd 89 (118)
..-..-|.++|...| ..-+.--+.+|.+-|.+.+.. ....+.|+.-++..
T Consensus 9 ~~~~~~A~~~C~~~~---~~L~~~~~~~e~~~i~~~~~~--~~~~~~wvg~~~~~ 58 (116)
T cd00037 9 KLTWEEAQEYCRSLG---GHLASIHSEEENDFLASLLKK--SSSSDVWIGLNDLS 58 (116)
T ss_pred ccCHHHHHHHHHHcC---CEEcccCCHHHHHHHHHHHhC--CCCCCEEEcccccC
Confidence 456778999999999 344555577999999999974 34467898666553
No 153
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=39.15 E-value=14 Score=32.95 Aligned_cols=50 Identities=22% Similarity=0.369 Sum_probs=35.6
Q ss_pred ccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 16 ~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
.+-..-..+.+.-.|..|.|||+++|..|++.+| +. ..+..-+.+++.++
T Consensus 557 yhr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~-~~i~~As~eeL~~v 606 (621)
T PRK14671 557 YHRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFG-SV-EKVAKASLEELAAV 606 (621)
T ss_pred hChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcC-CH-HHHHhCCHHHHHHH
Confidence 3445555566777889999999999999999996 21 23444577776554
No 154
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=38.85 E-value=20 Score=24.43 Aligned_cols=60 Identities=20% Similarity=0.366 Sum_probs=37.4
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcc--h-hccc-----cccCCCccceeeh
Q 033487 40 LANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDW--F-LNRQ-----KDYKDGKYSQVVS 100 (118)
Q Consensus 40 ~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w--~-~nr~-----kd~~tg~~~h~i~ 100 (118)
.+..|++++|+. ...+...=+.=++.|.+++.+-+...++.| | ...| ++|.||+..++-+
T Consensus 7 li~~ia~~~~l~-k~~a~~~v~~~~~~i~~aL~~G~~V~l~gFG~F~v~~R~aR~GRNPkTGe~i~I~a 74 (94)
T COG0776 7 LIDAIAEKAGLS-KKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAARTGRNPKTGEEIKIPA 74 (94)
T ss_pred HHHHHHHHcCCC-HHHHHHHHHHHHHHHHHHHHcCCeEEEeeeeeeEeeccCCCCCCCCCCCCeEeecC
Confidence 466777887733 223444444556667777775444555655 3 5666 8999999877643
No 155
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=38.29 E-value=19 Score=25.46 Aligned_cols=27 Identities=7% Similarity=0.119 Sum_probs=22.7
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNK 54 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~ 54 (118)
+.|-.-+|...-+..+||+++||+..+
T Consensus 13 ~~Ll~~k~~~~ITV~~I~~~AgvsR~T 39 (176)
T TIGR02366 13 KDLMEVQAFSKISVSDIMSTAQIRRQT 39 (176)
T ss_pred HHHHHHCCCccCCHHHHHHHhCCCHHH
Confidence 345678999999999999999999654
No 156
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=37.67 E-value=21 Score=22.65 Aligned_cols=27 Identities=15% Similarity=0.079 Sum_probs=19.3
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
.+.-...|+.-++||+..|..|++.+.
T Consensus 19 ~~~S~S~lQR~~rIGynrAariid~LE 45 (65)
T PF09397_consen 19 GKASISLLQRKFRIGYNRAARIIDQLE 45 (65)
T ss_dssp TCECHHHHHHHHT--HHHHHHHHHHHH
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344455689999999999999997763
No 157
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=37.56 E-value=20 Score=29.19 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CCcchhccccc
Q 033487 58 ELSAAELDNLMVVVANPRQFK------------------IPDWFLNRQKD 89 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~------------------ip~w~~nr~kd 89 (118)
-+|..|++.|+++++.. .|+ |-.||-|||.-
T Consensus 147 iFT~~Qle~LEkaFkea-HYPDv~Are~la~ktelpEDRIqVWfQNRRAK 195 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEA-HYPDVYAREMLADKTELPEDRIQVWFQNRRAK 195 (332)
T ss_pred hhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence 35999999999999863 232 34699999854
No 158
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=37.43 E-value=17 Score=33.03 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=22.0
Q ss_pred ehhhhhhhhcccCcchHHHHHHHhC
Q 033487 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
.+.-.|..|.|||+.++..+++.+|
T Consensus 634 ~~~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 634 ALTGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred hhHhHHhhCCCCCHHHHHHHHHHhC
Confidence 3456788999999999999999988
No 159
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.24 E-value=16 Score=28.16 Aligned_cols=22 Identities=27% Similarity=0.385 Sum_probs=18.1
Q ss_pred hhhhcccCcchHHHHHHHhCCC
Q 033487 30 LTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
|++|.|||+..|.+|+....+.
T Consensus 62 L~~i~GiG~aka~~l~a~~El~ 83 (218)
T TIGR00608 62 LSSVPGIGEAKAIQLKAAVELA 83 (218)
T ss_pred HHhCcCCcHHHHHHHHHHHHHH
Confidence 7889999999999887666554
No 160
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=37.11 E-value=52 Score=26.10 Aligned_cols=60 Identities=15% Similarity=0.130 Sum_probs=44.4
Q ss_pred chhhcccc-CCCCeehhhhh---hhhcccC----cchHHHHHHHhCCCC--CCcCCCCCHHHHHHHHHHH
Q 033487 12 ILRVLNTN-VDGKQKIMFAL---TSIKGIG----RRLANIVCKKADVDM--NKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 12 mvrI~g~~-i~~~K~v~~aL---t~IyGIG----~~~A~~Ic~~lgi~~--~~r~~~Ls~~qi~~L~~~i 71 (118)
+-++.... +++.-++.-.| ..+||.. ...+.++++.+|+.. +.+++.||..+-.++.=+.
T Consensus 80 igy~~~~~~~~~~lT~~e~l~~~~~l~~~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ia~ 149 (293)
T COG1131 80 IGYVPQEPSLYPELTVRENLEFFARLYGLSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLSIAL 149 (293)
T ss_pred eEEEccCCCCCccccHHHHHHHHHHHhCCChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHHHHH
Confidence 44444433 56666666555 5788887 467889999999998 7889999999988765443
No 161
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=36.75 E-value=28 Score=21.47 Aligned_cols=31 Identities=19% Similarity=0.425 Sum_probs=21.6
Q ss_pred CCcCCCCCHHHHHHHHHHHhCCCCccCCcchhcccc
Q 033487 53 NKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQK 88 (118)
Q Consensus 53 ~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~k 88 (118)
..++|.||++ |++++.=. ....|.|+++-|+
T Consensus 3 ~~kPG~lS~~----LR~ALG~~-~~~pPPWl~~Mq~ 33 (54)
T smart00581 3 HFKPGRISDE----LREALGLP-PGQPPPWLYRMRR 33 (54)
T ss_pred CccCCcCCHH----HHHHcCCC-CCCCChHHHHHHH
Confidence 4677888864 77777732 2457999988765
No 162
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=36.25 E-value=21 Score=22.68 Aligned_cols=51 Identities=12% Similarity=0.158 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHHHHHHHHHHHhC
Q 033487 56 AGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKI 117 (118)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I 117 (118)
+.++|.+|+..-...+.. .+ +|-|---.|| ++-.+..-+.++-||.|+++|
T Consensus 9 lr~ls~~eL~~~l~elk~--el------f~LRfq~atg---ql~n~~~ir~~RrdIARikTi 59 (67)
T CHL00154 9 IIDLTDSEISEEIIKTKK--EL------FDLRLKKATR---QNFKPHLFKHKKHRLAQLLTL 59 (67)
T ss_pred HHhCCHHHHHHHHHHHHH--HH------HHHHHHHHhC---cccChHHHHHHHHHHHHHHHH
Confidence 456788887765555554 23 3444444444 345566678899999999875
No 163
>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=36.25 E-value=20 Score=33.93 Aligned_cols=34 Identities=12% Similarity=0.166 Sum_probs=25.6
Q ss_pred cccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 7 ~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
++|-.+.-++|+|-. ..|.|||+.+|.+|++..|
T Consensus 854 ~qli~laiL~G~DY~---------~GI~GIGpktAl~li~~~~ 887 (1034)
T TIGR00600 854 NKLINLAYLLGSDYT---------EGIPTVGPVSAMEILNEFP 887 (1034)
T ss_pred HHHHHHHHeeCCCCC---------CCCCcccHHHHHHHHHHcC
Confidence 345555666666553 3699999999999999987
No 164
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=35.93 E-value=19 Score=32.60 Aligned_cols=43 Identities=7% Similarity=0.184 Sum_probs=30.1
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
.+.+.-.|..|.|||+.+...+++.+|== ..+..-|.+||.++
T Consensus 603 k~~~~s~L~~IpGiG~kr~~~LL~~FgS~--~~i~~As~eel~~v 645 (691)
T PRK14672 603 KKELVLSFERLPHVGKVRAHRLLAHFGSF--RSLQSATPQDIATA 645 (691)
T ss_pred hhhcccccccCCCCCHHHHHHHHHHhcCH--HHHHhCCHHHHHhC
Confidence 34455788999999999999999887632 33444455555443
No 165
>PF13551 HTH_29: Winged helix-turn helix
Probab=35.48 E-value=92 Score=19.99 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=34.6
Q ss_pred hhhhhhcccCcchHHHHHHHh---C---CCC----CCcCCC-CCHHHHHHHHHHHhC
Q 033487 28 FALTSIKGIGRRLANIVCKKA---D---VDM----NKRAGE-LSAAELDNLMVVVAN 73 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~l---g---i~~----~~r~~~-Ls~~qi~~L~~~i~~ 73 (118)
.......||++.+.....+.+ | +.+ .-+... |++++...|.+++.+
T Consensus 16 ~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 16 AEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 345678899999999998772 3 333 224444 999999999999996
No 166
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.22 E-value=26 Score=32.99 Aligned_cols=47 Identities=19% Similarity=0.348 Sum_probs=33.0
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDNLMV 69 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi-~~---------~~r~~~Ls~~qi~~L~~ 69 (118)
+..|+++|+.|+|||...|.+|.+.-.- .| .+..+.++...++.|..
T Consensus 819 ~~~i~~gl~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R~~~~~~~~~~le~Li~ 875 (1022)
T TIGR00594 819 DKGIRYGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRVDFKKLNKKVLEALIK 875 (1022)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHHH
Confidence 4579999999999999999999865421 11 12234567777776653
No 167
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=34.92 E-value=77 Score=24.98 Aligned_cols=47 Identities=9% Similarity=0.225 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCcccee------ehhhHHHHHHHHHHHHH
Q 033487 56 AGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQV------VSNALDMKLRDDLERLK 115 (118)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~------i~~dL~~~~~~dI~rl~ 115 (118)
+.-+|.||.+.....|.. -| |||||....+ ||-=+-+.-+.+||+..
T Consensus 157 m~PmTkEEyearQSvIRr--Vv-----------DpETGRtRLIkGdGEilEEIVSkERHkeINkqA 209 (225)
T PF10500_consen 157 MAPMTKEEYEARQSVIRR--VV-----------DPETGRTRLIKGDGEILEEIVSKERHKEINKQA 209 (225)
T ss_pred cCCCCHHHHHHHHhhhee--ee-----------cCCCCceeeecccchHHHHHhhHHHHHHHHHhh
Confidence 566899999999999986 35 9999999864 34445556666777643
No 168
>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=34.63 E-value=33 Score=24.91 Aligned_cols=37 Identities=14% Similarity=0.066 Sum_probs=32.5
Q ss_pred CcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 37 GRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 37 G~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
....|.+.++.+|+..=..++..+.+-++.|.++|++
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 3456788999999999999999999999999999863
No 169
>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=34.59 E-value=24 Score=22.13 Aligned_cols=21 Identities=24% Similarity=0.281 Sum_probs=17.6
Q ss_pred hhhhhhcccCcchHHHHHHHh
Q 033487 28 FALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~l 48 (118)
.-|.+++|+|.....+|.+.+
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 357899999999999988765
No 170
>cd00349 Ribosomal_L11 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been im
Probab=34.07 E-value=92 Score=22.20 Aligned_cols=38 Identities=8% Similarity=0.241 Sum_probs=31.5
Q ss_pred cC-cchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhC
Q 033487 36 IG-RRLANIVCKKADVDMN------KRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 36 IG-~~~A~~Ic~~lgi~~~------~r~~~Ls~~qi~~L~~~i~~ 73 (118)
|+ +.+|.-|.+.+|+... ..+++||-+|+..|.+.-..
T Consensus 62 v~~Pp~s~ll~ka~g~~kgs~~~~~~~~g~it~~~v~eIA~~K~~ 106 (131)
T cd00349 62 VKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLP 106 (131)
T ss_pred EcCCCHHHHHHHHhCCCCCCCCCCCeeeeeecHHHHHHHHHHHHh
Confidence 45 8888889999998763 44799999999999988875
No 171
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=33.98 E-value=34 Score=17.98 Aligned_cols=13 Identities=23% Similarity=0.263 Sum_probs=7.1
Q ss_pred CHHHHHHHHHHHh
Q 033487 60 SAAELDNLMVVVA 72 (118)
Q Consensus 60 s~~qi~~L~~~i~ 72 (118)
+.+.+.++.+++.
T Consensus 38 ~~~~~~~i~~~~~ 50 (56)
T smart00530 38 SLETLKKLAKALG 50 (56)
T ss_pred CHHHHHHHHHHhC
Confidence 5555555555553
No 172
>PRK00024 hypothetical protein; Reviewed
Probab=33.42 E-value=20 Score=27.65 Aligned_cols=23 Identities=35% Similarity=0.413 Sum_probs=18.7
Q ss_pred hhhhhcccCcchHHHHHHHhCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.|..+.|||+..|..|+....+.
T Consensus 67 eL~~i~GIG~akA~~L~a~~El~ 89 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALELA 89 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHHH
Confidence 48889999999999887666554
No 173
>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=33.01 E-value=20 Score=31.98 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=17.3
Q ss_pred hhhhhhhhcccCcchHHHHHHHhC
Q 033487 26 IMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+.+|| .|.|||+.+|+.+++.+|
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 788899998888888776
No 174
>PF12114 Period_C: Period protein 2/3C-terminal region; InterPro: IPR022728 This domain is found in eukaryotes and is typically between 164 to 200 amino acids in length. Sequences represented by this entry are found C-terminal to PF08447 from PFAM.
Probab=32.90 E-value=30 Score=26.54 Aligned_cols=40 Identities=25% Similarity=0.361 Sum_probs=32.7
Q ss_pred CCcchhccccccCCCccceeehhhHHHHHHHHHHHHHhCC
Q 033487 79 IPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 79 ip~w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
=|.|++.-+-|..-==..++=..|+...+++|.++|+.++
T Consensus 94 dPiWl~~~~t~~~vmmtYQ~p~R~~e~VLkeD~ekLk~mq 133 (195)
T PF12114_consen 94 DPIWLMMANTDEDVMMTYQMPERDLEEVLKEDREKLKSMQ 133 (195)
T ss_pred CCcchhhccCChhHeEEeecCcccHHHHHHHHHHHHHHHH
Confidence 3999988877766555677788999999999999998763
No 175
>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=32.86 E-value=44 Score=19.98 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=12.7
Q ss_pred CCCHHHHHHHHHHH
Q 033487 58 ELSAAELDNLMVVV 71 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i 71 (118)
.||++|+..|..+|
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 69999999999886
No 176
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=32.35 E-value=1.2e+02 Score=22.22 Aligned_cols=49 Identities=12% Similarity=0.264 Sum_probs=37.5
Q ss_pred cchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHHHHH
Q 033487 38 RRLANIVCKKADVDMN------KRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD 109 (118)
Q Consensus 38 ~~~A~~Ic~~lgi~~~------~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~~~~ 109 (118)
+..|.-|.+.+|+.+. .++++||-+|+..|.+.=.. - +...||+..+++
T Consensus 72 PPas~LlkKa~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~K~~---d--------------------l~a~~l~aA~k~ 126 (141)
T COG0080 72 PPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMP---D--------------------LNAKDLEAAVKE 126 (141)
T ss_pred CCHHHHHHHHhCCCCCCCCCCcceeeeeeHHHHHHHHHHhhh---h--------------------hhhHHHHHHHHH
Confidence 5677788888888643 67899999999999887653 2 577888877664
No 177
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=32.31 E-value=28 Score=20.72 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=13.9
Q ss_pred hhhhhhhcccCcchHHHHHH
Q 033487 27 MFALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~ 46 (118)
..++..-|||+.++...|++
T Consensus 25 ~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 25 KRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 55677888888888888775
No 178
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=31.96 E-value=39 Score=17.89 Aligned_cols=14 Identities=21% Similarity=0.252 Sum_probs=7.1
Q ss_pred CCCHHHHHHHHHHH
Q 033487 58 ELSAAELDNLMVVV 71 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i 71 (118)
..+.+.+..+.+++
T Consensus 38 ~~~~~~~~~i~~~~ 51 (58)
T cd00093 38 NPSLETLEKLAKAL 51 (58)
T ss_pred CCCHHHHHHHHHHh
Confidence 44555555555544
No 179
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=31.73 E-value=23 Score=28.82 Aligned_cols=19 Identities=16% Similarity=0.184 Sum_probs=14.2
Q ss_pred CCHHHHHHHHHHHhCCCCcc
Q 033487 59 LSAAELDNLMVVVANPRQFK 78 (118)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~ 78 (118)
.|+-|+..|++.++. ++|-
T Consensus 179 FT~~Ql~~LEkrF~~-QKYL 197 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEK-QKYL 197 (309)
T ss_pred hhHHHHHHHHHHHHH-hhcc
Confidence 588899999988874 3553
No 180
>PRK05755 DNA polymerase I; Provisional
Probab=31.49 E-value=25 Score=32.22 Aligned_cols=20 Identities=20% Similarity=0.429 Sum_probs=16.8
Q ss_pred hhhhcccCcchHHHHHHHhC
Q 033487 30 LTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lg 49 (118)
...+.|||+++|..++++.|
T Consensus 189 ipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 189 IPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred CCCCCCccHHHHHHHHHHcC
Confidence 34589999999999998765
No 181
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.39 E-value=26 Score=32.49 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=15.7
Q ss_pred hhcccCcchHHHHHHHhC
Q 033487 32 SIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lg 49 (118)
.+.|||+++|.++++..|
T Consensus 189 GVpGIG~KtA~kLL~~yg 206 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG 206 (887)
T ss_pred CCCCcCHHHHHHHHHHcC
Confidence 489999999999998755
No 182
>KOG0821 consensus Predicted ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=31.36 E-value=65 Score=26.04 Aligned_cols=35 Identities=23% Similarity=0.263 Sum_probs=31.6
Q ss_pred chHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 39 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 39 ~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
..|-.+++++.|+|..+.-+|+=||...|.+.-+.
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 35778999999999999999999999999988764
No 183
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=31.36 E-value=18 Score=32.37 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=24.7
Q ss_pred hhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033487 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~ 65 (118)
+|.|+|++++.++.+..+|..-.-+-.|+.+++.
T Consensus 449 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~ 482 (665)
T PRK07956 449 DIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLL 482 (665)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHh
Confidence 6899999999999999998753333344444443
No 184
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=31.33 E-value=76 Score=18.58 Aligned_cols=37 Identities=16% Similarity=0.245 Sum_probs=22.7
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.|.+--||++.+...++. -++..++-+.+.+|..++.
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 455666788888777775 2356788899999999986
No 185
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=31.16 E-value=31 Score=31.78 Aligned_cols=39 Identities=26% Similarity=0.342 Sum_probs=27.9
Q ss_pred hhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
..+ |..++|||+..|..|++.+| .=..+-+.|.+|+..+
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 455 77999999999999999744 3334445566666553
No 186
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=31.01 E-value=38 Score=32.36 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=31.6
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCCCCC---------CcCCCCCHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMN---------KRAGELSAAELDNLM 68 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~---------~r~~~Ls~~qi~~L~ 68 (118)
+..|+++|..|+|||...+.+|.+.=.=.|- ...+.++...++.|.
T Consensus 797 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~~~~~~nk~~le~Li 851 (1107)
T PRK06920 797 GNAIRYSLLSIRNIGMATVTALYEEREKKMFEDLFEFCLRMPSKFVTERNLEAFV 851 (1107)
T ss_pred CCeeEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHhccCCCHHHHHHHH
Confidence 4579999999999999999999865422221 122346666666554
No 187
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=30.90 E-value=22 Score=28.25 Aligned_cols=61 Identities=20% Similarity=0.242 Sum_probs=37.9
Q ss_pred CCCCCccccccchhhccccCCCCeehhhhhhhh-------cccCcchHHHHHHHh---CCCCCCcCCCCCHHHH
Q 033487 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSI-------KGIGRRLANIVCKKA---DVDMNKRAGELSAAEL 64 (118)
Q Consensus 1 ~~~~~~~~~~~mvrI~g~~i~~~K~v~~aLt~I-------yGIG~~~A~~Ic~~l---gi~~~~r~~~Ls~~qi 64 (118)
||+.|-..+.+|..+.|+.+|. .+.-.|... .-+|-..|.++|+.+ |+ +...+-.++.++.
T Consensus 197 ~pi~s~~~~~~~~~~~Gi~vP~--~l~~~l~~~~~~~~~~~~~gi~~a~~~~~~l~~~G~-~giH~~t~n~~~~ 267 (281)
T TIGR00677 197 MPINNYASFLRRAKWSKTKIPQ--EIMSRLEPIKDDDEAVRDYGIELIVEMCQKLLASGI-KGLHFYTLNLEKA 267 (281)
T ss_pred cccCCHHHHHHHHhcCCCCCCH--HHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHCCC-CeeEEeccCchHH
Confidence 6777766788888899999988 454444322 225667777777653 33 2344555555544
No 188
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=30.40 E-value=45 Score=31.64 Aligned_cols=25 Identities=36% Similarity=0.579 Sum_probs=22.4
Q ss_pred CeehhhhhhhhcccCcchHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKK 47 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~ 47 (118)
++.|+++|..|+|||...+..|.+.
T Consensus 745 ~~~Ir~GL~aIkgvg~~~~~~I~~~ 769 (1034)
T PRK07279 745 NKKIYLGLKNIKGLPRDLAYWIIEN 769 (1034)
T ss_pred CCEEEeehhhcCCCCHHHHHHHHHC
Confidence 5579999999999999999999764
No 189
>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=30.37 E-value=23 Score=31.66 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=23.4
Q ss_pred hhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
+|.|+|++++.++.+..+|..=.-+-.|+.+++
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 689999999999999988874333334444443
No 190
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=30.30 E-value=24 Score=34.02 Aligned_cols=44 Identities=20% Similarity=0.289 Sum_probs=34.7
Q ss_pred ccccchhhccccCC---CCeehhhhhhhhcccCcchHHHHHHHhCCC
Q 033487 8 DFQHILRVLNTNVD---GKQKIMFALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 8 ~~~~mvrI~g~~i~---~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
+|=.++-+.|++|+ .|..-.-+|+.|-|+|+++|..+++.+-=+
T Consensus 783 ~~Vd~vn~VGVDIN~a~~n~~~~~lLqyI~GlGpRKa~~lLKsl~~~ 829 (1299)
T KOG1856|consen 783 AFVDIVNEVGVDINKAANNPYYANLLQYICGLGPRKATSLLKSLKRN 829 (1299)
T ss_pred HHHHhHhhhhhhHHHHhcChhhhhhHHHhcCCCcccHHHHHHHHHHc
Confidence 45567777888885 466667789999999999999999877443
No 191
>PF11174 DUF2970: Protein of unknown function (DUF2970); InterPro: IPR021344 This short family is conserved in Proteobacteria. The function is not known.
Probab=30.10 E-value=9.7 Score=23.53 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=15.8
Q ss_pred hccccccCCCccceeehhhH
Q 033487 84 LNRQKDYKDGKYSQVVSNAL 103 (118)
Q Consensus 84 ~nr~kd~~tg~~~h~i~~dL 103 (118)
.||++|+.+|.-.|.|-.-+
T Consensus 19 ~~~e~Df~~~~p~~~Ii~gi 38 (56)
T PF11174_consen 19 KNRERDFAQGSPVHFIIVGI 38 (56)
T ss_pred hhHHHHHHcCCCchHHHHHH
Confidence 48999999999988875443
No 192
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=29.78 E-value=47 Score=22.28 Aligned_cols=44 Identities=14% Similarity=0.296 Sum_probs=29.7
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
|+|..+...|-. ......+||.-|.+=.+.+++-+++|.++.++
T Consensus 34 Fsl~ELkaaGi~--~~~ArtiGI~VD~RRrn~~~eNVerLk~y~sk 77 (83)
T PRK12277 34 FSIGELEAAGLD--IKNARKLGIRVDKRRKTVHEENVEALKKFLEQ 77 (83)
T ss_pred cCHHHHHHcCCC--HHHhcccCeeecccccCCCHHHHHHHHHHHHH
Confidence 444444433322 23344567777888889999999999999885
No 193
>PRK13622 psbV cytochrome c-550; Provisional
Probab=29.78 E-value=66 Score=24.45 Aligned_cols=26 Identities=15% Similarity=0.295 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHHHHhCCCCccCCcch
Q 033487 57 GELSAAELDNLMVVVANPRQFKIPDWF 83 (118)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~~~~~~ip~w~ 83 (118)
+.||++||+.+..+|-.. .-..|.|=
T Consensus 141 ~~LsdeEI~~VA~yIl~q-a~~~~~Wg 166 (180)
T PRK13622 141 RNLTDEDLKLIAGYILVQ-AKTVPGWG 166 (180)
T ss_pred cCCCHHHHHHHHHHHHhC-cccCCccC
Confidence 589999999999999852 22246663
No 194
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=29.30 E-value=34 Score=22.57 Aligned_cols=58 Identities=16% Similarity=0.268 Sum_probs=34.0
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcc--hhccc------cccCCCcccee
Q 033487 40 LANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDW--FLNRQ------KDYKDGKYSQV 98 (118)
Q Consensus 40 ~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w--~~nr~------kd~~tg~~~h~ 98 (118)
.+..|++..|++. ..+...=+.=++.|.+.+.+.....+|.| |-.+. ++|.||+...+
T Consensus 6 li~~ia~~~~~s~-~~~~~~v~~~~~~i~~~L~~~~~v~l~gfG~F~v~~r~aR~grNP~Tge~i~i 71 (90)
T PRK10664 6 LIDKIAAGADISK-AAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITI 71 (90)
T ss_pred HHHHHHHHhCCCH-HHHHHHHHHHHHHHHHHHhCCCEEEECCcEEEEEEEeCCccccCCCCCCEEEE
Confidence 3556667666542 23333334445566667776555667888 43332 58888887543
No 195
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=29.14 E-value=34 Score=27.87 Aligned_cols=23 Identities=17% Similarity=0.411 Sum_probs=19.7
Q ss_pred hhhhhcccCcchHHHHHHHhCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
-|+.++|||.+.|.+|-+.+.=+
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~tG 71 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIETG 71 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHHhC
Confidence 58899999999999999886633
No 196
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.11 E-value=1.6e+02 Score=21.98 Aligned_cols=64 Identities=8% Similarity=0.105 Sum_probs=38.4
Q ss_pred cchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccce---eehhhHHHHHHHHHHHH
Q 033487 38 RRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQ---VVSNALDMKLRDDLERL 114 (118)
Q Consensus 38 ~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h---~i~~dL~~~~~~dI~rl 114 (118)
..++..|.+.+|++ ..++.++-..+... .+. -..|+||..+|...+ +-...+...+..++.++
T Consensus 36 ~~tdeeLA~~Lgi~---------~~~VRk~L~~L~e~-gLv----~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~ 101 (178)
T PRK06266 36 EVTDEEIAEQTGIK---------LNTVRKILYKLYDA-RLA----DYKREKDEETNWYTYTWKPELEKLPEIIKKKKMEE 101 (178)
T ss_pred CcCHHHHHHHHCCC---------HHHHHHHHHHHHHC-CCe----EEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHH
Confidence 45555555555543 35666666666641 231 146779989999887 44566666666666555
Q ss_pred H
Q 033487 115 K 115 (118)
Q Consensus 115 ~ 115 (118)
.
T Consensus 102 ~ 102 (178)
T PRK06266 102 L 102 (178)
T ss_pred H
Confidence 3
No 197
>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=29.10 E-value=7.9 Score=25.56 Aligned_cols=39 Identities=10% Similarity=0.256 Sum_probs=28.7
Q ss_pred chhhcc-ccCCCCeehhhhhhhhcccCcchHHHHHHHhCC
Q 033487 12 ILRVLN-TNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (118)
Q Consensus 12 mvrI~g-~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi 50 (118)
+...++ ...-..+.+.+.+...+|.|...+..|++.+|.
T Consensus 7 l~~~~~~~~~~~~~~~kivvD~~~G~~~~~~~~ll~~lg~ 46 (104)
T PF02879_consen 7 LLSFIDILEAIKKSGLKIVVDCMNGAGSDILPRLLERLGC 46 (104)
T ss_dssp HHHTSCHHHHHHHTTCEEEEE-TTSTTHHHHHHHHHHTTC
T ss_pred HhhhccchhhcccCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence 344444 333345566788899999999999999999997
No 198
>PRK03352 DNA polymerase IV; Validated
Probab=29.05 E-value=42 Score=26.89 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=25.5
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~ 65 (118)
-+..+.|||+.++..+ +.+||..=--+-.++..++.
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 3578899999999885 78999864444444555553
No 199
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=28.94 E-value=39 Score=21.35 Aligned_cols=26 Identities=15% Similarity=0.051 Sum_probs=20.3
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhC
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+.-.-.|+.-+.||++.|..|++.+.
T Consensus 19 ~~S~S~lQR~~~IGynrAariid~lE 44 (63)
T smart00843 19 KASTSLLQRRLRIGYNRAARLIDQLE 44 (63)
T ss_pred CCChHHHHHHHhcchhHHHHHHHHHH
Confidence 33345678999999999999997663
No 200
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=28.78 E-value=70 Score=23.87 Aligned_cols=17 Identities=12% Similarity=0.075 Sum_probs=15.3
Q ss_pred CCCCHHHHHHHHHHHhC
Q 033487 57 GELSAAELDNLMVVVAN 73 (118)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (118)
+.||++|+..|..+|-.
T Consensus 131 ~~LsdeEL~aVAaYIl~ 147 (163)
T CHL00133 131 RSLTDEDLYAIAGHILL 147 (163)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 57999999999999874
No 201
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=28.48 E-value=35 Score=27.28 Aligned_cols=27 Identities=41% Similarity=0.567 Sum_probs=22.2
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+..-.+.|..++|||...|..+++..|
T Consensus 177 ~e~q~~il~s~pgig~~~a~~ll~~fg 203 (254)
T COG1948 177 KELQLYILESIPGIGPKLAERLLKKFG 203 (254)
T ss_pred HHHHHHHHHcCCCccHHHHHHHHHHhc
Confidence 334456779999999999999998876
No 202
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=28.47 E-value=32 Score=28.21 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=7.3
Q ss_pred CCcchhccc
Q 033487 79 IPDWFLNRQ 87 (118)
Q Consensus 79 ip~w~~nr~ 87 (118)
|.=||-|||
T Consensus 197 VKIWFQNrR 205 (307)
T KOG0842|consen 197 VKIWFQNRR 205 (307)
T ss_pred eeeeeecch
Confidence 556999997
No 203
>PRK02406 DNA polymerase IV; Validated
Probab=28.45 E-value=37 Score=27.14 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=25.3
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~ 65 (118)
-++.++|||+.++..+ +.+||..=--+-.++.+++.
T Consensus 169 pi~~l~giG~~~~~~L-~~~Gi~ti~dl~~l~~~~L~ 204 (343)
T PRK02406 169 PVEKIPGVGKVTAEKL-HALGIYTCADLQKYDLAELI 204 (343)
T ss_pred CcchhcCCCHHHHHHH-HHcCCCcHHHHHhCCHHHHH
Confidence 5688999999999886 68899754444444555543
No 204
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=28.29 E-value=34 Score=28.36 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=16.3
Q ss_pred hhhhhcccCcchHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~l 48 (118)
++|.+.|||+.+|..|-..+
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred ccCCCCCccHHHHHHHHHHH
Confidence 48899999999998886543
No 205
>PRK02362 ski2-like helicase; Provisional
Probab=28.08 E-value=36 Score=30.42 Aligned_cols=39 Identities=15% Similarity=0.288 Sum_probs=31.0
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
..|..|.|||+..|.++-+ +||..-..+-.++++++..|
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 4567899999999976664 99998777777788887764
No 206
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.69 E-value=38 Score=28.22 Aligned_cols=34 Identities=15% Similarity=0.310 Sum_probs=25.1
Q ss_pred ccchhhccccCCCCeehhhhhhhhcccCcchHHHHHH
Q 033487 10 QHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCK 46 (118)
Q Consensus 10 ~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~ 46 (118)
+.++.-.|-.+|.+.. .|..+.|||+.+|.+|+.
T Consensus 98 ~~v~~~~~G~~P~~~~---~l~~LpGiG~yTa~Ail~ 131 (342)
T COG1194 98 QEVVERHGGEFPDDEE---ELAALPGVGPYTAGAILS 131 (342)
T ss_pred HHHHHHcCCCCCCCHH---HHHhCCCCcHHHHHHHHH
Confidence 4455666667777654 456699999999999874
No 207
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=27.68 E-value=32 Score=23.96 Aligned_cols=21 Identities=38% Similarity=0.507 Sum_probs=17.6
Q ss_pred CCcCCCCCHHHHHHHHHHHhC
Q 033487 53 NKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 53 ~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.+|+.+||++|+++|.+.|++
T Consensus 84 qkRle~l~~eE~~~L~~eiee 104 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIEE 104 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhcC
Confidence 467889999999999988763
No 208
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=27.17 E-value=35 Score=32.31 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=23.1
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHh
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
++.|.++|+.|+|||...|..|.+.=
T Consensus 811 ~~~I~~gl~~Ikgvg~~~~~~Iv~~R 836 (1046)
T PRK05672 811 GPAVRLGLRLVRGLGEEAAERIVAAR 836 (1046)
T ss_pred CCcEEechhhcCCCCHHHHHHHHHHh
Confidence 46799999999999999999998754
No 209
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=26.95 E-value=1.6e+02 Score=18.66 Aligned_cols=47 Identities=6% Similarity=0.002 Sum_probs=34.0
Q ss_pred ehhhhhhhhcccCcchHHHHH--------------HHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 25 KIMFALTSIKGIGRRLANIVC--------------KKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic--------------~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.-+.|+.++.++-+..|..-+ ..+|..+.. ..+|..|+..|...+..
T Consensus 8 k~ELA~lYfP~~~~~sA~r~L~rwI~~~~~L~~~L~~~Gy~~~~--r~~TP~QV~lIv~~LGe 68 (69)
T PF14053_consen 8 KSELAQLYFPDLTPSSAVRKLRRWIRRNPELLEELEATGYHPRQ--RSFTPRQVRLIVRYLGE 68 (69)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHCHHHHHHHHHcCCCCCC--EecCHHHHHHHHHHcCC
Confidence 346677888888777765433 456777655 56999999999988765
No 210
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=26.74 E-value=70 Score=19.15 Aligned_cols=29 Identities=14% Similarity=0.130 Sum_probs=20.1
Q ss_pred CCCCee-hhhhhhhhcccCcchHHHHHHHh
Q 033487 20 VDGKQK-IMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 20 i~~~K~-v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
-+|.+- -...|...||+++.++.+.+..|
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 334444 67889999999999998877665
No 211
>PRK03858 DNA polymerase IV; Validated
Probab=26.67 E-value=49 Score=26.96 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=24.0
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
-++.+.|||+.++..+ +.+||..=--+..++.+++
T Consensus 174 pl~~l~Gig~~~~~~L-~~~Gi~t~~dl~~l~~~~L 208 (396)
T PRK03858 174 PVRRLWGVGPVTAAKL-RAHGITTVGDVAELPESAL 208 (396)
T ss_pred ChhhcCCCCHHHHHHH-HHhCCCcHHHHhcCCHHHH
Confidence 4578899999998887 5689985333444444433
No 212
>PRK00919 GMP synthase subunit B; Validated
Probab=26.54 E-value=1.3e+02 Score=24.40 Aligned_cols=50 Identities=10% Similarity=0.159 Sum_probs=37.1
Q ss_pred CCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHH
Q 033487 50 VDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMK 106 (118)
Q Consensus 50 i~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~ 106 (118)
+..-..+.+|+++|+.++... +++|.|+.+|.+=+..|.-.-+.| ++...
T Consensus 154 ~~Ii~PL~~l~K~EVr~la~~------lGLp~~~~~r~p~~~pcLa~Ri~g-~vt~e 203 (307)
T PRK00919 154 LKIVEPLRDLYKDEVREVARA------LGLPEEISERMPFPGPGLAVRIIG-EVTEE 203 (307)
T ss_pred CCcccCchhCcHHHHHHHHHH------cCCChhhhCCCCCCCCceeEEeec-ccCHH
Confidence 334455677888888877754 468999999999999998877765 55443
No 213
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=26.46 E-value=30 Score=31.02 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=16.6
Q ss_pred hhhhhhhhcccCcchHHHHHHHhC
Q 033487 26 IMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+.+|| .|.|||..+|+.|++..+
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 688888888888887664
No 214
>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat
Probab=26.25 E-value=38 Score=20.49 Aligned_cols=51 Identities=22% Similarity=0.287 Sum_probs=30.2
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHHHHHHHHHHHhC
Q 033487 56 AGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKI 117 (118)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I 117 (118)
+.++|.+|+......+.+ .+ ++-|-.-.||. +-..-.-+.++-||.|+.++
T Consensus 3 ir~ls~~eL~~~l~~l~~--el------f~Lr~q~~~~~---~~~~~~~~~~Rr~IARi~Ti 53 (57)
T cd00427 3 LREKSDEELQEKLDELKK--EL------FNLRFQKATGQ---LENPHRIRKVRKDIARIKTV 53 (57)
T ss_pred HHHCCHHHHHHHHHHHHH--HH------HHHHHHHHHCC---CcCcHHHHHHHHHHHHHHHH
Confidence 456777777765555554 23 23333333443 34445567889999998875
No 215
>KOG1647 consensus Vacuolar H+-ATPase V1 sector, subunit D [Energy production and conversion]
Probab=26.18 E-value=54 Score=26.08 Aligned_cols=52 Identities=27% Similarity=0.313 Sum_probs=39.7
Q ss_pred HHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHHHHHHHHHHHhC
Q 033487 41 ANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKI 117 (118)
Q Consensus 41 A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I 117 (118)
|..++..+=...|.|++.|..--|-+|++-+. | |.++|+..-++|.=||++|
T Consensus 154 sf~~Lde~ik~TNrRVNAiEhvIIPrlenTi~----Y---------------------I~sELdE~eRedF~RLKKi 205 (255)
T KOG1647|consen 154 SFRTLDEAIKVTNRRVNAIEHVIIPRLENTIA----Y---------------------IVSELDELEREDFYRLKKI 205 (255)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHH----H---------------------HHHHHHHHHHHHHHHHHHH
Confidence 34445555556677787777777777777774 5 8899999999999999987
No 216
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=26.16 E-value=47 Score=27.54 Aligned_cols=36 Identities=11% Similarity=0.287 Sum_probs=26.4
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~ 65 (118)
-+..++|||+.++..+ +.+||..=.-+..++.+.+.
T Consensus 180 Pv~~l~GiG~~~~~~L-~~lGi~TigdL~~~~~~~L~ 215 (422)
T PRK03609 180 PVEEVWGVGRRISKKL-NAMGIKTALDLADTNIRFIR 215 (422)
T ss_pred ChhhcCCccHHHHHHH-HHcCCCcHHHHhcCCHHHHH
Confidence 3578999999998887 57999975555555665554
No 217
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=25.91 E-value=37 Score=19.24 Aligned_cols=22 Identities=18% Similarity=0.185 Sum_probs=18.3
Q ss_pred hhcccCcchHHHHHHHhCCCCC
Q 033487 32 SIKGIGRRLANIVCKKADVDMN 53 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~~~ 53 (118)
.-.|+...+...||+.+|+++.
T Consensus 10 ~~~G~~~~s~~~Ia~~~gvs~~ 31 (47)
T PF00440_consen 10 AEKGYEAVSIRDIARRAGVSKG 31 (47)
T ss_dssp HHHHTTTSSHHHHHHHHTSCHH
T ss_pred HHhCHHhCCHHHHHHHHccchh
Confidence 3468888999999999999853
No 218
>KOG2355 consensus Predicted ABC-type transport, ATPase component/CCR4 associated factor [General function prediction only; Transcription]
Probab=25.76 E-value=47 Score=26.68 Aligned_cols=65 Identities=9% Similarity=0.197 Sum_probs=55.8
Q ss_pred ccccchhhcc-ccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 8 DFQHILRVLN-TNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 8 ~~~~mvrI~g-~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
+..+++-|+| +.+.++-.+...+..+-|+-+..-..+.+.+.||-.-|+..+|+.|-.++.-.+.
T Consensus 96 eW~~~~~~agevplq~D~sae~mifgV~g~dp~Rre~LI~iLDIdl~WRmHkvSDGqrRRVQicMG 161 (291)
T KOG2355|consen 96 EWSKTVGIAGEVPLQGDISAEHMIFGVGGDDPERREKLIDILDIDLRWRMHKVSDGQRRRVQICMG 161 (291)
T ss_pred cccccccccccccccccccHHHHHhhccCCChhHhhhhhhheeccceEEEeeccccchhhhHHHHh
Confidence 5677788887 7777888888888888888899999999999999999999999999987766554
No 219
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=25.68 E-value=1.2e+02 Score=22.48 Aligned_cols=44 Identities=14% Similarity=0.110 Sum_probs=37.1
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCC-cCCCCCHHHHHHHHHHHh
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNK-RAGELSAAELDNLMVVVA 72 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~-r~~~Ls~~qi~~L~~~i~ 72 (118)
.+..+||+...-...--+.+|+.+.. |+..+++++-..|=..-+
T Consensus 92 mm~~~FGls~~ev~~rR~llgi~~~~GR~~~~~ee~~~~iW~~W~ 136 (180)
T PF11198_consen 92 MMQRLFGLSSAEVAARRRLLGIPVRKGRPPALSEEEEAAIWRRWQ 136 (180)
T ss_pred HHHHHHCCCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 35789999888888888999999877 999999998887776665
No 220
>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=25.66 E-value=40 Score=26.52 Aligned_cols=34 Identities=26% Similarity=0.309 Sum_probs=20.7
Q ss_pred hhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
+..+.|||+.++..+. ..||..-.-+...+.+++
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L 34 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKEL 34 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHH
Confidence 3578899988887765 456654444444444444
No 221
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, 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. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=25.64 E-value=27 Score=28.92 Aligned_cols=24 Identities=25% Similarity=0.329 Sum_probs=20.0
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
..+..++|||+.++..+.+ +||..
T Consensus 172 lpv~~l~GiG~~~~~kL~~-~GI~t 195 (379)
T cd01703 172 HDLRKIPGIGYKTAAKLEA-HGISS 195 (379)
T ss_pred CCccccCCcCHHHHHHHHH-cCCCc
Confidence 4578999999999988875 79884
No 222
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=25.46 E-value=51 Score=26.06 Aligned_cols=21 Identities=29% Similarity=0.471 Sum_probs=19.1
Q ss_pred hhhhhcccCcchHHHHHHHhC
Q 033487 29 ALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lg 49 (118)
.|..+.|||...|..|.+.++
T Consensus 37 EL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 37 ELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHHccCCCHHHHHHHHHHhc
Confidence 478999999999999999887
No 223
>PRK00254 ski2-like helicase; Provisional
Probab=25.29 E-value=33 Score=30.56 Aligned_cols=39 Identities=21% Similarity=0.182 Sum_probs=29.9
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
..|..+.|||+.+|.. |-+.|+..-..+...+++++..+
T Consensus 645 ~~L~~ipgig~~~~~~-l~~~g~~s~~~i~~a~~~el~~~ 683 (720)
T PRK00254 645 LELMRLPMIGRKRARA-LYNAGFRSIEDIVNAKPSELLKV 683 (720)
T ss_pred hhhhcCCCCCHHHHHH-HHHccCCCHHHHHhCCHHHHhcC
Confidence 3466899999999988 55778877777777777777665
No 224
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.27 E-value=62 Score=30.28 Aligned_cols=31 Identities=6% Similarity=0.119 Sum_probs=26.8
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHH
Q 033487 40 LANIVCKKADVDMNKRAGELSAAELDNLMVV 70 (118)
Q Consensus 40 ~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~ 70 (118)
.-..+|+..||+.++..++|+++|.+.|-.=
T Consensus 321 ~l~~~~~~~g~~~~~p~~~l~~~~~~~ll~G 351 (924)
T TIGR00630 321 MLKSLAEHYGFDLDTPWKDLPEEVQKAVLYG 351 (924)
T ss_pred HHHHHHHHcCCCCCCChHHCCHHHHHHHhcC
Confidence 4567899999999999999999999988643
No 225
>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=25.26 E-value=43 Score=26.93 Aligned_cols=24 Identities=17% Similarity=0.379 Sum_probs=20.1
Q ss_pred hhhhhcccCcchHHHHHHHhCCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
.+++++|||+++|..|.+-+-=..
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG~ 69 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETGK 69 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcCC
Confidence 568999999999999998876443
No 226
>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=25.24 E-value=72 Score=19.01 Aligned_cols=16 Identities=25% Similarity=0.333 Sum_probs=14.6
Q ss_pred CCCHHHHHHHHHHHhC
Q 033487 58 ELSAAELDNLMVVVAN 73 (118)
Q Consensus 58 ~Ls~~qi~~L~~~i~~ 73 (118)
.||++|+..|..+|.+
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 7999999999999974
No 227
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=25.22 E-value=49 Score=20.61 Aligned_cols=51 Identities=22% Similarity=0.358 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcchhccccccCCCccceeehhhHHHHHHHHHHHHHhC
Q 033487 56 AGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKI 117 (118)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~rl~~I 117 (118)
+.++|.+|+......+.+ .+ ++-|-.-.||. +-..-..+.++-||.|+.++
T Consensus 6 lr~ls~~eL~~~l~~lkk--eL------~~lR~~~~~~~---~~n~~~i~~~rk~IARi~Tv 56 (66)
T PRK00306 6 LRELSVEELNEKLLELKK--EL------FNLRFQKATGQ---LENTHRLREVRRDIARIKTV 56 (66)
T ss_pred HhhCCHHHHHHHHHHHHH--HH------HHHHHHHHhCC---CcCcHHHHHHHHHHHHHHHH
Confidence 567888888877766665 33 34444444553 33445567888999998765
No 228
>PLN00131 hypothetical protein; Provisional
Probab=24.92 E-value=30 Score=26.25 Aligned_cols=49 Identities=18% Similarity=0.261 Sum_probs=29.0
Q ss_pred chHHHHHHHhCCCCCCc----------CCCCCHHHHHHHHH--HHhCCCCccCCcchhccc
Q 033487 39 RLANIVCKKADVDMNKR----------AGELSAAELDNLMV--VVANPRQFKIPDWFLNRQ 87 (118)
Q Consensus 39 ~~A~~Ic~~lgi~~~~r----------~~~Ls~~qi~~L~~--~i~~~~~~~ip~w~~nr~ 87 (118)
+.|.+++..+|++..+. ..+|+++|-.++.+ .++...-..+.-||+||.
T Consensus 156 kiadqlldwmgldnetdrtllddlynhlydlseeqgrrvgqpqmfsskgikslklwflnrk 216 (218)
T PLN00131 156 KIADQLLDWMGLDNETDRTLLDDLYNHLYDLSEEQGRRVGQPQMFSSKGIKSLKLWFLNRK 216 (218)
T ss_pred HHHHHHHHHhccCccchHHHHHHHHHHHhhhhHHhccccCCchhhcccchhhhhhhhcccc
Confidence 56888999999986543 34556666555432 222211112467999985
No 229
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=24.63 E-value=39 Score=23.08 Aligned_cols=33 Identities=18% Similarity=0.348 Sum_probs=26.8
Q ss_pred cCCCCCHHHHHHHHHHHhCCCCccCCcchhcccc
Q 033487 55 RAGELSAAELDNLMVVVANPRQFKIPDWFLNRQK 88 (118)
Q Consensus 55 r~~~Ls~~qi~~L~~~i~~~~~~~ip~w~~nr~k 88 (118)
....||++|+......++.+. -.+=.|+.|+..
T Consensus 40 ~~~~lsd~el~~f~~LLe~~D-~dL~~Wi~g~~~ 72 (94)
T COG2938 40 EFDSLSDEELDEFERLLECED-NDLFNWIMGHGE 72 (94)
T ss_pred HHhhCCHHHHHHHHHHHcCCc-HHHHHHHhCCCC
Confidence 457899999999999999764 335589998887
No 230
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=24.50 E-value=46 Score=18.06 Aligned_cols=16 Identities=6% Similarity=0.156 Sum_probs=8.3
Q ss_pred hhcccCcchHHHHHHH
Q 033487 32 SIKGIGRRLANIVCKK 47 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~ 47 (118)
...||++.+....++.
T Consensus 9 ~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 9 EYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHCCCHHHHHHHHHc
Confidence 3445555555555544
No 231
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=24.36 E-value=1.4e+02 Score=21.51 Aligned_cols=37 Identities=11% Similarity=0.232 Sum_probs=31.0
Q ss_pred CcchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhC
Q 033487 37 GRRLANIVCKKADVDMN------KRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 37 G~~~A~~Ic~~lgi~~~------~r~~~Ls~~qi~~L~~~i~~ 73 (118)
-+.+|.-|.+.+|+... -.+++||-+|+..|.+.-..
T Consensus 72 ~Pp~s~ll~k~~g~~~gs~~p~~~~vG~it~~~v~eIA~~K~~ 114 (141)
T PRK00140 72 TPPASVLLKKAAGIEKGSGEPNKEKVGKITRAQVREIAETKMP 114 (141)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeEEeeEcHHHHHHHHHHHHH
Confidence 67889999999999875 44689999999999988764
No 232
>PRK13620 psbV cytochrome c-550; Provisional
Probab=24.34 E-value=85 Score=24.57 Aligned_cols=17 Identities=12% Similarity=0.118 Sum_probs=14.9
Q ss_pred CCCCCHHHHHHHHHHHh
Q 033487 56 AGELSAAELDNLMVVVA 72 (118)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~ 72 (118)
+++||++|+..|..+|=
T Consensus 182 ~r~LtdedL~aIa~~IL 198 (215)
T PRK13620 182 MRNLTEDDLVAISGHIL 198 (215)
T ss_pred cCCCCHHHHHHHHHHHh
Confidence 47899999999999875
No 233
>KOG3200 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.16 E-value=79 Score=24.49 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCCcc--hhccccccC
Q 033487 56 AGELSAAELDNLMVVVANPRQFKIPDW--FLNRQKDYK 91 (118)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~ip~w--~~nr~kd~~ 91 (118)
++-+++||-.++-.-|++ -.-|.| ++|||=--+
T Consensus 18 PnfIt~EEe~~~lshIe~---ap~pkW~~L~NRRLqNy 52 (224)
T KOG3200|consen 18 PNFITEEEENLYLSHIEN---APQPKWRVLANRRLQNY 52 (224)
T ss_pred CCccChHHHHHHHHHHhc---CCCchhHHHHhhhhhhc
Confidence 567899999999999986 446999 789985443
No 234
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=24.07 E-value=41 Score=32.11 Aligned_cols=26 Identities=23% Similarity=0.477 Sum_probs=23.0
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHh
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
+..|.++|..|+|||...|..|.+.=
T Consensus 815 ~~~I~~gL~~Ikgvg~~~~~~I~~~R 840 (1135)
T PRK05673 815 DGDIRYGLGAIKGVGEGAVEAIVEAR 840 (1135)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHH
Confidence 45799999999999999999998654
No 235
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=24.04 E-value=66 Score=27.38 Aligned_cols=46 Identities=13% Similarity=0.074 Sum_probs=39.7
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANP 74 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~ 74 (118)
--|+.|.|||+..+. .+..+||..--.+-.++++++..+...+.-+
T Consensus 323 DDLk~I~GIGpk~e~-~Ln~~Gi~~f~QIA~wt~~eia~vd~~l~f~ 368 (400)
T PRK12373 323 DDLKLISGVGPKIEA-TLNELGIFTFDQVAAWKKAERAWVDGYLNFK 368 (400)
T ss_pred hhhhhccCCChHHHH-HHHhcCCCCHHHHhCCCHHHhHHhhhcccCC
Confidence 358999999998875 5789999999999999999999888888643
No 236
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=24.04 E-value=1.5e+02 Score=21.51 Aligned_cols=36 Identities=8% Similarity=0.131 Sum_probs=30.1
Q ss_pred cchHHHHHHHhCCCCCC--------cCCCCCHHHHHHHHHHHhC
Q 033487 38 RRLANIVCKKADVDMNK--------RAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 38 ~~~A~~Ic~~lgi~~~~--------r~~~Ls~~qi~~L~~~i~~ 73 (118)
+..|.-|.+.+|+.... .+++||-+|+..|.+.-..
T Consensus 50 Pp~s~ll~k~ag~~~~~~~~~~~~~~vG~it~~qv~eIAk~K~~ 93 (140)
T PTZ00105 50 PTASSLLIKALKEPPRDRKKVKNIKHSGNLTFDQVIKIARTMRP 93 (140)
T ss_pred CCHHHHHHHHhCCCCCCCCCCCcceeeeEeeHHHHHHHHHHHHh
Confidence 89999999999986332 6889999999999987664
No 237
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=23.93 E-value=66 Score=20.71 Aligned_cols=17 Identities=12% Similarity=0.102 Sum_probs=12.5
Q ss_pred CCCCHHHHHHHHHHHhC
Q 033487 57 GELSAAELDNLMVVVAN 73 (118)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (118)
=.||++|++.|.++|.+
T Consensus 46 V~Lt~eqv~~LN~~l~~ 62 (73)
T PF14794_consen 46 VFLTEEQVAKLNQALQK 62 (73)
T ss_dssp ----HHHHHHHHHHHHH
T ss_pred EEcCHHHHHHHHHHHHH
Confidence 36899999999999996
No 238
>cd01401 PncB_like Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi.
Probab=23.84 E-value=1.3e+02 Score=25.30 Aligned_cols=35 Identities=14% Similarity=0.095 Sum_probs=29.7
Q ss_pred chHHHHHHHhCCCCCCc----CCCCCHHHHHHHHHHHhC
Q 033487 39 RLANIVCKKADVDMNKR----AGELSAAELDNLMVVVAN 73 (118)
Q Consensus 39 ~~A~~Ic~~lgi~~~~r----~~~Ls~~qi~~L~~~i~~ 73 (118)
..+....+++|++|..| =+.|+++.+..|.+.++.
T Consensus 289 ~k~r~~~~~~Gi~p~~K~iv~Sd~Lde~~i~~L~~~~~g 327 (377)
T cd01401 289 EKAIAHYEKLGIDPKTKTLVFSDGLDVEKALELYEYFKG 327 (377)
T ss_pred HHHHHHHHHcCCCCCCcEEEEcCCCCHHHHHHHHHHHcC
Confidence 45677889999999988 678999999999998773
No 239
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=23.77 E-value=1.2e+02 Score=18.08 Aligned_cols=38 Identities=8% Similarity=0.041 Sum_probs=26.7
Q ss_pred hhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033487 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.+.|-..-...+|++.+|+.....+=.++.++ +.+.++
T Consensus 7 ~V~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~---~~~~l~ 44 (69)
T PF08478_consen 7 EVSGNSYLSKEEILQALGIQKGKNLFSLDLKK---IEQRLE 44 (69)
T ss_dssp EEES-SSS-HHHHHHHHCTTSTTTCCCSHHHH---HHHCCC
T ss_pred EEECCCcCCHHHHHHHhCcCCCCeEEEECHHH---HHHHHH
Confidence 46788888999999999999977777765444 445554
No 240
>TIGR02019 BchJ bacteriochlorophyll 4-vinyl reductase. This model represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the "dark" protochlorophyllide reductase enzymes BchN, BchB and BchL. This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll.
Probab=23.75 E-value=2e+02 Score=21.88 Aligned_cols=44 Identities=18% Similarity=0.148 Sum_probs=36.1
Q ss_pred hhhhhhcccCcchHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~---~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
-||...+ |+..+.++.+.+|.+ .+..-..+++.++..|.+.++.
T Consensus 12 ~al~~~~--g~~~~~~~~~~~g~~~~~~~~p~~mv~E~~~~aL~~aL~~ 58 (188)
T TIGR02019 12 PALEAAY--GPGAADRALAAAGQGVLRPGPPSGMLPESQFSTLHRWLRD 58 (188)
T ss_pred HHHHHhc--CHHHHHHHHHHcCcccccCCCchhcCCHHHHHHHHHHHHH
Confidence 4555554 688899999999999 4666677899999999999986
No 241
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=23.64 E-value=1.2e+02 Score=20.20 Aligned_cols=36 Identities=22% Similarity=0.402 Sum_probs=23.7
Q ss_pred hhhhhhcccCcch-HHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 28 FALTSIKGIGRRL-ANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 28 ~aLt~IyGIG~~~-A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
+++...+|-|.++ |..+++.+|+.- ...+.+..++.
T Consensus 2 I~i~G~~GsGKst~a~~la~~~~~~~-~~~~~i~~e~~ 38 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLAKKLGLPY-LDTGGIRTEEV 38 (147)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCce-eccccCCHHHH
Confidence 3566778999988 778888888742 22334555443
No 242
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=23.60 E-value=1.8e+02 Score=18.43 Aligned_cols=36 Identities=8% Similarity=0.208 Sum_probs=27.5
Q ss_pred cchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhC
Q 033487 38 RRLANIVCKKADVDMN------KRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 38 ~~~A~~Ic~~lgi~~~------~r~~~Ls~~qi~~L~~~i~~ 73 (118)
+.++.-|.+.+|+... -.+++||-+|+..|.+.-..
T Consensus 3 Pp~s~llkkaagi~kGs~~p~~~~vG~it~~~i~eIAk~K~~ 44 (69)
T PF00298_consen 3 PPTSWLLKKAAGIKKGSSKPGKEKVGTITLKQIYEIAKIKQK 44 (69)
T ss_dssp STHHHHHHHHHTTSSSSSSTTTSSSEEEEHHHHHHHHHHHTT
T ss_pred CChHHHHHHHhCCCCCCCCCCCceeeeecHHHHHHHHHHhhc
Confidence 3567778888888533 34788999999999988764
No 243
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=23.58 E-value=35 Score=30.08 Aligned_cols=63 Identities=10% Similarity=0.141 Sum_probs=41.3
Q ss_pred CCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC-CCCccCCcchhc
Q 033487 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN-PRQFKIPDWFLN 85 (118)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~-~~~~~ip~w~~n 85 (118)
..++...|||.-+|=-.....++|+.|||+ +.-++.=.+.++..-.+-++- .....+|+||..
T Consensus 160 ~k~~~ilgLTASPGs~~ekI~eV~~nLgIe-~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ 223 (542)
T COG1111 160 AKNPLILGLTASPGSDLEKIQEVVENLGIE-KVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKE 223 (542)
T ss_pred ccCceEEEEecCCCCCHHHHHHHHHhCCcc-eEEEecCCCccHHHhhccceeEEEeccCcHHHHH
Confidence 445589999999999999999999999998 444554444444443333321 111334666643
No 244
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.54 E-value=38 Score=20.05 Aligned_cols=20 Identities=5% Similarity=0.096 Sum_probs=13.0
Q ss_pred cccCcchHHHHHHHhCCCCC
Q 033487 34 KGIGRRLANIVCKKADVDMN 53 (118)
Q Consensus 34 yGIG~~~A~~Ic~~lgi~~~ 53 (118)
.-++...+..||+.+|++++
T Consensus 37 ~~~~~~~l~~i~~~~~v~~~ 56 (64)
T PF12844_consen 37 RKPSVSTLKKIAEALGVSLD 56 (64)
T ss_dssp S--BHHHHHHHHHHHTS-HH
T ss_pred cCCCHHHHHHHHHHhCCCHH
Confidence 35667778888888888864
No 245
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=23.52 E-value=86 Score=19.59 Aligned_cols=54 Identities=7% Similarity=0.144 Sum_probs=40.2
Q ss_pred cCCCCeehhhhhhhhcccCcchHHHHHH----HhC---CCCCCcCCCCCHHHHHHHHHHHh
Q 033487 19 NVDGKQKIMFALTSIKGIGRRLANIVCK----KAD---VDMNKRAGELSAAELDNLMVVVA 72 (118)
Q Consensus 19 ~i~~~K~v~~aLt~IyGIG~~~A~~Ic~----~lg---i~~~~r~~~Ls~~qi~~L~~~i~ 72 (118)
.+..+++|..-+..+.++|.+.+.+..- ..| +....++.++++..-..|..+++
T Consensus 13 ~l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~~vi~ 73 (74)
T PF14213_consen 13 ALKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIKRVIE 73 (74)
T ss_pred HHhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHHHHHh
Confidence 4556667899999999999999987653 334 44567777888887777777765
No 246
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=23.50 E-value=93 Score=22.14 Aligned_cols=27 Identities=22% Similarity=0.366 Sum_probs=23.9
Q ss_pred chHHHHHHHhCCCCC-CcCCCCCHHHHH
Q 033487 39 RLANIVCKKADVDMN-KRAGELSAAELD 65 (118)
Q Consensus 39 ~~A~~Ic~~lgi~~~-~r~~~Ls~~qi~ 65 (118)
..|.++++..||+.+ .+.+.+++++..
T Consensus 48 ~~a~~vl~e~Gid~~~~~~k~i~~~~~~ 75 (139)
T COG0394 48 PRAVEVLAEHGIDISGHRSKQLTEEDFD 75 (139)
T ss_pred HHHHHHHHHcCCCcCCccCccCchhhhh
Confidence 468899999999999 799999999884
No 247
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=23.28 E-value=40 Score=22.23 Aligned_cols=15 Identities=27% Similarity=0.102 Sum_probs=9.2
Q ss_pred chHHHHHHHhCCCCC
Q 033487 39 RLANIVCKKADVDMN 53 (118)
Q Consensus 39 ~~A~~Ic~~lgi~~~ 53 (118)
..|.++|+.+|++++
T Consensus 14 ~~A~~vl~~lGls~S 28 (80)
T PRK11235 14 ARAYAVLEKLGVTPS 28 (80)
T ss_pred HHHHHHHHHhCCCHH
Confidence 346666666666653
No 248
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=23.27 E-value=37 Score=23.66 Aligned_cols=32 Identities=25% Similarity=0.275 Sum_probs=24.3
Q ss_pred cccCcchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033487 34 KGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (118)
Q Consensus 34 yGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~ 66 (118)
+|||+..+.++ +.+||+....+-+.++.+..+
T Consensus 1 pgi~~~~~~~L-~~~GI~t~~~Ll~~~~~~~~r 32 (122)
T PF14229_consen 1 PGIGPKEAAKL-KAAGIKTTGDLLEAGDTPLGR 32 (122)
T ss_pred CCCCHHHHHHH-HHcCCCcHHHHHHcCCCHHHH
Confidence 48899998888 899998766666666666665
No 249
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=23.27 E-value=38 Score=25.57 Aligned_cols=39 Identities=8% Similarity=0.116 Sum_probs=31.0
Q ss_pred CCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033487 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (118)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~ 66 (118)
+.+.-+..|....|||+..|++++++|+.- .+|.+|+..
T Consensus 133 ~sk~rR~~lg~~L~IGy~N~KqllkrLn~f------~it~~e~~~ 171 (174)
T TIGR00334 133 ASKCKRLRLCNLLKLGYFNHKQLFKRLNLF------QIKKSDVMS 171 (174)
T ss_pred cHHHHHHHHHHHhCCCCCcHHHHHHHHHHc------CCCHHHHHH
Confidence 677788889999999999999999988754 356666654
No 250
>smart00649 RL11 Ribosomal protein L11/L12.
Probab=23.13 E-value=1.9e+02 Score=20.58 Aligned_cols=37 Identities=11% Similarity=0.218 Sum_probs=30.2
Q ss_pred CcchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhC
Q 033487 37 GRRLANIVCKKADVDMN------KRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 37 G~~~A~~Ic~~lgi~~~------~r~~~Ls~~qi~~L~~~i~~ 73 (118)
-+.+|.-|.+.+|+... ..++++|-+|+..+.+.-..
T Consensus 64 ~P~~s~ll~k~~g~~kgs~~p~~~~~g~it~~~v~eIA~~K~~ 106 (132)
T smart00649 64 TPPASFLLKKAAGIEKGSKKPGKKKVGNITLDQVYEIAKIKRP 106 (132)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeeeeEEcHHHHHHHHHHHHH
Confidence 47788888899998855 34789999999999988764
No 251
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=23.13 E-value=1.5e+02 Score=25.95 Aligned_cols=89 Identities=12% Similarity=0.300 Sum_probs=54.7
Q ss_pred CeehhhhhhhhcccCcc---hHHHHHHHhCCC-CCCcCCCCCHHHHHHHHHHHh-C-C---CCccCCcchhccccccCCC
Q 033487 23 KQKIMFALTSIKGIGRR---LANIVCKKADVD-MNKRAGELSAAELDNLMVVVA-N-P---RQFKIPDWFLNRQKDYKDG 93 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~---~A~~Ic~~lgi~-~~~r~~~Ls~~qi~~L~~~i~-~-~---~~~~ip~w~~nr~kd~~tg 93 (118)
+||....|.+..-.... .+.++-++.++. -....-+|+++++..|-+.+= . | .++.+|.|.--=..|
T Consensus 180 ~kPfiivlN~~dp~~~et~~l~~~l~eky~vpvl~v~c~~l~~~DI~~il~~vL~EFPv~Ei~~~~P~Wve~L~~~---- 255 (492)
T TIGR02836 180 NKPFIILLNSTHPYHPETEALRQELEEKYDVPVLAMDVESMRESDILSVLEEVLYEFPILEINIDLPSWVEVLDEN---- 255 (492)
T ss_pred CCCEEEEEECcCCCCchhHHHHHHHHHHhCCceEEEEHHHcCHHHHHHHHHHHHhcCCceEEEeeCchHHHhcCCC----
Confidence 45555555444422222 134555666754 356677899999997665543 2 0 123479997554444
Q ss_pred ccceeehhhHHHHHHHHHHHHHhCC
Q 033487 94 KYSQVVSNALDMKLRDDLERLKKIR 118 (118)
Q Consensus 94 ~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (118)
|.+-.++...+++-.+.+.+||
T Consensus 256 ---Hwlk~~~~~~i~~~~~~i~~ir 277 (492)
T TIGR02836 256 ---HWLKENFQSSVKETVKDVYRLR 277 (492)
T ss_pred ---chHHHHHHHHHHHHHHhhhHHh
Confidence 8999999888887776666554
No 252
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=23.09 E-value=44 Score=32.06 Aligned_cols=47 Identities=19% Similarity=0.345 Sum_probs=31.9
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDNLMV 69 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi-~~---------~~r~~~Ls~~qi~~L~~ 69 (118)
+..|.++|..|+|||...|..|.+.=.- .| ....+.++...++.|..
T Consensus 830 ~~~Ir~GL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~LI~ 886 (1170)
T PRK07374 830 GNRILFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRLPSNVLNRRSLESLIH 886 (1170)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccccCCHHHHHHHHH
Confidence 4469999999999999999999865421 11 11223466666666653
No 253
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=23.08 E-value=71 Score=27.65 Aligned_cols=33 Identities=21% Similarity=0.328 Sum_probs=23.7
Q ss_pred ccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhC
Q 033487 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (118)
Q Consensus 8 ~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lg 49 (118)
+|-.+-=++|.|--.+ |.|||+.+|..+.+..|
T Consensus 218 ~fidL~lLlGCDYc~~---------I~Gig~~~al~lir~~~ 250 (449)
T KOG2519|consen 218 SFIDLCLLLGCDYCPT---------IRGIGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHhcCccccc---------ccccChHHHHHHHHHhc
Confidence 3444444555555443 99999999999999988
No 254
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=23.06 E-value=2.1e+02 Score=20.67 Aligned_cols=37 Identities=11% Similarity=0.270 Sum_probs=29.8
Q ss_pred CcchHHHHHHHhCCCCCC------cCCCCCHHHHHHHHHHHhC
Q 033487 37 GRRLANIVCKKADVDMNK------RAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 37 G~~~A~~Ic~~lgi~~~~------r~~~Ls~~qi~~L~~~i~~ 73 (118)
-+.+|.-|.+.+|+.... .+++||-+|+..|.+.-..
T Consensus 72 ~Pp~s~ll~ka~gi~~gs~~p~~~~~G~it~~~v~eIA~~K~~ 114 (140)
T CHL00127 72 TPPASVLLAKAAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLP 114 (140)
T ss_pred CCCHHHHHHHHhCCCcCCCCCCCeecceecHHHHHHHHHHHhh
Confidence 577888888999987654 4788999999999888763
No 255
>PF02745 MCR_alpha_N: Methyl-coenzyme M reductase alpha subunit, N-terminal domain; InterPro: IPR003183 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the N-terminal domain of the alpha subunit, which has a ferredoxin-like alpha/beta-sandwich fold with a duplicated beta-alpha-beta topology. ; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity, 0015948 methanogenesis; PDB: 1HBU_D 3M2V_D 3POT_A 3M2U_A 1HBN_A 1HBO_A 3M30_A 3M2R_A 3M1V_A 1HBM_A ....
Probab=22.86 E-value=45 Score=26.56 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=26.4
Q ss_pred chhccccccCCCccceeehhhHHHHHHHHHHH
Q 033487 82 WFLNRQKDYKDGKYSQVVSNALDMKLRDDLER 113 (118)
Q Consensus 82 w~~nr~kd~~tg~~~h~i~~dL~~~~~~dI~r 113 (118)
+.++---.+.-|+++|.+.+---.+.-+||+|
T Consensus 71 y~~sgTd~~vegDDLHfvNNaAmQQ~wDDirR 102 (267)
T PF02745_consen 71 YQVSGTDTFVEGDDLHFVNNAAMQQMWDDIRR 102 (267)
T ss_dssp EEBTTSS-EEEGGGGSGGG-HHHHHHHHHHHT
T ss_pred EEecCCceeeccccceeechHHHHHHHHHhhh
Confidence 45667778899999999999999999999998
No 256
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=22.82 E-value=73 Score=29.89 Aligned_cols=32 Identities=9% Similarity=0.159 Sum_probs=26.9
Q ss_pred chHHHHHHHhCCCCCCcCCCCCHHHHHHHHHH
Q 033487 39 RLANIVCKKADVDMNKRAGELSAAELDNLMVV 70 (118)
Q Consensus 39 ~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~ 70 (118)
..-..+|+..||+.+++.++|+++|.+.|-.=
T Consensus 322 ~~l~~~~~~~g~~~~~p~~~l~~~~~~~ll~g 353 (943)
T PRK00349 322 QMLKSLAEHYGFDLDTPWKDLPEEVQDIILYG 353 (943)
T ss_pred HHHHHHHHHcCCCCCCchHHCCHHHHHHHcCC
Confidence 44567899999999999999999998877554
No 257
>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=22.81 E-value=63 Score=29.14 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=28.0
Q ss_pred hhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033487 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71 (118)
Q Consensus 31 t~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i 71 (118)
..++|||..+|-+|...+|+.++-.-+ |...=+..|.++.
T Consensus 184 ~~i~gigF~~aD~iA~~~g~~~~d~~R-i~a~i~~~L~~~~ 223 (720)
T TIGR01448 184 EDVKGIGFLTADQLAQALGIALNDPRR-ITAGLVYSLQQAC 223 (720)
T ss_pred hhcCCCCHHHHHHHHHHcCCCCCCHHH-HHHHHHHHHHHHh
Confidence 469999999999999999998763322 3333344455555
No 258
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=22.54 E-value=49 Score=31.76 Aligned_cols=47 Identities=21% Similarity=0.296 Sum_probs=36.7
Q ss_pred eehhhhhhhhcccCcchHHHHHHHh---------CCCCCCcCCCCCHHHHHHHHHH
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKA---------DVDMNKRAGELSAAELDNLMVV 70 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~l---------gi~~~~r~~~Ls~~qi~~L~~~ 70 (118)
+.|.++|..|+|||...+..|.+.- .+-.....+.++...++.|.++
T Consensus 819 ~~I~~gL~~IKGvg~~~i~~Iv~~R~~~~~~~~~df~~r~~~~~l~kr~lE~Lika 874 (1139)
T COG0587 819 KAIRLGLGAIKGVGEDAIEEIVEARKEKPFKSLEDFCDRIDRKGLNKRVLESLIKA 874 (1139)
T ss_pred CcEEEhhhhhcCCcHHHHHHHHHHhhcccCCcHhHHHHHhhhccCCHHHHHHHHHc
Confidence 6999999999999999999988774 2333444556788888877766
No 259
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=22.46 E-value=1.3e+02 Score=18.23 Aligned_cols=15 Identities=13% Similarity=0.062 Sum_probs=13.8
Q ss_pred CCHHHHHHHHHHHhC
Q 033487 59 LSAAELDNLMVVVAN 73 (118)
Q Consensus 59 Ls~~qi~~L~~~i~~ 73 (118)
||+.|.+.|..+++.
T Consensus 1 LT~~Q~e~L~~A~~~ 15 (53)
T PF04967_consen 1 LTDRQREILKAAYEL 15 (53)
T ss_pred CCHHHHHHHHHHHHc
Confidence 789999999999996
No 260
>PF00288 GHMP_kinases_N: GHMP kinases N terminal domain; InterPro: IPR006204 The galacto- (2.7.1.6 from EC), homoserine (2.7.1.39 from EC), mevalonate (2.7.1.36 from EC) and phosphomevalonate (2.7.4.2 from EC) kinases contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP [, ]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).; GO: 0005524 ATP binding, 0016301 kinase activity, 0016310 phosphorylation; PDB: 3F0N_B 1PIE_A 2AJ4_A 1K47_E 3GON_A 2R3V_C 3HUL_A 1KVK_A 2R42_A 3D4J_A ....
Probab=22.36 E-value=65 Score=19.40 Aligned_cols=40 Identities=25% Similarity=0.168 Sum_probs=28.6
Q ss_pred hcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 33 IKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 33 IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
=.|+|.+.|..+|-...+..-... +++++|+.++....++
T Consensus 11 ~~GLgSSaa~~~a~~~a~~~~~~~-~~~~~~l~~~a~~~e~ 50 (67)
T PF00288_consen 11 GSGLGSSAALAVALAAALNKLFGL-PLSKEELAKLAQEAER 50 (67)
T ss_dssp TSSSSHHHHHHHHHHHHHHHHTTT-SSBHHHHHHHHHHHHH
T ss_pred CCcccHHHHHHHHHHHHHHHHccc-cccHHHHHHHHHHHHH
Confidence 368888887777655555544444 4799999999888884
No 261
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=22.14 E-value=51 Score=31.82 Aligned_cols=25 Identities=20% Similarity=0.478 Sum_probs=22.5
Q ss_pred eehhhhhhhhcccCcchHHHHHHHh
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
..|.++|..|.|||...|.+|.+.-
T Consensus 1146 ~~I~~~l~aI~glg~~~a~~Iv~~R 1170 (1213)
T TIGR01405 1146 NTLIPPFNAIPGLGENVANSIVEAR 1170 (1213)
T ss_pred CEEEeehhhcCCCCHHHHHHHHHHH
Confidence 4699999999999999999999765
No 262
>PRK15482 transcriptional regulator MurR; Provisional
Probab=22.09 E-value=64 Score=25.02 Aligned_cols=24 Identities=13% Similarity=0.084 Sum_probs=21.6
Q ss_pred hhhhhcccCcchHHHHHHHhCCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
.|.+--|+...+..++|+++|++.
T Consensus 39 elA~~~~vS~aTv~Rf~kkLGf~G 62 (285)
T PRK15482 39 KMAKQLGISQSSIVKFAQKLGAQG 62 (285)
T ss_pred HHHHHhCCCHHHHHHHHHHhCCCC
Confidence 567788999999999999999995
No 263
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=22.01 E-value=43 Score=29.77 Aligned_cols=42 Identities=24% Similarity=0.256 Sum_probs=30.4
Q ss_pred eehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
..+.-.|-.|.|||+.+..++++..|= -..+..-|.+|+..+
T Consensus 526 ~~~~s~Ld~I~GiG~~r~~~LL~~Fgs--~~~i~~As~eel~~v 567 (581)
T COG0322 526 AMLQSSLDDIPGIGPKRRKALLKHFGS--LKGIKSASVEELAKV 567 (581)
T ss_pred hhhcCccccCCCcCHHHHHHHHHHhhC--HHHHHhcCHHHHHHc
Confidence 345567889999999999999998773 234555566666554
No 264
>cd03067 PDI_b_PDIR_N PDIb family, PDIR subfamily, N-terminal TRX-like b domain; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity. The TRX-like b domain of PDIR is critical for its chaperone activity.
Probab=21.90 E-value=82 Score=22.18 Aligned_cols=32 Identities=25% Similarity=0.397 Sum_probs=24.8
Q ss_pred hhhhhhcccC--------cchHHHHHHHhCCCCCCcCCCC
Q 033487 28 FALTSIKGIG--------RRLANIVCKKADVDMNKRAGEL 59 (118)
Q Consensus 28 ~aLt~IyGIG--------~~~A~~Ic~~lgi~~~~r~~~L 59 (118)
-+-+.++|.| ..=++.+|+++-++|+.++..+
T Consensus 42 ~~A~~vkG~gT~~~vdCgd~e~kKLCKKlKv~~~~kp~~~ 81 (112)
T cd03067 42 DVAQAVKGQGTIAWIDCGDSESRKLCKKLKVDPSSKPKPV 81 (112)
T ss_pred HHHHHhcCceeEEEEecCChHHHHHHHHHccCCCCCCCcc
Confidence 3446788876 4459999999999988887763
No 265
>PF07316 DUF1463: Protein of unknown function (DUF1463); InterPro: IPR009925 This entry represents a family of hypothetical proteins of around 140 residues in length found in Borrelia species. The function of this family is unknown.
Probab=21.82 E-value=62 Score=23.51 Aligned_cols=47 Identities=13% Similarity=0.072 Sum_probs=34.3
Q ss_pred CCCCCccccccchhhccccCCCCeehhhhh-----hhhcccCcchHHHHHHH
Q 033487 1 MSLVANEDFQHILRVLNTNVDGKQKIMFAL-----TSIKGIGRRLANIVCKK 47 (118)
Q Consensus 1 ~~~~~~~~~~~mvrI~g~~i~~~K~v~~aL-----t~IyGIG~~~A~~Ic~~ 47 (118)
+|+.|=.|=+.+++|+++.+.-.--=...| .++||++..+..++++.
T Consensus 42 ~Pi~SfRDP~Ti~~IFniEvt~gS~dY~~LtelS~~QFY~~~~sk~eK~l~l 93 (140)
T PF07316_consen 42 FPIVSFRDPKTITHIFNIEVTLGSYDYKLLTELSDEQFYNMDESKEEKLLSL 93 (140)
T ss_pred CccccccCCCeEEEEEEEEEEeccchhhHHhhhhHhhcccCCccHHHHHHHh
Confidence 466666778899999999886655444444 47899998888877643
No 266
>TIGR03872 cytochrome_MoxG cytochrome c(L), periplasmic. This model describes a periplasmic c-type cytochrome that serves as the primary electron acceptor for the quinoprotein methanol dehydrogenase, a PQQ enzyme. The member from Paracoccus denitrificans is also characterized as an electron acceptor for methylamine dehydrogenase, a tryptophan tryptophylquinone enzyme. This protein is called cytochrome c(L) in methylotrophic bacteria such Methylobacterium extorquens, but c551i in Paracoccus denitrificans.
Probab=21.81 E-value=1.2e+02 Score=21.45 Aligned_cols=17 Identities=24% Similarity=0.450 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHHHHhC
Q 033487 57 GELSAAELDNLMVVVAN 73 (118)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (118)
+.|+++|+..|..+|..
T Consensus 104 ~~LsdeeI~aLaaYI~s 120 (133)
T TIGR03872 104 GNLTLDEMLQIMAWIRH 120 (133)
T ss_pred cCCCHHHHHHHHHHHHH
Confidence 57999999999999984
No 267
>TIGR01632 L11_bact 50S ribosomal protein L11. This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11.
Probab=21.81 E-value=1.6e+02 Score=21.24 Aligned_cols=37 Identities=11% Similarity=0.278 Sum_probs=30.7
Q ss_pred CcchHHHHHHHhCCCCCC------cCCCCCHHHHHHHHHHHhC
Q 033487 37 GRRLANIVCKKADVDMNK------RAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 37 G~~~A~~Ic~~lgi~~~~------r~~~Ls~~qi~~L~~~i~~ 73 (118)
-+.+|.-|.+.+|+.+.. .++++|-+|+..|.+.-..
T Consensus 71 ~Pp~s~ll~kaag~~~gs~~p~~~~~G~it~~qv~eIA~~K~~ 113 (140)
T TIGR01632 71 TPPVSYLLKKAAGVEKGSKNPKKEKVGKITRKQVREIAEIKMS 113 (140)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeEEeEecHHHHHHHHHHHHH
Confidence 577888899999988763 5689999999999988764
No 268
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=21.70 E-value=1.2e+02 Score=20.75 Aligned_cols=65 Identities=11% Similarity=0.070 Sum_probs=58.0
Q ss_pred cccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 9 ~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
-.|-|.+++=++..---|...|.+++|.....|.+|+-.+.-....-++.-+.+.-+.....+..
T Consensus 26 ~~y~ViL~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~G~avv~~~~~e~AE~~~~~l~~ 90 (100)
T PRK00033 26 PMYKVLLHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNEGKAVVGVCTREVAETKVEQVHQ 90 (100)
T ss_pred CceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCcEEEEEEcHHHHHHHHHHHHc
Confidence 45788888888888888999999999999999999999999999999998899998888888864
No 269
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=21.59 E-value=21 Score=22.97 Aligned_cols=65 Identities=12% Similarity=0.079 Sum_probs=51.0
Q ss_pred cccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 9 ~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
=++.+.+.+=+...-..|..+|..+.|.-...|.++...+.-....-+..-+.++.+...+.+.+
T Consensus 5 ~~~~vvL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~avv~~~~~e~ae~~~~~l~~ 69 (82)
T PF02617_consen 5 DMYRVVLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREGRAVVGTGSREEAEEYAEKLQR 69 (82)
T ss_dssp -EEEEEEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHSEEEEEEEEHHHHHHHHHHHHH
T ss_pred CceEEEEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcCCEeeeeCCHHHHHHHHHHHHH
Confidence 45677788888888888999999999999999999999888888888888899998888888764
No 270
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=21.39 E-value=74 Score=26.22 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=30.8
Q ss_pred hhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033487 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73 (118)
Q Consensus 32 ~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~ 73 (118)
.-.|||+..|.++|+ =|++ =.-++ =|++.++++.+.|++
T Consensus 57 aTDGIGKayA~eLAk-rG~n-vvLIs-Rt~~KL~~v~kEI~~ 95 (312)
T KOG1014|consen 57 ATDGIGKAYARELAK-RGFN-VVLIS-RTQEKLEAVAKEIEE 95 (312)
T ss_pred CCCcchHHHHHHHHH-cCCE-EEEEe-CCHHHHHHHHHHHHH
Confidence 357999999999998 6776 22222 289999999999997
No 271
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=21.34 E-value=1.5e+02 Score=15.95 Aligned_cols=25 Identities=12% Similarity=0.096 Sum_probs=13.1
Q ss_pred HHHHHHhCCCCCCcCCCCCHHHHHHHHHH
Q 033487 42 NIVCKKADVDMNKRAGELSAAELDNLMVV 70 (118)
Q Consensus 42 ~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~ 70 (118)
+++|+..|++.+=+ ..+=+++|.++
T Consensus 10 k~~l~~~gL~~~G~----K~~Li~Rl~~~ 34 (35)
T PF02037_consen 10 KEELKERGLSTSGK----KAELIERLKEH 34 (35)
T ss_dssp HHHHHHTTS-STSS----HHHHHHHHHHH
T ss_pred HHHHHHCCCCCCCC----HHHHHHHHHHh
Confidence 56777777774322 44444455544
No 272
>PRK08609 hypothetical protein; Provisional
Probab=21.19 E-value=56 Score=28.65 Aligned_cols=31 Identities=26% Similarity=0.417 Sum_probs=23.0
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGEL 59 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~L 59 (118)
.|+.|+|||...|.+|.+.+.=..-.+..+|
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l 79 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETGESSVLQEL 79 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhCChHHHHHH
Confidence 5899999999999999988755443333333
No 273
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=21.07 E-value=52 Score=31.56 Aligned_cols=46 Identities=15% Similarity=0.394 Sum_probs=31.8
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDNLM 68 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi-~~---------~~r~~~Ls~~qi~~L~ 68 (118)
+..|+++|..|+|||...|..|.+.=.- .| ....+.++...++.|.
T Consensus 819 ~~~Ir~gL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~Li 874 (1151)
T PRK06826 819 GDKIRFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERVDTSQINKRAVESLI 874 (1151)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHH
Confidence 4579999999999999999999865421 11 1123356666666665
No 274
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=21.00 E-value=68 Score=25.36 Aligned_cols=50 Identities=16% Similarity=0.335 Sum_probs=34.1
Q ss_pred hHHHHHHHhCCCCCCcCCC-CCHHHHHHHHHHHhCCCCcc-----------------CCcchhccccc
Q 033487 40 LANIVCKKADVDMNKRAGE-LSAAELDNLMVVVANPRQFK-----------------IPDWFLNRQKD 89 (118)
Q Consensus 40 ~A~~Ic~~lgi~~~~r~~~-Ls~~qi~~L~~~i~~~~~~~-----------------ip~w~~nr~kd 89 (118)
.+-.+|...-=-++.++.. .|-.|+..|++.+.+.+++. |.-||-|||.-
T Consensus 131 ~~p~~C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAK 198 (246)
T KOG0492|consen 131 MSPTTCTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAK 198 (246)
T ss_pred CCcccchhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHH
Confidence 3444576666666666664 58899999998887653221 67799999853
No 275
>KOG3908 consensus Queuine-tRNA ribosyltransferase [RNA processing and modification]
Probab=20.79 E-value=20 Score=29.78 Aligned_cols=40 Identities=15% Similarity=0.331 Sum_probs=36.4
Q ss_pred cccccchhhccccCCCCeehhhhhhhhcccCcchHHHHHHHhCCC
Q 033487 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD 51 (118)
Q Consensus 7 ~~~~~mvrI~g~~i~~~K~v~~aLt~IyGIG~~~A~~Ic~~lgi~ 51 (118)
.+|-.||...-..+|.+|| .+.-|+|+..-.-+|-.+|.|
T Consensus 230 ~~Fwr~V~~ct~~LP~dkP-----RYlMGVGya~DlVVCvaLG~D 269 (396)
T KOG3908|consen 230 SEFWRMVAFCTSSLPPDKP-----RYLMGVGYAEDLVVCVALGSD 269 (396)
T ss_pred HHHHHHHHHHHccCCCCCC-----ceeeccCcccceeeeehhCCc
Confidence 3699999999999999999 567899999999999999987
No 276
>PRK01172 ski2-like helicase; Provisional
Probab=20.76 E-value=60 Score=28.55 Aligned_cols=39 Identities=18% Similarity=0.178 Sum_probs=30.7
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L 67 (118)
..|.+|+|+|+..|.+ |..+|+..-.-+-.++++++.+|
T Consensus 612 ~~L~~ip~~~~~~a~~-l~~~g~~~~~di~~~~~~~~~~i 650 (674)
T PRK01172 612 IDLVLIPKVGRVRARR-LYDAGFKTVDDIARSSPERIKKI 650 (674)
T ss_pred HhhcCCCCCCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHH
Confidence 4567899999998765 78899998777777777777665
No 277
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=20.76 E-value=1e+02 Score=25.75 Aligned_cols=48 Identities=15% Similarity=0.287 Sum_probs=36.5
Q ss_pred hhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccC
Q 033487 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKI 79 (118)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~i 79 (118)
+..++|||++.|..|-+-+.=..-..+.....++..+..+++.+ -++|
T Consensus 58 a~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtn--ifGv 105 (353)
T KOG2534|consen 58 AEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTN--IFGV 105 (353)
T ss_pred hcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHH--Hhcc
Confidence 45699999999999998887776666666666667777777776 4554
No 278
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.73 E-value=1e+02 Score=17.24 Aligned_cols=22 Identities=14% Similarity=0.119 Sum_probs=12.7
Q ss_pred hhhhhhhcccCcchHHHHHHHh
Q 033487 27 MFALTSIKGIGRRLANIVCKKA 48 (118)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~l 48 (118)
.-.|...+|+++.++.+.++.+
T Consensus 23 ~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 23 ERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 3445666666666666655544
No 279
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=20.59 E-value=67 Score=19.88 Aligned_cols=25 Identities=16% Similarity=0.093 Sum_probs=19.5
Q ss_pred hhhhhhcccCc--chHHHHHHHhCCCC
Q 033487 28 FALTSIKGIGR--RLANIVCKKADVDM 52 (118)
Q Consensus 28 ~aLt~IyGIG~--~~A~~Ic~~lgi~~ 52 (118)
..|..+..-|. .+|.+|++.+|+++
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~ 36 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLPK 36 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCCH
Confidence 34555666677 89999999999985
No 280
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=20.49 E-value=51 Score=31.09 Aligned_cols=46 Identities=20% Similarity=0.306 Sum_probs=32.1
Q ss_pred CeehhhhhhhhcccCcchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHH
Q 033487 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDNLM 68 (118)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~lgi-~~---------~~r~~~Ls~~qi~~L~ 68 (118)
++.|+++|+.|+|||...|..|.+.-.- .| ....+.++...++.|.
T Consensus 748 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li 803 (973)
T PRK07135 748 NGKIFLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLI 803 (973)
T ss_pred CCEEEECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhccccCCCHHHHHHHH
Confidence 4569999999999999999999865421 11 1122456777766665
No 281
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.46 E-value=1.5e+02 Score=16.17 Aligned_cols=38 Identities=13% Similarity=0.154 Sum_probs=17.8
Q ss_pred hhhcccCcchHHHHHHHhCCCCCCcC---CCCCHHHHHHHH
Q 033487 31 TSIKGIGRRLANIVCKKADVDMNKRA---GELSAAELDNLM 68 (118)
Q Consensus 31 t~IyGIG~~~A~~Ic~~lgi~~~~r~---~~Ls~~qi~~L~ 68 (118)
..+.||.+.+....++.-.+.|.... ...+++++.+|.
T Consensus 7 a~~~gv~~~tlr~~~~~g~l~~~~~~~~~~~y~~~~v~~l~ 47 (49)
T cd04761 7 AKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLR 47 (49)
T ss_pred HHHHCcCHHHHHHHHHCCCCCCCcCCCCCEEeCHHHHHHhh
Confidence 34555666555555444444432222 114555555554
No 282
>PRK14133 DNA polymerase IV; Provisional
Probab=20.39 E-value=70 Score=25.66 Aligned_cols=36 Identities=17% Similarity=0.241 Sum_probs=25.6
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~ 65 (118)
-+..+.|||+.++..+ ..+||..=.-+-.++.+++.
T Consensus 174 pv~~l~gig~~~~~~L-~~~Gi~ti~dl~~l~~~~L~ 209 (347)
T PRK14133 174 PISKVHGIGKKSVEKL-NNIGIYTIEDLLKLSREFLI 209 (347)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhhCCHHHHH
Confidence 3577899999999885 68899864444445555553
No 283
>PRK03348 DNA polymerase IV; Provisional
Probab=20.34 E-value=68 Score=27.16 Aligned_cols=37 Identities=22% Similarity=0.313 Sum_probs=26.4
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 66 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi~~ 66 (118)
-+..+.|||+.++..+ +.+||..=.-+-.|+..++.+
T Consensus 181 Pv~~L~GIG~~t~~~L-~~lGI~TigDLa~l~~~~L~~ 217 (454)
T PRK03348 181 PVRRLWGIGPVTEEKL-HRLGIETIGDLAALSEAEVAN 217 (454)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhcCCHHHHHH
Confidence 4678999999988876 789998644444456655543
No 284
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=20.29 E-value=1.6e+02 Score=15.70 Aligned_cols=11 Identities=18% Similarity=0.021 Sum_probs=7.2
Q ss_pred HHHHHHHhCCC
Q 033487 41 ANIVCKKADVD 51 (118)
Q Consensus 41 A~~Ic~~lgi~ 51 (118)
-+++|+..|++
T Consensus 9 Lk~~l~~~gl~ 19 (35)
T smart00513 9 LKDELKKRGLS 19 (35)
T ss_pred HHHHHHHcCCC
Confidence 45667777766
No 285
>PRK03103 DNA polymerase IV; Reviewed
Probab=20.19 E-value=79 Score=25.97 Aligned_cols=35 Identities=11% Similarity=0.312 Sum_probs=23.8
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
-++.+.|||+.++..+ +.+||..=--+..++.+++
T Consensus 182 pi~~l~gig~~~~~~L-~~~Gi~tigdl~~~~~~~L 216 (409)
T PRK03103 182 PVRKLFGVGSRMEKHL-RRMGIRTIGQLANTPLERL 216 (409)
T ss_pred CHhhcCCccHHHHHHH-HHcCCCCHHHHhcCCHHHH
Confidence 4578899999988875 6889975333333455444
No 286
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=20.18 E-value=66 Score=25.29 Aligned_cols=25 Identities=28% Similarity=0.295 Sum_probs=20.7
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCC
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
-.|+.+.|||..+|.++...+.+..
T Consensus 66 ~el~~v~GiG~aka~~l~a~~El~~ 90 (224)
T COG2003 66 EELSSVKGIGLAKAIQIKAAIELGK 90 (224)
T ss_pred HHHhhCCCccHHHHHHHHHHHHHHH
Confidence 4578999999999999998776653
No 287
>PRK08118 topology modulation protein; Reviewed
Probab=20.18 E-value=1.9e+02 Score=20.68 Aligned_cols=43 Identities=14% Similarity=0.146 Sum_probs=26.4
Q ss_pred hhhhhcccCcch-HHHHHHHhCCC---CCCcC-----CCCCHHHHHHHHHHH
Q 033487 29 ALTSIKGIGRRL-ANIVCKKADVD---MNKRA-----GELSAAELDNLMVVV 71 (118)
Q Consensus 29 aLt~IyGIG~~~-A~~Ic~~lgi~---~~~r~-----~~Ls~~qi~~L~~~i 71 (118)
.+..-.|-|++| |++|++.+|+. .+.-. ...+++++..+.+.+
T Consensus 5 ~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~~~~~~~~~~ 56 (167)
T PRK08118 5 ILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVPKEEQITVQNEL 56 (167)
T ss_pred EEECCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcCCCHHHHHHHHHHH
Confidence 344557888887 88888888865 33222 234566666555443
No 288
>cd08532 SAM_PNT-PDEF-like Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor. SAM Pointed domain of PDEF-like (Prostate-Derived ETS Factor) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. In human males this activator is highly expressed in the prostate gland and enhances androgen-mediated activation of the PSA promoter though interaction with the DNA binding domain of androgen receptor. PDEF may play a role in prostate cancer development as well as in goblet cell formation and mucus production in the epithelial lining of respiratory and intestinal tracts.
Probab=20.09 E-value=69 Score=20.80 Aligned_cols=33 Identities=18% Similarity=0.448 Sum_probs=25.4
Q ss_pred HHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCc
Q 033487 45 CKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPD 81 (118)
Q Consensus 45 c~~lgi~~~~r~~~Ls~~qi~~L~~~i~~~~~~~ip~ 81 (118)
|+++||.++ +..-|.++|..=..+..+ .|.+|.
T Consensus 1 c~~L~ip~D--P~~Ws~~~V~~WL~w~~~--ef~L~~ 33 (76)
T cd08532 1 CKLLGISPD--PYQWSPANVQKWLLWTEH--QYRLPP 33 (76)
T ss_pred CCcCCCCCC--hhhcCHHHHHHHHHHHHH--HhCCCC
Confidence 678888854 788999999987777666 577655
No 289
>PRK01810 DNA polymerase IV; Validated
Probab=20.09 E-value=73 Score=26.17 Aligned_cols=35 Identities=17% Similarity=0.276 Sum_probs=23.9
Q ss_pred hhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
-++.+.|||+.++..+ ..+||..=--+..++.+++
T Consensus 180 pv~~l~giG~~~~~~L-~~~Gi~tigdL~~~~~~~L 214 (407)
T PRK01810 180 PVGEMHGIGEKTAEKL-KDIGIQTIGDLAKADEHIL 214 (407)
T ss_pred CHhhcCCcCHHHHHHH-HHcCCCcHHHHHhCCHHHH
Confidence 4567899999999775 7899985433444444444
No 290
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=20.06 E-value=74 Score=24.97 Aligned_cols=24 Identities=13% Similarity=0.134 Sum_probs=20.0
Q ss_pred hhhhhcccCcchHHHHHHHhCCCC
Q 033487 29 ALTSIKGIGRRLANIVCKKADVDM 52 (118)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~lgi~~ 52 (118)
.|..--||++.+..++|+++|++.
T Consensus 41 elA~~a~VS~aTv~Rf~~kLGf~G 64 (281)
T COG1737 41 ELAERAGVSPATVVRFARKLGFEG 64 (281)
T ss_pred HHHHHhCCCHHHHHHHHHHcCCCC
Confidence 356677999999999999999884
No 291
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=20.04 E-value=80 Score=25.06 Aligned_cols=36 Identities=25% Similarity=0.313 Sum_probs=23.3
Q ss_pred hhhhhhcccCcchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033487 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (118)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~r~~~Ls~~qi 64 (118)
..|..++|||+.+|..+ ...||..-.-+-+++.+++
T Consensus 6 ~~l~~l~gIg~~~a~~L-~~~Gi~t~~dl~~~~~~~L 41 (317)
T PRK04301 6 KDLEDLPGVGPATAEKL-REAGYDTVEAIAVASPKEL 41 (317)
T ss_pred ccHhhcCCCCHHHHHHH-HHcCCCCHHHHHcCCHHHH
Confidence 45788999998887665 5667775444444444444
Done!