Query 037180
Match_columns 66
No_of_seqs 123 out of 1319
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 09:29:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037180hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01476 LysM: LysM domain; I 99.6 2.6E-16 5.6E-21 76.2 3.8 43 19-61 1-44 (44)
2 PRK14125 cell division suppres 99.5 3.6E-14 7.7E-19 80.4 7.0 53 13-65 33-93 (103)
3 TIGR02899 spore_safA spore coa 99.4 8.8E-13 1.9E-17 63.0 4.7 41 21-61 1-43 (44)
4 cd00118 LysM Lysin domain, fou 99.4 3E-12 6.4E-17 60.2 5.8 44 18-61 2-46 (46)
5 PRK06347 autolysin; Reviewed 99.4 1.6E-12 3.5E-17 90.8 6.2 46 16-61 547-592 (592)
6 PRK13914 invasion associated s 99.3 4.5E-12 9.8E-17 86.7 7.0 50 15-64 26-75 (481)
7 PRK10871 nlpD lipoprotein NlpD 99.3 3.8E-12 8.2E-17 83.6 5.6 47 16-62 60-107 (319)
8 TIGR02907 spore_VI_D stage VI 99.3 6.2E-12 1.3E-16 82.8 6.6 48 14-61 291-338 (338)
9 PRK10783 mltD membrane-bound l 99.3 1.5E-11 3.3E-16 83.9 6.7 49 15-63 401-449 (456)
10 PRK06347 autolysin; Reviewed 99.2 2.4E-11 5.3E-16 85.0 6.7 48 16-63 479-526 (592)
11 smart00257 LysM Lysin motif. 99.2 7.2E-11 1.6E-15 54.8 5.1 43 18-60 1-44 (44)
12 PRK13914 invasion associated s 99.2 1E-10 2.3E-15 80.1 7.6 49 15-63 198-246 (481)
13 COG1388 LytE FOG: LysM repeat 99.2 1.6E-10 3.4E-15 66.3 6.4 47 16-62 66-112 (124)
14 PRK11198 LysM domain/BON super 99.1 1.7E-10 3.7E-15 68.6 6.1 47 15-61 94-146 (147)
15 PRK10783 mltD membrane-bound l 99.0 6.3E-10 1.4E-14 76.0 6.4 49 16-64 343-391 (456)
16 PF04225 OapA: Opacity-associa 98.2 2.9E-06 6.4E-11 46.5 4.4 47 17-63 3-54 (85)
17 COG1652 XkdP Uncharacterized p 98.1 7.9E-07 1.7E-11 57.0 1.0 46 18-63 212-264 (269)
18 TIGR03505 FimV_core FimV N-ter 98.0 8.2E-06 1.8E-10 43.8 2.7 40 25-64 1-53 (74)
19 PRK10190 L,D-transpeptidase; P 97.9 6.2E-05 1.3E-09 49.8 6.1 46 17-62 38-86 (310)
20 PRK10260 L,D-transpeptidase; P 97.8 7.1E-05 1.5E-09 49.4 6.1 46 17-62 41-89 (306)
21 COG3858 Predicted glycosyl hyd 97.6 0.00011 2.3E-09 50.3 4.3 52 13-64 46-98 (423)
22 PRK11649 putative peptidase; P 97.4 0.00084 1.8E-08 46.2 6.7 46 17-62 96-143 (439)
23 COG3170 FimV Tfp pilus assembl 96.9 0.0016 3.5E-08 47.2 4.5 51 13-63 185-248 (755)
24 COG3061 OapA Cell envelope opa 96.8 0.0062 1.3E-07 38.9 5.8 50 15-64 158-212 (242)
25 PF05489 Phage_tail_X: Phage T 95.9 0.026 5.6E-07 29.0 4.1 46 18-64 3-55 (60)
26 COG3858 Predicted glycosyl hyd 95.8 0.005 1.1E-07 42.3 1.5 46 17-62 2-47 (423)
27 COG4784 Putative Zn-dependent 95.7 0.024 5.2E-07 38.7 4.5 48 14-61 426-477 (479)
28 COG1388 LytE FOG: LysM repeat 95.3 0.014 3E-07 33.2 2.0 33 30-62 1-35 (124)
29 COG0739 NlpD Membrane proteins 93.8 0.22 4.7E-06 31.3 5.0 47 17-63 2-49 (277)
30 PF13518 HTH_28: Helix-turn-he 92.8 0.14 3.1E-06 24.4 2.4 24 22-45 10-33 (52)
31 KOG2850 Predicted peptidoglyca 92.1 0.14 3.1E-06 31.9 2.3 32 18-49 11-42 (186)
32 PF01527 HTH_Tnp_1: Transposas 91.2 0.14 3E-06 26.4 1.4 25 21-45 20-44 (76)
33 PF02796 HTH_7: Helix-turn-hel 90.3 0.45 9.8E-06 22.6 2.6 24 21-44 18-41 (45)
34 PRK09413 IS2 repressor TnpA; R 87.4 0.83 1.8E-05 26.0 2.8 25 21-45 26-50 (121)
35 PF13384 HTH_23: Homeodomain-l 87.2 0.99 2.1E-05 21.4 2.7 23 22-44 15-37 (50)
36 COG4254 Uncharacterized protei 84.7 1.1 2.3E-05 30.1 2.6 46 17-62 6-55 (339)
37 PF05225 HTH_psq: helix-turn-h 84.5 1.1 2.3E-05 21.5 2.0 24 21-44 12-36 (45)
38 PF04545 Sigma70_r4: Sigma-70, 84.0 2.2 4.7E-05 20.3 3.0 23 22-44 18-40 (50)
39 COG2963 Transposase and inacti 83.6 1.6 3.5E-05 24.4 2.8 24 21-44 21-45 (116)
40 PF04218 CENP-B_N: CENP-B N-te 83.2 0.63 1.4E-05 23.0 0.9 24 21-44 19-42 (53)
41 cd00569 HTH_Hin_like Helix-tur 81.6 2.8 6.1E-05 17.1 2.8 22 22-43 19-40 (42)
42 PF13936 HTH_38: Helix-turn-he 81.1 2.7 5.9E-05 19.8 2.7 23 21-43 17-39 (44)
43 PHA00675 hypothetical protein 80.9 2.6 5.5E-05 22.8 2.7 24 22-45 37-60 (78)
44 PF13542 HTH_Tnp_ISL3: Helix-t 80.1 3 6.5E-05 19.8 2.7 21 24-44 27-47 (52)
45 TIGR01764 excise DNA binding d 79.9 4.5 9.8E-05 18.4 3.7 36 26-61 3-39 (49)
46 PF04255 DUF433: Protein of un 78.6 3 6.5E-05 20.7 2.5 23 22-44 29-52 (56)
47 PF09012 FeoC: FeoC like trans 78.2 2.8 6.1E-05 21.5 2.4 20 25-44 15-34 (69)
48 PF13693 HTH_35: Winged helix- 76.1 3.9 8.5E-05 22.0 2.6 22 22-43 13-34 (78)
49 PF08765 Mor: Mor transcriptio 75.7 3.9 8.4E-05 22.9 2.6 20 24-43 72-91 (108)
50 PF10668 Phage_terminase: Phag 75.3 4.7 0.0001 20.7 2.7 23 24-46 22-44 (60)
51 PF12471 GTP_CH_N: GTP cyclohy 75.0 2.6 5.5E-05 26.4 1.9 25 20-44 166-190 (194)
52 PF01710 HTH_Tnp_IS630: Transp 73.1 2.9 6.4E-05 23.7 1.7 25 21-45 15-39 (119)
53 cd04762 HTH_MerR-trunc Helix-T 72.6 6.5 0.00014 17.7 2.7 20 26-45 2-21 (49)
54 PF04967 HTH_10: HTH DNA bindi 72.1 5 0.00011 20.0 2.3 28 16-43 15-42 (53)
55 PF13510 Fer2_4: 2Fe-2S iron-s 71.6 5.6 0.00012 21.2 2.6 27 16-42 10-36 (82)
56 smart00421 HTH_LUXR helix_turn 70.3 9.4 0.0002 17.6 3.0 23 22-44 16-38 (58)
57 PF12298 Bot1p: Eukaryotic mit 69.2 7.5 0.00016 23.9 3.0 23 21-43 30-52 (172)
58 cd04761 HTH_MerR-SF Helix-Turn 68.9 8.5 0.00018 17.7 2.6 20 26-45 2-21 (49)
59 cd01104 HTH_MlrA-CarA Helix-Tu 67.9 8.3 0.00018 19.1 2.6 20 26-45 2-21 (68)
60 PF00356 LacI: Bacterial regul 67.7 10 0.00022 18.2 2.7 19 26-44 1-19 (46)
61 PF13613 HTH_Tnp_4: Helix-turn 67.4 6.4 0.00014 19.1 2.0 23 21-43 16-38 (53)
62 PRK12845 3-ketosteroid-delta-1 67.1 6.9 0.00015 27.9 2.9 26 21-46 421-450 (564)
63 PF08281 Sigma70_r4_2: Sigma-7 66.9 9.3 0.0002 18.2 2.6 21 23-43 25-45 (54)
64 PF01371 Trp_repressor: Trp re 66.8 10 0.00022 20.8 3.0 25 22-46 47-71 (87)
65 PRK12837 3-ketosteroid-delta-1 66.8 7.3 0.00016 27.2 2.9 26 21-46 372-401 (513)
66 PF11268 DUF3071: Protein of u 66.5 6.2 0.00013 24.2 2.2 27 19-45 64-90 (170)
67 smart00422 HTH_MERR helix_turn 66.2 9.5 0.00021 18.9 2.7 20 26-45 2-21 (70)
68 PF13411 MerR_1: MerR HTH fami 65.5 9.8 0.00021 18.9 2.6 20 26-45 2-21 (69)
69 PF00376 MerR: MerR family reg 65.2 10 0.00022 17.3 2.4 21 26-46 1-21 (38)
70 PF12244 DUF3606: Protein of u 64.5 11 0.00023 18.9 2.6 24 21-44 17-40 (57)
71 PRK12839 hypothetical protein; 63.7 8.9 0.00019 27.3 2.9 26 21-46 424-453 (572)
72 PF04760 IF2_N: Translation in 62.7 6.9 0.00015 19.0 1.6 19 26-44 5-23 (54)
73 smart00351 PAX Paired Box doma 62.7 13 0.00028 21.3 3.0 23 22-44 31-53 (125)
74 PRK10344 DNA-binding transcrip 62.6 13 0.00028 20.8 2.8 21 22-42 19-39 (92)
75 PF11242 DUF2774: Protein of u 62.5 15 0.00033 19.0 2.9 23 22-44 11-33 (63)
76 PF00392 GntR: Bacterial regul 62.5 10 0.00023 18.8 2.4 23 22-44 19-44 (64)
77 PF14493 HTH_40: Helix-turn-he 62.2 13 0.00028 20.0 2.8 23 21-43 10-32 (91)
78 PF12728 HTH_17: Helix-turn-he 62.2 16 0.00034 17.2 3.7 36 26-61 3-39 (51)
79 TIGR02531 yecD_yerC TrpR-relat 62.1 10 0.00022 20.7 2.4 26 21-46 47-72 (88)
80 PF08984 DUF1858: Domain of un 62.0 11 0.00024 18.7 2.3 21 22-42 39-59 (59)
81 TIGR02937 sigma70-ECF RNA poly 61.8 13 0.00028 20.4 2.9 23 22-44 124-146 (158)
82 PF13551 HTH_29: Winged helix- 61.4 11 0.00023 20.3 2.4 24 21-44 8-32 (112)
83 PF06627 DUF1153: Protein of u 61.0 9.8 0.00021 21.1 2.2 26 21-46 45-71 (90)
84 PF06056 Terminase_5: Putative 60.9 17 0.00037 18.2 3.0 24 23-46 12-35 (58)
85 COG3415 Transposase and inacti 60.8 13 0.00028 22.1 2.8 25 21-45 18-42 (138)
86 cd04764 HTH_MlrA-like_sg1 Heli 60.1 15 0.00032 18.3 2.7 20 26-45 2-21 (67)
87 COG3721 HugX Putative heme iro 59.6 15 0.00033 22.5 3.0 24 21-44 24-47 (176)
88 PF08220 HTH_DeoR: DeoR-like h 58.7 14 0.0003 18.2 2.4 19 25-43 15-33 (57)
89 PRK07843 3-ketosteroid-delta-1 58.7 12 0.00027 26.4 2.9 26 21-46 413-442 (557)
90 COG3753 Uncharacterized protei 58.4 12 0.00025 22.4 2.3 20 24-43 90-109 (143)
91 cd06170 LuxR_C_like C-terminal 58.0 19 0.00041 16.6 3.1 23 22-44 13-35 (57)
92 PRK06481 fumarate reductase fl 57.4 14 0.0003 25.8 2.9 26 21-46 375-404 (506)
93 cd04763 HTH_MlrA-like Helix-Tu 57.0 17 0.00038 18.1 2.7 20 26-45 2-21 (68)
94 PF00165 HTH_AraC: Bacterial r 56.6 19 0.00041 16.3 2.5 21 23-43 7-27 (42)
95 PF13011 LZ_Tnp_IS481: leucine 56.5 16 0.00034 20.1 2.5 25 21-45 22-46 (85)
96 PRK06134 putative FAD-binding 56.4 14 0.00031 26.3 2.9 26 21-46 426-455 (581)
97 TIGR03826 YvyF flagellar opero 55.6 20 0.00042 21.3 3.0 24 22-45 42-67 (137)
98 PRK12842 putative succinate de 55.5 14 0.00031 26.1 2.8 26 21-46 423-452 (574)
99 PRK12843 putative FAD-binding 55.4 15 0.00033 26.1 2.9 26 21-46 428-457 (578)
100 cd00131 PAX Paired Box domain 54.5 16 0.00034 21.1 2.5 24 21-44 30-53 (128)
101 smart00345 HTH_GNTR helix_turn 54.1 23 0.00049 16.6 2.7 18 26-43 22-39 (60)
102 COG1102 Cmk Cytidylate kinase 53.7 16 0.00034 22.7 2.5 26 20-45 28-53 (179)
103 cd06171 Sigma70_r4 Sigma70, re 53.2 22 0.00047 15.9 3.0 22 23-44 25-46 (55)
104 smart00342 HTH_ARAC helix_turn 53.1 23 0.00049 17.5 2.7 18 26-43 3-20 (84)
105 PRK07569 bidirectional hydroge 52.9 17 0.00036 23.0 2.5 28 16-43 10-37 (234)
106 PRK12844 3-ketosteroid-delta-1 52.6 18 0.00039 25.6 2.9 25 21-45 406-434 (557)
107 COG2442 Uncharacterized conser 52.2 25 0.00055 18.9 2.9 24 21-44 40-64 (79)
108 TIGR01813 flavo_cyto_c flavocy 51.8 19 0.0004 24.4 2.8 25 21-45 317-345 (439)
109 TIGR02007 fdx_isc ferredoxin, 51.7 23 0.00051 19.7 2.8 28 14-41 13-40 (110)
110 PRK12835 3-ketosteroid-delta-1 51.7 19 0.00041 25.8 2.9 26 21-46 427-456 (584)
111 PF15508 NAAA-beta: beta subun 51.5 22 0.00048 19.3 2.6 23 24-46 69-91 (95)
112 smart00760 Bac_DnaA_C Bacteria 51.4 14 0.00029 18.3 1.6 22 25-46 4-25 (60)
113 PF11020 DUF2610: Domain of un 50.9 23 0.00051 19.3 2.6 20 25-44 55-74 (82)
114 PRK00118 putative DNA-binding 50.8 28 0.0006 19.7 3.0 23 22-44 31-53 (104)
115 PF01381 HTH_3: Helix-turn-hel 50.4 28 0.0006 16.3 2.7 23 22-44 7-29 (55)
116 PF13443 HTH_26: Cro/C1-type H 50.1 24 0.00053 17.1 2.5 24 22-45 8-31 (63)
117 cd01666 TGS_DRG_C TGS_DRG_C: 49.9 25 0.00054 18.6 2.6 34 5-38 5-38 (75)
118 TIGR02485 CobZ_N-term precorri 49.0 22 0.00047 24.1 2.8 26 22-47 313-342 (432)
119 PRK07121 hypothetical protein; 49.0 22 0.00047 24.6 2.8 26 21-46 358-387 (492)
120 PRK08274 tricarballylate dehyd 48.7 23 0.0005 24.1 2.9 27 21-47 321-351 (466)
121 PF13404 HTH_AsnC-type: AsnC-t 47.5 30 0.00065 16.1 2.4 18 25-42 18-35 (42)
122 TIGR03879 near_KaiC_dom probab 47.3 38 0.00083 18.0 3.0 23 22-44 30-52 (73)
123 COG3784 Uncharacterized protei 47.2 18 0.00038 20.7 1.8 34 26-59 66-100 (109)
124 PF00196 GerE: Bacterial regul 47.1 26 0.00056 17.0 2.3 22 22-43 16-37 (58)
125 cd01109 HTH_YyaN Helix-Turn-He 46.6 29 0.00062 19.3 2.7 20 26-45 2-21 (113)
126 PHA02591 hypothetical protein; 46.6 49 0.0011 18.0 4.3 34 15-48 36-72 (83)
127 PF08299 Bac_DnaA_C: Bacterial 46.5 25 0.00053 18.1 2.2 18 26-43 5-22 (70)
128 TIGR02008 fdx_plant ferredoxin 46.5 28 0.00061 18.9 2.6 28 16-43 14-41 (97)
129 COG5004 P2-like prophage tail 46.2 43 0.00093 17.6 3.0 44 18-61 4-54 (70)
130 cd07377 WHTH_GntR Winged helix 46.0 35 0.00076 16.2 2.7 18 26-43 27-44 (66)
131 PRK12834 putative FAD-binding 45.9 26 0.00057 24.7 2.9 25 21-45 393-424 (549)
132 TIGR02885 spore_sigF RNA polym 45.9 31 0.00068 21.3 3.0 22 23-44 198-219 (231)
133 TIGR02844 spore_III_D sporulat 45.9 33 0.00071 18.4 2.7 20 25-44 20-39 (80)
134 PF14451 Ub-Mut7C: Mut7-C ubiq 45.9 24 0.00053 18.9 2.2 48 16-63 24-76 (81)
135 PF10543 ORF6N: ORF6N domain; 45.7 28 0.00062 18.7 2.5 23 22-44 10-32 (88)
136 COG2739 Uncharacterized protei 45.7 23 0.0005 20.2 2.1 19 25-43 34-52 (105)
137 TIGR02985 Sig70_bacteroi1 RNA 45.3 36 0.00079 19.1 3.0 22 22-43 127-148 (161)
138 COG3413 Predicted DNA binding 45.1 24 0.00053 21.8 2.4 28 17-44 171-198 (215)
139 PF14502 HTH_41: Helix-turn-he 45.1 36 0.00078 16.7 2.5 20 25-44 7-26 (48)
140 cd01279 HTH_HspR-like Helix-Tu 44.9 32 0.0007 18.7 2.6 20 26-45 3-22 (98)
141 PTZ00305 NADH:ubiquinone oxido 44.7 21 0.00045 24.0 2.1 32 16-47 75-107 (297)
142 PHA01976 helix-turn-helix prot 44.7 40 0.00086 16.5 3.0 23 22-44 13-35 (67)
143 COG5484 Uncharacterized conser 44.4 26 0.00057 23.2 2.5 23 24-46 19-41 (279)
144 COG2771 CsgD DNA-binding HTH d 43.4 36 0.00079 16.2 2.5 22 21-42 16-37 (65)
145 cd04768 HTH_BmrR-like Helix-Tu 43.1 36 0.00078 18.4 2.6 21 26-46 2-22 (96)
146 PF13413 HTH_25: Helix-turn-he 43.0 40 0.00087 17.0 2.7 24 21-44 7-30 (62)
147 cd04766 HTH_HspR Helix-Turn-He 42.2 38 0.00083 18.0 2.7 21 26-46 3-23 (91)
148 PF08279 HTH_11: HTH domain; 42.1 34 0.00074 16.1 2.2 18 25-42 16-33 (55)
149 COG3423 Nlp Predicted transcri 42.0 41 0.0009 18.3 2.6 23 22-44 19-41 (82)
150 PF04539 Sigma70_r3: Sigma-70 42.0 40 0.00086 17.1 2.6 21 25-45 21-41 (78)
151 cd04772 HTH_TioE_rpt1 First He 41.9 39 0.00084 18.4 2.7 21 26-46 2-22 (99)
152 TIGR02997 Sig70-cyanoRpoD RNA 41.8 38 0.00083 22.0 3.0 23 22-44 267-289 (298)
153 PRK06596 RNA polymerase factor 41.6 39 0.00084 21.9 3.0 22 23-44 247-268 (284)
154 PRK04217 hypothetical protein; 41.5 46 0.001 18.9 3.0 23 22-44 56-78 (110)
155 cd04775 HTH_Cfa-like Helix-Tur 41.3 40 0.00086 18.5 2.7 21 26-46 3-23 (102)
156 PHA00542 putative Cro-like pro 41.3 46 0.001 17.5 2.8 24 21-44 28-51 (82)
157 TIGR02392 rpoH_proteo alternat 41.0 40 0.00086 21.6 3.0 22 23-44 235-256 (270)
158 cd00207 fer2 2Fe-2S iron-sulfu 40.9 51 0.0011 16.7 3.0 24 16-39 9-32 (84)
159 cd01106 HTH_TipAL-Mta Helix-Tu 40.9 41 0.00088 18.3 2.7 20 26-45 2-21 (103)
160 TIGR03070 couple_hipB transcri 40.9 41 0.00089 15.5 2.9 24 22-45 13-36 (58)
161 cd00592 HTH_MerR-like Helix-Tu 40.7 42 0.00091 17.9 2.7 21 26-46 2-22 (100)
162 TIGR02950 SigM_subfam RNA poly 40.6 46 0.00099 18.8 3.0 22 22-43 119-140 (154)
163 PTZ00306 NADH-dependent fumara 40.4 31 0.00067 26.9 2.7 26 21-46 765-794 (1167)
164 PF12116 SpoIIID: Stage III sp 40.2 9.7 0.00021 20.8 0.0 24 18-41 13-36 (82)
165 PF01402 RHH_1: Ribbon-helix-h 40.0 38 0.00082 14.9 2.5 19 25-43 12-30 (39)
166 cd04788 HTH_NolA-AlbR Helix-Tu 39.9 44 0.00094 18.1 2.7 21 26-46 2-22 (96)
167 cd01108 HTH_CueR Helix-Turn-He 39.9 41 0.00088 19.2 2.6 20 26-45 2-21 (127)
168 cd00086 homeodomain Homeodomai 39.9 31 0.00067 16.2 1.9 20 25-44 28-47 (59)
169 PF13412 HTH_24: Winged helix- 39.7 43 0.00092 15.4 2.9 22 22-43 15-36 (48)
170 cd01107 HTH_BmrR Helix-Turn-He 39.5 43 0.00093 18.5 2.6 20 26-45 2-21 (108)
171 PRK11426 hypothetical protein; 39.3 28 0.00061 20.6 1.9 20 24-43 72-91 (132)
172 PF10007 DUF2250: Uncharacteri 39.2 50 0.0011 18.2 2.8 21 24-44 21-41 (92)
173 PF08769 Spo0A_C: Sporulation 39.1 36 0.00077 19.2 2.3 19 25-43 41-59 (106)
174 PRK13413 mpi multiple promoter 39.0 47 0.001 20.2 3.0 24 22-45 170-193 (200)
175 cd00093 HTH_XRE Helix-turn-hel 39.0 39 0.00084 14.7 2.9 24 22-45 10-33 (58)
176 cd04789 HTH_Cfa Helix-Turn-Hel 38.9 46 0.00099 18.2 2.7 20 26-45 3-22 (102)
177 PF00111 Fer2: 2Fe-2S iron-sul 38.9 42 0.00091 16.9 2.4 22 17-38 8-31 (78)
178 cd01105 HTH_GlnR-like Helix-Tu 38.9 47 0.001 17.7 2.6 21 26-46 3-23 (88)
179 PF07638 Sigma70_ECF: ECF sigm 38.9 45 0.00097 20.0 2.8 22 22-43 149-170 (185)
180 cd04782 HTH_BltR Helix-Turn-He 38.8 46 0.001 18.0 2.7 21 26-46 2-22 (97)
181 PRK05901 RNA polymerase sigma 38.8 43 0.00093 24.0 3.0 24 22-45 465-488 (509)
182 TIGR00270 conserved hypothetic 38.6 53 0.0011 19.7 3.1 37 25-61 112-153 (154)
183 TIGR02044 CueR Cu(I)-responsiv 38.6 44 0.00095 19.0 2.6 20 26-45 2-21 (127)
184 cd04770 HTH_HMRTR Helix-Turn-H 38.4 46 0.00099 18.6 2.7 21 26-46 2-22 (123)
185 PRK07921 RNA polymerase sigma 38.3 47 0.001 22.2 3.0 21 24-44 282-302 (324)
186 TIGR02812 fadR_gamma fatty aci 38.0 32 0.00069 21.3 2.1 25 20-44 23-50 (235)
187 PRK01777 hypothetical protein; 37.9 50 0.0011 18.3 2.7 44 17-60 19-73 (95)
188 cd04774 HTH_YfmP Helix-Turn-He 37.9 49 0.0011 18.0 2.7 21 26-46 2-22 (96)
189 TIGR00370 conserved hypothetic 37.8 49 0.0011 20.7 2.9 23 23-45 89-111 (202)
190 PRK05572 sporulation sigma fac 37.7 50 0.0011 20.8 3.0 24 22-45 216-239 (252)
191 cd01282 HTH_MerR-like_sg3 Heli 37.7 49 0.0011 18.4 2.7 21 26-46 2-22 (112)
192 PRK09652 RNA polymerase sigma 37.7 54 0.0012 18.8 3.0 21 22-42 142-162 (182)
193 PRK03837 transcriptional regul 37.6 41 0.00089 20.7 2.6 26 19-44 29-57 (241)
194 PF14174 YycC: YycC-like prote 37.3 28 0.0006 17.4 1.4 22 24-45 8-29 (53)
195 cd04769 HTH_MerR2 Helix-Turn-H 37.2 49 0.0011 18.5 2.7 21 26-46 2-22 (116)
196 PF09824 ArsR: ArsR transcript 37.1 81 0.0018 19.3 3.7 36 25-60 122-157 (160)
197 TIGR03643 conserved hypothetic 37.1 58 0.0012 17.4 2.7 20 24-43 13-32 (72)
198 PRK07198 hypothetical protein; 37.0 25 0.00054 24.7 1.6 25 20-44 170-194 (418)
199 PRK04984 fatty acid metabolism 37.0 32 0.0007 21.2 2.1 25 20-44 24-51 (239)
200 PF09339 HTH_IclR: IclR helix- 36.9 52 0.0011 15.5 2.4 20 25-44 19-38 (52)
201 PF07022 Phage_CI_repr: Bacter 36.8 23 0.00051 17.8 1.2 19 24-42 41-59 (66)
202 PRK10225 DNA-binding transcrip 36.6 35 0.00077 21.4 2.2 25 20-44 26-53 (257)
203 cd04785 HTH_CadR-PbrR-like Hel 36.3 51 0.0011 18.7 2.7 20 26-45 2-21 (126)
204 PF04297 UPF0122: Putative hel 36.2 49 0.0011 18.6 2.5 20 23-42 32-51 (101)
205 cd01795 USP48_C USP ubiquitin- 36.2 46 0.001 19.0 2.4 48 14-61 14-75 (107)
206 PRK06759 RNA polymerase factor 36.2 61 0.0013 18.3 3.0 23 22-44 120-142 (154)
207 PF09035 Tn916-Xis: Excisionas 36.0 68 0.0015 16.7 3.1 36 26-61 15-53 (67)
208 PRK12514 RNA polymerase sigma 35.6 56 0.0012 19.1 2.9 21 22-42 143-163 (179)
209 TIGR02051 MerR Hg(II)-responsi 34.8 54 0.0012 18.6 2.6 21 26-46 1-21 (124)
210 PF07836 DmpG_comm: DmpG-like 34.7 49 0.0011 17.3 2.2 15 28-42 26-40 (66)
211 PF13994 PgaD: PgaD-like prote 34.6 56 0.0012 19.0 2.7 23 25-47 101-123 (138)
212 PF06413 Neugrin: Neugrin; In 34.5 46 0.001 21.3 2.5 19 26-44 31-49 (225)
213 COG5566 Uncharacterized conser 34.5 57 0.0012 19.4 2.7 21 24-44 102-122 (137)
214 cd04767 HTH_HspR-like_MBC Heli 34.4 57 0.0012 18.8 2.7 20 26-45 3-22 (120)
215 PRK11924 RNA polymerase sigma 34.3 65 0.0014 18.4 3.0 22 22-43 139-160 (179)
216 PRK12537 RNA polymerase sigma 34.0 62 0.0013 19.1 2.9 21 22-42 147-167 (182)
217 PF01418 HTH_6: Helix-turn-hel 33.8 59 0.0013 16.8 2.5 22 24-45 34-55 (77)
218 cd06571 Bac_DnaA_C C-terminal 33.6 73 0.0016 16.9 2.9 19 23-41 43-62 (90)
219 PF04921 XAP5: XAP5, circadian 33.6 49 0.0011 21.5 2.5 17 18-34 114-130 (239)
220 PRK09990 DNA-binding transcrip 33.5 50 0.0011 20.6 2.5 25 20-44 24-51 (251)
221 PF08822 DUF1804: Protein of u 33.5 58 0.0012 20.0 2.7 26 20-45 15-40 (165)
222 PF10985 DUF2805: Protein of u 33.4 71 0.0015 17.1 2.7 20 24-43 12-31 (73)
223 PRK09210 RNA polymerase sigma 33.4 60 0.0013 21.9 3.0 22 23-44 324-345 (367)
224 PF15145 DUF4577: Domain of un 33.1 49 0.0011 19.3 2.2 29 19-47 84-115 (128)
225 PF04447 DUF550: Protein of un 33.0 61 0.0013 18.4 2.5 18 27-44 51-68 (100)
226 PRK07500 rpoH2 RNA polymerase 32.9 66 0.0014 20.9 3.1 22 23-44 244-265 (289)
227 PF09607 BrkDBD: Brinker DNA-b 32.9 59 0.0013 16.6 2.3 19 27-45 28-46 (58)
228 smart00530 HTH_XRE Helix-turn- 32.8 50 0.0011 14.2 2.9 23 23-45 9-31 (56)
229 cd04765 HTH_MlrA-like_sg2 Heli 32.7 65 0.0014 17.6 2.6 19 26-44 2-20 (99)
230 smart00341 HRDC Helicase and R 32.2 48 0.001 16.8 2.0 31 18-48 26-56 (81)
231 cd04773 HTH_TioE_rpt2 Second H 32.2 67 0.0014 17.8 2.7 21 26-46 2-22 (108)
232 PRK13182 racA polar chromosome 32.1 61 0.0013 19.9 2.7 20 26-45 2-21 (175)
233 PF04405 ScdA_N: Domain of Unk 31.8 74 0.0016 15.8 2.6 20 24-43 31-50 (56)
234 TIGR02850 spore_sigG RNA polym 31.8 72 0.0016 20.1 3.1 22 23-44 221-242 (254)
235 PRK11923 algU RNA polymerase s 31.5 75 0.0016 18.8 3.0 21 22-42 152-172 (193)
236 cd04780 HTH_MerR-like_sg5 Heli 31.5 71 0.0015 17.3 2.7 20 26-45 2-21 (95)
237 PLN02593 adrenodoxin-like ferr 31.5 64 0.0014 18.3 2.5 24 17-40 13-36 (117)
238 CHL00134 petF ferredoxin; Vali 31.5 90 0.0019 17.0 3.1 25 17-41 17-41 (99)
239 PRK11523 DNA-binding transcrip 31.5 44 0.00096 20.9 2.0 25 20-44 25-52 (253)
240 cd04784 HTH_CadR-PbrR Helix-Tu 31.3 69 0.0015 18.1 2.7 20 26-45 2-21 (127)
241 KOG3309 Ferredoxin [Energy pro 31.3 43 0.00094 20.5 1.8 23 18-40 57-79 (159)
242 TIGR02989 Sig-70_gvs1 RNA poly 31.3 81 0.0018 17.8 3.0 22 22-43 125-146 (159)
243 PF12085 DUF3562: Protein of u 31.3 53 0.0011 17.2 2.0 20 25-44 8-27 (66)
244 TIGR02393 RpoD_Cterm RNA polym 31.2 73 0.0016 19.8 3.0 23 22-44 194-216 (238)
245 PRK13690 hypothetical protein; 31.2 58 0.0012 20.4 2.4 16 50-65 21-36 (184)
246 cd04783 HTH_MerR1 Helix-Turn-H 31.0 69 0.0015 18.1 2.6 20 26-45 2-21 (126)
247 PRK07405 RNA polymerase sigma 30.8 72 0.0016 21.1 3.0 22 23-44 275-296 (317)
248 PF00046 Homeobox: Homeobox do 30.7 69 0.0015 15.1 2.6 20 25-44 28-47 (57)
249 PRK10014 DNA-binding transcrip 30.7 64 0.0014 20.6 2.7 20 25-44 7-26 (342)
250 PRK09464 pdhR transcriptional 30.5 62 0.0013 20.2 2.6 25 20-44 27-54 (254)
251 TIGR02607 antidote_HigA addict 30.5 80 0.0017 15.8 3.0 25 20-44 14-38 (78)
252 cd04777 HTH_MerR-like_sg1 Heli 30.5 65 0.0014 17.6 2.4 20 26-45 2-21 (107)
253 cd04781 HTH_MerR-like_sg6 Heli 30.5 73 0.0016 17.9 2.7 21 26-46 2-22 (120)
254 PRK12518 RNA polymerase sigma 30.5 80 0.0017 18.2 2.9 22 22-43 134-155 (175)
255 PRK09641 RNA polymerase sigma 30.3 81 0.0018 18.4 3.0 22 23-44 151-172 (187)
256 PRK07406 RNA polymerase sigma 30.2 74 0.0016 21.8 3.0 22 23-44 330-351 (373)
257 TIGR00241 CoA_E_activ CoA-subs 30.0 92 0.002 19.5 3.3 23 23-45 126-148 (248)
258 PRK08215 sporulation sigma fac 29.8 81 0.0018 19.9 3.0 22 23-44 224-245 (258)
259 smart00389 HOX Homeodomain. DN 29.6 56 0.0012 15.2 1.8 20 25-44 28-47 (56)
260 TIGR02043 ZntR Zn(II)-responsi 29.6 76 0.0017 18.2 2.7 22 26-47 3-24 (131)
261 TIGR02954 Sig70_famx3 RNA poly 29.6 84 0.0018 18.1 2.9 22 22-43 133-154 (169)
262 PF12844 HTH_19: Helix-turn-he 29.5 76 0.0017 15.3 2.6 22 23-44 11-32 (64)
263 cd08010 yceG_like proteins sim 29.5 1.3E+02 0.0028 19.4 3.9 28 17-44 29-60 (245)
264 smart00418 HTH_ARSR helix_turn 29.4 69 0.0015 14.7 2.7 20 23-42 9-28 (66)
265 cd01111 HTH_MerD Helix-Turn-He 29.3 81 0.0018 17.5 2.7 20 26-45 2-21 (107)
266 PF12964 DUF3853: Protein of u 29.3 54 0.0012 18.4 1.9 35 27-61 48-85 (96)
267 PRK10219 DNA-binding transcrip 29.3 84 0.0018 16.9 2.7 20 24-43 21-40 (107)
268 PRK10421 DNA-binding transcrip 29.2 66 0.0014 20.1 2.5 24 20-43 19-45 (253)
269 PF13022 HTH_Tnp_1_2: Helix-tu 29.2 73 0.0016 19.2 2.5 22 24-45 34-55 (142)
270 PF07027 DUF1318: Protein of u 29.1 46 0.00099 18.5 1.6 34 27-60 53-87 (95)
271 PF08356 EF_assoc_2: EF hand a 28.9 26 0.00056 19.3 0.6 17 21-37 42-60 (89)
272 PRK09639 RNA polymerase sigma 28.9 92 0.002 17.8 3.0 21 23-43 126-146 (166)
273 PRK07408 RNA polymerase sigma 28.7 86 0.0019 19.9 3.0 22 23-44 218-239 (256)
274 PF14453 ThiS-like: ThiS-like 28.6 71 0.0015 16.1 2.1 44 16-60 7-53 (57)
275 TIGR02980 SigBFG RNA polymeras 28.5 88 0.0019 19.2 3.0 22 23-44 193-214 (227)
276 PRK09648 RNA polymerase sigma 28.4 93 0.002 18.3 3.0 22 22-43 153-174 (189)
277 PRK05911 RNA polymerase sigma 28.3 88 0.0019 19.9 3.0 23 22-44 219-241 (257)
278 cd01110 HTH_SoxR Helix-Turn-He 28.2 81 0.0018 18.3 2.6 21 26-46 3-23 (139)
279 PF12824 MRP-L20: Mitochondria 28.1 73 0.0016 19.4 2.5 20 26-45 106-125 (164)
280 TIGR02047 CadR-PbrR Cd(II)/Pb( 27.9 85 0.0018 17.9 2.7 20 26-45 2-21 (127)
281 PRK05803 sporulation sigma fac 27.7 94 0.002 19.3 3.0 23 22-44 193-215 (233)
282 PRK14548 50S ribosomal protein 27.6 90 0.002 16.9 2.6 21 16-36 63-83 (84)
283 PRK05949 RNA polymerase sigma 27.5 88 0.0019 20.9 3.0 22 23-44 285-306 (327)
284 PRK12534 RNA polymerase sigma 27.3 91 0.002 18.3 2.8 20 23-42 152-171 (187)
285 PF02082 Rrf2: Transcriptional 27.3 84 0.0018 16.3 2.4 19 25-43 26-44 (83)
286 TIGR02054 MerD mercuric resist 27.2 91 0.002 17.9 2.7 21 25-45 4-24 (120)
287 PRK09638 RNA polymerase sigma 27.2 94 0.002 18.0 2.8 21 22-42 140-160 (176)
288 PRK09514 zntR zinc-responsive 27.1 86 0.0019 18.2 2.6 20 26-45 3-22 (140)
289 TIGR02983 SigE-fam_strep RNA p 27.1 99 0.0021 17.6 2.9 22 22-43 124-145 (162)
290 COG2049 DUR1 Allophanate hydro 27.0 93 0.002 20.0 2.9 23 23-45 96-118 (223)
291 PF10975 DUF2802: Protein of u 27.0 62 0.0013 16.8 1.8 22 20-41 40-61 (70)
292 KOG1577 Aldo/keto reductase fa 26.7 54 0.0012 22.0 1.9 23 20-42 218-240 (300)
293 PF13467 RHH_4: Ribbon-helix-h 26.7 53 0.0012 17.1 1.5 19 25-43 24-42 (67)
294 TIGR03541 reg_near_HchA LuxR f 26.6 1E+02 0.0022 19.2 3.1 23 21-43 183-205 (232)
295 PRK12513 RNA polymerase sigma 26.5 1.1E+02 0.0023 18.2 3.0 21 22-42 153-173 (194)
296 PRK12547 RNA polymerase sigma 26.5 1.1E+02 0.0024 17.6 3.1 20 23-42 127-146 (164)
297 TIGR00721 tfx DNA-binding prot 26.5 1.1E+02 0.0025 18.0 3.0 22 22-43 19-40 (137)
298 cd04776 HTH_GnyR Helix-Turn-He 26.4 95 0.0021 17.5 2.7 21 26-46 2-22 (118)
299 PF00570 HRDC: HRDC domain Blo 26.3 44 0.00095 16.4 1.2 30 20-49 25-54 (68)
300 COG2012 RPB5 DNA-directed RNA 26.2 95 0.0021 16.9 2.4 45 18-62 17-65 (80)
301 PF03398 Ist1: Regulator of Vp 25.9 51 0.0011 19.9 1.5 14 25-38 152-165 (165)
302 COG0568 RpoD DNA-directed RNA 25.7 93 0.002 21.3 2.9 22 23-44 298-319 (342)
303 PF13560 HTH_31: Helix-turn-he 25.7 95 0.0021 15.1 2.6 22 23-44 13-34 (64)
304 PF14549 P22_Cro: DNA-binding 25.6 1E+02 0.0022 15.5 2.7 20 26-45 11-30 (60)
305 PRK10072 putative transcriptio 25.6 1.2E+02 0.0026 16.7 2.9 25 21-45 43-67 (96)
306 cd04787 HTH_HMRTR_unk Helix-Tu 25.6 1E+02 0.0022 17.7 2.7 20 26-45 2-21 (133)
307 PF00440 TetR_N: Bacterial reg 25.6 83 0.0018 14.4 2.8 20 24-43 16-35 (47)
308 TIGR03209 P21_Cbot clostridium 25.4 85 0.0018 17.6 2.4 19 23-41 122-140 (142)
309 PRK12541 RNA polymerase sigma 25.4 1.2E+02 0.0026 17.3 3.0 22 22-43 126-147 (161)
310 PRK12519 RNA polymerase sigma 25.4 1.1E+02 0.0025 18.0 3.0 21 22-42 155-175 (194)
311 PRK06437 hypothetical protein; 25.3 69 0.0015 16.2 1.8 45 16-60 12-60 (67)
312 PRK13749 transcriptional regul 25.2 90 0.002 18.0 2.4 20 26-45 5-24 (121)
313 cd04790 HTH_Cfa-like_unk Helix 25.2 97 0.0021 18.7 2.7 21 26-46 3-23 (172)
314 PRK15002 redox-sensitivie tran 25.2 99 0.0021 18.5 2.7 22 25-46 12-33 (154)
315 PRK05658 RNA polymerase sigma 25.1 93 0.002 22.6 2.9 22 23-44 575-596 (619)
316 PRK07037 extracytoplasmic-func 25.1 1.2E+02 0.0027 17.2 3.1 22 22-43 123-144 (163)
317 TIGR02952 Sig70_famx2 RNA poly 25.1 1.1E+02 0.0025 17.4 2.9 21 23-43 137-157 (170)
318 PRK05602 RNA polymerase sigma 25.0 1.2E+02 0.0025 17.9 3.0 22 22-43 142-163 (186)
319 PRK09726 antitoxin HipB; Provi 25.0 1.2E+02 0.0026 16.0 2.9 23 22-44 23-45 (88)
320 cd04786 HTH_MerR-like_sg7 Heli 24.8 1.1E+02 0.0023 17.7 2.7 20 26-45 2-21 (131)
321 TIGR02939 RpoE_Sigma70 RNA pol 24.8 1.2E+02 0.0026 17.6 3.0 21 22-42 152-172 (190)
322 PRK12515 RNA polymerase sigma 24.7 1.1E+02 0.0024 18.0 2.9 22 22-43 145-166 (189)
323 PRK09570 rpoH DNA-directed RNA 24.7 1.2E+02 0.0026 16.3 2.7 46 19-64 15-64 (79)
324 TIGR02405 trehalos_R_Ecol treh 24.5 96 0.0021 19.6 2.7 19 26-44 3-21 (311)
325 PRK06944 sulfur carrier protei 24.5 67 0.0014 15.7 1.6 45 16-60 7-58 (65)
326 PRK12427 flagellar biosynthesi 24.5 1.2E+02 0.0025 19.0 3.0 24 22-45 197-220 (231)
327 PRK10401 DNA-binding transcrip 24.5 96 0.0021 19.9 2.7 19 26-44 3-21 (346)
328 PF08784 RPA_C: Replication pr 24.4 92 0.002 16.8 2.3 25 20-44 61-85 (102)
329 PF08972 DUF1902: Domain of un 24.4 30 0.00065 17.4 0.3 28 21-48 25-52 (54)
330 PRK09651 RNA polymerase sigma 24.4 1.3E+02 0.0027 17.6 3.0 22 22-43 133-154 (172)
331 COG0497 RecN ATPase involved i 24.3 84 0.0018 23.0 2.6 20 25-44 307-326 (557)
332 PF13984 MsyB: MsyB protein 24.3 22 0.00049 20.5 -0.2 14 17-30 36-49 (122)
333 PRK09943 DNA-binding transcrip 24.3 1.2E+02 0.0026 18.1 2.9 19 25-43 50-68 (185)
334 smart00455 RBD Raf-like Ras-bi 24.3 1.1E+02 0.0024 15.7 2.5 45 17-61 12-68 (70)
335 cd04779 HTH_MerR-like_sg4 Heli 24.2 1E+02 0.0023 17.9 2.6 20 26-45 2-21 (134)
336 smart00550 Zalpha Z-DNA-bindin 24.1 1.1E+02 0.0024 15.4 2.9 21 24-44 22-42 (68)
337 COG0789 SoxR Predicted transcr 24.1 1.1E+02 0.0025 16.7 2.7 20 26-45 2-21 (124)
338 PRK09526 lacI lac repressor; R 24.0 98 0.0021 19.7 2.7 20 25-44 6-25 (342)
339 PRK11511 DNA-binding transcrip 24.0 1.1E+02 0.0025 17.2 2.7 19 25-43 26-44 (127)
340 PRK09415 RNA polymerase factor 24.0 1.3E+02 0.0028 17.7 3.0 22 22-43 141-162 (179)
341 COG3661 AguA Alpha-glucuronida 24.0 98 0.0021 22.5 2.8 29 17-45 598-627 (684)
342 PF14210 DUF4322: Domain of un 23.9 74 0.0016 16.6 1.7 21 23-43 42-62 (66)
343 TIGR02859 spore_sigH RNA polym 23.9 1.3E+02 0.0027 17.7 3.0 21 22-42 163-183 (198)
344 PRK13503 transcriptional activ 23.9 1E+02 0.0022 19.2 2.7 22 23-44 186-207 (278)
345 PF10654 DUF2481: Protein of u 23.9 81 0.0018 18.4 2.0 22 23-44 79-100 (126)
346 TIGR02948 SigW_bacill RNA poly 23.8 1.2E+02 0.0027 17.5 3.0 22 22-43 150-171 (187)
347 PF05263 DUF722: Protein of un 23.8 1.2E+02 0.0025 17.9 2.7 26 20-45 95-120 (130)
348 TIGR01950 SoxR redox-sensitive 23.8 1.1E+02 0.0024 17.9 2.7 21 26-46 3-23 (142)
349 PRK15431 ferrous iron transpor 23.7 1.3E+02 0.0028 16.2 2.7 20 25-44 17-36 (78)
350 PRK15340 transcriptional regul 23.7 1.3E+02 0.0028 19.2 3.1 23 22-44 123-145 (216)
351 PRK06083 sulfur carrier protei 23.6 62 0.0013 17.4 1.5 45 16-60 25-77 (84)
352 PRK09492 treR trehalose repres 23.6 93 0.002 19.6 2.5 20 25-44 5-24 (315)
353 PF02682 AHS1: Allophanate hyd 23.4 83 0.0018 19.6 2.2 23 23-45 98-120 (202)
354 PF06114 DUF955: Domain of unk 23.2 1.1E+02 0.0025 16.0 2.5 17 26-42 102-118 (122)
355 TIGR02479 FliA_WhiG RNA polyme 23.1 1.3E+02 0.0029 18.4 3.1 22 22-43 189-210 (224)
356 PRK10227 DNA-binding transcrip 23.0 1.2E+02 0.0026 17.6 2.7 21 26-46 2-22 (135)
357 smart00796 AHS1 Allophanate hy 23.0 1.3E+02 0.0028 18.7 2.9 23 24-46 100-122 (201)
358 TIGR03595 Obg_CgtA_exten Obg f 23.0 1.2E+02 0.0027 15.5 2.8 43 18-61 10-63 (69)
359 PRK05713 hypothetical protein; 22.9 1.1E+02 0.0023 19.9 2.7 27 15-41 7-33 (312)
360 PRK12528 RNA polymerase sigma 22.9 1.3E+02 0.0029 17.1 2.9 21 22-42 127-147 (161)
361 PF10410 DnaB_bind: DnaB-helic 22.8 34 0.00074 16.4 0.3 14 27-40 45-58 (59)
362 PF06262 DUF1025: Possibl zinc 22.7 90 0.002 17.3 2.0 17 27-43 78-94 (97)
363 PRK09642 RNA polymerase sigma 22.6 1.4E+02 0.003 17.0 3.0 21 22-42 120-140 (160)
364 PF03921 ICAM_N: Intercellular 22.5 34 0.00074 18.9 0.3 16 50-65 13-28 (91)
365 smart00354 HTH_LACI helix_turn 22.5 1.2E+02 0.0026 15.2 2.7 19 26-44 2-20 (70)
366 cd01670 Death Death Domain: a 22.5 1.1E+02 0.0024 15.3 2.3 21 24-44 10-30 (79)
367 PRK12512 RNA polymerase sigma 22.5 1.4E+02 0.0029 17.5 2.9 21 23-43 146-166 (184)
368 PRK12542 RNA polymerase sigma 22.5 1.4E+02 0.003 17.5 3.0 22 22-43 136-157 (185)
369 PRK06811 RNA polymerase factor 22.3 1.4E+02 0.003 17.7 3.0 22 22-43 145-166 (189)
370 PRK06930 positive control sigm 22.2 1.4E+02 0.0031 18.0 3.0 23 22-44 128-150 (170)
371 smart00419 HTH_CRP helix_turn_ 22.2 93 0.002 13.7 3.2 23 21-43 5-27 (48)
372 TIGR02941 Sigma_B RNA polymera 22.1 1.4E+02 0.003 18.7 3.1 23 22-44 219-241 (255)
373 TIGR02984 Sig-70_plancto1 RNA 21.9 1.4E+02 0.0029 17.4 2.8 21 23-43 155-175 (189)
374 PF03374 ANT: Phage antirepres 21.9 1.3E+02 0.0028 16.3 2.6 21 24-44 24-44 (111)
375 PRK12536 RNA polymerase sigma 21.4 1.5E+02 0.0033 17.3 3.0 22 22-43 143-164 (181)
376 COG2186 FadR Transcriptional r 21.3 76 0.0016 20.1 1.7 25 20-44 27-54 (241)
377 cd05717 Ig1_Necl-1-3_like Firs 21.1 49 0.0011 17.3 0.7 19 45-63 1-20 (95)
378 PRK08583 RNA polymerase sigma 21.1 1.5E+02 0.0033 18.6 3.1 23 22-44 219-241 (257)
379 PRK13752 putative transcriptio 21.1 1.3E+02 0.0028 17.7 2.6 20 26-45 9-28 (144)
380 PRK13919 putative RNA polymera 21.0 1.6E+02 0.0034 17.2 3.0 21 22-42 149-169 (186)
381 PF07750 GcrA: GcrA cell cycle 20.9 93 0.002 18.8 2.0 22 21-42 15-37 (162)
382 cd01392 HTH_LacI Helix-turn-he 20.7 1.1E+02 0.0023 14.0 1.9 17 29-45 2-18 (52)
383 PRK12523 RNA polymerase sigma 20.7 1.7E+02 0.0036 17.0 3.0 22 22-43 133-154 (172)
384 TIGR03636 L23_arch archaeal ri 20.6 1.5E+02 0.0033 15.7 2.6 20 17-36 57-76 (77)
385 PRK09644 RNA polymerase sigma 20.6 1.5E+02 0.0032 17.0 2.8 22 22-43 122-143 (165)
386 PRK09640 RNA polymerase sigma 20.6 1.6E+02 0.0035 17.3 3.0 22 22-43 148-169 (188)
387 PF07374 DUF1492: Protein of u 20.5 1.6E+02 0.0036 16.0 3.0 22 23-44 70-91 (100)
388 cd08306 Death_FADD Fas-associa 20.5 1.4E+02 0.003 15.9 2.4 21 24-44 13-33 (86)
389 PRK12532 RNA polymerase sigma 20.5 1.6E+02 0.0034 17.5 3.0 22 22-43 150-171 (195)
390 PF12840 HTH_20: Helix-turn-he 20.5 1.3E+02 0.0027 14.6 2.6 21 22-42 22-42 (61)
391 PRK09649 RNA polymerase sigma 20.4 1.6E+02 0.0035 17.4 3.0 21 22-42 144-164 (185)
392 cd08805 Death_ank1 Death domai 20.3 1.6E+02 0.0035 15.8 2.7 21 24-44 15-35 (84)
393 PRK06986 fliA flagellar biosyn 20.3 1.6E+02 0.0035 18.2 3.1 22 22-43 198-219 (236)
394 cd08318 Death_NMPP84 Death dom 20.3 1.3E+02 0.0028 16.0 2.3 21 24-44 18-38 (86)
395 PF00984 UDPG_MGDP_dh: UDP-glu 20.2 1.6E+02 0.0035 16.0 2.7 20 27-46 25-44 (96)
396 PF14117 DUF4287: Domain of un 20.2 1.4E+02 0.0031 15.2 2.4 18 27-44 6-23 (61)
397 PRK09637 RNA polymerase sigma 20.1 1.6E+02 0.0034 17.5 2.9 21 22-42 120-140 (181)
398 cd08319 Death_RAIDD Death doma 20.1 1.5E+02 0.0032 15.9 2.5 21 24-44 13-33 (83)
399 PRK06288 RNA polymerase sigma 20.1 1.6E+02 0.0035 18.7 3.0 21 22-42 226-246 (268)
400 PF12668 DUF3791: Protein of u 20.0 1.4E+02 0.0029 14.8 2.5 16 27-42 8-23 (62)
401 TIGR02947 SigH_actino RNA poly 20.0 1.6E+02 0.0036 17.3 3.0 22 22-43 145-166 (193)
No 1
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.64 E-value=2.6e-16 Score=76.21 Aligned_cols=43 Identities=26% Similarity=0.480 Sum_probs=36.3
Q ss_pred EEEccCCcHHHHHHHhCCCHHHHHHhh-CCCCCCcCCCCEEEEc
Q 037180 19 VEILRGDTLWGFSMKCGVSIDAIKEAN-GLSGDTIYYSIICIFL 61 (66)
Q Consensus 19 y~V~~GdTl~~Ia~~~~~~~~~l~~~N-~l~~~~l~~G~~l~i~ 61 (66)
|+|++|||||+||++|++++++|+++| ++....+.+||.|.||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 899999999999999999999999999 7777559999999986
No 2
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.54 E-value=3.6e-14 Score=80.38 Aligned_cols=53 Identities=21% Similarity=0.314 Sum_probs=44.9
Q ss_pred CCCccEEEEccCCcHHHHHHHhCCC--------HHHHHHhhCCCCCCcCCCCEEEEcccCC
Q 037180 13 PASCRIVEILRGDTLWGFSMKCGVS--------IDAIKEANGLSGDTIYYSIICIFLCLSS 65 (66)
Q Consensus 13 ~~~~~~y~V~~GdTl~~Ia~~~~~~--------~~~l~~~N~l~~~~l~~G~~l~i~~~~~ 65 (66)
...-..|+|++|||||+||++|+.+ ++.|++.|+++++.+++||.|.||...+
T Consensus 33 ~~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~~ 93 (103)
T PRK14125 33 KNQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLKS 93 (103)
T ss_pred CCCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCCC
Confidence 3455689999999999999999765 5677888999888899999999997643
No 3
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=99.40 E-value=8.8e-13 Score=62.99 Aligned_cols=41 Identities=37% Similarity=0.604 Sum_probs=36.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhhC-CCC-CCcCCCCEEEEc
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEANG-LSG-DTIYYSIICIFL 61 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N~-l~~-~~l~~G~~l~i~ 61 (66)
|++|||||+||++|++++++|.++|+ +.. ..+.+|+.|.|+
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip 43 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIP 43 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence 57899999999999999999999997 444 679999999987
No 4
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=99.37 E-value=3e-12 Score=60.21 Aligned_cols=44 Identities=25% Similarity=0.381 Sum_probs=40.5
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCCC-CCCcCCCCEEEEc
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGLS-GDTIYYSIICIFL 61 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~-~~~l~~G~~l~i~ 61 (66)
+|+|++|||+|+||++|+++..++.++|+.. ...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 6899999999999999999999999999984 4789999999875
No 5
>PRK06347 autolysin; Reviewed
Probab=99.36 E-value=1.6e-12 Score=90.82 Aligned_cols=46 Identities=24% Similarity=0.394 Sum_probs=43.4
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFL 61 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~ 61 (66)
...|+|++|||||+||++||+++++|++||++..+.|++||.|.|+
T Consensus 547 ~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 547 VKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred ceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence 4689999999999999999999999999999988889999999885
No 6
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.33 E-value=4.5e-12 Score=86.74 Aligned_cols=50 Identities=36% Similarity=0.484 Sum_probs=46.0
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcccC
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCLS 64 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~~ 64 (66)
...+|.|++|||||+||++||+++++|+++|++..+.|++||.|+|+-.+
T Consensus 26 sa~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~~~I~~Gq~L~Ip~~~ 75 (481)
T PRK13914 26 SASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKLQVNEVA 75 (481)
T ss_pred cCceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCcccccCCCEEEeCCCC
Confidence 44689999999999999999999999999999988899999999998654
No 7
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=99.32 E-value=3.8e-12 Score=83.64 Aligned_cols=47 Identities=13% Similarity=0.140 Sum_probs=43.6
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
..+|+|++|||||.||.+||+++.+|.++|++.+ ..|++||.|+|+.
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~ 107 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGN 107 (319)
T ss_pred CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCC
Confidence 4589999999999999999999999999999966 8899999999964
No 8
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=99.32 E-value=6.2e-12 Score=82.80 Aligned_cols=48 Identities=17% Similarity=0.195 Sum_probs=44.2
Q ss_pred CCccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEc
Q 037180 14 ASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFL 61 (66)
Q Consensus 14 ~~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~ 61 (66)
..-.+|+|++|||||.||++||+++..|+++|++....+++|+.|.||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 344689999999999999999999999999999988889999999986
No 9
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.27 E-value=1.5e-11 Score=83.88 Aligned_cols=49 Identities=14% Similarity=0.176 Sum_probs=44.0
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEccc
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCL 63 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~ 63 (66)
...+|+|++|||||+||++||+++++|++||++....|.+||+|.|...
T Consensus 401 ~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pGq~L~l~v~ 449 (456)
T PRK10783 401 DSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPGDKLTLFVK 449 (456)
T ss_pred cceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCCCEEEEecC
Confidence 3458999999999999999999999999999986668999999998753
No 10
>PRK06347 autolysin; Reviewed
Probab=99.24 E-value=2.4e-11 Score=84.98 Aligned_cols=48 Identities=25% Similarity=0.385 Sum_probs=44.6
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEccc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCL 63 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~ 63 (66)
...|+|++|||||+||++||+++++|++||++..+.|++||.|.|+..
T Consensus 479 ~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~ 526 (592)
T PRK06347 479 AKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVSAG 526 (592)
T ss_pred ceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCcccccCCcEEEEecC
Confidence 357999999999999999999999999999998888999999999864
No 11
>smart00257 LysM Lysin motif.
Probab=99.20 E-value=7.2e-11 Score=54.75 Aligned_cols=43 Identities=21% Similarity=0.332 Sum_probs=38.2
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCC-CCCCcCCCCEEEE
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGL-SGDTIYYSIICIF 60 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l-~~~~l~~G~~l~i 60 (66)
+|+|++|||+|+||++|+++..++.++|+. ....+.+|+.+.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 478999999999999999999999999995 4477899998864
No 12
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.19 E-value=1e-10 Score=80.14 Aligned_cols=49 Identities=31% Similarity=0.457 Sum_probs=45.2
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEccc
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCL 63 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~ 63 (66)
...+|+|++|||||.||++|++++++|+++|++....+++||.|.|+..
T Consensus 198 ~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIKQT 246 (481)
T ss_pred CCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEecCC
Confidence 4468999999999999999999999999999998888999999999854
No 13
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.16 E-value=1.6e-10 Score=66.30 Aligned_cols=47 Identities=28% Similarity=0.328 Sum_probs=44.2
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLC 62 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~ 62 (66)
..+|+|+.||+|+.||++|+++..+|+++|++..+.+++||.|.++.
T Consensus 66 ~~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~~ 112 (124)
T COG1388 66 VVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLPV 112 (124)
T ss_pred CceEEEecCCCHHHHHHHhCCCHHHHHHHhccCCCceecCcEEEEec
Confidence 35899999999999999999999999999999888999999999975
No 14
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=99.14 E-value=1.7e-10 Score=68.64 Aligned_cols=47 Identities=28% Similarity=0.286 Sum_probs=40.6
Q ss_pred CccEEEEccCCcHHHHHHHhC---CCHHHHHHhhC--CCC-CCcCCCCEEEEc
Q 037180 15 SCRIVEILRGDTLWGFSMKCG---VSIDAIKEANG--LSG-DTIYYSIICIFL 61 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~---~~~~~l~~~N~--l~~-~~l~~G~~l~i~ 61 (66)
...+|+|++|||||+||++|. ..+.+|+++|+ +.. ..+++||.|.||
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 556899999999999999984 45789999997 655 789999999987
No 15
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.04 E-value=6.3e-10 Score=76.01 Aligned_cols=49 Identities=24% Similarity=0.276 Sum_probs=45.1
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcccC
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLCLS 64 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~~~ 64 (66)
..+|+|++|||||+||++||++..+|.++|++....+.+||.|.|++.+
T Consensus 343 ~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~ 391 (456)
T PRK10783 343 SRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIGAGS 391 (456)
T ss_pred ceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEecCCc
Confidence 4579999999999999999999999999999977889999999999853
No 16
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=98.23 E-value=2.9e-06 Score=46.46 Aligned_cols=47 Identities=15% Similarity=0.027 Sum_probs=28.2
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhC-----CCCCCcCCCCEEEEccc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANG-----LSGDTIYYSIICIFLCL 63 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~-----l~~~~l~~G~~l~i~~~ 63 (66)
..|+|++||||..|-+++|++..++.++=. ..-..|+|||.|.+..-
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 379999999999999999999988776542 22267999999987653
No 17
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=98.13 E-value=7.9e-07 Score=56.98 Aligned_cols=46 Identities=37% Similarity=0.436 Sum_probs=39.5
Q ss_pred EEEEccCCcHHHHHHHh---CCCHHHHHHhhC---CCC-CCcCCCCEEEEccc
Q 037180 18 IVEILRGDTLWGFSMKC---GVSIDAIKEANG---LSG-DTIYYSIICIFLCL 63 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~---~~~~~~l~~~N~---l~~-~~l~~G~~l~i~~~ 63 (66)
+|+|+.|||||.|++++ +..+..|..+|+ +.. +.|.+||.++||-.
T Consensus 212 ~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 212 TNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred EEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 89999999999999986 455777999998 555 89999999999854
No 18
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=97.96 E-value=8.2e-06 Score=43.75 Aligned_cols=40 Identities=28% Similarity=0.417 Sum_probs=31.4
Q ss_pred CcHHHHHHHh---C-CCHH----HHHHhhC---C-CC-CCcCCCCEEEEcccC
Q 037180 25 DTLWGFSMKC---G-VSID----AIKEANG---L-SG-DTIYYSIICIFLCLS 64 (66)
Q Consensus 25 dTl~~Ia~~~---~-~~~~----~l~~~N~---l-~~-~~l~~G~~l~i~~~~ 64 (66)
||||+||++| + +++. .|.+.|+ . .. +.|++|+.|.||..+
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~~ 53 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSEE 53 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCHH
Confidence 8999999999 4 6766 5667885 1 22 789999999999754
No 19
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.87 E-value=6.2e-05 Score=49.76 Aligned_cols=46 Identities=15% Similarity=0.012 Sum_probs=39.3
Q ss_pred cEEEEccCC--cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 17 RIVEILRGD--TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~Gd--Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
.+|+|+++| +|.+||++|++...+|+++|+--+ ....+|++|.|+.
T Consensus 38 ~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~ 86 (310)
T PRK10190 38 LTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQ 86 (310)
T ss_pred EEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecC
Confidence 468998866 699999999999999999998544 5568999999985
No 20
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.85 E-value=7.1e-05 Score=49.38 Aligned_cols=46 Identities=15% Similarity=0.081 Sum_probs=39.3
Q ss_pred cEEEEccCC--cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 17 RIVEILRGD--TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~Gd--Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
..|+|++|+ +|.+||++|++...+|+++|+--+ ....+|++|.|+.
T Consensus 41 ~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~ 89 (306)
T PRK10260 41 QVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQ 89 (306)
T ss_pred EEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCC
Confidence 479999966 599999999999999999998544 5567999999975
No 21
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=97.61 E-value=0.00011 Score=50.25 Aligned_cols=52 Identities=21% Similarity=0.222 Sum_probs=43.3
Q ss_pred CCCccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEcccC
Q 037180 13 PASCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFLCLS 64 (66)
Q Consensus 13 ~~~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~~~~ 64 (66)
++...+|.|++|||+++||++++++.+++..+|.+.. ..+.+|=.+.++...
T Consensus 46 ~~~~~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~ 98 (423)
T COG3858 46 PPSGHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSAR 98 (423)
T ss_pred CCcceEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCCC
Confidence 4455789999999999999999999999999997655 667777777777553
No 22
>PRK11649 putative peptidase; Provisional
Probab=97.40 E-value=0.00084 Score=46.15 Aligned_cols=46 Identities=13% Similarity=0.107 Sum_probs=38.2
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCC-C-CCCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGL-S-GDTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l-~-~~~l~~G~~l~i~~ 62 (66)
..|+|++||||.+|-+++|++..++.++-.. . ...|++||.+.+..
T Consensus 96 ~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~ 143 (439)
T PRK11649 96 HEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTL 143 (439)
T ss_pred EEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEE
Confidence 3799999999999999999999998877432 2 26799999998753
No 23
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=96.95 E-value=0.0016 Score=47.17 Aligned_cols=51 Identities=18% Similarity=0.317 Sum_probs=38.4
Q ss_pred CCCccEEEEccCCcHHHHHHHh----CCCHHH----HHHhhCC---CC--CCcCCCCEEEEccc
Q 037180 13 PASCRIVEILRGDTLWGFSMKC----GVSIDA----IKEANGL---SG--DTIYYSIICIFLCL 63 (66)
Q Consensus 13 ~~~~~~y~V~~GdTl~~Ia~~~----~~~~~~----l~~~N~l---~~--~~l~~G~~l~i~~~ 63 (66)
.....+|++++|||||+||.+. +++.+. |.+.|+- +. +.++.|.+|+|+..
T Consensus 185 ~a~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 185 AAPGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred CCCCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 4566799999999999999986 344444 6677852 22 57899999999864
No 24
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=96.80 E-value=0.0062 Score=38.86 Aligned_cols=50 Identities=10% Similarity=0.082 Sum_probs=42.3
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC-----CCcCCCCEEEEcccC
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAIKEANGLSG-----DTIYYSIICIFLCLS 64 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~-----~~l~~G~~l~i~~~~ 64 (66)
.-.+|+|+.|+||..+-+.+++++.++.++-.... ..|+.||.|.|+...
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 44689999999999999999999999988875422 578999999998754
No 25
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=95.89 E-value=0.026 Score=28.99 Aligned_cols=46 Identities=24% Similarity=0.318 Sum_probs=34.4
Q ss_pred EEEEccCCcHHHHHHHh-CCC---HHHHHHhhC-CCC--CCcCCCCEEEEcccC
Q 037180 18 IVEILRGDTLWGFSMKC-GVS---IDAIKEANG-LSG--DTIYYSIICIFLCLS 64 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~-~~~---~~~l~~~N~-l~~--~~l~~G~~l~i~~~~ 64 (66)
.|+. .||||-.|+.|+ |.. .+.++++|+ +.. ..+..|..|.+|-..
T Consensus 3 v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~ 55 (60)
T PF05489_consen 3 VYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP 55 (60)
T ss_pred EEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence 3444 899999999986 553 367899996 333 567889999998654
No 26
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=95.78 E-value=0.005 Score=42.29 Aligned_cols=46 Identities=13% Similarity=0.065 Sum_probs=40.9
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i~~ 62 (66)
..|.|++||++..|+++|+.+..+|...|.+..+.+-+||++.|+.
T Consensus 2 ~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~d~~~~~q~~~v~~ 47 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTNDDLVDGQTFVVPP 47 (423)
T ss_pred EEEEccCCceeeeehhhccccccccccccccccccccCceeEEECC
Confidence 3689999999999999999999999777777668899999999986
No 27
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=95.72 E-value=0.024 Score=38.73 Aligned_cols=48 Identities=19% Similarity=0.276 Sum_probs=38.2
Q ss_pred CCccEEEEccCCcHHHHHHHh-CC--CHHHHHHhhCCCC-CCcCCCCEEEEc
Q 037180 14 ASCRIVEILRGDTLWGFSMKC-GV--SIDAIKEANGLSG-DTIYYSIICIFL 61 (66)
Q Consensus 14 ~~~~~y~V~~GdTl~~Ia~~~-~~--~~~~l~~~N~l~~-~~l~~G~~l~i~ 61 (66)
-.....+|++|+|+.++|.+. |+ +++.+.-+|.+.. ..+.||+.+.|-
T Consensus 426 lrirvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 426 LRIRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred eEEEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 344568899999999999885 43 4666778899877 889999999773
No 28
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=95.32 E-value=0.014 Score=33.18 Aligned_cols=33 Identities=33% Similarity=0.407 Sum_probs=29.9
Q ss_pred HHHHhCCCHHHHHHhhCCC--CCCcCCCCEEEEcc
Q 037180 30 FSMKCGVSIDAIKEANGLS--GDTIYYSIICIFLC 62 (66)
Q Consensus 30 Ia~~~~~~~~~l~~~N~l~--~~~l~~G~~l~i~~ 62 (66)
||.+|+++++++.++|.+. .+.+.+|+++.++.
T Consensus 1 ia~~~~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~ 35 (124)
T COG1388 1 IASKYGVSVKALKKANALTGKSDAIKPGQVLKIPG 35 (124)
T ss_pred CcccccccHHHHHHHhcccCCCCccccCceEEccC
Confidence 5788999999999999987 78999999999885
No 29
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=93.82 E-value=0.22 Score=31.30 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=40.8
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHhhCCCCC-CcCCCCEEEEccc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEANGLSGD-TIYYSIICIFLCL 63 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~~-~l~~G~~l~i~~~ 63 (66)
..+.++.|+++..++++++.+...+...|..... .+..|+.+.++..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeeccc
Confidence 3588999999999999999999999999987664 7888998888764
No 30
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.75 E-value=0.14 Score=24.43 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=20.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..|.++..+|++||++...+..|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 468899999999999999988774
No 31
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=92.11 E-value=0.14 Score=31.87 Aligned_cols=32 Identities=28% Similarity=0.343 Sum_probs=28.7
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGLSG 49 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~ 49 (66)
..++++||||..||-+|.....++.+.|++..
T Consensus 11 ~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r 42 (186)
T KOG2850|consen 11 EVTIQEGDTLQAIALNYESDVADIKRVNNDDR 42 (186)
T ss_pred eeeeccCchhhhHHhhcccchhhheeeccchh
Confidence 56899999999999999999999999996543
No 32
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. 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; PDB: 2JN6_A 2RN7_A.
Probab=91.20 E-value=0.14 Score=26.42 Aligned_cols=25 Identities=12% Similarity=0.231 Sum_probs=21.1
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
...|.|+.++|++||+++..|..|=
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHH
Confidence 3679999999999999999998773
No 33
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=90.28 E-value=0.45 Score=22.59 Aligned_cols=24 Identities=17% Similarity=0.189 Sum_probs=17.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
...|-+..+||+.+|++...+.+.
T Consensus 18 ~~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 18 YAEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HHTT--HHHHHHHTTS-HHHHHHH
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 357899999999999999988764
No 34
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=87.38 E-value=0.83 Score=26.04 Aligned_cols=25 Identities=16% Similarity=0.018 Sum_probs=22.5
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+..|.+..++|++||++...|..|=
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 5679999999999999999999883
No 35
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=87.15 E-value=0.99 Score=21.39 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=17.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|.+...||+.+|++...+.+|
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w 37 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRW 37 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 34999999999999999998876
No 36
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.71 E-value=1.1 Score=30.13 Aligned_cols=46 Identities=17% Similarity=-0.069 Sum_probs=36.7
Q ss_pred cEEEEccCCcHHHHHHHhCCCHH---HHHHhhCCCC-CCcCCCCEEEEcc
Q 037180 17 RIVEILRGDTLWGFSMKCGVSID---AIKEANGLSG-DTIYYSIICIFLC 62 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~---~l~~~N~l~~-~~l~~G~~l~i~~ 62 (66)
-+|.|+.||||-.+...|-...+ .++..|...+ ..+.+|..|.|+.
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~ 55 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPL 55 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCC
Confidence 68999999999999999966544 4566787755 6788898888875
No 37
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=84.50 E-value=1.1 Score=21.47 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=16.9
Q ss_pred EccC-CcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRG-DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~G-dTl~~Ia~~~~~~~~~l~~~ 44 (66)
|+.| -++...|++||++...|.+.
T Consensus 12 v~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HHTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 3456 89999999999999988753
No 38
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=84.04 E-value=2.2 Score=20.29 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=18.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|+.+||+.+|++...+...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 46889999999999999887643
No 39
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.62 E-value=1.6 Score=24.38 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=20.2
Q ss_pred EccCCcHHHHHHHhCC-CHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGV-SIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~-~~~~l~~~ 44 (66)
.++|.|...||++||+ +...|..|
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHH
Confidence 4579999999999996 88887754
No 40
>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=83.20 E-value=0.63 Score=23.02 Aligned_cols=24 Identities=17% Similarity=0.302 Sum_probs=16.7
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+..|.+..+||++||++...+..+
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 467889999999999987776543
No 41
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=81.58 E-value=2.8 Score=17.10 Aligned_cols=22 Identities=18% Similarity=0.305 Sum_probs=18.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
..|.+...+++.+|++...+..
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4678999999999999887764
No 42
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=81.08 E-value=2.7 Score=19.80 Aligned_cols=23 Identities=13% Similarity=0.263 Sum_probs=14.9
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.+.|.+...||+++|.+...+.+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHH
Confidence 35799999999999999887754
No 43
>PHA00675 hypothetical protein
Probab=80.89 E-value=2.6 Score=22.84 Aligned_cols=24 Identities=21% Similarity=0.091 Sum_probs=21.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+.|.+...||++||++...+...-
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHH
Confidence 689999999999999999887654
No 44
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=80.08 E-value=3 Score=19.80 Aligned_cols=21 Identities=14% Similarity=0.261 Sum_probs=17.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.-|+.+||+.+|+++..+.+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHH
Confidence 348999999999999988753
No 45
>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=79.88 E-value=4.5 Score=18.41 Aligned_cols=36 Identities=14% Similarity=-0.104 Sum_probs=24.2
Q ss_pred cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEc
Q 037180 26 TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFL 61 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~ 61 (66)
|+.++|+.+|++...+.++-.-.. .....|....++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~ 39 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGELPAYRVGRHYRIP 39 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCCCCeEEeCCeEEEe
Confidence 567899999999999988754332 223336655553
No 46
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=78.56 E-value=3 Score=20.68 Aligned_cols=23 Identities=13% Similarity=0.258 Sum_probs=15.9
Q ss_pred ccCCcHHHHHHHhC-CCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCG-VSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~-~~~~~l~~~ 44 (66)
..|.+..+|++.|. ++.+++..+
T Consensus 29 ~~G~s~eeI~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 29 AAGESPEEIAEDYPSLTLEDIRAA 52 (56)
T ss_dssp HTT--HHHHHHHSTT--HHHHHHH
T ss_pred HcCCCHHHHHHHCCCCCHHHHHHH
Confidence 77999999999997 898888754
No 47
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=78.22 E-value=2.8 Score=21.45 Aligned_cols=20 Identities=20% Similarity=0.302 Sum_probs=15.3
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-++.+||++|+++++.+..+
T Consensus 15 ~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 15 VSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp EEHHHHHHHTT--HHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHH
Confidence 47889999999999988765
No 48
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=76.11 E-value=3.9 Score=22.04 Aligned_cols=22 Identities=27% Similarity=0.487 Sum_probs=16.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
+.|-||..||+.+|++...+..
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~n 34 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRN 34 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHHH
Confidence 4799999999999999877663
No 49
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=75.71 E-value=3.9 Score=22.89 Aligned_cols=20 Identities=25% Similarity=0.290 Sum_probs=14.9
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
|.+...+|++||++...+.+
T Consensus 72 G~n~~eLA~kyglS~r~I~~ 91 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYR 91 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHH
Confidence 88999999999999887764
No 50
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=75.32 E-value=4.7 Score=20.70 Aligned_cols=23 Identities=26% Similarity=0.201 Sum_probs=20.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHhhC
Q 037180 24 GDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+-++-+||.++|++...|..|-.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhh
Confidence 35889999999999999998864
No 51
>PF12471 GTP_CH_N: GTP cyclohydrolase N terminal ; InterPro: IPR022163 This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N-terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=75.01 E-value=2.6 Score=26.44 Aligned_cols=25 Identities=20% Similarity=0.179 Sum_probs=20.0
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|.+==-|.+||+|||++..+|.+.
T Consensus 166 AvEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 166 AVEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred EecccccchhhHHHcCCCHHHHHHH
Confidence 4555556789999999999999864
No 52
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=73.06 E-value=2.9 Score=23.72 Aligned_cols=25 Identities=20% Similarity=0.263 Sum_probs=21.5
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+..|.+...+|++|+++...+.+|=
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W~ 39 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRWL 39 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHHH
Confidence 4568999999999999998888774
No 53
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=72.64 E-value=6.5 Score=17.69 Aligned_cols=20 Identities=20% Similarity=0.018 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++.++|+.+|++...+..|=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998874
No 54
>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=72.06 E-value=5 Score=19.97 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=23.1
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHH
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
..+|-+.++-|+.++|+.+|++...+-.
T Consensus 15 ~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 15 LGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred cCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 3467788899999999999999887653
No 55
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=71.61 E-value=5.6 Score=21.16 Aligned_cols=27 Identities=22% Similarity=0.366 Sum_probs=18.7
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHH
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
...+.+.+|+|+.+.+.+.|+.+-.+.
T Consensus 10 G~~v~~~~G~til~al~~~gi~ip~~c 36 (82)
T PF13510_consen 10 GKPVEVPPGETILEALLAAGIDIPRLC 36 (82)
T ss_dssp TEEEEEEET-BHHHHHHHTT--B-EET
T ss_pred CEEEEEcCCCHHHHHHHHCCCeEEEee
Confidence 457899999999999999887655443
No 56
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=70.32 E-value=9.4 Score=17.62 Aligned_cols=23 Identities=22% Similarity=0.205 Sum_probs=19.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|.+...||+.+|++...+...
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 56889999999999999887654
No 57
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=69.24 E-value=7.5 Score=23.88 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=18.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.+.|.++..+|++||++..++.+
T Consensus 30 ~~~~~sv~~vS~~ygi~~~RV~A 52 (172)
T PF12298_consen 30 MQDGKSVREVSQKYGIKIQRVEA 52 (172)
T ss_pred HhCCCCHHHHHHHhCCCHHHHHH
Confidence 36788999999999999766543
No 58
>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=68.90 E-value=8.5 Score=17.69 Aligned_cols=20 Identities=20% Similarity=0.198 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++.++|+.+|++...|..|-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998874
No 59
>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=67.88 E-value=8.3 Score=19.11 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|++...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998764
No 60
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=67.71 E-value=10 Score=18.20 Aligned_cols=19 Identities=21% Similarity=0.333 Sum_probs=15.8
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
|+.+||++.|++...+-++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ 19 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRV 19 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 6889999999998886543
No 61
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=67.37 E-value=6.4 Score=19.13 Aligned_cols=23 Identities=13% Similarity=0.236 Sum_probs=18.9
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.+.|.+...+|.+||++....-+
T Consensus 16 LR~~~~~~~La~~FgIs~stvsr 38 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSR 38 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHH
Confidence 46788999999999999877554
No 62
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=67.06 E-value=6.9 Score=27.86 Aligned_cols=26 Identities=31% Similarity=0.410 Sum_probs=21.2
Q ss_pred EccCCcHHHHHHHhCCCHHHHH----HhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK----EANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~----~~N~ 46 (66)
+.++|||.++|++.|++.+.|. ++|.
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~ 450 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNE 450 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 4579999999999999977654 6773
No 63
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=66.95 E-value=9.3 Score=18.16 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=14.5
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|-+..+||+.+|++...+..
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKR 45 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHH
Confidence 578899999999999988764
No 64
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=66.84 E-value=10 Score=20.78 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=22.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhhC
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
..|-+-.+|++++|++...|-+.|+
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4788999999999999999998874
No 65
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=66.80 E-value=7.3 Score=27.20 Aligned_cols=26 Identities=38% Similarity=0.450 Sum_probs=21.0
Q ss_pred EccCCcHHHHHHHhCCCHHHHH----HhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK----EANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~----~~N~ 46 (66)
+.+.|||.++|++.|++.+.|. ++|.
T Consensus 372 ~~kaDTleELA~k~gid~~~L~~Tv~~yN~ 401 (513)
T PRK12837 372 WRTADTLEELAAKIGVPADALTATVARFNG 401 (513)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 4478999999999999977654 6773
No 66
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=66.47 E-value=6.2 Score=24.24 Aligned_cols=27 Identities=15% Similarity=0.289 Sum_probs=23.5
Q ss_pred EEEccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 19 VEILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 19 y~V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-.++.|.|..++|..+|++++.+.+.-
T Consensus 64 arIRaGas~eeVA~~~G~~~~rV~rfa 90 (170)
T PF11268_consen 64 ARIRAGASAEEVAEEAGVPVERVRRFA 90 (170)
T ss_pred HHHHCCCCHHHHHHHhCCCHHHhhhcc
Confidence 458899999999999999999987653
No 67
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=66.17 E-value=9.5 Score=18.92 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++.++|+.+|++...|..|-
T Consensus 2 s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999874
No 68
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=65.50 E-value=9.8 Score=18.91 Aligned_cols=20 Identities=20% Similarity=0.159 Sum_probs=17.3
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
|..++|+.+|++...|..|=
T Consensus 2 ti~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999999875
No 69
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=65.24 E-value=10 Score=17.35 Aligned_cols=21 Identities=19% Similarity=0.115 Sum_probs=16.2
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|..++|+.+|+++..|..+=.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356799999999999987753
No 70
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=64.50 E-value=11 Score=18.92 Aligned_cols=24 Identities=17% Similarity=0.291 Sum_probs=18.3
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+..-..+...+++||++.++|.++
T Consensus 17 ~~e~~ev~ywa~~~gvt~~~L~~A 40 (57)
T PF12244_consen 17 LSEPYEVRYWAKRFGVTEEQLREA 40 (57)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHH
Confidence 344445678899999999998865
No 71
>PRK12839 hypothetical protein; Provisional
Probab=63.70 E-value=8.9 Score=27.35 Aligned_cols=26 Identities=31% Similarity=0.552 Sum_probs=20.9
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N~ 46 (66)
+.++|||.++|++.|++.+.| .++|.
T Consensus 424 ~~kadTleELA~k~gid~~~L~~TV~~yN~ 453 (572)
T PRK12839 424 LTRGRTIEELAEKCGIDPAGLEATVAEFNE 453 (572)
T ss_pred EEECCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 346899999999999997665 46774
No 72
>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=62.71 E-value=6.9 Score=18.98 Aligned_cols=19 Identities=16% Similarity=0.189 Sum_probs=15.0
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
++.++|+.+|++..++.+.
T Consensus 5 ~V~elAk~l~v~~~~ii~~ 23 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKK 23 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHHH
Confidence 4568999999999987643
No 73
>smart00351 PAX Paired Box domain.
Probab=62.68 E-value=13 Score=21.27 Aligned_cols=23 Identities=17% Similarity=0.091 Sum_probs=20.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|.+...||++||++...+..|
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kw 53 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKI 53 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57999999999999998877665
No 74
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=62.63 E-value=13 Score=20.76 Aligned_cols=21 Identities=19% Similarity=0.290 Sum_probs=18.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
+.|-||..|++++|++...|.
T Consensus 19 KrG~sLa~lsr~~Gls~~TL~ 39 (92)
T PRK10344 19 KKGTSMAAESRRNGLSSSTLA 39 (92)
T ss_pred HcCCcHHHHHHHcCCChHHHH
Confidence 569999999999999987765
No 75
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=62.52 E-value=15 Score=19.03 Aligned_cols=23 Identities=17% Similarity=0.283 Sum_probs=18.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-++-+||+.+|++..+...+
T Consensus 11 E~g~~FveIAr~~~i~a~e~a~~ 33 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEVAKA 33 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHHHHH
Confidence 34889999999999998876543
No 76
>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=62.45 E-value=10 Score=18.82 Aligned_cols=23 Identities=35% Similarity=0.508 Sum_probs=15.6
Q ss_pred ccCCcH---HHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTL---WGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl---~~Ia~~~~~~~~~l~~~ 44 (66)
++|+.| .+||++|+++...+.++
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~a 44 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREA 44 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHH
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHH
Confidence 456544 78999999998776643
No 77
>PF14493 HTH_40: Helix-turn-helix domain
Probab=62.20 E-value=13 Score=19.96 Aligned_cols=23 Identities=13% Similarity=0.123 Sum_probs=19.7
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.+.|-|+.+||++-+++...+..
T Consensus 10 ~~~G~si~eIA~~R~L~~sTI~~ 32 (91)
T PF14493_consen 10 FQKGLSIEEIAKIRGLKESTIYG 32 (91)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHH
Confidence 46799999999999999888764
No 78
>PF12728 HTH_17: Helix-turn-helix domain
Probab=62.18 E-value=16 Score=17.15 Aligned_cols=36 Identities=8% Similarity=-0.142 Sum_probs=24.9
Q ss_pred cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEEc
Q 037180 26 TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIFL 61 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i~ 61 (66)
|..++|+.+|++...+.++=.-.. ..+..|....++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g~i~~~~~g~~~~~~ 39 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQGKIPPFKIGRKWRIP 39 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCeEEeCCEEEEe
Confidence 567899999999999888753322 333466666654
No 79
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=62.09 E-value=10 Score=20.72 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=22.6
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..|.|..+||+++|++...+.++.+
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46799999999999999999887654
No 80
>PF08984 DUF1858: Domain of unknown function (DUF1858); InterPro: IPR015077 This protein has no known function. It is found in various hypothetical bacterial proteins. ; PDB: 2K53_A 2K5E_A 2FI0_A.
Probab=61.98 E-value=11 Score=18.73 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=15.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-+..|+...|+.+|++++.|.
T Consensus 39 ~~~~Tl~~aa~~~gid~~~li 59 (59)
T PF08984_consen 39 AKFETLEQAAKMHGIDLEKLI 59 (59)
T ss_dssp HHHSBHHHHHHHHT--HHHHH
T ss_pred cccCCHHHHHHHcCCCHHHhC
Confidence 456899999999999998874
No 81
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=61.82 E-value=13 Score=20.37 Aligned_cols=23 Identities=22% Similarity=0.328 Sum_probs=19.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-+..+||+.+|++...+...
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 36999999999999999887753
No 82
>PF13551 HTH_29: Winged helix-turn helix
Probab=61.42 E-value=11 Score=20.31 Aligned_cols=24 Identities=17% Similarity=0.221 Sum_probs=19.8
Q ss_pred EccCC-cHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGD-TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~Gd-Tl~~Ia~~~~~~~~~l~~~ 44 (66)
+..|. |...||+.+|++...+.+|
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~ 32 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRW 32 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHH
Confidence 35677 5999999999998887765
No 83
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=60.97 E-value=9.8 Score=21.14 Aligned_cols=26 Identities=12% Similarity=0.109 Sum_probs=19.7
Q ss_pred EccC-CcHHHHHHHhCCCHHHHHHhhC
Q 037180 21 ILRG-DTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 21 V~~G-dTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|..| -|+.+..++|+++.++|..|=.
T Consensus 45 V~~Glis~~EA~~rY~Ls~eEf~~W~~ 71 (90)
T PF06627_consen 45 VRGGLISVEEACRRYGLSEEEFESWQR 71 (90)
T ss_dssp HHCTTS-HHHHHHCTTSSHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3344 5677888999999999999863
No 84
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=60.86 E-value=17 Score=18.23 Aligned_cols=24 Identities=13% Similarity=0.145 Sum_probs=20.5
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhhC
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
.|=+..+||+..|++...+..|-.
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHH
Confidence 488899999999999888887754
No 85
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=60.79 E-value=13 Score=22.08 Aligned_cols=25 Identities=20% Similarity=0.155 Sum_probs=21.3
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+..|.+.-.||++||++...+..|=
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv 42 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWV 42 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHH
Confidence 3579999999999999999887663
No 86
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. 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-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=60.15 E-value=15 Score=18.33 Aligned_cols=20 Identities=20% Similarity=0.137 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+.+|++...|..|=
T Consensus 2 ~i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999883
No 87
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=59.62 E-value=15 Score=22.54 Aligned_cols=24 Identities=21% Similarity=0.075 Sum_probs=21.3
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
-+|.-++..+|++|++++.++.+.
T Consensus 24 ~qPdg~~eamA~~~~v~~~eIv~a 47 (176)
T COG3721 24 TQPDGTLEAMAEQYNVTELEIVRA 47 (176)
T ss_pred hCCCCcHHHHHHHhCCCHHHHHHh
Confidence 477889999999999999998875
No 88
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=58.75 E-value=14 Score=18.22 Aligned_cols=19 Identities=21% Similarity=0.209 Sum_probs=15.6
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
-++.++|++|+++...+.+
T Consensus 15 ~s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRR 33 (57)
T ss_pred EEHHHHHHHHCcCHHHHHH
Confidence 3677999999999888763
No 89
>PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=58.72 E-value=12 Score=26.42 Aligned_cols=26 Identities=42% Similarity=0.639 Sum_probs=21.0
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N~ 46 (66)
+.++|||.++|++.|++.+.| .++|.
T Consensus 413 ~~kadTleELA~~~gid~~~L~aTV~~yN~ 442 (557)
T PRK07843 413 IVKADTLAELAAKIGVPADALTATVQRFNG 442 (557)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 457899999999999997665 46774
No 90
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.38 E-value=12 Score=22.45 Aligned_cols=20 Identities=25% Similarity=0.328 Sum_probs=17.5
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-++|.+||+++|++..++..
T Consensus 90 ~~~l~~la~~~Gld~~El~~ 109 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELLK 109 (143)
T ss_pred hhHHHHHHHHhCCCHHHHHH
Confidence 48999999999999988763
No 91
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=57.98 E-value=19 Score=16.63 Aligned_cols=23 Identities=22% Similarity=0.186 Sum_probs=19.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-+...||+.++++...+...
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999998887654
No 92
>PRK06481 fumarate reductase flavoprotein subunit; Validated
Probab=57.44 E-value=14 Score=25.83 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=20.9
Q ss_pred EccCCcHHHHHHHhCCCHHHHH----HhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK----EANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~----~~N~ 46 (66)
+.++|||.++|++.|++.+.|. ++|.
T Consensus 375 ~~kadTleeLA~~~gid~~~L~~tv~~yN~ 404 (506)
T PRK06481 375 VEEGKTIDELAKKINVPAETLTKTLDTWNK 404 (506)
T ss_pred EEEcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4468999999999999987755 5673
No 93
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-like proteins in this group appear to lack the long dimerization helix seen
Probab=56.96 E-value=17 Score=18.12 Aligned_cols=20 Identities=10% Similarity=0.209 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|++.|++...|..|-
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye 21 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999884
No 94
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=56.59 E-value=19 Score=16.26 Aligned_cols=21 Identities=19% Similarity=0.112 Sum_probs=14.3
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.+-++.+||.+.|++..-+.+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r 27 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSR 27 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
Confidence 356888999999998877664
No 95
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=56.55 E-value=16 Score=20.06 Aligned_cols=25 Identities=16% Similarity=0.008 Sum_probs=20.7
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
|..|-++..+|+.||++......|=
T Consensus 22 v~~g~~~a~aA~~~gVS~~Ta~kW~ 46 (85)
T PF13011_consen 22 VEQGWPVAHAAAEFGVSRRTAYKWL 46 (85)
T ss_pred HHcCCcHHHHHHHhCCCHHHHHHHH
Confidence 4568899999999999988777664
No 96
>PRK06134 putative FAD-binding dehydrogenase; Reviewed
Probab=56.42 E-value=14 Score=26.28 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=20.8
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N~ 46 (66)
+.++|||.++|++.|++.+.| .++|.
T Consensus 426 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 455 (581)
T PRK06134 426 LKRGASLEELARACGIDPDGLEATVARYNR 455 (581)
T ss_pred EEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 456899999999999997665 46673
No 97
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=55.60 E-value=20 Score=21.31 Aligned_cols=24 Identities=21% Similarity=0.062 Sum_probs=21.1
Q ss_pred ccC--CcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRG--DTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~G--dTl~~Ia~~~~~~~~~l~~~N 45 (66)
.++ -|+..|++..|+++..|..|=
T Consensus 42 ~p~~~ati~eV~e~tgVs~~~I~~~I 67 (137)
T TIGR03826 42 HENRQATVSEIVEETGVSEKLILKFI 67 (137)
T ss_pred CCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 466 899999999999999999874
No 98
>PRK12842 putative succinate dehydrogenase; Reviewed
Probab=55.48 E-value=14 Score=26.15 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=20.8
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N~ 46 (66)
+.++|||.++|++.|++.+.| .++|.
T Consensus 423 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 452 (574)
T PRK12842 423 LIKGDTLAELAGKAGIDAAGLEATVRRYNE 452 (574)
T ss_pred EEEcCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 456899999999999996664 46774
No 99
>PRK12843 putative FAD-binding dehydrogenase; Reviewed
Probab=55.43 E-value=15 Score=26.14 Aligned_cols=26 Identities=23% Similarity=0.256 Sum_probs=20.7
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N~ 46 (66)
+.+.|||.++|++.|++.+.| .++|.
T Consensus 428 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 457 (578)
T PRK12843 428 LTVASTLDELAPKLGIDPAALAATVQRHNQ 457 (578)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 346899999999999997665 46673
No 100
>cd00131 PAX Paired Box domain
Probab=54.54 E-value=16 Score=21.09 Aligned_cols=24 Identities=17% Similarity=0.070 Sum_probs=20.5
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+..|.+...||++|+++...+.+|
T Consensus 30 ~~~G~s~~~iA~~~~Vs~~tV~r~ 53 (128)
T cd00131 30 AQSGIRPCDISRQLRVSHGCVSKI 53 (128)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHH
Confidence 367999999999999998877665
No 101
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=54.14 E-value=23 Score=16.57 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=15.3
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 037180 26 TLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~ 43 (66)
+..++|++|+++...+.+
T Consensus 22 s~~~la~~~~vs~~tv~~ 39 (60)
T smart00345 22 SERELAAQLGVSRTTVRE 39 (60)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 678999999999877665
No 102
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=53.73 E-value=16 Score=22.74 Aligned_cols=26 Identities=12% Similarity=0.234 Sum_probs=22.7
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
.|..|+++-++|++.|++.+++.+.-
T Consensus 28 ~vsaG~iFR~~A~e~gmsl~ef~~~A 53 (179)
T COG1102 28 LVSAGTIFREMARERGMSLEEFSRYA 53 (179)
T ss_pred eeeccHHHHHHHHHcCCCHHHHHHHH
Confidence 46789999999999999999987664
No 103
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=53.20 E-value=22 Score=15.88 Aligned_cols=22 Identities=14% Similarity=0.205 Sum_probs=18.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-+...||+.+|++...+..+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6888999999999999887654
No 104
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=53.05 E-value=23 Score=17.48 Aligned_cols=18 Identities=22% Similarity=0.241 Sum_probs=13.7
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 037180 26 TLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~ 43 (66)
++..+|+++|++...+.+
T Consensus 3 ~~~~la~~~~~s~~~l~~ 20 (84)
T smart00342 3 TLEDLAEALGMSPRHLQR 20 (84)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 577888888888777654
No 105
>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated
Probab=52.88 E-value=17 Score=22.98 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=23.0
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHH
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
...+.+.+|+|+.+.+.+.|+.+..+-.
T Consensus 10 g~~~~~~~g~til~a~~~~gi~ip~~C~ 37 (234)
T PRK07569 10 DQLVSAREGETLLEAAREAGIPIPTLCH 37 (234)
T ss_pred CEEEEeCCCCHHHHHHHHcCCCCCcCcC
Confidence 4568999999999999999988766543
No 106
>PRK12844 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=52.59 E-value=18 Score=25.65 Aligned_cols=25 Identities=24% Similarity=0.334 Sum_probs=20.2
Q ss_pred EccCCcHHHHHHHhCCCHHHHH----Hhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK----EAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~----~~N 45 (66)
+.++|||.++|++.|++.+.|. ++|
T Consensus 406 ~~kadTleELA~k~gid~~~L~atv~~yN 434 (557)
T PRK12844 406 MKRADTIEELAGKTGIDPAGLAATVERFN 434 (557)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3468999999999999976654 567
No 107
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=52.19 E-value=25 Score=18.87 Aligned_cols=24 Identities=13% Similarity=0.331 Sum_probs=19.7
Q ss_pred EccCCcHHHHHHHhC-CCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCG-VSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~-~~~~~l~~~ 44 (66)
.+.|.|..+|+..|. ++.++|.++
T Consensus 40 l~~G~s~eeil~dyp~Lt~~dI~aa 64 (79)
T COG2442 40 LAAGESIEEILADYPDLTLEDIRAA 64 (79)
T ss_pred HHCCCCHHHHHHhCCCCCHHHHHHH
Confidence 467899999999997 888888764
No 108
>TIGR01813 flavo_cyto_c flavocytochrome c. This model describes a family of redox proteins related to the succinate dehydrogenases and fumarate reductases of E. coli, mitochondria, and other well-characterized systems. A member of this family from Shewanella frigidimarina NCIMB400 is characterized as a water-soluble periplasmic protein with four heme groups, a non-covalently bound FAD, and essentially unidirectional fumarate reductase activity. At least seven distinct members of this family are found in Shewanella oneidensis, a species able to use a wide variety of pathways for respiraton.
Probab=51.78 E-value=19 Score=24.35 Aligned_cols=25 Identities=28% Similarity=0.504 Sum_probs=20.3
Q ss_pred EccCCcHHHHHHHhCCCHHHH----HHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAI----KEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l----~~~N 45 (66)
+.+.|||.++|++.|++.+.| .++|
T Consensus 317 ~~~adtleeLa~~~g~~~~~l~~tv~~yN 345 (439)
T TIGR01813 317 AYKGDSLEELAKQFGIPAAALKKTVKDYN 345 (439)
T ss_pred EEEeCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 346899999999999987665 4777
No 109
>TIGR02007 fdx_isc ferredoxin, 2Fe-2S type, ISC system. This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes.
Probab=51.75 E-value=23 Score=19.73 Aligned_cols=28 Identities=21% Similarity=0.429 Sum_probs=23.0
Q ss_pred CCccEEEEccCCcHHHHHHHhCCCHHHH
Q 037180 14 ASCRIVEILRGDTLWGFSMKCGVSIDAI 41 (66)
Q Consensus 14 ~~~~~y~V~~GdTl~~Ia~~~~~~~~~l 41 (66)
+...++.+.+|++|-+.+++.|+.+..-
T Consensus 13 p~~~~~~~~~g~tLL~a~~~~gi~i~~~ 40 (110)
T TIGR02007 13 PEGAVVEAKPGETILDVALDNGIEIEHA 40 (110)
T ss_pred CCCeEEEECCCChHHHHHHHcCCCcccc
Confidence 3556789999999999999999886543
No 110
>PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=51.69 E-value=19 Score=25.79 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=20.7
Q ss_pred EccCCcHHHHHHHhCCCHHH----HHHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDA----IKEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~----l~~~N~ 46 (66)
+.+.|||.++|++.|++.+. +.++|.
T Consensus 427 ~~kAdTleeLA~~~gida~~L~aTV~~yN~ 456 (584)
T PRK12835 427 VKKADTWDELAAKIGVPAENLRATAERFNG 456 (584)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 34689999999999999665 457784
No 111
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=51.51 E-value=22 Score=19.33 Aligned_cols=23 Identities=17% Similarity=0.322 Sum_probs=19.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHhhC
Q 037180 24 GDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
.+=+.+||+..|++..++..+|-
T Consensus 69 ~~EirGIA~~~gi~l~~iv~lN~ 91 (95)
T PF15508_consen 69 AEEIRGIAKAAGIPLGDIVLLNL 91 (95)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 35578899999999999999883
No 112
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=51.40 E-value=14 Score=18.34 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=17.2
Q ss_pred CcHHHHHHHhCCCHHHHHHhhC
Q 037180 25 DTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+.+..+++.||++.++|..-..
T Consensus 4 ~I~~~Va~~~~i~~~~i~s~~R 25 (60)
T smart00760 4 EIIEAVAEYFGVKPEDLKSKSR 25 (60)
T ss_pred HHHHHHHHHhCCCHHHHhcCCC
Confidence 3456789999999999986554
No 113
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=50.85 E-value=23 Score=19.28 Aligned_cols=20 Identities=15% Similarity=0.240 Sum_probs=15.9
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|..+|+++|++.++|...
T Consensus 55 ~kL~~La~~N~v~feeLc~Y 74 (82)
T PF11020_consen 55 SKLYKLAKENNVSFEELCVY 74 (82)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 35778899999999998753
No 114
>PRK00118 putative DNA-binding protein; Validated
Probab=50.77 E-value=28 Score=19.66 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=19.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|..+||+.+|++...+...
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~ 53 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDN 53 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 45889999999999998887643
No 115
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=50.41 E-value=28 Score=16.32 Aligned_cols=23 Identities=22% Similarity=0.222 Sum_probs=16.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+.|-|..++|++.|++...+.++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~ 29 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRI 29 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHH
Confidence 45778888999999988887765
No 116
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=50.08 E-value=24 Score=17.08 Aligned_cols=24 Identities=25% Similarity=0.230 Sum_probs=14.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+.|-|..++|++.|++...+.++=
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~ 31 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRIL 31 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 356677888888888888777653
No 117
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=49.88 E-value=25 Score=18.58 Aligned_cols=34 Identities=21% Similarity=0.195 Sum_probs=25.3
Q ss_pred cCCCCCCCCCCccEEEEccCCcHHHHHHHhCCCH
Q 037180 5 FMDKSEPEPASCRIVEILRGDTLWGFSMKCGVSI 38 (66)
Q Consensus 5 ~~~~~~~~~~~~~~y~V~~GdTl~~Ia~~~~~~~ 38 (66)
|+.+....+.-...+.+..|.|..+++.+.+.+.
T Consensus 5 ytk~~g~~~d~~~~liL~~GaTV~D~a~~iH~di 38 (75)
T cd01666 5 YTKPKGQEPDFDEPVILRRGSTVEDVCNKIHKDL 38 (75)
T ss_pred EeCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHH
Confidence 4555555555666789999999999999877443
No 118
>TIGR02485 CobZ_N-term precorrin 3B synthase CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the N-terminal portion of the R. capsulatus gene which, in other species exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (TIGR02484).
Probab=49.03 E-value=22 Score=24.11 Aligned_cols=26 Identities=23% Similarity=0.280 Sum_probs=21.0
Q ss_pred ccCCcHHHHHHHhCCCHHHH----HHhhCC
Q 037180 22 LRGDTLWGFSMKCGVSIDAI----KEANGL 47 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l----~~~N~l 47 (66)
.++|||.++|++.|++.+.| .++|..
T Consensus 313 ~~adtleeLA~~~gid~~~l~~tv~~yN~~ 342 (432)
T TIGR02485 313 LSADTLEELAGLLGIDPGGLAETLDRPNAA 342 (432)
T ss_pred eecCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 47899999999999997665 467753
No 119
>PRK07121 hypothetical protein; Validated
Probab=49.02 E-value=22 Score=24.58 Aligned_cols=26 Identities=15% Similarity=0.246 Sum_probs=21.2
Q ss_pred EccCCcHHHHHHHhCCCHHH----HHHhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDA----IKEANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~----l~~~N~ 46 (66)
+.+.|||.++|++.|++.+. +.++|.
T Consensus 358 ~~kadtleeLA~~~gid~~~l~~tv~~yN~ 387 (492)
T PRK07121 358 AWKAETVEELARKLGIPPGGLQATVDAYNR 387 (492)
T ss_pred ccccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45689999999999999874 557774
No 120
>PRK08274 tricarballylate dehydrogenase; Validated
Probab=48.72 E-value=23 Score=24.15 Aligned_cols=27 Identities=26% Similarity=0.239 Sum_probs=21.4
Q ss_pred EccCCcHHHHHHHhCCCHHHHH----HhhCC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK----EANGL 47 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~----~~N~l 47 (66)
+.+.|||.++|++.|++.+.|. ++|..
T Consensus 321 ~~~adtleeLA~~~gi~~~~l~~tv~~yN~~ 351 (466)
T PRK08274 321 PIQADTLEELAEKLGLDPAAFLRTVAAFNAA 351 (466)
T ss_pred ccccCCHHHHHHHhCcCHHHHHHHHHHHHHh
Confidence 4578999999999999986655 56743
No 121
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=47.52 E-value=30 Score=16.08 Aligned_cols=18 Identities=11% Similarity=0.231 Sum_probs=13.4
Q ss_pred CcHHHHHHHhCCCHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~ 42 (66)
-++..||++.|++...+.
T Consensus 18 ~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVR 35 (42)
T ss_dssp S-HHHHHHHHTS-HHHHH
T ss_pred ccHHHHHHHHCcCHHHHH
Confidence 567899999999988765
No 122
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=47.31 E-value=38 Score=17.95 Aligned_cols=23 Identities=13% Similarity=0.169 Sum_probs=19.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|..+||++.|++...+...
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~ 52 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNH 52 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999999887754
No 123
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.21 E-value=18 Score=20.67 Aligned_cols=34 Identities=12% Similarity=0.045 Sum_probs=24.5
Q ss_pred cHHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEE
Q 037180 26 TLWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICI 59 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~ 59 (66)
....+|++.|++++++..+-+-+. ....|||-++
T Consensus 66 ~Yq~lA~~n~~s~~~vak~agqklv~Ra~~GqYvq 100 (109)
T COG3784 66 SYQQLAKKNGASTEEVAKLAGQKLVARAAPGQYVQ 100 (109)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCeee
Confidence 456788888999999888775544 4556777664
No 124
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=47.13 E-value=26 Score=16.95 Aligned_cols=22 Identities=18% Similarity=0.225 Sum_probs=17.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|.+...||...++++..+..
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~ 37 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKS 37 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHH
T ss_pred HhcCCcchhHHhcCcchhhHHH
Confidence 4689999999999999887653
No 125
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=46.59 E-value=29 Score=19.28 Aligned_cols=20 Identities=25% Similarity=0.327 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+.+|+++..|..+=
T Consensus 2 ~i~e~a~~~gvs~~tlr~ye 21 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYYE 21 (113)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998775
No 126
>PHA02591 hypothetical protein; Provisional
Probab=46.58 E-value=49 Score=18.05 Aligned_cols=34 Identities=18% Similarity=0.206 Sum_probs=24.7
Q ss_pred CccEEEEccCCcHHHHHHHh---CCCHHHHHHhhCCC
Q 037180 15 SCRIVEILRGDTLWGFSMKC---GVSIDAIKEANGLS 48 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~---~~~~~~l~~~N~l~ 48 (66)
....|-|...|.+-++|++. |.++++|.+.=+++
T Consensus 36 ~~~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~LGVs 72 (83)
T PHA02591 36 GQTRYFVESEDDLISVTHELARKGFTVEKIASLLGVS 72 (83)
T ss_pred CCEEEEEeccchHHHHHHHHHHcCCCHHHHHHHhCCC
Confidence 34568888888888888865 88888887665443
No 127
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=46.48 E-value=25 Score=18.10 Aligned_cols=18 Identities=22% Similarity=0.359 Sum_probs=12.9
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 037180 26 TLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~ 43 (66)
.+..+++.||++.++|..
T Consensus 5 Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 5 IIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp HHHHHHHHTT--HHHHHS
T ss_pred HHHHHHHHHCCCHHHHhC
Confidence 456789999999999874
No 128
>TIGR02008 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins.
Probab=46.46 E-value=28 Score=18.88 Aligned_cols=28 Identities=7% Similarity=0.068 Sum_probs=22.6
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHH
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
...+.+.+|++|-+.+.+.|+.+.---+
T Consensus 14 ~~~~~~~~g~tLLda~~~~Gi~i~~~C~ 41 (97)
T TIGR02008 14 EETIECPDDQYILDAAEEAGIDLPYSCR 41 (97)
T ss_pred EEEEEECCCCcHHHHHHHcCCCCCcCCC
Confidence 3578899999999999999987654443
No 129
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=46.21 E-value=43 Score=17.61 Aligned_cols=44 Identities=25% Similarity=0.330 Sum_probs=30.6
Q ss_pred EEEEccCCcHHHHHHHh-CCC---HHHHHHhhC-CCC--CCcCCCCEEEEc
Q 037180 18 IVEILRGDTLWGFSMKC-GVS---IDAIKEANG-LSG--DTIYYSIICIFL 61 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~-~~~---~~~l~~~N~-l~~--~~l~~G~~l~i~ 61 (66)
.++...|||+-.+..|+ |-. .+++..+|+ +.+ ..+.-|-.|.+|
T Consensus 4 ~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lP 54 (70)
T COG5004 4 IVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLP 54 (70)
T ss_pred EEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecC
Confidence 57778899999999885 433 456777885 433 455667666665
No 130
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=45.99 E-value=35 Score=16.23 Aligned_cols=18 Identities=22% Similarity=0.315 Sum_probs=15.2
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 037180 26 TLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~ 43 (66)
+..+||++++++...+.+
T Consensus 27 ~~~~la~~~~is~~~v~~ 44 (66)
T cd07377 27 SERELAEELGVSRTTVRE 44 (66)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 577999999999888665
No 131
>PRK12834 putative FAD-binding dehydrogenase; Reviewed
Probab=45.92 E-value=26 Score=24.68 Aligned_cols=25 Identities=8% Similarity=0.096 Sum_probs=20.5
Q ss_pred EccCCcHHHHHHHhC-------CCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCG-------VSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~-------~~~~~l~~~N 45 (66)
+.+.|||.++|++.| ++.+.|.+.+
T Consensus 393 ~~kAdTleELA~k~g~~~~~~~id~~~L~~tv 424 (549)
T PRK12834 393 FVVADDLEELVAGMNALTGEPLLDYAHLRRQI 424 (549)
T ss_pred EEEeCCHHHHHHHhcccccccCCCHHHHHHHH
Confidence 446899999999998 8888877544
No 132
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=45.90 E-value=31 Score=21.26 Aligned_cols=22 Identities=14% Similarity=0.083 Sum_probs=19.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+++|++...+.+.
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6889999999999999887754
No 133
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=45.85 E-value=33 Score=18.45 Aligned_cols=20 Identities=20% Similarity=0.209 Sum_probs=17.0
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-|+.+||+.+|++...+-+.
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~ 39 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKD 39 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHH
Confidence 57899999999999887753
No 134
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=45.85 E-value=24 Score=18.92 Aligned_cols=48 Identities=13% Similarity=-0.089 Sum_probs=37.4
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHH--HhhCC--CC-CCcCCCCEEEEccc
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIK--EANGL--SG-DTIYYSIICIFLCL 63 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~--~~N~l--~~-~~l~~G~~l~i~~~ 63 (66)
...+....+.|+..+.+.+|++..++- ..|+. .. ..+..|+.+.|-..
T Consensus 24 ~~~~~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 24 PFTHPFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAVYPV 76 (81)
T ss_pred ceEEecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEEEec
Confidence 346788999999999999999988854 45764 22 56889999977544
No 135
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=45.67 E-value=28 Score=18.69 Aligned_cols=23 Identities=22% Similarity=0.078 Sum_probs=18.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
++--|.++||+-||++...+.+.
T Consensus 10 ~rV~t~~~lA~~yg~~~~~i~~~ 32 (88)
T PF10543_consen 10 QRVMTDEDLAELYGVETKTINRN 32 (88)
T ss_pred EEEEEHHHHHHHhCcCHHHHHHH
Confidence 34458899999999998887653
No 136
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.65 E-value=23 Score=20.18 Aligned_cols=19 Identities=26% Similarity=0.167 Sum_probs=15.5
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
=++..||..|+++-+++..
T Consensus 34 lSl~EIAee~~VSRqAIyD 52 (105)
T COG2739 34 LSLSEIAEEFNVSRQAIYD 52 (105)
T ss_pred ccHHHHHHHhCccHHHHHH
Confidence 3688999999999887653
No 137
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=45.26 E-value=36 Score=19.09 Aligned_cols=22 Identities=14% Similarity=0.368 Sum_probs=17.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~ 148 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEY 148 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3588899999999999887653
No 138
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=45.11 E-value=24 Score=21.78 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=23.4
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHHHHh
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
++|-..+.-++.+||+.+|++...+.+.
T Consensus 171 GYFd~PR~~~l~dLA~~lGISkst~~eh 198 (215)
T COG3413 171 GYFDYPRRVSLKDLAKELGISKSTLSEH 198 (215)
T ss_pred CCCCCCccCCHHHHHHHhCCCHHHHHHH
Confidence 4677788899999999999998887653
No 139
>PF14502 HTH_41: Helix-turn-helix domain
Probab=45.10 E-value=36 Score=16.70 Aligned_cols=20 Identities=40% Similarity=0.459 Sum_probs=16.3
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|..+++++|+++...++.+
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~A 26 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNA 26 (48)
T ss_pred CCHHHHHHHhCcchhHHHHH
Confidence 47789999999998887744
No 140
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription 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 conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=44.92 E-value=32 Score=18.74 Aligned_cols=20 Identities=5% Similarity=0.027 Sum_probs=17.3
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++..+|+.+|++...|..|=
T Consensus 3 ~i~eva~~~gVs~~tLR~ye 22 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYD 22 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999988774
No 141
>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional
Probab=44.74 E-value=21 Score=23.96 Aligned_cols=32 Identities=22% Similarity=0.157 Sum_probs=26.2
Q ss_pred ccEEEE-ccCCcHHHHHHHhCCCHHHHHHhhCC
Q 037180 16 CRIVEI-LRGDTLWGFSMKCGVSIDAIKEANGL 47 (66)
Q Consensus 16 ~~~y~V-~~GdTl~~Ia~~~~~~~~~l~~~N~l 47 (66)
...+.| .+|.|+.+.|++.|+.+-.|.....+
T Consensus 75 Gk~VeV~~~G~TILeAAr~~GI~IPtLCy~~~L 107 (297)
T PTZ00305 75 KRPVEIIPQEENLLEVLEREGIRVPKFCYHPIL 107 (297)
T ss_pred CEEEEecCCCChHHHHHHHcCCCcCccccCCCC
Confidence 346778 88999999999999998888766544
No 142
>PHA01976 helix-turn-helix protein
Probab=44.67 E-value=40 Score=16.50 Aligned_cols=23 Identities=22% Similarity=0.121 Sum_probs=15.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+.|-|..++|++.|++...+.++
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~ 35 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDF 35 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 45667777777777777766654
No 143
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=44.40 E-value=26 Score=23.18 Aligned_cols=23 Identities=35% Similarity=0.322 Sum_probs=19.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHhhC
Q 037180 24 GDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|--+-+||.+||+++..|..|-.
T Consensus 19 gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH
Confidence 55678999999999999998874
No 144
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=43.38 E-value=36 Score=16.20 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=18.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
+..|.+.+.||...+++...+.
T Consensus 16 ~~~G~s~~eia~~l~is~~tV~ 37 (65)
T COG2771 16 VAQGKSNKEIARILGISEETVK 37 (65)
T ss_pred HHCCCCHHHHHHHHCCCHHHHH
Confidence 4678999999999999987765
No 145
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.11 E-value=36 Score=18.41 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|..++|+.+|+++..|.-+=.
T Consensus 2 ti~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999987653
No 146
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=43.04 E-value=40 Score=16.96 Aligned_cols=24 Identities=13% Similarity=0.161 Sum_probs=16.9
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.+.|-|+.++|++.+++..-|..+
T Consensus 7 ~~~glsl~~va~~t~I~~~~l~ai 30 (62)
T PF13413_consen 7 EAKGLSLEDVAEETKISVSYLEAI 30 (62)
T ss_dssp HCTT--HHHHHHHCS--HHHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 357889999999999999988765
No 147
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.22 E-value=38 Score=18.01 Aligned_cols=21 Identities=5% Similarity=-0.024 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+.+|+++..|..|-.
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998864
No 148
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=42.10 E-value=34 Score=16.14 Aligned_cols=18 Identities=28% Similarity=0.202 Sum_probs=13.9
Q ss_pred CcHHHHHHHhCCCHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~ 42 (66)
=|...||++++++...+.
T Consensus 16 it~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIR 33 (55)
T ss_dssp BEHHHHHHHCTS-HHHHH
T ss_pred cCHHHHHHHhCCCHHHHH
Confidence 478899999999977655
No 149
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=42.03 E-value=41 Score=18.26 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=19.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+.|-+|.+++++-|++...|...
T Consensus 19 k~G~Sl~~LS~~agls~~tL~n~ 41 (82)
T COG3423 19 KKGTSLAALSREAGLSSSTLANA 41 (82)
T ss_pred HccccHHHHHHHcCCCHHHHHHH
Confidence 56889999999999998887743
No 150
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=41.99 E-value=40 Score=17.09 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=15.7
Q ss_pred CcHHHHHHHhCCCHHHHHHhh
Q 037180 25 DTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N 45 (66)
-|...||+..|++++++..+-
T Consensus 21 Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 21 PTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp -BHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHcccHHHHHHHH
Confidence 467799999999999877553
No 151
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=41.91 E-value=39 Score=18.45 Aligned_cols=21 Identities=10% Similarity=0.180 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..++|+.+|++...|..+-.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998764
No 152
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=41.85 E-value=38 Score=22.00 Aligned_cols=23 Identities=13% Similarity=0.063 Sum_probs=19.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|+..||+.+|++.+.+.+.
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~ 289 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQI 289 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHH
Confidence 46889999999999999987653
No 153
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=41.63 E-value=39 Score=21.91 Aligned_cols=22 Identities=23% Similarity=0.386 Sum_probs=19.2
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+.+||+.+|++...+.+.
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi 268 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQI 268 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHH
Confidence 5789999999999999988764
No 154
>PRK04217 hypothetical protein; Provisional
Probab=41.45 E-value=46 Score=18.94 Aligned_cols=23 Identities=26% Similarity=0.150 Sum_probs=19.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|..+||+.+|++...+...
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r~ 78 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWRA 78 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36789999999999998887643
No 155
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil
Probab=41.29 E-value=40 Score=18.45 Aligned_cols=21 Identities=29% Similarity=0.205 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..++|+++|+++..|.-+=.
T Consensus 3 ~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466899999999999987753
No 156
>PHA00542 putative Cro-like protein
Probab=41.26 E-value=46 Score=17.54 Aligned_cols=24 Identities=21% Similarity=0.001 Sum_probs=20.5
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
...|-|..++|+..|++...+.++
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~ 51 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRI 51 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 356889999999999999998876
No 157
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=41.01 E-value=40 Score=21.56 Aligned_cols=22 Identities=27% Similarity=0.332 Sum_probs=18.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+.+|++...+.+.
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~ 256 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQI 256 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHH
Confidence 4789999999999999887643
No 158
>cd00207 fer2 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin.
Probab=40.92 E-value=51 Score=16.66 Aligned_cols=24 Identities=29% Similarity=0.404 Sum_probs=20.1
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHH
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSID 39 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~ 39 (66)
..++.+.+|++|-+.+.+.|+.+.
T Consensus 9 ~~~~~~~~g~~ll~al~~~g~~~~ 32 (84)
T cd00207 9 GVEVEVPEGETLLDAAREAGIDIP 32 (84)
T ss_pred CEEEEECCCCcHHHHHHHcCCCcc
Confidence 457889999999999999887754
No 159
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=40.88 E-value=41 Score=18.31 Aligned_cols=20 Identities=20% Similarity=0.218 Sum_probs=16.9
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+.+|++...|..+=
T Consensus 2 ti~eva~~~gvs~~tlR~ye 21 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYD 21 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998763
No 160
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=40.86 E-value=41 Score=15.54 Aligned_cols=24 Identities=21% Similarity=0.225 Sum_probs=18.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+.|-|..++|++.|++...+-++=
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457788888888888888877763
No 161
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=40.74 E-value=42 Score=17.94 Aligned_cols=21 Identities=19% Similarity=0.208 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..++|+.+|++...|..|-.
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999988753
No 162
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=40.63 E-value=46 Score=18.78 Aligned_cols=22 Identities=9% Similarity=0.095 Sum_probs=19.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|+++..+..
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~ 140 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKS 140 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHH
Confidence 3699999999999999888764
No 163
>PTZ00306 NADH-dependent fumarate reductase; Provisional
Probab=40.36 E-value=31 Score=26.91 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=21.4
Q ss_pred EccCCcHHHHHHHhCCCHHHHH----HhhC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIK----EANG 46 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~----~~N~ 46 (66)
+.+.|||.++|++.|++++.|. ++|.
T Consensus 765 ~~kADTleELA~~~gid~~~L~aTV~rYN~ 794 (1167)
T PTZ00306 765 FQRVDDVKGLAKLIGCPVENLHRTLETYER 794 (1167)
T ss_pred EEEeCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4578999999999999987655 6774
No 164
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=40.21 E-value=9.7 Score=20.80 Aligned_cols=24 Identities=21% Similarity=0.057 Sum_probs=15.6
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHH
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAI 41 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l 41 (66)
.|.+....|+-..|+.||+|-..+
T Consensus 13 ~yIi~~~aTVR~~Ak~FGvSKSTV 36 (82)
T PF12116_consen 13 NYIIETKATVRQAAKVFGVSKSTV 36 (82)
T ss_dssp HHHHHH---HHHHHHHHTS-HHHH
T ss_pred HHHHHcccHHHHHHHHHCCcHHHH
Confidence 356677899999999999996543
No 165
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=40.02 E-value=38 Score=14.89 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=15.3
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
+-|..+|++.|++..++.+
T Consensus 12 ~~l~~~a~~~g~s~s~~ir 30 (39)
T PF01402_consen 12 ERLDELAKELGRSRSELIR 30 (39)
T ss_dssp HHHHHHHHHHTSSHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHH
Confidence 4577889999999888765
No 166
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.90 E-value=44 Score=18.07 Aligned_cols=21 Identities=10% Similarity=0.289 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+.+|++...|.-+=.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 2 KIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999987753
No 167
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=39.88 E-value=41 Score=19.15 Aligned_cols=20 Identities=15% Similarity=0.096 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|.-+=
T Consensus 2 ~I~e~a~~~gvs~~tlRyYe 21 (127)
T cd01108 2 NIGEAAKLTGLSAKMIRYYE 21 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998664
No 168
>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=39.86 E-value=31 Score=16.23 Aligned_cols=20 Identities=10% Similarity=0.059 Sum_probs=16.8
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
+.+..||...|++...+..|
T Consensus 28 ~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 28 EEREELAKELGLTERQVKIW 47 (59)
T ss_pred HHHHHHHHHHCcCHHHHHHH
Confidence 56778999999999988765
No 169
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=39.66 E-value=43 Score=15.40 Aligned_cols=22 Identities=18% Similarity=0.087 Sum_probs=15.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.++-|..+||++.|++...+.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~ 36 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNR 36 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHH
Confidence 4567888999999999877653
No 170
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.49 E-value=43 Score=18.48 Aligned_cols=20 Identities=25% Similarity=0.323 Sum_probs=16.7
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|.-+=
T Consensus 2 ~i~eva~~~gis~~tlR~ye 21 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYD 21 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998664
No 171
>PRK11426 hypothetical protein; Provisional
Probab=39.31 E-value=28 Score=20.61 Aligned_cols=20 Identities=15% Similarity=0.233 Sum_probs=17.5
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|++..+|+++|++.+++..
T Consensus 72 ~d~i~~lA~q~Gl~~~~~~~ 91 (132)
T PRK11426 72 TNAVSDLGQKLGVDTSTASS 91 (132)
T ss_pred hHHHHHHHHHHCcCHHHHHH
Confidence 48999999999999998663
No 172
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=39.18 E-value=50 Score=18.25 Aligned_cols=21 Identities=14% Similarity=0.291 Sum_probs=18.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|.-|.||++.+++.+++...
T Consensus 21 ~Dy~k~ia~~l~~~~~~v~~~ 41 (92)
T PF10007_consen 21 PDYAKSIARRLKIPLEEVREA 41 (92)
T ss_pred CCcHHHHHHHHCCCHHHHHHH
Confidence 588999999999998887654
No 173
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=39.13 E-value=36 Score=19.15 Aligned_cols=19 Identities=11% Similarity=0.177 Sum_probs=14.1
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
+--..||++|++++..+.+
T Consensus 41 ~LYp~IA~k~~TT~s~VER 59 (106)
T PF08769_consen 41 ELYPDIAKKYGTTPSRVER 59 (106)
T ss_dssp THHHHHHHHTTS-HHHHHH
T ss_pred hHHHHHHHHHCCCHHHHHH
Confidence 4456899999999887654
No 174
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=39.04 E-value=47 Score=20.17 Aligned_cols=24 Identities=21% Similarity=0.149 Sum_probs=20.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..|.++..||+.+|++...+.+.-
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~ 193 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFL 193 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Confidence 568999999999999999887654
No 175
>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=38.99 E-value=39 Score=14.72 Aligned_cols=24 Identities=29% Similarity=0.232 Sum_probs=18.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
+.|-+...+|+..|++...+..+-
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~ 33 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIE 33 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 347788899999999888877654
No 176
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=38.94 E-value=46 Score=18.23 Aligned_cols=20 Identities=20% Similarity=0.223 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|..+=
T Consensus 3 ~i~eva~~~gvs~~tlR~ye 22 (102)
T cd04789 3 TISELAEKAGISRSTLLYYE 22 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998664
No 177
>PF00111 Fer2: 2Fe-2S iron-sulfur cluster binding domain; InterPro: IPR001041 The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities. This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [, , , ]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3 1JQ4_A 1DOX_A 1DOY_A 2KAJ_A ....
Probab=38.93 E-value=42 Score=16.93 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=17.6
Q ss_pred cEEEEccCCc-HHHHHHHh-CCCH
Q 037180 17 RIVEILRGDT-LWGFSMKC-GVSI 38 (66)
Q Consensus 17 ~~y~V~~GdT-l~~Ia~~~-~~~~ 38 (66)
.++.+.+|++ |-+.+++. ++.+
T Consensus 8 ~~~~~~~~~~~ll~~~~~~~gi~i 31 (78)
T PF00111_consen 8 VTVEVPPGETLLLDALERAGGIGI 31 (78)
T ss_dssp EEEEEETTSBBHHHHHHHTTTTTS
T ss_pred EEEEeCCCccHHHHHHHHcCCCCc
Confidence 4677899999 99999987 6654
No 178
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription 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 conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=38.91 E-value=47 Score=17.68 Aligned_cols=21 Identities=19% Similarity=0.059 Sum_probs=18.4
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
++.++|+.+|++...|..|-.
T Consensus 3 ti~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998864
No 179
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=38.90 E-value=45 Score=20.02 Aligned_cols=22 Identities=14% Similarity=0.308 Sum_probs=18.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-|..+||+..|+++..+.+
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r 170 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRR 170 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHH
Confidence 3689999999999999887654
No 180
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.82 E-value=46 Score=18.00 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+.+|++...|.-+-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999997753
No 181
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=38.78 E-value=43 Score=24.02 Aligned_cols=24 Identities=21% Similarity=0.202 Sum_probs=20.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..+-||..||+.+|++.+++.+.-
T Consensus 465 ~e~~TL~EIa~~lGVSrERVRQIe 488 (509)
T PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIE 488 (509)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
Confidence 357899999999999999987653
No 182
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=38.61 E-value=53 Score=19.71 Aligned_cols=37 Identities=0% Similarity=-0.251 Sum_probs=21.6
Q ss_pred CcHHHHHHHhCCCHHHHHHhh----CCC-CCCcCCCCEEEEc
Q 037180 25 DTLWGFSMKCGVSIDAIKEAN----GLS-GDTIYYSIICIFL 61 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N----~l~-~~~l~~G~~l~i~ 61 (66)
+++..|++.||+++.++..-. .-. ...+..|+.+.|+
T Consensus 112 ~~l~kLa~~Lgvsl~el~~e~~~~~~~~~~~~~TlGd~v~ik 153 (154)
T TIGR00270 112 KVVEKLEKLLKIKLREQVPEIKIEKSGRKSLGPTLGDFIKIK 153 (154)
T ss_pred HHHHHHHHHhCCCHHHHccchhhccccCccCCCCCcceeEec
Confidence 567777777777777765222 211 1345567777664
No 183
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=38.58 E-value=44 Score=18.98 Aligned_cols=20 Identities=15% Similarity=0.115 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+++|+++..|.-+=
T Consensus 2 ~I~e~a~~~gvs~~tlRyYe 21 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIRYYE 21 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998664
No 184
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=38.45 E-value=46 Score=18.63 Aligned_cols=21 Identities=24% Similarity=0.264 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+++|+++..|.-+-.
T Consensus 2 ~I~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 2 KIGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999987753
No 185
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=38.28 E-value=47 Score=22.19 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=18.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+-||.+||+.+|++.+.+.+.
T Consensus 282 ~~Tl~eIa~~lgvS~eRVrQI 302 (324)
T PRK07921 282 PRTLDQIGKLFGLSRERVRQI 302 (324)
T ss_pred CcCHHHHHHHHCCCHHHHHHH
Confidence 469999999999999988765
No 186
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=37.98 E-value=32 Score=21.26 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=19.2
Q ss_pred EEccCCcHH---HHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLW---GFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~---~Ia~~~~~~~~~l~~~ 44 (66)
..++||.|. +++++||+|-.-+.++
T Consensus 23 ~l~pG~~LpsE~~La~~lgVSRtpVREA 50 (235)
T TIGR02812 23 RFPPGSILPAERELSELIGVTRTTLREV 50 (235)
T ss_pred CCCCCCcCcCHHHHHHHHCcCHHHHHHH
Confidence 467898884 7999999996655543
No 187
>PRK01777 hypothetical protein; Validated
Probab=37.95 E-value=50 Score=18.25 Aligned_cols=44 Identities=11% Similarity=-0.075 Sum_probs=32.7
Q ss_pred cEEEEccCCcHHHHHHHhCCCHH--HH------HHhhCC--CC-CCcCCCCEEEE
Q 037180 17 RIVEILRGDTLWGFSMKCGVSID--AI------KEANGL--SG-DTIYYSIICIF 60 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~--~l------~~~N~l--~~-~~l~~G~~l~i 60 (66)
....+..|-|+.++.+..|+..+ ++ ...|+- .. ..+..|++|-|
T Consensus 19 ~~l~vp~GtTv~dal~~sgi~~~~pei~~~~~~vgI~Gk~v~~d~~L~dGDRVeI 73 (95)
T PRK01777 19 QRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEI 73 (95)
T ss_pred EEEEcCCCCcHHHHHHHcCCCccCcccccccceEEEeCeECCCCCcCCCCCEEEE
Confidence 45678999999999999999877 55 223432 22 57889999866
No 188
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.94 E-value=49 Score=18.00 Aligned_cols=21 Identities=10% Similarity=0.101 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
++..+|+++|++...|..|-.
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999998853
No 189
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=37.81 E-value=49 Score=20.69 Aligned_cols=23 Identities=13% Similarity=0.071 Sum_probs=19.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-|..|..+|+..|++.+++.+.=
T Consensus 89 ~g~DL~~vA~~~gLs~eevi~~H 111 (202)
T TIGR00370 89 FGPDLEEVAKINQLSPEEVIDIH 111 (202)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHH
Confidence 36689999999999999988764
No 190
>PRK05572 sporulation sigma factor SigF; Validated
Probab=37.72 E-value=50 Score=20.78 Aligned_cols=24 Identities=13% Similarity=0.187 Sum_probs=20.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..|-|+..||+.+|+++..+...-
T Consensus 216 ~~~~s~~eIA~~lgis~~~V~~~~ 239 (252)
T PRK05572 216 FKDKTQSEVAKRLGISQVQVSRLE 239 (252)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHH
Confidence 468899999999999999887653
No 191
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=37.71 E-value=49 Score=18.41 Aligned_cols=21 Identities=14% Similarity=0.306 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+.+|+++..|.-+=.
T Consensus 2 ~i~eva~~~gvs~~tlR~Ye~ 22 (112)
T cd01282 2 RIGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456899999999999987753
No 192
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.70 E-value=54 Score=18.80 Aligned_cols=21 Identities=14% Similarity=0.268 Sum_probs=17.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|++...+.
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~ 162 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVR 162 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHH
Confidence 468899999999999988875
No 193
>PRK03837 transcriptional regulator NanR; Provisional
Probab=37.61 E-value=41 Score=20.73 Aligned_cols=26 Identities=35% Similarity=0.337 Sum_probs=19.8
Q ss_pred EEEccCCcH---HHHHHHhCCCHHHHHHh
Q 037180 19 VEILRGDTL---WGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 19 y~V~~GdTl---~~Ia~~~~~~~~~l~~~ 44 (66)
-..++||-| ..+|++||++..-+.++
T Consensus 29 g~l~pG~~Lp~E~~Lae~~gVSRt~VREA 57 (241)
T PRK03837 29 GEFGPGDQLPSERELMAFFGVGRPAVREA 57 (241)
T ss_pred CCCCCCCCCCCHHHHHHHhCCCHHHHHHH
Confidence 357889966 68999999997665543
No 194
>PF14174 YycC: YycC-like protein
Probab=37.34 E-value=28 Score=17.36 Aligned_cols=22 Identities=23% Similarity=0.291 Sum_probs=17.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHhh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-||--.+|++.|++.+.|+.+-
T Consensus 8 ~eTA~kLs~~L~vPlE~lMHmP 29 (53)
T PF14174_consen 8 PETAVKLSKKLGVPLEQLMHMP 29 (53)
T ss_pred HHHHHHHHHHHCCcHHHHhcCc
Confidence 3677789999999999988653
No 195
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=37.21 E-value=49 Score=18.45 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|...+|+.+|++...|.-+-.
T Consensus 2 ~ige~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 2 YIGELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998764
No 196
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=37.09 E-value=81 Score=19.33 Aligned_cols=36 Identities=19% Similarity=-0.012 Sum_probs=26.1
Q ss_pred CcHHHHHHHhCCCHHHHHHhhCCCCCCcCCCCEEEE
Q 037180 25 DTLWGFSMKCGVSIDAIKEANGLSGDTIYYSIICIF 60 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N~l~~~~l~~G~~l~i 60 (66)
-++.+|++++|+++--|...-.-....---||.|.+
T Consensus 122 ~Sl~~lsr~l~~sp~firglAKRs~~L~VkGq~lel 157 (160)
T PF09824_consen 122 TSLSDLSRKLGISPVFIRGLAKRSPKLDVKGQRLEL 157 (160)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHhccCcceecceEEe
Confidence 578899999999998888776544433334787765
No 197
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=37.05 E-value=58 Score=17.36 Aligned_cols=20 Identities=10% Similarity=0.149 Sum_probs=15.9
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
--++..|..+||++..++..
T Consensus 13 RtpFeaI~~~fGL~E~eVi~ 32 (72)
T TIGR03643 13 RTPFEAIEQQFGLSEKEVIK 32 (72)
T ss_pred CCCHHHHHHHHCCCHHHHHH
Confidence 45688999999999887553
No 198
>PRK07198 hypothetical protein; Validated
Probab=36.98 E-value=25 Score=24.66 Aligned_cols=25 Identities=24% Similarity=0.166 Sum_probs=19.5
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|.|==-|..+|+|||++...|.+.
T Consensus 170 av~pvwylpgva~rfg~~e~~lrr~ 194 (418)
T PRK07198 170 AIEPVWYLPGVAERFGVSETDLRRT 194 (418)
T ss_pred eecccccccchHHHcCCCHHHHHHH
Confidence 3455556778999999999998765
No 199
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=36.97 E-value=32 Score=21.23 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=19.5
Q ss_pred EEccCCcHH---HHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLW---GFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~---~Ia~~~~~~~~~l~~~ 44 (66)
..++||-|. .++++||+|-.-+.++
T Consensus 24 ~l~pG~~LPsE~eLae~~gVSRt~VReA 51 (239)
T PRK04984 24 RFPPGSILPAERELSELIGVTRTTLREV 51 (239)
T ss_pred CCCCCCcCCCHHHHHHHHCCCHHHHHHH
Confidence 467898874 7999999997766544
No 200
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=36.86 E-value=52 Score=15.54 Aligned_cols=20 Identities=15% Similarity=0.129 Sum_probs=15.2
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-++.+||++.|++...+.+.
T Consensus 19 ~t~~eia~~~gl~~stv~r~ 38 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRL 38 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 38999999999998776543
No 201
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=36.79 E-value=23 Score=17.84 Aligned_cols=19 Identities=26% Similarity=0.408 Sum_probs=12.9
Q ss_pred CCcHHHHHHHhCCCHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~ 42 (66)
-|.+..||+++|++++-|.
T Consensus 41 ~~~l~~ia~~~gvsl~WLl 59 (66)
T PF07022_consen 41 AEWLIKIALETGVSLDWLL 59 (66)
T ss_dssp HHHHHHHHHHH---HHHHH
T ss_pred HHHHHHHHHHHCcCHHHHH
Confidence 4667788999999998876
No 202
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=36.55 E-value=35 Score=21.38 Aligned_cols=25 Identities=20% Similarity=0.187 Sum_probs=19.3
Q ss_pred EEccCCcHH---HHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLW---GFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~---~Ia~~~~~~~~~l~~~ 44 (66)
..++|+-|. .+|++||+|..-+.++
T Consensus 26 ~l~pG~~LpsE~eLa~~~gVSRtpVREA 53 (257)
T PRK10225 26 PYNPGERLPPEREIAEMLDVTRTVVREA 53 (257)
T ss_pred CCCCCCcCcCHHHHHHHhCCCHHHHHHH
Confidence 578898884 7999999996665543
No 203
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.30 E-value=51 Score=18.72 Aligned_cols=20 Identities=15% Similarity=0.386 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+.+|+++..|.-+=
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye 21 (126)
T cd04785 2 SIGELARRTGVNVETIRYYE 21 (126)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998664
No 204
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=36.22 E-value=49 Score=18.64 Aligned_cols=20 Identities=20% Similarity=0.194 Sum_probs=13.4
Q ss_pred cCCcHHHHHHHhCCCHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~ 42 (66)
..=++..||..+|++.+.+.
T Consensus 32 eDlSlsEIAe~~~iSRqaV~ 51 (101)
T PF04297_consen 32 EDLSLSEIAEELGISRQAVY 51 (101)
T ss_dssp S---HHHHHHHCTS-HHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHH
Confidence 45688999999999987754
No 205
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=36.20 E-value=46 Score=19.03 Aligned_cols=48 Identities=8% Similarity=-0.031 Sum_probs=31.3
Q ss_pred CCccEEEEccCCcHH----HHHHHhCCCHHH--HHHh--------hCCCCCCcCCCCEEEEc
Q 037180 14 ASCRIVEILRGDTLW----GFSMKCGVSIDA--IKEA--------NGLSGDTIYYSIICIFL 61 (66)
Q Consensus 14 ~~~~~y~V~~GdTl~----~Ia~~~~~~~~~--l~~~--------N~l~~~~l~~G~~l~i~ 61 (66)
+....-.|.+++|+- .|.++|++.+.+ |... +.+....+.+|..|.+.
T Consensus 14 ~~~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Ll 75 (107)
T cd01795 14 RGEKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLK 75 (107)
T ss_pred CCCceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEE
Confidence 345567899999999 788889998773 3221 12333456667766554
No 206
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.20 E-value=61 Score=18.27 Aligned_cols=23 Identities=9% Similarity=0.183 Sum_probs=18.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
-.|-+..+||+..|++...+...
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~ 142 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWI 142 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 35888999999999998887643
No 207
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=35.97 E-value=68 Score=16.68 Aligned_cols=36 Identities=8% Similarity=-0.011 Sum_probs=24.7
Q ss_pred cHHHHHHHhCCCHHHHHHhh---CCCCCCcCCCCEEEEc
Q 037180 26 TLWGFSMKCGVSIDAIKEAN---GLSGDTIYYSIICIFL 61 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N---~l~~~~l~~G~~l~i~ 61 (66)
|+.+.|+=||+....|.++- +-.+-.+..|.++.|.
T Consensus 15 Ti~EAa~Y~gIG~~klr~l~~~~~~~~f~~~~G~r~lIk 53 (67)
T PF09035_consen 15 TIEEAAEYFGIGEKKLRELAEENPDCPFVLWIGNRRLIK 53 (67)
T ss_dssp EHHHHHHHT-S-HHHHHHHHHH-TT-SSEEEETTEEEEE
T ss_pred CHHHHHHHhCccHHHHHHHHHhCCCCCEEEEECCEEEEe
Confidence 66788888999999888776 2233467889988874
No 208
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=35.63 E-value=56 Score=19.06 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=17.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|+++..+.
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~ 163 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMR 163 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHH
Confidence 368888899999999888765
No 209
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=34.82 E-value=54 Score=18.57 Aligned_cols=21 Identities=19% Similarity=0.339 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|...+|+++|+++..|..+-.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER 21 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999987753
No 210
>PF07836 DmpG_comm: DmpG-like communication domain; InterPro: IPR012425 This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain []. The communication domain is thought to play an important role in the heterodimerisation of the enzyme []. Members of this entry heterodimerise with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase [].; GO: 0016833 oxo-acid-lyase activity, 0019439 aromatic compound catabolic process; PDB: 1NVM_E.
Probab=34.68 E-value=49 Score=17.31 Aligned_cols=15 Identities=20% Similarity=0.067 Sum_probs=10.4
Q ss_pred HHHHHHhCCCHHHHH
Q 037180 28 WGFSMKCGVSIDAIK 42 (66)
Q Consensus 28 ~~Ia~~~~~~~~~l~ 42 (66)
..+|++||+++.+|.
T Consensus 26 ~raa~~ygVd~r~il 40 (66)
T PF07836_consen 26 ERAAERYGVDPRDIL 40 (66)
T ss_dssp HHHHHHHT--HHHHH
T ss_pred HHHHHHhCcCHHHHH
Confidence 467899999988865
No 211
>PF13994 PgaD: PgaD-like protein
Probab=34.58 E-value=56 Score=19.01 Aligned_cols=23 Identities=9% Similarity=0.055 Sum_probs=19.8
Q ss_pred CcHHHHHHHhCCCHHHHHHhhCC
Q 037180 25 DTLWGFSMKCGVSIDAIKEANGL 47 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N~l 47 (66)
-+..++|+.|+++.+.+.++.+-
T Consensus 101 ~~~~elA~~f~l~~~~l~~lr~~ 123 (138)
T PF13994_consen 101 VSDEELARSFGLSPEQLQQLRQA 123 (138)
T ss_pred CCHHHHHHHcCCCHHHHHHHHhC
Confidence 67789999999999999988653
No 212
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=34.55 E-value=46 Score=21.30 Aligned_cols=19 Identities=26% Similarity=0.225 Sum_probs=16.4
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
|...+|..|+++++.|.+.
T Consensus 31 t~~~Lae~F~vspe~irrI 49 (225)
T PF06413_consen 31 TVERLAESFKVSPEAIRRI 49 (225)
T ss_pred CHHHHHhhCCCCHHHHHHH
Confidence 6778999999999988765
No 213
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=34.52 E-value=57 Score=19.39 Aligned_cols=21 Identities=19% Similarity=0.203 Sum_probs=17.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|....+++++|.++...+.+.
T Consensus 102 G~n~~eLaKkYrlS~~~Iy~V 122 (137)
T COG5566 102 GSNYVELAKKYRLSENHIYRV 122 (137)
T ss_pred CccHHHHHHHhcccHHHHHHH
Confidence 888899999999998877653
No 214
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=34.35 E-value=57 Score=18.83 Aligned_cols=20 Identities=0% Similarity=-0.076 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++..+|+++|+++..|..|=
T Consensus 3 sI~eVA~~~GVs~~TLR~wE 22 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWE 22 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998774
No 215
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.32 E-value=65 Score=18.42 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
..|-+..+||+.+|++...+..
T Consensus 139 ~~~~~~~eIA~~lgis~~tv~~ 160 (179)
T PRK11924 139 VEGLSYREIAEILGVPVGTVKS 160 (179)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3588899999999999887764
No 216
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=33.99 E-value=62 Score=19.07 Aligned_cols=21 Identities=14% Similarity=0.308 Sum_probs=16.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|++...+.
T Consensus 147 ~~~~s~~eIA~~lgis~~tV~ 167 (182)
T PRK12537 147 VDGCSHAEIAQRLGAPLGTVK 167 (182)
T ss_pred HcCCCHHHHHHHHCCChhhHH
Confidence 468888889999888887755
No 217
>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=33.84 E-value=59 Score=16.77 Aligned_cols=22 Identities=23% Similarity=0.095 Sum_probs=15.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHhh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..|..+||+..+++...+.+.=
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~ 55 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFC 55 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHH
Confidence 4678899999999998887653
No 218
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=33.64 E-value=73 Score=16.95 Aligned_cols=19 Identities=16% Similarity=0.137 Sum_probs=14.6
Q ss_pred cCCcHHHHHHHhC-CCHHHH
Q 037180 23 RGDTLWGFSMKCG-VSIDAI 41 (66)
Q Consensus 23 ~GdTl~~Ia~~~~-~~~~~l 41 (66)
-|.++.+|++.|| .+-..+
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV 62 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTV 62 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHH
Confidence 3899999999998 665443
No 219
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=33.56 E-value=49 Score=21.49 Aligned_cols=17 Identities=47% Similarity=1.064 Sum_probs=14.6
Q ss_pred EEEEccCCcHHHHHHHh
Q 037180 18 IVEILRGDTLWGFSMKC 34 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~ 34 (66)
..+|+.|||+|.+-.+.
T Consensus 114 ~v~vKKGdtI~~FL~~~ 130 (239)
T PF04921_consen 114 TVRVKKGDTIWQFLEKC 130 (239)
T ss_pred eEEEcCCCCHHHHHHHH
Confidence 78999999999887764
No 220
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=33.46 E-value=50 Score=20.57 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=19.5
Q ss_pred EEccCCcH---HHHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTL---WGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl---~~Ia~~~~~~~~~l~~~ 44 (66)
..++||-| ..+|++||++-.-+.++
T Consensus 24 ~l~pG~~LPsE~eLa~~~gVSRtpVREA 51 (251)
T PRK09990 24 VLKVGQALPSERRLCEKLGFSRSALREG 51 (251)
T ss_pred CCCCCCcCcCHHHHHHHHCCCHHHHHHH
Confidence 46889988 48999999997665543
No 221
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.46 E-value=58 Score=20.03 Aligned_cols=26 Identities=23% Similarity=0.276 Sum_probs=22.3
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-|-.+-+|..+|..+|++.....+|-
T Consensus 15 YV~~~~sLe~aA~~~gVs~~TarrWK 40 (165)
T PF08822_consen 15 YVFDRLSLEQAAAKCGVSYATARRWK 40 (165)
T ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHH
Confidence 45568899999999999999988886
No 222
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=33.39 E-value=71 Score=17.06 Aligned_cols=20 Identities=10% Similarity=0.137 Sum_probs=15.9
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.++..|...||++..++..
T Consensus 12 RtpFeaI~~qfGl~E~eVi~ 31 (73)
T PF10985_consen 12 RTPFEAIERQFGLSEKEVIK 31 (73)
T ss_pred CCCHHHHHHHHCCCHHHHHH
Confidence 45788999999999887553
No 223
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=33.38 E-value=60 Score=21.93 Aligned_cols=22 Identities=27% Similarity=0.306 Sum_probs=19.0
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.+-|+..||+.+|++.+++.+.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi 345 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQI 345 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHH
Confidence 3479999999999999988765
No 224
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=33.10 E-value=49 Score=19.29 Aligned_cols=29 Identities=28% Similarity=0.429 Sum_probs=24.8
Q ss_pred EEEccCCcHHHHHHHh---CCCHHHHHHhhCC
Q 037180 19 VEILRGDTLWGFSMKC---GVSIDAIKEANGL 47 (66)
Q Consensus 19 y~V~~GdTl~~Ia~~~---~~~~~~l~~~N~l 47 (66)
-.+|.|.-+.++++|. |-++++|...|.+
T Consensus 84 LiiQTgnkMddvSrRL~aEgKdIdeLKKiN~m 115 (128)
T PF15145_consen 84 LIIQTGNKMDDVSRRLTAEGKDIDELKKINSM 115 (128)
T ss_pred heeeccchHHHHHHHHHhccCCHHHHHHHHHH
Confidence 3589999999999997 8889999988854
No 225
>PF04447 DUF550: Protein of unknown function (DUF550); InterPro: IPR007538 This entry represents the N terminus of a protein of unknown function, found in a range of Proteobacteria and a few P22-like dsDNA virus particles.
Probab=33.04 E-value=61 Score=18.36 Aligned_cols=18 Identities=33% Similarity=0.639 Sum_probs=14.4
Q ss_pred HHHHHHHhCCCHHHHHHh
Q 037180 27 LWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~~ 44 (66)
+|+-+.|.|++.++|..+
T Consensus 51 l~D~~~RaGis~~~i~~A 68 (100)
T PF04447_consen 51 LWDGARRAGISPEQIIDA 68 (100)
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 577888999999888743
No 226
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=32.93 E-value=66 Score=20.94 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=19.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+.+|++...+.+.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~ 265 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQI 265 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
Confidence 6889999999999998887643
No 227
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=32.92 E-value=59 Score=16.57 Aligned_cols=19 Identities=16% Similarity=0.066 Sum_probs=14.8
Q ss_pred HHHHHHHhCCCHHHHHHhh
Q 037180 27 LWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~~N 45 (66)
.-..|++||++...+..|=
T Consensus 28 ~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 28 QRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHhCccHHHHHHHH
Confidence 4568999999999888874
No 228
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=32.82 E-value=50 Score=14.19 Aligned_cols=23 Identities=26% Similarity=0.266 Sum_probs=18.4
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
.|-+..++|+..|++...+..+-
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 46678899999999988887664
No 229
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=32.70 E-value=65 Score=17.63 Aligned_cols=19 Identities=5% Similarity=0.020 Sum_probs=16.7
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
+..++|+.+|++...|..|
T Consensus 2 ti~EvA~~~gVs~~tLR~y 20 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYW 20 (99)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4568999999999999977
No 230
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=32.23 E-value=48 Score=16.78 Aligned_cols=31 Identities=13% Similarity=0.205 Sum_probs=25.6
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCCC
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGLS 48 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~ 48 (66)
.|.|-..++|..||++.-.+..++....++.
T Consensus 26 ~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~ 56 (81)
T smart00341 26 PYFVLPDETLIKMAAALPTNVSELLAIDGVG 56 (81)
T ss_pred CeEEECHHHHHHHHHHCCCCHHHHhcCCCCC
Confidence 5778888999999999999988888776554
No 231
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=32.15 E-value=67 Score=17.76 Aligned_cols=21 Identities=14% Similarity=0.156 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..++|+..|+++..|..+-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466899999999999987753
No 232
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=32.13 E-value=61 Score=19.89 Aligned_cols=20 Identities=20% Similarity=0.002 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+++|+++..|..|-
T Consensus 2 ti~evA~~lGVS~~TLRrw~ 21 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWV 21 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998885
No 233
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=31.81 E-value=74 Score=15.81 Aligned_cols=20 Identities=15% Similarity=0.141 Sum_probs=16.8
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
+.+|...+++.|++++++.+
T Consensus 31 ~~~L~eA~~~~~ld~~~vl~ 50 (56)
T PF04405_consen 31 NRSLEEACEEKGLDPEEVLE 50 (56)
T ss_pred CchHHHHHHHcCCCHHHHHH
Confidence 47899999999999998653
No 234
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=31.75 E-value=72 Score=20.10 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=18.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+++|++...+.+.
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~ 242 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRL 242 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHH
Confidence 5789999999999999887654
No 235
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=31.54 E-value=75 Score=18.77 Aligned_cols=21 Identities=5% Similarity=0.140 Sum_probs=17.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|.+..+||+.+|++...+.
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~ 172 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVR 172 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHH
Confidence 468999999999999987765
No 236
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=31.50 E-value=71 Score=17.33 Aligned_cols=20 Identities=30% Similarity=0.318 Sum_probs=16.8
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++.++|++.|++...|..+=
T Consensus 2 ~I~eva~~~gvs~~tlR~Ye 21 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYL 21 (95)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999988765
No 237
>PLN02593 adrenodoxin-like ferredoxin protein
Probab=31.49 E-value=64 Score=18.28 Aligned_cols=24 Identities=17% Similarity=0.245 Sum_probs=19.3
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHH
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDA 40 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~ 40 (66)
.+..+..|+||-.++++.|+.+..
T Consensus 13 ~~v~~~~G~tLl~a~~~~gi~i~~ 36 (117)
T PLN02593 13 RTVKAPVGMSLLEAAHENDIELEG 36 (117)
T ss_pred EEEEECCCCcHHHHHHHcCCCCCc
Confidence 356678999999999999887543
No 238
>CHL00134 petF ferredoxin; Validated
Probab=31.48 E-value=90 Score=17.00 Aligned_cols=25 Identities=4% Similarity=0.015 Sum_probs=20.9
Q ss_pred cEEEEccCCcHHHHHHHhCCCHHHH
Q 037180 17 RIVEILRGDTLWGFSMKCGVSIDAI 41 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~~~~~l 41 (66)
.++.+.+|+||-+.+.+.|+.+.--
T Consensus 17 ~~~~~~~~~tLL~a~~~~Gi~i~~~ 41 (99)
T CHL00134 17 VTIDCPDDVYILDAAEEQGIDLPYS 41 (99)
T ss_pred EEEEECCCCcHHHHHHHcCCCCCcC
Confidence 4689999999999999998876443
No 239
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=31.47 E-value=44 Score=20.92 Aligned_cols=25 Identities=32% Similarity=0.236 Sum_probs=19.5
Q ss_pred EEccCCcHH---HHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLW---GFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~---~Ia~~~~~~~~~l~~~ 44 (66)
..++||-|. .+|++||++..-+.++
T Consensus 25 ~l~pG~~LpsE~eLae~~gVSRtpVREA 52 (253)
T PRK11523 25 VYLVGDKLPAERFIADEKNVSRTVVREA 52 (253)
T ss_pred CCCCCCCCCCHHHHHHHHCCCHHHHHHH
Confidence 568899883 6999999997665544
No 240
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.33 E-value=69 Score=18.10 Aligned_cols=20 Identities=20% Similarity=0.341 Sum_probs=16.8
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|.-+=
T Consensus 2 ~IgevA~~~gvs~~tLRyYe 21 (127)
T cd04784 2 KIGELAKKTGCSVETIRYYE 21 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999988664
No 241
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=31.30 E-value=43 Score=20.47 Aligned_cols=23 Identities=17% Similarity=0.239 Sum_probs=18.8
Q ss_pred EEEEccCCcHHHHHHHhCCCHHH
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDA 40 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~ 40 (66)
.+..+.|||+-++|.++|+..+-
T Consensus 57 ~i~g~vGdtlLd~ah~n~idleG 79 (159)
T KOG3309|consen 57 KIKGKVGDTLLDAAHENNLDLEG 79 (159)
T ss_pred EeeeecchHHHHHHHHcCCCccc
Confidence 46678899999999999887543
No 242
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=31.29 E-value=81 Score=17.82 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=17.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 125 ~~g~~~~eIA~~l~is~~tv~~ 146 (159)
T TIGR02989 125 QRGVSLTALAEQLGRTVNAVYK 146 (159)
T ss_pred hcCCCHHHHHHHhCCCHHHHHH
Confidence 3588889999999999887664
No 243
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=31.26 E-value=53 Score=17.19 Aligned_cols=20 Identities=5% Similarity=0.337 Sum_probs=16.5
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
|.+-+||++.+++.+.+.++
T Consensus 8 e~i~~iA~~t~~P~e~V~~m 27 (66)
T PF12085_consen 8 EVIRSIAEETGTPAETVRRM 27 (66)
T ss_pred HHHHHHHHHHCCCHHHHHHH
Confidence 56789999999998887654
No 244
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=31.19 E-value=73 Score=19.85 Aligned_cols=23 Identities=22% Similarity=0.185 Sum_probs=19.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|+..||+.+|++...+.+.
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~ 216 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQI 216 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHH
Confidence 36789999999999999987764
No 245
>PRK13690 hypothetical protein; Provisional
Probab=31.16 E-value=58 Score=20.41 Aligned_cols=16 Identities=19% Similarity=0.279 Sum_probs=14.1
Q ss_pred CCcCCCCEEEEcccCC
Q 037180 50 DTIYYSIICIFLCLSS 65 (66)
Q Consensus 50 ~~l~~G~~l~i~~~~~ 65 (66)
..+.+|+.+.|=|.||
T Consensus 21 a~l~~g~i~VvGcSTS 36 (184)
T PRK13690 21 ANLKPGQIFVLGCSTS 36 (184)
T ss_pred hCCCCCCEEEEecchH
Confidence 6778899999999987
No 246
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.97 E-value=69 Score=18.10 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=16.7
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+.+|+++..|.-+=
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye 21 (126)
T cd04783 2 TIGELAKAAGVNVETIRYYQ 21 (126)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999997664
No 247
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=30.75 E-value=72 Score=21.09 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=18.6
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.+-|+.+||+.+|++.+.+.+.
T Consensus 275 ~~~Tl~EIa~~lgiS~erVRqi 296 (317)
T PRK07405 275 QPLTLAKIGERLNISRERVRQI 296 (317)
T ss_pred CCcCHHHHHHHHCcCHHHHHHH
Confidence 4679999999999999887653
No 248
>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=30.68 E-value=69 Score=15.11 Aligned_cols=20 Identities=10% Similarity=0.119 Sum_probs=15.9
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
+....||...|++...+..|
T Consensus 28 ~~~~~la~~l~l~~~~V~~W 47 (57)
T PF00046_consen 28 EEREELAKELGLTERQVKNW 47 (57)
T ss_dssp HHHHHHHHHHTSSHHHHHHH
T ss_pred cccccccccccccccccccC
Confidence 44668999999999888765
No 249
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=30.66 E-value=64 Score=20.60 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=16.3
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-|+.+||+++|+|....-++
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~ 26 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLV 26 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHH
Confidence 48999999999998775543
No 250
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=30.54 E-value=62 Score=20.21 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=19.2
Q ss_pred EEccCCcH---HHHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTL---WGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl---~~Ia~~~~~~~~~l~~~ 44 (66)
..++||-| -.+|++||++-.-+.++
T Consensus 27 ~l~pG~~LpsE~eLa~~lgVSRtpVREA 54 (254)
T PRK09464 27 TLRPGEKLPPERELAKQFDVSRPSLREA 54 (254)
T ss_pred CCCCCCcCCCHHHHHHHhCCCHHHHHHH
Confidence 57889966 57999999996665543
No 251
>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=30.49 E-value=80 Score=15.80 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=19.5
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..+.|-|..++|++.|++...+-.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~ 38 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRI 38 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 4456778888888888888887765
No 252
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=30.47 E-value=65 Score=17.62 Aligned_cols=20 Identities=20% Similarity=0.358 Sum_probs=16.3
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+++|++...|.-+=
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe 21 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYI 21 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999987654
No 253
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an
Probab=30.46 E-value=73 Score=17.85 Aligned_cols=21 Identities=5% Similarity=0.150 Sum_probs=17.3
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..++|+++|++...|.-+=.
T Consensus 2 ~IgevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 2 DIAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466899999999999986653
No 254
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=30.46 E-value=80 Score=18.25 Aligned_cols=22 Identities=9% Similarity=0.084 Sum_probs=18.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~ 155 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKS 155 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH
Confidence 4688999999999999887653
No 255
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.27 E-value=81 Score=18.35 Aligned_cols=22 Identities=14% Similarity=0.108 Sum_probs=17.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-+...||+.+|++...+...
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~ 172 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTR 172 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHH
Confidence 6888899999999998876643
No 256
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=30.22 E-value=74 Score=21.80 Aligned_cols=22 Identities=23% Similarity=0.202 Sum_probs=18.6
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.+-|+..||+.+|++.+.+.+.
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQi 351 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQI 351 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHH
Confidence 3579999999999999887654
No 257
>TIGR00241 CoA_E_activ CoA-substrate-specific enzyme activase, putative. This domain may be involved in generating or regenerating the active sites of enzymes related to (R)-2-hydroxyglutaryl-CoA dehydratase and benzoyl-CoA reductase.
Probab=29.98 E-value=92 Score=19.54 Aligned_cols=23 Identities=22% Similarity=0.250 Sum_probs=19.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-|.-+..+|+++|++++++..+-
T Consensus 126 tg~f~e~~a~~l~~~~~e~~~~~ 148 (248)
T TIGR00241 126 TGRFLEVTARRLGVSVEELGSLA 148 (248)
T ss_pred ccHHHHHHHHHcCCCHHHHHHHH
Confidence 35678999999999999987653
No 258
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=29.80 E-value=81 Score=19.89 Aligned_cols=22 Identities=18% Similarity=0.288 Sum_probs=18.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+.+|++...+...
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~ 245 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRL 245 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 5889999999999998887654
No 259
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=29.60 E-value=56 Score=15.22 Aligned_cols=20 Identities=20% Similarity=0.129 Sum_probs=16.2
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
+....||...|++...+..|
T Consensus 28 ~~~~~la~~~~l~~~qV~~W 47 (56)
T smart00389 28 EEREELAAKLGLSERQVKVW 47 (56)
T ss_pred HHHHHHHHHHCcCHHHHHHh
Confidence 56778999999998887765
No 260
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=29.58 E-value=76 Score=18.16 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=18.2
Q ss_pred cHHHHHHHhCCCHHHHHHhhCC
Q 037180 26 TLWGFSMKCGVSIDAIKEANGL 47 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~l 47 (66)
+...+|+++|++...|.-+-..
T Consensus 3 ~I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 3 QIGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4668999999999999877643
No 261
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=29.57 E-value=84 Score=18.13 Aligned_cols=22 Identities=9% Similarity=-0.020 Sum_probs=17.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|+++..+..
T Consensus 133 ~~g~s~~eiA~~lgis~~tv~~ 154 (169)
T TIGR02954 133 YHDLTIKEIAEVMNKPEGTVKT 154 (169)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3588888999999998887653
No 262
>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=29.52 E-value=76 Score=15.26 Aligned_cols=22 Identities=27% Similarity=0.315 Sum_probs=11.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|...+|+..|++...+..+
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~ 32 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKI 32 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 4556666666666665555543
No 263
>cd08010 yceG_like proteins similar to Escherichia coli yceG. The gene product of Escherichia coli yceG has been erroneously annotated as an aminodeoxychorismate lyase. Its overexpression has been reported to cause abnormal biofilm architecture, and it has been reported to be part of a putative five-gene operon. It might function as a periplasmic solute-binding protein. The family also includes Streptomyces caeruleus NovB, an uncharacterized member of the novobiocin biosynthetic gene cluster.
Probab=29.46 E-value=1.3e+02 Score=19.36 Aligned_cols=28 Identities=29% Similarity=0.165 Sum_probs=21.6
Q ss_pred cEEEEccCCcHHHHHHHh----CCCHHHHHHh
Q 037180 17 RIVEILRGDTLWGFSMKC----GVSIDAIKEA 44 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~----~~~~~~l~~~ 44 (66)
...++.+|.|+++|+++. +++.+++...
T Consensus 29 ~~vti~eG~t~~~i~~~l~~~~~~~~~~f~~~ 60 (245)
T cd08010 29 VKVTIPEGYTLKQIAKALSKAGGLSDAEFLAA 60 (245)
T ss_pred EEEEEcCCccHHHHHHHHHhccCCCHHHHHHH
Confidence 468899999999999876 5666665543
No 264
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=29.40 E-value=69 Score=14.70 Aligned_cols=20 Identities=10% Similarity=0.072 Sum_probs=15.6
Q ss_pred cCCcHHHHHHHhCCCHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~ 42 (66)
..-++.+|+++++++...+.
T Consensus 9 ~~~~~~~i~~~l~is~~~v~ 28 (66)
T smart00418 9 GELCVCELAEILGLSQSTVS 28 (66)
T ss_pred CCccHHHHHHHHCCCHHHHH
Confidence 34578899999999877654
No 265
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=29.31 E-value=81 Score=17.50 Aligned_cols=20 Identities=15% Similarity=0.419 Sum_probs=16.9
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+.+|+++..|..+=
T Consensus 2 ~Ige~A~~~gvs~~tlR~ye 21 (107)
T cd01111 2 SISQLALDAGVSVHIVRDYL 21 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998774
No 266
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=29.29 E-value=54 Score=18.43 Aligned_cols=35 Identities=14% Similarity=0.095 Sum_probs=25.1
Q ss_pred HHHHHHHhCCCHHHHHHhhC---CCCCCcCCCCEEEEc
Q 037180 27 LWGFSMKCGVSIDAIKEANG---LSGDTIYYSIICIFL 61 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~~N~---l~~~~l~~G~~l~i~ 61 (66)
+.+||+-||.++..-.++-. +++.-...|.++.+.
T Consensus 48 ~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~IivD 85 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKIIVD 85 (96)
T ss_pred HHHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEEEEe
Confidence 56899999999877666552 344556678888774
No 267
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=29.27 E-value=84 Score=16.86 Aligned_cols=20 Identities=15% Similarity=-0.077 Sum_probs=15.0
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.-++.++|+++|++...|.+
T Consensus 21 ~~~~~~lA~~~~~S~~~l~r 40 (107)
T PRK10219 21 PLNIDVVAKKSGYSKWYLQR 40 (107)
T ss_pred CCCHHHHHHHHCCCHHHHHH
Confidence 35788899988888776653
No 268
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=29.18 E-value=66 Score=20.15 Aligned_cols=24 Identities=29% Similarity=0.487 Sum_probs=18.4
Q ss_pred EEccCCcH---HHHHHHhCCCHHHHHH
Q 037180 20 EILRGDTL---WGFSMKCGVSIDAIKE 43 (66)
Q Consensus 20 ~V~~GdTl---~~Ia~~~~~~~~~l~~ 43 (66)
..++||-| -++|++||++..-+.+
T Consensus 19 ~l~pG~~LpsE~eLae~~gVSRtpVRE 45 (253)
T PRK10421 19 NLEAGMKLPAERQLAMQLGVSRNSLRE 45 (253)
T ss_pred CCCCCCcCCCHHHHHHHhCCCHHHHHH
Confidence 46789877 3799999999665543
No 269
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=29.17 E-value=73 Score=19.15 Aligned_cols=22 Identities=14% Similarity=0.077 Sum_probs=16.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHhh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
--|...||+..|++...|.+|-
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHH
T ss_pred cchHHHHHHHhCCCHHHHHHHH
Confidence 3678999999999999998874
No 270
>PF07027 DUF1318: Protein of unknown function (DUF1318); InterPro: IPR008309 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.05 E-value=46 Score=18.48 Aligned_cols=34 Identities=6% Similarity=0.005 Sum_probs=22.0
Q ss_pred HHHHHHHhCCCHHHHHHhhCCCC-CCcCCCCEEEE
Q 037180 27 LWGFSMKCGVSIDAIKEANGLSG-DTIYYSIICIF 60 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~~N~l~~-~~l~~G~~l~i 60 (66)
...||++.|++++++...-.-.. ....+|+-+..
T Consensus 53 Y~~iA~~ng~t~~~V~~~~a~k~~~~a~~G~~vq~ 87 (95)
T PF07027_consen 53 YQEIAKKNGITVEQVAATAAQKWIERAPPGQYVQD 87 (95)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhCCCCcEEEC
Confidence 45788888999888776654322 44455665543
No 271
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=28.93 E-value=26 Score=19.31 Aligned_cols=17 Identities=41% Similarity=0.671 Sum_probs=13.5
Q ss_pred EccC--CcHHHHHHHhCCC
Q 037180 21 ILRG--DTLWGFSMKCGVS 37 (66)
Q Consensus 21 V~~G--dTl~~Ia~~~~~~ 37 (66)
+++| ||.|.|=++||=+
T Consensus 42 ierGR~ETtW~vLR~FgY~ 60 (89)
T PF08356_consen 42 IERGRHETTWTVLRKFGYD 60 (89)
T ss_pred HHhCcchHHHHHHHHcCCC
Confidence 4556 9999999998765
No 272
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=28.87 E-value=92 Score=17.77 Aligned_cols=21 Identities=10% Similarity=0.155 Sum_probs=18.0
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|-+..+||+.+|++...+..
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~ 146 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGT 146 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHH
Confidence 789999999999999887653
No 273
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=28.68 E-value=86 Score=19.90 Aligned_cols=22 Identities=14% Similarity=0.022 Sum_probs=18.5
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+.+|++...+.+.
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~ 239 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRR 239 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHH
Confidence 5889999999999998887653
No 274
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=28.55 E-value=71 Score=16.13 Aligned_cols=44 Identities=16% Similarity=0.116 Sum_probs=32.3
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCCC--C-CCcCCCCEEEE
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGLS--G-DTIYYSIICIF 60 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~--~-~~l~~G~~l~i 60 (66)
...+.+..+-||..+.++++-..+ +.=.|+.. . ..+..|+.|.+
T Consensus 7 ~k~~~~~~~~tl~~lr~~~k~~~D-I~I~NGF~~~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 7 EKEIETEENTTLFELRKESKPDAD-IVILNGFPTKEDIELKEGDEVFL 53 (57)
T ss_pred CEEEEcCCCcCHHHHHHhhCCCCC-EEEEcCcccCCccccCCCCEEEE
Confidence 456778888999999999877554 55678753 2 56788888754
No 275
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=28.52 E-value=88 Score=19.15 Aligned_cols=22 Identities=14% Similarity=0.119 Sum_probs=17.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-+...||+.+|++...+...
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~ 214 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRL 214 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 5788899999999988887654
No 276
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.40 E-value=93 Score=18.34 Aligned_cols=22 Identities=14% Similarity=0.078 Sum_probs=17.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-++.+||+.+|++...+..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~ 174 (189)
T PRK09648 153 VVGLSAEETAEAVGSTPGAVRV 174 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3588999999999999887653
No 277
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=28.34 E-value=88 Score=19.89 Aligned_cols=23 Identities=17% Similarity=0.078 Sum_probs=19.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-|+.+||+.+|++...+...
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~ 241 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQI 241 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999998887654
No 278
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=28.20 E-value=81 Score=18.33 Aligned_cols=21 Identities=14% Similarity=0.246 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+++|+++..|.-+=.
T Consensus 3 ~I~EvA~~~Gvs~~tLRyYE~ 23 (139)
T cd01110 3 SVGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999987753
No 279
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 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 essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=28.09 E-value=73 Score=19.39 Aligned_cols=20 Identities=15% Similarity=-0.089 Sum_probs=15.3
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
|...+|++||++.--+...-
T Consensus 106 Tr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 106 TRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred hHHHHHHHhCCCHHHHHHhc
Confidence 67789999999877665543
No 280
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=27.93 E-value=85 Score=17.87 Aligned_cols=20 Identities=25% Similarity=0.384 Sum_probs=16.9
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+++|++...|.-+=
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye 21 (127)
T TIGR02047 2 KIGELAQKTGVSVETIRFYE 21 (127)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998664
No 281
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=27.68 E-value=94 Score=19.25 Aligned_cols=23 Identities=13% Similarity=0.088 Sum_probs=19.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|-+..+||+.+|++...+...
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~ 215 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRI 215 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999999888644
No 282
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=27.61 E-value=90 Score=16.90 Aligned_cols=21 Identities=14% Similarity=0.074 Sum_probs=17.5
Q ss_pred ccEEEEccCCcHHHHHHHhCC
Q 037180 16 CRIVEILRGDTLWGFSMKCGV 36 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~ 36 (66)
....++.+|++-+++|.+.|+
T Consensus 63 KA~V~L~~g~~A~~va~kig~ 83 (84)
T PRK14548 63 KAYVKLAEEYDAEEIASRLGV 83 (84)
T ss_pred EEEEEeCCCCcHHHHHHhhcc
Confidence 346788999999999998775
No 283
>PRK05949 RNA polymerase sigma factor; Validated
Probab=27.54 E-value=88 Score=20.86 Aligned_cols=22 Identities=9% Similarity=0.135 Sum_probs=18.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|+..||+.+|++.+.+...
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~ 306 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQL 306 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHH
Confidence 5689999999999999887643
No 284
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=27.33 E-value=91 Score=18.31 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=15.8
Q ss_pred cCCcHHHHHHHhCCCHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~ 42 (66)
.|-+...||..+|+++..+.
T Consensus 152 ~g~s~~eIA~~lgis~~~v~ 171 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVK 171 (187)
T ss_pred cCCCHHHHHHHhCCChhHHH
Confidence 57888888888888877765
No 285
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=27.29 E-value=84 Score=16.29 Aligned_cols=19 Identities=11% Similarity=0.139 Sum_probs=14.6
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
-+..+||+++++++..+.+
T Consensus 26 ~s~~eiA~~~~i~~~~l~k 44 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRK 44 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHH
Confidence 4788999999999877654
No 286
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=27.23 E-value=91 Score=17.85 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=17.8
Q ss_pred CcHHHHHHHhCCCHHHHHHhh
Q 037180 25 DTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N 45 (66)
=+..++|+++|+++..|.-+=
T Consensus 4 ~tI~elA~~~gvs~~tlR~Ye 24 (120)
T TIGR02054 4 YTISRLAEDAGVSVHVVRDYL 24 (120)
T ss_pred CcHHHHHHHHCcCHHHHHHHH
Confidence 367789999999999998764
No 287
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=27.20 E-value=94 Score=17.96 Aligned_cols=21 Identities=14% Similarity=0.088 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|++...+.
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~ 160 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVK 160 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHH
Confidence 479999999999999988764
No 288
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=27.12 E-value=86 Score=18.22 Aligned_cols=20 Identities=10% Similarity=0.086 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|.-+=
T Consensus 3 ~I~e~a~~~gvs~~tlR~Ye 22 (140)
T PRK09514 3 RIGELAKLAEVTPDTLRFYE 22 (140)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998775
No 289
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=27.10 E-value=99 Score=17.60 Aligned_cols=22 Identities=14% Similarity=0.155 Sum_probs=18.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 124 ~~g~s~~eIA~~lgis~~tV~~ 145 (162)
T TIGR02983 124 YEDLSEAQVAEALGISVGTVKS 145 (162)
T ss_pred HhcCCHHHHHHHhCCCHHHHHH
Confidence 4688999999999999887653
No 290
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=27.02 E-value=93 Score=20.02 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=20.0
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-|-.|..+|+++|++.+++.++-
T Consensus 96 ~GpDL~~va~~~gls~~evI~~H 118 (223)
T COG2049 96 YGPDLAEVARHNGLSVEEVIELH 118 (223)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHh
Confidence 37889999999999999988764
No 291
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=27.01 E-value=62 Score=16.84 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=18.1
Q ss_pred EEccCCcHHHHHHHhCCCHHHH
Q 037180 20 EILRGDTLWGFSMKCGVSIDAI 41 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l 41 (66)
.|+.|-+...|++..|++..+-
T Consensus 40 lv~~Ga~~~el~~~CgL~~aEA 61 (70)
T PF10975_consen 40 LVRQGASVEELMEECGLSRAEA 61 (70)
T ss_pred HHHcCCCHHHHHHHcCCCHHHH
Confidence 4778999999999999987763
No 292
>KOG1577 consensus Aldo/keto reductase family proteins [General function prediction only]
Probab=26.74 E-value=54 Score=22.02 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=19.2
Q ss_pred EEccCCcHHHHHHHhCCCHHHHH
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
.+-..+++-+||++||.+++++.
T Consensus 218 ~ll~~~~l~~iA~K~~kt~aQIl 240 (300)
T KOG1577|consen 218 DLLEDPVLKEIAKKYNKTPAQIL 240 (300)
T ss_pred ccccCHHHHHHHHHhCCCHHHHH
Confidence 45557889999999999998865
No 293
>PF13467 RHH_4: Ribbon-helix-helix domain; PDB: 3KK4_C.
Probab=26.71 E-value=53 Score=17.09 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=13.5
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
+.|.+||++-|++..+|..
T Consensus 24 ~~L~eiA~~~g~s~~~li~ 42 (67)
T PF13467_consen 24 DALEEIAAREGLSLNALIA 42 (67)
T ss_dssp HHHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 5677899999999888764
No 294
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=26.58 E-value=1e+02 Score=19.23 Aligned_cols=23 Identities=13% Similarity=0.140 Sum_probs=19.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
+..|-|.++||+..|++...+..
T Consensus 183 ~a~G~t~~eIa~~l~is~~Tv~~ 205 (232)
T TIGR03541 183 TALGRRQADIAAILGISERTVEN 205 (232)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHH
Confidence 46899999999999999887664
No 295
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=26.49 E-value=1.1e+02 Score=18.16 Aligned_cols=21 Identities=19% Similarity=0.110 Sum_probs=18.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+..|++...+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~ 173 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVK 173 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHH
Confidence 579999999999999998875
No 296
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=1.1e+02 Score=17.62 Aligned_cols=20 Identities=25% Similarity=0.425 Sum_probs=16.3
Q ss_pred cCCcHHHHHHHhCCCHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~ 42 (66)
.|-+..+||+.+|++...+.
T Consensus 127 ~g~s~~eIA~~lgis~~tV~ 146 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIK 146 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHH
Confidence 68888888888888877765
No 297
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=26.47 E-value=1.1e+02 Score=18.03 Aligned_cols=22 Identities=5% Similarity=-0.011 Sum_probs=18.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
..|-|..+||++.|++...+..
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~ 40 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSA 40 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHH
Confidence 4789999999999999887663
No 298
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.45 E-value=95 Score=17.48 Aligned_cols=21 Identities=10% Similarity=0.099 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+.+|+++..|.-+=.
T Consensus 2 ~Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 2 TISELAREFDVTPRTLRFYED 22 (118)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999987653
No 299
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=26.35 E-value=44 Score=16.44 Aligned_cols=30 Identities=20% Similarity=0.365 Sum_probs=20.7
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHhhCCCC
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEANGLSG 49 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~ 49 (66)
.|-+.++|..||++.-.+.++|.+..++..
T Consensus 25 ~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~ 54 (68)
T PF00570_consen 25 RILSDEALLEIAKRLPTSIEELLQIPGMGK 54 (68)
T ss_dssp HHS-HHHHHHHHHH--SSHHHHHTSTTCGH
T ss_pred cccCHHHHHHHHHhCCCCHHHHHHccCCCH
Confidence 445567888999998889999888776643
No 300
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=26.15 E-value=95 Score=16.86 Aligned_cols=45 Identities=7% Similarity=-0.027 Sum_probs=33.1
Q ss_pred EEEEccCCcHHHHHHHhCCCHHHHHHhhCCCC----CCcCCCCEEEEcc
Q 037180 18 IVEILRGDTLWGFSMKCGVSIDAIKEANGLSG----DTIYYSIICIFLC 62 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~----~~l~~G~~l~i~~ 62 (66)
.|.|-+-|....+-++|++.+++|-+.-.-++ -...+|+.+.|-=
T Consensus 17 eH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~lgak~GdvVkIvR 65 (80)
T COG2012 17 EHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKIVR 65 (80)
T ss_pred ceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHccCCCCcEEEEEe
Confidence 46777778889999999999999876543322 3457788887643
No 301
>PF03398 Ist1: Regulator of Vps4 activity in the MVB pathway; InterPro: IPR005061 This is a eukaryotic protein family of unknown function.; PDB: 3GGZ_B 3GGY_B 3FRR_A 3FRS_A.
Probab=25.90 E-value=51 Score=19.85 Aligned_cols=14 Identities=14% Similarity=0.193 Sum_probs=10.5
Q ss_pred CcHHHHHHHhCCCH
Q 037180 25 DTLWGFSMKCGVSI 38 (66)
Q Consensus 25 dTl~~Ia~~~~~~~ 38 (66)
..|.+||+.||+++
T Consensus 152 ~~L~eIA~e~~i~w 165 (165)
T PF03398_consen 152 KYLKEIAKEYGIPW 165 (165)
T ss_dssp HHHHHHHHHCT-SH
T ss_pred HHHHHHHHHcCCCC
Confidence 46789999999875
No 302
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=25.69 E-value=93 Score=21.29 Aligned_cols=22 Identities=18% Similarity=0.302 Sum_probs=18.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..-||..|++.||++-+++.+.
T Consensus 298 ~~~TLeevg~~~~isrERvRQI 319 (342)
T COG0568 298 EPKTLEELGEEFGISRERVRQI 319 (342)
T ss_pred CcchHHHHHHHhCCcHHHHHHH
Confidence 4679999999999998887654
No 303
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=25.68 E-value=95 Score=15.10 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=15.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|=|...+|++.|++...+.++
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~i 34 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRI 34 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 4667778888888888777665
No 304
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.64 E-value=1e+02 Score=15.52 Aligned_cols=20 Identities=20% Similarity=0.124 Sum_probs=16.0
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+.+|++...+..|.
T Consensus 11 ~~~~lAkalGVs~~aVs~W~ 30 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQWG 30 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHhc
Confidence 34578999999999999994
No 305
>PRK10072 putative transcriptional regulator; Provisional
Probab=25.63 E-value=1.2e+02 Score=16.72 Aligned_cols=25 Identities=28% Similarity=0.247 Sum_probs=19.2
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-+.|-|-..+|+..|++...+..|=
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE 67 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWE 67 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4457788888888888888887773
No 306
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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. This subgroup lacks one of the c
Probab=25.62 E-value=1e+02 Score=17.66 Aligned_cols=20 Identities=15% Similarity=0.219 Sum_probs=16.7
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|.-+=
T Consensus 2 ~IgE~A~~~gvs~~TLRyYE 21 (133)
T cd04787 2 KVKELANAAGVTPDTVRFYT 21 (133)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999997664
No 307
>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=25.59 E-value=83 Score=14.42 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=15.7
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 037180 24 GDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~ 43 (66)
+-|+.+|+++-|++...+..
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~ 35 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYR 35 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHH
T ss_pred hCCHHHHHHHHccchhhHHH
Confidence 45788899998888887764
No 308
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=25.45 E-value=85 Score=17.56 Aligned_cols=19 Identities=11% Similarity=0.039 Sum_probs=11.8
Q ss_pred cCCcHHHHHHHhCCCHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAI 41 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l 41 (66)
.|-+..+||+..|+++..+
T Consensus 122 ~~~s~~EIA~~l~is~~tV 140 (142)
T TIGR03209 122 EDMKEIDIAKKLHISRQSV 140 (142)
T ss_pred cCCCHHHHHHHHCcCHHhh
Confidence 4556666666666666543
No 309
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=25.38 E-value=1.2e+02 Score=17.30 Aligned_cols=22 Identities=18% Similarity=0.184 Sum_probs=17.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+...||+.+|++...+..
T Consensus 126 ~~~~s~~eIA~~lgis~~tv~~ 147 (161)
T PRK12541 126 YYGFSYKEIAEMTGLSLAKVKI 147 (161)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH
Confidence 4678888899999988877653
No 310
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=25.36 E-value=1.1e+02 Score=17.98 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=18.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|++...+.
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~ 175 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVK 175 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHH
Confidence 468999999999999988766
No 311
>PRK06437 hypothetical protein; Provisional
Probab=25.34 E-value=69 Score=16.25 Aligned_cols=45 Identities=13% Similarity=0.075 Sum_probs=32.5
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHH-HhhC--CCC-CCcCCCCEEEE
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIK-EANG--LSG-DTIYYSIICIF 60 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~-~~N~--l~~-~~l~~G~~l~i 60 (66)
.+.+.+..+-|+.++.++++++.+.+. ..|+ +.. ..+..|++|.|
T Consensus 12 ~~~~~i~~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Vei 60 (67)
T PRK06437 12 NKTIEIDHELTVNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLI 60 (67)
T ss_pred ceEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEE
Confidence 356778888999999999999766543 3454 333 56788888855
No 312
>PRK13749 transcriptional regulator MerD; Provisional
Probab=25.24 E-value=90 Score=17.97 Aligned_cols=20 Identities=20% Similarity=0.419 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+..++|+++|+++..|.-+=
T Consensus 5 tIgelA~~~gvS~~tiR~YE 24 (121)
T PRK13749 5 TVSRLALDAGVSVHIVRDYL 24 (121)
T ss_pred cHHHHHHHHCCCHHHHHHHH
Confidence 56789999999999998664
No 313
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=25.23 E-value=97 Score=18.70 Aligned_cols=21 Identities=14% Similarity=0.131 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
++..+|+++|++...|..+=.
T Consensus 3 ~I~evA~~~gvs~~tLRyYe~ 23 (172)
T cd04790 3 TISQLARQFGLSRSTLLYYER 23 (172)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999887653
No 314
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=25.18 E-value=99 Score=18.48 Aligned_cols=22 Identities=18% Similarity=0.149 Sum_probs=18.1
Q ss_pred CcHHHHHHHhCCCHHHHHHhhC
Q 037180 25 DTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
=+...+|+++|++...|.-+=.
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE~ 33 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYES 33 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHHH
Confidence 3567899999999999987753
No 315
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=25.15 E-value=93 Score=22.57 Aligned_cols=22 Identities=18% Similarity=0.211 Sum_probs=19.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.+-||..|++.||++.+++.+.
T Consensus 575 ~~~tl~ei~~~lgvs~eRVrQi 596 (619)
T PRK05658 575 TDHTLEEVGKQFDVTRERIRQI 596 (619)
T ss_pred CCccHHHHHHHhCCCHHHHHHH
Confidence 5679999999999999888754
No 316
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=25.11 E-value=1.2e+02 Score=17.21 Aligned_cols=22 Identities=27% Similarity=0.303 Sum_probs=17.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 123 ~~~~s~~EIA~~lgis~~tV~~ 144 (163)
T PRK07037 123 LHGETQKDIARELGVSPTLVNF 144 (163)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3578888899999988877654
No 317
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=25.10 E-value=1.1e+02 Score=17.37 Aligned_cols=21 Identities=14% Similarity=0.036 Sum_probs=17.2
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|-+..+||+.+|++...+..
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~ 157 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKI 157 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHH
Confidence 588888999999999877653
No 318
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.05 E-value=1.2e+02 Score=17.88 Aligned_cols=22 Identities=18% Similarity=0.234 Sum_probs=18.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 142 ~~g~s~~EIA~~lgis~~tV~~ 163 (186)
T PRK05602 142 YQGLSNIEAAAVMDISVDALES 163 (186)
T ss_pred hcCCCHHHHHHHhCcCHHHHHH
Confidence 4689999999999999888654
No 319
>PRK09726 antitoxin HipB; Provisional
Probab=25.03 E-value=1.2e+02 Score=15.97 Aligned_cols=23 Identities=22% Similarity=0.170 Sum_probs=18.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
+.|-|...+|++.|++...+.++
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~ 45 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNF 45 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 45777888888888888887765
No 320
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 su
Probab=24.81 E-value=1.1e+02 Score=17.72 Aligned_cols=20 Identities=10% Similarity=0.210 Sum_probs=16.9
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
++..+|+.+|++...|.-+=
T Consensus 2 ~Ige~a~~~gvs~~tLRyYE 21 (131)
T cd04786 2 KIGELAKRSGMAASRIRFYE 21 (131)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998774
No 321
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=24.77 E-value=1.2e+02 Score=17.65 Aligned_cols=21 Identities=10% Similarity=0.189 Sum_probs=17.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|++...+.
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~ 172 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVR 172 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHH
Confidence 478999999999999987765
No 322
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.70 E-value=1.1e+02 Score=18.02 Aligned_cols=22 Identities=9% Similarity=0.148 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|+++..+..
T Consensus 145 ~~~~s~~eIA~~lgis~~tV~~ 166 (189)
T PRK12515 145 YHEKSVEEVGEIVGIPESTVKT 166 (189)
T ss_pred HcCCCHHHHHHHHCcCHHHHHH
Confidence 3688899999999999887753
No 323
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=24.67 E-value=1.2e+02 Score=16.34 Aligned_cols=46 Identities=11% Similarity=0.012 Sum_probs=32.6
Q ss_pred EEEccCCcHHHHHHHhCCCHHHHHHhhCCCC----CCcCCCCEEEEcccC
Q 037180 19 VEILRGDTLWGFSMKCGVSIDAIKEANGLSG----DTIYYSIICIFLCLS 64 (66)
Q Consensus 19 y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l~~----~~l~~G~~l~i~~~~ 64 (66)
|.+-.-+-...+-++|++...+|...-.-++ -.+.+||.+.|-=.|
T Consensus 15 H~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S 64 (79)
T PRK09570 15 HEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRKS 64 (79)
T ss_pred eEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEEEECC
Confidence 4555556667888999999999876654333 367889999884433
No 324
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=24.50 E-value=96 Score=19.63 Aligned_cols=19 Identities=16% Similarity=0.244 Sum_probs=15.1
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
|+.+||++.|++....-++
T Consensus 3 ti~dIA~~agVS~sTVSr~ 21 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRV 21 (311)
T ss_pred cHHHHHHHhCCCHHHHHHH
Confidence 7889999999998765543
No 325
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=24.47 E-value=67 Score=15.73 Aligned_cols=45 Identities=11% Similarity=-0.013 Sum_probs=29.6
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHHHhhCC--C-----CCCcCCCCEEEE
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIKEANGL--S-----GDTIYYSIICIF 60 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~~~N~l--~-----~~~l~~G~~l~i 60 (66)
...+.+.+|-|+.++-+.++....-....|+. . ...+..|++|-|
T Consensus 7 g~~~~~~~~~tl~~ll~~l~~~~~~~v~vN~~~v~~~~~~~~~L~~gD~vei 58 (65)
T PRK06944 7 QQTLSLPDGATVADALAAYGARPPFAVAVNGDFVARTQHAARALAAGDRLDL 58 (65)
T ss_pred CEEEECCCCCcHHHHHHhhCCCCCeEEEECCEEcCchhcccccCCCCCEEEE
Confidence 34567778889999988887764333345642 1 235788888855
No 326
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=24.47 E-value=1.2e+02 Score=19.05 Aligned_cols=24 Identities=13% Similarity=0.050 Sum_probs=19.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
..|-|+..||+.+|++...+.+.-
T Consensus 197 ~~~~t~~EIA~~lgis~~~V~q~~ 220 (231)
T PRK12427 197 QHEMSLKEIALVLDLTEARICQLN 220 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 358899999999999998876543
No 327
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=24.46 E-value=96 Score=19.93 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=15.3
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
|+.+||++.|++...+-++
T Consensus 3 ti~dIA~~aGVS~~TVSrv 21 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRV 21 (346)
T ss_pred CHHHHHHHhCCCHHHHHHH
Confidence 7889999999998775543
No 328
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=24.42 E-value=92 Score=16.76 Aligned_cols=25 Identities=16% Similarity=0.219 Sum_probs=17.7
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.-..|=.+..|+++++++..++..+
T Consensus 61 ~~~~Gv~v~~I~~~l~~~~~~v~~a 85 (102)
T PF08784_consen 61 NSEEGVHVDEIAQQLGMSENEVRKA 85 (102)
T ss_dssp --TTTEEHHHHHHHSTS-HHHHHHH
T ss_pred CCCCcccHHHHHHHhCcCHHHHHHH
Confidence 3456788889999999998887754
No 329
>PF08972 DUF1902: Domain of unknown function (DUF1902); InterPro: IPR015066 Members of these prokaryotic proteins adopt a fold consisting of one alpha-helix and four beta-strands. Their function has not, as yet, been elucidated []. ; PDB: 1WV8_A.
Probab=24.36 E-value=30 Score=17.41 Aligned_cols=28 Identities=32% Similarity=0.343 Sum_probs=20.8
Q ss_pred EccCCcHHHHHHHhCCCHHHHHHhhCCC
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKEANGLS 48 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~~N~l~ 48 (66)
|-..+|+..+.+|...-..+|...|+..
T Consensus 25 vtEA~Tle~L~~kl~~~ipeLLelN~~~ 52 (54)
T PF08972_consen 25 VTEADTLEELIEKLRVMIPELLELNGVP 52 (54)
T ss_dssp --EESSHHHHHHHHHHHHHHHHHHS---
T ss_pred eecCccHHHHHHHHHHHHHHHHHhcCCC
Confidence 4457999999999988899999998754
No 330
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.35 E-value=1.3e+02 Score=17.56 Aligned_cols=22 Identities=36% Similarity=0.480 Sum_probs=18.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+..|+++..+..
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~ 154 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKK 154 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHH
Confidence 4688999999999999888763
No 331
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=24.33 E-value=84 Score=22.96 Aligned_cols=20 Identities=30% Similarity=0.353 Sum_probs=16.7
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
..|..++++||.+++++.++
T Consensus 307 ~~L~~l~RKY~~~~~~l~~~ 326 (557)
T COG0497 307 FALKSLARKYGVTIEDLLEY 326 (557)
T ss_pred HHHHHHHHHhCCCHHHHHHH
Confidence 45788999999999998764
No 332
>PF13984 MsyB: MsyB protein
Probab=24.28 E-value=22 Score=20.47 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=11.9
Q ss_pred cEEEEccCCcHHHH
Q 037180 17 RIVEILRGDTLWGF 30 (66)
Q Consensus 17 ~~y~V~~GdTl~~I 30 (66)
..|.+|.||++|..
T Consensus 36 QKYvmqDGdimWqa 49 (122)
T PF13984_consen 36 QKYVMQDGDIMWQA 49 (122)
T ss_pred HHHhhhccchHHHH
Confidence 46899999999975
No 333
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=24.28 E-value=1.2e+02 Score=18.14 Aligned_cols=19 Identities=21% Similarity=0.200 Sum_probs=12.5
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
+++..||+.|++++.+|..
T Consensus 50 ~~l~~ia~~l~v~~~~l~~ 68 (185)
T PRK09943 50 STLQKLLKVYGLSLSEFFS 68 (185)
T ss_pred HHHHHHHHHhCCCHHHHcc
Confidence 3466677777777777653
No 334
>smart00455 RBD Raf-like Ras-binding domain.
Probab=24.28 E-value=1.1e+02 Score=15.68 Aligned_cols=45 Identities=13% Similarity=0.054 Sum_probs=26.4
Q ss_pred cEEEEccCCcHH----HHHHHhCCCHHHHHHh----h-CC--CC-CCcCCCCEEEEc
Q 037180 17 RIVEILRGDTLW----GFSMKCGVSIDAIKEA----N-GL--SG-DTIYYSIICIFL 61 (66)
Q Consensus 17 ~~y~V~~GdTl~----~Ia~~~~~~~~~l~~~----N-~l--~~-~~l~~G~~l~i~ 61 (66)
....+++|.|+. .+-+++|+.+++..-. + .+ .. .....|+.+.+.
T Consensus 12 ~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ldl~~~~~~l~~~el~ve 68 (70)
T smart00455 12 TVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLDLNQPISSLDGQELVVE 68 (70)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCcceecCCccccccCceEEEE
Confidence 457889996655 5566788887773211 1 12 22 334467777664
No 335
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=24.20 E-value=1e+02 Score=17.91 Aligned_cols=20 Identities=20% Similarity=0.140 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+.+|+++..|..|=
T Consensus 2 ~I~e~a~~~gvs~~TLR~Ye 21 (134)
T cd04779 2 RIGQLAHLAGVSKRTIDYYT 21 (134)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998875
No 336
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=24.13 E-value=1.1e+02 Score=15.40 Aligned_cols=21 Identities=10% Similarity=0.186 Sum_probs=16.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|-+..+||+..|++...+.+.
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~ 42 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHH
Confidence 468999999999998776544
No 337
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=24.09 E-value=1.1e+02 Score=16.70 Aligned_cols=20 Identities=20% Similarity=0.228 Sum_probs=16.7
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+.+|+++..|.-+=
T Consensus 2 ~I~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 2 TIGEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred cHHHHHHHhCCCHHHHHHHH
Confidence 45679999999999998775
No 338
>PRK09526 lacI lac repressor; Reviewed
Probab=24.00 E-value=98 Score=19.72 Aligned_cols=20 Identities=25% Similarity=0.375 Sum_probs=15.9
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-|+.+||++.|++....=++
T Consensus 6 ~ti~dIA~~aGVS~~TVSrv 25 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRV 25 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHH
Confidence 38999999999997765443
No 339
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=23.97 E-value=1.1e+02 Score=17.16 Aligned_cols=19 Identities=21% Similarity=0.064 Sum_probs=14.2
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 037180 25 DTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~ 43 (66)
-++.++|+..|+++..|.+
T Consensus 26 ~sl~~lA~~~g~S~~~l~r 44 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQR 44 (127)
T ss_pred CCHHHHHHHHCcCHHHHHH
Confidence 5778888888888776654
No 340
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.96 E-value=1.3e+02 Score=17.65 Aligned_cols=22 Identities=14% Similarity=0.164 Sum_probs=17.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+...||+.+|++...+..
T Consensus 141 ~~g~s~~EIA~~l~is~~tv~~ 162 (179)
T PRK09415 141 YEELSIKEIAEVTGVNENTVKT 162 (179)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH
Confidence 3588899999999999887653
No 341
>COG3661 AguA Alpha-glucuronidase [Carbohydrate transport and metabolism]
Probab=23.95 E-value=98 Score=22.54 Aligned_cols=29 Identities=21% Similarity=0.298 Sum_probs=22.6
Q ss_pred cEEEEccCCcHHH-HHHHhCCCHHHHHHhh
Q 037180 17 RIVEILRGDTLWG-FSMKCGVSIDAIKEAN 45 (66)
Q Consensus 17 ~~y~V~~GdTl~~-Ia~~~~~~~~~l~~~N 45 (66)
..|+.+.|+|||. +-.+|.-.++....+|
T Consensus 598 ydhrLKSG~Tl~q~myd~hf~Gve~ve~~~ 627 (684)
T COG3661 598 YDHRLKSGDTLWQGMYDRHFRGVEYVEGMN 627 (684)
T ss_pred ccccccccccHHHHHHHHhcccHHHHHHHH
Confidence 4689999999986 6667777777777666
No 342
>PF14210 DUF4322: Domain of unknown function (DUF4322)
Probab=23.89 E-value=74 Score=16.57 Aligned_cols=21 Identities=19% Similarity=0.178 Sum_probs=16.7
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|+...-++.|+++++.+..
T Consensus 42 ~nDSvEnksk~y~vspqtVrn 62 (66)
T PF14210_consen 42 WNDSVENKSKAYNVSPQTVRN 62 (66)
T ss_pred hcchhhhhhhccCCChHHHHh
Confidence 368888888999999988763
No 343
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=23.89 E-value=1.3e+02 Score=17.74 Aligned_cols=21 Identities=14% Similarity=0.262 Sum_probs=16.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|+++..+.
T Consensus 163 ~~~~s~~eIA~~l~~s~~tV~ 183 (198)
T TIGR02859 163 LDGKSYQEIACDLNRHVKSID 183 (198)
T ss_pred HcCCCHHHHHHHHCCCHHHHH
Confidence 358888899999998887764
No 344
>PRK13503 transcriptional activator RhaS; Provisional
Probab=23.87 E-value=1e+02 Score=19.17 Aligned_cols=22 Identities=5% Similarity=0.072 Sum_probs=17.3
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
..-|+.++|+.+|++...+.+.
T Consensus 186 ~~~tl~~lA~~~~lS~~~l~r~ 207 (278)
T PRK13503 186 EEVNWEALADQFSLSLRTLHRQ 207 (278)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
Confidence 3568899999999998876643
No 345
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.87 E-value=81 Score=18.44 Aligned_cols=22 Identities=14% Similarity=0.084 Sum_probs=18.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.|-|..+||..|+++-..+...
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nf 100 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNF 100 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHH
Confidence 5889999999999998776543
No 346
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.80 E-value=1.2e+02 Score=17.55 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=17.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+...||+.+|++...+..
T Consensus 150 ~~g~s~~eIA~~lgis~~~v~~ 171 (187)
T TIGR02948 150 MEDLSLKEISEILDLPVGTVKT 171 (187)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH
Confidence 4688888999999998877653
No 347
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.80 E-value=1.2e+02 Score=17.90 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=21.8
Q ss_pred EEccCCcHHHHHHHhCCCHHHHHHhh
Q 037180 20 EILRGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 20 ~V~~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
.=..|-|+..||.+.+++.....++.
T Consensus 95 ~~r~~~TW~~IA~~l~i~erta~r~~ 120 (130)
T PF05263_consen 95 DRRSRRTWYQIAQKLHISERTARRWR 120 (130)
T ss_pred cccccchHHHHHHHhCccHHHHHHHH
Confidence 34468999999999999998888775
No 348
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=23.76 E-value=1.1e+02 Score=17.93 Aligned_cols=21 Identities=19% Similarity=0.314 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+...+|+++|+++..|.-+=.
T Consensus 3 ~IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 3 TVGELAKRSGVAVSALHFYES 23 (142)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999987753
No 349
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=23.72 E-value=1.3e+02 Score=16.23 Aligned_cols=20 Identities=10% Similarity=-0.105 Sum_probs=16.0
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-++..||++|++++..+..+
T Consensus 17 ~s~~~Ls~~~~~p~~~VeaM 36 (78)
T PRK15431 17 MEAAQISQTLNTPQPMINAM 36 (78)
T ss_pred ccHHHHHHHHCcCHHHHHHH
Confidence 45778999999998876654
No 350
>PRK15340 transcriptional regulator InvF; Provisional
Probab=23.71 E-value=1.3e+02 Score=19.18 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=18.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
....++.++|+++|++...+.+.
T Consensus 123 ~~~~sleeLA~~~gvS~r~f~Rl 145 (216)
T PRK15340 123 TSGNTMRMLGEDYGVSYTHFRRL 145 (216)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHH
Confidence 34678999999999998877654
No 351
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=23.60 E-value=62 Score=17.42 Aligned_cols=45 Identities=4% Similarity=-0.078 Sum_probs=31.5
Q ss_pred ccEEEEccCCcHHHHHHHhCCCHHHHH-HhhC-------CCCCCcCCCCEEEE
Q 037180 16 CRIVEILRGDTLWGFSMKCGVSIDAIK-EANG-------LSGDTIYYSIICIF 60 (66)
Q Consensus 16 ~~~y~V~~GdTl~~Ia~~~~~~~~~l~-~~N~-------l~~~~l~~G~~l~i 60 (66)
...+.+..+-|+.++-..++.....+. +.|+ .....+..|+.|-|
T Consensus 25 G~~~~~~~~~tl~~LL~~l~~~~~~vAVevNg~iVpr~~w~~t~L~egD~IEI 77 (84)
T PRK06083 25 DQSIQVDISSSLAQIIAQLSLPELGCVFAINNQVVPRSEWQSTVLSSGDAISL 77 (84)
T ss_pred CeEEEcCCCCcHHHHHHHcCCCCceEEEEECCEEeCHHHcCcccCCCCCEEEE
Confidence 346778888899888888888766544 6664 33345777888755
No 352
>PRK09492 treR trehalose repressor; Provisional
Probab=23.58 E-value=93 Score=19.56 Aligned_cols=20 Identities=15% Similarity=0.159 Sum_probs=16.0
Q ss_pred CcHHHHHHHhCCCHHHHHHh
Q 037180 25 DTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 25 dTl~~Ia~~~~~~~~~l~~~ 44 (66)
-|+.+||++.|++...+-++
T Consensus 5 ~ti~dIA~~agVS~~TVSrv 24 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRV 24 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHH
Confidence 48899999999997775543
No 353
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=23.40 E-value=83 Score=19.58 Aligned_cols=23 Identities=17% Similarity=0.254 Sum_probs=18.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHHhh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~N 45 (66)
-|..|..+|+..|++.+++.+.=
T Consensus 98 ~g~DL~~vA~~~gls~~evi~~H 120 (202)
T PF02682_consen 98 FGPDLEEVAEHNGLSVEEVIRLH 120 (202)
T ss_dssp THTTHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCHHHHHHHhCcCHHHHHHHH
Confidence 37889999999999999988753
No 354
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=23.20 E-value=1.1e+02 Score=15.97 Aligned_cols=17 Identities=29% Similarity=0.310 Sum_probs=11.2
Q ss_pred cHHHHHHHhCCCHHHHH
Q 037180 26 TLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~ 42 (66)
+...+|+.|+++.+.+.
T Consensus 102 ~~~~la~~f~vs~~~~~ 118 (122)
T PF06114_consen 102 SIEELAEYFGVSPEAIA 118 (122)
T ss_dssp SHHHHHHHHT--HHHHH
T ss_pred hHHHHHHHHCCCHHHHh
Confidence 34449999999988765
No 355
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=23.09 E-value=1.3e+02 Score=18.37 Aligned_cols=22 Identities=9% Similarity=0.063 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-|+.+||+.+|++...+..
T Consensus 189 ~~~~s~~eIA~~lgis~~tV~~ 210 (224)
T TIGR02479 189 YEELNLKEIGEVLGLTESRVSQ 210 (224)
T ss_pred hCCCCHHHHHHHhCCCHHHHHH
Confidence 4678999999999999888764
No 356
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=22.99 E-value=1.2e+02 Score=17.59 Aligned_cols=21 Identities=14% Similarity=0.145 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHhhC
Q 037180 26 TLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..++|+++|++...|.-+-.
T Consensus 2 ~Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 2 NISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 356899999999999987754
No 357
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=22.96 E-value=1.3e+02 Score=18.74 Aligned_cols=23 Identities=22% Similarity=0.276 Sum_probs=19.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHhhC
Q 037180 24 GDTLWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~N~ 46 (66)
|-.|..+|+..|++.+++.+.-.
T Consensus 100 gpDL~~vA~~~gLs~~evi~~Hs 122 (201)
T smart00796 100 GPDLEFVARHNGLSVDEVIRLHS 122 (201)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHh
Confidence 44899999999999999987753
No 358
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=22.96 E-value=1.2e+02 Score=15.50 Aligned_cols=43 Identities=7% Similarity=0.041 Sum_probs=29.0
Q ss_pred EEEEccCCcHHHHHHHhCCC-HHHHHHhh------CC----CCCCcCCCCEEEEc
Q 037180 18 IVEILRGDTLWGFSMKCGVS-IDAIKEAN------GL----SGDTIYYSIICIFL 61 (66)
Q Consensus 18 ~y~V~~GdTl~~Ia~~~~~~-~~~l~~~N------~l----~~~~l~~G~~l~i~ 61 (66)
.|.| .|.-+..+.+++... .+.+.+.+ ++ ....+..|++|.|-
T Consensus 10 ~~~V-~g~~ier~~~~~~~~~~e~~~~f~~~L~~~Gv~~~L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 10 VFVV-SGKKIERWVAKTPFNNDENLRRFARKLKKLGVEDALRKAGAKDGDTVRIG 63 (69)
T ss_pred eEEE-echHHHHHHHHcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEc
Confidence 4555 699999999998774 44444443 32 34678889988874
No 359
>PRK05713 hypothetical protein; Provisional
Probab=22.95 E-value=1.1e+02 Score=19.92 Aligned_cols=27 Identities=19% Similarity=0.144 Sum_probs=21.9
Q ss_pred CccEEEEccCCcHHHHHHHhCCCHHHH
Q 037180 15 SCRIVEILRGDTLWGFSMKCGVSIDAI 41 (66)
Q Consensus 15 ~~~~y~V~~GdTl~~Ia~~~~~~~~~l 41 (66)
...++.+.+|+||-+.+.+.|+.+.--
T Consensus 7 ~~~~~~~~~g~tlL~a~~~~gi~~~~~ 33 (312)
T PRK05713 7 GERRWSVPAGSNLLDALNAAGVAVPYS 33 (312)
T ss_pred CCeEEEECCCCcHHHHHHHcCCCCCcC
Confidence 345788999999999999998876443
No 360
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.85 E-value=1.3e+02 Score=17.08 Aligned_cols=21 Identities=19% Similarity=0.330 Sum_probs=16.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|+++..+.
T Consensus 127 ~~g~s~~EIA~~l~is~~tV~ 147 (161)
T PRK12528 127 VDGLGYGEIATELGISLATVK 147 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHH
Confidence 357888888888888887765
No 361
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=22.85 E-value=34 Score=16.35 Aligned_cols=14 Identities=29% Similarity=0.454 Sum_probs=8.4
Q ss_pred HHHHHHHhCCCHHH
Q 037180 27 LWGFSMKCGVSIDA 40 (66)
Q Consensus 27 l~~Ia~~~~~~~~~ 40 (66)
+..+|+++|++.++
T Consensus 45 ~~~la~~~~i~~~~ 58 (59)
T PF10410_consen 45 IRELAERLGISEDA 58 (59)
T ss_dssp HHHHHHHCT-SSTT
T ss_pred HHHHHHHhCcCccc
Confidence 45677777776554
No 362
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=22.71 E-value=90 Score=17.31 Aligned_cols=17 Identities=12% Similarity=0.288 Sum_probs=11.8
Q ss_pred HHHHHHHhCCCHHHHHH
Q 037180 27 LWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~ 43 (66)
+..||..||++.+++..
T Consensus 78 vhEiah~fG~~~e~l~~ 94 (97)
T PF06262_consen 78 VHEIAHHFGISDEDLDA 94 (97)
T ss_dssp HHHHHHHTT--HHHHHC
T ss_pred HHHHHHHcCCCHHHhhh
Confidence 56788899999988764
No 363
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.59 E-value=1.4e+02 Score=16.96 Aligned_cols=21 Identities=5% Similarity=0.259 Sum_probs=16.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+..|++...+.
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~ 140 (160)
T PRK09642 120 LEEKSYQEIALQEKIEVKTVE 140 (160)
T ss_pred HhCCCHHHHHHHHCCCHHHHH
Confidence 457788888888888887764
No 364
>PF03921 ICAM_N: Intercellular adhesion molecule (ICAM), N-terminal domain; InterPro: IPR013768 Intercellular adhesion molecules (ICAMs) and vascular cell adhesion molecule-1 (VCAM-1) are part of the immunoglobulin superfamily. They are important in inflammation, immune responses and in intracellular signalling events []. The ICAM family consists of five members, designated ICAM-1 to ICAM-5. They are known to bind to leucocyte integrins CD11/CD18 during inflammation and in immune responses. In addition, ICAMs may exist in soluble forms in human plasma, due to activation and proteolysis mechanisms at cell surfaces. ICAM-1 (CD54) contains five Ig-like domains. It is expressed on leucocytes, endothelial and epithelial cells, and is upregulated in response to bacterial invasion. The protein is a ligand for lymphocyte-function associated (LFA) antigens and also a receptor for CD11a,b/CD18, fibrinogen, human rhinovirus and Plasmodium falciparum-infected erythrocytes. ICAM-1 binding sites for CD11a/CD18 and its other binding partners are located in the first domain and are overlapping. ICAM-1 domain 2 seems to play an important role in maintaining the conformation of domain 1 and particularly the structural integrity of the LFA-1 ligand-binding site []. The 3-dimensional atomic structure of the tandem N-terminal Ig-like domains (D1 and D2) of ICAM-1 has been determined to 2.2A resolution and fitted into a cryoelectron microscopy reconstruction of a rhinovirus-ICAM-1 complex []. Extensive charge interactions between ICAM-1 and human rhinovirusesare largely conserved in major and minor receptor groups of rhinoviruses. The interaction of ICAMs with LFA-1 is mediated by a divalent cation bound to the insertion (I)-domain on the alpha chain of LFA-1 and the carboxyl group of a conserved glutamic acid residue on ICAMs. ICAM-2 (CD102) has two Ig-like domains. It is expressed on endothelial cells, leucocytes and platelets, and binds to CD11a'b/CD18. The protein is refractory to proinflammatory cytokines, and plays an important role in the adhesion of leucocytes to the uninduced endothelium []. ICAM-3 (CD50) contains five Ig-like domains and binds to leucocyte integrins CD11a'd/CD18. The protein plays an important role in the immune response and perhaps in signal transduction []. ICAM-4 (LW blood group Ag) is red blood cell (RBC) specific and binds to CD11a'b/CD18. It is associated with the RBC Rh antigens and could be important in retaining immature red cells in the bone marrow, or in the uptake of senescent cells into the spleen []. ICAM-5 (telencephalin) has nine Ig-like domains and is confined to the telencephalon of the brain. The role of this CD11a/CD18 binding molecule is not yet known []. VCAM-1 was first described as a cytokine-inducible endothelial adhesion molecule. It can bind to leucocyte integrin VL-4 (very late antigen-4) to recruit leucocytes to sites of inflammation []. The predominant form of VCAM-1 in vivo has an N-terminal extracellular region comprising seven Ig-like domains []. A conserved integrin-binding motif has been identified in domains 1 and 4, variants of which are present in the N-terminal domain of all members of the integrin-binding subgroup of the immunoglobulin superfamily. The structure of a VLA-4-binding fragment comprising the first two domains of VCAM-1 has been determined to 1.8A resolution. The integrin-binding motif is exposed and forms the N-terminal region of the loop between beta-strands C and D of domain 1 []. VCAM-1 domains 1 and 2 are structurally similar to ICAM-1 and ICAM-2 []. This entry represents the N-terminal domain of ICAM proteins such as ICAM-2, ICAM-3 and ICAM-4.; PDB: 3BN3_B 1T0P_B 1ZXQ_A 3TCX_A 1MQ8_A 1Z7Z_I 1IC1_A 1IAM_A.
Probab=22.55 E-value=34 Score=18.85 Aligned_cols=16 Identities=13% Similarity=-0.025 Sum_probs=12.7
Q ss_pred CCcCCCCEEEEcccCC
Q 037180 50 DTIYYSIICIFLCLSS 65 (66)
Q Consensus 50 ~~l~~G~~l~i~~~~~ 65 (66)
..+.+|..+.|.|.+|
T Consensus 13 ~vV~~G~Sv~VNCSts 28 (91)
T PF03921_consen 13 PVVPPGGSVWVNCSTS 28 (91)
T ss_dssp EEEETTEEEEEEEEES
T ss_pred cEECCCCCEEEEEcCC
Confidence 3467899999999876
No 365
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=22.54 E-value=1.2e+02 Score=15.20 Aligned_cols=19 Identities=21% Similarity=0.246 Sum_probs=13.7
Q ss_pred cHHHHHHHhCCCHHHHHHh
Q 037180 26 TLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~ 44 (66)
|+.+||++-|++...+-++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ 20 (70)
T smart00354 2 TIKDVARLAGVSKATVSRV 20 (70)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4667888888887766544
No 366
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=22.53 E-value=1.1e+02 Score=15.27 Aligned_cols=21 Identities=24% Similarity=0.275 Sum_probs=15.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|..+..+|++.|++..+|...
T Consensus 10 g~~W~~la~~Lgl~~~~I~~i 30 (79)
T cd01670 10 GKDWKKLARKLGLSDGEIDQI 30 (79)
T ss_pred hhHHHHHHHHhCCCHHHHHHH
Confidence 466778888888887776654
No 367
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=22.49 E-value=1.4e+02 Score=17.49 Aligned_cols=21 Identities=19% Similarity=0.232 Sum_probs=17.3
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|-+..+||+.+|++...+..
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~ 166 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRV 166 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHH
Confidence 588889999999999887664
No 368
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.49 E-value=1.4e+02 Score=17.54 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=18.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 136 ~~g~s~~EIA~~lgis~~tVk~ 157 (185)
T PRK12542 136 FYNLTYQEISSVMGITEANVRK 157 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4688889999999999887664
No 369
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=22.31 E-value=1.4e+02 Score=17.69 Aligned_cols=22 Identities=27% Similarity=0.412 Sum_probs=18.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 145 ~~g~s~~EIAe~lgis~~~V~~ 166 (189)
T PRK06811 145 LLGEKIEEIAKKLGLTRSAIDN 166 (189)
T ss_pred HccCCHHHHHHHHCCCHHHHHH
Confidence 3688999999999999887653
No 370
>PRK06930 positive control sigma-like factor; Validated
Probab=22.21 E-value=1.4e+02 Score=17.99 Aligned_cols=23 Identities=4% Similarity=-0.055 Sum_probs=19.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
-.|-+..+||+.+|++...+...
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~ 150 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSM 150 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 47899999999999998887644
No 371
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=22.20 E-value=93 Score=13.73 Aligned_cols=23 Identities=9% Similarity=0.014 Sum_probs=17.4
Q ss_pred EccCCcHHHHHHHhCCCHHHHHH
Q 037180 21 ILRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
+...-+..+||+.+|++...+.+
T Consensus 5 ~~~~~s~~~la~~l~~s~~tv~~ 27 (48)
T smart00419 5 VRLPLTRQEIAELLGLTRETVSR 27 (48)
T ss_pred EEeccCHHHHHHHHCCCHHHHHH
Confidence 33456778999999999877654
No 372
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=22.11 E-value=1.4e+02 Score=18.73 Aligned_cols=23 Identities=9% Similarity=-0.061 Sum_probs=18.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
-.|-|+..||+.+|++...+...
T Consensus 219 ~~g~s~~eIA~~lgis~~~V~~~ 241 (255)
T TIGR02941 219 EENLSQKETGERLGISQMHVSRL 241 (255)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999998887543
No 373
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=21.91 E-value=1.4e+02 Score=17.38 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=16.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 037180 23 RGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
.|-+...||..+|++...+..
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~ 175 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSM 175 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHH
Confidence 688888899998888877653
No 374
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=21.89 E-value=1.3e+02 Score=16.32 Aligned_cols=21 Identities=10% Similarity=-0.051 Sum_probs=17.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.-++.++|+.+|++..+|.++
T Consensus 24 ~~ti~~~AK~L~i~~~~l~~~ 44 (111)
T PF03374_consen 24 LYTIREAAKLLGIGRNKLFQW 44 (111)
T ss_pred CccHHHHHHHhCCCHHHHHHH
Confidence 367889999999998887654
No 375
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.36 E-value=1.5e+02 Score=17.33 Aligned_cols=22 Identities=27% Similarity=0.250 Sum_probs=17.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
..|-+..+||+.+|++...+..
T Consensus 143 ~~g~s~~EIA~~l~is~~tV~~ 164 (181)
T PRK12536 143 LEGLSVAETAQLTGLSESAVKV 164 (181)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4688888888888888887663
No 376
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=21.34 E-value=76 Score=20.07 Aligned_cols=25 Identities=36% Similarity=0.497 Sum_probs=18.9
Q ss_pred EEccCCcHH---HHHHHhCCCHHHHHHh
Q 037180 20 EILRGDTLW---GFSMKCGVSIDAIKEA 44 (66)
Q Consensus 20 ~V~~GdTl~---~Ia~~~~~~~~~l~~~ 44 (66)
..++||.|. .++++||++-..+.++
T Consensus 27 ~~~~G~~LP~EreLae~fgVSR~~vREA 54 (241)
T COG2186 27 ELPPGDRLPSERELAERFGVSRTVVREA 54 (241)
T ss_pred CCCCCCCCCCHHHHHHHHCCCcHHHHHH
Confidence 467787765 8999999997666544
No 377
>cd05717 Ig1_Necl-1-3_like First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-3 (also known as cell adhesion molecules CADM3, CADM1, and CADM2 respectively). Ig1_Necl-1-3_like: N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), and Necl-3 (CADM2). At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the form
Probab=21.15 E-value=49 Score=17.25 Aligned_cols=19 Identities=16% Similarity=0.139 Sum_probs=11.6
Q ss_pred hCCCC-CCcCCCCEEEEccc
Q 037180 45 NGLSG-DTIYYSIICIFLCL 63 (66)
Q Consensus 45 N~l~~-~~l~~G~~l~i~~~ 63 (66)
|++.. -.+..|+.+.+.|.
T Consensus 1 ~~~~~~~~v~~G~~v~L~C~ 20 (95)
T cd05717 1 NPVTQDVTVVEGGTATLKCR 20 (95)
T ss_pred CCcCCcEEEcCCCCEEEEEE
Confidence 34443 34567888888774
No 378
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.10 E-value=1.5e+02 Score=18.59 Aligned_cols=23 Identities=9% Similarity=0.020 Sum_probs=18.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHh
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
-.|-++..||+.+|++...+...
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~ 241 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRL 241 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHH
Confidence 36888999999999998887643
No 379
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=21.08 E-value=1.3e+02 Score=17.66 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHhh
Q 037180 26 TLWGFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 26 Tl~~Ia~~~~~~~~~l~~~N 45 (66)
+...+|+++|+++..|.-+=
T Consensus 9 ~IgevAk~~Gvs~~TLRyYE 28 (144)
T PRK13752 9 TIGVFAKAAGVNVETIRFYQ 28 (144)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998664
No 380
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.97 E-value=1.6e+02 Score=17.23 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=15.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+...||+..|+++..+.
T Consensus 149 ~~~~s~~eIA~~lgis~~~V~ 169 (186)
T PRK13919 149 YQGYTHREAAQLLGLPLGTLK 169 (186)
T ss_pred HcCCCHHHHHHHHCcCHHHHH
Confidence 357777788888888776655
No 381
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=20.93 E-value=93 Score=18.79 Aligned_cols=22 Identities=23% Similarity=0.181 Sum_probs=18.5
Q ss_pred EccCCcHHHHHHHhC-CCHHHHH
Q 037180 21 ILRGDTLWGFSMKCG-VSIDAIK 42 (66)
Q Consensus 21 V~~GdTl~~Ia~~~~-~~~~~l~ 42 (66)
...|-|...||+++| ++-+.++
T Consensus 15 w~~G~SasqIA~~lg~vsRnAVi 37 (162)
T PF07750_consen 15 WAEGLSASQIARQLGGVSRNAVI 37 (162)
T ss_pred HHcCCCHHHHHHHhCCcchhhhh
Confidence 367999999999999 8877765
No 382
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=20.69 E-value=1.1e+02 Score=13.99 Aligned_cols=17 Identities=18% Similarity=0.333 Sum_probs=12.9
Q ss_pred HHHHHhCCCHHHHHHhh
Q 037180 29 GFSMKCGVSIDAIKEAN 45 (66)
Q Consensus 29 ~Ia~~~~~~~~~l~~~N 45 (66)
+||++.|++...+-++-
T Consensus 2 ~lA~~~gvs~~tvs~~l 18 (52)
T cd01392 2 DIARAAGVSVATVSRVL 18 (52)
T ss_pred cHHHHHCcCHHHHHHHH
Confidence 47888888888777664
No 383
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.69 E-value=1.7e+02 Score=16.98 Aligned_cols=22 Identities=23% Similarity=0.363 Sum_probs=17.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~ 154 (172)
T PRK12523 133 LDGMGHAEIAERLGVSVSRVRQ 154 (172)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3578888999999999887653
No 384
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=20.61 E-value=1.5e+02 Score=15.72 Aligned_cols=20 Identities=15% Similarity=0.134 Sum_probs=16.8
Q ss_pred cEEEEccCCcHHHHHHHhCC
Q 037180 17 RIVEILRGDTLWGFSMKCGV 36 (66)
Q Consensus 17 ~~y~V~~GdTl~~Ia~~~~~ 36 (66)
...++.+|++--++|.+.|+
T Consensus 57 A~VtL~~g~~a~~va~k~g~ 76 (77)
T TIGR03636 57 AYVKLAEEYAAEEIASRLGV 76 (77)
T ss_pred EEEEECCCCcHHHHHHhhcc
Confidence 46778999999999998775
No 385
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.59 E-value=1.5e+02 Score=17.00 Aligned_cols=22 Identities=9% Similarity=-0.005 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+.+|++...+..
T Consensus 122 ~~g~s~~eIA~~lgis~~tv~~ 143 (165)
T PRK09644 122 VHELTYEEAASVLDLKLNTYKS 143 (165)
T ss_pred HhcCCHHHHHHHHCCCHHHHHH
Confidence 4688899999999999887653
No 386
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.57 E-value=1.6e+02 Score=17.33 Aligned_cols=22 Identities=9% Similarity=-0.031 Sum_probs=18.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+..+||+..|++...+..
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~ 169 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKM 169 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH
Confidence 4789999999999999887653
No 387
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=20.53 E-value=1.6e+02 Score=15.96 Aligned_cols=22 Identities=9% Similarity=-0.120 Sum_probs=17.6
Q ss_pred cCCcHHHHHHHhCCCHHHHHHh
Q 037180 23 RGDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 23 ~GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
.+.+++.|+.+.+++...+.++
T Consensus 70 ~~~~~~~I~~~l~~S~~t~yr~ 91 (100)
T PF07374_consen 70 NKLTWEQIAEELNISRRTYYRI 91 (100)
T ss_pred cCCCHHHHHHHHCCCHHHHHHH
Confidence 4688999999999998776654
No 388
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=20.52 E-value=1.4e+02 Score=15.91 Aligned_cols=21 Identities=24% Similarity=0.289 Sum_probs=16.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|..+..+|++.|++..+|...
T Consensus 13 G~~Wk~laR~LGlse~~Id~i 33 (86)
T cd08306 13 GRDWRKLARKLGLSETKIESI 33 (86)
T ss_pred hhhHHHHHHHcCCCHHHHHHH
Confidence 667788999999988877643
No 389
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=20.50 E-value=1.6e+02 Score=17.46 Aligned_cols=22 Identities=18% Similarity=0.270 Sum_probs=17.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+...||+.+|+++..+..
T Consensus 150 ~~g~s~~EIA~~lgis~~tVk~ 171 (195)
T PRK12532 150 ILGFSSDEIQQMCGISTSNYHT 171 (195)
T ss_pred HhCCCHHHHHHHHCCCHHHHHH
Confidence 4688889999999999877653
No 390
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=20.49 E-value=1.3e+02 Score=14.59 Aligned_cols=21 Identities=14% Similarity=0.108 Sum_probs=16.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
..+-|+.+||+++|++...+.
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s 42 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVS 42 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHH
Confidence 456788999999999987754
No 391
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.42 E-value=1.6e+02 Score=17.38 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=17.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|+++..+.
T Consensus 144 ~~g~s~~EIA~~lgis~~tVk 164 (185)
T PRK09649 144 LLGLSYADAAAVCGCPVGTIR 164 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHH
Confidence 468888999999999987765
No 392
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=20.32 E-value=1.6e+02 Score=15.82 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=15.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|..+..+|++.|++..+|-..
T Consensus 15 G~dW~~Lar~L~vs~~dI~~I 35 (84)
T cd08805 15 GLSWAELARELQFSVEDINRI 35 (84)
T ss_pred cchHHHHHHHcCCCHHHHHHH
Confidence 666778888888887776543
No 393
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.31 E-value=1.6e+02 Score=18.18 Aligned_cols=22 Identities=18% Similarity=0.093 Sum_probs=18.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-|...||+.+|++...+..
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~ 219 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQ 219 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHH
Confidence 4688999999999999888763
No 394
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.26 E-value=1.3e+02 Score=15.97 Aligned_cols=21 Identities=10% Similarity=0.118 Sum_probs=16.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|..+..+|++.|++..+|...
T Consensus 18 G~~Wk~Lar~LGls~~dI~~i 38 (86)
T cd08318 18 GEDWKTLAPHLEMKDKEIRAI 38 (86)
T ss_pred hhhHHHHHHHcCCCHHHHHHH
Confidence 677788888888888777654
No 395
>PF00984 UDPG_MGDP_dh: UDP-glucose/GDP-mannose dehydrogenase family, central domain; InterPro: IPR014026 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents an alpha helical region that serves as the dimerisation interface for these enzymes [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 2O3J_A 3OJO_A 3OJL_A 3PLR_A 3PJG_A 3PID_A 3PLN_A 3PHL_A 3TDK_B 2Q3E_A ....
Probab=20.25 E-value=1.6e+02 Score=16.02 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCHHHHHHhhC
Q 037180 27 LWGFSMKCGVSIDAIKEANG 46 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~~N~ 46 (66)
+..+++++|++..++.+.=+
T Consensus 25 l~~lce~~giD~~~V~~~~~ 44 (96)
T PF00984_consen 25 LARLCEKLGIDVYEVIEAAN 44 (96)
T ss_dssp HHHHHHHHTSBHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHc
Confidence 56789999999999886643
No 396
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=20.16 E-value=1.4e+02 Score=15.16 Aligned_cols=18 Identities=22% Similarity=0.200 Sum_probs=14.1
Q ss_pred HHHHHHHhCCCHHHHHHh
Q 037180 27 LWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~~~ 44 (66)
+..|-+++|-+++++.+.
T Consensus 6 ~~~Ie~kTGk~~~~W~~~ 23 (61)
T PF14117_consen 6 LPNIEKKTGKTLDEWLAL 23 (61)
T ss_pred HhHhHHHHCcCHHHHHHH
Confidence 457888899998887765
No 397
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.06 E-value=1.6e+02 Score=17.48 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=17.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
-.|-+..+||+.+|++...+.
T Consensus 120 ~~g~~~~EIA~~lgis~~tV~ 140 (181)
T PRK09637 120 LEGLSQKEIAEKLGLSLSGAK 140 (181)
T ss_pred hcCCCHHHHHHHhCCCHHHHH
Confidence 368888999999999987765
No 398
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=20.06 E-value=1.5e+02 Score=15.93 Aligned_cols=21 Identities=19% Similarity=0.174 Sum_probs=15.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHh
Q 037180 24 GDTLWGFSMKCGVSIDAIKEA 44 (66)
Q Consensus 24 GdTl~~Ia~~~~~~~~~l~~~ 44 (66)
|..+..+|++.|++..+|.+.
T Consensus 13 G~~W~~Lar~Lgls~~~I~~i 33 (83)
T cd08319 13 GPEWEQVLLDLGLSQTDIYRC 33 (83)
T ss_pred hhhHHHHHHHcCCCHHHHHHH
Confidence 566778888888887776654
No 399
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.05 E-value=1.6e+02 Score=18.69 Aligned_cols=21 Identities=24% Similarity=0.134 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIK 42 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~ 42 (66)
..|-|...||+.+|++...+.
T Consensus 226 ~~~~s~~eIA~~lgis~~tV~ 246 (268)
T PRK06288 226 YEDLTLKEIGKVLGVTESRIS 246 (268)
T ss_pred HcCCCHHHHHHHHCcCHHHHH
Confidence 468899999999999988876
No 400
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=20.05 E-value=1.4e+02 Score=14.83 Aligned_cols=16 Identities=19% Similarity=0.150 Sum_probs=12.4
Q ss_pred HHHHHHHhCCCHHHHH
Q 037180 27 LWGFSMKCGVSIDAIK 42 (66)
Q Consensus 27 l~~Ia~~~~~~~~~l~ 42 (66)
+...|+++|++..+..
T Consensus 8 Ie~~A~~~~~s~~ea~ 23 (62)
T PF12668_consen 8 IEEFAKKLNISGEEAY 23 (62)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 3578899999988755
No 401
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=20.00 E-value=1.6e+02 Score=17.34 Aligned_cols=22 Identities=14% Similarity=0.173 Sum_probs=18.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 037180 22 LRGDTLWGFSMKCGVSIDAIKE 43 (66)
Q Consensus 22 ~~GdTl~~Ia~~~~~~~~~l~~ 43 (66)
-.|-+...||+..|+++..+..
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~ 166 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMS 166 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH
Confidence 5789999999999999887653
Done!