Query 036926
Match_columns 168
No_of_seqs 151 out of 221
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:47:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02042 RWP-RK: RWP-RK domain 99.9 3.8E-27 8.2E-32 160.1 3.7 45 1-45 8-52 (52)
2 PF01418 HTH_6: Helix-turn-hel 96.5 0.002 4.4E-08 45.3 2.3 35 5-39 31-65 (77)
3 TIGR01764 excise DNA binding d 95.9 0.01 2.2E-07 36.4 3.3 28 9-36 2-29 (49)
4 PF02796 HTH_7: Helix-turn-hel 95.6 0.0097 2.1E-07 38.2 2.2 24 8-31 21-44 (45)
5 PF12728 HTH_17: Helix-turn-he 95.3 0.023 5E-07 36.4 3.2 29 9-37 2-30 (51)
6 cd04762 HTH_MerR-trunc Helix-T 95.2 0.026 5.7E-07 34.2 3.2 27 9-35 1-27 (49)
7 cd04761 HTH_MerR-SF Helix-Turn 95.2 0.028 6E-07 35.1 3.3 31 9-41 1-31 (49)
8 PF02954 HTH_8: Bacterial regu 95.1 0.03 6.4E-07 35.5 3.2 28 5-32 15-42 (42)
9 cd04763 HTH_MlrA-like Helix-Tu 95.1 0.031 6.7E-07 37.8 3.5 27 9-35 1-27 (68)
10 cd04764 HTH_MlrA-like_sg1 Heli 95.0 0.033 7.1E-07 37.5 3.6 27 9-35 1-27 (67)
11 PRK11302 DNA-binding transcrip 95.0 0.021 4.5E-07 47.4 2.9 37 5-41 31-67 (284)
12 PRK15482 transcriptional regul 94.8 0.024 5.1E-07 47.8 2.9 38 5-42 31-68 (285)
13 cd04765 HTH_MlrA-like_sg2 Heli 94.6 0.4 8.6E-06 35.6 8.7 27 9-35 1-27 (99)
14 COG1737 RpiR Transcriptional r 94.3 0.029 6.4E-07 47.9 2.4 38 6-43 34-71 (281)
15 cd01104 HTH_MlrA-CarA Helix-Tu 94.2 0.067 1.5E-06 35.6 3.5 26 9-34 1-26 (68)
16 PRK11557 putative DNA-binding 93.9 0.047 1E-06 45.5 2.8 37 5-41 27-63 (278)
17 PRK00430 fis global DNA-bindin 93.9 0.073 1.6E-06 39.7 3.5 29 6-34 66-94 (95)
18 PF13936 HTH_38: Helix-turn-he 93.8 0.065 1.4E-06 34.4 2.7 25 8-32 20-44 (44)
19 PF13384 HTH_23: Homeodomain-l 93.8 0.06 1.3E-06 34.1 2.5 25 8-32 17-41 (50)
20 PRK11337 DNA-binding transcrip 93.7 0.055 1.2E-06 45.5 2.9 34 6-39 44-77 (292)
21 PF04967 HTH_10: HTH DNA bindi 93.3 0.11 2.4E-06 35.4 3.2 27 5-31 16-46 (53)
22 smart00342 HTH_ARAC helix_turn 93.1 0.12 2.6E-06 34.0 3.2 32 8-39 1-33 (84)
23 smart00421 HTH_LUXR helix_turn 92.9 0.11 2.4E-06 32.0 2.7 31 8-38 18-52 (58)
24 PRK09413 IS2 repressor TnpA; R 92.9 0.98 2.1E-05 34.2 8.3 26 8-33 29-54 (121)
25 PRK13182 racA polar chromosome 92.8 0.12 2.6E-06 42.6 3.4 27 9-35 1-27 (175)
26 PRK01905 DNA-binding protein F 92.6 0.16 3.4E-06 36.1 3.5 28 7-34 49-76 (77)
27 cd01106 HTH_TipAL-Mta Helix-Tu 92.6 0.54 1.2E-05 34.4 6.3 25 9-34 1-25 (103)
28 cd04776 HTH_GnyR Helix-Turn-He 92.4 1.2 2.6E-05 33.8 8.3 25 9-34 1-25 (118)
29 smart00422 HTH_MERR helix_turn 92.1 0.71 1.5E-05 30.6 6.0 26 9-34 1-26 (70)
30 PF02001 DUF134: Protein of un 92.1 0.18 4E-06 38.8 3.4 28 3-30 52-79 (106)
31 PF13411 MerR_1: MerR HTH fami 91.9 0.19 4.1E-06 33.5 3.0 26 9-34 1-26 (69)
32 cd04789 HTH_Cfa Helix-Turn-Hel 91.6 1.3 2.9E-05 32.6 7.5 26 9-35 2-27 (102)
33 PF13542 HTH_Tnp_ISL3: Helix-t 91.6 0.23 5.1E-06 31.6 3.0 27 6-32 24-51 (52)
34 PF00165 HTH_AraC: Bacterial r 91.4 0.25 5.4E-06 30.7 2.9 27 8-34 8-35 (42)
35 cd04774 HTH_YfmP Helix-Turn-He 91.2 0.26 5.7E-06 36.2 3.4 30 9-40 1-30 (96)
36 PF01710 HTH_Tnp_IS630: Transp 90.9 0.26 5.7E-06 37.3 3.2 33 3-35 66-98 (119)
37 PF08281 Sigma70_r4_2: Sigma-7 90.8 0.34 7.4E-06 31.1 3.2 27 4-30 22-48 (54)
38 cd04766 HTH_HspR Helix-Turn-He 90.8 3.2 6.9E-05 29.7 8.6 25 9-34 2-26 (91)
39 PF13518 HTH_28: Helix-turn-he 90.7 0.32 6.9E-06 30.6 3.0 25 8-32 12-36 (52)
40 cd01109 HTH_YyaN Helix-Turn-He 90.7 1.8 3.9E-05 32.2 7.4 26 9-34 1-26 (113)
41 PF04545 Sigma70_r4: Sigma-70, 90.2 0.42 9E-06 30.5 3.2 24 8-31 20-43 (50)
42 PF01381 HTH_3: Helix-turn-hel 90.1 0.32 6.8E-06 31.0 2.6 29 3-31 4-32 (55)
43 PRK10219 DNA-binding transcrip 89.9 0.43 9.2E-06 34.5 3.5 26 9-34 22-48 (107)
44 cd01282 HTH_MerR-like_sg3 Heli 89.8 1.6 3.5E-05 32.6 6.6 27 9-36 1-27 (112)
45 cd04787 HTH_HMRTR_unk Helix-Tu 89.7 4.6 9.9E-05 31.0 9.2 30 9-40 1-30 (133)
46 PF01527 HTH_Tnp_1: Transposas 89.4 0.41 8.9E-06 32.3 2.9 33 8-40 23-57 (76)
47 PF13404 HTH_AsnC-type: AsnC-t 89.4 0.43 9.2E-06 30.7 2.8 26 7-32 16-41 (42)
48 PF07453 NUMOD1: NUMOD1 domain 89.1 0.31 6.6E-06 29.8 1.9 20 10-29 18-37 (37)
49 smart00497 IENR1 Intron encode 88.8 0.48 1E-05 30.1 2.7 22 10-31 19-40 (53)
50 cd04788 HTH_NolA-AlbR Helix-Tu 88.7 3.5 7.5E-05 30.0 7.6 25 9-34 1-25 (96)
51 TIGR02531 yecD_yerC TrpR-relat 88.6 0.48 1E-05 35.1 3.0 23 8-30 50-72 (88)
52 PF03374 ANT: Phage antirepres 88.2 0.57 1.2E-05 34.3 3.2 40 8-47 24-64 (111)
53 cd01105 HTH_GlnR-like Helix-Tu 87.9 0.68 1.5E-05 33.3 3.4 30 9-40 2-31 (88)
54 PF05225 HTH_psq: helix-turn-h 87.7 0.6 1.3E-05 30.3 2.7 22 9-30 17-38 (45)
55 PF03683 UPF0175: Uncharacteri 87.6 0.95 2.1E-05 32.1 3.9 31 8-39 34-64 (76)
56 TIGR03070 couple_hipB transcri 87.5 0.74 1.6E-05 28.8 3.0 28 3-30 10-37 (58)
57 cd04785 HTH_CadR-PbrR-like Hel 87.2 3.2 6.9E-05 31.6 6.8 26 9-34 1-26 (126)
58 cd04790 HTH_Cfa-like_unk Helix 87.0 2.9 6.2E-05 33.8 6.8 25 9-34 2-26 (172)
59 PF13412 HTH_24: Winged helix- 86.7 0.82 1.8E-05 28.8 2.8 26 7-32 16-41 (48)
60 PF13560 HTH_31: Helix-turn-he 86.7 0.44 9.6E-06 31.8 1.7 36 3-38 9-45 (64)
61 TIGR02047 CadR-PbrR Cd(II)/Pb( 86.4 3.9 8.4E-05 31.3 6.9 23 9-31 1-23 (127)
62 PF06056 Terminase_5: Putative 86.3 0.94 2E-05 31.0 3.2 27 8-34 13-39 (58)
63 PRK14101 bifunctional glucokin 86.2 0.59 1.3E-05 44.2 2.8 34 6-39 372-405 (638)
64 PRK15043 transcriptional regul 86.1 0.9 1.9E-05 39.4 3.7 32 8-40 3-34 (243)
65 cd04782 HTH_BltR Helix-Turn-He 86.0 7.9 0.00017 28.2 8.1 25 9-34 1-25 (97)
66 cd04775 HTH_Cfa-like Helix-Tur 85.8 1 2.2E-05 33.2 3.4 26 9-35 2-27 (102)
67 cd04773 HTH_TioE_rpt2 Second H 85.8 1 2.2E-05 33.6 3.4 25 9-34 1-25 (108)
68 PRK09637 RNA polymerase sigma 85.6 0.96 2.1E-05 35.7 3.4 27 4-30 118-144 (181)
69 PRK12533 RNA polymerase sigma 85.4 0.95 2.1E-05 37.3 3.4 28 4-31 146-173 (216)
70 PF04760 IF2_N: Translation in 85.4 0.6 1.3E-05 30.6 1.8 27 9-35 4-31 (54)
71 cd00592 HTH_MerR-like Helix-Tu 85.2 1.3 2.8E-05 31.7 3.6 30 9-40 1-30 (100)
72 PF12844 HTH_19: Helix-turn-he 85.1 1.3 2.7E-05 29.1 3.2 27 2-28 6-32 (64)
73 cd01279 HTH_HspR-like Helix-Tu 85.0 1.1 2.3E-05 33.0 3.1 25 9-34 2-26 (98)
74 cd04768 HTH_BmrR-like Helix-Tu 85.0 3.2 7E-05 30.2 5.7 25 9-34 1-25 (96)
75 PF13011 LZ_Tnp_IS481: leucine 84.9 1 2.2E-05 33.6 3.0 25 8-32 25-49 (85)
76 PRK11511 DNA-binding transcrip 84.8 1.1 2.5E-05 33.9 3.3 27 8-34 25-52 (127)
77 PRK12511 RNA polymerase sigma 84.7 1.1 2.5E-05 35.4 3.4 27 4-30 123-149 (182)
78 cd01108 HTH_CueR Helix-Turn-He 84.6 4.1 8.9E-05 31.0 6.3 23 9-31 1-23 (127)
79 PRK04217 hypothetical protein; 84.6 1.2 2.6E-05 34.4 3.3 26 6-31 56-81 (110)
80 TIGR01321 TrpR trp operon repr 84.4 0.98 2.1E-05 34.3 2.7 26 8-33 55-80 (94)
81 PF13443 HTH_26: Cro/C1-type H 84.3 1.1 2.5E-05 29.2 2.8 38 7-45 9-46 (63)
82 cd06170 LuxR_C_like C-terminal 84.2 1.4 3E-05 27.3 3.0 23 8-30 15-37 (57)
83 PF00356 LacI: Bacterial regul 84.1 1.1 2.4E-05 29.4 2.6 23 10-32 1-23 (46)
84 TIGR02297 HpaA 4-hydroxyphenyl 83.7 4.3 9.4E-05 33.4 6.5 33 8-42 202-235 (287)
85 cd01110 HTH_SoxR Helix-Turn-He 83.2 1.5 3.3E-05 34.2 3.5 28 8-36 1-28 (139)
86 cd06171 Sigma70_r4 Sigma70, re 83.1 1.8 3.9E-05 25.8 3.1 25 7-31 25-49 (55)
87 smart00354 HTH_LACI helix_turn 83.1 1.2 2.6E-05 30.6 2.5 24 9-32 1-24 (70)
88 COG1522 Lrp Transcriptional re 83.0 1.2 2.6E-05 33.6 2.8 30 3-32 17-46 (154)
89 cd01107 HTH_BmrR Helix-Turn-He 83.0 1.4 3E-05 32.8 3.0 25 9-34 1-25 (108)
90 cd00569 HTH_Hin_like Helix-tur 82.4 1.7 3.8E-05 23.0 2.6 21 8-28 21-41 (42)
91 PRK00118 putative DNA-binding 82.3 9.1 0.0002 29.2 7.3 26 5-30 30-55 (104)
92 COG1476 Predicted transcriptio 82.3 1.2 2.7E-05 31.9 2.5 27 2-28 8-34 (68)
93 COG1342 Predicted DNA-binding 82.1 1.2 2.7E-05 34.3 2.5 26 3-28 44-69 (99)
94 PF01371 Trp_repressor: Trp re 81.6 1.7 3.7E-05 32.3 3.0 26 8-33 49-74 (87)
95 PHA01976 helix-turn-helix prot 81.4 2.3 5E-05 28.1 3.4 29 3-31 10-38 (67)
96 PRK09636 RNA polymerase sigma 81.3 1.7 3.6E-05 36.9 3.3 28 3-30 126-153 (293)
97 PF13744 HTH_37: Helix-turn-he 81.2 3.8 8.2E-05 28.9 4.6 45 4-56 27-72 (80)
98 smart00345 HTH_GNTR helix_turn 81.1 2 4.4E-05 26.9 2.9 25 9-33 20-45 (60)
99 PF01498 HTH_Tnp_Tc3_2: Transp 81.1 0.95 2.1E-05 30.7 1.4 38 8-45 13-55 (72)
100 PF12833 HTH_18: Helix-turn-he 81.0 7.2 0.00016 26.4 5.8 21 14-34 1-22 (81)
101 TIGR02607 antidote_HigA addict 81.0 2.9 6.3E-05 28.2 3.8 28 3-30 13-40 (78)
102 PRK09514 zntR zinc-responsive 81.0 9.4 0.0002 29.8 7.2 25 9-34 2-26 (140)
103 PRK12516 RNA polymerase sigma 80.9 1.9 4.2E-05 34.2 3.4 28 3-30 127-154 (187)
104 TIGR02044 CueR Cu(I)-responsiv 80.9 4.5 9.8E-05 30.7 5.3 25 9-34 1-25 (127)
105 PF13551 HTH_29: Winged helix- 80.7 1.9 4.1E-05 30.4 3.0 25 8-32 11-36 (112)
106 PF06970 RepA_N: Replication i 80.7 1.5 3.2E-05 31.6 2.4 28 5-32 49-76 (76)
107 TIGR02959 SigZ RNA polymerase 80.6 2.1 4.6E-05 33.1 3.4 26 4-29 112-137 (170)
108 PRK08241 RNA polymerase factor 80.5 1.8 4E-05 37.0 3.3 28 3-30 164-191 (339)
109 PF10668 Phage_terminase: Phag 80.5 1.6 3.5E-05 30.6 2.5 24 8-31 22-45 (60)
110 PF05930 Phage_AlpA: Prophage 80.4 1.3 2.8E-05 28.9 1.8 26 9-34 4-29 (51)
111 smart00351 PAX Paired Box doma 80.1 12 0.00025 28.6 7.3 25 8-32 33-57 (125)
112 PRK09635 sigI RNA polymerase s 80.0 1.9 4.2E-05 37.2 3.3 28 3-30 129-156 (290)
113 TIGR03879 near_KaiC_dom probab 80.0 2 4.4E-05 31.1 2.9 25 7-31 31-55 (73)
114 PRK15418 transcriptional regul 80.0 2 4.3E-05 37.8 3.4 42 8-49 29-77 (318)
115 KOG0251 Clathrin assembly prot 79.9 2.1 4.5E-05 40.7 3.7 55 3-57 224-289 (491)
116 smart00419 HTH_CRP helix_turn_ 79.8 2.4 5.1E-05 25.8 2.8 32 6-37 6-37 (48)
117 PRK09726 antitoxin HipB; Provi 79.7 2.1 4.5E-05 30.6 2.9 28 3-30 20-47 (88)
118 cd04770 HTH_HMRTR Helix-Turn-H 79.6 5.5 0.00012 29.7 5.3 25 9-34 1-25 (123)
119 cd00092 HTH_CRP helix_turn_hel 79.5 2.5 5.3E-05 27.4 3.0 28 5-32 22-49 (67)
120 TIGR02960 SigX5 RNA polymerase 79.5 2.1 4.5E-05 36.2 3.3 28 3-30 153-180 (324)
121 PF00126 HTH_1: Bacterial regu 79.5 2.4 5.2E-05 28.1 3.0 22 9-30 14-35 (60)
122 PRK12540 RNA polymerase sigma 79.4 2.3 5.1E-05 33.6 3.4 28 4-31 123-150 (182)
123 COG2207 AraC AraC-type DNA-bin 79.0 2.8 6.2E-05 29.3 3.4 27 9-35 37-64 (127)
124 TIGR02957 SigX4 RNA polymerase 79.0 2.3 4.9E-05 36.1 3.4 28 3-30 119-146 (281)
125 PHA00542 putative Cro-like pro 79.0 2.1 4.5E-05 30.6 2.7 45 7-55 30-74 (82)
126 PRK01381 Trp operon repressor; 78.9 1.2 2.5E-05 34.2 1.5 27 8-34 55-81 (99)
127 PRK10072 putative transcriptio 78.8 2.8 6E-05 31.5 3.5 31 2-32 40-70 (96)
128 smart00418 HTH_ARSR helix_turn 78.4 2.8 6.1E-05 25.9 2.9 32 8-39 10-41 (66)
129 PF00196 GerE: Bacterial regul 77.7 2.4 5.1E-05 27.8 2.5 28 8-35 18-49 (58)
130 PRK09647 RNA polymerase sigma 77.6 2.7 5.9E-05 34.0 3.4 29 4-32 150-178 (203)
131 PRK15411 rcsA colanic acid cap 77.2 3.1 6.8E-05 33.8 3.6 27 8-34 152-182 (207)
132 PF08279 HTH_11: HTH domain; 77.1 3 6.5E-05 26.7 2.8 24 9-32 16-39 (55)
133 TIGR03830 CxxCG_CxxCG_HTH puta 77.0 2.6 5.6E-05 31.0 2.8 29 2-30 72-100 (127)
134 PRK12546 RNA polymerase sigma 77.0 3 6.5E-05 33.3 3.4 28 3-30 124-151 (188)
135 TIGR01950 SoxR redox-sensitive 76.7 3.1 6.8E-05 32.8 3.3 25 9-34 2-26 (142)
136 PF04552 Sigma54_DBD: Sigma-54 76.3 0.64 1.4E-05 37.7 -0.7 26 9-34 50-75 (160)
137 smart00342 HTH_ARAC helix_turn 75.9 3.7 7.9E-05 26.7 3.0 27 8-34 50-78 (84)
138 PF01710 HTH_Tnp_IS630: Transp 75.9 6.9 0.00015 29.5 4.9 23 8-30 18-40 (119)
139 COG2345 Predicted transcriptio 75.1 15 0.00033 31.5 7.3 94 6-107 23-149 (218)
140 PRK09978 DNA-binding transcrip 74.8 3.6 7.9E-05 36.0 3.5 27 8-34 158-184 (274)
141 smart00513 SAP Putative DNA-bi 74.7 3.5 7.5E-05 25.1 2.5 21 19-39 3-23 (35)
142 PF08280 HTH_Mga: M protein tr 74.7 4 8.6E-05 27.3 3.0 26 8-33 19-44 (59)
143 PRK11169 leucine-responsive tr 74.4 3.3 7.2E-05 32.6 3.0 30 3-32 23-52 (164)
144 PF09339 HTH_IclR: IclR helix- 74.3 3.3 7.2E-05 26.7 2.5 25 8-32 18-42 (52)
145 PRK09191 two-component respons 74.2 3.7 8.1E-05 32.7 3.3 27 4-30 100-126 (261)
146 cd04784 HTH_CadR-PbrR Helix-Tu 74.1 21 0.00045 26.9 7.2 25 9-34 1-25 (127)
147 PF04218 CENP-B_N: CENP-B N-te 74.1 2.8 6.1E-05 27.9 2.1 23 8-30 22-44 (53)
148 PRK06704 RNA polymerase factor 74.1 3.6 7.9E-05 34.7 3.3 27 4-30 128-154 (228)
149 smart00344 HTH_ASNC helix_turn 73.6 4.2 9.2E-05 29.1 3.1 31 3-33 12-42 (108)
150 PRK15044 transcriptional regul 73.4 15 0.00032 32.9 7.1 27 8-34 208-234 (295)
151 TIGR02051 MerR Hg(II)-responsi 73.0 12 0.00026 28.4 5.7 26 10-36 1-26 (124)
152 cd04779 HTH_MerR-like_sg4 Heli 73.0 24 0.00052 27.6 7.5 30 9-40 1-30 (134)
153 PRK10227 DNA-binding transcrip 72.8 19 0.00041 28.0 6.8 23 9-31 1-23 (135)
154 cd01111 HTH_MerD Helix-Turn-He 72.7 5.3 0.00011 29.9 3.5 27 9-36 1-27 (107)
155 COG5484 Uncharacterized conser 72.7 3.4 7.4E-05 36.9 2.9 27 8-34 19-45 (279)
156 TIGR02293 TAS_TIGR02293 putati 72.4 3.2 7E-05 32.1 2.4 31 2-32 30-60 (133)
157 PRK15186 AraC family transcrip 71.5 5.2 0.00011 34.9 3.8 33 8-40 197-229 (291)
158 PRK11179 DNA-binding transcrip 71.3 4.3 9.3E-05 31.6 2.9 25 8-32 23-47 (153)
159 cd00093 HTH_XRE Helix-turn-hel 70.9 13 0.00029 21.4 4.4 38 6-45 10-47 (58)
160 PRK11303 DNA-binding transcrip 70.9 4.2 9E-05 33.6 2.9 24 9-32 1-24 (328)
161 TIGR03338 phnR_burk phosphonat 70.7 42 0.0009 26.6 8.5 35 7-41 33-71 (212)
162 PRK11922 RNA polymerase sigma 70.7 4.6 0.0001 33.0 3.1 26 5-30 162-187 (231)
163 smart00530 HTH_XRE Helix-turn- 70.5 10 0.00022 21.8 3.8 26 5-30 7-32 (56)
164 PRK09685 DNA-binding transcrip 70.3 5.8 0.00013 33.0 3.6 33 9-43 215-247 (302)
165 PF13545 HTH_Crp_2: Crp-like h 70.1 5.4 0.00012 26.7 2.9 37 6-42 26-65 (76)
166 COG1709 Predicted transcriptio 69.9 2.3 4.9E-05 37.3 1.2 45 4-52 36-80 (241)
167 TIGR03453 partition_RepA plasm 69.5 5.5 0.00012 35.3 3.5 27 8-34 33-59 (387)
168 cd06571 Bac_DnaA_C C-terminal 69.4 6.5 0.00014 28.3 3.3 29 4-32 40-69 (90)
169 cd00131 PAX Paired Box domain 69.1 5.3 0.00011 30.8 2.9 24 8-31 33-56 (128)
170 PF13613 HTH_Tnp_4: Helix-turn 68.8 5.4 0.00012 26.1 2.6 24 8-31 19-42 (53)
171 PRK09393 ftrA transcriptional 68.8 5.5 0.00012 34.0 3.3 28 8-35 234-262 (322)
172 cd04769 HTH_MerR2 Helix-Turn-H 68.4 20 0.00043 26.8 5.9 25 9-34 1-25 (116)
173 PF12802 MarR_2: MarR family; 68.3 5.2 0.00011 25.7 2.4 25 9-33 22-46 (62)
174 PF00392 GntR: Bacterial regul 68.3 5.2 0.00011 26.6 2.4 26 8-33 23-49 (64)
175 PRK10703 DNA-binding transcrip 67.9 4.7 0.0001 33.6 2.6 22 9-30 2-23 (341)
176 PRK13502 transcriptional activ 67.8 6.3 0.00014 32.5 3.3 28 8-35 192-220 (282)
177 cd04772 HTH_TioE_rpt1 First He 67.7 8.6 0.00019 28.2 3.7 25 9-34 1-25 (99)
178 COG2944 Predicted transcriptio 67.2 4.7 0.0001 31.2 2.3 29 2-30 51-79 (104)
179 cd04781 HTH_MerR-like_sg6 Heli 66.5 8 0.00017 29.1 3.4 25 9-34 1-25 (120)
180 cd04767 HTH_HspR-like_MBC Heli 65.7 6.8 0.00015 30.6 3.0 25 9-34 2-26 (120)
181 PRK03975 tfx putative transcri 65.4 7.4 0.00016 31.2 3.2 26 6-31 19-44 (141)
182 PHA02591 hypothetical protein; 65.3 7.6 0.00016 29.2 3.0 23 8-30 59-81 (83)
183 PF14549 P22_Cro: DNA-binding 65.3 6.2 0.00013 27.4 2.4 26 2-28 4-29 (60)
184 PF09862 DUF2089: Protein of u 63.9 13 0.00029 29.0 4.2 17 10-26 51-67 (113)
185 PRK11534 DNA-binding transcrip 63.5 7.3 0.00016 31.4 2.9 33 8-40 30-66 (224)
186 PF13556 HTH_30: PucR C-termin 63.5 9.9 0.00022 25.3 3.1 28 2-29 4-33 (59)
187 cd01392 HTH_LacI Helix-turn-he 63.5 5.4 0.00012 25.0 1.7 20 13-32 2-21 (52)
188 COG3415 Transposase and inacti 63.0 8 0.00017 31.0 3.0 28 6-33 19-46 (138)
189 PF00440 TetR_N: Bacterial reg 63.0 10 0.00023 23.8 3.0 23 5-27 13-35 (47)
190 TIGR03001 Sig-70_gmx1 RNA poly 63.0 8.6 0.00019 32.4 3.3 27 4-30 173-199 (244)
191 PF07750 GcrA: GcrA cell cycle 63.0 6.1 0.00013 32.0 2.3 34 3-36 11-47 (162)
192 PRK09706 transcriptional repre 62.9 9.9 0.00021 28.9 3.4 34 2-35 12-45 (135)
193 PRK11475 DNA-binding transcrip 62.8 11 0.00023 31.1 3.7 27 8-34 149-179 (207)
194 PF05344 DUF746: Domain of Unk 62.6 8.9 0.00019 27.5 2.8 24 8-31 13-36 (65)
195 TIGR02405 trehalos_R_Ecol treh 62.2 7.1 0.00015 32.3 2.6 22 9-30 2-23 (311)
196 cd04786 HTH_MerR-like_sg7 Heli 62.1 15 0.00032 28.5 4.3 24 9-33 1-24 (131)
197 PF05043 Mga: Mga helix-turn-h 61.7 6.7 0.00015 27.4 2.1 24 8-31 30-53 (87)
198 cd00090 HTH_ARSR Arsenical Res 61.7 8.2 0.00018 24.3 2.3 32 9-40 21-52 (78)
199 PF01325 Fe_dep_repress: Iron 61.6 9.7 0.00021 25.9 2.8 25 8-32 22-46 (60)
200 PRK09526 lacI lac repressor; R 61.6 7.3 0.00016 32.3 2.6 22 9-30 6-27 (342)
201 PF08535 KorB: KorB domain; I 61.0 10 0.00022 27.3 3.0 27 7-33 2-28 (93)
202 PF00376 MerR: MerR family reg 60.8 13 0.00028 23.3 3.1 24 10-34 1-24 (38)
203 PRK15340 transcriptional regul 60.7 8.7 0.00019 32.8 2.9 28 8-35 125-153 (216)
204 PRK15185 transcriptional regul 60.3 11 0.00023 33.9 3.6 27 8-34 222-248 (309)
205 COG2452 Predicted site-specifi 60.3 10 0.00022 32.4 3.2 27 8-34 1-27 (193)
206 PF08220 HTH_DeoR: DeoR-like h 59.8 9 0.00019 25.5 2.3 29 4-32 10-38 (57)
207 PRK09940 transcriptional regul 59.7 12 0.00025 32.6 3.6 28 8-35 150-177 (253)
208 PRK09492 treR trehalose repres 59.6 7.9 0.00017 31.7 2.5 22 9-30 5-26 (315)
209 TIGR02054 MerD mercuric resist 59.6 14 0.00029 28.6 3.6 28 8-36 3-30 (120)
210 PF08822 DUF1804: Protein of u 59.5 63 0.0014 26.9 7.7 78 8-97 19-103 (165)
211 cd04777 HTH_MerR-like_sg1 Heli 59.2 67 0.0015 23.4 8.5 25 9-34 1-25 (107)
212 COG3093 VapI Plasmid maintenan 59.1 9 0.0002 29.7 2.5 30 3-32 18-47 (104)
213 PRK04984 fatty acid metabolism 59.0 9.9 0.00021 30.9 2.9 25 8-32 30-55 (239)
214 smart00346 HTH_ICLR helix_turn 59.0 12 0.00026 25.7 3.0 25 8-32 20-44 (91)
215 PRK13890 conjugal transfer pro 58.9 11 0.00023 28.9 2.9 30 3-32 13-42 (120)
216 COG0789 SoxR Predicted transcr 58.7 8.5 0.00018 28.1 2.3 27 9-35 1-27 (124)
217 PRK10014 DNA-binding transcrip 58.3 9 0.0002 31.8 2.6 22 9-30 7-28 (342)
218 PF09035 Tn916-Xis: Excisionas 58.1 11 0.00024 26.9 2.7 29 5-33 10-38 (67)
219 PF02037 SAP: SAP domain; Int 58.1 8.1 0.00018 23.7 1.8 18 20-37 4-21 (35)
220 cd04780 HTH_MerR-like_sg5 Heli 57.8 13 0.00029 27.2 3.2 26 9-34 1-26 (95)
221 PRK10423 transcriptional repre 57.6 7.1 0.00015 32.1 1.9 20 11-30 1-20 (327)
222 COG2771 CsgD DNA-binding HTH d 57.6 19 0.00041 22.9 3.6 28 7-34 18-49 (65)
223 PF11112 PyocinActivator: Pyoc 57.3 17 0.00036 26.4 3.5 40 3-43 6-50 (76)
224 smart00420 HTH_DEOR helix_turn 57.0 15 0.00033 22.2 2.9 26 8-33 14-39 (53)
225 PRK10225 DNA-binding transcrip 56.9 11 0.00024 31.1 2.9 25 8-32 32-57 (257)
226 PRK13503 transcriptional activ 56.1 14 0.00029 30.2 3.3 27 8-34 187-214 (278)
227 PF02082 Rrf2: Transcriptional 56.1 12 0.00026 26.2 2.6 24 9-32 26-49 (83)
228 PRK10572 DNA-binding transcrip 56.0 15 0.00032 30.5 3.5 28 8-35 199-227 (290)
229 PRK11014 transcriptional repre 55.9 12 0.00025 28.7 2.7 32 9-40 26-61 (141)
230 PRK13719 conjugal transfer tra 55.9 16 0.00034 31.5 3.7 27 8-34 158-188 (217)
231 TIGR02812 fadR_gamma fatty aci 55.8 12 0.00026 30.4 2.9 25 8-32 29-54 (235)
232 TIGR00637 ModE_repress ModE mo 55.6 12 0.00027 27.7 2.7 21 8-28 16-36 (99)
233 TIGR02612 mob_myst_A mobile my 55.5 13 0.00028 29.9 3.0 30 2-31 32-61 (150)
234 TIGR01481 ccpA catabolite cont 55.5 11 0.00023 31.2 2.6 22 9-30 2-23 (329)
235 PF13730 HTH_36: Helix-turn-he 55.3 15 0.00032 23.4 2.7 23 10-32 27-49 (55)
236 smart00550 Zalpha Z-DNA-bindin 55.2 15 0.00032 25.3 2.9 22 9-30 23-44 (68)
237 PRK10840 transcriptional regul 55.2 13 0.00029 29.1 3.0 24 8-31 165-188 (216)
238 PRK14987 gluconate operon tran 55.2 9.2 0.0002 31.8 2.2 22 9-30 6-27 (331)
239 COG1309 AcrR Transcriptional r 55.1 9.9 0.00021 26.7 2.0 22 6-27 30-51 (201)
240 PRK10401 DNA-binding transcrip 54.5 11 0.00025 31.5 2.6 22 9-30 2-23 (346)
241 PRK10371 DNA-binding transcrip 54.4 15 0.00032 31.5 3.4 28 8-35 207-235 (302)
242 PF10078 DUF2316: Uncharacteri 54.3 12 0.00026 28.2 2.4 53 2-57 14-70 (89)
243 PF06870 RNA_pol_I_A49: A49-li 54.1 11 0.00023 33.5 2.5 29 6-34 317-345 (385)
244 TIGR00721 tfx DNA-binding prot 53.3 16 0.00034 29.2 3.1 26 6-31 19-44 (137)
245 PRK09483 response regulator; P 53.2 16 0.00034 27.7 3.0 28 7-34 162-193 (217)
246 PRK11523 DNA-binding transcrip 53.0 14 0.0003 30.5 2.9 33 8-40 31-68 (253)
247 PF12116 SpoIIID: Stage III sp 53.0 12 0.00025 28.1 2.2 23 8-30 19-41 (82)
248 PF01047 MarR: MarR family; I 52.9 16 0.00035 23.3 2.6 31 4-34 13-43 (59)
249 PRK10339 DNA-binding transcrip 52.8 11 0.00024 31.3 2.3 24 9-32 2-25 (327)
250 PRK10727 DNA-binding transcrip 52.8 12 0.00025 31.4 2.4 21 10-30 3-23 (343)
251 TIGR02043 ZntR Zn(II)-responsi 52.4 20 0.00044 27.5 3.5 27 9-36 2-28 (131)
252 TIGR02417 fruct_sucro_rep D-fr 52.2 14 0.00029 30.6 2.7 23 10-32 1-23 (327)
253 cd04783 HTH_MerR1 Helix-Turn-H 52.2 22 0.00048 26.8 3.7 25 9-34 1-25 (126)
254 PRK10421 DNA-binding transcrip 52.1 15 0.00032 30.3 2.9 33 8-40 25-62 (253)
255 PRK08359 transcription factor; 51.9 16 0.00034 30.4 3.0 26 3-28 93-118 (176)
256 COG2390 DeoR Transcriptional r 51.8 16 0.00036 32.7 3.3 27 8-34 26-55 (321)
257 TIGR02844 spore_III_D sporulat 51.4 14 0.0003 27.1 2.3 23 7-29 18-40 (80)
258 PF01978 TrmB: Sugar-specific 51.2 16 0.00035 24.4 2.5 25 8-32 22-46 (68)
259 PRK15002 redox-sensitivie tran 50.0 16 0.00035 29.3 2.7 24 8-31 11-34 (154)
260 PF08784 RPA_C: Replication pr 49.9 17 0.00037 26.2 2.6 26 7-32 64-89 (102)
261 PF10075 PCI_Csn8: COP9 signal 49.2 18 0.00039 27.7 2.8 29 5-33 94-122 (143)
262 COG2522 Predicted transcriptio 49.1 44 0.00096 26.3 5.0 27 8-34 22-48 (119)
263 TIGR00122 birA_repr_reg BirA b 49.0 18 0.00039 24.3 2.5 30 9-38 14-43 (69)
264 PF07860 CCD: WisP family C-Te 49.0 6.6 0.00014 31.3 0.4 13 32-45 53-65 (141)
265 PRK11161 fumarate/nitrate redu 48.9 16 0.00034 29.2 2.6 39 8-46 184-225 (235)
266 PHA00675 hypothetical protein 48.7 19 0.00041 26.8 2.7 24 8-31 39-62 (78)
267 COG1654 BirA Biotin operon rep 48.4 21 0.00046 26.0 2.9 26 4-29 15-40 (79)
268 TIGR02944 suf_reg_Xantho FeS a 48.3 19 0.00041 26.9 2.7 24 9-32 26-49 (130)
269 PRK13752 putative transcriptio 48.2 22 0.00049 28.0 3.3 26 8-34 7-32 (144)
270 PRK11414 colanic acid/biofilm 47.7 17 0.00038 29.2 2.6 28 5-32 31-58 (221)
271 PF12840 HTH_20: Helix-turn-he 47.6 22 0.00048 23.4 2.7 25 7-31 23-47 (61)
272 PRK09990 DNA-binding transcrip 46.8 20 0.00043 29.4 2.9 25 8-32 30-55 (251)
273 PRK13500 transcriptional activ 46.6 23 0.00049 30.3 3.3 27 8-34 222-249 (312)
274 smart00352 POU Found in Pit-Oc 46.6 24 0.00052 25.9 2.9 26 3-28 19-50 (75)
275 PRK10046 dpiA two-component re 46.5 21 0.00045 28.5 2.9 23 8-30 177-199 (225)
276 PRK03837 transcriptional regul 46.3 21 0.00046 28.8 2.9 26 8-33 36-62 (241)
277 PRK09943 DNA-binding transcrip 45.8 23 0.00049 28.1 3.0 29 3-31 15-43 (185)
278 PRK09413 IS2 repressor TnpA; R 45.6 56 0.0012 24.6 5.0 33 13-45 20-52 (121)
279 PRK10430 DNA-binding transcrip 45.4 21 0.00045 28.7 2.7 26 7-32 177-202 (239)
280 COG2973 TrpR Trp operon repres 45.2 14 0.00031 28.7 1.6 20 8-27 60-79 (103)
281 PF09048 Cro: Cro; InterPro: 44.8 25 0.00054 24.9 2.7 20 11-30 15-34 (59)
282 PRK09464 pdhR transcriptional 44.8 23 0.00049 29.1 2.9 25 8-32 33-58 (254)
283 PRK13869 plasmid-partitioning 44.4 27 0.00058 31.7 3.6 23 9-31 49-71 (405)
284 PRK10130 transcriptional regul 44.3 25 0.00055 31.4 3.3 33 9-43 257-290 (350)
285 PHA02535 P terminase ATPase su 44.2 65 0.0014 31.5 6.3 26 8-33 18-43 (581)
286 PF06163 DUF977: Bacterial pro 43.9 24 0.00052 28.3 2.8 28 5-32 23-50 (127)
287 PRK07452 DNA polymerase III su 42.3 1.2E+02 0.0025 25.8 6.9 50 10-61 259-309 (326)
288 PRK13698 plasmid-partitioning 41.7 32 0.00069 31.3 3.6 33 3-35 171-203 (323)
289 TIGR01610 phage_O_Nterm phage 41.6 30 0.00066 25.1 2.9 28 6-33 45-72 (95)
290 PRK06424 transcription factor; 41.5 29 0.00063 27.8 3.0 30 3-32 92-121 (144)
291 PRK13501 transcriptional activ 41.4 30 0.00065 28.8 3.2 26 8-33 192-217 (290)
292 smart00529 HTH_DTXR Helix-turn 40.9 29 0.00063 24.1 2.6 30 11-40 2-31 (96)
293 TIGR00270 conserved hypothetic 40.7 31 0.00066 27.8 3.0 28 3-30 77-104 (154)
294 PRK15121 right oriC-binding tr 40.3 37 0.0008 28.6 3.6 28 8-35 21-49 (289)
295 PRK13749 transcriptional regul 40.2 42 0.00092 26.1 3.6 27 8-35 3-29 (121)
296 COG2197 CitB Response regulato 40.2 23 0.00049 29.0 2.3 23 8-30 163-185 (211)
297 PF13309 HTH_22: HTH domain 40.1 24 0.00052 24.2 2.0 18 11-28 45-62 (64)
298 PRK05932 RNA polymerase factor 39.8 36 0.00079 31.8 3.7 36 9-44 344-383 (455)
299 PF08299 Bac_DnaA_C: Bacterial 39.8 43 0.00094 23.2 3.3 28 4-31 41-69 (70)
300 cd07377 WHTH_GntR Winged helix 39.7 39 0.00085 21.3 2.9 20 11-30 28-47 (66)
301 cd08804 Death_ank2 Death domai 39.5 37 0.00079 24.5 3.0 30 3-32 10-39 (84)
302 COG1609 PurR Transcriptional r 39.3 26 0.00056 30.5 2.6 21 10-30 2-22 (333)
303 PF13022 HTH_Tnp_1_2: Helix-tu 39.3 27 0.00059 28.5 2.5 20 9-28 35-54 (142)
304 COG2963 Transposase and inacti 38.7 32 0.0007 25.2 2.7 34 8-41 24-60 (116)
305 TIGR00373 conserved hypothetic 38.5 33 0.00072 27.4 2.9 25 8-32 28-52 (158)
306 PF11121 DUF2639: Protein of u 38.4 24 0.00052 23.3 1.7 21 29-49 12-32 (40)
307 PRK09954 putative kinase; Prov 38.3 31 0.00067 29.9 2.9 25 8-32 17-41 (362)
308 TIGR02787 codY_Gpos GTP-sensin 37.8 32 0.00069 30.5 2.9 25 8-32 198-222 (251)
309 PF07022 Phage_CI_repr: Bacter 37.7 11 0.00025 25.6 0.1 31 4-34 7-39 (66)
310 TIGR02433 lysidine_TilS_C tRNA 37.5 17 0.00036 22.8 0.8 17 21-37 19-35 (47)
311 TIGR00180 parB_part ParB-like 37.5 45 0.00098 26.8 3.6 27 6-32 118-144 (187)
312 PF11972 HTH_13: HTH DNA bindi 37.3 45 0.00099 23.1 3.0 25 10-34 15-39 (54)
313 PRK13348 chromosome replicatio 37.2 30 0.00066 28.2 2.5 27 8-34 16-46 (294)
314 PRK03902 manganese transport t 37.0 39 0.00084 25.8 3.0 25 9-33 23-47 (142)
315 PRK10341 DNA-binding transcrip 36.9 34 0.00075 28.5 2.9 27 8-34 21-51 (312)
316 PF05732 RepL: Firmicute plasm 36.6 31 0.00066 28.0 2.4 28 6-33 73-100 (165)
317 PRK10082 cell density-dependen 36.5 33 0.00072 28.4 2.7 22 8-29 25-46 (303)
318 PRK11050 manganese transport r 36.4 40 0.00086 26.4 3.0 30 8-37 51-80 (152)
319 PRK11233 nitrogen assimilation 36.4 35 0.00076 28.3 2.8 23 8-30 15-37 (305)
320 COG1802 GntR Transcriptional r 36.3 28 0.0006 28.3 2.2 34 8-41 39-76 (230)
321 TIGR03495 phage_LysB phage lys 36.1 55 0.0012 26.3 3.7 28 70-97 84-111 (135)
322 PRK10837 putative DNA-binding 35.9 34 0.00074 27.6 2.6 27 8-34 17-47 (290)
323 PRK12682 transcriptional regul 35.9 34 0.00074 28.4 2.7 27 8-34 16-46 (309)
324 PF13413 HTH_25: Helix-turn-he 35.7 39 0.00084 23.1 2.5 25 4-28 6-30 (62)
325 TIGR02424 TF_pcaQ pca operon t 35.3 38 0.00082 27.7 2.8 23 8-30 17-39 (300)
326 cd08915 V_Alix_like Protein-in 35.2 1.8E+02 0.0038 25.5 7.1 74 30-103 112-203 (342)
327 PRK09791 putative DNA-binding 35.1 36 0.00078 28.0 2.7 22 9-30 20-41 (302)
328 PF00085 Thioredoxin: Thioredo 35.0 29 0.00064 23.3 1.8 30 11-40 39-75 (103)
329 COG2826 Tra8 Transposase and i 34.6 87 0.0019 28.7 5.2 39 8-47 23-61 (318)
330 PF13463 HTH_27: Winged helix 34.5 46 0.001 21.5 2.7 25 8-32 18-42 (68)
331 PRK12469 RNA polymerase factor 34.4 70 0.0015 30.4 4.8 26 9-34 370-395 (481)
332 PRK10086 DNA-binding transcrip 34.3 38 0.00081 28.3 2.7 27 8-34 28-58 (311)
333 PRK15435 bifunctional DNA-bind 34.3 46 0.001 29.9 3.4 29 7-35 98-127 (353)
334 PRK10411 DNA-binding transcrip 33.9 32 0.0007 28.9 2.3 34 6-39 16-49 (240)
335 cd08315 Death_TRAILR_DR4_DR5 D 33.9 51 0.0011 24.4 3.1 32 1-32 4-43 (96)
336 TIGR03418 chol_sulf_TF putativ 33.9 40 0.00087 27.4 2.7 26 9-34 16-45 (291)
337 PRK15320 transcriptional activ 33.6 39 0.00085 29.8 2.7 38 8-45 179-220 (251)
338 PF12342 DUF3640: Protein of u 33.4 33 0.00073 20.7 1.6 15 24-38 4-18 (26)
339 PRK11062 nhaR transcriptional 33.4 44 0.00096 27.6 3.0 27 8-34 18-48 (296)
340 PHA02519 plasmid partition pro 33.3 46 0.00099 30.2 3.3 27 8-34 39-65 (387)
341 TIGR03339 phn_lysR aminoethylp 33.3 38 0.00082 27.0 2.5 27 8-34 11-41 (279)
342 PRK11886 bifunctional biotin-- 33.2 40 0.00086 29.1 2.7 30 8-37 18-47 (319)
343 PRK09906 DNA-binding transcrip 33.2 35 0.00076 27.8 2.3 26 9-34 16-45 (296)
344 TIGR00738 rrf2_super rrf2 fami 33.1 48 0.001 24.5 2.8 26 8-33 25-50 (132)
345 PRK03601 transcriptional regul 32.9 41 0.0009 27.5 2.7 27 8-34 15-45 (275)
346 PRK14997 LysR family transcrip 32.9 46 0.001 27.3 3.0 27 8-34 16-46 (301)
347 PRK09508 leuO leucine transcri 32.7 42 0.0009 28.0 2.7 27 8-34 36-66 (314)
348 PF12244 DUF3606: Protein of u 32.6 40 0.00086 22.9 2.1 21 14-34 26-46 (57)
349 TIGR02702 SufR_cyano iron-sulf 32.6 46 0.00099 27.0 2.9 25 8-32 15-39 (203)
350 PRK12679 cbl transcriptional r 32.5 38 0.00083 28.4 2.5 26 9-34 17-46 (316)
351 PF04859 DUF641: Plant protein 32.5 1.4E+02 0.0031 23.8 5.5 25 13-39 44-72 (131)
352 PRK13509 transcriptional repre 32.4 42 0.00091 28.3 2.7 30 3-32 14-43 (251)
353 PF00325 Crp: Bacterial regula 32.3 58 0.0013 20.1 2.6 24 8-31 2-25 (32)
354 TIGR03631 bact_S13 30S ribosom 32.3 38 0.00081 26.1 2.2 28 16-45 19-46 (113)
355 PRK09391 fixK transcriptional 32.2 48 0.001 26.9 2.9 26 7-32 178-203 (230)
356 PF06322 Phage_NinH: Phage Nin 32.2 42 0.0009 24.2 2.2 23 10-32 18-40 (64)
357 TIGR03697 NtcA_cyano global ni 31.9 53 0.0012 25.0 3.0 26 7-32 142-167 (193)
358 TIGR02337 HpaR homoprotocatech 31.9 50 0.0011 24.1 2.7 26 8-33 42-67 (118)
359 PF01022 HTH_5: Bacterial regu 31.4 53 0.0012 20.6 2.5 23 8-30 15-37 (47)
360 PF02002 TFIIE_alpha: TFIIE al 31.4 46 0.00099 24.2 2.4 25 8-32 27-51 (105)
361 cd00283 GIY-YIG_Cterm GIYX(10- 31.2 36 0.00079 26.1 2.0 19 10-28 82-100 (113)
362 PRK11151 DNA-binding transcrip 31.1 44 0.00095 27.5 2.6 27 8-34 15-45 (305)
363 PRK10632 transcriptional regul 31.1 51 0.0011 27.5 3.0 27 8-34 16-46 (309)
364 PRK10094 DNA-binding transcrip 31.0 45 0.00098 27.9 2.7 27 8-34 16-46 (308)
365 TIGR02036 dsdC D-serine deamin 30.8 47 0.001 27.6 2.7 27 8-34 22-52 (302)
366 cd08316 Death_FAS_TNFRSF6 Deat 30.7 51 0.0011 24.8 2.6 30 13-54 13-42 (97)
367 TIGR03298 argP transcriptional 30.5 54 0.0012 26.8 3.0 27 8-34 15-45 (292)
368 PF07374 DUF1492: Protein of u 30.5 66 0.0014 23.6 3.2 23 8-30 71-93 (100)
369 PRK15090 DNA-binding transcrip 30.3 52 0.0011 27.4 2.9 31 8-38 28-62 (257)
370 PF14817 HAUS5: HAUS augmin-li 30.1 48 0.0011 32.6 3.0 32 14-45 10-49 (632)
371 PRK09986 DNA-binding transcrip 29.9 42 0.00092 27.1 2.3 26 9-34 22-51 (294)
372 KOG2577 Transcription factor E 29.9 96 0.0021 28.7 4.7 65 8-84 91-181 (354)
373 PRK11242 DNA-binding transcrip 29.8 48 0.001 26.9 2.5 27 8-34 15-45 (296)
374 cd08313 Death_TNFR1 Death doma 29.8 2.2E+02 0.0048 20.7 6.1 64 19-99 8-71 (80)
375 PF04539 Sigma70_r3: Sigma-70 29.5 64 0.0014 21.7 2.8 23 10-32 22-44 (78)
376 COG3645 Uncharacterized phage- 29.4 55 0.0012 26.5 2.8 26 9-34 48-73 (135)
377 PRK11074 putative DNA-binding 29.4 51 0.0011 27.2 2.7 27 8-34 16-46 (300)
378 COG0583 LysR Transcriptional r 29.3 49 0.0011 26.2 2.5 27 8-34 15-45 (297)
379 TIGR03613 RutR pyrimidine util 29.3 52 0.0011 25.4 2.6 34 6-52 26-59 (202)
380 PRK05179 rpsM 30S ribosomal pr 29.1 45 0.00099 26.0 2.2 28 16-45 21-48 (122)
381 cd08805 Death_ank1 Death domai 29.0 77 0.0017 23.2 3.3 30 3-32 10-39 (84)
382 PRK10216 DNA-binding transcrip 29.0 52 0.0011 27.5 2.7 28 8-35 22-53 (319)
383 CHL00137 rps13 ribosomal prote 28.9 49 0.0011 25.9 2.3 28 16-45 21-48 (122)
384 COG2901 Fis Factor for inversi 28.9 63 0.0014 24.9 2.8 30 5-34 68-97 (98)
385 PRK15201 fimbriae regulatory p 28.9 64 0.0014 27.7 3.2 24 8-31 148-171 (198)
386 PRK09801 transcriptional activ 28.8 52 0.0011 27.7 2.7 27 8-34 20-50 (310)
387 PRK10434 srlR DNA-bindng trans 28.8 46 0.001 28.1 2.4 30 3-32 14-43 (256)
388 CHL00180 rbcR LysR transcripti 28.6 47 0.001 27.5 2.4 27 8-34 19-49 (305)
389 PF12668 DUF3791: Protein of u 28.3 78 0.0017 21.4 3.0 25 10-34 7-31 (62)
390 COG1318 Predicted transcriptio 28.3 60 0.0013 27.6 2.9 40 5-44 58-101 (182)
391 PRK11482 putative DNA-binding 28.2 53 0.0012 27.8 2.7 23 8-30 43-65 (317)
392 PRK00409 recombination and DNA 28.2 1.5E+02 0.0031 29.7 6.0 38 12-55 491-528 (782)
393 COG2186 FadR Transcriptional r 28.1 50 0.0011 27.7 2.4 24 9-32 34-58 (241)
394 PF13744 HTH_37: Helix-turn-he 28.0 83 0.0018 22.0 3.2 33 2-34 36-73 (80)
395 PRK04140 hypothetical protein; 28.0 59 0.0013 29.3 3.0 29 2-30 133-161 (317)
396 PRK08154 anaerobic benzoate ca 28.0 67 0.0014 27.8 3.3 29 3-31 36-64 (309)
397 PF08965 DUF1870: Domain of un 27.9 55 0.0012 25.9 2.5 26 2-27 8-35 (118)
398 PRK13918 CRP/FNR family transc 27.9 66 0.0014 24.9 2.9 39 7-45 148-189 (202)
399 PF10087 DUF2325: Uncharacteri 27.8 50 0.0011 23.7 2.1 30 23-53 65-94 (97)
400 PF12792 CSS-motif: CSS motif 27.7 1.9E+02 0.0041 22.0 5.4 58 65-124 17-75 (208)
401 PRK07914 hypothetical protein; 27.6 2.8E+02 0.0061 23.9 7.0 49 10-60 251-299 (320)
402 PRK15481 transcriptional regul 27.3 61 0.0013 28.6 2.9 27 6-32 26-53 (431)
403 PRK11139 DNA-binding transcrip 27.0 60 0.0013 26.6 2.7 27 9-35 21-51 (297)
404 PRK11569 transcriptional repre 26.9 61 0.0013 27.4 2.8 24 9-32 44-67 (274)
405 PRK15421 DNA-binding transcrip 26.3 63 0.0014 27.4 2.8 27 8-34 16-46 (317)
406 cd08317 Death_ank Death domain 26.3 90 0.0019 22.1 3.2 21 11-34 7-27 (84)
407 PRK11920 rirA iron-responsive 26.3 68 0.0015 25.3 2.8 24 9-32 25-48 (153)
408 PF00416 Ribosomal_S13: Riboso 26.2 60 0.0013 24.3 2.4 29 16-46 19-47 (107)
409 PRK14999 histidine utilization 26.2 66 0.0014 26.4 2.8 23 10-32 38-60 (241)
410 PF08765 Mor: Mor transcriptio 26.2 82 0.0018 23.4 3.1 28 6-33 70-97 (108)
411 TIGR02404 trehalos_R_Bsub treh 26.2 67 0.0015 26.1 2.8 22 11-32 27-48 (233)
412 PF04463 DUF523: Protein of un 26.0 30 0.00064 27.2 0.7 12 32-43 45-56 (143)
413 PRK03635 chromosome replicatio 25.9 63 0.0014 26.6 2.6 27 8-34 16-46 (294)
414 COG3023 ampD N-acetyl-anhydrom 25.9 3.2E+02 0.007 24.4 7.1 72 26-99 171-254 (257)
415 COG4367 Uncharacterized protei 25.7 64 0.0014 24.9 2.4 28 2-29 14-44 (97)
416 PRK05743 ileS isoleucyl-tRNA s 25.7 1.8E+02 0.0039 29.5 6.2 77 5-109 96-178 (912)
417 PRK12681 cysB transcriptional 25.7 59 0.0013 27.7 2.5 26 9-34 17-46 (324)
418 PRK12680 transcriptional regul 25.7 59 0.0013 27.8 2.5 26 9-34 17-46 (327)
419 PRK09430 djlA Dna-J like membr 25.7 4.3E+02 0.0093 22.8 7.8 15 12-26 155-169 (267)
420 TIGR02395 rpoN_sigma RNA polym 25.6 42 0.00091 31.1 1.7 26 9-34 319-344 (429)
421 PRK06266 transcription initiat 25.5 72 0.0016 26.1 2.9 25 8-32 36-60 (178)
422 TIGR02431 pcaR_pcaU beta-ketoa 25.5 73 0.0016 26.3 2.9 25 8-32 24-48 (248)
423 PRK00215 LexA repressor; Valid 25.3 80 0.0017 25.3 3.1 26 8-33 23-49 (205)
424 PF02609 Exonuc_VII_S: Exonucl 25.2 1.8E+02 0.004 19.0 4.3 36 68-104 3-38 (53)
425 PF07498 Rho_N: Rho terminatio 25.2 56 0.0012 20.8 1.8 33 20-55 5-37 (43)
426 TIGR03826 YvyF flagellar opero 24.9 97 0.0021 24.8 3.4 32 9-40 47-78 (137)
427 PRK04053 rps13p 30S ribosomal 24.9 62 0.0013 26.2 2.3 28 16-45 29-56 (149)
428 PRK13705 plasmid-partitioning 24.9 77 0.0017 28.6 3.2 30 8-38 39-68 (388)
429 PRK09039 hypothetical protein; 24.8 1.6E+02 0.0035 26.4 5.2 60 39-102 136-202 (343)
430 KOG1789 Endocytosis protein RM 24.8 2.4E+02 0.0052 31.0 6.9 50 3-52 1214-1267(2235)
431 PF04977 DivIC: Septum formati 24.7 1.4E+02 0.003 20.0 3.8 41 37-84 14-54 (80)
432 PLN03184 chloroplast Hsp70; Pr 24.6 4E+02 0.0087 26.0 8.1 41 63-103 591-631 (673)
433 PRK13832 plasmid partitioning 24.3 78 0.0017 30.7 3.3 26 6-32 116-141 (520)
434 cd04786 HTH_MerR-like_sg7 Heli 24.3 3.4E+02 0.0073 21.0 8.5 71 12-90 50-122 (131)
435 cd09236 V_AnPalA_UmRIM20_like 24.3 5.1E+02 0.011 23.0 9.0 73 31-103 114-205 (353)
436 PRK11013 DNA-binding transcrip 24.2 69 0.0015 26.7 2.6 27 8-34 18-48 (309)
437 TIGR00268 conserved hypothetic 24.1 70 0.0015 26.8 2.6 20 18-37 142-161 (252)
438 PRK12683 transcriptional regul 24.1 66 0.0014 27.0 2.5 26 9-34 17-46 (309)
439 PRK08311 putative RNA polymera 24.0 66 0.0014 27.4 2.5 20 8-27 187-206 (237)
440 PRK11512 DNA-binding transcrip 24.0 89 0.0019 23.6 3.0 32 8-39 54-89 (144)
441 TIGR01069 mutS2 MutS2 family p 23.9 1.9E+02 0.0041 28.9 5.8 38 12-55 486-523 (771)
442 PRK10402 DNA-binding transcrip 23.7 79 0.0017 25.4 2.8 38 7-44 168-208 (226)
443 COG0099 RpsM Ribosomal protein 23.7 56 0.0012 26.1 1.8 22 16-37 21-42 (121)
444 PRK12684 transcriptional regul 23.7 65 0.0014 27.0 2.3 25 10-34 18-46 (313)
445 PRK09552 mtnX 2-hydroxy-3-keto 23.6 1.9E+02 0.0041 23.1 4.9 41 13-56 174-216 (219)
446 PRK03573 transcriptional regul 23.6 87 0.0019 23.5 2.8 29 9-37 47-75 (144)
447 PRK10668 DNA-binding transcrip 23.2 3.6E+02 0.0079 21.0 7.1 35 18-52 27-62 (215)
448 COG4565 CitB Response regulato 23.1 71 0.0015 27.9 2.5 21 8-28 173-193 (224)
449 TIGR02325 C_P_lyase_phnF phosp 23.0 84 0.0018 25.3 2.8 23 10-32 34-56 (238)
450 PRK04424 fatty acid biosynthes 23.0 71 0.0015 25.9 2.4 30 5-34 18-47 (185)
451 cd08803 Death_ank3 Death domai 22.7 1.2E+02 0.0026 22.0 3.3 30 3-32 10-39 (84)
452 PRK10668 DNA-binding transcrip 22.7 77 0.0017 24.8 2.5 24 5-28 28-51 (215)
453 PRK13756 tetracycline represso 22.7 1.1E+02 0.0024 25.0 3.5 42 11-52 9-55 (205)
454 TIGR02366 DHAK_reg probable di 22.6 60 0.0013 24.7 1.8 36 17-52 18-54 (176)
455 PRK05629 hypothetical protein; 22.6 4.7E+02 0.01 22.4 7.5 48 10-59 251-298 (318)
456 smart00347 HTH_MARR helix_turn 22.6 1E+02 0.0022 20.7 2.8 22 9-30 25-46 (101)
457 PF04297 UPF0122: Putative hel 22.5 1E+02 0.0022 23.5 3.0 21 8-28 33-53 (101)
458 PRK09744 DNA-binding transcrip 22.5 70 0.0015 23.6 2.0 25 2-27 5-29 (75)
459 TIGR03337 phnR transcriptional 22.5 88 0.0019 25.1 2.8 23 10-32 27-49 (231)
460 PF05659 RPW8: Arabidopsis bro 22.3 3.2E+02 0.007 21.7 5.9 28 63-90 65-92 (147)
461 cd01670 Death Death Domain: a 22.3 98 0.0021 20.7 2.6 20 12-34 3-22 (79)
462 COG1813 Predicted transcriptio 22.1 84 0.0018 26.2 2.6 26 5-30 89-114 (165)
463 PF07098 DUF1360: Protein of u 22.0 34 0.00073 26.3 0.3 15 151-165 52-66 (105)
464 TIGR03629 arch_S13P archaeal r 21.8 79 0.0017 25.4 2.4 28 16-45 25-52 (144)
465 TIGR02684 dnstrm_HI1420 probab 21.7 86 0.0019 23.0 2.4 29 4-34 41-69 (89)
466 PF09012 FeoC: FeoC like trans 21.7 93 0.002 21.0 2.4 22 8-29 14-35 (69)
467 PF07900 DUF1670: Protein of u 21.6 89 0.0019 27.2 2.8 32 8-40 105-140 (220)
468 PTZ00134 40S ribosomal protein 21.6 78 0.0017 25.9 2.3 28 16-45 34-61 (154)
469 PRK10870 transcriptional repre 21.5 1E+02 0.0022 24.7 2.9 29 9-37 72-100 (176)
470 cd02961 PDI_a_family Protein D 21.3 98 0.0021 20.1 2.4 20 20-39 55-74 (101)
471 PRK15092 DNA-binding transcrip 21.3 87 0.0019 26.5 2.7 27 8-34 25-55 (310)
472 PRK09764 DNA-binding transcrip 21.1 96 0.0021 25.4 2.8 24 9-32 29-53 (240)
473 TIGR02047 CadR-PbrR Cd(II)/Pb( 21.1 3.8E+02 0.0081 20.3 7.6 18 14-31 52-69 (127)
474 PRK11402 DNA-binding transcrip 21.0 97 0.0021 25.3 2.8 23 10-32 35-57 (241)
475 PRK10163 DNA-binding transcrip 21.0 99 0.0021 26.2 2.9 25 8-32 40-64 (271)
476 PRK00441 argR arginine repress 20.8 1.1E+02 0.0025 24.3 3.1 34 5-38 15-53 (149)
477 COG4152 ABC-type uncharacteriz 20.7 1.8E+02 0.0039 26.5 4.5 75 8-102 101-176 (300)
478 COG1321 TroR Mn-dependent tran 20.5 99 0.0021 24.8 2.7 36 7-43 23-63 (154)
479 PF04963 Sigma54_CBD: Sigma-54 20.3 1.2E+02 0.0026 24.8 3.2 25 4-28 48-72 (194)
480 PRK11235 bifunctional antitoxi 20.3 1.5E+02 0.0032 21.8 3.3 23 12-34 17-44 (80)
481 PF14282 FlxA: FlxA-like prote 20.1 3.8E+02 0.0083 20.0 5.8 42 40-81 19-64 (106)
No 1
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=99.93 E-value=3.8e-27 Score=160.11 Aligned_cols=45 Identities=64% Similarity=1.051 Sum_probs=43.8
Q ss_pred ChhhhhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 1 ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 1 e~l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
|||++|||||++|||++||||+|+|||+||++||+||||||++||
T Consensus 8 ~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~RWP~Rkl~Sl 52 (52)
T PF02042_consen 8 EDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIPRWPYRKLKSL 52 (52)
T ss_pred HHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCCCCCchhhccC
Confidence 589999999999999999999999999999999999999999986
No 2
>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=96.46 E-value=0.002 Score=45.34 Aligned_cols=35 Identities=17% Similarity=0.413 Sum_probs=28.4
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~ 39 (168)
..-.+++.+.|+.+|||.+++=|.|+++|...|+-
T Consensus 31 ~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~e 65 (77)
T PF01418_consen 31 EIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKE 65 (77)
T ss_dssp HHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHH
T ss_pred HHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHH
Confidence 44579999999999999999999999999987764
No 3
>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=95.94 E-value=0.01 Score=36.43 Aligned_cols=28 Identities=18% Similarity=0.196 Sum_probs=25.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
|.+.|||+.||||.+++.+.+++-.|+.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence 6789999999999999999999877764
No 4
>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=95.58 E-value=0.0097 Score=38.21 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=19.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
++|+.++|+.+|||.+++.|+.++
T Consensus 21 G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp T--HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 589999999999999999998764
No 5
>PF12728 HTH_17: Helix-turn-helix domain
Probab=95.27 E-value=0.023 Score=36.40 Aligned_cols=29 Identities=17% Similarity=0.286 Sum_probs=25.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RW 37 (168)
|...|||+.||||.+++.+.+++-+|+..
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence 57899999999999999999999988543
No 6
>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=95.24 E-value=0.026 Score=34.24 Aligned_cols=27 Identities=22% Similarity=0.358 Sum_probs=23.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+.+.|||+.|||+.++|.+.+++-.++
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 468899999999999999999986665
No 7
>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=95.18 E-value=0.028 Score=35.07 Aligned_cols=31 Identities=26% Similarity=0.163 Sum_probs=25.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCchh
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHRK 41 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RK 41 (168)
+++.|+|+.|||+..+|++.+++-.|+ |.|.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~--~~~~ 31 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS--PART 31 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC--CCcC
Confidence 578999999999999999887776665 6553
No 8
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=95.07 E-value=0.03 Score=35.52 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=22.1
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
..++--+.+||+.|||+.++|.+..+++
T Consensus 15 ~~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 15 ERCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 3456778999999999999999988775
No 9
>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=95.07 E-value=0.031 Score=37.83 Aligned_cols=27 Identities=19% Similarity=0.186 Sum_probs=24.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+++.|+|+.+||+.++|+..+++.|+.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~ 27 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLL 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999998864
No 10
>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=95.04 E-value=0.033 Score=37.51 Aligned_cols=27 Identities=19% Similarity=0.241 Sum_probs=24.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+++.|+|+.+||++++|+..+++.|++
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~ 27 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLY 27 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999998886
No 11
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=94.95 E-value=0.021 Score=47.44 Aligned_cols=37 Identities=27% Similarity=0.384 Sum_probs=32.4
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchh
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRK 41 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RK 41 (168)
....+++.+.|++.|||.+++=|.||++|...||-=|
T Consensus 31 ~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~k 67 (284)
T PRK11302 31 TAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFK 67 (284)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHH
Confidence 3457999999999999999999999999999886433
No 12
>PRK15482 transcriptional regulator MurR; Provisional
Probab=94.80 E-value=0.024 Score=47.77 Aligned_cols=38 Identities=16% Similarity=0.246 Sum_probs=33.5
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhh
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKL 42 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKl 42 (168)
....+.+.+.|++.|||.+++=|.|+++|...|+-=|.
T Consensus 31 ~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~ 68 (285)
T PRK15482 31 ELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRM 68 (285)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHH
Confidence 34579999999999999999999999999999976543
No 13
>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=94.62 E-value=0.4 Score=35.55 Aligned_cols=27 Identities=19% Similarity=0.142 Sum_probs=24.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+++.|+|+.+||+.++|...+++.|+.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gli 27 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQL 27 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence 478999999999999999999997753
No 14
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=94.33 E-value=0.029 Score=47.86 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=33.5
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhh
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLM 43 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlk 43 (168)
.-++.+.|.|+..|||.+++=|.||++|-..||==|+.
T Consensus 34 ~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~ 71 (281)
T COG1737 34 VALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLA 71 (281)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHH
Confidence 34688999999999999999999999999999866653
No 15
>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=94.23 E-value=0.067 Score=35.59 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=23.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.|+|+.+||+.++|.+..++.|+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~ 26 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGL 26 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCC
Confidence 47899999999999999999988886
No 16
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=93.93 E-value=0.047 Score=45.51 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=32.4
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchh
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRK 41 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RK 41 (168)
..-.+.+.+.|++.|||.+++=|.||++|...|+-=|
T Consensus 27 ~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk 63 (278)
T PRK11557 27 TARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALK 63 (278)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHH
Confidence 3447899999999999999999999999999886544
No 17
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=93.92 E-value=0.073 Score=39.67 Aligned_cols=29 Identities=24% Similarity=0.284 Sum_probs=26.2
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.++-.+.+||+.|||+.++|.+..+++||
T Consensus 66 ~~~gn~s~AAr~LGIsRsTL~rKLkr~gi 94 (95)
T PRK00430 66 YTRGNQTRAALMLGINRGTLRKKLKKYGM 94 (95)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 34567899999999999999999999998
No 18
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=93.79 E-value=0.065 Score=34.39 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=18.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
++++.++|+.||++.+|+.+-+++.
T Consensus 20 G~s~~~IA~~lg~s~sTV~relkR~ 44 (44)
T PF13936_consen 20 GMSIREIAKRLGRSRSTVSRELKRN 44 (44)
T ss_dssp ---HHHHHHHTT--HHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCcHHHHHHHhcC
Confidence 7899999999999999999998863
No 19
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.76 E-value=0.06 Score=34.15 Aligned_cols=25 Identities=20% Similarity=0.197 Sum_probs=18.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+++..++|+.||||.+++.+..+++
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 7899999999999999999987664
No 20
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=93.73 E-value=0.055 Score=45.53 Aligned_cols=34 Identities=15% Similarity=0.206 Sum_probs=30.8
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCc
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~ 39 (168)
...+++.+.|++.|||.+++=|.||++|...|+-
T Consensus 44 v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~e 77 (292)
T PRK11337 44 SEATALKDIAEALAVSEAMIVKVAKKLGFSGFRN 77 (292)
T ss_pred HHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHH
Confidence 4468999999999999999999999999988863
No 21
>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=93.26 E-value=0.11 Score=35.37 Aligned_cols=27 Identities=26% Similarity=0.537 Sum_probs=23.4
Q ss_pred hhccCc----HHHHHHHcCCChhHHHHHHHH
Q 036926 5 QYFYMP----ITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 5 ~yF~lP----i~eAAr~LgVs~T~LKr~CR~ 31 (168)
.||+.| +.|.|++||||.+++-..-|+
T Consensus 16 GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 16 GYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 689887 899999999999998777664
No 22
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=93.14 E-value=0.12 Score=33.96 Aligned_cols=32 Identities=9% Similarity=0.071 Sum_probs=25.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC-CCCCCc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN-IRRWPH 39 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG-I~RWP~ 39 (168)
.+++.++|+.+|++.+.|.+++++.. +.-..+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~ 33 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQY 33 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHH
Confidence 36899999999999999999998865 544333
No 23
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.90 E-value=0.11 Score=32.05 Aligned_cols=31 Identities=19% Similarity=0.278 Sum_probs=23.7
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCCCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNIRRWP 38 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI~RWP 38 (168)
+++..++|+.||||..++++. ++++|+..+|
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~ 52 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRT 52 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Confidence 789999999999999887766 4455554443
No 24
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.85 E-value=0.98 Score=34.17 Aligned_cols=26 Identities=15% Similarity=0.141 Sum_probs=23.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
+.++.++|+++||+.++|.+..+++.
T Consensus 29 g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 29 GMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 68999999999999999999999874
No 25
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=92.80 E-value=0.12 Score=42.59 Aligned_cols=27 Identities=26% Similarity=0.372 Sum_probs=25.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
|.+.++|+.+|||.+||.+.+++.||+
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~ 27 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLP 27 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 578999999999999999999999986
No 26
>PRK01905 DNA-binding protein Fis; Provisional
Probab=92.65 E-value=0.16 Score=36.09 Aligned_cols=28 Identities=18% Similarity=0.128 Sum_probs=25.2
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
++-...+||+.|||+.++|.++-+++||
T Consensus 49 ~~gn~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 49 AGGNQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 3456889999999999999999999997
No 27
>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=92.58 E-value=0.54 Score=34.41 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=20.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+.+.|+|+.+||++++|+...+ .|+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~-~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE-IGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 4689999999999999997765 453
No 28
>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=92.43 E-value=1.2 Score=33.82 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=21.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
++|.|+|+.+|||+.+|.-.-+. |+
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~-GL 25 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK-GL 25 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 47899999999999999887775 75
No 29
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=92.13 E-value=0.71 Score=30.57 Aligned_cols=26 Identities=23% Similarity=0.097 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+.+.|+|+.+||+..+|.+..++--|
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gli 26 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGLL 26 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 46899999999999999998874444
No 30
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=92.07 E-value=0.18 Score=38.82 Aligned_cols=28 Identities=14% Similarity=0.212 Sum_probs=24.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|..|.+|.+.|||..+|||.+|+-++-.
T Consensus 52 L~D~egl~QeeaA~~MgVSR~T~~ril~ 79 (106)
T PF02001_consen 52 LVDYEGLSQEEAAERMGVSRPTFQRILE 79 (106)
T ss_pred HHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence 4578899999999999999999987754
No 31
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=91.95 E-value=0.19 Score=33.51 Aligned_cols=26 Identities=31% Similarity=0.229 Sum_probs=23.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+.+.|+|+.+||+..+|+..+++.-+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gll 26 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGLL 26 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTSS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcCc
Confidence 46899999999999999999987765
No 32
>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=91.63 E-value=1.3 Score=32.63 Aligned_cols=26 Identities=12% Similarity=0.087 Sum_probs=22.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+++.|+|+.+||++++|....+. |+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 68999999999999999988886 753
No 33
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=91.59 E-value=0.23 Score=31.62 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=22.8
Q ss_pred hccC-cHHHHHHHcCCChhHHHHHHHHc
Q 036926 6 YFYM-PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 6 yF~l-Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
..+. +++++|+.+|||.++++++-.++
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4455 99999999999999999987653
No 34
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=91.41 E-value=0.25 Score=30.65 Aligned_cols=27 Identities=4% Similarity=0.165 Sum_probs=21.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI 34 (168)
.+++.++|..+|+|.+.|.|..++. |+
T Consensus 8 ~~~l~~iA~~~g~S~~~f~r~Fk~~~g~ 35 (42)
T PF00165_consen 8 KLTLEDIAEQAGFSPSYFSRLFKKETGM 35 (42)
T ss_dssp S--HHHHHHHHTS-HHHHHHHHHHHTSS
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCc
Confidence 4789999999999999999999987 65
No 35
>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=91.23 E-value=0.26 Score=36.25 Aligned_cols=30 Identities=23% Similarity=0.255 Sum_probs=25.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
|++.++|+.+||+.++|+..++. |+-. |.|
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~-p~r 30 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLVS-PER 30 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCc
Confidence 57899999999999999999985 8654 644
No 36
>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=90.94 E-value=0.26 Score=37.26 Aligned_cols=33 Identities=15% Similarity=0.207 Sum_probs=29.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
|..+=++++.|.|+.||||.+++-+...++|+.
T Consensus 66 v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t 98 (119)
T PF01710_consen 66 VEENPDATLRELAERLGVSPSTIWRALKRLGIT 98 (119)
T ss_pred HHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCch
Confidence 445668899999999999999999999999984
No 37
>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=90.82 E-value=0.34 Score=31.09 Aligned_cols=27 Identities=22% Similarity=0.290 Sum_probs=19.0
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.-+.++|..|+|+.||||.++++..-+
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 456799999999999999999887644
No 38
>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=90.81 E-value=3.2 Score=29.71 Aligned_cols=25 Identities=24% Similarity=0.157 Sum_probs=22.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.++|+.+||++++|....+ .|+
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 6899999999999999999987 474
No 39
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.70 E-value=0.32 Score=30.56 Aligned_cols=25 Identities=8% Similarity=0.177 Sum_probs=21.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.++.++|+++|||.+++.+..+++
T Consensus 12 g~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 12 GESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHHHH
Confidence 4589999999999999998887654
No 40
>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=90.66 E-value=1.8 Score=32.16 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=22.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.|+|+.+|||+.+|....+.--|
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57999999999999999988776445
No 41
>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=90.17 E-value=0.42 Score=30.53 Aligned_cols=24 Identities=8% Similarity=0.256 Sum_probs=20.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
++++.|+|+.||+|..+++++.++
T Consensus 20 ~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 20 GLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp T-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCcHHHHHHHHHH
Confidence 899999999999999999988764
No 42
>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=90.12 E-value=0.32 Score=31.01 Aligned_cols=29 Identities=7% Similarity=0.070 Sum_probs=23.6
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
++.--++++.+.|+.+||+.+++.++.+-
T Consensus 4 ~r~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 4 LRKEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 45567899999999999999999999876
No 43
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=89.88 E-value=0.43 Score=34.49 Aligned_cols=26 Identities=19% Similarity=0.188 Sum_probs=24.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc-CC
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL-NI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l-GI 34 (168)
+++.++|+.+|+|...|.|+|++. |+
T Consensus 22 ~~~~~lA~~~~~S~~~l~r~f~~~~g~ 48 (107)
T PRK10219 22 LNIDVVAKKSGYSKWYLQRMFRTVTHQ 48 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCc
Confidence 889999999999999999999996 76
No 44
>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=89.76 E-value=1.6 Score=32.61 Aligned_cols=27 Identities=19% Similarity=0.150 Sum_probs=23.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
|.|.|+|+.+|||+.+|+-..+. |+-.
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~-GLl~ 27 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ-GLLV 27 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC-CCCC
Confidence 57899999999999999998875 7543
No 45
>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=89.73 E-value=4.6 Score=30.99 Aligned_cols=30 Identities=20% Similarity=0.329 Sum_probs=23.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
|.|.|+|+.+|||+.+| |.--+.|+-. |.|
T Consensus 1 m~IgE~A~~~gvs~~TL-RyYE~~GLl~-p~r 30 (133)
T cd04787 1 MKVKELANAAGVTPDTV-RFYTRIGLLR-PTR 30 (133)
T ss_pred CCHHHHHHHHCcCHHHH-HHHHHCCCCC-CCc
Confidence 57899999999999999 5556889643 544
No 46
>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=89.41 E-value=0.41 Score=32.34 Aligned_cols=33 Identities=12% Similarity=0.253 Sum_probs=24.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc--CCCCCCch
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL--NIRRWPHR 40 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l--GI~RWP~R 40 (168)
+.++.++|+++||++++|.+..+++ |...=|..
T Consensus 23 g~sv~~va~~~gi~~~~l~~W~~~~~~~~~~~~~~ 57 (76)
T PF01527_consen 23 GESVSEVAREYGISPSTLYNWRKQYREGQSAFPAK 57 (76)
T ss_dssp HCHHHHHHHHHTS-HHHHHHHHHHHH--STT-SSS
T ss_pred CCceEeeecccccccccccHHHHHHhcCCCCCCcc
Confidence 6789999999999999999988888 45555554
No 47
>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=89.35 E-value=0.43 Score=30.66 Aligned_cols=26 Identities=23% Similarity=0.293 Sum_probs=20.4
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
=-.|..+.|+.+|+|.+++.++-+++
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 35799999999999999998887764
No 48
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=89.13 E-value=0.31 Score=29.82 Aligned_cols=20 Identities=25% Similarity=0.321 Sum_probs=17.6
Q ss_pred cHHHHHHHcCCChhHHHHHH
Q 036926 10 PITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~C 29 (168)
.+.|||+.|||+.+++.+.|
T Consensus 18 Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 18 SIREAARYLGISHSTISKYL 37 (37)
T ss_pred CHHHHHHHhCCCHHHHHHhC
Confidence 57899999999999998764
No 49
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=88.81 E-value=0.48 Score=30.09 Aligned_cols=22 Identities=27% Similarity=0.291 Sum_probs=20.5
Q ss_pred cHHHHHHHcCCChhHHHHHHHH
Q 036926 10 PITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.+.|||+.||++.+++.+.|+.
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhC
Confidence 6889999999999999999985
No 50
>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=88.72 E-value=3.5 Score=30.01 Aligned_cols=25 Identities=12% Similarity=0.204 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.+.|+|+.+||++.+|....+ .|+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~-~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH-IGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5789999999999999998876 453
No 51
>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=88.57 E-value=0.48 Score=35.09 Aligned_cols=23 Identities=9% Similarity=0.024 Sum_probs=21.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+.+.+++|+.||||.+|++|++|
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999999887
No 52
>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=88.21 E-value=0.57 Score=34.29 Aligned_cols=40 Identities=25% Similarity=0.189 Sum_probs=30.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCC-CchhhhcHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRW-PHRKLMSLQT 47 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RW-P~RKlkSL~~ 47 (168)
.+.+.++|+.|||+...|-+..|+.||-.. +-++...-+.
T Consensus 24 ~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~~~~~~~p~q~ 64 (111)
T PF03374_consen 24 LYTIREAAKLLGIGRNKLFQWLREKGWLYRRGKGRNLPYQK 64 (111)
T ss_pred CccHHHHHHHhCCCHHHHHHHHHhCCceEECCCCCcccChh
Confidence 478999999999999999999999996333 3334443333
No 53
>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=87.92 E-value=0.68 Score=33.31 Aligned_cols=30 Identities=17% Similarity=0.151 Sum_probs=24.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
+++.|+|+.+||+..+|+...++ |+-. |.|
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~-p~r 31 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GLIK-SIR 31 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCc
Confidence 68999999999999999999887 5433 544
No 54
>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=87.75 E-value=0.6 Score=30.32 Aligned_cols=22 Identities=45% Similarity=0.582 Sum_probs=16.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+++.+||+..||+.|+|-++-+
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHc
Confidence 8999999999999999996654
No 55
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=87.65 E-value=0.95 Score=32.12 Aligned_cols=31 Identities=16% Similarity=0.021 Sum_probs=28.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCCc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~ 39 (168)
.+....||+-+|+|.-.+-..++++||+ +.|
T Consensus 34 ~iS~gkAAelag~s~~eF~~~L~~~gI~-~~~ 64 (76)
T PF03683_consen 34 KISLGKAAELAGMSRWEFLELLKERGIP-INY 64 (76)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHCCCC-CCC
Confidence 6789999999999999999999999998 554
No 56
>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=87.50 E-value=0.74 Score=28.84 Aligned_cols=28 Identities=14% Similarity=0.145 Sum_probs=24.8
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++.-.++.+.++|+.+||+.+++.++.+
T Consensus 10 ~r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 10 RRKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4566799999999999999999999965
No 57
>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=87.20 E-value=3.2 Score=31.58 Aligned_cols=26 Identities=12% Similarity=0.079 Sum_probs=20.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|+|.|+|+.+|||+.+|.-..+.--|
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll 26 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLL 26 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 67999999999999999866553334
No 58
>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=86.95 E-value=2.9 Score=33.79 Aligned_cols=25 Identities=16% Similarity=0.319 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
++|.|+|+.+|||+++|.-.-+ .|+
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~-~GL 26 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER-IGL 26 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 6899999999999999987766 464
No 59
>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=86.72 E-value=0.82 Score=28.83 Aligned_cols=26 Identities=12% Similarity=0.204 Sum_probs=20.9
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
=.+++.|+|+.+|+|.+++.+..+++
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 35889999999999999999888764
No 60
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=86.67 E-value=0.44 Score=31.75 Aligned_cols=36 Identities=11% Similarity=0.007 Sum_probs=25.7
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHcC-CCCCC
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRELN-IRRWP 38 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lG-I~RWP 38 (168)
++.--++.+.++|+.+|||.+++.++.+--. .+.|+
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~ 45 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPD 45 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHH
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHH
Confidence 3445589999999999999999999988544 44443
No 61
>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=86.35 E-value=3.9 Score=31.28 Aligned_cols=23 Identities=17% Similarity=0.245 Sum_probs=20.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
|+|.|+|+.+|||+.+|.-..+.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~ 23 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEKQ 23 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC
Confidence 57999999999999999887764
No 62
>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=86.33 E-value=0.94 Score=31.04 Aligned_cols=27 Identities=19% Similarity=0.074 Sum_probs=25.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
++++.++|+.|||+.+++..-..+.|=
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W 39 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYKW 39 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhCc
Confidence 789999999999999999999998883
No 63
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=86.22 E-value=0.59 Score=44.24 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=30.6
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCc
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~ 39 (168)
.-.+.+.|.|++.|||.+++-|.||++|..-|+-
T Consensus 372 v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~e 405 (638)
T PRK14101 372 IINDPIVDIARKADVSQPTVIRFCRSLGCQGLSD 405 (638)
T ss_pred HHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHH
Confidence 3478999999999999999999999999988754
No 64
>PRK15043 transcriptional regulator MirA; Provisional
Probab=86.11 E-value=0.9 Score=39.40 Aligned_cols=32 Identities=19% Similarity=0.281 Sum_probs=28.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
.++|.|+|+.+||++.+|....|++|+.. |.|
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~-P~R 34 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLK-PQR 34 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCC-Ccc
Confidence 47899999999999999999999999765 655
No 65
>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=86.02 E-value=7.9 Score=28.19 Aligned_cols=25 Identities=12% Similarity=0.078 Sum_probs=22.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.|+|+.+|||..+|+...+ .|+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK-IGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5789999999999999998876 575
No 66
>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=85.84 E-value=1 Score=33.18 Aligned_cols=26 Identities=12% Similarity=0.075 Sum_probs=22.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+++.|+|+.+|||+++|.-..++ |+-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 68999999999999999777775 754
No 67
>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=85.77 E-value=1 Score=33.59 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=22.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|++.|+|+.+|||+.+|+...+. |+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57999999999999999999886 64
No 68
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=85.63 E-value=0.96 Score=35.67 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=23.4
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.-+.++|+.|+|..||||..++|.+..
T Consensus 118 ~~~~g~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 118 TELEGLSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345799999999999999999998763
No 69
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=85.44 E-value=0.95 Score=37.33 Aligned_cols=28 Identities=14% Similarity=0.050 Sum_probs=24.7
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.-+.++|.+|+|..||||..++|.+.++
T Consensus 146 ~y~eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 146 RELEDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4567999999999999999999998874
No 70
>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=85.40 E-value=0.6 Score=30.62 Aligned_cols=27 Identities=30% Similarity=0.330 Sum_probs=22.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRE-LNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~-lGI~ 35 (168)
+.+.|.|++|||+...|-+.|++ +||.
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 45789999999999999999966 9996
No 71
>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=85.19 E-value=1.3 Score=31.75 Aligned_cols=30 Identities=27% Similarity=0.330 Sum_probs=23.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
+.+.|+|+.+||+.++|+...++ |+-. |.|
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~-Gll~-~~~ 30 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEK-GLLP-PER 30 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCcC-CCc
Confidence 46899999999999999988874 6433 543
No 72
>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=85.07 E-value=1.3 Score=29.11 Aligned_cols=27 Identities=11% Similarity=0.113 Sum_probs=19.7
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
+++...++.+.++|+.+||+.+++.++
T Consensus 6 ~~r~~~~lt~~~~a~~~~i~~~~i~~~ 32 (64)
T PF12844_consen 6 ELREEKGLTQKDLAEKLGISRSTISKI 32 (64)
T ss_dssp HHHHHCT--HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 456777999999999999988777665
No 73
>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=85.02 E-value=1.1 Score=32.98 Aligned_cols=25 Identities=32% Similarity=0.385 Sum_probs=22.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.++|+.+||+.++|+...+ .|+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5899999999999999998876 674
No 74
>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=84.96 E-value=3.2 Score=30.18 Aligned_cols=25 Identities=20% Similarity=0.193 Sum_probs=22.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.|+|+.+||++.+|+-..++ |+
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 47899999999999999998887 75
No 75
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=84.93 E-value=1 Score=33.59 Aligned_cols=25 Identities=24% Similarity=0.189 Sum_probs=21.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.|+.+||+++|||..+.+|.-.++
T Consensus 25 g~~~a~aA~~~gVS~~Ta~kW~~Ry 49 (85)
T PF13011_consen 25 GWPVAHAAAEFGVSRRTAYKWLARY 49 (85)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 5899999999999999998865543
No 76
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=84.84 E-value=1.1 Score=33.87 Aligned_cols=27 Identities=7% Similarity=0.051 Sum_probs=24.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI 34 (168)
.+++.++|+.+|||++.|.|++++. |+
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~~G~ 52 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKETGH 52 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 4789999999999999999999987 87
No 77
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=84.67 E-value=1.1 Score=35.43 Aligned_cols=27 Identities=19% Similarity=0.101 Sum_probs=23.5
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.-+.+++.+|+|..||||.+++|.+..
T Consensus 123 ~~~eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 123 VAIEGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred HHHcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 446799999999999999999998863
No 78
>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=84.62 E-value=4.1 Score=31.00 Aligned_cols=23 Identities=22% Similarity=0.176 Sum_probs=20.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
|.|.|+|+.+||++.+|+-..+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57999999999999999977766
No 79
>PRK04217 hypothetical protein; Provisional
Probab=84.55 E-value=1.2 Score=34.35 Aligned_cols=26 Identities=15% Similarity=0.128 Sum_probs=23.2
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+-+++++|+|+.||||.++++++.++
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34689999999999999999998874
No 80
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=84.37 E-value=0.98 Score=34.26 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=23.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
++|++|+|+.||||.+++-|..+-++
T Consensus 55 ~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 55 NMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred CCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 58999999999999999999888776
No 81
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=84.34 E-value=1.1 Score=29.24 Aligned_cols=38 Identities=8% Similarity=-0.034 Sum_probs=22.6
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
-++.+.+.|+..||+.++|.+++..- +..|+.-.+..+
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~-~~~~~~~~l~~i 46 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK-PSNPSLDTLEKI 46 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT------HHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc-cccccHHHHHHH
Confidence 46789999999999999999999833 456665444433
No 82
>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=84.24 E-value=1.4 Score=27.28 Aligned_cols=23 Identities=17% Similarity=0.081 Sum_probs=19.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+++..++|+.||+|..++++..+
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 68999999999999988877654
No 83
>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=84.07 E-value=1.1 Score=29.39 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=19.9
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.++++|+.+|||.+++-|.-...
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 47899999999999999887654
No 84
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=83.74 E-value=4.3 Score=33.36 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=28.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH-cCCCCCCchhh
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE-LNIRRWPHRKL 42 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~-lGI~RWP~RKl 42 (168)
++++.+.|+.+|+|.+.|-|+|++ .|++ |..=|
T Consensus 202 ~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t--~~~yi 235 (287)
T TIGR02297 202 HLRLPEYADRLGISESRLNDICRRFSALS--PKRLI 235 (287)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHhCCC--HHHHH
Confidence 579999999999999999999999 8885 44433
No 85
>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=83.21 E-value=1.5 Score=34.23 Aligned_cols=28 Identities=14% Similarity=0.163 Sum_probs=24.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
.|+|.|+|+.+||++.+|.-..++ |+-.
T Consensus 1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~ 28 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQK-GLIA 28 (139)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 378999999999999999998887 7533
No 86
>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=83.15 E-value=1.8 Score=25.78 Aligned_cols=25 Identities=12% Similarity=0.161 Sum_probs=21.1
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
-+++..++|+.||++..++++.-++
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4889999999999999998776443
No 87
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=83.06 E-value=1.2 Score=30.60 Aligned_cols=24 Identities=13% Similarity=0.061 Sum_probs=21.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+++.+.|+.+|||.+++-+.|+.-
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~ 24 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGN 24 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCC
Confidence 468899999999999999999753
No 88
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=82.99 E-value=1.2 Score=33.59 Aligned_cols=30 Identities=10% Similarity=0.201 Sum_probs=24.7
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|+.-+-.|+.+.|+.||+|.+++.++-++|
T Consensus 17 L~~d~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 17 LQEDARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHhCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 455667999999999999999888877643
No 89
>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=82.98 E-value=1.4 Score=32.75 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=22.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.|+|+.+||++++|+-.+++ |+
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GL 25 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CC
Confidence 57899999999999999999997 74
No 90
>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=82.37 E-value=1.7 Score=23.03 Aligned_cols=21 Identities=19% Similarity=0.208 Sum_probs=17.5
Q ss_pred cCcHHHHHHHcCCChhHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~ 28 (168)
+.+..++|+.+||+.+++.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 568899999999999888764
No 91
>PRK00118 putative DNA-binding protein; Validated
Probab=82.30 E-value=9.1 Score=29.25 Aligned_cols=26 Identities=15% Similarity=0.115 Sum_probs=22.2
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
-+-+++..|+|+.+|||..+++++-+
T Consensus 30 y~eg~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45589999999999999999987654
No 92
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=82.30 E-value=1.2 Score=31.95 Aligned_cols=27 Identities=11% Similarity=0.023 Sum_probs=23.4
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
+++..+++.+.+.|+.+|||..++-.+
T Consensus 8 ~~R~~~~ltQ~elA~~vgVsRQTi~~i 34 (68)
T COG1476 8 ELRAELGLTQEELAKLVGVSRQTIIAI 34 (68)
T ss_pred HHHHHhCcCHHHHHHHcCcCHHHHHHH
Confidence 578899999999999999998877544
No 93
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=82.08 E-value=1.2 Score=34.28 Aligned_cols=26 Identities=12% Similarity=0.130 Sum_probs=22.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
|..|-+|.+.|||..+|||..||-+.
T Consensus 44 LvD~~~l~QeeAA~rMgISr~Tfwr~ 69 (99)
T COG1342 44 LVDYEGLTQEEAALRMGISRQTFWRL 69 (99)
T ss_pred HHhHhhccHHHHHHHhcccHHHHHHH
Confidence 45788999999999999999998543
No 94
>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=81.63 E-value=1.7 Score=32.32 Aligned_cols=26 Identities=19% Similarity=0.218 Sum_probs=23.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
++|..++|+.+|||.+++-|..|.+.
T Consensus 49 g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 49 GKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp TSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 68999999999999999999888764
No 95
>PHA01976 helix-turn-helix protein
Probab=81.38 E-value=2.3 Score=28.10 Aligned_cols=29 Identities=7% Similarity=-0.028 Sum_probs=24.7
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
++.--++.+.++|+.+||+.+++.+.-+.
T Consensus 10 ~R~~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 10 ARNARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 55667899999999999999999987543
No 96
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=81.34 E-value=1.7 Score=36.87 Aligned_cols=28 Identities=14% Similarity=0.229 Sum_probs=24.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|+.+|+++.+|+|+.||+|..++|.+..
T Consensus 126 L~~~~g~s~~EIA~~lg~s~~tVk~~l~ 153 (293)
T PRK09636 126 LHDVFGVPFDEIASTLGRSPAACRQLAS 153 (293)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567999999999999999999987765
No 97
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=81.22 E-value=3.8 Score=28.86 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=28.6
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH-HcCCCCCCchhhhcHHHHHHHHHHHh
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR-ELNIRRWPHRKLMSLQTLIKNVQELQ 56 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR-~lGI~RWP~RKlkSL~~li~~l~~~~ 56 (168)
..--++.+.++|+.|||+.+.+-++=+ +. .--|+++++.-+..++
T Consensus 27 ~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~--------~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 27 REERGLTQAELAERLGISQPRVSRLENGKI--------DDFSLDTLLRYLEALG 72 (80)
T ss_dssp HHCCT--HHHHHHHHTS-HHHHHHHHTT-G--------CC--HHHHHHHHHHTT
T ss_pred HHHcCCCHHHHHHHHCCChhHHHHHHcCcc--------cCCCHHHHHHHHHHcC
Confidence 344589999999999999999988864 21 1136677777666554
No 98
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=81.12 E-value=2 Score=26.90 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=21.6
Q ss_pred C-cHHHHHHHcCCChhHHHHHHHHcC
Q 036926 9 M-PITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 9 l-Pi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
+ ++.+.|+.+|||.+++.+...+|-
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5 599999999999999998887664
No 99
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=81.06 E-value=0.95 Score=30.71 Aligned_cols=38 Identities=26% Similarity=0.383 Sum_probs=27.1
Q ss_pred cCcHHHHHHHc-----CCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 8 YMPITKAAKEL-----NVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 8 ~lPi~eAAr~L-----gVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
+.+..+++.+| +||.+|+.++.++.|...|.-++---|
T Consensus 13 ~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g~~~~~~~~kP~L 55 (72)
T PF01498_consen 13 RISAREIAQELQEAGISVSKSTIRRRLREAGLKKRKARKKPFL 55 (72)
T ss_dssp ---HHHHHHHT---T--S-HHHHHHHHHHT-EEEETTEEEES-
T ss_pred CCCHHHHHHHHHHccCCcCHHHHHHHHHHcCccccccccCCCC
Confidence 46788999988 899999999999999988887775444
No 100
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=80.98 E-value=7.2 Score=26.40 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=18.4
Q ss_pred HHHHcCCChhHHHHHHHH-cCC
Q 036926 14 AAKELNVGLTLLKKRCRE-LNI 34 (168)
Q Consensus 14 AAr~LgVs~T~LKr~CR~-lGI 34 (168)
.|+.||||...|.++|++ .|+
T Consensus 1 lA~~~~~s~~~l~~~f~~~~g~ 22 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKETGM 22 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHHSS
T ss_pred ChHHhCcCHHHHHHHHHHHHCc
Confidence 489999999999999999 887
No 101
>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=80.97 E-value=2.9 Score=28.25 Aligned_cols=28 Identities=21% Similarity=0.209 Sum_probs=24.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+..--++++.++|+.+||+.+++-+++.
T Consensus 13 ~~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 13 FLEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4455689999999999999999999876
No 102
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=80.96 E-value=9.4 Score=29.76 Aligned_cols=25 Identities=20% Similarity=0.125 Sum_probs=22.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
++|.|+|+.+|||+.+|.-..++ |+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GL 26 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQ-GL 26 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 78999999999999999988776 54
No 103
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=80.90 E-value=1.9 Score=34.22 Aligned_cols=28 Identities=14% Similarity=0.089 Sum_probs=23.6
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|.-+-+++.+|+|+.||||..++|.+-.
T Consensus 127 L~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 127 LVGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456699999999999999999997654
No 104
>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=80.89 E-value=4.5 Score=30.72 Aligned_cols=25 Identities=20% Similarity=0.216 Sum_probs=20.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.|.|+|+.+|||+.+|.-.. +.|+
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe-~~GL 25 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYE-EKGL 25 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence 679999999999999998655 4553
No 105
>PF13551 HTH_29: Winged helix-turn helix
Probab=80.71 E-value=1.9 Score=30.44 Aligned_cols=25 Identities=12% Similarity=0.203 Sum_probs=21.4
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.+ +.++|+.||||..++.+..+++
T Consensus 11 g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 11 GVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 454 9999999999999998887764
No 106
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=80.70 E-value=1.5 Score=31.58 Aligned_cols=28 Identities=25% Similarity=0.315 Sum_probs=24.8
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
-||..|+.+.++.||+|..++.+.-++|
T Consensus 49 vYi~~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 49 VYIIFSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred EEEEeeHHHHHHHHCCCHHHHHHHHHcC
Confidence 4889999999999999999998887764
No 107
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=80.58 E-value=2.1 Score=33.14 Aligned_cols=26 Identities=19% Similarity=0.211 Sum_probs=22.6
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~C 29 (168)
.-+.+++++|+|+.||++..++|.+-
T Consensus 112 ~~~~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 112 TELEGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 45679999999999999999998764
No 108
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=80.53 E-value=1.8 Score=37.04 Aligned_cols=28 Identities=7% Similarity=0.140 Sum_probs=23.8
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|+-+++++.+|+|..||||..++|.+-.
T Consensus 164 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 191 (339)
T PRK08241 164 LRDVLGWSAAEVAELLDTSVAAVNSALQ 191 (339)
T ss_pred hHHhhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567899999999999999999887643
No 109
>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=80.50 E-value=1.6 Score=30.58 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=20.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.++.+++|.+|||+.+++.+--.+
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 589999999999999999865444
No 110
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=80.38 E-value=1.3 Score=28.91 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=20.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+.++|+++.+|||.|++.+..++-..
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g~F 29 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDGKF 29 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHHH-
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcccC
Confidence 46789999999999999999985433
No 111
>smart00351 PAX Paired Box domain.
Probab=80.07 E-value=12 Score=28.64 Aligned_cols=25 Identities=12% Similarity=0.015 Sum_probs=21.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.++.++|+.||||.+++.+..+++
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 6789999999999999988876654
No 112
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=80.03 E-value=1.9 Score=37.21 Aligned_cols=28 Identities=11% Similarity=0.254 Sum_probs=24.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|..+|+++..|+|+.||+|..++|.+.+
T Consensus 129 L~~~~g~s~~EIA~~Lgis~~tVr~~l~ 156 (290)
T PRK09635 129 LHEIFGLPYQQIATTIGSQASTCRQLAH 156 (290)
T ss_pred HHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 5678999999999999999988887654
No 113
>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=80.01 E-value=2 Score=31.13 Aligned_cols=25 Identities=12% Similarity=0.058 Sum_probs=22.5
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
-++++.|+|+.||||..++|.+-+.
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 5899999999999999999988664
No 114
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=79.96 E-value=2 Score=37.83 Aligned_cols=42 Identities=12% Similarity=0.158 Sum_probs=30.0
Q ss_pred cCcHHHHHHHcCCChhHHH---HHHHHcCCCC----CCchhhhcHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLK---KRCRELNIRR----WPHRKLMSLQTLI 49 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LK---r~CR~lGI~R----WP~RKlkSL~~li 49 (168)
+|++.|+|++||||.+++- +.||+.||=+ =|+-....|...+
T Consensus 29 g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L 77 (318)
T PRK15418 29 GLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENAL 77 (318)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHH
Confidence 8999999999999986554 5699999633 2554444444443
No 115
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=79.92 E-value=2.1 Score=40.67 Aligned_cols=55 Identities=22% Similarity=0.349 Sum_probs=41.5
Q ss_pred hhhhccCcHHHHHHHcCCChhHHH---------HHHHHcCCCCC-Cchhhhc-HHHHHHHHHHHhh
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLK---------KRCRELNIRRW-PHRKLMS-LQTLIKNVQELQT 57 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LK---------r~CR~lGI~RW-P~RKlkS-L~~li~~l~~~~~ 57 (168)
|.+||+|...+|.+.|.|-.+.++ +.||.+||.|| .+=.|+. ..++++.+++...
T Consensus 224 lekffem~~~~a~~al~iykr~~~q~e~L~~f~~~ck~~g~~r~~~iP~l~~i~~s~l~~lEe~l~ 289 (491)
T KOG0251|consen 224 LEKFFEMSKHDAIKALDIYKRFLSQTEKLSEFLKVCKSVGVDRGFEIPVLKRIPISLLEALEEHLR 289 (491)
T ss_pred HHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCcchhhcCHHHHHHHHHHHh
Confidence 568999999999999999877666 78999999999 5555543 2345555555544
No 116
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=79.83 E-value=2.4 Score=25.80 Aligned_cols=32 Identities=9% Similarity=0.083 Sum_probs=25.8
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RW 37 (168)
-|.+++.++|+.+|++.+++.+..+++-=..|
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~ 37 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKEGL 37 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 46789999999999999999888876644343
No 117
>PRK09726 antitoxin HipB; Provisional
Probab=79.70 E-value=2.1 Score=30.57 Aligned_cols=28 Identities=11% Similarity=0.038 Sum_probs=25.3
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++.-.++.+.++|+.+||+.+++.+.++
T Consensus 20 ~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 20 VRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4566799999999999999999999988
No 118
>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=79.65 E-value=5.5 Score=29.74 Aligned_cols=25 Identities=20% Similarity=0.290 Sum_probs=21.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.|.|+|+.+||++.+| |..-+.|+
T Consensus 1 ~~I~eva~~~gvs~~tL-RyYe~~GL 25 (123)
T cd04770 1 MKIGELAKAAGVSPDTI-RYYERIGL 25 (123)
T ss_pred CCHHHHHHHHCcCHHHH-HHHHHCCC
Confidence 57999999999999999 56667775
No 119
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=79.50 E-value=2.5 Score=27.44 Aligned_cols=28 Identities=14% Similarity=0.139 Sum_probs=23.0
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
..+.+++.++|+.+|++.+++.+..+++
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L 49 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3467899999999999999888877544
No 120
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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.
Probab=79.49 E-value=2.1 Score=36.22 Aligned_cols=28 Identities=7% Similarity=0.062 Sum_probs=24.0
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|.-+++++.+|+|+.||||..++|.+-.
T Consensus 153 L~~~~g~s~~EIA~~lgis~~tV~~~l~ 180 (324)
T TIGR02960 153 LRDVLGWRAAETAELLGTSTASVNSALQ 180 (324)
T ss_pred hHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567899999999999999999887644
No 121
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=79.47 E-value=2.4 Score=28.10 Aligned_cols=22 Identities=23% Similarity=0.394 Sum_probs=17.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
-.+..||+.|||+.+++.+..+
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~ 35 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIK 35 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHH
T ss_pred CCHHHHHHHhhccchHHHHHHH
Confidence 3678999999999988765544
No 122
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=79.36 E-value=2.3 Score=33.59 Aligned_cols=28 Identities=14% Similarity=0.035 Sum_probs=24.0
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.-+.+++..|+|..||||..++|.+..+
T Consensus 123 ~~~~g~s~~EIA~~Lgis~~tV~~~l~R 150 (182)
T PRK12540 123 VGASGFSYEDAAAICGCAVGTIKSRVNR 150 (182)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4467999999999999999999987653
No 123
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=78.97 E-value=2.8 Score=29.33 Aligned_cols=27 Identities=15% Similarity=0.267 Sum_probs=24.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHH-HcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCR-ELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR-~lGI~ 35 (168)
+.+.+.|+.+|+|.+.|.+.++ ..|+.
T Consensus 37 ~~l~~la~~~g~S~~~l~r~f~~~~g~s 64 (127)
T COG2207 37 LTLEDLARRLGMSRRTLSRLFKKETGTS 64 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCC
Confidence 6799999999999999999999 78874
No 124
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=78.96 E-value=2.3 Score=36.10 Aligned_cols=28 Identities=11% Similarity=0.123 Sum_probs=23.8
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|..+|+++..|+|+.||+|..++|.+..
T Consensus 119 L~~~~g~s~~EIA~~lg~s~~tVr~~l~ 146 (281)
T TIGR02957 119 LREVFDYPYEEIASIVGKSEANCRQLVS 146 (281)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4568999999999999999988876543
No 125
>PHA00542 putative Cro-like protein
Probab=78.95 E-value=2.1 Score=30.61 Aligned_cols=45 Identities=13% Similarity=0.071 Sum_probs=30.7
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQEL 55 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~ 55 (168)
-++.+.++|+.+||+.+++-++++--. +=| .+..+.++.+-+.++
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~~--~~p--~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGRH--KDP--RYSVVEKLRHLVLNL 74 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCCC--CCC--CHHHHHHHHHHHHHh
Confidence 378999999999999999999987542 112 234444444444443
No 126
>PRK01381 Trp operon repressor; Provisional
Probab=78.88 E-value=1.2 Score=34.22 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=24.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.+|+.|+|.+||||.+++-|-.|.|+-
T Consensus 55 ~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 55 ELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred CcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 389999999999999999999988875
No 127
>PRK10072 putative transcriptional regulator; Provisional
Probab=78.84 E-value=2.8 Score=31.47 Aligned_cols=31 Identities=16% Similarity=0.158 Sum_probs=26.2
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.|+.-.++.+.++|+.||||.+++.+..+..
T Consensus 40 ~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 40 QLRKGTGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 3566779999999999999999999887644
No 128
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=78.39 E-value=2.8 Score=25.88 Aligned_cols=32 Identities=9% Similarity=0.097 Sum_probs=25.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCCc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~ 39 (168)
.++..++|+.|||+.+++.+..+++-=..|..
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 35788999999999999999988776555554
No 129
>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=77.70 E-value=2.4 Score=27.79 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=21.0
Q ss_pred cCcHHHHHHHcCCChhHHH----HHHHHcCCC
Q 036926 8 YMPITKAAKELNVGLTLLK----KRCRELNIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LK----r~CR~lGI~ 35 (168)
+++..++|+.||||..+++ ++++++|++
T Consensus 18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred cCCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 7899999999999997765 556677763
No 130
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=77.61 E-value=2.7 Score=34.00 Aligned_cols=29 Identities=17% Similarity=0.119 Sum_probs=24.7
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.-+.++|.+|+|+.|||+..++|....+.
T Consensus 150 ~~~~g~s~~EIA~~Lgis~~tV~~~l~RA 178 (203)
T PRK09647 150 CDIEGLSYEEIAATLGVKLGTVRSRIHRG 178 (203)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34568999999999999999999887654
No 131
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=77.25 E-value=3.1 Score=33.76 Aligned_cols=27 Identities=7% Similarity=0.111 Sum_probs=22.5
Q ss_pred cCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLK----KRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LK----r~CR~lGI 34 (168)
+++.+|+|++||||..|+| ++++++|+
T Consensus 152 G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 152 GQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 6889999999999986654 66778887
No 132
>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=77.11 E-value=3 Score=26.72 Aligned_cols=24 Identities=25% Similarity=0.427 Sum_probs=19.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
++..+.|+.||||..++.+-...+
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHH
Confidence 899999999999999988765543
No 133
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=77.04 E-value=2.6 Score=31.05 Aligned_cols=29 Identities=21% Similarity=0.232 Sum_probs=25.2
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.++.-.++.+.++|+.||++..++.+.-+
T Consensus 72 ~~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 72 RIRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 35677899999999999999999998844
No 134
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=77.01 E-value=3 Score=33.31 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=23.7
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
|.-+.+++..|+|..||||..++|.+-.
T Consensus 124 L~~~~g~s~~EIA~~LgiS~~tVk~~l~ 151 (188)
T PRK12546 124 LVGASGFSYEEAAEMCGVAVGTVKSRAN 151 (188)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456799999999999999999987654
No 135
>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=76.67 E-value=3.1 Score=32.76 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=22.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.|.|+|+.+||++.+|+-..++ |+
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~-GL 26 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK-GL 26 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999988876 64
No 136
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=76.25 E-value=0.64 Score=37.73 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=0.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.++++|.+|||+.+|+-|.++---|
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~~Ky~ 75 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVKNKYI 75 (160)
T ss_dssp --------------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHcCcee
Confidence 67899999999999999999985443
No 137
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=75.91 E-value=3.7 Score=26.71 Aligned_cols=27 Identities=11% Similarity=0.304 Sum_probs=23.1
Q ss_pred cCcHHHHHHHcCC-ChhHHHHHHHHc-CC
Q 036926 8 YMPITKAAKELNV-GLTLLKKRCREL-NI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgV-s~T~LKr~CR~l-GI 34 (168)
++++.++|..+|+ +.+.|-|.+++. |+
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~ 78 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLFGV 78 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHCc
Confidence 5899999999999 999999998653 44
No 138
>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=75.89 E-value=6.9 Score=29.51 Aligned_cols=23 Identities=22% Similarity=0.199 Sum_probs=20.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+.++.+||+.+|||..++.+...
T Consensus 18 g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 18 GKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred cchHHHHHHHhCcHHHHHHHHHH
Confidence 56899999999999999988766
No 139
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=75.09 E-value=15 Score=31.53 Aligned_cols=94 Identities=20% Similarity=0.243 Sum_probs=61.7
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHH---------------------------HcCCCCCCchhhhcHHHHHHHHHHHhhc
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCR---------------------------ELNIRRWPHRKLMSLQTLIKNVQELQTE 58 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR---------------------------~lGI~RWP~RKlkSL~~li~~l~~~~~~ 58 (168)
.=.+...|+|++|||+....++--- +-|+...||+-..=+-.+++.|.+...
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~~~y~~l~~~~l~~l~~~~G- 101 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFPKRYGELALALLDALEETGG- 101 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcchhhHHHHHHHHHHHHHhcc-
Confidence 3356788999999999998887654 345566677766666666666665433
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHh-----hCC-CCCCcHHHHHHHHHHHHHhhhhh
Q 036926 59 GEGSEERLREALGILERERKLIE-----ERP-DLEMEDTTKRLRQACFKANYKKR 107 (168)
Q Consensus 59 g~~s~~~l~~ai~~Lerek~lIe-----e~P-~~~L~~~tKrlRQa~FK~~yk~R 107 (168)
++.+...+ ++..+.+. ..+ +.++++.+++|=+..++.+|-..
T Consensus 102 ----~~~l~~~l---~~r~~~~~~~~~~~~~~~~~~ee~~e~Lv~l~~~~gy~~e 149 (218)
T COG2345 102 ----EEALNAFL---EKRAQAIGAQYRPAMGGDADLEEKVERLVELLSDLGYMPE 149 (218)
T ss_pred ----HHHHHHHH---HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhCCcccc
Confidence 12222222 22211111 134 59999999999999999998776
No 140
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=74.75 E-value=3.6 Score=36.03 Aligned_cols=27 Identities=33% Similarity=0.389 Sum_probs=25.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.+++.++|+.+|+|++.|.|++++.|.
T Consensus 158 ~lsl~~lA~~~g~S~~~L~R~Fk~~G~ 184 (274)
T PRK09978 158 EWTLARIASELLMSPSLLKKKLREEET 184 (274)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCC
Confidence 478999999999999999999999875
No 141
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=74.70 E-value=3.5 Score=25.08 Aligned_cols=21 Identities=10% Similarity=0.127 Sum_probs=17.4
Q ss_pred CCChhHHHHHHHHcCCCCCCc
Q 036926 19 NVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 19 gVs~T~LKr~CR~lGI~RWP~ 39 (168)
.++...||..|+++|++.+--
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G~ 23 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSGT 23 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCCC
Confidence 467889999999999987653
No 142
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=74.67 E-value=4 Score=27.35 Aligned_cols=26 Identities=31% Similarity=0.520 Sum_probs=22.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.+++.++|..||+|..+|++.+-++.
T Consensus 19 ~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 19 WITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp SBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56889999999999999999998876
No 143
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=74.43 E-value=3.3 Score=32.65 Aligned_cols=30 Identities=17% Similarity=0.149 Sum_probs=24.7
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|++-.-++..+.|+++|+|.+++.++-++|
T Consensus 23 Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL 52 (164)
T PRK11169 23 LQKDGRISNVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred hccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 455667899999999999999988876654
No 144
>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=74.30 E-value=3.3 Score=26.72 Aligned_cols=25 Identities=12% Similarity=0.256 Sum_probs=21.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+++.|+|+++|++.+++-|++..|
T Consensus 18 ~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 18 PLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp CEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3679999999999999999998765
No 145
>PRK09191 two-component response regulator; Provisional
Probab=74.24 E-value=3.7 Score=32.69 Aligned_cols=27 Identities=15% Similarity=0.026 Sum_probs=22.9
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..+-+++..|+|..||+|..++|.+.+
T Consensus 100 ~~~~~~s~~eIA~~l~~s~~tV~~~l~ 126 (261)
T PRK09191 100 TALEGFSVEEAAEILGVDPAEAEALLD 126 (261)
T ss_pred HHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 345689999999999999988887765
No 146
>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=74.14 E-value=21 Score=26.95 Aligned_cols=25 Identities=16% Similarity=0.202 Sum_probs=20.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|+|.|+|+.+|||+.+|.-..+ .|+
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~-~GL 25 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEK-EGL 25 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 6799999999999999976665 554
No 147
>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=74.11 E-value=2.8 Score=27.86 Aligned_cols=23 Identities=13% Similarity=0.082 Sum_probs=16.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+....++|+.+||+.|++..+..
T Consensus 22 g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 22 GESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp TT-HHHHHHHHT--CCHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 34678999999999999987764
No 148
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=74.07 E-value=3.6 Score=34.68 Aligned_cols=27 Identities=22% Similarity=0.140 Sum_probs=23.2
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.-+++++.+|+|+.||+|..++|.+-.
T Consensus 128 ~~~eg~S~~EIAe~LgiS~~tVksrL~ 154 (228)
T PRK06704 128 KDVFQYSIADIAKVCSVSEGAVKASLF 154 (228)
T ss_pred HHhhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 346799999999999999999987653
No 149
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=73.62 E-value=4.2 Score=29.12 Aligned_cols=31 Identities=13% Similarity=0.312 Sum_probs=25.3
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
|.+.-.+|..++|+.+|++.+++.++.+++-
T Consensus 12 L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~ 42 (108)
T smart00344 12 LQKDARISLAELAKKVGLSPSTVHNRVKRLE 42 (108)
T ss_pred HHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3444578999999999999999988887663
No 150
>PRK15044 transcriptional regulator SirC; Provisional
Probab=73.38 E-value=15 Score=32.93 Aligned_cols=27 Identities=15% Similarity=0.195 Sum_probs=24.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.+.+.+.|+.+|+|.++|+|++++.|.
T Consensus 208 ~~SLeeLA~~lgmS~~tL~R~Fk~eg~ 234 (295)
T PRK15044 208 KWSQAEVAGKLFMSVSSLKRKLAAEEV 234 (295)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 478899999999999999999999875
No 151
>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=73.04 E-value=12 Score=28.37 Aligned_cols=26 Identities=15% Similarity=0.161 Sum_probs=20.0
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 10 PITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
+|.|+|+.+|||+.+|+-. -+.|+-.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Y-e~~GLl~ 26 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYY-ERKGLLP 26 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH-HHCCCCC
Confidence 4789999999999999544 5556533
No 152
>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=72.98 E-value=24 Score=27.65 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=24.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
+.+.|+|+.+|||+.+|+..-+. |+-. |.|
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~-GLl~-p~r 30 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNL-GLLT-PER 30 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-Ccc
Confidence 46899999999999999998755 7544 665
No 153
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=72.81 E-value=19 Score=28.04 Aligned_cols=23 Identities=17% Similarity=0.118 Sum_probs=19.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
|.|.|+|+.+||++.+|.-..+.
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~~ 23 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEK 23 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67999999999999999766553
No 154
>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=72.68 E-value=5.3 Score=29.94 Aligned_cols=27 Identities=11% Similarity=0.221 Sum_probs=22.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
++|.|+|+.+|||+.+|.-..++ |+-+
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~ 27 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLLH 27 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 57899999999999999888776 7533
No 155
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=72.68 E-value=3.4 Score=36.87 Aligned_cols=27 Identities=22% Similarity=0.170 Sum_probs=25.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+|+.+++|..||||+.++|..-|+.|-
T Consensus 19 gmk~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHhcCC
Confidence 599999999999999999999999983
No 156
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=72.44 E-value=3.2 Score=32.10 Aligned_cols=31 Identities=10% Similarity=0.106 Sum_probs=25.4
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+..+++++.++.|..|||+.+||.|+-++.
T Consensus 30 ~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~ 60 (133)
T TIGR02293 30 RLAHLLAIGKAEIFKATGIPKATLQRRKMAH 60 (133)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHHhhcC
Confidence 3567889999999999999999998876543
No 157
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=71.52 E-value=5.2 Score=34.93 Aligned_cols=33 Identities=12% Similarity=0.101 Sum_probs=27.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
.+.+.+.|+.+|+|.++|.|++++.|..=-++.
T Consensus 197 ~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~ 229 (291)
T PRK15186 197 KWALKDISDSLYMSCSTLKRKLKQENTSFSEVY 229 (291)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHH
Confidence 578999999999999999999999886444433
No 158
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.27 E-value=4.3 Score=31.59 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=21.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
-.|..+.|++||+|.+++.++-++|
T Consensus 23 R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 23 RTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4789999999999999988776643
No 159
>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=70.90 E-value=13 Score=21.39 Aligned_cols=38 Identities=16% Similarity=0.053 Sum_probs=26.5
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
-.++...++|+.+|++..++.+.+. |-..+|.-.+..+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~--g~~~~~~~~~~~i 47 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN--GKRNPSLETLEKL 47 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc--CCCCCCHHHHHHH
Confidence 3478899999999999999888755 4334554444333
No 160
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=70.88 E-value=4.2 Score=33.56 Aligned_cols=24 Identities=17% Similarity=0.034 Sum_probs=20.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|.|+++|+..|||.+|+-|.....
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~ 24 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGK 24 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Confidence 478999999999999999887654
No 161
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=70.73 E-value=42 Score=26.64 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=27.6
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc---C-CCCCCchh
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL---N-IRRWPHRK 41 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l---G-I~RWP~RK 41 (168)
-.+|..+.|+.||||.|.+...-+.| | |...|++-
T Consensus 33 ~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G 71 (212)
T TIGR03338 33 AKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRG 71 (212)
T ss_pred CEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCC
Confidence 35788999999999999988877765 4 56677763
No 162
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=70.67 E-value=4.6 Score=33.03 Aligned_cols=26 Identities=15% Similarity=0.156 Sum_probs=22.6
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
-+.+++.+|+|..||||.+++|.+-+
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~ 187 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLH 187 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999999999987653
No 163
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=70.55 E-value=10 Score=21.78 Aligned_cols=26 Identities=15% Similarity=0.070 Sum_probs=21.8
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.--++...+.|+.+||+..++.+...
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34578899999999999999988765
No 164
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=70.29 E-value=5.8 Score=32.96 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=27.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhh
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLM 43 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlk 43 (168)
+.+.++|+++|||+..|.+.+++.|.. |++-|.
T Consensus 215 ls~~~lA~~~giS~r~L~r~Fk~~G~T--~~~yi~ 247 (302)
T PRK09685 215 LRPEWIAGELGISVRSLYRLFAEQGLV--VAQYIR 247 (302)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHcCCC--HHHHHH
Confidence 788999999999999999999999874 444443
No 165
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=70.10 E-value=5.4 Score=26.68 Aligned_cols=37 Identities=16% Similarity=0.139 Sum_probs=26.7
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHc---CCCCCCchhh
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCREL---NIRRWPHRKL 42 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~l---GI~RWP~RKl 42 (168)
.|.++..+.|..+|+|..++-|..+++ |+-.+-++++
T Consensus 26 ~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~~i 65 (76)
T PF13545_consen 26 PLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRGKI 65 (76)
T ss_dssp EEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEE
T ss_pred EecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCCEE
Confidence 467899999999999998877766543 5444444443
No 166
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=69.92 E-value=2.3 Score=37.27 Aligned_cols=45 Identities=20% Similarity=0.363 Sum_probs=30.2
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNV 52 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l 52 (168)
+.+|+..+.|.|+.||||+++.--. +-|-+.-|- ...+.+..+.|
T Consensus 36 R~~F~vSQ~elA~~l~vSpSVISDY--E~GRRk~Pg--~~~vkk~V~AL 80 (241)
T COG1709 36 REIFNVSQTELARELGVSPSVISDY--ESGRRKSPG--IAFVKKFVEAL 80 (241)
T ss_pred HHHhCccHHHHHHHhCCCcceeehh--hccCccCcc--HHHHHHHHHHH
Confidence 5689999999999999999998653 445433343 23344444444
No 167
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=69.48 E-value=5.5 Score=35.34 Aligned_cols=27 Identities=22% Similarity=0.075 Sum_probs=24.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.+++.|+|+.+||+.++|+...++..+
T Consensus 33 ~~~i~eva~~~gv~~~tlr~~e~~~~~ 59 (387)
T TIGR03453 33 KFTSGEVAKLLGVSDSYLRQLSLEGKG 59 (387)
T ss_pred cCCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 369999999999999999999888764
No 168
>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=69.38 E-value=6.5 Score=28.25 Aligned_cols=29 Identities=3% Similarity=0.142 Sum_probs=24.2
Q ss_pred hhhccCcHHHHHHHcC-CChhHHHHHHHHc
Q 036926 4 SQYFYMPITKAAKELN-VGLTLLKKRCREL 32 (168)
Q Consensus 4 ~~yF~lPi~eAAr~Lg-Vs~T~LKr~CR~l 32 (168)
..++++|..++|+.|| .+.|++-.-|++.
T Consensus 40 ~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri 69 (90)
T cd06571 40 RELTGLSLPEIGRAFGGRDHSTVLHAVRKI 69 (90)
T ss_pred HHHhCCCHHHHHHHhCCCCHhHHHHHHHHH
Confidence 4678999999999999 9999988877654
No 169
>cd00131 PAX Paired Box domain
Probab=69.05 E-value=5.3 Score=30.83 Aligned_cols=24 Identities=13% Similarity=0.075 Sum_probs=20.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+++..++|+.||||.+++.+...+
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r 56 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNR 56 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 789999999999999887766554
No 170
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=68.84 E-value=5.4 Score=26.14 Aligned_cols=24 Identities=8% Similarity=0.177 Sum_probs=22.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+++..+.|..+|||.++..|++++
T Consensus 19 ~~~~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 19 NLTFQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred CCcHhHHhhheeecHHHHHHHHHH
Confidence 788999999999999999999875
No 171
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=68.76 E-value=5.5 Score=33.96 Aligned_cols=28 Identities=7% Similarity=0.071 Sum_probs=25.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI~ 35 (168)
.+++.++|+.+|+|...|.|+|++. |+.
T Consensus 234 ~~sl~~lA~~~~~S~~~l~r~fk~~~g~s 262 (322)
T PRK09393 234 PHTVASLAARAAMSPRTFLRRFEAATGMT 262 (322)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 4789999999999999999999986 873
No 172
>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=68.42 E-value=20 Score=26.78 Aligned_cols=25 Identities=16% Similarity=0.218 Sum_probs=21.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.+.|+|+.+|||+.+|.-..+. |+
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~-GL 25 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEK-GL 25 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57899999999999999877765 64
No 173
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=68.33 E-value=5.2 Score=25.72 Aligned_cols=25 Identities=12% Similarity=0.304 Sum_probs=21.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
+++.+.|+.||++.+++.+..++|=
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 7899999999999999988887653
No 174
>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=68.31 E-value=5.2 Score=26.65 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=20.5
Q ss_pred cC-cHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YM-PITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~l-Pi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.+ ...+.|+.+|||.+++++.++.|-
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHH
Confidence 45 678999999999999999888763
No 175
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=67.95 E-value=4.7 Score=33.55 Aligned_cols=22 Identities=23% Similarity=0.194 Sum_probs=19.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++++++|+++|||.+|+.|...
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 4789999999999999988875
No 176
>PRK13502 transcriptional activator RhaR; Provisional
Probab=67.81 E-value=6.3 Score=32.48 Aligned_cols=28 Identities=7% Similarity=0.177 Sum_probs=24.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE-LNIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~-lGI~ 35 (168)
.+.+.+.|..+|||++.|.|++++ .|+.
T Consensus 192 ~~~~~~lA~~~~iS~~~L~r~fk~~~G~t 220 (282)
T PRK13502 192 PFALDAFCQQEQCSERVLRQQFRAQTGMT 220 (282)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 456789999999999999999998 7973
No 177
>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=67.75 E-value=8.6 Score=28.21 Aligned_cols=25 Identities=8% Similarity=0.162 Sum_probs=21.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.|+|+.+|||..+|+...+ -|+
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~-~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYES-LGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-cCC
Confidence 3789999999999999998877 453
No 178
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=67.18 E-value=4.7 Score=31.16 Aligned_cols=29 Identities=17% Similarity=0.193 Sum_probs=25.3
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.|++-++|.+.+=|+.||||+.+|.+.=+
T Consensus 51 ~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEq 79 (104)
T COG2944 51 AIREKLGLSQPVFARYLGVSVSTVRKWEQ 79 (104)
T ss_pred HHHHHhCCCHHHHHHHHCCCHHHHHHHHc
Confidence 57888999999999999999999987533
No 179
>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=66.47 E-value=8 Score=29.08 Aligned_cols=25 Identities=12% Similarity=0.227 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.|.|+|+..||++.+|.-..++ |+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~-GL 25 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK-GL 25 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57899999999999999877765 64
No 180
>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=65.67 E-value=6.8 Score=30.58 Aligned_cols=25 Identities=28% Similarity=0.316 Sum_probs=22.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+++.++|+.+||++.+|...-++ |+
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~-GL 26 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH-GL 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999987776 64
No 181
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=65.38 E-value=7.4 Score=31.21 Aligned_cols=26 Identities=8% Similarity=-0.105 Sum_probs=23.0
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+-++++.|+|+.||+|.++++++.++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35899999999999999999988764
No 182
>PHA02591 hypothetical protein; Provisional
Probab=65.35 E-value=7.6 Score=29.16 Aligned_cols=23 Identities=17% Similarity=0.216 Sum_probs=20.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++.+.++|+.|||+..++++.-+
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Confidence 78999999999999999988754
No 183
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=65.28 E-value=6.2 Score=27.37 Aligned_cols=26 Identities=27% Similarity=0.281 Sum_probs=20.7
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
++-.||+ .+..+|+.|||+...+-+.
T Consensus 4 ~aI~~~G-~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 4 DAIKYFG-GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHS-SHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHC-CHHHHHHHHCCCHHHHHHh
Confidence 4567887 6789999999999998766
No 184
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=63.86 E-value=13 Score=29.02 Aligned_cols=17 Identities=18% Similarity=0.403 Sum_probs=11.3
Q ss_pred cHHHHHHHcCCChhHHH
Q 036926 10 PITKAAKELNVGLTLLK 26 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LK 26 (168)
.+++.|+.||||=.|++
T Consensus 51 nlKe~e~~lgiSYPTvR 67 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVR 67 (113)
T ss_pred CHHHHHHHHCCCcHHHH
Confidence 46677777777755554
No 185
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=63.54 E-value=7.3 Score=31.41 Aligned_cols=33 Identities=9% Similarity=0.214 Sum_probs=27.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc---C-CCCCCch
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL---N-IRRWPHR 40 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l---G-I~RWP~R 40 (168)
-+|..+.|+.||||.|.+....++| | |..-|.|
T Consensus 30 ~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~ 66 (224)
T PRK11534 30 KLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK 66 (224)
T ss_pred cCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence 5789999999999999999888866 4 4567776
No 186
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=63.54 E-value=9.9 Score=25.32 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=19.4
Q ss_pred hhhhhc--cCcHHHHHHHcCCChhHHHHHH
Q 036926 2 TISQYF--YMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 2 ~l~~yF--~lPi~eAAr~LgVs~T~LKr~C 29 (168)
.|.-|| +..+.+||++|+|...||+-+-
T Consensus 4 TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl 33 (59)
T PF13556_consen 4 TLRAYLENNGNISKTARALHIHRNTLRYRL 33 (59)
T ss_dssp HHHHHHHTTT-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 445555 4789999999999998876543
No 187
>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=63.47 E-value=5.4 Score=24.98 Aligned_cols=20 Identities=10% Similarity=0.125 Sum_probs=17.6
Q ss_pred HHHHHcCCChhHHHHHHHHc
Q 036926 13 KAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 13 eAAr~LgVs~T~LKr~CR~l 32 (168)
+.|+.+|||.+++-+.++--
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999998744
No 188
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.03 E-value=8 Score=30.95 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=22.9
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
+=++.+.+||+.+|||.+|..+.-+++.
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 3489999999999999998887665543
No 189
>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=63.01 E-value=10 Score=23.83 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=14.1
Q ss_pred hhccCcHHHHHHHcCCChhHHHH
Q 036926 5 QYFYMPITKAAKELNVGLTLLKK 27 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr 27 (168)
.|-++.+.++|+++||+.++|-+
T Consensus 13 G~~~~s~~~Ia~~~gvs~~~~y~ 35 (47)
T PF00440_consen 13 GYEAVSIRDIARRAGVSKGSFYR 35 (47)
T ss_dssp HTTTSSHHHHHHHHTSCHHHHHH
T ss_pred CHHhCCHHHHHHHHccchhhHHH
Confidence 34456666666666666666644
No 190
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=62.97 E-value=8.6 Score=32.39 Aligned_cols=27 Identities=4% Similarity=-0.042 Sum_probs=22.8
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.-+-+++.+|+|..|||+..++|.+-+
T Consensus 173 ~~~eg~S~~EIA~~Lgis~~TVk~rl~ 199 (244)
T TIGR03001 173 HFVDGLSMDRIGAMYQVHRSTVSRWVA 199 (244)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345689999999999999999997654
No 191
>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=62.96 E-value=6.1 Score=32.04 Aligned_cols=34 Identities=12% Similarity=0.288 Sum_probs=28.8
Q ss_pred hhhhc--cCcHHHHHHHcC-CChhHHHHHHHHcCCCC
Q 036926 3 ISQYF--YMPITKAAKELN-VGLTLLKKRCRELNIRR 36 (168)
Q Consensus 3 l~~yF--~lPi~eAAr~Lg-Vs~T~LKr~CR~lGI~R 36 (168)
|++.+ ++...++|++|| ||...+--.+++||+..
T Consensus 11 L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~ 47 (162)
T PF07750_consen 11 LRKLWAEGLSASQIARQLGGVSRNAVIGKAHRLGLSG 47 (162)
T ss_pred HHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcccccc
Confidence 44444 689999999999 99999999999999855
No 192
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=62.87 E-value=9.9 Score=28.87 Aligned_cols=34 Identities=12% Similarity=0.047 Sum_probs=27.2
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
.++.-.++.+.++|+.+||+.+++-++.+--..|
T Consensus 12 ~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p 45 (135)
T PRK09706 12 YRRKQLKLSQRSLAKAVKVSHVSISQWERDETEP 45 (135)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 3566779999999999999999999876654443
No 193
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=62.78 E-value=11 Score=31.09 Aligned_cols=27 Identities=11% Similarity=0.194 Sum_probs=22.6
Q ss_pred cCcHHHHHHHcCCChhHH----HHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLL----KKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~L----Kr~CR~lGI 34 (168)
+++.+|+|.+||||..|+ +++++++|+
T Consensus 149 G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 149 GYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 688999999999998555 567788887
No 194
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=62.56 E-value=8.9 Score=27.51 Aligned_cols=24 Identities=17% Similarity=0.282 Sum_probs=20.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.+|+.+||+.||+...++.+.-+.
T Consensus 13 ~~s~~~Aa~~lG~~~~~v~~wv~~ 36 (65)
T PF05344_consen 13 QISVAQAADRLGTDPGTVRRWVRM 36 (65)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHH
Confidence 578899999999999988877654
No 195
>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=62.16 E-value=7.1 Score=32.29 Aligned_cols=22 Identities=18% Similarity=0.270 Sum_probs=18.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..++++|+..|||.+|+.|.-.
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 4689999999999998887764
No 196
>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=62.12 E-value=15 Score=28.49 Aligned_cols=24 Identities=17% Similarity=0.087 Sum_probs=19.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
|+|.|+|+.+||++.+|.-.- +.|
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE-~~G 24 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYE-AEG 24 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCC
Confidence 689999999999999997554 444
No 197
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=61.74 E-value=6.7 Score=27.36 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=18.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+..+.+.|.+++||.|+++|..++
T Consensus 30 ~~s~~~la~~~~iS~sti~~~i~~ 53 (87)
T PF05043_consen 30 YVSIEDLAEELFISRSTIYRDIKK 53 (87)
T ss_dssp EEEHHHHHHHHT--HHHHHHHHHH
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 467899999999999999887654
No 198
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=61.72 E-value=8.2 Score=24.27 Aligned_cols=32 Identities=9% Similarity=0.237 Sum_probs=25.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
+...++|+.+|++.+++.+.++.+-=..|..+
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 67889999999999999998887644455544
No 199
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=61.62 E-value=9.7 Score=25.88 Aligned_cols=25 Identities=16% Similarity=0.169 Sum_probs=18.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.....+.|+.|||++++.-..+++|
T Consensus 22 ~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 22 PVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp SBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CccHHHHHHHHCCChHHHHHHHHHH
Confidence 3567899999999988776666654
No 200
>PRK09526 lacI lac repressor; Reviewed
Probab=61.60 E-value=7.3 Score=32.34 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=19.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..|+|+|+..|||.+|+-|.-.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhc
Confidence 4799999999999999887765
No 201
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=61.03 E-value=10 Score=27.27 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=19.7
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
|++.+.|+|+.||-|.+.+.+.-+=+.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll~ 28 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLALLD 28 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHGGGS
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHc
Confidence 789999999999999999988766444
No 202
>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=60.75 E-value=13 Score=23.29 Aligned_cols=24 Identities=33% Similarity=0.318 Sum_probs=19.0
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 10 PITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.|.|+|+.+||++.+|...=++ |+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~-Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE-GL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT-TS
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-CC
Confidence 3789999999999999877665 64
No 203
>PRK15340 transcriptional regulator InvF; Provisional
Probab=60.71 E-value=8.7 Score=32.76 Aligned_cols=28 Identities=11% Similarity=0.205 Sum_probs=25.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI~ 35 (168)
..++.+.|+.+|+|++.|.|+|++. |++
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~G~t 153 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRALGGK 153 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 5789999999999999999999985 875
No 204
>PRK15185 transcriptional regulator HilD; Provisional
Probab=60.31 E-value=11 Score=33.93 Aligned_cols=27 Identities=19% Similarity=0.219 Sum_probs=24.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.+++.+.|+.+|+|++.|.|++++.|.
T Consensus 222 ~~SledLA~~lgmS~~tL~R~FK~~G~ 248 (309)
T PRK15185 222 QWKLTDVADHIFMSTSTLKRKLAEEGT 248 (309)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCC
Confidence 568999999999999999999998776
No 205
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=60.25 E-value=10 Score=32.40 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=23.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+|.++|||..||||.+||.|..|+=-|
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~G~i 27 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIREGKI 27 (193)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHcCcc
Confidence 477899999999999999999986444
No 206
>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=59.83 E-value=9 Score=25.49 Aligned_cols=29 Identities=14% Similarity=0.211 Sum_probs=22.8
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.=.+.+.++|..||||..|++|=...|
T Consensus 10 ~~~~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 10 KEKGKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred HHcCCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 34446789999999999999998866543
No 207
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=59.65 E-value=12 Score=32.55 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=25.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
.+++.+.|+.+|+|.+.|+|..++.|.+
T Consensus 150 ~~tl~~LA~~~gmS~s~l~R~FK~~G~T 177 (253)
T PRK09940 150 PWKLKDICDCLYISESLLKKKLKQEQTT 177 (253)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence 3679999999999999999999999864
No 208
>PRK09492 treR trehalose repressor; Provisional
Probab=59.60 E-value=7.9 Score=31.74 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=18.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+.++|+|+..|||.+|+-|.-.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhC
Confidence 4789999999999988776553
No 209
>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=59.57 E-value=14 Score=28.65 Aligned_cols=28 Identities=11% Similarity=0.226 Sum_probs=24.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
.++|.|+|+..|||+.+|+-..+. |+-.
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~ 30 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLR-GLLH 30 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 478999999999999999988877 7544
No 210
>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=59.50 E-value=63 Score=26.87 Aligned_cols=78 Identities=17% Similarity=0.276 Sum_probs=45.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH---HcCCCCCCchhhhcHHHHHHHHHHHhhcCCCCHHH----HHHHHHHHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR---ELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEER----LREALGILERERKLI 80 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR---~lGI~RWP~RKlkSL~~li~~l~~~~~~g~~s~~~----l~~ai~~Lerek~lI 80 (168)
.+|+..||..+|||..|..|.-+ +.| .-| +++... ..+. |.+-++- +...+.+-+.-...|
T Consensus 19 ~~sLe~aA~~~gVs~~TarrWK~~Ak~~G-DDW--------Dk~RaA-~~la--ggg~e~v~~~~l~~f~~Q~~~tmeel 86 (165)
T PF08822_consen 19 RLSLEQAAAKCGVSYATARRWKREAKAKG-DDW--------DKARAA-HTLA--GGGIEDVARQMLEDFVVQYQATMEEL 86 (165)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHcC-CcH--------HHHHHH-HHhc--cCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 49999999999999988865544 556 466 333221 1111 1111211 222233334445556
Q ss_pred hhCCCCCCcHHHHHHHH
Q 036926 81 EERPDLEMEDTTKRLRQ 97 (168)
Q Consensus 81 ee~P~~~L~~~tKrlRQ 97 (168)
.++++++..+.++-|-.
T Consensus 87 ~~~~~~~~~~k~~~Las 103 (165)
T PF08822_consen 87 KENEDMPPQEKVELLAS 103 (165)
T ss_pred hcccCCCHHHHHHHHHH
Confidence 67888888888776653
No 211
>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=59.23 E-value=67 Score=23.43 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=20.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.|.|+|+..|||..+|.-.. +.|+
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe-~~GL 25 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYI-DLGL 25 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence 578999999999999996554 4554
No 212
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=59.13 E-value=9 Score=29.70 Aligned_cols=30 Identities=13% Similarity=0.051 Sum_probs=25.2
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+-.-|++.+.++|+.|||...++-.+|..-
T Consensus 18 flep~glt~~~lA~~lgV~r~~is~ling~ 47 (104)
T COG3093 18 FLEPLGLTQTELAEALGVTRNTISELINGR 47 (104)
T ss_pred HhccccCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 334568999999999999999999999743
No 213
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=59.01 E-value=9.9 Score=30.87 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=21.9
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
-|| ..+.|++||||.|+++...++|
T Consensus 30 ~LPsE~eLae~~gVSRt~VReAL~~L 55 (239)
T PRK04984 30 ILPAERELSELIGVTRTTLREVLQRL 55 (239)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 476 8899999999999999988866
No 214
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=58.98 E-value=12 Score=25.67 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=21.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.+.++|+.+||+.+++.|....+
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5789999999999999998887654
No 215
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=58.93 E-value=11 Score=28.92 Aligned_cols=30 Identities=10% Similarity=0.067 Sum_probs=25.7
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+....++.+.|.|+.+|||.+++-++++.-
T Consensus 13 ll~~~Glsq~eLA~~~Gis~~~is~iE~g~ 42 (120)
T PRK13890 13 LLDERHMTKKELSERSGVSISFLSDLTTGK 42 (120)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 445679999999999999999999998654
No 216
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=58.69 E-value=8.5 Score=28.13 Aligned_cols=27 Identities=22% Similarity=0.123 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
++|.|+|+.+|||+.+|.-.=+.-.|+
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GLl~ 27 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLS 27 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCCCC
Confidence 578999999999999997665554453
No 217
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=58.34 E-value=9 Score=31.78 Aligned_cols=22 Identities=14% Similarity=0.128 Sum_probs=19.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..++|+|++.|||.+|+.|.-.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHC
Confidence 5799999999999999887754
No 218
>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=58.13 E-value=11 Score=26.86 Aligned_cols=29 Identities=21% Similarity=0.320 Sum_probs=22.1
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.-+.|++.|||.=.|||...|++++++..
T Consensus 10 eK~~LTi~EAa~Y~gIG~~klr~l~~~~~ 38 (67)
T PF09035_consen 10 EKYTLTIEEAAEYFGIGEKKLRELAEENP 38 (67)
T ss_dssp TSSEEEHHHHHHHT-S-HHHHHHHHHH-T
T ss_pred HhhccCHHHHHHHhCccHHHHHHHHHhCC
Confidence 34568999999999999999999996544
No 219
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=58.07 E-value=8.1 Score=23.69 Aligned_cols=18 Identities=17% Similarity=0.209 Sum_probs=13.8
Q ss_pred CChhHHHHHHHHcCCCCC
Q 036926 20 VGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 20 Vs~T~LKr~CR~lGI~RW 37 (168)
+.+..||..|+++|++-.
T Consensus 4 l~v~eLk~~l~~~gL~~~ 21 (35)
T PF02037_consen 4 LTVAELKEELKERGLSTS 21 (35)
T ss_dssp SHHHHHHHHHHHTTS-ST
T ss_pred CcHHHHHHHHHHCCCCCC
Confidence 456789999999999543
No 220
>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=57.80 E-value=13 Score=27.18 Aligned_cols=26 Identities=23% Similarity=0.253 Sum_probs=21.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.+.|+|+.+||+..+|+-..++--|
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GLl 26 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLL 26 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999887765444
No 221
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=57.64 E-value=7.1 Score=32.08 Aligned_cols=20 Identities=10% Similarity=0.121 Sum_probs=15.0
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q 036926 11 ITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~CR 30 (168)
++|+|+.+|||.+|+.|.-.
T Consensus 1 i~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 1 MKDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred ChhHHHHhCCcHHHHHHHhC
Confidence 46788888888888777654
No 222
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=57.59 E-value=19 Score=22.87 Aligned_cols=28 Identities=18% Similarity=0.151 Sum_probs=21.1
Q ss_pred ccCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 036926 7 FYMPITKAAKELNVGLTLLK----KRCRELNI 34 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LK----r~CR~lGI 34 (168)
.+.+..|.|..||+|.-+++ ++.+++|+
T Consensus 18 ~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 18 QGKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 46889999999999986554 45566666
No 223
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=57.28 E-value=17 Score=26.37 Aligned_cols=40 Identities=18% Similarity=0.409 Sum_probs=33.8
Q ss_pred hhhhc---cCcHHHHHHHc--CCChhHHHHHHHHcCCCCCCchhhh
Q 036926 3 ISQYF---YMPITKAAKEL--NVGLTLLKKRCRELNIRRWPHRKLM 43 (168)
Q Consensus 3 l~~yF---~lPi~eAAr~L--gVs~T~LKr~CR~lGI~RWP~RKlk 43 (168)
+.+|| .+|+.++++.. |++..++++..+...| .||.=++.
T Consensus 6 ma~~~~~~~IpL~~v~~~yf~~lt~~~a~rk~~~g~l-plPv~rl~ 50 (76)
T PF11112_consen 6 MAQYFGDPVIPLEEVCEDYFPHLTPKTAKRKANAGEL-PLPVFRLD 50 (76)
T ss_pred HHHHcCCCCCcHHHHHHHHHccCCHHHHHHHHHCCCC-CCceeecC
Confidence 45665 68999999885 9999999999999999 89987774
No 224
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=57.02 E-value=15 Score=22.18 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=19.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.+++.+.|+.|||+.+++.+.-..+-
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36788899999999888877665543
No 225
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=56.89 E-value=11 Score=31.09 Aligned_cols=25 Identities=24% Similarity=0.288 Sum_probs=21.1
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
-|| ..+.|+.||||.|++...-++|
T Consensus 32 ~LpsE~eLa~~~gVSRtpVREAL~~L 57 (257)
T PRK10225 32 RLPPEREIAEMLDVTRTVVREALIML 57 (257)
T ss_pred cCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 576 8899999999999988777654
No 226
>PRK13503 transcriptional activator RhaS; Provisional
Probab=56.12 E-value=14 Score=30.20 Aligned_cols=27 Identities=11% Similarity=0.249 Sum_probs=24.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI 34 (168)
.+++.+.|+.+|+|.+.|.|.|++. |+
T Consensus 187 ~~tl~~lA~~~~lS~~~l~r~Fk~~~G~ 214 (278)
T PRK13503 187 EVNWEALADQFSLSLRTLHRQLKQQTGL 214 (278)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHhCc
Confidence 4678999999999999999999776 76
No 227
>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=56.06 E-value=12 Score=26.19 Aligned_cols=24 Identities=21% Similarity=0.342 Sum_probs=20.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
++..+.|+.+|++.+.|.++..+|
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L 49 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKL 49 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 789999999999999999887754
No 228
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=56.05 E-value=15 Score=30.53 Aligned_cols=28 Identities=18% Similarity=0.192 Sum_probs=25.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI~ 35 (168)
++.+.+.|+++|+|++.|-|++++. |+.
T Consensus 199 ~isl~~lA~~~~lS~~~l~r~Fk~~~G~t 227 (290)
T PRK10572 199 EFDIESVAQHVCLSPSRLAHLFRQQLGIS 227 (290)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 6789999999999999999999986 874
No 229
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=55.95 E-value=12 Score=28.75 Aligned_cols=32 Identities=13% Similarity=0.152 Sum_probs=25.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc---C-CCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL---N-IRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l---G-I~RWP~R 40 (168)
+++.+.|+.+|||.+.|.++.++| | |..+|.+
T Consensus 26 ~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~ 61 (141)
T PRK11014 26 TSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGK 61 (141)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCC
Confidence 567999999999999999998765 4 4455544
No 230
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=55.85 E-value=16 Score=31.55 Aligned_cols=27 Identities=15% Similarity=0.037 Sum_probs=23.4
Q ss_pred cCcHHHHHHHcCCChhHH----HHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLL----KKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~L----Kr~CR~lGI 34 (168)
+++.+|+|++||||..|+ +++++++|+
T Consensus 158 G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 158 GFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 789999999999998665 567889998
No 231
>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=55.85 E-value=12 Score=30.41 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=21.3
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
-|| ..+.|+.||||.|.+....++|
T Consensus 29 ~LpsE~~La~~lgVSRtpVREAL~~L 54 (235)
T TIGR02812 29 ILPAERELSELIGVTRTTLREVLQRL 54 (235)
T ss_pred cCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 475 8899999999999988877765
No 232
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=55.65 E-value=12 Score=27.67 Aligned_cols=21 Identities=19% Similarity=0.147 Sum_probs=16.5
Q ss_pred cCcHHHHHHHcCCChhHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~ 28 (168)
+-.+..||+.||||.+++-+.
T Consensus 16 ~gSis~AA~~L~iS~stvs~~ 36 (99)
T TIGR00637 16 MGSISQAAKDAGISYKSAWDY 36 (99)
T ss_pred hCCHHHHHHHHCCCHHHHHHH
Confidence 346789999999999887544
No 233
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=55.52 E-value=13 Score=29.93 Aligned_cols=30 Identities=17% Similarity=0.080 Sum_probs=25.8
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.++.-.+|++.+.|..+|||..++.++.+-
T Consensus 32 ~~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 32 AIRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 356678999999999999999999998864
No 234
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=55.52 E-value=11 Score=31.16 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=18.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.+++++|++.|||.+|+-|.-.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 4689999999999998877654
No 235
>PF13730 HTH_36: Helix-turn-helix domain
Probab=55.33 E-value=15 Score=23.42 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=19.9
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+...|+.+|+|..++.|...+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 58999999999999998887765
No 236
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.19 E-value=15 Score=25.27 Aligned_cols=22 Identities=14% Similarity=0.051 Sum_probs=17.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++..++|++|||+.+++.|.-.
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHH
Confidence 7889999999999887766543
No 237
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=55.16 E-value=13 Score=29.07 Aligned_cols=24 Identities=21% Similarity=0.286 Sum_probs=20.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+++.+|+|++||||..|+|..-++
T Consensus 165 G~s~~eIA~~l~iS~~TV~~h~~~ 188 (216)
T PRK10840 165 GFLVTEIAKKLNRSIKTISSQKKS 188 (216)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 688999999999999999876543
No 238
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=55.16 E-value=9.2 Score=31.77 Aligned_cols=22 Identities=14% Similarity=0.117 Sum_probs=19.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..++|+|+..|||.+|+-|...
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhC
Confidence 5789999999999999887764
No 239
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=55.12 E-value=9.9 Score=26.74 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=12.7
Q ss_pred hccCcHHHHHHHcCCChhHHHH
Q 036926 6 YFYMPITKAAKELNVGLTLLKK 27 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr 27 (168)
|-++++.+.|+++||+.+++.+
T Consensus 30 ~~~~t~~~Ia~~agvs~~~~Y~ 51 (201)
T COG1309 30 YAATTVDEIAKAAGVSKGTLYR 51 (201)
T ss_pred cCCCCHHHHHHHhCCCcchhHH
Confidence 3455666666666666666543
No 240
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=54.50 E-value=11 Score=31.50 Aligned_cols=22 Identities=14% Similarity=0.294 Sum_probs=18.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..++++|+..|||.+|+-|.-.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHC
Confidence 4689999999999998877653
No 241
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=54.38 E-value=15 Score=31.47 Aligned_cols=28 Identities=7% Similarity=0.169 Sum_probs=25.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI~ 35 (168)
.+.+.+.|+.+|||.+.|.|.+++. |+.
T Consensus 207 ~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t 235 (302)
T PRK10371 207 ALTINDVAEHVKLNANYAMGIFQRVMQLT 235 (302)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhCCC
Confidence 5889999999999999999999994 874
No 242
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=54.31 E-value=12 Score=28.19 Aligned_cols=53 Identities=15% Similarity=0.266 Sum_probs=35.6
Q ss_pred hhhhhc---cCcHHHHHHHcCCChhHHHHHHHHcCCC-CCCchhhhcHHHHHHHHHHHhh
Q 036926 2 TISQYF---YMPITKAAKELNVGLTLLKKRCRELNIR-RWPHRKLMSLQTLIKNVQELQT 57 (168)
Q Consensus 2 ~l~~yF---~lPi~eAAr~LgVs~T~LKr~CR~lGI~-RWP~RKlkSL~~li~~l~~~~~ 57 (168)
+|+..| ++++.++|..||+|..-|-++- .+. +=|+-=+.=-+-+.+++++.+.
T Consensus 14 ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL---~l~~~~~~~vW~lRdyL~~~i~~~G~ 70 (89)
T PF10078_consen 14 ELQANFELSGLSLEQIAADLGTSPEHLEQVL---NLKQPFPEDVWILRDYLNDKIKEQGK 70 (89)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH---cCCCCCcccchHHHHHHHHHHHHcCC
Confidence 455555 7999999999999999888764 332 3355544444556666666544
No 243
>PF06870 RNA_pol_I_A49: A49-like RNA polymerase I associated factor ; InterPro: IPR009668 Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3NFG_A 3NFH_B.
Probab=54.08 E-value=11 Score=33.48 Aligned_cols=29 Identities=31% Similarity=0.409 Sum_probs=24.5
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
-|-+++.+.|+.|+++...|...||++|-
T Consensus 317 ~f~~d~~~L~~dLkl~~~~l~~~~r~LGC 345 (385)
T PF06870_consen 317 NFSVDITDLARDLKLSPKKLTQYFRELGC 345 (385)
T ss_dssp TTEEEHHHHHHHHT--HHHHHHHHHHTT-
T ss_pred CcccChHHHHHHhCCCHHHHHHHHHHhCC
Confidence 46789999999999999999999999995
No 244
>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=53.31 E-value=16 Score=29.24 Aligned_cols=26 Identities=15% Similarity=-0.006 Sum_probs=22.0
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+-++++.|+|+.||+|.++++++=++
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 35799999999999999999876543
No 245
>PRK09483 response regulator; Provisional
Probab=53.21 E-value=16 Score=27.70 Aligned_cols=28 Identities=18% Similarity=0.254 Sum_probs=22.2
Q ss_pred ccCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 036926 7 FYMPITKAAKELNVGLTLLK----KRCRELNI 34 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LK----r~CR~lGI 34 (168)
-+++.+++|+.||||..|+| ++.+++|+
T Consensus 162 ~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 36788999999999987765 45667776
No 246
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=53.02 E-value=14 Score=30.48 Aligned_cols=33 Identities=21% Similarity=0.175 Sum_probs=25.8
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc---C-CCCCCch
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL---N-IRRWPHR 40 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l---G-I~RWP~R 40 (168)
-|| ..+.|+.||||.|.+....+.| | |..-|.+
T Consensus 31 ~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~ 68 (253)
T PRK11523 31 KLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGS 68 (253)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 577 7899999999999998887755 4 4455655
No 247
>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=53.01 E-value=12 Score=28.11 Aligned_cols=23 Identities=22% Similarity=0.251 Sum_probs=16.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
..++.+||+.+|||.|++-+=..
T Consensus 19 ~aTVR~~Ak~FGvSKSTVHkDvt 41 (82)
T PF12116_consen 19 KATVRQAAKVFGVSKSTVHKDVT 41 (82)
T ss_dssp ---HHHHHHHHTS-HHHHHHHHT
T ss_pred ccHHHHHHHHHCCcHHHHHHHHH
Confidence 46789999999999999876554
No 248
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=52.91 E-value=16 Score=23.34 Aligned_cols=31 Identities=10% Similarity=0.100 Sum_probs=24.1
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
..+=++++.+.|+.+|++.+++-+.+++|-=
T Consensus 13 ~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 13 YENGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 3444678999999999999999988887643
No 249
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=52.82 E-value=11 Score=31.29 Aligned_cols=24 Identities=17% Similarity=0.173 Sum_probs=20.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
..++++|+..|||.+|+.|.....
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~ 25 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDD 25 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCC
Confidence 368999999999999998887544
No 250
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=52.79 E-value=12 Score=31.39 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=17.8
Q ss_pred cHHHHHHHcCCChhHHHHHHH
Q 036926 10 PITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR 30 (168)
+|+++|+..|||.+|+-|.-.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 689999999999998876654
No 251
>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=52.36 E-value=20 Score=27.47 Aligned_cols=27 Identities=19% Similarity=0.133 Sum_probs=22.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRR 36 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~R 36 (168)
+.|.|+|+.+|||+.+|.-.-++ |+-.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~ 28 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN-GLIK 28 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 68999999999999999887766 6433
No 252
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=52.18 E-value=14 Score=30.61 Aligned_cols=23 Identities=17% Similarity=0.004 Sum_probs=17.5
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+|+++|+..|||.+|+-|.-..-
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~~ 23 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVINGK 23 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Confidence 47888888888888887776443
No 253
>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=52.16 E-value=22 Score=26.82 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=20.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|++.|+|+.+|||+.+|.-. -+.|+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Y-e~~GL 25 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYY-QRRGL 25 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHH-HHCCC
Confidence 57999999999999999544 55563
No 254
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=52.13 E-value=15 Score=30.34 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=25.5
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc---C-CCCCCch
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL---N-IRRWPHR 40 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l---G-I~RWP~R 40 (168)
-|| ..+.|+.||||.|.+...-+.| | |...|.+
T Consensus 25 ~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~ 62 (253)
T PRK10421 25 KLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGG 62 (253)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 476 8899999999999988776654 4 4566765
No 255
>PRK08359 transcription factor; Validated
Probab=51.89 E-value=16 Score=30.42 Aligned_cols=26 Identities=12% Similarity=0.112 Sum_probs=22.0
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
++.--+|.+.+.|..|||+.+++.++
T Consensus 93 aRe~kglSQeeLA~~lgvs~stI~~i 118 (176)
T PRK08359 93 AIQKSGLSYEELSHEVGLSVNDLRRI 118 (176)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 45556899999999999999999765
No 256
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=51.83 E-value=16 Score=32.72 Aligned_cols=27 Identities=19% Similarity=0.318 Sum_probs=22.9
Q ss_pred cCcHHHHHHHcCCChhHHHH---HHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKK---RCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr---~CR~lGI 34 (168)
++.+.|+|++||||.+++-| .+|+-||
T Consensus 26 gltQ~eIA~~LgiSR~~v~rlL~~Ar~~Gi 55 (321)
T COG2390 26 GLTQSEIAERLGISRATVSRLLAKAREEGI 55 (321)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCe
Confidence 78999999999999876655 6889995
No 257
>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=51.44 E-value=14 Score=27.05 Aligned_cols=23 Identities=17% Similarity=0.192 Sum_probs=19.5
Q ss_pred ccCcHHHHHHHcCCChhHHHHHH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~C 29 (168)
=.+++.++|+.+|||.+++-|.-
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 46789999999999999988844
No 258
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=51.17 E-value=16 Score=24.40 Aligned_cols=25 Identities=16% Similarity=0.216 Sum_probs=20.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.+.++|+.+|++.+++.+..++|
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~L 46 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKSL 46 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4678899999999998887776654
No 259
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=49.97 E-value=16 Score=29.35 Aligned_cols=24 Identities=17% Similarity=0.117 Sum_probs=20.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
-|.|.|+|+.+||++.+|.-..+.
T Consensus 11 ~~~IgevAk~~gvs~~TlRyYE~~ 34 (154)
T PRK15002 11 LLTPGEVAKRSGVAVSALHFYESK 34 (154)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHC
Confidence 378999999999999999877654
No 260
>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=49.90 E-value=17 Score=26.25 Aligned_cols=26 Identities=15% Similarity=0.110 Sum_probs=20.5
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.++++.++|+.||++...++..|..|
T Consensus 64 ~Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 64 EGVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp TTEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred CcccHHHHHHHhCcCHHHHHHHHHHH
Confidence 36788899999999888888888765
No 261
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=49.16 E-value=18 Score=27.65 Aligned_cols=29 Identities=17% Similarity=0.198 Sum_probs=23.9
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.|=.+++..+|+-||++...|.+.|.+.|
T Consensus 94 aY~sIs~~~la~~Lg~~~~el~~~~~~~g 122 (143)
T PF10075_consen 94 AYSSISLSDLAEMLGLSEEELEKFIKSRG 122 (143)
T ss_dssp H-SEE-HHHHHHHTTS-HHHHHHHHHHHT
T ss_pred HHhHcCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 46689999999999999999999999985
No 262
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=49.07 E-value=44 Score=26.28 Aligned_cols=27 Identities=11% Similarity=-0.049 Sum_probs=24.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|+.+.++|+.|||+++.+.+.-+.-+-
T Consensus 22 G~Sq~~iA~LLGltqaAVS~Yls~krg 48 (119)
T COG2522 22 GLSQYRIAKLLGLTQAAVSQYLSGKRG 48 (119)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHccCCc
Confidence 899999999999999999998876554
No 263
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=49.05 E-value=18 Score=24.28 Aligned_cols=30 Identities=17% Similarity=0.102 Sum_probs=23.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWP 38 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP 38 (168)
++..+.|..||||.+++.+.-+.+-=..||
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 458899999999999988877766444555
No 264
>PF07860 CCD: WisP family C-Terminal Region; InterPro: IPR012421 This entry represents the C-terminal domain found in the Tropheryma whipplei WisP family of proteins [].
Probab=49.05 E-value=6.6 Score=31.30 Aligned_cols=13 Identities=46% Similarity=0.917 Sum_probs=10.3
Q ss_pred cCCCCCCchhhhcH
Q 036926 32 LNIRRWPHRKLMSL 45 (168)
Q Consensus 32 lGI~RWP~RKlkSL 45 (168)
+|| -||+||+-.-
T Consensus 53 hgi-twpfrklfgs 65 (141)
T PF07860_consen 53 HGI-TWPFRKLFGS 65 (141)
T ss_pred hcc-cchHHHHhCC
Confidence 688 8999998543
No 265
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=48.93 E-value=16 Score=29.20 Aligned_cols=39 Identities=5% Similarity=0.006 Sum_probs=31.0
Q ss_pred cCcHHHHHHHcCCChhHHHHH---HHHcCCCCCCchhhhcHH
Q 036926 8 YMPITKAAKELNVGLTLLKKR---CRELNIRRWPHRKLMSLQ 46 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~---CR~lGI~RWP~RKlkSL~ 46 (168)
.++.++.|..||++..+|-|. -++-|+-+|.++++.=+|
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d 225 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIEN 225 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEcC
Confidence 477899999999998777664 456788889998886554
No 266
>PHA00675 hypothetical protein
Probab=48.67 E-value=19 Score=26.78 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=21.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+....+.|+.+|||.+++-.+|+.
T Consensus 39 G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 39 GMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred CccHHHHHHHhCCCHHHHHHHHcc
Confidence 456679999999999999999985
No 267
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=48.41 E-value=21 Score=26.04 Aligned_cols=26 Identities=23% Similarity=0.137 Sum_probs=20.1
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~C 29 (168)
..+.-.+-.+.|.+||+|.|.+.|.-
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaVwK~I 40 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAVWKHI 40 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHHHHHH
Confidence 34555778899999999999887653
No 268
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=48.26 E-value=19 Score=26.94 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=21.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
++..+.|+.+||+.+++.++.+.|
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L 49 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQL 49 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHH
Confidence 688999999999999999888755
No 269
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=48.24 E-value=22 Score=28.00 Aligned_cols=26 Identities=19% Similarity=0.171 Sum_probs=22.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.++|.|+|+..|||+.+|.-..+ .|+
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~-~GL 32 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQR-KGL 32 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 48999999999999999988775 464
No 270
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=47.67 E-value=17 Score=29.22 Aligned_cols=28 Identities=14% Similarity=0.139 Sum_probs=22.9
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.--.+|..+.|+.||||.|.+...-+.|
T Consensus 31 pG~~L~e~~La~~lgVSRtpVREAL~~L 58 (221)
T PRK11414 31 PGARLITKNLAEQLGMSITPVREALLRL 58 (221)
T ss_pred CCCccCHHHHHHHHCCCchhHHHHHHHH
Confidence 3346899999999999999988777655
No 271
>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=47.59 E-value=22 Score=23.42 Aligned_cols=25 Identities=16% Similarity=0.231 Sum_probs=19.4
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
=.+++.++|+.||++.+++.+--+.
T Consensus 23 ~~~t~~ela~~l~~~~~t~s~hL~~ 47 (61)
T PF12840_consen 23 GPMTVSELAEELGISQSTVSYHLKK 47 (61)
T ss_dssp STBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3678899999999999998776553
No 272
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=46.79 E-value=20 Score=29.37 Aligned_cols=25 Identities=16% Similarity=0.268 Sum_probs=21.3
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
-|| ..+.|+.||||.|.+...-++|
T Consensus 30 ~LPsE~eLa~~~gVSRtpVREAL~~L 55 (251)
T PRK09990 30 ALPSERRLCEKLGFSRSALREGLTVL 55 (251)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 574 7899999999999998877765
No 273
>PRK13500 transcriptional activator RhaR; Provisional
Probab=46.62 E-value=23 Score=30.31 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=24.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI 34 (168)
.+.+.+.|+.+|||+..|-|.+++. |.
T Consensus 222 ~isl~~lA~~~~iS~~~L~r~FK~~tG~ 249 (312)
T PRK13500 222 PFALDKFCDEASCSERVLRQQFRQQTGM 249 (312)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 3778999999999999999999986 87
No 274
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=46.58 E-value=24 Score=25.89 Aligned_cols=26 Identities=8% Similarity=-0.064 Sum_probs=21.3
Q ss_pred hhhhccCcHHHHHHHcC------CChhHHHHH
Q 036926 3 ISQYFYMPITKAAKELN------VGLTLLKKR 28 (168)
Q Consensus 3 l~~yF~lPi~eAAr~Lg------Vs~T~LKr~ 28 (168)
.+.-.++.+.++|+.+| +|.+++-|+
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~ 50 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRF 50 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHH
Confidence 45567999999999999 488888764
No 275
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=46.46 E-value=21 Score=28.49 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=19.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++..+|+|+.||||..|+|+.-.
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHH
Confidence 57899999999999999988653
No 276
>PRK03837 transcriptional regulator NanR; Provisional
Probab=46.30 E-value=21 Score=28.82 Aligned_cols=26 Identities=12% Similarity=0.163 Sum_probs=21.8
Q ss_pred cC-cHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YM-PITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~l-Pi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
-| +..+.|+.||||.|++....+.|-
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L~ 62 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQALK 62 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46 488999999999999998887653
No 277
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=45.80 E-value=23 Score=28.13 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=24.4
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+++-.++.+.++|+.+|||.++|.++-+.
T Consensus 15 ~R~~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 15 IRQQQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 45567899999999999999999988754
No 278
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=45.57 E-value=56 Score=24.55 Aligned_cols=33 Identities=3% Similarity=-0.223 Sum_probs=21.8
Q ss_pred HHHHHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 13 KAAKELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 13 eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
+|....--+-.++..+|++|||...-..++...
T Consensus 20 ~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 20 AIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344443334446678899999988777777543
No 279
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=45.39 E-value=21 Score=28.66 Aligned_cols=26 Identities=15% Similarity=0.133 Sum_probs=22.3
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
-+++.+++|+.||+|.+|+|+.-..+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 36789999999999999999887754
No 280
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=45.17 E-value=14 Score=28.73 Aligned_cols=20 Identities=15% Similarity=0.331 Sum_probs=17.9
Q ss_pred cCcHHHHHHHcCCChhHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKK 27 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr 27 (168)
.+|+.|+|..||||.+++-|
T Consensus 60 e~sQREi~~~LgvsiAtITR 79 (103)
T COG2973 60 ELSQREIAQKLGVSIATITR 79 (103)
T ss_pred cccHHHHHHHhCcchhhhcc
Confidence 68999999999999988765
No 281
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=44.85 E-value=25 Score=24.87 Aligned_cols=20 Identities=35% Similarity=0.393 Sum_probs=16.5
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q 036926 11 ITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~CR 30 (168)
+.+||+.|||..+.+-|.-|
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr 34 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALR 34 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred hHHHHHHcCCcHHHHHHHHH
Confidence 78999999999999887665
No 282
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=44.77 E-value=23 Score=29.10 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=20.6
Q ss_pred cCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
-|| ..+.|+.||||.|++...-+.|
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 464 8899999999999988776654
No 283
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=44.40 E-value=27 Score=31.68 Aligned_cols=23 Identities=17% Similarity=0.198 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
+.+.|||+.|||+.++|++.+++
T Consensus 49 ft~~e~A~~lgvs~~tlr~~~~~ 71 (405)
T PRK13869 49 FTSGEAARLMKISDSTLRKMTLA 71 (405)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHc
Confidence 48999999999999999999987
No 284
>PRK10130 transcriptional regulator EutR; Provisional
Probab=44.28 E-value=25 Score=31.39 Aligned_cols=33 Identities=21% Similarity=0.318 Sum_probs=27.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH-cCCCCCCchhhh
Q 036926 9 MPITKAAKELNVGLTLLKKRCRE-LNIRRWPHRKLM 43 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~-lGI~RWP~RKlk 43 (168)
+.+.+.|+.+|||..+|.+.+++ +|+. |..-|+
T Consensus 257 ltv~~lA~~~gvS~r~L~r~Fk~~~G~s--p~~ylr 290 (350)
T PRK10130 257 VTVLDLCNQLHVSRRTLQNAFHAILGIG--PNAWLK 290 (350)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcC--HHHHHH
Confidence 78999999999999999999988 6875 444443
No 285
>PHA02535 P terminase ATPase subunit; Provisional
Probab=44.20 E-value=65 Score=31.51 Aligned_cols=26 Identities=12% Similarity=0.022 Sum_probs=24.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
+.++.++|++|||+.++|-+-+++.+
T Consensus 18 G~sv~eIA~~LGv~~~Tl~~W~kr~~ 43 (581)
T PHA02535 18 GWTVAEIAEELGLKSRTIYSWKERDG 43 (581)
T ss_pred CCCHHHHHHHhCCChhHHHHHhcccc
Confidence 78999999999999999999999875
No 286
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=43.90 E-value=24 Score=28.33 Aligned_cols=28 Identities=18% Similarity=0.165 Sum_probs=24.1
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.=-+++.+++..+|++..++++.+|++
T Consensus 23 e~GRiTi~ql~~~TGasR~Tvk~~lreL 50 (127)
T PF06163_consen 23 EHGRITIKQLVAKTGASRNTVKRYLREL 50 (127)
T ss_pred HcCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 3445789999999999999999999975
No 287
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=42.30 E-value=1.2e+02 Score=25.84 Aligned_cols=50 Identities=16% Similarity=0.271 Sum_probs=31.5
Q ss_pred cHHHHHHHcCCC-hhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHhhcCCC
Q 036926 10 PITKAAKELNVG-LTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEG 61 (168)
Q Consensus 10 Pi~eAAr~LgVs-~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~~~g~~ 61 (168)
+..++|+.|||. +-.++..-++ +.+|+..++..+-..+..+....+.|..
T Consensus 259 ~~~~ia~~lgi~~p~~~~~~~~~--~~~~s~~~L~~~l~~L~~~D~~iK~g~~ 309 (326)
T PRK07452 259 DVKVIAKAAGIGNPKRIYFLRKE--VQGLSSQQLLKLLPLLLDLEASLKQGAN 309 (326)
T ss_pred cHHHHHHHhCCCCcHHHHHHHHH--HhcCCHHHHHHHHHHHHHHHHHHhcCCC
Confidence 355688999995 4333333233 3689998887776666666666665543
No 288
>PRK13698 plasmid-partitioning protein; Provisional
Probab=41.75 E-value=32 Score=31.27 Aligned_cols=33 Identities=12% Similarity=0.178 Sum_probs=29.2
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
|-..|++.+++.|+.||+|.+.+-+.-|-+.++
T Consensus 171 L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP 203 (323)
T PRK13698 171 LQNEFAGNISALADAENISRKIITRCINTAKLP 203 (323)
T ss_pred HHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcCC
Confidence 445789999999999999999999999988875
No 289
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=41.63 E-value=30 Score=25.11 Aligned_cols=28 Identities=14% Similarity=0.011 Sum_probs=22.9
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
...+++.|.|..+|++.+++-|...+|=
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4568899999999999999888776653
No 290
>PRK06424 transcription factor; Provisional
Probab=41.50 E-value=29 Score=27.79 Aligned_cols=30 Identities=10% Similarity=-0.010 Sum_probs=23.9
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
++.-.+|++.+.|+.+||+.+++.++-+-.
T Consensus 92 lRe~~GLSQ~eLA~~iGvs~stIskiE~G~ 121 (144)
T PRK06424 92 ARERLSMSQADLAAKIFERKNVIASIERGD 121 (144)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 455668899999999999999888886633
No 291
>PRK13501 transcriptional activator RhaR; Provisional
Probab=41.44 E-value=30 Score=28.85 Aligned_cols=26 Identities=15% Similarity=0.186 Sum_probs=22.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.+.+.+.|+.+|+|.+.|.|++++.-
T Consensus 192 ~~sl~~lA~~~~lS~~~l~r~Fk~~~ 217 (290)
T PRK13501 192 YFDMADFCHKNQLVERSLKQLFRQQT 217 (290)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35799999999999999999998653
No 292
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=40.88 E-value=29 Score=24.13 Aligned_cols=30 Identities=17% Similarity=0.170 Sum_probs=21.3
Q ss_pred HHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 11 ITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
+.++|+.|||+.+++-+.-++|-=..|=.|
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r 31 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEY 31 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 578999999999888777665543334333
No 293
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=40.66 E-value=31 Score=27.83 Aligned_cols=28 Identities=18% Similarity=0.018 Sum_probs=23.1
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
++.--+|++.+.|..+||+.+++.++-+
T Consensus 77 ~Re~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 77 EREKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3455689999999999999999988864
No 294
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=40.28 E-value=37 Score=28.64 Aligned_cols=28 Identities=7% Similarity=0.103 Sum_probs=25.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL-NIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l-GI~ 35 (168)
.+++.+.|+.+|+|...|.|+.++. |++
T Consensus 21 ~~~l~~lA~~~~~S~~~l~r~F~~~~g~s 49 (289)
T PRK15121 21 PLSLDNVAAKAGYSKWHLQRMFKDVTGHA 49 (289)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 4789999999999999999999986 874
No 295
>PRK13749 transcriptional regulator MerD; Provisional
Probab=40.24 E-value=42 Score=26.08 Aligned_cols=27 Identities=7% Similarity=0.187 Sum_probs=22.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~ 35 (168)
+|.|.|+|+..|||+.+|.-..+. |+-
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~-GLl 29 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLR-GLL 29 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHC-CCC
Confidence 478999999999999999876654 643
No 296
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=40.19 E-value=23 Score=29.02 Aligned_cols=23 Identities=22% Similarity=0.228 Sum_probs=20.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+++.+|+|++|++|..|+|-.-.
T Consensus 163 G~snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 163 GLSNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHH
Confidence 78899999999999999997644
No 297
>PF13309 HTH_22: HTH domain
Probab=40.08 E-value=24 Score=24.24 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=15.2
Q ss_pred HHHHHHHcCCChhHHHHH
Q 036926 11 ITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~ 28 (168)
+..+|+.||||..|+-+.
T Consensus 45 v~~vA~~L~iS~~TVY~Y 62 (64)
T PF13309_consen 45 VEYVAEKLGISRATVYRY 62 (64)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 678999999999888664
No 298
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=39.76 E-value=36 Score=31.77 Aligned_cols=36 Identities=11% Similarity=0.198 Sum_probs=26.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC----CCCCchhhhc
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI----RRWPHRKLMS 44 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI----~RWP~RKlkS 44 (168)
|.++++|.+|||..||+-|.+.---| .=+|-|-+=|
T Consensus 344 LtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs 383 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFS 383 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcc
Confidence 67899999999999999999984332 1156555544
No 299
>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=39.76 E-value=43 Score=23.18 Aligned_cols=28 Identities=4% Similarity=0.086 Sum_probs=20.7
Q ss_pred hhhccCcHHHHHHHcC-CChhHHHHHHHH
Q 036926 4 SQYFYMPITKAAKELN-VGLTLLKKRCRE 31 (168)
Q Consensus 4 ~~yF~lPi~eAAr~Lg-Vs~T~LKr~CR~ 31 (168)
+.+++++..++++.|| -.-|++-.-||+
T Consensus 41 r~~~~~sl~~Ig~~fg~rdHstV~~a~~k 69 (70)
T PF08299_consen 41 RELTGLSLSEIGRYFGGRDHSTVIHAIRK 69 (70)
T ss_dssp HHHS---HHHHHHHCTSSTHHHHHHHHHH
T ss_pred HHHhCCCHHHHHHHhCCCCHHHHHHHHHh
Confidence 4677899999999999 888888877775
No 300
>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=39.70 E-value=39 Score=21.27 Aligned_cols=20 Identities=30% Similarity=0.331 Sum_probs=14.3
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q 036926 11 ITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~CR 30 (168)
..+.|+.+|||..++.+.-.
T Consensus 28 ~~~la~~~~is~~~v~~~l~ 47 (66)
T cd07377 28 ERELAEELGVSRTTVREALR 47 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 77888888888777655433
No 301
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) 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-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. 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
Probab=39.46 E-value=37 Score=24.52 Aligned_cols=30 Identities=20% Similarity=0.140 Sum_probs=19.0
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|+...+---++.|++|||+-+.+.++..++
T Consensus 10 ia~~LG~dWk~LAr~Lg~se~dI~~i~~~~ 39 (84)
T cd08804 10 IADHLGFSWTELARELDFTEEQIHQIRIEN 39 (84)
T ss_pred HHHHHhhhHHHHHHHcCCCHHHHHHHHHHC
Confidence 444445555667777777777777766653
No 302
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=39.34 E-value=26 Score=30.47 Aligned_cols=21 Identities=19% Similarity=0.148 Sum_probs=17.3
Q ss_pred cHHHHHHHcCCChhHHHHHHH
Q 036926 10 PITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR 30 (168)
.|+++|+..|||.+|+-|.-.
T Consensus 2 TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 589999999999998766543
No 303
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=39.30 E-value=27 Score=28.49 Aligned_cols=20 Identities=15% Similarity=0.192 Sum_probs=15.8
Q ss_pred CcHHHHHHHcCCChhHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~ 28 (168)
.+..+.|+++||+.++|-+.
T Consensus 35 ~T~~eiAee~Gis~~tLYrW 54 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRW 54 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHH
T ss_pred chHHHHHHHhCCCHHHHHHH
Confidence 45889999999999999864
No 304
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.71 E-value=32 Score=25.17 Aligned_cols=34 Identities=18% Similarity=-0.006 Sum_probs=22.1
Q ss_pred cCcHHHHHHHcCC-ChhHHHHHHH--HcCCCCCCchh
Q 036926 8 YMPITKAAKELNV-GLTLLKKRCR--ELNIRRWPHRK 41 (168)
Q Consensus 8 ~lPi~eAAr~LgV-s~T~LKr~CR--~lGI~RWP~RK 41 (168)
+..+.++|+++|| +.+.|.+.-+ +.+-..+|-.+
T Consensus 24 g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~~ 60 (116)
T COG2963 24 GDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSGK 60 (116)
T ss_pred CccHHHHHHHhCCCChHHHHHHHHHHHHcccccccCc
Confidence 4568889999995 8888884333 33344555443
No 305
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=38.47 E-value=33 Score=27.44 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=21.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.-.+.|+.|||+...+.|+|..|
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L 52 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYAL 52 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4678999999999999999999754
No 306
>PF11121 DUF2639: Protein of unknown function (DUF2639); InterPro: IPR022580 This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Probab=38.41 E-value=24 Score=23.28 Aligned_cols=21 Identities=48% Similarity=0.567 Sum_probs=16.9
Q ss_pred HHHcCCCCCCchhhhcHHHHH
Q 036926 29 CRELNIRRWPHRKLMSLQTLI 49 (168)
Q Consensus 29 CR~lGI~RWP~RKlkSL~~li 49 (168)
-+++||.+-|-|||.|-..-+
T Consensus 12 LKk~GI~~h~~rKlesyK~~~ 32 (40)
T PF11121_consen 12 LKKLGIRRHEGRKLESYKTHI 32 (40)
T ss_pred HHHhCccccchhHHHHHHHHH
Confidence 357899999999998876543
No 307
>PRK09954 putative kinase; Provisional
Probab=38.29 E-value=31 Score=29.85 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=21.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.++..+.|+.||||.++.+++-++|
T Consensus 17 ~~s~~~la~~l~~s~~~v~~~i~~L 41 (362)
T PRK09954 17 LIQQNEIADILQISRSRVAAHIMDL 41 (362)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5889999999999998888777643
No 308
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=37.80 E-value=32 Score=30.48 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=20.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
-+|..+.|+++|||.|++.++-|+|
T Consensus 198 rlse~eLAerlGVSRs~ireAlrkL 222 (251)
T TIGR02787 198 LLVASKIADRVGITRSVIVNALRKL 222 (251)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHH
Confidence 4788899999999999888877765
No 309
>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=37.72 E-value=11 Score=25.60 Aligned_cols=31 Identities=13% Similarity=0.120 Sum_probs=18.2
Q ss_pred hhhccCcH-HHHHHHcCCChhHHH-HHHHHcCC
Q 036926 4 SQYFYMPI-TKAAKELNVGLTLLK-KRCRELNI 34 (168)
Q Consensus 4 ~~yF~lPi-~eAAr~LgVs~T~LK-r~CR~lGI 34 (168)
...++..- .+.|+.||||.+++- ..-++--+
T Consensus 7 ~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~ 39 (66)
T PF07022_consen 7 KEALGVKSDKELAERLGISKSTLSNNWKKRGSI 39 (66)
T ss_dssp HHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS-
T ss_pred HHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCC
Confidence 34455544 599999999999998 44444334
No 310
>TIGR02433 lysidine_TilS_C tRNA(Ile)-lysidine synthetase, C-terminal domain. TIGRFAMs model TIGR02432 describes the family of the N-terminal domain of tRNA(Ile)-lysidine synthetase. This family (TIGR02433) describes a small C-terminal domain of about 50 residues present in about half the members of family TIGR02432,and in no other protein. Characterized examples of tRNA(Ile)-lysidine synthetase from E. coli and Bacillus subtilis both contain this domain.
Probab=37.53 E-value=17 Score=22.76 Aligned_cols=17 Identities=29% Similarity=0.497 Sum_probs=14.7
Q ss_pred ChhHHHHHHHHcCCCCC
Q 036926 21 GLTLLKKRCRELNIRRW 37 (168)
Q Consensus 21 s~T~LKr~CR~lGI~RW 37 (168)
+...||+++-+.+|+.|
T Consensus 19 ~~k~lkk~~~e~kiP~~ 35 (47)
T TIGR02433 19 GSKKLKKLFIDAKVPPW 35 (47)
T ss_pred CCchHHHHHHHcCCCHH
Confidence 35679999999999987
No 311
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=37.53 E-value=45 Score=26.75 Aligned_cols=27 Identities=22% Similarity=0.197 Sum_probs=22.3
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.|++...++|+.||+|.++++++-+=.
T Consensus 118 ~~g~s~~~iA~~lg~s~~~V~r~l~l~ 144 (187)
T TIGR00180 118 KFSMTQEDLAKKIGKSRAHITNLLRLL 144 (187)
T ss_pred HhCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 378899999999999999888765543
No 312
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=37.28 E-value=45 Score=23.07 Aligned_cols=25 Identities=28% Similarity=0.278 Sum_probs=21.6
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 10 PITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
....+|++|||+.-.-.+.-.++|.
T Consensus 15 sa~mva~~L~vT~~~A~~li~eLg~ 39 (54)
T PF11972_consen 15 SAPMVAKELGVTPQAAQRLIAELGL 39 (54)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 4567899999999888888899987
No 313
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=37.19 E-value=30 Score=28.25 Aligned_cols=27 Identities=22% Similarity=0.274 Sum_probs=20.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
+-.+..||++||||.+++-+.- .++|+
T Consensus 16 ~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~ 46 (294)
T PRK13348 16 TGSFERAARRLHVTPSAVSQRIKALEESLGQ 46 (294)
T ss_pred cCCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 4568899999999987765544 46675
No 314
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=37.02 E-value=39 Score=25.77 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=20.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.++.++|+.|||+.+++-+..++|-
T Consensus 23 ~~~~ela~~l~vs~~svs~~l~~L~ 47 (142)
T PRK03902 23 ARVSDIAEALSVHPSSVTKMVQKLD 47 (142)
T ss_pred cCHHHHHHHhCCChhHHHHHHHHHH
Confidence 5788999999999988877776554
No 315
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=36.92 E-value=34 Score=28.49 Aligned_cols=27 Identities=26% Similarity=0.208 Sum_probs=20.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
+..+..||++||||.+++-+.-+ ++|+
T Consensus 21 ~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 51 (312)
T PRK10341 21 SGSIGSAAKELGLTQPAVSKIINDIEDYFGV 51 (312)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 45678999999999987765544 5675
No 316
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=36.62 E-value=31 Score=27.99 Aligned_cols=28 Identities=14% Similarity=0.220 Sum_probs=23.3
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.|.+.+.+.|..+|+|.+++.|.-..|-
T Consensus 73 ~v~~t~~~ia~~l~iS~~Tv~r~ik~L~ 100 (165)
T PF05732_consen 73 AVVATQKEIAEKLGISKPTVSRAIKELE 100 (165)
T ss_pred eEEeeHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4567889999999999999988877654
No 317
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=36.51 E-value=33 Score=28.38 Aligned_cols=22 Identities=23% Similarity=0.234 Sum_probs=16.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C 29 (168)
.-.+..||+.||||.+++-+.-
T Consensus 25 ~gS~t~AA~~L~iSQpavS~~I 46 (303)
T PRK10082 25 CRNFSQAAVSRNVSQPAFSRRI 46 (303)
T ss_pred cCCHHHHHHHhCCChHHHHHHH
Confidence 3467899999999998765443
No 318
>PRK11050 manganese transport regulator MntR; Provisional
Probab=36.36 E-value=40 Score=26.44 Aligned_cols=30 Identities=17% Similarity=0.059 Sum_probs=23.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RW 37 (168)
..++.++|+.|||+.+++-+..+++--..|
T Consensus 51 ~~t~~eLA~~l~is~stVsr~l~~Le~~Gl 80 (152)
T PRK11050 51 EARQVDIAARLGVSQPTVAKMLKRLARDGL 80 (152)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 468899999999999888887765543333
No 319
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=36.36 E-value=35 Score=28.34 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=18.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+..+..||+.|||+.+++-+.-+
T Consensus 15 ~~S~s~AA~~L~isQ~avS~~I~ 37 (305)
T PRK11233 15 IGSLTQAAEVLHIAQPALSQQVA 37 (305)
T ss_pred cCCHHHHHHHhCCCchHHHHHHH
Confidence 45788999999999987755444
No 320
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=36.26 E-value=28 Score=28.29 Aligned_cols=34 Identities=26% Similarity=0.343 Sum_probs=26.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC----CCCCCchh
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN----IRRWPHRK 41 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG----I~RWP~RK 41 (168)
-+...+.|..||||.|.+....++|- |.+=|.|-
T Consensus 39 ~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG 76 (230)
T COG1802 39 RLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRG 76 (230)
T ss_pred CccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCC
Confidence 57789999999999999888877663 55557763
No 321
>TIGR03495 phage_LysB phage lysis regulatory protein, LysB family. Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin.
Probab=36.07 E-value=55 Score=26.27 Aligned_cols=28 Identities=32% Similarity=0.439 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHhhCCCCCCcHHHHHHHH
Q 036926 70 LGILERERKLIEERPDLEMEDTTKRLRQ 97 (168)
Q Consensus 70 i~~Lerek~lIee~P~~~L~~~tKrlRQ 97 (168)
|+.|..|-+.+..=-+.+||+.+.||||
T Consensus 84 i~rL~~ENe~lR~Wa~t~LPd~V~RL~~ 111 (135)
T TIGR03495 84 IERLKRENEDLRRWADTPLPDDVIRLRQ 111 (135)
T ss_pred HHHHHHcCHHHHHHhcCCCcHHHHHHhc
Confidence 4444444444445557899999999997
No 322
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=35.95 E-value=34 Score=27.63 Aligned_cols=27 Identities=15% Similarity=0.112 Sum_probs=20.1
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+-.+..||++|||+.+++-+. =.++|.
T Consensus 17 ~~s~t~AA~~L~isqpavS~~I~~LE~~lg~ 47 (290)
T PRK10837 17 SGSTTQASVMLALSQSAVSAALTDLEGQLGV 47 (290)
T ss_pred cCCHHHHHHHhCCCccHHHHHHHHHHHHhCC
Confidence 557889999999998776544 446664
No 323
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=35.86 E-value=34 Score=28.40 Aligned_cols=27 Identities=33% Similarity=0.343 Sum_probs=20.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
+..+..||++||||.+++-|.-+ ++|.
T Consensus 16 ~~s~s~AA~~L~isq~avSr~I~~LE~~lg~ 46 (309)
T PRK12682 16 NLNLTEAAKALHTSQPGVSKAIIELEEELGI 46 (309)
T ss_pred cCCHHHHHHHhcCccHHHHHHHHHHHHHhCC
Confidence 35889999999999877655544 5674
No 324
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=35.74 E-value=39 Score=23.11 Aligned_cols=25 Identities=12% Similarity=0.194 Sum_probs=17.3
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
+.--++.+.++|..++|++..|+.+
T Consensus 6 R~~~glsl~~va~~t~I~~~~l~ai 30 (62)
T PF13413_consen 6 REAKGLSLEDVAEETKISVSYLEAI 30 (62)
T ss_dssp HHCTT--HHHHHHHCS--HHHHHHH
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 4445789999999999999988876
No 325
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=35.26 E-value=38 Score=27.69 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=17.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+..+..||++||||.+++-+.-+
T Consensus 17 ~gS~s~AA~~L~isq~avS~~I~ 39 (300)
T TIGR02424 17 QGSVKRAAEALHITQPAVSKTLR 39 (300)
T ss_pred hCCHHHHHHHhCCChHHHHHHHH
Confidence 45688999999999987655444
No 326
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=35.17 E-value=1.8e+02 Score=25.46 Aligned_cols=74 Identities=12% Similarity=0.234 Sum_probs=48.7
Q ss_pred HHcCCCCC----CchhhhcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHhh--------CCC------CCCcHH
Q 036926 30 RELNIRRW----PHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEE--------RPD------LEMEDT 91 (168)
Q Consensus 30 R~lGI~RW----P~RKlkSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~lIee--------~P~------~~L~~~ 91 (168)
.++|-.+| ...--..+..-+..++.....+..++..+...+...+....++.. .|+ ......
T Consensus 112 ~k~g~~~w~~~~S~~~~~~l~~~~~k~~~~L~~A~~sD~~l~~~~~~~~~~l~lL~~~~~~l~~~~Ps~~~~~~~~~~~~ 191 (342)
T cd08915 112 AKFGTLRWRRPSSDEAAKELYEKVTKLRGYLEQASNSDNEVLQCYESIDPNLVLLCGGYKELKAFIPSPYPALDPEVSEV 191 (342)
T ss_pred HHhCcccCCCCChHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhcCChHHHHHhCCCccccCCchhhHH
Confidence 37888899 244556666667777776666666777777777666665555533 231 123467
Q ss_pred HHHHHHHHHHHh
Q 036926 92 TKRLRQACFKAN 103 (168)
Q Consensus 92 tKrlRQa~FK~~ 103 (168)
+..||+.+=|.+
T Consensus 192 v~~Lr~~l~~l~ 203 (342)
T cd08915 192 VSSLRPLLNEVS 203 (342)
T ss_pred HHHHHHHHHHHH
Confidence 889999997774
No 327
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=35.08 E-value=36 Score=27.99 Aligned_cols=22 Identities=27% Similarity=0.280 Sum_probs=17.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
-.+..||++|||+.+++-+.-+
T Consensus 20 gs~s~AA~~L~isQ~avS~~i~ 41 (302)
T PRK09791 20 GSIRGASRMLNMSQPALTKSIQ 41 (302)
T ss_pred CCHHHHHHHhCCChHHHHHHHH
Confidence 4678999999999988766554
No 328
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=34.99 E-value=29 Score=23.31 Aligned_cols=30 Identities=27% Similarity=0.410 Sum_probs=22.1
Q ss_pred HHHHHHHcC-------CChhHHHHHHHHcCCCCCCch
Q 036926 11 ITKAAKELN-------VGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 11 i~eAAr~Lg-------Vs~T~LKr~CR~lGI~RWP~R 40 (168)
+.++|+.++ |....-+..|+++||..+|.=
T Consensus 39 ~~~~~~~~~~~v~~~~vd~~~~~~l~~~~~v~~~Pt~ 75 (103)
T PF00085_consen 39 LEKLAKEYKDNVKFAKVDCDENKELCKKYGVKSVPTI 75 (103)
T ss_dssp HHHHHHHTTTTSEEEEEETTTSHHHHHHTTCSSSSEE
T ss_pred ecccccccccccccchhhhhccchhhhccCCCCCCEE
Confidence 456666666 334556889999999999963
No 329
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=34.58 E-value=87 Score=28.69 Aligned_cols=39 Identities=18% Similarity=0.186 Sum_probs=32.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQT 47 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~ 47 (168)
++++.|+|+.||.+.+|+-|=-|++-+.. =|+-..+-..
T Consensus 23 ~~S~reIA~~LgRh~sTIsRElkRn~~~~-~Y~a~~A~~~ 61 (318)
T COG2826 23 KMSIREIAKQLNRHHSTISRELKRNRTRD-IYSAVKAQER 61 (318)
T ss_pred CCCHHHHHHHhCCCcchhhHHHhcCCccc-eeeHHHHHHH
Confidence 78999999999999999999999888877 4665555544
No 330
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=34.53 E-value=46 Score=21.50 Aligned_cols=25 Identities=16% Similarity=0.258 Sum_probs=15.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+++.+.|+.+|++.+++-+..+++
T Consensus 18 ~~t~~~l~~~~~~~~~~vs~~i~~L 42 (68)
T PF13463_consen 18 PMTQSDLAERLGISKSTVSRIIKKL 42 (68)
T ss_dssp -BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4567888888888877776655543
No 331
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=34.42 E-value=70 Score=30.39 Aligned_cols=26 Identities=12% Similarity=0.220 Sum_probs=22.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.++++|.+|||..||+-|.+..--|
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~~KY~ 395 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATGNKYM 395 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhcCcee
Confidence 67899999999999999999985443
No 332
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=34.27 E-value=38 Score=28.32 Aligned_cols=27 Identities=30% Similarity=0.343 Sum_probs=19.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
+-.+..||+.||||.+++-+.- .++|+
T Consensus 28 ~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 58 (311)
T PRK10086 28 HQSFALAADELSLTPSAVSHRINQLEEELGI 58 (311)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 3467899999999987765443 45665
No 333
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=34.25 E-value=46 Score=29.86 Aligned_cols=29 Identities=7% Similarity=0.090 Sum_probs=25.9
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCRE-LNIR 35 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~-lGI~ 35 (168)
-.+++.+.|+.+|+|.+.|.|++++ .|+.
T Consensus 98 ~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~T 127 (353)
T PRK15435 98 TPVTLEALADQVAMSPFHLHRLFKATTGMT 127 (353)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3578999999999999999999988 4886
No 334
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=33.90 E-value=32 Score=28.94 Aligned_cols=34 Identities=18% Similarity=0.145 Sum_probs=27.2
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCc
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~ 39 (168)
.=.+...|+|+.||||..+++|-..++....++-
T Consensus 16 ~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 16 HTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3367899999999999999999999875544443
No 335
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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=33.87 E-value=51 Score=24.43 Aligned_cols=32 Identities=16% Similarity=0.240 Sum_probs=20.7
Q ss_pred Chhhhhc-----cCc---HHHHHHHcCCChhHHHHHHHHc
Q 036926 1 ETISQYF-----YMP---ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 1 e~l~~yF-----~lP---i~eAAr~LgVs~T~LKr~CR~l 32 (168)
|.|++|| ++| -++.|+.||+|.+.+..+--.+
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~i~~~~ 43 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDVAKANE 43 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHHHHHHC
Confidence 3566666 345 3457777777777777776654
No 336
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=33.85 E-value=40 Score=27.40 Aligned_cols=26 Identities=27% Similarity=0.299 Sum_probs=18.9
Q ss_pred CcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
-.+..||+.|||+.+++-+. =.++|+
T Consensus 16 gs~s~AA~~L~itqpavS~~Ik~LE~~lg~ 45 (291)
T TIGR03418 16 ASFTAAARELGSTQPAVSQQVKRLEEELGT 45 (291)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 46789999999998776543 345564
No 337
>PRK15320 transcriptional activator SprB; Provisional
Probab=33.61 E-value=39 Score=29.76 Aligned_cols=38 Identities=21% Similarity=0.247 Sum_probs=29.0
Q ss_pred cCcHHHHHHHcCCChhHHH----HHHHHcCCCCCCchhhhcH
Q 036926 8 YMPITKAAKELNVGLTLLK----KRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LK----r~CR~lGI~RWP~RKlkSL 45 (168)
+++.+|+|.+|++|.++++ |+..++|+.-=|---++.|
T Consensus 179 G~SNKEIAekL~LS~KTVSTYKnRLLeKLgAkN~~~~~~~~~ 220 (251)
T PRK15320 179 GHPAIELAKKFGLGTKTVSIYRKKVMYRLGMDSSPLSLFRGL 220 (251)
T ss_pred CCCHHHHHHHhccchhhHHHHHHHHHHHcCCCCCchHHHccc
Confidence 6789999999999987665 5566888888776544444
No 338
>PF12342 DUF3640: Protein of unknown function (DUF3640) ; InterPro: IPR022101 This entry defines the N-terminal domain of the polyprotein of GB virus C; its function is not known.
Probab=33.43 E-value=33 Score=20.71 Aligned_cols=15 Identities=27% Similarity=0.818 Sum_probs=12.4
Q ss_pred HHHHHHHHcCCCCCC
Q 036926 24 LLKKRCRELNIRRWP 38 (168)
Q Consensus 24 ~LKr~CR~lGI~RWP 38 (168)
..-+.||++.++.|-
T Consensus 4 Ltnr~crrvdkdqwG 18 (26)
T PF12342_consen 4 LTNRMCRRVDKDQWG 18 (26)
T ss_pred HHHHHHhhhcccccC
Confidence 446899999999993
No 339
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=33.40 E-value=44 Score=27.62 Aligned_cols=27 Identities=15% Similarity=0.073 Sum_probs=20.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
+..+..||++|||+.+++-+.-+ ++|+
T Consensus 18 ~gs~s~AA~~L~isqpavS~~I~~LE~~lg~ 48 (296)
T PRK11062 18 EGSVVGAAEALFLTPQTITGQIKALEERLQG 48 (296)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHHHHHHcCc
Confidence 45678999999999987765544 5564
No 340
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=33.29 E-value=46 Score=30.17 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=23.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
.+++.|||+.|||+..+|++.-.+.++
T Consensus 39 ~f~~~eaA~l~gvs~~~lr~~~~~g~~ 65 (387)
T PHA02519 39 RWGITEVADLIGVTPQAIRDAEKSGRL 65 (387)
T ss_pred CcCHHHHHHHhCcCHHHHHHHHHcCCC
Confidence 467999999999999999999776665
No 341
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=33.26 E-value=38 Score=26.95 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=19.6
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+-.+..||+.|||+.+++-+. =.++|+
T Consensus 11 ~gs~~~AA~~L~isqsavS~~i~~LE~~lg~ 41 (279)
T TIGR03339 11 CGSFTRAAERLGLSQPTVTDQVRKLEERYGV 41 (279)
T ss_pred cCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 346789999999998776544 345664
No 342
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=33.21 E-value=40 Score=29.13 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=24.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RW 37 (168)
..+..+.|++||||.+++.+..+.|-=..|
T Consensus 18 ~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 18 FHSGEQLGEELGISRAAIWKHIQTLEEWGL 47 (319)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 467889999999999999988876654444
No 343
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=33.19 E-value=35 Score=27.81 Aligned_cols=26 Identities=23% Similarity=0.372 Sum_probs=19.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
-.+..||+.||||.+++-|.-+ ++|+
T Consensus 16 gs~s~AA~~L~isQ~avSr~i~~LE~~lg~ 45 (296)
T PRK09906 16 LNFTKAAEKLHTAQPSLSQQIKDLENCVGV 45 (296)
T ss_pred CCHHHHHHHhCCCCcHHHHHHHHHHHHhCC
Confidence 4678999999999877655444 4565
No 344
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=33.14 E-value=48 Score=24.48 Aligned_cols=26 Identities=19% Similarity=0.277 Sum_probs=20.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.++..+.|+.+|++.+.+.++-+.|-
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~ 50 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLR 50 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 36788889999999888888876553
No 345
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=32.94 E-value=41 Score=27.55 Aligned_cols=27 Identities=15% Similarity=0.113 Sum_probs=19.7
Q ss_pred cCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKK----RCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr----~CR~lGI 34 (168)
+-.+..||++||||.+++-+ +=.++|+
T Consensus 15 ~gs~s~AA~~L~isqpavS~~I~~LE~~lG~ 45 (275)
T PRK03601 15 TRHFGRAAESLYLTQSAVSFRIRQLENQLGV 45 (275)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 45678999999999877644 4445675
No 346
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=32.90 E-value=46 Score=27.26 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=20.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
+-.+..||++|||+.+++-+.-+ ++|+
T Consensus 16 ~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (301)
T PRK14997 16 EGGFAAAGRALDEPKSKLSRRIAQLEERLGV 46 (301)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 55788999999999987655544 5675
No 347
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=32.67 E-value=42 Score=28.03 Aligned_cols=27 Identities=22% Similarity=0.183 Sum_probs=19.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
+-.+..||+.|||+.+++-+.- .++|+
T Consensus 36 ~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 66 (314)
T PRK09508 36 EQNITRAAHNLGMSQPAVSNAVARLKVMFND 66 (314)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHhhCC
Confidence 3457899999999987765544 45665
No 348
>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=32.61 E-value=40 Score=22.92 Aligned_cols=21 Identities=24% Similarity=0.224 Sum_probs=15.7
Q ss_pred HHHHcCCChhHHHHHHHHcCC
Q 036926 14 AAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 14 AAr~LgVs~T~LKr~CR~lGI 34 (168)
-|++|||+...|+..-++.|=
T Consensus 26 wa~~~gvt~~~L~~AV~~vG~ 46 (57)
T PF12244_consen 26 WAKRFGVTEEQLREAVRAVGN 46 (57)
T ss_pred HHHHHCcCHHHHHHHHHHHCc
Confidence 467788888888877777773
No 349
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=32.59 E-value=46 Score=26.96 Aligned_cols=25 Identities=12% Similarity=0.254 Sum_probs=22.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.+.+.|+.|||+.+++.+...+|
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4789999999999999999998876
No 350
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=32.50 E-value=38 Score=28.42 Aligned_cols=26 Identities=23% Similarity=0.249 Sum_probs=19.9
Q ss_pred CcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
..+..||++||||.+++-+.- .++|.
T Consensus 17 ~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~ 46 (316)
T PRK12679 17 YNLTEVANMLFTSQSGVSRHIRELEDELGI 46 (316)
T ss_pred CCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 478999999999998765544 45664
No 351
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=32.45 E-value=1.4e+02 Score=23.79 Aligned_cols=25 Identities=40% Similarity=0.435 Sum_probs=18.4
Q ss_pred HHHHHcCCC----hhHHHHHHHHcCCCCCCc
Q 036926 13 KAAKELNVG----LTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 13 eAAr~LgVs----~T~LKr~CR~lGI~RWP~ 39 (168)
.||..+=|+ ++.||+++++-+- ||-
T Consensus 44 ~aAD~~vVsEL~~Ls~LK~~y~~~~~--~~~ 72 (131)
T PF04859_consen 44 QAADEAVVSELRRLSELKRRYRKKQS--DPS 72 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCC--CCC
Confidence 567777776 5889999988765 555
No 352
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=32.38 E-value=42 Score=28.32 Aligned_cols=30 Identities=13% Similarity=0.318 Sum_probs=24.9
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|.+.=.+.+.|.|+.||||..+..|--++|
T Consensus 14 l~~~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 14 LAQLGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred HHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334456889999999999999999888876
No 353
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 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. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=32.27 E-value=58 Score=20.11 Aligned_cols=24 Identities=13% Similarity=0.070 Sum_probs=16.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
.|.-.|.|..||+++-++-|.-.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHH
Confidence 366789999999998777666544
No 354
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=32.26 E-value=38 Score=26.07 Aligned_cols=28 Identities=18% Similarity=0.222 Sum_probs=21.1
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
.--||+..+-+.+|+++||.. ..++..|
T Consensus 19 ~i~GIG~~~a~~i~~~lgi~~--~~~~~~L 46 (113)
T TIGR03631 19 YIYGIGRTRARKILEKAGIDP--DKRVKDL 46 (113)
T ss_pred eeecccHHHHHHHHHHhCcCc--ccccccC
Confidence 346999999999999999964 3444444
No 355
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=32.21 E-value=48 Score=26.90 Aligned_cols=26 Identities=15% Similarity=0.199 Sum_probs=20.1
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.++.++.|..||+++.+|-|..+++
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L 203 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQL 203 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45678999999999998887755443
No 356
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.15 E-value=42 Score=24.17 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=19.2
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
-+.|+|+.||++.-+++|..+..
T Consensus 18 nqtEvaR~l~c~R~TVrKY~~D~ 40 (64)
T PF06322_consen 18 NQTEVARRLGCNRATVRKYSRDK 40 (64)
T ss_pred cHHHHHHHhcccHHHHHHHhccc
Confidence 46899999999999998877643
No 357
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=31.94 E-value=53 Score=25.03 Aligned_cols=26 Identities=8% Similarity=0.115 Sum_probs=20.9
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.++..+.|..||++..++-|.-+++
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l 167 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDL 167 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHH
Confidence 56789999999999998887665554
No 358
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=31.93 E-value=50 Score=24.10 Aligned_cols=26 Identities=19% Similarity=0.078 Sum_probs=18.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
.+++.++|+.+|++.+++-+...++=
T Consensus 42 ~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 42 SMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred CcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 46677888888888777766665544
No 359
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=31.39 E-value=53 Score=20.64 Aligned_cols=23 Identities=13% Similarity=0.307 Sum_probs=17.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
.+...|.|+.||++.+++.+--+
T Consensus 15 ~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 15 PLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCchhhHHHhccccchHHHHHHH
Confidence 45688999999999998876544
No 360
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=31.38 E-value=46 Score=24.19 Aligned_cols=25 Identities=20% Similarity=0.131 Sum_probs=18.9
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.-.+.|+.+|+.+..+.++|..|
T Consensus 27 ~l~de~la~~~~l~~~~vRkiL~~L 51 (105)
T PF02002_consen 27 ELTDEDLAKKLGLKPKEVRKILYKL 51 (105)
T ss_dssp -B-HHHHHHTT-S-HHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5778899999999999999999865
No 361
>cd00283 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing sit
Probab=31.23 E-value=36 Score=26.10 Aligned_cols=19 Identities=32% Similarity=0.279 Sum_probs=16.7
Q ss_pred cHHHHHHHcCCChhHHHHH
Q 036926 10 PITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~ 28 (168)
.+.|||+.||++..++.++
T Consensus 82 S~~EAar~lgi~~~tIs~~ 100 (113)
T cd00283 82 STTEAARFLKVHSGTISKN 100 (113)
T ss_pred CHHHHHHHHCCCcchhHHH
Confidence 5889999999998888776
No 362
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=31.10 E-value=44 Score=27.54 Aligned_cols=27 Identities=22% Similarity=0.235 Sum_probs=19.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
+-.+..||++|||+.+++-+.- ..+|.
T Consensus 15 ~gS~s~AA~~L~itQpavS~~i~~LE~~lg~ 45 (305)
T PRK11151 15 HRHFRRAADSCHVSQPTLSGQIRKLEDELGV 45 (305)
T ss_pred hCCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 3468899999999987765444 45564
No 363
>PRK10632 transcriptional regulator; Provisional
Probab=31.08 E-value=51 Score=27.50 Aligned_cols=27 Identities=22% Similarity=0.427 Sum_probs=20.4
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+..+..||++||||.+++-+. =.++|+
T Consensus 16 ~gS~t~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK10632 16 FGSFTAAARQLQMSVSSISQTVSKLEDELQV 46 (309)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 567899999999999776544 445675
No 364
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=30.96 E-value=45 Score=27.94 Aligned_cols=27 Identities=19% Similarity=0.132 Sum_probs=19.9
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+-.+..||++||||.+++-+. =.++|+
T Consensus 16 ~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 46 (308)
T PRK10094 16 TGSFSKAAERLCKTTATISYRIKLLEENTGV 46 (308)
T ss_pred hCCHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 456789999999998776544 445664
No 365
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=30.83 E-value=47 Score=27.63 Aligned_cols=27 Identities=30% Similarity=0.374 Sum_probs=20.5
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
+-.+..||+.||||.+++-+.-+ ++|+
T Consensus 22 ~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 52 (302)
T TIGR02036 22 HQSFSLAAEELSLTPSAISHRINQLEEELGI 52 (302)
T ss_pred hCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 34678999999999988766554 5565
No 366
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. 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 sign
Probab=30.66 E-value=51 Score=24.79 Aligned_cols=30 Identities=20% Similarity=0.237 Sum_probs=19.2
Q ss_pred HHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHH
Q 036926 13 KAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQE 54 (168)
Q Consensus 13 eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~ 54 (168)
.+|..+ +....|+..|++|+. +.-|+.++.
T Consensus 13 ~Ia~~~--~~~~wK~faR~lgls----------e~~Id~I~~ 42 (97)
T cd08316 13 DIADVM--TLKDVKKFVRKSGLS----------EPKIDEIKL 42 (97)
T ss_pred HHHHHc--CHHHHHHHHHHcCCC----------HHHHHHHHH
Confidence 455544 445678888888884 555666554
No 367
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=30.51 E-value=54 Score=26.76 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=20.2
Q ss_pred cCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKK----RCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr----~CR~lGI 34 (168)
+..+..||++||||.+++-+ .=.++|+
T Consensus 15 ~~s~t~AA~~L~isQpavS~~I~~LE~~lg~ 45 (292)
T TIGR03298 15 EGSFERAAAALSVTPSAVSQRIKALEERLGQ 45 (292)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 55788999999999877644 4446674
No 368
>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=30.50 E-value=66 Score=23.62 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=19.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+++..++|.+||+|.+++-|.=+
T Consensus 71 ~~~~~~I~~~l~~S~~t~yr~~~ 93 (100)
T PF07374_consen 71 KLTWEQIAEELNISRRTYYRIHK 93 (100)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 67889999999999988776543
No 369
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=30.27 E-value=52 Score=27.39 Aligned_cols=31 Identities=6% Similarity=0.086 Sum_probs=25.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc---C-CCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL---N-IRRWP 38 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l---G-I~RWP 38 (168)
.+...|+|+.||++.+++-|+++.| | +.+.|
T Consensus 28 ~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~ 62 (257)
T PRK15090 28 EIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEG 62 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 4779999999999999999999754 5 44555
No 370
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=30.09 E-value=48 Score=32.60 Aligned_cols=32 Identities=22% Similarity=0.346 Sum_probs=24.7
Q ss_pred HHHHcCCC------hhHHHHHHHHcCCCCCCc--hhhhcH
Q 036926 14 AAKELNVG------LTLLKKRCRELNIRRWPH--RKLMSL 45 (168)
Q Consensus 14 AAr~LgVs------~T~LKr~CR~lGI~RWP~--RKlkSL 45 (168)
|+++||.. ..+|+|+||=.|++=|=| +.++|-
T Consensus 10 a~eEmg~p~~~~P~~~~lrrlC~G~~~~IWkfli~~V~s~ 49 (632)
T PF14817_consen 10 AQEEMGYPPASLPSDDYLRRLCRGNMAPIWKFLIQHVRSQ 49 (632)
T ss_pred HHHHhCCCCCCCCCHHHHHHHhccCChHHHHHHHHHcCcH
Confidence 56677776 579999999999999987 344443
No 371
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=29.91 E-value=42 Score=27.15 Aligned_cols=26 Identities=23% Similarity=0.282 Sum_probs=19.0
Q ss_pred CcHHHHHHHcCCChhHHH----HHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLK----KRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LK----r~CR~lGI 34 (168)
-.+..||+.|||+.+++- ++=+++|.
T Consensus 22 gs~t~AA~~L~itq~avS~~i~~LE~~lg~ 51 (294)
T PRK09986 22 LHFGRAAARLNISQPPLSIHIKELEDQLGT 51 (294)
T ss_pred cCHHHHHHHhCCCCCHHHHHHHHHHHHhCC
Confidence 467899999999986654 44456673
No 372
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=29.88 E-value=96 Score=28.75 Aligned_cols=65 Identities=26% Similarity=0.422 Sum_probs=39.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----------------HcCCCCCCchhhhc----------HHHHHHHHHHHhhcCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----------------ELNIRRWPHRKLMS----------LQTLIKNVQELQTEGEG 61 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----------------~lGI~RWP~RKlkS----------L~~li~~l~~~~~~g~~ 61 (168)
.+-+++||..|+|. |||-. ++.| ||=-.-..+ |..-+..|+.
T Consensus 91 vldLn~aA~~L~Vq----KRRIYDITNVLEGI~LIeKksKN~I-qW~G~~~~~~~~~~e~~~~l~~e~~~L~~------- 158 (354)
T KOG2577|consen 91 VLDLNKAAEVLNVQ----KRRIYDITNVLEGIGLIEKKSKNNI-QWIGGDFNSTGGVPERLNGLEAEVEDLSQ------- 158 (354)
T ss_pred eeeHHHHHHHhccc----cceeeehhhhhhcccceeeccccce-eeecCCCccccccHHHHHHHHHHHHHHHH-------
Confidence 46789999999998 44332 4556 787666655 2222222221
Q ss_pred CHHHHHHHHHHHHHHHHHHhhCC
Q 036926 62 SEERLREALGILERERKLIEERP 84 (168)
Q Consensus 62 s~~~l~~ai~~Lerek~lIee~P 84 (168)
.++.+...|..+.+..+.+.+++
T Consensus 159 ~E~~LD~~i~~~q~~L~~lted~ 181 (354)
T KOG2577|consen 159 EEDDLDQLIRDCQQNLRLLTEDV 181 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHhcch
Confidence 23456666777777777777655
No 373
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=29.83 E-value=48 Score=26.89 Aligned_cols=27 Identities=26% Similarity=0.284 Sum_probs=19.5
Q ss_pred cCcHHHHHHHcCCChhHH----HHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLL----KKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~L----Kr~CR~lGI 34 (168)
+-.+..||++|||+.+++ |++=+++|+
T Consensus 15 ~gs~s~AA~~L~isqsavS~~i~~LE~~lg~ 45 (296)
T PRK11242 15 HGNFTRAAEALHVSQPTLSQQIRQLEESLGV 45 (296)
T ss_pred hCCHHHHHHHcCCCchHHHHHHHHHHHHhCC
Confidence 346789999999998654 555556664
No 374
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=29.79 E-value=2.2e+02 Score=20.66 Aligned_cols=64 Identities=17% Similarity=0.128 Sum_probs=32.4
Q ss_pred CCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHhhCCCCCCcHHHHHHHHH
Q 036926 19 NVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEERPDLEMEDTTKRLRQA 98 (168)
Q Consensus 19 gVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~lIee~P~~~L~~~tKrlRQa 98 (168)
.|....-|+..|++|+. +..|+.+++... ... +...++|..=+ .-.-.+...+..-++.||++
T Consensus 8 ~v~~~~wk~~~R~LGls----------e~~Id~ie~~~~---~~~---Eq~yqmL~~W~-~~~g~~~At~~~L~~aLr~~ 70 (80)
T cd08313 8 EVPPRRWKEFVRRLGLS----------DNEIERVELDHR---RCR---DAQYQMLKVWK-ERGPRPYATLQHLLSVLRDM 70 (80)
T ss_pred hCCHHHHHHHHHHcCCC----------HHHHHHHHHhCC---ChH---HHHHHHHHHHH-HhcCCCcchHHHHHHHHHHc
Confidence 35566678888888874 455666554211 111 12233333222 11111356666667777765
Q ss_pred H
Q 036926 99 C 99 (168)
Q Consensus 99 ~ 99 (168)
.
T Consensus 71 ~ 71 (80)
T cd08313 71 E 71 (80)
T ss_pred C
Confidence 4
No 375
>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=29.47 E-value=64 Score=21.74 Aligned_cols=23 Identities=13% Similarity=0.176 Sum_probs=17.7
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
...|+|+.|||++..+..+....
T Consensus 22 t~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHHhC
Confidence 46789999999998888877654
No 376
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=29.45 E-value=55 Score=26.55 Aligned_cols=26 Identities=27% Similarity=0.212 Sum_probs=24.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+-+.|+|+.|||+.+.|-..-|++|+
T Consensus 48 i~~re~AK~lkige~~l~~~L~e~~~ 73 (135)
T COG3645 48 ILFRELAKLLKIGENRLFAWLRENKY 73 (135)
T ss_pred eeHHHHHHHHccCHHHHHHHHHHCCE
Confidence 56899999999999999999999995
No 377
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=29.38 E-value=51 Score=27.22 Aligned_cols=27 Identities=19% Similarity=0.057 Sum_probs=19.6
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+-.+..||+.|||+.+++-+. =.++|+
T Consensus 16 ~~s~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (300)
T PRK11074 16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAV 46 (300)
T ss_pred hCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 346789999999999876544 445564
No 378
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=29.30 E-value=49 Score=26.16 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=19.6
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+-.+..||++||||.+.+-+. =.++|+
T Consensus 15 ~~s~t~AA~~L~isqsavS~~I~~LE~~lg~ 45 (297)
T COG0583 15 EGSFTRAAERLGLSQSAVSRQIKRLEEELGV 45 (297)
T ss_pred cCcHHHHHHHhCCCChHHHHHHHHHHHHhCc
Confidence 346789999999998775444 345675
No 379
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=29.26 E-value=52 Score=25.43 Aligned_cols=34 Identities=21% Similarity=0.091 Sum_probs=19.7
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHH
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNV 52 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l 52 (168)
|-+.++.++|++.|||..+| |+..+|-+.++..+
T Consensus 26 ~~~~s~~~IA~~agvs~~~l-------------Y~hF~sKe~L~~av 59 (202)
T TIGR03613 26 FHGTSLEQIAELAGVSKTNL-------------LYYFPSKDALYLAV 59 (202)
T ss_pred cccCCHHHHHHHhCCCHHHH-------------HHHcCCHHHHHHHH
Confidence 44566666666666666665 44555555555444
No 380
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=29.07 E-value=45 Score=25.98 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=21.5
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
.-.|||.++=+.+|+++||.. ..++..|
T Consensus 21 ~I~GIG~~~a~~i~~~lgi~~--~~~~~~L 48 (122)
T PRK05179 21 YIYGIGRTRAKEILAAAGIDP--DTRVKDL 48 (122)
T ss_pred ccccccHHHHHHHHHHhCcCc--ccccccC
Confidence 457999999999999999953 4444444
No 381
>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=28.99 E-value=77 Score=23.21 Aligned_cols=30 Identities=17% Similarity=0.171 Sum_probs=21.0
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|+...+.--.+.|++||||.+.+-++.-++
T Consensus 10 Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~ 39 (84)
T cd08805 10 IREHLGLSWAELARELQFSVEDINRIRVEN 39 (84)
T ss_pred HHHHhcchHHHHHHHcCCCHHHHHHHHHhC
Confidence 455556666777888888888777776665
No 382
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=28.96 E-value=52 Score=27.49 Aligned_cols=28 Identities=29% Similarity=0.179 Sum_probs=20.7
Q ss_pred cCcHHHHHHHcCCChhHH----HHHHHHcCCC
Q 036926 8 YMPITKAAKELNVGLTLL----KKRCRELNIR 35 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~L----Kr~CR~lGI~ 35 (168)
+-.+..||+.||||.+++ |++=+++|++
T Consensus 22 ~gs~t~AA~~L~iSQpavS~~I~~LE~~lg~~ 53 (319)
T PRK10216 22 ERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDP 53 (319)
T ss_pred hCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Confidence 456889999999998765 4555567753
No 383
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=28.89 E-value=49 Score=25.85 Aligned_cols=28 Identities=29% Similarity=0.323 Sum_probs=22.2
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
.-.|||.++-+.+|+++||. |..++..|
T Consensus 21 ~i~GIG~~~A~~ic~~lgi~--~~~~~~~L 48 (122)
T CHL00137 21 YIYGIGLTSAKEILEKANID--PDIRTKDL 48 (122)
T ss_pred ccccccHHHHHHHHHHcCcC--cCcCcccC
Confidence 45799999999999999995 45555554
No 384
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=28.87 E-value=63 Score=24.95 Aligned_cols=30 Identities=27% Similarity=0.308 Sum_probs=25.4
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+|-.=-+..||.-|||-..+|.|.-.++|.
T Consensus 68 ~~~~gNQtrAa~mLGinR~TLRKKLkqygl 97 (98)
T COG2901 68 QYTRGNQTRAALMLGINRGTLRKKLKKYGL 97 (98)
T ss_pred HHhcccHHHHHHHHcccHHHHHHHHHHhCC
Confidence 444456788999999999999999999986
No 385
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=28.86 E-value=64 Score=27.71 Aligned_cols=24 Identities=17% Similarity=0.073 Sum_probs=20.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
++..+|+|+.||||..+++...++
T Consensus 148 GkTnKEIAe~L~IS~rTVkth~sr 171 (198)
T PRK15201 148 GYHLSETAALLSLSEEQTKSLRRS 171 (198)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 678899999999999999876543
No 386
>PRK09801 transcriptional activator TtdR; Provisional
Probab=28.84 E-value=52 Score=27.66 Aligned_cols=27 Identities=22% Similarity=0.193 Sum_probs=20.1
Q ss_pred cCcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
.-.+..||+.||||.+++-+.- .++|+
T Consensus 20 ~gs~t~AA~~L~iSQpavS~~I~~LE~~LG~ 50 (310)
T PRK09801 20 SGSFSAAAATLGQTPAFVTKRIQILENTLAT 50 (310)
T ss_pred cCCHHHHHHHhCcCHHHHHHHHHHHHHHhCC
Confidence 3467899999999998765544 46775
No 387
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=28.84 E-value=46 Score=28.15 Aligned_cols=30 Identities=13% Similarity=0.064 Sum_probs=23.9
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|.+.=.+.+.|.|+.||||..|+.|-..+|
T Consensus 14 L~~~~~v~v~eLa~~l~VS~~TIRRDL~~L 43 (256)
T PRK10434 14 LQKQGKTSVEELAQYFDTTGTTIRKDLVIL 43 (256)
T ss_pred HHHcCCEEHHHHHHHHCCCHHHHHHHHHHH
Confidence 334445789999999999999998877754
No 388
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=28.59 E-value=47 Score=27.49 Aligned_cols=27 Identities=26% Similarity=0.304 Sum_probs=20.2
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI 34 (168)
+-.+..||++||||.+++-+.-+ ++|.
T Consensus 19 ~gs~s~AA~~L~isqpavS~~i~~LE~~lg~ 49 (305)
T CHL00180 19 EGSFKKAAESLYISQPAVSLQIKNLEKQLNI 49 (305)
T ss_pred cCCHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 45678999999999887665544 5564
No 389
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=28.32 E-value=78 Score=21.37 Aligned_cols=25 Identities=20% Similarity=0.134 Sum_probs=22.1
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 10 PITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
=|...|+++|+|....-++..+.|+
T Consensus 7 ~Ie~~A~~~~~s~~ea~~~~~~~~~ 31 (62)
T PF12668_consen 7 CIEEFAKKLNISGEEAYNYFKRSGV 31 (62)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHcCc
Confidence 4678999999999999999999987
No 390
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=28.27 E-value=60 Score=27.57 Aligned_cols=40 Identities=20% Similarity=0.143 Sum_probs=29.2
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHH----HcCCCCCCchhhhc
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCR----ELNIRRWPHRKLMS 44 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR----~lGI~RWP~RKlkS 44 (168)
.-+++++.++|++||.+..+.++.-+ ..|+.+=-|++++.
T Consensus 58 ekag~Ti~EIAeelG~TeqTir~hlkgetkAG~lv~etY~~lK~ 101 (182)
T COG1318 58 EKAGMTISEIAEELGRTEQTVRNHLKGETKAGQLVRETYEKLKE 101 (182)
T ss_pred HHccCcHHHHHHHhCCCHHHHHHHHhcchhhhhHHHHHHHHHHc
Confidence 45789999999999999998888766 23344444555544
No 391
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=28.23 E-value=53 Score=27.78 Aligned_cols=23 Identities=26% Similarity=0.234 Sum_probs=18.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+-.+..||++|||+.+++-+.-+
T Consensus 43 ~gs~s~AA~~L~isQpavS~~I~ 65 (317)
T PRK11482 43 HKGIVNAAKILNLTPSAISQSIQ 65 (317)
T ss_pred cCCHHHHHHHhCCChHHHHHHHH
Confidence 44678999999999988766555
No 392
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=28.15 E-value=1.5e+02 Score=29.71 Aligned_cols=38 Identities=21% Similarity=0.284 Sum_probs=28.8
Q ss_pred HHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHH
Q 036926 12 TKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQEL 55 (168)
Q Consensus 12 ~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~ 55 (168)
-++|+.+|+...++.+.-.-++- .-..++.+|..|++.
T Consensus 491 ~~iA~~~Glp~~ii~~A~~~~~~------~~~~~~~li~~l~~~ 528 (782)
T PRK00409 491 FEIAKRLGLPENIIEEAKKLIGE------DKEKLNELIASLEEL 528 (782)
T ss_pred HHHHHHhCcCHHHHHHHHHHHhh------hhhHHHHHHHHHHHH
Confidence 47899999999999988887763 334667777777654
No 393
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=28.08 E-value=50 Score=27.71 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=20.4
Q ss_pred Cc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
|| -.|.|..||||.|+|.-.-+.|
T Consensus 34 LP~EreLae~fgVSR~~vREAl~~L 58 (241)
T COG2186 34 LPSERELAERFGVSRTVVREALKRL 58 (241)
T ss_pred CCCHHHHHHHHCCCcHHHHHHHHHH
Confidence 55 7899999999999999887754
No 394
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=28.03 E-value=83 Score=21.97 Aligned_cols=33 Identities=9% Similarity=0.111 Sum_probs=25.3
Q ss_pred hhhhhccCcHHHHHHHc-----CCChhHHHHHHHHcCC
Q 036926 2 TISQYFYMPITKAAKEL-----NVGLTLLKKRCRELNI 34 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~L-----gVs~T~LKr~CR~lGI 34 (168)
++++.+++++..+++-+ ++|..+|-+.+..+|.
T Consensus 36 e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~ 73 (80)
T PF13744_consen 36 ELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGG 73 (80)
T ss_dssp HHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTE
T ss_pred HHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCC
Confidence 57788899999999888 6788888888888884
No 395
>PRK04140 hypothetical protein; Provisional
Probab=27.97 E-value=59 Score=29.26 Aligned_cols=29 Identities=17% Similarity=0.151 Sum_probs=24.5
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+++.-.++.+.+.|+.+|||.+++-++-+
T Consensus 133 ~lRe~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 133 EAREELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 35667899999999999999999887755
No 396
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=27.95 E-value=67 Score=27.84 Aligned_cols=29 Identities=14% Similarity=-0.057 Sum_probs=23.4
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHH
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~ 31 (168)
++.--+|++.+.|+.+|||.+++.++.+-
T Consensus 36 ~R~~~gltq~~lA~~~gvs~~~i~~~E~g 64 (309)
T PRK08154 36 LRARRGMSRKVLAQASGVSERYLAQLESG 64 (309)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 55667899999999999998877666543
No 397
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=27.91 E-value=55 Score=25.90 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=17.9
Q ss_pred hhhhhccCcHHHHHHHcC--CChhHHHH
Q 036926 2 TISQYFYMPITKAAKELN--VGLTLLKK 27 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~Lg--Vs~T~LKr 27 (168)
.|++.|.|.+.|||..+| |+..+-.+
T Consensus 8 alR~~l~lt~~EaA~~Ia~~v~~~tWq~ 35 (118)
T PF08965_consen 8 ALRQILGLTVEEAAYYIAQDVSSRTWQQ 35 (118)
T ss_dssp HHHHHTT--HHHHHHHTSSS--HHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHccCCHHHHHH
Confidence 478999999999999999 76655443
No 398
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=27.87 E-value=66 Score=24.86 Aligned_cols=39 Identities=15% Similarity=0.017 Sum_probs=27.8
Q ss_pred ccCcHHHHHHHcCCChhHHHHHHH---HcCCCCCCchhhhcH
Q 036926 7 FYMPITKAAKELNVGLTLLKKRCR---ELNIRRWPHRKLMSL 45 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~CR---~lGI~RWP~RKlkSL 45 (168)
+.++..+.|..||++..++-|.-+ +-|+-..-+++|.=+
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 467899999999999876655444 446656666766533
No 399
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.81 E-value=50 Score=23.70 Aligned_cols=30 Identities=17% Similarity=0.186 Sum_probs=19.6
Q ss_pred hHHHHHHHHcCCCCCCchhhhcHHHHHHHHH
Q 036926 23 TLLKKRCRELNIRRWPHRKLMSLQTLIKNVQ 53 (168)
Q Consensus 23 T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~ 53 (168)
-.+|+.|++.|||=|+.+. .++..+...|+
T Consensus 65 ~~vk~~akk~~ip~~~~~~-~~~~~l~~~l~ 94 (97)
T PF10087_consen 65 WKVKKAAKKYGIPIIYSRS-RGVSSLERALE 94 (97)
T ss_pred HHHHHHHHHcCCcEEEECC-CCHHHHHHHHH
Confidence 3579999999998887762 23334444333
No 400
>PF12792 CSS-motif: CSS motif domain associated with EAL ; InterPro: IPR024744 This domain, with its characteristic highly conserved CSS sequence motif, is found N-terminal to the EAL domain (PF00563 from PFAM), found in many putative cyclic diguanylate phosphodiesterases.
Probab=27.67 E-value=1.9e+02 Score=22.02 Aligned_cols=58 Identities=16% Similarity=0.126 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCCcHH-HHHHHHHHHHHhhhhhhhccccCCCcccccCCC
Q 036926 65 RLREALGILERERKLIEERPDLEMEDT-TKRLRQACFKANYKKRKFMGTMMGPMVSTSSCS 124 (168)
Q Consensus 65 ~l~~ai~~Lerek~lIee~P~~~L~~~-tKrlRQa~FK~~yk~Rr~~~~~~~~~~~~~~~~ 124 (168)
+++.++.........+......++++. +..||+..|...|=+== +.-..+.+--||..
T Consensus 17 ~~e~~~~~~~~~~~~~~~~~~~~Cs~~~~~~Lr~~~~~~~~ir~i--~~~~~g~i~CSS~~ 75 (208)
T PF12792_consen 17 RIESVLDQARQALDALLPLTGQPCSPAHLNALRQIVARSPYIRDI--GLVRNGRIYCSSLW 75 (208)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhchhhhhe--eEEeCCeEEecCCC
Confidence 455566666667777777778899999 99999999999887543 33344444444444
No 401
>PRK07914 hypothetical protein; Reviewed
Probab=27.57 E-value=2.8e+02 Score=23.87 Aligned_cols=49 Identities=14% Similarity=0.201 Sum_probs=30.7
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHhhcCC
Q 036926 10 PITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGE 60 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~~~g~ 60 (168)
+..++|+.+||.+-..|+..+ ...||+-.++..+-..+..+....+.|.
T Consensus 251 ~~~~i~~~l~i~p~~~~~~~~--~~~~~s~~~L~~~l~~l~~~D~~lK~~~ 299 (320)
T PRK07914 251 DPYRLAGELGMPPWRVQKAQK--QARRWSRDTVATAMRVVAALNADVKGAA 299 (320)
T ss_pred CHHHHHHHcCCCHHHHHHHHH--HHcCCCHHHHHHHHHHHHHHHHHhhcCC
Confidence 667777777777655555533 3457777777666666666655555443
No 402
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=27.29 E-value=61 Score=28.63 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=22.2
Q ss_pred hccCc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 6 YFYMP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 6 yF~lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
-..|| +.+.|+.||||.+++.+.-.+|
T Consensus 26 g~~lps~r~la~~~~vsr~tv~~a~~~L 53 (431)
T PRK15481 26 GDSLPPVRELASELGVNRNTVAAAYKRL 53 (431)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34675 7899999999999999886654
No 403
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=27.02 E-value=60 Score=26.62 Aligned_cols=27 Identities=30% Similarity=0.311 Sum_probs=20.1
Q ss_pred CcHHHHHHHcCCChhHH----HHHHHHcCCC
Q 036926 9 MPITKAAKELNVGLTLL----KKRCRELNIR 35 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~L----Kr~CR~lGI~ 35 (168)
-.+..||+.|||+.+++ |++=.++|++
T Consensus 21 gs~s~AA~~L~isq~avS~~i~~LE~~lg~~ 51 (297)
T PRK11139 21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLK 51 (297)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCch
Confidence 46789999999998765 4455567754
No 404
>PRK11569 transcriptional repressor IclR; Provisional
Probab=26.88 E-value=61 Score=27.40 Aligned_cols=24 Identities=8% Similarity=0.144 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+.+.|+|+.||++.+++-|++..|
T Consensus 44 ~~lseia~~lglpksTv~RlL~tL 67 (274)
T PRK11569 44 VALTELAQQAGLPNSTTHRLLTTM 67 (274)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 789999999999999999999853
No 405
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=26.33 E-value=63 Score=27.35 Aligned_cols=27 Identities=19% Similarity=0.193 Sum_probs=20.0
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+-.+..||++||||.+++-+. =.++|+
T Consensus 16 ~gs~s~AA~~L~iSqpaVS~~Ik~LE~~lg~ 46 (317)
T PRK15421 16 CGSLAAAAATLHQTQSALSHQFSDLEQRLGF 46 (317)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 446889999999998776544 446664
No 406
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. 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. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=26.30 E-value=90 Score=22.05 Aligned_cols=21 Identities=19% Similarity=0.294 Sum_probs=10.8
Q ss_pred HHHHHHHcCCChhHHHHHHHHcCC
Q 036926 11 ITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+..+|+.|| +.-|++.|+||+
T Consensus 7 l~~ia~~lG---~dW~~LAr~Lg~ 27 (84)
T cd08317 7 LADISNLLG---SDWPQLARELGV 27 (84)
T ss_pred HHHHHHHHh---hHHHHHHHHcCC
Confidence 444555554 444555555554
No 407
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=26.29 E-value=68 Score=25.32 Aligned_cols=24 Identities=25% Similarity=0.202 Sum_probs=20.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+++.+.|+.+||+...|.|+...|
T Consensus 25 ~s~~eIA~~~~is~~~L~kIl~~L 48 (153)
T PRK11920 25 SRIPEIARAYGVSELFLFKILQPL 48 (153)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHH
Confidence 578999999999999999887654
No 408
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=26.25 E-value=60 Score=24.27 Aligned_cols=29 Identities=31% Similarity=0.564 Sum_probs=22.3
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcHH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSLQ 46 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~ 46 (168)
+--||+.+.=+.+|.++||. |..++..|.
T Consensus 19 ~IyGIG~~~A~~Ic~~lgi~--~~~~~~~Ls 47 (107)
T PF00416_consen 19 KIYGIGRRKAKQICKKLGIN--PNKKVGDLS 47 (107)
T ss_dssp TSTTBCHHHHHHHHHHTTS---SSSBTTTST
T ss_pred hhhccCHHHHHHHHHHcCCC--hhhhcccCC
Confidence 44799999999999999995 555665553
No 409
>PRK14999 histidine utilization repressor; Provisional
Probab=26.23 E-value=66 Score=26.38 Aligned_cols=23 Identities=13% Similarity=0.190 Sum_probs=19.6
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+..+.|+++|||.+|+++.-..|
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L 60 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALREL 60 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 47899999999999999987644
No 410
>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=26.22 E-value=82 Score=23.37 Aligned_cols=28 Identities=7% Similarity=0.165 Sum_probs=19.3
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHcC
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCRELN 33 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~lG 33 (168)
|=+..+.+.|++.|+|...+.+++++.+
T Consensus 70 f~G~n~~eLA~kyglS~r~I~~Ii~~~~ 97 (108)
T PF08765_consen 70 FNGMNVRELARKYGLSERQIYRIIKRVR 97 (108)
T ss_dssp --SS-HHHHHHHHT--HHHHHHHHHHHH
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3467888999999999988888888765
No 411
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR 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 Gram-positive lineages and does not include the TreR from E. coli.
Probab=26.21 E-value=67 Score=26.05 Aligned_cols=22 Identities=9% Similarity=0.046 Sum_probs=18.9
Q ss_pred HHHHHHHcCCChhHHHHHHHHc
Q 036926 11 ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 11 i~eAAr~LgVs~T~LKr~CR~l 32 (168)
..|.|.++|||.+|+++.-..|
T Consensus 27 E~eLa~~~gVSR~TVR~Al~~L 48 (233)
T TIGR02404 27 EHELMDQYGASRETVRKALNLL 48 (233)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 6799999999999999876643
No 412
>PF04463 DUF523: Protein of unknown function (DUF523); InterPro: IPR007553 This entry contains uncharacterised bacterial proteins.
Probab=25.96 E-value=30 Score=27.23 Aligned_cols=12 Identities=33% Similarity=0.351 Sum_probs=10.8
Q ss_pred cCCCCCCchhhh
Q 036926 32 LNIRRWPHRKLM 43 (168)
Q Consensus 32 lGI~RWP~RKlk 43 (168)
||+||||.|.+.
T Consensus 45 Lg~PR~p~~~v~ 56 (143)
T PF04463_consen 45 LGVPRPPIRLVG 56 (143)
T ss_pred CCcCCcCeEEee
Confidence 789999999876
No 413
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=25.88 E-value=63 Score=26.61 Aligned_cols=27 Identities=15% Similarity=0.146 Sum_probs=20.8
Q ss_pred cCcHHHHHHHcCCChhHH----HHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLL----KKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~L----Kr~CR~lGI 34 (168)
+..+..||++|||+.+++ |++=.++|+
T Consensus 16 ~gs~s~AA~~L~isq~avS~~I~~LE~~lg~ 46 (294)
T PRK03635 16 EGSFERAAQKLHITQSAVSQRIKALEERVGQ 46 (294)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 456889999999998765 555567785
No 414
>COG3023 ampD N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]
Probab=25.87 E-value=3.2e+02 Score=24.35 Aligned_cols=72 Identities=17% Similarity=0.098 Sum_probs=39.2
Q ss_pred HHHHHHcCCCCCCc----------hhhhcHHHHHHHHHHHhh--cCCCCHHHHHHHHHHHHHHHHHHhhCCCCCCcHHHH
Q 036926 26 KKRCRELNIRRWPH----------RKLMSLQTLIKNVQELQT--EGEGSEERLREALGILERERKLIEERPDLEMEDTTK 93 (168)
Q Consensus 26 Kr~CR~lGI~RWP~----------RKlkSL~~li~~l~~~~~--~g~~s~~~l~~ai~~Lerek~lIee~P~~~L~~~tK 93 (168)
|+++..+||.+||- ++..+...+...|..++= +....++..+.+|..-+..-+. .+||.+.|-+|.
T Consensus 171 k~l~~~~gigaw~~~~~~~~~~~~~~~~~v~~lq~~L~~YGY~v~~~~~d~~t~~vv~aFQ~hfrp--~~~dg~~d~et~ 248 (257)
T COG3023 171 KRLAEALGIGAWLDTAQVQKYLALLKGEDVAALQEMLARYGYGVEIGVFDQETQQVVRAFQMHFRP--GLYDGEADVETI 248 (257)
T ss_pred HHHHhhcCcccCCcHhhhhhhhhhhccCCHHHHHHHHHHhCcCCCcchhhHHHHHHHHHHHHHhCC--CCCCCCCChHHH
Confidence 77888889999982 122333344444444432 1222334444444444444333 577888888877
Q ss_pred HHHHHH
Q 036926 94 RLRQAC 99 (168)
Q Consensus 94 rlRQa~ 99 (168)
..=|+.
T Consensus 249 a~l~al 254 (257)
T COG3023 249 AILQAL 254 (257)
T ss_pred HHHHHH
Confidence 665554
No 415
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.71 E-value=64 Score=24.85 Aligned_cols=28 Identities=21% Similarity=0.134 Sum_probs=22.6
Q ss_pred hhhhhc---cCcHHHHHHHcCCChhHHHHHH
Q 036926 2 TISQYF---YMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 2 ~l~~yF---~lPi~eAAr~LgVs~T~LKr~C 29 (168)
+|+..| .|...++|.+||++.-.|-|+-
T Consensus 14 elqan~el~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 14 ELQANFELCPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred HHHHhhhhccccHHHHHHHhCCCHHHHHHHH
Confidence 455555 5789999999999998888775
No 416
>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=25.69 E-value=1.8e+02 Score=29.46 Aligned_cols=77 Identities=18% Similarity=0.266 Sum_probs=48.1
Q ss_pred hhccCcHHHHHHH-c-----CCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 036926 5 QYFYMPITKAAKE-L-----NVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERK 78 (168)
Q Consensus 5 ~yF~lPi~eAAr~-L-----gVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~ 78 (168)
.++++|+.-+|.+ | ++++..+.+.||++-- +......+.++.++-.++
T Consensus 96 D~~Glpie~~~ek~l~~~~~~~~~~~f~~~c~~~~~--------~~~~~~~~~~~~lG~~~d------------------ 149 (912)
T PRK05743 96 DCHGLPIELKVEKKLGKKGKKLSAAEFRKKCREYAL--------EQVDIQREDFKRLGVLGD------------------ 149 (912)
T ss_pred CCCccHhHHHHHHHcCCccccCCHHHHHHHHHHHHH--------HHHHHHHHHHHHhCCccc------------------
Confidence 3579999999976 5 5666666667755421 111222233333322111
Q ss_pred HHhhCCCCCCcHHHHHHHHHHHHHhhhhhhh
Q 036926 79 LIEERPDLEMEDTTKRLRQACFKANYKKRKF 109 (168)
Q Consensus 79 lIee~P~~~L~~~tKrlRQa~FK~~yk~Rr~ 109 (168)
-.+|...+++...+.=|..|+.-|++--.
T Consensus 150 --w~~~~~T~~~~~~~~v~~~f~~l~~~Gli 178 (912)
T PRK05743 150 --WDNPYLTMDFKYEANIIRALGKMAKKGYL 178 (912)
T ss_pred --CCCCcCCCCHHHHHHHHHHHHHHHHCCCE
Confidence 24678889999999999999988875433
No 417
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=25.68 E-value=59 Score=27.67 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=20.0
Q ss_pred CcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
..+..||++||||.+++-+.- .++|+
T Consensus 17 ~S~s~AA~~L~iSQpavS~~I~~LE~~lG~ 46 (324)
T PRK12681 17 LNVSATAEGLYTSQPGISKQVRMLEDELGI 46 (324)
T ss_pred CCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 378999999999987765544 46775
No 418
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=25.68 E-value=59 Score=27.79 Aligned_cols=26 Identities=31% Similarity=0.299 Sum_probs=20.2
Q ss_pred CcHHHHHHHcCCChhHHHHHH----HHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRC----RELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~C----R~lGI 34 (168)
..+..||+.|||+.+++-+.- .++|+
T Consensus 17 gS~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (327)
T PRK12680 17 LNITLAAARVHATQPGLSKQLKQLEDELGF 46 (327)
T ss_pred CCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 578999999999998765554 46675
No 419
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=25.67 E-value=4.3e+02 Score=22.84 Aligned_cols=15 Identities=20% Similarity=0.096 Sum_probs=7.2
Q ss_pred HHHHHHcCCChhHHH
Q 036926 12 TKAAKELNVGLTLLK 26 (168)
Q Consensus 12 ~eAAr~LgVs~T~LK 26 (168)
.++|..|||+...+-
T Consensus 155 ~~Ia~~Lgis~~df~ 169 (267)
T PRK09430 155 YVIAEELGFSRFQFD 169 (267)
T ss_pred HHHHHHcCCCHHHHH
Confidence 345555555544333
No 420
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. 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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=25.62 E-value=42 Score=31.09 Aligned_cols=26 Identities=12% Similarity=0.266 Sum_probs=22.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
|.++++|.+|||+.||+-|.++.--|
T Consensus 319 LtlkdiA~~lglheSTVSRav~~Kyi 344 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAINNKYL 344 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhcCceE
Confidence 67899999999999999999985443
No 421
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.53 E-value=72 Score=26.13 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=22.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+...+.|..|||+...+.|.+..|
T Consensus 36 ~~tdeeLA~~Lgi~~~~VRk~L~~L 60 (178)
T PRK06266 36 EVTDEEIAEQTGIKLNTVRKILYKL 60 (178)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4678899999999999999999754
No 422
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=25.50 E-value=73 Score=26.29 Aligned_cols=25 Identities=12% Similarity=0.119 Sum_probs=22.3
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+...|+|++||++.+++-|+...|
T Consensus 24 ~~~l~eia~~lglpksT~~RlL~tL 48 (248)
T TIGR02431 24 RLTLTDVAEATGLTRAAARRFLLTL 48 (248)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3789999999999999999999854
No 423
>PRK00215 LexA repressor; Validated
Probab=25.29 E-value=80 Score=25.27 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=20.6
Q ss_pred cCcHHHHHHHcCC-ChhHHHHHHHHcC
Q 036926 8 YMPITKAAKELNV-GLTLLKKRCRELN 33 (168)
Q Consensus 8 ~lPi~eAAr~LgV-s~T~LKr~CR~lG 33 (168)
.+.+.|.|+.+|+ +.+++-++...|-
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 4578899999999 9888877776554
No 424
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=25.23 E-value=1.8e+02 Score=19.00 Aligned_cols=36 Identities=19% Similarity=0.210 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHhh
Q 036926 68 EALGILERERKLIEERPDLEMEDTTKRLRQACFKANY 104 (168)
Q Consensus 68 ~ai~~Lerek~lIee~P~~~L~~~tKrlRQa~FK~~y 104 (168)
+++..|+.=.+.| ++++++|++.++.+.++.--.++
T Consensus 3 e~~~~Le~Iv~~L-e~~~~sLdes~~lyeeg~~l~~~ 38 (53)
T PF02609_consen 3 EAMERLEEIVEKL-ESGELSLDESLKLYEEGMELIKK 38 (53)
T ss_dssp HHHHHHHHHHHHH-HTT-S-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH-HcCCCCHHHHHHHHHHHHHHHHH
Confidence 4455666666665 47888888888888776544433
No 425
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=25.21 E-value=56 Score=20.79 Aligned_cols=33 Identities=27% Similarity=0.343 Sum_probs=19.4
Q ss_pred CChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHH
Q 036926 20 VGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQEL 55 (168)
Q Consensus 20 Vs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~ 55 (168)
.+++-|+.+|+++||+. +.+++. +-+|..+...
T Consensus 5 ~~~~eL~~iAk~lgI~~--~~~~~K-~eLI~~Il~~ 37 (43)
T PF07498_consen 5 MTLSELREIAKELGIEG--YSKMRK-QELIFAILKA 37 (43)
T ss_dssp S-HHHHHHHHHCTT-TT--GCCS-H-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCC--CCcCCH-HHHHHHHHHH
Confidence 56789999999999963 223332 3455555443
No 426
>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=24.92 E-value=97 Score=24.81 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=28.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCCch
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRWPHR 40 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~R 40 (168)
.++.++|.++||+...+++.-|+=.|.-|++-
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~ 78 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQLKHFP 78 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCeeccCCC
Confidence 78899999999999999999999888777654
No 427
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=24.87 E-value=62 Score=26.22 Aligned_cols=28 Identities=21% Similarity=0.159 Sum_probs=21.6
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
.--|||.+.-+.+|+++||..+ .++..|
T Consensus 29 ~IyGIG~~~a~~Ic~~lgi~~~--~~~~~L 56 (149)
T PRK04053 29 GIKGIGRRTARAIARKLGLDPN--AKLGYL 56 (149)
T ss_pred ccccccHHHHHHHHHHcCcCCC--CccCcC
Confidence 4579999999999999999643 444444
No 428
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=24.85 E-value=77 Score=28.64 Aligned_cols=30 Identities=17% Similarity=0.148 Sum_probs=23.0
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWP 38 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP 38 (168)
-+++.|+|+.+||+..+|... .+.|...=|
T Consensus 39 ~~~i~e~A~~~gvs~~tiR~y-e~~gll~~~ 68 (388)
T PRK13705 39 RWRIGEAADLVGVSSQAIRDA-EKAGRLPHP 68 (388)
T ss_pred CCCHHHHHHHHCcCHHHHHHH-HHcCCCCCC
Confidence 467999999999999999966 555543334
No 429
>PRK09039 hypothetical protein; Validated
Probab=24.80 E-value=1.6e+02 Score=26.39 Aligned_cols=60 Identities=13% Similarity=0.148 Sum_probs=30.7
Q ss_pred chhhhcHHHHHHHHHHHhh-------cCCCCHHHHHHHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH
Q 036926 39 HRKLMSLQTLIKNVQELQT-------EGEGSEERLREALGILERERKLIEERPDLEMEDTTKRLRQACFKA 102 (168)
Q Consensus 39 ~RKlkSL~~li~~l~~~~~-------~g~~s~~~l~~ai~~Lerek~lIee~P~~~L~~~tKrlRQa~FK~ 102 (168)
|+++.-|+..|..|+.... ..+......+..|+.|+.+....... -.+++.++|..+|..
T Consensus 136 ~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~----~~~~l~~~~~~~~~~ 202 (343)
T PRK09039 136 LAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQ----RVQELNRYRSEFFGR 202 (343)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHhHHHHHHH
Confidence 5666666666666655432 12222233444555565554444321 234567777777654
No 430
>KOG1789 consensus Endocytosis protein RME-8, contains DnaJ domain [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=24.79 E-value=2.4e+02 Score=31.04 Aligned_cols=50 Identities=24% Similarity=0.458 Sum_probs=37.2
Q ss_pred hhhhccCcH---HHHHHHcCCChhHHHHHHHHcCCCCCCchh-hhcHHHHHHHH
Q 036926 3 ISQYFYMPI---TKAAKELNVGLTLLKKRCRELNIRRWPHRK-LMSLQTLIKNV 52 (168)
Q Consensus 3 l~~yF~lPi---~eAAr~LgVs~T~LKr~CR~lGI~RWP~RK-lkSL~~li~~l 52 (168)
|.+|--+|+ -|.+.+|=+..=-||.+|-+...|.||-+- .+=|+..+...
T Consensus 1214 LYqYcPiP~i~YPeL~~ElfCh~YYLr~LCD~~rFPdWPI~dpV~fL~~~L~~W 1267 (2235)
T KOG1789|consen 1214 LYQYCPIPLIDYPELAQELFCHVYYLRHLCDKQRFPDWPIRDPVPFLRCCLATW 1267 (2235)
T ss_pred HHHcCCCCCCCcHHHHHHHHHHHHHHHHHhccccCCCCcccCchHHHHHHHHHH
Confidence 345555665 478899999999999999999999999883 33444444444
No 431
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=24.66 E-value=1.4e+02 Score=19.96 Aligned_cols=41 Identities=17% Similarity=0.185 Sum_probs=22.0
Q ss_pred CCchhhhcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHhhCC
Q 036926 37 WPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEERP 84 (168)
Q Consensus 37 WP~RKlkSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~lIee~P 84 (168)
+.+..+.+++..+..++.... .++...+.|+.+.+.+..+|
T Consensus 14 ~~~~~~~~~~~ei~~l~~~i~-------~l~~e~~~L~~ei~~l~~~~ 54 (80)
T PF04977_consen 14 SGYSRYYQLNQEIAELQKEIE-------ELKKENEELKEEIERLKNDP 54 (80)
T ss_pred chHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHhcCCH
Confidence 455666666666666655332 33444555555555553333
No 432
>PLN03184 chloroplast Hsp70; Provisional
Probab=24.63 E-value=4e+02 Score=25.99 Aligned_cols=41 Identities=15% Similarity=0.187 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHh
Q 036926 63 EERLREALGILERERKLIEERPDLEMEDTTKRLRQACFKAN 103 (168)
Q Consensus 63 ~~~l~~ai~~Lerek~lIee~P~~~L~~~tKrlRQa~FK~~ 103 (168)
++...+..+.|......|+.+..-.+....+.+.+.+.+..
T Consensus 591 ~eer~~l~~~l~~~e~wL~~~d~~~ik~~~~~l~~~l~~l~ 631 (673)
T PLN03184 591 ADVKEKVEAKLKELKDAIASGSTQKMKDAMAALNQEVMQIG 631 (673)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 33334445556666667766533456666667777776665
No 433
>PRK13832 plasmid partitioning protein; Provisional
Probab=24.34 E-value=78 Score=30.71 Aligned_cols=26 Identities=19% Similarity=0.112 Sum_probs=22.5
Q ss_pred hccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 6 YFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 6 yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
-+++++.++|+.||+|.+.+++ .+.|
T Consensus 116 e~G~T~EeIA~~lG~S~~~V~r-lllL 141 (520)
T PRK13832 116 ALGWTEEAIAVALALPVRQIRK-LRLL 141 (520)
T ss_pred hcCCCHHHHHHHHCCCHHHHHH-HHHH
Confidence 3789999999999999999997 5655
No 434
>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=24.32 E-value=3.4e+02 Score=20.95 Aligned_cols=71 Identities=24% Similarity=0.414 Sum_probs=36.2
Q ss_pred HHHHHHcCCChhHHHHHHHHcCCCCCCchhh-hcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHhhCCC-CCCc
Q 036926 12 TKAAKELNVGLTLLKKRCRELNIRRWPHRKL-MSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEERPD-LEME 89 (168)
Q Consensus 12 ~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKl-kSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~lIee~P~-~~L~ 89 (168)
-..++.+|+|+..+|.+-.... ..|+...+ ..|+..+..+++. ..+++.....|+.....++.+|+ .+++
T Consensus 50 I~~lr~~GfsL~eI~~ll~~~~-~~~~~~~~~~~l~~k~~~i~~~-------i~~L~~~~~~L~~~i~~~~~~~~~~~~~ 121 (131)
T cd04786 50 ISSAQQAGFSLDEIRQLLPADA-SNWQHDELLAALERKVADIEAL-------EARLAQNKAQLLVLIDLIESKPDEMDCA 121 (131)
T ss_pred HHHHHHcCCCHHHHHHHHhccc-CCCCHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence 3457889999888888765322 23443222 2223333333322 22344445556666666666665 3443
Q ss_pred H
Q 036926 90 D 90 (168)
Q Consensus 90 ~ 90 (168)
+
T Consensus 122 ~ 122 (131)
T cd04786 122 D 122 (131)
T ss_pred H
Confidence 3
No 435
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=24.27 E-value=5.1e+02 Score=23.05 Aligned_cols=73 Identities=19% Similarity=0.248 Sum_probs=48.0
Q ss_pred HcCCCCC---Cch-hhhcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHh--------hCCCC-------CCcHH
Q 036926 31 ELNIRRW---PHR-KLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIE--------ERPDL-------EMEDT 91 (168)
Q Consensus 31 ~lGI~RW---P~R-KlkSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~lIe--------e~P~~-------~L~~~ 91 (168)
++|-.|| |.. --..|..-+..++.+...+..++..+...+...+....++. ..|.. .+...
T Consensus 114 k~g~~~Wtr~~S~~~~~~l~~~~~~~~~~L~~A~~sD~~v~~k~~~~~~~l~lL~~~~~~l~~~~Ps~~~~~~~~~~~~~ 193 (353)
T cd09236 114 KFGTDRWTRPDSHEANPKLYTQAAEYEGYLKQAGASDELVRRKLDEWEDLIQILTGDERDLENFVPSSRRPSIPPELERH 193 (353)
T ss_pred HcCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHcCCHHHHHHhCCCCCCCCCCchhhHH
Confidence 7887799 433 34466666777776666666677777777666665555552 23442 35567
Q ss_pred HHHHHHHHHHHh
Q 036926 92 TKRLRQACFKAN 103 (168)
Q Consensus 92 tKrlRQa~FK~~ 103 (168)
+.+||+.+=|.+
T Consensus 194 i~~Lr~~l~~l~ 205 (353)
T cd09236 194 VRALRVSLEELD 205 (353)
T ss_pred HHHHHHHHHHHH
Confidence 899999987775
No 436
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=24.19 E-value=69 Score=26.66 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=19.8
Q ss_pred cCcHHHHHHHcCCChhHHHHH----HHHcCC
Q 036926 8 YMPITKAAKELNVGLTLLKKR----CRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~----CR~lGI 34 (168)
+..+..||+.|||+.+++-+. =.++|.
T Consensus 18 ~gS~s~AAe~L~isqsavS~~Ik~LE~~lg~ 48 (309)
T PRK11013 18 AGSLTEAARLLHTSQPTVSRELARFEKVIGL 48 (309)
T ss_pred hCcHHHHHHHHCCCcHHHHHHHHHHHHHhCc
Confidence 356889999999998766544 445664
No 437
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=24.13 E-value=70 Score=26.81 Aligned_cols=20 Identities=10% Similarity=0.124 Sum_probs=17.9
Q ss_pred cCCChhHHHHHHHHcCCCCC
Q 036926 18 LNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 18 LgVs~T~LKr~CR~lGI~RW 37 (168)
+|++...+...++++|++-|
T Consensus 142 ~~l~K~eIr~la~~~gl~~~ 161 (252)
T TIGR00268 142 FGITKKEIREIAKSLGISFP 161 (252)
T ss_pred cCCCHHHHHHHHHHcCCCcc
Confidence 46788899999999999988
No 438
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=24.05 E-value=66 Score=26.96 Aligned_cols=26 Identities=23% Similarity=0.259 Sum_probs=19.8
Q ss_pred CcHHHHHHHcCCChhHH----HHHHHHcCC
Q 036926 9 MPITKAAKELNVGLTLL----KKRCRELNI 34 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~L----Kr~CR~lGI 34 (168)
..+..||++|||+.+++ |++=.++|.
T Consensus 17 ~S~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK12683 17 FNLTEVANALYTSQSGVSKQIKDLEDELGV 46 (309)
T ss_pred CCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 47889999999998765 445556774
No 439
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=24.04 E-value=66 Score=27.36 Aligned_cols=20 Identities=20% Similarity=0.429 Sum_probs=18.7
Q ss_pred cCcHHHHHHHcCCChhHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKK 27 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr 27 (168)
.||+++.++.+||+.-||.|
T Consensus 187 ~LP~k~l~~~~~v~rktier 206 (237)
T PRK08311 187 KLPLKELEKRVKVSRKTLER 206 (237)
T ss_pred CCCHHHHHHHcCCCHHHHHh
Confidence 69999999999999999986
No 440
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=23.99 E-value=89 Score=23.64 Aligned_cols=32 Identities=25% Similarity=0.365 Sum_probs=21.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc---C-CCCCCc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL---N-IRRWPH 39 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l---G-I~RWP~ 39 (168)
.+++.+.|+.+||+.+++-+...++ | |.|.|.
T Consensus 54 ~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~ 89 (144)
T PRK11512 54 CITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPN 89 (144)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccC
Confidence 4677888888888887776666544 3 455543
No 441
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=23.91 E-value=1.9e+02 Score=28.94 Aligned_cols=38 Identities=11% Similarity=0.100 Sum_probs=27.2
Q ss_pred HHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHH
Q 036926 12 TKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQEL 55 (168)
Q Consensus 12 ~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~ 55 (168)
-++|+.+|+...++.+.-.-++- .-..++.+|.+|++.
T Consensus 486 ~~iA~~~Glp~~ii~~A~~~~~~------~~~~~~~li~~L~~~ 523 (771)
T TIGR01069 486 FEIAQRYGIPHFIIEQAKTFYGE------FKEEINVLIEKLSAL 523 (771)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHh------hHHHHHHHHHHHHHH
Confidence 36899999999999988776652 123556777776553
No 442
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=23.72 E-value=79 Score=25.45 Aligned_cols=38 Identities=18% Similarity=0.050 Sum_probs=27.3
Q ss_pred ccCcHHHHHHHcCCChhHHHHHH---HHcCCCCCCchhhhc
Q 036926 7 FYMPITKAAKELNVGLTLLKKRC---RELNIRRWPHRKLMS 44 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~LKr~C---R~lGI~RWP~RKlkS 44 (168)
+.++..++|..||++.-+|-|.- ++-|+-....|++.=
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I 208 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLI 208 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEE
Confidence 45688999999999987776644 455765666666543
No 443
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=23.70 E-value=56 Score=26.06 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=18.9
Q ss_pred HHcCCChhHHHHHHHHcCCCCC
Q 036926 16 KELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RW 37 (168)
---|||.+.=+.+|.++||..|
T Consensus 21 ~IyGIG~~~a~~I~~~~gi~~~ 42 (121)
T COG0099 21 YIYGIGRRRAKEICKKAGIDPD 42 (121)
T ss_pred hhccccHHHHHHHHHHcCCCHh
Confidence 3679999999999999999643
No 444
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=23.70 E-value=65 Score=27.01 Aligned_cols=25 Identities=28% Similarity=0.260 Sum_probs=19.4
Q ss_pred cHHHHHHHcCCChhHHH----HHHHHcCC
Q 036926 10 PITKAAKELNVGLTLLK----KRCRELNI 34 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LK----r~CR~lGI 34 (168)
.+..||++|||+.+++- ++=.++|.
T Consensus 18 S~s~AA~~L~isQpavS~~ik~LE~~lg~ 46 (313)
T PRK12684 18 NLTEAAKALYTSQPGVSKAIIELEDELGV 46 (313)
T ss_pred CHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 78999999999987654 44456675
No 445
>PRK09552 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed
Probab=23.62 E-value=1.9e+02 Score=23.13 Aligned_cols=41 Identities=22% Similarity=0.374 Sum_probs=27.5
Q ss_pred HHHHHcCCC--hhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHh
Q 036926 13 KAAKELNVG--LTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQ 56 (168)
Q Consensus 13 eAAr~LgVs--~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~ 56 (168)
+||+.-|+. ...|...|++.| |||-.+.+..-.+..|+.+.
T Consensus 174 ~aa~~Ag~~~a~~~l~~~~~~~~---~~~~~~~~f~ei~~~l~~~~ 216 (219)
T PRK09552 174 EAAKQADKVFARDFLITKCEELG---IPYTPFETFHDVQTELKHLL 216 (219)
T ss_pred HHHHHCCcceeHHHHHHHHHHcC---CCccccCCHHHHHHHHHHHh
Confidence 467776664 345667777765 67888888877776666543
No 446
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=23.60 E-value=87 Score=23.49 Aligned_cols=29 Identities=14% Similarity=0.147 Sum_probs=18.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RW 37 (168)
+.+.+.|+.+|++.+++.+...++-=..|
T Consensus 47 ~t~~eLa~~l~~~~~tvt~~v~~Le~~Gl 75 (144)
T PRK03573 47 QSQIQLAKAIGIEQPSLVRTLDQLEEKGL 75 (144)
T ss_pred CCHHHHHHHhCCChhhHHHHHHHHHHCCC
Confidence 45677888888887777666665543333
No 447
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=23.22 E-value=3.6e+02 Score=20.97 Aligned_cols=35 Identities=14% Similarity=0.116 Sum_probs=20.8
Q ss_pred cCCChhHHHHHHHHcCC-CCCCchhhhcHHHHHHHH
Q 036926 18 LNVGLTLLKKRCRELNI-RRWPHRKLMSLQTLIKNV 52 (168)
Q Consensus 18 LgVs~T~LKr~CR~lGI-~RWP~RKlkSL~~li~~l 52 (168)
=|+.-|++..+|++.|| +.=-|+.+.|-+.++..+
T Consensus 27 ~G~~~~t~~~Ia~~agvs~~tlY~~F~sKe~Ll~~v 62 (215)
T PRK10668 27 QGVSATSLADIAKAAGVTRGAIYWHFKNKSDLFSEI 62 (215)
T ss_pred cCcccCCHHHHHHHhCCChHHHHHHCCCHHHHHHHH
Confidence 35666666666666665 334466667767665554
No 448
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=23.11 E-value=71 Score=27.91 Aligned_cols=21 Identities=10% Similarity=0.161 Sum_probs=18.2
Q ss_pred cCcHHHHHHHcCCChhHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~ 28 (168)
.+...|+|+++|+|.|+..|.
T Consensus 173 ~~Taeela~~~giSRvTaRRY 193 (224)
T COG4565 173 ELTAEELAQALGISRVTARRY 193 (224)
T ss_pred ccCHHHHHHHhCccHHHHHHH
Confidence 467899999999999998775
No 449
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=23.04 E-value=84 Score=25.28 Aligned_cols=23 Identities=13% Similarity=0.184 Sum_probs=18.8
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+..|.|+.+|||.+|+.+.-..|
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L 56 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAAL 56 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 35689999999999999876643
No 450
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=23.03 E-value=71 Score=25.92 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=25.5
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+.=.+.+.+.|+.||||..|+.|=..+|.-
T Consensus 18 ~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 18 ENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred HCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 334568899999999999999999988876
No 451
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) 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-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=22.73 E-value=1.2e+02 Score=22.03 Aligned_cols=30 Identities=20% Similarity=0.223 Sum_probs=22.8
Q ss_pred hhhhccCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 3 ISQYFYMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
|+...+---.+.|++|||+.+.+..+.-++
T Consensus 10 ia~~LG~dW~~LA~eLg~s~~dI~~i~~e~ 39 (84)
T cd08803 10 VADHLGLSWTELARELNFSVDEINQIRVEN 39 (84)
T ss_pred HHHHhhccHHHHHHHcCCCHHHHHHHHHhC
Confidence 455556666788999999999998886554
No 452
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=22.70 E-value=77 Score=24.80 Aligned_cols=24 Identities=13% Similarity=-0.050 Sum_probs=20.5
Q ss_pred hhccCcHHHHHHHcCCChhHHHHH
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
.|-+.++.++|++.|||..+|-+.
T Consensus 28 G~~~~t~~~Ia~~agvs~~tlY~~ 51 (215)
T PRK10668 28 GVSATSLADIAKAAGVTRGAIYWH 51 (215)
T ss_pred CcccCCHHHHHHHhCCChHHHHHH
Confidence 455789999999999999998764
No 453
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=22.66 E-value=1.1e+02 Score=25.02 Aligned_cols=42 Identities=14% Similarity=0.191 Sum_probs=28.6
Q ss_pred HHHHHHHc----CCChhHHHHHHHHcCCCC-CCchhhhcHHHHHHHH
Q 036926 11 ITKAAKEL----NVGLTLLKKRCRELNIRR-WPHRKLMSLQTLIKNV 52 (168)
Q Consensus 11 i~eAAr~L----gVs~T~LKr~CR~lGI~R-WP~RKlkSL~~li~~l 52 (168)
|-+||.+| |+...++.++++++|+.+ =-|+.+++-+.++..+
T Consensus 9 Il~aA~~l~~e~G~~~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~~~ 55 (205)
T PRK13756 9 VIDSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDAL 55 (205)
T ss_pred HHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcCCHHHHHHHH
Confidence 34455553 777788888888888743 3477888877776555
No 454
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=22.65 E-value=60 Score=24.65 Aligned_cols=36 Identities=11% Similarity=0.001 Sum_probs=22.3
Q ss_pred HcCCChhHHHHHHHHcCCCCC-CchhhhcHHHHHHHH
Q 036926 17 ELNVGLTLLKKRCRELNIRRW-PHRKLMSLQTLIKNV 52 (168)
Q Consensus 17 ~LgVs~T~LKr~CR~lGI~RW-P~RKlkSL~~li~~l 52 (168)
+=|...++++.+|.+.||.|= =|+-.++..-++..+
T Consensus 18 ~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~dLl~~~ 54 (176)
T TIGR02366 18 VQAFSKISVSDIMSTAQIRRQTFYNHFQDKYELLTWI 54 (176)
T ss_pred HCCCccCCHHHHHHHhCCCHHHHHHHCCCHHHHHHHH
Confidence 335666666666666666432 266777777777665
No 455
>PRK05629 hypothetical protein; Validated
Probab=22.63 E-value=4.7e+02 Score=22.40 Aligned_cols=48 Identities=17% Similarity=0.237 Sum_probs=28.3
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHhhcC
Q 036926 10 PITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEG 59 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~~~g 59 (168)
+..++|+.+||.+-..|+.-+ -.++|+...+..+-..+..+....+.+
T Consensus 251 ~~~~ia~~l~i~p~~~~~~~~--~ar~~s~~~L~~~l~~l~~~D~~~K~~ 298 (318)
T PRK05629 251 DSFELAKELGMPPFVVEKTAK--VARNWSGDAVSEAVILMADLDAAVKGQ 298 (318)
T ss_pred CHHHHHHHcCCChHHHHHHHH--HHhCCCHHHHHHHHHHHHHHHHHhhCC
Confidence 566777777777655544322 245777766665555555555555543
No 456
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=22.62 E-value=1e+02 Score=20.69 Aligned_cols=22 Identities=18% Similarity=0.315 Sum_probs=12.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 036926 9 MPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+...++|+.++++.+++.+.-+
T Consensus 25 ~~~~~la~~~~~s~~~i~~~l~ 46 (101)
T smart00347 25 LSVSELAKRLGVSPSTVTRVLD 46 (101)
T ss_pred cCHHHHHHHHCCCchhHHHHHH
Confidence 4566666666666555444433
No 457
>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=22.54 E-value=1e+02 Score=23.55 Aligned_cols=21 Identities=14% Similarity=0.268 Sum_probs=14.0
Q ss_pred cCcHHHHHHHcCCChhHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~ 28 (168)
++.+.|+|..+|||...+...
T Consensus 33 DlSlsEIAe~~~iSRqaV~d~ 53 (101)
T PF04297_consen 33 DLSLSEIAEELGISRQAVYDS 53 (101)
T ss_dssp ---HHHHHHHCTS-HHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHH
Confidence 688999999999998765543
No 458
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=22.50 E-value=70 Score=23.64 Aligned_cols=25 Identities=24% Similarity=0.220 Sum_probs=20.0
Q ss_pred hhhhhccCcHHHHHHHcCCChhHHHH
Q 036926 2 TISQYFYMPITKAAKELNVGLTLLKK 27 (168)
Q Consensus 2 ~l~~yF~lPi~eAAr~LgVs~T~LKr 27 (168)
|+-.||+ ....+|+.|||+.+.+-.
T Consensus 5 Dvi~yFG-s~~kvA~aLGIs~~AVsQ 29 (75)
T PRK09744 5 DAIAFFG-SKTKLANAAGVRLASVAA 29 (75)
T ss_pred HHHHHhC-cHHHHHHHHCCCHHHHHH
Confidence 5667884 577899999999988754
No 459
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=22.49 E-value=88 Score=25.05 Aligned_cols=23 Identities=9% Similarity=0.174 Sum_probs=18.9
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+..+.|+.+|||.+|+.+.-+.|
T Consensus 27 sE~eLa~~~~Vsr~Tvr~Al~~L 49 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQQL 49 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 46789999999999998887643
No 460
>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].
Probab=22.26 E-value=3.2e+02 Score=21.75 Aligned_cols=28 Identities=18% Similarity=0.363 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCCcH
Q 036926 63 EERLREALGILERERKLIEERPDLEMED 90 (168)
Q Consensus 63 ~~~l~~ai~~Lerek~lIee~P~~~L~~ 90 (168)
.++++...+.|++-++++.+.+....+.
T Consensus 65 ~ee~e~L~~~L~~g~~LV~k~sk~~r~n 92 (147)
T PF05659_consen 65 QEEIERLKELLEKGKELVEKCSKVRRWN 92 (147)
T ss_pred hHHHHHHHHHHHHHHHHHHHhccccHHH
Confidence 4667777888899999999887765443
No 461
>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=22.26 E-value=98 Score=20.67 Aligned_cols=20 Identities=40% Similarity=0.441 Sum_probs=12.0
Q ss_pred HHHHHHcCCChhHHHHHHHHcCC
Q 036926 12 TKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 12 ~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
..+|+.|| ..-|+++|++|+
T Consensus 3 ~~ia~~lg---~~W~~la~~Lgl 22 (79)
T cd01670 3 DKLAKKLG---KDWKKLARKLGL 22 (79)
T ss_pred HHHHHHHh---hHHHHHHHHhCC
Confidence 34556666 556666666664
No 462
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=22.09 E-value=84 Score=26.17 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=20.1
Q ss_pred hhccCcHHHHHHHcCCChhHHHHHHH
Q 036926 5 QYFYMPITKAAKELNVGLTLLKKRCR 30 (168)
Q Consensus 5 ~yF~lPi~eAAr~LgVs~T~LKr~CR 30 (168)
+--+|.+.+.|..|++..++++++=+
T Consensus 89 E~~G~SqedLA~ki~ek~svI~~iE~ 114 (165)
T COG1813 89 EKRGLSQEDLAAKLKEKVSVIRRIER 114 (165)
T ss_pred HHcCCCHHHHHHHhcccHHHHHHHHh
Confidence 33578888888888888888887654
No 463
>PF07098 DUF1360: Protein of unknown function (DUF1360); InterPro: IPR010773 This entry is represented by Mycobacterium phage PG1, Gp7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of around 115 residues in length. Members of this family are found in Bacillus species and Streptomyces coelicolor, the function of the family is unknown.
Probab=22.01 E-value=34 Score=26.30 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=12.2
Q ss_pred HhhhhhhcCCCcccc
Q 036926 151 EEMGSLFSCSSSNSI 165 (168)
Q Consensus 151 ~~~~~~~~~~~~~~~ 165 (168)
.-+++||+|+||-++
T Consensus 52 ~~vGeLlsCpwC~gv 66 (105)
T PF07098_consen 52 HWVGELLSCPWCTGV 66 (105)
T ss_pred HHHHHHhcChhHHHH
Confidence 458899999999654
No 464
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=21.77 E-value=79 Score=25.41 Aligned_cols=28 Identities=21% Similarity=0.259 Sum_probs=21.4
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
.--|||.+.-..+|+++||.. ..++..|
T Consensus 25 ~I~GIG~~~a~~I~~~lgi~~--~~~~~~L 52 (144)
T TIGR03629 25 GIKGIGRRFARAIARKLGVDP--NAKLGYL 52 (144)
T ss_pred ceeccCHHHHHHHHHHcCcCC--CCCcccC
Confidence 356999999999999999963 3444444
No 465
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=21.71 E-value=86 Score=23.01 Aligned_cols=29 Identities=14% Similarity=-0.014 Sum_probs=20.1
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHHHHHcCC
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKRCRELNI 34 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI 34 (168)
+.-.++. +.|+..||+.++|-++.+..+-
T Consensus 41 r~~~glS--qLAe~~GIs~stLs~iE~g~~~ 69 (89)
T TIGR02684 41 ARARGMT--QLARKTGLSRESLYKALSGKGN 69 (89)
T ss_pred HHHCChH--HHHHHHCCCHHHHHHHHcCCCC
Confidence 3444555 5888888888888877765543
No 466
>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=21.68 E-value=93 Score=21.04 Aligned_cols=22 Identities=9% Similarity=0.214 Sum_probs=15.7
Q ss_pred cCcHHHHHHHcCCChhHHHHHH
Q 036926 8 YMPITKAAKELNVGLTLLKKRC 29 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~C 29 (168)
-+.+.+.|++||+++.+|.-.-
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL 35 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAML 35 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHH
Confidence 4678899999999998876543
No 467
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=21.63 E-value=89 Score=27.18 Aligned_cols=32 Identities=19% Similarity=0.236 Sum_probs=24.4
Q ss_pred cCcHHHHHHHcCCChhHHHHHHH----HcCCCCCCch
Q 036926 8 YMPITKAAKELNVGLTLLKKRCR----ELNIRRWPHR 40 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR----~lGI~RWP~R 40 (168)
-|.+.+.|..||+|++++.+.-+ ++|+ -=|+|
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~-vvPtr 140 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQKEHGV-VVPTR 140 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHHHHcCc-eeccC
Confidence 47899999999999999877665 5574 33555
No 468
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=21.61 E-value=78 Score=25.86 Aligned_cols=28 Identities=14% Similarity=0.218 Sum_probs=22.0
Q ss_pred HHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926 16 KELNVGLTLLKKRCRELNIRRWPHRKLMSL 45 (168)
Q Consensus 16 r~LgVs~T~LKr~CR~lGI~RWP~RKlkSL 45 (168)
.--|||.++=+.+|+++||. |..++..|
T Consensus 34 ~I~GIG~~~A~~I~~~lgi~--~~~~~~~L 61 (154)
T PTZ00134 34 AIKGIGRRFAYLVCKKAGID--VTKRAGEL 61 (154)
T ss_pred ccccccHHHHHHHHHHcCcC--cCCCcccC
Confidence 45699999999999999995 44555554
No 469
>PRK10870 transcriptional repressor MprA; Provisional
Probab=21.53 E-value=1e+02 Score=24.70 Aligned_cols=29 Identities=21% Similarity=0.281 Sum_probs=19.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCC
Q 036926 9 MPITKAAKELNVGLTLLKKRCRELNIRRW 37 (168)
Q Consensus 9 lPi~eAAr~LgVs~T~LKr~CR~lGI~RW 37 (168)
+.+.+.|+.||++.+++-+.+.++-=..|
T Consensus 72 it~~eLa~~l~l~~~tvsr~v~rLe~kGl 100 (176)
T PRK10870 72 IQPSELSCALGSSRTNATRIADELEKRGW 100 (176)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 45578888888887777766665543334
No 470
>cd02961 PDI_a_family Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies
Probab=21.34 E-value=98 Score=20.14 Aligned_cols=20 Identities=30% Similarity=0.549 Sum_probs=15.9
Q ss_pred CChhHHHHHHHHcCCCCCCc
Q 036926 20 VGLTLLKKRCRELNIRRWPH 39 (168)
Q Consensus 20 Vs~T~LKr~CR~lGI~RWP~ 39 (168)
|....-+..|+++||...|.
T Consensus 55 v~~~~~~~~~~~~~i~~~Pt 74 (101)
T cd02961 55 VDCTANNDLCSEYGVRGYPT 74 (101)
T ss_pred eeccchHHHHHhCCCCCCCE
Confidence 44445679999999999995
No 471
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=21.33 E-value=87 Score=26.54 Aligned_cols=27 Identities=7% Similarity=-0.013 Sum_probs=20.0
Q ss_pred cCcHHHHHHHcCCChhHH----HHHHHHcCC
Q 036926 8 YMPITKAAKELNVGLTLL----KKRCRELNI 34 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~L----Kr~CR~lGI 34 (168)
+-.+..||+.|+||.+++ |++=.++|.
T Consensus 25 ~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (310)
T PRK15092 25 LNTFAAAAAAVCRTQSAVSQQMQRLEQLVGK 55 (310)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 456789999999998765 444456675
No 472
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=21.09 E-value=96 Score=25.45 Aligned_cols=24 Identities=21% Similarity=0.391 Sum_probs=19.9
Q ss_pred Cc-HHHHHHHcCCChhHHHHHHHHc
Q 036926 9 MP-ITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 9 lP-i~eAAr~LgVs~T~LKr~CR~l 32 (168)
|| -.+.|+++|||.+|+++.-..|
T Consensus 29 LPsE~eL~~~~~VSR~TvR~Al~~L 53 (240)
T PRK09764 29 LPTESALQTEFGVSRVTVRQALRQL 53 (240)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 54 5899999999999999877644
No 473
>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=21.06 E-value=3.8e+02 Score=20.32 Aligned_cols=18 Identities=17% Similarity=0.337 Sum_probs=12.7
Q ss_pred HHHHcCCChhHHHHHHHH
Q 036926 14 AAKELNVGLTLLKKRCRE 31 (168)
Q Consensus 14 AAr~LgVs~T~LKr~CR~ 31 (168)
.++.+|+|+..+|.+..-
T Consensus 52 ~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 52 NCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred HHHHcCCCHHHHHHHHHh
Confidence 457777777777777653
No 474
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=21.02 E-value=97 Score=25.32 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=19.2
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 036926 10 PITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 10 Pi~eAAr~LgVs~T~LKr~CR~l 32 (168)
+-.|.|+.+|||.+|+++.-..|
T Consensus 35 sE~eLa~~~~VSR~TvR~Al~~L 57 (241)
T PRK11402 35 TENELCTQYNVSRITIRKAISDL 57 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 45789999999999999877654
No 475
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=20.96 E-value=99 Score=26.16 Aligned_cols=25 Identities=12% Similarity=0.150 Sum_probs=21.8
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHc
Q 036926 8 YMPITKAAKELNVGLTLLKKRCREL 32 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~l 32 (168)
.+.+.|+|++||++.+++-|++..|
T Consensus 40 ~~tl~eIa~~lglpkStv~RlL~tL 64 (271)
T PRK10163 40 SSSVSDISLNLDLPLSTTFRLLKVL 64 (271)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3678999999999999999998754
No 476
>PRK00441 argR arginine repressor; Provisional
Probab=20.81 E-value=1.1e+02 Score=24.34 Aligned_cols=34 Identities=18% Similarity=0.154 Sum_probs=28.2
Q ss_pred hhccCcHHHHHHHc-----CCChhHHHHHHHHcCCCCCC
Q 036926 5 QYFYMPITKAAKEL-----NVGLTLLKKRCRELNIRRWP 38 (168)
Q Consensus 5 ~yF~lPi~eAAr~L-----gVs~T~LKr~CR~lGI~RWP 38 (168)
+.=-..+.|.++.| +||..|+.|-.+++|+-+=|
T Consensus 15 ~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L~lvKv~ 53 (149)
T PRK00441 15 SKEIETQEELAEELKKMGFDVTQATVSRDIKELKLIKVL 53 (149)
T ss_pred HcCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHcCcEEeE
Confidence 33345788999997 99999999999999987655
No 477
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=20.65 E-value=1.8e+02 Score=26.52 Aligned_cols=75 Identities=19% Similarity=0.272 Sum_probs=46.6
Q ss_pred cCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHhhCCCCC
Q 036926 8 YMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEERPDLE 87 (168)
Q Consensus 8 ~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL~~li~~l~~~~~~g~~s~~~l~~ai~~Lerek~lIee~P~~~ 87 (168)
+||-+||.+++ .-.-.+++|.--+++|+++|.+= +.++++=....+++=--+|..-|...
T Consensus 101 Gm~~~e~~~~~-------~~wLer~~i~~~~~~kIk~LSKG-------------nqQKIQfisaviHePeLlILDEPFSG 160 (300)
T COG4152 101 GMPKAEIQKKL-------QAWLERLEIVGKKTKKIKELSKG-------------NQQKIQFISAVIHEPELLILDEPFSG 160 (300)
T ss_pred CCcHHHHHHHH-------HHHHHhccccccccchHHHhhhh-------------hhHHHHHHHHHhcCCCEEEecCCccC
Confidence 67777777654 55677899999999999988532 22233222222222233344567777
Q ss_pred CcH-HHHHHHHHHHHH
Q 036926 88 MED-TTKRLRQACFKA 102 (168)
Q Consensus 88 L~~-~tKrlRQa~FK~ 102 (168)
||+ -++-|++++|-.
T Consensus 161 LDPVN~elLk~~I~~l 176 (300)
T COG4152 161 LDPVNVELLKDAIFEL 176 (300)
T ss_pred CChhhHHHHHHHHHHH
Confidence 765 467777777754
No 478
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.47 E-value=99 Score=24.76 Aligned_cols=36 Identities=19% Similarity=0.181 Sum_probs=24.8
Q ss_pred ccCcHHHHHHHcCCChhHH----HHHHHHcC-CCCCCchhhh
Q 036926 7 FYMPITKAAKELNVGLTLL----KKRCRELN-IRRWPHRKLM 43 (168)
Q Consensus 7 F~lPi~eAAr~LgVs~T~L----Kr~CR~lG-I~RWP~RKlk 43 (168)
......+.|+.|||++.+. ||+.+ .| |..=||+.+.
T Consensus 23 ~~~~~~diA~~L~Vsp~sVt~ml~rL~~-~GlV~~~~y~gi~ 63 (154)
T COG1321 23 GFARTKDIAERLKVSPPSVTEMLKRLER-LGLVEYEPYGGVT 63 (154)
T ss_pred CcccHHHHHHHhCCCcHHHHHHHHHHHH-CCCeEEecCCCeE
Confidence 3467889999999997554 44443 45 5555888764
No 479
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=20.35 E-value=1.2e+02 Score=24.77 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=18.9
Q ss_pred hhhccCcHHHHHHHcCCChhHHHHH
Q 036926 4 SQYFYMPITKAAKELNVGLTLLKKR 28 (168)
Q Consensus 4 ~~yF~lPi~eAAr~LgVs~T~LKr~ 28 (168)
..||..++.++|+.+||+...+.+.
T Consensus 48 ~GyL~~~~~eia~~l~~~~~~v~~~ 72 (194)
T PF04963_consen 48 DGYLTESLEEIAEELGVSEEEVEKA 72 (194)
T ss_dssp TSTCSS-HHHHHHHCTS-HHHHHHH
T ss_pred CCccCCCHHHHHHHhCCCHHHHHHH
Confidence 4789999999999999888766554
No 480
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.29 E-value=1.5e+02 Score=21.77 Aligned_cols=23 Identities=13% Similarity=0.060 Sum_probs=15.9
Q ss_pred HHHHHHcCCChhH-----HHHHHHHcCC
Q 036926 12 TKAAKELNVGLTL-----LKKRCRELNI 34 (168)
Q Consensus 12 ~eAAr~LgVs~T~-----LKr~CR~lGI 34 (168)
.++.+.||+++|. +|++.++.||
T Consensus 17 ~~vl~~lGls~S~Ai~~fl~qi~~~~~i 44 (80)
T PRK11235 17 YAVLEKLGVTPSEALRLLLQYVAENGRL 44 (80)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 5677889999865 4555566655
No 481
>PF14282 FlxA: FlxA-like protein
Probab=20.06 E-value=3.8e+02 Score=20.02 Aligned_cols=42 Identities=19% Similarity=0.332 Sum_probs=25.2
Q ss_pred hhhhcHHHHHHHHHHHhh----cCCCCHHHHHHHHHHHHHHHHHHh
Q 036926 40 RKLMSLQTLIKNVQELQT----EGEGSEERLREALGILERERKLIE 81 (168)
Q Consensus 40 RKlkSL~~li~~l~~~~~----~g~~s~~~l~~ai~~Lerek~lIe 81 (168)
..|.+|++.|..|++... ..+.+.+.....+..|..+...|+
T Consensus 19 ~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~Lq 64 (106)
T PF14282_consen 19 SQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQ 64 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHH
Confidence 457777777777766554 123344555555666666666654
Done!