Query 041600
Match_columns 160
No_of_seqs 114 out of 229
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:51:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041600.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041600hhsearch_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 2.3E-28 5.1E-33 164.1 4.8 51 68-118 2-52 (52)
2 PF01418 HTH_6: Helix-turn-hel 96.7 0.0026 5.7E-08 44.5 4.1 40 73-112 26-65 (77)
3 PF02001 DUF134: Protein of un 96.0 0.019 4.2E-07 43.7 5.7 49 53-101 24-77 (106)
4 cd04765 HTH_MlrA-like_sg2 Heli 95.9 0.049 1.1E-06 40.1 7.5 74 82-155 1-96 (99)
5 PF02796 HTH_7: Helix-turn-hel 95.9 0.012 2.5E-07 37.5 3.5 32 73-104 11-44 (45)
6 cd04766 HTH_HspR Helix-Turn-He 95.8 0.06 1.3E-06 38.4 7.2 73 82-156 2-86 (91)
7 cd01106 HTH_TipAL-Mta Helix-Tu 95.6 0.05 1.1E-06 39.6 6.4 72 82-154 1-92 (103)
8 TIGR01764 excise DNA binding d 95.6 0.015 3.3E-07 35.4 3.1 28 82-109 2-29 (49)
9 cd04768 HTH_BmrR-like Helix-Tu 95.1 0.099 2.1E-06 37.9 6.5 73 82-155 1-93 (96)
10 PRK09413 IS2 repressor TnpA; R 95.1 0.11 2.4E-06 39.0 6.9 42 65-106 11-54 (121)
11 PF12728 HTH_17: Helix-turn-he 94.8 0.034 7.4E-07 35.3 3.1 28 82-109 2-29 (51)
12 cd04762 HTH_MerR-trunc Helix-T 94.8 0.039 8.5E-07 33.3 3.1 27 82-108 1-27 (49)
13 PRK11302 DNA-binding transcrip 94.7 0.035 7.6E-07 45.9 3.5 38 75-112 28-65 (284)
14 PF02954 HTH_8: Bacterial regu 94.6 0.065 1.4E-06 33.6 3.9 28 78-105 15-42 (42)
15 PRK15482 transcriptional regul 94.6 0.035 7.7E-07 46.5 3.5 46 69-114 22-67 (285)
16 cd04789 HTH_Cfa Helix-Turn-Hel 94.5 0.14 3E-06 37.6 6.1 69 82-154 2-90 (102)
17 PF13936 HTH_38: Helix-turn-he 94.5 0.038 8.3E-07 35.1 2.6 25 81-105 20-44 (44)
18 cd04763 HTH_MlrA-like Helix-Tu 94.2 0.055 1.2E-06 36.3 3.1 27 82-108 1-27 (68)
19 cd01279 HTH_HspR-like Helix-Tu 94.1 0.33 7.3E-06 35.4 7.3 25 82-107 2-26 (98)
20 cd04761 HTH_MerR-SF Helix-Turn 94.1 0.061 1.3E-06 33.3 2.9 30 82-113 1-30 (49)
21 COG1342 Predicted DNA-binding 94.0 0.14 3E-06 38.8 5.1 45 67-124 30-79 (99)
22 cd04764 HTH_MlrA-like_sg1 Heli 94.0 0.07 1.5E-06 35.6 3.3 27 82-108 1-27 (67)
23 PRK00430 fis global DNA-bindin 93.9 0.1 2.2E-06 38.5 4.3 31 77-107 64-94 (95)
24 cd01107 HTH_BmrR Helix-Turn-He 93.9 0.25 5.4E-06 36.4 6.4 72 82-154 1-94 (108)
25 PRK11557 putative DNA-binding 93.8 0.063 1.4E-06 44.6 3.4 39 76-114 25-63 (278)
26 COG1737 RpiR Transcriptional r 93.8 0.055 1.2E-06 46.0 3.0 40 76-115 31-70 (281)
27 PF13384 HTH_23: Homeodomain-l 93.7 0.059 1.3E-06 33.9 2.3 24 81-104 17-40 (50)
28 TIGR03070 couple_hipB transcri 93.6 0.33 7.2E-06 30.3 5.7 34 73-108 7-40 (58)
29 PF01381 HTH_3: Helix-turn-hel 93.6 0.34 7.4E-06 30.6 5.8 42 74-118 2-44 (55)
30 smart00342 HTH_ARAC helix_turn 93.5 0.19 4E-06 32.9 4.6 46 81-126 1-47 (84)
31 cd04788 HTH_NolA-AlbR Helix-Tu 93.5 0.39 8.4E-06 34.8 6.6 74 82-156 1-94 (96)
32 PRK11337 DNA-binding transcrip 93.4 0.082 1.8E-06 44.3 3.4 35 77-111 42-76 (292)
33 PRK13182 racA polar chromosome 93.4 0.24 5.3E-06 40.4 6.0 27 82-108 1-27 (175)
34 cd01104 HTH_MlrA-CarA Helix-Tu 93.4 0.11 2.4E-06 34.3 3.4 26 82-107 1-26 (68)
35 cd04774 HTH_YfmP Helix-Turn-He 93.3 0.24 5.3E-06 36.1 5.3 27 82-109 1-27 (96)
36 PRK00118 putative DNA-binding 93.1 0.52 1.1E-05 35.6 7.1 61 77-149 29-89 (104)
37 cd04782 HTH_BltR Helix-Turn-He 93.1 0.52 1.1E-05 34.1 6.8 73 82-155 1-94 (97)
38 PF04967 HTH_10: HTH DNA bindi 93.0 0.12 2.5E-06 34.8 3.0 28 77-104 15-46 (53)
39 PF13542 HTH_Tnp_ISL3: Helix-t 92.9 0.14 3.1E-06 32.4 3.2 30 75-104 20-50 (52)
40 cd01110 HTH_SoxR Helix-Turn-He 92.5 0.97 2.1E-05 35.0 8.0 27 81-108 1-27 (139)
41 PRK04217 hypothetical protein; 92.4 0.57 1.2E-05 35.7 6.5 41 78-127 55-95 (110)
42 cd01282 HTH_MerR-like_sg3 Heli 92.4 0.87 1.9E-05 33.8 7.3 26 82-108 1-26 (112)
43 PRK01905 DNA-binding protein F 92.4 0.25 5.5E-06 34.7 4.2 30 78-107 47-76 (77)
44 PRK09706 transcriptional repre 92.3 1.5 3.2E-05 33.2 8.7 82 73-154 10-121 (135)
45 PRK09641 RNA polymerase sigma 92.2 0.28 6.1E-06 37.6 4.7 39 77-124 148-186 (187)
46 cd04775 HTH_Cfa-like Helix-Tur 92.1 0.59 1.3E-05 34.2 6.0 26 82-108 2-27 (102)
47 PF00165 HTH_AraC: Bacterial r 92.1 0.18 3.9E-06 31.0 2.8 27 81-107 8-35 (42)
48 PF01710 HTH_Tnp_IS630: Transp 91.8 0.27 5.9E-06 36.9 4.1 39 70-108 56-98 (119)
49 smart00421 HTH_LUXR helix_turn 91.8 0.26 5.7E-06 30.2 3.3 23 80-102 17-39 (58)
50 cd01109 HTH_YyaN Helix-Turn-He 91.7 0.64 1.4E-05 34.3 5.9 26 82-107 1-26 (113)
51 PRK10219 DNA-binding transcrip 91.7 0.6 1.3E-05 33.5 5.6 33 76-108 14-49 (107)
52 PRK09645 RNA polymerase sigma 91.6 0.4 8.6E-06 36.6 4.9 37 78-123 131-167 (173)
53 PRK09643 RNA polymerase sigma 91.4 0.49 1.1E-05 37.3 5.3 40 80-128 149-188 (192)
54 PRK11361 acetoacetate metaboli 91.4 0.27 5.8E-06 43.2 4.2 31 78-108 427-457 (457)
55 PRK12536 RNA polymerase sigma 91.4 0.38 8.2E-06 37.3 4.6 36 78-122 142-177 (181)
56 PRK13413 mpi multiple promoter 91.3 0.22 4.8E-06 39.9 3.3 27 81-107 172-198 (200)
57 COG1595 RpoE DNA-directed RNA 91.3 0.42 9.2E-06 37.2 4.8 40 76-124 138-177 (182)
58 PF01527 HTH_Tnp_1: Transposas 91.1 0.22 4.8E-06 33.5 2.7 33 73-105 13-47 (76)
59 PRK09642 RNA polymerase sigma 91.1 0.54 1.2E-05 35.4 5.1 38 77-123 118-155 (160)
60 PRK11608 pspF phage shock prot 91.1 0.32 6.9E-06 42.2 4.3 30 78-107 296-325 (326)
61 PRK09637 RNA polymerase sigma 91.0 0.52 1.1E-05 37.0 5.1 38 78-124 119-156 (181)
62 cd04773 HTH_TioE_rpt2 Second H 91.0 1.7 3.8E-05 32.0 7.6 25 82-107 1-25 (108)
63 PRK12532 RNA polymerase sigma 90.9 0.55 1.2E-05 36.8 5.2 39 76-123 147-185 (195)
64 PRK09047 RNA polymerase factor 90.8 0.64 1.4E-05 34.8 5.2 36 79-123 120-155 (161)
65 PRK15115 response regulator Gl 90.8 0.34 7.4E-06 42.5 4.2 31 78-108 408-438 (444)
66 PF08281 Sigma70_r4_2: Sigma-7 90.7 0.42 9E-06 30.4 3.6 27 76-102 21-47 (54)
67 cd04790 HTH_Cfa-like_unk Helix 90.7 2.1 4.7E-05 34.2 8.5 72 82-154 2-93 (172)
68 PRK07037 extracytoplasmic-func 90.7 0.61 1.3E-05 35.1 5.1 36 78-122 122-157 (163)
69 PF13560 HTH_31: Helix-turn-he 90.7 0.32 6.9E-06 32.2 3.1 38 74-111 7-45 (64)
70 cd04787 HTH_HMRTR_unk Helix-Tu 90.7 1 2.2E-05 34.4 6.3 27 82-109 1-27 (133)
71 PRK12513 RNA polymerase sigma 90.7 0.43 9.4E-06 37.2 4.3 36 79-123 153-188 (194)
72 PRK12515 RNA polymerase sigma 90.6 0.24 5.2E-06 38.6 2.9 25 78-102 144-168 (189)
73 PF04545 Sigma70_r4: Sigma-70, 90.6 0.32 7E-06 30.8 3.0 24 81-104 20-43 (50)
74 PRK12522 RNA polymerase sigma 90.6 0.69 1.5E-05 35.5 5.3 39 77-124 131-169 (173)
75 PF13411 MerR_1: MerR HTH fami 90.5 0.3 6.4E-06 32.3 2.9 26 82-107 1-26 (69)
76 PRK12543 RNA polymerase sigma 90.4 0.75 1.6E-05 35.6 5.4 43 78-129 130-172 (179)
77 PRK05602 RNA polymerase sigma 90.3 0.63 1.4E-05 36.1 5.0 39 77-124 140-178 (186)
78 PRK10820 DNA-binding transcrip 90.3 0.4 8.7E-06 44.2 4.5 26 83-108 488-513 (520)
79 TIGR02947 SigH_actino RNA poly 90.3 0.59 1.3E-05 36.5 4.8 40 78-126 144-183 (193)
80 cd00592 HTH_MerR-like Helix-Tu 90.3 2.6 5.5E-05 30.0 7.7 72 82-154 1-96 (100)
81 PRK11923 algU RNA polymerase s 90.2 0.7 1.5E-05 35.9 5.2 38 78-124 151-188 (193)
82 PRK12511 RNA polymerase sigma 90.2 0.69 1.5E-05 36.5 5.2 40 78-126 124-163 (182)
83 cd04772 HTH_TioE_rpt1 First He 90.2 3.5 7.5E-05 30.0 8.5 25 82-107 1-25 (99)
84 TIGR02948 SigW_bacill RNA poly 90.2 0.53 1.1E-05 36.1 4.4 37 78-123 149-185 (187)
85 PRK12527 RNA polymerase sigma 90.1 0.79 1.7E-05 34.6 5.2 38 78-124 118-155 (159)
86 PF13518 HTH_28: Helix-turn-he 90.1 0.37 8E-06 30.0 2.9 25 81-105 12-36 (52)
87 PRK05022 anaerobic nitric oxid 90.0 0.45 9.7E-06 43.6 4.4 31 78-108 478-508 (509)
88 PF13404 HTH_AsnC-type: AsnC-t 90.0 0.58 1.3E-05 29.7 3.7 31 75-105 11-41 (42)
89 PF13443 HTH_26: Cro/C1-type H 89.9 0.64 1.4E-05 30.2 4.0 44 74-118 3-46 (63)
90 PRK12520 RNA polymerase sigma 89.8 0.84 1.8E-05 35.6 5.3 38 78-124 144-181 (191)
91 PRK12530 RNA polymerase sigma 89.7 0.8 1.7E-05 36.0 5.2 37 78-123 147-183 (189)
92 TIGR02954 Sig70_famx3 RNA poly 89.6 0.69 1.5E-05 35.2 4.6 36 78-122 132-167 (169)
93 PRK12542 RNA polymerase sigma 89.6 0.66 1.4E-05 36.0 4.6 36 78-122 135-170 (185)
94 PF00356 LacI: Bacterial regul 89.6 1.2 2.7E-05 28.8 5.1 21 83-103 1-21 (46)
95 PRK12516 RNA polymerase sigma 89.6 0.83 1.8E-05 36.1 5.2 39 78-125 129-167 (187)
96 COG1522 Lrp Transcriptional re 89.4 0.55 1.2E-05 35.3 3.8 33 73-105 14-46 (154)
97 PRK12538 RNA polymerase sigma 89.3 0.74 1.6E-05 38.1 4.9 41 77-126 183-223 (233)
98 PRK10923 glnG nitrogen regulat 89.3 0.53 1.1E-05 41.7 4.2 31 78-108 439-469 (469)
99 PF12844 HTH_19: Helix-turn-he 89.2 0.7 1.5E-05 30.1 3.8 33 73-107 4-36 (64)
100 TIGR02915 PEP_resp_reg putativ 89.2 0.56 1.2E-05 41.2 4.3 30 78-107 415-444 (445)
101 TIGR02044 CueR Cu(I)-responsiv 89.1 1.6 3.5E-05 32.9 6.3 25 82-107 1-25 (127)
102 PRK12519 RNA polymerase sigma 89.1 0.96 2.1E-05 35.2 5.2 36 79-123 155-190 (194)
103 COG3284 AcoR Transcriptional a 89.1 0.35 7.7E-06 46.4 3.2 31 79-109 576-606 (606)
104 PRK09646 RNA polymerase sigma 89.1 0.75 1.6E-05 36.2 4.6 36 78-122 155-190 (194)
105 PRK12545 RNA polymerase sigma 89.0 0.84 1.8E-05 36.3 4.9 38 78-124 152-189 (201)
106 TIGR02999 Sig-70_X6 RNA polyme 89.0 0.92 2E-05 34.8 4.9 24 79-102 148-171 (183)
107 PRK12533 RNA polymerase sigma 88.9 0.76 1.6E-05 37.7 4.7 37 77-122 146-182 (216)
108 PF13412 HTH_24: Winged helix- 88.9 0.74 1.6E-05 28.8 3.6 31 75-105 11-41 (48)
109 TIGR02939 RpoE_Sigma70 RNA pol 88.8 0.84 1.8E-05 35.0 4.6 36 79-123 152-187 (190)
110 TIGR02051 MerR Hg(II)-responsi 88.8 1.7 3.6E-05 32.9 6.1 24 83-107 1-24 (124)
111 TIGR02952 Sig70_famx2 RNA poly 88.8 0.76 1.6E-05 34.6 4.3 24 79-102 136-159 (170)
112 TIGR02943 Sig70_famx1 RNA poly 88.8 1.1 2.3E-05 35.3 5.3 38 78-124 144-181 (188)
113 PRK09640 RNA polymerase sigma 88.8 0.93 2E-05 35.4 4.9 39 79-126 148-186 (188)
114 PRK12535 RNA polymerase sigma 88.7 0.69 1.5E-05 36.9 4.2 41 77-126 145-185 (196)
115 TIGR02983 SigE-fam_strep RNA p 88.7 0.88 1.9E-05 34.2 4.5 36 78-122 123-158 (162)
116 PRK09652 RNA polymerase sigma 88.6 1.3 2.7E-05 33.4 5.4 36 79-123 142-177 (182)
117 COG1476 Predicted transcriptio 88.5 0.57 1.2E-05 33.2 3.2 29 73-101 6-34 (68)
118 TIGR02959 SigZ RNA polymerase 88.5 1.3 2.7E-05 34.2 5.4 40 77-125 112-151 (170)
119 TIGR02531 yecD_yerC TrpR-relat 88.3 0.49 1.1E-05 34.7 2.8 23 81-103 50-72 (88)
120 PRK12531 RNA polymerase sigma 88.3 1.1 2.4E-05 35.2 5.1 33 81-122 157-189 (194)
121 cd04781 HTH_MerR-like_sg6 Heli 88.3 2.3 4.9E-05 31.8 6.5 25 82-107 1-25 (120)
122 PRK12539 RNA polymerase sigma 88.3 1 2.2E-05 35.1 4.8 36 79-123 145-180 (184)
123 PRK09638 RNA polymerase sigma 88.2 0.74 1.6E-05 35.1 3.9 36 78-122 139-174 (176)
124 PRK14101 bifunctional glucokin 88.2 0.26 5.7E-06 46.3 1.7 35 78-112 371-405 (638)
125 PRK09647 RNA polymerase sigma 88.1 1.2 2.7E-05 35.8 5.3 38 78-124 151-188 (203)
126 PRK12547 RNA polymerase sigma 88.1 1.2 2.6E-05 33.9 5.0 25 78-102 125-149 (164)
127 TIGR02960 SigX5 RNA polymerase 88.0 1.9 4.1E-05 36.3 6.6 40 76-124 153-192 (324)
128 PRK12524 RNA polymerase sigma 87.8 1.2 2.7E-05 35.0 5.0 42 79-129 150-191 (196)
129 PRK12515 RNA polymerase sigma 87.7 1.4 3E-05 34.3 5.3 46 66-111 143-189 (189)
130 TIGR02989 Sig-70_gvs1 RNA poly 87.6 0.8 1.7E-05 34.1 3.7 25 78-102 124-148 (159)
131 TIGR02047 CadR-PbrR Cd(II)/Pb( 87.6 2 4.4E-05 32.6 6.0 25 82-107 1-25 (127)
132 PRK09415 RNA polymerase factor 87.6 1.2 2.5E-05 34.6 4.7 26 77-102 139-164 (179)
133 PHA01976 helix-turn-helix prot 87.6 2.7 5.9E-05 27.5 5.9 33 73-107 7-39 (67)
134 PRK08295 RNA polymerase factor 87.4 1.1 2.5E-05 35.0 4.7 38 78-124 167-204 (208)
135 PRK12540 RNA polymerase sigma 87.3 1.4 3.1E-05 34.6 5.1 38 78-124 124-161 (182)
136 cd04770 HTH_HMRTR Helix-Turn-H 87.2 2.3 5E-05 31.6 5.9 25 82-107 1-25 (123)
137 PF07453 NUMOD1: NUMOD1 domain 87.1 0.53 1.2E-05 28.4 2.1 21 82-102 17-37 (37)
138 TIGR01950 SoxR redox-sensitive 87.1 4.4 9.6E-05 31.6 7.7 25 82-107 2-26 (142)
139 TIGR02984 Sig-70_plancto1 RNA 87.0 1.2 2.5E-05 34.1 4.4 25 78-102 153-177 (189)
140 cd01108 HTH_CueR Helix-Turn-He 87.0 2.2 4.7E-05 32.3 5.8 23 82-104 1-23 (127)
141 PRK08301 sporulation sigma fac 86.9 1.5 3.3E-05 35.5 5.3 35 81-124 198-232 (234)
142 cd04776 HTH_GnyR Helix-Turn-He 86.8 1.9 4.1E-05 32.4 5.4 25 82-107 1-25 (118)
143 PRK09726 antitoxin HipB; Provi 86.6 0.98 2.1E-05 32.0 3.5 31 73-103 17-47 (88)
144 PRK12514 RNA polymerase sigma 86.5 1.4 2.9E-05 33.9 4.5 33 80-121 144-176 (179)
145 smart00497 IENR1 Intron encode 86.5 0.77 1.7E-05 28.9 2.6 23 82-104 18-40 (53)
146 PRK12541 RNA polymerase sigma 86.4 1.4 3E-05 33.3 4.5 25 78-102 125-149 (161)
147 PRK10072 putative transcriptio 86.3 1.3 2.9E-05 32.8 4.2 31 73-103 38-68 (96)
148 PRK09649 RNA polymerase sigma 86.3 1.4 3E-05 34.6 4.5 27 76-102 141-167 (185)
149 PRK09639 RNA polymerase sigma 86.2 1.7 3.6E-05 32.7 4.8 39 78-125 124-162 (166)
150 PF03374 ANT: Phage antirepres 86.0 0.86 1.9E-05 33.1 3.0 28 81-108 24-51 (111)
151 cd04783 HTH_MerR1 Helix-Turn-H 86.0 8.2 0.00018 28.9 8.5 25 82-107 1-25 (126)
152 PRK09644 RNA polymerase sigma 85.8 1.9 4E-05 32.8 4.9 38 78-124 121-158 (165)
153 smart00422 HTH_MERR helix_turn 85.8 1 2.2E-05 29.7 3.0 25 82-107 1-25 (70)
154 PRK15002 redox-sensitivie tran 85.7 6.6 0.00014 31.2 8.2 24 82-106 12-35 (154)
155 TIGR03830 CxxCG_CxxCG_HTH puta 85.6 1.8 3.9E-05 31.7 4.7 41 65-107 59-102 (127)
156 PRK11303 DNA-binding transcrip 85.6 1.7 3.7E-05 35.8 5.0 24 82-105 1-24 (328)
157 PRK12537 RNA polymerase sigma 85.5 1.7 3.7E-05 33.7 4.7 25 78-102 146-170 (182)
158 PRK09648 RNA polymerase sigma 85.5 1.8 3.9E-05 33.6 4.8 24 79-102 153-176 (189)
159 PRK12529 RNA polymerase sigma 85.5 1.1 2.4E-05 34.8 3.6 25 78-102 140-164 (178)
160 cd04784 HTH_CadR-PbrR Helix-Tu 85.4 3.2 6.9E-05 31.2 6.0 25 82-107 1-25 (127)
161 PF05225 HTH_psq: helix-turn-h 85.4 1.4 2.9E-05 28.3 3.4 22 82-103 17-38 (45)
162 PRK11511 DNA-binding transcrip 85.4 2.8 6E-05 31.5 5.6 28 81-108 25-53 (127)
163 TIGR01817 nifA Nif-specific re 85.3 1.2 2.6E-05 40.9 4.2 31 78-108 500-530 (534)
164 TIGR02985 Sig70_bacteroi1 RNA 85.2 1.5 3.4E-05 32.1 4.1 24 79-102 127-150 (161)
165 PRK09413 IS2 repressor TnpA; R 85.1 2 4.4E-05 32.2 4.8 33 86-118 20-52 (121)
166 PRK12518 RNA polymerase sigma 85.1 1.7 3.7E-05 33.0 4.4 37 79-124 134-170 (175)
167 PF08535 KorB: KorB domain; I 85.0 5.9 0.00013 28.2 7.0 26 80-105 2-27 (93)
168 PRK12546 RNA polymerase sigma 84.9 1.9 4.2E-05 34.2 4.8 38 78-124 126-163 (188)
169 smart00419 HTH_CRP helix_turn_ 84.8 1.2 2.5E-05 27.0 2.8 27 80-106 7-33 (48)
170 PRK13919 putative RNA polymera 84.7 2 4.3E-05 33.1 4.7 24 79-102 149-172 (186)
171 TIGR02835 spore_sigmaE RNA pol 84.7 1.4 3.1E-05 36.0 4.1 36 81-125 198-233 (234)
172 PRK15429 formate hydrogenlyase 84.5 0.89 1.9E-05 43.1 3.1 24 85-108 661-684 (686)
173 TIGR02950 SigM_subfam RNA poly 84.3 1.5 3.3E-05 32.5 3.7 24 79-102 119-142 (154)
174 PRK12517 RNA polymerase sigma 84.3 2.8 6E-05 33.1 5.5 39 78-125 141-179 (188)
175 PRK12544 RNA polymerase sigma 84.3 2.4 5.2E-05 34.2 5.2 38 78-124 161-198 (206)
176 PRK12526 RNA polymerase sigma 84.3 2.2 4.7E-05 34.1 4.9 37 78-123 165-202 (206)
177 PF06056 Terminase_5: Putative 84.3 1.3 2.8E-05 30.0 3.0 27 81-107 13-39 (58)
178 PF13744 HTH_37: Helix-turn-he 84.3 3.1 6.8E-05 29.0 5.1 30 73-102 23-52 (80)
179 TIGR01321 TrpR trp operon repr 84.2 1 2.2E-05 33.8 2.7 26 81-106 55-80 (94)
180 PRK03975 tfx putative transcri 84.2 2.3 5E-05 33.7 4.9 25 79-103 19-43 (141)
181 PF13011 LZ_Tnp_IS481: leucine 84.2 1.1 2.5E-05 32.9 2.9 24 81-104 25-48 (85)
182 TIGR03209 P21_Cbot clostridium 84.1 0.78 1.7E-05 34.0 2.1 22 79-100 121-142 (142)
183 PRK12512 RNA polymerase sigma 84.0 2.3 5E-05 32.8 4.8 23 80-102 146-168 (184)
184 PF10668 Phage_terminase: Phag 83.9 1 2.2E-05 31.2 2.4 22 81-102 22-43 (60)
185 PRK06704 RNA polymerase factor 83.9 2.1 4.6E-05 35.8 4.9 37 78-123 129-165 (228)
186 PRK11924 RNA polymerase sigma 83.8 3 6.4E-05 31.2 5.2 24 79-102 139-162 (179)
187 smart00354 HTH_LACI helix_turn 83.8 1 2.2E-05 30.7 2.4 24 82-105 1-24 (70)
188 cd01105 HTH_GlnR-like Helix-Tu 83.6 1.2 2.6E-05 31.7 2.8 25 82-107 2-26 (88)
189 PRK09514 zntR zinc-responsive 83.5 4.4 9.5E-05 31.3 6.1 25 82-107 2-26 (140)
190 PRK12523 RNA polymerase sigma 83.4 2.6 5.6E-05 32.3 4.8 25 78-102 132-156 (172)
191 cd06571 Bac_DnaA_C C-terminal 83.3 4.2 9E-05 29.0 5.5 34 71-104 34-68 (90)
192 PF07638 Sigma70_ECF: ECF sigm 83.2 1.6 3.5E-05 34.6 3.7 28 78-105 148-175 (185)
193 PF03683 UPF0175: Uncharacteri 83.1 1.8 3.9E-05 30.4 3.5 31 81-112 34-64 (76)
194 PRK11388 DNA-binding transcrip 83.0 1.8 3.8E-05 40.6 4.4 34 78-111 601-634 (638)
195 PRK09393 ftrA transcriptional 82.8 3.1 6.7E-05 35.3 5.5 45 81-125 234-279 (322)
196 TIGR02607 antidote_HigA addict 82.7 4.9 0.00011 26.9 5.5 37 75-113 12-48 (78)
197 cd00093 HTH_XRE Helix-turn-hel 82.7 7.1 0.00015 22.5 5.8 42 75-118 6-47 (58)
198 TIGR02859 spore_sigH RNA polym 82.7 1.7 3.6E-05 33.7 3.5 25 78-102 161-186 (198)
199 PRK08241 RNA polymerase factor 82.5 1.9 4.1E-05 36.8 4.1 27 76-102 164-190 (339)
200 cd06170 LuxR_C_like C-terminal 82.5 1.7 3.8E-05 26.7 3.0 23 81-103 15-37 (57)
201 PRK11169 leucine-responsive tr 82.4 1.5 3.4E-05 34.3 3.3 31 75-105 22-52 (164)
202 PRK09636 RNA polymerase sigma 82.4 2 4.4E-05 36.2 4.2 27 76-102 126-152 (293)
203 TIGR02043 ZntR Zn(II)-responsi 82.4 5.8 0.00013 30.2 6.3 25 82-107 2-26 (131)
204 TIGR02040 PpsR-CrtJ transcript 82.0 2.1 4.5E-05 37.5 4.2 30 78-107 413-442 (442)
205 PF04218 CENP-B_N: CENP-B N-te 81.9 2 4.4E-05 28.2 3.2 36 68-103 4-44 (53)
206 cd04785 HTH_CadR-PbrR-like Hel 81.9 4.9 0.00011 30.3 5.8 22 82-103 1-22 (126)
207 PRK15043 transcriptional regul 81.9 1.5 3.2E-05 37.7 3.2 29 81-109 3-31 (243)
208 PRK09685 DNA-binding transcrip 81.9 4.1 9E-05 33.7 5.8 51 75-125 205-258 (302)
209 cd00569 HTH_Hin_like Helix-tur 81.8 1.8 3.9E-05 22.9 2.5 21 81-101 21-41 (42)
210 PRK12534 RNA polymerase sigma 81.7 3 6.5E-05 32.2 4.6 24 79-102 151-174 (187)
211 cd06171 Sigma70_r4 Sigma70, re 81.7 2.1 4.5E-05 25.4 3.0 23 80-102 25-47 (55)
212 PHA00542 putative Cro-like pro 81.6 8.7 0.00019 27.1 6.6 27 78-104 28-54 (82)
213 smart00345 HTH_GNTR helix_turn 81.2 1.8 3.9E-05 27.0 2.7 24 82-105 20-44 (60)
214 PRK10339 DNA-binding transcrip 81.2 2.7 6E-05 34.8 4.5 24 82-105 2-25 (327)
215 smart00342 HTH_ARAC helix_turn 81.0 2.8 6.1E-05 27.1 3.7 25 81-105 50-75 (84)
216 cd00092 HTH_CRP helix_turn_hel 80.9 2.1 4.5E-05 27.6 3.0 26 79-104 23-48 (67)
217 TIGR02846 spore_sigmaK RNA pol 80.8 2.6 5.6E-05 34.3 4.2 22 81-102 194-215 (227)
218 TIGR02054 MerD mercuric resist 80.7 7.3 0.00016 29.8 6.4 28 81-109 3-30 (120)
219 smart00344 HTH_ASNC helix_turn 80.7 2.8 6E-05 29.9 3.8 31 75-105 11-41 (108)
220 cd04786 HTH_MerR-like_sg7 Heli 80.7 7.3 0.00016 29.9 6.4 24 82-106 1-24 (131)
221 TIGR03879 near_KaiC_dom probab 80.6 2.7 5.9E-05 30.0 3.7 24 80-103 31-54 (73)
222 cd01111 HTH_MerD Helix-Turn-He 80.5 15 0.00032 27.3 7.8 26 82-108 1-26 (107)
223 PRK11922 RNA polymerase sigma 80.4 2.8 6E-05 34.2 4.2 38 78-124 162-199 (231)
224 KOG0251 Clathrin assembly prot 80.2 1.4 3.1E-05 41.4 2.7 56 75-130 223-289 (491)
225 PRK06986 fliA flagellar biosyn 80.1 3.3 7.2E-05 33.7 4.6 23 80-102 199-221 (236)
226 TIGR02957 SigX4 RNA polymerase 80.0 3.1 6.7E-05 35.1 4.5 27 76-102 119-145 (281)
227 cd04777 HTH_MerR-like_sg1 Heli 79.7 8.4 0.00018 28.0 6.2 73 82-155 1-101 (107)
228 PRK05803 sporulation sigma fac 79.7 3.6 7.8E-05 33.5 4.7 35 81-124 195-229 (233)
229 PF01498 HTH_Tnp_Tc3_2: Transp 79.7 0.95 2.1E-05 30.5 1.1 35 82-116 14-53 (72)
230 smart00530 HTH_XRE Helix-turn- 79.5 9.4 0.0002 21.8 5.8 29 75-103 4-32 (56)
231 PRK12528 RNA polymerase sigma 79.4 2.9 6.2E-05 31.6 3.7 25 78-102 126-150 (161)
232 PRK09635 sigI RNA polymerase s 79.4 2.2 4.8E-05 36.6 3.5 28 75-102 128-155 (290)
233 PF13556 HTH_30: PucR C-termin 79.3 10 0.00022 25.0 6.0 28 74-101 3-32 (59)
234 PF01371 Trp_repressor: Trp re 79.2 1.5 3.3E-05 32.2 2.1 26 81-106 49-74 (87)
235 PRK10703 DNA-binding transcrip 79.2 4.4 9.6E-05 33.6 5.1 22 82-103 2-23 (341)
236 PRK15186 AraC family transcrip 79.1 4.1 8.9E-05 35.3 5.1 34 81-114 197-230 (291)
237 smart00351 PAX Paired Box doma 79.1 2.1 4.5E-05 32.5 2.9 25 81-105 33-57 (125)
238 PF10078 DUF2316: Uncharacteri 79.0 2.4 5.1E-05 31.5 3.1 32 71-102 10-44 (89)
239 TIGR02293 TAS_TIGR02293 putati 78.8 8.3 0.00018 29.5 6.2 58 72-129 27-85 (133)
240 PF13551 HTH_29: Winged helix- 78.7 2.3 5E-05 29.9 2.9 24 81-104 11-35 (112)
241 COG3829 RocR Transcriptional r 78.6 1.8 3.9E-05 41.4 2.9 27 82-108 534-560 (560)
242 PF04760 IF2_N: Translation in 78.5 1.3 2.7E-05 28.8 1.3 27 82-108 4-31 (54)
243 TIGR03001 Sig-70_gmx1 RNA poly 78.4 5.1 0.00011 33.5 5.3 38 78-124 174-211 (244)
244 TIGR02937 sigma70-ECF RNA poly 78.4 2.6 5.6E-05 29.8 3.0 24 80-103 125-148 (158)
245 COG2207 AraC AraC-type DNA-bin 78.3 8.5 0.00018 26.8 5.7 27 82-108 37-64 (127)
246 smart00418 HTH_ARSR helix_turn 78.3 2.8 6E-05 25.8 2.8 31 81-111 10-40 (66)
247 PRK06759 RNA polymerase factor 78.0 4.6 0.0001 29.9 4.5 23 80-102 121-143 (154)
248 PRK01381 Trp operon repressor; 78.0 1.4 3E-05 33.4 1.6 27 81-107 55-81 (99)
249 cd04779 HTH_MerR-like_sg4 Heli 77.9 5.9 0.00013 30.8 5.1 27 82-109 1-27 (134)
250 PRK09651 RNA polymerase sigma 77.6 3 6.5E-05 32.1 3.4 27 76-102 130-156 (172)
251 PRK09526 lacI lac repressor; R 77.6 5.3 0.00011 33.1 5.1 22 82-103 6-27 (342)
252 PF05930 Phage_AlpA: Prophage 77.5 1.6 3.5E-05 28.1 1.6 24 82-105 4-27 (51)
253 PF06970 RepA_N: Replication i 77.4 2 4.2E-05 30.6 2.2 28 78-105 49-76 (76)
254 TIGR02417 fruct_sucro_rep D-fr 77.4 4.8 0.0001 33.2 4.8 23 83-105 1-23 (327)
255 PRK15424 propionate catabolism 77.3 3.6 7.9E-05 38.8 4.5 31 78-108 507-537 (538)
256 COG3413 Predicted DNA binding 77.3 2.5 5.3E-05 34.4 3.0 34 70-103 155-200 (215)
257 TIGR02974 phageshock_pspF psp 77.3 3.3 7.2E-05 36.1 4.0 28 78-105 302-329 (329)
258 PF14817 HAUS5: HAUS augmin-li 77.1 3.9 8.6E-05 39.5 4.7 67 87-154 10-98 (632)
259 COG2944 Predicted transcriptio 77.0 3.2 7E-05 31.6 3.3 29 73-101 49-77 (104)
260 PRK06930 positive control sigm 76.9 5.9 0.00013 31.8 5.0 24 79-102 128-151 (170)
261 PF00376 MerR: MerR family reg 76.8 2.2 4.7E-05 26.5 2.0 24 83-107 1-24 (38)
262 PRK09492 treR trehalose repres 76.5 5.6 0.00012 32.5 4.9 22 82-103 5-26 (315)
263 PRK06288 RNA polymerase sigma 76.5 6.8 0.00015 32.7 5.5 37 81-126 228-264 (268)
264 PF00126 HTH_1: Bacterial regu 76.5 3.2 6.9E-05 27.2 2.9 21 81-101 13-33 (60)
265 PF08279 HTH_11: HTH domain; 76.5 3.1 6.8E-05 26.4 2.8 22 81-102 15-36 (55)
266 PRK15411 rcsA colanic acid cap 76.3 3.2 6.9E-05 33.5 3.4 33 70-102 137-173 (207)
267 PRK10227 DNA-binding transcrip 76.1 10 0.00022 29.3 6.0 21 82-102 1-21 (135)
268 PRK15418 transcriptional regul 75.8 4.3 9.3E-05 35.5 4.3 47 78-124 24-79 (318)
269 PRK10840 transcriptional regul 75.7 3.6 7.8E-05 32.2 3.5 38 70-107 150-195 (216)
270 PF00196 GerE: Bacterial regul 75.5 2.5 5.5E-05 27.4 2.2 21 81-101 18-38 (58)
271 TIGR02405 trehalos_R_Ecol treh 75.4 6.5 0.00014 32.4 5.1 21 82-102 2-22 (311)
272 COG5484 Uncharacterized conser 75.4 2.6 5.6E-05 37.1 2.8 27 81-107 19-45 (279)
273 PHA00675 hypothetical protein 75.4 3.2 7E-05 30.3 2.8 39 67-105 19-63 (78)
274 PRK08359 transcription factor; 75.3 8.1 0.00018 31.8 5.5 29 78-108 95-123 (176)
275 PF08220 HTH_DeoR: DeoR-like h 75.3 4.5 9.7E-05 26.7 3.4 30 74-103 7-36 (57)
276 TIGR02297 HpaA 4-hydroxyphenyl 75.2 6.1 0.00013 32.3 4.9 35 81-117 202-237 (287)
277 cd04769 HTH_MerR2 Helix-Turn-H 75.1 12 0.00026 27.7 6.0 25 82-107 1-25 (116)
278 TIGR02392 rpoH_proteo alternat 74.9 3.5 7.5E-05 34.6 3.4 23 81-103 236-258 (270)
279 PF00416 Ribosomal_S13: Riboso 74.8 6.7 0.00015 29.1 4.5 65 83-149 12-81 (107)
280 TIGR01818 ntrC nitrogen regula 74.5 4.3 9.4E-05 35.7 4.0 26 79-104 437-462 (463)
281 TIGR02394 rpoS_proteo RNA poly 74.3 4.8 0.0001 34.0 4.1 34 81-123 242-275 (285)
282 PF09339 HTH_IclR: IclR helix- 74.2 2.9 6.4E-05 26.7 2.2 24 82-105 19-42 (52)
283 PF13613 HTH_Tnp_4: Helix-turn 74.1 3.3 7.1E-05 26.9 2.4 24 81-104 19-42 (53)
284 PRK09191 two-component respons 73.9 4.4 9.6E-05 32.2 3.6 25 78-102 101-125 (261)
285 COG1709 Predicted transcriptio 73.7 2.1 4.4E-05 37.0 1.7 37 73-111 32-68 (241)
286 PRK06811 RNA polymerase factor 73.0 7 0.00015 30.5 4.5 24 79-102 145-168 (189)
287 PRK13752 putative transcriptio 72.9 15 0.00033 28.7 6.3 26 82-108 8-33 (144)
288 PF12802 MarR_2: MarR family; 72.6 5.5 0.00012 25.4 3.2 24 82-105 22-45 (62)
289 PRK14987 gluconate operon tran 72.5 7.2 0.00016 32.3 4.7 24 82-105 6-29 (331)
290 PRK13890 conjugal transfer pro 72.4 5.2 0.00011 30.3 3.5 32 73-104 10-41 (120)
291 PRK06596 RNA polymerase factor 72.2 8.4 0.00018 32.8 5.1 23 81-103 248-270 (284)
292 PRK09978 DNA-binding transcrip 72.1 7.6 0.00016 33.7 4.9 27 81-107 158-184 (274)
293 PRK11179 DNA-binding transcrip 71.8 6.1 0.00013 30.5 3.8 30 76-105 18-47 (153)
294 PRK15340 transcriptional regul 71.7 7 0.00015 33.0 4.4 28 81-108 125-153 (216)
295 PRK00118 putative DNA-binding 71.5 14 0.0003 27.9 5.6 65 67-135 30-94 (104)
296 PF13545 HTH_Crp_2: Crp-like h 71.2 4.6 0.0001 26.8 2.7 25 80-104 27-51 (76)
297 PF07750 GcrA: GcrA cell cycle 71.2 4.6 0.0001 32.4 3.1 37 73-109 8-47 (162)
298 PRK10403 transcriptional regul 71.2 6.2 0.00014 29.2 3.7 27 81-107 168-198 (215)
299 PF08280 HTH_Mga: M protein tr 71.0 5.3 0.00012 26.4 2.9 26 81-106 19-44 (59)
300 TIGR02479 FliA_WhiG RNA polyme 70.8 8.9 0.00019 30.9 4.7 22 81-102 191-212 (224)
301 COG2204 AtoC Response regulato 70.8 6.3 0.00014 36.9 4.3 35 78-112 427-461 (464)
302 PRK05911 RNA polymerase sigma 70.7 10 0.00023 31.7 5.3 34 81-123 221-254 (257)
303 CHL00137 rps13 ribosomal prote 70.7 9 0.00019 29.6 4.5 59 88-148 20-82 (122)
304 PRK08583 RNA polymerase sigma 70.7 8.9 0.00019 31.6 4.8 24 79-102 219-242 (257)
305 PRK10727 DNA-binding transcrip 70.7 9.4 0.0002 31.8 5.0 22 82-103 2-23 (343)
306 PRK08154 anaerobic benzoate ca 70.6 40 0.00087 29.0 9.0 30 72-101 32-61 (309)
307 cd00131 PAX Paired Box domain 70.5 4.6 0.0001 30.9 2.9 24 81-104 33-56 (128)
308 TIGR03631 bact_S13 30S ribosom 70.5 10 0.00022 28.8 4.7 59 88-148 18-80 (113)
309 COG2452 Predicted site-specifi 70.4 10 0.00022 32.0 5.0 69 81-149 1-80 (193)
310 PF07352 Phage_Mu_Gam: Bacteri 70.3 4.4 9.6E-05 31.5 2.8 49 110-158 7-55 (149)
311 PRK09940 transcriptional regul 70.2 9 0.0002 32.9 4.9 28 81-108 150-177 (253)
312 PF01325 Fe_dep_repress: Iron 70.1 4.9 0.00011 27.0 2.6 25 81-105 22-46 (60)
313 PRK10572 DNA-binding transcrip 70.0 8.9 0.00019 31.7 4.7 45 81-125 199-244 (290)
314 PTZ00134 40S ribosomal protein 69.8 10 0.00022 30.6 4.8 37 88-124 33-75 (154)
315 TIGR01481 ccpA catabolite cont 69.6 11 0.00024 31.0 5.1 23 82-104 2-24 (329)
316 PRK15185 transcriptional regul 69.5 9.3 0.0002 34.0 4.9 28 81-108 222-249 (309)
317 PRK02944 OxaA-like protein pre 69.5 9 0.0002 32.7 4.7 39 113-151 86-124 (255)
318 PRK15044 transcriptional regul 69.2 9.9 0.00021 33.7 5.0 28 81-108 208-235 (295)
319 PF00392 GntR: Bacterial regul 69.2 4.4 9.6E-05 26.7 2.2 25 81-105 23-48 (64)
320 PRK12525 RNA polymerase sigma 69.0 11 0.00025 28.7 4.8 22 81-102 134-155 (168)
321 TIGR02980 SigBFG RNA polymeras 69.0 10 0.00022 30.4 4.7 22 81-102 194-215 (227)
322 PRK05949 RNA polymerase sigma 68.8 13 0.00028 32.6 5.7 40 81-129 286-325 (327)
323 PRK05179 rpsM 30S ribosomal pr 68.6 11 0.00024 29.0 4.7 59 88-148 20-82 (122)
324 PF14549 P22_Cro: DNA-binding 68.3 6 0.00013 27.1 2.8 28 73-101 2-29 (60)
325 TIGR02612 mob_myst_A mobile my 68.0 7.4 0.00016 31.0 3.7 29 73-101 30-58 (150)
326 PRK09483 response regulator; P 68.0 6.6 0.00014 29.7 3.3 23 80-102 162-184 (217)
327 PRK05657 RNA polymerase sigma 67.9 8.1 0.00018 33.8 4.2 34 81-123 282-315 (325)
328 COG0216 PrfA Protein chain rel 67.8 14 0.00031 33.7 5.8 43 112-154 52-95 (363)
329 PRK07670 RNA polymerase sigma 67.6 9.9 0.00021 31.4 4.5 22 81-102 217-238 (251)
330 COG3283 TyrR Transcriptional r 67.5 8 0.00017 36.3 4.2 38 71-108 460-508 (511)
331 COG1609 PurR Transcriptional r 67.2 12 0.00027 32.2 5.2 23 83-105 2-24 (333)
332 PF14257 DUF4349: Domain of un 67.1 14 0.0003 30.9 5.3 44 113-156 139-183 (262)
333 COG2963 Transposase and inacti 66.9 23 0.0005 25.8 5.9 34 68-101 9-45 (116)
334 PRK04053 rps13p 30S ribosomal 66.9 12 0.00025 30.0 4.6 23 88-110 28-50 (149)
335 smart00346 HTH_ICLR helix_turn 66.9 10 0.00022 25.9 3.8 25 81-105 20-44 (91)
336 PRK10371 DNA-binding transcrip 66.0 12 0.00026 31.8 4.8 46 81-126 207-253 (302)
337 smart00352 POU Found in Pit-Oc 65.9 9.7 0.00021 27.5 3.6 29 73-101 16-50 (75)
338 cd00090 HTH_ARSR Arsenical Res 65.9 7.4 0.00016 24.4 2.7 31 82-112 21-51 (78)
339 TIGR02844 spore_III_D sporulat 65.7 9 0.00019 27.7 3.4 29 74-103 13-41 (80)
340 PRK11534 DNA-binding transcrip 65.4 6.2 0.00013 31.6 2.8 33 81-113 30-66 (224)
341 PRK13749 transcriptional regul 65.4 10 0.00022 29.2 3.9 27 81-108 3-29 (121)
342 PHA02591 hypothetical protein; 65.1 7.5 0.00016 28.7 2.9 24 80-103 58-81 (83)
343 PRK13502 transcriptional activ 65.1 13 0.00028 30.5 4.7 28 81-108 192-220 (282)
344 cd01392 HTH_LacI Helix-turn-he 65.0 4.5 9.8E-05 25.1 1.6 20 86-105 2-21 (52)
345 PRK09943 DNA-binding transcrip 64.9 9.1 0.0002 30.2 3.6 30 73-102 12-41 (185)
346 PF09048 Cro: Cro; InterPro: 64.8 6.3 0.00014 27.4 2.3 32 70-103 3-34 (59)
347 PRK13503 transcriptional activ 64.8 20 0.00043 29.1 5.7 33 76-108 180-215 (278)
348 TIGR02393 RpoD_Cterm RNA polym 64.8 12 0.00025 30.7 4.3 22 81-102 196-217 (238)
349 PF09862 DUF2089: Protein of u 64.6 18 0.00039 27.9 5.1 32 70-101 33-69 (113)
350 cd04767 HTH_HspR-like_MBC Heli 64.5 7.1 0.00015 30.1 2.8 25 82-107 2-26 (120)
351 PF12833 HTH_18: Helix-turn-he 64.2 13 0.00028 25.0 3.8 22 87-108 1-23 (81)
352 PRK07405 RNA polymerase sigma 64.1 18 0.00038 31.5 5.6 40 81-129 276-315 (317)
353 COG0099 RpsM Ribosomal protein 63.9 21 0.00047 28.0 5.4 59 89-149 21-83 (121)
354 PRK10365 transcriptional regul 63.9 8.6 0.00019 33.5 3.6 24 78-101 415-438 (441)
355 PRK07500 rpoH2 RNA polymerase 63.7 13 0.00029 31.7 4.7 22 81-102 245-266 (289)
356 PF01047 MarR: MarR family; I 63.6 12 0.00025 23.8 3.3 31 75-105 11-41 (59)
357 smart00513 SAP Putative DNA-bi 63.5 7.7 0.00017 23.2 2.3 20 92-111 3-22 (35)
358 PRK07408 RNA polymerase sigma 63.4 15 0.00032 30.7 4.8 22 81-102 219-240 (256)
359 COG3415 Transposase and inacti 63.1 7.6 0.00017 30.7 2.8 28 79-106 19-46 (138)
360 PRK11475 DNA-binding transcrip 63.1 9.9 0.00021 31.0 3.6 38 70-107 134-179 (207)
361 PF00440 TetR_N: Bacterial reg 63.1 9.9 0.00021 23.7 2.9 23 78-100 13-35 (47)
362 TIGR00721 tfx DNA-binding prot 63.0 16 0.00034 28.9 4.6 24 79-102 19-42 (137)
363 PF05344 DUF746: Domain of Unk 62.7 9 0.00019 27.1 2.8 24 81-104 13-36 (65)
364 PF13234 rRNA_proc-arch: rRNA- 62.6 25 0.00054 29.5 6.0 73 72-154 188-268 (268)
365 PHA02535 P terminase ATPase su 62.5 29 0.00063 33.5 7.1 48 81-128 18-67 (581)
366 TIGR03338 phnR_burk phosphonat 62.3 7.3 0.00016 30.8 2.6 25 81-105 34-58 (212)
367 PRK10014 DNA-binding transcrip 62.2 6.8 0.00015 32.4 2.5 21 82-102 7-27 (342)
368 PRK09645 RNA polymerase sigma 61.8 8 0.00017 29.3 2.7 43 67-109 131-173 (173)
369 COG3093 VapI Plasmid maintenan 61.6 7.8 0.00017 29.6 2.5 35 70-104 12-46 (104)
370 PRK11014 transcriptional repre 61.5 7.9 0.00017 29.5 2.6 24 82-105 26-49 (141)
371 COG2522 Predicted transcriptio 61.2 45 0.00099 25.9 6.8 30 75-105 17-46 (119)
372 PF11112 PyocinActivator: Pyoc 61.2 15 0.00032 26.3 3.8 57 73-130 3-69 (76)
373 TIGR00270 conserved hypothetic 61.1 30 0.00064 27.6 5.9 28 78-107 79-106 (154)
374 PF02082 Rrf2: Transcriptional 61.0 8.4 0.00018 26.7 2.5 24 82-105 26-49 (83)
375 TIGR03629 arch_S13P archaeal r 60.6 14 0.0003 29.4 3.9 22 88-109 24-45 (144)
376 COG0789 SoxR Predicted transcr 60.5 7.4 0.00016 28.3 2.2 24 82-106 1-24 (124)
377 COG4367 Uncharacterized protei 60.2 10 0.00023 28.6 2.9 32 71-102 10-44 (97)
378 PF11855 DUF3375: Protein of u 60.1 22 0.00049 32.8 5.7 44 114-157 123-166 (478)
379 PRK10423 transcriptional repre 59.8 5.6 0.00012 32.6 1.6 20 84-103 1-20 (327)
380 PRK05572 sporulation sigma fac 59.8 19 0.00041 29.7 4.8 21 81-101 218-238 (252)
381 PRK06424 transcription factor; 59.7 13 0.00028 29.4 3.6 27 76-102 92-118 (144)
382 PRK04984 fatty acid metabolism 59.7 9.1 0.0002 30.9 2.8 25 81-105 30-55 (239)
383 PRK10225 DNA-binding transcrip 59.2 9.3 0.0002 31.3 2.8 25 81-105 32-57 (257)
384 PRK13500 transcriptional activ 59.0 15 0.00032 31.3 4.1 35 74-108 213-250 (312)
385 PF04977 DivIC: Septum formati 59.0 25 0.00055 23.5 4.6 37 110-147 14-50 (80)
386 PRK10401 DNA-binding transcrip 58.9 8.3 0.00018 32.2 2.5 20 83-102 3-22 (346)
387 PRK10651 transcriptional regul 58.5 15 0.00033 27.3 3.6 37 71-107 156-200 (216)
388 PF07022 Phage_CI_repr: Bacter 58.4 5.5 0.00012 26.9 1.1 43 73-118 3-47 (66)
389 TIGR02812 fadR_gamma fatty aci 58.4 9.8 0.00021 30.7 2.8 25 81-105 29-54 (235)
390 smart00420 HTH_DEOR helix_turn 58.2 22 0.00047 21.3 3.8 23 81-103 14-36 (53)
391 COG2771 CsgD DNA-binding HTH d 58.0 18 0.00038 22.8 3.5 23 80-102 18-40 (65)
392 PRK08215 sporulation sigma fac 57.9 18 0.0004 29.9 4.4 21 81-101 225-245 (258)
393 PRK11414 colanic acid/biofilm 57.4 9.5 0.00021 30.6 2.5 25 81-105 34-58 (221)
394 PF05008 V-SNARE: Vesicle tran 57.3 52 0.0011 22.4 6.0 45 112-156 31-75 (79)
395 PRK15121 right oriC-binding tr 57.1 22 0.00047 29.9 4.7 46 81-126 21-67 (289)
396 PRK14997 LysR family transcrip 57.0 15 0.00033 30.0 3.7 21 81-101 16-36 (301)
397 PRK03573 transcriptional regul 57.0 68 0.0015 23.9 7.0 73 82-154 47-140 (144)
398 PF09278 MerR-DNA-bind: MerR, 57.0 7 0.00015 25.6 1.4 16 87-102 9-24 (65)
399 PF13730 HTH_36: Helix-turn-he 57.0 13 0.00028 23.5 2.6 23 83-105 27-49 (55)
400 TIGR03453 partition_RepA plasm 56.7 11 0.00024 33.2 3.1 26 82-107 34-59 (387)
401 PRK13501 transcriptional activ 56.3 16 0.00036 30.2 3.9 33 73-105 182-216 (290)
402 PRK11753 DNA-binding transcrip 56.2 8.4 0.00018 29.9 2.0 36 80-115 167-205 (211)
403 PRK13348 chromosome replicatio 56.0 16 0.00034 29.8 3.6 21 81-101 16-36 (294)
404 cd08804 Death_ank2 Death domai 56.0 16 0.00034 26.1 3.2 36 70-105 4-39 (84)
405 PF05043 Mga: Mga helix-turn-h 55.9 13 0.00029 25.6 2.8 22 81-102 30-51 (87)
406 TIGR01453 grpIintron_endo grou 55.9 9.9 0.00021 31.3 2.5 25 82-106 180-204 (214)
407 TIGR02329 propionate_PrpR prop 55.7 14 0.0003 34.8 3.6 25 78-102 500-524 (526)
408 PRK07598 RNA polymerase sigma 55.6 23 0.00049 32.7 4.9 21 82-102 371-391 (415)
409 COG2197 CitB Response regulato 55.4 13 0.00028 30.2 3.1 38 70-107 148-193 (211)
410 PRK10421 DNA-binding transcrip 55.3 12 0.00026 30.7 2.8 25 81-105 25-50 (253)
411 smart00550 Zalpha Z-DNA-bindin 55.2 22 0.00048 24.1 3.7 20 82-101 23-42 (68)
412 TIGR02036 dsdC D-serine deamin 55.1 19 0.00041 29.8 4.0 35 67-101 4-42 (302)
413 PF12116 SpoIIID: Stage III sp 55.1 9.8 0.00021 28.1 2.0 22 81-102 19-40 (82)
414 PF01191 RNA_pol_Rpb5_C: RNA p 55.0 7.2 0.00016 27.9 1.3 33 5-37 16-48 (74)
415 PRK11482 putative DNA-binding 54.9 18 0.00039 30.5 3.9 36 66-101 24-63 (317)
416 PRK11523 DNA-binding transcrip 54.7 12 0.00027 30.6 2.8 25 81-105 31-56 (253)
417 PF13591 MerR_2: MerR HTH fami 54.5 74 0.0016 22.4 8.5 70 83-154 2-82 (84)
418 PRK10130 transcriptional regul 54.2 23 0.0005 31.4 4.7 44 82-125 257-301 (350)
419 PF04420 CHD5: CHD5-like prote 54.1 52 0.0011 26.1 6.2 46 111-156 38-87 (161)
420 PF01710 HTH_Tnp_IS630: Transp 54.0 12 0.00026 27.9 2.5 23 81-103 18-40 (119)
421 TIGR02607 antidote_HigA addict 53.8 39 0.00084 22.5 4.8 43 66-108 14-60 (78)
422 PRK10094 DNA-binding transcrip 53.7 19 0.00041 30.1 3.8 21 81-101 16-36 (308)
423 TIGR00637 ModE_repress ModE mo 53.6 14 0.00031 27.0 2.8 21 81-101 16-36 (99)
424 PRK10046 dpiA two-component re 52.9 11 0.00025 29.9 2.3 22 81-102 177-198 (225)
425 COG4565 CitB Response regulato 52.7 9.8 0.00021 32.7 2.0 37 66-102 153-194 (224)
426 PF04859 DUF641: Plant protein 52.5 26 0.00056 27.6 4.2 68 86-156 44-122 (131)
427 PRK10086 DNA-binding transcrip 52.4 21 0.00046 29.7 3.9 34 68-101 11-48 (311)
428 COG3604 FhlA Transcriptional r 52.4 14 0.00031 35.4 3.2 28 81-108 519-546 (550)
429 PRK13719 conjugal transfer tra 52.3 19 0.0004 30.7 3.6 42 66-107 139-188 (217)
430 PF08965 DUF1870: Domain of un 51.8 36 0.00078 26.6 4.8 46 71-118 4-51 (118)
431 cd04780 HTH_MerR-like_sg5 Heli 51.6 15 0.00033 26.6 2.6 25 82-107 1-25 (95)
432 TIGR02850 spore_sigG RNA polym 51.5 21 0.00045 29.6 3.7 21 81-101 222-242 (254)
433 TIGR00180 parB_part ParB-like 51.5 26 0.00057 27.9 4.2 26 78-103 117-142 (187)
434 TIGR02684 dnstrm_HI1420 probab 51.4 24 0.00052 25.6 3.6 33 72-106 36-68 (89)
435 PRK09954 putative kinase; Prov 51.3 21 0.00045 30.7 3.8 32 74-105 10-41 (362)
436 TIGR01637 phage_arpU phage tra 51.2 40 0.00087 25.1 4.9 27 3-29 8-34 (132)
437 TIGR02944 suf_reg_Xantho FeS a 51.2 15 0.00033 27.2 2.7 24 82-105 26-49 (130)
438 PHA01976 helix-turn-helix prot 51.1 39 0.00084 21.9 4.3 43 66-108 11-57 (67)
439 PF09035 Tn916-Xis: Excisionas 50.8 16 0.00035 25.7 2.5 27 80-106 12-38 (67)
440 PRK15369 two component system 50.5 22 0.00048 25.9 3.4 22 81-102 164-185 (211)
441 cd08317 Death_ank Death domain 50.5 28 0.0006 24.4 3.7 37 69-105 3-39 (84)
442 PRK11233 nitrogen assimilation 50.3 23 0.00049 29.3 3.8 21 81-101 15-35 (305)
443 TIGR02941 Sigma_B RNA polymera 50.2 32 0.00068 28.3 4.6 23 80-102 220-242 (255)
444 COG1309 AcrR Transcriptional r 50.1 13 0.00028 26.1 2.0 24 78-101 29-52 (201)
445 PRK15435 bifunctional DNA-bind 49.9 41 0.0009 29.9 5.6 29 80-108 98-127 (353)
446 PRK10100 DNA-binding transcrip 49.8 42 0.00092 27.4 5.3 78 22-102 104-191 (216)
447 PRK13558 bacterio-opsin activa 49.6 16 0.00035 33.7 3.0 27 78-104 623-653 (665)
448 PRK07122 RNA polymerase sigma 49.4 27 0.00058 29.4 4.1 22 81-102 231-252 (264)
449 PF10075 PCI_Csn8: COP9 signal 49.4 18 0.00038 27.5 2.8 29 78-106 94-122 (143)
450 TIGR00122 birA_repr_reg BirA b 49.3 23 0.00051 23.5 3.1 30 82-111 14-43 (69)
451 TIGR01610 phage_O_Nterm phage 49.2 26 0.00057 25.2 3.5 27 79-105 45-71 (95)
452 PRK11074 putative DNA-binding 49.2 23 0.0005 29.2 3.6 21 81-101 16-36 (300)
453 PF01978 TrmB: Sugar-specific 49.2 22 0.00048 23.5 2.9 24 81-104 22-45 (68)
454 PF09012 FeoC: FeoC like trans 48.9 20 0.00044 24.1 2.7 21 81-101 14-34 (69)
455 COG3382 Solo B3/4 domain (OB-f 48.9 6.2 0.00013 33.9 0.2 52 108-159 167-220 (229)
456 TIGR02885 spore_sigF RNA polym 48.7 29 0.00062 28.0 4.1 21 81-101 199-219 (231)
457 PRK10430 DNA-binding transcrip 48.7 17 0.00036 29.1 2.7 26 80-105 177-202 (239)
458 PRK09210 RNA polymerase sigma 48.5 40 0.00087 29.9 5.2 28 75-102 313-346 (367)
459 PRK06746 peptide chain release 48.4 53 0.0011 29.6 6.0 43 112-154 30-73 (326)
460 PRK09791 putative DNA-binding 48.3 29 0.00063 28.4 4.1 32 70-101 4-39 (302)
461 cd08805 Death_ank1 Death domai 48.1 29 0.00063 25.1 3.6 37 69-105 3-39 (84)
462 PRK03837 transcriptional regul 47.9 19 0.00041 29.0 2.9 25 81-105 36-61 (241)
463 PRK09464 pdhR transcriptional 47.7 19 0.00041 29.4 2.9 25 81-105 33-58 (254)
464 PF02037 SAP: SAP domain; Int 47.6 13 0.00027 22.5 1.4 17 93-109 4-20 (35)
465 PF12840 HTH_20: Helix-turn-he 47.5 32 0.00069 22.4 3.5 23 80-102 23-45 (61)
466 PRK11886 bifunctional biotin-- 47.4 24 0.00053 30.2 3.6 26 81-106 18-43 (319)
467 PRK10411 DNA-binding transcrip 47.4 27 0.00058 29.2 3.8 35 73-107 10-44 (240)
468 PRK13698 plasmid-partitioning 47.3 30 0.00066 31.1 4.3 34 76-109 171-204 (323)
469 PF02002 TFIIE_alpha: TFIIE al 47.0 28 0.00061 25.1 3.4 33 73-105 19-51 (105)
470 COG2826 Tra8 Transposase and i 47.0 45 0.00098 30.1 5.3 43 81-125 23-65 (318)
471 PF04552 Sigma54_DBD: Sigma-54 46.8 6.5 0.00014 31.6 0.0 25 81-105 49-73 (160)
472 PF13744 HTH_37: Helix-turn-he 46.5 39 0.00084 23.4 3.9 42 66-107 27-73 (80)
473 PRK13869 plasmid-partitioning 46.0 18 0.00039 32.5 2.7 24 81-104 48-71 (405)
474 PF14335 DUF4391: Domain of un 45.9 30 0.00066 28.5 3.8 40 112-151 181-221 (221)
475 PF10945 DUF2629: Protein of u 45.8 11 0.00025 24.7 1.1 20 73-92 6-28 (44)
476 PRK10837 putative DNA-binding 45.7 28 0.00062 28.0 3.6 21 81-101 17-37 (290)
477 PRK09990 DNA-binding transcrip 45.7 21 0.00045 29.1 2.8 25 81-105 30-55 (251)
478 PRK11062 nhaR transcriptional 45.6 33 0.00072 28.2 4.0 31 71-101 4-38 (296)
479 PRK09508 leuO leucine transcri 45.6 32 0.00069 28.6 4.0 33 69-101 20-56 (314)
480 PF08784 RPA_C: Replication pr 45.4 21 0.00046 25.5 2.6 25 81-105 65-89 (102)
481 COG2973 TrpR Trp operon repres 45.3 15 0.00031 28.2 1.7 21 81-101 60-80 (103)
482 PRK12682 transcriptional regul 45.3 31 0.00068 28.5 3.9 21 81-101 16-36 (309)
483 PRK13509 transcriptional repre 45.2 29 0.00064 29.0 3.7 33 73-105 11-43 (251)
484 KOG0723 Molecular chaperone (D 45.1 18 0.00039 28.1 2.2 31 81-117 52-82 (112)
485 PF12674 Zn_ribbon_2: Putative 45.0 22 0.00048 25.6 2.6 60 40-99 5-78 (81)
486 PF00440 TetR_N: Bacterial reg 45.0 15 0.00032 22.8 1.5 36 88-123 9-45 (47)
487 PRK11020 hypothetical protein; 45.0 55 0.0012 25.7 4.8 42 115-156 7-52 (118)
488 PF13413 HTH_25: Helix-turn-he 44.8 33 0.00072 23.1 3.3 35 75-111 4-39 (62)
489 COG1802 GntR Transcriptional r 44.4 18 0.00038 29.3 2.2 25 81-105 39-63 (230)
490 COG1654 BirA Biotin operon rep 44.4 31 0.00068 24.8 3.2 25 77-101 15-39 (79)
491 PRK10082 cell density-dependen 44.3 33 0.00071 28.3 3.8 33 69-101 9-45 (303)
492 PF14282 FlxA: FlxA-like prote 44.3 91 0.002 23.1 5.9 42 113-154 19-70 (106)
493 TIGR00373 conserved hypothetic 44.2 32 0.0007 27.2 3.6 25 81-105 28-52 (158)
494 TIGR02424 TF_pcaQ pca operon t 43.8 34 0.00073 27.9 3.8 21 81-101 17-37 (300)
495 PRK07914 hypothetical protein; 43.8 73 0.0016 27.3 6.0 48 83-132 251-298 (320)
496 PRK15201 fimbriae regulatory p 43.7 31 0.00067 29.2 3.5 43 65-107 128-178 (198)
497 TIGR02702 SufR_cyano iron-sulf 43.4 35 0.00076 27.4 3.8 28 78-105 12-39 (203)
498 smart00529 HTH_DTXR Helix-turn 43.3 25 0.00053 24.3 2.5 22 84-105 2-23 (96)
499 PRK09570 rpoH DNA-directed RNA 43.3 13 0.00027 27.1 1.1 33 5-37 19-51 (79)
500 PRK04140 hypothetical protein; 43.0 31 0.00067 30.7 3.6 30 72-101 130-159 (317)
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=99.95 E-value=2.3e-28 Score=164.06 Aligned_cols=51 Identities=55% Similarity=0.946 Sum_probs=49.3
Q ss_pred cCCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600 68 TGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118 (160)
Q Consensus 68 ~~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl 118 (160)
+++||++||++|||+|++|||++||||+|+|||+||++||.||||||++||
T Consensus 2 ~~~lt~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~RWP~Rkl~Sl 52 (52)
T PF02042_consen 2 TKSLTLEDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIPRWPYRKLKSL 52 (52)
T ss_pred CCccCHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCCCCCchhhccC
Confidence 468999999999999999999999999999999999999999999999986
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=96.70 E-value=0.0026 Score=44.46 Aligned_cols=40 Identities=18% Similarity=0.408 Sum_probs=31.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy 112 (160)
++.....-.+++.|.|+.+|||++++=|.|+++|...|+-
T Consensus 26 l~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~e 65 (77)
T PF01418_consen 26 LENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKE 65 (77)
T ss_dssp HH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHH
T ss_pred HhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHH
Confidence 4444566689999999999999999999999999988773
No 3
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.00 E-value=0.019 Score=43.66 Aligned_cols=49 Identities=29% Similarity=0.289 Sum_probs=36.3
Q ss_pred CCCCCCCCchhhhhccCCCCHHHHH-----hhcCCcHHHHHHHcCCChhHHHHH
Q 041600 53 DYSQPPMTNSVQRERTGKLTLRDLM-----IYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 53 ~~~~ps~s~s~~r~r~~~lt~~~L~-----~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
..+.|.....+.....-.|++|++. .|.+|++.|||..+|||.+|+-++
T Consensus 24 ~~F~P~g~~~~~~~~~V~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ri 77 (106)
T PF02001_consen 24 RCFKPAGPGSELEKEPVVLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRI 77 (106)
T ss_pred CEEeCCCCCCCCCcceEEeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHH
Confidence 3445544222223345678999876 778999999999999999999888
No 4
>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=95.95 E-value=0.049 Score=40.06 Aligned_cols=74 Identities=18% Similarity=0.197 Sum_probs=50.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC---C-------ChhHH------HhhH-H---HHHHHHhhhccC--CcHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH---R-------WPHRK------IKSI-Q---RRMSVASGRLRS--NDAEERAN 139 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~---R-------WPyRk------ikSl-~---~~i~~L~~~~~~--~~~eerar 139 (160)
+++.|+|+.+|||+++|+...++.|+. | |.... |+++ + -.|+.+..+++. +....++.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~ 80 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEE 80 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhh
Confidence 468999999999999999999886642 2 33222 3332 1 124555666653 23356778
Q ss_pred HHHHHHHHHHHHHHHh
Q 041600 140 AQIEIQRLQEEMAAAC 155 (160)
Q Consensus 140 ~~~eIerL~~Em~~~c 155 (160)
+..++.++..|+..+.
T Consensus 81 ~~~~~~~~~~~~~~l~ 96 (99)
T cd04765 81 AEERLPSIRAELLDLR 96 (99)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8888999999988764
No 5
>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=95.92 E-value=0.012 Score=37.48 Aligned_cols=32 Identities=13% Similarity=0.342 Sum_probs=23.2
Q ss_pred HHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 73 LRDLMIYF--HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 73 ~~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
++++...+ ++|+.++|+.+|||.+|+.|+.++
T Consensus 11 ~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 11 IEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45555555 599999999999999999998653
No 6
>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=95.77 E-value=0.06 Score=38.44 Aligned_cols=73 Identities=21% Similarity=0.263 Sum_probs=46.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC----------ChhHHHhhHHHHHHHHhhhcc--CCcHHHHHHHHHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR----------WPHRKIKSIQRRMSVASGRLR--SNDAEERANAQIEIQRLQE 149 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R----------WPyRkikSl~~~i~~L~~~~~--~~~~eerar~~~eIerL~~ 149 (160)
+++.++|+.+||++++|+...+ .|+-. .+...+..+.. |..|..... -.+-.+-.....+++.|++
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~p~r~~~g~R~y~~~dv~~l~~-i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~ 79 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLLSPSRTDGGTRRYSERDIERLRR-IQRLTQELGVNLAGVKRILELEEELAELRA 79 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCeeECHHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 6899999999999999998876 46433 23334444443 444444221 1233334456688888888
Q ss_pred HHHHHhc
Q 041600 150 EMAAACA 156 (160)
Q Consensus 150 Em~~~c~ 156 (160)
|+..+-.
T Consensus 80 ~l~~l~~ 86 (91)
T cd04766 80 ELDELRA 86 (91)
T ss_pred HHHHHHH
Confidence 8887653
No 7
>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=95.63 E-value=0.05 Score=39.62 Aligned_cols=72 Identities=14% Similarity=0.107 Sum_probs=46.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC----CCCh--hHH--------------HhhHHHHHHHHhhhccCCcHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL----HRWP--HRK--------------IKSIQRRMSVASGRLRSNDAEERANAQ 141 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI----~RWP--yRk--------------ikSl~~~i~~L~~~~~~~~~eerar~~ 141 (160)
+.+.|+|+.+||++++|+...+ .|+ .|.| ||. ++.+.--|+.++..+...+++..+...
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~-~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~ 79 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE-IGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALR 79 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHH
Confidence 4688999999999999997764 454 2344 221 222223355566666654455566666
Q ss_pred HHHHHHHHHHHHH
Q 041600 142 IEIQRLQEEMAAA 154 (160)
Q Consensus 142 ~eIerL~~Em~~~ 154 (160)
.++..|++++.++
T Consensus 80 ~~~~~l~~~i~~l 92 (103)
T cd01106 80 EQKELLEEKKERL 92 (103)
T ss_pred HHHHHHHHHHHHH
Confidence 7777777777665
No 8
>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=95.62 E-value=0.015 Score=35.44 Aligned_cols=28 Identities=25% Similarity=0.348 Sum_probs=24.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
|.+.|||+.||||.+++.+.+++..|+.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence 6789999999999999999998876753
No 9
>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=95.10 E-value=0.099 Score=37.88 Aligned_cols=73 Identities=16% Similarity=0.125 Sum_probs=49.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC---CC-h--hHH--------------HhhHHHHHHHHhhhccCCcHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH---RW-P--HRK--------------IKSIQRRMSVASGRLRSNDAEERANAQ 141 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~---RW-P--yRk--------------ikSl~~~i~~L~~~~~~~~~eerar~~ 141 (160)
+++.|+|+.+||++.||+-..++ |+- +. + ||. ++.+.-.++.+++.+...+.+-..-..
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~l~ 79 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLL 79 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHHHH
Confidence 47899999999999999988766 753 22 2 341 122222355666666654555566677
Q ss_pred HHHHHHHHHHHHHh
Q 041600 142 IEIQRLQEEMAAAC 155 (160)
Q Consensus 142 ~eIerL~~Em~~~c 155 (160)
.+++.|++++.++-
T Consensus 80 ~~~~~l~~~i~~l~ 93 (96)
T cd04768 80 EKKQAIQQKIDRLQ 93 (96)
T ss_pred HHHHHHHHHHHHHH
Confidence 88888888888764
No 10
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=95.08 E-value=0.11 Score=39.01 Aligned_cols=42 Identities=14% Similarity=0.130 Sum_probs=31.7
Q ss_pred hhccCCCCHHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 65 RERTGKLTLRDLMIYF--HLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 65 r~r~~~lt~~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
|..+..+-.+-+..++ +.+..++|+++||+.++|-+-.+++.
T Consensus 11 r~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3444444455555555 68999999999999999999988763
No 11
>PF12728 HTH_17: Helix-turn-helix domain
Probab=94.83 E-value=0.034 Score=35.32 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=25.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
|...|||+.||||.+++.+.+++-+|+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~ 29 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPP 29 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCe
Confidence 6789999999999999999999888843
No 12
>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=94.76 E-value=0.039 Score=33.27 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=23.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+.+.|||+.||||.++|.+.+++-.++
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 468999999999999999998875553
No 13
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=94.67 E-value=0.035 Score=45.92 Aligned_cols=38 Identities=18% Similarity=0.329 Sum_probs=33.4
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy 112 (160)
.......+++.+.|++.|||++|+=|.||++|..-++-
T Consensus 28 n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e 65 (284)
T PRK11302 28 SPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPD 65 (284)
T ss_pred CHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHH
Confidence 33455689999999999999999999999999999873
No 14
>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=94.63 E-value=0.065 Score=33.56 Aligned_cols=28 Identities=11% Similarity=0.058 Sum_probs=21.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
..++--+.+||+.|||+.++|.+..+++
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 4567789999999999999999887654
No 15
>PRK15482 transcriptional regulator MurR; Provisional
Probab=94.63 E-value=0.035 Score=46.51 Aligned_cols=46 Identities=7% Similarity=0.180 Sum_probs=37.4
Q ss_pred CCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600 69 GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK 114 (160)
Q Consensus 69 ~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk 114 (160)
.+.=++.....-.+++.|.|++.|||++|+=|.|+++|..-|+-=|
T Consensus 22 a~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk 67 (285)
T PRK15482 22 ADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELR 67 (285)
T ss_pred HHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHH
Confidence 3333444456668999999999999999999999999999998433
No 16
>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=94.54 E-value=0.14 Score=37.57 Aligned_cols=69 Identities=16% Similarity=0.183 Sum_probs=41.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCh------hH-----HHhhHH------H---HHHHHhhhccCCcHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHRWP------HR-----KIKSIQ------R---RMSVASGRLRSNDAEERANAQ 141 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP------yR-----kikSl~------~---~i~~L~~~~~~~~~eerar~~ 141 (160)
+++.|+|+.+|||++||+-..+. |+-. | || .+.-+. . .++.+...++.. ...+...
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~-~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~~~--~~~~~l~ 77 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLIT-GTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGK--LTRSLLL 77 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCcCCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC--cHHHHHH
Confidence 68999999999999999987765 6532 2 22 222222 1 223344444332 2234566
Q ss_pred HHHHHHHHHHHHH
Q 041600 142 IEIQRLQEEMAAA 154 (160)
Q Consensus 142 ~eIerL~~Em~~~ 154 (160)
.+++.|++++..+
T Consensus 78 ~~~~~l~~~i~~l 90 (102)
T cd04789 78 ERLSSLAEQIARK 90 (102)
T ss_pred HHHHHHHHHHHHH
Confidence 6777777777665
No 17
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=94.49 E-value=0.038 Score=35.09 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=18.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++++.++|+.||++.+|+.+.++++
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 6999999999999999999998863
No 18
>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=94.21 E-value=0.055 Score=36.32 Aligned_cols=27 Identities=30% Similarity=0.281 Sum_probs=24.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+++.|+|+.+||++++|+..+++.|+.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~ 27 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLL 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999987764
No 19
>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=94.10 E-value=0.33 Score=35.36 Aligned_cols=25 Identities=32% Similarity=0.453 Sum_probs=21.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.++|+.+|||+++|+...+ .|+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5899999999999999998865 664
No 20
>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=94.06 E-value=0.061 Score=33.27 Aligned_cols=30 Identities=27% Similarity=0.334 Sum_probs=23.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHRWPHR 113 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR 113 (160)
+++.|+|+.|||++.+|++..++-.|+ |.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~--~~~ 30 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS--PAR 30 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC--CCc
Confidence 578999999999999999876554443 544
No 21
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.00 E-value=0.14 Score=38.84 Aligned_cols=45 Identities=27% Similarity=0.321 Sum_probs=35.6
Q ss_pred ccCCCCHHHHH-----hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 67 RTGKLTLRDLM-----IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 67 r~~~lt~~~L~-----~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
..-.||+++|. .|-+|.+.|||.++|||..||-+. ++|-++++.+
T Consensus 30 ~~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~-------------l~sAR~KvA~ 79 (99)
T COG1342 30 EPVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRL-------------LTSARKKVAD 79 (99)
T ss_pred cceeecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHH-------------HHHHHHHHHH
Confidence 34568888875 788999999999999999998665 5666665554
No 22
>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=94.00 E-value=0.07 Score=35.63 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=24.3
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+++.|+|+.+||++++|+...++.|+.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~ 27 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLY 27 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999987775
No 23
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=93.93 E-value=0.1 Score=38.49 Aligned_cols=31 Identities=19% Similarity=0.210 Sum_probs=27.5
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
-..++-.+.+||+.|||+.++|.+..+++||
T Consensus 64 L~~~~gn~s~AAr~LGIsRsTL~rKLkr~gi 94 (95)
T PRK00430 64 MQYTRGNQTRAALMLGINRGTLRKKLKKYGM 94 (95)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 3455678999999999999999999999997
No 24
>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=93.91 E-value=0.25 Score=36.42 Aligned_cols=72 Identities=21% Similarity=0.247 Sum_probs=45.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC-C-C--h---hHH-----------HhhH---HHHHHHHhhhccCCcH-HHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH-R-W--P---HRK-----------IKSI---QRRMSVASGRLRSNDA-EERAN 139 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~-R-W--P---yRk-----------ikSl---~~~i~~L~~~~~~~~~-eerar 139 (160)
+++.|+|+.+||+++||+-.+++ |+- . + + ||. |+.+ .-.++.+...++..+. +-.+-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~~~~~~~ 79 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKL 79 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHH
Confidence 57899999999999999998876 752 2 2 3 453 1111 2234455555554443 44445
Q ss_pred HHHHHHHHHHHHHHH
Q 041600 140 AQIEIQRLQEEMAAA 154 (160)
Q Consensus 140 ~~~eIerL~~Em~~~ 154 (160)
...+++.|++++..+
T Consensus 80 l~~~~~~l~~~i~~l 94 (108)
T cd01107 80 LREKLAELEAEIEEL 94 (108)
T ss_pred HHHHHHHHHHHHHHH
Confidence 667777777777665
No 25
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=93.85 E-value=0.063 Score=44.56 Aligned_cols=39 Identities=21% Similarity=0.234 Sum_probs=33.6
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK 114 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk 114 (160)
....-.+++.+.|++.|||++|+=|.||++|...|+-=|
T Consensus 25 ~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk 63 (278)
T PRK11557 25 PDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALK 63 (278)
T ss_pred HHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHH
Confidence 345557999999999999999999999999999987433
No 26
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=93.77 E-value=0.055 Score=45.97 Aligned_cols=40 Identities=25% Similarity=0.316 Sum_probs=34.3
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI 115 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki 115 (160)
-...-+++++|.|+..|||++|+=|.||++|-.-||-=|+
T Consensus 31 ~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~ 70 (281)
T COG1737 31 PDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKL 70 (281)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHH
Confidence 3345579999999999999999999999999999994443
No 27
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.67 E-value=0.059 Score=33.92 Aligned_cols=24 Identities=25% Similarity=0.390 Sum_probs=18.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+++..++|+.||||.+|+.+..++
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 899999999999999999998655
No 28
>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=93.57 E-value=0.33 Score=30.29 Aligned_cols=34 Identities=12% Similarity=0.098 Sum_probs=28.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+..++.-.++.+.++|+.+||+++++.++. .|-.
T Consensus 7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e--~g~~ 40 (58)
T TIGR03070 7 VRARRKALGLTQADLADLAGVGLRFIRDVE--NGKP 40 (58)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH--CCCC
Confidence 556777889999999999999999999994 4543
No 29
>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=93.55 E-value=0.34 Score=30.61 Aligned_cols=42 Identities=24% Similarity=0.382 Sum_probs=29.3
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh-hHHHhhH
Q 041600 74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP-HRKIKSI 118 (160)
Q Consensus 74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP-yRkikSl 118 (160)
..++.-.++++.+.|+.+||+.+++.++. .| .+.| ...+..+
T Consensus 2 k~~r~~~gls~~~la~~~gis~~~i~~~~--~g-~~~~~~~~~~~i 44 (55)
T PF01381_consen 2 KELRKEKGLSQKELAEKLGISRSTISRIE--NG-KRNPSLDTLKKI 44 (55)
T ss_dssp HHHHHHTTS-HHHHHHHHTS-HHHHHHHH--TT-SSTSBHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHhCCCcchhHHHh--cC-CCCCCHHHHHHH
Confidence 45666778999999999999999999995 55 3444 4444443
No 30
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=93.48 E-value=0.19 Score=32.91 Aligned_cols=46 Identities=11% Similarity=0.263 Sum_probs=33.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC-CCCChhHHHhhHHHHHHHHh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDG-LHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWPyRkikSl~~~i~~L~ 126 (160)
.+++.++|+.+|+|.+.|.+++++.. ++-..|.+...+++.+..|.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~a~~~l~ 47 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLR 47 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 36889999999999999999998764 65455555444555444444
No 31
>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=93.47 E-value=0.39 Score=34.77 Aligned_cols=74 Identities=20% Similarity=0.236 Sum_probs=48.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC-----------CChhHHHhhHH---------HHHHHHhhhccCCcHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH-----------RWPHRKIKSIQ---------RRMSVASGRLRSNDAEERANAQ 141 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~-----------RWPyRkikSl~---------~~i~~L~~~~~~~~~eerar~~ 141 (160)
|.+.|+|+.+|||+.+|+-..+ .|+- .+.-..+..+. -.++.++..++..+.+-.+-..
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~-~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~l~ 79 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH-IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLR 79 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChhHHHHHH
Confidence 5789999999999999997764 4432 12222222222 2245555556544445567778
Q ss_pred HHHHHHHHHHHHHhc
Q 041600 142 IEIQRLQEEMAAACA 156 (160)
Q Consensus 142 ~eIerL~~Em~~~c~ 156 (160)
.+++.|++++.++..
T Consensus 80 ~~~~~l~~~i~~l~~ 94 (96)
T cd04788 80 RQLARLEEQLELATR 94 (96)
T ss_pred HHHHHHHHHHHHHHh
Confidence 899999999988753
No 32
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=93.44 E-value=0.082 Score=44.30 Aligned_cols=35 Identities=9% Similarity=0.249 Sum_probs=31.7
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP 111 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP 111 (160)
.....+++.+.|+..|||++|+=|.||++|..-|+
T Consensus 42 ~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~ 76 (292)
T PRK11337 42 DLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFR 76 (292)
T ss_pred HHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHH
Confidence 34557899999999999999999999999999887
No 33
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=93.39 E-value=0.24 Score=40.37 Aligned_cols=27 Identities=15% Similarity=0.319 Sum_probs=24.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
|.+.++|+.+|||++||.+..++.||+
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~ 27 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLP 27 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 478999999999999999999988885
No 34
>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=93.36 E-value=0.11 Score=34.30 Aligned_cols=26 Identities=31% Similarity=0.419 Sum_probs=23.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+||+.++|++..++.|+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~ 26 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGL 26 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCC
Confidence 47899999999999999999887776
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=93.27 E-value=0.24 Score=36.08 Aligned_cols=27 Identities=26% Similarity=0.356 Sum_probs=23.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
+++.|+|+.+||++++|+...+. |+-.
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~ 27 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLVS 27 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 57899999999999999999864 7644
No 36
>PRK00118 putative DNA-binding protein; Validated
Probab=93.15 E-value=0.52 Score=35.59 Aligned_cols=61 Identities=16% Similarity=0.048 Sum_probs=38.9
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQE 149 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~ 149 (160)
.-+-+++.+|+|+.+|||+.+++++- +|-.+.+...++.|.-.-+ -.++...-+.++++.+
T Consensus 29 ~y~eg~S~~EIAe~lGIS~~TV~r~L---------~RArkkLr~~~~~~~~~~~---~~~~~~~~~~~~~~~~ 89 (104)
T PRK00118 29 YYLDDYSLGEIAEEFNVSRQAVYDNI---------KRTEKLLEDYEEKLHLYEK---FIERNELFDKIAYLKE 89 (104)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHHChHHH---HHHHHHHHHHHHHHHH
Confidence 34557999999999999999999884 5555666665555543322 2333344445555443
No 37
>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=93.06 E-value=0.52 Score=34.14 Aligned_cols=73 Identities=14% Similarity=0.093 Sum_probs=47.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC--C-CCh---hHH--------------HhhHHHHHHHHhhhccCCcH-HHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL--H-RWP---HRK--------------IKSIQRRMSVASGRLRSNDA-EERANA 140 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI--~-RWP---yRk--------------ikSl~~~i~~L~~~~~~~~~-eerar~ 140 (160)
+++.|+|+.+|||+.+|+-..+ .|+ + +-+ ||. ++.+.-.++.+++.+...+. +-..-.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l 79 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK-IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELL 79 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHH
Confidence 4789999999999999997764 576 2 222 332 22222335555665554333 345667
Q ss_pred HHHHHHHHHHHHHHh
Q 041600 141 QIEIQRLQEEMAAAC 155 (160)
Q Consensus 141 ~~eIerL~~Em~~~c 155 (160)
+.+++.|++++..+-
T Consensus 80 ~~~~~~l~~~i~~l~ 94 (97)
T cd04782 80 KKQEKEIKEEIEELQ 94 (97)
T ss_pred HHHHHHHHHHHHHHH
Confidence 788889999888763
No 38
>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=93.03 E-value=0.12 Score=34.80 Aligned_cols=28 Identities=32% Similarity=0.605 Sum_probs=23.5
Q ss_pred HhhcCCc----HHHHHHHcCCChhHHHHHHHH
Q 041600 77 MIYFHLP----IEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 77 ~~yF~lP----~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
..||+.| +.|.|+.||||.+++-..-|+
T Consensus 15 ~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 15 LGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3789877 899999999999998877554
No 39
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=92.93 E-value=0.14 Score=32.40 Aligned_cols=30 Identities=20% Similarity=0.291 Sum_probs=24.6
Q ss_pred HHHhhcCC-cHHHHHHHcCCChhHHHHHHHH
Q 041600 75 DLMIYFHL-PIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 75 ~L~~yF~l-P~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
-+....+. +++++|+.+|||.++++++-.+
T Consensus 20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 20 ILKLLRESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34455556 9999999999999999999755
No 40
>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=92.47 E-value=0.97 Score=35.03 Aligned_cols=27 Identities=22% Similarity=0.350 Sum_probs=23.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.|+|.|+|+.+||++.||+-..++ |+-
T Consensus 1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl 27 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQK-GLI 27 (139)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 378999999999999999988766 753
No 41
>PRK04217 hypothetical protein; Provisional
Probab=92.44 E-value=0.57 Score=35.73 Aligned_cols=41 Identities=22% Similarity=0.196 Sum_probs=31.4
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhh
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASG 127 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~ 127 (160)
.+-+++++|+|+.||||.+|++++. +|-.+.|...+..-..
T Consensus 55 ~~eGlS~~EIAk~LGIS~sTV~r~L---------~RArkkLre~L~~~~~ 95 (110)
T PRK04217 55 DYEGLTQEEAGKRMGVSRGTVWRAL---------TSARKKVAQMLVEGRE 95 (110)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHhccc
Confidence 3346999999999999999999996 4556666666655444
No 42
>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=92.40 E-value=0.87 Score=33.81 Aligned_cols=26 Identities=23% Similarity=0.264 Sum_probs=21.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
|++.|+|+.+|||+.||+-..+. |+-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~-GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ-GLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC-CCC
Confidence 57899999999999999987764 643
No 43
>PRK01905 DNA-binding protein Fis; Provisional
Probab=92.39 E-value=0.25 Score=34.70 Aligned_cols=30 Identities=17% Similarity=0.068 Sum_probs=26.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
...+-...+||+.|||+.++|.+.-+++||
T Consensus 47 ~~~~gn~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 47 EQAGGNQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 334567999999999999999999999987
No 44
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=92.34 E-value=1.5 Score=33.21 Aligned_cols=82 Identities=10% Similarity=0.059 Sum_probs=46.5
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHH---------------HHHHHcCCC-CChhHHH--------------hhHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVK---------------KICRRDGLH-RWPHRKI--------------KSIQRRM 122 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LK---------------r~CR~~GI~-RWPyRki--------------kSl~~~i 122 (160)
+..++.-.++.+.+.|+.+||+.+++- ++|+-+||+ -|=.--- ..+...-
T Consensus 10 lk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~l~~g~~~~~~~~~~~~~~~~~l~~~~ 89 (135)
T PRK09706 10 IRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDEDKQPTPPVPLNQPVELSEDQ 89 (135)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcCCCcCCCCCcccccCCCCCCHHH
Confidence 456677778899999999999865554 455555552 1211000 0011112
Q ss_pred HHHhhhccCCcHHHHHHHHHHHHHHHHHHHHH
Q 041600 123 SVASGRLRSNDAEERANAQIEIQRLQEEMAAA 154 (160)
Q Consensus 123 ~~L~~~~~~~~~eerar~~~eIerL~~Em~~~ 154 (160)
..|-..++.-+++++..+...++.+.++|+++
T Consensus 90 ~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~ 121 (135)
T PRK09706 90 KELLELFDALPESEQDAQLSEMRARVENFNKL 121 (135)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Confidence 23333444456777777777766666666654
No 45
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=92.24 E-value=0.28 Score=37.60 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=30.7
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
.-+.++|.+|+|..||||+.+++... +|=.+.|.+.+..
T Consensus 148 ~~~~~~s~~eIA~~lgis~~~v~~~l---------~Rar~~Lr~~l~~ 186 (187)
T PRK09641 148 KYIEDLSLKEISEILDLPVGTVKTRI---------HRGREALRKQLRH 186 (187)
T ss_pred HHhhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHhc
Confidence 35678999999999999999999885 5656666665543
No 46
>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=92.08 E-value=0.59 Score=34.17 Aligned_cols=26 Identities=15% Similarity=0.201 Sum_probs=22.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+++.|+|+.+|||++||+-.-++ |+-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 68999999999999999876654 754
No 47
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=92.07 E-value=0.18 Score=30.97 Aligned_cols=27 Identities=19% Similarity=0.593 Sum_probs=21.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI 107 (160)
.+++.++|..+|+|++.|.|+.++. |+
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 4889999999999999999999887 66
No 48
>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=91.83 E-value=0.27 Score=36.90 Aligned_cols=39 Identities=21% Similarity=0.330 Sum_probs=32.4
Q ss_pred CCCHHHHH----hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 70 KLTLRDLM----IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 70 ~lt~~~L~----~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.|..+.|. .+=++++.|.|+.||||.+++-+...++|+.
T Consensus 56 Kid~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t 98 (119)
T PF01710_consen 56 KIDRDELKALVEENPDATLRELAERLGVSPSTIWRALKRLGIT 98 (119)
T ss_pred cccHHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCch
Confidence 34455554 5568999999999999999999999999994
No 49
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=91.75 E-value=0.26 Score=30.19 Aligned_cols=23 Identities=26% Similarity=0.215 Sum_probs=20.0
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++..++|+.||||.+++++.-
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 36899999999999999887763
No 50
>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=91.73 E-value=0.64 Score=34.28 Aligned_cols=26 Identities=19% Similarity=0.241 Sum_probs=21.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+|||+.||+...+.--|
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999987654334
No 51
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=91.69 E-value=0.6 Score=33.51 Aligned_cols=33 Identities=12% Similarity=0.108 Sum_probs=27.3
Q ss_pred HHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600 76 LMIYFH--LPIEEAARRMKLCPTVVKKICRRD-GLH 108 (160)
Q Consensus 76 L~~yF~--lP~~eAA~~Lgv~~T~LKr~CR~~-GI~ 108 (160)
|...++ +++.++|+.+|+|+.+|.|++++. |++
T Consensus 14 i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 14 IDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred HHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 344444 899999999999999999999997 763
No 52
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=91.61 E-value=0.4 Score=36.58 Aligned_cols=37 Identities=14% Similarity=0.195 Sum_probs=29.4
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
-+-+++.+|+|+.||++.+++|... ||=++.|++.+.
T Consensus 131 ~~~g~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~ 167 (173)
T PRK09645 131 YYRGWSTAQIAADLGIPEGTVKSRL---------HYALRALRLALQ 167 (173)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHhh
Confidence 3448999999999999999999886 666666666544
No 53
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=91.40 E-value=0.49 Score=37.33 Aligned_cols=40 Identities=18% Similarity=0.243 Sum_probs=33.8
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhh
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGR 128 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~ 128 (160)
-+++.+|+|..|||+.+++|... +|-.+.|.+.+..+...
T Consensus 149 ~g~s~~EIA~~lg~s~~tV~~rl---------~rar~~Lr~~l~~~~~~ 188 (192)
T PRK09643 149 QGYSVADAARMLGVAEGTVKSRC---------ARGRARLAELLGYLRAG 188 (192)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHhcCC
Confidence 46999999999999999999996 77778888888776644
No 54
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=91.40 E-value=0.27 Score=43.15 Aligned_cols=31 Identities=6% Similarity=-0.080 Sum_probs=27.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
..++--..+||+.||||.+||.|..+++||.
T Consensus 427 ~~~~gn~~~aA~~LGisr~tL~rkl~~~~i~ 457 (457)
T PRK11361 427 EQQEGNRTRTALMLGISRRALMYKLQEYGID 457 (457)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence 3456789999999999999999999999983
No 55
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=91.36 E-value=0.38 Score=37.33 Aligned_cols=36 Identities=25% Similarity=0.304 Sum_probs=29.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.+++.+|+|+.||+|+.++|... ||-++.|.+.+
T Consensus 142 ~~~g~s~~EIA~~l~is~~tV~~~l---------~rar~~Lr~~l 177 (181)
T PRK12536 142 KLEGLSVAETAQLTGLSESAVKVGI---------HRGLKALAAKI 177 (181)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHh
Confidence 3568999999999999999999985 66666665544
No 56
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=91.31 E-value=0.22 Score=39.88 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=25.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
++++.++|+.||||.+|+.|++...|+
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~~~~ 198 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKTRGL 198 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhccc
Confidence 579999999999999999999998887
No 57
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=91.28 E-value=0.42 Score=37.19 Aligned_cols=40 Identities=25% Similarity=0.250 Sum_probs=31.5
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
|..+.+++..|+|+.|||+.+|+|... +|-++.|.+.+..
T Consensus 138 l~~~~gls~~EIA~~l~i~~~tVks~l---------~ra~~~l~~~l~~ 177 (182)
T COG1595 138 LRYLEGLSYEEIAEILGISVGTVKSRL---------HRARKKLREQLEE 177 (182)
T ss_pred hHhhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHhh
Confidence 346668999999999999999999985 5666666665544
No 58
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=91.12 E-value=0.22 Score=33.47 Aligned_cols=33 Identities=18% Similarity=0.273 Sum_probs=24.7
Q ss_pred HHHHHhh--cCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 73 LRDLMIY--FHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 73 ~~~L~~y--F~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
..-|..+ -+.++.++|+++||++++|.+-.+++
T Consensus 13 ~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 13 LQAVREYLESGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHCCCceEeeecccccccccccHHHHHH
Confidence 3344444 36899999999999999999887666
No 59
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=91.11 E-value=0.54 Score=35.40 Aligned_cols=38 Identities=18% Similarity=0.043 Sum_probs=29.4
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
.-+.+++.+|+|+.||+|..++|..- ||=.+.|++.+.
T Consensus 118 ~~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~ 155 (160)
T PRK09642 118 HYLEEKSYQEIALQEKIEVKTVEMKL---------YRARKWIKKHWK 155 (160)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHh
Confidence 34558999999999999999999885 555555555543
No 60
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=91.07 E-value=0.32 Score=42.16 Aligned_cols=30 Identities=10% Similarity=0.133 Sum_probs=27.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
...+--..+||+.||||.+||-|..+++||
T Consensus 296 ~~~~gn~~~aA~~LGIsR~tLyrklk~~gi 325 (326)
T PRK11608 296 QQAKFNQKRAAELLGLTYHQLRALLKKHQI 325 (326)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 335778999999999999999999999998
No 61
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=91.02 E-value=0.52 Score=36.99 Aligned_cols=38 Identities=16% Similarity=0.087 Sum_probs=31.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.++|+.|+|..||||+.++|.+. +|-+++|...+..
T Consensus 119 ~~~g~~~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~ 156 (181)
T PRK09637 119 ELEGLSQKEIAEKLGLSLSGAKSRV---------QRGRVKLKELLEG 156 (181)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 4568999999999999999999885 6666777766654
No 62
>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=91.02 E-value=1.7 Score=32.03 Aligned_cols=25 Identities=24% Similarity=0.438 Sum_probs=21.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|++.|+|+.+|||+.||+...+. |+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57899999999999999988764 64
No 63
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=90.91 E-value=0.55 Score=36.77 Aligned_cols=39 Identities=15% Similarity=0.227 Sum_probs=31.2
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
|.-+.+++.+|+|+.||+++.++|... ||=++.|++.+.
T Consensus 147 L~~~~g~s~~EIA~~lgis~~tVk~~l---------~Rar~~Lr~~l~ 185 (195)
T PRK12532 147 LKEILGFSSDEIQQMCGISTSNYHTIM---------HRARESLRQCLQ 185 (195)
T ss_pred hHHHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 345568999999999999999999885 666666666554
No 64
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=90.78 E-value=0.64 Score=34.75 Aligned_cols=36 Identities=19% Similarity=0.365 Sum_probs=28.4
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+-+++.+|+|..||||+.++|.+- +|=++.|...+.
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~ 155 (161)
T PRK09047 120 WEDMDVAETAAAMGCSEGSVKTHC---------SRATHALAKALE 155 (161)
T ss_pred HhcCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 447999999999999999999884 555666655544
No 65
>PRK15115 response regulator GlrR; Provisional
Probab=90.78 E-value=0.34 Score=42.52 Aligned_cols=31 Identities=23% Similarity=0.073 Sum_probs=27.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
...+-...+||+.||||.+||-|..+++||.
T Consensus 408 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~~~ 438 (444)
T PRK15115 408 QITKGNVTHAARMAGRNRTEFYKLLSRHELD 438 (444)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 3446789999999999999999999999995
No 66
>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=90.74 E-value=0.42 Score=30.43 Aligned_cols=27 Identities=19% Similarity=0.241 Sum_probs=19.1
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+.-+.++|..|+|+.||+|++++++.-
T Consensus 21 l~~~~g~s~~eIa~~l~~s~~~v~~~l 47 (54)
T PF08281_consen 21 LRYFQGMSYAEIAEILGISESTVKRRL 47 (54)
T ss_dssp HHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence 345568999999999999999999774
No 67
>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=90.73 E-value=2.1 Score=34.23 Aligned_cols=72 Identities=17% Similarity=0.204 Sum_probs=42.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC----Ch--hH-----HHhhHH---------HHHHHHhhhccCCcHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR----WP--HR-----KIKSIQ---------RRMSVASGRLRSNDAEERANAQ 141 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R----WP--yR-----kikSl~---------~~i~~L~~~~~~~~~eerar~~ 141 (160)
+++.|+|+.+|||++||.-.-+ .|+-. =+ || .+..+. -.++.++..++..+........
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~ 80 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER-IGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLR 80 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhHHHHHH
Confidence 6899999999999999987654 46421 11 33 233331 1233444445443334444556
Q ss_pred HHHHHHHHHHHHH
Q 041600 142 IEIQRLQEEMAAA 154 (160)
Q Consensus 142 ~eIerL~~Em~~~ 154 (160)
.+++.|.+|+..+
T Consensus 81 ~~~~~l~~ei~~L 93 (172)
T cd04790 81 RRLAELNREIQRL 93 (172)
T ss_pred HHHHHHHHHHHHH
Confidence 6677777776654
No 68
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=90.72 E-value=0.61 Score=35.11 Aligned_cols=36 Identities=14% Similarity=0.228 Sum_probs=27.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.+++.+|+|+.||+|+.++|..- +|-++.|++.+
T Consensus 122 ~~~~~s~~EIA~~lgis~~tV~~~l---------~ra~~~lr~~l 157 (163)
T PRK07037 122 RLHGETQKDIARELGVSPTLVNFMI---------RDALVHCRKCL 157 (163)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHH
Confidence 3458999999999999999999863 55555555544
No 69
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=90.72 E-value=0.32 Score=32.20 Aligned_cols=38 Identities=21% Similarity=0.121 Sum_probs=26.3
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC-CCCCh
Q 041600 74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDG-LHRWP 111 (160)
Q Consensus 74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWP 111 (160)
..++.--++.+.++|+.+|||.+++.++.+--. .+.|+
T Consensus 7 r~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~ 45 (64)
T PF13560_consen 7 RRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPD 45 (64)
T ss_dssp HHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHH
Confidence 445566689999999999999999999965333 33344
No 70
>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=90.68 E-value=1 Score=34.35 Aligned_cols=27 Identities=30% Similarity=0.425 Sum_probs=21.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
|.+.|+|+.+|||+.||+-. -+.|+-.
T Consensus 1 m~IgE~A~~~gvs~~TLRyY-E~~GLl~ 27 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFY-TRIGLLR 27 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHH-HHCCCCC
Confidence 57899999999999999544 5778643
No 71
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=90.65 E-value=0.43 Score=37.24 Aligned_cols=36 Identities=17% Similarity=0.138 Sum_probs=28.7
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+.++|.+|+|+.||+|+.++|.+- ||-++.|+..+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~ 188 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRL---------RYALQKLRELLA 188 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 458999999999999999999774 566666666554
No 72
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=90.64 E-value=0.24 Score=38.62 Aligned_cols=25 Identities=20% Similarity=0.257 Sum_probs=21.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+.+++.+|+|+.||+|++++|.+-
T Consensus 144 ~~~~~s~~eIA~~lgis~~tV~~~l 168 (189)
T PRK12515 144 YYHEKSVEEVGEIVGIPESTVKTRM 168 (189)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4467999999999999999998773
No 73
>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=90.61 E-value=0.32 Score=30.77 Aligned_cols=24 Identities=33% Similarity=0.602 Sum_probs=20.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
++++.|+|+.||+|..+++++.++
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 699999999999999999988643
No 74
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=90.60 E-value=0.69 Score=35.46 Aligned_cols=39 Identities=13% Similarity=0.107 Sum_probs=30.5
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
.-+-++|.+|+|..||+|+.++|..- +|=.+.|.+.+..
T Consensus 131 ~~~~~~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 131 YYYEQYSYKEMSEILNIPIGTVKYRL---------NYAKKQMREHLEG 169 (173)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 34568999999999999999999885 6666666665544
No 75
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=90.55 E-value=0.3 Score=32.32 Aligned_cols=26 Identities=23% Similarity=0.361 Sum_probs=22.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+||++.+|+...++.-+
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 46899999999999999999876554
No 76
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=90.36 E-value=0.75 Score=35.60 Aligned_cols=43 Identities=19% Similarity=0.212 Sum_probs=34.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhc
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL 129 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~ 129 (160)
-+-+++.+|+|+.||||..++|..- +|-++.|++.+..+..-+
T Consensus 130 ~~e~~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~~~~~~~ 172 (179)
T PRK12543 130 YLHDYSQEEIAQLLQIPIGTVKSRI---------HAALKKLRQKEQIEEIFL 172 (179)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHHHHHH
Confidence 3457999999999999999999873 677777777777765544
No 77
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=90.35 E-value=0.63 Score=36.07 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=31.2
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
.-+.+++..|+|+.||+++.++|.+- ||-++.|.+.+..
T Consensus 140 ~~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~ 178 (186)
T PRK05602 140 QYYQGLSNIEAAAVMDISVDALESLL---------ARGRRALRAQLAD 178 (186)
T ss_pred HHhcCCCHHHHHHHhCcCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 34558999999999999999999885 6666666666654
No 78
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=90.29 E-value=0.4 Score=44.24 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=24.4
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 83 PIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
...+||+.||||.|||-|.-|++||.
T Consensus 488 ~~~~aA~~LGisr~tL~rkl~~~gi~ 513 (520)
T PRK10820 488 STRKLAKRLGVSHTAIANKLREYGLS 513 (520)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 77899999999999999999999994
No 79
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=90.28 E-value=0.59 Score=36.53 Aligned_cols=40 Identities=18% Similarity=0.071 Sum_probs=32.4
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~ 126 (160)
-+.+++.+|+|+.||+|+.++|.+- +|=++.|.+.+....
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l---------~Rar~~Lr~~l~~~~ 183 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRL---------HRGRKQLRKQLVDVA 183 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHHH
Confidence 4458999999999999999999885 676777777776544
No 80
>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=90.28 E-value=2.6 Score=29.98 Aligned_cols=72 Identities=18% Similarity=0.251 Sum_probs=43.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC----------Chh------HHHhhHHH---HHHHHhhhccCC-c----HHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR----------WPH------RKIKSIQR---RMSVASGRLRSN-D----AEER 137 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R----------WPy------RkikSl~~---~i~~L~~~~~~~-~----~eer 137 (160)
+.+.|+|+.+||++++|+...+ .|+-. +.. +.++.+.+ .++.+...+... . ++.+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~-~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~~~~~~~~~~~ 79 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE-KGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALL 79 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccccchHHHHH
Confidence 4689999999999999998876 45422 111 22333332 234444444321 1 2345
Q ss_pred HHHHHHHHHHHHHHHHH
Q 041600 138 ANAQIEIQRLQEEMAAA 154 (160)
Q Consensus 138 ar~~~eIerL~~Em~~~ 154 (160)
.-....++.|++++..+
T Consensus 80 ~~~~~~~~~l~~~~~~l 96 (100)
T cd00592 80 ALLDEKLAELEEKIARL 96 (100)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55667777777777765
No 81
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=90.22 E-value=0.7 Score=35.94 Aligned_cols=38 Identities=18% Similarity=0.170 Sum_probs=31.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+-+++.+|+|..||++..+++... +|-.+.|++.++.
T Consensus 151 ~~~g~s~~eIA~~lgis~~tv~~~l---------~Rar~~Lr~~l~~ 188 (193)
T PRK11923 151 EFDGLSYEDIASVMQCPVGTVRSRI---------FRAREAIDKALQP 188 (193)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 3447999999999999999999986 7777777777765
No 82
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=90.20 E-value=0.69 Score=36.48 Aligned_cols=40 Identities=13% Similarity=-0.025 Sum_probs=32.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~ 126 (160)
-+.+++.+|+|..||||++++|... +|=++.|.+.+....
T Consensus 124 ~~eg~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~~~~~~ 163 (182)
T PRK12511 124 AIEGLSYQEAAAVLGIPIGTLMSRI---------GRARAALRAFEEGTG 163 (182)
T ss_pred HHcCCCHHHHHHHhCcCHHHHHHHH---------HHHHHHHHHHHHhcC
Confidence 4557999999999999999999986 666777777666554
No 83
>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=90.20 E-value=3.5 Score=30.04 Aligned_cols=25 Identities=28% Similarity=0.365 Sum_probs=21.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+|||+.||+...+ .|+
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 4789999999999999998765 454
No 84
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=90.15 E-value=0.53 Score=36.07 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=28.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
-+.+++.+|+|+.||+++.+++... +|-.+.|...+.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l---------~Rar~~Lr~~l~ 185 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRI---------HRGREALRKQLR 185 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHhh
Confidence 3458999999999999999999885 555555555544
No 85
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=90.14 E-value=0.79 Score=34.56 Aligned_cols=38 Identities=18% Similarity=0.190 Sum_probs=29.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+-++|.+|+|..||+|.+++|..- +|=++.|...|..
T Consensus 118 ~~~~~s~~eIA~~lgis~~tv~~~l---------~ra~~~Lr~~l~~ 155 (159)
T PRK12527 118 KLEGLSHQQIAEHLGISRSLVEKHI---------VNAMKHCRVRMRQ 155 (159)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 3447999999999999999999884 5666666666553
No 86
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.12 E-value=0.37 Score=30.03 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=21.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+.++.++|+.+|||.++|.+..+++
T Consensus 12 g~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 12 GESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHHHH
Confidence 4699999999999999999887554
No 87
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=89.97 E-value=0.45 Score=43.63 Aligned_cols=31 Identities=23% Similarity=0.278 Sum_probs=27.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
..++-.+.+||+.|||+.+||-|..+++||.
T Consensus 478 ~~~~gn~~~aA~~LGisr~tL~rklk~~gi~ 508 (509)
T PRK05022 478 AQHQGNWAAAARALELDRANLHRLAKRLGLK 508 (509)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 4457788999999999999999999999994
No 88
>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=89.95 E-value=0.58 Score=29.65 Aligned_cols=31 Identities=23% Similarity=0.104 Sum_probs=22.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.|+.-=-.|..+.|+.+|+|.+++.++-+++
T Consensus 11 ~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 11 LLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 3444446899999999999999998886553
No 89
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=89.92 E-value=0.64 Score=30.23 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=25.5
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600 74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118 (160)
Q Consensus 74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl 118 (160)
.++..--++.+.+.|+..||+.++|.+++..- +..|+.-.+..+
T Consensus 3 ~~~m~~~~it~~~La~~~gis~~tl~~~~~~~-~~~~~~~~l~~i 46 (63)
T PF13443_consen 3 KELMAERGITQKDLARKTGISRSTLSRILNGK-PSNPSLDTLEKI 46 (63)
T ss_dssp HHHHHHTT--HHHHHHHHT--HHHHHHHHTTT------HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc-cccccHHHHHHH
Confidence 44555567899999999999999999998632 355655444433
No 90
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=89.78 E-value=0.84 Score=35.60 Aligned_cols=38 Identities=13% Similarity=0.218 Sum_probs=30.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++.+|+|..||+|..++|... ||=++.|++.+..
T Consensus 144 ~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~ 181 (191)
T PRK12520 144 EWLELETEEICQELQITATNAWVLL---------YRARMRLRECLDL 181 (191)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 4558999999999999999999886 6666666665554
No 91
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=89.68 E-value=0.8 Score=36.00 Aligned_cols=37 Identities=16% Similarity=0.239 Sum_probs=29.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
-+.+++.+|+|..||+|+.++|.+. ||=++.|+..+.
T Consensus 147 ~~~g~s~~EIA~~lgis~~tVk~~l---------~RAr~~Lr~~l~ 183 (189)
T PRK12530 147 EYLELSSEQICQECDISTSNLHVLL---------YRARLQLQACLS 183 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 3458999999999999999999885 555566655543
No 92
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=89.62 E-value=0.69 Score=35.23 Aligned_cols=36 Identities=33% Similarity=0.501 Sum_probs=27.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.+++.+|+|+.|||++.++|..- +|=++.|.+.+
T Consensus 132 ~~~g~s~~eiA~~lgis~~tv~~~l---------~Ra~~~Lr~~l 167 (169)
T TIGR02954 132 YYHDLTIKEIAEVMNKPEGTVKTYL---------HRALKKLKKRL 167 (169)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHh
Confidence 3457999999999999999999874 55555555543
No 93
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=89.59 E-value=0.66 Score=36.01 Aligned_cols=36 Identities=22% Similarity=0.404 Sum_probs=28.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.+++.+|+|..||+|++++|... +|=.+.|.+.+
T Consensus 135 ~~~g~s~~EIA~~lgis~~tVk~~l---------~Rar~~Lr~~l 170 (185)
T PRK12542 135 VFYNLTYQEISSVMGITEANVRKQF---------ERARKRVQNMI 170 (185)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHH
Confidence 4457999999999999999999884 56566665544
No 94
>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=89.59 E-value=1.2 Score=28.78 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=18.4
Q ss_pred cHHHHHHHcCCChhHHHHHHH
Q 041600 83 PIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR 103 (160)
+++|+|+.+|||.+|+-|.-.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 478999999999999998843
No 95
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=89.59 E-value=0.83 Score=36.10 Aligned_cols=39 Identities=18% Similarity=0.111 Sum_probs=31.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
-+-+++.+|+|+.||+|+.++|..- +|=++.|.+.+...
T Consensus 129 ~~~g~s~~EIA~~Lgis~~tVk~~l---------~Rar~~Lr~~l~~~ 167 (187)
T PRK12516 129 GASGFAYEEAAEICGCAVGTIKSRV---------NRARQRLQEILQIE 167 (187)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHhh
Confidence 4558999999999999999999885 66677777766553
No 96
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=89.39 E-value=0.55 Score=35.34 Aligned_cols=33 Identities=30% Similarity=0.288 Sum_probs=27.8
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+..|+.-.-.|+.+.|+.||+|++++.++-+++
T Consensus 14 L~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 14 LRLLQEDARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred HHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 556677778999999999999999998887654
No 97
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=89.28 E-value=0.74 Score=38.08 Aligned_cols=41 Identities=12% Similarity=0.079 Sum_probs=32.2
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~ 126 (160)
.-+-+++.+|+|+.||+|..++|.+- +|-++.|++.+...+
T Consensus 183 ~~~eg~s~~EIA~~Lgis~~tVk~~l---------~RAr~kLr~~l~~~~ 223 (233)
T PRK12538 183 SYHENMSNGEIAEVMDTTVAAVESLL---------KRGRQQLRDLLRRHE 223 (233)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHhh
Confidence 34558999999999999999999885 666777776665443
No 98
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=89.25 E-value=0.53 Score=41.73 Aligned_cols=31 Identities=16% Similarity=0.087 Sum_probs=27.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
..++--..+||+.||||.+||-|..+++||.
T Consensus 439 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~i~ 469 (469)
T PRK10923 439 RHTQGHKQEAARLLGWGRNTLTRKLKELGME 469 (469)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 3457789999999999999999999999983
No 99
>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=89.24 E-value=0.7 Score=30.14 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=24.8
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+.+++.-.++.+.++|+.+|++.+++.++ +.|-
T Consensus 4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~--e~g~ 36 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLGISRSTISKI--ENGK 36 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHTS-HHHHHHH--HTTS
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCC
Confidence 56778888999999999999998888888 5663
No 100
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=89.22 E-value=0.56 Score=41.17 Aligned_cols=30 Identities=13% Similarity=0.229 Sum_probs=26.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
..++--..+||+.||||.+||-|.-+++||
T Consensus 415 ~~~~gn~~~aA~~Lgisr~tl~rkl~~~~i 444 (445)
T TIGR02915 415 ARVDGNIARAAELLGITRPTLYDLMKKHGI 444 (445)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 445678899999999999999999999998
No 101
>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=89.13 E-value=1.6 Score=32.88 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=20.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|.+.|+|+.+|||+.||+-.- +.|+
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 578999999999999998554 4554
No 102
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=89.12 E-value=0.96 Score=35.20 Aligned_cols=36 Identities=19% Similarity=0.255 Sum_probs=28.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+.+++.+|+|..||+|.+++|.+- +|-++.|.+.+.
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~ 190 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARA---------RQGLLKLRELLQ 190 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 457999999999999999999874 566666666554
No 103
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=89.10 E-value=0.35 Score=46.44 Aligned_cols=31 Identities=23% Similarity=0.327 Sum_probs=27.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
--.--+.+||+.||||.|||-|.-|+|||.+
T Consensus 576 ~~~~~is~aa~~lgi~R~T~yrklk~~gi~~ 606 (606)
T COG3284 576 ATNGNISEAARLLGISRSTLYRKLKRHGISK 606 (606)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhCCCC
Confidence 3367899999999999999999999999953
No 104
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=89.07 E-value=0.75 Score=36.16 Aligned_cols=36 Identities=19% Similarity=0.195 Sum_probs=28.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.+++.+|+|+.||||.+++|... +|-++.|...+
T Consensus 155 ~~~~~s~~EIA~~Lgis~~tVk~~l---------~ra~~~Lr~~l 190 (194)
T PRK09646 155 YYGGLTYREVAERLAVPLGTVKTRM---------RDGLIRLRDCL 190 (194)
T ss_pred HHcCCCHHHHHHHhCCChHhHHHHH---------HHHHHHHHHHh
Confidence 3458999999999999999999885 55555555544
No 105
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=89.03 E-value=0.84 Score=36.33 Aligned_cols=38 Identities=11% Similarity=0.222 Sum_probs=30.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++.+|+|..||+|++++|.+- +|=++.|++.+..
T Consensus 152 ~~eg~s~~EIA~~lgis~~tVk~~l---------~RAr~~Lr~~l~~ 189 (201)
T PRK12545 152 EFLDFEIDDICTELTLTANHCSVLL---------YRARTRLRTCLSE 189 (201)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 3457999999999999999999874 5666666666654
No 106
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=89.03 E-value=0.92 Score=34.80 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=21.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++.+|+|..||+|+.++|.+.
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 148 FAGLTVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 346999999999999999999885
No 107
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=88.92 E-value=0.76 Score=37.65 Aligned_cols=37 Identities=11% Similarity=-0.023 Sum_probs=28.9
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
.-+.++|.+|+|..||||+.++|.+. ||=++.|.+.+
T Consensus 146 ~y~eg~s~~EIAe~LgiS~~tVk~~L---------~RAr~~Lr~~l 182 (216)
T PRK12533 146 RELEDMSYREIAAIADVPVGTVMSRL---------ARARRRLAALL 182 (216)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHH
Confidence 34568999999999999999999986 55555555544
No 108
>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=88.89 E-value=0.74 Score=28.77 Aligned_cols=31 Identities=13% Similarity=0.148 Sum_probs=22.8
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.|...=.+++.|+|+.+|+|.+++.+..+++
T Consensus 11 ~l~~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 11 YLRENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3444446899999999999999999887654
No 109
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=88.85 E-value=0.84 Score=35.04 Aligned_cols=36 Identities=25% Similarity=0.200 Sum_probs=29.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+.+++.+|+|..||++..++|... ||=.+.|.+.+.
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l---------~rar~~Lr~~l~ 187 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRI---------FRAREAIAIRLR 187 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHhh
Confidence 347999999999999999999886 666667766654
No 110
>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=88.84 E-value=1.7 Score=32.85 Aligned_cols=24 Identities=25% Similarity=0.311 Sum_probs=18.6
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 83 PIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
++.|+|+.+|||+.||+-.. +.|+
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye-~~GL 24 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYE-RKGL 24 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHH-HCCC
Confidence 47899999999999996554 4554
No 111
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=88.81 E-value=0.76 Score=34.56 Aligned_cols=24 Identities=33% Similarity=0.295 Sum_probs=21.5
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+.+++.+|+|+.||||.++++..-
T Consensus 136 ~~g~s~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 136 GQNLPIAEVARILGKTEGAVKILQ 159 (170)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHH
Confidence 348999999999999999999885
No 112
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 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=88.80 E-value=1.1 Score=35.34 Aligned_cols=38 Identities=11% Similarity=0.180 Sum_probs=30.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+-+++.+|+|..||++++++|.+. +|=++.|++.+..
T Consensus 144 ~~~g~s~~EIA~~lgis~~tvk~rl---------~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 144 EVLGFESDEICQELEISTSNCHVLL---------YRARLSLRACLSI 181 (188)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 4457999999999999999999885 6666666665543
No 113
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=88.79 E-value=0.93 Score=35.35 Aligned_cols=39 Identities=15% Similarity=0.212 Sum_probs=31.2
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~ 126 (160)
+-+++.+|+|..||||..++|..- +|=++.|+..+..+.
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~~~~ 186 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKMRY---------KRALDKLREKFAGLA 186 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHHh
Confidence 347999999999999999999873 666777777666554
No 114
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=88.73 E-value=0.69 Score=36.89 Aligned_cols=41 Identities=12% Similarity=0.090 Sum_probs=32.9
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~ 126 (160)
.-+.+++.+|+|..||||+.++|... +|=++.|++.+...+
T Consensus 145 ~~~~g~s~~EIAe~lgis~~tV~~~l---------~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 145 TQVLGYTYEEAAKIADVRVGTIRSRV---------ARARADLIAATATGQ 185 (196)
T ss_pred HHHhCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHhcccc
Confidence 34568999999999999999999885 676777777666544
No 115
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=88.66 E-value=0.88 Score=34.23 Aligned_cols=36 Identities=17% Similarity=0.237 Sum_probs=27.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.+++.+|+|..||+|.+++|..- +|-++.|++.+
T Consensus 123 ~~~g~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l 158 (162)
T TIGR02983 123 YYEDLSEAQVAEALGISVGTVKSRL---------SRALARLRELL 158 (162)
T ss_pred HHhcCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHh
Confidence 4457999999999999999999884 55555555443
No 116
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=88.64 E-value=1.3 Score=33.36 Aligned_cols=36 Identities=19% Similarity=0.146 Sum_probs=26.9
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+-++|.+|+|+.|||++++++..- +|-++.|.+.+.
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~ 177 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRSRI---------FRAREALRAKLQ 177 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 348999999999999999998763 454555555444
No 117
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=88.51 E-value=0.57 Score=33.22 Aligned_cols=29 Identities=24% Similarity=0.300 Sum_probs=26.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+.+++..+++.+.+.|+.+|||..|+-.+
T Consensus 6 ~k~~R~~~~ltQ~elA~~vgVsRQTi~~i 34 (68)
T COG1476 6 LKELRAELGLTQEELAKLVGVSRQTIIAI 34 (68)
T ss_pred HHHHHHHhCcCHHHHHHHcCcCHHHHHHH
Confidence 67889999999999999999998887665
No 118
>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=88.47 E-value=1.3 Score=34.22 Aligned_cols=40 Identities=18% Similarity=0.154 Sum_probs=31.1
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
.-+.+++.+|+|+.||+|+.++|..- +|-.+.|...+...
T Consensus 112 ~~~~g~s~~eIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~~ 151 (170)
T TIGR02959 112 TELEGLSQQEIAEKLGLSLSGAKSRV---------QRGRKKLKELLETC 151 (170)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHh
Confidence 34568999999999999999999874 66666666666543
No 119
>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=88.33 E-value=0.49 Score=34.67 Aligned_cols=23 Identities=4% Similarity=0.098 Sum_probs=21.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+++.+++|+.||||.+|++|++|
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 57999999999999999999886
No 120
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=88.32 E-value=1.1 Score=35.17 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=26.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
+++.+|+|..||||++++|.+. ||=++.|++.+
T Consensus 157 g~s~~EIA~~lgis~~tVk~rl---------~ra~~~Lr~~l 189 (194)
T PRK12531 157 ELPHQQVAEMFDIPLGTVKSRL---------RLAVEKLRHSM 189 (194)
T ss_pred CCCHHHHHHHhCcCHHHHHHHH---------HHHHHHHHHHh
Confidence 7999999999999999999874 55555555544
No 121
>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=88.32 E-value=2.3 Score=31.81 Aligned_cols=25 Identities=32% Similarity=0.430 Sum_probs=20.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|.+.|+|+..|||+.||+-..++ |+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~-GL 25 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK-GL 25 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 57899999999999999866543 54
No 122
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=88.29 E-value=1 Score=35.07 Aligned_cols=36 Identities=28% Similarity=0.363 Sum_probs=29.1
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+-+++.+|+|+.||||..++|.+- ||-++.|.+.+.
T Consensus 145 ~~g~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~ 180 (184)
T PRK12539 145 LEGLSVAEAATRSGMSESAVKVSV---------HRGLKALAALIG 180 (184)
T ss_pred HcCCcHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHh
Confidence 347999999999999999999885 666666666553
No 123
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=88.23 E-value=0.74 Score=35.09 Aligned_cols=36 Identities=25% Similarity=0.407 Sum_probs=28.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i 122 (160)
-+.++|.+|+|..||+++.+++... ||=++.|.+.+
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l---------~ra~~~l~~~l 174 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRV---------HHGIKQLRKEW 174 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHH---------HHHHHHHHHHh
Confidence 3457999999999999999999886 55555555543
No 124
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=88.18 E-value=0.26 Score=46.29 Aligned_cols=35 Identities=23% Similarity=0.393 Sum_probs=31.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy 112 (160)
..-.+++.|.|++.|||.+|+=|.||++|..-++-
T Consensus 371 ~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~e 405 (638)
T PRK14101 371 SIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSD 405 (638)
T ss_pred HHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHH
Confidence 44578999999999999999999999999988873
No 125
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=88.08 E-value=1.2 Score=35.77 Aligned_cols=38 Identities=18% Similarity=0.159 Sum_probs=31.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+-++|.+|+|+.|||+..++|... +|-.+.|++.+..
T Consensus 151 ~~~g~s~~EIA~~Lgis~~tV~~~l---------~RArk~Lr~~l~~ 188 (203)
T PRK09647 151 DIEGLSYEEIAATLGVKLGTVRSRI---------HRGRQQLRAALAA 188 (203)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 4558999999999999999999886 6667777766665
No 126
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=88.05 E-value=1.2 Score=33.95 Aligned_cols=25 Identities=16% Similarity=-0.037 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+-+++.+|+|+.||+|+.++|...
T Consensus 125 ~~~g~s~~eIA~~lgis~~tV~~~l 149 (164)
T PRK12547 125 GASGFSYEDAAAICGCAVGTIKSRV 149 (164)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3457999999999999999999885
No 127
>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=87.99 E-value=1.9 Score=36.35 Aligned_cols=40 Identities=13% Similarity=0.042 Sum_probs=30.8
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
|.-+++++.+|+|+.||+|+.++|.+- ||=++.|++.+..
T Consensus 153 L~~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 153 LRDVLGWRAAETAELLGTSTASVNSAL---------QRARATLDEVGPS 192 (324)
T ss_pred hHHHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHhccc
Confidence 345678999999999999999999884 5555566555443
No 128
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=87.76 E-value=1.2 Score=34.97 Aligned_cols=42 Identities=17% Similarity=0.158 Sum_probs=34.1
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhc
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL 129 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~ 129 (160)
+-+++.+|+|+.|||++.++|.+- +|=++.|.+.+..+...+
T Consensus 150 ~~g~s~~eIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~~~~~~~ 191 (196)
T PRK12524 150 IEGLSNPEIAEVMEIGVEAVESLT---------ARGKRALAALLAGQRAEL 191 (196)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHhccccc
Confidence 346999999999999999999884 777778888777765544
No 129
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=87.74 E-value=1.4 Score=34.30 Aligned_cols=46 Identities=15% Similarity=0.321 Sum_probs=40.7
Q ss_pred hccCCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC-Ch
Q 041600 66 ERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR-WP 111 (160)
Q Consensus 66 ~r~~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R-WP 111 (160)
..-..+++++|...+++|...+...|.-+...|++.....|+.| ||
T Consensus 143 ~~~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~ 189 (189)
T PRK12515 143 VYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAGVERGWP 189 (189)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccccCCC
Confidence 34577999999999999999999999999999999999988866 88
No 130
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=87.63 E-value=0.8 Score=34.14 Aligned_cols=25 Identities=12% Similarity=0.016 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+.+++.+|+|+.||||+++++...
T Consensus 124 ~~~g~~~~eIA~~l~is~~tv~~~l 148 (159)
T TIGR02989 124 YQRGVSLTALAEQLGRTVNAVYKAL 148 (159)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4558999999999999999999875
No 131
>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=87.61 E-value=2 Score=32.56 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=20.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|++.|+|+.+|||+.||+-..+ .|+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~-~GL 25 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK-QGL 25 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5789999999999999987664 443
No 132
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=87.61 E-value=1.2 Score=34.64 Aligned_cols=26 Identities=27% Similarity=0.252 Sum_probs=22.8
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.-+.+++.+|+|+.||+|..++|..-
T Consensus 139 ~~~~g~s~~EIA~~l~is~~tv~~~l 164 (179)
T PRK09415 139 FYYEELSIKEIAEVTGVNENTVKTRL 164 (179)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34568999999999999999999885
No 133
>PHA01976 helix-turn-helix protein
Probab=87.60 E-value=2.7 Score=27.52 Aligned_cols=33 Identities=12% Similarity=0.024 Sum_probs=27.7
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+..++.--++.+.++|+.+||+.+++.++ +.|.
T Consensus 7 l~~~R~~~glt~~~lA~~~gvs~~~v~~~--e~g~ 39 (67)
T PHA01976 7 LIKARNARAWSAPELSRRAGVRHSLIYDF--EADK 39 (67)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HcCC
Confidence 55677888999999999999999999998 4443
No 134
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=87.44 E-value=1.1 Score=34.97 Aligned_cols=38 Identities=8% Similarity=0.084 Sum_probs=29.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++.+|+|..||||++++|..- +|-.+.|.+.+..
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l---------~rar~~Lr~~l~~ 204 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNAL---------QRVKRKLEKYLEN 204 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 3447999999999999999999763 5556666665544
No 135
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=87.28 E-value=1.4 Score=34.60 Aligned_cols=38 Identities=16% Similarity=0.044 Sum_probs=31.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++.+|+|..||+|..++|... ||=.+.|++.+..
T Consensus 124 ~~~g~s~~EIA~~Lgis~~tV~~~l---------~RAr~~Lr~~l~~ 161 (182)
T PRK12540 124 GASGFSYEDAAAICGCAVGTIKSRV---------NRARSKLSALLYV 161 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 4568999999999999999999986 6667777666654
No 136
>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=87.19 E-value=2.3 Score=31.57 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=20.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|++.|+|+.+||++.||+ .--+.|+
T Consensus 1 ~~I~eva~~~gvs~~tLR-yYe~~GL 25 (123)
T cd04770 1 MKIGELAKAAGVSPDTIR-YYERIGL 25 (123)
T ss_pred CCHHHHHHHHCcCHHHHH-HHHHCCC
Confidence 578999999999999995 5556664
No 137
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=87.10 E-value=0.53 Score=28.39 Aligned_cols=21 Identities=29% Similarity=0.339 Sum_probs=18.3
Q ss_pred CcHHHHHHHcCCChhHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-.+.|||+.||++.+++.+.|
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKYL 37 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHhC
Confidence 578999999999999998764
No 138
>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=87.08 E-value=4.4 Score=31.61 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=21.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|+|.|+|+.+|||+.||+-..+. |+
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~-GL 26 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK-GL 26 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999877654 54
No 139
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=87.01 E-value=1.2 Score=34.12 Aligned_cols=25 Identities=24% Similarity=0.191 Sum_probs=22.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+.++|.+|+|..||||+.++++.-
T Consensus 153 ~~~g~s~~eIA~~lgis~~~v~~~l 177 (189)
T TIGR02984 153 HLEGLSFAEVAERMDRSEGAVSMLW 177 (189)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3457999999999999999999885
No 140
>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=86.96 E-value=2.2 Score=32.26 Aligned_cols=23 Identities=22% Similarity=0.239 Sum_probs=20.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
|++.|+|+.+|||+.||+-..+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999977654
No 141
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=86.93 E-value=1.5 Score=35.46 Aligned_cols=35 Identities=14% Similarity=0.302 Sum_probs=27.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
+++.+|+|..||||+.++|++- +|=++.|++.+..
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~---------~rA~~~Lr~~l~~ 232 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLE---------KRIIKRLKKEINK 232 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 7999999999999999999884 5555666655543
No 142
>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=86.78 E-value=1.9 Score=32.44 Aligned_cols=25 Identities=28% Similarity=0.474 Sum_probs=20.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
++|.|+|+.+|||+.||+-.-+. |+
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~-GL 25 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK-GL 25 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 46889999999999999866543 65
No 143
>PRK09726 antitoxin HipB; Provisional
Probab=86.63 E-value=0.98 Score=32.00 Aligned_cols=31 Identities=6% Similarity=0.062 Sum_probs=27.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+..++.-.++.+.++|+.+||+.+++.++.+
T Consensus 17 lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 17 MKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 5566777899999999999999999999976
No 144
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=86.51 E-value=1.4 Score=33.90 Aligned_cols=33 Identities=15% Similarity=0.157 Sum_probs=26.2
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRR 121 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~ 121 (160)
-+++.+|+|+.||+++.++|..- +|=++.|.+.
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l---------~Rar~~Lr~~ 176 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWL---------RRSLLKLREC 176 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHH---------HHHHHHHHHH
Confidence 38999999999999999999874 5555555544
No 145
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=86.46 E-value=0.77 Score=28.90 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=20.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
-.+.|||+.||++.+++.+.|+.
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHhC
Confidence 47899999999999999999875
No 146
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=86.40 E-value=1.4 Score=33.28 Aligned_cols=25 Identities=24% Similarity=0.186 Sum_probs=22.4
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+.++|.+|+|..||+|..++|...
T Consensus 125 ~~~~~s~~eIA~~lgis~~tv~~~l 149 (161)
T PRK12541 125 DYYGFSYKEIAEMTGLSLAKVKIEL 149 (161)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4578999999999999999999874
No 147
>PRK10072 putative transcriptional regulator; Provisional
Probab=86.33 E-value=1.3 Score=32.85 Aligned_cols=31 Identities=23% Similarity=0.199 Sum_probs=27.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+..|+.-.++.+.++|+.||||.+++.+..+
T Consensus 38 ik~LR~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 38 FEQLRKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 6667788899999999999999999998854
No 148
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=86.26 E-value=1.4 Score=34.56 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=23.5
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
|.-+.+++.+|+|..||+|+.++|...
T Consensus 141 L~~~~g~s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 141 LTQLLGLSYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred hHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 345568999999999999999999885
No 149
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=86.18 E-value=1.7 Score=32.73 Aligned_cols=39 Identities=13% Similarity=0.102 Sum_probs=30.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
.|.+++.+|+|..|||+..++|+.- +|=++.|...+...
T Consensus 124 ~~~g~s~~eIA~~lgis~~tV~~~i---------~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 124 RFSGYSYKEIAEALGIKESSVGTTL---------ARAKKKFRKIYEQM 162 (166)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHh
Confidence 4478999999999999999999873 55566666655543
No 150
>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=86.00 E-value=0.86 Score=33.14 Aligned_cols=28 Identities=21% Similarity=0.219 Sum_probs=25.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.+.+.++|+.|||+...|-+..|+.||-
T Consensus 24 ~~ti~~~AK~L~i~~~~l~~~Lr~~g~l 51 (111)
T PF03374_consen 24 LYTIREAAKLLGIGRNKLFQWLREKGWL 51 (111)
T ss_pred CccHHHHHHHhCCCHHHHHHHHHhCCce
Confidence 4889999999999999999999999973
No 151
>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=85.97 E-value=8.2 Score=28.94 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=19.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|++.|+|+.+|||+.||+-.. +.|+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye-~~GL 25 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQ-RRGL 25 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence 578999999999999996554 4453
No 152
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=85.84 E-value=1.9 Score=32.79 Aligned_cols=38 Identities=24% Similarity=0.146 Sum_probs=29.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++.+|+|..||+|..+++..- +|=.+.|++.+..
T Consensus 121 ~~~g~s~~eIA~~lgis~~tv~~~l---------~Rar~~Lr~~l~~ 158 (165)
T PRK09644 121 DVHELTYEEAASVLDLKLNTYKSHL---------FRGRKRLKALLKE 158 (165)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 4568999999999999999998773 5555556555543
No 153
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=85.76 E-value=1 Score=29.66 Aligned_cols=25 Identities=24% Similarity=0.244 Sum_probs=21.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+||++.+|++..+ .|+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~-~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER-IGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 4689999999999999998876 443
No 154
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=85.69 E-value=6.6 Score=31.23 Aligned_cols=24 Identities=21% Similarity=0.225 Sum_probs=20.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
|.+.|+|+.+||++.||+-.. +.|
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE-~~G 35 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYE-SKG 35 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHH-HCC
Confidence 799999999999999998765 444
No 155
>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=85.65 E-value=1.8 Score=31.67 Aligned_cols=41 Identities=24% Similarity=0.199 Sum_probs=31.1
Q ss_pred hhccCCCCH---HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 65 RERTGKLTL---RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 65 r~r~~~lt~---~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
++....++- ..++...++.+.++|+.||++.+++.+. +.|-
T Consensus 59 ~~~~~~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~--e~g~ 102 (127)
T TIGR03830 59 RKVDGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRY--ERGE 102 (127)
T ss_pred HHccCCcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HCCC
Confidence 344444444 4456888999999999999999999998 4554
No 156
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=85.60 E-value=1.7 Score=35.76 Aligned_cols=24 Identities=17% Similarity=0.238 Sum_probs=20.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
|.++|+|+..|||.+|+-|.-...
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~ 24 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGK 24 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Confidence 478999999999999999996544
No 157
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=85.52 E-value=1.7 Score=33.68 Aligned_cols=25 Identities=20% Similarity=-0.028 Sum_probs=21.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+-++|.+|+|+.||||+.++|..-
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHHHH
Confidence 3457999999999999999999873
No 158
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=85.50 E-value=1.8 Score=33.62 Aligned_cols=24 Identities=25% Similarity=0.236 Sum_probs=21.3
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+.+++.+|+|..|||++.++|..-
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 153 VVGLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 458999999999999999999773
No 159
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=85.46 E-value=1.1 Score=34.82 Aligned_cols=25 Identities=16% Similarity=0.170 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+-+++.+|+|..||||+.++|...
T Consensus 140 ~~~g~s~~EIA~~lgis~~tVk~~l 164 (178)
T PRK12529 140 TLDGMKQKDIAQALDIALPTVKKYI 164 (178)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4457999999999999999999885
No 160
>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=85.43 E-value=3.2 Score=31.16 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=19.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|++.|+|+.+|||+.||.-.- +.|+
T Consensus 1 m~IgevA~~~gvs~~tLRyYe-~~GL 25 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYE-KEGL 25 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence 578899999999999987554 3443
No 161
>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=85.43 E-value=1.4 Score=28.28 Aligned_cols=22 Identities=18% Similarity=0.380 Sum_probs=16.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+++.+||+..||+.|||-++-+
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 9999999999999999997643
No 162
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=85.38 E-value=2.8 Score=31.51 Aligned_cols=28 Identities=14% Similarity=0.347 Sum_probs=25.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~ 108 (160)
.+++.++|+.+|+|+++|.|++++. |++
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 3899999999999999999999987 873
No 163
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=85.28 E-value=1.2 Score=40.88 Aligned_cols=31 Identities=19% Similarity=0.118 Sum_probs=27.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
..++--..+||+.||||.+||.+..|++||.
T Consensus 500 ~~~~gn~~~aA~~LGisr~tLy~klk~~gi~ 530 (534)
T TIGR01817 500 EQAGWVQAKAARLLGMTPRQVGYALRKLNIE 530 (534)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCC
Confidence 4456678999999999999999999999983
No 164
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=85.20 E-value=1.5 Score=32.09 Aligned_cols=24 Identities=13% Similarity=0.095 Sum_probs=21.3
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+.++|..|+|+.||||..+++.+-
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~~~ 150 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEYHI 150 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 348999999999999999999874
No 165
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=85.08 E-value=2 Score=32.17 Aligned_cols=33 Identities=9% Similarity=-0.033 Sum_probs=22.5
Q ss_pred HHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600 86 EAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118 (160)
Q Consensus 86 eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl 118 (160)
+|...+--+-.++..+|+++||+..-..++...
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 344444334446788999999988777777554
No 166
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=85.08 E-value=1.7 Score=33.05 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=29.3
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
+.+++..|+|..||+|+.++|..- +|-.+.|...+.+
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l---------~Rar~~L~~~l~~ 170 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRL---------FYARRQLRKFLQQ 170 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence 457999999999999999999874 6666666665544
No 167
>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=85.02 E-value=5.9 Score=28.24 Aligned_cols=26 Identities=23% Similarity=0.141 Sum_probs=18.1
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
|++.+.|+|++||-|.+.+.+.-+=+
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll 27 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLALL 27 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999988775433
No 168
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=84.90 E-value=1.9 Score=34.16 Aligned_cols=38 Identities=18% Similarity=0.106 Sum_probs=30.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++..|+|..||||..++|..- ||=.+.|++.+..
T Consensus 126 ~~~g~s~~EIA~~LgiS~~tVk~~l---------~Rar~~Lr~~l~~ 163 (188)
T PRK12546 126 GASGFSYEEAAEMCGVAVGTVKSRA---------NRARARLAELLQL 163 (188)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHhc
Confidence 4568999999999999999999885 6666666665543
No 169
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=84.84 E-value=1.2 Score=27.00 Aligned_cols=27 Identities=22% Similarity=0.231 Sum_probs=22.6
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
|.+++.+.|+.+|++.+++.+..+++-
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~ 33 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLE 33 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999988866553
No 170
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=84.75 E-value=2 Score=33.11 Aligned_cols=24 Identities=25% Similarity=0.171 Sum_probs=21.5
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++.+|+|..||||+.++|..-
T Consensus 149 ~~~~s~~eIA~~lgis~~~V~~~l 172 (186)
T PRK13919 149 YQGYTHREAAQLLGLPLGTLKTRA 172 (186)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 457999999999999999999874
No 171
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=84.67 E-value=1.4 Score=35.99 Aligned_cols=36 Identities=11% Similarity=0.274 Sum_probs=27.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
+++.+|+|+.||||..++++.- +|=++.|++.+..|
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l---------~ra~~~LR~~l~~~ 233 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLE---------KRILKRLKKEINRM 233 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHhhcc
Confidence 5999999999999999998773 45556666655543
No 172
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=84.50 E-value=0.89 Score=43.11 Aligned_cols=24 Identities=29% Similarity=0.357 Sum_probs=22.6
Q ss_pred HHHHHHcCCChhHHHHHHHHcCCC
Q 041600 85 EEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 85 ~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.+||+.|||+.|||-|..+++||.
T Consensus 661 ~~aA~~LGi~R~tL~rklk~~gi~ 684 (686)
T PRK15429 661 KGAAQRLGLKRTTLLSRMKRLGID 684 (686)
T ss_pred HHHHHHhCCCHHHHHHHHHHcCCC
Confidence 599999999999999999999994
No 173
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=84.33 E-value=1.5 Score=32.49 Aligned_cols=24 Identities=21% Similarity=0.213 Sum_probs=21.3
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++.+|+|..||+++.+++..-
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l 142 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNL 142 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHH
Confidence 347999999999999999999874
No 174
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=84.32 E-value=2.8 Score=33.05 Aligned_cols=39 Identities=15% Similarity=0.110 Sum_probs=31.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
-+-+++.+|+|..||||..+++... +|=++.|...+..-
T Consensus 141 ~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 141 VIGGFSGEEIAEILDLNKNTVMTRL---------FRARNQLKEALEKP 179 (188)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 3447999999999999999999885 66667776666543
No 175
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=84.29 E-value=2.4 Score=34.20 Aligned_cols=38 Identities=11% Similarity=0.155 Sum_probs=31.0
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+-+++.+|+|..||++..++|... ||=++.|.+.+..
T Consensus 161 ~~~g~s~~EIAe~lgis~~tV~~~l---------~RAr~~Lr~~l~~ 198 (206)
T PRK12544 161 EFIELETNEICHAVDLSVSNLNVLL---------YRARLRLRECLEN 198 (206)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 4558999999999999999999885 6767777776653
No 176
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=84.29 E-value=2.2 Score=34.06 Aligned_cols=37 Identities=22% Similarity=0.371 Sum_probs=28.5
Q ss_pred hhc-CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 78 IYF-HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 78 ~yF-~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
.|| +++.+|+|..||||..++|..- ||-++.|.+.+.
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~ 202 (206)
T PRK12526 165 VYFQELSQEQLAQQLNVPLGTVKSRL---------RLALAKLKVQMG 202 (206)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHh
Confidence 344 7999999999999999999773 555566655554
No 177
>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=84.28 E-value=1.3 Score=29.99 Aligned_cols=27 Identities=19% Similarity=0.090 Sum_probs=24.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++++++|+.|||+.+|+..-..+.+=
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W 39 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYKW 39 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhCc
Confidence 699999999999999999999888764
No 178
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=84.28 E-value=3.1 Score=29.01 Aligned_cols=30 Identities=23% Similarity=0.258 Sum_probs=23.8
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+.++..--++++.++|+.|||+.+.+-++=
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHH
Confidence 667777789999999999999999999985
No 179
>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=84.25 E-value=1 Score=33.78 Aligned_cols=26 Identities=8% Similarity=0.120 Sum_probs=22.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
.+|++|+|+.||||.+++-|.-+-+.
T Consensus 55 ~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 55 NMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred CCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 59999999999999999998865544
No 180
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=84.20 E-value=2.3 Score=33.73 Aligned_cols=25 Identities=20% Similarity=0.061 Sum_probs=22.3
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+-+++++|+|+.||+|.++++++.+
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ 43 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEK 43 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3579999999999999999999864
No 181
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=84.18 E-value=1.1 Score=32.90 Aligned_cols=24 Identities=21% Similarity=0.236 Sum_probs=21.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+.|+.+||+++|||.+|.+|.-.+
T Consensus 25 g~~~a~aA~~~gVS~~Ta~kW~~R 48 (85)
T PF13011_consen 25 GWPVAHAAAEFGVSRRTAYKWLAR 48 (85)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHH
Confidence 589999999999999999987544
No 182
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=84.09 E-value=0.78 Score=34.03 Aligned_cols=22 Identities=14% Similarity=0.259 Sum_probs=19.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKK 100 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr 100 (160)
+-+++.+|+|..||+|+.|+||
T Consensus 121 ~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 121 FEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HcCCCHHHHHHHHCcCHHhhcC
Confidence 4479999999999999999985
No 183
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=83.99 E-value=2.3 Score=32.77 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=21.2
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++..|+|..||+|..+++...
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 47999999999999999999885
No 184
>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=83.89 E-value=1 Score=31.20 Aligned_cols=22 Identities=9% Similarity=0.353 Sum_probs=19.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.++.+++|+.|||+.+++++-=
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHh
Confidence 5899999999999999998764
No 185
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=83.88 E-value=2.1 Score=35.77 Aligned_cols=37 Identities=16% Similarity=0.173 Sum_probs=29.7
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
-+.+++.+|+|+.||+|..++|..- +|-++.|...+.
T Consensus 129 ~~eg~S~~EIAe~LgiS~~tVksrL---------~Rark~Lr~~l~ 165 (228)
T PRK06704 129 DVFQYSIADIAKVCSVSEGAVKASL---------FRSRNRLKTVSE 165 (228)
T ss_pred HhhCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHH
Confidence 4568999999999999999999885 666666666554
No 186
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=83.80 E-value=3 Score=31.21 Aligned_cols=24 Identities=21% Similarity=0.019 Sum_probs=21.3
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+.+++..|+|+.||+|+.++++.-
T Consensus 139 ~~~~~~~eIA~~lgis~~tv~~~~ 162 (179)
T PRK11924 139 VEGLSYREIAEILGVPVGTVKSRL 162 (179)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 458999999999999999999873
No 187
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=83.80 E-value=1 Score=30.68 Aligned_cols=24 Identities=17% Similarity=0.296 Sum_probs=21.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+++.|.|+.+|||.+++-++|+..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~ 24 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGN 24 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCC
Confidence 368899999999999999999653
No 188
>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=83.61 E-value=1.2 Score=31.73 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+||++.+|+...++ |+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999988765 54
No 189
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=83.50 E-value=4.4 Score=31.34 Aligned_cols=25 Identities=24% Similarity=0.392 Sum_probs=21.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+|||+.||+-.-++ |+
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 68999999999999999877654 54
No 190
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=83.41 E-value=2.6 Score=32.32 Aligned_cols=25 Identities=16% Similarity=0.105 Sum_probs=22.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+-+++.+|+|..||||.+++|..-
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 132 RLDGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4457999999999999999999874
No 191
>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=83.25 E-value=4.2 Score=28.99 Aligned_cols=34 Identities=15% Similarity=0.093 Sum_probs=27.4
Q ss_pred CCHHHHHhhcCCcHHHHHHHcC-CChhHHHHHHHH
Q 041600 71 LTLRDLMIYFHLPIEEAARRMK-LCPTVVKKICRR 104 (160)
Q Consensus 71 lt~~~L~~yF~lP~~eAA~~Lg-v~~T~LKr~CR~ 104 (160)
+-.--+..++++|..++|+.|| .+.|++-.-|++
T Consensus 34 ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~r 68 (90)
T cd06571 34 IAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRK 68 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHH
Confidence 3444556888999999999999 999999888654
No 192
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=83.25 E-value=1.6 Score=34.57 Aligned_cols=28 Identities=29% Similarity=0.478 Sum_probs=23.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-+=+++..|+|+.||||+.|++|..+..
T Consensus 148 ~~~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 148 FFEGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3447999999999999999999886543
No 193
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=83.11 E-value=1.8 Score=30.39 Aligned_cols=31 Identities=10% Similarity=0.126 Sum_probs=28.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy 112 (160)
.++...||+.+|+|.-.+-..++++||+ +.|
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 6999999999999999999999999998 544
No 194
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=82.96 E-value=1.8 Score=40.56 Aligned_cols=34 Identities=15% Similarity=0.094 Sum_probs=28.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP 111 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP 111 (160)
..++--+.+||+.||||.+||-|.-+++||..=|
T Consensus 601 ~~~~gn~~~aA~~LGisR~TLyrklk~~~i~~~~ 634 (638)
T PRK11388 601 QVCGGRIQEMAALLGIGRTTLWRKMKQHGIDAGQ 634 (638)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCCccc
Confidence 4456789999999999999999999999995433
No 195
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=82.81 E-value=3.1 Score=35.33 Aligned_cols=45 Identities=11% Similarity=0.118 Sum_probs=32.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L 125 (160)
.+++.++|+.+|+|+.+|.|++++. |++-=-|.+...+++....|
T Consensus 234 ~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~~~~~~~Rl~~A~~lL 279 (322)
T PRK09393 234 PHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLL 279 (322)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3889999999999999999999986 87533343334444433433
No 196
>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=82.74 E-value=4.9 Score=26.93 Aligned_cols=37 Identities=14% Similarity=0.260 Sum_probs=28.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHR 113 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR 113 (160)
.+..--++++.++|+.+||+.+++-++.. |-...+..
T Consensus 12 ~~~~~~~~t~~~lA~~~gis~~tis~~~~--g~~~~~~~ 48 (78)
T TIGR02607 12 EFLEPLGLSIRALAKALGVSRSTLSRIVN--GRRGITAD 48 (78)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc--CCCCCCHH
Confidence 45666789999999999999999999864 54333333
No 197
>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=82.70 E-value=7.1 Score=22.51 Aligned_cols=42 Identities=17% Similarity=0.215 Sum_probs=28.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl 118 (160)
.+..-.++...++|+.+|++..++.+... |-...|.-.+..+
T Consensus 6 ~~~~~~~~s~~~~a~~~~~~~~~v~~~~~--g~~~~~~~~~~~i 47 (58)
T cd00093 6 ELRKEKGLTQEELAEKLGVSRSTISRIEN--GKRNPSLETLEKL 47 (58)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHc--CCCCCCHHHHHHH
Confidence 34445578899999999999999988743 4444555444444
No 198
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=82.67 E-value=1.7 Score=33.69 Aligned_cols=25 Identities=12% Similarity=0.110 Sum_probs=21.1
Q ss_pred hhc-CCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYF-HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF-~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.|| +++.+|+|+.||+|.+++|..-
T Consensus 161 ~~~~~~s~~eIA~~l~~s~~tV~~~l 186 (198)
T TIGR02859 161 SYLDGKSYQEIACDLNRHVKSIDNAL 186 (198)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344 6999999999999999998653
No 199
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=82.54 E-value=1.9 Score=36.77 Aligned_cols=27 Identities=15% Similarity=0.054 Sum_probs=23.6
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
|.-+.+++.+|+|..||+|+.++|.+-
T Consensus 164 L~~~~g~s~~EIA~~lgis~~tVk~~l 190 (339)
T PRK08241 164 LRDVLGWSAAEVAELLDTSVAAVNSAL 190 (339)
T ss_pred hHHhhCCCHHHHHHHhCCCHHHHHHHH
Confidence 345678999999999999999999874
No 200
>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=82.50 E-value=1.7 Score=26.66 Aligned_cols=23 Identities=22% Similarity=0.138 Sum_probs=20.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+++..++|+.||+|+.++++.-+
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 58999999999999999887743
No 201
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=82.42 E-value=1.5 Score=34.28 Aligned_cols=31 Identities=26% Similarity=0.223 Sum_probs=25.5
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.|+.-.-++..+.|+++|+|.+++.++-++|
T Consensus 22 ~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL 52 (164)
T PRK11169 22 ELQKDGRISNVELSKRVGLSPTPCLERVRRL 52 (164)
T ss_pred HhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4456667999999999999999998886654
No 202
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=82.41 E-value=2 Score=36.16 Aligned_cols=27 Identities=22% Similarity=0.454 Sum_probs=24.1
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
|.-+++++.+|+|+.||+|..++|.+.
T Consensus 126 L~~~~g~s~~EIA~~lg~s~~tVk~~l 152 (293)
T PRK09636 126 LHDVFGVPFDEIASTLGRSPAACRQLA 152 (293)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 346789999999999999999999885
No 203
>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=82.39 E-value=5.8 Score=30.22 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=20.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+.+.|+|+.+|||+.||.-.-++ |+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GL 26 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN-GL 26 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999866654 54
No 204
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=81.97 E-value=2.1 Score=37.52 Aligned_cols=30 Identities=23% Similarity=0.079 Sum_probs=26.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
..++-.+..||+.|||+.++|.+..+++||
T Consensus 413 ~~~~~n~~~aa~~lgi~r~~l~~~l~~~~~ 442 (442)
T TIGR02040 413 ELTRDNRASAAEILGLSRQSLYVKLRRYGL 442 (442)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHhCc
Confidence 445677999999999999999999999886
No 205
>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=81.91 E-value=2 Score=28.22 Aligned_cols=36 Identities=19% Similarity=0.251 Sum_probs=21.5
Q ss_pred cCCCCHHHHH---hhc--CCcHHHHHHHcCCChhHHHHHHH
Q 041600 68 TGKLTLRDLM---IYF--HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 68 ~~~lt~~~L~---~yF--~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
-..||+++=. ..+ +....++|+.+||+.||+..+..
T Consensus 4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred CccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3456665432 222 46889999999999999988853
No 206
>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=81.90 E-value=4.9 Score=30.29 Aligned_cols=22 Identities=27% Similarity=0.274 Sum_probs=18.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
|++.|+|+.+|||+.||.-.-+
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYES 22 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999985543
No 207
>PRK15043 transcriptional regulator MirA; Provisional
Probab=81.89 E-value=1.5 Score=37.70 Aligned_cols=29 Identities=28% Similarity=0.337 Sum_probs=25.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
.++|.|+|+.+||++.||....|+.|+-.
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~ 31 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLK 31 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCC
Confidence 47999999999999999999998888654
No 208
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=81.86 E-value=4.1 Score=33.68 Aligned_cols=51 Identities=12% Similarity=0.030 Sum_probs=34.9
Q ss_pred HHHhhcC---CcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 75 DLMIYFH---LPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 75 ~L~~yF~---lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
-|..+++ +.+.++|+.+|||+..|.+++++.|.+--=|-.-..|++....|
T Consensus 205 ~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~~~yi~~~RL~~A~~lL 258 (302)
T PRK09685 205 LIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCADDL 258 (302)
T ss_pred HHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Confidence 3445553 78899999999999999999999887522233333344434444
No 209
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=81.83 E-value=1.8 Score=22.90 Aligned_cols=21 Identities=19% Similarity=0.316 Sum_probs=18.2
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+.+..++|+.+|++.+++.++
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 569999999999999988764
No 210
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=81.74 E-value=3 Score=32.21 Aligned_cols=24 Identities=25% Similarity=0.142 Sum_probs=21.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++.+|+|..||||+.+++.+-
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l 174 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWI 174 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHH
Confidence 348999999999999999999885
No 211
>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=81.66 E-value=2.1 Score=25.38 Aligned_cols=23 Identities=22% Similarity=0.206 Sum_probs=20.4
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++..++|+.||++..++++.-
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~ 47 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRL 47 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 47999999999999999998764
No 212
>PHA00542 putative Cro-like protein
Probab=81.58 E-value=8.7 Score=27.11 Aligned_cols=27 Identities=15% Similarity=0.117 Sum_probs=23.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.--++.+.++|+.+||+.+++-++.+-
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 344899999999999999999999643
No 213
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=81.23 E-value=1.8 Score=26.95 Aligned_cols=24 Identities=25% Similarity=0.259 Sum_probs=20.4
Q ss_pred C-cHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 L-PIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 l-P~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+ ++.+.|+.+|||.+++.+..+++
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5 59999999999999999886654
No 214
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=81.20 E-value=2.7 Score=34.80 Aligned_cols=24 Identities=13% Similarity=0.225 Sum_probs=20.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+++|+|+..|||.+|+.|.-...
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~ 25 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDD 25 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCC
Confidence 368999999999999999997543
No 215
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=80.97 E-value=2.8 Score=27.14 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=22.2
Q ss_pred CCcHHHHHHHcCC-ChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKL-CPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv-~~T~LKr~CR~~ 105 (160)
++++.++|..+|+ +++.|-+.+++.
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 5899999999999 999999998654
No 216
>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=80.90 E-value=2.1 Score=27.64 Aligned_cols=26 Identities=19% Similarity=0.221 Sum_probs=21.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.+.+++.++|+.+|++.+++.+..++
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34689999999999999998887643
No 217
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=80.84 E-value=2.6 Score=34.30 Aligned_cols=22 Identities=18% Similarity=0.212 Sum_probs=20.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+|+|+.||+++++++++.
T Consensus 194 ~~S~~EIAe~lgis~~tV~~~~ 215 (227)
T TIGR02846 194 RKTQREIAKILGISRSYVSRIE 215 (227)
T ss_pred CcCHHHHHHHHCCCHHHHHHHH
Confidence 5899999999999999999885
No 218
>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=80.74 E-value=7.3 Score=29.80 Aligned_cols=28 Identities=25% Similarity=0.273 Sum_probs=23.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
.++|.|+|+..|||+.||+-..+. |+-.
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~ 30 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLR-GLLH 30 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 478999999999999999987755 7543
No 219
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=80.69 E-value=2.8 Score=29.91 Aligned_cols=31 Identities=23% Similarity=0.375 Sum_probs=25.3
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.|...-.+|..++|+.+|++.+++.++.+++
T Consensus 11 ~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 11 ELQKDARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred HHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445557999999999999999998887655
No 220
>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=80.67 E-value=7.3 Score=29.94 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=18.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
|+|.|+|+.+||++.||.-.= +.|
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE-~~G 24 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYE-AEG 24 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCC
Confidence 578999999999999997443 444
No 221
>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=80.64 E-value=2.7 Score=30.03 Aligned_cols=24 Identities=13% Similarity=0.059 Sum_probs=21.9
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
-++++.|+|+.||||+.++|.+-+
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHh
Confidence 579999999999999999998855
No 222
>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=80.50 E-value=15 Score=27.27 Aligned_cols=26 Identities=23% Similarity=0.280 Sum_probs=21.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+++.|+|+.+|||+.||+-..+. |+-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 47899999999999999977654 753
No 223
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=80.41 E-value=2.8 Score=34.15 Aligned_cols=38 Identities=24% Similarity=0.324 Sum_probs=30.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+.+++.+|+|..||||.+++|.+- +|-++.|++.+..
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l---------~Rar~kLr~~l~~ 199 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRL---------HRARRLLRESLAR 199 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 3457999999999999999999884 6666666666653
No 224
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=80.17 E-value=1.4 Score=41.35 Aligned_cols=56 Identities=20% Similarity=0.363 Sum_probs=41.7
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHH---------HHHHHcCCCCC-hhHHHhhH-HHHHHHHhhhcc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVK---------KICRRDGLHRW-PHRKIKSI-QRRMSVASGRLR 130 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LK---------r~CR~~GI~RW-PyRkikSl-~~~i~~L~~~~~ 130 (160)
-|..||+|...+|.+.|.+-.+.++ +.||.+|+.|| .|=.|+.. .+.++.|++.++
T Consensus 223 Llekffem~~~~a~~al~iykr~~~q~e~L~~f~~~ck~~g~~r~~~iP~l~~i~~s~l~~lEe~l~ 289 (491)
T KOG0251|consen 223 LLEKFFEMSKHDAIKALDIYKRFLSQTEKLSEFLKVCKSVGVDRGFEIPVLKRIPISLLEALEEHLR 289 (491)
T ss_pred HHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCcchhhcCHHHHHHHHHHHh
Confidence 3457999999999999999866665 78999999999 55544433 455666666554
No 225
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=80.05 E-value=3.3 Score=33.70 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=20.9
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++.+|+|+.||||..++|++-
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~ 221 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIH 221 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 46999999999999999999884
No 226
>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=79.98 E-value=3.1 Score=35.05 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=24.1
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
|.-+|+++.+|+|+.||+|..++|..-
T Consensus 119 L~~~~g~s~~EIA~~lg~s~~tVr~~l 145 (281)
T TIGR02957 119 LREVFDYPYEEIASIVGKSEANCRQLV 145 (281)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 456789999999999999999999874
No 227
>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=79.74 E-value=8.4 Score=28.03 Aligned_cols=73 Identities=11% Similarity=0.103 Sum_probs=41.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC---------CCChhHH---------HhhHHHHHHHHhhhccCC---c-------
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL---------HRWPHRK---------IKSIQRRMSVASGRLRSN---D------- 133 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI---------~RWPyRk---------ikSl~~~i~~L~~~~~~~---~------- 133 (160)
|.+.|+|+..|||+.||+-.. +.|+ .+..... ++.+.-.++.+++++... +
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe-~~GLl~p~~~~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~ 79 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYI-DLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQ 79 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCCcCCccCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcccccccchhhH
Confidence 578999999999999997443 4454 2222111 122222344455555321 0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 041600 134 AEERANAQIEIQRLQEEMAAAC 155 (160)
Q Consensus 134 ~eerar~~~eIerL~~Em~~~c 155 (160)
++-++-...+++.|++++.++-
T Consensus 80 ~~~~~~l~~~~~~l~~~i~~l~ 101 (107)
T cd04777 80 DYYKSFLKNKKDELEKEIEDLK 101 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 1224556678888888887764
No 228
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=79.71 E-value=3.6 Score=33.50 Aligned_cols=35 Identities=17% Similarity=0.275 Sum_probs=26.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
+++.+|+|..||||.++++++. +|-++.|.+.+..
T Consensus 195 ~~S~~EIA~~lgis~~tV~~~~---------~rA~~kLr~~l~~ 229 (233)
T PRK05803 195 EKTQREIAKALGISRSYVSRIE---------KRALKKLFKELYR 229 (233)
T ss_pred CcCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 4799999999999999998885 4555556555443
No 229
>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=79.68 E-value=0.95 Score=30.47 Aligned_cols=35 Identities=20% Similarity=0.393 Sum_probs=24.7
Q ss_pred CcHHHHHHHc-----CCChhHHHHHHHHcCCCCChhHHHh
Q 041600 82 LPIEEAARRM-----KLCPTVVKKICRRDGLHRWPHRKIK 116 (160)
Q Consensus 82 lP~~eAA~~L-----gv~~T~LKr~CR~~GI~RWPyRkik 116 (160)
.+..+++..| +||.+|+.++.++.|+..|.-++.-
T Consensus 14 ~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g~~~~~~~~kP 53 (72)
T PF01498_consen 14 ISAREIAQELQEAGISVSKSTIRRRLREAGLKKRKARKKP 53 (72)
T ss_dssp --HHHHHHHT---T--S-HHHHHHHHHHT-EEEETTEEEE
T ss_pred CCHHHHHHHHHHccCCcCHHHHHHHHHHcCccccccccCC
Confidence 6677777777 8999999999999999888766543
No 230
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=79.47 E-value=9.4 Score=21.80 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=22.4
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
.+...-++...+.|+.+||+.+++.+...
T Consensus 4 ~~~~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 4 ELREEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34445578889999999999999988743
No 231
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=79.39 E-value=2.9 Score=31.55 Aligned_cols=25 Identities=20% Similarity=0.101 Sum_probs=21.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+.++|.+|+|+.||+|+.++|..-
T Consensus 126 ~~~g~s~~EIA~~l~is~~tV~~~l 150 (161)
T PRK12528 126 QVDGLGYGEIATELGISLATVKRYL 150 (161)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3458999999999999999999774
No 232
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=79.35 E-value=2.2 Score=36.56 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=25.0
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.|..+|+++.+|+|+.||+|+.++|.+.
T Consensus 128 ~L~~~~g~s~~EIA~~Lgis~~tVr~~l 155 (290)
T PRK09635 128 VLHEIFGLPYQQIATTIGSQASTCRQLA 155 (290)
T ss_pred hHHHHhCCCHHHHHHHHCcCHHHHHHHH
Confidence 4567899999999999999999999885
No 233
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=79.30 E-value=10 Score=24.97 Aligned_cols=28 Identities=18% Similarity=0.294 Sum_probs=19.9
Q ss_pred HHHHhhc--CCcHHHHHHHcCCChhHHHHH
Q 041600 74 RDLMIYF--HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 74 ~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+.|..|+ +..+.+||+.|+|...||+-+
T Consensus 3 ~TL~~yl~~~~n~~~tA~~L~iHrNTl~yR 32 (59)
T PF13556_consen 3 ETLRAYLENNGNISKTARALHIHRNTLRYR 32 (59)
T ss_dssp -HHHHHHHTTT-HHHHHHHHTS-HHHHHHH
T ss_pred hHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 3455565 478999999999999998865
No 234
>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=79.20 E-value=1.5 Score=32.16 Aligned_cols=26 Identities=12% Similarity=0.096 Sum_probs=23.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
++|+.++|+.+|||.+|+-|..|.+.
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 69999999999999999999977664
No 235
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=79.19 E-value=4.4 Score=33.59 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=19.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
++++|+|+.+|||.+|+.|...
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 4789999999999999999974
No 236
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=79.13 E-value=4.1 Score=35.28 Aligned_cols=34 Identities=3% Similarity=0.058 Sum_probs=28.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK 114 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk 114 (160)
.+.+.+.|+.+|+|.++|.|..++.|..=-+|..
T Consensus 197 ~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~ 230 (291)
T PRK15186 197 KWALKDISDSLYMSCSTLKRKLKQENTSFSEVYL 230 (291)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHH
Confidence 4889999999999999999999998765444443
No 237
>smart00351 PAX Paired Box domain.
Probab=79.09 E-value=2.1 Score=32.49 Aligned_cols=25 Identities=20% Similarity=0.174 Sum_probs=22.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+.+..++|+.||||.+++-++.+++
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 6899999999999999998887764
No 238
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=79.02 E-value=2.4 Score=31.52 Aligned_cols=32 Identities=22% Similarity=0.366 Sum_probs=28.1
Q ss_pred CCHHHHHhhc---CCcHHHHHHHcCCChhHHHHHH
Q 041600 71 LTLRDLMIYF---HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 71 lt~~~L~~yF---~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.|-++|+..| +++..++|..||+|+.-|-++-
T Consensus 10 ~T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 10 ATRQELQANFELSGLSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4678899888 6999999999999999999874
No 239
>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=78.79 E-value=8.3 Score=29.54 Aligned_cols=58 Identities=10% Similarity=0.079 Sum_probs=38.2
Q ss_pred CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC-CCCChhHHHhhHHHHHHHHhhhc
Q 041600 72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDG-LHRWPHRKIKSIQRRMSVASGRL 129 (160)
Q Consensus 72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWPyRkikSl~~~i~~L~~~~ 129 (160)
.+..+..+++++.++.|+.|||+.+|++|.-+..+ +.+=-.-++-.+-+.+..+..+.
T Consensus 27 ~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l~ri~~~a~~vf 85 (133)
T TIGR02293 27 ALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARVARVWKAAVDVF 85 (133)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45667888999999999999999999998865432 21112334444444445444444
No 240
>PF13551 HTH_29: Winged helix-turn helix
Probab=78.74 E-value=2.3 Score=29.86 Aligned_cols=24 Identities=29% Similarity=0.432 Sum_probs=20.9
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+.+ +.++|+.||||..|+.+.-++
T Consensus 11 g~~~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 11 GVSTIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 464 999999999999999988766
No 241
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=78.63 E-value=1.8 Score=41.41 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=24.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
--...||+.||||.|||-+.++++||.
T Consensus 534 gn~~~aAk~LgIsrttL~rKlkk~~l~ 560 (560)
T COG3829 534 GNKSKAAKELGISRTTLYRKLKKYGLR 560 (560)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHhcCC
Confidence 477899999999999999999999983
No 242
>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=78.48 E-value=1.3 Score=28.78 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRR-DGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~-~GI~ 108 (160)
+.+.|.|+.|||++..|=+.|++ +||.
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 45779999999999999999966 9993
No 243
>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=78.39 E-value=5.1 Score=33.50 Aligned_cols=38 Identities=8% Similarity=0.095 Sum_probs=29.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~ 124 (160)
-+-+++.+|+|..||||..++|..- +|=++.|.+.+.+
T Consensus 174 ~~eg~S~~EIA~~Lgis~~TVk~rl---------~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 174 FVDGLSMDRIGAMYQVHRSTVSRWV---------AQARERLLERTRR 211 (244)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence 3457999999999999999999884 5556666555543
No 244
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=78.36 E-value=2.6 Score=29.82 Aligned_cols=24 Identities=21% Similarity=0.177 Sum_probs=21.3
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
-+++..++|+.||||+.+++++..
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999998853
No 245
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=78.30 E-value=8.5 Score=26.77 Aligned_cols=27 Identities=22% Similarity=0.521 Sum_probs=24.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHH-HcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICR-RDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR-~~GI~ 108 (160)
+.+.+.|..+|+|++.|.++++ ..|+.
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 7799999999999999999999 77874
No 246
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=78.26 E-value=2.8 Score=25.81 Aligned_cols=31 Identities=16% Similarity=0.056 Sum_probs=24.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWP 111 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP 111 (160)
.++..++|+.||++.+++.+..+++-=..|.
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i 40 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKKLREAGLV 40 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 3678899999999999999988776544444
No 247
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=77.99 E-value=4.6 Score=29.93 Aligned_cols=23 Identities=17% Similarity=0.065 Sum_probs=20.7
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++..|+|+.||+|.++++.+-
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~ 143 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIY 143 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 37999999999999999999873
No 248
>PRK01381 Trp operon repressor; Provisional
Probab=77.99 E-value=1.4 Score=33.41 Aligned_cols=27 Identities=7% Similarity=0.031 Sum_probs=23.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
.+|+.|+|+.||||.+++-|-.|.+.-
T Consensus 55 ~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 55 ELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred CcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 389999999999999999988766543
No 249
>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=77.93 E-value=5.9 Score=30.79 Aligned_cols=27 Identities=15% Similarity=0.101 Sum_probs=21.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
+.+.|+|+.+|||+.||+..- +.|+-.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye-~~GLl~ 27 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYT-NLGLLT 27 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCCCC
Confidence 468899999999999999876 446543
No 250
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=77.62 E-value=3 Score=32.12 Aligned_cols=27 Identities=26% Similarity=0.228 Sum_probs=22.8
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
|.-+.+++.+|+|+.||+|..++|..-
T Consensus 130 l~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 130 LSQLDGLTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred hhhccCCCHHHHHHHhCCCHHHHHHHH
Confidence 344568999999999999999999773
No 251
>PRK09526 lacI lac repressor; Reviewed
Probab=77.56 E-value=5.3 Score=33.07 Aligned_cols=22 Identities=14% Similarity=0.232 Sum_probs=19.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
.+++|+|+..|||.+|+-|.-.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhc
Confidence 4789999999999999999864
No 252
>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=77.48 E-value=1.6 Score=28.11 Aligned_cols=24 Identities=17% Similarity=0.344 Sum_probs=19.4
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+.++|+++.+|||.|++-+..++-
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 578999999999999999988743
No 253
>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=77.40 E-value=2 Score=30.60 Aligned_cols=28 Identities=21% Similarity=0.272 Sum_probs=24.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|+..|++|.++.||+|..++.++-++|
T Consensus 49 vYi~~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 49 VYIIFSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred EEEEeeHHHHHHHHCCCHHHHHHHHHcC
Confidence 5888999999999999999999886654
No 254
>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=77.36 E-value=4.8 Score=33.16 Aligned_cols=23 Identities=9% Similarity=0.144 Sum_probs=19.4
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 041600 83 PIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+++|+|+..|||.+|+-|.-...
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~~ 23 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVINGK 23 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Confidence 47899999999999999997443
No 255
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=77.33 E-value=3.6 Score=38.78 Aligned_cols=31 Identities=13% Similarity=0.060 Sum_probs=26.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.-++--..+||+.||||.|||-|.-+++|..
T Consensus 507 ~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~~ 537 (538)
T PRK15424 507 ERFNGDKTAAANYLGISRTTLWRRLKAEAKA 537 (538)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4456789999999999999999988888863
No 256
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=77.29 E-value=2.5 Score=34.42 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=26.6
Q ss_pred CCCHHHHH--------hhcCCc----HHHHHHHcCCChhHHHHHHH
Q 041600 70 KLTLRDLM--------IYFHLP----IEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 70 ~lt~~~L~--------~yF~lP----~~eAA~~Lgv~~T~LKr~CR 103 (160)
.||=.+++ .||+.| ++|.|+.||||.+++-..-|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 46665554 899876 78999999999999876643
No 257
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=77.25 E-value=3.3 Score=36.10 Aligned_cols=28 Identities=14% Similarity=0.145 Sum_probs=22.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
..++--+.+||+.||||.++|.+..+++
T Consensus 302 ~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 302 AEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 3456789999999999999998776653
No 258
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=77.07 E-value=3.9 Score=39.54 Aligned_cols=67 Identities=19% Similarity=0.410 Sum_probs=44.4
Q ss_pred HHHHcCCC------hhHHHHHHHHcCCCCChh--HHHhhHHHHHHHHhhhc----cCCcH----------HHHHHHHHHH
Q 041600 87 AARRMKLC------PTVVKKICRRDGLHRWPH--RKIKSIQRRMSVASGRL----RSNDA----------EERANAQIEI 144 (160)
Q Consensus 87 AA~~Lgv~------~T~LKr~CR~~GI~RWPy--RkikSl~~~i~~L~~~~----~~~~~----------eerar~~~eI 144 (160)
|.++||.. ..+|||+||=.|++=|=| ++++|-+. +..++..+ ...++ .+|...+.+|
T Consensus 10 a~eEmg~p~~~~P~~~~lrrlC~G~~~~IWkfli~~V~s~rt-V~~iRgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~ev 88 (632)
T PF14817_consen 10 AQEEMGYPPASLPSDDYLRRLCRGNMAPIWKFLIQHVRSQRT-VRKIRGNLLWYGHQQSKERKKSRENEARRRRELEKEV 88 (632)
T ss_pred HHHHhCCCCCCCCCHHHHHHHhccCChHHHHHHHHHcCcHhH-HHHHHcceeeccccccccchhhhHHHHHHHHHHHHHH
Confidence 45567766 678999999999999987 45555433 44444332 11122 4566777888
Q ss_pred HHHHHHHHHH
Q 041600 145 QRLQEEMAAA 154 (160)
Q Consensus 145 erL~~Em~~~ 154 (160)
++|+.|+..+
T Consensus 89 erLraei~~l 98 (632)
T PF14817_consen 89 ERLRAEIQEL 98 (632)
T ss_pred HHHHHHHHHH
Confidence 8888887665
No 259
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=76.96 E-value=3.2 Score=31.65 Aligned_cols=29 Identities=17% Similarity=0.186 Sum_probs=26.8
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..|+.-++|.+.+=|+.||||+.||.+.
T Consensus 49 Ik~iRe~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 49 IKAIREKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHH
Confidence 66678999999999999999999999987
No 260
>PRK06930 positive control sigma-like factor; Validated
Probab=76.95 E-value=5.9 Score=31.77 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=21.5
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++.+|+|+.||+|++++|..-
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l 151 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMI 151 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 357999999999999999999885
No 261
>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=76.83 E-value=2.2 Score=26.49 Aligned_cols=24 Identities=29% Similarity=0.491 Sum_probs=18.4
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 83 PIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
.|.|+|+.+||++.+|...=++ |+
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 3789999999999999876543 64
No 262
>PRK09492 treR trehalose repressor; Provisional
Probab=76.52 E-value=5.6 Score=32.51 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=17.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
++++|+|+..|||.+|+-|.-.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhC
Confidence 4688888888888888888753
No 263
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=76.51 E-value=6.8 Score=32.71 Aligned_cols=37 Identities=5% Similarity=0.286 Sum_probs=29.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~ 126 (160)
+++.+|+|..||||+.+++++- +|=++.|++.+..++
T Consensus 228 ~~s~~eIA~~lgis~~tV~~~~---------~ra~~~Lr~~l~~~~ 264 (268)
T PRK06288 228 DLTLKEIGKVLGVTESRISQLH---------TKAVLQLRAKLAEIK 264 (268)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHHh
Confidence 6999999999999999999774 455666666666554
No 264
>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=76.48 E-value=3.2 Score=27.22 Aligned_cols=21 Identities=19% Similarity=0.253 Sum_probs=17.6
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+-.+..||+.||||.+++.+.
T Consensus 13 ~gs~~~AA~~l~is~~~vs~~ 33 (60)
T PF00126_consen 13 TGSISAAAEELGISQSAVSRQ 33 (60)
T ss_dssp HSSHHHHHHHCTSSHHHHHHH
T ss_pred hCCHHHHHHHhhccchHHHHH
Confidence 357889999999999988765
No 265
>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=76.45 E-value=3.1 Score=26.37 Aligned_cols=22 Identities=9% Similarity=0.212 Sum_probs=18.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.++..+.|+.||||..|+.+--
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHH
Confidence 3899999999999999998763
No 266
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=76.26 E-value=3.2 Score=33.51 Aligned_cols=33 Identities=9% Similarity=-0.029 Sum_probs=24.6
Q ss_pred CCCHHHHH--h--hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 70 KLTLRDLM--I--YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 70 ~lt~~~L~--~--yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.||--|+. . .=+++.+|+|++||+|..|+|...
T Consensus 137 ~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~ 173 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHK 173 (207)
T ss_pred cCCHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH
Confidence 36666654 2 227999999999999988877653
No 267
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=76.14 E-value=10 Score=29.33 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=18.0
Q ss_pred CcHHHHHHHcCCChhHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~C 102 (160)
|.|.|+|+.+||++.||+-.-
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE 21 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYE 21 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 578999999999999998554
No 268
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=75.83 E-value=4.3 Score=35.48 Aligned_cols=47 Identities=19% Similarity=0.304 Sum_probs=35.5
Q ss_pred hhc--CCcHHHHHHHcCCChhHHHH---HHHHcCCCC----ChhHHHhhHHHHHHH
Q 041600 78 IYF--HLPIEEAARRMKLCPTVVKK---ICRRDGLHR----WPHRKIKSIQRRMSV 124 (160)
Q Consensus 78 ~yF--~lP~~eAA~~Lgv~~T~LKr---~CR~~GI~R----WPyRkikSl~~~i~~ 124 (160)
-|| +|++.|+|++||||.+++-| .+|+.||-+ =|+.....|.+.+.+
T Consensus 24 lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~ 79 (318)
T PRK15418 24 FYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQ 79 (318)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHH
Confidence 454 69999999999999777655 589999865 376666666666554
No 269
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=75.70 E-value=3.6 Score=32.17 Aligned_cols=38 Identities=11% Similarity=0.271 Sum_probs=26.9
Q ss_pred CCCHHHHH---hhc-CCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 041600 70 KLTLRDLM---IYF-HLPIEEAARRMKLCPTVVK----KICRRDGL 107 (160)
Q Consensus 70 ~lt~~~L~---~yF-~lP~~eAA~~Lgv~~T~LK----r~CR~~GI 107 (160)
.||--|.. -+. +++.+++|++||+|..|+| ++.+++|+
T Consensus 150 ~Lt~rE~evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 150 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred cCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 36655543 222 7999999999999977765 55666666
No 270
>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=75.52 E-value=2.5 Score=27.40 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=17.6
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+++.+++|+.||||+.+++..
T Consensus 18 G~~~~eIA~~l~is~~tV~~~ 38 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSH 38 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHH
T ss_pred cCCcchhHHhcCcchhhHHHH
Confidence 789999999999998887654
No 271
>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=75.45 E-value=6.5 Score=32.41 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=18.4
Q ss_pred CcHHHHHHHcCCChhHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.+++|+|+..|||.+|+.|.-
T Consensus 2 ~ti~dIA~~agVS~sTVSr~L 22 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVL 22 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHh
Confidence 468899999999999999885
No 272
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=75.38 E-value=2.6 Score=37.09 Aligned_cols=27 Identities=26% Similarity=0.565 Sum_probs=25.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+|+.+++|..||||+.++|.--|++|-
T Consensus 19 gmk~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHhcCC
Confidence 499999999999999999999999874
No 273
>PHA00675 hypothetical protein
Probab=75.35 E-value=3.2 Score=30.32 Aligned_cols=39 Identities=21% Similarity=0.287 Sum_probs=28.7
Q ss_pred ccCCCCHHHHHhhcC------CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 67 RTGKLTLRDLMIYFH------LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 67 r~~~lt~~~L~~yF~------lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
..+.||-.+....+. +...+.|+.+|||.+++-.||+.-
T Consensus 19 ~~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk 63 (78)
T PHA00675 19 PNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYE 63 (78)
T ss_pred CCcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccc
Confidence 345666666654443 446799999999999999999743
No 274
>PRK08359 transcription factor; Validated
Probab=75.30 E-value=8.1 Score=31.76 Aligned_cols=29 Identities=21% Similarity=0.193 Sum_probs=24.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.--+|.+.+.|+.|||+.+++.++ +.|-.
T Consensus 95 e~kglSQeeLA~~lgvs~stI~~i--E~G~~ 123 (176)
T PRK08359 95 QKSGLSYEELSHEVGLSVNDLRRI--AHGEY 123 (176)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH--HCCCc
Confidence 334899999999999999999888 66653
No 275
>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=75.30 E-value=4.5 Score=26.66 Aligned_cols=30 Identities=10% Similarity=0.074 Sum_probs=23.7
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 74 RDLMIYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+-|...=.+.+.++|..||||..|++|=..
T Consensus 7 ~~l~~~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 7 ELLKEKGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred HHHHHcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 334555578999999999999999987643
No 276
>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=75.23 E-value=6.1 Score=32.33 Aligned_cols=35 Identities=37% Similarity=0.656 Sum_probs=29.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH-cCCCCChhHHHhh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR-DGLHRWPHRKIKS 117 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~-~GI~RWPyRkikS 117 (160)
++++++.|+.+|+|++.|-|++++ .|++ |..=|..
T Consensus 202 ~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t--~~~yi~~ 237 (287)
T TIGR02297 202 HLRLPEYADRLGISESRLNDICRRFSALS--PKRLIIE 237 (287)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHhCCC--HHHHHHH
Confidence 579999999999999999999999 8886 5444433
No 277
>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=75.05 E-value=12 Score=27.71 Aligned_cols=25 Identities=20% Similarity=0.260 Sum_probs=20.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|.+.|+|+.+|||+.||.-..+ .|+
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~-~GL 25 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEE-KGL 25 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5789999999999999986654 364
No 278
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=74.91 E-value=3.5 Score=34.62 Aligned_cols=23 Identities=17% Similarity=0.343 Sum_probs=20.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+++++|+|+.||||..+++++.+
T Consensus 236 ~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 236 KLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 48999999999999999998853
No 279
>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=74.81 E-value=6.7 Score=29.14 Aligned_cols=65 Identities=17% Similarity=0.343 Sum_probs=41.2
Q ss_pred cHHHH-HHHcCCChhHHHHHHHHcCCCCChhHHHhhH-HHHHHHHhhhccC---CcHHHHHHHHHHHHHHHH
Q 041600 83 PIEEA-ARRMKLCPTVVKKICRRDGLHRWPHRKIKSI-QRRMSVASGRLRS---NDAEERANAQIEIQRLQE 149 (160)
Q Consensus 83 P~~eA-A~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl-~~~i~~L~~~~~~---~~~eerar~~~eIerL~~ 149 (160)
|+.-| .+--||+.++=+.+|.++||..+ .++..| +.+++.|...+.. -..+-+....+.|++|..
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~--~~~~~Ls~~~i~~l~~~i~~~~~i~~~L~~~~~~~i~rl~~ 81 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLGINPN--KKVGDLSDEQIDKLRKIIEKNHLIENDLKRQVRENIKRLKK 81 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTTS-SS--SBTTTSTHHHHHHHHHHHHTHSTCHHHHHHHHHHHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHHHcCCChh--hhcccCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHH
Confidence 44444 56779999999999999999642 333333 2345555554443 345666677788887753
No 280
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=74.46 E-value=4.3 Score=35.74 Aligned_cols=26 Identities=12% Similarity=-0.015 Sum_probs=21.4
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.++-.+.+||+.||||.+||-|..++
T Consensus 437 ~~~gn~~~aA~~Lgisr~tL~rkl~~ 462 (463)
T TIGR01818 437 HTRGHKQEAAALLGWGRNTLTRKLKE 462 (463)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 45778999999999999999766544
No 281
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=74.27 E-value=4.8 Score=34.01 Aligned_cols=34 Identities=24% Similarity=0.335 Sum_probs=26.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+++.+|+|..||||.+++|.+- +|=++.|++.+.
T Consensus 242 ~~s~~EIA~~Lgis~~tVk~~l---------~rAlkkLr~~l~ 275 (285)
T TIGR02394 242 PATLEEVAAEVGLTRERVRQIQ---------VEALKKLRRILE 275 (285)
T ss_pred CccHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence 6899999999999999999884 555555555444
No 282
>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=74.17 E-value=2.9 Score=26.68 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=20.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+++.|+|+.+|++.+++-|++..+
T Consensus 19 ~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 689999999999999999887654
No 283
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=74.11 E-value=3.3 Score=26.87 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=21.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+++..+.|..+|||.++..|++++
T Consensus 19 ~~~~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 19 NLTFQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred CCcHhHHhhheeecHHHHHHHHHH
Confidence 689999999999999999999754
No 284
>PRK09191 two-component response regulator; Provisional
Probab=73.90 E-value=4.4 Score=32.18 Aligned_cols=25 Identities=20% Similarity=0.244 Sum_probs=22.2
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.+-+++.+|+|+.||+|..++|.+.
T Consensus 101 ~~~~~s~~eIA~~l~~s~~tV~~~l 125 (261)
T PRK09191 101 ALEGFSVEEAAEILGVDPAEAEALL 125 (261)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHH
Confidence 4457999999999999999999886
No 285
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=73.65 E-value=2.1 Score=37.03 Aligned_cols=37 Identities=27% Similarity=0.485 Sum_probs=28.7
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP 111 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP 111 (160)
+.--+.+|++.|.|.|+.||||+++.--. +-|-..-|
T Consensus 32 lrKWR~~F~vSQ~elA~~l~vSpSVISDY--E~GRRk~P 68 (241)
T COG1709 32 LRKWREIFNVSQTELARELGVSPSVISDY--ESGRRKSP 68 (241)
T ss_pred HHHHHHHhCccHHHHHHHhCCCcceeehh--hccCccCc
Confidence 44567999999999999999999988654 55544444
No 286
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=72.96 E-value=7 Score=30.49 Aligned_cols=24 Identities=21% Similarity=0.304 Sum_probs=21.2
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-++|.+|+|+.||+|.++++..-
T Consensus 145 ~~g~s~~EIAe~lgis~~~V~~~l 168 (189)
T PRK06811 145 LLGEKIEEIAKKLGLTRSAIDNRL 168 (189)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHH
Confidence 348999999999999999999773
No 287
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=72.86 E-value=15 Score=28.67 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
++|.|+|+.+|||+.||+=.-+ .|+-
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE~-~GLl 33 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQR-KGLL 33 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence 8999999999999999986653 4643
No 288
>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=72.58 E-value=5.5 Score=25.42 Aligned_cols=24 Identities=29% Similarity=0.437 Sum_probs=20.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+++.+.|+.||++.+++.++.+++
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 789999999999999999886654
No 289
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=72.54 E-value=7.2 Score=32.27 Aligned_cols=24 Identities=17% Similarity=0.288 Sum_probs=19.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+++|+|+..|||.+|+-|.....
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~~ 29 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRNP 29 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCCC
Confidence 578899999999999999887543
No 290
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=72.43 E-value=5.2 Score=30.31 Aligned_cols=32 Identities=13% Similarity=0.157 Sum_probs=26.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+..+....++.+.|.|+.+|||.+++-++.+-
T Consensus 10 l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 10 VLRLLDERHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 45666778999999999999999999988643
No 291
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=72.17 E-value=8.4 Score=32.81 Aligned_cols=23 Identities=17% Similarity=0.260 Sum_probs=20.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+++++|+|+.||||...++++-+
T Consensus 248 ~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 248 KSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 58999999999999999999853
No 292
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=72.15 E-value=7.6 Score=33.72 Aligned_cols=27 Identities=19% Similarity=0.367 Sum_probs=24.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
.+++.++|+.+|+|+++|.|++++.|.
T Consensus 158 ~lsl~~lA~~~g~S~~~L~R~Fk~~G~ 184 (274)
T PRK09978 158 EWTLARIASELLMSPSLLKKKLREEET 184 (274)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCC
Confidence 378999999999999999999999875
No 293
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.79 E-value=6.1 Score=30.51 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=23.5
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
|+.-=-.|..+.|+.||+|.+++.++-+++
T Consensus 18 Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL 47 (153)
T PRK11179 18 LMENARTPYAELAKQFGVSPGTIHVRVEKM 47 (153)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334335899999999999999998876643
No 294
>PRK15340 transcriptional regulator InvF; Provisional
Probab=71.71 E-value=7 Score=32.97 Aligned_cols=28 Identities=14% Similarity=0.249 Sum_probs=25.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~ 108 (160)
+.++.+.|+.+|+|+++|.|+|++. |++
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~G~t 153 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRALGGK 153 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 5799999999999999999999986 764
No 295
>PRK00118 putative DNA-binding protein; Validated
Probab=71.51 E-value=14 Score=27.87 Aligned_cols=65 Identities=8% Similarity=0.029 Sum_probs=51.3
Q ss_pred ccCCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhccCCcHH
Q 041600 67 RTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAE 135 (160)
Q Consensus 67 r~~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~~~~~~e 135 (160)
....+|..+|...+++|...+-+.+.-+...|+.+-..+|. +.+.+.=+..+..++......+.+
T Consensus 30 y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 94 (104)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL----YEKFIERNELFDKIAYLKEKYPDD 94 (104)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh----HHHHHHHHHHHHHHHHHHHccccc
Confidence 45679999999999999999999999999999999999996 555555556666666665544434
No 296
>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=71.20 E-value=4.6 Score=26.84 Aligned_cols=25 Identities=28% Similarity=0.383 Sum_probs=20.8
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+.+++++.|..+|+|..++-|..++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~ 51 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKR 51 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5689999999999998888777554
No 297
>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=71.17 E-value=4.6 Score=32.42 Aligned_cols=37 Identities=22% Similarity=0.274 Sum_probs=31.4
Q ss_pred HHHHHhhc--CCcHHHHHHHcC-CChhHHHHHHHHcCCCC
Q 041600 73 LRDLMIYF--HLPIEEAARRMK-LCPTVVKKICRRDGLHR 109 (160)
Q Consensus 73 ~~~L~~yF--~lP~~eAA~~Lg-v~~T~LKr~CR~~GI~R 109 (160)
++.|++.+ ++...++|+.|| ||...+--..++||+..
T Consensus 8 ~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~ 47 (162)
T PF07750_consen 8 VERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRLGLSG 47 (162)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcccccc
Confidence 45666666 599999999999 99999999999999854
No 298
>PRK10403 transcriptional regulator NarP; Provisional
Probab=71.17 E-value=6.2 Score=29.24 Aligned_cols=27 Identities=11% Similarity=0.273 Sum_probs=22.0
Q ss_pred CCcHHHHHHHcCCChhH----HHHHHHHcCC
Q 041600 81 HLPIEEAARRMKLCPTV----VKKICRRDGL 107 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~----LKr~CR~~GI 107 (160)
+++-+++|+.||+|..| ++++++++|+
T Consensus 168 g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 58899999999999887 5666666666
No 299
>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=70.97 E-value=5.3 Score=26.43 Aligned_cols=26 Identities=12% Similarity=0.276 Sum_probs=21.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
.+++.|+|+.||+|..++++-+-++.
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 57889999999999999999876554
No 300
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=70.80 E-value=8.9 Score=30.89 Aligned_cols=22 Identities=23% Similarity=0.321 Sum_probs=20.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+|+|+.||||..++|++-
T Consensus 191 ~~s~~eIA~~lgis~~tV~~~~ 212 (224)
T TIGR02479 191 ELNLKEIGEVLGLTESRVSQIH 212 (224)
T ss_pred CCCHHHHHHHhCCCHHHHHHHH
Confidence 7999999999999999999874
No 301
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=70.78 E-value=6.3 Score=36.86 Aligned_cols=35 Identities=17% Similarity=0.094 Sum_probs=30.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy 112 (160)
..++--+.+||+.|||+.+||-+.-+++||.+=++
T Consensus 427 ~~~~g~~~~aA~~LGi~R~tLy~Klk~~g~~~~~~ 461 (464)
T COG2204 427 ERTGGNKSEAAERLGISRKTLYRKLKEYGIDRSDV 461 (464)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHhCCCcccc
Confidence 46678899999999999999999999999976443
No 302
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=70.74 E-value=10 Score=31.65 Aligned_cols=34 Identities=15% Similarity=0.314 Sum_probs=26.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+++.+|+|..||||.++++++- +|=++.|++.+.
T Consensus 221 ~~t~~EIA~~lgis~~~V~~~~---------~ral~kLr~~l~ 254 (257)
T PRK05911 221 ELVLKEIGKILGVSESRVSQIH---------SKALLKLRATLS 254 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHH
Confidence 6999999999999999999885 444555555544
No 303
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=70.69 E-value=9 Score=29.62 Aligned_cols=59 Identities=15% Similarity=0.226 Sum_probs=36.5
Q ss_pred HHHcCCChhHHHHHHHHcCCCCChhHHHhhH-HHHHHHHhhhccC---CcHHHHHHHHHHHHHHH
Q 041600 88 ARRMKLCPTVVKKICRRDGLHRWPHRKIKSI-QRRMSVASGRLRS---NDAEERANAQIEIQRLQ 148 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl-~~~i~~L~~~~~~---~~~eerar~~~eIerL~ 148 (160)
..-.||+.++-+.+|+++||.. ..++..| +.+++.|...+++ -..+=+...++.|++|.
T Consensus 20 t~i~GIG~~~A~~ic~~lgi~~--~~~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~ 82 (122)
T CHL00137 20 TYIYGIGLTSAKEILEKANIDP--DIRTKDLTDEQISALREIIEENYQVEGDLRRFESLNIKRLM 82 (122)
T ss_pred cccccccHHHHHHHHHHcCcCc--CcCcccCCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHH
Confidence 4467999999999999999964 3343333 2234444444421 23344556677777765
No 304
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=70.69 E-value=8.9 Score=31.60 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=21.2
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++.+|+|+.|||+..++|++-
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~ 242 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQ 242 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHH
Confidence 347999999999999999999873
No 305
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=70.66 E-value=9.4 Score=31.84 Aligned_cols=22 Identities=18% Similarity=0.292 Sum_probs=19.1
Q ss_pred CcHHHHHHHcCCChhHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
.+++|+|+..|||.+|+-|.-.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhC
Confidence 3689999999999999998853
No 306
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=70.59 E-value=40 Score=28.99 Aligned_cols=30 Identities=10% Similarity=0.079 Sum_probs=23.7
Q ss_pred CHHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.+..++.--++++.+.|+.+|||.+++.++
T Consensus 32 rl~~~R~~~gltq~~lA~~~gvs~~~i~~~ 61 (309)
T PRK08154 32 RVRTLRARRGMSRKVLAQASGVSERYLAQL 61 (309)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 355667777899999999999987777666
No 307
>cd00131 PAX Paired Box domain
Probab=70.52 E-value=4.6 Score=30.88 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=21.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
+++..++|+.||||.+++-++..+
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r 56 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNR 56 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 799999999999999998887665
No 308
>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=70.47 E-value=10 Score=28.84 Aligned_cols=59 Identities=15% Similarity=0.328 Sum_probs=37.1
Q ss_pred HHHcCCChhHHHHHHHHcCCCCChhHHHhhH-HHHHHHHhhhccC---CcHHHHHHHHHHHHHHH
Q 041600 88 ARRMKLCPTVVKKICRRDGLHRWPHRKIKSI-QRRMSVASGRLRS---NDAEERANAQIEIQRLQ 148 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl-~~~i~~L~~~~~~---~~~eerar~~~eIerL~ 148 (160)
..--||+..+-+.+|+++||..| .++..| +.+++.|...+++ -..+=+....+.|++|.
T Consensus 18 ~~i~GIG~~~a~~i~~~lgi~~~--~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~rl~ 80 (113)
T TIGR03631 18 TYIYGIGRTRARKILEKAGIDPD--KRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLM 80 (113)
T ss_pred eeeecccHHHHHHHHHHhCcCcc--cccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence 34569999999999999999643 333333 3345555555532 23344566677777765
No 309
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=70.45 E-value=10 Score=31.97 Aligned_cols=69 Identities=17% Similarity=0.236 Sum_probs=39.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCC---------CCChhHHHhhHHHHHHHHhhh--ccCCcHHHHHHHHHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGL---------HRWPHRKIKSIQRRMSVASGR--LRSNDAEERANAQIEIQRLQE 149 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI---------~RWPyRkikSl~~~i~~L~~~--~~~~~~eerar~~~eIerL~~ 149 (160)
+|.++|||+.||||.+||.|..|.=-| -|-|.--+..+-..+..=.-. .+-.+..+|.....||..|+.
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~G~i~~~~~~~gr~~~~ee~v~~~~~~~~~~k~vlYARVSSadQK~DL~rQv~~l~~ 80 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIREGKIRVVTTEGGKYRIPEEEIKKYLGKREKRKTVLYARVSSADQKEDLERQINYLTN 80 (193)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHcCcccceEecCceEeccHhHHHHHhchhhhcceEEEEEeccccchHHHHHHHHHHHH
Confidence 478899999999999999998874333 122332222222211111111 122345566677777777664
No 310
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=70.35 E-value=4.4 Score=31.51 Aligned_cols=49 Identities=24% Similarity=0.288 Sum_probs=39.7
Q ss_pred ChhHHHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHHHHHHHhccc
Q 041600 110 WPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGL 158 (160)
Q Consensus 110 WPyRkikSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~Em~~~c~~~ 158 (160)
|=-|+|..+++.++.++..++..=.+-+++++.+++.|+.++..+-+++
T Consensus 7 ~al~ki~~l~~~~~~i~~~~~~~I~~i~~~~~~~~~~l~~~i~~l~~~l 55 (149)
T PF07352_consen 7 WALRKIAELQREIARIEAEANDEIARIKEWYEAEIAPLQNRIEYLEGLL 55 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6679999999999999988864334556778889999999998887775
No 311
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=70.21 E-value=9 Score=32.90 Aligned_cols=28 Identities=7% Similarity=0.202 Sum_probs=25.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.+++.+.|+.+|+|+++|+|..++.|.+
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 3789999999999999999999999864
No 312
>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=70.14 E-value=4.9 Score=27.01 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=19.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.....++|+.||||+++.-..+++|
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 4778999999999988877776654
No 313
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=70.00 E-value=8.9 Score=31.66 Aligned_cols=45 Identities=22% Similarity=0.363 Sum_probs=33.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L 125 (160)
++.+.+.|+.+|+|++.|-|++++. |++-=-|.....+++...-|
T Consensus 199 ~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~l~~~Rl~~A~~lL 244 (290)
T PRK10572 199 EFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLL 244 (290)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999999997 77543355555555544444
No 314
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=69.77 E-value=10 Score=30.62 Aligned_cols=37 Identities=11% Similarity=0.233 Sum_probs=25.4
Q ss_pred HHHcCCChhHHHHHHHHcCCCC------ChhHHHhhHHHHHHH
Q 041600 88 ARRMKLCPTVVKKICRRDGLHR------WPHRKIKSIQRRMSV 124 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~R------WPyRkikSl~~~i~~ 124 (160)
..--||+.++=+.+|+++||.. ..--++.+|...|++
T Consensus 33 t~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 75 (154)
T PTZ00134 33 TAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIAN 75 (154)
T ss_pred cccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhc
Confidence 4567999999999999999953 333444455554443
No 315
>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=69.56 E-value=11 Score=31.02 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=19.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.+++|+|+..|||.+|+-|.-..
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 47899999999999999998643
No 316
>PRK15185 transcriptional regulator HilD; Provisional
Probab=69.54 E-value=9.3 Score=33.97 Aligned_cols=28 Identities=11% Similarity=0.281 Sum_probs=25.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.+++.+.|+.+|+|+++|.|..++.|.+
T Consensus 222 ~~SledLA~~lgmS~~tL~R~FK~~G~S 249 (309)
T PRK15185 222 QWKLTDVADHIFMSTSTLKRKLAEEGTS 249 (309)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence 4789999999999999999999987764
No 317
>PRK02944 OxaA-like protein precursor; Validated
Probab=69.46 E-value=9 Score=32.66 Aligned_cols=39 Identities=18% Similarity=0.289 Sum_probs=31.7
Q ss_pred HHHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHHHH
Q 041600 113 RKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEM 151 (160)
Q Consensus 113 RkikSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~Em 151 (160)
+|++.++-+++.+++...+++++++++.++|+.+|.+|-
T Consensus 86 ~km~~iqPe~~~iq~kyk~~~~~~~~k~~~e~~~Lyk~~ 124 (255)
T PRK02944 86 KAMQALQPEMQKLKEKYSSKDQATQQKLQQEMMQLFQKN 124 (255)
T ss_pred HHHHHccHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHc
Confidence 566777778888888777678888999999999998773
No 318
>PRK15044 transcriptional regulator SirC; Provisional
Probab=69.17 E-value=9.9 Score=33.69 Aligned_cols=28 Identities=11% Similarity=0.165 Sum_probs=25.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
.+.+.+.|+.+|+|+++|+|++++.|..
T Consensus 208 ~~SLeeLA~~lgmS~~tL~R~Fk~eg~T 235 (295)
T PRK15044 208 KWSQAEVAGKLFMSVSSLKRKLAAEEVS 235 (295)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 4788999999999999999999998753
No 319
>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=69.16 E-value=4.4 Score=26.73 Aligned_cols=25 Identities=32% Similarity=0.337 Sum_probs=19.3
Q ss_pred CC-cHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HL-PIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~l-P~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+ ...+.|+.+|||.+++++..+++
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 46 67888999999999999887655
No 320
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=68.99 E-value=11 Score=28.66 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=20.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+|+|+.||+|..++|..-
T Consensus 134 g~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 134 GLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
Confidence 6899999999999999999763
No 321
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=68.95 E-value=10 Score=30.42 Aligned_cols=22 Identities=18% Similarity=0.249 Sum_probs=20.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++++|+|+.||||+++++++-
T Consensus 194 ~~s~~eIA~~lgis~~~v~~~~ 215 (227)
T TIGR02980 194 DKTQSEIAERLGISQMHVSRLL 215 (227)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 7999999999999999999874
No 322
>PRK05949 RNA polymerase sigma factor; Validated
Probab=68.83 E-value=13 Score=32.62 Aligned_cols=40 Identities=20% Similarity=0.404 Sum_probs=28.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL 129 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~ 129 (160)
+++++|+|+.||||..++|.+= +|=++.|++....|..++
T Consensus 286 ~~Tl~EIa~~lgiS~erVrq~~---------~rAl~kLr~~~~~l~~~~ 325 (327)
T PRK05949 286 ELSLAKVGERLNLSRERVRQLE---------HQALAHLRRRRANVKEYL 325 (327)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHHHHHH
Confidence 3899999999999999999884 444555555444454443
No 323
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=68.63 E-value=11 Score=29.04 Aligned_cols=59 Identities=15% Similarity=0.251 Sum_probs=37.5
Q ss_pred HHHcCCChhHHHHHHHHcCCCCChhHHHhhH-HHHHHHHhhhccC---CcHHHHHHHHHHHHHHH
Q 041600 88 ARRMKLCPTVVKKICRRDGLHRWPHRKIKSI-QRRMSVASGRLRS---NDAEERANAQIEIQRLQ 148 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl-~~~i~~L~~~~~~---~~~eerar~~~eIerL~ 148 (160)
..-.||+.++=+.+|+++||..| .++..| +.+++.|...+++ -..+=+....+.|++|.
T Consensus 20 ~~I~GIG~~~a~~i~~~lgi~~~--~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~ 82 (122)
T PRK05179 20 TYIYGIGRTRAKEILAAAGIDPD--TRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKRLM 82 (122)
T ss_pred cccccccHHHHHHHHHHhCcCcc--cccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHH
Confidence 44679999999999999999643 344443 3345555555432 23344556677777775
No 324
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=68.27 E-value=6 Score=27.06 Aligned_cols=28 Identities=21% Similarity=0.401 Sum_probs=22.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.+++..||+ .+..+|+.|||++.++-.-
T Consensus 2 k~~aI~~~G-~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 2 KKDAIKYFG-GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHS-SHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHC-CHHHHHHHHCCCHHHHHHh
Confidence 467788997 7889999999999998755
No 325
>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=68.02 E-value=7.4 Score=30.99 Aligned_cols=29 Identities=17% Similarity=0.283 Sum_probs=17.2
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..++.-.+|++.+.|+.+|||..++.++
T Consensus 30 Ir~~R~~lGmTq~eLAerlGVS~~tIs~i 58 (150)
T TIGR02612 30 VRAIRKALGMSGAQLAGRLGVTPQRVEAL 58 (150)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 44555556666666666666665555444
No 326
>PRK09483 response regulator; Provisional
Probab=67.96 E-value=6.6 Score=29.71 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=19.3
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++.+++|+.|++|..|+|..-
T Consensus 162 ~G~~~~~Ia~~l~is~~TV~~~~ 184 (217)
T PRK09483 162 KGQKVNEISEQLNLSPKTVNSYR 184 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Confidence 46899999999999988887653
No 327
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=67.85 E-value=8.1 Score=33.77 Aligned_cols=34 Identities=18% Similarity=0.340 Sum_probs=26.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~ 123 (160)
+++++|+|+.|||+..++|.+- +|=++.|++.+.
T Consensus 282 ~~s~~EIA~~Lgis~~tV~~~~---------~rAl~kLr~~l~ 315 (325)
T PRK05657 282 AATLEDVAREIGLTRERVRQIQ---------VEALRRLREILQ 315 (325)
T ss_pred CcCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHH
Confidence 5899999999999999999884 555555555443
No 328
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=67.82 E-value=14 Score=33.73 Aligned_cols=43 Identities=28% Similarity=0.319 Sum_probs=37.2
Q ss_pred hHHHhhHHHHHHHHhhhccC-CcHHHHHHHHHHHHHHHHHHHHH
Q 041600 112 HRKIKSIQRRMSVASGRLRS-NDAEERANAQIEIQRLQEEMAAA 154 (160)
Q Consensus 112 yRkikSl~~~i~~L~~~~~~-~~~eerar~~~eIerL~~Em~~~ 154 (160)
|++++++...+...+.++.. .|+|.+.-++.||..++.++..+
T Consensus 52 ~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~~~~~~~l 95 (363)
T COG0216 52 YREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEEL 95 (363)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999975 48999988888888888887765
No 329
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=67.65 E-value=9.9 Score=31.36 Aligned_cols=22 Identities=18% Similarity=0.375 Sum_probs=20.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+|+|..||||..++|.+-
T Consensus 217 ~~s~~EIA~~lgis~~tV~~~~ 238 (251)
T PRK07670 217 ELTLTEIGQVLNLSTSRISQIH 238 (251)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 7999999999999999999874
No 330
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=67.54 E-value=8 Score=36.27 Aligned_cols=38 Identities=21% Similarity=0.393 Sum_probs=30.1
Q ss_pred CCHHHHHhhc----------CCc-HHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 71 LTLRDLMIYF----------HLP-IEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 71 lt~~~L~~yF----------~lP-~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
=|+++|...| .+| -...|++||||-|+.-..-|++||.
T Consensus 460 gsLdei~~~fE~~VL~rly~~yPStRkLAkRLgvSHTaIAnKLRqyGi~ 508 (511)
T COG3283 460 GSLDEIVSRFERSVLTRLYRSYPSTRKLAKRLGVSHTAIANKLRQYGIG 508 (511)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCcHHHHHHHhCCcHHHHHHHHHHhCCC
Confidence 3577776544 345 4567999999999999999999995
No 331
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=67.22 E-value=12 Score=32.23 Aligned_cols=23 Identities=13% Similarity=0.273 Sum_probs=19.4
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 041600 83 PIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.++|+|+..|||.+|+-|.-...
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~ 24 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGS 24 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Confidence 58999999999999999885443
No 332
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=67.10 E-value=14 Score=30.89 Aligned_cols=44 Identities=14% Similarity=0.213 Sum_probs=35.3
Q ss_pred HHHhhHHHHHHHHhhhccC-CcHHHHHHHHHHHHHHHHHHHHHhc
Q 041600 113 RKIKSIQRRMSVASGRLRS-NDAEERANAQIEIQRLQEEMAAACA 156 (160)
Q Consensus 113 RkikSl~~~i~~L~~~~~~-~~~eerar~~~eIerL~~Em~~~c~ 156 (160)
.++++++...+.|.++++. .+.++..+++.+|.+++.|++.+-|
T Consensus 139 arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~ 183 (262)
T PF14257_consen 139 ARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEG 183 (262)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888888888888864 4788888888899888888887654
No 333
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=66.91 E-value=23 Score=25.76 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=25.2
Q ss_pred cCCCCHHHHHhhc--CCcHHHHHHHcCC-ChhHHHHH
Q 041600 68 TGKLTLRDLMIYF--HLPIEEAARRMKL-CPTVVKKI 101 (160)
Q Consensus 68 ~~~lt~~~L~~yF--~lP~~eAA~~Lgv-~~T~LKr~ 101 (160)
+..+-++-+..|+ +.++.++|+++|| +.++|.+-
T Consensus 9 s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 9 SPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred CHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHH
Confidence 3344455566666 5789999999995 99999954
No 334
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=66.90 E-value=12 Score=30.05 Aligned_cols=23 Identities=17% Similarity=0.164 Sum_probs=19.4
Q ss_pred HHHcCCChhHHHHHHHHcCCCCC
Q 041600 88 ARRMKLCPTVVKKICRRDGLHRW 110 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~RW 110 (160)
..--||+.++-+.+|+++||..+
T Consensus 28 t~IyGIG~~~a~~Ic~~lgi~~~ 50 (149)
T PRK04053 28 TGIKGIGRRTARAIARKLGLDPN 50 (149)
T ss_pred cccccccHHHHHHHHHHcCcCCC
Confidence 45679999999999999999653
No 335
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=66.86 E-value=10 Score=25.86 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=21.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+...++|+.+|++.+++.|....+
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5889999999999999998887644
No 336
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=65.97 E-value=12 Score=31.84 Aligned_cols=46 Identities=22% Similarity=0.155 Sum_probs=32.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~ 126 (160)
.+.+.+.|+.+|+|++.|.|++++. |++--=|.+...+++....|.
T Consensus 207 ~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~A~~lL~ 253 (302)
T PRK10371 207 ALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLS 253 (302)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999999999994 774333444444444444443
No 337
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=65.94 E-value=9.7 Score=27.50 Aligned_cols=29 Identities=7% Similarity=0.174 Sum_probs=23.6
Q ss_pred HHHHHhhcCCcHHHHHHHcC------CChhHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMK------LCPTVVKKI 101 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lg------v~~T~LKr~ 101 (160)
+...+.-.++.+.++|+.+| +|.|++-|+
T Consensus 16 lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~ 50 (75)
T smart00352 16 FKQRRIKLGFTQADVGLALGALYGPDFSQTTICRF 50 (75)
T ss_pred HHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHH
Confidence 44455677999999999999 499998876
No 338
>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=65.88 E-value=7.4 Score=24.37 Aligned_cols=31 Identities=19% Similarity=0.225 Sum_probs=23.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy 112 (160)
+...++|+.+|++.+++.+.++++-=..|..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 7788999999999999988887663334443
No 339
>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=65.71 E-value=9 Score=27.67 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=22.7
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 74 RDLMIYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+-|.. =..++.++|+.+|||.+|+-+.-.
T Consensus 13 e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 13 KYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 34455 568999999999999999988643
No 340
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=65.41 E-value=6.2 Score=31.64 Aligned_cols=33 Identities=9% Similarity=0.041 Sum_probs=25.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc---C-CCCChhH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD---G-LHRWPHR 113 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~---G-I~RWPyR 113 (160)
-+|..+.|+.||||.|+++...++| | |..-|.+
T Consensus 30 ~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~ 66 (224)
T PRK11534 30 KLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK 66 (224)
T ss_pred cCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence 4899999999999999999888866 4 2345554
No 341
>PRK13749 transcriptional regulator MerD; Provisional
Probab=65.39 E-value=10 Score=29.16 Aligned_cols=27 Identities=15% Similarity=0.167 Sum_probs=21.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
++.|.|+|+..|||+.+|+-.. +.|+-
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE-~~GLl 29 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYL-LRGLL 29 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHH-HCCCC
Confidence 4789999999999999998655 34643
No 342
>PHA02591 hypothetical protein; Provisional
Probab=65.15 E-value=7.5 Score=28.69 Aligned_cols=24 Identities=13% Similarity=0.160 Sum_probs=21.1
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
-++.+.++|+.|||+..++++.-+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 479999999999999999998743
No 343
>PRK13502 transcriptional activator RhaR; Provisional
Probab=65.11 E-value=13 Score=30.45 Aligned_cols=28 Identities=11% Similarity=0.301 Sum_probs=24.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH-cCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR-DGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~-~GI~ 108 (160)
.+.+.+.|..+|||++.|.|++++ .|++
T Consensus 192 ~~~~~~lA~~~~iS~~~L~r~fk~~~G~t 220 (282)
T PRK13502 192 PFALDAFCQQEQCSERVLRQQFRAQTGMT 220 (282)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 367889999999999999999998 7874
No 344
>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=65.03 E-value=4.5 Score=25.11 Aligned_cols=20 Identities=15% Similarity=0.250 Sum_probs=17.3
Q ss_pred HHHHHcCCChhHHHHHHHHc
Q 041600 86 EAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 86 eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+.|+.+|||.+++-++++-.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999998633
No 345
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=64.85 E-value=9.1 Score=30.18 Aligned_cols=30 Identities=20% Similarity=0.137 Sum_probs=25.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+..++.-.++.+.++|+.+|||.++|.++-
T Consensus 12 l~~~R~~~glt~~elA~~~gis~~~is~~E 41 (185)
T PRK09943 12 LSEIRQQQGLSQRRAAELSGLTHSAISTIE 41 (185)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 556677778999999999999999988884
No 346
>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=64.84 E-value=6.3 Score=27.38 Aligned_cols=32 Identities=22% Similarity=0.322 Sum_probs=24.3
Q ss_pred CCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 70 KLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 70 ~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
.+||.|.-.-++ +.+||+.|||..+.+-|.-|
T Consensus 3 ~i~L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr 34 (59)
T PF09048_consen 3 RITLAEYVKEHG--QAKAARALGVTQSAISKALR 34 (59)
T ss_dssp EEEHHHHHHHHH--HHHHHHHHTS-HHHHHHHHH
T ss_pred eeeHHHHHHHhC--hHHHHHHcCCcHHHHHHHHH
Confidence 356777766666 89999999999999877644
No 347
>PRK13503 transcriptional activator RhaS; Provisional
Probab=64.84 E-value=20 Score=29.13 Aligned_cols=33 Identities=21% Similarity=0.293 Sum_probs=26.7
Q ss_pred HHhhc--CCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600 76 LMIYF--HLPIEEAARRMKLCPTVVKKICRRD-GLH 108 (160)
Q Consensus 76 L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~ 108 (160)
|..+| .+++.+.|+.+|+|++.|.|.+++. |++
T Consensus 180 I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S 215 (278)
T PRK13503 180 LEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLT 215 (278)
T ss_pred HHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcC
Confidence 34444 4778999999999999999999776 663
No 348
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=64.77 E-value=12 Score=30.69 Aligned_cols=22 Identities=14% Similarity=0.302 Sum_probs=20.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++++|+|+.||||.++++++-
T Consensus 196 ~~t~~EIA~~lgis~~~V~q~~ 217 (238)
T TIGR02393 196 PHTLEEVGKEFNVTRERIRQIE 217 (238)
T ss_pred CccHHHHHHHHCCCHHHHHHHH
Confidence 4899999999999999999885
No 349
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=64.63 E-value=18 Score=27.89 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=22.5
Q ss_pred CCCHHHHH--hhc---CCcHHHHHHHcCCChhHHHHH
Q 041600 70 KLTLRDLM--IYF---HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 70 ~lt~~~L~--~yF---~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.|+-+++. ..| .=.+++.|+.||||=+|++.+
T Consensus 33 ~L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~r 69 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNR 69 (113)
T ss_pred cCCHHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHH
Confidence 45555554 333 457899999999998877765
No 350
>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=64.52 E-value=7.1 Score=30.14 Aligned_cols=25 Identities=28% Similarity=0.477 Sum_probs=21.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.++|+.+||++.+|...-++ |+
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~-GL 26 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH-GL 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999977664 65
No 351
>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=64.20 E-value=13 Score=24.97 Aligned_cols=22 Identities=14% Similarity=0.403 Sum_probs=18.3
Q ss_pred HHHHcCCChhHHHHHHHH-cCCC
Q 041600 87 AARRMKLCPTVVKKICRR-DGLH 108 (160)
Q Consensus 87 AA~~Lgv~~T~LKr~CR~-~GI~ 108 (160)
.|+.||||+..|.++|++ .|++
T Consensus 1 lA~~~~~s~~~l~~~f~~~~g~s 23 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKETGMS 23 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHHSS-
T ss_pred ChHHhCcCHHHHHHHHHHHHCcC
Confidence 489999999999999999 7873
No 352
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=64.08 E-value=18 Score=31.50 Aligned_cols=40 Identities=15% Similarity=0.314 Sum_probs=28.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL 129 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~ 129 (160)
.++++|+|..||||..+++.+= +|=++.|++....|..++
T Consensus 276 ~~Tl~EIa~~lgiS~erVRqi~---------~rAl~kLr~~~~~l~~~~ 315 (317)
T PRK07405 276 PLTLAKIGERLNISRERVRQIE---------REALSKLRKRKANIQEYL 315 (317)
T ss_pred CcCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHHHHHH
Confidence 3899999999999999999884 444555555444444433
No 353
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=63.94 E-value=21 Score=27.98 Aligned_cols=59 Identities=14% Similarity=0.400 Sum_probs=40.0
Q ss_pred HHcCCChhHHHHHHHHcCCCCChhHHHhhH-HHHHHHHhhhccC---CcHHHHHHHHHHHHHHHH
Q 041600 89 RRMKLCPTVVKKICRRDGLHRWPHRKIKSI-QRRMSVASGRLRS---NDAEERANAQIEIQRLQE 149 (160)
Q Consensus 89 ~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl-~~~i~~L~~~~~~---~~~eerar~~~eIerL~~ 149 (160)
.--||+.++=+.||.++||.. ..++.-| +-+|..|.+.+.+ -.++-+....+.|++|.+
T Consensus 21 ~IyGIG~~~a~~I~~~~gi~~--~~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkRl~~ 83 (121)
T COG0099 21 YIYGIGRRRAKEICKKAGIDP--DKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKRLMK 83 (121)
T ss_pred hhccccHHHHHHHHHHcCCCH--hHhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHHHHH
Confidence 367999999999999999964 4455544 3455666555541 234455677788888763
No 354
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=63.89 E-value=8.6 Score=33.49 Aligned_cols=24 Identities=17% Similarity=-0.010 Sum_probs=19.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
..++--..+||+.||||.+||-|.
T Consensus 415 ~~~~gn~~~aa~~Lgisr~tl~rk 438 (441)
T PRK10365 415 EKTGGNKTEAARQLGITRKTLLAK 438 (441)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHH
Confidence 345678999999999999998654
No 355
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=63.72 E-value=13 Score=31.73 Aligned_cols=22 Identities=14% Similarity=0.221 Sum_probs=20.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+|+|+.||||..+++++=
T Consensus 245 ~~t~~EIa~~lgvs~~~V~q~~ 266 (289)
T PRK07500 245 GATLEALGEELGISKERVRQIE 266 (289)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
Confidence 5899999999999999999884
No 356
>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=63.59 E-value=12 Score=23.84 Aligned_cols=31 Identities=19% Similarity=0.175 Sum_probs=24.1
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.|..+=.+++.+.|+.++++.+++-++.+++
T Consensus 11 ~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 11 ILYENGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp HHHHHSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHcCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 3445557899999999999999999887654
No 357
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=63.52 E-value=7.7 Score=23.20 Aligned_cols=20 Identities=25% Similarity=0.233 Sum_probs=16.5
Q ss_pred CCChhHHHHHHHHcCCCCCh
Q 041600 92 KLCPTVVKKICRRDGLHRWP 111 (160)
Q Consensus 92 gv~~T~LKr~CR~~GI~RWP 111 (160)
.++.+.||.+|+.+|++.+-
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G 22 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSG 22 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCC
Confidence 35678899999999997665
No 358
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=63.38 E-value=15 Score=30.67 Aligned_cols=22 Identities=32% Similarity=0.505 Sum_probs=20.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++++|+|..||||..+++++-
T Consensus 219 ~~s~~eIA~~lgvs~~~V~~~~ 240 (256)
T PRK07408 219 DLTQKEAAERLGISPVTVSRRV 240 (256)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 6999999999999999999884
No 359
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.11 E-value=7.6 Score=30.71 Aligned_cols=28 Identities=29% Similarity=0.232 Sum_probs=23.1
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
+=++.+.+||+.+|||.+|..+.-++..
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 4479999999999999999887765543
No 360
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=63.06 E-value=9.9 Score=31.01 Aligned_cols=38 Identities=8% Similarity=0.169 Sum_probs=27.0
Q ss_pred CCCHHHHH--hh--cCCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 041600 70 KLTLRDLM--IY--FHLPIEEAARRMKLCPTVVK----KICRRDGL 107 (160)
Q Consensus 70 ~lt~~~L~--~y--F~lP~~eAA~~Lgv~~T~LK----r~CR~~GI 107 (160)
.||--|.. .. =+++.+++|++|++|..|+| ++.+++|+
T Consensus 134 ~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 134 MLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 46665554 11 27999999999999977665 56666666
No 361
>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=63.06 E-value=9.9 Score=23.68 Aligned_cols=23 Identities=22% Similarity=0.248 Sum_probs=13.8
Q ss_pred hhcCCcHHHHHHHcCCChhHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKK 100 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr 100 (160)
.|-++.+.++|+++||+.+++-+
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 44556666666666666666543
No 362
>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=63.01 E-value=16 Score=28.86 Aligned_cols=24 Identities=25% Similarity=0.146 Sum_probs=21.6
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHH
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+-+++++|+|+.||+|.++++++=
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e 42 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIE 42 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 457999999999999999999884
No 363
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=62.74 E-value=9 Score=27.07 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=20.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.+|..+||+.||+...++.+.-+.
T Consensus 13 ~~s~~~Aa~~lG~~~~~v~~wv~~ 36 (65)
T PF05344_consen 13 QISVAQAADRLGTDPGTVRRWVRM 36 (65)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHH
Confidence 478899999999999998877443
No 364
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=62.64 E-value=25 Score=29.48 Aligned_cols=73 Identities=23% Similarity=0.392 Sum_probs=43.2
Q ss_pred CHHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhccCC------cHHHHHHHHHH
Q 041600 72 TLRDLMIYF--HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSN------DAEERANAQIE 143 (160)
Q Consensus 72 t~~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~~~~------~~eerar~~~e 143 (160)
++.++...| ++|.=+-.+.|+|.-..|+++ ++++..|.+.+.+-.-..... .=.+|+.++.+
T Consensus 188 ~l~el~~r~~~giP~LDPi~DmkI~d~~~~e~----------~~k~~~Le~rl~~~~~~~~~~~~~~~~~~~~k~~l~~~ 257 (268)
T PF13234_consen 188 SLQELLKRFPDGIPLLDPIKDMKIKDPEFVEL----------VKKIEALEKRLSSHPLHKCPDFEEHYALYHEKAELQEE 257 (268)
T ss_dssp HHHHHHHHSSS--TCHHCHHHH----HHHHHH----------HHHHHHHHHHHHHSCHCCSSSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhCCCCCCccChHHhCCCCcHHHHHH----------HHHHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHHHHH
Confidence 455665555 467777777777777777777 567777777776633222111 22457778889
Q ss_pred HHHHHHHHHHH
Q 041600 144 IQRLQEEMAAA 154 (160)
Q Consensus 144 IerL~~Em~~~ 154 (160)
|+.|+.+|..+
T Consensus 258 i~~Lk~~l~~a 268 (268)
T PF13234_consen 258 IKALKRQLSDA 268 (268)
T ss_dssp HHHHHHHHHH-
T ss_pred HHHHHHHHhcC
Confidence 99999888764
No 365
>PHA02535 P terminase ATPase subunit; Provisional
Probab=62.55 E-value=29 Score=33.51 Aligned_cols=48 Identities=23% Similarity=0.340 Sum_probs=34.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCC-ChhHHH-hhHHHHHHHHhhh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHR-WPHRKI-KSIQRRMSVASGR 128 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R-WPyRki-kSl~~~i~~L~~~ 128 (160)
+.++.++|+.|||++++|-+-+++.+=.. =|.-++ .++...|..|-..
T Consensus 18 G~sv~eIA~~LGv~~~Tl~~W~kr~~w~~~~~~~~v~~~~~~r~~~l~~k 67 (581)
T PHA02535 18 GWTVAEIAEELGLKSRTIYSWKERDGWRDLLPEERIEESIEARLIQLIEK 67 (581)
T ss_pred CCCHHHHHHHhCCChhHHHHHhccccccccCCcccHHHHHHHHHHHHHcc
Confidence 79999999999999999999998875211 133333 3446666666543
No 366
>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=62.35 E-value=7.3 Score=30.81 Aligned_cols=25 Identities=20% Similarity=0.205 Sum_probs=21.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+|..+.|+.||||.|+++..-++|
T Consensus 34 ~L~e~~La~~lgVSRtpVReAL~~L 58 (212)
T TIGR03338 34 KLNESDIAARLGVSRGPVREAFRAL 58 (212)
T ss_pred EecHHHHHHHhCCChHHHHHHHHHH
Confidence 5789999999999999998877755
No 367
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=62.15 E-value=6.8 Score=32.41 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=14.4
Q ss_pred CcHHHHHHHcCCChhHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.+++|+|+..|||.+|+.|.-
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~L 27 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVL 27 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHH
Confidence 466777777777777776664
No 368
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=61.83 E-value=8 Score=29.35 Aligned_cols=43 Identities=9% Similarity=0.158 Sum_probs=34.9
Q ss_pred ccCCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 67 RTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 67 r~~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
.-..++.++|...+++|...+-..|.-+...||+...+.|+.|
T Consensus 131 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~ 173 (173)
T PRK09645 131 YYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERGVTR 173 (173)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccccCC
Confidence 3467888888888888888888888888888888887777754
No 369
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=61.63 E-value=7.8 Score=29.64 Aligned_cols=35 Identities=9% Similarity=0.172 Sum_probs=29.3
Q ss_pred CCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600 70 KLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 70 ~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.|=.+++-.-|++.+.++|+.|||...++-.+|.-
T Consensus 12 EiL~eeflep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFLEPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 45566777778999999999999999999998853
No 370
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=61.53 E-value=7.9 Score=29.46 Aligned_cols=24 Identities=17% Similarity=0.113 Sum_probs=21.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++..+.|+.+|||.+.|.++.++|
T Consensus 26 ~s~~~ia~~~~is~~~vrk~l~~L 49 (141)
T PRK11014 26 TSISEVTEVYGVSRNHMVKIINQL 49 (141)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 678999999999999999998765
No 371
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=61.16 E-value=45 Score=25.88 Aligned_cols=30 Identities=17% Similarity=0.141 Sum_probs=24.6
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+|..- ++.+.++|+.||++++.+.+.-+..
T Consensus 17 ~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 17 ELIEE-GLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred HHHHc-CCcHHHHHHHhCCCHHHHHHHHccC
Confidence 44444 9999999999999999999885543
No 372
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=61.16 E-value=15 Score=26.27 Aligned_cols=57 Identities=19% Similarity=0.354 Sum_probs=38.2
Q ss_pred HHHHHhhc---CCcHHHHHHHc--CCChhHHHHHHHHcCCCCChhHHHhhHHH-----HHHHHhhhcc
Q 041600 73 LRDLMIYF---HLPIEEAARRM--KLCPTVVKKICRRDGLHRWPHRKIKSIQR-----RMSVASGRLR 130 (160)
Q Consensus 73 ~~~L~~yF---~lP~~eAA~~L--gv~~T~LKr~CR~~GI~RWPyRkikSl~~-----~i~~L~~~~~ 130 (160)
+.-|.+|| .+|+.++++.. |+++.++++..+...| .||.=++-.=++ .+.+|-.+|+
T Consensus 3 flLma~~~~~~~IpL~~v~~~yf~~lt~~~a~rk~~~g~l-plPv~rl~~SqKs~~~V~v~dLA~yiD 69 (76)
T PF11112_consen 3 FLLMAQYFGDPVIPLEEVCEDYFPHLTPKTAKRKANAGEL-PLPVFRLDDSQKSPKFVHVQDLAAYID 69 (76)
T ss_pred HHHHHHHcCCCCCcHHHHHHHHHccCCHHHHHHHHHCCCC-CCceeecCCcccCCceeeHHHHHHHHH
Confidence 44566675 48888887665 9999999999888777 899655532111 2455555554
No 373
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=61.11 E-value=30 Score=27.61 Aligned_cols=28 Identities=18% Similarity=0.184 Sum_probs=23.5
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
.--+|++.+.|..+|++.+++.++ +.|-
T Consensus 79 e~~glSqeeLA~~lgvs~s~Isri--E~G~ 106 (154)
T TIGR00270 79 EKRGWSQEQLAKKIQEKESLIKKI--ENAE 106 (154)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH--HCCC
Confidence 445899999999999999999998 4554
No 374
>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=60.97 E-value=8.4 Score=26.74 Aligned_cols=24 Identities=25% Similarity=0.486 Sum_probs=19.9
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++.++.|+.+|++++.|.++..+|
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 789999999999999999986543
No 375
>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=60.61 E-value=14 Score=29.36 Aligned_cols=22 Identities=14% Similarity=0.194 Sum_probs=18.5
Q ss_pred HHHcCCChhHHHHHHHHcCCCC
Q 041600 88 ARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~R 109 (160)
..--||+.+.-..+|+++||..
T Consensus 24 t~I~GIG~~~a~~I~~~lgi~~ 45 (144)
T TIGR03629 24 TGIKGIGRRFARAIARKLGVDP 45 (144)
T ss_pred cceeccCHHHHHHHHHHcCcCC
Confidence 3457999999999999999964
No 376
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=60.52 E-value=7.4 Score=28.28 Aligned_cols=24 Identities=21% Similarity=0.243 Sum_probs=19.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
+++.|+|+.+|||+.||.-.= +.|
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE-~~G 24 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYE-RKG 24 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHH-HcC
Confidence 578999999999999998554 444
No 377
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.21 E-value=10 Score=28.61 Aligned_cols=32 Identities=28% Similarity=0.279 Sum_probs=27.6
Q ss_pred CCHHHHHhhc---CCcHHHHHHHcCCChhHHHHHH
Q 041600 71 LTLRDLMIYF---HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 71 lt~~~L~~yF---~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.|.+||+..| .|...++|..||++.-.|-|+-
T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred HHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHH
Confidence 4678999888 4789999999999999888875
No 378
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=60.09 E-value=22 Score=32.83 Aligned_cols=44 Identities=14% Similarity=0.216 Sum_probs=31.7
Q ss_pred HHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHHHHHHHhcc
Q 041600 114 KIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAG 157 (160)
Q Consensus 114 kikSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~Em~~~c~~ 157 (160)
++.++-..+.+|....+.+.....+....+|+.|++||..+-.|
T Consensus 123 Rl~tv~~~l~~la~~~~~Dp~~Ri~~Le~e~~~i~~EI~~l~aG 166 (478)
T PF11855_consen 123 RLNTVFDALRQLAEGTDPDPERRIAELEREIAEIDAEIDRLEAG 166 (478)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence 56666667777776676544444566678999999999988877
No 379
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=59.85 E-value=5.6 Score=32.63 Aligned_cols=20 Identities=15% Similarity=0.326 Sum_probs=15.2
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q 041600 84 IEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 84 ~~eAA~~Lgv~~T~LKr~CR 103 (160)
++|+|+.+|||.+|+.|.-.
T Consensus 1 i~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 1 MKDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred ChhHHHHhCCcHHHHHHHhC
Confidence 46788888888888877754
No 380
>PRK05572 sporulation sigma factor SigF; Validated
Probab=59.82 E-value=19 Score=29.69 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=19.8
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
++++.++|+.|||++++++++
T Consensus 218 ~~s~~eIA~~lgis~~~V~~~ 238 (252)
T PRK05572 218 DKTQSEVAKRLGISQVQVSRL 238 (252)
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 799999999999999999877
No 381
>PRK06424 transcription factor; Provisional
Probab=59.75 E-value=13 Score=29.44 Aligned_cols=27 Identities=11% Similarity=0.039 Sum_probs=22.5
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
++.-.+|++.+.|+.+|++.+++.++-
T Consensus 92 lRe~~GLSQ~eLA~~iGvs~stIskiE 118 (144)
T PRK06424 92 ARERLSMSQADLAAKIFERKNVIASIE 118 (144)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 445668999999999999999988883
No 382
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=59.73 E-value=9.1 Score=30.90 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=21.6
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|++||||.|+++.-.++|
T Consensus 30 ~LPsE~eLae~~gVSRt~VReAL~~L 55 (239)
T PRK04984 30 ILPAERELSELIGVTRTTLREVLQRL 55 (239)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 376 8899999999999999887765
No 383
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=59.21 E-value=9.3 Score=31.34 Aligned_cols=25 Identities=28% Similarity=0.272 Sum_probs=21.1
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|+.||||.|+++..-++|
T Consensus 32 ~LpsE~eLa~~~gVSRtpVREAL~~L 57 (257)
T PRK10225 32 RLPPEREIAEMLDVTRTVVREALIML 57 (257)
T ss_pred cCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 586 8899999999999988777654
No 384
>PRK13500 transcriptional activator RhaR; Provisional
Probab=59.02 E-value=15 Score=31.27 Aligned_cols=35 Identities=11% Similarity=0.289 Sum_probs=28.7
Q ss_pred HHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600 74 RDLMIYFH--LPIEEAARRMKLCPTVVKKICRRD-GLH 108 (160)
Q Consensus 74 ~~L~~yF~--lP~~eAA~~Lgv~~T~LKr~CR~~-GI~ 108 (160)
+-|..+|. +.+.+.|+.+|+|+..|-|++++. |.+
T Consensus 213 ~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T 250 (312)
T PRK13500 213 TRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMT 250 (312)
T ss_pred HHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 44555553 789999999999999999999986 763
No 385
>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=59.02 E-value=25 Score=23.47 Aligned_cols=37 Identities=14% Similarity=0.171 Sum_probs=21.4
Q ss_pred ChhHHHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHH
Q 041600 110 WPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRL 147 (160)
Q Consensus 110 WPyRkikSl~~~i~~L~~~~~~~~~eerar~~~eIerL 147 (160)
+.+..+.+++..+..|+..+.. -..+....+.+|+.|
T Consensus 14 ~~~~~~~~~~~ei~~l~~~i~~-l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 14 SGYSRYYQLNQEIAELQKEIEE-LKKENEELKEEIERL 50 (80)
T ss_pred chHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHh
Confidence 4567778888888887766642 122233344444444
No 386
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=58.94 E-value=8.3 Score=32.20 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=14.1
Q ss_pred cHHHHHHHcCCChhHHHHHH
Q 041600 83 PIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~C 102 (160)
+++|+|+..|||.+|+-|.-
T Consensus 3 ti~dIA~~aGVS~~TVSrvL 22 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVL 22 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHH
Confidence 56777777777777766654
No 387
>PRK10651 transcriptional regulator NarL; Provisional
Probab=58.49 E-value=15 Score=27.28 Aligned_cols=37 Identities=30% Similarity=0.376 Sum_probs=25.0
Q ss_pred CCHHHHH---hhc-CCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 041600 71 LTLRDLM---IYF-HLPIEEAARRMKLCPTVVKK----ICRRDGL 107 (160)
Q Consensus 71 lt~~~L~---~yF-~lP~~eAA~~Lgv~~T~LKr----~CR~~GI 107 (160)
||..+.. -+. +++.+++|+.|++|..|++. +.+++|+
T Consensus 156 Lt~rE~~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 156 LTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 5555543 222 47999999999999877664 4445554
No 388
>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=58.41 E-value=5.5 Score=26.88 Aligned_cols=43 Identities=16% Similarity=0.269 Sum_probs=24.9
Q ss_pred HHHHHhhcCCcH-HHHHHHcCCChhHHH-HHHHHcCCCCChhHHHhhH
Q 041600 73 LRDLMIYFHLPI-EEAARRMKLCPTVVK-KICRRDGLHRWPHRKIKSI 118 (160)
Q Consensus 73 ~~~L~~yF~lP~-~eAA~~Lgv~~T~LK-r~CR~~GI~RWPyRkikSl 118 (160)
++.|...++..- .+.|+.||||.+++- ..-++.-+ |+-.+-.+
T Consensus 3 i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~---P~~~l~~i 47 (66)
T PF07022_consen 3 IERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSI---PAEWLIKI 47 (66)
T ss_dssp HHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS-----HHHHHHH
T ss_pred HHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCC---CHHHHHHH
Confidence 345666666555 599999999999999 44444334 55555444
No 389
>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=58.41 E-value=9.8 Score=30.71 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=21.2
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|++||||.|+++...++|
T Consensus 29 ~LpsE~~La~~lgVSRtpVREAL~~L 54 (235)
T TIGR02812 29 ILPAERELSELIGVTRTTLREVLQRL 54 (235)
T ss_pred cCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 485 8899999999999998877754
No 390
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=58.24 E-value=22 Score=21.32 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=17.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
.+++.+.|+.||++.+++.+.-.
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~ 36 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLN 36 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 36778888888888888776643
No 391
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=58.02 E-value=18 Score=22.84 Aligned_cols=23 Identities=22% Similarity=0.107 Sum_probs=18.9
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.+.+..|.|..||+|..|++.-.
T Consensus 18 ~G~s~~eia~~l~is~~tV~~h~ 40 (65)
T COG2771 18 QGKSNKEIARILGISEETVKTHL 40 (65)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Confidence 46999999999999977766554
No 392
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=57.88 E-value=18 Score=29.90 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=19.8
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+++++|+|+.||||.++++++
T Consensus 225 ~~t~~eIA~~lgis~~~V~~~ 245 (258)
T PRK08215 225 GKTQMEVAEEIGISQAQVSRL 245 (258)
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 799999999999999999887
No 393
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=57.39 E-value=9.5 Score=30.58 Aligned_cols=25 Identities=20% Similarity=0.173 Sum_probs=21.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+|..+.|+.||||.|+++..-++|
T Consensus 34 ~L~e~~La~~lgVSRtpVREAL~~L 58 (221)
T PRK11414 34 RLITKNLAEQLGMSITPVREALLRL 58 (221)
T ss_pred ccCHHHHHHHHCCCchhHHHHHHHH
Confidence 6899999999999999988777655
No 394
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=57.35 E-value=52 Score=22.36 Aligned_cols=45 Identities=13% Similarity=0.187 Sum_probs=33.0
Q ss_pred hHHHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHHHHHHHhc
Q 041600 112 HRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACA 156 (160)
Q Consensus 112 yRkikSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~Em~~~c~ 156 (160)
-+.|...+..|..++--+++.++.+|..+...|...+.|+..+-.
T Consensus 31 e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~ 75 (79)
T PF05008_consen 31 ERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKK 75 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666667777777666777788999999888888888877643
No 395
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=57.12 E-value=22 Score=29.85 Aligned_cols=46 Identities=7% Similarity=0.099 Sum_probs=32.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS 126 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~ 126 (160)
.+++.+.|+.+|+|+.+|.|+.++. |++-==|.+...|.+....|.
T Consensus 21 ~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~~~L~ 67 (289)
T PRK15121 21 PLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALR 67 (289)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999987 874322444444444444443
No 396
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=57.05 E-value=15 Score=29.98 Aligned_cols=21 Identities=10% Similarity=0.021 Sum_probs=18.1
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..+..||++||||.+++-+.
T Consensus 16 ~gs~s~AA~~L~isQpavS~~ 36 (301)
T PRK14997 16 EGGFAAAGRALDEPKSKLSRR 36 (301)
T ss_pred cCCHHHHHHHhCCCHHHHHHH
Confidence 678899999999999988654
No 397
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.00 E-value=68 Score=23.88 Aligned_cols=73 Identities=12% Similarity=0.100 Sum_probs=45.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH--------------------HhhHHHHHHHHhh-hccCCcHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK--------------------IKSIQRRMSVASG-RLRSNDAEERANA 140 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk--------------------ikSl~~~i~~L~~-~~~~~~~eerar~ 140 (160)
+++.+.|+.+|++.+++.+...++-=..|=.|. +..+......+.. .+..-++++....
T Consensus 47 ~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~~~~~~~~~l~~ee~~~l 126 (144)
T PRK03573 47 QSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVINKTRAEILHGISAEEIEQL 126 (144)
T ss_pred CCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence 568999999999988888777655322222211 2223333333333 2344688888888
Q ss_pred HHHHHHHHHHHHHH
Q 041600 141 QIEIQRLQEEMAAA 154 (160)
Q Consensus 141 ~~eIerL~~Em~~~ 154 (160)
..-+.+|...+.++
T Consensus 127 ~~~l~~l~~~l~~~ 140 (144)
T PRK03573 127 ITLIAKLEKNIIEL 140 (144)
T ss_pred HHHHHHHHHHHHHh
Confidence 88888887766554
No 398
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=57.00 E-value=7 Score=25.58 Aligned_cols=16 Identities=6% Similarity=0.233 Sum_probs=7.5
Q ss_pred HHHHcCCChhHHHHHH
Q 041600 87 AARRMKLCPTVVKKIC 102 (160)
Q Consensus 87 AA~~Lgv~~T~LKr~C 102 (160)
.++.||+|...+|.+.
T Consensus 9 ~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 9 RLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHTT--HHHHHHHH
T ss_pred HHHHcCCCHHHHHHHH
Confidence 3455555555555554
No 399
>PF13730 HTH_36: Helix-turn-helix domain
Probab=56.98 E-value=13 Score=23.49 Aligned_cols=23 Identities=13% Similarity=0.189 Sum_probs=19.0
Q ss_pred cHHHHHHHcCCChhHHHHHHHHc
Q 041600 83 PIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+...|+.+|+|..|+.|...+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 58889999999999988876554
No 400
>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=56.74 E-value=11 Score=33.19 Aligned_cols=26 Identities=8% Similarity=0.144 Sum_probs=23.2
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
+++.|+|+.+||+.++|+...++..+
T Consensus 34 ~~i~eva~~~gv~~~tlr~~e~~~~~ 59 (387)
T TIGR03453 34 FTSGEVAKLLGVSDSYLRQLSLEGKG 59 (387)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 79999999999999999998877653
No 401
>PRK13501 transcriptional activator RhaR; Provisional
Probab=56.33 E-value=16 Score=30.23 Aligned_cols=33 Identities=12% Similarity=0.277 Sum_probs=27.4
Q ss_pred HHHHHhhcC--CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 73 LRDLMIYFH--LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 73 ~~~L~~yF~--lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++-|..+|+ +++++.|+.+|+|++.|.|++++.
T Consensus 182 ~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~ 216 (290)
T PRK13501 182 MSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQ 216 (290)
T ss_pred HHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 455566664 679999999999999999999865
No 402
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=56.22 E-value=8.4 Score=29.87 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=25.8
Q ss_pred cCCcHHHHHHHcCCChhHHHHH---HHHcCCCCChhHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKI---CRRDGLHRWPHRKI 115 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~---CR~~GI~RWPyRki 115 (160)
+.++.++.|..||+++.++-|+ .++-||-+|..++|
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i 205 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTI 205 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEE
Confidence 3578899999999998877664 34556666665544
No 403
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=56.03 E-value=16 Score=29.83 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=17.7
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+-.+..||++||||.+++-+.
T Consensus 16 ~gs~t~AA~~L~iSQ~avS~~ 36 (294)
T PRK13348 16 TGSFERAARRLHVTPSAVSQR 36 (294)
T ss_pred cCCHHHHHHHhCCCchHHHHH
Confidence 578899999999998887554
No 404
>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=56.03 E-value=16 Score=26.13 Aligned_cols=36 Identities=14% Similarity=0.147 Sum_probs=31.5
Q ss_pred CCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 70 KLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 70 ~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+.+.+|+...+---++.|++||++.+.+.++-.++
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~~ 39 (84)
T cd08804 4 EERLAVIADHLGFSWTELARELDFTEEQIHQIRIEN 39 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHC
Confidence 466888999999999999999999999999987664
No 405
>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=55.92 E-value=13 Score=25.60 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=17.7
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+..+.+.|..++||.|+++|..
T Consensus 30 ~~s~~~la~~~~iS~sti~~~i 51 (87)
T PF05043_consen 30 YVSIEDLAEELFISRSTIYRDI 51 (87)
T ss_dssp EEEHHHHHHHHT--HHHHHHHH
T ss_pred CcCHHHHHHHHCCCHHHHHHHH
Confidence 5789999999999999998774
No 406
>TIGR01453 grpIintron_endo group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.
Probab=55.88 E-value=9.9 Score=31.34 Aligned_cols=25 Identities=24% Similarity=0.306 Sum_probs=21.8
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
-.+.|||+.||++.+++++.|+.-.
T Consensus 180 ~S~~eAa~~l~i~~~tI~~~l~~~~ 204 (214)
T TIGR01453 180 DSIAEAARHLGISRGTISKYIKSGK 204 (214)
T ss_pred cCHHHHHHHhCCCHHHHHHHHcccc
Confidence 6899999999999999999887544
No 407
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=55.69 E-value=14 Score=34.76 Aligned_cols=25 Identities=16% Similarity=0.089 Sum_probs=20.6
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
.-.+-...+||+.||||.|||-|.-
T Consensus 500 ~~~~Gn~~~aA~~LGIsRtTL~Rkl 524 (526)
T TIGR02329 500 ERFGGDRDAAAKALGISRTTLWRRL 524 (526)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3446789999999999999997654
No 408
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=55.57 E-value=23 Score=32.69 Aligned_cols=21 Identities=24% Similarity=0.376 Sum_probs=19.8
Q ss_pred CcHHHHHHHcCCChhHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~C 102 (160)
++++|+|+.||||..++|.+=
T Consensus 371 ~Tl~EIA~~LGvS~erVRqie 391 (415)
T PRK07598 371 YSLAEIGRALDLSRERVRQIE 391 (415)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 899999999999999999884
No 409
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=55.40 E-value=13 Score=30.22 Aligned_cols=38 Identities=34% Similarity=0.341 Sum_probs=27.3
Q ss_pred CCCHHHHH--h--hcCCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 041600 70 KLTLRDLM--I--YFHLPIEEAARRMKLCPTVVKK----ICRRDGL 107 (160)
Q Consensus 70 ~lt~~~L~--~--yF~lP~~eAA~~Lgv~~T~LKr----~CR~~GI 107 (160)
.+|-.++. + --+++.+|+|++|++|..|+|. +-+++|+
T Consensus 148 ~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 148 LLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 45555543 2 2379999999999999888874 5556666
No 410
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=55.34 E-value=12 Score=30.71 Aligned_cols=25 Identities=12% Similarity=0.219 Sum_probs=20.8
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|+.||||.|++...-++|
T Consensus 25 ~LpsE~eLae~~gVSRtpVREAL~~L 50 (253)
T PRK10421 25 KLPAERQLAMQLGVSRNSLREALAKL 50 (253)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 486 8899999999999988776654
No 411
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.18 E-value=22 Score=24.14 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=17.3
Q ss_pred CcHHHHHHHcCCChhHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~ 101 (160)
++..|+|+.|||+.+++.|.
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~ 42 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHH
Confidence 88999999999998887766
No 412
>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=55.07 E-value=19 Score=29.83 Aligned_cols=35 Identities=20% Similarity=0.364 Sum_probs=26.9
Q ss_pred ccCCCCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 67 RTGKLTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 67 r~~~lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+-..+++++|+-+. +-.+..||++||||.++|-+.
T Consensus 4 ~~~~~~l~~L~~F~~va~~gs~s~AA~~L~isQpavS~~ 42 (302)
T TIGR02036 4 RLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHR 42 (302)
T ss_pred cccCcCHHHHHHHHHHHHhCCHHHHHHHHCCCHHHHHHH
Confidence 45667887776444 578899999999999998654
No 413
>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=55.06 E-value=9.8 Score=28.05 Aligned_cols=22 Identities=18% Similarity=0.258 Sum_probs=15.8
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
..++.+||+.+|||.||+-+=.
T Consensus 19 ~aTVR~~Ak~FGvSKSTVHkDv 40 (82)
T PF12116_consen 19 KATVRQAAKVFGVSKSTVHKDV 40 (82)
T ss_dssp ---HHHHHHHHTS-HHHHHHHH
T ss_pred ccHHHHHHHHHCCcHHHHHHHH
Confidence 5788999999999999987654
No 414
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=54.98 E-value=7.2 Score=27.94 Aligned_cols=33 Identities=27% Similarity=0.376 Sum_probs=28.3
Q ss_pred chHHHHHHHHHHHHHHhhCCceeecCchhHHHH
Q 041600 5 SIENVKEYLVQYCEERKQAGFMMLPDPLSDFYE 37 (160)
Q Consensus 5 s~~~vk~~L~~y~~~r~~~g~~~~qd~~s~f~~ 37 (160)
|.||.+++|..|..+..|.=-|..-||++.||.
T Consensus 16 s~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g 48 (74)
T PF01191_consen 16 SEEEKKELLKKYNIKPEQLPKILSSDPVARYLG 48 (74)
T ss_dssp -HHHHHHHHHHTT--TTCSSEEETTSHHHHHTT
T ss_pred CHHHHHHHHHHhCCChhhCCcccccChhhhhcC
Confidence 679999999999999999999999999999984
No 415
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=54.87 E-value=18 Score=30.47 Aligned_cols=36 Identities=25% Similarity=0.372 Sum_probs=27.3
Q ss_pred hccCCCCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 66 ERTGKLTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 66 ~r~~~lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+.-..+++..|+-+. +-.+..||++|||+.+++-+.
T Consensus 24 ~~~~~m~l~~L~~f~av~e~gs~s~AA~~L~isQpavS~~ 63 (317)
T PRK11482 24 RTLRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQS 63 (317)
T ss_pred hcccccchhHHHHHHHHHHcCCHHHHHHHhCCChHHHHHH
Confidence 344567888885333 578999999999999988755
No 416
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=54.70 E-value=12 Score=30.63 Aligned_cols=25 Identities=24% Similarity=0.153 Sum_probs=21.5
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|+.||||.|+++.-.+.|
T Consensus 31 ~LpsE~eLae~~gVSRtpVREAL~~L 56 (253)
T PRK11523 31 KLPAERFIADEKNVSRTVVREAIIML 56 (253)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 587 7899999999999998877755
No 417
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=54.45 E-value=74 Score=22.44 Aligned_cols=70 Identities=14% Similarity=0.263 Sum_probs=45.2
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCC---------CChhHHHhhHHHHHHHHhhhccC--CcHHHHHHHHHHHHHHHHHH
Q 041600 83 PIEEAARRMKLCPTVVKKICRRDGLH---------RWPHRKIKSIQRRMSVASGRLRS--NDAEERANAQIEIQRLQEEM 151 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~GI~---------RWPyRkikSl~~~i~~L~~~~~~--~~~eerar~~~eIerL~~Em 151 (160)
++.|.|...||+++.|...- ++|+- .-+...+..+.+ +..|+.-++- .+.+--.....+|+.|++|+
T Consensus 2 s~~e~~~~~~i~~~~l~~lv-e~Gli~p~~~~~~~~f~~~~l~rl~~-~~rL~~Dl~in~~gi~lil~LLd~i~~L~~el 79 (84)
T PF13591_consen 2 SLEEFCEACGIEPEFLRELV-EEGLIEPEGEEEEWYFSEEDLARLRR-IRRLHRDLGINLEGIALILDLLDRIEQLRREL 79 (84)
T ss_pred CHHHHHHHHCcCHHHHHHHH-HCCCeeecCCCCeeeECHHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666677777776553 55541 234566666666 6666666642 24444667779999999998
Q ss_pred HHH
Q 041600 152 AAA 154 (160)
Q Consensus 152 ~~~ 154 (160)
..+
T Consensus 80 ~~L 82 (84)
T PF13591_consen 80 REL 82 (84)
T ss_pred HHh
Confidence 875
No 418
>PRK10130 transcriptional regulator EutR; Provisional
Probab=54.24 E-value=23 Score=31.37 Aligned_cols=44 Identities=5% Similarity=0.032 Sum_probs=31.7
Q ss_pred CcHHHHHHHcCCChhHHHHHHHH-cCCCCChhHHHhhHHHHHHHH
Q 041600 82 LPIEEAARRMKLCPTVVKKICRR-DGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~-~GI~RWPyRkikSl~~~i~~L 125 (160)
+.+.+.|+.+|||..+|.+.+++ +|++-==|-+...|++....|
T Consensus 257 ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~~ylr~~RL~~ar~lL 301 (350)
T PRK10130 257 VTVLDLCNQLHVSRRTLQNAFHAILGIGPNAWLKRIRLNAVRREL 301 (350)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999988 577432244444444444444
No 419
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=54.08 E-value=52 Score=26.10 Aligned_cols=46 Identities=11% Similarity=0.261 Sum_probs=33.6
Q ss_pred hhHHHhhHHHHHHHHhhhccC-C---cHHHHHHHHHHHHHHHHHHHHHhc
Q 041600 111 PHRKIKSIQRRMSVASGRLRS-N---DAEERANAQIEIQRLQEEMAAACA 156 (160)
Q Consensus 111 PyRkikSl~~~i~~L~~~~~~-~---~~eerar~~~eIerL~~Em~~~c~ 156 (160)
+.++.+.++++|.++++..++ . .=..=+|.+.+++++++|++++-.
T Consensus 38 ~~~~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~~~ 87 (161)
T PF04420_consen 38 SSKEQRQLRKEILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKLNK 87 (161)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367788889999998887654 1 223356778999999999987643
No 420
>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=54.05 E-value=12 Score=27.92 Aligned_cols=23 Identities=26% Similarity=0.328 Sum_probs=21.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
+.++.+||+.+|||..|+.+..+
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 57999999999999999998876
No 421
>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=53.81 E-value=39 Score=22.45 Aligned_cols=43 Identities=12% Similarity=0.145 Sum_probs=36.5
Q ss_pred hccCCCCHHHHHhhcCCcHHHHHHHc----CCChhHHHHHHHHcCCC
Q 041600 66 ERTGKLTLRDLMIYFHLPIEEAARRM----KLCPTVVKKICRRDGLH 108 (160)
Q Consensus 66 ~r~~~lt~~~L~~yF~lP~~eAA~~L----gv~~T~LKr~CR~~GI~ 108 (160)
.....+|..+|....+++...+.+-+ .++..++.++|+-+|+.
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~ 60 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTS 60 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 45577999999999999999988755 46788999999999984
No 422
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=53.73 E-value=19 Score=30.07 Aligned_cols=21 Identities=14% Similarity=0.078 Sum_probs=18.0
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+-.+..||++||||.+++-+.
T Consensus 16 ~gs~s~AA~~L~iSQpavS~~ 36 (308)
T PRK10094 16 TGSFSKAAERLCKTTATISYR 36 (308)
T ss_pred hCCHHHHHHHhcCCHHHHHHH
Confidence 578899999999999988654
No 423
>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=53.55 E-value=14 Score=27.03 Aligned_cols=21 Identities=14% Similarity=0.023 Sum_probs=17.5
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+-.+..||+.||||.+++-+.
T Consensus 16 ~gSis~AA~~L~iS~stvs~~ 36 (99)
T TIGR00637 16 MGSISQAAKDAGISYKSAWDY 36 (99)
T ss_pred hCCHHHHHHHHCCCHHHHHHH
Confidence 567899999999999987544
No 424
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=52.89 E-value=11 Score=29.85 Aligned_cols=22 Identities=14% Similarity=0.247 Sum_probs=19.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+|+|+.||+|..|+|+.-
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~ 198 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYL 198 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHH
Confidence 4799999999999999999763
No 425
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=52.69 E-value=9.8 Score=32.66 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=30.2
Q ss_pred hccCCCCHHHHHhhcC-----CcHHHHHHHcCCChhHHHHHH
Q 041600 66 ERTGKLTLRDLMIYFH-----LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 66 ~r~~~lt~~~L~~yF~-----lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+....+|+..+...|. ++..|+|+.+|+|.||.+|.-
T Consensus 153 kGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYL 194 (224)
T COG4565 153 KGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYL 194 (224)
T ss_pred CCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHH
Confidence 4556788888888776 568999999999999988763
No 426
>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=52.52 E-value=26 Score=27.63 Aligned_cols=68 Identities=18% Similarity=0.193 Sum_probs=36.7
Q ss_pred HHHHHcCCC----hhHHHHHHHHcCCCCChhHHH-------hhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHHHHHHH
Q 041600 86 EAARRMKLC----PTVVKKICRRDGLHRWPHRKI-------KSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAA 154 (160)
Q Consensus 86 eAA~~Lgv~----~T~LKr~CR~~GI~RWPyRki-------kSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~Em~~~ 154 (160)
.+|..+=|+ ++-||+.+++.+. ||-.+. ..++..|...+-.++.-. .+-..-..||..|++++..+
T Consensus 44 ~aAD~~vVsEL~~Ls~LK~~y~~~~~--~~~~~~~~l~a~~~e~qsli~~yE~~~~kLe-~e~~~Kdsei~~Lr~~L~~~ 120 (131)
T PF04859_consen 44 QAADEAVVSELRRLSELKRRYRKKQS--DPSPQVARLAAEIQEQQSLIKTYEIVVKKLE-AELRAKDSEIDRLREKLDEL 120 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCC--CCCccccccccchHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 456666676 7789999887764 454222 223333333333332111 11123347888888888776
Q ss_pred hc
Q 041600 155 CA 156 (160)
Q Consensus 155 c~ 156 (160)
-.
T Consensus 121 ~~ 122 (131)
T PF04859_consen 121 NR 122 (131)
T ss_pred HH
Confidence 43
No 427
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=52.43 E-value=21 Score=29.65 Aligned_cols=34 Identities=24% Similarity=0.297 Sum_probs=26.5
Q ss_pred cCCCCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 68 TGKLTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 68 ~~~lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
..++++.+|+-+. +-.+..||+.||||.+++-+.
T Consensus 11 ~~~~~l~~L~~f~~va~~gs~s~AA~~L~iSQpavS~~ 48 (311)
T PRK10086 11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHR 48 (311)
T ss_pred hcCCcHHHHHHHHHHHHcCCHHHHHHHHCCCHHHHHHH
Confidence 4577888876443 578899999999999888654
No 428
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=52.37 E-value=14 Score=35.40 Aligned_cols=28 Identities=25% Similarity=0.232 Sum_probs=25.6
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLH 108 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~ 108 (160)
+.-+..||+.||..+++|-++.|++||.
T Consensus 519 ~~~~a~AAr~LGl~~~~L~~~~kRlGI~ 546 (550)
T COG3604 519 NGNWAGAARRLGLTRRTLLYRMKRLGIK 546 (550)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 5678889999999999999999999994
No 429
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=52.30 E-value=19 Score=30.70 Aligned_cols=42 Identities=21% Similarity=0.155 Sum_probs=29.8
Q ss_pred hccCCCCHHHHH----hhcCCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 041600 66 ERTGKLTLRDLM----IYFHLPIEEAARRMKLCPTVVK----KICRRDGL 107 (160)
Q Consensus 66 ~r~~~lt~~~L~----~yF~lP~~eAA~~Lgv~~T~LK----r~CR~~GI 107 (160)
+....+|-.++. -.-+++.+|+|++|++|+.|+| ++.+++|+
T Consensus 139 ~~~~~LS~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 139 EAKNKVTKYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hccCCCCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344556666544 2237999999999999987766 46666666
No 430
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=51.78 E-value=36 Score=26.55 Aligned_cols=46 Identities=24% Similarity=0.325 Sum_probs=30.1
Q ss_pred CCHHHHHhhcCCcHHHHHHHcC--CChhHHHHHHHHcCCCCChhHHHhhH
Q 041600 71 LTLRDLMIYFHLPIEEAARRMK--LCPTVVKKICRRDGLHRWPHRKIKSI 118 (160)
Q Consensus 71 lt~~~L~~yF~lP~~eAA~~Lg--v~~T~LKr~CR~~GI~RWPyRkikSl 118 (160)
+.|.-|+..|.|.+.|||..++ |+..+-++- +.|=.-=|..=+..+
T Consensus 4 ~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~W--E~G~~~IP~~Vie~l 51 (118)
T PF08965_consen 4 LELQALRQILGLTVEEAAYYIAQDVSSRTWQQW--EKGERPIPDDVIEEL 51 (118)
T ss_dssp HHHHHHHHHTT--HHHHHHHTSSS--HHHHHHH--HTTSS---HHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHH--HcCCCCCCHHHHHHH
Confidence 4578899999999999999999 988888876 677555565544333
No 431
>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=51.57 E-value=15 Score=26.62 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=20.5
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
|.+.|+|+.+||++.+|+-.-+ .|+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~-~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR-EGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5789999999999999997654 443
No 432
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=51.52 E-value=21 Score=29.55 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=19.5
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+++++++|+.||||..++.++
T Consensus 222 ~~t~~eIA~~lgis~~~V~~~ 242 (254)
T TIGR02850 222 GKTQMEVAEEIGISQAQVSRL 242 (254)
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 689999999999999999877
No 433
>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=51.50 E-value=26 Score=27.92 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=22.1
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICR 103 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR 103 (160)
..+++..+++|+.||+|.+++++.-+
T Consensus 117 ~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 117 EKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred HHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34789999999999999999988744
No 434
>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=51.44 E-value=24 Score=25.64 Aligned_cols=33 Identities=18% Similarity=0.141 Sum_probs=25.0
Q ss_pred CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
.+.+++.-.++. +.|+..||+.++|-++-+..+
T Consensus 36 ~l~~~r~~~glS--qLAe~~GIs~stLs~iE~g~~ 68 (89)
T TIGR02684 36 ALGYIARARGMT--QLARKTGLSRESLYKALSGKG 68 (89)
T ss_pred HHHHHHHHCChH--HHHHHHCCCHHHHHHHHcCCC
Confidence 366777777776 499999999999888865443
No 435
>PRK09954 putative kinase; Provisional
Probab=51.25 E-value=21 Score=30.74 Aligned_cols=32 Identities=13% Similarity=-0.085 Sum_probs=24.9
Q ss_pred HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+.|++.=.++..+.|+.||||.++++++-++|
T Consensus 10 ~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L 41 (362)
T PRK09954 10 AILRRNPLIQQNEIADILQISRSRVAAHIMDL 41 (362)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44455446999999999999999998876543
No 436
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=51.24 E-value=40 Score=25.15 Aligned_cols=27 Identities=41% Similarity=0.576 Sum_probs=22.7
Q ss_pred ccchHHHHHHHHHHHHHHhhCCceeec
Q 041600 3 KKSIENVKEYLVQYCEERKQAGFMMLP 29 (160)
Q Consensus 3 ~ks~~~vk~~L~~y~~~r~~~g~~~~q 29 (160)
.++..+|+.||.+|-.-+..+|--+.+
T Consensus 8 ~kT~~~v~~~L~~y~~~~~~~~~~~~~ 34 (132)
T TIGR01637 8 KKTRANVKRFLEDYRRLRRIAGRSLTP 34 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCcccC
Confidence 478899999999999999888876444
No 437
>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=51.20 E-value=15 Score=27.22 Aligned_cols=24 Identities=25% Similarity=0.238 Sum_probs=20.0
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHc
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++..|.|+.+|++.+++.++.+.+
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L 49 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQL 49 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHH
Confidence 688889999999999988887644
No 438
>PHA01976 helix-turn-helix protein
Probab=51.12 E-value=39 Score=21.90 Aligned_cols=43 Identities=5% Similarity=-0.100 Sum_probs=34.4
Q ss_pred hccCCCCHHHHHhhcCCcHHHHHHHc-C---CChhHHHHHHHHcCCC
Q 041600 66 ERTGKLTLRDLMIYFHLPIEEAARRM-K---LCPTVVKKICRRDGLH 108 (160)
Q Consensus 66 ~r~~~lt~~~L~~yF~lP~~eAA~~L-g---v~~T~LKr~CR~~GI~ 108 (160)
.....+|.++|....+++...+.+-. | .+..+|.++|+-+||+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~ 57 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVT 57 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcC
Confidence 44567999999999999999888733 3 3567899999999983
No 439
>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=50.77 E-value=16 Score=25.67 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=20.7
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
+.|++.|||.=.||+...|+++.+.+.
T Consensus 12 ~~LTi~EAa~Y~gIG~~klr~l~~~~~ 38 (67)
T PF09035_consen 12 YTLTIEEAAEYFGIGEKKLRELAEENP 38 (67)
T ss_dssp SEEEHHHHHHHT-S-HHHHHHHHHH-T
T ss_pred hccCHHHHHHHhCccHHHHHHHHHhCC
Confidence 458999999999999999999995543
No 440
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=50.54 E-value=22 Score=25.87 Aligned_cols=22 Identities=9% Similarity=0.095 Sum_probs=18.5
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++.+++|+.|++|..|++..-
T Consensus 164 g~~~~~Ia~~l~~s~~tv~~~~ 185 (211)
T PRK15369 164 GYTNRDIAEQLSISIKTVETHR 185 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHH
Confidence 5789999999999988877653
No 441
>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=50.47 E-value=28 Score=24.44 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=31.5
Q ss_pred CCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 69 GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 69 ~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.++.+..|+...+.--++.|++||++.+.+..+-..+
T Consensus 3 ~~~~l~~ia~~lG~dW~~LAr~Lg~~~~dI~~i~~~~ 39 (84)
T cd08317 3 ADIRLADISNLLGSDWPQLARELGVSETDIDLIKAEN 39 (84)
T ss_pred ccchHHHHHHHHhhHHHHHHHHcCCCHHHHHHHHHHC
Confidence 4567888898889899999999999999999887655
No 442
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=50.33 E-value=23 Score=29.32 Aligned_cols=21 Identities=10% Similarity=0.154 Sum_probs=18.1
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..+..||++|||+.+++-+.
T Consensus 15 ~~S~s~AA~~L~isQ~avS~~ 35 (305)
T PRK11233 15 IGSLTQAAEVLHIAQPALSQQ 35 (305)
T ss_pred cCCHHHHHHHhCCCchHHHHH
Confidence 578899999999999988655
No 443
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=50.25 E-value=32 Score=28.31 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=20.4
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-+++..|+|+.||||..+++++-
T Consensus 220 ~g~s~~eIA~~lgis~~~V~~~~ 242 (255)
T TIGR02941 220 ENLSQKETGERLGISQMHVSRLQ 242 (255)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHH
Confidence 36999999999999999998773
No 444
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=50.08 E-value=13 Score=26.15 Aligned_cols=24 Identities=13% Similarity=0.151 Sum_probs=17.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHH
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.|-++++.+.|+++||+.+++-+.
T Consensus 29 G~~~~t~~~Ia~~agvs~~~~Y~~ 52 (201)
T COG1309 29 GYAATTVDEIAKAAGVSKGTLYRH 52 (201)
T ss_pred CcCCCCHHHHHHHhCCCcchhHHH
Confidence 555677888888888887777554
No 445
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=49.92 E-value=41 Score=29.92 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=26.0
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRD-GLH 108 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~ 108 (160)
-.+++.+.|+.+|+|++.|.|++++. |++
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 35899999999999999999999885 875
No 446
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=49.84 E-value=42 Score=27.43 Aligned_cols=78 Identities=17% Similarity=0.077 Sum_probs=43.4
Q ss_pred hCCceeecCchhHHHHHh---hcccccCCCCCCC---CCCCCCCCchhhhhccCCCCHHHHH----hhcCCcHHHHHHHc
Q 041600 22 QAGFMMLPDPLSDFYEAV---CVGLVLDDNLTTD---DYSQPPMTNSVQRERTGKLTLRDLM----IYFHLPIEEAARRM 91 (160)
Q Consensus 22 ~~g~~~~qd~~s~f~~al---c~~~~~~~~~~~d---~~~~ps~s~s~~r~r~~~lt~~~L~----~yF~lP~~eAA~~L 91 (160)
..||+.-.++...+-+|+ .-|-.|.+..-.. ....+..... .....||-.+.+ -+-+++.+|+|+.|
T Consensus 104 a~G~l~K~~~~~~L~~aI~~v~~G~~~~~~~~~~~l~~~~~~~~~~~---~~~~~Lt~rE~~Vl~l~~~G~s~~eIA~~L 180 (216)
T PRK10100 104 INGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITHSGNYRYNS---TESALLTHREKEILNKLRIGASNNEIARSL 180 (216)
T ss_pred CeEEEECCCCHHHHHHHHHHHHcCCcccCHHHHHHHHHhhcccccCC---CccCCCCHHHHHHHHHHHcCCCHHHHHHHh
Confidence 347888888888877765 3455554321000 0000000000 001236655554 23389999999999
Q ss_pred CCChhHHHHHH
Q 041600 92 KLCPTVVKKIC 102 (160)
Q Consensus 92 gv~~T~LKr~C 102 (160)
++|..|+|..-
T Consensus 181 ~iS~~TVk~~~ 191 (216)
T PRK10100 181 FISENTVKTHL 191 (216)
T ss_pred CCCHHHHHHHH
Confidence 99988877653
No 447
>PRK13558 bacterio-opsin activator; Provisional
Probab=49.60 E-value=16 Score=33.74 Aligned_cols=27 Identities=30% Similarity=0.384 Sum_probs=23.0
Q ss_pred hhcCCc----HHHHHHHcCCChhHHHHHHHH
Q 041600 78 IYFHLP----IEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 78 ~yF~lP----~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.||..| ..|.|.+||||.+|+-..-|+
T Consensus 623 gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~ 653 (665)
T PRK13558 623 GYFEWPRRVEGEELAESMGISRSTFHQHLRA 653 (665)
T ss_pred CCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 889765 789999999999999877554
No 448
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=49.42 E-value=27 Score=29.42 Aligned_cols=22 Identities=14% Similarity=0.262 Sum_probs=20.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
+++++|+|+.||||.++++++-
T Consensus 231 ~~t~~EIA~~lgis~~~V~~~~ 252 (264)
T PRK07122 231 SMTQTQIAERVGISQMHVSRLL 252 (264)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 7999999999999999999873
No 449
>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=49.37 E-value=18 Score=27.46 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=23.9
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
.|=.+++..+|+-||++...|.+.|.+.|
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 56689999999999999999999999885
No 450
>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=49.30 E-value=23 Score=23.49 Aligned_cols=30 Identities=13% Similarity=0.009 Sum_probs=22.6
Q ss_pred CcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600 82 LPIEEAARRMKLCPTVVKKICRRDGLHRWP 111 (160)
Q Consensus 82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP 111 (160)
++..+.|..||||.+++.+.-+++-=..||
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 568999999999999988876655333444
No 451
>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=49.22 E-value=26 Score=25.18 Aligned_cols=27 Identities=15% Similarity=-0.048 Sum_probs=22.0
Q ss_pred hcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 79 YFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
...+++.|.|+.+|++.+++-|...++
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 346889999999999999988876544
No 452
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=49.20 E-value=23 Score=29.15 Aligned_cols=21 Identities=19% Similarity=0.237 Sum_probs=17.8
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..+..||+.|||+.+++-+.
T Consensus 16 ~~s~s~AA~~L~isQpavS~~ 36 (300)
T PRK11074 16 TGSFSAAAQELHRVPSAVSYT 36 (300)
T ss_pred hCCHHHHHHHhCCCHHHHHHH
Confidence 568899999999999988654
No 453
>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=49.17 E-value=22 Score=23.47 Aligned_cols=24 Identities=17% Similarity=0.224 Sum_probs=19.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.+...|+|+.+|++.+++-+.-++
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 578899999999998888776544
No 454
>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=48.93 E-value=20 Score=24.11 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=15.3
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.+++.+.|++||+++.+|.-.
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHH
Confidence 478888888889888888765
No 455
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=48.89 E-value=6.2 Score=33.90 Aligned_cols=52 Identities=12% Similarity=0.105 Sum_probs=33.3
Q ss_pred CCChhHHHh--hHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHHHHHHHhcccC
Q 041600 108 HRWPHRKIK--SIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGLT 159 (160)
Q Consensus 108 ~RWPyRkik--Sl~~~i~~L~~~~~~~~~eerar~~~eIerL~~Em~~~c~~~~ 159 (160)
.|||||+=. .+....++.--.+..-++.+......-++.|.+.+.+++||.+
T Consensus 167 r~~~~Rds~rT~vt~~Tk~~l~I~e~vp~~~~~~l~~a~~~l~~~l~~~~gG~~ 220 (229)
T COG3382 167 RRWNWRDSVRTMVTESTKNVLLIAEGVPGVEVEDLVEALDSLADLLEKLLGGTR 220 (229)
T ss_pred eecccccceeeehhhccceEEEEEecCCCccHHHHHHHHHHHHHHHHHhcCCcc
Confidence 579999522 2222222222222333555566888899999999999999975
No 456
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=48.74 E-value=29 Score=27.99 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=19.7
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+++++|+|+.||||+.++.++
T Consensus 199 ~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 199 DKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 789999999999999999877
No 457
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=48.65 E-value=17 Score=29.07 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=22.7
Q ss_pred cCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 80 FHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-+++.+++|+.||+|.+|+|+.-+.+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 36899999999999999999887644
No 458
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=48.46 E-value=40 Score=29.92 Aligned_cols=28 Identities=18% Similarity=0.267 Sum_probs=23.0
Q ss_pred HHHhhcC------CcHHHHHHHcCCChhHHHHHH
Q 041600 75 DLMIYFH------LPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 75 ~L~~yF~------lP~~eAA~~Lgv~~T~LKr~C 102 (160)
-|.-+|+ ++++|+|+.||||...++++-
T Consensus 313 Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~ 346 (367)
T PRK09210 313 VLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIE 346 (367)
T ss_pred HHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHH
Confidence 3455664 799999999999999998884
No 459
>PRK06746 peptide chain release factor 2; Provisional
Probab=48.39 E-value=53 Score=29.57 Aligned_cols=43 Identities=16% Similarity=0.291 Sum_probs=35.5
Q ss_pred hHHHhhHHHHHHHHhhhcc-CCcHHHHHHHHHHHHHHHHHHHHH
Q 041600 112 HRKIKSIQRRMSVASGRLR-SNDAEERANAQIEIQRLQEEMAAA 154 (160)
Q Consensus 112 yRkikSl~~~i~~L~~~~~-~~~~eerar~~~eIerL~~Em~~~ 154 (160)
|++++.....+..+.+++. ..|++.+.-+..+++.|++++..+
T Consensus 30 ~~~~~~~~~d~~~~~el~~~~~d~e~~~~a~~e~~~l~~~l~~l 73 (326)
T PRK06746 30 FRQLDETFENLEITHELLKEEYDEDLHEELESEVKGLIQEMNEY 73 (326)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 7788888888888888874 358888989999999999988765
No 460
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=48.30 E-value=29 Score=28.41 Aligned_cols=32 Identities=13% Similarity=0.317 Sum_probs=23.7
Q ss_pred CCCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 70 KLTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 70 ~lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.+++..|+-+. +-.+..||++||||.+++-+.
T Consensus 4 ~~~l~~L~~f~~v~~~gs~s~AA~~L~isQ~avS~~ 39 (302)
T PRK09791 4 QVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKS 39 (302)
T ss_pred cccHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHH
Confidence 45666665322 468899999999999998755
No 461
>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=48.14 E-value=29 Score=25.13 Aligned_cols=37 Identities=14% Similarity=0.182 Sum_probs=32.2
Q ss_pred CCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 69 GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 69 ~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.++.+.+|+...+.-=.+.|++||||.+-+-++.-++
T Consensus 3 ~~~~l~~Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~ 39 (84)
T cd08805 3 VEMKMAVIREHLGLSWAELARELQFSVEDINRIRVEN 39 (84)
T ss_pred hhhHHHHHHHHhcchHHHHHHHcCCCHHHHHHHHHhC
Confidence 3677899999999999999999999999999886554
No 462
>PRK03837 transcriptional regulator NanR; Provisional
Probab=47.94 E-value=19 Score=28.97 Aligned_cols=25 Identities=12% Similarity=0.038 Sum_probs=21.4
Q ss_pred CC-cHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HL-PIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~l-P~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-+ +..+.|+.||||.|+++..-+.|
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L 61 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQAL 61 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47 48999999999999999887765
No 463
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=47.67 E-value=19 Score=29.43 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=20.6
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|+.||||.|+++..-++|
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 474 8999999999999988776654
No 464
>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=47.62 E-value=13 Score=22.51 Aligned_cols=17 Identities=24% Similarity=0.303 Sum_probs=12.8
Q ss_pred CChhHHHHHHHHcCCCC
Q 041600 93 LCPTVVKKICRRDGLHR 109 (160)
Q Consensus 93 v~~T~LKr~CR~~GI~R 109 (160)
+.+..||.+|+++|++-
T Consensus 4 l~v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 4 LTVAELKEELKERGLST 20 (35)
T ss_dssp SHHHHHHHHHHHTTS-S
T ss_pred CcHHHHHHHHHHCCCCC
Confidence 44677999999999854
No 465
>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=47.54 E-value=32 Score=22.38 Aligned_cols=23 Identities=13% Similarity=0.134 Sum_probs=17.8
Q ss_pred cCCcHHHHHHHcCCChhHHHHHH
Q 041600 80 FHLPIEEAARRMKLCPTVVKKIC 102 (160)
Q Consensus 80 F~lP~~eAA~~Lgv~~T~LKr~C 102 (160)
=.++..++|+.||++.+++.+--
T Consensus 23 ~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 23 GPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp STBEHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Confidence 46889999999999998887653
No 466
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=47.37 E-value=24 Score=30.21 Aligned_cols=26 Identities=8% Similarity=-0.001 Sum_probs=22.1
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDG 106 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G 106 (160)
.++..+.|++||||.+++.+..+++-
T Consensus 18 ~~s~~~LA~~lgvsr~tV~~~l~~L~ 43 (319)
T PRK11886 18 FHSGEQLGEELGISRAAIWKHIQTLE 43 (319)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 47888999999999999988877654
No 467
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=47.37 E-value=27 Score=29.18 Aligned_cols=35 Identities=11% Similarity=0.093 Sum_probs=27.3
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL 107 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI 107 (160)
++.|.+.=.+...|.|+.||||..|++|-..++..
T Consensus 10 l~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 10 VDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34444545689999999999999999999887643
No 468
>PRK13698 plasmid-partitioning protein; Provisional
Probab=47.28 E-value=30 Score=31.06 Aligned_cols=34 Identities=15% Similarity=0.148 Sum_probs=28.7
Q ss_pred HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600 76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR 109 (160)
Q Consensus 76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R 109 (160)
|...|++.+++.|+.||+|.+++-+.-|-+.++.
T Consensus 171 L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP~ 204 (323)
T PRK13698 171 LQNEFAGNISALADAENISRKIITRCINTAKLPK 204 (323)
T ss_pred HHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcCCH
Confidence 4456789999999999999999999888777643
No 469
>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=47.03 E-value=28 Score=25.08 Aligned_cols=33 Identities=30% Similarity=0.320 Sum_probs=22.6
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++-|...=.+.-.+.|+.+|+.+..++++|..|
T Consensus 19 l~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L 51 (105)
T PF02002_consen 19 LDALLRKGELTDEDLAKKLGLKPKEVRKILYKL 51 (105)
T ss_dssp HHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHH
T ss_pred HHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 444554556889999999999999999999765
No 470
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=47.02 E-value=45 Score=30.08 Aligned_cols=43 Identities=14% Similarity=0.264 Sum_probs=34.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA 125 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L 125 (160)
++++.|+|+.||.+++|+-|--|++-... =|+-..+..+ +..+
T Consensus 23 ~~S~reIA~~LgRh~sTIsRElkRn~~~~-~Y~a~~A~~~-~~~~ 65 (318)
T COG2826 23 KMSIREIAKQLNRHHSTISRELKRNRTRD-IYSAVKAQER-YRML 65 (318)
T ss_pred CCCHHHHHHHhCCCcchhhHHHhcCCccc-eeeHHHHHHH-HHHh
Confidence 79999999999999999999999888776 4666666655 4444
No 471
>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=46.81 E-value=6.5 Score=31.62 Aligned_cols=25 Identities=16% Similarity=0.340 Sum_probs=0.0
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|.++++|..||+++||+-|.++--
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~~K 73 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVKNK 73 (160)
T ss_dssp -------------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHcCc
Confidence 3789999999999999999988743
No 472
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=46.49 E-value=39 Score=23.42 Aligned_cols=42 Identities=12% Similarity=0.053 Sum_probs=31.4
Q ss_pred hccCCCCHHHHHhhcCCcHHHHHHHc-----CCChhHHHHHHHHcCC
Q 041600 66 ERTGKLTLRDLMIYFHLPIEEAARRM-----KLCPTVVKKICRRDGL 107 (160)
Q Consensus 66 ~r~~~lt~~~L~~yF~lP~~eAA~~L-----gv~~T~LKr~CR~~GI 107 (160)
-+...+|-.++...+++++..+++-+ ++|..+|-+.+..+|.
T Consensus 27 ~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~ 73 (80)
T PF13744_consen 27 REERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGG 73 (80)
T ss_dssp HHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTE
T ss_pred HHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCC
Confidence 44577999999999999999999887 6778888888888874
No 473
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=45.96 E-value=18 Score=32.53 Aligned_cols=24 Identities=29% Similarity=0.405 Sum_probs=21.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRR 104 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~ 104 (160)
.+++.|||+.|||+.++|++.+++
T Consensus 48 ~ft~~e~A~~lgvs~~tlr~~~~~ 71 (405)
T PRK13869 48 KFTSGEAARLMKISDSTLRKMTLA 71 (405)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHc
Confidence 358999999999999999999886
No 474
>PF14335 DUF4391: Domain of unknown function (DUF4391)
Probab=45.93 E-value=30 Score=28.50 Aligned_cols=40 Identities=10% Similarity=0.400 Sum_probs=33.4
Q ss_pred hHHHhhHHHHHHHHhhhccC-CcHHHHHHHHHHHHHHHHHH
Q 041600 112 HRKIKSIQRRMSVASGRLRS-NDAEERANAQIEIQRLQEEM 151 (160)
Q Consensus 112 yRkikSl~~~i~~L~~~~~~-~~~eerar~~~eIerL~~Em 151 (160)
.+++..|.+.|+.|+..+.. ....++...-.+|.++++|+
T Consensus 181 ~~~i~~L~kei~~L~~~~~kEkq~nrkveln~elk~l~~eL 221 (221)
T PF14335_consen 181 LEQIEKLEKEIAKLKKKIKKEKQFNRKVELNTELKKLKKEL 221 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHhcC
Confidence 46888999999999988864 46778888899999999885
No 475
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=45.82 E-value=11 Score=24.71 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=11.5
Q ss_pred HHHHHhhcCCcH---HHHHHHcC
Q 041600 73 LRDLMIYFHLPI---EEAARRMK 92 (160)
Q Consensus 73 ~~~L~~yF~lP~---~eAA~~Lg 92 (160)
+.-|+++|++|- .+++++.+
T Consensus 6 i~~L~~~fslp~~~Y~DIsr~e~ 28 (44)
T PF10945_consen 6 IAALSQAFSLPDINYIDISREER 28 (44)
T ss_pred HHHHHHHhCCCCccHHHHHHHHH
Confidence 455677777663 45555444
No 476
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=45.69 E-value=28 Score=27.99 Aligned_cols=21 Identities=14% Similarity=0.110 Sum_probs=17.9
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..+..||++||||.+++-+.
T Consensus 17 ~~s~t~AA~~L~isqpavS~~ 37 (290)
T PRK10837 17 SGSTTQASVMLALSQSAVSAA 37 (290)
T ss_pred cCCHHHHHHHhCCCccHHHHH
Confidence 678999999999998887654
No 477
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=45.66 E-value=21 Score=29.09 Aligned_cols=25 Identities=8% Similarity=0.126 Sum_probs=21.3
Q ss_pred CCc-HHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLP-IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP-~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
-|| ..+.|+.||||.|++...-++|
T Consensus 30 ~LPsE~eLa~~~gVSRtpVREAL~~L 55 (251)
T PRK09990 30 ALPSERRLCEKLGFSRSALREGLTVL 55 (251)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 584 8899999999999998877755
No 478
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=45.63 E-value=33 Score=28.22 Aligned_cols=31 Identities=16% Similarity=0.302 Sum_probs=22.9
Q ss_pred CCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 71 LTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 71 lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+++++|+-+. +..+..||++|||+.+++-+.
T Consensus 4 m~l~~L~~F~~v~e~gs~s~AA~~L~isqpavS~~ 38 (296)
T PRK11062 4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQ 38 (296)
T ss_pred cCHHHHHHHHHHHhcCCHHHHHHHhCCChHHHHHH
Confidence 4555554332 678899999999999988654
No 479
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=45.62 E-value=32 Score=28.59 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=25.1
Q ss_pred CCCCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 69 GKLTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 69 ~~lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
..+++.+|+-+. +-.+..||+.|||+.+++-+.
T Consensus 20 ~~~~l~~L~~f~avae~gs~s~AA~~L~isQpavS~~ 56 (314)
T PRK09508 20 RMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNA 56 (314)
T ss_pred cccChHHHHHHHHHHhcCCHHHHHHHhCCCHHHHHHH
Confidence 357788875333 578899999999998887655
No 480
>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=45.45 E-value=21 Score=25.51 Aligned_cols=25 Identities=16% Similarity=0.208 Sum_probs=20.4
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++++.++|+.||++...++..|..|
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHH
Confidence 6899999999999988888887654
No 481
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=45.33 E-value=15 Score=28.20 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=18.2
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.+|+.|+|..||||.+++-|=
T Consensus 60 e~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 60 ELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred cccHHHHHHHhCcchhhhccc
Confidence 599999999999998887653
No 482
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=45.33 E-value=31 Score=28.49 Aligned_cols=21 Identities=29% Similarity=0.354 Sum_probs=17.7
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..+..||++||||.+++-+.
T Consensus 16 ~~s~s~AA~~L~isq~avSr~ 36 (309)
T PRK12682 16 NLNLTEAAKALHTSQPGVSKA 36 (309)
T ss_pred cCCHHHHHHHhcCccHHHHHH
Confidence 358999999999998887654
No 483
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=45.16 E-value=29 Score=29.02 Aligned_cols=33 Identities=15% Similarity=0.235 Sum_probs=27.1
Q ss_pred HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
++.|...=.+++.|.|+.||||..|+.|--+++
T Consensus 11 l~~l~~~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 11 LELLAQLGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 455566667999999999999999998887765
No 484
>KOG0723 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=45.13 E-value=18 Score=28.06 Aligned_cols=31 Identities=26% Similarity=0.365 Sum_probs=24.9
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhh
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKS 117 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikS 117 (160)
-|.-.||+..|||++|+-|.--|+. |||+--
T Consensus 52 kMsr~EA~lIL~v~~s~~k~Kikea------HrriM~ 82 (112)
T KOG0723|consen 52 KMSRREAALILGVTPSLDKDKIKEA------HRRIML 82 (112)
T ss_pred ccchHHHHHHhCCCccccHHHHHHH------HHHHHH
Confidence 4788999999999999888776665 676643
No 485
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=44.99 E-value=22 Score=25.55 Aligned_cols=60 Identities=17% Similarity=0.217 Sum_probs=33.1
Q ss_pred hcccccCCCCCCCCCCCCCCCch------hhhhccCCCCHHHHHhh--------cCCcHHHHHHHcCCChhHHH
Q 041600 40 CVGLVLDDNLTTDDYSQPPMTNS------VQRERTGKLTLRDLMIY--------FHLPIEEAARRMKLCPTVVK 99 (160)
Q Consensus 40 c~~~~~~~~~~~d~~~~ps~s~s------~~r~r~~~lt~~~L~~y--------F~lP~~eAA~~Lgv~~T~LK 99 (160)
|-||+.+.+....+--+.|.|.. ..=+-+.++|++++... ..++..+|...+..-.++||
T Consensus 5 SCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~~~t~eemie~~~~~~~~~~~~~~~~a~~~~~~~lp~Lk 78 (81)
T PF12674_consen 5 SCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQDITMEEMIEFCVPFMDEFNGMTPEEARKMMPRYLPTLK 78 (81)
T ss_pred cCcCccCCccccccccCCCCchhHHHHHhcCCceeecCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCc
Confidence 35777777664444444444322 22234448899988733 33566666666555555555
No 486
>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=44.97 E-value=15 Score=22.85 Aligned_cols=36 Identities=17% Similarity=0.152 Sum_probs=27.3
Q ss_pred HHHcCCChhHHHHHHHHcCCCCC-hhHHHhhHHHHHH
Q 041600 88 ARRMKLCPTVVKKICRRDGLHRW-PHRKIKSIQRRMS 123 (160)
Q Consensus 88 A~~Lgv~~T~LKr~CR~~GI~RW-PyRkikSl~~~i~ 123 (160)
..+.|+..+++..+|++.|+++= -|+...+.+..+.
T Consensus 9 ~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~~ 45 (47)
T PF00440_consen 9 FAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKDDLLR 45 (47)
T ss_dssp HHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHHHHHH
T ss_pred HHHhCHHhCCHHHHHHHHccchhhHHHHcCCHHHHHh
Confidence 45779999999999999999762 3666666665544
No 487
>PRK11020 hypothetical protein; Provisional
Probab=44.96 E-value=55 Score=25.67 Aligned_cols=42 Identities=29% Similarity=0.329 Sum_probs=29.3
Q ss_pred HhhHHHHHHHHhhhc----cCCcHHHHHHHHHHHHHHHHHHHHHhc
Q 041600 115 IKSIQRRMSVASGRL----RSNDAEERANAQIEIQRLQEEMAAACA 156 (160)
Q Consensus 115 ikSl~~~i~~L~~~~----~~~~~eerar~~~eIerL~~Em~~~c~ 156 (160)
|+.|+..++.+++.+ ..+|.+--+....||+.|..|+..+.+
T Consensus 7 iq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~ 52 (118)
T PRK11020 7 IKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIARLKE 52 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455555544433 235788888899999999999988765
No 488
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=44.79 E-value=33 Score=23.12 Aligned_cols=35 Identities=20% Similarity=0.344 Sum_probs=22.5
Q ss_pred HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC-CCCCh
Q 041600 75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDG-LHRWP 111 (160)
Q Consensus 75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWP 111 (160)
..+.--++++.++|+.++|++..|+.+ +.| ...-|
T Consensus 4 ~~R~~~glsl~~va~~t~I~~~~l~ai--E~~~~~~lp 39 (62)
T PF13413_consen 4 EAREAKGLSLEDVAEETKISVSYLEAI--ENGDFDSLP 39 (62)
T ss_dssp HHHHCTT--HHHHHHHCS--HHHHHHH--HCT-GCCSS
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHH--HCcChhhCC
Confidence 344555789999999999999999988 655 44444
No 489
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=44.45 E-value=18 Score=29.29 Aligned_cols=25 Identities=32% Similarity=0.339 Sum_probs=22.2
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.+...+.|+.||||.|.++...++|
T Consensus 39 ~l~e~~La~~~gvSrtPVReAL~rL 63 (230)
T COG1802 39 RLSEEELAEELGVSRTPVREALRRL 63 (230)
T ss_pred CccHHHHHHHhCCCCccHHHHHHHH
Confidence 5889999999999999998888766
No 490
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=44.37 E-value=31 Score=24.83 Aligned_cols=25 Identities=20% Similarity=0.092 Sum_probs=20.8
Q ss_pred HhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 77 MIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 77 ~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
..+.-++-.+.|+.||+|.|++.|.
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaVwK~ 39 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAVWKH 39 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHHHHH
Confidence 3554588999999999999998876
No 491
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=44.33 E-value=33 Score=28.26 Aligned_cols=33 Identities=9% Similarity=0.083 Sum_probs=24.8
Q ss_pred CCCCHHHHHhhc----CCcHHHHHHHcCCChhHHHHH
Q 041600 69 GKLTLRDLMIYF----HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 69 ~~lt~~~L~~yF----~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.++++..|+-+- +-.+..||+.||||.+++-+.
T Consensus 9 ~~m~~~~l~~F~av~e~gS~t~AA~~L~iSQpavS~~ 45 (303)
T PRK10082 9 HNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRR 45 (303)
T ss_pred cccchHHHHHHHHHHhcCCHHHHHHHhCCChHHHHHH
Confidence 357777774322 578899999999999988654
No 492
>PF14282 FlxA: FlxA-like protein
Probab=44.28 E-value=91 Score=23.12 Aligned_cols=42 Identities=29% Similarity=0.432 Sum_probs=22.8
Q ss_pred HHHhhHHHHHHHHhhhccC------CcHHHH----HHHHHHHHHHHHHHHHH
Q 041600 113 RKIKSIQRRMSVASGRLRS------NDAEER----ANAQIEIQRLQEEMAAA 154 (160)
Q Consensus 113 RkikSl~~~i~~L~~~~~~------~~~eer----ar~~~eIerL~~Em~~~ 154 (160)
.+|.+|++.|..|...|.. .+++++ ..++.+|.-|+..|..+
T Consensus 19 ~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~ql 70 (106)
T PF14282_consen 19 SQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQL 70 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666665521 255543 33445666666655443
No 493
>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=44.19 E-value=32 Score=27.22 Aligned_cols=25 Identities=16% Similarity=0.042 Sum_probs=22.3
Q ss_pred CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 81 HLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
.++-.|.|+.||++...+.|+|..|
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L 52 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYAL 52 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5889999999999999999999754
No 494
>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=43.83 E-value=34 Score=27.88 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=18.0
Q ss_pred CCcHHHHHHHcCCChhHHHHH
Q 041600 81 HLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 81 ~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
+..+..||+.||||.+++-+.
T Consensus 17 ~gS~s~AA~~L~isq~avS~~ 37 (300)
T TIGR02424 17 QGSVKRAAEALHITQPAVSKT 37 (300)
T ss_pred hCCHHHHHHHhCCChHHHHHH
Confidence 578899999999999988654
No 495
>PRK07914 hypothetical protein; Reviewed
Probab=43.83 E-value=73 Score=27.27 Aligned_cols=48 Identities=15% Similarity=0.256 Sum_probs=36.1
Q ss_pred cHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhccCC
Q 041600 83 PIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSN 132 (160)
Q Consensus 83 P~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~~~~ 132 (160)
+..++|+.+||.+-..|+..+ ...||+-.++..+-..+..+...+.+.
T Consensus 251 ~~~~i~~~l~i~p~~~~~~~~--~~~~~s~~~L~~~l~~l~~~D~~lK~~ 298 (320)
T PRK07914 251 DPYRLAGELGMPPWRVQKAQK--QARRWSRDTVATAMRVVAALNADVKGA 298 (320)
T ss_pred CHHHHHHHcCCCHHHHHHHHH--HHcCCCHHHHHHHHHHHHHHHHHhhcC
Confidence 777888888887766666633 357888888888888888888888753
No 496
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=43.70 E-value=31 Score=29.18 Aligned_cols=43 Identities=16% Similarity=0.146 Sum_probs=29.8
Q ss_pred hhccCCCCHHHHHh----hcCCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 041600 65 RERTGKLTLRDLMI----YFHLPIEEAARRMKLCPTVVKK----ICRRDGL 107 (160)
Q Consensus 65 r~r~~~lt~~~L~~----yF~lP~~eAA~~Lgv~~T~LKr----~CR~~GI 107 (160)
...+..||-.|+.= .=++..+|+|+.||+|+.|++. +.+++|+
T Consensus 128 ~~~~~~LSpRErEVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 128 YCTTRHFSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred ccCCCCCCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34555677666541 1279999999999999887765 4455555
No 497
>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=43.42 E-value=35 Score=27.40 Aligned_cols=28 Identities=11% Similarity=0.095 Sum_probs=23.3
Q ss_pred hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600 78 IYFHLPIEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
..=.+.+.+.|+.|||+++++.+...+|
T Consensus 12 ~~~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 12 KQGQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3335889999999999999999988865
No 498
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=43.33 E-value=25 Score=24.32 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=17.9
Q ss_pred HHHHHHHcCCChhHHHHHHHHc
Q 041600 84 IEEAARRMKLCPTVVKKICRRD 105 (160)
Q Consensus 84 ~~eAA~~Lgv~~T~LKr~CR~~ 105 (160)
+.++|+.|||+.+++-+.-+++
T Consensus 2 ~~ela~~l~is~stvs~~l~~L 23 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKL 23 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHH
Confidence 5789999999998888776544
No 499
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=43.28 E-value=13 Score=27.09 Aligned_cols=33 Identities=24% Similarity=0.242 Sum_probs=30.7
Q ss_pred chHHHHHHHHHHHHHHhhCCceeecCchhHHHH
Q 041600 5 SIENVKEYLVQYCEERKQAGFMMLPDPLSDFYE 37 (160)
Q Consensus 5 s~~~vk~~L~~y~~~r~~~g~~~~qd~~s~f~~ 37 (160)
|.||.+++|..|-....|.=-|..-||++.+|.
T Consensus 19 s~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g 51 (79)
T PRK09570 19 SEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIG 51 (79)
T ss_pred CHHHHHHHHHHcCCCHHHCCceeccChhhhhcC
Confidence 679999999999999999999999999998873
No 500
>PRK04140 hypothetical protein; Provisional
Probab=42.99 E-value=31 Score=30.72 Aligned_cols=30 Identities=20% Similarity=0.261 Sum_probs=24.5
Q ss_pred CHHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600 72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKI 101 (160)
Q Consensus 72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~ 101 (160)
.+..++.-.++++.+.|+.+|||.+++-++
T Consensus 130 rLk~lRe~~GlSq~eLA~~lGVSr~tIsky 159 (317)
T PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKY 159 (317)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 355667778899999999999998888777
Done!