Query 023462
Match_columns 282
No_of_seqs 124 out of 222
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 04:13:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023462.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023462hhsearch_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 1.1E-26 2.3E-31 168.9 5.7 51 26-76 2-52 (52)
2 PF01418 HTH_6: Helix-turn-hel 96.2 0.0057 1.2E-07 46.2 3.4 37 33-69 28-64 (77)
3 PF02796 HTH_7: Helix-turn-hel 95.3 0.024 5.2E-07 39.1 3.6 33 30-62 10-44 (45)
4 TIGR01764 excise DNA binding d 95.1 0.03 6.4E-07 36.8 3.4 27 40-66 2-28 (49)
5 cd04764 HTH_MlrA-like_sg1 Heli 95.0 0.068 1.5E-06 38.6 5.3 27 40-66 1-27 (67)
6 cd04763 HTH_MlrA-like Helix-Tu 94.7 0.1 2.2E-06 37.9 5.6 27 40-66 1-27 (68)
7 cd01104 HTH_MlrA-CarA Helix-Tu 94.6 0.058 1.3E-06 38.5 4.0 27 40-66 1-27 (68)
8 PF02954 HTH_8: Bacterial regu 94.3 0.091 2E-06 35.8 4.3 28 36-63 15-42 (42)
9 PF12728 HTH_17: Helix-turn-he 94.1 0.066 1.4E-06 36.8 3.3 45 40-87 2-48 (51)
10 cd04762 HTH_MerR-trunc Helix-T 94.1 0.074 1.6E-06 34.5 3.4 27 40-66 1-27 (49)
11 PF13411 MerR_1: MerR HTH fami 93.8 0.24 5.2E-06 35.4 5.9 26 40-65 1-26 (69)
12 cd04761 HTH_MerR-SF Helix-Turn 93.7 0.094 2E-06 35.0 3.5 32 40-73 1-32 (49)
13 PRK11302 DNA-binding transcrip 93.7 0.058 1.3E-06 47.9 3.1 34 36-69 31-64 (284)
14 COG2207 AraC AraC-type DNA-bin 93.6 0.45 9.8E-06 35.8 7.3 75 40-126 37-120 (127)
15 PRK15482 transcriptional regul 93.6 0.061 1.3E-06 48.5 3.1 39 34-72 29-67 (285)
16 PRK00430 fis global DNA-bindin 93.2 0.16 3.4E-06 40.8 4.5 31 36-66 65-95 (95)
17 PF13384 HTH_23: Homeodomain-l 92.6 0.16 3.5E-06 34.5 3.4 25 39-63 17-41 (50)
18 PF02001 DUF134: Protein of un 92.5 0.18 4E-06 41.8 4.2 38 25-62 38-80 (106)
19 PF13936 HTH_38: Helix-turn-he 92.5 0.13 2.7E-06 35.6 2.7 26 38-63 19-44 (44)
20 PRK10219 DNA-binding transcrip 92.5 0.75 1.6E-05 35.6 7.4 34 33-66 13-49 (107)
21 PRK11557 putative DNA-binding 92.3 0.11 2.4E-06 46.3 2.9 36 36-71 27-62 (278)
22 COG1737 RpiR Transcriptional r 92.2 0.098 2.1E-06 47.9 2.4 39 36-74 33-71 (281)
23 PRK11337 DNA-binding transcrip 92.1 0.13 2.7E-06 46.4 3.0 35 36-70 43-77 (292)
24 PRK11361 acetoacetate metaboli 91.9 0.22 4.7E-06 47.0 4.4 31 36-66 427-457 (457)
25 cd04765 HTH_MlrA-like_sg2 Heli 91.5 0.42 9.1E-06 38.1 5.0 27 40-66 1-27 (99)
26 PF13542 HTH_Tnp_ISL3: Helix-t 91.4 0.21 4.6E-06 34.2 2.9 34 30-63 17-51 (52)
27 PF04967 HTH_10: HTH DNA bindi 91.3 0.26 5.7E-06 36.2 3.4 28 35-62 15-46 (53)
28 PRK15115 response regulator Gl 91.2 0.29 6.3E-06 46.1 4.5 31 36-66 408-438 (444)
29 PRK11608 pspF phage shock prot 91.1 0.3 6.6E-06 45.6 4.5 31 36-66 296-326 (326)
30 PRK11511 DNA-binding transcrip 91.1 1.9 4.2E-05 35.1 8.6 83 34-128 18-111 (127)
31 PRK01905 DNA-binding protein F 90.8 0.47 1E-05 36.2 4.5 29 38-66 49-77 (77)
32 PRK13413 mpi multiple promoter 89.8 0.37 8E-06 41.6 3.6 28 39-66 172-199 (200)
33 PF01710 HTH_Tnp_IS630: Transp 89.8 0.52 1.1E-05 38.3 4.2 39 28-66 56-98 (119)
34 PF01381 HTH_3: Helix-turn-hel 89.8 0.59 1.3E-05 32.0 3.9 31 32-62 2-32 (55)
35 PRK05022 anaerobic nitric oxid 89.7 0.47 1E-05 46.9 4.7 31 36-66 478-508 (509)
36 TIGR02915 PEP_resp_reg putativ 89.6 0.51 1.1E-05 44.6 4.6 30 36-65 415-444 (445)
37 PRK10923 glnG nitrogen regulat 89.5 0.48 1E-05 45.1 4.5 31 36-66 439-469 (469)
38 PRK10820 DNA-binding transcrip 89.5 0.51 1.1E-05 47.1 4.7 26 41-66 488-513 (520)
39 TIGR03070 couple_hipB transcri 89.4 0.6 1.3E-05 31.4 3.7 32 31-62 7-38 (58)
40 PRK09393 ftrA transcriptional 89.4 2.3 4.9E-05 39.0 8.5 77 34-122 227-314 (322)
41 PRK13182 racA polar chromosome 89.1 0.65 1.4E-05 41.1 4.6 27 40-66 1-27 (175)
42 PF00165 HTH_AraC: Bacterial r 89.0 0.52 1.1E-05 31.5 3.1 27 39-65 8-35 (42)
43 cd01105 HTH_GlnR-like Helix-Tu 89.0 1 2.3E-05 34.8 5.2 31 40-72 2-32 (88)
44 smart00422 HTH_MERR helix_turn 88.8 1.9 4.2E-05 30.6 6.2 25 40-65 1-25 (70)
45 cd04774 HTH_YfmP Helix-Turn-He 88.7 0.56 1.2E-05 37.1 3.6 30 40-71 1-30 (96)
46 PRK12515 RNA polymerase sigma 88.6 0.72 1.6E-05 38.7 4.4 26 34-59 142-167 (189)
47 COG3284 AcoR Transcriptional a 88.5 0.4 8.8E-06 49.9 3.4 30 38-67 577-606 (606)
48 smart00421 HTH_LUXR helix_turn 88.5 0.51 1.1E-05 31.1 2.8 25 38-62 17-41 (58)
49 PRK13502 transcriptional activ 88.4 2.4 5.2E-05 37.5 7.8 74 39-124 192-274 (282)
50 PRK09685 DNA-binding transcrip 88.4 3 6.5E-05 37.2 8.4 65 33-109 205-279 (302)
51 smart00342 HTH_ARAC helix_turn 88.4 1 2.2E-05 31.6 4.4 26 39-64 1-26 (84)
52 PF13518 HTH_28: Helix-turn-he 88.3 0.62 1.3E-05 31.4 3.1 25 39-63 12-36 (52)
53 PF11112 PyocinActivator: Pyoc 87.8 2.3 5E-05 33.3 6.4 58 30-88 2-70 (76)
54 PF04545 Sigma70_r4: Sigma-70, 87.5 1.2 2.7E-05 30.5 4.3 24 39-62 20-43 (50)
55 PF08281 Sigma70_r4_2: Sigma-7 87.4 0.91 2E-05 31.3 3.6 29 33-61 20-48 (54)
56 cd04766 HTH_HspR Helix-Turn-He 87.3 1.2 2.5E-05 34.5 4.5 30 40-71 2-31 (91)
57 cd04773 HTH_TioE_rpt2 Second H 87.3 1.2 2.6E-05 35.7 4.7 25 40-65 1-25 (108)
58 PRK09978 DNA-binding transcrip 87.1 3 6.4E-05 39.3 7.9 75 39-125 158-240 (274)
59 PF13412 HTH_24: Winged helix- 87.0 1.2 2.6E-05 30.3 3.9 32 32-63 10-41 (48)
60 PF13404 HTH_AsnC-type: AsnC-t 86.7 1.3 2.7E-05 30.8 4.0 32 32-63 10-41 (42)
61 smart00351 PAX Paired Box doma 86.6 2.5 5.4E-05 34.8 6.4 67 39-105 33-107 (125)
62 COG1342 Predicted DNA-binding 86.3 0.82 1.8E-05 38.0 3.3 36 24-59 29-69 (99)
63 cd04768 HTH_BmrR-like Helix-Tu 86.0 1.7 3.6E-05 34.1 4.8 27 40-67 1-27 (96)
64 PF12844 HTH_19: Helix-turn-he 86.0 1.5 3.2E-05 31.0 4.2 29 31-59 4-32 (64)
65 TIGR02989 Sig-70_gvs1 RNA poly 86.0 1.1 2.4E-05 35.9 4.0 28 35-62 123-150 (159)
66 cd04775 HTH_Cfa-like Helix-Tur 86.0 1.5 3.2E-05 34.8 4.6 30 40-71 2-31 (102)
67 smart00497 IENR1 Intron encode 85.9 0.91 2E-05 31.0 2.9 22 41-62 19-40 (53)
68 COG1522 Lrp Transcriptional re 85.9 1.2 2.6E-05 36.1 4.1 33 31-63 14-46 (154)
69 PRK11388 DNA-binding transcrip 85.8 1.2 2.6E-05 44.9 4.9 35 36-70 601-635 (638)
70 PRK15043 transcriptional regul 85.7 1.5 3.2E-05 41.0 5.1 33 39-72 3-35 (243)
71 COG1595 RpoE DNA-directed RNA 85.6 1 2.2E-05 37.8 3.7 31 32-62 136-166 (182)
72 PRK00118 putative DNA-binding 85.6 0.69 1.5E-05 38.1 2.6 29 34-62 28-56 (104)
73 TIGR01817 nifA Nif-specific re 85.2 1.2 2.6E-05 44.0 4.5 31 36-66 500-530 (534)
74 TIGR02531 yecD_yerC TrpR-relat 85.1 0.96 2.1E-05 36.1 3.1 23 39-61 50-72 (88)
75 TIGR02297 HpaA 4-hydroxyphenyl 84.8 5.1 0.00011 35.3 7.8 64 34-109 195-266 (287)
76 PF13560 HTH_31: Helix-turn-he 84.7 1.3 2.8E-05 31.8 3.3 34 31-64 6-39 (64)
77 cd01282 HTH_MerR-like_sg3 Heli 84.4 2.3 5.1E-05 34.2 5.1 31 40-72 1-31 (112)
78 cd04789 HTH_Cfa Helix-Turn-Hel 84.4 2.1 4.5E-05 34.0 4.7 30 40-71 2-31 (102)
79 PF07453 NUMOD1: NUMOD1 domain 84.4 0.83 1.8E-05 30.1 2.1 21 40-60 17-37 (37)
80 PRK14101 bifunctional glucokin 83.7 0.94 2E-05 46.0 3.1 34 37-70 372-405 (638)
81 cd01279 HTH_HspR-like Helix-Tu 83.6 2.5 5.5E-05 33.4 4.9 26 40-66 2-27 (98)
82 PRK13503 transcriptional activ 83.5 8.7 0.00019 33.7 8.7 64 34-109 180-251 (278)
83 cd00131 PAX Paired Box domain 83.3 5 0.00011 33.4 6.7 66 39-105 33-107 (128)
84 KOG0251 Clathrin assembly prot 83.2 1.3 2.8E-05 45.1 3.9 55 33-87 223-289 (491)
85 PHA01976 helix-turn-helix prot 83.0 2.4 5.2E-05 30.2 4.2 33 30-62 6-38 (67)
86 PRK09645 RNA polymerase sigma 82.9 1.8 3.8E-05 35.6 3.9 27 36-62 131-157 (173)
87 PF03374 ANT: Phage antirepres 82.7 1.5 3.2E-05 34.5 3.3 28 39-66 24-51 (111)
88 PRK09413 IS2 repressor TnpA; R 82.6 8 0.00017 31.5 7.6 42 23-64 11-54 (121)
89 PRK10572 DNA-binding transcrip 82.5 9.4 0.0002 34.0 8.6 58 39-108 199-262 (290)
90 PF00356 LacI: Bacterial regul 82.4 2.9 6.2E-05 29.7 4.3 23 41-63 1-23 (46)
91 PRK15429 formate hydrogenlyase 82.3 1.2 2.7E-05 45.5 3.4 24 43-66 661-684 (686)
92 PRK13500 transcriptional activ 82.3 7.8 0.00017 35.6 8.2 82 32-125 213-305 (312)
93 COG1476 Predicted transcriptio 82.2 1.6 3.5E-05 33.9 3.2 32 30-61 5-36 (68)
94 TIGR02999 Sig-70_X6 RNA polyme 82.1 2 4.3E-05 35.5 4.0 26 37-62 148-173 (183)
95 PRK12533 RNA polymerase sigma 82.0 1.7 3.7E-05 38.5 3.8 28 35-62 146-173 (216)
96 PRK12529 RNA polymerase sigma 81.9 2 4.4E-05 36.0 4.0 27 35-61 139-165 (178)
97 PRK09642 RNA polymerase sigma 81.9 2.1 4.5E-05 34.7 3.9 27 35-61 118-144 (160)
98 PRK09726 antitoxin HipB; Provi 81.7 2.1 4.5E-05 32.9 3.7 32 30-61 16-47 (88)
99 PRK09649 RNA polymerase sigma 81.7 2 4.3E-05 36.4 3.9 29 34-62 141-169 (185)
100 cd00592 HTH_MerR-like Helix-Tu 81.7 3.9 8.4E-05 31.5 5.2 30 40-71 1-30 (100)
101 PRK04217 hypothetical protein; 81.7 2.1 4.5E-05 35.6 3.9 26 37-62 56-81 (110)
102 PHA00542 putative Cro-like pro 81.4 2.1 4.5E-05 33.0 3.6 28 36-63 28-55 (82)
103 PF05225 HTH_psq: helix-turn-h 81.2 2.8 6.1E-05 29.4 3.9 23 40-62 17-39 (45)
104 cd01106 HTH_TipAL-Mta Helix-Tu 81.0 5.7 0.00012 31.2 6.0 25 40-65 1-25 (103)
105 smart00419 HTH_CRP helix_turn_ 80.7 2.2 4.8E-05 28.0 3.1 28 37-64 6-33 (48)
106 PF03683 UPF0175: Uncharacteri 80.5 2.9 6.3E-05 32.0 4.1 31 39-70 34-64 (76)
107 PRK12511 RNA polymerase sigma 80.4 2.3 5E-05 36.2 3.9 26 36-61 124-149 (182)
108 PF04218 CENP-B_N: CENP-B N-te 80.3 3.1 6.6E-05 29.9 3.9 38 24-61 2-44 (53)
109 PF12833 HTH_18: Helix-turn-he 80.3 4.4 9.5E-05 29.6 4.8 22 45-66 1-23 (81)
110 PRK15418 transcriptional regul 80.2 1.6 3.5E-05 41.3 3.2 29 39-67 29-60 (318)
111 PRK09641 RNA polymerase sigma 80.1 2.4 5.3E-05 34.9 3.8 29 34-62 147-175 (187)
112 PRK09637 RNA polymerase sigma 80.1 2.4 5.2E-05 35.9 3.9 27 35-61 118-144 (181)
113 TIGR02040 PpsR-CrtJ transcript 80.1 2.6 5.6E-05 39.7 4.5 30 36-65 413-442 (442)
114 cd04767 HTH_HspR-like_MBC Heli 80.0 4.8 0.0001 33.9 5.5 30 40-71 2-31 (120)
115 PRK12541 RNA polymerase sigma 79.5 2.7 5.8E-05 34.2 3.8 29 34-62 123-151 (161)
116 smart00342 HTH_ARAC helix_turn 79.4 3.5 7.6E-05 28.8 3.9 27 39-65 50-78 (84)
117 smart00354 HTH_LACI helix_turn 79.3 1.9 4E-05 31.9 2.6 24 40-63 1-24 (70)
118 PRK09638 RNA polymerase sigma 79.3 2.1 4.5E-05 35.2 3.1 27 36-62 139-165 (176)
119 PF01527 HTH_Tnp_1: Transposas 79.2 1.6 3.4E-05 31.7 2.2 45 27-71 9-57 (76)
120 PRK10072 putative transcriptio 79.1 3.4 7.4E-05 33.5 4.3 33 31-63 38-70 (96)
121 PRK12532 RNA polymerase sigma 79.1 2.6 5.7E-05 35.5 3.8 28 34-61 147-174 (195)
122 PRK07037 extracytoplasmic-func 79.1 3 6.5E-05 33.8 4.0 24 36-59 122-145 (163)
123 PRK13501 transcriptional activ 78.9 14 0.0003 33.2 8.5 86 31-128 182-278 (290)
124 PRK12536 RNA polymerase sigma 78.8 2.8 6E-05 35.1 3.8 27 36-62 142-168 (181)
125 PRK12530 RNA polymerase sigma 78.7 2.7 5.9E-05 35.6 3.8 27 36-62 147-173 (189)
126 cd01110 HTH_SoxR Helix-Turn-He 78.6 3.8 8.2E-05 34.5 4.5 31 39-71 1-31 (139)
127 PF07638 Sigma70_ECF: ECF sigm 78.6 2.9 6.3E-05 35.8 4.0 30 34-63 146-175 (185)
128 COG3829 RocR Transcriptional r 78.6 1.9 4.2E-05 44.8 3.3 28 39-66 533-560 (560)
129 PRK09047 RNA polymerase factor 78.4 3.2 6.9E-05 33.4 3.9 26 36-61 119-144 (161)
130 TIGR02952 Sig70_famx2 RNA poly 78.3 3.3 7.1E-05 33.5 4.0 26 37-62 136-161 (170)
131 cd06170 LuxR_C_like C-terminal 78.3 3 6.6E-05 27.7 3.2 25 39-63 15-39 (57)
132 PRK11169 leucine-responsive tr 78.2 2.7 5.9E-05 35.6 3.6 34 32-65 21-57 (164)
133 PRK12520 RNA polymerase sigma 78.2 3.1 6.7E-05 35.0 3.9 27 36-62 144-170 (191)
134 TIGR02047 CadR-PbrR Cd(II)/Pb( 77.9 5.3 0.00011 32.9 5.1 27 40-67 1-27 (127)
135 PF06056 Terminase_5: Putative 77.8 3.1 6.7E-05 30.8 3.4 26 39-64 13-38 (58)
136 PRK09646 RNA polymerase sigma 77.7 3.2 6.8E-05 35.2 3.9 27 35-61 154-180 (194)
137 PRK10130 transcriptional regul 77.5 14 0.0003 35.5 8.5 57 40-108 257-322 (350)
138 TIGR02974 phageshock_pspF psp 77.4 3.3 7.1E-05 39.1 4.3 28 36-63 302-329 (329)
139 COG3413 Predicted DNA binding 77.2 2.6 5.6E-05 37.1 3.3 35 28-62 155-201 (215)
140 cd01109 HTH_YyaN Helix-Turn-He 77.1 5.3 0.00012 31.9 4.8 26 40-65 1-26 (113)
141 TIGR01321 TrpR trp operon repr 76.9 2.5 5.4E-05 34.6 2.9 26 39-64 55-80 (94)
142 PRK09636 RNA polymerase sigma 76.9 3.2 7E-05 37.8 3.9 28 34-61 126-153 (293)
143 smart00344 HTH_ASNC helix_turn 76.6 4.3 9.4E-05 31.3 4.1 32 32-63 10-41 (108)
144 PRK12547 RNA polymerase sigma 76.5 3.8 8.3E-05 33.7 4.0 27 36-62 125-151 (164)
145 cd06171 Sigma70_r4 Sigma70, re 76.5 4 8.8E-05 26.0 3.3 25 38-62 25-49 (55)
146 smart00345 HTH_GNTR helix_turn 76.3 3.5 7.5E-05 27.8 3.1 24 40-63 20-44 (60)
147 TIGR02954 Sig70_famx3 RNA poly 76.2 3.8 8.2E-05 33.6 3.8 27 35-61 131-157 (169)
148 PF13011 LZ_Tnp_IS481: leucine 76.1 3.1 6.7E-05 33.6 3.2 36 39-74 25-69 (85)
149 PRK15044 transcriptional regul 76.1 9.9 0.00021 36.7 7.1 60 39-110 208-272 (295)
150 PRK12542 RNA polymerase sigma 76.0 3.8 8.3E-05 34.2 3.9 27 35-61 134-160 (185)
151 PF13443 HTH_26: Cro/C1-type H 76.0 3.8 8.2E-05 28.8 3.3 41 32-73 3-43 (63)
152 TIGR03879 near_KaiC_dom probab 75.9 4.6 0.0001 31.7 4.0 27 36-62 29-55 (73)
153 PF04760 IF2_N: Translation in 75.9 2.8 6.1E-05 29.6 2.6 27 40-66 4-31 (54)
154 TIGR02947 SigH_actino RNA poly 75.9 2.9 6.3E-05 35.2 3.2 27 36-62 144-170 (193)
155 PRK09415 RNA polymerase factor 75.8 3.9 8.4E-05 34.2 3.8 29 34-62 138-166 (179)
156 PRK12513 RNA polymerase sigma 75.7 2.8 6E-05 35.3 3.0 24 37-60 153-176 (194)
157 TIGR01818 ntrC nitrogen regula 75.7 3.9 8.4E-05 38.8 4.3 27 37-63 437-463 (463)
158 PRK12531 RNA polymerase sigma 75.6 4 8.6E-05 34.6 3.9 24 38-61 156-179 (194)
159 PRK12528 RNA polymerase sigma 75.6 4.3 9.3E-05 33.0 4.0 28 35-62 125-152 (161)
160 cd00569 HTH_Hin_like Helix-tur 75.6 3.8 8.3E-05 23.2 2.8 21 39-59 21-41 (42)
161 cd00092 HTH_CRP helix_turn_hel 75.4 3.8 8.3E-05 28.6 3.2 28 36-63 22-49 (67)
162 PRK08241 RNA polymerase factor 75.3 3.4 7.5E-05 38.0 3.7 28 34-61 164-191 (339)
163 PRK15424 propionate catabolism 75.3 4.2 9.2E-05 41.5 4.7 31 36-66 507-537 (538)
164 PF06970 RepA_N: Replication i 75.3 2.5 5.5E-05 32.8 2.4 28 36-63 49-76 (76)
165 PRK09643 RNA polymerase sigma 75.3 4 8.8E-05 34.7 3.9 27 36-62 147-173 (192)
166 PRK05602 RNA polymerase sigma 75.3 4 8.7E-05 34.1 3.8 29 34-62 139-167 (186)
167 PRK12516 RNA polymerase sigma 75.2 4.1 8.9E-05 34.8 3.9 27 35-61 128-154 (187)
168 PRK09635 sigI RNA polymerase s 75.0 3.5 7.6E-05 38.3 3.7 29 33-61 128-156 (290)
169 PF13551 HTH_29: Winged helix- 74.9 3.5 7.7E-05 31.2 3.1 25 39-63 11-36 (112)
170 TIGR02960 SigX5 RNA polymerase 74.9 3.8 8.1E-05 37.2 3.8 28 34-61 153-180 (324)
171 TIGR02943 Sig70_famx1 RNA poly 74.8 4.2 9.2E-05 34.5 3.9 27 36-62 144-170 (188)
172 TIGR02948 SigW_bacill RNA poly 74.8 4.1 8.9E-05 33.5 3.7 27 36-62 149-175 (187)
173 PF01498 HTH_Tnp_Tc3_2: Transp 74.7 2 4.2E-05 31.4 1.6 38 39-76 13-55 (72)
174 PRK12523 RNA polymerase sigma 74.5 4.6 0.0001 33.4 4.0 27 35-61 131-157 (172)
175 PRK12540 RNA polymerase sigma 74.2 4.4 9.6E-05 34.4 3.9 27 36-62 124-150 (182)
176 PF01371 Trp_repressor: Trp re 74.1 3.8 8.3E-05 32.9 3.2 26 39-64 49-74 (87)
177 TIGR02983 SigE-fam_strep RNA p 74.1 4.5 9.8E-05 32.7 3.7 28 35-62 122-149 (162)
178 PRK15121 right oriC-binding tr 74.1 16 0.00036 33.1 7.7 75 39-125 21-104 (289)
179 TIGR02043 ZntR Zn(II)-responsi 73.9 7.4 0.00016 32.2 5.0 27 40-67 2-28 (131)
180 TIGR03830 CxxCG_CxxCG_HTH puta 73.7 4 8.6E-05 32.3 3.3 33 30-62 69-101 (127)
181 PRK12545 RNA polymerase sigma 73.6 4.6 0.0001 34.6 3.9 26 36-61 152-177 (201)
182 TIGR02957 SigX4 RNA polymerase 73.6 4.4 9.5E-05 36.9 3.9 29 33-61 118-146 (281)
183 PRK12522 RNA polymerase sigma 73.5 4.9 0.00011 33.2 3.9 26 36-61 132-157 (173)
184 PF10668 Phage_terminase: Phag 73.4 6.5 0.00014 29.9 4.2 24 39-62 22-45 (60)
185 TIGR02984 Sig-70_plancto1 RNA 73.4 5.2 0.00011 32.9 4.0 26 36-61 153-178 (189)
186 TIGR02959 SigZ RNA polymerase 73.2 5.2 0.00011 33.3 4.0 27 34-60 111-137 (170)
187 TIGR01950 SoxR redox-sensitive 73.2 5.8 0.00013 33.7 4.3 27 40-67 2-28 (142)
188 TIGR02985 Sig70_bacteroi1 RNA 73.1 5.6 0.00012 31.3 4.0 26 37-62 127-152 (161)
189 TIGR02607 antidote_HigA addict 73.1 5.4 0.00012 29.0 3.6 29 33-61 12-40 (78)
190 PF05930 Phage_AlpA: Prophage 73.0 2.7 5.8E-05 29.6 1.9 26 40-65 4-29 (51)
191 cd04782 HTH_BltR Helix-Turn-He 73.0 8 0.00017 30.4 4.8 26 40-66 1-26 (97)
192 PRK12527 RNA polymerase sigma 72.9 5.5 0.00012 32.3 4.0 26 36-61 118-143 (159)
193 TIGR03209 P21_Cbot clostridium 72.7 2.6 5.7E-05 33.6 2.0 23 36-58 120-142 (142)
194 PRK11534 DNA-binding transcrip 72.1 14 0.0003 32.1 6.5 36 39-74 30-69 (224)
195 TIGR02293 TAS_TIGR02293 putati 72.1 5.1 0.00011 33.4 3.7 34 30-63 27-60 (133)
196 smart00418 HTH_ARSR helix_turn 72.1 5.1 0.00011 26.5 3.1 32 39-70 10-41 (66)
197 TIGR02937 sigma70-ECF RNA poly 72.0 5 0.00011 30.4 3.3 27 37-63 124-150 (158)
198 PRK15185 transcriptional regul 71.8 20 0.00042 34.8 8.0 27 39-65 222-248 (309)
199 PRK09940 transcriptional regul 71.7 19 0.00042 33.6 7.7 73 39-123 150-229 (253)
200 PRK12519 RNA polymerase sigma 71.6 5.2 0.00011 33.5 3.7 26 36-61 154-179 (194)
201 PRK09652 RNA polymerase sigma 71.4 6.1 0.00013 31.9 3.9 23 37-59 142-164 (182)
202 TIGR02939 RpoE_Sigma70 RNA pol 71.4 5.4 0.00012 32.9 3.7 26 37-62 152-177 (190)
203 PRK10703 DNA-binding transcrip 71.3 6 0.00013 35.3 4.2 23 40-62 2-24 (341)
204 smart00530 HTH_XRE Helix-turn- 71.1 8 0.00017 23.9 3.7 29 33-61 4-32 (56)
205 PRK12535 RNA polymerase sigma 71.1 5.4 0.00012 34.4 3.7 27 35-61 145-171 (196)
206 cd00093 HTH_XRE Helix-turn-hel 71.1 8.7 0.00019 23.9 3.8 29 33-61 6-34 (58)
207 TIGR02392 rpoH_proteo alternat 71.0 5.6 0.00012 36.1 4.0 24 39-62 236-259 (270)
208 PRK09647 RNA polymerase sigma 70.8 5.9 0.00013 34.5 3.9 28 36-63 151-178 (203)
209 PRK09651 RNA polymerase sigma 70.8 5.6 0.00012 33.0 3.7 27 34-60 130-156 (172)
210 PRK11923 algU RNA polymerase s 70.3 6.2 0.00013 33.0 3.8 27 36-62 151-177 (193)
211 PRK12514 RNA polymerase sigma 70.2 6 0.00013 32.7 3.7 25 37-61 143-167 (179)
212 PRK10371 DNA-binding transcrip 70.1 20 0.00043 33.1 7.4 60 39-110 207-272 (302)
213 PRK01381 Trp operon repressor; 70.1 2.7 5.8E-05 34.8 1.6 27 39-65 55-81 (99)
214 cd04781 HTH_MerR-like_sg6 Heli 69.8 10 0.00023 30.7 4.9 27 40-67 1-27 (120)
215 PRK09648 RNA polymerase sigma 69.4 7.1 0.00015 32.7 4.0 25 36-60 152-176 (189)
216 PRK12546 RNA polymerase sigma 69.4 6.5 0.00014 33.8 3.8 28 35-62 125-152 (188)
217 PRK12539 RNA polymerase sigma 69.4 6.3 0.00014 33.0 3.7 26 36-61 144-169 (184)
218 PRK13919 putative RNA polymera 69.2 7 0.00015 32.4 3.9 27 36-62 148-174 (186)
219 PRK09191 two-component respons 69.2 6.6 0.00014 33.5 3.8 29 34-62 99-127 (261)
220 cd04772 HTH_TioE_rpt1 First He 69.1 11 0.00024 29.8 4.8 27 40-67 1-27 (99)
221 COG2204 AtoC Response regulato 69.1 7.7 0.00017 39.4 4.8 36 36-71 427-462 (464)
222 cd04770 HTH_HMRTR Helix-Turn-H 68.8 13 0.00027 29.9 5.2 29 40-69 1-29 (123)
223 COG2963 Transposase and inacti 68.8 20 0.00043 28.4 6.2 49 24-72 7-60 (116)
224 PF09339 HTH_IclR: IclR helix- 68.8 4.7 0.0001 28.0 2.4 24 40-63 19-42 (52)
225 PF13744 HTH_37: Helix-turn-he 68.7 7.1 0.00015 29.6 3.5 31 31-61 23-53 (80)
226 PF08220 HTH_DeoR: DeoR-like h 68.6 7.8 0.00017 27.9 3.5 32 32-63 7-38 (57)
227 PRK10840 transcriptional regul 68.4 6.9 0.00015 33.0 3.7 39 28-66 150-196 (216)
228 PF00196 GerE: Bacterial regul 68.4 5.5 0.00012 28.1 2.7 28 39-66 18-49 (58)
229 PRK12537 RNA polymerase sigma 67.9 7.5 0.00016 32.5 3.8 25 36-60 146-170 (182)
230 PRK12538 RNA polymerase sigma 67.8 6.4 0.00014 35.2 3.6 28 35-62 183-210 (233)
231 PF08279 HTH_11: HTH domain; 67.5 5.9 0.00013 27.3 2.6 24 40-63 16-39 (55)
232 cd04787 HTH_HMRTR_unk Helix-Tu 67.3 13 0.00028 30.7 5.1 30 40-71 1-30 (133)
233 TIGR03338 phnR_burk phosphonat 67.2 19 0.00042 30.7 6.3 36 39-74 34-73 (212)
234 PF10078 DUF2316: Uncharacteri 67.1 7.2 0.00016 31.8 3.4 33 28-60 9-44 (89)
235 PF00126 HTH_1: Bacterial regu 66.6 7 0.00015 27.9 3.0 24 39-62 13-36 (60)
236 PRK06596 RNA polymerase factor 66.6 7.8 0.00017 35.8 4.0 24 39-62 248-271 (284)
237 PRK06759 RNA polymerase factor 66.4 9.3 0.0002 30.5 4.0 25 37-61 120-144 (154)
238 COG2944 Predicted transcriptio 66.4 7.9 0.00017 32.4 3.6 35 25-59 40-77 (104)
239 cd06571 Bac_DnaA_C C-terminal 66.2 8.9 0.00019 29.7 3.7 38 27-64 32-70 (90)
240 PRK11924 RNA polymerase sigma 66.1 9 0.0002 30.8 3.8 25 37-61 139-163 (179)
241 PF13545 HTH_Crp_2: Crp-like h 66.0 7 0.00015 28.2 2.9 38 37-74 26-66 (76)
242 PF08280 HTH_Mga: M protein tr 65.9 7 0.00015 28.3 2.8 27 39-65 19-45 (59)
243 PRK11179 DNA-binding transcrip 65.8 9.6 0.00021 31.9 4.1 35 32-66 16-53 (153)
244 PF07022 Phage_CI_repr: Bacter 65.8 3.8 8.2E-05 30.2 1.5 32 31-62 3-36 (66)
245 cd01107 HTH_BmrR Helix-Turn-He 65.7 17 0.00037 29.0 5.3 26 40-66 1-26 (108)
246 cd04785 HTH_CadR-PbrR-like Hel 65.6 14 0.00031 30.2 5.0 25 40-65 1-25 (126)
247 PRK11161 fumarate/nitrate redu 65.5 8.1 0.00018 33.1 3.7 38 39-76 184-224 (235)
248 PF07750 GcrA: GcrA cell cycle 65.5 6.9 0.00015 34.2 3.3 37 31-67 8-47 (162)
249 PRK12534 RNA polymerase sigma 65.3 9.1 0.0002 31.9 3.9 26 37-62 151-176 (187)
250 PRK12543 RNA polymerase sigma 65.2 9.4 0.0002 31.8 3.9 25 36-60 130-154 (179)
251 PRK06704 RNA polymerase factor 65.2 7.7 0.00017 35.2 3.6 28 34-61 127-154 (228)
252 PRK10430 DNA-binding transcrip 65.2 7.5 0.00016 33.5 3.4 26 38-63 177-202 (239)
253 PRK10365 transcriptional regul 65.1 8 0.00017 36.3 3.8 26 36-61 415-440 (441)
254 cd04780 HTH_MerR-like_sg5 Heli 65.1 17 0.00036 28.8 5.1 26 40-65 1-26 (95)
255 TIGR02846 spore_sigmaK RNA pol 65.0 8.5 0.00018 33.8 3.8 24 39-62 194-217 (227)
256 PRK15186 AraC family transcrip 65.0 22 0.00047 33.5 6.7 28 39-66 197-224 (291)
257 PRK13890 conjugal transfer pro 64.9 9 0.0002 31.6 3.7 33 31-63 10-42 (120)
258 PRK09644 RNA polymerase sigma 64.8 8.8 0.00019 31.4 3.6 25 36-60 121-145 (165)
259 PF12802 MarR_2: MarR family; 64.8 10 0.00022 26.2 3.5 24 40-63 22-45 (62)
260 PRK11753 DNA-binding transcrip 64.7 6.2 0.00014 33.0 2.8 37 38-74 167-206 (211)
261 PF13613 HTH_Tnp_4: Helix-turn 64.6 6.7 0.00015 27.8 2.5 25 39-63 19-43 (53)
262 PRK11303 DNA-binding transcrip 64.3 6.4 0.00014 34.8 2.9 24 40-63 1-24 (328)
263 cd04788 HTH_NolA-AlbR Helix-Tu 64.1 19 0.00041 28.2 5.2 27 40-67 1-27 (96)
264 cd01111 HTH_MerD Helix-Turn-He 64.1 10 0.00022 30.7 3.7 29 40-69 1-29 (107)
265 cd00090 HTH_ARSR Arsenical Res 63.9 14 0.00029 25.0 3.9 32 40-71 21-52 (78)
266 PRK12512 RNA polymerase sigma 63.8 10 0.00023 31.4 3.9 26 37-62 145-170 (184)
267 PRK12517 RNA polymerase sigma 63.4 9.7 0.00021 32.4 3.7 26 37-62 142-167 (188)
268 PRK09726 antitoxin HipB; Provi 63.3 15 0.00032 28.2 4.4 63 1-66 1-67 (88)
269 smart00530 HTH_XRE Helix-turn- 63.2 28 0.0006 21.4 5.0 40 27-66 9-52 (56)
270 cd01108 HTH_CueR Helix-Turn-He 63.1 18 0.00039 29.7 5.1 26 40-66 1-26 (127)
271 PRK09706 transcriptional repre 63.0 12 0.00027 30.5 4.1 31 31-61 10-40 (135)
272 PRK10403 transcriptional regul 62.9 11 0.00025 29.9 3.8 28 39-66 168-199 (215)
273 PRK12518 RNA polymerase sigma 62.8 8.7 0.00019 31.5 3.2 25 36-60 133-157 (175)
274 smart00346 HTH_ICLR helix_turn 62.6 14 0.0003 27.3 4.0 31 33-63 13-44 (91)
275 PRK15435 bifunctional DNA-bind 62.3 47 0.001 32.2 8.5 77 38-126 98-182 (353)
276 TIGR02054 MerD mercuric resist 62.2 17 0.00038 30.3 4.9 32 39-71 3-34 (120)
277 PF01710 HTH_Tnp_IS630: Transp 61.8 15 0.00033 29.9 4.4 60 39-99 18-79 (119)
278 PRK12524 RNA polymerase sigma 61.4 12 0.00026 31.8 3.9 25 37-61 150-174 (196)
279 COG5484 Uncharacterized conser 61.2 7.8 0.00017 37.3 3.0 26 39-64 19-44 (279)
280 PRK08301 sporulation sigma fac 61.0 12 0.00027 32.6 4.0 24 39-62 198-221 (234)
281 TIGR02950 SigM_subfam RNA poly 60.9 10 0.00022 30.3 3.2 24 38-61 120-143 (154)
282 PRK12526 RNA polymerase sigma 60.8 12 0.00027 32.2 4.0 22 38-59 168-189 (206)
283 PF00392 GntR: Bacterial regul 60.7 8.6 0.00019 27.6 2.5 25 39-63 23-48 (64)
284 PRK10423 transcriptional repre 60.5 11 0.00023 33.3 3.6 20 42-61 1-20 (327)
285 PRK09639 RNA polymerase sigma 60.2 13 0.00028 30.1 3.8 25 36-60 124-148 (166)
286 PRK13752 putative transcriptio 60.1 20 0.00042 30.6 5.0 27 40-67 8-34 (144)
287 PF13556 HTH_30: PucR C-termin 60.0 15 0.00032 26.5 3.7 31 32-62 3-35 (59)
288 cd04776 HTH_GnyR Helix-Turn-He 59.8 12 0.00027 30.5 3.6 30 40-71 1-30 (118)
289 PRK12544 RNA polymerase sigma 59.8 12 0.00026 32.6 3.8 27 36-62 161-187 (206)
290 COG1709 Predicted transcriptio 59.3 5.7 0.00012 37.5 1.7 69 31-103 32-101 (241)
291 PRK06986 fliA flagellar biosyn 59.3 13 0.00028 32.7 3.9 25 37-61 198-222 (236)
292 PRK06811 RNA polymerase factor 59.2 14 0.0003 31.2 3.9 25 37-61 145-169 (189)
293 PRK11922 RNA polymerase sigma 59.1 8.6 0.00019 33.8 2.8 26 36-61 162-187 (231)
294 PRK09514 zntR zinc-responsive 58.8 21 0.00046 30.0 4.9 27 40-67 2-28 (140)
295 cd04779 HTH_MerR-like_sg4 Heli 58.4 18 0.0004 30.6 4.5 31 40-72 1-31 (134)
296 cd08804 Death_ank2 Death domai 58.0 13 0.00029 29.0 3.4 37 27-63 3-39 (84)
297 PRK09640 RNA polymerase sigma 57.9 12 0.00027 31.4 3.4 24 37-60 148-171 (188)
298 COG3415 Transposase and inacti 57.9 11 0.00024 32.6 3.1 28 37-64 19-46 (138)
299 TIGR02612 mob_myst_A mobile my 57.8 14 0.00031 32.1 3.8 32 31-62 30-61 (150)
300 PRK03975 tfx putative transcri 57.7 12 0.00026 32.4 3.4 26 37-62 19-44 (141)
301 PRK08295 RNA polymerase factor 57.6 12 0.00027 31.4 3.4 26 36-61 167-192 (208)
302 TIGR03453 partition_RepA plasm 56.7 13 0.00028 35.5 3.7 31 40-71 34-64 (387)
303 COG3283 TyrR Transcriptional r 56.3 16 0.00036 37.4 4.5 38 29-66 460-508 (511)
304 PF01047 MarR: MarR family; I 56.0 18 0.0004 24.9 3.5 33 32-64 10-42 (59)
305 smart00513 SAP Putative DNA-bi 55.9 13 0.00027 24.5 2.5 20 50-69 3-22 (35)
306 PRK15340 transcriptional regul 55.6 12 0.00026 34.4 3.1 28 39-66 125-153 (216)
307 PRK10651 transcriptional regul 55.4 18 0.00039 28.9 3.8 37 29-65 156-200 (216)
308 PRK10296 DNA-binding transcrip 55.3 48 0.001 29.4 6.8 59 40-110 189-253 (278)
309 TIGR02859 spore_sigH RNA polym 55.3 14 0.00031 30.7 3.4 23 38-60 164-186 (198)
310 cd04786 HTH_MerR-like_sg7 Heli 55.1 23 0.00049 29.7 4.5 26 40-66 1-26 (131)
311 TIGR03001 Sig-70_gmx1 RNA poly 55.0 17 0.00036 33.0 3.9 26 36-61 174-199 (244)
312 COG3093 VapI Plasmid maintenan 55.0 16 0.00036 30.6 3.6 39 24-62 8-46 (104)
313 TIGR02393 RpoD_Cterm RNA polym 54.9 17 0.00038 32.1 4.0 24 39-62 196-219 (238)
314 TIGR01453 grpIintron_endo grou 54.9 11 0.00023 33.8 2.7 26 39-64 179-204 (214)
315 cd01392 HTH_LacI Helix-turn-he 54.7 9.1 0.0002 25.8 1.7 20 44-63 2-21 (52)
316 PRK09526 lacI lac repressor; R 54.5 11 0.00023 33.6 2.6 21 41-61 7-27 (342)
317 PRK13749 transcriptional regul 54.4 28 0.00061 29.3 4.9 32 39-71 3-34 (121)
318 PRK12525 RNA polymerase sigma 53.8 20 0.00044 29.6 4.0 24 37-60 132-155 (168)
319 TIGR02405 trehalos_R_Ecol treh 53.7 12 0.00026 33.3 2.7 20 41-60 3-22 (311)
320 cd08805 Death_ank1 Death domai 53.7 21 0.00045 28.4 3.8 39 26-64 2-40 (84)
321 cd04777 HTH_MerR-like_sg1 Heli 53.6 29 0.00064 27.4 4.7 26 40-66 1-26 (107)
322 TIGR02044 CueR Cu(I)-responsiv 53.6 30 0.00065 28.3 4.9 27 40-67 1-27 (127)
323 smart00352 POU Found in Pit-Oc 53.4 21 0.00045 28.4 3.8 31 31-61 16-52 (75)
324 PRK06930 positive control sigm 53.3 18 0.00039 31.6 3.7 27 36-62 127-153 (170)
325 TIGR02329 propionate_PrpR prop 53.0 16 0.00034 37.2 3.8 26 36-61 500-525 (526)
326 PF00376 MerR: MerR family reg 53.0 20 0.00043 24.4 3.1 26 41-67 1-26 (38)
327 PRK08359 transcription factor; 52.7 19 0.00041 32.4 3.8 22 38-59 97-118 (176)
328 PF00440 TetR_N: Bacterial reg 52.7 21 0.00046 24.3 3.3 25 35-59 12-36 (47)
329 TIGR02479 FliA_WhiG RNA polyme 52.6 20 0.00044 31.2 4.0 23 39-61 191-213 (224)
330 PHA02591 hypothetical protein; 52.5 17 0.00036 29.6 3.1 24 38-61 58-81 (83)
331 PRK10227 DNA-binding transcrip 52.3 30 0.00064 29.1 4.8 26 40-66 1-26 (135)
332 PF05344 DUF746: Domain of Unk 51.6 18 0.00039 28.2 3.0 25 39-63 13-37 (65)
333 PF05043 Mga: Mga helix-turn-h 51.6 12 0.00025 28.2 2.0 25 39-63 30-54 (87)
334 PRK09492 treR trehalose repres 51.4 13 0.00028 32.8 2.6 37 29-65 5-48 (315)
335 PF09048 Cro: Cro; InterPro: 51.4 17 0.00037 27.9 2.9 32 28-61 3-34 (59)
336 PF01325 Fe_dep_repress: Iron 51.3 18 0.00038 26.6 2.9 26 38-63 21-46 (60)
337 PRK13558 bacterio-opsin activa 51.2 15 0.00033 36.6 3.3 27 36-62 623-653 (665)
338 PRK08583 RNA polymerase sigma 51.1 22 0.00047 31.8 4.0 25 37-61 219-243 (257)
339 PRK10339 DNA-binding transcrip 50.8 13 0.00028 33.2 2.5 23 41-63 3-25 (327)
340 TIGR02607 antidote_HigA addict 50.4 46 0.001 24.0 5.0 43 24-66 14-60 (78)
341 PRK09943 DNA-binding transcrip 50.4 22 0.00047 30.4 3.8 33 30-62 11-43 (185)
342 TIGR02844 spore_III_D sporulat 49.9 24 0.00052 27.9 3.6 30 31-61 12-41 (80)
343 PF14549 P22_Cro: DNA-binding 49.9 29 0.00062 26.1 3.9 28 31-59 2-29 (60)
344 PRK11475 DNA-binding transcrip 49.8 23 0.00049 31.4 3.9 27 39-65 149-179 (207)
345 PRK13698 plasmid-partitioning 49.8 72 0.0016 31.3 7.5 35 33-67 170-204 (323)
346 KOG3917 Beta-1,4-galactosyltra 49.8 10 0.00022 36.5 1.8 14 167-180 198-211 (310)
347 PHA00675 hypothetical protein 49.6 21 0.00046 28.8 3.3 41 23-63 17-63 (78)
348 smart00420 HTH_DEOR helix_turn 49.6 37 0.0008 22.1 4.0 25 39-63 14-38 (53)
349 PRK10082 cell density-dependen 49.4 23 0.00049 31.6 3.8 38 27-65 9-55 (303)
350 PRK15411 rcsA colanic acid cap 49.3 18 0.00039 31.6 3.1 37 29-65 138-182 (207)
351 TIGR00180 parB_part ParB-like 49.3 26 0.00056 30.4 4.1 28 36-63 117-144 (187)
352 TIGR02980 SigBFG RNA polymeras 49.3 24 0.00052 30.6 3.9 24 39-62 194-217 (227)
353 PRK05803 sporulation sigma fac 49.2 19 0.00041 31.7 3.3 23 39-61 195-217 (233)
354 PF02082 Rrf2: Transcriptional 49.0 27 0.00058 26.4 3.7 24 40-63 26-49 (83)
355 CHL00137 rps13 ribosomal prote 48.9 59 0.0013 27.5 6.0 56 47-104 21-85 (122)
356 PRK10014 DNA-binding transcrip 48.9 16 0.00034 32.6 2.7 20 41-60 8-27 (342)
357 PF08535 KorB: KorB domain; I 48.5 18 0.0004 28.0 2.8 29 38-66 2-30 (93)
358 cd08317 Death_ank Death domain 48.1 31 0.00068 26.4 4.0 39 26-64 2-40 (84)
359 TIGR02036 dsdC D-serine deamin 48.0 32 0.00069 30.8 4.6 42 24-65 3-52 (302)
360 PF01381 HTH_3: Helix-turn-hel 47.9 40 0.00086 22.8 4.1 41 26-66 7-51 (55)
361 PRK13869 plasmid-partitioning 47.7 35 0.00076 33.3 5.1 24 39-62 48-71 (405)
362 TIGR02051 MerR Hg(II)-responsi 47.6 77 0.0017 25.9 6.4 30 41-71 1-30 (124)
363 COG2452 Predicted site-specifi 47.6 20 0.00044 33.0 3.3 34 39-73 1-34 (193)
364 PF13730 HTH_36: Helix-turn-he 47.4 23 0.00051 24.3 2.9 23 41-63 27-49 (55)
365 PRK10094 DNA-binding transcrip 47.4 26 0.00056 31.6 3.9 36 29-65 2-46 (308)
366 COG2197 CitB Response regulato 47.3 25 0.00054 31.0 3.7 40 28-67 148-195 (211)
367 PRK08215 sporulation sigma fac 47.0 27 0.00059 31.3 4.0 23 39-61 225-247 (258)
368 PF01978 TrmB: Sugar-specific 46.9 24 0.00053 25.4 3.0 28 36-63 19-46 (68)
369 PRK14987 gluconate operon tran 46.8 14 0.00031 32.9 2.1 21 41-61 7-27 (331)
370 COG1802 GntR Transcriptional r 46.7 64 0.0014 28.2 6.2 36 39-74 39-78 (230)
371 TIGR02835 spore_sigmaE RNA pol 46.6 22 0.00048 31.4 3.3 22 39-60 198-219 (234)
372 PF13443 HTH_26: Cro/C1-type H 46.6 39 0.00084 23.6 4.0 40 27-66 9-53 (63)
373 cd04783 HTH_MerR1 Helix-Turn-H 46.4 52 0.0011 26.8 5.2 27 40-67 1-27 (126)
374 PRK04984 fatty acid metabolism 46.2 21 0.00045 31.2 3.1 25 39-63 30-55 (239)
375 smart00550 Zalpha Z-DNA-bindin 46.2 37 0.00081 25.2 4.0 24 40-63 23-46 (68)
376 TIGR00373 conserved hypothetic 45.9 1.3E+02 0.0029 25.9 7.9 36 37-74 26-64 (158)
377 TIGR02850 spore_sigG RNA polym 45.4 30 0.00065 31.0 4.0 23 39-61 222-244 (254)
378 PRK10401 DNA-binding transcrip 45.4 19 0.00041 32.4 2.8 20 41-60 3-22 (346)
379 TIGR01481 ccpA catabolite cont 45.4 19 0.00041 31.9 2.7 22 40-61 2-23 (329)
380 PRK09645 RNA polymerase sigma 45.3 23 0.00051 29.0 3.1 39 28-66 134-172 (173)
381 TIGR02394 rpoS_proteo RNA poly 45.1 19 0.00041 32.9 2.7 23 39-61 242-264 (285)
382 PRK13348 chromosome replicatio 45.1 29 0.00062 30.5 3.7 27 39-65 16-46 (294)
383 cd04784 HTH_CadR-PbrR Helix-Tu 44.8 58 0.0013 26.5 5.3 31 40-71 1-31 (127)
384 TIGR00270 conserved hypothetic 44.6 31 0.00068 30.0 3.9 26 36-61 79-104 (154)
385 PRK14997 LysR family transcrip 44.5 31 0.00067 30.4 3.9 27 39-65 16-46 (301)
386 COG4367 Uncharacterized protei 44.2 28 0.00061 29.0 3.3 35 26-60 7-44 (97)
387 PRK11014 transcriptional repre 44.1 23 0.0005 29.2 2.9 32 40-71 26-61 (141)
388 TIGR00721 tfx DNA-binding prot 44.0 26 0.00057 30.2 3.3 26 37-62 19-44 (137)
389 COG0789 SoxR Predicted transcr 43.9 20 0.00044 28.2 2.4 26 40-65 1-26 (124)
390 KOG4721 Serine/threonine prote 43.4 64 0.0014 35.1 6.5 83 77-169 439-536 (904)
391 PF13744 HTH_37: Helix-turn-he 43.4 53 0.0012 24.9 4.5 41 25-65 28-73 (80)
392 PRK10727 DNA-binding transcrip 43.3 21 0.00045 32.1 2.7 21 41-61 3-23 (343)
393 PRK09954 putative kinase; Prov 43.2 33 0.00072 31.9 4.1 32 32-63 10-41 (362)
394 PRK06424 transcription factor; 43.1 32 0.0007 29.7 3.7 29 34-62 92-120 (144)
395 TIGR01610 phage_O_Nterm phage 43.0 39 0.00085 26.5 3.9 28 36-63 44-71 (95)
396 COG4565 CitB Response regulato 42.9 29 0.00064 32.6 3.6 58 16-73 145-219 (224)
397 PRK09483 response regulator; P 42.9 28 0.00061 28.3 3.2 28 38-65 162-193 (217)
398 TIGR03298 argP transcriptional 42.6 34 0.00075 30.0 3.9 34 39-74 15-55 (292)
399 PF09035 Tn916-Xis: Excisionas 42.6 22 0.00047 27.5 2.3 29 36-64 10-38 (67)
400 PRK10225 DNA-binding transcrip 42.6 25 0.00054 31.2 3.0 33 39-71 32-69 (257)
401 TIGR02417 fruct_sucro_rep D-fr 42.4 21 0.00047 31.6 2.6 22 41-62 1-22 (327)
402 PF12840 HTH_20: Helix-turn-he 42.0 44 0.00096 23.7 3.7 28 36-63 21-48 (61)
403 cd04769 HTH_MerR2 Helix-Turn-H 41.9 38 0.00083 27.2 3.7 27 40-67 1-27 (116)
404 PF06163 DUF977: Bacterial pro 41.8 39 0.00085 29.4 4.0 32 32-63 19-50 (127)
405 TIGR02812 fadR_gamma fatty aci 41.8 26 0.00057 30.5 3.0 33 39-71 29-66 (235)
406 PRK11074 putative DNA-binding 41.8 35 0.00075 30.4 3.8 27 39-65 16-46 (300)
407 PF08965 DUF1870: Domain of un 41.6 25 0.00054 30.1 2.7 31 28-58 3-35 (118)
408 PRK11886 bifunctional biotin-- 41.5 35 0.00076 31.7 3.9 36 33-68 12-47 (319)
409 PRK07670 RNA polymerase sigma 41.5 37 0.00079 30.3 3.9 24 39-62 217-240 (251)
410 COG2522 Predicted transcriptio 40.9 66 0.0014 27.4 5.1 31 33-64 17-47 (119)
411 COG1609 PurR Transcriptional r 40.9 42 0.00091 31.4 4.4 24 41-64 2-25 (333)
412 TIGR00122 birA_repr_reg BirA b 40.9 41 0.00089 24.4 3.5 31 40-70 14-44 (69)
413 PRK12679 cbl transcriptional r 40.8 29 0.00062 31.4 3.2 26 40-65 17-46 (316)
414 PRK10411 DNA-binding transcrip 40.8 39 0.00084 30.7 4.0 41 31-71 10-50 (240)
415 PRK10402 DNA-binding transcrip 40.6 39 0.00084 29.3 3.8 47 38-85 168-217 (226)
416 COG2390 DeoR Transcriptional r 40.6 30 0.00065 33.5 3.5 28 39-66 26-56 (321)
417 PRK13719 conjugal transfer tra 40.5 36 0.00079 31.6 3.8 29 38-66 157-189 (217)
418 COG1309 AcrR Transcriptional r 40.2 22 0.00047 26.8 2.0 25 36-60 29-53 (201)
419 PRK07500 rpoH2 RNA polymerase 40.2 31 0.00068 32.0 3.4 23 39-61 245-267 (289)
420 PRK13509 transcriptional repre 40.1 40 0.00086 30.7 4.0 33 31-63 11-43 (251)
421 PRK09391 fixK transcriptional 40.0 34 0.00074 29.9 3.4 37 38-74 178-218 (230)
422 PF02037 SAP: SAP domain; Int 40.0 22 0.00048 23.6 1.7 16 51-66 4-19 (35)
423 PRK09210 RNA polymerase sigma 39.9 38 0.00081 32.7 4.0 29 34-62 314-348 (367)
424 PRK07408 RNA polymerase sigma 39.6 40 0.00087 30.5 3.9 23 39-61 219-241 (256)
425 PRK15092 DNA-binding transcrip 39.5 37 0.0008 31.0 3.7 41 24-65 6-55 (310)
426 PF00416 Ribosomal_S13: Riboso 39.4 1.3E+02 0.0028 24.4 6.4 37 47-85 19-57 (107)
427 PRK11414 colanic acid/biofilm 39.4 27 0.00059 30.3 2.7 35 38-72 33-71 (221)
428 PRK05911 RNA polymerase sigma 39.1 42 0.0009 30.5 3.9 24 39-62 221-244 (257)
429 PHA01976 helix-turn-helix prot 39.0 85 0.0018 22.1 4.8 43 24-66 11-57 (67)
430 PRK10421 DNA-binding transcrip 38.9 31 0.00067 30.6 3.0 35 39-73 25-64 (253)
431 CHL00180 rbcR LysR transcripti 38.8 38 0.00082 30.2 3.6 37 28-65 4-49 (305)
432 TIGR00637 ModE_repress ModE mo 38.7 34 0.00074 27.4 3.0 25 39-63 16-40 (99)
433 PRK11523 DNA-binding transcrip 38.6 32 0.00069 30.6 3.1 36 39-74 31-71 (253)
434 PRK11233 nitrogen assimilation 38.4 42 0.00092 30.0 3.8 27 39-65 15-45 (305)
435 PRK15002 redox-sensitivie tran 38.0 32 0.00069 29.9 2.9 25 40-65 12-36 (154)
436 TIGR02997 Sig70-cyanoRpoD RNA 38.0 44 0.00096 30.9 4.0 24 39-62 269-292 (298)
437 PRK06288 RNA polymerase sigma 37.9 45 0.00097 30.1 4.0 23 39-61 228-250 (268)
438 TIGR02944 suf_reg_Xantho FeS a 37.8 34 0.00074 27.5 2.9 24 40-63 26-49 (130)
439 PF10075 PCI_Csn8: COP9 signal 37.6 31 0.00068 28.4 2.7 29 36-64 94-122 (143)
440 PRK10086 DNA-binding transcrip 37.1 51 0.0011 29.6 4.2 40 26-65 11-58 (311)
441 PRK10434 srlR DNA-bindng trans 37.0 41 0.00089 30.7 3.6 33 31-63 11-43 (256)
442 PRK10046 dpiA two-component re 36.9 35 0.00076 29.2 3.0 33 29-61 162-199 (225)
443 PF06870 RNA_pol_I_A49: A49-li 36.9 27 0.00058 33.3 2.5 30 36-65 316-345 (385)
444 cd04790 HTH_Cfa-like_unk Helix 36.9 86 0.0019 27.3 5.4 26 40-66 2-27 (172)
445 PF08784 RPA_C: Replication pr 36.4 32 0.0007 26.8 2.5 26 38-63 64-89 (102)
446 PF04552 Sigma54_DBD: Sigma-54 36.3 12 0.00026 32.8 0.0 69 39-107 49-137 (160)
447 PRK05657 RNA polymerase sigma 35.9 34 0.00073 32.5 2.9 23 39-61 282-304 (325)
448 COG3604 FhlA Transcriptional r 35.8 37 0.0008 35.6 3.4 28 39-66 519-546 (550)
449 PRK12682 transcriptional regul 35.8 51 0.0011 29.4 3.9 27 39-65 16-46 (309)
450 PF02002 TFIIE_alpha: TFIIE al 35.7 48 0.001 26.0 3.3 33 31-63 19-51 (105)
451 PRK05572 sporulation sigma fac 35.1 53 0.0011 29.4 3.9 23 39-61 218-240 (252)
452 PF12116 SpoIIID: Stage III sp 35.0 33 0.00071 27.9 2.3 23 39-61 19-41 (82)
453 COG1654 BirA Biotin operon rep 35.0 56 0.0012 25.8 3.6 31 33-63 13-43 (79)
454 PF08299 Bac_DnaA_C: Bacterial 34.9 57 0.0012 24.5 3.5 35 28-62 34-69 (70)
455 TIGR02366 DHAK_reg probable di 34.8 29 0.00063 28.4 2.1 23 36-58 20-42 (176)
456 COG1191 FliA DNA-directed RNA 34.8 38 0.00082 31.8 3.0 24 39-62 212-235 (247)
457 COG2973 TrpR Trp operon repres 34.8 26 0.00056 29.6 1.8 21 39-59 60-80 (103)
458 PRK03837 transcriptional regul 34.3 42 0.00091 29.2 3.1 25 39-63 36-61 (241)
459 PTZ00134 40S ribosomal protein 34.2 1.1E+02 0.0025 26.9 5.7 40 46-87 33-74 (154)
460 TIGR03697 NtcA_cyano global ni 34.1 39 0.00086 27.7 2.8 37 38-74 142-181 (193)
461 TIGR02941 Sigma_B RNA polymera 34.1 53 0.0012 29.2 3.8 24 38-61 220-243 (255)
462 PRK09508 leuO leucine transcri 33.7 60 0.0013 29.1 4.1 39 27-65 20-66 (314)
463 TIGR02787 codY_Gpos GTP-sensin 33.4 49 0.0011 31.6 3.6 26 38-63 197-222 (251)
464 COG1321 TroR Mn-dependent tran 33.3 1.4E+02 0.0031 25.8 6.2 40 36-75 21-64 (154)
465 PRK11062 nhaR transcriptional 33.1 63 0.0014 28.7 4.1 37 29-65 4-48 (296)
466 PRK09801 transcriptional activ 33.0 50 0.0011 29.9 3.5 27 39-65 20-50 (310)
467 cd08803 Death_ank3 Death domai 32.6 59 0.0013 25.7 3.4 37 27-63 3-39 (84)
468 PRK10837 putative DNA-binding 32.4 59 0.0013 28.2 3.7 27 39-65 17-47 (290)
469 cd08315 Death_TRAILR_DR4_DR5 D 32.4 69 0.0015 25.7 3.8 34 31-64 3-44 (96)
470 TIGR02885 spore_sigF RNA polym 32.4 60 0.0013 28.3 3.7 22 39-60 199-220 (231)
471 PRK15090 DNA-binding transcrip 32.3 60 0.0013 29.1 3.8 26 39-64 28-53 (257)
472 PRK13918 CRP/FNR family transc 32.3 47 0.001 27.6 3.0 46 38-84 148-196 (202)
473 PF08822 DUF1804: Protein of u 32.2 55 0.0012 29.4 3.5 40 30-70 7-52 (165)
474 PRK11139 DNA-binding transcrip 32.2 60 0.0013 28.7 3.7 37 29-66 6-51 (297)
475 PF05732 RepL: Firmicute plasm 31.8 38 0.00082 29.6 2.4 29 36-64 72-100 (165)
476 PF09012 FeoC: FeoC like trans 31.4 47 0.001 24.4 2.5 24 39-62 14-37 (69)
477 PRK09935 transcriptional regul 31.3 78 0.0017 25.3 4.0 27 39-65 164-194 (210)
478 PRK12681 cysB transcriptional 31.2 61 0.0013 29.7 3.7 26 40-65 17-46 (324)
479 PRK09464 pdhR transcriptional 30.9 50 0.0011 29.1 3.1 33 39-71 33-70 (254)
480 PRK04053 rps13p 30S ribosomal 30.8 1.8E+02 0.0038 25.6 6.3 38 47-86 29-68 (149)
481 PF00325 Crp: Bacterial regula 30.8 63 0.0014 21.8 2.8 24 40-63 3-26 (32)
482 TIGR02424 TF_pcaQ pca operon t 30.6 71 0.0015 28.1 3.9 27 39-65 17-47 (300)
483 COG2901 Fis Factor for inversi 30.4 87 0.0019 26.2 4.1 34 32-65 64-97 (98)
484 PRK07122 RNA polymerase sigma 30.4 68 0.0015 29.4 3.9 23 39-61 231-253 (264)
485 PRK00441 argR arginine repress 30.3 74 0.0016 27.5 3.9 39 31-69 10-53 (149)
486 TIGR02337 HpaR homoprotocatech 30.2 81 0.0017 24.8 3.8 29 36-64 39-67 (118)
487 PF12833 HTH_18: Helix-turn-he 30.1 94 0.002 22.5 3.9 35 31-65 37-73 (81)
488 PRK09990 DNA-binding transcrip 30.0 54 0.0012 28.9 3.1 33 39-71 30-67 (251)
489 PF13413 HTH_25: Helix-turn-he 30.0 74 0.0016 23.5 3.4 29 32-60 3-31 (62)
490 PRK12427 flagellar biosynthesi 29.8 69 0.0015 28.6 3.8 21 39-59 199-219 (231)
491 COG2771 CsgD DNA-binding HTH d 29.7 81 0.0018 21.5 3.4 29 37-65 17-49 (65)
492 PRK00215 LexA repressor; Valid 29.7 77 0.0017 27.4 3.9 30 39-68 23-53 (205)
493 TIGR02702 SufR_cyano iron-sulf 29.5 81 0.0017 27.5 4.1 30 34-63 10-39 (203)
494 PRK04140 hypothetical protein; 29.3 68 0.0015 31.1 3.8 32 30-61 130-161 (317)
495 cd07377 WHTH_GntR Winged helix 29.2 73 0.0016 21.6 3.0 22 42-63 28-49 (66)
496 smart00529 HTH_DTXR Helix-turn 29.1 58 0.0013 24.4 2.7 22 42-63 2-23 (96)
497 PRK09958 DNA-binding transcrip 29.0 86 0.0019 25.2 3.9 28 39-66 158-189 (204)
498 PRK08154 anaerobic benzoate ca 28.9 75 0.0016 29.7 4.0 33 30-62 32-64 (309)
499 PF07860 CCD: WisP family C-Te 28.8 20 0.00044 30.9 0.2 12 63-75 53-64 (141)
500 COG4977 Transcriptional regula 28.8 1.6E+02 0.0035 28.8 6.3 57 39-107 236-298 (328)
No 1
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=99.93 E-value=1.1e-26 Score=168.92 Aligned_cols=51 Identities=55% Similarity=1.013 Sum_probs=49.4
Q ss_pred CCCcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhhh
Q 023462 26 TKSLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLSG 76 (282)
Q Consensus 26 ~~~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkSL 76 (282)
+.+||++||++|||||++|||++||||.|+|||+||++||.||||||++|+
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 578999999999999999999999999999999999999999999999986
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=96.15 E-value=0.0057 Score=46.21 Aligned_cols=37 Identities=19% Similarity=0.416 Sum_probs=28.8
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCC
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWP 69 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWP 69 (282)
.......+++.|+|+.+|||.+++=|.|+++|...|+
T Consensus 28 ~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~ 64 (77)
T PF01418_consen 28 NPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFK 64 (77)
T ss_dssp -HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHH
T ss_pred CHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHH
Confidence 3445568999999999999999999999999987654
No 3
>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=95.30 E-value=0.024 Score=39.12 Aligned_cols=33 Identities=15% Similarity=0.446 Sum_probs=24.5
Q ss_pred CHHHHHhhc--CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 30 SFDDISKYF--SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 30 TledL~~yF--~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.++++...+ ++|+.++|+.+|||.+||.|++++
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 356666555 699999999999999999999864
No 4
>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=95.10 E-value=0.03 Score=36.79 Aligned_cols=27 Identities=26% Similarity=0.439 Sum_probs=24.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|.+.|||+.||||.++|.+.|++-.|+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 678999999999999999999987665
No 5
>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=94.97 E-value=0.068 Score=38.61 Aligned_cols=27 Identities=15% Similarity=0.229 Sum_probs=25.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+||+.++|...+++.++.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~ 27 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLY 27 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 578999999999999999999998886
No 6
>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=94.68 E-value=0.1 Score=37.90 Aligned_cols=27 Identities=26% Similarity=0.286 Sum_probs=24.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+||+.++|+..|++.|+.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~ 27 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLL 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence 478999999999999999999998875
No 7
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=94.57 E-value=0.058 Score=38.54 Aligned_cols=27 Identities=26% Similarity=0.320 Sum_probs=24.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+||+.++|.+.+++.|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~~ 27 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGLP 27 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCCC
Confidence 478999999999999999999888874
No 8
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=94.27 E-value=0.091 Score=35.85 Aligned_cols=28 Identities=21% Similarity=0.190 Sum_probs=23.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..++-.+.+||+.|||+.++|.+..++|
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 5668889999999999999999998875
No 9
>PF12728 HTH_17: Helix-turn-helix domain
Probab=94.10 E-value=0.066 Score=36.83 Aligned_cols=45 Identities=20% Similarity=0.343 Sum_probs=32.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhh-hh-cHHHHHHHHH
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLS-GK-SIEDIKKYAA 87 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkS-Lk-sI~~l~e~a~ 87 (282)
|...|||+.||||.++|.+.|++-.|+.- ++-. .. .-++|.++.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~---~~g~~~~~~~~~l~~~~~ 48 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF---KIGRKWRIPKSDLDRWLE 48 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE---EeCCEEEEeHHHHHHHHH
Confidence 67899999999999999999999988533 3321 11 4556665544
No 10
>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=94.08 E-value=0.074 Score=34.52 Aligned_cols=27 Identities=33% Similarity=0.503 Sum_probs=24.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|.+.|||+.|||+.++|.+.+++-.++
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 578999999999999999999986664
No 11
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=93.77 E-value=0.24 Score=35.43 Aligned_cols=26 Identities=31% Similarity=0.385 Sum_probs=23.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|++.|+|+.+||+..+|+..+++.-|
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 47899999999999999999988775
No 12
>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=93.74 E-value=0.094 Score=35.05 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=26.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchh
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKF 73 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKl 73 (282)
|++.|+|+.|||+..+|++.+++--|+ |.|.-
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~--~~~~~ 32 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS--PARTE 32 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC--CCcCC
Confidence 578999999999999999887666554 76654
No 13
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=93.69 E-value=0.058 Score=47.92 Aligned_cols=34 Identities=15% Similarity=0.318 Sum_probs=31.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWP 69 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWP 69 (282)
....+++.+.|++.|||.+++=|.||++|..-++
T Consensus 31 ~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~ 64 (284)
T PRK11302 31 TAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFP 64 (284)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHH
Confidence 4458999999999999999999999999998776
No 14
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=93.56 E-value=0.45 Score=35.82 Aligned_cols=75 Identities=25% Similarity=0.451 Sum_probs=52.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHH-HcCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCccCCc--
Q 023462 40 LPLSDAANHLGVCVSVLKKICR-DNGLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQPLSN-- 111 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR-~lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~~~n~-- 111 (282)
+.+.+.|+.+|+|.+.|.|+++ ..|+. |+ +.+. ..+.++++.++. |..|+..-||...+.
T Consensus 37 ~~l~~la~~~g~S~~~l~r~f~~~~g~s--~~---------~~~~-~~Rl~~A~~lL~~~~~~i~~iA~~~Gf~~~s~F~ 104 (127)
T COG2207 37 LTLEDLARRLGMSRRTLSRLFKKETGTS--PS---------QYLR-QLRLEEARRLLRSTDLSITEIALRLGYSSPSHFS 104 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCC--HH---------HHHH-HHHHHHHHHHHHcCCCCHHHHHHHhCcCCHHHHH
Confidence 6799999999999999999999 67874 21 1122 234556666664 888888888885432
Q ss_pred -ccccccCCCCCCccc
Q 023462 112 -ETSKLHGVTSPPNLQ 126 (282)
Q Consensus 112 -~~sk~qgv~~~~~~~ 126 (282)
.--+..|++|.+...
T Consensus 105 ~~Fk~~~g~tP~~~r~ 120 (127)
T COG2207 105 RAFKRLFGVTPSEYRK 120 (127)
T ss_pred HHHHHHhCCChHHHHH
Confidence 344667888765443
No 15
>PRK15482 transcriptional regulator MurR; Provisional
Probab=93.56 E-value=0.061 Score=48.51 Aligned_cols=39 Identities=21% Similarity=0.297 Sum_probs=33.4
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcch
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRK 72 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRK 72 (282)
......+++.|.|++.|||.+++=|.||++|..-|+-=|
T Consensus 29 ~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk 67 (285)
T PRK15482 29 VSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELR 67 (285)
T ss_pred HHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHH
Confidence 335568999999999999999999999999998886433
No 16
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=93.17 E-value=0.16 Score=40.77 Aligned_cols=31 Identities=26% Similarity=0.342 Sum_probs=27.5
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++-.+.+||+.|||+.++|.|..+++||.
T Consensus 65 ~~~~gn~s~AAr~LGIsRsTL~rKLkr~gi~ 95 (95)
T PRK00430 65 QYTRGNQTRAALMLGINRGTLRKKLKKYGMN 95 (95)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4456779999999999999999999999983
No 17
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=92.60 E-value=0.16 Score=34.55 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=19.1
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++++.++|+.||||.+|+.+..+++
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 8999999999999999999997764
No 18
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=92.54 E-value=0.18 Score=41.82 Aligned_cols=38 Identities=24% Similarity=0.451 Sum_probs=32.4
Q ss_pred CCCCcCHHHHH-----hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 25 STKSLSFDDIS-----KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 25 ~~~~iTledL~-----~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
....|++|++. .|.+|++.|||..+|||.+|+-|+...
T Consensus 38 ~~V~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ 80 (106)
T PF02001_consen 38 EPVVLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILES 80 (106)
T ss_pred ceEEeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHH
Confidence 45678888876 788999999999999999999887653
No 19
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=92.51 E-value=0.13 Score=35.64 Aligned_cols=26 Identities=19% Similarity=0.319 Sum_probs=19.2
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
-++++.++|+.||++.+|+.+.|+++
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relkR~ 44 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELKRN 44 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHhcC
Confidence 48999999999999999999999874
No 20
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=92.49 E-value=0.75 Score=35.65 Aligned_cols=34 Identities=18% Similarity=0.139 Sum_probs=27.9
Q ss_pred HHHhhcC--CcHHHHHHHhCCChHHHHHHHHHc-CCC
Q 023462 33 DISKYFS--LPLSDAANHLGVCVSVLKKICRDN-GLD 66 (282)
Q Consensus 33 dL~~yF~--lPi~EAAr~LGVs~T~LKR~CR~l-GI~ 66 (282)
-|...++ +++.++|+.+|+|..+|.|+|++. |+.
T Consensus 13 ~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 13 WIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred HHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3444444 789999999999999999999997 763
No 21
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=92.34 E-value=0.11 Score=46.32 Aligned_cols=36 Identities=25% Similarity=0.266 Sum_probs=31.5
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
..-.+++.|.|++.|||.+++=|.||++|...|+-=
T Consensus 27 ~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~ef 62 (278)
T PRK11557 27 TARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPAL 62 (278)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHH
Confidence 444799999999999999999999999999877543
No 22
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=92.17 E-value=0.098 Score=47.91 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=33.6
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhh
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFL 74 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlk 74 (282)
..-++++.|.|+..|||.+++=|.||++|..-||==|+.
T Consensus 33 ~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~ 71 (281)
T COG1737 33 EVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLA 71 (281)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHH
Confidence 344789999999999999999999999999988755544
No 23
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=92.11 E-value=0.13 Score=46.43 Aligned_cols=35 Identities=20% Similarity=0.278 Sum_probs=30.9
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPY 70 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPy 70 (282)
....+++.+.|++.|||.+++=|.||++|..-|+-
T Consensus 43 ~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~e 77 (292)
T PRK11337 43 LSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRN 77 (292)
T ss_pred HHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHH
Confidence 34478999999999999999999999999987753
No 24
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=91.91 E-value=0.22 Score=46.95 Aligned_cols=31 Identities=19% Similarity=0.163 Sum_probs=27.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++....+||+.||||.+||.|..++|||.
T Consensus 427 ~~~~gn~~~aA~~LGisr~tL~rkl~~~~i~ 457 (457)
T PRK11361 427 EQQEGNRTRTALMLGISRRALMYKLQEYGID 457 (457)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence 3457789999999999999999999999983
No 25
>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=91.46 E-value=0.42 Score=38.09 Aligned_cols=27 Identities=19% Similarity=0.153 Sum_probs=24.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+||+.++|...+++.|+.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gli 27 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQL 27 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence 478999999999999999999998864
No 26
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=91.42 E-value=0.21 Score=34.24 Aligned_cols=34 Identities=21% Similarity=0.190 Sum_probs=27.4
Q ss_pred CHHHHHhhcCC-cHHHHHHHhCCChHHHHHHHHHc
Q 023462 30 SFDDISKYFSL-PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 30 TledL~~yF~l-Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
...-+....+. +++++|+.+|||.++++|+..++
T Consensus 17 ~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 17 EQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 33445566667 99999999999999999998764
No 27
>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=91.26 E-value=0.26 Score=36.19 Aligned_cols=28 Identities=32% Similarity=0.584 Sum_probs=24.5
Q ss_pred HhhcCCc----HHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLP----LSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lP----i~EAAr~LGVs~T~LKR~CR~ 62 (282)
..||+.| +.|.|++||||.+++-..-|+
T Consensus 15 ~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 15 LGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3799988 899999999999998877765
No 28
>PRK15115 response regulator GlrR; Provisional
Probab=91.19 E-value=0.29 Score=46.14 Aligned_cols=31 Identities=19% Similarity=0.143 Sum_probs=28.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++....+||+.||||.+||.|..++|||.
T Consensus 408 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~~~ 438 (444)
T PRK15115 408 QITKGNVTHAARMAGRNRTEFYKLLSRHELD 438 (444)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 3457789999999999999999999999996
No 29
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=91.15 E-value=0.3 Score=45.65 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=27.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++.-..+||+.||||.++|.|..++|||.
T Consensus 296 ~~~~gn~~~aA~~LGIsR~tLyrklk~~gi~ 326 (326)
T PRK11608 296 QQAKFNQKRAAELLGLTYHQLRALLKKHQIL 326 (326)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 3457789999999999999999999999983
No 30
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=91.10 E-value=1.9 Score=35.05 Aligned_cols=83 Identities=13% Similarity=0.205 Sum_probs=49.3
Q ss_pred HHhhc--CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHH-----HHHHHHHhhcC
Q 023462 34 ISKYF--SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKEL-----AELSKIARKSG 105 (282)
Q Consensus 34 L~~yF--~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~l-----lel~k~~~~~~ 105 (282)
|..+| .+++.++|+.+|||+.+|.|+|++. |+. | ..+ |+ ..+.+++..+ +.|..|+.+-|
T Consensus 18 I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s--~-~~~--------l~-~~Rl~~A~~~L~~t~~~i~eIA~~~G 85 (127)
T PRK11511 18 IEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHS--L-GQY--------IR-SRKMTEIAQKLKESNEPILYLAERYG 85 (127)
T ss_pred HHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC--H-HHH--------HH-HHHHHHHHHHHHcCCCCHHHHHHHhC
Confidence 34444 4789999999999999999999988 873 1 111 11 1122222222 24677778888
Q ss_pred CccCCcc---cccccCCCCCCccccc
Q 023462 106 FQPLSNE---TSKLHGVTSPPNLQQQ 128 (282)
Q Consensus 106 ~~~~n~~---~sk~qgv~~~~~~~Qq 128 (282)
|.-.+.- =-+.-|++|-+-..+.
T Consensus 86 f~s~s~F~r~Fkk~~G~tP~~yR~~~ 111 (127)
T PRK11511 86 FESQQTLTRTFKNYFDVPPHKYRMTN 111 (127)
T ss_pred CCCHHHHHHHHHHHHCcCHHHHHHhc
Confidence 7744321 1245566655544333
No 31
>PRK01905 DNA-binding protein Fis; Provisional
Probab=90.78 E-value=0.47 Score=36.25 Aligned_cols=29 Identities=31% Similarity=0.234 Sum_probs=26.0
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
++-.+.+||+.|||+.++|.++-+++||.
T Consensus 49 ~~gn~s~aAr~LGIsrstL~rklkk~gi~ 77 (77)
T PRK01905 49 AGGNQSLAAEYLGINRNTLRKKLQQHGLL 77 (77)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence 45679999999999999999999999973
No 32
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=89.82 E-value=0.37 Score=41.63 Aligned_cols=28 Identities=29% Similarity=0.447 Sum_probs=25.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
++++.++|+.||||.+|+.|++...|+.
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~~~~~ 199 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKTRGLR 199 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhcccC
Confidence 5799999999999999999999998873
No 33
>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=89.79 E-value=0.52 Score=38.33 Aligned_cols=39 Identities=21% Similarity=0.327 Sum_probs=33.0
Q ss_pred CcCHHHHH----hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 28 SLSFDDIS----KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 28 ~iTledL~----~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
.|..+.|. .+=++++.|.|+.||||.++|-+..+++||.
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 44555555 5568999999999999999999999999985
No 34
>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=89.78 E-value=0.59 Score=31.97 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=25.6
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
..++.-.++++.|.|+.+||+.+++.++++-
T Consensus 2 k~~r~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 2 KELRKEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 4567778999999999999999999999876
No 35
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=89.72 E-value=0.47 Score=46.91 Aligned_cols=31 Identities=19% Similarity=0.184 Sum_probs=28.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++-.+.+||+.|||+.+||.|+.++|||.
T Consensus 478 ~~~~gn~~~aA~~LGisr~tL~rklk~~gi~ 508 (509)
T PRK05022 478 AQHQGNWAAAARALELDRANLHRLAKRLGLK 508 (509)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 4457789999999999999999999999995
No 36
>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=89.59 E-value=0.51 Score=44.58 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=27.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
..++-...+||+.||||.+||.|+.++|||
T Consensus 415 ~~~~gn~~~aA~~Lgisr~tl~rkl~~~~i 444 (445)
T TIGR02915 415 ARVDGNIARAAELLGITRPTLYDLMKKHGI 444 (445)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 445778999999999999999999999998
No 37
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=89.54 E-value=0.48 Score=45.14 Aligned_cols=31 Identities=19% Similarity=0.213 Sum_probs=27.9
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++....+||+.||||.+||.|..++|||.
T Consensus 439 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~i~ 469 (469)
T PRK10923 439 RHTQGHKQEAARLLGWGRNTLTRKLKELGME 469 (469)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4468889999999999999999999999983
No 38
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=89.46 E-value=0.51 Score=47.07 Aligned_cols=26 Identities=27% Similarity=0.417 Sum_probs=24.6
Q ss_pred cHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 41 PLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
...+||+.||||.|+|.|..|+|||.
T Consensus 488 ~~~~aA~~LGisr~tL~rkl~~~gi~ 513 (520)
T PRK10820 488 STRKLAKRLGVSHTAIANKLREYGLS 513 (520)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 78899999999999999999999994
No 39
>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=89.41 E-value=0.6 Score=31.45 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=28.2
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+..++...++.+.++|+.+||+.+++.++.+-
T Consensus 7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 7 VRARRKALGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 56778888999999999999999999999753
No 40
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=89.41 E-value=2.3 Score=38.97 Aligned_cols=77 Identities=12% Similarity=0.218 Sum_probs=48.3
Q ss_pred HHhhc--CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcC
Q 023462 34 ISKYF--SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSG 105 (282)
Q Consensus 34 L~~yF--~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~ 105 (282)
|..++ .+++.++|+.+|||..+|.|+|++. |+. |.+-+ ...+-++++.++. +.+|+.+-|
T Consensus 227 i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s--~~~~~----------~~~Rl~~A~~lL~~~~~~i~~IA~~~G 294 (322)
T PRK09393 227 MRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMT--PAEWL----------LRERLARARDLLESSALSIDQIAERAG 294 (322)
T ss_pred HHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC--HHHHH----------HHHHHHHHHHHHHcCCCCHHHHHHHhC
Confidence 44444 4789999999999999999999986 874 22111 1233444444443 677778888
Q ss_pred CccCCcc---cccccCCCCC
Q 023462 106 FQPLSNE---TSKLHGVTSP 122 (282)
Q Consensus 106 ~~~~n~~---~sk~qgv~~~ 122 (282)
|.-.+.- --+..|++|-
T Consensus 295 f~~~s~F~r~Fk~~~G~tP~ 314 (322)
T PRK09393 295 FGSEESLRHHFRRRAATSPA 314 (322)
T ss_pred CCCHHHHHHHHHHHHCcCHH
Confidence 7654331 1234456543
No 41
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=89.06 E-value=0.65 Score=41.15 Aligned_cols=27 Identities=19% Similarity=0.268 Sum_probs=25.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|.+.|+|+.+|||..||.+.+++.+|+
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~ 27 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLP 27 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 578999999999999999999999985
No 42
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=89.02 E-value=0.52 Score=31.46 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc-CC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN-GL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l-GI 65 (282)
.+++.++|..+|+|...|.|++++. |+
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 5789999999999999999999987 76
No 43
>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=89.02 E-value=1 Score=34.82 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=25.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcch
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYRK 72 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRK 72 (282)
+++.|+|+.+||+..+|+...++ |+.. |-|.
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~-p~r~ 32 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GLIK-SIRS 32 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCcc
Confidence 68999999999999999998887 5544 6543
No 44
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=88.85 E-value=1.9 Score=30.60 Aligned_cols=25 Identities=32% Similarity=0.440 Sum_probs=21.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|++.|+|+.+||+..+|.+.++ .|+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~-~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER-IGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 5689999999999999998887 554
No 45
>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=88.66 E-value=0.56 Score=37.11 Aligned_cols=30 Identities=30% Similarity=0.372 Sum_probs=26.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
|++.|+|+.+||+..+|+..++. |+.. |-|
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~-p~r 30 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLVS-PER 30 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCc
Confidence 57899999999999999999985 8766 755
No 46
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=88.56 E-value=0.72 Score=38.70 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=21.7
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
++-+.+++.+|+|+.|||+..+++.+
T Consensus 142 l~~~~~~s~~eIA~~lgis~~tV~~~ 167 (189)
T PRK12515 142 LVYYHEKSVEEVGEIVGIPESTVKTR 167 (189)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 34557999999999999999988655
No 47
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=88.54 E-value=0.4 Score=49.93 Aligned_cols=30 Identities=27% Similarity=0.396 Sum_probs=27.1
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
-.--+.+||+.|||+.|||.|+-|+|||.+
T Consensus 577 ~~~~is~aa~~lgi~R~T~yrklk~~gi~~ 606 (606)
T COG3284 577 TNGNISEAARLLGISRSTLYRKLKRHGISK 606 (606)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhCCCC
Confidence 366799999999999999999999999964
No 48
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=88.47 E-value=0.51 Score=31.12 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=21.5
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+++..++|+.||||..+++++.++
T Consensus 17 ~g~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 17 EGLTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3789999999999999998877554
No 49
>PRK13502 transcriptional activator RhaR; Provisional
Probab=88.43 E-value=2.4 Score=37.49 Aligned_cols=74 Identities=16% Similarity=0.221 Sum_probs=50.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH-cCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCccCCc-
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD-NGLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQPLSN- 111 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~-lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~~~n~- 111 (282)
.+.+.++|..+|||++.|.|+|++ .|+. | .+.|. ..+-+++++||. |.+|+.+-||.-.+.
T Consensus 192 ~~~~~~lA~~~~iS~~~L~r~fk~~~G~t--~---------~~yi~-~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F 259 (282)
T PRK13502 192 PFALDAFCQQEQCSERVLRQQFRAQTGMT--I---------NQYLR-QVRICHAQYLLQHSPLMISEISMQCGFEDSNYF 259 (282)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC--H---------HHHHH-HHHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHH
Confidence 456889999999999999999998 6874 1 12222 345667777765 788899988885433
Q ss_pred --ccccccCCCCCCc
Q 023462 112 --ETSKLHGVTSPPN 124 (282)
Q Consensus 112 --~~sk~qgv~~~~~ 124 (282)
-==|.-|++|-+=
T Consensus 260 ~r~FKk~~G~tP~~y 274 (282)
T PRK13502 260 SVVFTRETGMTPSQW 274 (282)
T ss_pred HHHHHHHHCcCHHHH
Confidence 1223456665443
No 50
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=88.39 E-value=3 Score=37.17 Aligned_cols=65 Identities=22% Similarity=0.248 Sum_probs=45.6
Q ss_pred HHHhhcC---CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHH-------HHHHHHh
Q 023462 33 DISKYFS---LPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLSGKSIEDIKKYAAREKSKELA-------ELSKIAR 102 (282)
Q Consensus 33 dL~~yF~---lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~ll-------el~k~~~ 102 (282)
-|..+|+ +.+.++|+.+|||...|.|.+++.|.. |++-|.. .+.++++.+| -|.+|+.
T Consensus 205 ~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T--~~~yi~~----------~RL~~A~~lL~~~~~~~sI~eIA~ 272 (302)
T PRK09685 205 LIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLV--VAQYIRN----------RRLDRCADDLRPAADDEKITSIAY 272 (302)
T ss_pred HHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCC--HHHHHHH----------HHHHHHHHHhhhhccCCCHHHHHH
Confidence 3455653 788999999999999999999999874 4443332 2344444444 3777777
Q ss_pred hcCCccC
Q 023462 103 KSGFQPL 109 (282)
Q Consensus 103 ~~~~~~~ 109 (282)
.-||.-.
T Consensus 273 ~~GF~d~ 279 (302)
T PRK09685 273 KWGFSDS 279 (302)
T ss_pred HhCCCCH
Confidence 7787743
No 51
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=88.36 E-value=1 Score=31.58 Aligned_cols=26 Identities=27% Similarity=0.465 Sum_probs=23.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.+++.++|+.+||+...|.+++++..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36889999999999999999999874
No 52
>PF13518 HTH_28: Helix-turn-helix domain
Probab=88.26 E-value=0.62 Score=31.42 Aligned_cols=25 Identities=12% Similarity=0.230 Sum_probs=22.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+.++.++|+++|||.++|.+.++++
T Consensus 12 g~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 12 GESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHHHH
Confidence 4599999999999999999988765
No 53
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=87.82 E-value=2.3 Score=33.32 Aligned_cols=58 Identities=21% Similarity=0.409 Sum_probs=46.6
Q ss_pred CHHHHHhhc---CCcHHHHHHHh--CCChHHHHHHHHHcCCCCCCcchhh-hhh-----cHHHHHHHHHH
Q 023462 30 SFDDISKYF---SLPLSDAANHL--GVCVSVLKKICRDNGLDRWPYRKFL-SGK-----SIEDIKKYAAR 88 (282)
Q Consensus 30 TledL~~yF---~lPi~EAAr~L--GVs~T~LKR~CR~lGI~RWPyRKlk-SLk-----sI~~l~e~a~~ 88 (282)
++.-|.+|| .+|+.++++.. |++..+++|..+...| .+|.=++- |.| .|.+|-.|...
T Consensus 2 ~flLma~~~~~~~IpL~~v~~~yf~~lt~~~a~rk~~~g~l-plPv~rl~~SqKs~~~V~v~dLA~yiD~ 70 (76)
T PF11112_consen 2 TFLLMAQYFGDPVIPLEEVCEDYFPHLTPKTAKRKANAGEL-PLPVFRLDDSQKSPKFVHVQDLAAYIDK 70 (76)
T ss_pred HHHHHHHHcCCCCCcHHHHHHHHHccCCHHHHHHHHHCCCC-CCceeecCCcccCCceeeHHHHHHHHHH
Confidence 466677886 67899999885 9999999999999999 79999986 655 37777777543
No 54
>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=87.54 E-value=1.2 Score=30.51 Aligned_cols=24 Identities=29% Similarity=0.564 Sum_probs=21.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
++++.|+|+.||||..+++++.++
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 899999999999999999988765
No 55
>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=87.37 E-value=0.91 Score=31.30 Aligned_cols=29 Identities=21% Similarity=0.338 Sum_probs=20.5
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+.-++++|..|+|+.|||+..+++..-+
T Consensus 20 ~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 20 LLRYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34567799999999999999999987654
No 56
>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=87.35 E-value=1.2 Score=34.46 Aligned_cols=30 Identities=33% Similarity=0.298 Sum_probs=25.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
+++.++|+.+||++++|....+ .|+-. |.|
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~-p~r 31 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLLS-PSR 31 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCcC-CCc
Confidence 6899999999999999999987 57644 543
No 57
>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=87.25 E-value=1.2 Score=35.74 Aligned_cols=25 Identities=32% Similarity=0.522 Sum_probs=22.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|++.|+|+.+|||+.+|...++. |+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence 68999999999999999999886 65
No 58
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=87.10 E-value=3 Score=39.35 Aligned_cols=75 Identities=20% Similarity=0.292 Sum_probs=50.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCccCCcc-
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQPLSNE- 112 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~~~n~~- 112 (282)
.+++.++|+.+|||+++|.|++++.|+. +.++ |. ..+-++++.++. |++|+.+-||.-.+.-
T Consensus 158 ~lsl~~lA~~~g~S~~~L~R~Fk~~G~S---~~~y--------l~-~~Rl~~A~~LL~~t~~sI~eIA~~~GF~s~S~Fs 225 (274)
T PRK09978 158 EWTLARIASELLMSPSLLKKKLREEETS---YSQL--------LT-ECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFI 225 (274)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCC---HHHH--------HH-HHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHH
Confidence 4689999999999999999999998753 2222 11 244555555554 7788888888754331
Q ss_pred --cccccCCCCCCcc
Q 023462 113 --TSKLHGVTSPPNL 125 (282)
Q Consensus 113 --~sk~qgv~~~~~~ 125 (282)
--+..|++|-+-.
T Consensus 226 r~FKk~~G~TPs~yR 240 (274)
T PRK09978 226 YVFRNYYGMTPTEYQ 240 (274)
T ss_pred HHHHHHHCcCHHHHH
Confidence 2245677754443
No 59
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=87.01 E-value=1.2 Score=30.27 Aligned_cols=32 Identities=13% Similarity=0.230 Sum_probs=24.8
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..|...=.+++.|+|+.+|++.+++.++.+++
T Consensus 10 ~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 10 NYLRENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34455557999999999999999999998875
No 60
>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=86.73 E-value=1.3 Score=30.76 Aligned_cols=32 Identities=16% Similarity=0.149 Sum_probs=23.9
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..|+.-=-.|..++|+.+|||.+++.++-+++
T Consensus 10 ~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 10 RLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 34555567899999999999999999888765
No 61
>smart00351 PAX Paired Box domain.
Probab=86.61 E-value=2.5 Score=34.81 Aligned_cols=67 Identities=19% Similarity=0.117 Sum_probs=40.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc---CCCC--CC-cchhh--hhhcHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN---GLDR--WP-YRKFL--SGKSIEDIKKYAAREKSKELAELSKIARKSG 105 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l---GI~R--WP-yRKlk--SLksI~~l~e~a~~EK~k~llel~k~~~~~~ 105 (282)
++++.++|+.||||.+++-++.+++ |... .. +++-. +-.....|.++..+.-...+.||.+.+...+
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~g 107 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEG 107 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 6899999999999999998887765 5421 11 11111 1122334554445555566777766655443
No 62
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=86.30 E-value=0.82 Score=38.04 Aligned_cols=36 Identities=17% Similarity=0.351 Sum_probs=30.2
Q ss_pred CCCCCcCHHHHH-----hhcCCcHHHHHHHhCCChHHHHHH
Q 023462 24 TSTKSLSFDDIS-----KYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 24 ~~~~~iTledL~-----~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
.....||+|+|. .|-+|.+.|||..+|||..||-+.
T Consensus 29 ~~~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~ 69 (99)
T COG1342 29 LEPVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRL 69 (99)
T ss_pred CcceeecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHH
Confidence 355678888865 789999999999999999998654
No 63
>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=86.05 E-value=1.7 Score=34.15 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=23.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
+++.|+|+.+||++.+|+-.+++ |+..
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gll~ 27 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GLFK 27 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 57899999999999999988887 8643
No 64
>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=86.03 E-value=1.5 Score=30.99 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=21.1
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
+-+++...++.+.++|+.+||+.++|.++
T Consensus 4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~ 32 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLGISRSTISKI 32 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 45778888999999999999987776665
No 65
>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=86.03 E-value=1.1 Score=35.92 Aligned_cols=28 Identities=21% Similarity=0.198 Sum_probs=24.2
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.-+.+++++|+|+.|||+..+++.++.+
T Consensus 123 ~~~~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 123 RYQRGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3556999999999999999999988654
No 66
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=85.99 E-value=1.5 Score=34.78 Aligned_cols=30 Identities=23% Similarity=0.210 Sum_probs=24.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
+++.|+|+.+|||+.+|....++ |+.. |.|
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll~-~~r 31 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLIP-SAR 31 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCC
Confidence 68999999999999999777775 8762 444
No 67
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=85.88 E-value=0.91 Score=31.00 Aligned_cols=22 Identities=27% Similarity=0.400 Sum_probs=20.8
Q ss_pred cHHHHHHHhCCChHHHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+.|||+.|||+.+++.+.|+.
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhC
Confidence 7899999999999999999986
No 68
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=85.86 E-value=1.2 Score=36.10 Aligned_cols=33 Identities=9% Similarity=0.126 Sum_probs=29.5
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+..|+.-+-+|+.+.|++||+|.+++.++-++|
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 567778888999999999999999999998876
No 69
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=85.83 E-value=1.2 Score=44.95 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=30.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPY 70 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPy 70 (282)
..++-.+.+||+.||||.+||.|..++|||..=|+
T Consensus 601 ~~~~gn~~~aA~~LGisR~TLyrklk~~~i~~~~~ 635 (638)
T PRK11388 601 QVCGGRIQEMAALLGIGRTTLWRKMKQHGIDAGQF 635 (638)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCCcccc
Confidence 44677899999999999999999999999955443
No 70
>PRK15043 transcriptional regulator MirA; Provisional
Probab=85.67 E-value=1.5 Score=40.98 Aligned_cols=33 Identities=21% Similarity=0.241 Sum_probs=29.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcch
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRK 72 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRK 72 (282)
.|+|.|+|+.+||+..||....|++|+.. |.|.
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~-P~Rt 35 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLK-PQRT 35 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCC-CccC
Confidence 48999999999999999999999999876 7663
No 71
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=85.63 E-value=1 Score=37.79 Aligned_cols=31 Identities=19% Similarity=0.165 Sum_probs=26.4
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-.|..+.+++..|+|+.|||+++++|.+.++
T Consensus 136 ~~l~~~~gls~~EIA~~l~i~~~tVks~l~r 166 (182)
T COG1595 136 FLLRYLEGLSYEEIAEILGISVGTVKSRLHR 166 (182)
T ss_pred hhhHhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3455777999999999999999999987764
No 72
>PRK00118 putative DNA-binding protein; Validated
Probab=85.59 E-value=0.69 Score=38.09 Aligned_cols=29 Identities=10% Similarity=0.095 Sum_probs=24.4
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.-+.++++.|+|+.||||..+++++-++
T Consensus 28 L~y~eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 28 LYYLDDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44556899999999999999999887664
No 73
>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=85.16 E-value=1.2 Score=44.04 Aligned_cols=31 Identities=16% Similarity=0.119 Sum_probs=27.6
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++--+.+||+.|||+.++|.|+.|+|||.
T Consensus 500 ~~~~gn~~~aA~~LGisr~tLy~klk~~gi~ 530 (534)
T TIGR01817 500 EQAGWVQAKAARLLGMTPRQVGYALRKLNIE 530 (534)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCC
Confidence 4456779999999999999999999999994
No 74
>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=85.15 E-value=0.96 Score=36.13 Aligned_cols=23 Identities=17% Similarity=0.317 Sum_probs=21.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++.+++|+.||||.+|++|++|
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 57999999999999999999887
No 75
>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=84.77 E-value=5.1 Score=35.33 Aligned_cols=64 Identities=28% Similarity=0.488 Sum_probs=44.1
Q ss_pred HHhhc--CCcHHHHHHHhCCChHHHHHHHHH-cCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcC
Q 023462 34 ISKYF--SLPLSDAANHLGVCVSVLKKICRD-NGLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSG 105 (282)
Q Consensus 34 L~~yF--~lPi~EAAr~LGVs~T~LKR~CR~-lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~ 105 (282)
|..+| ++++.+.|+.+|||.+.|-|+|++ .|+. |. +.|.+ -+.++++.||. |.+|+..-|
T Consensus 195 I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t--~~---------~yi~~-~Rl~~A~~lL~~t~~sI~eIA~~~G 262 (287)
T TIGR02297 195 IEENYKQHLRLPEYADRLGISESRLNDICRRFSALS--PK---------RLIIE-RVMQEARRLLLFTQHSINQIAYDLG 262 (287)
T ss_pred HHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCC--HH---------HHHHH-HHHHHHHHHHHcCCCCHHHHHHHhC
Confidence 34444 669999999999999999999999 6875 32 22232 23455555544 677777777
Q ss_pred CccC
Q 023462 106 FQPL 109 (282)
Q Consensus 106 ~~~~ 109 (282)
|.-.
T Consensus 263 F~s~ 266 (287)
T TIGR02297 263 YKDP 266 (287)
T ss_pred CCCH
Confidence 7643
No 76
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=84.69 E-value=1.3 Score=31.77 Aligned_cols=34 Identities=24% Similarity=0.343 Sum_probs=26.6
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
+-.++..-++.+.++|+.+|||.+++.++.+--.
T Consensus 6 lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 6 LRRLRERAGLSQAQLADRLGVSQSTVSRIERGRR 39 (64)
T ss_dssp HHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCC
Confidence 4456677799999999999999999999988443
No 77
>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=84.43 E-value=2.3 Score=34.20 Aligned_cols=31 Identities=29% Similarity=0.397 Sum_probs=26.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcch
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYRK 72 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRK 72 (282)
|.+.|+|+.+||+..+|.-..+. |+-. |.|.
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~-GLl~-p~r~ 31 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ-GLLV-PERS 31 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC-CCCC-CCcC
Confidence 67899999999999999998885 8765 6553
No 78
>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=84.41 E-value=2.1 Score=34.05 Aligned_cols=30 Identities=27% Similarity=0.245 Sum_probs=25.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
|++.|+|+.+||++.||....+. |+.. |.|
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~-~~r 31 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLIT-GTR 31 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCc
Confidence 68999999999999999988886 8654 533
No 79
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=84.37 E-value=0.83 Score=30.08 Aligned_cols=21 Identities=29% Similarity=0.358 Sum_probs=18.4
Q ss_pred CcHHHHHHHhCCChHHHHHHH
Q 023462 40 LPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~C 60 (282)
-.+.|||+.|||+.+++.+.|
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKYL 37 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHhC
Confidence 368999999999999998865
No 80
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=83.70 E-value=0.94 Score=46.02 Aligned_cols=34 Identities=21% Similarity=0.336 Sum_probs=30.4
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCc
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPY 70 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPy 70 (282)
.-.+++.|.|++.|||.+++=|.||++|..-++-
T Consensus 372 v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~e 405 (638)
T PRK14101 372 IINDPIVDIARKADVSQPTVIRFCRSLGCQGLSD 405 (638)
T ss_pred HHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHH
Confidence 3478999999999999999999999999987654
No 81
>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=83.65 E-value=2.5 Score=33.39 Aligned_cols=26 Identities=38% Similarity=0.447 Sum_probs=22.9
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+||+.++|....+ .|+.
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gli 27 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGLV 27 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence 6899999999999999998876 7764
No 82
>PRK13503 transcriptional activator RhaS; Provisional
Probab=83.48 E-value=8.7 Score=33.65 Aligned_cols=64 Identities=19% Similarity=0.354 Sum_probs=44.2
Q ss_pred HHhhc--CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcC
Q 023462 34 ISKYF--SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSG 105 (282)
Q Consensus 34 L~~yF--~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~ 105 (282)
|..+| .+++.+.|+.+|||.+.|.|+|++. |+. | .+.|. ..+-+++++|+. |.+|+..-|
T Consensus 180 I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S--~---------~~yi~-~~Rl~~A~~LL~~~~~sI~eIA~~~G 247 (278)
T PRK13503 180 LEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLT--P---------QRYLN-RLRLLKARHLLRHSDASVTDIAYRCG 247 (278)
T ss_pred HHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcC--H---------HHHHH-HHHHHHHHHHHHcCCCCHHHHHHHhC
Confidence 44444 4678999999999999999999877 763 1 22222 244556666554 677778778
Q ss_pred CccC
Q 023462 106 FQPL 109 (282)
Q Consensus 106 ~~~~ 109 (282)
|.-.
T Consensus 248 F~~~ 251 (278)
T PRK13503 248 FGDS 251 (278)
T ss_pred CCCH
Confidence 7754
No 83
>cd00131 PAX Paired Box domain
Probab=83.26 E-value=5 Score=33.39 Aligned_cols=66 Identities=17% Similarity=0.162 Sum_probs=39.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc---C-C-CC----CCcchhhhhhcHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN---G-L-DR----WPYRKFLSGKSIEDIKKYAAREKSKELAELSKIARKSG 105 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l---G-I-~R----WPyRKlkSLksI~~l~e~a~~EK~k~llel~k~~~~~~ 105 (282)
+++..+||+.||||.+++-|+.+++ | + ++ +++|++. ......|..+.++.-...+.||.+.+...+
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~-~~~~~~i~~~v~~~p~~Tl~El~~~L~~~g 107 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVAT-PEVVKKIEIYKQENPGMFAWEIRDRLLQEG 107 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCC-HHHHHHHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 8899999999999999888877654 3 2 11 2233322 222344444445554566677766644333
No 84
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=83.17 E-value=1.3 Score=45.07 Aligned_cols=55 Identities=22% Similarity=0.365 Sum_probs=44.4
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHH---------HHHHHcCCCCC-Ccchhhh--hhcHHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLK---------KICRDNGLDRW-PYRKFLS--GKSIEDIKKYAA 87 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LK---------R~CR~lGI~RW-PyRKlkS--LksI~~l~e~a~ 87 (282)
-|.+||+|...+|.+.|.|-.+.++ ++||.+||.|| .|=.|+. .+.++.++|+..
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 3557999999999999999887776 78999999999 7777773 456777776543
No 85
>PHA01976 helix-turn-helix protein
Probab=82.99 E-value=2.4 Score=30.16 Aligned_cols=33 Identities=12% Similarity=0.090 Sum_probs=27.9
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+..++...++.+.++|+.+||+.+++.++-+.
T Consensus 6 rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 356778888999999999999999999987543
No 86
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=82.92 E-value=1.8 Score=35.58 Aligned_cols=27 Identities=19% Similarity=0.164 Sum_probs=23.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+-+++.+|+|+.|||+..++|.+.++
T Consensus 131 ~~~g~s~~EIA~~lgis~~tV~~~l~r 157 (173)
T PRK09645 131 YYRGWSTAQIAADLGIPEGTVKSRLHY 157 (173)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 445999999999999999999887654
No 87
>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=82.67 E-value=1.5 Score=34.50 Aligned_cols=28 Identities=25% Similarity=0.298 Sum_probs=25.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
.+.+.++|+.|||+...|-+..|+.||.
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 4789999999999999999999999963
No 88
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=82.64 E-value=8 Score=31.47 Aligned_cols=42 Identities=19% Similarity=0.151 Sum_probs=32.9
Q ss_pred CCCCCCcCHHHHHhhc--CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 23 STSTKSLSFDDISKYF--SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 23 k~~~~~iTledL~~yF--~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
+.....+-.+.+..++ ++++.++|+++||+.++|.+-++++.
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 3444445555666665 68999999999999999999999974
No 89
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=82.47 E-value=9.4 Score=34.04 Aligned_cols=58 Identities=19% Similarity=0.343 Sum_probs=41.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCcc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQP 108 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~~ 108 (282)
++.+.+.|+.+|+|.+.|-|++|+. |+. | .+.|+ ..+.++++.||. |++|+.+-||.-
T Consensus 199 ~isl~~lA~~~~lS~~~l~r~Fk~~~G~t--p---------~~~l~-~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d 262 (290)
T PRK10572 199 EFDIESVAQHVCLSPSRLAHLFRQQLGIS--V---------LRWRE-DQRISRAKLLLQTTRMPIATIGRNVGYDD 262 (290)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCcC--H---------HHHHH-HHHHHHHHHHHHcCCCCHHHHHHHhCCCC
Confidence 7889999999999999999999997 874 1 22222 344555665553 567777777763
No 90
>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=82.37 E-value=2.9 Score=29.69 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=20.1
Q ss_pred cHHHHHHHhCCChHHHHHHHHHc
Q 023462 41 PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.++|+|+.+|||.+|+-|.....
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 47899999999999999987654
No 91
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=82.33 E-value=1.2 Score=45.47 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=22.7
Q ss_pred HHHHHHhCCChHHHHHHHHHcCCC
Q 023462 43 SDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 43 ~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
.+||+.|||+.|||.|+.++|||.
T Consensus 661 ~~aA~~LGi~R~tL~rklk~~gi~ 684 (686)
T PRK15429 661 KGAAQRLGLKRTTLLSRMKRLGID 684 (686)
T ss_pred HHHHHHhCCCHHHHHHHHHHcCCC
Confidence 499999999999999999999994
No 92
>PRK13500 transcriptional activator RhaR; Provisional
Probab=82.26 E-value=7.8 Score=35.61 Aligned_cols=82 Identities=15% Similarity=0.239 Sum_probs=55.2
Q ss_pred HHHHhhc--CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhh
Q 023462 32 DDISKYF--SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARK 103 (282)
Q Consensus 32 edL~~yF--~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~ 103 (282)
+-|..+| .+.+.+.|+.+|||...|-|+|++. |+. | .+.|. ..+.++|++||. |++|+..
T Consensus 213 ~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T--~---------~~yi~-~~RL~~A~~LL~~t~~sI~eIA~~ 280 (312)
T PRK13500 213 TRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMT--I---------NQYLR-QVRVCHAQYLLQHSRLLISDISTE 280 (312)
T ss_pred HHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC--H---------HHHHH-HHHHHHHHHHHHcCCCCHHHHHHH
Confidence 3445555 4779999999999999999999987 874 2 22223 345666666664 7888888
Q ss_pred cCCccCCccc---ccccCCCCCCcc
Q 023462 104 SGFQPLSNET---SKLHGVTSPPNL 125 (282)
Q Consensus 104 ~~~~~~n~~~---sk~qgv~~~~~~ 125 (282)
-||.-.|.-+ =|.-|++|-+-.
T Consensus 281 ~GF~d~s~Fsr~FKk~~G~TP~~yR 305 (312)
T PRK13500 281 CGFEDSNYFSVVFTRETGMTPSQWR 305 (312)
T ss_pred hCCCCHHHHHHHHHHHHCcCHHHHH
Confidence 8888654411 244566654433
No 93
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=82.21 E-value=1.6 Score=33.91 Aligned_cols=32 Identities=16% Similarity=0.281 Sum_probs=27.3
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+.+++..++|.+.+.|+.+|||..|+-.+=+
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 46789999999999999999999988765433
No 94
>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=82.08 E-value=2 Score=35.45 Aligned_cols=26 Identities=27% Similarity=0.399 Sum_probs=22.6
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+++.+|+|..|||+..++|.+.++
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 148 FAGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 34799999999999999999987664
No 95
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=81.96 E-value=1.7 Score=38.47 Aligned_cols=28 Identities=11% Similarity=0.016 Sum_probs=24.3
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.-|.+++.+|+|+.|||+..++|.++++
T Consensus 146 ~y~eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 146 RELEDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3556899999999999999999988774
No 96
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=81.92 E-value=2 Score=36.00 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=23.3
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+-+++.+|+|..||||..++|.+.+
T Consensus 139 ~~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 139 ATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345589999999999999999998765
No 97
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.87 E-value=2.1 Score=34.70 Aligned_cols=27 Identities=7% Similarity=-0.110 Sum_probs=23.2
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+.+++.+|+|+.|||+..++|.+..
T Consensus 118 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 118 HYLEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999987765
No 98
>PRK09726 antitoxin HipB; Provisional
Probab=81.71 E-value=2.1 Score=32.94 Aligned_cols=32 Identities=9% Similarity=0.167 Sum_probs=28.1
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+..++.-.++.+.++|+.+||+.++|.++++
T Consensus 16 ~lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 16 AMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 45567777899999999999999999999988
No 99
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=81.70 E-value=2 Score=36.35 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=24.7
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
|+-+.+++.+|+|..||||..++|.+.++
T Consensus 141 L~~~~g~s~~EIA~~lgis~~tVk~~l~R 169 (185)
T PRK09649 141 LTQLLGLSYADAAAVCGCPVGTIRSRVAR 169 (185)
T ss_pred hHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44667999999999999999999987654
No 100
>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=81.69 E-value=3.9 Score=31.48 Aligned_cols=30 Identities=33% Similarity=0.469 Sum_probs=24.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
|.+.|+|+.+||+.++|+..++ .|+.. |.|
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~-~Gll~-~~~ 30 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE-KGLLP-PER 30 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCcC-CCc
Confidence 5789999999999999998887 46644 644
No 101
>PRK04217 hypothetical protein; Provisional
Probab=81.66 E-value=2.1 Score=35.61 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=23.4
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+++++|+|+.||||.++++++.++
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34799999999999999999999885
No 102
>PHA00542 putative Cro-like protein
Probab=81.37 E-value=2.1 Score=32.98 Aligned_cols=28 Identities=11% Similarity=0.050 Sum_probs=24.6
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.--++.+.++|+.+||+.+++-++++--
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 4448999999999999999999998754
No 103
>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=81.17 E-value=2.8 Score=29.36 Aligned_cols=23 Identities=30% Similarity=0.434 Sum_probs=17.7
Q ss_pred CcHHHHHHHhCCChHHHHHHHHH
Q 023462 40 LPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
|++.+||+..||+.+||-++-+.
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 99999999999999999976554
No 104
>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=81.02 E-value=5.7 Score=31.19 Aligned_cols=25 Identities=28% Similarity=0.337 Sum_probs=21.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
+.+.|+|+.+||+.++|+..++ .|+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~-~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE-IGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 4689999999999999997765 564
No 105
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=80.73 E-value=2.2 Score=27.95 Aligned_cols=28 Identities=14% Similarity=0.207 Sum_probs=24.3
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.|.+++.++|+.||++.+++.|..+++-
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~ 33 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLE 33 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3678899999999999999999888763
No 106
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=80.53 E-value=2.9 Score=31.96 Aligned_cols=31 Identities=19% Similarity=0.365 Sum_probs=28.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPY 70 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPy 70 (282)
.+++-.||+.+||+.-.+-..++++||+ +.|
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 7899999999999999999999999998 554
No 107
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=80.36 E-value=2.3 Score=36.21 Aligned_cols=26 Identities=23% Similarity=0.226 Sum_probs=22.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+.+++.+|+|..|||+..++|.++.
T Consensus 124 ~~eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 124 AIEGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred HHcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 45689999999999999999998764
No 108
>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=80.31 E-value=3.1 Score=29.93 Aligned_cols=38 Identities=26% Similarity=0.347 Sum_probs=23.4
Q ss_pred CCCCCcCHHHHH---hhc--CCcHHHHHHHhCCChHHHHHHHH
Q 023462 24 TSTKSLSFDDIS---KYF--SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 24 ~~~~~iTledL~---~yF--~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+.+..||+++=. .++ +....++|+.+||+.|++..+.+
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred CCCccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345566766532 222 56899999999999999988865
No 109
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=80.28 E-value=4.4 Score=29.59 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=18.4
Q ss_pred HHHHhCCChHHHHHHHHH-cCCC
Q 023462 45 AANHLGVCVSVLKKICRD-NGLD 66 (282)
Q Consensus 45 AAr~LGVs~T~LKR~CR~-lGI~ 66 (282)
.|+.||||...|.++|++ .|+.
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 6874
No 110
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=80.22 E-value=1.6 Score=41.26 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=25.0
Q ss_pred CCcHHHHHHHhCCChHHHHH---HHHHcCCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKK---ICRDNGLDR 67 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR---~CR~lGI~R 67 (282)
+|+|.|+|++||||.+++-| .||+.||-+
T Consensus 29 g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~ 60 (318)
T PRK15418 29 GLTQSEIGERLGLTRLKVSRLLEKGRQSGIIR 60 (318)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEE
Confidence 89999999999999877655 699999853
No 111
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=80.13 E-value=2.4 Score=34.87 Aligned_cols=29 Identities=17% Similarity=0.179 Sum_probs=24.3
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.-+++++.+|+|..|||+..+++...++
T Consensus 147 l~~~~~~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T PRK09641 147 LKYIEDLSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred hHHhhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34567999999999999999999877654
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=80.12 E-value=2.4 Score=35.89 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=23.4
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+.++|+.|+|..||||..++|.+..
T Consensus 118 ~~~~g~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 118 TELEGLSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345799999999999999999988764
No 113
>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=80.10 E-value=2.6 Score=39.73 Aligned_cols=30 Identities=27% Similarity=0.187 Sum_probs=27.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
..++-.+..||+.|||+.++|.++.+++||
T Consensus 413 ~~~~~n~~~aa~~lgi~r~~l~~~l~~~~~ 442 (442)
T TIGR02040 413 ELTRDNRASAAEILGLSRQSLYVKLRRYGL 442 (442)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHhCc
Confidence 456777999999999999999999999986
No 114
>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=79.99 E-value=4.8 Score=33.91 Aligned_cols=30 Identities=30% Similarity=0.429 Sum_probs=24.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
|++.++|+.+||++.+|...-++ |+.. |-|
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~-GLl~-p~r 31 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH-GLIK-PAR 31 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CcC
Confidence 68999999999999999987776 7543 433
No 115
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=79.50 E-value=2.7 Score=34.20 Aligned_cols=29 Identities=14% Similarity=0.348 Sum_probs=23.7
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
|+-+.++|..|+|..|||+..++|.+..+
T Consensus 123 l~~~~~~s~~eIA~~lgis~~tv~~~l~R 151 (161)
T PRK12541 123 LRDYYGFSYKEIAEMTGLSLAKVKIELHR 151 (161)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33467999999999999999998876543
No 116
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=79.44 E-value=3.5 Score=28.80 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=24.1
Q ss_pred CCcHHHHHHHhCC-ChHHHHHHHHHc-CC
Q 023462 39 SLPLSDAANHLGV-CVSVLKKICRDN-GL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGV-s~T~LKR~CR~l-GI 65 (282)
++++.++|..+|+ +.+.|-|.+++. |+
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~ 78 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLFGV 78 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHCc
Confidence 5899999999999 999999999765 65
No 117
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=79.28 E-value=1.9 Score=31.94 Aligned_cols=24 Identities=21% Similarity=0.364 Sum_probs=21.3
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++.|.|+.+|||.+++-|+|+..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~ 24 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGN 24 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCC
Confidence 468899999999999999999754
No 118
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=79.25 E-value=2.1 Score=35.16 Aligned_cols=27 Identities=15% Similarity=0.305 Sum_probs=23.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+++++.+|+|..|||+..+++..+++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~r 165 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHH 165 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHH
Confidence 456899999999999999999877653
No 119
>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=79.17 E-value=1.6 Score=31.66 Aligned_cols=45 Identities=18% Similarity=0.364 Sum_probs=32.5
Q ss_pred CCcCHHHHHhh--cCCcHHHHHHHhCCChHHHHHHHHHc--CCCCCCcc
Q 023462 27 KSLSFDDISKY--FSLPLSDAANHLGVCVSVLKKICRDN--GLDRWPYR 71 (282)
Q Consensus 27 ~~iTledL~~y--F~lPi~EAAr~LGVs~T~LKR~CR~l--GI~RWPyR 71 (282)
.++-..-|..| =+.++.++|+++||+.++|.+-.+++ |...=|..
T Consensus 9 ~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~~~~~~~~~~ 57 (76)
T PF01527_consen 9 PEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYREGQSAFPAK 57 (76)
T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH--STT-SSS
T ss_pred HHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHhcCCCCCCcc
Confidence 34444555555 48999999999999999999999998 55555555
No 120
>PRK10072 putative transcriptional regulator; Provisional
Probab=79.11 E-value=3.4 Score=33.45 Aligned_cols=33 Identities=30% Similarity=0.423 Sum_probs=28.6
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+..|+.-.++.+.++|+.|||+.+++.+.++..
T Consensus 38 ik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 38 FEQLRKGTGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 556667789999999999999999999988754
No 121
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=79.07 E-value=2.6 Score=35.50 Aligned_cols=28 Identities=11% Similarity=0.244 Sum_probs=23.4
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
|+-+.+++..|+|+.|||+..++|.+..
T Consensus 147 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 147 LKEILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred hHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456699999999999999999987654
No 122
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=79.06 E-value=3 Score=33.79 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=21.5
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
-+.+++.+|+|+.|||+..++|.+
T Consensus 122 ~~~~~s~~EIA~~lgis~~tV~~~ 145 (163)
T PRK07037 122 RLHGETQKDIARELGVSPTLVNFM 145 (163)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHH
Confidence 456999999999999999999975
No 123
>PRK13501 transcriptional activator RhaR; Provisional
Probab=78.91 E-value=14 Score=33.16 Aligned_cols=86 Identities=17% Similarity=0.252 Sum_probs=56.5
Q ss_pred HHHHHhhcC--CcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHh
Q 023462 31 FDDISKYFS--LPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIAR 102 (282)
Q Consensus 31 ledL~~yF~--lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~ 102 (282)
+..|..+|. +++.+.|+.+|+|...|-|+|++. |+. -++.|+ .-+.++|++||. |++|+.
T Consensus 182 ~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T-----------~~qyi~-~~Ri~~A~~LL~~t~~sI~eIA~ 249 (290)
T PRK13501 182 MSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMS-----------ISHYLR-QIRLCHAKCLLRGSEHRISDIAA 249 (290)
T ss_pred HHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcC-----------HHHHHH-HHHHHHHHHHHHcCCCCHHHHHH
Confidence 455556664 569999999999999999999986 542 133333 345666777764 788889
Q ss_pred hcCCccCCc---ccccccCCCCCCccccc
Q 023462 103 KSGFQPLSN---ETSKLHGVTSPPNLQQQ 128 (282)
Q Consensus 103 ~~~~~~~n~---~~sk~qgv~~~~~~~Qq 128 (282)
+-||.-.+. -=-+.-|+||-+-..++
T Consensus 250 ~~GF~~~s~F~r~FKk~~G~TP~~yR~~~ 278 (290)
T PRK13501 250 RCGFEDSNYFSAVFTREAGMTPRDYRQRF 278 (290)
T ss_pred HhCCCCHHHHHHHHHHHHCcCHHHHHHHh
Confidence 989875433 12244566654443333
No 124
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=78.77 E-value=2.8 Score=35.07 Aligned_cols=27 Identities=22% Similarity=0.213 Sum_probs=23.5
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++.+|+|+.||||..++|.+..+
T Consensus 142 ~~~g~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 142 KLEGLSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 456899999999999999999988644
No 125
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=78.70 E-value=2.7 Score=35.63 Aligned_cols=27 Identities=15% Similarity=0.240 Sum_probs=23.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++.+|+|..|||+..++|.+.++
T Consensus 147 ~~~g~s~~EIA~~lgis~~tVk~~l~R 173 (189)
T PRK12530 147 EYLELSSEQICQECDISTSNLHVLLYR 173 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 456899999999999999999987553
No 126
>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=78.64 E-value=3.8 Score=34.48 Aligned_cols=31 Identities=32% Similarity=0.458 Sum_probs=26.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
.|+|.|+|+.+||++.+|.-..++ |+-. |.|
T Consensus 1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~-p~r 31 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQK-GLIA-SWR 31 (139)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCc
Confidence 378999999999999999998888 8765 644
No 127
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=78.63 E-value=2.9 Score=35.78 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=25.6
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+.-+-+++..|+|+.||||..+++|..+..
T Consensus 146 l~~~~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 146 LRFFEGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334458999999999999999999988765
No 128
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=78.56 E-value=1.9 Score=44.76 Aligned_cols=28 Identities=29% Similarity=0.336 Sum_probs=25.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+-....||+.||||.|+|-|.|+++||.
T Consensus 533 ~gn~~~aAk~LgIsrttL~rKlkk~~l~ 560 (560)
T COG3829 533 GGNKSKAAKELGISRTTLYRKLKKYGLR 560 (560)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhcCC
Confidence 3468899999999999999999999984
No 129
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=78.38 E-value=3.2 Score=33.37 Aligned_cols=26 Identities=15% Similarity=0.378 Sum_probs=22.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+-+++.+|+|..|||+..++|.+-.
T Consensus 119 ~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 119 YWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 34589999999999999999987654
No 130
>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=78.27 E-value=3.3 Score=33.49 Aligned_cols=26 Identities=23% Similarity=0.257 Sum_probs=22.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.+++..|+|+.|||+..+++.+.++
T Consensus 136 ~~g~s~~eIA~~l~is~~tv~~~l~r 161 (170)
T TIGR02952 136 GQNLPIAEVARILGKTEGAVKILQFR 161 (170)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45999999999999999999877643
No 131
>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=78.26 E-value=3 Score=27.67 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=21.5
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++..++|+.|||+..++++..++.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999988876643
No 132
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=78.23 E-value=2.7 Score=35.65 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.5
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc---CC
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN---GL 65 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l---GI 65 (282)
..|+.-.-++..|.|++||+|.+++.++-++| ||
T Consensus 21 ~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 21 NELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 35667789999999999999999999998876 76
No 133
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=78.18 E-value=3.1 Score=34.97 Aligned_cols=27 Identities=7% Similarity=0.140 Sum_probs=23.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++.+|+|..|||+..++|.+..+
T Consensus 144 ~~~g~s~~EIA~~lgis~~tV~~~l~R 170 (191)
T PRK12520 144 EWLELETEEICQELQITATNAWVLLYR 170 (191)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 456999999999999999999887654
No 134
>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=77.85 E-value=5.3 Score=32.92 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=22.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|+|.|+|+.+||++.+|.-..+ .|+-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~-~GLl~ 27 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK-QGLLP 27 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH-CCCCC
Confidence 6789999999999999987766 45543
No 135
>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=77.75 E-value=3.1 Score=30.79 Aligned_cols=26 Identities=19% Similarity=0.153 Sum_probs=24.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
++++.|+|+.|||+.+|+..-+.+.+
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 88999999999999999999999987
No 136
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=77.73 E-value=3.2 Score=35.20 Aligned_cols=27 Identities=26% Similarity=0.324 Sum_probs=22.7
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+.+++.+|+|+.|||+..++|.+.+
T Consensus 154 ~~~~~~s~~EIA~~Lgis~~tVk~~l~ 180 (194)
T PRK09646 154 AYYGGLTYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred HHHcCCCHHHHHHHhCCChHhHHHHHH
Confidence 345689999999999999999987753
No 137
>PRK10130 transcriptional regulator EutR; Provisional
Probab=77.54 E-value=14 Score=35.54 Aligned_cols=57 Identities=19% Similarity=0.196 Sum_probs=41.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHH-cCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH--------HHHHHhhcCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRD-NGLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE--------LSKIARKSGFQP 108 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~-lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle--------l~k~~~~~~~~~ 108 (282)
+.+.+.|+.+|||..+|.+.+++ +|+. |+. .|+ ..+.++++.+|. |.+|+.+-||.-
T Consensus 257 ltv~~lA~~~gvS~r~L~r~Fk~~~G~s--p~~---------ylr-~~RL~~ar~lL~~~~~~~~sI~eIA~~~GF~~ 322 (350)
T PRK10130 257 VTVLDLCNQLHVSRRTLQNAFHAILGIG--PNA---------WLK-RIRLNAVRRELISPWSQSTTVKDAAMQWGFWH 322 (350)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcC--HHH---------HHH-HHHHHHHHHHHhccCCCCCCHHHHHHHhCCCC
Confidence 78999999999999999999988 4874 333 333 344555555542 788888888764
No 138
>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=77.43 E-value=3.3 Score=39.13 Aligned_cols=28 Identities=21% Similarity=0.249 Sum_probs=24.5
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..++.-+.+||+.|||+.++|.|..++|
T Consensus 302 ~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 302 AEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 3457889999999999999999998875
No 139
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=77.23 E-value=2.6 Score=37.08 Aligned_cols=35 Identities=34% Similarity=0.557 Sum_probs=27.6
Q ss_pred CcCHHHHH--------hhcCCc----HHHHHHHhCCChHHHHHHHHH
Q 023462 28 SLSFDDIS--------KYFSLP----LSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 28 ~iTledL~--------~yF~lP----i~EAAr~LGVs~T~LKR~CR~ 62 (282)
.||=.+++ .||+.| ++|.|+.||||.+++-..-|+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45655554 899988 899999999999988766554
No 140
>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=77.12 E-value=5.3 Score=31.89 Aligned_cols=26 Identities=15% Similarity=0.307 Sum_probs=22.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|++.|+|+.+||++.+|....+.--|
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57999999999999999988776434
No 141
>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=76.87 E-value=2.5 Score=34.63 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=24.0
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.+|+.|+|+.||||.+++-|..|-+.
T Consensus 55 ~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 55 NMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred CCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 58999999999999999999988776
No 142
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=76.86 E-value=3.2 Score=37.76 Aligned_cols=28 Identities=18% Similarity=0.478 Sum_probs=24.4
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
|+.+|+++.+|+|+.||++..++|.+..
T Consensus 126 L~~~~g~s~~EIA~~lg~s~~tVk~~l~ 153 (293)
T PRK09636 126 LHDVFGVPFDEIASTLGRSPAACRQLAS 153 (293)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4467899999999999999999987765
No 143
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=76.62 E-value=4.3 Score=31.28 Aligned_cols=32 Identities=16% Similarity=0.322 Sum_probs=27.2
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..|...-.+|..++|+.||++.+++.++.+++
T Consensus 10 ~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 10 EELQKDARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred HHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44556667999999999999999999988876
No 144
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=76.52 E-value=3.8 Score=33.68 Aligned_cols=27 Identities=22% Similarity=0.206 Sum_probs=23.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+-+++.+|+|+.|||+..++|.+.++
T Consensus 125 ~~~g~s~~eIA~~lgis~~tV~~~l~R 151 (164)
T PRK12547 125 GASGFSYEDAAAICGCAVGTIKSRVSR 151 (164)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 456899999999999999999887654
No 145
>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=76.51 E-value=4 Score=26.04 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=21.6
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-++++.++|+.|||+..+++++-++
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5899999999999999999876544
No 146
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=76.25 E-value=3.5 Score=27.78 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=21.6
Q ss_pred C-cHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 L-PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 l-Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+ ++.+.|+.+|||.+++.+.+++|
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5 59999999999999999998876
No 147
>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=76.22 E-value=3.8 Score=33.61 Aligned_cols=27 Identities=15% Similarity=0.205 Sum_probs=22.4
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+.+++.+|+|+.|||+..++|.+-.
T Consensus 131 ~~~~g~s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 131 RYYHDLTIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345689999999999999999887543
No 148
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=76.12 E-value=3.1 Score=33.55 Aligned_cols=36 Identities=25% Similarity=0.246 Sum_probs=28.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc---CC------CCCCcchhh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN---GL------DRWPYRKFL 74 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l---GI------~RWPyRKlk 74 (282)
++|+.+||+++|||..|.+|...+| |. ..-|+|.-.
T Consensus 25 g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~ 69 (85)
T PF13011_consen 25 GWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPR 69 (85)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCc
Confidence 6899999999999999999876655 43 456776654
No 149
>PRK15044 transcriptional regulator SirC; Provisional
Probab=76.08 E-value=9.9 Score=36.67 Aligned_cols=60 Identities=22% Similarity=0.238 Sum_probs=41.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHH-----HHHHHHhhcCCccCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLSGKSIEDIKKYAAREKSKELA-----ELSKIARKSGFQPLS 110 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~ll-----el~k~~~~~~~~~~n 110 (282)
.+.+.+.|+.+|+|.++|+|++++.|.. | .++ + . ..+-++++.++ -+.+|+.+-||.-.+
T Consensus 208 ~~SLeeLA~~lgmS~~tL~R~Fk~eg~T--~-~~y-----~---~-~~RL~~A~~LL~~t~~sIseIA~~~GFss~S 272 (295)
T PRK15044 208 KWSQAEVAGKLFMSVSSLKRKLAAEEVS--F-SKI-----Y---L-DARMNQAIKLLRMGAGNISQVATMCGYDTPS 272 (295)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHcCCC--H-HHH-----H---H-HHHHHHHHHHHHcCCCCHHHHHHHhCCCChH
Confidence 4778999999999999999999998753 2 111 1 1 13345555555 366777787877543
No 150
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=76.05 E-value=3.8 Score=34.24 Aligned_cols=27 Identities=11% Similarity=0.373 Sum_probs=23.1
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-+.+++.+|+|..|||+..++|.+..
T Consensus 134 ~~~~g~s~~EIA~~lgis~~tVk~~l~ 160 (185)
T PRK12542 134 KVFYNLTYQEISSVMGITEANVRKQFE 160 (185)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345689999999999999999998754
No 151
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=76.03 E-value=3.8 Score=28.80 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=23.9
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchh
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKF 73 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKl 73 (282)
.++-.--++.+.+.|+..||+.++|.++|..- +.+|+.-.+
T Consensus 3 ~~~m~~~~it~~~La~~~gis~~tl~~~~~~~-~~~~~~~~l 43 (63)
T PF13443_consen 3 KELMAERGITQKDLARKTGISRSTLSRILNGK-PSNPSLDTL 43 (63)
T ss_dssp HHHHHHTT--HHHHHHHHT--HHHHHHHHTTT------HHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc-cccccHHHH
Confidence 34445557899999999999999999999843 334444333
No 152
>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=75.94 E-value=4.6 Score=31.66 Aligned_cols=27 Identities=15% Similarity=0.150 Sum_probs=23.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+-++++.|+|+.||||..++|.+-+.
T Consensus 29 ~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 29 EEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 346999999999999999999998764
No 153
>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=75.91 E-value=2.8 Score=29.57 Aligned_cols=27 Identities=26% Similarity=0.250 Sum_probs=22.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHH-cCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRD-NGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~-lGI~ 66 (282)
+.+.|.|++|||+...|-+.|++ +||.
T Consensus 4 i~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 4 IRVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp E-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred eEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 45789999999999999999966 9996
No 154
>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=75.91 E-value=2.9 Score=35.18 Aligned_cols=27 Identities=7% Similarity=0.101 Sum_probs=22.9
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++.+|+|+.|||+..++|.+..+
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~R 170 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHR 170 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455899999999999999999987543
No 155
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=75.77 E-value=3.9 Score=34.24 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=23.8
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
|.-+.+++.+|+|+.||||..++|.+..+
T Consensus 138 l~~~~g~s~~EIA~~l~is~~tv~~~l~R 166 (179)
T PRK09415 138 LFYYEELSIKEIAEVTGVNENTVKTRLKK 166 (179)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33557999999999999999999876543
No 156
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=75.73 E-value=2.8 Score=35.26 Aligned_cols=24 Identities=25% Similarity=0.130 Sum_probs=20.9
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
+.++|.+|+|+.|||++.++|.+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l 176 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRL 176 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHH
Confidence 458999999999999999998553
No 157
>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=75.72 E-value=3.9 Score=38.83 Aligned_cols=27 Identities=19% Similarity=0.049 Sum_probs=23.9
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.++-.+.+||+.||||.+||.|..+++
T Consensus 437 ~~~gn~~~aA~~Lgisr~tL~rkl~~~ 463 (463)
T TIGR01818 437 HTRGHKQEAAALLGWGRNTLTRKLKEL 463 (463)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 467889999999999999999988765
No 158
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=75.62 E-value=4 Score=34.61 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=20.9
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+++.+|+|..|||+..++|.+.+
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ 179 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLR 179 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHH
Confidence 389999999999999999987643
No 159
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=75.58 E-value=4.3 Score=33.01 Aligned_cols=28 Identities=18% Similarity=0.339 Sum_probs=23.1
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.-+.+++.+|+|+.|||++.++|.+..+
T Consensus 125 ~~~~g~s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 125 AQVDGLGYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3456999999999999999998876543
No 160
>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=75.56 E-value=3.8 Score=23.24 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=18.4
Q ss_pred CCcHHHHHHHhCCChHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~ 59 (282)
+.+..++|+.+||+.+++.++
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 569999999999999998764
No 161
>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=75.45 E-value=3.8 Score=28.56 Aligned_cols=28 Identities=14% Similarity=0.244 Sum_probs=24.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..+.+++.++|+.+|++..++.|..+++
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L 49 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4467999999999999999998888655
No 162
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=75.33 E-value=3.4 Score=37.99 Aligned_cols=28 Identities=11% Similarity=0.227 Sum_probs=24.0
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
|+-+++|+.+|+|..|||+..++|.+.+
T Consensus 164 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 191 (339)
T PRK08241 164 LRDVLGWSAAEVAELLDTSVAAVNSALQ 191 (339)
T ss_pred hHHhhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4467899999999999999999987644
No 163
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=75.33 E-value=4.2 Score=41.54 Aligned_cols=31 Identities=23% Similarity=0.235 Sum_probs=27.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
..++-...+||+.||||.|||.|..+++|..
T Consensus 507 ~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~~ 537 (538)
T PRK15424 507 ERFNGDKTAAANYLGISRTTLWRRLKAEAKA 537 (538)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4557789999999999999999999999853
No 164
>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=75.33 E-value=2.5 Score=32.81 Aligned_cols=28 Identities=14% Similarity=0.207 Sum_probs=25.4
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
-||..|++|.++.||+|..++.++-++|
T Consensus 49 vYi~~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 49 VYIIFSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred EEEEeeHHHHHHHHCCCHHHHHHHHHcC
Confidence 5889999999999999999999987765
No 165
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=75.31 E-value=4 Score=34.68 Aligned_cols=27 Identities=30% Similarity=0.448 Sum_probs=23.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+-+++.+|+|..|||+..++|.++++
T Consensus 147 ~~~g~s~~EIA~~lg~s~~tV~~rl~r 173 (192)
T PRK09643 147 DMQGYSVADAARMLGVAEGTVKSRCAR 173 (192)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345899999999999999999988754
No 166
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=75.31 E-value=4 Score=34.06 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=24.4
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.-+.+++..|+|+.|||+..++|.+.++
T Consensus 139 l~~~~g~s~~EIA~~lgis~~tV~~~l~R 167 (186)
T PRK05602 139 LQYYQGLSNIEAAAVMDISVDALESLLAR 167 (186)
T ss_pred HHHhcCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 44567999999999999999999987643
No 167
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=75.23 E-value=4.1 Score=34.76 Aligned_cols=27 Identities=19% Similarity=0.192 Sum_probs=22.3
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+.+++.+|+|+.|||+..++|.+..
T Consensus 128 ~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 128 VGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999887644
No 168
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=75.00 E-value=3.5 Score=38.28 Aligned_cols=29 Identities=21% Similarity=0.426 Sum_probs=25.0
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.|+.+|+++..|+|+.||++..++|.+.+
T Consensus 128 ~L~~~~g~s~~EIA~~Lgis~~tVr~~l~ 156 (290)
T PRK09635 128 VLHEIFGLPYQQIATTIGSQASTCRQLAH 156 (290)
T ss_pred hHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34578999999999999999999987654
No 169
>PF13551 HTH_29: Winged helix-turn helix
Probab=74.94 E-value=3.5 Score=31.19 Aligned_cols=25 Identities=12% Similarity=0.313 Sum_probs=21.9
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++ +.++|+.||||..|+.+..+++
T Consensus 11 g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 11 GVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 454 9999999999999999988874
No 170
>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=74.87 E-value=3.8 Score=37.22 Aligned_cols=28 Identities=11% Similarity=0.241 Sum_probs=24.0
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
|+-+++++.+|+|+.||||..++|.+..
T Consensus 153 L~~~~g~s~~EIA~~lgis~~tV~~~l~ 180 (324)
T TIGR02960 153 LRDVLGWRAAETAELLGTSTASVNSALQ 180 (324)
T ss_pred hHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4467899999999999999999987644
No 171
>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=74.83 E-value=4.2 Score=34.53 Aligned_cols=27 Identities=7% Similarity=0.112 Sum_probs=23.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++.+|+|..||++..++|.+..+
T Consensus 144 ~~~g~s~~EIA~~lgis~~tvk~rl~R 170 (188)
T TIGR02943 144 EVLGFESDEICQELEISTSNCHVLLYR 170 (188)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 456899999999999999999887543
No 172
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=74.82 E-value=4.1 Score=33.54 Aligned_cols=27 Identities=19% Similarity=0.162 Sum_probs=23.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++.+|+|+.|||+..+++.+..+
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345899999999999999999887654
No 173
>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=74.67 E-value=2 Score=31.41 Aligned_cols=38 Identities=24% Similarity=0.276 Sum_probs=25.9
Q ss_pred CCcHHHHHHHh-----CCChHHHHHHHHHcCCCCCCcchhhhh
Q 023462 39 SLPLSDAANHL-----GVCVSVLKKICRDNGLDRWPYRKFLSG 76 (282)
Q Consensus 39 ~lPi~EAAr~L-----GVs~T~LKR~CR~lGI~RWPyRKlkSL 76 (282)
+.+..+++.+| .||.+|+.++.++.|+..|.-++..-|
T Consensus 13 ~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g~~~~~~~~kP~L 55 (72)
T PF01498_consen 13 RISAREIAQELQEAGISVSKSTIRRRLREAGLKKRKARKKPFL 55 (72)
T ss_dssp ---HHHHHHHT---T--S-HHHHHHHHHHT-EEEETTEEEES-
T ss_pred CCCHHHHHHHHHHccCCcCHHHHHHHHHHcCccccccccCCCC
Confidence 36677777777 899999999999999988777775544
No 174
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=74.46 E-value=4.6 Score=33.35 Aligned_cols=27 Identities=22% Similarity=0.330 Sum_probs=22.7
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.-+.+++.+|+|..||||..++|.+.+
T Consensus 131 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK12523 131 NRLDGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999887653
No 175
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=74.22 E-value=4.4 Score=34.41 Aligned_cols=27 Identities=22% Similarity=0.212 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++..|+|..|||+..++|.+.++
T Consensus 124 ~~~g~s~~EIA~~Lgis~~tV~~~l~R 150 (182)
T PRK12540 124 GASGFSYEDAAAICGCAVGTIKSRVNR 150 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 456899999999999999998877553
No 176
>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=74.15 E-value=3.8 Score=32.89 Aligned_cols=26 Identities=15% Similarity=0.300 Sum_probs=24.0
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
++|+.|+|+.+|||.+|+-|..|.+.
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 69999999999999999999988764
No 177
>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=74.13 E-value=4.5 Score=32.72 Aligned_cols=28 Identities=25% Similarity=0.318 Sum_probs=23.3
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.-+.+++.+|+|..|||+..++|....+
T Consensus 122 ~~~~g~s~~eIA~~lgis~~tV~~~l~r 149 (162)
T TIGR02983 122 RYYEDLSEAQVAEALGISVGTVKSRLSR 149 (162)
T ss_pred HHHhcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3456899999999999999999876543
No 178
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=74.05 E-value=16 Score=33.07 Aligned_cols=75 Identities=17% Similarity=0.102 Sum_probs=48.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCccCCc-
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQPLSN- 111 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~~~n~- 111 (282)
.+++.++|+.+|+|...|.|++++. |+. |..-++ ..+.++++.++. |.+|+..-+|.-.+.
T Consensus 21 ~~~l~~lA~~~~~S~~~l~r~F~~~~g~s--~~~yi~----------~~Rl~~A~~~L~~~~~~i~~iA~~~Gf~s~~~f 88 (289)
T PRK15121 21 PLSLDNVAAKAGYSKWHLQRMFKDVTGHA--IGAYIR----------ARRLSKAAVALRLTSRPILDIALQYRFDSQQTF 88 (289)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC--HHHHHH----------HHHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHH
Confidence 4789999999999999999999987 874 221111 233445544443 677777878764332
Q ss_pred --ccccccCCCCCCcc
Q 023462 112 --ETSKLHGVTSPPNL 125 (282)
Q Consensus 112 --~~sk~qgv~~~~~~ 125 (282)
.--+..|++|-+-.
T Consensus 89 ~r~Fk~~~g~sP~~~r 104 (289)
T PRK15121 89 TRAFKKQFAQTPALYR 104 (289)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 12245566655443
No 179
>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=73.90 E-value=7.4 Score=32.21 Aligned_cols=27 Identities=22% Similarity=0.364 Sum_probs=23.3
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|.+.|+|+.+||++.||...-++ |+.+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~ 28 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN-GLIK 28 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 68999999999999999877766 7654
No 180
>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=73.75 E-value=4 Score=32.29 Aligned_cols=33 Identities=27% Similarity=0.331 Sum_probs=28.8
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+..++...++.+.++|+.|||+..++.|..+-
T Consensus 69 ~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 69 EIRRIRKKLGLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 466778899999999999999999999988543
No 181
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=73.62 E-value=4.6 Score=34.65 Aligned_cols=26 Identities=8% Similarity=0.239 Sum_probs=22.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+.+++.+|+|..|||+..++|.+-.
T Consensus 152 ~~eg~s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 152 EFLDFEIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999999999996643
No 182
>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=73.59 E-value=4.4 Score=36.94 Aligned_cols=29 Identities=14% Similarity=0.314 Sum_probs=24.4
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.|+.+|+++.+|+|+.||+|..++|.+.+
T Consensus 118 ~L~~~~g~s~~EIA~~lg~s~~tVr~~l~ 146 (281)
T TIGR02957 118 VLREVFDYPYEEIASIVGKSEANCRQLVS 146 (281)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34578999999999999999999886643
No 183
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=73.54 E-value=4.9 Score=33.16 Aligned_cols=26 Identities=12% Similarity=0.149 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+-+++.+|+|..|||+..++|.+..
T Consensus 132 ~~~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 132 YYEQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45699999999999999999987654
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=73.43 E-value=6.5 Score=29.86 Aligned_cols=24 Identities=33% Similarity=0.448 Sum_probs=20.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.++++++|.+|||+.+++.+--.+
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 689999999999999999876544
No 185
>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=73.35 E-value=5.2 Score=32.91 Aligned_cols=26 Identities=8% Similarity=0.146 Sum_probs=21.6
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+.++|.+|+|..|||+..+++.+..
T Consensus 153 ~~~g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 153 HLEGLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44689999999999999988887754
No 186
>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=73.22 E-value=5.2 Score=33.29 Aligned_cols=27 Identities=22% Similarity=0.294 Sum_probs=22.1
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
|.-+.+++++|+|+.|||+..++|.+-
T Consensus 111 l~~~~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 111 LTELEGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 445678999999999999998888754
No 187
>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=73.15 E-value=5.8 Score=33.67 Aligned_cols=27 Identities=33% Similarity=0.374 Sum_probs=23.9
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|.|.|+|+.+||++.+|+-..+. |+-.
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~-GLl~ 28 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK-GLIT 28 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 78999999999999999988887 8654
No 188
>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=73.07 E-value=5.6 Score=31.33 Aligned_cols=26 Identities=15% Similarity=0.268 Sum_probs=21.6
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.++|..|+|+.||||..+++.+-++
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45899999999999999998765443
No 189
>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=73.06 E-value=5.4 Score=28.99 Aligned_cols=29 Identities=28% Similarity=0.408 Sum_probs=25.8
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.++.--++++.++|+.+||+.+++-+++.
T Consensus 12 ~~~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 12 EFLEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 56677799999999999999999999886
No 190
>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=73.03 E-value=2.7 Score=29.58 Aligned_cols=26 Identities=27% Similarity=0.492 Sum_probs=20.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
+.++|+++.+|||.++|.+.+++-..
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g~F 29 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDGKF 29 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHHH-
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcccC
Confidence 56899999999999999999996543
No 191
>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=72.97 E-value=8 Score=30.36 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=22.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+||+..+|+..++ .|+-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gll 26 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK-IGLF 26 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence 5789999999999999988876 5873
No 192
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=72.87 E-value=5.5 Score=32.32 Aligned_cols=26 Identities=31% Similarity=0.367 Sum_probs=21.9
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+-++|.+|+|..|||+.++++.+-+
T Consensus 118 ~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 118 KLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34589999999999999999987644
No 193
>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=72.66 E-value=2.6 Score=33.63 Aligned_cols=23 Identities=17% Similarity=0.141 Sum_probs=19.9
Q ss_pred hhcCCcHHHHHHHhCCChHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKK 58 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR 58 (282)
-|-+++.+|+|..||||+.++|+
T Consensus 120 ~~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 120 FFEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HHcCCCHHHHHHHHCcCHHhhcC
Confidence 34489999999999999999874
No 194
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=72.13 E-value=14 Score=32.06 Aligned_cols=36 Identities=14% Similarity=0.104 Sum_probs=30.5
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc---CC-CCCCcchhh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN---GL-DRWPYRKFL 74 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyRKlk 74 (282)
-+|..+.|++||||.|.+....++| |+ ..-|.|-..
T Consensus 30 ~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~ 69 (224)
T PRK11534 30 KLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYR 69 (224)
T ss_pred cCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceE
Confidence 5789999999999999999999887 64 568888655
No 195
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=72.10 E-value=5.1 Score=33.37 Aligned_cols=34 Identities=9% Similarity=0.215 Sum_probs=29.2
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.+..+..+++++.+|+|..|||+.+||.|+-++.
T Consensus 27 ~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~ 60 (133)
T TIGR02293 27 ALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAH 60 (133)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcC
Confidence 4667789999999999999999999999877643
No 196
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=72.08 E-value=5.1 Score=26.53 Aligned_cols=32 Identities=16% Similarity=0.080 Sum_probs=25.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPY 70 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPy 70 (282)
.++..++|+.|||+.+++.++.+++-=..|..
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 46788999999999999999998875444444
No 197
>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=71.96 E-value=5 Score=30.39 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=23.0
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+-+++..|+|+.|||+..+++++.++.
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~~~~~ 150 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRRLKRA 150 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 348999999999999999998877653
No 198
>PRK15185 transcriptional regulator HilD; Provisional
Probab=71.84 E-value=20 Score=34.80 Aligned_cols=27 Identities=30% Similarity=0.444 Sum_probs=24.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
.+++.+.|+.+|+|..+|.|++++.|+
T Consensus 222 ~~SledLA~~lgmS~~tL~R~FK~~G~ 248 (309)
T PRK15185 222 QWKLTDVADHIFMSTSTLKRKLAEEGT 248 (309)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCC
Confidence 568999999999999999999998876
No 199
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=71.68 E-value=19 Score=33.61 Aligned_cols=73 Identities=25% Similarity=0.273 Sum_probs=45.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHH----HHHHHHhhcCCccCCcc--
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLSGKSIEDIKKYAAREKSKELA----ELSKIARKSGFQPLSNE-- 112 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~ll----el~k~~~~~~~~~~n~~-- 112 (282)
.+++.+.|+.+|+|.++|+|++++.|.. |+.-+.- .+-++++.|+ -+.+|+..-||...+.-
T Consensus 150 ~~tl~~LA~~~gmS~s~l~R~FK~~G~T--~~eyl~~----------~Rl~~A~~LL~~~~sI~eIA~~~GF~s~S~Fsr 217 (253)
T PRK09940 150 PWKLKDICDCLYISESLLKKKLKQEQTT--FSQILLD----------ARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIY 217 (253)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCC--HHHHHHH----------HHHHHHHHHHccCCCHHHHHHHhCCCCHHHHHH
Confidence 4679999999999999999999998863 2222211 2222333332 46677777777754331
Q ss_pred -cccccCCCCCC
Q 023462 113 -TSKLHGVTSPP 123 (282)
Q Consensus 113 -~sk~qgv~~~~ 123 (282)
--+.-|++|-+
T Consensus 218 ~FKr~~G~TPs~ 229 (253)
T PRK09940 218 AFRKHFGNSPKR 229 (253)
T ss_pred HHHHHHCcCHHH
Confidence 12344777543
No 200
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=71.57 E-value=5.2 Score=33.51 Aligned_cols=26 Identities=31% Similarity=0.425 Sum_probs=22.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+.+++.+|+|..|||+.++++.+-+
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34699999999999999999997643
No 201
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=71.39 E-value=6.1 Score=31.85 Aligned_cols=23 Identities=13% Similarity=0.225 Sum_probs=20.1
Q ss_pred hcCCcHHHHHHHhCCChHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
+.+++.+|+|+.|||+.++++.+
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~~ 164 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRSR 164 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 34899999999999999999765
No 202
>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=71.35 E-value=5.4 Score=32.91 Aligned_cols=26 Identities=15% Similarity=0.088 Sum_probs=22.6
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.+++..|+|..|||+..++|.++++
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~r 177 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFR 177 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34899999999999999999988754
No 203
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=71.28 E-value=6 Score=35.29 Aligned_cols=23 Identities=17% Similarity=0.380 Sum_probs=20.3
Q ss_pred CcHHHHHHHhCCChHHHHHHHHH
Q 023462 40 LPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
++++|+|+++|||.+|+.|....
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 47899999999999999999853
No 204
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=71.14 E-value=8 Score=23.88 Aligned_cols=29 Identities=28% Similarity=0.362 Sum_probs=21.2
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+...-++.+.+.|+.+||+..++.+.++
T Consensus 4 ~~~~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 4 ELREEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34455577888888888888888877654
No 205
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=71.08 E-value=5.4 Score=34.37 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=23.2
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-|.+++..|+|..|||+..++|.+.+
T Consensus 145 ~~~~g~s~~EIAe~lgis~~tV~~~l~ 171 (196)
T PRK12535 145 TQVLGYTYEEAAKIADVRVGTIRSRVA 171 (196)
T ss_pred HHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 456799999999999999999998753
No 206
>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=71.07 E-value=8.7 Score=23.89 Aligned_cols=29 Identities=28% Similarity=0.371 Sum_probs=22.0
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+....++.+.++|+.+|++..++.+.+.
T Consensus 6 ~~~~~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 6 ELRKEKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 34455578888999999998888877655
No 207
>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=70.96 E-value=5.6 Score=36.13 Aligned_cols=24 Identities=25% Similarity=0.469 Sum_probs=21.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.++++|+|+.||||..+++++.++
T Consensus 236 ~~t~~eIA~~lgvS~~~V~q~~~~ 259 (270)
T TIGR02392 236 KLTLQELAAEYGVSAERIRQIEKN 259 (270)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 489999999999999999988764
No 208
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=70.84 E-value=5.9 Score=34.48 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=24.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
-+.++|.+|+|+.|||+..++|...++-
T Consensus 151 ~~~g~s~~EIA~~Lgis~~tV~~~l~RA 178 (203)
T PRK09647 151 DIEGLSYEEIAATLGVKLGTVRSRIHRG 178 (203)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4568999999999999999999887654
No 209
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=70.82 E-value=5.6 Score=33.04 Aligned_cols=27 Identities=41% Similarity=0.507 Sum_probs=22.5
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
|.-+.+++..|+|+.|||+..++|.+-
T Consensus 130 l~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 130 LSQLDGLTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred hhhccCCCHHHHHHHhCCCHHHHHHHH
Confidence 445679999999999999999887643
No 210
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=70.32 E-value=6.2 Score=33.03 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=22.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+-+++.+|+|..|||+..+++.++++
T Consensus 151 ~~~g~s~~eIA~~lgis~~tv~~~l~R 177 (193)
T PRK11923 151 EFDGLSYEDIASVMQCPVGTVRSRIFR 177 (193)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344899999999999999999888654
No 211
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=70.24 E-value=6 Score=32.72 Aligned_cols=25 Identities=16% Similarity=0.196 Sum_probs=21.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-+++.+|+|+.|||+..++|.+..
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHH
Confidence 3499999999999999999986643
No 212
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=70.10 E-value=20 Score=33.06 Aligned_cols=60 Identities=20% Similarity=0.244 Sum_probs=40.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHH-----HHHHHHhhcCCccCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELA-----ELSKIARKSGFQPLS 110 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~ll-----el~k~~~~~~~~~~n 110 (282)
.+.+.++|+.+|||.+.|.|++++. |+. |.+-+ + ..+.++++.++ -|.+|+..-||.-.+
T Consensus 207 ~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t--~~~~l---------~-~~Rl~~A~~lL~~~~~si~eIA~~~Gf~~~s 272 (302)
T PRK10371 207 ALTINDVAEHVKLNANYAMGIFQRVMQLT--MKQYI---------T-AMRINHVRALLSDTDKSILDIALTAGFRSSS 272 (302)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhCCC--HHHHH---------H-HHHHHHHHHHHhcCCCCHHHHHHHcCCCCHH
Confidence 5889999999999999999999995 763 22222 2 23344444443 366677777776443
No 213
>PRK01381 Trp operon repressor; Provisional
Probab=70.09 E-value=2.7 Score=34.85 Aligned_cols=27 Identities=15% Similarity=0.227 Sum_probs=24.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
.+|+.|+|.+||||.+++-|..|.+..
T Consensus 55 ~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 55 ELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred CcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 489999999999999999999988764
No 214
>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=69.81 E-value=10 Score=30.68 Aligned_cols=27 Identities=26% Similarity=0.340 Sum_probs=23.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|.|.|+|+..||++.+|.-..+. |+..
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~-GLl~ 27 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK-GLIA 27 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 57899999999999999887775 7654
No 215
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=69.41 E-value=7.1 Score=32.68 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=21.4
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
-+.+++.+|+|..|||+..+++.+-
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 152 VVVGLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3459999999999999999888764
No 216
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=69.38 E-value=6.5 Score=33.75 Aligned_cols=28 Identities=21% Similarity=0.228 Sum_probs=23.0
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.-+.+++..|+|..||||..++|.+.++
T Consensus 125 ~~~~g~s~~EIA~~LgiS~~tVk~~l~R 152 (188)
T PRK12546 125 VGASGFSYEEAAEMCGVAVGTVKSRANR 152 (188)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3567999999999999999988876543
No 217
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=69.36 E-value=6.3 Score=33.00 Aligned_cols=26 Identities=27% Similarity=0.313 Sum_probs=22.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+-+++..|+|+.|||+..++|.+.+
T Consensus 144 ~~~g~s~~eIA~~lgis~~tV~~~l~ 169 (184)
T PRK12539 144 KLEGLSVAEAATRSGMSESAVKVSVH 169 (184)
T ss_pred HHcCCcHHHHHHHHCcCHHHHHHHHH
Confidence 34589999999999999999987763
No 218
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=69.23 E-value=7 Score=32.41 Aligned_cols=27 Identities=30% Similarity=0.361 Sum_probs=22.4
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+-+++.+|+|..|||+..++|.+.++
T Consensus 148 ~~~~~s~~eIA~~lgis~~~V~~~l~r 174 (186)
T PRK13919 148 YYQGYTHREAAQLLGLPLGTLKTRARR 174 (186)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345899999999999999999876543
No 219
>PRK09191 two-component response regulator; Provisional
Probab=69.20 E-value=6.6 Score=33.54 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=24.3
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
|..+-+++.+|+|+.||+|..++|.+.++
T Consensus 99 l~~~~~~s~~eIA~~l~~s~~tV~~~l~r 127 (261)
T PRK09191 99 LTALEGFSVEEAAEILGVDPAEAEALLDD 127 (261)
T ss_pred HHHHhcCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44566899999999999999998888763
No 220
>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=69.12 E-value=11 Score=29.80 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=22.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
+++.|+|+.+|||..||+...+ .|+-.
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~-~Gll~ 27 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYES-LGLIP 27 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-cCCCC
Confidence 4789999999999999998877 56544
No 221
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=69.11 E-value=7.7 Score=39.44 Aligned_cols=36 Identities=25% Similarity=0.301 Sum_probs=31.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
..++--+.+||+.|||+.+||.+.-++|||.+=+|.
T Consensus 427 ~~~~g~~~~aA~~LGi~R~tLy~Klk~~g~~~~~~~ 462 (464)
T COG2204 427 ERTGGNKSEAAERLGISRKTLYRKLKEYGIDRSDVE 462 (464)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHhCCCccccC
Confidence 467888999999999999999999999999876553
No 222
>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=68.85 E-value=13 Score=29.92 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=23.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWP 69 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWP 69 (282)
|.|.|+|+.+||++.+| |..-+.|+-.=|
T Consensus 1 ~~I~eva~~~gvs~~tL-RyYe~~GLl~p~ 29 (123)
T cd04770 1 MKIGELAKAAGVSPDTI-RYYERIGLLPPP 29 (123)
T ss_pred CCHHHHHHHHCcCHHHH-HHHHHCCCCCCC
Confidence 57999999999999999 566777875433
No 223
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=68.81 E-value=20 Score=28.36 Aligned_cols=49 Identities=18% Similarity=0.241 Sum_probs=35.0
Q ss_pred CCCCCcCHHHHHhhc--CCcHHHHHHHhCC-ChHHHHH--HHHHcCCCCCCcch
Q 023462 24 TSTKSLSFDDISKYF--SLPLSDAANHLGV-CVSVLKK--ICRDNGLDRWPYRK 72 (282)
Q Consensus 24 ~~~~~iTledL~~yF--~lPi~EAAr~LGV-s~T~LKR--~CR~lGI~RWPyRK 72 (282)
+-...+-++-+..|+ +.++.++|+++|| +.++|.+ +.-+.+-..++-.+
T Consensus 7 ~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~~ 60 (116)
T COG2963 7 KYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSGK 60 (116)
T ss_pred cCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccCc
Confidence 444455666677777 6789999999995 9999994 44444555676655
No 224
>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=68.75 E-value=4.7 Score=28.05 Aligned_cols=24 Identities=29% Similarity=0.401 Sum_probs=21.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++.|+|+++|++.+++-|++..|
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 689999999999999999999876
No 225
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=68.69 E-value=7.1 Score=29.62 Aligned_cols=31 Identities=13% Similarity=0.282 Sum_probs=22.9
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+.++..--++++.|+|+.|||+.+.+-++-+
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 5667777789999999999999998888763
No 226
>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=68.57 E-value=7.8 Score=27.90 Aligned_cols=32 Identities=9% Similarity=0.152 Sum_probs=26.5
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+-|...=.+.+.|+|..||||..|++|=+..|
T Consensus 7 ~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 7 ELLKEKGKVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred HHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 44566668899999999999999999877654
No 227
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=68.44 E-value=6.9 Score=32.97 Aligned_cols=39 Identities=13% Similarity=0.237 Sum_probs=28.0
Q ss_pred CcCHHHHH---hhc-CCcHHHHHHHhCCChHHHH----HHHHHcCCC
Q 023462 28 SLSFDDIS---KYF-SLPLSDAANHLGVCVSVLK----KICRDNGLD 66 (282)
Q Consensus 28 ~iTledL~---~yF-~lPi~EAAr~LGVs~T~LK----R~CR~lGI~ 66 (282)
.||--|+. -+. +++.+|+|++|+||..|+| ++++++|+.
T Consensus 150 ~Lt~rE~evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~ 196 (216)
T PRK10840 150 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVE 196 (216)
T ss_pred cCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 46655543 222 8999999999999987764 667778874
No 228
>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=68.43 E-value=5.5 Score=28.11 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=21.0
Q ss_pred CCcHHHHHHHhCCChHHHHH----HHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKK----ICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR----~CR~lGI~ 66 (282)
+++.+|+|+.|||+..+++. +++++|+.
T Consensus 18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred cCCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 78999999999999988764 55566653
No 229
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=67.86 E-value=7.5 Score=32.52 Aligned_cols=25 Identities=16% Similarity=0.107 Sum_probs=21.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
-+-+++.+|+|..||||+.++|.+-
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHHHH
Confidence 3458999999999999999888654
No 230
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=67.79 E-value=6.4 Score=35.21 Aligned_cols=28 Identities=11% Similarity=0.151 Sum_probs=23.8
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+.+++.+|+|+.|||+..++|.+.++
T Consensus 183 ~~~eg~s~~EIA~~Lgis~~tVk~~l~R 210 (233)
T PRK12538 183 SYHENMSNGEIAEVMDTTVAAVESLLKR 210 (233)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4556899999999999999999987643
No 231
>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=67.48 E-value=5.9 Score=27.33 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=20.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++..+.|+.||||..|+.+-...+
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHH
Confidence 899999999999999999877655
No 232
>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=67.31 E-value=13 Score=30.71 Aligned_cols=30 Identities=30% Similarity=0.461 Sum_probs=24.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
|.|.|+|+.+||++.+|. .--+.|+-. |.|
T Consensus 1 m~IgE~A~~~gvs~~TLR-yYE~~GLl~-p~r 30 (133)
T cd04787 1 MKVKELANAAGVTPDTVR-FYTRIGLLR-PTR 30 (133)
T ss_pred CCHHHHHHHHCcCHHHHH-HHHHCCCCC-CCc
Confidence 678999999999999994 445789754 544
No 233
>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=67.17 E-value=19 Score=30.69 Aligned_cols=36 Identities=31% Similarity=0.329 Sum_probs=30.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc---CC-CCCCcchhh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN---GL-DRWPYRKFL 74 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyRKlk 74 (282)
.+|..+.|++||||.|.+....++| |+ ...|+|-..
T Consensus 34 ~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~ 73 (212)
T TIGR03338 34 KLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVF 73 (212)
T ss_pred EecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeE
Confidence 5789999999999999999888877 64 678888665
No 234
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=67.11 E-value=7.2 Score=31.76 Aligned_cols=33 Identities=21% Similarity=0.362 Sum_probs=28.9
Q ss_pred CcCHHHHHhhc---CCcHHHHHHHhCCChHHHHHHH
Q 023462 28 SLSFDDISKYF---SLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 28 ~iTledL~~yF---~lPi~EAAr~LGVs~T~LKR~C 60 (282)
..|-++|+..| ++++.++|..||+|...|-++-
T Consensus 9 ~~T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 9 RATRQELQANFELSGLSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 45888999888 7899999999999999988764
No 235
>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=66.62 E-value=7 Score=27.89 Aligned_cols=24 Identities=25% Similarity=0.392 Sum_probs=19.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-.+..||+.|||+.+++-+..++
T Consensus 13 ~gs~~~AA~~l~is~~~vs~~i~~ 36 (60)
T PF00126_consen 13 TGSISAAAEELGISQSAVSRQIKQ 36 (60)
T ss_dssp HSSHHHHHHHCTSSHHHHHHHHHH
T ss_pred hCCHHHHHHHhhccchHHHHHHHH
Confidence 347899999999999987666554
No 236
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=66.57 E-value=7.8 Score=35.77 Aligned_cols=24 Identities=21% Similarity=0.371 Sum_probs=21.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++++|+|+.||||...++++.++
T Consensus 248 ~~Tl~EIA~~lgvS~~rVrqi~~~ 271 (284)
T PRK06596 248 KSTLQELAAEYGVSAERVRQIEKN 271 (284)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 589999999999999999998875
No 237
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=66.38 E-value=9.3 Score=30.53 Aligned_cols=25 Identities=12% Similarity=0.165 Sum_probs=21.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-++++.|+|+.|||+..+++.+-.
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3489999999999999999887643
No 238
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=66.36 E-value=7.9 Score=32.36 Aligned_cols=35 Identities=34% Similarity=0.397 Sum_probs=28.9
Q ss_pred CCCCcC---HHHHHhhcCCcHHHHHHHhCCChHHHHHH
Q 023462 25 STKSLS---FDDISKYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 25 ~~~~iT---ledL~~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
....++ +..||+-++|.+.+-|+.||||+.+|...
T Consensus 40 ~~~~ls~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 40 KVKTLSPTEIKAIREKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred cCCCCCHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHH
Confidence 334455 66778999999999999999999999864
No 239
>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=66.21 E-value=8.9 Score=29.72 Aligned_cols=38 Identities=13% Similarity=0.137 Sum_probs=31.6
Q ss_pred CCcCHHHHHhhcCCcHHHHHHHhC-CChHHHHHHHHHcC
Q 023462 27 KSLSFDDISKYFSLPLSDAANHLG-VCVSVLKKICRDNG 64 (282)
Q Consensus 27 ~~iTledL~~yF~lPi~EAAr~LG-Vs~T~LKR~CR~lG 64 (282)
..+-.--++.+++++..++|+.|| .+.|++-.-|++.-
T Consensus 32 R~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~ 70 (90)
T cd06571 32 RQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIE 70 (90)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHH
Confidence 345556677889999999999999 99999999888753
No 240
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=66.09 E-value=9 Score=30.80 Aligned_cols=25 Identities=32% Similarity=0.311 Sum_probs=21.3
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+.+++..|+|+.|||+..+++++-+
T Consensus 139 ~~~~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 139 VEGLSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4589999999999999998887643
No 241
>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=65.97 E-value=7 Score=28.16 Aligned_cols=38 Identities=21% Similarity=0.291 Sum_probs=30.3
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHc---CCCCCCcchhh
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDN---GLDRWPYRKFL 74 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~l---GI~RWPyRKlk 74 (282)
.|.+++++.|..+|||..++-|..+++ ||-+.-+++|.
T Consensus 26 ~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~~i~ 66 (76)
T PF13545_consen 26 PLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRGKII 66 (76)
T ss_dssp EEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEEE
T ss_pred EecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCCEEE
Confidence 367889999999999999988887766 77666666554
No 242
>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=65.87 E-value=7 Score=28.26 Aligned_cols=27 Identities=15% Similarity=0.175 Sum_probs=23.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
.+++.|+|..||||..+|++.|.++..
T Consensus 19 ~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 19 WITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp SBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 678899999999999999999998763
No 243
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=65.84 E-value=9.6 Score=31.90 Aligned_cols=35 Identities=14% Similarity=0.275 Sum_probs=28.6
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc---CCC
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN---GLD 66 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l---GI~ 66 (282)
+.|+.-=-.|..+.|+.||+|.+++.++-+++ ||-
T Consensus 16 ~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 16 EALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence 44555567899999999999999999988876 753
No 244
>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=65.78 E-value=3.8 Score=30.20 Aligned_cols=32 Identities=16% Similarity=0.307 Sum_probs=20.7
Q ss_pred HHHHHhhcCCcH-HHHHHHhCCChHHHH-HHHHH
Q 023462 31 FDDISKYFSLPL-SDAANHLGVCVSVLK-KICRD 62 (282)
Q Consensus 31 ledL~~yF~lPi-~EAAr~LGVs~T~LK-R~CR~ 62 (282)
++.|...++..- .|.|+.|||+.++|- ..-++
T Consensus 3 i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 3 IERLKEALGVKSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp HHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhC
Confidence 355666666665 599999999999998 44343
No 245
>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=65.71 E-value=17 Score=29.01 Aligned_cols=26 Identities=15% Similarity=0.216 Sum_probs=23.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|++.|+|+.+||++++|+-.+++ |+.
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CCC
Confidence 57899999999999999999997 864
No 246
>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=65.63 E-value=14 Score=30.20 Aligned_cols=25 Identities=28% Similarity=0.404 Sum_probs=20.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|+|.|+|+.+||++.+|.-..+ .|+
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~-~Gl 25 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYES-IGL 25 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 6799999999999999986655 444
No 247
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=65.55 E-value=8.1 Score=33.15 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=31.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH---cCCCCCCcchhhhh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD---NGLDRWPYRKFLSG 76 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~---lGI~RWPyRKlkSL 76 (282)
.+++++.|..|||+..+|-|+.++ -|+-+|.+++|.-+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i~ 224 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIE 224 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEc
Confidence 478899999999999988886654 49989999987644
No 248
>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=65.47 E-value=6.9 Score=34.21 Aligned_cols=37 Identities=24% Similarity=0.354 Sum_probs=32.1
Q ss_pred HHHHHhhc--CCcHHHHHHHhC-CChHHHHHHHHHcCCCC
Q 023462 31 FDDISKYF--SLPLSDAANHLG-VCVSVLKKICRDNGLDR 67 (282)
Q Consensus 31 ledL~~yF--~lPi~EAAr~LG-Vs~T~LKR~CR~lGI~R 67 (282)
++.|++++ ++...|+|++|| ||...+-=.+++||+..
T Consensus 8 ~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~ 47 (162)
T PF07750_consen 8 VERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRLGLSG 47 (162)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcccccc
Confidence 45677776 799999999999 99999999999999854
No 249
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=65.33 E-value=9.1 Score=31.87 Aligned_cols=26 Identities=12% Similarity=0.190 Sum_probs=21.7
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+++.+|+|..|||+..+++.+..+
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHH
Confidence 34899999999999999988877654
No 250
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=65.18 E-value=9.4 Score=31.84 Aligned_cols=25 Identities=12% Similarity=0.115 Sum_probs=21.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
-+.+++.+|+|..|||+..++|..-
T Consensus 130 ~~e~~s~~EIA~~lgis~~tV~~~l 154 (179)
T PRK12543 130 YLHDYSQEEIAQLLQIPIGTVKSRI 154 (179)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHH
Confidence 4468999999999999999988653
No 251
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=65.16 E-value=7.7 Score=35.22 Aligned_cols=28 Identities=18% Similarity=0.216 Sum_probs=23.2
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
|.-+++++.+|+|+.||||..++|.+..
T Consensus 127 L~~~eg~S~~EIAe~LgiS~~tVksrL~ 154 (228)
T PRK06704 127 LKDVFQYSIADIAKVCSVSEGAVKASLF 154 (228)
T ss_pred hHHhhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3356799999999999999999987643
No 252
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=65.15 E-value=7.5 Score=33.55 Aligned_cols=26 Identities=12% Similarity=0.089 Sum_probs=23.4
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
-+++.+++|+.||+|..|+|+.-+.+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 46899999999999999999988855
No 253
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=65.09 E-value=8 Score=36.32 Aligned_cols=26 Identities=19% Similarity=0.123 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
..++.-..+||+.||||.+||.|..+
T Consensus 415 ~~~~gn~~~aa~~Lgisr~tl~rk~~ 440 (441)
T PRK10365 415 EKTGGNKTEAARQLGITRKTLLAKLS 440 (441)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHhh
Confidence 34677899999999999999988765
No 254
>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=65.06 E-value=17 Score=28.78 Aligned_cols=26 Identities=27% Similarity=0.418 Sum_probs=21.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|.+.|+|+.+||+..+|+...++--|
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GLl 26 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLL 26 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 67899999999999999877764334
No 255
>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=65.00 E-value=8.5 Score=33.83 Aligned_cols=24 Identities=21% Similarity=0.277 Sum_probs=21.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++.+|+|+.|||++.+++++.++
T Consensus 194 ~~S~~EIAe~lgis~~tV~~~~~r 217 (227)
T TIGR02846 194 RKTQREIAKILGISRSYVSRIEKR 217 (227)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 689999999999999999887543
No 256
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=65.00 E-value=22 Score=33.48 Aligned_cols=28 Identities=21% Similarity=0.300 Sum_probs=25.5
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
.+.+.+.|+.+|+|.++|.|++++.|..
T Consensus 197 ~~sl~~lA~~~gmS~stl~R~Fk~~g~s 224 (291)
T PRK15186 197 KWALKDISDSLYMSCSTLKRKLKQENTS 224 (291)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence 5789999999999999999999998753
No 257
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=64.90 E-value=9 Score=31.60 Aligned_cols=33 Identities=12% Similarity=0.173 Sum_probs=28.7
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+..+....+|.+.|.|+.+||+.+++-++++..
T Consensus 10 l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~ 42 (120)
T PRK13890 10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGK 42 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 556777889999999999999999999998654
No 258
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=64.81 E-value=8.8 Score=31.41 Aligned_cols=25 Identities=20% Similarity=0.210 Sum_probs=20.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
-+.+++..|+|..|||+..+++.+-
T Consensus 121 ~~~g~s~~eIA~~lgis~~tv~~~l 145 (165)
T PRK09644 121 DVHELTYEEAASVLDLKLNTYKSHL 145 (165)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHH
Confidence 4568999999999999988886543
No 259
>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=64.78 E-value=10 Score=26.24 Aligned_cols=24 Identities=29% Similarity=0.451 Sum_probs=21.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++.|+|+.|+++.+++-+++++|
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 899999999999999999999877
No 260
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=64.66 E-value=6.2 Score=32.99 Aligned_cols=37 Identities=11% Similarity=0.228 Sum_probs=29.9
Q ss_pred cCCcHHHHHHHhCCChHHHHHHH---HHcCCCCCCcchhh
Q 023462 38 FSLPLSDAANHLGVCVSVLKKIC---RDNGLDRWPYRKFL 74 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~C---R~lGI~RWPyRKlk 74 (282)
+.+++++.|..||++..++-|+- ++-||-++..|+|.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~ 206 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIV 206 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEE
Confidence 46888999999999998887754 45588888888764
No 261
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=64.62 E-value=6.7 Score=27.75 Aligned_cols=25 Identities=24% Similarity=0.432 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++..+.|..+|||.++..|++++.
T Consensus 19 ~~~~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 19 NLTFQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred CCcHhHHhhheeecHHHHHHHHHHH
Confidence 7889999999999999999999863
No 262
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=64.28 E-value=6.4 Score=34.81 Aligned_cols=24 Identities=17% Similarity=0.249 Sum_probs=19.9
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
|.|+|+|+..|||.+|+-|.....
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~ 24 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGK 24 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Confidence 468899999999999998887543
No 263
>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=64.11 E-value=19 Score=28.19 Aligned_cols=27 Identities=22% Similarity=0.281 Sum_probs=22.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|.+.|+|+.+||++.+|....+ .|+-.
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~-~Gll~ 27 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH-IGLLS 27 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCC
Confidence 6789999999999999988886 66543
No 264
>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=64.08 E-value=10 Score=30.67 Aligned_cols=29 Identities=24% Similarity=0.241 Sum_probs=23.9
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWP 69 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWP 69 (282)
+++.|+|+.+||++.||....+. |+.+=|
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~p~ 29 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLLHPV 29 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCC
Confidence 57899999999999999877776 875444
No 265
>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=63.92 E-value=14 Score=25.00 Aligned_cols=32 Identities=19% Similarity=0.184 Sum_probs=25.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
+...|+|+.|||+.+++.+.++++-=..|..+
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 78899999999999999999987733344443
No 266
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=63.81 E-value=10 Score=31.43 Aligned_cols=26 Identities=8% Similarity=0.118 Sum_probs=22.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+++..|+|..|||+..+++.++.+
T Consensus 145 ~~g~s~~eIA~~l~is~~tV~~~l~r 170 (184)
T PRK12512 145 VEGASIKETAAKLSMSEGAVRVALHR 170 (184)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 34899999999999999999887654
No 267
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=63.37 E-value=9.7 Score=32.43 Aligned_cols=26 Identities=8% Similarity=-0.098 Sum_probs=21.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+++.+|+|..|||+..+++.+..+
T Consensus 142 ~~g~s~~EIA~~lgis~~tV~~~l~R 167 (188)
T PRK12517 142 IGGFSGEEIAEILDLNKNTVMTRLFR 167 (188)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44889999999999999988877643
No 268
>PRK09726 antitoxin HipB; Provisional
Probab=63.35 E-value=15 Score=28.20 Aligned_cols=63 Identities=14% Similarity=0.181 Sum_probs=46.4
Q ss_pred CCcccccccCchhhhhhhhcCCCCCCCCcCHHHHHhhcCCcHHHHHHHh----CCChHHHHHHHHHcCCC
Q 023462 1 MMSSLSLHNNSSISKAAASSSISTSTKSLSFDDISKYFSLPLSDAANHL----GVCVSVLKKICRDNGLD 66 (282)
Q Consensus 1 ~~~~~~~~~~~~~~ka~as~~~k~~~~~iTledL~~yF~lPi~EAAr~L----GVs~T~LKR~CR~lGI~ 66 (282)
||+-+..-+.+.+....... +....+|.++|....+++...+.+-+ .++..+|.++|+.+||.
T Consensus 1 ~~~~~~~~~~~~l~~~lk~~---R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~ 67 (88)
T PRK09726 1 MMSFQKIYSPTQLANAMKLV---RQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELS 67 (88)
T ss_pred CCccccccCHHHHHHHHHHH---HHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCC
Confidence 56665555555554443322 34557999999999999999998865 36789999999999985
No 269
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=63.20 E-value=28 Score=21.38 Aligned_cols=40 Identities=18% Similarity=0.301 Sum_probs=32.9
Q ss_pred CCcCHHHHHhhcCCcHHHHHHHh----CCChHHHHHHHHHcCCC
Q 023462 27 KSLSFDDISKYFSLPLSDAANHL----GVCVSVLKKICRDNGLD 66 (282)
Q Consensus 27 ~~iTledL~~yF~lPi~EAAr~L----GVs~T~LKR~CR~lGI~ 66 (282)
..++..++....+++...+.+-+ .++..++.++|+.+|+.
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~ 52 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCC
Confidence 46788899999999988887754 35789999999999984
No 270
>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=63.13 E-value=18 Score=29.68 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=22.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|.|.|+|+.+||++.+|.-..+. |+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~-GLl 26 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEI-GLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 67999999999999999988776 543
No 271
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=62.98 E-value=12 Score=30.55 Aligned_cols=31 Identities=16% Similarity=0.085 Sum_probs=24.2
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+..++...+|.+.++|+.+||+.+++-++.+
T Consensus 10 lk~~R~~~gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 10 IRYRRKQLKLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4567788899999999999998876665544
No 272
>PRK10403 transcriptional regulator NarP; Provisional
Probab=62.91 E-value=11 Score=29.89 Aligned_cols=28 Identities=14% Similarity=0.250 Sum_probs=23.8
Q ss_pred CCcHHHHHHHhCCChHH----HHHHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSV----LKKICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~----LKR~CR~lGI~ 66 (282)
+++.+++|+.|++|..| ++++++++|+.
T Consensus 168 g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 68899999999999886 67788888874
No 273
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=62.80 E-value=8.7 Score=31.46 Aligned_cols=25 Identities=24% Similarity=0.263 Sum_probs=21.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
-+.+++..|+|..||++..++|.+-
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l 157 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRL 157 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3468999999999999999888654
No 274
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=62.57 E-value=14 Score=27.32 Aligned_cols=31 Identities=19% Similarity=0.277 Sum_probs=24.6
Q ss_pred HHHhh-cCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 33 DISKY-FSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 33 dL~~y-F~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.|... =.+.+.|+|+.+||+.+++.|..+.+
T Consensus 13 ~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 13 ALAEEPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34443 36889999999999999999988765
No 275
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=62.33 E-value=47 Score=32.16 Aligned_cols=77 Identities=14% Similarity=0.211 Sum_probs=49.3
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHH----HHHHHHHhhcCCccCCc-
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKEL----AELSKIARKSGFQPLSN- 111 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~l----lel~k~~~~~~~~~~n~- 111 (282)
-.+++.++|+.+|+|...|.|++++. |+. |..-+..+ +.++++.+ +-|.+|+...||.-.+.
T Consensus 98 ~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~T--P~~yl~~~----------Rl~~A~~lL~~~~sI~eIA~~~Gf~s~s~F 165 (353)
T PRK15435 98 TPVTLEALADQVAMSPFHLHRLFKATTGMT--PKAWQQAW----------RARRLREALAKGESVTTSILNAGFPDSSSY 165 (353)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHCcC--HHHHHHHH----------HHHHHHHHHhCCCCHHHHHHHhCCCChHHH
Confidence 46889999999999999999999986 885 33332222 22223322 23566667777764432
Q ss_pred --ccccccCCCCCCccc
Q 023462 112 --ETSKLHGVTSPPNLQ 126 (282)
Q Consensus 112 --~~sk~qgv~~~~~~~ 126 (282)
.--+.-|++|-+-..
T Consensus 166 ~~~Fkk~~G~TPs~yR~ 182 (353)
T PRK15435 166 YRKADETLGMTAKQFRH 182 (353)
T ss_pred HHHHHHHHCcCchhHHh
Confidence 234566888666543
No 276
>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=62.15 E-value=17 Score=30.27 Aligned_cols=32 Identities=28% Similarity=0.288 Sum_probs=26.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
.|+|.|+|+..||++.+|+-..+. |+..=|.|
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~p~~r 34 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLR-GLLHPVRR 34 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHC-CCCCCCcc
Confidence 478999999999999999988887 87653333
No 277
>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=61.76 E-value=15 Score=29.85 Aligned_cols=60 Identities=17% Similarity=0.172 Sum_probs=34.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH--cCCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD--NGLDRWPYRKFLSGKSIEDIKKYAAREKSKELAELSK 99 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~--lGI~RWPyRKlkSLksI~~l~e~a~~EK~k~llel~k 99 (282)
+.++.+||+.++||..++.+.+++ .|-.+=..|.-.-+ ..+.|+++.+.....++.||++
T Consensus 18 g~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Ki-d~~~L~~~v~~~pd~tl~Ela~ 79 (119)
T PF01710_consen 18 GKSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKI-DRDELKALVEENPDATLRELAE 79 (119)
T ss_pred cchHHHHHHHhCcHHHHHHHHHHhcccccccccccccccc-cHHHHHHHHHHCCCcCHHHHHH
Confidence 568999999999999999999774 34221111211111 2344555444444455555543
No 278
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=61.41 E-value=12 Score=31.78 Aligned_cols=25 Identities=12% Similarity=0.167 Sum_probs=19.9
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-+++.+|+|+.|||+..++|.+-+
T Consensus 150 ~~g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 150 IEGLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4478899999999999888876543
No 279
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=61.20 E-value=7.8 Score=37.33 Aligned_cols=26 Identities=35% Similarity=0.544 Sum_probs=25.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
+|+.+++|..||||+.++|.--|++|
T Consensus 19 gmk~~dIAeklGvspntiksWKrr~g 44 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRRDG 44 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHhcC
Confidence 59999999999999999999999998
No 280
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=60.99 E-value=12 Score=32.65 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=21.1
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++.+|+|..|||+..++|++..+
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~~r 221 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 899999999999999999877543
No 281
>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=60.86 E-value=10 Score=30.27 Aligned_cols=24 Identities=13% Similarity=0.110 Sum_probs=20.5
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+++..|+|..|||+..+++.+-.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~ 143 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLF 143 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHH
Confidence 489999999999999999887644
No 282
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=60.81 E-value=12 Score=32.18 Aligned_cols=22 Identities=23% Similarity=0.217 Sum_probs=19.8
Q ss_pred cCCcHHHHHHHhCCChHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~ 59 (282)
-+++.+|+|..|||+..++|.+
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~ 189 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSR 189 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHH
Confidence 3999999999999999999765
No 283
>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=60.65 E-value=8.6 Score=27.63 Aligned_cols=25 Identities=20% Similarity=0.282 Sum_probs=20.6
Q ss_pred CC-cHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SL-PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~l-Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.+ ...+.|+.+|||.+++.+.+++|
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 45 68899999999999999999877
No 284
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=60.47 E-value=11 Score=33.31 Aligned_cols=20 Identities=25% Similarity=0.408 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q 023462 42 LSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 42 i~EAAr~LGVs~T~LKR~CR 61 (282)
++|+|+.+|||.+|+.|...
T Consensus 1 i~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 1 MKDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred ChhHHHHhCCcHHHHHHHhC
Confidence 47889999999999888875
No 285
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=60.20 E-value=13 Score=30.08 Aligned_cols=25 Identities=16% Similarity=0.258 Sum_probs=20.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
.|.+++.+|+|..|||+..+++.+-
T Consensus 124 ~~~g~s~~eIA~~lgis~~tV~~~i 148 (166)
T PRK09639 124 RFSGYSYKEIAEALGIKESSVGTTL 148 (166)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3478999999999999998888654
No 286
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=60.11 E-value=20 Score=30.58 Aligned_cols=27 Identities=30% Similarity=0.315 Sum_probs=23.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|+|.|+|+.+|||+.||.-..+ .|+-.
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE~-~GLl~ 34 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQR-KGLLP 34 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHHH-CCCCC
Confidence 8999999999999999988875 57654
No 287
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=60.05 E-value=15 Score=26.46 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=21.8
Q ss_pred HHHHhhc--CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 32 DDISKYF--SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 32 edL~~yF--~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+.|..|| +..+.+||+.|+|...||+.+-++
T Consensus 3 ~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~k 35 (59)
T PF13556_consen 3 ETLRAYLENNGNISKTARALHIHRNTLRYRLKK 35 (59)
T ss_dssp -HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred hHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4566676 578999999999999987655443
No 288
>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=59.81 E-value=12 Score=30.52 Aligned_cols=30 Identities=27% Similarity=0.319 Sum_probs=24.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
++|.|+|+.+|||+.||.-..+. |+-. |-|
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~-GLl~-p~r 30 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK-GLLS-PER 30 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CcC
Confidence 57899999999999999888776 8754 433
No 289
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=59.79 E-value=12 Score=32.63 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=22.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-|-+++..|+|..|||+..++|.+..+
T Consensus 161 ~~~g~s~~EIAe~lgis~~tV~~~l~R 187 (206)
T PRK12544 161 EFIELETNEICHAVDLSVSNLNVLLYR 187 (206)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 456999999999999999999877543
No 290
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=59.33 E-value=5.7 Score=37.55 Aligned_cols=69 Identities=19% Similarity=0.273 Sum_probs=41.7
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchhhhh-hcHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKFLSG-KSIEDIKKYAAREKSKELAELSKIARK 103 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKlkSL-ksI~~l~e~a~~EK~k~llel~k~~~~ 103 (282)
+---+.+|+..|.|.|+.||||++++-- .+-|-+.-|-= ... |-++.|-++.++.=-+-+.++++++..
T Consensus 32 lrKWR~~F~vSQ~elA~~l~vSpSVISD--YE~GRRk~Pg~--~~vkk~V~ALIeID~eRGg~vik~l~~~l~~ 101 (241)
T COG1709 32 LRKWREIFNVSQTELARELGVSPSVISD--YESGRRKSPGI--AFVKKFVEALIEIDEERGGKVIKALARVLGS 101 (241)
T ss_pred HHHHHHHhCccHHHHHHHhCCCcceeeh--hhccCccCccH--HHHHHHHHHHHhhhHhhcchHHHHHHHHhcc
Confidence 4446789999999999999999999764 34443323321 111 223344443333333666666666665
No 291
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=59.28 E-value=13 Score=32.74 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=21.1
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-+++.+|+|+.|||+..++|.+-+
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3478999999999999999987644
No 292
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=59.23 E-value=14 Score=31.21 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=21.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+.+++.+|+|+.|||+..+++.+-.
T Consensus 145 ~~g~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 145 LLGEKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHH
Confidence 4589999999999999998887643
No 293
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=59.12 E-value=8.6 Score=33.80 Aligned_cols=26 Identities=19% Similarity=0.193 Sum_probs=22.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+.+++.+|+|..|||+..++|.+-+
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~ 187 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLH 187 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999999999987643
No 294
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=58.80 E-value=21 Score=29.98 Aligned_cols=27 Identities=19% Similarity=0.191 Sum_probs=23.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|++.|+|+.+||++.+|....++ |+..
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~ 28 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQ-GLMD 28 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 78999999999999999888776 7643
No 295
>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=58.36 E-value=18 Score=30.57 Aligned_cols=31 Identities=23% Similarity=0.250 Sum_probs=25.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcch
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYRK 72 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRK 72 (282)
|.+.|+|+.+||+..+|+...+. |+-. |.|.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~-GLl~-p~r~ 31 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNL-GLLT-PERS 31 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CccC
Confidence 46899999999999999998755 7655 7664
No 296
>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=58.03 E-value=13 Score=28.96 Aligned_cols=37 Identities=16% Similarity=0.219 Sum_probs=33.2
Q ss_pred CCcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 27 KSLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 27 ~~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.++-+.+|+...+---++.|++|||+.+.+.++..++
T Consensus 3 ~~~~l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~~ 39 (84)
T cd08804 3 KEERLAVIADHLGFSWTELARELDFTEEQIHQIRIEN 39 (84)
T ss_pred hhhHHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHC
Confidence 4677889999999999999999999999999998875
No 297
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=57.92 E-value=12 Score=31.39 Aligned_cols=24 Identities=17% Similarity=0.134 Sum_probs=20.5
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
+-+++.+|+|..|||+..++|.+-
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~~l 171 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKMRY 171 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHH
Confidence 347999999999999999988753
No 298
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.86 E-value=11 Score=32.58 Aligned_cols=28 Identities=25% Similarity=0.288 Sum_probs=24.2
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
|=+|.+.+||+.||||.+|..+.-+++.
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 4489999999999999999988777664
No 299
>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=57.77 E-value=14 Score=32.06 Aligned_cols=32 Identities=19% Similarity=0.264 Sum_probs=27.4
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+..++.-.+|++.+.|..+||+..++.++.+.
T Consensus 30 Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 30 VRAIRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 67788888999999999999998888887764
No 300
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=57.71 E-value=12 Score=32.38 Aligned_cols=26 Identities=19% Similarity=0.188 Sum_probs=23.5
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-+++++|+|+.||+|..+++++.++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46899999999999999999998875
No 301
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=57.58 E-value=12 Score=31.40 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=21.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+.+++.+|+|..|||+..++|.+-+
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l~ 192 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNALQ 192 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 45689999999999999999986443
No 302
>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=56.72 E-value=13 Score=35.50 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=26.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
+++.|+|+.+||+.++|+..+++..+.. |.|
T Consensus 34 ~~i~eva~~~gv~~~tlr~~e~~~~~~~-~~r 64 (387)
T TIGR03453 34 FTSGEVAKLLGVSDSYLRQLSLEGKGPE-PET 64 (387)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCC-CCc
Confidence 6999999999999999999988887543 433
No 303
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=56.32 E-value=16 Score=37.37 Aligned_cols=38 Identities=32% Similarity=0.474 Sum_probs=31.5
Q ss_pred cCHHHHHhhc----------CCc-HHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 29 LSFDDISKYF----------SLP-LSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 29 iTledL~~yF----------~lP-i~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
=++++|-..| .+| -...|++||||.|.+-..-|+|||.
T Consensus 460 gsLdei~~~fE~~VL~rly~~yPStRkLAkRLgvSHTaIAnKLRqyGi~ 508 (511)
T COG3283 460 GSLDEIVSRFERSVLTRLYRSYPSTRKLAKRLGVSHTAIANKLRQYGIG 508 (511)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCcHHHHHHHhCCcHHHHHHHHHHhCCC
Confidence 3778887666 344 5689999999999999999999995
No 304
>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=56.03 E-value=18 Score=24.93 Aligned_cols=33 Identities=18% Similarity=0.212 Sum_probs=26.7
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
..|..+=.+++.+.|+.++++.+++-+.++++-
T Consensus 10 ~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 10 RILYENGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp HHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 345566678999999999999999999998873
No 305
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=55.95 E-value=13 Score=24.47 Aligned_cols=20 Identities=30% Similarity=0.245 Sum_probs=16.4
Q ss_pred CCChHHHHHHHHHcCCCCCC
Q 023462 50 GVCVSVLKKICRDNGLDRWP 69 (282)
Q Consensus 50 GVs~T~LKR~CR~lGI~RWP 69 (282)
.++...||.+|+.+|++..-
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G 22 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSG 22 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCC
Confidence 35688899999999987654
No 306
>PRK15340 transcriptional regulator InvF; Provisional
Probab=55.55 E-value=12 Score=34.41 Aligned_cols=28 Identities=14% Similarity=0.356 Sum_probs=25.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc-CCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN-GLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l-GI~ 66 (282)
..++.++|+.+|||.++|.|+|+++ |+.
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~G~t 153 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRALGGK 153 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 6789999999999999999999997 875
No 307
>PRK10651 transcriptional regulator NarL; Provisional
Probab=55.38 E-value=18 Score=28.87 Aligned_cols=37 Identities=22% Similarity=0.190 Sum_probs=25.1
Q ss_pred cCHHHHH---hhc-CCcHHHHHHHhCCChHHHHH----HHHHcCC
Q 023462 29 LSFDDIS---KYF-SLPLSDAANHLGVCVSVLKK----ICRDNGL 65 (282)
Q Consensus 29 iTledL~---~yF-~lPi~EAAr~LGVs~T~LKR----~CR~lGI 65 (282)
||-.+.+ -+. +++.+++|++|+||..|++. +++++|+
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 5554443 223 47999999999999877664 4555554
No 308
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=55.35 E-value=48 Score=29.38 Aligned_cols=59 Identities=22% Similarity=0.271 Sum_probs=42.3
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCccCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQPLS 110 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~~~n 110 (282)
..+.+.|+.+|||...|-|.||+. |+. | .+.|+ ..+-++|+.+|. |.+|+..-||.-.+
T Consensus 189 ~~l~~lA~~~~~s~~~l~r~fk~~~G~t--~---------~~yi~-~~Rl~~A~~lL~~t~~sI~eIA~~~GF~~~s 253 (278)
T PRK10296 189 SALENMVRLSGKSQEYLTRATRRYYGKT--P---------MQIIN-EIRINFAKKQLEMTNYSVTDIAFEAGYSSPS 253 (278)
T ss_pred hhHHHHHHHhCCCHHHHHHHHHHHHCcC--H---------HHHHH-HHHHHHHHHHHHcCCCCHHHHHHHhCCCCHH
Confidence 357889999999999999999886 653 1 22222 345666777776 78888888887543
No 309
>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=55.27 E-value=14 Score=30.70 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=19.5
Q ss_pred cCCcHHHHHHHhCCChHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~C 60 (282)
-+++++|+|+.|||+..+++.+.
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l 186 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNAL 186 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 38999999999999999987543
No 310
>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=55.05 E-value=23 Score=29.69 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=20.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|+|.|+|+.+||++.+|.-. -+.|+-
T Consensus 1 m~Ige~a~~~gvs~~tLRyY-E~~GLl 26 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFY-EAEGLL 26 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHH-HHCCCC
Confidence 67899999999999999544 455543
No 311
>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=55.03 E-value=17 Score=33.05 Aligned_cols=26 Identities=12% Similarity=0.009 Sum_probs=21.9
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+-+++.+|+|..|||+..++|.+-+
T Consensus 174 ~~eg~S~~EIA~~Lgis~~TVk~rl~ 199 (244)
T TIGR03001 174 FVDGLSMDRIGAMYQVHRSTVSRWVA 199 (244)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34589999999999999999987644
No 312
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=54.98 E-value=16 Score=30.57 Aligned_cols=39 Identities=13% Similarity=0.245 Sum_probs=33.9
Q ss_pred CCCCCcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 24 TSTKSLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 24 ~~~~~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.++.+|=.|++-.-|++.+.++|+.|||...++-.+|.-
T Consensus 8 ~~PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 8 AHPGEILREEFLEPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred CCchHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 456667778888888999999999999999999999974
No 313
>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=54.92 E-value=17 Score=32.14 Aligned_cols=24 Identities=13% Similarity=0.239 Sum_probs=20.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.++++|+|..||||..+++++..+
T Consensus 196 ~~t~~EIA~~lgis~~~V~q~~~~ 219 (238)
T TIGR02393 196 PHTLEEVGKEFNVTRERIRQIESK 219 (238)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHH
Confidence 488999999999999999887654
No 314
>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=54.85 E-value=11 Score=33.81 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=22.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.-.+.|||+.|||+.++++++|+.-.
T Consensus 179 F~S~~eAa~~l~i~~~tI~~~l~~~~ 204 (214)
T TIGR01453 179 FDSIAEAARHLGISRGTISKYIKSGK 204 (214)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHcccc
Confidence 34799999999999999999998654
No 315
>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=54.74 E-value=9.1 Score=25.83 Aligned_cols=20 Identities=25% Similarity=0.444 Sum_probs=17.8
Q ss_pred HHHHHhCCChHHHHHHHHHc
Q 023462 44 DAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 44 EAAr~LGVs~T~LKR~CR~l 63 (282)
+.|+.+||+.+++-++|+--
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999744
No 316
>PRK09526 lacI lac repressor; Reviewed
Probab=54.51 E-value=11 Score=33.60 Aligned_cols=21 Identities=24% Similarity=0.350 Sum_probs=13.4
Q ss_pred cHHHHHHHhCCChHHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR 61 (282)
.|+|+|+..|||.+|+-|...
T Consensus 7 ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 7 TLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHhc
Confidence 566666666776666665553
No 317
>PRK13749 transcriptional regulator MerD; Provisional
Probab=54.43 E-value=28 Score=29.26 Aligned_cols=32 Identities=25% Similarity=0.201 Sum_probs=24.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
.|.|.|+|+..|||+.+|.-..+. |+..=|.|
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~-GLl~p~~r 34 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLR-GLLRPVAC 34 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHC-CCCCCCCc
Confidence 478999999999999999766654 86554434
No 318
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=53.82 E-value=20 Score=29.55 Aligned_cols=24 Identities=21% Similarity=0.319 Sum_probs=20.5
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
|=+++..|+|..|||+..++|..-
T Consensus 132 ~eg~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 132 LEGLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 338899999999999999988654
No 319
>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=53.75 E-value=12 Score=33.28 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=13.3
Q ss_pred cHHHHHHHhCCChHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~C 60 (282)
+++|+|+.+|||.+|+.|.-
T Consensus 3 ti~dIA~~agVS~sTVSr~L 22 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVL 22 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHh
Confidence 46677777777776666554
No 320
>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=53.74 E-value=21 Score=28.37 Aligned_cols=39 Identities=18% Similarity=0.250 Sum_probs=34.7
Q ss_pred CCCcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 26 TKSLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 26 ~~~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
+.++.+.+|....+..=.+.|++|||+.+-+-++.-++-
T Consensus 2 ~~~~~l~~Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~p 40 (84)
T cd08805 2 RVEMKMAVIREHLGLSWAELARELQFSVEDINRIRVENP 40 (84)
T ss_pred chhhHHHHHHHHhcchHHHHHHHcCCCHHHHHHHHHhCC
Confidence 457889999999999999999999999999999888764
No 321
>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=53.64 E-value=29 Score=27.37 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=20.9
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|.|.|+|+..|||..+|.-. -+.|+-
T Consensus 1 m~Ige~a~~~gvs~~tlRyY-e~~GLl 26 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHY-IDLGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHH-HHCCCc
Confidence 67899999999999999654 456654
No 322
>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=53.64 E-value=30 Score=28.29 Aligned_cols=27 Identities=15% Similarity=0.303 Sum_probs=22.0
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|.|.|+|+.+|||+.+|.-.. +.|+-.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe-~~GLl~ 27 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYE-EKGLIP 27 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-HCCCCC
Confidence 679999999999999998655 566544
No 323
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=53.38 E-value=21 Score=28.37 Aligned_cols=31 Identities=13% Similarity=0.195 Sum_probs=24.6
Q ss_pred HHHHHhhcCCcHHHHHHHhC------CChHHHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLG------VCVSVLKKICR 61 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LG------Vs~T~LKR~CR 61 (282)
|.+.+.-.+|.+.++|+.|| |+.+++-|+=+
T Consensus 16 lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 16 FKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 44556777999999999999 58999877543
No 324
>PRK06930 positive control sigma-like factor; Validated
Probab=53.34 E-value=18 Score=31.56 Aligned_cols=27 Identities=19% Similarity=0.313 Sum_probs=22.7
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+.+++..|+|..|||+..+++.+.++
T Consensus 127 ~~eg~s~~EIA~~lgiS~~tVk~~l~R 153 (170)
T PRK06930 127 RGYGLSYSEIADYLNIKKSTVQSMIER 153 (170)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345899999999999999998877653
No 325
>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=53.04 E-value=16 Score=37.25 Aligned_cols=26 Identities=23% Similarity=0.256 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
..++-...+||+.||||.|||.|..+
T Consensus 500 ~~~~Gn~~~aA~~LGIsRtTL~Rklk 525 (526)
T TIGR02329 500 ERFGGDRDAAAKALGISRTTLWRRLK 525 (526)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 44577899999999999999988765
No 326
>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=52.98 E-value=20 Score=24.37 Aligned_cols=26 Identities=31% Similarity=0.431 Sum_probs=19.4
Q ss_pred cHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 41 PLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
.|.|+|+.+||++.+|...=++ |+..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~-Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE-GLLP 26 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT-TSS-
T ss_pred CHHHHHHHHCCCHHHHHHHHHC-CCCC
Confidence 3789999999999999776655 7643
No 327
>PRK08359 transcription factor; Validated
Probab=52.73 E-value=19 Score=32.35 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=18.6
Q ss_pred cCCcHHHHHHHhCCChHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~ 59 (282)
-+|.+.|.|..|||+.+++.++
T Consensus 97 kglSQeeLA~~lgvs~stI~~i 118 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRI 118 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHH
Confidence 3888999999999999998665
No 328
>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=52.67 E-value=21 Score=24.27 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=19.2
Q ss_pred HhhcCCcHHHHHHHhCCChHHHHHH
Q 023462 35 SKYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 35 ~~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
..|-.+.+.++|+++||+.++|-+.
T Consensus 12 ~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 12 KGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred hCHHhCCHHHHHHHHccchhhHHHH
Confidence 4677788888888888888887654
No 329
>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=52.62 E-value=20 Score=31.19 Aligned_cols=23 Identities=26% Similarity=0.361 Sum_probs=20.5
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|+.|||+..+++++.+
T Consensus 191 ~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 191 ELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 88999999999999999987644
No 330
>PHA02591 hypothetical protein; Provisional
Probab=52.55 E-value=17 Score=29.63 Aligned_cols=24 Identities=21% Similarity=0.325 Sum_probs=21.5
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-++.+.++|+.|||+..++++.-+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 389999999999999999998765
No 331
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=52.30 E-value=30 Score=29.13 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=20.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|.|.|+|+.+||++.+|.-..+ .|+-
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~-~GLl 26 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEE-KGLV 26 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence 6789999999999999976655 4443
No 332
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=51.64 E-value=18 Score=28.18 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=21.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.+|+.+||+.||+...++.+..+.+
T Consensus 13 ~~s~~~Aa~~lG~~~~~v~~wv~~f 37 (65)
T PF05344_consen 13 QISVAQAADRLGTDPGTVRRWVRMF 37 (65)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHHH
Confidence 4678999999999999998877754
No 333
>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=51.62 E-value=12 Score=28.21 Aligned_cols=25 Identities=16% Similarity=0.154 Sum_probs=19.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
...+.+.|.+|+||.++++|.++++
T Consensus 30 ~~s~~~la~~~~iS~sti~~~i~~l 54 (87)
T PF05043_consen 30 YVSIEDLAEELFISRSTIYRDIKKL 54 (87)
T ss_dssp EEEHHHHHHHHT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6779999999999999999877654
No 334
>PRK09492 treR trehalose repressor; Provisional
Probab=51.43 E-value=13 Score=32.76 Aligned_cols=37 Identities=19% Similarity=0.342 Sum_probs=19.6
Q ss_pred cCHHHHHhhcCCcHHHHHHHhC----CChHHHHH---HHHHcCC
Q 023462 29 LSFDDISKYFSLPLSDAANHLG----VCVSVLKK---ICRDNGL 65 (282)
Q Consensus 29 iTledL~~yF~lPi~EAAr~LG----Vs~T~LKR---~CR~lGI 65 (282)
+|+.||.+.+++...-+.+.|+ ||..+=+| .++++|.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY 48 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGF 48 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCC
Confidence 4555555555555555555553 44444333 3566774
No 335
>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=51.38 E-value=17 Score=27.87 Aligned_cols=32 Identities=28% Similarity=0.363 Sum_probs=25.5
Q ss_pred CcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 28 SLSFDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 28 ~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.|+|.|.-.-++ +.+||+.|||..+.+-+.-|
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 467777777776 99999999999999877665
No 336
>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=51.34 E-value=18 Score=26.63 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=20.7
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
-.....++|+.|||+.++.-..+++|
T Consensus 21 ~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 21 GPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp SSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCCChHHHHHHHHHH
Confidence 35678999999999999888877776
No 337
>PRK13558 bacterio-opsin activator; Provisional
Probab=51.20 E-value=15 Score=36.55 Aligned_cols=27 Identities=26% Similarity=0.480 Sum_probs=24.2
Q ss_pred hhcCCc----HHHHHHHhCCChHHHHHHHHH
Q 023462 36 KYFSLP----LSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 36 ~yF~lP----i~EAAr~LGVs~T~LKR~CR~ 62 (282)
.||+.| ..|+|.+||||.+++-.+-|+
T Consensus 623 gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~ 653 (665)
T PRK13558 623 GYFEWPRRVEGEELAESMGISRSTFHQHLRA 653 (665)
T ss_pred CCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 899887 899999999999999887775
No 338
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=51.12 E-value=22 Score=31.76 Aligned_cols=25 Identities=16% Similarity=0.310 Sum_probs=21.3
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+-+++++|+|+.|||+..+++++-+
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3488999999999999999987644
No 339
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=50.80 E-value=13 Score=33.22 Aligned_cols=23 Identities=26% Similarity=0.483 Sum_probs=19.3
Q ss_pred cHHHHHHHhCCChHHHHHHHHHc
Q 023462 41 PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+++|+|+..|||.+|+-|.....
T Consensus 3 ti~dIA~~agVS~~TVSrvln~~ 25 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLNDD 25 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcCC
Confidence 68899999999999998887543
No 340
>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=50.45 E-value=46 Score=24.05 Aligned_cols=43 Identities=14% Similarity=0.254 Sum_probs=37.0
Q ss_pred CCCCCcCHHHHHhhcCCcHHHHHHHh----CCChHHHHHHHHHcCCC
Q 023462 24 TSTKSLSFDDISKYFSLPLSDAANHL----GVCVSVLKKICRDNGLD 66 (282)
Q Consensus 24 ~~~~~iTledL~~yF~lPi~EAAr~L----GVs~T~LKR~CR~lGI~ 66 (282)
.....+|.++|....+++...+.+-+ .++..++.++|+-+|+.
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~ 60 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTS 60 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 34567899999999999999999877 47889999999999984
No 341
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=50.38 E-value=22 Score=30.38 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=28.1
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+..++.-.++.+.++|+.+||+.++|-++-+-
T Consensus 11 ~l~~~R~~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 456777888999999999999999999988754
No 342
>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=49.93 E-value=24 Score=27.94 Aligned_cols=30 Identities=20% Similarity=0.155 Sum_probs=24.2
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
++-|.. =.+++.++|+.+|||.+++-|.-.
T Consensus 12 ~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 12 GKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 345556 678999999999999999988553
No 343
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=49.89 E-value=29 Score=26.05 Aligned_cols=28 Identities=32% Similarity=0.389 Sum_probs=22.8
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHH
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~ 59 (282)
.+++-.||+ .+..+|+.|||+...+-+-
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 467788998 7889999999999998665
No 344
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=49.84 E-value=23 Score=31.38 Aligned_cols=27 Identities=11% Similarity=0.315 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCChHHHH----HHHHHcCC
Q 023462 39 SLPLSDAANHLGVCVSVLK----KICRDNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LK----R~CR~lGI 65 (282)
+++.+|+|++|+||..|+| ++++++|+
T Consensus 149 G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 149 GYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 8999999999999987765 56666665
No 345
>PRK13698 plasmid-partitioning protein; Provisional
Probab=49.75 E-value=72 Score=31.33 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=30.2
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
.|...|++.++++|+.||+|.+.+-+.-|-+.++.
T Consensus 170 ~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP~ 204 (323)
T PRK13698 170 RLQNEFAGNISALADAENISRKIITRCINTAKLPK 204 (323)
T ss_pred HHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcCCH
Confidence 35567899999999999999999999999888743
No 346
>KOG3917 consensus Beta-1,4-galactosyltransferase B4GALT7/SQV-3 [Carbohydrate transport and metabolism]
Probab=49.75 E-value=10 Score=36.52 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.8
Q ss_pred ccccccccCCCCCC
Q 023462 167 TASYKWWGGRSSDG 180 (282)
Q Consensus 167 t~s~KWWG~~~~~~ 180 (282)
.-|||.|||.--|+
T Consensus 198 GMSN~yWGWGlEDD 211 (310)
T KOG3917|consen 198 GMSNKYWGWGLEDD 211 (310)
T ss_pred CccccccccCcccc
Confidence 45899999986654
No 347
>PHA00675 hypothetical protein
Probab=49.63 E-value=21 Score=28.76 Aligned_cols=41 Identities=15% Similarity=0.272 Sum_probs=29.5
Q ss_pred CCCCCCcCHHHHHhhc------CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 23 STSTKSLSFDDISKYF------SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 23 k~~~~~iTledL~~yF------~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+-....||-.+....+ .+...+.|+.||||.+++-.||+.-
T Consensus 17 ~h~~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk 63 (78)
T PHA00675 17 DHPNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYE 63 (78)
T ss_pred CCCCcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccc
Confidence 3445556655554433 4557799999999999999999853
No 348
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=49.59 E-value=37 Score=22.06 Aligned_cols=25 Identities=16% Similarity=0.251 Sum_probs=20.0
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.+++.+.|+.|+|+.+++.+.-..+
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L 38 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKL 38 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4788888888999988887776655
No 349
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=49.44 E-value=23 Score=31.57 Aligned_cols=38 Identities=18% Similarity=0.169 Sum_probs=29.0
Q ss_pred CCcCHHHHHhhc-----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 27 KSLSFDDISKYF-----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 27 ~~iTledL~~yF-----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
.++++..| +|| +-.+..||+.|+||.+++-+.-+ ++|+
T Consensus 9 ~~m~~~~l-~~F~av~e~gS~t~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (303)
T PRK10082 9 HNIETKWL-YDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGV 55 (303)
T ss_pred cccchHHH-HHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCC
Confidence 55777777 444 67899999999999988766555 5675
No 350
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=49.34 E-value=18 Score=31.63 Aligned_cols=37 Identities=14% Similarity=0.116 Sum_probs=26.8
Q ss_pred cCHHHHH--hh--cCCcHHHHHHHhCCChHHHH----HHHHHcCC
Q 023462 29 LSFDDIS--KY--FSLPLSDAANHLGVCVSVLK----KICRDNGL 65 (282)
Q Consensus 29 iTledL~--~y--F~lPi~EAAr~LGVs~T~LK----R~CR~lGI 65 (282)
||--|+. .+ =+++.+|+|++|+||..|+| ++++++|+
T Consensus 138 LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 138 LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 6655544 11 28899999999999988765 55666776
No 351
>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=49.33 E-value=26 Score=30.35 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=23.6
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..|++...++|+.||++.++++|+-+=.
T Consensus 117 ~~~g~s~~~iA~~lg~s~~~V~r~l~l~ 144 (187)
T TIGR00180 117 EKFSMTQEDLAKKIGKSRAHITNLLRLL 144 (187)
T ss_pred HHhCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3478999999999999999998876654
No 352
>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=49.26 E-value=24 Score=30.61 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=20.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++++|+|+.|||+..+++++-++
T Consensus 194 ~~s~~eIA~~lgis~~~v~~~~~r 217 (227)
T TIGR02980 194 DKTQSEIAERLGISQMHVSRLLRR 217 (227)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 789999999999999998877543
No 353
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=49.21 E-value=19 Score=31.70 Aligned_cols=23 Identities=22% Similarity=0.319 Sum_probs=20.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++.+|+|..|||+..+++++.+
T Consensus 195 ~~S~~EIA~~lgis~~tV~~~~~ 217 (233)
T PRK05803 195 EKTQREIAKALGISRSYVSRIEK 217 (233)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 47999999999999999988743
No 354
>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=49.02 E-value=27 Score=26.39 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=20.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++.+|.|+.+||+...|.++..+|
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 789999999999999999998865
No 355
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=48.90 E-value=59 Score=27.47 Aligned_cols=56 Identities=13% Similarity=0.191 Sum_probs=37.5
Q ss_pred HHhCCChHHHHHHHHHcCCCCCCcchhhhhh--cHHHHHHHHHH-------HHHHHHHHHHHHHhhc
Q 023462 47 NHLGVCVSVLKKICRDNGLDRWPYRKFLSGK--SIEDIKKYAAR-------EKSKELAELSKIARKS 104 (282)
Q Consensus 47 r~LGVs~T~LKR~CR~lGI~RWPyRKlkSLk--sI~~l~e~a~~-------EK~k~llel~k~~~~~ 104 (282)
...||+.++-+.+|+++||. |..++..|. -|+.|.++... =+...-.+|+++.+=+
T Consensus 21 ~i~GIG~~~A~~ic~~lgi~--~~~~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~~I~ 85 (122)
T CHL00137 21 YIYGIGLTSAKEILEKANID--PDIRTKDLTDEQISALREIIEENYQVEGDLRRFESLNIKRLMEIN 85 (122)
T ss_pred ccccccHHHHHHHHHHcCcC--cCcCcccCCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHHHhC
Confidence 45699999999999999995 778888663 46666655431 1333345555555444
No 356
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=48.85 E-value=16 Score=32.60 Aligned_cols=20 Identities=30% Similarity=0.368 Sum_probs=11.1
Q ss_pred cHHHHHHHhCCChHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~C 60 (282)
+++|+|++.|||.+|+.|.-
T Consensus 8 Ti~dIA~~agVS~~TVSr~L 27 (342)
T PRK10014 8 TIHDVALAAGVSVSTVSLVL 27 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHH
Confidence 45555555555555555543
No 357
>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=48.49 E-value=18 Score=27.98 Aligned_cols=29 Identities=21% Similarity=0.146 Sum_probs=20.4
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
|++.+.|+|++||.|.+.+-++-+=+..+
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP 30 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLALLDLP 30 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHGGGS--
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHcCC
Confidence 78999999999999999999887766554
No 358
>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=48.06 E-value=31 Score=26.40 Aligned_cols=39 Identities=23% Similarity=0.305 Sum_probs=33.3
Q ss_pred CCCcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 26 TKSLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 26 ~~~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
..++.|..|....+.--++.|++||++.+.+..+..++.
T Consensus 2 ~~~~~l~~ia~~lG~dW~~LAr~Lg~~~~dI~~i~~~~~ 40 (84)
T cd08317 2 RADIRLADISNLLGSDWPQLARELGVSETDIDLIKAENP 40 (84)
T ss_pred cccchHHHHHHHHhhHHHHHHHHcCCCHHHHHHHHHHCC
Confidence 346778889999999999999999999999999888764
No 359
>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=48.04 E-value=32 Score=30.79 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=31.9
Q ss_pred CCCCCcCHHHHHhhc----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 24 TSTKSLSFDDISKYF----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 24 ~~~~~iTledL~~yF----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
++-..+++.+|+-+. +-.+..||+.|||+.++|-|.-+ ++|+
T Consensus 3 ~~~~~~~l~~L~~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 52 (302)
T TIGR02036 3 RRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGI 52 (302)
T ss_pred ccccCcCHHHHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 455677887775433 66899999999999998877766 4575
No 360
>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=47.94 E-value=40 Score=22.82 Aligned_cols=41 Identities=22% Similarity=0.316 Sum_probs=33.0
Q ss_pred CCCcCHHHHHhhcCCcHHHHHHHh----CCChHHHHHHHHHcCCC
Q 023462 26 TKSLSFDDISKYFSLPLSDAANHL----GVCVSVLKKICRDNGLD 66 (282)
Q Consensus 26 ~~~iTledL~~yF~lPi~EAAr~L----GVs~T~LKR~CR~lGI~ 66 (282)
...+|..+|....+++..-+.+-+ .++..++.++|+-+|++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~ 51 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVS 51 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSE
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCC
Confidence 456889999999999999998886 37788999999999873
No 361
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=47.69 E-value=35 Score=33.29 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=22.0
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+.+.|||+.|||+.++|++.+++
T Consensus 48 ~ft~~e~A~~lgvs~~tlr~~~~~ 71 (405)
T PRK13869 48 KFTSGEAARLMKISDSTLRKMTLA 71 (405)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHc
Confidence 447999999999999999999987
No 362
>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=47.62 E-value=77 Score=25.92 Aligned_cols=30 Identities=27% Similarity=0.378 Sum_probs=22.5
Q ss_pred cHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 41 PLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
+|.|+|+.+||++.|| |..-+.|+-.=|.|
T Consensus 1 ~I~e~a~~~gvs~~tl-R~Ye~~GLl~~~~r 30 (124)
T TIGR02051 1 TIGELAKAAGVNVETI-RYYERKGLLPEPDR 30 (124)
T ss_pred CHHHHHHHHCcCHHHH-HHHHHCCCCCCCcc
Confidence 4789999999999999 44455676554444
No 363
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=47.57 E-value=20 Score=32.96 Aligned_cols=34 Identities=24% Similarity=0.232 Sum_probs=26.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcchh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLDRWPYRKF 73 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyRKl 73 (282)
+|.++|||..||||.+||.|..|+=-| |=|-++.
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~G~i-~~~~~~~ 34 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIREGKI-RVVTTEG 34 (193)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHcCcc-cceEecC
Confidence 478999999999999999999987555 3444433
No 364
>PF13730 HTH_36: Helix-turn-helix domain
Probab=47.37 E-value=23 Score=24.31 Aligned_cols=23 Identities=17% Similarity=0.289 Sum_probs=20.9
Q ss_pred cHHHHHHHhCCChHHHHHHHHHc
Q 023462 41 PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++...|+.+|+|..++.|...+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 58999999999999999988876
No 365
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=47.36 E-value=26 Score=31.63 Aligned_cols=36 Identities=17% Similarity=0.276 Sum_probs=26.1
Q ss_pred cCHHHHHhhc-----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 29 LSFDDISKYF-----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 29 iTledL~~yF-----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+++++|+ || +-.+..||++|||+.++|-|.-+ ++|+
T Consensus 2 ~~~~~L~-~f~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 46 (308)
T PRK10094 2 FDPETLR-TFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGV 46 (308)
T ss_pred CCHHHHH-HHHHHHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 4455555 33 67899999999999988766555 5575
No 366
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=47.29 E-value=25 Score=31.02 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=29.1
Q ss_pred CcCHHHHH--h--hcCCcHHHHHHHhCCChHHHH----HHHHHcCCCC
Q 023462 28 SLSFDDIS--K--YFSLPLSDAANHLGVCVSVLK----KICRDNGLDR 67 (282)
Q Consensus 28 ~iTledL~--~--yF~lPi~EAAr~LGVs~T~LK----R~CR~lGI~R 67 (282)
.+|-.++. + --+++.+|+|++|++|..|+| ++.+++|+..
T Consensus 148 ~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~ 195 (211)
T COG2197 148 LLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRN 195 (211)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCC
Confidence 45554443 2 238999999999999998887 5667777754
No 367
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=46.95 E-value=27 Score=31.29 Aligned_cols=23 Identities=9% Similarity=0.287 Sum_probs=20.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|+.|||+..+++++-+
T Consensus 225 ~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 225 GKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 88999999999999999887644
No 368
>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=46.91 E-value=24 Score=25.41 Aligned_cols=28 Identities=18% Similarity=0.178 Sum_probs=23.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..=.+...|+|+.+||+.+++-+..++|
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L 46 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSL 46 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHH
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445689999999999999998888766
No 369
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=46.77 E-value=14 Score=32.90 Aligned_cols=21 Identities=29% Similarity=0.468 Sum_probs=13.5
Q ss_pred cHHHHHHHhCCChHHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR 61 (282)
+++|+|+..|||.+|+-|...
T Consensus 7 ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhC
Confidence 566667777777666666553
No 370
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=46.68 E-value=64 Score=28.20 Aligned_cols=36 Identities=25% Similarity=0.347 Sum_probs=30.5
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc---C-CCCCCcchhh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN---G-LDRWPYRKFL 74 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l---G-I~RWPyRKlk 74 (282)
-+...+.|+.||||.|.+....++| | |.+=|.|-..
T Consensus 39 ~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~ 78 (230)
T COG1802 39 RLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAF 78 (230)
T ss_pred CccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCe
Confidence 6789999999999999999888887 5 4566888776
No 371
>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=46.61 E-value=22 Score=31.37 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=19.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~C 60 (282)
+++.+|+|+.|||+..+++++-
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l 219 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
Confidence 5999999999999999997663
No 372
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.61 E-value=39 Score=23.61 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=24.8
Q ss_pred CCcCHHHHHhhcCCcHHHHHHHh-----CCChHHHHHHHHHcCCC
Q 023462 27 KSLSFDDISKYFSLPLSDAANHL-----GVCVSVLKKICRDNGLD 66 (282)
Q Consensus 27 ~~iTledL~~yF~lPi~EAAr~L-----GVs~T~LKR~CR~lGI~ 66 (282)
..+|..+|+..-+++.....+.+ .++..+|.++|.-+|+.
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~ 53 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCS 53 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCC
Confidence 35677788888888877777766 47788999999999874
No 373
>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=46.44 E-value=52 Score=26.79 Aligned_cols=27 Identities=26% Similarity=0.393 Sum_probs=21.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|++.|+|+.+||++.||.-. -+.|+-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Y-e~~GLl~ 27 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYY-QRRGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHH-HHCCCCC
Confidence 67999999999999999555 4556543
No 374
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=46.22 E-value=21 Score=31.18 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=22.5
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l 63 (282)
-|| ..+.|++||||.|+++...++|
T Consensus 30 ~LPsE~eLae~~gVSRt~VReAL~~L 55 (239)
T PRK04984 30 ILPAERELSELIGVTRTTLREVLQRL 55 (239)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 475 8899999999999999999877
No 375
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=46.15 E-value=37 Score=25.19 Aligned_cols=24 Identities=13% Similarity=0.102 Sum_probs=20.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++..|+|+.|||+.+++.|.-..|
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 889999999999999988876544
No 376
>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=45.91 E-value=1.3e+02 Score=25.95 Aligned_cols=36 Identities=17% Similarity=0.201 Sum_probs=28.9
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHHc---CCCCCCcchhh
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRDN---GLDRWPYRKFL 74 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~l---GI~RWPyRKlk 74 (282)
.=.+.-.|.|+.|||+...+.|+|..| |+.. |||.+
T Consensus 26 ~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~--~~r~r 64 (158)
T TIGR00373 26 KGEFTDEEISLELGIKLNEVRKALYALYDAGLAD--YKRRK 64 (158)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce--eeeee
Confidence 336889999999999999999999865 7765 55544
No 377
>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=45.45 E-value=30 Score=31.01 Aligned_cols=23 Identities=9% Similarity=0.287 Sum_probs=19.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|+.|||+..++.++-+
T Consensus 222 ~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 222 GKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 68999999999999998877643
No 378
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=45.42 E-value=19 Score=32.40 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=13.3
Q ss_pred cHHHHHHHhCCChHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~C 60 (282)
+++|+|+.+|||.+|+-|.-
T Consensus 3 ti~dIA~~aGVS~~TVSrvL 22 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVL 22 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHH
Confidence 56677777777777666554
No 379
>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=45.39 E-value=19 Score=31.89 Aligned_cols=22 Identities=18% Similarity=0.460 Sum_probs=17.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHH
Q 023462 40 LPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+++|+|+..|||.+|+-|.-+
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 4678888888888888877654
No 380
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=45.28 E-value=23 Score=28.96 Aligned_cols=39 Identities=15% Similarity=0.281 Sum_probs=22.9
Q ss_pred CcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 28 SLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 28 ~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
.+++++|...+++|..-+-..|.-+...|++...+.|+.
T Consensus 134 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~ 172 (173)
T PRK09645 134 GWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERGVT 172 (173)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccccC
Confidence 455566666666666666666666666666555555554
No 381
>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=45.08 E-value=19 Score=32.90 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=20.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|..|||+..++|++-+
T Consensus 242 ~~s~~EIA~~Lgis~~tVk~~l~ 264 (285)
T TIGR02394 242 PATLEEVAAEVGLTRERVRQIQV 264 (285)
T ss_pred CccHHHHHHHHCCCHHHHHHHHH
Confidence 68999999999999999988754
No 382
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=45.06 E-value=29 Score=30.52 Aligned_cols=27 Identities=22% Similarity=0.202 Sum_probs=21.5
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+-.+..||++|||+.+++-+.-+ ++|+
T Consensus 16 ~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~ 46 (294)
T PRK13348 16 TGSFERAARRLHVTPSAVSQRIKALEESLGQ 46 (294)
T ss_pred cCCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 56899999999999888766555 5675
No 383
>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=44.80 E-value=58 Score=26.47 Aligned_cols=31 Identities=23% Similarity=0.380 Sum_probs=23.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
|+|.|+|+.+||++.+|.-..+ .|+-.=|.|
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~-~GLl~p~~r 31 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEK-EGLLPAPAR 31 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCc
Confidence 6799999999999999976655 665443333
No 384
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=44.57 E-value=31 Score=29.99 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=21.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.--+|++.+.|..+||+.+++.++-+
T Consensus 79 e~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 79 EKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 33489999999999999999988864
No 385
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=44.48 E-value=31 Score=30.42 Aligned_cols=27 Identities=19% Similarity=0.065 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+..+..||++|||+.+++-+.-+ ++|+
T Consensus 16 ~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (301)
T PRK14997 16 EGGFAAAGRALDEPKSKLSRRIAQLEERLGV 46 (301)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 67899999999999998766665 5575
No 386
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.16 E-value=28 Score=29.02 Aligned_cols=35 Identities=23% Similarity=0.228 Sum_probs=29.8
Q ss_pred CCCcCHHHHHhhc---CCcHHHHHHHhCCChHHHHHHH
Q 023462 26 TKSLSFDDISKYF---SLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 26 ~~~iTledL~~yF---~lPi~EAAr~LGVs~T~LKR~C 60 (282)
...+|.+||+..| .|...++|.+||++.-.|-|+-
T Consensus 7 q~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 7 QKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred HHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHH
Confidence 3456889999988 5679999999999999888876
No 387
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=44.11 E-value=23 Score=29.22 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=26.5
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc---C-CCCCCcc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN---G-LDRWPYR 71 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l---G-I~RWPyR 71 (282)
+++.+.|+.+|||.+.|.++.++| | |...|.+
T Consensus 26 ~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~ 61 (141)
T PRK11014 26 TSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGK 61 (141)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCC
Confidence 578999999999999999999877 6 3556655
No 388
>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=44.05 E-value=26 Score=30.18 Aligned_cols=26 Identities=15% Similarity=0.092 Sum_probs=22.4
Q ss_pred hcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+-++++.|+|+.||+|..+++++-++
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 56899999999999999999876543
No 389
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=43.93 E-value=20 Score=28.15 Aligned_cols=26 Identities=27% Similarity=0.313 Sum_probs=20.8
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|++.|+|+.+||++.||.-.=+.--|
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GLl 26 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLL 26 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCCC
Confidence 57899999999999999665554445
No 390
>KOG4721 consensus Serine/threonine protein kinase, contains leucine zipper domain [Signal transduction mechanisms]
Probab=43.45 E-value=64 Score=35.11 Aligned_cols=83 Identities=24% Similarity=0.293 Sum_probs=45.5
Q ss_pred hcHHHHHHHHH--HHHHHHHHHHHHHHhhcC---Cc-c----CCc--ccccccCCCCCCcccccCCCCCCCCCCcccchh
Q 023462 77 KSIEDIKKYAA--REKSKELAELSKIARKSG---FQ-P----LSN--ETSKLHGVTSPPNLQQQGSKNSPVGQPHVLLNA 144 (282)
Q Consensus 77 ksI~~l~e~a~--~EK~k~llel~k~~~~~~---~~-~----~n~--~~sk~qgv~~~~~~~QqGs~~~~~g~~~~~~n~ 144 (282)
++...|...+- ++|.++|+|.++.+..+- .+ | .|- ++.+.-| +|+|..||--+.-.--.|-
T Consensus 439 ~ly~eLs~cm~qLelkEkElaerEq~l~rr~pg~~~kp~r~~~nt~~k~~krrg--~p~n~g~qs~~pD~~~~p~----- 511 (904)
T KOG4721|consen 439 NLYMELSACMLQLELKEKELAEREQALERRCPGHLYKPSRLHGNTMEKLIKRRG--VPQNLGPQSQRPDILKAPS----- 511 (904)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcCCCccccchHHHHHHHHhcC--CCcccCcccCCCccccCcc-----
Confidence 34444444432 778899999998877662 11 1 011 3445555 6889888876554322221
Q ss_pred hhhccccccccc---ccCCCCCCccccc
Q 023462 145 NLTKGIMALDEF---KHGFPSDGLSTAS 169 (282)
Q Consensus 145 ~~~K~i~t~DeF---K~GFPS~GLst~s 169 (282)
.++|.+|-= --|.||++++..+
T Consensus 512 ---r~~p~~dsn~s~as~l~ssp~~~~s 536 (904)
T KOG4721|consen 512 ---RLLPKLDSNLSSASGLPSSPKAPPS 536 (904)
T ss_pred ---cCCccccccCCcCCCCCCCCCCCCC
Confidence 244443322 3467777776544
No 391
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=43.40 E-value=53 Score=24.85 Aligned_cols=41 Identities=7% Similarity=0.140 Sum_probs=32.1
Q ss_pred CCCCcCHHHHHhhcCCcHHHHHHHh-----CCChHHHHHHHHHcCC
Q 023462 25 STKSLSFDDISKYFSLPLSDAANHL-----GVCVSVLKKICRDNGL 65 (282)
Q Consensus 25 ~~~~iTledL~~yF~lPi~EAAr~L-----GVs~T~LKR~CR~lGI 65 (282)
....+|-.++...+++++..+++.+ +++..+|-+.+..+|.
T Consensus 28 ~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~ 73 (80)
T PF13744_consen 28 EERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGG 73 (80)
T ss_dssp HCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTE
T ss_pred HHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCC
Confidence 3467899999999999999999998 6889999999999984
No 392
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=43.30 E-value=21 Score=32.12 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=16.2
Q ss_pred cHHHHHHHhCCChHHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR 61 (282)
+|+|+|+..|||.+|+-|.-.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 578888888888888776653
No 393
>PRK09954 putative kinase; Provisional
Probab=43.22 E-value=33 Score=31.90 Aligned_cols=32 Identities=13% Similarity=0.025 Sum_probs=26.2
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+.|++.=.++..|.|+.||||.+++.++-++|
T Consensus 10 ~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L 41 (362)
T PRK09954 10 AILRRNPLIQQNEIADILQISRSRVAAHIMDL 41 (362)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44555557999999999999999998887755
No 394
>PRK06424 transcription factor; Provisional
Probab=43.13 E-value=32 Score=29.75 Aligned_cols=29 Identities=21% Similarity=0.185 Sum_probs=23.4
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
++...+|++.+.|+.+||+.+++.++-+-
T Consensus 92 lRe~~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 92 ARERLSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 44556899999999999998888887653
No 395
>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=43.03 E-value=39 Score=26.51 Aligned_cols=28 Identities=11% Similarity=0.027 Sum_probs=22.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
....+++.|.|..+|++.+++-|...+|
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3557788888888888888888877766
No 396
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=42.94 E-value=29 Score=32.60 Aligned_cols=58 Identities=14% Similarity=0.306 Sum_probs=43.2
Q ss_pred hhhhcCCCCCCCCcCHHHHHhhcC-----CcHHHHHHHhCCChHHHHHHHH------------HcCCCCCCcchh
Q 023462 16 AAASSSISTSTKSLSFDDISKYFS-----LPLSDAANHLGVCVSVLKKICR------------DNGLDRWPYRKF 73 (282)
Q Consensus 16 a~as~~~k~~~~~iTledL~~yF~-----lPi~EAAr~LGVs~T~LKR~CR------------~lGI~RWPyRKl 73 (282)
........+....+|+..+...|. ++..|+|+.+|+|.|+..|..- .+|..--|.|..
T Consensus 145 ~~~~~~LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~yG~vGRP~r~Y 219 (224)
T COG4565 145 EQPPDDLPKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIHYGKVGRPERRY 219 (224)
T ss_pred ccCcccCCCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEeeccccCCcceee
Confidence 444445556778889999998887 5589999999999999988643 456555576654
No 397
>PRK09483 response regulator; Provisional
Probab=42.92 E-value=28 Score=28.28 Aligned_cols=28 Identities=4% Similarity=0.147 Sum_probs=22.3
Q ss_pred cCCcHHHHHHHhCCChHHHHH----HHHHcCC
Q 023462 38 FSLPLSDAANHLGVCVSVLKK----ICRDNGL 65 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR----~CR~lGI 65 (282)
-+++.+++|+.|+||..|+|. +++++|+
T Consensus 162 ~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 478999999999999988765 4456665
No 398
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=42.59 E-value=34 Score=29.98 Aligned_cols=34 Identities=21% Similarity=0.136 Sum_probs=25.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC---CCCCcchhh
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL---DRWPYRKFL 74 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI---~RWPyRKlk 74 (282)
+..+..||++|||+.++|-+.-+ ++|+ .| - |++.
T Consensus 15 ~~s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R-~-r~~~ 55 (292)
T TIGR03298 15 EGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-T-QPCR 55 (292)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHhCchheec-C-CCCc
Confidence 67899999999999887755554 5685 56 4 6655
No 399
>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=42.57 E-value=22 Score=27.48 Aligned_cols=29 Identities=21% Similarity=0.480 Sum_probs=22.0
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.-+.|++.|||.-.||+...|.++++++.
T Consensus 10 eK~~LTi~EAa~Y~gIG~~klr~l~~~~~ 38 (67)
T PF09035_consen 10 EKYTLTIEEAAEYFGIGEKKLRELAEENP 38 (67)
T ss_dssp TSSEEEHHHHHHHT-S-HHHHHHHHHH-T
T ss_pred HhhccCHHHHHHHhCccHHHHHHHHHhCC
Confidence 34568899999999999999999996654
No 400
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=42.57 E-value=25 Score=31.20 Aligned_cols=33 Identities=24% Similarity=0.218 Sum_probs=25.8
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc---CC-CCCCcc
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN---GL-DRWPYR 71 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyR 71 (282)
-|| ..+.|++||||.|++....++| |+ ..=|.|
T Consensus 32 ~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~ 69 (257)
T PRK10225 32 RLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGA 69 (257)
T ss_pred cCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 576 8899999999999998888766 54 344554
No 401
>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=42.45 E-value=21 Score=31.61 Aligned_cols=22 Identities=27% Similarity=0.296 Sum_probs=15.6
Q ss_pred cHHHHHHHhCCChHHHHHHHHH
Q 023462 41 PLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+|+|+|+..|||.+|+-|....
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3677788888887777776643
No 402
>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=41.97 E-value=44 Score=23.74 Aligned_cols=28 Identities=18% Similarity=0.202 Sum_probs=21.8
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
..-.+++.|+|+.||++.+++.+--+.|
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L 48 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKL 48 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4457889999999999999988766644
No 403
>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=41.88 E-value=38 Score=27.25 Aligned_cols=27 Identities=19% Similarity=0.329 Sum_probs=22.2
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDR 67 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~R 67 (282)
|.+.|+|+.+|||+.+|.-..+. |+-.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~-GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEK-GLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence 67899999999999999776665 7643
No 404
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=41.84 E-value=39 Score=29.35 Aligned_cols=32 Identities=9% Similarity=0.162 Sum_probs=28.0
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
|-+++.=-+++.+++..+|++..++++.+|++
T Consensus 19 ElVRe~GRiTi~ql~~~TGasR~Tvk~~lreL 50 (127)
T PF06163_consen 19 ELVREHGRITIKQLVAKTGASRNTVKRYLREL 50 (127)
T ss_pred HHHHHcCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 44556668899999999999999999999986
No 405
>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=41.81 E-value=26 Score=30.54 Aligned_cols=33 Identities=18% Similarity=0.267 Sum_probs=25.8
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc---CC-CCCCcc
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN---GL-DRWPYR 71 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyR 71 (282)
-|| ..+.|++||||.|.+....++| |+ ..=|.|
T Consensus 29 ~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~ 66 (235)
T TIGR02812 29 ILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK 66 (235)
T ss_pred cCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 575 8899999999999999888877 54 334444
No 406
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=41.76 E-value=35 Score=30.36 Aligned_cols=27 Identities=22% Similarity=0.081 Sum_probs=21.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+-.+..||+.|||+.+++-+.-+ ++|+
T Consensus 16 ~~s~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (300)
T PRK11074 16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAV 46 (300)
T ss_pred hCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 56789999999999988755554 5675
No 407
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=41.64 E-value=25 Score=30.08 Aligned_cols=31 Identities=16% Similarity=0.339 Sum_probs=22.9
Q ss_pred CcCHHHHHhhcCCcHHHHHHHhC--CChHHHHH
Q 023462 28 SLSFDDISKYFSLPLSDAANHLG--VCVSVLKK 58 (282)
Q Consensus 28 ~iTledL~~yF~lPi~EAAr~LG--Vs~T~LKR 58 (282)
.+.|..||..|.|.+.|||..++ |+..+-.+
T Consensus 3 ~~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~ 35 (118)
T PF08965_consen 3 NLELQALRQILGLTVEEAAYYIAQDVSSRTWQQ 35 (118)
T ss_dssp HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHccCCHHHHHH
Confidence 35788999999999999999999 88776554
No 408
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=41.51 E-value=35 Score=31.70 Aligned_cols=36 Identities=8% Similarity=-0.135 Sum_probs=27.0
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCC
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRW 68 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RW 68 (282)
.|...=.++..+.|++||||.+++.+..+++-=..+
T Consensus 12 ~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 12 LLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGL 47 (319)
T ss_pred HHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 344434578889999999999999998887743333
No 409
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=41.50 E-value=37 Score=30.35 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=21.0
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++.+|+|..||||..++|.+-++
T Consensus 217 ~~s~~EIA~~lgis~~tV~~~~~r 240 (251)
T PRK07670 217 ELTLTEIGQVLNLSTSRISQIHSK 240 (251)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 889999999999999999877543
No 410
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=40.95 E-value=66 Score=27.41 Aligned_cols=31 Identities=13% Similarity=0.176 Sum_probs=26.2
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
+|..- +|.+.++|+.|||+++.+.+.-+...
T Consensus 17 ~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 17 ELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred HHHHc-CCcHHHHHHHhCCCHHHHHHHHccCC
Confidence 44555 99999999999999999999877654
No 411
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=40.92 E-value=42 Score=31.38 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=18.4
Q ss_pred cHHHHHHHhCCChHHHHHHHHHcC
Q 023462 41 PLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 41 Pi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.|+|+|+..|||.+|+-|.-...+
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~~ 25 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGSP 25 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 578889999999888877665443
No 412
>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=40.88 E-value=41 Score=24.35 Aligned_cols=31 Identities=10% Similarity=-0.034 Sum_probs=24.7
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCCCCCc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLDRWPY 70 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPy 70 (282)
++..+.|..||||.+++.+.-+++-=..||.
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4599999999999999998888774345553
No 413
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=40.79 E-value=29 Score=31.37 Aligned_cols=26 Identities=27% Similarity=0.305 Sum_probs=21.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
..+..||++|+||.+++-|.-+ ++|+
T Consensus 17 ~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~ 46 (316)
T PRK12679 17 YNLTEVANMLFTSQSGVSRHIRELEDELGI 46 (316)
T ss_pred CCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 5889999999999998766665 5575
No 414
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=40.78 E-value=39 Score=30.66 Aligned_cols=41 Identities=17% Similarity=0.097 Sum_probs=31.0
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCCCCCCcc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDNGLDRWPYR 71 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI~RWPyR 71 (282)
++.|.++=.+...|+|+.||||..|++|-+.++-....+-|
T Consensus 10 l~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 10 VDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34455555789999999999999999999998754334433
No 415
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=40.62 E-value=39 Score=29.34 Aligned_cols=47 Identities=19% Similarity=0.195 Sum_probs=34.1
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc---CCCCCCcchhhhhhcHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN---GLDRWPYRKFLSGKSIEDIKKY 85 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l---GI~RWPyRKlkSLksI~~l~e~ 85 (282)
+.++..++|..||++.-+|-|.-+++ ||-..-.|+|.-+ .++.|.++
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~-d~~~L~~~ 217 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIK-NRKQLSGL 217 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEe-CHHHHHHH
Confidence 45689999999999999888876655 8767777777643 24455543
No 416
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=40.56 E-value=30 Score=33.47 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=24.0
Q ss_pred CCcHHHHHHHhCCChHHHHH---HHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKK---ICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR---~CR~lGI~ 66 (282)
+|.+.|+|++||||.+++-| .+|+.||-
T Consensus 26 gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV 56 (321)
T COG2390 26 GLTQSEIAERLGISRATVSRLLAKAREEGIV 56 (321)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCeE
Confidence 68899999999999887766 57888974
No 417
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=40.53 E-value=36 Score=31.64 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=24.5
Q ss_pred cCCcHHHHHHHhCCChHHHH----HHHHHcCCC
Q 023462 38 FSLPLSDAANHLGVCVSVLK----KICRDNGLD 66 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LK----R~CR~lGI~ 66 (282)
-+++.+|+|++|+||..|+| ++++++|+.
T Consensus 157 ~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 157 FGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 38999999999999987765 678888874
No 418
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=40.23 E-value=22 Score=26.78 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=18.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
.|-++++.+.|+++||+.++|.+..
T Consensus 29 G~~~~t~~~Ia~~agvs~~~~Y~~f 53 (201)
T COG1309 29 GYAATTVDEIAKAAGVSKGTLYRHF 53 (201)
T ss_pred CcCCCCHHHHHHHhCCCcchhHHHc
Confidence 5667778888888888887776543
No 419
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=40.20 E-value=31 Score=32.00 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=20.1
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|+.||||..+++++-+
T Consensus 245 ~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 245 GATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 58999999999999999887754
No 420
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=40.14 E-value=40 Score=30.67 Aligned_cols=33 Identities=6% Similarity=0.138 Sum_probs=28.7
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++.|.++=.+.+.|.|+.||||..|+.|-.+++
T Consensus 11 l~~l~~~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 11 LELLAQLGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456667778999999999999999999999877
No 421
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=39.96 E-value=34 Score=29.90 Aligned_cols=37 Identities=19% Similarity=0.277 Sum_probs=29.4
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc---CCCCCCc-chhh
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN---GLDRWPY-RKFL 74 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l---GI~RWPy-RKlk 74 (282)
+.+++++.|..|||+..+|-|+.+++ ||-.+-+ ++|.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 45778999999999999998877655 8777775 4565
No 422
>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=39.96 E-value=22 Score=23.62 Aligned_cols=16 Identities=31% Similarity=0.520 Sum_probs=13.1
Q ss_pred CChHHHHHHHHHcCCC
Q 023462 51 VCVSVLKKICRDNGLD 66 (282)
Q Consensus 51 Vs~T~LKR~CR~lGI~ 66 (282)
+.+..||..|+++|++
T Consensus 4 l~v~eLk~~l~~~gL~ 19 (35)
T PF02037_consen 4 LTVAELKEELKERGLS 19 (35)
T ss_dssp SHHHHHHHHHHHTTS-
T ss_pred CcHHHHHHHHHHCCCC
Confidence 4577899999999985
No 423
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=39.89 E-value=38 Score=32.67 Aligned_cols=29 Identities=17% Similarity=0.299 Sum_probs=23.2
Q ss_pred HHhhcC------CcHHHHHHHhCCChHHHHHHHHH
Q 023462 34 ISKYFS------LPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 34 L~~yF~------lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
|.-||+ +++.|+|+.|||+...++++.++
T Consensus 314 l~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~ 348 (367)
T PRK09210 314 LRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAK 348 (367)
T ss_pred HHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 445665 79999999999999988887554
No 424
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=39.63 E-value=40 Score=30.48 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=20.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|..|||+..+++++-+
T Consensus 219 ~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 219 DLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 78999999999999999988754
No 425
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=39.50 E-value=37 Score=30.98 Aligned_cols=41 Identities=17% Similarity=0.134 Sum_probs=30.0
Q ss_pred CCCCCcCHHHHHhhc-----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 24 TSTKSLSFDDISKYF-----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 24 ~~~~~iTledL~~yF-----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+...++++.+| .|| +-.+..||+.|+||..+|-+.-+ ++|.
T Consensus 6 ~~~~~m~l~~L-~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (310)
T PRK15092 6 RPIINLDLDLL-RTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGK 55 (310)
T ss_pred hhhhcCCHHHH-HHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 33446888777 445 67899999999999887655544 5575
No 426
>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=39.41 E-value=1.3e+02 Score=24.38 Aligned_cols=37 Identities=24% Similarity=0.475 Sum_probs=27.9
Q ss_pred HHhCCChHHHHHHHHHcCCCCCCcchhhhhh--cHHHHHHH
Q 023462 47 NHLGVCVSVLKKICRDNGLDRWPYRKFLSGK--SIEDIKKY 85 (282)
Q Consensus 47 r~LGVs~T~LKR~CR~lGI~RWPyRKlkSLk--sI~~l~e~ 85 (282)
+.-||+.++=+.+|.++||. |..++..|. -++.|.++
T Consensus 19 ~IyGIG~~~A~~Ic~~lgi~--~~~~~~~Ls~~~i~~l~~~ 57 (107)
T PF00416_consen 19 KIYGIGRRKAKQICKKLGIN--PNKKVGDLSDEQIDKLRKI 57 (107)
T ss_dssp TSTTBCHHHHHHHHHHTTS---SSSBTTTSTHHHHHHHHHH
T ss_pred hhhccCHHHHHHHHHHcCCC--hhhhcccCCHHHHHHHHHH
Confidence 34699999999999999995 777777664 36666653
No 427
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=39.41 E-value=27 Score=30.25 Aligned_cols=35 Identities=14% Similarity=0.162 Sum_probs=27.0
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc---CC-CCCCcch
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN---GL-DRWPYRK 72 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyRK 72 (282)
-.||..+.|+.||||.|.+...-++| |+ ..=|.|-
T Consensus 33 ~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g 71 (221)
T PRK11414 33 ARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQA 71 (221)
T ss_pred CccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCc
Confidence 47899999999999999998877766 54 3345553
No 428
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=39.09 E-value=42 Score=30.47 Aligned_cols=24 Identities=29% Similarity=0.367 Sum_probs=21.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++++|+|..||||..+++++.++
T Consensus 221 ~~t~~EIA~~lgis~~~V~~~~~r 244 (257)
T PRK05911 221 ELVLKEIGKILGVSESRVSQIHSK 244 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 889999999999999999887654
No 429
>PHA01976 helix-turn-helix protein
Probab=39.03 E-value=85 Score=22.13 Aligned_cols=43 Identities=12% Similarity=0.118 Sum_probs=35.0
Q ss_pred CCCCCcCHHHHHhhcCCcHHHHHHHh-C---CChHHHHHHHHHcCCC
Q 023462 24 TSTKSLSFDDISKYFSLPLSDAANHL-G---VCVSVLKKICRDNGLD 66 (282)
Q Consensus 24 ~~~~~iTledL~~yF~lPi~EAAr~L-G---Vs~T~LKR~CR~lGI~ 66 (282)
+....+|.++|....+++...+.+-. | .+..+|.++|+-+||.
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 34566899999999999999888865 2 4678899999999984
No 430
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=38.92 E-value=31 Score=30.61 Aligned_cols=35 Identities=23% Similarity=0.171 Sum_probs=27.5
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc---CC-CCCCcchh
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN---GL-DRWPYRKF 73 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyRKl 73 (282)
-|| ..|.|+.||||.|.+....++| |+ ...|.+-.
T Consensus 25 ~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~ 64 (253)
T PRK10421 25 KLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGT 64 (253)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeE
Confidence 576 8899999999999998888766 64 46776643
No 431
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=38.81 E-value=38 Score=30.20 Aligned_cols=37 Identities=11% Similarity=0.231 Sum_probs=26.9
Q ss_pred CcCHHHHHhhc-----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 28 SLSFDDISKYF-----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 28 ~iTledL~~yF-----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
.|++..| +|| +-.+..||++|+|+.+++-|.-+ ++|.
T Consensus 4 ~~~l~~L-~~f~~v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg~ 49 (305)
T CHL00180 4 PFTLDQL-RILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNI 49 (305)
T ss_pred cccHHHH-HHHHHHHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 3455555 344 67899999999999988776666 4574
No 432
>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=38.70 E-value=34 Score=27.36 Aligned_cols=25 Identities=20% Similarity=0.126 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
+-.+..||+.||||.+++-+.-+++
T Consensus 16 ~gSis~AA~~L~iS~stvs~~I~~L 40 (99)
T TIGR00637 16 MGSISQAAKDAGISYKSAWDYIRAM 40 (99)
T ss_pred hCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5678999999999999876666544
No 433
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=38.60 E-value=32 Score=30.55 Aligned_cols=36 Identities=17% Similarity=0.071 Sum_probs=28.8
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc---CC-CCCCcchhh
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN---GL-DRWPYRKFL 74 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyRKlk 74 (282)
-|| ..+.|+.||||.|++....+.| |+ ..-|+|-..
T Consensus 31 ~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~ 71 (253)
T PRK11523 31 KLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIH 71 (253)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCeeE
Confidence 677 7899999999999999888876 64 567776543
No 434
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=38.36 E-value=42 Score=29.96 Aligned_cols=27 Identities=19% Similarity=0.139 Sum_probs=21.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+..+..||++|||+.+++-+.-+ ++|.
T Consensus 15 ~~S~s~AA~~L~isQ~avS~~I~~LE~~lg~ 45 (305)
T PRK11233 15 IGSLTQAAEVLHIAQPALSQQVATLEGELNQ 45 (305)
T ss_pred cCCHHHHHHHhCCCchHHHHHHHHHHHHhCC
Confidence 66899999999999998766665 4574
No 435
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=38.00 E-value=32 Score=29.86 Aligned_cols=25 Identities=36% Similarity=0.424 Sum_probs=21.3
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
|.|.|+|+.+||++.||...++ .|+
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE~-~GL 36 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYES-KGL 36 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 8899999999999999977665 454
No 436
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=37.98 E-value=44 Score=30.87 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=20.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.++++|+|+.||||..+++.+-.+
T Consensus 269 ~~Tl~EIa~~lgiS~erVrq~~~r 292 (298)
T TIGR02997 269 PLTLAEIGRRLNLSRERVRQIEAK 292 (298)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 689999999999999999887543
No 437
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=37.88 E-value=45 Score=30.15 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=19.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++.+|+|..|||+..+++++-+
T Consensus 228 ~~s~~eIA~~lgis~~tV~~~~~ 250 (268)
T PRK06288 228 DLTLKEIGKVLGVTESRISQLHT 250 (268)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 78999999999999999886653
No 438
>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=37.76 E-value=34 Score=27.54 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=21.4
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++..|.|+.|||+.+++.++.+.|
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L 49 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQL 49 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHH
Confidence 688999999999999999998866
No 439
>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=37.57 E-value=31 Score=28.37 Aligned_cols=29 Identities=38% Similarity=0.564 Sum_probs=24.3
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.|=.+++..+|+.||++...|.+.|.+.|
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 56689999999999999999999999996
No 440
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=37.08 E-value=51 Score=29.62 Aligned_cols=40 Identities=13% Similarity=0.218 Sum_probs=29.8
Q ss_pred CCCcCHHHHHhhc----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 26 TKSLSFDDISKYF----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 26 ~~~iTledL~~yF----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
..++++.+|+-+. +-.+..||+.|||+.+++-+.-+ ++|+
T Consensus 11 ~~~~~l~~L~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 58 (311)
T PRK10086 11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGI 58 (311)
T ss_pred hcCCcHHHHHHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 4577887775333 67899999999999988765554 5676
No 441
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=37.01 E-value=41 Score=30.69 Aligned_cols=33 Identities=9% Similarity=-0.006 Sum_probs=28.3
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++.|.++=.+.+.|.|+.||||..|+.|-..+|
T Consensus 11 l~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~L 43 (256)
T PRK10434 11 LEYLQKQGKTSVEELAQYFDTTGTTIRKDLVIL 43 (256)
T ss_pred HHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHH
Confidence 556667677999999999999999999988865
No 442
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=36.94 E-value=35 Score=29.25 Aligned_cols=33 Identities=15% Similarity=0.307 Sum_probs=24.8
Q ss_pred cCHHHHHhhc-----CCcHHHHHHHhCCChHHHHHHHH
Q 023462 29 LSFDDISKYF-----SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 29 iTledL~~yF-----~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+|..++..++ +++.+|+|+.||||..|+|+.-.
T Consensus 162 Lt~r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 162 LTLNAVRKLFKEPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 5555544433 57999999999999999987543
No 443
>PF06870 RNA_pol_I_A49: A49-like RNA polymerase I associated factor ; InterPro: IPR009668 Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3NFG_A 3NFH_B.
Probab=36.90 E-value=27 Score=33.34 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=25.1
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
.-|-+++.+.|+.|+|+...|..+||++|-
T Consensus 316 d~f~~d~~~L~~dLkl~~~~l~~~~r~LGC 345 (385)
T PF06870_consen 316 DNFSVDITDLARDLKLSPKKLTQYFRELGC 345 (385)
T ss_dssp TTTEEEHHHHHHHHT--HHHHHHHHHHTT-
T ss_pred cCcccChHHHHHHhCCCHHHHHHHHHHhCC
Confidence 457789999999999999999999999995
No 444
>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=36.87 E-value=86 Score=27.29 Aligned_cols=26 Identities=35% Similarity=0.360 Sum_probs=22.3
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+++.|+|+.+|||+++|....+ .|+-
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~-~GLl 27 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER-IGLL 27 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence 6899999999999999987776 5763
No 445
>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=36.44 E-value=32 Score=26.75 Aligned_cols=26 Identities=15% Similarity=0.165 Sum_probs=22.2
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.++++.++|+.|+++...++..|..|
T Consensus 64 ~Gv~v~~I~~~l~~~~~~v~~al~~L 89 (102)
T PF08784_consen 64 EGVHVDEIAQQLGMSENEVRKALDFL 89 (102)
T ss_dssp TTEEHHHHHHHSTS-HHHHHHHHHHH
T ss_pred CcccHHHHHHHhCcCHHHHHHHHHHH
Confidence 36889999999999999999999876
No 446
>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=36.32 E-value=12 Score=32.83 Aligned_cols=69 Identities=25% Similarity=0.488 Sum_probs=13.8
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCC----CCCCcchhhhhh------------cH-HHHHHHHHHH-HHH--HHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGL----DRWPYRKFLSGK------------SI-EDIKKYAARE-KSK--ELAELS 98 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI----~RWPyRKlkSLk------------sI-~~l~e~a~~E-K~k--~llel~ 98 (282)
-|.++++|..|||+.+|+-|.++.--| .-+|.|.+-+-. .| ..|++..+.| +.+ .=.+|+
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~ 128 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIA 128 (160)
T ss_dssp ------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHH
T ss_pred CCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 367899999999999999999884322 236777776421 12 2444443332 332 234566
Q ss_pred HHHhhcCCc
Q 023462 99 KIARKSGFQ 107 (282)
Q Consensus 99 k~~~~~~~~ 107 (282)
+++++.++.
T Consensus 129 ~~L~~~gi~ 137 (160)
T PF04552_consen 129 ELLKEEGIK 137 (160)
T ss_dssp HHHTTTTS-
T ss_pred HHHHHcCCC
Confidence 666666644
No 447
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=35.93 E-value=34 Score=32.52 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=19.9
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|+.|||+..++|.+-+
T Consensus 282 ~~s~~EIA~~Lgis~~tV~~~~~ 304 (325)
T PRK05657 282 AATLEDVAREIGLTRERVRQIQV 304 (325)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 58999999999999999887643
No 448
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=35.79 E-value=37 Score=35.63 Aligned_cols=28 Identities=21% Similarity=0.208 Sum_probs=25.7
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lGI~ 66 (282)
+.-+..||+.||.-+++|-++.|+|||.
T Consensus 519 ~~~~a~AAr~LGl~~~~L~~~~kRlGI~ 546 (550)
T COG3604 519 NGNWAGAARRLGLTRRTLLYRMKRLGIK 546 (550)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 5668889999999999999999999994
No 449
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=35.78 E-value=51 Score=29.41 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+..+..||++|||+.+++-|.-+ ++|.
T Consensus 16 ~~s~s~AA~~L~isq~avSr~I~~LE~~lg~ 46 (309)
T PRK12682 16 NLNLTEAAKALHTSQPGVSKAIIELEEELGI 46 (309)
T ss_pred cCCHHHHHHHhcCccHHHHHHHHHHHHHhCC
Confidence 35999999999999988766655 5575
No 450
>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=35.74 E-value=48 Score=26.02 Aligned_cols=33 Identities=24% Similarity=0.226 Sum_probs=23.7
Q ss_pred HHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 31 FDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
++.|..+=.+.-.+.|+.+|+....+.++|..|
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 455555667889999999999999999999876
No 451
>PRK05572 sporulation sigma factor SigF; Validated
Probab=35.10 E-value=53 Score=29.35 Aligned_cols=23 Identities=17% Similarity=0.329 Sum_probs=20.0
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
++++.|+|+.|||+.++++++-+
T Consensus 218 ~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 218 DKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 89999999999999999877543
No 452
>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=34.99 E-value=33 Score=27.91 Aligned_cols=23 Identities=26% Similarity=0.281 Sum_probs=16.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
..++.++|+.+|||.||+-+=..
T Consensus 19 ~aTVR~~Ak~FGvSKSTVHkDvt 41 (82)
T PF12116_consen 19 KATVRQAAKVFGVSKSTVHKDVT 41 (82)
T ss_dssp ---HHHHHHHHTS-HHHHHHHHT
T ss_pred ccHHHHHHHHHCCcHHHHHHHHH
Confidence 67899999999999999877654
No 453
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=34.97 E-value=56 Score=25.85 Aligned_cols=31 Identities=13% Similarity=-0.009 Sum_probs=24.5
Q ss_pred HHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 33 DISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 33 dL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.+..+.-.+-.+.|++||||.|.+-+.-.++
T Consensus 13 ~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~L 43 (79)
T COG1654 13 LLLTGNFVSGEKLAEELGISRTAVWKHIQQL 43 (79)
T ss_pred HHcCCCcccHHHHHHHHCccHHHHHHHHHHH
Confidence 3446667889999999999999998766544
No 454
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=34.87 E-value=57 Score=24.48 Aligned_cols=35 Identities=17% Similarity=0.141 Sum_probs=25.5
Q ss_pred CcCHHHHHhhcCCcHHHHHHHhC-CChHHHHHHHHH
Q 023462 28 SLSFDDISKYFSLPLSDAANHLG-VCVSVLKKICRD 62 (282)
Q Consensus 28 ~iTledL~~yF~lPi~EAAr~LG-Vs~T~LKR~CR~ 62 (282)
.+-.--++.++++++.++++.|| -..|++-.-||+
T Consensus 34 ~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~k 69 (70)
T PF08299_consen 34 QVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRK 69 (70)
T ss_dssp HHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHh
Confidence 33445566888999999999999 999998888875
No 455
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=34.84 E-value=29 Score=28.40 Aligned_cols=23 Identities=9% Similarity=0.156 Sum_probs=14.7
Q ss_pred hhcCCcHHHHHHHhCCChHHHHH
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKK 58 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR 58 (282)
+|-.++++|+|++-||+.+|+-+
T Consensus 20 ~~~~ITV~~I~~~AgvsR~TFY~ 42 (176)
T TIGR02366 20 AFSKISVSDIMSTAQIRRQTFYN 42 (176)
T ss_pred CCccCCHHHHHHHhCCCHHHHHH
Confidence 45566666667777777666544
No 456
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=34.81 E-value=38 Score=31.75 Aligned_cols=24 Identities=21% Similarity=0.382 Sum_probs=20.1
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
+++++|+|+.||||.+.+-|+-++
T Consensus 212 elt~kEI~~~LgISes~VSql~kk 235 (247)
T COG1191 212 ELTQKEIAEVLGISESRVSRLHKK 235 (247)
T ss_pred ccCHHHHHHHhCccHHHHHHHHHH
Confidence 599999999999999977666443
No 457
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=34.80 E-value=26 Score=29.56 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=18.8
Q ss_pred CCcHHHHHHHhCCChHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~ 59 (282)
.+|+.|+|..||||.+++-|=
T Consensus 60 e~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 60 ELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred cccHHHHHHHhCcchhhhccc
Confidence 799999999999999987653
No 458
>PRK03837 transcriptional regulator NanR; Provisional
Probab=34.27 E-value=42 Score=29.18 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=22.1
Q ss_pred CC-cHHHHHHHhCCChHHHHHHHHHc
Q 023462 39 SL-PLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 39 ~l-Pi~EAAr~LGVs~T~LKR~CR~l 63 (282)
-| +..+.|+.||||.|++....+.|
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L 61 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQAL 61 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47 48999999999999999888876
No 459
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=34.21 E-value=1.1e+02 Score=26.94 Aligned_cols=40 Identities=20% Similarity=0.263 Sum_probs=29.9
Q ss_pred HHHhCCChHHHHHHHHHcCCCCCCcchhhhhh--cHHHHHHHHH
Q 023462 46 ANHLGVCVSVLKKICRDNGLDRWPYRKFLSGK--SIEDIKKYAA 87 (282)
Q Consensus 46 Ar~LGVs~T~LKR~CR~lGI~RWPyRKlkSLk--sI~~l~e~a~ 87 (282)
...-||+.++=+.+|+++||. |..++..|. -|+.|.++..
T Consensus 33 t~I~GIG~~~A~~I~~~lgi~--~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 33 TAIKGIGRRFAYLVCKKAGID--VTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred cccccccHHHHHHHHHHcCcC--cCCCcccCCHHHHHHHHHHHh
Confidence 345699999999999999995 777887653 4666665443
No 460
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=34.10 E-value=39 Score=27.71 Aligned_cols=37 Identities=16% Similarity=0.197 Sum_probs=29.1
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHH---cCCCCCCcchhh
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRD---NGLDRWPYRKFL 74 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~---lGI~RWPyRKlk 74 (282)
+.++.+|.|..||++..++-|.-++ -||-+--+++|.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~ 181 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKIT 181 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEE
Confidence 5678999999999999988886554 487677777765
No 461
>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=34.08 E-value=53 Score=29.25 Aligned_cols=24 Identities=17% Similarity=0.332 Sum_probs=20.0
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
-+++..|+|..|||+..+++++-+
T Consensus 220 ~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 220 ENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 378999999999999998877643
No 462
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=33.72 E-value=60 Score=29.12 Aligned_cols=39 Identities=10% Similarity=0.163 Sum_probs=28.8
Q ss_pred CCcCHHHHHhhc----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 27 KSLSFDDISKYF----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 27 ~~iTledL~~yF----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
..+++.+|+-+. +-.+..||+.|||+.+++-|.-+ ++|+
T Consensus 20 ~~~~l~~L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 66 (314)
T PRK09508 20 RMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFND 66 (314)
T ss_pred cccChHHHHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCC
Confidence 357888874332 66799999999999988766555 5676
No 463
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=33.38 E-value=49 Score=31.62 Aligned_cols=26 Identities=27% Similarity=0.222 Sum_probs=23.7
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
--+|..+.|+++|||.|++.++-|+|
T Consensus 197 grlse~eLAerlGVSRs~ireAlrkL 222 (251)
T TIGR02787 197 GLLVASKIADRVGITRSVIVNALRKL 222 (251)
T ss_pred ccccHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999999877
No 464
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=33.33 E-value=1.4e+02 Score=25.78 Aligned_cols=40 Identities=20% Similarity=0.213 Sum_probs=28.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHH---cCCCCC-Ccchhhh
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRD---NGLDRW-PYRKFLS 75 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~---lGI~RW-PyRKlkS 75 (282)
........+.|+.|+|++.++...-++ .|..-- ||+.+.-
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~L 64 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTL 64 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEE
Confidence 344578999999999997776444443 465444 9998873
No 465
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=33.14 E-value=63 Score=28.75 Aligned_cols=37 Identities=8% Similarity=0.112 Sum_probs=26.5
Q ss_pred cCHHHHHhhc----CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 29 LSFDDISKYF----SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 29 iTledL~~yF----~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+++.+|+-+. +..+..||++|||+.+++-|.-+ ++|+
T Consensus 4 m~l~~L~~F~~v~e~gs~s~AA~~L~isqpavS~~I~~LE~~lg~ 48 (296)
T PRK11062 4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQG 48 (296)
T ss_pred cCHHHHHHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCc
Confidence 4555554322 67889999999999998776665 4564
No 466
>PRK09801 transcriptional activator TtdR; Provisional
Probab=33.05 E-value=50 Score=29.92 Aligned_cols=27 Identities=26% Similarity=0.170 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+-.+..||+.||||.++|-+.-+ ++|+
T Consensus 20 ~gs~t~AA~~L~iSQpavS~~I~~LE~~LG~ 50 (310)
T PRK09801 20 SGSFSAAAATLGQTPAFVTKRIQILENTLAT 50 (310)
T ss_pred cCCHHHHHHHhCcCHHHHHHHHHHHHHHhCC
Confidence 56789999999999988766555 5675
No 467
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=32.60 E-value=59 Score=25.65 Aligned_cols=37 Identities=16% Similarity=0.302 Sum_probs=32.2
Q ss_pred CCcCHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 27 KSLSFDDISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 27 ~~iTledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
.++.+.+|....+--=.+.|++|||+.+.+.++.-++
T Consensus 3 ~d~~l~~ia~~LG~dW~~LA~eLg~s~~dI~~i~~e~ 39 (84)
T cd08803 3 TDIRMAIVADHLGLSWTELARELNFSVDEINQIRVEN 39 (84)
T ss_pred hHHHHHHHHHHhhccHHHHHHHcCCCHHHHHHHHHhC
Confidence 4567888999999999999999999999999996655
No 468
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=32.43 E-value=59 Score=28.24 Aligned_cols=27 Identities=19% Similarity=0.148 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+..+..||++|||+.+++-|.-+ ++|.
T Consensus 17 ~~s~t~AA~~L~isqpavS~~I~~LE~~lg~ 47 (290)
T PRK10837 17 SGSTTQASVMLALSQSAVSAALTDLEGQLGV 47 (290)
T ss_pred cCCHHHHHHHhCCCccHHHHHHHHHHHHhCC
Confidence 67899999999999887765555 5575
No 469
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.41 E-value=69 Score=25.70 Aligned_cols=34 Identities=12% Similarity=0.283 Sum_probs=27.0
Q ss_pred HHHHHhhc-----CCc---HHHHHHHhCCChHHHHHHHHHcC
Q 023462 31 FDDISKYF-----SLP---LSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 31 ledL~~yF-----~lP---i~EAAr~LGVs~T~LKR~CR~lG 64 (282)
-+.|+.|| ++| -++.||.||++.+.+..+.-.+-
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~i~~~~~ 44 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDVAKANER 44 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHHHHHHCC
Confidence 46677777 566 46789999999999999988763
No 470
>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=32.40 E-value=60 Score=28.33 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=19.4
Q ss_pred CCcHHHHHHHhCCChHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~C 60 (282)
++++.|+|+.||||..++.++=
T Consensus 199 ~~t~~eIA~~lgis~~~V~~~~ 220 (231)
T TIGR02885 199 DKTQTEVANMLGISQVQVSRLE 220 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 8899999999999998887664
No 471
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=32.32 E-value=60 Score=29.11 Aligned_cols=26 Identities=4% Similarity=0.133 Sum_probs=23.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
.+.+.|+|+.||++.+++-|+++.|-
T Consensus 28 ~l~l~eia~~lgl~kstv~Rll~tL~ 53 (257)
T PRK15090 28 EIGITELSQRVMMSKSTVYRFLQTMK 53 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 47899999999999999999998763
No 472
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=32.31 E-value=47 Score=27.63 Aligned_cols=46 Identities=15% Similarity=0.191 Sum_probs=32.4
Q ss_pred cCCcHHHHHHHhCCChHHHHHHHHHc---CCCCCCcchhhhhhcHHHHHH
Q 023462 38 FSLPLSDAANHLGVCVSVLKKICRDN---GLDRWPYRKFLSGKSIEDIKK 84 (282)
Q Consensus 38 F~lPi~EAAr~LGVs~T~LKR~CR~l---GI~RWPyRKlkSLksI~~l~e 84 (282)
+.++.++.|..||++..++-|.-+++ ||-..-+++|.-+ ..+.|++
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~-d~~~L~~ 196 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL-DLKGLEE 196 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE-CHHHHHH
Confidence 46789999999999988887766655 7767677776532 2344443
No 473
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.20 E-value=55 Score=29.40 Aligned_cols=40 Identities=28% Similarity=0.506 Sum_probs=30.2
Q ss_pred CHHHHHhhcC---CcHHHHHHHhCCChHHHHHHHH---HcCCCCCCc
Q 023462 30 SFDDISKYFS---LPLSDAANHLGVCVSVLKKICR---DNGLDRWPY 70 (282)
Q Consensus 30 TledL~~yF~---lPi~EAAr~LGVs~T~LKR~CR---~lGI~RWPy 70 (282)
+-+.+|.+|- +|+..||..+|||..|..|.-+ ..| .-|=-
T Consensus 7 ~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~G-DDWDk 52 (165)
T PF08822_consen 7 TRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKG-DDWDK 52 (165)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcC-CcHHH
Confidence 3456777774 9999999999999999866544 567 56753
No 474
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=32.16 E-value=60 Score=28.66 Aligned_cols=37 Identities=22% Similarity=0.255 Sum_probs=26.0
Q ss_pred cCHHHHHhhc-----CCcHHHHHHHhCCChHHHHHH----HHHcCCC
Q 023462 29 LSFDDISKYF-----SLPLSDAANHLGVCVSVLKKI----CRDNGLD 66 (282)
Q Consensus 29 iTledL~~yF-----~lPi~EAAr~LGVs~T~LKR~----CR~lGI~ 66 (282)
+++.+| +|| .-.+..||++|+|+.+++-+. =.++|++
T Consensus 6 ~~l~~l-~~f~~v~~~gs~s~AA~~L~isq~avS~~i~~LE~~lg~~ 51 (297)
T PRK11139 6 PPLNAL-RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLK 51 (297)
T ss_pred CchHHH-HHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCch
Confidence 455555 344 567899999999998876554 4566864
No 475
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=31.83 E-value=38 Score=29.63 Aligned_cols=29 Identities=10% Similarity=0.205 Sum_probs=25.2
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
..|.+.+.++|+.||||.+++.|..+.|-
T Consensus 72 N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~ 100 (165)
T PF05732_consen 72 NAVVATQKEIAEKLGISKPTVSRAIKELE 100 (165)
T ss_pred CeEEeeHHHHHHHhCCCHHHHHHHHHHHH
Confidence 35678899999999999999999998773
No 476
>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=31.38 E-value=47 Score=24.38 Aligned_cols=24 Identities=13% Similarity=0.375 Sum_probs=15.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
-+++.|.|++|++++.+|.-.-..
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 567788888888888877665443
No 477
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=31.26 E-value=78 Score=25.29 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=21.5
Q ss_pred CCcHHHHHHHhCCChHHHHH----HHHHcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKK----ICRDNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR----~CR~lGI 65 (282)
+++.+|+|+.|+++..|++. +.+++|+
T Consensus 164 g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 164 GLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 89999999999999977765 4445554
No 478
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=31.21 E-value=61 Score=29.71 Aligned_cols=26 Identities=27% Similarity=0.296 Sum_probs=21.1
Q ss_pred CcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 40 LPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
..+..||++|+|+.+++-+.-+ ++|+
T Consensus 17 ~S~s~AA~~L~iSQpavS~~I~~LE~~lG~ 46 (324)
T PRK12681 17 LNVSATAEGLYTSQPGISKQVRMLEDELGI 46 (324)
T ss_pred CCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 4899999999999988766665 5575
No 479
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=30.89 E-value=50 Score=29.15 Aligned_cols=33 Identities=24% Similarity=0.267 Sum_probs=24.9
Q ss_pred CC-cHHHHHHHhCCChHHHHHHHHHc---CC-CCCCcc
Q 023462 39 SL-PLSDAANHLGVCVSVLKKICRDN---GL-DRWPYR 71 (282)
Q Consensus 39 ~l-Pi~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyR 71 (282)
-| +..+.|+.||||.|++...-++| |+ ..=|.+
T Consensus 33 ~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~ 70 (254)
T PRK09464 33 KLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGG 70 (254)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCc
Confidence 46 48999999999999988777765 53 344554
No 480
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=30.81 E-value=1.8e+02 Score=25.56 Aligned_cols=38 Identities=29% Similarity=0.319 Sum_probs=28.9
Q ss_pred HHhCCChHHHHHHHHHcCCCCCCcchhhhhh--cHHHHHHHH
Q 023462 47 NHLGVCVSVLKKICRDNGLDRWPYRKFLSGK--SIEDIKKYA 86 (282)
Q Consensus 47 r~LGVs~T~LKR~CR~lGI~RWPyRKlkSLk--sI~~l~e~a 86 (282)
...||+.++-+.+|+++||. |..++..|. -|+.|.++.
T Consensus 29 ~IyGIG~~~a~~Ic~~lgi~--~~~~~~~Lt~~qi~~l~~~i 68 (149)
T PRK04053 29 GIKGIGRRTARAIARKLGLD--PNAKLGYLSDEEIEKIEEAL 68 (149)
T ss_pred ccccccHHHHHHHHHHcCcC--CCCccCcCCHHHHHHHHHHH
Confidence 45699999999999999996 666777653 466666654
No 481
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=30.77 E-value=63 Score=21.76 Aligned_cols=24 Identities=21% Similarity=0.343 Sum_probs=14.6
Q ss_pred CcHHHHHHHhCCChHHHHHHHHHc
Q 023462 40 LPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 40 lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
|+..|.|..||++.-++-|...++
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHH
Confidence 556777888888777776665543
No 482
>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=30.65 E-value=71 Score=28.06 Aligned_cols=27 Identities=22% Similarity=0.164 Sum_probs=21.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH----HcCC
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR----DNGL 65 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR----~lGI 65 (282)
+..+..||+.|||+.+++-|.-+ ++|+
T Consensus 17 ~gS~s~AA~~L~isq~avS~~I~~LE~~lg~ 47 (300)
T TIGR02424 17 QGSVKRAAEALHITQPAVSKTLRELEEILGT 47 (300)
T ss_pred hCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 66899999999999988766655 5574
No 483
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=30.44 E-value=87 Score=26.23 Aligned_cols=34 Identities=29% Similarity=0.336 Sum_probs=27.9
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHHHHcCC
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKICRDNGL 65 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~CR~lGI 65 (282)
+.+-+|-.=-+..||..|||-..||.|.-.++|+
T Consensus 64 ~~vM~~~~gNQtrAa~mLGinR~TLRKKLkqygl 97 (98)
T COG2901 64 DMVMQYTRGNQTRAALMLGINRGTLRKKLKKYGL 97 (98)
T ss_pred HHHHHHhcccHHHHHHHHcccHHHHHHHHHHhCC
Confidence 3444555556889999999999999999999986
No 484
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=30.35 E-value=68 Score=29.35 Aligned_cols=23 Identities=13% Similarity=0.306 Sum_probs=20.3
Q ss_pred CCcHHHHHHHhCCChHHHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
+++++|+|..|||+..+++++-+
T Consensus 231 ~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 231 SMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 89999999999999999988643
No 485
>PRK00441 argR arginine repressor; Provisional
Probab=30.34 E-value=74 Score=27.45 Aligned_cols=39 Identities=13% Similarity=0.044 Sum_probs=33.3
Q ss_pred HHHHHhhcCCcHHHHHHHh-----CCChHHHHHHHHHcCCCCCC
Q 023462 31 FDDISKYFSLPLSDAANHL-----GVCVSVLKKICRDNGLDRWP 69 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~L-----GVs~T~LKR~CR~lGI~RWP 69 (282)
++.|+.+=-..+.|.++.| +||..|+.|-.+++||.+=|
T Consensus 10 ~~ll~~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L~lvKv~ 53 (149)
T PRK00441 10 LEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKELKLIKVL 53 (149)
T ss_pred HHHHHHcCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHcCcEEeE
Confidence 4556666677899999998 99999999999999998766
No 486
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=30.18 E-value=81 Score=24.83 Aligned_cols=29 Identities=17% Similarity=0.071 Sum_probs=24.6
Q ss_pred hhcCCcHHHHHHHhCCChHHHHHHHHHcC
Q 023462 36 KYFSLPLSDAANHLGVCVSVLKKICRDNG 64 (282)
Q Consensus 36 ~yF~lPi~EAAr~LGVs~T~LKR~CR~lG 64 (282)
..=.+++.++|+.+||+.+++-+.+.++=
T Consensus 39 ~~~~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 39 EQGSMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred HcCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 44468899999999999999999998873
No 487
>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=30.13 E-value=94 Score=22.50 Aligned_cols=35 Identities=14% Similarity=0.267 Sum_probs=24.7
Q ss_pred HHHHHhhcCCcHHHHHHHhCCC-hHHHHHHHHHc-CC
Q 023462 31 FDDISKYFSLPLSDAANHLGVC-VSVLKKICRDN-GL 65 (282)
Q Consensus 31 ledL~~yF~lPi~EAAr~LGVs-~T~LKR~CR~l-GI 65 (282)
.+.|..+=++|+.|+|..+|.+ .+.+-|.|++. |+
T Consensus 37 ~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~~g~ 73 (81)
T PF12833_consen 37 KELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRYFGM 73 (81)
T ss_dssp HHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHHHSS
T ss_pred HHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHHHCc
Confidence 3445455589999999999988 88888888765 65
No 488
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=29.98 E-value=54 Score=28.93 Aligned_cols=33 Identities=24% Similarity=0.263 Sum_probs=25.7
Q ss_pred CCc-HHHHHHHhCCChHHHHHHHHHc---CC-CCCCcc
Q 023462 39 SLP-LSDAANHLGVCVSVLKKICRDN---GL-DRWPYR 71 (282)
Q Consensus 39 ~lP-i~EAAr~LGVs~T~LKR~CR~l---GI-~RWPyR 71 (282)
-|| ..+.|+.||||.|.+....++| |+ ..=|.|
T Consensus 30 ~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~ 67 (251)
T PRK09990 30 ALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGR 67 (251)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 574 8899999999999999888876 53 344554
No 489
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=29.97 E-value=74 Score=23.54 Aligned_cols=29 Identities=28% Similarity=0.297 Sum_probs=19.2
Q ss_pred HHHHhhcCCcHHHHHHHhCCChHHHHHHH
Q 023462 32 DDISKYFSLPLSDAANHLGVCVSVLKKIC 60 (282)
Q Consensus 32 edL~~yF~lPi~EAAr~LGVs~T~LKR~C 60 (282)
...+.--++++.++|+.++|++..|..+=
T Consensus 3 r~~R~~~glsl~~va~~t~I~~~~l~aiE 31 (62)
T PF13413_consen 3 REAREAKGLSLEDVAEETKISVSYLEAIE 31 (62)
T ss_dssp HHHHHCTT--HHHHHHHCS--HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556668889999999999998888763
No 490
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=29.81 E-value=69 Score=28.64 Aligned_cols=21 Identities=14% Similarity=0.219 Sum_probs=17.5
Q ss_pred CCcHHHHHHHhCCChHHHHHH
Q 023462 39 SLPLSDAANHLGVCVSVLKKI 59 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~ 59 (282)
+++++|+|+.||||...+.++
T Consensus 199 ~~t~~EIA~~lgis~~~V~q~ 219 (231)
T PRK12427 199 EMSLKEIALVLDLTEARICQL 219 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 689999999999999866544
No 491
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=29.73 E-value=81 Score=21.49 Aligned_cols=29 Identities=21% Similarity=0.215 Sum_probs=21.9
Q ss_pred hcCCcHHHHHHHhCCChHHHHHH----HHHcCC
Q 023462 37 YFSLPLSDAANHLGVCVSVLKKI----CRDNGL 65 (282)
Q Consensus 37 yF~lPi~EAAr~LGVs~T~LKR~----CR~lGI 65 (282)
..+++..|.|..|++|.-+++-- .+++|+
T Consensus 17 ~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 17 AQGKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 34799999999999998776544 445555
No 492
>PRK00215 LexA repressor; Validated
Probab=29.73 E-value=77 Score=27.36 Aligned_cols=30 Identities=13% Similarity=0.160 Sum_probs=23.4
Q ss_pred CCcHHHHHHHhCC-ChHHHHHHHHHcCCCCC
Q 023462 39 SLPLSDAANHLGV-CVSVLKKICRDNGLDRW 68 (282)
Q Consensus 39 ~lPi~EAAr~LGV-s~T~LKR~CR~lGI~RW 68 (282)
.+.+.|.|+.||+ +.+++-+++++|--..|
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~ 53 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALERKGF 53 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCCC
Confidence 4578899999999 99998888877643333
No 493
>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=29.51 E-value=81 Score=27.54 Aligned_cols=30 Identities=13% Similarity=0.125 Sum_probs=25.1
Q ss_pred HHhhcCCcHHHHHHHhCCChHHHHHHHHHc
Q 023462 34 ISKYFSLPLSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 34 L~~yF~lPi~EAAr~LGVs~T~LKR~CR~l 63 (282)
|...=.+.+.++|+.|||+.+++.+...+|
T Consensus 10 L~~~~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 10 LLKQGQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 333445889999999999999999999876
No 494
>PRK04140 hypothetical protein; Provisional
Probab=29.32 E-value=68 Score=31.15 Aligned_cols=32 Identities=22% Similarity=0.334 Sum_probs=27.7
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICR 61 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR 61 (282)
.+.+++.-.++++.+.|+.+|||..++-++.+
T Consensus 130 rLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45677888999999999999999999988765
No 495
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=29.20 E-value=73 Score=21.62 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=16.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHc
Q 023462 42 LSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 42 i~EAAr~LGVs~T~LKR~CR~l 63 (282)
..+.|+.+|||..++.+.-.++
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 28 ERELAEELGVSRTTVREALREL 49 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 8888888888888776654443
No 496
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=29.13 E-value=58 Score=24.41 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHc
Q 023462 42 LSDAANHLGVCVSVLKKICRDN 63 (282)
Q Consensus 42 i~EAAr~LGVs~T~LKR~CR~l 63 (282)
+.++|+.|||+.+++-+.-+++
T Consensus 2 ~~ela~~l~is~stvs~~l~~L 23 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKL 23 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHH
Confidence 5789999999999988877766
No 497
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=29.03 E-value=86 Score=25.20 Aligned_cols=28 Identities=7% Similarity=0.057 Sum_probs=22.7
Q ss_pred CCcHHHHHHHhCCChHHHH----HHHHHcCCC
Q 023462 39 SLPLSDAANHLGVCVSVLK----KICRDNGLD 66 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LK----R~CR~lGI~ 66 (282)
+.+.+++|+.|+++..|++ ++++++|+.
T Consensus 158 g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~ 189 (204)
T PRK09958 158 GKDNNDIAEKMFISNKTVSTYKSRLMEKLECK 189 (204)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 6799999999999976654 677788864
No 498
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=28.94 E-value=75 Score=29.66 Aligned_cols=33 Identities=12% Similarity=0.064 Sum_probs=25.8
Q ss_pred CHHHHHhhcCCcHHHHHHHhCCChHHHHHHHHH
Q 023462 30 SFDDISKYFSLPLSDAANHLGVCVSVLKKICRD 62 (282)
Q Consensus 30 TledL~~yF~lPi~EAAr~LGVs~T~LKR~CR~ 62 (282)
.+..++.--+|++.+.|+.+||+.+++-++.+-
T Consensus 32 rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g 64 (309)
T PRK08154 32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESG 64 (309)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 456677888999999999999888777665543
No 499
>PF07860 CCD: WisP family C-Terminal Region; InterPro: IPR012421 This entry represents the C-terminal domain found in the Tropheryma whipplei WisP family of proteins [].
Probab=28.85 E-value=20 Score=30.88 Aligned_cols=12 Identities=42% Similarity=1.376 Sum_probs=9.9
Q ss_pred cCCCCCCcchhhh
Q 023462 63 NGLDRWPYRKFLS 75 (282)
Q Consensus 63 lGI~RWPyRKlkS 75 (282)
+|| -|||||+-.
T Consensus 53 hgi-twpfrklfg 64 (141)
T PF07860_consen 53 HGI-TWPFRKLFG 64 (141)
T ss_pred hcc-cchHHHHhC
Confidence 688 599999863
No 500
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=28.77 E-value=1.6e+02 Score=28.82 Aligned_cols=57 Identities=28% Similarity=0.518 Sum_probs=40.6
Q ss_pred CCcHHHHHHHhCCChHHHHHHHHHc-CCCCCCcchhhhhhcHHHHHHHHHHHHHHHHHH-----HHHHHhhcCCc
Q 023462 39 SLPLSDAANHLGVCVSVLKKICRDN-GLDRWPYRKFLSGKSIEDIKKYAAREKSKELAE-----LSKIARKSGFQ 107 (282)
Q Consensus 39 ~lPi~EAAr~LGVs~T~LKR~CR~l-GI~RWPyRKlkSLksI~~l~e~a~~EK~k~lle-----l~k~~~~~~~~ 107 (282)
-+++.+.|+.+|||.-+|-|+++++ |+. |.+-+ . ..+.+++|.|++ +.+|+---||.
T Consensus 236 plsl~~LA~~~~~S~R~leRlF~~~lG~s--P~~yy---------~-~lRL~~Ar~LL~~t~~si~~IA~~~GF~ 298 (328)
T COG4977 236 PLSLEELADRAGLSRRQLERLFRAELGVS--PARYY---------L-RLRLERARRLLEQTRLSIAEIAVACGFS 298 (328)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHhCCC--HHHHH---------H-HHHHHHHHHHHHhCCCcHHHHHHHhCCC
Confidence 4678999999999999999999976 753 33322 2 245677777765 55566666665
Done!