Query 011262
Match_columns 490
No_of_seqs 243 out of 1048
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 23:24:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011262.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011262hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1598 Transcription initiati 100.0 2E-66 4.3E-71 543.3 21.5 410 1-471 74-492 (521)
2 COG1405 SUA7 Transcription ini 100.0 5.8E-40 1.3E-44 328.9 18.7 175 1-184 104-278 (285)
3 PRK00423 tfb transcription ini 100.0 1.7E-39 3.7E-44 331.1 20.9 174 1-183 129-302 (310)
4 KOG1597 Transcription initiati 100.0 2.1E-37 4.6E-42 304.1 18.1 190 1-198 111-300 (308)
5 PF07741 BRF1: Brf1-like TBP-b 100.0 1.3E-29 2.9E-34 216.6 1.6 96 346-466 1-97 (97)
6 PF00382 TFIIB: Transcription 99.7 8.6E-18 1.9E-22 135.4 9.2 71 1-73 1-71 (71)
7 PF00382 TFIIB: Transcription 99.6 7.1E-16 1.5E-20 124.3 8.9 71 102-174 1-71 (71)
8 PRK00423 tfb transcription ini 99.4 5.7E-13 1.2E-17 136.4 10.9 85 1-87 223-307 (310)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.3 6.3E-11 1.4E-15 120.9 17.6 153 1-160 63-226 (305)
10 KOG0835 Cyclin L [General func 99.3 6.4E-11 1.4E-15 119.0 17.0 173 1-180 30-224 (367)
11 COG1405 SUA7 Transcription ini 99.2 9.1E-11 2E-15 118.5 9.2 86 1-88 198-283 (285)
12 KOG0834 CDK9 kinase-activating 99.1 4.2E-10 9.1E-15 115.2 11.1 152 1-159 46-214 (323)
13 KOG1597 Transcription initiati 99.1 4.4E-10 9.6E-15 111.8 9.0 83 1-85 207-289 (308)
14 COG5333 CCL1 Cdk activating ki 99.0 3.1E-09 6.7E-14 106.8 11.8 152 1-159 52-211 (297)
15 cd00043 CYCLIN Cyclin box fold 98.9 1.2E-08 2.7E-13 82.3 9.7 78 1-80 9-87 (88)
16 cd00043 CYCLIN Cyclin box fold 98.9 1.2E-08 2.5E-13 82.5 9.4 84 96-181 3-87 (88)
17 smart00385 CYCLIN domain prese 98.9 1.1E-08 2.3E-13 82.0 8.9 78 1-81 3-82 (83)
18 smart00385 CYCLIN domain prese 98.9 1.7E-08 3.8E-13 80.7 9.3 81 100-182 1-82 (83)
19 KOG0794 CDK8 kinase-activating 98.6 5.4E-07 1.2E-11 87.3 11.9 172 1-181 48-234 (264)
20 KOG0656 G1/S-specific cyclin D 98.3 1.7E-05 3.6E-10 81.8 15.1 171 2-179 86-268 (335)
21 KOG1598 Transcription initiati 98.2 9.1E-07 2E-11 94.8 4.7 155 1-157 170-334 (521)
22 KOG4557 Origin recognition com 97.7 0.0013 2.9E-08 63.4 14.9 157 1-172 3-168 (262)
23 KOG2496 Cdk activating kinase 97.4 0.0016 3.4E-08 66.0 12.1 139 9-151 73-219 (325)
24 PF00134 Cyclin_N: Cyclin, N-t 97.4 0.00098 2.1E-08 58.4 9.1 84 2-87 39-125 (127)
25 KOG0653 Cyclin B and related k 97.2 0.002 4.4E-08 68.4 10.8 147 3-158 167-317 (391)
26 PF02984 Cyclin_C: Cyclin, C-t 97.2 0.0011 2.4E-08 57.0 6.9 84 97-182 2-86 (118)
27 PF01857 RB_B: Retinoblastoma- 97.0 0.0021 4.4E-08 58.6 6.7 66 1-68 18-85 (135)
28 COG5024 Cyclin [Cell division 96.7 0.0089 1.9E-07 64.1 10.0 144 4-157 223-370 (440)
29 PF02984 Cyclin_C: Cyclin, C-t 94.1 0.15 3.2E-06 43.6 6.5 72 14-85 18-90 (118)
30 PF00134 Cyclin_N: Cyclin, N-t 93.9 0.2 4.3E-06 43.7 7.0 67 99-167 35-102 (127)
31 KOG0835 Cyclin L [General func 93.5 0.31 6.7E-06 50.3 8.3 100 3-110 147-247 (367)
32 TIGR00569 ccl1 cyclin ccl1. Un 92.9 0.4 8.6E-06 49.5 8.3 67 101-167 62-128 (305)
33 PF13404 HTH_AsnC-type: AsnC-t 91.0 0.42 9.2E-06 34.7 4.2 32 151-182 11-42 (42)
34 KOG0834 CDK9 kinase-activating 90.9 0.34 7.3E-06 50.3 5.1 82 99-182 43-128 (323)
35 PF05460 ORC6: Origin recognit 89.5 0.1 2.2E-06 54.8 0.0 87 2-88 2-89 (353)
36 smart00342 HTH_ARAC helix_turn 89.2 3 6.5E-05 32.7 8.4 26 157-182 50-76 (84)
37 smart00342 HTH_ARAC helix_turn 87.4 1.5 3.4E-05 34.4 5.6 72 1-81 4-76 (84)
38 KOG0655 G1/S-specific cyclin E 86.5 9.2 0.0002 39.9 11.6 164 4-181 155-331 (408)
39 KOG2496 Cdk activating kinase 86.4 1.6 3.4E-05 44.8 6.1 70 99-168 60-129 (325)
40 PF01857 RB_B: Retinoblastoma- 86.3 2.7 5.8E-05 38.3 7.1 64 101-166 17-82 (135)
41 PF13412 HTH_24: Winged helix- 85.7 1.4 3.1E-05 32.1 4.2 29 155-183 15-43 (48)
42 PF13384 HTH_23: Homeodomain-l 85.4 1.1 2.4E-05 32.9 3.5 29 157-185 17-45 (50)
43 PRK05657 RNA polymerase sigma 84.6 37 0.0008 35.3 15.5 27 156-182 281-307 (325)
44 PF08613 Cyclin: Cyclin; Inte 84.5 10 0.00023 34.7 10.2 84 2-87 59-148 (149)
45 PRK11169 leucine-responsive tr 83.6 1.5 3.2E-05 40.8 4.3 37 149-185 20-56 (164)
46 KOG4557 Origin recognition com 82.9 3.3 7.2E-05 40.6 6.3 81 1-84 96-181 (262)
47 PF13730 HTH_36: Helix-turn-he 82.7 2.6 5.7E-05 31.5 4.6 26 159-184 27-52 (55)
48 PF13936 HTH_38: Helix-turn-he 81.9 1.9 4.1E-05 31.4 3.4 30 150-179 13-42 (44)
49 PRK00135 scpB segregation and 81.5 14 0.0003 35.6 10.1 118 38-177 5-124 (188)
50 PRK11179 DNA-binding transcrip 81.5 2 4.4E-05 39.4 4.3 37 149-185 15-51 (153)
51 PF08279 HTH_11: HTH domain; 81.4 2.7 5.8E-05 31.5 4.2 31 154-184 12-42 (55)
52 PRK09210 RNA polymerase sigma 81.1 58 0.0013 34.4 15.6 25 156-180 324-348 (367)
53 PF13542 HTH_Tnp_ISL3: Helix-t 80.4 5.9 0.00013 29.2 5.8 25 157-181 27-51 (52)
54 PF04545 Sigma70_r4: Sigma-70, 77.9 3.9 8.4E-05 30.1 4.0 28 154-181 17-44 (50)
55 TIGR03697 NtcA_cyano global ni 77.8 8.7 0.00019 35.6 7.4 29 156-184 142-170 (193)
56 PF13545 HTH_Crp_2: Crp-like h 77.3 4 8.6E-05 32.3 4.3 29 156-184 27-55 (76)
57 PRK07405 RNA polymerase sigma 77.2 94 0.002 32.1 15.4 26 155-180 274-299 (317)
58 PF02796 HTH_7: Helix-turn-hel 77.2 1.4 2.9E-05 32.3 1.3 28 152-179 16-43 (45)
59 PF10668 Phage_terminase: Phag 76.9 5.9 0.00013 31.2 4.9 40 137-179 5-44 (60)
60 KOG4164 Cyclin ik3-1/CABLES [C 76.9 4.1 8.9E-05 43.2 5.2 83 2-86 390-477 (497)
61 PF00356 LacI: Bacterial regul 76.9 2.2 4.7E-05 31.7 2.4 22 159-180 1-22 (46)
62 PF00325 Crp: Bacterial regula 76.7 3.9 8.5E-05 28.1 3.4 27 56-82 2-28 (32)
63 PF01325 Fe_dep_repress: Iron 76.3 5.5 0.00012 31.0 4.6 37 146-183 12-48 (60)
64 PRK10572 DNA-binding transcrip 76.1 38 0.00082 33.8 12.0 58 135-197 224-284 (290)
65 cd00092 HTH_CRP helix_turn_hel 75.8 7.5 0.00016 29.8 5.3 30 155-184 23-52 (67)
66 TIGR02393 RpoD_Cterm RNA polym 75.3 85 0.0018 30.7 16.1 26 156-181 195-220 (238)
67 COG5333 CCL1 Cdk activating ki 75.1 3.1 6.7E-05 42.7 3.7 56 99-156 49-104 (297)
68 TIGR02297 HpaA 4-hydroxyphenyl 74.9 61 0.0013 32.1 13.0 37 155-196 249-286 (287)
69 TIGR03697 NtcA_cyano global ni 74.2 11 0.00024 34.9 7.0 48 36-83 113-170 (193)
70 PF04967 HTH_10: HTH DNA bindi 73.7 6.9 0.00015 30.0 4.5 24 158-181 24-47 (53)
71 TIGR02395 rpoN_sigma RNA polym 73.5 12 0.00027 40.4 8.0 188 2-197 117-359 (429)
72 smart00419 HTH_CRP helix_turn_ 73.4 4.3 9.3E-05 29.0 3.2 30 155-184 6-35 (48)
73 PF08613 Cyclin: Cyclin; Inte 73.0 21 0.00045 32.7 8.4 78 96-175 52-135 (149)
74 PF08220 HTH_DeoR: DeoR-like h 72.5 3.6 7.7E-05 31.6 2.7 30 155-184 12-41 (57)
75 TIGR02010 IscR iron-sulfur clu 72.5 8.2 0.00018 34.7 5.5 48 36-83 5-52 (135)
76 smart00344 HTH_ASNC helix_turn 71.8 5.7 0.00012 33.8 4.1 30 155-184 15-44 (108)
77 KOG0794 CDK8 kinase-activating 71.2 7.8 0.00017 38.5 5.3 57 99-157 45-101 (264)
78 PF00165 HTH_AraC: Bacterial r 71.1 9.9 0.00021 26.9 4.6 36 155-195 6-41 (42)
79 PF00325 Crp: Bacterial regula 70.8 4.7 0.0001 27.7 2.7 27 157-183 2-28 (32)
80 TIGR00122 birA_repr_reg BirA b 70.7 7 0.00015 30.8 4.1 31 153-183 9-39 (69)
81 COG1522 Lrp Transcriptional re 70.6 5.9 0.00013 35.7 4.2 32 153-184 18-49 (154)
82 smart00345 HTH_GNTR helix_turn 70.6 6 0.00013 29.3 3.5 30 155-184 17-47 (60)
83 TIGR03879 near_KaiC_dom probab 70.4 11 0.00023 30.9 5.1 27 156-182 31-57 (73)
84 PF02082 Rrf2: Transcriptional 70.0 6.9 0.00015 32.1 4.0 45 39-83 8-52 (83)
85 PF13545 HTH_Crp_2: Crp-like h 68.8 13 0.00028 29.4 5.3 46 41-86 3-58 (76)
86 PF01325 Fe_dep_repress: Iron 67.8 16 0.00034 28.5 5.4 38 45-83 12-49 (60)
87 smart00421 HTH_LUXR helix_turn 67.1 6.9 0.00015 28.4 3.2 26 157-182 18-43 (58)
88 cd06571 Bac_DnaA_C C-terminal 67.0 31 0.00067 28.8 7.5 71 14-86 2-75 (90)
89 PF13518 HTH_28: Helix-turn-he 65.8 12 0.00027 27.1 4.4 26 159-184 14-39 (52)
90 TIGR02394 rpoS_proteo RNA poly 65.6 1.6E+02 0.0034 29.7 15.6 26 156-181 241-266 (285)
91 PF12802 MarR_2: MarR family; 65.5 13 0.00028 28.1 4.5 38 147-184 11-48 (62)
92 PF01022 HTH_5: Bacterial regu 65.1 11 0.00025 27.4 4.0 32 153-184 11-42 (47)
93 PRK05949 RNA polymerase sigma 65.0 1.8E+02 0.0039 30.3 16.0 25 156-180 285-309 (327)
94 PF09862 DUF2089: Protein of u 64.9 22 0.00047 31.6 6.3 71 37-116 35-106 (113)
95 PF08279 HTH_11: HTH domain; 64.8 16 0.00035 27.1 4.9 33 52-84 11-43 (55)
96 PF05225 HTH_psq: helix-turn-h 64.6 11 0.00024 27.6 3.8 27 154-181 14-40 (45)
97 PRK10857 DNA-binding transcrip 64.3 15 0.00032 34.5 5.5 47 37-83 6-52 (164)
98 PRK05932 RNA polymerase factor 64.0 50 0.0011 36.1 10.3 185 2-197 142-384 (455)
99 COG2207 AraC AraC-type DNA-bin 63.7 88 0.0019 26.2 10.6 39 41-80 22-60 (127)
100 PF13613 HTH_Tnp_4: Helix-turn 63.3 8.4 0.00018 29.0 3.0 36 148-183 10-45 (53)
101 PRK11920 rirA iron-responsive 63.2 17 0.00037 33.6 5.7 46 37-83 6-51 (153)
102 PF08281 Sigma70_r4_2: Sigma-7 62.9 9.7 0.00021 28.2 3.3 28 154-181 23-50 (54)
103 KOG1010 Rb (Retinoblastoma tum 62.5 9.4 0.0002 44.2 4.5 65 1-67 684-750 (920)
104 PF13613 HTH_Tnp_4: Helix-turn 62.3 14 0.00031 27.8 4.1 43 40-87 8-50 (53)
105 PRK07406 RNA polymerase sigma 62.1 63 0.0014 34.4 10.4 26 156-181 330-355 (373)
106 PRK13918 CRP/FNR family transc 61.3 30 0.00064 32.3 7.1 29 156-184 148-176 (202)
107 PF13542 HTH_Tnp_ISL3: Helix-t 61.1 29 0.00062 25.4 5.6 43 35-80 9-51 (52)
108 smart00420 HTH_DEOR helix_turn 61.0 20 0.00044 25.6 4.7 27 157-183 14-40 (53)
109 cd00092 HTH_CRP helix_turn_hel 60.7 30 0.00065 26.3 5.9 30 54-83 23-52 (67)
110 PRK09393 ftrA transcriptional 60.5 1.1E+02 0.0024 31.2 11.7 36 157-197 283-319 (322)
111 TIGR01610 phage_O_Nterm phage 60.3 20 0.00043 30.3 5.2 31 154-184 44-74 (95)
112 PRK11161 fumarate/nitrate redu 60.3 31 0.00068 33.2 7.3 30 156-185 183-212 (235)
113 PF08280 HTH_Mga: M protein tr 59.9 12 0.00027 28.8 3.5 30 155-184 17-46 (59)
114 PF02082 Rrf2: Transcriptional 59.8 11 0.00023 31.0 3.3 39 146-184 14-52 (83)
115 PRK05911 RNA polymerase sigma 59.7 1.3E+02 0.0029 29.9 11.8 27 155-181 219-245 (257)
116 PF02954 HTH_8: Bacterial regu 59.4 12 0.00026 26.8 3.1 26 156-181 17-42 (42)
117 PF13551 HTH_29: Winged helix- 59.3 19 0.00041 30.3 4.9 27 159-185 14-40 (112)
118 PHA02591 hypothetical protein; 59.2 11 0.00024 31.2 3.2 31 149-179 51-81 (83)
119 cd04762 HTH_MerR-trunc Helix-T 59.2 10 0.00022 26.7 2.8 23 159-181 2-24 (49)
120 PF00392 GntR: Bacterial regul 58.8 11 0.00023 29.3 3.0 30 154-183 20-50 (64)
121 PF02042 RWP-RK: RWP-RK domain 58.6 11 0.00024 28.8 3.0 27 156-182 14-40 (52)
122 PF00440 TetR_N: Bacterial reg 58.6 20 0.00044 26.0 4.3 35 144-179 3-38 (47)
123 PF00356 LacI: Bacterial regul 58.5 12 0.00025 27.8 3.0 19 58-76 1-19 (46)
124 cd06170 LuxR_C_like C-terminal 58.3 13 0.00028 27.0 3.3 26 157-182 15-40 (57)
125 PF00165 HTH_AraC: Bacterial r 58.3 14 0.00031 26.1 3.4 27 54-80 6-32 (42)
126 PF04079 DUF387: Putative tran 58.0 84 0.0018 29.4 9.3 107 42-181 3-120 (159)
127 PRK11511 DNA-binding transcrip 57.4 34 0.00074 30.3 6.4 44 37-81 7-50 (127)
128 PF01978 TrmB: Sugar-specific 57.3 10 0.00022 29.6 2.7 38 146-184 12-49 (68)
129 PF01371 Trp_repressor: Trp re 57.2 16 0.00034 30.9 3.9 32 153-184 45-76 (87)
130 PRK05901 RNA polymerase sigma 57.2 73 0.0016 35.4 10.1 25 155-179 465-489 (509)
131 PRK10219 DNA-binding transcrip 56.4 42 0.00091 28.4 6.6 39 41-80 7-45 (107)
132 TIGR01764 excise DNA binding d 56.4 12 0.00025 26.5 2.7 23 158-180 2-24 (49)
133 PRK11161 fumarate/nitrate redu 55.9 42 0.00092 32.2 7.4 53 34-86 152-214 (235)
134 PF05344 DUF746: Domain of Unk 55.7 17 0.00037 29.1 3.6 31 152-182 8-38 (65)
135 PF07638 Sigma70_ECF: ECF sigm 55.7 19 0.0004 34.0 4.7 25 158-182 152-176 (185)
136 PRK07122 RNA polymerase sigma 55.7 71 0.0015 32.0 9.1 27 155-181 229-255 (264)
137 PRK13413 mpi multiple promoter 55.6 35 0.00075 32.5 6.6 25 157-181 172-196 (200)
138 smart00418 HTH_ARSR helix_turn 55.4 22 0.00048 26.1 4.2 29 155-183 8-36 (66)
139 PRK10434 srlR DNA-bindng trans 55.1 13 0.00029 37.1 3.7 28 156-183 18-45 (256)
140 TIGR00738 rrf2_super rrf2 fami 54.9 27 0.00058 30.7 5.3 46 38-83 7-52 (132)
141 PRK11014 transcriptional repre 54.5 17 0.00038 32.8 4.1 38 146-183 14-51 (141)
142 cd00569 HTH_Hin_like Helix-tur 54.4 12 0.00027 23.6 2.4 21 157-177 21-41 (42)
143 TIGR02997 Sig70-cyanoRpoD RNA 54.4 2.5E+02 0.0054 28.5 15.7 26 155-180 267-292 (298)
144 TIGR02944 suf_reg_Xantho FeS a 54.4 32 0.00069 30.4 5.7 46 37-83 7-52 (130)
145 PRK10870 transcriptional repre 54.2 55 0.0012 30.8 7.6 30 155-184 69-98 (176)
146 PRK10219 DNA-binding transcrip 54.0 58 0.0013 27.5 7.1 51 142-198 7-57 (107)
147 PF12802 MarR_2: MarR family; 53.9 32 0.00069 25.9 4.9 41 43-83 8-48 (62)
148 cd04761 HTH_MerR-SF Helix-Turn 53.8 13 0.00028 26.7 2.6 23 159-181 2-24 (49)
149 cd06171 Sigma70_r4 Sigma70, re 53.7 24 0.00051 24.8 4.0 27 156-182 25-51 (55)
150 PRK15418 transcriptional regul 53.7 11 0.00023 39.1 2.9 45 149-193 21-65 (318)
151 PRK04217 hypothetical protein; 53.5 17 0.00036 32.1 3.7 27 156-182 57-83 (110)
152 PRK11511 DNA-binding transcrip 53.5 63 0.0014 28.6 7.5 54 138-197 7-60 (127)
153 cd00090 HTH_ARSR Arsenical Res 53.4 26 0.00055 26.5 4.4 27 158-184 21-47 (78)
154 PRK09391 fixK transcriptional 53.2 53 0.0012 31.8 7.6 29 156-184 178-206 (230)
155 cd07377 WHTH_GntR Winged helix 52.9 20 0.00044 26.9 3.7 26 159-184 27-52 (66)
156 PRK07500 rpoH2 RNA polymerase 52.7 2.7E+02 0.0058 28.3 13.9 27 155-181 243-269 (289)
157 TIGR02844 spore_III_D sporulat 52.3 22 0.00047 29.6 3.9 24 156-179 18-41 (80)
158 COG3877 Uncharacterized protei 52.3 72 0.0016 28.1 7.1 70 37-116 43-114 (122)
159 PRK14088 dnaA chromosomal repl 51.5 1.1E+02 0.0024 33.1 10.4 51 131-183 360-413 (440)
160 PRK10402 DNA-binding transcrip 51.4 37 0.0008 32.8 6.1 30 156-185 168-197 (226)
161 PF01726 LexA_DNA_bind: LexA D 51.4 16 0.00036 28.9 3.0 32 152-183 20-52 (65)
162 PRK13501 transcriptional activ 51.3 2.6E+02 0.0057 27.8 14.0 81 101-197 194-277 (290)
163 smart00419 HTH_CRP helix_turn_ 51.3 24 0.00053 24.9 3.7 30 54-83 6-35 (48)
164 PRK08215 sporulation sigma fac 51.2 2.6E+02 0.0055 27.7 15.1 26 156-181 224-249 (258)
165 PF12833 HTH_18: Helix-turn-he 51.2 58 0.0013 25.9 6.3 67 4-80 1-70 (81)
166 COG1510 Predicted transcriptio 51.0 32 0.0007 32.8 5.3 59 119-184 10-68 (177)
167 PF13022 HTH_Tnp_1_2: Helix-tu 50.9 33 0.00072 31.6 5.2 42 138-179 12-56 (142)
168 PRK13509 transcriptional repre 50.9 15 0.00032 36.7 3.3 29 155-183 17-45 (251)
169 cd01104 HTH_MlrA-CarA Helix-Tu 50.8 15 0.00033 28.3 2.8 23 159-181 2-24 (68)
170 COG1318 Predicted transcriptio 50.8 21 0.00045 34.0 4.0 72 114-197 28-99 (182)
171 TIGR01321 TrpR trp operon repr 50.5 18 0.0004 31.0 3.3 29 154-182 52-80 (94)
172 PRK07408 RNA polymerase sigma 50.3 2.7E+02 0.0058 27.6 14.3 28 155-182 217-244 (256)
173 PF12728 HTH_17: Helix-turn-he 50.2 18 0.00039 26.5 2.9 23 158-180 2-24 (51)
174 PRK09526 lacI lac repressor; R 50.0 16 0.00036 36.8 3.6 45 157-203 5-49 (342)
175 TIGR02944 suf_reg_Xantho FeS a 49.8 34 0.00074 30.2 5.2 38 146-184 15-52 (130)
176 PRK07598 RNA polymerase sigma 49.5 3.8E+02 0.0081 29.1 16.3 26 155-180 368-393 (415)
177 PRK00118 putative DNA-binding 49.3 20 0.00043 31.3 3.4 27 156-182 32-58 (104)
178 PF09339 HTH_IclR: IclR helix- 49.3 22 0.00048 26.4 3.3 31 154-184 15-45 (52)
179 smart00550 Zalpha Z-DNA-bindin 48.9 36 0.00078 27.0 4.6 33 152-184 16-49 (68)
180 KOG1010 Rb (Retinoblastoma tum 48.7 75 0.0016 37.2 8.6 54 3-59 40-93 (920)
181 PF04545 Sigma70_r4: Sigma-70, 48.5 36 0.00077 24.9 4.3 31 54-84 18-48 (50)
182 PRK11753 DNA-binding transcrip 48.0 77 0.0017 29.7 7.6 47 37-83 140-195 (211)
183 smart00346 HTH_ICLR helix_turn 47.9 47 0.001 26.9 5.4 29 156-184 19-47 (91)
184 PF09862 DUF2089: Protein of u 47.3 18 0.0004 32.0 2.9 26 158-183 50-75 (113)
185 PF13412 HTH_24: Winged helix- 47.3 58 0.0013 23.4 5.2 28 55-82 16-43 (48)
186 PRK09413 IS2 repressor TnpA; R 47.2 34 0.00073 30.2 4.7 31 153-183 25-55 (121)
187 PRK10703 DNA-binding transcrip 46.5 18 0.0004 36.5 3.3 43 158-202 2-44 (341)
188 PRK10402 DNA-binding transcrip 46.3 54 0.0012 31.6 6.4 48 37-84 150-197 (226)
189 PF00196 GerE: Bacterial regul 46.2 19 0.00041 27.3 2.5 27 156-182 17-43 (58)
190 PF12840 HTH_20: Helix-turn-he 46.2 29 0.00063 26.6 3.6 31 154-184 21-51 (61)
191 PF04703 FaeA: FaeA-like prote 46.2 29 0.00063 27.4 3.6 30 155-184 13-42 (62)
192 PF05460 ORC6: Origin recognit 46.1 6.7 0.00015 41.4 0.0 79 105-183 4-83 (353)
193 PRK10572 DNA-binding transcrip 46.0 54 0.0012 32.7 6.6 71 2-81 203-274 (290)
194 TIGR02985 Sig70_bacteroi1 RNA 45.9 20 0.00043 31.8 3.1 27 156-182 128-154 (161)
195 PF12116 SpoIIID: Stage III sp 45.8 14 0.00029 30.9 1.7 34 147-180 9-42 (82)
196 PRK11753 DNA-binding transcrip 45.5 82 0.0018 29.5 7.4 29 156-184 167-195 (211)
197 PRK10014 DNA-binding transcrip 45.4 21 0.00046 36.0 3.5 24 156-179 5-28 (342)
198 PF03444 HrcA_DNA-bdg: Winged 45.3 28 0.0006 28.9 3.5 29 154-182 20-48 (78)
199 COG1309 AcrR Transcriptional r 45.2 23 0.00049 30.9 3.3 39 142-181 17-56 (201)
200 PF13443 HTH_26: Cro/C1-type H 44.6 36 0.00079 25.8 4.0 42 156-201 9-50 (63)
201 PF14502 HTH_41: Helix-turn-he 44.5 23 0.0005 26.7 2.6 29 158-186 7-35 (48)
202 PF05732 RepL: Firmicute plasm 44.5 31 0.00067 32.4 4.2 27 158-184 76-102 (165)
203 PRK09642 RNA polymerase sigma 44.5 11 0.00023 34.1 1.1 27 156-182 121-147 (160)
204 PF13556 HTH_30: PucR C-termin 44.4 27 0.00058 26.8 3.2 30 156-185 11-40 (59)
205 COG1386 scpB Chromosome segreg 44.3 1.8E+02 0.0038 28.0 9.3 120 39-182 10-131 (184)
206 PRK09492 treR trehalose repres 44.2 20 0.00043 35.8 3.1 24 157-180 4-27 (315)
207 TIGR02405 trehalos_R_Ecol treh 43.9 17 0.00037 36.5 2.5 45 157-203 1-45 (311)
208 PF13011 LZ_Tnp_IS481: leucine 43.9 45 0.00097 28.1 4.6 36 148-183 16-51 (85)
209 PRK15121 right oriC-binding tr 43.7 48 0.001 33.4 5.8 53 39-105 5-57 (289)
210 cd04764 HTH_MlrA-like_sg1 Heli 43.5 24 0.00052 27.4 2.8 23 159-181 2-24 (67)
211 smart00351 PAX Paired Box doma 43.5 31 0.00067 30.7 3.9 29 157-185 33-61 (125)
212 PF00376 MerR: MerR family reg 43.5 17 0.00037 25.7 1.7 20 159-178 1-20 (38)
213 COG1725 Predicted transcriptio 43.4 24 0.00052 31.9 3.1 30 153-182 30-60 (125)
214 cd00131 PAX Paired Box domain 43.3 31 0.00067 31.0 3.8 30 156-185 32-61 (128)
215 TIGR02392 rpoH_proteo alternat 43.1 3.5E+02 0.0076 27.0 14.7 27 155-181 234-260 (270)
216 smart00421 HTH_LUXR helix_turn 42.8 46 0.001 23.8 4.2 31 57-87 19-49 (58)
217 PRK06030 hypothetical protein; 42.5 60 0.0013 29.2 5.5 69 14-84 26-97 (124)
218 PF13411 MerR_1: MerR HTH fami 42.3 19 0.00042 27.9 2.1 24 159-182 2-25 (69)
219 PF00196 GerE: Bacterial regul 42.3 37 0.00079 25.7 3.6 33 55-87 17-49 (58)
220 PRK10371 DNA-binding transcrip 42.2 2.6E+02 0.0057 28.4 10.9 40 40-80 192-231 (302)
221 TIGR02479 FliA_WhiG RNA polyme 42.2 3.2E+02 0.0069 26.2 16.2 26 156-181 190-215 (224)
222 PF01418 HTH_6: Helix-turn-hel 42.1 18 0.00039 29.3 2.0 27 156-182 33-59 (77)
223 TIGR02147 Fsuc_second hypothet 42.0 3.9E+02 0.0085 27.2 12.3 122 47-184 17-166 (271)
224 COG3415 Transposase and inacti 42.0 36 0.00079 31.2 4.1 32 154-185 18-49 (138)
225 TIGR02999 Sig-70_X6 RNA polyme 42.0 24 0.00052 32.5 3.1 26 156-181 149-174 (183)
226 PHA00542 putative Cro-like pro 41.9 22 0.00047 29.3 2.4 42 153-198 27-68 (82)
227 PRK12529 RNA polymerase sigma 41.8 24 0.00053 32.7 3.1 25 156-180 142-166 (178)
228 COG1959 Predicted transcriptio 41.7 58 0.0013 30.0 5.5 46 38-83 7-52 (150)
229 PRK10411 DNA-binding transcrip 41.7 25 0.00055 34.8 3.3 28 156-183 17-44 (240)
230 PRK09391 fixK transcriptional 41.6 1.1E+02 0.0024 29.6 7.7 48 36-83 153-206 (230)
231 PRK09685 DNA-binding transcrip 41.4 1.1E+02 0.0024 30.6 7.9 55 138-198 195-249 (302)
232 PF04703 FaeA: FaeA-like prote 41.2 56 0.0012 25.8 4.5 34 54-87 13-46 (62)
233 PRK13918 CRP/FNR family transc 41.0 96 0.0021 28.8 7.1 30 55-84 148-177 (202)
234 smart00354 HTH_LACI helix_turn 40.5 25 0.00053 27.9 2.5 35 158-197 1-35 (70)
235 PF01527 HTH_Tnp_1: Transposas 40.4 26 0.00057 27.6 2.6 26 157-182 23-48 (76)
236 cd04763 HTH_MlrA-like Helix-Tu 40.3 28 0.00061 27.1 2.8 23 159-181 2-24 (68)
237 smart00422 HTH_MERR helix_turn 40.3 26 0.00057 27.0 2.6 22 159-180 2-23 (70)
238 smart00550 Zalpha Z-DNA-bindin 40.2 76 0.0017 25.1 5.3 38 46-83 11-49 (68)
239 PF10668 Phage_terminase: Phag 40.0 69 0.0015 25.3 4.8 24 53-76 19-42 (60)
240 PRK09480 slmA division inhibit 39.9 34 0.00074 31.5 3.8 43 138-180 11-53 (194)
241 PF13463 HTH_27: Winged helix 39.8 59 0.0013 24.8 4.5 37 46-83 9-45 (68)
242 PF04218 CENP-B_N: CENP-B N-te 39.7 18 0.00039 27.4 1.5 23 158-180 23-45 (53)
243 TIGR02980 SigBFG RNA polymeras 39.6 3.5E+02 0.0076 25.9 14.6 26 156-181 193-218 (227)
244 cd06170 LuxR_C_like C-terminal 39.6 58 0.0013 23.5 4.3 32 56-87 15-46 (57)
245 TIGR00281 segregation and cond 39.4 2.9E+02 0.0063 26.6 10.0 120 39-181 3-125 (186)
246 PRK09392 ftrB transcriptional 39.4 81 0.0018 30.3 6.4 30 156-185 172-201 (236)
247 PRK01381 Trp operon repressor; 39.3 23 0.0005 30.7 2.2 37 149-185 47-83 (99)
248 PF01381 HTH_3: Helix-turn-hel 39.2 27 0.00059 25.7 2.4 39 155-198 7-45 (55)
249 PF01047 MarR: MarR family; I 39.2 83 0.0018 23.4 5.2 38 44-83 7-44 (59)
250 PRK10130 transcriptional regul 39.2 65 0.0014 33.9 6.1 54 38-105 239-292 (350)
251 PRK09645 RNA polymerase sigma 39.0 29 0.00063 31.7 3.1 26 156-181 133-158 (173)
252 PF07278 DUF1441: Protein of u 38.7 26 0.00057 32.7 2.6 26 157-182 1-26 (152)
253 PF13744 HTH_37: Helix-turn-he 38.7 51 0.0011 26.8 4.2 46 149-198 23-68 (80)
254 TIGR02702 SufR_cyano iron-sulf 38.5 51 0.0011 31.6 4.8 28 157-184 15-42 (203)
255 TIGR02010 IscR iron-sulfur clu 38.5 50 0.0011 29.6 4.5 40 145-184 13-52 (135)
256 PRK09047 RNA polymerase factor 38.4 30 0.00066 31.0 3.1 27 156-182 121-147 (161)
257 smart00345 HTH_GNTR helix_turn 38.2 58 0.0012 23.8 4.1 26 58-83 22-47 (60)
258 PRK06759 RNA polymerase factor 38.0 38 0.00083 30.1 3.6 26 156-181 121-146 (154)
259 PF05043 Mga: Mga helix-turn-h 37.7 35 0.00075 27.9 3.0 30 153-182 26-55 (87)
260 PF09339 HTH_IclR: IclR helix- 37.6 60 0.0013 24.0 4.1 34 49-82 11-44 (52)
261 PRK14962 DNA polymerase III su 37.5 4.1E+02 0.009 29.2 12.1 50 96-145 274-327 (472)
262 PRK12543 RNA polymerase sigma 37.4 45 0.00099 30.8 4.2 27 156-182 132-158 (179)
263 TIGR02937 sigma70-ECF RNA poly 37.3 42 0.00092 28.8 3.7 27 156-182 125-151 (158)
264 PRK12523 RNA polymerase sigma 36.9 31 0.00068 31.6 3.0 25 156-180 134-158 (172)
265 TIGR02885 spore_sigF RNA polym 36.8 3.9E+02 0.0085 25.7 14.6 27 155-181 197-223 (231)
266 PF04552 Sigma54_DBD: Sigma-54 36.7 25 0.00054 33.0 2.2 45 36-80 20-73 (160)
267 KOG3915 Transcription regulato 36.7 1.1E+02 0.0023 33.6 7.0 18 362-383 530-547 (641)
268 PRK12525 RNA polymerase sigma 36.5 34 0.00073 31.3 3.1 26 156-181 133-158 (168)
269 TIGR02947 SigH_actino RNA poly 36.3 33 0.00072 32.1 3.1 27 156-182 146-172 (193)
270 COG3620 Predicted transcriptio 36.1 35 0.00076 32.3 3.0 43 155-197 16-73 (187)
271 PRK09954 putative kinase; Prov 36.0 47 0.001 34.5 4.4 30 154-183 14-43 (362)
272 PRK12520 RNA polymerase sigma 35.9 49 0.0011 30.9 4.2 27 156-182 146-172 (191)
273 PF07900 DUF1670: Protein of u 35.5 2.3E+02 0.0049 28.2 8.6 105 51-176 100-216 (220)
274 PRK00430 fis global DNA-bindin 35.5 1.6E+02 0.0035 25.1 6.8 26 157-182 68-93 (95)
275 PRK12528 RNA polymerase sigma 35.5 37 0.0008 30.7 3.2 26 156-181 128-153 (161)
276 PRK12531 RNA polymerase sigma 35.4 34 0.00074 32.1 3.0 27 156-182 156-182 (194)
277 PRK11512 DNA-binding transcrip 35.4 52 0.0011 29.5 4.1 30 155-184 52-81 (144)
278 PF08220 HTH_DeoR: DeoR-like h 35.3 56 0.0012 24.9 3.7 31 54-84 12-42 (57)
279 PRK09685 DNA-binding transcrip 35.3 2.2E+02 0.0047 28.4 9.0 43 37-79 195-237 (302)
280 TIGR01610 phage_O_Nterm phage 35.3 1.1E+02 0.0025 25.7 5.9 42 42-83 27-74 (95)
281 smart00347 HTH_MARR helix_turn 35.2 87 0.0019 25.3 5.1 28 157-184 24-51 (101)
282 TIGR01481 ccpA catabolite cont 35.1 27 0.00058 35.1 2.4 44 158-203 2-45 (329)
283 PF01047 MarR: MarR family; I 35.1 63 0.0014 24.1 3.9 27 157-183 17-43 (59)
284 PRK14987 gluconate operon tran 35.1 24 0.00052 35.6 2.0 24 157-180 5-28 (331)
285 PRK10906 DNA-binding transcrip 34.7 32 0.00069 34.4 2.8 28 156-183 18-45 (252)
286 COG0664 Crp cAMP-binding prote 34.6 1.5E+02 0.0033 27.0 7.3 29 156-184 170-198 (214)
287 COG1725 Predicted transcriptio 34.6 49 0.0011 29.9 3.6 26 58-83 37-62 (125)
288 PF01498 HTH_Tnp_Tc3_2: Transp 34.6 38 0.00082 26.7 2.7 27 156-182 12-43 (72)
289 PF05930 Phage_AlpA: Prophage 34.6 39 0.00085 25.1 2.6 23 158-180 4-26 (51)
290 PF05344 DUF746: Domain of Unk 34.5 1E+02 0.0023 24.7 5.1 45 50-103 7-51 (65)
291 PF01710 HTH_Tnp_IS630: Transp 34.5 1.2E+02 0.0027 26.5 6.2 34 52-85 67-100 (119)
292 TIGR02954 Sig70_famx3 RNA poly 34.5 52 0.0011 29.9 4.0 27 156-182 134-160 (169)
293 PRK15340 transcriptional regul 34.5 2.1E+02 0.0045 28.3 8.3 29 52-80 121-149 (216)
294 TIGR00498 lexA SOS regulatory 34.4 42 0.00091 31.9 3.5 32 153-184 21-53 (199)
295 PRK09863 putative frv operon r 34.3 1.6E+02 0.0035 32.9 8.5 104 55-184 16-119 (584)
296 PRK11303 DNA-binding transcrip 34.2 29 0.00062 34.8 2.4 22 159-180 2-23 (328)
297 COG3355 Predicted transcriptio 33.9 70 0.0015 29.0 4.5 38 147-184 32-69 (126)
298 PRK12527 RNA polymerase sigma 33.8 40 0.00086 30.4 3.1 26 156-181 120-145 (159)
299 PRK07670 RNA polymerase sigma 33.8 4.7E+02 0.01 25.7 16.5 27 155-181 215-241 (251)
300 TIGR02417 fruct_sucro_rep D-fr 33.7 29 0.00063 34.9 2.3 22 159-180 1-22 (327)
301 TIGR03070 couple_hipB transcri 33.7 47 0.001 24.2 3.0 39 155-198 13-51 (58)
302 PRK10072 putative transcriptio 33.6 42 0.00091 28.8 3.0 29 154-182 43-71 (96)
303 PRK09393 ftrA transcriptional 33.6 75 0.0016 32.4 5.4 26 55-80 282-308 (322)
304 PRK11014 transcriptional repre 33.6 82 0.0018 28.3 5.1 46 38-83 7-52 (141)
305 PRK09649 RNA polymerase sigma 33.6 40 0.00086 31.6 3.1 27 156-182 145-171 (185)
306 PRK12542 RNA polymerase sigma 33.5 40 0.00086 31.3 3.1 42 156-197 137-181 (185)
307 PRK15435 bifunctional DNA-bind 33.3 1.3E+02 0.0027 31.8 7.1 51 39-105 85-135 (353)
308 TIGR02950 SigM_subfam RNA poly 33.3 39 0.00085 30.0 2.9 26 156-181 120-145 (154)
309 COG1191 FliA DNA-directed RNA 33.2 3.5E+02 0.0075 27.2 9.8 27 155-181 210-236 (247)
310 TIGR02531 yecD_yerC TrpR-relat 33.1 53 0.0011 27.8 3.4 22 157-178 50-71 (88)
311 PRK09956 hypothetical protein; 33.1 1.3E+02 0.0029 31.0 7.1 79 97-176 224-305 (308)
312 TIGR02366 DHAK_reg probable di 33.1 53 0.0011 30.0 3.8 41 141-181 7-47 (176)
313 PRK09639 RNA polymerase sigma 33.0 53 0.0011 29.6 3.8 27 156-182 126-152 (166)
314 PRK08301 sporulation sigma fac 32.8 38 0.00083 32.9 3.0 26 156-181 197-222 (234)
315 PF08281 Sigma70_r4_2: Sigma-7 32.7 70 0.0015 23.5 3.8 27 57-83 27-53 (54)
316 TIGR02952 Sig70_famx2 RNA poly 32.6 52 0.0011 29.7 3.7 27 156-182 137-163 (170)
317 PF04967 HTH_10: HTH DNA bindi 32.3 2.3E+02 0.005 21.7 6.7 44 21-82 6-49 (53)
318 COG3711 BglG Transcriptional a 32.3 2E+02 0.0043 31.1 8.7 110 52-181 15-124 (491)
319 cd06571 Bac_DnaA_C C-terminal 32.1 80 0.0017 26.3 4.4 37 145-183 34-71 (90)
320 PRK06288 RNA polymerase sigma 32.1 5.2E+02 0.011 25.7 15.4 25 156-180 227-251 (268)
321 COG2973 TrpR Trp operon repres 32.0 92 0.002 27.0 4.7 41 144-184 47-87 (103)
322 PF13404 HTH_AsnC-type: AsnC-t 32.0 99 0.0021 22.3 4.3 29 52-80 13-41 (42)
323 COG1595 RpoE DNA-directed RNA 31.9 45 0.00097 31.0 3.2 26 156-181 142-167 (182)
324 PRK12545 RNA polymerase sigma 31.9 43 0.00094 31.8 3.1 26 156-181 154-179 (201)
325 PRK12519 RNA polymerase sigma 31.8 41 0.0009 31.4 2.9 26 156-181 156-181 (194)
326 PRK10339 DNA-binding transcrip 31.7 29 0.00062 35.0 2.0 23 158-180 2-24 (327)
327 smart00351 PAX Paired Box doma 31.7 1.8E+02 0.0039 25.8 6.9 60 2-66 37-103 (125)
328 PF13730 HTH_36: Helix-turn-he 31.5 1.1E+02 0.0023 22.6 4.6 25 58-82 27-51 (55)
329 COG1476 Predicted transcriptio 31.3 37 0.0008 27.5 2.1 24 156-179 13-36 (68)
330 PRK10401 DNA-binding transcrip 31.3 34 0.00074 34.7 2.5 43 158-202 2-44 (346)
331 PRK11920 rirA iron-responsive 31.3 77 0.0017 29.2 4.6 39 145-184 13-51 (153)
332 PRK12547 RNA polymerase sigma 31.2 46 0.001 30.3 3.1 27 156-182 127-153 (164)
333 PRK06704 RNA polymerase factor 31.1 59 0.0013 32.1 4.0 27 156-182 131-157 (228)
334 PRK10727 DNA-binding transcrip 30.9 34 0.00073 34.7 2.3 22 158-179 2-23 (343)
335 TIGR00738 rrf2_super rrf2 fami 30.7 1.1E+02 0.0025 26.7 5.4 42 143-184 10-52 (132)
336 PF07900 DUF1670: Protein of u 30.6 47 0.001 32.8 3.1 25 158-182 106-130 (220)
337 COG4565 CitB Response regulato 30.5 66 0.0014 31.9 4.0 47 139-185 152-201 (224)
338 TIGR02939 RpoE_Sigma70 RNA pol 30.4 49 0.0011 30.5 3.2 27 156-182 153-179 (190)
339 PRK13501 transcriptional activ 30.4 1.9E+02 0.004 28.9 7.6 70 2-81 196-267 (290)
340 PRK05932 RNA polymerase factor 30.4 82 0.0018 34.5 5.3 43 36-78 314-365 (455)
341 TIGR02983 SigE-fam_strep RNA p 30.3 48 0.001 29.8 3.0 27 156-182 125-151 (162)
342 PRK13698 plasmid-partitioning 30.2 57 0.0012 34.1 3.8 35 148-182 167-201 (323)
343 PRK13919 putative RNA polymera 30.2 48 0.001 30.7 3.0 26 156-181 150-175 (186)
344 PRK09651 RNA polymerase sigma 30.1 59 0.0013 29.9 3.6 27 155-181 133-159 (172)
345 TIGR00721 tfx DNA-binding prot 30.1 59 0.0013 29.8 3.5 27 156-182 20-46 (137)
346 TIGR02607 antidote_HigA addict 30.0 61 0.0013 25.6 3.3 41 153-198 14-54 (78)
347 PRK12530 RNA polymerase sigma 30.0 49 0.0011 31.0 3.1 26 156-181 149-174 (189)
348 PRK09802 DNA-binding transcrip 30.0 70 0.0015 32.3 4.4 27 157-183 31-57 (269)
349 PRK12537 RNA polymerase sigma 30.0 48 0.001 30.8 3.0 26 156-181 148-173 (182)
350 COG1321 TroR Mn-dependent tran 30.0 77 0.0017 29.5 4.3 36 146-182 14-49 (154)
351 PRK12533 RNA polymerase sigma 29.9 48 0.001 32.2 3.1 27 156-182 149-175 (216)
352 COG1349 GlpR Transcriptional r 29.9 39 0.00085 33.7 2.5 27 156-182 18-44 (253)
353 TIGR02297 HpaA 4-hydroxyphenyl 29.9 3.3E+02 0.0071 26.8 9.2 44 148-197 194-237 (287)
354 PRK07037 extracytoplasmic-func 29.8 52 0.0011 29.6 3.2 25 156-180 124-148 (163)
355 PRK03902 manganese transport t 29.8 84 0.0018 28.2 4.5 29 156-184 21-49 (142)
356 PF00126 HTH_1: Bacterial regu 29.8 68 0.0015 24.4 3.3 26 159-184 15-40 (60)
357 PRK09415 RNA polymerase factor 29.8 51 0.0011 30.5 3.1 27 156-182 142-168 (179)
358 PRK10681 DNA-binding transcrip 29.5 51 0.0011 32.8 3.3 27 156-182 20-46 (252)
359 PRK09392 ftrB transcriptional 29.5 1.5E+02 0.0033 28.4 6.5 48 36-83 147-200 (236)
360 PRK04424 fatty acid biosynthes 29.4 80 0.0017 30.1 4.4 29 156-184 20-48 (185)
361 PRK11050 manganese transport r 29.4 88 0.0019 28.7 4.6 30 155-184 49-78 (152)
362 PRK12536 RNA polymerase sigma 29.2 52 0.0011 30.5 3.1 26 156-181 144-169 (181)
363 PRK12532 RNA polymerase sigma 29.2 49 0.0011 31.0 2.9 27 156-182 151-177 (195)
364 TIGR02989 Sig-70_gvs1 RNA poly 29.2 54 0.0012 29.3 3.1 27 156-182 126-152 (159)
365 PF06056 Terminase_5: Putative 29.1 65 0.0014 25.0 3.1 28 156-183 12-39 (58)
366 COG2390 DeoR Transcriptional r 29.1 64 0.0014 33.7 4.0 43 150-192 19-61 (321)
367 cd04765 HTH_MlrA-like_sg2 Heli 29.0 52 0.0011 28.1 2.8 24 159-182 2-25 (99)
368 smart00530 HTH_XRE Helix-turn- 29.0 62 0.0013 22.1 2.8 39 155-198 8-46 (56)
369 smart00418 HTH_ARSR helix_turn 29.0 1.4E+02 0.003 21.6 4.9 30 54-83 8-37 (66)
370 PF13936 HTH_38: Helix-turn-he 28.9 99 0.0021 22.3 3.9 25 54-78 18-42 (44)
371 COG2207 AraC AraC-type DNA-bin 28.8 1.2E+02 0.0026 25.4 5.1 38 143-181 23-60 (127)
372 PRK07921 RNA polymerase sigma 28.8 6.8E+02 0.015 26.0 14.9 24 155-178 280-303 (324)
373 PRK09652 RNA polymerase sigma 28.7 63 0.0014 29.3 3.5 26 156-181 143-168 (182)
374 TIGR02337 HpaR homoprotocatech 28.6 79 0.0017 27.3 4.0 30 155-184 40-69 (118)
375 TIGR02850 spore_sigG RNA polym 28.5 5.8E+02 0.012 25.1 15.0 27 155-181 220-246 (254)
376 PRK09646 RNA polymerase sigma 28.5 76 0.0016 29.8 4.1 26 156-181 157-182 (194)
377 PRK09643 RNA polymerase sigma 28.5 53 0.0011 30.9 3.0 26 156-181 149-174 (192)
378 PRK10840 transcriptional regul 28.4 65 0.0014 30.4 3.7 27 156-182 164-190 (216)
379 PRK12518 RNA polymerase sigma 28.4 54 0.0012 29.9 3.0 27 156-182 135-161 (175)
380 PF01978 TrmB: Sugar-specific 28.2 74 0.0016 24.7 3.4 31 53-83 19-49 (68)
381 PF13463 HTH_27: Winged helix 28.1 1.2E+02 0.0026 23.0 4.5 31 154-184 15-45 (68)
382 COG4977 Transcriptional regula 28.0 3.7E+02 0.0081 28.2 9.3 78 56-185 236-314 (328)
383 PRK12517 RNA polymerase sigma 28.0 55 0.0012 30.8 3.1 27 156-182 143-169 (188)
384 PRK14165 winged helix-turn-hel 28.0 66 0.0014 31.7 3.6 30 155-184 19-48 (217)
385 PRK11924 RNA polymerase sigma 27.9 62 0.0013 29.2 3.3 26 156-181 140-165 (179)
386 PRK14088 dnaA chromosomal repl 27.9 1.2E+02 0.0025 32.9 5.9 68 14-84 345-415 (440)
387 PF13384 HTH_23: Homeodomain-l 27.9 97 0.0021 22.3 3.7 27 56-82 17-43 (50)
388 PF13560 HTH_31: Helix-turn-he 27.8 68 0.0015 24.6 3.1 40 155-198 12-51 (64)
389 PRK12541 RNA polymerase sigma 27.8 59 0.0013 29.3 3.1 26 156-181 127-152 (161)
390 PRK12516 RNA polymerase sigma 27.8 56 0.0012 30.7 3.1 27 156-182 131-157 (187)
391 cd07377 WHTH_GntR Winged helix 27.7 91 0.002 23.2 3.7 26 58-83 27-52 (66)
392 TIGR02835 spore_sigmaE RNA pol 27.6 59 0.0013 31.7 3.3 25 156-180 197-221 (234)
393 PRK09978 DNA-binding transcrip 27.6 3.7E+02 0.0081 27.4 9.1 53 139-198 141-193 (274)
394 PRK13502 transcriptional activ 27.6 2.1E+02 0.0045 28.3 7.3 70 2-81 196-267 (282)
395 PRK15481 transcriptional regul 27.6 1.1E+02 0.0024 32.5 5.6 30 154-183 25-55 (431)
396 smart00420 HTH_DEOR helix_turn 27.5 1.8E+02 0.0039 20.4 5.2 29 55-83 13-41 (53)
397 PRK05602 RNA polymerase sigma 27.4 58 0.0013 30.2 3.1 27 156-182 143-169 (186)
398 TIGR02959 SigZ RNA polymerase 27.4 60 0.0013 29.8 3.2 27 156-182 115-141 (170)
399 PRK12524 RNA polymerase sigma 27.4 57 0.0012 30.7 3.0 27 156-182 151-177 (196)
400 PRK12526 RNA polymerase sigma 27.4 56 0.0012 31.1 3.1 26 156-181 168-193 (206)
401 PRK10430 DNA-binding transcrip 27.4 93 0.002 30.0 4.6 33 153-185 174-206 (239)
402 PRK12511 RNA polymerase sigma 27.1 56 0.0012 30.6 2.9 27 156-182 126-152 (182)
403 PRK10141 DNA-binding transcrip 27.0 1E+02 0.0022 27.4 4.4 30 155-184 28-57 (117)
404 PF04552 Sigma54_DBD: Sigma-54 26.9 21 0.00046 33.5 0.0 42 156-197 48-90 (160)
405 PF01726 LexA_DNA_bind: LexA D 26.9 1.1E+02 0.0023 24.3 4.0 33 51-83 20-53 (65)
406 TIGR03338 phnR_burk phosphonat 26.8 61 0.0013 30.8 3.2 30 153-182 30-59 (212)
407 TIGR03209 P21_Cbot clostridium 26.7 33 0.00072 30.3 1.2 21 156-176 122-142 (142)
408 PRK11923 algU RNA polymerase s 26.7 69 0.0015 29.8 3.5 27 156-182 153-179 (193)
409 PHA01976 helix-turn-helix prot 26.6 63 0.0014 24.8 2.7 38 156-198 14-51 (67)
410 PRK14999 histidine utilization 26.6 69 0.0015 31.3 3.6 29 154-182 32-61 (241)
411 PRK12522 RNA polymerase sigma 26.5 60 0.0013 29.7 3.0 27 156-182 134-160 (173)
412 TIGR02943 Sig70_famx1 RNA poly 26.5 58 0.0012 30.6 2.9 27 156-182 146-172 (188)
413 COG2169 Ada Adenosine deaminas 26.5 1.2E+02 0.0027 29.2 5.1 44 37-82 80-123 (187)
414 PRK13870 transcriptional regul 26.5 89 0.0019 30.8 4.3 27 156-182 187-213 (234)
415 PRK13500 transcriptional activ 26.3 3.5E+02 0.0076 27.5 8.9 87 54-197 220-307 (312)
416 PRK04984 fatty acid metabolism 26.3 73 0.0016 30.9 3.7 29 154-182 27-56 (239)
417 PRK12469 RNA polymerase factor 26.3 1.3E+02 0.0029 33.1 6.0 128 36-177 340-480 (481)
418 PRK13503 transcriptional activ 26.2 75 0.0016 31.2 3.8 27 54-80 185-211 (278)
419 TIGR03384 betaine_BetI transcr 26.2 99 0.0021 28.2 4.4 41 138-179 9-50 (189)
420 PRK09640 RNA polymerase sigma 26.1 63 0.0014 30.1 3.1 26 156-181 149-174 (188)
421 PRK12513 RNA polymerase sigma 26.1 64 0.0014 30.1 3.1 26 156-181 154-179 (194)
422 PRK12534 RNA polymerase sigma 26.1 61 0.0013 30.0 3.0 27 156-182 152-178 (187)
423 PF03428 RP-C: Replication pro 26.1 2.2E+02 0.0048 27.1 6.8 57 113-184 41-98 (177)
424 PRK15340 transcriptional regul 26.0 1.6E+02 0.0036 29.0 6.0 24 56-79 174-198 (216)
425 PRK10857 DNA-binding transcrip 25.9 1E+02 0.0023 28.8 4.5 40 145-184 13-52 (164)
426 PRK09644 RNA polymerase sigma 25.8 63 0.0014 29.3 3.0 27 156-182 123-149 (165)
427 PRK12514 RNA polymerase sigma 25.8 62 0.0013 29.7 2.9 26 156-181 144-169 (179)
428 PF05269 Phage_CII: Bacterioph 25.7 31 0.00067 29.5 0.8 24 158-181 24-47 (91)
429 PRK12539 RNA polymerase sigma 25.7 63 0.0014 30.0 3.0 26 156-181 146-171 (184)
430 PF05066 HARE-HTH: HB1, ASXL, 25.7 66 0.0014 25.5 2.7 32 20-51 20-53 (72)
431 PF01022 HTH_5: Bacterial regu 25.4 1.9E+02 0.0042 20.8 4.9 32 51-82 10-41 (47)
432 PRK10130 transcriptional regul 25.3 2E+02 0.0043 30.2 6.9 53 140-198 240-292 (350)
433 PF00392 GntR: Bacterial regul 25.1 1.1E+02 0.0024 23.5 3.8 30 54-83 21-51 (64)
434 PRK08583 RNA polymerase sigma 25.1 77 0.0017 31.3 3.6 27 155-181 219-245 (257)
435 PRK03573 transcriptional regul 25.1 1.2E+02 0.0026 27.0 4.7 30 155-184 44-73 (144)
436 PF08280 HTH_Mga: M protein tr 25.1 81 0.0018 24.2 3.0 33 54-86 17-49 (59)
437 PRK05658 RNA polymerase sigma 25.1 3.3E+02 0.0072 30.9 9.1 27 53-79 480-506 (619)
438 COG2512 Predicted membrane-ass 25.0 81 0.0017 31.9 3.7 34 151-184 204-237 (258)
439 PRK09648 RNA polymerase sigma 24.9 70 0.0015 29.7 3.1 26 156-181 154-179 (189)
440 PRK09637 RNA polymerase sigma 24.8 69 0.0015 29.9 3.1 27 156-182 121-147 (181)
441 TIGR03001 Sig-70_gmx1 RNA poly 24.7 66 0.0014 31.9 3.1 27 156-182 176-202 (244)
442 PRK13182 racA polar chromosome 24.7 62 0.0013 30.8 2.7 24 159-182 2-25 (175)
443 PRK13503 transcriptional activ 24.7 2.6E+02 0.0055 27.4 7.3 70 2-81 191-262 (278)
444 KOG0654 G2/Mitotic-specific cy 24.6 5.4E+02 0.012 27.4 9.9 134 43-182 184-320 (359)
445 PRK10188 DNA-binding transcrip 24.5 1E+02 0.0022 30.4 4.4 27 156-182 193-219 (240)
446 TIGR02859 spore_sigH RNA polym 24.4 76 0.0017 29.5 3.3 27 157-183 165-191 (198)
447 PRK08295 RNA polymerase factor 24.4 71 0.0015 30.0 3.1 27 156-182 169-195 (208)
448 PRK12515 RNA polymerase sigma 24.4 72 0.0016 29.7 3.1 27 156-182 146-172 (189)
449 TIGR02948 SigW_bacill RNA poly 24.2 78 0.0017 29.1 3.3 27 156-182 151-177 (187)
450 TIGR02787 codY_Gpos GTP-sensin 24.0 1.3E+02 0.0029 30.3 4.9 29 156-184 197-225 (251)
451 COG3413 Predicted DNA binding 23.9 1.1E+02 0.0024 29.6 4.4 26 157-182 178-203 (215)
452 TIGR02404 trehalos_R_Bsub treh 23.9 72 0.0016 30.9 3.1 28 155-182 21-49 (233)
453 PRK11886 bifunctional biotin-- 23.9 1.1E+02 0.0023 31.5 4.5 29 155-183 16-44 (319)
454 TIGR02018 his_ut_repres histid 23.9 83 0.0018 30.5 3.5 29 154-182 21-50 (230)
455 smart00529 HTH_DTXR Helix-turn 23.8 77 0.0017 26.0 2.9 25 160-184 2-26 (96)
456 TIGR02325 C_P_lyase_phnF phosp 23.7 73 0.0016 30.8 3.1 28 155-182 29-57 (238)
457 PRK01905 DNA-binding protein F 23.6 1.1E+02 0.0024 24.8 3.7 24 158-181 51-74 (77)
458 COG4753 Response regulator con 23.5 2.6E+02 0.0056 30.9 7.5 32 51-82 383-414 (475)
459 PRK06811 RNA polymerase factor 23.4 72 0.0016 29.8 2.9 26 156-181 146-171 (189)
460 PRK12423 LexA repressor; Provi 23.4 1.4E+02 0.0031 28.6 5.0 31 153-183 21-52 (202)
461 PRK03837 transcriptional regul 23.4 92 0.002 30.2 3.7 29 154-182 33-62 (241)
462 PF02796 HTH_7: Helix-turn-hel 23.3 94 0.002 22.4 2.9 21 57-77 22-42 (45)
463 PRK06986 fliA flagellar biosyn 23.3 96 0.0021 30.2 3.9 26 156-181 199-224 (236)
464 PRK09638 RNA polymerase sigma 23.3 77 0.0017 28.9 3.0 26 156-181 141-166 (176)
465 PRK11552 putative DNA-binding 23.2 1.1E+02 0.0023 29.7 4.2 38 141-179 17-54 (225)
466 cd04768 HTH_BmrR-like Helix-Tu 23.2 63 0.0014 27.3 2.2 22 159-180 2-23 (96)
467 PRK12538 RNA polymerase sigma 23.1 74 0.0016 31.3 3.0 27 156-182 186-212 (233)
468 PRK00118 putative DNA-binding 23.1 1.9E+02 0.0041 25.3 5.2 60 56-129 33-92 (104)
469 PF07022 Phage_CI_repr: Bacter 23.1 95 0.0021 24.3 3.1 26 153-179 9-35 (66)
470 TIGR01884 cas_HTH CRISPR locus 23.0 1.2E+02 0.0025 29.1 4.3 28 157-184 157-184 (203)
471 PRK03975 tfx putative transcri 22.9 80 0.0017 29.1 3.0 26 156-181 20-45 (141)
472 PRK09647 RNA polymerase sigma 22.9 74 0.0016 30.4 2.9 27 156-182 153-179 (203)
473 PRK09641 RNA polymerase sigma 22.9 79 0.0017 29.0 3.1 26 156-181 151-176 (187)
474 TIGR03541 reg_near_HchA LuxR f 22.8 1.2E+02 0.0026 29.7 4.4 27 156-182 185-211 (232)
475 COG1510 Predicted transcriptio 22.8 1E+02 0.0022 29.4 3.7 37 46-82 31-67 (177)
476 PF09241 Herp-Cyclin: Herpesvi 22.8 4.7E+02 0.01 22.1 7.4 83 3-86 10-100 (106)
477 PRK09726 antitoxin HipB; Provi 22.8 1.9E+02 0.004 23.9 5.0 40 155-199 23-62 (88)
478 PRK12535 RNA polymerase sigma 22.7 78 0.0017 30.0 3.0 26 156-181 148-173 (196)
479 PRK03573 transcriptional regul 22.7 4E+02 0.0087 23.6 7.6 65 16-83 8-73 (144)
480 cd00090 HTH_ARSR Arsenical Res 22.7 2.1E+02 0.0046 21.2 5.0 27 57-83 21-47 (78)
481 PRK09764 DNA-binding transcrip 22.6 91 0.002 30.5 3.6 29 154-182 25-54 (240)
482 PRK05572 sporulation sigma fac 22.6 7.3E+02 0.016 24.3 12.8 26 156-181 217-242 (252)
483 PRK12540 RNA polymerase sigma 22.6 82 0.0018 29.4 3.1 27 156-182 126-152 (182)
484 PRK06930 positive control sigm 22.6 1E+02 0.0022 29.1 3.7 28 155-182 128-155 (170)
485 PF01638 HxlR: HxlR-like helix 22.5 1.4E+02 0.003 24.7 4.2 30 155-184 16-46 (90)
486 PRK12546 RNA polymerase sigma 22.5 82 0.0018 29.7 3.1 27 156-182 128-154 (188)
487 COG1654 BirA Biotin operon rep 22.5 1.7E+02 0.0036 24.3 4.5 32 153-184 15-46 (79)
488 PRK10079 phosphonate metabolis 22.5 80 0.0017 30.9 3.1 24 159-182 37-60 (241)
489 COG1609 PurR Transcriptional r 22.3 64 0.0014 33.4 2.5 25 158-182 1-25 (333)
490 cd00131 PAX Paired Box domain 22.3 5.6E+02 0.012 22.8 8.5 75 2-78 37-125 (128)
491 PRK09940 transcriptional regul 22.2 4E+02 0.0088 26.8 8.1 39 154-198 147-185 (253)
492 TIGR00180 parB_part ParB-like 22.2 1.3E+02 0.0028 28.4 4.4 43 136-181 102-144 (187)
493 TIGR03613 RutR pyrimidine util 21.8 1.2E+02 0.0026 28.2 4.1 40 141-181 12-52 (202)
494 COG1321 TroR Mn-dependent tran 21.7 1.7E+02 0.0036 27.3 4.9 37 45-82 14-50 (154)
495 PF09904 HTH_43: Winged helix- 21.6 97 0.0021 26.4 3.0 37 146-182 10-46 (90)
496 TIGR01889 Staph_reg_Sar staphy 21.6 1.6E+02 0.0036 25.1 4.6 33 152-184 38-70 (109)
497 TIGR01889 Staph_reg_Sar staphy 21.6 3.2E+02 0.007 23.3 6.4 35 50-84 37-71 (109)
498 COG2944 Predicted transcriptio 21.4 78 0.0017 27.7 2.4 24 154-177 54-77 (104)
499 PF06163 DUF977: Bacterial pro 21.4 1.1E+02 0.0023 27.8 3.3 29 156-184 25-53 (127)
500 TIGR02984 Sig-70_plancto1 RNA 21.4 1.1E+02 0.0023 28.1 3.6 26 156-181 155-180 (189)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=2e-66 Score=543.34 Aligned_cols=410 Identities=32% Similarity=0.448 Sum_probs=326.4
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|..++.+|+|+ . +++.|++||++|.++||++||+...|+|||+|++||+++++++|+||+++++|+||.||.+|++|
T Consensus 74 i~~~~~~l~l~--~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l 150 (521)
T KOG1598|consen 74 IEELTERLNLG--N-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEV 150 (521)
T ss_pred HHHHHHhcCcc--h-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHH
Confidence 56789999999 7 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccccccccccCCccchHHHHHhhhC-CCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCC
Q 011262 81 CQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFS 159 (490)
Q Consensus 81 ~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~-~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t 159 (490)
++.|.++.. +.+++||+.||+||++.|. |+.+++|+.+|.+|+++|++|||++||+|+||||||||+|||+||+++|
T Consensus 151 ~~~L~i~en--~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rs 228 (521)
T KOG1598|consen 151 TDSLSIGEN--VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRT 228 (521)
T ss_pred HHHhccccc--cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCcccc
Confidence 999999842 3457999999999999997 8888999999999999999999999999999999999999999999999
Q ss_pred HhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHhhhcccCCCCCCCCCCCCchh--------hhhhcccCCC
Q 011262 160 KSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHEGVAANLPNNGPKVSGMNE--------VLCKHKDTGK 231 (490)
Q Consensus 160 ~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le~e~~~~~p~~~~~~~~~~e--------~~~~~k~~~~ 231 (490)
+.||+.++|||+.||++||+||.+|+++.||+++|+++ |+|.+ .|||+|+....+..+ +.|.|....
T Consensus 229 i~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~--d~e~~--~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e- 303 (521)
T KOG1598|consen 229 IGDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELAEI--DLEYE--SDPPSFTASPSKEAKYVEDKKKMLSRTMQLVE- 303 (521)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhccccccccHHHHHhh--hhhhc--cCcchhhcccchhhhhhhhhhhhhhhhhhhhh-
Confidence 99999999999999999999999999999999999999 99998 999999976432222 222222222
Q ss_pred CcccCchhhhhhhhhhcccCCCCCCCCchhHHHHHHHHHHhhhhhcchhhhccCCcccccccccCCCCCCCCCCCCCCCc
Q 011262 232 PFACGLCRSCYEEFMTISEGLEGGADPPAFQVAERERMVKASAEENSSFERESDSPFMSRVDKVQSPEPESIGVPKNCTT 311 (490)
Q Consensus 232 ~~~~g~~~~~~~~~~~~~~~~~~~~~ppa~~~~e~~r~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 311 (490)
.+..+.|..||..+..+++|+.++..++.++..+.++-..... + ..+.+. ..+...+........ .
T Consensus 304 ~~~~~~~~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~~~~~~~-e-----~~~ssE----~~dk~~~g~~~~~~~--~-- 369 (521)
T KOG1598|consen 304 LANETWLVTLRHSLPVITGGLFLAWQDLQPRDRLVESYDDLAS-E-----CPLSSE----DEDKPASGRLAELLA--V-- 369 (521)
T ss_pred cccchhhhccccCCcccchhhhcccccchhhhhhhhhhhhhhh-c-----Cccccc----ccCCcCccccchhhh--c--
Confidence 6778899999999999999999999999998776654100000 0 001110 000000000000000 0
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHHH
Q 011262 312 QTASNEGEGDHTKTPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAAL 391 (490)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lsdiDD~Eid~~il~eeE~~~K~~iW~~~N~dyl~eq~~Ke~~~~~~~~~~ 391 (490)
..+. ..............+....++++||.+++.++|++++.+.++.+ | +|++||.|+..+.++++++++.
T Consensus 370 ---~sd~---~~~~~~~~~~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ak~~~~- 440 (521)
T KOG1598|consen 370 ---LSDM---AEQLASVWLRVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKAAKEREE- 440 (521)
T ss_pred ---cccc---chhhhhcchhhhhccccccccccCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhhhHhhhh-
Confidence 0000 00000001112345677889999999999999999999999999 7 9999999999988766543221
Q ss_pred HHhhcCCCcchHHHHHHHHHHHHHHhhhhhHHHhhhhhhhcCCCCCCCHHHHHHHHHHhcCCCccCCHHHHhhhhCCCCc
Q 011262 392 EASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQKRAAEAKNSGPAQTALEATRRMLTKKRLSSKINYDVLEKLFDDSVC 471 (490)
Q Consensus 392 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~rk~kk~k~~~~~~~~~~a~ta~EA~~~ml~~k~~S~KINYdvl~~L~~~~~~ 471 (490)
++ .+ ++++..+.++.+++.||.||++.|++.+.+|++|||++|++|||....
T Consensus 441 -----------------------g~-~~----~~~k~~~r~~s~~~~t~~eavk~~~~i~~~s~~in~~~L~~i~d~~~e 492 (521)
T KOG1598|consen 441 -----------------------GI-NS----LSKKVGERRNSPELLTAPEAVKSMKEIKPVSSVINYSVLENISDAEIE 492 (521)
T ss_pred -----------------------cc-cc----cccccccccCCCcccccHHHHHHHHhccccccchHHHHHHHHhhhhcc
Confidence 11 11 123344567899999999999999999999999999999999986544
No 2
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=5.8e-40 Score=328.93 Aligned_cols=175 Identities=29% Similarity=0.522 Sum_probs=170.1
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|.++|++|+|| .++.++|..||++++++++++||+.++++|||||+|||+++.|+||.||+.+++|++++|+++|+.+
T Consensus 104 l~~~~~~l~LP--~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rtyr~~ 181 (285)
T COG1405 104 LERIASALGLP--ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTYRLL 181 (285)
T ss_pred HHHHHHHhCCC--chHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCH
Q 011262 81 CQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 160 (490)
Q Consensus 81 ~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~ 160 (490)
.+.|++..+| ++|.+||+|||+.|+ ++++|...|.+|++.+.+.|++.||+|.||||||||+|++++|+++||
T Consensus 182 ~~~L~l~~~~-----~~p~~yi~rf~s~L~--l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq 254 (285)
T COG1405 182 VRELKLKIPP-----VDPSDYIPRFASKLG--LSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQ 254 (285)
T ss_pred HHhcCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHH
Confidence 9999998876 899999999999999 899999999999999999999999999999999999999999999999
Q ss_pred hhHHhHhccCHHHHHHHHHHHhcC
Q 011262 161 SDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 161 ~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++|+.++|||++|||+||+|+.+.
T Consensus 255 ~eva~v~~vtevTIrnrykel~~~ 278 (285)
T COG1405 255 KEVAKVAGVTEVTIRNRYKELADA 278 (285)
T ss_pred HHHHHHhCCeeeHHHHHHHHHHHh
Confidence 999999999999999999998643
No 3
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=1.7e-39 Score=331.11 Aligned_cols=174 Identities=26% Similarity=0.428 Sum_probs=169.5
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|+++|+.|+|| +.|+++|..||++++++++++||+.+.++|||||+|||++++|+||+||+.++++++++|+++|+.|
T Consensus 129 I~~~~~~L~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l 206 (310)
T PRK00423 129 LDRIASQLGLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFL 206 (310)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57899999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCH
Q 011262 81 CQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 160 (490)
Q Consensus 81 ~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~ 160 (490)
.+.|+++.++ ++|..||+|||+.|+ ++..|.+.|.+|++.+.+.|++.||+|.+||||||||||+++|.++|+
T Consensus 207 ~k~L~~~~~~-----~~p~~~i~r~~~~L~--L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~ 279 (310)
T PRK00423 207 LRELNLKLPP-----TDPIDYVPRFASELG--LSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQ 279 (310)
T ss_pred HHHhCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCH
Confidence 9999998765 899999999999999 899999999999999999999999999999999999999999999999
Q ss_pred hhHHhHhccCHHHHHHHHHHHhc
Q 011262 161 SDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 161 ~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
++|+.++||++.||++||++|..
T Consensus 280 keIa~v~~Vs~~tI~~~ykel~~ 302 (310)
T PRK00423 280 REVAEVAGVTEVTVRNRYKELAE 302 (310)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHH
Confidence 99999999999999999999974
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2.1e-37 Score=304.14 Aligned_cols=190 Identities=20% Similarity=0.320 Sum_probs=179.2
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|..||++|+|| ..|.++|.++|+++.+.+.+|||+.++++|||||+|||++++|||++||+.+++|+.++|||+++.|
T Consensus 111 I~~m~d~~~Lp--~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEIgr~~K~i 188 (308)
T KOG1597|consen 111 ITAMCDRLSLP--ATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEIGRCVKLI 188 (308)
T ss_pred HHHHHHHhCCc--hHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHHHHHHHHH
Confidence 67899999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCH
Q 011262 81 CQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 160 (490)
Q Consensus 81 ~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~ 160 (490)
.+.|++.++-+ .+...+||+|||+.|. ++..+++.|.++++++....+..||+|.+||||+|||++++.+.++|+
T Consensus 189 ~~~l~~s~~~~---s~~t~~~m~RFCs~L~--L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~ 263 (308)
T KOG1597|consen 189 GEALETSVDLI---SISTGDFMPRFCSNLG--LPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQ 263 (308)
T ss_pred HHHHhccchhh---hhhHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccH
Confidence 99999876531 3557899999999999 899999999999999999999999999999999999999999999999
Q ss_pred hhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 161 SDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 161 ~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
++|..++||+|+|||+.|++++ ++...|.+.+|....
T Consensus 264 keI~~vtgVaE~TIr~sYK~Ly-p~~~~liP~~~a~~~ 300 (308)
T KOG1597|consen 264 KEIGEVTGVAEVTIRNSYKDLY-PHADKLIPSWYANAV 300 (308)
T ss_pred HHHHHHhhhhHHHHHHHHHHHh-hchhhhChhhhcccc
Confidence 9999999999999999999996 556788899997764
No 5
>PF07741 BRF1: Brf1-like TBP-binding domain; InterPro: IPR011665 The Vaccinia virus has an infection-induced host cell cycle control mechanism. p53 and Rb, which are associated with the is inactivated Rb, which are associated with the RNA polymerase III transcription factor B (TFIIIB) subunits, TBP and Brf1, are inactivated [, ]. TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound pre-initiation complex, whereas Brf1 and Brf2 are involved in the recruitment of Pol III. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1 []. It is suggested that the structure of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. Entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box []. This region covers both the Brf homology II and III regions []. ; GO: 0008270 zinc ion binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NGM_J.
Probab=99.95 E-value=1.3e-29 Score=216.63 Aligned_cols=96 Identities=54% Similarity=0.796 Sum_probs=34.3
Q ss_pred hHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHHhhhhhHHHh
Q 011262 346 DFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQ 425 (490)
Q Consensus 346 D~Eid~~il~eeE~~~K~~iW~~~N~dyl~eq~~Ke~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~rk~kk~ 425 (490)
|+|||.|||||+|+++|++||+++|+|||++|++|++..+++.+ .. .+++|++++
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~----------------------~~---~~~~k~k~~ 55 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEE----------------------AG---AKSRKKKKK 55 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----------------------hc---cCCCccccc
Confidence 56999999999999999999999999999999999976543211 11 112222222
Q ss_pred hhhhhhcC-CCCCCCHHHHHHHHHHhcCCCccCCHHHHhhhh
Q 011262 426 KRAAEAKN-SGPAQTALEATRRMLTKKRLSSKINYDVLEKLF 466 (490)
Q Consensus 426 k~~~~~~~-~~~a~ta~EA~~~ml~~k~~S~KINYdvl~~L~ 466 (490)
+++...++ .+||.||+||+++||++|+||+|||||+|++||
T Consensus 56 rk~~~~~~~~~~a~ta~EA~~~ml~~k~~S~KINYd~L~~LF 97 (97)
T PF07741_consen 56 RKRRKKKNQAPPAETAAEAARKMLKKKKFSKKINYDALESLF 97 (97)
T ss_dssp ------------------------------------------
T ss_pred cccccccCCCCCCCCHHHHHHHHHHhcCcccccCHHHHHhhC
Confidence 22223334 899999999999999999999999999999998
No 6
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.74 E-value=8.6e-18 Score=135.45 Aligned_cols=71 Identities=27% Similarity=0.516 Sum_probs=66.4
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 73 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~L 73 (490)
|++||+.|+|| .+|.+.|.++|+.+.+.++++||++..++|||||+|||+++.|+|++||+++++|++++|
T Consensus 1 I~r~~~~L~L~--~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLP--EDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCC--HHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 68999999999 999999999999999999999999999999999999999999999999999999999886
No 7
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.64 E-value=7.1e-16 Score=124.27 Aligned_cols=71 Identities=18% Similarity=0.365 Sum_probs=66.8
Q ss_pred HHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHH
Q 011262 102 LHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATL 174 (490)
Q Consensus 102 I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TI 174 (490)
|+|||+.|+ +++.|.+.|.+|++.+.+.|+..||+|.+|||||||+||+.+|.++|++||+++++|++.||
T Consensus 1 I~r~~~~L~--L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLG--LPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcC--CCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 789999999 89999999999999999999999999999999999999999999999999999999999997
No 8
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.43 E-value=5.7e-13 Score=136.42 Aligned_cols=85 Identities=15% Similarity=0.225 Sum_probs=82.3
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|.++|+.|+|| ..+.+.|..+++.+.+.+++.||++.++||||||+|||.+|.|+|++||+++++|+..+|++.|+.|
T Consensus 223 i~r~~~~L~L~--~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel 300 (310)
T PRK00423 223 VPRFASELGLS--GEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL 300 (310)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 57899999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccc
Q 011262 81 CQVLYIA 87 (490)
Q Consensus 81 ~~~L~i~ 87 (490)
.+.|++.
T Consensus 301 ~~~l~~~ 307 (310)
T PRK00423 301 AEKLDIK 307 (310)
T ss_pred HHHhCcc
Confidence 9999864
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.32 E-value=6.3e-11 Score=120.91 Aligned_cols=153 Identities=17% Similarity=0.142 Sum_probs=128.1
Q ss_pred CHHHHHhcC--CCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcC----HHHHH
Q 011262 1 MRQMKNALN--IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNIN----VYELG 74 (490)
Q Consensus 1 I~~ia~~L~--Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vs----v~~Lg 74 (490)
|.++|..|+ || +.|+-+|..+|++.+-.+-+.--.+..|+++|||+||+.+..|+++.+|...+.-+ ...|.
T Consensus 63 i~~~~~~lkp~Lp--q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~~~~~~~~Il 140 (305)
T TIGR00569 63 LLDFCSAFKPTMP--TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKALEQVL 140 (305)
T ss_pred HHHHHHHhcCCCC--chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCCchhhHHHHH
Confidence 578999999 99 99999999999999998888888999999999999999999999999999876544 37888
Q ss_pred HHHHHHHHHhcccccccccccCCccchHHHHHhhhC-----CCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHH
Q 011262 75 AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-----PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYV 149 (490)
Q Consensus 75 r~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~-----~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALyl 149 (490)
..-..|.+.|+++... ..|..++..|...|. ......+...|..+++.+....+.-=-.|+-||.||||+
T Consensus 141 ~~E~~lL~~L~F~L~V-----~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~l 215 (305)
T TIGR00569 141 EYELLLIQQLNFHLIV-----HNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILH 215 (305)
T ss_pred HHHHHHHHHCCCcEEe-----eCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHH
Confidence 8899999999987654 679888888775442 123456888899998877665444448999999999999
Q ss_pred HHHhcCCCCCH
Q 011262 150 SALTHGLKFSK 160 (490)
Q Consensus 150 Aar~~g~~~t~ 160 (490)
|++.+|.+..-
T Consensus 216 A~~~~~~~l~~ 226 (305)
T TIGR00569 216 TASRAGLNMES 226 (305)
T ss_pred HHHHhCCCCcc
Confidence 99999987654
No 10
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.31 E-value=6.4e-11 Score=119.01 Aligned_cols=173 Identities=13% Similarity=0.138 Sum_probs=146.9
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCc----------C-
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI----------N- 69 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~v----------s- 69 (490)
|++-|-.|+|| +.++-+++.+|.......-..+-..++|++|||.+|.+.+..|++++||..|++- .
T Consensus 30 Iqea~ILL~L~--q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~~~ 107 (367)
T KOG0835|consen 30 IQEAGILLNLP--QVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEAAEH 107 (367)
T ss_pred HHhhhHhhcCc--HHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccCcch
Confidence 45667789999 9999999999999998888888999999999999999999999999999887731 0
Q ss_pred ----------HHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCCh
Q 011262 70 ----------VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKP 139 (490)
Q Consensus 70 ----------v~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~P 139 (490)
...+-++...|.+.||+..+. .+|..+|-.|..-|+..-+..+.+.++...+...+..+..--+|
T Consensus 108 ~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv-----~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~p 182 (367)
T KOG0835|consen 108 LILARLYINLKMQVIRAERRILRELGFDVHV-----EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSP 182 (367)
T ss_pred hhhhhHHhhhhhHHHHHHHHHHHHhCCeeee-----eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCH
Confidence 124557778999999998876 89999999999999844455689999999999999888899999
Q ss_pred hHHHHHHHHHHHHhcCCCCC-HhhHHhHhccCHHHHHHHHHH
Q 011262 140 SGLCGAALYVSALTHGLKFS-KSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 140 sgIaaAALylAar~~g~~~t-~~dIa~v~~Vse~TIrkR~kE 180 (490)
.+||+||||||||..+++++ +..+-.+++++..-|..+...
T Consensus 183 e~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~ 224 (367)
T KOG0835|consen 183 ESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYR 224 (367)
T ss_pred HHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHH
Confidence 99999999999999997754 458888888888766544433
No 11
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.16 E-value=9.1e-11 Score=118.51 Aligned_cols=86 Identities=17% Similarity=0.225 Sum_probs=83.2
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|.+||+.|||| +.+...|.++.+++...|++-||++..+||||||+||+.+|.++|.++|+.+++|++.+|.+.|+.|
T Consensus 198 i~rf~s~L~l~--~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel 275 (285)
T COG1405 198 IPRFASKLGLS--DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKEL 275 (285)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHH
Confidence 57899999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccc
Q 011262 81 CQVLYIAD 88 (490)
Q Consensus 81 ~~~L~i~~ 88 (490)
...+++..
T Consensus 276 ~~~~~i~~ 283 (285)
T COG1405 276 ADALDIEV 283 (285)
T ss_pred HHhhcccc
Confidence 99998753
No 12
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.10 E-value=4.2e-10 Score=115.18 Aligned_cols=152 Identities=21% Similarity=0.264 Sum_probs=122.5
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhC--cCH--HHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN--INV--YELGAV 76 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~--vsv--~~Lgr~ 76 (490)
|.+++.+|++| ...+.+|..||.+.+-....+.-....||++|||+||+.++.|+.+.||..+.. .++ .++...
T Consensus 46 I~elg~~L~~~--~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~~~ 123 (323)
T KOG0834|consen 46 IQELGVRLKMP--QKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLELEEV 123 (323)
T ss_pred HHHHHHHcCCC--ccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccHHHH
Confidence 67899999999 899999999999999988888888899999999999999999999999988752 232 233333
Q ss_pred H-----------HHHHHHhcccccccccccCCccchHHHHHhhhCCCCc--HHHHHHHHHHHHHhhccccccCCChhHHH
Q 011262 77 Y-----------LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN--KKVCDTARDILASMKRDWITTGRKPSGLC 143 (490)
Q Consensus 77 y-----------k~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~--~~V~~~A~~Iv~~~~~~~l~~GR~PsgIa 143 (490)
| +.|++.|+++... -.|..|+-+++..|..+.+ ..++..|..+++......+.---.|..||
T Consensus 124 ~~~~~~~Iv~~E~~lL~tl~Fdl~v-----~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IA 198 (323)
T KOG0834|consen 124 YWELKERIVQLELLLLETLGFDLNV-----EHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIA 198 (323)
T ss_pred HHHHHHHHHHHHHHHHHHccCceec-----cCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEE
Confidence 3 4455666666543 6799999999999973233 25889999999988775544556899999
Q ss_pred HHHHHHHHHhcCCCCC
Q 011262 144 GAALYVSALTHGLKFS 159 (490)
Q Consensus 144 aAALylAar~~g~~~t 159 (490)
.||||+|+.+.|....
T Consensus 199 va~i~lA~~~~~~~~~ 214 (323)
T KOG0834|consen 199 VACIHLAAKLLGVELP 214 (323)
T ss_pred eehhhHHHHHcCCCCC
Confidence 9999999999997544
No 13
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.06 E-value=4.4e-10 Score=111.84 Aligned_cols=83 Identities=12% Similarity=0.151 Sum_probs=80.9
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
|.++|+.|+|| .+++..|.++.+.+.+.++..||++.+||||.||++|+....+++++||.+++||...+|..+|+.|
T Consensus 207 m~RFCs~L~L~--~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~L 284 (308)
T KOG1597|consen 207 MPRFCSNLGLP--KSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDL 284 (308)
T ss_pred HHHHHHhcCCC--HHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHH
Confidence 57999999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhc
Q 011262 81 CQVLY 85 (490)
Q Consensus 81 ~~~L~ 85 (490)
..++.
T Consensus 285 yp~~~ 289 (308)
T KOG1597|consen 285 YPHAD 289 (308)
T ss_pred hhchh
Confidence 99875
No 14
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=98.99 E-value=3.1e-09 Score=106.79 Aligned_cols=152 Identities=18% Similarity=0.188 Sum_probs=126.2
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHh--------CcCHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL--------NINVYE 72 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~--------~vsv~~ 72 (490)
|+.+|.+|+|| ..+..+|..+|++.+-.+..++-+...|+++|||+||+.+.+|+-+.-.+-.. --+...
T Consensus 52 i~~l~~~L~lp--~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr~~ 129 (297)
T COG5333 52 IMDLCTRLNLP--QTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRER 129 (297)
T ss_pred HHHHHHhcCCC--cchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccHHH
Confidence 57899999999 99999999999999999999999999999999999999999765444333333 346678
Q ss_pred HHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHH
Q 011262 73 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 152 (490)
Q Consensus 73 Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar 152 (490)
|-..-..|.+.|+.+... ..|..++..|...+.....-++.+.|+.++..+-+..++-=-.|..||.|||++|+.
T Consensus 130 Il~~E~~lLEaL~fd~~V-----~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~ 204 (297)
T COG5333 130 ILEYEFELLEALDFDLHV-----HHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACE 204 (297)
T ss_pred HHHHHHHHHHHcccceEe-----ccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHH
Confidence 888888899999987664 679999999988885212347999999999998876655556899999999999999
Q ss_pred hcCCCCC
Q 011262 153 THGLKFS 159 (490)
Q Consensus 153 ~~g~~~t 159 (490)
..|.+.-
T Consensus 205 ~~~~~~~ 211 (297)
T COG5333 205 VLGMPII 211 (297)
T ss_pred hcCCccc
Confidence 9987744
No 15
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.89 E-value=1.2e-08 Score=82.34 Aligned_cols=78 Identities=23% Similarity=0.262 Sum_probs=73.7
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCc-CHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 79 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~v-sv~~Lgr~yk~ 79 (490)
|.+++..++++ ..+...|..+++++...+.+.|+++..+++||||+||+.++.|.++.+|..+++. +..+|.+.++.
T Consensus 9 l~~~~~~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~e~~ 86 (88)
T cd00043 9 LRRVAKALGLS--PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRMEKL 86 (88)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHHHHH
Confidence 46899999999 9999999999999999999999999999999999999999999999999999999 99999988876
Q ss_pred H
Q 011262 80 L 80 (490)
Q Consensus 80 L 80 (490)
|
T Consensus 87 i 87 (88)
T cd00043 87 L 87 (88)
T ss_pred h
Confidence 5
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.88 E-value=1.2e-08 Score=82.52 Aligned_cols=84 Identities=23% Similarity=0.276 Sum_probs=79.1
Q ss_pred CCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhcc-CHHHH
Q 011262 96 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATL 174 (490)
Q Consensus 96 vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~V-se~TI 174 (490)
..|..||.++++.++ ++..+...|..+++++...+...|++|..||+||||+|+++.+...+.++++.+++. +..+|
T Consensus 3 ~~~~~~l~~~~~~~~--~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 3 PTPLDFLRRVAKALG--LSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred chHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHH
Confidence 357889999999998 899999999999999998888899999999999999999999999999999999999 99999
Q ss_pred HHHHHHH
Q 011262 175 MKRLIEF 181 (490)
Q Consensus 175 rkR~kE~ 181 (490)
.+.++++
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9998876
No 17
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.88 E-value=1.1e-08 Score=81.96 Aligned_cols=78 Identities=22% Similarity=0.293 Sum_probs=71.7
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHh-CCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCc-CHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVA-RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYL 78 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~-~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~v-sv~~Lgr~yk 78 (490)
|.+++..+++| ..+...|..+++++.. .++++ +++..++|||||+||+.++.+.+..++...+++ +..+|.+.++
T Consensus 3 l~~~~~~~~~~--~~~~~~a~~~~~~~l~~~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~ 79 (83)
T smart00385 3 LRRVCKALNLD--PETLNLAVNLLDRFLSDYKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEK 79 (83)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHHHHHHHhhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHH
Confidence 57899999999 9999999999999998 55655 999999999999999999999999999999999 9999999888
Q ss_pred HHH
Q 011262 79 QLC 81 (490)
Q Consensus 79 ~L~ 81 (490)
.|.
T Consensus 80 ~il 82 (83)
T smart00385 80 LLL 82 (83)
T ss_pred HHh
Confidence 775
No 18
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.85 E-value=1.7e-08 Score=80.72 Aligned_cols=81 Identities=20% Similarity=0.214 Sum_probs=74.3
Q ss_pred chHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhcc-CHHHHHHHH
Q 011262 100 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRL 178 (490)
Q Consensus 100 ~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~V-se~TIrkR~ 178 (490)
.||.|+++.++ +++++...|..+++++....-..+++|..||+||||+|+++.+.+.+..+++..+++ ++.+|.+.+
T Consensus 1 ~~l~~~~~~~~--~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 1 DFLRRVCKALN--LDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred CHHHHHHHHcC--CCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 48999999999 799999999999999988544556999999999999999999999999999999999 999999999
Q ss_pred HHHh
Q 011262 179 IEFE 182 (490)
Q Consensus 179 kE~~ 182 (490)
+++.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 9874
No 19
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.58 E-value=5.4e-07 Score=87.32 Aligned_cols=172 Identities=16% Similarity=0.205 Sum_probs=121.5
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCC----cCHHHHHHHh----------
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP----FLLIDFSNYL---------- 66 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~p----rtL~DIa~v~---------- 66 (490)
|+.++..|+|. +.|+-+|..+|++.+-++-.++-.+..+|+-|||+||+.+..| |+|.--+.++
T Consensus 48 I~~lg~~lklR--Q~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~e~ 125 (264)
T KOG0794|consen 48 IQKLGQHLKLR--QRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWPEK 125 (264)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccchhh
Confidence 56789999999 9999999999999999999999999999999999999999988 2222222222
Q ss_pred -CcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHH
Q 011262 67 -NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGA 145 (490)
Q Consensus 67 -~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaA 145 (490)
..+...|-..-..|.+.|+--.- .-.|..=+..|...++. .+......+..|++..-+..++-=-.|.-||-|
T Consensus 126 ~~~~~~~I~e~Ef~llE~Ld~~LI-----VhHPYrsL~q~~qd~gi-~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalA 199 (264)
T KOG0794|consen 126 FPYERKDILEMEFYLLEALDCYLI-----VHHPYRSLLQFVQDMGI-NDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALA 199 (264)
T ss_pred cCCCcCcchhhhhhHHhhhceeEE-----EecCCccHHHHHHHhcc-cchhhhhhhHhhhcchhhcceeeecCHHHHHHH
Confidence 11222333334455666653211 13565557788887772 256688999999998888777777899999999
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
|||+|+..+|-..+ +..-..+.|--.-|.....++
T Consensus 200 cl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I 234 (264)
T KOG0794|consen 200 CLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEI 234 (264)
T ss_pred HHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHH
Confidence 99999998886664 233333344444444444443
No 20
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.29 E-value=1.7e-05 Score=81.81 Aligned_cols=171 Identities=15% Similarity=0.196 Sum_probs=132.0
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCC-CCCCC--ChHHHHHHHHHHHHHhcCC--CcCHHHHHHH--hCcCHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARN-FTKGR--RTEQVQASCLYLACRQKSK--PFLLIDFSNY--LNINVYELG 74 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~-~~rGR--~~~~VaAACLYiACR~~~~--prtL~DIa~v--~~vsv~~Lg 74 (490)
-++|...+.. ..+.=-|.+|+.+.+.-. +-+++ -...+++|||.+|.+.+.+ |.++.=.... .-...++|.
T Consensus 86 l~V~~~~~~~--~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~ 163 (335)
T KOG0656|consen 86 LKVCEEYNFE--PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQ 163 (335)
T ss_pred HHHHHHhCCc--hHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHH
Confidence 4677788888 889999999999988754 44433 3789999999999998765 6554444443 235789999
Q ss_pred HHHHHHHHHhcccccccccccCCccchHHHHHhhhC--CCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHH
Q 011262 75 AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL--PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 152 (490)
Q Consensus 75 r~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~--~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar 152 (490)
|.-+.++..|+=.... +.|..||..|+++++ ....+.+...+.+++-....+.-..+-.|+.||||++..++.
T Consensus 164 rmELLVLstL~Wrl~a-----VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~ 238 (335)
T KOG0656|consen 164 RMELLVLSTLKWRLRA-----VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSA 238 (335)
T ss_pred HHHHHHHhhccccccC-----CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHH
Confidence 9999999999977666 899999999999997 234567888888888777777777889999999998876654
Q ss_pred -hcCCC--CCHhhHHhHhccCHHHHHHHHH
Q 011262 153 -THGLK--FSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 153 -~~g~~--~t~~dIa~v~~Vse~TIrkR~k 179 (490)
+.+.. ....-+.....|+.-.+++.|.
T Consensus 239 ~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 239 SVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred hhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 34433 2245566777888888888877
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.24 E-value=9.1e-07 Score=94.76 Aligned_cols=155 Identities=14% Similarity=0.185 Sum_probs=101.6
Q ss_pred CHHHHHhcCCCCc-hHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHH
Q 011262 1 MRQMKNALNIGES-DEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 79 (490)
Q Consensus 1 I~~ia~~L~Lp~~-~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~ 79 (490)
|.+++..|-..+. ..|+.+|.++......-=...||++..++.||||||||.||+++|..||+.++.|+..+|.+.|+.
T Consensus 170 i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~E 249 (521)
T KOG1598|consen 170 IVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKE 249 (521)
T ss_pred eechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHH
Confidence 4566666655411 234455544444443323456999999999999999999999999999999999999999999999
Q ss_pred HHHHhccccccc------ccccCCccchHHHH--Hh-hhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHH
Q 011262 80 LCQVLYIADESN------VLKQVDPSIFLHKF--TD-RLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVS 150 (490)
Q Consensus 80 L~~~L~i~~~~~------~~~~vdP~~~I~Rf--~s-~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylA 150 (490)
|...+..+.+.. ...-.||-.|-..= .. ... ...+....-...+.-+...|..+++.+...+-+.++.+
T Consensus 250 f~~T~s~~Lti~ef~~~d~e~~~~ppsft~~~~~~~k~~~--~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~~ 327 (521)
T KOG1598|consen 250 FSDTLSGDLTIDELAEIDLEYESDPPSFTASPSKEAKYVE--DKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFLA 327 (521)
T ss_pred HhccccccccHHHHHhhhhhhccCcchhhcccchhhhhhh--hhhhhhhhhhhhhhcccchhhhccccCCcccchhhhcc
Confidence 999876543220 00112333321100 00 000 11223333445566677789999999999999999888
Q ss_pred HHhcCCC
Q 011262 151 ALTHGLK 157 (490)
Q Consensus 151 ar~~g~~ 157 (490)
++-....
T Consensus 328 ~q~~~~~ 334 (521)
T KOG1598|consen 328 WQDLQPR 334 (521)
T ss_pred cccchhh
Confidence 8654443
No 22
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.69 E-value=0.0013 Score=63.39 Aligned_cols=157 Identities=15% Similarity=0.159 Sum_probs=121.3
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhC--CCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYL 78 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~--~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk 78 (490)
|.+++.+|||.+.+.+.+.|.+|.++..-+ +..-|-.-..-+.-|+-+|.-.-++|.--.-.-...|.+.....+.|+
T Consensus 3 I~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~~ 82 (262)
T KOG4557|consen 3 ISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSFN 82 (262)
T ss_pred HHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHHH
Confidence 688999999965579999999998877543 455566656667779999888888887766667778999999999999
Q ss_pred HHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhcc-------ccccCCChhHHHHHHHHHHH
Q 011262 79 QLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-------WITTGRKPSGLCGAALYVSA 151 (490)
Q Consensus 79 ~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~-------~l~~GR~PsgIaaAALylAa 151 (490)
.+...||++... -|..+|-.|+ -.+|++.|..|+...+.. +... -+| -.++||+|.||
T Consensus 83 sfe~llgln~~~----------~VrdlaVQfg---c~evi~~a~~vl~syk~~lpaT~~~~~D~-SrP-~ft~aA~~~ac 147 (262)
T KOG4557|consen 83 SFENLLGLNIKL----------NVRDLAVQFG---CVEVIKSAQNVLSSYKERLPATRRANADF-SRP-VFTAAAFYLAC 147 (262)
T ss_pred HHHHHhcchhhc----------CHHHHHHHHh---HHHHHHHHHHHHHHHHhcCchhhhcCCcc-cch-HHHHHHHHHHH
Confidence 999999986432 3566787887 577888999888877652 1111 234 47888999999
Q ss_pred HhcCCCCCHhhHHhHhccCHH
Q 011262 152 LTHGLKFSKSDIVKIVHICEA 172 (490)
Q Consensus 152 r~~g~~~t~~dIa~v~~Vse~ 172 (490)
+....+++......+.|++++
T Consensus 148 k~lKlKVdK~kli~~sg~~~s 168 (262)
T KOG4557|consen 148 KKLKLKVDKLKLIEVSGTSES 168 (262)
T ss_pred HHHHHhhhHhhcccccCCCHH
Confidence 999888888777777776664
No 23
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=97.44 E-value=0.0016 Score=65.96 Aligned_cols=139 Identities=19% Similarity=0.169 Sum_probs=91.3
Q ss_pred CCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhC----cCHHHHHHHHHHHHHHh
Q 011262 9 NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN----INVYELGAVYLQLCQVL 84 (490)
Q Consensus 9 ~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~----vsv~~Lgr~yk~L~~~L 84 (490)
+|| .+|+-+|..+|++++=.+.+..-++..|.++|+|+||+.+..-+++-+|..-.. -+...+-+.-..+.+.|
T Consensus 73 ~lp--~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~E~~llqsL 150 (325)
T KOG2496|consen 73 NLP--TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKYEFLLLQSL 150 (325)
T ss_pred CCc--hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhchHHHHHhh
Confidence 688 999999999999999999999999999999999999999999999999998776 44455555555666767
Q ss_pred cccccccccccCCc-cchHHHHHhhhCCCCcHH-HHHHHH--HHHHHhhccccccCCChhHHHHHHHHHHH
Q 011262 85 YIADESNVLKQVDP-SIFLHKFTDRLLPGGNKK-VCDTAR--DILASMKRDWITTGRKPSGLCGAALYVSA 151 (490)
Q Consensus 85 ~i~~~~~~~~~vdP-~~~I~Rf~s~L~~~l~~~-V~~~A~--~Iv~~~~~~~l~~GR~PsgIaaAALylAa 151 (490)
...... ..+-.| +-|+..+-..|-+-.++. ...... +.++++.-....-=-.|+-||-|||+.++
T Consensus 151 ~f~L~v--h~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~ 219 (325)
T KOG2496|consen 151 KFSLTV--HNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAA 219 (325)
T ss_pred hhhhee--cCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHh
Confidence 654321 112344 335444444432101222 222222 33333322112222589999999995544
No 24
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.39 E-value=0.00098 Score=58.38 Aligned_cols=84 Identities=13% Similarity=0.265 Sum_probs=69.8
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-CcCHHHHHHHhC--cCHHHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYELGAVYL 78 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~-prtL~DIa~v~~--vsv~~Lgr~yk 78 (490)
..++..++++ ..+.-.|..+|.+..............+++||+|+||+.+.. +.++.++....+ .+..+|-..-.
T Consensus 39 ~~~~~~~~l~--~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~ 116 (127)
T PF00134_consen 39 IELCQRLKLS--PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMER 116 (127)
T ss_dssp HHHHHHTT-B--HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHH
T ss_pred HHHHHhcccc--hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHH
Confidence 4688999999 999999999999999988888889999999999999998766 788899988873 57888888888
Q ss_pred HHHHHhccc
Q 011262 79 QLCQVLYIA 87 (490)
Q Consensus 79 ~L~~~L~i~ 87 (490)
.|...|+.+
T Consensus 117 ~iL~~L~f~ 125 (127)
T PF00134_consen 117 EILSALNFD 125 (127)
T ss_dssp HHHHHTTT-
T ss_pred HHHHHCCCC
Confidence 888888764
No 25
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.22 E-value=0.002 Score=68.41 Aligned_cols=147 Identities=14% Similarity=0.096 Sum_probs=117.1
Q ss_pred HHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHH-HHHHhcCC-CcCHHHHHHHhC--cCHHHHHHHHH
Q 011262 3 QMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLY-LACRQKSK-PFLLIDFSNYLN--INVYELGAVYL 78 (490)
Q Consensus 3 ~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLY-iACR~~~~-prtL~DIa~v~~--vsv~~Lgr~yk 78 (490)
.+-..++|. ....-.|..|+.+......+..+....|..+||+ |||+.+.. +-++.|+.-+++ .+...|.+.-+
T Consensus 167 evh~~F~L~--~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~ 244 (391)
T KOG0653|consen 167 EVHEKFGLS--PETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEK 244 (391)
T ss_pred HhhhhcCcC--HHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHH
Confidence 455678898 8999999999999998866888888889888856 99996433 334777776664 68899999999
Q ss_pred HHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCC
Q 011262 79 QLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKF 158 (490)
Q Consensus 79 ~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~ 158 (490)
.+...|+..... ..|-.|+.||..... ........+..++....-+.-+....|+.++||+.+++.++.+.+.
T Consensus 245 ~il~~L~f~l~~-----p~~~~FLrr~~ka~~--~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~ 317 (391)
T KOG0653|consen 245 YILNVLEFDLSV-----PTPLSFLRRFLKAAD--YDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGD 317 (391)
T ss_pred HHHhccCeeecC-----CchHHHHHHHHHhhh--cchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCC
Confidence 999999876543 678999999988877 4556667777777777666656678899999999999999887664
No 26
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=97.18 E-value=0.0011 Score=56.98 Aligned_cols=84 Identities=19% Similarity=0.168 Sum_probs=67.0
Q ss_pred CccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCC-CCCHhhHHhHhccCHHHHH
Q 011262 97 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIVHICEATLM 175 (490)
Q Consensus 97 dP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~-~~t~~dIa~v~~Vse~TIr 175 (490)
.|..|+.+|....+ .+..+...|..|++.+.-+.-..+-+|+.||+||||+|..+.+. +.-...+...+|+....|+
T Consensus 2 Tp~~Fl~~~~~~~~--~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~ 79 (118)
T PF02984_consen 2 TPYDFLRRFLKISN--ADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLK 79 (118)
T ss_dssp -HHHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHHHHcC--CcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHH
Confidence 47889999944333 46789999999999988887788899999999999999999875 3445568888899999999
Q ss_pred HHHHHHh
Q 011262 176 KRLIEFE 182 (490)
Q Consensus 176 kR~kE~~ 182 (490)
..++.|.
T Consensus 80 ~c~~~i~ 86 (118)
T PF02984_consen 80 ECIELIQ 86 (118)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8888885
No 27
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=96.95 E-value=0.0021 Score=58.58 Aligned_cols=66 Identities=11% Similarity=0.268 Sum_probs=54.8
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHh--CCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCc
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI 68 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~--~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~v 68 (490)
|+.+|+.|+|+ +.+.+....+|..+.. ..++++|..++++..|+|+.||..+.+.+++||-..-.-
T Consensus 18 l~~LC~~L~l~--~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 18 LQDLCERLDLS--SDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHTTS--TTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHcCCc--HHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 46899999999 8999999999998775 468899999999999999999999999999999876543
No 28
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.69 E-value=0.0089 Score=64.12 Aligned_cols=144 Identities=14% Similarity=0.064 Sum_probs=107.0
Q ss_pred HHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-CcCHHHHHHHh--CcCHHHHHHHHHHH
Q 011262 4 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYL--NINVYELGAVYLQL 80 (490)
Q Consensus 4 ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~-prtL~DIa~v~--~vsv~~Lgr~yk~L 80 (490)
+=..+++- +.....|..|..+.+..+.+.=-+...|+++||+|||+-+.+ +-++.+++-++ ..++..|.++.+.+
T Consensus 223 vH~~F~ll--peTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~m 300 (440)
T COG5024 223 VHGKFGLL--PETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYM 300 (440)
T ss_pred hccccccc--chHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHH
Confidence 33456776 678888999999999988887778899999999999998754 55688998887 46899999999999
Q ss_pred HHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccc-cccCCChhHHHHHHHHHHHHhcCCC
Q 011262 81 CQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDW-ITTGRKPSGLCGAALYVSALTHGLK 157 (490)
Q Consensus 81 ~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~-l~~GR~PsgIaaAALylAar~~g~~ 157 (490)
...|+.++.- ..|..|+.|+..... ........+..+..-..-+. +...+ |+.+++||-|++-.+.+..
T Consensus 301 l~~l~f~is~-----P~P~sFLRriSka~d--yd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~~~~ 370 (440)
T COG5024 301 LEVLDFNISW-----PSPMSFLRRISKASD--YDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKILSQN 370 (440)
T ss_pred hhhcccccCC-----CChHHHHHHHHhhcc--cchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhhccC
Confidence 9999986533 678889888766655 23333334444444332222 33445 9999999999988877643
No 29
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=94.12 E-value=0.15 Score=43.63 Aligned_cols=72 Identities=13% Similarity=0.110 Sum_probs=56.8
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-CcCHHHHHHHhCcCHHHHHHHHHHHHHHhc
Q 011262 14 DEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQVLY 85 (490)
Q Consensus 14 ~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~-prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~ 85 (490)
..+...|..+...+.-....-+-++..+||||||+|.+..+. +.--..+...++++...|..++..|...+.
T Consensus 18 ~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~~~i~~~~~ 90 (118)
T PF02984_consen 18 QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHHHHHHHHHHH
Confidence 568888888888766554455688999999999999999765 555566788889999999999999998875
No 30
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=93.92 E-value=0.2 Score=43.68 Aligned_cols=67 Identities=15% Similarity=0.095 Sum_probs=51.5
Q ss_pred cchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCC-CCCHhhHHhHh
Q 011262 99 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIV 167 (490)
Q Consensus 99 ~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~-~~t~~dIa~v~ 167 (490)
..||...+..++ +++.+...|..++.++..........+.-|++||+++|+.+.+. ..+..+++...
T Consensus 35 ~~~i~~~~~~~~--l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 35 IDWIIELCQRLK--LSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHTT---BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHHhcc--cchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 347778888887 89999999999999987766677789999999999999998876 34455555443
No 31
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=93.52 E-value=0.31 Score=50.28 Aligned_cols=100 Identities=17% Similarity=0.301 Sum_probs=67.3
Q ss_pred HHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHH-HHHHHhCcCHHHHHHHHHHHH
Q 011262 3 QMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLI-DFSNYLNINVYELGAVYLQLC 81 (490)
Q Consensus 3 ~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~-DIa~v~~vsv~~Lgr~yk~L~ 81 (490)
.+-.-|++|.+..+...+.+|.....--.+..--+++.||+||+|+|.|..++|.+.. ..-.+++++..+|-.....+.
T Consensus 147 ~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~ 226 (367)
T KOG0835|consen 147 MYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLI 226 (367)
T ss_pred HHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHH
Confidence 3556789984445677777777777666665557899999999999999999876654 444567777777766655555
Q ss_pred HHhcccccccccccCCccchHHHHHhhhC
Q 011262 82 QVLYIADESNVLKQVDPSIFLHKFTDRLL 110 (490)
Q Consensus 82 ~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~ 110 (490)
....... | -..+|.-|+..+.
T Consensus 227 ~lY~~~~-p-------~~~li~~~vd~~k 247 (367)
T KOG0835|consen 227 PLYKRAK-P-------DETLIEAFVDRLK 247 (367)
T ss_pred HHHHhcc-c-------CHHHHHHHHHHhh
Confidence 5433211 1 1346666666553
No 32
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=92.93 E-value=0.4 Score=49.51 Aligned_cols=67 Identities=13% Similarity=0.099 Sum_probs=53.8
Q ss_pred hHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHh
Q 011262 101 FLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV 167 (490)
Q Consensus 101 ~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~ 167 (490)
+|..+|..|.-.++..|..+|.-+.+|.--.+-+.--.|.-|+++|||+||..-++++++.+++..+
T Consensus 62 ~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 4566677665236889999999999987655444557899999999999999999999988887654
No 33
>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=90.99 E-value=0.42 Score=34.70 Aligned_cols=32 Identities=19% Similarity=0.294 Sum_probs=24.7
Q ss_pred HHhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 151 ALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 151 ar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
....+-+.|..+|++.+|+|+.|+.+|++.++
T Consensus 11 ~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 11 LLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 33456789999999999999999999998763
No 34
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=90.92 E-value=0.34 Score=50.35 Aligned_cols=82 Identities=17% Similarity=0.137 Sum_probs=64.0
Q ss_pred cchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhc----cCHHHH
Q 011262 99 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH----ICEATL 174 (490)
Q Consensus 99 ~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~----Vse~TI 174 (490)
..||..++.+|+ ++..-..+|.-+.+|.--..-+.+-.|..||++|||+|+...+.++..+||..+.. ....+.
T Consensus 43 ~~fI~elg~~L~--~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~ 120 (323)
T KOG0834|consen 43 AKFIQELGVRLK--MPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLEL 120 (323)
T ss_pred HHHHHHHHHHcC--CCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccH
Confidence 347888888887 56666788888888877666667778899999999999999999999999988752 222366
Q ss_pred HHHHHHHh
Q 011262 175 MKRLIEFE 182 (490)
Q Consensus 175 rkR~kE~~ 182 (490)
..+|-+++
T Consensus 121 ~~~~~~~~ 128 (323)
T KOG0834|consen 121 EEVYWELK 128 (323)
T ss_pred HHHHHHHH
Confidence 66666665
No 35
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=89.54 E-value=0.1 Score=54.83 Aligned_cols=87 Identities=13% Similarity=0.090 Sum_probs=0.0
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHH-hCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~-~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
.+|+-.++++.+..++..|..+|++.. ....+++..-.+-+.+|+||||...+.++-+.-+....++++....+.|..|
T Consensus 2 ~~l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~ 81 (353)
T PF05460_consen 2 SDLIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTF 81 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHH
Confidence 456666666544899999999999998 4566777777778899999999999999888777778899998888888888
Q ss_pred HHHhcccc
Q 011262 81 CQVLYIAD 88 (490)
Q Consensus 81 ~~~L~i~~ 88 (490)
...|+...
T Consensus 82 ~~~L~~~s 89 (353)
T PF05460_consen 82 ENLLGNSS 89 (353)
T ss_dssp --------
T ss_pred HHHHhCCC
Confidence 88887643
No 36
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=89.24 E-value=3 Score=32.70 Aligned_cols=26 Identities=12% Similarity=0.165 Sum_probs=23.8
Q ss_pred CCCHhhHHhHhcc-CHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHI-CEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~V-se~TIrkR~kE~~ 182 (490)
+.++.+||..+|+ +..++.+.++...
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7999999999999 9999999998773
No 37
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.36 E-value=1.5 Score=34.40 Aligned_cols=72 Identities=8% Similarity=0.155 Sum_probs=45.0
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCc-CHHHHHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 79 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~v-sv~~Lgr~yk~ 79 (490)
|..||..+|++ ..... ++|+......+..-.....+.-|+-|+.- .+.++.|||..+|+ +...+.+.|++
T Consensus 4 ~~~la~~~~~s--~~~l~---~~f~~~~~~s~~~~~~~~r~~~a~~~l~~----~~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 4 LEDLAEALGMS--PRHLQ---RLFKKETGTTPKQYLRDRRLERARRLLRD----TDLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHhCCC--HHHHH---HHHHHHhCcCHHHHHHHHHHHHHHHHHHc----CCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 46789999999 54433 33333332222111122334445555532 28999999999999 99999998876
Q ss_pred HH
Q 011262 80 LC 81 (490)
Q Consensus 80 L~ 81 (490)
..
T Consensus 75 ~~ 76 (84)
T smart00342 75 LF 76 (84)
T ss_pred HH
Confidence 64
No 38
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=86.46 E-value=9.2 Score=39.90 Aligned_cols=164 Identities=12% Similarity=0.041 Sum_probs=96.3
Q ss_pred HHHhcCCCCchHHHHHHHHHHHHHHhCC-CCCCCChHHHHHHHHHHHHHhcCC-CcCHHHHHHHhC--cCHHHHHHHHHH
Q 011262 4 MKNALNIGESDEIVHVAKRFYGIAVARN-FTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYELGAVYLQ 79 (490)
Q Consensus 4 ia~~L~Lp~~~~v~d~A~~iyk~A~~~~-~~rGR~~~~VaAACLYiACR~~~~-prtL~DIa~v~~--vsv~~Lgr~yk~ 79 (490)
+|..-.|- ...-=-|..||.+...-. -+.--....|--+|||||.+.+.+ |--++|||-++. ++...|.+.-+.
T Consensus 155 VCEvykLH--RETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~i 232 (408)
T KOG0655|consen 155 VCEVYKLH--RETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELI 232 (408)
T ss_pred HHHHHHHh--hhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHH
Confidence 44444555 455556777776554321 112234566777899999998765 888999999984 688999999999
Q ss_pred HHHHhcccccccccccCCccchHHHHHhhhC-CCCc-----HHHHHHHHHHHH---HhhccccccCCChhHHHHHHHHHH
Q 011262 80 LCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGN-----KKVCDTARDILA---SMKRDWITTGRKPSGLCGAALYVS 150 (490)
Q Consensus 80 L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~-~~l~-----~~V~~~A~~Iv~---~~~~~~l~~GR~PsgIaaAALylA 150 (490)
|.+.|+-...| +..-.++.-|..-+. ++.+ .-....=..|++ -+.-+.-.---.-..|||||||.-
T Consensus 233 ilkal~W~l~P-----iTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaqlLDlc~ldids~~fsYrilaAAal~h~ 307 (408)
T KOG0655|consen 233 ILKALKWELSP-----ITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQLLDLCILDIDSLEFSYRILAAAALCHF 307 (408)
T ss_pred HHHHhcccccc-----eehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHH
Confidence 99999977655 444455555554443 2111 111122222222 222121112255667888888742
Q ss_pred HHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 151 ALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 151 ar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
. +..-+-+++|.--..|.+..+=+
T Consensus 308 ~-------s~e~v~kaSG~~w~~ie~cv~wm 331 (408)
T KOG0655|consen 308 T-------SIEVVKKASGLEWDSIEECVDWM 331 (408)
T ss_pred h-------HHHHHHHcccccHHHHHHHHHHH
Confidence 2 22223355677777777766554
No 39
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=86.40 E-value=1.6 Score=44.79 Aligned_cols=70 Identities=14% Similarity=0.191 Sum_probs=62.1
Q ss_pred cchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhc
Q 011262 99 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 168 (490)
Q Consensus 99 ~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~ 168 (490)
+..+-.||+++.-.++..|+.+|.....|+--.|-.+--+|..|.++|+|+||....+.+|..+++.-.+
T Consensus 60 E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 60 ELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred HHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 4567789999975589999999999999998888888889999999999999999999999999987665
No 40
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=86.26 E-value=2.7 Score=38.33 Aligned_cols=64 Identities=16% Similarity=0.124 Sum_probs=49.3
Q ss_pred hHHHHHhhhCCCCcHHHHHHHHHHHHHhh--ccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhH
Q 011262 101 FLHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKI 166 (490)
Q Consensus 101 ~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~--~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v 166 (490)
=|..+|++|+ +++++....+.+++.+. ...+..+|+-.-|.-.|||+.|++++..+|.++|-..
T Consensus 17 Rl~~LC~~L~--l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~ 82 (135)
T PF01857_consen 17 RLQDLCERLD--LSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKA 82 (135)
T ss_dssp HHHHHHHHHT--TSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHH
T ss_pred HHHHHHHHcC--CcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHH
Confidence 4566889998 67777788888887765 4578899999999999999999999988888888764
No 41
>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=85.68 E-value=1.4 Score=32.13 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=24.4
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+-..|+++||+.+|+|..|++++++++.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45599999999999999999999999864
No 42
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=85.44 E-value=1.1 Score=32.89 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=19.3
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
..|.++||+.+|||..||++.++.|.+.-
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 78999999999999999999999987543
No 43
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=84.62 E-value=37 Score=35.30 Aligned_cols=27 Identities=7% Similarity=0.069 Sum_probs=23.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||..+|||..||++++..-.
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl 307 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEAL 307 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 569999999999999999999877653
No 44
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=84.45 E-value=10 Score=34.67 Aligned_cols=84 Identities=11% Similarity=0.100 Sum_probs=62.4
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHh---CC--CCCCCChHHHHHHHHHHHHHh-cCCCcCHHHHHHHhCcCHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVA---RN--FTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINVYELGA 75 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~---~~--~~rGR~~~~VaAACLYiACR~-~~~prtL~DIa~v~~vsv~~Lgr 75 (490)
.++....+++ ..+.-.|..+..+... .. .+...+...+..+||-+|.+- .....+.+.+|.+.|+++.+|.+
T Consensus 59 ~ri~~~~~~s--~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln~ 136 (149)
T PF08613_consen 59 SRILKYTQCS--PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELNE 136 (149)
T ss_dssp HHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHcCCC--hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHHH
Confidence 4677778888 8899899988888877 22 234567788999999999996 68899999999999999999999
Q ss_pred HHHHHHHHhccc
Q 011262 76 VYLQLCQVLYIA 87 (490)
Q Consensus 76 ~yk~L~~~L~i~ 87 (490)
.-..+...|+.+
T Consensus 137 lE~~fL~~l~~~ 148 (149)
T PF08613_consen 137 LEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHTTT-
T ss_pred HHHHHHHHCCCc
Confidence 999998888753
No 45
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=83.64 E-value=1.5 Score=40.84 Aligned_cols=37 Identities=16% Similarity=0.291 Sum_probs=31.3
Q ss_pred HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 149 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 149 lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
|.+...+-+.|..+||+.+|+|++|+++|++.+.+..
T Consensus 20 L~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 20 LNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3444567789999999999999999999999997654
No 46
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=82.92 E-value=3.3 Score=40.57 Aligned_cols=81 Identities=15% Similarity=0.173 Sum_probs=55.4
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhC-----CCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHH
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVAR-----NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 75 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~-----~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr 75 (490)
|+++|-++|+- .++..|.++.+...++ ..--.-+.-..++|++|.|||..+..+.-.-+-.+.|+++..+..
T Consensus 96 VrdlaVQfgc~---evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F~~ 172 (262)
T KOG4557|consen 96 VRDLAVQFGCV---EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEFSC 172 (262)
T ss_pred HHHHHHHHhHH---HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHHHH
Confidence 45677788877 6778888887766552 111123456788999999999988776666666677888776666
Q ss_pred HHHHHHHHh
Q 011262 76 VYLQLCQVL 84 (490)
Q Consensus 76 ~yk~L~~~L 84 (490)
..+++.+..
T Consensus 173 l~kqler~~ 181 (262)
T KOG4557|consen 173 LSKQLERNY 181 (262)
T ss_pred HHHHHHHHH
Confidence 555555543
No 47
>PF13730 HTH_36: Helix-turn-helix domain
Probab=82.65 E-value=2.6 Score=31.51 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=24.0
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|++.|++.+|++..||++.++++.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 79999999999999999999999753
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=81.90 E-value=1.9 Score=31.43 Aligned_cols=30 Identities=17% Similarity=0.079 Sum_probs=20.6
Q ss_pred HHHhcCCCCCHhhHHhHhccCHHHHHHHHH
Q 011262 150 SALTHGLKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 150 Aar~~g~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
...++....|+++||+.+|++.+||.+-++
T Consensus 13 I~~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 345567789999999999999999998765
No 49
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=81.48 E-value=14 Score=35.61 Aligned_cols=118 Identities=13% Similarity=0.186 Sum_probs=68.3
Q ss_pred hHHHHHHHHHHHHHhcCCC-cCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHH
Q 011262 38 TEQVQASCLYLACRQKSKP-FLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 116 (490)
Q Consensus 38 ~~~VaAACLYiACR~~~~p-rtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~ 116 (490)
...++=|.||+ .|-| .++.+|+.+++++...+..+...|...+.-...+.....+ ...| +|+ ..++
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~-~~~y--~l~------tk~e 71 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEF-NDVY--KLV------TKEE 71 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEE-CCEE--EEE------EcHH
Confidence 45667788887 5777 9999999999999999999999998877532111000000 1111 111 1222
Q ss_pred HHHHHHHHHHHhhccccccCCChhHHHHHHHH-HHHHhcCCCCCHhhHHhHhccCHHHHHHH
Q 011262 117 VCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKR 177 (490)
Q Consensus 117 V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALy-lAar~~g~~~t~~dIa~v~~Vse~TIrkR 177 (490)
......+++ ...+|.-+--|+|= +|...+..++|..+|+++.||+-.-+-+.
T Consensus 72 ~~~~v~~~~---------~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~~~ii~~ 124 (188)
T PRK00135 72 NADYLQKLV---------KTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNSDGALQT 124 (188)
T ss_pred HHHHHHHHh---------cccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHH
Confidence 222222221 11223334444443 34445678999999999999996444333
No 50
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.45 E-value=2 Score=39.42 Aligned_cols=37 Identities=14% Similarity=0.250 Sum_probs=31.2
Q ss_pred HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 149 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 149 lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
+.+...+-+.|..+||+.+|+|+.|+++|++.+.+..
T Consensus 15 l~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 15 LEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4444566789999999999999999999999997554
No 51
>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=81.38 E-value=2.7 Score=31.48 Aligned_cols=31 Identities=6% Similarity=0.164 Sum_probs=26.1
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++.++|..++|+.++||..||++-++++.+.
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 4445999999999999999999999999643
No 52
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=81.06 E-value=58 Score=34.39 Aligned_cols=25 Identities=4% Similarity=0.034 Sum_probs=21.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|+.+|++.+|||..+||+..+.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~~ 348 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAK 348 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 6799999999999999999976544
No 53
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=80.39 E-value=5.9 Score=29.17 Aligned_cols=25 Identities=12% Similarity=0.146 Sum_probs=22.8
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
..|+++||+..|||..||++.++.+
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3899999999999999999998765
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=77.87 E-value=3.9 Score=30.12 Aligned_cols=28 Identities=14% Similarity=0.059 Sum_probs=24.0
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
+....|+.+||...|+|..||+++++.-
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 3678999999999999999999988764
No 55
>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=77.83 E-value=8.7 Score=35.58 Aligned_cols=29 Identities=17% Similarity=0.306 Sum_probs=26.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++.|+.+||..+|+|..||.+-+++|.+-
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 67899999999999999999999999754
No 56
>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=77.31 E-value=4 Score=32.34 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=26.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++.|+.+||..+|+|..|+.+-+++|.+-
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999999999754
No 57
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=77.24 E-value=94 Score=32.14 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=22.5
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
+...|+.+|+..+|||..|||++...
T Consensus 274 ~~~~Tl~EIa~~lgiS~erVRqi~~r 299 (317)
T PRK07405 274 GQPLTLAKIGERLNISRERVRQIERE 299 (317)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 36799999999999999999987544
No 58
>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=77.22 E-value=1.4 Score=32.25 Aligned_cols=28 Identities=18% Similarity=0.131 Sum_probs=20.3
Q ss_pred HhcCCCCCHhhHHhHhccCHHHHHHHHH
Q 011262 152 LTHGLKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 152 r~~g~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
+|+....|+.+||+.+|||..||.+.++
T Consensus 16 ~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 16 ELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 3444459999999999999999998764
No 59
>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=76.94 E-value=5.9 Score=31.22 Aligned_cols=40 Identities=23% Similarity=0.236 Sum_probs=32.0
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHH
Q 011262 137 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 137 R~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
|+|.-=-|=-||+ -++-.++.+|||..+||++.|||+.=.
T Consensus 5 Rsp~rdkA~e~y~---~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 5 RSPNRDKAFEIYK---ESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CCcCHHHHHHHHH---HhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 5666666666775 467889999999999999999997643
No 60
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=76.94 E-value=4.1 Score=43.19 Aligned_cols=83 Identities=17% Similarity=0.257 Sum_probs=56.5
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCC-cC---HHH-HHHHhCcCHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP-FL---LID-FSNYLNINVYELGAV 76 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~p-rt---L~D-Ia~v~~vsv~~Lgr~ 76 (490)
.+|+..-+|. ...+.+|..||.+..=+|++.-.++..+|.|||.+|.+.+... .+ |+| .-+.+..+..+|-..
T Consensus 390 r~l~~d~~id--~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~ 467 (497)
T KOG4164|consen 390 RELGEDCGID--VVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAF 467 (497)
T ss_pred HHhhhccCcc--ceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhh
Confidence 3445455666 6788999999999988899988889999999999999987542 22 222 233456666555544
Q ss_pred HHHHHHHhcc
Q 011262 77 YLQLCQVLYI 86 (490)
Q Consensus 77 yk~L~~~L~i 86 (490)
-.-++-.|.+
T Consensus 468 Ef~VlvaLef 477 (497)
T KOG4164|consen 468 EFPVLVALEF 477 (497)
T ss_pred hhhHHHhhhh
Confidence 4444444444
No 61
>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=76.91 E-value=2.2 Score=31.66 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=19.8
Q ss_pred CHhhHHhHhccCHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|++|||+.+|||..|+.+-|..
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6899999999999999998754
No 62
>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=76.66 E-value=3.9 Score=28.12 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=22.3
Q ss_pred CcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 56 PFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 56 prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
|.+-.|||+.+|++..++.|++++|.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 667889999999999999999999876
No 63
>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=76.34 E-value=5.5 Score=31.05 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+||.... .+..++..+||+..+|+.+|+..-++.|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 4665555 678899999999999999999999998864
No 64
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=76.10 E-value=38 Score=33.81 Aligned_cols=58 Identities=12% Similarity=0.023 Sum_probs=37.3
Q ss_pred cCCChhHHHHHHHHHHHH--hcCCCCCHhhHHhHhccC-HHHHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 135 TGRKPSGLCGAALYVSAL--THGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 135 ~GR~PsgIaaAALylAar--~~g~~~t~~dIa~v~~Vs-e~TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
+|..|....=-.-+..|+ +..-+.++.+||..+|.+ ...-.+.+|... .+||.+|++.
T Consensus 224 ~G~tp~~~l~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~SP~~yR~~ 284 (290)
T PRK10572 224 LGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCT-----GASPSEFRAR 284 (290)
T ss_pred HCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 455555544433333222 223468889999999887 567788877773 5788888876
No 65
>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=75.75 E-value=7.5 Score=29.75 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=26.6
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
....|+.+|++.+|++..|+.+.++.|.+-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 366899999999999999999999999643
No 66
>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=75.33 E-value=85 Score=30.68 Aligned_cols=26 Identities=4% Similarity=-0.019 Sum_probs=23.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++||...|||..+|+++.+.-
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~a 220 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKA 220 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 56999999999999999999886654
No 67
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=75.06 E-value=3.1 Score=42.72 Aligned_cols=56 Identities=11% Similarity=0.030 Sum_probs=49.3
Q ss_pred cchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCC
Q 011262 99 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL 156 (490)
Q Consensus 99 ~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~ 156 (490)
..+|.++|.+|. ++..+..+|.-+.+|..-..-..+-.|..||.+|||+|++.-+-
T Consensus 49 ~k~i~~l~~~L~--lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~ 104 (297)
T COG5333 49 LKLIMDLCTRLN--LPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT 104 (297)
T ss_pred HHHHHHHHHhcC--CCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccc
Confidence 357899999998 88999999999999987666688999999999999999987663
No 68
>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=74.86 E-value=61 Score=32.12 Aligned_cols=37 Identities=14% Similarity=-0.014 Sum_probs=25.5
Q ss_pred CCCCCHhhHHhHhccC-HHHHHHHHHHHhcCCCCCCCHHHHHH
Q 011262 155 GLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMA 196 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vs-e~TIrkR~kE~~~t~s~~Lt~~ef~~ 196 (490)
.-+.++.+||..+|.+ .++-.+.+|... .+||.+|++
T Consensus 249 ~t~~sI~eIA~~~GF~s~s~Fsr~FKk~~-----G~tP~~yR~ 286 (287)
T TIGR02297 249 FTQHSINQIAYDLGYKDPAYFARFFQKET-----GLSPSAFRD 286 (287)
T ss_pred cCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHhc
Confidence 4557888888888875 457777777663 466777754
No 69
>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=74.19 E-value=11 Score=34.93 Aligned_cols=48 Identities=13% Similarity=0.101 Sum_probs=37.7
Q ss_pred CChHHHHHHHHHHHHHhcC----------CCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 36 RRTEQVQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~~----------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+...-+|..|+.-|+..+ .|.|..|||+.+|++..++.|++++|.+.
T Consensus 113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 4555556666655555432 68899999999999999999999999986
No 70
>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=73.71 E-value=6.9 Score=29.98 Aligned_cols=24 Identities=13% Similarity=0.223 Sum_probs=22.0
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
.|..|||+.+|||.+|+..+++.-
T Consensus 24 ~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 789999999999999999998865
No 71
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=73.52 E-value=12 Score=40.44 Aligned_cols=188 Identities=14% Similarity=0.205 Sum_probs=99.0
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC------------------CcCHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK------------------PFLLIDFS 63 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~------------------prtL~DIa 63 (490)
..||..|+++ ...++.|..+.+...-.|+.. |+. .=||.+=.+..+. ..-+..|+
T Consensus 117 ~eia~~l~~~--~~~ve~~l~~iq~leP~GIgA-r~L----~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~ 189 (429)
T TIGR02395 117 EEIADELEVS--EEEVEKVLELIQRLDPAGVGA-RDL----QECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLA 189 (429)
T ss_pred HHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CCH----HHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHH
Confidence 5688889998 888888888887765555532 222 1244444443221 12346678
Q ss_pred HHhCcCHHHHHHHHHHHHHHhcccccccc-----cccCCccchHHHHHhhhC----------CCCcHHHHH--------H
Q 011262 64 NYLNINVYELGAVYLQLCQVLYIADESNV-----LKQVDPSIFLHKFTDRLL----------PGGNKKVCD--------T 120 (490)
Q Consensus 64 ~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~-----~~~vdP~~~I~Rf~s~L~----------~~l~~~V~~--------~ 120 (490)
..++++..++..++..|.. |+-.....+ ...+-|..+|.+.-..+. ..+++.... .
T Consensus 190 ~~l~is~~~v~~~~~~I~~-L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~~ 268 (429)
T TIGR02395 190 KKLGLSEEELKEALDLIKS-LSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEKEA 268 (429)
T ss_pred HHHCcCHHHHHHHHHHHhC-CCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccchH
Confidence 8899999999887766554 531100000 012334444332211110 001111110 0
Q ss_pred H-HHHHHHhhc-ccccc--CCChhHHHHHHHHHHHH-----hcC----CCCCHhhHHhHhccCHHHHHHHHHH-HhcCCC
Q 011262 121 A-RDILASMKR-DWITT--GRKPSGLCGAALYVSAL-----THG----LKFSKSDIVKIVHICEATLMKRLIE-FENTDS 186 (490)
Q Consensus 121 A-~~Iv~~~~~-~~l~~--GR~PsgIaaAALylAar-----~~g----~~~t~~dIa~v~~Vse~TIrkR~kE-~~~t~s 186 (490)
+ ..|-+.+.+ .|+.. -+|-.+|.-.+-.|+-+ ..| .++|+++||..+||+++||.+..+. ...||-
T Consensus 269 ~~~ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~~Kyi~tp~ 348 (429)
T TIGR02395 269 AAQYLKQKLKEARWLIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAINNKYLQTPR 348 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhcCceEecCC
Confidence 0 011111111 23322 13344444444444443 345 3689999999999999999988765 346666
Q ss_pred CCCCHHHHHHh
Q 011262 187 GSLTIEDFMAR 197 (490)
Q Consensus 187 ~~Lt~~ef~~~ 197 (490)
+-+-...|-+.
T Consensus 349 Gi~~lk~FFs~ 359 (429)
T TIGR02395 349 GVFELKYFFSR 359 (429)
T ss_pred ceEEHHHhcCC
Confidence 66666666544
No 72
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=73.40 E-value=4.3 Score=28.95 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=26.8
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.++.++.+|++.++++..|+++.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 467899999999999999999999999754
No 73
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=73.01 E-value=21 Score=32.70 Aligned_cols=78 Identities=14% Similarity=0.040 Sum_probs=53.2
Q ss_pred CCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhc---c--ccccCCChhHHHHHHHHHHHHhcC-CCCCHhhHHhHhcc
Q 011262 96 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR---D--WITTGRKPSGLCGAALYVSALTHG-LKFSKSDIVKIVHI 169 (490)
Q Consensus 96 vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~---~--~l~~GR~PsgIaaAALylAar~~g-~~~t~~dIa~v~~V 169 (490)
++-..|+.|+..... .+..+.-.|+-.+.++.. . .......+.-+-.+||.+|+.+++ ...+.+..+++.||
T Consensus 52 i~i~~fl~ri~~~~~--~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gi 129 (149)
T PF08613_consen 52 ISIRDFLSRILKYTQ--CSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGI 129 (149)
T ss_dssp S-HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS
T ss_pred CcHHHHHHHHHHHcC--CChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCC
Confidence 455678888887776 788999999999998877 1 123456677788899999998764 56889999999998
Q ss_pred CHHHHH
Q 011262 170 CEATLM 175 (490)
Q Consensus 170 se~TIr 175 (490)
+..-|.
T Consensus 130 s~~eln 135 (149)
T PF08613_consen 130 SLKELN 135 (149)
T ss_dssp -HHHHH
T ss_pred CHHHHH
Confidence 755443
No 74
>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=72.53 E-value=3.6 Score=31.60 Aligned_cols=30 Identities=20% Similarity=0.247 Sum_probs=26.1
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.-.++..+++..++||+.|||+=+..+.+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 356899999999999999999999988643
No 75
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=72.46 E-value=8.2 Score=34.69 Aligned_cols=48 Identities=21% Similarity=0.268 Sum_probs=40.4
Q ss_pred CChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 36 RRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
++...-+.+++|+|-+..+.|.+..+||..++++...+.+....|.+.
T Consensus 5 ~~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 5 TKGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred cHHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344566778999997766779999999999999999999988888874
No 76
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=71.84 E-value=5.7 Score=33.77 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=27.0
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+-+.|..+|++.+|+++.|++++++.+.+.
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457999999999999999999999999754
No 77
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=71.16 E-value=7.8 Score=38.51 Aligned_cols=57 Identities=16% Similarity=0.109 Sum_probs=44.2
Q ss_pred cchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCC
Q 011262 99 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLK 157 (490)
Q Consensus 99 ~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~ 157 (490)
..+|..++.+|. +...|..+|.-..+|.--..-..+-.|.-+|..|||+||..-..+
T Consensus 45 ~n~I~~lg~~lk--lRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 45 ANVIQKLGQHLK--LRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 346677777777 788999999988887543333678999999999999999866554
No 78
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=71.06 E-value=9.9 Score=26.91 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFM 195 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~ 195 (490)
..+.++.|||..+|+|...+++.+++.- .+|+-+|.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~-----g~tp~~y~ 41 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET-----GMTPKQYR 41 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT-----SS-HHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHh
Confidence 3568999999999999999999999872 45666664
No 79
>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=70.85 E-value=4.7 Score=27.73 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=22.1
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+.|..|||+.+|++..|+.+-++.|.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 568899999999999999999999964
No 80
>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=70.72 E-value=7 Score=30.77 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=26.8
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+.+-..+..+++..++||..||+++++.+.+
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3444678999999999999999999999965
No 81
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=70.56 E-value=5.9 Score=35.72 Aligned_cols=32 Identities=16% Similarity=0.407 Sum_probs=28.1
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
..+.+.|+.+||+.+|+|..|+++|++.+.+.
T Consensus 18 ~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 18 QEDARISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 44567999999999999999999999999644
No 82
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=70.55 E-value=6 Score=29.31 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=25.9
Q ss_pred CCCC-CHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKF-SKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~-t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|... |..++++.++||..||++.++.+.+.
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3445 89999999999999999999999754
No 83
>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=70.44 E-value=11 Score=30.91 Aligned_cols=27 Identities=19% Similarity=0.064 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|+++||+.+|||+.||++++....
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 457999999999999999999998653
No 84
>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=69.97 E-value=6.9 Score=32.09 Aligned_cols=45 Identities=22% Similarity=0.244 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 39 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 39 ~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
..-.-+.+|++-...+.|.+..+||+.++++...+.+....|.+.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 444556788877777778999999999999999999999999884
No 85
>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=68.78 E-value=13 Score=29.36 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhcC----------CCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcc
Q 011262 41 VQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 86 (490)
Q Consensus 41 VaAACLYiACR~~~----------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i 86 (490)
+|.--++++.+... .|.+..+||+.+|++..++.++++.|.+.=-+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I 58 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGII 58 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 44445555555432 57899999999999999999999999986333
No 86
>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=67.75 E-value=16 Score=28.46 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=31.5
Q ss_pred HHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 45 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 45 CLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+||.... .+.+.+..|||..++|+..++..++++|.+.
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 4555555 7889999999999999999999999998874
No 87
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=67.06 E-value=6.9 Score=28.39 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.3
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..+..+||..++||..||++++..+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36999999999999999999998764
No 88
>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=66.99 E-value=31 Score=28.79 Aligned_cols=71 Identities=13% Similarity=0.222 Sum_probs=48.9
Q ss_pred hHHHHHHHHHHHHHHhC--CCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhC-cCHHHHHHHHHHHHHHhcc
Q 011262 14 DEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQLCQVLYI 86 (490)
Q Consensus 14 ~~v~d~A~~iyk~A~~~--~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~-vsv~~Lgr~yk~L~~~L~i 86 (490)
+.|++.....|..-.+. +-.|++.....=..|+|++-+..| .++.+|+..++ .+-.++..+++.+.+.+..
T Consensus 2 ~~Ii~~Va~~~~v~~~~i~~~~R~~~~~~aR~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 2 ELIIEAVAEYFGISVEDLRSKSRKKEIALARQIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHHhCCCHHHHhcCCCCcCcchHHHHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 45666666666443332 222333333334468888776654 67899999999 9999999999999998864
No 89
>PF13518 HTH_28: Helix-turn-helix domain
Probab=65.77 E-value=12 Score=27.13 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=24.0
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|+.+||..+|||..||.+.++.|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~ 39 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREG 39 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhc
Confidence 99999999999999999999998753
No 90
>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=65.58 E-value=1.6e+02 Score=29.75 Aligned_cols=26 Identities=8% Similarity=0.043 Sum_probs=23.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++||..+|||..||++++..-
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rA 266 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEA 266 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 46999999999999999999887654
No 91
>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=65.52 E-value=13 Score=28.09 Aligned_cols=38 Identities=18% Similarity=0.298 Sum_probs=27.8
Q ss_pred HHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 147 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 147 LylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|+......+..+|+.+|++.++++..|+.+.++.|.+-
T Consensus 11 L~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 11 LMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 33333333334899999999999999999999998643
No 92
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=65.08 E-value=11 Score=27.41 Aligned_cols=32 Identities=9% Similarity=0.189 Sum_probs=26.8
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+..-+.+..+|++.++++.+||...++.+.+.
T Consensus 11 L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 11 LSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 44567899999999999999999999998753
No 93
>PRK05949 RNA polymerase sigma factor; Validated
Probab=65.01 E-value=1.8e+02 Score=30.27 Aligned_cols=25 Identities=4% Similarity=0.050 Sum_probs=22.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|..+|+..+|||..|||.+...
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~r 309 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEHQ 309 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 6799999999999999999987543
No 94
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=64.91 E-value=22 Score=31.61 Aligned_cols=71 Identities=14% Similarity=0.082 Sum_probs=53.8
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhC-CCCcH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNK 115 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~-~~l~~ 115 (490)
+.+...=.=+|+-|| =.|+|++..+||+-.+++..+..|.+.|+....+ ..........+.++|. |+++.
T Consensus 35 ~~E~~~Fi~~Fi~~r-----GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~----~~~~~~~~~~IL~~L~~GeIs~ 105 (113)
T PF09862_consen 35 SPEQLEFIKLFIKNR-----GNLKEMEKELGISYPTVRNRLDKIIEKLGYEEDE----EEEEEDERKEILDKLEKGEISV 105 (113)
T ss_pred CHHHHHHHHHHHHhc-----CCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCc----ccccchhHHHHHHHHHcCCCCH
Confidence 445555556666665 3799999999999999999999999999983222 1345567888889996 77765
Q ss_pred H
Q 011262 116 K 116 (490)
Q Consensus 116 ~ 116 (490)
+
T Consensus 106 e 106 (113)
T PF09862_consen 106 E 106 (113)
T ss_pred H
Confidence 4
No 95
>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=64.80 E-value=16 Score=27.11 Aligned_cols=33 Identities=9% Similarity=0.096 Sum_probs=28.1
Q ss_pred hcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 52 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 52 ~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
.++-|+|..+||+.++|+..+|.+....|...+
T Consensus 11 ~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 11 ESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 456679999999999999999999999997765
No 96
>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=64.65 E-value=11 Score=27.63 Aligned_cols=27 Identities=26% Similarity=0.209 Sum_probs=21.0
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
.|. .|++..|+..||..+||+.|++.-
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 555 999999999999999999988765
No 97
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=64.31 E-value=15 Score=34.53 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=39.4
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+...-..+++|+|-...+-|.++.+||+.++++...|.+.+..|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45566788899995555679999999999999999999988888874
No 98
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=64.00 E-value=50 Score=36.13 Aligned_cols=185 Identities=14% Similarity=0.201 Sum_probs=100.4
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcC-C------------------CcCHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKS-K------------------PFLLIDF 62 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~-~------------------prtL~DI 62 (490)
..||..|+++ ...++.|..+.....-.|+.. |+. .=||.+=.+..+ . ..-+..|
T Consensus 142 ~eia~~l~~~--~~~v~~~l~~lQ~leP~GigA-r~L----~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~i 214 (455)
T PRK05932 142 EEIAESLGVE--LDEVEAVLKRIQSFDPAGVGA-RDL----QECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRTL 214 (455)
T ss_pred HHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CCH----HHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHHH
Confidence 5688889998 888888888888766555532 221 224444333311 1 1235668
Q ss_pred HHHhCcCHHHHHHHHHHHHHHhcccccccc----cccCCccchHHH----------------------HHhhhCCCCcHH
Q 011262 63 SNYLNINVYELGAVYLQLCQVLYIADESNV----LKQVDPSIFLHK----------------------FTDRLLPGGNKK 116 (490)
Q Consensus 63 a~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~----~~~vdP~~~I~R----------------------f~s~L~~~l~~~ 116 (490)
+..++++..+|..+...|. .|+-.....+ ...+-|..+|.+ |...+......+
T Consensus 215 a~~l~is~~~v~~~~~~Ir-~L~P~Pg~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~in~~Y~~~~~~~~~~e 293 (455)
T PRK05932 215 AKKLGVKEEDLQEALDLIR-SLDPKPGAGFGTEEPEYVVPDVFVRKINGGWLVELNPDSLPRLRINQEYAALVSRSARDE 293 (455)
T ss_pred HHHHCcCHHHHHHHHHHHh-CCCCCCccccCCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHHhccchH
Confidence 8889999999998886654 4531100000 112334444322 111121000011
Q ss_pred HHHHHHHHHHHhhc-ccccc--CCChhHHHHHHHHHHHH-----hcC----CCCCHhhHHhHhccCHHHHHHHHHH-Hhc
Q 011262 117 VCDTARDILASMKR-DWITT--GRKPSGLCGAALYVSAL-----THG----LKFSKSDIVKIVHICEATLMKRLIE-FEN 183 (490)
Q Consensus 117 V~~~A~~Iv~~~~~-~~l~~--GR~PsgIaaAALylAar-----~~g----~~~t~~dIa~v~~Vse~TIrkR~kE-~~~ 183 (490)
+. ..|-+++.+ .|+.. .+|-.+|.--+-.|+-+ ..| .++|+++||..+|++++||.+..+. +..
T Consensus 294 ~~---~ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~Kyv~ 370 (455)
T PRK05932 294 DK---QFLREKLQEAKWLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTNKYMA 370 (455)
T ss_pred HH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcCceee
Confidence 11 111112111 24332 14445555544444443 234 3589999999999999999988765 456
Q ss_pred CCCCCCCHHHHHHh
Q 011262 184 TDSGSLTIEDFMAR 197 (490)
Q Consensus 184 t~s~~Lt~~ef~~~ 197 (490)
||-+-+-...|-+.
T Consensus 371 tp~Gi~~lk~FFs~ 384 (455)
T PRK05932 371 TPRGIFELKYFFSS 384 (455)
T ss_pred cCCceEEHHHhccc
Confidence 77666666666554
No 99
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=63.69 E-value=88 Score=26.20 Aligned_cols=39 Identities=15% Similarity=0.277 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 41 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 41 VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
+.-++-||.- ....+.++.++|..++++...|.+.|+..
T Consensus 22 ~~~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~ 60 (127)
T COG2207 22 LARALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKE 60 (127)
T ss_pred HHHHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3345555555 66667999999999999999998866644
No 100
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=63.34 E-value=8.4 Score=29.02 Aligned_cols=36 Identities=14% Similarity=0.193 Sum_probs=29.1
Q ss_pred HHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 148 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 148 ylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+++-...-...+..++|...|||++|+.+.+.++.+
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 333444557899999999999999999999998854
No 101
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=63.20 E-value=17 Score=33.59 Aligned_cols=46 Identities=13% Similarity=0.100 Sum_probs=38.3
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+.+.-+-+++|+| ...+.+.+..+||+..+++...|.+.+..|.+.
T Consensus 6 ~~~YAlr~L~~LA-~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCA-ANDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHH-hCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4456667889999 445668899999999999999999999888884
No 102
>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=62.94 E-value=9.7 Score=28.25 Aligned_cols=28 Identities=29% Similarity=0.286 Sum_probs=20.7
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
+-...|..+||+..|+|+.||++++..-
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3467899999999999999999998754
No 103
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=62.50 E-value=9.4 Score=44.20 Aligned_cols=65 Identities=11% Similarity=0.267 Sum_probs=55.9
Q ss_pred CHHHHHhcCCCCchHHHHHHHHHHHHHHhC--CCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhC
Q 011262 1 MRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN 67 (490)
Q Consensus 1 I~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~--~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~ 67 (490)
|+.+|.+|.|. +.+...-..+|.-...+ .+++.|..+++.-.|+|+.||..+...++.+|-....
T Consensus 684 L~~Lc~rL~l~--~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR 750 (920)
T KOG1010|consen 684 LNDLCERLSLS--DELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYR 750 (920)
T ss_pred HHHHHHHhhhh--hHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHh
Confidence 57899999999 88999888888865543 5788999999999999999999999999998876543
No 104
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=62.27 E-value=14 Score=27.75 Aligned_cols=43 Identities=16% Similarity=0.325 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhccc
Q 011262 40 QVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 87 (490)
Q Consensus 40 ~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 87 (490)
.+....+|+ +.-.+..++|..+||+..++.+.+..+...|...
T Consensus 8 ~lll~L~~L-----R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 8 QLLLTLMYL-----RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHHHHH-----HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 444444454 3457899999999999999999999999988643
No 105
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=62.07 E-value=63 Score=34.42 Aligned_cols=26 Identities=8% Similarity=0.018 Sum_probs=22.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++|+..+|||..+||+....-
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rA 355 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKA 355 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46999999999999999999876654
No 106
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=61.34 E-value=30 Score=32.35 Aligned_cols=29 Identities=14% Similarity=0.177 Sum_probs=26.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++.|+.+||..+|++..|+.+-+++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 56899999999999999999999999754
No 107
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=61.13 E-value=29 Score=25.44 Aligned_cols=43 Identities=9% Similarity=0.062 Sum_probs=30.0
Q ss_pred CCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 35 GRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 35 GR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
+.+...-...-++-.|+.. .++.+||..++|+..++.+.|...
T Consensus 9 ~~r~T~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 9 YCRITKRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCcHHHHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3344444444444444433 799999999999999999988753
No 108
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=60.97 E-value=20 Score=25.58 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=24.8
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
..++.+|++.++++..|+++.++.|..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 489999999999999999999999964
No 109
>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=60.67 E-value=30 Score=26.29 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=27.0
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
..+.+..|||+.++++..++.+.+..|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 467899999999999999999999998884
No 110
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=60.52 E-value=1.1e+02 Score=31.17 Aligned_cols=36 Identities=14% Similarity=0.143 Sum_probs=24.4
Q ss_pred CCCHhhHHhHhccC-HHHHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 157 KFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 157 ~~t~~dIa~v~~Vs-e~TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
..++.+||..+|.+ .....+.++.+. .+||.+|++.
T Consensus 283 ~~~i~~IA~~~Gf~~~s~F~r~Fk~~~-----G~tP~~yr~~ 319 (322)
T PRK09393 283 ALSIDQIAERAGFGSEESLRHHFRRRA-----ATSPAAYRKR 319 (322)
T ss_pred CCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 45777788777764 467777777663 4667777654
No 111
>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=60.30 E-value=20 Score=30.34 Aligned_cols=31 Identities=3% Similarity=0.128 Sum_probs=27.2
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
....+|+.+||+.+|++..|+.+.+++|.+-
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3567999999999999999999999999643
No 112
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=60.27 E-value=31 Score=33.16 Aligned_cols=30 Identities=20% Similarity=0.357 Sum_probs=26.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
.++|+++||..+|+|..|+.+-+++|.+..
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g 212 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSG 212 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 578999999999999999999999997543
No 113
>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=59.86 E-value=12 Score=28.75 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=25.5
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.-..+..++|...|+|+.||++-+.++.+.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 345889999999999999999999999744
No 114
>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=59.82 E-value=11 Score=30.98 Aligned_cols=39 Identities=23% Similarity=0.324 Sum_probs=28.6
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.+|+|..-.+.+.|.++||+.+++++.++++-+..+...
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 344544433345999999999999999999999998643
No 115
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=59.66 E-value=1.3e+02 Score=29.89 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=23.8
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|.++||...|||..||++++...
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ra 245 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKA 245 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467999999999999999999987654
No 116
>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=59.39 E-value=12 Score=26.84 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=19.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
..=.+...|+.+||+..|+.++++.+
T Consensus 17 ~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 17 CGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 33456789999999999999999863
No 117
>PF13551 HTH_29: Winged helix-turn helix
Probab=59.30 E-value=19 Score=30.27 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=24.6
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
|+.+||+.+|||..||.+.++.|.+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999997554
No 118
>PHA02591 hypothetical protein; Provisional
Probab=59.21 E-value=11 Score=31.21 Aligned_cols=31 Identities=13% Similarity=0.142 Sum_probs=26.0
Q ss_pred HHHHhcCCCCCHhhHHhHhccCHHHHHHHHH
Q 011262 149 VSALTHGLKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 149 lAar~~g~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
+|..+...-.|+.+||+.+||+..||++-++
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4555666778999999999999999998765
No 119
>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=59.17 E-value=10 Score=26.68 Aligned_cols=23 Identities=13% Similarity=0.232 Sum_probs=20.5
Q ss_pred CHhhHHhHhccCHHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
|..+||+.+||+..||++..+.-
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 67899999999999999888764
No 120
>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=58.79 E-value=11 Score=29.29 Aligned_cols=30 Identities=17% Similarity=0.290 Sum_probs=25.0
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
.|..+ |..++++..+||..|+|+.|..+..
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 46778 8999999999999999999999864
No 121
>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=58.62 E-value=11 Score=28.79 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=25.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|..++.+.|+.+|||..+++++++++.
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 778999999999999999999999874
No 122
>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=58.60 E-value=20 Score=26.00 Aligned_cols=35 Identities=23% Similarity=0.232 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcC-CCCCHhhHHhHhccCHHHHHHHHH
Q 011262 144 GAALYVSALTHG-LKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 144 aAALylAar~~g-~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
-|++-+..+ .| ...|.++|++.+||+.++|-+.+.
T Consensus 3 ~aa~~l~~~-~G~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 3 EAALELFAE-KGYEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHH-HHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHHHHHHHH-hCHHhCCHHHHHHHHccchhhHHHHcC
Confidence 345555443 45 459999999999999999987664
No 123
>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=58.48 E-value=12 Score=27.78 Aligned_cols=19 Identities=11% Similarity=0.148 Sum_probs=17.2
Q ss_pred CHHHHHHHhCcCHHHHHHH
Q 011262 58 LLIDFSNYLNINVYELGAV 76 (490)
Q Consensus 58 tL~DIa~v~~vsv~~Lgr~ 76 (490)
||+|||..+||+..++.++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ 19 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRV 19 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 6899999999999999874
No 124
>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=58.30 E-value=13 Score=27.03 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=23.5
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..+.++||...+++..||+++++.+.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46999999999999999999988764
No 125
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=58.30 E-value=14 Score=26.09 Aligned_cols=27 Identities=7% Similarity=0.114 Sum_probs=20.0
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
..+.++.|||..++++...+.|.|++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457899999999999999998877654
No 126
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=57.97 E-value=84 Score=29.43 Aligned_cols=107 Identities=19% Similarity=0.281 Sum_probs=61.1
Q ss_pred HHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhccccccc--------ccccCCc--cchHHHHHhhhCC
Q 011262 42 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESN--------VLKQVDP--SIFLHKFTDRLLP 111 (490)
Q Consensus 42 aAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~--------~~~~vdP--~~~I~Rf~s~L~~ 111 (490)
+=|.||.+ +-|.++.+|+.+++ +...+......|.+.+.-..... +.-.+.| ..||.+|...
T Consensus 3 iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~--- 74 (159)
T PF04079_consen 3 IEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK--- 74 (159)
T ss_dssp HHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT---
T ss_pred hHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc---
Confidence 44677764 67999999999999 99999999999999883221111 0001111 1222222211
Q ss_pred CCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHH-HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 112 GGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 112 ~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALy-lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
++|..+--|++= +|.-.+..++|..+|..+-||.-..+-+.|.+.
T Consensus 75 -------------------------~~~~~LS~aalEtLAiIAY~QPiTr~eIe~IRGv~s~~~i~~L~e~ 120 (159)
T PF04079_consen 75 -------------------------PKPPKLSQAALETLAIIAYKQPITRAEIEEIRGVNSDSVIKTLLER 120 (159)
T ss_dssp -------------------------CCCHHHHHHHHHHHHHHHHH-SEEHHHHHHHHTS--HCHHHHHHHT
T ss_pred -------------------------CccCCCCHHHHHHHHHHHhcCCcCHHHHHHHcCCChHHHHHHHHHC
Confidence 234444444443 333456689999999999999865555555554
No 127
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=57.41 E-value=34 Score=30.29 Aligned_cols=44 Identities=9% Similarity=0.128 Sum_probs=32.5
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 81 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~ 81 (490)
....+..+.-||--... .+.++.++|+.+++++..|.+.|+...
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34455566666665544 479999999999999999988776543
No 128
>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=57.35 E-value=10 Score=29.65 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-+|.+-. ..-..|..+|++.++++..|+.+.++.+.+-
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4454443 4467899999999999999999999998643
No 129
>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=57.22 E-value=16 Score=30.94 Aligned_cols=32 Identities=13% Similarity=-0.049 Sum_probs=27.3
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+.....|+++|++.+|||..||.+-=+.+..-
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~~ 76 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLKYG 76 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHHS
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence 66677899999999999999999888877643
No 130
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=57.18 E-value=73 Score=35.43 Aligned_cols=25 Identities=8% Similarity=0.068 Sum_probs=21.3
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
+...|+.+|+..+|||...||+.-+
T Consensus 465 ~e~~TL~EIa~~lGVSrERVRQIe~ 489 (509)
T PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIES 489 (509)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3579999999999999999986543
No 131
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=56.45 E-value=42 Score=28.40 Aligned_cols=39 Identities=8% Similarity=0.135 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 41 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 41 VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
+..++-|+... ...|.++.++|+.++++...|.+.|+..
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44455565554 3467999999999999999998877764
No 132
>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=56.41 E-value=12 Score=26.53 Aligned_cols=23 Identities=9% Similarity=0.260 Sum_probs=20.6
Q ss_pred CCHhhHHhHhccCHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
.|.+++|+.+||+..||++.+++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 47899999999999999998865
No 133
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=55.90 E-value=42 Score=32.22 Aligned_cols=53 Identities=17% Similarity=0.221 Sum_probs=38.5
Q ss_pred CCCChHHHHHHHHHHHHHhcC----------CCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcc
Q 011262 34 KGRRTEQVQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 86 (490)
Q Consensus 34 rGR~~~~VaAACLYiACR~~~----------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i 86 (490)
..++...-.|..|+.-++..+ .|.|..+||+.+|++..++.|..++|.+.=-|
T Consensus 152 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I 214 (235)
T PRK11161 152 SKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGML 214 (235)
T ss_pred hCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCE
Confidence 345655555555554443332 58899999999999999999999998885433
No 134
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=55.73 E-value=17 Score=29.12 Aligned_cols=31 Identities=10% Similarity=0.012 Sum_probs=29.3
Q ss_pred HhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 152 LTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 152 r~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
++.+..+|..+.++.+|+.+.||++.+..|+
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR 38 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFR 38 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6789999999999999999999999999995
No 135
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=55.71 E-value=19 Score=34.03 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=23.3
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|..|||..+|||+.||++++.-++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5999999999999999999998875
No 136
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=55.66 E-value=71 Score=32.04 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=23.5
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|+++||..+|||..||+++++..
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ra 255 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKT 255 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999987654
No 137
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=55.60 E-value=35 Score=32.54 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=22.6
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
..|..+||+.+|||.+|+.+.+++.
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 4699999999999999999998864
No 138
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=55.44 E-value=22 Score=26.08 Aligned_cols=29 Identities=10% Similarity=0.276 Sum_probs=26.2
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+-..|..+|++.++++..||++.++.|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56689999999999999999999999964
No 139
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=55.13 E-value=13 Score=37.14 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=25.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
-.++..|+++.++||+.|||+.++++.+
T Consensus 18 ~~v~v~eLa~~l~VS~~TIRRDL~~Le~ 45 (256)
T PRK10434 18 GKTSVEELAQYFDTTGTTIRKDLVILEH 45 (256)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4589999999999999999999999853
No 140
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=54.92 E-value=27 Score=30.72 Aligned_cols=46 Identities=20% Similarity=0.155 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 38 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 38 ~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
...-..+.+|++-...+.|.+..+||..++++...+.+....|.+.
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3445566677763223459999999999999999999988888873
No 141
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=54.48 E-value=17 Score=32.78 Aligned_cols=38 Identities=16% Similarity=0.359 Sum_probs=31.2
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
.||++..-.|...+.++||+..+|+..+||+.+..+..
T Consensus 14 ~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~ 51 (141)
T PRK11014 14 LIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSR 51 (141)
T ss_pred HHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45555545566789999999999999999999999853
No 142
>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=54.38 E-value=12 Score=23.59 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.6
Q ss_pred CCCHhhHHhHhccCHHHHHHH
Q 011262 157 KFSKSDIVKIVHICEATLMKR 177 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR 177 (490)
..+..+|++.++++..||.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999999875
No 143
>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=54.38 E-value=2.5e+02 Score=28.52 Aligned_cols=26 Identities=8% Similarity=0.160 Sum_probs=23.0
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
+...|..+|+..+|||..|||++...
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~r 292 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEAK 292 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35799999999999999999988764
No 144
>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=54.37 E-value=32 Score=30.43 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=37.6
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
..+....+.+|++- ..+.+.+..|||+.++++...+.+....|.+.
T Consensus 7 ~~~yal~~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 7 LTDYATLVLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHhHHHHHHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44566777888874 34668999999999999999999988888874
No 145
>PRK10870 transcriptional repressor MprA; Provisional
Probab=54.20 E-value=55 Score=30.78 Aligned_cols=30 Identities=10% Similarity=0.067 Sum_probs=26.5
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+..+|+.+|++.++++.+|+.+.++.+..-
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~k 98 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEKR 98 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 456899999999999999999999998643
No 146
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.01 E-value=58 Score=27.53 Aligned_cols=51 Identities=8% Similarity=0.094 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 142 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 142 IaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
|.-+.-|+... ...+.++.+||+.+|+|..++.+++++. ..+|+.+|....
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~-----~g~s~~~~i~~~ 57 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV-----THQTLGDYIRQR 57 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH-----HCcCHHHHHHHH
Confidence 34444555554 3457999999999999999999999997 357778876653
No 147
>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=53.86 E-value=32 Score=25.86 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=32.3
Q ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 43 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 43 AACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
..+|++..+..+...++.||++.++++...+.+..+.|.+.
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44566666655556899999999999999999999998874
No 148
>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=53.76 E-value=13 Score=26.67 Aligned_cols=23 Identities=13% Similarity=0.026 Sum_probs=20.0
Q ss_pred CHhhHHhHhccCHHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
|..++|+.+||+..||+...++-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999876654
No 149
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=53.67 E-value=24 Score=24.83 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+..+|+...|++..||.++.....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 557999999999999999999887764
No 150
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=53.66 E-value=11 Score=39.15 Aligned_cols=45 Identities=9% Similarity=0.039 Sum_probs=37.0
Q ss_pred HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHH
Q 011262 149 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 193 (490)
Q Consensus 149 lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~e 193 (490)
+|...+-...||.|||+..|||..||.+-|++=++..-=+++|..
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~ 65 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINS 65 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeC
Confidence 444556778999999999999999999999998877766666643
No 151
>PRK04217 hypothetical protein; Provisional
Probab=53.50 E-value=17 Score=32.08 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=23.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|+.+||+..|||..||++++....
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 446999999999999999999998764
No 152
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=53.46 E-value=63 Score=28.59 Aligned_cols=54 Identities=4% Similarity=0.022 Sum_probs=41.7
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 138 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 138 ~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
....|..+.-||-.... .+.++.+||+.+|+|..++.+.+++.. .+|+.+|...
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~-----G~s~~~~l~~ 60 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET-----GHSLGQYIRS 60 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 34455566666766654 479999999999999999999999873 4678888655
No 153
>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=53.39 E-value=26 Score=26.49 Aligned_cols=27 Identities=15% Similarity=0.383 Sum_probs=24.7
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.+..+|++.++++..||++.++.|...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHC
Confidence 999999999999999999999998643
No 154
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=53.16 E-value=53 Score=31.81 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=26.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++.|+.+||..+|++..|+.+.+++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999999999755
No 155
>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=52.86 E-value=20 Score=26.93 Aligned_cols=26 Identities=19% Similarity=0.328 Sum_probs=23.7
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|..+|++.++||..||++.++.|.+-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 59999999999999999999999653
No 156
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=52.67 E-value=2.7e+02 Score=28.32 Aligned_cols=27 Identities=4% Similarity=-0.141 Sum_probs=23.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|+++|+...|||..||+++...-
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~A 269 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARA 269 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999999887665
No 157
>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=52.30 E-value=22 Score=29.61 Aligned_cols=24 Identities=17% Similarity=0.265 Sum_probs=21.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
-..|+.+||+.+|||..||++.+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 567999999999999999999663
No 158
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.29 E-value=72 Score=28.10 Aligned_cols=70 Identities=17% Similarity=0.189 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccch-HHHHHhhhC-CCCc
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIF-LHKFTDRLL-PGGN 114 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~-I~Rf~s~L~-~~l~ 114 (490)
..+.+--.-||+-||- .|++|-..+|++-.+++.-+..+.+.+|.+... .+|... =..+.+.|+ |+++
T Consensus 43 t~d~LeFv~lf~r~RG-----nlKEvEr~lg~sYptvR~kld~vlramgy~p~~-----e~~~~i~~~~i~~qle~Gei~ 112 (122)
T COG3877 43 TSDQLEFVELFLRCRG-----NLKEVERELGISYPTVRTKLDEVLRAMGYNPDS-----ENSVNIGKKKIIDQLEKGEIS 112 (122)
T ss_pred CHhHhHHHHHHHHHcc-----CHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCC-----CChhhhhHHHHHHHHHcCCCC
Confidence 3466677789999984 599999999999999999999999999987544 444433 234677786 7777
Q ss_pred HH
Q 011262 115 KK 116 (490)
Q Consensus 115 ~~ 116 (490)
++
T Consensus 113 pe 114 (122)
T COG3877 113 PE 114 (122)
T ss_pred HH
Confidence 64
No 159
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=51.51 E-value=1.1e+02 Score=33.14 Aligned_cols=51 Identities=14% Similarity=0.143 Sum_probs=41.4
Q ss_pred cccccCCChhHHHHH---HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 131 DWITTGRKPSGLCGA---ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 131 ~~l~~GR~PsgIaaA---ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
..|..+++-..|+-| |.|++-.+.+. |..+|++.+|.+.+||...++.+..
T Consensus 360 ~~l~s~~R~~~i~~aR~iamyl~r~~~~~--s~~~Ig~~fgr~hstV~~a~~~i~~ 413 (440)
T PRK14088 360 EEILSNSRNVKALLARRIGMYVAKNYLGS--SLRTIAEKFNRSHPVVVDSVKKVKD 413 (440)
T ss_pred HHHhCCCCCccccHHHHHHHHHHHHHhCC--CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345566666778888 99999776554 9999999999999999998888864
No 160
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=51.45 E-value=37 Score=32.76 Aligned_cols=30 Identities=10% Similarity=0.139 Sum_probs=26.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
++.|+.+||+.+|+|..|+.+-+++|.+-.
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 457899999999999999999999997543
No 161
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=51.35 E-value=16 Score=28.93 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=25.3
Q ss_pred HhcCCCCCHhhHHhHhccC-HHHHHHHHHHHhc
Q 011262 152 LTHGLKFSKSDIVKIVHIC-EATLMKRLIEFEN 183 (490)
Q Consensus 152 r~~g~~~t~~dIa~v~~Vs-e~TIrkR~kE~~~ 183 (490)
.-+|++-|++||++.+|++ .+|+...++.+.+
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3578999999999999996 9999999998853
No 162
>PRK13501 transcriptional activator RhaR; Provisional
Probab=51.32 E-value=2.6e+02 Score=27.83 Aligned_cols=81 Identities=14% Similarity=0.093 Sum_probs=52.6
Q ss_pred hHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHH-HHHHh-cCCCCCHhhHHhHhccCH-HHHHHH
Q 011262 101 FLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALT-HGLKFSKSDIVKIVHICE-ATLMKR 177 (490)
Q Consensus 101 ~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALy-lAar~-~g~~~t~~dIa~v~~Vse-~TIrkR 177 (490)
-|..+|..++ +++.-. .++.++. +|..|.-..---.. .|+++ ..-..++.+||..+|-+. +.-.+.
T Consensus 194 sl~~lA~~~~--lS~~~l---~r~Fk~~------~G~T~~qyi~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~ 262 (290)
T PRK13501 194 DMADFCHKNQ--LVERSL---KQLFRQQ------TGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAV 262 (290)
T ss_pred CHHHHHHHHC--cCHHHH---HHHHHHH------HCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHH
Confidence 3566777776 554322 3344433 57777776655554 33333 456689999999999855 566777
Q ss_pred HHHHhcCCCCCCCHHHHHHh
Q 011262 178 LIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 178 ~kE~~~t~s~~Lt~~ef~~~ 197 (490)
+|... .+|+.+|++.
T Consensus 263 FKk~~-----G~TP~~yR~~ 277 (290)
T PRK13501 263 FTREA-----GMTPRDYRQR 277 (290)
T ss_pred HHHHH-----CcCHHHHHHH
Confidence 77663 5899999887
No 163
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=51.31 E-value=24 Score=24.89 Aligned_cols=30 Identities=10% Similarity=0.136 Sum_probs=26.7
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
..|.+..|||+.++++..++.+.+..|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999999888874
No 164
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=51.21 E-value=2.6e+02 Score=27.67 Aligned_cols=26 Identities=8% Similarity=0.049 Sum_probs=22.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++||..+|||..||+++.+..
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~a 249 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAA 249 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999876643
No 165
>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=51.16 E-value=58 Score=25.86 Aligned_cols=67 Identities=7% Similarity=0.161 Sum_probs=37.8
Q ss_pred HHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhc--CCCcCHHHHHHHhCc-CHHHHHHHHHHH
Q 011262 4 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK--SKPFLLIDFSNYLNI-NVYELGAVYLQL 80 (490)
Q Consensus 4 ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~--~~prtL~DIa~v~~v-sv~~Lgr~yk~L 80 (490)
||+.++++ .. .-.++|+......+. ..+...-+-.|++.- +...++.|||..+|. +...+.+.|+..
T Consensus 1 lA~~~~~s--~~---~l~~~f~~~~g~s~~-----~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 1 LADELGMS--ER---YLSRIFKKETGMSFK-----QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp HHHHCTS---HH---HHHHHHHHHHSS-HH-----HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred ChHHhCcC--HH---HHHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 57888888 33 334555555443332 233444455555532 467899999999987 567777766655
No 166
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=51.03 E-value=32 Score=32.76 Aligned_cols=59 Identities=14% Similarity=0.150 Sum_probs=42.2
Q ss_pred HHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 119 DTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 119 ~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.-...+++-|.+.++- +-.|..=|+|| +..-+.|..||+.++|+|.+.+...++++...
T Consensus 10 ~~Ie~fae~m~r~G~n---rtVG~iYgily----ls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~ 68 (177)
T COG1510 10 IFIEHFAETMSRWGIN---RTVGQIYGILY----LSRKPLTLDEIAEALGMSKSNVSMGLKKLQDW 68 (177)
T ss_pred HHHHHHHHHHHHhCCc---chHHHHhhhhe----ecCCCccHHHHHHHHCCCcchHHHHHHHHHhc
Confidence 3344566666665442 23444445555 56789999999999999999999999999533
No 167
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=50.95 E-value=33 Score=31.60 Aligned_cols=42 Identities=19% Similarity=0.097 Sum_probs=28.9
Q ss_pred ChhHHHHHHHHHHHHhcC---CCCCHhhHHhHhccCHHHHHHHHH
Q 011262 138 KPSGLCGAALYVSALTHG---LKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 138 ~PsgIaaAALylAar~~g---~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
+|.-+-||.|+++--++. -++|+.+||.-+||+++|+-++-+
T Consensus 12 ~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 12 TLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp -HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 455566777766666665 469999999999999999988774
No 168
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=50.89 E-value=15 Score=36.70 Aligned_cols=29 Identities=10% Similarity=0.102 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+-.++++++++.++||+.|||+.+++|.+
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45689999999999999999999999853
No 169
>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=50.84 E-value=15 Score=28.32 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=20.6
Q ss_pred CHhhHHhHhccCHHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
|..+||+.+||+..|||+..+++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999988764
No 170
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=50.76 E-value=21 Score=33.97 Aligned_cols=72 Identities=21% Similarity=0.301 Sum_probs=47.7
Q ss_pred cHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHH
Q 011262 114 NKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 193 (490)
Q Consensus 114 ~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~e 193 (490)
.+.|.........+. .|+.+ ..+||+++ +| .-.-.|..+||+-.|.|+.|||+.++. +|.+++|--+-
T Consensus 28 ~~evlkli~~~~~~l--TWvdS----LavAAga~---ar-ekag~Ti~EIAeelG~TeqTir~hlkg--etkAG~lv~et 95 (182)
T COG1318 28 RPEVLKLIKDPYERL--TWVDS----LAVAAGAL---AR-EKAGMTISEIAEELGRTEQTVRNHLKG--ETKAGQLVRET 95 (182)
T ss_pred cHHHHHHHhCccccc--chhhH----HHHHHHHH---HH-HHccCcHHHHHHHhCCCHHHHHHHHhc--chhhhhHHHHH
Confidence 455655555444444 35432 35555544 34 456799999999999999999999985 46667766555
Q ss_pred HHHh
Q 011262 194 FMAR 197 (490)
Q Consensus 194 f~~~ 197 (490)
|...
T Consensus 96 Y~~l 99 (182)
T COG1318 96 YEKL 99 (182)
T ss_pred HHHH
Confidence 5544
No 171
>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=50.45 E-value=18 Score=31.02 Aligned_cols=29 Identities=14% Similarity=0.159 Sum_probs=25.0
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..-..||++|+..+|||.+||.+-=+.+.
T Consensus 52 l~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 52 LNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 34679999999999999999998777765
No 172
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=50.27 E-value=2.7e+02 Score=27.64 Aligned_cols=28 Identities=11% Similarity=0.090 Sum_probs=24.3
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
....|+++||..+|||..||++++....
T Consensus 217 ~~~~s~~eIA~~lgvs~~~V~~~~~ra~ 244 (256)
T PRK07408 217 LHDLTQKEAAERLGISPVTVSRRVKKGL 244 (256)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3578999999999999999999987653
No 173
>PF12728 HTH_17: Helix-turn-helix domain
Probab=50.16 E-value=18 Score=26.52 Aligned_cols=23 Identities=9% Similarity=0.309 Sum_probs=20.0
Q ss_pred CCHhhHHhHhccCHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
.|..|+|+.+|||..||++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 47899999999999999987754
No 174
>PRK09526 lacI lac repressor; Reviewed
Probab=50.02 E-value=16 Score=36.84 Aligned_cols=45 Identities=18% Similarity=0.141 Sum_probs=31.7
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHhhh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHE 203 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le~ 203 (490)
+.|++|||+.+|||.+|+++-|+.- ..-+.-|-+..+..+++|-.
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn~~--~~vs~~tr~rV~~~a~elgY 49 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLNQA--SHVSAKTREKVEAAMAELNY 49 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhcCC--CCCCHHHHHHHHHHHHHHCC
Confidence 4799999999999999999999742 22334445555555555444
No 175
>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=49.83 E-value=34 Score=30.20 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.+|++. ..+-+.+..+|++.++++..+++++++.+.+.
T Consensus 15 l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 15 LTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 445543 34567899999999999999999999999754
No 176
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=49.53 E-value=3.8e+02 Score=29.13 Aligned_cols=26 Identities=12% Similarity=0.226 Sum_probs=22.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|...|+++|+..+|||..|||+++..
T Consensus 368 ~~~~Tl~EIA~~LGvS~erVRqie~r 393 (415)
T PRK07598 368 GHTYSLAEIGRALDLSRERVRQIESK 393 (415)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 36799999999999999999988654
No 177
>PRK00118 putative DNA-binding protein; Validated
Probab=49.28 E-value=20 Score=31.29 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=24.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||+.+|||..||.+++....
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RAr 58 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTE 58 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 578999999999999999999988664
No 178
>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=49.27 E-value=22 Score=26.36 Aligned_cols=31 Identities=16% Similarity=0.244 Sum_probs=25.6
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++...|+.||++.+|++.+|+.+-++.|.+.
T Consensus 15 ~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 15 SGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp TBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4455799999999999999999999998643
No 179
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=48.94 E-value=36 Score=26.96 Aligned_cols=33 Identities=12% Similarity=0.120 Sum_probs=27.7
Q ss_pred HhcCC-CCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 152 LTHGL-KFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 152 r~~g~-~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.-+|- ..|..+|+..+||+..|+++.|..|.+-
T Consensus 16 ~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 16 ENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 34555 4999999999999999999999998643
No 180
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=48.73 E-value=75 Score=37.21 Aligned_cols=54 Identities=26% Similarity=0.330 Sum_probs=43.6
Q ss_pred HHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCH
Q 011262 3 QMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLL 59 (490)
Q Consensus 3 ~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL 59 (490)
..|..|+++ ......|...|.-+.++--+-| +-.++.|.+||.+||..++|.-.
T Consensus 40 ~~c~~lnld--~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~v~ 93 (920)
T KOG1010|consen 40 ELCRPLNLD--EQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPTVG 93 (920)
T ss_pred hhhhhhccc--chhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCccC
Confidence 468889999 8999999999998876544444 47899999999999998766433
No 181
>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=48.52 E-value=36 Score=24.88 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=25.8
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
....|+.|||..+|++..++.+......+.|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5678999999999999999998887776655
No 182
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=47.96 E-value=77 Score=29.67 Aligned_cols=47 Identities=13% Similarity=0.013 Sum_probs=35.4
Q ss_pred ChHHHHHHHHHHHHHhc---------CCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQK---------SKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~---------~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+...-+|..|+.-|... ..|.|..+||+.+|++..++.|.+++|.+.
T Consensus 140 ~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 140 DVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred ChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 44455566555444432 248899999999999999999999999885
No 183
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=47.88 E-value=47 Score=26.92 Aligned_cols=29 Identities=7% Similarity=0.139 Sum_probs=26.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-+.|..+|++.++++.+|+++.++.+.+.
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47999999999999999999999999643
No 184
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=47.31 E-value=18 Score=32.04 Aligned_cols=26 Identities=19% Similarity=0.109 Sum_probs=23.5
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
=++++|++..|||=.|+|+|+.++-.
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 46899999999999999999999853
No 185
>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=47.29 E-value=58 Score=23.44 Aligned_cols=28 Identities=11% Similarity=0.086 Sum_probs=23.0
Q ss_pred CCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 55 KPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 55 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
-+.|..|||..++++..++.+.++.|.+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3489999999999999999998888876
No 186
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=47.18 E-value=34 Score=30.17 Aligned_cols=31 Identities=6% Similarity=0.100 Sum_probs=26.9
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
......|+.+||+..||+..||.+..+.|..
T Consensus 25 ~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 25 SFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 3445789999999999999999999999864
No 187
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=46.50 E-value=18 Score=36.53 Aligned_cols=43 Identities=21% Similarity=0.136 Sum_probs=29.6
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHhh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELH 202 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le 202 (490)
.|++|||+.+|||.+|+++-|+.- ...+.-|.+..++.+++|-
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~--~~vs~~tr~~V~~~a~elg 44 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKT--RFVAEETRNAVWAAIKELH 44 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC--CCCCHHHHHHHHHHHHHHC
Confidence 489999999999999999999631 2233444444555544443
No 188
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=46.28 E-value=54 Score=31.57 Aligned_cols=48 Identities=19% Similarity=0.038 Sum_probs=36.5
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
+...-+|.-|+........|.+..|||+.+|++..+|.|++++|.+.=
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 455555665654333344677899999999999999999999999953
No 189
>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=46.19 E-value=19 Score=27.29 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||...+|++.||+.+.+.+.
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 557889999999999999999988874
No 190
>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=46.19 E-value=29 Score=26.56 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=27.2
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.+-+.|..+|++.++++.+|+...++.+.+.
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5678999999999999999999999999754
No 191
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=46.16 E-value=29 Score=27.45 Aligned_cols=30 Identities=10% Similarity=0.050 Sum_probs=24.7
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+.+++-+|||+.+|+|..|+|.-|..+...
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~e 42 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKE 42 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 567899999999999999999999888543
No 192
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=46.07 E-value=6.7 Score=41.36 Aligned_cols=79 Identities=14% Similarity=0.049 Sum_probs=0.0
Q ss_pred HHhhhCCCCcHHHHHHHHHHHHHhh-ccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 105 FTDRLLPGGNKKVCDTARDILASMK-RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 105 f~s~L~~~l~~~V~~~A~~Iv~~~~-~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
++..+++..+++++..|..|++... ...+..|-.=.+=+.+|+||||..++....+.......++......+-|..|.+
T Consensus 4 l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~ 83 (353)
T PF05460_consen 4 LIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFEN 83 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHH
Confidence 4455554467888888888888776 455666666667788999999999998888888888999999999999988875
No 193
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=46.00 E-value=54 Score=32.67 Aligned_cols=71 Identities=6% Similarity=0.150 Sum_probs=36.0
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCc-CHHHHHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQL 80 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~v-sv~~Lgr~yk~L 80 (490)
..+|..++++ . ..-.++|++.....+..=....-+..|+..+ .....++.+||..+|- +...+.|.|++.
T Consensus 203 ~~lA~~~~lS--~---~~l~r~Fk~~~G~tp~~~l~~~Rl~~A~~lL----~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~ 273 (290)
T PRK10572 203 ESVAQHVCLS--P---SRLAHLFRQQLGISVLRWREDQRISRAKLLL----QTTRMPIATIGRNVGYDDQLYFSRVFKKC 273 (290)
T ss_pred HHHHHHHCCC--H---HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 4566666666 3 2334555555444433322222233333222 1345777777777776 366666666554
Q ss_pred H
Q 011262 81 C 81 (490)
Q Consensus 81 ~ 81 (490)
.
T Consensus 274 ~ 274 (290)
T PRK10572 274 T 274 (290)
T ss_pred H
Confidence 3
No 194
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=45.86 E-value=20 Score=31.81 Aligned_cols=27 Identities=15% Similarity=-0.017 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||.++|||+.||++++.-..
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567999999999999999999887653
No 195
>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=45.84 E-value=14 Score=30.89 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=22.1
Q ss_pred HHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 147 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 147 LylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|-++.-+.+.+.|++..|.++|||.+||-+=+.|
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvte 42 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTE 42 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHH
Confidence 3444445567899999999999999999764443
No 196
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=45.45 E-value=82 Score=29.47 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=26.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
++.|+++||..+|+|..|+.+-+++|.+-
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 57999999999999999999999999744
No 197
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=45.38 E-value=21 Score=36.04 Aligned_cols=24 Identities=17% Similarity=0.119 Sum_probs=22.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
.+.|++|||+.+|||.+|+++.|+
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHC
Confidence 468999999999999999999986
No 198
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=45.31 E-value=28 Score=28.92 Aligned_cols=29 Identities=17% Similarity=0.247 Sum_probs=25.5
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|.++.-++|++.++++.+||||-+..+.
T Consensus 20 ~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred cCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 46788889999999999999999888875
No 199
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=45.21 E-value=23 Score=30.95 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCC-CCHhhHHhHhccCHHHHHHHHHHH
Q 011262 142 LCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 142 IaaAALylAar~~g~~-~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
|..+++.+... +|+. .|.++|++.+||+..||.+.+..-
T Consensus 17 ii~aa~~l~~~-~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K 56 (201)
T COG1309 17 ILDAALRLFAE-KGYAATTVDEIAKAAGVSKGTLYRHFPSK 56 (201)
T ss_pred HHHHHHHHHHH-cCcCCCCHHHHHHHhCCCcchhHHHcCCH
Confidence 44444444443 8875 999999999999999999888754
No 200
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.64 E-value=36 Score=25.79 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=26.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 201 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~l 201 (490)
..+|+.++|+.+||+..||.+-++ -....++.+.+..+++-|
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~----~~~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILN----GKPSNPSLDTLEKIAKAL 50 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHT----TT-----HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHh----cccccccHHHHHHHHHHc
Confidence 456999999999999999998887 223578888888886533
No 201
>PF14502 HTH_41: Helix-turn-helix domain
Probab=44.52 E-value=23 Score=26.68 Aligned_cols=29 Identities=14% Similarity=0.133 Sum_probs=25.6
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcCCC
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENTDS 186 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t~s 186 (490)
.|+.|.++.++||..||++.++.+.+...
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~ga 35 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGA 35 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCc
Confidence 57889999999999999999999976653
No 202
>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=44.52 E-value=31 Score=32.45 Aligned_cols=27 Identities=19% Similarity=0.354 Sum_probs=24.9
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.|+++|+..+++|..||.+.+++|.+.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 789999999999999999999999754
No 203
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.51 E-value=11 Score=34.13 Aligned_cols=27 Identities=19% Similarity=0.015 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||..+|+++.||++++.--.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999998887654
No 204
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=44.44 E-value=27 Score=26.82 Aligned_cols=30 Identities=27% Similarity=0.189 Sum_probs=23.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
...+....|+..+|+..|++.|++-+.+.-
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~ 40 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELL 40 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 356788899999999999999999996543
No 205
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=44.27 E-value=1.8e+02 Score=28.01 Aligned_cols=120 Identities=15% Similarity=0.209 Sum_probs=69.3
Q ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHhCc-CHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHH
Q 011262 39 EQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV 117 (490)
Q Consensus 39 ~~VaAACLYiACR~~~~prtL~DIa~v~~v-sv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V 117 (490)
..++.|.||. .+.|.++++++.++++ +...+......+.....-. . +.-. .+.....+ .+..
T Consensus 10 ~~~vEall~a----~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~r--g-----~~L~----~~~~~~r~-~t~~- 72 (184)
T COG1386 10 KALIEALLFA----GGEPLSLKELAEILGIVSADAIIDALAELKEEYEDR--G-----LELV----EVAEGWRL-QTKQ- 72 (184)
T ss_pred HHHHHHHHHh----cCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCC--C-----eeEE----EEcCceeE-EehH-
Confidence 4555566654 4789999999999998 7777777777777664211 0 0000 01110000 0111
Q ss_pred HHHHHHHHHHhhccccccCCChhHHHHHHH-HHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 118 CDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 118 ~~~A~~Iv~~~~~~~l~~GR~PsgIaaAAL-ylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..-..+.++.. . +.+..+--|++ -+|.-.+..++|..+|..+-||...++-+.|.++.
T Consensus 73 --~~~~~~~~l~~----~-~~~~~LSraalEtLAiIAY~QPiTR~eI~~iRGv~~~~~i~~L~e~g 131 (184)
T COG1386 73 --EYAEYLEKLQE----Q-RPKRELSRAALETLAIIAYKQPVTRSEIEEIRGVAVSQVISTLLERG 131 (184)
T ss_pred --HHHHHHHHHhc----c-cccccccHHHHHHHHHHHHcCCccHHHHHHHhCccHHHHHHHHHHCC
Confidence 11112222211 1 11123444444 46666788999999999999999988888888773
No 206
>PRK09492 treR trehalose repressor; Provisional
Probab=44.20 E-value=20 Score=35.76 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=22.0
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHH
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
+.|++|||+.+|||.+|+.+.|+.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCC
Confidence 579999999999999999999974
No 207
>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=43.90 E-value=17 Score=36.46 Aligned_cols=45 Identities=16% Similarity=0.086 Sum_probs=30.3
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHhhh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHE 203 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le~ 203 (490)
+.|++|||+.+|||.+|+++.++.- ..-+.-|-+..+..+++|-.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~~--~~vs~~tr~rV~~~a~~lgY 45 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNE--PKVSIETRERVEQVIQQSGF 45 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCCC--CCCCHHHHHHHHHHHHHHCC
Confidence 4689999999999999999999642 12234444444444444433
No 208
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=43.88 E-value=45 Score=28.15 Aligned_cols=36 Identities=8% Similarity=0.039 Sum_probs=30.1
Q ss_pred HHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 148 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 148 ylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
.|+-++.+...++.++|..+|||..|..+.+.-|..
T Consensus 16 ~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 16 RLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred HHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 355556667789999999999999999999988863
No 209
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=43.74 E-value=48 Score=33.37 Aligned_cols=53 Identities=8% Similarity=0.169 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 011262 39 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 105 (490)
Q Consensus 39 ~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf 105 (490)
..+..++-||-... ..+.++.++|..++++...|.|.|+.... ..|..||.+.
T Consensus 5 ~~i~~~~~~i~~~~-~~~~~l~~lA~~~~~S~~~l~r~F~~~~g-------------~s~~~yi~~~ 57 (289)
T PRK15121 5 GIIRDLLIWLEGHL-DQPLSLDNVAAKAGYSKWHLQRMFKDVTG-------------HAIGAYIRAR 57 (289)
T ss_pred HHHHHHHHHHHhcc-cCCCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH
Confidence 45566777777554 45799999999999999999987776543 3466676654
No 210
>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=43.54 E-value=24 Score=27.40 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=20.2
Q ss_pred CHhhHHhHhccCHHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
+..+||+.+||+..|||..-+++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 67899999999999999887664
No 211
>smart00351 PAX Paired Box domain.
Probab=43.51 E-value=31 Score=30.72 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.7
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
..+..+||+.++||..||.+.++-|.++.
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G 61 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETG 61 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence 46889999999999999999999987664
No 212
>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=43.51 E-value=17 Score=25.73 Aligned_cols=20 Identities=15% Similarity=0.207 Sum_probs=15.9
Q ss_pred CHhhHHhHhccCHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRL 178 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~ 178 (490)
|..++|+.+||+..|||..=
T Consensus 1 ti~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 46789999999999998643
No 213
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=43.43 E-value=24 Score=31.88 Aligned_cols=30 Identities=23% Similarity=0.223 Sum_probs=25.9
Q ss_pred hcCCC-CCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 153 THGLK-FSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 153 ~~g~~-~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..|.+ -|+++.|..++|...|+++.|+++.
T Consensus 30 ~pGdkLPSvRelA~~~~VNpnTv~raY~eLE 60 (125)
T COG1725 30 KPGDKLPSVRELAKDLGVNPNTVQRAYQELE 60 (125)
T ss_pred CCCCCCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34666 4699999999999999999999985
No 214
>cd00131 PAX Paired Box domain
Probab=43.28 E-value=31 Score=30.95 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=26.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
...+..+||+.++||..||.+..+-|.++.
T Consensus 32 ~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G 61 (128)
T cd00131 32 SGIRPCDISRQLRVSHGCVSKILNRYYETG 61 (128)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence 457999999999999999999999998764
No 215
>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=43.12 E-value=3.5e+02 Score=26.97 Aligned_cols=27 Identities=4% Similarity=-0.025 Sum_probs=22.8
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
+...|+++||..+|||..||+++.+.-
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 347999999999999999999766543
No 216
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.76 E-value=46 Score=23.83 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=27.9
Q ss_pred cCHHHHHHHhCcCHHHHHHHHHHHHHHhccc
Q 011262 57 FLLIDFSNYLNINVYELGAVYLQLCQVLYIA 87 (490)
Q Consensus 57 rtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 87 (490)
.+..+||..++++..++.+....+.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5889999999999999999999998888764
No 217
>PRK06030 hypothetical protein; Provisional
Probab=42.46 E-value=60 Score=29.24 Aligned_cols=69 Identities=10% Similarity=0.143 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCCC-hHHHH--HHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 14 DEIVHVAKRFYGIAVARNFTKGRR-TEQVQ--ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 14 ~~v~d~A~~iyk~A~~~~~~rGR~-~~~Va--AACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
+.|++....+|..-.+.=..+.|+ ...+. -.|+|++-...+ .++.+|+..||-+-.++..+++.+.+.+
T Consensus 26 d~Ii~~Va~~f~I~~~di~sk~R~rk~i~~aRqIAMYL~r~~~~--~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 26 EAVIDLLALAFGVSGAEIASPLRGRREVSRIRQIAMYVAHVSLG--WPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHHhCCCHHHHhCCCCCCcccchHHHHHHHHHHHHcC--CCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 677888888887555543333332 22222 258888876655 5899999999999999999999888765
No 218
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=42.31 E-value=19 Score=27.85 Aligned_cols=24 Identities=17% Similarity=0.098 Sum_probs=21.3
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|..|||+.+||+..|||..-+++.
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC
Confidence 578999999999999999887774
No 219
>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=42.30 E-value=37 Score=25.66 Aligned_cols=33 Identities=9% Similarity=0.045 Sum_probs=28.0
Q ss_pred CCcCHHHHHHHhCcCHHHHHHHHHHHHHHhccc
Q 011262 55 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 87 (490)
Q Consensus 55 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 87 (490)
...+..+||..+++++.++......|.+.|++.
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 346789999999999999999999999999875
No 220
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=42.17 E-value=2.6e+02 Score=28.37 Aligned_cols=40 Identities=10% Similarity=0.159 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 40 QVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 40 ~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
.+..++-||...-. .+.++.+||+.+++++..|.|.|++.
T Consensus 192 ~i~~~~~~i~~~~~-~~~tl~~lA~~~~~S~~~l~r~Fk~~ 231 (302)
T PRK10371 192 YVSQMLGFIAENYD-QALTINDVAEHVKLNANYAMGIFQRV 231 (302)
T ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35566666666544 57899999999999998888877764
No 221
>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=42.16 E-value=3.2e+02 Score=26.21 Aligned_cols=26 Identities=8% Similarity=0.123 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+|||..||++++..-
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra 215 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQA 215 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56799999999999999999887643
No 222
>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=42.13 E-value=18 Score=29.30 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=21.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||+.++||++||.+-.+.+.
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 458899999999999999999988874
No 223
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=42.04 E-value=3.9e+02 Score=27.19 Aligned_cols=122 Identities=12% Similarity=0.089 Sum_probs=68.3
Q ss_pred HHHHHhcCC-CcCHHHHHHHhCcCH-HHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHH-----
Q 011262 47 YLACRQKSK-PFLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCD----- 119 (490)
Q Consensus 47 YiACR~~~~-prtL~DIa~v~~vsv-~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~----- 119 (490)
|+..|.... -.|+++||..+|++. .-|. ..+.-.-+ + +...+.+++..|+ ++..-..
T Consensus 17 ~ye~rk~~~p~fS~R~fa~~~G~ss~s~L~-------~v~~Gkr~------L-s~~~~~k~a~~l~--L~~~E~~yF~~l 80 (271)
T TIGR02147 17 YYEERKKTDPAFSWRFFAEKAGFSSTSYLN-------DIIKGKKN------L-TKRMIPKFAEALG--LDEKEAAYFEAM 80 (271)
T ss_pred HHHHHhccCcCcCHHHHHHHhCCCCHHHHH-------HHHcCCCC------C-CHHHHHHHHHHcC--CCHHHHHHHHHH
Confidence 667777644 689999999999875 3332 22221111 1 3556777777777 3333222
Q ss_pred -------------HHHHHHHHhhc---cccccC---CChhHHHHHHHHHHHHhcCCCCCHhhHHhHhc--cCHHHHHHHH
Q 011262 120 -------------TARDILASMKR---DWITTG---RKPSGLCGAALYVSALTHGLKFSKSDIVKIVH--ICEATLMKRL 178 (490)
Q Consensus 120 -------------~A~~Iv~~~~~---~~l~~G---R~PsgIaaAALylAar~~g~~~t~~dIa~v~~--Vse~TIrkR~ 178 (490)
.|..=++.+.. ..++.+ +--....-.+|.-.+.+.++.-+..+||+.++ ||...++..+
T Consensus 81 V~f~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL 160 (271)
T TIGR02147 81 VNFGQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESL 160 (271)
T ss_pred HHHhccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHH
Confidence 22211111111 011111 11112333355555556677777889999998 9999999999
Q ss_pred HHHhcC
Q 011262 179 IEFENT 184 (490)
Q Consensus 179 kE~~~t 184 (490)
.-+.+.
T Consensus 161 ~~L~~~ 166 (271)
T TIGR02147 161 DLLERL 166 (271)
T ss_pred HHHHHC
Confidence 887644
No 224
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.03 E-value=36 Score=31.22 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=28.0
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
.....|.++||..+|||.+||.+.++.++++-
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G 49 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWVRRYRETG 49 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHHHHhcccc
Confidence 34668899999999999999999999998765
No 225
>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=42.01 E-value=24 Score=32.52 Aligned_cols=26 Identities=8% Similarity=0.092 Sum_probs=23.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.+|||+.+|+|+.||++|+.--
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Ra 174 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFA 174 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999998654
No 226
>PHA00542 putative Cro-like protein
Probab=41.93 E-value=22 Score=29.34 Aligned_cols=42 Identities=7% Similarity=0.033 Sum_probs=29.5
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
+.....|+.++|+.+||+..||.+....-.. ..+++...++.
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~g~~~----~p~~~~l~ki~ 68 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYSGRHK----DPRYSVVEKLR 68 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHcCCCC----CCCHHHHHHHH
Confidence 3345689999999999999999988765421 23445555544
No 227
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=41.77 E-value=24 Score=32.70 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=22.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|.+|||..+|+|++||+.|+.-
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~r 166 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQ 166 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5689999999999999999999864
No 228
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=41.75 E-value=58 Score=30.01 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 38 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 38 ~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
....+=|-+|+|....+-|.++.+||...+++..-|.+.+..|.+.
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 3456667889998877669999999999999999999999988884
No 229
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=41.72 E-value=25 Score=34.83 Aligned_cols=28 Identities=11% Similarity=0.322 Sum_probs=25.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
-..++.++++.++||+.|||+-+++|.+
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4799999999999999999999999964
No 230
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=41.63 E-value=1.1e+02 Score=29.64 Aligned_cols=48 Identities=17% Similarity=0.193 Sum_probs=37.0
Q ss_pred CChHHHHHHHHHHHHHhcC------CCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 36 RRTEQVQASCLYLACRQKS------KPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~~------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+...-.|..|+.-++..+ .|.+..|||+.+|++..+|.|+.++|.+.
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4555556666655455433 57889999999999999999999999985
No 231
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=41.36 E-value=1.1e+02 Score=30.60 Aligned_cols=55 Identities=9% Similarity=0.121 Sum_probs=42.4
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 138 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 138 ~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
.+.-+.-+.-||...+....+|+.+||+.+|||..++.+-+++. .+|+-+|....
T Consensus 195 ~~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~------G~T~~~yi~~~ 249 (302)
T PRK09685 195 RERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ------GLVVAQYIRNR 249 (302)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc------CCCHHHHHHHH
Confidence 34445566667877777777999999999999999999988764 36778876653
No 232
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.19 E-value=56 Score=25.82 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=27.1
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhccc
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 87 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 87 (490)
+.|.+-.|||+.++++.++..+....|.+.=.+.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 7899999999999999999999888777764443
No 233
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=40.98 E-value=96 Score=28.84 Aligned_cols=30 Identities=7% Similarity=-0.199 Sum_probs=27.7
Q ss_pred CCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 55 KPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 55 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
.|.|..+||+.+|++..++.|.+++|.+.=
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCC
Confidence 688999999999999999999999999853
No 234
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=40.50 E-value=25 Score=27.91 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=24.9
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
.|++|||+.+|||..||.+.+.. ...++.+-...+
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~-----~~~v~~~t~~~i 35 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG-----NGRVSEETREKV 35 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC-----CCCCCHHHHHHH
Confidence 37899999999999999987742 133454444444
No 235
>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=40.44 E-value=26 Score=27.60 Aligned_cols=26 Identities=19% Similarity=0.184 Sum_probs=23.3
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..|+.+||...||+..||.++.+.+.
T Consensus 23 g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 23 GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCceEeeecccccccccccHHHHHHh
Confidence 48899999999999999999999996
No 236
>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=40.32 E-value=28 Score=27.14 Aligned_cols=23 Identities=17% Similarity=0.156 Sum_probs=20.4
Q ss_pred CHhhHHhHhccCHHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
+..++|+.+||+..|||...+++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~ 24 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 67899999999999999887765
No 237
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=40.30 E-value=26 Score=27.04 Aligned_cols=22 Identities=14% Similarity=0.064 Sum_probs=19.2
Q ss_pred CHhhHHhHhccCHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|..+||+.+||+..|||...++
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999977554
No 238
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=40.19 E-value=76 Score=25.09 Aligned_cols=38 Identities=11% Similarity=0.102 Sum_probs=29.8
Q ss_pred HHHHHHhcCC-CcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 46 LYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 46 LYiACR~~~~-prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
|+..-+..|- +.++.|||..++++..++.+....|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3344445555 4999999999999999999888877775
No 239
>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=40.00 E-value=69 Score=25.27 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=19.8
Q ss_pred cCCCcCHHHHHHHhCcCHHHHHHH
Q 011262 53 KSKPFLLIDFSNYLNINVYELGAV 76 (490)
Q Consensus 53 ~~~prtL~DIa~v~~vsv~~Lgr~ 76 (490)
++--++++|||+.++|+..+|++.
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHHH
Confidence 344578999999999999999864
No 240
>PRK09480 slmA division inhibitor protein; Provisional
Probab=39.91 E-value=34 Score=31.50 Aligned_cols=43 Identities=14% Similarity=0.198 Sum_probs=31.4
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 138 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 138 ~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
+..-|.-|++-+...-.|...|+++|++.+||+.+||-..++.
T Consensus 11 ~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 11 RREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 3445555655544434467799999999999999999877654
No 241
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=39.79 E-value=59 Score=24.82 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=26.9
Q ss_pred HHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 46 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 46 LYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
|+..+ ..+-+.++.+|++.++++...+.+..+.|.+.
T Consensus 9 L~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 9 LRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp HHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred HHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34444 56778899999999999999999999999885
No 242
>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=39.68 E-value=18 Score=27.42 Aligned_cols=23 Identities=26% Similarity=0.247 Sum_probs=17.5
Q ss_pred CCHhhHHhHhccCHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
.++.+||+.+||+.+||++.++.
T Consensus 23 ~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 23 ESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp T-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Confidence 38999999999999999987763
No 243
>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=39.64 E-value=3.5e+02 Score=25.92 Aligned_cols=26 Identities=15% Similarity=0.143 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++||+..|||..||+++++..
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra 218 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRA 218 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56899999999999999999987654
No 244
>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=39.58 E-value=58 Score=23.46 Aligned_cols=32 Identities=9% Similarity=0.027 Sum_probs=28.6
Q ss_pred CcCHHHHHHHhCcCHHHHHHHHHHHHHHhccc
Q 011262 56 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 87 (490)
Q Consensus 56 prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 87 (490)
..+..+||..+++++.++.+....+.+.++.+
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 36899999999999999999999999988764
No 245
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=39.36 E-value=2.9e+02 Score=26.57 Aligned_cols=120 Identities=17% Similarity=0.181 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHHhcCCC-cCHHHHHHHhCcCH-HHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHH
Q 011262 39 EQVQASCLYLACRQKSKP-FLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 116 (490)
Q Consensus 39 ~~VaAACLYiACR~~~~p-rtL~DIa~v~~vsv-~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~ 116 (490)
.+++=|.||++ |-| +++.+|+.+++++. ..+......|.....-+..+. -|..+.........++
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl---------~l~~~~~~y~l~tk~e 69 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGI---------EIIKFGQSYSLVTKPA 69 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCE---------EEEEECCEEEEEEhHH
Confidence 45667888877 788 99999999999984 455555555555543211110 0111111110001222
Q ss_pred HHHHHHHHHHHhhccccccCCChhHHHHHHHH-HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 117 VCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 117 V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALy-lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
......+++.. .+++ +.-|++= +|.-.+..++|..+|-.+-||.-..+-+.|.+.
T Consensus 70 ~~~~i~~~~~~--------~~~~--LS~aaLEtLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~er 125 (186)
T TIGR00281 70 FADYIHRFLPA--------KLKN--LNSASLEVLAIIAYKQPITRARINEIRGVKSYQIVDDLVEK 125 (186)
T ss_pred HHHHHHHHhcc--------cccc--CCHHHHHHHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHHC
Confidence 22222222111 1111 3333332 444567789999999999999865555555554
No 246
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=39.36 E-value=81 Score=30.31 Aligned_cols=30 Identities=10% Similarity=0.247 Sum_probs=26.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
++.|+.+||..+|++..|+.+-+++|.+..
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 356789999999999999999999997654
No 247
>PRK01381 Trp operon repressor; Provisional
Probab=39.27 E-value=23 Score=30.71 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=29.7
Q ss_pred HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 149 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 149 lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
|+..+..-..|+++|+...|||.+||.+-=+.++..+
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~ 83 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLKTAP 83 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCC
Confidence 3444555679999999999999999999888886444
No 248
>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=39.24 E-value=27 Score=25.66 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=28.1
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
....|++++|+.+||+..||.+..+. ...++++....++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g-----~~~~~~~~~~~ia 45 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG-----KRNPSLDTLKKIA 45 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT-----SSTSBHHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC-----CCCCCHHHHHHHH
Confidence 35689999999999999999988766 2346666665554
No 249
>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=39.20 E-value=83 Score=23.39 Aligned_cols=38 Identities=11% Similarity=0.101 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 44 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 44 ACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+|++.....+ .++.+||..++++...+.+..+.|.+.
T Consensus 7 ~iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 7 RILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 34444444444 899999999999999999999999884
No 250
>PRK10130 transcriptional regulator EutR; Provisional
Probab=39.19 E-value=65 Score=33.86 Aligned_cols=54 Identities=19% Similarity=0.376 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 011262 38 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 105 (490)
Q Consensus 38 ~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf 105 (490)
...|..++=||.-.. ..|+++.|||..++++..+|.+.|+.. +| ..|..||.++
T Consensus 239 ~~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~---~G----------~sp~~ylr~~ 292 (350)
T PRK10130 239 RRLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAI---LG----------IGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH
Confidence 445666777776443 458999999999999999999888765 33 3577787754
No 251
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.99 E-value=29 Score=31.71 Aligned_cols=26 Identities=27% Similarity=0.186 Sum_probs=22.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+.+|+++.||++++.--
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra 158 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYA 158 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46889999999999999998887654
No 252
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=38.69 E-value=26 Score=32.69 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.7
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
+.++..||.++|++..||++|++++.
T Consensus 1 ~~nI~qlA~~~g~~R~TV~~RL~~~~ 26 (152)
T PF07278_consen 1 KWNINQLAEAFGLHRQTVAKRLKGAN 26 (152)
T ss_pred CCCHHHHHHHHcccHHHHHHHHccCC
Confidence 35778899999999999999999997
No 253
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=38.67 E-value=51 Score=26.82 Aligned_cols=46 Identities=4% Similarity=0.166 Sum_probs=29.4
Q ss_pred HHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 149 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 149 lAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
+...+-....||.++|+.+||+.++|.+-.+ -.....|++.+....
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~----g~~~~~sl~~L~~~l 68 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN----GKIDDFSLDTLLRYL 68 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT----T-GCC--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc----CcccCCCHHHHHHHH
Confidence 4445566789999999999999999976443 233567788777663
No 254
>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=38.52 E-value=51 Score=31.59 Aligned_cols=28 Identities=11% Similarity=0.280 Sum_probs=25.6
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
..|+.+|++.++|+..||++.|+.|.+-
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4999999999999999999999999643
No 255
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=38.51 E-value=50 Score=29.56 Aligned_cols=40 Identities=15% Similarity=0.075 Sum_probs=32.8
Q ss_pred HHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 145 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 145 AALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+.+|||.+-.+...|..+|++..+|+...+++-+..+...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4667776544457999999999999999999999999654
No 256
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=38.37 E-value=30 Score=31.00 Aligned_cols=27 Identities=4% Similarity=0.012 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||...|+|..||++++..-.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999998887653
No 257
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=38.23 E-value=58 Score=23.82 Aligned_cols=26 Identities=8% Similarity=0.004 Sum_probs=24.5
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 58 LLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 58 tL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+..++|+.++++..++.+.+..|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999999874
No 258
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=37.95 E-value=38 Score=30.14 Aligned_cols=26 Identities=4% Similarity=-0.143 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.+|||...|+|..||++++.-.
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra 146 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQA 146 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999997654
No 259
>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=37.67 E-value=35 Score=27.91 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=24.5
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
+.+...++.++|....||.+||.+.++.+.
T Consensus 26 l~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 26 LNNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp HH-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HcCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356789999999999999999999999985
No 260
>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=37.60 E-value=60 Score=23.98 Aligned_cols=34 Identities=15% Similarity=0.228 Sum_probs=26.5
Q ss_pred HHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 49 ACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 49 ACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
+-..++-|.++.||+..++++..++-|....|..
T Consensus 11 ~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 11 ALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp CHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3345566789999999999999999887777766
No 261
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=37.46 E-value=4.1e+02 Score=29.18 Aligned_cols=50 Identities=10% Similarity=0.223 Sum_probs=30.9
Q ss_pred CCccchHHHHHhhhC---CCCc-HHHHHHHHHHHHHhhccccccCCChhHHHHH
Q 011262 96 VDPSIFLHKFTDRLL---PGGN-KKVCDTARDILASMKRDWITTGRKPSGLCGA 145 (490)
Q Consensus 96 vdP~~~I~Rf~s~L~---~~l~-~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaA 145 (490)
.||..++.|+...+. |-.+ +.....+..+++....-++-.|+.|.+=.+-
T Consensus 274 edp~~i~r~l~~~~~edi~~a~~~~~~~~~~~~~~~~~~i~~~e~~~~l~~~~~ 327 (472)
T PRK14962 274 KDYEVLIQQAIEDLVEDLERERANDIIQVSRQLLNILREIKFAEEKRLVCKLGS 327 (472)
T ss_pred CCHHHHHHHHHHHHHHHccCCCchHHHHHHHHHHHHHHHhCCcchHHHHHHHHH
Confidence 577777777766551 2123 5566666666666666667777777655554
No 262
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=37.37 E-value=45 Score=30.81 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||..+|+++.||+.++..-.
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456999999999999999999887764
No 263
>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=37.28 E-value=42 Score=28.82 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=24.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+..+||...|||+.||++++....
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 457999999999999999999998764
No 264
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=36.88 E-value=31 Score=31.62 Aligned_cols=25 Identities=8% Similarity=0.155 Sum_probs=22.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|.++||+++|+|..||+.++.-
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999998754
No 265
>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=36.79 E-value=3.9e+02 Score=25.68 Aligned_cols=27 Identities=4% Similarity=0.091 Sum_probs=23.3
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|+.+||...|||..||++..+..
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~~~~a 223 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRLEKKV 223 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356899999999999999999887654
No 266
>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=36.72 E-value=25 Score=33.00 Aligned_cols=45 Identities=20% Similarity=0.273 Sum_probs=0.0
Q ss_pred CChHHHHHHHHHHHHHhcC---------CCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 36 RRTEQVQASCLYLACRQKS---------KPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~~---------~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
++...+...+-+|+-+|.. .|.|+.|||+.+|+++.+|.|+...-
T Consensus 20 ~R~~TL~~v~~~iv~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~K 73 (160)
T PF04552_consen 20 QRNETLLRVAQAIVERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKNK 73 (160)
T ss_dssp ------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcCc
Confidence 3444555555666655532 59999999999999999999976643
No 267
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=36.67 E-value=1.1e+02 Score=33.63 Aligned_cols=18 Identities=22% Similarity=0.376 Sum_probs=12.9
Q ss_pred HHHHHhhhCHHHHHHHHHHHHH
Q 011262 362 KKIIWEEMNREYLEEQAAKEAA 383 (490)
Q Consensus 362 K~~iW~~~N~dyl~eq~~Ke~~ 383 (490)
|+.||| |+|+|++-|+-.
T Consensus 530 k~ELkm----d~lrerelresl 547 (641)
T KOG3915|consen 530 KTELKM----DFLRERELRESL 547 (641)
T ss_pred HHHHHH----HHHHHHHHHHHH
Confidence 677887 677777777654
No 268
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=36.45 E-value=34 Score=31.34 Aligned_cols=26 Identities=8% Similarity=0.115 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|..+||+.+|++..||++++..-
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra 158 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEA 158 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999988654
No 269
>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=36.27 E-value=33 Score=32.08 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=23.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+++|+|..||++|+.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 458999999999999999999987654
No 270
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=36.06 E-value=35 Score=32.33 Aligned_cols=43 Identities=16% Similarity=0.326 Sum_probs=33.1
Q ss_pred CCCCCHhhHHhHhccCH---------------HHHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 155 GLKFSKSDIVKIVHICE---------------ATLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse---------------~TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
...+||+|.|+.+|||. +|+++-|..|.+....++|....|..
T Consensus 16 ~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~s 73 (187)
T COG3620 16 ELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHS 73 (187)
T ss_pred HcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccC
Confidence 45689999999999998 46677777777777777777777664
No 271
>PRK09954 putative kinase; Provisional
Probab=35.99 E-value=47 Score=34.48 Aligned_cols=30 Identities=10% Similarity=0.329 Sum_probs=27.0
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
.+-++|+.+|++.++||..||++|++.|.+
T Consensus 14 ~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 14 RNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 334899999999999999999999999975
No 272
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=35.92 E-value=49 Score=30.87 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+..|+|+.||++++.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 458899999999999999999987654
No 273
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=35.50 E-value=2.3e+02 Score=28.15 Aligned_cols=105 Identities=11% Similarity=0.172 Sum_probs=61.4
Q ss_pred HhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccc--cccccCCcc-----chHHHHHhhhCCCCcHHHHHHHHH
Q 011262 51 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADES--NVLKQVDPS-----IFLHKFTDRLLPGGNKKVCDTARD 123 (490)
Q Consensus 51 R~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~--~~~~~vdP~-----~~I~Rf~s~L~~~l~~~V~~~A~~ 123 (490)
...|.-.|..|++..+++++.+|++-.+.+.+.-|+-+|- .... +-|. ..|..| |.|.-+.+|.+....
T Consensus 100 y~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~D-iGp~~tHK~~ii~~~---l~g~~~~eiar~t~H 175 (220)
T PF07900_consen 100 YDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHD-IGPGVTHKKIIIRLY---LKGKPTPEIARRTNH 175 (220)
T ss_pred HHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccc-cCCcchHHHHHHHHH---HcCCCHHHHHHHhcc
Confidence 3445567999999999999999999999999987654332 0000 1132 122333 222223333322221
Q ss_pred HHHHhhccccccCCChhHHHHHHHHHHH-----HhcCCCCCHhhHHhHhccCHHHHHH
Q 011262 124 ILASMKRDWITTGRKPSGLCGAALYVSA-----LTHGLKFSKSDIVKIVHICEATLMK 176 (490)
Q Consensus 124 Iv~~~~~~~l~~GR~PsgIaaAALylAa-----r~~g~~~t~~dIa~v~~Vse~TIrk 176 (490)
+|.+| -=|+-. .+.+...+..+|+.++|.|+..|..
T Consensus 176 --------------S~~av---~rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~e 216 (220)
T PF07900_consen 176 --------------SPEAV---DRYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKE 216 (220)
T ss_pred --------------CHHHH---HHHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 11111 112211 1356778899999999999988764
No 274
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=35.47 E-value=1.6e+02 Score=25.08 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.2
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.-.+...|+.+||+..|++++++.+.
T Consensus 68 ~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 68 RGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 34577899999999999999999863
No 275
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=35.47 E-value=37 Score=30.66 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=23.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+.+|++..||+.|+.--
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999998754
No 276
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.40 E-value=34 Score=32.13 Aligned_cols=27 Identities=15% Similarity=0.135 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+.+|||..||++|+.-..
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 468999999999999999999986553
No 277
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.37 E-value=52 Score=29.51 Aligned_cols=30 Identities=10% Similarity=0.121 Sum_probs=26.4
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.-.+|+.+|++.++++.+||.+.++.+.+-
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~ 81 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCK 81 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 446999999999999999999999998644
No 278
>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=35.30 E-value=56 Score=24.89 Aligned_cols=31 Identities=3% Similarity=-0.022 Sum_probs=27.2
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
+-..++.|+++.++|+..++.+-+..|.+.-
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4578999999999999999999999888753
No 279
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=35.30 E-value=2.2e+02 Score=28.41 Aligned_cols=43 Identities=16% Similarity=0.107 Sum_probs=32.6
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 79 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~ 79 (490)
....+..++-||.-....-..++.+||..+++++..|.+.|+.
T Consensus 195 ~~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 195 RERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE 237 (302)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3445566777776665555589999999999999999888763
No 280
>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=35.28 E-value=1.1e+02 Score=25.70 Aligned_cols=42 Identities=10% Similarity=0.050 Sum_probs=32.9
Q ss_pred HHHHHHHHHHh------cCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 42 QASCLYLACRQ------KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 42 aAACLYiACR~------~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+.||..-+|+ ...+.+..|||+.++++..++.++...|.+.
T Consensus 27 ~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 27 EFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred HHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34444434453 4678999999999999999999999998874
No 281
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.15 E-value=87 Score=25.27 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=25.7
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
..++++|++.++++..||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 5899999999999999999999999754
No 282
>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=35.07 E-value=27 Score=35.09 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=29.0
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHhhh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHE 203 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le~ 203 (490)
.|++|||+.+|||.+|+.+-|+.- ..-+.=|.+.-++.+++|-.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~--~~vs~~tr~rV~~~a~~lgY 45 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGN--PNVKPATRKKVLEVIKRLDY 45 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCC--CCCCHHHHHHHHHHHHHHCC
Confidence 489999999999999999998642 11223333444445444444
No 283
>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=35.06 E-value=63 Score=24.09 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=23.6
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
..++.+|++.++++.+|+.+.++.+..
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 399999999999999999999998864
No 284
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=35.06 E-value=24 Score=35.57 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=21.9
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHH
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
+.|++|||+.+|||.+|+++.|+.
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCC
Confidence 479999999999999999999964
No 285
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=34.66 E-value=32 Score=34.38 Aligned_cols=28 Identities=14% Similarity=0.230 Sum_probs=25.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
-.+++.|+++.++||+.|||+-+.++.+
T Consensus 18 ~~~~~~ela~~l~vS~~TiRRdL~~Le~ 45 (252)
T PRK10906 18 GYVSTEELVEHFSVSPQTIRRDLNDLAE 45 (252)
T ss_pred CCEeHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4589999999999999999999998854
No 286
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=34.61 E-value=1.5e+02 Score=27.03 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=26.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+++|..+|+..+|++..|+.+.+.+|...
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~ 198 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKD 198 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhC
Confidence 57999999999999999999999999744
No 287
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=34.59 E-value=49 Score=29.91 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=24.6
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 58 LLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 58 tL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
|.+++|..++|++.++.|+|..|.+.
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 78999999999999999999999985
No 288
>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=34.56 E-value=38 Score=26.66 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=18.5
Q ss_pred CCCCHhhHHhHh-----ccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIV-----HICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~-----~Vse~TIrkR~kE~~ 182 (490)
-..|..+|+..+ +||..||+++|++..
T Consensus 12 p~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g 43 (72)
T PF01498_consen 12 PRISAREIAQELQEAGISVSKSTIRRRLREAG 43 (72)
T ss_dssp ----HHHHHHHT---T--S-HHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHHHccCCcCHHHHHHHHHHcC
Confidence 347889999977 899999999999974
No 289
>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=34.55 E-value=39 Score=25.12 Aligned_cols=23 Identities=4% Similarity=0.346 Sum_probs=18.6
Q ss_pred CCHhhHHhHhccCHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
++.++|++.+|+|..||.+..++
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhc
Confidence 46789999999999999988874
No 290
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=34.51 E-value=1e+02 Score=24.69 Aligned_cols=45 Identities=18% Similarity=0.078 Sum_probs=36.4
Q ss_pred HHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHH
Q 011262 50 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLH 103 (490)
Q Consensus 50 CR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~ 103 (490)
.|..+.|+++.+.|+.+|+++..+.+....+.+-|-. .||+-...
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~---------LDPSG~~E 51 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ---------LDPSGHWE 51 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH---------cCCCCChH
Confidence 3667899999999999999999999998888886632 57765444
No 291
>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=34.50 E-value=1.2e+02 Score=26.51 Aligned_cols=34 Identities=9% Similarity=0.037 Sum_probs=26.3
Q ss_pred hcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhc
Q 011262 52 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLY 85 (490)
Q Consensus 52 ~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~ 85 (490)
.++--.|+.|+|..++|+..+|++..+.|--...
T Consensus 67 ~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~K 100 (119)
T PF01710_consen 67 EENPDATLRELAERLGVSPSTIWRALKRLGITRK 100 (119)
T ss_pred HHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhc
Confidence 4455689999999999999999987766554443
No 292
>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=34.47 E-value=52 Score=29.94 Aligned_cols=27 Identities=15% Similarity=0.140 Sum_probs=23.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+.+|||..||++++.-..
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~ 160 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRAL 160 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999999887553
No 293
>PRK15340 transcriptional regulator InvF; Provisional
Probab=34.46 E-value=2.1e+02 Score=28.27 Aligned_cols=29 Identities=3% Similarity=-0.020 Sum_probs=23.0
Q ss_pred hcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 52 QKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 52 ~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
....+.++.++|..+++++..+.|.|++.
T Consensus 121 ~~~~~~sleeLA~~~gvS~r~f~RlFk~~ 149 (216)
T PRK15340 121 QSTSGNTMRMLGEDYGVSYTHFRRLCSRA 149 (216)
T ss_pred CccCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34567899999999999998888866654
No 294
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=34.42 E-value=42 Score=31.87 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=28.3
Q ss_pred hcCCCCCHhhHHhHhccC-HHHHHHHHHHHhcC
Q 011262 153 THGLKFSKSDIVKIVHIC-EATLMKRLIEFENT 184 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vs-e~TIrkR~kE~~~t 184 (490)
-+++..|+++||+.++++ .+|+.++++.|.+-
T Consensus 21 ~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 21 STGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 357889999999999998 99999999999644
No 295
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=34.30 E-value=1.6e+02 Score=32.95 Aligned_cols=104 Identities=8% Similarity=0.015 Sum_probs=61.4
Q ss_pred CCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccc
Q 011262 55 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWIT 134 (490)
Q Consensus 55 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~ 134 (490)
-|+|..++|..++||..+|.+-...|...|.-...... .....| .|.. .+..-. ..+.+.
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i---~~~~Gy------~l~~-~~~~~~---~~~~~~------- 75 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSI---SGSAKY------HLEI-LNRRSL---FQLLQK------- 75 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhhe---ecCCce------EEEe-CCHHHH---HHHHhc-------
Confidence 48999999999999999999999999887753211100 000011 1210 011100 111110
Q ss_pred cCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 135 TGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 135 ~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
..|.-. . ++...+....++..++|+...||++||.+-+++++..
T Consensus 76 --~~~e~~---~-il~~Ll~~~~~~~~~La~~l~vS~sTi~~dl~~v~~~ 119 (584)
T PRK09863 76 --SDNEDR---L-LLLRLLLNTFTPMAQLASALNLSRTWVAERLPRLNQR 119 (584)
T ss_pred --CCHHHH---H-HHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence 012222 1 1211223457899999999999999999999888653
No 296
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=34.21 E-value=29 Score=34.83 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=20.5
Q ss_pred CHhhHHhHhccCHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|++|||+.+|||.+|+.+-|+.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999964
No 297
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=33.95 E-value=70 Score=28.97 Aligned_cols=38 Identities=13% Similarity=0.292 Sum_probs=31.2
Q ss_pred HHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 147 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 147 LylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+|.+-.-.+-+.|..+||+.++.+.+|+.+.++-+.+.
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 45544435678999999999999999999999998644
No 298
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=33.82 E-value=40 Score=30.38 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=23.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||...|+|++||+.|+.--
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra 145 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNA 145 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999987654
No 299
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=33.81 E-value=4.7e+02 Score=25.67 Aligned_cols=27 Identities=4% Similarity=0.133 Sum_probs=23.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|.++||...|||..||++++...
T Consensus 215 ~~~~s~~EIA~~lgis~~tV~~~~~ra 241 (251)
T PRK07670 215 KEELTLTEIGQVLNLSTSRISQIHSKA 241 (251)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 367899999999999999999998664
No 300
>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=33.72 E-value=29 Score=34.87 Aligned_cols=22 Identities=23% Similarity=0.231 Sum_probs=20.1
Q ss_pred CHhhHHhHhccCHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|++|||+.+|||.+|+.+-|+.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6799999999999999999954
No 301
>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=33.68 E-value=47 Score=24.19 Aligned_cols=39 Identities=5% Similarity=0.089 Sum_probs=29.1
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
....|+.++|..+||+..||++..+-- ...+++.+..++
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g~-----~~~~~~~~~~i~ 51 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENGK-----PTVRLDKVLRVL 51 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCCC-----CCCCHHHHHHHH
Confidence 357899999999999999999876432 235666666654
No 302
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.62 E-value=42 Score=28.81 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=24.8
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.....|+.++|+.+|||..||++...--.
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 45689999999999999999999876553
No 303
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=33.61 E-value=75 Score=32.41 Aligned_cols=26 Identities=4% Similarity=0.009 Sum_probs=17.8
Q ss_pred CCcCHHHHHHHhCc-CHHHHHHHHHHH
Q 011262 55 KPFLLIDFSNYLNI-NVYELGAVYLQL 80 (490)
Q Consensus 55 ~prtL~DIa~v~~v-sv~~Lgr~yk~L 80 (490)
...++.+||..+|. +...+.|.|++.
T Consensus 282 ~~~~i~~IA~~~Gf~~~s~F~r~Fk~~ 308 (322)
T PRK09393 282 SALSIDQIAERAGFGSEESLRHHFRRR 308 (322)
T ss_pred CCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 35777888877776 556776666554
No 304
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=33.60 E-value=82 Score=28.33 Aligned_cols=46 Identities=11% Similarity=0.162 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 38 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 38 ~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.++-.-+.+|++-...|.+.+..+||..++|+...|.+++..|.+.
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 3444556677775556778899999999999999999999999885
No 305
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.59 E-value=40 Score=31.55 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.+|||..+|+|+.||++++.--.
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar 171 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARAR 171 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999986553
No 306
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=33.53 E-value=40 Score=31.33 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=29.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhc---CCCCCCCHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFEN---TDSGSLTIEDFMAR 197 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~---t~s~~Lt~~ef~~~ 197 (490)
...|.++||.++|+|..||++++.--.. ......+.++|.+.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~~~ 181 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEFKEL 181 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHHHHH
Confidence 4589999999999999999988654321 11244555666443
No 307
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=33.33 E-value=1.3e+02 Score=31.83 Aligned_cols=51 Identities=12% Similarity=0.374 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 011262 39 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 105 (490)
Q Consensus 39 ~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf 105 (490)
..+..++-||-- +.+.++.+||..++++...|.|.|++... ..|..|+.++
T Consensus 85 ~~i~~a~~~I~~---~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G-------------~TP~~yl~~~ 135 (353)
T PRK15435 85 DKITHACRLLEQ---ETPVTLEALADQVAMSPFHLHRLFKATTG-------------MTPKAWQQAW 135 (353)
T ss_pred HHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHHC-------------cCHHHHHHHH
Confidence 446666777633 56899999999999999999888776543 3577777553
No 308
>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=33.27 E-value=39 Score=30.00 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|..+||..+|+++.||++++.-.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra 145 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRA 145 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999988654
No 309
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=33.15 E-value=3.5e+02 Score=27.25 Aligned_cols=27 Identities=11% Similarity=0.228 Sum_probs=22.7
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+|+++|++++|||+++|.+.-+..
T Consensus 210 ~eelt~kEI~~~LgISes~VSql~kka 236 (247)
T COG1191 210 KEELTQKEIAEVLGISESRVSRLHKKA 236 (247)
T ss_pred HhccCHHHHHHHhCccHHHHHHHHHHH
Confidence 467999999999999999998665543
No 310
>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=33.13 E-value=53 Score=27.76 Aligned_cols=22 Identities=23% Similarity=0.057 Sum_probs=19.1
Q ss_pred CCCHhhHHhHhccCHHHHHHHH
Q 011262 157 KFSKSDIVKIVHICEATLMKRL 178 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~ 178 (490)
..|.++||+.+|||..||.+..
T Consensus 50 G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 3699999999999999998833
No 311
>PRK09956 hypothetical protein; Provisional
Probab=33.12 E-value=1.3e+02 Score=31.01 Aligned_cols=79 Identities=13% Similarity=0.196 Sum_probs=54.6
Q ss_pred CccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhccccccCC---ChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHH
Q 011262 97 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR---KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEAT 173 (490)
Q Consensus 97 dP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~GR---~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~T 173 (490)
++..++..+...+.. ....++..|..+-+.....++..|| .=.|..-+++-+|-++.....+...|++++|.|...
T Consensus 224 ~~~~~i~~l~~~~~~-~~e~iMTiAe~l~qeG~e~G~q~G~~eG~qeG~~e~~~eiA~~mL~~G~~~~~i~~~tgLs~ee 302 (308)
T PRK09956 224 RFTRFIQEIAERSPL-QKERLMTIAERLRQEGHQIGWQEGKLEGLQEGMHEQAIKIALRMLEQGFDRDQVLAATQLSEAD 302 (308)
T ss_pred hHHHHHHHHHHhCcc-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHH
Confidence 466777777777641 2345777777776665554555554 112344456778888888889999999999999998
Q ss_pred HHH
Q 011262 174 LMK 176 (490)
Q Consensus 174 Irk 176 (490)
|.+
T Consensus 303 l~~ 305 (308)
T PRK09956 303 LAA 305 (308)
T ss_pred HHH
Confidence 875
No 312
>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=33.12 E-value=53 Score=30.00 Aligned_cols=41 Identities=20% Similarity=0.129 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 141 GLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 141 gIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
-|..|++=|.....=.++|+++||+.+||+.+|.-..|+.-
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK 47 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK 47 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence 46666665555333346999999999999999998877665
No 313
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=33.01 E-value=53 Score=29.63 Aligned_cols=27 Identities=19% Similarity=0.222 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||...||++.||++++..-.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~ 152 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAK 152 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678999999999999999999986653
No 314
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=32.79 E-value=38 Score=32.89 Aligned_cols=26 Identities=4% Similarity=0.142 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+|||..||++++.--
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA 222 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999886543
No 315
>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=32.71 E-value=70 Score=23.51 Aligned_cols=27 Identities=7% Similarity=0.038 Sum_probs=19.9
Q ss_pred cCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 57 FLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 57 rtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+..|||..+|+++.++...+..-.+.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 578999999999999998877665544
No 316
>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=32.60 E-value=52 Score=29.67 Aligned_cols=27 Identities=7% Similarity=0.084 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||...|+|+.||++++.-..
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAI 163 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999987653
No 317
>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=32.35 E-value=2.3e+02 Score=21.67 Aligned_cols=44 Identities=11% Similarity=0.094 Sum_probs=30.5
Q ss_pred HHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 21 KRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 21 ~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
.++++.|++.|+..--+ -.++.|+|+.+||+..++....+.-.+
T Consensus 6 ~e~L~~A~~~GYfd~PR------------------~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 6 REILKAAYELGYFDVPR------------------RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred HHHHHHHHHcCCCCCCC------------------cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45666777777654211 258999999999999888776655444
No 318
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=32.28 E-value=2e+02 Score=31.14 Aligned_cols=110 Identities=8% Similarity=0.057 Sum_probs=62.3
Q ss_pred hcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhcc
Q 011262 52 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD 131 (490)
Q Consensus 52 ~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~ 131 (490)
..+.+.+..++|+.++||..+|++-...|...|.-...+.. ..+. ...+.+ .... +......-...
T Consensus 15 ~~~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~---~~~~------~~~~~~-~~~~----~~~~~~~~~~~ 80 (491)
T COG3711 15 LKNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPII---KRKG------GGYILE-EDER----ALELEELQELT 80 (491)
T ss_pred HhCCCCCHHHHHHHhCccHHHHHHHHHHHHHHHHhCCceEE---ecCC------CcEEec-CcHH----HHHHHhccccc
Confidence 45678899999999999999999999999999975443311 0111 000000 0000 00000000000
Q ss_pred ccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 132 WITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 132 ~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
... ..--..+.+...+.+..++..++++.+.||.+||.+-++..
T Consensus 81 ~~~------~~er~~~~ll~~~~~~~~~l~~La~~l~vs~~ti~~dl~~v 124 (491)
T COG3711 81 SYD------KDERIIIILLLLLLSELLSLHELADELFVSKSTIINDLKDV 124 (491)
T ss_pred ccC------hHHHHHHHHHHHHhcChhhHHHHHHHHHhHHHHHHHHHHHH
Confidence 000 11111122222222267899999999999999999988863
No 319
>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=32.14 E-value=80 Score=26.28 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=29.7
Q ss_pred HHHHHHHHhcCCCCCHhhHHhHhc-cCHHHHHHHHHHHhc
Q 011262 145 AALYVSALTHGLKFSKSDIVKIVH-ICEATLMKRLIEFEN 183 (490)
Q Consensus 145 AALylAar~~g~~~t~~dIa~v~~-Vse~TIrkR~kE~~~ 183 (490)
-|.|++-... ..|..+|++.+| .+.+||...++-+..
T Consensus 34 ia~yl~~~~~--~~s~~~Ig~~fg~r~hStV~~a~~ri~~ 71 (90)
T cd06571 34 IAMYLARELT--GLSLPEIGRAFGGRDHSTVLHAVRKIEE 71 (90)
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence 4667766654 578899999999 999999988888753
No 320
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=32.08 E-value=5.2e+02 Score=25.66 Aligned_cols=25 Identities=12% Similarity=0.213 Sum_probs=22.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|.++||..+|+|..||++++..
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~r 251 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTK 251 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5689999999999999999987754
No 321
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=32.02 E-value=92 Score=27.05 Aligned_cols=41 Identities=12% Similarity=0.160 Sum_probs=32.2
Q ss_pred HHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 144 GAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 144 aAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|.=+-|...+..-..||++|+.-.|||-+||.+--..++-.
T Consensus 47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~ 87 (103)
T COG2973 47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTA 87 (103)
T ss_pred HHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccC
Confidence 33445666677788999999999999999998877777533
No 322
>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=31.98 E-value=99 Score=22.27 Aligned_cols=29 Identities=10% Similarity=0.063 Sum_probs=22.4
Q ss_pred hcCCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 52 QKSKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 52 ~~~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
+.+..+++.+||..+|++..++.+.+..|
T Consensus 13 q~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 13 QEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 44567899999999999999999888776
No 323
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=31.92 E-value=45 Score=30.99 Aligned_cols=26 Identities=27% Similarity=0.272 Sum_probs=23.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|..|||..+||+..||++|+..=
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra 167 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRA 167 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999988754
No 324
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=31.86 E-value=43 Score=31.78 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=22.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+|+|+.||+.|+.--
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RA 179 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRA 179 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56889999999999999999887654
No 325
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.80 E-value=41 Score=31.36 Aligned_cols=26 Identities=27% Similarity=0.139 Sum_probs=22.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+.+|+|..||+.++.--
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra 181 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQG 181 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45899999999999999999877543
No 326
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=31.74 E-value=29 Score=35.00 Aligned_cols=23 Identities=22% Similarity=0.150 Sum_probs=20.9
Q ss_pred CCHhhHHhHhccCHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
.|++|||+.+|||.+|+++.++.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcC
Confidence 48999999999999999999953
No 327
>smart00351 PAX Paired Box domain.
Probab=31.74 E-value=1.8e+02 Score=25.78 Aligned_cols=60 Identities=12% Similarity=0.145 Sum_probs=33.2
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCC-----CCChHHH-HHHHHHHH-HHhcCCCcCHHHHHHHh
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTK-----GRRTEQV-QASCLYLA-CRQKSKPFLLIDFSNYL 66 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~r-----GR~~~~V-aAACLYiA-CR~~~~prtL~DIa~v~ 66 (490)
..||..||++ ..++..-. +++.+.|.+. |+++..+ .....||. .+.++-..++.+|++.+
T Consensus 37 ~~iA~~~gvs--~~tV~kwi---~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L 103 (125)
T smart00351 37 CDISRQLCVS--HGCVSKIL---GRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRL 103 (125)
T ss_pred HHHHHHHCcC--HHHHHHHH---HHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 5789999999 66555444 4444443332 3232222 12223333 45666677888888765
No 328
>PF13730 HTH_36: Helix-turn-helix domain
Probab=31.50 E-value=1.1e+02 Score=22.61 Aligned_cols=25 Identities=8% Similarity=0.017 Sum_probs=23.4
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 58 LLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 58 tL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
+...||+.++++..++.++.+.|.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999998876
No 329
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=31.34 E-value=37 Score=27.47 Aligned_cols=24 Identities=17% Similarity=0.351 Sum_probs=20.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
...||.+.|+.+|||..||-.-=+
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHc
Confidence 568999999999999999965433
No 330
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=31.33 E-value=34 Score=34.74 Aligned_cols=43 Identities=21% Similarity=0.147 Sum_probs=29.4
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHHHhh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELH 202 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le 202 (490)
.|++|||+.+|||.+|+.+-|+.= ..-+.-|-+-.++.+++|-
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~--~~Vs~~tr~kV~~~a~elg 44 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNS--ALVSADTREAVMKAVSELG 44 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCC--CCCCHHHHHHHHHHHHHHC
Confidence 589999999999999999999631 1223444444555544443
No 331
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=31.32 E-value=77 Score=29.23 Aligned_cols=39 Identities=21% Similarity=0.258 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 145 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 145 AALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+.+|||. ..+..++.++||+..+|+..-+++-+..+...
T Consensus 13 ~L~~LA~-~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 13 MLMYCAA-NDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHHHHHh-CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4567774 34556899999999999999999999998643
No 332
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=31.22 E-value=46 Score=30.29 Aligned_cols=27 Identities=22% Similarity=0.193 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||...|+|..||++++.--.
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar 153 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRAR 153 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 567899999999999999999887654
No 333
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=31.14 E-value=59 Score=32.11 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=23.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.+|||+.+|+|+.||++|+.--.
T Consensus 131 eg~S~~EIAe~LgiS~~tVksrL~Rar 157 (228)
T PRK06704 131 FQYSIADIAKVCSVSEGAVKASLFRSR 157 (228)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 458999999999999999998876543
No 334
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=30.92 E-value=34 Score=34.74 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=20.5
Q ss_pred CCHhhHHhHhccCHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~k 179 (490)
.|++|||+.+|||.+|+.+-|+
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhC
Confidence 4899999999999999999985
No 335
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=30.74 E-value=1.1e+02 Score=26.66 Aligned_cols=42 Identities=24% Similarity=0.101 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhcC-CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 143 CGAALYVSALTHG-LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 143 aaAALylAar~~g-~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
|-.++++-++..+ .+.|..+|++.++++..++++-+..+...
T Consensus 10 al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 10 ALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3334444444444 37999999999999999999999999643
No 336
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=30.59 E-value=47 Score=32.82 Aligned_cols=25 Identities=20% Similarity=0.474 Sum_probs=23.7
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|+.|++-.+++|..||++.++++.
T Consensus 106 LT~~Dla~LL~~S~~TI~~~i~~yq 130 (220)
T PF07900_consen 106 LTQEDLAMLLGISPRTISKDIKEYQ 130 (220)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 7899999999999999999999995
No 337
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=30.55 E-value=66 Score=31.85 Aligned_cols=47 Identities=15% Similarity=0.161 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHhcC---CCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 139 PSGLCGAALYVSALTHG---LKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 139 PsgIaaAALylAar~~g---~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
|.||-...+=....... ...|-.++|+.+|+|.+|+|+.+.-+....
T Consensus 152 PkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~ 201 (224)
T COG4565 152 PKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNG 201 (224)
T ss_pred CCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcC
No 338
>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=30.43 E-value=49 Score=30.51 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+..+||+.+|+++.||++++.-.+
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar 179 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAR 179 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 568899999999999999999886654
No 339
>PRK13501 transcriptional activator RhaR; Provisional
Probab=30.42 E-value=1.9e+02 Score=28.91 Aligned_cols=70 Identities=9% Similarity=0.091 Sum_probs=36.5
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHh-cCCCcCHHHHHHHhCc-CHHHHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNI-NVYELGAVYLQ 79 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~-~~~prtL~DIa~v~~v-sv~~Lgr~yk~ 79 (490)
.++|..++++ .. .-.++|++.....+.+ .+---=|-.||+. .....++.|||..+|- +...+.|.|++
T Consensus 196 ~~lA~~~~lS--~~---~l~r~Fk~~~G~T~~q-----yi~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FKk 265 (290)
T PRK13501 196 ADFCHKNQLV--ER---SLKQLFRQQTGMSISH-----YLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTR 265 (290)
T ss_pred HHHHHHHCcC--HH---HHHHHHHHHHCcCHHH-----HHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 4566666666 22 2244555544433322 2222234445554 3455677777777776 55666666655
Q ss_pred HH
Q 011262 80 LC 81 (490)
Q Consensus 80 L~ 81 (490)
..
T Consensus 266 ~~ 267 (290)
T PRK13501 266 EA 267 (290)
T ss_pred HH
Confidence 43
No 340
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=30.41 E-value=82 Score=34.47 Aligned_cols=43 Identities=19% Similarity=0.303 Sum_probs=32.3
Q ss_pred CChHHHHHHHHHHHHHhc-----C----CCcCHHHHHHHhCcCHHHHHHHHH
Q 011262 36 RRTEQVQASCLYLACRQK-----S----KPFLLIDFSNYLNINVYELGAVYL 78 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~-----~----~prtL~DIa~v~~vsv~~Lgr~yk 78 (490)
++..++.-.+-+|+-+|. | .|.|++|||+.+|+.+.||.|+..
T Consensus 314 ~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 314 QRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence 344556666666666664 2 599999999999999999998643
No 341
>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=30.26 E-value=48 Score=29.83 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||..+|+|..||++++.-..
T Consensus 125 ~g~s~~eIA~~lgis~~tV~~~l~ra~ 151 (162)
T TIGR02983 125 EDLSEAQVAEALGISVGTVKSRLSRAL 151 (162)
T ss_pred hcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 468899999999999999999887653
No 342
>PRK13698 plasmid-partitioning protein; Provisional
Probab=30.17 E-value=57 Score=34.14 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=29.4
Q ss_pred HHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 148 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 148 ylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|....+.++..|+.+||+.+|+|.++|.+.++-+.
T Consensus 167 y~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~ 201 (323)
T PRK13698 167 YASRLQNEFAGNISALADAENISRKIITRCINTAK 201 (323)
T ss_pred HHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHc
Confidence 43444567889999999999999999999998873
No 343
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.16 E-value=48 Score=30.66 Aligned_cols=26 Identities=12% Similarity=0.166 Sum_probs=22.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+.++||+..|+|..||++++.--
T Consensus 150 ~~~s~~eIA~~lgis~~~V~~~l~ra 175 (186)
T PRK13919 150 QGYTHREAAQLLGLPLGTLKTRARRA 175 (186)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46889999999999999999887654
No 344
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=30.10 E-value=59 Score=29.86 Aligned_cols=27 Identities=11% Similarity=0.069 Sum_probs=23.4
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|..+||+.+|++..||++++.--
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~Ra 159 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVAKA 159 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 456889999999999999999988653
No 345
>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=30.06 E-value=59 Score=29.78 Aligned_cols=27 Identities=15% Similarity=0.043 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|+++||+.+|+|+.||+++.+...
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 567999999999999999998777654
No 346
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=30.03 E-value=61 Score=25.56 Aligned_cols=41 Identities=15% Similarity=0.113 Sum_probs=30.2
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
+.....|+.++|+.+||+..||.+.++-- ..++++....++
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~g~-----~~~~~~~~~~l~ 54 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVNGR-----RGITADMALRLA 54 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCC-----CCCCHHHHHHHH
Confidence 44567899999999999999999976522 345666655554
No 347
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.02 E-value=49 Score=31.05 Aligned_cols=26 Identities=23% Similarity=0.253 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+|+|+.||+.|+.--
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~RA 174 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLYRA 174 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46889999999999999999887654
No 348
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=30.01 E-value=70 Score=32.28 Aligned_cols=27 Identities=15% Similarity=0.236 Sum_probs=24.5
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
.++..++++.++||+.|||+=+.++.+
T Consensus 31 ~vtv~eLa~~l~VS~~TIRRDL~~Le~ 57 (269)
T PRK09802 31 SVQVNDLSALYGVSTVTIRNDLAFLEK 57 (269)
T ss_pred CEeHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 389999999999999999999998853
No 349
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=30.00 E-value=48 Score=30.76 Aligned_cols=26 Identities=12% Similarity=-0.032 Sum_probs=23.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+..|||..|+++++.--
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra 173 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRS 173 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHH
Confidence 56899999999999999999988654
No 350
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=29.99 E-value=77 Score=29.47 Aligned_cols=36 Identities=14% Similarity=0.146 Sum_probs=29.5
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
+||.... .+.....++||+..+|+.+|+.+-++.+.
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~ 49 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLE 49 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHH
Confidence 5665554 56678899999999999999998888875
No 351
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=29.94 E-value=48 Score=32.19 Aligned_cols=27 Identities=26% Similarity=0.295 Sum_probs=24.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+.+|||+.||++++.-..
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr 175 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARAR 175 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999988764
No 352
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=29.91 E-value=39 Score=33.75 Aligned_cols=27 Identities=26% Similarity=0.377 Sum_probs=24.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
-.+++.|+++.++||+.|||+=+.++.
T Consensus 18 g~v~v~eLa~~~~VS~~TIRRDL~~Le 44 (253)
T COG1349 18 GKVSVEELAELFGVSEMTIRRDLNELE 44 (253)
T ss_pred CcEEHHHHHHHhCCCHHHHHHhHHHHH
Confidence 358899999999999999999888884
No 353
>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=29.89 E-value=3.3e+02 Score=26.82 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=35.5
Q ss_pred HHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 148 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 148 ylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
||... +...+|+.+||+.+|+|..++.+.++..- .+|+-+|...
T Consensus 194 ~I~~~-~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~-----G~t~~~yi~~ 237 (287)
T TIGR02297 194 LIEEN-YKQHLRLPEYADRLGISESRLNDICRRFS-----ALSPKRLIIE 237 (287)
T ss_pred HHHHh-hccCCCHHHHHHHHCCCHHHHHHHHHHHh-----CCCHHHHHHH
Confidence 55444 34589999999999999999999999973 5678888554
No 354
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=29.79 E-value=52 Score=29.61 Aligned_cols=25 Identities=8% Similarity=0.070 Sum_probs=21.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|.+|||+.+|++..||+.++.-
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~r 148 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRD 148 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4688999999999999999988553
No 355
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=29.77 E-value=84 Score=28.22 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=24.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-..++++|++.++|+.+||+..++.+.+-
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 34588999999999999999999998543
No 356
>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=29.76 E-value=68 Score=24.43 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=23.2
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+....|+..+||.+||.++++.+.+.
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~ 40 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEE 40 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHH
Confidence 78889999999999999999999643
No 357
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=29.76 E-value=51 Score=30.51 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||...|+|..||++|+.--.
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~ 168 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAK 168 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999987654
No 358
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=29.47 E-value=51 Score=32.81 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=24.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
-.+++.++++.++||+.|||+=++++.
T Consensus 20 ~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 20 DKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 458999999999999999999998874
No 359
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=29.45 E-value=1.5e+02 Score=28.43 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=35.1
Q ss_pred CChHHHHHHHHHHHHHhcC------CCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 36 RRTEQVQASCLYLACRQKS------KPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~~------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
++...-.|..|+--+...+ +|.+..|||+.+|++..++.|+++.|.+.
T Consensus 147 ~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~ 200 (236)
T PRK09392 147 RSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASH 200 (236)
T ss_pred CCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhC
Confidence 4555555555554333332 47778999999999999999999998874
No 360
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=29.44 E-value=80 Score=30.06 Aligned_cols=29 Identities=7% Similarity=0.059 Sum_probs=25.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-.+++.++++.++||+.|||+=+.++.+-
T Consensus 20 ~~~~~~~La~~~~vS~~TiRRDl~~L~~~ 48 (185)
T PRK04424 20 PFITDEELAEKFGVSIQTIRLDRMELGIP 48 (185)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence 35899999999999999999999999644
No 361
>PRK11050 manganese transport regulator MntR; Provisional
Probab=29.44 E-value=88 Score=28.71 Aligned_cols=30 Identities=17% Similarity=0.144 Sum_probs=27.0
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+-.+++.+|++.++|+.+||++.++.|...
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~ 78 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARD 78 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 457899999999999999999999999754
No 362
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.19 E-value=52 Score=30.45 Aligned_cols=26 Identities=8% Similarity=0.086 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+|+|+.||++++..-
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~ra 169 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRG 169 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998654
No 363
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=29.19 E-value=49 Score=31.01 Aligned_cols=27 Identities=19% Similarity=0.268 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||+.+|++..||++++.--.
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar 177 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRAR 177 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999887653
No 364
>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=29.18 E-value=54 Score=29.26 Aligned_cols=27 Identities=11% Similarity=0.069 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||+.+|+|..||+.++.-.+
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar 152 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLR 152 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568999999999999999999876653
No 365
>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=29.13 E-value=65 Score=24.98 Aligned_cols=28 Identities=11% Similarity=0.099 Sum_probs=24.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
..-++++||+.+||+..||.+..+...-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~~W 39 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRYKW 39 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhhCc
Confidence 4678999999999999999999888753
No 366
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=29.05 E-value=64 Score=33.72 Aligned_cols=43 Identities=19% Similarity=0.167 Sum_probs=33.0
Q ss_pred HHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHH
Q 011262 150 SALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIE 192 (490)
Q Consensus 150 Aar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ 192 (490)
|+..+....||.+||+..|||+.||++-+..-++---=++++.
T Consensus 19 A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~ 61 (321)
T COG2390 19 AWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN 61 (321)
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence 3344567899999999999999999999988766544444443
No 367
>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=29.00 E-value=52 Score=28.10 Aligned_cols=24 Identities=21% Similarity=0.220 Sum_probs=21.1
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|..+||+.+||+..|||...+++.
T Consensus 2 ti~EvA~~~gVs~~tLR~ye~~~g 25 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYWETEFP 25 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcC
Confidence 678999999999999998887753
No 368
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.00 E-value=62 Score=22.06 Aligned_cols=39 Identities=8% Similarity=0.112 Sum_probs=27.1
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
..++|..++++.+|++..||.+.... . ...+.+.+..+.
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~~----~-~~~~~~~~~~i~ 46 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIENG----K-RKPSLETLKKLA 46 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC----C-CCCCHHHHHHHH
Confidence 35689999999999999999775431 1 233566655553
No 369
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=28.97 E-value=1.4e+02 Score=21.64 Aligned_cols=30 Identities=7% Similarity=0.144 Sum_probs=26.5
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+-|.++.||+..++++..++.+....|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 567899999999999999999988888873
No 370
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.93 E-value=99 Score=22.31 Aligned_cols=25 Identities=4% Similarity=0.006 Sum_probs=16.8
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHH
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYL 78 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk 78 (490)
..-.++.+||..++++..+|.+..+
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 3448899999999999999988654
No 371
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=28.79 E-value=1.2e+02 Score=25.38 Aligned_cols=38 Identities=13% Similarity=0.165 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 143 CGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 143 aaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
.-+.-|+.. ....+.++.+||..+|+|..++.++++..
T Consensus 23 ~~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~ 60 (127)
T COG2207 23 ARALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKE 60 (127)
T ss_pred HHHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 355555655 66666999999999999999999999954
No 372
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=28.77 E-value=6.8e+02 Score=26.01 Aligned_cols=24 Identities=13% Similarity=0.098 Sum_probs=20.7
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRL 178 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~ 178 (490)
+.+.|+.+|++.+|||...||+--
T Consensus 280 ~~~~Tl~eIa~~lgvS~eRVrQIe 303 (324)
T PRK07921 280 GQPRTLDQIGKLFGLSRERVRQIE 303 (324)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHH
Confidence 357999999999999999998653
No 373
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=28.69 E-value=63 Score=29.26 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=22.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||...|+++.||++++..-
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra 168 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRA 168 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56799999999999999999887654
No 374
>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=28.64 E-value=79 Score=27.26 Aligned_cols=30 Identities=13% Similarity=0.117 Sum_probs=26.3
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+-..|+.+|++.++++.+|+.+.++.+.+-
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 346899999999999999999999998644
No 375
>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=28.54 E-value=5.8e+02 Score=25.10 Aligned_cols=27 Identities=7% Similarity=-0.032 Sum_probs=23.1
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|+++||..+|||..+|++..+.-
T Consensus 220 ~~~~t~~eIA~~lgis~~~V~~~~~ra 246 (254)
T TIGR02850 220 FEGKTQMEVAEEIGISQAQVSRLEKAA 246 (254)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356899999999999999999887654
No 376
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=28.51 E-value=76 Score=29.76 Aligned_cols=26 Identities=8% Similarity=0.062 Sum_probs=22.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|..+||+..|++..||++++.--
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra 182 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDG 182 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHH
Confidence 45999999999999999999887543
No 377
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=28.49 E-value=53 Score=30.88 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=22.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+||+..||++|+.--
T Consensus 149 ~g~s~~EIA~~lg~s~~tV~~rl~ra 174 (192)
T PRK09643 149 QGYSVADAARMLGVAEGTVKSRCARG 174 (192)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45899999999999999999998543
No 378
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=28.45 E-value=65 Score=30.38 Aligned_cols=27 Identities=15% Similarity=0.046 Sum_probs=23.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+..++|+.||+.....+.
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 457888999999999999999988874
No 379
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=28.36 E-value=54 Score=29.88 Aligned_cols=27 Identities=22% Similarity=0.301 Sum_probs=23.3
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||..+|+|..||++++.--.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar 161 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYAR 161 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567899999999999999998886653
No 380
>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=28.19 E-value=74 Score=24.69 Aligned_cols=31 Identities=16% Similarity=0.086 Sum_probs=27.1
Q ss_pred cCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 53 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 53 ~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
..-+.|..|||..++++..++.++.+.|.+.
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4457899999999999999999998888874
No 381
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=28.10 E-value=1.2e+02 Score=23.02 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=24.2
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
.+-+.++.+|++.++++..|+.+.++.+.+-
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4677999999999999999999999998644
No 382
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=28.01 E-value=3.7e+02 Score=28.24 Aligned_cols=78 Identities=13% Similarity=0.219 Sum_probs=0.0
Q ss_pred CcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhcccccc
Q 011262 56 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITT 135 (490)
Q Consensus 56 prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l~~ 135 (490)
|+++.++|+.++++.-+|-|.|++-.. ..|..|..++ =.+.|.+|+..
T Consensus 236 plsl~~LA~~~~~S~R~leRlF~~~lG-------------~sP~~yy~~l-----------RL~~Ar~LL~~-------- 283 (328)
T COG4977 236 PLSLEELADRAGLSRRQLERLFRAELG-------------VSPARYYLRL-----------RLERARRLLEQ-------- 283 (328)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHhC-------------CCHHHHHHHH-----------HHHHHHHHHHh--------
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhc-cCHHHHHHHHHHHhcCC
Q 011262 136 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH-ICEATLMKRLIEFENTD 185 (490)
Q Consensus 136 GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~-Vse~TIrkR~kE~~~t~ 185 (490)
-+.++.+||..+| ++.+..++.|++....+
T Consensus 284 --------------------t~~si~~IA~~~GF~sa~~fsr~fr~~fg~~ 314 (328)
T COG4977 284 --------------------TRLSIAEIAVACGFSSASHFSRAFRRQFGLS 314 (328)
T ss_pred --------------------CCCcHHHHHHHhCCCCHHHHHHHHHHHhCCC
No 383
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=28.01 E-value=55 Score=30.76 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||..+|+|+.||+.++.-..
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRAR 169 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999987664
No 384
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=27.96 E-value=66 Score=31.72 Aligned_cols=30 Identities=20% Similarity=0.245 Sum_probs=26.6
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
...+|+.++++.++++..|+.++++.|.+-
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 356899999999999999999999999643
No 385
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.89 E-value=62 Score=29.22 Aligned_cols=26 Identities=23% Similarity=0.212 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+..+||...|+|..||++++..-
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra 165 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRA 165 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999887664
No 386
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=27.88 E-value=1.2e+02 Score=32.94 Aligned_cols=68 Identities=13% Similarity=0.151 Sum_probs=48.6
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCCChHHHHHH---HHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 14 DEIVHVAKRFYGIAVARNFTKGRRTEQVQAS---CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 14 ~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAA---CLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
+.|++..+.+|..-.+.=..++|. ..++-| |+|++-+ -+..++.+|+..+|.+-.++.+++++|.+.+
T Consensus 345 ~~I~~~V~~~~~i~~~~l~s~~R~-~~i~~aR~iamyl~r~--~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 345 DELIEIVAKVTGVSREEILSNSRN-VKALLARRIGMYVAKN--YLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHHcCCcHHHHhCCCCC-ccccHHHHHHHHHHHH--HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 567777888875443322223333 344445 8888844 4456999999999999999999999999965
No 387
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.88 E-value=97 Score=22.32 Aligned_cols=27 Identities=4% Similarity=0.018 Sum_probs=18.2
Q ss_pred CcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 56 PFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 56 prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
..+..+||..++|+..++.+..+...+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 678899999999999999988776654
No 388
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=27.83 E-value=68 Score=24.58 Aligned_cols=40 Identities=5% Similarity=0.032 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
....|+.++|+.+|||.+||.+--+ -.....+++.+....
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~----G~~~~p~~~~l~~l~ 51 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIER----GRRPRPSPDTLQRLA 51 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHT----TSSSS-BHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC----CCCCCCCHHHHHHHH
Confidence 3458999999999999999876432 222246677776664
No 389
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=27.80 E-value=59 Score=29.30 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=22.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|..+||..+|+|..||+.++.--
T Consensus 127 ~~~s~~eIA~~lgis~~tv~~~l~Ra 152 (161)
T PRK12541 127 YGFSYKEIAEMTGLSLAKVKIELHRG 152 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999887654
No 390
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.79 E-value=56 Score=30.73 Aligned_cols=27 Identities=15% Similarity=0.162 Sum_probs=24.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.+|||+.+|+|+.||++++.--.
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar 157 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRAR 157 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999987764
No 391
>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=27.68 E-value=91 Score=23.22 Aligned_cols=26 Identities=8% Similarity=0.008 Sum_probs=23.7
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 58 LLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 58 tL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
+..+|++.++++..++.+.+..|.+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 68999999999999999999998873
No 392
>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=27.64 E-value=59 Score=31.73 Aligned_cols=25 Identities=4% Similarity=0.154 Sum_probs=22.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE 180 (490)
...|.++||+..|||..||++++.-
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~r 221 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5699999999999999999988744
No 393
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=27.64 E-value=3.7e+02 Score=27.42 Aligned_cols=53 Identities=11% Similarity=0.120 Sum_probs=40.7
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 139 PSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 139 PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
|.-+.-+.-||-.... .+.++.+||..+|+|..++.+.+++. ..|+.+|....
T Consensus 141 ~~~~~~v~~yI~~~~~-~~lsl~~lA~~~g~S~~~L~R~Fk~~------G~S~~~yl~~~ 193 (274)
T PRK09978 141 PNMRTRVCTVINNNIA-HEWTLARIASELLMSPSLLKKKLREE------ETSYSQLLTEC 193 (274)
T ss_pred HHHHHHHHHHHHhccc-CCCCHHHHHHHHCcCHHHHHHHHHhc------CCCHHHHHHHH
Confidence 4445556667766654 48999999999999999999999753 37888887653
No 394
>PRK13502 transcriptional activator RhaR; Provisional
Probab=27.58 E-value=2.1e+02 Score=28.28 Aligned_cols=70 Identities=7% Similarity=0.106 Sum_probs=37.0
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhc-CCCcCHHHHHHHhCc-CHHHHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK-SKPFLLIDFSNYLNI-NVYELGAVYLQ 79 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~-~~prtL~DIa~v~~v-sv~~Lgr~yk~ 79 (490)
..+|..+|++ .. .-.++|+......+. +.+.-.-|=.|++.- ....++.|||..+|- |...+.|.|++
T Consensus 196 ~~lA~~~~iS--~~---~L~r~fk~~~G~t~~-----~yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~r~FKk 265 (282)
T PRK13502 196 DAFCQQEQCS--ER---VLRQQFRAQTGMTIN-----QYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTR 265 (282)
T ss_pred HHHHHHHCcC--HH---HHHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence 3556666666 22 223444444333322 233333444455543 345777888887776 56667666665
Q ss_pred HH
Q 011262 80 LC 81 (490)
Q Consensus 80 L~ 81 (490)
..
T Consensus 266 ~~ 267 (282)
T PRK13502 266 ET 267 (282)
T ss_pred HH
Confidence 44
No 395
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=27.56 E-value=1.1e+02 Score=32.49 Aligned_cols=30 Identities=7% Similarity=0.096 Sum_probs=26.3
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
.|.++ +.+++++..+||..||++.|.++..
T Consensus 25 ~g~~lps~r~la~~~~vsr~tv~~a~~~L~~ 55 (431)
T PRK15481 25 PGDSLPPVRELASELGVNRNTVAAAYKRLVT 55 (431)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35777 6899999999999999999999853
No 396
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=27.45 E-value=1.8e+02 Score=20.40 Aligned_cols=29 Identities=7% Similarity=0.075 Sum_probs=25.7
Q ss_pred CCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 55 KPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 55 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
-+.+..+|+..++++..++.+....|.+.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 46899999999999999999988888775
No 397
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=27.45 E-value=58 Score=30.19 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=23.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||++.|++..||++++.--.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGR 169 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 578999999999999999999886553
No 398
>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=27.40 E-value=60 Score=29.79 Aligned_cols=27 Identities=11% Similarity=0.078 Sum_probs=24.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||..+|+|+.||++++.-..
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar 141 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGR 141 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999987764
No 399
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=27.39 E-value=57 Score=30.69 Aligned_cols=27 Identities=11% Similarity=0.092 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||+..||+..||++++.--.
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 567899999999999999999887653
No 400
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=27.38 E-value=56 Score=31.11 Aligned_cols=26 Identities=15% Similarity=0.179 Sum_probs=22.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||..+|||+.||+.++..-
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra 193 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLA 193 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999887654
No 401
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=27.36 E-value=93 Score=29.95 Aligned_cols=33 Identities=24% Similarity=0.345 Sum_probs=28.3
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCC
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENTD 185 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~ 185 (490)
..+...|.++||+.+++|+.||++.+.-+.+..
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 356778999999999999999999999886553
No 402
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.05 E-value=56 Score=30.61 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=23.4
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||..+|||..||++++.--.
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar 152 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRAR 152 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 468899999999999999999986553
No 403
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=26.99 E-value=1e+02 Score=27.36 Aligned_cols=30 Identities=7% Similarity=0.190 Sum_probs=26.7
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+-..++.+|++.++++.+||.+.++.+.+.
T Consensus 28 ~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 28 SGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 346889999999999999999999999755
No 404
>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=26.85 E-value=21 Score=33.47 Aligned_cols=42 Identities=21% Similarity=0.422 Sum_probs=0.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHH-HhcCCCCCCCHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIE-FENTDSGSLTIEDFMAR 197 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE-~~~t~s~~Lt~~ef~~~ 197 (490)
.++|++|||..+|++++||.+..+. ...||.+-+-+..|-..
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~ 90 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSR 90 (160)
T ss_dssp -------------------------------------S-----
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccc
Confidence 4689999999999999999887765 34566666656666554
No 405
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=26.85 E-value=1.1e+02 Score=24.27 Aligned_cols=33 Identities=9% Similarity=0.096 Sum_probs=24.2
Q ss_pred HhcCCCcCHHHHHHHhCcC-HHHHHHHHHHHHHH
Q 011262 51 RQKSKPFLLIDFSNYLNIN-VYELGAVYLQLCQV 83 (490)
Q Consensus 51 R~~~~prtL~DIa~v~~vs-v~~Lgr~yk~L~~~ 83 (490)
..+|.|=|++||++.++++ ...+.+..+.|.+.
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 3579999999999999996 88887777776653
No 406
>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=26.85 E-value=61 Score=30.79 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=27.1
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
..|.+++..++++..|||.+|||..++.+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~ 59 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALE 59 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHH
Confidence 347889999999999999999999999985
No 407
>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=26.69 E-value=33 Score=30.32 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=18.9
Q ss_pred CCCCHhhHHhHhccCHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMK 176 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrk 176 (490)
...|.+|||..+|+|.+||++
T Consensus 122 ~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 122 EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred cCCCHHHHHHHHCcCHHhhcC
Confidence 558999999999999999974
No 408
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=26.69 E-value=69 Score=29.80 Aligned_cols=27 Identities=19% Similarity=0.201 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+..|+++.||++++.-.+
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar 179 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAR 179 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999987654
No 409
>PHA01976 helix-turn-helix protein
Probab=26.63 E-value=63 Score=24.77 Aligned_cols=38 Identities=3% Similarity=0.039 Sum_probs=27.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
..+|+.++|+.+||+..||.+..+-- ...+++.+..++
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g~-----~~p~~~~l~~ia 51 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEADK-----RLPNLKTLLRLA 51 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCC-----CCCCHHHHHHHH
Confidence 45899999999999999999854322 234556665554
No 410
>PRK14999 histidine utilization repressor; Provisional
Probab=26.57 E-value=69 Score=31.31 Aligned_cols=29 Identities=17% Similarity=0.219 Sum_probs=25.3
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|.++ |-.++|+..|||..|||+.+.++.
T Consensus 32 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~ 61 (241)
T PRK14999 32 PHDRIPSEAELVAQYGFSRMTINRALRELT 61 (241)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35666 688999999999999999999984
No 411
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=26.55 E-value=60 Score=29.69 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||..+|++..||++++.-..
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAK 160 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568999999999999999999987553
No 412
>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=26.54 E-value=58 Score=30.56 Aligned_cols=27 Identities=19% Similarity=0.237 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||..+|++..||++|+.-..
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar 172 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRAR 172 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568999999999999999999987654
No 413
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=26.52 E-value=1.2e+02 Score=29.20 Aligned_cols=44 Identities=14% Similarity=0.270 Sum_probs=35.1
Q ss_pred ChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 37 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 37 ~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
+...|..||-+|-- +-.+++|.++++.+++|.+++.+.|+.+..
T Consensus 80 ~~~~V~~a~~~ie~--~~~~~~le~la~~lg~sp~~~~R~FK~~~G 123 (187)
T COG2169 80 RSGLVATACRLIEQ--NPEKRWLEELADELGVSPSTLHRLFKAITG 123 (187)
T ss_pred ccHHHHHHHHHHHc--CCCcccHHHHHHHhCCChHHHHHHHHHHhC
Confidence 34567777777653 377999999999999999999998887643
No 414
>PRK13870 transcriptional regulator TraR; Provisional
Probab=26.48 E-value=89 Score=30.81 Aligned_cols=27 Identities=11% Similarity=0.071 Sum_probs=22.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.-+|-.||+.+.|||+.||...++...
T Consensus 187 ~GKT~~EIa~ILgISe~TV~~Hl~na~ 213 (234)
T PRK13870 187 VGKTMEEIADVEGVKYNSVRVKLREAM 213 (234)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346677899999999999999888764
No 415
>PRK13500 transcriptional activator RhaR; Provisional
Probab=26.34 E-value=3.5e+02 Score=27.46 Aligned_cols=87 Identities=15% Similarity=0.114 Sum_probs=54.5
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhhcccc
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWI 133 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~~~~l 133 (490)
..++++.++|+.+++++..|.+.|++.. | ..|..||.++ -...|.+++
T Consensus 220 ~e~isl~~lA~~~~iS~~~L~r~FK~~t---G----------~T~~~yi~~~-----------RL~~A~~LL-------- 267 (312)
T PRK13500 220 KSPFALDKFCDEASCSERVLRQQFRQQT---G----------MTINQYLRQV-----------RVCHAQYLL-------- 267 (312)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHH---C----------cCHHHHHHHH-----------HHHHHHHHH--------
Confidence 4578888888888888888887766543 2 3455666554 111222221
Q ss_pred ccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHH-HHHHHHHHHhcCCCCCCCHHHHHHh
Q 011262 134 TTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA-TLMKRLIEFENTDSGSLTIEDFMAR 197 (490)
Q Consensus 134 ~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~-TIrkR~kE~~~t~s~~Lt~~ef~~~ 197 (490)
..-..++.+||..+|.+.. ...+.+|... .+||.+|++.
T Consensus 268 --------------------~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~TP~~yRk~ 307 (312)
T PRK13500 268 --------------------QHSRLLISDISTECGFEDSNYFSVVFTRET-----GMTPSQWRHL 307 (312)
T ss_pred --------------------HcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 1235678888888887554 5566666553 4777888765
No 416
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.27 E-value=73 Score=30.92 Aligned_cols=29 Identities=14% Similarity=0.320 Sum_probs=26.4
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|.++ |-.++++..|||..|||..++.+.
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VReAL~~L~ 56 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLREVLQRLA 56 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 47788 699999999999999999999985
No 417
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=26.26 E-value=1.3e+02 Score=33.13 Aligned_cols=128 Identities=18% Similarity=0.237 Sum_probs=0.0
Q ss_pred CChHHHHHHHHHHHHHhcC---------CCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHH
Q 011262 36 RRTEQVQASCLYLACRQKS---------KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFT 106 (490)
Q Consensus 36 R~~~~VaAACLYiACR~~~---------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~ 106 (490)
.+..++.-.+-+|+-+|.+ .|.+|+|||+.+|+.+.||.|+...=.-......-+ +=.-|.
T Consensus 340 qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~Gife----------LK~FFs 409 (481)
T PRK12469 340 QRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATGNKYMATPRGTFE----------FKHFFP 409 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEe----------HHHhhc
Q ss_pred hhhCCCCcHHHHHHHHH-HHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHH---hHhccCHHHHHHH
Q 011262 107 DRLLPGGNKKVCDTARD-ILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIV---KIVHICEATLMKR 177 (490)
Q Consensus 107 s~L~~~l~~~V~~~A~~-Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa---~v~~Vse~TIrkR 177 (490)
+.+..+....+...+.+ .++.+.... ..++|.+=-.=+-.|... |++++-+.|| +..||..+.-|||
T Consensus 410 ~~v~~~~g~~~Ss~~Ik~~Ik~lI~~E--d~~kPLSD~~I~~~L~~~--GI~IARRTVAKYRe~L~IpsS~~RKr 480 (481)
T PRK12469 410 RKLEAAGGGECSAAAVRALIKEMIAAE--QAGDPLSDVALAEMLAGR--GVLIARRTVAKYREAMKIPPAELRRR 480 (481)
T ss_pred cccCCCCCccccHHHHHHHHHHHHHhc--CCCCCCCHHHHHHHHHhc--CCCeechhHHHHHHHcCCCChhhccC
No 418
>PRK13503 transcriptional activator RhaS; Provisional
Probab=26.23 E-value=75 Score=31.24 Aligned_cols=27 Identities=7% Similarity=0.062 Sum_probs=21.5
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHH
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQL 80 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L 80 (490)
..++|+.|+|..++++...|.+.|+..
T Consensus 185 ~~~~tl~~lA~~~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 185 AEEVNWEALADQFSLSLRTLHRQLKQQ 211 (278)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 357888999999999988888877643
No 419
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=26.21 E-value=99 Score=28.19 Aligned_cols=41 Identities=10% Similarity=0.119 Sum_probs=31.2
Q ss_pred ChhHHHHHHHHHHHHhcCCC-CCHhhHHhHhccCHHHHHHHHH
Q 011262 138 KPSGLCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 138 ~PsgIaaAALylAar~~g~~-~t~~dIa~v~~Vse~TIrkR~k 179 (490)
+..-|..||+-+-+ -+|+. .|+++|++.+||+.+||-..+.
T Consensus 9 rr~~Il~aA~~lf~-~~G~~~~s~~~IA~~agvsk~~ly~~F~ 50 (189)
T TIGR03384 9 RRAELIDATIESIG-ERGSLDVTIAQIARRAGVSSGIISHYFG 50 (189)
T ss_pred HHHHHHHHHHHHHH-hcCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence 44556666665555 46754 9999999999999999988874
No 420
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=26.15 E-value=63 Score=30.12 Aligned_cols=26 Identities=15% Similarity=0.181 Sum_probs=22.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||...|||..||++++.--
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45789999999999999999887543
No 421
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=26.13 E-value=64 Score=30.11 Aligned_cols=26 Identities=19% Similarity=0.178 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|..+||...|+|..||++++..-
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra 179 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYA 179 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999887644
No 422
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=26.09 E-value=61 Score=30.03 Aligned_cols=27 Identities=4% Similarity=-0.143 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||..+|+|..||++++.-..
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar 178 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGL 178 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHH
Confidence 568999999999999999999987653
No 423
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=26.07 E-value=2.2e+02 Score=27.14 Aligned_cols=57 Identities=18% Similarity=0.221 Sum_probs=37.7
Q ss_pred CcHHHHHHHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHh-ccCHHHHHHHHHHHhcC
Q 011262 113 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV-HICEATLMKRLIEFENT 184 (490)
Q Consensus 113 l~~~V~~~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~-~Vse~TIrkR~kE~~~t 184 (490)
+++.....-..++.....+.+..|+.|. +--|...++..+ |+++.||++.+..+.+.
T Consensus 41 l~~~~l~vL~aLls~~~~~d~~~~~~pi---------------VfpSN~~La~r~~G~s~~tlrR~l~~Lvea 98 (177)
T PF03428_consen 41 LSDRALAVLDALLSFTPPDDWEPGRRPI---------------VFPSNAQLAERLNGMSERTLRRHLARLVEA 98 (177)
T ss_pred CChhHHHHHHHHHHhCCcccccCCCCce---------------eecCHHHHHHHHcCCCHHHHHHHHHHHHHC
Confidence 4544444444455555444446777764 223556788888 99999999999999644
No 424
>PRK15340 transcriptional regulator InvF; Provisional
Probab=25.97 E-value=1.6e+02 Score=28.96 Aligned_cols=24 Identities=0% Similarity=-0.129 Sum_probs=12.3
Q ss_pred CcCHHHHHHHhCc-CHHHHHHHHHH
Q 011262 56 PFLLIDFSNYLNI-NVYELGAVYLQ 79 (490)
Q Consensus 56 prtL~DIa~v~~v-sv~~Lgr~yk~ 79 (490)
..++.|||..+|. +...+.+.|++
T Consensus 174 ~~sItdIA~~~GY~d~ShFsr~FKk 198 (216)
T PRK15340 174 HENITQLAVNHGYSSPSHFSSEIKE 198 (216)
T ss_pred CCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 3555666655554 44445444443
No 425
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=25.88 E-value=1e+02 Score=28.81 Aligned_cols=40 Identities=18% Similarity=0.084 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 145 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 145 AALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+.+|+|..-.+.++|.++||+..+++..-+++-+..+...
T Consensus 13 ~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 13 AMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3556663333457999999999999999999999998644
No 426
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=25.79 E-value=63 Score=29.30 Aligned_cols=27 Identities=7% Similarity=0.096 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+..+||..+|+++.||+.++.-.+
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar 149 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGR 149 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999887664
No 427
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=62 Score=29.75 Aligned_cols=26 Identities=12% Similarity=-0.006 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+..|+++.||++++.--
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Ra 169 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRS 169 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHH
Confidence 45789999999999999999987654
No 428
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=25.74 E-value=31 Score=29.46 Aligned_cols=24 Identities=13% Similarity=0.291 Sum_probs=21.0
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
++|+.||+..||+++||.+.-.++
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~ 47 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDF 47 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhH
Confidence 578999999999999999986654
No 429
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.72 E-value=63 Score=29.99 Aligned_cols=26 Identities=8% Similarity=-0.021 Sum_probs=22.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+..+||+.+|++..||+.|+.--
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra 171 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRG 171 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887543
No 430
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=25.72 E-value=66 Score=25.48 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCC--CCChHHHHHHHHHHHHH
Q 011262 20 AKRFYGIAVARNFTK--GRRTEQVQASCLYLACR 51 (490)
Q Consensus 20 A~~iyk~A~~~~~~r--GR~~~~VaAACLYiACR 51 (490)
..+|++.+.+.++.. |+.+...++|.||--++
T Consensus 20 ~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 20 FKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 456788888888877 89999999999999888
No 431
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=25.39 E-value=1.9e+02 Score=20.81 Aligned_cols=32 Identities=9% Similarity=0.154 Sum_probs=25.5
Q ss_pred HhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 51 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 51 R~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
-...-|.+..||++.++++..++.+-.+.|.+
T Consensus 10 ~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 10 LLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 34457899999999999999999987766655
No 432
>PRK10130 transcriptional regulator EutR; Provisional
Probab=25.32 E-value=2e+02 Score=30.24 Aligned_cols=53 Identities=17% Similarity=0.174 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 140 SGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 140 sgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
.-|.-+.-||-... +.++|+.+||+.+|||..|+.+.+++.. .+|+-+|....
T Consensus 240 ~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~~-----G~sp~~ylr~~ 292 (350)
T PRK10130 240 RLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAIL-----GIGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 33455555666554 4579999999999999999999999873 46778887653
No 433
>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=25.11 E-value=1.1e+02 Score=23.51 Aligned_cols=30 Identities=3% Similarity=-0.007 Sum_probs=24.6
Q ss_pred CCCc-CHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 54 SKPF-LLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 54 ~~pr-tL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
|... +..+|+..++|+..++.+++..|...
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 4456 88999999999999999999999874
No 434
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.10 E-value=77 Score=31.29 Aligned_cols=27 Identities=7% Similarity=-0.017 Sum_probs=23.3
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
....|+++||...||+..||++++..-
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ra 245 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQRQA 245 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 466899999999999999999887643
No 435
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=25.10 E-value=1.2e+02 Score=26.96 Aligned_cols=30 Identities=20% Similarity=0.286 Sum_probs=26.1
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+-..|+.+|++.++++.+||.+-++.+..-
T Consensus 44 ~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~ 73 (144)
T PRK03573 44 PPEQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred CCCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence 345899999999999999999999998644
No 436
>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=25.07 E-value=81 Score=24.16 Aligned_cols=33 Identities=18% Similarity=0.111 Sum_probs=26.0
Q ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcc
Q 011262 54 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 86 (490)
Q Consensus 54 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i 86 (490)
+-..++.|+|..++++..+|.+....|...|.-
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~ 49 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEFFPE 49 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--T
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhh
Confidence 445799999999999999999999888887753
No 437
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=25.06 E-value=3.3e+02 Score=30.86 Aligned_cols=27 Identities=7% Similarity=-0.027 Sum_probs=21.7
Q ss_pred cCCCcCHHHHHHHhCcCHHHHHHHHHH
Q 011262 53 KSKPFLLIDFSNYLNINVYELGAVYLQ 79 (490)
Q Consensus 53 ~~~prtL~DIa~v~~vsv~~Lgr~yk~ 79 (490)
.|..-|..+||..+++++..+.+..+.
T Consensus 480 ~gr~pt~~eiA~~l~~~~~~v~~~~~~ 506 (619)
T PRK05658 480 IGREPTPEELAERLGMPEDKVRKVLKI 506 (619)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 455557999999999999999887543
No 438
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=24.99 E-value=81 Score=31.93 Aligned_cols=34 Identities=12% Similarity=0.290 Sum_probs=30.1
Q ss_pred HHhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 151 ALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 151 ar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-+-+|=+++|+|+.+.+|.+++|+.++++.+.+-
T Consensus 204 i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~ 237 (258)
T COG2512 204 IRERGGRITQAELRRALGLSKTTVSRILRRLEKR 237 (258)
T ss_pred HHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC
Confidence 3567889999999999999999999999998643
No 439
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.94 E-value=70 Score=29.72 Aligned_cols=26 Identities=8% Similarity=-0.001 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||...|++..||+.++.--
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~Ra 179 (189)
T PRK09648 154 VGLSAEETAEAVGSTPGAVRVAQHRA 179 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46889999999999999999987643
No 440
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.80 E-value=69 Score=29.87 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=24.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+..+||..+|+|..||++++.--.
T Consensus 121 ~g~~~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 121 EGLSQKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568899999999999999999987664
No 441
>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=24.73 E-value=66 Score=31.93 Aligned_cols=27 Identities=11% Similarity=0.112 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.+|||.++||+..||+.++.--.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr 202 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQAR 202 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 558899999999999999999987764
No 442
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=24.70 E-value=62 Score=30.85 Aligned_cols=24 Identities=8% Similarity=0.166 Sum_probs=21.4
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
+..+||+.+|||..|||+.++...
T Consensus 2 ti~evA~~lGVS~~TLRrw~k~g~ 25 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVKQLN 25 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 678999999999999999998753
No 443
>PRK13503 transcriptional activator RhaS; Provisional
Probab=24.67 E-value=2.6e+02 Score=27.41 Aligned_cols=70 Identities=6% Similarity=0.007 Sum_probs=39.3
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhc-CCCcCHHHHHHHhCc-CHHHHHHHHHH
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK-SKPFLLIDFSNYLNI-NVYELGAVYLQ 79 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~~~~~rGR~~~~VaAACLYiACR~~-~~prtL~DIa~v~~v-sv~~Lgr~yk~ 79 (490)
.++|..++++ .. .-.++|+......+. +.+--.=|..|++.- ....++.|||..+|- +...+.|.|++
T Consensus 191 ~~lA~~~~lS--~~---~l~r~Fk~~~G~S~~-----~yi~~~Rl~~A~~LL~~~~~sI~eIA~~~GF~~~s~F~r~FKk 260 (278)
T PRK13503 191 EALADQFSLS--LR---TLHRQLKQQTGLTPQ-----RYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRR 260 (278)
T ss_pred HHHHHHHCCC--HH---HHHHHHHHHhCcCHH-----HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 5677777777 22 234455554433222 233344455566653 345678888888776 55666666665
Q ss_pred HH
Q 011262 80 LC 81 (490)
Q Consensus 80 L~ 81 (490)
..
T Consensus 261 ~~ 262 (278)
T PRK13503 261 EF 262 (278)
T ss_pred HH
Confidence 44
No 444
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=24.64 E-value=5.4e+02 Score=27.42 Aligned_cols=134 Identities=17% Similarity=0.167 Sum_probs=80.0
Q ss_pred HHHHHHHHHhc-CCCcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCc--cchHHHHHhhhCCCCcHHHHH
Q 011262 43 ASCLYLACRQK-SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDP--SIFLHKFTDRLLPGGNKKVCD 119 (490)
Q Consensus 43 AACLYiACR~~-~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP--~~~I~Rf~s~L~~~l~~~V~~ 119 (490)
-+|-+|+.+-+ ..+..+.||.-.+. +-+..++++......+..-.-. .+.| ..|+.||...-.+ -.-++..
T Consensus 184 ~s~m~I~sk~ee~~~~~~~ef~~itd-~ty~~~qv~~~~~~il~~l~~~----~~~pt~~~~l~~~~~~~~~-~~~~~e~ 257 (359)
T KOG0654|consen 184 ISAMLIASKYEEIKEPRVEEFCYITD-NTYTYWQVLRMEIDILNALTFE----LVRPTSKTFLRRFLRVAQT-PELQVEP 257 (359)
T ss_pred cccceeeccchhhcchHHHHHHhhhh-hhhHHHHHHHHHHHHHHHhHHH----HhCchHHHHHHHHHHhhcc-hhHHHHH
Confidence 34555565543 44555556655543 3345555555555544321111 1333 5688888433221 2345666
Q ss_pred HHHHHHHHhhccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 120 TARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 120 ~A~~Iv~~~~~~~l~~GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
++..|..--.-+....--.|+-|||||+++|-..++..-=-..+..-++++-.++...+..+.
T Consensus 258 ~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 258 LANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 666666654434334445799999999999988777332244577788899888888888885
No 445
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=24.50 E-value=1e+02 Score=30.43 Aligned_cols=27 Identities=19% Similarity=0.172 Sum_probs=23.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..|||.+.+||+.||+..++.+.
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~ 219 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQ 219 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 447788999999999999999998874
No 446
>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=24.42 E-value=76 Score=29.48 Aligned_cols=27 Identities=11% Similarity=-0.013 Sum_probs=0.0
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
..|.++||+.+|++..||+.++.-.+.
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
No 447
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.41 E-value=71 Score=30.00 Aligned_cols=27 Identities=11% Similarity=-0.004 Sum_probs=23.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||...|+|..||++++.-.+
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 469999999999999999999887654
No 448
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.36 E-value=72 Score=29.69 Aligned_cols=27 Identities=26% Similarity=0.235 Sum_probs=23.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+..+||..+|+|..||++++.-.+
T Consensus 146 ~~~s~~eIA~~lgis~~tV~~~l~Rar 172 (189)
T PRK12515 146 HEKSVEEVGEIVGIPESTVKTRMFYAR 172 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 678999999999999999999986654
No 449
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.16 E-value=78 Score=29.08 Aligned_cols=27 Identities=19% Similarity=0.189 Sum_probs=23.7
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||+.+|++..||++++.-.+
T Consensus 151 ~g~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999987653
No 450
>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=23.97 E-value=1.3e+02 Score=30.29 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-+.+..++|+.+|||.++|++|++.|...
T Consensus 197 grlse~eLAerlGVSRs~ireAlrkLE~a 225 (251)
T TIGR02787 197 GLLVASKIADRVGITRSVIVNALRKLESA 225 (251)
T ss_pred ccccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 47899999999999999999999999643
No 451
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=23.94 E-value=1.1e+02 Score=29.56 Aligned_cols=26 Identities=31% Similarity=0.362 Sum_probs=22.7
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
+++.+|+|+..|||.+|+..+|+.-.
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 37799999999999999999888653
No 452
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=23.93 E-value=72 Score=30.90 Aligned_cols=28 Identities=18% Similarity=0.170 Sum_probs=24.2
Q ss_pred CCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 155 GLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 155 g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|.++ |-.+++...|||..|||+.+.++.
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNLLT 49 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4554 477999999999999999999985
No 453
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=23.87 E-value=1.1e+02 Score=31.47 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhc
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFEN 183 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~ 183 (490)
+...+..+||+.++||..||+++++.+.+
T Consensus 16 ~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 16 GDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45678889999999999999999999975
No 454
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=23.85 E-value=83 Score=30.47 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=25.1
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|.++ |-.++++..|||..|||+.+.++.
T Consensus 21 ~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~ 50 (230)
T TIGR02018 21 PGHRIPSEHELVAQYGCSRMTVNRALRELT 50 (230)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35566 688999999999999999999985
No 455
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=23.76 E-value=77 Score=26.04 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=22.3
Q ss_pred HhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 160 KSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 160 ~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
+.++++.++|+.+||++.++.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~ 26 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD 26 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHC
Confidence 5789999999999999999999653
No 456
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=23.71 E-value=73 Score=30.77 Aligned_cols=28 Identities=7% Similarity=0.150 Sum_probs=24.4
Q ss_pred CCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 155 GLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 155 g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|.++ |-.++++..|||..|||+.+.++.
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~L~ 57 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAALV 57 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555 678999999999999999999985
No 457
>PRK01905 DNA-binding protein Fis; Provisional
Probab=23.56 E-value=1.1e+02 Score=24.81 Aligned_cols=24 Identities=25% Similarity=0.173 Sum_probs=20.9
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHH
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
-++...|+.+||+..|++++++.+
T Consensus 51 gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 51 GNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHh
Confidence 447778999999999999999876
No 458
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=23.52 E-value=2.6e+02 Score=30.91 Aligned_cols=32 Identities=22% Similarity=0.324 Sum_probs=28.1
Q ss_pred HhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 51 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 51 R~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
+....+.||.+||+++++++.-||..|++...
T Consensus 383 ~h~se~LtL~~la~~f~in~~Ylgqlfk~~~~ 414 (475)
T COG4753 383 KHFSENLTLKDLAKVFHINPVYLGQLFKKETG 414 (475)
T ss_pred HHhcCCCCHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 45678999999999999999999999887655
No 459
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.44 E-value=72 Score=29.79 Aligned_cols=26 Identities=19% Similarity=0.163 Sum_probs=23.0
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+.+|+|..||++++.-.
T Consensus 146 ~g~s~~EIAe~lgis~~~V~~~l~Ra 171 (189)
T PRK06811 146 LGEKIEEIAKKLGLTRSAIDNRLSRG 171 (189)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45899999999999999999997655
No 460
>PRK12423 LexA repressor; Provisional
Probab=23.40 E-value=1.4e+02 Score=28.58 Aligned_cols=31 Identities=13% Similarity=0.128 Sum_probs=26.6
Q ss_pred hcCCCCCHhhHHhHhc-cCHHHHHHHHHHHhc
Q 011262 153 THGLKFSKSDIVKIVH-ICEATLMKRLIEFEN 183 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~-Vse~TIrkR~kE~~~ 183 (490)
.+|+.-|.++||+.+| +|..|+++.++.|.+
T Consensus 21 ~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 21 QAGQPPSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3466689999999999 599999999999864
No 461
>PRK03837 transcriptional regulator NanR; Provisional
Probab=23.35 E-value=92 Score=30.16 Aligned_cols=29 Identities=10% Similarity=0.266 Sum_probs=26.5
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|.++ +..++++..|||..|||..++.+.
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~ 62 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVREALQALK 62 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 47788 899999999999999999999985
No 462
>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=23.27 E-value=94 Score=22.43 Aligned_cols=21 Identities=0% Similarity=0.064 Sum_probs=15.7
Q ss_pred cCHHHHHHHhCcCHHHHHHHH
Q 011262 57 FLLIDFSNYLNINVYELGAVY 77 (490)
Q Consensus 57 rtL~DIa~v~~vsv~~Lgr~y 77 (490)
.+..+||..++|+..+|-|..
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 889999999999999987643
No 463
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.27 E-value=96 Score=30.20 Aligned_cols=26 Identities=8% Similarity=0.114 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||...|||..||++++..-
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra 224 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQA 224 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 55799999999999999999887654
No 464
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=23.25 E-value=77 Score=28.89 Aligned_cols=26 Identities=23% Similarity=0.342 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+..+||...|++..||++++.--
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra 166 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHG 166 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 45889999999999999999887654
No 465
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=23.25 E-value=1.1e+02 Score=29.71 Aligned_cols=38 Identities=24% Similarity=0.097 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHH
Q 011262 141 GLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 179 (490)
Q Consensus 141 gIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~k 179 (490)
-|..||+-+-+ -+|+..|+++||+.+||+..||...+.
T Consensus 17 ~Il~aA~~lF~-~~Gy~~s~~~IA~~AGvsk~tiy~~F~ 54 (225)
T PRK11552 17 QLIAAALAQFG-EYGLHATTRDIAAQAGQNIAAITYYFG 54 (225)
T ss_pred HHHHHHHHHHH-HhCccCCHHHHHHHhCCCHHHHHHHcC
Confidence 35555554444 357668999999999999999987764
No 466
>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=23.24 E-value=63 Score=27.27 Aligned_cols=22 Identities=14% Similarity=0.022 Sum_probs=18.4
Q ss_pred CHhhHHhHhccCHHHHHHHHHH
Q 011262 159 SKSDIVKIVHICEATLMKRLIE 180 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE 180 (490)
|..+||+.+|||..|||-.=++
T Consensus 2 ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999865443
No 467
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.15 E-value=74 Score=31.25 Aligned_cols=27 Identities=15% Similarity=0.142 Sum_probs=23.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||+.+|+|+.||++++.--.
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RAr 212 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRGR 212 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 568899999999999999998876543
No 468
>PRK00118 putative DNA-binding protein; Validated
Probab=23.14 E-value=1.9e+02 Score=25.26 Aligned_cols=60 Identities=12% Similarity=0.103 Sum_probs=40.1
Q ss_pred CcCHHHHHHHhCcCHHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCcHHHHHHHHHHHHHhh
Q 011262 56 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMK 129 (490)
Q Consensus 56 prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~vdP~~~I~Rf~s~L~~~l~~~V~~~A~~Iv~~~~ 129 (490)
-.|..+||..+|++..++.+.+....+.|.-- +.--.|+.|+.+. +.+...+.++.+...
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~--------~~~~~~~~~~~~~------~~~~~~~~~~~~~~~ 92 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY--------EEKLHLYEKFIER------NELFDKIAYLKEKYP 92 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--------HHHHChHHHHHHH------HHHHHHHHHHHHccc
Confidence 36789999999999999988877776666421 2333466777654 335555566655543
No 469
>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=23.08 E-value=95 Score=24.31 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=18.1
Q ss_pred hcCCCCCHhhHHhHhccCHHHHH-HHHH
Q 011262 153 THGLKFSKSDIVKIVHICEATLM-KRLI 179 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIr-kR~k 179 (490)
.+|++ ++.++|+.+||+.+||. ++.+
T Consensus 9 ~~g~~-~~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 9 ALGVK-SDKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp HHT-S-SCHHHHCCTT--HHHHH-HHHH
T ss_pred HhCCC-CHHHHHHHhCcCHHHhhHHHHh
Confidence 34544 77899999999999999 5554
No 470
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=22.95 E-value=1.2e+02 Score=29.09 Aligned_cols=28 Identities=25% Similarity=0.258 Sum_probs=25.2
Q ss_pred CCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 157 KFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 157 ~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
..++.+|++.++++.+|+++.++.+.+.
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le~~ 184 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELEKK 184 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5899999999999999999999998644
No 471
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=22.91 E-value=80 Score=29.10 Aligned_cols=26 Identities=12% Similarity=0.101 Sum_probs=22.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++||+.+|+|..||++..+-.
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra 45 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRA 45 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56999999999999999998776543
No 472
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.88 E-value=74 Score=30.42 Aligned_cols=27 Identities=15% Similarity=0.079 Sum_probs=24.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...+.++||+.+|+++.||++++.--.
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~~~l~RAr 179 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVRSRIHRGR 179 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999987764
No 473
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=22.85 E-value=79 Score=29.01 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=23.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+..+||+.+|||..||++++.-.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Ra 176 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRG 176 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 67899999999999999999887654
No 474
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=22.82 E-value=1.2e+02 Score=29.71 Aligned_cols=27 Identities=30% Similarity=0.317 Sum_probs=24.5
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||.+.+||+.||+.+++...
T Consensus 185 ~G~t~~eIa~~l~is~~Tv~~~l~~~~ 211 (232)
T TIGR03541 185 LGRRQADIAAILGISERTVENHLRSAR 211 (232)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 458999999999999999999998874
No 475
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=22.80 E-value=1e+02 Score=29.43 Aligned_cols=37 Identities=16% Similarity=0.189 Sum_probs=30.8
Q ss_pred HHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 46 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 46 LYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
||-..-..+.|.|+.||+.++|+|...+.-+.+.|..
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 4444445689999999999999999999888888776
No 476
>PF09241 Herp-Cyclin: Herpesviridae viral cyclin; InterPro: IPR015322 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry represents a domain found in a family of viral cyclins that specifically activate CDK6 of host cells to a very high degree []. This domain adopts a helical structure consisting of five alpha-helices, with one helix surrounded by the others.; PDB: 1XO2_A 1JOW_A 2F2C_A 2EUF_A 1BU2_A.
Probab=22.79 E-value=4.7e+02 Score=22.08 Aligned_cols=83 Identities=17% Similarity=0.140 Sum_probs=52.7
Q ss_pred HHHHhcCCCCc--hHHHHHHHH-HHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-----CcCHHHHHHHhCcCHHHHH
Q 011262 3 QMKNALNIGES--DEIVHVAKR-FYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-----PFLLIDFSNYLNINVYELG 74 (490)
Q Consensus 3 ~ia~~L~Lp~~--~~v~d~A~~-iyk~A~~~~~~rGR~~~~VaAACLYiACR~~~~-----prtL~DIa~v~~vsv~~Lg 74 (490)
-+|++|+||+. +..-+.+.. |.|-.++-|+ .=-++-.++|.-|.-....+++ .+-|.|++.+++.+..+++
T Consensus 10 p~c~alkipe~~wpql~e~~s~tickaliqpni-all~p~licaggllttiet~ntn~~~wt~yledl~~ilnfstntir 88 (106)
T PF09241_consen 10 PVCHALKIPEDFWPQLFEATSITICKALIQPNI-ALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNFSTNTIR 88 (106)
T ss_dssp HHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGG-GGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTCHHHHHH
T ss_pred HhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCc-cccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhcccchhh
Confidence 37999999932 233333333 3333333222 2245677888888877776654 3568999999999999999
Q ss_pred HHHHHHHHHhcc
Q 011262 75 AVYLQLCQVLYI 86 (490)
Q Consensus 75 r~yk~L~~~L~i 86 (490)
.+-.++.+.+..
T Consensus 89 t~kdqv~ea~~~ 100 (106)
T PF09241_consen 89 TVKDQVSEAFST 100 (106)
T ss_dssp HHHHHHHHHHHT
T ss_pred hHHHHHHHHHHh
Confidence 888888887754
No 477
>PRK09726 antitoxin HipB; Provisional
Probab=22.77 E-value=1.9e+02 Score=23.85 Aligned_cols=40 Identities=18% Similarity=0.208 Sum_probs=30.8
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhHH
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 199 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~ 199 (490)
....|+.++|+.+||+..||.+-.+- ....+++.+..+++
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e~g-----~~~ps~~~l~~ia~ 62 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFENN-----PDNTTLTTFFKILQ 62 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC-----CCCCCHHHHHHHHH
Confidence 35689999999999999999876652 23467777777754
No 478
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=78 Score=30.02 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=22.6
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|.++||+.+|++..||++++.--
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Ra 173 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARA 173 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45789999999999999999987644
No 479
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=22.69 E-value=4e+02 Score=23.56 Aligned_cols=65 Identities=11% Similarity=-0.011 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHhCCCCC-CCChHHHHHHHHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 16 IVHVAKRFYGIAVARNFTK-GRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 16 v~d~A~~iyk~A~~~~~~r-GR~~~~VaAACLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+..+.+.+....+..+.. |-+..++ ..|+..++ .+-+.+..||++.++++..++.+....|.+.
T Consensus 8 ~l~~~~~~~~~~~~~~l~~~glt~~q~--~vL~~l~~-~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~ 73 (144)
T PRK03573 8 DLARLVRIWRALIDHRLKPLELTQTHW--VTLHNIHQ-LPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHH--HHHHHHHH-cCCCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence 3455555555555543321 4333333 23443333 3345789999999999999999999999884
No 480
>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=22.66 E-value=2.1e+02 Score=21.21 Aligned_cols=27 Identities=7% Similarity=0.150 Sum_probs=24.2
Q ss_pred cCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 011262 57 FLLIDFSNYLNINVYELGAVYLQLCQV 83 (490)
Q Consensus 57 rtL~DIa~v~~vsv~~Lgr~yk~L~~~ 83 (490)
.+..||+..++++..++.+.+..|...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHC
Confidence 889999999999999999988888664
No 481
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=22.62 E-value=91 Score=30.49 Aligned_cols=29 Identities=14% Similarity=0.182 Sum_probs=25.4
Q ss_pred cCCCC-CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 154 HGLKF-SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 154 ~g~~~-t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|.++ |-.++++..|||..|||+.+.++.
T Consensus 25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~ 54 (240)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLV 54 (240)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45677 678999999999999999999984
No 482
>PRK05572 sporulation sigma factor SigF; Validated
Probab=22.60 E-value=7.3e+02 Score=24.27 Aligned_cols=26 Identities=12% Similarity=0.149 Sum_probs=22.9
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...|+++||...|||..||+++.+..
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ra 242 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKI 242 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56999999999999999999877654
No 483
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.59 E-value=82 Score=29.43 Aligned_cols=27 Identities=22% Similarity=0.181 Sum_probs=24.1
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|..+||+.+|+|+.||+.++.--.
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr 152 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRAR 152 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999987664
No 484
>PRK06930 positive control sigma-like factor; Validated
Probab=22.56 E-value=1e+02 Score=29.09 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=24.6
Q ss_pred CCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 155 GLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 155 g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
....|.++||..+|+|..||+.++....
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~ 155 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMIERAE 155 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4678999999999999999999987664
No 485
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=22.55 E-value=1.4e+02 Score=24.72 Aligned_cols=30 Identities=23% Similarity=0.264 Sum_probs=25.3
Q ss_pred CCCCCHhhHHhHh-ccCHHHHHHHHHHHhcC
Q 011262 155 GLKFSKSDIVKIV-HICEATLMKRLIEFENT 184 (490)
Q Consensus 155 g~~~t~~dIa~v~-~Vse~TIrkR~kE~~~t 184 (490)
.-+....++.+.+ +||..++.+|++++.+.
T Consensus 16 ~g~~rf~el~~~l~~is~~~L~~~L~~L~~~ 46 (90)
T PF01638_consen 16 QGPMRFSELQRRLPGISPKVLSQRLKELEEA 46 (90)
T ss_dssp TSSEEHHHHHHHSTTS-HHHHHHHHHHHHHT
T ss_pred hCCCcHHHHHHhcchhHHHHHHHHHHHHHHc
Confidence 3578899999999 99999999999999654
No 486
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.48 E-value=82 Score=29.69 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=24.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
...|.++||..+|+|..||++++.-..
T Consensus 128 ~g~s~~EIA~~LgiS~~tVk~~l~Rar 154 (188)
T PRK12546 128 SGFSYEEAAEMCGVAVGTVKSRANRAR 154 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 668999999999999999999987764
No 487
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=22.47 E-value=1.7e+02 Score=24.34 Aligned_cols=32 Identities=13% Similarity=0.195 Sum_probs=27.8
Q ss_pred hcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 153 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 153 ~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
..+...|-.+|++..|+|+.+|-+..+.+++-
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~ 46 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAVWKHIQQLREE 46 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHHHHHHHHHHHh
Confidence 34567999999999999999999999999744
No 488
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.46 E-value=80 Score=30.86 Aligned_cols=24 Identities=8% Similarity=0.160 Sum_probs=22.1
Q ss_pred CHhhHHhHhccCHHHHHHHHHHHh
Q 011262 159 SKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 159 t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
|-.++|+..|||..|||+.+.++.
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~ 60 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLV 60 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 577999999999999999999985
No 489
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=22.28 E-value=64 Score=33.37 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=21.9
Q ss_pred CCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 158 FSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 158 ~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
.|++|||+.+|||..|+.+.++.-.
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~ 25 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSP 25 (333)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 3789999999999999999987653
No 490
>cd00131 PAX Paired Box domain
Probab=22.28 E-value=5.6e+02 Score=22.79 Aligned_cols=75 Identities=9% Similarity=0.088 Sum_probs=42.4
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHHHHh--CCCCCCCChHH--HHHHHHHHHHHhcCCCcCHHHHHHHh---Cc------
Q 011262 2 RQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQ--VQASCLYLACRQKSKPFLLIDFSNYL---NI------ 68 (490)
Q Consensus 2 ~~ia~~L~Lp~~~~v~d~A~~iyk~A~~--~~~~rGR~~~~--VaAACLYiACR~~~~prtL~DIa~v~---~v------ 68 (490)
..+|..|+++ ..++..-..-|+.--+ .+-..|+++.. -...+..+.....+-..|+.|+++.+ ++
T Consensus 37 ~~iA~~~~Vs--~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~ 114 (128)
T cd00131 37 CDISRQLRVS--HGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNV 114 (128)
T ss_pred HHHHHHHCcC--HHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCC
Confidence 4688999999 7776666666654321 11111332222 12234334444556667899998875 33
Q ss_pred -CHHHHHHHHH
Q 011262 69 -NVYELGAVYL 78 (490)
Q Consensus 69 -sv~~Lgr~yk 78 (490)
++.+|++.++
T Consensus 115 ~s~stI~R~L~ 125 (128)
T cd00131 115 PSVSSINRILR 125 (128)
T ss_pred CCHHHHHHHHH
Confidence 6777777644
No 491
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=22.23 E-value=4e+02 Score=26.83 Aligned_cols=39 Identities=21% Similarity=0.219 Sum_probs=32.1
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHhH
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 198 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 198 (490)
...+.|+.+||+.+|+|+.++.+++++. + .|+-+|....
T Consensus 147 ~~~~~tl~~LA~~~gmS~s~l~R~FK~~-----G-~T~~eyl~~~ 185 (253)
T PRK09940 147 LAHPWKLKDICDCLYISESLLKKKLKQE-----Q-TTFSQILLDA 185 (253)
T ss_pred hcCCCCHHHHHHHHCcCHHHHHHHHHHc-----C-CCHHHHHHHH
Confidence 4457999999999999999999999874 2 5788886653
No 492
>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=22.21 E-value=1.3e+02 Score=28.44 Aligned_cols=43 Identities=14% Similarity=0.114 Sum_probs=31.3
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 136 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 136 GR~PsgIaaAALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
.-+|.-.+.+..-+. ..+..|+.+||+.+|+|..+|+++++-.
T Consensus 102 ~lt~~e~a~~~~~l~---~~~g~s~~~iA~~lg~s~~~V~r~l~l~ 144 (187)
T TIGR00180 102 DLSPIEEAQAYKRLL---EKFSMTQEDLAKKIGKSRAHITNLLRLL 144 (187)
T ss_pred CCCHHHHHHHHHHHH---HHhCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 345666655443322 2256799999999999999999999875
No 493
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=21.79 E-value=1.2e+02 Score=28.22 Aligned_cols=40 Identities=18% Similarity=0.218 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhcCCC-CCHhhHHhHhccCHHHHHHHHHHH
Q 011262 141 GLCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 141 gIaaAALylAar~~g~~-~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
-|..||+=+.+ -.|+. .|+.+||+.+|||..||-..++.-
T Consensus 12 ~Il~aA~~lf~-e~G~~~~s~~~IA~~agvs~~~lY~hF~sK 52 (202)
T TIGR03613 12 AILSAALDTFS-RFGFHGTSLEQIAELAGVSKTNLLYYFPSK 52 (202)
T ss_pred HHHHHHHHHHH-HhCcccCCHHHHHHHhCCCHHHHHHHcCCH
Confidence 34444443333 35654 999999999999999998877543
No 494
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=21.67 E-value=1.7e+02 Score=27.25 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=31.1
Q ss_pred HHHHHHHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHH
Q 011262 45 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 82 (490)
Q Consensus 45 CLYiACR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 82 (490)
+||..-+ .+-+....|||..++|+..++....++|.+
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~ 50 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLER 50 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHH
Confidence 4565555 667788999999999999999998888887
No 495
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=21.63 E-value=97 Score=26.45 Aligned_cols=37 Identities=11% Similarity=0.168 Sum_probs=26.6
Q ss_pred HHHHHHHhcCCCCCHhhHHhHhccCHHHHHHHHHHHh
Q 011262 146 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 182 (490)
Q Consensus 146 ALylAar~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~ 182 (490)
=||+|..+-....++..+.+++|..+.||+..++.|.
T Consensus 10 rlyla~li~~~~~nvp~L~~~TGmPrRT~Qd~i~aL~ 46 (90)
T PF09904_consen 10 RLYLAYLIDSGERNVPALMEATGMPRRTIQDTIKALP 46 (90)
T ss_dssp HHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGG
T ss_pred HHHHHHHHhcCCccHHHHHHHhCCCHhHHHHHHHHhh
Confidence 3788887744334999999999999999999999885
No 496
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=21.62 E-value=1.6e+02 Score=25.10 Aligned_cols=33 Identities=18% Similarity=0.263 Sum_probs=27.9
Q ss_pred HhcCCCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 152 LTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 152 r~~g~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
...+-.+++.+|+..++++.+||.+-++.+.+-
T Consensus 38 ~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 38 ENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK 70 (109)
T ss_pred hccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 334567999999999999999999999988543
No 497
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=21.60 E-value=3.2e+02 Score=23.27 Aligned_cols=35 Identities=11% Similarity=0.043 Sum_probs=31.1
Q ss_pred HHhcCCCcCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 011262 50 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 84 (490)
Q Consensus 50 CR~~~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 84 (490)
|...+-+.++.+|+..++++..++.+....|.+.=
T Consensus 37 ~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg 71 (109)
T TIGR01889 37 LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKG 71 (109)
T ss_pred hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 56667889999999999999999999999998853
No 498
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=21.43 E-value=78 Score=27.74 Aligned_cols=24 Identities=17% Similarity=0.217 Sum_probs=21.6
Q ss_pred cCCCCCHhhHHhHhccCHHHHHHH
Q 011262 154 HGLKFSKSDIVKIVHICEATLMKR 177 (490)
Q Consensus 154 ~g~~~t~~dIa~v~~Vse~TIrkR 177 (490)
-+..+||.+.|+..|||..|++++
T Consensus 54 e~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 54 EKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHH
Confidence 457899999999999999999986
No 499
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.40 E-value=1.1e+02 Score=27.84 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=26.2
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHHhcC
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEFENT 184 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~~~t 184 (490)
-+.|.++++..+|++..|+++.++++..+
T Consensus 25 GRiTi~ql~~~TGasR~Tvk~~lreLVa~ 53 (127)
T PF06163_consen 25 GRITIKQLVAKTGASRNTVKRYLRELVAR 53 (127)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 36899999999999999999999999654
No 500
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=21.37 E-value=1.1e+02 Score=28.13 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=22.8
Q ss_pred CCCCHhhHHhHhccCHHHHHHHHHHH
Q 011262 156 LKFSKSDIVKIVHICEATLMKRLIEF 181 (490)
Q Consensus 156 ~~~t~~dIa~v~~Vse~TIrkR~kE~ 181 (490)
...+.++||...|||..||++++.-.
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra 180 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRG 180 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56799999999999999999887654
Done!