Query 010919
Match_columns 497
No_of_seqs 246 out of 1064
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 06:03:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010919.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010919hhsearch_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 7E-68 1.5E-72 555.1 22.4 417 1-478 67-492 (521)
2 PRK00423 tfb transcription ini 100.0 2.5E-40 5.4E-45 337.9 22.1 181 1-190 122-302 (310)
3 COG1405 SUA7 Transcription ini 100.0 6.5E-40 1.4E-44 329.1 19.8 181 1-190 97-277 (285)
4 KOG1597 Transcription initiati 100.0 6.6E-38 1.4E-42 308.1 19.2 197 1-205 104-300 (308)
5 PF07741 BRF1: Brf1-like TBP-b 100.0 8.2E-30 1.8E-34 218.3 1.7 96 353-473 1-97 (97)
6 PF00382 TFIIB: Transcription 99.7 1.5E-17 3.2E-22 134.3 10.1 71 8-80 1-71 (71)
7 PF00382 TFIIB: Transcription 99.6 1.6E-15 3.4E-20 122.5 8.7 71 109-181 1-71 (71)
8 KOG0835 Cyclin L [General func 99.5 5.6E-13 1.2E-17 133.8 18.2 177 4-187 26-224 (367)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.5 3.1E-12 6.8E-17 130.6 19.1 166 3-176 58-234 (305)
10 PRK00423 tfb transcription ini 99.4 6E-13 1.3E-17 136.5 12.3 89 4-94 219-307 (310)
11 KOG0834 CDK9 kinase-activating 99.4 9.5E-13 2.1E-17 134.7 11.6 158 2-166 40-214 (323)
12 COG1405 SUA7 Transcription ini 99.2 7.8E-11 1.7E-15 119.2 10.4 90 4-95 194-283 (285)
13 COG5333 CCL1 Cdk activating ki 99.2 2.6E-10 5.5E-15 114.7 13.0 157 3-166 47-211 (297)
14 KOG1597 Transcription initiati 99.1 4.9E-10 1.1E-14 111.7 10.3 87 4-92 203-289 (308)
15 cd00043 CYCLIN Cyclin box fold 99.0 4.4E-09 9.5E-14 85.2 11.2 83 3-87 4-87 (88)
16 KOG0794 CDK8 kinase-activating 98.9 2E-08 4.2E-13 97.3 12.9 175 5-188 45-234 (264)
17 smart00385 CYCLIN domain prese 98.9 9.3E-09 2E-13 82.5 8.9 79 7-88 2-82 (83)
18 cd00043 CYCLIN Cyclin box fold 98.9 1.5E-08 3.2E-13 82.1 9.2 84 103-188 3-87 (88)
19 smart00385 CYCLIN domain prese 98.8 1.8E-08 3.9E-13 80.8 9.2 81 107-189 1-82 (83)
20 KOG0656 G1/S-specific cyclin D 98.6 1.5E-06 3.1E-11 89.7 16.6 177 3-186 80-268 (335)
21 KOG1598 Transcription initiati 98.3 3.6E-07 7.9E-12 97.9 4.6 157 7-165 169-335 (521)
22 PF00134 Cyclin_N: Cyclin, N-t 97.8 0.00027 5.8E-09 62.1 10.8 90 3-94 33-125 (127)
23 KOG4557 Origin recognition com 97.7 0.0013 2.7E-08 63.7 15.0 159 7-179 2-168 (262)
24 KOG2496 Cdk activating kinase 97.6 0.0008 1.7E-08 68.1 11.8 146 9-158 64-219 (325)
25 KOG0653 Cyclin B and related k 97.5 0.00072 1.6E-08 71.9 11.5 151 6-165 163-317 (391)
26 PF02984 Cyclin_C: Cyclin, C-t 97.2 0.00074 1.6E-08 58.2 6.4 84 104-189 2-86 (118)
27 PF01857 RB_B: Retinoblastoma- 97.1 0.0018 3.8E-08 59.1 8.0 71 3-75 13-85 (135)
28 COG5024 Cyclin [Cell division 97.0 0.0039 8.4E-08 66.9 10.6 148 6-163 218-369 (440)
29 KOG0835 Cyclin L [General func 95.6 0.073 1.6E-06 54.8 9.5 106 4-117 141-247 (367)
30 PF02984 Cyclin_C: Cyclin, C-t 94.9 0.11 2.4E-06 44.6 7.6 87 4-92 3-90 (118)
31 PF00134 Cyclin_N: Cyclin, N-t 93.7 0.22 4.8E-06 43.5 6.8 67 106-174 35-102 (127)
32 TIGR00569 ccl1 cyclin ccl1. Un 93.0 0.38 8.3E-06 49.7 8.2 68 108-175 62-129 (305)
33 PF13404 HTH_AsnC-type: AsnC-t 91.1 0.41 8.9E-06 34.8 4.3 31 158-188 11-41 (42)
34 PF08613 Cyclin: Cyclin; Inte 91.1 3.6 7.8E-05 37.8 11.6 88 5-94 55-148 (149)
35 KOG0655 G1/S-specific cyclin E 91.0 3.6 7.9E-05 42.8 12.4 169 5-188 149-331 (408)
36 KOG0834 CDK9 kinase-activating 90.4 0.4 8.7E-06 49.9 5.1 83 106-190 43-129 (323)
37 smart00342 HTH_ARAC helix_turn 89.6 2.8 6.1E-05 32.9 8.5 26 164-189 50-76 (84)
38 PF05460 ORC6: Origin recognit 88.6 0.13 2.9E-06 54.1 0.0 87 9-95 2-89 (353)
39 smart00342 HTH_ARAC helix_turn 88.1 1.8 3.9E-05 34.1 6.4 72 8-88 4-76 (84)
40 PF13384 HTH_23: Homeodomain-l 87.4 0.76 1.7E-05 33.8 3.5 29 164-192 17-45 (50)
41 PF01857 RB_B: Retinoblastoma- 87.2 2.1 4.5E-05 39.1 6.9 64 109-174 18-83 (135)
42 KOG2496 Cdk activating kinase 87.0 1.3 2.9E-05 45.4 5.9 70 106-175 60-129 (325)
43 KOG4164 Cyclin ik3-1/CABLES [C 86.9 1.5 3.2E-05 46.4 6.4 91 4-96 385-480 (497)
44 PF13412 HTH_24: Winged helix- 86.3 1.3 2.8E-05 32.4 4.2 29 162-190 15-43 (48)
45 PRK09210 RNA polymerase sigma 84.7 41 0.00089 35.6 16.2 25 163-187 324-348 (367)
46 KOG4557 Origin recognition com 84.7 2.9 6.3E-05 41.0 6.7 81 8-91 96-181 (262)
47 PRK11169 leucine-responsive tr 84.1 1.5 3.3E-05 40.9 4.6 37 156-192 20-56 (164)
48 PF13936 HTH_38: Helix-turn-he 83.9 1.4 3.1E-05 32.1 3.4 30 157-186 13-42 (44)
49 PRK05657 RNA polymerase sigma 83.8 59 0.0013 33.9 16.9 27 163-189 281-307 (325)
50 PF13730 HTH_36: Helix-turn-he 83.2 2.5 5.3E-05 31.7 4.6 26 166-191 27-52 (55)
51 PRK11179 DNA-binding transcrip 81.8 2 4.3E-05 39.6 4.3 37 156-192 15-51 (153)
52 PF08279 HTH_11: HTH domain; 81.4 2.7 5.8E-05 31.5 4.2 31 161-191 12-42 (55)
53 PF13542 HTH_Tnp_ISL3: Helix-t 80.9 5.8 0.00012 29.3 5.8 25 164-188 27-51 (52)
54 PF04967 HTH_10: HTH DNA bindi 80.0 3.7 8E-05 31.5 4.5 34 155-188 9-47 (53)
55 PRK05932 RNA polymerase factor 79.7 17 0.00037 39.7 11.3 184 8-204 141-384 (455)
56 PF02796 HTH_7: Helix-turn-hel 79.6 1 2.3E-05 32.9 1.4 28 159-186 16-43 (45)
57 PF13545 HTH_Crp_2: Crp-like h 78.4 3.6 7.8E-05 32.7 4.3 29 163-191 27-55 (76)
58 PRK10572 DNA-binding transcrip 78.4 31 0.00068 34.5 12.1 37 163-204 247-284 (290)
59 PF10668 Phage_terminase: Phag 77.6 5.6 0.00012 31.4 4.9 40 144-186 5-44 (60)
60 PRK07405 RNA polymerase sigma 77.5 94 0.002 32.2 16.1 25 163-187 275-299 (317)
61 PRK00135 scpB segregation and 77.4 16 0.00034 35.3 9.0 119 45-185 5-125 (188)
62 cd00092 HTH_CRP helix_turn_hel 77.1 6.5 0.00014 30.2 5.3 29 162-190 23-51 (67)
63 TIGR03697 NtcA_cyano global ni 76.9 8.6 0.00019 35.7 7.1 30 163-192 142-171 (193)
64 PF01325 Fe_dep_repress: Iron 76.9 5.3 0.00011 31.2 4.7 37 153-190 12-48 (60)
65 TIGR02395 rpoN_sigma RNA polym 76.9 13 0.00028 40.4 9.2 182 8-204 116-359 (429)
66 PF04545 Sigma70_r4: Sigma-70, 76.7 4.4 9.6E-05 29.9 4.1 27 162-188 18-44 (50)
67 TIGR02393 RpoD_Cterm RNA polym 76.5 80 0.0017 30.9 15.9 26 163-188 195-220 (238)
68 PF00356 LacI: Bacterial regul 76.4 2.6 5.7E-05 31.3 2.7 34 166-204 1-34 (46)
69 PF00325 Crp: Bacterial regula 75.1 2.8 6E-05 28.9 2.3 27 164-190 2-28 (32)
70 TIGR02297 HpaA 4-hydroxyphenyl 74.9 60 0.0013 32.2 13.0 96 50-203 190-286 (287)
71 smart00419 HTH_CRP helix_turn_ 74.5 3.9 8.4E-05 29.2 3.2 30 162-191 6-35 (48)
72 PF00325 Crp: Bacterial regula 74.5 4.7 0.0001 27.8 3.3 27 63-89 2-28 (32)
73 COG5333 CCL1 Cdk activating ki 74.4 2.3 5E-05 43.7 2.6 55 106-162 49-103 (297)
74 PF08220 HTH_DeoR: DeoR-like h 73.3 3.3 7.3E-05 31.8 2.7 30 162-191 12-41 (57)
75 TIGR02010 IscR iron-sulfur clu 72.8 8.1 0.00018 34.8 5.5 47 44-90 6-52 (135)
76 KOG0794 CDK8 kinase-activating 72.7 5.6 0.00012 39.6 4.6 57 106-164 45-101 (264)
77 smart00344 HTH_ASNC helix_turn 72.5 5.5 0.00012 33.9 4.2 30 162-191 15-44 (108)
78 TIGR03879 near_KaiC_dom probab 72.3 8.3 0.00018 31.6 4.8 27 163-189 31-57 (73)
79 COG1522 Lrp Transcriptional re 72.1 5.3 0.00011 36.1 4.2 33 159-191 17-49 (154)
80 smart00345 HTH_GNTR helix_turn 71.9 5.4 0.00012 29.6 3.6 30 162-191 17-47 (60)
81 PF00165 HTH_AraC: Bacterial r 71.1 10 0.00022 26.9 4.7 36 162-202 6-41 (42)
82 PF08613 Cyclin: Cyclin; Inte 71.1 32 0.00068 31.5 9.1 79 103-183 52-136 (149)
83 TIGR00122 birA_repr_reg BirA b 70.5 7.2 0.00016 30.7 4.2 31 160-190 9-39 (69)
84 PRK07406 RNA polymerase sigma 70.1 38 0.00083 36.1 10.7 26 163-188 330-355 (373)
85 KOG1010 Rb (Retinoblastoma tum 70.1 8.4 0.00018 44.7 5.9 80 4-85 680-761 (920)
86 TIGR03697 NtcA_cyano global ni 70.0 15 0.00033 34.0 6.9 48 43-90 113-170 (193)
87 PF02082 Rrf2: Transcriptional 69.2 7.3 0.00016 32.0 4.1 45 46-90 8-52 (83)
88 PF01325 Fe_dep_repress: Iron 68.3 14 0.00031 28.7 5.3 38 52-90 12-49 (60)
89 PF13518 HTH_28: Helix-turn-he 68.1 7.5 0.00016 28.4 3.5 26 166-191 14-39 (52)
90 PRK07408 RNA polymerase sigma 68.0 1.3E+02 0.0029 29.9 14.6 27 163-189 218-244 (256)
91 smart00421 HTH_LUXR helix_turn 67.7 6.9 0.00015 28.4 3.3 26 164-189 18-43 (58)
92 COG2207 AraC AraC-type DNA-bin 66.7 77 0.0017 26.6 10.9 39 48-87 22-60 (127)
93 PF05225 HTH_psq: helix-turn-h 66.7 9.9 0.00021 28.0 3.9 27 161-188 14-40 (45)
94 COG1508 RpoN DNA-directed RNA 66.2 91 0.002 34.1 12.5 41 164-204 330-371 (444)
95 PF13545 HTH_Crp_2: Crp-like h 66.1 15 0.00033 29.0 5.3 32 62-93 27-58 (76)
96 PRK07122 RNA polymerase sigma 65.7 41 0.0009 33.8 9.5 27 162-188 229-255 (264)
97 PF13613 HTH_Tnp_4: Helix-turn 65.5 7.4 0.00016 29.4 3.1 36 155-190 10-45 (53)
98 PRK10857 DNA-binding transcrip 65.2 14 0.00031 34.7 5.6 47 44-90 6-52 (164)
99 PF12802 MarR_2: MarR family; 64.6 14 0.00029 28.0 4.5 27 164-190 21-47 (62)
100 PF02042 RWP-RK: RWP-RK domain 64.5 7.9 0.00017 29.7 3.0 28 162-189 13-40 (52)
101 PRK05949 RNA polymerase sigma 64.2 1.9E+02 0.0041 30.2 16.7 25 163-187 285-309 (327)
102 PRK09393 ftrA transcriptional 64.0 96 0.0021 31.7 12.0 99 48-204 220-319 (322)
103 TIGR01610 phage_O_Nterm phage 64.0 16 0.00034 31.0 5.2 30 161-190 44-73 (95)
104 PHA02591 hypothetical protein; 63.8 8.4 0.00018 32.0 3.2 31 156-186 51-81 (83)
105 TIGR02479 FliA_WhiG RNA polyme 63.7 1.4E+02 0.0031 28.7 15.9 26 163-188 190-215 (224)
106 smart00420 HTH_DEOR helix_turn 63.6 17 0.00038 26.0 4.8 27 164-190 14-40 (53)
107 PF13022 HTH_Tnp_1_2: Helix-tu 63.0 13 0.00027 34.4 4.6 42 145-186 12-56 (142)
108 PRK11920 rirA iron-responsive 62.9 17 0.00037 33.6 5.6 46 44-90 6-51 (153)
109 PRK11511 DNA-binding transcrip 62.8 33 0.00072 30.4 7.3 55 145-205 7-61 (127)
110 TIGR02850 spore_sigG RNA polym 62.5 1.1E+02 0.0025 30.2 11.9 26 163-188 221-246 (254)
111 PF00392 GntR: Bacterial regul 62.5 8.4 0.00018 29.9 3.0 30 161-190 20-50 (64)
112 PF01022 HTH_5: Bacterial regu 62.3 14 0.0003 27.0 4.0 32 160-191 11-42 (47)
113 PF08281 Sigma70_r4_2: Sigma-7 62.3 10 0.00022 28.2 3.4 27 162-188 24-50 (54)
114 PF02954 HTH_8: Bacterial regu 62.3 9.5 0.00021 27.4 3.0 26 163-188 17-42 (42)
115 PF13551 HTH_29: Winged helix- 62.1 12 0.00025 31.7 4.1 27 166-192 14-40 (112)
116 PF08279 HTH_11: HTH domain; 62.0 18 0.0004 26.9 4.7 33 59-91 11-43 (55)
117 PRK05901 RNA polymerase sigma 61.9 2.6E+02 0.0056 31.2 15.4 25 163-187 466-490 (509)
118 cd04762 HTH_MerR-trunc Helix-T 61.1 8.9 0.00019 27.0 2.8 23 166-188 2-24 (49)
119 PF00165 HTH_AraC: Bacterial r 60.5 12 0.00026 26.5 3.3 27 61-87 6-32 (42)
120 PF13613 HTH_Tnp_4: Helix-turn 60.3 16 0.00034 27.6 4.1 34 61-94 17-50 (53)
121 PRK13918 CRP/FNR family transc 59.4 30 0.00065 32.4 6.8 30 163-192 148-177 (202)
122 cd06170 LuxR_C_like C-terminal 59.2 12 0.00027 27.2 3.3 27 164-190 15-41 (57)
123 TIGR01764 excise DNA binding d 59.2 9.9 0.00021 27.0 2.7 23 165-187 2-24 (49)
124 PF09862 DUF2089: Protein of u 59.1 32 0.0007 30.6 6.3 72 44-124 35-107 (113)
125 PF07638 Sigma70_ECF: ECF sigm 58.6 16 0.00034 34.6 4.7 25 165-189 152-176 (185)
126 cd00092 HTH_CRP helix_turn_hel 58.5 34 0.00074 26.0 5.9 30 61-90 23-52 (67)
127 PF01978 TrmB: Sugar-specific 58.5 9.7 0.00021 29.9 2.8 37 153-190 12-48 (68)
128 PF05344 DUF746: Domain of Unk 58.2 15 0.00032 29.5 3.7 31 159-189 8-38 (65)
129 PRK11161 fumarate/nitrate redu 58.0 32 0.0007 33.1 7.0 30 163-192 183-212 (235)
130 PF13011 LZ_Tnp_IS481: leucine 57.9 20 0.00043 30.3 4.6 37 154-190 15-51 (85)
131 PRK13413 mpi multiple promoter 57.8 28 0.0006 33.3 6.4 25 164-188 172-196 (200)
132 PF00440 TetR_N: Bacterial reg 57.7 22 0.00047 25.9 4.3 35 152-187 4-39 (47)
133 PF08280 HTH_Mga: M protein tr 57.5 14 0.0003 28.5 3.4 30 162-191 17-46 (59)
134 PF01371 Trp_repressor: Trp re 57.4 15 0.00032 31.2 3.8 31 160-190 45-75 (87)
135 PRK11511 DNA-binding transcrip 57.1 34 0.00073 30.4 6.3 56 43-112 6-61 (127)
136 smart00418 HTH_ARSR helix_turn 56.2 21 0.00046 26.2 4.3 29 162-190 8-36 (66)
137 PRK15418 transcriptional regul 56.0 8 0.00017 40.2 2.4 45 156-200 21-65 (318)
138 PRK07921 RNA polymerase sigma 55.9 82 0.0018 32.9 9.9 24 163-186 281-304 (324)
139 PRK10434 srlR DNA-bindng trans 55.7 13 0.00028 37.3 3.8 28 163-190 18-45 (256)
140 PF00356 LacI: Bacterial regul 55.7 14 0.00029 27.5 2.9 20 65-84 1-20 (46)
141 cd00090 HTH_ARSR Arsenical Res 55.6 23 0.00049 26.8 4.5 26 165-190 21-46 (78)
142 TIGR02844 spore_III_D sporulat 55.6 17 0.00037 30.3 3.8 23 163-185 18-40 (80)
143 cd04761 HTH_MerR-SF Helix-Turn 55.3 11 0.00024 27.0 2.5 23 166-188 2-24 (49)
144 PRK14088 dnaA chromosomal repl 55.3 95 0.0021 33.7 10.6 51 138-190 360-413 (440)
145 cd00569 HTH_Hin_like Helix-tur 55.3 12 0.00026 23.7 2.4 21 164-184 21-41 (42)
146 TIGR01321 TrpR trp operon repr 54.9 14 0.00031 31.8 3.3 30 160-189 51-80 (94)
147 PRK04217 hypothetical protein; 54.6 16 0.00035 32.3 3.7 27 163-189 57-83 (110)
148 PRK10219 DNA-binding transcrip 54.5 68 0.0015 27.2 7.6 51 149-205 7-57 (107)
149 PF02082 Rrf2: Transcriptional 54.4 14 0.00029 30.4 3.1 37 154-190 15-51 (83)
150 PRK10219 DNA-binding transcrip 54.2 47 0.001 28.1 6.6 39 48-87 7-45 (107)
151 cd06171 Sigma70_r4 Sigma70, re 53.7 24 0.00052 24.9 4.1 27 163-189 25-51 (55)
152 cd07377 WHTH_GntR Winged helix 53.7 15 0.00034 27.6 3.2 26 166-191 27-52 (66)
153 PRK11161 fumarate/nitrate redu 53.5 48 0.001 31.9 7.3 53 41-93 152-214 (235)
154 PRK09391 fixK transcriptional 53.2 48 0.001 32.2 7.3 30 163-192 178-207 (230)
155 cd01104 HTH_MlrA-CarA Helix-Tu 53.1 13 0.00029 28.8 2.7 23 166-188 2-24 (68)
156 PF12728 HTH_17: Helix-turn-he 52.9 15 0.00033 26.9 2.9 23 165-187 2-24 (51)
157 PF01726 LexA_DNA_bind: LexA D 52.9 15 0.00033 29.2 3.0 32 159-190 20-52 (65)
158 PRK11014 transcriptional repre 52.7 18 0.00039 32.7 3.9 38 153-190 14-51 (141)
159 PRK09413 IS2 repressor TnpA; R 52.6 25 0.00055 31.1 4.7 30 161-190 26-55 (121)
160 PRK06288 RNA polymerase sigma 52.5 2.5E+02 0.0055 28.0 15.8 25 163-187 227-251 (268)
161 TIGR00738 rrf2_super rrf2 fami 52.5 32 0.0007 30.3 5.5 45 46-90 8-52 (132)
162 TIGR02944 suf_reg_Xantho FeS a 52.4 31 0.00066 30.6 5.3 38 153-191 15-52 (130)
163 TIGR02944 suf_reg_Xantho FeS a 52.4 35 0.00076 30.2 5.7 46 44-90 7-52 (130)
164 PF13542 HTH_Tnp_ISL3: Helix-t 52.1 55 0.0012 23.9 5.9 42 43-87 10-51 (52)
165 TIGR02997 Sig70-cyanoRpoD RNA 51.9 2.8E+02 0.006 28.3 16.9 25 163-187 268-292 (298)
166 smart00550 Zalpha Z-DNA-bindin 51.7 31 0.00068 27.4 4.7 37 154-190 11-48 (68)
167 PF12116 SpoIIID: Stage III sp 51.7 9.8 0.00021 31.7 1.7 35 153-187 8-42 (82)
168 PRK07500 rpoH2 RNA polymerase 51.6 2.8E+02 0.006 28.2 15.1 28 162-189 243-270 (289)
169 PRK13501 transcriptional activ 51.6 2.6E+02 0.0057 27.9 14.2 58 142-204 217-277 (290)
170 TIGR02394 rpoS_proteo RNA poly 51.5 2.7E+02 0.0059 28.1 17.1 26 163-188 241-266 (285)
171 PRK13509 transcriptional repre 51.5 14 0.00031 36.9 3.3 29 162-190 17-45 (251)
172 PF09339 HTH_IclR: IclR helix- 50.7 19 0.00042 26.7 3.2 32 160-191 14-45 (52)
173 PRK10402 DNA-binding transcrip 50.4 34 0.00074 33.1 5.7 30 163-192 168-197 (226)
174 smart00351 PAX Paired Box doma 50.2 21 0.00046 31.8 3.9 29 164-192 33-61 (125)
175 cd00131 PAX Paired Box domain 49.9 21 0.00046 32.0 3.9 30 163-192 32-61 (128)
176 PRK00118 putative DNA-binding 49.9 20 0.00043 31.4 3.5 27 163-189 32-58 (104)
177 PRK10870 transcriptional repre 49.6 62 0.0013 30.5 7.2 30 162-191 69-98 (176)
178 smart00419 HTH_CRP helix_turn_ 49.6 27 0.00058 24.7 3.7 30 61-90 6-35 (48)
179 PF12802 MarR_2: MarR family; 49.5 38 0.00082 25.5 4.7 41 50-90 8-48 (62)
180 KOG0654 G2/Mitotic-specific cy 49.5 1.5E+02 0.0033 31.5 10.6 133 51-189 185-320 (359)
181 PRK05911 RNA polymerase sigma 49.1 2.8E+02 0.0061 27.6 13.5 27 162-188 219-245 (257)
182 PRK10572 DNA-binding transcrip 49.1 57 0.0012 32.6 7.3 26 62-87 247-273 (290)
183 COG3415 Transposase and inacti 48.9 24 0.00053 32.4 4.1 33 161-193 18-50 (138)
184 PF07900 DUF1670: Protein of u 48.8 2.3E+02 0.005 28.1 11.0 101 63-183 105-216 (220)
185 PF13412 HTH_24: Winged helix- 48.5 53 0.0012 23.7 5.2 29 61-89 15-43 (48)
186 cd06571 Bac_DnaA_C C-terminal 48.4 46 0.001 27.8 5.5 45 47-93 30-75 (90)
187 PRK07598 RNA polymerase sigma 48.2 4E+02 0.0086 29.0 17.3 86 6-91 186-306 (415)
188 COG1318 Predicted transcriptio 48.2 24 0.00053 33.6 4.0 72 121-204 28-99 (182)
189 PRK11753 DNA-binding transcrip 48.1 75 0.0016 29.8 7.6 47 44-90 140-195 (211)
190 smart00346 HTH_ICLR helix_turn 47.9 47 0.001 27.0 5.4 28 163-190 19-46 (91)
191 TIGR02985 Sig70_bacteroi1 RNA 47.8 18 0.00039 32.2 3.1 27 163-189 128-154 (161)
192 COG1309 AcrR Transcriptional r 47.3 20 0.00044 31.4 3.3 39 149-188 17-56 (201)
193 PF04545 Sigma70_r4: Sigma-70, 46.9 38 0.00083 24.7 4.2 31 61-91 18-48 (50)
194 PF14502 HTH_41: Helix-turn-he 46.8 21 0.00045 27.0 2.7 29 165-193 7-35 (48)
195 PF00196 GerE: Bacterial regul 46.8 18 0.0004 27.4 2.6 27 163-189 17-43 (58)
196 COG1725 Predicted transcriptio 46.4 20 0.00044 32.4 3.1 30 161-190 31-61 (125)
197 PF13443 HTH_26: Cro/C1-type H 46.4 35 0.00075 26.0 4.1 41 163-207 9-49 (63)
198 PRK10402 DNA-binding transcrip 46.1 55 0.0012 31.6 6.4 47 44-90 150-196 (226)
199 PHA00542 putative Cro-like pro 45.7 18 0.00039 29.9 2.5 42 160-205 27-68 (82)
200 PRK09642 RNA polymerase sigma 45.5 9.1 0.0002 34.7 0.8 27 163-189 121-147 (160)
201 PRK06030 hypothetical protein; 45.2 51 0.0011 29.8 5.5 69 21-91 26-97 (124)
202 PRK11753 DNA-binding transcrip 45.2 76 0.0016 29.8 7.1 29 163-191 167-195 (211)
203 PF12840 HTH_20: Helix-turn-he 45.0 37 0.0008 26.0 4.1 31 161-191 21-51 (61)
204 PF05732 RepL: Firmicute plasm 44.8 31 0.00067 32.5 4.2 27 165-191 76-102 (165)
205 TIGR02405 trehalos_R_Ecol treh 44.7 16 0.00035 36.7 2.5 24 164-187 1-24 (311)
206 PF09862 DUF2089: Protein of u 44.6 22 0.00047 31.7 2.9 26 165-190 50-75 (113)
207 PF12833 HTH_18: Helix-turn-he 44.5 54 0.0012 26.1 5.2 67 11-87 1-70 (81)
208 PF00196 GerE: Bacterial regul 44.2 32 0.0007 26.0 3.6 33 62-94 17-49 (58)
209 PRK10371 DNA-binding transcrip 44.1 2.5E+02 0.0054 28.6 11.2 40 47-87 192-231 (302)
210 PF01527 HTH_Tnp_1: Transposas 43.9 21 0.00047 28.2 2.7 26 164-189 23-48 (76)
211 PRK01381 Trp operon repressor; 43.8 18 0.00039 31.4 2.3 37 156-192 47-83 (99)
212 PF13556 HTH_30: PucR C-termin 43.5 28 0.00062 26.7 3.2 29 163-191 11-39 (59)
213 PF04218 CENP-B_N: CENP-B N-te 43.1 15 0.00033 27.9 1.5 23 165-187 23-45 (53)
214 PRK12529 RNA polymerase sigma 42.9 23 0.0005 33.0 3.1 25 163-187 142-166 (178)
215 COG3877 Uncharacterized protei 42.6 1.3E+02 0.0028 26.6 7.3 70 44-123 43-114 (122)
216 PF05460 ORC6: Origin recognit 42.5 8.3 0.00018 40.8 0.0 79 112-190 4-83 (353)
217 PRK09526 lacI lac repressor; R 42.4 20 0.00043 36.4 2.7 45 164-210 5-49 (342)
218 PF01381 HTH_3: Helix-turn-hel 42.3 23 0.00049 26.1 2.4 39 162-205 7-45 (55)
219 cd04764 HTH_MlrA-like_sg1 Heli 42.2 25 0.00055 27.3 2.8 23 166-188 2-24 (67)
220 PRK10411 DNA-binding transcrip 42.2 25 0.00054 35.0 3.4 28 163-190 17-44 (240)
221 PF04079 DUF387: Putative tran 42.2 2.1E+02 0.0045 26.8 9.3 107 49-188 3-120 (159)
222 TIGR02999 Sig-70_X6 RNA polyme 42.2 24 0.00052 32.6 3.1 26 163-188 149-174 (183)
223 smart00354 HTH_LACI helix_turn 42.0 22 0.00049 28.2 2.5 35 165-204 1-35 (70)
224 PRK09685 DNA-binding transcrip 42.0 98 0.0021 31.0 7.7 55 145-205 195-249 (302)
225 PF07278 DUF1441: Protein of u 41.8 21 0.00046 33.3 2.6 26 164-189 1-26 (152)
226 PRK15121 right oriC-binding tr 41.8 54 0.0012 33.1 5.8 53 46-112 5-57 (289)
227 PF13411 MerR_1: MerR HTH fami 41.7 20 0.00044 27.8 2.1 24 166-189 2-25 (69)
228 smart00421 HTH_LUXR helix_turn 41.6 52 0.0011 23.6 4.3 31 64-94 19-49 (58)
229 PRK10703 DNA-binding transcrip 41.5 25 0.00054 35.7 3.3 22 165-186 2-23 (341)
230 PF04703 FaeA: FaeA-like prote 41.5 41 0.00089 26.6 3.8 29 162-190 13-41 (62)
231 PF00376 MerR: MerR family reg 41.4 19 0.00041 25.5 1.7 21 166-186 1-21 (38)
232 PRK10130 transcriptional regul 40.7 59 0.0013 34.2 6.1 54 45-112 239-292 (350)
233 PRK09492 treR trehalose repres 40.6 19 0.00041 36.0 2.3 24 164-187 4-27 (315)
234 smart00422 HTH_MERR helix_turn 40.5 25 0.00054 27.2 2.5 22 166-187 2-23 (70)
235 cd04763 HTH_MlrA-like Helix-Tu 40.5 27 0.00059 27.3 2.7 23 166-188 2-24 (68)
236 COG1959 Predicted transcriptio 40.5 65 0.0014 29.8 5.6 45 46-90 8-52 (150)
237 PRK09391 fixK transcriptional 40.4 1.1E+02 0.0025 29.5 7.7 48 43-90 153-206 (230)
238 PRK09645 RNA polymerase sigma 40.1 27 0.00058 32.0 3.0 26 163-188 133-158 (173)
239 PRK10014 DNA-binding transcrip 40.0 22 0.00048 36.0 2.7 37 163-204 5-41 (342)
240 cd06170 LuxR_C_like C-terminal 39.7 57 0.0012 23.5 4.3 32 63-94 15-46 (57)
241 PF13744 HTH_37: Helix-turn-he 39.7 49 0.0011 27.0 4.2 46 156-205 23-68 (80)
242 PRK09047 RNA polymerase factor 39.5 28 0.00061 31.3 3.1 27 163-189 121-147 (161)
243 TIGR02702 SufR_cyano iron-sulf 39.4 49 0.0011 31.8 4.9 28 164-191 15-42 (203)
244 PRK09480 slmA division inhibit 39.3 35 0.00076 31.5 3.8 44 144-187 10-53 (194)
245 smart00550 Zalpha Z-DNA-bindin 39.1 79 0.0017 25.0 5.2 38 53-90 11-49 (68)
246 PRK13918 CRP/FNR family transc 39.0 1.1E+02 0.0023 28.6 7.0 30 62-91 148-177 (202)
247 PRK06759 RNA polymerase factor 38.7 30 0.00065 30.9 3.1 26 163-188 121-146 (154)
248 PF01418 HTH_6: Helix-turn-hel 38.7 26 0.00057 28.4 2.4 28 163-190 33-60 (77)
249 smart00345 HTH_GNTR helix_turn 38.7 55 0.0012 24.0 4.1 26 65-90 22-47 (60)
250 PRK12543 RNA polymerase sigma 38.3 43 0.00094 31.0 4.2 27 163-189 132-158 (179)
251 TIGR00281 segregation and cond 38.3 3E+02 0.0065 26.5 9.9 120 46-188 3-125 (186)
252 KOG3915 Transcription regulato 38.0 97 0.0021 34.0 7.0 18 369-390 530-547 (641)
253 TIGR02937 sigma70-ECF RNA poly 38.0 41 0.00089 29.0 3.8 27 163-189 125-151 (158)
254 PRK12525 RNA polymerase sigma 37.9 31 0.00067 31.7 3.1 26 163-188 133-158 (168)
255 PRK08215 sporulation sigma fac 37.8 4.1E+02 0.0089 26.2 17.6 26 163-188 224-249 (258)
256 PF13463 HTH_27: Winged helix 37.7 62 0.0013 24.7 4.4 32 59-90 14-45 (68)
257 COG1476 Predicted transcriptio 37.6 25 0.00055 28.4 2.1 24 163-186 13-36 (68)
258 PF01710 HTH_Tnp_IS630: Transp 37.6 1.3E+02 0.0029 26.4 6.9 75 7-91 20-99 (119)
259 PRK12523 RNA polymerase sigma 37.6 31 0.00068 31.7 3.1 25 163-187 134-158 (172)
260 PF04552 Sigma54_DBD: Sigma-54 37.5 9.2 0.0002 36.0 -0.5 41 164-204 49-90 (160)
261 COG3355 Predicted transcriptio 37.4 58 0.0013 29.5 4.6 38 154-191 32-69 (126)
262 COG4977 Transcriptional regula 37.2 2.2E+02 0.0048 29.9 9.5 80 61-192 234-314 (328)
263 TIGR02980 SigBFG RNA polymeras 37.2 3.8E+02 0.0083 25.7 16.1 26 163-188 193-218 (227)
264 PF10668 Phage_terminase: Phag 37.1 90 0.002 24.7 5.0 24 60-83 19-42 (60)
265 PF05930 Phage_AlpA: Prophage 36.9 34 0.00074 25.5 2.6 23 165-187 4-26 (51)
266 PF05043 Mga: Mga helix-turn-h 36.8 37 0.00081 27.8 3.1 30 160-189 26-55 (87)
267 PRK12531 RNA polymerase sigma 36.8 32 0.00069 32.4 3.0 26 163-188 156-181 (194)
268 PRK10072 putative transcriptio 36.8 35 0.00077 29.3 3.0 29 161-189 43-71 (96)
269 PRK09954 putative kinase; Prov 36.7 46 0.00099 34.6 4.5 29 162-190 15-43 (362)
270 TIGR02947 SigH_actino RNA poly 36.7 32 0.00068 32.3 3.0 27 163-189 146-172 (193)
271 PRK15340 transcriptional regul 36.4 4.3E+02 0.0094 26.1 11.7 29 60-88 122-150 (216)
272 PRK09685 DNA-binding transcrip 36.4 2E+02 0.0044 28.7 9.0 43 44-86 195-237 (302)
273 TIGR02531 yecD_yerC TrpR-relat 36.4 44 0.00096 28.3 3.5 23 163-186 49-71 (88)
274 TIGR02885 spore_sigF RNA polym 36.3 4E+02 0.0087 25.7 16.4 27 162-188 197-223 (231)
275 smart00347 HTH_MARR helix_turn 36.3 83 0.0018 25.4 5.2 28 164-191 24-51 (101)
276 PF01047 MarR: MarR family; I 36.0 65 0.0014 24.1 4.1 27 164-190 17-43 (59)
277 PRK09392 ftrB transcriptional 36.0 88 0.0019 30.1 6.1 30 163-192 172-201 (236)
278 PRK12528 RNA polymerase sigma 35.8 35 0.00077 30.9 3.1 26 163-188 128-153 (161)
279 PF13730 HTH_36: Helix-turn-he 35.5 1E+02 0.0022 22.7 5.1 25 65-89 27-51 (55)
280 TIGR02147 Fsuc_second hypothet 35.5 5E+02 0.011 26.5 12.5 124 54-191 17-166 (271)
281 TIGR03070 couple_hipB transcri 35.3 43 0.00094 24.4 3.0 39 162-205 13-51 (58)
282 PRK12527 RNA polymerase sigma 35.3 36 0.00079 30.7 3.1 26 163-188 120-145 (159)
283 PRK11014 transcriptional repre 35.1 78 0.0017 28.5 5.2 45 46-90 8-52 (141)
284 PF13463 HTH_27: Winged helix 35.1 52 0.0011 25.2 3.5 31 161-191 15-45 (68)
285 PRK10906 DNA-binding transcrip 35.0 31 0.00068 34.5 2.8 28 163-190 18-45 (252)
286 PRK07670 RNA polymerase sigma 35.0 4.5E+02 0.0097 25.8 17.5 27 163-189 216-242 (251)
287 TIGR02952 Sig70_famx2 RNA poly 35.0 37 0.0008 30.8 3.1 27 163-189 137-163 (170)
288 PRK14962 DNA polymerase III su 35.0 6.5E+02 0.014 27.7 13.7 88 63-151 229-326 (472)
289 cd06571 Bac_DnaA_C C-terminal 35.0 68 0.0015 26.7 4.5 37 152-190 34-71 (90)
290 TIGR02010 IscR iron-sulfur clu 34.9 62 0.0013 29.0 4.5 40 152-191 13-52 (135)
291 KOG1010 Rb (Retinoblastoma tum 34.9 89 0.0019 36.7 6.5 56 6-64 36-91 (920)
292 PF01047 MarR: MarR family; I 34.8 99 0.0021 23.0 5.0 37 52-90 8-44 (59)
293 PRK14987 gluconate operon tran 34.5 25 0.00054 35.5 2.0 24 164-187 5-28 (331)
294 TIGR01481 ccpA catabolite cont 34.4 28 0.0006 35.1 2.4 23 165-187 2-24 (329)
295 TIGR02954 Sig70_famx3 RNA poly 34.4 53 0.0011 30.0 4.0 27 163-189 134-160 (169)
296 PRK09393 ftrA transcriptional 34.4 93 0.002 31.8 6.3 83 8-112 237-320 (322)
297 PRK00430 fis global DNA-bindin 34.4 91 0.002 26.6 5.2 26 164-189 68-93 (95)
298 PRK09649 RNA polymerase sigma 34.3 37 0.00081 31.8 3.1 27 163-189 145-171 (185)
299 TIGR02950 SigM_subfam RNA poly 34.3 38 0.00083 30.2 3.0 26 163-188 120-145 (154)
300 PRK13698 plasmid-partitioning 34.3 45 0.00096 35.0 3.8 35 155-189 167-201 (323)
301 COG3620 Predicted transcriptio 34.2 41 0.0009 31.9 3.2 44 161-204 15-73 (187)
302 PF04703 FaeA: FaeA-like prote 33.9 79 0.0017 25.0 4.3 34 61-94 13-46 (62)
303 PRK11303 DNA-binding transcrip 33.9 30 0.00066 34.7 2.5 22 166-187 2-23 (328)
304 TIGR01610 phage_O_Nterm phage 33.9 1.2E+02 0.0026 25.6 5.9 31 60-90 44-74 (95)
305 PF09339 HTH_IclR: IclR helix- 33.8 69 0.0015 23.7 3.9 35 55-89 10-44 (52)
306 PRK15435 bifunctional DNA-bind 33.7 1.2E+02 0.0026 32.0 7.1 50 46-111 85-134 (353)
307 PRK08301 sporulation sigma fac 33.7 37 0.00081 33.0 3.1 26 163-188 197-222 (234)
308 PRK12542 RNA polymerase sigma 33.6 39 0.00085 31.4 3.1 42 163-204 137-181 (185)
309 PRK11512 DNA-binding transcrip 33.3 66 0.0014 28.9 4.4 29 162-190 52-80 (144)
310 PRK12520 RNA polymerase sigma 33.2 38 0.00081 31.7 2.9 27 163-189 146-172 (191)
311 PRK12519 RNA polymerase sigma 33.2 39 0.00086 31.6 3.0 25 163-187 156-180 (194)
312 TIGR00498 lexA SOS regulatory 33.2 69 0.0015 30.4 4.7 32 160-191 21-53 (199)
313 PF03444 HrcA_DNA-bdg: Winged 33.1 93 0.002 25.9 4.7 29 161-189 20-48 (78)
314 PRK09639 RNA polymerase sigma 33.1 53 0.0011 29.7 3.8 27 163-189 126-152 (166)
315 PF01498 HTH_Tnp_Tc3_2: Transp 32.7 43 0.00094 26.4 2.8 27 163-189 12-43 (72)
316 PF05269 Phage_CII: Bacterioph 32.6 19 0.00042 30.7 0.7 24 165-188 24-47 (91)
317 TIGR02417 fruct_sucro_rep D-fr 32.5 31 0.00067 34.7 2.3 22 166-187 1-22 (327)
318 PF00126 HTH_1: Bacterial regu 32.4 78 0.0017 24.1 4.1 25 166-190 15-39 (60)
319 PRK12545 RNA polymerase sigma 32.1 40 0.00086 32.1 2.9 26 163-188 154-179 (201)
320 COG3711 BglG Transcriptional a 32.0 2.2E+02 0.0047 30.9 8.9 108 59-187 15-123 (491)
321 PRK13919 putative RNA polymera 31.9 43 0.00093 31.1 3.0 26 163-188 150-175 (186)
322 PRK14088 dnaA chromosomal repl 31.9 75 0.0016 34.5 5.3 68 21-91 345-415 (440)
323 PRK12547 RNA polymerase sigma 31.8 44 0.00096 30.5 3.1 27 163-189 127-153 (164)
324 TIGR00721 tfx DNA-binding prot 31.8 54 0.0012 30.1 3.5 27 163-189 20-46 (137)
325 PRK10130 transcriptional regul 31.8 2.6E+02 0.0055 29.5 9.1 53 147-205 240-292 (350)
326 PRK09802 DNA-binding transcrip 31.7 63 0.0014 32.6 4.4 27 164-190 31-57 (269)
327 COG1595 RpoE DNA-directed RNA 31.7 45 0.00098 31.0 3.2 26 163-188 142-167 (182)
328 TIGR02983 SigE-fam_strep RNA p 31.6 44 0.00095 30.1 3.0 27 163-189 125-151 (162)
329 TIGR02607 antidote_HigA addict 31.6 56 0.0012 25.8 3.3 41 160-205 14-54 (78)
330 COG4753 Response regulator con 31.5 1.9E+02 0.004 32.1 8.1 32 58-89 383-414 (475)
331 PF13560 HTH_31: Helix-turn-he 31.5 55 0.0012 25.2 3.1 40 162-205 12-51 (64)
332 COG2390 DeoR Transcriptional r 31.5 55 0.0012 34.2 4.0 43 157-199 19-61 (321)
333 PRK10339 DNA-binding transcrip 31.4 29 0.00064 35.0 2.0 37 165-204 2-38 (327)
334 PRK09652 RNA polymerase sigma 31.4 46 0.00099 30.3 3.1 26 163-188 143-168 (182)
335 PF04967 HTH_10: HTH DNA bindi 31.3 2.4E+02 0.0052 21.6 6.4 44 28-89 6-49 (53)
336 PRK10401 DNA-binding transcrip 31.3 34 0.00075 34.8 2.5 23 165-187 2-24 (346)
337 PF08220 HTH_DeoR: DeoR-like h 31.2 69 0.0015 24.5 3.5 31 61-91 12-42 (57)
338 PRK04424 fatty acid biosynthes 31.1 73 0.0016 30.4 4.5 29 163-191 20-48 (185)
339 PRK04984 fatty acid metabolism 31.1 53 0.0012 31.9 3.7 30 161-190 27-57 (239)
340 TIGR03338 phnR_burk phosphonat 31.1 45 0.00098 31.8 3.1 30 161-190 31-60 (212)
341 PRK09415 RNA polymerase factor 31.0 46 0.001 30.9 3.1 27 163-189 142-168 (179)
342 COG1725 Predicted transcriptio 30.9 60 0.0013 29.4 3.6 26 65-90 37-62 (125)
343 PRK12530 RNA polymerase sigma 30.9 46 0.001 31.3 3.1 26 163-188 149-174 (189)
344 PRK09651 RNA polymerase sigma 30.8 47 0.001 30.6 3.1 27 162-188 133-159 (172)
345 COG1349 GlpR Transcriptional r 30.8 37 0.00081 34.0 2.6 27 163-189 18-44 (253)
346 TIGR02939 RpoE_Sigma70 RNA pol 30.8 47 0.001 30.7 3.1 27 163-189 153-179 (190)
347 TIGR02989 Sig-70_gvs1 RNA poly 30.7 48 0.001 29.7 3.0 27 163-189 126-152 (159)
348 COG1321 TroR Mn-dependent tran 30.6 74 0.0016 29.6 4.3 37 153-190 14-50 (154)
349 PRK10681 DNA-binding transcrip 30.6 48 0.001 33.1 3.3 27 163-189 20-46 (252)
350 PRK07037 extracytoplasmic-func 30.6 48 0.001 29.9 3.1 25 163-187 124-148 (163)
351 TIGR02366 DHAK_reg probable di 30.5 61 0.0013 29.6 3.8 40 148-188 7-47 (176)
352 PRK11050 manganese transport r 30.5 90 0.0019 28.7 4.9 30 162-191 49-78 (152)
353 PRK12533 RNA polymerase sigma 30.5 46 0.001 32.4 3.1 27 163-189 149-175 (216)
354 COG0664 Crp cAMP-binding prote 30.4 1.7E+02 0.0036 26.8 6.8 29 163-191 170-198 (214)
355 PRK03902 manganese transport t 30.4 81 0.0018 28.4 4.5 29 163-191 21-49 (142)
356 PF08281 Sigma70_r4_2: Sigma-7 30.2 79 0.0017 23.2 3.7 27 64-90 27-53 (54)
357 PRK14999 histidine utilization 30.2 55 0.0012 32.1 3.6 29 162-190 33-62 (241)
358 PRK12537 RNA polymerase sigma 30.2 46 0.00099 31.0 2.9 26 163-188 148-173 (182)
359 PRK06704 RNA polymerase factor 30.1 63 0.0014 31.9 4.0 27 163-189 131-157 (228)
360 TIGR00738 rrf2_super rrf2 fami 30.1 1.3E+02 0.0029 26.3 5.7 43 149-191 9-52 (132)
361 PRK12469 RNA polymerase factor 30.1 66 0.0014 35.6 4.5 185 8-204 163-410 (481)
362 COG1510 Predicted transcriptio 30.1 62 0.0013 31.0 3.6 56 128-190 12-67 (177)
363 PRK10727 DNA-binding transcrip 30.0 36 0.00078 34.6 2.3 35 165-204 2-36 (343)
364 PF05344 DUF746: Domain of Unk 30.0 1.3E+02 0.0029 24.1 5.0 35 57-91 7-41 (65)
365 smart00530 HTH_XRE Helix-turn- 29.9 59 0.0013 22.2 2.9 39 162-205 8-46 (56)
366 PF03428 RP-C: Replication pro 29.9 1.8E+02 0.004 27.8 6.9 57 120-191 41-98 (177)
367 PRK12532 RNA polymerase sigma 29.9 49 0.0011 31.1 3.1 27 163-189 151-177 (195)
368 TIGR02337 HpaR homoprotocatech 29.9 74 0.0016 27.5 4.0 30 162-191 40-69 (118)
369 PRK13501 transcriptional activ 29.8 1.5E+02 0.0033 29.6 6.9 71 8-88 195-267 (290)
370 PRK09978 DNA-binding transcrip 29.7 2.8E+02 0.006 28.4 8.6 53 146-205 141-193 (274)
371 PRK09643 RNA polymerase sigma 29.7 49 0.0011 31.2 3.1 26 163-188 149-174 (192)
372 COG3413 Predicted DNA binding 29.6 76 0.0016 30.7 4.4 25 164-188 178-202 (215)
373 PF06056 Terminase_5: Putative 29.5 65 0.0014 25.0 3.1 28 163-190 12-39 (58)
374 PRK12536 RNA polymerase sigma 29.5 51 0.0011 30.6 3.1 26 163-188 144-169 (181)
375 smart00351 PAX Paired Box doma 29.4 2.7E+02 0.0058 24.7 7.6 61 8-73 36-103 (125)
376 TIGR02404 trehalos_R_Bsub treh 29.3 51 0.0011 32.1 3.2 29 162-190 21-50 (233)
377 PF13404 HTH_AsnC-type: AsnC-t 29.3 1.2E+02 0.0027 21.8 4.4 29 59-87 13-41 (42)
378 TIGR03209 P21_Cbot clostridium 29.2 29 0.00064 30.7 1.4 21 163-183 122-142 (142)
379 PRK14165 winged helix-turn-hel 28.9 60 0.0013 32.0 3.6 30 162-191 19-48 (217)
380 PRK12518 RNA polymerase sigma 28.9 52 0.0011 30.1 3.0 27 163-189 135-161 (175)
381 PRK09975 DNA-binding transcrip 28.9 83 0.0018 29.6 4.5 39 148-187 15-54 (213)
382 COG2207 AraC AraC-type DNA-bin 28.9 1.2E+02 0.0026 25.4 5.1 47 151-203 24-70 (127)
383 TIGR02325 C_P_lyase_phnF phosp 28.8 52 0.0011 31.9 3.2 29 162-190 29-58 (238)
384 PF13936 HTH_38: Helix-turn-he 28.8 97 0.0021 22.4 3.8 26 60-85 17-42 (44)
385 TIGR02392 rpoH_proteo alternat 28.8 75 0.0016 31.9 4.4 27 162-188 234-260 (270)
386 PRK12517 RNA polymerase sigma 28.8 52 0.0011 31.0 3.1 27 163-189 143-169 (188)
387 cd04765 HTH_MlrA-like_sg2 Heli 28.7 63 0.0014 27.7 3.3 24 166-189 2-25 (99)
388 PHA01976 helix-turn-helix prot 28.7 65 0.0014 24.7 3.1 38 163-205 14-51 (67)
389 PF07037 DUF1323: Putative tra 28.5 56 0.0012 29.4 2.9 24 165-188 1-24 (122)
390 PRK09646 RNA polymerase sigma 28.5 77 0.0017 29.8 4.2 26 163-188 157-182 (194)
391 PRK12524 RNA polymerase sigma 28.4 53 0.0011 31.0 3.1 27 163-189 151-177 (196)
392 PRK05602 RNA polymerase sigma 28.4 54 0.0012 30.5 3.0 27 163-189 143-169 (186)
393 PRK15481 transcriptional regul 28.3 1E+02 0.0023 32.7 5.6 30 162-191 26-56 (431)
394 PRK09956 hypothetical protein; 28.2 1.6E+02 0.0034 30.5 6.7 79 104-183 224-305 (308)
395 PRK11924 RNA polymerase sigma 28.1 61 0.0013 29.3 3.3 26 163-188 140-165 (179)
396 PRK12541 RNA polymerase sigma 28.0 58 0.0013 29.4 3.2 26 163-188 127-152 (161)
397 PRK09392 ftrB transcriptional 28.0 1.7E+02 0.0036 28.2 6.5 48 43-90 147-200 (236)
398 TIGR02959 SigZ RNA polymerase 27.9 58 0.0013 30.0 3.2 27 163-189 115-141 (170)
399 PRK12511 RNA polymerase sigma 27.8 56 0.0012 30.7 3.0 27 163-189 126-152 (182)
400 PRK12522 RNA polymerase sigma 27.7 56 0.0012 30.0 3.0 27 163-189 134-160 (173)
401 PRK12516 RNA polymerase sigma 27.7 56 0.0012 30.8 3.1 27 163-189 131-157 (187)
402 PF07900 DUF1670: Protein of u 27.7 57 0.0012 32.3 3.1 27 164-190 105-131 (220)
403 TIGR02943 Sig70_famx1 RNA poly 27.7 53 0.0012 30.9 2.9 27 163-189 146-172 (188)
404 PRK10430 DNA-binding transcrip 27.6 91 0.002 30.1 4.6 33 160-192 174-206 (239)
405 PRK10079 phosphonate metabolis 27.6 56 0.0012 32.0 3.2 25 166-190 37-61 (241)
406 PRK12526 RNA polymerase sigma 27.6 56 0.0012 31.2 3.1 26 163-188 168-193 (206)
407 smart00418 HTH_ARSR helix_turn 27.5 1.5E+02 0.0032 21.5 4.8 30 61-90 8-37 (66)
408 COG4565 CitB Response regulato 27.4 1.5E+02 0.0033 29.4 5.9 54 137-192 148-201 (224)
409 PF13384 HTH_23: Homeodomain-l 27.3 97 0.0021 22.3 3.7 27 63-89 17-43 (50)
410 PRK03837 transcriptional regul 27.2 70 0.0015 31.0 3.8 30 161-190 33-63 (241)
411 PRK11923 algU RNA polymerase s 27.2 67 0.0015 30.0 3.5 27 163-189 153-179 (193)
412 PRK09640 RNA polymerase sigma 27.1 59 0.0013 30.4 3.1 26 163-188 149-174 (188)
413 PRK11920 rirA iron-responsive 27.1 1E+02 0.0022 28.5 4.5 38 152-190 13-50 (153)
414 PRK15185 transcriptional regul 27.1 3.7E+02 0.008 28.1 9.1 80 8-112 225-307 (309)
415 PRK12514 RNA polymerase sigma 27.0 57 0.0012 30.1 2.9 26 163-188 144-169 (179)
416 TIGR02835 spore_sigmaE RNA pol 27.0 57 0.0012 31.9 3.1 25 163-187 197-221 (234)
417 PRK03573 transcriptional regul 26.9 1.1E+02 0.0024 27.3 4.7 30 162-191 44-73 (144)
418 COG2512 Predicted membrane-ass 26.9 76 0.0016 32.2 4.0 36 155-190 201-236 (258)
419 PRK13503 transcriptional activ 26.9 71 0.0015 31.5 3.8 51 48-112 173-223 (278)
420 PRK09863 putative frv operon r 26.8 2.4E+02 0.0053 31.5 8.4 104 62-191 16-119 (584)
421 TIGR00180 parB_part ParB-like 26.8 96 0.0021 29.4 4.5 43 143-188 102-144 (187)
422 COG2169 Ada Adenosine deaminas 26.8 1.3E+02 0.0028 29.2 5.2 44 44-89 80-123 (187)
423 PRK10840 transcriptional regul 26.7 76 0.0017 29.9 3.8 28 162-189 163-190 (216)
424 cd07377 WHTH_GntR Winged helix 26.7 95 0.0021 23.1 3.7 26 65-90 27-52 (66)
425 PRK10141 DNA-binding transcrip 26.7 1.1E+02 0.0024 27.2 4.6 30 162-191 28-57 (117)
426 PRK12534 RNA polymerase sigma 26.6 57 0.0012 30.3 2.9 27 163-189 152-178 (187)
427 PRK10870 transcriptional repre 26.6 2.9E+02 0.0063 25.9 7.7 39 52-90 60-98 (176)
428 TIGR03384 betaine_BetI transcr 26.6 96 0.0021 28.3 4.4 42 145-187 9-51 (189)
429 PRK09764 DNA-binding transcrip 26.5 69 0.0015 31.4 3.6 28 162-189 26-54 (240)
430 PF09904 HTH_43: Winged helix- 26.4 69 0.0015 27.4 3.0 38 153-190 10-47 (90)
431 PRK12539 RNA polymerase sigma 26.4 60 0.0013 30.2 3.0 26 163-188 146-171 (184)
432 TIGR02948 SigW_bacill RNA poly 26.3 61 0.0013 29.8 3.0 27 163-189 151-177 (187)
433 PRK09648 RNA polymerase sigma 26.2 63 0.0014 30.1 3.1 26 163-188 154-179 (189)
434 PRK12423 LexA repressor; Provi 26.2 1.2E+02 0.0026 29.2 5.1 31 160-190 21-52 (202)
435 PRK09644 RNA polymerase sigma 26.1 63 0.0014 29.4 3.0 27 163-189 123-149 (165)
436 TIGR02018 his_ut_repres histid 26.0 63 0.0014 31.4 3.2 29 162-190 22-51 (230)
437 PRK12513 RNA polymerase sigma 25.9 63 0.0014 30.2 3.1 26 163-188 154-179 (194)
438 COG1654 BirA Biotin operon rep 25.9 1.3E+02 0.0028 25.0 4.5 31 161-191 16-46 (79)
439 PF01978 TrmB: Sugar-specific 25.9 92 0.002 24.2 3.5 31 60-90 19-49 (68)
440 PF06892 Phage_CP76: Phage reg 25.8 58 0.0012 30.6 2.7 37 166-205 22-58 (162)
441 PRK09726 antitoxin HipB; Provi 25.7 1.6E+02 0.0034 24.3 5.1 40 162-206 23-62 (88)
442 COG2188 PhnF Transcriptional r 25.6 63 0.0014 31.8 3.1 25 166-190 33-57 (236)
443 COG2973 TrpR Trp operon repres 25.5 1.5E+02 0.0032 25.9 4.8 38 152-189 48-85 (103)
444 PRK09637 RNA polymerase sigma 25.5 65 0.0014 30.1 3.0 27 163-189 121-147 (181)
445 PF00392 GntR: Bacterial regul 25.5 1E+02 0.0022 23.7 3.7 30 61-90 21-51 (64)
446 PRK01905 DNA-binding protein F 25.4 99 0.0021 25.1 3.7 24 165-188 51-74 (77)
447 TIGR03001 Sig-70_gmx1 RNA poly 25.3 63 0.0014 32.1 3.1 27 163-189 176-202 (244)
448 PRK11886 bifunctional biotin-- 25.3 99 0.0021 31.8 4.6 29 162-190 16-44 (319)
449 PRK09990 DNA-binding transcrip 25.2 78 0.0017 31.1 3.7 30 161-190 27-57 (251)
450 PRK06986 fliA flagellar biosyn 25.0 65 0.0014 31.4 3.1 26 163-188 199-224 (236)
451 PRK13182 racA polar chromosome 25.0 61 0.0013 31.0 2.7 24 166-189 2-25 (175)
452 PRK08583 RNA polymerase sigma 25.0 79 0.0017 31.3 3.7 27 162-188 219-245 (257)
453 PRK11552 putative DNA-binding 24.9 94 0.002 30.2 4.1 38 148-186 17-54 (225)
454 smart00529 HTH_DTXR Helix-turn 24.8 72 0.0016 26.3 2.9 24 167-190 2-25 (96)
455 PRK08295 RNA polymerase factor 24.7 68 0.0015 30.2 3.0 27 163-189 169-195 (208)
456 TIGR02859 spore_sigH RNA polym 24.7 75 0.0016 29.6 3.3 27 164-190 165-191 (198)
457 PRK12515 RNA polymerase sigma 24.7 70 0.0015 29.8 3.1 27 163-189 146-172 (189)
458 PF01710 HTH_Tnp_IS630: Transp 24.4 1E+02 0.0023 27.0 4.0 32 162-193 69-100 (119)
459 PF01022 HTH_5: Bacterial regu 24.3 1.9E+02 0.0041 20.9 4.7 33 57-89 9-41 (47)
460 PRK13500 transcriptional activ 24.2 4E+02 0.0087 27.1 8.8 99 48-204 208-307 (312)
461 PF07022 Phage_CI_repr: Bacter 24.2 87 0.0019 24.6 3.1 26 160-186 9-35 (66)
462 PRK09638 RNA polymerase sigma 24.2 72 0.0016 29.2 3.0 26 163-188 141-166 (176)
463 PRK12535 RNA polymerase sigma 24.1 70 0.0015 30.4 3.0 26 163-188 148-173 (196)
464 PF02796 HTH_7: Helix-turn-hel 24.0 86 0.0019 22.7 2.8 22 63-84 21-42 (45)
465 PRK11534 DNA-binding transcrip 24.0 85 0.0018 30.2 3.6 29 161-189 27-55 (224)
466 COG0568 RpoD DNA-directed RNA 24.0 8.8E+02 0.019 25.7 11.5 112 61-183 203-318 (342)
467 PRK10421 DNA-binding transcrip 24.0 85 0.0018 30.9 3.7 30 161-190 22-52 (253)
468 COG1191 FliA DNA-directed RNA 23.9 7.6E+02 0.016 24.9 15.5 66 5-70 33-109 (247)
469 PRK06930 positive control sigm 23.8 81 0.0018 29.8 3.3 28 162-189 128-155 (170)
470 PF04552 Sigma54_DBD: Sigma-54 23.8 26 0.00057 32.9 0.0 25 62-86 48-72 (160)
471 TIGR02787 codY_Gpos GTP-sensin 23.7 1.3E+02 0.0028 30.4 4.8 28 163-190 197-224 (251)
472 PRK03975 tfx putative transcri 23.7 78 0.0017 29.2 3.1 25 163-187 20-44 (141)
473 PRK12538 RNA polymerase sigma 23.6 71 0.0015 31.4 3.1 26 163-188 186-211 (233)
474 TIGR02984 Sig-70_plancto1 RNA 23.6 77 0.0017 29.2 3.2 26 163-188 155-180 (189)
475 PRK11414 colanic acid/biofilm 23.6 77 0.0017 30.5 3.2 30 161-190 31-60 (221)
476 PRK09647 RNA polymerase sigma 23.5 74 0.0016 30.5 3.1 27 163-189 153-179 (203)
477 PRK11402 DNA-binding transcrip 23.5 74 0.0016 31.1 3.2 29 162-190 30-59 (241)
478 PRK06811 RNA polymerase factor 23.5 74 0.0016 29.8 3.0 26 163-188 146-171 (189)
479 TIGR03337 phnR transcriptional 23.4 81 0.0018 30.4 3.4 26 166-191 27-52 (231)
480 PRK09641 RNA polymerase sigma 23.4 76 0.0017 29.2 3.1 26 163-188 151-176 (187)
481 TIGR01884 cas_HTH CRISPR locus 23.4 1.2E+02 0.0025 29.2 4.4 28 164-191 157-184 (203)
482 PF06163 DUF977: Bacterial pro 23.2 93 0.002 28.2 3.4 29 163-191 25-53 (127)
483 PF01726 LexA_DNA_bind: LexA D 23.2 1.3E+02 0.0029 23.8 4.0 33 58-90 20-53 (65)
484 TIGR02297 HpaA 4-hydroxyphenyl 23.2 2.5E+02 0.0054 27.7 7.0 44 155-204 194-237 (287)
485 PRK13500 transcriptional activ 23.1 2.3E+02 0.005 28.9 6.8 27 61-87 269-296 (312)
486 PRK12546 RNA polymerase sigma 23.1 77 0.0017 29.9 3.1 27 163-189 128-154 (188)
487 COG1321 TroR Mn-dependent tran 23.0 1.5E+02 0.0032 27.6 4.9 38 51-89 13-50 (154)
488 PRK12540 RNA polymerase sigma 22.9 78 0.0017 29.6 3.1 27 163-189 126-152 (182)
489 TIGR02812 fadR_gamma fatty aci 22.8 93 0.002 30.2 3.7 30 161-190 26-56 (235)
490 PF01846 FF: FF domain; Inter 22.8 1.1E+02 0.0024 22.4 3.2 36 447-482 2-37 (51)
491 PRK09464 pdhR transcriptional 22.8 93 0.002 30.6 3.7 30 161-190 30-60 (254)
492 PF05066 HARE-HTH: HB1, ASXL, 22.6 81 0.0018 25.0 2.7 31 28-58 21-53 (72)
493 PF08280 HTH_Mga: M protein tr 22.6 93 0.002 23.9 2.9 32 61-92 17-48 (59)
494 PRK10857 DNA-binding transcrip 22.5 1.3E+02 0.0029 28.2 4.5 39 153-191 14-52 (164)
495 COG1609 PurR Transcriptional r 22.5 63 0.0014 33.5 2.5 35 165-204 1-35 (333)
496 PRK10225 DNA-binding transcrip 22.4 94 0.002 30.6 3.7 30 161-190 29-59 (257)
497 cd01392 HTH_LacI Helix-turn-he 22.4 60 0.0013 23.6 1.7 19 168-186 1-19 (52)
498 COG4861 Uncharacterized protei 22.3 76 0.0017 32.5 2.9 54 139-192 134-191 (345)
499 PRK08154 anaerobic benzoate ca 22.2 8.5E+02 0.019 24.9 12.0 120 60-181 38-179 (309)
500 cd04768 HTH_BmrR-like Helix-Tu 22.1 65 0.0014 27.2 2.1 22 166-187 2-23 (96)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=7e-68 Score=555.08 Aligned_cols=417 Identities=32% Similarity=0.436 Sum_probs=334.0
Q ss_pred ChHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHH
Q 010919 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 80 (497)
Q Consensus 1 L~~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~L 80 (497)
+++|++.|..++.+|+|+ . +++.|++||++|.++||++||+...|+|||+|++||+++++++|+||+++++|+||.|
T Consensus 67 ~~n~r~~i~~~~~~l~l~--~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~L 143 (521)
T KOG1598|consen 67 IYNARRLIEELTERLNLG--N-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDL 143 (521)
T ss_pred HHHHHhHHHHHHHhcCcc--h-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhh
Confidence 468999999999999999 7 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcccccccccccCCccchHHHHHhhhC-CCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHH
Q 010919 81 GAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 159 (497)
Q Consensus 81 gr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~-~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar 159 (497)
|++|++|++.|.|+.. +.+++||+.||+||+.+|. ++.+++|+.+|.+|+++|++|||++||+|+||||||||+|||
T Consensus 144 G~~~l~l~~~L~i~en--~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar 221 (521)
T KOG1598|consen 144 GSNFLEVTDSLSIGEN--VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAAR 221 (521)
T ss_pred hHHHHHHHHHhccccc--cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHH
Confidence 9999999999999842 3447999999999999997 888899999999999999999999999999999999999999
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhhhcccCCCCCCCCCCCCch--------hhhh
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHEGVAANLPNNGPKVSGMN--------EVLC 231 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~~dle~e~~~~pp~~~~~~~~~~--------~~~~ 231 (497)
+||+++|..||+.++|||+.||++||+||.+|+++.||+++|+++ |+|.+ +|||+|+....+.. .+.+
T Consensus 222 ~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~--d~e~~--~~ppsft~~~~~~~k~~~~~k~~l~~ 297 (521)
T KOG1598|consen 222 MHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELAEI--DLEYE--SDPPSFTASPSKEAKYVEDKKKMLSR 297 (521)
T ss_pred HcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccccHHHHHhh--hhhhc--cCcchhhcccchhhhhhhhhhhhhhh
Confidence 999999999999999999999999999999999999999999999 99998 99999997653222 2222
Q ss_pred hcccCCCCcccCchhhhhhhhhhcccCCCCCCCCchhHHHHHHHHHHhhhhhcchhhhccCCcccccccccCCCCCCCCC
Q 010919 232 KHKDTGKPFACGLCRSCYEEFMTISEGLEGGADPPAFQVAERERMVKASAEENSSFERESDSPFMSRVDKVQSPEPESIG 311 (497)
Q Consensus 232 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ppa~~~~e~~r~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 311 (497)
.|... .++..+.|..||..+..+++|+.++..++.++..+.++-..... + ..+... ..+...+......
T Consensus 298 ~~~~~-e~~~~~~~~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~~~~~~~-e-----~~~ssE----~~dk~~~g~~~~~ 366 (521)
T KOG1598|consen 298 TMQLV-ELANETWLVTLRHSLPVITGGLFLAWQDLQPRDRLVESYDDLAS-E-----CPLSSE----DEDKPASGRLAEL 366 (521)
T ss_pred hhhhh-hcccchhhhccccCCcccchhhhcccccchhhhhhhhhhhhhhh-c-----Cccccc----ccCCcCccccchh
Confidence 22222 17778999999999999999999999999998776654100000 0 000000 0000000000000
Q ss_pred CCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHH
Q 010919 312 VPKNCTTQTASNEGEGDHTKTPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAA 391 (497)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lsdiDD~Eid~~iL~eeE~~~K~~iW~~~N~dyL~eq~~Ke~~~ 391 (497)
.. . ..+. ..............+....++++||.+++.++|++++.+.++.+ | +|++||.|+..+.+++
T Consensus 367 ~~--~-----~sd~---~~~~~~~~~~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ 434 (521)
T KOG1598|consen 367 LA--V-----LSDM---AEQLASVWLRVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKA 434 (521)
T ss_pred hh--c-----cccc---chhhhhcchhhhhccccccccccCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhh
Confidence 00 0 0000 00000001112345677889999999999999999999999999 7 9999999999988876
Q ss_pred HHHHHHHHHhhcCCCcchHHHHHHHHHHHHHHhhhhhHHHhhhhhhhcCCCCCCCHHHHHHHHHHhcCCCccCCHHHHhh
Q 010919 392 AAAKAALEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQKRAAEAKNSGPAQTALEATRRMLTKKRLSSKINYDVLEK 471 (497)
Q Consensus 392 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~kk~k~~~~~~~~~~a~ta~EA~~~ml~~k~~S~KINYdvl~~ 471 (497)
+++++. |+ .. ++++..+.++++++.||.||+++|++.+.+|++|||++|+.
T Consensus 435 ak~~~~------------------------g~-~~----~~~k~~~r~~s~~~~t~~eavk~~~~i~~~s~~in~~~L~~ 485 (521)
T KOG1598|consen 435 AKEREE------------------------GI-NS----LSKKVGERRNSPELLTAPEAVKSMKEIKPVSSVINYSVLEN 485 (521)
T ss_pred hHhhhh------------------------cc-cc----cccccccccCCCcccccHHHHHHHHhccccccchHHHHHHH
Confidence 643321 11 01 12344456789999999999999999999999999999999
Q ss_pred hhCCCCc
Q 010919 472 LFDDSVC 478 (497)
Q Consensus 472 L~~~~~~ 478 (497)
|||....
T Consensus 486 i~d~~~e 492 (521)
T KOG1598|consen 486 ISDAEIE 492 (521)
T ss_pred Hhhhhcc
Confidence 9986543
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=2.5e-40 Score=337.95 Aligned_cols=181 Identities=25% Similarity=0.424 Sum_probs=176.2
Q ss_pred ChHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHH
Q 010919 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 80 (497)
Q Consensus 1 L~~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~L 80 (497)
|..|++.|+++|+.|+|| +.|+++|..+|+++++.++++||+.+.++|||||+|||++++|+||+||+.++++++++|
T Consensus 122 l~~a~~~I~~~~~~L~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i 199 (310)
T PRK00423 122 LAFALSELDRIASQLGLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEI 199 (310)
T ss_pred HHHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHH
Confidence 467999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHh
Q 010919 81 GAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALT 160 (497)
Q Consensus 81 gr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~ 160 (497)
|++|+.|.+.|+++.++ ++|+.||+|||+.|+ ++..|.+.|.+|++.+.+.|++.||+|.+|||||||+||++
T Consensus 200 ~~~~~~l~k~L~~~~~~-----~~p~~~i~r~~~~L~--L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~ 272 (310)
T PRK00423 200 GRCYRFLLRELNLKLPP-----TDPIDYVPRFASELG--LSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLL 272 (310)
T ss_pred HHHHHHHHHHhCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH
Confidence 99999999999998766 899999999999999 79999999999999999999999999999999999999999
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+|.++|+++|+.++||++.||++||++|..
T Consensus 273 ~g~~~t~keIa~v~~Vs~~tI~~~ykel~~ 302 (310)
T PRK00423 273 LGERRTQREVAEVAGVTEVTVRNRYKELAE 302 (310)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999974
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=6.5e-40 Score=329.12 Aligned_cols=181 Identities=29% Similarity=0.522 Sum_probs=176.6
Q ss_pred ChHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHH
Q 010919 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 80 (497)
Q Consensus 1 L~~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~L 80 (497)
|..++.+|..+|+.|+|| .+++++|..||+++++.++++||+.++++|||||+|||+++.|+||.||+++++|+++.|
T Consensus 97 l~~a~~~l~~~~~~l~LP--~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei 174 (285)
T COG1405 97 LITALEELERIASALGLP--ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEI 174 (285)
T ss_pred HHHHHHHHHHHHHHhCCC--chHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHH
Confidence 457999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHh
Q 010919 81 GAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALT 160 (497)
Q Consensus 81 gr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~ 160 (497)
+++|+.+.+.|++..+| ++|.+||+|||+.|+ ++.+|...|.+|++.+.+.|+..||+|.||||||||+|+++
T Consensus 175 ~rtyr~~~~~L~l~~~~-----~~p~~yi~rf~s~L~--l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l 247 (285)
T COG1405 175 GRTYRLLVRELKLKIPP-----VDPSDYIPRFASKLG--LSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLL 247 (285)
T ss_pred HHHHHHHHHhcCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHH
Confidence 99999999999998877 899999999999999 78999999999999999999999999999999999999999
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+|+++||++|+.++|||++|||+||+|+.+
T Consensus 248 ~~~~~tq~eva~v~~vtevTIrnrykel~~ 277 (285)
T COG1405 248 LGERRTQKEVAKVAGVTEVTIRNRYKELAD 277 (285)
T ss_pred hCCchHHHHHHHHhCCeeeHHHHHHHHHHH
Confidence 999999999999999999999999999865
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=6.6e-38 Score=308.13 Aligned_cols=197 Identities=20% Similarity=0.336 Sum_probs=186.5
Q ss_pred ChHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHH
Q 010919 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 80 (497)
Q Consensus 1 L~~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~L 80 (497)
|..||..|..||++|+|| ..|.|+|.++|+++.+.+.+|||+.++++|||||+|||+++.|||++||+.+.+|+.++|
T Consensus 104 ~~~a~~~I~~m~d~~~Lp--~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEI 181 (308)
T KOG1597|consen 104 LKAAFKEITAMCDRLSLP--ATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEI 181 (308)
T ss_pred HHHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHH
Confidence 357999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHh
Q 010919 81 GAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALT 160 (497)
Q Consensus 81 gr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~ 160 (497)
||+++.|.+.|++..+.+ .+...+||+|||+.|. ++..+++.|.++++.+....+..||+|.+||||+|||++++
T Consensus 182 gr~~K~i~~~l~~s~~~~---s~~t~~~m~RFCs~L~--L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisql 256 (308)
T KOG1597|consen 182 GRCVKLIGEALETSVDLI---SISTGDFMPRFCSNLG--LPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQL 256 (308)
T ss_pred HHHHHHHHHHHhccchhh---hhhHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHh
Confidence 999999999999876542 3567899999999999 89999999999999999999999999999999999999999
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
.+.++|+++|..++||+|+|||+.||+|. ++...|.|.+|....
T Consensus 257 s~~kkt~keI~~vtgVaE~TIr~sYK~Ly-p~~~~liP~~~a~~~ 300 (308)
T KOG1597|consen 257 SDEKKTQKEIGEVTGVAEVTIRNSYKDLY-PHADKLIPSWYANAV 300 (308)
T ss_pred ccCcccHHHHHHHhhhhHHHHHHHHHHHh-hchhhhChhhhcccc
Confidence 99999999999999999999999999995 678889999998764
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=8.2e-30 Score=218.30 Aligned_cols=96 Identities=54% Similarity=0.796 Sum_probs=34.3
Q ss_pred hHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHHHHhhhhhHHHh
Q 010919 353 DFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQ 432 (497)
Q Consensus 353 D~Eid~~iL~eeE~~~K~~iW~~~N~dyL~eq~~Ke~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~kk~ 432 (497)
|+|||.|||||+|+++|++||+++|+|||++|++|+++.+++.+ .++ +++|++++
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~----------------------~~~---~~~k~k~~ 55 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEE----------------------AGA---KSRKKKKK 55 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----------------------hcc---CCCccccc
Confidence 56999999999999999999999999999999999976543211 111 22222222
Q ss_pred hhhhhhcC-CCCCCCHHHHHHHHHHhcCCCccCCHHHHhhhh
Q 010919 433 KRAAEAKN-SGPAQTALEATRRMLTKKRLSSKINYDVLEKLF 473 (497)
Q Consensus 433 k~~~~~~~-~~~a~ta~EA~~~ml~~k~~S~KINYdvl~~L~ 473 (497)
+++...++ .+||.||+||+++||++|+||+|||||+|++||
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 33333344 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=99.73 E-value=1.5e-17 Score=134.30 Aligned_cols=71 Identities=27% Similarity=0.516 Sum_probs=66.4
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 80 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~L 80 (497)
|++||+.|+|| .+|++.|..+|+.+.+.++++||++..++|||||+|||+++.|+|++||+++++|++++|
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 78999999999 999999999999999999999999999999999999999999999999999999999876
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=99.62 E-value=1.6e-15 Score=122.50 Aligned_cols=71 Identities=18% Similarity=0.365 Sum_probs=66.7
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHH
Q 010919 109 LHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATL 181 (497)
Q Consensus 109 I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TI 181 (497)
|+|||+.|+ ++..|...|.+|++.+.+.|+..||+|.+|||||||+|||.+|.++|++||++++||++.||
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 689999999 89999999999999999999999999999999999999999999999999999999999997
No 8
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.52 E-value=5.6e-13 Score=133.84 Aligned_cols=177 Identities=12% Similarity=0.119 Sum_probs=154.2
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc--------
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-------- 75 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~v-------- 75 (497)
|...|++-|-.|+|| +.++-++..+|.......-+.+...+.|+.|||.+|.+.+..|++++||..|++.
T Consensus 26 G~e~Iqea~ILL~L~--q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~ 103 (367)
T KOG0835|consen 26 GCELIQEAGILLNLP--QVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESE 103 (367)
T ss_pred hHHHHHhhhHhhcCc--HHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhcc
Confidence 678999999999999 9999999999999998888888999999999999999999999999999988752
Q ss_pred -------------ChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccC
Q 010919 76 -------------NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITT 142 (497)
Q Consensus 76 -------------sv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~ 142 (497)
-.-.+-++..+|++.||+..+. .+|+.+|-.|.+-|+..-+..+.+.+|.+.+...+..++.
T Consensus 104 ~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv-----~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~v 178 (367)
T KOG0835|consen 104 AAEHLILARLYINLKMQVIRAERRILRELGFDVHV-----EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFV 178 (367)
T ss_pred CcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeee-----eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceee
Confidence 1123456678899999999887 8999999999999985445578999999999999888999
Q ss_pred CCChhHHHHHHHHHHHHhcCCCC-CHhhHHHHhccCHHHHHHHHHH
Q 010919 143 GRKPSGLCGAALYVSALTHGLKF-SKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 143 GR~P~~IaaAaLylAar~~g~~~-t~~eIa~v~~Vse~TIrkr~kE 187 (497)
--+|.+||+||||||||-.++++ .+..+..+++++...|..+.-.
T Consensus 179 ry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~ 224 (367)
T KOG0835|consen 179 RYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYR 224 (367)
T ss_pred ecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHH
Confidence 99999999999999999999774 3558999999998877654433
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.46 E-value=3.1e-12 Score=130.63 Aligned_cols=166 Identities=16% Similarity=0.110 Sum_probs=138.0
Q ss_pred HHHHHHHHHHHHcC--CCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcC----
Q 010919 3 KAFDDMRQMKNALN--IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNIN---- 76 (497)
Q Consensus 3 ~a~~~I~~ia~~L~--Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vs---- 76 (497)
.+...|.++|..|+ || +.|+-+|..||++.+-.+.+.-..+..|+++|||+||+.+..|+++.+|...+.-+
T Consensus 58 ~y~~~i~~~~~~lkp~Lp--q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~~~~~ 135 (305)
T TIGR00569 58 YYEKRLLDFCSAFKPTMP--TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKA 135 (305)
T ss_pred HHHHHHHHHHHHhcCCCC--chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCCchhh
Confidence 35678999999999 99 99999999999999999988888999999999999999999999999999876543
Q ss_pred hHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhC-----CCCCHHHHHHHHHHHHHhccccccCCCChhHHHH
Q 010919 77 VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-----PGGNKKVCDTARDILASMKRDWITTGRKPSGLCG 151 (497)
Q Consensus 77 v~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~-----~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~Iaa 151 (497)
...|...-..|++.|+++... ..|..++..|...|. ......+...|+.+++.+....++--..|.-||.
T Consensus 136 ~~~Il~~E~~lL~~L~F~L~V-----~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAl 210 (305)
T TIGR00569 136 LEQVLEYELLLIQQLNFHLIV-----HNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIAL 210 (305)
T ss_pred HHHHHHHHHHHHHHCCCcEEe-----eCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHH
Confidence 377888889999999998765 789998888876553 1234568889999998776655555699999999
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhcc
Q 010919 152 AALYVSALTHGLKFSKSDIVKIVHI 176 (497)
Q Consensus 152 AaLylAar~~g~~~t~~eIa~v~~V 176 (497)
||||+|++.+|++..-.+. ++..+
T Consensus 211 AAI~lA~~~~~~~l~~~~~-e~~~~ 234 (305)
T TIGR00569 211 AAILHTASRAGLNMESYLT-EQLSV 234 (305)
T ss_pred HHHHHHHHHhCCCCcccch-hhhcc
Confidence 9999999999987654332 44444
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.44 E-value=6e-13 Score=136.55 Aligned_cols=89 Identities=16% Similarity=0.227 Sum_probs=86.0
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 83 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~ 83 (497)
...+|.++|+.|+|| ..+.+.|..+++.+.+.+++.||++..+||||||+|||.+|.|+|++||+++++|+..+|++.
T Consensus 219 p~~~i~r~~~~L~L~--~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ 296 (310)
T PRK00423 219 PIDYVPRFASELGLS--GEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNR 296 (310)
T ss_pred HHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 568999999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccc
Q 010919 84 YLQLCQVLYIA 94 (497)
Q Consensus 84 yk~L~~~L~i~ 94 (497)
|+.|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999864
No 11
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.42 E-value=9.5e-13 Score=134.67 Aligned_cols=158 Identities=20% Similarity=0.248 Sum_probs=132.1
Q ss_pred hHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--cCh--
Q 010919 2 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN--INV-- 77 (497)
Q Consensus 2 ~~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~--vsv-- 77 (497)
+.+.+.|.++|.+|++| ...+.+|..||.+++-....+.-....||++|||+||+.++.|+.+.||..+.. .++
T Consensus 40 ~~~~~fI~elg~~L~~~--~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~ 117 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMP--QKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKD 117 (323)
T ss_pred HHHHHHHHHHHHHcCCC--ccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccc
Confidence 36889999999999999 899999999999999999889888899999999999999999999999998752 333
Q ss_pred HHHHHHH-----------HHHHHHhcccccccccccCCccchHHHHHhhhCCCCC--HHHHHHHHHHHHHhccccccCCC
Q 010919 78 YELGAVY-----------LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN--KKVCDTARDILASMKRDWITTGR 144 (497)
Q Consensus 78 ~~Lgr~y-----------k~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~--~~V~~~A~~Lv~~~~~~~l~~GR 144 (497)
.++...| +.|++.|+++... -+|+.|+.+|+..|..+.+ ..++..|+.+++......++---
T Consensus 118 ~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v-----~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y 192 (323)
T KOG0834|consen 118 LELEEVYWELKERIVQLELLLLETLGFDLNV-----EHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQY 192 (323)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHccCceec-----cCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEee
Confidence 2444444 4566677776654 6899999999999973233 25899999999988776666678
Q ss_pred ChhHHHHHHHHHHHHhcCCCCC
Q 010919 145 KPSGLCGAALYVSALTHGLKFS 166 (497)
Q Consensus 145 ~P~~IaaAaLylAar~~g~~~t 166 (497)
.|..||.||||+|+.++|+..+
T Consensus 193 ~p~~IAva~i~lA~~~~~~~~~ 214 (323)
T KOG0834|consen 193 SPHSIAVACIHLAAKLLGVELP 214 (323)
T ss_pred cCcEEEeehhhHHHHHcCCCCC
Confidence 9999999999999999997543
No 12
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.19 E-value=7.8e-11 Score=119.21 Aligned_cols=90 Identities=18% Similarity=0.213 Sum_probs=86.7
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 83 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~ 83 (497)
-..+|.+||+.|+|+ +.+...|.++.+++...|.+-||++..+||||||+||+.++.++|.++|+.+++|++.+|.+.
T Consensus 194 p~~yi~rf~s~L~l~--~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnr 271 (285)
T COG1405 194 PSDYIPRFASKLGLS--DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNR 271 (285)
T ss_pred HHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHH
Confidence 467999999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccc
Q 010919 84 YLQLCQVLYIAD 95 (497)
Q Consensus 84 yk~L~~~L~i~~ 95 (497)
|+.|.+.+++..
T Consensus 272 ykel~~~~~i~~ 283 (285)
T COG1405 272 YKELADALDIEV 283 (285)
T ss_pred HHHHHHhhcccc
Confidence 999999998753
No 13
>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=99.17 E-value=2.6e-10 Score=114.67 Aligned_cols=157 Identities=18% Similarity=0.169 Sum_probs=132.4
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHh--------C
Q 010919 3 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL--------N 74 (497)
Q Consensus 3 ~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~--------~ 74 (497)
.++..|..+|.+|+|| ..+..+|..+|++.+-.+..++.+...|+++|||+||+.+.+|+-+.=.+-.. -
T Consensus 47 ~~~k~i~~l~~~L~lp--~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~ 124 (297)
T COG5333 47 YYLKLIMDLCTRLNLP--QTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPK 124 (297)
T ss_pred HHHHHHHHHHHhcCCC--cchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhcccccccc
Confidence 3678999999999999 99999999999999999999999999999999999999999754433222222 2
Q ss_pred cChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHH
Q 010919 75 INVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAAL 154 (497)
Q Consensus 75 vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaL 154 (497)
-+...|-..-..|++.|+++.+. .+|..++..|...+......++.+.||.++..+-+..++-=-.|..||.|||
T Consensus 125 ~sr~~Il~~E~~lLEaL~fd~~V-----~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l 199 (297)
T COG5333 125 SSRERILEYEFELLEALDFDLHV-----HHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAAL 199 (297)
T ss_pred ccHHHHHHHHHHHHHHcccceEe-----ccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHH
Confidence 46677777788899999998776 7899999999988862123579999999999998877777789999999999
Q ss_pred HHHHHhcCCCCC
Q 010919 155 YVSALTHGLKFS 166 (497)
Q Consensus 155 ylAar~~g~~~t 166 (497)
++|+...|.+.-
T Consensus 200 ~ia~~~~~~~~~ 211 (297)
T COG5333 200 LIACEVLGMPII 211 (297)
T ss_pred HHHHHhcCCccc
Confidence 999999887643
No 14
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.08 E-value=4.9e-10 Score=111.72 Aligned_cols=87 Identities=13% Similarity=0.128 Sum_probs=84.0
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 83 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~ 83 (497)
.-.+|.+||+.|+|| ..++..|.++.+.+.+.++..||++.+||||.||++|+....+++++||.+++||...+|..+
T Consensus 203 t~~~m~RFCs~L~L~--~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~s 280 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLP--KSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNS 280 (308)
T ss_pred HHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHH
Confidence 567899999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhc
Q 010919 84 YLQLCQVLY 92 (497)
Q Consensus 84 yk~L~~~L~ 92 (497)
|+.|...+.
T Consensus 281 YK~Lyp~~~ 289 (308)
T KOG1597|consen 281 YKDLYPHAD 289 (308)
T ss_pred HHHHhhchh
Confidence 999998775
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=99.00 E-value=4.4e-09 Score=85.19 Aligned_cols=83 Identities=23% Similarity=0.257 Sum_probs=78.8
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-ChHHHH
Q 010919 3 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELG 81 (497)
Q Consensus 3 ~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~v-sv~~Lg 81 (497)
.++..|.+++..++++ ..+...|..+++++...+.+.|+++..+++||||+||+.++.|.++.+|..+++. +..+|.
T Consensus 4 ~~~~~l~~~~~~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~ 81 (88)
T cd00043 4 TPLDFLRRVAKALGLS--PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEIL 81 (88)
T ss_pred hHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHH
Confidence 5788999999999999 9999999999999999999999999999999999999999999999999999999 999999
Q ss_pred HHHHHH
Q 010919 82 AVYLQL 87 (497)
Q Consensus 82 r~yk~L 87 (497)
+.++.|
T Consensus 82 ~~e~~i 87 (88)
T cd00043 82 RMEKLL 87 (88)
T ss_pred HHHHHh
Confidence 888765
No 16
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.90 E-value=2e-08 Score=97.26 Aligned_cols=175 Identities=16% Similarity=0.208 Sum_probs=128.5
Q ss_pred HHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCC----CHHHHHHHh----C--
Q 010919 5 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF----LLIDFSNYL----N-- 74 (497)
Q Consensus 5 ~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~pr----tL~DIa~v~----~-- 74 (497)
.+.|+.+|..|+|. +.|+.+|..+|++.+-++..++-.+..+|+.|||+||+.+..|+ +|.--+.++ +
T Consensus 45 ~n~I~~lg~~lklR--Q~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~ 122 (264)
T KOG0794|consen 45 ANVIQKLGQHLKLR--QRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYW 122 (264)
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccc
Confidence 35799999999999 99999999999999999999999999999999999999999982 222112222 1
Q ss_pred -----cChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHH
Q 010919 75 -----INVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGL 149 (497)
Q Consensus 75 -----vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~I 149 (497)
.....|-..-..|.+.|+--.-+ -+|..=+..|.+.++. .+......++.|++..-+..++-=..|.-|
T Consensus 123 ~e~~~~~~~~I~e~Ef~llE~Ld~~LIV-----hHPYrsL~q~~qd~gi-~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~I 196 (264)
T KOG0794|consen 123 PEKFPYERKDILEMEFYLLEALDCYLIV-----HHPYRSLLQFVQDMGI-NDQKLLQLAWSIVNDSYRMDLCLLYPPHQI 196 (264)
T ss_pred hhhcCCCcCcchhhhhhHHhhhceeEEE-----ecCCccHHHHHHHhcc-cchhhhhhhHhhhcchhhcceeeecCHHHH
Confidence 12223333334556666532221 4676668888888872 256688999999999888888888999999
Q ss_pred HHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 150 CGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 150 aaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
|-||||+|+...|-..+ +..-..+.|.-.-+.....++
T Consensus 197 alAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I 234 (264)
T KOG0794|consen 197 ALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEI 234 (264)
T ss_pred HHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHH
Confidence 99999999988876654 444444555555555555554
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=98.89 E-value=9.3e-09 Score=82.50 Aligned_cols=79 Identities=22% Similarity=0.270 Sum_probs=72.8
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHh-CCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-ChHHHHHHH
Q 010919 7 DMRQMKNALNIGESDEIVHVAKRFYGIAVA-RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVY 84 (497)
Q Consensus 7 ~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~-~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~v-sv~~Lgr~y 84 (497)
.|.+++..++++ ..+...|..+++++.. .++++ +++..++|||||+|||.++.+.+..++..++++ +..+|.+.+
T Consensus 2 ~l~~~~~~~~~~--~~~~~~a~~~~~~~l~~~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 2 FLRRVCKALNLD--PETLNLAVNLLDRFLSDYKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred HHHHHHHHcCCC--HHHHHHHHHHHHHHHHHhhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 588999999999 9999999999999998 55554 999999999999999999999999999999999 999999988
Q ss_pred HHHH
Q 010919 85 LQLC 88 (497)
Q Consensus 85 k~L~ 88 (497)
+.|.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 8775
No 18
>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=98.86 E-value=1.5e-08 Score=82.06 Aligned_cols=84 Identities=23% Similarity=0.276 Sum_probs=79.2
Q ss_pred CCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhcc-CHHHH
Q 010919 103 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATL 181 (497)
Q Consensus 103 idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~V-se~TI 181 (497)
..|..||.+++..++ .+..+...|..+++++...+...|++|..||+||||+|+++.+...+.++++.+++. ++.+|
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 010919 182 MKRLIEF 188 (497)
Q Consensus 182 rkr~kE~ 188 (497)
.+.++++
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9998876
No 19
>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=98.84 E-value=1.8e-08 Score=80.85 Aligned_cols=81 Identities=20% Similarity=0.214 Sum_probs=74.5
Q ss_pred chHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhcc-CHHHHHHHH
Q 010919 107 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRL 185 (497)
Q Consensus 107 ~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~V-se~TIrkr~ 185 (497)
.||.||+..++ .++.+...|..+++++..+.-..+++|..||+||||+|+++.+.+++.++++..+|+ ++.+|.+.+
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 789999999999999987545556999999999999999999999999999999999 999999999
Q ss_pred HHHh
Q 010919 186 IEFE 189 (497)
Q Consensus 186 kE~~ 189 (497)
+++.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 9885
No 20
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.60 E-value=1.5e-06 Score=89.68 Aligned_cols=177 Identities=16% Similarity=0.195 Sum_probs=142.8
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCC-CCC--ChHHHHHHHHHHHHHhcCC--CCCHHHHHHH--hCc
Q 010919 3 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFT-KGR--RTEQVQASCLYLACRQKSK--PFLLIDFSNY--LNI 75 (497)
Q Consensus 3 ~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~-rGR--~~~~VaAACLYiACR~e~~--prtL~DIa~v--~~v 75 (497)
.|...|-++|...+.. ..+.=-|.+++.+.+...-+ +++ -...+|+|||.+|.+.+.+ |.++-=.... .-+
T Consensus 80 ~A~~WIl~V~~~~~~~--~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~f 157 (335)
T KOG0656|consen 80 QALDWILKVCEEYNFE--PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVF 157 (335)
T ss_pred HHHHHHHHHHHHhCCc--hHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccc
Confidence 5889999999999999 89999999999998875444 333 3788999999999999866 6554444444 346
Q ss_pred ChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhC--CCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHH
Q 010919 76 NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL--PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA 153 (497)
Q Consensus 76 sv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~--~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAa 153 (497)
..++|.|.-+.|+..|+=.... +.|..||..|+.+++ ....+.+...+..++-....+.-+.+-.|+.||||+
T Consensus 158 eaktI~rmELLVLstL~Wrl~a-----VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~ 232 (335)
T KOG0656|consen 158 EAKTIQRMELLVLSTLKWRLRA-----VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA 232 (335)
T ss_pred cHHHHHHHHHHHHhhccccccC-----CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence 7899999999999999987776 899999999999997 334567888888888888888888899999999998
Q ss_pred HHHHHHh-cCCC--CCHhhHHHHhccCHHHHHHHHH
Q 010919 154 LYVSALT-HGLK--FSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 154 LylAar~-~g~~--~t~~eIa~v~~Vse~TIrkr~k 186 (497)
+..++.. .+.. .....+.....|+.-.+++.|.
T Consensus 233 ~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 233 ILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 8766653 3433 2346677778889988888887
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.34 E-value=3.6e-07 Score=97.90 Aligned_cols=157 Identities=14% Similarity=0.172 Sum_probs=106.5
Q ss_pred HHHHHHHHcCCCCh-hHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHH
Q 010919 7 DMRQMKNALNIGES-DEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYL 85 (497)
Q Consensus 7 ~I~~ia~~L~Lp~~-~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk 85 (497)
+|.+++..|-..+. ..|+.+|.++...+..-=...||++..++.||||||||.||+++|+.||+.+..|+..+|.+.|+
T Consensus 169 ~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~ 248 (521)
T KOG1598|consen 169 YIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLK 248 (521)
T ss_pred eeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHH
Confidence 56777777766521 23555555555554333345699999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccc------ccccCCccchHHHHH---hhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHH
Q 010919 86 QLCQVLYIADESN------VLKQVDPSIFLHKFT---DRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYV 156 (497)
Q Consensus 86 ~L~~~L~i~~~~~------~~~~idP~~~I~Rf~---~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLyl 156 (497)
+|.+.+..+.... ...-.||..|-..=- .... ...+....-...+.-+...|..+++.+...+-+.++.
T Consensus 249 Ef~~T~s~~Lti~ef~~~d~e~~~~ppsft~~~~~~~k~~~--~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~ 326 (521)
T KOG1598|consen 249 EFSDTLSGDLTIDELAEIDLEYESDPPSFTASPSKEAKYVE--DKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFL 326 (521)
T ss_pred HHhccccccccHHHHHhhhhhhccCcchhhcccchhhhhhh--hhhhhhhhhhhhhhcccchhhhccccCCcccchhhhc
Confidence 9999876543220 011234443322110 0000 1223333444556667778999999999999999998
Q ss_pred HHHhcCCCC
Q 010919 157 SALTHGLKF 165 (497)
Q Consensus 157 Aar~~g~~~ 165 (497)
+++-.....
T Consensus 327 ~~q~~~~~~ 335 (521)
T KOG1598|consen 327 AWQDLQPRD 335 (521)
T ss_pred ccccchhhh
Confidence 877554443
No 22
>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=97.77 E-value=0.00027 Score=62.13 Aligned_cols=90 Identities=13% Similarity=0.242 Sum_probs=75.8
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHh--CcChHH
Q 010919 3 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYL--NINVYE 79 (497)
Q Consensus 3 ~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~-prtL~DIa~v~--~vsv~~ 79 (497)
...+.|..++..++++ ..+.-.|..+|.+......+...+...++++|+|+||+.+.. +.++.++.... ..+...
T Consensus 33 ~~~~~i~~~~~~~~l~--~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~ 110 (127)
T PF00134_consen 33 IIIDWIIELCQRLKLS--PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKD 110 (127)
T ss_dssp HHHHHHHHHHHHTT-B--HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHH
T ss_pred HHHHHHHHHHHhcccc--hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHH
Confidence 4578899999999999 999999999999999988888889999999999999999866 88889998887 367888
Q ss_pred HHHHHHHHHHHhccc
Q 010919 80 LGAVYLQLCQVLYIA 94 (497)
Q Consensus 80 Lgr~yk~L~~~L~i~ 94 (497)
|-..-..|...|+.+
T Consensus 111 i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 111 ILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHCCCC
Confidence 888888898888764
No 23
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.71 E-value=0.0013 Score=63.68 Aligned_cols=159 Identities=14% Similarity=0.158 Sum_probs=123.4
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHh--CCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHH
Q 010919 7 DMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 84 (497)
Q Consensus 7 ~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~--~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~y 84 (497)
.|.+++.+|||.+.+.++..|.+|.++..- -+..-|-.-..-+.-|+-+|.-.-++|.-=.-.-...|.+.....+.|
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~ 81 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSF 81 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHH
Confidence 488999999995557999999999888754 355556666677888999998888888877777778899999999999
Q ss_pred HHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhcccc-----ccCC-CChhHHHHHHHHHHH
Q 010919 85 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDW-----ITTG-RKPSGLCGAALYVSA 158 (497)
Q Consensus 85 k~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~-----l~~G-R~P~~IaaAaLylAa 158 (497)
+-+...||++..- -|..+|-.|+ -.+|++.|..|+...+..- +-+. -+| -.++||+|.||
T Consensus 82 ~sfe~llgln~~~----------~VrdlaVQfg---c~evi~~a~~vl~syk~~lpaT~~~~~D~SrP-~ft~aA~~~ac 147 (262)
T KOG4557|consen 82 NSFENLLGLNIKL----------NVRDLAVQFG---CVEVIKSAQNVLSSYKERLPATRRANADFSRP-VFTAAAFYLAC 147 (262)
T ss_pred HHHHHHhcchhhc----------CHHHHHHHHh---HHHHHHHHHHHHHHHHhcCchhhhcCCcccch-HHHHHHHHHHH
Confidence 9999999986432 3566777787 5788899999888876521 1111 234 47888999999
Q ss_pred HhcCCCCCHhhHHHHhccCHH
Q 010919 159 LTHGLKFSKSDIVKIVHICEA 179 (497)
Q Consensus 159 r~~g~~~t~~eIa~v~~Vse~ 179 (497)
+....+++......+.|++++
T Consensus 148 k~lKlKVdK~kli~~sg~~~s 168 (262)
T KOG4557|consen 148 KKLKLKVDKLKLIEVSGTSES 168 (262)
T ss_pred HHHHHhhhHhhcccccCCCHH
Confidence 999888888777777776664
No 24
>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=97.56 E-value=0.0008 Score=68.11 Aligned_cols=146 Identities=18% Similarity=0.174 Sum_probs=95.8
Q ss_pred HHHHHHc--CCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhC----cChHHHHH
Q 010919 9 RQMKNAL--NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN----INVYELGA 82 (497)
Q Consensus 9 ~~ia~~L--~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~----vsv~~Lgr 82 (497)
-++|+.+ +|| .+|+-+|..+|++++=.+.+..-++..+.++|+|+||+.+..-+++-+|+.-.. -+...+-+
T Consensus 64 ~~f~~k~~p~lp--~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk 141 (325)
T KOG2496|consen 64 VNFYSKFKPNLP--TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLK 141 (325)
T ss_pred HHHHHHhcCCCc--hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHh
Confidence 3455555 788 999999999999999999999999999999999999999999999999998876 44445555
Q ss_pred HHHHHHHHhcccccccccccCCc-cchHHHHHhhhCCCCCHHHH-HHH--HHHHHHhccccccCCCChhHHHHHHHHHHH
Q 010919 83 VYLQLCQVLYIADESNVLKQVDP-SIFLHKFTDRLLPGGNKKVC-DTA--RDILASMKRDWITTGRKPSGLCGAALYVSA 158 (497)
Q Consensus 83 ~yk~L~~~L~i~~~~~~~~~idP-~~~I~Rf~~~L~~~~~~~V~-~~A--~~Lv~~~~~~~l~~GR~P~~IaaAaLylAa 158 (497)
--..+++.|...... ..+-.| +-|+..+-..|.+-.++... ... ...++++.-....-=..|+=||-|||+.++
T Consensus 142 ~E~~llqsL~f~L~v--h~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~ 219 (325)
T KOG2496|consen 142 YEFLLLQSLKFSLTV--HNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAA 219 (325)
T ss_pred chHHHHHhhhhhhee--cCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHh
Confidence 455667777765432 112344 33554444443211122221 111 133333322223334789999999995443
No 25
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.51 E-value=0.00072 Score=71.92 Aligned_cols=151 Identities=15% Similarity=0.095 Sum_probs=122.4
Q ss_pred HHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHH-HHHHhcCC-CCCHHHHHHHhC--cChHHHH
Q 010919 6 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLY-LACRQKSK-PFLLIDFSNYLN--INVYELG 81 (497)
Q Consensus 6 ~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLY-iACR~e~~-prtL~DIa~v~~--vsv~~Lg 81 (497)
+.+-++-..++|. ..+.-.|..++.+......+..+....|..+|++ |||+.+.. +-++.|+.-+++ ++...|.
T Consensus 163 dwlvevh~~F~L~--~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il 240 (391)
T KOG0653|consen 163 DWLVEVHEKFGLS--PETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEIL 240 (391)
T ss_pred HHHHHhhhhcCcC--HHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHH
Confidence 4567788899999 8999999999999998866888888888888856 99996433 334677766654 7889999
Q ss_pred HHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhc
Q 010919 82 AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTH 161 (497)
Q Consensus 82 r~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~ 161 (497)
+.-+.+...|+..... ..|..|+.||..... ........+..++....-+.-+....|+.++||+.+++.++.
T Consensus 241 ~mE~~il~~L~f~l~~-----p~~~~FLrr~~ka~~--~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~ 313 (391)
T KOG0653|consen 241 RMEKYILNVLEFDLSV-----PTPLSFLRRFLKAAD--YDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRML 313 (391)
T ss_pred HHHHHHHhccCeeecC-----CchHHHHHHHHHhhh--cchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHh
Confidence 9999999999877654 679999999988887 456666777777777766666677899999999999999998
Q ss_pred CCCC
Q 010919 162 GLKF 165 (497)
Q Consensus 162 g~~~ 165 (497)
+.+.
T Consensus 314 ~~~~ 317 (391)
T KOG0653|consen 314 SKGD 317 (391)
T ss_pred ccCC
Confidence 7664
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=97.23 E-value=0.00074 Score=58.21 Aligned_cols=84 Identities=19% Similarity=0.168 Sum_probs=67.4
Q ss_pred CccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCC-CCCHhhHHHHhccCHHHHH
Q 010919 104 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIVHICEATLM 182 (497)
Q Consensus 104 dP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~-~~t~~eIa~v~~Vse~TIr 182 (497)
.|..|+.+|....+ .+..+...|..|++.+..+.-+.+-+|+.||+||||+|....+. ..-...+...+|+....|+
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 46789999999999988887788999999999999999999875 3445668888899999999
Q ss_pred HHHHHHh
Q 010919 183 KRLIEFE 189 (497)
Q Consensus 183 kr~kE~~ 189 (497)
..++.+.
T Consensus 80 ~c~~~i~ 86 (118)
T PF02984_consen 80 ECIELIQ 86 (118)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9988885
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=97.14 E-value=0.0018 Score=59.12 Aligned_cols=71 Identities=11% Similarity=0.225 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHh--CCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc
Q 010919 3 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI 75 (497)
Q Consensus 3 ~a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~--~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~v 75 (497)
-|...|+.+|+.|+|+ +.+.+....+|.-+.. ..++++|..++++-.|+|..||.++.+.+++||-....-
T Consensus 13 la~~Rl~~LC~~L~l~--~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 13 LAAVRLQDLCERLDLS--SDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHHHHHHTTS--TTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHHHHHHcCCc--HHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 3678899999999999 8899999999998775 467899999999999999999999999999999887554
No 28
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=97.03 E-value=0.0039 Score=66.94 Aligned_cols=148 Identities=14% Similarity=0.065 Sum_probs=110.9
Q ss_pred HHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHh--CcChHHHHH
Q 010919 6 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYL--NINVYELGA 82 (497)
Q Consensus 6 ~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~-prtL~DIa~v~--~vsv~~Lgr 82 (497)
+.|.++=..++|- +.+...|..|..+.+..+.+.=-+...|+++|++|||+.+.+ +-++.++.-++ .+++..|.+
T Consensus 218 ~wlvevH~~F~ll--peTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~ 295 (440)
T COG5024 218 DWLVEVHGKFGLL--PETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIR 295 (440)
T ss_pred HHHHHhccccccc--chHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHH
Confidence 3456667778888 789999999999999988888778899999999999998754 55688998886 478999999
Q ss_pred HHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhcccc-ccCCCChhHHHHHHHHHHHHhc
Q 010919 83 VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDW-ITTGRKPSGLCGAALYVSALTH 161 (497)
Q Consensus 83 ~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~-l~~GR~P~~IaaAaLylAar~~ 161 (497)
+.+.+...|+.+... ..|.-|+.|+....+ ....-...+..++....-+. +...+ |+.+++||-|++-.+.
T Consensus 296 aE~~ml~~l~f~is~-----P~P~sFLRriSka~d--yd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~ 367 (440)
T COG5024 296 AERYMLEVLDFNISW-----PSPMSFLRRISKASD--YDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKIL 367 (440)
T ss_pred HHHHHhhhcccccCC-----CChHHHHHHHHhhcc--cchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhh
Confidence 999999999987644 678889777766555 23333333444433332222 23344 9999999999998877
Q ss_pred CC
Q 010919 162 GL 163 (497)
Q Consensus 162 g~ 163 (497)
+-
T Consensus 368 ~~ 369 (440)
T COG5024 368 SQ 369 (440)
T ss_pred cc
Confidence 64
No 29
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=95.56 E-value=0.073 Score=54.80 Aligned_cols=106 Identities=16% Similarity=0.275 Sum_probs=78.2
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHH-HHHHHhCcChHHHHH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLI-DFSNYLNINVYELGA 82 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~-DIa~v~~vsv~~Lgr 82 (497)
-.+.|-.+.+-|+||++..+...+.+|.....--.+..-.+++.||+||+|+|.|..++|.+.. ..-.+++++..+|-.
T Consensus 141 Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ 220 (367)
T KOG0835|consen 141 PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDE 220 (367)
T ss_pred cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHH
Confidence 3467888999999996555688888888887777776668899999999999999999876554 445677888888877
Q ss_pred HHHHHHHHhcccccccccccCCccchHHHHHhhhC
Q 010919 83 VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL 117 (497)
Q Consensus 83 ~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~ 117 (497)
....+........ | -..+|.-|+..+.
T Consensus 221 ic~~l~~lY~~~~-p-------~~~li~~~vd~~k 247 (367)
T KOG0835|consen 221 ICYRLIPLYKRAK-P-------DETLIEAFVDRLK 247 (367)
T ss_pred HHHHHHHHHHhcc-c-------CHHHHHHHHHHhh
Confidence 6666666543311 1 2346777777664
No 30
>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=94.94 E-value=0.11 Score=44.55 Aligned_cols=87 Identities=14% Similarity=0.149 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhCcChHHHHH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLNINVYELGA 82 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~-prtL~DIa~v~~vsv~~Lgr 82 (497)
.+..|..+....+.. ..+...|.-+...+.-....-+-++..+||||+|+|.+..+. +.--..+...++++...|..
T Consensus 3 p~~Fl~~~~~~~~~~--~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~ 80 (118)
T PF02984_consen 3 PYDFLRRFLKISNAD--QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKE 80 (118)
T ss_dssp HHHHHHHHHTSSSHH--HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHcCCc--HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHH
Confidence 456777774444445 678888888888866554455688999999999999999765 55556678888999999999
Q ss_pred HHHHHHHHhc
Q 010919 83 VYLQLCQVLY 92 (497)
Q Consensus 83 ~yk~L~~~L~ 92 (497)
++..|.+.+.
T Consensus 81 c~~~i~~~~~ 90 (118)
T PF02984_consen 81 CIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 9999998775
No 31
>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=93.66 E-value=0.22 Score=43.47 Aligned_cols=67 Identities=15% Similarity=0.095 Sum_probs=51.5
Q ss_pred cchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCC-CCCHhhHHHHh
Q 010919 106 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIV 174 (497)
Q Consensus 106 ~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~-~~t~~eIa~v~ 174 (497)
..||...+..++ +++.+...|..++.++..........+.-|++||+++|+.+.+. ..+..+++...
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 347777888887 89999999999999987666677889999999999999998876 34455555443
No 32
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=92.97 E-value=0.38 Score=49.72 Aligned_cols=68 Identities=13% Similarity=0.101 Sum_probs=54.0
Q ss_pred hHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc
Q 010919 108 FLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 175 (497)
Q Consensus 108 ~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~ 175 (497)
+|..+|..|.-.++..|..+|.-+++++--.+-+.-..|.-|+++||||||..-++.+++.+++..+.
T Consensus 62 ~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~ 129 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhcc
Confidence 45566666652268899999999999876544455679999999999999999999999888876543
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=91.12 E-value=0.41 Score=34.82 Aligned_cols=31 Identities=16% Similarity=0.265 Sum_probs=24.4
Q ss_pred HHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 158 ALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 158 ar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
....+-++|..+|++.+|+|+.|+.+|++.+
T Consensus 11 ~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 11 LLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 3445678999999999999999999999876
No 34
>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=91.07 E-value=3.6 Score=37.82 Aligned_cols=88 Identities=11% Similarity=0.095 Sum_probs=67.9
Q ss_pred HHHHHHHHHHcCCCChhHHHHHHHHHHHHHHh---CC--CCCCCChHHHHHHHHHHHHHh-cCCCCCHHHHHHHhCcChH
Q 010919 5 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVA---RN--FTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINVY 78 (497)
Q Consensus 5 ~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~---~~--~~rGR~~~~VaAACLYiACR~-e~~prtL~DIa~v~~vsv~ 78 (497)
.++|.++....+++ ..+.-.|..|..+... .. .+...+...+..+||-+|.+- .....+.+.+|.+.|+++.
T Consensus 55 ~~fl~ri~~~~~~s--~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~ 132 (149)
T PF08613_consen 55 RDFLSRILKYTQCS--PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLK 132 (149)
T ss_dssp HHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHcCCC--hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHH
Confidence 56899999999999 8999999999888877 22 234567788999999999996 6889999999999999999
Q ss_pred HHHHHHHHHHHHhccc
Q 010919 79 ELGAVYLQLCQVLYIA 94 (497)
Q Consensus 79 ~Lgr~yk~L~~~L~i~ 94 (497)
+|.+.-..+...|+.+
T Consensus 133 eln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 133 ELNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHCCCc
Confidence 9999999998888753
No 35
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=91.03 E-value=3.6 Score=42.80 Aligned_cols=169 Identities=12% Similarity=0.071 Sum_probs=107.5
Q ss_pred HHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhC-CCCCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cChHHH
Q 010919 5 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR-NFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYEL 80 (497)
Q Consensus 5 ~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~-~~~rGR~~~~VaAACLYiACR~e~~-prtL~DIa~v~~--vsv~~L 80 (497)
++.+-++|.--.|. ..+---|..||.+...- .-+.--....+--+|||||.+.+.+ |--++|||-++. ++...|
T Consensus 149 lDWlmEVCEvykLH--RETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddI 226 (408)
T KOG0655|consen 149 LDWLMEVCEVYKLH--RETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDI 226 (408)
T ss_pred HHHHHHHHHHHHHh--hhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHH
Confidence 45677888888888 88888899998886542 1122234456677899999999765 888999999874 789999
Q ss_pred HHHHHHHHHHhcccccccccccCCccchHHHHHhhhC-CCCC---------HHHHHHHHHHHHHhccccccCCCChhHHH
Q 010919 81 GAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGN---------KKVCDTARDILASMKRDWITTGRKPSGLC 150 (497)
Q Consensus 81 gr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~-~~~~---------~~V~~~A~~Lv~~~~~~~l~~GR~P~~Ia 150 (497)
...-+.|++.|+-...| +..-.++.-|.+-+. ++.+ ...+++|. |+....-+-=..--+-..||
T Consensus 227 ltmE~iilkal~W~l~P-----iTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaq-lLDlc~ldids~~fsYrila 300 (408)
T KOG0655|consen 227 LTMELIILKALKWELSP-----ITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQ-LLDLCILDIDSLEFSYRILA 300 (408)
T ss_pred HHHHHHHHHHhcccccc-----eehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHH-HHHHHHhccccccchHHHHH
Confidence 99999999999977666 444445555555443 1111 22223322 33322211111224555777
Q ss_pred HHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 151 GAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 151 aAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
|||||.-. +..-|-+++|.--..|.++.+=+
T Consensus 301 AAal~h~~-------s~e~v~kaSG~~w~~ie~cv~wm 331 (408)
T KOG0655|consen 301 AAALCHFT-------SIEVVKKASGLEWDSIEECVDWM 331 (408)
T ss_pred HHHHHHHh-------HHHHHHHcccccHHHHHHHHHHH
Confidence 88776422 22234455677777777776554
No 36
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=90.38 E-value=0.4 Score=49.89 Aligned_cols=83 Identities=17% Similarity=0.139 Sum_probs=63.3
Q ss_pred cchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc----cCHHHH
Q 010919 106 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH----ICEATL 181 (497)
Q Consensus 106 ~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~----Vse~TI 181 (497)
..||...+.+|+ .+..-..+|.-+.+++---.-+.+-.|..||++|||||+...+..+..++|..+.. ....+.
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 347777888887 55556778888888877655667788899999999999999999999999988763 222356
Q ss_pred HHHHHHHhc
Q 010919 182 MKRLIEFEN 190 (497)
Q Consensus 182 rkr~kE~~~ 190 (497)
..+|-++++
T Consensus 121 ~~~~~~~~~ 129 (323)
T KOG0834|consen 121 EEVYWELKE 129 (323)
T ss_pred HHHHHHHHH
Confidence 666666653
No 37
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=89.61 E-value=2.8 Score=32.93 Aligned_cols=26 Identities=12% Similarity=0.165 Sum_probs=23.9
Q ss_pred CCCHhhHHHHhcc-CHHHHHHHHHHHh
Q 010919 164 KFSKSDIVKIVHI-CEATLMKRLIEFE 189 (497)
Q Consensus 164 ~~t~~eIa~v~~V-se~TIrkr~kE~~ 189 (497)
+.++.+||..+|+ +..++.+.++...
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 8999999999999 9999999998864
No 38
>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=88.56 E-value=0.13 Score=54.10 Aligned_cols=87 Identities=13% Similarity=0.090 Sum_probs=0.0
Q ss_pred HHHHHHcCCCChhHHHHHHHHHHHHHH-hCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 9 RQMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 9 ~~ia~~L~Lp~~~~i~d~A~~iyk~a~-~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
..|+..++++.+..++..|..+|++.. ....+++..-.+-+.+|+||||...+.++-+.-+....+++.....+.|..|
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 344555555433899999999999998 4566677777788899999999999999888887788899998888888888
Q ss_pred HHHhcccc
Q 010919 88 CQVLYIAD 95 (497)
Q Consensus 88 ~~~L~i~~ 95 (497)
.+.|+...
T Consensus 82 ~~~L~~~s 89 (353)
T PF05460_consen 82 ENLLGNSS 89 (353)
T ss_dssp --------
T ss_pred HHHHhCCC
Confidence 88887653
No 39
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=88.14 E-value=1.8 Score=34.09 Aligned_cols=72 Identities=7% Similarity=0.123 Sum_probs=45.9
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-ChHHHHHHHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 86 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~v-sv~~Lgr~yk~ 86 (497)
|..+|..+|++ ...... +|+......+..-.....+.-|+-|+... +.++.|||..+|+ +...+.+.|++
T Consensus 4 ~~~la~~~~~s--~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~~----~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 4 LEDLAEALGMS--PRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRDT----DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHhCCC--HHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHcC----CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 67899999999 444333 33333222221112223344455555332 8999999999999 99999998876
Q ss_pred HH
Q 010919 87 LC 88 (497)
Q Consensus 87 L~ 88 (497)
..
T Consensus 75 ~~ 76 (84)
T smart00342 75 LF 76 (84)
T ss_pred HH
Confidence 64
No 40
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=87.37 E-value=0.76 Score=33.82 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=19.4
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
..|.++||+.+|||..||.+.++.|.+..
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 78999999999999999999999987644
No 41
>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=87.19 E-value=2.1 Score=39.14 Aligned_cols=64 Identities=16% Similarity=0.134 Sum_probs=50.1
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHHHHhc--cccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHh
Q 010919 109 LHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV 174 (497)
Q Consensus 109 I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~--~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~ 174 (497)
|..+|++|+ ++.++....|.+++.+. ...+..+|.-.-|.-.|||+.|++++..+|.++|...-
T Consensus 18 l~~LC~~L~--l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Y 83 (135)
T PF01857_consen 18 LQDLCERLD--LSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAY 83 (135)
T ss_dssp HHHHHHHHT--TSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHH
T ss_pred HHHHHHHcC--CcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHH
Confidence 556888998 67778888888888876 46788999999999999999999999888888887643
No 42
>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=86.97 E-value=1.3 Score=45.39 Aligned_cols=70 Identities=14% Similarity=0.191 Sum_probs=62.1
Q ss_pred cchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc
Q 010919 106 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 175 (497)
Q Consensus 106 ~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~ 175 (497)
+..+..||+++.-.++..|+.+|.....++--.|-..--.|..|.++|+|+||....+.+|..+++.-..
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 4567789999975589999999999999998888888999999999999999999999999999887665
No 43
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=86.90 E-value=1.5 Score=46.42 Aligned_cols=91 Identities=18% Similarity=0.215 Sum_probs=67.1
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCC----CCHHHH-HHHhCcChH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP----FLLIDF-SNYLNINVY 78 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~p----rtL~DI-a~v~~vsv~ 78 (497)
-.++|.+++..-+|. ..++.+|..||.+..=+|++.-.++..+|.|||.+|.+.+... .+|+|= -+.+..+..
T Consensus 385 lKREMr~l~~d~~id--~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrr 462 (497)
T KOG4164|consen 385 LKREMRELGEDCGID--VVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRR 462 (497)
T ss_pred HHHHHHHhhhccCcc--ceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHH
Confidence 356788888777888 7899999999999988898887888999999999999988653 233332 345677766
Q ss_pred HHHHHHHHHHHHhccccc
Q 010919 79 ELGAVYLQLCQVLYIADE 96 (497)
Q Consensus 79 ~Lgr~yk~L~~~L~i~~~ 96 (497)
+|-.--.-++-.|.+..+
T Consensus 463 dLia~Ef~VlvaLefaL~ 480 (497)
T KOG4164|consen 463 DLIAFEFPVLVALEFALH 480 (497)
T ss_pred hhhhhhhhHHHhhhhhcc
Confidence 665554455555555443
No 44
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=86.31 E-value=1.3 Score=32.41 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=24.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+-..|+++||+.+|+|..|+++.+++|.+
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 45699999999999999999999999865
No 45
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=84.70 E-value=41 Score=35.60 Aligned_cols=25 Identities=4% Similarity=0.034 Sum_probs=21.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|+.+|+..+|||..+||+..+.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~~ 348 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAK 348 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 5699999999999999999876554
No 46
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=84.68 E-value=2.9 Score=41.02 Aligned_cols=81 Identities=15% Similarity=0.173 Sum_probs=55.4
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhC-----CCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVAR-----NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 82 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~-----~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr 82 (497)
|+.+|-+||+. .++..|.++.+...++ ..--.-+....++|++|.|||.-+....-.-+-.+.|++...+..
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 56777777777 5777777777766542 111123556788999999999887766666666677777777766
Q ss_pred HHHHHHHHh
Q 010919 83 VYLQLCQVL 91 (497)
Q Consensus 83 ~yk~L~~~L 91 (497)
..+++-+..
T Consensus 173 l~kqler~~ 181 (262)
T KOG4557|consen 173 LSKQLERNY 181 (262)
T ss_pred HHHHHHHHH
Confidence 666665543
No 47
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=84.14 E-value=1.5 Score=40.92 Aligned_cols=37 Identities=16% Similarity=0.291 Sum_probs=31.5
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 156 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 156 lAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
|.+...+-+.|..+||+.+|+|++|+++|++.|.+..
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 4444567789999999999999999999999997654
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=83.89 E-value=1.4 Score=32.10 Aligned_cols=30 Identities=17% Similarity=0.079 Sum_probs=20.8
Q ss_pred HHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 010919 157 SALTHGLKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 157 Aar~~g~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
...++....|+++||+.+|++.+||.+-++
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 345667789999999999999999998765
No 49
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=83.78 E-value=59 Score=33.85 Aligned_cols=27 Identities=7% Similarity=0.069 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+||+..||++++..-.
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl 307 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEAL 307 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 469999999999999999999877653
No 50
>PF13730 HTH_36: Helix-turn-helix domain
Probab=83.16 E-value=2.5 Score=31.73 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=24.0
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
|++.|++.+|+++.||++.++++.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 89999999999999999999999753
No 51
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.77 E-value=2 Score=39.58 Aligned_cols=37 Identities=14% Similarity=0.250 Sum_probs=31.4
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 156 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 156 lAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
+.+...+-+.|..+||+.+|+|++|+++|++.|.+..
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 4445566789999999999999999999999997654
No 52
>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=81.44 E-value=2.7 Score=31.52 Aligned_cols=31 Identities=6% Similarity=0.164 Sum_probs=26.0
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
++-.+|..++|+.++||+.||++-++++.+.
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 53
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=80.91 E-value=5.8 Score=29.30 Aligned_cols=25 Identities=12% Similarity=0.146 Sum_probs=22.8
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
..|+++||+..||+..||++.++.+
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
>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=80.02 E-value=3.7 Score=31.54 Aligned_cols=34 Identities=15% Similarity=0.247 Sum_probs=26.9
Q ss_pred HHHHHhcCC-----CCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 155 YVSALTHGL-----KFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 155 ylAar~~g~-----~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
+.+|...|+ ++|+.|||+.+|||.+|+..+++.-
T Consensus 9 L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 9 LKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344555553 3789999999999999999998864
No 55
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=79.66 E-value=17 Score=39.73 Aligned_cols=184 Identities=14% Similarity=0.210 Sum_probs=106.3
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcC-C------------------CCCHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKS-K------------------PFLLID 68 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~-~------------------prtL~D 68 (497)
+..+|..|+++ ...++.|..+...+.-.|+.. |+. .=||.+=.+..+ . ..-+..
T Consensus 141 ~~eia~~l~~~--~~~v~~~l~~lQ~leP~GigA-r~L----~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~ 213 (455)
T PRK05932 141 LEEIAESLGVE--LDEVEAVLKRIQSFDPAGVGA-RDL----QECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRT 213 (455)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CCH----HHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHH
Confidence 57788899998 888888888888766566532 221 224444433321 1 123566
Q ss_pred HHHHhCcChHHHHHHHHHHHHHhccccccc--c----cccCCccchHHH----------------------HHhhhCCCC
Q 010919 69 FSNYLNINVYELGAVYLQLCQVLYIADESN--V----LKQVDPSIFLHK----------------------FTDRLLPGG 120 (497)
Q Consensus 69 Ia~v~~vsv~~Lgr~yk~L~~~L~i~~~~~--~----~~~idP~~~I~R----------------------f~~~L~~~~ 120 (497)
|+..++++..+|..+...|. .|+= .|- + ...+-|..+|.+ |...+....
T Consensus 214 ia~~l~is~~~v~~~~~~Ir-~L~P--~Pg~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~in~~Y~~~~~~~~ 290 (455)
T PRK05932 214 LAKKLGVKEEDLQEALDLIR-SLDP--KPGAGFGTEEPEYVVPDVFVRKINGGWLVELNPDSLPRLRINQEYAALVSRSA 290 (455)
T ss_pred HHHHHCcCHHHHHHHHHHHh-CCCC--CCccccCCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHHhcc
Confidence 88889999999999886664 4531 121 1 112334444322 222221000
Q ss_pred CHHHHHHHHHHHHHhcc-ccccC--CCChhHHHHHHHHHHHH-----hcCC----CCCHhhHHHHhccCHHHHHHHHHH-
Q 010919 121 NKKVCDTARDILASMKR-DWITT--GRKPSGLCGAALYVSAL-----THGL----KFSKSDIVKIVHICEATLMKRLIE- 187 (497)
Q Consensus 121 ~~~V~~~A~~Lv~~~~~-~~l~~--GR~P~~IaaAaLylAar-----~~g~----~~t~~eIa~v~~Vse~TIrkr~kE- 187 (497)
..++.. .|-+++.+ .|+.. .+|-.+|.--+-.++-+ ..|. +.|+++||..+|++++||.+..+.
T Consensus 291 ~~e~~~---ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~K 367 (455)
T PRK05932 291 RDEDKQ---FLREKLQEAKWLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTNK 367 (455)
T ss_pred chHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcCc
Confidence 011111 11111111 24332 24555555545444443 2343 579999999999999999998876
Q ss_pred HhcCCCCCCCHHHHHHH
Q 010919 188 FENTDSGSLTIEDFMAR 204 (497)
Q Consensus 188 ~~~t~~~~Lt~~ef~~~ 204 (497)
+..||-+-+-+..|.+.
T Consensus 368 yv~tp~Gi~~lk~FFs~ 384 (455)
T PRK05932 368 YMATPRGIFELKYFFSS 384 (455)
T ss_pred eeecCCceEEHHHhccc
Confidence 66888888888888876
No 56
>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=79.64 E-value=1 Score=32.90 Aligned_cols=28 Identities=18% Similarity=0.131 Sum_probs=20.5
Q ss_pred HhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 010919 159 LTHGLKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 159 r~~g~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
+|+.-..|+.+||+.+|||..||.+.++
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 4444559999999999999999998764
No 57
>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=78.40 E-value=3.6 Score=32.66 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=26.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
++.|+.+||..+|+|..|+.+-+++|.+-
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 56899999999999999999999999753
No 58
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=78.36 E-value=31 Score=34.50 Aligned_cols=37 Identities=14% Similarity=0.134 Sum_probs=28.4
Q ss_pred CCCCHhhHHHHhccC-HHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 163 LKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vs-e~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
-+.|+.+||..+|-+ .+...+.+|..- .+||.+|++.
T Consensus 247 t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~SP~~yR~~ 284 (290)
T PRK10572 247 TRMPIATIGRNVGYDDQLYFSRVFKKCT-----GASPSEFRAR 284 (290)
T ss_pred CCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 468888888888876 667788887764 5788888876
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=77.62 E-value=5.6 Score=31.38 Aligned_cols=40 Identities=23% Similarity=0.236 Sum_probs=31.8
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 010919 144 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 144 R~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
|+|.-=-|=-||+ -++-.++.++||..+||++.|||+.=.
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 5666556666774 467899999999999999999997643
No 60
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=77.47 E-value=94 Score=32.22 Aligned_cols=25 Identities=12% Similarity=0.072 Sum_probs=22.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|+++|+..+|||..|||++...
T Consensus 275 ~~~Tl~EIa~~lgiS~erVRqi~~r 299 (317)
T PRK07405 275 QPLTLAKIGERLNISRERVRQIERE 299 (317)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5699999999999999999987554
No 61
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=77.40 E-value=16 Score=35.33 Aligned_cols=119 Identities=14% Similarity=0.206 Sum_probs=68.0
Q ss_pred hHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHH
Q 010919 45 TEQVQASCLYLACRQKSKP-FLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 123 (497)
Q Consensus 45 ~~~VaAACLYiACR~e~~p-rtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~ 123 (497)
...++=|.||. .+.| .++.+|+.+++++...+..+...|...+.-.........+ ...| + |. ..++
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--K----LV--TKEE 71 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEE-CCEE--E----EE--EcHH
Confidence 34566677777 5777 9999999999999989999999998877532211000000 0111 0 11 1222
Q ss_pred HHHHHHHHHHHhccccccCCCChhHHHHHHHH-HHHHhcCCCCCHhhHHHHhccCHHHHHHHH
Q 010919 124 VCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKRL 185 (497)
Q Consensus 124 V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLy-lAar~~g~~~t~~eIa~v~~Vse~TIrkr~ 185 (497)
......+++ ...+|.-+--|+|= +|.-.+..++|..+|+++.||+..-+-+.|
T Consensus 72 ~~~~v~~~~---------~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~~~ii~~L 125 (188)
T PRK00135 72 NADYLQKLV---------KTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNSDGALQTL 125 (188)
T ss_pred HHHHHHHHh---------cccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 222222221 11222233333442 444456789999999999999974443333
No 62
>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=77.14 E-value=6.5 Score=30.15 Aligned_cols=29 Identities=21% Similarity=0.414 Sum_probs=26.3
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
....|+.+|++.+|++..|+.+.++.|.+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35689999999999999999999999865
No 63
>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=76.91 E-value=8.6 Score=35.72 Aligned_cols=30 Identities=17% Similarity=0.301 Sum_probs=27.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
++.|+.+||..+|+|..||.+-+++|.+-.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 171 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKKK 171 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 678999999999999999999999997643
No 64
>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=76.88 E-value=5.3 Score=31.21 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+||.... .+..++..+||+.++|+.+|+..-++.|.+
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 677899999999999999999999998864
No 65
>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=76.87 E-value=13 Score=40.41 Aligned_cols=182 Identities=14% Similarity=0.194 Sum_probs=104.9
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCC------------------CCCHHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK------------------PFLLIDF 69 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~------------------prtL~DI 69 (497)
+..+|..|+++ ...++.|..++..+.-.|+.. |+. .=||.+=.+..+. ..-+..|
T Consensus 116 ~~eia~~l~~~--~~~ve~~l~~iq~leP~GIgA-r~L----~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i 188 (429)
T TIGR02395 116 LEEIADELEVS--EEEVEKVLELIQRLDPAGVGA-RDL----QECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRL 188 (429)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CCH----HHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHH
Confidence 57788999999 888888888887766555532 222 2244444443221 1235678
Q ss_pred HHHhCcChHHHHHHHHHHHHHhcccccccc-----cccCCccchHHHHH----------------------hhhCCCCCH
Q 010919 70 SNYLNINVYELGAVYLQLCQVLYIADESNV-----LKQVDPSIFLHKFT----------------------DRLLPGGNK 122 (497)
Q Consensus 70 a~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~-----~~~idP~~~I~Rf~----------------------~~L~~~~~~ 122 (497)
+..++++..++..++..|.. |+-.+...+ ...+-|..+|.+.- ..+......
T Consensus 189 ~~~l~is~~~v~~~~~~I~~-L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~ 267 (429)
T TIGR02395 189 AKKLGLSEEELKEALDLIKS-LSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEKE 267 (429)
T ss_pred HHHHCcCHHHHHHHHHHHhC-CCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccch
Confidence 88899999999887766555 431100001 11233444443221 111100001
Q ss_pred HH-------HHHHHHHHHHhccccccCCCChhHHHHHHHHHHHH-----hcC----CCCCHhhHHHHhccCHHHHHHHHH
Q 010919 123 KV-------CDTARDILASMKRDWITTGRKPSGLCGAALYVSAL-----THG----LKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 123 ~V-------~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar-----~~g----~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
++ ...|..|++.+ -+|-.+|--.+-.++-+ ..| .+.|+++||..+||+++||.+..+
T Consensus 268 ~~~~ylk~k~~~A~~li~~i-------~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 268 AAAQYLKQKLKEARWLIKAL-------EQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 11 11223232222 24444554444444443 245 258999999999999999999887
Q ss_pred H-HhcCCCCCCCHHHHHHH
Q 010919 187 E-FENTDSGSLTIEDFMAR 204 (497)
Q Consensus 187 E-~~~t~~~~Lt~~ef~~~ 204 (497)
. +..||-+-+-+..|.+.
T Consensus 341 ~Kyi~tp~Gi~~lk~FFs~ 359 (429)
T TIGR02395 341 NKYLQTPRGVFELKYFFSR 359 (429)
T ss_pred CceEecCCceEEHHHhcCC
Confidence 6 66888888888888876
No 66
>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=76.66 E-value=4.4 Score=29.86 Aligned_cols=27 Identities=15% Similarity=0.089 Sum_probs=23.6
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
....|..+||...|+|..||+++++..
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 567999999999999999999998764
No 67
>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=76.49 E-value=80 Score=30.94 Aligned_cols=26 Identities=4% Similarity=-0.019 Sum_probs=22.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|+++||..+|||..+|+++.+.-
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~a 220 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKA 220 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 46999999999999999999886654
No 68
>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=76.43 E-value=2.6 Score=31.26 Aligned_cols=34 Identities=15% Similarity=0.070 Sum_probs=25.6
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
|++|||+.+|||..|+.+.|..= ..++.+-..++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~-----~~vs~~tr~rI 34 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP-----PRVSEETRERI 34 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC-----SSSTHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC-----CCCCHHHHHHH
Confidence 68999999999999999987532 45555554444
No 69
>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=75.06 E-value=2.8 Score=28.90 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=22.1
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+.|..|||+.+|++..|+.+-++.|..
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 468899999999999999999999965
No 70
>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=74.88 E-value=60 Score=32.21 Aligned_cols=96 Identities=13% Similarity=0.122 Sum_probs=57.0
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHH
Q 010919 50 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTAR 129 (497)
Q Consensus 50 AACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~ 129 (497)
.++-||...- ..++++.++|+.+++|...|.+.|++... ..|..||.+. +| ..|.
T Consensus 190 ~~~~~I~~~~-~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G-------------~t~~~yi~~~--Rl---------~~A~ 244 (287)
T TIGR02297 190 RFNFLIEENY-KQHLRLPEYADRLGISESRLNDICRRFSA-------------LSPKRLIIER--VM---------QEAR 244 (287)
T ss_pred HHHHHHHHhh-ccCCCHHHHHHHHCCCHHHHHHHHHHHhC-------------CCHHHHHHHH--HH---------HHHH
Confidence 3444555433 34788888888888888888777766442 3455565544 11 1222
Q ss_pred HHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccC-HHHHHHHHHHHhcCCCCCCCHHHHHH
Q 010919 130 DILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMA 203 (497)
Q Consensus 130 ~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vs-e~TIrkr~kE~~~t~~~~Lt~~ef~~ 203 (497)
++ +..-+.|+.+||..+|-+ .++-.+.+|... .+||.+|++
T Consensus 245 ~l----------------------------L~~t~~sI~eIA~~~GF~s~s~Fsr~FKk~~-----G~tP~~yR~ 286 (287)
T TIGR02297 245 RL----------------------------LLFTQHSINQIAYDLGYKDPAYFARFFQKET-----GLSPSAFRD 286 (287)
T ss_pred HH----------------------------HHcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHhc
Confidence 21 113456778888888864 556777777653 366666653
No 71
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=74.55 E-value=3.9 Score=29.24 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=26.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.++.++.+|++.+|++..|+++.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 467899999999999999999999999753
No 72
>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=74.46 E-value=4.7 Score=27.77 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=22.2
Q ss_pred CCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 63 PFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 63 prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
|.+-.|||+.++++..++.|.+++|.+
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 567889999999999999999999876
No 73
>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=74.36 E-value=2.3 Score=43.68 Aligned_cols=55 Identities=11% Similarity=0.038 Sum_probs=48.6
Q ss_pred cchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcC
Q 010919 106 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHG 162 (497)
Q Consensus 106 ~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g 162 (497)
..+|.++|.+|. ++..+..+|.-+.++..-..-..+-.|..||.+|||+||+.-+
T Consensus 49 ~k~i~~l~~~L~--lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed 103 (297)
T COG5333 49 LKLIMDLCTRLN--LPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED 103 (297)
T ss_pred HHHHHHHHHhcC--CCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccc
Confidence 457889999998 7999999999999998766668899999999999999999766
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=73.33 E-value=3.3 Score=31.81 Aligned_cols=30 Identities=20% Similarity=0.247 Sum_probs=26.1
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.-.++..+++..++||+.|||+=+..|.+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 346899999999999999999999888643
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=72.80 E-value=8.1 Score=34.78 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=39.9
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+...-..+++|+|-+..+.|.+..+||..++++...|.+....|.+.
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44566778999998766779999999999999999999988888874
No 76
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=72.66 E-value=5.6 Score=39.58 Aligned_cols=57 Identities=16% Similarity=0.109 Sum_probs=43.9
Q ss_pred cchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCC
Q 010919 106 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLK 164 (497)
Q Consensus 106 ~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~ 164 (497)
..+|..++.+|. +...|+.+|.-.++|.--..-..+-.|.-+|..|||+||..-...
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 346667777776 788999999988888543333778999999999999999855444
No 77
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=72.49 E-value=5.5 Score=33.94 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=27.0
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+-+.|..+|++.+|+++.|++++++.|.+.
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457899999999999999999999999753
No 78
>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=72.28 E-value=8.3 Score=31.63 Aligned_cols=27 Identities=19% Similarity=0.064 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||+.+|||+.||++++....
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 457999999999999999999998653
No 79
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=72.13 E-value=5.3 Score=36.13 Aligned_cols=33 Identities=18% Similarity=0.435 Sum_probs=28.6
Q ss_pred HhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 159 LTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 159 r~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
...+.++|+.+||+.+|+|..|+++|++.+.+.
T Consensus 17 L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 17 LQEDARISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344667999999999999999999999999654
No 80
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=71.95 E-value=5.4 Score=29.63 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=25.8
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
|... |..++++.++||..||++.++.|.+.
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3345 89999999999999999999999753
No 81
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=71.12 E-value=10 Score=26.88 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=26.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFM 202 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~ 202 (497)
..+.++.+||..+|+|...+++.++... .+|+.+|.
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 3468999999999999999999999873 46677765
No 82
>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=71.09 E-value=32 Score=31.55 Aligned_cols=79 Identities=14% Similarity=0.045 Sum_probs=53.7
Q ss_pred CCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhcc---c--cccCCCChhHHHHHHHHHHHHhcC-CCCCHhhHHHHhcc
Q 010919 103 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR---D--WITTGRKPSGLCGAALYVSALTHG-LKFSKSDIVKIVHI 176 (497)
Q Consensus 103 idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~---~--~l~~GR~P~~IaaAaLylAar~~g-~~~t~~eIa~v~~V 176 (497)
++-..||.|+..... .++.+.-.|+-++.++.. . .......+.-+-.+||.+|+.+++ ...+.+.++++.||
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 555678888877776 788999999999999877 1 123456677788999999998865 55889999999998
Q ss_pred CHHHHHH
Q 010919 177 CEATLMK 183 (497)
Q Consensus 177 se~TIrk 183 (497)
+...|.+
T Consensus 130 s~~eln~ 136 (149)
T PF08613_consen 130 SLKELNE 136 (149)
T ss_dssp -HHHHHH
T ss_pred CHHHHHH
Confidence 7655543
No 83
>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=70.51 E-value=7.2 Score=30.74 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=26.6
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+.+-..+..+++..+|||..||+++++.+.+
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3344578999999999999999999999964
No 84
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=70.14 E-value=38 Score=36.12 Aligned_cols=26 Identities=8% Similarity=0.018 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|+++|+..+|||..+||+....-
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rA 355 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKA 355 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999876653
No 85
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=70.09 E-value=8.4 Score=44.66 Aligned_cols=80 Identities=13% Similarity=0.222 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHcCCCChhHHHHHHHHHHHHHHh--CCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHH
Q 010919 4 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELG 81 (497)
Q Consensus 4 a~~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~--~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lg 81 (497)
|..+|+.+|.+|.|. +.+...-..+|.-... -.+.+.|..+++.-.|+|+.||..+...++.+|-...+--..-..
T Consensus 680 AavRL~~Lc~rL~l~--~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~ 757 (920)
T KOG1010|consen 680 AAVRLNDLCERLSLS--DELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVS 757 (920)
T ss_pred HHHHHHHHHHHhhhh--hHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhh
Confidence 667899999999999 8888888888776554 357789999999999999999999999999998776543333333
Q ss_pred HHHH
Q 010919 82 AVYL 85 (497)
Q Consensus 82 r~yk 85 (497)
.+|+
T Consensus 758 ~vyR 761 (920)
T KOG1010|consen 758 LVYR 761 (920)
T ss_pred hhhh
Confidence 3343
No 86
>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=69.99 E-value=15 Score=34.05 Aligned_cols=48 Identities=13% Similarity=0.101 Sum_probs=37.3
Q ss_pred CChHHHHHHHHHHHHHhcC----------CCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 43 RRTEQVQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 43 R~~~~VaAACLYiACR~e~----------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
++...-.|..|+.-|+..+ .|.|..|||+.+|++..++.|++++|.+.
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 4455556666655455432 68899999999999999999999999885
No 87
>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=69.24 E-value=7.3 Score=31.98 Aligned_cols=45 Identities=22% Similarity=0.244 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 46 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
....-+.+|+|-...+.|.+..+||+.++++...|.+....|.+.
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 344556778887777788999999999999999999999999884
No 88
>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=68.35 E-value=14 Score=28.73 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=32.0
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 52 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 52 CLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+||.... .+.+.+..|||..++|+..++....++|.+.
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 5666665 8889999999999999999999999998873
No 89
>PF13518 HTH_28: Helix-turn-helix domain
Probab=68.08 E-value=7.5 Score=28.41 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=24.0
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
|+.+||..+||+..||.+.++.|.+.
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
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=68.05 E-value=1.3e+02 Score=29.87 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|+++||..+||+..||++++....
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~ 244 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGL 244 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 578999999999999999999987653
No 91
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=67.69 E-value=6.9 Score=28.43 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.3
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
..+.++||..+|||..||++++..+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36999999999999999999988764
No 92
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=66.70 E-value=77 Score=26.61 Aligned_cols=39 Identities=15% Similarity=0.277 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 48 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 48 VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
+.-++-||.- ....+.++.++|..++++...|.+.|+..
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 66667999999999999999998876644
No 93
>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=66.69 E-value=9.9 Score=27.96 Aligned_cols=27 Identities=26% Similarity=0.209 Sum_probs=20.9
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
.|- .|++..|+..||..+||++|++.-
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 455 999999999999999999988764
No 94
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=66.24 E-value=91 Score=34.10 Aligned_cols=41 Identities=15% Similarity=0.336 Sum_probs=37.1
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH-HhcCCCCCCCHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIE-FENTDSGSLTIEDFMAR 204 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE-~~~t~~~~Lt~~ef~~~ 204 (497)
+.++++||..+|++++||.+.... +..||.+-+-+..|...
T Consensus 330 PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~ 371 (444)
T COG1508 330 PLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSS 371 (444)
T ss_pred cccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHH
Confidence 467899999999999999988876 77899999999999988
No 95
>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=66.12 E-value=15 Score=28.96 Aligned_cols=32 Identities=13% Similarity=0.163 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCcChHHHHHHHHHHHHHhcc
Q 010919 62 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 93 (497)
Q Consensus 62 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i 93 (497)
.|.+..+||+.+|++..++.++++.|.+.=-+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I 58 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGII 58 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 57899999999999999999999999885433
No 96
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=65.73 E-value=41 Score=33.79 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=23.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
....|+++||..+|||..||+++++..
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ra 255 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKT 255 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999987654
No 97
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=65.50 E-value=7.4 Score=29.37 Aligned_cols=36 Identities=14% Similarity=0.193 Sum_probs=29.0
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 155 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 155 ylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
++.-...-...+..++|..+||+++|+.+.+.++.+
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 333334457799999999999999999999998754
No 98
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=65.17 E-value=14 Score=34.70 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=39.2
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+...-..+++|+|-...+.|.++.+||+.++++...|.+....|.+.
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 34566778899995555679999999999999999999988888874
No 99
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=64.61 E-value=14 Score=28.03 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=23.9
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.+|+.+|++.++++.+|+.+.++.|.+
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 389999999999999999999999864
No 100
>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=64.53 E-value=7.9 Score=29.66 Aligned_cols=28 Identities=14% Similarity=0.169 Sum_probs=25.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
-|..++.+.|..+|||..+++++.+++.
T Consensus 13 ~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 13 YFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 3789999999999999999999999874
No 101
>PRK05949 RNA polymerase sigma factor; Validated
Probab=64.20 E-value=1.9e+02 Score=30.20 Aligned_cols=25 Identities=4% Similarity=0.050 Sum_probs=22.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.++|+..+|||..|||.+...
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~r 309 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEHQ 309 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5799999999999999999987554
No 102
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=64.04 E-value=96 Score=31.69 Aligned_cols=99 Identities=12% Similarity=0.146 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHH
Q 010919 48 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDT 127 (497)
Q Consensus 48 VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~ 127 (497)
+.-+.-||-- .-..++++.++|..++++...|.+.|++.. | ..|..|+.++ -...
T Consensus 220 ~~~~~~~i~~-~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~---g----------~s~~~~~~~~-----------Rl~~ 274 (322)
T PRK09393 220 LGPLIDWMRA-HLAEPHTVASLAARAAMSPRTFLRRFEAAT---G----------MTPAEWLLRE-----------RLAR 274 (322)
T ss_pred HHHHHHHHHh-ccCCCCCHHHHHHHHCcCHHHHHHHHHHHH---C----------cCHHHHHHHH-----------HHHH
Confidence 3334444443 334578889999999998888877666543 2 3465565544 1112
Q ss_pred HHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhcc-CHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 128 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 128 A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~V-se~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
|..++. .-..++.+||..+|- +.+...+.++.+. .+||.+|++.
T Consensus 275 A~~lL~----------------------------~~~~~i~~IA~~~Gf~~~s~F~r~Fk~~~-----G~tP~~yr~~ 319 (322)
T PRK09393 275 ARDLLE----------------------------SSALSIDQIAERAGFGSEESLRHHFRRRA-----ATSPAAYRKR 319 (322)
T ss_pred HHHHHH----------------------------cCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 222221 124477778888876 4467777777763 4677777754
No 103
>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=64.02 E-value=16 Score=31.01 Aligned_cols=30 Identities=3% Similarity=0.134 Sum_probs=26.9
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
....+|+.+||..+|++..|+.+.+++|..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 356799999999999999999999999864
No 104
>PHA02591 hypothetical protein; Provisional
Probab=63.77 E-value=8.4 Score=31.96 Aligned_cols=31 Identities=13% Similarity=0.142 Sum_probs=26.5
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 010919 156 VSALTHGLKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 156 lAar~~g~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
+|..+.....|+.+||+.+||+..||++-++
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 5556667788999999999999999998765
No 105
>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=63.69 E-value=1.4e+02 Score=28.70 Aligned_cols=26 Identities=8% Similarity=0.123 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+||+..||++++..-
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra 215 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQA 215 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56799999999999999999887653
No 106
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=63.65 E-value=17 Score=26.01 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=24.9
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..++.+|+..++++..|+++.++.|..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 489999999999999999999999864
No 107
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=63.01 E-value=13 Score=34.35 Aligned_cols=42 Identities=19% Similarity=0.097 Sum_probs=28.9
Q ss_pred ChhHHHHHHHHHHHHhcC---CCCCHhhHHHHhccCHHHHHHHHH
Q 010919 145 KPSGLCGAALYVSALTHG---LKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 145 ~P~~IaaAaLylAar~~g---~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
.|.=+-||.|+++-.++. -++|+.+||.-+||+++|+-++-+
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 344556677777666665 459999999999999999988774
No 108
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=62.94 E-value=17 Score=33.65 Aligned_cols=46 Identities=13% Similarity=0.108 Sum_probs=37.9
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+.+.-+-+.+|+|- ..+.+.+..+||+..+++...|.+.+..|.+.
T Consensus 6 ~~~YAlr~L~~LA~-~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCAA-NDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHHh-CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34555668899994 45668899999999999999999999988884
No 109
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=62.82 E-value=33 Score=30.45 Aligned_cols=55 Identities=4% Similarity=0.038 Sum_probs=42.8
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 145 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 145 ~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
....|..+.-||-.... .+.++.+||+.+|+++.++.+.+++.. .+|+.+|....
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~-----G~s~~~~l~~~ 61 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET-----GHSLGQYIRSR 61 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 44555666667766654 469999999999999999999999874 47888887553
No 110
>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=62.53 E-value=1.1e+02 Score=30.21 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|+++||..+|||..+|++..+.-
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ra 246 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAA 246 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887653
No 111
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=62.46 E-value=8.4 Score=29.92 Aligned_cols=30 Identities=17% Similarity=0.290 Sum_probs=24.8
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|..+ |..++++..+||..|+|+.|..|..
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 35677 9999999999999999999999864
No 112
>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=62.34 E-value=14 Score=26.98 Aligned_cols=32 Identities=9% Similarity=0.189 Sum_probs=26.8
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+..-+.++.+|++.+|++.+||..-++.+.+.
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 113
>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=62.29 E-value=10 Score=28.17 Aligned_cols=27 Identities=30% Similarity=0.324 Sum_probs=20.3
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
-...|..+||...|+|+.||++++.--
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 466899999999999999999998754
No 114
>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=62.25 E-value=9.5 Score=27.39 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=19.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
..=.+...|+.+||+..|+.++++.+
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 115
>PF13551 HTH_29: Winged helix-turn helix
Probab=62.10 E-value=12 Score=31.69 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=24.7
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
|+.+||+.+||+..||.+.++.|.+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999997654
No 116
>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=61.97 E-value=18 Score=26.88 Aligned_cols=33 Identities=9% Similarity=0.096 Sum_probs=28.1
Q ss_pred hcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 59 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 59 ~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
.++-|+|..+||+.++||..++.+-...|...+
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 456679999999999999999999999997755
No 117
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=61.91 E-value=2.6e+02 Score=31.25 Aligned_cols=25 Identities=4% Similarity=-0.004 Sum_probs=21.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|+.+|+..+|||...||+.-+.
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~k 490 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIESK 490 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999865433
No 118
>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=61.10 E-value=8.9 Score=27.03 Aligned_cols=23 Identities=13% Similarity=0.232 Sum_probs=20.5
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
|..|||+.+||+..||++..+.-
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 67899999999999999888763
No 119
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=60.47 E-value=12 Score=26.50 Aligned_cols=27 Identities=7% Similarity=0.114 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
..+.++.|||..++++...+.+.|++.
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 457899999999999999998877764
No 120
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=60.30 E-value=16 Score=27.57 Aligned_cols=34 Identities=12% Similarity=0.251 Sum_probs=29.7
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 94 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 94 (497)
+.-.+..++|..+||+..++.+.+..+...|...
T Consensus 17 R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 17 RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 4457899999999999999999999999988654
No 121
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=59.35 E-value=30 Score=32.39 Aligned_cols=30 Identities=13% Similarity=0.172 Sum_probs=26.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
++.|+.+||..+|++..|+.+-+++|.+..
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCC
Confidence 568999999999999999999999997643
No 122
>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=59.21 E-value=12 Score=27.21 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=23.8
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..|.++||..++++..||+++++.+..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 469999999999999999999887643
No 123
>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=59.16 E-value=9.9 Score=26.99 Aligned_cols=23 Identities=9% Similarity=0.260 Sum_probs=20.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.|.+|+|+.+||+..||++..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 47899999999999999998865
No 124
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=59.14 E-value=32 Score=30.58 Aligned_cols=72 Identities=14% Similarity=0.072 Sum_probs=54.3
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhC-CCCCH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNK 122 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~-~~~~~ 122 (497)
+.+...=.=+|+-|| =+|++++..++||-.+++.....|.+.|+....+ ..........+.++|. |+++.
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 445555566677666 3799999999999999999999999999983322 1344567788888996 77765
Q ss_pred HH
Q 010919 123 KV 124 (497)
Q Consensus 123 ~V 124 (497)
+-
T Consensus 106 ee 107 (113)
T PF09862_consen 106 EE 107 (113)
T ss_pred HH
Confidence 43
No 125
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=58.63 E-value=16 Score=34.59 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=23.3
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
.|..|||..+|||+.||++++.-+.
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 126
>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=58.46 E-value=34 Score=26.03 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..+.+..|||+.++++..++.+.+..|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 457899999999999999999999998884
No 127
>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=58.46 E-value=9.7 Score=29.85 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=29.9
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.+|.+-. ..-..|..+|++.+|++..|+.+.++.|.+
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4454443 446789999999999999999999999864
No 128
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=58.23 E-value=15 Score=29.48 Aligned_cols=31 Identities=10% Similarity=0.012 Sum_probs=29.3
Q ss_pred HhcCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 159 LTHGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 159 r~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
++.+..+|+.+.++.+|+.+.||+++...|.
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR 38 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFR 38 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6789999999999999999999999999996
No 129
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=58.02 E-value=32 Score=33.12 Aligned_cols=30 Identities=20% Similarity=0.357 Sum_probs=26.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
+++|+++||..+|++..|+.+-+++|.+..
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g 212 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSG 212 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 568999999999999999999999987543
No 130
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=57.93 E-value=20 Score=30.27 Aligned_cols=37 Identities=11% Similarity=0.073 Sum_probs=31.1
Q ss_pred HHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 154 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 154 LylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+.|+-++.+...++.++|..+|||..|..|++.-|..
T Consensus 15 ~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 15 LRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred HHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455566677899999999999999999999988864
No 131
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=57.80 E-value=28 Score=33.27 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=22.6
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
..|..+||+.+|||.+|+.+.+++.
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 132
>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=57.66 E-value=22 Score=25.89 Aligned_cols=35 Identities=23% Similarity=0.294 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCC-CCCHhhHHHHhccCHHHHHHHHHH
Q 010919 152 AALYVSALTHGL-KFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 152 AaLylAar~~g~-~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
|++-+.. -.|+ ..|.++|++.+||+..++-+.+..
T Consensus 4 aa~~l~~-~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47)
T PF00440_consen 4 AALELFA-EKGYEAVSIRDIARRAGVSKGSFYRYFPS 39 (47)
T ss_dssp HHHHHHH-HHHTTTSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred HHHHHHH-HhCHHhCCHHHHHHHHccchhhHHHHcCC
Confidence 4444444 3455 599999999999999999877643
No 133
>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=57.54 E-value=14 Score=28.51 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=25.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.-..+..++|..+|+|+.||++-+.++.+.
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 345899999999999999999999999753
No 134
>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=57.40 E-value=15 Score=31.18 Aligned_cols=31 Identities=13% Similarity=-0.039 Sum_probs=27.3
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+..-..|+++|++.+|||-.||.+-=+.+..
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 6667899999999999999999988777764
No 135
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=57.06 E-value=34 Score=30.40 Aligned_cols=56 Identities=7% Similarity=0.094 Sum_probs=39.3
Q ss_pred CChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 010919 43 RRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 112 (497)
Q Consensus 43 R~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf 112 (497)
.....+..+.-||--... .+.++.++|+.+++++..|.+.|+.... ..|..||.+.
T Consensus 6 ~~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~G-------------~s~~~~l~~~ 61 (127)
T PRK11511 6 TDAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKETG-------------HSLGQYIRSR 61 (127)
T ss_pred ccHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH
Confidence 344455556666666544 4799999999999999999887766533 3466666554
No 136
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=56.23 E-value=21 Score=26.23 Aligned_cols=29 Identities=10% Similarity=0.276 Sum_probs=26.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+-..|..+|++.++|+..|+++.++.|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55689999999999999999999999864
No 137
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=56.01 E-value=8 Score=40.20 Aligned_cols=45 Identities=9% Similarity=0.039 Sum_probs=36.9
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHH
Q 010919 156 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 200 (497)
Q Consensus 156 lAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~e 200 (497)
+|...+-...||.|||+.+|||+.||.+-|++-++..-=+++|..
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 444456678999999999999999999999998887766666643
No 138
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=55.88 E-value=82 Score=32.86 Aligned_cols=24 Identities=8% Similarity=-0.027 Sum_probs=20.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
...|+++|+..+|||...||+--+
T Consensus 281 ~~~Tl~eIa~~lgvS~eRVrQIe~ 304 (324)
T PRK07921 281 QPRTLDQIGKLFGLSRERVRQIER 304 (324)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999999985433
No 139
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=55.75 E-value=13 Score=37.28 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=25.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
-.++..|+++.++||+.|||+.+++|.+
T Consensus 18 ~~v~v~eLa~~l~VS~~TIRRDL~~Le~ 45 (256)
T PRK10434 18 GKTSVEELAQYFDTTGTTIRKDLVILEH 45 (256)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4589999999999999999999998853
No 140
>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=55.71 E-value=14 Score=27.47 Aligned_cols=20 Identities=10% Similarity=0.140 Sum_probs=17.7
Q ss_pred CHHHHHHHhCcChHHHHHHH
Q 010919 65 LLIDFSNYLNINVYELGAVY 84 (497)
Q Consensus 65 tL~DIa~v~~vsv~~Lgr~y 84 (497)
||+|||..+||+..++.+++
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 68999999999999998754
No 141
>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=55.63 E-value=23 Score=26.85 Aligned_cols=26 Identities=15% Similarity=0.390 Sum_probs=24.3
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
++..+|++.++++..||++.++.|..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 99999999999999999999999864
No 142
>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=55.58 E-value=17 Score=30.29 Aligned_cols=23 Identities=17% Similarity=0.286 Sum_probs=21.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRL 185 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~ 185 (497)
-..|+.+||+.+|||..||++.+
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 56799999999999999999966
No 143
>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=55.33 E-value=11 Score=27.05 Aligned_cols=23 Identities=13% Similarity=0.026 Sum_probs=20.1
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
|..++|+.+||+..||+...++-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999876654
No 144
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=55.31 E-value=95 Score=33.72 Aligned_cols=51 Identities=14% Similarity=0.139 Sum_probs=41.3
Q ss_pred ccccCCCChhHHHHH---HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 138 DWITTGRKPSGLCGA---ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 138 ~~l~~GR~P~~IaaA---aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..|..++|-..|+-| |.|++-++.+ .|..+|+..+|.+.+||...++.+.+
T Consensus 360 ~~l~s~~R~~~i~~aR~iamyl~r~~~~--~s~~~Ig~~fgr~hstV~~a~~~i~~ 413 (440)
T PRK14088 360 EEILSNSRNVKALLARRIGMYVAKNYLG--SSLRTIAEKFNRSHPVVVDSVKKVKD 413 (440)
T ss_pred HHHhCCCCCccccHHHHHHHHHHHHHhC--CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345666666778888 9999977555 49999999999999999988888864
No 145
>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=55.26 E-value=12 Score=23.73 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.7
Q ss_pred CCCHhhHHHHhccCHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKR 184 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr 184 (497)
..+..+|+..+|++..||.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999999875
No 146
>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=54.92 E-value=14 Score=31.76 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=25.6
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
+..-..||++|+..+|||.+||.+-=+.+.
T Consensus 51 Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 51 LLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 344679999999999999999998777765
No 147
>PRK04217 hypothetical protein; Provisional
Probab=54.60 E-value=16 Score=32.25 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|+++||+.+|||..||++++....
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 148
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.45 E-value=68 Score=27.16 Aligned_cols=51 Identities=8% Similarity=0.111 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 149 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 149 IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
|.-+.-|+...+ ..++++.+||+.+|+|..++.+++++.. .+|+.+|....
T Consensus 7 ~~~~~~~i~~~~-~~~~~~~~lA~~~~~S~~~l~r~f~~~~-----g~s~~~~i~~~ 57 (107)
T PRK10219 7 IQTLIAWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTVT-----HQTLGDYIRQR 57 (107)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 344445555543 4569999999999999999999999973 57888887653
No 149
>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=54.41 E-value=14 Score=30.38 Aligned_cols=37 Identities=24% Similarity=0.346 Sum_probs=27.2
Q ss_pred HHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 154 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 154 LylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+|+|..-.+...|.++||+.+++++.++++-+..|..
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 3444333333489999999999999999999999864
No 150
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.22 E-value=47 Score=28.13 Aligned_cols=39 Identities=8% Similarity=0.137 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 48 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 48 VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
+..++-|+.... ..|.++.++|+.++++...|.+.|++.
T Consensus 7 ~~~~~~~i~~~~-~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344555665553 457999999999999999999887775
No 151
>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=53.73 E-value=24 Score=24.85 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+..+|+..+|++..||.++.....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 557999999999999999999887764
No 152
>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=53.71 E-value=15 Score=27.65 Aligned_cols=26 Identities=19% Similarity=0.328 Sum_probs=23.7
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
|..+|++.++|+..||++.++.|.+-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 59999999999999999999999753
No 153
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=53.47 E-value=48 Score=31.91 Aligned_cols=53 Identities=17% Similarity=0.221 Sum_probs=37.7
Q ss_pred CCCChHHHHHHHHHHHHHhcC----------CCCCHHHHHHHhCcChHHHHHHHHHHHHHhcc
Q 010919 41 KGRRTEQVQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 93 (497)
Q Consensus 41 rGR~~~~VaAACLYiACR~e~----------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i 93 (497)
..++...-.|.-|+.=++..+ .|.|..+||+.+|++..++.|..++|.+.=-|
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 345555555555554333322 58899999999999999999999988885333
No 154
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=53.19 E-value=48 Score=32.19 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=26.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
++.|+.+||..+|++..|+.+.+++|.+..
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~G 207 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDRG 207 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 568999999999999999999999997653
No 155
>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=53.13 E-value=13 Score=28.77 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=20.6
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
|..|||+.+||+..||++..+++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999988764
No 156
>PF12728 HTH_17: Helix-turn-helix domain
Probab=52.87 E-value=15 Score=26.94 Aligned_cols=23 Identities=9% Similarity=0.309 Sum_probs=20.1
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.|.+|+|+.+|||..||++..+.
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 157
>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=52.87 E-value=15 Score=29.19 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=25.3
Q ss_pred HhcCCCCCHhhHHHHhccC-HHHHHHHHHHHhc
Q 010919 159 LTHGLKFSKSDIVKIVHIC-EATLMKRLIEFEN 190 (497)
Q Consensus 159 r~~g~~~t~~eIa~v~~Vs-e~TIrkr~kE~~~ 190 (497)
..+|+.-|++||++.+|++ .+|+...++-|.+
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 9999999998854
No 158
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=52.74 E-value=18 Score=32.70 Aligned_cols=38 Identities=16% Similarity=0.359 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.||++..-.|...+.++||+..+|+..+||+.+..+..
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 44555444556689999999999999999999999864
No 159
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=52.61 E-value=25 Score=31.06 Aligned_cols=30 Identities=7% Similarity=0.087 Sum_probs=26.7
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..-..|+.+||+..||+..||.++.+.|..
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 445789999999999999999999999864
No 160
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=52.55 E-value=2.5e+02 Score=27.99 Aligned_cols=25 Identities=12% Similarity=0.213 Sum_probs=22.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.++||..+||+..||++++..
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~r 251 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTK 251 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4689999999999999999987754
No 161
>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=52.51 E-value=32 Score=30.28 Aligned_cols=45 Identities=18% Similarity=0.140 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 46 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..-..+.+|++-...+.|.+..+||..++++...+.+....|.+.
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344556667763323459999999999999999999998888873
No 162
>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=52.40 E-value=31 Score=30.58 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=30.5
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.+|++. ..+-..|..+|++.++++.++++++++.+...
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 34556899999999999999999999999754
No 163
>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=52.35 E-value=35 Score=30.19 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=37.3
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..+....+.+|++- ..+.+.+..|||+.++++...+.+....|.+.
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 34556677888874 34668999999999999999999988888874
No 164
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=52.12 E-value=55 Score=23.91 Aligned_cols=42 Identities=10% Similarity=0.095 Sum_probs=28.6
Q ss_pred CChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 43 RRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 43 R~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
.+...-...-|+-.|+.. .++++||..++|+..++.+.|...
T Consensus 10 ~r~T~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 10 CRITKRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CcHHHHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 333333334344444433 799999999999999999988753
No 165
>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=51.87 E-value=2.8e+02 Score=28.27 Aligned_cols=25 Identities=4% Similarity=0.078 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|+++|+..+|||..|||++...
T Consensus 268 ~~~Tl~EIa~~lgiS~erVrq~~~r 292 (298)
T TIGR02997 268 EPLTLAEIGRRLNLSRERVRQIEAK 292 (298)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4699999999999999999988765
No 166
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=51.68 E-value=31 Score=27.37 Aligned_cols=37 Identities=11% Similarity=0.079 Sum_probs=29.4
Q ss_pred HHHHHHhcCC-CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 154 LYVSALTHGL-KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 154 LylAar~~g~-~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|+..-..+|- .+|..+||..+||+..|+++.|..|.+
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3333344555 499999999999999999999998864
No 167
>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=51.65 E-value=9.8 Score=31.75 Aligned_cols=35 Identities=14% Similarity=0.203 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
+|-++.-+.+.+.|++..|.++|||.+||-+=+.|
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvte 42 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTE 42 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHH
Confidence 34444555566889999999999999999765544
No 168
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=51.64 E-value=2.8e+02 Score=28.24 Aligned_cols=28 Identities=4% Similarity=-0.169 Sum_probs=24.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
....|+++|+..+|||..||+++...-.
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al 270 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARAL 270 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3579999999999999999998877653
No 169
>PRK13501 transcriptional activator RhaR; Provisional
Probab=51.60 E-value=2.6e+02 Score=27.89 Aligned_cols=58 Identities=17% Similarity=0.086 Sum_probs=38.0
Q ss_pred CCCChhHHHHHHHH-HHHHh-cCCCCCHhhHHHHhcc-CHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 142 TGRKPSGLCGAALY-VSALT-HGLKFSKSDIVKIVHI-CEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 142 ~GR~P~~IaaAaLy-lAar~-~g~~~t~~eIa~v~~V-se~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
+|..|.-..---.. .|+++ ..-..|+.+||..+|- +.+.-.+.+|... .+||.+|++.
T Consensus 217 ~G~T~~qyi~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FKk~~-----G~TP~~yR~~ 277 (290)
T PRK13501 217 TGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREA-----GMTPRDYRQR 277 (290)
T ss_pred HCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 45555554444433 23333 3455789999999998 4556677777764 4899999887
No 170
>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=51.52 E-value=2.7e+02 Score=28.06 Aligned_cols=26 Identities=8% Similarity=0.043 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|+++||..+||+..||++++..-
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rA 266 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEA 266 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 35899999999999999999887664
No 171
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.49 E-value=14 Score=36.87 Aligned_cols=29 Identities=10% Similarity=0.102 Sum_probs=25.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+-.++++++++.+|||+.|||+.+++|.+
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45689999999999999999999999853
No 172
>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=50.75 E-value=19 Score=26.74 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=26.0
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.++-..|+.||++.+|++.+|+.+-++.|.+.
T Consensus 14 ~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 14 ESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp CTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34455799999999999999999999988653
No 173
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=50.41 E-value=34 Score=33.06 Aligned_cols=30 Identities=10% Similarity=0.139 Sum_probs=26.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
+..|+.+||+.+|+|..|+.+-+++|.+-.
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 456899999999999999999999997643
No 174
>smart00351 PAX Paired Box domain.
Probab=50.23 E-value=21 Score=31.81 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.9
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
..+..+||+.+||+..||.+.++-|.++.
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G 61 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETG 61 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence 46899999999999999999999997664
No 175
>cd00131 PAX Paired Box domain
Probab=49.95 E-value=21 Score=32.03 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=26.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
...+..+||..++|+..||.+..+-|.++.
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 176
>PRK00118 putative DNA-binding protein; Validated
Probab=49.86 E-value=20 Score=31.39 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=24.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||+.+|||+.||.+++....
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RAr 58 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTE 58 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 478999999999999999999988654
No 177
>PRK10870 transcriptional repressor MprA; Provisional
Probab=49.61 E-value=62 Score=30.50 Aligned_cols=30 Identities=10% Similarity=0.067 Sum_probs=26.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+..+|+.+|++.++++.+|+.+.++.|..-
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~k 98 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEKR 98 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 456899999999999999999999988643
No 178
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=49.56 E-value=27 Score=24.73 Aligned_cols=30 Identities=10% Similarity=0.136 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..|.+..|+|+.++++..++.+.+..|.+.
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 179
>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=49.54 E-value=38 Score=25.50 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=31.9
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 50 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 50 AACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..+|++.....+...++.||++.++++...+.+..+.|.+.
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 44555555555556899999999999999999999998874
No 180
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=49.52 E-value=1.5e+02 Score=31.50 Aligned_cols=133 Identities=17% Similarity=0.170 Sum_probs=81.2
Q ss_pred HHHHHHHHhc-CCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCc--cchHHHHHhhhCCCCCHHHHHH
Q 010919 51 SCLYLACRQK-SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDP--SIFLHKFTDRLLPGGNKKVCDT 127 (497)
Q Consensus 51 ACLYiACR~e-~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP--~~~I~Rf~~~L~~~~~~~V~~~ 127 (497)
+|-+|+.+-+ ..+..+.||.-.+. +-+...+++......|.+-.-. ++.| ..|+.||...-.+ -.-.+...
T Consensus 185 s~m~I~sk~ee~~~~~~~ef~~itd-~ty~~~qv~~~~~~il~~l~~~----~~~pt~~~~l~~~~~~~~~-~~~~~e~~ 258 (359)
T KOG0654|consen 185 SAMLIASKYEEIKEPRVEEFCYITD-NTYTYWQVLRMEIDILNALTFE----LVRPTSKTFLRRFLRVAQT-PELQVEPL 258 (359)
T ss_pred ccceeeccchhhcchHHHHHHhhhh-hhhHHHHHHHHHHHHHHHhHHH----HhCchHHHHHHHHHHhhcc-hhHHHHHH
Confidence 4556666643 44555666665544 3355555555554444321111 1334 5678887433321 23345555
Q ss_pred HHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 128 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 128 A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
+..|..-..-+..+.--.|+-|||||+++|-..+++.-=...+..-+|++-.++.-....+.
T Consensus 259 ~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 259 ANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 55555554334445567999999999999988887544455678889999999998888885
No 181
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=49.09 E-value=2.8e+02 Score=27.58 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=23.7
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
....|.++||..+|||..||++++...
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ra 245 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKA 245 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999887664
No 182
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=49.08 E-value=57 Score=32.60 Aligned_cols=26 Identities=4% Similarity=0.111 Sum_probs=15.2
Q ss_pred CCCCHHHHHHHhCcC-hHHHHHHHHHH
Q 010919 62 KPFLLIDFSNYLNIN-VYELGAVYLQL 87 (497)
Q Consensus 62 ~prtL~DIa~v~~vs-v~~Lgr~yk~L 87 (497)
...++.+||..+|.+ ...+.|.|++.
T Consensus 247 t~~sI~eIA~~~GF~d~s~Fsr~FKk~ 273 (290)
T PRK10572 247 TRMPIATIGRNVGYDDQLYFSRVFKKC 273 (290)
T ss_pred CCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 456666666666654 55555555543
No 183
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.88 E-value=24 Score=32.39 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=28.5
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCC
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 193 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~ 193 (497)
.....|.++||..+|||.+||.+.++.+.++.+
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~ 50 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWVRRYRETGL 50 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHHHHhccccc
Confidence 346689999999999999999999999987653
No 184
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=48.79 E-value=2.3e+02 Score=28.15 Aligned_cols=101 Identities=12% Similarity=0.178 Sum_probs=59.5
Q ss_pred CCCHHHHHHHhCcChHHHHHHHHHHHHHhccccccc-ccccCCcc-----chHHHHHhhhCCCCCHHHHHHHHHHHHHhc
Q 010919 63 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESN-VLKQVDPS-----IFLHKFTDRLLPGGNKKVCDTARDILASMK 136 (497)
Q Consensus 63 prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~-~~~~idP~-----~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~ 136 (497)
-.|..|+|..+++|+.+|++-.+.+.+.-++-.|.- ...-+-|. .-|..| |.|..+.+|.+...
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~---l~g~~~~eiar~t~------- 174 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLY---LKGKPTPEIARRTN------- 174 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHH---HcCCCHHHHHHHhc-------
Confidence 358899999999999999999999999877644321 00011132 122222 22222333333322
Q ss_pred cccccCCCChhHHHHHHHHHHH-----HhcCCCCCHhhHHHHhccCHHHHHH
Q 010919 137 RDWITTGRKPSGLCGAALYVSA-----LTHGLKFSKSDIVKIVHICEATLMK 183 (497)
Q Consensus 137 ~~~l~~GR~P~~IaaAaLylAa-----r~~g~~~t~~eIa~v~~Vse~TIrk 183 (497)
++|.+|= =|+-. .+.+...+..+|+.++|.|+..|..
T Consensus 175 -------HS~~av~---rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~e 216 (220)
T PF07900_consen 175 -------HSPEAVD---RYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKE 216 (220)
T ss_pred -------cCHHHHH---HHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 2222221 12211 1346778999999999999988764
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=48.46 E-value=53 Score=23.70 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
+-+.+..|||..++++..++.+.++.|.+
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 33489999999999999999999888876
No 186
>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=48.39 E-value=46 Score=27.78 Aligned_cols=45 Identities=11% Similarity=0.084 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhC-cChHHHHHHHHHHHHHhcc
Q 010919 47 QVQASCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQLCQVLYI 93 (497)
Q Consensus 47 ~VaAACLYiACR~e~~prtL~DIa~v~~-vsv~~Lgr~yk~L~~~L~i 93 (497)
..=..|.|++-+..| .++.+|+..++ .+-.++..+++++.+.+.-
T Consensus 30 ~aR~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 30 LARQIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred hHHHHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 333468888877664 67899999999 9999999999999998854
No 187
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=48.20 E-value=4e+02 Score=29.01 Aligned_cols=86 Identities=13% Similarity=0.059 Sum_probs=50.6
Q ss_pred HHHHHHHHHc---CCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHH------HHHHHH-------------------H
Q 010919 6 DDMRQMKNAL---NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA------SCLYLA-------------------C 57 (497)
Q Consensus 6 ~~I~~ia~~L---~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaA------ACLYiA-------------------C 57 (497)
+.+-.+|.++ ++.-.+-|.+...-+++-+..-.-.+|.+..+.+- -+-+++ -
T Consensus 186 rLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lr 265 (415)
T PRK07598 186 RLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIK 265 (415)
T ss_pred HHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHH
Confidence 3444555543 22211555666666777776666677766555443 222332 1
Q ss_pred -------HhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 58 -------RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 58 -------R~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
...|.+-+..+||..+++++..+..+.......+
T Consensus 266 k~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~ 306 (415)
T PRK07598 266 KAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSV 306 (415)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCc
Confidence 1135566789999999999999988766544333
No 188
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=48.17 E-value=24 Score=33.58 Aligned_cols=72 Identities=21% Similarity=0.296 Sum_probs=47.6
Q ss_pred CHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHH
Q 010919 121 NKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 200 (497)
Q Consensus 121 ~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~e 200 (497)
.+.|.........+. .|+. -.++||+|+ +| .-...|..+||.-+|.|+.|||+-++. +|.+++|--+-
T Consensus 28 ~~evlkli~~~~~~l--TWvd----SLavAAga~---ar-ekag~Ti~EIAeelG~TeqTir~hlkg--etkAG~lv~et 95 (182)
T COG1318 28 RPEVLKLIKDPYERL--TWVD----SLAVAAGAL---AR-EKAGMTISEIAEELGRTEQTVRNHLKG--ETKAGQLVRET 95 (182)
T ss_pred cHHHHHHHhCccccc--chhh----HHHHHHHHH---HH-HHccCcHHHHHHHhCCCHHHHHHHHhc--chhhhhHHHHH
Confidence 455555554444433 3432 235555544 34 557799999999999999999999986 56677776666
Q ss_pred HHHH
Q 010919 201 FMAR 204 (497)
Q Consensus 201 f~~~ 204 (497)
|...
T Consensus 96 Y~~l 99 (182)
T COG1318 96 YEKL 99 (182)
T ss_pred HHHH
Confidence 6554
No 189
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=48.05 E-value=75 Score=29.81 Aligned_cols=47 Identities=13% Similarity=0.013 Sum_probs=34.9
Q ss_pred ChHHHHHHHHHHHHHhc---------CCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQK---------SKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e---------~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+...-+|..|+.-|... ..|.+..+||+.+|++..++.|.+++|.+.
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 44445555555444432 248899999999999999999999999885
No 190
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=47.85 E-value=47 Score=26.99 Aligned_cols=28 Identities=7% Similarity=0.159 Sum_probs=25.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
-..|..+|++.+|++.+|+++.++.|.+
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999999864
No 191
>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=47.76 E-value=18 Score=32.20 Aligned_cols=27 Identities=15% Similarity=-0.017 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|..|||..+|||+.||++++.-..
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467999999999999999999887653
No 192
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=47.26 E-value=20 Score=31.36 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhcCCC-CCHhhHHHHhccCHHHHHHHHHHH
Q 010919 149 LCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 149 IaaAaLylAar~~g~~-~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
|..+++.+... +|+. +|.++|++.+||+..||.+.+..-
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 44455554444 8875 999999999999999999888754
No 193
>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=46.88 E-value=38 Score=24.75 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=25.7
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
..+.|+.|||..+|++..++.+......+.|
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 194
>PF14502 HTH_41: Helix-turn-helix domain
Probab=46.79 E-value=21 Score=26.99 Aligned_cols=29 Identities=14% Similarity=0.133 Sum_probs=25.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhcCCC
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFENTDS 193 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~t~~ 193 (497)
.|+.|.++.++|+..||++.++.+.+...
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~ga 35 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGA 35 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCc
Confidence 47899999999999999999999976554
No 195
>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=46.77 E-value=18 Score=27.38 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||...+|++.||+.+.+.+.
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 567899999999999999999888764
No 196
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=46.39 E-value=20 Score=32.38 Aligned_cols=30 Identities=23% Similarity=0.225 Sum_probs=25.9
Q ss_pred cCCC-CCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLK-FSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~-~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.+ -|+++.|.-++|...|+++.|++|..
T Consensus 31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 31 PGDKLPSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3556 47999999999999999999999853
No 197
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.35 E-value=35 Score=25.96 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=26.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKE 207 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~~d 207 (497)
..+|+.++|+.+||+..||.+-++ -....++.+.+.++++-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~----~~~~~~~~~~l~~ia~~ 49 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILN----GKPSNPSLDTLEKIAKA 49 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHT----TT-----HHHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHh----cccccccHHHHHHHHHH
Confidence 456999999999999999998887 22357888888887643
No 198
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=46.08 E-value=55 Score=31.59 Aligned_cols=47 Identities=19% Similarity=0.070 Sum_probs=35.5
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+...-.|.-|+........|.+..|||+.+|++..+|.|++++|.+.
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 44555555555433333457789999999999999999999999985
No 199
>PHA00542 putative Cro-like protein
Probab=45.72 E-value=18 Score=29.90 Aligned_cols=42 Identities=7% Similarity=0.018 Sum_probs=29.8
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
+.....|+.++|+.+||+..||.+....-. ...+++...++.
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~g~~----~~p~~~~l~ki~ 68 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYSGRH----KDPRYSVVEKLR 68 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHcCCC----CCCCHHHHHHHH
Confidence 334568999999999999999998876542 124455555554
No 200
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=45.48 E-value=9.1 Score=34.69 Aligned_cols=27 Identities=19% Similarity=0.015 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+|+++.||++++.-..
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999998876654
No 201
>PRK06030 hypothetical protein; Provisional
Probab=45.24 E-value=51 Score=29.75 Aligned_cols=69 Identities=10% Similarity=0.140 Sum_probs=48.4
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCCC-hHHHHH--HHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 21 DEIVHVAKRFYGIAVARNFTKGRR-TEQVQA--SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 21 ~~i~d~A~~iyk~a~~~~~~rGR~-~~~VaA--ACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
+.|++....+|..-.+.=..+.|+ ...+.| .|+|++-...+ .++.+|+..||-+-.++..+++.+.+.+
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 577777777777655433333332 222222 48888877755 4899999999999999999999888755
No 202
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=45.16 E-value=76 Score=29.79 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=26.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
++.|+++||..+|++..|+.+-+++|.+-
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47899999999999999999999999753
No 203
>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=44.96 E-value=37 Score=26.01 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=27.2
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.+-+.|..+|++.+|++.+|+...++.|.+.
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 5678999999999999999999999999764
No 204
>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=44.83 E-value=31 Score=32.54 Aligned_cols=27 Identities=19% Similarity=0.354 Sum_probs=24.8
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.|+++|+..+|+|..||.+.+++|.+.
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 689999999999999999999999753
No 205
>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=44.70 E-value=16 Score=36.69 Aligned_cols=24 Identities=21% Similarity=0.374 Sum_probs=21.7
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
+.|++|||+.+|||.+|+++.++.
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCC
Confidence 468999999999999999999963
No 206
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=44.59 E-value=22 Score=31.65 Aligned_cols=26 Identities=19% Similarity=0.109 Sum_probs=23.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
=++++|++..|||=.|+|+||.++..
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 47999999999999999999999854
No 207
>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=44.46 E-value=54 Score=26.08 Aligned_cols=67 Identities=7% Similarity=0.181 Sum_probs=36.0
Q ss_pred HHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHh--cCCCCCHHHHHHHhCcC-hHHHHHHHHHH
Q 010919 11 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ--KSKPFLLIDFSNYLNIN-VYELGAVYLQL 87 (497)
Q Consensus 11 ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~--e~~prtL~DIa~v~~vs-v~~Lgr~yk~L 87 (497)
+|+.|+++ ... -.++|+......+. ..+...-+-.|++. .+...++.|||..+|.+ ...+.+.|+..
T Consensus 1 lA~~~~~s--~~~---l~~~f~~~~g~s~~-----~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 1 LADELGMS--ERY---LSRIFKKETGMSFK-----QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp HHHHCTS---HHH---HHHHHHHHHSS-HH-----HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred ChHHhCcC--HHH---HHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 57788888 332 24455554443332 23333344455553 24678999999999875 66676666654
No 208
>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=44.21 E-value=32 Score=26.01 Aligned_cols=33 Identities=9% Similarity=0.045 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010919 62 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 94 (497)
Q Consensus 62 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 94 (497)
...+..+||..++++..++......|.+.|++.
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 356889999999999999999999999999875
No 209
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=44.12 E-value=2.5e+02 Score=28.58 Aligned_cols=40 Identities=10% Similarity=0.159 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 47 QVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 47 ~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
.+..++-||..... .+.++.++|+.++++...|.+.|++.
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 35666667776654 58999999999999999998888774
No 210
>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=43.90 E-value=21 Score=28.16 Aligned_cols=26 Identities=19% Similarity=0.184 Sum_probs=23.5
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
..|+.+||...||+.+||.++.+.+.
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 48999999999999999999999996
No 211
>PRK01381 Trp operon repressor; Provisional
Probab=43.76 E-value=18 Score=31.40 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=29.9
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 156 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 156 lAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
++..+..-..|+++|+.-+|||.+||.+-=+.++..+
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~ 83 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLKTAP 83 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCC
Confidence 4444555679999999999999999999888886543
No 212
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=43.49 E-value=28 Score=26.72 Aligned_cols=29 Identities=28% Similarity=0.241 Sum_probs=23.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
...+....|+..+|+..|++.|++.+.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l 39 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEEL 39 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 35678889999999999999999998654
No 213
>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=43.14 E-value=15 Score=27.89 Aligned_cols=23 Identities=26% Similarity=0.247 Sum_probs=17.5
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.++.+||+.+||+.+||++-++.
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 39999999999999999987763
No 214
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=42.92 E-value=23 Score=32.97 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.+|||..+||++.||+.++.-
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 215
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.64 E-value=1.3e+02 Score=26.57 Aligned_cols=70 Identities=17% Similarity=0.189 Sum_probs=53.8
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccch-HHHHHhhhC-CCCC
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIF-LHKFTDRLL-PGGN 121 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~-I~Rf~~~L~-~~~~ 121 (497)
.++.+--.-||+-||- .|++|-..+|++-.+++.-+-.+.+.++.+... .+|... =..+.+.|. |+++
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 4566777789999984 599999999999999999999999999987544 344332 234677786 7677
Q ss_pred HH
Q 010919 122 KK 123 (497)
Q Consensus 122 ~~ 123 (497)
++
T Consensus 113 pe 114 (122)
T COG3877 113 PE 114 (122)
T ss_pred HH
Confidence 64
No 216
>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=42.45 E-value=8.3 Score=40.77 Aligned_cols=79 Identities=14% Similarity=0.049 Sum_probs=0.0
Q ss_pred HHhhhCCCCCHHHHHHHHHHHHHhc-cccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 112 FTDRLLPGGNKKVCDTARDILASMK-RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 112 f~~~L~~~~~~~V~~~A~~Lv~~~~-~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
++..+++..++.++..|..|++... ...+..+-.=.+=+.+|+||||..++....+.......++......+-|+.|..
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 3445554457788888888887776 455666666677788999999999998888888889999999999999888865
No 217
>PRK09526 lacI lac repressor; Reviewed
Probab=42.39 E-value=20 Score=36.36 Aligned_cols=45 Identities=18% Similarity=0.141 Sum_probs=30.3
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhhh
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHE 210 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~~dle~ 210 (497)
+.|.+|||+.+|||.+|+++.|+.- ..-+.-|-+--+..+++|-.
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 4699999999999999999999742 12233344444444444433
No 218
>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=42.29 E-value=23 Score=26.14 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=28.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
....|++++|+.+||+..||.+..+. ....+++....++
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 35689999999999999999988765 3456666666554
No 219
>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=42.24 E-value=25 Score=27.30 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=20.1
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
+..+||+.+||+..|||..-+++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 67899999999999999877664
No 220
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=42.19 E-value=25 Score=34.96 Aligned_cols=28 Identities=11% Similarity=0.322 Sum_probs=25.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
-.+++.++++.++||+.|||+-+++|.+
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4699999999999999999999999954
No 221
>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=42.16 E-value=2.1e+02 Score=26.83 Aligned_cols=107 Identities=19% Similarity=0.278 Sum_probs=60.5
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhccccccc--------ccccCCc--cchHHHHHhhhCC
Q 010919 49 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESN--------VLKQVDP--SIFLHKFTDRLLP 118 (497)
Q Consensus 49 aAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~--------~~~~idP--~~~I~Rf~~~L~~ 118 (497)
+=|.||. .+.|.++.+|+++++ +...+......|.+.+.-..... +.-.+.| ..||.+|...
T Consensus 3 iEAlLF~----s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~--- 74 (159)
T PF04079_consen 3 IEALLFA----SGEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK--- 74 (159)
T ss_dssp HHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT---
T ss_pred hHhhHHH----cCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc---
Confidence 3466666 466999999999999 99999999999999883222111 0001112 1222222211
Q ss_pred CCCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHH-HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 119 GGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 119 ~~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLy-lAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
+++..+--|++= ||.-.+..++|..+|..+=||.-..+-+.|.+.
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 234444444442 333455689999999999999866555555554
No 222
>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=42.15 E-value=24 Score=32.62 Aligned_cols=26 Identities=8% Similarity=0.092 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|+++.||+.++.--
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 223
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=42.04 E-value=22 Score=28.18 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=25.6
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
.|+++||+.+|||..||.+.+.. ...++.+-...+
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 234555555554
No 224
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=41.99 E-value=98 Score=30.99 Aligned_cols=55 Identities=9% Similarity=0.121 Sum_probs=42.9
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 145 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 145 ~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
.+.-+.-+.-||...+..-.+|+.+||+.+|||+.++.+-+++. .+|+-+|....
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 34445566667877777777999999999999999999988763 46788887653
No 225
>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=41.84 E-value=21 Score=33.33 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.6
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
+.++..||.++|+...||++|++++.
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 226
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=41.80 E-value=54 Score=33.08 Aligned_cols=53 Identities=8% Similarity=0.169 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 010919 46 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 112 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf 112 (497)
..+..++-||-.... .+.++.++|..+++|...|.|.|+.... ..|..||.+.
T Consensus 5 ~~i~~~~~~i~~~~~-~~~~l~~lA~~~~~S~~~l~r~F~~~~g-------------~s~~~yi~~~ 57 (289)
T PRK15121 5 GIIRDLLIWLEGHLD-QPLSLDNVAAKAGYSKWHLQRMFKDVTG-------------HAIGAYIRAR 57 (289)
T ss_pred HHHHHHHHHHHhccc-CCCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH
Confidence 345667777776544 5799999999999999999988876543 3466666654
No 227
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.70 E-value=20 Score=27.79 Aligned_cols=24 Identities=17% Similarity=0.098 Sum_probs=21.3
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHh
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
|..|||+.+||+..|||..-+.+.
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 578999999999999999887764
No 228
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=41.65 E-value=52 Score=23.61 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=28.0
Q ss_pred CCHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010919 64 FLLIDFSNYLNINVYELGAVYLQLCQVLYIA 94 (497)
Q Consensus 64 rtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 94 (497)
.+..+||..++++..++.+....+.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5889999999999999999999998888764
No 229
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=41.55 E-value=25 Score=35.66 Aligned_cols=22 Identities=14% Similarity=0.151 Sum_probs=20.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~k 186 (497)
.|++|||+.+|||.+|+++.|+
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 4899999999999999999996
No 230
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.51 E-value=41 Score=26.63 Aligned_cols=29 Identities=10% Similarity=0.053 Sum_probs=24.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+.+++-+|||+++|+|..|+|.-|..+..
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~ 41 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEK 41 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56789999999999999999999988854
No 231
>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=41.41 E-value=19 Score=25.50 Aligned_cols=21 Identities=14% Similarity=0.159 Sum_probs=16.4
Q ss_pred CHhhHHHHhccCHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~k 186 (497)
|..++|+.+||+..|||..=+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999986543
No 232
>PRK10130 transcriptional regulator EutR; Provisional
Probab=40.68 E-value=59 Score=34.24 Aligned_cols=54 Identities=17% Similarity=0.343 Sum_probs=40.5
Q ss_pred hHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 010919 45 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 112 (497)
Q Consensus 45 ~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf 112 (497)
...|..++-||--.. ..|+++.|||..++|+...|.+.|++.. + ..|..||.++
T Consensus 239 ~~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~~---G----------~sp~~ylr~~ 292 (350)
T PRK10130 239 RRLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAIL---G----------IGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHHH---C----------cCHHHHHHHH
Confidence 345666677776544 4589999999999999999998887653 3 4577787754
No 233
>PRK09492 treR trehalose repressor; Provisional
Probab=40.63 E-value=19 Score=36.01 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=21.9
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
+.|++|||+.+|||.+|+.+.|+.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCC
Confidence 479999999999999999999963
No 234
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=40.54 E-value=25 Score=27.24 Aligned_cols=22 Identities=14% Similarity=0.064 Sum_probs=19.3
Q ss_pred CHhhHHHHhccCHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE 187 (497)
|..+||+.+||+..||+...++
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999977654
No 235
>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=40.51 E-value=27 Score=27.25 Aligned_cols=23 Identities=17% Similarity=0.156 Sum_probs=20.3
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
+..++|+.+||+..|||...+++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~ 24 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 67899999999999999887764
No 236
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=40.48 E-value=65 Score=29.76 Aligned_cols=45 Identities=20% Similarity=0.183 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 46 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
....=|-+|+|....+.|.++.+||...+++...|.+.+..|.+.
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 345567789998887779999999999999999999999998884
No 237
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=40.37 E-value=1.1e+02 Score=29.53 Aligned_cols=48 Identities=17% Similarity=0.193 Sum_probs=36.6
Q ss_pred CChHHHHHHHHHHHHHhcC------CCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 43 RRTEQVQASCLYLACRQKS------KPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 43 R~~~~VaAACLYiACR~e~------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
.+...-.|..|+.-+...+ .|.+..|||+.+|++..+|.|+.++|.+.
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 4555555665554445433 57889999999999999999999999885
No 238
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=40.05 E-value=27 Score=32.04 Aligned_cols=26 Identities=27% Similarity=0.186 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||+.+|+++.||++++.--
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra 158 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYA 158 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999998887654
No 239
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=40.05 E-value=22 Score=35.97 Aligned_cols=37 Identities=14% Similarity=0.074 Sum_probs=27.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
-+.|.+|||+.+|||.+|+++.|+. ...++.+--.++
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~-----~~~vs~~tr~~V 41 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSG-----KGRISTATGERV 41 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCC-----CCCCCHHHHHHH
Confidence 3589999999999999999999862 234554444444
No 240
>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=39.74 E-value=57 Score=23.52 Aligned_cols=32 Identities=9% Similarity=0.027 Sum_probs=28.7
Q ss_pred CCCHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010919 63 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 94 (497)
Q Consensus 63 prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 94 (497)
..+..+||..+++++.++.+....+.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46999999999999999999999999888764
No 241
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=39.72 E-value=49 Score=27.00 Aligned_cols=46 Identities=4% Similarity=0.166 Sum_probs=29.4
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 156 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 156 lAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
+...+-....||.++|+.+||+.++|.+-.+ -.....|++.+....
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 233567888777663
No 242
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=39.52 E-value=28 Score=31.27 Aligned_cols=27 Identities=4% Similarity=0.012 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||+.++..-.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999998877643
No 243
>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=39.39 E-value=49 Score=31.76 Aligned_cols=28 Identities=11% Similarity=0.280 Sum_probs=25.6
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
..|+.+|+..+||+..||++.|+.|.+-
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4999999999999999999999999653
No 244
>PRK09480 slmA division inhibitor protein; Provisional
Probab=39.31 E-value=35 Score=31.49 Aligned_cols=44 Identities=14% Similarity=0.197 Sum_probs=32.4
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 144 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 144 R~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.+..-|.-|++-+...-.|...|+++|++.+||+..||-..++.
T Consensus 10 ~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 10 ERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred hHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 34445666665554444467799999999999999999877755
No 245
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=39.13 E-value=79 Score=25.03 Aligned_cols=38 Identities=11% Similarity=0.102 Sum_probs=29.7
Q ss_pred HHHHHHhcCC-CCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 53 LYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 53 LYiACR~e~~-prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
|+..-+..+- +.++.|||..++++..++.+....|.+.
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 3444455555 4999999999999999999887777764
No 246
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=39.04 E-value=1.1e+02 Score=28.62 Aligned_cols=30 Identities=7% Similarity=-0.199 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 62 KPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 62 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
.|.|..+||+.+|++..++.|..++|.+.=
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCC
Confidence 588999999999999999999999999853
No 247
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=38.69 E-value=30 Score=30.91 Aligned_cols=26 Identities=4% Similarity=-0.143 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|+++.||++++.-.
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra 146 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQA 146 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46889999999999999999987654
No 248
>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=38.69 E-value=26 Score=28.36 Aligned_cols=28 Identities=11% Similarity=0.106 Sum_probs=22.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
...|..+||+.+|||++||.+-.+.+.-
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG~ 60 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLGF 60 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCTT
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhCC
Confidence 4689999999999999999999888753
No 249
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=38.67 E-value=55 Score=23.95 Aligned_cols=26 Identities=8% Similarity=0.004 Sum_probs=24.4
Q ss_pred CHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 65 LLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 65 tL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+..++|+.++++..++.+.+..|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999999874
No 250
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=38.34 E-value=43 Score=31.01 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=23.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+|+++.||+.++..-.
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 446999999999999999998887764
No 251
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=38.25 E-value=3e+02 Score=26.50 Aligned_cols=120 Identities=17% Similarity=0.202 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHHhcCCC-CCHHHHHHHhCcCh-HHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHH
Q 010919 46 EQVQASCLYLACRQKSKP-FLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 123 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~p-rtL~DIa~v~~vsv-~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~ 123 (497)
.+++=|.||.+ +.| +++.+|+.+++++. ..+......|.....-+..+ + -|..+.+.......++
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~g-----l----~l~~~~~~y~l~tk~e 69 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAG-----I----EIIKFGQSYSLVTKPA 69 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCC-----E----EEEEECCEEEEEEhHH
Confidence 35566778877 788 99999999999984 45555555555543321111 0 0011111110001222
Q ss_pred HHHHHHHHHHHhccccccCCCChhHHHHHHH-HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 124 VCDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 124 V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaL-ylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
......+++.. .+++ +.-|++ -||.-.+..++|..+|-.+=||.-..+-+.|.+.
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 333333 2444466789999999999999866665555554
No 252
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=38.02 E-value=97 Score=33.96 Aligned_cols=18 Identities=22% Similarity=0.376 Sum_probs=13.1
Q ss_pred HHHHHhhhCHHHHHHHHHHHHH
Q 010919 369 KKIIWEEMNREYLEEQAAKEAA 390 (497)
Q Consensus 369 K~~iW~~~N~dyL~eq~~Ke~~ 390 (497)
|+.||| |+|+|++-|+-.
T Consensus 530 k~ELkm----d~lrerelresl 547 (641)
T KOG3915|consen 530 KTELKM----DFLRERELRESL 547 (641)
T ss_pred HHHHHH----HHHHHHHHHHHH
Confidence 677887 677887777654
No 253
>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=37.98 E-value=41 Score=28.97 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=24.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|..+||...||++.||++++....
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467999999999999999999998764
No 254
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=37.89 E-value=31 Score=31.66 Aligned_cols=26 Identities=8% Similarity=0.115 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||+.+|+++.||++++.--
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra 158 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEA 158 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998654
No 255
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=37.77 E-value=4.1e+02 Score=26.22 Aligned_cols=26 Identities=8% Similarity=0.049 Sum_probs=22.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|+++||..+|||..||+++.+..
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~a 249 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAA 249 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999876653
No 256
>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=37.74 E-value=62 Score=24.73 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=24.9
Q ss_pred hcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 59 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 59 ~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..+-+.++.+|++.++++...+.+..+.|.+.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56788999999999999999999999999884
No 257
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=37.65 E-value=25 Score=28.44 Aligned_cols=24 Identities=17% Similarity=0.351 Sum_probs=20.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
...||.+.|..+|||+.||-.-=+
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHc
Confidence 568999999999999999975433
No 258
>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=37.62 E-value=1.3e+02 Score=26.39 Aligned_cols=75 Identities=12% Similarity=0.139 Sum_probs=44.9
Q ss_pred HHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCC----CCCCC-hHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHH
Q 010919 7 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNF----TKGRR-TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELG 81 (497)
Q Consensus 7 ~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~----~rGR~-~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lg 81 (497)
-+.++|..++++ ..++ .++++.. +.|- .+|++ .. .=-..+.=.++-..++.|+|..++|+..+|+
T Consensus 20 s~~eaa~~F~VS--~~Tv---~~W~k~~-~~G~~~~k~r~~~Kid----~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~ 89 (119)
T PF01710_consen 20 SIREAAKRFGVS--RNTV---YRWLKRK-ETGDLEPKPRGRKKID----RDELKALVEENPDATLRELAERLGVSPSTIW 89 (119)
T ss_pred hHHHHHHHhCcH--HHHH---HHHHHhc-cccccccccccccccc----HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHH
Confidence 467888888888 5444 4555522 2222 23332 11 1112333344566899999999999999998
Q ss_pred HHHHHHHHHh
Q 010919 82 AVYLQLCQVL 91 (497)
Q Consensus 82 r~yk~L~~~L 91 (497)
+..++|--..
T Consensus 90 ~~Lkrlg~t~ 99 (119)
T PF01710_consen 90 RALKRLGITR 99 (119)
T ss_pred HHHHHcCchh
Confidence 7766654333
No 259
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=37.62 E-value=31 Score=31.70 Aligned_cols=25 Identities=8% Similarity=0.155 Sum_probs=22.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.+|||+.+|+++.||+.++.-
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999998865
No 260
>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=37.54 E-value=9.2 Score=35.96 Aligned_cols=41 Identities=22% Similarity=0.449 Sum_probs=0.8
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH-HhcCCCCCCCHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIE-FENTDSGSLTIEDFMAR 204 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE-~~~t~~~~Lt~~ef~~~ 204 (497)
++|+++||..+|++++||.+..+. ...||.+-+-+..|...
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~ 90 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSR 90 (160)
T ss_dssp ------------------------------------S-----
T ss_pred CCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccc
Confidence 579999999999999999988776 56778887777777766
No 261
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=37.41 E-value=58 Score=29.53 Aligned_cols=38 Identities=13% Similarity=0.292 Sum_probs=31.3
Q ss_pred HHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 154 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 154 LylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+|.+-.-.+-+.|+.+||+.++.+.+|+.+.++-+.+.
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 35544435678999999999999999999999998654
No 262
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=37.24 E-value=2.2e+02 Score=29.93 Aligned_cols=80 Identities=13% Similarity=0.220 Sum_probs=0.0
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccc
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWI 140 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l 140 (497)
..|+++.++|+.++++.-+|-|.|++-.. ..|..|..++ =...|.+|++.
T Consensus 234 e~plsl~~LA~~~~~S~R~leRlF~~~lG-------------~sP~~yy~~l-----------RL~~Ar~LL~~------ 283 (328)
T COG4977 234 EEPLSLEELADRAGLSRRQLERLFRAELG-------------VSPARYYLRL-----------RLERARRLLEQ------ 283 (328)
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHhC-------------CCHHHHHHHH-----------HHHHHHHHHHh------
Q ss_pred cCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc-cCHHHHHHHHHHHhcCC
Q 010919 141 TTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH-ICEATLMKRLIEFENTD 192 (497)
Q Consensus 141 ~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~-Vse~TIrkr~kE~~~t~ 192 (497)
-+.++.+||..+| ++.+..++.|+...-.+
T Consensus 284 ----------------------t~~si~~IA~~~GF~sa~~fsr~fr~~fg~~ 314 (328)
T COG4977 284 ----------------------TRLSIAEIAVACGFSSASHFSRAFRRQFGLS 314 (328)
T ss_pred ----------------------CCCcHHHHHHHhCCCCHHHHHHHHHHHhCCC
No 263
>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=37.22 E-value=3.8e+02 Score=25.69 Aligned_cols=26 Identities=15% Similarity=0.143 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|+++||+.+||+..||+++++..
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra 218 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRA 218 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999987654
No 264
>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=37.07 E-value=90 Score=24.65 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=19.9
Q ss_pred cCCCCCHHHHHHHhCcChHHHHHH
Q 010919 60 KSKPFLLIDFSNYLNINVYELGAV 83 (497)
Q Consensus 60 e~~prtL~DIa~v~~vsv~~Lgr~ 83 (497)
++--++++|||+.++|+..+|++.
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 265
>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=36.86 E-value=34 Score=25.49 Aligned_cols=23 Identities=4% Similarity=0.346 Sum_probs=18.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
++.++|++.+|+|.+||.+..++
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 266
>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=36.80 E-value=37 Score=27.77 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=24.3
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
+.+-.+++.++|....||++||.+.++.+.
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 356779999999999999999999999985
No 267
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=36.79 E-value=32 Score=32.44 Aligned_cols=26 Identities=15% Similarity=0.165 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+||+..||++|+.-.
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra 181 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLA 181 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 46899999999999999999998654
No 268
>PRK10072 putative transcriptional regulator; Provisional
Probab=36.75 E-value=35 Score=29.32 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=24.9
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
.....|+.++|+.+||+..||+++..--.
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 269
>PRK09954 putative kinase; Provisional
Probab=36.71 E-value=46 Score=34.64 Aligned_cols=29 Identities=10% Similarity=0.334 Sum_probs=26.6
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+-++|+.+|++.++||.+||++|++.|.+
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34899999999999999999999999975
No 270
>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=36.70 E-value=32 Score=32.32 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=23.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+|+++.||+.++.--.
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 271
>PRK15340 transcriptional regulator InvF; Provisional
Probab=36.41 E-value=4.3e+02 Score=26.08 Aligned_cols=29 Identities=0% Similarity=-0.069 Sum_probs=23.8
Q ss_pred cCCCCCHHHHHHHhCcChHHHHHHHHHHH
Q 010919 60 KSKPFLLIDFSNYLNINVYELGAVYLQLC 88 (497)
Q Consensus 60 e~~prtL~DIa~v~~vsv~~Lgr~yk~L~ 88 (497)
...+.++.++|+.+++++..+.|.|++..
T Consensus 122 ~~~~~sleeLA~~~gvS~r~f~RlFk~~~ 150 (216)
T PRK15340 122 STSGNTMRMLGEDYGVSYTHFRRLCSRAL 150 (216)
T ss_pred ccCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34578999999999999999988776543
No 272
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=36.39 E-value=2e+02 Score=28.71 Aligned_cols=43 Identities=16% Similarity=0.107 Sum_probs=33.6
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 86 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~ 86 (497)
....+..++-||.-....-..++.+||..+++|+..|.+.|+.
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 3445566777777776665589999999999999999888863
No 273
>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=36.37 E-value=44 Score=28.27 Aligned_cols=23 Identities=22% Similarity=0.086 Sum_probs=19.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
...|.++||+.+|||..||.+ ++
T Consensus 49 ~G~S~~eIA~~LgISrsTIyR-i~ 71 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISR-VK 71 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHH-HH
Confidence 346999999999999999988 44
No 274
>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=36.34 E-value=4e+02 Score=25.66 Aligned_cols=27 Identities=4% Similarity=0.091 Sum_probs=23.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
....|+++||..+|||..||++..+..
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~~~~a 223 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRLEKKV 223 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356899999999999999999887654
No 275
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=36.29 E-value=83 Score=25.44 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=25.7
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
..++++|+..++++..||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 6899999999999999999999999753
No 276
>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=36.01 E-value=65 Score=24.06 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=23.7
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..++.+|++.++++.+|+.+.++.+..
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 277
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=35.98 E-value=88 Score=30.14 Aligned_cols=30 Identities=10% Similarity=0.247 Sum_probs=26.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
++.|+++||..+|++..|+.+-+++|.+..
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 278
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=35.78 E-value=35 Score=30.86 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|++..||+.|+.--
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998754
No 279
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.51 E-value=1e+02 Score=22.74 Aligned_cols=25 Identities=8% Similarity=0.017 Sum_probs=23.4
Q ss_pred CHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 65 LLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 65 tL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
+...||+.++++..++.++.+.|.+
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 280
>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=35.48 E-value=5e+02 Score=26.49 Aligned_cols=124 Identities=11% Similarity=0.067 Sum_probs=68.4
Q ss_pred HHHHHhcCC-CCCHHHHHHHhCcCh-HHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCC------------
Q 010919 54 YLACRQKSK-PFLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPG------------ 119 (497)
Q Consensus 54 YiACR~e~~-prtL~DIa~v~~vsv-~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~------------ 119 (497)
|+..|.... -.|+++||..+|++. ..|.. .+.=.-+ + +...+.+++..|++.
T Consensus 17 ~ye~rk~~~p~fS~R~fa~~~G~ss~s~L~~-------v~~Gkr~------L-s~~~~~k~a~~l~L~~~E~~yF~~lV~ 82 (271)
T TIGR02147 17 YYEERKKTDPAFSWRFFAEKAGFSSTSYLND-------IIKGKKN------L-TKRMIPKFAEALGLDEKEAAYFEAMVN 82 (271)
T ss_pred HHHHHhccCcCcCHHHHHHHhCCCCHHHHHH-------HHcCCCC------C-CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 677777655 689999999999876 33332 2211111 1 344667777777611
Q ss_pred ----CCHHHHHHHHHHHHHhcc---ccccCC---CChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc--cCHHHHHHHHHH
Q 010919 120 ----GNKKVCDTARDILASMKR---DWITTG---RKPSGLCGAALYVSALTHGLKFSKSDIVKIVH--ICEATLMKRLIE 187 (497)
Q Consensus 120 ----~~~~V~~~A~~Lv~~~~~---~~l~~G---R~P~~IaaAaLylAar~~g~~~t~~eIa~v~~--Vse~TIrkr~kE 187 (497)
.+......+..=++.+.. ..++.+ +--....-.+|.-.+.+.++.-+..+||+.++ ||...++..+.-
T Consensus 83 f~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~ 162 (271)
T TIGR02147 83 FGQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDL 162 (271)
T ss_pred HhccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHH
Confidence 122222222221121111 111111 11112333355555556677777889999998 999999999987
Q ss_pred HhcC
Q 010919 188 FENT 191 (497)
Q Consensus 188 ~~~t 191 (497)
|...
T Consensus 163 L~~~ 166 (271)
T TIGR02147 163 LERL 166 (271)
T ss_pred HHHC
Confidence 7644
No 281
>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=35.30 E-value=43 Score=24.42 Aligned_cols=39 Identities=5% Similarity=0.089 Sum_probs=29.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
....|+.++|..+||+..||++..+-- ...+++.+..+.
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 245677766664
No 282
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=35.30 E-value=36 Score=30.71 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+|+++.||+.++.--
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra 145 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNA 145 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999987653
No 283
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=35.13 E-value=78 Score=28.55 Aligned_cols=45 Identities=9% Similarity=0.147 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 46 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+.-.-+.+|++-...|.+.+..+||..++|+...|.+++..|.+.
T Consensus 8 ~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 8 DYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred hHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 344556677776556778899999999999999999999999885
No 284
>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=35.11 E-value=52 Score=25.16 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=24.1
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.+-..++.+|++.++++..|+.+.++.+.+-
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 3567899999999999999999999998643
No 285
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=35.00 E-value=31 Score=34.49 Aligned_cols=28 Identities=14% Similarity=0.230 Sum_probs=25.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
-.+++.|+++.++||+.|||+-+++|.+
T Consensus 18 ~~~~~~ela~~l~vS~~TiRRdL~~Le~ 45 (252)
T PRK10906 18 GYVSTEELVEHFSVSPQTIRRDLNDLAE 45 (252)
T ss_pred CCEeHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4589999999999999999999988854
No 286
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=34.99 E-value=4.5e+02 Score=25.84 Aligned_cols=27 Identities=4% Similarity=0.112 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|||+.||++++....
T Consensus 216 ~~~s~~EIA~~lgis~~tV~~~~~ra~ 242 (251)
T PRK07670 216 EELTLTEIGQVLNLSTSRISQIHSKAL 242 (251)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 678999999999999999999886643
No 287
>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=34.98 E-value=37 Score=30.76 Aligned_cols=27 Identities=7% Similarity=0.084 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||++++.-..
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAI 163 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999887643
No 288
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=34.96 E-value=6.5e+02 Score=27.70 Aligned_cols=88 Identities=10% Similarity=0.131 Sum_probs=44.9
Q ss_pred CCCHHHHHHHhCcChHHHH-HHHHHHHH-----HhcccccccccccCCccchHHHHHhhhC---CCCC-HHHHHHHHHHH
Q 010919 63 PFLLIDFSNYLNINVYELG-AVYLQLCQ-----VLYIADESNVLKQVDPSIFLHKFTDRLL---PGGN-KKVCDTARDIL 132 (497)
Q Consensus 63 prtL~DIa~v~~vsv~~Lg-r~yk~L~~-----~L~i~~~~~~~~~idP~~~I~Rf~~~L~---~~~~-~~V~~~A~~Lv 132 (497)
.++..++..+++......- ...+.|.. .+.+ ..-.+....||..++.|+...+. +-.+ +.....+..++
T Consensus 229 ~It~e~V~~~l~~~~~~~i~~li~si~~~d~~~Al~~-l~~ll~~Gedp~~i~r~l~~~~~edi~~a~~~~~~~~~~~~~ 307 (472)
T PRK14962 229 KITLETVHEALGLIPIEVVRDYINAIFNGDVKRVFTV-LDDVYYSGKDYEVLIQQAIEDLVEDLERERANDIIQVSRQLL 307 (472)
T ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHcCCHHHHHHH-HHHHHHcCCCHHHHHHHHHHHHHHHccCCCchHHHHHHHHHH
Confidence 4899999888876543221 11111110 0000 00001123678777887776552 2123 55555666666
Q ss_pred HHhccccccCCCChhHHHH
Q 010919 133 ASMKRDWITTGRKPSGLCG 151 (497)
Q Consensus 133 ~~~~~~~l~~GR~P~~Iaa 151 (497)
+....-++-.|+.|.+=.+
T Consensus 308 ~~~~~i~~~e~~~~l~~~~ 326 (472)
T PRK14962 308 NILREIKFAEEKRLVCKLG 326 (472)
T ss_pred HHHHHhCCcchHHHHHHHH
Confidence 6665556667777655444
No 289
>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=34.96 E-value=68 Score=26.74 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhc-cCHHHHHHHHHHHhc
Q 010919 152 AALYVSALTHGLKFSKSDIVKIVH-ICEATLMKRLIEFEN 190 (497)
Q Consensus 152 AaLylAar~~g~~~t~~eIa~v~~-Vse~TIrkr~kE~~~ 190 (497)
-|.|++-+.. ..|..+|+..+| .+.+||...++-+.+
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 678999999999 999999988887753
No 290
>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=34.93 E-value=62 Score=29.02 Aligned_cols=40 Identities=15% Similarity=0.075 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 152 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 152 AaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+.+|||.+-.+...|.++|++..+|+...+++-+..|...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4566766534456899999999999999999999998654
No 291
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=34.90 E-value=89 Score=36.70 Aligned_cols=56 Identities=27% Similarity=0.357 Sum_probs=45.5
Q ss_pred HHHHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCC
Q 010919 6 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF 64 (497)
Q Consensus 6 ~~I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~pr 64 (497)
......|..|+++ ..+...|...|..+...--+-| +-.++.|.+||.+||..++|.
T Consensus 36 q~~~~~c~~lnld--~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~ 91 (920)
T KOG1010|consen 36 QDSDELCRPLNLD--EQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPT 91 (920)
T ss_pred hhhhhhhhhhccc--chhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCc
Confidence 4556789999999 8999999999998876544444 468999999999999987653
No 292
>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=34.85 E-value=99 Score=23.03 Aligned_cols=37 Identities=11% Similarity=0.088 Sum_probs=28.3
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 52 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 52 CLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+|++..... +.++.+||+.++++...+.+..+.|.+.
T Consensus 8 iL~~l~~~~--~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 8 ILRILYENG--GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHS--SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcC--CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 444444433 3899999999999999999999999874
No 293
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=34.48 E-value=25 Score=35.54 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=21.8
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
+.|.+|||+.+|||.+|+++.|+.
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCC
Confidence 479999999999999999999964
No 294
>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=34.43 E-value=28 Score=35.05 Aligned_cols=23 Identities=13% Similarity=0.141 Sum_probs=21.0
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.|++|||+.+|||.+|+.+-|+.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 58999999999999999999864
No 295
>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=34.42 E-value=53 Score=29.97 Aligned_cols=27 Identities=15% Similarity=0.140 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||+.+|||+.||++++.-..
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~ 160 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRAL 160 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999998886543
No 296
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=34.39 E-value=93 Score=31.81 Aligned_cols=83 Identities=10% Similarity=0.115 Sum_probs=45.2
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-ChHHHHHHHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 86 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~v-sv~~Lgr~yk~ 86 (497)
|..+|..++++ .... .+.|+......+.+=.+..-+.-|+-.+ .....++.+||..+|. +...+.+.|++
T Consensus 237 l~~lA~~~~~S--~~~l---~r~fk~~~g~s~~~~~~~~Rl~~A~~lL----~~~~~~i~~IA~~~Gf~~~s~F~r~Fk~ 307 (322)
T PRK09393 237 VASLAARAAMS--PRTF---LRRFEAATGMTPAEWLLRERLARARDLL----ESSALSIDQIAERAGFGSEESLRHHFRR 307 (322)
T ss_pred HHHHHHHHCcC--HHHH---HHHHHHHHCcCHHHHHHHHHHHHHHHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 56677777777 3222 3445554433322211222222232222 2346889999998887 46777777766
Q ss_pred HHHHhcccccccccccCCccchHHHH
Q 010919 87 LCQVLYIADESNVLKQVDPSIFLHKF 112 (497)
Q Consensus 87 L~~~L~i~~~~~~~~~idP~~~I~Rf 112 (497)
... ..|..|-.++
T Consensus 308 ~~G-------------~tP~~yr~~~ 320 (322)
T PRK09393 308 RAA-------------TSPAAYRKRF 320 (322)
T ss_pred HHC-------------cCHHHHHHHh
Confidence 532 3466666655
No 297
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=34.35 E-value=91 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.1
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
.-.+...|+.+||+..|++++++.+.
T Consensus 68 ~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 68 RGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 34577889999999999999999863
No 298
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.34 E-value=37 Score=31.79 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+|+++.||++++.--.
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar 171 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARAR 171 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999986643
No 299
>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=34.30 E-value=38 Score=30.16 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+|+++.||++++.-.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra 145 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRA 145 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999887654
No 300
>PRK13698 plasmid-partitioning protein; Provisional
Probab=34.28 E-value=45 Score=34.96 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=29.6
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 155 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 155 ylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
|....+.++..|+++||+.+|+|+++|.+.++-+.
T Consensus 167 y~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~ 201 (323)
T PRK13698 167 YASRLQNEFAGNISALADAENISRKIITRCINTAK 201 (323)
T ss_pred HHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHc
Confidence 44444567889999999999999999999998873
No 301
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=34.24 E-value=41 Score=31.93 Aligned_cols=44 Identities=16% Similarity=0.317 Sum_probs=32.4
Q ss_pred cCCCCCHhhHHHHhccCHH---------------HHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 161 HGLKFSKSDIVKIVHICEA---------------TLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~---------------TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
....+||+++|+.+|||.+ |+++-|.-|.+....++|....|..
T Consensus 15 k~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~s 73 (187)
T COG3620 15 KELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHS 73 (187)
T ss_pred HHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccC
Confidence 3467899999999999985 5566666676666666776666654
No 302
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=33.91 E-value=79 Score=25.03 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=26.9
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 94 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~ 94 (497)
+.|.+-.|||+.++++.+...+....|.+.=.+.
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 7899999999999999999998777777754443
No 303
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=33.89 E-value=30 Score=34.74 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=20.4
Q ss_pred CHhhHHHHhccCHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE 187 (497)
|++|||+.+|||.+|+.+-|..
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999964
No 304
>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=33.89 E-value=1.2e+02 Score=25.57 Aligned_cols=31 Identities=6% Similarity=0.033 Sum_probs=27.8
Q ss_pred cCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 60 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 60 e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
...+.+..|||+.++++..++.++...|.+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4678999999999999999999999998874
No 305
>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=33.85 E-value=69 Score=23.70 Aligned_cols=35 Identities=14% Similarity=0.195 Sum_probs=26.8
Q ss_pred HHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 55 LACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 55 iACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
-+-..++.|.++.||+..++++..++-+....|.+
T Consensus 10 ~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 10 EALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33445566789999999999999999887777765
No 306
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=33.73 E-value=1.2e+02 Score=31.99 Aligned_cols=50 Identities=12% Similarity=0.358 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHH
Q 010919 46 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHK 111 (497)
Q Consensus 46 ~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~R 111 (497)
..+..++-||-- +.+.++.+||..++++...|.+.|++... ..|..|+.+
T Consensus 85 ~~i~~a~~~I~~---~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G-------------~TP~~yl~~ 134 (353)
T PRK15435 85 DKITHACRLLEQ---ETPVTLEALADQVAMSPFHLHRLFKATTG-------------MTPKAWQQA 134 (353)
T ss_pred HHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHHC-------------cCHHHHHHH
Confidence 346666667633 56899999999999999999988876543 457777654
No 307
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=33.68 E-value=37 Score=33.01 Aligned_cols=26 Identities=4% Similarity=0.142 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+||++.||++++.-.
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA 222 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999886543
No 308
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=33.60 E-value=39 Score=31.45 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=29.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc---CCCCCCCHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN---TDSGSLTIEDFMAR 204 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~---t~~~~Lt~~ef~~~ 204 (497)
...|.++||..+|+++.||++++.--.. ......+.++|.+.
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 12244556666444
No 309
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=33.32 E-value=66 Score=28.90 Aligned_cols=29 Identities=10% Similarity=0.124 Sum_probs=26.0
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.-.+|+.+|++.++++.+|+.+-++.+.+
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44699999999999999999999999864
No 310
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=38 Score=31.74 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+|+++.||+.++.-.+
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999999987654
No 311
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=33.21 E-value=39 Score=31.57 Aligned_cols=25 Identities=28% Similarity=0.214 Sum_probs=22.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.+|||..+|+++.||+.++.-
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~R 180 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQ 180 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3589999999999999999987654
No 312
>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=33.15 E-value=69 Score=30.45 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=28.3
Q ss_pred hcCCCCCHhhHHHHhccC-HHHHHHHHHHHhcC
Q 010919 160 THGLKFSKSDIVKIVHIC-EATLMKRLIEFENT 191 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vs-e~TIrkr~kE~~~t 191 (497)
.+++..|+++||+.+|++ .+|+.++++.|.+-
T Consensus 21 ~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 21 STGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 457889999999999998 99999999999653
No 313
>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=33.09 E-value=93 Score=25.90 Aligned_cols=29 Identities=17% Similarity=0.247 Sum_probs=25.3
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
.|.++.-++|++.++++.+|||+-+..+.
T Consensus 20 ~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred cCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 46778888999999999999999888774
No 314
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=33.09 E-value=53 Score=29.68 Aligned_cols=27 Identities=19% Similarity=0.222 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||..+||++.||++++.--.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~ 152 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAK 152 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678999999999999999999886653
No 315
>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=32.74 E-value=43 Score=26.36 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=18.5
Q ss_pred CCCCHhhHHHHh-----ccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIV-----HICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~-----~Vse~TIrkr~kE~~ 189 (497)
-..|..+|+..+ +||..||+++|++..
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 347899999977 899999999999964
No 316
>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=32.64 E-value=19 Score=30.73 Aligned_cols=24 Identities=13% Similarity=0.291 Sum_probs=21.1
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
++++.||+.+||+++||.+.-.++
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 317
>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=32.53 E-value=31 Score=34.72 Aligned_cols=22 Identities=23% Similarity=0.231 Sum_probs=20.1
Q ss_pred CHhhHHHHhccCHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE 187 (497)
|.+|||+.+|||.+|+.+-|..
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6799999999999999999954
No 318
>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=32.39 E-value=78 Score=24.13 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=22.7
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+....|+..+|+.+||.++++.+.+
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~ 39 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEE 39 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHhhccchHHHHHHHHHHH
Confidence 7888999999999999999999853
No 319
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=32.13 E-value=40 Score=32.12 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|+++.||+.|+.--
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 320
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=31.96 E-value=2.2e+02 Score=30.95 Aligned_cols=108 Identities=8% Similarity=0.063 Sum_probs=61.9
Q ss_pred hcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhc-c
Q 010919 59 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMK-R 137 (497)
Q Consensus 59 ~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~-~ 137 (497)
..+.+.+..++|+.++||..+|++-...|...|.-...+... .+ + ...+.+ ... .+......-. .
T Consensus 15 ~~~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~---~~-----~-~~~~~~-~~~----~~~~~~~~~~~~ 80 (491)
T COG3711 15 LKNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIK---RK-----G-GGYILE-EDE----RALELEELQELT 80 (491)
T ss_pred HhCCCCCHHHHHHHhCccHHHHHHHHHHHHHHHHhCCceEEe---cC-----C-CcEEec-CcH----HHHHHHhccccc
Confidence 456788999999999999999999999999998755433110 01 1 000000 000 0000000000 0
Q ss_pred ccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 138 DWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 138 ~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.+- ..--..+.+.....+..++..++++.+.||.+||.+-++.
T Consensus 81 ~~~-------~~er~~~~ll~~~~~~~~~l~~La~~l~vs~~ti~~dl~~ 123 (491)
T COG3711 81 SYD-------KDERIIIILLLLLLSELLSLHELADELFVSKSTIINDLKD 123 (491)
T ss_pred ccC-------hHHHHHHHHHHHHhcChhhHHHHHHHHHhHHHHHHHHHHH
Confidence 000 1111111222222226789999999999999999998886
No 321
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=31.92 E-value=43 Score=31.05 Aligned_cols=26 Identities=12% Similarity=0.166 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...+.++||..+|+++.||++++.-.
T Consensus 150 ~~~s~~eIA~~lgis~~~V~~~l~ra 175 (186)
T PRK13919 150 QGYTHREAAQLLGLPLGTLKTRARRA 175 (186)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887654
No 322
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=31.85 E-value=75 Score=34.51 Aligned_cols=68 Identities=13% Similarity=0.151 Sum_probs=48.5
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCCChHHHHHH---HHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 21 DEIVHVAKRFYGIAVARNFTKGRRTEQVQAS---CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 21 ~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAA---CLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
+.|++..+.+|..-.+.=..++|. ..++-| |.|++-+ -+..++.+|+..+|.+-.++.+++++|.+.+
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 567777777775543322223333 344445 8888844 4556999999999999999999999999865
No 323
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=31.84 E-value=44 Score=30.47 Aligned_cols=27 Identities=22% Similarity=0.193 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+|+++.||+.++.--.
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 324
>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=31.80 E-value=54 Score=30.09 Aligned_cols=27 Identities=15% Similarity=0.043 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|+++||+.+|+|+.||+++.+...
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 567999999999999999998777654
No 325
>PRK10130 transcriptional regulator EutR; Provisional
Probab=31.77 E-value=2.6e+02 Score=29.51 Aligned_cols=53 Identities=17% Similarity=0.174 Sum_probs=40.6
Q ss_pred hHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 147 SGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 147 ~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
.-|.-+.-||-... +.++|+.+||+.+|||..|+.+.+++.. .+|+-+|....
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 4569999999999999999999999974 46888887653
No 326
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=31.74 E-value=63 Score=32.64 Aligned_cols=27 Identities=15% Similarity=0.236 Sum_probs=24.4
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.++..++++.++||+.|||+=+.+|.+
T Consensus 31 ~vtv~eLa~~l~VS~~TIRRDL~~Le~ 57 (269)
T PRK09802 31 SVQVNDLSALYGVSTVTIRNDLAFLEK 57 (269)
T ss_pred CEeHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 389999999999999999999988843
No 327
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=31.70 E-value=45 Score=31.02 Aligned_cols=26 Identities=27% Similarity=0.272 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|..|||..+||+..||+.|+..-
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra 167 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRA 167 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999988764
No 328
>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=31.63 E-value=44 Score=30.15 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||++++.-..
T Consensus 125 ~g~s~~eIA~~lgis~~tV~~~l~ra~ 151 (162)
T TIGR02983 125 EDLSEAQVAEALGISVGTVKSRLSRAL 151 (162)
T ss_pred hcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 368999999999999999998886653
No 329
>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=31.61 E-value=56 Score=25.84 Aligned_cols=41 Identities=15% Similarity=0.138 Sum_probs=30.6
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
+.....|+.++|+.+||+..||.+.++. ...++++....++
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~g-----~~~~~~~~~~~l~ 54 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVNG-----RRGITADMALRLA 54 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC-----CCCCCHHHHHHHH
Confidence 4456789999999999999999997642 2356666666654
No 330
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=31.51 E-value=1.9e+02 Score=32.05 Aligned_cols=32 Identities=22% Similarity=0.324 Sum_probs=27.9
Q ss_pred HhcCCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 58 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 58 R~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
+....|.||++||+++++|+..||..|++...
T Consensus 383 ~h~se~LtL~~la~~f~in~~Ylgqlfk~~~~ 414 (475)
T COG4753 383 KHFSENLTLKDLAKVFHINPVYLGQLFKKETG 414 (475)
T ss_pred HHhcCCCCHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 44578999999999999999999999887655
No 331
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.50 E-value=55 Score=25.18 Aligned_cols=40 Identities=5% Similarity=0.032 Sum_probs=25.9
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
.-..|+.++|+.+||+.+||.+--+ -.....+++.+....
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 3468999999999999999886432 222246677776664
No 332
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=31.46 E-value=55 Score=34.21 Aligned_cols=43 Identities=19% Similarity=0.167 Sum_probs=33.2
Q ss_pred HHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHH
Q 010919 157 SALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIE 199 (497)
Q Consensus 157 Aar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ 199 (497)
|+..+....||.+||+..|||+.||++-+...++..-=++++.
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 3344567899999999999999999999998776554444443
No 333
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=31.39 E-value=29 Score=35.01 Aligned_cols=37 Identities=16% Similarity=-0.014 Sum_probs=26.4
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
.|++|||+.+|||.+|+++.++.- +...++.+--.++
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~---~~~~vs~~tr~rV 38 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDD---PTLNVKEETKHRI 38 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCC---CCCCcCHHHHHHH
Confidence 489999999999999999999532 2113555544444
No 334
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=31.39 E-value=46 Score=30.26 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+|+++.||++++...
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra 168 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRA 168 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46799999999999999999887654
No 335
>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=31.32 E-value=2.4e+02 Score=21.61 Aligned_cols=44 Identities=11% Similarity=0.094 Sum_probs=31.0
Q ss_pred HHHHHHHHhCCCCCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 28 KRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 28 ~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
.++++.|++.|+..--+ -.++.|+|+.++|+..++....+.-.+
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 45677777777764211 258999999999999888776655443
No 336
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=31.28 E-value=34 Score=34.82 Aligned_cols=23 Identities=17% Similarity=0.248 Sum_probs=21.0
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
.|++|||+.+|||.+|+.+.|+.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~ 24 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNN 24 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 58999999999999999999963
No 337
>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=31.18 E-value=69 Score=24.45 Aligned_cols=31 Identities=3% Similarity=-0.022 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
+-..++.|+|+.++||..++.+-+..|.+.-
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4578999999999999999999999887753
No 338
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=31.14 E-value=73 Score=30.39 Aligned_cols=29 Identities=7% Similarity=0.059 Sum_probs=25.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
-.+++.++++.++||+.|||+=+.+|.+-
T Consensus 20 ~~~~~~~La~~~~vS~~TiRRDl~~L~~~ 48 (185)
T PRK04424 20 PFITDEELAEKFGVSIQTIRLDRMELGIP 48 (185)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence 35899999999999999999999999653
No 339
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=31.11 E-value=53 Score=31.93 Aligned_cols=30 Identities=13% Similarity=0.313 Sum_probs=26.5
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ |-.++++.+|||..|||..++.|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VReAL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLREVLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36778 6999999999999999999999853
No 340
>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=31.10 E-value=45 Score=31.76 Aligned_cols=30 Identities=20% Similarity=0.348 Sum_probs=26.9
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.+++..++++.+|||.+|||..++.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVReAL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVREAFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHHHHHHHHHH
Confidence 477889999999999999999999999853
No 341
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=30.97 E-value=46 Score=30.87 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=23.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|++..||++++.-.+
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~ 168 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAK 168 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999887654
No 342
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=30.94 E-value=60 Score=29.38 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=24.6
Q ss_pred CHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 65 LLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 65 tL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
|.+++|..++||+-++.|+|..|.+.
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 78999999999999999999999884
No 343
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.92 E-value=46 Score=31.29 Aligned_cols=26 Identities=23% Similarity=0.253 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|+++.||+.|+.--
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~RA 174 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLYRA 174 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 36889999999999999998887654
No 344
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=30.80 E-value=47 Score=30.62 Aligned_cols=27 Identities=11% Similarity=0.069 Sum_probs=23.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
-...|.+|||+.+|++..||++++.--
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~Ra 159 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVAKA 159 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 356889999999999999999988653
No 345
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=30.78 E-value=37 Score=33.97 Aligned_cols=27 Identities=26% Similarity=0.377 Sum_probs=24.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
-.+++.|+++.++||+.|||+=+.+|.
T Consensus 18 g~v~v~eLa~~~~VS~~TIRRDL~~Le 44 (253)
T COG1349 18 GKVSVEELAELFGVSEMTIRRDLNELE 44 (253)
T ss_pred CcEEHHHHHHHhCCCHHHHHHhHHHHH
Confidence 458999999999999999999888874
No 346
>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=30.78 E-value=47 Score=30.74 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+..+||..+|+++.||++++.-.+
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar 179 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAR 179 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 568999999999999999998876553
No 347
>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=30.69 E-value=48 Score=29.69 Aligned_cols=27 Identities=11% Similarity=0.069 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||..+|+|..||+.++.-.+
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar 152 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLR 152 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568999999999999999999876543
No 348
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=30.63 E-value=74 Score=29.62 Aligned_cols=37 Identities=14% Similarity=0.145 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+||.... .+.....++||..++|+.+|+.+-++.+..
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 5665554 556788999999999999999988888753
No 349
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=30.60 E-value=48 Score=33.09 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=24.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
-.+++.++++.++||+.|||+=++++.
T Consensus 20 ~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 20 DKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 458999999999999999999988764
No 350
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=30.59 E-value=48 Score=29.92 Aligned_cols=25 Identities=8% Similarity=0.070 Sum_probs=21.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.+|||+.+|++..||+.++.-
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~r 148 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRD 148 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4688999999999999999987654
No 351
>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=30.54 E-value=61 Score=29.63 Aligned_cols=40 Identities=20% Similarity=0.215 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhcCC-CCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 148 GLCGAALYVSALTHGL-KFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 148 ~IaaAaLylAar~~g~-~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
-|..|++=|.. ..|+ ++|+++|++.+||+.+|.-..|+.-
T Consensus 7 ~I~~a~~~Ll~-~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK 47 (176)
T TIGR02366 7 KIAKAFKDLME-VQAFSKISVSDIMSTAQIRRQTFYNHFQDK 47 (176)
T ss_pred HHHHHHHHHHH-HCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence 46666665555 4555 5999999999999999998777654
No 352
>PRK11050 manganese transport regulator MntR; Provisional
Probab=30.53 E-value=90 Score=28.71 Aligned_cols=30 Identities=17% Similarity=0.144 Sum_probs=26.9
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+-.+++.+|++.++|+.+||++.++.|...
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 353
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=30.47 E-value=46 Score=32.40 Aligned_cols=27 Identities=26% Similarity=0.295 Sum_probs=24.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+||++.||++++.-.+
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr 175 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARAR 175 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 578999999999999999999988654
No 354
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=30.43 E-value=1.7e+02 Score=26.80 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=26.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+.+|..+|+..+|++..|+.+.+.+|...
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~ 198 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKD 198 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhC
Confidence 57899999999999999999999999753
No 355
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=30.37 E-value=81 Score=28.38 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=24.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
-..++++|++.++|+.+||+..++.|.+-
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 34588999999999999999999988643
No 356
>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=30.24 E-value=79 Score=23.24 Aligned_cols=27 Identities=7% Similarity=0.038 Sum_probs=19.8
Q ss_pred CCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 64 FLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 64 rtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
.+..|||..+++++.++...+..-.+.
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 477999999999999998877665544
No 357
>PRK14999 histidine utilization repressor; Provisional
Probab=30.22 E-value=55 Score=32.10 Aligned_cols=29 Identities=17% Similarity=0.257 Sum_probs=25.2
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|.++ |-.++|+..|||..|||+.+.+|..
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~ 62 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRELTD 62 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4556 7899999999999999999999853
No 358
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=30.18 E-value=46 Score=30.95 Aligned_cols=26 Identities=12% Similarity=-0.032 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|||+.|+++++.-.
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra 173 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRS 173 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHH
Confidence 56899999999999999999888654
No 359
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=30.14 E-value=63 Score=31.95 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||+.+|+++.||++++.--.
T Consensus 131 eg~S~~EIAe~LgiS~~tVksrL~Rar 157 (228)
T PRK06704 131 FQYSIADIAKVCSVSEGAVKASLFRSR 157 (228)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 359999999999999999998876543
No 360
>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=30.10 E-value=1.3e+02 Score=26.30 Aligned_cols=43 Identities=23% Similarity=0.111 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhcCC-CCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 149 LCGAALYVSALTHGL-KFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 149 IaaAaLylAar~~g~-~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.|-.++++-++..+- ..|..+|++.++++..++++-+..|...
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344444444444443 7899999999999999999999998653
No 361
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=30.07 E-value=66 Score=35.58 Aligned_cols=185 Identities=13% Similarity=0.211 Sum_probs=103.7
Q ss_pred HHHHHHH----cCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHh-------------------cCC-C
Q 010919 8 MRQMKNA----LNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ-------------------KSK-P 63 (497)
Q Consensus 8 I~~ia~~----L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~-------------------e~~-p 63 (497)
+..++.. |+++ ...++.|..+...+.-.|+.. |+. .=||.+=.+. +.. -
T Consensus 163 ~~eia~~~~~~l~~~--~~~ve~vL~~iQ~leP~GVgA-RdL----~ECL~lQL~~~~~~~~~~~~a~~il~~~le~La~ 235 (481)
T PRK12469 163 LSELAEAADPELGLS--EQELEVALRLVQSLDPPGVAA-RDL----SECLLLQLDALPADTPALEEAKEIARHHLERLAR 235 (481)
T ss_pred HHHHHhccccccCCC--HHHHHHHHHHHhcCCCCccCc-CCH----HHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHc
Confidence 4567777 8888 888888888887765555422 221 1233333332 111 2
Q ss_pred CCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccc----cccCCccchHHHH----------------------HhhhC
Q 010919 64 FLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNV----LKQVDPSIFLHKF----------------------TDRLL 117 (497)
Q Consensus 64 rtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~----~~~idP~~~I~Rf----------------------~~~L~ 117 (497)
+-+..|+..++++..+|..+...|.. |+=.....+ ...+-|..+|.+. ...+.
T Consensus 236 ~~~~~i~~~l~~~~~~l~~a~~~Ir~-L~P~Pg~~f~~~~~~yi~PDv~V~~~~~~~~V~lN~~~~P~l~in~~Y~~~l~ 314 (481)
T PRK12469 236 RETAEIQRRIGCDQETLREACALVRR-LDPRPGNHFGSARADYVVPDVIVRQVRGKWVVTINPAVLPRARIHRRYAELFA 314 (481)
T ss_pred cCHHHHHHHhCcCHHHHHHHHHHHhC-CCCCCcccccCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHH
Confidence 34556778889999999887765554 431100001 1124455444331 22221
Q ss_pred CCCCHHHHHHHHHHHHHhc-cccccC--CCChhHHHHHHHHHHHH-----hcCC----CCCHhhHHHHhccCHHHHHHHH
Q 010919 118 PGGNKKVCDTARDILASMK-RDWITT--GRKPSGLCGAALYVSAL-----THGL----KFSKSDIVKIVHICEATLMKRL 185 (497)
Q Consensus 118 ~~~~~~V~~~A~~Lv~~~~-~~~l~~--GR~P~~IaaAaLylAar-----~~g~----~~t~~eIa~v~~Vse~TIrkr~ 185 (497)
... .. ....+-+.+. -.|+.. -+|-.+|--.+-.++-+ .+|. +.++++||..+|++++||.+..
T Consensus 315 ~~~-~~---~~~yl~~kl~~A~wli~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~ 390 (481)
T PRK12469 315 QSS-GE---RRSPLNQQLQEARWLIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRAT 390 (481)
T ss_pred hcc-hh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHh
Confidence 000 00 0011111111 134322 24445555444444443 3443 4799999999999999999887
Q ss_pred HH-HhcCCCCCCCHHHHHHH
Q 010919 186 IE-FENTDSGSLTIEDFMAR 204 (497)
Q Consensus 186 kE-~~~t~~~~Lt~~ef~~~ 204 (497)
.- +..||-+-+-...|.+.
T Consensus 391 ~~KY~~tp~GifeLK~FFs~ 410 (481)
T PRK12469 391 GNKYMATPRGTFEFKHFFPR 410 (481)
T ss_pred cCceeecCCceEeHHHhhcc
Confidence 65 67889899989999887
No 362
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=30.05 E-value=62 Score=30.96 Aligned_cols=56 Identities=13% Similarity=0.210 Sum_probs=39.2
Q ss_pred HHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 128 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 128 A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
...+++-|.+.++- +-.| .||-+--++.-+.|..||+.++|+|.+.+...++++..
T Consensus 12 Ie~fae~m~r~G~n---rtVG----~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 12 IEHFAETMSRWGIN---RTVG----QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HHHHHHHHHHhCCc---chHH----HHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 34455555554432 2223 34444446778999999999999999999999999953
No 363
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=30.02 E-value=36 Score=34.64 Aligned_cols=35 Identities=14% Similarity=0.157 Sum_probs=27.0
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
.|++|||+.+|||.+|+.+-|+. ...++.+--.++
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~-----~~~Vs~~tr~rV 36 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINN-----SPKASEASRLAV 36 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCC-----CCCCCHHHHHHH
Confidence 48999999999999999999953 245665555554
No 364
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=29.98 E-value=1.3e+02 Score=24.14 Aligned_cols=35 Identities=14% Similarity=0.009 Sum_probs=30.8
Q ss_pred HHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010919 57 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 91 (497)
Q Consensus 57 CR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L 91 (497)
.|.-+.|+++.+.|+.+++++..+.+....+.+-|
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wl 41 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWL 41 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 35678999999999999999999999988887765
No 365
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.93 E-value=59 Score=22.22 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=27.6
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
..++|..++++.+|++..||.+.... ....+.+.+..+.
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~~-----~~~~~~~~~~~i~ 46 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIENG-----KRKPSLETLKKLA 46 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC-----CCCCCHHHHHHHH
Confidence 35689999999999999999875431 1233666666553
No 366
>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=29.93 E-value=1.8e+02 Score=27.75 Aligned_cols=57 Identities=18% Similarity=0.221 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHh-ccCHHHHHHHHHHHhcC
Q 010919 120 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV-HICEATLMKRLIEFENT 191 (497)
Q Consensus 120 ~~~~V~~~A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~-~Vse~TIrkr~kE~~~t 191 (497)
+++.....-..|+.....+.+..|+.|. +-.|...++..+ |+++.||++.+..+.+.
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 4554444444455555544447777764 234566788889 99999999999999654
No 367
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=29.86 E-value=49 Score=31.09 Aligned_cols=27 Identities=19% Similarity=0.268 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|++..||+.++.-..
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar 177 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRAR 177 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999998887653
No 368
>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=29.86 E-value=74 Score=27.48 Aligned_cols=30 Identities=13% Similarity=0.117 Sum_probs=26.3
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+-..|+.+|++.++++.+|+.+.++.|.+-
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 346899999999999999999999998653
No 369
>PRK13501 transcriptional activator RhaR; Provisional
Probab=29.81 E-value=1.5e+02 Score=29.57 Aligned_cols=71 Identities=10% Similarity=0.120 Sum_probs=35.9
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHh-cCCCCCHHHHHHHhCc-ChHHHHHHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNI-NVYELGAVYL 85 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~VaAACLYiACR~-e~~prtL~DIa~v~~v-sv~~Lgr~yk 85 (497)
|.++|..++++ .... .++|++.....+.+ .+.--=|-.||+. .....++.|||..+|. +...+.|.|+
T Consensus 195 l~~lA~~~~lS--~~~l---~r~Fk~~~G~T~~q-----yi~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FK 264 (290)
T PRK13501 195 MADFCHKNQLV--ERSL---KQLFRQQTGMSISH-----YLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFT 264 (290)
T ss_pred HHHHHHHHCcC--HHHH---HHHHHHHHCcCHHH-----HHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHH
Confidence 45566666666 2222 44555444333322 1122223344554 3455677777777776 4566666665
Q ss_pred HHH
Q 010919 86 QLC 88 (497)
Q Consensus 86 ~L~ 88 (497)
+..
T Consensus 265 k~~ 267 (290)
T PRK13501 265 REA 267 (290)
T ss_pred HHH
Confidence 543
No 370
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=29.70 E-value=2.8e+02 Score=28.37 Aligned_cols=53 Identities=11% Similarity=0.120 Sum_probs=40.7
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 146 PSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 146 P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
|.-+.-+.-|+-.... .+.++.+||..+|+|..++.+.+++. ..|+.+|....
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 4445556666666554 48999999999999999999999853 37889987653
No 371
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=29.70 E-value=49 Score=31.18 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+||+..||++|+.--
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 372
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.56 E-value=76 Score=30.75 Aligned_cols=25 Identities=28% Similarity=0.328 Sum_probs=22.4
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
+++.++||+.+|||.+|+..+|+.-
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4789999999999999999888865
No 373
>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=29.50 E-value=65 Score=25.04 Aligned_cols=28 Identities=11% Similarity=0.099 Sum_probs=24.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..-++++||+.+||...||.+..+...-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~~W 39 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRYKW 39 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhhCc
Confidence 4578999999999999999998887753
No 374
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.47 E-value=51 Score=30.61 Aligned_cols=26 Identities=8% Similarity=0.086 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|+++.||++++..-
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~ra 169 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRG 169 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999988654
No 375
>smart00351 PAX Paired Box domain.
Probab=29.43 E-value=2.7e+02 Score=24.74 Aligned_cols=61 Identities=11% Similarity=0.152 Sum_probs=35.0
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCC-----CCChHHHH-HHHHHHH-HHhcCCCCCHHHHHHHh
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTK-----GRRTEQVQ-ASCLYLA-CRQKSKPFLLIDFSNYL 73 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~r-----GR~~~~Va-AACLYiA-CR~e~~prtL~DIa~v~ 73 (497)
+..+|..|+++ ..++.. +.+++.+.|.+. |+++..+. ....||. .+.++-..++.+|++.+
T Consensus 36 ~~~iA~~~gvs--~~tV~k---wi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L 103 (125)
T smart00351 36 PCDISRQLCVS--HGCVSK---ILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRL 103 (125)
T ss_pred HHHHHHHHCcC--HHHHHH---HHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 56889999999 665554 444444443332 32332222 2233333 55666678888888765
No 376
>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=29.34 E-value=51 Score=32.07 Aligned_cols=29 Identities=17% Similarity=0.174 Sum_probs=24.8
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|.++ |-.+++...|||..|||+.+.+|.+
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~ 50 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNLLTE 50 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4454 6889999999999999999999853
No 377
>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=29.32 E-value=1.2e+02 Score=21.80 Aligned_cols=29 Identities=10% Similarity=0.063 Sum_probs=22.5
Q ss_pred hcCCCCCHHHHHHHhCcChHHHHHHHHHH
Q 010919 59 QKSKPFLLIDFSNYLNINVYELGAVYLQL 87 (497)
Q Consensus 59 ~e~~prtL~DIa~v~~vsv~~Lgr~yk~L 87 (497)
+.+..++..+||..+|++..++.+.+..|
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 378
>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=29.17 E-value=29 Score=30.73 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=18.9
Q ss_pred CCCCHhhHHHHhccCHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMK 183 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrk 183 (497)
...|.+|||..+|+++.||++
T Consensus 122 ~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 122 EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred cCCCHHHHHHHHCcCHHhhcC
Confidence 458999999999999999975
No 379
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=28.94 E-value=60 Score=32.04 Aligned_cols=30 Identities=20% Similarity=0.245 Sum_probs=26.7
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
...+|+.++++.++++..|+.++++.|.+-
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 356899999999999999999999999653
No 380
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=28.93 E-value=52 Score=30.11 Aligned_cols=27 Identities=22% Similarity=0.301 Sum_probs=23.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||+.++.--+
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar 161 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYAR 161 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467899999999999999998886643
No 381
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=28.93 E-value=83 Score=29.63 Aligned_cols=39 Identities=15% Similarity=0.196 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhcCCC-CCHhhHHHHhccCHHHHHHHHHH
Q 010919 148 GLCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 148 ~IaaAaLylAar~~g~~-~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
-|.-||+-+.+ ..|+. .|+++||+.+|||..||-..|..
T Consensus 15 ~Il~aa~~lf~-~~G~~~~ti~~Ia~~agvsk~t~Y~~F~s 54 (213)
T PRK09975 15 ELIETAIAQFA-LRGVSNTTLNDIADAANVTRGAIYWHFEN 54 (213)
T ss_pred HHHHHHHHHHH-HcCcccCCHHHHHHHcCCCHHHHHHHcCC
Confidence 34445554443 36875 99999999999999999887754
No 382
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=28.89 E-value=1.2e+02 Score=25.44 Aligned_cols=47 Identities=11% Similarity=0.175 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHH
Q 010919 151 GAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMA 203 (497)
Q Consensus 151 aAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~ 203 (497)
-+.-|+.. ....+.++.+||..+|+|+.++.++++... ..|+-+|..
T Consensus 24 ~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~~-----g~s~~~~~~ 70 (127)
T COG2207 24 RALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKET-----GTSPSQYLR 70 (127)
T ss_pred HHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CCCHHHHHH
Confidence 44555555 555669999999999999999999999543 345555554
No 383
>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=28.81 E-value=52 Score=31.88 Aligned_cols=29 Identities=7% Similarity=0.155 Sum_probs=24.9
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|.++ |-.++++..|||..|||+.+.+|.+
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~ 58 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAALVE 58 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4454 7889999999999999999999853
No 384
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.79 E-value=97 Score=22.40 Aligned_cols=26 Identities=4% Similarity=-0.021 Sum_probs=17.2
Q ss_pred cCCCCCHHHHHHHhCcChHHHHHHHH
Q 010919 60 KSKPFLLIDFSNYLNINVYELGAVYL 85 (497)
Q Consensus 60 e~~prtL~DIa~v~~vsv~~Lgr~yk 85 (497)
.....++.+||..++++..+|.+..+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 34558999999999999999987654
No 385
>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=28.78 E-value=75 Score=31.90 Aligned_cols=27 Identities=4% Similarity=-0.025 Sum_probs=22.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
+...|+++||..+|||..||+++.+..
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 346899999999999999999766553
No 386
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=28.76 E-value=52 Score=30.97 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.+|||..+|+++.||+.++.-..
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRAR 169 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999887654
No 387
>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=28.71 E-value=63 Score=27.66 Aligned_cols=24 Identities=21% Similarity=0.220 Sum_probs=21.0
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHh
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
|..+||+.+||+..|||...+++.
T Consensus 2 ti~EvA~~~gVs~~tLR~ye~~~g 25 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYWETEFP 25 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcC
Confidence 678999999999999998887753
No 388
>PHA01976 helix-turn-helix protein
Probab=28.68 E-value=65 Score=24.73 Aligned_cols=38 Identities=3% Similarity=0.069 Sum_probs=28.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
..+|+.++|+.+||+..||.+..+- ....+++.+.+++
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g-----~~~p~~~~l~~ia 51 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD-----KRLPNLKTLLRLA 51 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC-----CCCCCHHHHHHHH
Confidence 5589999999999999999985432 2345566666664
No 389
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=28.55 E-value=56 Score=29.37 Aligned_cols=24 Identities=4% Similarity=0.160 Sum_probs=21.9
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
.|..|+|..+|++..||.++.++-
T Consensus 1 MT~eELA~~tG~srQTINrWvRke 24 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRKE 24 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHhc
Confidence 378999999999999999999884
No 390
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=28.48 E-value=77 Score=29.79 Aligned_cols=26 Identities=8% Similarity=0.062 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||+.+|++..||++++.--
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra 182 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDG 182 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHH
Confidence 45999999999999999999887553
No 391
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.44 E-value=53 Score=30.96 Aligned_cols=27 Identities=11% Similarity=0.092 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||+.+||+..||++++.--+
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467899999999999999999887653
No 392
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.42 E-value=54 Score=30.49 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|..+||..+|++..||+.++.--.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGR 169 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 478999999999999999998876553
No 393
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=28.32 E-value=1e+02 Score=32.73 Aligned_cols=30 Identities=7% Similarity=0.114 Sum_probs=26.3
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
|.++ |.+++++..|||..||++.|.++..-
T Consensus 26 g~~lps~r~la~~~~vsr~tv~~a~~~L~~~ 56 (431)
T PRK15481 26 GDSLPPVRELASELGVNRNTVAAAYKRLVTA 56 (431)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5676 78999999999999999999998643
No 394
>PRK09956 hypothetical protein; Provisional
Probab=28.24 E-value=1.6e+02 Score=30.52 Aligned_cols=79 Identities=13% Similarity=0.196 Sum_probs=53.1
Q ss_pred CccchHHHHHhhhCCCCCHHHHHHHHHHHHHhccccccCCC---ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHH
Q 010919 104 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR---KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEAT 180 (497)
Q Consensus 104 dP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~~GR---~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~T 180 (497)
++..++..+...+.. ....++..|..+-+.....++..|+ .-.|..-+++-+|-++.....+...|++++|.|...
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 456677777766541 2345666677776665444444553 112344456778888888889999999999999998
Q ss_pred HHH
Q 010919 181 LMK 183 (497)
Q Consensus 181 Irk 183 (497)
|.+
T Consensus 303 l~~ 305 (308)
T PRK09956 303 LAA 305 (308)
T ss_pred HHH
Confidence 875
No 395
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.10 E-value=61 Score=29.30 Aligned_cols=26 Identities=23% Similarity=0.212 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...+..+||..+|+++.||++++..-
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra 165 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRA 165 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999887664
No 396
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=28.02 E-value=58 Score=29.41 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|..+||..+|++..||+.++.--
T Consensus 127 ~~~s~~eIA~~lgis~~tv~~~l~Ra 152 (161)
T PRK12541 127 YGFSYKEIAEMTGLSLAKVKIELHRG 152 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999887654
No 397
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=27.96 E-value=1.7e+02 Score=28.20 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=34.4
Q ss_pred CChHHHHHHHHHHHHHhcC------CCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 43 RRTEQVQASCLYLACRQKS------KPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 43 R~~~~VaAACLYiACR~e~------~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
++...-.|..|+--+...+ .|.+..|||+.+|++..++.|+.++|.+.
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 4555555555543333322 47778999999999999999999998774
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=27.94 E-value=58 Score=29.97 Aligned_cols=27 Identities=11% Similarity=0.078 Sum_probs=24.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||..+|+++.||+.++.-..
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
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.77 E-value=56 Score=30.69 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=23.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+||+..||+.++.--.
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar 152 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRAR 152 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 468899999999999999999986543
No 400
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=27.71 E-value=56 Score=29.99 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=23.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||..+|++..||+.++.-..
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAK 160 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568999999999999999999987553
No 401
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.71 E-value=56 Score=30.78 Aligned_cols=27 Identities=15% Similarity=0.162 Sum_probs=24.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||+.+|+++.||+.++.--.
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 402
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=27.68 E-value=57 Score=32.30 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=24.5
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
=.|+.|++-.+++|..||++.++++.+
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq~ 131 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQK 131 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 379999999999999999999999953
No 403
>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=27.68 E-value=53 Score=30.86 Aligned_cols=27 Identities=19% Similarity=0.237 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||..+|++..||+.|+.-.+
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar 172 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRAR 172 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 468999999999999999999876654
No 404
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=27.63 E-value=91 Score=30.09 Aligned_cols=33 Identities=24% Similarity=0.345 Sum_probs=28.2
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 160 THGLKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
..+...|.++||+.+++|+.||++-+.-+.+..
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 356778999999999999999999998886543
No 405
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=27.58 E-value=56 Score=32.01 Aligned_cols=25 Identities=8% Similarity=0.166 Sum_probs=22.8
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|-.++++..|||..|||+.+.+|..
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~ 61 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVE 61 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6889999999999999999999853
No 406
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=27.58 E-value=56 Score=31.21 Aligned_cols=26 Identities=15% Similarity=0.179 Sum_probs=22.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+||++.||+.++..-
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra 193 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLA 193 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999887654
No 407
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=27.50 E-value=1.5e+02 Score=21.50 Aligned_cols=30 Identities=7% Similarity=0.144 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+-|.++.||+..++++..++.+....|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 567899999999999999999988888763
No 408
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=27.40 E-value=1.5e+02 Score=29.40 Aligned_cols=54 Identities=11% Similarity=0.086 Sum_probs=0.0
Q ss_pred cccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 137 RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 137 ~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
.+.+-.|-.+.++-.-.-.+. ..+...|-.++|+.+|+|.+|+|+.+.-+...+
T Consensus 148 ~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~ 201 (224)
T COG4565 148 PDDLPKGLDELTLQKVREALK--EPDQELTAEELAQALGISRVTARRYLEYLVSNG 201 (224)
T ss_pred cccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHHHhCccHHHHHHHHHHHHhcC
No 409
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.33 E-value=97 Score=22.35 Aligned_cols=27 Identities=4% Similarity=0.018 Sum_probs=18.1
Q ss_pred CCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 63 PFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 63 prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
..+..+||..++|+..++.+..+...+
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 678899999999999999887766543
No 410
>PRK03837 transcriptional regulator NanR; Provisional
Probab=27.23 E-value=70 Score=31.03 Aligned_cols=30 Identities=10% Similarity=0.261 Sum_probs=26.6
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ +..++++.+|||..|||..++.|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVREALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 36778 8999999999999999999999853
No 411
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=27.19 E-value=67 Score=29.95 Aligned_cols=27 Identities=19% Similarity=0.201 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||++++.-.+
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar 179 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAR 179 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999877654
No 412
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=27.13 E-value=59 Score=30.39 Aligned_cols=26 Identities=15% Similarity=0.181 Sum_probs=22.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+||+..||+.++.--
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35789999999999999999887643
No 413
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=27.13 E-value=1e+02 Score=28.52 Aligned_cols=38 Identities=21% Similarity=0.259 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 152 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 152 AaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+.+|||. ..+-.+|.++||+..+|+..-+++-+..|..
T Consensus 13 ~L~~LA~-~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~ 50 (153)
T PRK11920 13 MLMYCAA-NDGKLSRIPEIARAYGVSELFLFKILQPLVE 50 (153)
T ss_pred HHHHHHh-CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4567774 3455679999999999999999999999865
No 414
>PRK15185 transcriptional regulator HilD; Provisional
Probab=27.10 E-value=3.7e+02 Score=28.09 Aligned_cols=80 Identities=8% Similarity=0.056 Sum_probs=0.0
Q ss_pred HHHHHHHcCCCChhHHHHHHHHHHHHHHhCCCCCCCChHH-HHHHHHHHHHHh-cCCCCCHHHHHHHhCc-ChHHHHHHH
Q 010919 8 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQ-VQASCLYLACRQ-KSKPFLLIDFSNYLNI-NVYELGAVY 84 (497)
Q Consensus 8 I~~ia~~L~Lp~~~~i~d~A~~iyk~a~~~~~~rGR~~~~-VaAACLYiACR~-e~~prtL~DIa~v~~v-sv~~Lgr~y 84 (497)
+..+|..++++ ...+.+.... + |.++.. +.-.-+-.|++. .....++.+||..+|. +...+.+.|
T Consensus 225 ledLA~~lgmS---------~~tL~R~FK~-~--G~S~~~yl~~~Ri~~A~~LL~~t~~sIseIA~~~GFss~S~FsR~F 292 (309)
T PRK15185 225 LTDVADHIFMS---------TSTLKRKLAE-E--GTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCF 292 (309)
T ss_pred HHHHHHHHCcC---------HHHHHHHHHH-c--CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHH
Q ss_pred HHHHHHhcccccccccccCCccchHHHH
Q 010919 85 LQLCQVLYIADESNVLKQVDPSIFLHKF 112 (497)
Q Consensus 85 k~L~~~L~i~~~~~~~~~idP~~~I~Rf 112 (497)
++... ..|..|..+.
T Consensus 293 Kk~~G-------------~TPseYRk~~ 307 (309)
T PRK15185 293 KKYFK-------------TTPSTFIKMA 307 (309)
T ss_pred HHHHC-------------cCHHHHHHhh
No 415
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=27.00 E-value=57 Score=30.06 Aligned_cols=26 Identities=12% Similarity=-0.006 Sum_probs=22.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+|+++.||++++.--
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Ra 169 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRS 169 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHH
Confidence 45789999999999999999887654
No 416
>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=26.99 E-value=57 Score=31.91 Aligned_cols=25 Identities=4% Similarity=0.154 Sum_probs=22.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|.+|||..+||+..||++++.-
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~r 221 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999988744
No 417
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=26.88 E-value=1.1e+02 Score=27.32 Aligned_cols=30 Identities=20% Similarity=0.286 Sum_probs=26.1
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+-.+|+.+|++.++++.+||.+.++.|..-
T Consensus 44 ~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~ 73 (144)
T PRK03573 44 PPEQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred CCCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence 345899999999999999999999988643
No 418
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=26.87 E-value=76 Score=32.17 Aligned_cols=36 Identities=11% Similarity=0.230 Sum_probs=30.9
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 155 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 155 ylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.-+-+.+|-+++|+|+.+.+|.+++|+.++++.+.+
T Consensus 201 l~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 201 LDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred HHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh
Confidence 334456789999999999999999999999999854
No 419
>PRK13503 transcriptional activator RhaS; Provisional
Probab=26.87 E-value=71 Score=31.47 Aligned_cols=51 Identities=10% Similarity=0.142 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 010919 48 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 112 (497)
Q Consensus 48 VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf 112 (497)
+-.+.=||--. -..++|+.|+|+.++++...|.+.|++. .| ..|..||.+.
T Consensus 173 i~~~~~~I~~~-~~~~~tl~~lA~~~~lS~~~l~r~Fk~~---~G----------~S~~~yi~~~ 223 (278)
T PRK13503 173 LNQLLAWLEDH-FAEEVNWEALADQFSLSLRTLHRQLKQQ---TG----------LTPQRYLNRL 223 (278)
T ss_pred HHHHHHHHHHh-hcCCCCHHHHHHHHCCCHHHHHHHHHHH---hC----------cCHHHHHHHH
Confidence 44444444332 3458999999999999999998877754 32 3566676654
No 420
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=26.82 E-value=2.4e+02 Score=31.53 Aligned_cols=104 Identities=9% Similarity=0.011 Sum_probs=60.5
Q ss_pred CCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHHHHHHHHhcccccc
Q 010919 62 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWIT 141 (497)
Q Consensus 62 ~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A~~Lv~~~~~~~l~ 141 (497)
.|+|..++|..++||..+|.+-...|...|.-....... -.. -| .|.. .+..-. ..+.+.
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~--~~~-Gy------~l~~-~~~~~~---~~~~~~------- 75 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSIS--GSA-KY------HLEI-LNRRSL---FQLLQK------- 75 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhhee--cCC-ce------EEEe-CCHHHH---HHHHhc-------
Confidence 589999999999999999999999888876432111000 000 11 1210 011100 111110
Q ss_pred CCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 142 TGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 142 ~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
..|.-. .+ +...+....++..++|+...||++||.+-++++...
T Consensus 76 --~~~e~~---~i-l~~Ll~~~~~~~~~La~~l~vS~sTi~~dl~~v~~~ 119 (584)
T PRK09863 76 --SDNEDR---LL-LLRLLLNTFTPMAQLASALNLSRTWVAERLPRLNQR 119 (584)
T ss_pred --CCHHHH---HH-HHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence 012222 11 111222456899999999999999999999888653
No 421
>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=26.77 E-value=96 Score=29.42 Aligned_cols=43 Identities=14% Similarity=0.114 Sum_probs=31.1
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 143 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 143 GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
.-.|.-.+.+..-+. ..+..|+.+||+.+|++..+|+++++-.
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 345666555433322 2256899999999999999999999875
No 422
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=26.77 E-value=1.3e+02 Score=29.19 Aligned_cols=44 Identities=14% Similarity=0.266 Sum_probs=35.2
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 44 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 44 ~~~~VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
+...|..+|-+|--. ..++++.++++.+++|.+.+.+.|+.+..
T Consensus 80 ~~~~V~~a~~~ie~~--~~~~~le~la~~lg~sp~~~~R~FK~~~G 123 (187)
T COG2169 80 RSGLVATACRLIEQN--PEKRWLEELADELGVSPSTLHRLFKAITG 123 (187)
T ss_pred ccHHHHHHHHHHHcC--CCcccHHHHHHHhCCChHHHHHHHHHHhC
Confidence 345677777776543 77899999999999999999999887643
No 423
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=26.72 E-value=76 Score=29.94 Aligned_cols=28 Identities=14% Similarity=0.050 Sum_probs=24.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
....|.++||+..++|+.||+...+.+.
T Consensus 163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3457899999999999999999888764
No 424
>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=26.69 E-value=95 Score=23.14 Aligned_cols=26 Identities=8% Similarity=0.008 Sum_probs=23.7
Q ss_pred CHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 65 LLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 65 tL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
+..+||+.++++...+.+.+..|.+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 68999999999999999999999873
No 425
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=26.66 E-value=1.1e+02 Score=27.18 Aligned_cols=30 Identities=7% Similarity=0.190 Sum_probs=26.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+-..++.+|++.++++.+||.+.++.|.+.
T Consensus 28 ~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 28 SGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 346899999999999999999999999764
No 426
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=26.62 E-value=57 Score=30.31 Aligned_cols=27 Identities=4% Similarity=-0.143 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||++++.-..
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar 178 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGL 178 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHH
Confidence 568999999999999999999887543
No 427
>PRK10870 transcriptional repressor MprA; Provisional
Probab=26.61 E-value=2.9e+02 Score=25.94 Aligned_cols=39 Identities=13% Similarity=-0.008 Sum_probs=32.0
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 52 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 52 CLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
.|+...+..+.+.+..|||+.++++..++.+....|.+.
T Consensus 60 iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~k 98 (176)
T PRK10870 60 ALITLESQENHSIQPSELSCALGSSRTNATRIADELEKR 98 (176)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344444555678999999999999999999999998874
No 428
>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=26.55 E-value=96 Score=28.32 Aligned_cols=42 Identities=10% Similarity=0.110 Sum_probs=31.6
Q ss_pred ChhHHHHHHHHHHHHhcCCC-CCHhhHHHHhccCHHHHHHHHHH
Q 010919 145 KPSGLCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 145 ~P~~IaaAaLylAar~~g~~-~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
+..-|..||+-+-+ .+|+. .|+++||+.+||+..||-..|..
T Consensus 9 rr~~Il~aA~~lf~-~~G~~~~s~~~IA~~agvsk~~ly~~F~s 51 (189)
T TIGR03384 9 RRAELIDATIESIG-ERGSLDVTIAQIARRAGVSSGIISHYFGG 51 (189)
T ss_pred HHHHHHHHHHHHHH-hcCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence 44555555655544 46765 89999999999999999888843
No 429
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=26.51 E-value=69 Score=31.38 Aligned_cols=28 Identities=14% Similarity=0.202 Sum_probs=25.0
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHh
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
|.++ |-.++++..|||..|||+.+.+|.
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR~Al~~L~ 54 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVRQALRQLV 54 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5566 689999999999999999999985
No 430
>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=26.39 E-value=69 Score=27.38 Aligned_cols=38 Identities=11% Similarity=0.171 Sum_probs=27.0
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
=||+|..+-....++..+.+++|..+.||+..++.|.+
T Consensus 10 rlyla~li~~~~~nvp~L~~~TGmPrRT~Qd~i~aL~~ 47 (90)
T PF09904_consen 10 RLYLAYLIDSGERNVPALMEATGMPRRTIQDTIKALPE 47 (90)
T ss_dssp HHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGG
T ss_pred HHHHHHHHhcCCccHHHHHHHhCCCHhHHHHHHHHhhc
Confidence 36888877544449999999999999999999998853
No 431
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=26.37 E-value=60 Score=30.18 Aligned_cols=26 Identities=8% Similarity=-0.021 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...+.++||+.+|++..||+.++.--
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra 171 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRG 171 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 47899999999999999999887653
No 432
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.34 E-value=61 Score=29.84 Aligned_cols=27 Identities=19% Similarity=0.189 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+++.||++++.-.+
T Consensus 151 ~g~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999987643
No 433
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.20 E-value=63 Score=30.11 Aligned_cols=26 Identities=8% Similarity=-0.001 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+||+..||+.++.--
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~Ra 179 (189)
T PRK09648 154 VGLSAEETAEAVGSTPGAVRVAQHRA 179 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 36889999999999999999887653
No 434
>PRK12423 LexA repressor; Provisional
Probab=26.16 E-value=1.2e+02 Score=29.17 Aligned_cols=31 Identities=13% Similarity=0.128 Sum_probs=26.9
Q ss_pred hcCCCCCHhhHHHHhc-cCHHHHHHHHHHHhc
Q 010919 160 THGLKFSKSDIVKIVH-ICEATLMKRLIEFEN 190 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~-Vse~TIrkr~kE~~~ 190 (497)
.+|+.-|.+|||+.+| ++.+|+++.++.|.+
T Consensus 21 ~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 21 QAGQPPSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4566789999999999 599999999998865
No 435
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=26.08 E-value=63 Score=29.38 Aligned_cols=27 Identities=7% Similarity=0.096 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+..+||..+|+++.||+.++.-.+
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar 149 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGR 149 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999998887654
No 436
>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=25.97 E-value=63 Score=31.37 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=25.1
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|.++ |-.++++..|||..|||+.+.+|.+
T Consensus 22 g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~ 51 (230)
T TIGR02018 22 GHRIPSEHELVAQYGCSRMTVNRALRELTD 51 (230)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4555 7889999999999999999999853
No 437
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=25.90 E-value=63 Score=30.22 Aligned_cols=26 Identities=19% Similarity=0.178 Sum_probs=22.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|++..||++++..-
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra 179 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYA 179 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999876643
No 438
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=25.86 E-value=1.3e+02 Score=24.98 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=27.2
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.+...|..+|++.+|+|+.+|-+..+.+++-
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~ 46 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVWKHIQQLREE 46 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHHHHHHHHHHh
Confidence 4557999999999999999999999998753
No 439
>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=25.86 E-value=92 Score=24.21 Aligned_cols=31 Identities=16% Similarity=0.086 Sum_probs=27.2
Q ss_pred cCCCCCHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 60 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 60 e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
..-+.|..|||..++++..++.++.+.|.+.
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 4557899999999999999999999888874
No 440
>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This entry is represented by Bacteriophage 186, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny [].
Probab=25.81 E-value=58 Score=30.64 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=31.1
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 205 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~ 205 (497)
..++||..+|++..|+|+++.-= . .-+||+.|+..+.
T Consensus 22 ~~~~lA~~lGm~~~~LrNKLNP~-q--~H~Lt~~el~~i~ 58 (162)
T PF06892_consen 22 NMAALAERLGMNPQTLRNKLNPE-Q--PHKLTVDELIAIT 58 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHcCCC-C--CCCCCHHHHHHHH
Confidence 37899999999999999998753 3 3589999998874
No 441
>PRK09726 antitoxin HipB; Provisional
Probab=25.72 E-value=1.6e+02 Score=24.32 Aligned_cols=40 Identities=18% Similarity=0.208 Sum_probs=31.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 206 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~~~ 206 (497)
....|+.++|+.+||+..||.+-.+. ....+++.+..+++
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 45789999999999999999876652 23567888877753
No 442
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=25.63 E-value=63 Score=31.84 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=22.6
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|-.++|+..|||..|||+.+.+|.+
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~ 57 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDELVE 57 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 5779999999999999999999853
No 443
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=25.52 E-value=1.5e+02 Score=25.87 Aligned_cols=38 Identities=11% Similarity=0.106 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 152 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 152 AaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
.=+-+...+..-+.||+||+.-.||+-+||.+--..++
T Consensus 48 ~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK 85 (103)
T COG2973 48 TRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLK 85 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhc
Confidence 34556666777899999999999999999988766664
No 444
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=25.50 E-value=65 Score=30.12 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=24.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+..+||..+|+|..||++++.--.
T Consensus 121 ~g~~~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 121 EGLSQKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 568999999999999999999987664
No 445
>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=25.47 E-value=1e+02 Score=23.72 Aligned_cols=30 Identities=3% Similarity=-0.007 Sum_probs=24.6
Q ss_pred CCCC-CHHHHHHHhCcChHHHHHHHHHHHHH
Q 010919 61 SKPF-LLIDFSNYLNINVYELGAVYLQLCQV 90 (497)
Q Consensus 61 ~~pr-tL~DIa~v~~vsv~~Lgr~yk~L~~~ 90 (497)
|... +..+|+..++|+..++.+++..|...
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 446
>PRK01905 DNA-binding protein Fis; Provisional
Probab=25.38 E-value=99 Score=25.14 Aligned_cols=24 Identities=25% Similarity=0.173 Sum_probs=21.0
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
-++...|+.+||+..|++++++.+
T Consensus 51 gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 51 GNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHh
Confidence 457778999999999999999876
No 447
>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=25.35 E-value=63 Score=32.12 Aligned_cols=27 Identities=11% Similarity=0.112 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.+|||..+||++.||+.++.--.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr 202 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQAR 202 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 468899999999999999999987754
No 448
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=25.33 E-value=99 Score=31.82 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=26.0
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+-..+..+||+.+|||.+||+++++.+.+
T Consensus 16 ~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 16 GDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45678889999999999999999999985
No 449
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=25.19 E-value=78 Score=31.06 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=26.8
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ +..++++.+|||..|||..++.|..
T Consensus 27 pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~ 57 (251)
T PRK09990 27 VGQALPSERRLCEKLGFSRSALREGLTVLRG 57 (251)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46788 7999999999999999999999853
No 450
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.03 E-value=65 Score=31.43 Aligned_cols=26 Identities=8% Similarity=0.114 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.++||..+||+..||++++..-
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra 224 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQA 224 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45799999999999999999887654
No 451
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=24.98 E-value=61 Score=30.95 Aligned_cols=24 Identities=8% Similarity=0.166 Sum_probs=21.4
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHh
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
+..+||+.+|||..|||+.++...
T Consensus 2 ti~evA~~lGVS~~TLRrw~k~g~ 25 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVKQLN 25 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 678999999999999999998753
No 452
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=24.95 E-value=79 Score=31.30 Aligned_cols=27 Identities=7% Similarity=-0.017 Sum_probs=23.3
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
....|.++||..+||++.||++++..-
T Consensus 219 ~~g~s~~eIA~~l~is~~tV~~~~~ra 245 (257)
T PRK08583 219 IENLSQKETGERLGISQMHVSRLQRQA 245 (257)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 356899999999999999999887653
No 453
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=24.86 E-value=94 Score=30.16 Aligned_cols=38 Identities=24% Similarity=0.097 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 010919 148 GLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 148 ~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~k 186 (497)
-|..||+-+-+ .+|+..|+++||+.+||+..||...+.
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 34445554433 357779999999999999999988774
No 454
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=24.75 E-value=72 Score=26.27 Aligned_cols=24 Identities=21% Similarity=0.375 Sum_probs=22.0
Q ss_pred HhhHHHHhccCHHHHHHHHHHHhc
Q 010919 167 KSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 167 ~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
+.++++.+||+.+||++.++.|..
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 578999999999999999999965
No 455
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.74 E-value=68 Score=30.23 Aligned_cols=27 Identities=11% Similarity=-0.004 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|++..||+.++.-.+
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 469999999999999999998887654
No 456
>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=24.72 E-value=75 Score=29.59 Aligned_cols=27 Identities=11% Similarity=-0.013 Sum_probs=0.0
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
..|.++||..+|++..||+.++.-...
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
No 457
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.72 E-value=70 Score=29.83 Aligned_cols=27 Identities=26% Similarity=0.235 Sum_probs=23.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|+|..||++++.-.+
T Consensus 146 ~~~s~~eIA~~lgis~~tV~~~l~Rar 172 (189)
T PRK12515 146 HEKSVEEVGEIVGIPESTVKTRMFYAR 172 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 678999999999999999999886653
No 458
>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=24.41 E-value=1e+02 Score=27.03 Aligned_cols=32 Identities=9% Similarity=0.143 Sum_probs=28.1
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHhcCCC
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFENTDS 193 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~ 193 (497)
+-..|+.|+|..+||+.+||...|+-+.-|.-
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~K 100 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRALKRLGITRK 100 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHHcCchhc
Confidence 46789999999999999999999999976654
No 459
>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=24.30 E-value=1.9e+02 Score=20.87 Aligned_cols=33 Identities=9% Similarity=0.121 Sum_probs=26.2
Q ss_pred HHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 57 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 57 CR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
.-..+-|.+..||++.++++..++.+-.+.|.+
T Consensus 9 ~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 9 KLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 334557899999999999999999987777765
No 460
>PRK13500 transcriptional activator RhaR; Provisional
Probab=24.20 E-value=4e+02 Score=27.10 Aligned_cols=99 Identities=15% Similarity=0.108 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHH
Q 010919 48 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDT 127 (497)
Q Consensus 48 VaAACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~ 127 (497)
+...+-||--. ...++++.++|+.++++...|.+.|++-.. ..|..||.++ ....
T Consensus 208 l~~i~~yI~~~-~~e~isl~~lA~~~~iS~~~L~r~FK~~tG-------------~T~~~yi~~~-----------RL~~ 262 (312)
T PRK13500 208 LDKLITRLAAS-LKSPFALDKFCDEASCSERVLRQQFRQQTG-------------MTINQYLRQV-----------RVCH 262 (312)
T ss_pred HHHHHHHHHHc-ccCCCCHHHHHHHHCcCHHHHHHHHHHHHC-------------cCHHHHHHHH-----------HHHH
Confidence 34444444433 355799999999999999999987776432 3466676655 1122
Q ss_pred HHHHHHHhccccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHH-HHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 128 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA-TLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 128 A~~Lv~~~~~~~l~~GR~P~~IaaAaLylAar~~g~~~t~~eIa~v~~Vse~-TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
|.+++. .-+.|+.|||..+|-... ...+.+|... .+||.+|++.
T Consensus 263 A~~LL~----------------------------~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~TP~~yRk~ 307 (312)
T PRK13500 263 AQYLLQ----------------------------HSRLLISDISTECGFEDSNYFSVVFTRET-----GMTPSQWRHL 307 (312)
T ss_pred HHHHHH----------------------------cCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 222221 235678888888887444 5666666653 4778888765
No 461
>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=24.18 E-value=87 Score=24.57 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=18.2
Q ss_pred hcCCCCCHhhHHHHhccCHHHHH-HHHH
Q 010919 160 THGLKFSKSDIVKIVHICEATLM-KRLI 186 (497)
Q Consensus 160 ~~g~~~t~~eIa~v~~Vse~TIr-kr~k 186 (497)
..|++ +++++|+.+||+.+||. ++.+
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 34554 77899999999999999 5554
No 462
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=24.17 E-value=72 Score=29.15 Aligned_cols=26 Identities=23% Similarity=0.342 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...+.++||..+|++..||++++.-.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra 166 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHG 166 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 46899999999999999999887654
No 463
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.05 E-value=70 Score=30.38 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||+.+|++..||+.++.--
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Ra 173 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARA 173 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45789999999999999999887644
No 464
>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=24.02 E-value=86 Score=22.66 Aligned_cols=22 Identities=0% Similarity=0.037 Sum_probs=16.0
Q ss_pred CCCHHHHHHHhCcChHHHHHHH
Q 010919 63 PFLLIDFSNYLNINVYELGAVY 84 (497)
Q Consensus 63 prtL~DIa~v~~vsv~~Lgr~y 84 (497)
..++.+||..++|+..+|-|..
T Consensus 21 G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 21 GMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp T--HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 3889999999999999887643
No 465
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=24.02 E-value=85 Score=30.22 Aligned_cols=29 Identities=14% Similarity=0.037 Sum_probs=26.3
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
.|.+++..++++.+|||.++||..++.|.
T Consensus 27 pG~~L~e~eLae~lgVSRtpVREAL~~L~ 55 (224)
T PRK11534 27 PDEKLRMSLLTSRYALGVGPLREALSQLV 55 (224)
T ss_pred CCCcCCHHHHHHHHCCChHHHHHHHHHHH
Confidence 36788999999999999999999999885
No 466
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=24.01 E-value=8.8e+02 Score=25.71 Aligned_cols=112 Identities=5% Similarity=-0.014 Sum_probs=58.2
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHhhhC-C-CCCHHHHHHHHHHHHHhccc
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-P-GGNKKVCDTARDILASMKRD 138 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~-~-~~~~~V~~~A~~Lv~~~~~~ 138 (497)
+.+-+..+||..+++++..+....+....-..++.+. .-|-.. .+.+-|. . ..++........+ +.-...
T Consensus 203 ~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~i----g~ded~---~l~d~leD~~~~~p~~~~~~~~~-~~~~~~ 274 (342)
T COG0568 203 GREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPI----GDDEDS---ELGDFLEDDKSVSPEDAVERESL-KEDLNE 274 (342)
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcC----CCCccc---HHHHHhhcCCcCCHHHHHHHHHH-HHHHHH
Confidence 3445788999999999987776655555533343322 111111 2333342 1 1233322222222 222233
Q ss_pred cccCCCChhHHHHHHHHHHHHhc--CCCCCHhhHHHHhccCHHHHHH
Q 010919 139 WITTGRKPSGLCGAALYVSALTH--GLKFSKSDIVKIVHICEATLMK 183 (497)
Q Consensus 139 ~l~~GR~P~~IaaAaLylAar~~--g~~~t~~eIa~v~~Vse~TIrk 183 (497)
|+...=.|.-- -|+..=... +.+.|+.+|+..+|||.--||+
T Consensus 275 ~L~~~Lt~rE~---~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQ 318 (342)
T COG0568 275 VLAEALTERER---RVIRLRFGLDDGEPKTLEELGEEFGISRERVRQ 318 (342)
T ss_pred HHHhcCCHHHH---HHHHHHhccCCCCcchHHHHHHHhCCcHHHHHH
Confidence 43332233221 222111122 4579999999999999999984
No 467
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=23.99 E-value=85 Score=30.93 Aligned_cols=30 Identities=13% Similarity=0.334 Sum_probs=26.5
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ +..++++.+|||.+|||..++.|..
T Consensus 22 pG~~LpsE~eLae~~gVSRtpVREAL~~Le~ 52 (253)
T PRK10421 22 AGMKLPAERQLAMQLGVSRNSLREALAKLVS 52 (253)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46788 6899999999999999999999853
No 468
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=23.90 E-value=7.6e+02 Score=24.89 Aligned_cols=66 Identities=11% Similarity=0.141 Sum_probs=38.6
Q ss_pred HHHHHHHHHHc--CCC-ChhHHHHHH-HHHHHHHHhCCCCCCCChHHHHHHHH----HHHHHhcC---CCCCHHHHH
Q 010919 5 FDDMRQMKNAL--NIG-ESDEIVHVA-KRFYGIAVARNFTKGRRTEQVQASCL----YLACRQKS---KPFLLIDFS 70 (497)
Q Consensus 5 ~~~I~~ia~~L--~Lp-~~~~i~d~A-~~iyk~a~~~~~~rGR~~~~VaAACL----YiACR~e~---~prtL~DIa 70 (497)
...+..++.++ ++| +-++.+..+ .-+.+-+..-...+|.+..+.|.=|| +-=+|.++ .||++++.+
T Consensus 33 lpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~~v~vpR~~~~~~ 109 (247)
T COG1191 33 LPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLRELG 109 (247)
T ss_pred HHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCCCccCcHHHHHHH
Confidence 34555666665 233 113444444 44455555567888988888777665 44466655 577777664
No 469
>PRK06930 positive control sigma-like factor; Validated
Probab=23.78 E-value=81 Score=29.77 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=24.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 162 GLKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 162 g~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
....|.++||..+|++..||+.++....
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~ 155 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMIERAE 155 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4678999999999999999999987654
No 470
>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=23.75 E-value=26 Score=32.90 Aligned_cols=25 Identities=16% Similarity=0.297 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHhCcChHHHHHHHHH
Q 010919 62 KPFLLIDFSNYLNINVYELGAVYLQ 86 (497)
Q Consensus 62 ~prtL~DIa~v~~vsv~~Lgr~yk~ 86 (497)
.|.+++|||+.+++++.+|.|+...
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~~ 72 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVKN 72 (160)
T ss_dssp -------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHcC
Confidence 5899999999999999999987653
No 471
>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=23.71 E-value=1.3e+02 Score=30.36 Aligned_cols=28 Identities=21% Similarity=0.239 Sum_probs=25.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
-+.+..++|+.+|||.++|+.|++.|..
T Consensus 197 grlse~eLAerlGVSRs~ireAlrkLE~ 224 (251)
T TIGR02787 197 GLLVASKIADRVGITRSVIVNALRKLES 224 (251)
T ss_pred ccccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4789999999999999999999999964
No 472
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=23.68 E-value=78 Score=29.19 Aligned_cols=25 Identities=12% Similarity=0.135 Sum_probs=21.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE 187 (497)
...|+++||+.+|+|..||++..+-
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5699999999999999999876654
No 473
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.63 E-value=71 Score=31.42 Aligned_cols=26 Identities=15% Similarity=0.142 Sum_probs=22.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||..+|+++.||+.++.--
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RA 211 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRG 211 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887654
No 474
>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=23.63 E-value=77 Score=29.15 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...+.++||..+|||..||++++.-.
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra 180 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRG 180 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56799999999999999999887643
No 475
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=23.60 E-value=77 Score=30.51 Aligned_cols=30 Identities=7% Similarity=0.243 Sum_probs=26.8
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.+++..++++.+|||.++||..++.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVREAL~~L~~ 60 (221)
T PRK11414 31 PGARLITKNLAEQLGMSITPVREALLRLVS 60 (221)
T ss_pred CCCccCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 377888899999999999999999999854
No 476
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.55 E-value=74 Score=30.51 Aligned_cols=27 Identities=15% Similarity=0.079 Sum_probs=24.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...+.++||+.+|+++.||++++.-.+
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~~~l~RAr 179 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVRSRIHRGR 179 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999887764
No 477
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.54 E-value=74 Score=31.11 Aligned_cols=29 Identities=10% Similarity=0.261 Sum_probs=24.5
Q ss_pred CCC-CCHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 162 GLK-FSKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 162 g~~-~t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
|.+ -|-.++++..|||..|||+.+.+|.+
T Consensus 30 g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~ 59 (241)
T PRK11402 30 GQQIPTENELCTQYNVSRITIRKAISDLVA 59 (241)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344 36789999999999999999999854
No 478
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.46 E-value=74 Score=29.77 Aligned_cols=26 Identities=19% Similarity=0.163 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...|.+|||+.+|+|..||++++.-.
T Consensus 146 ~g~s~~EIAe~lgis~~~V~~~l~Ra 171 (189)
T PRK06811 146 LGEKIEEIAKKLGLTRSAIDNRLSRG 171 (189)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45899999999999999999987654
No 479
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=23.42 E-value=81 Score=30.38 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=23.3
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 166 SKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
+-.++++..|||..|+|+++..+...
T Consensus 27 sE~eLa~~~~Vsr~Tvr~Al~~L~~e 52 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQQLEAE 52 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 67899999999999999999998643
No 480
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=23.38 E-value=76 Score=29.20 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEF 188 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~ 188 (497)
...+..+||+.+|||..||++++.-.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Ra 176 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRG 176 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999999887644
No 481
>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=23.36 E-value=1.2e+02 Score=29.18 Aligned_cols=28 Identities=25% Similarity=0.258 Sum_probs=25.3
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 164 KFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 164 ~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
..++.+|++.++++.+|+++.++.|.+.
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le~~ 184 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELEKK 184 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5899999999999999999999998643
No 482
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.25 E-value=93 Score=28.24 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=26.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
-+.|.++++..+|++..|+++.++++..+
T Consensus 25 GRiTi~ql~~~TGasR~Tvk~~lreLVa~ 53 (127)
T PF06163_consen 25 GRITIKQLVAKTGASRNTVKRYLRELVAR 53 (127)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 47899999999999999999999998754
No 483
>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=23.22 E-value=1.3e+02 Score=23.76 Aligned_cols=33 Identities=9% Similarity=0.096 Sum_probs=23.6
Q ss_pred HhcCCCCCHHHHHHHhCcC-hHHHHHHHHHHHHH
Q 010919 58 RQKSKPFLLIDFSNYLNIN-VYELGAVYLQLCQV 90 (497)
Q Consensus 58 R~e~~prtL~DIa~v~~vs-v~~Lgr~yk~L~~~ 90 (497)
..+|.|=|++||++.++++ ...+.+..+.|.+.
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 3578999999999999997 77777766666653
No 484
>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=23.18 E-value=2.5e+02 Score=27.73 Aligned_cols=44 Identities=11% Similarity=0.140 Sum_probs=35.6
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 155 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 155 ylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
||.... ...+|+.+||+.+|+|..++.+.++... .+|+-+|...
T Consensus 194 ~I~~~~-~~~~sl~~lA~~~~~S~~~l~r~Fk~~~-----G~t~~~yi~~ 237 (287)
T TIGR02297 194 LIEENY-KQHLRLPEYADRLGISESRLNDICRRFS-----ALSPKRLIIE 237 (287)
T ss_pred HHHHhh-ccCCCHHHHHHHHCCCHHHHHHHHHHHh-----CCCHHHHHHH
Confidence 454443 4589999999999999999999999964 5788998654
No 485
>PRK13500 transcriptional activator RhaR; Provisional
Probab=23.15 E-value=2.3e+02 Score=28.87 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=17.7
Q ss_pred CCCCCHHHHHHHhCc-ChHHHHHHHHHH
Q 010919 61 SKPFLLIDFSNYLNI-NVYELGAVYLQL 87 (497)
Q Consensus 61 ~~prtL~DIa~v~~v-sv~~Lgr~yk~L 87 (497)
....++.|||..+|. |...+.+.|++.
T Consensus 269 ~t~~sI~eIA~~~GF~d~s~Fsr~FKk~ 296 (312)
T PRK13500 269 HSRLLISDISTECGFEDSNYFSVVFTRE 296 (312)
T ss_pred cCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 446777788877776 456666666554
No 486
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.11 E-value=77 Score=29.94 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=24.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||..+|||..||+.++.-.+
T Consensus 128 ~g~s~~EIA~~LgiS~~tVk~~l~Rar 154 (188)
T PRK12546 128 SGFSYEEAAEMCGVAVGTVKSRANRAR 154 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678999999999999999999887764
No 487
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=23.02 E-value=1.5e+02 Score=27.61 Aligned_cols=38 Identities=11% Similarity=0.072 Sum_probs=32.2
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcChHHHHHHHHHHHH
Q 010919 51 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 89 (497)
Q Consensus 51 ACLYiACR~e~~prtL~DIa~v~~vsv~~Lgr~yk~L~~ 89 (497)
-+||..-+ .+-+....|||..++|+..++....++|.+
T Consensus 13 ~~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~ 50 (154)
T COG1321 13 ETIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLER 50 (154)
T ss_pred HHHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHH
Confidence 35676666 677889999999999999999998888877
No 488
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.94 E-value=78 Score=29.63 Aligned_cols=27 Identities=22% Similarity=0.181 Sum_probs=24.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHh
Q 010919 163 LKFSKSDIVKIVHICEATLMKRLIEFE 189 (497)
Q Consensus 163 ~~~t~~eIa~v~~Vse~TIrkr~kE~~ 189 (497)
...|.++||+.+|+++.||+.++.--.
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr 152 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRAR 152 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568899999999999999999987764
No 489
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=22.84 E-value=93 Score=30.20 Aligned_cols=30 Identities=13% Similarity=0.313 Sum_probs=26.6
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ |..++++.+|||.++||..++.|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVREAL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLREVLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36788 7999999999999999999998853
No 490
>PF01846 FF: FF domain; InterPro: IPR002713 The FF domain may be involved in protein-protein interaction []. It often occurs as multiple copies and often accompanies WW domains IPR001202 from INTERPRO. PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [].; PDB: 3HFH_B 2KIS_A 2DOD_A 2JUC_A 2LKS_A 1UZC_A 2KZG_A 2L9V_A 2DOF_A 2KFD_A ....
Probab=22.84 E-value=1.1e+02 Score=22.42 Aligned_cols=36 Identities=14% Similarity=0.260 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcCCCccCCHHHHhhhhCCCCccccc
Q 010919 447 ALEATRRMLTKKRLSSKINYDVLEKLFDDSVCLYSI 482 (497)
Q Consensus 447 a~EA~~~ml~~k~~S~KINYdvl~~L~~~~~~~~~~ 482 (497)
|.++.++||+...++....|+-+..++...+-+..+
T Consensus 2 a~~~F~~lL~e~~i~~~s~W~~~~~~l~~dpry~~i 37 (51)
T PF01846_consen 2 AREAFKELLKEHKITPYSSWEEVKPKLSKDPRYKAI 37 (51)
T ss_dssp HHHHHHHHHHHTTS-TTSSHHHHHHHHTTSCHHHHS
T ss_pred HHHHHHHHHHhCCCCCCCcHHHHHHHHccCHHHHHh
Confidence 568899999999999999999999999877666554
No 491
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=22.80 E-value=93 Score=30.57 Aligned_cols=30 Identities=17% Similarity=0.352 Sum_probs=26.6
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ +..++++.+|||..|||..++.|..
T Consensus 30 pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~ 60 (254)
T PRK09464 30 PGEKLPPERELAKQFDVSRPSLREAIQRLEA 60 (254)
T ss_pred CCCcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46788 7999999999999999999999853
No 492
>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=22.63 E-value=81 Score=25.00 Aligned_cols=31 Identities=26% Similarity=0.377 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCCC--CCChHHHHHHHHHHHHH
Q 010919 28 KRFYGIAVARNFTK--GRRTEQVQASCLYLACR 58 (497)
Q Consensus 28 ~~iyk~a~~~~~~r--GR~~~~VaAACLYiACR 58 (497)
.+|++.+.+.++.. |+.+...++|.||--++
T Consensus 21 ~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 21 KEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 46777777777776 99999999999999888
No 493
>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=22.57 E-value=93 Score=23.86 Aligned_cols=32 Identities=19% Similarity=0.143 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCcChHHHHHHHHHHHHHhc
Q 010919 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLY 92 (497)
Q Consensus 61 ~~prtL~DIa~v~~vsv~~Lgr~yk~L~~~L~ 92 (497)
+-..++.|+|..++++..+|..-...|...|.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~ 48 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEFFP 48 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 44578999999999999999999888887765
No 494
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=22.53 E-value=1.3e+02 Score=28.17 Aligned_cols=39 Identities=15% Similarity=0.066 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHhcC
Q 010919 153 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 191 (497)
Q Consensus 153 aLylAar~~g~~~t~~eIa~v~~Vse~TIrkr~kE~~~t 191 (497)
.+|+|..-.+-.+|.++||+..+++..-+.+-+..|...
T Consensus 14 l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 14 MLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 455553333456899999999999999999999998654
No 495
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=22.50 E-value=63 Score=33.49 Aligned_cols=35 Identities=17% Similarity=0.116 Sum_probs=26.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 010919 165 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 204 (497)
Q Consensus 165 ~t~~eIa~v~~Vse~TIrkr~kE~~~t~~~~Lt~~ef~~~ 204 (497)
.|++|||+.+|||..|+.+.|+.-. .++.+--.++
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~-----~Vs~eTr~kV 35 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSP-----YVSEETREKV 35 (333)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC-----CCCHHHHHHH
Confidence 3789999999999999999987543 4555544444
No 496
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=22.44 E-value=94 Score=30.64 Aligned_cols=30 Identities=17% Similarity=0.386 Sum_probs=26.3
Q ss_pred cCCCC-CHhhHHHHhccCHHHHHHHHHHHhc
Q 010919 161 HGLKF-SKSDIVKIVHICEATLMKRLIEFEN 190 (497)
Q Consensus 161 ~g~~~-t~~eIa~v~~Vse~TIrkr~kE~~~ 190 (497)
.|.++ |..++|+.+|||..|||..++.|..
T Consensus 29 pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~ 59 (257)
T PRK10225 29 PGERLPPEREIAEMLDVTRTVVREALIMLEI 59 (257)
T ss_pred CCCcCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46778 6999999999999999999999853
No 497
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=22.37 E-value=60 Score=23.57 Aligned_cols=19 Identities=26% Similarity=0.317 Sum_probs=16.5
Q ss_pred hhHHHHhccCHHHHHHHHH
Q 010919 168 SDIVKIVHICEATLMKRLI 186 (497)
Q Consensus 168 ~eIa~v~~Vse~TIrkr~k 186 (497)
++||+.+||+..||.+.++
T Consensus 1 ~~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 1 KDIARAAGVSVATVSRVLN 19 (52)
T ss_pred CcHHHHHCcCHHHHHHHHc
Confidence 3789999999999998775
No 498
>COG4861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.34 E-value=76 Score=32.47 Aligned_cols=54 Identities=9% Similarity=0.047 Sum_probs=37.2
Q ss_pred cccCCCChhHHHHHHHHHHHHhcC----CCCCHhhHHHHhccCHHHHHHHHHHHhcCC
Q 010919 139 WITTGRKPSGLCGAALYVSALTHG----LKFSKSDIVKIVHICEATLMKRLIEFENTD 192 (497)
Q Consensus 139 ~l~~GR~P~~IaaAaLylAar~~g----~~~t~~eIa~v~~Vse~TIrkr~kE~~~t~ 192 (497)
...+||.-+..-.-..-+.+-+.. ++.+.+|||.++||+..|....+..+.++.
T Consensus 134 ~~~~~RpA~~ftp~raqv~~ALL~aP~lv~~P~REIAasAgVsvGTa~~t~d~LrE~G 191 (345)
T COG4861 134 GLHSDRPANPFTPKRAQVVCALLDAPQLVDAPLREIAASAGVSVGTAKETMDTLRETG 191 (345)
T ss_pred cCCCCCCCCCCChhhhhHhHhhhCCHHHhcchHHHHHHhccceechHHHHHHHHHhcc
Confidence 345565544444444444443333 468999999999999999999999887653
No 499
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=22.18 E-value=8.5e+02 Score=24.88 Aligned_cols=120 Identities=11% Similarity=0.032 Sum_probs=65.6
Q ss_pred cCCCCCHHHHHHHhCcChHHHHHH-----------HHHHHHHhcccccccccccCCccchHHHHHhhhCCCCCHHHHHHH
Q 010919 60 KSKPFLLIDFSNYLNINVYELGAV-----------YLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTA 128 (497)
Q Consensus 60 e~~prtL~DIa~v~~vsv~~Lgr~-----------yk~L~~~L~i~~~~~~~~~idP~~~I~Rf~~~L~~~~~~~V~~~A 128 (497)
.....|+.++|+.++++...|++. +.+|.+.|++...-.+....++..-..++...|.. ++++-...+
T Consensus 38 ~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l~~~~~~~~~~~~~l~~~l~~-l~~~~~~~~ 116 (309)
T PRK08154 38 ARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVDTSSPDWLLIRELLEQ-ASPAQLARV 116 (309)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHhCCCCCCChHHHHHHHHHhc-CCHHHHHHH
Confidence 344567788888888888777765 35667777664322111111122222345555532 667666777
Q ss_pred HHHHHHhcc---------ccccCCCChhHHHHHHHHHHHHhcCCC-C-CHhhHHHHhccCHHHH
Q 010919 129 RDILASMKR---------DWITTGRKPSGLCGAALYVSALTHGLK-F-SKSDIVKIVHICEATL 181 (497)
Q Consensus 129 ~~Lv~~~~~---------~~l~~GR~P~~IaaAaLylAar~~g~~-~-t~~eIa~v~~Vse~TI 181 (497)
..+++.+.. ..+++|..-+|=...+-.+|-++ |.+ + +-..|.+..|++...|
T Consensus 117 ~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~La~~L-g~~~id~D~~i~~~~G~~i~ei 179 (309)
T PRK08154 117 RDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARL-GVPFVELNREIEREAGLSVSEI 179 (309)
T ss_pred HHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHHHHHHc-CCCEEeHHHHHHHHhCCCHHHH
Confidence 777766443 22455666555555555555443 443 1 3345666667665544
No 500
>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=22.09 E-value=65 Score=27.20 Aligned_cols=22 Identities=14% Similarity=0.022 Sum_probs=18.6
Q ss_pred CHhhHHHHhccCHHHHHHHHHH
Q 010919 166 SKSDIVKIVHICEATLMKRLIE 187 (497)
Q Consensus 166 t~~eIa~v~~Vse~TIrkr~kE 187 (497)
|..+||+.+|||..|||-.=++
T Consensus 2 ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999865444
Done!