Query 023151
Match_columns 286
No_of_seqs 141 out of 259
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:48:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023151.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023151hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4557 Origin recognition com 100.0 9.6E-59 2.1E-63 412.9 18.7 255 1-276 1-262 (262)
2 COG1405 SUA7 Transcription ini 100.0 5E-38 1.1E-42 293.6 19.2 170 1-183 102-277 (285)
3 PRK00423 tfb transcription ini 100.0 3.4E-33 7.4E-38 263.4 21.2 169 2-183 128-302 (310)
4 KOG1597 Transcription initiati 100.0 2.5E-28 5.5E-33 226.6 18.5 175 2-189 110-292 (308)
5 KOG1598 Transcription initiati 99.7 9.8E-17 2.1E-21 159.2 12.4 170 1-184 72-253 (521)
6 PF00382 TFIIB: Transcription 99.6 3.8E-15 8.3E-20 111.7 8.8 71 3-77 1-71 (71)
7 PF00382 TFIIB: Transcription 99.5 1.6E-13 3.4E-18 103.0 8.9 70 96-174 1-71 (71)
8 PRK00423 tfb transcription ini 99.3 8.7E-12 1.9E-16 118.1 11.2 87 3-93 223-309 (310)
9 PF05460 ORC6: Origin recognit 99.1 1.3E-11 2.9E-16 119.1 0.0 89 3-92 1-89 (353)
10 COG1405 SUA7 Transcription ini 99.0 1E-09 2.2E-14 103.4 9.3 88 2-93 197-284 (285)
11 TIGR00569 ccl1 cyclin ccl1. Un 98.9 1.1E-07 2.3E-12 90.5 18.3 167 3-183 63-250 (305)
12 cd00043 CYCLIN Cyclin box fold 98.6 3.1E-07 6.7E-12 67.8 9.7 78 3-84 9-87 (88)
13 smart00385 CYCLIN domain prese 98.6 3.2E-07 6.9E-12 67.2 9.3 79 95-182 2-82 (83)
14 smart00385 CYCLIN domain prese 98.6 2.9E-07 6.3E-12 67.4 9.1 79 3-85 3-82 (83)
15 cd00043 CYCLIN Cyclin box fold 98.4 3E-06 6.4E-11 62.5 9.8 78 95-181 8-87 (88)
16 KOG1597 Transcription initiati 98.3 3E-06 6.5E-11 79.9 8.7 82 3-88 207-288 (308)
17 KOG0834 CDK9 kinase-activating 98.2 1.3E-05 2.9E-10 76.9 11.6 168 3-183 46-243 (323)
18 COG5333 CCL1 Cdk activating ki 98.1 3.4E-05 7.3E-10 73.2 11.7 146 3-161 52-213 (297)
19 KOG0835 Cyclin L [General func 97.8 0.001 2.2E-08 64.0 15.3 167 9-187 36-231 (367)
20 KOG0794 CDK8 kinase-activating 97.5 0.0015 3.3E-08 60.3 11.6 166 3-182 48-235 (264)
21 KOG1598 Transcription initiati 96.6 0.003 6.6E-08 64.0 5.5 89 4-94 171-260 (521)
22 PF00134 Cyclin_N: Cyclin, N-t 96.3 0.032 7E-07 44.7 9.0 85 3-91 38-125 (127)
23 PF02984 Cyclin_C: Cyclin, C-t 96.2 0.018 3.8E-07 45.3 6.5 83 95-186 6-90 (118)
24 KOG2496 Cdk activating kinase 96.0 0.1 2.3E-06 50.0 11.7 57 11-71 73-129 (325)
25 PF01857 RB_B: Retinoblastoma- 95.4 0.077 1.7E-06 45.1 7.7 78 3-82 18-95 (135)
26 TIGR00569 ccl1 cyclin ccl1. Un 94.5 0.21 4.7E-06 47.8 9.0 67 95-170 62-131 (305)
27 KOG4557 Origin recognition com 93.0 0.74 1.6E-05 42.5 9.2 82 95-183 2-86 (262)
28 PF02984 Cyclin_C: Cyclin, C-t 92.6 0.51 1.1E-05 36.9 6.8 71 17-89 19-90 (118)
29 PF00134 Cyclin_N: Cyclin, N-t 91.9 1.2 2.6E-05 35.5 8.2 78 95-181 37-118 (127)
30 COG1191 FliA DNA-directed RNA 90.3 16 0.00034 34.2 16.1 151 17-181 53-236 (247)
31 KOG0656 G1/S-specific cyclin D 89.5 3 6.5E-05 40.7 9.9 163 7-187 89-268 (335)
32 COG5024 Cyclin [Cell division 89.3 2.1 4.6E-05 43.2 9.0 170 7-189 224-403 (440)
33 TIGR02393 RpoD_Cterm RNA polym 88.6 9 0.0002 34.6 11.9 28 155-182 194-221 (238)
34 smart00342 HTH_ARAC helix_turn 87.6 4.1 8.9E-05 29.2 7.5 25 157-181 50-75 (84)
35 KOG0834 CDK9 kinase-activating 86.7 2.6 5.6E-05 40.9 7.5 78 95-181 45-127 (323)
36 KOG0835 Cyclin L [General func 85.3 1.2 2.6E-05 43.4 4.4 75 7-83 149-225 (367)
37 PF13412 HTH_24: Winged helix- 85.1 2.3 4.9E-05 28.9 4.7 29 155-183 15-43 (48)
38 PF00325 Crp: Bacterial regula 85.0 1.2 2.7E-05 28.9 3.1 27 157-183 2-28 (32)
39 cd06571 Bac_DnaA_C C-terminal 83.8 5.6 0.00012 30.9 7.0 73 17-91 3-76 (90)
40 TIGR02997 Sig70-cyanoRpoD RNA 83.1 16 0.00035 34.3 11.1 27 155-181 267-293 (298)
41 PF13545 HTH_Crp_2: Crp-like h 82.8 1.9 4.1E-05 31.6 3.8 28 156-183 27-54 (76)
42 PRK07405 RNA polymerase sigma 82.4 14 0.00031 35.3 10.5 27 155-181 274-300 (317)
43 PRK07598 RNA polymerase sigma 82.1 17 0.00037 36.4 11.3 112 57-181 275-394 (415)
44 COG0177 Nth Predicted EndoIII- 80.4 10 0.00022 34.8 8.3 47 58-107 103-152 (211)
45 TIGR03697 NtcA_cyano global ni 79.9 4.7 0.0001 34.2 5.7 29 155-183 141-169 (193)
46 PF13404 HTH_AsnC-type: AsnC-t 79.2 4.4 9.4E-05 27.6 4.2 30 153-182 13-42 (42)
47 PRK11179 DNA-binding transcrip 79.2 3.6 7.8E-05 34.9 4.7 39 150-193 16-54 (153)
48 PF05460 ORC6: Origin recognit 78.9 0.63 1.4E-05 45.4 0.0 79 97-183 2-83 (353)
49 PF12802 MarR_2: MarR family; 78.7 6.3 0.00014 27.6 5.2 45 137-183 3-47 (62)
50 PRK11169 leucine-responsive tr 78.4 4 8.6E-05 35.1 4.8 39 150-193 21-59 (164)
51 cd00092 HTH_CRP helix_turn_hel 77.7 9.4 0.0002 26.9 5.9 29 155-183 23-51 (67)
52 PRK09210 RNA polymerase sigma 77.6 28 0.00061 33.9 11.0 26 156-181 324-349 (367)
53 PF01325 Fe_dep_repress: Iron 77.6 7.4 0.00016 28.3 5.4 37 146-183 12-48 (60)
54 KOG0794 CDK8 kinase-activating 76.5 7.6 0.00017 36.4 6.3 73 95-189 47-120 (264)
55 TIGR01610 phage_O_Nterm phage 76.1 12 0.00026 29.5 6.6 37 154-195 44-80 (95)
56 PF03444 HrcA_DNA-bdg: Winged 76.1 5.3 0.00011 31.2 4.4 34 155-193 21-54 (78)
57 PF13730 HTH_36: Helix-turn-he 76.1 14 0.00031 25.4 6.3 27 157-183 25-51 (55)
58 PRK05949 RNA polymerase sigma 76.0 32 0.0007 33.1 10.8 27 155-181 284-310 (327)
59 smart00345 HTH_GNTR helix_turn 76.0 5.6 0.00012 27.2 4.2 29 155-183 17-46 (60)
60 PF01857 RB_B: Retinoblastoma- 75.5 17 0.00037 30.9 7.8 79 96-181 18-97 (135)
61 smart00419 HTH_CRP helix_turn_ 75.2 5.3 0.00012 26.3 3.8 28 156-183 7-34 (48)
62 PF08613 Cyclin: Cyclin; Inte 75.1 44 0.00096 28.2 10.3 86 3-90 58-147 (149)
63 TIGR02392 rpoH_proteo alternat 74.7 49 0.0011 30.5 11.4 31 155-185 234-264 (270)
64 PRK07406 RNA polymerase sigma 74.7 35 0.00077 33.6 10.8 26 156-181 330-355 (373)
65 PF08279 HTH_11: HTH domain; 74.6 5.6 0.00012 27.5 3.9 32 153-184 11-42 (55)
66 TIGR03697 NtcA_cyano global ni 74.5 14 0.00031 31.2 7.2 49 39-87 112-170 (193)
67 PRK05901 RNA polymerase sigma 74.4 82 0.0018 32.5 13.7 27 155-181 465-491 (509)
68 TIGR02980 SigBFG RNA polymeras 73.8 64 0.0014 28.5 12.5 30 156-185 193-222 (227)
69 PRK11161 fumarate/nitrate redu 73.6 7.1 0.00015 34.5 5.3 35 156-195 183-217 (235)
70 PF13384 HTH_23: Homeodomain-l 73.5 6.1 0.00013 26.8 3.8 27 157-183 17-43 (50)
71 smart00342 HTH_ARAC helix_turn 73.3 17 0.00037 25.9 6.4 71 2-84 3-75 (84)
72 PRK07122 RNA polymerase sigma 73.2 45 0.00097 30.9 10.7 165 5-183 55-257 (264)
73 PRK11753 DNA-binding transcrip 72.4 9.7 0.00021 32.8 5.7 28 156-183 167-194 (211)
74 PF08280 HTH_Mga: M protein tr 71.0 4.6 9.9E-05 29.1 2.8 42 75-117 2-44 (59)
75 KOG0653 Cyclin B and related k 70.7 48 0.001 32.7 10.7 154 5-172 167-332 (391)
76 PF09756 DDRGK: DDRGK domain; 70.0 3.1 6.7E-05 37.4 2.1 83 80-168 100-184 (188)
77 COG1522 Lrp Transcriptional re 69.7 8.6 0.00019 31.8 4.6 36 155-195 20-55 (154)
78 TIGR02850 spore_sigG RNA polym 68.9 69 0.0015 29.2 10.8 28 156-183 221-248 (254)
79 PF13542 HTH_Tnp_ISL3: Helix-t 68.6 16 0.00034 24.9 5.0 39 142-180 12-50 (52)
80 PF00325 Crp: Bacterial regula 68.1 7.1 0.00015 25.4 2.9 28 59-86 1-28 (32)
81 PRK13918 CRP/FNR family transc 67.6 7.1 0.00015 33.5 3.8 34 155-193 147-180 (202)
82 PF13936 HTH_38: Helix-turn-he 67.0 9 0.0002 26.0 3.5 28 152-179 15-42 (44)
83 PRK06596 RNA polymerase factor 66.8 91 0.002 29.1 11.4 33 75-107 133-165 (284)
84 PRK07921 RNA polymerase sigma 66.5 84 0.0018 30.3 11.3 27 155-181 280-306 (324)
85 KOG4164 Cyclin ik3-1/CABLES [C 66.4 15 0.00033 36.9 6.2 53 2-58 388-440 (497)
86 PRK06986 fliA flagellar biosyn 66.3 90 0.0019 27.9 10.9 28 156-183 199-226 (236)
87 PRK09863 putative frv operon r 66.2 56 0.0012 33.5 10.6 36 152-187 87-122 (584)
88 PRK05657 RNA polymerase sigma 65.9 68 0.0015 30.8 10.5 32 155-186 280-311 (325)
89 COG1476 Predicted transcriptio 65.6 6 0.00013 30.1 2.6 25 156-180 13-37 (68)
90 PF13613 HTH_Tnp_4: Helix-turn 65.3 12 0.00026 26.3 4.0 38 147-184 9-46 (53)
91 PF01381 HTH_3: Helix-turn-hel 65.3 7.1 0.00015 26.8 2.7 26 155-180 7-32 (55)
92 PF02082 Rrf2: Transcriptional 64.8 12 0.00025 28.5 4.1 45 146-195 14-58 (83)
93 TIGR03070 couple_hipB transcri 64.6 8 0.00017 26.2 2.9 25 155-179 13-37 (58)
94 PRK00135 scpB segregation and 64.4 39 0.00086 30.2 8.0 120 43-183 6-127 (188)
95 PF13545 HTH_Crp_2: Crp-like h 64.4 8.9 0.00019 28.0 3.3 29 59-87 27-55 (76)
96 smart00344 HTH_ASNC helix_turn 64.4 14 0.0003 28.9 4.6 29 155-183 15-43 (108)
97 PRK06288 RNA polymerase sigma 64.1 96 0.0021 28.5 10.8 26 156-181 227-252 (268)
98 COG5333 CCL1 Cdk activating ki 63.7 3.5 7.7E-05 39.6 1.2 64 83-155 37-103 (297)
99 PRK12427 flagellar biosynthesi 63.5 1.2E+02 0.0025 27.5 11.8 152 17-182 47-224 (231)
100 PF13744 HTH_37: Helix-turn-he 63.4 15 0.00032 27.9 4.5 31 149-179 23-53 (80)
101 PRK09391 fixK transcriptional 63.4 9.4 0.0002 34.1 3.9 29 155-183 177-205 (230)
102 PRK11512 DNA-binding transcrip 62.3 29 0.00064 28.7 6.5 53 136-197 37-89 (144)
103 PF01371 Trp_repressor: Trp re 62.1 14 0.0003 29.2 4.2 36 148-183 39-75 (87)
104 PRK07500 rpoH2 RNA polymerase 61.9 1.4E+02 0.0031 28.0 12.4 32 155-186 243-274 (289)
105 PF13443 HTH_26: Cro/C1-type H 61.7 7.9 0.00017 27.4 2.5 24 157-180 10-33 (63)
106 PRK08215 sporulation sigma fac 61.5 87 0.0019 28.5 10.0 27 156-182 224-250 (258)
107 TIGR02394 rpoS_proteo RNA poly 61.4 83 0.0018 29.2 10.0 29 155-183 240-268 (285)
108 PRK03573 transcriptional regul 60.3 44 0.00096 27.5 7.2 59 137-203 29-87 (144)
109 PRK13719 conjugal transfer tra 60.3 26 0.00057 32.3 6.2 60 58-117 156-216 (217)
110 COG1510 Predicted transcriptio 60.0 15 0.00033 32.8 4.5 40 47-86 28-67 (177)
111 PF13022 HTH_Tnp_1_2: Helix-tu 59.8 28 0.00061 30.1 5.9 42 137-178 11-55 (142)
112 TIGR01321 TrpR trp operon repr 59.7 11 0.00025 30.3 3.3 32 151-182 49-80 (94)
113 PRK13918 CRP/FNR family transc 59.7 55 0.0012 27.9 7.9 49 39-87 118-176 (202)
114 PRK05911 RNA polymerase sigma 59.6 88 0.0019 28.7 9.7 169 3-184 36-248 (257)
115 PRK07408 RNA polymerase sigma 59.6 95 0.0021 28.4 9.9 30 156-185 218-247 (256)
116 PRK05572 sporulation sigma fac 59.3 1.1E+02 0.0024 27.8 10.2 30 156-185 217-246 (252)
117 TIGR03879 near_KaiC_dom probab 59.1 22 0.00047 27.4 4.6 28 156-183 31-58 (73)
118 PF00392 GntR: Bacterial regul 59.0 15 0.00033 26.4 3.6 37 154-195 20-57 (64)
119 TIGR01889 Staph_reg_Sar staphy 58.7 44 0.00094 26.6 6.6 54 137-197 23-78 (109)
120 TIGR02479 FliA_WhiG RNA polyme 58.4 99 0.0021 27.4 9.6 26 156-181 190-215 (224)
121 TIGR02885 spore_sigF RNA polym 58.3 1.2E+02 0.0025 27.0 10.0 28 156-183 198-225 (231)
122 smart00420 HTH_DEOR helix_turn 58.1 40 0.00086 22.1 5.5 28 156-183 13-40 (53)
123 PF04545 Sigma70_r4: Sigma-70, 58.0 21 0.00046 24.3 4.1 27 155-181 18-44 (50)
124 PHA01976 helix-turn-helix prot 57.5 13 0.00027 26.6 3.0 25 155-179 13-37 (67)
125 PF13443 HTH_26: Cro/C1-type H 57.2 30 0.00066 24.3 5.0 40 62-107 12-54 (63)
126 TIGR02297 HpaA 4-hydroxyphenyl 55.7 95 0.0021 28.1 9.2 32 51-83 194-225 (287)
127 PF13560 HTH_31: Helix-turn-he 55.6 13 0.00027 26.7 2.7 25 155-179 12-36 (64)
128 cd07377 WHTH_GntR Winged helix 55.6 20 0.00044 24.8 3.8 25 159-183 27-51 (66)
129 PRK10402 DNA-binding transcrip 55.5 17 0.00036 32.3 4.1 27 157-183 169-195 (226)
130 PF13518 HTH_28: Helix-turn-he 55.3 32 0.00069 23.0 4.6 26 158-183 13-38 (52)
131 PF00126 HTH_1: Bacterial regu 55.3 24 0.00053 25.0 4.2 30 62-91 15-44 (60)
132 PRK11014 transcriptional repre 55.1 23 0.00051 29.5 4.7 46 146-196 14-59 (141)
133 PF00196 GerE: Bacterial regul 55.0 16 0.00035 25.7 3.2 37 58-94 16-52 (58)
134 TIGR01764 excise DNA binding d 54.9 16 0.00035 23.8 3.0 23 158-180 2-24 (49)
135 PF01047 MarR: MarR family; I 54.7 29 0.00063 24.0 4.5 27 157-183 17-43 (59)
136 KOG0656 G1/S-specific cyclin D 53.6 34 0.00075 33.5 6.1 58 95-158 84-142 (335)
137 PF01418 HTH_6: Helix-turn-hel 53.6 22 0.00047 26.8 3.9 43 139-181 16-58 (77)
138 cd04762 HTH_MerR-trunc Helix-T 52.8 19 0.00041 23.3 3.1 22 159-180 2-23 (49)
139 PF13463 HTH_27: Winged helix 52.7 37 0.0008 24.0 4.8 38 153-195 14-51 (68)
140 PF01978 TrmB: Sugar-specific 52.6 18 0.00039 26.2 3.2 44 146-195 12-55 (68)
141 PF08279 HTH_11: HTH domain; 52.5 30 0.00065 23.8 4.2 16 92-107 14-29 (55)
142 PRK04217 hypothetical protein; 52.5 30 0.00066 28.5 4.8 34 156-189 57-90 (110)
143 PRK10072 putative transcriptio 52.3 17 0.00036 29.2 3.2 27 153-179 42-68 (96)
144 COG1725 Predicted transcriptio 52.1 21 0.00046 30.1 3.9 34 158-196 36-69 (125)
145 PRK11161 fumarate/nitrate redu 52.1 61 0.0013 28.5 7.1 28 59-86 183-210 (235)
146 PF02001 DUF134: Protein of un 52.0 19 0.00041 29.6 3.5 29 155-183 55-83 (106)
147 cd00092 HTH_CRP helix_turn_hel 51.5 68 0.0015 22.3 6.1 28 59-86 24-51 (67)
148 PRK11753 DNA-binding transcrip 51.4 76 0.0017 27.2 7.5 29 59-87 167-195 (211)
149 PF10668 Phage_terminase: Phag 51.3 21 0.00046 26.5 3.3 35 142-179 10-44 (60)
150 PHA00542 putative Cro-like pro 51.2 18 0.00039 27.7 3.1 27 154-180 28-54 (82)
151 PF02796 HTH_7: Helix-turn-hel 50.8 11 0.00023 25.6 1.6 29 151-179 15-43 (45)
152 PF01381 HTH_3: Helix-turn-hel 50.8 26 0.00056 23.8 3.6 41 60-107 9-52 (55)
153 PF00392 GntR: Bacterial regul 50.2 46 0.001 23.8 5.0 42 77-118 2-50 (64)
154 PRK06030 hypothetical protein; 50.1 90 0.0019 26.2 7.4 71 16-88 26-97 (124)
155 TIGR02607 antidote_HigA addict 50.1 19 0.00042 26.3 3.0 27 153-179 14-40 (78)
156 smart00354 HTH_LACI helix_turn 50.1 20 0.00043 26.4 3.1 23 158-180 1-23 (70)
157 PF13730 HTH_36: Helix-turn-he 50.1 80 0.0017 21.5 6.5 25 62-86 27-51 (55)
158 PRK10870 transcriptional repre 50.0 51 0.0011 28.7 6.2 55 137-198 53-107 (176)
159 smart00421 HTH_LUXR helix_turn 49.9 57 0.0012 21.4 5.2 26 157-182 18-43 (58)
160 cd00171 Sec7 Sec7 domain; Doma 49.4 1.8E+02 0.004 25.5 15.0 119 59-182 45-181 (185)
161 cd02418 Peptidase_C39B A sub-f 48.9 27 0.00058 27.8 4.0 32 41-72 8-39 (136)
162 PF07900 DUF1670: Protein of u 48.9 58 0.0013 30.1 6.5 27 158-184 106-132 (220)
163 PF07471 Phage_Nu1: Phage DNA 48.5 10 0.00022 33.3 1.5 25 156-180 1-25 (164)
164 smart00419 HTH_CRP helix_turn_ 48.3 35 0.00076 22.2 3.8 29 58-86 6-34 (48)
165 TIGR02337 HpaR homoprotocatech 48.3 56 0.0012 26.0 5.8 44 136-183 25-68 (118)
166 PRK09391 fixK transcriptional 48.1 89 0.0019 27.8 7.6 48 40-87 153-206 (230)
167 PRK09726 antitoxin HipB; Provi 48.0 20 0.00043 27.6 2.9 27 154-180 22-48 (88)
168 cd02423 Peptidase_C39G A sub-f 47.7 36 0.00078 26.8 4.5 38 35-72 2-40 (129)
169 COG1318 Predicted transcriptio 47.6 34 0.00074 30.7 4.6 28 154-181 58-85 (182)
170 COG0533 QRI7 Metal-dependent p 47.4 54 0.0012 32.2 6.4 96 74-195 157-254 (342)
171 PF12728 HTH_17: Helix-turn-he 47.3 24 0.00051 24.0 3.0 22 158-179 2-23 (51)
172 cd00090 HTH_ARSR Arsenical Res 47.1 59 0.0013 22.3 5.1 26 158-183 21-46 (78)
173 cd04761 HTH_MerR-SF Helix-Turn 47.1 20 0.00044 23.7 2.5 22 159-180 2-23 (49)
174 PF08220 HTH_DeoR: DeoR-like h 47.0 30 0.00065 24.6 3.5 29 155-183 12-40 (57)
175 smart00530 HTH_XRE Helix-turn- 46.9 25 0.00055 22.1 3.0 25 154-178 7-31 (56)
176 PRK10402 DNA-binding transcrip 46.8 55 0.0012 29.0 6.0 47 41-87 150-196 (226)
177 COG1725 Predicted transcriptio 46.6 23 0.00049 30.0 3.2 25 94-118 36-61 (125)
178 PF02954 HTH_8: Bacterial regu 46.5 25 0.00054 23.5 2.9 23 158-180 19-41 (42)
179 PF09339 HTH_IclR: IclR helix- 46.3 40 0.00086 23.2 4.0 28 156-183 17-44 (52)
180 cd06170 LuxR_C_like C-terminal 46.1 54 0.0012 21.8 4.6 34 60-93 15-48 (57)
181 PF12651 RHH_3: Ribbon-helix-h 46.0 18 0.00039 24.8 2.1 24 2-26 16-39 (44)
182 PF03412 Peptidase_C39: Peptid 45.6 15 0.00033 29.3 2.0 58 36-107 4-61 (131)
183 PRK13777 transcriptional regul 45.4 65 0.0014 28.7 6.2 52 136-196 42-93 (185)
184 cd02421 Peptidase_C39_likeD A 45.1 29 0.00063 27.3 3.6 48 46-93 8-56 (124)
185 PF13551 HTH_29: Winged helix- 45.0 1.4E+02 0.003 22.8 8.7 82 96-180 15-110 (112)
186 smart00421 HTH_LUXR helix_turn 44.8 46 0.00099 21.9 4.1 33 61-93 19-51 (58)
187 PF02082 Rrf2: Transcriptional 44.8 45 0.00097 25.2 4.4 14 94-107 26-39 (83)
188 PRK00118 putative DNA-binding 44.8 42 0.00091 27.4 4.5 33 157-189 33-65 (104)
189 TIGR00122 birA_repr_reg BirA b 44.1 57 0.0012 23.6 4.7 34 153-186 9-42 (69)
190 cd02420 Peptidase_C39D A sub-f 43.7 42 0.0009 26.4 4.3 28 45-72 12-39 (125)
191 PF04539 Sigma70_r3: Sigma-70 43.6 75 0.0016 23.3 5.4 31 75-107 4-34 (78)
192 PRK09483 response regulator; P 43.5 50 0.0011 27.8 5.0 45 61-105 164-208 (217)
193 COG1510 Predicted transcriptio 42.6 1.3E+02 0.0029 27.0 7.5 45 146-195 30-74 (177)
194 PRK09392 ftrB transcriptional 42.5 29 0.00062 30.7 3.5 29 155-183 171-199 (236)
195 TIGR02941 Sigma_B RNA polymera 42.5 2.6E+02 0.0056 25.3 12.1 26 156-181 220-245 (255)
196 PHA02591 hypothetical protein; 42.3 33 0.00071 27.0 3.3 31 149-179 51-81 (83)
197 PF08281 Sigma70_r4_2: Sigma-7 41.8 45 0.00097 22.8 3.7 26 157-182 26-51 (54)
198 PHA01976 helix-turn-helix prot 41.7 43 0.00093 23.8 3.7 41 61-107 16-58 (67)
199 PRK09706 transcriptional repre 41.7 27 0.00059 28.8 3.0 27 154-180 15-41 (135)
200 smart00550 Zalpha Z-DNA-bindin 41.7 84 0.0018 23.1 5.3 37 147-183 11-48 (68)
201 COG3093 VapI Plasmid maintenan 40.9 31 0.00066 28.4 3.1 25 156-180 22-46 (104)
202 PF00165 HTH_AraC: Bacterial r 40.5 48 0.001 21.7 3.5 26 156-181 7-32 (42)
203 PF05225 HTH_psq: helix-turn-h 40.3 69 0.0015 21.9 4.4 30 151-181 11-40 (45)
204 PF00356 LacI: Bacterial regul 39.9 34 0.00073 23.7 2.7 21 62-82 1-21 (46)
205 PRK09958 DNA-binding transcrip 39.7 65 0.0014 26.7 5.1 43 62-104 160-202 (204)
206 PRK00149 dnaA chromosomal repl 39.6 92 0.002 30.9 6.9 75 16-92 360-435 (450)
207 smart00418 HTH_ARSR helix_turn 39.5 61 0.0013 21.6 4.1 29 155-183 8-36 (66)
208 PF00165 HTH_AraC: Bacterial r 39.5 51 0.0011 21.5 3.6 30 58-90 6-35 (42)
209 TIGR02787 codY_Gpos GTP-sensin 39.5 1.7E+02 0.0037 27.7 8.1 78 108-195 153-231 (251)
210 COG3355 Predicted transcriptio 39.5 1.5E+02 0.0034 25.0 7.2 56 58-117 10-68 (126)
211 TIGR02010 IscR iron-sulfur clu 39.4 71 0.0015 26.4 5.2 39 48-86 13-51 (135)
212 PF06971 Put_DNA-bind_N: Putat 39.0 24 0.00053 25.1 2.0 21 156-176 27-47 (50)
213 KOG3054 Uncharacterized conser 39.0 1.2E+02 0.0026 28.8 7.0 84 79-168 200-285 (299)
214 PF14502 HTH_41: Helix-turn-he 38.8 51 0.0011 23.5 3.5 25 94-118 7-32 (48)
215 cd02417 Peptidase_C39_likeA A 38.6 53 0.0012 25.6 4.1 27 46-72 8-34 (121)
216 PF13551 HTH_29: Winged helix- 38.5 50 0.0011 25.4 3.9 30 154-183 8-38 (112)
217 PF09339 HTH_IclR: IclR helix- 38.5 57 0.0012 22.4 3.8 27 59-85 17-43 (52)
218 cd00093 HTH_XRE Helix-turn-hel 38.5 49 0.0011 20.9 3.3 25 155-179 10-34 (58)
219 PF00356 LacI: Bacterial regul 38.5 43 0.00093 23.2 3.1 21 160-180 2-22 (46)
220 PRK09935 transcriptional regul 38.3 68 0.0015 26.5 5.0 42 61-102 165-206 (210)
221 TIGR02684 dnstrm_HI1420 probab 38.3 1.6E+02 0.0035 23.1 6.8 72 20-107 15-86 (89)
222 TIGR01610 phage_O_Nterm phage 38.2 1.2E+02 0.0026 23.7 6.1 30 57-86 44-73 (95)
223 PRK12523 RNA polymerase sigma 38.2 57 0.0012 27.4 4.5 43 147-191 127-169 (172)
224 PRK13509 transcriptional repre 38.1 46 0.00099 30.6 4.2 29 155-183 17-45 (251)
225 PRK15121 right oriC-binding tr 38.1 3.3E+02 0.0071 25.1 10.4 56 56-112 17-89 (289)
226 PRK05658 RNA polymerase sigma 38.0 2.3E+02 0.0049 29.7 9.7 150 17-181 409-600 (619)
227 TIGR02366 DHAK_reg probable di 38.0 59 0.0013 27.2 4.6 48 142-189 8-55 (176)
228 TIGR02702 SufR_cyano iron-sulf 37.9 92 0.002 27.5 6.0 33 157-194 15-47 (203)
229 PRK12525 RNA polymerase sigma 37.9 56 0.0012 27.4 4.4 33 157-189 134-166 (168)
230 PF08299 Bac_DnaA_C: Bacterial 37.5 1.2E+02 0.0026 22.5 5.7 66 17-84 4-70 (70)
231 PRK15340 transcriptional regul 37.4 1.6E+02 0.0034 27.1 7.5 88 17-112 97-193 (216)
232 smart00550 Zalpha Z-DNA-bindin 37.3 96 0.0021 22.8 5.1 26 61-86 23-48 (68)
233 cd04763 HTH_MlrA-like Helix-Tu 37.2 39 0.00085 24.4 2.9 22 160-181 3-24 (68)
234 cd02419 Peptidase_C39C A sub-f 37.2 59 0.0013 25.5 4.3 28 45-72 12-39 (127)
235 PRK10086 DNA-binding transcrip 37.1 1.4E+02 0.0031 27.4 7.3 56 61-121 29-90 (311)
236 PRK10219 DNA-binding transcrip 37.0 2E+02 0.0043 22.3 8.4 27 57-83 18-44 (107)
237 PRK15369 two component system 37.0 82 0.0018 25.6 5.2 43 62-104 166-208 (211)
238 TIGR00637 ModE_repress ModE mo 36.6 67 0.0014 25.6 4.4 31 61-91 17-47 (99)
239 cd06171 Sigma70_r4 Sigma70, re 36.4 79 0.0017 20.2 4.1 27 156-182 25-51 (55)
240 TIGR03830 CxxCG_CxxCG_HTH puta 36.3 41 0.00088 26.9 3.2 28 152-179 73-100 (127)
241 TIGR02405 trehalos_R_Ecol treh 35.8 35 0.00075 31.2 3.0 23 157-179 1-23 (311)
242 PRK11511 DNA-binding transcrip 35.7 1.4E+02 0.0031 24.3 6.4 39 142-181 11-49 (127)
243 cd06170 LuxR_C_like C-terminal 35.7 79 0.0017 20.9 4.1 27 157-183 15-41 (57)
244 TIGR02944 suf_reg_Xantho FeS a 35.5 1.3E+02 0.0028 24.4 6.1 49 142-195 10-58 (130)
245 PF00376 MerR: MerR family reg 35.5 40 0.00088 22.3 2.5 19 161-179 3-21 (38)
246 cd04764 HTH_MlrA-like_sg1 Heli 35.4 45 0.00097 23.9 3.0 21 161-181 4-24 (67)
247 PRK11242 DNA-binding transcrip 35.2 1.1E+02 0.0025 27.3 6.3 56 61-121 16-77 (296)
248 PRK12529 RNA polymerase sigma 35.2 63 0.0014 27.5 4.3 33 156-188 142-174 (178)
249 PF08220 HTH_DeoR: DeoR-like h 35.1 64 0.0014 22.9 3.7 29 84-112 5-34 (57)
250 PRK10219 DNA-binding transcrip 35.1 1.7E+02 0.0036 22.7 6.5 40 141-181 6-45 (107)
251 PRK11511 DNA-binding transcrip 35.0 2.5E+02 0.0054 22.8 10.5 51 57-110 22-91 (127)
252 PF05930 Phage_AlpA: Prophage 34.9 47 0.001 23.0 2.9 22 158-179 4-25 (51)
253 PRK14088 dnaA chromosomal repl 34.9 1.4E+02 0.0029 30.0 7.2 70 17-88 346-415 (440)
254 PF12844 HTH_19: Helix-turn-he 34.7 42 0.00091 23.6 2.7 26 155-180 10-35 (64)
255 cd02259 Peptidase_C39_like Pep 34.5 64 0.0014 24.9 4.0 28 44-71 6-33 (122)
256 PRK09801 transcriptional activ 34.5 1.5E+02 0.0033 27.4 7.1 55 62-121 22-82 (310)
257 PF00196 GerE: Bacterial regul 34.5 1E+02 0.0022 21.4 4.7 28 156-183 17-44 (58)
258 cd00569 HTH_Hin_like Helix-tur 34.3 61 0.0013 18.4 3.1 20 158-177 22-41 (42)
259 PRK11920 rirA iron-responsive 34.2 1.3E+02 0.0027 25.8 6.0 50 141-196 8-58 (153)
260 PF00288 GHMP_kinases_N: GHMP 34.1 70 0.0015 22.9 3.8 30 41-70 16-45 (67)
261 PF01022 HTH_5: Bacterial regu 33.9 1E+02 0.0022 20.7 4.4 32 152-183 10-41 (47)
262 PF01726 LexA_DNA_bind: LexA D 33.8 62 0.0013 23.9 3.5 29 57-85 22-51 (65)
263 PRK09954 putative kinase; Prov 33.4 72 0.0016 30.3 4.9 29 155-183 15-43 (362)
264 PRK10411 DNA-binding transcrip 33.3 56 0.0012 29.9 3.9 28 156-183 17-44 (240)
265 PF05269 Phage_CII: Bacterioph 33.3 24 0.00052 28.3 1.3 26 158-183 24-49 (91)
266 PRK10341 DNA-binding transcrip 33.3 1.4E+02 0.0029 27.5 6.5 55 61-120 22-82 (312)
267 PF06056 Terminase_5: Putative 33.2 74 0.0016 23.1 3.8 32 143-180 5-36 (58)
268 cd01104 HTH_MlrA-CarA Helix-Tu 32.8 57 0.0012 23.1 3.2 23 159-181 2-24 (68)
269 PF12181 MogR_DNAbind: DNA bin 32.8 72 0.0016 27.5 4.1 99 95-195 18-128 (148)
270 smart00346 HTH_ICLR helix_turn 32.6 1.7E+02 0.0036 21.7 5.9 28 156-183 19-46 (91)
271 PRK13890 conjugal transfer pro 32.6 46 0.00099 27.4 2.9 25 156-180 17-41 (120)
272 TIGR03338 phnR_burk phosphonat 32.5 57 0.0012 28.4 3.7 36 155-195 32-67 (212)
273 PRK14165 winged helix-turn-hel 32.4 63 0.0014 29.6 4.1 34 150-183 14-47 (217)
274 PRK13503 transcriptional activ 32.4 1.2E+02 0.0026 27.2 5.9 31 58-91 185-215 (278)
275 TIGR03418 chol_sulf_TF putativ 32.1 1.7E+02 0.0038 26.2 7.0 55 62-121 17-77 (291)
276 PF01978 TrmB: Sugar-specific 32.1 49 0.0011 23.8 2.7 29 58-86 20-48 (68)
277 PRK03975 tfx putative transcri 32.0 73 0.0016 27.4 4.1 26 156-181 20-45 (141)
278 TIGR00721 tfx DNA-binding prot 31.9 66 0.0014 27.5 3.9 27 156-182 20-46 (137)
279 PRK09651 RNA polymerase sigma 31.9 76 0.0016 26.8 4.3 31 156-186 134-164 (172)
280 cd02424 Peptidase_C39E A sub-f 31.8 86 0.0019 25.1 4.4 33 41-73 8-41 (129)
281 PRK09492 treR trehalose repres 31.7 47 0.001 30.2 3.2 25 156-180 3-27 (315)
282 PF02509 Rota_NS35: Rotavirus 31.3 28 0.00061 33.2 1.6 55 119-177 57-111 (316)
283 PF12793 SgrR_N: Sugar transpo 31.1 1E+02 0.0022 25.4 4.7 41 89-131 15-55 (115)
284 PF04967 HTH_10: HTH DNA bindi 31.1 96 0.0021 22.3 4.0 26 157-182 23-48 (53)
285 TIGR00738 rrf2_super rrf2 fami 31.1 1.5E+02 0.0033 23.8 5.8 42 142-183 9-51 (132)
286 PF04703 FaeA: FaeA-like prote 31.0 66 0.0014 23.8 3.3 29 155-183 13-41 (62)
287 PRK14997 LysR family transcrip 30.9 1.8E+02 0.004 26.3 6.9 55 61-120 17-77 (301)
288 TIGR00498 lexA SOS regulatory 30.8 1.1E+02 0.0025 26.5 5.4 32 152-183 20-52 (199)
289 COG2771 CsgD DNA-binding HTH d 30.8 1.5E+02 0.0033 20.3 5.1 44 61-104 20-63 (65)
290 PRK09392 ftrB transcriptional 30.6 1.5E+02 0.0033 26.0 6.2 48 40-87 147-200 (236)
291 PF05732 RepL: Firmicute plasm 30.6 60 0.0013 28.4 3.5 27 157-183 75-101 (165)
292 PRK10130 transcriptional regul 30.5 4.9E+02 0.011 25.3 10.1 58 55-112 251-327 (350)
293 cd02425 Peptidase_C39F A sub-f 30.4 93 0.002 24.2 4.3 28 45-72 12-39 (126)
294 COG2512 Predicted membrane-ass 30.4 50 0.0011 31.0 3.2 41 151-196 204-244 (258)
295 TIGR02010 IscR iron-sulfur clu 30.3 1.1E+02 0.0023 25.3 4.8 50 141-195 8-58 (135)
296 PF07022 Phage_CI_repr: Bacter 30.2 28 0.00061 25.4 1.2 20 159-178 14-34 (66)
297 smart00422 HTH_MERR helix_turn 30.1 51 0.0011 23.4 2.5 20 160-179 3-22 (70)
298 PRK10857 DNA-binding transcrip 30.1 1.2E+02 0.0026 26.4 5.2 39 48-86 13-51 (164)
299 TIGR02531 yecD_yerC TrpR-relat 29.9 76 0.0017 25.0 3.6 23 156-178 49-71 (88)
300 TIGR02985 Sig70_bacteroi1 RNA 29.8 93 0.002 25.0 4.4 28 156-183 128-155 (161)
301 TIGR02036 dsdC D-serine deamin 29.8 1.8E+02 0.004 26.5 6.8 56 61-121 23-84 (302)
302 PRK14616 4-diphosphocytidyl-2- 29.7 1.1E+02 0.0025 28.4 5.4 39 126-167 91-129 (287)
303 TIGR02612 mob_myst_A mobile my 29.6 57 0.0012 28.2 3.1 30 151-180 32-61 (150)
304 PF02042 RWP-RK: RWP-RK domain 29.5 78 0.0017 22.8 3.3 26 156-181 14-39 (52)
305 cd01392 HTH_LacI Helix-turn-he 29.5 35 0.00077 22.9 1.5 18 162-179 2-19 (52)
306 TIGR03541 reg_near_HchA LuxR f 29.4 1.7E+02 0.0037 26.3 6.4 13 95-107 188-200 (232)
307 TIGR02844 spore_III_D sporulat 29.3 59 0.0013 25.3 2.9 23 156-178 18-40 (80)
308 PRK10840 transcriptional regul 29.3 1.2E+02 0.0025 26.2 5.1 24 94-117 166-191 (216)
309 PRK01381 Trp operon repressor; 29.2 42 0.00092 27.3 2.1 36 148-183 46-81 (99)
310 PRK09906 DNA-binding transcrip 29.2 1.5E+02 0.0033 26.6 6.1 31 62-92 17-47 (296)
311 PRK10094 DNA-binding transcrip 29.1 1.9E+02 0.0041 26.6 6.8 55 62-121 18-78 (308)
312 PRK00343 ipk 4-diphosphocytidy 28.9 2E+02 0.0043 26.8 6.9 55 16-70 68-133 (271)
313 PRK08583 RNA polymerase sigma 28.9 4.4E+02 0.0094 23.8 12.3 28 156-183 220-247 (257)
314 PRK10082 cell density-dependen 28.9 2.3E+02 0.005 25.8 7.3 55 61-120 26-86 (303)
315 KOG0654 G2/Mitotic-specific cy 28.9 1.1E+02 0.0024 30.4 5.3 49 134-182 272-320 (359)
316 PRK10014 DNA-binding transcrip 28.8 55 0.0012 30.1 3.1 25 156-180 5-29 (342)
317 PRK08359 transcription factor; 28.7 58 0.0012 29.1 3.1 24 156-179 97-120 (176)
318 PRK14611 4-diphosphocytidyl-2- 28.6 2.2E+02 0.0048 26.3 7.1 56 16-71 61-127 (275)
319 PRK11139 DNA-binding transcrip 28.5 2E+02 0.0044 25.9 6.8 56 61-121 21-82 (297)
320 PRK11169 leucine-responsive tr 28.4 1E+02 0.0022 26.3 4.6 40 78-117 13-54 (164)
321 PRK14987 gluconate operon tran 28.4 53 0.0011 30.2 2.9 25 156-180 4-28 (331)
322 COG1321 TroR Mn-dependent tran 28.4 1.2E+02 0.0027 26.1 5.0 44 146-195 14-57 (154)
323 smart00347 HTH_MARR helix_turn 28.4 2.1E+02 0.0044 21.1 5.8 27 157-183 24-50 (101)
324 PF01726 LexA_DNA_bind: LexA D 28.4 1.3E+02 0.0028 22.2 4.5 31 153-183 21-52 (65)
325 smart00345 HTH_GNTR helix_turn 28.1 1.2E+02 0.0026 20.3 4.0 25 62-86 22-46 (60)
326 PF01325 Fe_dep_repress: Iron 28.1 1.9E+02 0.0041 20.8 5.3 15 93-107 22-36 (60)
327 PRK12528 RNA polymerase sigma 27.9 1E+02 0.0022 25.5 4.3 30 157-186 129-158 (161)
328 PRK11233 nitrogen assimilation 27.7 1.9E+02 0.0041 26.4 6.5 55 62-121 17-77 (305)
329 PRK15121 right oriC-binding tr 27.4 4E+02 0.0088 24.5 8.7 94 74-195 4-102 (289)
330 PRK06424 transcription factor; 27.4 84 0.0018 27.0 3.8 31 149-179 89-119 (144)
331 PRK09526 lacI lac repressor; R 27.3 69 0.0015 29.4 3.5 25 156-180 4-28 (342)
332 PRK11074 putative DNA-binding 27.2 1.9E+02 0.004 26.4 6.3 31 62-92 18-48 (300)
333 PRK10703 DNA-binding transcrip 27.1 58 0.0012 30.0 2.9 23 158-180 2-24 (341)
334 COG2207 AraC AraC-type DNA-bin 27.1 2.2E+02 0.0048 21.6 5.9 40 142-182 22-61 (127)
335 TIGR02424 TF_pcaQ pca operon t 27.1 2.6E+02 0.0057 25.1 7.3 55 61-120 18-78 (300)
336 PRK10632 transcriptional regul 27.1 2.3E+02 0.005 26.0 7.0 55 61-120 17-77 (309)
337 PF13411 MerR_1: MerR HTH fami 27.0 64 0.0014 22.9 2.6 22 160-181 3-24 (69)
338 PF09862 DUF2089: Protein of u 27.0 2.2E+02 0.0047 23.7 6.0 30 61-90 50-79 (113)
339 PF08613 Cyclin: Cyclin; Inte 26.9 3.8E+02 0.0082 22.5 10.1 85 95-183 57-143 (149)
340 TIGR02937 sigma70-ECF RNA poly 26.8 1.1E+02 0.0024 23.7 4.3 27 157-183 126-152 (158)
341 PRK10702 endonuclease III; Pro 26.8 3E+02 0.0064 24.9 7.4 47 58-107 103-152 (211)
342 TIGR00738 rrf2_super rrf2 fami 26.8 1.8E+02 0.0039 23.4 5.5 28 59-86 24-51 (132)
343 PRK12543 RNA polymerase sigma 26.8 3.4E+02 0.0073 22.9 7.5 41 147-189 125-165 (179)
344 smart00529 HTH_DTXR Helix-turn 26.7 88 0.0019 23.7 3.5 24 160-183 2-25 (96)
345 PF06323 Phage_antiter_Q: Phag 26.6 1.4E+02 0.003 27.9 5.2 36 151-186 159-200 (230)
346 PF07638 Sigma70_ECF: ECF sigm 26.6 1E+02 0.0022 26.7 4.3 30 158-187 152-181 (185)
347 PRK09464 pdhR transcriptional 26.6 96 0.0021 27.9 4.2 36 155-195 31-67 (254)
348 PRK15421 DNA-binding transcrip 26.6 2.2E+02 0.0048 26.4 6.8 55 62-121 18-78 (317)
349 smart00352 POU Found in Pit-Oc 26.5 69 0.0015 24.8 2.8 26 154-179 21-52 (75)
350 PF00440 TetR_N: Bacterial reg 26.4 99 0.0022 20.7 3.3 35 149-183 8-42 (47)
351 cd08318 Death_NMPP84 Death dom 26.3 2.4E+02 0.0051 21.7 5.8 56 60-122 4-59 (86)
352 PRK09393 ftrA transcriptional 26.3 5.4E+02 0.012 24.0 10.8 93 74-194 217-314 (322)
353 TIGR03339 phn_lysR aminoethylp 26.2 1.9E+02 0.0041 25.5 6.0 31 61-91 12-42 (279)
354 PF09862 DUF2089: Protein of u 26.1 80 0.0017 26.3 3.3 26 158-183 50-75 (113)
355 PRK12682 transcriptional regul 26.1 2.3E+02 0.0051 25.8 6.8 56 61-121 17-79 (309)
356 smart00418 HTH_ARSR helix_turn 26.1 1.3E+02 0.0028 19.9 3.9 29 58-86 8-36 (66)
357 COG3355 Predicted transcriptio 26.0 1.6E+02 0.0034 25.0 5.0 30 57-86 39-68 (126)
358 CHL00180 rbcR LysR transcripti 26.0 2E+02 0.0043 26.3 6.3 30 62-91 21-50 (305)
359 PF13556 HTH_30: PucR C-termin 25.9 1.1E+02 0.0025 21.7 3.7 28 158-185 13-40 (59)
360 PF11467 LEDGF: Lens epitheliu 25.9 69 0.0015 26.3 2.8 58 66-124 11-80 (106)
361 TIGR02147 Fsuc_second hypothet 25.8 5.7E+02 0.012 24.1 15.2 133 51-194 17-171 (271)
362 PF09012 FeoC: FeoC like trans 25.8 56 0.0012 23.9 2.1 35 83-117 4-39 (69)
363 COG3877 Uncharacterized protei 25.7 4E+02 0.0086 22.3 7.2 67 46-117 48-121 (122)
364 PRK09986 DNA-binding transcrip 25.4 1.8E+02 0.0039 26.0 5.8 54 62-120 23-82 (294)
365 TIGR01083 nth endonuclease III 25.3 2.6E+02 0.0057 24.4 6.7 56 59-117 101-161 (191)
366 PRK15243 transcriptional regul 25.3 2.5E+02 0.0055 26.3 7.0 56 61-121 19-80 (297)
367 PRK14611 4-diphosphocytidyl-2- 25.3 1.6E+02 0.0034 27.3 5.5 31 138-168 97-127 (275)
368 PF04218 CENP-B_N: CENP-B N-te 25.2 50 0.0011 23.3 1.7 23 158-180 23-45 (53)
369 PRK10188 DNA-binding transcrip 25.0 1.4E+02 0.0031 27.2 5.1 45 61-105 195-239 (240)
370 PRK00430 fis global DNA-bindin 24.9 3.4E+02 0.0074 21.5 6.6 29 153-181 64-92 (95)
371 TIGR02404 trehalos_R_Bsub treh 24.9 1.8E+02 0.004 25.8 5.7 42 77-118 2-50 (233)
372 PF09904 HTH_43: Winged helix- 24.9 66 0.0014 25.8 2.5 33 58-92 20-52 (90)
373 PRK12531 RNA polymerase sigma 24.8 1.2E+02 0.0027 26.0 4.4 33 156-188 156-188 (194)
374 PRK09943 DNA-binding transcrip 24.8 80 0.0017 27.3 3.3 28 153-180 16-43 (185)
375 PRK10572 DNA-binding transcrip 24.7 5.3E+02 0.011 23.4 10.8 30 58-90 197-226 (290)
376 PRK10225 DNA-binding transcrip 24.7 1.1E+02 0.0023 27.7 4.2 36 155-195 30-66 (257)
377 PRK11013 DNA-binding transcrip 24.7 2.8E+02 0.0061 25.4 7.0 31 61-91 19-49 (309)
378 KOG1010 Rb (Retinoblastoma tum 24.6 1.1E+02 0.0024 33.7 4.7 81 3-85 684-764 (920)
379 PRK15481 transcriptional regul 24.6 1E+02 0.0022 30.0 4.2 36 155-195 26-62 (431)
380 PRK10421 DNA-binding transcrip 24.6 1.1E+02 0.0024 27.7 4.2 36 155-195 23-59 (253)
381 COG2197 CitB Response regulato 24.4 1.4E+02 0.003 26.6 4.8 23 95-117 165-189 (211)
382 PRK13500 transcriptional activ 24.3 5.9E+02 0.013 23.7 10.1 25 58-82 220-244 (312)
383 PRK14086 dnaA chromosomal repl 24.0 2.4E+02 0.0052 30.0 7.0 73 17-91 528-600 (617)
384 PRK12518 RNA polymerase sigma 24.0 1.3E+02 0.0029 25.0 4.4 34 156-189 135-168 (175)
385 PRK12527 RNA polymerase sigma 23.9 1.4E+02 0.0031 24.5 4.5 41 147-189 113-153 (159)
386 PRK11920 rirA iron-responsive 23.8 1.9E+02 0.004 24.7 5.3 39 48-87 13-51 (153)
387 PRK12519 RNA polymerase sigma 23.8 1.4E+02 0.003 25.5 4.5 31 157-187 157-187 (194)
388 PRK15092 DNA-binding transcrip 23.7 4.3E+02 0.0094 24.5 8.2 56 61-121 26-87 (310)
389 TIGR02018 his_ut_repres histid 23.7 2E+02 0.0044 25.5 5.7 37 94-133 26-63 (230)
390 PRK00215 LexA repressor; Valid 23.6 2.9E+02 0.0063 24.1 6.6 32 152-183 18-50 (205)
391 PRK09480 slmA division inhibit 23.5 1.3E+02 0.0029 25.2 4.3 42 142-183 15-56 (194)
392 COG0083 ThrB Homoserine kinase 23.5 60 0.0013 31.3 2.3 47 37-83 89-136 (299)
393 PRK11050 manganese transport r 23.4 3E+02 0.0065 23.3 6.5 59 25-90 22-80 (152)
394 PRK15186 AraC family transcrip 23.4 4.9E+02 0.011 24.6 8.5 29 55-83 192-220 (291)
395 COG3620 Predicted transcriptio 23.1 76 0.0017 28.4 2.7 30 154-183 15-59 (187)
396 PRK09639 RNA polymerase sigma 23.1 1.5E+02 0.0032 24.4 4.5 34 156-189 126-159 (166)
397 TIGR01481 ccpA catabolite cont 23.0 70 0.0015 29.2 2.7 23 158-180 2-24 (329)
398 PRK10339 DNA-binding transcrip 23.0 68 0.0015 29.5 2.6 22 158-179 2-23 (327)
399 COG3711 BglG Transcriptional a 22.9 7.4E+02 0.016 24.5 10.1 28 156-183 99-126 (491)
400 PRK01212 homoserine kinase; Pr 22.9 2.4E+02 0.0053 26.1 6.3 56 16-71 62-128 (301)
401 PRK10434 srlR DNA-bindng trans 22.9 89 0.0019 28.8 3.3 27 157-183 19-45 (256)
402 COG1846 MarR Transcriptional r 22.9 2.4E+02 0.0052 21.3 5.4 32 161-197 40-71 (126)
403 PF14549 P22_Cro: DNA-binding 22.9 93 0.002 22.8 2.8 19 159-177 11-29 (60)
404 PRK03188 4-diphosphocytidyl-2- 22.9 1.7E+02 0.0038 27.2 5.3 30 138-167 100-129 (300)
405 PRK09645 RNA polymerase sigma 22.8 1.5E+02 0.0032 24.7 4.4 27 157-183 134-160 (173)
406 TIGR02944 suf_reg_Xantho FeS a 22.8 2.8E+02 0.006 22.4 5.9 14 94-107 26-39 (130)
407 PRK01212 homoserine kinase; Pr 22.7 1.9E+02 0.0041 26.8 5.5 41 138-178 98-138 (301)
408 PRK03188 4-diphosphocytidyl-2- 22.7 2.8E+02 0.0062 25.7 6.7 55 16-70 64-129 (300)
409 PF13961 DUF4219: Domain of un 22.7 49 0.0011 20.3 1.1 11 242-252 4-14 (27)
410 PF04297 UPF0122: Putative hel 22.7 1.2E+02 0.0027 24.6 3.7 29 94-122 34-67 (101)
411 PF01402 RHH_1: Ribbon-helix-h 22.7 78 0.0017 20.2 2.1 22 2-24 13-34 (39)
412 PRK04984 fatty acid metabolism 22.5 1.3E+02 0.0028 26.8 4.2 36 155-195 28-64 (239)
413 PRK12683 transcriptional regul 22.5 3.2E+02 0.007 25.1 7.0 56 61-121 17-79 (309)
414 PRK14999 histidine utilization 22.3 1.3E+02 0.0028 27.0 4.2 36 155-195 33-69 (241)
415 PRK01905 DNA-binding protein F 22.3 3.4E+02 0.0075 20.3 7.1 34 148-181 41-74 (77)
416 PF09999 DUF2240: Uncharacteri 22.2 1.4E+02 0.0031 25.7 4.2 83 20-106 37-136 (144)
417 PRK09940 transcriptional regul 22.2 3.4E+02 0.0073 25.4 7.0 29 55-83 145-173 (253)
418 PF08776 VASP_tetra: VASP tetr 22.2 73 0.0016 21.9 1.9 17 242-258 3-19 (40)
419 PRK09047 RNA polymerase factor 22.2 1.5E+02 0.0033 24.1 4.3 32 156-187 121-152 (161)
420 PRK10079 phosphonate metabolis 22.2 2.2E+02 0.0047 25.5 5.7 42 77-118 14-61 (241)
421 TIGR02999 Sig-70_X6 RNA polyme 22.1 1.1E+02 0.0023 25.8 3.5 26 157-182 150-175 (183)
422 PF13613 HTH_Tnp_4: Helix-turn 22.1 1.6E+02 0.0034 20.4 3.8 33 57-89 16-48 (53)
423 COG4565 CitB Response regulato 22.1 3.1E+02 0.0066 25.6 6.5 52 34-87 149-200 (224)
424 PRK03837 transcriptional regul 22.1 1.4E+02 0.0029 26.5 4.3 36 155-195 34-70 (241)
425 PF00288 GHMP_kinases_N: GHMP 22.1 1.5E+02 0.0031 21.2 3.7 31 138-168 16-46 (67)
426 PRK03902 manganese transport t 22.0 2.1E+02 0.0045 23.6 5.1 27 157-183 22-48 (142)
427 TIGR03337 phnR transcriptional 22.0 2.3E+02 0.005 24.8 5.7 25 94-118 26-51 (231)
428 PF12840 HTH_20: Helix-turn-he 21.9 1.6E+02 0.0034 20.7 3.8 30 154-183 21-50 (61)
429 PF03428 RP-C: Replication pro 21.9 1.8E+02 0.004 25.8 5.0 25 159-183 72-97 (177)
430 TIGR02684 dnstrm_HI1420 probab 21.8 1.7E+02 0.0037 22.9 4.3 37 140-180 30-66 (89)
431 PRK00650 4-diphosphocytidyl-2- 21.7 3.1E+02 0.0067 26.1 6.8 58 12-69 57-125 (288)
432 PRK11050 manganese transport r 21.7 1.7E+02 0.0037 24.8 4.6 30 154-183 48-77 (152)
433 PRK11534 DNA-binding transcrip 21.6 1.4E+02 0.003 26.4 4.2 36 155-195 28-63 (224)
434 PRK11924 RNA polymerase sigma 21.5 1.6E+02 0.0036 24.1 4.4 32 156-187 140-171 (179)
435 PRK11523 DNA-binding transcrip 21.5 1.4E+02 0.003 26.9 4.3 36 155-195 29-65 (253)
436 PF04539 Sigma70_r3: Sigma-70 21.4 1.2E+02 0.0025 22.2 3.2 34 55-88 15-48 (78)
437 PRK09726 antitoxin HipB; Provi 21.2 2.2E+02 0.0047 21.7 4.7 42 60-107 25-68 (88)
438 PF05344 DUF746: Domain of Unk 21.2 2.2E+02 0.0048 21.5 4.5 33 54-86 7-39 (65)
439 PRK14101 bifunctional glucokin 21.1 9.6E+02 0.021 25.0 11.8 113 61-181 229-398 (638)
440 PRK11557 putative DNA-binding 21.1 1.2E+02 0.0027 27.6 3.9 25 157-181 30-54 (278)
441 TIGR02293 TAS_TIGR02293 putati 21.0 1.2E+02 0.0027 25.2 3.5 34 144-179 25-58 (133)
442 PRK14999 histidine utilization 20.9 2.5E+02 0.0054 25.1 5.8 56 76-134 13-75 (241)
443 PRK11303 DNA-binding transcrip 20.9 88 0.0019 28.5 2.9 22 159-180 2-23 (328)
444 KOG2072 Translation initiation 20.8 4.6E+02 0.01 29.2 8.3 74 42-117 316-394 (988)
445 COG0664 Crp cAMP-binding prote 20.7 4.9E+02 0.011 21.5 8.9 29 155-183 169-197 (214)
446 KOG2496 Cdk activating kinase 20.7 4.3E+02 0.0093 25.9 7.4 65 95-168 62-129 (325)
447 PRK11151 DNA-binding transcrip 20.6 2.6E+02 0.0055 25.4 5.9 30 62-91 17-46 (305)
448 PRK11302 DNA-binding transcrip 20.6 1.3E+02 0.0028 27.4 3.9 25 157-181 34-58 (284)
449 PRK12517 RNA polymerase sigma 20.6 1.6E+02 0.0036 25.3 4.4 33 157-189 144-176 (188)
450 TIGR02018 his_ut_repres histid 20.5 1.5E+02 0.0032 26.3 4.2 32 159-195 27-58 (230)
451 TIGR02835 spore_sigmaE RNA pol 20.5 1.7E+02 0.0036 26.3 4.5 30 156-185 197-226 (234)
452 PF04967 HTH_10: HTH DNA bindi 20.5 2.1E+02 0.0046 20.4 4.2 31 57-87 18-50 (53)
453 TIGR02325 C_P_lyase_phnF phosp 20.4 1.1E+02 0.0023 27.1 3.3 25 94-118 33-58 (238)
454 COG2390 DeoR Transcriptional r 20.4 1.6E+02 0.0034 28.6 4.6 43 142-194 16-58 (321)
455 PF12833 HTH_18: Helix-turn-he 20.3 2E+02 0.0043 20.9 4.2 45 67-111 17-63 (81)
456 TIGR01884 cas_HTH CRISPR locus 20.3 1.9E+02 0.0042 25.4 4.8 34 157-195 157-190 (203)
457 PF01710 HTH_Tnp_IS630: Transp 20.2 4.7E+02 0.01 21.1 7.6 41 148-196 62-102 (119)
458 TIGR00191 thrB homoserine kina 20.2 2.5E+02 0.0054 26.3 5.8 63 77-167 63-126 (302)
459 TIGR02812 fadR_gamma fatty aci 20.2 1.5E+02 0.0033 26.3 4.2 36 155-195 27-63 (235)
460 PRK09956 hypothetical protein; 20.2 6.9E+02 0.015 23.8 8.9 76 96-177 229-306 (308)
461 PF05344 DUF746: Domain of Unk 20.1 2.4E+02 0.0051 21.4 4.5 38 152-189 8-45 (65)
462 PRK13413 mpi multiple promoter 20.1 3.5E+02 0.0076 23.6 6.4 26 156-181 171-196 (200)
463 PRK09791 putative DNA-binding 20.1 3.1E+02 0.0066 24.8 6.3 30 62-91 21-50 (302)
No 1
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=100.00 E-value=9.6e-59 Score=412.88 Aligned_cols=255 Identities=58% Similarity=0.948 Sum_probs=227.7
Q ss_pred CcHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHH
Q 023151 1 MDLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRS 80 (286)
Q Consensus 1 mei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~ 80 (286)
|.|.+|+.+|||.+.|.++++|+||.|++..+|++++.|.+++|++++|+++|+.+++||||++.++++||++++.|.++
T Consensus 1 ~lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~ 80 (262)
T KOG4557|consen 1 MLISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRS 80 (262)
T ss_pred CcHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHH
Confidence 78999999999977789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCCCcHHHHHHHhCCcchHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCH
Q 023151 81 FNSLQNSIGFKNELDIRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDK 160 (286)
Q Consensus 81 yr~l~~~LgL~~~~~I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ 160 (286)
+++|+++||||..++|++||+||||.+|++.|++||..|+++ ||+.++.++||++|+|++||||+||+++|.|||+
T Consensus 81 ~~sfe~llgln~~~~VrdlaVQfgc~evi~~a~~vl~syk~~----lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK 156 (262)
T KOG4557|consen 81 FNSFENLLGLNIKLNVRDLAVQFGCVEVIKSAQNVLSSYKER----LPATRRANADFSRPVFTAAAFYLACKKLKLKVDK 156 (262)
T ss_pred HHHHHHHhcchhhcCHHHHHHHHhHHHHHHHHHHHHHHHHhc----CchhhhcCCcccchHHHHHHHHHHHHHHHHhhhH
Confidence 999999999999999999999999999999999999988864 7889999999999999999999999999999999
Q ss_pred HHHHHHhCCCHHHHHHHHHHHHHhhh------hhhhcccccCChhhhhccchhcccCcccccchhhhhcchhhhhhchhc
Q 023151 161 LKLIEVCGTSETEFASVSTTMKDLCH------DVFGIAKEKKDPRELKSNRELLDVLPEKRKFEDVEYLSADEAEVSSYK 234 (286)
Q Consensus 161 ~kla~~sgvt~vt~rnr~ke~~~~c~------d~~~i~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~k 234 (286)
.+++++||+++.+|+.++++|+.--. |-+++++.+++.+.+++|+++++.+|.|+ ||
T Consensus 157 ~kli~~sg~~~s~F~~l~kqler~~~qv~~e~~~V~~s~~k~~k~~v~~n~~~~~~~~~k~-----------------hk 219 (262)
T KOG4557|consen 157 LKLIEVSGTSESEFSCLSKQLERNYKQVSTEMDCVGISKEKKDKKDVKGNRDLLDVLPGKR-----------------HK 219 (262)
T ss_pred hhcccccCCCHHHHHHHHHHHHHHHHHhcCCccccCCChhhhhhhhccCcHHHhhhccccC-----------------CC
Confidence 99999999999999999999975221 22344555555555555555555555552 55
Q ss_pred ccCccc-hhHHHHHHHHHhhhhhhcccCCcccccccccccccc
Q 023151 235 RHKKTE-KVAYEEWKTSVLASNRNKAKAPCKRTTQAGLNFQKK 276 (286)
Q Consensus 235 ~~~~~~-~~~Ye~WK~~il~~~~~~~~~~~~~~~~~~~~~~~~ 276 (286)
+....+ ++|||+||++||++++.++|...++..|+.+||+++
T Consensus 220 p~~~~~~~~dYE~WK~~vl~~a~~~~k~~~~~~~~~~~~~~~~ 262 (262)
T KOG4557|consen 220 PDGGYSEEADYEDWKSTVLNSAKKNPKKGTKRVIQASLNFPKK 262 (262)
T ss_pred CCCCcchhhhHHHHHHHHHHHHHhchHHhHHHHHHHhhccccC
Confidence 555444 789999999999999999999999999999999874
No 2
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=5e-38 Score=293.64 Aligned_cols=170 Identities=21% Similarity=0.214 Sum_probs=163.5
Q ss_pred CcHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHH
Q 023151 1 MDLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRS 80 (286)
Q Consensus 1 mei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~ 80 (286)
++|++++++||||+ +|++.|..|||++..+ ++++|||+++++|||+|+|||.+|+|++++++++.++++++.++++
T Consensus 102 ~~l~~~~~~l~LP~--~v~e~A~~iyr~a~~~--~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rt 177 (285)
T COG1405 102 EELERIASALGLPE--SVRETAARIYRKAVDK--GLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRT 177 (285)
T ss_pred HHHHHHHHHhCCCc--hHHHHHHHHHHHHhhc--CCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHH
Confidence 36899999999997 6999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCCCC-----cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhC
Q 023151 81 FNSLQNSIGFKNEL-----DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKH 154 (286)
Q Consensus 81 yr~l~~~LgL~~~~-----~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~ 154 (286)
|+.+.+.|+++.++ |||+||+.|||++ +...|.+|++.+++. +++.|+ +|.|+||||+|+||.++
T Consensus 178 yr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~---g~~~Gk------~P~glAaaaiy~as~l~ 248 (285)
T COG1405 178 YRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRA---GLTAGK------SPAGLAAAAIYLASLLL 248 (285)
T ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh---CcccCC------CchhHHHHHHHHHHHHh
Confidence 99999999999875 8999999999999 999999999999988 556899 69999999999999999
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++++||+++|+++|||++||||+|++|.+
T Consensus 249 ~~~~tq~eva~v~~vtevTIrnrykel~~ 277 (285)
T COG1405 249 GERRTQKEVAKVAGVTEVTIRNRYKELAD 277 (285)
T ss_pred CCchHHHHHHHHhCCeeeHHHHHHHHHHH
Confidence 99999999999999999999999999965
No 3
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=3.4e-33 Score=263.44 Aligned_cols=169 Identities=20% Similarity=0.203 Sum_probs=161.0
Q ss_pred cHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSF 81 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~y 81 (286)
+|++|+.+||||+ .|+++|.+|||++..+ ++++|++.+++++||||+|||.+++|++++||+.+++++++++.++|
T Consensus 128 ~I~~~~~~L~Lp~--~v~e~A~~iyk~~~~~--~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~ 203 (310)
T PRK00423 128 ELDRIASQLGLPR--SVREEAAVIYRKAVEK--GLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCY 203 (310)
T ss_pred HHHHHHHHcCCCH--HHHHHHHHHHHHHHhc--CcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 6899999999996 7999999999999998 89999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCCC-----cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCC
Q 023151 82 NSLQNSIGFKNEL-----DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHK 155 (286)
Q Consensus 82 r~l~~~LgL~~~~-----~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k 155 (286)
+.|.+.||++.++ +|++||+.|+++. +.+.|.+|++.+.+. ++..|+ +|.++||||+|+||+++|
T Consensus 204 ~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~---~l~~Gr------~P~sIAAAaIYlA~~~~g 274 (310)
T PRK00423 204 RFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEK---GLTSGK------GPTGLAAAAIYIASLLLG 274 (310)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc---CcccCC------CHHHHHHHHHHHHHHHhC
Confidence 9999999987764 7999999999999 999999999988765 567898 699999999999999999
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.++||++|+.++||+++||+++|++|..
T Consensus 275 ~~~t~keIa~v~~Vs~~tI~~~ykel~~ 302 (310)
T PRK00423 275 ERRTQREVAEVAGVTEVTVRNRYKELAE 302 (310)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 9999999999999999999999999965
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.96 E-value=2.5e-28 Score=226.61 Aligned_cols=175 Identities=17% Similarity=0.194 Sum_probs=162.5
Q ss_pred cHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSF 81 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~y 81 (286)
+|..|+.+|+||- .+.+.|.++|.+.... .+++|++.++++|||||+|||..++|||++||..++++++|++.+++
T Consensus 110 ~I~~m~d~~~Lp~--~I~d~A~~ifk~v~~~--k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kKEIgr~~ 185 (308)
T KOG1597|consen 110 EITAMCDRLSLPA--TIKDRANEIFKLVEDS--KLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKKEIGRCV 185 (308)
T ss_pred HHHHHHHHhCCch--HHHHHHHHHHHHHHHh--hhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHHHHHHHH
Confidence 5889999999995 7999999999999976 68999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCCC-------cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHh
Q 023151 82 NSLQNSIGFKNEL-------DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKK 153 (286)
Q Consensus 82 r~l~~~LgL~~~~-------~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~ 153 (286)
+.|...|+..... +++|||+.|+|+. ++..|.++.+.+.+... -.|| +|--+|||++|++|++
T Consensus 186 K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~---~~gR------sPiSIAAa~IYmisql 256 (308)
T KOG1597|consen 186 KLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDI---RAGR------SPISIAAAAIYMISQL 256 (308)
T ss_pred HHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhcc---ccCC------CchhHHHHHHHHHHHh
Confidence 9999999987764 6999999999999 99999999999998744 4678 6888999999999999
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
..++.+|++|.+++||+++|||+.|++|..+-.+++
T Consensus 257 s~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~li 292 (308)
T KOG1597|consen 257 SDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKLI 292 (308)
T ss_pred ccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhhC
Confidence 999999999999999999999999999977555554
No 5
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=99.70 E-value=9.8e-17 Score=159.19 Aligned_cols=170 Identities=13% Similarity=0.112 Sum_probs=155.2
Q ss_pred CcHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHH
Q 023151 1 MDLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRS 80 (286)
Q Consensus 1 mei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~ 80 (286)
|-|+.+..+|+|++ +++.|--+|++|..+ ++++||...-++++|+|++||..+.+.=+=+.+.+..++--.+.++
T Consensus 72 ~~i~~~~~~l~l~~---~~~~a~~~~k~a~~~--nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~ 146 (521)
T KOG1598|consen 72 RLIEELTERLNLGN---KTEVAFNFFKLAPDR--NFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSN 146 (521)
T ss_pred hHHHHHHHhcCcch---HHHHHHHHHHHHhhC--CCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHH
Confidence 34788999999994 999999999999999 9999999999999999999999999998888888888999999999
Q ss_pred HHHHHHHhCCC---CC-----CcHHHHHHHhCCcc----hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHH
Q 023151 81 FNSLQNSIGFK---NE-----LDIRELGIRFGCIR----LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFY 148 (286)
Q Consensus 81 yr~l~~~LgL~---~~-----~~I~~ia~qlg~s~----v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY 148 (286)
|..|.+.|.++ .+ +||++++..|..-. |...|..|++..+.-++. .|++ |.|+..||||
T Consensus 147 ~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~---tGRR------PsglcGAaLl 217 (521)
T KOG1598|consen 147 FLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQ---TGRR------PSGLCGAALL 217 (521)
T ss_pred HHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHH---hCCC------ccchhHHHHH
Confidence 99999999998 33 38999998874433 999999999999988776 6885 9999999999
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 023151 149 LCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDL 184 (286)
Q Consensus 149 ~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~ 184 (286)
+||+.||+++|..+|+.++.|.+.||+.||+|+.++
T Consensus 218 iAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T 253 (521)
T KOG1598|consen 218 IAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDT 253 (521)
T ss_pred HHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999998653
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=99.60 E-value=3.8e-15 Score=111.72 Aligned_cols=71 Identities=27% Similarity=0.333 Sum_probs=65.1
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAY 77 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y 77 (286)
|++++++||||+ +|.+.|.+||+.+... ++..||+..++++||||+|||.+|+|++++++++.+|++++.+
T Consensus 1 I~r~~~~L~L~~--~v~~~A~~i~~~~~~~--~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPE--DVRERAKEIYKKAQER--GLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--H--HHHHHHHHHHHHHHHT--TTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCH--HHHHHHHHHHHHHHHc--CCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 689999999996 7999999999999998 8999999999999999999999999999999999999998865
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=99.49 E-value=1.6e-13 Score=102.96 Aligned_cols=70 Identities=19% Similarity=0.246 Sum_probs=62.8
Q ss_pred HHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHH
Q 023151 96 IRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEF 174 (286)
Q Consensus 96 I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~ 174 (286)
|++||..||++. +.+.|.+|++...+. ++..|+ +|.+++|||+|+||++++.++|+++|++++||++.||
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~---~~~~Gr------~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQER---GLLKGR------SPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHT---TTSTTS-------HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHc---CCcccC------CHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 689999999999 999999999988777 556898 6999999999999999999999999999999999997
No 8
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.33 E-value=8.7e-12 Score=118.10 Aligned_cols=87 Identities=20% Similarity=0.283 Sum_probs=82.8
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
|.|++++|+||+ .|.+.|.+|++.+... +++.|++..+++|||||+||+.+|+|+|.++|++++|+++..+.+.|+
T Consensus 223 i~r~~~~L~L~~--~v~~~A~~i~~~a~~~--~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~yk 298 (310)
T PRK00423 223 VPRFASELGLSG--EVQKKAIEILQKAKEK--GLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298 (310)
T ss_pred HHHHHHHcCCCH--HHHHHHHHHHHHHHhc--CcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 689999999996 7999999999999987 899999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCCC
Q 023151 83 SLQNSIGFKNE 93 (286)
Q Consensus 83 ~l~~~LgL~~~ 93 (286)
.|.+.||+..+
T Consensus 299 el~~~l~~~~~ 309 (310)
T PRK00423 299 ELAEKLDIKIP 309 (310)
T ss_pred HHHHHhCcccC
Confidence 99999998653
No 9
>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=99.10 E-value=1.3e-11 Score=119.08 Aligned_cols=89 Identities=37% Similarity=0.488 Sum_probs=0.0
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
|.+|+.++|++.++.|+++|++|||+++ ++.+.+.|..+.|++++|+|+||..+++++|+..+++++|++++.|.+.|+
T Consensus 1 L~~l~p~~~~~~~~~ll~~a~~L~~ls~-~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~ 79 (353)
T PF05460_consen 1 LSDLIPKLGGGLPPKLLSKASELYRLSR-QKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLN 79 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ChhhhhccCCCCCHHHHHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHH
Confidence 5689999999977899999999999999 455788999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCC
Q 023151 83 SLQNSIGFKN 92 (286)
Q Consensus 83 ~l~~~LgL~~ 92 (286)
.|++.|+...
T Consensus 80 ~~~~~L~~~s 89 (353)
T PF05460_consen 80 TFENLLGNSS 89 (353)
T ss_dssp ----------
T ss_pred HHHHHHhCCC
Confidence 9999999987
No 10
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.02 E-value=1e-09 Score=103.43 Aligned_cols=88 Identities=24% Similarity=0.303 Sum_probs=83.5
Q ss_pred cHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSF 81 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~y 81 (286)
.|.|+++.||||+ .|..+|.+|.+++..+ |++.|++..++|+||+|+||..+|+++|-.++++++|+.+-.+.+.|
T Consensus 197 yi~rf~s~L~l~~--~v~~~a~ei~~~~~~~--g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnry 272 (285)
T COG1405 197 YIPRFASKLGLSD--EVRRKAIEIVKKAKRA--GLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRY 272 (285)
T ss_pred HHHHHHHHcCCCH--HHHHHHHHHHHHHHHh--CcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHH
Confidence 3789999999996 7999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCCC
Q 023151 82 NSLQNSIGFKNE 93 (286)
Q Consensus 82 r~l~~~LgL~~~ 93 (286)
+.|...|++...
T Consensus 273 kel~~~~~i~~~ 284 (285)
T COG1405 273 KELADALDIEVT 284 (285)
T ss_pred HHHHHhhccccC
Confidence 999999987653
No 11
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=98.91 E-value=1.1e-07 Score=90.52 Aligned_cols=167 Identities=12% Similarity=0.092 Sum_probs=123.3
Q ss_pred HHHHHHHhC--CCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCC----HHH
Q 023151 3 LSDIAKKLG--LSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMS----EKA 76 (286)
Q Consensus 3 i~ria~kLg--L~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~----~k~ 76 (286)
|.+++.+|+ ||. .|+.+|..||++.-.+ +.+.--...-++++|||+||.....|+++++++...+-. +..
T Consensus 63 i~~~~~~lkp~Lpq--~viaTAivyf~RFy~~--~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~~~~~~~~ 138 (305)
T TIGR00569 63 LLDFCSAFKPTMPT--SVVGTAIMYFKRFYLN--NSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKETPLKALEQ 138 (305)
T ss_pred HHHHHHHhcCCCCc--hHHHHHHHHHhHHhcc--CchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCCchhhHHH
Confidence 678999999 997 7999999999999997 556667889999999999999999999999999866544 356
Q ss_pred HHHHHHHHHHHhCCCCCC---------cHHHHHHHh-CCc--c-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHH
Q 023151 77 YNRSFNSLQNSIGFKNEL---------DIRELGIRF-GCI--R-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFT 143 (286)
Q Consensus 77 y~~~yr~l~~~LgL~~~~---------~I~~ia~ql-g~s--~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~A 143 (286)
+-.+=..|-+.||-+..+ ++-+|-..+ ++. + +...|-.+|+. .+.+ ...+-|.|+.+|
T Consensus 139 Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lnd---sl~T------d~~L~y~Ps~IA 209 (305)
T TIGR00569 139 VLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNR---TLLT------DAYLLYTPSQIA 209 (305)
T ss_pred HHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHH---HHcC------CceecCCHHHHH
Confidence 666767777888866543 233333333 222 1 55556666553 4333 235668899999
Q ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCC--CHHHHHHHHHHHHH
Q 023151 144 AVAFYLCAKKHKLKVDKLKLIEVCGT--SETEFASVSTTMKD 183 (286)
Q Consensus 144 AAAlY~A~~~~k~kvtQ~kla~~sgv--t~vt~rnr~ke~~~ 183 (286)
+||+|+|++.++++++.-.- ++-++ .+.+...++..|.+
T Consensus 210 lAAI~lA~~~~~~~l~~~~~-e~~~~~~~~~~~~~l~~~~~~ 250 (305)
T TIGR00569 210 LAAILHTASRAGLNMESYLT-EQLSVPGNREELPQLIDIMRE 250 (305)
T ss_pred HHHHHHHHHHhCCCCcccch-hhhcccccHHHHHHHHHHHHH
Confidence 99999999999998877543 66666 55666666666644
No 12
>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=98.64 E-value=3.1e-07 Score=67.82 Aligned_cols=78 Identities=26% Similarity=0.230 Sum_probs=72.0
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCC-CHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGM-SEKAYNRSF 81 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~-~~k~y~~~y 81 (286)
|.+++..++++. .+...|..++.++... +...|.+....+++||++||+..+.|.+.+++..++|. +..++.+.+
T Consensus 9 l~~~~~~~~~~~--~~~~~A~~~~~~~~~~--~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~e 84 (88)
T cd00043 9 LRRVAKALGLSP--ETLTLAVNLLDRFLLD--YSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRME 84 (88)
T ss_pred HHHHHHHcCCCH--HHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHHH
Confidence 678999999995 7999999999999997 56779999999999999999999999999999999999 999998887
Q ss_pred HHH
Q 023151 82 NSL 84 (286)
Q Consensus 82 r~l 84 (286)
+.+
T Consensus 85 ~~i 87 (88)
T cd00043 85 KLL 87 (88)
T ss_pred HHh
Confidence 764
No 13
>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=98.63 E-value=3.2e-07 Score=67.21 Aligned_cols=79 Identities=19% Similarity=0.241 Sum_probs=68.3
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCC-CHH
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGT-SET 172 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgv-t~v 172 (286)
++.+++..++++. +...|..+++.+..... ...++|..+||||+|+||+..+..++..++...+|+ ++.
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~---------~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~ 72 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYK---------FLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEE 72 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhh---------cccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHH
Confidence 5789999999998 99999999997765311 112478889999999999999999999999999999 999
Q ss_pred HHHHHHHHHH
Q 023151 173 EFASVSTTMK 182 (286)
Q Consensus 173 t~rnr~ke~~ 182 (286)
+|.+.+.+|.
T Consensus 73 ~i~~~~~~il 82 (83)
T smart00385 73 EILRMEKLLL 82 (83)
T ss_pred HHHHHHHHHh
Confidence 9999999883
No 14
>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=98.63 E-value=2.9e-07 Score=67.43 Aligned_cols=79 Identities=19% Similarity=0.129 Sum_probs=70.7
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCC-CHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGM-SEKAYNRSF 81 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~-~~k~y~~~y 81 (286)
|.+++..++++. .+...|..|++++... ....+.+...++++|+|+||+..+.+....++..++|. +..++.+++
T Consensus 3 l~~~~~~~~~~~--~~~~~a~~~~~~~l~~--~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 3 LRRVCKALNLDP--ETLNLAVNLLDRFLSD--YKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred HHHHHHHcCCCH--HHHHHHHHHHHHHHHH--hhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 678999999985 7999999999999885 23445999999999999999999999999999999999 999999988
Q ss_pred HHHH
Q 023151 82 NSLQ 85 (286)
Q Consensus 82 r~l~ 85 (286)
+.|.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 8764
No 15
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.42 E-value=3e-06 Score=62.52 Aligned_cols=78 Identities=22% Similarity=0.260 Sum_probs=68.5
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCC-CHH
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGT-SET 172 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgv-t~v 172 (286)
++.+++..++++. +...|..+++.+...+.. . .++|-.+|+||+|+||+..+...+..++...++. ++.
T Consensus 8 ~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~---~------~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~ 78 (88)
T cd00043 8 FLRRVAKALGLSPETLTLAVNLLDRFLLDYSV---L------GRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEE 78 (88)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHhccc---c------cCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHH
Confidence 6899999999999 999999999977655332 1 3478889999999999999999999999999999 999
Q ss_pred HHHHHHHHH
Q 023151 173 EFASVSTTM 181 (286)
Q Consensus 173 t~rnr~ke~ 181 (286)
+|.+.+.++
T Consensus 79 ~i~~~e~~i 87 (88)
T cd00043 79 EILRMEKLL 87 (88)
T ss_pred HHHHHHHHh
Confidence 999988876
No 16
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.28 E-value=3e-06 Score=79.93 Aligned_cols=82 Identities=17% Similarity=0.205 Sum_probs=77.2
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
|.|.++.|+||. .+.+-|.|+-+++... +..+||+..+++||++|++|+....+.+..+|.+++|+.+-.+.++|+
T Consensus 207 m~RFCs~L~L~~--~~q~aA~e~a~ka~~~--~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK 282 (308)
T KOG1597|consen 207 MPRFCSNLGLPK--SAQEAATEIAEKAEEM--DIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYK 282 (308)
T ss_pred HHHHHHhcCCCH--HHHHHHHHHHHHHHHh--ccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHH
Confidence 679999999996 7999999999999998 889999999999999999999999999999999999999999999999
Q ss_pred HHHHHh
Q 023151 83 SLQNSI 88 (286)
Q Consensus 83 ~l~~~L 88 (286)
-|.-.+
T Consensus 283 ~Lyp~~ 288 (308)
T KOG1597|consen 283 DLYPHA 288 (308)
T ss_pred HHhhch
Confidence 886543
No 17
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.21 E-value=1.3e-05 Score=76.90 Aligned_cols=168 Identities=13% Similarity=0.094 Sum_probs=121.1
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCC--CH------
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGM--SE------ 74 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~--~~------ 74 (286)
|.+++.+||+|. .-+..|..||-+.... ....+-.-+-.|++||++|+...+.|+-+++|+.++.- ++
T Consensus 46 I~elg~~L~~~~--~ti~tA~~~~hRFy~~--~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~ 121 (323)
T KOG0834|consen 46 IQELGVRLKMPQ--KTIATAIVIFHRFYMF--HSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLELE 121 (323)
T ss_pred HHHHHHHcCCCc--cchhhhhhhhhhhhhh--cccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccHH
Confidence 778999999997 5799999999999997 33555566899999999999999999999999987753 33
Q ss_pred HHHHHHHHHH-------HHHhCCCCC-----CcHHHHHHHhCCcc-----hHHHHHHHHHHHHHhhhhccccccccCCCC
Q 023151 75 KAYNRSFNSL-------QNSIGFKNE-----LDIRELGIRFGCIR-----LIPLVQKGLSLFKDRFTAALPASRKTSADF 137 (286)
Q Consensus 75 k~y~~~yr~l-------~~~LgL~~~-----~~I~~ia~qlg~s~-----v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~ 137 (286)
..|++-...+ -..|+.... .+|-+++..|+-.. +...|-.+++. -+.+. -.+-|
T Consensus 122 ~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD---~~~t~------~cL~y 192 (323)
T KOG0834|consen 122 EVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVND---SLRTT------LCLQY 192 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhch---hheee------eeEee
Confidence 4555554433 233443332 26888888876655 34444444442 22221 22336
Q ss_pred ChhHHHHHHHHHHHHhCCCCCCHHH---HHHHhC--CCHHHHHHHHHHHHH
Q 023151 138 SRPVFTAVAFYLCAKKHKLKVDKLK---LIEVCG--TSETEFASVSTTMKD 183 (286)
Q Consensus 138 ~pp~~AAAAlY~A~~~~k~kvtQ~k---la~~sg--vt~vt~rnr~ke~~~ 183 (286)
.|..+|+||+|+|+...|..++-.. --...+ ||...++.++.++.+
T Consensus 193 ~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~ 243 (323)
T KOG0834|consen 193 SPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLD 243 (323)
T ss_pred cCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHH
Confidence 8999999999999999999665421 235556 999999999999865
No 18
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=98.10 E-value=3.4e-05 Score=73.15 Aligned_cols=146 Identities=13% Similarity=0.067 Sum_probs=106.3
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhC--------CCH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSG--------MSE 74 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg--------~~~ 74 (286)
|.+++.+|.||- .|+++|-.+|++...+ ..+.+.+.+..+++|||+||++...|++.....-..+ -++
T Consensus 52 i~~l~~~L~lp~--~~laTAi~~f~Rf~Lk--~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr 127 (297)
T COG5333 52 IMDLCTRLNLPQ--TVLATAILFFSRFYLK--NSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSR 127 (297)
T ss_pred HHHHHHhcCCCc--chHHHHHHHHHHHHhh--cccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccH
Confidence 678999999997 7999999999999999 5589999999999999999999998888765544443 467
Q ss_pred HHHHHHHHHHHHHhCCCCC---CcHHHHHH----HhCCc-chHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHH
Q 023151 75 KAYNRSFNSLQNSIGFKNE---LDIRELGI----RFGCI-RLIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVA 146 (286)
Q Consensus 75 k~y~~~yr~l~~~LgL~~~---~~I~~ia~----qlg~s-~v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAA 146 (286)
+.+...=..+-..|+-... |+-+-... |+... ++...|-.++..+-.. ....=+.|..+|.||
T Consensus 128 ~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t---------~~~llypphiIA~a~ 198 (297)
T COG5333 128 ERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRT---------DLCLLYPPHIIALAA 198 (297)
T ss_pred HHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhc---------eeeeecChHHHHHHH
Confidence 7777777777777776543 23222211 11222 2555555555542211 222334688899999
Q ss_pred HHHHHHhCCCCCCHH
Q 023151 147 FYLCAKKHKLKVDKL 161 (286)
Q Consensus 147 lY~A~~~~k~kvtQ~ 161 (286)
+++||..+|.++-..
T Consensus 199 l~ia~~~~~~~~~~~ 213 (297)
T COG5333 199 LLIACEVLGMPIIKL 213 (297)
T ss_pred HHHHHHhcCCccchh
Confidence 999999999988776
No 19
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=97.77 E-value=0.001 Score=64.04 Aligned_cols=167 Identities=13% Similarity=0.089 Sum_probs=116.9
Q ss_pred HhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCC----------------
Q 023151 9 KLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGM---------------- 72 (286)
Q Consensus 9 kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~---------------- 72 (286)
-|.||. ...-++..||++.-.. ....+-..+..+.|||-+|......|+...+++-+..-
T Consensus 36 LL~L~q--~a~atgqVLFqRf~~~--ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~~~~~~~ 111 (367)
T KOG0835|consen 36 LLNLPQ--VAMATGQVLFQRFCYS--KSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEAAEHLILA 111 (367)
T ss_pred hhcCcH--HHHHHHHHHHHHHHhc--cccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccCcchhhhh
Confidence 467775 5777888888877665 34566789999999999999999999999998654321
Q ss_pred -----CHHHHHHHHHHHHHHhCCCCCC-----cHHHHHHHhCCcchHHHHHHHHHHHHHhhhhcccccc--ccCCCCChh
Q 023151 73 -----SEKAYNRSFNSLQNSIGFKNEL-----DIRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPASR--KTSADFSRP 140 (286)
Q Consensus 73 -----~~k~y~~~yr~l~~~LgL~~~~-----~I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~gk--~~~~D~~pp 140 (286)
-+....++-+.+.++||.-+.+ .|--+--.|+|+.-.. |++..- .|.. .+. ...+-|.|-
T Consensus 112 ~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~----l~Q~~w-NfmN---DslRT~v~vry~pe 183 (367)
T KOG0835|consen 112 RLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLK----LLQAAW-NFMN---DSLRTDVFVRYSPE 183 (367)
T ss_pred hHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchh----HHHHHH-Hhhh---hccccceeeecCHH
Confidence 1234456777889999987765 2444455677877222 233222 1221 122 234667899
Q ss_pred HHHHHHHHHHHHhCCCCCC-HHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 141 VFTAVAFYLCAKKHKLKVD-KLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 141 ~~AAAAlY~A~~~~k~kvt-Q~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
.+||||+|+|++-..+... +.-.-.+-++++..|+.+|-.+..+--+
T Consensus 184 ~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 184 SIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred HHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 9999999999999996553 4577788899999999888776554443
No 20
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=97.49 E-value=0.0015 Score=60.26 Aligned_cols=166 Identities=11% Similarity=0.111 Sum_probs=102.0
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCC-CCHHHHHHHh-----------
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVI-FDRKTAIKLS----------- 70 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~ip-rd~~e~~k~s----------- 70 (286)
|..++..|.|.. .|+.+|-.+||+...+ ..+++.+.+.+|.-|||+||.....| .....++-..
T Consensus 48 I~~lg~~lklRQ--~ViATAivY~rRfy~r--~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~ 123 (264)
T KOG0794|consen 48 IQKLGQHLKLRQ--RVIATAIVYFRRFYLR--KSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWP 123 (264)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHH--HhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccch
Confidence 566788888986 7999999999999999 66899999999999999999988887 1111111111
Q ss_pred ---CCCHHHHHHHHHHHHHHhCC----CCCC-cHHHHHHHhCC-cc-hHHHHHHHHHHHHHhhhhccccccccCCCCChh
Q 023151 71 ---GMSEKAYNRSFNSLQNSIGF----KNEL-DIRELGIRFGC-IR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRP 140 (286)
Q Consensus 71 ---g~~~k~y~~~yr~l~~~LgL----~~~~-~I~~ia~qlg~-s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp 140 (286)
..+.+.+..+==.|...|+- ..|. ++.++--..|. ++ ..+.+=.|++. .|.. +..+=+-|-
T Consensus 124 e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivND---Syr~------Dl~Ll~PPh 194 (264)
T KOG0794|consen 124 EKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVND---SYRM------DLCLLYPPH 194 (264)
T ss_pred hhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhcc---hhhc------ceeeecCHH
Confidence 11111111111122222221 1111 46666666666 33 55556555553 3322 112223466
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 141 VFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 141 ~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
.+|-||+|+||..++-..++.=.++ ..|--.-+.+...+|.
T Consensus 195 ~IalAcl~Ia~~~~~k~~~~~w~~e-l~vD~ekV~~~v~~I~ 235 (264)
T KOG0794|consen 195 QIALACLYIACVIDEKDIPKAWFAE-LSVDMEKVKDIVQEIL 235 (264)
T ss_pred HHHHHHHHHHHhhcCCChHHHHHHH-HhccHHHHHHHHHHHH
Confidence 7999999999999988877544444 4455555555555553
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=96.62 E-value=0.003 Score=63.96 Aligned_cols=89 Identities=12% Similarity=0.055 Sum_probs=69.8
Q ss_pred HHHHHHhCCCCChhHHHHHHHHHHHhhhhcCC-CCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 4 SDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDS-SIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 4 ~ria~kLgL~e~~~V~ekAael~Rla~~k~~~-l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
.|.+.+|-..+. . .+-+-..+|+++....+ +..||-..++..|||++|||++|++++..+|+++.-+....+..-|.
T Consensus 171 ~Rfa~~L~~g~~-~-~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~ 248 (521)
T KOG1598|consen 171 VRFSCRLLFGDK-T-EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLK 248 (521)
T ss_pred echhHhhhcCCc-h-HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHH
Confidence 455556655542 3 44555556666553222 56799999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCCCC
Q 023151 83 SLQNSIGFKNEL 94 (286)
Q Consensus 83 ~l~~~LgL~~~~ 94 (286)
.|...++.+.++
T Consensus 249 Ef~~T~s~~Lti 260 (521)
T KOG1598|consen 249 EFSDTLSGDLTI 260 (521)
T ss_pred HHhccccccccH
Confidence 999998876553
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=96.33 E-value=0.032 Score=44.70 Aligned_cols=85 Identities=15% Similarity=0.138 Sum_probs=68.0
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCC-CCCHHHHHHHhC--CCHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDV-IFDRKTAIKLSG--MSEKAYNR 79 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~i-prd~~e~~k~sg--~~~k~y~~ 79 (286)
|-.++..++++. .++-.|..|+.+...+ ..+........+++|+++||+.... +.+.++++..++ .+.+++..
T Consensus 38 i~~~~~~~~l~~--~~~~~A~~~~dr~~~~--~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~ 113 (127)
T PF00134_consen 38 IIELCQRLKLSP--ETLHLAIYLFDRFLSK--RPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILE 113 (127)
T ss_dssp HHHHHHHTT-BH--HHHHHHHHHHHHHHTT--S-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHH
T ss_pred HHHHHHhcccch--hHHHHHHHHHHHHHhh--cccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHH
Confidence 456889999995 7999999999999988 4466778889999999999999976 888999999884 57888888
Q ss_pred HHHHHHHHhCCC
Q 023151 80 SFNSLQNSIGFK 91 (286)
Q Consensus 80 ~yr~l~~~LgL~ 91 (286)
.=+.+-+.||-+
T Consensus 114 ~E~~iL~~L~f~ 125 (127)
T PF00134_consen 114 MEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHTTT-
T ss_pred HHHHHHHHCCCC
Confidence 888888877753
No 23
>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=96.16 E-value=0.018 Score=45.34 Aligned_cols=83 Identities=14% Similarity=0.038 Sum_probs=57.7
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCC-CCCHHHHHHHhCCCHH
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKL-KVDKLKLIEVCGTSET 172 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~-kvtQ~kla~~sgvt~v 172 (286)
++..+..-.+.+. +...|.-+++..-- ....++|.|..+||||+|+|...++. ..-...+...+|++..
T Consensus 6 Fl~~~~~~~~~~~~~~~~a~~l~el~l~---------~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~ 76 (118)
T PF02984_consen 6 FLRRFLKISNADQEVRNLARYLLELSLL---------DYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKE 76 (118)
T ss_dssp HHHHHHTSSSHHHHHHHHHHHHHHHHHH---------SHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HH
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHHHHHh---------hccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHH
Confidence 4555522223333 67777777764221 12256788999999999999999875 5666789999999999
Q ss_pred HHHHHHHHHHHhhh
Q 023151 173 EFASVSTTMKDLCH 186 (286)
Q Consensus 173 t~rnr~ke~~~~c~ 186 (286)
.+...++.|.++..
T Consensus 77 ~l~~c~~~i~~~~~ 90 (118)
T PF02984_consen 77 DLKECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999976443
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=95.99 E-value=0.1 Score=49.99 Aligned_cols=57 Identities=14% Similarity=0.148 Sum_probs=51.8
Q ss_pred CCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhC
Q 023151 11 GLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSG 71 (286)
Q Consensus 11 gL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg 71 (286)
.|| ++|+.+|.++|+++-.. +.+.-.+.-.+.+.|+++||.+...-++.+++++-+.
T Consensus 73 ~lp--~~Vv~TA~~fFkRffL~--nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 73 NLP--TSVVSTAIEFFKRFFLE--NSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred CCc--hHHHHHHHHHHHHHHHh--cchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 466 47999999999999998 7888888999999999999999999999999999766
No 25
>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=95.40 E-value=0.077 Score=45.14 Aligned_cols=78 Identities=14% Similarity=0.015 Sum_probs=62.3
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
|+.|+.+|+|++ .+.++.-.+|.-+....+.|+.+|-+-=...-|+|+.|+..+.+.+..+|.+..+--+-.-...||
T Consensus 18 l~~LC~~L~l~~--~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~~~Vyr 95 (135)
T PF01857_consen 18 LQDLCERLDLSS--DLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQASSHVYR 95 (135)
T ss_dssp HHHHHHHHTTST--THHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--THHHH
T ss_pred HHHHHHHcCCcH--HHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcccccccceE
Confidence 678999999997 699999999999998888999999999999999999999999999999999988764433333444
No 26
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=94.52 E-value=0.21 Score=47.80 Aligned_cols=67 Identities=9% Similarity=0.173 Sum_probs=55.2
Q ss_pred cHHHHHHHhC--Ccc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCC
Q 023151 95 DIRELGIRFG--CIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTS 170 (286)
Q Consensus 95 ~I~~ia~qlg--~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt 170 (286)
.|.++|..|+ ++. |.-.|.-++. ||.. +++-.+++|-.++++|||+||+.-...++=.+++...+-+
T Consensus 62 ~i~~~~~~lkp~Lpq~viaTAivyf~----RFy~-----~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGTAIMYFK----RFYL-----NNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHh----HHhc-----cCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 4888999999 999 9999999988 5543 3456778999999999999999999988877777655544
No 27
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=93.04 E-value=0.74 Score=42.51 Aligned_cols=82 Identities=15% Similarity=0.237 Sum_probs=68.0
Q ss_pred cHHHHHHHhCCc-c--hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCH
Q 023151 95 DIRELGIRFGCI-R--LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSE 171 (286)
Q Consensus 95 ~I~~ia~qlg~s-~--v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~ 171 (286)
.|.+|+-+|||. + +.+.|.||+....-++- +++.|- +-.+=|..|+=+|+..+++..|+..+...||+++
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~-~~~~~v------~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k 74 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFD-SSIIGV------GEICKAVICLDLAATRLQIIFDRQAAVKLSGLSK 74 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhcc-Cccccc------cchhHHHHhHHHHHHHhcccccHHHHHHhccccH
Confidence 378899999993 3 99999999998876655 334443 3567788899999999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 023151 172 TEFASVSTTMKD 183 (286)
Q Consensus 172 vt~rnr~ke~~~ 183 (286)
.+..+-.++++.
T Consensus 75 ~~Y~~~~~sfe~ 86 (262)
T KOG4557|consen 75 KAYSRSFNSFEN 86 (262)
T ss_pred HHHHHHHHHHHH
Confidence 999988887654
No 28
>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=92.64 E-value=0.51 Score=36.92 Aligned_cols=71 Identities=13% Similarity=0.109 Sum_probs=57.3
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDV-IFDRKTAIKLSGMSEKAYNRSFNSLQNSIG 89 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~i-prd~~e~~k~sg~~~k~y~~~yr~l~~~Lg 89 (286)
.+..-|..|..++.... -..+-...-+|+||+++|...++. +.-...+..++|.+...+..|+..|...+-
T Consensus 19 ~~~~~a~~l~el~l~~~--~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~~~i~~~~~ 90 (118)
T PF02984_consen 19 EVRNLARYLLELSLLDY--EFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHHHHHSH--HHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhc--cccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHHHHHHHHHHH
Confidence 58888888888877752 256677889999999999999986 555667899999999999999999988764
No 29
>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=91.86 E-value=1.2 Score=35.51 Aligned_cols=78 Identities=15% Similarity=0.180 Sum_probs=51.3
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCC-CCHHHHHHHhC--CC
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLK-VDKLKLIEVCG--TS 170 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~k-vtQ~kla~~sg--vt 170 (286)
++-+++..++++. +.-.|..+++.|-.. .+..+ .++..+++||+|+||+..... .+=.++...++ .|
T Consensus 37 ~i~~~~~~~~l~~~~~~~A~~~~dr~~~~----~~~~~-----~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~ 107 (127)
T PF00134_consen 37 WIIELCQRLKLSPETLHLAIYLFDRFLSK----RPVNR-----SKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFT 107 (127)
T ss_dssp HHHHHHHHTT-BHHHHHHHHHHHHHHHTT----S-TTC-----CGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSH
T ss_pred HHHHHHHhcccchhHHHHHHHHHHHHHhh----ccccc-----chhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCC
Confidence 5778999999999 999999999955433 22222 257789999999999988773 33345555542 45
Q ss_pred HHHHHHHHHHH
Q 023151 171 ETEFASVSTTM 181 (286)
Q Consensus 171 ~vt~rnr~ke~ 181 (286)
...+......+
T Consensus 108 ~~~i~~~E~~i 118 (127)
T PF00134_consen 108 KKDILEMEREI 118 (127)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 55554444444
No 30
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=90.26 E-value=16 Score=34.19 Aligned_cols=151 Identities=14% Similarity=0.060 Sum_probs=93.1
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHh----hCC---CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAAS----RFD---VIFDRKTAIKLSGMSEKAYNRSFNSLQNSIG 89 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr----~~~---iprd~~e~~k~sg~~~k~y~~~yr~l~~~Lg 89 (286)
..+.-.+.=+=.|..+| +...|.+-.+.|+-|+-.|.. -.+ +||...+.. ..+..+...|..+||
T Consensus 53 DLiqiG~iGLi~Aiery-d~~kg~kF~tyA~~~I~Gei~d~LR~~~~v~vpR~~~~~~-------~~i~~~~~~l~~el~ 124 (247)
T COG1191 53 DLIQIGMIGLIKAIERY-DPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLRELG-------RRIEEAIDELEQELG 124 (247)
T ss_pred HHHHHHHHHHHHHHHHc-CcccCcchHHHHHHHHHHHHHHHHHhCCCccCcHHHHHHH-------HHHHHHHHHHHHHhC
Confidence 45555566566677777 467888888888888877753 222 455444433 357777888888888
Q ss_pred CCCCCcHHHHHHHhCCcc--hHHHHHHHHHHHHHhhhhccccccccCCCC-----C-hh------HHHHHHHHHHHHhCC
Q 023151 90 FKNELDIRELGIRFGCIR--LIPLVQKGLSLFKDRFTAALPASRKTSADF-----S-RP------VFTAVAFYLCAKKHK 155 (286)
Q Consensus 90 L~~~~~I~~ia~qlg~s~--v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~-----~-pp------~~AAAAlY~A~~~~k 155 (286)
..|+..+||..||++. +...-..+ +-+ .++ ++-..-..+.|. . +| ..-...++-|-..+.
T Consensus 125 --r~pt~~EIA~~L~i~~ee~~~~~~~~-~~~--~~~-sld~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~ai~~L~ 198 (247)
T COG1191 125 --REPTDEEIAEELGIDKEEYIEALLAI-NGS--QLL-SLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAIEPLP 198 (247)
T ss_pred --CCCcHHHHHHHhCCCHHHHHHHHHHh-ccc--ccc-chhhhhccccccchhhccccchhHHHHHHHHHHHHHHHHccC
Confidence 6678999999999987 33221111 100 011 111100001111 1 11 133456666655544
Q ss_pred C------------CCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 L------------KVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~------------kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+ -.||++|+++.|||+..+.++-+..
T Consensus 199 EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kka 236 (247)
T COG1191 199 EREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKA 236 (247)
T ss_pred HHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHH
Confidence 4 6999999999999999999998876
No 31
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=89.49 E-value=3 Score=40.68 Aligned_cols=163 Identities=12% Similarity=0.074 Sum_probs=100.7
Q ss_pred HHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCc--chHHHHHHHHHHHHhhCC--CCCCHHHHHHHh--CCCHHHHHHH
Q 023151 7 AKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGV--GEVCKAVICLELAASRFD--VIFDRKTAIKLS--GMSEKAYNRS 80 (286)
Q Consensus 7 a~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Gr--s~~~~aaacLylAcr~~~--iprd~~e~~k~s--g~~~k~y~~~ 80 (286)
++..|... .+.==|.-|+-+...- .++..+. -..-+|||||-+|+++.. +|...+-.+..+ -...+.+.+.
T Consensus 89 ~~~~~~~~--~~~~LA~NYlDRFls~-~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rm 165 (335)
T KOG0656|consen 89 CEEYNFEP--LVFLLAMNYLDRFLSS-QKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRM 165 (335)
T ss_pred HHHhCCch--HHHHHHHHHHHHhhcc-cccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHH
Confidence 33444443 3555555555555541 1343333 367899999999999886 489888888763 3478999999
Q ss_pred HHHHHHHhCCCCCC-----cHHHHHHHhCCcc-----hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHH
Q 023151 81 FNSLQNSIGFKNEL-----DIRELGIRFGCIR-----LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLC 150 (286)
Q Consensus 81 yr~l~~~LgL~~~~-----~I~~ia~qlg~s~-----v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A 150 (286)
=-.+...|+=+... |+.=|..+++... +...+..++- ...+.+ ..+.|.|..+||||.-.+
T Consensus 166 ELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll-------~~~~d~--~Fl~y~pSviAaa~~~~v 236 (335)
T KOG0656|consen 166 ELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLL-------SVITDI--KFLEYPPSVIAAAAILSV 236 (335)
T ss_pred HHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHH-------HHhhhh--hhhcCChHHHHHHHHHHH
Confidence 88888999877642 6888888888854 3333433332 222222 356778999999987555
Q ss_pred HHh-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 151 AKK-HKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 151 ~~~-~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
+.. .+....=.. ....++-.+.++....|++
T Consensus 237 ~~~~~~l~~~~~~------~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 237 SASVDGLDFREYE------NNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHhhcchhhhhhh------HHHHHHHHhhHHhhhcchh
Confidence 432 222111100 2334455666677777777
No 32
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=89.27 E-value=2.1 Score=43.17 Aligned_cols=170 Identities=13% Similarity=0.035 Sum_probs=110.5
Q ss_pred HHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCC-CCCHHHHHHHhC--CCHHHHHHHHHH
Q 023151 7 AKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDV-IFDRKTAIKLSG--MSEKAYNRSFNS 83 (286)
Q Consensus 7 a~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~i-prd~~e~~k~sg--~~~k~y~~~yr~ 83 (286)
=.++||.. ..+.-|.-|.-+...+ ..+.=--.--.++.||.+||....+ +..+++.+-++. .+++.+.++.+.
T Consensus 224 H~~F~llp--eTL~lainiiDrfLs~--~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ 299 (440)
T COG5024 224 HGKFGLLP--ETLFLAINIIDRFLSS--RVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERY 299 (440)
T ss_pred cccccccc--hHHHHHHHHHHHHhcc--CcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHH
Confidence 34555552 4566666666666554 2111112345789999999998864 333555555443 389999999999
Q ss_pred HHHHhCCCCCC-----cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCC
Q 023151 84 LQNSIGFKNEL-----DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLK 157 (286)
Q Consensus 84 l~~~LgL~~~~-----~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~k 157 (286)
+...|+-+... ++++|...-+-+- ....+.-+++- +---...+-+.|...+|||.|.+-+.++..
T Consensus 300 ml~~l~f~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~---------s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~ 370 (440)
T COG5024 300 MLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEI---------SPVDYKFIQISPSWCAAAAMYLSRKILSQN 370 (440)
T ss_pred HhhhcccccCCCChHHHHHHHHhhcccchhhhhhHhhhCCc---------hHhhhhhccCCchHHHHHHHHHHHhhhccC
Confidence 99999876542 7888877666555 44444333331 111111233458889999999999988776
Q ss_pred CCHHHHHHHhC-CCHHHHHHHHHHHHHhhhhhh
Q 023151 158 VDKLKLIEVCG-TSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 158 vtQ~kla~~sg-vt~vt~rnr~ke~~~~c~d~~ 189 (286)
-=...+...+| -+...+...+..+.+.|..-.
T Consensus 371 ~w~~~l~~ySg~y~~~~l~~~~~~~~~~l~~~~ 403 (440)
T COG5024 371 QWDRTLIHYSGNYTNPDLKPLNESNKENLQNPS 403 (440)
T ss_pred CCCccccccCCCCCchhHHHHHHHHHHHhcccc
Confidence 55566788888 666689999988877665443
No 33
>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=88.60 E-value=9 Score=34.59 Aligned_cols=28 Identities=0% Similarity=-0.098 Sum_probs=24.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
....|..+||+..|||+.+++++.+...
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~~al 221 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIESKAL 221 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4678999999999999999999988763
No 34
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.56 E-value=4.1 Score=29.24 Aligned_cols=25 Identities=12% Similarity=0.182 Sum_probs=23.5
Q ss_pred CCCHHHHHHHhCC-CHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGT-SETEFASVSTTM 181 (286)
Q Consensus 157 kvtQ~kla~~sgv-t~vt~rnr~ke~ 181 (286)
..+=.+||..+|. ++..|.+.+++.
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 6788999999999 999999999998
No 35
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=86.74 E-value=2.6 Score=40.95 Aligned_cols=78 Identities=19% Similarity=0.202 Sum_probs=57.9
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHh----CC
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVC----GT 169 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~s----gv 169 (286)
+|-+++.+||++. ....|.-+..+|--. ...-.|++-.+|++|+|+|++..+..+.=.+|..++ +.
T Consensus 45 fI~elg~~L~~~~~ti~tA~~~~hRFy~~---------~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~ 115 (323)
T KOG0834|consen 45 FIQELGVRLKMPQKTIATAIVIFHRFYMF---------HSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNP 115 (323)
T ss_pred HHHHHHHHcCCCccchhhhhhhhhhhhhh---------cccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCc
Confidence 7999999999999 888888888865522 112235566899999999999999999999998877 22
Q ss_pred CHHHHHHHHHHH
Q 023151 170 SETEFASVSTTM 181 (286)
Q Consensus 170 t~vt~rnr~ke~ 181 (286)
...+....|.++
T Consensus 116 ~~~~~~~~~~~~ 127 (323)
T KOG0834|consen 116 KDLELEEVYWEL 127 (323)
T ss_pred ccccHHHHHHHH
Confidence 223555555553
No 36
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=85.31 E-value=1.2 Score=43.40 Aligned_cols=75 Identities=13% Similarity=0.139 Sum_probs=46.7
Q ss_pred HHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHH-HHHHHhCCCHHHHHH-HHHH
Q 023151 7 AKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRK-TAIKLSGMSEKAYNR-SFNS 83 (286)
Q Consensus 7 a~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~-e~~k~sg~~~k~y~~-~yr~ 83 (286)
..-|++|.+.. +.+++-.|=---.+ +.+.---+.+++|+||+|+|+|..+||+... ---++.+..+..|.. ||+.
T Consensus 149 LqtL~~~~~~~-l~Q~~wNfmNDslR-T~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l 225 (367)
T KOG0835|consen 149 LQTLQLPPNLK-LLQAAWNFMNDSLR-TDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRL 225 (367)
T ss_pred HHHhcCCCchh-HHHHHHHhhhhccc-cceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHH
Confidence 35688887532 44444444322222 1343345789999999999999999876432 456677777766643 4443
No 37
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=85.12 E-value=2.3 Score=28.89 Aligned_cols=29 Identities=14% Similarity=0.252 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+-..|+.+||+..|+|..|+....++|.+
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 44599999999999999999999999976
No 38
>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=85.02 E-value=1.2 Score=28.94 Aligned_cols=27 Identities=4% Similarity=0.219 Sum_probs=22.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++|+.+||+..|+|+.|+.+..+.+++
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 578999999999999999999999976
No 39
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=83.80 E-value=5.6 Score=30.93 Aligned_cols=73 Identities=11% Similarity=0.006 Sum_probs=54.8
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHhCCC
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSG-MSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg-~~~k~y~~~yr~l~~~LgL~ 91 (286)
.|++..|+.|........+-.+++.+.--=-+|+|+|-+..| .++.+|.+..| .+.+.+..+++.++..+.-+
T Consensus 3 ~Ii~~Va~~~~v~~~~i~~~~R~~~~~~aR~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~d 76 (90)
T cd06571 3 LIIEAVAEYFGISVEDLRSKSRKKEIALARQIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVRKIEELLEED 76 (90)
T ss_pred HHHHHHHHHhCCCHHHHhcCCCCcCcchHHHHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHHHHHHHHHhC
Confidence 577777888876666543444444444444577888888775 57899999999 99999999999999998754
No 40
>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=83.13 E-value=16 Score=34.28 Aligned_cols=27 Identities=4% Similarity=-0.054 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
....|..+||+..|||+.+||++...-
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~rA 293 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEAKA 293 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467899999999999999999987653
No 41
>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=82.78 E-value=1.9 Score=31.60 Aligned_cols=28 Identities=18% Similarity=0.376 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+||.+||+.+|+|..|+.+..+.|.+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999999987
No 42
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=82.45 E-value=14 Score=35.27 Aligned_cols=27 Identities=11% Similarity=0.021 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+...|-.+|++..|||+.++|++.+.-
T Consensus 274 ~~~~Tl~EIa~~lgiS~erVRqi~~rA 300 (317)
T PRK07405 274 GQPLTLAKIGERLNISRERVRQIEREA 300 (317)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467899999999999999999998764
No 43
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=82.12 E-value=17 Score=36.44 Aligned_cols=112 Identities=7% Similarity=-0.025 Sum_probs=57.6
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCc------HHHHHHHhCCcchHHHHHHHHHHHHHhhhhccccc
Q 023151 57 FDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELD------IRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPAS 130 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~------I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~g 130 (286)
+|.+-+.+++++..|++...+..........+-|..+++ +.++...-+.+.-.....+.+...-...+..|+.-
T Consensus 275 lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~~r 354 (415)
T PRK07598 275 KGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLTSR 354 (415)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCCHH
Confidence 455566677777777777777766665544444443321 22211110111111111111111112334344444
Q ss_pred cccCCCCChhHHHHHHHHHHHHh--CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 131 RKTSADFSRPVFTAVAFYLCAKK--HKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 131 k~~~~D~~pp~~AAAAlY~A~~~--~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
.+ -|+...-. -+...|..+|++..|||..+++++...-
T Consensus 355 eR-------------~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rA 394 (415)
T PRK07598 355 ER-------------DVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKA 394 (415)
T ss_pred HH-------------HHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 32 12222222 2467899999999999999999997664
No 44
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=80.39 E-value=10 Score=34.77 Aligned_cols=47 Identities=21% Similarity=0.353 Sum_probs=37.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC---CCCcHHHHHHHhCCcc
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK---NELDIRELGIRFGCIR 107 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~---~~~~I~~ia~qlg~s~ 107 (286)
.+|-|++++.++-|+.+|.-.-. |....|.+ +-..|-|++..+|++.
T Consensus 103 ~vP~~~~eL~~LPGVGrKTAnvV---L~~a~g~p~i~VDTHV~Rvs~R~gl~~ 152 (211)
T COG0177 103 EVPDTREELLSLPGVGRKTANVV---LSFAFGIPAIAVDTHVHRVSNRLGLVP 152 (211)
T ss_pred CCCchHHHHHhCCCcchHHHHHH---HHhhcCCCcccccchHHHHHHHhCCCC
Confidence 69999999999999999975443 44455555 2336999999999996
No 45
>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=79.86 E-value=4.7 Score=34.19 Aligned_cols=29 Identities=10% Similarity=0.330 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..++||.+||+.+|+|+.|+.+..++|.+
T Consensus 141 ~~~~t~~~iA~~lG~tretvsR~l~~l~~ 169 (193)
T TIGR03697 141 DLRLSHQAIAEAIGSTRVTITRLLGDLRK 169 (193)
T ss_pred cCCCCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 46799999999999999999999999987
No 46
>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=79.24 E-value=4.4 Score=27.57 Aligned_cols=30 Identities=17% Similarity=0.137 Sum_probs=22.9
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
..+-+.+-.+||+..|+|+.|+.+|.+.|+
T Consensus 13 q~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 13 QEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 334567788999999999999999998873
No 47
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=79.18 E-value=3.6 Score=34.90 Aligned_cols=39 Identities=21% Similarity=0.149 Sum_probs=32.5
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccc
Q 023151 150 CAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAK 193 (286)
Q Consensus 150 A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~ 193 (286)
.....+-+.+..+||+..|+|+.|+++|.+.|++ .|+-.
T Consensus 16 ~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~-----~GvI~ 54 (153)
T PRK11179 16 EALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ-----AGIIT 54 (153)
T ss_pred HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCee
Confidence 3445556789999999999999999999999988 66554
No 48
>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=78.89 E-value=0.63 Score=45.42 Aligned_cols=79 Identities=14% Similarity=0.118 Sum_probs=0.0
Q ss_pred HHHHHHhCCc--c-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHH
Q 023151 97 RELGIRFGCI--R-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETE 173 (286)
Q Consensus 97 ~~ia~qlg~s--~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt 173 (286)
.+|+-.+|.. . +.+.|.+++...+ .+...|.... -..=+.+|+|+||..++.+++.......+|+.+..
T Consensus 2 ~~l~p~~~~~~~~~ll~~a~~L~~ls~-~~~~~l~~~~-------EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~ 73 (353)
T PF05460_consen 2 SDLIPKLGGGLPPKLLSKASELYRLSR-QKKSSLKPEE-------EIARAHICAELACERLKEKLDLPYAIKRSPLPPKV 73 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhhhccCCCCCHHHHHHHHHHHHHHH-hcCCCCCCHH-------HHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHH
Confidence 3455556555 3 9999999999877 4333332221 34456799999999999999999999999999999
Q ss_pred HHHHHHHHHH
Q 023151 174 FASVSTTMKD 183 (286)
Q Consensus 174 ~rnr~ke~~~ 183 (286)
..+.|+.|+.
T Consensus 74 y~~l~~~~~~ 83 (353)
T PF05460_consen 74 YKKLLNTFEN 83 (353)
T ss_dssp ----------
T ss_pred HHHHHHHHHH
Confidence 9999999965
No 49
>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=78.72 E-value=6.3 Score=27.56 Aligned_cols=45 Identities=13% Similarity=0.249 Sum_probs=31.4
Q ss_pred CChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 137 FSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 137 ~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++++.|. .|+.-...-+..+++.+|++..++++.++....+.|++
T Consensus 3 lt~~q~~--vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 3 LTPSQFR--VLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp STHHHHH--HHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCHHHHH--HHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444443 23333333333489999999999999999999999977
No 50
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=78.36 E-value=4 Score=35.11 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=32.7
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccc
Q 023151 150 CAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAK 193 (286)
Q Consensus 150 A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~ 193 (286)
...+.+-+.+-.+||+..|+|+.|+++|.+.|++ .|+-+
T Consensus 21 ~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~-----~GvI~ 59 (164)
T PRK11169 21 NELQKDGRISNVELSKRVGLSPTPCLERVRRLER-----QGFIQ 59 (164)
T ss_pred HHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCeE
Confidence 3455666788999999999999999999999988 66644
No 51
>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=77.71 E-value=9.4 Score=26.90 Aligned_cols=29 Identities=7% Similarity=0.274 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...+++.+||+..|+++.|+....+.|.+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45689999999999999999999999976
No 52
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=77.62 E-value=28 Score=33.92 Aligned_cols=26 Identities=8% Similarity=0.079 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...|..+|++..|||+..||++...-
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~~A 349 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAKA 349 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998764
No 53
>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=77.57 E-value=7.4 Score=28.31 Aligned_cols=37 Identities=16% Similarity=0.190 Sum_probs=32.4
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 146 AFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 146 AlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++|.... .+..++-.+||+..||+++|+....+.|.+
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 5777776 888999999999999999999999999977
No 54
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=76.55 E-value=7.6 Score=36.37 Aligned_cols=73 Identities=19% Similarity=0.213 Sum_probs=52.4
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHH
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETE 173 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt 173 (286)
.|..++..+.+-+ |...|.-.+.+|-- |.+-.+|+|-.+|+-|+|+||+. |.++ -+-
T Consensus 47 ~I~~lg~~lklRQ~ViATAivY~rRfy~---------r~S~k~~~p~lla~TClyLAcKv-----------EE~~--i~~ 104 (264)
T KOG0794|consen 47 VIQKLGQHLKLRQRVIATAIVYFRRFYL---------RKSLKEIEPRLLAPTCLYLACKV-----------EECP--IVH 104 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHhhhccCHHHHHHHHHHHHhhh-----------hhcc--hHH
Confidence 4888999999988 88888887774432 34456789999999999999974 3344 355
Q ss_pred HHHHHHHHHHhhhhhh
Q 023151 174 FASVSTTMKDLCHDVF 189 (286)
Q Consensus 174 ~rnr~ke~~~~c~d~~ 189 (286)
+|.++.+...+|.-..
T Consensus 105 ~r~l~~~a~~L~~~f~ 120 (264)
T KOG0794|consen 105 IRLLVNEAKVLKTRFS 120 (264)
T ss_pred HHHHHHHHHHHhhhcc
Confidence 6666666666654433
No 55
>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=76.09 E-value=12 Score=29.47 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=32.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
....++|.+||+.+|+++.|+.+..++|++ .|+-...
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~-----~GlI~r~ 80 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR-----RRIIFRQ 80 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCeeee
Confidence 678999999999999999999999999987 6665543
No 56
>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=76.07 E-value=5.3 Score=31.18 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccc
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAK 193 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~ 193 (286)
+..|.=+.|++..++++.||||-...+++ +|+-.
T Consensus 21 ~~PVgSk~ia~~l~~s~aTIRN~M~~Le~-----lGlve 54 (78)
T PF03444_consen 21 GEPVGSKTIAEELGRSPATIRNEMADLEE-----LGLVE 54 (78)
T ss_pred CCCcCHHHHHHHHCCChHHHHHHHHHHHH-----CCCcc
Confidence 45577788999999999999999999988 66554
No 57
>PF13730 HTH_36: Helix-turn-helix domain
Probab=76.06 E-value=14 Score=25.44 Aligned_cols=27 Identities=11% Similarity=0.099 Sum_probs=24.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
-.++..||+.+|+++.||++..+++++
T Consensus 25 ~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 25 FPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 348999999999999999999999976
No 58
>PRK05949 RNA polymerase sigma factor; Validated
Probab=76.04 E-value=32 Score=33.11 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+...|-.+|++..|+|..++|++...-
T Consensus 284 ~e~~Tl~EIa~~lgiS~erVrq~~~rA 310 (327)
T PRK05949 284 GKELSLAKVGERLNLSRERVRQLEHQA 310 (327)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 367899999999999999999997664
No 59
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=76.02 E-value=5.6 Score=27.16 Aligned_cols=29 Identities=17% Similarity=0.176 Sum_probs=25.9
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+..+ +..+||+..|+|..|++..++.|.+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3345 8999999999999999999999987
No 60
>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=75.46 E-value=17 Score=30.86 Aligned_cols=79 Identities=14% Similarity=0.083 Sum_probs=49.5
Q ss_pred HHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHH
Q 023151 96 IRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEF 174 (286)
Q Consensus 96 I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~ 174 (286)
+.+||..|++++ +.+..-.+.+..-. ....|=-++ .-.++---|+|..|+..+..++-++|...-.--|..-
T Consensus 18 l~~LC~~L~l~~~~~~~iwt~fe~~l~-~~t~L~~dR------HLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~ 90 (135)
T PF01857_consen 18 LQDLCERLDLSSDLREKIWTCFEHSLT-HHTELMKDR------HLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQAS 90 (135)
T ss_dssp HHHHHHHHTTSTTHHHHHHHHHHHHHH-HSGGGGTTS-------HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--
T ss_pred HHHHHHHcCCcHHHHHHHHHHHHHHHH-hhHHHHhcc------hHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhccccc
Confidence 778999999999 77766665554332 122332333 4577999999999999998888888877665554444
Q ss_pred HHHHHHH
Q 023151 175 ASVSTTM 181 (286)
Q Consensus 175 rnr~ke~ 181 (286)
...|.+.
T Consensus 91 ~~Vyr~V 97 (135)
T PF01857_consen 91 SHVYRSV 97 (135)
T ss_dssp THHHHSE
T ss_pred ccceEEE
Confidence 4444443
No 61
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.22 E-value=5.3 Score=26.31 Aligned_cols=28 Identities=11% Similarity=0.284 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+++.+||+..|++..|+.+..+.|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999999976
No 62
>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=75.07 E-value=44 Score=28.21 Aligned_cols=86 Identities=19% Similarity=0.092 Sum_probs=60.9
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhh---hcCCCCCCcchHHHHHHHHHHHHhhC-CCCCCHHHHHHHhCCCHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDV---QFDSSIIGVGEVCKAVICLELAASRF-DVIFDRKTAIKLSGMSEKAYN 78 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~---k~~~l~~Grs~~~~aaacLylAcr~~-~iprd~~e~~k~sg~~~k~y~ 78 (286)
+.+|.....++. .+.=-|-.|++++.. .....+...+..-+..+||-+|.+.+ ....+-...++++|++.+++.
T Consensus 58 l~ri~~~~~~s~--~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~eln 135 (149)
T PF08613_consen 58 LSRILKYTQCSP--ECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKELN 135 (149)
T ss_dssp HHHHHHHTT--H--HHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHcCCCh--HHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHHH
Confidence 567888888874 577777777666666 32122445688899999999999987 589999999999999999999
Q ss_pred HHHHHHHHHhCC
Q 023151 79 RSFNSLQNSIGF 90 (286)
Q Consensus 79 ~~yr~l~~~LgL 90 (286)
..=+.+-..||-
T Consensus 136 ~lE~~fL~~l~~ 147 (149)
T PF08613_consen 136 ELEREFLKLLDY 147 (149)
T ss_dssp HHHHHHHHHTTT
T ss_pred HHHHHHHHHCCC
Confidence 888888777764
No 63
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=74.74 E-value=49 Score=30.52 Aligned_cols=31 Identities=13% Similarity=0.090 Sum_probs=26.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLC 185 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c 185 (286)
....|+++||+..|||+.+++++.+.....+
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3478999999999999999999998865433
No 64
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=74.67 E-value=35 Score=33.65 Aligned_cols=26 Identities=0% Similarity=-0.000 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...|..+|++..|||..+||++.+.-
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rA 355 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKA 355 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999999875
No 65
>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=74.63 E-value=5.6 Score=27.51 Aligned_cols=32 Identities=16% Similarity=0.188 Sum_probs=27.1
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVSTTMKDL 184 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~ 184 (286)
..+..+|-.+||+..|||+.||++-.++|.+.
T Consensus 11 ~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 11 ESKEPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp HTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred HcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 35556999999999999999999999999773
No 66
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=74.47 E-value=14 Score=31.24 Aligned_cols=49 Identities=12% Similarity=0.156 Sum_probs=36.9
Q ss_pred CcchHHHHHHHHHHHHhhCC----------CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 39 GVGEVCKAVICLELAASRFD----------VIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 39 Grs~~~~aaacLylAcr~~~----------iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
..+.....+..|..=|...| +|++.++++.+.|+++..+.+.++.|.+.
T Consensus 112 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 112 HRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred hCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 34666777777654444432 68889999999999999999999888875
No 67
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=74.43 E-value=82 Score=32.52 Aligned_cols=27 Identities=7% Similarity=0.085 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+...|..+|+...|||+..||++.+.-
T Consensus 465 ~e~~TL~EIa~~lGVSrERVRQIe~kA 491 (509)
T PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIESKT 491 (509)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999999998875
No 68
>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=73.83 E-value=64 Score=28.55 Aligned_cols=30 Identities=10% Similarity=0.034 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLC 185 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c 185 (286)
...+.++||+..|+|+.|++.+.......+
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 467999999999999999999987765433
No 69
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=73.57 E-value=7.1 Score=34.48 Aligned_cols=35 Identities=11% Similarity=0.152 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
+++||.+||+..|+|++|+.+..++|.+ .|+-.-.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~-----~g~I~~~ 217 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQK-----SGMLAVK 217 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHH-----CCCEEec
Confidence 6799999999999999999999999977 6554433
No 70
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=73.46 E-value=6.1 Score=26.77 Aligned_cols=27 Identities=7% Similarity=0.032 Sum_probs=19.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+..+||...||++.||++..+.+.+
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 688999999999999999999988865
No 71
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=73.32 E-value=17 Score=25.90 Aligned_cols=71 Identities=24% Similarity=0.318 Sum_probs=39.1
Q ss_pred cHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhC-CCCCCHHHHHHHhCC-CHHHHHH
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRF-DVIFDRKTAIKLSGM-SEKAYNR 79 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~-~iprd~~e~~k~sg~-~~k~y~~ 79 (286)
-|.+||..+|++.. .+.|.....+ +.... .... -.=+..|+..+ ..+.++++++..+|+ +...+.+
T Consensus 3 ~~~~la~~~~~s~~--------~l~~~f~~~~-~~s~~--~~~~-~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r 70 (84)
T smart00342 3 TLEDLAEALGMSPR--------HLQRLFKKET-GTTPK--QYLR-DRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSR 70 (84)
T ss_pred CHHHHHHHhCCCHH--------HHHHHHHHHh-CcCHH--HHHH-HHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHH
Confidence 37899999999852 2333333321 11111 1110 01122233322 227999999999999 8888877
Q ss_pred HHHHH
Q 023151 80 SFNSL 84 (286)
Q Consensus 80 ~yr~l 84 (286)
.++..
T Consensus 71 ~Fk~~ 75 (84)
T smart00342 71 AFKKL 75 (84)
T ss_pred HHHHH
Confidence 76543
No 72
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=73.24 E-value=45 Score=30.90 Aligned_cols=165 Identities=17% Similarity=0.070 Sum_probs=84.4
Q ss_pred HHHHHh---CCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHH----hhCC----CCCCHHHHHHHhCCC
Q 023151 5 DIAKKL---GLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAA----SRFD----VIFDRKTAIKLSGMS 73 (286)
Q Consensus 5 ria~kL---gL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAc----r~~~----iprd~~e~~k~sg~~ 73 (286)
.+|.++ |++- ..++..+..=+=+|..+|+ ..+|..-.+.|+-.+.-+. +..+ +|+...+.
T Consensus 55 ~iA~~y~~~g~~~-~DLiQeG~iGLi~AierFD-p~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~Pr~~~~~------- 125 (264)
T PRK07122 55 HIARRFDGRGEPR-DDLVQVARVGLVNAVNRFD-VETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKEL------- 125 (264)
T ss_pred HHHHHHHhCCCCH-HHHHHHHHHHHHHHHHHcC-CCCCCChHHHHHHHHHHHHHHHHHHcCCccccCHHHHHH-------
Confidence 344444 5544 2555555553444666674 4677766666555554444 2222 45554432
Q ss_pred HHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccc----cc---cCCCCCh-hH--H
Q 023151 74 EKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPAS----RK---TSADFSR-PV--F 142 (286)
Q Consensus 74 ~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~g----k~---~~~D~~p-p~--~ 142 (286)
-..+.++.+.+...|| ..|++.+||..||++. -...+...... ....||..- .. .-.|+.+ +. +
T Consensus 126 ~~~i~~~~~~l~~~lg--~~pt~~eiA~~lg~~~~~v~~~~~~~~~---~~~~SLd~~~~~~~~~~~~~~d~~~~~~~~~ 200 (264)
T PRK07122 126 HLRLGRATAELSQRLG--RAPTASELAAELGMDREEVVEGLVAGSA---YNTLSIDSGGGSGDDDARAIADTLGDVDAGL 200 (264)
T ss_pred HHHHHHHHHHHHHHhC--CCCCHHHHHHHhCCCHHHHHHHHHHhhc---CCCCcccccccCCCCCcccchhccCCcHHHH
Confidence 2345566677777776 3446888888888877 22222221111 111122211 00 0111111 10 0
Q ss_pred ----HHHHHHHHH------------HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 143 ----TAVAFYLCA------------KKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 143 ----AAAAlY~A~------------~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
....|.-+- .......|..+||+..|+|..+++++.+....
T Consensus 201 e~~~~~~~l~~~l~~L~~rer~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~ 257 (264)
T PRK07122 201 DQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLA 257 (264)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 011111111 11235789999999999999999998876644
No 73
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=72.37 E-value=9.7 Score=32.80 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.++||.+||+..|+|+.|+.+..++|.+
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5799999999999999999999999987
No 74
>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=71.00 E-value=4.6 Score=29.06 Aligned_cols=42 Identities=17% Similarity=0.195 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc-hHHHHHHHHH
Q 023151 75 KAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR-LIPLVQKGLS 117 (286)
Q Consensus 75 k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~-v~~~A~eiL~ 117 (286)
+.+.|-++.|+-+++ +..+++.+||.++|||+ ..+.-..-|+
T Consensus 2 k~i~rq~~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 2 KDIKRQLKLLELLLK-NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567788888888888 88889999999999999 4443333333
No 75
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=70.65 E-value=48 Score=32.71 Aligned_cols=154 Identities=16% Similarity=0.049 Sum_probs=98.8
Q ss_pred HHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHH-HHHhh--CCCCCCHHHHHHHhC--CCHHHHHH
Q 023151 5 DIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLE-LAASR--FDVIFDRKTAIKLSG--MSEKAYNR 79 (286)
Q Consensus 5 ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLy-lAcr~--~~iprd~~e~~k~sg--~~~k~y~~ 79 (286)
.+-.+.||.. ..+=-|=-|+-+...+ ..+...-..++++.||. +||+. ...|. .++.+-++. .+++.+-+
T Consensus 167 evh~~F~L~~--ETL~LaVnliDRfL~~--~~v~~~~lqLvgvsalf~IA~K~EE~~~P~-v~dlv~isd~~~s~~~il~ 241 (391)
T KOG0653|consen 167 EVHEKFGLSP--ETLYLAVNLIDRFLSK--VKVPLKKLQLVGVSALLSIACKYEEISLPS-VEDLVLITDGAYSREEILR 241 (391)
T ss_pred HhhhhcCcCH--HHHHHHHHHHHHHHHH--hcccHHHhhHHhHHHHHHHHHhhhhccCCc-cceeEeeeCCccchHHHHH
Confidence 4456677764 4666666666666665 23556667888888855 99997 34453 444444333 47788888
Q ss_pred HHHHHHHHhCCCCC-----CcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHh
Q 023151 80 SFNSLQNSIGFKNE-----LDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKK 153 (286)
Q Consensus 80 ~yr~l~~~LgL~~~-----~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~ 153 (286)
+=+.+.+.|+-... .|++++....+..- ....+.-+++.+.=.+. .+-+.|+..|||++|++-..
T Consensus 242 mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~---------~~~~~~s~~aaa~~~~~~~~ 312 (391)
T KOG0653|consen 242 MEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYS---------MLSIPPSSSAAASFTLALRM 312 (391)
T ss_pred HHHHHHhccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhH---------HhccCcHHHHHHHHHHHHHH
Confidence 87777777765443 27999988888544 55555555554332221 12235788999999999998
Q ss_pred CCCCC-CHHHHHHHhCCCHH
Q 023151 154 HKLKV-DKLKLIEVCGTSET 172 (286)
Q Consensus 154 ~k~kv-tQ~kla~~sgvt~v 172 (286)
...+. =...+..-+|=+..
T Consensus 313 ~~~~~~w~~~~~~~sg~~~~ 332 (391)
T KOG0653|consen 313 LSKGDVWSPTLEHYSGYSES 332 (391)
T ss_pred hccCCccCCCCeeccCCCcH
Confidence 88874 44456666664433
No 76
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=70.03 E-value=3.1 Score=37.42 Aligned_cols=83 Identities=17% Similarity=0.146 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCCCcHHHHHHHhCCcc--hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCC
Q 023151 80 SFNSLQNSIGFKNELDIRELGIRFGCIR--LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLK 157 (286)
Q Consensus 80 ~yr~l~~~LgL~~~~~I~~ia~qlg~s~--v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~k 157 (286)
.+..|.+-+-.+..+.|-+||+.|||+. ++++-..|+.. .-++|+-..++..|=.++--+.|.|-|+-.+ -+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~---g~ltGv~DdrGkfIyIs~eE~~~va~fi~~r---GR 173 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAE---GRLTGVIDDRGKFIYISEEEMEAVAKFIKQR---GR 173 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHH---SSS-EEE-TT--EEE---------------------
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHC---CCceeeEcCCCCeEEecHHHHHHHHHHHHHc---CC
Confidence 5666666666677789999999999998 88877777764 5566666666666656888899999998664 45
Q ss_pred CCHHHHHHHhC
Q 023151 158 VDKLKLIEVCG 168 (286)
Q Consensus 158 vtQ~kla~~sg 168 (286)
|+-.+|+..|+
T Consensus 174 vsi~el~~~~N 184 (188)
T PF09756_consen 174 VSISELAQESN 184 (188)
T ss_dssp -----------
T ss_pred ccHHHHHHHHH
Confidence 67777777665
No 77
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=69.67 E-value=8.6 Score=31.83 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
+-+.++.+||+..|+|+.|+++|.+.|++ .||-+..
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~-----~GiI~~~ 55 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEE-----EGVIKGY 55 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHH-----CCceeeE
Confidence 34489999999999999999999999988 6655543
No 78
>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=68.92 E-value=69 Score=29.15 Aligned_cols=28 Identities=11% Similarity=0.182 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...|+.+||+..|+|+.+++.+.+....
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ral~ 248 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAALK 248 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4679999999999999999999877643
No 79
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=68.61 E-value=16 Score=24.93 Aligned_cols=39 Identities=10% Similarity=-0.099 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
++...-.....++....|.+.||...||+..|++++..+
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 333333344444455599999999999999999999875
No 80
>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=68.12 E-value=7.1 Score=25.39 Aligned_cols=28 Identities=14% Similarity=0.341 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+|.+.++++.+.|+++..+.|.+..|++
T Consensus 1 l~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 1 LPMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp EE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 3678888888888888888888887765
No 81
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=67.57 E-value=7.1 Score=33.51 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=29.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccc
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAK 193 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~ 193 (286)
..++||.+||+..|+|+.|+.+..++|.+ .|+-.
T Consensus 147 ~~~~t~~~iA~~lG~tretvsR~l~~l~~-----~g~I~ 180 (202)
T PRK13918 147 MIYATHDELAAAVGSVRETVTKVIGELSR-----EGYIR 180 (202)
T ss_pred EecCCHHHHHHHhCccHHHHHHHHHHHHH-----CCCEE
Confidence 45799999999999999999999999987 55554
No 82
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=66.96 E-value=9 Score=26.02 Aligned_cols=28 Identities=7% Similarity=0.006 Sum_probs=19.2
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 152 KKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
.++....+..+||...|+++.||.+-.+
T Consensus 15 ~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 15 ALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 4456779999999999999999988654
No 83
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=66.84 E-value=91 Score=29.14 Aligned_cols=33 Identities=9% Similarity=0.234 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc
Q 023151 75 KAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR 107 (286)
Q Consensus 75 k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~ 107 (286)
+.+...++.+...||...++++.+||..||++.
T Consensus 133 ~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~ 165 (284)
T PRK06596 133 RKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSE 165 (284)
T ss_pred HHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCH
Confidence 455666777888888656678999999999998
No 84
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=66.48 E-value=84 Score=30.28 Aligned_cols=27 Identities=7% Similarity=0.041 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+...|..+|++..|||+..||++.+.-
T Consensus 280 ~~~~Tl~eIa~~lgvS~eRVrQIe~~A 306 (324)
T PRK07921 280 GQPRTLDQIGKLFGLSRERVRQIEREV 306 (324)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 356899999999999999999998774
No 85
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=66.37 E-value=15 Score=36.88 Aligned_cols=53 Identities=19% Similarity=0.128 Sum_probs=42.7
Q ss_pred cHHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCC
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFD 58 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~ 58 (286)
|+++|..--||.. ..+..|=.||.++..+ |++.-.+--+.|.|||-+|+.+..
T Consensus 388 EMr~l~~d~~id~--~TVa~AyVYFEKliLk--glisK~NRKlcAGAclLlaaKmnD 440 (497)
T KOG4164|consen 388 EMRELGEDCGIDV--VTVAMAYVYFEKLILK--GLISKQNRKLCAGACLLLAAKMND 440 (497)
T ss_pred HHHHhhhccCccc--eeehhHHHHHHHHHHh--hhhhhhhhhHHHHHHHHHHHHhhh
Confidence 4455555555543 5789999999999999 888888889999999999999874
No 86
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=66.26 E-value=90 Score=27.93 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...|..+||+..|+|+.|++++...-..
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3578999999999999999998876544
No 87
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=66.20 E-value=56 Score=33.55 Aligned_cols=36 Identities=11% Similarity=-0.084 Sum_probs=30.5
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 152 KKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
.+....++-.++|+...||+.|+.+-.+.++..+..
T Consensus 87 Ll~~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~~ 122 (584)
T PRK09863 87 LLLNTFTPMAQLASALNLSRTWVAERLPRLNQRYER 122 (584)
T ss_pred HHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHhhhc
Confidence 344567899999999999999999999999876654
No 88
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=65.94 E-value=68 Score=30.76 Aligned_cols=32 Identities=3% Similarity=-0.070 Sum_probs=26.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhh
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCH 186 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~ 186 (286)
-...|..+||+..|||+.|++++...-.....
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr 311 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRLR 311 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999877654333
No 89
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=65.59 E-value=6 Score=30.08 Aligned_cols=25 Identities=16% Similarity=0.315 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
...||.++|...|||+.||-++.++
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 3579999999999999999887665
No 90
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=65.30 E-value=12 Score=26.25 Aligned_cols=38 Identities=16% Similarity=0.124 Sum_probs=33.1
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 023151 147 FYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDL 184 (286)
Q Consensus 147 lY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~ 184 (286)
+++.-..+....+...||..-||++.|+.+.++.|.+.
T Consensus 9 lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~ 46 (53)
T PF13613_consen 9 LLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPL 46 (53)
T ss_pred HHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHH
Confidence 45566677889999999999999999999999999763
No 91
>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=65.26 E-value=7.1 Score=26.75 Aligned_cols=26 Identities=15% Similarity=0.247 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
....||.++|+.+|+++.|+.+....
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 45689999999999999999988765
No 92
>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=64.81 E-value=12 Score=28.48 Aligned_cols=45 Identities=18% Similarity=0.281 Sum_probs=33.4
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 146 AFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 146 AlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
-+|+|..-.+..++-.+||+..|+++..++.+.+.+.+ -|+-...
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~-----~Gli~s~ 58 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK-----AGLIESS 58 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH-----TTSEEEE
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh-----CCeeEec
Confidence 34454444444599999999999999999999999987 6665555
No 93
>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=64.60 E-value=8 Score=26.24 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
....||.++|+.+|+++.|+.+..+
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3468999999999999999988764
No 94
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=64.44 E-value=39 Score=30.21 Aligned_cols=120 Identities=10% Similarity=0.080 Sum_probs=73.0
Q ss_pred HHHHHHHHHHHHhhCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC-CCCCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 43 VCKAVICLELAASRFDVI-FDRKTAIKLSGMSEKAYNRSFNSLQNSIGF-KNELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 43 ~~~aaacLylAcr~~~ip-rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL-~~~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
...+=|.||+ .|-| +++++++++.|++...+..+...|.....- +.++-|.+++.-+-+. +...-.+.+.
T Consensus 6 ~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~-tk~e~~~~v~--- 77 (188)
T PRK00135 6 KSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLV-TKEENADYLQ--- 77 (188)
T ss_pred HHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEE-EcHHHHHHHH---
Confidence 3444455554 6777 999999999999999999999999888753 3334343333322111 1222222333
Q ss_pred HhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 121 DRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 121 e~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++.. ..+ ...++++.+-. +|..-.+.++|+.+|++.-||+. .+..+++.+
T Consensus 78 -~~~~---~~~--~~~LS~aaLEt----LaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~ 127 (188)
T PRK00135 78 -KLVK---TPI--KQSLSQAALEV----LAIIAYKQPITRIEIDEIRGVNS---DGALQTLLA 127 (188)
T ss_pred -HHhc---ccc--cCCCCHHHHHH----HHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence 2221 111 11223333222 33445778999999999999996 788888766
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=64.44 E-value=8.9 Score=27.96 Aligned_cols=29 Identities=14% Similarity=0.337 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
+|++.++++.++|+++..+.+.++.|.+.
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 68899999999999999999999999874
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=64.40 E-value=14 Score=28.94 Aligned_cols=29 Identities=10% Similarity=0.213 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+-..+..+|++..|+++.|++++.+.|.+
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34689999999999999999999999987
No 97
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=64.09 E-value=96 Score=28.46 Aligned_cols=26 Identities=15% Similarity=0.224 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...|..+||+..|+|+.|++++....
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~ra 252 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTKA 252 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 36889999999999999999887554
No 98
>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=63.70 E-value=3.5 Score=39.57 Aligned_cols=64 Identities=16% Similarity=0.150 Sum_probs=46.4
Q ss_pred HHHHHhCCCCC--CcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCC
Q 023151 83 SLQNSIGFKNE--LDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHK 155 (286)
Q Consensus 83 ~l~~~LgL~~~--~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k 155 (286)
++.+++++..- ..|.++|.+|.++. +...|.-+..+|-= +..-..+++-.++++|||+||+..+
T Consensus 37 ~~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~L---------k~sv~e~~~~~vv~tcv~LA~K~ed 103 (297)
T COG5333 37 TLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYL---------KNSVEEISLYSVVTTCVYLACKVED 103 (297)
T ss_pred chhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHh---------hcccccccHHHHHHhheeeeeeccc
Confidence 34444444332 25999999999999 98999888885442 2223335678899999999999877
No 99
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=63.54 E-value=1.2e+02 Score=27.52 Aligned_cols=152 Identities=7% Similarity=-0.062 Sum_probs=79.6
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHh----h-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAAS----R-FDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr----~-~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
.++..+-.-+=.+..+|+. ..| +-.+.+.-.+.-++. . ...|++..+- .+.+.++.+.+...+|
T Consensus 47 DLvQeg~igL~~a~~~fd~-~~~-~F~tYa~~~Ir~~il~~lr~~~~~~r~vr~~-------~~~i~~~~~~l~~~~g-- 115 (231)
T PRK12427 47 DMEQIALMGLLEALRRYGH-PDE-QFAAYAVHRIRGAILDELRELDWRPRRLRQK-------THKTNDAIREIAKRLG-- 115 (231)
T ss_pred HHHHHHHHHHHHHHHhcCC-CCC-ChHHHHHHHHHHHHHHHHHhcCCCCHHHHHH-------HHHHHHHHHHHHHHHC--
Confidence 4545554423334455653 234 555666666666653 2 2345554332 2456788888888888
Q ss_pred CCCcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccc--cccC---CCCC-hh--HHHHHHHHHHHHhC--------
Q 023151 92 NELDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPAS--RKTS---ADFS-RP--VFTAVAFYLCAKKH-------- 154 (286)
Q Consensus 92 ~~~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~g--k~~~---~D~~-pp--~~AAAAlY~A~~~~-------- 154 (286)
..|++.+||..||++. -...+..... -....||..- .... ++.. +. ......|-.+...+
T Consensus 116 ~~pt~~eiA~~lg~~~~~v~~~~~~~~---~~~~~SLd~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~er~vi 192 (231)
T PRK12427 116 HEPNFEEISAELNLTAEEYQEYLLLEN---AGTLESLDELLALEAHNDILQSRDLEENIIIEDNLKQALSQLDEREQLIL 192 (231)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHhc---cCCceeccCcccCCCcccccCCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 3457999999999987 2222222110 0111111110 0000 1001 11 11111122222122
Q ss_pred ----CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 155 ----KLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 155 ----k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
....|..+||+..|+|+.+++++-+...
T Consensus 193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~ 224 (231)
T PRK12427 193 HLYYQHEMSLKEIALVLDLTEARICQLNKKIA 224 (231)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 2478999999999999999998887764
No 100
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=63.41 E-value=15 Score=27.88 Aligned_cols=31 Identities=13% Similarity=0.217 Sum_probs=24.1
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 149 LCAKKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 149 ~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
+.......+.||.++|+..|+++.+|.++..
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 5666777889999999999999999998775
No 101
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=63.35 E-value=9.4 Score=34.11 Aligned_cols=29 Identities=10% Similarity=0.250 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..++||.+||+..|+++.|+.+..++|.+
T Consensus 177 ~i~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 177 ALPMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred EecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35789999999999999999999999987
No 102
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=62.34 E-value=29 Score=28.71 Aligned_cols=53 Identities=9% Similarity=0.108 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccCC
Q 023151 136 DFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKKD 197 (286)
Q Consensus 136 D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~~ 197 (286)
|+++++|..-.+ ......+++.+|++..|+++.|+....+.|++ -|.-....+
T Consensus 37 glt~~q~~vL~~----l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~-----~GlI~R~~~ 89 (144)
T PRK11512 37 DITAAQFKVLCS----IRCAACITPVELKKVLSVDLGALTRMLDRLVC-----KGWVERLPN 89 (144)
T ss_pred CCCHHHHHHHHH----HHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEeccC
Confidence 456777644332 22345699999999999999999999999977 555555543
No 103
>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=62.13 E-value=14 Score=29.24 Aligned_cols=36 Identities=22% Similarity=0.147 Sum_probs=31.3
Q ss_pred HHHHH-hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 148 YLCAK-KHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 148 Y~A~~-~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+..++ ++....||++|++..|||-.||.+.-+.+..
T Consensus 39 ~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 39 WQVAKELLDEGKSYREIAEETGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 44455 8888999999999999999999999998865
No 104
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=61.87 E-value=1.4e+02 Score=27.99 Aligned_cols=32 Identities=13% Similarity=0.009 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhh
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCH 186 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~ 186 (286)
....|..+||+..|||+.+++++...-.....
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr 274 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARALEKLR 274 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999988655433
No 105
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=61.68 E-value=7.9 Score=27.36 Aligned_cols=24 Identities=13% Similarity=0.232 Sum_probs=17.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.+|+.+||..+|+++.||.+.++.
T Consensus 10 ~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 10 GITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp T--HHHHHHHHT--HHHHHHHHTT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 459999999999999999998864
No 106
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=61.50 E-value=87 Score=28.53 Aligned_cols=27 Identities=11% Similarity=0.197 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
...|+.+||+..|+|+.+++.+.+...
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~al 250 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAAL 250 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467999999999999999999877653
No 107
>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=61.43 E-value=83 Score=29.20 Aligned_cols=29 Identities=3% Similarity=-0.019 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
-...|..+||+..|+|+.|++++...-..
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlk 268 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALK 268 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999876433
No 108
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=60.34 E-value=44 Score=27.46 Aligned_cols=59 Identities=5% Similarity=0.180 Sum_probs=41.1
Q ss_pred CChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccCChhhhhc
Q 023151 137 FSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKKDPRELKS 203 (286)
Q Consensus 137 ~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~~~~~~~~ 203 (286)
++++.|.. ++..+ ..+...+|.+|++..|+++.|+....+.|++ -|.-....+|..-+.
T Consensus 29 lt~~q~~v--L~~l~-~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~-----~GlV~r~~~~~DrR~ 87 (144)
T PRK03573 29 LTQTHWVT--LHNIH-QLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE-----KGLISRQTCASDRRA 87 (144)
T ss_pred CCHHHHHH--HHHHH-HcCCCCCHHHHHHHhCCChhhHHHHHHHHHH-----CCCEeeecCCCCcCe
Confidence 45666542 22222 2345689999999999999999999999987 677666655444443
No 109
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=60.28 E-value=26 Score=32.25 Aligned_cols=60 Identities=10% Similarity=0.053 Sum_probs=51.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc-hHHHHHHHHH
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR-LIPLVQKGLS 117 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~-v~~~A~eiL~ 117 (286)
....+-.+|++..+++.+.+.+-...+-+.||++....+-.+|.+.|+.. +-..+.+|+.
T Consensus 156 a~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~eLv~~A~~~gli~~~~~~~~~ii~ 216 (217)
T PRK13719 156 SFGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDELLIILHTSEMIFYLYKKVFEIIN 216 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence 44688999999999999999999999999999988887778888888877 7777777653
No 110
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=60.01 E-value=15 Score=32.78 Aligned_cols=40 Identities=15% Similarity=-0.001 Sum_probs=31.7
Q ss_pred HHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 47 VICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 47 aacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
|.-+|++-=+.+-|.|++|+++..|+|++.+..+.+-|+.
T Consensus 28 VG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 28 VGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 4445555445688999999999999999999988887764
No 111
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=59.82 E-value=28 Score=30.12 Aligned_cols=42 Identities=10% Similarity=0.053 Sum_probs=29.3
Q ss_pred CChhHHHHHHHHHHHHhCC---CCCCHHHHHHHhCCCHHHHHHHH
Q 023151 137 FSRPVFTAVAFYLCAKKHK---LKVDKLKLIEVCGTSETEFASVS 178 (286)
Q Consensus 137 ~~pp~~AAAAlY~A~~~~k---~kvtQ~kla~~sgvt~vt~rnr~ 178 (286)
+++-+.-||.+...--++. .+.|+.+||+.+||++.|+=+.-
T Consensus 11 L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 11 LTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp S-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHH
Confidence 3577788888877776666 56999999999999999975544
No 112
>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=59.71 E-value=11 Score=30.29 Aligned_cols=32 Identities=13% Similarity=0.102 Sum_probs=27.1
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 151 AKKHKLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 151 ~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
..+.+...||++||+..|||..||.+..+.+.
T Consensus 49 ~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 49 NELLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHHHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 33556779999999999999999999888774
No 113
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=59.66 E-value=55 Score=27.90 Aligned_cols=49 Identities=8% Similarity=0.024 Sum_probs=35.5
Q ss_pred CcchHHHHHHHHHHHHhh----------CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 39 GVGEVCKAVICLELAASR----------FDVIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 39 Grs~~~~aaacLylAcr~----------~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
+.+...+.+.-|.--+.. ..+|++.++++.+.|+++..+.|.++.|.+.
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 345667777655433332 2368899999999999999999999998863
No 114
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=59.59 E-value=88 Score=28.73 Aligned_cols=169 Identities=14% Similarity=0.056 Sum_probs=91.3
Q ss_pred HHHHHHHh--CCCC---ChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhh-----CCCCCCHHHHHHHhCC
Q 023151 3 LSDIAKKL--GLSD---SKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASR-----FDVIFDRKTAIKLSGM 72 (286)
Q Consensus 3 i~ria~kL--gL~e---~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~-----~~iprd~~e~~k~sg~ 72 (286)
+..+|.++ |++. -+.++..+-.=+=.+..+|+ -.+|..-...+.-.+--++.- ..+|+...+.
T Consensus 36 V~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd-~~~g~~F~tya~~~Ir~~i~~~lr~~~~~pr~~~~~------ 108 (257)
T PRK05911 36 VKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFD-PEKSRRFEGYALFLIKAAIIDDLRKQDWVPRSVHQK------ 108 (257)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcC-CccCCCHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH------
Confidence 34566665 5552 12455555553334555563 457766677666666655532 2244433321
Q ss_pred CHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccc----ccc---------CCC--
Q 023151 73 SEKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPAS----RKT---------SAD-- 136 (286)
Q Consensus 73 ~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~g----k~~---------~~D-- 136 (286)
-+.+..+.+.+...|| ..|++.+||..+|++. -.. +++.........+|... ... -.|
T Consensus 109 -~~~l~~~~~~l~~~~g--r~pt~~eiA~~l~i~~~~v~---~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l~d~~ 182 (257)
T PRK05911 109 -ANKLADAMDSLRQSLG--KEPTDGELCEYLNISQQELS---GWFSSARPALILSLNEEFPCQSDDEAGLALEERIADER 182 (257)
T ss_pred -HHHHHHHHHHHHHHHC--cCCCHHHHHHHhCcCHHHHH---HHHHHhhccceeeccccCCCCCCCccccchhhhccCCC
Confidence 1356667777888888 4567899999999987 322 23322221111222110 000 001
Q ss_pred CChhH------HHHHHHHHHHHhC------------CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 023151 137 FSRPV------FTAVAFYLCAKKH------------KLKVDKLKLIEVCGTSETEFASVSTTMKDL 184 (286)
Q Consensus 137 ~~pp~------~AAAAlY~A~~~~------------k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~ 184 (286)
..+|- -....|..|-..+ ....|..+||+..|+|+.+++++.......
T Consensus 183 ~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ral~k 248 (257)
T PRK05911 183 AETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLK 248 (257)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 11221 1122333332222 347899999999999999999998876543
No 115
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=59.55 E-value=95 Score=28.45 Aligned_cols=30 Identities=13% Similarity=0.013 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLC 185 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c 185 (286)
...|..+||+..|+|+.+|+++........
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~kL 247 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGLDQL 247 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 478999999999999999999988765433
No 116
>PRK05572 sporulation sigma factor SigF; Validated
Probab=59.25 E-value=1.1e+02 Score=27.78 Aligned_cols=30 Identities=7% Similarity=0.104 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLC 185 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c 185 (286)
...|..+||+..|+|+.+++++.+.....+
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kL 246 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQM 246 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 468999999999999999999988765433
No 117
>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=59.09 E-value=22 Score=27.37 Aligned_cols=28 Identities=11% Similarity=0.029 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...|+.+||+..|+|+.|++++...+.+
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 4469999999999999999999987633
No 118
>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=59.01 E-value=15 Score=26.37 Aligned_cols=37 Identities=16% Similarity=0.226 Sum_probs=28.7
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 154 HKLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 154 ~k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
.|.++ +..+|++..|||..|+|..+..|.+ .|+-...
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~-----~g~i~~~ 57 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEA-----EGLIERR 57 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH-----TTSEEEE
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHH-----CCcEEEE
Confidence 34567 8999999999999999999999977 6655443
No 119
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=58.70 E-value=44 Score=26.57 Aligned_cols=54 Identities=9% Similarity=0.174 Sum_probs=39.7
Q ss_pred CChhHHHHHHHHHHH--HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccCC
Q 023151 137 FSRPVFTAVAFYLCA--KKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKKD 197 (286)
Q Consensus 137 ~~pp~~AAAAlY~A~--~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~~ 197 (286)
++++.|.. ++.-+ ...+...++.+|++..++++.|+....+.|++ -|.-....+
T Consensus 23 ls~~q~~v--L~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~-----kg~I~r~~~ 78 (109)
T TIGR01889 23 LSLEELLI--LYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSK-----KGYLSKERS 78 (109)
T ss_pred CCHHHHHH--HHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEeccCC
Confidence 46676653 33333 44557799999999999999999999999977 565554443
No 120
>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=58.42 E-value=99 Score=27.38 Aligned_cols=26 Identities=15% Similarity=0.266 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...|.++||+..|+|+.|++++...-
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra 215 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQA 215 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45789999999999999999987653
No 121
>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=58.29 E-value=1.2e+02 Score=27.03 Aligned_cols=28 Identities=7% Similarity=0.179 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...|..+||+..|+|+.+|+++.+....
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~~~~al~ 225 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRLEKKVLK 225 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4679999999999999999999877643
No 122
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=58.11 E-value=40 Score=22.12 Aligned_cols=28 Identities=25% Similarity=0.248 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..++..+|++..|+++.|+++..+.|.+
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4589999999999999999999999976
No 123
>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=58.00 E-value=21 Score=24.26 Aligned_cols=27 Identities=11% Similarity=0.033 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
....|..+||+..|+|..|++++.+..
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 677899999999999999999998875
No 124
>PHA01976 helix-turn-helix protein
Probab=57.50 E-value=13 Score=26.61 Aligned_cols=25 Identities=8% Similarity=0.005 Sum_probs=21.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
....||.++|+.+||++.++.+...
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3457999999999999999987654
No 125
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=57.24 E-value=30 Score=24.25 Aligned_cols=40 Identities=18% Similarity=0.378 Sum_probs=24.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---cHHHHHHHhCCcc
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNEL---DIRELGIRFGCIR 107 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~---~I~~ia~qlg~s~ 107 (286)
+..++++.+|+++..+.+-++ |-...+ .+.+||..|||+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~------~~~~~~~~~~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILN------GKPSNPSLDTLEKIAKALNCSP 54 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHT------TT-----HHHHHHHHHHHT--H
T ss_pred CHHHHHHHHCcCHHHHHHHHh------cccccccHHHHHHHHHHcCCCH
Confidence 889999999999887766555 211223 5999999999975
No 126
>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=55.74 E-value=95 Score=28.11 Aligned_cols=32 Identities=13% Similarity=0.108 Sum_probs=23.5
Q ss_pred HHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 51 ELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNS 83 (286)
Q Consensus 51 ylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~ 83 (286)
|+... ...+++++++++.+|++++.+.+.++.
T Consensus 194 ~I~~~-~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 194 LIEEN-YKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHh-hccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44433 356899999999999998888766554
No 127
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=55.59 E-value=13 Score=26.65 Aligned_cols=25 Identities=12% Similarity=0.307 Sum_probs=19.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
....||.++|+.+|+++.++.++.+
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 3468999999999999999988764
No 128
>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=55.59 E-value=20 Score=24.76 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=23.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 159 DKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+..+|++..|++..|++...+.|.+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999999987
No 129
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=55.52 E-value=17 Score=32.30 Aligned_cols=27 Identities=15% Similarity=0.082 Sum_probs=25.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..||.+||+..|+|+.|+.+..++|.+
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~ 195 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQ 195 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 358999999999999999999999987
No 130
>PF13518 HTH_28: Helix-turn-helix domain
Probab=55.32 E-value=32 Score=23.03 Aligned_cols=26 Identities=8% Similarity=0.054 Sum_probs=24.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.+..++|...||+..|+++..+....
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 39999999999999999999999976
No 131
>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=55.29 E-value=24 Score=25.03 Aligned_cols=30 Identities=23% Similarity=0.386 Sum_probs=27.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
+...+++..|++...+.+..+.|++.||.+
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 678899999999999999999999999975
No 132
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=55.09 E-value=23 Score=29.49 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=37.3
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccC
Q 023151 146 AFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKK 196 (286)
Q Consensus 146 AlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~ 196 (286)
.+|+|-..-|..++-.+||+..||++..+|.....+.. .|+-....
T Consensus 14 ~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~-----~Glv~s~~ 59 (141)
T PRK11014 14 LIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSR-----AGYVTAVR 59 (141)
T ss_pred HHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHh-----CCEEEEec
Confidence 34555555667889999999999999999999999987 77776664
No 133
>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=55.04 E-value=16 Score=25.67 Aligned_cols=37 Identities=22% Similarity=0.247 Sum_probs=30.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNEL 94 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~ 94 (286)
....+..+|++..|++.+.+..-.+.+.+-||++...
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~ 52 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRA 52 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHH
T ss_pred HhcCCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHH
Confidence 3457889999999999999999999999999987654
No 134
>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=54.94 E-value=16 Score=23.79 Aligned_cols=23 Identities=13% Similarity=0.070 Sum_probs=19.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.|-.++|+..||++.||++.+++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 46689999999999999998754
No 135
>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=54.75 E-value=29 Score=24.01 Aligned_cols=27 Identities=15% Similarity=0.278 Sum_probs=24.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.+++.+|++..+++..++.+..+.|++
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 389999999999999999999999977
No 136
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=53.58 E-value=34 Score=33.47 Aligned_cols=58 Identities=14% Similarity=0.172 Sum_probs=41.5
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCC
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKV 158 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kv 158 (286)
.|=+.|...+|.+ +.-.|...|+ ||+++..--+. -++---.+|+||+.+|++.....|
T Consensus 84 WIl~V~~~~~~~~~~~~LA~NYlD----RFls~~~l~k~--k~W~lQLlAvaCLsLAsKmeE~~v 142 (335)
T KOG0656|consen 84 WILKVCEEYNFEPLVFLLAMNYLD----RFLSSQKLPKD--KPWMLQLLAVACLSLASKMEETDV 142 (335)
T ss_pred HHHHHHHHhCCchHHHHHHHHHHH----HhhcccccCCC--chHHHHHHHHHHHHHHHhhcCcCC
Confidence 4788899999999 9999999998 77764222221 001122399999999999877643
No 137
>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=53.58 E-value=22 Score=26.77 Aligned_cols=43 Identities=12% Similarity=0.083 Sum_probs=27.4
Q ss_pred hhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 139 RPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 139 pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+..--.|-+.+.-...-...|-.+||+.+|||+.||-+.|+.|
T Consensus 16 ~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 16 PTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 3333334433443444446788999999999999999999886
No 138
>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=52.81 E-value=19 Score=23.25 Aligned_cols=22 Identities=14% Similarity=0.129 Sum_probs=19.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 023151 159 DKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr~ke 180 (286)
+..++|+..||++.||++..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 5678999999999999988775
No 139
>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=52.71 E-value=37 Score=23.97 Aligned_cols=38 Identities=13% Similarity=0.269 Sum_probs=28.5
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
..+...+..+|++..+++..++.+..++|.+ .|+-...
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~-----~glv~~~ 51 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEE-----KGLVEKE 51 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHH-----TTSEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCEEec
Confidence 4688899999999999999999999999977 5555444
No 140
>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=52.64 E-value=18 Score=26.16 Aligned_cols=44 Identities=14% Similarity=0.217 Sum_probs=33.0
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 146 AFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 146 AlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
.+|.+-. ..-..|-.+||+.+|+++.|+.+..+.|.+ .|+-...
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~-----~GlV~~~ 55 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE-----KGLVERE 55 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH-----TTSEEEE
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCEEEE
Confidence 3444333 344578889999999999999999999987 5665554
No 141
>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=52.52 E-value=30 Score=23.77 Aligned_cols=16 Identities=25% Similarity=0.468 Sum_probs=8.7
Q ss_pred CCCcHHHHHHHhCCcc
Q 023151 92 NELDIRELGIRFGCIR 107 (286)
Q Consensus 92 ~~~~I~~ia~qlg~s~ 107 (286)
.++++.+||.+||+|.
T Consensus 14 ~~it~~eLa~~l~vS~ 29 (55)
T PF08279_consen 14 EPITAKELAEELGVSR 29 (55)
T ss_dssp TSBEHHHHHHHCTS-H
T ss_pred CCcCHHHHHHHhCCCH
Confidence 3355666666666665
No 142
>PRK04217 hypothetical protein; Provisional
Probab=52.52 E-value=30 Score=28.48 Aligned_cols=34 Identities=9% Similarity=0.010 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
...|..+||+..|+|+.||.++.......+.+.+
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5569999999999999999999988766444444
No 143
>PRK10072 putative transcriptional regulator; Provisional
Probab=52.31 E-value=17 Score=29.19 Aligned_cols=27 Identities=11% Similarity=0.058 Sum_probs=22.8
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
..+.++||.++|+..||+..||.+...
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345678999999999999999988654
No 144
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=52.11 E-value=21 Score=30.13 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=30.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccC
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKK 196 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~ 196 (286)
.+-+++|...||++-|+++.|++|++ .||-..++
T Consensus 36 PSvRelA~~~~VNpnTv~raY~eLE~-----eG~i~t~r 69 (125)
T COG1725 36 PSVRELAKDLGVNPNTVQRAYQELER-----EGIVETKR 69 (125)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHH-----CCCEEEec
Confidence 35689999999999999999999998 88887775
No 145
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=52.09 E-value=61 Score=28.48 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+|++.++++.+.|+++..+.|.++.|++
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~ 210 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQK 210 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 4566666666666666666666666655
No 146
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=51.96 E-value=19 Score=29.60 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
-+..+|.+.|+..|||..||.++|.+=..
T Consensus 55 ~egl~QeeaA~~MgVSR~T~~ril~~ARk 83 (106)
T PF02001_consen 55 YEGLSQEEAAERMGVSRPTFQRILESARK 83 (106)
T ss_pred HcCCCHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 35699999999999999999999988643
No 147
>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=51.50 E-value=68 Score=22.33 Aligned_cols=28 Identities=14% Similarity=0.392 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
.+.+..++++..|+++..+.+.++.|..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4555666666666666666655555554
No 148
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=51.44 E-value=76 Score=27.16 Aligned_cols=29 Identities=17% Similarity=0.330 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
+|++..+++...|+++..+.|.++.|..+
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47778888888888888888888777653
No 149
>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=51.29 E-value=21 Score=26.45 Aligned_cols=35 Identities=20% Similarity=0.202 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
--|=-+|. .++-+++=++||+..||++.|||..=.
T Consensus 10 dkA~e~y~---~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 10 DKAFEIYK---ESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHH---HhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 34445563 356678889999999999999997543
No 150
>PHA00542 putative Cro-like protein
Probab=51.17 E-value=18 Score=27.72 Aligned_cols=27 Identities=4% Similarity=0.095 Sum_probs=23.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.....||.++|+.+||+..||.+.+..
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 345689999999999999999988754
No 151
>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=50.84 E-value=11 Score=25.62 Aligned_cols=29 Identities=7% Similarity=-0.012 Sum_probs=20.5
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 151 AKKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 151 ~~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
-.++....+-.+||...||+..||.+...
T Consensus 15 ~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 15 KELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 34445558899999999999999987654
No 152
>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=50.81 E-value=26 Score=23.84 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=28.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---cHHHHHHHhCCcc
Q 023151 60 IFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNEL---DIRELGIRFGCIR 107 (286)
Q Consensus 60 prd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~---~I~~ia~qlg~s~ 107 (286)
..+..++++..|+++..|.+-.+- +..| .+.+||..|||+.
T Consensus 9 gls~~~la~~~gis~~~i~~~~~g-------~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 9 GLSQKELAEKLGISRSTISRIENG-------KRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHTT-------SSTSBHHHHHHHHHHHTSEH
T ss_pred CCCHHHHHHHhCCCcchhHHHhcC-------CCCCCHHHHHHHHHHHCCCH
Confidence 456788999999888877654332 3333 5899999999875
No 153
>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=50.23 E-value=46 Score=23.76 Aligned_cols=42 Identities=24% Similarity=0.397 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhC---CCC--C-CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 77 YNRSFNSLQNSIG---FKN--E-LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 77 y~~~yr~l~~~Lg---L~~--~-~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
|...|..|...+- ++. . |+..+||..||+|. +.+.|...|..
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 4445555554432 333 2 38999999999999 88888888774
No 154
>PRK06030 hypothetical protein; Provisional
Probab=50.15 E-value=90 Score=26.25 Aligned_cols=71 Identities=10% Similarity=0.040 Sum_probs=54.5
Q ss_pred hhHHHHHHHHHHHhhhhcCCCCCCcc-hHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 023151 16 KQLIRKAAEIRRLCDVQFDSSIIGVG-EVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSI 88 (286)
Q Consensus 16 ~~V~ekAael~Rla~~k~~~l~~Grs-~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~L 88 (286)
+.|++..|++|-.......+..+++. +.--=-+|+|++-..++. ++.+|.+.+|-+.+.+..+.+.+++.+
T Consensus 26 d~Ii~~Va~~f~I~~~di~sk~R~rk~i~~aRqIAMYL~r~~~~~--sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 26 EAVIDLLALAFGVSGAEIASPLRGRREVSRIRQIAMYVAHVSLGW--PMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHHhCCCHHHHhCCCCCCcccchHHHHHHHHHHHHcCC--CHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 37888899999877776444555522 222234789999888776 789999999999999999999888875
No 155
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=50.12 E-value=19 Score=26.34 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=22.9
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
.....+||.++|+.+|+++.||.+.+.
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 455668999999999999999998754
No 156
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=50.09 E-value=20 Score=26.44 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=19.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke 180 (286)
+++.+||..+||+..|+...+..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 47889999999999999876643
No 157
>PF13730 HTH_36: Helix-turn-helix domain
Probab=50.06 E-value=80 Score=21.54 Aligned_cols=25 Identities=24% Similarity=0.387 Sum_probs=21.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+.+++++.+|++++.+.++.+.|+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7888888899998888888888764
No 158
>PRK10870 transcriptional repressor MprA; Provisional
Probab=49.98 E-value=51 Score=28.67 Aligned_cols=55 Identities=13% Similarity=0.241 Sum_probs=38.9
Q ss_pred CChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccCCh
Q 023151 137 FSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKKDP 198 (286)
Q Consensus 137 ~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~~~ 198 (286)
++++.|..- +.-....+..+++.+|++..+++..|+....+.|+. -|+-....+|
T Consensus 53 Lt~~q~~iL--~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~-----kGlV~R~~~~ 107 (176)
T PRK10870 53 INETLFMAL--ITLESQENHSIQPSELSCALGSSRTNATRIADELEK-----RGWIERRESD 107 (176)
T ss_pred CCHHHHHHH--HHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEecCCC
Confidence 355555442 222233356799999999999999999999999977 5666555433
No 159
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=49.92 E-value=57 Score=21.41 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=23.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
..+..+||+..|+|+.|++++...+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36899999999999999999988763
No 160
>cd00171 Sec7 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Probab=49.38 E-value=1.8e+02 Score=25.53 Aligned_cols=119 Identities=13% Similarity=0.127 Sum_probs=79.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC---CCcHHHHHHHhCCcchHHHHHHHHHHHHHhhhhccccccccCC
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN---ELDIRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPASRKTSA 135 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~---~~~I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~gk~~~~ 135 (286)
..++++.+.++.|-....-...++.....++..- ...++.++..|.+++=......||+.|-++|... +++.
T Consensus 45 ~~l~k~~ig~~L~~~~~~~~~vL~~y~~~f~f~~~~i~~ALR~~l~~f~lpgE~Q~Idrile~Fs~~y~~~-----Np~~ 119 (185)
T cd00171 45 EGLNKKAIGEYLGENNEFNSLVLHEFVDLFDFSGLRLDEALRKFLQSFRLPGEAQKIDRLLEKFSERYCEC-----NPGI 119 (185)
T ss_pred CCCCHHHHHHHHcCCchHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHHHH-----CCCC
Confidence 4689999999999876555666666777766543 3379999999999996678889999999999863 2211
Q ss_pred CC-ChhH---HHHHHHHHHHHhC----CCCCCHHHHHHHh-------CCCHHHHHHHHHHHH
Q 023151 136 DF-SRPV---FTAVAFYLCAKKH----KLKVDKLKLIEVC-------GTSETEFASVSTTMK 182 (286)
Q Consensus 136 D~-~pp~---~AAAAlY~A~~~~----k~kvtQ~kla~~s-------gvt~vt~rnr~ke~~ 182 (286)
-+ ++.. ++-|.+.+-.-+| +.|.|+.+-.... +++...+..+|..|.
T Consensus 120 ~~~~~d~v~~l~~sllmLnTdlHn~~~~~kmt~~~Fi~~~~~~~~~~~~~~~~L~~iY~~I~ 181 (185)
T cd00171 120 FSSSADAAYTLAYSIIMLNTDLHNPNVKKKMTLEDFIKNLRGINDGEDFPREFLKELYDSIK 181 (185)
T ss_pred CCCChhHHHHHHHHHHHHhHHhcCcccCCCCCHHHHHHHHhcccCCCCCCHHHHHHHHHHHH
Confidence 11 2222 3344444444444 5566776666543 566777777777664
No 161
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=48.89 E-value=27 Score=27.77 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=25.2
Q ss_pred chHHHHHHHHHHHHhhCCCCCCHHHHHHHhCC
Q 023151 41 GEVCKAVICLELAASRFDVIFDRKTAIKLSGM 72 (286)
Q Consensus 41 s~~~~aaacLylAcr~~~iprd~~e~~k~sg~ 72 (286)
+...-+.+||-+.++.+|++++.+.+....+.
T Consensus 8 ~~~~~gl~~l~~~~~~~g~~~~~~~l~~~~~~ 39 (136)
T cd02418 8 DEMDCGAACLAMIAKYYGKNYSLAKLRELAGT 39 (136)
T ss_pred CcccHHHHHHHHHHHHhCCCCCHHHHHHHcCC
Confidence 34456778899999999999999998765544
No 162
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=48.87 E-value=58 Score=30.15 Aligned_cols=27 Identities=11% Similarity=0.081 Sum_probs=25.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKDL 184 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~~ 184 (286)
.||.+||-..|+|+.||++..+++...
T Consensus 106 LT~~Dla~LL~~S~~TI~~~i~~yq~e 132 (220)
T PF07900_consen 106 LTQEDLAMLLGISPRTISKDIKEYQKE 132 (220)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 799999999999999999999999763
No 163
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=48.45 E-value=10 Score=33.27 Aligned_cols=25 Identities=32% Similarity=0.445 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
++|+|++||++.|||+.||++...+
T Consensus 1 ~~vnk~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 1 MKVNKKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp -EEEHHHHHHHTT--HHHHHHHTTT
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHC
Confidence 4689999999999999999987644
No 164
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=48.28 E-value=35 Score=22.22 Aligned_cols=29 Identities=17% Similarity=0.423 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
.+|.+..++++..|+++..+.+.++.|.+
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35667777777777777777777776665
No 165
>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=48.28 E-value=56 Score=25.99 Aligned_cols=44 Identities=2% Similarity=0.057 Sum_probs=33.4
Q ss_pred CCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 136 DFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 136 D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+++++.|..- .+...+-..++.+|++..|+++.|+....+.|++
T Consensus 25 ~lt~~q~~iL----~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 25 GLTEQQWRIL----RILAEQGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred CCCHHHHHHH----HHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 3467776532 2222345689999999999999999999999977
No 166
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=48.12 E-value=89 Score=27.80 Aligned_cols=48 Identities=15% Similarity=0.241 Sum_probs=32.2
Q ss_pred cchHHHHHHHHHHHHhhCC------CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 40 VGEVCKAVICLELAASRFD------VIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 40 rs~~~~aaacLylAcr~~~------iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
.+...+.+..|..-+...| +|++.++++.+.|+++..+.|.++.|++.
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 4566666665554444332 56777888888888888888888777764
No 167
>PRK09726 antitoxin HipB; Provisional
Probab=47.96 E-value=20 Score=27.58 Aligned_cols=27 Identities=7% Similarity=0.135 Sum_probs=23.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
....+||.++|+.+||++.||.+..+.
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 345789999999999999999987764
No 168
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=47.71 E-value=36 Score=26.76 Aligned_cols=38 Identities=8% Similarity=0.055 Sum_probs=28.7
Q ss_pred CCCCCcchHHHHHHHHHHHHhhCC-CCCCHHHHHHHhCC
Q 023151 35 SSIIGVGEVCKAVICLELAASRFD-VIFDRKTAIKLSGM 72 (286)
Q Consensus 35 ~l~~Grs~~~~aaacLylAcr~~~-iprd~~e~~k~sg~ 72 (286)
|++...+..--+.+|+-+.++.+| ++.+.+++....+.
T Consensus 2 ~~~~q~~~~~~~l~~l~~~~~~~g~~~~~~~~l~~~~~~ 40 (129)
T cd02423 2 GVVRQSYDFSCGPAALATLLRYYGGINITEQEVLKLMLI 40 (129)
T ss_pred CceecCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHhCc
Confidence 444445555567888888999999 99999999876554
No 169
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=47.57 E-value=34 Score=30.66 Aligned_cols=28 Identities=14% Similarity=0.083 Sum_probs=25.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
.+.-.|=.+||+-.|.|+.|+||..+.=
T Consensus 58 ekag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 58 EKAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred HHccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 7777888999999999999999998763
No 170
>COG0533 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=47.40 E-value=54 Score=32.22 Aligned_cols=96 Identities=18% Similarity=0.287 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHHHHhCCCCCC--cHHHHHHHhCCcchHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHH
Q 023151 74 EKAYNRSFNSLQNSIGFKNEL--DIRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCA 151 (286)
Q Consensus 74 ~k~y~~~yr~l~~~LgL~~~~--~I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~ 151 (286)
...+.++|..+.|.|||.-|- -|.++|.+ --.. ++.-..+.-++...|||-+|+-+|++...-
T Consensus 157 DdA~Gea~DKvAR~lGL~yPGGp~Ie~lA~~------------G~~~---~~~fP~~~~~~~~~DfSFSGLkTa~~~~~~ 221 (342)
T COG0533 157 DDAAGEAFDKVARLLGLGYPGGPAIEKLAKK------------GDPD---AFEFPRPMVKGKNLDFSFSGLKTAVLRLLK 221 (342)
T ss_pred hhhhhHHHHHHHHHhCCCCCCcHHHHHHHhc------------CCCC---ceeCCccccCCCCcceehHhHHHHHHHHHH
Confidence 467899999999999997763 34444432 1110 111111222344689999999999887765
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 152 KKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
.... + .+..+.++++++.++.+.-+|.. +.+.+
T Consensus 222 ~~~~-~---------~~~~~~d~~dia~sfQ~av~~~L-~~kt~ 254 (342)
T COG0533 222 KLKQ-K---------EELNEEDKEDIAASFQEAVFDML-VEKTE 254 (342)
T ss_pred hccc-c---------cccchhhHHHHHHHHHHHHHHHH-HHHHH
Confidence 4332 1 37888889999999988888877 44444
No 171
>PF12728 HTH_17: Helix-turn-helix domain
Probab=47.34 E-value=24 Score=24.00 Aligned_cols=22 Identities=14% Similarity=0.066 Sum_probs=18.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~k 179 (286)
.|-.++|+..||++.|+++..+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3668999999999999998764
No 172
>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=47.15 E-value=59 Score=22.33 Aligned_cols=26 Identities=15% Similarity=0.218 Sum_probs=24.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++..+|++..|++..|++.....|.+
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 99999999999999999999999966
No 173
>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=47.12 E-value=20 Score=23.73 Aligned_cols=22 Identities=14% Similarity=0.122 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 023151 159 DKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr~ke 180 (286)
+=.++|+..||++.|||...++
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 3468999999999999987544
No 174
>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=46.96 E-value=30 Score=24.62 Aligned_cols=29 Identities=28% Similarity=0.225 Sum_probs=25.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+-.++=.+||+..|||+.|+|+=...|++
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~ 40 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEK 40 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44677889999999999999999999976
No 175
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=46.89 E-value=25 Score=22.08 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=20.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVS 178 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ 178 (286)
...++++.++++..|+++.+|.+..
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3457899999999999999997643
No 176
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=46.80 E-value=55 Score=28.95 Aligned_cols=47 Identities=9% Similarity=-0.077 Sum_probs=30.8
Q ss_pred chHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 41 GEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 41 s~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
+...+.+.-|...+.....|.+..+++...|+++..+.|.++.|++.
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 55666666555433323356677777777777777777777777764
No 177
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=46.57 E-value=23 Score=29.95 Aligned_cols=25 Identities=20% Similarity=0.230 Sum_probs=23.3
Q ss_pred CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 94 LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 94 ~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
|+|++||..+|++. ++++|.+.|+.
T Consensus 36 PSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 36 PSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 69999999999999 99999999985
No 178
>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=46.52 E-value=25 Score=23.46 Aligned_cols=23 Identities=13% Similarity=0.021 Sum_probs=18.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke 180 (286)
=++.+.|...|+++.|+.+..+.
T Consensus 19 gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 19 GNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 45688999999999999988764
No 179
>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=46.29 E-value=40 Score=23.21 Aligned_cols=28 Identities=7% Similarity=0.100 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...+-.+|++.+|+++.|+.+....|.+
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3467789999999999999999999976
No 180
>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=46.11 E-value=54 Score=21.75 Aligned_cols=34 Identities=21% Similarity=0.321 Sum_probs=29.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCC
Q 023151 60 IFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNE 93 (286)
Q Consensus 60 prd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~ 93 (286)
..+..++++..|++...+.+..+.+.+.||.+..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~~ 48 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVKSR 48 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCH
Confidence 3588999999999999999999998888888654
No 181
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=45.97 E-value=18 Score=24.80 Aligned_cols=24 Identities=29% Similarity=0.531 Sum_probs=20.5
Q ss_pred cHHHHHHHhCCCCChhHHHHHHHHH
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAEIR 26 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAael~ 26 (286)
.|+.++...|+|.+ .++++|-+.|
T Consensus 16 ~L~~ls~~t~i~~S-~Ll~eAle~~ 39 (44)
T PF12651_consen 16 KLKELSEETGIPKS-KLLREALEDY 39 (44)
T ss_pred HHHHHHHHHCCCHH-HHHHHHHHHH
Confidence 47899999999997 8889887765
No 182
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=45.60 E-value=15 Score=29.28 Aligned_cols=58 Identities=14% Similarity=0.237 Sum_probs=33.9
Q ss_pred CCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc
Q 023151 36 SIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR 107 (286)
Q Consensus 36 l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~ 107 (286)
.+.+.+...-+.+||.+.++.+|++.|.+++....+.+.. |+ ....+.+++..+|+..
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~~g~~~s~~~l~~~~~~~~~-------------g~-s~~~L~~~~~~~gl~~ 61 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKYYGIPVSEEELRRQLGTSEE-------------GT-SLADLKRAARKYGLKA 61 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHHTT----HHHHHCCTT-BTT-------------B---CCCHHHHHHHTTEEE
T ss_pred eEEeCCCCCHHHHHHHHHHHHhCCCchHHHHHHHhcCCcc-------------CC-CHHHHHHHHHhcccce
Confidence 4556677778889999999999999999988876655322 11 1125777777777765
No 183
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=45.41 E-value=65 Score=28.70 Aligned_cols=52 Identities=10% Similarity=0.038 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccC
Q 023151 136 DFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKK 196 (286)
Q Consensus 136 D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~ 196 (286)
|++++.+. .++ +......++|++|++..+++..|+.+..+.|++ -|+-....
T Consensus 42 gLt~~q~~--iL~--~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~-----kGlI~R~~ 93 (185)
T PRK13777 42 DLNINEHH--ILW--IAYHLKGASISEIAKFGVMHVSTAFNFSKKLEE-----RGYLTFSK 93 (185)
T ss_pred CCCHHHHH--HHH--HHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHH-----CCCEEecC
Confidence 45677774 233 333445799999999999999999999999987 45555443
No 184
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=45.15 E-value=29 Score=27.32 Aligned_cols=48 Identities=17% Similarity=0.224 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHHhCCCH-HHHHHHHHHHHHHhCCCCC
Q 023151 46 AVICLELAASRFDVIFDRKTAIKLSGMSE-KAYNRSFNSLQNSIGFKNE 93 (286)
Q Consensus 46 aaacLylAcr~~~iprd~~e~~k~sg~~~-k~y~~~yr~l~~~LgL~~~ 93 (286)
+..||-+.|+.+|+|.+.+.+....+... ..-...+..+.+.+|++..
T Consensus 8 ~l~~l~~i~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl~~~ 56 (124)
T cd02421 8 LLDCLVLLARQFGKPASRDSLVAGLPLDDGRLSPALFPRAAARAGLSAR 56 (124)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHhcCCCCCCCcCHHHHHHHHHHCCCcce
Confidence 45688889999999999999988766531 1222333334445666553
No 185
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.01 E-value=1.4e+02 Score=22.81 Aligned_cols=82 Identities=15% Similarity=0.128 Sum_probs=39.3
Q ss_pred HHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhcccc-cccc--CCC-CChhHHHHHHHHHHHHh-CC-CCCCHHHHHHH--
Q 023151 96 IRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPA-SRKT--SAD-FSRPVFTAVAFYLCAKK-HK-LKVDKLKLIEV-- 166 (286)
Q Consensus 96 I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~-gk~~--~~D-~~pp~~AAAAlY~A~~~-~k-~kvtQ~kla~~-- 166 (286)
+.++|-.|||+. ++ ...++.|.+.++.++.. +.+. .-. +++...+..-=++...- .| ...+-..|++.
T Consensus 15 ~~~ia~~lg~s~~Tv---~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~ 91 (112)
T PF13551_consen 15 IAEIARRLGISRRTV---YRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLI 91 (112)
T ss_pred HHHHHHHHCcCHHHH---HHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHH
Confidence 666777777665 32 24555555555444443 1110 010 22333321111111110 11 13556677763
Q ss_pred -----hCCCHHHHHHHHHH
Q 023151 167 -----CGTSETEFASVSTT 180 (286)
Q Consensus 167 -----sgvt~vt~rnr~ke 180 (286)
..+++.||+++.+.
T Consensus 92 ~~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 92 EEEFGIDVSPSTIRRILKR 110 (112)
T ss_pred HhccCccCCHHHHHHHHHH
Confidence 37889999888765
No 186
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.80 E-value=46 Score=21.91 Aligned_cols=33 Identities=18% Similarity=0.387 Sum_probs=27.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNE 93 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~ 93 (286)
.+..+|++..|++...+.+..+.+...||.+..
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~ 51 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVRSR 51 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 477889999999998888888888888887554
No 187
>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=44.77 E-value=45 Score=25.19 Aligned_cols=14 Identities=21% Similarity=0.404 Sum_probs=8.0
Q ss_pred CcHHHHHHHhCCcc
Q 023151 94 LDIRELGIRFGCIR 107 (286)
Q Consensus 94 ~~I~~ia~qlg~s~ 107 (286)
+++.+||..+|++.
T Consensus 26 ~s~~eiA~~~~i~~ 39 (83)
T PF02082_consen 26 VSSKEIAERLGISP 39 (83)
T ss_dssp BEHHHHHHHHTS-H
T ss_pred CCHHHHHHHHCcCH
Confidence 45666666666665
No 188
>PRK00118 putative DNA-binding protein; Validated
Probab=44.76 E-value=42 Score=27.36 Aligned_cols=33 Identities=12% Similarity=-0.013 Sum_probs=26.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
..|..+||+..|+|+.||.++.......+.+.+
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999877655444444
No 189
>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=44.14 E-value=57 Score=23.62 Aligned_cols=34 Identities=21% Similarity=0.089 Sum_probs=28.0
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhh
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCH 186 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~ 186 (286)
+.+-..+-.+|++..|||..|+++..+.|.+..+
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 3344577899999999999999999999987333
No 190
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=43.66 E-value=42 Score=26.42 Aligned_cols=28 Identities=7% Similarity=0.030 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHhCC
Q 023151 45 KAVICLELAASRFDVIFDRKTAIKLSGM 72 (286)
Q Consensus 45 ~aaacLylAcr~~~iprd~~e~~k~sg~ 72 (286)
-+.+||-.+|+.+|++.+.+++....+.
T Consensus 12 ~gl~~l~~i~~~~g~~~~~~~l~~~~~~ 39 (125)
T cd02420 12 CGAASLAIILAYYGRYVPLSELRIACGV 39 (125)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 4566777899999999999999887654
No 191
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=43.58 E-value=75 Score=23.29 Aligned_cols=31 Identities=19% Similarity=0.266 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc
Q 023151 75 KAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR 107 (286)
Q Consensus 75 k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~ 107 (286)
+.|.++++.|...||- .|+..+||..+|++.
T Consensus 4 ~~i~~a~~~L~~~lgr--~Pt~eEiA~~lgis~ 34 (78)
T PF04539_consen 4 RKIERARRELEQELGR--EPTDEEIAEELGISV 34 (78)
T ss_dssp HHHHHHHHHHHHHHSS----BHHHHHHHHTS-H
T ss_pred HHHHHHHHHHHHHhCC--CCCHHHHHHHHcccH
Confidence 5688999999999995 578999999999997
No 192
>PRK09483 response regulator; Provisional
Probab=43.48 E-value=50 Score=27.77 Aligned_cols=45 Identities=16% Similarity=0.226 Sum_probs=24.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFGC 105 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~ 105 (286)
.+.++|+...+++.+.+.+-.+.+.+.||++....+-.+|.+.|+
T Consensus 164 ~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~~l~~~a~~~~~ 208 (217)
T PRK09483 164 QKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGL 208 (217)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCC
Confidence 344555555566666665555555555555554444444444444
No 193
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=42.58 E-value=1.3e+02 Score=26.95 Aligned_cols=45 Identities=13% Similarity=0.177 Sum_probs=37.6
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 146 AFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 146 AlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
.+|..--+...+.|=.+|+++.|+|..-+..-.++|.+ .++.+..
T Consensus 30 ~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~-----~~lV~~~ 74 (177)
T COG1510 30 QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD-----WNLVKKV 74 (177)
T ss_pred HHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh-----cchHHhh
Confidence 35554445678899999999999999999999999988 7777775
No 194
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=42.51 E-value=29 Score=30.67 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=26.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
....+|.+||+..|+|+.|+.+..++|.+
T Consensus 171 ~i~~t~~~iA~~lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 171 TLPYEKRVLASYLGMTPENLSRAFAALAS 199 (236)
T ss_pred EeeCCHHHHHHHhCCChhHHHHHHHHHHh
Confidence 35678999999999999999999999987
No 195
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=42.50 E-value=2.6e+02 Score=25.25 Aligned_cols=26 Identities=12% Similarity=0.092 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...|..+||+..|+|+.|++++...-
T Consensus 220 ~g~s~~eIA~~lgis~~~V~~~~~ra 245 (255)
T TIGR02941 220 ENLSQKETGERLGISQMHVSRLQRQA 245 (255)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46789999999999999999998654
No 196
>PHA02591 hypothetical protein; Provisional
Probab=42.33 E-value=33 Score=27.01 Aligned_cols=31 Identities=10% Similarity=0.040 Sum_probs=26.5
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 149 LCAKKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 149 ~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
+|-.+.....||.+||...||+..++++-..
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 5566777889999999999999999998654
No 197
>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=41.78 E-value=45 Score=22.76 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=19.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
..|..+||+..|+|+.|+++++..-.
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46889999999999999999887643
No 198
>PHA01976 helix-turn-helix protein
Probab=41.73 E-value=43 Score=23.78 Aligned_cols=41 Identities=7% Similarity=0.049 Sum_probs=29.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCC--CcHHHHHHHhCCcc
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNE--LDIRELGIRFGCIR 107 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~--~~I~~ia~qlg~s~ 107 (286)
++.+++++..|+++..|.+- ++ |-..| -.+.+||..||++.
T Consensus 16 lt~~~lA~~~gvs~~~v~~~----e~--g~~~p~~~~l~~ia~~l~v~~ 58 (67)
T PHA01976 16 WSAPELSRRAGVRHSLIYDF----EA--DKRLPNLKTLLRLADALGVTL 58 (67)
T ss_pred CCHHHHHHHhCCCHHHHHHH----Hc--CCCCCCHHHHHHHHHHHCcCH
Confidence 68899999999998777652 22 33222 25899999999875
No 199
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=41.72 E-value=27 Score=28.83 Aligned_cols=27 Identities=15% Similarity=0.210 Sum_probs=22.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.....||.++|+.+||++.||.+..+.
T Consensus 15 ~~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 15 KQLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 344689999999999999999997644
No 200
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=41.67 E-value=84 Score=23.11 Aligned_cols=37 Identities=14% Similarity=0.123 Sum_probs=29.6
Q ss_pred HHHHHHhCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 147 FYLCAKKHKL-KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 147 lY~A~~~~k~-kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++..-...+. .++..+||...|++..+++.....|++
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 3333444455 489999999999999999999999977
No 201
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=40.94 E-value=31 Score=28.39 Aligned_cols=25 Identities=16% Similarity=0.296 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
+.+|+.++|++.||++.||.+++..
T Consensus 22 ~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 22 LGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3689999999999999999998865
No 202
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=40.52 E-value=48 Score=21.68 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
.+.+=.+||+.+|+++..|.+++++.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45667899999999999999999998
No 203
>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=40.29 E-value=69 Score=21.90 Aligned_cols=30 Identities=13% Similarity=0.037 Sum_probs=21.8
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 151 AKKHKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 151 ~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+...|. .+..+.|..-||...|++++++.-
T Consensus 11 ~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 11 AVKNGK-MSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp HHHTTS-S-HHHHHHHHT--HHHHHHHHHHT
T ss_pred HHHhCC-CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 334555 999999999999999999887654
No 204
>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=39.88 E-value=34 Score=23.74 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=16.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr 82 (286)
|+.+|++.+|++...+.++++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 578899999999888776643
No 205
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=39.73 E-value=65 Score=26.74 Aligned_cols=43 Identities=16% Similarity=0.135 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFG 104 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg 104 (286)
+.++|+...+++.+.+..-.+.|.+.||.+....+-.+|.+.|
T Consensus 160 ~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l~~~~~~~~ 202 (204)
T PRK09958 160 DNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNK 202 (204)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhC
Confidence 3444444444444444444444444444444333333443333
No 206
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=39.65 E-value=92 Score=30.92 Aligned_cols=75 Identities=11% Similarity=0.022 Sum_probs=52.7
Q ss_pred hhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCC
Q 023151 16 KQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLS-GMSEKAYNRSFNSLQNSIGFKN 92 (286)
Q Consensus 16 ~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~s-g~~~k~y~~~yr~l~~~LgL~~ 92 (286)
+.|++..|++|........+-.+.+.+.--=-+|+|+|-+..+. ++.+|.+.. |-+.+.+..+++.+++.+.-+.
T Consensus 360 ~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~~--s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~d~ 435 (450)
T PRK00149 360 ENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTDL--SLPEIGRAFGGRDHTTVLHAVRKIEKLLEEDP 435 (450)
T ss_pred HHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcCC--CHHHHHHHcCCCCHhHHHHHHHHHHHHHHhCH
Confidence 36778888888766665433344444444445678888777775 778888888 4788888888888888876543
No 207
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=39.54 E-value=61 Score=21.64 Aligned_cols=29 Identities=14% Similarity=0.219 Sum_probs=26.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
....+..+|++..|++..|++...+.|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56788999999999999999999999976
No 208
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=39.51 E-value=51 Score=21.53 Aligned_cols=30 Identities=17% Similarity=0.337 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGF 90 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL 90 (286)
..++++++++...|++...+.+.++ +.+|+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk---~~~g~ 35 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFK---KETGM 35 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHH---HHTSS
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHH---HHHCc
Confidence 4578889999999998777765544 44554
No 209
>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=39.50 E-value=1.7e+02 Score=27.67 Aligned_cols=78 Identities=9% Similarity=0.095 Sum_probs=51.5
Q ss_pred hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhh
Q 023151 108 LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKH-KLKVDKLKLIEVCGTSETEFASVSTTMKDLCH 186 (286)
Q Consensus 108 v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~-k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~ 186 (286)
+...+.++=+..+++-...+.-+- +|.+-+-|.-=-+..... .-+++-.+||+..|||+.++|++.+.|+.
T Consensus 153 lr~~~~~iEee~Rkka~Vq~Ai~t-----LSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~--- 224 (251)
T TIGR02787 153 LRAQAEEIEEEARKKAAVQMAINT-----LSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLES--- 224 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh-----ccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHH---
Confidence 566667777777666443222221 244444444433344333 36999999999999999999999999977
Q ss_pred hhhhccccc
Q 023151 187 DVFGIAKEK 195 (286)
Q Consensus 187 d~~~i~~~~ 195 (286)
.|+-+..
T Consensus 225 --aGvIe~r 231 (251)
T TIGR02787 225 --AGVIESR 231 (251)
T ss_pred --CCCEEec
Confidence 6665544
No 210
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=39.48 E-value=1.5e+02 Score=25.04 Aligned_cols=56 Identities=21% Similarity=0.172 Sum_probs=38.9
Q ss_pred CCCCCHHHHHH-HhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc--hHHHHHHHHH
Q 023151 58 DVIFDRKTAIK-LSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR--LIPLVQKGLS 117 (286)
Q Consensus 58 ~iprd~~e~~k-~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~--v~~~A~eiL~ 117 (286)
+..++.+++++ +.|++...+.--...|+ -+.+.++-+||..++.+. |.+....|++
T Consensus 10 ~~~~~~~dvl~c~~GLs~~Dv~v~~~LL~----~~~~~tvdelae~lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 10 RKEFRCEDVLKCVYGLSELDVEVYKALLE----ENGPLTVDELAEILNRSRSTVYRSLQNLLE 68 (126)
T ss_pred cccCcHHHHHHHHhCCcHHHHHHHHHHHh----hcCCcCHHHHHHHHCccHHHHHHHHHHHHH
Confidence 34566777776 67999988754333333 556679999999999998 5555555555
No 211
>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=39.39 E-value=71 Score=26.41 Aligned_cols=39 Identities=18% Similarity=0.127 Sum_probs=26.2
Q ss_pred HHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 48 ICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 48 acLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+.+|+|-...+-|++.+++++..+++...+..-++.|.+
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~ 51 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRK 51 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456666554455777777777777777777776666655
No 212
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=39.01 E-value=24 Score=25.06 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFAS 176 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rn 176 (286)
..++=.+||+.+|+++++||.
T Consensus 27 ~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 27 ERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp SEE-HHHHHHHHTS-HHHHHH
T ss_pred eeECHHHHHHHHCCCHHHhcc
Confidence 357788999999999999996
No 213
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.99 E-value=1.2e+02 Score=28.82 Aligned_cols=84 Identities=18% Similarity=0.165 Sum_probs=58.1
Q ss_pred HHHHHHHHHhCCCCCCcHHHHHHHhCCcc--hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCC
Q 023151 79 RSFNSLQNSIGFKNELDIRELGIRFGCIR--LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKL 156 (286)
Q Consensus 79 ~~yr~l~~~LgL~~~~~I~~ia~qlg~s~--v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~ 156 (286)
+-++-|..-..-+.-+-+-+||++|||-. ++++-.++|.. -.++|.-.-++..|=.++--|+|.|=|+=- --
T Consensus 200 nll~eFv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~e---g~ltGVmDDRGKfIYIS~eEl~AVAkfIkq---rG 273 (299)
T KOG3054|consen 200 NLLSEFVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAE---GLLTGVMDDRGKFIYISMEELAAVAKFIKQ---RG 273 (299)
T ss_pred HHHHHHHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHh---hhheeeecCCCceEEecHHHHHHHHHHHHH---cC
Confidence 44555555555566678999999999987 88877777764 335554455555555688889999988732 33
Q ss_pred CCCHHHHHHHhC
Q 023151 157 KVDKLKLIEVCG 168 (286)
Q Consensus 157 kvtQ~kla~~sg 168 (286)
+|+=.+||+.|+
T Consensus 274 RVSIaelAe~SN 285 (299)
T KOG3054|consen 274 RVSIAELAEKSN 285 (299)
T ss_pred ceeHHHHHHhhc
Confidence 566677777664
No 214
>PF14502 HTH_41: Helix-turn-helix domain
Probab=38.79 E-value=51 Score=23.49 Aligned_cols=25 Identities=32% Similarity=0.260 Sum_probs=22.6
Q ss_pred CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 94 LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 94 ~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
+.|.+++.+|+++. ++..|...|+.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~ 32 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEE 32 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHH
Confidence 58999999999999 99999888885
No 215
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=38.57 E-value=53 Score=25.58 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=22.7
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHHhCC
Q 023151 46 AVICLELAASRFDVIFDRKTAIKLSGM 72 (286)
Q Consensus 46 aaacLylAcr~~~iprd~~e~~k~sg~ 72 (286)
..+||-+.|+.+|+|.+.+.+....+.
T Consensus 8 ~l~~l~~i~~~~g~~~~~~~l~~~~~~ 34 (121)
T cd02417 8 GLLALVLLARYHGIAADPEQLRHEFGL 34 (121)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhcC
Confidence 456788899999999999999987654
No 216
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.52 E-value=50 Score=25.37 Aligned_cols=30 Identities=10% Similarity=0.007 Sum_probs=25.7
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 154 HKLKV-DKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 154 ~k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+.... +..++|...|+++.||.+..+.+.+
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 33445 6999999999999999999999975
No 217
>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=38.50 E-value=57 Score=22.42 Aligned_cols=27 Identities=11% Similarity=0.160 Sum_probs=13.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQ 85 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~ 85 (286)
-|.++.++++..|+++..+.+.+++|.
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334555555555555555555554444
No 218
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=38.47 E-value=49 Score=20.87 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
....++.+++...|+++.++.+...
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 3478999999999999999887543
No 219
>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=38.47 E-value=43 Score=23.20 Aligned_cols=21 Identities=14% Similarity=0.167 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCHHHHHHHHHH
Q 023151 160 KLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 160 Q~kla~~sgvt~vt~rnr~ke 180 (286)
=++||..+|||..|+.+....
T Consensus 2 i~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHhC
Confidence 368999999999999887543
No 220
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=38.31 E-value=68 Score=26.52 Aligned_cols=42 Identities=10% Similarity=0.157 Sum_probs=18.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIR 102 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~q 102 (286)
.+.+++++..+++.+.+....+.+.+.||++....+-.+|.+
T Consensus 165 ~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~~~a~~ 206 (210)
T PRK09935 165 LSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKL 206 (210)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 444444444444444444444444444444433333333333
No 221
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=38.31 E-value=1.6e+02 Score=23.09 Aligned_cols=72 Identities=14% Similarity=0.087 Sum_probs=48.4
Q ss_pred HHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHH
Q 023151 20 RKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIREL 99 (286)
Q Consensus 20 ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~i 99 (286)
+.|+.|+--+.+. | ......+++--+|...|+. ++++.+|+++..+.+.. +--+-+....+.+|
T Consensus 15 ~~~~~~l~~~le~------~--~~~~~~~~l~~~r~~~glS----qLAe~~GIs~stLs~iE----~g~~~Ps~~tL~kI 78 (89)
T TIGR02684 15 EAIAEYLAQALED------G--DPAYIAHALGYIARARGMT----QLARKTGLSRESLYKAL----SGKGNPTFDTILKV 78 (89)
T ss_pred HHHHHHHHHHHHc------C--CHHHHHHHHHHHHHHCChH----HHHHHHCCCHHHHHHHH----cCCCCCCHHHHHHH
Confidence 4577777777664 3 3334666677888888765 59999999998886543 22221111268899
Q ss_pred HHHhCCcc
Q 023151 100 GIRFGCIR 107 (286)
Q Consensus 100 a~qlg~s~ 107 (286)
|..||++=
T Consensus 79 ~~aLgi~l 86 (89)
T TIGR02684 79 TKALGLKL 86 (89)
T ss_pred HHHcCCce
Confidence 99999864
No 222
>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=38.18 E-value=1.2e+02 Score=23.68 Aligned_cols=30 Identities=17% Similarity=0.191 Sum_probs=20.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 57 FDVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
...+.+-.+++++.|+++..+.++++.|++
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445666777777777777777776666654
No 223
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=38.18 E-value=57 Score=27.41 Aligned_cols=43 Identities=12% Similarity=0.063 Sum_probs=33.4
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhc
Q 023151 147 FYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGI 191 (286)
Q Consensus 147 lY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i 191 (286)
+|...... ..+.++||+..|+++.|++++..-=...|.+-.+.
T Consensus 127 v~~L~~~~--g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 127 AFLYNRLD--GMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred HHHHHHHc--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 33444443 47889999999999999999998888888776643
No 224
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=38.08 E-value=46 Score=30.63 Aligned_cols=29 Identities=21% Similarity=0.062 Sum_probs=26.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+-.++..+|++..|||+.|+|+-.++|++
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34589999999999999999999999976
No 225
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=38.05 E-value=3.3e+02 Score=25.11 Aligned_cols=56 Identities=11% Similarity=0.170 Sum_probs=38.4
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHH-----------------HHHhCCCCCCcHHHHHHHhCCcchHHHH
Q 023151 56 RFDVIFDRKTAIKLSGMSEKAYNRSFNSL-----------------QNSIGFKNELDIRELGIRFGCIRLIPLV 112 (286)
Q Consensus 56 ~~~iprd~~e~~k~sg~~~k~y~~~yr~l-----------------~~~LgL~~~~~I~~ia~qlg~s~v~~~A 112 (286)
.+..+.+++++++.+|+++..+.+.++.. ..+|. ....+|.+||..+|-+......
T Consensus 17 ~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~~~L~-~~~~~i~~iA~~~Gf~s~~~f~ 89 (289)
T PRK15121 17 HLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALR-LTSRPILDIALQYRFDSQQTFT 89 (289)
T ss_pred cccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH-cCCCCHHHHHHHHCCCCHHHHH
Confidence 35668899999999988888887766653 11121 1344789999999887755544
No 226
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=38.02 E-value=2.3e+02 Score=29.71 Aligned_cols=150 Identities=17% Similarity=0.114 Sum_probs=83.7
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHh--------hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAAS--------RFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSI 88 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr--------~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~L 88 (286)
.++.....=+=+|..+|+ -.+|..-.+.|+-++.-|-. .-.+|++..+.+ ..+.++.+.+...|
T Consensus 409 DLiQeG~iGL~~Av~kfd-~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~-------~k~~~~~~~~~~~~ 480 (619)
T PRK05658 409 DLIQEGNIGLMKAVDKFE-YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI-------NKLNRISRQMLQEI 480 (619)
T ss_pred HHHHHHHHHHHHHHHhcC-ccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHH-------HHHHHHHHHHHHHh
Confidence 344444443444556663 45776666666666655542 224666655432 35677778888888
Q ss_pred CCCCCCcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhcccc--cccc---CCCC------ChhHHHHH------HHH--
Q 023151 89 GFKNELDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPA--SRKT---SADF------SRPVFTAV------AFY-- 148 (286)
Q Consensus 89 gL~~~~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~--gk~~---~~D~------~pp~~AAA------AlY-- 148 (286)
|- .|++.+||..||++. -+..+..+. . . ..||.. |-.. ..|| ..|.-.+. .+.
T Consensus 481 gr--~pt~~eiA~~l~~~~~~v~~~~~~~---~-~-~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~ 553 (619)
T PRK05658 481 GR--EPTPEELAERLGMPEDKVRKVLKIA---K-E-PISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDV 553 (619)
T ss_pred CC--CCCHHHHHHHhCCCHHHHHHHHHhc---C-C-CCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHH
Confidence 73 457899999999998 334333332 2 2 123322 1111 1111 12221111 111
Q ss_pred ----------HHHHhCC----CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 149 ----------LCAKKHK----LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 149 ----------~A~~~~k----~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+--...| ...|..+|+...|||...||++.+.-
T Consensus 554 l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~a 600 (619)
T PRK05658 554 LASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 600 (619)
T ss_pred HHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHH
Confidence 1111132 57899999999999999999998764
No 227
>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=37.97 E-value=59 Score=27.20 Aligned_cols=48 Identities=10% Similarity=0.036 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
+..|++=+....-=.++|=++|++.|||+..||=+.|++..++-...+
T Consensus 8 I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~dLl~~~~ 55 (176)
T TIGR02366 8 IAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDKYELLTWIF 55 (176)
T ss_pred HHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCHHHHHHHHH
Confidence 334444444444445789999999999999999999988776655543
No 228
>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=37.92 E-value=92 Score=27.49 Aligned_cols=33 Identities=12% Similarity=0.094 Sum_probs=28.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccc
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKE 194 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~ 194 (286)
.+|..+||+..|+++.|++..++.|++ .|+-..
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le~-----~GlV~r 47 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLET-----EGLIEY 47 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCeEE
Confidence 389999999999999999999999988 555543
No 229
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=37.91 E-value=56 Score=27.42 Aligned_cols=33 Identities=15% Similarity=0.149 Sum_probs=29.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
..+..+||+..|+++.|++++...-...|.+.+
T Consensus 134 g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 134 GLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 478899999999999999999999888887754
No 230
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=37.49 E-value=1.2e+02 Score=22.47 Aligned_cols=66 Identities=12% Similarity=0.030 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhC-CCHHHHHHHHHHH
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSG-MSEKAYNRSFNSL 84 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg-~~~k~y~~~yr~l 84 (286)
.|++.-++.|..-.....+-.+++.+.--=-+|+|++-..++ .++.+|.+..| -+.+.+..+++.+
T Consensus 4 ~Ii~~Va~~~~v~~~~i~s~~R~~~i~~aR~va~yL~r~~~~--~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 4 DIIEAVAEYFGVSVEDIRSKSRKRKIVEARQVAMYLARELTG--LSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHTT--HHHHHSS---HHHHHHHHHHHHHHHHHS-----HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHhCCCCChhhcchHHHHHHHHHHHhC--CCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 455555666655555422222332222222344677777665 67889999999 8888888887753
No 231
>PRK15340 transcriptional regulator InvF; Provisional
Probab=37.42 E-value=1.6e+02 Score=27.09 Aligned_cols=88 Identities=14% Similarity=0.169 Sum_probs=47.6
Q ss_pred hHHHHHHHHHHHhhhh------cCCCCCCcchHHHHHHHHHHHHhhCCC-CCCHHH-HHHHhCCCHHHHHHHHHHHHHHh
Q 023151 17 QLIRKAAEIRRLCDVQ------FDSSIIGVGEVCKAVICLELAASRFDV-IFDRKT-AIKLSGMSEKAYNRSFNSLQNSI 88 (286)
Q Consensus 17 ~V~ekAael~Rla~~k------~~~l~~Grs~~~~aaacLylAcr~~~i-prd~~e-~~k~sg~~~k~y~~~yr~l~~~L 88 (286)
+..+.++.+.|....= ......+.+ ++--|+..|+ ++.+.. .-+..|++.+.|-+.+|.-...+
T Consensus 97 ~~~~~~~~~~r~~e~y~l~~~Ll~~~~~~~s--------leeLA~~~gvS~r~f~RlFk~~~G~tpk~yl~~~Rl~~all 168 (216)
T PRK15340 97 PAFNKVLALLRKSESYWLVGYLLAQSTSGNT--------MRMLGEDYGVSYTHFRRLCSRALGGKAKSELRNWRMAQSLL 168 (216)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhCccCCCC--------HHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 5677777777777221 001111222 2333333443 233332 33456777777777777655555
Q ss_pred CC-CCCCcHHHHHHHhCCcchHHHH
Q 023151 89 GF-KNELDIRELGIRFGCIRLIPLV 112 (286)
Q Consensus 89 gL-~~~~~I~~ia~qlg~s~v~~~A 112 (286)
.+ +...+|.+||..+|-+......
T Consensus 169 ~L~~s~~sItdIA~~~GY~d~ShFs 193 (216)
T PRK15340 169 NSVEGHENITQLAVNHGYSSPSHFS 193 (216)
T ss_pred hhhcCCCCHHHHHHHhCCCCHHHHH
Confidence 54 3456788888888877754433
No 232
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=37.32 E-value=96 Score=22.80 Aligned_cols=26 Identities=27% Similarity=0.264 Sum_probs=11.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
++..++++..|++++.+.+.+..|++
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44444444444444444444444433
No 233
>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=37.19 E-value=39 Score=24.36 Aligned_cols=22 Identities=5% Similarity=-0.013 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHH
Q 023151 160 KLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 160 Q~kla~~sgvt~vt~rnr~ke~ 181 (286)
=.++|+.+||++.|+|..+++.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~~ 24 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWEREF 24 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 3689999999999999876654
No 234
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=37.17 E-value=59 Score=25.53 Aligned_cols=28 Identities=18% Similarity=0.138 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHhCC
Q 023151 45 KAVICLELAASRFDVIFDRKTAIKLSGM 72 (286)
Q Consensus 45 ~aaacLylAcr~~~iprd~~e~~k~sg~ 72 (286)
-+.+||-..|+.+|+|.+.+.+....+.
T Consensus 12 ~~l~~l~~~~~~~g~~~~~~~l~~~~~~ 39 (127)
T cd02419 12 CGLACLAMIASYHGHHVDLASLRQRFPV 39 (127)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 4556778899999999999999876554
No 235
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=37.09 E-value=1.4e+02 Score=27.42 Aligned_cols=56 Identities=18% Similarity=0.260 Sum_probs=41.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.+...+++..|++...+.+..+.|+.+||++- ++.+...+..| ...|.++++.+.+
T Consensus 29 gs~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~~LT~~G~~l-----~~~a~~~l~~~~~ 90 (311)
T PRK10086 29 QSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRV-----FWALKSSLDTLNQ 90 (311)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCeeEEEcCCCcccCHhHHHH-----HHHHHHHHHHHHH
Confidence 46678899999999999999999999999853 23444554444 5556666665553
No 236
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=37.03 E-value=2e+02 Score=22.30 Aligned_cols=27 Identities=26% Similarity=0.291 Sum_probs=18.4
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 57 FDVIFDRKTAIKLSGMSEKAYNRSFNS 83 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~~k~y~~~yr~ 83 (286)
...|++++++++..|+++..+.+.++.
T Consensus 18 ~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 18 IDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455677788877777777766555443
No 237
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=36.97 E-value=82 Score=25.58 Aligned_cols=43 Identities=9% Similarity=0.139 Sum_probs=21.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFG 104 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg 104 (286)
+..+|++..+++.+.+.+..+.+.+.||++..+.+-..+-++|
T Consensus 166 ~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~~~~~~~~ 208 (211)
T PRK15369 166 TNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLG 208 (211)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcC
Confidence 3455555555555555555555555555544433333333333
No 238
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=36.60 E-value=67 Score=25.56 Aligned_cols=31 Identities=23% Similarity=0.085 Sum_probs=28.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
-+...+++..|++.+.+++..+.|+..||.+
T Consensus 17 gSis~AA~~L~iS~stvs~~I~~LE~~lg~~ 47 (99)
T TIGR00637 17 GSISQAAKDAGISYKSAWDYIRAMNNLSGEP 47 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 4567889999999999999999999999984
No 239
>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=36.40 E-value=79 Score=20.17 Aligned_cols=27 Identities=11% Similarity=0.054 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
...++.+||+..|+++.|+.++.....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 457999999999999999988877654
No 240
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=36.30 E-value=41 Score=26.94 Aligned_cols=28 Identities=18% Similarity=0.279 Sum_probs=22.9
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 152 KKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
......+||.++|+..|+++.||++..+
T Consensus 73 ~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 73 IRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3455688999999999999999987643
No 241
>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=35.83 E-value=35 Score=31.23 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=20.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
|+|-++||+.+|||..|+++...
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Confidence 57889999999999999998885
No 242
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=35.69 E-value=1.4e+02 Score=24.31 Aligned_cols=39 Identities=10% Similarity=0.053 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+..+.-|+-... ....+=.+||+.+|+++.+|..++++.
T Consensus 11 i~~~~~~I~~~~-~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 11 IHSILDWIEDNL-ESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445555555554 456899999999999999999999998
No 243
>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=35.67 E-value=79 Score=20.91 Aligned_cols=27 Identities=11% Similarity=0.167 Sum_probs=23.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+-.+||+..|+++.|++++...+..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 468999999999999999999988744
No 244
>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=35.53 E-value=1.3e+02 Score=24.38 Aligned_cols=49 Identities=12% Similarity=0.209 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
||-.++-.-+...+..++=.+|++..|+++.+++++...|.+ -|+-...
T Consensus 10 yal~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~-----~Gli~~~ 58 (130)
T TIGR02944 10 YATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL-----AGIVTSK 58 (130)
T ss_pred HHHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH-----CCcEEec
Confidence 444444333444567899999999999999999999999987 6666554
No 245
>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=35.48 E-value=40 Score=22.30 Aligned_cols=19 Identities=11% Similarity=0.102 Sum_probs=15.0
Q ss_pred HHHHHHhCCCHHHHHHHHH
Q 023151 161 LKLIEVCGTSETEFASVST 179 (286)
Q Consensus 161 ~kla~~sgvt~vt~rnr~k 179 (286)
.++|+.+||++.|+|...+
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4799999999999997543
No 246
>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=35.42 E-value=45 Score=23.92 Aligned_cols=21 Identities=10% Similarity=0.172 Sum_probs=18.2
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 023151 161 LKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 161 ~kla~~sgvt~vt~rnr~ke~ 181 (286)
.++|+.+||++.|+|...++.
T Consensus 4 ~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHhc
Confidence 589999999999999877664
No 247
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=35.18 E-value=1.1e+02 Score=27.32 Aligned_cols=56 Identities=13% Similarity=0.212 Sum_probs=41.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.++..+++..|++...+.+..+.|++.||.+- ++.+.+.+.. +.+.|.+|++.+.+
T Consensus 16 gs~s~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~-----l~~~~~~il~~~~~ 77 (296)
T PRK11242 16 GNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEV-----YLRYARRALQDLEA 77 (296)
T ss_pred CCHHHHHHHcCCCchHHHHHHHHHHHHhCCeeEeEcCCceeechhHHH-----HHHHHHHHHHHHHH
Confidence 36778899999999999999999999999853 2234444443 36667777766654
No 248
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=35.15 E-value=63 Score=27.51 Aligned_cols=33 Identities=3% Similarity=-0.013 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHDV 188 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~ 188 (286)
...+..+||+..|+|+.|++++..--...|.+-
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 457889999999999999999999887777664
No 249
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=35.14 E-value=64 Score=22.89 Aligned_cols=29 Identities=21% Similarity=0.294 Sum_probs=20.1
Q ss_pred HHHHhCCCCCCcHHHHHHHhCCcc-hHHHH
Q 023151 84 LQNSIGFKNELDIRELGIRFGCIR-LIPLV 112 (286)
Q Consensus 84 l~~~LgL~~~~~I~~ia~qlg~s~-v~~~A 112 (286)
|...|.-+..+++.+||..||+|+ +.++=
T Consensus 5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRD 34 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFGVSEMTIRRD 34 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHCcCHHHHHHH
Confidence 444454455678999999999998 55543
No 250
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=35.06 E-value=1.7e+02 Score=22.72 Aligned_cols=40 Identities=8% Similarity=0.059 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 141 VFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 141 ~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
.+..+.-|+... ....++=.+||+.+|+|+.++.+++++.
T Consensus 6 ~~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 6 IIQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344555566655 3456899999999999999999999998
No 251
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=34.98 E-value=2.5e+02 Score=22.85 Aligned_cols=51 Identities=20% Similarity=0.238 Sum_probs=29.4
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC-------------------CCCCcHHHHHHHhCCcchHH
Q 023151 57 FDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGF-------------------KNELDIRELGIRFGCIRLIP 110 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL-------------------~~~~~I~~ia~qlg~s~v~~ 110 (286)
...+++++++++..|+++..+.+.++ +.+|+ .....|.+||.++|-+....
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk---~~~G~s~~~~l~~~Rl~~A~~~L~~t~~~i~eIA~~~Gf~s~s~ 91 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFK---KETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQT 91 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHH---HHHCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHH
Confidence 34567777777777777766544333 23333 23345666776666666444
No 252
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=34.89 E-value=47 Score=23.00 Aligned_cols=22 Identities=14% Similarity=0.194 Sum_probs=17.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~k 179 (286)
++-+++++..|++..||.+..+
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHh
Confidence 4668999999999999998877
No 253
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=34.89 E-value=1.4e+02 Score=29.96 Aligned_cols=70 Identities=16% Similarity=0.126 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSI 88 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~L 88 (286)
.|++..|.+|........+..+++.+.--=-+|+|+|-+..+. ++.+|.+..|.+.+.+..+++.++..+
T Consensus 346 ~I~~~V~~~~~i~~~~l~s~~R~~~i~~aR~iamyl~r~~~~~--s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 346 ELIEIVAKVTGVSREEILSNSRNVKALLARRIGMYVAKNYLGS--SLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHcCCcHHHHhCCCCCccccHHHHHHHHHHHHHhCC--CHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4555566665544333222222222222223456666444343 666666666666666666666666644
No 254
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=34.71 E-value=42 Score=23.60 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=18.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
....||.++|+..|+++.+|.+....
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 34679999999999998888776543
No 255
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=34.55 E-value=64 Score=24.88 Aligned_cols=28 Identities=14% Similarity=0.288 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHHhC
Q 023151 44 CKAVICLELAASRFDVIFDRKTAIKLSG 71 (286)
Q Consensus 44 ~~aaacLylAcr~~~iprd~~e~~k~sg 71 (286)
.-..+||-+.++.+|++.+.+.+....+
T Consensus 6 ~~gl~~l~~i~~~~g~~~~~~~l~~~~~ 33 (122)
T cd02259 6 DCGLACLQMLLRYFGIPVRRDVLLNAQQ 33 (122)
T ss_pred chHHHHHHHHHHHcCCCCCHHHHHHHHh
Confidence 3456788899999999999999865544
No 256
>PRK09801 transcriptional activator TtdR; Provisional
Probab=34.51 E-value=1.5e+02 Score=27.39 Aligned_cols=55 Identities=15% Similarity=0.162 Sum_probs=39.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
++..+++..+++...+.+..+.|+.+||.+- .+.+.+.+..| .+.|..+++.+.+
T Consensus 22 s~t~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~R~~r~~~lT~~G~~l-----~~~a~~il~~~~~ 82 (310)
T PRK09801 22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRC-----YEHALEILTQYQR 82 (310)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHhCCEeeeecCCCCcccHhHHHH-----HHHHHHHHHHHHH
Confidence 4567889999999999999999999999852 23444444433 5566666665553
No 257
>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=34.46 E-value=1e+02 Score=21.43 Aligned_cols=28 Identities=18% Similarity=0.171 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...+-.+||+..|+++.||++....+..
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 3478889999999999999999999843
No 258
>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=34.29 E-value=61 Score=18.37 Aligned_cols=20 Identities=10% Similarity=0.084 Sum_probs=17.8
Q ss_pred CCHHHHHHHhCCCHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASV 177 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr 177 (286)
.+..++++..|++..||.+.
T Consensus 22 ~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 22 ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHCCCHHHHHHh
Confidence 48899999999999999875
No 259
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=34.24 E-value=1.3e+02 Score=25.77 Aligned_cols=50 Identities=10% Similarity=0.173 Sum_probs=39.7
Q ss_pred HHHH-HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccC
Q 023151 141 VFTA-VAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKK 196 (286)
Q Consensus 141 ~~AA-AAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~ 196 (286)
-||- |-+|+| ...+..++-.+||+..|+++.-++++...|.+ -|+-.+.+
T Consensus 8 ~YAlr~L~~LA-~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~-----aGlv~S~r 58 (153)
T PRK11920 8 NYAIRMLMYCA-ANDGKLSRIPEIARAYGVSELFLFKILQPLVE-----AGLVETVR 58 (153)
T ss_pred hHHHHHHHHHH-hCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH-----CCCEEeec
Confidence 3555 444555 55666789999999999999999999999987 67777764
No 260
>PF00288 GHMP_kinases_N: GHMP kinases N terminal domain; InterPro: IPR006204 The galacto- (2.7.1.6 from EC), homoserine (2.7.1.39 from EC), mevalonate (2.7.1.36 from EC) and phosphomevalonate (2.7.4.2 from EC) kinases contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP [, ]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).; GO: 0005524 ATP binding, 0016301 kinase activity, 0016310 phosphorylation; PDB: 3F0N_B 1PIE_A 2AJ4_A 1K47_E 3GON_A 2R3V_C 3HUL_A 1KVK_A 2R42_A 3D4J_A ....
Probab=34.08 E-value=70 Score=22.93 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=22.6
Q ss_pred chHHHHHHHHHHHHhhCCCCCCHHHHHHHh
Q 023151 41 GEVCKAVICLELAASRFDVIFDRKTAIKLS 70 (286)
Q Consensus 41 s~~~~aaacLylAcr~~~iprd~~e~~k~s 70 (286)
|-.+.+++.+.+..+.++.+++.+++++++
T Consensus 16 SSaa~~~a~~~a~~~~~~~~~~~~~l~~~a 45 (67)
T PF00288_consen 16 SSAALAVALAAALNKLFGLPLSKEELAKLA 45 (67)
T ss_dssp HHHHHHHHHHHHHHHHTTTSSBHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHccccccHHHHHHHH
Confidence 456677788888888889998887775544
No 261
>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=33.93 E-value=1e+02 Score=20.72 Aligned_cols=32 Identities=13% Similarity=0.109 Sum_probs=26.2
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 152 KKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.+.+-..+-.+|++..|+++.|+....+.|.+
T Consensus 10 ~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 10 LLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 34445677789999999999999999999977
No 262
>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=33.78 E-value=62 Score=23.92 Aligned_cols=29 Identities=10% Similarity=0.119 Sum_probs=12.4
Q ss_pred CCCCCCHHHHHHHhCCC-HHHHHHHHHHHH
Q 023151 57 FDVIFDRKTAIKLSGMS-EKAYNRSFNSLQ 85 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~-~k~y~~~yr~l~ 85 (286)
+|.|-+..||++..|++ ...+...++.|+
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLKALE 51 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 34455555555555543 444444444444
No 263
>PRK09954 putative kinase; Provisional
Probab=33.39 E-value=72 Score=30.34 Aligned_cols=29 Identities=7% Similarity=0.112 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+-++++.+||+..|||+.|++++.+.|++
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34799999999999999999999999987
No 264
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=33.33 E-value=56 Score=29.94 Aligned_cols=28 Identities=11% Similarity=0.060 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
-.++..+|++..|||+.|+|+-.++|.+
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3689999999999999999999999966
No 265
>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=33.33 E-value=24 Score=28.28 Aligned_cols=26 Identities=19% Similarity=0.311 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
++|+.+|+..||++.||.+.-.++..
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~ 49 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIE 49 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHH
Confidence 78999999999999999997666543
No 266
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=33.28 E-value=1.4e+02 Score=27.51 Aligned_cols=55 Identities=15% Similarity=0.176 Sum_probs=39.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
.++..+++..+++...+.+..+.|+.+||.+- .+.+.+.+..| .+.|.++++.+.
T Consensus 22 gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~~G~~l-----~~~a~~il~~~~ 82 (312)
T PRK10341 22 GSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVL-----LSRSESITREMK 82 (312)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCceEChhHHHH-----HHHHHHHHHHHH
Confidence 45677899999999999999999999999752 23344444433 555556665554
No 267
>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=33.20 E-value=74 Score=23.06 Aligned_cols=32 Identities=19% Similarity=0.159 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 143 TAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 143 AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.|-.||.- ..+.++||+..||++.|+.+-.+-
T Consensus 5 ~A~~LY~~------G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 5 QARSLYLQ------GWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHHc------CCCHHHHHHHHCCChHHHHHHHHh
Confidence 34556653 378899999999999999887654
No 268
>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=32.85 E-value=57 Score=23.12 Aligned_cols=23 Identities=9% Similarity=0.053 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Q 023151 159 DKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+-.++|+.+||++.|+|+..++.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 44689999999999999977653
No 269
>PF12181 MogR_DNAbind: DNA binding domain of the motility gene repressor (MogR); InterPro: IPR021009 This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in the transcriptional repressor of flagellar motility genes, such as flaA, during extracellular growth at 37 degrees Celsius and during intracellular infection. It binds directly to gene promoter region and probably prevents RNA polymerase binding. At low temperatures, MogR repression activity is modulated by the DegU response regulator in an unknown mechanism. MogR is required for full virulence []. MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR []. ; PDB: 3FDQ_B.
Probab=32.76 E-value=72 Score=27.48 Aligned_cols=99 Identities=15% Similarity=0.180 Sum_probs=46.1
Q ss_pred cHHHHHHHhCCcc--hHHHHHHHHHHHHHhhhh-ccccccccCCCCChhH-HHHHHHHHHHHhCCCCCCHHHHHHHhC--
Q 023151 95 DIRELGIRFGCIR--LIPLVQKGLSLFKDRFTA-ALPASRKTSADFSRPV-FTAVAFYLCAKKHKLKVDKLKLIEVCG-- 168 (286)
Q Consensus 95 ~I~~ia~qlg~s~--v~~~A~eiL~~~ke~~~~-~L~~gk~~~~D~~pp~-~AAAAlY~A~~~~k~kvtQ~kla~~sg-- 168 (286)
.+..|+.+|+++. ++..=..+..-|++--.. |+..--.+.+-|=... =---++|.-|..+++++- ++++...
T Consensus 18 e~kkieke~~i~y~el~dlY~~mv~Fq~~vEk~GG~~~Ye~S~isWLKsELELLy~~YQf~q~h~lni~--diSk~~Skn 95 (148)
T PF12181_consen 18 EIKKIEKEFQIDYEELVDLYNRMVLFQIDVEKNGGIEAYEHSNISWLKSELELLYACYQFCQRHGLNIL--DISKMLSKN 95 (148)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHTSSEEE-HHHHHHHHHHHHHHHHTT--HH--HHHHHHSTT
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHccCHHHHHHhhhHHHHHHHHHHHHHHHHHHHcCCccc--cHHHHhhhh
Confidence 5788888888876 444444444433332111 0000001111111111 122478999999999863 3444332
Q ss_pred ------CCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 169 ------TSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 169 ------vt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
-||.+++|.|=-+...-...+.|.+.+
T Consensus 96 ~L~lFpKTeSQLQNTYYKLKk~~i~fEnI~K~K 128 (148)
T PF12181_consen 96 DLNLFPKTESQLQNTYYKLKKEEIPFENIKKNK 128 (148)
T ss_dssp TT-SSSS-HHHHHHHHHHHHTTSS-SS-EE---
T ss_pred hhccCCCCHHHHHHHHHHHHhhhcchhhccccC
Confidence 378999999988866444444444444
No 270
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=32.62 E-value=1.7e+02 Score=21.71 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..++-.+|++..|++..|+++....|++
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3688899999999999999999999976
No 271
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=32.55 E-value=46 Score=27.42 Aligned_cols=25 Identities=24% Similarity=0.244 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
..+||.+||..+|+++.|+.++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 3579999999999999999988753
No 272
>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=32.53 E-value=57 Score=28.44 Aligned_cols=36 Identities=11% Similarity=0.249 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.+++..+|++..|||.+++|.-...|+. .|+-...
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~-----eGlv~~~ 67 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEE-----AGLVRNE 67 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHH-----CCCEEEe
Confidence 66789999999999999999999999977 6665543
No 273
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=32.40 E-value=63 Score=29.61 Aligned_cols=34 Identities=21% Similarity=0.290 Sum_probs=29.8
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 150 CAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 150 A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.+.....++|+.+|++..|+++.|+.++.+.|++
T Consensus 14 g~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe 47 (217)
T PRK14165 14 GAVNNTVKISSSEFANHTGTSSKTAARILKQLED 47 (217)
T ss_pred hccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3445556799999999999999999999999987
No 274
>PRK13503 transcriptional activator RhaS; Provisional
Probab=32.39 E-value=1.2e+02 Score=27.23 Aligned_cols=31 Identities=10% Similarity=0.169 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
..+++++++++..|+++..+.+.++ +..|..
T Consensus 185 ~~~~tl~~lA~~~~lS~~~l~r~Fk---~~~G~S 215 (278)
T PRK13503 185 AEEVNWEALADQFSLSLRTLHRQLK---QQTGLT 215 (278)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHH---HHhCcC
Confidence 4689999999999999998876654 566653
No 275
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=32.15 E-value=1.7e+02 Score=26.18 Aligned_cols=55 Identities=22% Similarity=0.314 Sum_probs=39.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
++..+++..+++...+.+..+.|+.+||.+. ++.+.+.+.. +...|..+++.+.+
T Consensus 17 s~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~~~lT~~G~~-----l~~~a~~il~~~~~ 77 (291)
T TIGR03418 17 SFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDGQR-----LFEAVRAGLDTIDL 77 (291)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCceeEcHhHHH-----HHHHHHHHHHHHHH
Confidence 6778899999999999999999999999742 1223333333 35666666665553
No 276
>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=32.11 E-value=49 Score=23.85 Aligned_cols=29 Identities=17% Similarity=0.192 Sum_probs=22.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
.-+.|.++|++.+|+++..+.+.++.|.+
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34577888888888888888888777765
No 277
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=32.03 E-value=73 Score=27.37 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...||.+||+..|+|+.|+.++.+..
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra 45 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRA 45 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998775
No 278
>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=31.95 E-value=66 Score=27.51 Aligned_cols=27 Identities=4% Similarity=0.097 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
...||.+||+..|+|+.|++++.+...
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 557999999999999999999988863
No 279
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.87 E-value=76 Score=26.78 Aligned_cols=31 Identities=10% Similarity=0.107 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCH 186 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~ 186 (286)
...+..+||+..|++..|++++..--...|.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4567999999999999999999988777775
No 280
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=31.83 E-value=86 Score=25.08 Aligned_cols=33 Identities=3% Similarity=0.046 Sum_probs=26.8
Q ss_pred chHHHHHHHHHHHHhh-CCCCCCHHHHHHHhCCC
Q 023151 41 GEVCKAVICLELAASR-FDVIFDRKTAIKLSGMS 73 (286)
Q Consensus 41 s~~~~aaacLylAcr~-~~iprd~~e~~k~sg~~ 73 (286)
+...-+.+||-+.++. +|++.+.+++....+.+
T Consensus 8 ~~~dcgla~l~~i~~~~~g~~~~~~~l~~~~~~~ 41 (129)
T cd02424 8 DLNDCGIAVIQMLYNHYYKKKYDLNELKIKANLK 41 (129)
T ss_pred CccchHHHHHHHHHHHhcCCCccHHHHHHHhCCC
Confidence 3445678899999999 99999999998876643
No 281
>PRK09492 treR trehalose repressor; Provisional
Probab=31.66 E-value=47 Score=30.15 Aligned_cols=25 Identities=12% Similarity=0.209 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.++|-++||+.+|||..|+++....
T Consensus 3 ~~~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CCCcHHHHHHHhCCCHHHHhHHhCC
Confidence 4689999999999999999988763
No 282
>PF02509 Rota_NS35: Rotavirus non-structural protein 35; InterPro: IPR003668 Rotavirus non-structural protein 2 (NSP2) is a basic protein which possesses RNA-binding activity and is essential for genome replication []. It may also be important for viral RNA packaging.; GO: 0003723 RNA binding, 0019079 viral genome replication; PDB: 2GU0_B 2R8F_A 2R7P_A 2R7C_A 1L9V_A 2R7J_A.
Probab=31.32 E-value=28 Score=33.23 Aligned_cols=55 Identities=20% Similarity=0.442 Sum_probs=39.8
Q ss_pred HHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHH
Q 023151 119 FKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASV 177 (286)
Q Consensus 119 ~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr 177 (286)
|++||.++ -....+||+.+.|.-.|.-+|=.+++++++|.+++++... .+.+|-+
T Consensus 57 fkkR~ntn---~nsrGmnyet~mf~kva~ll~e~LN~ik~t~~~~~~il~~-vvsVRHL 111 (316)
T PF02509_consen 57 FKKRFNTN---DNSRGMNYETDMFDKVAILLCEALNSIKMTQSKVANILSR-VVSVRHL 111 (316)
T ss_dssp GGGGB-BT---TBSSSB-TTSHHHHHHHHHHHHHHHCCTBBCCCHHHHCC--B--HHHH
T ss_pred HHhhccCC---CCccCcccchHHHHHHHHHHHHHhhcccccHHHHHHHHHH-heeHHHH
Confidence 56677752 3335689999999999999999999999999998888752 3444433
No 283
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=31.14 E-value=1e+02 Score=25.38 Aligned_cols=41 Identities=20% Similarity=0.170 Sum_probs=29.0
Q ss_pred CCCCCCcHHHHHHHhCCcchHHHHHHHHHHHHHhhhhcccccc
Q 023151 89 GFKNELDIRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPASR 131 (286)
Q Consensus 89 gL~~~~~I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~gk 131 (286)
|-+..++|.+||..|.||+ +-|..||..+.+.+-..-..|+
T Consensus 15 ~~~~~vtl~elA~~l~cS~--Rn~r~lLkkm~~~gWi~W~pg~ 55 (115)
T PF12793_consen 15 GQPVEVTLDELAELLFCSR--RNARTLLKKMQEEGWITWQPGR 55 (115)
T ss_pred CCCcceeHHHHHHHhCCCH--HHHHHHHHHHHHCCCeeeeCCC
Confidence 5566679999999999997 4455677777776554444443
No 284
>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=31.09 E-value=96 Score=22.25 Aligned_cols=26 Identities=15% Similarity=0.178 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
.+|-.+||+..||++.||..+...-+
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 57889999999999999998876653
No 285
>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=31.09 E-value=1.5e+02 Score=23.76 Aligned_cols=42 Identities=17% Similarity=0.140 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 142 FTAVAFYLCAKKHK-LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 142 ~AAAAlY~A~~~~k-~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+|-.+++.-++..+ ..++-.+|++..|+++.+++++...|.+
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44445544445433 3899999999999999999999999987
No 286
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.98 E-value=66 Score=23.80 Aligned_cols=29 Identities=7% Similarity=0.021 Sum_probs=24.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+-.++=.+||+.+|+|..|.|.....|++
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 44577789999999999999999999976
No 287
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=30.88 E-value=1.8e+02 Score=26.25 Aligned_cols=55 Identities=15% Similarity=0.184 Sum_probs=39.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
.+...+++..+++...+.+..+.|+..||.+- .+.+.+.+..| ...|..+|..+.
T Consensus 17 gs~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~~~lT~~G~~l-----~~~a~~il~~~~ 77 (301)
T PRK14997 17 GGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTF-----YEHCKAMLVEAQ 77 (301)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeeccCcceEcHhHHHH-----HHHHHHHHHHHH
Confidence 45677899999999999999999999999852 22343443333 566666666554
No 288
>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=30.83 E-value=1.1e+02 Score=26.53 Aligned_cols=32 Identities=3% Similarity=0.020 Sum_probs=28.4
Q ss_pred HhCCCCCCHHHHHHHhCCC-HHHHHHHHHHHHH
Q 023151 152 KKHKLKVDKLKLIEVCGTS-ETEFASVSTTMKD 183 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt-~vt~rnr~ke~~~ 183 (286)
...+...+.++||+..|++ +.|+.++.+.|++
T Consensus 20 ~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 20 ESTGYPPSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred HhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3456668999999999998 9999999999987
No 289
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=30.81 E-value=1.5e+02 Score=20.26 Aligned_cols=44 Identities=23% Similarity=0.500 Sum_probs=35.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFG 104 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg 104 (286)
.+..+++...|++...+..-.+.+.+.||++....+-.++..++
T Consensus 20 ~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~~~~~ 63 (65)
T COG2771 20 KSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLG 63 (65)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhc
Confidence 78899999999999999999999999999877655544444443
No 290
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=30.61 E-value=1.5e+02 Score=26.04 Aligned_cols=48 Identities=15% Similarity=0.239 Sum_probs=29.5
Q ss_pred cchHHHHHHHHHHHHhhC------CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 40 VGEVCKAVICLELAASRF------DVIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 40 rs~~~~aaacLylAcr~~------~iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
.+.....+--|.--+... .+|.+.++++.+.|+++..+.+.++.|.+.
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 455555555443222222 246777788888888888888877776653
No 291
>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=30.61 E-value=60 Score=28.36 Aligned_cols=27 Identities=11% Similarity=0.209 Sum_probs=25.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
-.||++||+..|+|..||.+..++|++
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 368999999999999999999999987
No 292
>PRK10130 transcriptional regulator EutR; Provisional
Probab=30.53 E-value=4.9e+02 Score=25.27 Aligned_cols=58 Identities=7% Similarity=0.162 Sum_probs=38.9
Q ss_pred hhCCCCCCHHHHHHHhCCCHHHHHHHHHHH-----------------HHHhCC--CCCCcHHHHHHHhCCcchHHHH
Q 023151 55 SRFDVIFDRKTAIKLSGMSEKAYNRSFNSL-----------------QNSIGF--KNELDIRELGIRFGCIRLIPLV 112 (286)
Q Consensus 55 r~~~iprd~~e~~k~sg~~~k~y~~~yr~l-----------------~~~LgL--~~~~~I~~ia~qlg~s~v~~~A 112 (286)
.....|++++++++..|+++..+.+.++.. .++|-- ....+|.+||.++|-...-..+
T Consensus 251 ~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~~ylr~~RL~~ar~lL~~~~~~~~sI~eIA~~~GF~~~s~Fs 327 (350)
T PRK10130 251 ENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGPNAWLKRIRLNAVRRELISPWSQSTTVKDAAMQWGFWHLGQFA 327 (350)
T ss_pred hhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHhCCCCHHHHH
Confidence 345678999999999999998888777653 223311 1234677788777777765544
No 293
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=30.43 E-value=93 Score=24.24 Aligned_cols=28 Identities=7% Similarity=0.106 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHhCC
Q 023151 45 KAVICLELAASRFDVIFDRKTAIKLSGM 72 (286)
Q Consensus 45 ~aaacLylAcr~~~iprd~~e~~k~sg~ 72 (286)
-..+|+-+.|+.+|++++.+.+....+.
T Consensus 12 ~~l~~l~~~~~~~~~~~~~~~l~~~~~~ 39 (126)
T cd02425 12 CGLACYAMILNYFGYKVSLNELREKYEL 39 (126)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHhccC
Confidence 4566888899999999999998776544
No 294
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=30.36 E-value=50 Score=31.02 Aligned_cols=41 Identities=15% Similarity=0.290 Sum_probs=35.1
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccC
Q 023151 151 AKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKK 196 (286)
Q Consensus 151 ~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~ 196 (286)
=+.+|=+++|.+|....|.+++|+.++.+.+++ .|+-+..|
T Consensus 204 i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk-----~GlIe~~K 244 (258)
T COG2512 204 IRERGGRITQAELRRALGLSKTTVSRILRRLEK-----RGLIEKEK 244 (258)
T ss_pred HHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh-----CCceEEEE
Confidence 344566699999999999999999999999998 88877764
No 295
>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=30.31 E-value=1.1e+02 Score=25.31 Aligned_cols=50 Identities=14% Similarity=0.158 Sum_probs=38.1
Q ss_pred HHHH-HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 141 VFTA-VAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 141 ~~AA-AAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
-||- +.+|+|....+..++-.+||+..++++..++.+...|.+ -|+-...
T Consensus 8 ~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~-----~glv~s~ 58 (135)
T TIGR02010 8 RYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRK-----AGLVKSV 58 (135)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH-----CCceEEE
Confidence 3555 445555544455799999999999999999999999987 5665554
No 296
>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=30.20 E-value=28 Score=25.45 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=15.5
Q ss_pred CHHHHHHHhCCCHHHHH-HHH
Q 023151 159 DKLKLIEVCGTSETEFA-SVS 178 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~r-nr~ 178 (286)
++.++|+..||++.||. +..
T Consensus 14 ~~~~lA~~lgis~st~s~~~~ 34 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWK 34 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHH
T ss_pred CHHHHHHHhCcCHHHhhHHHH
Confidence 67799999999999999 554
No 297
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=30.12 E-value=51 Score=23.43 Aligned_cols=20 Identities=10% Similarity=0.072 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 023151 160 KLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 160 Q~kla~~sgvt~vt~rnr~k 179 (286)
=.++|+.+||++.|+|...+
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999999998754
No 298
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=30.05 E-value=1.2e+02 Score=26.39 Aligned_cols=39 Identities=15% Similarity=0.111 Sum_probs=29.0
Q ss_pred HHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 48 ICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 48 acLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+.+|+|....+-|++.++|++..|++...+.+-++.|.+
T Consensus 13 ~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~ 51 (164)
T PRK10857 13 AMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRK 51 (164)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456666444456888888888888888888888887776
No 299
>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=29.87 E-value=76 Score=25.03 Aligned_cols=23 Identities=13% Similarity=0.072 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVS 178 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ 178 (286)
...+..+||+..|++..||.++.
T Consensus 49 ~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHH
Confidence 34699999999999999998844
No 300
>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=29.82 E-value=93 Score=25.04 Aligned_cols=28 Identities=11% Similarity=-0.067 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...+..+||+..|+|+.|++++..-...
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3568999999999999999999877644
No 301
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=29.78 E-value=1.8e+02 Score=26.54 Aligned_cols=56 Identities=14% Similarity=0.236 Sum_probs=39.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.++..+++..|++...+.+..+.|+.+||.+- .+.+..-+..| ...|.++++.+.+
T Consensus 23 gs~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l-----~~~a~~~l~~~~~ 84 (302)
T TIGR02036 23 QSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRI-----YWALKSSLDTLNQ 84 (302)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCceEEECCCceeECHhHHHH-----HHHHHHHHHHHHH
Confidence 45677889999999999999999999999863 23343343333 4555555554443
No 302
>PRK14616 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=29.73 E-value=1.1e+02 Score=28.37 Aligned_cols=39 Identities=8% Similarity=0.026 Sum_probs=30.1
Q ss_pred ccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHh
Q 023151 126 ALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVC 167 (286)
Q Consensus 126 ~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~s 167 (286)
.+|.|.+- ++.+..+||+++.+..+.+.+.+..++++.+
T Consensus 91 ~IP~~~GL---GssSA~aaA~l~al~~l~g~~ls~~el~~~a 129 (287)
T PRK14616 91 RVPFGAGL---GGGSSDAATVLRVLNELWEINAPSADLHRLA 129 (287)
T ss_pred CCCCcCCc---hHHHHHHHHHHHHHHHHhCCCcCHHHHHHHH
Confidence 44444432 2467799999999999999999999988765
No 303
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=29.55 E-value=57 Score=28.20 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=25.2
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 151 AKKHKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 151 ~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
........||.+||+.+|||+.+|.+..+.
T Consensus 32 ~~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 32 AIRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 335566789999999999999999998864
No 304
>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=29.53 E-value=78 Score=22.77 Aligned_cols=26 Identities=12% Similarity=0.101 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...++.+.|...||+..++.++|.++
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 35788999999999999999999876
No 305
>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=29.53 E-value=35 Score=22.92 Aligned_cols=18 Identities=17% Similarity=0.255 Sum_probs=15.2
Q ss_pred HHHHHhCCCHHHHHHHHH
Q 023151 162 KLIEVCGTSETEFASVST 179 (286)
Q Consensus 162 kla~~sgvt~vt~rnr~k 179 (286)
+||+.+||+..||.+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 689999999999987664
No 306
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=29.45 E-value=1.7e+02 Score=26.32 Aligned_cols=13 Identities=8% Similarity=0.158 Sum_probs=6.0
Q ss_pred cHHHHHHHhCCcc
Q 023151 95 DIRELGIRFGCIR 107 (286)
Q Consensus 95 ~I~~ia~qlg~s~ 107 (286)
+..+||..||+++
T Consensus 188 t~~eIa~~l~is~ 200 (232)
T TIGR03541 188 RQADIAAILGISE 200 (232)
T ss_pred CHHHHHHHHCcCH
Confidence 4444444444444
No 307
>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=29.28 E-value=59 Score=25.30 Aligned_cols=23 Identities=17% Similarity=0.117 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVS 178 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ 178 (286)
-.+|-.+||+.+|||..|++...
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 34688899999999999999843
No 308
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=29.26 E-value=1.2e+02 Score=26.16 Aligned_cols=24 Identities=4% Similarity=0.086 Sum_probs=12.3
Q ss_pred CcHHHHHHHhCCcc--hHHHHHHHHH
Q 023151 94 LDIRELGIRFGCIR--LIPLVQKGLS 117 (286)
Q Consensus 94 ~~I~~ia~qlg~s~--v~~~A~eiL~ 117 (286)
.+..+||..|++|. |...-..|+.
T Consensus 166 ~s~~eIA~~l~iS~~TV~~h~~~i~~ 191 (216)
T PRK10840 166 FLVTEIAKKLNRSIKTISSQKKSAMM 191 (216)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35555555555555 4444444444
No 309
>PRK01381 Trp operon repressor; Provisional
Probab=29.17 E-value=42 Score=27.32 Aligned_cols=36 Identities=8% Similarity=0.119 Sum_probs=29.7
Q ss_pred HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 148 YLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 148 Y~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
=++..++.-..+|++|++..||+-.||.+--+.+..
T Consensus 46 ~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 46 RIVEELLRGELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 345556777899999999999999999988887743
No 310
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=29.16 E-value=1.5e+02 Score=26.64 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=28.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN 92 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~ 92 (286)
+...+++..+++...+.+..+.|+..||.+-
T Consensus 17 s~s~AA~~L~isQ~avSr~i~~LE~~lg~~L 47 (296)
T PRK09906 17 NFTKAAEKLHTAQPSLSQQIKDLENCVGVPL 47 (296)
T ss_pred CHHHHHHHhCCCCcHHHHHHHHHHHHhCCee
Confidence 6778999999999999999999999999853
No 311
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=29.10 E-value=1.9e+02 Score=26.63 Aligned_cols=55 Identities=13% Similarity=0.142 Sum_probs=40.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
++..+++..+++...+.+..+.|+.+||.+. .+.+.+.+.. +.+.|..||+.+.+
T Consensus 18 s~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~-----l~~~a~~il~~~~~ 78 (308)
T PRK10094 18 SFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEH-----LLSQARDWLSWLES 78 (308)
T ss_pred CHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeCCCceeECHhHHH-----HHHHHHHHHHHHHH
Confidence 6678899999999999999999999999853 2233333333 36667777766654
No 312
>PRK00343 ipk 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=28.95 E-value=2e+02 Score=26.79 Aligned_cols=55 Identities=18% Similarity=0.125 Sum_probs=39.2
Q ss_pred hhHHHHHHHHHHHhhhhcC--------CCCCCcch---HHHHHHHHHHHHhhCCCCCCHHHHHHHh
Q 023151 16 KQLIRKAAEIRRLCDVQFD--------SSIIGVGE---VCKAVICLELAASRFDVIFDRKTAIKLS 70 (286)
Q Consensus 16 ~~V~ekAael~Rla~~k~~--------~l~~Grs~---~~~aaacLylAcr~~~iprd~~e~~k~s 70 (286)
++.+-+|...++..-...+ ++..|.+. .+.++|.+.++.+.++.+++.+++++++
T Consensus 68 ~N~v~~a~~~l~~~~~~~~~~~i~i~k~IP~gaGLGssSs~aaa~l~al~~l~~~~ls~~el~~la 133 (271)
T PRK00343 68 DNLIVRAARLLQKATGTPLGADISLDKRLPMGGGLGGGSSDAATTLVALNRLWQLGLSRDELAELG 133 (271)
T ss_pred ccHHHHHHHHHHHHhCCCCCeEEEEEcCCCCcCCCCcchHHHHHHHHHHHHHhCCCcCHHHHHHHH
Confidence 4777777777765422111 23345444 7888999999999999999999998875
No 313
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=28.88 E-value=4.4e+02 Score=23.80 Aligned_cols=28 Identities=11% Similarity=0.067 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...+..+||+..|+++.|++++...-..
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999999999999999876533
No 314
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=28.87 E-value=2.3e+02 Score=25.77 Aligned_cols=55 Identities=22% Similarity=0.315 Sum_probs=39.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
-++..+++..+++...+.+..+.|+.+||.+- .+.+.+.+..| .+.|..+++.+.
T Consensus 26 gS~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R~~r~~~lT~~G~~l-----~~~a~~~l~~~e 86 (303)
T PRK10082 26 RNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIF-----HSQIRHLLQQLE 86 (303)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEecCCCCccCHHHHHH-----HHHHHHHHHHHH
Confidence 35677899999999999999999999999842 23344444433 555666666554
No 315
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=28.87 E-value=1.1e+02 Score=30.36 Aligned_cols=49 Identities=10% Similarity=0.136 Sum_probs=41.7
Q ss_pred CCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 134 SADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 134 ~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
..-|.|+.+||||||+|=-.++..-==..|.+-.|.+-.++.....+|.
T Consensus 272 ~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 272 FLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 4446799999999999998888555557899999999999999999995
No 316
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=28.84 E-value=55 Score=30.08 Aligned_cols=25 Identities=16% Similarity=0.117 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.++|-++||+.+|||..|+++....
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCC
Confidence 3689999999999999999998754
No 317
>PRK08359 transcription factor; Validated
Probab=28.68 E-value=58 Score=29.06 Aligned_cols=24 Identities=13% Similarity=0.141 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
...||.+||+.+||+..||+++..
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~ 120 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAH 120 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 368999999999999999987743
No 318
>PRK14611 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=28.55 E-value=2.2e+02 Score=26.32 Aligned_cols=56 Identities=13% Similarity=0.112 Sum_probs=38.4
Q ss_pred hhHHHHHHHHHHHhhhhcCC----------CCCCc-chHHHHHHHHHHHHhhCCCCCCHHHHHHHhC
Q 023151 16 KQLIRKAAEIRRLCDVQFDS----------SIIGV-GEVCKAVICLELAASRFDVIFDRKTAIKLSG 71 (286)
Q Consensus 16 ~~V~ekAael~Rla~~k~~~----------l~~Gr-s~~~~aaacLylAcr~~~iprd~~e~~k~sg 71 (286)
.+.+-+|...++.......+ ..+|. |..+.+||.+.+++...|.+.+.+++.+++.
T Consensus 61 ~n~v~~a~~~~~~~~g~~~~~~i~i~k~IP~~~GLGSSsA~aaA~l~al~~~~~~~l~~~~l~~la~ 127 (275)
T PRK14611 61 ENIVYKALRLFERYTGIDINYSIFIEKNIPVGAGLGGGSSNAAVVLKYLNELLGNPLSEEELFELAS 127 (275)
T ss_pred ccHHHHHHHHHHHHhCCCCCeEEEEEeCCCCcCCccHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 46777777777654321111 22343 4667888889999999999999998877654
No 319
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=28.53 E-value=2e+02 Score=25.93 Aligned_cols=56 Identities=16% Similarity=0.229 Sum_probs=40.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.++..+++..+++...+.+..+.|+.+||.+- ++.+.+.+..| ...+.++++.+.+
T Consensus 21 gs~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~r~l~lT~~G~~l-----~~~~~~~l~~~~~ 82 (297)
T PRK11139 21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRY-----FLDIREIFDQLAE 82 (297)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCchheEecCCceeECHhHHHH-----HHHHHHHHHHHHH
Confidence 45677889999999999999999999999853 23455555443 5556666665553
No 320
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=28.43 E-value=1e+02 Score=26.28 Aligned_cols=40 Identities=18% Similarity=0.145 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhCCCCCCcHHHHHHHhCCcc--hHHHHHHHHH
Q 023151 78 NRSFNSLQNSIGFKNELDIRELGIRFGCIR--LIPLVQKGLS 117 (286)
Q Consensus 78 ~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~--v~~~A~eiL~ 117 (286)
...=+.|-+.|--+...+..+||.++|+|+ +.++..+|.+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 333456777888888899999999999999 7777777766
No 321
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=28.43 E-value=53 Score=30.20 Aligned_cols=25 Identities=4% Similarity=0.033 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.++|-++||+.+|||..|+++....
T Consensus 4 ~~~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 4 KRPVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CCCcHHHHHHHhCCCHHHhhhhhCC
Confidence 3689999999999999999988743
No 322
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=28.41 E-value=1.2e+02 Score=26.11 Aligned_cols=44 Identities=11% Similarity=0.135 Sum_probs=36.4
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 146 AFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 146 AlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
++|.... .+..+...+||+..+|++.|+....+.|.+ .|.-...
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~-----~GlV~~~ 57 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLER-----LGLVEYE 57 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHH-----CCCeEEe
Confidence 5666665 777889999999999999999999999977 6666654
No 323
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=28.40 E-value=2.1e+02 Score=21.06 Aligned_cols=27 Identities=15% Similarity=0.197 Sum_probs=25.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+..+|++..++++.++....+.|.+
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 589999999999999999999999987
No 324
>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=28.38 E-value=1.3e+02 Score=22.16 Aligned_cols=31 Identities=6% Similarity=0.079 Sum_probs=25.2
Q ss_pred hCCCCCCHHHHHHHhCCC-HHHHHHHHHHHHH
Q 023151 153 KHKLKVDKLKLIEVCGTS-ETEFASVSTTMKD 183 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt-~vt~rnr~ke~~~ 183 (286)
.+|...|-++|++..|++ ..|+....+.|++
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 467778889999999997 9999999999976
No 325
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=28.10 E-value=1.2e+02 Score=20.30 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+..++++..|+++..+.++++.|++
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6677777777777777777777765
No 326
>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=28.10 E-value=1.9e+02 Score=20.82 Aligned_cols=15 Identities=13% Similarity=0.379 Sum_probs=9.7
Q ss_pred CCcHHHHHHHhCCcc
Q 023151 93 ELDIRELGIRFGCIR 107 (286)
Q Consensus 93 ~~~I~~ia~qlg~s~ 107 (286)
++...+||..||++.
T Consensus 22 ~v~~~~iA~~L~vs~ 36 (60)
T PF01325_consen 22 PVRTKDIAERLGVSP 36 (60)
T ss_dssp SBBHHHHHHHHTS-H
T ss_pred CccHHHHHHHHCCCh
Confidence 456777777777776
No 327
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=27.86 E-value=1e+02 Score=25.48 Aligned_cols=30 Identities=10% Similarity=0.000 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhh
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCH 186 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~ 186 (286)
..+-.+||+..|++..|++++..--...|.
T Consensus 129 g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 129 GLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 367789999999999999999988777775
No 328
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=27.67 E-value=1.9e+02 Score=26.42 Aligned_cols=55 Identities=11% Similarity=0.113 Sum_probs=40.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
+...+++..|++...+.+..+.|+.+||.+- .+.+...+..| ...|.++++.+.+
T Consensus 17 S~s~AA~~L~isQ~avS~~I~~LE~~lg~~LF~R~~r~v~lT~~G~~l-----~~~a~~~l~~~~~ 77 (305)
T PRK11233 17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKIL-----YTHARAILRQCEQ 77 (305)
T ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHhCCceEEeCCCCceECHhHHHH-----HHHHHHHHHHHHH
Confidence 6678899999999999999999999999853 22344444433 5666666666554
No 329
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=27.40 E-value=4e+02 Score=24.48 Aligned_cols=94 Identities=10% Similarity=0.085 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc--hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHH-HHHHH
Q 023151 74 EKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR--LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAV-AFYLC 150 (286)
Q Consensus 74 ~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~--v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAA-AlY~A 150 (286)
...+.++...|+..|+ .++++.+||..+|+|. +.+.=.+.. |. ++..|.-. =+-.|
T Consensus 4 ~~~i~~~~~~i~~~~~--~~~~l~~lA~~~~~S~~~l~r~F~~~~-------------g~------s~~~yi~~~Rl~~A 62 (289)
T PRK15121 4 AGIIRDLLIWLEGHLD--QPLSLDNVAAKAGYSKWHLQRMFKDVT-------------GH------AIGAYIRARRLSKA 62 (289)
T ss_pred HHHHHHHHHHHHhccc--CCCCHHHHHHHHCcCHHHHHHHHHHHH-------------Cc------CHHHHHHHHHHHHH
Confidence 4567788888887766 4579999999999999 444322221 22 22222111 12223
Q ss_pred HHhCC-CCCCHHHHHHHhCC-CHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 151 AKKHK-LKVDKLKLIEVCGT-SETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 151 ~~~~k-~kvtQ~kla~~sgv-t~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
+.++. -..+=.+||..+|- +...|.+.++.+ +|+.+..
T Consensus 63 ~~~L~~~~~~i~~iA~~~Gf~s~~~f~r~Fk~~-------~g~sP~~ 102 (289)
T PRK15121 63 AVALRLTSRPILDIALQYRFDSQQTFTRAFKKQ-------FAQTPAL 102 (289)
T ss_pred HHHHHcCCCCHHHHHHHHCCCCHHHHHHHHHHH-------HCcCHHH
Confidence 33222 35677889999987 788999999988 7777663
No 330
>PRK06424 transcription factor; Provisional
Probab=27.37 E-value=84 Score=27.00 Aligned_cols=31 Identities=13% Similarity=0.158 Sum_probs=25.3
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 149 LCAKKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 149 ~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
+-.......+||.+||+.+|+++.+|.++..
T Consensus 89 Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 89 VKNARERLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4444566789999999999999999987764
No 331
>PRK09526 lacI lac repressor; Reviewed
Probab=27.25 E-value=69 Score=29.45 Aligned_cols=25 Identities=16% Similarity=0.118 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.++|-++||..+|||..|+++....
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcC
Confidence 4579999999999999999988764
No 332
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=27.22 E-value=1.9e+02 Score=26.35 Aligned_cols=31 Identities=10% Similarity=-0.027 Sum_probs=27.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN 92 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~ 92 (286)
++..+++..|++...+.+..+.|+.+||.+.
T Consensus 18 s~s~AA~~L~isQpavS~~I~~LE~~lg~~L 48 (300)
T PRK11074 18 SFSAAAQELHRVPSAVSYTVRQLEEWLAVPL 48 (300)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCee
Confidence 5677899999999999999999999999853
No 333
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=27.10 E-value=58 Score=30.01 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke 180 (286)
+|-++||+.+|||..|+++....
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 58899999999999999998764
No 334
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=27.09 E-value=2.2e+02 Score=21.59 Aligned_cols=40 Identities=10% Similarity=0.045 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
+.-+.-|+.. ......+-.+||..+|+++.++..+++...
T Consensus 22 ~~~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~~ 61 (127)
T COG2207 22 LARALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKET 61 (127)
T ss_pred HHHHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4466667777 777779999999999999999999999873
No 335
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=27.08 E-value=2.6e+02 Score=25.12 Aligned_cols=55 Identities=15% Similarity=0.231 Sum_probs=39.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
.+...+++..|++...+.+..+.|+..||.+- ++.+.+.+..| .+.|..+++.+.
T Consensus 18 gS~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~~~~~~lT~~G~~l-----~~~a~~~l~~~~ 78 (300)
T TIGR02424 18 GSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELF-----LRHAGASLAALR 78 (300)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCccccHhHHHH-----HHHHHHHHHHHH
Confidence 36778899999999999999999999999853 22344444433 455555555444
No 336
>PRK10632 transcriptional regulator; Provisional
Probab=27.05 E-value=2.3e+02 Score=25.98 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=39.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
.+...+++..+++...+.+..+.|+.+||.+- .+.+.+.+..| ...|..+++.+.
T Consensus 17 gS~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~i~lT~~G~~l-----~~~a~~il~~~~ 77 (309)
T PRK10632 17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIY-----YQGCRRMLHEVQ 77 (309)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeecccCCCceechhHHHH-----HHHHHHHHHHHH
Confidence 45677899999999999999999999999853 23344444433 455555555544
No 337
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.01 E-value=64 Score=22.94 Aligned_cols=22 Identities=9% Similarity=0.063 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHH
Q 023151 160 KLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 160 Q~kla~~sgvt~vt~rnr~ke~ 181 (286)
-.++|+.+||++.|+|...+.-
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 3689999999999999876543
No 338
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.99 E-value=2.2e+02 Score=23.69 Aligned_cols=30 Identities=17% Similarity=0.239 Sum_probs=23.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGF 90 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL 90 (286)
=+++++.+..|++-..+.+-+..|...||+
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 567788888888888888877777777777
No 339
>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=26.95 E-value=3.8e+02 Score=22.47 Aligned_cols=85 Identities=14% Similarity=0.063 Sum_probs=52.6
Q ss_pred cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHH-hCCCCCCHHHHHHHhCCCHH
Q 023151 95 DIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAK-KHKLKVDKLKLIEVCGTSET 172 (286)
Q Consensus 95 ~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~-~~k~kvtQ~kla~~sgvt~v 172 (286)
|+.+|.....|+. +.-.|.-.|+++..... .+... --..+.--+-.+|+-+|++ ..+...+-+.-+.++|++..
T Consensus 57 fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~--~~~~~--~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~ 132 (149)
T PF08613_consen 57 FLSRILKYTQCSPECLILALIYLDRLRQRSR--KPNIP--LNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLK 132 (149)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHHHHHH--H---TT-----STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HH
T ss_pred HHHHHHHHcCCChHHHHHHHHHHHHHHHhhc--ccccc--cccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHH
Confidence 6888888888988 77777777887665100 00010 0011333466677778888 67788899999999999999
Q ss_pred HHHHHHHHHHH
Q 023151 173 EFASVSTTMKD 183 (286)
Q Consensus 173 t~rnr~ke~~~ 183 (286)
.+.....++..
T Consensus 133 eln~lE~~fL~ 143 (149)
T PF08613_consen 133 ELNELEREFLK 143 (149)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 99988888754
No 340
>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=26.81 E-value=1.1e+02 Score=23.72 Aligned_cols=27 Identities=11% Similarity=0.105 Sum_probs=24.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+..+||+..|+|+.+++++......
T Consensus 126 g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 126 GLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 578999999999999999999988754
No 341
>PRK10702 endonuclease III; Provisional
Probab=26.79 E-value=3e+02 Score=24.89 Aligned_cols=47 Identities=23% Similarity=0.227 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCC---CcHHHHHHHhCCcc
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNE---LDIRELGIRFGCIR 107 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~---~~I~~ia~qlg~s~ 107 (286)
.+|-+++++.++-|+.++.-.- .+.-.+|-+.. ..|.|++..+|+..
T Consensus 103 ~~p~~~~~Ll~lpGVG~ktA~~---ill~a~~~~~~~VDt~v~Rv~~r~g~~~ 152 (211)
T PRK10702 103 EVPEDRAALEALPGVGRKTANV---VLNTAFGWPTIAVDTHIFRVCNRTQFAP 152 (211)
T ss_pred CCCchHHHHhcCCcccHHHHHH---HHHHHcCCCcccccchHHHHHHHhCCCC
Confidence 4799999999999999985433 22333554332 37999999999876
No 342
>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=26.78 E-value=1.8e+02 Score=23.36 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
-|.+.+++++..|+++..+.+..+.|.+
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3677777777777777777777777665
No 343
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=26.77 E-value=3.4e+02 Score=22.85 Aligned_cols=41 Identities=5% Similarity=-0.087 Sum_probs=30.3
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 147 FYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 147 lY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
++..+...| .+-++||+..|+|+.|++++...-...|-..+
T Consensus 125 i~~l~~~e~--~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 125 VIILRYLHD--YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred HHHHHHHcc--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 334444444 48899999999999999999887766555544
No 344
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=26.67 E-value=88 Score=23.65 Aligned_cols=24 Identities=8% Similarity=0.120 Sum_probs=22.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 160 KLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 160 Q~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+.+|++..|+++.|+...++.|++
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 568999999999999999999987
No 345
>PF06323 Phage_antiter_Q: Phage antitermination protein Q; InterPro: IPR010455 This entry is represented by Bacteriophage 82, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 82 gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [].
Probab=26.63 E-value=1.4e+02 Score=27.91 Aligned_cols=36 Identities=19% Similarity=0.276 Sum_probs=27.3
Q ss_pred HHhCCCC--CCHHHHHHHhCCCHHHHHHHHHH----HHHhhh
Q 023151 151 AKKHKLK--VDKLKLIEVCGTSETEFASVSTT----MKDLCH 186 (286)
Q Consensus 151 ~~~~k~k--vtQ~kla~~sgvt~vt~rnr~ke----~~~~c~ 186 (286)
+.+++.. -++.+||+.+||++.||+..|.. |.+.|.
T Consensus 159 ~~l~~~~~~y~~~~LA~L~GV~~~nW~~~y~~~W~~m~~~~~ 200 (230)
T PF06323_consen 159 AELNGREYKYTYAELAELVGVSRSNWSKNYAPRWLRMKSIFK 200 (230)
T ss_pred HHHcCCCccccHHHHHHHhCCChhhhhhhhHHHHHHHHHHHH
Confidence 4445443 59999999999999999999865 555443
No 346
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.62 E-value=1e+02 Score=26.68 Aligned_cols=30 Identities=13% Similarity=0.082 Sum_probs=25.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
.|..+||+..|+|+.|++++..-+...+.+
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 699999999999999999999887654443
No 347
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=26.57 E-value=96 Score=27.92 Aligned_cols=36 Identities=11% Similarity=0.141 Sum_probs=31.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +..+|++..|||..++|.-...|.. +|+-...
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~-----eGlv~~~ 67 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEA-----KGLLLRR 67 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 5678 7999999999999999999999977 7766654
No 348
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=26.56 E-value=2.2e+02 Score=26.39 Aligned_cols=55 Identities=18% Similarity=0.291 Sum_probs=41.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
+...+++..+++...+.+..+.|+.+||.+. ++.+.+.+..| ...|.++++.+.+
T Consensus 18 s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~LF~R~~r~v~lT~~G~~l-----~~~a~~il~~~~~ 78 (317)
T PRK15421 18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEIL-----LQLANQVLPQISQ 78 (317)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEEEEecCCCceECHhHHHH-----HHHHHHHHHHHHH
Confidence 6778899999999999999999999999852 23344444433 6667777766654
No 349
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=26.51 E-value=69 Score=24.83 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=21.0
Q ss_pred CCCCCCHHHHHHHhCC------CHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGT------SETEFASVST 179 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgv------t~vt~rnr~k 179 (286)
.....||.+||+..|+ |++||.+..+
T Consensus 21 ~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 21 IKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 3456899999999994 9999988654
No 350
>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=26.38 E-value=99 Score=20.69 Aligned_cols=35 Identities=23% Similarity=0.188 Sum_probs=26.0
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 149 LCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 149 ~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+....-=..+|=.+|++.+|+++.+|-+.+.+..+
T Consensus 8 l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~ 42 (47)
T PF00440_consen 8 LFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKDD 42 (47)
T ss_dssp HHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHHH
T ss_pred HHHHhCHHhCCHHHHHHHHccchhhHHHHcCCHHH
Confidence 33333334678899999999999999988776644
No 351
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=26.30 E-value=2.4e+02 Score=21.75 Aligned_cols=56 Identities=13% Similarity=0.230 Sum_probs=40.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcchHHHHHHHHHHHHHh
Q 023151 60 IFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIRLIPLVQKGLSLFKDR 122 (286)
Q Consensus 60 prd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~v~~~A~eiL~~~ke~ 122 (286)
|+|.+++-.++ +.+..--+.|.+.||++.. .|..|-.. -+.+...+.++|...+++
T Consensus 4 ~~t~~~l~~ia----~~iG~~Wk~Lar~LGls~~-dI~~i~~~--~~~~~eq~~~mL~~W~~r 59 (86)
T cd08318 4 PVTGEQITVFA----NKLGEDWKTLAPHLEMKDK-EIRAIESD--SEDIKMQAKQLLVAWQDR 59 (86)
T ss_pred CCCHHHHHHHH----HHHhhhHHHHHHHcCCCHH-HHHHHHhc--CCCHHHHHHHHHHHHHHh
Confidence 66677776665 5677788888999998433 56666544 345889999999998877
No 352
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=26.27 E-value=5.4e+02 Score=23.98 Aligned_cols=93 Identities=8% Similarity=0.043 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCCcc--hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHH-HHHH
Q 023151 74 EKAYNRSFNSLQNSIGFKNELDIRELGIRFGCIR--LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVA-FYLC 150 (286)
Q Consensus 74 ~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~s~--v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAA-lY~A 150 (286)
...+.+.+..|...++ .++++.+||..+|+|+ +.+. +++. -|. +|..|.--. +-.|
T Consensus 217 ~~~~~~~~~~i~~~~~--~~~sl~~lA~~~~~S~~~l~r~-------fk~~------~g~------s~~~~~~~~Rl~~A 275 (322)
T PRK09393 217 SDRLGPLIDWMRAHLA--EPHTVASLAARAAMSPRTFLRR-------FEAA------TGM------TPAEWLLRERLARA 275 (322)
T ss_pred hHHHHHHHHHHHhccC--CCCCHHHHHHHHCcCHHHHHHH-------HHHH------HCc------CHHHHHHHHHHHHH
Confidence 3567777777777544 4578999999999998 4332 2222 122 344332222 2233
Q ss_pred HHhC-CCCCCHHHHHHHhCC-CHHHHHHHHHHHHHhhhhhhhcccc
Q 023151 151 AKKH-KLKVDKLKLIEVCGT-SETEFASVSTTMKDLCHDVFGIAKE 194 (286)
Q Consensus 151 ~~~~-k~kvtQ~kla~~sgv-t~vt~rnr~ke~~~~c~d~~~i~~~ 194 (286)
+.++ .-..+=.+||..+|- +...|.+.++.+ +|+.+.
T Consensus 276 ~~lL~~~~~~i~~IA~~~Gf~~~s~F~r~Fk~~-------~G~tP~ 314 (322)
T PRK09393 276 RDLLESSALSIDQIAERAGFGSEESLRHHFRRR-------AATSPA 314 (322)
T ss_pred HHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH-------HCcCHH
Confidence 3333 235677899999998 568999999998 666654
No 353
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=26.22 E-value=1.9e+02 Score=25.45 Aligned_cols=31 Identities=16% Similarity=0.187 Sum_probs=28.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
.+...+++..+++...+.+..+.|+..||.+
T Consensus 12 gs~~~AA~~L~isqsavS~~i~~LE~~lg~~ 42 (279)
T TIGR03339 12 GSFTRAAERLGLSQPTVTDQVRKLEERYGVE 42 (279)
T ss_pred CCHHHHHHHhcCCchHHHHHHHHHHHHhCCc
Confidence 3677889999999999999999999999985
No 354
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.11 E-value=80 Score=26.25 Aligned_cols=26 Identities=8% Similarity=-0.013 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
=+=++|+...|||-.|+|||..+|..
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 34579999999999999999999853
No 355
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=26.09 E-value=2.3e+02 Score=25.82 Aligned_cols=56 Identities=16% Similarity=0.276 Sum_probs=42.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CC-cHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------EL-DIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~-~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.+...+++..|++...+.+..+.|+..||.+- .+ .+.+.+.. +.+.|.++++.+.+
T Consensus 17 ~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~-----l~~~~~~~l~~~~~ 79 (309)
T PRK12682 17 LNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKA-----VLDVIERILREVGN 79 (309)
T ss_pred CCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEEECCCCcCccCHhHHH-----HHHHHHHHHHHHHH
Confidence 36678899999999999999999999999743 22 24444444 47777777777664
No 356
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=26.07 E-value=1.3e+02 Score=19.94 Aligned_cols=29 Identities=10% Similarity=0.163 Sum_probs=24.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
+-|.+..++++..|+++..+.+.++.|..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56788889999999999888888888775
No 357
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.03 E-value=1.6e+02 Score=25.02 Aligned_cols=30 Identities=13% Similarity=0.069 Sum_probs=25.4
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 57 FDVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
.+-|.|.+++++-.+.+++.++++++.|..
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLE 68 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHH
Confidence 578999999999999999988777766653
No 358
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=26.01 E-value=2e+02 Score=26.27 Aligned_cols=30 Identities=17% Similarity=0.160 Sum_probs=27.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
+...+++..+++...+.+..+.|+.+||.+
T Consensus 21 s~s~AA~~L~isqpavS~~i~~LE~~lg~~ 50 (305)
T CHL00180 21 SFKKAAESLYISQPAVSLQIKNLEKQLNIP 50 (305)
T ss_pred CHHHHHHHhcCCChHHHHHHHHHHHHhCCE
Confidence 667788999999999999999999999984
No 359
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=25.94 E-value=1.1e+02 Score=21.65 Aligned_cols=28 Identities=7% Similarity=-0.022 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 023151 158 VDKLKLIEVCGTSETEFASVSTTMKDLC 185 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke~~~~c 185 (286)
-+-.+.|+..+|.+.|++.|.+.|++.+
T Consensus 13 ~n~~~tA~~L~iHrNTl~yRl~ki~~l~ 40 (59)
T PF13556_consen 13 GNISKTARALHIHRNTLRYRLKKIEELL 40 (59)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4667889999999999999999998743
No 360
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=25.90 E-value=69 Score=26.25 Aligned_cols=58 Identities=10% Similarity=0.133 Sum_probs=40.9
Q ss_pred HHHHhCCCHHHHHHHHHHHHHHhCCCCCC-----------cHHHHHHHhCCcc-hHHHHHHHHHHHHHhhh
Q 023151 66 AIKLSGMSEKAYNRSFNSLQNSIGFKNEL-----------DIRELGIRFGCIR-LIPLVQKGLSLFKDRFT 124 (286)
Q Consensus 66 ~~k~sg~~~k~y~~~yr~l~~~LgL~~~~-----------~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~ 124 (286)
|-...+++...+.+|+..|..+..|+... +|++| -.|.-+. |...|..|.+.|+..|+
T Consensus 11 Ik~~L~~~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~Tlkkl-RrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 11 IKSSLKVDNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKL-RRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp HHHTCETTEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHH-TT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHH-HHhhccHHHHHHHHHHHHHHHHHhC
Confidence 34455778889999999999999987753 35443 3444556 99999999999999987
No 361
>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=25.79 E-value=5.7e+02 Score=24.13 Aligned_cols=133 Identities=16% Similarity=0.141 Sum_probs=81.5
Q ss_pred HHHHhhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---cHHHHHHHhCCcchHHHHHHHHHHHH------
Q 023151 51 ELAASRF-DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNEL---DIRELGIRFGCIRLIPLVQKGLSLFK------ 120 (286)
Q Consensus 51 ylAcr~~-~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~---~I~~ia~qlg~s~v~~~A~eiL~~~k------ 120 (286)
|...|.. +--+++.++++..|++.+.| |...+.-+.++ +++++|..|||++-+..=-+.|-.|-
T Consensus 17 ~ye~rk~~~p~fS~R~fa~~~G~ss~s~------L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~~yF~~lV~f~~ak~~~ 90 (271)
T TIGR02147 17 YYEERKKTDPAFSWRFFAEKAGFSSTSY------LNDIIKGKKNLTKRMIPKFAEALGLDEKEAAYFEAMVNFGQAKTDT 90 (271)
T ss_pred HHHHHhccCcCcCHHHHHHHhCCCCHHH------HHHHHcCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCCHH
Confidence 4455554 44789999999999977655 45566656554 59999999999994433222221110
Q ss_pred --Hh----hhhccccccccCCCCC----hhHHHHHHHHHHHHhCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHhhhhh
Q 023151 121 --DR----FTAALPASRKTSADFS----RPVFTAVAFYLCAKKHKLKVDKLKLIEVCG--TSETEFASVSTTMKDLCHDV 188 (286)
Q Consensus 121 --e~----~~~~L~~gk~~~~D~~----pp~~AAAAlY~A~~~~k~kvtQ~kla~~sg--vt~vt~rnr~ke~~~~c~d~ 188 (286)
+. ...--+..+..-+|-+ -.-+...++.....+++...+=..||..++ ||..++++-..=|++
T Consensus 91 ~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~----- 165 (271)
T TIGR02147 91 EKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLER----- 165 (271)
T ss_pred HHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHH-----
Confidence 00 0000000111111111 112345577777778888877778999998 999999999998877
Q ss_pred hhcccc
Q 023151 189 FGIAKE 194 (286)
Q Consensus 189 ~~i~~~ 194 (286)
.|+-+.
T Consensus 166 ~glikk 171 (271)
T TIGR02147 166 LGLIKK 171 (271)
T ss_pred CCCeeE
Confidence 555554
No 362
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=25.78 E-value=56 Score=23.90 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=21.3
Q ss_pred HHHHHhCCCCCCcHHHHHHHhCCcc-hHHHHHHHHH
Q 023151 83 SLQNSIGFKNELDIRELGIRFGCIR-LIPLVQKGLS 117 (286)
Q Consensus 83 ~l~~~LgL~~~~~I~~ia~qlg~s~-v~~~A~eiL~ 117 (286)
.|...|.-+..+++.+||..|+++. ..+...+.|.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~ 39 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLI 39 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3444455556679999999999999 5554444443
No 363
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.66 E-value=4e+02 Score=22.29 Aligned_cols=67 Identities=12% Similarity=0.064 Sum_probs=48.9
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC------cHHHHHHHhCCcc-hHHHHHHHHH
Q 023151 46 AVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNEL------DIRELGIRFGCIR-LIPLVQKGLS 117 (286)
Q Consensus 46 aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~------~I~~ia~qlg~s~-v~~~A~eiL~ 117 (286)
--.-||+-|| =+++|+-+..|++-..+..-+..+-+.+|.++.- +=.+|-.|+.=-+ ....|.++|+
T Consensus 48 eFv~lf~r~R-----GnlKEvEr~lg~sYptvR~kld~vlramgy~p~~e~~~~i~~~~i~~qle~Gei~peeA~~~L~ 121 (122)
T COG3877 48 EFVELFLRCR-----GNLKEVERELGISYPTVRTKLDEVLRAMGYNPDSENSVNIGKKKIIDQLEKGEISPEEAIKMLN 121 (122)
T ss_pred HHHHHHHHHc-----cCHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCCCChhhhhHHHHHHHHHcCCCCHHHHHHHhc
Confidence 3345677666 4789999999999999999999999999998742 3455777775555 4444555543
No 364
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=25.44 E-value=1.8e+02 Score=26.02 Aligned_cols=54 Identities=11% Similarity=0.093 Sum_probs=38.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHH
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFK 120 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~k 120 (286)
+...+++..+++...+.+..+.|+.+||.+- .+.+...+..| .+.|..+++...
T Consensus 23 s~t~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~~l-----~~~a~~~l~~~~ 82 (294)
T PRK09986 23 HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKIL-----MEESRRLLDNAE 82 (294)
T ss_pred CHHHHHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCCCceeECHhHHHH-----HHHHHHHHHHHH
Confidence 5667888999999999999999999999743 23344444433 455555555444
No 365
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=25.30 E-value=2.6e+02 Score=24.43 Aligned_cols=56 Identities=25% Similarity=0.310 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC---CCcHHHHHHHhCCcc--hHHHHHHHHH
Q 023151 59 VIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN---ELDIRELGIRFGCIR--LIPLVQKGLS 117 (286)
Q Consensus 59 iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~---~~~I~~ia~qlg~s~--v~~~A~eiL~ 117 (286)
+|-+++++.++-|+.++.-.-. +...+|-+. -..|.+++..+|+.. -.....+.++
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~i---ll~~~~~~~~~vD~~v~Ri~~r~g~~~~~~~~~~~~~l~ 161 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVV---LNVAFGIPAIAVDTHVFRVSNRLGLSKGKDPDKVEEELL 161 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHH---HHHHcCCCccccchhHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 5667889999999998854433 233355333 236999999999875 3333444443
No 366
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=25.26 E-value=2.5e+02 Score=26.30 Aligned_cols=56 Identities=11% Similarity=0.077 Sum_probs=40.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.+...+++..+++...+.+..+.|+.+||.+- ++.+..-+.. +...|.++|+.+.+
T Consensus 19 gSfs~AA~~L~isQpavS~~Ik~LE~eLG~~LF~R~~r~~~LT~aG~~-----ll~~a~~il~~~~~ 80 (297)
T PRK15243 19 GSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQT-----IYRKVKSHYIFLHA 80 (297)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCccEEeCCCCeeECHHHHH-----HHHHHHHHHHHHHH
Confidence 35677899999999999999999999999853 2334444333 36666666665553
No 367
>PRK14611 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=25.26 E-value=1.6e+02 Score=27.30 Aligned_cols=31 Identities=13% Similarity=0.067 Sum_probs=26.2
Q ss_pred ChhHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Q 023151 138 SRPVFTAVAFYLCAKKHKLKVDKLKLIEVCG 168 (286)
Q Consensus 138 ~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sg 168 (286)
+-+..+||+++.+....+...+..+|++.+.
T Consensus 97 SSsA~aaA~l~al~~~~~~~l~~~~l~~la~ 127 (275)
T PRK14611 97 GGSSNAAVVLKYLNELLGNPLSEEELFELAS 127 (275)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 4677889999999999999999998877653
No 368
>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=25.19 E-value=50 Score=23.28 Aligned_cols=23 Identities=13% Similarity=0.215 Sum_probs=18.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke 180 (286)
.++.+||..-||+..|++++.+.
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 48999999999999999998875
No 369
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=25.00 E-value=1.4e+02 Score=27.17 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=28.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFGC 105 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg~ 105 (286)
.+-.||+...|++...+....+.+.+.||.....-.-.+|..+|+
T Consensus 195 ~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~v~~a~~~gl 239 (240)
T PRK10188 195 KTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGL 239 (240)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcCC
Confidence 455667777777777777777777777776655444345555543
No 370
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=24.94 E-value=3.4e+02 Score=21.48 Aligned_cols=29 Identities=3% Similarity=0.003 Sum_probs=23.4
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
+....-++.+.|...|+++.|+++..+.+
T Consensus 64 L~~~~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 64 MQYTRGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 33345678999999999999999988764
No 371
>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=24.91 E-value=1.8e+02 Score=25.76 Aligned_cols=42 Identities=21% Similarity=0.335 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHh---CCCCC---CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 77 YNRSFNSLQNSI---GFKNE---LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 77 y~~~yr~l~~~L---gL~~~---~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
|..-+..|.... .++++ |+-.+||.+||+|. ++++|.+.|..
T Consensus 2 y~qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~ 50 (233)
T TIGR02404 2 YEQIYQDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTE 50 (233)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
No 372
>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=24.90 E-value=66 Score=25.82 Aligned_cols=33 Identities=12% Similarity=0.322 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN 92 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~ 92 (286)
+.. ++..+.+++|+.+..++.++.+|. ++|+..
T Consensus 20 ~~~-nvp~L~~~TGmPrRT~Qd~i~aL~-~~~I~~ 52 (90)
T PF09904_consen 20 GER-NVPALMEATGMPRRTIQDTIKALP-ELGIEC 52 (90)
T ss_dssp S-B--HHHHHHHH---HHHHHHHHHGGG-GGT-EE
T ss_pred CCc-cHHHHHHHhCCCHhHHHHHHHHhh-cCCeEE
Confidence 344 899999999999999999999999 888743
No 373
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=24.82 E-value=1.2e+02 Score=26.02 Aligned_cols=33 Identities=6% Similarity=-0.055 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHDV 188 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~ 188 (286)
...+-.+||+..|+|..|++++.......+...
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999999987765544433
No 374
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=24.80 E-value=80 Score=27.28 Aligned_cols=28 Identities=7% Similarity=0.312 Sum_probs=23.4
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 153 KHKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 153 ~~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
......||.++|+.+|+++.|+.++.+.
T Consensus 16 R~~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 16 RQQQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 4456789999999999999999987753
No 375
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=24.74 E-value=5.3e+02 Score=23.37 Aligned_cols=30 Identities=17% Similarity=0.289 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGF 90 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL 90 (286)
..+++++++++..|+++..+.+.+ .+.+|+
T Consensus 197 ~~~isl~~lA~~~~lS~~~l~r~F---k~~~G~ 226 (290)
T PRK10572 197 ASEFDIESVAQHVCLSPSRLAHLF---RQQLGI 226 (290)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHH---HHHHCc
Confidence 467788888888888876665443 344565
No 376
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=24.69 E-value=1.1e+02 Score=27.71 Aligned_cols=36 Identities=8% Similarity=0.125 Sum_probs=31.1
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +..+|++..|||..++|.-...|+. .|+-...
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~-----eGlV~~~ 66 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEI-----KGLVEVR 66 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 5678 6999999999999999999999987 7776654
No 377
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=24.69 E-value=2.8e+02 Score=25.36 Aligned_cols=31 Identities=23% Similarity=0.289 Sum_probs=28.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
.+...+++..+++...+.+..+.|+.+||.+
T Consensus 19 gS~s~AAe~L~isqsavS~~Ik~LE~~lg~~ 49 (309)
T PRK11013 19 GSLTEAARLLHTSQPTVSRELARFEKVIGLK 49 (309)
T ss_pred CcHHHHHHHHCCCcHHHHHHHHHHHHHhCce
Confidence 3677899999999999999999999999975
No 378
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=24.63 E-value=1.1e+02 Score=33.68 Aligned_cols=81 Identities=12% Similarity=0.006 Sum_probs=70.3
Q ss_pred HHHHHHHhCCCCChhHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 3 LSDIAKKLGLSDSKQLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 3 i~ria~kLgL~e~~~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
|+.|+.+|.|.+ .+.++-=-+|.=....++.|++.|-.-=..--|+|+-|+..+...+..+|.+..+--.-.....||
T Consensus 684 L~~Lc~rL~l~~--e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~~vyR 761 (920)
T KOG1010|consen 684 LNDLCERLSLSD--ELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVSLVYR 761 (920)
T ss_pred HHHHHHHhhhhh--HHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhhhhhh
Confidence 678999999997 688888888888888777888888888889999999999999999999999998887777777787
Q ss_pred HHH
Q 023151 83 SLQ 85 (286)
Q Consensus 83 ~l~ 85 (286)
.+-
T Consensus 762 sV~ 764 (920)
T KOG1010|consen 762 SVL 764 (920)
T ss_pred hee
Confidence 653
No 379
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=24.62 E-value=1e+02 Score=30.04 Aligned_cols=36 Identities=14% Similarity=0.161 Sum_probs=29.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +.++|++..|||..|+++-|.+++. .|+-...
T Consensus 26 g~~lps~r~la~~~~vsr~tv~~a~~~L~~-----~g~i~~~ 62 (431)
T PRK15481 26 GDSLPPVRELASELGVNRNTVAAAYKRLVT-----AGLAQSQ 62 (431)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 3566 7899999999999999999999987 6655543
No 380
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=24.60 E-value=1.1e+02 Score=27.65 Aligned_cols=36 Identities=14% Similarity=0.208 Sum_probs=31.1
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +..+|++..|||..++|.-.+.|+. .|+-...
T Consensus 23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~-----~GlV~~~ 59 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSRNSLREALAKLVS-----EGVLLSR 59 (253)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 5678 6999999999999999999999987 7776654
No 381
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=24.45 E-value=1.4e+02 Score=26.57 Aligned_cols=23 Identities=13% Similarity=0.091 Sum_probs=13.2
Q ss_pred cHHHHHHHhCCcc--hHHHHHHHHH
Q 023151 95 DIRELGIRFGCIR--LIPLVQKGLS 117 (286)
Q Consensus 95 ~I~~ia~qlg~s~--v~~~A~eiL~ 117 (286)
+..+||.+|++|+ |......|+.
T Consensus 165 snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 165 SNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 5566666666666 5555555554
No 382
>PRK13500 transcriptional activator RhaR; Provisional
Probab=24.27 E-value=5.9e+02 Score=23.73 Aligned_cols=25 Identities=16% Similarity=0.199 Sum_probs=16.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 58 DVIFDRKTAIKLSGMSEKAYNRSFN 82 (286)
Q Consensus 58 ~iprd~~e~~k~sg~~~k~y~~~yr 82 (286)
..+++++++++..|++++.+.+.++
T Consensus 220 ~e~isl~~lA~~~~iS~~~L~r~FK 244 (312)
T PRK13500 220 KSPFALDKFCDEASCSERVLRQQFR 244 (312)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4467777777777777666655444
No 383
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=24.04 E-value=2.4e+02 Score=29.97 Aligned_cols=73 Identities=10% Similarity=-0.004 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 17 QLIRKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 17 ~V~ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
.|++..+.+|-.......+-.+++.+.--=-+|+|++-...+. ++.+|.+.+|-+.+.+..+.+.|++.+.-+
T Consensus 528 ~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~lt~~--Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~d 600 (617)
T PRK14086 528 AIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCRELTDL--SLPKIGQQFGRDHTTVMHADRKIRALMAER 600 (617)
T ss_pred HHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHHHcCC--CHHHHHHHhCCChhHHHHHHHHHHHHHHhC
Confidence 5777777777655554333334444444445678877776654 567888888877788888888888877654
No 384
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.96 E-value=1.3e+02 Score=24.98 Aligned_cols=34 Identities=6% Similarity=-0.005 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
...+..+||+..|+|+.|++++..--...|.+.+
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999999988877666655
No 385
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.91 E-value=1.4e+02 Score=24.48 Aligned_cols=41 Identities=15% Similarity=0.156 Sum_probs=31.1
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 147 FYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 147 lY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
+|...... ..+-.+||+..|+|+.|++++..--...|.+.+
T Consensus 113 v~~l~~~~--~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 113 SFLLRKLE--GLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 44444433 467889999999999999999887766666554
No 386
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=23.83 E-value=1.9e+02 Score=24.72 Aligned_cols=39 Identities=15% Similarity=0.077 Sum_probs=29.4
Q ss_pred HHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 48 ICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 48 acLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
+.+|+|.. .+-+.+.++|++..|+++..+.+-+..|.+.
T Consensus 13 ~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 13 MLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45677733 4557788888888888888888888888773
No 387
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.81 E-value=1.4e+02 Score=25.51 Aligned_cols=31 Identities=3% Similarity=-0.065 Sum_probs=25.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
..+.++||+..|+|+.|++++..--...+.+
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4889999999999999999988765554443
No 388
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=23.75 E-value=4.3e+02 Score=24.46 Aligned_cols=56 Identities=16% Similarity=0.169 Sum_probs=41.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CCcHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------ELDIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.++..+++..+++...+.+..+.|+..||.+- ++.+.+.+.+| .+.|.++++.+.+
T Consensus 26 gs~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~~~~~LT~~G~~l-----~~~a~~il~~~~~ 87 (310)
T PRK15092 26 NTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQL-----LGYARKILRFNDE 87 (310)
T ss_pred CCHHHHHHHhCCChHHHHHHHHHHHHHhCcceEEECCCCceECHhHHHH-----HHHHHHHHHHHHH
Confidence 35577899999999999999999999999853 22344444444 6666667766654
No 389
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=23.74 E-value=2e+02 Score=25.47 Aligned_cols=37 Identities=19% Similarity=0.146 Sum_probs=28.1
Q ss_pred CcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhcccccccc
Q 023151 94 LDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKT 133 (286)
Q Consensus 94 ~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~ 133 (286)
|+-.+||.+||+|. ++++|...|.. .++..--.|++.
T Consensus 26 PsE~eLa~~~~VSR~TVR~Al~~L~~---eGli~r~~G~Gt 63 (230)
T TIGR02018 26 PSEHELVAQYGCSRMTVNRALRELTD---AGLLERRQGVGT 63 (230)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEecCCEE
Confidence 58999999999999 99999888874 444333445554
No 390
>PRK00215 LexA repressor; Validated
Probab=23.61 E-value=2.9e+02 Score=24.09 Aligned_cols=32 Identities=6% Similarity=0.131 Sum_probs=28.4
Q ss_pred HhCCCCCCHHHHHHHhCC-CHHHHHHHHHHHHH
Q 023151 152 KKHKLKVDKLKLIEVCGT-SETEFASVSTTMKD 183 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgv-t~vt~rnr~ke~~~ 183 (286)
..++...+..+|++..|+ ++.|+.++.+.|++
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 345777899999999999 99999999999976
No 391
>PRK09480 slmA division inhibitor protein; Provisional
Probab=23.50 E-value=1.3e+02 Score=25.17 Aligned_cols=42 Identities=12% Similarity=0.055 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
+..||.=+-....|..+|=.+||+.+||++.||-..+++-.+
T Consensus 15 Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 15 ILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 334443333334458899999999999999999888866543
No 392
>COG0083 ThrB Homoserine kinase [Amino acid transport and metabolism]
Probab=23.46 E-value=60 Score=31.30 Aligned_cols=47 Identities=13% Similarity=0.068 Sum_probs=36.9
Q ss_pred CCCc-chHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 37 IIGV-GEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNS 83 (286)
Q Consensus 37 ~~Gr-s~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~ 83 (286)
.+|. |.-|.+||++++|-..++.|++.++++++.+.-+-++.|.-=.
T Consensus 89 ~rGLGSSaAsiVAal~aan~l~~~~L~~~~ll~~a~~~EgHpDNVapa 136 (299)
T COG0083 89 GRGLGSSAASIVAALAAANELAGLPLSKEELLQLALEIEGHPDNVAPA 136 (299)
T ss_pred CCCCcHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCCchHHHH
Confidence 3444 4667889999999999999999999999888766666655433
No 393
>PRK11050 manganese transport regulator MntR; Provisional
Probab=23.45 E-value=3e+02 Score=23.28 Aligned_cols=59 Identities=10% Similarity=-0.054 Sum_probs=36.9
Q ss_pred HHHHhhhhcCCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 023151 25 IRRLCDVQFDSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGF 90 (286)
Q Consensus 25 l~Rla~~k~~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL 90 (286)
.||.+... .+++......-.|+.+... +-+.+..++++..|+++..+.+.++.|+.. |+
T Consensus 22 ~~~~~~~~-----~~~~~~e~~l~~I~~~l~~-~~~~t~~eLA~~l~is~stVsr~l~~Le~~-Gl 80 (152)
T PRK11050 22 GFRQVREA-----HRRELIEDYVELIADLIAE-VGEARQVDIAARLGVSQPTVAKMLKRLARD-GL 80 (152)
T ss_pred HHHHHHHH-----HhHHHHHHHHHHHHHHHHh-cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CC
Confidence 55555443 1333343333344433332 346788888888888888888888888886 54
No 394
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=23.41 E-value=4.9e+02 Score=24.60 Aligned_cols=29 Identities=17% Similarity=0.072 Sum_probs=25.1
Q ss_pred hhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 55 SRFDVIFDRKTAIKLSGMSEKAYNRSFNS 83 (286)
Q Consensus 55 r~~~iprd~~e~~k~sg~~~k~y~~~yr~ 83 (286)
.....+++++++++..|++++.+.+.++.
T Consensus 192 ~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 192 SDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred hCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34567999999999999999999888775
No 395
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=23.15 E-value=76 Score=28.44 Aligned_cols=30 Identities=13% Similarity=0.313 Sum_probs=23.0
Q ss_pred CCCCCCHHHHHHHhCCCHH---------------HHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSET---------------EFASVSTTMKD 183 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~v---------------t~rnr~ke~~~ 183 (286)
....+||++||..+|||.. ||+.+|.-+++
T Consensus 15 k~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e 59 (187)
T COG3620 15 KELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEE 59 (187)
T ss_pred HHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHH
Confidence 3456899999999999985 66666666655
No 396
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.10 E-value=1.5e+02 Score=24.38 Aligned_cols=34 Identities=12% Similarity=0.184 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
...+..+||+..|+|+.|++++..--...+...+
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999999877655444433
No 397
>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=23.02 E-value=70 Score=29.21 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=19.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~ke 180 (286)
+|-++||+.+|||..|+.+....
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 57789999999999999987643
No 398
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=22.99 E-value=68 Score=29.49 Aligned_cols=22 Identities=14% Similarity=0.057 Sum_probs=19.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 023151 158 VDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 158 vtQ~kla~~sgvt~vt~rnr~k 179 (286)
+|-++||+.+|||..|+++...
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhc
Confidence 5788999999999999998864
No 399
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=22.94 E-value=7.4e+02 Score=24.49 Aligned_cols=28 Identities=7% Similarity=-0.078 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..++-..+++..+|++.|+.+-.+.+..
T Consensus 99 ~~~~l~~La~~l~vs~~ti~~dl~~v~~ 126 (491)
T COG3711 99 ELLSLHELADELFVSKSTIINDLKDVRL 126 (491)
T ss_pred ChhhHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 6888999999999999999998876543
No 400
>PRK01212 homoserine kinase; Provisional
Probab=22.94 E-value=2.4e+02 Score=26.06 Aligned_cols=56 Identities=16% Similarity=0.059 Sum_probs=38.7
Q ss_pred hhHHHHHHHHHHHhhhhcC--------CCCC--Cc-chHHHHHHHHHHHHhhCCCCCCHHHHHHHhC
Q 023151 16 KQLIRKAAEIRRLCDVQFD--------SSII--GV-GEVCKAVICLELAASRFDVIFDRKTAIKLSG 71 (286)
Q Consensus 16 ~~V~ekAael~Rla~~k~~--------~l~~--Gr-s~~~~aaacLylAcr~~~iprd~~e~~k~sg 71 (286)
++++-+|.+.++......+ ++.. |. |-.+.++|.+.++.+.+|.+++.+++++++.
T Consensus 62 ~Nli~~a~~~~~~~~~~~~~~~I~i~k~IP~~~GLGssSa~aaA~l~al~~l~~~~l~~~eL~~~a~ 128 (301)
T PRK01212 62 KNLVYQAALKFLEKLGKPPGLRIELEKNIPLGRGLGSSAASIVAGLVAANELAGLPLSKEELLQLAT 128 (301)
T ss_pred cccHHHHHHHHHHHcCCCCCeEEEEEeCCCCCCCCcHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 4788888888766432101 1222 33 4567888888899999999999999988754
No 401
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=22.92 E-value=89 Score=28.79 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=24.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.++=.+||+..|||+.|||+-...|++
T Consensus 19 ~v~v~eLa~~l~VS~~TIRRDL~~Le~ 45 (256)
T PRK10434 19 KTSVEELAQYFDTTGTTIRKDLVILEH 45 (256)
T ss_pred CEEHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 367789999999999999999999976
No 402
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=22.87 E-value=2.4e+02 Score=21.31 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=27.4
Q ss_pred HHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccCC
Q 023151 161 LKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKKD 197 (286)
Q Consensus 161 ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~~ 197 (286)
.+|++..++++.++.+..+.|+. .|.-....+
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~-----~glv~r~~~ 71 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED-----KGLIERLRD 71 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH-----CCCeeecCC
Confidence 89999999999999999999977 566665543
No 403
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=22.86 E-value=93 Score=22.85 Aligned_cols=19 Identities=21% Similarity=0.226 Sum_probs=16.6
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 023151 159 DKLKLIEVCGTSETEFASV 177 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr 177 (286)
++.+||.++|||+.+|...
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 6889999999999999887
No 404
>PRK03188 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=22.85 E-value=1.7e+02 Score=27.20 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=26.3
Q ss_pred ChhHHHHHHHHHHHHhCCCCCCHHHHHHHh
Q 023151 138 SRPVFTAVAFYLCAKKHKLKVDKLKLIEVC 167 (286)
Q Consensus 138 ~pp~~AAAAlY~A~~~~k~kvtQ~kla~~s 167 (286)
+-+..++|+++.+..+.+.+.+..+|++.+
T Consensus 100 SSSA~a~A~l~al~~~~g~~ls~~el~~~a 129 (300)
T PRK03188 100 GGSADAAAALVACDALWGLGLSRDELLELA 129 (300)
T ss_pred HHHHHHHHHHHHHHHHhCCCcCHHHHHHHH
Confidence 467789999999999999999999988766
No 405
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=22.78 E-value=1.5e+02 Score=24.73 Aligned_cols=27 Identities=11% Similarity=-0.045 Sum_probs=23.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
..+..+||+..|+++.|++++..--..
T Consensus 134 g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 134 GWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 578899999999999999999766544
No 406
>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=22.78 E-value=2.8e+02 Score=22.42 Aligned_cols=14 Identities=14% Similarity=0.104 Sum_probs=8.4
Q ss_pred CcHHHHHHHhCCcc
Q 023151 94 LDIRELGIRFGCIR 107 (286)
Q Consensus 94 ~~I~~ia~qlg~s~ 107 (286)
+++.+||..+|++.
T Consensus 26 ~s~~eia~~l~is~ 39 (130)
T TIGR02944 26 YSAAEIAEQTGLNA 39 (130)
T ss_pred ccHHHHHHHHCcCH
Confidence 45666666666665
No 407
>PRK01212 homoserine kinase; Provisional
Probab=22.74 E-value=1.9e+02 Score=26.81 Aligned_cols=41 Identities=15% Similarity=0.151 Sum_probs=31.0
Q ss_pred ChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 023151 138 SRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVS 178 (286)
Q Consensus 138 ~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ 178 (286)
+-+..+||++..+..+.+.+.+..+|++.+.--+...++..
T Consensus 98 ssSa~aaA~l~al~~l~~~~l~~~eL~~~a~~~e~~~ddv~ 138 (301)
T PRK01212 98 SSAASIVAGLVAANELAGLPLSKEELLQLATEGEGHPDNVA 138 (301)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCHHHHH
Confidence 46678999999999999999999999887754443333333
No 408
>PRK03188 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=22.69 E-value=2.8e+02 Score=25.75 Aligned_cols=55 Identities=18% Similarity=0.175 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHHhhhhcCC----------CCCCc-chHHHHHHHHHHHHhhCCCCCCHHHHHHHh
Q 023151 16 KQLIRKAAEIRRLCDVQFDS----------SIIGV-GEVCKAVICLELAASRFDVIFDRKTAIKLS 70 (286)
Q Consensus 16 ~~V~ekAael~Rla~~k~~~----------l~~Gr-s~~~~aaacLylAcr~~~iprd~~e~~k~s 70 (286)
++++-++.+.++......++ ..+|. |-.+.++|.+.++++.+|.+++.+++.+++
T Consensus 64 ~nl~~~~~~~~~~~~~~~~~~~I~i~s~IP~~~GLGSSSA~a~A~l~al~~~~g~~ls~~el~~~a 129 (300)
T PRK03188 64 SNLAWRAAELLAEHVGRAPDVHLHIDKGIPVAGGMAGGSADAAAALVACDALWGLGLSRDELLELA 129 (300)
T ss_pred ccHHHHHHHHHHHHhCCCCCeEEEEEcCCcccCcchHHHHHHHHHHHHHHHHhCCCcCHHHHHHHH
Confidence 46777777666443321111 22343 567788899999999999999999998765
No 409
>PF13961 DUF4219: Domain of unknown function (DUF4219)
Probab=22.68 E-value=49 Score=20.34 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=9.4
Q ss_pred hHHHHHHHHHh
Q 023151 242 VAYEEWKTSVL 252 (286)
Q Consensus 242 ~~Ye~WK~~il 252 (286)
..|..||.+|=
T Consensus 4 ~NY~~W~~~M~ 14 (27)
T PF13961_consen 4 TNYSTWKIRMK 14 (27)
T ss_pred cCHHHHHHHHH
Confidence 58999999984
No 410
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=22.67 E-value=1.2e+02 Score=24.62 Aligned_cols=29 Identities=24% Similarity=0.440 Sum_probs=16.4
Q ss_pred CcHHHHHHHhCCcc-----hHHHHHHHHHHHHHh
Q 023151 94 LDIRELGIRFGCIR-----LIPLVQKGLSLFKDR 122 (286)
Q Consensus 94 ~~I~~ia~qlg~s~-----v~~~A~eiL~~~ke~ 122 (286)
.++.+||..+|+|. ..++|.+.|..|.++
T Consensus 34 lSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k 67 (101)
T PF04297_consen 34 LSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK 67 (101)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 36777777777765 345566666655544
No 411
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=22.66 E-value=78 Score=20.21 Aligned_cols=22 Identities=50% Similarity=0.706 Sum_probs=15.8
Q ss_pred cHHHHHHHhCCCCChhHHHHHHH
Q 023151 2 DLSDIAKKLGLSDSKQLIRKAAE 24 (286)
Q Consensus 2 ei~ria~kLgL~e~~~V~ekAae 24 (286)
.|+++|.+.|++-+ .+++.|-.
T Consensus 13 ~l~~~a~~~g~s~s-~~ir~ai~ 34 (39)
T PF01402_consen 13 RLDELAKELGRSRS-ELIREAIR 34 (39)
T ss_dssp HHHHHHHHHTSSHH-HHHHHHHH
T ss_pred HHHHHHHHHCcCHH-HHHHHHHH
Confidence 36788999998876 66665544
No 412
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=22.50 E-value=1.3e+02 Score=26.78 Aligned_cols=36 Identities=17% Similarity=0.156 Sum_probs=30.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +-.+|++..|||..|+|.-...|+. .|+-...
T Consensus 28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~-----eGlv~~~ 64 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLREVLQRLAR-----DGWLTIQ 64 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 5678 6999999999999999999999987 6666554
No 413
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=22.49 E-value=3.2e+02 Score=25.10 Aligned_cols=56 Identities=16% Similarity=0.291 Sum_probs=41.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC------CC-cHHHHHHHhCCcchHHHHHHHHHHHHH
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKN------EL-DIRELGIRFGCIRLIPLVQKGLSLFKD 121 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~------~~-~I~~ia~qlg~s~v~~~A~eiL~~~ke 121 (286)
.++..+++..|++...+.+..+.|+..||.+- .+ .+...+..| .+.|.++|+.+.+
T Consensus 17 ~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~~~~lT~~G~~l-----~~~a~~il~~~~~ 79 (309)
T PRK12683 17 FNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKEL-----LQIVERMLLDAEN 79 (309)
T ss_pred CCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEeeCCCCcCCcCHHHHHH-----HHHHHHHHHHHHH
Confidence 36777899999999999999999999999743 22 234444443 6777777776554
No 414
>PRK14999 histidine utilization repressor; Provisional
Probab=22.31 E-value=1.3e+02 Score=26.97 Aligned_cols=36 Identities=14% Similarity=0.165 Sum_probs=29.5
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +-.+|++.-|||..|+|+-...+.+ .|+-...
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~-----eGli~r~ 69 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRELTD-----EGWLVRL 69 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 3455 7899999999999999999999987 6655444
No 415
>PRK01905 DNA-binding protein Fis; Provisional
Probab=22.25 E-value=3.4e+02 Score=20.33 Aligned_cols=34 Identities=9% Similarity=-0.028 Sum_probs=25.0
Q ss_pred HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 148 YLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 148 Y~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
|+...+..-.-++.+.|...|+++.|++.+.+.+
T Consensus 41 ~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 41 LLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 3333444444678899999999999999887764
No 416
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=22.23 E-value=1.4e+02 Score=25.74 Aligned_cols=83 Identities=12% Similarity=0.019 Sum_probs=51.5
Q ss_pred HHHHHHHHHhhhhcCCCCCCcchHHHHHHHHHHHHhh-------------CC--CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 20 RKAAEIRRLCDVQFDSSIIGVGEVCKAVICLELAASR-------------FD--VIFDRKTAIKLSGMSEKAYNRSFNSL 84 (286)
Q Consensus 20 ekAael~Rla~~k~~~l~~Grs~~~~aaacLylAcr~-------------~~--iprd~~e~~k~sg~~~k~y~~~yr~l 84 (286)
++|..+...|... ||+...+. ..++..+.+.-. .. .-+-++.|+.-.|++++++....+.+
T Consensus 37 dqAk~li~~A~~e--GLl~~~~~--~l~~~Fd~~~v~iP~~FkP~~~~l~e~~~fe~ild~ia~~~g~~~~evv~~in~~ 112 (144)
T PF09999_consen 37 DQAKRLIDEAIEE--GLLEEEGG--YLVPNFDPSEVEIPLGFKPDEEILQERDPFERILDYIAAKTGIEKQEVVAEINEL 112 (144)
T ss_pred HHHHHHHHHHHHC--CCeeecCC--EEEEecCccccccCCCCCCcHHHHhcccHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 7899999999998 88765322 222222222211 11 12234677888999999999999999
Q ss_pred HHHhC--CCCCCcHHHHHHHhCCc
Q 023151 85 QNSIG--FKNELDIRELGIRFGCI 106 (286)
Q Consensus 85 ~~~Lg--L~~~~~I~~ia~qlg~s 106 (286)
+..|| |...+-.-=+|-..||+
T Consensus 113 q~~~~~~l~~e~aall~ake~Gvd 136 (144)
T PF09999_consen 113 QEELGGLLDPEAAALLYAKEKGVD 136 (144)
T ss_pred HHHHhccCCHHHHHHHHHHHhCCC
Confidence 99999 54433222255555554
No 417
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=22.23 E-value=3.4e+02 Score=25.43 Aligned_cols=29 Identities=10% Similarity=0.098 Sum_probs=24.7
Q ss_pred hhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 55 SRFDVIFDRKTAIKLSGMSEKAYNRSFNS 83 (286)
Q Consensus 55 r~~~iprd~~e~~k~sg~~~k~y~~~yr~ 83 (286)
....-|+++++++...|+++..+.+.++.
T Consensus 145 ~~~~~~~tl~~LA~~~gmS~s~l~R~FK~ 173 (253)
T PRK09940 145 MKLAHPWKLKDICDCLYISESLLKKKLKQ 173 (253)
T ss_pred HhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34467899999999999999999888765
No 418
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=22.22 E-value=73 Score=21.90 Aligned_cols=17 Identities=24% Similarity=0.339 Sum_probs=14.1
Q ss_pred hHHHHHHHHHhhhhhhc
Q 023151 242 VAYEEWKTSVLASNRNK 258 (286)
Q Consensus 242 ~~Ye~WK~~il~~~~~~ 258 (286)
.|+|.||+-||+.-...
T Consensus 3 ~dle~~KqEIL~EvrkE 19 (40)
T PF08776_consen 3 SDLERLKQEILEEVRKE 19 (40)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 58999999999886643
No 419
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.22 E-value=1.5e+02 Score=24.13 Aligned_cols=32 Identities=13% Similarity=0.084 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
...+.++||+..|+|+.|++++..--...+..
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999998776554433
No 420
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.15 E-value=2.2e+02 Score=25.50 Aligned_cols=42 Identities=14% Similarity=0.213 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHh--CCCCC---CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 77 YNRSFNSLQNSI--GFKNE---LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 77 y~~~yr~l~~~L--gL~~~---~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
|.+-++.|...+ .+.++ |+=.+||.+||+|. ++++|...|..
T Consensus 14 Y~qi~~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~ 61 (241)
T PRK10079 14 YQEIAAKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVE 61 (241)
T ss_pred HHHHHHHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHH
No 421
>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=22.12 E-value=1.1e+02 Score=25.76 Aligned_cols=26 Identities=12% Similarity=0.043 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMK 182 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~ 182 (286)
..+..+||+..|+++.|++++..--.
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 150 GLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 47889999999999999999986543
No 422
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=22.11 E-value=1.6e+02 Score=20.43 Aligned_cols=33 Identities=12% Similarity=0.102 Sum_probs=22.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 023151 57 FDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIG 89 (286)
Q Consensus 57 ~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~Lg 89 (286)
+..-++.+.++...|++++.+.+.++.+...|.
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~ 48 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLY 48 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHHHHHHHHHHH
Confidence 344466677777777777777777777766654
No 423
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=22.11 E-value=3.1e+02 Score=25.56 Aligned_cols=52 Identities=17% Similarity=0.144 Sum_probs=40.1
Q ss_pred CCCCCCcchHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 34 DSSIIGVGEVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 34 ~~l~~Grs~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
..|..|.+...+-.++--+. ..+.++|-+|+++..|+++....+-+..++..
T Consensus 149 ~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~~~giSRvTaRRYLeyl~~~ 200 (224)
T COG4565 149 DDLPKGLDELTLQKVREALK--EPDQELTAEELAQALGISRVTARRYLEYLVSN 200 (224)
T ss_pred ccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHHHhCccHHHHHHHHHHHHhc
Confidence 35777877777666666555 56789999999999999998888888877653
No 424
>PRK03837 transcriptional regulator NanR; Provisional
Probab=22.09 E-value=1.4e+02 Score=26.53 Aligned_cols=36 Identities=11% Similarity=0.199 Sum_probs=31.5
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +..+|++..|||..++|.-...++. .|+-...
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~-----eGlv~~~ 70 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKR-----KGLVQIS 70 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 6678 8999999999999999999999987 7776664
No 425
>PF00288 GHMP_kinases_N: GHMP kinases N terminal domain; InterPro: IPR006204 The galacto- (2.7.1.6 from EC), homoserine (2.7.1.39 from EC), mevalonate (2.7.1.36 from EC) and phosphomevalonate (2.7.4.2 from EC) kinases contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP [, ]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).; GO: 0005524 ATP binding, 0016301 kinase activity, 0016310 phosphorylation; PDB: 3F0N_B 1PIE_A 2AJ4_A 1K47_E 3GON_A 2R3V_C 3HUL_A 1KVK_A 2R42_A 3D4J_A ....
Probab=22.07 E-value=1.5e+02 Score=21.22 Aligned_cols=31 Identities=16% Similarity=0.103 Sum_probs=25.1
Q ss_pred ChhHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Q 023151 138 SRPVFTAVAFYLCAKKHKLKVDKLKLIEVCG 168 (286)
Q Consensus 138 ~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sg 168 (286)
+-..+++|.++......+.++++.++++.+-
T Consensus 16 SSaa~~~a~~~a~~~~~~~~~~~~~l~~~a~ 46 (67)
T PF00288_consen 16 SSAALAVALAAALNKLFGLPLSKEELAKLAQ 46 (67)
T ss_dssp HHHHHHHHHHHHHHHHTTTSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHccccccHHHHHHHHH
Confidence 4567899999999999999998888765543
No 426
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=22.01 E-value=2.1e+02 Score=23.63 Aligned_cols=27 Identities=4% Similarity=0.068 Sum_probs=24.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.++..+||+..||++.|++...+.|.+
T Consensus 22 ~~~~~ela~~l~vs~~svs~~l~~L~~ 48 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMVQKLDK 48 (142)
T ss_pred CcCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 346789999999999999999999977
No 427
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=22.00 E-value=2.3e+02 Score=24.84 Aligned_cols=25 Identities=32% Similarity=0.368 Sum_probs=22.3
Q ss_pred CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 94 LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 94 ~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
|+-++||.+||+|. +.+.|...|..
T Consensus 26 PsE~eLa~~~~Vsr~Tvr~Al~~L~~ 51 (231)
T TIGR03337 26 PSERDLGERFNTTRVTIREALQQLEA 51 (231)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58999999999999 89999888874
No 428
>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=21.95 E-value=1.6e+02 Score=20.74 Aligned_cols=30 Identities=13% Similarity=0.129 Sum_probs=26.4
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.+...|-.+|++..|+++.|+....+.|++
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 566788899999999999999999999987
No 429
>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=21.94 E-value=1.8e+02 Score=25.78 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=22.3
Q ss_pred CHHHHHHHh-CCCHHHHHHHHHHHHH
Q 023151 159 DKLKLIEVC-GTSETEFASVSTTMKD 183 (286)
Q Consensus 159 tQ~kla~~s-gvt~vt~rnr~ke~~~ 183 (286)
+-..|++-. |+++.|+++....+.+
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~Lve 97 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVE 97 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 445899999 9999999999999976
No 430
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=21.81 E-value=1.7e+02 Score=22.94 Aligned_cols=37 Identities=19% Similarity=0.255 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 023151 140 PVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 140 p~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke 180 (286)
|.+-.++|=..+...|+ || ||+.+||++.|+.+....
T Consensus 30 ~~~~~~~l~~~r~~~gl--Sq--LAe~~GIs~stLs~iE~g 66 (89)
T TIGR02684 30 PAYIAHALGYIARARGM--TQ--LARKTGLSRESLYKALSG 66 (89)
T ss_pred HHHHHHHHHHHHHHCCh--HH--HHHHHCCCHHHHHHHHcC
Confidence 55555667677777764 44 999999999999887644
No 431
>PRK00650 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=21.73 E-value=3.1e+02 Score=26.14 Aligned_cols=58 Identities=17% Similarity=0.097 Sum_probs=39.5
Q ss_pred CCCChhHHHHHHHHHHHhhhhcCC----------CCCCc-chHHHHHHHHHHHHhhCCCCCCHHHHHHH
Q 023151 12 LSDSKQLIRKAAEIRRLCDVQFDS----------SIIGV-GEVCKAVICLELAASRFDVIFDRKTAIKL 69 (286)
Q Consensus 12 L~e~~~V~ekAael~Rla~~k~~~----------l~~Gr-s~~~~aaacLylAcr~~~iprd~~e~~k~ 69 (286)
++..++++-+|..+++......++ ..+|. |-.+-+|+.|.++.+..+.+++.+++.++
T Consensus 57 ~~~~~Nlv~ra~~~l~~~~g~~~~v~I~i~K~IP~gaGLGggSS~aAa~L~~ln~l~~~~ls~~eL~~l 125 (288)
T PRK00650 57 LETPSNSIWKSVALFRRYTGITTPVSWRVVKQIPIGAGLAGGSSNAATALFALNQIFQTGLSDEELRSL 125 (288)
T ss_pred CCccccHHHHHHHHHHHHhCCCCCeEEEEeeCCCCcCCcCcchhHHHHHHHHHHHHhCCCcCHHHHHHH
Confidence 443358888888888865432111 22233 46677888888888999999998888654
No 432
>PRK11050 manganese transport regulator MntR; Provisional
Probab=21.69 E-value=1.7e+02 Score=24.78 Aligned_cols=30 Identities=10% Similarity=0.138 Sum_probs=27.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 154 HKLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 154 ~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
.+...+..+||+..++++.++....+.|++
T Consensus 48 ~~~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 48 EVGEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356789999999999999999999999987
No 433
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=21.58 E-value=1.4e+02 Score=26.35 Aligned_cols=36 Identities=6% Similarity=-0.086 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.+++..+|++..|||..++|.-...++. .|+-...
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~-----eGlv~~~ 63 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVA-----ERLVTVV 63 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHH-----CCCEEEe
Confidence 67789999999999999999999999987 7766654
No 434
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.52 E-value=1.6e+02 Score=24.09 Aligned_cols=32 Identities=13% Similarity=0.132 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLCHD 187 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d 187 (286)
...+..+||+..|+|+.|++++..--...+..
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35888999999999999999998776554433
No 435
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=21.49 E-value=1.4e+02 Score=26.95 Aligned_cols=36 Identities=11% Similarity=0.011 Sum_probs=30.9
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +..+|++..|||..++|.-.+.|+. .|+-...
T Consensus 29 G~~LpsE~eLae~~gVSRtpVREAL~~L~~-----eGlV~~~ 65 (253)
T PRK11523 29 GDKLPAERFIADEKNVSRTVVREAIIMLEV-----EGYVEVR 65 (253)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 5678 4899999999999999999999987 7766554
No 436
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.41 E-value=1.2e+02 Score=22.21 Aligned_cols=34 Identities=6% Similarity=0.049 Sum_probs=25.5
Q ss_pred hhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 023151 55 SRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSI 88 (286)
Q Consensus 55 r~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~L 88 (286)
..+|.+-|.++|++..|++.+.|...+....+-.
T Consensus 15 ~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~ 48 (78)
T PF04539_consen 15 QELGREPTDEEIAEELGISVEEVRELLQASRRPV 48 (78)
T ss_dssp HHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCE
T ss_pred HHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCe
Confidence 3467888999999999999999999888765433
No 437
>PRK09726 antitoxin HipB; Provisional
Probab=21.18 E-value=2.2e+02 Score=21.71 Aligned_cols=42 Identities=12% Similarity=0.070 Sum_probs=30.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCC-C-cHHHHHHHhCCcc
Q 023151 60 IFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNE-L-DIRELGIRFGCIR 107 (286)
Q Consensus 60 prd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~-~-~I~~ia~qlg~s~ 107 (286)
..+..++++..|++...|.+- ++ |-..+ + .+.+||..||++-
T Consensus 25 gltq~elA~~~gvs~~tis~~----e~--g~~~ps~~~l~~ia~~lgv~~ 68 (88)
T PRK09726 25 GWTQSELAKKIGIKQATISNF----EN--NPDNTTLTTFFKILQSLELSM 68 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHH----HC--CCCCCCHHHHHHHHHHcCCCc
Confidence 468899999999998777543 33 33222 2 5889999999986
No 438
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=21.17 E-value=2.2e+02 Score=21.50 Aligned_cols=33 Identities=9% Similarity=0.024 Sum_probs=23.8
Q ss_pred HhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 54 ASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQN 86 (286)
Q Consensus 54 cr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~ 86 (286)
.+.++.|++..++++..|++...+.+-.+.+..
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQ 39 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 466777888888888888887777766665544
No 439
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=21.10 E-value=9.6e+02 Score=25.04 Aligned_cols=113 Identities=13% Similarity=0.198 Sum_probs=66.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcHHHHHHHhC------Ccc-hHHHHHHHHH--HHHHhhhhcccccc
Q 023151 61 FDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELDIRELGIRFG------CIR-LIPLVQKGLS--LFKDRFTAALPASR 131 (286)
Q Consensus 61 rd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~I~~ia~qlg------~s~-v~~~A~eiL~--~~ke~~~~~L~~gk 131 (286)
.+-.++...+.-....-...++.+.+.||. .+..++..|+ +-+ |.+...+++. .+.++|.. .|+
T Consensus 229 ~~~~~i~~~a~~gd~~A~~~~~~~~~~lg~----~~~nl~~~~~~p~~vvigGGIs~~~~~~l~~~~f~~~f~~---kg~ 301 (638)
T PRK14101 229 VDTAEIVERAHAGDALALEAVECFCAILGT----FAGNLALTLGALGGIYIGGGVVPKLGELFTRSSFRARFEA---KGR 301 (638)
T ss_pred CCHHHHHHHHHCCCHHHHHHHHHHHHHHHH----HHHHHHHHhCCCCcEEEeCcHHHHHHHHcChHHHHHHHHh---CCC
Confidence 567788877766666666777777777774 5666666665 222 4333333332 34445442 122
Q ss_pred cc----------CCCCChhHHHHHHHHHHHHhCCC--------------------------------------CCCHHHH
Q 023151 132 KT----------SADFSRPVFTAVAFYLCAKKHKL--------------------------------------KVDKLKL 163 (286)
Q Consensus 132 ~~----------~~D~~pp~~AAAAlY~A~~~~k~--------------------------------------kvtQ~kl 163 (286)
-. -.| ..|++-.||-|..=.++.- ..|=.+|
T Consensus 302 ~~~~~~~ipv~~i~~-~~~~l~Gaa~~~~~~~~~~~~~~~~~l~~~I~~~~~~Lt~~E~~IA~yIl~n~~~v~~~si~eL 380 (638)
T PRK14101 302 FEAYLANIPTYLITA-EYPAFLGVSAILAEQLSNRTGGASSAVFERIRQMRDALTPAERRVADLALNHPRSIINDPIVDI 380 (638)
T ss_pred hHHHHhcCCEEEEeC-CChhHHHHHHHHHHHhccccCCchHHHHHHHHHHHhhcCHHHHHHHHHHHhCHHHHHhccHHHH
Confidence 10 122 2355444433333333221 4466789
Q ss_pred HHHhCCCHHHHHHHHHHH
Q 023151 164 IEVCGTSETEFASVSTTM 181 (286)
Q Consensus 164 a~~sgvt~vt~rnr~ke~ 181 (286)
|+.++||+.||-+.|+.|
T Consensus 381 A~~~~vS~aTV~Rf~kkL 398 (638)
T PRK14101 381 ARKADVSQPTVIRFCRSL 398 (638)
T ss_pred HHHhCCCHHHHHHHHHHh
Confidence 999999999999999986
No 440
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=21.08 E-value=1.2e+02 Score=27.61 Aligned_cols=25 Identities=12% Similarity=0.298 Sum_probs=22.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
..|=.+||+.+|||+.||-+.|+.|
T Consensus 30 ~~si~elA~~~~vS~aTv~Rf~kkl 54 (278)
T PRK11557 30 HLSSQQLANEAGVSQSSVVKFAQKL 54 (278)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 3567899999999999999999876
No 441
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=20.96 E-value=1.2e+02 Score=25.19 Aligned_cols=34 Identities=12% Similarity=0.106 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 023151 144 AVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVST 179 (286)
Q Consensus 144 AAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~k 179 (286)
+.++--.+... .+++.+++...|+++.|+.++-+
T Consensus 25 ~~~~~~l~~~l--~ls~~el~~~lgis~~Tl~R~~~ 58 (133)
T TIGR02293 25 IGALDRLAHLL--AIGKAEIFKATGIPKATLQRRKM 58 (133)
T ss_pred HHHHHHHHHHH--CCCHHHHHHHHCCCHHHHHHHhh
Confidence 34443444443 36889999999999999987764
No 442
>PRK14999 histidine utilization repressor; Provisional
Probab=20.92 E-value=2.5e+02 Score=25.14 Aligned_cols=56 Identities=16% Similarity=0.049 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHh---CCCCC---CcHHHHHHHhCCcc-hHHHHHHHHHHHHHhhhhccccccccC
Q 023151 76 AYNRSFNSLQNSI---GFKNE---LDIRELGIRFGCIR-LIPLVQKGLSLFKDRFTAALPASRKTS 134 (286)
Q Consensus 76 ~y~~~yr~l~~~L---gL~~~---~~I~~ia~qlg~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~ 134 (286)
.|..-+..|...+ .++++ |+-++||.+||+|. ++++|...|.. .++.---.|++..
T Consensus 13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~---eGli~r~~GkGTf 75 (241)
T PRK14999 13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTD---EGWLVRLQGVGTF 75 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEecCcEEE
Confidence 4666666665544 23332 58999999999999 99999888874 4443334566543
No 443
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=20.89 E-value=88 Score=28.55 Aligned_cols=22 Identities=18% Similarity=0.151 Sum_probs=18.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 023151 159 DKLKLIEVCGTSETEFASVSTT 180 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr~ke 180 (286)
|-++||+.+|||..|+.+....
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6689999999999999987753
No 444
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=20.84 E-value=4.6e+02 Score=29.17 Aligned_cols=74 Identities=16% Similarity=0.170 Sum_probs=51.2
Q ss_pred hHHHHHHHHHHHHhhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCc----HHHHHHHhCCcc-hHHHHHHHH
Q 023151 42 EVCKAVICLELAASRFDVIFDRKTAIKLSGMSEKAYNRSFNSLQNSIGFKNELD----IRELGIRFGCIR-LIPLVQKGL 116 (286)
Q Consensus 42 ~~~~aaacLylAcr~~~iprd~~e~~k~sg~~~k~y~~~yr~l~~~LgL~~~~~----I~~ia~qlg~s~-v~~~A~eiL 116 (286)
+.-..+.-+.+|+=.--+|.+..++..+.-+..-.+.+.. .|.++|||+.+|+ |.+++. +|+.+ +-..+.+|.
T Consensus 316 e~q~~as~VlLaaLSIP~~~~~~~~~r~~e~e~~~~ek~~-rla~LL~L~~~PTR~~ll~e~v~-~gV~~~v~qe~kdLY 393 (988)
T KOG2072|consen 316 ELQRMASRVLLAALSIPIPDARSDSARLIEIEDIGKEKNL-RLANLLGLPAPPTRKGLLKEAVR-EGVLSKVDQEVKDLY 393 (988)
T ss_pred HHHHHHHHHHHHHhcCCCCCcccccccccccccchhhHHH-HHHHHhCCCCCccHHHHHHHHHH-hccHhhhhHHHHHHH
Confidence 4455667777777666777888888888888777677665 4789999999884 555444 77766 555554444
Q ss_pred H
Q 023151 117 S 117 (286)
Q Consensus 117 ~ 117 (286)
+
T Consensus 394 ~ 394 (988)
T KOG2072|consen 394 N 394 (988)
T ss_pred H
Confidence 3
No 445
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=20.74 E-value=4.9e+02 Score=21.49 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 023151 155 KLKVDKLKLIEVCGTSETEFASVSTTMKD 183 (286)
Q Consensus 155 k~kvtQ~kla~~sgvt~vt~rnr~ke~~~ 183 (286)
...+++..+|..+|++..|+.+...++.+
T Consensus 169 ~~~~~~~~ia~~~g~~~~~vsr~l~~l~~ 197 (214)
T COG0664 169 PLPLTHKDLAEYLGLSRETVSRILKELRK 197 (214)
T ss_pred eccCCHHHHHHHhCCchhhHHHHHHHHHh
Confidence 36899999999999999999999999976
No 446
>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=20.71 E-value=4.3e+02 Score=25.90 Aligned_cols=65 Identities=14% Similarity=0.277 Sum_probs=48.3
Q ss_pred cHHHHHHHh--CCcc-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Q 023151 95 DIRELGIRF--GCIR-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCG 168 (286)
Q Consensus 95 ~I~~ia~ql--g~s~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sg 168 (286)
++-++|..| .++. |+..|..- |+.-|+. ..-.|++|-.+.++|||+||++....|+=.+.+.-+.
T Consensus 62 ~l~~f~~k~~p~lp~~Vv~TA~~f---FkRffL~------nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLPTSVVSTAIEF---FKRFFLE------NSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred HHHHHHHHhcCCCchHHHHHHHHH---HHHHHHh------cchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 466777777 4555 77777554 4446664 3445678999999999999999999999888876665
No 447
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=20.59 E-value=2.6e+02 Score=25.40 Aligned_cols=30 Identities=13% Similarity=0.242 Sum_probs=27.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
++..+++..+++...+.+..+.|+..||.+
T Consensus 17 S~s~AA~~L~itQpavS~~i~~LE~~lg~~ 46 (305)
T PRK11151 17 HFRRAADSCHVSQPTLSGQIRKLEDELGVM 46 (305)
T ss_pred CHHHHHHHhCCCchHHHHHHHHHHHHhCch
Confidence 667789999999999999999999999974
No 448
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=20.57 E-value=1.3e+02 Score=27.44 Aligned_cols=25 Identities=12% Similarity=0.182 Sum_probs=22.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
..|=.+||+.+|||+.||-+.|+.|
T Consensus 34 ~~si~~lA~~~~vS~aTv~Rf~kkl 58 (284)
T PRK11302 34 HSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 3577899999999999999999886
No 449
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=1.6e+02 Score=25.29 Aligned_cols=33 Identities=3% Similarity=0.065 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
..+..+||+..|+|+.|++++..-....+-..+
T Consensus 144 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 144 GFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999877655444444
No 450
>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=20.49 E-value=1.5e+02 Score=26.34 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=27.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 159 DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 159 tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
+-.+|++.-|||..|+|+-...|.+ .|+-...
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~-----eGli~r~ 58 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTD-----AGLLERR 58 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH-----CCCEEEe
Confidence 7889999999999999999999987 5654444
No 451
>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=20.49 E-value=1.7e+02 Score=26.26 Aligned_cols=30 Identities=7% Similarity=0.139 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTMKDLC 185 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c 185 (286)
...+..+||+..|+|+.|++++..-....+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~L 226 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRL 226 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 678999999999999999999986654433
No 452
>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=20.48 E-value=2.1e+02 Score=20.44 Aligned_cols=31 Identities=16% Similarity=0.203 Sum_probs=24.8
Q ss_pred CCCCC--CHHHHHHHhCCCHHHHHHHHHHHHHH
Q 023151 57 FDVIF--DRKTAIKLSGMSEKAYNRSFNSLQNS 87 (286)
Q Consensus 57 ~~ipr--d~~e~~k~sg~~~k~y~~~yr~l~~~ 87 (286)
+++|| +++++++..|+++..+..-+|.-++-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 45665 67999999999999998888876654
No 453
>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=20.43 E-value=1.1e+02 Score=27.12 Aligned_cols=25 Identities=24% Similarity=0.187 Sum_probs=0.0
Q ss_pred CcHHHHHHHhCCcc-hHHHHHHHHHH
Q 023151 94 LDIRELGIRFGCIR-LIPLVQKGLSL 118 (286)
Q Consensus 94 ~~I~~ia~qlg~s~-v~~~A~eiL~~ 118 (286)
|+-++||.+||+|. ++++|...|..
T Consensus 33 PsE~eLa~~~~VSR~TvR~Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVRRAIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
No 454
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=20.37 E-value=1.6e+02 Score=28.62 Aligned_cols=43 Identities=19% Similarity=0.216 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccc
Q 023151 142 FTAVAFYLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKE 194 (286)
Q Consensus 142 ~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~ 194 (286)
.-+|-+|. -...||.+||+..|+|..++++..+.-.+ .||-+=
T Consensus 16 ~~~A~lYY-----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~-----~GiV~I 58 (321)
T COG2390 16 ARAAWLYY-----VEGLTQSEIAERLGISRATVSRLLAKARE-----EGIVKI 58 (321)
T ss_pred HHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH-----CCeEEE
Confidence 34455554 35799999999999999999999998876 555543
No 455
>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=20.33 E-value=2e+02 Score=20.89 Aligned_cols=45 Identities=24% Similarity=0.250 Sum_probs=28.5
Q ss_pred HHHhCCCHHHHHHHHHHHHHHhCC--CCCCcHHHHHHHhCCcchHHH
Q 023151 67 IKLSGMSEKAYNRSFNSLQNSIGF--KNELDIRELGIRFGCIRLIPL 111 (286)
Q Consensus 67 ~k~sg~~~k~y~~~yr~l~~~LgL--~~~~~I~~ia~qlg~s~v~~~ 111 (286)
.+..|++..+|.+.+|...-.--| ....+|.+||..+|-+.....
T Consensus 17 ~~~~g~s~~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f 63 (81)
T PF12833_consen 17 KKETGMSFKQYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHF 63 (81)
T ss_dssp HHHHSS-HHHHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHH
T ss_pred HHHHCcCHHHHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHH
Confidence 345888888888877765544433 256789999999998885443
No 456
>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=20.30 E-value=1.9e+02 Score=25.44 Aligned_cols=34 Identities=12% Similarity=0.186 Sum_probs=28.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 157 KVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 157 kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
.++..+|++..|+++.|+++..+.|++ .|+-...
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le~-----~GlI~r~ 190 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELEK-----KGLVEQK 190 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCEEEE
Confidence 589999999999999999999999987 4554443
No 457
>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=20.24 E-value=4.7e+02 Score=21.10 Aligned_cols=41 Identities=20% Similarity=0.209 Sum_probs=31.4
Q ss_pred HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhcccccC
Q 023151 148 YLCAKKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEKK 196 (286)
Q Consensus 148 Y~A~~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~~ 196 (286)
..+-....-..|..++|+-.||+..||-...+.| |+...++
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl--------g~t~KK~ 102 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRL--------GITRKKK 102 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc--------CchhccC
Confidence 3455556777899999999999999998887776 5665553
No 458
>TIGR00191 thrB homoserine kinase. P.aeruginosa homoserine kinase seems not to be homologous (see PROSITE:PDOC0054)
Probab=20.23 E-value=2.5e+02 Score=26.28 Aligned_cols=63 Identities=13% Similarity=0.211 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhCCC-CCCcHHHHHHHhCCcchHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCC
Q 023151 77 YNRSFNSLQNSIGFK-NELDIRELGIRFGCIRLIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHK 155 (286)
Q Consensus 77 y~~~yr~l~~~LgL~-~~~~I~~ia~qlg~s~v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k 155 (286)
+.++++.+.+.+|.+ .++.| .....+|.|++- ++-+..++|+++.+..+.+
T Consensus 63 v~~a~~~~~~~~g~~~~g~~i-------------------------~i~~~IP~~~GL---GSSsa~~vA~l~a~~~l~~ 114 (302)
T TIGR00191 63 IYQVAKRFLDQLGIRMPPVKV-------------------------TLEKNIPLGRGL---GSSAAAIVAALAAANELCG 114 (302)
T ss_pred HHHHHHHHHHHcCCCCCCEEE-------------------------EEEcCCCCcCCC---ChHHHHHHHHHHHHHHHcC
Q ss_pred CCCCHHHHHHHh
Q 023151 156 LKVDKLKLIEVC 167 (286)
Q Consensus 156 ~kvtQ~kla~~s 167 (286)
.+.+..+|+..+
T Consensus 115 ~~l~~~el~~~a 126 (302)
T TIGR00191 115 LPLSKERLLDYA 126 (302)
T ss_pred CCcCHHHHHHHH
No 459
>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=20.23 E-value=1.5e+02 Score=26.28 Aligned_cols=36 Identities=17% Similarity=0.156 Sum_probs=31.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhhhhhhhccccc
Q 023151 155 KLKV-DKLKLIEVCGTSETEFASVSTTMKDLCHDVFGIAKEK 195 (286)
Q Consensus 155 k~kv-tQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~~i~~~~ 195 (286)
|.++ +..+|++..|||..++|.-...|+. .|+-...
T Consensus 27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~-----eGlV~~~ 63 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLREVLQRLAR-----DGWLTIQ 63 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHHHHHHHHHH-----CCCEEEe
Confidence 6678 7999999999999999999999977 6766654
No 460
>PRK09956 hypothetical protein; Provisional
Probab=20.16 E-value=6.9e+02 Score=23.81 Aligned_cols=76 Identities=12% Similarity=0.064 Sum_probs=48.2
Q ss_pred HHHHHHHhCCc-c-hHHHHHHHHHHHHHhhhhccccccccCCCCChhHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHH
Q 023151 96 IRELGIRFGCI-R-LIPLVQKGLSLFKDRFTAALPASRKTSADFSRPVFTAVAFYLCAKKHKLKVDKLKLIEVCGTSETE 173 (286)
Q Consensus 96 I~~ia~qlg~s-~-v~~~A~eiL~~~ke~~~~~L~~gk~~~~D~~pp~~AAAAlY~A~~~~k~kvtQ~kla~~sgvt~vt 173 (286)
+..|+..+.=- + +...|+++-+...+.++ ..|+... ---|..-+++-+|-+++...++...|+++.|+|+.+
T Consensus 229 i~~l~~~~~~~~e~iMTiAe~l~qeG~e~G~---q~G~~eG---~qeG~~e~~~eiA~~mL~~G~~~~~i~~~tgLs~ee 302 (308)
T PRK09956 229 IQEIAERSPLQKERLMTIAERLRQEGHQIGW---QEGKLEG---LQEGMHEQAIKIALRMLEQGFDRDQVLAATQLSEAD 302 (308)
T ss_pred HHHHHHhCcccchHHHHHHHHHHHHHHHHHH---HHHHHHH---HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHH
Confidence 55555553211 2 56666666665544322 2332100 012344567889999999999999999999999999
Q ss_pred HHHH
Q 023151 174 FASV 177 (286)
Q Consensus 174 ~rnr 177 (286)
+.++
T Consensus 303 l~~~ 306 (308)
T PRK09956 303 LAAN 306 (308)
T ss_pred HHHh
Confidence 8764
No 461
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=20.08 E-value=2.4e+02 Score=21.35 Aligned_cols=38 Identities=5% Similarity=0.004 Sum_probs=32.1
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhhhhh
Q 023151 152 KKHKLKVDKLKLIEVCGTSETEFASVSTTMKDLCHDVF 189 (286)
Q Consensus 152 ~~~k~kvtQ~kla~~sgvt~vt~rnr~ke~~~~c~d~~ 189 (286)
++++..++=.+.|+..|+++.++++....|...|-..-
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LD 45 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLD 45 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcC
Confidence 46777788889999999999999999999988665543
No 462
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=20.06 E-value=3.5e+02 Score=23.57 Aligned_cols=26 Identities=23% Similarity=0.175 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 023151 156 LKVDKLKLIEVCGTSETEFASVSTTM 181 (286)
Q Consensus 156 ~kvtQ~kla~~sgvt~vt~rnr~ke~ 181 (286)
...+..+||...||+..||.+..++.
T Consensus 171 ~g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 171 KGTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 34799999999999999999988753
No 463
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=20.05 E-value=3.1e+02 Score=24.84 Aligned_cols=30 Identities=20% Similarity=0.345 Sum_probs=27.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Q 023151 62 DRKTAIKLSGMSEKAYNRSFNSLQNSIGFK 91 (286)
Q Consensus 62 d~~e~~k~sg~~~k~y~~~yr~l~~~LgL~ 91 (286)
++..+++..|++...+.+..+.|+..||.+
T Consensus 21 s~s~AA~~L~isQ~avS~~i~~LE~~lG~~ 50 (302)
T PRK09791 21 SIRGASRMLNMSQPALTKSIQELEEGLAAQ 50 (302)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCCe
Confidence 677899999999999999999999999984
Done!