Query 009725
Match_columns 527
No_of_seqs 130 out of 280
Neff 7.9
Searched_HMMs 46136
Date Thu Mar 28 16:35:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2587 RNA polymerase III (C) 100.0 6.2E-81 1.3E-85 630.3 40.2 500 2-527 1-551 (551)
2 PF05645 RNA_pol_Rpc82: RNA po 99.9 1.1E-24 2.3E-29 216.0 11.4 115 256-370 98-258 (258)
3 PF08221 HTH_9: RNA polymerase 99.8 2.6E-19 5.6E-24 136.8 6.3 61 8-68 1-61 (62)
4 PF02002 TFIIE_alpha: TFIIE al 99.5 2.3E-14 4.9E-19 122.4 4.7 103 374-478 2-104 (105)
5 TIGR00373 conserved hypothetic 98.9 1.2E-08 2.6E-13 93.3 11.6 106 374-481 3-108 (158)
6 PRK06266 transcription initiat 98.8 2.5E-08 5.4E-13 92.8 11.5 109 371-481 6-116 (178)
7 COG1675 TFA1 Transcription ini 98.6 2.5E-07 5.5E-12 84.9 11.2 104 374-482 10-113 (176)
8 smart00531 TFIIE Transcription 98.4 8.4E-07 1.8E-11 80.3 7.1 93 388-481 4-98 (147)
9 PF02002 TFIIE_alpha: TFIIE al 98.0 8.6E-06 1.9E-10 69.4 5.8 89 8-100 1-89 (105)
10 KOG2587 RNA polymerase III (C) 97.7 0.007 1.5E-07 63.6 20.9 101 259-379 368-481 (551)
11 TIGR00373 conserved hypothetic 97.3 0.0022 4.8E-08 58.7 11.1 88 9-100 3-90 (158)
12 PF08221 HTH_9: RNA polymerase 97.2 0.00053 1.1E-08 52.4 4.7 60 374-434 2-61 (62)
13 PRK06266 transcription initiat 96.6 0.013 2.8E-07 54.7 9.6 84 13-100 13-98 (178)
14 PF01978 TrmB: Sugar-specific 96.0 0.021 4.6E-07 44.2 6.2 46 20-65 8-53 (68)
15 PHA02943 hypothetical protein; 95.6 0.084 1.8E-06 47.1 8.8 73 390-472 16-88 (165)
16 smart00550 Zalpha Z-DNA-bindin 95.6 0.017 3.7E-07 45.0 4.0 44 388-432 9-54 (68)
17 KOG2593 Transcription initiati 95.1 0.1 2.2E-06 54.2 8.8 142 373-519 17-198 (436)
18 smart00531 TFIIE Transcription 94.9 0.07 1.5E-06 48.3 6.5 74 24-100 5-80 (147)
19 PF13412 HTH_24: Winged helix- 94.7 0.049 1.1E-06 39.0 4.0 43 388-431 6-48 (48)
20 PF13601 HTH_34: Winged helix 94.6 0.16 3.4E-06 40.9 7.1 75 24-107 4-78 (80)
21 PHA02943 hypothetical protein; 94.4 0.75 1.6E-05 41.2 11.3 102 23-158 14-118 (165)
22 smart00550 Zalpha Z-DNA-bindin 94.3 0.12 2.6E-06 40.2 5.7 46 20-65 6-53 (68)
23 PF01978 TrmB: Sugar-specific 93.1 0.13 2.8E-06 39.7 3.9 46 388-434 11-56 (68)
24 PF13412 HTH_24: Winged helix- 92.9 0.28 6E-06 35.0 5.1 44 22-65 5-48 (48)
25 COG3355 Predicted transcriptio 92.6 0.95 2.1E-05 39.5 8.9 61 10-70 15-78 (126)
26 PF04337 DUF480: Protein of un 92.4 2.1 4.6E-05 38.1 10.8 120 22-167 5-143 (148)
27 TIGR02702 SufR_cyano iron-sulf 92.2 2.7 5.8E-05 40.0 12.6 66 22-92 3-68 (203)
28 PF09339 HTH_IclR: IclR helix- 92.0 0.24 5.1E-06 36.2 3.9 44 22-65 5-49 (52)
29 PF04703 FaeA: FaeA-like prote 91.9 0.21 4.6E-06 38.0 3.5 56 390-451 5-61 (62)
30 PRK10141 DNA-binding transcrip 91.8 1.7 3.7E-05 37.7 9.5 64 17-90 12-76 (117)
31 smart00418 HTH_ARSR helix_turn 91.6 0.77 1.7E-05 34.1 6.6 57 25-92 2-58 (66)
32 KOG2593 Transcription initiati 91.4 0.7 1.5E-05 48.2 7.8 101 7-109 16-116 (436)
33 COG3355 Predicted transcriptio 91.1 2.7 5.8E-05 36.8 10.0 96 375-473 15-117 (126)
34 PF09339 HTH_IclR: IclR helix- 90.8 0.22 4.7E-06 36.4 2.6 46 386-431 4-49 (52)
35 cd00090 HTH_ARSR Arsenical Res 90.1 1.7 3.6E-05 33.3 7.4 47 20-67 7-53 (78)
36 COG1675 TFA1 Transcription ini 89.8 2.4 5.2E-05 39.4 9.1 80 14-97 11-91 (176)
37 PF03965 Penicillinase_R: Peni 89.8 3.9 8.5E-05 35.1 10.2 100 19-131 2-106 (115)
38 PF01022 HTH_5: Bacterial regu 89.8 0.58 1.2E-05 33.3 4.1 42 23-65 5-46 (47)
39 smart00347 HTH_MARR helix_turn 89.8 3.1 6.7E-05 33.9 9.3 67 19-92 9-75 (101)
40 PF09012 FeoC: FeoC like trans 89.3 0.67 1.4E-05 36.0 4.4 47 23-69 3-49 (69)
41 smart00420 HTH_DEOR helix_turn 89.2 1 2.2E-05 32.2 5.2 42 24-65 4-45 (53)
42 TIGR02698 CopY_TcrY copper tra 89.1 5.8 0.00013 35.0 10.9 98 21-131 5-107 (130)
43 PF03962 Mnd1: Mnd1 family; I 88.2 5.2 0.00011 37.7 10.4 84 392-481 3-92 (188)
44 PF05645 RNA_pol_Rpc82: RNA po 88.1 0.92 2E-05 45.0 5.7 42 357-398 102-143 (258)
45 PF04703 FaeA: FaeA-like prote 87.9 1.8 3.8E-05 33.0 5.7 56 25-88 5-61 (62)
46 COG1510 Predicted transcriptio 87.7 1.7 3.7E-05 39.9 6.5 48 20-67 26-74 (177)
47 COG5647 Cullin, a subunit of E 87.6 3.1 6.7E-05 46.3 9.6 138 24-167 612-764 (773)
48 PF10771 DUF2582: Protein of u 87.6 0.85 1.9E-05 35.1 3.9 54 15-69 3-56 (65)
49 PRK00135 scpB segregation and 87.2 5.3 0.00011 37.7 9.8 136 291-451 6-149 (188)
50 COG1378 Predicted transcriptio 87.1 4.6 0.0001 39.8 9.8 50 16-65 10-61 (247)
51 smart00344 HTH_ASNC helix_turn 86.8 3.5 7.5E-05 34.7 7.8 63 388-451 6-72 (108)
52 smart00346 HTH_ICLR helix_turn 86.8 1.8 3.8E-05 35.1 5.8 45 22-66 7-52 (91)
53 PF12840 HTH_20: Helix-turn-he 86.4 1.5 3.2E-05 33.1 4.6 51 385-436 10-60 (61)
54 PF12840 HTH_20: Helix-turn-he 86.3 3.1 6.6E-05 31.3 6.4 46 20-65 10-55 (61)
55 PRK11239 hypothetical protein; 86.3 14 0.00031 35.1 12.0 123 18-167 5-153 (215)
56 PF08220 HTH_DeoR: DeoR-like h 86.1 1.7 3.7E-05 32.3 4.8 43 23-65 3-45 (57)
57 COG2345 Predicted transcriptio 85.0 4 8.8E-05 39.2 7.9 66 385-453 11-76 (218)
58 PF14947 HTH_45: Winged helix- 84.8 8.1 0.00018 30.6 8.5 70 20-104 6-75 (77)
59 COG2345 Predicted transcriptio 84.7 15 0.00032 35.4 11.5 93 17-124 8-100 (218)
60 PF06163 DUF977: Bacterial pro 84.5 2.5 5.4E-05 36.7 5.6 46 20-65 12-57 (127)
61 smart00344 HTH_ASNC helix_turn 84.5 2 4.4E-05 36.2 5.1 43 23-65 6-48 (108)
62 PRK00135 scpB segregation and 83.9 22 0.00048 33.5 12.3 121 21-167 5-135 (188)
63 PF01638 HxlR: HxlR-like helix 83.7 11 0.00024 30.8 9.1 63 22-92 7-70 (90)
64 PF12802 MarR_2: MarR family; 83.3 2.9 6.4E-05 31.1 5.1 47 20-66 5-53 (62)
65 PF10557 Cullin_Nedd8: Cullin 82.2 4.2 9E-05 31.5 5.6 56 112-167 9-64 (68)
66 PF01047 MarR: MarR family; I 81.8 2.8 6E-05 31.0 4.4 49 388-437 6-54 (59)
67 PF02082 Rrf2: Transcriptional 81.7 4.8 0.0001 32.3 6.1 42 24-65 12-56 (83)
68 PF13463 HTH_27: Winged helix 80.8 6.5 0.00014 29.8 6.3 45 25-69 8-53 (68)
69 TIGR02702 SufR_cyano iron-sulf 80.5 3.9 8.4E-05 38.9 6.0 63 388-453 4-66 (203)
70 PHA00738 putative HTH transcri 80.2 5.8 0.00012 33.6 6.1 60 23-92 15-74 (108)
71 PF03965 Penicillinase_R: Peni 80.1 32 0.0007 29.3 11.1 72 388-465 6-81 (115)
72 PHA02701 ORF020 dsRNA-binding 79.7 2.5 5.4E-05 39.3 4.1 46 387-433 6-52 (183)
73 TIGR02337 HpaR homoprotocatech 79.7 34 0.00073 29.2 11.2 65 20-91 28-92 (118)
74 PF01047 MarR: MarR family; I 79.2 3.7 8E-05 30.3 4.3 45 25-69 8-52 (59)
75 PRK11169 leucine-responsive tr 79.1 4.8 0.0001 37.0 5.9 43 388-431 17-59 (164)
76 PF01022 HTH_5: Bacterial regu 78.6 2.4 5.2E-05 30.1 3.0 42 388-431 5-46 (47)
77 cd00092 HTH_CRP helix_turn_hel 77.4 6.2 0.00013 29.7 5.2 36 31-66 22-57 (67)
78 COG3388 Predicted transcriptio 77.4 1.7 3.8E-05 35.5 2.1 42 24-65 18-59 (101)
79 PF12802 MarR_2: MarR family; 77.3 3.9 8.4E-05 30.4 4.0 51 386-437 6-58 (62)
80 PRK15090 DNA-binding transcrip 77.2 5 0.00011 39.6 5.9 43 24-66 18-60 (257)
81 COG3682 Predicted transcriptio 77.1 36 0.00078 29.7 10.2 102 18-131 4-109 (123)
82 smart00346 HTH_ICLR helix_turn 76.7 3.8 8.3E-05 33.1 4.1 46 386-432 6-52 (91)
83 PF13463 HTH_27: Winged helix 76.3 7.4 0.00016 29.5 5.4 50 388-438 6-56 (68)
84 PRK11179 DNA-binding transcrip 76.1 9.9 0.00022 34.4 7.0 47 385-432 9-55 (153)
85 COG3682 Predicted transcriptio 75.9 7.1 0.00015 34.0 5.6 54 109-166 4-57 (123)
86 smart00420 HTH_DEOR helix_turn 75.4 5 0.00011 28.4 4.0 43 389-432 4-46 (53)
87 PF10771 DUF2582: Protein of u 74.8 3 6.4E-05 32.1 2.7 55 381-436 4-58 (65)
88 COG1378 Predicted transcriptio 74.7 23 0.00051 34.8 9.7 74 385-466 16-89 (247)
89 TIGR01889 Staph_reg_Sar staphy 74.6 49 0.0011 27.9 10.6 91 371-465 9-106 (109)
90 COG1414 IclR Transcriptional r 74.4 7.3 0.00016 38.4 6.1 43 24-66 8-51 (246)
91 PRK03902 manganese transport t 73.5 7.9 0.00017 34.5 5.6 46 21-66 9-54 (142)
92 PF04079 DUF387: Putative tran 73.2 6.9 0.00015 35.8 5.2 129 293-446 2-137 (159)
93 PF09824 ArsR: ArsR transcript 72.6 23 0.0005 32.1 8.1 116 16-136 12-132 (160)
94 PF08220 HTH_DeoR: DeoR-like h 72.5 5.8 0.00013 29.5 3.8 41 389-430 4-44 (57)
95 PF02082 Rrf2: Transcriptional 72.4 5.2 0.00011 32.1 3.8 47 386-432 9-57 (83)
96 TIGR02787 codY_Gpos GTP-sensin 71.9 7.3 0.00016 37.9 5.2 46 20-65 183-229 (251)
97 PF02295 z-alpha: Adenosine de 71.9 3.7 8.1E-05 31.7 2.6 44 388-432 7-52 (66)
98 PRK06474 hypothetical protein; 71.6 11 0.00024 35.2 6.3 68 20-92 11-80 (178)
99 TIGR01610 phage_O_Nterm phage 71.3 8.3 0.00018 31.9 4.9 48 18-65 20-78 (95)
100 smart00418 HTH_ARSR helix_turn 71.3 5.6 0.00012 29.2 3.6 43 389-433 1-43 (66)
101 TIGR02698 CopY_TcrY copper tra 71.1 51 0.0011 28.9 10.1 70 388-465 7-82 (130)
102 PF08784 RPA_C: Replication pr 70.8 10 0.00023 31.6 5.5 53 17-70 44-100 (102)
103 COG1522 Lrp Transcriptional re 70.8 5.9 0.00013 35.5 4.2 69 383-452 6-78 (154)
104 PF13404 HTH_AsnC-type: AsnC-t 69.6 12 0.00026 26.0 4.5 36 23-58 6-41 (42)
105 cd07377 WHTH_GntR Winged helix 69.3 8.2 0.00018 28.7 4.1 47 19-65 4-56 (66)
106 PF05402 PqqD: Coenzyme PQQ sy 68.8 7.4 0.00016 29.7 3.8 55 108-164 14-68 (68)
107 PF06163 DUF977: Bacterial pro 68.7 15 0.00033 32.0 5.9 49 111-167 12-60 (127)
108 PRK11169 leucine-responsive tr 68.5 8.6 0.00019 35.2 4.8 49 20-68 14-62 (164)
109 PRK11512 DNA-binding transcrip 68.5 48 0.001 29.4 9.6 44 24-67 44-87 (144)
110 TIGR01889 Staph_reg_Sar staphy 68.2 22 0.00048 30.0 7.0 53 14-66 17-75 (109)
111 COG4190 Predicted transcriptio 67.8 20 0.00044 31.4 6.5 51 19-70 63-113 (144)
112 COG3132 Uncharacterized protei 67.3 39 0.00085 31.2 8.5 120 20-167 7-151 (215)
113 PF13601 HTH_34: Winged helix 66.8 14 0.0003 29.6 5.1 48 388-436 3-50 (80)
114 PF08280 HTH_Mga: M protein tr 66.6 12 0.00027 27.9 4.5 36 24-59 9-44 (59)
115 smart00347 HTH_MARR helix_turn 66.6 48 0.001 26.6 8.7 48 385-433 10-57 (101)
116 PRK10163 DNA-binding transcrip 66.5 25 0.00055 35.0 8.1 43 24-66 29-72 (271)
117 PHA02701 ORF020 dsRNA-binding 66.4 15 0.00033 34.2 5.8 46 20-65 4-50 (183)
118 TIGR01610 phage_O_Nterm phage 65.8 10 0.00022 31.3 4.3 36 397-433 45-80 (95)
119 TIGR02337 HpaR homoprotocatech 65.7 34 0.00074 29.2 7.8 49 384-433 27-75 (118)
120 PF13730 HTH_36: Helix-turn-he 65.6 9.3 0.0002 27.8 3.6 29 36-64 27-55 (55)
121 PF08279 HTH_11: HTH domain; 65.6 15 0.00033 26.6 4.8 48 388-436 3-50 (55)
122 smart00419 HTH_CRP helix_turn_ 65.5 10 0.00022 26.3 3.7 32 34-65 8-39 (48)
123 PRK13777 transcriptional regul 65.1 45 0.00098 31.3 8.9 62 388-453 48-109 (185)
124 PRK11179 DNA-binding transcrip 64.7 14 0.00029 33.5 5.3 48 20-67 9-56 (153)
125 COG1386 scpB Chromosome segreg 64.0 81 0.0017 29.6 10.3 135 290-447 9-148 (184)
126 PF08679 DsrD: Dissimilatory s 63.9 18 0.00038 27.8 4.8 35 36-70 21-56 (67)
127 PF00392 GntR: Bacterial regul 63.9 7.8 0.00017 29.3 3.0 35 31-65 19-55 (64)
128 PRK09834 DNA-binding transcrip 63.7 16 0.00034 36.2 6.0 42 24-65 15-57 (263)
129 PRK15431 ferrous iron transpor 63.7 19 0.00041 28.7 5.1 45 24-68 6-50 (78)
130 PRK11512 DNA-binding transcrip 63.5 19 0.00041 32.0 6.0 63 387-453 42-104 (144)
131 TIGR02844 spore_III_D sporulat 62.7 14 0.0003 29.7 4.3 35 20-55 6-40 (80)
132 PF01325 Fe_dep_repress: Iron 62.2 25 0.00053 26.5 5.4 45 22-66 10-54 (60)
133 PRK15090 DNA-binding transcrip 61.9 8.9 0.00019 37.8 3.8 45 386-431 15-59 (257)
134 TIGR02010 IscR iron-sulfur clu 61.8 13 0.00028 32.8 4.5 74 385-467 8-83 (135)
135 COG3398 Uncharacterized protei 61.1 1.1E+02 0.0023 29.6 10.5 121 18-164 98-219 (240)
136 smart00419 HTH_CRP helix_turn_ 60.9 9.1 0.0002 26.6 2.7 32 402-433 10-41 (48)
137 cd00090 HTH_ARSR Arsenical Res 60.9 14 0.0003 27.9 4.1 45 386-432 8-52 (78)
138 COG1733 Predicted transcriptio 60.7 35 0.00075 29.7 6.8 62 19-88 22-84 (120)
139 PRK11569 transcriptional repre 60.5 19 0.00042 35.9 6.0 40 26-65 34-74 (274)
140 TIGR00281 segregation and cond 60.2 1.2E+02 0.0025 28.6 10.7 134 292-450 4-145 (186)
141 PF09012 FeoC: FeoC like trans 59.2 17 0.00037 28.0 4.3 49 389-438 4-52 (69)
142 TIGR02944 suf_reg_Xantho FeS a 58.8 12 0.00026 32.7 3.7 51 382-432 6-57 (130)
143 PF08784 RPA_C: Replication pr 58.7 9.9 0.00021 31.7 3.0 48 383-431 45-96 (102)
144 smart00345 HTH_GNTR helix_turn 58.7 14 0.00031 26.7 3.6 33 33-65 18-51 (60)
145 PHA03103 double-strand RNA-bin 58.6 10 0.00023 35.4 3.4 43 390-433 18-60 (183)
146 COG2512 Predicted membrane-ass 58.5 14 0.0003 36.7 4.4 51 388-438 198-248 (258)
147 cd00092 HTH_CRP helix_turn_hel 58.4 23 0.00051 26.4 4.9 55 98-167 5-59 (67)
148 PF01325 Fe_dep_repress: Iron 58.3 17 0.00036 27.4 3.9 43 390-433 13-55 (60)
149 cd07153 Fur_like Ferric uptake 57.4 31 0.00068 29.2 6.0 50 115-167 5-55 (116)
150 PF01726 LexA_DNA_bind: LexA D 57.3 30 0.00065 26.5 5.2 46 20-65 10-57 (65)
151 TIGR02431 pcaR_pcaU beta-ketoa 57.3 18 0.00038 35.5 5.0 40 26-65 15-55 (248)
152 PRK10163 DNA-binding transcrip 56.4 14 0.00031 36.8 4.2 46 386-431 26-71 (271)
153 PRK09834 DNA-binding transcrip 56.4 14 0.00031 36.6 4.2 45 386-431 12-57 (263)
154 PRK11569 transcriptional repre 56.2 14 0.0003 36.9 4.2 46 386-431 29-74 (274)
155 TIGR01884 cas_HTH CRISPR locus 55.6 22 0.00047 33.8 5.2 48 19-66 142-189 (203)
156 PHA03103 double-strand RNA-bin 55.5 24 0.00052 33.0 5.2 46 20-65 13-58 (183)
157 PRK11050 manganese transport r 55.3 28 0.0006 31.5 5.5 43 23-65 40-82 (152)
158 COG1414 IclR Transcriptional r 55.2 15 0.00033 36.1 4.1 91 386-483 5-97 (246)
159 TIGR02944 suf_reg_Xantho FeS a 55.1 28 0.00061 30.3 5.4 34 33-66 24-57 (130)
160 COG5625 Predicted transcriptio 55.1 12 0.00026 31.1 2.8 43 23-65 24-67 (113)
161 PF07848 PaaX: PaaX-like prote 54.9 31 0.00068 26.9 5.0 33 33-65 19-54 (70)
162 TIGR00738 rrf2_super rrf2 fami 54.6 18 0.00038 31.5 4.1 46 386-431 9-56 (132)
163 TIGR02431 pcaR_pcaU beta-ketoa 54.4 15 0.00031 36.1 3.9 45 386-431 10-55 (248)
164 PF05584 Sulfolobus_pRN: Sulfo 54.0 42 0.00092 26.3 5.5 42 23-65 8-49 (72)
165 PF09904 HTH_43: Winged helix- 53.4 20 0.00044 29.3 3.8 62 27-94 14-75 (90)
166 PF04157 EAP30: EAP30/Vps36 fa 52.4 40 0.00086 32.6 6.5 105 312-431 110-221 (223)
167 COG1777 Predicted transcriptio 51.8 2.2E+02 0.0049 27.2 11.8 51 16-67 10-61 (217)
168 TIGR00122 birA_repr_reg BirA b 51.0 30 0.00064 26.5 4.4 41 24-65 4-44 (69)
169 PF09681 Phage_rep_org_N: N-te 50.5 41 0.00088 29.3 5.5 48 33-92 52-99 (121)
170 TIGR01884 cas_HTH CRISPR locus 50.0 21 0.00046 33.8 4.1 51 382-433 140-190 (203)
171 COG1522 Lrp Transcriptional re 49.9 32 0.0007 30.6 5.2 49 21-69 9-57 (154)
172 PRK03573 transcriptional regul 49.8 1.8E+02 0.0039 25.5 11.2 61 388-452 34-95 (144)
173 PF09756 DDRGK: DDRGK domain; 49.2 12 0.00026 35.2 2.2 85 21-136 100-184 (188)
174 PF00392 GntR: Bacterial regul 49.2 37 0.0008 25.5 4.6 36 398-433 21-57 (64)
175 TIGR00738 rrf2_super rrf2 fami 49.1 42 0.0009 29.2 5.6 34 33-66 24-57 (132)
176 TIGR02010 IscR iron-sulfur clu 48.9 48 0.001 29.2 6.0 33 33-65 24-56 (135)
177 cd07153 Fur_like Ferric uptake 48.4 65 0.0014 27.2 6.6 46 24-69 5-56 (116)
178 PRK09462 fur ferric uptake reg 48.3 49 0.0011 29.6 6.0 53 112-167 18-72 (148)
179 PRK10870 transcriptional repre 47.3 1.6E+02 0.0034 27.2 9.4 51 17-67 50-104 (176)
180 PRK11014 transcriptional repre 47.1 28 0.0006 30.9 4.2 47 387-433 10-58 (141)
181 PF08279 HTH_11: HTH domain; 46.9 55 0.0012 23.5 5.1 40 23-62 3-43 (55)
182 PF07381 DUF1495: Winged helix 46.8 73 0.0016 26.2 6.1 60 23-91 12-83 (90)
183 PF12793 SgrR_N: Sugar transpo 46.1 67 0.0014 27.7 6.2 55 34-93 19-73 (115)
184 COG4189 Predicted transcriptio 45.8 52 0.0011 31.9 5.8 51 388-439 26-76 (308)
185 COG0735 Fur Fe2+/Zn2+ uptake r 45.6 57 0.0012 29.2 6.0 54 111-167 21-75 (145)
186 PF10007 DUF2250: Uncharacteri 44.8 38 0.00081 28.0 4.2 46 385-431 7-52 (92)
187 PF04079 DUF387: Putative tran 44.6 1.1E+02 0.0023 28.1 7.6 117 24-167 2-127 (159)
188 PF02796 HTH_7: Helix-turn-hel 44.4 38 0.00082 23.7 3.7 31 23-55 12-42 (45)
189 PF04492 Phage_rep_O: Bacterio 44.3 26 0.00056 29.4 3.2 52 372-432 35-86 (100)
190 COG1846 MarR Transcriptional r 43.9 1.8E+02 0.004 23.9 9.8 53 18-70 20-72 (126)
191 PF11994 DUF3489: Protein of u 43.9 91 0.002 24.5 5.9 43 23-65 13-57 (72)
192 PF01638 HxlR: HxlR-like helix 43.6 41 0.00089 27.3 4.3 47 113-167 7-53 (90)
193 PRK10344 DNA-binding transcrip 43.5 48 0.001 27.2 4.5 34 22-56 10-43 (92)
194 PRK10434 srlR DNA-bindng trans 43.2 38 0.00083 33.4 4.9 44 22-65 7-50 (256)
195 PF04337 DUF480: Protein of un 43.0 56 0.0012 29.3 5.2 49 17-65 85-140 (148)
196 PRK11534 DNA-binding transcrip 42.9 41 0.00089 32.2 5.0 50 16-65 11-61 (224)
197 PRK09775 putative DNA-binding 42.5 49 0.0011 35.6 5.9 41 25-67 4-44 (442)
198 PF14947 HTH_45: Winged helix- 42.2 32 0.00068 27.2 3.3 40 389-430 10-49 (77)
199 PRK13777 transcriptional regul 41.8 3E+02 0.0065 25.8 12.8 43 24-66 49-91 (185)
200 COG5625 Predicted transcriptio 41.8 99 0.0021 25.9 6.1 86 381-470 15-103 (113)
201 PRK09954 putative kinase; Prov 41.8 28 0.0006 36.1 3.8 43 388-431 6-48 (362)
202 PRK04424 fatty acid biosynthes 41.6 34 0.00073 32.1 4.0 44 22-65 9-52 (185)
203 TIGR03879 near_KaiC_dom probab 41.5 41 0.00088 26.5 3.7 46 20-65 18-63 (73)
204 COG1510 Predicted transcriptio 41.3 88 0.0019 28.9 6.4 69 368-436 5-77 (177)
205 PRK10906 DNA-binding transcrip 40.9 45 0.00097 32.9 4.9 43 23-65 8-50 (252)
206 PF01726 LexA_DNA_bind: LexA D 40.6 1E+02 0.0023 23.5 5.9 47 114-167 13-60 (65)
207 PLN02853 Probable phenylalanyl 40.3 4.1E+02 0.009 29.0 12.3 112 22-166 5-117 (492)
208 COG1959 Predicted transcriptio 40.1 41 0.00089 30.4 4.2 55 383-437 6-62 (150)
209 TIGR03859 PQQ_PqqD coenzyme PQ 40.0 63 0.0014 25.8 4.8 52 110-164 30-81 (81)
210 COG1321 TroR Mn-dependent tran 39.7 39 0.00085 30.7 3.9 43 390-433 15-57 (154)
211 PRK10857 DNA-binding transcrip 39.7 38 0.00082 31.1 3.9 49 385-433 8-58 (164)
212 PF10007 DUF2250: Uncharacteri 39.2 92 0.002 25.7 5.6 51 20-70 7-57 (92)
213 PF13730 HTH_36: Helix-turn-he 38.9 25 0.00054 25.4 2.1 29 402-430 27-55 (55)
214 PRK11014 transcriptional repre 38.6 45 0.00098 29.6 4.2 32 34-65 25-56 (141)
215 cd07377 WHTH_GntR Winged helix 38.5 27 0.00059 25.8 2.4 31 402-432 27-57 (66)
216 TIGR01714 phage_rep_org_N phag 38.1 68 0.0015 27.8 5.0 47 33-91 50-96 (119)
217 PF12793 SgrR_N: Sugar transpo 37.9 1E+02 0.0022 26.5 6.1 60 401-462 20-79 (115)
218 PF13545 HTH_Crp_2: Crp-like h 37.5 35 0.00075 26.3 2.9 32 402-433 30-61 (76)
219 PRK03573 transcriptional regul 37.0 2.9E+02 0.0062 24.2 12.1 44 25-68 36-80 (144)
220 PRK09462 fur ferric uptake reg 36.6 1.2E+02 0.0025 27.1 6.6 50 20-69 17-73 (148)
221 smart00345 HTH_GNTR helix_turn 36.4 35 0.00076 24.6 2.7 31 402-432 22-52 (60)
222 COG4344 Uncharacterized protei 36.1 31 0.00067 30.8 2.5 53 38-90 35-94 (175)
223 COG2238 RPS19A Ribosomal prote 36.0 1.1E+02 0.0025 27.2 5.9 57 111-167 53-115 (147)
224 PF04492 Phage_rep_O: Bacterio 35.9 1.3E+02 0.0028 25.2 6.2 32 34-65 54-85 (100)
225 COG3888 Predicted transcriptio 35.8 73 0.0016 31.5 5.2 42 389-430 8-50 (321)
226 PRK09802 DNA-binding transcrip 35.8 60 0.0013 32.4 5.0 45 21-65 18-62 (269)
227 COG1349 GlpR Transcriptional r 35.3 61 0.0013 32.0 4.9 47 113-167 7-53 (253)
228 PRK04172 pheS phenylalanyl-tRN 35.1 4.8E+02 0.01 28.4 12.2 112 22-165 8-119 (489)
229 PRK06474 hypothetical protein; 35.0 83 0.0018 29.3 5.5 47 114-167 14-61 (178)
230 COG3423 Nlp Predicted transcri 34.8 80 0.0017 25.0 4.3 33 23-56 11-43 (82)
231 COG1959 Predicted transcriptio 34.8 1.1E+02 0.0025 27.5 6.2 48 19-66 7-57 (150)
232 TIGR02787 codY_Gpos GTP-sensin 34.8 42 0.0009 32.8 3.4 48 388-436 186-234 (251)
233 COG0735 Fur Fe2+/Zn2+ uptake r 34.4 1.2E+02 0.0026 27.2 6.2 59 23-90 24-88 (145)
234 PF00325 Crp: Bacterial regula 34.4 59 0.0013 21.2 3.0 31 34-64 2-32 (32)
235 PF02295 z-alpha: Adenosine de 34.2 41 0.0009 25.8 2.7 46 20-65 4-51 (66)
236 KOG4562 Uncharacterized conser 34.0 38 0.00082 34.8 3.2 56 388-450 223-279 (329)
237 PF04182 B-block_TFIIIC: B-blo 34.0 2E+02 0.0044 22.4 6.8 49 402-450 20-70 (75)
238 PRK11920 rirA iron-responsive 33.9 1.4E+02 0.003 27.0 6.6 34 33-66 23-56 (153)
239 PF13814 Replic_Relax: Replica 33.8 91 0.002 28.8 5.7 62 392-454 2-66 (191)
240 PF09202 Rio2_N: Rio2, N-termi 33.4 52 0.0011 26.5 3.3 36 31-66 21-56 (82)
241 PF13404 HTH_AsnC-type: AsnC-t 33.3 71 0.0015 22.1 3.6 36 388-424 6-41 (42)
242 PRK11050 manganese transport r 33.2 1.4E+02 0.0031 26.8 6.6 42 389-431 41-82 (152)
243 PRK03902 manganese transport t 33.1 56 0.0012 28.9 3.9 41 390-431 13-53 (142)
244 PRK12423 LexA repressor; Provi 33.0 99 0.0022 29.3 5.8 45 21-65 11-57 (202)
245 PF01475 FUR: Ferric uptake re 32.9 92 0.002 26.5 5.1 53 113-168 10-63 (120)
246 PF09743 DUF2042: Uncharacteri 32.6 1.8E+02 0.0039 29.1 7.7 52 14-65 110-161 (272)
247 TIGR03338 phnR_burk phosphonat 32.3 57 0.0012 30.8 4.0 33 34-66 34-66 (212)
248 TIGR03879 near_KaiC_dom probab 32.2 36 0.00078 26.8 2.1 44 386-430 19-62 (73)
249 PF09397 Ftsk_gamma: Ftsk gamm 31.8 1.4E+02 0.0031 22.9 5.3 48 19-66 5-52 (65)
250 PRK10141 DNA-binding transcrip 31.7 3.4E+02 0.0073 23.4 10.3 58 388-453 19-76 (117)
251 PF14394 DUF4423: Domain of un 31.7 1.2E+02 0.0025 28.1 5.8 50 16-65 19-72 (171)
252 KOG2165 Anaphase-promoting com 31.6 6.7E+02 0.015 28.5 12.2 140 23-166 605-757 (765)
253 PRK11920 rirA iron-responsive 31.2 52 0.0011 29.8 3.4 52 383-434 6-58 (153)
254 PRK13918 CRP/FNR family transc 31.1 3.4E+02 0.0074 24.9 9.2 51 313-370 147-198 (202)
255 COG1802 GntR Transcriptional r 31.1 4.7E+02 0.01 24.9 10.3 53 398-457 37-89 (230)
256 COG4742 Predicted transcriptio 31.0 3.3E+02 0.0071 27.1 9.0 79 13-105 5-83 (260)
257 PRK10402 DNA-binding transcrip 30.9 1.4E+02 0.003 28.5 6.5 58 8-65 138-200 (226)
258 PF05379 Peptidase_C23: Carlav 30.6 1.5E+02 0.0032 24.3 5.6 69 274-361 2-70 (89)
259 PRK13509 transcriptional repre 30.6 94 0.002 30.6 5.3 44 22-65 7-50 (251)
260 PRK10857 DNA-binding transcrip 30.5 82 0.0018 28.9 4.6 34 33-66 24-57 (164)
261 PRK10434 srlR DNA-bindng trans 30.3 87 0.0019 30.9 5.1 47 113-167 7-53 (256)
262 PF10415 FumaraseC_C: Fumarase 30.2 86 0.0019 23.1 3.8 41 14-55 5-47 (55)
263 COG2512 Predicted membrane-ass 30.2 81 0.0018 31.3 4.7 54 15-68 190-244 (258)
264 PF14502 HTH_41: Helix-turn-he 30.2 78 0.0017 22.8 3.3 30 36-65 8-37 (48)
265 TIGR03882 cyclo_dehyd_2 bacter 29.8 1.2E+02 0.0025 28.7 5.6 47 112-166 31-77 (193)
266 COG1349 GlpR Transcriptional r 29.5 82 0.0018 31.1 4.7 43 23-65 8-50 (253)
267 COG1321 TroR Mn-dependent tran 29.4 4.3E+02 0.0094 23.9 10.0 42 25-66 15-56 (154)
268 PF10668 Phage_terminase: Phag 29.3 70 0.0015 24.2 3.1 25 29-53 17-41 (60)
269 PF13693 HTH_35: Winged helix- 29.0 48 0.001 26.5 2.4 32 23-55 5-36 (78)
270 PF09202 Rio2_N: Rio2, N-termi 28.8 62 0.0013 26.1 3.0 47 386-432 7-56 (82)
271 PRK03837 transcriptional regul 28.8 75 0.0016 30.6 4.3 42 25-66 26-69 (241)
272 PRK11414 colanic acid/biofilm 28.5 74 0.0016 30.3 4.1 33 34-66 34-66 (221)
273 PRK13509 transcriptional repre 28.4 68 0.0015 31.6 3.9 43 388-431 8-50 (251)
274 PRK00082 hrcA heat-inducible t 28.3 1.3E+02 0.0029 31.0 6.2 93 28-136 19-113 (339)
275 COG4738 Predicted transcriptio 28.0 3.9E+02 0.0085 23.0 9.9 105 7-122 14-118 (124)
276 COG1733 Predicted transcriptio 27.5 2.3E+02 0.0049 24.5 6.6 54 108-168 19-72 (120)
277 COG4189 Predicted transcriptio 27.1 1E+02 0.0023 29.9 4.6 42 24-65 27-68 (308)
278 PRK09990 DNA-binding transcrip 27.1 71 0.0015 31.1 3.8 58 106-167 5-65 (251)
279 TIGR02147 Fsuc_second hypothet 27.0 1.3E+02 0.0029 30.0 5.7 50 16-65 117-170 (271)
280 TIGR00122 birA_repr_reg BirA b 27.0 96 0.0021 23.6 3.8 42 388-431 3-44 (69)
281 TIGR00281 segregation and cond 26.3 5.5E+02 0.012 24.1 10.0 121 22-167 3-132 (186)
282 PF03551 PadR: Transcriptional 26.2 1.5E+02 0.0033 22.8 4.9 48 120-167 4-51 (75)
283 PRK11639 zinc uptake transcrip 26.0 1.5E+02 0.0033 27.2 5.5 53 112-167 27-80 (169)
284 PHA02591 hypothetical protein; 25.4 1.6E+02 0.0035 23.5 4.5 34 21-55 47-80 (83)
285 COG3398 Uncharacterized protei 25.3 2.5E+02 0.0054 27.2 6.7 65 16-90 170-234 (240)
286 PF09382 RQC: RQC domain; Int 25.0 2.7E+02 0.0058 22.9 6.5 56 111-166 4-75 (106)
287 PRK09954 putative kinase; Prov 25.0 1.3E+02 0.0028 31.1 5.5 99 23-125 6-108 (362)
288 PF08672 APC2: Anaphase promot 24.4 1.3E+02 0.0028 22.7 3.9 47 315-361 11-60 (60)
289 PRK10906 DNA-binding transcrip 23.9 86 0.0019 30.9 3.7 42 388-430 8-49 (252)
290 PF10330 Stb3: Putative Sin3 b 23.8 1.2E+02 0.0027 24.8 3.8 34 25-58 11-52 (92)
291 PRK10411 DNA-binding transcrip 23.4 1.5E+02 0.0034 28.8 5.4 43 23-65 7-49 (240)
292 TIGR03697 NtcA_cyano global ni 23.2 2.9E+02 0.0062 25.1 7.0 51 16-66 110-175 (193)
293 PRK04984 fatty acid metabolism 23.1 93 0.002 30.0 3.7 54 110-167 9-65 (239)
294 COG1846 MarR Transcriptional r 23.1 1.1E+02 0.0025 25.3 3.9 65 383-451 20-84 (126)
295 TIGR03882 cyclo_dehyd_2 bacter 23.1 1.8E+02 0.0039 27.4 5.5 46 19-66 29-76 (193)
296 PF03444 HrcA_DNA-bdg: Winged 23.0 1.4E+02 0.0031 23.8 4.0 38 396-433 19-56 (78)
297 PF01399 PCI: PCI domain; Int 22.9 1.2E+02 0.0026 24.5 3.9 37 30-66 56-92 (105)
298 PRK11239 hypothetical protein; 22.8 1.7E+02 0.0038 28.0 5.2 48 18-65 95-150 (215)
299 TIGR02812 fadR_gamma fatty aci 22.8 1E+02 0.0022 29.6 4.0 36 30-65 24-61 (235)
300 smart00088 PINT motif in prote 22.8 1.6E+02 0.0034 23.3 4.5 40 27-66 17-56 (88)
301 smart00753 PAM PCI/PINT associ 22.8 1.6E+02 0.0034 23.3 4.5 40 27-66 17-56 (88)
302 PF01454 MAGE: MAGE family; I 22.3 1.3E+02 0.0029 28.1 4.5 59 389-453 125-185 (195)
303 PRK03837 transcriptional regul 22.3 1.5E+02 0.0033 28.5 5.1 36 398-433 34-70 (241)
304 TIGR03338 phnR_burk phosphonat 21.9 1.4E+02 0.003 28.1 4.6 36 398-433 32-67 (212)
305 TIGR00498 lexA SOS regulatory 21.6 1.3E+02 0.0027 28.3 4.2 31 35-65 26-57 (199)
306 PRK00215 LexA repressor; Valid 21.6 2.1E+02 0.0045 26.9 5.7 44 22-65 10-55 (205)
307 PF05584 Sulfolobus_pRN: Sulfo 21.5 1.6E+02 0.0034 23.2 3.9 58 389-451 9-66 (72)
308 PRK09333 30S ribosomal protein 21.4 3E+02 0.0065 24.9 6.2 56 112-167 54-115 (150)
309 KOG2166 Cullins [Cell cycle co 21.4 3E+02 0.0065 31.7 7.7 127 32-166 578-717 (725)
310 cd06571 Bac_DnaA_C C-terminal 21.1 2.9E+02 0.0062 22.3 5.7 37 21-57 30-68 (90)
311 PF04157 EAP30: EAP30/Vps36 fa 20.9 1.2E+02 0.0026 29.2 4.0 47 19-65 173-221 (223)
312 PRK09464 pdhR transcriptional 20.8 1.6E+02 0.0034 28.7 4.9 57 365-433 10-67 (254)
313 PF05732 RepL: Firmicute plasm 20.8 1.5E+02 0.0033 27.2 4.4 65 16-93 51-121 (165)
314 TIGR02812 fadR_gamma fatty aci 20.8 1.7E+02 0.0036 28.1 5.0 36 398-433 27-63 (235)
315 PRK10402 DNA-binding transcrip 20.7 3.2E+02 0.0069 26.0 6.9 63 385-458 150-217 (226)
316 COG4190 Predicted transcriptio 20.5 5.8E+02 0.013 22.6 7.5 69 353-435 45-113 (144)
317 TIGR00331 hrcA heat shock gene 20.5 4.4E+02 0.0096 27.2 8.2 41 25-65 12-54 (337)
318 PF04255 DUF433: Protein of un 20.4 2.1E+02 0.0046 21.0 4.3 33 22-56 21-54 (56)
319 TIGR02404 trehalos_R_Bsub treh 20.3 1.1E+02 0.0024 29.4 3.6 30 36-65 26-55 (233)
320 PF05158 RNA_pol_Rpc34: RNA po 20.2 1.1E+02 0.0024 31.5 3.7 134 25-167 89-258 (327)
321 PRK09333 30S ribosomal protein 20.1 1.8E+02 0.0038 26.4 4.5 45 21-65 54-112 (150)
322 PF08281 Sigma70_r4_2: Sigma-7 20.1 2.3E+02 0.005 20.1 4.5 31 27-57 19-49 (54)
323 PF07278 DUF1441: Protein of u 20.0 2.1E+02 0.0045 26.0 4.9 45 14-63 95-150 (152)
No 1
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=100.00 E-value=6.2e-81 Score=630.31 Aligned_cols=500 Identities=26% Similarity=0.412 Sum_probs=386.3
Q ss_pred ccHHHHHHHHHHHHHhhchhHHHHHHHHHhcCCCC-HHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCC
Q 009725 2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLT-RQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPK 80 (527)
Q Consensus 2 ~~~~~~~Lc~~ii~~~FG~~v~~V~~~Ll~~G~~t-l~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~ 80 (527)
||+|+++||..||++|||++|++|+.+|++.|++| +.-+...++++..+||.+|++|||||||.|+....+ .+
T Consensus 1 msq~eielc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~------~g 74 (551)
T KOG2587|consen 1 MSQYEIELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRN------SG 74 (551)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCC------CC
Confidence 79999999999999999999999999999999999 888888899999999999999999999998776532 23
Q ss_pred cceEEEeehhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccC-----HHHHHHHHH
Q 009725 81 ANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVD-----LDSLRETLV 155 (527)
Q Consensus 81 ~~~~Y~~~~~~il~rlR~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~-----~~~l~~~f~ 155 (527)
..++|++.+++|+++||||+|+..++++||+.|+.|+++|+.+|++|++++++++..+.......+ ..-+.+.|.
T Consensus 75 ~vt~Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sIv~~Lls~GrLTv~e~i~rv~~~~~~~~~ss~~~ql~~lv~q~F~ 154 (551)
T KOG2587|consen 75 KVTTYEAQCSEILHILRYPRYIYITKTLYSQTAESIVEELLSNGRLTVSEVIKRVADRLTTTMESSKTMQLCALVSQTFV 154 (551)
T ss_pred ceEEEEehhhHHHHHHhcccceeeHHHHhhhHHHHHHHHHHhcCceeHHHHHHHHHhcccccchhhHHHHHHHHHHHHHH
Confidence 579999999999999999999999999999999999999999999999999999987543322111 133566666
Q ss_pred HHHhc---ccceecCCCCCCCCCCCCCCCcccccCCcCccccCCchhhhHHHHHHhCccchhhhhhhhcccccccccccC
Q 009725 156 KLVTA---HYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKN 232 (527)
Q Consensus 156 ~Lv~~---~~i~~v~~~~~~~~~~~~~~~~~~~~g~~~~k~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~ 232 (527)
.++.. ||..++|.+.+ ..+...++.+..+-+........++..+..+++.+-...+.+. .
T Consensus 155 ~~~~~~ekH~~~r~~e~~~-------------~~~~~a~~~~~e~~~~~~~~~q~lt~~pkis~~~~~~~~s~s~----~ 217 (551)
T KOG2587|consen 155 ELADPLEKHFVNRCPESVP-------------TVENSAAGPPPEAPTLVINEKQILTLVPKISLPGKGKRRSSSD----E 217 (551)
T ss_pred HhhCchhhHhhccCCCccc-------------ccccccCCCCcccccchhhhccccccccccccCCCCCcccccc----c
Confidence 66666 66666653211 1112222222222112222222233333344433221111111 1
Q ss_pred CCCCCCCCccccccccccccCCCCCCceEEEeehhHHHHHhhhhHHHHHHHhhcCccHHHHHHHHHHccchh-hhc-cc-
Q 009725 233 SNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSA-EKK-VK- 309 (527)
Q Consensus 233 ~~~~~~~~krk~~~~~~d~~~~~~~~~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~-~~~-~~- 309 (527)
.+...++.++|.- ..|......+.+++||+|+++|+.++||++|+++|..|.++.++.|+++||..+... +++ +.
T Consensus 218 ~d~~~~~~~~k~l--~~D~~~~~~d~ga~wr~N~~rf~~~lRd~~~v~~v~~r~~e~ts~v~~a~Lt~~tie~~r~~~~~ 295 (551)
T KOG2587|consen 218 DDRGEKKAKRKKL--TTDNKTPDPDDGAYWRINLDRFHQHLRDQAIVSAVANRMDEGTSEVLRAMLTRMTIELTRHSPAP 295 (551)
T ss_pred ccccCcccccccc--ccccCCCCCCCceeEehhhHHhhHHhhhHHHHHHHHhcccchhHHHHHHHHHhhhhhhccCCchh
Confidence 1122333333321 111112334678999999999999999999999999999999999999999443211 111 00
Q ss_pred ---------ccCCCcc------ChHHHHHHhhh-----cccCCCCCHHHHHHHHHHhccCC------CCCCCCCcEEEeh
Q 009725 310 ---------TKNSVPL------SLSSIYEEVIK-----SEAGRNMTLDHVRASLVQLGELS------FVDASSDSYSIDF 363 (527)
Q Consensus 310 ---------~~~s~p~------s~~~I~~~l~~-----~~~~~~~~~~~i~~~L~~La~~~------~~~~~~~~y~V~~ 363 (527)
...|.++ +...+-+.+.. ++++.+...+.+..|+..|++++ +|++|||+|.|||
T Consensus 296 l~~e~si~~~~~s~n~~s~~~~~~esl~~~~~l~Er~~~ee~~nl~~~~~~~ac~~l~d~slk~l~klges~~G~yiV~y 375 (551)
T KOG2587|consen 296 LDTELSINEIFRSLNVGSNGSISMESLDQYLTLLERGDTEEEENLDADTEDPACASLADDSLKFLGKLGESGGGMYIVNY 375 (551)
T ss_pred hhchhhhhhhccCcccccchHHHHHhhhhHHHHHhhccchhhccccccchhhHHHHhhcchHHHHHHhccCCCCEEEEEH
Confidence 0111111 11111111111 12344556678889999999888 6799999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccC--CC
Q 009725 364 EKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--AR 441 (527)
Q Consensus 364 ~~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~--~~ 441 (527)
++++..++..++|++|.++||..|.|+||+|..+|++ |||||++.|||+.||+|..||+|+++||+++||||||+ +|
T Consensus 376 ~k~i~vl~~~~~E~vI~~rfG~rAiRl~R~l~~k~~v-eekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~p 454 (551)
T KOG2587|consen 376 HKAIAVLATATYESVIQERFGSRAIRLFRLLLQKKHV-EEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAP 454 (551)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc-hHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCC
Confidence 9999999999999999999999999999999999877 99999999999999999999999999999999999999 99
Q ss_pred CceEEEEEEchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccccC-----------ChhhHHHHHHHHHHHHHH
Q 009725 442 QSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKR-----------TGPLQDRYNRIRKVRILL 510 (527)
Q Consensus 442 ~~t~~lw~v~~~~~~~~~~~~~yk~~~nl~~R~~~e~~~~k~ll~k~~~~~-----------~~~e~~~l~~~~~~~~~L 510 (527)
+||||||+||+.++++++++++||++.||+.|++||+.+++.||+|.++.+ -+.+..+++++...+..+
T Consensus 455 srtF~L~~v~~~~a~~~lld~ly~~iaNL~~R~~~eraEn~~LL~Ka~rve~~Ik~~e~~~~k~~qlael~~~~~~ql~l 534 (551)
T KOG2587|consen 455 SRTFYLYTVNILRAYRMLLDELYKSIANLIERLRHERAENKRLLEKAQRVEAIIKGREATGAKEAQLAELEEMYTAQLNL 534 (551)
T ss_pred cceEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccHhhhhhHHhhhhHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999976554 167788888888889999
Q ss_pred HHHHhhhhhhhhcccCC
Q 009725 511 ESSQMKLDDAILLFHDF 527 (527)
Q Consensus 511 ~~~~~rlD~~l~ll~d~ 527 (527)
+....|+|+++++|++|
T Consensus 535 f~r~s~l~~~~~vf~~~ 551 (551)
T KOG2587|consen 535 FKRASQLDETILVFESY 551 (551)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999999997
No 2
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2XV4_S 2XUB_A.
Probab=99.91 E-value=1.1e-24 Score=216.01 Aligned_cols=115 Identities=27% Similarity=0.398 Sum_probs=83.9
Q ss_pred CCCceEEEeehhHHHHHhhhhHHHHHHHhhcCccHHHHHHHHHHccchhhhccccc--------CCCccChHHHHHHhhh
Q 009725 256 DEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTK--------NSVPLSLSSIYEEVIK 327 (527)
Q Consensus 256 ~~~~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~~~~~~~~--------~s~p~s~~~I~~~l~~ 327 (527)
.+++++|||||++|+++|||+.|+++|+.|+|..||+||++||++++..++....+ .|.|+|+.+|.+.|.+
T Consensus 98 ~d~~v~~rvN~erF~~~lRn~~lv~~a~~r~g~~ta~Vy~~~L~~~e~~~~~~~~~~~~~~~~~~s~~is~~dI~~~l~~ 177 (258)
T PF05645_consen 98 LDPDVVWRVNYERFLVHLRNQRLVDLAERRIGSVTAEVYRAMLKLSESKTPSCRDPPSGEEEKQPSVPISANDIARHLPK 177 (258)
T ss_dssp --TTTSEEE-HHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHCTTTTS-TT-SB------------EEHHHHHHTS-T
T ss_pred CCCCeEEEEEHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHhhccccCCcccccccccccccCCceecHHHHHHHCcc
Confidence 35789999999999999999999999999999999999999999998877554444 5899999999998843
Q ss_pred ccc---C-----------------------------CCCCHHHHHHHHHHhccCC--C----CCCCCCcEEEehHHHHHH
Q 009725 328 SEA---G-----------------------------RNMTLDHVRASLVQLGELS--F----VDASSDSYSIDFEKIIEI 369 (527)
Q Consensus 328 ~~~---~-----------------------------~~~~~~~i~~~L~~La~~~--~----~~~~~~~y~V~~~~i~~~ 369 (527)
.-+ + .+.+.++|.+||++||+++ | +.+|+|+|+|||+++++.
T Consensus 178 ~~dl~~~i~K~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~i~qhL~LLa~~~~~Fl~~~~~~g~g~~~V~f~~l~~~ 257 (258)
T PF05645_consen 178 DLDLSGSIGKRPSSNSSPPNPKKLKTEDSDDDDEDNDPSRLSLIDQHLKLLAEDPLPFLRKCGPSGGGQYTVDFKKLAEQ 257 (258)
T ss_dssp T---HHH-----------------------------------HHHHHHHHHCSTTT-BEEE----SS-EEEEBHHHHHHH
T ss_pred ccCcccccccccccccccccccccccccccccccccchhhHHHHHHHHHHHhCCChhhhheecCCCCcEEEeEHHHHHhh
Confidence 211 0 1223459999999999999 4 478899999999999987
Q ss_pred H
Q 009725 370 A 370 (527)
Q Consensus 370 l 370 (527)
|
T Consensus 258 L 258 (258)
T PF05645_consen 258 L 258 (258)
T ss_dssp H
T ss_pred C
Confidence 5
No 3
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=99.78 E-value=2.6e-19 Score=136.84 Aligned_cols=61 Identities=51% Similarity=0.695 Sum_probs=56.3
Q ss_pred HHHHHHHHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccc
Q 009725 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (527)
Q Consensus 8 ~Lc~~ii~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~ 68 (527)
+||+.|++++||++|++|+++|+++|++|+++|++.|++|+++||+||++|||||||.|+.
T Consensus 1 ~L~~~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 1 ELCTLIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 5999999999999999999999999999999999999999999999999999999999765
No 4
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=99.49 E-value=2.3e-14 Score=122.40 Aligned_cols=103 Identities=23% Similarity=0.401 Sum_probs=60.9
Q ss_pred HHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 374 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 374 ~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+..+++..||.+|.+|+++|..+|.+ ++++|++.++|+.+++|++|++|.+.|||..+..... .++++.|+|++|.+
T Consensus 2 L~~~v~r~~yg~~~~~Il~~L~~~~~l-~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~-~~~~~~~yw~i~~~ 79 (105)
T PF02002_consen 2 LLKEVVRAFYGEEAVRILDALLRKGEL-TDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDD-ERGWTRYYWYIDYD 79 (105)
T ss_dssp ----HHHTTS-STTHHHHHHHHHH--B--HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE---------EEEEE-THH
T ss_pred hHHHHHHHHcCchHHHHHHHHHHcCCc-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcC-CCcEEEEEEEEcHH
Confidence 567899999999999999999999998 9999999999999999999999999999999866543 78899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 009725 454 ILWKHVLDEMFHAALNLSLRVSYEL 478 (527)
Q Consensus 454 ~~~~~~~~~~yk~~~nl~~R~~~e~ 478 (527)
.+...+...++++..++..|++.|.
T Consensus 80 ~~~~~ik~r~~~~~~~l~~~l~~e~ 104 (105)
T PF02002_consen 80 QIIDVIKYRIYKMREKLKKRLEFEE 104 (105)
T ss_dssp HH------------------SSS--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999988765
No 5
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=98.91 E-value=1.2e-08 Score=93.30 Aligned_cols=106 Identities=16% Similarity=0.188 Sum_probs=93.5
Q ss_pred HHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 374 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 374 ~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+..++..-+|..+..|+..|..+|.+ .+++||+...|+.+++|++||+|.+.|+|. ..-.+....+|..|+|++|.+
T Consensus 3 ~~~~~~~~~~g~~~v~Vl~aL~~~~~~-tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~-~~r~r~~~~gw~~Y~w~i~~~ 80 (158)
T TIGR00373 3 LLNEVVGRAAEEEVGLVLFSLGIKGEF-TDEEISLELGIKLNEVRKALYALYDAGLAD-YKRRKDDETGWYEYTWRINYE 80 (158)
T ss_pred HHHHHHHHHcChhHHHHHHHHhccCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCce-eeeeeecCCCcEEEEEEeCHH
Confidence 456788999999999999999988888 999999999999999999999999999997 332222266889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 009725 454 ILWKHVLDEMFHAALNLSLRVSYELDRE 481 (527)
Q Consensus 454 ~~~~~~~~~~yk~~~nl~~R~~~e~~~~ 481 (527)
.+...+..++.+.+.++..++++|.++.
T Consensus 81 ~i~d~Ik~~~~~~~~~lk~~l~~e~~~~ 108 (158)
T TIGR00373 81 KALDVLKRKLEETAKKLREKLEFETNNM 108 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence 9999999999999999999998876544
No 6
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=98.85 E-value=2.5e-08 Score=92.85 Aligned_cols=109 Identities=17% Similarity=0.238 Sum_probs=93.2
Q ss_pred HHHHHHHHHHHHc--CCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEE
Q 009725 371 QNEEVESVVSKRY--GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLW 448 (527)
Q Consensus 371 r~~~le~~v~~~~--G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw 448 (527)
....+.+++.+-. |..+.+|+..|..+|.+ .+++||+...|+.+++|++|++|.++|+|....+... ..+|..|+|
T Consensus 6 ~~~~v~~~l~~~~~~~~~~~~Vl~~L~~~g~~-tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~-~~Gr~~y~w 83 (178)
T PRK06266 6 NNPLVQKVLFEIMEGDEEGFEVLKALIKKGEV-TDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDE-ETNWYTYTW 83 (178)
T ss_pred cCHHHHHHHHHHhcCCccHhHHHHHHHHcCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeecc-CCCcEEEEE
Confidence 3344455555555 77799999999998888 9999999999999999999999999999986543332 678999999
Q ss_pred EEchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 009725 449 KVNRQILWKHVLDEMFHAALNLSLRVSYELDRE 481 (527)
Q Consensus 449 ~v~~~~~~~~~~~~~yk~~~nl~~R~~~e~~~~ 481 (527)
+++.+++...+..++++...++..|+++|.+..
T Consensus 84 ~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~ 116 (178)
T PRK06266 84 KPELEKLPEIIKKKKMEELKKLKEQLEEEENNM 116 (178)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCC
Confidence 999999999999999999999999999987653
No 7
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=98.64 E-value=2.5e-07 Score=84.90 Aligned_cols=104 Identities=18% Similarity=0.296 Sum_probs=91.3
Q ss_pred HHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 374 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 374 ~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+.+++. |++|.+|+..|.++|.+ ++++|++...|..+++|.+||.|++.|+|..--.... .+.+..|+|+++.+
T Consensus 10 ~~~~i~~---g~~~~~v~~~l~~kge~-tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~-~~~~~~y~w~~~~~ 84 (176)
T COG1675 10 LLKSIVR---GDEAVLVVDALLEKGEL-TDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDE-ESGWEEYTWYINYE 84 (176)
T ss_pred HHHHHcc---CchhhHHHHHHHhcCCc-ChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeeccc-CCCcEEEEEEechH
Confidence 3444444 99999999999999877 9999999999999999999999999999976533222 66799999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009725 454 ILWKHVLDEMFHAALNLSLRVSYELDREK 482 (527)
Q Consensus 454 ~~~~~~~~~~yk~~~nl~~R~~~e~~~~k 482 (527)
.+..++.....+.+-+|..++++|.+++-
T Consensus 85 ~v~~~l~~~~~~~le~Lk~~le~~~~~~~ 113 (176)
T COG1675 85 KVLEVLKGKKRKILEKLKRKLEKETENNY 113 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCCc
Confidence 99999999999999999999999887763
No 8
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=98.37 E-value=8.4e-07 Score=80.34 Aligned_cols=93 Identities=15% Similarity=0.241 Sum_probs=77.4
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccC-CC-CceEEEEEEchHHHHHHHHHHHHH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG-AR-QSQFLLWKVNRQILWKHVLDEMFH 465 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~-~~-~~t~~lw~v~~~~~~~~~~~~~yk 465 (527)
.-|+..|..+|.+ .+++|++...|+.+++|++||+|.+++++...-....+ .. +++.|+|++|.+.+...+...+++
T Consensus 4 ~~v~d~L~~~~~~-~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 4 FLVLDALMRNGCV-TEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred EeehHHHHhcCCc-CHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHH
Confidence 4577778788887 99999999999999999999999998876444333222 33 389999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhh
Q 009725 466 AALNLSLRVSYELDRE 481 (527)
Q Consensus 466 ~~~nl~~R~~~e~~~~ 481 (527)
...++-.|+++|.++.
T Consensus 83 ~~~~L~~~l~~e~~~~ 98 (147)
T smart00531 83 MRKRLEDKLEDETNNA 98 (147)
T ss_pred HHHHHHHHHhcccCCc
Confidence 9999999998876543
No 9
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=98.03 E-value=8.6e-06 Score=69.39 Aligned_cols=89 Identities=18% Similarity=0.348 Sum_probs=56.3
Q ss_pred HHHHHHHHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEe
Q 009725 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVV 87 (527)
Q Consensus 8 ~Lc~~ii~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~ 87 (527)
+|...+++..||+-+..|..+|+.+|.++=.+|+..++++++.||..|..|.+.++|.+....+++ +.....+|.+
T Consensus 1 ~L~~~v~r~~yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~----~~~~~~yw~i 76 (105)
T PF02002_consen 1 ELLKEVVRAFYGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDE----RGWTRYYWYI 76 (105)
T ss_dssp -----HHHTTS-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE------------EEEEE-
T ss_pred ChHHHHHHHHcCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCC----CcEEEEEEEE
Confidence 366789999999999999999999999999999999999999999999999999999865433211 1344588999
Q ss_pred ehhhHHHHhchhh
Q 009725 88 LFDNILHRVRFAK 100 (527)
Q Consensus 88 ~~~~il~rlR~p~ 100 (527)
|++.+...+.+-.
T Consensus 77 ~~~~~~~~ik~r~ 89 (105)
T PF02002_consen 77 DYDQIIDVIKYRI 89 (105)
T ss_dssp THHHH--------
T ss_pred cHHHHHHHHHHHH
Confidence 9999888776543
No 10
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=97.67 E-value=0.007 Score=63.58 Aligned_cols=101 Identities=15% Similarity=0.218 Sum_probs=72.4
Q ss_pred ceEEEeehhHHHHHhhhhHHHHHHHhhcCccHHHHHHHHHHccchhhhcccccCCCccChHHHHHHhhhcccCCCCCHHH
Q 009725 259 SVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDH 338 (527)
Q Consensus 259 ~~~~rvN~e~f~~~lR~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~~~~~~~~~s~p~s~~~I~~~l~~~~~~~~~~~~~ 338 (527)
+-.|-|||.+.+.-++.-.+...|.++||+.|..++|.+.+... +.-..|.+.- -|....
T Consensus 368 ~G~yiV~y~k~i~vl~~~~~E~vI~~rfG~rAiRl~R~l~~k~~-------------veekqv~~~A-------lm~~Kd 427 (551)
T KOG2587|consen 368 GGMYIVNYHKAIAVLATATYESVIQERFGSRAIRLFRLLLQKKH-------------VEEKQVEDFA-------LMPAKD 427 (551)
T ss_pred CCEEEEEHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhccc-------------chHHHHHHhh-------cccccc
Confidence 45699999999999999999999999999999999999998542 2222222211 122334
Q ss_pred HHHHHHHhccCCC------C---CCCCC----cEEEehHHHHHHHHHHHHHHHH
Q 009725 339 VRASLVQLGELSF------V---DASSD----SYSIDFEKIIEIAQNEEVESVV 379 (527)
Q Consensus 339 i~~~L~~La~~~~------~---~~~~~----~y~V~~~~i~~~lr~~~le~~v 379 (527)
+.+.|..|.++++ + +.++. .|+||..+....|...++.++.
T Consensus 428 ~r~~L~~m~~~g~v~lQeVprTaD~~psrtF~L~~v~~~~a~~~lld~ly~~ia 481 (551)
T KOG2587|consen 428 ARDMLYKMLEEGYVELQEVPRTADRAPSRTFYLYTVNILRAYRMLLDELYKSIA 481 (551)
T ss_pred HHHHHHHHHHcCceeeeecCCCCCCCCcceEEEEEeccHHHHHHHHHHHHHHHH
Confidence 5566666666661 1 23332 6899999999999999886653
No 11
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=97.34 E-value=0.0022 Score=58.70 Aligned_cols=88 Identities=14% Similarity=0.097 Sum_probs=72.0
Q ss_pred HHHHHHHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEee
Q 009725 9 HAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL 88 (527)
Q Consensus 9 Lc~~ii~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~ 88 (527)
|.-..+...+|+..-.|...|+.+|.+|-.+|+..+|++.+.||.+|..|.-.|+|.|.....+++ +....+|.++
T Consensus 3 ~~~~~~~~~~g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~----gw~~Y~w~i~ 78 (158)
T TIGR00373 3 LLNEVVGRAAEEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDET----GWYEYTWRIN 78 (158)
T ss_pred HHHHHHHHHcChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCC----CcEEEEEEeC
Confidence 455678889999999999999999999999999999999999999999999999998654322221 2234566799
Q ss_pred hhhHHHHhchhh
Q 009725 89 FDNILHRVRFAK 100 (527)
Q Consensus 89 ~~~il~rlR~p~ 100 (527)
.+.++..+++-.
T Consensus 79 ~~~i~d~Ik~~~ 90 (158)
T TIGR00373 79 YEKALDVLKRKL 90 (158)
T ss_pred HHHHHHHHHHHH
Confidence 999888877653
No 12
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=97.23 E-value=0.00053 Score=52.40 Aligned_cols=60 Identities=18% Similarity=0.218 Sum_probs=53.0
Q ss_pred HHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEE
Q 009725 374 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 434 (527)
Q Consensus 374 ~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQE 434 (527)
....+|++-||+.+.+|+..|..+|.+ .-.+|.+.+-+|.+.+|+.|..|.+.|+|...+
T Consensus 2 L~~~ii~~~fG~~~~~V~~~Ll~~G~l-tl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 2 LCTLIIEEHFGEIVAKVGEVLLSRGRL-TLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC-SE-EHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcChHHHHHHHHHHHcCCc-CHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 356789999999999999999999999 999999999999999999999999999998754
No 13
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=96.64 E-value=0.013 Score=54.69 Aligned_cols=84 Identities=13% Similarity=0.163 Sum_probs=65.3
Q ss_pred HHHHhh--chhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehh
Q 009725 13 VITNHF--GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (527)
Q Consensus 13 ii~~~F--G~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (527)
++.+.. |+..-.|...|..+|.+|-.+|+..++++...||..|..|...|+|.|.....++. .....+|.++.+
T Consensus 13 ~l~~~~~~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~----Gr~~y~w~l~~~ 88 (178)
T PRK06266 13 VLFEIMEGDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEET----NWYTYTWKPELE 88 (178)
T ss_pred HHHHHhcCCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCC----CcEEEEEEeCHH
Confidence 344444 77788999999999999999999999999999999999999999999644322121 234567778888
Q ss_pred hHHHHhchhh
Q 009725 91 NILHRVRFAK 100 (527)
Q Consensus 91 ~il~rlR~p~ 100 (527)
.+...+++-.
T Consensus 89 ~i~d~ik~~~ 98 (178)
T PRK06266 89 KLPEIIKKKK 98 (178)
T ss_pred HHHHHHHHHH
Confidence 8777766543
No 14
>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=96.01 E-value=0.021 Score=44.24 Aligned_cols=46 Identities=30% Similarity=0.361 Sum_probs=44.4
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.=++|..+|+.+|+.|..+|++.++++.+.|..+|-.|.+.|+|.
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 6778999999999999999999999999999999999999999998
No 15
>PHA02943 hypothetical protein; Provisional
Probab=95.60 E-value=0.084 Score=47.08 Aligned_cols=73 Identities=23% Similarity=0.367 Sum_probs=60.8
Q ss_pred HHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHHHHHHHHHHHHH
Q 009725 390 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALN 469 (527)
Q Consensus 390 I~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~~~~~~yk~~~n 469 (527)
|+++| +.|.- ...+|++...++-..|+-.||.|.++|.| ++|+++ .+=+|.++.+ .+...+.++++.+..
T Consensus 16 ILE~L-k~G~~-TtseIAkaLGlS~~qa~~~LyvLErEG~V--krV~~G-----~~tyw~l~~d-ay~~~v~~~~Relwr 85 (165)
T PHA02943 16 TLRLL-ADGCK-TTSRIANKLGVSHSMARNALYQLAKEGMV--LKVEIG-----RAAIWCLDED-AYTNLVFEIKRELWR 85 (165)
T ss_pred HHHHH-hcCCc-cHHHHHHHHCCCHHHHHHHHHHHHHcCce--EEEeec-----ceEEEEEChH-HHHHHHHHHHHHHHH
Confidence 67777 66777 99999999999999999999999999999 567776 4668999974 566668888888877
Q ss_pred HHH
Q 009725 470 LSL 472 (527)
Q Consensus 470 l~~ 472 (527)
++.
T Consensus 86 lv~ 88 (165)
T PHA02943 86 LVC 88 (165)
T ss_pred HHH
Confidence 653
No 16
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.59 E-value=0.017 Score=44.97 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=40.5
Q ss_pred HHHHHHHHHhCC--CcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 388 YRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 388 ~RI~r~l~~k~~--l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
-+|+.+|...|. + ..++|++...|+.+.++..||+|.++|||.-
T Consensus 9 ~~IL~~L~~~g~~~~-ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 9 EKILEFLENSGDETS-TALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHCCCCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 478999988877 7 9999999999999999999999999999954
No 17
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=95.08 E-value=0.1 Score=54.23 Aligned_cols=142 Identities=13% Similarity=0.160 Sum_probs=101.8
Q ss_pred HHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCce---EEEEE
Q 009725 373 EEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQ---FLLWK 449 (527)
Q Consensus 373 ~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t---~~lw~ 449 (527)
..+.-+|+-.||..++=|+..|+..+.+ -|+++++..-++.|++|.++..|-.+.||.++-..-++..+|+ .-+|+
T Consensus 17 ~l~k~vvr~fy~~~~~lild~llr~~~v-~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr~~~~~~Yyy 95 (436)
T KOG2593|consen 17 DLLKKVVRGFYGGEHVLILDALLRRQCV-REEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGRAVDKHTYYY 95 (436)
T ss_pred HHHHHHHHhcccchhHHHHHHHHHhhhc-chHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCcceeeeEEEE
Confidence 3445567888999999999999999888 9999999999999999999999999999988743334322333 35788
Q ss_pred EchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccc-----------------c------------------cccCCh
Q 009725 450 VNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNL-----------------P------------------ADKRTG 494 (527)
Q Consensus 450 v~~~~~~~~~~~~~yk~~~nl~~R~~~e~~~~k~ll~k-----------------~------------------~~~~~~ 494 (527)
+|+.+++..+.=. +..+..|++.+.......-.- . ..+..|
T Consensus 96 InY~~~idvVKyK----lh~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~ 171 (436)
T KOG2593|consen 96 INYAQVIDVVKYK----LHQMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLP 171 (436)
T ss_pred eehHHHHHHHHHH----HHHHHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCc
Confidence 9988766665544 445666666665544332110 0 001113
Q ss_pred hh--HHHHHHHHHHHHHHHHHHhhhhh
Q 009725 495 PL--QDRYNRIRKVRILLESSQMKLDD 519 (527)
Q Consensus 495 ~e--~~~l~~~~~~~~~L~~~~~rlD~ 519 (527)
++ +..+.++.+..+-|...+.++|.
T Consensus 172 ~~e~~~~l~~~~~Q~~pi~d~Lk~~e~ 198 (436)
T KOG2593|consen 172 SKESRTALNRLMEQLEPIIDLLKELEG 198 (436)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33 33588899999999999888887
No 18
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=94.93 E-value=0.07 Score=48.28 Aligned_cols=74 Identities=16% Similarity=0.354 Sum_probs=54.1
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccc--ccccccccCCCCCCCCCcceEEEeehhhHHHHhchhh
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNC--VQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~--V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~ 100 (527)
.|...|+.+|.+|=.+|+..++++.+.||..|..|-.+++ +.|-..-.++ +.....++|.+|.+.+...+++-.
T Consensus 5 ~v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~---~~~~~~~yw~i~y~~~~~vik~r~ 80 (147)
T smart00531 5 LVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPE---TKTWYRYYWYINYDTLLDVVKYKL 80 (147)
T ss_pred eehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCC---CceEEEEEEEecHHHHHHHHHHHH
Confidence 4778899999999999999999999999999999999555 5432222111 111334567788888777776643
No 19
>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=94.73 E-value=0.049 Score=39.03 Aligned_cols=43 Identities=16% Similarity=0.321 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+|+..|.+++.+ ..++|++...++...+...|.+|.++|+|+
T Consensus 6 ~~Il~~l~~~~~~-t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPRI-TQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTTS--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 5899999998888 999999999999999999999999999985
No 20
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.60 E-value=0.16 Score=40.92 Aligned_cols=75 Identities=19% Similarity=0.221 Sum_probs=56.8
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhhHHH
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLT 103 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~ 103 (527)
.|..+|...+.+++.+|...++++...+..-|-.|...|+|.... ...+ .++.++|++-..+ +-.|.+|+.
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k-~~~~-----~~p~t~~~lT~~G---r~~~~~~~~ 74 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEK-EFEG-----RRPRTWYSLTDKG---REAFERYVA 74 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEE-E-SS-----S--EEEEEE-HHH---HHHHHHHHH
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEE-eccC-----CCCeEEEEECHHH---HHHHHHHHH
Confidence 477889999999999999999999999999999999999998533 3222 3346899999887 666777777
Q ss_pred HHHH
Q 009725 104 ILSQ 107 (527)
Q Consensus 104 ~i~~ 107 (527)
..+.
T Consensus 75 ~L~~ 78 (80)
T PF13601_consen 75 ALRE 78 (80)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6654
No 21
>PHA02943 hypothetical protein; Provisional
Probab=94.39 E-value=0.75 Score=41.17 Aligned_cols=102 Identities=17% Similarity=0.149 Sum_probs=69.8
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhhHH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFL 102 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i 102 (527)
..|-++| ..|..|..+|++.+|+|..+++..|.+|-.-|+|.- ... +..++|.++.++..+.
T Consensus 14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr--V~~--------G~~tyw~l~~day~~~------- 75 (165)
T PHA02943 14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK--VEI--------GRAAIWCLDEDAYTNL------- 75 (165)
T ss_pred HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE--Eee--------cceEEEEEChHHHHHH-------
Confidence 3566677 889999999999999999999999999999999983 221 2258999998765544
Q ss_pred HHHHHHhhhhHHHHHHHHHHccc---CCHHHHHHHhhhcccCCCccCHHHHHHHHHHHH
Q 009725 103 TILSQEFDQQCVELVQGLLEHGR---LTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLV 158 (527)
Q Consensus 103 ~~i~~~yG~~a~~I~~~lL~~G~---~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv 158 (527)
+.+-+-+ +..++.+.+ ++++++..-+..+ .+..+.|.++|
T Consensus 76 --v~~~~Re-----lwrlv~s~~~kfi~p~~l~~li~kd---------~~a~~~~ak~v 118 (165)
T PHA02943 76 --VFEIKRE-----LWRLVCNSRLKFITPSRLLRLIAKD---------TEAHNIFAKYV 118 (165)
T ss_pred --HHHHHHH-----HHHHHHhccccccChHHHHHHHHhC---------HHHHHHHHHhc
Confidence 3222211 133444444 4577777776543 23566665543
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.33 E-value=0.12 Score=40.19 Aligned_cols=46 Identities=24% Similarity=0.259 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHhcCC--CCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~--~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.-.+|..+|..+|. +|..+|++..+++.+.|+..|..|..+|+|.
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 345689999999988 9999999999999999999999999999997
No 23
>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=93.08 E-value=0.13 Score=39.75 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=42.9
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEE
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 434 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQE 434 (527)
.+|+..|+.+|.. +.++|++..-+|...+...|.+|.+.|+|+..+
T Consensus 11 ~~vy~~Ll~~~~~-t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 11 AKVYLALLKNGPA-TAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHCHE-EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 6899999988999 999999999999999999999999999997665
No 24
>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=92.88 E-value=0.28 Score=35.02 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=38.8
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
-.+|..+|..+|++|..+|++.++++...|...|--|...|+|.
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 45788999999999999999999999999999999999999873
No 25
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.64 E-value=0.95 Score=39.54 Aligned_cols=61 Identities=25% Similarity=0.356 Sum_probs=52.7
Q ss_pred HHHHHHHhhc--hhHHHHHHHHH-hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccc
Q 009725 10 AVHVITNHFG--DLVAKVCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (527)
Q Consensus 10 c~~ii~~~FG--~~v~~V~~~Ll-~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~ 70 (527)
|..+|+=.|| +.=-.|...|+ .+|++|..+|+...+.+.+.|-.||--|+.-|+|.--..+
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeec
Confidence 5567777788 66667899999 7999999999999999999999999999999999854444
No 26
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=92.38 E-value=2.1 Score=38.09 Aligned_cols=120 Identities=24% Similarity=0.314 Sum_probs=80.7
Q ss_pred HHHHHHHHHh-------cCCCCHHHHHhhc----------CCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceE
Q 009725 22 VAKVCECLLR-------KGPLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQ 84 (527)
Q Consensus 22 v~~V~~~Ll~-------~G~~tl~~i~~~t----------~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~ 84 (527)
-++|..+|+. +-++||..|.-.+ +++...|..+|=.|...++|.- ... + .+ +..
T Consensus 5 E~RVLG~LiEK~~TTPd~YPLtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~-~~~--g-----sR-v~k 75 (148)
T PF04337_consen 5 EARVLGCLIEKEVTTPDQYPLTLNALTTACNQKSNREPVMNLSESEVQAALDELRAKGLVRE-SGF--G-----SR-VAK 75 (148)
T ss_dssp HHHHHHHHHHHHHH-GGG-SEEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEE--E---------SS---E
T ss_pred HhhHHHhhheecccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHHCcCeee-cCC--C-----cc-hHH
Confidence 3556666664 3588999997664 3678999999999999999973 222 1 12 578
Q ss_pred EEeehhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcc--c
Q 009725 85 YVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAH--Y 162 (527)
Q Consensus 85 Y~~~~~~il~rlR~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~--~ 162 (527)
|+=+..+. -.+......|+-.||..|-.|+.++-.+..--. +..+.++++..+..|++.+ +
T Consensus 76 y~Hr~~~~--------------l~l~~~e~All~~LlLRGpQT~GELR~Rs~Rl~---~F~d~~~Ve~~L~~L~~r~~pl 138 (148)
T PF04337_consen 76 YEHRFCNT--------------LQLSPQELALLCLLLLRGPQTPGELRTRSERLH---EFADVAEVEAVLERLAEREPPL 138 (148)
T ss_dssp EEE-HHHH--------------HT--HHHHHHHHHHHHH-SB-HHHHHHHHTTTS-----SSHHHHHHHHHHHHHTT--S
T ss_pred HHhhhhhh--------------cCCCHHHHHHHHHHHHcCCCchhHHHhhhcccc---CCCCHHHHHHHHHHHHhccchh
Confidence 98776665 134566788999999999999999988764311 2447889999999999999 8
Q ss_pred ceecC
Q 009725 163 VERCP 167 (527)
Q Consensus 163 i~~v~ 167 (527)
+.+.|
T Consensus 139 V~~Lp 143 (148)
T PF04337_consen 139 VVKLP 143 (148)
T ss_dssp EEEE-
T ss_pred heecC
Confidence 87776
No 27
>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=92.25 E-value=2.7 Score=40.04 Aligned_cols=66 Identities=15% Similarity=0.144 Sum_probs=51.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
-..|...|..+|++|..+|...+++++..|+..|-.|.+.|+|.......+. .+....|.+...+.
T Consensus 3 r~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~-----gRp~~~y~LT~~G~ 68 (203)
T TIGR02702 3 KEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGM-----GRPQYHYQLSRQGR 68 (203)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCC-----CCCceEEEECcchh
Confidence 3578889999999999999999999999999999999999999843221111 22245677776653
No 28
>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=92.01 E-value=0.24 Score=36.18 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=37.7
Q ss_pred HHHHHHHHHhcCC-CCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 22 VAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 22 v~~V~~~Ll~~G~-~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+-.|.++|...+. +|+.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 3456777777765 7999999999999999999999999999996
No 29
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=91.85 E-value=0.21 Score=38.04 Aligned_cols=56 Identities=25% Similarity=0.344 Sum_probs=41.0
Q ss_pred HHHHHHH-hCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEc
Q 009725 390 IFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 451 (527)
Q Consensus 390 I~r~l~~-k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~ 451 (527)
|+.+|.. ++-+ ...+||+.+.|+...||..|..|.++|.|+-.++.|+ . + + +|+++
T Consensus 5 Il~~i~~~~~p~-~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG-~-~-~--~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPL-KTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRG-K-S-T--YWRLN 61 (62)
T ss_dssp HHHHHHHHTS-E-EHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSS-S-S----EEEES
T ss_pred HHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCC-c-c-e--eeeec
Confidence 5556655 4555 9999999999999999999999999999855544444 2 2 2 59886
No 30
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=91.76 E-value=1.7 Score=37.65 Aligned_cols=64 Identities=11% Similarity=0.090 Sum_probs=51.6
Q ss_pred hhc-hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehh
Q 009725 17 HFG-DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (527)
Q Consensus 17 ~FG-~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (527)
.+| |.=-+|...|...|..+..+|+..++++++.|-+=|-+|.+-|+|.. ... + ...+|.+|.+
T Consensus 12 aLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~-~r~--G-------r~~~Y~l~~~ 76 (117)
T PRK10141 12 ILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLD-RKQ--G-------KWVHYRLSPH 76 (117)
T ss_pred HhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEE-EEE--c-------CEEEEEECch
Confidence 344 34447888888889999999999999999999999999999999973 222 1 1578999975
No 31
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=91.63 E-value=0.77 Score=34.05 Aligned_cols=57 Identities=19% Similarity=0.218 Sum_probs=44.7
Q ss_pred HHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 25 V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
|..+|. .+++|+.+|.+.++++...+...|-.|.+.|++...... + ..+|.++.+..
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~---------~-~~~~~~~~~~~ 58 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG---------K-RVYYSLTDEKV 58 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC---------C-EEEEEEchHHH
Confidence 456666 889999999999999999999999999999999732211 1 35677776533
No 32
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=91.38 E-value=0.7 Score=48.19 Aligned_cols=101 Identities=13% Similarity=0.293 Sum_probs=79.5
Q ss_pred HHHHHHHHHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEE
Q 009725 7 TKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYV 86 (527)
Q Consensus 7 ~~Lc~~ii~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~ 86 (527)
.+|.-..++..||..+.-|..+|++++++.=.+|....+++.+++|.-|..|--..+|...+.......|.....++||.
T Consensus 16 ~~l~k~vvr~fy~~~~~lild~llr~~~v~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr~~~~~~Yyy 95 (436)
T KOG2593|consen 16 NDLLKKVVRGFYGGEHVLILDALLRRQCVREEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGRAVDKHTYYY 95 (436)
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHhhhcchHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCcceeeeEEEE
Confidence 36777788999999999999999999999999999999999999999999999888888433221111121121258999
Q ss_pred eehhhHHHHhchhhHHHHHHHHh
Q 009725 87 VLFDNILHRVRFAKFLTILSQEF 109 (527)
Q Consensus 87 ~~~~~il~rlR~p~~i~~i~~~y 109 (527)
+|+..++..+||- |+++++++
T Consensus 96 InY~~~idvVKyK--lh~m~krl 116 (436)
T KOG2593|consen 96 INYAQVIDVVKYK--LHQMRKRL 116 (436)
T ss_pred eehHHHHHHHHHH--HHHHHHHH
Confidence 9999999999886 55665555
No 33
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=91.08 E-value=2.7 Score=36.76 Aligned_cols=96 Identities=19% Similarity=0.328 Sum_probs=68.6
Q ss_pred HHHHHHHHcCCch--HHHHHHHH-HhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEE-EE
Q 009725 375 VESVVSKRYGRDA--YRIFRLLS-KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLW-KV 450 (527)
Q Consensus 375 le~~v~~~~G~~~--~RI~r~l~-~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw-~v 450 (527)
+++++.=-||-.- ..++-.|+ ..|.+ +.++||+..-.+...+.+.|.+|...|+|+=--++- ..++..|+| -+
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~-tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~--~~Ggy~yiY~~i 91 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLEENGPL-TVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL--KGGGYYYLYKPI 91 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHhhcCCc-CHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc--CCCceeEEEecC
Confidence 3444444455443 35677777 56788 999999999999999999999999999994332221 456778888 89
Q ss_pred chHHHHHHHHH---HHHHHHHHHHHH
Q 009725 451 NRQILWKHVLD---EMFHAALNLSLR 473 (527)
Q Consensus 451 ~~~~~~~~~~~---~~yk~~~nl~~R 473 (527)
+++.+...++. ++|..+..+++.
T Consensus 92 ~~ee~k~~i~~~l~~w~~~~~~~i~~ 117 (126)
T COG3355 92 DPEEIKKKILKDLDEWYDKMKQLIEE 117 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99988866655 455555544443
No 34
>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=90.76 E-value=0.22 Score=36.38 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=40.5
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+.+|+++|...+.-+.-.+|++...+|...+..+|..|...|||+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 4788999998777644999999999999999999999999999995
No 35
>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=90.13 E-value=1.7 Score=33.26 Aligned_cols=47 Identities=21% Similarity=0.161 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
+....|..++...+ .+..+|.+.++++...+...|-.|.++|++...
T Consensus 7 ~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 7 PTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred hHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEE
Confidence 45667888877776 999999999999999999999999999999843
No 36
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=89.84 E-value=2.4 Score=39.36 Aligned_cols=80 Identities=16% Similarity=0.331 Sum_probs=61.8
Q ss_pred HHHhh-chhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 14 ITNHF-GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 14 i~~~F-G~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
+...+ |+-+-.|+.+|+.+|-.|=.+|+..+++....||..|..|--.|++.|-..-.+.. .-...+|.++.+.+
T Consensus 11 ~~~i~~g~~~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~----~~~~y~w~~~~~~v 86 (176)
T COG1675 11 LKSIVRGDEAVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEES----GWEEYTWYINYEKV 86 (176)
T ss_pred HHHHccCchhhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCC----CcEEEEEEechHHH
Confidence 33434 99999999999999999999999999999999999999999999999533221111 23346677777776
Q ss_pred HHHhc
Q 009725 93 LHRVR 97 (527)
Q Consensus 93 l~rlR 97 (527)
...++
T Consensus 87 ~~~l~ 91 (176)
T COG1675 87 LEVLK 91 (176)
T ss_pred HHHHH
Confidence 65554
No 37
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=89.84 E-value=3.9 Score=35.06 Aligned_cols=100 Identities=19% Similarity=0.255 Sum_probs=70.4
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhc----CCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehh-hHH
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYT----ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD-NIL 93 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t----~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~-~il 93 (527)
|+.=..|.++|=.+|++|..+|.... +.+++.|+..|-.|.+-|+|.+.... + ...|.+... +-+
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g---------r-~~~Y~p~is~~e~ 71 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG---------R-AYVYSPLISREEY 71 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET---------T-CEEEEESSSHHHH
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecC---------C-ceEEEeCCcHHHH
Confidence 44456789999999999999998774 47799999999999999999853322 1 245665533 333
Q ss_pred HHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHH
Q 009725 94 HRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 131 (527)
Q Consensus 94 ~rlR~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~l 131 (527)
..-... .+++..||.....++..|+....++.+++
T Consensus 72 ~~~~~~---~~l~~~~~gs~~~l~~~l~~~~~ls~~el 106 (115)
T PF03965_consen 72 LAQELR---QFLDRLFDGSIPQLVAALVESEELSPEEL 106 (115)
T ss_dssp HHHHHH---HHHHHHSTTHHHHHHHHHHHCT-S-HHHH
T ss_pred HHHHHH---HHHHHHhCCCHHHHHHHHHhcCCCCHHHH
Confidence 333333 34566788889999999999998887766
No 38
>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=89.83 E-value=0.58 Score=33.34 Aligned_cols=42 Identities=26% Similarity=0.322 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.+|...|.. |+++..+|++.++++.+.|.+-|-.|...|+|.
T Consensus 5 ~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 356666665 999999999999999999999999999999986
No 39
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=89.79 E-value=3.1 Score=33.94 Aligned_cols=67 Identities=13% Similarity=0.152 Sum_probs=52.3
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
...--.|...|..+|..+..+|.+.++++...|...|-.|.+.|+|....... ++...+|.+...+.
T Consensus 9 ~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~-------~~r~~~~~lT~~g~ 75 (101)
T smart00347 9 TPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPE-------DRRSVLVSLTEEGR 75 (101)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCC-------CCCeEEEEECHhHH
Confidence 35566788888889999999999999999999999999999999998443321 12246677766553
No 40
>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=89.30 E-value=0.67 Score=35.99 Aligned_cols=47 Identities=19% Similarity=0.303 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
..|-++|-.+|+.|+.+|++..++++..|+.-|-.|++-|.|.-...
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 35778899999999999999999999999999999999999984433
No 41
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.25 E-value=1 Score=32.17 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.|..+|..+|..+..+|.+..+++...|+..|-.|.+.|+|.
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 467777888999999999999999999999999999999997
No 42
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=89.14 E-value=5.8 Score=34.96 Aligned_cols=98 Identities=17% Similarity=0.277 Sum_probs=69.8
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhh----cCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehh-hHHHH
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRY----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD-NILHR 95 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~----t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~-~il~r 95 (527)
.=-.|..+|-..|+.|..+|... .++++..|...|-.|.+.|+|.+ ... .+ ...|++... +-+..
T Consensus 5 ~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~-~k~--------gr-~~~Y~p~vs~ee~~~ 74 (130)
T TIGR02698 5 AEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTT-EKE--------GR-KFIYTALVSEDEAVE 74 (130)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceee-ecC--------CC-cEEEEecCCHHHHHH
Confidence 33467888889999999997655 46899999999999999999984 322 12 246774322 32322
Q ss_pred hchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHH
Q 009725 96 VRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 131 (527)
Q Consensus 96 lR~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~l 131 (527)
-... .+++..||.....++..|+....++..++
T Consensus 75 ~~~~---~~~~~~f~gs~~~ll~~l~~~~~ls~eel 107 (130)
T TIGR02698 75 NAAQ---ELFSRICSRKVGAVIADLIEESPLSQTDI 107 (130)
T ss_pred HHHH---HHHHHHHCCCHHHHHHHHHhcCCCCHHHH
Confidence 2233 34455788888899999999888887665
No 43
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=88.19 E-value=5.2 Score=37.70 Aligned_cols=84 Identities=13% Similarity=0.190 Sum_probs=51.7
Q ss_pred HHHHHhCCCcchhhh----hhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHH--HHHHHHHHH
Q 009725 392 RLLSKSGRLLETDKI----SDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILW--KHVLDEMFH 465 (527)
Q Consensus 392 r~l~~k~~l~eek~i----~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~--~~~~~~~yk 465 (527)
.++.+.+....-|+| .+.+.|....++++|..|..+|.|+.- --+.+.|+|...-.... ..-++.+-+
T Consensus 3 ~~f~e~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~E------KiGssn~YWsFps~~~~~~~~~~~~l~~ 76 (188)
T PF03962_consen 3 EIFHESKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVE------KIGSSNYYWSFPSQAKQKRQNKLEKLQK 76 (188)
T ss_pred HHHhhcCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhh------hccCeeEEEecChHHHHHHHHHHHHHHH
Confidence 444444444455554 455899999999999999999999544 33456788887654432 444444444
Q ss_pred HHHHHHHHHHHHHHhh
Q 009725 466 AALNLSLRVSYELDRE 481 (527)
Q Consensus 466 ~~~nl~~R~~~e~~~~ 481 (527)
.+.++..++....+..
T Consensus 77 ~~~~~~~~i~~l~~~i 92 (188)
T PF03962_consen 77 EIEELEKKIEELEEKI 92 (188)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5555544444433333
No 44
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2XV4_S 2XUB_A.
Probab=88.11 E-value=0.92 Score=45.00 Aligned_cols=42 Identities=14% Similarity=0.382 Sum_probs=37.5
Q ss_pred CcEEEehHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhC
Q 009725 357 DSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSG 398 (527)
Q Consensus 357 ~~y~V~~~~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~ 398 (527)
=.|.|||+++...+|...+.+.++.|+|..++.|++.+++-.
T Consensus 102 v~~rvN~erF~~~lRn~~lv~~a~~r~g~~ta~Vy~~~L~~~ 143 (258)
T PF05645_consen 102 VVWRVNYERFLVHLRNQRLVDLAERRIGSVTAEVYRAMLKLS 143 (258)
T ss_dssp TSEEE-HHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHCT
T ss_pred eEEEEEHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHhhc
Confidence 369999999999999999999999999999999999998753
No 45
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=87.87 E-value=1.8 Score=33.03 Aligned_cols=56 Identities=20% Similarity=0.191 Sum_probs=41.2
Q ss_pred HHHHHHh-cCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEee
Q 009725 25 VCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL 88 (527)
Q Consensus 25 V~~~Ll~-~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~ 88 (527)
|-.+|-. +++++-.+|+..++++..++|.=|..|.+.|.|. ..+.. .+..++|.++
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~-~~~~~-------rG~~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE-RSPVR-------RGKSTYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE-EES-S-------SSSS-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCC-------CCcceeeeec
Confidence 4556666 8999999999999999999999999999999997 33322 1224677765
No 46
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=87.66 E-value=1.7 Score=39.86 Aligned_cols=48 Identities=23% Similarity=0.252 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHh-cCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 20 DLVAKVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 20 ~~v~~V~~~Ll~-~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
..|+.|..+|.- ++++|+.+|...+|++.+.|-.+|-.|.--|+|..-
T Consensus 26 rtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 26 RTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred chHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 356777777766 899999999999999999999999999999999953
No 47
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.63 E-value=3.1 Score=46.25 Aligned_cols=138 Identities=17% Similarity=0.224 Sum_probs=97.3
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEee--hhhHHHHhchhhH
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL--FDNILHRVRFAKF 101 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~--~~~il~rlR~p~~ 101 (527)
.|+.....+-.+|+.+|...|+|+...++..|..|+-.+++.- ..+ +..+. +.+.|.+| ......|++++-.
T Consensus 612 ~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l-~~~--~~~~~---p~~~fy~ne~f~~~~~rIki~~~ 685 (773)
T COG5647 612 LVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVL-LKD--DKLVS---PNTKFYVNENFSSKLERIKINYI 685 (773)
T ss_pred HHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheeee-ccc--cccCC---CCceEEEccccccccceeeeccc
Confidence 3444445566999999999999999999999999999998873 222 11111 12456666 3467777777766
Q ss_pred HHHHHHH--------hh-----hhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 102 LTILSQE--------FD-----QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 102 i~~i~~~--------yG-----~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
..-.... +. ..-++|+--+=..++++-.++++.+......--..+...++.++..|++.+||+|..
T Consensus 686 ~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~ 764 (773)
T COG5647 686 AESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQA 764 (773)
T ss_pred ccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 4332211 11 235778888888999999999998875422111336889999999999999999963
No 48
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=87.57 E-value=0.85 Score=35.06 Aligned_cols=54 Identities=28% Similarity=0.375 Sum_probs=48.3
Q ss_pred HHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccccc
Q 009725 15 TNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
++..|..++.|-+.|-.+|.+|+.+|.+.++++.+.+-.||==|.+-|=|. +..
T Consensus 3 ~~~IG~nAG~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~-~~~ 56 (65)
T PF10771_consen 3 KENIGENAGKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIE-FEE 56 (65)
T ss_dssp HHHHHHHHHHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE-EEE
T ss_pred hhHHHHHHHHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee-EEe
Confidence 355899999999999999999999999999999999999999999999886 443
No 49
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=87.19 E-value=5.3 Score=37.67 Aligned_cols=136 Identities=15% Similarity=0.156 Sum_probs=90.7
Q ss_pred HHHHHHHHHccchhhhcccccCCCc-cChHHHHHHhhhcccCCCCCHHHHHHHHHHhccCC------C-CCCCCCcEEEe
Q 009725 291 ANVLSAMLQATSSAEKKVKTKNSVP-LSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELS------F-VDASSDSYSID 362 (527)
Q Consensus 291 ~~v~~~~L~~~~~~~~~~~~~~s~p-~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~------~-~~~~~~~y~V~ 362 (527)
..+++|+|-.+ ..| +|+.+|.+-+.. ..+.+...|..|..+- + ...-+|.|.+-
T Consensus 6 ~~~iEA~LF~s-----------g~pgls~~~La~~l~~-------~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~ 67 (188)
T PRK00135 6 KSIIEALLFVS-----------GEEGLSLEQLAEILEL-------EPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLV 67 (188)
T ss_pred HHHHHHHHHHc-----------CCCCCCHHHHHHHHCC-------CHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEE
Confidence 34677777764 234 999999987732 2345666666664431 1 12335668887
Q ss_pred hHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCC
Q 009725 363 FEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQ 442 (527)
Q Consensus 363 ~~~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~ 442 (527)
.+.-..-.....+..--..++...++.++.++.-++-+ ...+|++.-.++. -.++.+|.+.|+|. |..+...++
T Consensus 68 tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPi-Tr~eI~~irGv~~---~~ii~~L~~~gLI~--e~gr~~~~G 141 (188)
T PRK00135 68 TKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPI-TRIEIDEIRGVNS---DGALQTLLAKGLIK--EVGRKEVPG 141 (188)
T ss_pred EcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCc-CHHHHHHHHCCCH---HHHHHHHHHCCCeE--EcCcCCCCC
Confidence 77666555555444433447899999999999887777 9999999998885 79999999999994 343333334
Q ss_pred ceEEEEEEc
Q 009725 443 SQFLLWKVN 451 (527)
Q Consensus 443 ~t~~lw~v~ 451 (527)
+ -++|.+.
T Consensus 142 r-p~ly~tT 149 (188)
T PRK00135 142 R-PILYGTT 149 (188)
T ss_pred C-Ceeeehh
Confidence 3 3444444
No 50
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=87.11 E-value=4.6 Score=39.78 Aligned_cols=50 Identities=24% Similarity=0.318 Sum_probs=46.7
Q ss_pred Hhhc--hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 16 NHFG--DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 16 ~~FG--~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.|| +-=++|..+|+.+|+.|..+|++.+++|..+|-..|-.|..-|+|.
T Consensus 10 ~~lGlt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~ 61 (247)
T COG1378 10 QKLGLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVE 61 (247)
T ss_pred HHcCCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEE
Confidence 3444 7789999999999999999999999999999999999999999998
No 51
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.82 E-value=3.5 Score=34.71 Aligned_cols=63 Identities=11% Similarity=0.187 Sum_probs=50.6
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce-EEEEec-cC--CCCceEEEEEEc
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL-MEKLVV-TG--ARQSQFLLWKVN 451 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~-lQEvpk-t~--~~~~t~~lw~v~ 451 (527)
.+|++.|...+.. .-.+|++...++...+++.+.+|.+.|+|. ..-... .. .+...+..|.++
T Consensus 6 ~~il~~L~~~~~~-~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~ 72 (108)
T smart00344 6 RKILEELQKDARI-SLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLE 72 (108)
T ss_pred HHHHHHHHHhCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEEC
Confidence 5899999888888 999999999999999999999999999997 332222 11 344566778877
No 52
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.81 E-value=1.8 Score=35.13 Aligned_cols=45 Identities=22% Similarity=0.186 Sum_probs=40.4
Q ss_pred HHHHHHHHHhc-CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 22 VAKVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 22 v~~V~~~Ll~~-G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
+-.|..+|..+ |++|+.+|++.++++.+.|..-|-.|.++|++..
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 45677778777 8999999999999999999999999999999973
No 53
>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=86.40 E-value=1.5 Score=33.07 Aligned_cols=51 Identities=22% Similarity=0.324 Sum_probs=43.4
Q ss_pred CchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEe
Q 009725 385 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 436 (527)
Q Consensus 385 ~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvp 436 (527)
+.-.+|++.|...+.+ .-.+|++...+|...+..-|..|.+.|+|+.....
T Consensus 10 p~R~~Il~~L~~~~~~-t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~g 60 (61)
T PF12840_consen 10 PTRLRILRLLASNGPM-TVSELAEELGISQSTVSYHLKKLEEAGLIEVEREG 60 (61)
T ss_dssp HHHHHHHHHHHHCSTB-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHhcCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeccC
Confidence 3446889999777788 99999999999999999999999999999877543
No 54
>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=86.33 E-value=3.1 Score=31.28 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=42.2
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
|.--+|...|...|++|..+|.+.++++...+..-|-.|...|+|.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 6677888888899999999999999999999999999999999997
No 55
>PRK11239 hypothetical protein; Provisional
Probab=86.32 E-value=14 Score=35.15 Aligned_cols=123 Identities=27% Similarity=0.379 Sum_probs=88.1
Q ss_pred hchhHHHHHHHHHhc-------CCCCHHHHHhhc----------CCCHHHHHHHHHHHHhcccccccccccCCCCCCCCC
Q 009725 18 FGDLVAKVCECLLRK-------GPLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPK 80 (527)
Q Consensus 18 FG~~v~~V~~~Ll~~-------G~~tl~~i~~~t----------~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~ 80 (527)
+-+.-++|..||+.+ -++||..|.-.+ +++-.+|..+|=.|...++|.-.... + .
T Consensus 5 Ls~~EaRVlG~LiEKe~TTPd~YPLSLNaL~~aCNQKsnRePVm~lsE~eV~~ald~L~~~~Lv~~~~~~--g-----s- 76 (215)
T PRK11239 5 LTALEARVIGCLLEKQVTTPEQYPLSVNGVVTACNQKTNREPVMNLSESEVQEQLDNLVKRHYLRTVSGF--G-----N- 76 (215)
T ss_pred cCHHHHHHHHHhhhhcccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHhCcCeeeecCC--C-----c-
Confidence 455667888888875 478899997664 37789999999999999999622111 1 1
Q ss_pred cceEEEeehhhHHHHhchhhHHHHH-HHHh-----hhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHH
Q 009725 81 ANTQYVVLFDNILHRVRFAKFLTIL-SQEF-----DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETL 154 (527)
Q Consensus 81 ~~~~Y~~~~~~il~rlR~p~~i~~i-~~~y-----G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f 154 (527)
|.+||-+.. .++| ......|+-.||..|-.|+.++-.+..--. +..+.++++..+
T Consensus 77 ----------------Rv~Ky~Hr~~~~ef~~l~l~~~~~All~~LlLRGPQT~gELRtRs~Rl~---~F~dv~~Ve~~L 137 (215)
T PRK11239 77 ----------------RVTKYEQRFCNSEFGDLKLSAAEVALITTLLLRGAQTPGELRSRAARMY---EFSDMAEVESTL 137 (215)
T ss_pred ----------------chHHHHHhcccccccccCCCHHHHHHHHHHHhcCCCChHHHHHhHhcCC---cCCCHHHHHHHH
Confidence 234444432 2333 356888999999999999999988754211 244788999999
Q ss_pred HHHHhcc---cceecC
Q 009725 155 VKLVTAH---YVERCP 167 (527)
Q Consensus 155 ~~Lv~~~---~i~~v~ 167 (527)
..|+... ++.+.|
T Consensus 138 ~~L~~r~~~plV~~Lp 153 (215)
T PRK11239 138 EQLANREDGPFVVRLA 153 (215)
T ss_pred HHHHhccCCceeeecC
Confidence 9999874 676665
No 56
>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=86.11 E-value=1.7 Score=32.34 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
..|..+|-.+|.+++.+|+...+.+...||.=|..|-+.|++.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK 45 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678899999999999999999999999999999999999986
No 57
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=84.98 E-value=4 Score=39.24 Aligned_cols=66 Identities=21% Similarity=0.311 Sum_probs=54.4
Q ss_pred CchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 385 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 385 ~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.---+|..+|.+.|-. .-.+|++...|+..-+|.-|-.|..+|+|+.+..+. +.+|+.++|+..-.
T Consensus 11 ~tr~~il~lL~~~g~~-sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~--g~GRP~~~y~Lt~~ 76 (218)
T COG2345 11 STRERILELLKKSGPV-SADELAEELGISPMAVRRHLDDLEAEGLVEVERQQG--GRGRPAKLYRLTEK 76 (218)
T ss_pred cHHHHHHHHHhccCCc-cHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccC--CCCCCceeeeeccc
Confidence 3345788888778888 999999999999999999999999999999994333 55777777777644
No 58
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=84.84 E-value=8.1 Score=30.62 Aligned_cols=70 Identities=11% Similarity=0.209 Sum_probs=46.4
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchh
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFA 99 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p 99 (527)
+++..|-..|. .|+.+..+|+..++|+++.+..-|--|++.|+|. .. ...|.+-..+--..-.+-
T Consensus 6 ~Ii~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~---~~-----------~~~Y~lTekG~~~l~~l~ 70 (77)
T PF14947_consen 6 EIIFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK---KK-----------DGKYRLTEKGKEFLEELE 70 (77)
T ss_dssp HHHHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE---EE-----------TTEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee---CC-----------CCEEEECccHHHHHHHHH
Confidence 34455555554 7999999999999999999999999999999994 12 136888776655555555
Q ss_pred hHHHH
Q 009725 100 KFLTI 104 (527)
Q Consensus 100 ~~i~~ 104 (527)
++..+
T Consensus 71 ~~~~~ 75 (77)
T PF14947_consen 71 ELIEL 75 (77)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 54443
No 59
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=84.66 E-value=15 Score=35.42 Aligned_cols=93 Identities=17% Similarity=0.233 Sum_probs=64.1
Q ss_pred hhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHh
Q 009725 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRV 96 (527)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rl 96 (527)
.=|..-.+|-..|..+|+.|+.+|+...++++-.||.=|-.|.--|+|.+.... +|-|. +...|.+--...=
T Consensus 8 ~~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~--~g~GR---P~~~y~Lt~~g~~--- 79 (218)
T COG2345 8 PSGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQ--GGRGR---PAKLYRLTEKGRE--- 79 (218)
T ss_pred CCccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeecc--CCCCC---Cceeeeecccchh---
Confidence 346777888899999999999999999999999999999999999999954222 22222 2345666544321
Q ss_pred chhhHHHHHHHHhhhhHHHHHHHHHHcc
Q 009725 97 RFAKFLTILSQEFDQQCVELVQGLLEHG 124 (527)
Q Consensus 97 R~p~~i~~i~~~yG~~a~~I~~~lL~~G 124 (527)
.....||+.+..++..|=..|
T Consensus 80 -------~f~~~y~~l~~~~l~~l~~~~ 100 (218)
T COG2345 80 -------QFPKRYGELALALLDALEETG 100 (218)
T ss_pred -------hcchhhHHHHHHHHHHHHHhc
Confidence 333445555555554444443
No 60
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=84.48 E-value=2.5 Score=36.72 Aligned_cols=46 Identities=24% Similarity=0.275 Sum_probs=43.2
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
++.++|.+.+=.+|+.|+.++...|+++...++.-|-.|+-.|-|+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeE
Confidence 5678889999999999999999999999999999999999999886
No 61
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=84.47 E-value=2 Score=36.18 Aligned_cols=43 Identities=19% Similarity=0.268 Sum_probs=40.8
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.+|...|..+|+.|..+|.+.+++++..|+..+-.|.+.|+|.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4788899999999999999999999999999999999999997
No 62
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=83.91 E-value=22 Score=33.46 Aligned_cols=121 Identities=14% Similarity=0.179 Sum_probs=80.9
Q ss_pred hHHHHHHHHHhcCC--CCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhch
Q 009725 21 LVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRF 98 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~--~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~ 98 (527)
..+.|=.+|+..|. +|+.+|.+.++++...|+.+|--|.++- .... .| .--....+-|.+.--
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y-----~~~~-~g---------i~i~~~~~~y~l~tk 69 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKY-----EGDD-RG---------LKLIEFNDVYKLVTK 69 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH-----hhCC-CC---------EEEEEECCEEEEEEc
Confidence 34567778888883 8999999999999999999999997751 1110 00 000111111222222
Q ss_pred hhHHHHHHH--------HhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 99 AKFLTILSQ--------EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 99 p~~i~~i~~--------~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
|.|-.+++. .+...+-+++..+..+|-+|-.++.+.-... ....+.+|++.|||..+.
T Consensus 70 ~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~-----------~~~ii~~L~~~gLI~e~g 135 (188)
T PRK00135 70 EENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVN-----------SDGALQTLLAKGLIKEVG 135 (188)
T ss_pred HHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCC-----------HHHHHHHHHHCCCeEEcC
Confidence 333333332 4667789999999999999999987764321 277899999999998764
No 63
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=83.74 E-value=11 Score=30.76 Aligned_cols=63 Identities=14% Similarity=0.197 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhc-CCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t-~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
...|...|.. |+..+.+|.+.. +++++.+...|-.|..+|+|.--..+ . .+..+.|.+-..+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~--~-----~p~~v~Y~LT~~G~ 70 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYP--E-----VPPRVEYSLTEKGK 70 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES--S-----SSSEEEEEE-HHHH
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccccc--C-----CCCCCccCCCcCHH
Confidence 4456666766 999999999987 89999999999999999999732222 1 12246888876543
No 64
>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=83.30 E-value=2.9 Score=31.12 Aligned_cols=47 Identities=19% Similarity=0.162 Sum_probs=40.7
Q ss_pred hhHHHHHHHHHhcCC--CCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 20 DLVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~--~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
+.-..|-.+|..+|+ +|..+|++.+++++..|-..+-.|++.|+|.-
T Consensus 5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r 53 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVER 53 (62)
T ss_dssp HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 334567788888988 99999999999999999999999999999983
No 65
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=82.16 E-value=4.2 Score=31.47 Aligned_cols=56 Identities=13% Similarity=0.239 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 112 QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 112 ~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.-+.|+.-+=..+.++..+|+..+.+.....-..+...++.++..|++.+||.|-+
T Consensus 9 I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 9 IDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEES
T ss_pred hhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 45788888999999999999999887554322347889999999999999999975
No 66
>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=81.81 E-value=2.8 Score=31.02 Aligned_cols=49 Identities=20% Similarity=0.409 Sum_probs=43.5
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEec
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 437 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpk 437 (527)
++++.+|...+.+ ...+|++..-++...+-.++.+|.+.|||.-+.-|.
T Consensus 6 ~~iL~~l~~~~~~-~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 6 FRILRILYENGGI-TQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp HHHHHHHHHHSSE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 5788888888898 999999999999999999999999999998886654
No 67
>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=81.67 E-value=4.8 Score=32.30 Aligned_cols=42 Identities=14% Similarity=0.277 Sum_probs=34.0
Q ss_pred HHHHHHHhcC---CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 24 KVCECLLRKG---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 24 ~V~~~Ll~~G---~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
++.-+|..++ ++|..+|+..+++|++.+++.|-.|.++|+|.
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 3444455444 38999999999999999999999999999997
No 68
>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=80.79 E-value=6.5 Score=29.77 Aligned_cols=45 Identities=20% Similarity=0.290 Sum_probs=34.5
Q ss_pred HHHHHH-hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccccc
Q 009725 25 VCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 25 V~~~Ll-~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
|-.+|. ..|++|..+|++.++++...+...|-.|+..|+|.-...
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~ 53 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERD 53 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC
Confidence 334454 689999999999999999999999999999999974333
No 69
>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=80.47 E-value=3.9 Score=38.94 Aligned_cols=63 Identities=17% Similarity=0.260 Sum_probs=51.4
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+|+..|...|.+ ...+|++...++...++..|..|.+.|+|+-...+. ..+|..++|++...
T Consensus 4 ~~IL~~L~~~~~~-t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~--~~gRp~~~y~LT~~ 66 (203)
T TIGR02702 4 EDILSYLLKQGQA-TAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQ--GMGRPQYHYQLSRQ 66 (203)
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeeccc--CCCCCceEEEECcc
Confidence 4788889888887 999999999999999999999999999997554333 23566677777744
No 70
>PHA00738 putative HTH transcription regulator
Probab=80.23 E-value=5.8 Score=33.63 Aligned_cols=60 Identities=17% Similarity=0.071 Sum_probs=49.0
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
-+|...|...+.++..+|+...+++.+.|-+=|-+|-+-|+|.. ... +..++|+++.+.-
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~s-rK~---------Gr~vyY~Ln~~~~ 74 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIEL-YKE---------GRTLYAKIRENSK 74 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEE-EEE---------CCEEEEEECCCcc
Confidence 45777777767899999999999999999999999999999983 322 1258999997753
No 71
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=80.07 E-value=32 Score=29.32 Aligned_cols=72 Identities=18% Similarity=0.239 Sum_probs=51.8
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCC----CcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHHHHHHH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFV----EKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEM 463 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami----~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~~~~~~ 463 (527)
..|+++|-+.|.+ .-.+|.+..-= +...++.+|.+|.+.|||..+...++ .+|.=.++.+......+.++
T Consensus 6 ~~IM~~lW~~~~~-t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~-----~~Y~p~is~~e~~~~~~~~~ 79 (115)
T PF03965_consen 6 LEIMEILWESGEA-TVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRA-----YVYSPLISREEYLAQELRQF 79 (115)
T ss_dssp HHHHHHHHHHSSE-EHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTC-----EEEEESSSHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCC-CHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCCc-----eEEEeCCcHHHHHHHHHHHH
Confidence 4678888888885 88888777543 47899999999999999988855333 34444667776666666655
Q ss_pred HH
Q 009725 464 FH 465 (527)
Q Consensus 464 yk 465 (527)
..
T Consensus 80 l~ 81 (115)
T PF03965_consen 80 LD 81 (115)
T ss_dssp HH
T ss_pred HH
Confidence 54
No 72
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=79.68 E-value=2.5 Score=39.26 Aligned_cols=46 Identities=33% Similarity=0.471 Sum_probs=41.8
Q ss_pred hHHHHHHHHHhC-CCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 387 AYRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 387 ~~RI~r~l~~k~-~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
+.||.-+|..+| ++ .-++|++...|...++-..||+|++.|+|..-
T Consensus 6 ~~~i~~~l~~~~~~~-~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 6 ASLILTLLSSSGDKL-PAKRIAKELGISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred HHHHHHHHHhcCCCC-cHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence 568999999888 66 99999999999999999999999999999654
No 73
>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=79.66 E-value=34 Score=29.16 Aligned_cols=65 Identities=9% Similarity=0.116 Sum_probs=49.9
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhh
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (527)
..--.|..+|..+|++|..+|++..+++...|-..|-.|...|+|.-...+. + .+ ...|.+...+
T Consensus 28 ~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~-D-----~R-~~~v~LT~~G 92 (118)
T TIGR02337 28 EQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASN-D-----QR-RVYISLTPKG 92 (118)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC-C-----CC-eeEEEECHhH
Confidence 3334678888889999999999999999999999999999999998443332 1 22 3566666554
No 74
>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=79.18 E-value=3.7 Score=30.33 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=38.6
Q ss_pred HHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccccc
Q 009725 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 25 V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
|-.+|-.+|++|..+|++..+++.+.+-..+--|++.|+|.-...
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence 455677899999999999999999999999999999999984333
No 75
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=79.13 E-value=4.8 Score=36.95 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=41.2
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+|++.|.+.+.. .-.+|++...++...++.-+.+|.+.|.|.
T Consensus 17 ~~IL~~Lq~d~R~-s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 17 RNILNELQKDGRI-SNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHhccCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 5899999999999 999999999999999999999999999996
No 76
>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=78.63 E-value=2.4 Score=30.09 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=37.5
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+|+..|.+ |.+ .-.+|++...++...+..-|..|.+.|+|+
T Consensus 5 ~~Il~~L~~-~~~-~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPL-TVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCC-chhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 578888866 888 999999999999999999999999999985
No 77
>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=77.42 E-value=6.2 Score=29.71 Aligned_cols=36 Identities=31% Similarity=0.419 Sum_probs=33.8
Q ss_pred hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 31 RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 31 ~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
..+++|..+|+..++++...|...|-.|.+.|+|..
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 568899999999999999999999999999999973
No 78
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=77.39 E-value=1.7 Score=35.49 Aligned_cols=42 Identities=24% Similarity=0.370 Sum_probs=39.8
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.|-.+++..++.-+-.|+.-||+|...||.+|-||-|-|++.
T Consensus 18 ~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~~iI~ 59 (101)
T COG3388 18 SVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQENIIS 59 (101)
T ss_pred HHHHHHHHhCCceeEeechhcCCchhhhhhhhhhhhhcCccC
Confidence 577889999999999999999999999999999999999997
No 79
>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=77.35 E-value=3.9 Score=30.44 Aligned_cols=51 Identities=18% Similarity=0.286 Sum_probs=43.0
Q ss_pred chHHHHHHHHHhCC--CcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEec
Q 009725 386 DAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 437 (527)
Q Consensus 386 ~~~RI~r~l~~k~~--l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpk 437 (527)
.-++|+..|...+. + ...+|++...+++..+-.++.+|.+.|||+-..-|.
T Consensus 6 ~q~~vL~~l~~~~~~~~-t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 6 SQFRVLMALARHPGEEL-TQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp HHHHHHHHHHHSTTSGE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred HHHHHHHHHHHCCCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 45688888888777 7 999999999999999999999999999998775443
No 80
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=77.25 E-value=5 Score=39.61 Aligned_cols=43 Identities=12% Similarity=0.092 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.|-++|...+++|+.+|++.+++|.+.+..-|-.|.++|+|..
T Consensus 18 ~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 18 GILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4455556678899999999999999999999999999999973
No 81
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=77.14 E-value=36 Score=29.69 Aligned_cols=102 Identities=21% Similarity=0.205 Sum_probs=71.1
Q ss_pred hchhHHHHHHHHHhcCCCCHHHHHhh----cCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHH
Q 009725 18 FGDLVAKVCECLLRKGPLTRQNVKRY----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNIL 93 (527)
Q Consensus 18 FG~~v~~V~~~Ll~~G~~tl~~i~~~----t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il 93 (527)
-|+.=..|.++|=.+|+.|..+|... ...+++.|+.-|-.|..-|+|...... + ...|++..+.--
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdg---------r-~~~y~pL~~~~~ 73 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDG---------R-AFRYSPLLTRDQ 73 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcC---------C-eeeeecccCHHH
Confidence 47777899999999999999999766 458999999999999999999833222 1 356777766543
Q ss_pred HHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHH
Q 009725 94 HRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 131 (527)
Q Consensus 94 ~rlR~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~l 131 (527)
.+ .+.--..+.+-|+.....++.++..+-.++..++
T Consensus 74 ~~--~~~~~~~l~k~~d~~~~~lv~~F~~~~~l~~~ei 109 (123)
T COG3682 74 YV--AGESQDLLDKICDGGLASLVAHFAEKEKLTADEI 109 (123)
T ss_pred HH--HHHHHHHHHHHHcccchHHHHHHHHhccCCHHHH
Confidence 32 2222334455555555666666666666665544
No 82
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=76.70 E-value=3.8 Score=33.10 Aligned_cols=46 Identities=22% Similarity=0.359 Sum_probs=40.7
Q ss_pred chHHHHHHHHHh-CCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 386 DAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 386 ~~~RI~r~l~~k-~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
.+.+|+.+|... +.+ .-.+|++..-+|...++..|..|.+.|||.-
T Consensus 6 r~~~Il~~l~~~~~~~-t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGL-TLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCc-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 467888888776 567 9999999999999999999999999999953
No 83
>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=76.25 E-value=7.4 Score=29.45 Aligned_cols=50 Identities=18% Similarity=0.341 Sum_probs=39.1
Q ss_pred HHHHHHHH-HhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEecc
Q 009725 388 YRIFRLLS-KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVT 438 (527)
Q Consensus 388 ~RI~r~l~-~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt 438 (527)
+.|++.|. .++.+ ...+|++...++...+-..+.+|.+.|||+-+.-|..
T Consensus 6 ~~vL~~l~~~~~~~-t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d 56 (68)
T PF13463_consen 6 WQVLRALAHSDGPM-TQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHD 56 (68)
T ss_dssp HHHHHHHT--TS-B-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSC
T ss_pred HHHHHHHHccCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCc
Confidence 56777776 56777 9999999999999999999999999999977665543
No 84
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=76.09 E-value=9.9 Score=34.37 Aligned_cols=47 Identities=13% Similarity=0.039 Sum_probs=43.0
Q ss_pred CchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 385 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 385 ~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
..=.+|++.|...+.. .-.+|++...++...++.-+-+|.+.|+|.-
T Consensus 9 ~~D~~Il~~Lq~d~R~-s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENART-PYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 3446899999998999 9999999999999999999999999999973
No 85
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=75.87 E-value=7.1 Score=33.97 Aligned_cols=54 Identities=15% Similarity=0.249 Sum_probs=47.2
Q ss_pred hhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009725 109 FDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (527)
Q Consensus 109 yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v 166 (527)
.|+.-.+||+.+=.+|-.|.+++++.+..+.+. +...+...+.+|+..|+|.+.
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ew----s~sTV~TLl~RL~KKg~l~~~ 57 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREW----SYSTVKTLLNRLVKKGLLTRK 57 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccc----cHHHHHHHHHHHHhccchhhh
Confidence 467778999999999999999999999876443 677899999999999999776
No 86
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=75.44 E-value=5 Score=28.42 Aligned_cols=43 Identities=23% Similarity=0.377 Sum_probs=37.7
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
.|++.|..++.+ ...+|++..-++...++..|..|.+.|+|.-
T Consensus 4 ~il~~l~~~~~~-s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKV-SVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHHcCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 466777676776 9999999999999999999999999999964
No 87
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=74.76 E-value=3 Score=32.11 Aligned_cols=55 Identities=16% Similarity=0.267 Sum_probs=48.6
Q ss_pred HHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEe
Q 009725 381 KRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 436 (527)
Q Consensus 381 ~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvp 436 (527)
+..|..|..||++|..+|.+ +-++|.+.+-++.+++--.+-=|.++|=|.+.+..
T Consensus 4 ~~IG~nAG~Vw~~L~~~~~~-s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~ 58 (65)
T PF10771_consen 4 ENIGENAGKVWQLLNENGEW-SVSELKKATGLSDKEVYLAIGWLARENKIEFEEKN 58 (65)
T ss_dssp HHHHHHHHHHHHHHCCSSSE-EHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEET
T ss_pred hHHHHHHHHHHHHHhhCCCc-CHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeC
Confidence 45788999999999887787 99999999999999999999999999999888543
No 88
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=74.72 E-value=23 Score=34.84 Aligned_cols=74 Identities=16% Similarity=0.150 Sum_probs=58.1
Q ss_pred CchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHHHHHHHH
Q 009725 385 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMF 464 (527)
Q Consensus 385 ~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~~~~~~y 464 (527)
.-=++++.-|+..|.. .-++|++.+.+|..-+=++|-.|-..|||+.| +++.-.+--++++.+.....+++-
T Consensus 16 ~yEa~vY~aLl~~g~~-tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~-------~g~P~~y~av~p~~~i~~~~~~~~ 87 (247)
T COG1378 16 EYEAKVYLALLCLGEA-TAKEISEASGVPRPKVYDVLRSLEKKGLVEVI-------EGRPKKYRAVPPEELIERIKEELQ 87 (247)
T ss_pred HHHHHHHHHHHHhCCc-cHHHHHHHcCCCchhHHHHHHHHHHCCCEEee-------CCCCceEEeCCHHHHHHHHHHHHH
Confidence 3347899999999999 99999999999999999999999999999777 234455566777765555554444
Q ss_pred HH
Q 009725 465 HA 466 (527)
Q Consensus 465 k~ 466 (527)
..
T Consensus 88 ~~ 89 (247)
T COG1378 88 EL 89 (247)
T ss_pred HH
Confidence 33
No 89
>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=74.60 E-value=49 Score=27.86 Aligned_cols=91 Identities=19% Similarity=0.277 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHHcCCch--HHHHHHHH----HhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCce
Q 009725 371 QNEEVESVVSKRYGRDA--YRIFRLLS----KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQ 444 (527)
Q Consensus 371 r~~~le~~v~~~~G~~~--~RI~r~l~----~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t 444 (527)
.-..+.+.+...||-.. ++|+.+|. ..|.+ ..++|++...++...+=..+.+|.+.|||.=+.-| ...|.
T Consensus 9 ~~~~~~~~l~~~~~ls~~q~~vL~~l~~~~~~~~~~-t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~---~D~R~ 84 (109)
T TIGR01889 9 YIKSLKRYLKKEFNLSLEELLILYYLGKLENNEGKL-TLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE---DDERK 84 (109)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHhhhccCCcC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc---ccCCe
Confidence 34456666676666544 56777776 44567 99999999999999999999999999999433111 44666
Q ss_pred EEEEEEchH-HHHHHHHHHHHH
Q 009725 445 FLLWKVNRQ-ILWKHVLDEMFH 465 (527)
Q Consensus 445 ~~lw~v~~~-~~~~~~~~~~yk 465 (527)
+++.--..- .....+.+.+++
T Consensus 85 ~~i~lT~~G~~~~~~~~~~~~~ 106 (109)
T TIGR01889 85 VIISINKEQRSKIESLISEIEQ 106 (109)
T ss_pred EEEEECHHHHHHHHHHHHHHHH
Confidence 665544433 233444444444
No 90
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=74.38 E-value=7.3 Score=38.36 Aligned_cols=43 Identities=16% Similarity=0.202 Sum_probs=36.0
Q ss_pred HHHHHHHhcCC-CCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 24 KVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 24 ~V~~~Ll~~G~-~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.|-++|...+. +++.+|++.+++|++.+..-|..|+++|+|.+
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~ 51 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQ 51 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE
Confidence 45555555443 67999999999999999999999999999983
No 91
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=73.46 E-value=7.9 Score=34.50 Aligned_cols=46 Identities=9% Similarity=0.096 Sum_probs=41.6
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
....|...+-.+|..++.+|++..++++..|...|-.|.+.|+|.+
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~ 54 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIY 54 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEE
Confidence 4567777888889999999999999999999999999999999973
No 92
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=73.23 E-value=6.9 Score=35.82 Aligned_cols=129 Identities=15% Similarity=0.207 Sum_probs=77.1
Q ss_pred HHHHHHHccchhhhcccccCCCccChHHHHHHhhhcccCCCCCHHHHHHHHHHhccC----C---CCCCCCCcEEEehHH
Q 009725 293 VLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGEL----S---FVDASSDSYSIDFEK 365 (527)
Q Consensus 293 v~~~~L~~~~~~~~~~~~~~s~p~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~----~---~~~~~~~~y~V~~~~ 365 (527)
+++|+|-.+ +.|++..+|.+.+. ..+.+.+.|..|... + -...-+|.|.+-.+.
T Consensus 2 ~iEAlLF~s-----------~~pvs~~~La~~l~--------~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~ 62 (159)
T PF04079_consen 2 IIEALLFAS-----------GEPVSIEELAEILG--------SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKP 62 (159)
T ss_dssp HHHHHHHH------------SS-B-HHHHHHHCT---------HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-G
T ss_pred hhHhhHHHc-----------CCCCCHHHHHHHhC--------CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhH
Confidence 466677654 34799999998884 244555555544433 1 113336777766555
Q ss_pred HHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceE
Q 009725 366 IIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQF 445 (527)
Q Consensus 366 i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~ 445 (527)
-..-.....+..--..++...++.++-++.-+.-. ...+|.+.=... +-..+.+|.+.|+| .++.+...|+|++
T Consensus 63 ~~~~~v~~~~~~~~~~~LS~aalEtLAiIAY~QPi-Tr~eIe~IRGv~---s~~~i~~L~e~glI--~~~gr~~~~Grp~ 136 (159)
T PF04079_consen 63 EYAEYVEKLFKKPKPPKLSQAALETLAIIAYKQPI-TRAEIEEIRGVN---SDSVIKTLLERGLI--EEVGRKDTPGRPI 136 (159)
T ss_dssp GGHHHHHHHHCTCCCHHHHHHHHHHHHHHHHH-SE-EHHHHHHHHTS-----HCHHHHHHHTTSE--EEEEE-TTTT--E
T ss_pred HHHHHHHHHhccCccCCCCHHHHHHHHHHHhcCCc-CHHHHHHHcCCC---hHHHHHHHHHCCCE--EecCcCCCCCCCe
Confidence 54433333333322347777889999999776555 999999888766 78899999999999 3445544677765
Q ss_pred E
Q 009725 446 L 446 (527)
Q Consensus 446 ~ 446 (527)
.
T Consensus 137 l 137 (159)
T PF04079_consen 137 L 137 (159)
T ss_dssp E
T ss_pred E
Confidence 4
No 93
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=72.60 E-value=23 Score=32.07 Aligned_cols=116 Identities=16% Similarity=0.200 Sum_probs=67.1
Q ss_pred HhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc-ccccccCCC-CC-CCCCcceEEEeehhhH
Q 009725 16 NHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ-AFTTEQPDG-FA-DGPKANTQYVVLFDNI 92 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~-~~~~~~~~~-~~-~~~~~~~~Y~~~~~~i 92 (527)
..||.-+-+=.--++..|.+|..+|....+-.. +.||.+|=+-|+|. -|..+.+++ +. ++..+.+...+|..--
T Consensus 12 ~~f~s~~~kkV~~~Ls~~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE~qWrmP~pG~kPeKEYhtsYs~vqaNFqcs 88 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSKGWMTEEELEEKYGKDV---RESLLILKKGGLIESQWRMPEPGEKPEKEYHTSYSKVQANFQCS 88 (160)
T ss_pred HHhCCHHHHHHHHHHHhccCCHHHHHHHHCcCH---HHHHHHHHHcCchhhccccCCCCCCchHHHHhhHhheeeeeEee
Confidence 468865555445555799999999999887655 89999999999998 355554331 10 1111111222222111
Q ss_pred HHHhchhhHHHHHHHHhh--hhHHHHHHHHHHcccCCHHHHHHHhh
Q 009725 93 LHRVRFAKFLTILSQEFD--QQCVELVQGLLEHGRLTLKQMFDRAK 136 (527)
Q Consensus 93 l~rlR~p~~i~~i~~~yG--~~a~~I~~~lL~~G~~~~~~li~~~~ 136 (527)
+- =.+.+|..+-.-+. .+...-++..+..|..+++++...+.
T Consensus 89 ~~--DLsdii~i~f~~deel~~~~e~i~~~v~~Gn~Sl~~lsr~l~ 132 (160)
T PF09824_consen 89 ME--DLSDIIYIAFMSDEELRDYVEKIEKEVEAGNTSLSDLSRKLG 132 (160)
T ss_pred HH--HHHHHHheeecCHHHHHHHHHHHHHHHHcCCCcHHHHHHHhC
Confidence 11 12233333322222 23455566667779999999987753
No 94
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=72.54 E-value=5.8 Score=29.46 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=38.4
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccc
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 430 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v 430 (527)
.|+.+|..++.+ .-+++++.--++...+|.-|..|.+.|+|
T Consensus 4 ~Il~~l~~~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 4 QILELLKEKGKV-SVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHcCCE-EHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 588888888888 99999999999999999999999999996
No 95
>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=72.42 E-value=5.2 Score=32.13 Aligned_cols=47 Identities=26% Similarity=0.264 Sum_probs=38.1
Q ss_pred chHHHHHHHHHhCC--CcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 386 DAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 386 ~~~RI~r~l~~k~~--l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
-|.|++-.|...+. .+.-++|++..-+|...+++++.+|.+.|+|+.
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s 57 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIES 57 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEe
Confidence 46788888865443 249999999999999999999999999999843
No 96
>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=71.90 E-value=7.3 Score=37.91 Aligned_cols=46 Identities=20% Similarity=0.248 Sum_probs=43.9
Q ss_pred hhHHHHHHHHHh-cCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~-~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.+.+|.+.|-. .|+++-.+|+...+++++.|++++-.|-+-|++.
T Consensus 183 eAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe 229 (251)
T TIGR02787 183 EAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIE 229 (251)
T ss_pred HHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 778999999998 5999999999999999999999999999999998
No 97
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=71.88 E-value=3.7 Score=31.66 Aligned_cols=44 Identities=27% Similarity=0.402 Sum_probs=33.9
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcC--CCcccHHHHHHHHHhcccceE
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTF--VEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~am--i~~k~~r~~L~~L~~~g~v~l 432 (527)
-+|..+|...|.. .-..++.... +|.|++-..||+|.+.|.|.-
T Consensus 7 e~Il~~L~~~g~~-~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k 52 (66)
T PF02295_consen 7 EKILDFLKELGGS-TATAIAKALGLSVPKKEVNRVLYRLEKQGKVCK 52 (66)
T ss_dssp HHHHHHHHHHTSS-EEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhcCCc-cHHHHHHHhCcchhHHHHHHHHHHHHHCCCEee
Confidence 3788888887754 6666666555 458999999999999999954
No 98
>PRK06474 hypothetical protein; Provisional
Probab=71.62 E-value=11 Score=35.19 Aligned_cols=68 Identities=12% Similarity=0.291 Sum_probs=50.6
Q ss_pred hhHHHHHHHHHhcCC-CCHHHHHhhc-CCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 20 DLVAKVCECLLRKGP-LTRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~-~tl~~i~~~t-~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
+.=-+|..+|..+|. +|..+|.... +++...|-.-|-.|..+|+|.......-+ ....-+|.++.+.+
T Consensus 11 p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~-----~~~ek~y~~~~~~~ 80 (178)
T PRK06474 11 PVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVR-----SVSEKYYAINEEDA 80 (178)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeeccccc-----CceeEEEEecccee
Confidence 344578888988876 9999999887 79999999999999999999843332111 12235788887654
No 99
>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=71.29 E-value=8.3 Score=31.92 Aligned_cols=48 Identities=23% Similarity=0.295 Sum_probs=40.2
Q ss_pred hchhHHHHHHHHH-----------hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 18 FGDLVAKVCECLL-----------RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 18 FG~~v~~V~~~Ll-----------~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
|-++.++++.+|+ ...++|-.+|+..+++++..|..+|-.|.+.|+|.
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4556666666555 35688999999999999999999999999999997
No 100
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=71.28 E-value=5.6 Score=29.17 Aligned_cols=43 Identities=21% Similarity=0.325 Sum_probs=36.7
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
+|+++|. .+.. ...+|++...++...++..|.+|.+.|+|...
T Consensus 1 ~il~~l~-~~~~-~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 1 KILKLLA-EGEL-CVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred CHHHHhh-cCCc-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 3667765 5666 88999999999999999999999999999633
No 101
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=71.13 E-value=51 Score=28.94 Aligned_cols=70 Identities=16% Similarity=0.257 Sum_probs=49.0
Q ss_pred HHHHHHHHHhCCCcchhhhhhhc----CCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEE--EchHHHHHHHHH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTT----FVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWK--VNRQILWKHVLD 461 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~a----mi~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~--v~~~~~~~~~~~ 461 (527)
.-|+++|-..|.. ..++|.+.. -+....++.+|.+|.+.|||..+ +. +|+ |+|+ ++.+........
T Consensus 7 ~~VM~vlW~~~~~-t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~---k~---gr~-~~Y~p~vs~ee~~~~~~~ 78 (130)
T TIGR02698 7 WEVMRVVWTLGET-TSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE---KE---GRK-FIYTALVSEDEAVENAAQ 78 (130)
T ss_pred HHHHHHHHcCCCC-CHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee---cC---CCc-EEEEecCCHHHHHHHHHH
Confidence 3467777677776 777755543 57788999999999999999655 22 444 4555 777777666666
Q ss_pred HHHH
Q 009725 462 EMFH 465 (527)
Q Consensus 462 ~~yk 465 (527)
++..
T Consensus 79 ~~~~ 82 (130)
T TIGR02698 79 ELFS 82 (130)
T ss_pred HHHH
Confidence 6654
No 102
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=70.81 E-value=10 Score=31.59 Aligned_cols=53 Identities=17% Similarity=0.234 Sum_probs=43.2
Q ss_pred hhchhHHHHHHHHHh----cCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccc
Q 009725 17 HFGDLVAKVCECLLR----KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (527)
Q Consensus 17 ~FG~~v~~V~~~Ll~----~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~ 70 (527)
..+++-.+|..+|-. .-.+++.+|++.++++..+||.+|--|+-.|.|+ .+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY-sTiD 100 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY-STID 100 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE-ESSS
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe-cccC
Confidence 467888899999987 3358999999999999999999999999999996 4443
No 103
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=70.77 E-value=5.9 Score=35.51 Aligned_cols=69 Identities=17% Similarity=0.246 Sum_probs=53.3
Q ss_pred cCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccC--CC--CceEEEEEEch
Q 009725 383 YGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--AR--QSQFLLWKVNR 452 (527)
Q Consensus 383 ~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~--~~--~~t~~lw~v~~ 452 (527)
....-.||+++|.+.+.. ...+|++...++...++..+.+|.+.|+|.--..--.. -. -..|..+.+..
T Consensus 6 lD~~D~~IL~~L~~d~r~-~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~ 78 (154)
T COG1522 6 LDDIDRRILRLLQEDARI-SNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLER 78 (154)
T ss_pred ccHHHHHHHHHHHHhCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecC
Confidence 344557999999998897 99999999999999999999999999999665442221 11 11666777665
No 104
>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=69.60 E-value=12 Score=26.01 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL 58 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vL 58 (527)
.+|...|...|+.|+.+|.+.+|++...|..-+--|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 467888999999999999999999999998766544
No 105
>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=69.28 E-value=8.2 Score=28.73 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=35.8
Q ss_pred chhHHHHHHHHHh----cCC--CCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 19 GDLVAKVCECLLR----KGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 19 G~~v~~V~~~Ll~----~G~--~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.++...+...+.. .|. .|..+|++..+++...|+++|..|.+-|+|.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444455555443 232 3488999999999999999999999999987
No 106
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=68.79 E-value=7.4 Score=29.68 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=35.1
Q ss_pred HhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccce
Q 009725 108 EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 164 (527)
Q Consensus 108 ~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~ 164 (527)
...+.|..|.+.+ .|..|++++++.+.+..+.........+..-+.+|.+.|+|+
T Consensus 14 ~Ln~~a~~Iw~~~--~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELL--DGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHc--cCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 3446677777776 789999999999988664322334677899999999999874
No 107
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=68.71 E-value=15 Score=31.96 Aligned_cols=49 Identities=24% Similarity=0.369 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 111 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 111 ~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
...+.|++-+=++|++|+.|+...... +...++..|.+||..|-|.+..
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGa--------sR~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGA--------SRNTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCC--------CHHHHHHHHHHHHHcCCeEeCC
Confidence 346889999999999999999887643 6788999999999999998864
No 108
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.55 E-value=8.6 Score=35.24 Aligned_cols=49 Identities=16% Similarity=0.251 Sum_probs=43.9
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~ 68 (527)
++=.+|...|...||.|..+|++.++++.+.|+.=+--|.+.|++.-|.
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~ 62 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYT 62 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 4456888999999999999999999999999999999999999997333
No 109
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=68.53 E-value=48 Score=29.39 Aligned_cols=44 Identities=16% Similarity=0.122 Sum_probs=38.6
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
.|...|..+|++|..+|+...+++++.|-..+-.|.+.|+|.-.
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 44555666899999999999999999999999999999999843
No 110
>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=68.17 E-value=22 Score=30.00 Aligned_cols=53 Identities=11% Similarity=0.156 Sum_probs=42.3
Q ss_pred HHHhhchhHH--HHHHHHH----hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 14 ITNHFGDLVA--KVCECLL----RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 14 i~~~FG~~v~--~V~~~Ll----~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++..||--.. .|..+|. ..|++|..+|+..++++.+.|-..+-.|.++|+|.-
T Consensus 17 l~~~~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r 75 (109)
T TIGR01889 17 LKKEFNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSK 75 (109)
T ss_pred HHHHcCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEec
Confidence 4445664333 3455555 458899999999999999999999999999999984
No 111
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=67.79 E-value=20 Score=31.44 Aligned_cols=51 Identities=12% Similarity=0.164 Sum_probs=44.3
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccc
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~ 70 (527)
-|-.-.....+-.+++.++.++++.++=.++.|...|..|+..|+|. |..+
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~-fe~~ 113 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIF-FEED 113 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEE-EecC
Confidence 34455667778889999999999999999999999999999999998 6653
No 112
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.33 E-value=39 Score=31.19 Aligned_cols=120 Identities=29% Similarity=0.369 Sum_probs=86.8
Q ss_pred hhHHHHHHHHHhc-------CCCCHHHHHhhc----------CCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcc
Q 009725 20 DLVAKVCECLLRK-------GPLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKAN 82 (527)
Q Consensus 20 ~~v~~V~~~Ll~~-------G~~tl~~i~~~t----------~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~ 82 (527)
++=++|..||+.+ -++|+.-++-.+ +|+..+|..+|--|++.++|. +.+. ++ .
T Consensus 7 a~eARViGcLlEKqvtTPe~YPLtlN~l~~AcNQKT~RdPVmnLse~eVq~~l~~L~~r~lvr--~~sg-------sR-v 76 (215)
T COG3132 7 ALEARVIGCLLEKQVTTPEQYPLTLNGLVTACNQKTNRDPVMNLSESEVQEQLDNLEKRHLVR--TVSG-------SR-V 76 (215)
T ss_pred hHHHHHHHHhhhcccCCcccccchHHHHHHHHhccccccchhcCCHHHHHHHHHHHHHhhhHH--Hhhc-------ch-H
Confidence 5667888888875 377888886553 478899999999999999997 2221 11 2
Q ss_pred eEEEeehhhHHHHhchhhHHHHHHHHhhh-----hHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHH
Q 009725 83 TQYVVLFDNILHRVRFAKFLTILSQEFDQ-----QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKL 157 (527)
Q Consensus 83 ~~Y~~~~~~il~rlR~p~~i~~i~~~yG~-----~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~L 157 (527)
+.|+ . .+...+||+ .-..++-.||..|-.|+.++..+..--.+ ..+..+++..+..|
T Consensus 77 ~kye----h-----------rfcnsefgdlkl~~~evali~lLlLRGaQTpgELrtRanRm~~---Fsdv~e~e~~Le~L 138 (215)
T COG3132 77 TKYE----H-----------RFCNSEFGDLKLSAAEVALITLLLLRGAQTPGELRTRANRMYE---FSDVAEVEHTLERL 138 (215)
T ss_pred HHHH----H-----------HHhhccccceeechHHHHHHHHHHHcCCCChhHHHHHHHhhhc---cchHHHHHHHHHHH
Confidence 3342 1 234456664 34567889999999999999988643211 33678899999999
Q ss_pred Hhcc---cceecC
Q 009725 158 VTAH---YVERCP 167 (527)
Q Consensus 158 v~~~---~i~~v~ 167 (527)
+..+ |+.+.|
T Consensus 139 a~R~~gplvv~l~ 151 (215)
T COG3132 139 ANREDGPLVVRLA 151 (215)
T ss_pred hcCCCCceeeecC
Confidence 9988 888775
No 113
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=66.78 E-value=14 Score=29.57 Aligned_cols=48 Identities=23% Similarity=0.255 Sum_probs=39.6
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEe
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 436 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvp 436 (527)
..|+-+|...+.+ +=++|.+..-++.......|..|.++|||+.....
T Consensus 3 l~Il~~L~~~~~~-~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 3 LAILALLYANEEA-TFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp HHHHHHHHHHSEE-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-
T ss_pred HHHHHHHhhcCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence 3577788777888 99999999999999999999999999999876443
No 114
>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=66.64 E-value=12 Score=27.90 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=31.2
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHH
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLI 59 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLi 59 (527)
.+...|+..+..|+.+|+..++++.+.|++-+--|-
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 577889999999999999999999999999887664
No 115
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=66.62 E-value=48 Score=26.64 Aligned_cols=48 Identities=19% Similarity=0.323 Sum_probs=42.4
Q ss_pred CchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 385 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 385 ~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
....+|+.+|...+.+ ..++|++..-++...+...+.+|.+.|+|...
T Consensus 10 ~~~~~il~~l~~~~~~-~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 10 PTQFLVLRILYEEGPL-SVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHHHHcCCc-CHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 4457889999887777 99999999999999999999999999999654
No 116
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=66.46 E-value=25 Score=34.99 Aligned_cols=43 Identities=16% Similarity=0.161 Sum_probs=36.4
Q ss_pred HHHHHHHhc-CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 24 KVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 24 ~V~~~Ll~~-G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.|-+++-.. +++|+.+|++.+++|.+.+..-|..|.++|+|.+
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ 72 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 344555444 5789999999999999999999999999999973
No 117
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=66.38 E-value=15 Score=34.22 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHhcC-CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G-~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+..++|+.+|-++| ++|..+|.+..+++.+.|=..|..|.+-+.|+
T Consensus 4 ~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~ 50 (183)
T PHA02701 4 DCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVS 50 (183)
T ss_pred hHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEe
Confidence 34678999999999 89999999999999999999999999999997
No 118
>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=65.82 E-value=10 Score=31.35 Aligned_cols=36 Identities=11% Similarity=0.201 Sum_probs=32.3
Q ss_pred hCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 397 SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 397 k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
...+ .+.+|++.+.++...+...|.+|.+.|+|..+
T Consensus 45 ~~~i-s~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRV-TATVIAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCcc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 3456 99999999999999999999999999999754
No 119
>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=65.72 E-value=34 Score=29.16 Aligned_cols=49 Identities=22% Similarity=0.448 Sum_probs=42.2
Q ss_pred CCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 384 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 384 G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
+..-.+|+..|..++.+ ...+|++...++...+-..+.+|.+.|||.-+
T Consensus 27 t~~q~~iL~~l~~~~~~-t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 27 TEQQWRILRILAEQGSM-EFTQLANQACILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred CHHHHHHHHHHHHcCCc-CHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence 34445688888787787 99999999999999999999999999999554
No 120
>PF13730 HTH_36: Helix-turn-helix domain
Probab=65.62 E-value=9.3 Score=27.76 Aligned_cols=29 Identities=14% Similarity=0.248 Sum_probs=27.2
Q ss_pred CHHHHHhhcCCCHHHHHHHHHHHHhcccc
Q 009725 36 TRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (527)
Q Consensus 36 tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V 64 (527)
+...|+..++++.+.|+.++-.|.++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 68999999999999999999999999975
No 121
>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=65.57 E-value=15 Score=26.59 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=37.3
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEe
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 436 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvp 436 (527)
.+|+.+|...+..+.-++|++..-++...++.-+..|-+.| +.+.-.|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~-~~I~~~~ 50 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG-IPIESKR 50 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT--EEEEET
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC-CeEEeeC
Confidence 36788886655545999999999999999999999999988 5554433
No 122
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=65.45 E-value=10 Score=26.33 Aligned_cols=32 Identities=31% Similarity=0.451 Sum_probs=30.4
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.|..+|++.++++...+...|-.|.++|++.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 57899999999999999999999999999997
No 123
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=65.09 E-value=45 Score=31.31 Aligned_cols=62 Identities=15% Similarity=0.100 Sum_probs=49.1
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+|+-+|...+.+ .+++|++...++...+-.++.+|.+.|||.-+.-| ...|..+++-.+.-
T Consensus 48 ~~iL~~L~~~~~i-tq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~---~DrR~~~I~LTekG 109 (185)
T PRK13777 48 HHILWIAYHLKGA-SISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE---DDKRNTYIELTEKG 109 (185)
T ss_pred HHHHHHHHhCCCc-CHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC---CCCCeeEEEECHHH
Confidence 4777777777777 99999999999999999999999999999533222 55787877766544
No 124
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=64.71 E-value=14 Score=33.48 Aligned_cols=48 Identities=10% Similarity=0.117 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
++=.+|...|...||.|..+|++..+++...|+.-+-.|...|++.-|
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 455678899999999999999999999999999999999999999733
No 125
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=63.95 E-value=81 Score=29.62 Aligned_cols=135 Identities=15% Similarity=0.191 Sum_probs=89.1
Q ss_pred HHHHHHHHHHccchhhhcccccCCCccChHHHHHHhhhcccCCCCCHHHHHHHHHHhccCC-----CCCCCCCcEEEehH
Q 009725 290 AANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELS-----FVDASSDSYSIDFE 364 (527)
Q Consensus 290 a~~v~~~~L~~~~~~~~~~~~~~s~p~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~-----~~~~~~~~y~V~~~ 364 (527)
.+.+++++|-+. ..|+|..++..-++.. ....+...|..|..+. -...-++.|..-..
T Consensus 9 ~~~~vEall~a~-----------~~pls~~~L~~il~~~------~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t~ 71 (184)
T COG1386 9 LKALIEALLFAG-----------GEPLSLKELAEILGIV------SADAIIDALAELKEEYEDRGLELVEVAEGWRLQTK 71 (184)
T ss_pred HHHHHHHHHHhc-----------CCCCCHHHHHHHhCCC------chHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEeh
Confidence 355677777754 4589999999988532 2333444444444332 11233455666556
Q ss_pred HHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCce
Q 009725 365 KIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQ 444 (527)
Q Consensus 365 ~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t 444 (527)
....-.-....+.-....++..+.+.+-++.-+ .-+..-+|.+.-..... .++..|...|+| .++++...|+|+
T Consensus 72 ~~~~~~~~~l~~~~~~~~LSraalEtLAiIAY~-QPiTR~eI~~iRGv~~~---~~i~~L~e~glI--~~~g~~~~~Grp 145 (184)
T COG1386 72 QEYAEYLEKLQEQRPKRELSRAALETLAIIAYK-QPVTRSEIEEIRGVAVS---QVISTLLERGLI--REVGRRDTPGRP 145 (184)
T ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHc-CCccHHHHHHHhCccHH---HHHHHHHHCCCe--EecCCCCCCCCc
Confidence 655555555666666667899999999999665 44588888888776654 389999999999 567766577776
Q ss_pred EEE
Q 009725 445 FLL 447 (527)
Q Consensus 445 ~~l 447 (527)
+.+
T Consensus 146 ~ly 148 (184)
T COG1386 146 YLY 148 (184)
T ss_pred eee
Confidence 543
No 126
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=63.95 E-value=18 Score=27.83 Aligned_cols=35 Identities=9% Similarity=0.242 Sum_probs=28.8
Q ss_pred CHHHHHh-hcCCCHHHHHHHHHHHHhcccccccccc
Q 009725 36 TRQNVKR-YTELSDEQVKNALLVLIQQNCVQAFTTE 70 (527)
Q Consensus 36 tl~~i~~-~t~l~~~~Vr~~L~vLiQhn~V~~~~~~ 70 (527)
=+.++.+ .....+++|++++..||+-+.+.||...
T Consensus 21 YfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yWSSG 56 (67)
T PF08679_consen 21 YFKDFYKAFPDAKPREVKKIVNELVNEGKLEYWSSG 56 (67)
T ss_dssp EHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred eHHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEEcCC
Confidence 3778877 5789999999999999999999988764
No 127
>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=63.89 E-value=7.8 Score=29.33 Aligned_cols=35 Identities=20% Similarity=0.279 Sum_probs=29.3
Q ss_pred hcC-CC-CHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 31 RKG-PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 31 ~~G-~~-tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
..| .+ +..+|++..+++...|+.||-.|.+.|+|.
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 344 56 789999999999999999999999999997
No 128
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=63.73 E-value=16 Score=36.24 Aligned_cols=42 Identities=24% Similarity=0.180 Sum_probs=36.8
Q ss_pred HHHHHHHhcC-CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 24 KVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 24 ~V~~~Ll~~G-~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.|-++|..++ ++++.+|.+.++++.+.+...|-.|.++|+|.
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4555666655 59999999999999999999999999999997
No 129
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=63.71 E-value=19 Score=28.73 Aligned_cols=45 Identities=11% Similarity=0.130 Sum_probs=41.6
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~ 68 (527)
.|-++|-.+|+.++.+|.+..+.|+.-|..=|-.|+.-|-|....
T Consensus 6 qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 577899999999999999999999999999999999999998543
No 130
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=63.51 E-value=19 Score=32.00 Aligned_cols=63 Identities=8% Similarity=0.091 Sum_probs=48.4
Q ss_pred hHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 387 AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 387 ~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
-++|+..|...+.+ .+++|++...+++..+=.++.+|.+.|||.-+.-| ...|..+++--+.-
T Consensus 42 q~~vL~~l~~~~~~-t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~---~DrR~~~l~LT~~G 104 (144)
T PRK11512 42 QFKVLCSIRCAACI-TPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP---NDKRGVLVKLTTSG 104 (144)
T ss_pred HHHHHHHHHHcCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc---ccCCeeEeEEChhH
Confidence 34667777666677 99999999999999999999999999999433222 55777777655533
No 131
>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=62.71 E-value=14 Score=29.72 Aligned_cols=35 Identities=11% Similarity=0.191 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHH
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L 55 (527)
+-...|.+.|.. |..|+.+|++.+|++...|+.+|
T Consensus 6 ~R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 6 ERVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 356788999999 99999999999999999999966
No 132
>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=62.24 E-value=25 Score=26.46 Aligned_cols=45 Identities=18% Similarity=0.248 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
...|+..--..+..+..+|++..+++++.|-..|-.|...|+|.|
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEe
Confidence 345666666788999999999999999999999999999999984
No 133
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=61.87 E-value=8.9 Score=37.83 Aligned_cols=45 Identities=16% Similarity=0.333 Sum_probs=40.1
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+++|+++|...+.+ .-.+|++...||...+..+|..|.+.|||+
T Consensus 15 r~l~IL~~l~~~~~l-~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 15 KVFGILQALGEEREI-GITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHHHHhhcCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 467888888776666 999999999999999999999999999983
No 134
>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=61.75 E-value=13 Score=32.84 Aligned_cols=74 Identities=14% Similarity=0.010 Sum_probs=51.6
Q ss_pred CchHHHHHHHHHh--CCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHHHHHH
Q 009725 385 RDAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDE 462 (527)
Q Consensus 385 ~~~~RI~r~l~~k--~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~~~~~ 462 (527)
.-|+|++-.|... +..+.-++|++..-+|..-++++|.+|.+.|+|..+ ++... -|.+.-+++. .-+.+
T Consensus 8 ~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~---~G~~G---gy~l~~~~~~---Itl~d 78 (135)
T TIGR02010 8 RYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV---RGPGG---GYQLGRPAED---ISVAD 78 (135)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE---eCCCC---CEeccCCHHH---CcHHH
Confidence 4478888888643 334599999999999999999999999999999643 22111 2555555543 33445
Q ss_pred HHHHH
Q 009725 463 MFHAA 467 (527)
Q Consensus 463 ~yk~~ 467 (527)
++.++
T Consensus 79 v~~a~ 83 (135)
T TIGR02010 79 IIDAV 83 (135)
T ss_pred HHHHh
Confidence 55444
No 135
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=61.12 E-value=1.1e+02 Score=29.58 Aligned_cols=121 Identities=7% Similarity=-0.004 Sum_probs=88.1
Q ss_pred hc-hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHh
Q 009725 18 FG-DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRV 96 (527)
Q Consensus 18 FG-~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rl 96 (527)
|+ ..=..|.++...+++..+.++....+++.+..|-=|-+|-.|+++....... . ..+|..|..
T Consensus 98 ~~ns~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g--~-------~~yfpa~~t------ 162 (240)
T COG3398 98 FLNSKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGG--A-------LRYFPADMT------ 162 (240)
T ss_pred HhhhhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCC--c-------eEEccCCCC------
Confidence 44 3345789999999999999999999999999999999999999998544331 0 122322211
Q ss_pred chhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccce
Q 009725 97 RFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 164 (527)
Q Consensus 97 R~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~ 164 (527)
..+.= +-..=|.....|+.++..++..+...+-.... .+.+.+.=...+|-+-|+|.
T Consensus 163 ~~~~e---~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~--------ls~aTV~~~lk~l~~~Gii~ 219 (240)
T COG3398 163 YGEAE---VLSLKNETSKAIIYEIQENKCNTNLLIAYELN--------LSVATVAYHLKKLEELGIIP 219 (240)
T ss_pred cccch---HHHhhchhHHHHHHHHhcCCcchHHHHHHHcC--------ccHHHHHHHHHHHHHcCCCc
Confidence 00000 22234677899999999999999888766542 35677888888998888873
No 136
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=60.93 E-value=9.1 Score=26.58 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=30.0
Q ss_pred chhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 402 ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 402 eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
..++|++...++...+...|.+|.+.|+|..+
T Consensus 10 s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 10 TRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 78899999999999999999999999999755
No 137
>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=60.88 E-value=14 Score=27.86 Aligned_cols=45 Identities=22% Similarity=0.303 Sum_probs=38.3
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
....|+..+...+ . ..++|++...++...++..|..|...|+|.-
T Consensus 8 ~~~~il~~l~~~~-~-~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 8 TRLRILRLLLEGP-L-TVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHHHHCC-c-CHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 3456777776654 5 9999999999999999999999999999954
No 138
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=60.70 E-value=35 Score=29.65 Aligned_cols=62 Identities=16% Similarity=0.239 Sum_probs=47.5
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhcC-CCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEee
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL 88 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t~-l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~ 88 (527)
|.-.--|...|.. |..-+.+|.+..+ ++.+-+-+.|-.|.++|+|.--..+. .+..+.|++-
T Consensus 22 ~kW~~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~-------~PprveY~LT 84 (120)
T COG1733 22 GKWTLLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYPE-------EPPRVEYRLT 84 (120)
T ss_pred CccHHHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEeeecCC-------CCceeEEEEh
Confidence 3556667777776 9999999999977 99999999999999999998322221 1225788875
No 139
>PRK11569 transcriptional repressor IclR; Provisional
Probab=60.52 E-value=19 Score=35.86 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=34.9
Q ss_pred HHHHHh-cCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 26 CECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 26 ~~~Ll~-~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
-++|.. .+++++.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 34 L~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 34 LEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 333444 4679999999999999999999999999999997
No 140
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=60.16 E-value=1.2e+02 Score=28.58 Aligned_cols=134 Identities=13% Similarity=0.216 Sum_probs=86.6
Q ss_pred HHHHHHHHccchhhhcccccCCCc-cChHHHHHHhhhcccCCCCCHHHHHHHHHHhccC----CC---CCCCCCcEEEeh
Q 009725 292 NVLSAMLQATSSAEKKVKTKNSVP-LSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGEL----SF---VDASSDSYSIDF 363 (527)
Q Consensus 292 ~v~~~~L~~~~~~~~~~~~~~s~p-~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~----~~---~~~~~~~y~V~~ 363 (527)
.+++|+|-.+ +.| +|..+|.+-+... ..+.+...++.|... +. ...-+|.|.+-.
T Consensus 4 ~~iEAlLF~s-----------g~pgls~~~La~il~~~------~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~t 66 (186)
T TIGR00281 4 AIIEALLFVS-----------GEPGVTLAELVRILGKE------KAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVT 66 (186)
T ss_pred HHHHHHHHHc-----------CCCCCCHHHHHHHhCCC------chHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEE
Confidence 4677777765 346 9999999887421 123344444444322 21 134467888887
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCc
Q 009725 364 EKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQS 443 (527)
Q Consensus 364 ~~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~ 443 (527)
+.-..-.....+..-... +...++..+-++.-+.-+ ...+|.+.-.++ +...+.+|.+.|+|.. +.+...|+|
T Consensus 67 k~e~~~~i~~~~~~~~~~-LS~aaLEtLAIIAY~QPI-Tr~eIe~IRGv~---s~~~l~~L~ergLI~~--~Gr~~~~Gr 139 (186)
T TIGR00281 67 KPAFADYIHRFLPAKLKN-LNSASLEVLAIIAYKQPI-TRARINEIRGVK---SYQIVDDLVEKGLVVE--LGRKDTPGR 139 (186)
T ss_pred hHHHHHHHHHHhcccccc-CCHHHHHHHHHHHHcCCc-CHHHHHHHcCCC---HHHHHHHHHHCCCeEe--cCcCCCCCC
Confidence 776665555555443333 778999999999766554 999999888877 6789999999999943 222225666
Q ss_pred eEEEEEE
Q 009725 444 QFLLWKV 450 (527)
Q Consensus 444 t~~lw~v 450 (527)
++ +|..
T Consensus 140 p~-ly~T 145 (186)
T TIGR00281 140 SF-IYET 145 (186)
T ss_pred Ce-eehh
Confidence 54 4443
No 141
>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=59.21 E-value=17 Score=27.95 Aligned_cols=49 Identities=16% Similarity=0.278 Sum_probs=38.9
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEecc
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVT 438 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt 438 (527)
.|..+|..+|.. +-.+|+...-+++..++..|-.|.+.|+|.-.+.+..
T Consensus 4 ~i~~~l~~~~~~-S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~~ 52 (69)
T PF09012_consen 4 EIRDYLRERGRV-SLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSSC 52 (69)
T ss_dssp HHHHHHHHS-SE-EHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE--
T ss_pred HHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCCC
Confidence 466778777777 9999999999999999999999999999987766553
No 142
>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=58.82 E-value=12 Score=32.74 Aligned_cols=51 Identities=18% Similarity=0.200 Sum_probs=42.7
Q ss_pred HcCCchHHHHHHHHHh-CCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 382 RYGRDAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 382 ~~G~~~~RI~r~l~~k-~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
+...-|.|++..|... +..+.-++|++...+|...++++|..|.+.|+|.-
T Consensus 6 ~~~~yal~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 6 KLTDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred hHHhHHHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 3456688999998754 33449999999999999999999999999999954
No 143
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=58.74 E-value=9.9 Score=31.74 Aligned_cols=48 Identities=13% Similarity=0.213 Sum_probs=35.9
Q ss_pred cCCchHHHHHHHHH----hCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 383 YGRDAYRIFRLLSK----SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 383 ~G~~~~RI~r~l~~----k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+....+||++|.. ...+ .-++|++..-++.+++|+.|..|..+|+|.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGV-HVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTE-EHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcc-cHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 34445567777755 1234 778899999999999999999999999985
No 144
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=58.70 E-value=14 Score=26.74 Aligned_cols=33 Identities=24% Similarity=0.259 Sum_probs=30.5
Q ss_pred CCC-CHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 33 GPL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 33 G~~-tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+++ |..+|++..+++...|+.+|-.|.+.|+|.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 356 799999999999999999999999999986
No 145
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=58.61 E-value=10 Score=35.36 Aligned_cols=43 Identities=28% Similarity=0.373 Sum_probs=36.3
Q ss_pred HHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 390 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 390 I~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
+.-.|...++. .-.+|++...|+.+++-..||+|++.|.|..-
T Consensus 18 ~~~~l~~~~~~-~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 18 EVKNLGLGEGI-TAIEISRKLNIEKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHhccCCCc-cHHHHHHHhCCCHHHHHHHHHHHHhcCceecC
Confidence 55556555566 99999999999999999999999999999543
No 146
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=58.46 E-value=14 Score=36.69 Aligned_cols=51 Identities=24% Similarity=0.277 Sum_probs=44.6
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEecc
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVT 438 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt 438 (527)
.-|+.++..+|.-+.|.+|.+...+|.-.+..+|.+|-+.|+|+.+-.-++
T Consensus 198 ~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~ 248 (258)
T COG2512 198 KEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRT 248 (258)
T ss_pred HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCe
Confidence 347778888887669999999999999999999999999999999866555
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=58.36 E-value=23 Score=26.43 Aligned_cols=55 Identities=25% Similarity=0.262 Sum_probs=39.5
Q ss_pred hhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 98 FAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 98 ~p~~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
...|+...-+.||. ....++.++..++.+.+.- +...+...+..|.+.|+|...+
T Consensus 5 ia~~l~~l~~~~~~-------~~~~~~~~s~~ela~~~g~--------s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 5 LASFLLNLSLRYGA-------GDLVQLPLTRQEIADYLGL--------TRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHHHHHcCC-------CccccCCcCHHHHHHHHCC--------CHHHHHHHHHHHHHCCCEEecC
Confidence 34444444445654 2335778898888887643 5778999999999999998875
No 148
>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=58.32 E-value=17 Score=27.41 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=36.7
Q ss_pred HHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 390 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 390 I~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
||++-. .+..+..++||+..-+++..+-+.+.+|.+.|||..+
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 677765 4555699999999999999999999999999999765
No 149
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=57.45 E-value=31 Score=29.17 Aligned_cols=50 Identities=26% Similarity=0.407 Sum_probs=40.2
Q ss_pred HHHHHHHH-cccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 115 ELVQGLLE-HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 115 ~I~~~lL~-~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.|++.|.. .++++++++.+.+....+ ..+...+-.++..|++.|+|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~---~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGP---SISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCC---CCCHHHHHHHHHHHHhCCCEEEEE
Confidence 46677776 468999999999865422 346788999999999999999985
No 150
>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=57.30 E-value=30 Score=26.53 Aligned_cols=46 Identities=17% Similarity=0.301 Sum_probs=38.4
Q ss_pred hhHHHHHHHHHhcC-CCCHHHHHhhcCCC-HHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKG-PLTRQNVKRYTELS-DEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G-~~tl~~i~~~t~l~-~~~Vr~~L~vLiQhn~V~ 65 (527)
++-..|..++-.+| +-|+.+|.+..+++ ++.|..-|-.|..-|++.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 45567778888888 55799999999996 999999999999999997
No 151
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=57.30 E-value=18 Score=35.49 Aligned_cols=40 Identities=25% Similarity=0.284 Sum_probs=34.8
Q ss_pred HHHHHh-cCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 26 CECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 26 ~~~Ll~-~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
-+++.. .+++++.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 15 L~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 15 IEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 333443 5679999999999999999999999999999997
No 152
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=56.42 E-value=14 Score=36.81 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=40.0
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+++|+++|...+.-+.-.+|++...||...+..+|..|.+.|||.
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678888887655434999999999999999999999999999993
No 153
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=56.39 E-value=14 Score=36.58 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=40.5
Q ss_pred chHHHHHHHHHhCC-CcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKSGR-LLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k~~-l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+.+|+++|...+. + ...+|++..-+|...+..+|..|.+.|||+
T Consensus 12 ral~iL~~l~~~~~~l-s~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 12 RGLMVLRALNRLDGGA-TVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHHHhcCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 57789999977654 6 999999999999999999999999999995
No 154
>PRK11569 transcriptional repressor IclR; Provisional
Probab=56.25 E-value=14 Score=36.89 Aligned_cols=46 Identities=7% Similarity=0.270 Sum_probs=39.9
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+++|+++|.+.+.-+.-.+|++...+|...+..+|..|.+.||+.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678888887654434999999999999999999999999999995
No 155
>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=55.59 E-value=22 Score=33.77 Aligned_cols=48 Identities=21% Similarity=0.158 Sum_probs=43.0
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.+.-..|...|..+|+.++.+|++.++++.+.+..-|-.|.+.|+|..
T Consensus 142 s~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r 189 (203)
T TIGR01884 142 SREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQ 189 (203)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 444557888888889999999999999999999999999999999983
No 156
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=55.47 E-value=24 Score=32.99 Aligned_cols=46 Identities=22% Similarity=0.237 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
++|.+++..|-..|..|..+|.+..+++.+.|=..|..|.+-+.|+
T Consensus 13 ~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~ 58 (183)
T PHA03103 13 ELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVY 58 (183)
T ss_pred HHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCcee
Confidence 7889999999999999999999999999999999999999999996
No 157
>PRK11050 manganese transport regulator MntR; Provisional
Probab=55.26 E-value=28 Score=31.51 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=38.2
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
..|...+...|+.+..+|++..+++.+.|...|-.|.+.|+|.
T Consensus 40 ~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 40 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3455666677999999999999999999999999999999986
No 158
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=55.25 E-value=15 Score=36.08 Aligned_cols=91 Identities=18% Similarity=0.153 Sum_probs=61.5
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHHHHHH--H
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDE--M 463 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~~~~~--~ 463 (527)
.|++|+.+|........-.+|++...+|...++.+|..|.+.|||.-- ....+|+|.---. .+-...+.. +
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d------~~~g~Y~Lg~~~~-~lg~~~l~~~~l 77 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQD------PEDGRYRLGPRLL-ELGAAALSSLDL 77 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEc------CCCCcEeehHHHH-HHHHHHHhcCCH
Confidence 578899999774442379999999999999999999999999999321 2233444432222 222344443 6
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 009725 464 FHAALNLSLRVSYELDREKE 483 (527)
Q Consensus 464 yk~~~nl~~R~~~e~~~~k~ 483 (527)
.+.+.-.+.++..+......
T Consensus 78 ~~~a~p~l~~L~~~tgetv~ 97 (246)
T COG1414 78 VSLARPLLEELAEETGETVH 97 (246)
T ss_pred HHHhHHHHHHHHHHhCCcEE
Confidence 77777777777776654433
No 159
>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=55.11 E-value=28 Score=30.33 Aligned_cols=34 Identities=21% Similarity=0.232 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++.+..+|++..++|++.|.+.|-.|.+.|+|..
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 5789999999999999999999999999999973
No 160
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=55.10 E-value=12 Score=31.12 Aligned_cols=43 Identities=21% Similarity=0.435 Sum_probs=39.0
Q ss_pred HHHHHHHHhcCC-CCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~-~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
=.|.+.|+.+|+ +-+++|.+..+++...|+.++.+|...|++-
T Consensus 24 I~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~ 67 (113)
T COG5625 24 IRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLA 67 (113)
T ss_pred hhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHH
Confidence 478899999887 8999999999999999999999999888876
No 161
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=54.92 E-value=31 Score=26.87 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=26.7
Q ss_pred CCCCHHHHHhh---cCCCHHHHHHHHHHHHhccccc
Q 009725 33 GPLTRQNVKRY---TELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 33 G~~tl~~i~~~---t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
|.++...|+.. .+++...||.||.-|.+.|.+.
T Consensus 19 ~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~ 54 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLE 54 (70)
T ss_dssp S-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEE
T ss_pred CceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCcee
Confidence 57788888776 5789999999999999999997
No 162
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=54.61 E-value=18 Score=31.54 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=38.3
Q ss_pred chHHHHHHHHHh--CCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k--~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.|.+++-.|... +..+.-++|++..-+|...++++|..|.+.|+|.
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 466777777643 2245999999999999999999999999999984
No 163
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=54.42 E-value=15 Score=36.09 Aligned_cols=45 Identities=18% Similarity=0.321 Sum_probs=39.6
Q ss_pred chHHHHHHHHHhC-CCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 386 DAYRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 386 ~~~RI~r~l~~k~-~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+.+|+.++...+ .+ .-.+|++...+|...+..+|..|...|||+
T Consensus 10 ral~IL~~l~~~~~~~-~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRL-TLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678888887544 45 999999999999999999999999999995
No 164
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=54.00 E-value=42 Score=26.32 Aligned_cols=42 Identities=19% Similarity=0.146 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
..|-.+|. ++++|+.+|...|+++.+.+--.|.-|...|+|.
T Consensus 8 ~~IL~~ls-~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 8 QKILIILS-KRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred HHHHHHHH-hccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 34444444 5599999999999999999999999999999997
No 165
>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=53.43 E-value=20 Score=29.29 Aligned_cols=62 Identities=10% Similarity=0.108 Sum_probs=38.4
Q ss_pred HHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHH
Q 009725 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILH 94 (527)
Q Consensus 27 ~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~ 94 (527)
..|+.+|.-+++.|...|++|.+.++.+|..|--.++..-|..+... ...-+|.+.-=+++.
T Consensus 14 a~li~~~~~nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~G~R------~~~GyY~i~~WG~id 75 (90)
T PF09904_consen 14 AYLIDSGERNVPALMEATGMPRRTIQDTIKALPELGIECEFVQDGER------NNAGYYRISDWGPID 75 (90)
T ss_dssp HHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-------S--EEEEEE-TTB-
T ss_pred HHHHhcCCccHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEecCcc------CCCCcEEeeecCCCC
Confidence 46788888899999999999999999999999999988766543211 112478876444443
No 166
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=52.43 E-value=40 Score=32.57 Aligned_cols=105 Identities=18% Similarity=0.225 Sum_probs=70.6
Q ss_pred CCCccChHHHHHHhhhcc-cCCCCCHHHHHHHHHHhccCC----CCCCCCCcEEEehHHHHHHHHHHHHHHHHHHHcCCc
Q 009725 312 NSVPLSLSSIYEEVIKSE-AGRNMTLDHVRASLVQLGELS----FVDASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRD 386 (527)
Q Consensus 312 ~s~p~s~~~I~~~l~~~~-~~~~~~~~~i~~~L~~La~~~----~~~~~~~~y~V~~~~i~~~lr~~~le~~v~~~~G~~ 386 (527)
++.-+++.+++..+.+.- ....++++.+.+.++.|..-+ ...-++|...|-.....+. +..
T Consensus 110 ~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~~~~e~--------------~~~ 175 (223)
T PF04157_consen 110 NGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSVPYSEL--------------SKD 175 (223)
T ss_dssp TTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECST-CHH---------------HH
T ss_pred CCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeCCchhh--------------hHH
Confidence 345788999999887754 223577889999999886554 1144556665555443331 223
Q ss_pred hHHHHHHH--HHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 387 AYRIFRLL--SKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 387 ~~RI~r~l--~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
..+|+.++ -..|.. +..++++....+..-|++.|..|..+|++-
T Consensus 176 ~~~il~~~~~~~~g~v-t~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 176 QSRILELAEEENGGGV-TASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp HHHHHHHH--TTTSEE-EHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhhcCCCC-CHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 34555565 344455 999999999999999999999999999974
No 167
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=51.84 E-value=2.2e+02 Score=27.21 Aligned_cols=51 Identities=18% Similarity=0.267 Sum_probs=40.9
Q ss_pred HhhchhHH-HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 16 NHFGDLVA-KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 16 ~~FG~~v~-~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
+..|.-.. +|-+.| .+-++-..+|++..+++++.|-.=|-.|-+-|+|..+
T Consensus 10 dvLGNetRR~Il~lL-t~~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ 61 (217)
T COG1777 10 DVLGNETRRRILQLL-TRRPCYVSEISRELGVSQKAVLKHLRILERAGLVESR 61 (217)
T ss_pred HHHcCcHHHHHHHHH-hcCchHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhh
Confidence 56675444 455544 5555899999999999999999999999999999953
No 168
>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=51.05 E-value=30 Score=26.47 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=35.5
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+|... +..|..+..+|+...+++.+.|++.+..|-+.|+..
T Consensus 4 ~il~~-L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 4 RLLAL-LADNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHH-HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 44555 457788999999999999999999999999999975
No 169
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=50.48 E-value=41 Score=29.32 Aligned_cols=48 Identities=15% Similarity=0.196 Sum_probs=38.5
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
.+-|..+|+..++-+...|+.||.+|.+.|++. ...+ .++|-.++.+.
T Consensus 52 ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe-~~ed-----------~~i~i~~~~~~ 99 (121)
T PF09681_consen 52 IPYTAEMLALEFDRPVDTVRLALAVFQKLGLIE-IDED-----------GVIYIPNWEKH 99 (121)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecC-----------CeEEeecHHHH
Confidence 366788888889999999999999999999998 3333 25777777654
No 170
>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=49.99 E-value=21 Score=33.83 Aligned_cols=51 Identities=16% Similarity=0.234 Sum_probs=44.3
Q ss_pred HcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 382 RYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 382 ~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
.......+|+..|..+|.. ..++|++..-++...++..|.+|.+.|||.-.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~-s~~eia~~l~is~stv~r~L~~Le~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEK-SVKNIAKKLGKSLSTISRHLRELEKKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3455566888888777787 99999999999999999999999999999755
No 171
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=49.90 E-value=32 Score=30.61 Aligned_cols=49 Identities=12% Similarity=0.231 Sum_probs=43.9
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccccc
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
.=.+|-..|...|+.|+.+|++..++|++.|+.=+--|...|++.-|..
T Consensus 9 ~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~ 57 (154)
T COG1522 9 IDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTA 57 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEE
Confidence 3457888999999999999999999999999999999999999985544
No 172
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=49.85 E-value=1.8e+02 Score=25.52 Aligned_cols=61 Identities=7% Similarity=0.067 Sum_probs=45.7
Q ss_pred HHHHHHHHHhC-CCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEch
Q 009725 388 YRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNR 452 (527)
Q Consensus 388 ~RI~r~l~~k~-~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~ 452 (527)
+.++..|...+ .. .+.+|++...++...+-.++.+|.+.|||+-..-| ...|..+++-.+.
T Consensus 34 ~~vL~~l~~~~~~~-t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~---~DrR~~~l~LT~~ 95 (144)
T PRK03573 34 WVTLHNIHQLPPEQ-SQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA---SDRRAKRIKLTEK 95 (144)
T ss_pred HHHHHHHHHcCCCC-CHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC---CCcCeeeeEEChH
Confidence 45666665544 46 89999999999999999999999999999544222 4467666665543
No 173
>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=49.19 E-value=12 Score=35.17 Aligned_cols=85 Identities=13% Similarity=0.246 Sum_probs=40.0
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhh
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~ 100 (527)
+.....+++-.+.-++|.+|+...+|+...+.+-+-.|...|.++=..++ . |+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd--r-------------------------Gk 152 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDD--R-------------------------GK 152 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T--T---------------------------
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC--C-------------------------CC
Confidence 67778889999999999999999999999999999999999998722221 1 45
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhh
Q 009725 101 FLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAK 136 (527)
Q Consensus 101 ~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~ 136 (527)
||++-.+.+ ..|...+-+.|++++++|...+.
T Consensus 153 fIyIs~eE~----~~va~fi~~rGRvsi~el~~~~N 184 (188)
T PF09756_consen 153 FIYISEEEM----EAVAKFIKQRGRVSISELAQESN 184 (188)
T ss_dssp EEE---------------------------------
T ss_pred eEEecHHHH----HHHHHHHHHcCCccHHHHHHHHH
Confidence 555555556 44556677899999999987654
No 174
>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=49.16 E-value=37 Score=25.52 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=30.5
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 398 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 398 ~~l~-eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
|..+ .+.+|++.--++...+|+.|..|..+|+|+..
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 4455 89999999999999999999999999999764
No 175
>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=49.06 E-value=42 Score=29.15 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++.|..+|+..+++|++.|++.|-.|.+.|+|..
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 4899999999999999999999999999999973
No 176
>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=48.88 E-value=48 Score=29.17 Aligned_cols=33 Identities=18% Similarity=0.275 Sum_probs=31.4
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
++.|..+|+...++|+.-+++.|-.|.+.|+|.
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~ 56 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVK 56 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence 468999999999999999999999999999997
No 177
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=48.41 E-value=65 Score=27.17 Aligned_cols=46 Identities=24% Similarity=0.278 Sum_probs=37.5
Q ss_pred HHHHHHHhc-CCCCHHHHHhhc-----CCCHHHHHHHHHHHHhccccccccc
Q 009725 24 KVCECLLRK-GPLTRQNVKRYT-----ELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 24 ~V~~~Ll~~-G~~tl~~i~~~t-----~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
.|.++|... +.+|..+|.... +++...|-.+|-.|.+.|+|.....
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 567777764 578999998774 6899999999999999999985443
No 178
>PRK09462 fur ferric uptake regulator; Provisional
Probab=48.29 E-value=49 Score=29.62 Aligned_cols=53 Identities=15% Similarity=0.226 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHc--ccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 112 QCVELVQGLLEH--GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 112 ~a~~I~~~lL~~--G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.=..|++.|... +++++.+|.+.+....+ ..+...|-.++..|++.|+|.++.
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~---~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGE---EIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHCCCEEEEE
Confidence 445677777763 69999999999865432 346788999999999999999875
No 179
>PRK10870 transcriptional repressor MprA; Provisional
Probab=47.30 E-value=1.6e+02 Score=27.24 Aligned_cols=51 Identities=8% Similarity=-0.089 Sum_probs=39.0
Q ss_pred hhchhHH--HHHHHHHh--cCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 17 HFGDLVA--KVCECLLR--KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 17 ~FG~~v~--~V~~~Ll~--~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
.+|-... .|-..|.. .|++|..+|++..+++...|-..+-.|.+.|+|.-.
T Consensus 50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 4553333 34444443 356899999999999999999999999999999843
No 180
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=47.08 E-value=28 Score=30.93 Aligned_cols=47 Identities=19% Similarity=0.377 Sum_probs=37.1
Q ss_pred hHHHHHHHHH--hCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 387 AYRIFRLLSK--SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 387 ~~RI~r~l~~--k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
|.|..=.+.. .|..+.+++|++...+|..-+|++|.+|.++|+|...
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~ 58 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV 58 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence 4454444432 3455699999999999999999999999999999544
No 181
>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=46.87 E-value=55 Score=23.53 Aligned_cols=40 Identities=18% Similarity=0.285 Sum_probs=33.5
Q ss_pred HHHHHHHH-hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcc
Q 009725 23 AKVCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQN 62 (527)
Q Consensus 23 ~~V~~~Ll-~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn 62 (527)
.+|...|+ ..++.|..+|+...+++.+.|++-|-.|-..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 35677784 45679999999999999999999999998888
No 182
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=46.82 E-value=73 Score=26.23 Aligned_cols=60 Identities=20% Similarity=0.117 Sum_probs=45.5
Q ss_pred HHHHHHHHhc--CCCCHHHHHhhcCCCHHHHHHHHH----------HHHhcccccccccccCCCCCCCCCcceEEEeehh
Q 009725 23 AKVCECLLRK--GPLTRQNVKRYTELSDEQVKNALL----------VLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (527)
Q Consensus 23 ~~V~~~Ll~~--G~~tl~~i~~~t~l~~~~Vr~~L~----------vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (527)
.+|..+|... .+.++.+|++.++.+++.|+-||. .|+..|+|...... .+ ..+|.+...
T Consensus 12 ~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~-~g--------~k~Y~lT~~ 82 (90)
T PF07381_consen 12 KKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEK-GG--------FKYYRLTEK 82 (90)
T ss_pred HHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeec-CC--------eeEEEeChh
Confidence 5678888887 356788999999999999999996 69999999422222 11 358888765
Q ss_pred h
Q 009725 91 N 91 (527)
Q Consensus 91 ~ 91 (527)
.
T Consensus 83 G 83 (90)
T PF07381_consen 83 G 83 (90)
T ss_pred h
Confidence 4
No 183
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=46.10 E-value=67 Score=27.66 Aligned_cols=55 Identities=9% Similarity=0.194 Sum_probs=44.3
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHH
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNIL 93 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il 93 (527)
..||.+|+....-+.+.+|.-|--|.+.|.+. |.+....| +.+...+..+++.++
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~-W~pg~GRG----~~S~L~~l~~~~~~~ 73 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQEEGWIT-WQPGRGRG----NRSQLTFLKSPEELL 73 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee-eeCCCCCC----CCCeeEEeeCHHHHH
Confidence 56999999999999999999999999999998 77664333 555566767766654
No 184
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=45.75 E-value=52 Score=31.93 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=47.1
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccC
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG 439 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~ 439 (527)
.+|+.+|..||-+ .-.+|++...+|...+-.-+..|.+.|+|+..-++-+.
T Consensus 26 v~Il~lL~~k~pl-NvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~kark 76 (308)
T COG4189 26 VAILQLLHRKGPL-NVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARK 76 (308)
T ss_pred HHHHHHHHHhCCC-CHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeecccc
Confidence 5799999999999 99999999999999999999999999999998887654
No 185
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=45.59 E-value=57 Score=29.23 Aligned_cols=54 Identities=24% Similarity=0.351 Sum_probs=43.7
Q ss_pred hhHHHHHHHHHHc-ccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 111 QQCVELVQGLLEH-GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 111 ~~a~~I~~~lL~~-G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
+.=..|++-|.++ |++++.++...+....+ ..+...|-+++..|.+.|+|.++.
T Consensus 21 ~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p---~islaTVYr~L~~l~e~Glv~~~~ 75 (145)
T COG0735 21 PQRLAVLELLLEADGHLSAEELYEELREEGP---GISLATVYRTLKLLEEAGLVHRLE 75 (145)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhCC---CCCHhHHHHHHHHHHHCCCEEEEE
Confidence 4456778888866 77999999999876433 356888999999999999999975
No 186
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=44.84 E-value=38 Score=28.01 Aligned_cols=46 Identities=22% Similarity=0.190 Sum_probs=39.2
Q ss_pred CchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 385 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 385 ~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
+....|+..|.+-|-= -.+.|+....+|..+++..|-+|.+.|+|+
T Consensus 7 ~l~~~IL~hl~~~~~D-y~k~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPD-YAKSIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred hhHHHHHHHHHHHCCC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4567788888766655 678899999999999999999999999994
No 187
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=44.56 E-value=1.1e+02 Score=28.05 Aligned_cols=117 Identities=13% Similarity=0.154 Sum_probs=70.9
Q ss_pred HHHHHHHhcC-CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhhHH
Q 009725 24 KVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFL 102 (527)
Q Consensus 24 ~V~~~Ll~~G-~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i 102 (527)
.|=..|+..| ++++.+|.+.++ +...|+.+|--|.+.- ...+ . ..--....+-|.+.--|.|-
T Consensus 2 ~iEAlLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y-----~~~~-~---------gl~l~~~~~~y~l~tk~~~~ 65 (159)
T PF04079_consen 2 IIEALLFASGEPVSIEELAEILG-SEDEVEEALEELQEEY-----NEED-R---------GLELVEVGGGYRLQTKPEYA 65 (159)
T ss_dssp HHHHHHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHHHHH-----HHCT-----------SEEEEEETTEEEEEE-GGGH
T ss_pred hhHhhHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHh-----ccCC-C---------CEEEEEECCEEEEEEhHHHH
Confidence 3445677775 899999999999 9999999999998753 1111 1 11222234444444556666
Q ss_pred HHHHHHhhh--------hHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 103 TILSQEFDQ--------QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 103 ~~i~~~yG~--------~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.++++.++. .+-+.+--+.-++=+|-.++-+-=.. .-...+.+|.+.|||..+.
T Consensus 66 ~~v~~~~~~~~~~~LS~aalEtLAiIAY~QPiTr~eIe~IRGv-----------~s~~~i~~L~e~glI~~~g 127 (159)
T PF04079_consen 66 EYVEKLFKKPKPPKLSQAALETLAIIAYKQPITRAEIEEIRGV-----------NSDSVIKTLLERGLIEEVG 127 (159)
T ss_dssp HHHHHHHCTCCCHHHHHHHHHHHHHHHHH-SEEHHHHHHHHTS-------------HCHHHHHHHTTSEEEEE
T ss_pred HHHHHHhccCccCCCCHHHHHHHHHHHhcCCcCHHHHHHHcCC-----------ChHHHHHHHHHCCCEEecC
Confidence 666666654 45566666666777776665433111 1356789999999999885
No 188
>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=44.43 E-value=38 Score=23.65 Aligned_cols=31 Identities=19% Similarity=0.291 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L 55 (527)
..|.. |+..| .|+.+|++.++++...|...|
T Consensus 12 ~~i~~-l~~~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKE-LYAEG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHH-HHHTT---HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHH-HHHCC-CCHHHHHHHHCcCHHHHHHHH
Confidence 34444 77888 899999999999999987654
No 189
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=44.26 E-value=26 Score=29.43 Aligned_cols=52 Identities=19% Similarity=0.342 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 372 NEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 372 ~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
..++..+++..||-. ++...+...|+++...++...+.+.+..|.+.|+|..
T Consensus 35 ~ki~~ai~RkTyG~n---------Kk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~ 86 (100)
T PF04492_consen 35 LKILLAIIRKTYGWN---------KKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIR 86 (100)
T ss_pred HHHHHHHHHHccCCC---------CccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 367888888888876 5555669999999999999999999999999999933
No 190
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=43.94 E-value=1.8e+02 Score=23.95 Aligned_cols=53 Identities=15% Similarity=0.146 Sum_probs=43.1
Q ss_pred hchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccc
Q 009725 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (527)
Q Consensus 18 FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~ 70 (527)
+++.--.|-.+|...|+.+..+|....+++++.|-..+-.|.+.|+|.-...+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~ 72 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP 72 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence 34555566777788888777999999999999999999999999999843333
No 191
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=43.85 E-value=91 Score=24.50 Aligned_cols=43 Identities=21% Similarity=0.099 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHH--Hhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL--IQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vL--iQhn~V~ 65 (527)
+.|...|..-+.-|+.+|+..|+-.+..||-+|.-+ =+.|+..
T Consensus 13 a~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i 57 (72)
T PF11994_consen 13 AQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTI 57 (72)
T ss_pred HHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEE
Confidence 678888999999999999999999999999999999 4555554
No 192
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=43.56 E-value=41 Score=27.30 Aligned_cols=47 Identities=21% Similarity=0.345 Sum_probs=37.8
Q ss_pred HHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 113 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 113 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
...|+..|.. |..+.+++.+.+.. .+...+.+.+..|.+.|+|.+..
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~-------is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPG-------ISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTT-------S-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcch-------hHHHHHHHHHHHHHHcchhhccc
Confidence 4566667766 99999999988743 25678999999999999999974
No 193
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=43.48 E-value=48 Score=27.16 Aligned_cols=34 Identities=29% Similarity=0.315 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHH
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~ 56 (527)
.+.|...|-.+|. ||..|.+..||+.+.++++|.
T Consensus 10 ~adI~AaL~KrG~-sLa~lsr~~Gls~~TL~nAL~ 43 (92)
T PRK10344 10 PADIIAGLRKKGT-SMAAESRRNGLSSSTLANALS 43 (92)
T ss_pred HHHHHHHHHHcCC-cHHHHHHHcCCChHHHHHHHc
Confidence 3567778888885 999999999999999999874
No 194
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.15 E-value=38 Score=33.44 Aligned_cols=44 Identities=18% Similarity=0.372 Sum_probs=41.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
=.+|.+.|-.+|+.++.+|++..+++...||.=|-.|-+.|+|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 35788899999999999999999999999999999999999886
No 195
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=42.97 E-value=56 Score=29.30 Aligned_cols=49 Identities=22% Similarity=0.263 Sum_probs=36.8
Q ss_pred hhchhHHHHHHHHHhcCCCCHHHHHhhcC-C----CHHHHHHHHHHHHhcc--ccc
Q 009725 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTE-L----SDEQVKNALLVLIQQN--CVQ 65 (527)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~-l----~~~~Vr~~L~vLiQhn--~V~ 65 (527)
.|.+--..|.-.|+-||++|..+|-..++ | +...|...|--|++++ +|.
T Consensus 85 ~l~~~e~All~~LlLRGpQT~GELR~Rs~Rl~~F~d~~~Ve~~L~~L~~r~~plV~ 140 (148)
T PF04337_consen 85 QLSPQELALLCLLLLRGPQTPGELRTRSERLHEFADVAEVEAVLERLAEREPPLVV 140 (148)
T ss_dssp T--HHHHHHHHHHHHH-SB-HHHHHHHHTTTS--SSHHHHHHHHHHHHHTT--SEE
T ss_pred CCCHHHHHHHHHHHHcCCCchhHHHhhhccccCCCCHHHHHHHHHHHHhccchhhe
Confidence 34456667778888999999999976654 2 6799999999999999 664
No 196
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=42.90 E-value=41 Score=32.16 Aligned_cols=50 Identities=14% Similarity=0.127 Sum_probs=39.0
Q ss_pred HhhchhHHHHHHHHHhcC-CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 16 NHFGDLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G-~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
..|..+-..|.+-=+.-| ++|-.+|+...+++..-||.||..|.+-|+|.
T Consensus 11 ~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~ 61 (224)
T PRK11534 11 DGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVT 61 (224)
T ss_pred HHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 334444444444444445 77899999999999999999999999999998
No 197
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=42.47 E-value=49 Score=35.56 Aligned_cols=41 Identities=24% Similarity=0.356 Sum_probs=36.7
Q ss_pred HHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccc
Q 009725 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (527)
Q Consensus 25 V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~ 67 (527)
...+++..|+.|..+|+...+++...|-+-|.+| .++|...
T Consensus 4 ~~~~~L~~g~~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~ 44 (442)
T PRK09775 4 LLTTLLLQGPLSAAELAARLGVSQATLSRLLAAL--GDQVVRF 44 (442)
T ss_pred HHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHHh--hcceeEe
Confidence 3467888999999999999999999999999999 8888743
No 198
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=42.24 E-value=32 Score=27.19 Aligned_cols=40 Identities=23% Similarity=0.311 Sum_probs=31.1
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccc
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 430 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v 430 (527)
.|+..+. +|.. .-.+|+..+-++.+.+.+.|..|.+.|+|
T Consensus 10 ~IL~~l~-~~~~-~~t~i~~~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 10 DILKILS-KGGA-KKTEIMYKANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp HHHHHH--TT-B--HHHHHTTST--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHH-cCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCcCe
Confidence 4556654 6777 88999999999999999999999999999
No 199
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=41.83 E-value=3e+02 Score=25.79 Aligned_cols=43 Identities=5% Similarity=-0.043 Sum_probs=39.6
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.|-.+|..+|++|..+|++.+.++.+.|-..|-.|...|+|.-
T Consensus 49 ~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R 91 (185)
T PRK13777 49 HILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTF 91 (185)
T ss_pred HHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEe
Confidence 6777888889999999999999999999999999999999984
No 200
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=41.82 E-value=99 Score=25.89 Aligned_cols=86 Identities=16% Similarity=0.227 Sum_probs=61.6
Q ss_pred HHcCCch--HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEE-chHHHHH
Q 009725 381 KRYGRDA--YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKV-NRQILWK 457 (527)
Q Consensus 381 ~~~G~~~--~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v-~~~~~~~ 457 (527)
+..|-+. .||+++|.+++.-+--.+|+-.-.|+.-.+|..+..|++.||+.=.=| ..++-=|.|.. .++....
T Consensus 15 ~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relv----qkgWvGYiya~~~P~k~le 90 (113)
T COG5625 15 EAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELV----QKGWVGYIYATTPPPKPLE 90 (113)
T ss_pred HHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHH----hccceeeEecCCCCchHHH
Confidence 3466666 899999998876338899999999999999999999999999931111 44566666654 4555555
Q ss_pred HHHHHHHHHHHHH
Q 009725 458 HVLDEMFHAALNL 470 (527)
Q Consensus 458 ~~~~~~yk~~~nl 470 (527)
.+-+.+.+.+..+
T Consensus 91 ei~~~i~keiEel 103 (113)
T COG5625 91 EIEEEIMKEIEEL 103 (113)
T ss_pred HHHHHHHHHHHHH
Confidence 5555555555444
No 201
>PRK09954 putative kinase; Provisional
Probab=41.76 E-value=28 Score=36.12 Aligned_cols=43 Identities=14% Similarity=0.325 Sum_probs=39.3
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+|+++|.+.+.+ ...+|++..-++...++..+.+|.++|+|.
T Consensus 6 ~~il~~l~~~~~~-s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRNPLI-QQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 3689999887777 999999999999999999999999999984
No 202
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=41.55 E-value=34 Score=32.10 Aligned_cols=44 Identities=9% Similarity=-0.006 Sum_probs=41.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
-..|...|..+|..++.+|++..+.|...||.=|..|-+.|+|.
T Consensus 9 ~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~ 52 (185)
T PRK04424 9 QKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRE 52 (185)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHH
Confidence 45788899999999999999999999999999999999999887
No 203
>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=41.47 E-value=41 Score=26.53 Aligned_cols=46 Identities=11% Similarity=0.057 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.+..++........+|..+|++..++|.+.|++-+..+.+.+.+.
T Consensus 18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 4455555555444788999999999999999999998888777553
No 204
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=41.28 E-value=88 Score=28.94 Aligned_cols=69 Identities=22% Similarity=0.178 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHHH--HHcCCc--hHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEe
Q 009725 368 EIAQNEEVESVVS--KRYGRD--AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 436 (527)
Q Consensus 368 ~~lr~~~le~~v~--~~~G~~--~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvp 436 (527)
+..++..++.+-+ .+||.. ..+|+-+|.-..+-..-.+|++...|+..-+=..+-+|...|+|+.+-.|
T Consensus 5 eqak~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~ 77 (177)
T COG1510 5 EQAKDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEK 77 (177)
T ss_pred HHHHHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhcc
Confidence 3444555555544 556643 45788888654444499999999999999999999999999999777555
No 205
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=40.89 E-value=45 Score=32.91 Aligned_cols=43 Identities=16% Similarity=0.239 Sum_probs=40.8
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.+|.+.|-.+|..++.+|.+..+++...||.=|..|-+.|++.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 5788899999999999999999999999999999999999986
No 206
>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=40.61 E-value=1e+02 Score=23.50 Aligned_cols=47 Identities=15% Similarity=0.211 Sum_probs=34.4
Q ss_pred HHHHHHHHHcccCC-HHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 114 VELVQGLLEHGRLT-LKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 114 ~~I~~~lL~~G~~~-~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
..|.+.+-.+|... ..+|.+.+.- .|...+...+..|.+.|||.+.|
T Consensus 13 ~~I~~~~~~~G~~Pt~rEIa~~~g~-------~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 13 EFIREYIEENGYPPTVREIAEALGL-------KSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHHSS---HHHHHHHHTS-------SSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCC-------CChHHHHHHHHHHHHCcCccCCC
Confidence 44566667788775 5666666542 26788999999999999999986
No 207
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=40.33 E-value=4.1e+02 Score=28.97 Aligned_cols=112 Identities=10% Similarity=0.083 Sum_probs=78.6
Q ss_pred HHHHHHHHHhcCC-CCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhh
Q 009725 22 VAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (527)
Q Consensus 22 v~~V~~~Ll~~G~-~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~ 100 (527)
-.+|-..|...|. .+..+|+..++++...|..++..|-..|+|.. .... ...|++..++--
T Consensus 5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~-~~~~----------~~~~~LT~eG~~------- 66 (492)
T PLN02853 5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDA-QDIK----------RETWVLTEEGKK------- 66 (492)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE-EEEE----------EEEEEECHHHHH-------
Confidence 3466677777775 89999999999999999999999999999983 3321 467888766511
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009725 101 FLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (527)
Q Consensus 101 ~i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v 166 (527)
+++ =|.--+.|+..|-..|.+.++++...+. ...+.-+|-.+.+.|||..-
T Consensus 67 ---~l~--~G~PE~rl~~~l~~~~~~~~~eL~~~l~----------~~~~~i~~g~a~k~gwi~i~ 117 (492)
T PLN02853 67 ---YAA--EGSPEVQLFAAVPAEGSISKDELQKKLD----------PAVFDIGFKQAMKNKWLEMG 117 (492)
T ss_pred ---HHH--cCCHHHHHHHHHhhcCCccHHHHHHhhC----------chhHHHHHHHHHHCCcEEEC
Confidence 111 2444455555555557778888865531 12466788899999998764
No 208
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=40.08 E-value=41 Score=30.37 Aligned_cols=55 Identities=22% Similarity=0.144 Sum_probs=45.4
Q ss_pred cCCchHHHHHHHHHhCC--CcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEec
Q 009725 383 YGRDAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 437 (527)
Q Consensus 383 ~G~~~~RI~r~l~~k~~--l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpk 437 (527)
.|.-|.+++=.|..+.. .+.-++|++.--+|+.-.++++.+|-+.|+|+-..=|+
T Consensus 6 ~~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~ 62 (150)
T COG1959 6 KGEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKG 62 (150)
T ss_pred hHhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCC
Confidence 45667888888865543 66899999999999999999999999999998775333
No 209
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=40.03 E-value=63 Score=25.81 Aligned_cols=52 Identities=13% Similarity=0.151 Sum_probs=40.1
Q ss_pred hhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccce
Q 009725 110 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 164 (527)
Q Consensus 110 G~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~ 164 (527)
.+.|..|.+.+ .|.-|+++++..+.+..+. ......++.+-+.+|.+.|+|.
T Consensus 30 n~~g~~Iw~ll--dg~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 30 NDSAGEILELC--DGKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred ChHHHHHHHHc--cCCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCcC
Confidence 35677777755 7888999999999887665 3345677888888899999873
No 210
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=39.73 E-value=39 Score=30.72 Aligned_cols=43 Identities=26% Similarity=0.365 Sum_probs=37.4
Q ss_pred HHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 390 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 390 I~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
|+.+...+|.. -.++||+..-+++..+.+.+.+|.+.|||...
T Consensus 15 Iy~l~~~~~~~-~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~ 57 (154)
T COG1321 15 IYELLEEKGFA-RTKDIAERLKVSPPSVTEMLKRLERLGLVEYE 57 (154)
T ss_pred HHHHHhccCcc-cHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEe
Confidence 66666666666 99999999999999999999999999999654
No 211
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=39.73 E-value=38 Score=31.12 Aligned_cols=49 Identities=14% Similarity=0.104 Sum_probs=40.6
Q ss_pred CchHHHHHHHHHh--CCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 385 RDAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 385 ~~~~RI~r~l~~k--~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
.-|+|++-.|... +..+.-++|++.-.+|.+-++++|.+|.+.|+|.-+
T Consensus 8 ~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 8 RYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 4467877777633 235599999999999999999999999999999754
No 212
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=39.20 E-value=92 Score=25.74 Aligned_cols=51 Identities=22% Similarity=0.273 Sum_probs=43.9
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~ 70 (527)
++.-.|...|-..|+=.-..|++.++++...|+..|--|.+-|+|..+...
T Consensus 7 ~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred hhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 445577888888898888899999999999999999999999999966543
No 213
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.90 E-value=25 Score=25.40 Aligned_cols=29 Identities=10% Similarity=0.282 Sum_probs=27.7
Q ss_pred chhhhhhhcCCCcccHHHHHHHHHhcccc
Q 009725 402 ETDKISDTTFVEKKDAPKILYKLWKDGYL 430 (527)
Q Consensus 402 eek~i~~~ami~~k~~r~~L~~L~~~g~v 430 (527)
..++|++...++.+.+++.+..|.+.|||
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 78999999999999999999999999986
No 214
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=38.64 E-value=45 Score=29.56 Aligned_cols=32 Identities=13% Similarity=0.079 Sum_probs=30.5
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
..+..+|+...++|+.-|+++|..|.++|+|.
T Consensus 25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~ 56 (141)
T PRK11014 25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVT 56 (141)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEE
Confidence 56889999999999999999999999999998
No 215
>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=38.46 E-value=27 Score=25.77 Aligned_cols=31 Identities=13% Similarity=0.177 Sum_probs=28.7
Q ss_pred chhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 402 ETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 402 eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
...+|++..-++...+++.|.+|.+.|+|..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 4889999999999999999999999999854
No 216
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=38.06 E-value=68 Score=27.84 Aligned_cols=47 Identities=6% Similarity=0.133 Sum_probs=36.5
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhh
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (527)
.+-|...|+.-++-+...|+.||.+|.+.|++. ...+ .++|-.|++.
T Consensus 50 ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe-~~d~-----------g~i~i~~~~~ 96 (119)
T TIGR01714 50 APYNAEMLATMFNRNVGDIRITLQTLESLGLIE-KKNN-----------GDIFLENWEK 96 (119)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecC-----------CcEEehhHHH
Confidence 455677788888999999999999999999998 3432 1467777654
No 217
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=37.86 E-value=1e+02 Score=26.51 Aligned_cols=60 Identities=17% Similarity=0.342 Sum_probs=47.3
Q ss_pred cchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHHHHHH
Q 009725 401 LETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDE 462 (527)
Q Consensus 401 ~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~~~~~ 462 (527)
+.-.+||+..--+.+-||.+|-+|.+.|.|.-|. ...=.+++..-|..+++.+....+.+
T Consensus 20 vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~p--g~GRG~~S~L~~l~~~~~~~~~~~~~ 79 (115)
T PF12793_consen 20 VTLDELAELLFCSRRNARTLLKKMQEEGWITWQP--GRGRGNRSQLTFLKSPEELLEQQAEE 79 (115)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeC--CCCCCCCCeeEEeeCHHHHHHHHHHH
Confidence 3778999999999999999999999999997773 11134677888889988776555443
No 218
>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=37.49 E-value=35 Score=26.33 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=30.3
Q ss_pred chhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 402 ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 402 eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
..++||+.+.++...+-..|.+|.++|+|+++
T Consensus 30 t~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 30 TQEEIADMLGVSRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp SHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence 89999999999999999999999999999754
No 219
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=36.97 E-value=2.9e+02 Score=24.18 Aligned_cols=44 Identities=7% Similarity=0.041 Sum_probs=36.8
Q ss_pred HHHHHHhc-CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccc
Q 009725 25 VCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (527)
Q Consensus 25 V~~~Ll~~-G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~ 68 (527)
|-..|... +++|..+|++.++++++.|-..+-.|.+.|+|.-..
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 44555555 468999999999999999999999999999998433
No 220
>PRK09462 fur ferric uptake regulator; Provisional
Probab=36.63 E-value=1.2e+02 Score=27.14 Aligned_cols=50 Identities=14% Similarity=0.062 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHhc--CCCCHHHHHhh-----cCCCHHHHHHHHHHHHhccccccccc
Q 009725 20 DLVAKVCECLLRK--GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTT 69 (527)
Q Consensus 20 ~~v~~V~~~Ll~~--G~~tl~~i~~~-----t~l~~~~Vr~~L~vLiQhn~V~~~~~ 69 (527)
+-=..|.++|... +.+|..+|... .++++..|-.+|-.|.+.|+|..+..
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~ 73 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNF 73 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEc
Confidence 4445788888863 69999999765 35889999999999999999975443
No 221
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.44 E-value=35 Score=24.56 Aligned_cols=31 Identities=13% Similarity=0.174 Sum_probs=28.8
Q ss_pred chhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 402 ETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 402 eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
.+.+|++..-++...+++.|.+|.++|+|..
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 7889999999999999999999999999853
No 222
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.07 E-value=31 Score=30.85 Aligned_cols=53 Identities=21% Similarity=0.277 Sum_probs=39.1
Q ss_pred HHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCC-------CCCCCcceEEEeehh
Q 009725 38 QNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGF-------ADGPKANTQYVVLFD 90 (527)
Q Consensus 38 ~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~-------~~~~~~~~~Y~~~~~ 90 (527)
..|.++|++|...|+..|--|..-|++.+++...-... .+-....+||.+|-+
T Consensus 35 K~i~r~tkiPl~~i~e~l~dL~elGLier~tgttiKrteAKfKksaEVHKHHTYYrl~re 94 (175)
T COG4344 35 KNITRYTKIPLPRIREYLKDLKELGLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNRE 94 (175)
T ss_pred HHHHHHccCChHHHHHHHHHHHHcCCeeeccCchhhhhHHHHHHhHHHHhchhhheechh
Confidence 46788999999999999999999999998765431100 111234689999955
No 223
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=35.98 E-value=1.1e+02 Score=27.19 Aligned_cols=57 Identities=16% Similarity=0.271 Sum_probs=43.5
Q ss_pred hhHHHHHHHHHHcccCCHHHHHHHhhhcccCCC------ccCHHHHHHHHHHHHhcccceecC
Q 009725 111 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGN------LVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 111 ~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~------~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.-||.|+-.+..+|.+.++-+-.....+..-+. .-+..-++.+|.+|-+.|||+..|
T Consensus 53 ~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~ 115 (147)
T COG2238 53 VRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP 115 (147)
T ss_pred HHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC
Confidence 347888888889999998888777765432221 124567899999999999999986
No 224
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=35.90 E-value=1.3e+02 Score=25.24 Aligned_cols=32 Identities=25% Similarity=0.391 Sum_probs=30.6
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.|..++...|++++..|..++-.|+.-|++.
T Consensus 54 ~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 54 RISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred eeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 78999999999999999999999999999995
No 225
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=35.85 E-value=73 Score=31.52 Aligned_cols=42 Identities=21% Similarity=0.359 Sum_probs=37.2
Q ss_pred HHHHHHHHhCC-CcchhhhhhhcCCCcccHHHHHHHHHhcccc
Q 009725 389 RIFRLLSKSGR-LLETDKISDTTFVEKKDAPKILYKLWKDGYL 430 (527)
Q Consensus 389 RI~r~l~~k~~-l~eek~i~~~ami~~k~~r~~L~~L~~~g~v 430 (527)
.+.|.|...|- -++|-+|.+...++...+-+.|..|-+.|.|
T Consensus 8 klir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv 50 (321)
T COG3888 8 KLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIV 50 (321)
T ss_pred HHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCee
Confidence 57788877765 2499999999999999999999999999999
No 226
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=35.83 E-value=60 Score=32.36 Aligned_cols=45 Identities=16% Similarity=0.221 Sum_probs=42.2
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
--.+|.+.|-.+|..++.+|++..+.+...||.=|..|-+.|++.
T Consensus 18 R~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 456788999999999999999999999999999999999999997
No 227
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=35.25 E-value=61 Score=31.95 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=41.8
Q ss_pred HHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 113 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 113 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
-..|++.|-++|.++++++.+.+.- |...++.=+..|.+.|+|.|++
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~V--------S~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGV--------SEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCC--------CHHHHHHhHHHHHHCCcEEEEe
Confidence 4689999999999999999998742 6778999999999999999985
No 228
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=35.09 E-value=4.8e+02 Score=28.40 Aligned_cols=112 Identities=16% Similarity=0.122 Sum_probs=77.0
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhhH
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKF 101 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~ 101 (527)
-..|-..|-.+|.++..+|++.++++...|-.++-.|-..|+|.. ... + ...|++-.++-
T Consensus 8 e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~-~~~---------~-~~~i~LTeeG~--------- 67 (489)
T PRK04172 8 EKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKV-EER---------V-EEVYVLTEEGK--------- 67 (489)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEE-Eee---------e-EEEEEECHHHH---------
Confidence 345667777889999999999999999999999999999999984 321 1 24566654431
Q ss_pred HHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhccccee
Q 009725 102 LTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVER 165 (527)
Q Consensus 102 i~~i~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~ 165 (527)
.+++ =|.....+++.+...|-.+++++...+. + .....-.+..|.+.||+..
T Consensus 68 -~~~~--~g~pE~rl~~~l~~~~g~~~~el~~~aL---~------~~~~~i~~~~l~k~g~i~i 119 (489)
T PRK04172 68 -KYAE--EGLPERRLLNALKDGGEVSLDELKEALL---D------KKEVGIALGNLARKGWAKI 119 (489)
T ss_pred -HHHH--hcCHHHHHHHhhHhcCCcCHHHHHHhhc---c------chhHHHHHHHHHHCCCeec
Confidence 1111 1233456666666556678888765421 1 1235677888889999876
No 229
>PRK06474 hypothetical protein; Provisional
Probab=34.97 E-value=83 Score=29.25 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=38.0
Q ss_pred HHHHHHHHHccc-CCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 114 VELVQGLLEHGR-LTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 114 ~~I~~~lL~~G~-~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
..|++.|..+|. +|+.++.+.+.. .+...+...+..|.+.|+|..++
T Consensus 14 ~~Il~~L~~~~~~~ta~el~~~l~~-------is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 14 MKICQVLMRNKEGLTPLELVKILKD-------VPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhcC-------CCHHHHHHHHHHHHHCCCEEEee
Confidence 457777777775 999999888632 25677999999999999999885
No 230
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=34.84 E-value=80 Score=25.02 Aligned_cols=33 Identities=30% Similarity=0.374 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~ 56 (527)
+.|...|-.+|. ||..|.+..+++++.++++|.
T Consensus 11 adI~A~Lkk~G~-Sl~~LS~~agls~~tL~n~L~ 43 (82)
T COG3423 11 ADIIAALKKKGT-SLAALSREAGLSSSTLANALD 43 (82)
T ss_pred HHHHHHHHHccc-cHHHHHHHcCCCHHHHHHHHc
Confidence 456667777776 999999999999999999874
No 231
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=34.82 E-value=1.1e+02 Score=27.50 Aligned_cols=48 Identities=15% Similarity=0.202 Sum_probs=38.7
Q ss_pred chhHHHHHHHHHhcC---CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 19 GDLVAKVCECLLRKG---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G---~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
|+.+=.+--+|..++ ..|+.+|+...++|++-+++.|.-|-+.|+|..
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S 57 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKS 57 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEe
Confidence 344445555566543 578999999999999999999999999999983
No 232
>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=34.80 E-value=42 Score=32.84 Aligned_cols=48 Identities=27% Similarity=0.250 Sum_probs=42.5
Q ss_pred HHHHHHHHH-hCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEe
Q 009725 388 YRIFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 436 (527)
Q Consensus 388 ~RI~r~l~~-k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvp 436 (527)
-+|++.|.. .|.+ .+.+|++...++..-+|+.+-+|...|+|+.+...
T Consensus 186 ~~IL~~L~~~egrl-se~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG 234 (251)
T TIGR02787 186 EHIFEELDGNEGLL-VASKIADRVGITRSVIVNALRKLESAGVIESRSLG 234 (251)
T ss_pred HHHHHHhccccccc-cHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence 368888876 4788 99999999999999999999999999999887644
No 233
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=34.44 E-value=1.2e+02 Score=27.19 Aligned_cols=59 Identities=25% Similarity=0.290 Sum_probs=43.9
Q ss_pred HHHHHHHHhc-CCCCHHHHHhh-----cCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehh
Q 009725 23 AKVCECLLRK-GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (527)
Q Consensus 23 ~~V~~~Ll~~-G~~tl~~i~~~-----t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (527)
..|.++|... +++|..+|.+. .++++..|-++|-.|...|+|.-+.... + .+.|+.+..
T Consensus 24 ~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~--~-------~~~y~~~~~ 88 (145)
T COG0735 24 LAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG--G-------KTRYELNSE 88 (145)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC--C-------EEEEecCCC
Confidence 3577888866 67888888655 4689999999999999999998555432 1 356666644
No 234
>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=34.40 E-value=59 Score=21.24 Aligned_cols=31 Identities=35% Similarity=0.539 Sum_probs=24.3
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhcccc
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V 64 (527)
++|-.+|+..+++++..|-..|-.|-+.|++
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 3577899999999999999999999888764
No 235
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=34.23 E-value=41 Score=25.85 Aligned_cols=46 Identities=26% Similarity=0.276 Sum_probs=39.5
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHhhcCC--CHHHHHHHHHHHHhccccc
Q 009725 20 DLVAKVCECLLRKGPLTRQNVKRYTEL--SDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 20 ~~v~~V~~~Ll~~G~~tl~~i~~~t~l--~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.-++|..+|...|+.|...|....+| +.+.|=..|..|...|.|.
T Consensus 4 ~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~ 51 (66)
T PF02295_consen 4 DLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVC 51 (66)
T ss_dssp HHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEe
Confidence 345789999999998898888887665 4899999999999999996
No 236
>KOG4562 consensus Uncharacterized conserved protein (tumor-rejection antigen MAGE in humans) [Function unknown]
Probab=34.05 E-value=38 Score=34.77 Aligned_cols=56 Identities=20% Similarity=0.273 Sum_probs=38.8
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHH-HHHHhcccceEEEEeccCCCCceEEEEEE
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKIL-YKLWKDGYLLMEKLVVTGARQSQFLLWKV 450 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L-~~L~~~g~v~lQEvpkt~~~~~t~~lw~v 450 (527)
.-||.+|..-|-. +.+.-.- --+.|+++ ..|.+++|++.++||.+ .|.+..|+|--
T Consensus 223 e~iWe~L~~lGv~-~g~~H~i-----fGeprkLiT~dlVqq~YLeYr~Vp~s-dP~~YEFlWGp 279 (329)
T KOG4562|consen 223 EEIWEVLRRLGVY-DGREHSI-----FGEPRKLLTQDLVQEKYLEYRQVPDS-DPPRYEFLWGP 279 (329)
T ss_pred HHHHHHHHHhcCC-CCccccc-----cCChHHHHHHHHHHhhceeeeecCCC-CCCceEEeecc
Confidence 4566666554544 3332221 24555555 68899999999999999 99999999974
No 237
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=33.97 E-value=2e+02 Score=22.37 Aligned_cols=49 Identities=16% Similarity=0.155 Sum_probs=39.5
Q ss_pred chhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccC--CCCceEEEEEE
Q 009725 402 ETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKV 450 (527)
Q Consensus 402 eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~--~~~~t~~lw~v 450 (527)
-+.++++..-++++.+-..+-.|...|+|.=|.++... ...+|..+|.-
T Consensus 20 ~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~l~ 70 (75)
T PF04182_consen 20 TQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLHLK 70 (75)
T ss_pred ehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEEEe
Confidence 78889999999999999999999999999999995322 44555566654
No 238
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=33.86 E-value=1.4e+02 Score=27.04 Aligned_cols=34 Identities=15% Similarity=0.088 Sum_probs=31.3
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
+..|..+|+...++|+.-+++.|..|.+.|+|..
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S 56 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVET 56 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 3468999999999999999999999999999983
No 239
>PF13814 Replic_Relax: Replication-relaxation
Probab=33.79 E-value=91 Score=28.79 Aligned_cols=62 Identities=26% Similarity=0.221 Sum_probs=47.2
Q ss_pred HHHHHhCCCcchhhhhhhcCCCcc---cHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHH
Q 009725 392 RLLSKSGRLLETDKISDTTFVEKK---DAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQI 454 (527)
Q Consensus 392 r~l~~k~~l~eek~i~~~ami~~k---~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~ 454 (527)
++|-+.+.+ +.+||+...-.+.+ .++..|.+|.+.|+|.--..+.+......-+.|++...-
T Consensus 2 ~~L~~~r~l-t~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G 66 (191)
T PF13814_consen 2 RLLARHRFL-TTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAG 66 (191)
T ss_pred hhHHHhcCc-CHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHH
Confidence 456565666 99999999999998 799999999999999777655322334455778877554
No 240
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=33.43 E-value=52 Score=26.53 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=30.5
Q ss_pred hcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 31 RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 31 ~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.+--.|+..|.+.++++.+.+...|-.|+.|++|.+
T Consensus 21 ~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 21 NHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp T-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred CCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 345679999999999999999999999999999996
No 241
>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=33.34 E-value=71 Score=22.08 Aligned_cols=36 Identities=19% Similarity=0.374 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKL 424 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L 424 (527)
.+|++.|...+.. .-.+|++...++...++.-+.+|
T Consensus 6 ~~Il~~Lq~d~r~-s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRR-SYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCc-cHHHHHHHHCcCHHHHHHHHHHh
Confidence 4789999998998 99999999999999999888777
No 242
>PRK11050 manganese transport regulator MntR; Provisional
Probab=33.16 E-value=1.4e+02 Score=26.81 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=36.6
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
-|.+++...+.. ...+|++...++...+...+.+|.+.|+|.
T Consensus 41 ~I~~~l~~~~~~-t~~eLA~~l~is~stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 41 LIADLIAEVGEA-RQVDIAARLGVSQPTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHHHhcCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 366677665666 999999999999999999999999999984
No 243
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=33.05 E-value=56 Score=28.95 Aligned_cols=41 Identities=29% Similarity=0.472 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 390 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 390 I~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
|++++...|.. ..++|++...+++..+...+.+|.+.|||.
T Consensus 13 I~~l~~~~~~~-~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 13 IYLLIEEKGYA-RVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHHHHhcCCCc-CHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 66666565556 999999999999999999999999999996
No 244
>PRK12423 LexA repressor; Provisional
Probab=32.97 E-value=99 Score=29.26 Aligned_cols=45 Identities=13% Similarity=0.251 Sum_probs=37.2
Q ss_pred hHHHHHHHHHhcC-CCCHHHHHhhcCC-CHHHHHHHHHHHHhccccc
Q 009725 21 LVAKVCECLLRKG-PLTRQNVKRYTEL-SDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 21 ~v~~V~~~Ll~~G-~~tl~~i~~~t~l-~~~~Vr~~L~vLiQhn~V~ 65 (527)
+...+.+.+..+| +-|..+|++..++ ++..|+..|-.|.+-|++.
T Consensus 11 il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 11 ILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 4455566666666 3599999999996 8999999999999999998
No 245
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=32.91 E-value=92 Score=26.55 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=40.6
Q ss_pred HHHHHHHHHHc-ccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009725 113 CVELVQGLLEH-GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 168 (527)
Q Consensus 113 a~~I~~~lL~~-G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~~ 168 (527)
-..|++.|..+ +++|+.++.+.+.... ...+.+.|-.++..|.+.|+|.+++.
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~ 63 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEF 63 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEc
Confidence 34567777775 5999999999987532 23477889999999999999999853
No 246
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=32.57 E-value=1.8e+02 Score=29.14 Aligned_cols=52 Identities=15% Similarity=0.241 Sum_probs=42.9
Q ss_pred HHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 14 ITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 14 i~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
=++++-.++..|-+.|-.+|..++.+|++..+||..-+++.++.-.-...+.
T Consensus 110 t~~Yld~l~~Eine~Lqe~G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~ 161 (272)
T PF09743_consen 110 TDSYLDSLAEEINEKLQESGQVSISELAKQYDLPSEFLKEELISKRLGKIIK 161 (272)
T ss_pred cHHHHHHHHHHHHHHHHHcCeEeHHHHHHhcCCcHHHHHHHHhhhhcCccee
Confidence 3567788999999999999999999999999999998887766664444443
No 247
>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=32.31 E-value=57 Score=30.81 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=30.6
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++|-.+|+...+++..-||.||..|-+.|+|..
T Consensus 34 ~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 34 KLNESDIAARLGVSRGPVREAFRALEEAGLVRN 66 (212)
T ss_pred EecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 667789999999999999999999999999984
No 248
>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=32.23 E-value=36 Score=26.83 Aligned_cols=44 Identities=16% Similarity=-0.008 Sum_probs=36.1
Q ss_pred chHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccc
Q 009725 386 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 430 (527)
Q Consensus 386 ~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v 430 (527)
....+|-+.+....+ +.++|++..-++.+.++..+..+..+|.+
T Consensus 19 ~~r~af~L~R~~eGl-S~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 19 LAEAAAALAREEAGK-TASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 344566665555788 99999999999999999999999988754
No 249
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=31.81 E-value=1.4e+02 Score=22.89 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=41.3
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
.++-..+..+++..|..+...|.+..++.+...-..+=.|-+.|+|..
T Consensus 5 D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 5 DPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp STTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred cHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 466778888899999999999999999999999999999999999973
No 250
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=31.74 E-value=3.4e+02 Score=23.42 Aligned_cols=58 Identities=21% Similarity=0.261 Sum_probs=45.6
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchH
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+|+++|...+.+ .-.+|++..-++...+=.-|-.|.+.|+|...-. ++ .-+|++|.+
T Consensus 19 l~IL~~L~~~~~~-~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~------Gr-~~~Y~l~~~ 76 (117)
T PRK10141 19 LGIVLLLRESGEL-CVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ------GK-WVHYRLSPH 76 (117)
T ss_pred HHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE------cC-EEEEEECch
Confidence 4788888776677 8889999999999999999999999999965532 22 234666754
No 251
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=31.68 E-value=1.2e+02 Score=28.13 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=39.6
Q ss_pred HhhchhHHHHHHHHHhc--CCCCHHHHHhhc--CCCHHHHHHHHHHHHhccccc
Q 009725 16 NHFGDLVAKVCECLLRK--GPLTRQNVKRYT--ELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~--G~~tl~~i~~~t--~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
++|....--|..-|+.- |.-+...|.+.+ +++..+|++||-.|.+.|++.
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~ 72 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIK 72 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeE
Confidence 45555555555555544 334899999998 999999999999999999997
No 252
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=31.61 E-value=6.7e+02 Score=28.53 Aligned_cols=140 Identities=15% Similarity=0.156 Sum_probs=81.5
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccccccccc-CCCC---------CCCCCcceEEEeehhhH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQ-PDGF---------ADGPKANTQYVVLFDNI 92 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~-~~~~---------~~~~~~~~~Y~~~~~~i 92 (527)
+.|...-......|+.+++..+++|+..++.=|-..||||++.--+... ++.+ +. ....+.-+...++
T Consensus 605 A~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEse~d~~q-~~~~~~~e~eee~- 682 (765)
T KOG2165|consen 605 AAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPIISDTGTLTVIESEMDFDQ-AEGTVLLEAEEEN- 682 (765)
T ss_pred HHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCCCCCceeeeccccccccc-cCCCccccccccc-
Confidence 4444444556778999999999999999999999999999997322110 0000 00 0001111111111
Q ss_pred HHHhchhhHHHHHHHHhhhhHHHHHHHHHHc-ccCCHHHHHHHhhhcc-cCCC-ccCHHHHHHHHHHHHhcccceec
Q 009725 93 LHRVRFAKFLTILSQEFDQQCVELVQGLLEH-GRLTLKQMFDRAKSSE-KEGN-LVDLDSLRETLVKLVTAHYVERC 166 (527)
Q Consensus 93 l~rlR~p~~i~~i~~~yG~~a~~I~~~lL~~-G~~~~~~li~~~~~~~-~~~~-~~~~~~l~~~f~~Lv~~~~i~~v 166 (527)
.=.+-.-++..-+++++-.-.- ++..|.| |.+.++-+-..+.=-. +.+. ..+..+++.-+..+|.+|-++-.
T Consensus 683 -~e~~~as~vdqle~el~~~~~f-I~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~ 757 (765)
T KOG2165|consen 683 -YESHNASEVDQLEEELTLFRSF-IVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFI 757 (765)
T ss_pred -chhhhhhHHHHHHHHHHHHHHH-HHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEe
Confidence 1122334455556666544333 4444444 9998766544432111 2223 34788999999999999988654
No 253
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=31.24 E-value=52 Score=29.78 Aligned_cols=52 Identities=21% Similarity=0.153 Sum_probs=42.8
Q ss_pred cCCchHHHHHHHHH-hCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEE
Q 009725 383 YGRDAYRIFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 434 (527)
Q Consensus 383 ~G~~~~RI~r~l~~-k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQE 434 (527)
...-|+|++-.|.. .+..+.-++|++.--+|.+-.+++|..|.+.|+|.-..
T Consensus 6 ~~~YAlr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 6 QTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred HHhHHHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 34567888888853 34445889999999999999999999999999996664
No 254
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=31.11 E-value=3.4e+02 Score=24.92 Aligned_cols=51 Identities=12% Similarity=0.164 Sum_probs=37.9
Q ss_pred CCccChHHHHHHhhhcccCCCCCHHHHHHHHHHhccCCCCCCCCCcE-EEehHHHHHHH
Q 009725 313 SVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVDASSDSY-SIDFEKIIEIA 370 (527)
Q Consensus 313 s~p~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~~~~~~~~~y-~V~~~~i~~~l 370 (527)
..|+|-.+|.+.++ ++.+.+.+.|+.|.+.+....+++.. ..|++++.+..
T Consensus 147 ~~~~t~~~iA~~lG-------~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 198 (202)
T PRK13918 147 MIYATHDELAAAVG-------SVRETVTKVIGELSREGYIRSGYGKIQLLDLKGLEELA 198 (202)
T ss_pred EecCCHHHHHHHhC-------ccHHHHHHHHHHHHHCCCEEcCCCEEEEECHHHHHHHH
Confidence 45788899998883 67889999999999888555555544 44787776543
No 255
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=31.07 E-value=4.7e+02 Score=24.92 Aligned_cols=53 Identities=13% Similarity=0.182 Sum_probs=42.0
Q ss_pred CCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHH
Q 009725 398 GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWK 457 (527)
Q Consensus 398 ~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~ 457 (527)
|.-+.+.+|++.-.++.-=+|+.|.+|..+|+|... |++-++.=.++.+.+..
T Consensus 37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~-------p~rG~~V~~~~~~~~~e 89 (230)
T COG1802 37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE-------PNRGAFVAPLSLAEARE 89 (230)
T ss_pred CCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec-------CCCCCeeCCCCHHHHHH
Confidence 533499999999999999999999999999999654 44455666666665544
No 256
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=30.96 E-value=3.3e+02 Score=27.08 Aligned_cols=79 Identities=18% Similarity=0.167 Sum_probs=62.3
Q ss_pred HHHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhH
Q 009725 13 VITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (527)
Q Consensus 13 ii~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (527)
++.-.|...-.+=.=.||..|+.|+.+|....+.++..|-.-|-.|.-.|+|.. .. -.|++-.-+-
T Consensus 5 ll~~if~SekRk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~--~~------------~~Y~LS~~G~ 70 (260)
T COG4742 5 LLDLLFLSEKRKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQ--EG------------DRYSLSSLGK 70 (260)
T ss_pred HHHHHHccHHHHHHHHHHHhCCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEe--cC------------CEEEecchHH
Confidence 455666666666666788889999999999999999999999999999999972 22 2699887776
Q ss_pred HHHhchhhHHHHH
Q 009725 93 LHRVRFAKFLTIL 105 (527)
Q Consensus 93 l~rlR~p~~i~~i 105 (527)
+.......++..+
T Consensus 71 iiv~km~~ll~tl 83 (260)
T COG4742 71 IIVEKMEPLLDTL 83 (260)
T ss_pred HHHHHHHHHHHHH
Confidence 6666666665544
No 257
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=30.92 E-value=1.4e+02 Score=28.55 Aligned_cols=58 Identities=16% Similarity=0.193 Sum_probs=46.0
Q ss_pred HHHHHHHHHhhchhHHHHHHHHHhc---C--CCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 8 KHAVHVITNHFGDLVAKVCECLLRK---G--PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 8 ~Lc~~ii~~~FG~~v~~V~~~Ll~~---G--~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.+...+......++-++|+.+|+.. + +.|-.+|+...++++..|-..|--|.+.|++.
T Consensus 138 ~~~~~~~~~~~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 138 RNIVSLTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred HHHHHHHHhccChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 3334444444557889999999853 2 35779999999999999999999999999997
No 258
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 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 cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=30.63 E-value=1.5e+02 Score=24.30 Aligned_cols=69 Identities=13% Similarity=0.301 Sum_probs=47.4
Q ss_pred hhhHHHHHHHhhcCccHHHHHHHHHHccchhhhcccccCCCccChHHHHHHhhhcccCCCCCHHHHHHHHHHhccCCCCC
Q 009725 274 RHKGCIDHVRAHLDDGAANVLSAMLQATSSAEKKVKTKNSVPLSLSSIYEEVIKSEAGRNMTLDHVRASLVQLGELSFVD 353 (527)
Q Consensus 274 R~~~iv~~v~~r~~~~a~~v~~~~L~~~~~~~~~~~~~~s~p~s~~~I~~~l~~~~~~~~~~~~~i~~~L~~La~~~~~~ 353 (527)
||..++.++.+-+|.....|++.+-+... .++.+.+. .|..++.+++..+++.+.=...+.
T Consensus 2 kN~Cvi~AiA~aL~R~~~dVl~Vl~~~~~----------------~~~~~~l~---~G~Gl~l~~le~~f~~F~I~A~v~ 62 (89)
T PF05379_consen 2 KNGCVIRAIAEALGRREQDVLAVLSRKCG----------------EELLEELW---SGEGLDLEDLEELFELFDICAHVN 62 (89)
T ss_pred CccchhHHHHHHhCCCHHHHHHHHHhccC----------------HHHHHHHH---cCCCcCHHHHHHHHHHcCeEEEEE
Confidence 67788999999999999999888877442 35677763 466788888888888664332233
Q ss_pred CCCCcEEE
Q 009725 354 ASSDSYSI 361 (527)
Q Consensus 354 ~~~~~y~V 361 (527)
.+++.+.+
T Consensus 63 ~~g~~~~l 70 (89)
T PF05379_consen 63 FGGETFVL 70 (89)
T ss_pred ECCEEEEE
Confidence 44444443
No 259
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=30.57 E-value=94 Score=30.57 Aligned_cols=44 Identities=16% Similarity=0.107 Sum_probs=41.0
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
-.+|-..|-.+|..+..+|++..+++...||.=|-.|-+.|++.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 7 HQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 45688899999999999999999999999999999999999996
No 260
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=30.51 E-value=82 Score=28.91 Aligned_cols=34 Identities=15% Similarity=0.239 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 33 G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++.|..+|++..++|..-+.+.|-.|-+.|+|..
T Consensus 24 ~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 24 GPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 4789999999999999999999999999999983
No 261
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=30.30 E-value=87 Score=30.91 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=41.3
Q ss_pred HHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 113 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 113 a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
-..|++.|-.+|++++.++.+.+.- +...++.-+..|.+.|+|.|+.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~V--------S~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDT--------TGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCC--------CHHHHHHHHHHHHHCCCEEEEE
Confidence 4789999999999999999988742 6778999999999999999974
No 262
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=30.23 E-value=86 Score=23.15 Aligned_cols=41 Identities=20% Similarity=0.329 Sum_probs=30.8
Q ss_pred HHHhhc-hhHHHHHHHHHhcCCCCHHHHHhhcC-CCHHHHHHHH
Q 009725 14 ITNHFG-DLVAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNAL 55 (527)
Q Consensus 14 i~~~FG-~~v~~V~~~Ll~~G~~tl~~i~~~t~-l~~~~Vr~~L 55 (527)
+.-++| +.+++|+..=+..|+ |+++++...+ |+..++...|
T Consensus 5 L~p~iGYe~aa~iAk~A~~~g~-svre~v~~~g~lt~ee~d~ll 47 (55)
T PF10415_consen 5 LNPYIGYEKAAEIAKEALAEGR-SVREVVLEEGLLTEEELDELL 47 (55)
T ss_dssp GHHHHHHHHHHHHHHHHHHHT---HHHHHHHTTSS-HHHHHHHT
T ss_pred ccchhccHHHHHHHHHHHHcCC-CHHHHHHHcCCCCHHHHHHHc
Confidence 346778 889999999999998 9999988877 6888877654
No 263
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=30.18 E-value=81 Score=31.30 Aligned_cols=54 Identities=15% Similarity=0.228 Sum_probs=47.3
Q ss_pred HHhhchhHHHHHHHHHhcC-CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccc
Q 009725 15 TNHFGDLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (527)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~G-~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~ 68 (527)
+..|-+.=..|..+|..|| +.+-++|.+.+++|...|-..|.-|-+-|+|.-+.
T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEE
Confidence 3566677788999999996 59999999999999999999999999999998443
No 264
>PF14502 HTH_41: Helix-turn-helix domain
Probab=30.17 E-value=78 Score=22.78 Aligned_cols=30 Identities=20% Similarity=0.228 Sum_probs=28.5
Q ss_pred CHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 36 TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 36 tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
|+.++....+++...|.+||-.|-..++|.
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 788999999999999999999999999997
No 265
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=29.83 E-value=1.2e+02 Score=28.69 Aligned_cols=47 Identities=19% Similarity=0.195 Sum_probs=36.5
Q ss_pred hHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009725 112 QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (527)
Q Consensus 112 ~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v 166 (527)
....|+. +..|+.|.+++++.+.... +..++.+++.+|.+.|||...
T Consensus 31 ~~~~L~~--lLdG~rt~~eI~~~l~~~~------p~~~v~~~L~~L~~~G~l~~~ 77 (193)
T TIGR03882 31 LYCQLAP--LLDGRRTLDEIIAALAGRF------PAEEVLYALDRLERRGYLVED 77 (193)
T ss_pred hHHHHHH--HHcCCCCHHHHHHHhhccC------CHHHHHHHHHHHHHCCCEecc
Confidence 3444444 5689999999999986532 467799999999999999864
No 266
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=29.49 E-value=82 Score=31.07 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=41.3
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.+|.+.|-.+|..++.+|+...+.+...||.=|..|-+.|++.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 8 QKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 5788999999999999999999999999999999999999997
No 267
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=29.38 E-value=4.3e+02 Score=23.91 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=37.2
Q ss_pred HHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 25 V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
|....-..|.....+|++..+++++.|...|--|..-|+|.|
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~ 56 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEY 56 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEE
Confidence 334444789999999999999999999999999999999995
No 268
>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=29.35 E-value=70 Score=24.20 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=21.8
Q ss_pred HHhcCCCCHHHHHhhcCCCHHHHHH
Q 009725 29 LLRKGPLTRQNVKRYTELSDEQVKN 53 (527)
Q Consensus 29 Ll~~G~~tl~~i~~~t~l~~~~Vr~ 53 (527)
+-..|.+++.+|+...++++++|+.
T Consensus 17 ~~~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHhCCCccHHHHHHHHCCCHHHHHH
Confidence 4456899999999999999999984
No 269
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=29.00 E-value=48 Score=26.48 Aligned_cols=32 Identities=28% Similarity=0.421 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L 55 (527)
+.|-..|-.+| .||..|.+..+++.+.++++|
T Consensus 5 adI~AaL~krG-~sL~~lsr~~Gl~~~tl~nal 36 (78)
T PF13693_consen 5 ADIKAALRKRG-TSLAALSREAGLSSSTLRNAL 36 (78)
T ss_dssp HHHHHHHCTTS---HHHHHHHHSS-HHHHHHTT
T ss_pred HHHHHHHHHcC-CCHHHHHHHcCCCHHHHHHHH
Confidence 45666676677 599999999999999999886
No 270
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=28.85 E-value=62 Score=26.10 Aligned_cols=47 Identities=17% Similarity=0.246 Sum_probs=36.5
Q ss_pred chHHHHHHHH---HhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 386 DAYRIFRLLS---KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 386 ~~~RI~r~l~---~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
.-.||++.+- +++.++-.+.|.+.+-++.+++...|.+|.+.++|.-
T Consensus 7 ~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 7 EDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp HHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 4456666662 3456779999999999999999999999999999965
No 271
>PRK03837 transcriptional regulator NanR; Provisional
Probab=28.84 E-value=75 Score=30.63 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=34.2
Q ss_pred HHHHHHhcC-CC-CHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 25 VCECLLRKG-PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 25 V~~~Ll~~G-~~-tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
|.+-=+.-| ++ +-.+|+...+++...||.||..|-+.|+|..
T Consensus 26 I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~ 69 (241)
T PRK03837 26 IRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQI 69 (241)
T ss_pred HHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 333333445 56 6889999999999999999999999999984
No 272
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=28.54 E-value=74 Score=30.35 Aligned_cols=33 Identities=27% Similarity=0.346 Sum_probs=30.9
Q ss_pred CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 34 ~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++|-.+|+...+++...||.||..|.+-|+|..
T Consensus 34 ~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~ 66 (221)
T PRK11414 34 RLITKNLAEQLGMSITPVREALLRLVSVNALSV 66 (221)
T ss_pred ccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEe
Confidence 678889999999999999999999999999983
No 273
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=28.38 E-value=68 Score=31.57 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=38.8
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+|.++|.++|.. ..++|++..-++...+|.-|..|.+.|.|.
T Consensus 8 ~~Il~~l~~~~~~-~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 8 QILLELLAQLGFV-TVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3588888887777 999999999999999999999999999983
No 274
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=28.35 E-value=1.3e+02 Score=31.01 Aligned_cols=93 Identities=10% Similarity=0.204 Sum_probs=58.4
Q ss_pred HHHhcCCCCHHHHHhh--cCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhhHHHHH
Q 009725 28 CLLRKGPLTRQNVKRY--TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTIL 105 (527)
Q Consensus 28 ~Ll~~G~~tl~~i~~~--t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i~~i 105 (527)
++-..++.+-++|++. .++++..||+-+..|-+.|++.. +++.++.-|...-..|+++ +. +...
T Consensus 19 yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~---~h~sagrIPT~kGYR~YVd--~L---~~~~------ 84 (339)
T PRK00082 19 YIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEK---PHTSSGRIPTDKGYRYFVD--HL---LEVK------ 84 (339)
T ss_pred HHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCC---CcCCCCCCcCHHHHHHHHH--Hh---CCCC------
Confidence 5667789999999966 88999999999999999999973 2212111222222233333 21 1110
Q ss_pred HHHhhhhHHHHHHHHHHcccCCHHHHHHHhh
Q 009725 106 SQEFDQQCVELVQGLLEHGRLTLKQMFDRAK 136 (527)
Q Consensus 106 ~~~yG~~a~~I~~~lL~~G~~~~~~li~~~~ 136 (527)
.+.++-...+...+......++++++.+.
T Consensus 85 --~~~~~~~~~i~~~~~~~~~~~~~~l~~aa 113 (339)
T PRK00082 85 --PLSEEERRAIEKFLDERGVSLEDVLQEAA 113 (339)
T ss_pred --CCCHHHHHHHHHHHHhccCCHHHHHHHHH
Confidence 23444455666666666678888887753
No 275
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=28.03 E-value=3.9e+02 Score=23.00 Aligned_cols=105 Identities=13% Similarity=0.173 Sum_probs=77.1
Q ss_pred HHHHHHHHHHhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEE
Q 009725 7 TKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYV 86 (527)
Q Consensus 7 ~~Lc~~ii~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~ 86 (527)
.++...+=.-..---+|...-||...+-.+=.+|-+.+||-...|--|+--|-..|-|.--.....|. .++.-.|.
T Consensus 14 ~~~ie~L~~lgi~R~vA~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~eKKkGK----GRPik~Y~ 89 (124)
T COG4738 14 YEIIELLRILGIPRNVATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDEREEKKKGK----GRPIKLYR 89 (124)
T ss_pred HHHHHHHHHcCCCchHHHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccchHHhcccCC----CCCceEEE
Confidence 34444444444556788888899999999999999999999999999999999999998433332222 23345787
Q ss_pred eehhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHH
Q 009725 87 VLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLE 122 (527)
Q Consensus 87 ~~~~~il~rlR~p~~i~~i~~~yG~~a~~I~~~lL~ 122 (527)
+-. -|+.+++.+.+.+-.+...|+.++=+
T Consensus 90 Lt~-------~~~eIvs~iee~~~ke~k~i~~~ier 118 (124)
T COG4738 90 LTV-------PFDEIVSEIEEEIIKESKEIIYNIER 118 (124)
T ss_pred ecC-------cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 653 36778888888888888777776644
No 276
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=27.48 E-value=2.3e+02 Score=24.54 Aligned_cols=54 Identities=17% Similarity=0.115 Sum_probs=39.4
Q ss_pred HhhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecCC
Q 009725 108 EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 168 (527)
Q Consensus 108 ~yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~~ 168 (527)
..|.--..+|-..|..|..+.+++...+.. .+...+.+.+..|.++|+|.|...
T Consensus 19 ~ig~kW~~lIl~~L~~g~~RF~eL~r~i~~-------Is~k~Ls~~Lk~Le~~Glv~R~~~ 72 (120)
T COG1733 19 VIGGKWTLLILRDLFDGPKRFNELRRSIGG-------ISPKMLSRRLKELEEDGLVERVVY 72 (120)
T ss_pred HHcCccHHHHHHHHhcCCCcHHHHHHHccc-------cCHHHHHHHHHHHHHCCCEEeeec
Confidence 344443444444444499999999888643 256779999999999999999854
No 277
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=27.15 E-value=1e+02 Score=29.91 Aligned_cols=42 Identities=21% Similarity=0.361 Sum_probs=39.3
Q ss_pred HHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 24 ~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.|-+.|-..|++.+.+|+...+||.+.+-..+-+|..-|++.
T Consensus 27 ~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlir 68 (308)
T COG4189 27 AILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIR 68 (308)
T ss_pred HHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCcee
Confidence 566778888999999999999999999999999999999998
No 278
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=27.13 E-value=71 Score=31.14 Aligned_cols=58 Identities=21% Similarity=0.210 Sum_probs=0.0
Q ss_pred HHHhhhhHHHHHHHHHHcccCCHHHHH---HHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 106 SQEFDQQCVELVQGLLEHGRLTLKQMF---DRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 106 ~~~yG~~a~~I~~~lL~~G~~~~~~li---~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
+....+....-+.+.+..|.+.+++-+ ..+.+.... |+.-+++++..|...|+|...|
T Consensus 5 ~~~~~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gV----SRtpVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 5 RRPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGF----SRSALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred cccHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeC
No 279
>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=27.04 E-value=1.3e+02 Score=29.99 Aligned_cols=50 Identities=20% Similarity=0.155 Sum_probs=41.8
Q ss_pred HhhchhHHHHHHHHHhc--CCCCHHHHHhhcC--CCHHHHHHHHHHHHhccccc
Q 009725 16 NHFGDLVAKVCECLLRK--GPLTRQNVKRYTE--LSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~--G~~tl~~i~~~t~--l~~~~Vr~~L~vLiQhn~V~ 65 (527)
++|....--|..-|+.- |..+...|++.++ ++..+|+.+|-.|.+.|++.
T Consensus 117 ~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik 170 (271)
T TIGR02147 117 EYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIK 170 (271)
T ss_pred HHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee
Confidence 35667777788888744 6667888999987 89999999999999999997
No 280
>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=26.99 E-value=96 Score=23.57 Aligned_cols=42 Identities=17% Similarity=0.259 Sum_probs=36.9
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccce
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 431 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~ 431 (527)
.+|+++|. .+.. .-++|++..-++...++..+..|.+.|+.-
T Consensus 3 ~~il~~L~-~~~~-~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 3 LRLLALLA-DNPF-SGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHHHHH-cCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 47888875 4677 799999999999999999999999999963
No 281
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=26.27 E-value=5.5e+02 Score=24.10 Aligned_cols=121 Identities=15% Similarity=0.168 Sum_probs=67.9
Q ss_pred HHHHHHHHHhcC-C-CCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchh
Q 009725 22 VAKVCECLLRKG-P-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFA 99 (527)
Q Consensus 22 v~~V~~~Ll~~G-~-~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p 99 (527)
.+.|=..|+..| + +|+.+|.+.++.+.......++-+++... ..+. .| .--....+-|.+.--|
T Consensus 3 ~~~iEAlLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l~~~~----~~~~-~g---------l~l~~~~~~y~l~tk~ 68 (186)
T TIGR00281 3 KAIIEALLFVSGEPGVTLAELVRILGKEKAEKLNAIMELLEDYL----SRDT-AG---------IEIIKFGQSYSLVTKP 68 (186)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHH----hcCC-CC---------EEEEEECCEEEEEEhH
Confidence 455667788887 3 99999999999885544444444443321 1110 00 0001111222222223
Q ss_pred hHHHHHHHH-------hhhhHHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 100 KFLTILSQE-------FDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 100 ~~i~~i~~~-------yG~~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.|-.+++.. +...+-+.+--+.-++=+|-.+|-+-=.. .-...+.+|++.|||..+.
T Consensus 69 e~~~~i~~~~~~~~~~LS~aaLEtLAIIAY~QPITr~eIe~IRGv-----------~s~~~l~~L~ergLI~~~G 132 (186)
T TIGR00281 69 AFADYIHRFLPAKLKNLNSASLEVLAIIAYKQPITRARINEIRGV-----------KSYQIVDDLVEKGLVVELG 132 (186)
T ss_pred HHHHHHHHHhccccccCCHHHHHHHHHHHHcCCcCHHHHHHHcCC-----------CHHHHHHHHHHCCCeEecC
Confidence 333333333 44466667777777777776666443111 1357899999999998874
No 282
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=26.18 E-value=1.5e+02 Score=22.83 Aligned_cols=48 Identities=17% Similarity=0.075 Sum_probs=33.1
Q ss_pred HHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 120 LLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 120 lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
+|..|-++.-+|.+.+......--..+...|-.++.+|.++|||....
T Consensus 4 ~L~~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~ 51 (75)
T PF03551_consen 4 LLSEGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRW 51 (75)
T ss_dssp HHHHS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEE
T ss_pred hhccCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEee
Confidence 444477777777777655321111346888999999999999998863
No 283
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=26.04 E-value=1.5e+02 Score=27.23 Aligned_cols=53 Identities=15% Similarity=0.228 Sum_probs=41.1
Q ss_pred hHHHHHHHHHH-cccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 112 QCVELVQGLLE-HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 112 ~a~~I~~~lL~-~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.=..|++.|.. .+++++.+|.+.+.+..+ ..+...|-.++..|++.|+|.++.
T Consensus 27 qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~---~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 27 QRLEVLRLMSLQPGAISAYDLLDLLREAEP---QAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHhhCC---CCCcchHHHHHHHHHHCCCEEEEe
Confidence 34556666664 469999999999876432 346778999999999999999985
No 284
>PHA02591 hypothetical protein; Provisional
Probab=25.39 E-value=1.6e+02 Score=23.51 Aligned_cols=34 Identities=26% Similarity=0.252 Sum_probs=29.3
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHH
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L 55 (527)
..-.|+.-|...|- |..+|++..+++...|++-|
T Consensus 47 d~~~vA~eL~eqGl-SqeqIA~~LGVsqetVrKYL 80 (83)
T PHA02591 47 DLISVTHELARKGF-TVEKIASLLGVSVRKVRRYL 80 (83)
T ss_pred hHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHH
Confidence 44568888988887 99999999999999999865
No 285
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.31 E-value=2.5e+02 Score=27.20 Aligned_cols=65 Identities=12% Similarity=-0.021 Sum_probs=53.2
Q ss_pred HhhchhHHHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehh
Q 009725 16 NHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (527)
..=|+....|+..+...++.|...|.+..+++...|.-.+--|---|++. -... | + .+.|++|+.
T Consensus 170 ~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~-~~~~--G------r-~iiy~in~s 234 (240)
T COG3398 170 SLKNETSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIP-EDRE--G------R-SIIYSINPS 234 (240)
T ss_pred HhhchhHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCc-cccc--C------c-eEEEEeCHH
Confidence 34467779999999999999999999999999999999999999999996 2221 1 1 467889853
No 286
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=25.04 E-value=2.7e+02 Score=22.93 Aligned_cols=56 Identities=16% Similarity=0.265 Sum_probs=37.9
Q ss_pred hhHHHHHHHHHHc-ccCCHHHHHHHhhhcc---------------cCCCccCHHHHHHHHHHHHhcccceec
Q 009725 111 QQCVELVQGLLEH-GRLTLKQMFDRAKSSE---------------KEGNLVDLDSLRETLVKLVTAHYVERC 166 (527)
Q Consensus 111 ~~a~~I~~~lL~~-G~~~~~~li~~~~~~~---------------~~~~~~~~~~l~~~f~~Lv~~~~i~~v 166 (527)
++|..|+..+-.. |+.+...++.-+.... ..++..+...++..+.+|+..|||...
T Consensus 4 ~~a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~ 75 (106)
T PF09382_consen 4 EEAKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSED 75 (106)
T ss_dssp HHHHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceec
Confidence 4677777777775 6688888877664321 112345788999999999999999555
No 287
>PRK09954 putative kinase; Provisional
Probab=24.98 E-value=1.3e+02 Score=31.09 Aligned_cols=99 Identities=10% Similarity=0.076 Sum_probs=64.6
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHh-chhhH
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRV-RFAKF 101 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rl-R~p~~ 101 (527)
.+|.+.|..+++.|..+|.+..+++.+.|+.-|-.|.+-|++.-+..--... ....+.=.++.|-++..- ++|.-
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~----~~v~viG~~~vD~~~~~~~~~p~~ 81 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQ----EYCVVVGAINMDIRGMADIRYPQA 81 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCC----ccEEEEEEEEEEEEEeeCCcCcCC
Confidence 4688899999999999999999999999999999999999986333211000 111233344444433211 23321
Q ss_pred ---HHHHHHHhhhhHHHHHHHHHHccc
Q 009725 102 ---LTILSQEFDQQCVELVQGLLEHGR 125 (527)
Q Consensus 102 ---i~~i~~~yG~~a~~I~~~lL~~G~ 125 (527)
...+....|..+.-+...+-..|.
T Consensus 82 ~~~~~~~~~~~GG~~~NvA~~larLG~ 108 (362)
T PRK09954 82 ASHPGTIHCSAGGVGRNIAHNLALLGR 108 (362)
T ss_pred CCCCceEEEecCcHHHHHHHHHHHcCC
Confidence 122344467777777777777775
No 288
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=24.40 E-value=1.3e+02 Score=22.67 Aligned_cols=47 Identities=23% Similarity=0.344 Sum_probs=29.6
Q ss_pred ccChHHHHHHhhh---cccCCCCCHHHHHHHHHHhccCCCCCCCCCcEEE
Q 009725 315 PLSLSSIYEEVIK---SEAGRNMTLDHVRASLVQLGELSFVDASSDSYSI 361 (527)
Q Consensus 315 p~s~~~I~~~l~~---~~~~~~~~~~~i~~~L~~La~~~~~~~~~~~y~V 361 (527)
+++++.|+.-+.- .+.+.+.+.+.+.++|..+.++.-..-.+|.|.+
T Consensus 11 sl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~G~YkL 60 (60)
T PF08672_consen 11 SLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSGGSYKL 60 (60)
T ss_dssp SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--TTEEEE
T ss_pred CCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecCCEEeC
Confidence 3677777765532 2456678899999999999988733344888864
No 289
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=23.92 E-value=86 Score=30.89 Aligned_cols=42 Identities=17% Similarity=0.243 Sum_probs=38.4
Q ss_pred HHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccc
Q 009725 388 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 430 (527)
Q Consensus 388 ~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v 430 (527)
.+|..+|.+++.+ ..++|++.--++...+|.-|..|.+.|++
T Consensus 8 ~~Il~~l~~~~~~-~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 8 DAIIELVKQQGYV-STEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHcCCE-eHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 3578888887887 99999999999999999999999999997
No 290
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=23.75 E-value=1.2e+02 Score=24.84 Aligned_cols=34 Identities=26% Similarity=0.516 Sum_probs=24.1
Q ss_pred HHHHHHhcCCCCHHHHHhhc--------CCCHHHHHHHHHHH
Q 009725 25 VCECLLRKGPLTRQNVKRYT--------ELSDEQVKNALLVL 58 (527)
Q Consensus 25 V~~~Ll~~G~~tl~~i~~~t--------~l~~~~Vr~~L~vL 58 (527)
+-+.|+.+|+++++.|..+. ++|++.-|.-++.-
T Consensus 11 Lp~iLl~~GPLaIRhI~~~Lt~~vPgF~~ls~sKqRRLi~~A 52 (92)
T PF10330_consen 11 LPEILLNHGPLAIRHITGYLTTSVPGFSDLSPSKQRRLIMAA 52 (92)
T ss_pred hHHHHHhcCcHHHHHHHHHHhccCCCcccCCHHHHHHHHHHH
Confidence 34599999999999998762 46776655544433
No 291
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=23.41 E-value=1.5e+02 Score=28.84 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 23 ~~V~~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
.+|...|..+|..+..+|++..+++...||.=|-.|...|.+.
T Consensus 7 ~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 7 QAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4578889999999999999999999999999999999988876
No 292
>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=23.15 E-value=2.9e+02 Score=25.14 Aligned_cols=51 Identities=16% Similarity=0.152 Sum_probs=42.9
Q ss_pred HhhchhHHHHHHHHHh----cC-----------CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 16 NHFGDLVAKVCECLLR----KG-----------PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~----~G-----------~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
-.+.+.-++|+.+|+. .| ++|-.+|+...++++..|-.+|-.|-+.|+|.+
T Consensus 110 l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 110 LAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred HHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 3566788899998864 11 468899999999999999999999999999973
No 293
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=23.11 E-value=93 Score=30.01 Aligned_cols=54 Identities=13% Similarity=0.093 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHHcccCCHHHHHH---HhhhcccCCCccCHHHHHHHHHHHHhcccceecC
Q 009725 110 DQQCVELVQGLLEHGRLTLKQMFD---RAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 110 G~~a~~I~~~lL~~G~~~~~~li~---~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
.+.+...+.+-+..|.+.+++-+- .+.+.... |+.-+++++..|...|+|...|
T Consensus 9 ~~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gV----SRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 9 AGFAEEYIIESIWNNRFPPGSILPAERELSELIGV----TRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEEeC
No 294
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=23.08 E-value=1.1e+02 Score=25.29 Aligned_cols=65 Identities=11% Similarity=0.225 Sum_probs=47.6
Q ss_pred cCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEc
Q 009725 383 YGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 451 (527)
Q Consensus 383 ~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~ 451 (527)
++..-.+++.+|...+.. ...+|++...++...+-..+.+|.+.|||.-+.-| ...|..++.-.+
T Consensus 20 lt~~q~~~L~~l~~~~~~-~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~---~DrR~~~l~lT~ 84 (126)
T COG1846 20 LTPPQYQVLLALYEAGGI-TVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP---EDRRAVLVRLTE 84 (126)
T ss_pred CCHHHHHHHHHHHHhCCC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc---cccceeeEEECc
Confidence 455666777777776555 33999999999999999999999999999544322 335555555444
No 295
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=23.07 E-value=1.8e+02 Score=27.39 Aligned_cols=46 Identities=22% Similarity=0.227 Sum_probs=38.0
Q ss_pred chhHHHHHHHHHhcCCCCHHHHHhhc--CCCHHHHHHHHHHHHhcccccc
Q 009725 19 GDLVAKVCECLLRKGPLTRQNVKRYT--ELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 19 G~~v~~V~~~Ll~~G~~tl~~i~~~t--~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
|+.+..+...| .|+.|+.+|+... ..+...|.++|..|.+.|++..
T Consensus 29 ~~~~~~L~~lL--dG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~~ 76 (193)
T TIGR03882 29 GALYCQLAPLL--DGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLVE 76 (193)
T ss_pred chhHHHHHHHH--cCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEec
Confidence 66677777754 7888999998774 4688999999999999999973
No 296
>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=22.98 E-value=1.4e+02 Score=23.81 Aligned_cols=38 Identities=11% Similarity=0.083 Sum_probs=33.0
Q ss_pred HhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 396 KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 396 ~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
+.+.-+--+.|++..-+++-.+|+.+..|.+.|||+=|
T Consensus 19 ~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 19 ETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred hcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 44677788999999888999999999999999999544
No 297
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=22.91 E-value=1.2e+02 Score=24.54 Aligned_cols=37 Identities=22% Similarity=0.361 Sum_probs=33.7
Q ss_pred HhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 30 LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 30 l~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
..+.++++.+|++..+++...|..-|+-+|..|.+..
T Consensus 56 ~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~ 92 (105)
T PF01399_consen 56 KPYSSISISEIAKALQLSEEEVESILIDLISNGLIKA 92 (105)
T ss_dssp HC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEE
T ss_pred HHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEE
Confidence 3678999999999999999999999999999999983
No 298
>PRK11239 hypothetical protein; Provisional
Probab=22.84 E-value=1.7e+02 Score=27.98 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=38.3
Q ss_pred hchhHHHHHHHHHhcCCCCHHHHHhhcC-C----CHHHHHHHHHHHHhcc---ccc
Q 009725 18 FGDLVAKVCECLLRKGPLTRQNVKRYTE-L----SDEQVKNALLVLIQQN---CVQ 65 (527)
Q Consensus 18 FG~~v~~V~~~Ll~~G~~tl~~i~~~t~-l----~~~~Vr~~L~vLiQhn---~V~ 65 (527)
|.+--..|.-.|+-||++|..+|-..++ | +...|...|--|+++. +|.
T Consensus 95 l~~~~~All~~LlLRGPQT~gELRtRs~Rl~~F~dv~~Ve~~L~~L~~r~~~plV~ 150 (215)
T PRK11239 95 LSAAEVALITTLLLRGAQTPGELRSRAARMYEFSDMAEVESTLEQLANREDGPFVV 150 (215)
T ss_pred CCHHHHHHHHHHHhcCCCChHHHHHhHhcCCcCCCHHHHHHHHHHHHhccCCceee
Confidence 4455667778888999999999976654 2 6799999999999995 554
No 299
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=22.84 E-value=1e+02 Score=29.62 Aligned_cols=36 Identities=11% Similarity=0.265 Sum_probs=31.6
Q ss_pred HhcC-CC-CHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 30 LRKG-PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 30 l~~G-~~-tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+.-| ++ +-.+|+...+++..-||.||..|.+-|+|.
T Consensus 24 l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~ 61 (235)
T TIGR02812 24 FPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLT 61 (235)
T ss_pred CCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3344 67 588999999999999999999999999998
No 300
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=22.76 E-value=1.6e+02 Score=23.35 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=35.3
Q ss_pred HHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 27 ~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++.-.+...++.+|.+..+++...+-..++-+|..|.+..
T Consensus 17 ~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00088 17 QLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEE
Confidence 3344578999999999999999999999999999999974
No 301
>smart00753 PAM PCI/PINT associated module.
Probab=22.76 E-value=1.6e+02 Score=23.35 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=35.3
Q ss_pred HHHHhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhcccccc
Q 009725 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (527)
Q Consensus 27 ~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~ 66 (527)
++.-.+...++.+|.+..+++...+-..++-+|..|.+..
T Consensus 17 ~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00753 17 QLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEE
Confidence 3344578999999999999999999999999999999974
No 302
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=22.33 E-value=1.3e+02 Score=28.06 Aligned_cols=59 Identities=14% Similarity=0.316 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHH-HHHHhcccc-eEEEEeccCCCCceEEEEEEchH
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKIL-YKLWKDGYL-LMEKLVVTGARQSQFLLWKVNRQ 453 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L-~~L~~~g~v-~lQEvpkt~~~~~t~~lw~v~~~ 453 (527)
.+|+.|..= .+ ++. ...+.... +.++++ ..|.+.||+ +..++|.+ +|....|.|++-+.
T Consensus 125 ~L~~~L~~l-gi-~~~--~~~~~~g~-~~~~~i~~~~vkq~YL~~~k~~~~~-~~~~~~~~y~~G~R 185 (195)
T PF01454_consen 125 DLWKFLRRL-GI-DED--EKHPILGM-DIKKLILKEFVKQGYLVRYKQVPNS-DPEEYEFSYSWGPR 185 (195)
T ss_dssp HHHHHHHHT-T---TT--S-BTTTB---HHHHHHCHHHHCTSE-EEE-----------EEEE---HH
T ss_pred HHHHHHHhc-CC-Ccc--ccCccCCC-CHHHHHHHHHHHhcCHHheeecCCC-CCCceEEEeCCcCc
Confidence 466777543 33 333 24444443 445555 999999999 77778877 55667777987654
No 303
>PRK03837 transcriptional regulator NanR; Provisional
Probab=22.31 E-value=1.5e+02 Score=28.46 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=32.9
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 398 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 398 ~~l~-eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
|.-+ .|.+|++.-.++..-+|+.|..|..+|+|++.
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5545 89999999999999999999999999999875
No 304
>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=21.91 E-value=1.4e+02 Score=28.10 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=32.0
Q ss_pred CCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 398 GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 398 ~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
|.-+.|.+|++.-.++..-+|+.|..|..+|+|+.+
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence 533489999999999999999999999999999654
No 305
>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=21.59 E-value=1.3e+02 Score=28.28 Aligned_cols=31 Identities=13% Similarity=0.207 Sum_probs=29.6
Q ss_pred CCHHHHHhhcCCC-HHHHHHHHHHHHhccccc
Q 009725 35 LTRQNVKRYTELS-DEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 35 ~tl~~i~~~t~l~-~~~Vr~~L~vLiQhn~V~ 65 (527)
.|..+|++.++++ .+.|...|-.|.+.|++.
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~ 57 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIE 57 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEe
Confidence 6789999999998 999999999999999998
No 306
>PRK00215 LexA repressor; Validated
Probab=21.55 E-value=2.1e+02 Score=26.92 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=36.3
Q ss_pred HHHHHHHHHhcC-CCCHHHHHhhcCC-CHHHHHHHHHHHHhccccc
Q 009725 22 VAKVCECLLRKG-PLTRQNVKRYTEL-SDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 22 v~~V~~~Ll~~G-~~tl~~i~~~t~l-~~~~Vr~~L~vLiQhn~V~ 65 (527)
-..|..+...+| +.|+.+|++.+++ +.+.+..-|-.|.+.|++.
T Consensus 10 l~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~ 55 (205)
T PRK00215 10 LDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIR 55 (205)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 344444555555 5789999999999 9999999999999999997
No 307
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=21.54 E-value=1.6e+02 Score=23.20 Aligned_cols=58 Identities=14% Similarity=0.134 Sum_probs=43.1
Q ss_pred HHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEc
Q 009725 389 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 451 (527)
Q Consensus 389 RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~ 451 (527)
+|+-.+ .++.. .-+.+.+...++.+..--.|.+|.+.|.|.=.... -+++.+=.|.+.
T Consensus 9 ~IL~~l-s~~c~-TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~---~~gkk~R~YclK 66 (72)
T PF05584_consen 9 KILIIL-SKRCC-TLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRK---FGGKKYREYCLK 66 (72)
T ss_pred HHHHHH-HhccC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEE---ecCeEEEEEEec
Confidence 455555 44577 99999999999999999999999999999433222 345566666654
No 308
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=21.44 E-value=3e+02 Score=24.93 Aligned_cols=56 Identities=14% Similarity=0.202 Sum_probs=42.1
Q ss_pred hHHHHHHHHHHcccCCHHHHHHHhhhcccCC------CccCHHHHHHHHHHHHhcccceecC
Q 009725 112 QCVELVQGLLEHGRLTLKQMFDRAKSSEKEG------NLVDLDSLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 112 ~a~~I~~~lL~~G~~~~~~li~~~~~~~~~~------~~~~~~~l~~~f~~Lv~~~~i~~v~ 167 (527)
-|+.|+..|..+|-+.+..+-..+..+...+ ...+..-++.+|.+|-+.|||+..|
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 4788888998999999888877766532211 1124566999999999999998764
No 309
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=21.36 E-value=3e+02 Score=31.68 Aligned_cols=127 Identities=16% Similarity=0.217 Sum_probs=80.5
Q ss_pred cCCCCHHHHHhhcCCCHHHHHHHHHHH--HhcccccccccccCCCCCCCCCcceEEEeehh--hHHHHhchhh----HHH
Q 009725 32 KGPLTRQNVKRYTELSDEQVKNALLVL--IQQNCVQAFTTEQPDGFADGPKANTQYVVLFD--NILHRVRFAK----FLT 103 (527)
Q Consensus 32 ~G~~tl~~i~~~t~l~~~~Vr~~L~vL--iQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~--~il~rlR~p~----~i~ 103 (527)
+-++|+.+|...|+++.+.+..+|-.| +...+.. . +.+.. .....+++|.+ .-..|+.-|. --.
T Consensus 578 ~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~--~-~~s~~-----~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~ 649 (725)
T KOG2166|consen 578 TEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILL--K-PMSRT-----SPNDEFAFNSKFTSKMRRVKIPLPPMDERK 649 (725)
T ss_pred hhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhcc--C-ccccC-----CCCcEEEeeccccCcceeeccCCCCchhHH
Confidence 368999999999999999999999999 5522221 1 11100 11234555543 4444544442 223
Q ss_pred HHHHHhhhh-----HHHHHHHHHHcccCCHHHHHHHhhhcccCCCccCHHHHHHHHHHHHhcccceec
Q 009725 104 ILSQEFDQQ-----CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (527)
Q Consensus 104 ~i~~~yG~~-----a~~I~~~lL~~G~~~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~~i~~v 166 (527)
.+.+..+.+ -|+|+--+=..+++.-.+++..+.+...+.=..+...|+.++..|++.+||+|-
T Consensus 650 ~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~ 717 (725)
T KOG2166|consen 650 KVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD 717 (725)
T ss_pred HHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc
Confidence 334444432 567777777788888777777766432111112578899999999999999985
No 310
>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=21.14 E-value=2.9e+02 Score=22.32 Aligned_cols=37 Identities=19% Similarity=0.176 Sum_probs=25.0
Q ss_pred hHHHHHHHHHhc-CCCCHHHHHhhcC-CCHHHHHHHHHH
Q 009725 21 LVAKVCECLLRK-GPLTRQNVKRYTE-LSDEQVKNALLV 57 (527)
Q Consensus 21 ~v~~V~~~Ll~~-G~~tl~~i~~~t~-l~~~~Vr~~L~v 57 (527)
.+..|+-+|+.+ ..+|+.+|.+..+ -+.+.|-+++-.
T Consensus 30 ~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~r 68 (90)
T cd06571 30 LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRK 68 (90)
T ss_pred hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHH
Confidence 455566677766 3777777777776 777776666544
No 311
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=20.85 E-value=1.2e+02 Score=29.17 Aligned_cols=47 Identities=19% Similarity=0.127 Sum_probs=41.7
Q ss_pred chhHHHHHHHH--HhcCCCCHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 19 GDLVAKVCECL--LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 19 G~~v~~V~~~L--l~~G~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
+....+|...+ -..|..|..+|....+.++...+..|-.|++.|+++
T Consensus 173 ~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 173 SKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp -HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred hHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 46678888888 888999999999999999999999999999999986
No 312
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=20.81 E-value=1.6e+02 Score=28.73 Aligned_cols=57 Identities=14% Similarity=0.194 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCc-chhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 365 KIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 365 ~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~-eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
.+.+.+-....+.|+...|.. |.-+ .|.+|++...++..-+|+.|..|..+|+|++.
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~p------------G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRP------------GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCC------------CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
No 313
>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=20.80 E-value=1.5e+02 Score=27.17 Aligned_cols=65 Identities=17% Similarity=0.239 Sum_probs=49.9
Q ss_pred HhhchhHHHHHHHHHhcC------CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeeh
Q 009725 16 NHFGDLVAKVCECLLRKG------PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLF 89 (527)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G------~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~ 89 (527)
+..|.-..+|..+|+.+= -+|..+|+..++++...|..++-.|...+++.- .. .-.|.+|+
T Consensus 51 ~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k--~~-----------~G~Y~iNP 117 (165)
T PF05732_consen 51 DLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKK--IR-----------NGAYMINP 117 (165)
T ss_pred hhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEE--cc-----------CCeEEECc
Confidence 345666778888888662 357889999999999999999999999999862 11 12699998
Q ss_pred hhHH
Q 009725 90 DNIL 93 (527)
Q Consensus 90 ~~il 93 (527)
+-+.
T Consensus 118 ~~~~ 121 (165)
T PF05732_consen 118 NFFF 121 (165)
T ss_pred HHhe
Confidence 7553
No 314
>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=20.75 E-value=1.7e+02 Score=28.14 Aligned_cols=36 Identities=25% Similarity=0.494 Sum_probs=32.6
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHHhcccceEE
Q 009725 398 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 433 (527)
Q Consensus 398 ~~l~-eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQ 433 (527)
|.-+ .|.+|++.-.++..-+|+.|..|..+|+|+++
T Consensus 27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 5445 79999999999999999999999999999765
No 315
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=20.70 E-value=3.2e+02 Score=25.96 Aligned_cols=63 Identities=17% Similarity=0.180 Sum_probs=44.1
Q ss_pred CchHHHHHHHHHh---C--CCcchhhhhhhcCCCcccHHHHHHHHHhcccceEEEEeccCCCCceEEEEEEchHHHHHH
Q 009725 385 RDAYRIFRLLSKS---G--RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKH 458 (527)
Q Consensus 385 ~~~~RI~r~l~~k---~--~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~lQEvpkt~~~~~t~~lw~v~~~~~~~~ 458 (527)
..-.||.++|... + .+ ..++||....++...+-..|.+|.++|+|+.+ .+++. -.|.+.+.+.
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~-t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~--------~~~i~--I~d~~~L~~~ 217 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHE-KHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS--------KRGYL--IKNRKQLSGL 217 (226)
T ss_pred hHHHHHHHHHHhcccCCcccc-hHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee--------CCEEE--EeCHHHHHHH
Confidence 3445666655421 1 23 78999999999999999999999999999765 23333 3576655543
No 316
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=20.53 E-value=5.8e+02 Score=22.63 Aligned_cols=69 Identities=13% Similarity=0.263 Sum_probs=51.7
Q ss_pred CCCCCcEEEehHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHhCCCcchhhhhhhcCCCcccHHHHHHHHHhcccceE
Q 009725 353 DASSDSYSIDFEKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 432 (527)
Q Consensus 353 ~~~~~~y~V~~~~i~~~lr~~~le~~v~~~~G~~~~RI~r~l~~k~~l~eek~i~~~ami~~k~~r~~L~~L~~~g~v~l 432 (527)
+..+..|+-.|+.+.+.|- ..-.++++++..++-. +-.++++...=..|.+...|..|...|+|.+
T Consensus 45 ~~~Ptl~F~Sye~la~vLs-------------p~nleLl~~Ia~~~P~-Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~f 110 (144)
T COG4190 45 DATPTLWFTSYEDLARVLS-------------PRNLELLELIAQEEPA-SINELAELVGRDVKNVHRTLSTLADLGLIFF 110 (144)
T ss_pred cCCceeccccHHHHHHHhC-------------hhHHHHHHHHHhcCcc-cHHHHHHHhCcchHHHHHHHHHHHhcCeEEE
Confidence 4455556666666655544 3445788888887666 7777888888888889999999999999999
Q ss_pred EEE
Q 009725 433 EKL 435 (527)
Q Consensus 433 QEv 435 (527)
|+-
T Consensus 111 e~~ 113 (144)
T COG4190 111 EED 113 (144)
T ss_pred ecC
Confidence 983
No 317
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=20.51 E-value=4.4e+02 Score=27.18 Aligned_cols=41 Identities=17% Similarity=0.226 Sum_probs=37.0
Q ss_pred HHHHHHhcCCCCHHHHHhh--cCCCHHHHHHHHHHHHhccccc
Q 009725 25 VCECLLRKGPLTRQNVKRY--TELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 25 V~~~Ll~~G~~tl~~i~~~--t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
|-.+|-..++.+..+|++. .++++..||+-|..|-+.|++.
T Consensus 12 V~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~ 54 (337)
T TIGR00331 12 VEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIE 54 (337)
T ss_pred HHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCcc
Confidence 4456777899999999999 8899999999999999999997
No 318
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=20.35 E-value=2.1e+02 Score=20.97 Aligned_cols=33 Identities=21% Similarity=0.335 Sum_probs=22.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHhhcC-CCHHHHHHHHH
Q 009725 22 VAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNALL 56 (527)
Q Consensus 22 v~~V~~~Ll~~G~~tl~~i~~~t~-l~~~~Vr~~L~ 56 (527)
|..|...+ ..|- |..+|..... |+..+|+.||.
T Consensus 21 v~~i~~~~-~~G~-s~eeI~~~yp~Lt~~~i~aAl~ 54 (56)
T PF04255_consen 21 VRDILDLL-AAGE-SPEEIAEDYPSLTLEDIRAALA 54 (56)
T ss_dssp HHHHHHHH-HTT---HHHHHHHSTT--HHHHHHHHH
T ss_pred HHHHHHHH-HcCC-CHHHHHHHCCCCCHHHHHHHHH
Confidence 56666666 5555 9999987754 99999999985
No 319
>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=20.32 E-value=1.1e+02 Score=29.39 Aligned_cols=30 Identities=23% Similarity=0.298 Sum_probs=28.3
Q ss_pred CHHHHHhhcCCCHHHHHHHHHHHHhccccc
Q 009725 36 TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 36 tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~ 65 (527)
|=.+|+...+++...||+||-.|++.|+|.
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~ 55 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQ 55 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 478899999999999999999999999997
No 320
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=20.20 E-value=1.1e+02 Score=31.48 Aligned_cols=134 Identities=15% Similarity=0.169 Sum_probs=0.0
Q ss_pred HHHHHHhcC--CCCHHHHHhhcCCCHHHHHHHHHHHHhcccccccccccCCCCCCCCCcceEEEeehhhHHHHhchhhHH
Q 009725 25 VCECLLRKG--PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFL 102 (527)
Q Consensus 25 V~~~Ll~~G--~~tl~~i~~~t~l~~~~Vr~~L~vLiQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p~~i 102 (527)
|.+++-.-| ..-.++|...|+|+..+|..+|-.|.+.+++.....-...+ .+....|.+.+.. -+--|-+=
T Consensus 89 vy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~----rK~Yml~~l~Ps~---eiTGG~wy 161 (327)
T PF05158_consen 89 VYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPN----RKVYMLYDLEPSE---EITGGPWY 161 (327)
T ss_dssp HHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS------EEEESSS---------------
T ss_pred HHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCC----eEEEEEccCCcCc---ccCCCCcc
Q ss_pred HHHHHHhhhh-----HHHHHHHHHHccc-----------------------------CCHHHHHHHhhhcccCCCccCHH
Q 009725 103 TILSQEFDQQ-----CVELVQGLLEHGR-----------------------------LTLKQMFDRAKSSEKEGNLVDLD 148 (527)
Q Consensus 103 ~~i~~~yG~~-----a~~I~~~lL~~G~-----------------------------~~~~~li~~~~~~~~~~~~~~~~ 148 (527)
-..+|..+ ...++..+-..+. .|+.++.+.+....-.....+.+
T Consensus 162 --~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~fI~~sgIs~v~Ls~e 239 (327)
T PF05158_consen 162 --TDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEFINKSGISNVELSEE 239 (327)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --cCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHHHHHHHcCCCceecCHH
Q ss_pred HHHHHHHHHHhcccceecC
Q 009725 149 SLRETLVKLVTAHYVERCP 167 (527)
Q Consensus 149 ~l~~~f~~Lv~~~~i~~v~ 167 (527)
+|+..+..||-+|.|++++
T Consensus 240 DI~~LL~tLVyDgkIE~v~ 258 (327)
T PF05158_consen 240 DIESLLDTLVYDGKIEEVR 258 (327)
T ss_dssp -------------------
T ss_pred HHHHHHHHHhhCceeEEEe
No 321
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=20.12 E-value=1.8e+02 Score=26.40 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=39.3
Q ss_pred hHHHHHHHHHhcCCCCHHHHHhhcCC--------------CHHHHHHHHHHHHhccccc
Q 009725 21 LVAKVCECLLRKGPLTRQNVKRYTEL--------------SDEQVKNALLVLIQQNCVQ 65 (527)
Q Consensus 21 ~v~~V~~~Ll~~G~~tl~~i~~~t~l--------------~~~~Vr~~L~vLiQhn~V~ 65 (527)
-++.|.+.+-.+|+..+..|.+..+. +.+.||.+|-.|-+-++|.
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVe 112 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVE 112 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCee
Confidence 47889999999999999999888765 3456999999999999998
No 322
>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=20.09 E-value=2.3e+02 Score=20.07 Aligned_cols=31 Identities=16% Similarity=0.069 Sum_probs=21.2
Q ss_pred HHHHhcCCCCHHHHHhhcCCCHHHHHHHHHH
Q 009725 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLV 57 (527)
Q Consensus 27 ~~Ll~~G~~tl~~i~~~t~l~~~~Vr~~L~v 57 (527)
-.|..-...|..+|+...+++.+.|+..|..
T Consensus 19 ~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 19 FLLRYFQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp HHHHHTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3344456779999999999999999987754
No 323
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=20.05 E-value=2.1e+02 Score=26.02 Aligned_cols=45 Identities=22% Similarity=0.395 Sum_probs=34.4
Q ss_pred HHHhhchhHHHHHHHHHhcCCCCHHHHHhh-cCCCHHH----------HHHHHHHHHhccc
Q 009725 14 ITNHFGDLVAKVCECLLRKGPLTRQNVKRY-TELSDEQ----------VKNALLVLIQQNC 63 (527)
Q Consensus 14 i~~~FG~~v~~V~~~Ll~~G~~tl~~i~~~-t~l~~~~----------Vr~~L~vLiQhn~ 63 (527)
+.+.|+.++..|...|- |++++... .+|++.+ +|..|..-|++-|
T Consensus 95 V~~~~s~~~Kav~q~Le-----tlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 95 VRREMSEMAKAVVQVLE-----TLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHHHHHHHHHHHH-----HhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 66889999999999997 99999755 9999975 4555555555444
Done!