Query 003120
Match_columns 846
No_of_seqs 332 out of 936
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 17:23:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003120.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003120hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2165 Anaphase-promoting com 100.0 3E-131 6E-136 1112.6 58.9 712 13-838 3-716 (765)
2 KOG2167 Cullins [Cell cycle co 100.0 1.2E-43 2.6E-48 396.7 19.4 401 361-791 155-576 (661)
3 PF00888 Cullin: Cullin family 100.0 3.7E-40 8.1E-45 386.9 31.8 390 366-781 179-588 (588)
4 KOG2166 Cullins [Cell cycle co 100.0 8.8E-38 1.9E-42 369.3 31.5 397 368-790 225-641 (725)
5 COG5647 Cullin, a subunit of E 100.0 6.6E-36 1.4E-40 341.4 24.2 234 546-790 444-683 (773)
6 smart00182 CULLIN Cullin. 100.0 9.2E-32 2E-36 262.3 16.7 141 557-706 1-142 (142)
7 KOG2284 E3 ubiquitin ligase, C 99.9 2E-27 4.3E-32 256.5 11.6 292 448-786 322-633 (728)
8 KOG2285 E3 ubiquitin ligase, C 99.9 1.9E-23 4.1E-28 227.8 17.2 229 545-782 427-671 (777)
9 TIGR01610 phage_O_Nterm phage 95.7 0.028 6.2E-07 51.7 6.7 66 712-781 20-93 (95)
10 PF08672 APC2: Anaphase promot 95.5 0.004 8.6E-08 52.7 0.4 14 826-840 1-14 (60)
11 PF13412 HTH_24: Winged helix- 94.6 0.078 1.7E-06 42.2 5.3 47 716-762 2-48 (48)
12 PF02082 Rrf2: Transcriptional 94.3 0.17 3.8E-06 45.1 7.5 59 718-779 11-70 (83)
13 PF08220 HTH_DeoR: DeoR-like h 94.0 0.16 3.4E-06 42.4 6.0 48 719-766 2-49 (57)
14 PF12802 MarR_2: MarR family; 93.8 0.11 2.4E-06 43.0 4.9 51 715-765 3-55 (62)
15 PF09339 HTH_IclR: IclR helix- 93.7 0.12 2.5E-06 42.1 4.7 45 720-764 6-51 (52)
16 PF13463 HTH_27: Winged helix 93.0 0.32 7E-06 41.0 6.6 50 715-764 1-51 (68)
17 PF12840 HTH_20: Helix-turn-he 90.8 0.54 1.2E-05 39.4 5.4 49 716-764 9-57 (61)
18 PF01047 MarR: MarR family; I 90.8 0.36 7.8E-06 39.7 4.3 50 715-764 1-50 (59)
19 PF01022 HTH_5: Bacterial regu 90.4 0.82 1.8E-05 36.4 5.8 45 717-762 2-46 (47)
20 smart00346 HTH_ICLR helix_turn 90.4 0.76 1.7E-05 40.9 6.3 57 720-780 8-65 (91)
21 PF01978 TrmB: Sugar-specific 90.2 0.4 8.8E-06 40.9 4.2 52 715-766 6-57 (68)
22 smart00550 Zalpha Z-DNA-bindin 89.5 1.2 2.7E-05 38.4 6.7 48 717-764 6-55 (68)
23 smart00347 HTH_MARR helix_turn 89.5 1 2.2E-05 40.2 6.4 53 712-764 5-57 (101)
24 smart00420 HTH_DEOR helix_turn 89.0 0.88 1.9E-05 35.9 5.1 46 720-765 3-48 (53)
25 TIGR02337 HpaR homoprotocatech 88.4 0.86 1.9E-05 43.0 5.4 52 713-764 24-75 (118)
26 PRK15090 DNA-binding transcrip 87.1 1.4 2.9E-05 47.5 6.6 55 720-778 17-71 (257)
27 PF08784 RPA_C: Replication pr 86.6 1.3 2.8E-05 40.9 5.4 51 714-764 44-98 (102)
28 PF09012 FeoC: FeoC like trans 86.5 0.83 1.8E-05 39.4 3.7 41 724-764 7-47 (69)
29 smart00344 HTH_ASNC helix_turn 86.4 1.3 2.9E-05 40.9 5.4 47 717-763 3-49 (108)
30 smart00345 HTH_GNTR helix_turn 86.2 1.6 3.4E-05 35.3 5.1 40 726-765 14-54 (60)
31 smart00419 HTH_CRP helix_turn_ 86.1 1.8 3.9E-05 33.6 5.2 41 731-777 8-48 (48)
32 PRK11512 DNA-binding transcrip 86.1 1.4 3E-05 43.2 5.5 52 713-764 36-87 (144)
33 cd00090 HTH_ARSR Arsenical Res 85.7 2.2 4.8E-05 35.4 5.9 59 716-777 6-64 (78)
34 PRK11920 rirA iron-responsive 85.4 2.4 5.3E-05 42.4 6.9 47 720-766 13-59 (153)
35 PF13730 HTH_36: Helix-turn-he 85.3 2.3 4.9E-05 34.6 5.6 29 733-761 27-55 (55)
36 COG3355 Predicted transcriptio 85.1 2.2 4.8E-05 41.6 6.2 37 728-764 39-75 (126)
37 PRK10857 DNA-binding transcrip 84.7 2.9 6.3E-05 42.4 7.2 58 719-779 12-70 (164)
38 COG1414 IclR Transcriptional r 84.3 2.2 4.7E-05 46.0 6.5 56 720-779 7-63 (246)
39 TIGR02010 IscR iron-sulfur clu 84.2 2.7 5.9E-05 40.9 6.5 47 720-766 13-60 (135)
40 PF04703 FaeA: FaeA-like prote 83.8 2.7 5.9E-05 36.0 5.5 44 722-765 5-49 (62)
41 TIGR01889 Staph_reg_Sar staphy 82.9 3.9 8.5E-05 38.3 6.9 53 713-765 21-77 (109)
42 TIGR01884 cas_HTH CRISPR locus 82.7 3.5 7.5E-05 43.0 7.0 53 713-765 139-191 (203)
43 PRK11179 DNA-binding transcrip 82.2 2.4 5.2E-05 42.2 5.4 50 714-763 6-55 (153)
44 PRK10163 DNA-binding transcrip 82.2 3 6.6E-05 45.3 6.6 55 720-778 28-83 (271)
45 TIGR02431 pcaR_pcaU beta-ketoa 82.0 3.2 7E-05 44.3 6.7 53 720-778 12-65 (248)
46 PRK11569 transcriptional repre 81.9 2.9 6.4E-05 45.5 6.4 53 720-776 31-84 (274)
47 TIGR00738 rrf2_super rrf2 fami 81.9 3.5 7.5E-05 39.5 6.2 35 730-764 24-58 (132)
48 PF08279 HTH_11: HTH domain; 81.3 3.6 7.9E-05 33.4 5.3 41 720-760 3-44 (55)
49 TIGR02944 suf_reg_Xantho FeS a 80.1 4.2 9.2E-05 39.1 6.2 47 729-778 23-69 (130)
50 cd00092 HTH_CRP helix_turn_hel 79.8 4.6 0.0001 33.6 5.6 36 730-765 24-59 (67)
51 PRK09834 DNA-binding transcrip 79.5 3.7 8.1E-05 44.4 6.2 54 720-777 14-68 (263)
52 PRK11169 leucine-responsive tr 79.2 3.2 6.9E-05 41.8 5.2 49 715-763 12-60 (164)
53 PF04492 Phage_rep_O: Bacterio 79.0 7.3 0.00016 36.5 7.1 62 714-781 29-98 (100)
54 smart00418 HTH_ARSR helix_turn 79.0 5.5 0.00012 32.1 5.7 36 729-764 8-43 (66)
55 PF05732 RepL: Firmicute plasm 78.9 2.7 5.9E-05 42.7 4.6 50 732-786 76-125 (165)
56 PRK13777 transcriptional regul 77.7 6.8 0.00015 40.6 7.1 54 712-765 40-93 (185)
57 TIGR02702 SufR_cyano iron-sulf 77.7 5.6 0.00012 41.4 6.6 60 720-779 4-66 (203)
58 PRK10434 srlR DNA-bindng trans 76.8 3.5 7.6E-05 44.6 5.0 48 719-766 7-54 (256)
59 PRK11014 transcriptional repre 76.4 6.5 0.00014 38.5 6.3 41 726-766 20-60 (141)
60 PRK03573 transcriptional regul 75.9 4.8 0.0001 39.2 5.2 52 713-764 27-79 (144)
61 COG1959 Predicted transcriptio 75.2 7.2 0.00016 39.0 6.3 49 718-766 11-60 (150)
62 COG2345 Predicted transcriptio 74.8 7.5 0.00016 41.4 6.6 62 718-779 12-76 (218)
63 PF08221 HTH_9: RNA polymerase 72.1 6.5 0.00014 33.5 4.4 37 727-763 23-59 (62)
64 PHA00738 putative HTH transcri 72.0 11 0.00024 35.8 6.2 67 712-781 7-74 (108)
65 COG1522 Lrp Transcriptional re 71.6 7.5 0.00016 38.0 5.4 49 715-763 6-54 (154)
66 PRK10141 DNA-binding transcrip 70.7 11 0.00023 36.4 6.0 60 716-778 15-75 (117)
67 PF13601 HTH_34: Winged helix 70.7 5.5 0.00012 35.5 3.9 45 720-764 3-47 (80)
68 TIGR03879 near_KaiC_dom probab 70.6 4.3 9.3E-05 35.9 3.0 36 727-762 28-63 (73)
69 PRK10870 transcriptional repre 70.4 14 0.0003 37.8 7.2 53 713-765 51-105 (176)
70 PF13404 HTH_AsnC-type: AsnC-t 70.2 7.2 0.00016 30.7 3.9 36 720-755 6-41 (42)
71 PRK10906 DNA-binding transcrip 70.1 6.9 0.00015 42.3 5.2 49 718-766 6-54 (252)
72 PRK13509 transcriptional repre 70.0 7.5 0.00016 42.0 5.5 49 718-766 6-54 (251)
73 PRK06266 transcription initiat 69.9 8.2 0.00018 39.8 5.5 45 719-763 24-68 (178)
74 COG1349 GlpR Transcriptional r 69.9 6.3 0.00014 42.7 4.8 48 719-766 7-54 (253)
75 COG1846 MarR Transcriptional r 69.2 16 0.00035 33.4 6.9 51 715-765 20-70 (126)
76 TIGR00373 conserved hypothetic 68.9 13 0.00028 37.6 6.5 43 720-762 17-59 (158)
77 PRK09802 DNA-binding transcrip 68.7 7.2 0.00016 42.6 5.0 50 717-766 17-66 (269)
78 PF01726 LexA_DNA_bind: LexA D 67.7 14 0.0003 31.9 5.5 52 715-766 4-61 (65)
79 cd07377 WHTH_GntR Winged helix 67.1 17 0.00038 29.7 6.0 32 733-764 27-58 (66)
80 PF05584 Sulfolobus_pRN: Sulfo 66.8 15 0.00033 32.4 5.6 47 716-764 5-51 (72)
81 TIGR00498 lexA SOS regulatory 65.9 7.8 0.00017 40.0 4.4 52 715-766 4-61 (199)
82 PF01325 Fe_dep_repress: Iron 65.8 15 0.00033 31.0 5.3 43 722-764 13-55 (60)
83 PF00325 Crp: Bacterial regula 65.5 11 0.00025 28.1 3.9 30 732-761 3-32 (32)
84 PF00392 GntR: Bacterial regul 65.1 11 0.00024 31.7 4.4 40 727-766 19-59 (64)
85 PF13545 HTH_Crp_2: Crp-like h 64.6 15 0.00033 31.4 5.3 35 731-765 28-62 (76)
86 PRK00215 LexA repressor; Valid 64.6 14 0.00031 38.2 6.1 60 715-777 2-67 (205)
87 PF11994 DUF3489: Protein of u 64.0 19 0.00042 31.8 5.7 44 716-759 9-52 (72)
88 PF14394 DUF4423: Domain of un 62.3 25 0.00054 36.0 7.2 64 711-779 18-84 (171)
89 PRK04424 fatty acid biosynthes 60.8 9.7 0.00021 39.3 4.0 46 718-763 8-53 (185)
90 PRK10411 DNA-binding transcrip 59.2 16 0.00034 39.3 5.4 48 719-766 6-53 (240)
91 PRK06474 hypothetical protein; 59.1 26 0.00057 35.9 6.8 67 713-779 7-78 (178)
92 PRK04172 pheS phenylalanyl-tRN 58.8 16 0.00035 43.3 5.9 51 714-764 3-53 (489)
93 PF02002 TFIIE_alpha: TFIIE al 58.5 6.7 0.00014 36.5 2.1 46 719-764 15-60 (105)
94 PF13384 HTH_23: Homeodomain-l 57.5 10 0.00022 30.1 2.7 38 721-760 9-46 (50)
95 PF10007 DUF2250: Uncharacteri 57.1 22 0.00047 32.9 5.1 54 713-766 3-56 (92)
96 COG4189 Predicted transcriptio 54.9 18 0.0004 38.7 4.8 50 715-764 21-70 (308)
97 PF01638 HxlR: HxlR-like helix 52.8 31 0.00068 31.1 5.5 43 720-763 8-51 (90)
98 PF08280 HTH_Mga: M protein tr 52.6 19 0.00041 30.1 3.7 38 719-756 7-44 (59)
99 TIGR00122 birA_repr_reg BirA b 50.1 54 0.0012 27.9 6.2 52 722-779 5-56 (69)
100 PF04545 Sigma70_r4: Sigma-70, 48.7 43 0.00092 26.6 5.1 34 719-754 10-43 (50)
101 PRK09954 putative kinase; Prov 47.7 35 0.00077 38.4 6.1 43 720-762 6-48 (362)
102 PF01399 PCI: PCI domain; Int 47.5 43 0.00094 30.0 5.6 46 717-762 46-91 (105)
103 smart00421 HTH_LUXR helix_turn 47.0 42 0.0009 26.3 4.8 40 715-756 4-43 (58)
104 PF14947 HTH_45: Winged helix- 46.6 38 0.00081 29.9 4.8 52 720-778 9-60 (77)
105 cd07153 Fur_like Ferric uptake 46.5 44 0.00095 31.1 5.6 57 721-778 5-67 (116)
106 PRK14999 histidine utilization 46.1 34 0.00073 36.3 5.3 38 729-766 33-71 (241)
107 TIGR02404 trehalos_R_Bsub treh 45.1 32 0.00069 36.2 4.9 39 733-775 26-64 (233)
108 PRK03902 manganese transport t 44.8 39 0.00085 33.0 5.2 42 722-763 13-54 (142)
109 TIGR02325 C_P_lyase_phnF phosp 44.0 34 0.00073 36.0 4.9 34 733-766 34-67 (238)
110 PRK11050 manganese transport r 43.7 48 0.001 33.1 5.6 44 721-764 41-84 (152)
111 PRK10430 DNA-binding transcrip 43.4 39 0.00084 35.4 5.3 36 728-763 175-210 (239)
112 PF01475 FUR: Ferric uptake re 43.2 26 0.00057 33.1 3.6 64 714-778 5-74 (120)
113 PRK09764 DNA-binding transcrip 43.0 46 0.001 35.3 5.8 39 728-766 25-64 (240)
114 TIGR02018 his_ut_repres histid 41.9 37 0.0008 35.7 4.8 39 729-767 22-61 (230)
115 smart00753 PAM PCI/PINT associ 41.3 44 0.00095 29.5 4.5 35 728-762 21-55 (88)
116 smart00088 PINT motif in prote 41.3 44 0.00095 29.5 4.5 35 728-762 21-55 (88)
117 PF06784 UPF0240: Uncharacteri 41.0 44 0.00095 34.6 5.0 68 688-760 96-165 (179)
118 PF03444 HrcA_DNA-bdg: Winged 40.5 95 0.0021 28.0 6.3 46 718-763 10-55 (78)
119 PRK11402 DNA-binding transcrip 39.7 42 0.00091 35.6 4.9 34 733-766 35-68 (241)
120 COG0735 Fur Fe2+/Zn2+ uptake r 39.2 45 0.00098 33.1 4.6 53 712-764 16-74 (145)
121 COG4565 CitB Response regulato 39.1 57 0.0012 34.8 5.4 50 713-763 155-205 (224)
122 PF08281 Sigma70_r4_2: Sigma-7 38.9 62 0.0013 26.0 4.6 24 730-753 25-48 (54)
123 TIGR03338 phnR_burk phosphonat 38.4 42 0.00092 34.6 4.5 42 725-766 28-69 (212)
124 PF09681 Phage_rep_org_N: N-te 38.4 70 0.0015 31.0 5.6 47 727-778 49-95 (121)
125 TIGR03697 NtcA_cyano global ni 38.2 60 0.0013 32.5 5.5 34 732-765 144-177 (193)
126 PRK11534 DNA-binding transcrip 37.9 53 0.0012 34.3 5.2 43 724-766 23-65 (224)
127 PRK04984 fatty acid metabolism 37.9 55 0.0012 34.5 5.4 41 726-766 25-66 (239)
128 TIGR02698 CopY_TcrY copper tra 37.5 78 0.0017 30.8 5.9 50 715-764 2-55 (130)
129 cd06170 LuxR_C_like C-terminal 37.1 81 0.0018 24.7 5.1 39 716-756 2-40 (57)
130 PF02796 HTH_7: Helix-turn-hel 37.0 30 0.00066 27.3 2.4 32 721-754 13-44 (45)
131 COG1510 Predicted transcriptio 37.0 33 0.00071 35.3 3.2 58 723-781 34-91 (177)
132 TIGR02787 codY_Gpos GTP-sensin 37.0 60 0.0013 35.2 5.4 44 722-765 188-232 (251)
133 PRK10079 phosphonate metabolis 36.3 51 0.0011 35.0 4.8 35 733-767 37-71 (241)
134 PRK13918 CRP/FNR family transc 36.1 66 0.0014 32.6 5.5 34 731-764 149-182 (202)
135 PRK10681 DNA-binding transcrip 35.7 51 0.0011 35.6 4.8 42 718-759 8-49 (252)
136 PF14502 HTH_41: Helix-turn-he 35.3 57 0.0012 26.8 3.7 32 732-763 7-38 (48)
137 PRK11414 colanic acid/biofilm 35.3 52 0.0011 34.3 4.7 46 721-766 24-69 (221)
138 COG2188 PhnF Transcriptional r 35.0 52 0.0011 35.1 4.6 42 733-778 33-74 (236)
139 cd04761 HTH_MerR-SF Helix-Turn 34.9 69 0.0015 24.8 4.2 27 732-762 1-27 (49)
140 PRK11886 bifunctional biotin-- 34.8 93 0.002 34.7 6.8 44 721-764 8-52 (319)
141 PRK11161 fumarate/nitrate redu 34.5 67 0.0014 33.5 5.3 34 732-765 185-218 (235)
142 smart00529 HTH_DTXR Helix-turn 33.8 57 0.0012 29.2 4.1 32 734-765 2-33 (96)
143 PF04182 B-block_TFIIIC: B-blo 33.8 80 0.0017 27.7 4.8 49 716-764 1-51 (75)
144 PRK12423 LexA repressor; Provi 33.6 69 0.0015 33.4 5.2 52 715-766 4-61 (202)
145 PRK09391 fixK transcriptional 33.5 73 0.0016 33.5 5.4 33 732-764 180-212 (230)
146 TIGR02812 fadR_gamma fatty aci 33.3 60 0.0013 34.2 4.7 42 725-766 23-65 (235)
147 PRK10225 DNA-binding transcrip 33.3 62 0.0013 34.6 4.9 45 722-766 23-68 (257)
148 PRK09464 pdhR transcriptional 33.1 77 0.0017 33.8 5.6 42 725-766 27-69 (254)
149 PF00165 HTH_AraC: Bacterial r 33.0 57 0.0012 25.0 3.4 28 729-756 6-33 (42)
150 PF04967 HTH_10: HTH DNA bindi 33.0 60 0.0013 27.0 3.6 30 725-754 17-46 (53)
151 PRK10402 DNA-binding transcrip 32.7 70 0.0015 33.5 5.1 39 733-777 171-209 (226)
152 TIGR01714 phage_rep_org_N phag 32.2 87 0.0019 30.4 5.1 45 729-778 49-93 (119)
153 PRK11753 DNA-binding transcrip 32.1 79 0.0017 32.2 5.3 35 731-765 168-202 (211)
154 PF00376 MerR: MerR family reg 31.6 59 0.0013 25.0 3.2 26 733-762 1-26 (38)
155 COG1654 BirA Biotin operon rep 31.6 1.1E+02 0.0023 27.7 5.2 38 726-763 14-51 (79)
156 PF13411 MerR_1: MerR HTH fami 31.4 53 0.0011 27.6 3.2 29 732-764 1-29 (69)
157 PRK00135 scpB segregation and 31.4 3.8E+02 0.0082 28.0 10.1 98 668-781 34-153 (188)
158 PRK14165 winged helix-turn-hel 31.4 93 0.002 33.2 5.7 46 719-764 9-54 (217)
159 PRK03837 transcriptional regul 31.0 74 0.0016 33.5 5.0 42 725-766 30-72 (241)
160 COG1378 Predicted transcriptio 30.9 1E+02 0.0022 33.5 6.0 62 713-777 12-73 (247)
161 PF06163 DUF977: Bacterial pro 30.9 1.1E+02 0.0025 29.9 5.6 48 717-764 12-59 (127)
162 PRK09990 DNA-binding transcrip 30.7 82 0.0018 33.5 5.3 42 725-766 24-66 (251)
163 PRK10421 DNA-binding transcrip 30.3 86 0.0019 33.5 5.4 42 725-766 19-61 (253)
164 cd06171 Sigma70_r4 Sigma70, re 30.0 1E+02 0.0022 23.4 4.5 39 715-754 11-49 (55)
165 COG1733 Predicted transcriptio 29.9 1.5E+02 0.0032 28.7 6.3 58 720-778 26-85 (120)
166 COG4742 Predicted transcriptio 29.9 79 0.0017 34.7 5.0 43 722-765 18-60 (260)
167 TIGR02147 Fsuc_second hypothet 29.7 1.4E+02 0.0031 32.8 7.0 45 731-780 137-183 (271)
168 PRK15431 ferrous iron transpor 29.7 93 0.002 28.1 4.5 38 727-764 12-49 (78)
169 smart00531 TFIIE Transcription 29.3 69 0.0015 31.8 4.1 34 728-761 12-45 (147)
170 TIGR02844 spore_III_D sporulat 29.1 78 0.0017 28.6 4.0 33 719-752 8-40 (80)
171 TIGR02716 C20_methyl_CrtF C-20 29.1 70 0.0015 35.2 4.6 43 730-778 22-64 (306)
172 PRK10046 dpiA two-component re 28.9 81 0.0018 32.7 4.8 43 721-763 166-209 (225)
173 COG1321 TroR Mn-dependent tran 28.8 96 0.0021 31.3 5.0 43 722-764 15-57 (154)
174 cd04780 HTH_MerR-like_sg5 Heli 28.7 82 0.0018 29.0 4.2 29 732-764 1-29 (95)
175 PF00196 GerE: Bacterial regul 28.5 1.1E+02 0.0023 25.1 4.5 42 715-758 4-45 (58)
176 PF10771 DUF2582: Protein of u 28.4 86 0.0019 27.3 3.9 38 722-759 13-50 (65)
177 PF13518 HTH_28: Helix-turn-he 28.2 1.4E+02 0.0029 23.5 4.9 37 722-760 5-41 (52)
178 PRK04214 rbn ribonuclease BN/u 28.1 1.4E+02 0.0031 34.6 7.1 39 726-764 305-343 (412)
179 PRK09462 fur ferric uptake reg 27.9 1.1E+02 0.0024 30.2 5.2 65 712-777 12-83 (148)
180 PF09904 HTH_43: Winged helix- 27.8 1.1E+02 0.0025 28.2 4.8 55 723-778 14-70 (90)
181 PF03965 Penicillinase_R: Peni 27.6 95 0.0021 29.2 4.6 49 716-764 2-54 (115)
182 PF13551 HTH_29: Winged helix- 27.3 1.1E+02 0.0024 27.7 4.9 39 721-760 3-41 (112)
183 COG1318 Predicted transcriptio 27.0 84 0.0018 32.4 4.2 55 686-761 37-91 (182)
184 PF15469 Sec5: Exocyst complex 26.4 1.4E+02 0.003 30.4 5.9 49 407-466 134-182 (182)
185 PHA02943 hypothetical protein; 26.4 1.3E+02 0.0027 30.7 5.2 53 722-778 16-69 (165)
186 COG4190 Predicted transcriptio 25.6 1.4E+02 0.003 29.7 5.2 51 715-765 62-112 (144)
187 smart00422 HTH_MERR helix_turn 25.5 1.1E+02 0.0023 25.7 4.1 28 732-763 1-28 (70)
188 PF03428 RP-C: Replication pro 25.4 1.2E+02 0.0026 31.4 5.1 31 733-763 72-103 (177)
189 PRK11523 DNA-binding transcrip 25.3 97 0.0021 33.1 4.7 42 725-766 25-67 (253)
190 PF13936 HTH_38: Helix-turn-he 24.8 1.1E+02 0.0024 24.1 3.7 37 716-753 6-42 (44)
191 PF08222 HTH_CodY: CodY helix- 24.2 81 0.0017 26.9 2.9 32 732-763 5-36 (61)
192 TIGR03337 phnR transcriptional 23.6 1.1E+02 0.0024 32.0 4.6 34 733-766 27-60 (231)
193 KOG2796 Uncharacterized conser 23.4 5E+02 0.011 29.0 9.4 120 353-478 166-314 (366)
194 COG1802 GntR Transcriptional r 23.3 1E+02 0.0023 32.3 4.4 47 719-765 27-73 (230)
195 PF14493 HTH_40: Helix-turn-he 23.2 1.2E+02 0.0027 27.3 4.3 37 722-760 6-42 (91)
196 PRK09334 30S ribosomal protein 23.1 1.1E+02 0.0024 28.1 3.8 36 729-764 39-74 (86)
197 COG1725 Predicted transcriptio 22.9 1.3E+02 0.0029 29.4 4.6 35 732-766 36-70 (125)
198 PRK05658 RNA polymerase sigma 22.8 1.5E+03 0.032 27.9 21.6 67 407-473 383-459 (619)
199 TIGR00721 tfx DNA-binding prot 22.7 1.5E+02 0.0032 29.6 4.9 40 714-755 6-45 (137)
200 cd01107 HTH_BmrR Helix-Turn-He 22.7 91 0.002 29.2 3.4 28 732-763 1-28 (108)
201 PF04157 EAP30: EAP30/Vps36 fa 22.6 3.3E+02 0.0072 28.8 8.0 47 716-762 173-221 (223)
202 PF09114 MotA_activ: Transcrip 22.6 2.2E+02 0.0049 26.4 5.6 46 720-765 19-66 (96)
203 COG3398 Uncharacterized protei 22.4 1.9E+02 0.0041 31.2 5.9 61 718-780 175-235 (240)
204 PF08361 TetR_C_2: MAATS-type 22.3 6.7E+02 0.015 23.7 10.9 91 360-452 7-104 (121)
205 TIGR02989 Sig-70_gvs1 RNA poly 22.2 1.4E+02 0.0031 28.9 4.8 38 714-753 111-149 (159)
206 cd04789 HTH_Cfa Helix-Turn-Hel 21.7 1E+02 0.0022 28.7 3.4 28 732-763 2-29 (102)
207 cd04781 HTH_MerR-like_sg6 Heli 21.6 98 0.0021 29.5 3.5 29 732-764 1-29 (120)
208 TIGR00331 hrcA heat shock gene 21.4 1.8E+02 0.0039 33.0 6.0 48 719-766 9-58 (337)
209 COG5090 TFG2 Transcription ini 21.3 2.3E+02 0.005 30.7 6.2 36 720-755 198-233 (297)
210 PF01853 MOZ_SAS: MOZ/SAS fami 21.2 98 0.0021 32.4 3.5 37 726-765 145-181 (188)
211 PLN03238 probable histone acet 21.1 1.9E+02 0.0041 32.3 5.8 48 716-766 207-255 (290)
212 PF05331 DUF742: Protein of un 20.9 1.8E+02 0.0038 28.1 4.9 66 697-764 23-88 (114)
213 PLN02853 Probable phenylalanyl 20.9 1.6E+02 0.0034 35.3 5.5 47 717-763 3-50 (492)
214 cd00592 HTH_MerR-like Helix-Tu 20.8 1.3E+02 0.0029 27.3 4.0 27 732-762 1-27 (100)
215 cd01111 HTH_MerD Helix-Turn-He 20.6 1.4E+02 0.003 28.1 4.2 28 732-763 1-28 (107)
216 PTZ00326 phenylalanyl-tRNA syn 20.3 1.7E+02 0.0036 35.1 5.6 48 716-763 5-53 (494)
217 PRK05472 redox-sensing transcr 20.3 1.7E+02 0.0036 30.6 5.2 44 716-759 15-60 (213)
218 cd01106 HTH_TipAL-Mta Helix-Tu 20.2 1.5E+02 0.0033 27.3 4.4 28 732-763 1-28 (103)
219 PF09940 DUF2172: Domain of un 20.0 3E+02 0.0064 31.9 7.2 115 645-762 258-386 (386)
No 1
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.9e-131 Score=1112.57 Aligned_cols=712 Identities=39% Similarity=0.607 Sum_probs=602.1
Q ss_pred hhhccChhhHHHHHHHhhhhhccchhhccCCCCccchhhHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhhchhhhhccc
Q 003120 13 ILEKLNDESVQEIIESYNGFCATTNSLLNGGRDIAVGKEFVTHVRSLCKHGLQSLAHGHFLRSLEETFERTFVSKFWRHF 92 (846)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~fw~~~ 92 (846)
+-|++.++-.+ |+. +.|+..+..+ ++++++ +..++.||+.++..++|++++|..++.++. ||+||
T Consensus 3 ~sd~~~~~~~~-i~~-~~g~~~s~~s--------~~e~~~---~~~~~~~~~~s~s~~~~~~vl~~~~~~~~~--fw~~i 67 (765)
T KOG2165|consen 3 DSDTLWQTVSS-IFP-ILGDLNSVLS--------PMEDND---FKSLSQLGLPSLSIENFIKVLQFNNQKTIP--FWSAI 67 (765)
T ss_pred CcHHHHHHHHH-Hhh-hccchhhhcC--------cCchHH---HHHHHhcccchhhHHHHHHHHHHHHhhcch--HHHHH
Confidence 34455666566 777 6666655543 777777 888999999999999999999999999986 99999
Q ss_pred ccccchhhhhcCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCcccCCCCCCCCcchhhHHHHHHHHHHH
Q 003120 93 DVYSKVAVLEKNKPLIYDDEVHEVLCKALEEICMEIQYQEKCLFMLVHAIESPRDCSLEGKPILDSEVHLFAKYQLMVSS 172 (846)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 172 (846)
.++...+...++.- ...+.+.-. .+.+..++. .++++++. ..+-..++++|+|.
T Consensus 68 ~~~~~~~~~~~~i~--------~l~d~~~ll----~~~~~~yi~--~~~l~~~l------------~~g~~~~i~~~~r~ 121 (765)
T KOG2165|consen 68 NQSLAKSIVAKNIE--------NLLDKTGLL----SSFKDFYIF--QVRLRFFL------------LFGNGDRIKDCLRW 121 (765)
T ss_pred HHHHHhcchhhhHH--------HHHhHHhHH----HHHHHHHHH--HHHHHHHH------------HhCcccHHHHHHHH
Confidence 86654422111111 111111111 111122211 12221100 01111249999999
Q ss_pred HHhccCCCChHHHHHHHHhhhhhhhhhhhcccccCCCCCCCCCcccccccccccCCCCCcccccccccccchHHHHHHHH
Q 003120 173 VLMASLPPHFPEMLYWYFKGRLEELSTIMDGELEDGNDSQDKDDMDLDEKGKQRTGEMDIDQSNNHGKFSEKSKLVKHIG 252 (846)
Q Consensus 173 ~l~~~~p~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~ 252 (846)
.|++++|++|.+|+.+||+..|.+++..|.....+. | .|+|++ ..||+.....|+|...+++|+
T Consensus 122 ~~~~~lP~~f~~vl~~~~~~~l~~~~~~~~~~~~~~---d--~~~dl~-----------~~gc~t~~~k~~cd~~~~~f~ 185 (765)
T KOG2165|consen 122 ELYYELPLRFIEVLDVYFNEHLLELNKAMHLLLTRN---D--HDIDLD-----------LQGCSTRKDKLICDQLVDLFN 185 (765)
T ss_pred HHHHhcchhHHHHHHHHHHHHHHHHHHHHhhcccCC---C--cccCcc-----------ccccCchHHHHHHHHHHHHHH
Confidence 999999999999999999999999999997665431 1 113332 257777777788888999999
Q ss_pred HHHHHHHHcCchhhhHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHhhhcccchhHHHHHHHHhhCCCCCCCCCC
Q 003120 253 KVVHDLRTLGFTSMTENAYASAIFSLLKAKVHNLAGEDYRSSVLEPIKAWIQFVSQAVPLQFLNALLAYLGESESYDSPT 332 (846)
Q Consensus 253 ~~~~~L~~lgl~~~~~~~~~~~~~~~i~~~v~~~~~~~~~~~~l~~l~~Wi~~~~~~v~~~~l~~~~~~~~~~~~~~~~~ 332 (846)
++++.|.++||.+++.+|++++++..|+++++++|+|.|++++++++.+||+ +|+.+|+..|...
T Consensus 186 ~l~~~Lk~~~l~~~~~ea~~s~l~l~l~~~l~d~~~~~~~~s~l~s~~~wI~----~~~~~wl~~V~~~----------- 250 (765)
T KOG2165|consen 186 QLVQKLKSLNLSSVSTEAIVSVLYLKLKAFLEDRCSGVWDRSVLESFNKWIN----TVWGQWLKLVFSQ----------- 250 (765)
T ss_pred HHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHhcCc-----------
Confidence 9999999999988999999999999999999999999999999999999999 8999999887421
Q ss_pred CCCCCCCCCCCCCCCCCCCCchHHHHHHHHhhHHHHHHHHHHHHHHHHhhhhcCCCCchhHHHHHHHHhhcchhhHHHHH
Q 003120 333 AGLKSPLASRPLCCPGTHNPSEGLVRWRLRLEYFAYETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVES 412 (846)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~l~~~~y~~l~~lRi~ElFdIIv~yPdS~pai~DLr~cL~~~~~r~~Lv~~ 412 (846)
+...+|+.++++++|++|+++||+++|+||+|||+|.|||+|||.||+++++|.+||.+
T Consensus 251 ---------------------e~~~~~~~~l~~~~~~~fa~lr~~~~f~Iv~dyPdS~~aiedLK~cle~t~qr~~ltes 309 (765)
T KOG2165|consen 251 ---------------------ESDHAFKLTLDYFFYEIFARLRINEIFDIVLDYPDSKPAIEDLKYCLERTDQRVYLTES 309 (765)
T ss_pred ---------------------ccccceeeeeHHHHHHHHHHHHHhhHHHHHHhCCccchhHHHHHHHHHHhcchHHHHHH
Confidence 34568999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHHHhHHHHhhcCcccchhhhchhhHHHhhccCchHHHHHHhhcCCCCCCCCCCCCch
Q 003120 413 FISALKYRLLTAGASTNDILHQYVSTIKALRTIDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAG 492 (846)
Q Consensus 413 f~~~l~~RLLhpG~~T~dIL~~YIs~Ikal~~LDPsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~ 492 (846)
|++++++|||||||+|.|||++|||||||||+|||+||+|++||.|||+|||+|+|||+|||++|||..+.+ ..
T Consensus 310 fi~~l~~riL~asv~T~DIL~~YVstIkalr~lDptgV~Le~v~~pIR~YLr~R~DtVk~iVs~lt~~~k~~-----~~- 383 (765)
T KOG2165|consen 310 FISDLKTRILTASVDTVDILLRYVSTIKALRVLDPTGVILEKVTEPIRDYLRERKDTVKQIVSGLTDLPKSE-----GE- 383 (765)
T ss_pred HHHHHHhhhcCCCCcHHHHHHHHHHHHHHHHhhCCcceehHHhhHhHHHHHhhCccHHHHHHHHHhcCCccC-----Cc-
Confidence 999999999999999999999999999999999999999999999999999999999999999999764321 12
Q ss_pred hhHHHHhcc-CcccccccCCCCCCcchhHHhhhhcccCCCCCCCCCCCCCCCccchhhHHHhHhhhcCCHHHHHHHHHHH
Q 003120 493 DSLLEELNR-DEENQENIGVDDGFNIDDKQAWINAVCWEPDPVEADPLKGSRNRRKVDILGMIVGIIGSKDQLVNEYRVM 571 (846)
Q Consensus 493 ~~L~eeL~~-~~~~~~~~~~ddd~~~d~k~~~~~~~nW~PdPvda~p~~~~k~~k~lD~I~~Lf~il~sKDvF~~eYr~l 571 (846)
.++..|++. ++..++..+.++|+..+..+.|+ ..||+|||+||+|.+++++.++.|++++|+++|||||.|++|||++
T Consensus 384 ~Dl~~els~~d~~~~e~i~~n~D~~td~~~~~e-~~~W~PdPiDA~pg~~s~k~r~~Di~~mLVsIygSKElfv~EyRnL 462 (765)
T KOG2165|consen 384 KDLSAELSKVDTLHDEDIGENDDSPTDDFMNYE-ILNWMPDPIDADPGKGSSKYRKVDIFGMLVSIYGSKELFVKEYRNL 462 (765)
T ss_pred ccHHHHHhccCccchhhcccCcCCCcchhhhhh-hhhccCCCccCCCCCCCcccccccHHHHHHHHHcchHHHHHHHHHH
Confidence 256667766 55556677888888888888886 6799999999999999888999999999999999999999999999
Q ss_pred HHHHHccCCCCChHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcccCCccccceeEEe
Q 003120 572 LADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATI 651 (846)
Q Consensus 572 LAkRLL~~~s~s~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~~~~~~~~~~~~~~~~~l~~~~~~v~I 651 (846)
||+|||+..+|+.+.|++++++||.|||++.+|.|+|||+|+.+|+++|++|+...... .+....+.+.++++|
T Consensus 463 LAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~------r~~e~~~~~~i~~~I 536 (765)
T KOG2165|consen 463 LADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS------RGAEEVPDFGISATI 536 (765)
T ss_pred HHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh------cccccCCCCchhhhh
Confidence 99999999999999999999999999999999999999999999999999999753111 011223457899999
Q ss_pred eccCCCCCCCCCCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCc
Q 003120 652 ISSNFWPPMQDEALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTS 731 (846)
Q Consensus 652 LS~~fWP~~~~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~ 731 (846)
||+.|||++.++.|.||.+++..++.|.+.|+..|++|||.|++++|+|+|+++|+||+++++|||.||+||++|+++++
T Consensus 537 lS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~qA~iI~~Fqek~t 616 (765)
T KOG2165|consen 537 LSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPEQAAIINLFQEKNT 616 (765)
T ss_pred hhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHHHHHHHHHhcCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCCCCCCCCCCCCCcccccCCCCCC-cccccCH
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMVDSSKNGDNTGSCEELLGGDEDG-ERSVASV 810 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f~~~~~~~~~~~~~~~~~~~~~e~-~~~~~s~ 810 (846)
||++++++.+|||...++|+|.||+++|||++.++. .++.+|+++|+-.+..+..+ ..+..+|++. +++++|+
T Consensus 617 wt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~-s~tgt~T~iEse~d~~q~~~-----~~~~e~eee~~e~~~as~ 690 (765)
T KOG2165|consen 617 WTLEELSESLGIPVPALRRRLSFWIQKGVLREEPII-SDTGTLTVIESEMDFDQAEG-----TVLLEAEEENYESHNASE 690 (765)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCC-CCCceeeeccccccccccCC-----CcccccccccchhhhhhH
Confidence 999999999999999999999999999999987643 56789999997665544321 2233444444 8889999
Q ss_pred HHHHhccccccchhhHHHHHhhCcccch
Q 003120 811 EDQIRNEMTVYEPTLFLVRYVANILTQK 838 (846)
Q Consensus 811 e~q~~ee~~v~w~~~fI~gMLTN~~~~~ 838 (846)
.+|.++|+++||+ ||+|||||||+||
T Consensus 691 vdqle~el~~~~~--fI~gMLTNlgsm~ 716 (765)
T KOG2165|consen 691 VDQLEEELTLFRS--FIVGMLTNLGSMK 716 (765)
T ss_pred HHHHHHHHHHHHH--HHHHHhcCcccch
Confidence 9999999999999 9999999999994
No 2
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.2e-43 Score=396.75 Aligned_cols=401 Identities=18% Similarity=0.228 Sum_probs=328.4
Q ss_pred HHhhHHHHHHHHHHHHHHHHhhhhcCCCCchhHHHHHHHHhhcchhhHHHHHHHHHHHHhhccCCCChHHHHHHHHHHhH
Q 003120 361 LRLEYFAYETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVESFISALKYRLLTAGASTNDILHQYVSTIK 440 (846)
Q Consensus 361 ~~l~~~~y~~l~~lRi~ElFdIIv~yPdS~pai~DLr~cL~~~~~r~~Lv~~f~~~l~~RLLhpG~~T~dIL~~YIs~Ik 440 (846)
..++..-|-.|+.-|+.+--+.++.|=|+.+ ..++..++++.-.-.+|...+.+.+.. |-.+-.|.|+.+.|-..=+
T Consensus 155 Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st-~k~l~atV~~~LL~~hL~~IL~kgl~~--lvDm~q~~d~~rly~L~~r 231 (661)
T KOG2167|consen 155 QELEVPEYLEHVEGRLEEENDRVIEYFDSST-KKPLIATVERCLLSRHLDLILTKGLDS--LVDMRQTSDLTRLYMLFSR 231 (661)
T ss_pred hhcccHHHHHhhhhcccchHHHHHHhccccc-ccchHHHHHHHHHHHHHHHHHhcchHH--hhhhhhccchHhHHHHHHH
Confidence 4566677889999999999999999999887 777888888766555555444444331 3335588888888865544
Q ss_pred HHHhhcCcccchhhhchhhHHHhhccCchHHHHHHhhcCCCCCCCCCCCCchhhHHHHhcc-CcccccccCCC--CCCcc
Q 003120 441 ALRTIDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVD--DGFNI 517 (846)
Q Consensus 441 al~~LDPsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~d--dd~~~ 517 (846)
+. .| ...++.+++.|+++++ ..| ++|+..+ +.++++|++++.+ |.+.-.+|-.+ +.+..
T Consensus 232 ~~-----~g--~l~l~qq~sdylk~~G---~Kl---V~de~kD-----k~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~ 293 (661)
T KOG2167|consen 232 VQ-----GG--QLSLLQQWSDYLKKPG---FKL---VIDEEKD-----KDMVQELLDFKKKVDIIVDESFLKYVAEKFLN 293 (661)
T ss_pred Hh-----cc--hHHHHHHHHHHHhccc---cee---ccCchhh-----HHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHH
Confidence 32 23 3588899999999999 666 4565533 3577888888777 44333344333 66666
Q ss_pred hhHHhhhhcccCCC-CCCCCCC----------CCCC--Cc-cchhhHHHhHhhhcCCHHHHHHHHHHHHHHHHccCCCCC
Q 003120 518 DDKQAWINAVCWEP-DPVEADP----------LKGS--RN-RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYE 583 (846)
Q Consensus 518 d~k~~~~~~~nW~P-dPvda~p----------~~~~--k~-~k~lD~I~~Lf~il~sKDvF~~eYr~lLAkRLL~~~s~s 583 (846)
..+.+|+.+.|-.| +|++-.. .++. +- ....|.|+.||+|+.+||+|+.+|++.||+|||..+|.+
T Consensus 294 ~~~~afe~fink~~~rpAelIak~~dt~Lr~gnk~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAs 373 (661)
T KOG2167|consen 294 SMSKAFETFINKRRNRPAELIAKYVDTKLRAGNKETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSAS 373 (661)
T ss_pred HHHHHHHHHHhcccCCHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchh
Confidence 67889999999888 5776321 1111 11 356899999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcccCCccccceeEEeeccCCCCCCCCC
Q 003120 584 IDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDE 663 (846)
Q Consensus 584 ~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~~~~~~~~~~~~~~~~~l~~~~~~v~ILS~~fWP~~~~~ 663 (846)
.|.|..||.+||.+||..+|+++|+|++||..|++++..|+++...+. . .+..-+.+.|++.+|||++++.
T Consensus 374 vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~--------~-~~~~l~~v~vlt~~yWpty~~~ 444 (661)
T KOG2167|consen 374 VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANN--------R-LEGNLLTVNVLTMGYWPTYPPM 444 (661)
T ss_pred hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhc--------c-CcCCceEEEeecccccCCCCch
Confidence 999999999999999999999999999999999999999998853321 0 1112289999999999999999
Q ss_pred CcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCC
Q 003120 664 ALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGV 743 (846)
Q Consensus 664 ~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm 743 (846)
...||++|...++.|.+||..+|.||+|+|.++||+|.|+++|..|++++.||.+|++||++||+.+.||++||.+.|++
T Consensus 445 ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i 524 (661)
T KOG2167|consen 445 EVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGI 524 (661)
T ss_pred hccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHhC--Cccccc-CCC-CCCCCeEEEecCCCCCCCCCCCCC
Q 003120 744 PVDVLSRRINFWISK--GIIKES-VGT-GSNDHLYNLVEGMVDSSKNGDNTG 791 (846)
Q Consensus 744 ~~~~L~r~L~~wv~~--gVL~e~-~g~-~~~~d~f~vNe~f~~~~~~~~~~~ 791 (846)
.+.+|+|.|++|.+. +||... +|+ ..++|.|.||+.|+++..|++.+.
T Consensus 525 ~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinq 576 (661)
T KOG2167|consen 525 EDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQ 576 (661)
T ss_pred cHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhh
Confidence 999999999999875 577654 444 468899999999999999987543
No 3
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=3.7e-40 Score=386.85 Aligned_cols=390 Identities=22% Similarity=0.341 Sum_probs=280.2
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCCchhHHHHHHHHhhcchhhHHHHHHHHHHHHhhccCCCChHHHHHHHHHHhHHHHhh
Q 003120 366 FAYETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVESFISALKYRLLTAGASTNDILHQYVSTIKALRTI 445 (846)
Q Consensus 366 ~~y~~l~~lRi~ElFdIIv~yPdS~pai~DLr~cL~~~~~r~~Lv~~f~~~l~~RLLhpG~~T~dIL~~YIs~Ikal~~L 445 (846)
.-|-+.+..++.+--+.+..|..+. +...+..++...-...+ .+.+.+.+. -|+... ...+|-..|--..+
T Consensus 179 ~~Yl~~v~~~l~~E~~r~~~~l~~~-t~~ki~~~l~~~LI~~~-~~~l~~~~~-~ll~~~-~~~~L~~ly~l~~~----- 249 (588)
T PF00888_consen 179 SEYLKKVENRLKEEEERVQKYLHPS-TKEKIIKTLEEVLISDH-LDELSSGFR-DLLEED-DKEDLKRLYRLFSR----- 249 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCS-GG-GHHHHHHHHHHHHTGGG-HHHHHTCHH-HHHHTT--HHHHHHHHHHHTT-----
T ss_pred hhHHHHHHHHHHHHHHHHHhhcchh-hhhhHHHHHHHHHHHHH-HHHHHHHHH-HHHHhh-HHHHHHHHHHHhhc-----
Confidence 4577788889988888888877654 57778877776543322 122222222 233333 56666666643332
Q ss_pred cCcccchhhhchhhHHHhhccCchHHHHHHhhcCCCCCCCCCCCCchhhHHHHhcc-CcccccccCCCCCCcchhHHhhh
Q 003120 446 DPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVDDGFNIDDKQAWI 524 (846)
Q Consensus 446 DPsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~ddd~~~d~k~~~~ 524 (846)
-|. .++.+...++.|++..+ ..++....... .+...++.+++...+ ......+|+.+..+....+.+|+
T Consensus 250 ~~~--~~~~l~~~~~~~i~~~g---~~~~~~~~~~~-----~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~ 319 (588)
T PF00888_consen 250 VPN--GLESLRDAFKEYIKKEG---QNIIDSFEKSS-----DPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFE 319 (588)
T ss_dssp STT--HHHHHHHHHHHHHHHHH---HHHHHHHCCGG-----GCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHH
T ss_pred ccC--CCchHHHHHHHHHHHHh---HHHHhhccccc-----chHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHH
Confidence 123 36788999999999888 45544332100 011234455554444 23344566666666555667777
Q ss_pred hcccCCC-CCCCCC-------CCCCC------CccchhhHHHhHhhhcCCHHHHHHHHHHHHHHHHccCCCCChHHHHHH
Q 003120 525 NAVCWEP-DPVEAD-------PLKGS------RNRRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRT 590 (846)
Q Consensus 525 ~~~nW~P-dPvda~-------p~~~~------k~~k~lD~I~~Lf~il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~ 590 (846)
.+.|=.+ .+++.. -.++. ..+...+.++.||+++++||+|+++|+++||+|||..++++.+.|..+
T Consensus 320 ~~~n~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~ 399 (588)
T PF00888_consen 320 EFLNKNNNKIPELLAKYCDSLLRKSNKKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSM 399 (588)
T ss_dssp HHHHCSTSHHHHHHHHHHHHHHBSSCCCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHH
T ss_pred HHHHcCCcchHHHHHHHhhHhhhhcccccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHH
Confidence 6666662 233311 01111 235779999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcccCCccccceeEEeeccCCCCCCCCCC-cccCh
Q 003120 591 LELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDEA-LIVPG 669 (846)
Q Consensus 591 LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~~~~~~~~~~~~~~~~~l~~~~~~v~ILS~~fWP~~~~~~-~~LP~ 669 (846)
|++||.+||.+++++|++|++|+..|+++++.|++...+.. ....+++++++.|||+++||..+... +.+|+
T Consensus 400 i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~-------~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~ 472 (588)
T PF00888_consen 400 IEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNN-------IQLIPPFDFNVKVLSKGYWPKYPSENNIKLPP 472 (588)
T ss_dssp HHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT--------SS--CCEEEEEEEETTTS-S-S-SS-----H
T ss_pred HHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhcc-------ccccCCCceEEEEecCCCCCCCCCCccccCCH
Confidence 99999999999999999999999999999999998875321 00112478999999999999998766 99999
Q ss_pred HHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHH
Q 003120 670 HIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLS 749 (846)
Q Consensus 670 eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~ 749 (846)
+|+..++.|+++|..+|++|+|+|.+++|+|+|++++++++++++||++||+||++||+.+++|+++|++.+||+++.++
T Consensus 473 ~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~ 552 (588)
T PF00888_consen 473 ELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELK 552 (588)
T ss_dssp HHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHH
T ss_pred HHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCccccc---CC-CCCCCCeEEEecCCC
Q 003120 750 RRINFWISKGIIKES---VG-TGSNDHLYNLVEGMV 781 (846)
Q Consensus 750 r~L~~wv~~gVL~e~---~g-~~~~~d~f~vNe~f~ 781 (846)
++|.+|++.|+|... .+ ...+++.|+||++|+
T Consensus 553 ~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 553 RALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 999999999998632 22 256789999999995
No 4
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=8.8e-38 Score=369.30 Aligned_cols=397 Identities=18% Similarity=0.225 Sum_probs=289.8
Q ss_pred HHHHHHHHHHHHHhhhhcCCCCchhHHHHHHHHhhcchh---hHHHHHHHHHHHHhhccCCCChHHHHHHHHHHhHHHHh
Q 003120 368 YETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQH---SKLVESFISALKYRLLTAGASTNDILHQYVSTIKALRT 444 (846)
Q Consensus 368 y~~l~~lRi~ElFdIIv~yPdS~pai~DLr~cL~~~~~r---~~Lv~~f~~~l~~RLLhpG~~T~dIL~~YIs~Ikal~~ 444 (846)
|-.-++.|+.+--.-+..|-++...- .++..|+..-.. ..++..+-+.+. ++|. +....|+...|-..=|
T Consensus 225 yl~k~e~~l~~e~~r~~~yl~~~~e~-~~~~~le~~~~~~~~~~~~e~~~sgf~-~~l~-~~~~edl~~my~l~~r---- 297 (725)
T KOG2166|consen 225 YLKKIEECLKEERERVTHYLHSSTEP-KLVEVVEDELIVVFADDLEEMEHSGFR-ALLN-DDKLEDLSRMYRLFRR---- 297 (725)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhcccc-hhhHHHHHHHHHHHHHHHHHHhcchHH-HHHh-ccchhHHHHHHHHhhc----
Confidence 44456666666655666555543222 244444433221 112222222332 3333 3367777777743332
Q ss_pred hcCcccchhhhchhhHHHhhccCchHHHHHHhhcCCCCCCCCCCCCchhhHHHHhcc-CcccccccCCCCCCcchhHHhh
Q 003120 445 IDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVDDGFNIDDKQAW 523 (846)
Q Consensus 445 LDPsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~ddd~~~d~k~~~ 523 (846)
.|+| |..+..-+..|++.-| ..+++........+| ...+..++++..+ ......+++.|..+......++
T Consensus 298 -~~~g--l~~l~~~~~~~~~~eg---~~l~~r~~~~~~~~~---~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~ 368 (725)
T KOG2166|consen 298 -ILPG--LEPLASVFKQHVREEG---NALVARPAETAATNP---VEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAF 368 (725)
T ss_pred -cccc--chhHHHHHHHHHHhhH---HHHhhhhhhhcccch---HHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 3456 7888899999999988 555543322111111 1122233333222 2223345666665555455566
Q ss_pred hhcccCCCCCC-CC-------CCCCCCCc------cchhhHHHhHhhhcCCHHHHHHHHHHHHHHHHccCCCCChHHHHH
Q 003120 524 INAVCWEPDPV-EA-------DPLKGSRN------RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIR 589 (846)
Q Consensus 524 ~~~~nW~PdPv-da-------~p~~~~k~------~k~lD~I~~Lf~il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~ 589 (846)
..+.|-.-.+. +- .-.++++. +..++.++++|+|+.+||+|+++|+++||+|||+++|.|.|.|..
T Consensus 369 ~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~ 448 (725)
T KOG2166|consen 369 EEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKS 448 (725)
T ss_pred HHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHH
Confidence 66676665444 31 11122222 356788888999999999999999999999999999999999999
Q ss_pred HHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcccCCccccceeEEeeccCCCCCCCCCCcccCh
Q 003120 590 TLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDEALIVPG 669 (846)
Q Consensus 590 ~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~~~~~~~~~~~~~~~~~l~~~~~~v~ILS~~fWP~~~~~~~~LP~ 669 (846)
+|.+||..||.++|.|+++|++|+..|++++..|++..... ....++|.|.||+++|||.++..+|.||+
T Consensus 449 mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~~~~~----------~~~~~df~v~VLt~g~WP~~~~~~~~LP~ 518 (725)
T KOG2166|consen 449 LITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADYANYS----------ANLGIDFTVTVLTTGFWPSYKSTDINLPS 518 (725)
T ss_pred HHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhhhchh----------ccCCCceeEEEeecCCcCCccCCCCCCCh
Confidence 99999999999999999999999999999999999761110 11237899999999999998888899999
Q ss_pred HHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHH
Q 003120 670 HIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLS 749 (846)
Q Consensus 670 eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~ 749 (846)
++...++.|..+|..+|+||+|+|+++||+++|..+|.+++++++||++|++|+++||+.+.+|+++|.+.|+|+.+.+.
T Consensus 519 el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~ 598 (725)
T KOG2166|consen 519 EMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLA 598 (725)
T ss_pred hHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHH--hCCcccccCCCCCCCCeEEEecCCCCCCCCCCCC
Q 003120 750 RRINFWI--SKGIIKESVGTGSNDHLYNLVEGMVDSSKNGDNT 790 (846)
Q Consensus 750 r~L~~wv--~~gVL~e~~g~~~~~d~f~vNe~f~~~~~~~~~~ 790 (846)
+.|+++. +.+|+..+.++..+++.|.+|.+|.++..|+...
T Consensus 599 ~~L~Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~ 641 (725)
T KOG2166|consen 599 RLLQSLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIP 641 (725)
T ss_pred HHHHHHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccC
Confidence 9999994 4455554333346789999999999999997643
No 5
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.6e-36 Score=341.44 Aligned_cols=234 Identities=16% Similarity=0.248 Sum_probs=208.0
Q ss_pred chhhHHHhHhhhcCCHHHHHHHHHHHHHHHHccCCCCChHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHH
Q 003120 546 RKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKA 625 (846)
Q Consensus 546 k~lD~I~~Lf~il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~ 625 (846)
..+..|..||+|+.+||+|+++|+++||+|||++++.+.+.|..||++||..||..||+|+|+||+||..|+++...|++
T Consensus 444 ~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~ 523 (773)
T COG5647 444 DLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQH 523 (773)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhh
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred HHHhhhccCCCcccCCccccceeEEeeccCCCCC-CCCCCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEE
Q 003120 626 TIEKQSLAGSELGEEGVSLGLLDATIISSNFWPP-MQDEALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLEL 704 (846)
Q Consensus 626 ~~~~~~~~~~~~~~~~l~~~~~~v~ILS~~fWP~-~~~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel 704 (846)
.. ++ . .+..++.|.||++.|||. .++..+.||++|.+..+.|+++|.++|+||+|.|.++||+|+|++
T Consensus 524 s~-~s--------~--~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evka 592 (773)
T COG5647 524 SP-QS--------Y--NKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKA 592 (773)
T ss_pred Cc-hh--------h--ccccchhHHHHHHhcCCCCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEe
Confidence 43 11 0 123689999999999994 457899999999999999999999999999999999999999999
Q ss_pred EECCceeEE---EecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC-C-CCCCCCeEEEecC
Q 003120 705 QFDDRAMQF---TVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV-G-TGSNDHLYNLVEG 779 (846)
Q Consensus 705 ~f~dr~~el---~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~-g-~~~~~d~f~vNe~ 779 (846)
.|+.+++.+ +++.+|+.|+++||+.+++|+++|.+.|+|+.+.+.+.|+++++.+++...+ + ..++++.|.+|++
T Consensus 593 rf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~fy~ne~ 672 (773)
T COG5647 593 RFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNEN 672 (773)
T ss_pred eccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheeeeccccccCCCCceEEEccc
Confidence 999886544 4678999999999999999999999999999999999999999987654322 2 2467899999999
Q ss_pred CCCCCCCCCCC
Q 003120 780 MVDSSKNGDNT 790 (846)
Q Consensus 780 f~~~~~~~~~~ 790 (846)
|+++..+++.+
T Consensus 673 f~~~~~rIki~ 683 (773)
T COG5647 673 FSSKLERIKIN 683 (773)
T ss_pred cccccceeeec
Confidence 99999997643
No 6
>smart00182 CULLIN Cullin.
Probab=99.98 E-value=9.2e-32 Score=262.33 Aligned_cols=141 Identities=24% Similarity=0.400 Sum_probs=130.3
Q ss_pred hcCCHHHHHHHHHHHHHHHHccCCCCChHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCC
Q 003120 557 IIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSE 636 (846)
Q Consensus 557 il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~~~~~~~~~~~~ 636 (846)
|+++||+|+++|+++||+|||..++++.+.|..+|++||.+||.+++++|++||+||..|++++++|++...+..
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~----- 75 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS----- 75 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----
Confidence 689999999999999999999999999999999999999999999999999999999999999999998764310
Q ss_pred cccCCccccceeEEeeccCCCCCCCC-CCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEE
Q 003120 637 LGEEGVSLGLLDATIISSNFWPPMQD-EALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQF 706 (846)
Q Consensus 637 ~~~~~l~~~~~~v~ILS~~fWP~~~~-~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f 706 (846)
...+++++++|||+++||.++. ..+.||++|+..++.|+++|.++|++|+|+|.|+||+|+|+++|
T Consensus 76 ----~~~~~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 76 ----NKPIIDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred ----CCCCCceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 1123689999999999999887 89999999999999999999999999999999999999999865
No 7
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=2e-27 Score=256.48 Aligned_cols=292 Identities=20% Similarity=0.257 Sum_probs=227.8
Q ss_pred cccchhhhchhhHHHhhccCchHHHHHHhhcCCCCCCCCCCCCchhhHHHHhccCc-ccccccCCCCCCcchhHHhhhhc
Q 003120 448 TGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNRDE-ENQENIGVDDGFNIDDKQAWINA 526 (846)
Q Consensus 448 sGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~~~-~~~~~~~~ddd~~~d~k~~~~~~ 526 (846)
+| |..+..-+.+|++..| -..|+.||.+. .+.-.++++++--.+-. .....+..|..|......+...-
T Consensus 322 ~g--l~~mv~e~~~~v~~~g---l~a~s~lt~en-----~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~v 391 (728)
T KOG2284|consen 322 AG--LSVMVKEFEEYVKKKG---LEAVSRLTGEN-----VPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGV 391 (728)
T ss_pred cC--chHHHHHHHHHHHHHH---HHHHhhhcccc-----chHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHh
Confidence 45 6677788889998888 56667777542 12223444443322211 11112333444433322233222
Q ss_pred ccCC-C-CCCCCCC----------CC-CCCc------cchhhHHHhHhhhcCCHHHHHHHHHHHHHHHHccCCCCChHHH
Q 003120 527 VCWE-P-DPVEADP----------LK-GSRN------RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSE 587 (846)
Q Consensus 527 ~nW~-P-dPvda~p----------~~-~~k~------~k~lD~I~~Lf~il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E 587 (846)
.|.. | ..+--.| .+ +.|+ +.++|-...+|+|+++||+|.++|.++||+||+...+.+.|.|
T Consensus 392 vn~~epg~sv~ka~e~la~y~d~llkks~kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~e 471 (728)
T KOG2284|consen 392 VNSKEPGQSVPKASERLARYTDGLLKKSTKGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAE 471 (728)
T ss_pred hccCCCCccccchHHHHHHHhhhHHhhhhcCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchH
Confidence 3332 3 1111111 11 1122 4567888899999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcccCCccccceeEEeeccCCCCCCCCCCccc
Q 003120 588 IRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDEALIV 667 (846)
Q Consensus 588 ~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~fk~~~~~~~~~~~~~~~~~l~~~~~~v~ILS~~fWP~~~~~~~~L 667 (846)
..||++||..||.++++++- +.|+..|.++|.+|.+.+. +|.+
T Consensus 472 e~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~-----------------------------------nf~~ 514 (728)
T KOG2284|consen 472 ELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA-----------------------------------NFHL 514 (728)
T ss_pred HHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH-----------------------------------hccc
Confidence 99999999999999999998 8999999999999976542 1889
Q ss_pred ChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHH
Q 003120 668 PGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDV 747 (846)
Q Consensus 668 P~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~ 747 (846)
|.+++...+.|++||..+++||||+|++.+++++|++++-|+.|--.|+++|+++|++||..+.+++.+|.+.+||+.+.
T Consensus 515 pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~ 594 (728)
T KOG2284|consen 515 PQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDY 594 (728)
T ss_pred hHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHH
Confidence 99999999999999999999999999999999999999999999899999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCcccccCCCCCCCCeEEEecCCCCCCCC
Q 003120 748 LSRRINFWISKGIIKESVGTGSNDHLYNLVEGMVDSSKN 786 (846)
Q Consensus 748 L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f~~~~~~ 786 (846)
|.+.+.++.+-.+|.........+..|++|.+|+++..+
T Consensus 595 l~kti~tildv~~~~~d~~~~~a~s~~~lnm~~tskr~k 633 (728)
T KOG2284|consen 595 LLKTIRTILDVTLLTCDDQNLTADSLVRLNMSMTSKRMK 633 (728)
T ss_pred HHHHHHHHHhceeecccccccChhhhhhcccccccccee
Confidence 999999999999998765444556789999999988766
No 8
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=1.9e-23 Score=227.78 Aligned_cols=229 Identities=14% Similarity=0.251 Sum_probs=197.8
Q ss_pred cchhhHHHhHhhhcCCHHHHHHHHHHHHHHHHccCCCCChHHHHHHHHHHhhhhC--CChhHHHHHHHHHHHHHHHHHHH
Q 003120 545 RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFG--ESSMQRCEIMLNDLIDSKRTNAN 622 (846)
Q Consensus 545 ~k~lD~I~~Lf~il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~LelLK~rfG--~~~l~k~EvMLkDI~~Skrln~~ 622 (846)
+.++..+..+++|..+||+|+.+++.+|++||+...|.+.+.|..|++.|+ +|| .++.+++..|++||..|+++|+.
T Consensus 427 dakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~ 505 (777)
T KOG2285|consen 427 DAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSS 505 (777)
T ss_pred HHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHH
Confidence 356788889999999999999999999999999999999999999999998 566 67899999999999999999999
Q ss_pred HHHHHHhhhccCCCcccCCccccceeEEeeccCCCCCCC-CCCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceE
Q 003120 623 IKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQ-DEALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVK 701 (846)
Q Consensus 623 fk~~~~~~~~~~~~~~~~~l~~~~~~v~ILS~~fWP~~~-~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~ve 701 (846)
|+....... ...+...++.+||..|.|-... ...+.||.+++..+-..++||.++|+||||+|.|+++.++
T Consensus 506 Fk~~~~~~~--------~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~ 577 (777)
T KOG2285|consen 506 FKKALTGTN--------NNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGT 577 (777)
T ss_pred HHHHHhCCC--------CCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCe
Confidence 998775321 1123357899999999999764 4578999999999999999999999999999999999988
Q ss_pred EEEEECCceeEEEecHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhC-----Cc-ccccCC-----CC
Q 003120 702 LELQFDDRAMQFTVAPIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISK-----GI-IKESVG-----TG 768 (846)
Q Consensus 702 Lel~f~dr~~el~VS~~QAaILl~Fn~--~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~-----gV-L~e~~g-----~~ 768 (846)
|...-+=+.|.++|+++|++||.+||+ ++.+|++.|.-+|.+|..+|+|.|-+++.. .| |.+++. .+
T Consensus 578 itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDF 657 (777)
T KOG2285|consen 578 ITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDF 657 (777)
T ss_pred eEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccc
Confidence 886555578999999999999999997 468999999999999999999999999852 34 455432 13
Q ss_pred CCCCeEEEecCCCC
Q 003120 769 SNDHLYNLVEGMVD 782 (846)
Q Consensus 769 ~~~d~f~vNe~f~~ 782 (846)
.+++.|.||..|+-
T Consensus 658 te~T~F~iNqeF~v 671 (777)
T KOG2285|consen 658 TESTKFLINQEFNV 671 (777)
T ss_pred cccceEEeechhhh
Confidence 57789999999974
No 9
>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=95.72 E-value=0.028 Score=51.66 Aligned_cols=66 Identities=12% Similarity=0.065 Sum_probs=55.9
Q ss_pred EEEecHHHHHHHHHhc--------CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCC
Q 003120 712 QFTVAPIHAAIIMQFQ--------DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMV 781 (846)
Q Consensus 712 el~VS~~QAaILl~Fn--------~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f~ 781 (846)
.+.+++-|+.+|+... ....+|-.||++.+|++.+.+.++|..|.++|+|....| ...|.||.+..
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~----~~~~~~n~~~~ 93 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM----MGIVGVNTPLS 93 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC----CceeecCCCcc
Confidence 4678999999888655 466789999999999999999999999999999986543 36899998765
No 10
>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=95.55 E-value=0.004 Score=52.71 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=11.8
Q ss_pred HHHHHhhCcccchhh
Q 003120 826 FLVRYVANILTQKSL 840 (846)
Q Consensus 826 fI~gMLTN~~~~~~~ 840 (846)
||+|||||+++| ||
T Consensus 1 yI~gMLtN~gsl-~l 14 (60)
T PF08672_consen 1 YIVGMLTNLGSL-PL 14 (60)
T ss_dssp HHHHHHHHH-SE-EH
T ss_pred CHhHHhhcCCCC-CH
Confidence 899999999997 65
No 11
>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=94.63 E-value=0.078 Score=42.18 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=40.4
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
+..+..||....+++..|..||++.+|++...+.+.|+.|.+.|+++
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 45677888888888999999999999999999999999999999874
No 12
>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=94.31 E-value=0.17 Score=45.06 Aligned_cols=59 Identities=19% Similarity=0.290 Sum_probs=44.8
Q ss_pred HHHHHHHHhcCCCc-ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003120 718 IHAAIIMQFQDQTS-WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 779 (846)
Q Consensus 718 ~QAaILl~Fn~~~~-~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~ 779 (846)
+++.+.+..+.... +|.++|++.+++++..+++.++.|.+.|++....| .++-|.+...
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G---~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRG---RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETS---TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCC---CCCceeecCC
Confidence 34455555454443 99999999999999999999999999999987665 2467888664
No 13
>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=94.00 E-value=0.16 Score=42.42 Aligned_cols=48 Identities=25% Similarity=0.392 Sum_probs=43.0
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|..|+...+++..+|+++|++.+|+++.++++-|..|.+.|+++...|
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 456778888899999999999999999999999999999999977654
No 14
>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=93.82 E-value=0.11 Score=43.03 Aligned_cols=51 Identities=20% Similarity=0.383 Sum_probs=44.8
Q ss_pred ecHHHHHHHHHhcCCCc--ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 715 VAPIHAAIIMQFQDQTS--WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~--~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+|+.|+.||......+. +|..+|++.++++...+.+.+.-|.++|++....
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 57899999998887766 9999999999999999999999999999997543
No 15
>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=93.71 E-value=0.12 Score=42.07 Aligned_cols=45 Identities=18% Similarity=0.382 Sum_probs=38.7
Q ss_pred HHHHHHhcCCCc-ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 720 AAIIMQFQDQTS-WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 720 AaILl~Fn~~~~-~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..||..|.+... +|+.||++.+|+|...+.+.|+.|+..|++...
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 457888887654 899999999999999999999999999999753
No 16
>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=93.03 E-value=0.32 Score=40.96 Aligned_cols=50 Identities=18% Similarity=0.310 Sum_probs=40.7
Q ss_pred ecHHHHHHHHHhc-CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 715 VAPIHAAIIMQFQ-DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 715 VS~~QAaILl~Fn-~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+|+.|..||.... .....+..+|++.++++...+.+.|+.|+.+|++...
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 4778999999998 7888999999999999999999999999999999543
No 17
>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=90.82 E-value=0.54 Score=39.40 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=43.4
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+|.-..|+.++......|+.+|++.+|++...+.++|.-|.+.|++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 5777889999977789999999999999999999999999999998653
No 18
>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=90.82 E-value=0.36 Score=39.74 Aligned_cols=50 Identities=22% Similarity=0.357 Sum_probs=44.5
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.|+.|+.+|....+.+..+..+|++.++++...+.+.+..|.++|++...
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 37789999998888888999999999999999999999999999998653
No 19
>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=90.43 E-value=0.82 Score=36.39 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=38.8
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 717 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
|...-|+...-+ ...++.||++.+|++...+.++|..|.+.|++.
T Consensus 2 ~~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 2 PTRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 556677877777 679999999999999999999999999999875
No 20
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=90.36 E-value=0.76 Score=40.94 Aligned_cols=57 Identities=18% Similarity=0.261 Sum_probs=45.7
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCC
Q 003120 720 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGM 780 (846)
Q Consensus 720 AaILl~Fn~~-~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f 780 (846)
..|+..+... ..+|+.+|++.+|++...+.+.|..|.+.|+|.... .++.|++...+
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~----~~~~y~l~~~~ 65 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG----QNGRYRLGPKV 65 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC----CCCceeecHHH
Confidence 4467777765 689999999999999999999999999999997642 13567775543
No 21
>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=90.18 E-value=0.4 Score=40.90 Aligned_cols=52 Identities=15% Similarity=0.318 Sum_probs=44.0
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|..++.|+...-.....|..+|++.+|++...+.+.|..|.++|++....+
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 4556677776666778899999999999999999999999999999976543
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.53 E-value=1.2 Score=38.36 Aligned_cols=48 Identities=19% Similarity=0.281 Sum_probs=41.5
Q ss_pred HHHHHHHHHhcCCCc--ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 717 PIHAAIIMQFQDQTS--WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~--~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..+-.||..+.+... +|..||++.+|++...+++.|..|...|++...
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 445567788877655 999999999999999999999999999998754
No 23
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=89.45 E-value=1 Score=40.23 Aligned_cols=53 Identities=17% Similarity=0.337 Sum_probs=48.4
Q ss_pred EEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 712 QFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 712 el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
++.++..+..||........++..+|++.++++...+.+.|..|++.|++...
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 46788999999999988888999999999999999999999999999999754
No 24
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.03 E-value=0.88 Score=35.85 Aligned_cols=46 Identities=20% Similarity=0.277 Sum_probs=38.7
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
-.|+..+.....++..+|++.++++...+.+.|..|...|++....
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3456666666679999999999999999999999999999986543
No 25
>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=88.39 E-value=0.86 Score=43.01 Aligned_cols=52 Identities=13% Similarity=0.095 Sum_probs=47.8
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 713 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..+++.|+.||......+.+|..+|++.++++...+.+.+..|.++|++...
T Consensus 24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence 4579999999999988889999999999999999999999999999998754
No 26
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=87.13 E-value=1.4 Score=47.52 Aligned_cols=55 Identities=13% Similarity=0.161 Sum_probs=45.4
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
..||..|.....+|+.||++.+|+|...+.|.|+.|+..|.|.... .+..|++-.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~----~~~~Y~lG~ 71 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEG----ESEKYSLTL 71 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCcEEecH
Confidence 4588899887789999999999999999999999999999997542 124566544
No 27
>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=86.65 E-value=1.3 Score=40.95 Aligned_cols=51 Identities=12% Similarity=0.352 Sum_probs=43.6
Q ss_pred EecHHHHHHHHHhcC----CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 714 TVAPIHAAIIMQFQD----QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 714 ~VS~~QAaILl~Fn~----~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.+++.|-.|+..+.. ...+++++|++.++++...++.+|.+|++.|.+...
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEES
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecc
Confidence 688999999999987 456899999999999999999999999999998753
No 28
>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=86.54 E-value=0.83 Score=39.36 Aligned_cols=41 Identities=17% Similarity=0.293 Sum_probs=33.1
Q ss_pred HHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 724 MQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 724 l~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
....++...|+.||+..++++++.++..|..|+.+|-++..
T Consensus 7 ~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 7 DYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence 33456778999999999999999999999999999988754
No 29
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.43 E-value=1.3 Score=40.87 Aligned_cols=47 Identities=23% Similarity=0.369 Sum_probs=42.2
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 717 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
...-.|+..++.....|+.+|++.+|+++..+.+.++.|.+.|+++.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 34567888888888899999999999999999999999999999973
No 30
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=86.16 E-value=1.6 Score=35.35 Aligned_cols=40 Identities=15% Similarity=0.322 Sum_probs=34.6
Q ss_pred hcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 726 FQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 726 Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+.....+ |..+|++.+|++...++++|..|.+.|+|....
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4445567 899999999999999999999999999996554
No 31
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=86.13 E-value=1.8 Score=33.64 Aligned_cols=41 Identities=17% Similarity=0.287 Sum_probs=35.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 731 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 731 ~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
..+..+|++.+|++...+.+.|..|.+.|+|.... +.|.|+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~------~~~~i~ 48 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG------GRIVIL 48 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC------CEEEEC
Confidence 46889999999999999999999999999997543 367663
No 32
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=86.12 E-value=1.4 Score=43.18 Aligned_cols=52 Identities=13% Similarity=0.275 Sum_probs=47.4
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 713 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+.+|+.|+.||......+.+|..+|++.++++...+.+.+..|.++|++...
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 5688999999998877778999999999999999999999999999999754
No 33
>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=85.66 E-value=2.2 Score=35.45 Aligned_cols=59 Identities=19% Similarity=0.312 Sum_probs=45.8
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
+..+..|+..+.+.. .+..+|++.++++...+.+.|.-|.+.|++....+. ....|.++
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~--~~~~~~~~ 64 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG--RRVYYSLT 64 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec--cEEEEEeC
Confidence 456777888776666 999999999999999999999999999998754321 22455554
No 34
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=85.35 E-value=2.4 Score=42.41 Aligned_cols=47 Identities=17% Similarity=0.179 Sum_probs=38.8
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+.+.+..+.....+..+|++..++|+..|++.|+.|.+.|++....|
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG 59 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRG 59 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecC
Confidence 33444445555689999999999999999999999999999987665
No 35
>PF13730 HTH_36: Helix-turn-helix domain
Probab=85.35 E-value=2.3 Score=34.58 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=27.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGII 761 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL 761 (846)
|.+.|++.+|++...++++|..|.+.|+|
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 89999999999999999999999999975
No 36
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.09 E-value=2.2 Score=41.55 Aligned_cols=37 Identities=14% Similarity=0.277 Sum_probs=34.1
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 728 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 728 ~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.....|+++||+.++.+.+.+.++|+.|+..|++...
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence 6778999999999999999999999999999998544
No 37
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=84.66 E-value=2.9 Score=42.40 Aligned_cols=58 Identities=12% Similarity=0.186 Sum_probs=44.1
Q ss_pred HHHHHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003120 719 HAAIIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 779 (846)
Q Consensus 719 QAaILl~Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~ 779 (846)
.+.+.+.|+. ...+|.++|++.+++|...+.+.|+.|.+.|++....|. ++-|.+...
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~---~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGP---GGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCC---CCCeeccCC
Confidence 3444455665 357999999999999999999999999999999865442 234666443
No 38
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=84.26 E-value=2.2 Score=45.96 Aligned_cols=56 Identities=20% Similarity=0.318 Sum_probs=46.0
Q ss_pred HHHHHHhcCCCc-ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003120 720 AAIIMQFQDQTS-WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 779 (846)
Q Consensus 720 AaILl~Fn~~~~-~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~ 779 (846)
..||.+|...+. +++.||++.+|+|...+.|.|..|+..|.+..... +..|++-..
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~----~g~Y~Lg~~ 63 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPE----DGRYRLGPR 63 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCC----CCcEeehHH
Confidence 468889987655 68999999999999999999999999999987641 346776543
No 39
>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=84.18 E-value=2.7 Score=40.93 Aligned_cols=47 Identities=15% Similarity=0.260 Sum_probs=38.1
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 720 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 720 AaILl~Fn~~-~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+.+.+.++.. ..+|.++|++.+++|...+++.|..|.+.|++....|
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G 60 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG 60 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeC
Confidence 4444555543 4699999999999999999999999999999976444
No 40
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=83.76 E-value=2.7 Score=35.99 Aligned_cols=44 Identities=14% Similarity=0.247 Sum_probs=35.5
Q ss_pred HHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 722 IIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 722 ILl~Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
||..++. ....+..|||+.+|++...+++-|..|.+.|.+...+
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4555565 6778999999999999999999999999999887543
No 41
>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=82.95 E-value=3.9 Score=38.26 Aligned_cols=53 Identities=15% Similarity=0.201 Sum_probs=46.1
Q ss_pred EEecHHHHHHHHHhc----CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 713 FTVAPIHAAIIMQFQ----DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 713 l~VS~~QAaILl~Fn----~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+.+|+.|..||.... +....|..+|+..++++...+.+.+.-|.++|.+....
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 467899999987766 45679999999999999999999999999999997543
No 42
>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=82.71 E-value=3.5 Score=42.95 Aligned_cols=53 Identities=15% Similarity=0.256 Sum_probs=47.9
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 713 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
..++..|..|+..+.++...+..+|++.++++...+.+.|+.|.+.|++....
T Consensus 139 ~~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 139 AGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 35788899999999887889999999999999999999999999999997653
No 43
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=82.24 E-value=2.4 Score=42.19 Aligned_cols=50 Identities=18% Similarity=0.274 Sum_probs=45.6
Q ss_pred EecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 714 TVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 714 ~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
.+...--.||..++.....++.+|++.+|+++..+++.++.|...|+++.
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 45677788999999999999999999999999999999999999999973
No 44
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=82.17 E-value=3 Score=45.34 Aligned_cols=55 Identities=9% Similarity=0.164 Sum_probs=44.3
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 720 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 720 AaILl~Fn~~-~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
..||..|... ..+|+.||++.+|+|...+.|.|+.|+..|.|.... .+..|.+-.
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~----~~~~Y~lG~ 83 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS----QLGWWHIGL 83 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCeEEecH
Confidence 4588899764 579999999999999999999999999999996542 124565443
No 45
>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=81.97 E-value=3.2 Score=44.33 Aligned_cols=53 Identities=21% Similarity=0.268 Sum_probs=43.8
Q ss_pred HHHHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 720 AAIIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 720 AaILl~Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
..||..|.. ...+|+.||++.+|+|...+.|.|..|+..|.|.... ..|.+-.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~------~~Y~lG~ 65 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDG------RLFWLTP 65 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC------CEEEecH
Confidence 457888985 5679999999999999999999999999999997542 3566543
No 46
>PRK11569 transcriptional repressor IclR; Provisional
Probab=81.91 E-value=2.9 Score=45.49 Aligned_cols=53 Identities=13% Similarity=0.211 Sum_probs=43.3
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEE
Q 003120 720 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNL 776 (846)
Q Consensus 720 AaILl~Fn~~-~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~v 776 (846)
..||.+|.+. ..+|+.||++.+|+|...+.|.|..|+..|.|.... .+..|++
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~----~~~~Y~l 84 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG----ELGHWAI 84 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC----CCCeEec
Confidence 4578889864 569999999999999999999999999999996532 1345655
No 47
>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=81.87 E-value=3.5 Score=39.52 Aligned_cols=35 Identities=14% Similarity=0.254 Sum_probs=32.5
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 730 TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 730 ~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..+|.++|++.+++|...+++.|..|.+.|+|...
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 47999999999999999999999999999999754
No 48
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=81.35 E-value=3.6 Score=33.37 Aligned_cols=41 Identities=27% Similarity=0.355 Sum_probs=32.9
Q ss_pred HHHHHHh-cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003120 720 AAIIMQF-QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 760 (846)
Q Consensus 720 AaILl~F-n~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV 760 (846)
..|+..+ +..+.+|.++||+.++++...+++.|..+-..|+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~ 44 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWGI 44 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCC
Confidence 3455555 6666699999999999999999999999988884
No 49
>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=80.12 E-value=4.2 Score=39.09 Aligned_cols=47 Identities=17% Similarity=0.345 Sum_probs=38.2
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 729 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 729 ~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
...+|+.+|++.+++|...+.+.|..|.+.|++....|. ++.|.++.
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~---~ggy~l~~ 69 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGV---EGGYTLAR 69 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCC---CCChhhcC
Confidence 457999999999999999999999999999999754431 23566644
No 50
>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=79.79 E-value=4.6 Score=33.62 Aligned_cols=36 Identities=19% Similarity=0.311 Sum_probs=32.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 730 TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 730 ~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
..+|..+|++.+|++...+.+.|+-|.+.|++....
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 468999999999999999999999999999997643
No 51
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=79.51 E-value=3.7 Score=44.38 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=43.6
Q ss_pred HHHHHHhcCCC-cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 720 AAIIMQFQDQT-SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 720 AaILl~Fn~~~-~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
..||..|.+.. .+|+.||++.+|++...+.|.|..|...|+|..... +..|++-
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~----~~~Y~Lg 68 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSAS----DDSFRLT 68 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC----CCcEEEc
Confidence 45778887654 499999999999999999999999999999976431 2457664
No 52
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=79.16 E-value=3.2 Score=41.80 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=44.7
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+...-..||...+.....|+.+|++.+|+++..+.+.++-|.+.|+++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 4556778999999999999999999999999999999999999999963
No 53
>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=79.03 E-value=7.3 Score=36.49 Aligned_cols=62 Identities=15% Similarity=0.278 Sum_probs=47.0
Q ss_pred EecHHHHHHHHH-------hcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCC
Q 003120 714 TVAPIHAAIIMQ-------FQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMV 781 (846)
Q Consensus 714 ~VS~~QAaILl~-------Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f~ 781 (846)
.++.-|.-|++. ||. .+.+|..++++.+|++.+.+.+++..|+..|||.... ..+-+|.+.+
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~g------~~~G~N~~i~ 98 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRDG------KRIGVNKNIS 98 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC------cEEeeecccc
Confidence 455555555554 454 3568999999999999999999999999999997643 4666776543
No 54
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=79.03 E-value=5.5 Score=32.07 Aligned_cols=36 Identities=14% Similarity=0.259 Sum_probs=32.9
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 729 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 729 ~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.+..|+.+|++.+|++...+.+.|.-+.+.|++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 567899999999999999999999999999999743
No 55
>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=78.89 E-value=2.7 Score=42.72 Aligned_cols=50 Identities=24% Similarity=0.266 Sum_probs=43.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCCCCCCC
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMVDSSKN 786 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f~~~~~~ 786 (846)
+|..+|++.+|++...+.+++..|..+++|.... .+.|.||.++-.++.+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~-----~G~Y~iNP~~~~kG~~ 125 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR-----NGAYMINPNFFFKGDR 125 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc-----CCeEEECcHHheeCcH
Confidence 5889999999999999999999999999997654 3599999998765544
No 56
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=77.75 E-value=6.8 Score=40.64 Aligned_cols=54 Identities=9% Similarity=-0.058 Sum_probs=49.1
Q ss_pred EEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 712 QFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 712 el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
.+.+|+.|+.||......+.+|..+|++.++++...+.+.+.-|.++|++....
T Consensus 40 ~~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~ 93 (185)
T PRK13777 40 PYDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSK 93 (185)
T ss_pred HCCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecC
Confidence 457899999999999988899999999999999999999999999999997543
No 57
>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=77.73 E-value=5.6 Score=41.39 Aligned_cols=60 Identities=22% Similarity=0.303 Sum_probs=44.0
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc---CCCCCCCCeEEEecC
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES---VGTGSNDHLYNLVEG 779 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~---~g~~~~~d~f~vNe~ 779 (846)
..||......+..|..+|++.+|++...++++|..|.++|++... .+...+...|.+.+.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~ 66 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ 66 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence 345555555567999999999999999999999999999999643 121123345666544
No 58
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=76.84 E-value=3.5 Score=44.63 Aligned_cols=48 Identities=19% Similarity=0.232 Sum_probs=43.5
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|..|+...+.+..+++.||++.++++...+||-|..|.++|+|+...|
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~G 54 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYG 54 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEC
Confidence 567888889899999999999999999999999999999998876554
No 59
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=76.40 E-value=6.5 Score=38.54 Aligned_cols=41 Identities=15% Similarity=0.213 Sum_probs=35.6
Q ss_pred hcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 726 FQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 726 Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+......+..+|++.+|+|...++++|+.|.+.|++...+|
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence 44445689999999999999999999999999999976654
No 60
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=75.87 E-value=4.8 Score=39.22 Aligned_cols=52 Identities=19% Similarity=0.312 Sum_probs=45.9
Q ss_pred EEecHHHHHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 713 FTVAPIHAAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~-~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+.+|+.|..||...... +..|..+|++.++++...+.+.+..|.++|++...
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 56899999998887754 56899999999999999999999999999999654
No 61
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=75.19 E-value=7.2 Score=38.98 Aligned_cols=49 Identities=16% Similarity=0.278 Sum_probs=39.4
Q ss_pred HHHHHHHHhcCCC-cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 718 IHAAIIMQFQDQT-SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 718 ~QAaILl~Fn~~~-~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+++.+.+.-+..+ ..|+++||+..++|+..|.+.+..|.+.|+++...|
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG 60 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG 60 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence 3444445444444 578999999999999999999999999999987665
No 62
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=74.82 E-value=7.5 Score=41.36 Aligned_cols=62 Identities=19% Similarity=0.361 Sum_probs=47.9
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc---CCCCCCCCeEEEecC
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES---VGTGSNDHLYNLVEG 779 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~---~g~~~~~d~f~vNe~ 779 (846)
.-..|+...+.....|..||++.+|++...++++|..|...|++... .|..-+.-.|++.+.
T Consensus 12 tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~ 76 (218)
T COG2345 12 TRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEK 76 (218)
T ss_pred HHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeeccc
Confidence 34556677777889999999999999999999999999999988432 222234567877665
No 63
>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=72.12 E-value=6.5 Score=33.46 Aligned_cols=37 Identities=8% Similarity=0.218 Sum_probs=30.4
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 727 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 727 n~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
-.+...|+.+|...+++|...++.+|..|+++|++..
T Consensus 23 l~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 23 LSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeee
Confidence 3456889999999999999999999999999998753
No 64
>PHA00738 putative HTH transcription regulator
Probab=71.96 E-value=11 Score=35.83 Aligned_cols=67 Identities=9% Similarity=0.122 Sum_probs=53.7
Q ss_pred EEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc-CCCCCCCCeEEEecCCC
Q 003120 712 QFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES-VGTGSNDHLYNLVEGMV 781 (846)
Q Consensus 712 el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~-~g~~~~~d~f~vNe~f~ 781 (846)
++...|.--.||....+.+..++.+|++.++|+...+-++|.-|-..||+... .|+ .-.|++|++..
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr---~vyY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGR---TLYAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECC---EEEEEECCCcc
Confidence 45567777788888877778999999999999999999999999999999643 332 34677777643
No 65
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.58 E-value=7.5 Score=38.01 Aligned_cols=49 Identities=27% Similarity=0.401 Sum_probs=43.9
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+.....-||...+.....++.+|++.+|+++..+.+.+.-|.+.||++.
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceee
Confidence 4456677888899888899999999999999999999999999999874
No 66
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=70.72 E-value=11 Score=36.37 Aligned_cols=60 Identities=15% Similarity=0.253 Sum_probs=46.4
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc-CCCCCCCCeEEEec
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES-VGTGSNDHLYNLVE 778 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~-~g~~~~~d~f~vNe 778 (846)
.|.-..||...-+....++.||++.++++...+-++|..|.+.|++... .|+ .-.|++|.
T Consensus 15 dptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr---~~~Y~l~~ 75 (117)
T PRK10141 15 DETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGK---WVHYRLSP 75 (117)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcC---EEEEEECc
Confidence 4555567776655567999999999999999999999999999999643 332 23577754
No 67
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=70.66 E-value=5.5 Score=35.54 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=36.5
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..|+......+..++.+|.+.+|++...+.++|..|.+.|.+...
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence 345555566778999999999999999999999999999998643
No 68
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=70.59 E-value=4.3 Score=35.94 Aligned_cols=36 Identities=11% Similarity=0.165 Sum_probs=31.2
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 727 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 727 n~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
.....+|+.|||+.+|+++..++..+....+.|+|.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 334678999999999999999999999888888875
No 69
>PRK10870 transcriptional repressor MprA; Provisional
Probab=70.39 E-value=14 Score=37.78 Aligned_cols=53 Identities=13% Similarity=0.149 Sum_probs=45.4
Q ss_pred EEecHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 713 FTVAPIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~--~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+.+|+.|..||..... ...+|..+|++.++++...+.+.+.-|.++|++....
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4577889888887764 4568999999999999999999999999999996543
No 70
>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=70.16 E-value=7.2 Score=30.67 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 755 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~w 755 (846)
..||...+.....++.+|++.+|+++..+.+.++-|
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 467888888889999999999999999999988755
No 71
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=70.09 E-value=6.9 Score=42.33 Aligned_cols=49 Identities=22% Similarity=0.245 Sum_probs=43.7
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
-+..|+...+.+..+++.||++.++++..+++|-|..|.++|+|+...|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~G 54 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHG 54 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3567888888889999999999999999999999999999999977655
No 72
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=70.04 E-value=7.5 Score=41.95 Aligned_cols=49 Identities=16% Similarity=0.174 Sum_probs=43.7
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
-|..|+..++++..+++.||++.+|++...++|-|..|.+.|++....|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 3567888899999999999999999999999999999999999976544
No 73
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=69.94 E-value=8.2 Score=39.76 Aligned_cols=45 Identities=7% Similarity=0.149 Sum_probs=38.4
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
...|+...-.+..+|-++|++.+||+...+|++|..|...|++..
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 445566555667899999999999999999999999999999863
No 74
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=69.86 E-value=6.3 Score=42.67 Aligned_cols=48 Identities=21% Similarity=0.336 Sum_probs=43.6
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|-.|+.+.+++..++++||++.+++++.++||=|..|.++|+|+...|
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hG 54 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHG 54 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeC
Confidence 556888889999999999999999999999999999999999977554
No 75
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=69.19 E-value=16 Score=33.40 Aligned_cols=51 Identities=20% Similarity=0.340 Sum_probs=45.0
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+++.|..+|.........+..+|++.++++...+.+.+..|..+|++....
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 789999999888777666559999999999999999999999999997654
No 76
>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=68.87 E-value=13 Score=37.59 Aligned_cols=43 Identities=7% Similarity=0.310 Sum_probs=36.6
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
.-|+...=.+..+|-++||+.+||+...+++.|..|...|++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 4455544455679999999999999999999999999999994
No 77
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=68.69 E-value=7.2 Score=42.57 Aligned_cols=50 Identities=24% Similarity=0.346 Sum_probs=44.7
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 717 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
-=|..|+...+.+..+++.||++.+|++..++||-|..|.+.|+++...|
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~G 66 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYG 66 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeC
Confidence 45778888999888999999999999999999999999999999876554
No 78
>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=67.67 E-value=14 Score=31.87 Aligned_cols=52 Identities=17% Similarity=0.313 Sum_probs=37.5
Q ss_pred ecHHHHHHHHHhcC-----CCcccHHHHHHHhCCC-HHHHHHHHHHHHhCCcccccCC
Q 003120 715 VAPIHAAIIMQFQD-----QTSWTSKNLAAAVGVP-VDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 715 VS~~QAaILl~Fn~-----~~~~Ti~EL~~~lgm~-~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+|.-|.-||....+ .-.-|+.||++.+|+. ...+.+.|.-|..+|.|+..++
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 45566666654432 2346999999999996 9999999999999999987654
No 79
>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=67.11 E-value=17 Score=29.73 Aligned_cols=32 Identities=16% Similarity=0.369 Sum_probs=29.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
|..+|++.++++...+.+.|.-|.+.|+|...
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 59999999999999999999999999998654
No 80
>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=66.78 E-value=15 Score=32.43 Aligned_cols=47 Identities=17% Similarity=0.311 Sum_probs=36.9
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+..|..++. .... ..|++||.+.||++...|.-.|.-|.+.|++...
T Consensus 5 t~~~~IL~~-ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 5 TVTQKILII-LSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred hHHHHHHHH-HHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 344443333 3333 8999999999999999999999999999999653
No 81
>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=65.89 E-value=7.8 Score=39.98 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=43.9
Q ss_pred ecHHHHHHHHHhcCC-----CcccHHHHHHHhCCC-HHHHHHHHHHHHhCCcccccCC
Q 003120 715 VAPIHAAIIMQFQDQ-----TSWTSKNLAAAVGVP-VDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 715 VS~~QAaILl~Fn~~-----~~~Ti~EL~~~lgm~-~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+++.|..||....+. -..|+.||++.+|++ ...+.++|..|.++|+|....|
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCC
Confidence 478898888877642 247899999999998 9999999999999999987654
No 82
>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=65.81 E-value=15 Score=31.03 Aligned_cols=43 Identities=16% Similarity=0.261 Sum_probs=35.5
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
|..+-++....+..+||+.+|+++..+...+.-|...|++...
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 3334446778999999999999999999999999999998653
No 83
>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=65.45 E-value=11 Score=28.10 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=25.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGII 761 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL 761 (846)
+|-+||+..+|++.+.+-|.|..|..+|++
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 577899999999999999999999999875
No 84
>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=65.15 E-value=11 Score=31.74 Aligned_cols=40 Identities=18% Similarity=0.297 Sum_probs=32.6
Q ss_pred cCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 727 QDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 727 n~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
...+.+ |..+|++.+|++...++++|..|.+.|++...++
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 345678 9999999999999999999999999999976543
No 85
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=64.65 E-value=15 Score=31.44 Aligned_cols=35 Identities=26% Similarity=0.375 Sum_probs=31.8
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 731 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 731 ~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
.+|-++||+.+|++...+.+.|..|.+.|++....
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcC
Confidence 36889999999999999999999999999998654
No 86
>PRK00215 LexA repressor; Validated
Probab=64.58 E-value=14 Score=38.17 Aligned_cols=60 Identities=15% Similarity=0.272 Sum_probs=46.9
Q ss_pred ecHHHHHHHHHhcC-----CCcccHHHHHHHhCC-CHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 715 VAPIHAAIIMQFQD-----QTSWTSKNLAAAVGV-PVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 715 VS~~QAaILl~Fn~-----~~~~Ti~EL~~~lgm-~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
+|+-|..||....+ ....|+.||++.+|+ +...+.+.|+.|..+|+|....+ ..-.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~---~~r~~~l~ 67 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPG---RSRAIEVA 67 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCC---CcceEEec
Confidence 46788888876652 446899999999999 99999999999999999965432 12356664
No 87
>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=63.95 E-value=19 Score=31.85 Aligned_cols=44 Identities=14% Similarity=0.145 Sum_probs=39.7
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKG 759 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~g 759 (846)
.+=|+.+|-++...+.-|+++|++.+|--+..++-+|.-+++++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKk 52 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKK 52 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHh
Confidence 45689999999999999999999999999999999999997653
No 88
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=62.28 E-value=25 Score=36.00 Aligned_cols=64 Identities=16% Similarity=0.170 Sum_probs=48.3
Q ss_pred eEEEecHHHHHHHHHhcCCCc-ccHHHHHHHh--CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003120 711 MQFTVAPIHAAIIMQFQDQTS-WTSKNLAAAV--GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 779 (846)
Q Consensus 711 ~el~VS~~QAaILl~Fn~~~~-~Ti~EL~~~l--gm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~ 779 (846)
+++--+.+..+|..+..-.+. .+..+|+..+ +++.+.++.+|.+|.+.|+|+... ++.|...+.
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~-----~g~y~~t~~ 84 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDG-----DGKYVQTDK 84 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECC-----CCcEEEecc
Confidence 344445566666666654443 3899999999 999999999999999999998764 247777654
No 89
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=60.83 E-value=9.7 Score=39.32 Aligned_cols=46 Identities=13% Similarity=0.078 Sum_probs=42.0
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
=+..|+...+.+...++.+|++.+|++..++||=|..|...|+|..
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r 53 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRER 53 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHH
Confidence 4677888889999999999999999999999999999999998854
No 90
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.24 E-value=16 Score=39.30 Aligned_cols=48 Identities=27% Similarity=0.378 Sum_probs=42.1
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|..|+..++.+...++.||++.++++...++|-|..|...|.|+...|
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~G 53 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHG 53 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 566888888888999999999999999999999999999888865443
No 91
>PRK06474 hypothetical protein; Provisional
Probab=59.13 E-value=26 Score=35.94 Aligned_cols=67 Identities=18% Similarity=0.294 Sum_probs=49.9
Q ss_pred EEecHHHHHHHHHhcCCCc-ccHHHHHHHh-CCCHHHHHHHHHHHHhCCcccccCCC-C--CCCCeEEEecC
Q 003120 713 FTVAPIHAAIIMQFQDQTS-WTSKNLAAAV-GVPVDVLSRRINFWISKGIIKESVGT-G--SNDHLYNLVEG 779 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~~~-~Ti~EL~~~l-gm~~~~L~r~L~~wv~~gVL~e~~g~-~--~~~d~f~vNe~ 779 (846)
+-.+|....|+..+..... .|..+|++.+ +++...+-++|..|.+.|++.....+ . .-.-.|.+|..
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~ 78 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE 78 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc
Confidence 3456777888877766554 9999999999 79999999999999999999754321 1 11235777664
No 92
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=58.76 E-value=16 Score=43.32 Aligned_cols=51 Identities=20% Similarity=0.396 Sum_probs=46.9
Q ss_pred EecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 714 TVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 714 ~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.+|+.|..||......+..|..+|++.++++...+.+.+..|.++|++...
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~ 53 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVE 53 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEE
Confidence 478999999999998889999999999999999999999999999988643
No 93
>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=58.54 E-value=6.7 Score=36.46 Aligned_cols=46 Identities=13% Similarity=0.217 Sum_probs=33.1
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.+.|+..+..+..++-++|++.+||+...+++.|..|...|++...
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 3455666665678999999999999999999999999999998543
No 94
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=57.48 E-value=10 Score=30.11 Aligned_cols=38 Identities=24% Similarity=0.532 Sum_probs=22.8
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003120 721 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 760 (846)
Q Consensus 721 aILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV 760 (846)
.++.++.+ .+|..+|++.+|++...+.+-+.-|...|+
T Consensus 9 ~ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 9 QIIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp -HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred HHHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 35555554 789999999999999999998888876663
No 95
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=57.11 E-value=22 Score=32.93 Aligned_cols=54 Identities=13% Similarity=0.329 Sum_probs=47.5
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 713 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+..++....||.++.....=...-||..+++|.+.++..|.-|...|+|....|
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 456788889999998877777888999999999999999999999999987765
No 96
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=54.88 E-value=18 Score=38.74 Aligned_cols=50 Identities=20% Similarity=0.413 Sum_probs=44.6
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.|..-..||.+...+..+.+.|||+.+|+|...+..+++.|.+.|+++..
T Consensus 21 aS~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 21 ASKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 35566679999999999999999999999999999999999999999753
No 97
>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=52.84 E-value=31 Score=31.13 Aligned_cols=43 Identities=19% Similarity=0.298 Sum_probs=35.8
Q ss_pred HHHHHHhcCCCcccHHHHHHHh-CCCHHHHHHHHHHHHhCCcccc
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAV-GVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~l-gm~~~~L~r~L~~wv~~gVL~e 763 (846)
+.||..... ....+.||.+.+ |+++..|.+.|..|...|++..
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r 51 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVER 51 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhc
Confidence 456655555 678999999999 9999999999999999999954
No 98
>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=52.56 E-value=19 Score=30.13 Aligned_cols=38 Identities=16% Similarity=0.135 Sum_probs=30.9
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWI 756 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv 756 (846)
|.-+|.++-+++.+++.+|++.+|++...++.-|..+-
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566666557889999999999999999999988775
No 99
>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=50.13 E-value=54 Score=27.92 Aligned_cols=52 Identities=19% Similarity=0.342 Sum_probs=38.0
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 779 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~ 779 (846)
|+..+.+. ..+..+|++.+|++...+++.+..+.+.|+.....+ .-|.++..
T Consensus 5 il~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~-----~g~~l~~~ 56 (69)
T TIGR00122 5 LLALLADN-PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVG-----KGYRLPPP 56 (69)
T ss_pred HHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC-----CceEecCc
Confidence 33444443 467999999999999999999999999998543322 35666544
No 100
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=48.74 E-value=43 Score=26.65 Aligned_cols=34 Identities=15% Similarity=0.301 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINF 754 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~ 754 (846)
+..|.+.| ...+|+.||++.+|++...+++....
T Consensus 10 r~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 10 REVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 34455556 45789999999999999998877654
No 101
>PRK09954 putative kinase; Provisional
Probab=47.65 E-value=35 Score=38.37 Aligned_cols=43 Identities=16% Similarity=0.212 Sum_probs=39.0
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
.-||..+.+....|..||++.++++...+++.|..|.+.|++.
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 3478888888899999999999999999999999999999874
No 102
>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=47.49 E-value=43 Score=29.98 Aligned_cols=46 Identities=17% Similarity=0.135 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 717 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
....++...+....++++++|++.++++.+.+...+..++..|.|.
T Consensus 46 i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~ 91 (105)
T PF01399_consen 46 IRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIK 91 (105)
T ss_dssp HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSE
T ss_pred HHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEE
Confidence 3445555666678899999999999999999999999999999885
No 103
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=47.00 E-value=42 Score=26.28 Aligned_cols=40 Identities=13% Similarity=0.315 Sum_probs=31.1
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWI 756 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv 756 (846)
+++-|..++.++. ..++..+|++.+|++...+++.+.-..
T Consensus 4 l~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 4 LTPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4566666666663 457999999999999999998887654
No 104
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=46.63 E-value=38 Score=29.88 Aligned_cols=52 Identities=19% Similarity=0.266 Sum_probs=37.4
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
+-||.... ....+..+|+..++++...+.+.|..|.+.|++... ++.|.+-+
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~~------~~~Y~lTe 60 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKKK------DGKYRLTE 60 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEEE------TTEEEE-H
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeCC------CCEEEECc
Confidence 44555554 567788999999999999999999999999999653 35888754
No 105
>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=46.50 E-value=44 Score=31.13 Aligned_cols=57 Identities=14% Similarity=0.268 Sum_probs=41.9
Q ss_pred HHHHHhcC-CCcccHHHHHHHh-----CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 721 AIIMQFQD-QTSWTSKNLAAAV-----GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 721 aILl~Fn~-~~~~Ti~EL~~~l-----gm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
+|+..+.. ...+|.+||.+.+ +++..++-|+|..|+..|++.+.... ++...|..+.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~-~~~~~y~~~~ 67 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELG-DGKARYELNT 67 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeC-CCceEEEeCC
Confidence 45555554 4569999999998 68999999999999999999764321 1225676653
No 106
>PRK14999 histidine utilization repressor; Provisional
Probab=46.12 E-value=34 Score=36.35 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=33.6
Q ss_pred CCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 729 QTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 729 ~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.+.+ |-.+|++..|++..+++++|.-|+..|+|....|
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 71 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQG 71 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3445 8899999999999999999999999999977665
No 107
>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=45.05 E-value=32 Score=36.24 Aligned_cols=39 Identities=15% Similarity=0.285 Sum_probs=34.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEE
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYN 775 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~ 775 (846)
|-.||++.+|++..+++++|.-|+..|+|....|+ ++|.
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~----GTfV 64 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQGK----GSIV 64 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCc----eEEE
Confidence 78999999999999999999999999999876653 4564
No 108
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=44.80 E-value=39 Score=32.99 Aligned_cols=42 Identities=10% Similarity=0.106 Sum_probs=36.0
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
|..+.+.....++.+|++.++++...+.+.|.-|.+.|++..
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~ 54 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIY 54 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEE
Confidence 444455667789999999999999999999999999999864
No 109
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=43.96 E-value=34 Score=35.98 Aligned_cols=34 Identities=24% Similarity=0.453 Sum_probs=31.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|-.||++..|++..+++++|.-|+..|+|....|
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 67 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG 67 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 7889999999999999999999999999977665
No 110
>PRK11050 manganese transport regulator MntR; Provisional
Probab=43.71 E-value=48 Score=33.06 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=37.7
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 721 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 721 aILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.|+.++...+.++..+|++.++++...+.+.|..|...|++...
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34456666778999999999999999999999999999988653
No 111
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=43.43 E-value=39 Score=35.41 Aligned_cols=36 Identities=14% Similarity=0.218 Sum_probs=33.0
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 728 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 728 ~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
....+|.++|++.+++++.+++..+..+++.|+|.+
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~ 210 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFT 210 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEE
Confidence 356799999999999999999999999999999954
No 112
>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=43.23 E-value=26 Score=33.07 Aligned_cols=64 Identities=14% Similarity=0.302 Sum_probs=46.8
Q ss_pred EecHHHHHHHHHhcCC-CcccHHHHHHHh-----CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 714 TVAPIHAAIIMQFQDQ-TSWTSKNLAAAV-----GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 714 ~VS~~QAaILl~Fn~~-~~~Ti~EL~~~l-----gm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
.+|+-.-+||..+.+. ..+|.++|.+.+ +++..++-|+|..|...|++...... ++...|.++.
T Consensus 5 r~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~-~~~~~Y~~~~ 74 (120)
T PF01475_consen 5 RLTPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG-DGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET-TSEEEEEESS
T ss_pred CCCHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC-CCcceEeecC
Confidence 3567777888888764 478999998877 58889999999999999999764321 2335677766
No 113
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=43.02 E-value=46 Score=35.32 Aligned_cols=39 Identities=15% Similarity=0.248 Sum_probs=34.0
Q ss_pred CCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 728 DQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 728 ~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
..+.+ |-.+|++..|++..+++++|.-|+..|+|....|
T Consensus 25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G 64 (240)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQG 64 (240)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34455 7899999999999999999999999999987665
No 114
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=41.91 E-value=37 Score=35.72 Aligned_cols=39 Identities=15% Similarity=0.263 Sum_probs=33.9
Q ss_pred CCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCC
Q 003120 729 QTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGT 767 (846)
Q Consensus 729 ~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~ 767 (846)
.+.+ |-.+|++..|++..+++++|.-|+..|+|....|+
T Consensus 22 g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~ 61 (230)
T TIGR02018 22 GHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQGV 61 (230)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3444 88999999999999999999999999999776653
No 115
>smart00753 PAM PCI/PINT associated module.
Probab=41.30 E-value=44 Score=29.54 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=32.1
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 728 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 728 ~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
...++++++|++.++++.+.+.+.+..++..|.|.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~ 55 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEIS 55 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeE
Confidence 46789999999999999999999999999999884
No 116
>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=41.30 E-value=44 Score=29.54 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=32.1
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 728 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 728 ~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
...++++++|++.++++.+.+.+.+..++..|.|.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~ 55 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEIS 55 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeE
Confidence 46789999999999999999999999999999884
No 117
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=40.98 E-value=44 Score=34.60 Aligned_cols=68 Identities=12% Similarity=0.198 Sum_probs=52.3
Q ss_pred CceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003120 688 PRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 760 (846)
Q Consensus 688 ~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~--~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV 760 (846)
.|.-.|.+.+|..+++---. | .+|..||.-|+.-.. -.+||.+.||+..+++.+.++..|.++.--.|
T Consensus 96 ~r~~~~~~~fg~~ep~~vPk-G----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~~F~v 165 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEKVPK-G----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFKPFEV 165 (179)
T ss_pred CCCCcccccccccCcccCCC-C----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcCCcee
Confidence 45556888889888863332 2 478899988876543 35799999999999999999999998865444
No 118
>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=40.49 E-value=95 Score=28.02 Aligned_cols=46 Identities=13% Similarity=0.218 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
++|.|=..-+....+...+|++.+++++..+|..+..|-..|+|..
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 3444444445567789999999999999999999999999999964
No 119
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=39.73 E-value=42 Score=35.56 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=31.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|-.||++.+|++-.+++++|.-|+..|+|....|
T Consensus 35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 68 (241)
T PRK11402 35 TENELCTQYNVSRITIRKAISDLVADGVLIRWQG 68 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 7789999999999999999999999999977665
No 120
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=39.22 E-value=45 Score=33.10 Aligned_cols=53 Identities=9% Similarity=0.278 Sum_probs=44.5
Q ss_pred EEEecHHHHHHHHHhcCC-CcccHHHHHHHhC-----CCHHHHHHHHHHHHhCCccccc
Q 003120 712 QFTVAPIHAAIIMQFQDQ-TSWTSKNLAAAVG-----VPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 712 el~VS~~QAaILl~Fn~~-~~~Ti~EL~~~lg-----m~~~~L~r~L~~wv~~gVL~e~ 764 (846)
-+.+|+-+.+||..+.+. +..|.++|-..+. ++..++-|+|..|...|++...
T Consensus 16 glr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~ 74 (145)
T COG0735 16 GLRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRL 74 (145)
T ss_pred CCCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEE
Confidence 467899999999988865 4589988877665 7899999999999999999754
No 121
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=39.08 E-value=57 Score=34.84 Aligned_cols=50 Identities=18% Similarity=0.354 Sum_probs=39.3
Q ss_pred EEecHHHHHHHHHhc-CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 713 FTVAPIHAAIIMQFQ-DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 713 l~VS~~QAaILl~Fn-~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
++-.|+|.. ...|. .....|.+|+++++|++....||-|.++++.|+|..
T Consensus 155 i~~~Tl~~i-~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a 205 (224)
T COG4565 155 LDELTLQKV-REALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEA 205 (224)
T ss_pred cCHHHHHHH-HHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeE
Confidence 444555543 33444 346799999999999999999999999999999864
No 122
>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=38.86 E-value=62 Score=25.95 Aligned_cols=24 Identities=17% Similarity=0.401 Sum_probs=17.6
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHH
Q 003120 730 TSWTSKNLAAAVGVPVDVLSRRIN 753 (846)
Q Consensus 730 ~~~Ti~EL~~~lgm~~~~L~r~L~ 753 (846)
..+|+.||++.+|+++..++..+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999999887764
No 123
>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=38.43 E-value=42 Score=34.61 Aligned_cols=42 Identities=12% Similarity=0.257 Sum_probs=36.6
Q ss_pred HhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|...+.++-.+|++.+|++...++.+|.-|...|++...++
T Consensus 28 ~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 28 ELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred CCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecC
Confidence 455667889999999999999999999999999999976554
No 124
>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=38.38 E-value=70 Score=31.03 Aligned_cols=47 Identities=19% Similarity=0.307 Sum_probs=38.2
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 727 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 727 n~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
+..-..|.++||..++-+.+.++.+|..+.+.|++.... ++.|.+..
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~e-----d~~i~i~~ 95 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDE-----DGVIYIPN 95 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-----CCeEEeec
Confidence 344568999999999999999999999999999997642 34666543
No 125
>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=38.23 E-value=60 Score=32.51 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=31.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+|-++||..+|++.+.+-|.|+-|.+.|++....
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 5778999999999999999999999999998754
No 126
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=37.90 E-value=53 Score=34.29 Aligned_cols=43 Identities=12% Similarity=0.131 Sum_probs=37.3
Q ss_pred HHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 724 MQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 724 l~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
..|...+.++..+|++.+|++...++.+|.-|...|++...++
T Consensus 23 g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 23 GNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred CCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence 3466677889999999999999999999999999999976543
No 127
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=37.88 E-value=55 Score=34.49 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=35.8
Q ss_pred hcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 726 FQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 726 Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
|...+.+ |-.+|++.+|++...+|.+|.-|...|+|...+|
T Consensus 25 l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g 66 (239)
T PRK04984 25 FPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 66 (239)
T ss_pred CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4456678 7899999999999999999999999999976554
No 128
>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=37.49 E-value=78 Score=30.82 Aligned_cols=50 Identities=8% Similarity=0.108 Sum_probs=41.1
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHh----CCCHHHHHHHHHHHHhCCccccc
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAV----GVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~l----gm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+|..|..|+..+=+.+..|+.+|.+.+ +++...+...|.-|.++|+|...
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence 577888888777566678999976665 78899999999999999998643
No 129
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=37.12 E-value=81 Score=24.73 Aligned_cols=39 Identities=13% Similarity=0.274 Sum_probs=29.2
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWI 756 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv 756 (846)
++-|.-++.++- ..+|..+|++.++++...+++.+.-..
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555555543 457999999999999999998887543
No 130
>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=37.04 E-value=30 Score=27.27 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=22.6
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003120 721 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINF 754 (846)
Q Consensus 721 aILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~ 754 (846)
-|+-++++. .|+.+||+.+|++...+.+.|..
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHhc
Confidence 344555554 89999999999999999988754
No 131
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.01 E-value=33 Score=35.30 Aligned_cols=58 Identities=14% Similarity=0.250 Sum_probs=40.9
Q ss_pred HHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCC
Q 003120 723 IMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMV 781 (846)
Q Consensus 723 Ll~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f~ 781 (846)
++.++ .+.+|++||++.|||+...+-..+.-|..-|+.+...-+..-.+.|....+|.
T Consensus 34 ilyls-~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F~a~~df~ 91 (177)
T COG1510 34 ILYLS-RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYFEAEKDFS 91 (177)
T ss_pred hheec-CCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCcchhhhcccchHH
Confidence 33344 46899999999999999999999999999898765421111234555555554
No 132
>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=37.00 E-value=60 Score=35.21 Aligned_cols=44 Identities=18% Similarity=0.308 Sum_probs=38.8
Q ss_pred HHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 722 IIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 722 ILl~Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
||...+. ...++..+||+++|++...+++++..|...||+...+
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 6777777 4689999999999999999999999999999997554
No 133
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=36.32 E-value=51 Score=34.96 Aligned_cols=35 Identities=29% Similarity=0.403 Sum_probs=31.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCC
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGT 767 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~ 767 (846)
|-.+|++..|++..+++++|.-|+..|+|....|+
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~ 71 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGV 71 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 77899999999999999999999999999776653
No 134
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=36.09 E-value=66 Score=32.55 Aligned_cols=34 Identities=29% Similarity=0.330 Sum_probs=30.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 731 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 731 ~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.+|-++||+.+|++.+.+-|.|.-|.+.|++...
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC
Confidence 3577899999999999999999999999999854
No 135
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=35.73 E-value=51 Score=35.57 Aligned_cols=42 Identities=17% Similarity=0.173 Sum_probs=37.6
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKG 759 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~g 759 (846)
=|..|+.+.+.+..+++.+|++.+|+++.++||=|..+...+
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 367889999999999999999999999999999999887543
No 136
>PF14502 HTH_41: Helix-turn-helix domain
Probab=35.34 E-value=57 Score=26.76 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=29.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
-|++|+++.++++.-.++.+|.+|...|.+..
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~L 38 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKL 38 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEe
Confidence 48999999999999999999999999997754
No 137
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=35.29 E-value=52 Score=34.31 Aligned_cols=46 Identities=15% Similarity=0.190 Sum_probs=38.4
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 721 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 721 aILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.+-..+...+.++-.+|++.+|++...+|.+|..|...|++...++
T Consensus 24 I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~ 69 (221)
T PRK11414 24 LSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPA 69 (221)
T ss_pred HHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCC
Confidence 3334556677888899999999999999999999999999976543
No 138
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=35.04 E-value=52 Score=35.08 Aligned_cols=42 Identities=17% Similarity=0.321 Sum_probs=34.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
|=.||++..|++..+++++|.-|++.|+|....|+ ++|....
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~----GtfV~~~ 74 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDELVEEGLIVRRQGK----GTFVASP 74 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecC----eeEEcCc
Confidence 66799999999999999999999999999776653 4555543
No 139
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.88 E-value=69 Score=24.81 Aligned_cols=27 Identities=26% Similarity=0.480 Sum_probs=23.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
+|+.|+++.+|+++..|+ .|.+.|+|.
T Consensus 1 ~~~~e~a~~~gv~~~tlr----~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTLR----YYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHHH----HHHHCCCCC
Confidence 478999999999987665 799999986
No 140
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=34.78 E-value=93 Score=34.65 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=37.2
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc-cccc
Q 003120 721 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI-IKES 764 (846)
Q Consensus 721 aILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV-L~e~ 764 (846)
.||....+....+..+|++.+|++...+.++|+.|...|+ +...
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~ 52 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSV 52 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEe
Confidence 4566666667789999999999999999999999999998 5443
No 141
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=34.50 E-value=67 Score=33.49 Aligned_cols=34 Identities=18% Similarity=0.348 Sum_probs=31.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+|-++||+.+|++...+.|.|+-|.+.|++....
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~ 218 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKG 218 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 5678999999999999999999999999998754
No 142
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=33.83 E-value=57 Score=29.21 Aligned_cols=32 Identities=9% Similarity=0.216 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 734 SKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 734 i~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+.+|++.+|++...+.+.|..|.+.|++...+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 46899999999999999999999999997654
No 143
>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=33.79 E-value=80 Score=27.69 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=41.2
Q ss_pred cHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 716 APIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 716 S~~QAaILl~Fn~--~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
|..|..+|..-.. ....+-.+|+..+|+++..+-..++.|.+.|++...
T Consensus 1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~ 51 (75)
T PF04182_consen 1 TDIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQ 51 (75)
T ss_pred CchHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEE
Confidence 4567788877764 456788999999999999999999999999998653
No 144
>PRK12423 LexA repressor; Provisional
Probab=33.60 E-value=69 Score=33.38 Aligned_cols=52 Identities=19% Similarity=0.309 Sum_probs=41.9
Q ss_pred ecHHHHHHHHHhcCC---Cc--ccHHHHHHHhC-CCHHHHHHHHHHHHhCCcccccCC
Q 003120 715 VAPIHAAIIMQFQDQ---TS--WTSKNLAAAVG-VPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 715 VS~~QAaILl~Fn~~---~~--~Ti~EL~~~lg-m~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+|+-|-.|+....+. .. -|+.||++.+| .+...++++|.-|..+|+|....+
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence 467787777766542 23 49999999999 589999999999999999976543
No 145
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=33.47 E-value=73 Score=33.50 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=30.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+|-++||+.+|++.+.+-|.|+-|.+.|+|...
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence 467899999999999999999999999999754
No 146
>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=33.32 E-value=60 Score=34.18 Aligned_cols=42 Identities=17% Similarity=0.289 Sum_probs=36.6
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.+...+.+ |-.+|++.+|++...+|.+|.-|...|++...+|
T Consensus 23 ~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~ 65 (235)
T TIGR02812 23 RFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 65 (235)
T ss_pred CCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45566788 8999999999999999999999999999976554
No 147
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=33.31 E-value=62 Score=34.62 Aligned_cols=45 Identities=16% Similarity=0.273 Sum_probs=37.9
Q ss_pred HHHHhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 722 IIMQFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 722 ILl~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+-..|...+.+ |-.+|++.+|++...+|.+|.-|...|++...+|
T Consensus 23 ~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 23 IKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred HhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 33346667788 6899999999999999999999999999976554
No 148
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=33.08 E-value=77 Score=33.77 Aligned_cols=42 Identities=19% Similarity=0.260 Sum_probs=36.3
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 27 ~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 27 TLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred CCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 45556778 8999999999999999999999999999976554
No 149
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=33.04 E-value=57 Score=24.99 Aligned_cols=28 Identities=21% Similarity=0.193 Sum_probs=20.7
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003120 729 QTSWTSKNLAAAVGVPVDVLSRRINFWI 756 (846)
Q Consensus 729 ~~~~Ti~EL~~~lgm~~~~L~r~L~~wv 756 (846)
...|++++||+..|+++..+.+..+-..
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4579999999999999999999877554
No 150
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=33.03 E-value=60 Score=27.03 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=24.8
Q ss_pred HhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003120 725 QFQDQTSWTSKNLAAAVGVPVDVLSRRINF 754 (846)
Q Consensus 725 ~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~ 754 (846)
.|+.-...|++|||+.+||+...+..+|.-
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 566667899999999999999987777654
No 151
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=32.71 E-value=70 Score=33.46 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=33.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
|-++||+.+|++.+.|.|.|+-|.+.|++.... ..+.|.
T Consensus 171 t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~------~~i~I~ 209 (226)
T PRK10402 171 KHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSK------RGYLIK 209 (226)
T ss_pred hHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeC------CEEEEe
Confidence 468999999999999999999999999997653 356664
No 152
>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=32.19 E-value=87 Score=30.40 Aligned_cols=45 Identities=16% Similarity=0.123 Sum_probs=36.6
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 729 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 729 ~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
.-..+.++||..++-+.+.++.+|..+.+.|++.... ++.|.+..
T Consensus 49 ~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d-----~g~i~i~~ 93 (119)
T TIGR01714 49 LAPYNAEMLATMFNRNVGDIRITLQTLESLGLIEKKN-----NGDIFLEN 93 (119)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-----CCcEEehh
Confidence 3467999999999999999999999999999997643 24555543
No 153
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=32.11 E-value=79 Score=32.17 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=31.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 731 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 731 ~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
.+|-++||+.+|++...+.|.|+-|.+.|+++...
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~ 202 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHG 202 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecC
Confidence 36788999999999999999999999999998654
No 154
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=31.60 E-value=59 Score=25.00 Aligned_cols=26 Identities=23% Similarity=0.470 Sum_probs=20.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
|+.|+|+.+|++...| .+|-+.|+|.
T Consensus 1 ti~e~A~~~gvs~~tl----R~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTL----RYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS-HHHH----HHHHHTTSS-
T ss_pred CHHHHHHHHCCCHHHH----HHHHHCCCCC
Confidence 5789999999988665 5899999984
No 155
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=31.57 E-value=1.1e+02 Score=27.68 Aligned_cols=38 Identities=16% Similarity=0.216 Sum_probs=32.3
Q ss_pred hcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 726 FQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 726 Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
-++.+-.|-++|++.+|++...+-++++.|-..|+=.+
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred HcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 34556789999999999999999999999999887443
No 156
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=31.44 E-value=53 Score=27.59 Aligned_cols=29 Identities=24% Similarity=0.520 Sum_probs=23.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+|+.|+|+.+|++...|+ .|.+.|+|...
T Consensus 1 yti~eva~~~gvs~~tlr----~y~~~gll~~~ 29 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLR----YYEREGLLPPP 29 (69)
T ss_dssp EEHHHHHHHTTTTHHHHH----HHHHTTSSTTB
T ss_pred CcHHHHHHHHCcCHHHHH----HHHHhcCcccc
Confidence 478999999999987765 89999997543
No 157
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=31.42 E-value=3.8e+02 Score=28.01 Aligned_cols=98 Identities=18% Similarity=0.320 Sum_probs=64.6
Q ss_pred ChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcC-------------------
Q 003120 668 PGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQD------------------- 728 (846)
Q Consensus 668 P~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~------------------- 728 (846)
+..+...++...+.|.... |-+.-. ++ ++.|.|...|--+..+..|..
T Consensus 34 ~~~v~~~l~~L~~~y~~~~--~gi~i~----------~~-~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIa 100 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDD--RGLKLI----------EF-NDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIA 100 (188)
T ss_pred HHHHHHHHHHHHHHHhhCC--CCEEEE----------EE-CCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHH
Confidence 3578888888888887552 322221 12 455777777766666665533
Q ss_pred -CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCC--CCCCeEEEecCCC
Q 003120 729 -QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTG--SNDHLYNLVEGMV 781 (846)
Q Consensus 729 -~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~--~~~d~f~vNe~f~ 781 (846)
+..+|-.+|++..|++. ...+..|+..|++++..-.. .....|.+++.|-
T Consensus 101 y~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 101 YKQPITRIEIDEIRGVNS---DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HcCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 23568899999999987 56678889999997642111 1345787877764
No 158
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=31.41 E-value=93 Score=33.23 Aligned_cols=46 Identities=15% Similarity=0.240 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+.+.+..-++...+|..+|++.++++...+.+.|..|..+|++...
T Consensus 9 ~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~ 54 (217)
T PRK14165 9 KLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRT 54 (217)
T ss_pred HHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 3344455556667999999999999999999999999999999543
No 159
>PRK03837 transcriptional regulator NanR; Provisional
Probab=31.00 E-value=74 Score=33.46 Aligned_cols=42 Identities=21% Similarity=0.327 Sum_probs=36.2
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|...+.+ +..+|++.+|++...++.+|.-|...|++...+|
T Consensus 30 ~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 30 EFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred CCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34456678 8999999999999999999999999999976554
No 160
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=30.93 E-value=1e+02 Score=33.50 Aligned_cols=62 Identities=19% Similarity=0.255 Sum_probs=48.9
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 713 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 713 l~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
|-.|.++|-+-...=.....|..||++.+|+|..-+-..|.+|.++|+.....|+ ...|+-.
T Consensus 12 lGlt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~---P~~y~av 73 (247)
T COG1378 12 LGLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGR---PKKYRAV 73 (247)
T ss_pred cCCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCC---CceEEeC
Confidence 4556777776666666678899999999999999999999999999999776553 2455543
No 161
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.92 E-value=1.1e+02 Score=29.93 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 717 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
.+.+-|+.+--++..+|+.++...||++-..+++.+.-++..|-|..+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeC
Confidence 456778888888899999999999999999999999999999988764
No 162
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=30.73 E-value=82 Score=33.51 Aligned_cols=42 Identities=17% Similarity=0.345 Sum_probs=36.4
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 24 ~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 24 VLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 44556778 8899999999999999999999999999976554
No 163
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=30.29 E-value=86 Score=33.48 Aligned_cols=42 Identities=19% Similarity=0.371 Sum_probs=36.2
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 19 ~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~ 61 (253)
T PRK10421 19 NLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRG 61 (253)
T ss_pred CCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45566778 7899999999999999999999999999976543
No 164
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=30.00 E-value=1e+02 Score=23.37 Aligned_cols=39 Identities=10% Similarity=0.217 Sum_probs=28.3
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINF 754 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~ 754 (846)
+++.+..++..+- ...++..+|++.+|++...+.+.+..
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4555555554442 24579999999999999999887754
No 165
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=29.95 E-value=1.5e+02 Score=28.71 Aligned_cols=58 Identities=22% Similarity=0.311 Sum_probs=42.2
Q ss_pred HHHHHHhcCCCcccHHHHHHHhC-CCHHHHHHHHHHHHhCCcccccCC-CCCCCCeEEEec
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVG-VPVDVLSRRINFWISKGIIKESVG-TGSNDHLYNLVE 778 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lg-m~~~~L~r~L~~wv~~gVL~e~~g-~~~~~d~f~vNe 778 (846)
..||....+ ...-++||...++ |+...|.+.|+-|...|++..... ...+.-.|++.+
T Consensus 26 ~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~ 85 (120)
T COG1733 26 LLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTE 85 (120)
T ss_pred HHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhh
Confidence 345555544 6789999999999 999999999999999999865321 122334566543
No 166
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=29.86 E-value=79 Score=34.68 Aligned_cols=43 Identities=12% Similarity=0.253 Sum_probs=36.0
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
||++..+ ..-|++||...++++...+..+|..|.+.|++.+..
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~~ 60 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQEG 60 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEecC
Confidence 3444433 678999999999999999999999999999987754
No 167
>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=29.72 E-value=1.4e+02 Score=32.84 Aligned_cols=45 Identities=16% Similarity=0.274 Sum_probs=37.1
Q ss_pred cccHHHHHHHhC--CCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCC
Q 003120 731 SWTSKNLAAAVG--VPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGM 780 (846)
Q Consensus 731 ~~Ti~EL~~~lg--m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f 780 (846)
.++..+|++.++ |+.+.++.+|.+|++.|+|+... ++.|...+..
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~-----~g~y~~t~~~ 183 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE-----DGFYKQTDKA 183 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC-----CCcEEeecce
Confidence 457889999999 89999999999999999998753 3467776553
No 168
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=29.69 E-value=93 Score=28.08 Aligned_cols=38 Identities=8% Similarity=0.091 Sum_probs=33.0
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 727 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 727 n~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..+...+..+|+..+++|++.++..|.-|+.+|-+...
T Consensus 12 ~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 12 ALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 34567899999999999999999999999999877543
No 169
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.31 E-value=69 Score=31.83 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=30.1
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003120 728 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGII 761 (846)
Q Consensus 728 ~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL 761 (846)
....+|-++|++.+||+...|++.|..|-..|++
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLI 45 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcc
Confidence 3457899999999999999999999999987654
No 170
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=29.12 E-value=78 Score=28.59 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=29.6
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHH
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRI 752 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L 752 (846)
+..|+...+. ...|+.+|++.+|++...+.+.|
T Consensus 8 ~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 5677778888 89999999999999999999977
No 171
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=29.07 E-value=70 Score=35.18 Aligned_cols=43 Identities=19% Similarity=0.077 Sum_probs=36.7
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003120 730 TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 778 (846)
Q Consensus 730 ~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe 778 (846)
...|.+||++++|+++..+++-|..++..|+|.+.. +.|....
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~------~~y~~t~ 64 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED------GKWSLTE 64 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC------CcEecch
Confidence 468999999999999999999999999999998753 4566543
No 172
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=28.89 E-value=81 Score=32.74 Aligned_cols=43 Identities=19% Similarity=0.320 Sum_probs=35.5
Q ss_pred HHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 721 AIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 721 aILl~Fn~~-~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
-|+.+..+. ...|.+||++.+++++.++++.+.+++..|.+..
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~ 209 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIA 209 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEE
Confidence 455555443 2579999999999999999999999999998864
No 173
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=28.75 E-value=96 Score=31.26 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=37.0
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
|...+.++......+||+.+++++..+...++-|.+.|++...
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~ 57 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYE 57 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEe
Confidence 4445556778899999999999999999999999999998764
No 174
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.71 E-value=82 Score=29.01 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=24.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+++.|+|+.+|++...| .+|.+.|+|...
T Consensus 1 m~I~eva~~~gvs~~tl----R~Ye~~GLl~p~ 29 (95)
T cd04780 1 MRMSELSKRSGVSVATI----KYYLREGLLPEG 29 (95)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCC
Confidence 47899999999988755 589999999753
No 175
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=28.49 E-value=1.1e+02 Score=25.10 Aligned_cols=42 Identities=10% Similarity=0.213 Sum_probs=33.2
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhC
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISK 758 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~ 758 (846)
.|+-|..|+.++.. ..+..+|++.+++++..++..+..+.++
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 46677778877764 5788999999999999999999888764
No 176
>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=28.41 E-value=86 Score=27.26 Aligned_cols=38 Identities=13% Similarity=0.306 Sum_probs=31.1
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKG 759 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~g 759 (846)
|-...++...+|+.+|+..++++..++..+|--|...+
T Consensus 13 Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~ 50 (65)
T PF10771_consen 13 VWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAREN 50 (65)
T ss_dssp HHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTT
T ss_pred HHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccC
Confidence 44456777899999999999999999999998777653
No 177
>PF13518 HTH_28: Helix-turn-helix domain
Probab=28.22 E-value=1.4e+02 Score=23.45 Aligned_cols=37 Identities=19% Similarity=0.342 Sum_probs=28.4
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 760 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV 760 (846)
|+.++.+. .|+.+++..+||+...+.+-+.-+-..|+
T Consensus 5 iv~~~~~g--~s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYLEG--ESVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHcC--CCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 44444433 39999999999999999888877777775
No 178
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=28.13 E-value=1.4e+02 Score=34.58 Aligned_cols=39 Identities=8% Similarity=0.078 Sum_probs=35.5
Q ss_pred hcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 726 FQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 726 Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
|+....+|.++|++.+++|+..+++.|..|.+.|++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEec
Confidence 566678999999999999999999999999999999754
No 179
>PRK09462 fur ferric uptake regulator; Provisional
Probab=27.88 E-value=1.1e+02 Score=30.20 Aligned_cols=65 Identities=14% Similarity=0.228 Sum_probs=48.5
Q ss_pred EEEecHHHHHHHHHhcC--CCcccHHHHHHHh-----CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003120 712 QFTVAPIHAAIIMQFQD--QTSWTSKNLAAAV-----GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 777 (846)
Q Consensus 712 el~VS~~QAaILl~Fn~--~~~~Ti~EL~~~l-----gm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vN 777 (846)
-+.+|+-..+|+..+.. ...+|.+||.+.+ +++..++-|+|..|...|++.+.... ++...|.++
T Consensus 12 glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~-~~~~~y~~~ 83 (148)
T PRK09462 12 GLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFE-GGKSVFELT 83 (148)
T ss_pred CCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcC-CCcEEEEeC
Confidence 35678888899988864 3589999998877 36889999999999999999754311 123456654
No 180
>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=27.81 E-value=1.1e+02 Score=28.23 Aligned_cols=55 Identities=20% Similarity=0.264 Sum_probs=32.6
Q ss_pred HHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc--cCCCCCCCCeEEEec
Q 003120 723 IMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE--SVGTGSNDHLYNLVE 778 (846)
Q Consensus 723 Ll~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e--~~g~~~~~d~f~vNe 778 (846)
..+..+... ++..|.+.||||.-+++..|..|-.-||-.+ ..|.-+..+.|++..
T Consensus 14 a~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~~ 70 (90)
T PF09904_consen 14 AYLIDSGER-NVPALMEATGMPRRTIQDTIKALPELGIECEFVQDGERNNAGYYRISD 70 (90)
T ss_dssp HHHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE
T ss_pred HHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEeee
Confidence 344445555 9999999999999999999999998887432 233334456787753
No 181
>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=27.57 E-value=95 Score=29.23 Aligned_cols=49 Identities=12% Similarity=0.201 Sum_probs=40.6
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCC----HHHHHHHHHHHHhCCccccc
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVP----VDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~----~~~L~r~L~~wv~~gVL~e~ 764 (846)
|+.+..|+..+=+.+..|+.||.+.++=+ ..++...|..|+.+|+|...
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEe
Confidence 56777788777776779999999998755 89999999999999999654
No 182
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.33 E-value=1.1e+02 Score=27.74 Aligned_cols=39 Identities=21% Similarity=0.370 Sum_probs=31.4
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003120 721 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 760 (846)
Q Consensus 721 aILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV 760 (846)
.++.++.+... |..++|..+|++...+.+-+.-+...|+
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYREGGI 41 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHcccH
Confidence 35555555433 7999999999999999999999988884
No 183
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=27.00 E-value=84 Score=32.41 Aligned_cols=55 Identities=16% Similarity=0.227 Sum_probs=41.3
Q ss_pred CCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003120 686 KTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGII 761 (846)
Q Consensus 686 k~~RkL~W~~~LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL 761 (846)
.+.|+|+|.++| .-|+-...- +.-..|+++|++.+|..+.+++++|+-=.+.|=|
T Consensus 37 ~~~~~lTWvdSL--------------------avAAga~ar-ekag~Ti~EIAeelG~TeqTir~hlkgetkAG~l 91 (182)
T COG1318 37 DPYERLTWVDSL--------------------AVAAGALAR-EKAGMTISEIAEELGRTEQTVRNHLKGETKAGQL 91 (182)
T ss_pred CcccccchhhHH--------------------HHHHHHHHH-HHccCcHHHHHHHhCCCHHHHHHHHhcchhhhhH
Confidence 478999999754 223322223 5567899999999999999999999887777643
No 184
>PF15469 Sec5: Exocyst complex component Sec5
Probab=26.43 E-value=1.4e+02 Score=30.36 Aligned_cols=49 Identities=24% Similarity=0.463 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHHhhccCCCChHHHHHHHHHHhHHHHhhcCcccchhhhchhhHHHhhcc
Q 003120 407 SKLVESFISALKYRLLTAGASTNDILHQYVSTIKALRTIDPTGVFLEAVGEPIRDYLRGR 466 (846)
Q Consensus 407 ~~Lv~~f~~~l~~RLLhpG~~T~dIL~~YIs~Ikal~~LDPsGvlL~~V~~pIr~YLr~R 466 (846)
...+..|+..+..||+.|..+. ..+..+|+-|..|+|.| .||=.||..|
T Consensus 134 e~ii~~~r~~l~~~L~~~~~s~----~~~~~~i~~Ll~L~~~~-------dPi~~~l~~q 182 (182)
T PF15469_consen 134 EKIIEEFREKLWEKLLSPPSSQ----EEFLKLIRKLLELNVEE-------DPIWYWLESQ 182 (182)
T ss_pred HHHHHHHHHHHHHHHhCCCCCH----HHHHHHHHHHHhCCCCC-------CHHHHHHHcC
Confidence 4577899999999999999666 55788899999999988 7888888664
No 185
>PHA02943 hypothetical protein; Provisional
Probab=26.43 E-value=1.3e+02 Score=30.65 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=40.3
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC-CCCCCCCeEEEec
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV-GTGSNDHLYNLVE 778 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~-g~~~~~d~f~vNe 778 (846)
||..+ ....-|..||++.+|++-..++-.|.-|.+.|.+++.. | ....+.+++
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G---~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIG---RAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeec---ceEEEEECh
Confidence 44455 55667899999999999999999999999999887643 3 124555555
No 186
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=25.60 E-value=1.4e+02 Score=29.68 Aligned_cols=51 Identities=18% Similarity=0.229 Sum_probs=43.0
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 715 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 715 VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
.||---.+|-...+++..|+.|+++.+|-+...+.+.|.-+.+.||+....
T Consensus 62 Lsp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~ 112 (144)
T COG4190 62 LSPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEE 112 (144)
T ss_pred hChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEec
Confidence 344445567777888899999999999999999999999999999996543
No 187
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.49 E-value=1.1e+02 Score=25.68 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=23.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+|+.|+++.+|+++..|+ .|...|++.-
T Consensus 1 ~s~~eva~~~gvs~~tlr----~~~~~gli~~ 28 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLR----YYERIGLLPP 28 (70)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCC
Confidence 478999999999987766 7888999863
No 188
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=25.40 E-value=1.2e+02 Score=31.38 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=28.6
Q ss_pred cHHHHHHHh-CCCHHHHHHHHHHHHhCCcccc
Q 003120 733 TSKNLAAAV-GVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 733 Ti~EL~~~l-gm~~~~L~r~L~~wv~~gVL~e 763 (846)
|-.+|++.+ ||++..|+++|.-|+..|+|..
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~LveaGLI~r 103 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVEAGLIVR 103 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHCCCeee
Confidence 568999999 9999999999999999999865
No 189
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=25.35 E-value=97 Score=33.07 Aligned_cols=42 Identities=14% Similarity=0.166 Sum_probs=36.0
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 725 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 725 ~Fn~~~~~-Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|...+.+ +-.+|++.+|++...+|.+|.-|...|++...+|
T Consensus 25 ~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 25 VYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 45566778 5789999999999999999999999999976554
No 190
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=24.80 E-value=1.1e+02 Score=24.09 Aligned_cols=37 Identities=16% Similarity=0.298 Sum_probs=20.3
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHH
Q 003120 716 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRIN 753 (846)
Q Consensus 716 S~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~ 753 (846)
|+.|=..|..+-+ ..+|+.+||..+|.+...+.+.|.
T Consensus 6 t~~eR~~I~~l~~-~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 6 TPEERNQIEALLE-QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ------HHHHHHC-S---HHHHHHHTT--HHHHHHHHH
T ss_pred hhhHHHHHHHHHH-cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 4444445555544 458999999999999999988764
No 191
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=24.16 E-value=81 Score=26.90 Aligned_cols=32 Identities=22% Similarity=0.371 Sum_probs=26.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
++...||++.|+....+..+|..+-+.||+..
T Consensus 5 lvas~iAd~~GiTRSvIVNALRKleSaGvIes 36 (61)
T PF08222_consen 5 LVASKIADRVGITRSVIVNALRKLESAGVIES 36 (61)
T ss_dssp E-HHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred ehHHHHHHHhCccHHHHHHHHHHHHhcCceee
Confidence 56789999999999999999999999999964
No 192
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=23.56 E-value=1.1e+02 Score=31.98 Aligned_cols=34 Identities=9% Similarity=0.163 Sum_probs=31.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 733 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 733 Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+-.+|++.+|++..+++++|..|...|++....|
T Consensus 27 sE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 7889999999999999999999999999987665
No 193
>KOG2796 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.44 E-value=5e+02 Score=29.03 Aligned_cols=120 Identities=20% Similarity=0.337 Sum_probs=73.1
Q ss_pred chHHHHHHHHhhHHHHHHHHH--------HHHHHHHhhhhcCCCCchhHHH-H-HHHHhhcc--------hh--------
Q 003120 353 SEGLVRWRLRLEYFAYETLQD--------LRIAKLFEIIVDYPESSPAIED-L-KQCLEYTG--------QH-------- 406 (846)
Q Consensus 353 ~~~~~~w~~~l~~~~y~~l~~--------lRi~ElFdIIv~yPdS~pai~D-L-r~cL~~~~--------~r-------- 406 (846)
...++-|+.|+.+..|--..= +-..-+=.+|--||+-.|++.- | |.-|+--+ ++
T Consensus 166 ESsv~lW~KRl~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL 245 (366)
T KOG2796|consen 166 ESSIRLWRKRLGRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKL 245 (366)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhh
Confidence 356899999999987753321 1223333455578787777642 1 11222111 11
Q ss_pred hHHHHHHHHHHHHhhccCCCChHHHHHHHHHHhHHH---HhhcCcccchhhhchhhHHHhhccCchHHHHHHhhc
Q 003120 407 SKLVESFISALKYRLLTAGASTNDILHQYVSTIKAL---RTIDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLT 478 (846)
Q Consensus 407 ~~Lv~~f~~~l~~RLLhpG~~T~dIL~~YIs~Ikal---~~LDPsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~ 478 (846)
..+.....---.+|++|-|++. |+++.+++ .+.||+..+-.--..-+.-||+.=.|+|+.|-+++.
T Consensus 246 ~~~q~~~~V~~n~a~i~lg~nn------~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~ 314 (366)
T KOG2796|consen 246 DGLQGKIMVLMNSAFLHLGQNN------FAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQ 314 (366)
T ss_pred hccchhHHHHhhhhhheecccc------hHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 1122222233456888888764 77777776 345888765555556678999999999999977764
No 194
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=23.29 E-value=1e+02 Score=32.33 Aligned_cols=47 Identities=13% Similarity=0.204 Sum_probs=40.2
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
.+.+-..|.....++..+|++.+|++..-++.+|.-|...|++...+
T Consensus 27 ~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 27 EAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEP 73 (230)
T ss_pred HHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecC
Confidence 34445566778889999999999999999999999999999997654
No 195
>PF14493 HTH_40: Helix-turn-helix domain
Probab=23.22 E-value=1.2e+02 Score=27.30 Aligned_cols=37 Identities=16% Similarity=0.198 Sum_probs=32.3
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003120 722 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 760 (846)
Q Consensus 722 ILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gV 760 (846)
-+.+|++ .+|++|||+.-+++..++..+|.-++..|-
T Consensus 6 T~~l~~~--G~si~eIA~~R~L~~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 6 TYELFQK--GLSIEEIAKIRGLKESTIYGHLAELIESGE 42 (91)
T ss_pred HHHHHHc--CCCHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 3567774 689999999999999999999999998875
No 196
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=23.09 E-value=1.1e+02 Score=28.12 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=32.4
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 729 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 729 ~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
..-+|...|++++++.-...+++|.-|..+|+++..
T Consensus 39 ~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 39 EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 455799999999999999999999999999998653
No 197
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=22.86 E-value=1.3e+02 Score=29.38 Aligned_cols=35 Identities=23% Similarity=0.339 Sum_probs=32.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
-|+.+||..+|+.+.++.|+.+-|...|++....|
T Consensus 36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg 70 (125)
T COG1725 36 PSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG 70 (125)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 48999999999999999999999999999976654
No 198
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=22.78 E-value=1.5e+03 Score=27.88 Aligned_cols=67 Identities=15% Similarity=0.276 Sum_probs=48.8
Q ss_pred hHHHHH---HHHHHHHhhccCCCChHHHHH-HHHHHhHHHHhhcCc-ccchh-----hhchhhHHHhhccCchHHHH
Q 003120 407 SKLVES---FISALKYRLLTAGASTNDILH-QYVSTIKALRTIDPT-GVFLE-----AVGEPIRDYLRGRKDTIKCI 473 (846)
Q Consensus 407 ~~Lv~~---f~~~l~~RLLhpG~~T~dIL~-~YIs~Ikal~~LDPs-GvlL~-----~V~~pIr~YLr~R~DtVr~I 473 (846)
..|+.+ |...+-+|.-+-|+.-.|+++ .+|..|||..-.||+ |+-+. .|...|.+||+...-|||+=
T Consensus 383 ~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip 459 (619)
T PRK05658 383 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 459 (619)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecC
Confidence 456644 455566667777999999975 689999999999995 54443 36677888888877666643
No 199
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.71 E-value=1.5e+02 Score=29.56 Aligned_cols=40 Identities=8% Similarity=-0.022 Sum_probs=32.1
Q ss_pred EecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003120 714 TVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 755 (846)
Q Consensus 714 ~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~w 755 (846)
-.|+-|..|+.++ ...+|.+||++.+|++...+.+.+...
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 3578888999887 467999999999999999877554443
No 200
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.65 E-value=91 Score=29.20 Aligned_cols=28 Identities=18% Similarity=0.415 Sum_probs=23.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+++.|+++.+|++...+ .+|.+.|+|.-
T Consensus 1 ~~i~eva~~~gis~~tl----R~ye~~GLi~p 28 (108)
T cd01107 1 FTIGEFAKLSNLSIKAL----RYYDKIGLLKP 28 (108)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHcCCCCC
Confidence 47899999999998765 59999999953
No 201
>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=22.57 E-value=3.3e+02 Score=28.82 Aligned_cols=47 Identities=15% Similarity=0.177 Sum_probs=39.5
Q ss_pred cHHHHHHHHHh--cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 716 APIHAAIIMQF--QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 716 S~~QAaILl~F--n~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
+..|..|+..- ......|..+|++.+|.+....+..|.-++..|+|.
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 35677788777 667789999999999999999999999999999874
No 202
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=22.57 E-value=2.2e+02 Score=26.41 Aligned_cols=46 Identities=24% Similarity=0.345 Sum_probs=35.2
Q ss_pred HHHHHHhcCCCcccHHHHHHHh--CCCHHHHHHHHHHHHhCCcccccC
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAV--GVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~l--gm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+.|+-+.-+++-+|..++++.+ .+....+.+.+.-|+++|++.++.
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEKSG 66 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKGLIEKSG 66 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccccC
Confidence 3444455566778999999987 899999999999999999998763
No 203
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.36 E-value=1.9e+02 Score=31.16 Aligned_cols=61 Identities=20% Similarity=0.268 Sum_probs=50.5
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCC
Q 003120 718 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGM 780 (846)
Q Consensus 718 ~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vNe~f 780 (846)
.|=.|+...++.++.|.-+|+..+|++..++.-++.-+-.-|++.+... ...-.|++|+++
T Consensus 175 ~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~~~--Gr~iiy~in~s~ 235 (240)
T COG3398 175 TSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIPEDRE--GRSIIYSINPSI 235 (240)
T ss_pred hHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCccccc--CceEEEEeCHHH
Confidence 3456788888889999999999999999999999999999999976531 124589999865
No 204
>PF08361 TetR_C_2: MAATS-type transcriptional repressor, C-terminal region; InterPro: IPR013572 This entry is named after the various transcriptional regulatory proteins that it contains, including MtrR (Q6RV06 from SWISSPROT), AcrR (P34000 from SWISSPROT), ArpR (Q9KJC4 from SWISSPROT), TtgR (Q9AIU0 from SWISSPROT) and SmeT (Q8KLP4 from SWISSPROT). These are members of the TetR (tetracycline resistance) family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins [, , ]. ; GO: 0003677 DNA binding; PDB: 3BCG_B 2QOP_A 2UXP_B 2XDN_C 2UXH_A 2UXI_B 2UXO_A 2UXU_B 2WUI_A 2W53_A ....
Probab=22.26 E-value=6.7e+02 Score=23.68 Aligned_cols=91 Identities=18% Similarity=0.185 Sum_probs=57.1
Q ss_pred HHHhhHHHHHHHHHHHHHHHHhhhh---cCCCCchhHHH-HHHHHhhcchhhHHHHHHHHHHHHhhccCCCChHHHHHHH
Q 003120 360 RLRLEYFAYETLQDLRIAKLFEIIV---DYPESSPAIED-LKQCLEYTGQHSKLVESFISALKYRLLTAGASTNDILHQY 435 (846)
Q Consensus 360 ~~~l~~~~y~~l~~lRi~ElFdIIv---~yPdS~pai~D-Lr~cL~~~~~r~~Lv~~f~~~l~~RLLhpG~~T~dIL~~Y 435 (846)
+.-+.+.+-..-.+-|...+|+|+. +|-+...++.+ -+.+.. ..+..+...|..+.++..|+|+.+....-...
T Consensus 7 r~~~~~~l~~l~~d~~~Rrv~~I~~~kcE~~~e~~~~~~r~~~~~~--~~~~~i~~~l~~A~~~g~L~~~ld~~~AA~~l 84 (121)
T PF08361_consen 7 REALIEALRRLAEDERQRRVFEILFHKCEYVEEMAPVRERRREAQR--EALARIERLLRRAQARGQLPADLDPRLAAIML 84 (121)
T ss_dssp HHHHHHHHHHHHHSHHHHHHHHHHHHS--SSTTTHHHHHHHHHHHH--HHHHHHHHHHHHHHHTTSS-TTB-HHHHHHHH
T ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHHhcccCCcccHHHHHHHHHHH--HHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHH
Confidence 3344444445556778999999986 68665545544 444433 23567889999999999999998887766666
Q ss_pred HHHhHHHHh---hcCcccch
Q 003120 436 VSTIKALRT---IDPTGVFL 452 (846)
Q Consensus 436 Is~Ikal~~---LDPsGvlL 452 (846)
.+.+..+-. ++|..-=|
T Consensus 85 ~a~~~Gl~~~WL~~p~~fdL 104 (121)
T PF08361_consen 85 HALLSGLIQNWLLDPESFDL 104 (121)
T ss_dssp HHHHHHHHHHHHHSTTTS-H
T ss_pred HHHHHHHHHHHHcCCccCCH
Confidence 666554433 46654333
No 205
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=22.19 E-value=1.4e+02 Score=28.87 Aligned_cols=38 Identities=13% Similarity=0.279 Sum_probs=30.0
Q ss_pred EecHHHHHHHHH-hcCCCcccHHHHHHHhCCCHHHHHHHHH
Q 003120 714 TVAPIHAAIIMQ-FQDQTSWTSKNLAAAVGVPVDVLSRRIN 753 (846)
Q Consensus 714 ~VS~~QAaILl~-Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~ 753 (846)
.+++-|..|+.+ |- ..++++||++.+||+...++..+.
T Consensus 111 ~L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 467777777766 43 478999999999999999887764
No 206
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.66 E-value=1e+02 Score=28.67 Aligned_cols=28 Identities=25% Similarity=0.472 Sum_probs=24.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+++.|+|+.+|+++..|+ +|.+.|+|.-
T Consensus 2 ~~i~eva~~~gvs~~tlR----~ye~~Gll~~ 29 (102)
T cd04789 2 YTISELAEKAGISRSTLL----YYEKLGLITG 29 (102)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCC
Confidence 589999999999998877 8999999963
No 207
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=21.59 E-value=98 Score=29.49 Aligned_cols=29 Identities=24% Similarity=0.491 Sum_probs=24.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+|+.|+|+.+|++...| .+|.+.|+|.-.
T Consensus 1 m~IgevA~~~gvs~~tl----RyYe~~GLl~p~ 29 (120)
T cd04781 1 LDIAEVARQSGLPASTL----RYYEEKGLIASI 29 (120)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCC
Confidence 47899999999998765 499999999743
No 208
>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=21.42 E-value=1.8e+02 Score=33.01 Aligned_cols=48 Identities=15% Similarity=0.150 Sum_probs=40.4
Q ss_pred HHHHHHHhcCCCcccHHHHHHH--hCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 719 HAAIIMQFQDQTSWTSKNLAAA--VGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 719 QAaILl~Fn~~~~~Ti~EL~~~--lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
.|.|=........++..+|++. +++++.++|+-|..|.+.|+|..+.|
T Consensus 9 ~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~h~ 58 (337)
T TIGR00331 9 KAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKPHT 58 (337)
T ss_pred HHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCCCC
Confidence 3444456677889999999999 99999999999999999999977653
No 209
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=21.33 E-value=2.3e+02 Score=30.67 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=31.1
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003120 720 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 755 (846)
Q Consensus 720 AaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~w 755 (846)
-.+.-+|.+.+.||+..|++-+|-|+..|+..|...
T Consensus 198 D~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~i 233 (297)
T COG5090 198 DMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDI 233 (297)
T ss_pred HHHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHH
Confidence 346778999999999999999999999998887654
No 210
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=21.19 E-value=98 Score=32.39 Aligned_cols=37 Identities=16% Similarity=0.324 Sum_probs=26.4
Q ss_pred hcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003120 726 FQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 765 (846)
Q Consensus 726 Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~ 765 (846)
+.....+|+++|++.|||..+++..+|+.+ |+|+..+
T Consensus 145 ~~~~~~isi~~is~~Tgi~~~DIi~tL~~l---~~l~~~~ 181 (188)
T PF01853_consen 145 FKGKKSISIKDISQETGIRPEDIISTLQQL---GMLKYYK 181 (188)
T ss_dssp TSSE--EEHHHHHHHH-BTHHHHHHHHHHT---T-EEEET
T ss_pred cCCCCeEEHHHHHHHHCCCHHHHHHHHHHC---CCEEEEC
Confidence 333346999999999999999999888765 7776654
No 211
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=21.14 E-value=1.9e+02 Score=32.28 Aligned_cols=48 Identities=19% Similarity=0.249 Sum_probs=36.1
Q ss_pred cHHHHHHHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003120 716 APIHAAIIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 766 (846)
Q Consensus 716 S~~QAaILl~Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~~g 766 (846)
+-+..+|+..+.+ ...+|+++|+..|||..+++..+|+.+ |+|+..+|
T Consensus 207 ~YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l---~~l~~~~g 255 (290)
T PLN03238 207 SYWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL---NLIKYWKG 255 (290)
T ss_pred HHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC---CcEEEECC
Confidence 3455566666544 468999999999999999998888754 88876543
No 212
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=20.92 E-value=1.8e+02 Score=28.10 Aligned_cols=66 Identities=18% Similarity=0.281 Sum_probs=51.1
Q ss_pred CCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003120 697 LGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 764 (846)
Q Consensus 697 LG~veLel~f~dr~~el~VS~~QAaILl~Fn~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e~ 764 (846)
+.-.++-....+..-.-..++-|..|+.+... ..|+.||+..+++|...++=-+.-|+..|.+.-.
T Consensus 23 l~l~TlV~a~~~~~~~~~l~pE~~~Il~lC~~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 23 LDLETLVVATPGAPAPAGLGPEHRAILELCRR--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVR 88 (114)
T ss_pred CCeEEEEEecCCCCCCCCCCHHHHHHHHHHCC--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEe
Confidence 33444433333322246788999999998877 8899999999999999999999999999988654
No 213
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=20.89 E-value=1.6e+02 Score=35.27 Aligned_cols=47 Identities=13% Similarity=0.094 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCCc-ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 717 PIHAAIIMQFQDQTS-WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 717 ~~QAaILl~Fn~~~~-~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
..|..||..+.+.+. .+.++|++.+|++.+.+.+++..|..+|++..
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~ 50 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDA 50 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence 457788988888774 89999999999999999999999999998753
No 214
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.81 E-value=1.3e+02 Score=27.30 Aligned_cols=27 Identities=30% Similarity=0.591 Sum_probs=23.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
+++.|+++.+|+++..|+ .|.+.|+|.
T Consensus 1 ~~~~eva~~~gi~~~tlr----~~~~~Gll~ 27 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLR----YYEEKGLLP 27 (100)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCcC
Confidence 478999999999987766 789999986
No 215
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=20.57 E-value=1.4e+02 Score=28.08 Aligned_cols=28 Identities=21% Similarity=0.528 Sum_probs=23.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+|+.|+++.+|++...| .+|.+.|+|.-
T Consensus 1 y~Ige~A~~~gvs~~tl----R~ye~~GLl~p 28 (107)
T cd01111 1 YSISQLALDAGVSVHIV----RDYLLRGLLHP 28 (107)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCC
Confidence 47899999999998765 58999999964
No 216
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=20.31 E-value=1.7e+02 Score=35.13 Aligned_cols=48 Identities=15% Similarity=0.113 Sum_probs=41.9
Q ss_pred cHHHHHHHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 716 APIHAAIIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 716 S~~QAaILl~Fn~-~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
...|..||..+.+ ....+.++|++.+|++.+.+.+++.+|..+|++..
T Consensus 5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~ 53 (494)
T PTZ00326 5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYITT 53 (494)
T ss_pred hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence 3567888988887 56789999999999999999999999999998753
No 217
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=20.31 E-value=1.7e+02 Score=30.62 Aligned_cols=44 Identities=20% Similarity=0.394 Sum_probs=37.8
Q ss_pred cHHHHHHHHHhcCCC--cccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003120 716 APIHAAIIMQFQDQT--SWTSKNLAAAVGVPVDVLSRRINFWISKG 759 (846)
Q Consensus 716 S~~QAaILl~Fn~~~--~~Ti~EL~~~lgm~~~~L~r~L~~wv~~g 759 (846)
.+.+..|+...+.+. .+|..+|++.+|+++..++|=|..+-..|
T Consensus 15 ~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G 60 (213)
T PRK05472 15 LPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFG 60 (213)
T ss_pred hHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcC
Confidence 456677888888877 89999999999999999999998886655
No 218
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=20.24 E-value=1.5e+02 Score=27.28 Aligned_cols=28 Identities=29% Similarity=0.521 Sum_probs=23.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003120 732 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 763 (846)
Q Consensus 732 ~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~e 763 (846)
+|+.|+|+.+|+++..|+ +|.+.|+|..
T Consensus 1 ~ti~eva~~~gvs~~tlR----~ye~~Gll~~ 28 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLH----YYDEIGLLKP 28 (103)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCC
Confidence 478999999999998776 8999999853
No 219
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=20.02 E-value=3e+02 Score=31.94 Aligned_cols=115 Identities=14% Similarity=0.211 Sum_probs=58.0
Q ss_pred cceeEEeeccCC---CCCCC----CCCcccChHHHHHHHHHHhhhhccCCCceEE-----eecCCCceEEEEEECCceeE
Q 003120 645 GLLDATIISSNF---WPPMQ----DEALIVPGHIDQLLADYAKRFNEIKTPRKLL-----WKKNLGTVKLELQFDDRAMQ 712 (846)
Q Consensus 645 ~~~~v~ILS~~f---WP~~~----~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~-----W~~~LG~veLel~f~dr~~e 712 (846)
+++-+--+.+.- .|.|- +.+|.=|..|++.++.+.+..+..-.+|.-. =-|+||.=-|--+..++.
T Consensus 258 ~dLPv~~~~Rs~yg~ypEYHTS~Dnl~fi~p~~L~~s~~~~~~~i~~lE~n~~~~~~~~~gEPqLgkrgLY~~~~~~~-- 335 (386)
T PF09940_consen 258 FDLPVGSLMRSKYGEYPEYHTSLDNLDFISPEGLEGSFEVLLEAIEILENNRIYRNLKPLGEPQLGKRGLYPTISGKS-- 335 (386)
T ss_dssp T---EEEEESS-TT--TTTTBTTSSGGG--HHHHHHHHHHHHHHHHHHHH--EEEES--SS---TTS-------------
T ss_pred cCCceeeeecccccCCcccccCCCccccCCHHHHHHHHHHHHHHHHHHhcCCceecCCcccCCCCCcccCccccCCCc--
Confidence 455555555443 35542 4567889999999988888887654443322 235666655554444322
Q ss_pred EEecH-HHHHHHHHhc-CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003120 713 FTVAP-IHAAIIMQFQ-DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 762 (846)
Q Consensus 713 l~VS~-~QAaILl~Fn-~~~~~Ti~EL~~~lgm~~~~L~r~L~~wv~~gVL~ 762 (846)
+.+. .+++++...| ...+-++-|||+++|+|...+..++.-|..+|+|+
T Consensus 336 -~~~~~~~~~~l~~L~~~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 336 -DAGKAQQMAMLWVLNYSDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -------HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred -chhHHHHHHHHHHHHhccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 1111 2233333323 23457999999999999999999999999999874
Done!