Query 003173
Match_columns 842
No_of_seqs 338 out of 936
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 18:26:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003173.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003173hhsearch_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 5E-131 1E-135 1109.8 59.0 712 13-834 3-716 (765)
2 KOG2167 Cullins [Cell cycle co 100.0 6.3E-44 1.4E-48 398.7 20.2 400 357-786 155-575 (661)
3 PF00888 Cullin: Cullin family 100.0 1.4E-40 3E-45 390.5 32.7 390 362-777 179-588 (588)
4 KOG2166 Cullins [Cell cycle co 100.0 1.5E-38 3.2E-43 375.7 32.8 396 364-785 225-640 (725)
5 COG5647 Cullin, a subunit of E 100.0 7.5E-37 1.6E-41 348.9 24.6 399 364-786 250-683 (773)
6 smart00182 CULLIN Cullin. 100.0 7.8E-32 1.7E-36 262.8 16.9 141 553-702 1-142 (142)
7 KOG2284 E3 ubiquitin ligase, C 99.9 8.3E-28 1.8E-32 259.2 9.5 292 444-782 322-633 (728)
8 KOG2285 E3 ubiquitin ligase, C 99.9 3E-22 6.6E-27 218.3 26.0 229 541-778 427-671 (777)
9 TIGR01610 phage_O_Nterm phage 95.6 0.033 7.2E-07 51.2 6.7 66 708-777 20-93 (95)
10 PF08672 APC2: Anaphase promot 95.4 0.0048 1E-07 52.2 0.3 14 822-836 1-14 (60)
11 PF13412 HTH_24: Winged helix- 94.5 0.084 1.8E-06 41.9 5.4 47 712-758 2-48 (48)
12 PF02082 Rrf2: Transcriptional 94.1 0.19 4.2E-06 44.7 7.3 59 714-775 11-70 (83)
13 PF08220 HTH_DeoR: DeoR-like h 93.8 0.18 3.8E-06 42.0 6.0 48 715-762 2-49 (57)
14 PF12802 MarR_2: MarR family; 93.7 0.12 2.6E-06 42.8 4.9 50 711-760 3-54 (62)
15 PF09339 HTH_IclR: IclR helix- 93.6 0.12 2.7E-06 41.9 4.7 45 716-760 6-51 (52)
16 PF13463 HTH_27: Winged helix 93.0 0.35 7.5E-06 40.7 6.7 50 711-760 1-51 (68)
17 PF01047 MarR: MarR family; I 90.7 0.37 8E-06 39.6 4.3 50 711-760 1-50 (59)
18 PF12840 HTH_20: Helix-turn-he 90.5 0.59 1.3E-05 39.1 5.4 49 712-760 9-57 (61)
19 PF01022 HTH_5: Bacterial regu 90.2 0.9 1.9E-05 36.1 5.8 45 713-758 2-46 (47)
20 smart00346 HTH_ICLR helix_turn 89.9 0.88 1.9E-05 40.5 6.3 57 716-776 8-65 (91)
21 PF01978 TrmB: Sugar-specific 89.7 0.47 1E-05 40.5 4.2 51 711-761 6-56 (68)
22 smart00347 HTH_MARR helix_turn 89.2 0.99 2.1E-05 40.3 6.1 53 708-760 5-57 (101)
23 smart00420 HTH_DEOR helix_turn 89.1 0.85 1.8E-05 35.9 5.1 46 716-761 3-48 (53)
24 smart00550 Zalpha Z-DNA-bindin 89.0 1.4 3.1E-05 37.9 6.7 48 713-760 6-55 (68)
25 TIGR02337 HpaR homoprotocatech 87.7 0.99 2.1E-05 42.6 5.3 52 709-760 24-75 (118)
26 PF09012 FeoC: FeoC like trans 86.8 0.79 1.7E-05 39.5 3.8 41 720-760 7-47 (69)
27 PRK15090 DNA-binding transcrip 86.7 1.5 3.2E-05 47.2 6.6 55 716-774 17-71 (257)
28 PF08784 RPA_C: Replication pr 86.6 1.3 2.9E-05 40.9 5.4 51 710-760 44-98 (102)
29 PRK11512 DNA-binding transcrip 86.0 1.4 3.1E-05 43.1 5.5 52 709-760 36-87 (144)
30 smart00345 HTH_GNTR helix_turn 85.6 1.7 3.7E-05 35.1 5.0 40 722-761 14-54 (60)
31 smart00344 HTH_ASNC helix_turn 85.6 1.6 3.4E-05 40.4 5.3 47 713-759 3-49 (108)
32 smart00419 HTH_CRP helix_turn_ 85.3 2.1 4.5E-05 33.2 5.2 41 727-773 8-48 (48)
33 PF04703 FaeA: FaeA-like prote 84.8 2.3 5E-05 36.3 5.5 43 718-760 5-48 (62)
34 cd00090 HTH_ARSR Arsenical Res 84.7 2.6 5.6E-05 35.0 5.9 59 712-773 6-64 (78)
35 PF13730 HTH_36: Helix-turn-he 84.5 2.6 5.7E-05 34.2 5.6 29 729-757 27-55 (55)
36 COG3355 Predicted transcriptio 84.2 2.5 5.5E-05 41.1 6.2 37 724-760 39-75 (126)
37 PRK11920 rirA iron-responsive 84.1 3 6.5E-05 41.7 6.9 47 716-762 13-59 (153)
38 PRK10857 DNA-binding transcrip 83.7 3.2 7E-05 42.1 7.0 58 715-775 12-70 (164)
39 COG1414 IclR Transcriptional r 83.3 2.5 5.4E-05 45.5 6.4 56 716-775 7-63 (246)
40 TIGR02010 IscR iron-sulfur clu 83.2 3.2 6.8E-05 40.4 6.5 57 716-775 13-70 (135)
41 TIGR01889 Staph_reg_Sar staphy 82.8 4 8.7E-05 38.2 6.8 53 709-761 21-77 (109)
42 TIGR01884 cas_HTH CRISPR locus 81.9 3.9 8.4E-05 42.6 7.0 53 709-761 139-191 (203)
43 PF08279 HTH_11: HTH domain; 81.5 3.6 7.8E-05 33.4 5.3 41 716-756 3-44 (55)
44 PRK10163 DNA-binding transcrip 81.5 3.3 7.2E-05 45.0 6.6 55 716-774 28-83 (271)
45 TIGR02431 pcaR_pcaU beta-ketoa 81.4 3.5 7.5E-05 44.1 6.7 45 716-760 12-57 (248)
46 PRK11569 transcriptional repre 81.2 3.2 7E-05 45.2 6.4 45 716-760 31-76 (274)
47 PRK11179 DNA-binding transcrip 81.0 2.8 6E-05 41.7 5.4 50 710-759 6-55 (153)
48 TIGR00738 rrf2_super rrf2 fami 80.7 4.1 8.8E-05 39.0 6.2 35 726-760 24-58 (132)
49 TIGR02944 suf_reg_Xantho FeS a 78.7 5 0.00011 38.6 6.2 47 725-774 23-69 (130)
50 cd00092 HTH_CRP helix_turn_hel 78.7 5.2 0.00011 33.3 5.6 36 726-761 24-59 (67)
51 PRK09834 DNA-binding transcrip 78.6 4.1 8.9E-05 44.0 6.2 54 716-773 14-68 (263)
52 PRK11169 leucine-responsive tr 78.6 3.4 7.4E-05 41.6 5.2 49 711-759 12-60 (164)
53 PF05732 RepL: Firmicute plasm 78.6 2.8 6.1E-05 42.6 4.6 50 728-782 76-125 (165)
54 TIGR02702 SufR_cyano iron-sulf 78.1 5.4 0.00012 41.5 6.6 60 716-775 4-66 (203)
55 PRK13777 transcriptional regul 77.4 5.7 0.00012 41.2 6.4 54 708-761 40-93 (185)
56 PRK10434 srlR DNA-bindng trans 76.5 3.6 7.8E-05 44.5 5.0 49 714-762 6-54 (256)
57 PRK03573 transcriptional regul 75.3 5 0.00011 39.1 5.2 53 709-761 27-80 (144)
58 COG2345 Predicted transcriptio 75.2 7.2 0.00016 41.4 6.6 62 714-775 12-76 (218)
59 PF04492 Phage_rep_O: Bacterio 74.4 9.6 0.00021 35.7 6.5 62 710-777 29-98 (100)
60 smart00418 HTH_ARSR helix_turn 74.3 6.6 0.00014 31.6 4.9 36 725-760 8-43 (66)
61 PRK11014 transcriptional repre 73.7 8.3 0.00018 37.7 6.3 41 722-762 20-60 (141)
62 COG1959 Predicted transcriptio 73.1 8.7 0.00019 38.3 6.3 48 715-762 12-60 (150)
63 PF08221 HTH_9: RNA polymerase 72.5 6.3 0.00014 33.5 4.4 42 718-759 18-59 (62)
64 PRK10141 DNA-binding transcrip 71.8 9.7 0.00021 36.6 6.0 60 712-774 15-75 (117)
65 PHA00738 putative HTH transcri 71.7 11 0.00024 35.7 6.2 67 708-777 7-74 (108)
66 COG1522 Lrp Transcriptional re 71.2 5.9 0.00013 38.7 4.6 49 711-759 6-54 (154)
67 PF13404 HTH_AsnC-type: AsnC-t 71.0 6.7 0.00015 30.8 3.9 36 716-751 6-41 (42)
68 PRK10906 DNA-binding transcrip 69.7 7.1 0.00015 42.2 5.2 49 714-762 6-54 (252)
69 COG1349 GlpR Transcriptional r 69.6 6.4 0.00014 42.6 4.8 48 715-762 7-54 (253)
70 PRK10870 transcriptional repre 69.5 15 0.00032 37.5 7.2 53 709-761 51-105 (176)
71 PRK13509 transcriptional repre 69.5 7.8 0.00017 41.8 5.5 49 714-762 6-54 (251)
72 TIGR03879 near_KaiC_dom probab 69.4 5.3 0.00011 35.3 3.4 36 723-758 28-63 (73)
73 PF01325 Fe_dep_repress: Iron 68.6 12 0.00027 31.5 5.3 43 718-760 13-55 (60)
74 PRK09802 DNA-binding transcrip 68.4 7.4 0.00016 42.5 5.0 50 713-762 17-66 (269)
75 PF01726 LexA_DNA_bind: LexA D 68.3 14 0.0003 31.8 5.6 52 711-762 4-61 (65)
76 COG1846 MarR Transcriptional r 67.9 18 0.00038 33.1 6.9 51 711-761 20-70 (126)
77 PF13601 HTH_34: Winged helix 67.4 7.2 0.00016 34.8 3.9 45 716-760 3-47 (80)
78 TIGR00373 conserved hypothetic 66.0 16 0.00034 36.9 6.5 43 716-758 17-59 (158)
79 cd07377 WHTH_GntR Winged helix 65.9 14 0.0003 30.3 5.1 32 729-760 27-58 (66)
80 PRK06266 transcription initiat 65.9 11 0.00024 38.8 5.5 45 715-759 24-68 (178)
81 PF05584 Sulfolobus_pRN: Sulfo 65.8 17 0.00036 32.2 5.6 34 727-760 18-51 (72)
82 TIGR00498 lexA SOS regulatory 65.4 8 0.00017 39.9 4.4 52 711-762 4-61 (199)
83 PRK00215 LexA repressor; Valid 64.3 15 0.00032 38.1 6.1 60 711-773 2-67 (205)
84 PF00325 Crp: Bacterial regula 63.9 13 0.00028 27.8 3.9 30 728-757 3-32 (32)
85 PF00392 GntR: Bacterial regul 62.9 13 0.00028 31.3 4.4 39 723-761 19-58 (64)
86 PF13545 HTH_Crp_2: Crp-like h 62.7 17 0.00038 31.1 5.3 34 728-761 29-62 (76)
87 PF14394 DUF4423: Domain of un 60.9 27 0.00059 35.7 7.1 64 707-775 18-84 (171)
88 PRK04424 fatty acid biosynthes 60.7 9.8 0.00021 39.3 4.0 46 714-759 8-53 (185)
89 PF13384 HTH_23: Homeodomain-l 59.2 9 0.00019 30.3 2.7 39 716-756 8-46 (50)
90 PRK10411 DNA-binding transcrip 58.8 16 0.00035 39.2 5.4 49 714-762 5-53 (240)
91 PRK06474 hypothetical protein; 58.6 27 0.00059 35.8 6.8 67 709-775 7-78 (178)
92 PRK04172 pheS phenylalanyl-tRN 57.8 17 0.00037 43.1 5.9 51 710-760 3-53 (489)
93 PF10007 DUF2250: Uncharacteri 54.6 25 0.00054 32.5 5.1 54 709-762 3-56 (92)
94 PF08280 HTH_Mga: M protein tr 54.4 17 0.00037 30.3 3.7 38 715-752 7-44 (59)
95 PF11994 DUF3489: Protein of u 53.0 45 0.00097 29.6 6.1 43 712-754 9-51 (72)
96 COG4189 Predicted transcriptio 52.9 21 0.00045 38.3 4.8 49 712-760 22-70 (308)
97 PF02002 TFIIE_alpha: TFIIE al 52.5 12 0.00025 34.8 2.6 45 715-759 15-59 (105)
98 PF01638 HxlR: HxlR-like helix 52.1 34 0.00073 30.9 5.5 44 715-759 7-51 (90)
99 TIGR00122 birA_repr_reg BirA b 48.9 57 0.0012 27.7 6.2 52 718-775 5-56 (69)
100 PF14947 HTH_45: Winged helix- 48.8 34 0.00073 30.1 4.9 52 716-774 9-60 (77)
101 PF04545 Sigma70_r4: Sigma-70, 48.6 41 0.00089 26.7 4.9 34 715-750 10-43 (50)
102 smart00421 HTH_LUXR helix_turn 48.5 37 0.0008 26.6 4.7 41 711-753 4-44 (58)
103 PRK09954 putative kinase; Prov 46.6 37 0.00081 38.2 6.1 43 716-758 6-48 (362)
104 PF01399 PCI: PCI domain; Int 46.3 46 0.001 29.8 5.6 45 714-758 47-91 (105)
105 cd07153 Fur_like Ferric uptake 45.8 46 0.00099 31.0 5.6 58 716-774 4-67 (116)
106 PRK10430 DNA-binding transcrip 45.2 35 0.00076 35.7 5.3 37 724-760 175-211 (239)
107 PRK03902 manganese transport t 44.4 40 0.00087 32.9 5.2 44 717-760 12-55 (142)
108 PRK11050 manganese transport r 42.5 51 0.0011 32.8 5.6 44 717-760 41-84 (152)
109 COG4565 CitB Response regulato 41.9 48 0.001 35.3 5.5 50 709-759 155-205 (224)
110 PF01475 FUR: Ferric uptake re 41.8 28 0.00062 32.8 3.5 64 710-774 5-74 (120)
111 PRK14999 histidine utilization 40.9 45 0.00098 35.4 5.3 38 725-762 33-71 (241)
112 TIGR02404 trehalos_R_Bsub treh 40.3 42 0.00091 35.3 4.9 34 729-762 26-59 (233)
113 smart00753 PAM PCI/PINT associ 40.0 47 0.001 29.3 4.5 35 724-758 21-55 (88)
114 smart00088 PINT motif in prote 40.0 47 0.001 29.3 4.5 35 724-758 21-55 (88)
115 TIGR02325 C_P_lyase_phnF phosp 39.4 43 0.00094 35.1 4.9 34 729-762 34-67 (238)
116 PF08281 Sigma70_r4_2: Sigma-7 39.0 62 0.0013 25.9 4.7 24 726-749 25-48 (54)
117 COG0735 Fur Fe2+/Zn2+ uptake r 38.6 47 0.001 33.0 4.6 53 708-760 16-74 (145)
118 PF02796 HTH_7: Helix-turn-hel 38.4 28 0.00061 27.4 2.5 32 717-750 13-44 (45)
119 cd06170 LuxR_C_like C-terminal 38.3 74 0.0016 25.0 5.0 39 712-752 2-40 (57)
120 PRK09764 DNA-binding transcrip 38.0 62 0.0013 34.4 5.8 39 724-762 25-64 (240)
121 PF06784 UPF0240: Uncharacteri 37.9 52 0.0011 34.0 5.0 68 684-756 96-165 (179)
122 PF03444 HrcA_DNA-bdg: Winged 37.9 1.1E+02 0.0024 27.6 6.3 46 714-759 10-55 (78)
123 COG1510 Predicted transcriptio 37.6 32 0.0007 35.3 3.3 58 719-777 34-91 (177)
124 TIGR02018 his_ut_repres histid 37.4 48 0.001 34.9 4.8 38 725-762 22-60 (230)
125 TIGR02698 CopY_TcrY copper tra 36.7 82 0.0018 30.7 5.9 50 711-760 2-55 (130)
126 TIGR03697 NtcA_cyano global ni 36.5 66 0.0014 32.2 5.5 34 728-761 144-177 (193)
127 PRK10681 DNA-binding transcrip 36.2 50 0.0011 35.6 4.8 42 714-755 8-49 (252)
128 KOG2753 Uncharacterized conser 36.1 1.8E+02 0.0039 33.1 8.9 67 411-477 148-219 (378)
129 PRK11402 DNA-binding transcrip 35.3 54 0.0012 34.7 4.9 34 729-762 35-68 (241)
130 PF04967 HTH_10: HTH DNA bindi 35.3 49 0.0011 27.5 3.5 30 721-750 17-46 (53)
131 PF09681 Phage_rep_org_N: N-te 34.6 88 0.0019 30.3 5.6 47 723-774 49-95 (121)
132 PRK15431 ferrous iron transpor 34.5 57 0.0012 29.3 4.0 38 723-760 12-49 (78)
133 TIGR03338 phnR_burk phosphonat 34.2 54 0.0012 33.8 4.5 42 721-762 28-69 (212)
134 PRK13918 CRP/FNR family transc 34.1 74 0.0016 32.2 5.5 35 727-761 149-183 (202)
135 TIGR02787 codY_Gpos GTP-sensin 34.1 72 0.0016 34.6 5.4 44 718-761 188-232 (251)
136 PF00165 HTH_AraC: Bacterial r 33.9 54 0.0012 25.1 3.4 28 725-752 6-33 (42)
137 PRK11534 DNA-binding transcrip 33.4 69 0.0015 33.4 5.2 43 720-762 23-65 (224)
138 smart00529 HTH_DTXR Helix-turn 33.0 59 0.0013 29.1 4.0 32 730-761 2-33 (96)
139 PRK11886 bifunctional biotin-- 32.9 1E+02 0.0022 34.2 6.8 43 717-759 8-51 (319)
140 PRK12423 LexA repressor; Provi 32.8 72 0.0016 33.2 5.2 52 711-762 4-61 (202)
141 PRK11161 fumarate/nitrate redu 32.7 75 0.0016 33.1 5.3 34 728-761 185-218 (235)
142 cd04761 HTH_MerR-SF Helix-Turn 32.7 57 0.0012 25.3 3.4 27 728-758 1-27 (49)
143 PF14502 HTH_41: Helix-turn-he 32.5 67 0.0015 26.3 3.7 32 728-759 7-38 (48)
144 PRK10079 phosphonate metabolis 32.2 65 0.0014 34.1 4.8 34 729-762 37-70 (241)
145 COG1321 TroR Mn-dependent tran 31.3 81 0.0018 31.8 5.0 43 718-760 15-57 (154)
146 PF10771 DUF2582: Protein of u 31.3 66 0.0014 27.9 3.7 38 718-755 13-50 (65)
147 PRK04984 fatty acid metabolism 31.2 69 0.0015 33.7 4.8 41 722-762 25-66 (239)
148 PF00196 GerE: Bacterial regul 31.1 88 0.0019 25.6 4.4 42 711-754 4-45 (58)
149 cd06171 Sigma70_r4 Sigma70, re 31.0 97 0.0021 23.5 4.5 40 711-751 11-50 (55)
150 PRK09391 fixK transcriptional 31.0 85 0.0018 33.0 5.4 33 728-760 180-212 (230)
151 COG2188 PhnF Transcriptional r 30.9 67 0.0015 34.2 4.6 41 729-773 33-73 (236)
152 PF04182 B-block_TFIIIC: B-blo 30.7 1E+02 0.0022 27.0 4.9 49 712-760 1-51 (75)
153 PRK11414 colanic acid/biofilm 30.5 69 0.0015 33.4 4.6 46 717-762 24-69 (221)
154 PRK14165 winged helix-turn-hel 30.5 98 0.0021 33.0 5.7 46 715-760 9-54 (217)
155 PRK11753 DNA-binding transcrip 30.5 88 0.0019 31.8 5.3 35 727-761 168-202 (211)
156 PRK10046 dpiA two-component re 30.2 75 0.0016 33.0 4.8 43 717-759 166-209 (225)
157 PRK10402 DNA-binding transcrip 30.1 82 0.0018 32.9 5.1 39 729-773 171-209 (226)
158 COG1654 BirA Biotin operon rep 29.8 1.2E+02 0.0026 27.3 5.2 39 721-759 13-51 (79)
159 PF13518 HTH_28: Helix-turn-he 29.7 1.2E+02 0.0027 23.7 4.9 37 718-756 5-41 (52)
160 PRK10225 DNA-binding transcrip 29.5 78 0.0017 33.8 4.9 45 718-762 23-68 (257)
161 TIGR02844 spore_III_D sporulat 29.4 77 0.0017 28.6 4.0 34 714-748 7-40 (80)
162 PRK00135 scpB segregation and 29.4 4.4E+02 0.0096 27.5 10.2 99 664-778 34-154 (188)
163 COG1318 Predicted transcriptio 29.1 74 0.0016 32.8 4.2 55 682-757 37-91 (182)
164 PF13551 HTH_29: Winged helix- 28.9 1E+02 0.0022 28.0 4.9 39 717-756 3-41 (112)
165 PF04157 EAP30: EAP30/Vps36 fa 28.7 2.4E+02 0.0053 29.8 8.4 47 712-758 173-221 (223)
166 TIGR02812 fadR_gamma fatty aci 28.7 80 0.0017 33.2 4.7 42 721-762 23-65 (235)
167 COG1733 Predicted transcriptio 28.6 1.6E+02 0.0035 28.4 6.3 58 716-774 26-85 (120)
168 COG4742 Predicted transcriptio 28.6 85 0.0018 34.4 4.9 43 718-761 18-60 (260)
169 TIGR02147 Fsuc_second hypothet 28.3 1.6E+02 0.0034 32.5 7.0 45 727-776 137-183 (271)
170 PRK09462 fur ferric uptake reg 28.2 1.1E+02 0.0023 30.2 5.2 65 708-773 12-83 (148)
171 smart00531 TFIIE Transcription 27.8 75 0.0016 31.5 4.1 34 724-757 12-45 (147)
172 PF06163 DUF977: Bacterial pro 27.7 1.4E+02 0.003 29.3 5.6 48 713-760 12-59 (127)
173 PRK04214 rbn ribonuclease BN/u 27.7 1.4E+02 0.0031 34.6 6.9 39 722-760 305-343 (412)
174 PRK09464 pdhR transcriptional 27.6 91 0.002 33.2 5.0 42 721-762 27-69 (254)
175 TIGR02716 C20_methyl_CrtF C-20 27.4 78 0.0017 34.8 4.6 43 726-774 22-64 (306)
176 PRK03837 transcriptional regul 27.3 1E+02 0.0022 32.4 5.3 42 721-762 30-72 (241)
177 PF03965 Penicillinase_R: Peni 26.8 1E+02 0.0022 29.1 4.6 49 712-760 2-54 (115)
178 PF15469 Sec5: Exocyst complex 26.7 1.4E+02 0.0031 30.3 6.0 49 403-462 134-182 (182)
179 PF10826 DUF2551: Protein of u 26.6 1.6E+02 0.0034 26.9 5.4 68 710-777 8-80 (83)
180 PHA02943 hypothetical protein; 26.5 1.3E+02 0.0027 30.6 5.2 53 718-774 16-69 (165)
181 TIGR01714 phage_rep_org_N phag 26.4 1.3E+02 0.0027 29.3 5.1 36 725-760 49-84 (119)
182 COG1378 Predicted transcriptio 25.9 1.4E+02 0.003 32.4 6.0 62 709-773 12-73 (247)
183 PF13411 MerR_1: MerR HTH fami 25.6 78 0.0017 26.5 3.3 28 728-759 1-28 (69)
184 PF03428 RP-C: Replication pro 24.9 1.2E+02 0.0027 31.2 5.1 31 729-759 72-103 (177)
185 PRK10421 DNA-binding transcrip 24.7 1.2E+02 0.0025 32.5 5.1 42 721-762 19-61 (253)
186 PRK09990 DNA-binding transcrip 24.4 1E+02 0.0022 32.7 4.7 42 721-762 24-66 (251)
187 PF00376 MerR: MerR family reg 24.2 97 0.0021 23.8 3.2 26 729-758 1-26 (38)
188 PF13936 HTH_38: Helix-turn-he 24.1 1.2E+02 0.0025 23.9 3.7 37 712-749 6-42 (44)
189 TIGR00721 tfx DNA-binding prot 23.8 1.3E+02 0.0028 29.8 4.8 39 711-751 7-45 (137)
190 PF14493 HTH_40: Helix-turn-he 23.8 1.2E+02 0.0026 27.4 4.3 37 718-756 6-42 (91)
191 COG5090 TFG2 Transcription ini 23.7 1.9E+02 0.0042 31.2 6.2 35 717-751 199-233 (297)
192 COG4190 Predicted transcriptio 23.5 1.6E+02 0.0035 29.2 5.2 50 712-761 63-112 (144)
193 PF09904 HTH_43: Winged helix- 23.1 1.4E+02 0.003 27.6 4.5 56 718-774 13-70 (90)
194 smart00422 HTH_MERR helix_turn 23.1 98 0.0021 25.9 3.4 27 728-758 1-27 (70)
195 TIGR02989 Sig-70_gvs1 RNA poly 22.8 1.4E+02 0.0029 29.0 4.8 39 710-750 111-150 (159)
196 PRK09334 30S ribosomal protein 22.7 1.1E+02 0.0024 28.0 3.8 36 725-760 39-74 (86)
197 cd04780 HTH_MerR-like_sg5 Heli 22.3 1.3E+02 0.0027 27.7 4.2 29 728-760 1-29 (95)
198 PRK11523 DNA-binding transcrip 21.5 1.3E+02 0.0028 32.1 4.7 42 721-762 25-67 (253)
199 PRK05472 redox-sensing transcr 21.5 1.5E+02 0.0033 30.9 5.2 44 712-755 15-60 (213)
200 COG3398 Uncharacterized protei 21.4 2E+02 0.0044 30.9 5.9 60 714-776 175-235 (240)
201 TIGR00331 hrcA heat shock gene 21.2 1.8E+02 0.004 32.9 6.0 48 715-762 9-58 (337)
202 PF13542 HTH_Tnp_ISL3: Helix-t 21.0 2E+02 0.0044 22.7 4.7 34 715-750 17-50 (52)
203 PF09114 MotA_activ: Transcrip 21.0 2.3E+02 0.005 26.3 5.3 46 716-761 19-66 (96)
204 PF08222 HTH_CodY: CodY helix- 20.9 1E+02 0.0022 26.3 2.9 32 728-759 5-36 (61)
205 TIGR03337 phnR transcriptional 20.7 1.3E+02 0.0029 31.3 4.6 34 729-762 27-60 (231)
206 cd04789 HTH_Cfa Helix-Turn-Hel 20.5 1.1E+02 0.0024 28.4 3.4 28 728-759 2-29 (102)
207 PF05331 DUF742: Protein of un 20.5 1.8E+02 0.0039 28.0 4.9 67 692-760 22-88 (114)
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=5.1e-131 Score=1109.84 Aligned_cols=712 Identities=39% Similarity=0.604 Sum_probs=601.6
Q ss_pred hhhccChhhHHHHHHHhhhhhccchhhccCCCCccchhhHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhccchhhhccc
Q 003173 13 ILEKLNDESVQEIIESYNGFCATTNSLLNGGRDIAVGKEFVTHVRSLCKHGLQSLAHGHFLRSLEETFERTFVSKFWRHF 92 (842)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~p~fw~~f 92 (842)
+-|++.++-.+ |+. +.|+..+..+ ++++++ +..++.||+.++..++|+.++|..++.++. ||+||
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 34455666556 777 6666655543 777777 888999999999999999999999999986 99999
Q ss_pred ccccchhhhhcCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCccCCCCCCCCchhhHHHHHHHHHHHH
Q 003173 93 DVYSKVAVLEKNKPLIYDDEVHEVLCKALEEICMEIQYQEKCLFMLVHAIESPRDCSLEGKPILDSEVHLFAKYQLMVSS 172 (842)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 172 (842)
.++...+...++. ...++.+.- +.++...++ +.++++++.. .+-..++++|+|.
T Consensus 68 ~~~~~~~~~~~~i--------~~l~d~~~l----l~~~~~~yi--~~~~l~~~l~------------~g~~~~i~~~~r~ 121 (765)
T KOG2165|consen 68 NQSLAKSIVAKNI--------ENLLDKTGL----LSSFKDFYI--FQVRLRFFLL------------FGNGDRIKDCLRW 121 (765)
T ss_pred HHHHHhcchhhhH--------HHHHhHHhH----HHHHHHHHH--HHHHHHHHHH------------hCcccHHHHHHHH
Confidence 8665442211111 111111111 112222221 1122221111 1111239999999
Q ss_pred HHhhcCCCCHHHHHHHHHhhhHhhhhhhhcccccCCCCCCCCCcccccccccccCCCCCccccccccchhhhHHHHHHHH
Q 003173 173 VLMASLPPHFPEMLYWYFKGRLEELSTIMDGELEDGNDSQDKDDMDLDEKGKQRTGEMDIDQSNNHGKFSEKSKLVKHIG 252 (842)
Q Consensus 173 ~l~~~~p~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~ 252 (842)
.+++++|++|.+++..||...|.+++.+|+...+.. + .|+|.+ ..+|+.....|+|...+++|+
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 999999999999999999999999999997544321 1 113333 245666666666667999999
Q ss_pred HHHHHHHHcCccchhHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHhhhHHHHHHHHHhCCCCCCCCCCCCCC
Q 003173 253 KVVHDLRTLGFTSMTENAYASAIFSLLKAKVHNLAGEDYRSSVLEPIKAWIQAVPLQFLNALLAYLGESESYDSPTAGLK 332 (842)
Q Consensus 253 ~~~~~L~~lgl~~~~~~~~~~~~~~~i~~~v~~~~~~~~~~~~l~~l~~Wi~~v~~~~~~~vl~~~~~~~~~~~~~~~~~ 332 (842)
++++.|.++||.+++.++++++++..|+++++++|+|.|++++++++.+||++|+.+|+..|..+
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 QLVQKLKSLNLSSVSTEAIVSVLYLKLKAFLEDRCSGVWDRSVLESFNKWINTVWGQWLKLVFSQ--------------- 250 (765)
T ss_pred HHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc---------------
Confidence 99999999999889999999999999999999999999999999999999999999999998432
Q ss_pred CCCCCCCCCCCCCCCCchHHHHHHHHHhHHHHHHHHHHHHHHHHhhhhcCCCChhhHHHHHHHHhhcchhhHHHHHHHHH
Q 003173 333 SPLASRPLCCPGTHNPSEGLVRWRLRLEYFAYETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVESFISA 412 (842)
Q Consensus 333 ~~~~~~~~~~~~~~~~~~~~~~w~~~L~~~~y~~l~~lRi~ElFdIIvdyPdS~pai~DLr~cL~~~~~r~~Lv~~f~~~ 412 (842)
++..+|+.++++++|++|+.+||.++|+||+|||+|.|||+|||+||+++++|.+|+.+|+++
T Consensus 251 -----------------e~~~~~~~~l~~~~~~~fa~lr~~~~f~Iv~dyPdS~~aiedLK~cle~t~qr~~ltesfi~~ 313 (765)
T KOG2165|consen 251 -----------------ESDHAFKLTLDYFFYEIFARLRINEIFDIVLDYPDSKPAIEDLKYCLERTDQRVYLTESFISD 313 (765)
T ss_pred -----------------ccccceeeeeHHHHHHHHHHHHHhhHHHHHHhCCccchhHHHHHHHHHHhcchHHHHHHHHHH
Confidence 234569999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCCCChHHHHHHHHHHHHHHHhhcCCCcchhhhchhhHHHhhhcCcchhhhcccccccCCCCCCCCCCchhhHH
Q 003173 413 LKYRLLTAGASTNDILHQYVSTIKALRTIDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLL 492 (842)
Q Consensus 413 l~~RLLhpGa~T~dIL~~YIstIkal~~LDpsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~ 492 (842)
+++|||||||+|.|||++||+||||||+|||+||+|++||.|||+|||+|+|||+|||++|+|..+.+ .. .++.
T Consensus 314 l~~riL~asv~T~DIL~~YVstIkalr~lDptgV~Le~v~~pIR~YLr~R~DtVk~iVs~lt~~~k~~-----~~-~Dl~ 387 (765)
T KOG2165|consen 314 LKTRILTASVDTVDILLRYVSTIKALRVLDPTGVILEKVTEPIRDYLRERKDTVKQIVSGLTDLPKSE-----GE-KDLS 387 (765)
T ss_pred HHhhhcCCCCcHHHHHHHHHHHHHHHHhhCCcceehHHhhHhHHHHHhhCccHHHHHHHHHhcCCccC-----Cc-ccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999874322 11 2567
Q ss_pred HHhcc-CcccccccCCCCCCcchhHHhhhhccccCCCCCCCCCcCCCCccchhhHHhhHhhhcCCHHHHHHHHHHHHHHH
Q 003173 493 EELNR-DEENQENIGVDDGFNIDDKQAWINAVCWEPDPVEADPLKGSRNRRKVDILGMIVGIIGSKDQLVNEYRVMLADK 571 (842)
Q Consensus 493 eeL~~-~~~~~~~~~~ddd~~~d~k~~~~~~~nW~PdPvda~p~~~~k~~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkR 571 (842)
.|+++ ++..++..+.++|+..|..+.|+ ..||+|||+||+|.+++++.++.|++++|+++|||||.|++|||++||+|
T Consensus 388 ~els~~d~~~~e~i~~n~D~~td~~~~~e-~~~W~PdPiDA~pg~~s~k~r~~Di~~mLVsIygSKElfv~EyRnLLAdR 466 (765)
T KOG2165|consen 388 AELSKVDTLHDEDIGENDDSPTDDFMNYE-ILNWMPDPIDADPGKGSSKYRKVDIFGMLVSIYGSKELFVKEYRNLLADR 466 (765)
T ss_pred HHHhccCccchhhcccCcCCCcchhhhhh-hhhccCCCccCCCCCCCcccccccHHHHHHHHHcchHHHHHHHHHHHHHH
Confidence 77776 55566677888998888888896 78999999999999999899999999999999999999999999999999
Q ss_pred hcCCCCCChHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccCCccccceeEEeeccC
Q 003173 572 LLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSN 651 (842)
Q Consensus 572 LL~~~s~s~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~ 651 (842)
||...+|+.+.|+++|++||.|||++.+|.|+|||+|+.+|+++|++|+...... .+..+.+.+.++++|||+.
T Consensus 467 Ll~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~------r~~e~~~~~~i~~~IlS~~ 540 (765)
T KOG2165|consen 467 LLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS------RGAEEVPDFGISATILSSL 540 (765)
T ss_pred HhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh------cccccCCCCchhhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999853211 1112344578999999999
Q ss_pred CCCCCCCCCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHH
Q 003173 652 FWPPMQDEALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSK 731 (842)
Q Consensus 652 ~WP~~~~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~ 731 (842)
|||++.++.|.||.+++..++.|.+.|++.|++|||.|++++|+|+|+++|+||+.+++|||.||+||++|+++++||++
T Consensus 541 fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~qA~iI~~Fqek~twt~e 620 (765)
T KOG2165|consen 541 FWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPEQAAIINLFQEKNTWTLE 620 (765)
T ss_pred cCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHHHHHHHHHhcCcccccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCCCCCCCCCCCCCcccccCCCCCC-cccccCHHHHH
Q 003173 732 NLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMVDSSKNGDNTGSCEELLGGDEDG-ERSVASVEDQI 810 (842)
Q Consensus 732 EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f~~~~~~~~~~~~~~~~~~~~~e~-~~~~~s~e~~~ 810 (842)
++++.+|||...++|+|.||+++|||++.++. .++.+|+++|+-.+..+..+ ..+..+|++. +++++|+.+|.
T Consensus 621 else~l~ip~~~lrrrL~fWi~~GvL~e~~~~-s~tgt~T~iEse~d~~q~~~-----~~~~e~eee~~e~~~as~vdql 694 (765)
T KOG2165|consen 621 ELSESLGIPVPALRRRLSFWIQKGVLREEPII-SDTGTLTVIESEMDFDQAEG-----TVLLEAEEENYESHNASEVDQL 694 (765)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHcCeeecCCCC-CCCceeeeccccccccccCC-----CcccccccccchhhhhhHHHHH
Confidence 99999999999999999999999999987643 56789999997655544321 2233344444 88899999999
Q ss_pred hccccccchhhHHHHHhhCcccch
Q 003173 811 RNEMTVYEPTLFLVRYVANILTQK 834 (842)
Q Consensus 811 ~ee~~v~w~~~fI~gMLTN~~~~~ 834 (842)
++|+++||+ ||+|||||+|+||
T Consensus 695 e~el~~~~~--fI~gMLTNlgsm~ 716 (765)
T KOG2165|consen 695 EEELTLFRS--FIVGMLTNLGSMK 716 (765)
T ss_pred HHHHHHHHH--HHHHHhcCcccch
Confidence 999999999 9999999999995
No 2
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.3e-44 Score=398.69 Aligned_cols=400 Identities=18% Similarity=0.233 Sum_probs=329.9
Q ss_pred HHHhHHHHHHHHHHHHHHHHhhhhcCCCChhhHHHHHHHHhhcchhhHHHHHHHHHHHHhhccCCCChHHHHHHHHHHHH
Q 003173 357 LRLEYFAYETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVESFISALKYRLLTAGASTNDILHQYVSTIK 436 (842)
Q Consensus 357 ~~L~~~~y~~l~~lRi~ElFdIIvdyPdS~pai~DLr~cL~~~~~r~~Lv~~f~~~l~~RLLhpGa~T~dIL~~YIstIk 436 (842)
..++..-|-.|+.-|+.+--+.++.|=|+.+ ..++..+.+++-.-.+|...+.+.+.. |-.+-.|.|+.+.|-..=+
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 4666788999999999999999999999887 777888888776655555444444332 3345588889999844433
Q ss_pred HHHhhcCCCcchhhhchhhHHHhhhcCcchhhhcccccccCCCCCCCCCCchhhHHHHhcc-CcccccccCCC--CCCcc
Q 003173 437 ALRTIDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVD--DGFNI 513 (842)
Q Consensus 437 al~~LDpsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~d--dd~~~ 513 (842)
-.-| ...++.++..|+++++ ..|| +|+..+ ..++.+|++++.+ |.+.-.+|-.+ +.|..
T Consensus 232 -----~~~g--~l~l~qq~sdylk~~G---~KlV---~de~kD-----k~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~ 293 (661)
T KOG2167|consen 232 -----VQGG--QLSLLQQWSDYLKKPG---FKLV---IDEEKD-----KDMVQELLDFKKKVDIIVDESFLKYVAEKFLN 293 (661)
T ss_pred -----Hhcc--hHHHHHHHHHHHhccc---ceec---cCchhh-----HHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHH
Confidence 2334 5688999999999999 8888 776543 3567788887777 44433444333 55666
Q ss_pred hhHHhhhhccccCC-CCCCCCCc-------CCCC--c----cchhhHHhhHhhhcCCHHHHHHHHHHHHHHHhcCCCCCC
Q 003173 514 DDKQAWINAVCWEP-DPVEADPL-------KGSR--N----RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYE 579 (842)
Q Consensus 514 d~k~~~~~~~nW~P-dPvda~p~-------~~~k--~----~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkRLL~~~s~s 579 (842)
..+.+|+.+.|-.| +|++-.+. .|.| + ....|.|+.||+|+.+||+|+.+|++.||+|||..+|.+
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 67789999999888 57763221 0111 1 356899999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccCCccccceeEEeeccCCCCCCCCC
Q 003173 580 IDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDE 659 (842)
Q Consensus 580 ~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~~WP~~~~~ 659 (842)
.|.|..||.+||.+||..+|+++|+|++||..|++++..|+.+..... ..+..-+.+.|++.+|||++++.
T Consensus 374 vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~---------~~~~~l~~v~vlt~~yWpty~~~ 444 (661)
T KOG2167|consen 374 VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANN---------RLEGNLLTVNVLTMGYWPTYPPM 444 (661)
T ss_pred hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhc---------cCcCCceEEEeecccccCCCCch
Confidence 999999999999999999999999999999999999999998854321 01112289999999999999999
Q ss_pred CcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCC
Q 003173 660 ALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGV 739 (842)
Q Consensus 660 ~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m 739 (842)
.+.||+++...++.|.+||..+|.||+|.|.++||+|.|+++|..+++++.||.+|++||++||+.+.||++||.+.|++
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-CCCCCeEEEecCCCCCCCCCCCC
Q 003173 740 PVDVLSRRINFWISK--GIIKES-VGT-GSNDHLYNLVEGMVDSSKNGDNT 786 (842)
Q Consensus 740 ~~~~L~r~L~~wv~~--gVL~e~-~g~-~~~~d~f~vne~f~~~~~~~~~~ 786 (842)
...+|+|.|++|.+. +||... +|+ ..++|.|.||+.|+++..|++.+
T Consensus 525 ~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikin 575 (661)
T KOG2167|consen 525 EDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKIN 575 (661)
T ss_pred cHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHh
Confidence 999999999999975 678654 444 46889999999999999997644
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=1.4e-40 Score=390.55 Aligned_cols=390 Identities=22% Similarity=0.354 Sum_probs=284.7
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCChhhHHHHHHHHhhcchhhHHHHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHhh
Q 003173 362 FAYETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVESFISALKYRLLTAGASTNDILHQYVSTIKALRTI 441 (842)
Q Consensus 362 ~~y~~l~~lRi~ElFdIIvdyPdS~pai~DLr~cL~~~~~r~~Lv~~f~~~l~~RLLhpGa~T~dIL~~YIstIkal~~L 441 (842)
..|-+.+..++.+--+.+..|..+. +...+..++...-...+ .+.+.+.+.. |+... ...+|-..|- +...
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-LDELSSGFRD-LLEED-DKEDLKRLYR-----LFSR 249 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCS-GG-GHHHHHHHHHHHHTGGG-HHHHHTCHHH-HHHTT--HHHHHHHHH-----HHTT
T ss_pred hhHHHHHHHHHHHHHHHHHhhcchh-hhhhHHHHHHHHHHHHH-HHHHHHHHHH-HHHhh-HHHHHHHHHH-----Hhhc
Confidence 4578888999999999998887654 67888888876654333 1222333332 33333 6667766663 2222
Q ss_pred cCCCcchhhhchhhHHHhhhcCcchhhhcccccccCCCCCCCCCCchhhHHHHhcc-CcccccccCCCCCCcchhHHhhh
Q 003173 442 DPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVDDGFNIDDKQAWI 520 (842)
Q Consensus 442 DpsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~ddd~~~d~k~~~~ 520 (842)
-|.| ++.+...+++|++..+ ..++........ +...+..+++...+ ......+|+.+..+....+.+|+
T Consensus 250 ~~~~--~~~l~~~~~~~i~~~g---~~~~~~~~~~~~-----~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~ 319 (588)
T PF00888_consen 250 VPNG--LESLRDAFKEYIKKEG---QNIIDSFEKSSD-----PKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFE 319 (588)
T ss_dssp STTH--HHHHHHHHHHHHHHHH---HHHHHHHCCGGG-----CHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHH
T ss_pred ccCC--CchHHHHHHHHHHHHh---HHHHhhcccccc-----hHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHH
Confidence 2444 7889999999999988 444432211000 11234555554444 23344567666666666667787
Q ss_pred hccccCC-CCCCCCC-------cCCC------CccchhhHHhhHhhhcCCHHHHHHHHHHHHHHHhcCCCCCChHHHHHH
Q 003173 521 NAVCWEP-DPVEADP-------LKGS------RNRRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRT 586 (842)
Q Consensus 521 ~~~nW~P-dPvda~p-------~~~~------k~~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~ 586 (842)
.+.|=.+ .+++..+ .++. ......|.+..||+++++||+|+++|+++||+|||..++++.+.|..+
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 7777662 3333111 1111 235779999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccCCccccceeEEeeccCCCCCCCCCC-cccCh
Q 003173 587 LELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDEA-LIVPG 665 (842)
Q Consensus 587 LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~~WP~~~~~~-~~LP~ 665 (842)
+++||.+||.+++++|++|++|+..|+++++.|++...... ....+++++++.|||+++||.++... +.+|+
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 00012578999999999999998766 99999
Q ss_pred HHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHH
Q 003173 666 HIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLS 745 (842)
Q Consensus 666 eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~ 745 (842)
+|+..++.|+++|+.+|++|+|+|.+++|+|+|++++++++++++||++||+||++||+.+++|+++|++.+||+++.++
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 003173 746 RRINFWISKGIIKES---VG-TGSNDHLYNLVEGMV 777 (842)
Q Consensus 746 r~L~~wv~~gVL~e~---~g-~~~~~d~f~vne~f~ 777 (842)
++|.+|++.|+|... .+ ...+++.|+||++|+
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 356789999999985
No 4
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.5e-38 Score=375.74 Aligned_cols=396 Identities=18% Similarity=0.223 Sum_probs=298.5
Q ss_pred HHHHHHHHHHHHHhhhhcCCCChhhHHHHHHHHhhcchh---hHHHHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHh
Q 003173 364 YETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQH---SKLVESFISALKYRLLTAGASTNDILHQYVSTIKALRT 440 (842)
Q Consensus 364 y~~l~~lRi~ElFdIIvdyPdS~pai~DLr~cL~~~~~r---~~Lv~~f~~~l~~RLLhpGa~T~dIL~~YIstIkal~~ 440 (842)
|-.-++.|+.+.-.-+..|-++...- .++..|+..... ..++..+-+.+. ++|. +....|+...| .+.-
T Consensus 225 yl~k~e~~l~~e~~r~~~yl~~~~e~-~~~~~le~~~~~~~~~~~~e~~~sgf~-~~l~-~~~~edl~~my-----~l~~ 296 (725)
T KOG2166|consen 225 YLKKIEECLKEERERVTHYLHSSTEP-KLVEVVEDELIVVFADDLEEMEHSGFR-ALLN-DDKLEDLSRMY-----RLFR 296 (725)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhcccc-hhhHHHHHHHHHHHHHHHHHHhcchHH-HHHh-ccchhHHHHHH-----HHhh
Confidence 45556667777666666655544222 244444433322 223333444444 2233 33788998888 6666
Q ss_pred hcCCCcchhhhchhhHHHhhhcCcchhhhcccccccCCCCCCCCCCchhhHHHHhcc-CcccccccCCCCCCcchhHHhh
Q 003173 441 IDPTGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVDDGFNIDDKQAW 519 (842)
Q Consensus 441 LDpsGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~ddd~~~d~k~~~ 519 (842)
..++| |..+...+..|++.-| ..+++......+.+ +...+..++++..+ ......++..|..+......++
T Consensus 297 r~~~g--l~~l~~~~~~~~~~eg---~~l~~r~~~~~~~~---~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~ 368 (725)
T KOG2166|consen 297 RILPG--LEPLASVFKQHVREEG---NALVARPAETAATN---PVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAF 368 (725)
T ss_pred ccccc--chhHHHHHHHHHHhhH---HHHhhhhhhhcccc---hHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 77888 8999999999999999 55664332211111 11222233333222 2233456666666655555667
Q ss_pred hhccccCCCCC-CC-------CCcCCCCc------cchhhHHhhHhhhcCCHHHHHHHHHHHHHHHhcCCCCCChHHHHH
Q 003173 520 INAVCWEPDPV-EA-------DPLKGSRN------RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIR 585 (842)
Q Consensus 520 ~~~~nW~PdPv-da-------~p~~~~k~------~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~ 585 (842)
..+.|-.-.+. +- .-.++++. +..++.++++|+|+.+||+|+++|+++||+|||+.+|.|.|.|+.
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 67777666544 31 11122332 356788888999999999999999999999999999999999999
Q ss_pred HHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccCCccccceeEEeeccCCCCCCCCCCcccCh
Q 003173 586 TLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDEALIVPG 665 (842)
Q Consensus 586 ~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~~WP~~~~~~~~LP~ 665 (842)
+|.+||..||.+++.++++|++|+..|++++..|++..... ....++|.|.||+++|||.++..+|.||+
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 99999999999999999999999999999999999762110 11247899999999999998888899999
Q ss_pred HHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHH
Q 003173 666 HIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLS 745 (842)
Q Consensus 666 eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~ 745 (842)
++...++.|..||.++|+||+|+|+++||.++|..+|.+++++++||++|++|+++||+.+.+|+++|.+.|+|+.+.+.
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--hCCcccccCCCCCCCCeEEEecCCCCCCCCCCC
Q 003173 746 RRINFWI--SKGIIKESVGTGSNDHLYNLVEGMVDSSKNGDN 785 (842)
Q Consensus 746 r~L~~wv--~~gVL~e~~g~~~~~d~f~vne~f~~~~~~~~~ 785 (842)
+.|+++. +.+|+..+.++..+++.|.+|.+|.++..|+..
T Consensus 599 ~~L~Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i 640 (725)
T KOG2166|consen 599 RLLQSLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKI 640 (725)
T ss_pred HHHHHHHHHhHhhccCccccCCCCcEEEeeccccCcceeecc
Confidence 9999994 445554433333678999999999999998753
No 5
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.5e-37 Score=348.94 Aligned_cols=399 Identities=16% Similarity=0.170 Sum_probs=280.7
Q ss_pred HHHHHHHHHHHHHhhhhcCCCChhhHHHHHHHHhhcchhhHHHHHHHH--HHHHhhccCCCChHHHHHHHHHHHHHHHhh
Q 003173 364 YETLQDLRIAKLFEIIVDYPESSPAIEDLKQCLEYTGQHSKLVESFIS--ALKYRLLTAGASTNDILHQYVSTIKALRTI 441 (842)
Q Consensus 364 y~~l~~lRi~ElFdIIvdyPdS~pai~DLr~cL~~~~~r~~Lv~~f~~--~l~~RLLhpGa~T~dIL~~YIstIkal~~L 441 (842)
|-..+..|+++-=..+..|-.-. +-..|+..++.....++|-.-... .+. +++. ..+-..|...| .|..-
T Consensus 250 yL~ka~~~~~~E~~~v~~yl~~~-~~kpl~~~~edvLi~~hld~l~~~~s~f~-~~~d-~~~~e~l~~lY-----~l~se 321 (773)
T COG5647 250 YLEKAHKILEREEELVEIYLKVS-TKKPLLEVLEDVLITRHLDDLEEQGSGFR-EALD-ASNLEKLQVLY-----RLLSE 321 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc-ccchHHHHHHHhhhhccHHHHHhchHHHH-HHHH-hhhHHHHHHHH-----HHhhh
Confidence 44556666655555555554443 566777777777665543322221 222 1122 22556666666 55556
Q ss_pred cCCCcchhhhchhhHHHhhhcCcchhhhcc---------cccccCCCCCCCCCCchhhHHHHhcc-CcccccccCCCCCC
Q 003173 442 DPTGVFLEAVGEPIRDYLRGRKDTIKCIVT---------MLTDGTGGNPNGSGNAGDSLLEELNR-DEENQENIGVDDGF 511 (842)
Q Consensus 442 DpsGvlL~~V~~pIr~YLr~R~DtVr~IV~---------~L~d~~~~~~~~~~~~~~~L~eeL~~-~~~~~~~~~~ddd~ 511 (842)
++.|+ ..+...+.+|++.-+-.+..-.. +++...... +..-++.++..-.. .....+++..|...
T Consensus 322 ~~~~v--~pl~~~f~~yV~~~g~~~~i~~~~~~~~~~~~~~~~~~e~~---~~~~~q~lls~~~~~~~l~~~sf~~D~~~ 396 (773)
T COG5647 322 TKYGV--QPLQEVFERYVKDEGVLINIETNYIFHCKVDVGFLGSRECL---PKLYVQKLLSCHDLFPSLVNESFEGDGSI 396 (773)
T ss_pred hhhhh--hhHHHHHHHHHHhhchhhhhHHhhhhccchhhcccchhhhc---HHHHHHHHHHHHHHHHHHHhhccCCcchH
Confidence 77884 34677799999998822211111 111110000 00011112221111 12223445555444
Q ss_pred cchhHHhhhhccccC-C---CCCCCCCc------C-------CCCccchhhHHhhHhhhcCCHHHHHHHHHHHHHHHhcC
Q 003173 512 NIDDKQAWINAVCWE-P---DPVEADPL------K-------GSRNRRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLN 574 (842)
Q Consensus 512 ~~d~k~~~~~~~nW~-P---dPvda~p~------~-------~~k~~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkRLL~ 574 (842)
......+|..+.|-. - .|.+-.+. + ..+....+..|..||+|+.+||+|+++|+++||+|||+
T Consensus 397 ~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~ 476 (773)
T COG5647 397 VKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLN 476 (773)
T ss_pred HHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccccccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhc
Confidence 334456776666653 1 13331110 1 11222345678999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccCCccccceeEEeeccCCCC
Q 003173 575 KSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWP 654 (842)
Q Consensus 575 ~~s~s~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~~WP 654 (842)
+++.+.+.|..||++||..||..||+|+|+||+||..|+++...|++... + .....++.|.||++.|||
T Consensus 477 g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~-s----------~~~~~Dl~v~VLt~a~WP 545 (773)
T COG5647 477 GRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQ-S----------YNKYLDLFVWVLTQAYWP 545 (773)
T ss_pred CCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCch-h----------hccccchhHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999999986431 1 012478999999999999
Q ss_pred C-CCCCCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEE---EecHHHHHHHHHhcCCCcccH
Q 003173 655 P-MQDEALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQF---TVAPIHAAIIMQFQDQTSWTS 730 (842)
Q Consensus 655 ~-~~~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l---~VS~~QAaILllFn~~~~~Tv 730 (842)
. .++..+.||++|.+..+.|+++|.++|+||+|+|.++||+|+|++.|+.+++.+ +++.+|+.|+++||+.+++|+
T Consensus 546 ~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~ 625 (773)
T COG5647 546 LSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTF 625 (773)
T ss_pred CCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeH
Confidence 4 457899999999999999999999999999999999999999999999886544 467899999999999999999
Q ss_pred HHHHHHhCCCHHHHHHHHHHHHhCCcccccC-C-CCCCCCeEEEecCCCCCCCCCCCC
Q 003173 731 KNLAAAVGVPVDVLSRRINFWISKGIIKESV-G-TGSNDHLYNLVEGMVDSSKNGDNT 786 (842)
Q Consensus 731 ~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~-g-~~~~~d~f~vne~f~~~~~~~~~~ 786 (842)
++|.+.|+|+.+.+.+.|+++++.+++...+ + ..++++.|.+|++|..++.++..+
T Consensus 626 eei~e~T~l~~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~ 683 (773)
T COG5647 626 EEILELTKLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKIN 683 (773)
T ss_pred HHHHhhcCCChhhHHHHHHHHHhhheeeeccccccCCCCceEEEccccccccceeeec
Confidence 9999999999999999999999987654322 2 246789999999999999987533
No 6
>smart00182 CULLIN Cullin.
Probab=99.98 E-value=7.8e-32 Score=262.77 Aligned_cols=141 Identities=24% Similarity=0.400 Sum_probs=130.3
Q ss_pred hcCCHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 003173 553 IIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSE 632 (842)
Q Consensus 553 il~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~ 632 (842)
|+++||+|+++|+++||+|||..++++.+.|..+|++||.+||.+++++|++||+||..|++++++|++......
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 003173 633 LGEEGVSLGLLDATIISSNFWPPMQD-EALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQF 702 (842)
Q Consensus 633 ~~~~~l~~~~~~~~ILS~~~WP~~~~-~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f 702 (842)
...+++++++|||+++||.++. ..+.||++|+..++.|+++|.++|++|+|+|.++||+|+|+++|
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 1124789999999999999887 89999999999999999999999999999999999999999864
No 7
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=8.3e-28 Score=259.22 Aligned_cols=292 Identities=20% Similarity=0.262 Sum_probs=230.0
Q ss_pred CCcchhhhchhhHHHhhhcCcchhhhcccccccCCCCCCCCCCchhhHHHHhccCcc-cccccCCCCCCcchhHHhhhhc
Q 003173 444 TGVFLEAVGEPIRDYLRGRKDTIKCIVTMLTDGTGGNPNGSGNAGDSLLEELNRDEE-NQENIGVDDGFNIDDKQAWINA 522 (842)
Q Consensus 444 sGvlL~~V~~pIr~YLr~R~DtVr~IV~~L~d~~~~~~~~~~~~~~~L~eeL~~~~~-~~~~~~~ddd~~~d~k~~~~~~ 522 (842)
.| |.....-+.+|+++.| -..|+.||.+. .+..+++++++--.+-.. ....+..|..|......+...-
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 56 7778888899999988 66677777542 222344455443332111 1112333444443332333333
Q ss_pred cccC-C-CCCCCCC----------c-CCCCc------cchhhHHhhHhhhcCCHHHHHHHHHHHHHHHhcCCCCCChHHH
Q 003173 523 VCWE-P-DPVEADP----------L-KGSRN------RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSE 583 (842)
Q Consensus 523 ~nW~-P-dPvda~p----------~-~~~k~------~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkRLL~~~s~s~d~E 583 (842)
.|.. | ..+--.| . ++.|+ +.++|-...+|+|+++||+|.++|.++||+||+.+.+.+.|.|
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 3432 3 1111111 1 12222 3567888899999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhCCChhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccCCccccceeEEeeccCCCCCCCCCCccc
Q 003173 584 IRTLELLKIHFGESSMQRCEIMLNDLIDSKRTNANIKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQDEALIV 663 (842)
Q Consensus 584 ~~~LelLK~rfG~~~l~k~EvMLkDI~~Skrln~~f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~~WP~~~~~~~~L 663 (842)
..||++||+.||..+++++- +.|+..|.++|.+|.+.+. +|.+
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 99999999999999999988 8999999999999976542 2899
Q ss_pred ChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHH
Q 003173 664 PGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDV 743 (842)
Q Consensus 664 P~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~ 743 (842)
|.+++...+.|++||..+++||||+|++.+++++|++++-|+.|.-.|+++|+++|++||..+.+++.+|.+.+||+.+.
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCcccccCCCCCCCCeEEEecCCCCCCCC
Q 003173 744 LSRRINFWISKGIIKESVGTGSNDHLYNLVEGMVDSSKN 782 (842)
Q Consensus 744 L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f~~~~~~ 782 (842)
|.+.+..+..-.+|.........+..|++|.+|+++..+
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 999999999999987665445566789999999988766
No 8
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=3e-22 Score=218.26 Aligned_cols=229 Identities=14% Similarity=0.251 Sum_probs=198.0
Q ss_pred cchhhHHhhHhhhcCCHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHhhhhC--CChhHHHHHHHHHHHHHHHHHHH
Q 003173 541 RRKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFG--ESSMQRCEIMLNDLIDSKRTNAN 618 (842)
Q Consensus 541 ~k~lD~I~~Lfsil~sKDvF~~eYr~lLAkRLL~~~s~s~d~E~~~LelLK~rfG--~~~l~k~EvMLkDI~~Skrln~~ 618 (842)
+.++..+..++.|.++||+|..+++.+|.+||+...+.+.+.|..|++.|+ +|| .++.+++..|++||..|+++|+.
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 HHHHHHhhhhcCCCcccCCccccceeEEeeccCCCCCCC-CCCcccChHHHHHHHHHHhhhhccCCCceEEeecCCCceE
Q 003173 619 IKATIEKQSLAGSELGEEGVSLGLLDATIISSNFWPPMQ-DEALIVPGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVK 697 (842)
Q Consensus 619 f~~~~~~~~~~~~~~~~~~l~~~~~~~~ILS~~~WP~~~-~~~~~LP~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~ve 697 (842)
|+....+.. .......++.+||..|.|.... ...+.||.+++..+-..++||+++|+||||+|.|+++.++
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 4578999999999999999999999999999999999998
Q ss_pred EEEEECCceeEEEecHHHHHHHHHhcCC--CcccHHHHHHHhCCCHHHHHHHHHHHHhC-----Cc-ccccCC-----CC
Q 003173 698 LELQFDDRAMQFTVAPIHAAIIMQFQDQ--TSWTSKNLAAAVGVPVDVLSRRINFWISK-----GI-IKESVG-----TG 764 (842)
Q Consensus 698 Lel~f~dr~~~l~VS~~QAaILllFn~~--~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~-----gV-L~e~~g-----~~ 764 (842)
+...-+=+.+.++|+++|++||.+||+. +.+|++.|.-++.+|..+|+|.|-+++.- .| |.+++. .+
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 8875555789999999999999999974 67999999999999999999999999852 34 455532 14
Q ss_pred CCCCeEEEecCCCC
Q 003173 765 SNDHLYNLVEGMVD 778 (842)
Q Consensus 765 ~~~d~f~vne~f~~ 778 (842)
.+++.|.||..|+-
T Consensus 658 te~T~F~iNqeF~v 671 (777)
T KOG2285|consen 658 TESTKFLINQEFNV 671 (777)
T ss_pred cccceEEeechhhh
Confidence 56789999999974
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=95.61 E-value=0.033 Score=51.17 Aligned_cols=66 Identities=12% Similarity=0.065 Sum_probs=55.9
Q ss_pred EEEecHHHHHHHHHhc--------CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCC
Q 003173 708 QFTVAPIHAAIIMQFQ--------DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMV 777 (842)
Q Consensus 708 ~l~VS~~QAaILllFn--------~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f~ 777 (842)
.+.+++-|+.+|+... ....+|-.||++.+|++.+.+.++|..|.++|+|....| ..+|.||.+..
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 4678899999888655 456789999999999999999999999999999976543 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=95.39 E-value=0.0048 Score=52.16 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=11.6
Q ss_pred HHHHHhhCcccchhh
Q 003173 822 FLVRYVANILTQKSL 836 (842)
Q Consensus 822 fI~gMLTN~~~~~~~ 836 (842)
||+|||||+++| |+
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 55
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=94.54 E-value=0.084 Score=41.95 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=40.4
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
+..+..||....+.+..|..+|++.+|++...+.+.|..|.++|+++
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=94.10 E-value=0.19 Score=44.73 Aligned_cols=59 Identities=19% Similarity=0.291 Sum_probs=44.1
Q ss_pred HHHHHHHHhcCCC-cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003173 714 IHAAIIMQFQDQT-SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 775 (842)
Q Consensus 714 ~QAaILllFn~~~-~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~ 775 (842)
+++.+.+..+... .+|.++|++.+++|+..+++.++.|.+.|++....| .+.-|.+...
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 3444555544444 399999999999999999999999999999976655 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=93.81 E-value=0.18 Score=42.03 Aligned_cols=48 Identities=25% Similarity=0.392 Sum_probs=43.1
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|..|+...+++..+|+++|++.+|+++..+++-|..|.+.|+++...|
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 456788888899999999999999999999999999999999977654
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=93.70 E-value=0.12 Score=42.78 Aligned_cols=50 Identities=20% Similarity=0.404 Sum_probs=44.5
Q ss_pred ecHHHHHHHHHhcCCCc--ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 711 VAPIHAAIIMQFQDQTS--WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 711 VS~~QAaILllFn~~~~--~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|+.|+.||......+. +|..+|++.++++...+.+.+.-|.++|++...
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 57899999998887766 999999999999999999999999999999754
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=93.63 E-value=0.12 Score=41.89 Aligned_cols=45 Identities=18% Similarity=0.382 Sum_probs=38.7
Q ss_pred HHHHHHhcCCCc-ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 716 AAIIMQFQDQTS-WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 716 AaILllFn~~~~-~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..||..|.+... +|+.||++.+|+|...+.+.|..|+..|++...
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=92.95 E-value=0.35 Score=40.75 Aligned_cols=50 Identities=18% Similarity=0.310 Sum_probs=40.7
Q ss_pred ecHHHHHHHHHhc-CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 711 VAPIHAAIIMQFQ-DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 711 VS~~QAaILllFn-~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|+.|..||.... .....+..+|++.++++...+.+.|..++.+|++...
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
>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=90.74 E-value=0.37 Score=39.63 Aligned_cols=50 Identities=22% Similarity=0.357 Sum_probs=44.6
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|+.|+.+|....+.+..+..+|++.++++...+.+.+..|.++|++...
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 18
>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=90.54 E-value=0.59 Score=39.11 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=43.5
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|.-..|+.++......|+.+|++.+|++...+.++|.-|...|++...
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 5778889999977889999999999999999999999999999998643
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=90.16 E-value=0.9 Score=36.13 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 713 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 713 ~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
|...-|+...-+ ...++.||++.+|++...+.++|..|...|++.
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 556777887777 679999999999999999999999999999875
No 20
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=89.88 E-value=0.88 Score=40.51 Aligned_cols=57 Identities=18% Similarity=0.261 Sum_probs=45.6
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCC
Q 003173 716 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGM 776 (842)
Q Consensus 716 AaILllFn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f 776 (842)
..|+..+... ..+|+.+|++.+|++...+.+.|..|...|+|.... .++.|.+...+
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 4467777766 689999999999999999999999999999997642 13467775543
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=89.68 E-value=0.47 Score=40.46 Aligned_cols=51 Identities=14% Similarity=0.281 Sum_probs=43.7
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
.|..++.|+...-.....|..+|++.+|+|...+.+.|..|..+|++....
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 455677777766677889999999999999999999999999999997654
No 22
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=89.16 E-value=0.99 Score=40.26 Aligned_cols=53 Identities=17% Similarity=0.337 Sum_probs=48.4
Q ss_pred EEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 708 QFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 708 ~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
++.++..+..||........++..+|++.++++...+.+.|..|++.|++...
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 46788899999999988888999999999999999999999999999999754
No 23
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.14 E-value=0.85 Score=35.90 Aligned_cols=46 Identities=20% Similarity=0.277 Sum_probs=38.8
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
-.|+..+.....+++.+|++.++++...+.+.|..|...|++....
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 3456666666779999999999999999999999999999986543
No 24
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.99 E-value=1.4 Score=37.93 Aligned_cols=48 Identities=19% Similarity=0.281 Sum_probs=41.6
Q ss_pred HHHHHHHHHhcCCCc--ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 713 PIHAAIIMQFQDQTS--WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 713 ~~QAaILllFn~~~~--~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..+-.||..+.+... +|..+|++.+|++...+++.|..|...|.+...
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 455667888887755 999999999999999999999999999998654
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=87.71 E-value=0.99 Score=42.58 Aligned_cols=52 Identities=13% Similarity=0.095 Sum_probs=47.7
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 709 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 709 l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..+++.|+.||......+.+|..+|++.++++...+.+.+..|.++|++...
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 4578999999999988889999999999999999999999999999998754
No 26
>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=86.85 E-value=0.79 Score=39.47 Aligned_cols=41 Identities=17% Similarity=0.293 Sum_probs=33.1
Q ss_pred HHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 720 MQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 720 llFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
....++...|+.+|+..++++++.++..|..|+.+|-++..
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 34456778999999999999999999999999999988754
No 27
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=86.75 E-value=1.5 Score=47.24 Aligned_cols=55 Identities=13% Similarity=0.151 Sum_probs=45.2
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
..||..|.....+|+.||++.+|+|...+.+.|..|+..|.|..... +..|++-.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~----~~~Y~lG~ 71 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE----SEKYSLTL 71 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC----CCcEEecH
Confidence 45888998877899999999999999999999999999999965421 24566544
No 28
>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=86.59 E-value=1.3 Score=40.86 Aligned_cols=51 Identities=12% Similarity=0.352 Sum_probs=43.5
Q ss_pred EecHHHHHHHHHhcC----CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 710 TVAPIHAAIIMQFQD----QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 710 ~VS~~QAaILllFn~----~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.+++.|-.|+..+.. .+.+++++|+++++++...++.+|.+|++.|.+...
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 456899999999999999999999999999998643
No 29
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=85.97 E-value=1.4 Score=43.07 Aligned_cols=52 Identities=13% Similarity=0.275 Sum_probs=47.4
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 709 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 709 l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+.+|+.|+.||......+.+|..+|++.++++...+.+.+..|.++|++...
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 5688899999998877788999999999999999999999999999999754
No 30
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=85.62 E-value=1.7 Score=35.07 Aligned_cols=40 Identities=15% Similarity=0.322 Sum_probs=34.6
Q ss_pred hcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 722 FQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 722 Fn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+.....+ |..+|++.+|++...++++|..|.+.|+|....
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 899999999999999999999999999986544
No 31
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.55 E-value=1.6 Score=40.38 Aligned_cols=47 Identities=23% Similarity=0.369 Sum_probs=42.1
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 713 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 713 ~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
...-.|+..++.....|+.+|++.+|+++..+.+.+..|.+.|+++.
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 32
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=85.28 E-value=2.1 Score=33.23 Aligned_cols=41 Identities=17% Similarity=0.287 Sum_probs=34.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 727 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 727 ~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
..+..+|++.+|++...+.+.|..|.+.|++.... +.|.|+
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 366653
No 33
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=84.83 E-value=2.3 Score=36.35 Aligned_cols=43 Identities=14% Similarity=0.267 Sum_probs=35.1
Q ss_pred HHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 718 IIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 718 ILllFn~-~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
||..++. ....+..|||+.+|++...+++.|..|.+.|.++..
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4555565 677899999999999999999999999999988654
No 34
>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=84.69 E-value=2.6 Score=34.99 Aligned_cols=59 Identities=19% Similarity=0.312 Sum_probs=45.7
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
+..+..|+..+.+.. .+..+|++.++++...+.+.|.-|...|++....+. ....|.++
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 456777888777666 999999999999999999999999999998754321 22455554
No 35
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.48 E-value=2.6 Score=34.17 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=27.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGII 757 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL 757 (842)
|.+.|++.+|++...++++|..|.+.|+|
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=84.24 E-value=2.5 Score=41.09 Aligned_cols=37 Identities=14% Similarity=0.277 Sum_probs=34.2
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 724 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 724 ~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.....|+++||+.++.+.+.+.++|+.|+..|++...
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence 6778999999999999999999999999999998654
No 37
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=84.05 E-value=3 Score=41.71 Aligned_cols=47 Identities=17% Similarity=0.179 Sum_probs=38.5
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+.+.+..+.....+..+||+..++|+..|++.|+.|.+.|++....|
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 33444445555679999999999999999999999999999977655
No 38
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=83.69 E-value=3.2 Score=42.06 Aligned_cols=58 Identities=12% Similarity=0.186 Sum_probs=44.2
Q ss_pred HHHHHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003173 715 HAAIIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 775 (842)
Q Consensus 715 QAaILllFn~-~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~ 775 (842)
.+.+.+.|+. ...+|.++|++.+++|...+.+.|+.|.+.|++....|. .+-|.+...
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 234666544
No 39
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=83.32 E-value=2.5 Score=45.46 Aligned_cols=56 Identities=20% Similarity=0.318 Sum_probs=45.9
Q ss_pred HHHHHHhcCCCc-ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003173 716 AAIIMQFQDQTS-WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 775 (842)
Q Consensus 716 AaILllFn~~~~-~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~ 775 (842)
..||.+|...+. +++.||++.+|+|...+.|.|..|+..|.+..... +..|++-..
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 458889997655 68999999999999999999999999999987641 246776543
No 40
>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=83.19 E-value=3.2 Score=40.44 Aligned_cols=57 Identities=16% Similarity=0.229 Sum_probs=42.1
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003173 716 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 775 (842)
Q Consensus 716 AaILllFn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~ 775 (842)
+.+.+.++.. ..+|.++|++.+++|...+++.|..|.+.|++....|. .+-|.+...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~---~Ggy~l~~~ 70 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGP---GGGYQLGRP 70 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCC---CCCEeccCC
Confidence 4444555543 46999999999999999999999999999999754332 224555443
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=82.78 E-value=4 Score=38.16 Aligned_cols=53 Identities=15% Similarity=0.201 Sum_probs=46.1
Q ss_pred EEecHHHHHHHHHhc----CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 709 FTVAPIHAAIIMQFQ----DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 709 l~VS~~QAaILllFn----~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+.+|+.|..||.... +....|..+|+..++++...+.+.+..|.++|.+....
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 457889999987766 55679999999999999999999999999999997543
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=81.88 E-value=3.9 Score=42.56 Aligned_cols=53 Identities=15% Similarity=0.256 Sum_probs=47.9
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 709 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 709 l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
..++..|..|+..+.++...+..+|++.++++...+.+.|..|.+.|++....
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
>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=81.55 E-value=3.6 Score=33.36 Aligned_cols=41 Identities=27% Similarity=0.355 Sum_probs=32.9
Q ss_pred HHHHHHh-cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003173 716 AAIIMQF-QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 756 (842)
Q Consensus 716 AaILllF-n~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV 756 (842)
..||..+ +..+.+|.++||+.++++...+++.|..+-..|+
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 44
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=81.48 E-value=3.3 Score=45.01 Aligned_cols=55 Identities=9% Similarity=0.164 Sum_probs=44.2
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 716 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 716 AaILllFn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
..||.+|... ..+|+.||++.+|||...+.|.|..|+..|.|.... .+..|.+-.
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 4588899864 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=81.41 E-value=3.5 Score=44.06 Aligned_cols=45 Identities=20% Similarity=0.269 Sum_probs=40.0
Q ss_pred HHHHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 716 AAIIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 716 AaILllFn~-~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..||.+|.. ...+|+.||++.+|+|...+.|.|..|+..|.|...
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 457889986 567999999999999999999999999999999754
No 46
>PRK11569 transcriptional repressor IclR; Provisional
Probab=81.20 E-value=3.2 Score=45.16 Aligned_cols=45 Identities=16% Similarity=0.271 Sum_probs=39.7
Q ss_pred HHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 716 AAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 716 AaILllFn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..||.+|.+. ..+|+.||++.+|+|...+.|.|..|+..|.|...
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~ 76 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV 76 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 4578889864 56999999999999999999999999999999654
No 47
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.02 E-value=2.8 Score=41.67 Aligned_cols=50 Identities=18% Similarity=0.274 Sum_probs=45.4
Q ss_pred EecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 710 TVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 710 ~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
.+...--.||..++.....++.+||+.+|+++..+++++.-|...|+++.
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 45667788999999999999999999999999999999999999999973
No 48
>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=80.66 E-value=4.1 Score=39.02 Aligned_cols=35 Identities=14% Similarity=0.254 Sum_probs=32.5
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 726 TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 726 ~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..+|.++|++.+++|...+++.|..|.+.|+|...
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 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=78.74 E-value=5 Score=38.58 Aligned_cols=47 Identities=17% Similarity=0.345 Sum_probs=38.1
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 725 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 725 ~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
...+|+.+|++.+++|...+.+.|..|.+.|++....|. .+.|.++.
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 457999999999999999999999999999999754331 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=78.72 E-value=5.2 Score=33.27 Aligned_cols=36 Identities=19% Similarity=0.311 Sum_probs=32.8
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 726 TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 726 ~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
..+|..+|++.+|++...+.+.|.-|.+.|++....
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=78.61 E-value=4.1 Score=44.02 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=43.5
Q ss_pred HHHHHHhcCCC-cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 716 AAIIMQFQDQT-SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 716 AaILllFn~~~-~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
..||..|.+.. .+|+.||++.+|++...+.|.|..|...|+|..... +..|++-
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 499999999999999999999999999999975431 2456664
No 52
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=78.59 E-value=3.4 Score=41.57 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=44.5
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
+...-..||...+.....|+.+||+.+|+++..+.++++-|.+.|+++.
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 4456778999999999999999999999999999999999999999863
No 53
>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=78.57 E-value=2.8 Score=42.57 Aligned_cols=50 Identities=24% Similarity=0.266 Sum_probs=43.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCCCCCCC
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMVDSSKN 782 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f~~~~~~ 782 (842)
+|..+|++.+|++...+.+++..|..+++|.... ...|.||.++-.++.+
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 54
>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=78.08 E-value=5.4 Score=41.50 Aligned_cols=60 Identities=22% Similarity=0.303 Sum_probs=44.4
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc---CCCCCCCCeEEEecC
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES---VGTGSNDHLYNLVEG 775 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~---~g~~~~~d~f~vne~ 775 (842)
..||......+..|..+|++.+|++...++++|..|.++|++... .+...+...|.+.+.
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 445555555567999999999999999999999999999999643 122223445666644
No 55
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=77.41 E-value=5.7 Score=41.15 Aligned_cols=54 Identities=9% Similarity=-0.058 Sum_probs=49.0
Q ss_pred EEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 708 QFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 708 ~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
.+.+|+.|..||......+.+|..+|++.++++...+.+.+.-|.++|++....
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 357889999999999988899999999999999999999999999999997543
No 56
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=76.48 E-value=3.6 Score=44.49 Aligned_cols=49 Identities=18% Similarity=0.211 Sum_probs=44.1
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
=|..|+...+.+..+++.||++.+++++..+||-|..|.++|+|+...|
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~G 54 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYG 54 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEC
Confidence 3677888899999999999999999999999999999999998876654
No 57
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=75.34 E-value=5 Score=39.05 Aligned_cols=53 Identities=19% Similarity=0.307 Sum_probs=46.2
Q ss_pred EEecHHHHHHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 709 FTVAPIHAAIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 709 l~VS~~QAaILllFn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+.+|+.|..||...... +..|..+|++.++++...+.+.+..|.++|++....
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 56888999998887754 568999999999999999999999999999996543
No 58
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=75.21 E-value=7.2 Score=41.45 Aligned_cols=62 Identities=19% Similarity=0.361 Sum_probs=48.8
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc---CCCCCCCCeEEEecC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES---VGTGSNDHLYNLVEG 775 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~---~g~~~~~d~f~vne~ 775 (842)
.-..|+.+.+.....|.+||++.+|++...++++|..|...|++... .|..-+.-.|++.+.
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 34567777777889999999999999999999999999999988432 222335567887665
No 59
>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=74.42 E-value=9.6 Score=35.68 Aligned_cols=62 Identities=15% Similarity=0.292 Sum_probs=46.0
Q ss_pred EecHHHHHHHHH-------hcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCC
Q 003173 710 TVAPIHAAIIMQ-------FQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMV 777 (842)
Q Consensus 710 ~VS~~QAaILll-------Fn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f~ 777 (842)
.++.-|.-|++. ||.+ +.+|..++++.+|++.+.+.+++..|+..|||.... ..+-+|.+..
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 344455444443 5543 568999999999999999999999999999997643 3666666543
No 60
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=74.30 E-value=6.6 Score=31.56 Aligned_cols=36 Identities=14% Similarity=0.259 Sum_probs=32.8
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 725 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 725 ~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.+..|+.+|++.++++...+.+.|.-+.+.|++...
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 61
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=73.74 E-value=8.3 Score=37.74 Aligned_cols=41 Identities=15% Similarity=0.213 Sum_probs=35.4
Q ss_pred hcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 722 FQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 722 Fn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+......+..+|++.+|+|...++++|+.|.+.|++...+|
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 62
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=73.05 E-value=8.7 Score=38.34 Aligned_cols=48 Identities=17% Similarity=0.265 Sum_probs=38.8
Q ss_pred HHHHHHHhcCCC-cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 715 HAAIIMQFQDQT-SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 715 QAaILllFn~~~-~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+|.+.+.-+..+ ..|+++||+..++|+..|.+.+..|.+.|+++...|
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG 60 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG 60 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence 444444444444 578999999999999999999999999999987665
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=72.52 E-value=6.3 Score=33.50 Aligned_cols=42 Identities=7% Similarity=0.169 Sum_probs=32.4
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
|....-.+...|+.+|...+++|...++.+|..|+++|++..
T Consensus 18 V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 18 VGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeee
Confidence 333333456889999999999999999999999999998763
No 64
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=71.81 E-value=9.7 Score=36.60 Aligned_cols=60 Identities=15% Similarity=0.253 Sum_probs=46.7
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc-CCCCCCCCeEEEec
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES-VGTGSNDHLYNLVE 774 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~-~g~~~~~d~f~vne 774 (842)
.|.-..||...-+....++.||++.++++...+-++|.-|.+.|++... .|+ .-.|++|.
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 4555667776655567999999999999999999999999999999643 332 24577754
No 65
>PHA00738 putative HTH transcription regulator
Probab=71.68 E-value=11 Score=35.72 Aligned_cols=67 Identities=9% Similarity=0.122 Sum_probs=53.9
Q ss_pred EEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc-CCCCCCCCeEEEecCCC
Q 003173 708 QFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES-VGTGSNDHLYNLVEGMV 777 (842)
Q Consensus 708 ~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~-~g~~~~~d~f~vne~f~ 777 (842)
++...|.--.||....+.+..++.+|++.++|+...+-++|.-|-..|++... .|+ .-.|++|++..
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 45566777788888887778999999999999999999999999999999643 332 34678877643
No 66
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.15 E-value=5.9 Score=38.75 Aligned_cols=49 Identities=27% Similarity=0.401 Sum_probs=43.6
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
+...-.-||...+.....++.+|++.+|+++..+.+.+.-|...||++.
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 3445677888899888899999999999999999999999999999874
No 67
>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=71.01 E-value=6.7 Score=30.79 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=28.8
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 751 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~w 751 (842)
-.||...+.....++.+|++.+|+++..+.+.+.-|
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 457788888889999999999999999999998754
No 68
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=69.73 E-value=7.1 Score=42.21 Aligned_cols=49 Identities=22% Similarity=0.245 Sum_probs=44.0
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
-|..|+...+++..+++.||++.++++...++|-|..|.++|+|+...|
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 4567888888899999999999999999999999999999999977655
No 69
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=69.59 E-value=6.4 Score=42.57 Aligned_cols=48 Identities=21% Similarity=0.336 Sum_probs=43.9
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|-.|+.+.+++..++++||++.+++++.++||=|..|.++|+|+...|
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 567888899999999999999999999999999999999999987654
No 70
>PRK10870 transcriptional repressor MprA; Provisional
Probab=69.55 E-value=15 Score=37.55 Aligned_cols=53 Identities=13% Similarity=0.149 Sum_probs=45.2
Q ss_pred EEecHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 709 FTVAPIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 709 l~VS~~QAaILllFn~--~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+.+|+.|..||..... ...+|..+|++.++++...+.+.+.-|.++|++....
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 71
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=69.51 E-value=7.8 Score=41.80 Aligned_cols=49 Identities=16% Similarity=0.174 Sum_probs=43.9
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
-|..|+..++++..+++.||++.+|++...++|-|..|.+.|++....|
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 4567888999999999999999999999999999999999999976544
No 72
>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=69.43 E-value=5.3 Score=35.33 Aligned_cols=36 Identities=11% Similarity=0.165 Sum_probs=31.1
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 723 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 723 n~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
.....+|+.|||+.+|+++..++..+....+.|+|.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 334678999999999999999999999888888774
No 73
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=68.56 E-value=12 Score=31.51 Aligned_cols=43 Identities=16% Similarity=0.261 Sum_probs=35.6
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
|..+-++....+..+||+.+|+++..+...+.-|...|++...
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 3334446778999999999999999999999999999998654
No 74
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=68.41 E-value=7.4 Score=42.47 Aligned_cols=50 Identities=24% Similarity=0.346 Sum_probs=44.9
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 713 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 713 ~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
--|..|+...+.+..+++.||++.+|++...+||-|..|-+.|+++...|
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 45778898999998999999999999999999999999999999876654
No 75
>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=68.33 E-value=14 Score=31.81 Aligned_cols=52 Identities=17% Similarity=0.313 Sum_probs=37.5
Q ss_pred ecHHHHHHHHHhcC-----CCcccHHHHHHHhCCC-HHHHHHHHHHHHhCCcccccCC
Q 003173 711 VAPIHAAIIMQFQD-----QTSWTSKNLAAAVGVP-VDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 711 VS~~QAaILllFn~-----~~~~Tv~EL~~~l~m~-~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+|.-|.-||....+ .-.-|+.||++.+|+. ...+.+.|..|..+|.|+..++
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 45566666654443 2345999999999996 9999999999999999987654
No 76
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=67.93 E-value=18 Score=33.11 Aligned_cols=51 Identities=20% Similarity=0.340 Sum_probs=45.1
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+++.|..+|.........+..+|++.++++...+.+.+..|..+|++....
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 788999999888877666659999999999999999999999999997654
No 77
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=67.41 E-value=7.2 Score=34.78 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=36.7
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..|+......+..++.+|.+.+|++...+.++|..|.+.|.+...
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 455666666788999999999999999999999999999998643
No 78
>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=66.00 E-value=16 Score=36.88 Aligned_cols=43 Identities=7% Similarity=0.310 Sum_probs=36.5
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
.-|+...-.+..+|-++||+.+||+...+++.|..|...|++.
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 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=65.90 E-value=14 Score=30.34 Aligned_cols=32 Identities=16% Similarity=0.369 Sum_probs=29.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
|..+|++.++++...+.+.|.-|.+.|+|...
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
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.90 E-value=11 Score=38.76 Aligned_cols=45 Identities=7% Similarity=0.149 Sum_probs=38.4
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
...||...-.+..+|-++||+.+||+...+++.|..|...|++..
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 445666565667899999999999999999999999999999863
No 81
>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=65.77 E-value=17 Score=32.19 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=32.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 727 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 727 ~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+.|++||.+.||++...|.-.|.-|.+.|++...
T Consensus 18 c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 18 CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 8999999999999999999999999999999653
No 82
>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=65.36 E-value=8 Score=39.85 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=43.9
Q ss_pred ecHHHHHHHHHhcCC-----CcccHHHHHHHhCCC-HHHHHHHHHHHHhCCcccccCC
Q 003173 711 VAPIHAAIIMQFQDQ-----TSWTSKNLAAAVGVP-VDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 711 VS~~QAaILllFn~~-----~~~Tv~EL~~~l~m~-~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+++.|..||....+. -..|+.||++.+|++ ...+.++|..|.++|+|....|
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 478898888877742 247899999999998 9999999999999999976654
No 83
>PRK00215 LexA repressor; Validated
Probab=64.30 E-value=15 Score=38.09 Aligned_cols=60 Identities=15% Similarity=0.269 Sum_probs=47.0
Q ss_pred ecHHHHHHHHHhcC-----CCcccHHHHHHHhCC-CHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 711 VAPIHAAIIMQFQD-----QTSWTSKNLAAAVGV-PVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 711 VS~~QAaILllFn~-----~~~~Tv~EL~~~l~m-~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
+|+-|..||....+ ....|+.||++.+|+ +...+.+.|..|..+|+|....+. .-.+.|.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~---~r~~~l~ 67 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR---SRAIEVA 67 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC---cceEEec
Confidence 46788888876652 446799999999999 999999999999999999655321 2356664
No 84
>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=63.88 E-value=13 Score=27.80 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=25.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGII 757 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL 757 (842)
+|-+||++.+|++.+.+-|.|..|..+|++
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 85
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=62.91 E-value=13 Score=31.30 Aligned_cols=39 Identities=15% Similarity=0.248 Sum_probs=32.1
Q ss_pred cCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 723 QDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 723 n~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
...+.+ |..+|++.+|++...++++|..|.+.|++...+
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEEC
Confidence 345678 999999999999999999999999999997654
No 86
>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=62.74 E-value=17 Score=31.06 Aligned_cols=34 Identities=26% Similarity=0.382 Sum_probs=31.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+|-++||+.+|++...+.+.|..|.+.|++....
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcC
Confidence 5889999999999999999999999999998654
No 87
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=60.88 E-value=27 Score=35.68 Aligned_cols=64 Identities=16% Similarity=0.170 Sum_probs=48.0
Q ss_pred eEEEecHHHHHHHHHhcCCCc-ccHHHHHHHh--CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003173 707 MQFTVAPIHAAIIMQFQDQTS-WTSKNLAAAV--GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 775 (842)
Q Consensus 707 ~~l~VS~~QAaILllFn~~~~-~Tv~EL~~~l--~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~ 775 (842)
+++--+.+..+|..+..-.+. .+..+|+..+ +++.+.++.+|.+|.+.|+|+... ++.|...+.
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 344445556666666554443 3899999999 999999999999999999998764 247776654
No 88
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=60.70 E-value=9.8 Score=39.25 Aligned_cols=46 Identities=13% Similarity=0.078 Sum_probs=42.1
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
-+..|+...+.+...++.+|++.++++..++||=|..|..+|+|..
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 89
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=59.24 E-value=9 Score=30.35 Aligned_cols=39 Identities=26% Similarity=0.539 Sum_probs=23.1
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 756 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV 756 (842)
+.++.++.+ .+|..+||+.+|++...+.+-+.-|...|+
T Consensus 8 ~~ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 8 AQIIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp --HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred HHHHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 345555555 899999999999999999999888876653
No 90
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=58.79 E-value=16 Score=39.18 Aligned_cols=49 Identities=27% Similarity=0.354 Sum_probs=42.6
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
-|..|+..++.+...++.||++.++++...++|-|..|...|.|+...|
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~G 53 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHG 53 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 3567888888888999999999999999999999999999888765443
No 91
>PRK06474 hypothetical protein; Provisional
Probab=58.57 E-value=27 Score=35.81 Aligned_cols=67 Identities=18% Similarity=0.312 Sum_probs=49.8
Q ss_pred EEecHHHHHHHHHhcCCCc-ccHHHHHHHh-CCCHHHHHHHHHHHHhCCcccccCCC---CCCCCeEEEecC
Q 003173 709 FTVAPIHAAIIMQFQDQTS-WTSKNLAAAV-GVPVDVLSRRINFWISKGIIKESVGT---GSNDHLYNLVEG 775 (842)
Q Consensus 709 l~VS~~QAaILllFn~~~~-~Tv~EL~~~l-~m~~~~L~r~L~~wv~~gVL~e~~g~---~~~~d~f~vne~ 775 (842)
+-.+|....|+..+..... .|+.+|++.+ +++...+-++|..|...|++.....+ ..-.-.|.+|..
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 3346777888877766554 9999999999 79999999999999999999754321 111245777664
No 92
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=57.81 E-value=17 Score=43.08 Aligned_cols=51 Identities=20% Similarity=0.396 Sum_probs=46.9
Q ss_pred EecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 710 TVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 710 ~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.+|+.|..||......+..+..+|++.++++...+.+.+..|.++|++...
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
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=54.61 E-value=25 Score=32.50 Aligned_cols=54 Identities=13% Similarity=0.329 Sum_probs=47.8
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 709 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 709 l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+..++....||.++.....-...-||..+++|.+.++..|.-|...|+|....|
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 456778889999999887778888999999999999999999999999987765
No 94
>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=54.39 E-value=17 Score=30.33 Aligned_cols=38 Identities=16% Similarity=0.135 Sum_probs=31.2
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWI 752 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv 752 (842)
|.-+|.++-+.+.+++.+||+.+|++...++.-|..+-
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 55666666667889999999999999999999998875
No 95
>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=53.03 E-value=45 Score=29.57 Aligned_cols=43 Identities=14% Similarity=0.156 Sum_probs=39.3
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhC
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISK 754 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~ 754 (842)
.+=|+.+|-++...+.-|+++|++.+|--+-.++-+|.-++++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kK 51 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKK 51 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHH
Confidence 4568999999999999999999999999999999999999765
No 96
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=52.90 E-value=21 Score=38.33 Aligned_cols=49 Identities=20% Similarity=0.420 Sum_probs=44.2
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
|.....||.+...+..+.+.|||+.+|+|...+...++.|.+.|+++..
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 4566679999999999999999999999999999999999999999643
No 97
>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=52.52 E-value=12 Score=34.84 Aligned_cols=45 Identities=13% Similarity=0.223 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
.+.|+..+..+..++-++|++.+||+...+++.|..|...|++..
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~ 59 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSY 59 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEE
Confidence 345566666567899999999999999999999999999999854
No 98
>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=52.10 E-value=34 Score=30.89 Aligned_cols=44 Identities=18% Similarity=0.289 Sum_probs=36.3
Q ss_pred HHHHHHHhcCCCcccHHHHHHHh-CCCHHHHHHHHHHHHhCCcccc
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAV-GVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l-~m~~~~L~r~L~~wv~~gVL~e 759 (842)
-+.||..... ....+.||.+.+ |+++..|.++|..|...|++..
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r 51 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVER 51 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhc
Confidence 3456655555 678999999999 9999999999999999999954
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=48.92 E-value=57 Score=27.70 Aligned_cols=52 Identities=19% Similarity=0.342 Sum_probs=37.9
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecC
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEG 775 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~ 775 (842)
|+..+.+. ..+..+|++.+|++...+++.+..+-..|+.....+ .-|.++..
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 33344443 467999999999999999999999998898543322 35666544
No 100
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=48.84 E-value=34 Score=30.15 Aligned_cols=52 Identities=19% Similarity=0.266 Sum_probs=37.4
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
+-||.... ....+..+|+..++++...+.+.|..|.+.|++... ++.|.+.+
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 567789999999999999999999999999999653 35888754
No 101
>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=48.61 E-value=41 Score=26.72 Aligned_cols=34 Identities=15% Similarity=0.301 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINF 750 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~ 750 (842)
+..|.+.| ...+|+.||++.+|++...+++....
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 45789999999999999998887654
No 102
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=48.50 E-value=37 Score=26.56 Aligned_cols=41 Identities=12% Similarity=0.306 Sum_probs=31.6
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHh
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWIS 753 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~ 753 (842)
+++-+..++.++. ..++..+|++.+|++...+++.+.-...
T Consensus 4 l~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 4 LTPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4566666666663 4579999999999999999998876543
No 103
>PRK09954 putative kinase; Provisional
Probab=46.64 E-value=37 Score=38.16 Aligned_cols=43 Identities=16% Similarity=0.212 Sum_probs=39.1
Q ss_pred HHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
.-||..+.+....|..+|++.++++...+++.|..|.+.|++.
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 104
>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=46.28 E-value=46 Score=29.75 Aligned_cols=45 Identities=18% Similarity=0.157 Sum_probs=38.2
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
...++...+....++++++|++.++++.+.+...+..++..|.|.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~ 91 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIK 91 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSE
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEE
Confidence 445566666678899999999999999999999999999999885
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=45.84 E-value=46 Score=31.00 Aligned_cols=58 Identities=14% Similarity=0.256 Sum_probs=42.3
Q ss_pred HHHHHHhcC-CCcccHHHHHHHh-----CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 716 AAIIMQFQD-QTSWTSKNLAAAV-----GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 716 AaILllFn~-~~~~Tv~EL~~~l-----~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
.+|+..+.. ...+|.+||.+.+ +++..++-|+|..|+..|++.+.... .+...|..+.
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~-~~~~~y~~~~ 67 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELG-DGKARYELNT 67 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeC-CCceEEEeCC
Confidence 345555554 4569999999998 68999999999999999999764321 1125676653
No 106
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=45.23 E-value=35 Score=35.73 Aligned_cols=37 Identities=16% Similarity=0.232 Sum_probs=33.5
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 724 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 724 ~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
....+|.++||+.+++++.+++..+..+++.|++.+.
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~ 211 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTS 211 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEE
Confidence 3577999999999999999999999999999999543
No 107
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=44.39 E-value=40 Score=32.90 Aligned_cols=44 Identities=9% Similarity=0.101 Sum_probs=36.7
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|..+.+.....++.+|++.+++++..+.+.|.-|..+|++...
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 34444556677899999999999999999999999999998643
No 108
>PRK11050 manganese transport regulator MntR; Provisional
Probab=42.48 E-value=51 Score=32.82 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=37.8
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.|+.++...+.++..+|++.++++...+.+.|..|...|++...
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 44556666778999999999999999999999999999988643
No 109
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=41.87 E-value=48 Score=35.29 Aligned_cols=50 Identities=18% Similarity=0.354 Sum_probs=38.8
Q ss_pred EEecHHHHHHHHHhc-CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 709 FTVAPIHAAIIMQFQ-DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 709 l~VS~~QAaILllFn-~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
++-.|+|.. ...|. .....|.+|+++.+|++....||-|.++++.|+|..
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 334445543 33444 346799999999999999999999999999999864
No 110
>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=41.79 E-value=28 Score=32.80 Aligned_cols=64 Identities=14% Similarity=0.302 Sum_probs=47.0
Q ss_pred EecHHHHHHHHHhcCC-CcccHHHHHHHh-----CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 710 TVAPIHAAIIMQFQDQ-TSWTSKNLAAAV-----GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 710 ~VS~~QAaILllFn~~-~~~Tv~EL~~~l-----~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
.+|+-.-+||..+.+. ..+|.++|.+.+ +++...+-|+|..|...|++...... .+...|.++.
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 3567778888888864 478999998877 58889999999999999999754321 2235677765
No 111
>PRK14999 histidine utilization repressor; Provisional
Probab=40.93 E-value=45 Score=35.35 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=33.4
Q ss_pred CCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 725 QTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 725 ~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.+.+ |-.+|++..|++-.+++++|.-|+..|+|...+|
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 8899999999999999999999999999976655
No 112
>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=40.27 E-value=42 Score=35.33 Aligned_cols=34 Identities=18% Similarity=0.388 Sum_probs=31.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|-.||++..|++-.+++++|.-|+..|+|...+|
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 59 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQG 59 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 7899999999999999999999999999977665
No 113
>smart00753 PAM PCI/PINT associated module.
Probab=39.96 E-value=47 Score=29.30 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=32.0
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 724 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 724 ~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
...++++++|++.++++.+.+.+.+..++..|.|.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~ 55 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEIS 55 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeE
Confidence 46789999999999999999999999999999874
No 114
>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=39.96 E-value=47 Score=29.30 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=32.0
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 724 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 724 ~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
...++++++|++.++++.+.+.+.+..++..|.|.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~ 55 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEIS 55 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeE
Confidence 46789999999999999999999999999999874
No 115
>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=39.44 E-value=43 Score=35.12 Aligned_cols=34 Identities=24% Similarity=0.453 Sum_probs=31.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|-.||++..|++-.+++++|.-|+..|+|...+|
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 116
>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=39.01 E-value=62 Score=25.90 Aligned_cols=24 Identities=17% Similarity=0.401 Sum_probs=17.7
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHH
Q 003173 726 TSWTSKNLAAAVGVPVDVLSRRIN 749 (842)
Q Consensus 726 ~~~Tv~EL~~~l~m~~~~L~r~L~ 749 (842)
..+|+.||++.+|+++..++..+.
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 468999999999999999888774
No 117
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=38.64 E-value=47 Score=32.98 Aligned_cols=53 Identities=9% Similarity=0.278 Sum_probs=44.5
Q ss_pred EEEecHHHHHHHHHhcCC-CcccHHHHHHHhC-----CCHHHHHHHHHHHHhCCccccc
Q 003173 708 QFTVAPIHAAIIMQFQDQ-TSWTSKNLAAAVG-----VPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 708 ~l~VS~~QAaILllFn~~-~~~Tv~EL~~~l~-----m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
-+.+|+-+.+||..+.+. +..|.++|-..+. ++..++-|+|..|...|++...
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 4589988876655 8899999999999999999754
No 118
>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=38.40 E-value=28 Score=27.40 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=22.7
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINF 750 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~ 750 (842)
-|+-++++. .|+.+||+.+|++...+.+.|..
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 89999999999999999998754
No 119
>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=38.27 E-value=74 Score=24.96 Aligned_cols=39 Identities=13% Similarity=0.274 Sum_probs=29.4
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWI 752 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv 752 (842)
++-|.-++.++- ..++..+|++.++++...++..+.-..
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 458999999999999999998887554
No 120
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=38.01 E-value=62 Score=34.36 Aligned_cols=39 Identities=15% Similarity=0.248 Sum_probs=33.8
Q ss_pred CCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 724 DQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 724 ~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
..+.+ |-.+|++..|++...++++|.-|+..|+|...+|
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 34445 7899999999999999999999999999976655
No 121
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=37.88 E-value=52 Score=34.01 Aligned_cols=68 Identities=12% Similarity=0.198 Sum_probs=51.8
Q ss_pred CceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003173 684 PRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 756 (842)
Q Consensus 684 ~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~--~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV 756 (842)
.|.-.|.+..|.++++---. | .||..||.-|+.-.. -.+||.+.||+..+++.+.++..|.++.--.|
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 45556788888888763222 2 478899988776553 45799999999999999999999998864444
No 122
>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=37.88 E-value=1.1e+02 Score=27.59 Aligned_cols=46 Identities=13% Similarity=0.218 Sum_probs=37.6
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
++|.|=.+-+....+...+|++.+++++..+|..++.|-..|+|..
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 123
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.65 E-value=32 Score=35.32 Aligned_cols=58 Identities=14% Similarity=0.250 Sum_probs=40.8
Q ss_pred HHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCCC
Q 003173 719 IMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGMV 777 (842)
Q Consensus 719 LllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f~ 777 (842)
++.++ .+.+|++||++.|||+...+-..+.-|..-|+.+...-+..-.+.|....+|.
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 33444 46899999999999999999999999998898765422111234555555544
No 124
>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=37.37 E-value=48 Score=34.85 Aligned_cols=38 Identities=16% Similarity=0.270 Sum_probs=33.4
Q ss_pred CCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 725 QTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 725 ~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.+.+ |-.+|++..|++-.+++++|.-|+..|+|...+|
T Consensus 22 g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 60 (230)
T TIGR02018 22 GHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQG 60 (230)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3444 8899999999999999999999999999977665
No 125
>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=36.68 E-value=82 Score=30.65 Aligned_cols=50 Identities=8% Similarity=0.108 Sum_probs=41.3
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHh----CCCHHHHHHHHHHHHhCCccccc
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAV----GVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l----~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|..+..|+..+=+.+..|+.+|.+.+ +++...+...|.-|..+|++...
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 577888888777666778999976665 78899999999999999998643
No 126
>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=36.53 E-value=66 Score=32.18 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=31.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+|-++||..+|++.+.+-|.|+-|.+.|++....
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 5778999999999999999999999999998654
No 127
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=36.23 E-value=50 Score=35.63 Aligned_cols=42 Identities=17% Similarity=0.173 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKG 755 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~g 755 (842)
=|..|+.+.+.+..+++.+|++.+|+++.++||=|..+-..+
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 477899999999999999999999999999999999887543
No 128
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=36.06 E-value=1.8e+02 Score=33.07 Aligned_cols=67 Identities=21% Similarity=0.260 Sum_probs=43.4
Q ss_pred HHHHHhhccCCCChHHHHHHHHHHHHHHHhhcCCCcchhhhchhhHHHh-----hhcCcchhhhcccccccC
Q 003173 411 SALKYRLLTAGASTNDILHQYVSTIKALRTIDPTGVFLEAVGEPIRDYL-----RGRKDTIKCIVTMLTDGT 477 (842)
Q Consensus 411 ~~l~~RLLhpGa~T~dIL~~YIstIkal~~LDpsGvlL~~V~~pIr~YL-----r~R~DtVr~IV~~L~d~~ 477 (842)
+.+..+|-.-|+++.|--..|+..-|+++.-+...--...++.-+..|= .-|+|.+||||+.+.|++
T Consensus 148 k~~~~~lkew~~~vedqrel~r~v~~al~~~k~~~~s~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~ 219 (378)
T KOG2753|consen 148 KQLDDWLKEWNISVEDQRELLRAVHKALKDNKSVDESSKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPK 219 (378)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCc
Confidence 4567777888888888888888888888765531111122222222221 348899999998888764
No 129
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=35.32 E-value=54 Score=34.70 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=31.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|-.||++.+|++-.+++++|.-|+..|+|....|
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 7789999999999999999999999999976665
No 130
>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=35.31 E-value=49 Score=27.50 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=25.0
Q ss_pred HhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003173 721 QFQDQTSWTSKNLAAAVGVPVDVLSRRINF 750 (842)
Q Consensus 721 lFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~ 750 (842)
.|+.....|++|||+.+||+...+..+|.-
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 566667899999999999999987777653
No 131
>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=34.60 E-value=88 Score=30.33 Aligned_cols=47 Identities=19% Similarity=0.307 Sum_probs=38.0
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 723 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 723 n~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
+..-..|.++||..++-+.+.++.+|..+.+.|++.... ++.|.+..
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 344567999999999999999999999999999997642 34666543
No 132
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=34.53 E-value=57 Score=29.35 Aligned_cols=38 Identities=8% Similarity=0.091 Sum_probs=32.8
Q ss_pred cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 723 QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 723 n~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..+...+..+|+..+++|++.++..|..|+.+|-+...
T Consensus 12 ~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 12 ALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 34567899999999999999999999999999876543
No 133
>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=34.16 E-value=54 Score=33.81 Aligned_cols=42 Identities=12% Similarity=0.257 Sum_probs=36.5
Q ss_pred HhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|...+.++-.+|++.+|++...++.+|.-|...|++...++
T Consensus 28 ~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 28 ELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred CCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecC
Confidence 455667789999999999999999999999999999976543
No 134
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=34.14 E-value=74 Score=32.17 Aligned_cols=35 Identities=29% Similarity=0.310 Sum_probs=31.2
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 727 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 727 ~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
.+|-++||+.+|++.+.+.|.|.-|.+.|++....
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 183 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSGY 183 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCC
Confidence 35778999999999999999999999999998543
No 135
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=34.05 E-value=72 Score=34.62 Aligned_cols=44 Identities=18% Similarity=0.308 Sum_probs=38.8
Q ss_pred HHHHhcC-CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 718 IIMQFQD-QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 718 ILllFn~-~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
||...+. ...++..+||+++|++...+++++..|...||+...+
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 6777777 4689999999999999999999999999999997544
No 136
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=33.89 E-value=54 Score=25.08 Aligned_cols=28 Identities=21% Similarity=0.193 Sum_probs=20.9
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHH
Q 003173 725 QTSWTSKNLAAAVGVPVDVLSRRINFWI 752 (842)
Q Consensus 725 ~~~~Tv~EL~~~l~m~~~~L~r~L~~wv 752 (842)
...|++++||+.+|+++..+.+..+-..
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 4569999999999999999999887654
No 137
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=33.40 E-value=69 Score=33.42 Aligned_cols=43 Identities=12% Similarity=0.131 Sum_probs=37.1
Q ss_pred HHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 720 MQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 720 llFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
..|...+.++..+|++.+|++..-++.+|.-|...|++...++
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 3456677889999999999999999999999999999976543
No 138
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=33.03 E-value=59 Score=29.06 Aligned_cols=32 Identities=9% Similarity=0.216 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 730 SKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 730 v~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+.+|++.++++...+.+.+..|.+.|++...+
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 139
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=32.90 E-value=1e+02 Score=34.24 Aligned_cols=43 Identities=14% Similarity=0.244 Sum_probs=36.8
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc-ccc
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI-IKE 759 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV-L~e 759 (842)
.||....+....+..+||+.+|++...+.++|+.|...|+ +..
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~ 51 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS 51 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence 4566666667789999999999999999999999999998 544
No 140
>PRK12423 LexA repressor; Provisional
Probab=32.84 E-value=72 Score=33.21 Aligned_cols=52 Identities=19% Similarity=0.309 Sum_probs=41.9
Q ss_pred ecHHHHHHHHHhcCC---Cc--ccHHHHHHHhC-CCHHHHHHHHHHHHhCCcccccCC
Q 003173 711 VAPIHAAIIMQFQDQ---TS--WTSKNLAAAVG-VPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 711 VS~~QAaILllFn~~---~~--~Tv~EL~~~l~-m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+|+-|-.|+....+. .. -|+.||++.+| .+...++++|.-|..+|+|....+
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 467787777766642 33 49999999999 589999999999999999976543
No 141
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=32.70 E-value=75 Score=33.12 Aligned_cols=34 Identities=18% Similarity=0.348 Sum_probs=31.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+|.++||+.+|++...+.|.|+-|.+.|++....
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 5778999999999999999999999999998754
No 142
>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=32.66 E-value=57 Score=25.30 Aligned_cols=27 Identities=26% Similarity=0.480 Sum_probs=23.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
+|+.|+++.+|+++..|+ .|.++|+|.
T Consensus 1 ~~~~e~a~~~gv~~~tlr----~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTLR----YYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHHH----HHHHCCCCC
Confidence 478999999999998665 789999886
No 143
>PF14502 HTH_41: Helix-turn-helix domain
Probab=32.46 E-value=67 Score=26.30 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=29.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
-|++|+++.++++.-.++.+|.+|...|.++.
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 48999999999999999999999999987754
No 144
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=32.23 E-value=65 Score=34.14 Aligned_cols=34 Identities=29% Similarity=0.415 Sum_probs=31.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|-.+|++..|++-.+++++|.-|+..|+|....|
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 70 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG 70 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 7789999999999999999999999999976665
No 145
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=31.34 E-value=81 Score=31.76 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=36.9
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
|...+.++......+||+.+++++..+...++-|.+.|++...
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 3445556778899999999999999999999999999998764
No 146
>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=31.28 E-value=66 Score=27.90 Aligned_cols=38 Identities=13% Similarity=0.306 Sum_probs=31.6
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKG 755 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~g 755 (842)
|-...++...+|+.+|+..++++...+..+|-.|...+
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 44566777899999999999999999999998888754
No 147
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=31.19 E-value=69 Score=33.73 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=35.6
Q ss_pred hcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 722 FQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 722 Fn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
|...+.+ |-.+|++.+|++-..++.+|.-|...|+|...+|
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 148
>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=31.08 E-value=88 Score=25.63 Aligned_cols=42 Identities=10% Similarity=0.213 Sum_probs=33.4
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhC
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISK 754 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~ 754 (842)
.|+-|..|+.++.. ..+..+|++.+++++..++..+..+.++
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 46677778877765 5789999999999999999999888765
No 149
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=31.04 E-value=97 Score=23.51 Aligned_cols=40 Identities=10% Similarity=0.182 Sum_probs=28.6
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 751 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~w 751 (842)
+++.+..++..+- ...++..+|++.+|++...+.+.+..-
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4555555554442 245899999999999999998877643
No 150
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=30.97 E-value=85 Score=32.97 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=30.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+|-++||+.+|++.+.+.|.|+-|.+.|+|...
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence 567899999999999999999999999999754
No 151
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=30.87 E-value=67 Score=34.23 Aligned_cols=41 Identities=17% Similarity=0.332 Sum_probs=34.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
|=.+|++..|++..+++++|.-|+..|+|....|. ++|...
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~----GtfV~~ 73 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDELVEEGLIVRRQGK----GTFVAS 73 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecC----eeEEcC
Confidence 66799999999999999999999999999766553 455544
No 152
>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=30.73 E-value=1e+02 Score=27.03 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=41.1
Q ss_pred cHHHHHHHHHhcC--CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 712 APIHAAIIMQFQD--QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 712 S~~QAaILllFn~--~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
|..|..+|..-.. ....+-.+|+..+|+++..+-..+..|.+.|++...
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 356788999999999999999999999999998643
No 153
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=30.53 E-value=69 Score=33.40 Aligned_cols=46 Identities=15% Similarity=0.190 Sum_probs=38.2
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.+-..+...+.++..+|++.+|++...++.+|..|...|++...++
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 3334556667888899999999999999999999999999976543
No 154
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=30.49 E-value=98 Score=33.01 Aligned_cols=46 Identities=15% Similarity=0.240 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+.+.+..-++...+|..+|++.++++...+.+.|..|..+|++...
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 3444455556667999999999999999999999999999999643
No 155
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=30.45 E-value=88 Score=31.82 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=31.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 727 SWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 727 ~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
.+|-++||+.+|++...+.|.|.-|.+.|+++...
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 156
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=30.18 E-value=75 Score=32.99 Aligned_cols=43 Identities=19% Similarity=0.320 Sum_probs=35.5
Q ss_pred HHHHHhcCC-CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 717 AIIMQFQDQ-TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 717 aILllFn~~-~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
-|+.++.+. ...|.+||++.+++++.++++.+.+++..|.+..
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~ 209 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIA 209 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEE
Confidence 455555543 2579999999999999999999999999998864
No 157
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=30.06 E-value=82 Score=32.91 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=33.2
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
|-++||+.+|++.+.|.|.|.-|.+.|++.... ..+.|.
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 158
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=29.81 E-value=1.2e+02 Score=27.35 Aligned_cols=39 Identities=15% Similarity=0.197 Sum_probs=32.6
Q ss_pred HhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 721 QFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 721 lFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
.-++..-.|-++|++++|++...+-++++.|-..|+=.+
T Consensus 13 ~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 13 LLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred HHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 334555689999999999999999999999998887443
No 159
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.71 E-value=1.2e+02 Score=23.68 Aligned_cols=37 Identities=19% Similarity=0.342 Sum_probs=28.5
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 756 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV 756 (842)
|+.++.+. .|+.++|..+||+...+.+-+.-+-..|+
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 44444443 39999999999999999888877777675
No 160
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=29.54 E-value=78 Score=33.83 Aligned_cols=45 Identities=16% Similarity=0.273 Sum_probs=37.7
Q ss_pred HHHHhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 718 IIMQFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 718 ILllFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+-..|...+.+ |-.+|++.+|++...++.+|.-|...|++...+|
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 6899999999999999999999999999976543
No 161
>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=29.43 E-value=77 Score=28.59 Aligned_cols=34 Identities=18% Similarity=0.142 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHH
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRI 748 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L 748 (842)
=+..|+...+. ...|+.+|++.+|++...+.+.|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 36677888888 89999999999999999999977
No 162
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=29.39 E-value=4.4e+02 Score=27.47 Aligned_cols=99 Identities=19% Similarity=0.333 Sum_probs=65.0
Q ss_pred ChHHHHHHHHHHhhhhccCCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcC-------------------
Q 003173 664 PGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQD------------------- 724 (842)
Q Consensus 664 P~eL~~~~e~F~k~Y~~~k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~------------------- 724 (842)
|..+..+++...+.|.... |-+.-. ++ ++.|.|.+.|--+..+..|..
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 3578888999998887552 322222 12 456777777766666665543
Q ss_pred -CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCC--CCCCeEEEecCCCC
Q 003173 725 -QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTG--SNDHLYNLVEGMVD 778 (842)
Q Consensus 725 -~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~--~~~d~f~vne~f~~ 778 (842)
+..+|-.+|++..|++. ...+..|+..|++++..... .....|.+++.|-.
T Consensus 101 y~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~~ 154 (188)
T PRK00135 101 YKQPITRIEIDEIRGVNS---DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFLD 154 (188)
T ss_pred HcCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHHH
Confidence 23467899999999987 56678888999997632111 13457877777653
No 163
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=29.14 E-value=74 Score=32.76 Aligned_cols=55 Identities=16% Similarity=0.227 Sum_probs=41.5
Q ss_pred CCCceEEeecCCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003173 682 KTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGII 757 (842)
Q Consensus 682 k~~RkL~W~~~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL 757 (842)
.+.|+|+|.++| .-|+-.+.- +.-..|+++|++.+|.++.+++++|+-=.+.|=|
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 478999999854 223333333 5567899999999999999999999877776533
No 164
>PF13551 HTH_29: Winged helix-turn helix
Probab=28.87 E-value=1e+02 Score=28.02 Aligned_cols=39 Identities=21% Similarity=0.370 Sum_probs=31.5
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 756 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV 756 (842)
.+|.++.+... |+.++|..+|++...+.+-+.-|...|+
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 45555655433 7999999999999999999999988874
No 165
>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=28.70 E-value=2.4e+02 Score=29.79 Aligned_cols=47 Identities=15% Similarity=0.177 Sum_probs=39.6
Q ss_pred cHHHHHHHHHh--cCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 712 APIHAAIIMQF--QDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 712 S~~QAaILllF--n~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
+..|..|+..- ......|..+|++.+|.+....+..|..++..|+|.
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 35677888777 667789999999999999999999999999999874
No 166
>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=28.65 E-value=80 Score=33.21 Aligned_cols=42 Identities=17% Similarity=0.289 Sum_probs=36.5
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.+...+.+ +-.+|++.+|++...+|.+|.-|...|++...+|
T Consensus 23 ~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~ 65 (235)
T TIGR02812 23 RFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 65 (235)
T ss_pred CCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45566778 8999999999999999999999999999976543
No 167
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=28.57 E-value=1.6e+02 Score=28.40 Aligned_cols=58 Identities=22% Similarity=0.311 Sum_probs=42.5
Q ss_pred HHHHHHhcCCCcccHHHHHHHhC-CCHHHHHHHHHHHHhCCcccccCC-CCCCCCeEEEec
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAVG-VPVDVLSRRINFWISKGIIKESVG-TGSNDHLYNLVE 774 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l~-m~~~~L~r~L~~wv~~gVL~e~~g-~~~~~d~f~vne 774 (842)
..||....+ ...-++||...++ |+...|.+.|.-|...|++..... ...+.-.|++.+
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 445555544 6789999999999 999999999999999999864321 122344566544
No 168
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=28.57 E-value=85 Score=34.41 Aligned_cols=43 Identities=12% Similarity=0.253 Sum_probs=36.0
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
||++..+ ..-|++||...++++...+..+|..|...|++.+..
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 3444443 678999999999999999999999999999987653
No 169
>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=28.27 E-value=1.6e+02 Score=32.50 Aligned_cols=45 Identities=16% Similarity=0.274 Sum_probs=37.0
Q ss_pred cccHHHHHHHhC--CCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEecCC
Q 003173 727 SWTSKNLAAAVG--VPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVEGM 776 (842)
Q Consensus 727 ~~Tv~EL~~~l~--m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne~f 776 (842)
.++..+|++.++ |+.+.++.+|.+|++.|+|+... ++.|...+..
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 3467766553
No 170
>PRK09462 fur ferric uptake regulator; Provisional
Probab=28.19 E-value=1.1e+02 Score=30.24 Aligned_cols=65 Identities=14% Similarity=0.228 Sum_probs=48.5
Q ss_pred EEEecHHHHHHHHHhcC--CCcccHHHHHHHh-----CCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 708 QFTVAPIHAAIIMQFQD--QTSWTSKNLAAAV-----GVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 708 ~l~VS~~QAaILllFn~--~~~~Tv~EL~~~l-----~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
-+.+|+-..+||..+.. ...+|.+||.+.+ +++..++-|+|..|...|++...... .+...|.++
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 35678888889988864 3589999998877 37899999999999999999754211 123456654
No 171
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.80 E-value=75 Score=31.51 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=30.0
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcc
Q 003173 724 DQTSWTSKNLAAAVGVPVDVLSRRINFWISKGII 757 (842)
Q Consensus 724 ~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL 757 (842)
....+|-++|++.+||+...|++.|..|-..|++
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLI 45 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcc
Confidence 4457899999999999999999999999986654
No 172
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=27.72 E-value=1.4e+02 Score=29.30 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=42.9
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 713 PIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 713 ~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.+.+-|+.+--++..+|+.++...||++-..+++.+.-++..|-|...
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 356778888888999999999999999999999999999999887654
No 173
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=27.70 E-value=1.4e+02 Score=34.62 Aligned_cols=39 Identities=8% Similarity=0.078 Sum_probs=35.5
Q ss_pred hcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 722 FQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 722 Fn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
|+..+.+|.++|++.+++|+..+++.|..|.+.|++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEec
Confidence 556678999999999999999999999999999999754
No 174
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=27.55 E-value=91 Score=33.18 Aligned_cols=42 Identities=19% Similarity=0.260 Sum_probs=36.1
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 27 ~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 27 TLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred CCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 45556777 8999999999999999999999999999976543
No 175
>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=27.42 E-value=78 Score=34.79 Aligned_cols=43 Identities=19% Similarity=0.077 Sum_probs=36.6
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEec
Q 003173 726 TSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLVE 774 (842)
Q Consensus 726 ~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vne 774 (842)
...|.+|||+++|+++..+.+-|..++.-|+|.+.. +.|....
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 176
>PRK03837 transcriptional regulator NanR; Provisional
Probab=27.34 E-value=1e+02 Score=32.35 Aligned_cols=42 Identities=21% Similarity=0.327 Sum_probs=36.0
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|...+.+ +..+|++.+|++...++.+|.-|...|++...+|
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 34455678 8999999999999999999999999999976544
No 177
>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=26.84 E-value=1e+02 Score=29.06 Aligned_cols=49 Identities=12% Similarity=0.201 Sum_probs=40.7
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCC----HHHHHHHHHHHHhCCccccc
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVP----VDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~----~~~L~r~L~~wv~~gVL~e~ 760 (842)
|+.+..|+..+=+.+..|+.||.+.++=+ ...+...|.-|+.+|+|...
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 56777788877777779999999988755 89999999999999999654
No 178
>PF15469 Sec5: Exocyst complex component Sec5
Probab=26.66 E-value=1.4e+02 Score=30.30 Aligned_cols=49 Identities=24% Similarity=0.463 Sum_probs=41.4
Q ss_pred hHHHHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHhhcCCCcchhhhchhhHHHhhhc
Q 003173 403 SKLVESFISALKYRLLTAGASTNDILHQYVSTIKALRTIDPTGVFLEAVGEPIRDYLRGR 462 (842)
Q Consensus 403 ~~Lv~~f~~~l~~RLLhpGa~T~dIL~~YIstIkal~~LDpsGvlL~~V~~pIr~YLr~R 462 (842)
...+..|+..+..||+.|..+. ..+..+|+-|..|+|.| .||=.||..|
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 3577899999999999998666 55788899999999988 8988888765
No 179
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=26.58 E-value=1.6e+02 Score=26.87 Aligned_cols=68 Identities=16% Similarity=0.273 Sum_probs=44.6
Q ss_pred EecHHHHHHHHHhcCCCcccHHHHHHHh----CCCHHHHHHHHHHHHhC-CcccccCCCCCCCCeEEEecCCC
Q 003173 710 TVAPIHAAIIMQFQDQTSWTSKNLAAAV----GVPVDVLSRRINFWISK-GIIKESVGTGSNDHLYNLVEGMV 777 (842)
Q Consensus 710 ~VS~~QAaILllFn~~~~~Tv~EL~~~l----~m~~~~L~r~L~~wv~~-gVL~e~~g~~~~~d~f~vne~f~ 777 (842)
..+..-=+||..|=+..+.|+++|-+.+ .++...+-..+-...++ |||.-.+....+..+|.+-|.+.
T Consensus 8 D~~GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~Y~ 80 (83)
T PF10826_consen 8 DKDGIRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEKYA 80 (83)
T ss_pred CCccHHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHHhh
Confidence 4556677899999999999998876654 45554444444333333 99975332223457899887764
No 180
>PHA02943 hypothetical protein; Provisional
Probab=26.48 E-value=1.3e+02 Score=30.62 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=40.3
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC-CCCCCCCeEEEec
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV-GTGSNDHLYNLVE 774 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~-g~~~~~d~f~vne 774 (842)
||..+ ....-|..||++.+|++-..++-.|.-|-+.|.+++.. | ....|.+++
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 55667899999999999999999999999999887653 3 124555555
No 181
>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=26.37 E-value=1.3e+02 Score=29.27 Aligned_cols=36 Identities=17% Similarity=0.210 Sum_probs=32.4
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 725 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 725 ~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.-..+.++||..++-+.+.++.+|..+.+.|++...
T Consensus 49 ~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~ 84 (119)
T TIGR01714 49 LAPYNAEMLATMFNRNVGDIRITLQTLESLGLIEKK 84 (119)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 345799999999999999999999999999998764
No 182
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=25.91 E-value=1.4e+02 Score=32.43 Aligned_cols=62 Identities=19% Similarity=0.255 Sum_probs=48.7
Q ss_pred EEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCCCCCCCCeEEEe
Q 003173 709 FTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESVGTGSNDHLYNLV 773 (842)
Q Consensus 709 l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g~~~~~d~f~vn 773 (842)
|-.|.++|-+-...=.....|..||++.+|+|..-+-..|.+|.++|+.....|+ ...|+-.
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 4456777777666666678899999999999999999999999999998766553 2355543
No 183
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.57 E-value=78 Score=26.51 Aligned_cols=28 Identities=25% Similarity=0.534 Sum_probs=23.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
+|+.|+|+.+|++...|+ +|.+.|+|.-
T Consensus 1 yti~eva~~~gvs~~tlr----~y~~~gll~~ 28 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLR----YYEREGLLPP 28 (69)
T ss_dssp EEHHHHHHHTTTTHHHHH----HHHHTTSSTT
T ss_pred CcHHHHHHHHCcCHHHHH----HHHHhcCccc
Confidence 478999999999987665 7999999754
No 184
>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=24.87 E-value=1.2e+02 Score=31.24 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=28.6
Q ss_pred cHHHHHHHh-CCCHHHHHHHHHHHHhCCcccc
Q 003173 729 TSKNLAAAV-GVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 729 Tv~EL~~~l-~m~~~~L~r~L~~wv~~gVL~e 759 (842)
|-.+|++.+ ||++..|+++|..|+..|++..
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 9999999999999999999864
No 185
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=24.69 E-value=1.2e+02 Score=32.47 Aligned_cols=42 Identities=19% Similarity=0.371 Sum_probs=36.0
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 19 ~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~ 61 (253)
T PRK10421 19 NLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRG 61 (253)
T ss_pred CCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45566778 7899999999999999999999999999975543
No 186
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=24.39 E-value=1e+02 Score=32.73 Aligned_cols=42 Identities=17% Similarity=0.345 Sum_probs=36.2
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 24 ~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 24 VLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 44556778 8899999999999999999999999999976544
No 187
>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=24.17 E-value=97 Score=23.80 Aligned_cols=26 Identities=23% Similarity=0.470 Sum_probs=20.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
|+.|+|+.+|++...| .+|-+.|+|.
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 5789999999998665 5899999884
No 188
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=24.07 E-value=1.2e+02 Score=23.90 Aligned_cols=37 Identities=16% Similarity=0.298 Sum_probs=20.1
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHH
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRIN 749 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~ 749 (842)
|+.|=..|..+-+ ..+|+.+||..+|.+...+.+.|.
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 3444444555543 459999999999999999988764
No 189
>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=23.77 E-value=1.3e+02 Score=29.83 Aligned_cols=39 Identities=8% Similarity=-0.003 Sum_probs=32.0
Q ss_pred ecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003173 711 VAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 751 (842)
Q Consensus 711 VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~w 751 (842)
.|+-|..|+.++ ...+|.+|||+.+|++...+.+.+...
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 578888999887 468999999999999999887555443
No 190
>PF14493 HTH_40: Helix-turn-helix domain
Probab=23.76 E-value=1.2e+02 Score=27.38 Aligned_cols=37 Identities=16% Similarity=0.198 Sum_probs=32.3
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCc
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGI 756 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gV 756 (842)
-+.+|++ .+|++|||+.-+++..++..+|.-++..|-
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 689999999999999999999999998765
No 191
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=23.68 E-value=1.9e+02 Score=31.17 Aligned_cols=35 Identities=26% Similarity=0.391 Sum_probs=30.8
Q ss_pred HHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHH
Q 003173 717 AIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFW 751 (842)
Q Consensus 717 aILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~w 751 (842)
.+.-+|.+.+.||+..|++-+|-|+..|+..|...
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~i 233 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDI 233 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHH
Confidence 46678999999999999999999999998887654
No 192
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=23.49 E-value=1.6e+02 Score=29.21 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=42.3
Q ss_pred cHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC
Q 003173 712 APIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 712 S~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
||---.+|-+..+++..|+.|+|+.+|-+.+.+.+.|.-+.+-||+....
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~ 112 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEE 112 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEec
Confidence 44445567777888899999999999999999999999999999986543
No 193
>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=23.06 E-value=1.4e+02 Score=27.63 Aligned_cols=56 Identities=20% Similarity=0.268 Sum_probs=33.1
Q ss_pred HHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc-c-CCCCCCCCeEEEec
Q 003173 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKE-S-VGTGSNDHLYNLVE 774 (842)
Q Consensus 718 ILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e-~-~g~~~~~d~f~vne 774 (842)
+..+..+... ++..|.+.||||.-.++..|..|-.-||-.+ . .|.-...+.|++..
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~~ 70 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALPELGIECEFVQDGERNNAGYYRISD 70 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEeee
Confidence 3444455555 9999999999999999999999998887432 2 33333455777743
No 194
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.06 E-value=98 Score=25.88 Aligned_cols=27 Identities=26% Similarity=0.500 Sum_probs=23.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIK 758 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~ 758 (842)
+|+.|+++.+|+++..|+ +|...|++.
T Consensus 1 ~s~~eva~~~gvs~~tlr----~~~~~gli~ 27 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLR----YYERIGLLP 27 (70)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCC
Confidence 478999999999998776 678899986
No 195
>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=22.78 E-value=1.4e+02 Score=28.98 Aligned_cols=39 Identities=13% Similarity=0.244 Sum_probs=29.9
Q ss_pred EecHHHHHHHHH-hcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003173 710 TVAPIHAAIIMQ-FQDQTSWTSKNLAAAVGVPVDVLSRRINF 750 (842)
Q Consensus 710 ~VS~~QAaILll-Fn~~~~~Tv~EL~~~l~m~~~~L~r~L~~ 750 (842)
.+++-|..|+.+ |- ..++++||++.+|||...++..+.-
T Consensus 111 ~L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 456666666665 43 4789999999999999998877643
No 196
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=22.70 E-value=1.1e+02 Score=28.00 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=32.3
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 725 QTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 725 ~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
..-+|...|++++++.-...+++|.-|..+|+++..
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 455799999999999999999999999999998654
No 197
>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=22.35 E-value=1.3e+02 Score=27.74 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=24.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
+++.|+|+.+|++...| .+|.+.|+|...
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 47899999999998754 589999999753
No 198
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=21.52 E-value=1.3e+02 Score=32.14 Aligned_cols=42 Identities=14% Similarity=0.166 Sum_probs=35.8
Q ss_pred HhcCCCcc-cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 721 QFQDQTSW-TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 721 lFn~~~~~-Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|...+.+ +-.+|++.+|++...++.+|.-|...|++...+|
T Consensus 25 ~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 25 VYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 45566778 5789999999999999999999999999975544
No 199
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=21.46 E-value=1.5e+02 Score=30.89 Aligned_cols=44 Identities=20% Similarity=0.394 Sum_probs=37.8
Q ss_pred cHHHHHHHHHhcCCC--cccHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 003173 712 APIHAAIIMQFQDQT--SWTSKNLAAAVGVPVDVLSRRINFWISKG 755 (842)
Q Consensus 712 S~~QAaILllFn~~~--~~Tv~EL~~~l~m~~~~L~r~L~~wv~~g 755 (842)
.+.+..|+...+.+. .+|..+|++.+|+++..++|=|..+-..|
T Consensus 15 ~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G 60 (213)
T PRK05472 15 LPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFG 60 (213)
T ss_pred hHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcC
Confidence 456777888888887 89999999999999999999998886554
No 200
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.44 E-value=2e+02 Score=30.89 Aligned_cols=60 Identities=22% Similarity=0.311 Sum_probs=50.8
Q ss_pred HHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCcccccC-CCCCCCCeEEEecCC
Q 003173 714 IHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKESV-GTGSNDHLYNLVEGM 776 (842)
Q Consensus 714 ~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~-g~~~~~d~f~vne~f 776 (842)
.|=.|+...++.++.|.-+|+..+|++.+++.-++.-+-.-|++.+.. | ..-.|++|+.+
T Consensus 175 ~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~~~G---r~iiy~in~s~ 235 (240)
T COG3398 175 TSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIPEDREG---RSIIYSINPSI 235 (240)
T ss_pred hHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCcccccC---ceEEEEeCHHH
Confidence 455788888999999999999999999999999999999999997653 2 24689998865
No 201
>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=21.18 E-value=1.8e+02 Score=32.89 Aligned_cols=48 Identities=15% Similarity=0.150 Sum_probs=40.5
Q ss_pred HHHHHHHhcCCCcccHHHHHHH--hCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAA--VGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~--l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
.|.|=.+......++..+|++. +++++.++|+-|..|.+.|.|..+.|
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 3444456777889999999999 99999999999999999999977643
No 202
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=21.00 E-value=2e+02 Score=22.68 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=25.2
Q ss_pred HHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHH
Q 003173 715 HAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINF 750 (842)
Q Consensus 715 QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~ 750 (842)
++.|+.+--+. .|+.++|..+|++...+.+.+..
T Consensus 17 ~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 33444444332 69999999999999999998754
No 203
>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=20.99 E-value=2.3e+02 Score=26.29 Aligned_cols=46 Identities=24% Similarity=0.345 Sum_probs=35.1
Q ss_pred HHHHHHhcCCCcccHHHHHHHh--CCCHHHHHHHHHHHHhCCcccccC
Q 003173 716 AAIIMQFQDQTSWTSKNLAAAV--GVPVDVLSRRINFWISKGIIKESV 761 (842)
Q Consensus 716 AaILllFn~~~~~Tv~EL~~~l--~m~~~~L~r~L~~wv~~gVL~e~~ 761 (842)
+.|+-..-.++-+|..++++.+ .+....+.+.+.-|+++|++..+.
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 3444455566678999999987 899999999999999999998763
No 204
>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=20.93 E-value=1e+02 Score=26.25 Aligned_cols=32 Identities=22% Similarity=0.371 Sum_probs=26.7
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
++...||++.|+....+..+|..+-+.||+..
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 205
>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=20.75 E-value=1.3e+02 Score=31.28 Aligned_cols=34 Identities=9% Similarity=0.163 Sum_probs=31.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHhCCcccccCC
Q 003173 729 TSKNLAAAVGVPVDVLSRRINFWISKGIIKESVG 762 (842)
Q Consensus 729 Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~~g 762 (842)
+-.+|++.+|++..+++++|..|...|++....|
T Consensus 27 sE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 7889999999999999999999999999977665
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=20.53 E-value=1.1e+02 Score=28.39 Aligned_cols=28 Identities=25% Similarity=0.472 Sum_probs=24.8
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHhCCcccc
Q 003173 728 WTSKNLAAAVGVPVDVLSRRINFWISKGIIKE 759 (842)
Q Consensus 728 ~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e 759 (842)
+++.|+|+.+|+++..|+ +|-+.|+|.-
T Consensus 2 ~~i~eva~~~gvs~~tlR----~ye~~Gll~~ 29 (102)
T cd04789 2 YTISELAEKAGISRSTLL----YYEKLGLITG 29 (102)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCC
Confidence 588999999999998877 8999999963
No 207
>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=20.48 E-value=1.8e+02 Score=28.00 Aligned_cols=67 Identities=18% Similarity=0.288 Sum_probs=51.6
Q ss_pred CCCceEEEEEECCceeEEEecHHHHHHHHHhcCCCcccHHHHHHHhCCCHHHHHHHHHHHHhCCccccc
Q 003173 692 NLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNLAAAVGVPVDVLSRRINFWISKGIIKES 760 (842)
Q Consensus 692 ~LG~veLel~f~dr~~~l~VS~~QAaILllFn~~~~~Tv~EL~~~l~m~~~~L~r~L~~wv~~gVL~e~ 760 (842)
.+.-.++-....+..-.-..++-|..|+-+... ..|+.||+..+++|...++=-+.-|+..|.+.-.
T Consensus 22 ~l~l~TlV~a~~~~~~~~~l~pE~~~Il~lC~~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 22 DLDLETLVVATPGAPAPAGLGPEHRAILELCRR--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVR 88 (114)
T ss_pred CCCeEEEEEecCCCCCCCCCCHHHHHHHHHHCC--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEe
Confidence 344444444333322246788999999998887 8899999999999999999999999999988643
Done!