Query 004666
Match_columns 738
No_of_seqs 206 out of 1080
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 03:08:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004666.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004666hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 6E-120 1E-124 1018.4 66.8 718 3-736 5-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 6E-112 1E-116 908.9 64.6 721 4-738 16-773 (773)
3 KOG2167 Cullins [Cell cycle co 100.0 2E-109 4E-114 869.4 48.0 646 62-738 2-661 (661)
4 KOG2284 E3 ubiquitin ligase, C 100.0 4E-109 8E-114 828.3 48.2 680 2-738 5-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 2E-91 4.2E-96 707.3 57.6 714 4-738 9-777 (777)
6 PF00888 Cullin: Cullin family 100.0 1.9E-91 4.1E-96 811.1 60.9 586 12-642 1-588 (588)
7 smart00182 CULLIN Cullin. 100.0 2.1E-32 4.5E-37 255.2 17.8 141 422-563 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 2.5E-25 5.4E-30 239.4 40.7 303 415-727 441-757 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 7E-20 1.5E-24 146.3 1.8 67 666-732 2-68 (68)
10 PF08539 HbrB: HbrB-like; Int 97.0 0.02 4.4E-07 53.7 13.7 137 5-149 2-156 (158)
11 KOG2167 Cullins [Cell cycle co 94.4 1.3 2.9E-05 49.2 15.6 92 5-107 65-159 (661)
12 TIGR01610 phage_O_Nterm phage 92.8 0.34 7.4E-06 41.5 6.5 65 570-642 21-93 (95)
13 PF13412 HTH_24: Winged helix- 91.4 0.42 9E-06 35.0 4.7 42 573-614 2-43 (48)
14 PF02082 Rrf2: Transcriptional 90.9 0.75 1.6E-05 38.2 6.3 59 575-640 11-70 (83)
15 PF09339 HTH_IclR: IclR helix- 90.9 0.4 8.6E-06 35.9 4.2 45 577-623 6-51 (52)
16 PF12802 MarR_2: MarR family; 90.1 0.4 8.6E-06 37.2 3.8 51 572-624 3-55 (62)
17 PF08220 HTH_DeoR: DeoR-like h 87.4 1 2.2E-05 34.4 4.2 46 576-623 2-47 (57)
18 PF01047 MarR: MarR family; I 86.7 0.53 1.1E-05 36.1 2.4 50 572-623 1-50 (59)
19 PF13463 HTH_27: Winged helix 85.9 1.3 2.8E-05 34.9 4.4 50 572-623 1-51 (68)
20 PF12840 HTH_20: Helix-turn-he 85.8 1.1 2.4E-05 34.8 3.7 49 573-623 9-57 (61)
21 PF01022 HTH_5: Bacterial regu 85.7 2 4.4E-05 31.2 4.9 44 575-621 3-46 (47)
22 TIGR02337 HpaR homoprotocatech 85.0 1.7 3.8E-05 38.7 5.2 52 571-624 25-76 (118)
23 COG3682 Predicted transcriptio 83.3 1 2.2E-05 40.1 2.8 62 672-738 6-67 (123)
24 smart00550 Zalpha Z-DNA-bindin 83.0 2.5 5.5E-05 33.6 4.8 47 575-623 7-55 (68)
25 PF09012 FeoC: FeoC like trans 82.7 0.46 9.9E-06 38.0 0.4 44 678-729 6-49 (69)
26 TIGR02698 CopY_TcrY copper tra 82.5 1.1 2.5E-05 40.7 3.0 60 674-738 6-65 (130)
27 PRK11512 DNA-binding transcrip 82.1 2.8 6.2E-05 38.8 5.6 52 571-624 37-88 (144)
28 PF08279 HTH_11: HTH domain; 78.7 4.1 8.9E-05 30.6 4.5 37 578-614 4-41 (55)
29 TIGR01889 Staph_reg_Sar staphy 78.3 5.6 0.00012 34.9 5.9 52 571-624 22-77 (109)
30 PRK11920 rirA iron-responsive 77.6 7.2 0.00016 36.6 6.7 56 577-639 13-68 (153)
31 PF09763 Sec3_C: Exocyst compl 77.3 1.7E+02 0.0036 35.1 19.7 24 336-359 678-701 (701)
32 smart00347 HTH_MARR helix_turn 76.9 4.7 0.0001 34.2 5.0 52 570-623 6-57 (101)
33 PF03965 Penicillinase_R: Peni 76.2 2.4 5.2E-05 37.6 3.0 60 674-738 5-64 (115)
34 PRK10857 DNA-binding transcrip 75.7 8.8 0.00019 36.5 6.8 45 576-622 12-57 (164)
35 smart00346 HTH_ICLR helix_turn 75.2 6.7 0.00014 32.8 5.3 45 577-623 8-53 (91)
36 PF08318 COG4: COG4 transport 74.6 1.3E+02 0.0027 32.3 16.3 164 270-446 15-214 (331)
37 smart00420 HTH_DEOR helix_turn 74.1 6.7 0.00015 28.7 4.6 44 577-622 3-46 (53)
38 PF01978 TrmB: Sugar-specific 73.8 2.8 6.1E-05 33.2 2.5 49 573-623 7-55 (68)
39 PF13404 HTH_AsnC-type: AsnC-t 73.7 5 0.00011 28.5 3.4 36 577-612 6-41 (42)
40 TIGR02010 IscR iron-sulfur clu 72.0 11 0.00024 34.5 6.3 44 577-622 13-57 (135)
41 COG1959 Predicted transcriptio 71.2 11 0.00024 35.3 6.1 59 575-640 11-70 (150)
42 PF04703 FaeA: FaeA-like prote 71.2 9.1 0.0002 29.8 4.6 56 579-638 5-61 (62)
43 COG3355 Predicted transcriptio 71.0 10 0.00023 34.0 5.6 39 584-624 38-76 (126)
44 PF05584 Sulfolobus_pRN: Sulfo 70.3 11 0.00025 30.1 5.0 45 575-623 7-51 (72)
45 PRK13777 transcriptional regul 70.2 9.4 0.0002 37.0 5.6 53 570-624 41-93 (185)
46 PRK15090 DNA-binding transcrip 69.6 10 0.00022 38.9 6.2 46 577-624 17-62 (257)
47 PF04492 Phage_rep_O: Bacterio 69.5 17 0.00036 31.4 6.4 61 571-641 29-97 (100)
48 PHA00738 putative HTH transcri 69.2 11 0.00025 32.6 5.2 68 569-642 7-74 (108)
49 PF05732 RepL: Firmicute plasm 68.3 10 0.00022 36.1 5.3 48 588-644 75-122 (165)
50 PRK03573 transcriptional regul 68.1 10 0.00022 35.0 5.4 53 570-624 27-80 (144)
51 PF13601 HTH_34: Winged helix 65.9 5.4 0.00012 32.9 2.6 43 577-621 3-45 (80)
52 smart00419 HTH_CRP helix_turn_ 64.6 16 0.00035 26.1 4.7 34 588-623 8-41 (48)
53 PRK10870 transcriptional repre 63.8 17 0.00037 35.0 6.0 51 572-624 53-105 (176)
54 TIGR00738 rrf2_super rrf2 fami 63.1 20 0.00042 32.5 6.1 45 576-622 12-57 (132)
55 PF08784 RPA_C: Replication pr 63.0 12 0.00026 32.3 4.4 44 571-614 44-91 (102)
56 PF08280 HTH_Mga: M protein tr 62.8 9.8 0.00021 29.2 3.4 38 576-613 7-44 (59)
57 smart00345 HTH_GNTR helix_turn 62.4 17 0.00037 27.3 4.8 39 583-623 14-53 (60)
58 TIGR01884 cas_HTH CRISPR locus 61.9 13 0.00029 36.7 5.0 52 571-624 140-191 (203)
59 PF13463 HTH_27: Winged helix 61.5 6.4 0.00014 30.8 2.3 52 675-734 6-60 (68)
60 PF01978 TrmB: Sugar-specific 61.1 3.7 8.1E-05 32.5 0.8 53 677-737 13-65 (68)
61 PF08220 HTH_DeoR: DeoR-like h 61.0 3.5 7.6E-05 31.5 0.6 45 676-728 4-48 (57)
62 PRK10141 DNA-binding transcrip 61.0 18 0.00039 32.2 5.2 58 576-639 18-75 (117)
63 cd00090 HTH_ARSR Arsenical Res 59.3 21 0.00046 28.0 5.1 47 573-622 6-52 (78)
64 PF11994 DUF3489: Protein of u 59.1 22 0.00047 28.5 4.7 47 573-619 9-55 (72)
65 TIGR03879 near_KaiC_dom probab 58.9 11 0.00025 30.3 3.1 28 586-613 30-57 (73)
66 COG2345 Predicted transcriptio 58.8 13 0.00029 36.8 4.3 42 578-621 15-56 (218)
67 smart00344 HTH_ASNC helix_turn 58.6 17 0.00038 31.5 4.7 45 575-621 4-48 (108)
68 smart00550 Zalpha Z-DNA-bindin 58.6 8.1 0.00017 30.7 2.3 53 674-734 8-62 (68)
69 TIGR02944 suf_reg_Xantho FeS a 58.3 25 0.00055 31.8 5.9 44 577-622 12-57 (130)
70 smart00762 Cog4 COG4 transport 57.6 2.6E+02 0.0057 29.8 15.5 161 270-443 15-205 (324)
71 PF09756 DDRGK: DDRGK domain; 57.5 3.9 8.4E-05 39.6 0.3 57 674-738 101-157 (188)
72 PRK11569 transcriptional repre 57.3 21 0.00046 37.0 5.9 47 576-624 30-77 (274)
73 COG1414 IclR Transcriptional r 56.0 25 0.00054 35.9 6.0 46 577-624 7-53 (246)
74 PRK10163 DNA-binding transcrip 56.0 25 0.00054 36.5 6.1 46 577-624 28-74 (271)
75 PF10771 DUF2582: Protein of u 55.0 23 0.00049 27.9 4.2 38 577-614 11-48 (65)
76 PF04545 Sigma70_r4: Sigma-70, 54.0 33 0.00072 25.0 4.9 33 577-611 11-43 (50)
77 PF01325 Fe_dep_repress: Iron 53.7 30 0.00065 26.7 4.7 44 579-624 13-56 (60)
78 TIGR02431 pcaR_pcaU beta-ketoa 53.7 29 0.00063 35.4 6.1 44 577-622 12-56 (248)
79 smart00418 HTH_ARSR helix_turn 53.2 27 0.00059 26.3 4.6 36 586-623 8-43 (66)
80 PRK09834 DNA-binding transcrip 53.0 27 0.00058 36.0 5.8 46 577-624 14-60 (263)
81 PRK11014 transcriptional repre 51.2 47 0.001 30.6 6.5 40 583-624 20-59 (141)
82 COG1846 MarR Transcriptional r 50.9 30 0.00066 30.3 5.2 51 572-624 20-70 (126)
83 PF13730 HTH_36: Helix-turn-he 50.7 38 0.00083 25.2 4.9 24 590-613 27-50 (55)
84 smart00418 HTH_ARSR helix_turn 48.9 15 0.00033 27.8 2.5 44 679-731 4-47 (66)
85 PF08221 HTH_9: RNA polymerase 48.9 24 0.00052 27.4 3.5 34 585-620 24-57 (62)
86 PF12324 HTH_15: Helix-turn-he 48.5 45 0.00097 27.2 5.0 39 575-613 25-63 (77)
87 PF02002 TFIIE_alpha: TFIIE al 46.1 17 0.00037 31.6 2.6 44 576-621 15-58 (105)
88 PF05158 RNA_pol_Rpc34: RNA po 45.8 24 0.00053 37.6 4.1 143 571-730 81-260 (327)
89 cd00092 HTH_CRP helix_turn_hel 44.8 38 0.00082 26.1 4.2 35 587-623 24-58 (67)
90 PF08281 Sigma70_r4_2: Sigma-7 44.6 39 0.00085 25.0 4.1 24 587-610 25-48 (54)
91 PRK10434 srlR DNA-bindng trans 43.5 30 0.00065 35.5 4.3 47 575-623 6-52 (256)
92 PF01726 LexA_DNA_bind: LexA D 43.3 38 0.00081 26.7 3.8 55 669-730 7-62 (65)
93 PF09012 FeoC: FeoC like trans 43.2 26 0.00055 27.8 3.0 35 580-614 6-40 (69)
94 PF14394 DUF4423: Domain of un 43.2 63 0.0014 30.9 6.1 54 569-624 19-75 (171)
95 cd07153 Fur_like Ferric uptake 43.1 22 0.00048 31.3 2.9 57 677-736 6-63 (116)
96 PF00325 Crp: Bacterial regula 43.0 36 0.00078 22.7 3.0 26 588-613 2-27 (32)
97 PRK11169 leucine-responsive tr 42.7 39 0.00084 32.0 4.7 48 572-621 12-59 (164)
98 smart00421 HTH_LUXR helix_turn 42.2 53 0.0011 24.0 4.6 39 573-613 5-43 (58)
99 PRK06266 transcription initiat 42.0 37 0.0008 32.7 4.4 44 576-621 24-67 (178)
100 TIGR00373 conserved hypothetic 41.5 47 0.001 31.3 4.9 43 577-621 17-59 (158)
101 TIGR02844 spore_III_D sporulat 41.5 43 0.00093 27.6 4.0 35 575-610 7-41 (80)
102 PF02796 HTH_7: Helix-turn-hel 40.6 36 0.00078 24.4 3.1 30 579-610 14-43 (45)
103 PF13412 HTH_24: Winged helix- 40.2 12 0.00026 27.1 0.6 44 674-725 5-48 (48)
104 cd06170 LuxR_C_like C-terminal 40.1 60 0.0013 23.8 4.6 38 574-613 3-40 (57)
105 COG4189 Predicted transcriptio 39.8 46 0.00099 33.0 4.5 49 573-623 22-70 (308)
106 PRK11179 DNA-binding transcrip 39.7 45 0.00097 31.2 4.5 48 572-621 7-54 (153)
107 PF02186 TFIIE_beta: TFIIE bet 39.6 17 0.00036 28.7 1.3 54 674-738 7-61 (65)
108 cd07377 WHTH_GntR Winged helix 38.8 72 0.0016 24.3 5.0 38 584-623 20-58 (66)
109 PF01853 MOZ_SAS: MOZ/SAS fami 38.4 31 0.00068 33.3 3.2 26 588-613 150-175 (188)
110 TIGR02702 SufR_cyano iron-sulf 37.9 72 0.0016 31.4 5.9 44 578-623 5-48 (203)
111 COG1349 GlpR Transcriptional r 37.8 44 0.00095 34.2 4.5 47 575-623 6-52 (253)
112 COG4190 Predicted transcriptio 37.6 1.1E+02 0.0023 27.7 6.0 67 574-642 64-133 (144)
113 PF00196 GerE: Bacterial regul 37.4 53 0.0011 24.8 3.8 40 572-613 4-43 (58)
114 PF06784 UPF0240: Uncharacteri 35.9 65 0.0014 31.1 5.0 64 545-613 96-161 (179)
115 smart00344 HTH_ASNC helix_turn 35.9 19 0.00041 31.3 1.2 46 673-726 4-49 (108)
116 PF07106 TBPIP: Tat binding pr 35.9 2.5E+02 0.0054 26.6 9.1 59 576-640 3-64 (169)
117 COG1522 Lrp Transcriptional re 35.0 67 0.0015 29.7 5.0 49 572-622 6-54 (154)
118 PRK13509 transcriptional repre 34.7 62 0.0013 33.1 5.0 47 575-623 6-52 (251)
119 PF01726 LexA_DNA_bind: LexA D 34.5 60 0.0013 25.5 3.7 51 572-624 4-60 (65)
120 PLN02999 photosystem II oxygen 33.8 2.8E+02 0.0061 26.5 8.5 62 42-115 126-189 (190)
121 PRK00215 LexA repressor; Valid 33.8 86 0.0019 30.8 5.7 51 572-624 2-58 (205)
122 COG1318 Predicted transcriptio 33.5 62 0.0014 30.6 4.2 50 542-612 36-85 (182)
123 PRK10681 DNA-binding transcrip 32.7 60 0.0013 33.2 4.5 39 575-613 8-46 (252)
124 PF12802 MarR_2: MarR family; 32.7 22 0.00048 27.1 1.0 26 704-729 31-56 (62)
125 TIGR01714 phage_rep_org_N phag 32.1 72 0.0016 28.5 4.2 48 574-623 29-84 (119)
126 KOG3054 Uncharacterized conser 32.1 36 0.00077 33.9 2.5 54 677-738 205-258 (299)
127 PF01047 MarR: MarR family; I 31.7 17 0.00037 27.5 0.3 44 677-728 8-51 (59)
128 PF09681 Phage_rep_org_N: N-te 31.4 61 0.0013 29.1 3.7 38 584-623 49-86 (121)
129 COG1654 BirA Biotin operon rep 31.4 1.5E+02 0.0032 24.4 5.6 41 581-621 12-52 (79)
130 smart00420 HTH_DEOR helix_turn 31.2 24 0.00051 25.6 0.9 43 678-728 6-48 (53)
131 PRK13239 alkylmercury lyase; P 30.5 88 0.0019 30.8 5.0 39 575-613 23-61 (206)
132 cd06171 Sigma70_r4 Sigma70, re 29.9 1.1E+02 0.0024 21.7 4.5 39 573-612 12-50 (55)
133 PRK04424 fatty acid biosynthes 28.9 70 0.0015 31.0 4.0 40 575-614 8-47 (185)
134 PF00165 HTH_AraC: Bacterial r 28.6 90 0.002 21.7 3.5 27 586-612 6-32 (42)
135 PRK10906 DNA-binding transcrip 28.2 81 0.0018 32.3 4.6 47 575-623 6-52 (252)
136 TIGR02404 trehalos_R_Bsub treh 28.2 37 0.00079 34.2 2.0 33 702-735 32-64 (233)
137 cd07977 TFIIE_beta_winged_heli 28.1 38 0.00081 27.5 1.6 58 671-738 8-70 (75)
138 PRK09802 DNA-binding transcrip 28.0 78 0.0017 32.7 4.5 48 574-623 17-64 (269)
139 smart00531 TFIIE Transcription 27.9 70 0.0015 29.7 3.7 30 585-614 12-41 (147)
140 PRK09334 30S ribosomal protein 27.5 48 0.001 27.7 2.2 37 702-738 49-85 (86)
141 TIGR00498 lexA SOS regulatory 27.4 66 0.0014 31.4 3.7 50 572-623 4-59 (199)
142 KOG2747 Histone acetyltransfer 27.3 78 0.0017 34.3 4.3 64 548-613 282-354 (396)
143 PRK04172 pheS phenylalanyl-tRN 27.0 89 0.0019 35.5 5.0 50 571-622 3-52 (489)
144 PLN03238 probable histone acet 26.8 1E+02 0.0022 32.0 4.8 37 576-612 210-247 (290)
145 smart00345 HTH_GNTR helix_turn 26.8 44 0.00095 24.9 1.8 27 703-729 29-55 (60)
146 PF04967 HTH_10: HTH DNA bindi 26.7 1.3E+02 0.0028 22.6 4.2 31 582-612 17-47 (53)
147 PF01638 HxlR: HxlR-like helix 26.5 1.1E+02 0.0024 25.6 4.4 45 576-623 7-52 (90)
148 PF12395 DUF3658: Protein of u 26.1 79 0.0017 27.8 3.5 62 672-736 48-109 (111)
149 PRK11402 DNA-binding transcrip 26.0 42 0.0009 34.0 2.0 33 702-735 41-73 (241)
150 PHA02591 hypothetical protein; 25.9 84 0.0018 25.5 3.1 25 587-611 58-82 (83)
151 TIGR03433 padR_acidobact trans 25.9 90 0.0019 26.8 3.8 53 673-726 5-57 (100)
152 PF13384 HTH_23: Homeodomain-l 25.8 74 0.0016 23.0 2.8 32 579-612 10-41 (50)
153 PF00392 GntR: Bacterial regul 25.7 39 0.00084 26.2 1.3 28 702-729 32-59 (64)
154 COG3355 Predicted transcriptio 25.5 65 0.0014 29.0 2.8 41 681-729 37-77 (126)
155 COG4742 Predicted transcriptio 25.1 1.2E+02 0.0027 31.0 5.0 42 579-623 18-59 (260)
156 PF06163 DUF977: Bacterial pro 24.9 1.3E+02 0.0029 27.0 4.5 48 574-623 12-59 (127)
157 PF06163 DUF977: Bacterial pro 24.8 49 0.0011 29.6 1.9 52 670-729 10-61 (127)
158 PF13542 HTH_Tnp_ISL3: Helix-t 24.6 1.7E+02 0.0037 21.2 4.7 35 575-611 16-50 (52)
159 PF08672 APC2: Anaphase promot 24.6 63 0.0014 25.0 2.2 52 677-728 2-55 (60)
160 TIGR01889 Staph_reg_Sar staphy 24.3 57 0.0012 28.5 2.2 41 683-731 40-82 (109)
161 PRK10411 DNA-binding transcrip 23.9 1.1E+02 0.0023 31.1 4.5 40 575-614 5-44 (240)
162 TIGR02325 C_P_lyase_phnF phosp 23.9 48 0.001 33.4 2.0 33 702-735 40-72 (238)
163 PRK10079 phosphonate metabolis 23.7 49 0.0011 33.5 2.0 48 680-735 28-75 (241)
164 PF03444 HrcA_DNA-bdg: Winged 23.2 2.8E+02 0.0061 22.7 5.7 48 575-624 10-57 (78)
165 PF10007 DUF2250: Uncharacteri 23.2 1.6E+02 0.0034 25.0 4.5 53 570-624 3-55 (92)
166 PRK11050 manganese transport r 23.1 1.6E+02 0.0035 27.4 5.2 43 578-622 41-83 (152)
167 COG1522 Lrp Transcriptional re 22.8 46 0.00099 30.9 1.5 50 671-728 7-56 (154)
168 PHA03103 double-strand RNA-bin 22.7 1.8E+02 0.0039 28.1 5.4 44 578-623 17-60 (183)
169 PRK03902 manganese transport t 22.3 1.5E+02 0.0032 27.2 4.7 42 579-622 13-54 (142)
170 PF04760 IF2_N: Translation in 22.1 60 0.0013 24.2 1.7 23 587-609 2-24 (54)
171 PRK13719 conjugal transfer tra 21.5 1.6E+02 0.0035 29.3 4.9 42 571-614 143-184 (217)
172 PF09114 MotA_activ: Transcrip 21.4 1.5E+02 0.0032 24.9 3.8 47 577-625 19-67 (96)
173 PRK03573 transcriptional regul 21.4 64 0.0014 29.6 2.1 26 703-728 55-80 (144)
174 COG1510 Predicted transcriptio 21.3 1.2E+02 0.0026 28.9 3.7 41 579-622 33-73 (177)
175 PF00392 GntR: Bacterial regul 21.2 1.3E+02 0.0028 23.2 3.5 38 585-624 20-58 (64)
176 PRK14999 histidine utilization 21.1 56 0.0012 33.0 1.8 47 680-735 29-76 (241)
177 COG2188 PhnF Transcriptional r 21.1 57 0.0012 33.0 1.8 35 700-735 37-71 (236)
178 PF02270 TFIIF_beta: Transcrip 20.9 1.3E+02 0.0028 31.3 4.4 57 575-641 217-273 (275)
179 COG1321 TroR Mn-dependent tran 20.8 1.8E+02 0.0038 27.4 4.9 45 578-624 14-58 (154)
180 COG2771 CsgD DNA-binding HTH d 20.7 2.4E+02 0.0051 21.2 5.0 41 571-613 4-44 (65)
181 PF00356 LacI: Bacterial regul 20.5 1.2E+02 0.0026 22.0 2.8 21 590-610 1-21 (46)
182 smart00347 HTH_MARR helix_turn 20.4 78 0.0017 26.4 2.3 47 674-728 12-58 (101)
183 KOG1086 Cytosolic sorting prot 20.2 2.8E+02 0.0061 30.3 6.6 92 8-114 22-121 (594)
184 PF04182 B-block_TFIIIC: B-blo 20.2 1.5E+02 0.0033 23.8 3.8 48 574-623 2-51 (75)
185 TIGR00721 tfx DNA-binding prot 20.2 1.8E+02 0.004 26.7 4.7 39 572-612 7-45 (137)
186 PF09904 HTH_43: Winged helix- 20.0 1.8E+02 0.0039 24.5 4.1 33 581-614 15-47 (90)
187 PRK10434 srlR DNA-bindng trans 20.0 44 0.00095 34.3 0.7 45 675-727 8-52 (256)
188 PRK06474 hypothetical protein; 20.0 2.7E+02 0.0059 26.7 6.2 50 572-623 9-60 (178)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.4e-120 Score=1018.36 Aligned_cols=718 Identities=67% Similarity=1.101 Sum_probs=668.6
Q ss_pred CCCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccc
Q 004666 3 RKTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSL 82 (738)
Q Consensus 3 ~~~~~f~~~W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~~~~~l 82 (738)
+.+.+|+..|+.+++++.++.+..++-....++.-+++.+|+++|++|+++++.+.++.||+++++++.+|+.+.+.+..
T Consensus 5 ~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~ 84 (725)
T KOG2166|consen 5 PKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPAL 84 (725)
T ss_pred ccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999887753333346777899999999999999955555599999999999999998876666
Q ss_pred cccCchHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhcC-CCChHHHHH-HHHHHHHHHH-HHHHHHHHHHHHHHHHH
Q 004666 83 SEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARR-SLPALNEVG-LTCFREQVYD-ALKNKAKDAIIALIDKE 159 (738)
Q Consensus 83 ~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~-~~~~i~~l~-l~~f~~~i~~-~l~~~l~~~ll~~I~~~ 159 (738)
....++.+|..+...|.+|+.++.+++++|.||||+||.++ +..++++++ +.+|+..++. .+.++++++++.+|..+
T Consensus 85 ~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~e 164 (725)
T KOG2166|consen 85 REKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHKE 164 (725)
T ss_pred HhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHhh
Confidence 67778899999999999999999999999999999999976 666777766 8888888887 59999999999999999
Q ss_pred hCCCccCHHHHHHHHHHHHHhcCCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHcccc
Q 004666 160 REGEQIDRALLKNVLDIFVEIGMGQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYL 239 (738)
Q Consensus 160 R~g~~i~~~~l~~~i~~~~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~~E~~r~~~~l 239 (738)
|.|+.||+..|++++++++.+|.+...+|...||++|++.|..||..+++.|+...++++|+.+++.++.+|..|+..|+
T Consensus 165 R~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl 244 (725)
T KOG2166|consen 165 REGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYL 244 (725)
T ss_pred cccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999988999999999999999999999999
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhcCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHHHHHHhh
Q 004666 240 HSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQA 319 (738)
Q Consensus 240 ~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~g~~~ll~~~~~~~L~~ly~L~~~v~~~l~~l~~~~~~~I~~~g~~i~~~~ 319 (738)
+..+.+++...+...++..+++.++++.++||..|+.+++.++|.+||+|++++++|++.+++.++.|++.+|..++...
T Consensus 245 ~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~ 324 (725)
T KOG2166|consen 245 HSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARP 324 (725)
T ss_pred hhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888766
Q ss_pred HHhhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHhhcC
Q 004666 320 EDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKG 399 (738)
Q Consensus 320 ~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~ 399 (738)
.... ..+|+.+++.+++++++|..++..||.++..|.++++.||..|+|.+.. ..+|+||+|||.++|++
T Consensus 325 ~~~~--------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~lkk~ 394 (725)
T KOG2166|consen 325 AETA--------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDILKKG 394 (725)
T ss_pred hhhc--------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHHhccc
Confidence 4432 1478999999999999999999999999999999999999999999863 23799999999999995
Q ss_pred CCCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhHHhHHHHHHHHH
Q 004666 400 GNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLT 479 (738)
Q Consensus 400 ~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~ 479 (738)
..+.++++++..+++++.+|+|+.+||+|+.+|+++||+|||+++|.|++.|+.||.+|+++||.+||.+|++|++|+.
T Consensus 395 -~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~ 473 (725)
T KOG2166|consen 395 -SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLT 473 (725)
T ss_pred -ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHH
Confidence 4677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCCcCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEE
Q 004666 480 LARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNI 559 (738)
Q Consensus 480 ~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i 559 (738)
.|+++...|+++ .+ .....+++|.|.|||.|+||.+++.++.||++|.++++.|..||..+|+||+|.|+|++|.|+|
T Consensus 474 ~s~~l~~~F~~~-~~-~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei 551 (725)
T KOG2166|consen 474 LSRELQTAFADY-AN-YSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEI 551 (725)
T ss_pred HHHHHHHHHHhh-hc-hhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEE
Confidence 999999999987 21 1223579999999999999998877899999999999999999999999999999999999999
Q ss_pred EeeecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEcc
Q 004666 560 NGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 639 (738)
Q Consensus 560 ~~~~~~~~~~l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 639 (738)
.++|++++++|+||++||+|||+||+.+.+|+++|.+.|+++.+++.++|+||++.|.+++.+ |.++. ++++.|.+|.
T Consensus 552 ~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~ 629 (725)
T KOG2166|consen 552 NGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNS 629 (725)
T ss_pred EEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeec
Confidence 999999999999999999999999999999999999999999999999999999888777766 66666 7899999999
Q ss_pred CCCCCCcceeccCCChhhhhhHHHhHHHhhhhhhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhh
Q 004666 640 KFTDRMRRIKIPLPPVDERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLI 719 (738)
Q Consensus 640 ~f~~~~~~i~i~~~~~~e~~~~~~~i~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Li 719 (738)
+|+++.++++++.++..+.+++.+.+++||+..|+||||||||+||.+.|++|+.||.+|++++|.|++.+||+|||.||
T Consensus 630 ~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LI 709 (725)
T KOG2166|consen 630 KFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLI 709 (725)
T ss_pred cccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHH
Confidence 99999999999988888888889999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCCCCCCceee
Q 004666 720 TRDYLERDKENPNMFRY 736 (738)
Q Consensus 720 ekeyi~r~~~d~~~y~Y 736 (738)
|||||+|| +|+++|+|
T Consensus 710 EkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 710 EREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHhcc-CCCCcccC
Confidence 99999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.6e-112 Score=908.94 Aligned_cols=721 Identities=31% Similarity=0.528 Sum_probs=636.8
Q ss_pred CCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhhhccCCCCC------------chHHHHHHHHHHHH
Q 004666 4 KTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHD------------YSQQLYDKYKQAFE 71 (738)
Q Consensus 4 ~~~~f~~~W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~lc~~~~~~~------------~~e~LY~~l~~~l~ 71 (738)
+..||+.+|..+++||++|+.-+.. ++....||++|+.+|++|+++++.- .|..||+++....+
T Consensus 16 ~~~df~~~W~~i~~~I~~I~~~l~~----~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k 91 (773)
T COG5647 16 SEEDFESTWEFIERAIGQIFERLYD----SMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAK 91 (773)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHh----hhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999865543 3556679999999999999985421 37889999999999
Q ss_pred HHHHhcccccccccCchHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhc-----CCCChHHHHHHHHHHHHHHHHHHH
Q 004666 72 EYISSMVLPSLSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIAR-----RSLPALNEVGLTCFREQVYDALKN 146 (738)
Q Consensus 72 ~~l~~~~~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~-----~~~~~i~~l~l~~f~~~i~~~l~~ 146 (738)
+|+.+.- ++.+....+.||..++..|++|..++.+++.+|.||||.|++. .....+.++++..|+-.+|.++++
T Consensus 92 ~~i~~~~-~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~ 170 (773)
T COG5647 92 NYIEEYN-RGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVD 170 (773)
T ss_pred HHHHHhc-ccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhH
Confidence 9998753 3333334578999999999999999999999999999999993 334567789999999999999999
Q ss_pred HHHHHHHHHHHHHhCCCccCHHHHHHHHHHHHHhcC------CchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHH
Q 004666 147 KAKDAIIALIDKEREGEQIDRALLKNVLDIFVEIGM------GQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEY 220 (738)
Q Consensus 147 ~l~~~ll~~I~~~R~g~~i~~~~l~~~i~~~~~l~~------~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~~~~~Y 220 (738)
.+.+.+|..+.+.|.|+.+|+..+..++.|+..++. .++.+|.+.|||.||+.|.+||..++++.+...++.+|
T Consensus 171 ~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~ey 250 (773)
T COG5647 171 SLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEY 250 (773)
T ss_pred HHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHH
Confidence 999999999999999999999999999999999864 34589999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHccccCCCchhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhcCcHHHHHHHHHhhccCCCChHHH
Q 004666 221 MIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPV 300 (738)
Q Consensus 221 l~~v~~~l~~E~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~g~~~ll~~~~~~~L~~ly~L~~~v~~~l~~l 300 (738)
|.++..++++|..++..|++.++..++..+++++||..|.+.|.+.. +|+..+++....+.|+.||+++++++.++.++
T Consensus 251 L~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl 329 (773)
T COG5647 251 LEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQPL 329 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhH
Confidence 99999999999999999999999999999999999999999987654 89999999999999999999999999899999
Q ss_pred HHHHHHHHHHHHHHHHHhhHHhhhhcCCC-----CCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHh
Q 004666 301 ANVFKQHITAEGTVLVQQAEDAATNQGGS-----SGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFC 375 (738)
Q Consensus 301 ~~~~~~~I~~~g~~i~~~~~~~~~~~~~~-----~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~ 375 (738)
.+.|..||+..|.-+ ......+...... .....+..+++.++++++.+..++...|.+|..+.+++++||+.|+
T Consensus 330 ~~~f~~yV~~~g~~~-~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fi 408 (773)
T COG5647 330 QEVFERYVKDEGVLI-NIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFI 408 (773)
T ss_pred HHHHHHHHHhhchhh-hhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHh
Confidence 999999999999221 2111111100000 0124688999999999999999999999999999999999999999
Q ss_pred cCCCC-CCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHH
Q 004666 376 NKAVG-GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERS 454 (738)
Q Consensus 376 n~~~~-~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~ 454 (738)
|.+.+ ...++|+||+|+|.+||++++ +.....++..+..++.||+|+.+||+|+++|+++||||||+++|.+.+.|..
T Consensus 409 n~~~sa~~~~~e~Laky~D~~lkk~~k-~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~ 487 (773)
T COG5647 409 NGNESADSGPSEYLAKYIDGLLKKDGK-QSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELK 487 (773)
T ss_pred ccccccccccHHHHHHHhHHHhhcccc-ccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHH
Confidence 99642 247899999999999998652 2223457778899999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcChhHHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCC-CCCCcCChhHHHHHH
Q 004666 455 ILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYK-SSDLNLPSEMVKCVE 533 (738)
Q Consensus 455 ~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~-~~~~~lP~~l~~~~~ 533 (738)
||++||+.||.+||+|+++||+|+..|+++...|++.- +. ..+.+++.|.||+..+||..+ ...+.+|++|.+..+
T Consensus 488 mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~-~s--~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le 564 (773)
T COG5647 488 MISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSP-QS--YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILE 564 (773)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCc-hh--hccccchhHHHHHHhcCCCCccccccCCChHHHHHHH
Confidence 99999999999999999999999999999999987643 11 235789999999999999655 457999999999999
Q ss_pred HHHHHHhhcCCCceEEeccCCceEEEEeeecCeeEEEE---EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 004666 534 VFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELI---VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 610 (738)
Q Consensus 534 ~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~---~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~ 610 (738)
.|++||..+|+||+|.|.|+||+|+|++.|+.+.+.+. ++++|+.|+++||+++++|+++|.+.|+++..++++.|+
T Consensus 565 ~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~ 644 (773)
T COG5647 565 GFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQ 644 (773)
T ss_pred HHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHH
Confidence 99999999999999999999999999999987754443 567899999999999999999999999999999999999
Q ss_pred HhhhcccceeecCCCCCCCCCCCeEEEccCCCCCCcceeccCCCh----hhhhhHHHhHHHhhhhhhhheeeeccccccc
Q 004666 611 SLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DERKKIVEDVDKDRRYAIDAALVRIMKSRKV 686 (738)
Q Consensus 611 ~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~i~~~r~~~i~A~IVRimK~~k~ 686 (738)
+|+++|..++.+ +++.+++++.|.+|.+|+++..+|+++.+.. ++...+.+.+++||+..+|||||||||+||+
T Consensus 645 sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~ 722 (773)
T COG5647 645 SLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKK 722 (773)
T ss_pred HHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999876555554 4778889999999999999999999987653 3445567889999999999999999999999
Q ss_pred CChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 687 LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 687 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
|.|++|+++|+.+++.||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 723 l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 723 LKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred CcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 99999999999999999999999999999999999999999888 8999997
No 3
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.7e-109 Score=869.38 Aligned_cols=646 Identities=35% Similarity=0.609 Sum_probs=604.2
Q ss_pred HHHHHHHHHHHHHHhcccccccc--cCchHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhc-C-CCChHHHHHHHHHH
Q 004666 62 LYDKYKQAFEEYISSMVLPSLSE--KHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIAR-R-SLPALNEVGLTCFR 137 (738)
Q Consensus 62 LY~~l~~~l~~~l~~~~~~~l~~--~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~-~-~~~~i~~l~l~~f~ 137 (738)
||+.++..+++|+...+. .+.. .+...+|+.+.++|..|...+.+++.+|.||||.|+.. + ..+|+|++|+.+||
T Consensus 2 ly~~l~~~~~~~~~~~~~-q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR 80 (661)
T KOG2167|consen 2 LYKQLRQICEQHIKAQIE-QLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFR 80 (661)
T ss_pred hHHHHHHHHHHHHHHHHh-hCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHH
Confidence 799999999999987653 2322 23457999999999999999999999999999999988 3 46899999999999
Q ss_pred HHHHH----HHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHHHHhcCCchhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 004666 138 EQVYD----ALKNKAKDAIIALIDKEREGEQIDRALLKNVLDIFVEIGMGQMDSYEKDFEEHMLQDTGAYYSRKASNWIL 213 (738)
Q Consensus 138 ~~i~~----~l~~~l~~~ll~~I~~~R~g~~i~~~~l~~~i~~~~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~ 213 (738)
.+++. .+..++.++++..++++|.|+++|++.|++++.|+.++ .+|.+.|++.|++.+.++|.+++.....
T Consensus 81 ~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~-----~iY~esF~~~fls~f~~lY~aE~~d~~Q 155 (661)
T KOG2167|consen 81 AHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDL-----QIYKESFELTFLSLFRELYAAEGQDKRQ 155 (661)
T ss_pred HHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH-----HhhhhhhHHHHHHHHHHHHHHHhcchhh
Confidence 99997 47888999999999999999999999999999999985 6899999999999999999999999999
Q ss_pred cCChhHHHHHHHHHHHHHHHHHccccCCCchhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhcCcHHHHHHHHHhhccC
Q 004666 214 EDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKI 293 (738)
Q Consensus 214 ~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~g~~~ll~~~~~~~L~~ly~L~~~v 293 (738)
+..+++||++++..+.+|.+|+..+++.+|...+..++++.|+..|++.|+.+ |+..+++.++..++.+||.|++++
T Consensus 156 el~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~ 232 (661)
T KOG2167|consen 156 ELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRV 232 (661)
T ss_pred hcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHH
Confidence 99999999999999999999999999999977799999999999999999875 899999999999999999999999
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCC--hHHHHHHHHHH
Q 004666 294 PKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINH--TLFHKALKEAF 371 (738)
Q Consensus 294 ~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~--~~f~~~l~~af 371 (738)
.++...++..|++|++..|.+++.+.+ ....+|+.+++++++.+-++..||..+ ..|..++++||
T Consensus 233 ~~g~l~l~qq~sdylk~~G~KlV~de~-------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~af 299 (661)
T KOG2167|consen 233 QGGQLSLLQQWSDYLKKPGFKLVIDEE-------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAF 299 (661)
T ss_pred hcchHHHHHHHHHHHhcccceeccCch-------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence 888899999999999999999986543 256899999999999999999999988 89999999999
Q ss_pred HHHhcCCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHH
Q 004666 372 EIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDH 451 (738)
Q Consensus 372 ~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~ 451 (738)
+.|+|... .++||+||+|+|..|+.|. +..++++++..++.++.||+|+.+||+|+.+|++.||+|||.++|++.|.
T Consensus 300 e~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvda 376 (661)
T KOG2167|consen 300 ETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDA 376 (661)
T ss_pred HHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcc
Confidence 99999775 5799999999999999875 56678889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcChhHHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCCcCChhHHHH
Q 004666 452 ERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKC 531 (738)
Q Consensus 452 E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~ 531 (738)
|.+|+.+|+.+||..||++|++|++||..|++++..|+++...+.....++ +.+.|+|.++||.+++.++.||++|.++
T Consensus 377 e~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~ 455 (661)
T KOG2167|consen 377 EKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDC 455 (661)
T ss_pred hhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHH
Confidence 999999999999999999999999999999999999999865544333455 9999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCceEEeccCCceEEEEeeecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004666 532 VEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 611 (738)
Q Consensus 532 ~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~ 611 (738)
++.|..||..+|.||+|.|++++|+|++++.|..|+.++.+|++|++||++||+++.+|++||.+.||+...+|.++|++
T Consensus 456 ~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqs 535 (661)
T KOG2167|consen 456 QEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQS 535 (661)
T ss_pred HHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcccceeecCCCCCCCCCCCeEEEccCCCCCCcceeccCCCh----hhhhhHHHhHHHhhhhhhhheeeecccccccC
Q 004666 612 LSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DERKKIVEDVDKDRRYAIDAALVRIMKSRKVL 687 (738)
Q Consensus 612 L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~i~~~r~~~i~A~IVRimK~~k~l 687 (738)
|+|++.++|.+.|.|+.+.+++.|.+|..|+++..+|+|+++.. +|.+++.++|.+||++.||||||||||+||+|
T Consensus 536 l~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l 615 (661)
T KOG2167|consen 536 LACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTL 615 (661)
T ss_pred HhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999998754 56777889999999999999999999999999
Q ss_pred ChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 688 GHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 688 ~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
+|+.|+.++.++++ |+..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 616 ~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 616 SHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred chhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 99999999999997 99888 999999999999999999 45 9999998
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.9e-109 Score=828.33 Aligned_cols=680 Identities=27% Similarity=0.512 Sum_probs=621.8
Q ss_pred CCCCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhccccc
Q 004666 2 DRKTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPS 81 (738)
Q Consensus 2 ~~~~~~f~~~W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~~~~~ 81 (738)
-|++++||++|..|.+.|..|... +.+++.+|..-|+.||.+|.+- |.+-||+||+..+.++++|+++... .
T Consensus 5 kp~vv~fd~~w~~l~~si~~ii~l------~~i~~~~w~~~fsdvy~icvs~-p~pl~erly~e~k~~i~~hvrq~~~-~ 76 (728)
T KOG2284|consen 5 KPKVVEFDKVWVQLRPSIIDIINL------RPITNVQWHHKFSDVYDICVSI-PTPLSERLYNEVKACIQEHVRQKRQ-D 76 (728)
T ss_pred CceeeeHHHHHHHHHHHHHHHHhc------cchhccccccchhhHHHHHHhC-CCchhHHHHHHHHHHHHHHHHHHhh-h
Confidence 478999999999999999887653 3577888999999999999998 6778999999999999999996543 2
Q ss_pred ccccCchHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhcCC------------------CChHHHHHHHHHHHHHHHH
Q 004666 82 LSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARRS------------------LPALNEVGLTCFREQVYDA 143 (738)
Q Consensus 82 l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~------------------~~~i~~l~l~~f~~~i~~~ 143 (738)
.-..+++.+|..|.+.|+.|..+..++..+|.|||+.|++.++ +..|..+|+.+|++.+..+
T Consensus 77 ~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~ 156 (728)
T KOG2284|consen 77 IVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKT 156 (728)
T ss_pred hhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHH
Confidence 2333456699999999999999999999999999999998753 2346678899999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCccC-HHHHHHHHHHHHHhcC-----------------CchhchHHHHHHHHHHHHHHHHH
Q 004666 144 LKNKAKDAIIALIDKEREGEQID-RALLKNVLDIFVEIGM-----------------GQMDSYEKDFEEHMLQDTGAYYS 205 (738)
Q Consensus 144 l~~~l~~~ll~~I~~~R~g~~i~-~~~l~~~i~~~~~l~~-----------------~~~~~Y~~~FE~~~l~~t~~yY~ 205 (738)
+...|+..++..|.++|.|+..+ ...+.++|++|+.+.. -...+|++.||+|||.+|.+||+
T Consensus 157 i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~ 236 (728)
T KOG2284|consen 157 ILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYS 236 (728)
T ss_pred HHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHH
Confidence 99999999999999999999888 6689999999998753 13568999999999999999999
Q ss_pred HHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCchhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhcCcHHHHHH
Q 004666 206 RKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSR 285 (738)
Q Consensus 206 ~~s~~~l~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~g~~~ll~~~~~~~L~~ 285 (738)
++++..+.+.+|++|+.+|..++++|+-||+.||++++..+++-.|++.+|.+|.+.| +..|+.++.+.+..|++.
T Consensus 237 ~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~d~~n 312 (728)
T KOG2284|consen 237 ALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENKDLRN 312 (728)
T ss_pred HHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhhHHH
Confidence 9999999999999999999999999999999999999999999999999999999887 356999999999999999
Q ss_pred HHHhhccCCCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHH
Q 004666 286 MYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHK 365 (738)
Q Consensus 286 ly~L~~~v~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~ 365 (738)
||+|+..+..|+..+.+.|.+||..+|...++...++ +-|..||+.++.+|.+|.+++...|++|..|..
T Consensus 313 my~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~e----------n~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s 382 (728)
T KOG2284|consen 313 MYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTGE----------NVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSS 382 (728)
T ss_pred HHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhccc----------cchHHHHHHHHHHHHHHHHHHHHHhcCchhhhH
Confidence 9999999999999999999999999999888766432 368999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCC---CCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhc
Q 004666 366 ALKEAFEIFCNKAVG---GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLL 442 (738)
Q Consensus 366 ~l~~af~~~~n~~~~---~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL 442 (738)
+++.|+..++|...+ -.+.+|.||+|||.+|+++. +++++.+++.+|+..+.+|+|++|||+|.++|.++||+||+
T Consensus 383 ~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli 461 (728)
T KOG2284|consen 383 GLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLI 461 (728)
T ss_pred HHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHH
Confidence 999999999998764 25789999999999999974 78999999999999999999999999999999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHhhcChhHHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCC
Q 004666 443 FDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKSSDL 522 (738)
Q Consensus 443 ~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~ 522 (738)
.+.|.|.|.|+.||++||+.||++||+++. +.|+..|.+++++|.+.+.+ +
T Consensus 462 ~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~n---------------------------f 512 (728)
T KOG2284|consen 462 ASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIAN---------------------------F 512 (728)
T ss_pred hhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHHh---------------------------c
Confidence 999999999999999999999999999998 99999999999999876532 7
Q ss_pred cCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeeecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCH
Q 004666 523 NLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTH 602 (738)
Q Consensus 523 ~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~ 602 (738)
.+|.+|+...+.|+.||..+|+||+|+|++.++++++++++-++.|--.+.++||++||+||..+.+++.||.+.+|++.
T Consensus 513 ~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~ 592 (728)
T KOG2284|consen 513 HLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSG 592 (728)
T ss_pred cchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccH
Confidence 89999999999999999999999999999999999999999989998899999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCCcceeccCCCh-----hhhhhHHHhHHHhhhhhhhhee
Q 004666 603 DDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV-----DERKKIVEDVDKDRRYAIDAAL 677 (738)
Q Consensus 603 ~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~-----~e~~~~~~~i~~~r~~~i~A~I 677 (738)
+.|.+.+.++.. .++|+.. +..+..+..|++|.+|+++..+.++..|.+ +|.+.+...+.+||++.++|||
T Consensus 593 ~~l~kti~tild--v~~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~ai 668 (728)
T KOG2284|consen 593 DYLLKTIRTILD--VTLLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAI 668 (728)
T ss_pred HHHHHHHHHHHh--ceeeccc--ccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHH
Confidence 999999999974 4677654 345667788999999999999999987654 3445566788999999999999
Q ss_pred eecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 678 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 678 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
|||||+||.+.|+.|+.||+.+.+++|.|++++||+|||.||++-||+|.+.+ +.|.|+|
T Consensus 669 vrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 669 VRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 99999999999999999999999999999999999999999999999999875 9999997
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-91 Score=707.29 Aligned_cols=714 Identities=26% Similarity=0.459 Sum_probs=632.0
Q ss_pred CCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhccccccc
Q 004666 4 KTIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSLS 83 (738)
Q Consensus 4 ~~~~f~~~W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~~~~~l~ 83 (738)
+...|++.|+...|.+-++.+. ++++++.|.++|.+||..|.+. .....++|+.+.+.|.+|+.+...+-.+
T Consensus 9 ~r~qFee~W~~~rpIVlkLLrQ------~sVt~~~WqDLF~~Vh~vclWd--dkGpaKI~d~L~~dI~efi~qAq~rv~s 80 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLRQ------KSVTPAAWQDLFYHVHKVCLWD--DKGPAKIRDILTRDINEFIHQAQKRVRS 80 (777)
T ss_pred chhhhhhhccccchHHHHHHhh------ccCCHHHHHHHHhhheeeeeec--CCCcHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3457999999999999987762 4689999999999999999997 3357789999999999999875433333
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhcCC--------CChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004666 84 EKHDEYMLRELVKRWANHKVMVRWLSRFFHYLDRYFIARRS--------LPALNEVGLTCFREQVYDALKNKAKDAIIAL 155 (738)
Q Consensus 84 ~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~--------~~~i~~l~l~~f~~~i~~~l~~~l~~~ll~~ 155 (738)
...+..+|..|..+|.+|.....++...|.-|+..-..+.+ ..+|..+.+..|.+.||..++++|..+.+.+
T Consensus 81 ~q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmkl 160 (777)
T KOG2285|consen 81 LQTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKL 160 (777)
T ss_pred hccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567899999999999999999999999999987554421 2478999999999999999999999999999
Q ss_pred HHHHhCCCccCHHHHHHHHHHHHHhcC---CchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHH
Q 004666 156 IDKEREGEQIDRALLKNVLDIFVEIGM---GQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKER 232 (738)
Q Consensus 156 I~~~R~g~~i~~~~l~~~i~~~~~l~~---~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~~E~ 232 (738)
+..+|.|+.+|.+.+-++-++|+.+.. +.+.+|++.||..||++|.+||+..+..++++.++.+|++.+..-+++|+
T Consensus 161 VhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe 240 (777)
T KOG2285|consen 161 VHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEE 240 (777)
T ss_pred HHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHH
Confidence 999999999999999999999999875 56889999999999999999999999999999999999999999999999
Q ss_pred HHHccccCC--CchhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHhcCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHH
Q 004666 233 DRVSHYLHS--SSEPKLVEKVQHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITA 310 (738)
Q Consensus 233 ~r~~~~l~~--~t~~kl~~~l~~~LI~~~~~~ll~~~~~g~~~ll~~~~~~~L~~ly~L~~~v~~~l~~l~~~~~~~I~~ 310 (738)
.|+.+||.+ .|..+++..+.+.||.++.+.|+. .|+.|+...+++.|++||+|+.+++.|++++..-+..||+.
T Consensus 241 ~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~s 316 (777)
T KOG2285|consen 241 QRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRS 316 (777)
T ss_pred HHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHh
Confidence 999999976 688899999999999999999985 58899999999999999999999999999999999999999
Q ss_pred HHHHHHHhhHHhhhhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhcCCC-----------
Q 004666 311 EGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAV----------- 379 (738)
Q Consensus 311 ~g~~i~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~----------- 379 (738)
.|..-+....+.+ +.++..||+.|+.++++|..++.++|++||.|..+-+.||..++|...
T Consensus 317 aGLaDM~~aaE~i--------ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~k 388 (777)
T KOG2285|consen 317 AGLADMRNAAENI--------TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKK 388 (777)
T ss_pred hhHHHHHhhhhhc--------cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhc
Confidence 9987665543333 457889999999999999999999999999999999999999999863
Q ss_pred -------CCCCcHHHHHHHHHHHhhcCC-CCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHH
Q 004666 380 -------GGSSSSELLATFCDNILKKGG-NEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDH 451 (738)
Q Consensus 380 -------~~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~ 451 (738)
+..+.||+||.|||.++|+.. +++++.++++.+|++++-+++|+.+||+|..+++.+|++||+...|++.+.
T Consensus 389 grglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEk 468 (777)
T KOG2285|consen 389 GRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEK 468 (777)
T ss_pred CCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhH
Confidence 235789999999999999853 467889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhc--ChhHHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCCcCChhH
Q 004666 452 ERSILTKLKQQCG--GQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKS-SDLNLPSEM 528 (738)
Q Consensus 452 E~~~i~~Lk~~~G--~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~-~~~~lP~~l 528 (738)
|+.|+..|+ +|| .+|++++.+|++|++.|+++++.|+..+...+..++.-.+++.||+.|.|...+. ..+.||.+|
T Consensus 469 EE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~EL 547 (777)
T KOG2285|consen 469 EEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPREL 547 (777)
T ss_pred HHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhH
Confidence 999999998 577 5899999999999999999999999988776555566778999999999997643 458999999
Q ss_pred HHHHHHHHHHHhhcCCCceEEeccCCceEEEEeeecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHHHH
Q 004666 529 VKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLV 606 (738)
Q Consensus 529 ~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLl~fn~~--~~~t~~ei~~~~~~~~~~l~ 606 (738)
++.+-.-++||+++|.||+|.|.|+++.++|++.-+-|.|++.|+++||+||.+||+. +.+|++.+.-.|.+|..+|.
T Consensus 548 ED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELr 627 (777)
T KOG2285|consen 548 EDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELR 627 (777)
T ss_pred HHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHH
Confidence 9999999999999999999999999999999887666899999999999999999974 68999999999999999999
Q ss_pred HHHHHhhh-c--ccceeecCCCC----CCCCCCCeEEEccCCCC-C----CcceeccCCCh----hh--hhhHHHhHHHh
Q 004666 607 RLLHSLSC-A--KYKILLKEPNT----KTISQSDHFEFNSKFTD-R----MRRIKIPLPPV----DE--RKKIVEDVDKD 668 (738)
Q Consensus 607 ~~L~~L~~-~--k~~iL~~~~~~----~~i~~~~~~~~N~~f~~-~----~~~i~i~~~~~----~e--~~~~~~~i~~~ 668 (738)
+.|-||+. + |..||...|+. +.+.++..|.+|.+|.- + .++-+++.++- .| .++..+.+-+-
T Consensus 628 RTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqL 707 (777)
T KOG2285|consen 628 RTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQL 707 (777)
T ss_pred HHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHH
Confidence 99999963 3 57888877642 34667889999999972 1 11223332211 11 12234567788
Q ss_pred hhhhhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 669 RRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 669 r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
|....+-+|++|||.||+++..+|-.+..+.|+..|-|+..+||+.||.|||..|++||.+|-++|+|+|
T Consensus 708 RiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 708 RILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999997
No 6
>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=1.9e-91 Score=811.14 Aligned_cols=586 Identities=43% Similarity=0.772 Sum_probs=524.1
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCchHHH
Q 004666 12 WDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSLSEKHDEYML 91 (738)
Q Consensus 12 W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~~~~~l~~~~~~~~L 91 (738)
|+.|++||+.|+ .+ .+++.+||.+|++||++|..+ +|+.||+.+++.+.+|+... ...+...+++.+|
T Consensus 1 W~~l~~~i~~i~---~~----~~~~~~~~~lY~~vy~l~~~~----~~~~LY~~l~~~i~~~~~~~-~~~l~~~~~~~~l 68 (588)
T PF00888_consen 1 WEILEEAIDQIF---KK----SISKLSYMELYTCVYNLCDNK----YGEQLYDKLKEFISEYLKNI-IESLLSSSDEDLL 68 (588)
T ss_dssp HHHHHHHHHHHH---TT-----GCCSHHHHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHHH-HHHHCTTTTCHHH
T ss_pred ChHHHHHHHHHH---cC----CCChhHHHHHHHHHHhhcCCc----ccHHHHHHHHHHHHHHHHHH-HHHHHhcChhHHH
Confidence 999999999976 22 367788999999999998877 89999999999999999874 4555555778999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhchhhhhhhhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHH
Q 004666 92 RELVKRWANHKVMVRWLSRFFHYLDRYFIARRSLPALNEVGLTCFREQVYDALKNKAKDAIIALIDKEREGEQIDRALLK 171 (738)
Q Consensus 92 ~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~i~~l~l~~f~~~i~~~l~~~l~~~ll~~I~~~R~g~~i~~~~l~ 171 (738)
..|..+|.+|+.++.+|+++|+||||+|+.++ +|++.++.++.++++++++.+|.++|.|+.+|...++
T Consensus 69 ~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~-----------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~ 137 (588)
T PF00888_consen 69 EEYVQEWEKYKKAIKYISDIFSYLDRNYVKRN-----------LFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLK 137 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTT-----------HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhh-----------hHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Confidence 99999999999999999999999999999888 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCchhHHHHHH
Q 004666 172 NVLDIFVEIGMGQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKV 251 (738)
Q Consensus 172 ~~i~~~~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~kl~~~l 251 (738)
++++|++.+| ...+|.+.||++||+.|.+||+.++ +...++.+|+.+|++++++|.+|+..|++++|..++.+.+
T Consensus 138 ~~~~~~~~l~--~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l 212 (588)
T PF00888_consen 138 NVIEMFVELG--SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTL 212 (588)
T ss_dssp HHHHHHHHTT--HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHH
T ss_pred HHHHHHhccc--hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHH
Confidence 9999999998 5789999999999999999999999 5677999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhHHHHHhcCcHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhcCCCCC
Q 004666 252 QHELLVVYATELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSG 331 (738)
Q Consensus 252 ~~~LI~~~~~~ll~~~~~g~~~ll~~~~~~~L~~ly~L~~~v~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~ 331 (738)
.++||.+|.+.| .+|+..|+++++.++|++||+|+++++++++.+++.|++||...|..+++....
T Consensus 213 ~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~---------- 278 (588)
T PF00888_consen 213 EEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK---------- 278 (588)
T ss_dssp HHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------
T ss_pred HHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------
Confidence 999999999988 479999999999999999999999999999999999999999999999976531
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHH
Q 004666 332 AVQEQVLIRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEE 411 (738)
Q Consensus 332 ~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~ 411 (738)
...+..||+.+++++++|+.++.+||++++.|..++++||+.++|.. ...++++||+|||.++++++ .+.++++++.
T Consensus 279 ~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~ 355 (588)
T PF00888_consen 279 SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQ 355 (588)
T ss_dssp GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHH
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHH
Confidence 23678999999999999999999999999999999999999999998 36899999999999999875 5667888999
Q ss_pred HHHHHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhHHhHHHHHHHHHHhHHHHHHHHHH
Q 004666 412 TLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY 491 (738)
Q Consensus 412 ~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~ 491 (738)
.++.++.||+|+++||+|+.+|+++||+|||..++.+.+.|+.+|++|+.+||.+++++|++|++|+..|++++++|++.
T Consensus 356 ~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~ 435 (588)
T PF00888_consen 356 KLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQK 435 (588)
T ss_dssp HHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCC-CCcceEEEEeecCCCCCCCCCC-CcCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeeecCeeEE
Q 004666 492 LSNNQNAH-PGIDLSVTVLTTGFWPSYKSSD-LNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIE 569 (738)
Q Consensus 492 ~~~~~~~~-~~~~~~~~vLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~ 569 (738)
..+.+... ++++|+|.||++++||..+... +.+|++|+.+++.|++||+.+|+||+|.|++++|+|+|++++++++++
T Consensus 436 ~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~ 515 (588)
T PF00888_consen 436 QSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYE 515 (588)
T ss_dssp HHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEE
T ss_pred hhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCcee
Confidence 87655322 2799999999999999988666 999999999999999999999999999999999999999999999999
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 004666 570 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 642 (738)
Q Consensus 570 l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~ 642 (738)
+.||++||+||++||+++++|++||++.||++.++++++|.+|+..+..++.+.++++.+++++.|.+|.+|+
T Consensus 516 l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 516 LTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred EEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 9999999999999999999999999999999999999999999865433333677888999999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2.1e-32 Score=255.19 Aligned_cols=141 Identities=48% Similarity=0.896 Sum_probs=132.4
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhHHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCC
Q 004666 422 YISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPG 501 (738)
Q Consensus 422 ~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~~~~~~~~~~~ 501 (738)
|+++||+|+.+|+++||+|||..++.+.+.|..||++|+.+||.+++++|++|++|+..|++++++|++++.+++ ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999876532 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCCcCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeee
Q 004666 502 IDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKF 563 (738)
Q Consensus 502 ~~~~~~vLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~ 563 (738)
++|+|.|||+++||..+. .++.+|++|+.+++.|++||..+|+||+|.|++++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999998877 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=2.5e-25 Score=239.42 Aligned_cols=303 Identities=24% Similarity=0.322 Sum_probs=239.3
Q ss_pred HHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhHHhHHHHHHHHHHhHHHHHHHHHH--H
Q 004666 415 KVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--L 492 (738)
Q Consensus 415 ~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~D~~~S~~l~~~f~~~--~ 492 (738)
-+..++..+.+|+.|.+.||.+||.||+.....+.+.|..-++.||-.||.+..+.|++|++|+..|+++++.++.. .
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 34567777899999999999999999999999999999999999999999999999999999999999999999874 3
Q ss_pred hcCCCCCCCcceEEEEeecCCCCCCCCCCCcCChhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeeecCeeEEEEE
Q 004666 493 SNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIV 572 (738)
Q Consensus 493 ~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~ 572 (738)
.......+.+.+++.+||+.+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|.|+|++.|++++..++|
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tV 600 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTV 600 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEee
Confidence 22122345788999999999999887778999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCCcceeccC
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPL 652 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~ 652 (738)
|+.||+|+.+|.+.++||++|+++.+|+|.+.+++.|..|.+ .++|..+|. ++++++|++++.=.+..+--.-+.
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iEse~d~~q~~~~~~ 675 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIESEMDFDQAEGTVL 675 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeeccccccccccCCCcc
Confidence 999999999999999999999999999999999999999974 588887653 367889999985443322111111
Q ss_pred CChhh-h--hhHHHhHHHhh--hhhhhheeeecccccccCChhHHHHHHHHHhccCCCCC-------hhHHHHHHHhhhh
Q 004666 653 PPVDE-R--KKIVEDVDKDR--RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPD-------IKAIKKRMEDLIT 720 (738)
Q Consensus 653 ~~~~e-~--~~~~~~i~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~-------~~~ik~~Ie~Lie 720 (738)
...++ . ......+++-+ -..-...||-.+=.-+.|..+-+.+... .|.|. -++++.-+..++.
T Consensus 676 ~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~kV~ 750 (765)
T KOG2165|consen 676 LEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQRKVR 750 (765)
T ss_pred cccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHHHhh
Confidence 11111 1 11111222211 1233447777777779999988887442 45443 4566666666666
Q ss_pred hhhhccC
Q 004666 721 RDYLERD 727 (738)
Q Consensus 721 keyi~r~ 727 (738)
.|-++-.
T Consensus 751 e~kL~f~ 757 (765)
T KOG2165|consen 751 EGKLEFI 757 (765)
T ss_pred ccceEEe
Confidence 6655543
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.77 E-value=7e-20 Score=146.33 Aligned_cols=67 Identities=51% Similarity=0.962 Sum_probs=62.0
Q ss_pred HHhhhhhhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCC
Q 004666 666 DKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPN 732 (738)
Q Consensus 666 ~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~ 732 (738)
+++|...|+|+||||||++|+++|++|+.+|.++++++|.|+..+||++||.||++|||+||++|+|
T Consensus 2 ~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 2 EQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred cchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 5789999999999999999999999999999999998999999999999999999999999999876
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=96.98 E-value=0.02 Score=53.69 Aligned_cols=137 Identities=18% Similarity=0.252 Sum_probs=94.6
Q ss_pred CCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccc
Q 004666 5 TIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVLPSLSE 84 (738)
Q Consensus 5 ~~~f~~~W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~~~~~l~~ 84 (738)
.+..++.|+.++.++-.++ +|+... .+-.+.-++-+.--+.|.++. ....+-+.+++.+..=+.. ....+..
T Consensus 2 ~~~~~~~W~~~~~~vl~lF---~g~~l~-~~iEdlN~lv~~~i~~~~~~~---~~~~~~~dl~elL~tg~~~-L~~~l~~ 73 (158)
T PF08539_consen 2 NMSSDDAWNSLCAKVLPLF---QGERLR-LPIEDLNELVRFHIKLCIQSF---PPSYFLEDLEELLTTGMYI-LENQLNE 73 (158)
T ss_pred CCchhhhHHHHHHHHHHHH---cCCCCC-cCHHHHHHHHHHHHHHhhccc---chHHHHHHHHHHHHHHHHH-HHHHHhh
Confidence 4567899999999987754 576553 665555555555566677662 2334445555555543332 1234455
Q ss_pred cCchHHHHHHHHHHHHHHH-HHHHHHHHhchhhhhhhhc-----------------CCCChHHHHHHHHHHHHHHHHHHH
Q 004666 85 KHDEYMLRELVKRWANHKV-MVRWLSRFFHYLDRYFIAR-----------------RSLPALNEVGLTCFREQVYDALKN 146 (738)
Q Consensus 85 ~~~~~~L~~~~~~W~~~~~-~~~~l~~vf~YLdr~yv~~-----------------~~~~~i~~l~l~~f~~~i~~~l~~ 146 (738)
.+++.+|+.++..|.-|.. -+-++..+|..|++.+-.. ....+|..+++..||+.|+-+..+
T Consensus 74 ~~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvLP~y~ 153 (158)
T PF08539_consen 74 VPDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVLPYYQ 153 (158)
T ss_pred cchhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhhcchH
Confidence 6778999999999999655 5689999999999654322 234789999999999999987666
Q ss_pred HHH
Q 004666 147 KAK 149 (738)
Q Consensus 147 ~l~ 149 (738)
++.
T Consensus 154 ~l~ 156 (158)
T PF08539_consen 154 RLK 156 (158)
T ss_pred hhh
Confidence 653
No 11
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=94.39 E-value=1.3 Score=49.21 Aligned_cols=92 Identities=4% Similarity=-0.007 Sum_probs=54.9
Q ss_pred CCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhhh-hccCCCCCchHHHHHHHHHHHHHHHHhccc--cc
Q 004666 5 TIDLDQGWDYMQKGITKLKRILEGLPESPFSSEEYMMLYTTIYNM-CTQKPPHDYSQQLYDKYKQAFEEYISSMVL--PS 81 (738)
Q Consensus 5 ~~~f~~~W~~l~~ai~~i~~~~~~~~~~~~s~~~~~~lY~~vy~l-c~~~~~~~~~e~LY~~l~~~l~~~l~~~~~--~~ 81 (738)
..+....|....+++.+.+. .++.... ....+..++.. |... .|+.++..+-.-+..++..... ++
T Consensus 65 np~v~siWem~l~LFR~~f~---~~~~~~v----qs~~~N~ll~s~er~r----sgeAvdrslLrsll~MLsd~~iY~es 133 (661)
T KOG2167|consen 65 NPYVLSIWEMGLQLFRAHFS---QEPQPFV----QSKTFNGLLKSIERER----SGEAVDRSLLRSLLKMLSDLQIYKES 133 (661)
T ss_pred CCCcCCHHHhhHHHHHHHhh---ccCCchh----hccchHHHHHHHHHHh----hcchhhHHHHHHHHHHHHHHHhhhhh
Confidence 45778899999999988643 2211111 33455556553 4443 6888886655555556554211 11
Q ss_pred ccccCchHHHHHHHHHHHHHHHHHHH
Q 004666 82 LSEKHDEYMLRELVKRWANHKVMVRW 107 (738)
Q Consensus 82 l~~~~~~~~L~~~~~~W~~~~~~~~~ 107 (738)
......+.|...|..+|.++...+..
T Consensus 134 F~~~fls~f~~lY~aE~~d~~Qel~v 159 (661)
T KOG2167|consen 134 FELTFLSLFRELYAAEGQDKRQELEV 159 (661)
T ss_pred hHHHHHHHHHHHHHHHhcchhhhccc
Confidence 11122356788899999999887653
No 12
>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=92.82 E-value=0.34 Score=41.50 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=51.9
Q ss_pred EEEcHHHHHHHHhhc--------CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCC
Q 004666 570 LIVSTYQAATLLLFN--------TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 641 (738)
Q Consensus 570 l~~s~~Q~~iLl~fn--------~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 641 (738)
..++.-|+.+|+... ....+|-.||++.+|++.+.+.+.|..|. +-++|.+.. ....|++|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~~ 92 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTPL 92 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCCc
Confidence 457788998888665 45689999999999999999999999997 457776542 24679999876
Q ss_pred C
Q 004666 642 T 642 (738)
Q Consensus 642 ~ 642 (738)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 4
No 13
>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=91.41 E-value=0.42 Score=35.02 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=34.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
+..+..||....+++.+|..||++.+|++...+.++|..|..
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456778888888888999999999999999999999999963
No 14
>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=90.90 E-value=0.75 Score=38.22 Aligned_cols=59 Identities=15% Similarity=0.233 Sum_probs=41.3
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 004666 575 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 640 (738)
Q Consensus 575 ~Q~~iLl~fn~~~-~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 640 (738)
+++.+.+..+..+ .+|.++|++.++++...+.+.++.|. +.+++...+ ..++.|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-----G~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-----GRGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-----STTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-----CCCCceeecCC
Confidence 3444555444443 49999999999999999999999997 567876542 13567888764
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=90.88 E-value=0.4 Score=35.88 Aligned_cols=45 Identities=27% Similarity=0.294 Sum_probs=36.4
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 577 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 577 ~~iLl~fn~~~-~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
+.||.+|.+.+ .+|+.||++.+|++...+.+.|..|.. .+++.+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~--~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE--EGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CcCeecC
Confidence 45788888765 589999999999999999999999974 5677653
No 16
>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=90.15 E-value=0.4 Score=37.16 Aligned_cols=51 Identities=20% Similarity=0.337 Sum_probs=42.1
Q ss_pred EcHHHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 572 VSTYQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~--~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+|+.|+.||..+...+. +|..||++.++++...+.+.+..|. +.+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~--~~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLE--KKGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEeC
Confidence 46789999988877766 9999999999999999999999997 357777653
No 17
>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=87.36 E-value=1 Score=34.43 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=38.8
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 576 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 576 Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
|..|+.+.++++.+|++||++.+|++...+++-|..|.. .+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~--~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEK--QGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 456787888889999999999999999999999999974 4566554
No 18
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=86.73 E-value=0.53 Score=36.10 Aligned_cols=50 Identities=18% Similarity=0.357 Sum_probs=42.4
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
+|..|+.+|....+.+++|..+|++.++++...+.+.+..|. +.+++.+.
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEec
Confidence 367899999888888899999999999999999999999997 45777654
No 19
>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=85.94 E-value=1.3 Score=34.91 Aligned_cols=50 Identities=16% Similarity=0.279 Sum_probs=38.3
Q ss_pred EcHHHHHHHHhhc-CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 572 VSTYQAATLLLFN-TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 572 ~s~~Q~~iLl~fn-~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
+|..|..||.... ..+.++..+|++.++++...+-+.|..|.. .+++.+.
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~--~glv~~~ 51 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE--KGLVEKE 51 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH--TTSEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEec
Confidence 3667899998888 778999999999999999999999999974 4777654
No 20
>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=85.78 E-value=1.1 Score=34.75 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=39.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
++.-..||.++...+++|+.||++.+|++...+..+|..|. +.+++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 45566788888667799999999999999999999999996 45777644
No 21
>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=85.72 E-value=2 Score=31.23 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=34.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
...-||.++-+ ++.++.||++.+|++...+.++|..|. +.+++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 34567777766 689999999999999999999999996 345553
No 22
>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=84.96 E-value=1.7 Score=38.69 Aligned_cols=52 Identities=12% Similarity=0.201 Sum_probs=44.9
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 571 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
.++..|+.||..+..++.+|..+|++.+|++...+-+.+..|. +-+++.+.+
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~~ 76 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRLK 76 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEecc
Confidence 3577899999988888899999999999999999999999996 457887654
No 23
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=83.31 E-value=1 Score=40.07 Aligned_cols=62 Identities=21% Similarity=0.302 Sum_probs=52.9
Q ss_pred hhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 672 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 672 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
..++.|++||=.++..+.+|++.++.. .+.++..-|+--|..|..||.|.|..+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 457788999999999999999997765 477899999999999999999999975 46787754
No 24
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=83.03 E-value=2.5 Score=33.60 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=38.0
Q ss_pred HHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 575 YQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~--~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 34567777777665 9999999999999999999999996 34666654
No 25
>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=82.66 E-value=0.46 Score=37.98 Aligned_cols=44 Identities=18% Similarity=0.321 Sum_probs=34.2
Q ss_pred eecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCC
Q 004666 678 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 729 (738)
Q Consensus 678 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 729 (738)
-.+|+.++.++..+|-. +|..+++.+...|+.|+.+|||++.+.
T Consensus 6 ~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 34577788888887765 688999999999999999999998753
No 26
>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=82.53 E-value=1.1 Score=40.71 Aligned_cols=60 Identities=17% Similarity=0.201 Sum_probs=44.9
Q ss_pred hheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 674 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 674 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
+..|++++-..+.++..+++... .....+...-|...|+.|.+||||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l----~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRIL----AEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHH----hhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 34566777667778777766654 33456788899999999999999999864 45788865
No 27
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=82.06 E-value=2.8 Score=38.82 Aligned_cols=52 Identities=17% Similarity=0.161 Sum_probs=44.7
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 571 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
.+|..|+.||......+++|..+|++.+|++...+-+.+..|. +.+++.+.+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 4677899999877667789999999999999999999999997 567887764
No 28
>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=78.69 E-value=4.1 Score=30.58 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=29.0
Q ss_pred HHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 578 ATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 578 ~iLl~f-n~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
.||.++ +..+.+|.++|++.+|++...+.+.|..|..
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344444 6666799999999999999999999998853
No 29
>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=78.26 E-value=5.6 Score=34.91 Aligned_cols=52 Identities=25% Similarity=0.367 Sum_probs=43.1
Q ss_pred EEcHHHHHHHHhhc----CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 571 IVSTYQAATLLLFN----TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn----~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
.+|..|..||.... ..+++|..+|+..++++...+-+.+..|. +.+++.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 45778888887665 55689999999999999999999999997 457887764
No 30
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=77.65 E-value=7.2 Score=36.63 Aligned_cols=56 Identities=11% Similarity=0.076 Sum_probs=41.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEcc
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 639 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 639 (738)
+.+.|..+..+.+|..+|++..|+|...|.+.|..|. +.+++.... | .++.|.++.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~ 68 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGR 68 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecC
Confidence 3444555555678999999999999999999999996 568886542 1 245676655
No 31
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=77.29 E-value=1.7e+02 Score=35.05 Aligned_cols=24 Identities=8% Similarity=0.362 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC
Q 004666 336 QVLIRKIIELHDKYMEYVTNCFIN 359 (738)
Q Consensus 336 ~~~i~~ll~l~~~~~~l~~~~F~~ 359 (738)
..+-+..++.|.++..++..|+.|
T Consensus 678 ~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 678 SAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 445577889999999999999875
No 32
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=76.87 E-value=4.7 Score=34.22 Aligned_cols=52 Identities=21% Similarity=0.261 Sum_probs=44.4
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 570 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 570 l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
+.++..+..||.++...+.+|..+|++.++++...+.++|..|.. .+++.+.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~--~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK--KGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH--CCCeEec
Confidence 457788999998888777899999999999999999999999973 5677654
No 33
>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=76.24 E-value=2.4 Score=37.64 Aligned_cols=60 Identities=10% Similarity=0.197 Sum_probs=43.6
Q ss_pred hheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 674 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 674 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
+..|++++=..+.++..+++..+ .....+....|...+..|.+||||.|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~l----~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEAL----PEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHH----CTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHH----HhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 34556666666677777776644 44466788999999999999999999975 46888864
No 34
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=75.71 E-value=8.8 Score=36.48 Aligned_cols=45 Identities=16% Similarity=0.216 Sum_probs=36.0
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 576 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 576 Q~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
.+.+.+.|+.. ..+|.++|++.+|+|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s 57 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSS 57 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 34444556654 589999999999999999999999997 5678874
No 35
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=75.17 E-value=6.7 Score=32.84 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=37.2
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 577 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 577 ~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
..||..+... +++|..||++.+|++...+.+.|..|.. .+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeec
Confidence 4466677665 6899999999999999999999999963 5788764
No 36
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=74.58 E-value=1.3e+02 Score=32.29 Aligned_cols=164 Identities=12% Similarity=0.229 Sum_probs=88.8
Q ss_pred hHHHHHhcCcHHHHHHHHHhhccC---CCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhcCCCCCCcchHHHHHHHHHHH
Q 004666 270 GCRALLREDKVEDLSRMYRLYHKI---PKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELH 346 (738)
Q Consensus 270 g~~~ll~~~~~~~L~~ly~L~~~v---~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~ 346 (738)
.|..-.+.++.+.+.|.++||--+ +.|++.....+.+.|.....+.++.......+ ...+.-|+..|..++
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~------~~~~~~~~~~lt~LF 88 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSD------SRSPVFYADALTKLF 88 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc------ccccccHHHHHHHHH
Confidence 466777888999999999998655 35677777777777766666655543221100 123344555555555
Q ss_pred HHHH-------HHHHHhcCCChHH--HHHHHHHHHH----HhcCCCCCCCcHH---HHHHHHHHHhhc------------
Q 004666 347 DKYM-------EYVTNCFINHTLF--HKALKEAFEI----FCNKAVGGSSSSE---LLATFCDNILKK------------ 398 (738)
Q Consensus 347 ~~~~-------~l~~~~F~~~~~f--~~~l~~af~~----~~n~~~~~~~~~e---~La~y~d~~l~~------------ 398 (738)
+..- .+|..+|+..... ...|-.-+.. ++..-.....+.+ .+-.|-...+.+
T Consensus 89 e~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 168 (331)
T PF08318_consen 89 EHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSSSRA 168 (331)
T ss_pred HHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhcccccccccccccc
Confidence 5554 4566788866432 1111111111 1111000011111 222333222221
Q ss_pred -----CCCCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhcCCCC
Q 004666 399 -----GGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRS 446 (738)
Q Consensus 399 -----~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~ 446 (738)
+.....+.-+++..|+.+..++.... .|.++++.|.-....
T Consensus 169 ~~~~~~~~~~~d~reld~lL~Eis~i~~~w~-------lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 169 ASSSQSEDEGIDPRELDALLNEISLILQRWS-------LYCRFISRKWNEFSD 214 (331)
T ss_pred ccccccccCCCCHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhcccc
Confidence 00122344578888888888876544 899999999987543
No 37
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=74.15 E-value=6.7 Score=28.69 Aligned_cols=44 Identities=20% Similarity=0.263 Sum_probs=34.6
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
-.|+..+.+...+|..+|++.+|++...+.+.|..|.. .+++.+
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 34555556667899999999999999999999999964 355544
No 38
>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=73.81 E-value=2.8 Score=33.16 Aligned_cols=49 Identities=22% Similarity=0.274 Sum_probs=39.1
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
|-.++-|+..+-..+..|..||++.+|++...+.+.|..|.. .+++.+.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~--~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE--KGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 445666666554667899999999999999999999999974 4677654
No 39
>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=73.70 E-value=5 Score=28.51 Aligned_cols=36 Identities=28% Similarity=0.451 Sum_probs=27.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
..||-.+.+....++.+|++.+|++...+.+.+..|
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 456766777789999999999999999998877654
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=71.98 E-value=11 Score=34.47 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=34.7
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 577 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 577 ~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
+.+.|.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 3444555543 479999999999999999999999997 5678764
No 41
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=71.23 E-value=11 Score=35.28 Aligned_cols=59 Identities=15% Similarity=0.200 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 004666 575 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 640 (738)
Q Consensus 575 ~Q~~iLl~fn~~~-~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 640 (738)
+++.+.|.-+..+ ..|.++|++..|+|+..|.+.+..|. |.+++...+ | .++.|.++..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r-G----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR-G----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec-C----CCCCccCCCC
Confidence 4555555555554 68899999999999999999999996 568886442 1 2456766653
No 42
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=71.19 E-value=9.1 Score=29.80 Aligned_cols=56 Identities=21% Similarity=0.206 Sum_probs=37.4
Q ss_pred HHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEc
Q 004666 579 TLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFN 638 (738)
Q Consensus 579 iLl~fn~-~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N 638 (738)
||-.++. +.+++..||++.+|++.......|..|. +.+.+.+.|.++.- ...|.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG~--~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRGK--STYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSSS--S-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCCc--ceeeeec
Confidence 4555555 6789999999999999999999999996 44566655543221 1346665
No 43
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=71.04 E-value=10 Score=34.00 Aligned_cols=39 Identities=21% Similarity=0.260 Sum_probs=34.0
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 584 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 584 n~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+.+++.|+++|++.++.+...+.++|+.|.. .+++.+..
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Rek 76 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVEREK 76 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeeee
Confidence 3678999999999999999999999999974 57887753
No 44
>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=70.27 E-value=11 Score=30.07 Aligned_cols=45 Identities=18% Similarity=0.319 Sum_probs=34.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.|. ||+..... ..|++||.+.||++.+.|...|..|. +-+++.+.
T Consensus 7 ~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~Rk 51 (72)
T PF05584_consen 7 TQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIERK 51 (72)
T ss_pred HHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 444 44444444 89999999999999999999999996 45777653
No 45
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=70.23 E-value=9.4 Score=37.04 Aligned_cols=53 Identities=13% Similarity=-0.011 Sum_probs=45.0
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 570 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 570 l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+.+|..|+.||.....++++|..+|++.++++...+.+.+..|. +-+++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE--~kGlI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE--ERGYLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH--HCCCEEecC
Confidence 34677899999999888899999999999999999999999996 457887653
No 46
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=69.60 E-value=10 Score=38.94 Aligned_cols=46 Identities=11% Similarity=0.260 Sum_probs=39.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+.||.+|....++|+.||++.+|+|...+.+.|..|.. .+.|.+.+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 46888888877899999999999999999999999974 57787653
No 47
>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=69.53 E-value=17 Score=31.41 Aligned_cols=61 Identities=25% Similarity=0.377 Sum_probs=44.6
Q ss_pred EEcHHHHHHHHhh-------cC-CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCC
Q 004666 571 IVSTYQAATLLLF-------NT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 641 (738)
Q Consensus 571 ~~s~~Q~~iLl~f-------n~-~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 641 (738)
.+|.-|.-|++.. |. .+.+|..++++.||++...+.+++..|. +.++|... +..+-+|.+.
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i 97 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNI 97 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeeccc
Confidence 3455666666553 43 3589999999999999999999999997 56788654 3445566554
No 48
>PHA00738 putative HTH transcription regulator
Probab=69.16 E-value=11 Score=32.60 Aligned_cols=68 Identities=19% Similarity=0.094 Sum_probs=50.2
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCCC
Q 004666 569 ELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 642 (738)
Q Consensus 569 ~l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~ 642 (738)
++...+.=-.||.++.+++++++.+|++.++++.+.+-++|.-|. ..+|+.....|.. -.|++|.+-+
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~----vyY~Ln~~~~ 74 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRT----LYAKIRENSK 74 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCE----EEEEECCCcc
Confidence 344455555677666777789999999999999999999999996 3688876654432 3477777643
No 49
>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=68.28 E-value=10 Score=36.13 Aligned_cols=48 Identities=19% Similarity=0.266 Sum_probs=40.0
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCCCCC
Q 004666 588 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDR 644 (738)
Q Consensus 588 ~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~ 644 (738)
-+|..+|++.+|++...+.+++..|.. .++|.+.. .+.|.+|++|..+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e--~~iI~k~~-------~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEE--KNIIKKIR-------NGAYMINPNFFFK 122 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHh--CCcEEEcc-------CCeEEECcHHhee
Confidence 478899999999999999999999974 57887652 4689999997654
No 50
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=68.15 E-value=10 Score=34.97 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=43.7
Q ss_pred EEEcHHHHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 570 LIVSTYQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 570 l~~s~~Q~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+.+|..|..+|...... +..|..||++.+|++...+.+.+..|. +-+++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le--~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE--EKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH--HCCCEeeec
Confidence 34677898888877654 468999999999999999999999997 457887654
No 51
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=65.91 E-value=5.4 Score=32.87 Aligned_cols=43 Identities=26% Similarity=0.351 Sum_probs=33.2
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
..||.+.+..+.+++.+|.+.+|++...+-++|..|.. .+.+.
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~--~GyV~ 45 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE--AGYVE 45 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEE
Confidence 45666666677899999999999999999999999974 45554
No 52
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=64.57 E-value=16 Score=26.11 Aligned_cols=34 Identities=32% Similarity=0.436 Sum_probs=28.9
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 588 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 588 ~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
++|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 57899999999999999999999996 35777643
No 53
>PRK10870 transcriptional repressor MprA; Provisional
Probab=63.82 E-value=17 Score=34.98 Aligned_cols=51 Identities=14% Similarity=0.217 Sum_probs=42.0
Q ss_pred EcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 572 VSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~--~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+|..|..||..... ..++|..||++.+|++...+.+.+..|. +-+++.+.+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 55678888877754 4579999999999999999999999997 457887764
No 54
>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=63.13 E-value=20 Score=32.49 Aligned_cols=45 Identities=20% Similarity=0.278 Sum_probs=34.4
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 576 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 576 Q~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
++.+.+.-++. ..+|.++|++.+|+|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 44444443433 389999999999999999999999997 4577764
No 55
>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=63.00 E-value=12 Score=32.27 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=36.9
Q ss_pred EEcHHHHHHHHhhcC----CCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 571 IVSTYQAATLLLFNT----SDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~----~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
.++..|-.||-.+.+ .+.+++++|++.++++.++++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 578889999988877 35799999999999999999999999975
No 56
>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=62.79 E-value=9.8 Score=29.20 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=29.5
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 576 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 576 Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
|.-+|-++-+.+.+|++||++.+|++...++.-+.-|.
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 55556444447799999999999999999998887774
No 57
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=62.44 E-value=17 Score=27.27 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=31.8
Q ss_pred hcCCCCc-CHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 583 FNTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 583 fn~~~~~-t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
+..++.+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~--~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEA--EGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4455567 8999999999999999999999974 4677654
No 58
>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=61.86 E-value=13 Score=36.65 Aligned_cols=52 Identities=17% Similarity=0.179 Sum_probs=44.8
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 571 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
.++..|..||..+.+++.++..+|++.+|++...+.++|..|. +.+++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 4677899999999887789999999999999999999999996 457887653
No 59
>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=61.54 E-value=6.4 Score=30.84 Aligned_cols=52 Identities=10% Similarity=0.185 Sum_probs=32.8
Q ss_pred heeeeccc-ccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccC--CCCCCce
Q 004666 675 AALVRIMK-SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD--KENPNMF 734 (738)
Q Consensus 675 A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~--~~d~~~y 734 (738)
..|.+.+. ..+.++..+|.. .+..+...+-+.|+.|+++|||++. +.|....
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 34455555 566666666655 3556778899999999999999665 4444433
No 60
>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=61.07 E-value=3.7 Score=32.45 Aligned_cols=53 Identities=11% Similarity=0.260 Sum_probs=38.1
Q ss_pred eeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeec
Q 004666 677 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 737 (738)
Q Consensus 677 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yi 737 (738)
|-..|-.++.++..+|...+ ..+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 13 vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 13 VYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 33333366667777766533 357788999999999999999998766556554
No 61
>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=61.04 E-value=3.5 Score=31.46 Aligned_cols=45 Identities=13% Similarity=0.343 Sum_probs=39.0
Q ss_pred eeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 676 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 676 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
.|+..++.++.++..+|.+ .|..|..-|.+=+..|-++|.|+|.-
T Consensus 4 ~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 4677788899999988877 47889999999999999999999864
No 62
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=61.03 E-value=18 Score=32.21 Aligned_cols=58 Identities=22% Similarity=0.359 Sum_probs=42.7
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEcc
Q 004666 576 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 639 (738)
Q Consensus 576 Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 639 (738)
-..||.+.-+.++.++.||++.+|++...+-+||.-|. ..+++.....|. .-.|++|.
T Consensus 18 Rl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 18 RLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 33455555455679999999999999999999999996 468887665443 23477765
No 63
>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=59.26 E-value=21 Score=27.97 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=37.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
+..+..|+..+.+.+ ++..||++.+|++...+.+.|..|.. .+++..
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~--~g~i~~ 52 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEE--AGLVES 52 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHH--CCCeEE
Confidence 345777887777665 99999999999999999999999863 356654
No 64
>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=59.06 E-value=22 Score=28.50 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=39.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccce
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKI 619 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~i 619 (738)
.+=|+.++-++...+..|+++|++.||.....+.-+|..+...|.++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl 55 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGL 55 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCc
Confidence 34688899888888899999999999999999999998885434444
No 65
>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=58.89 E-value=11 Score=30.28 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=24.5
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 586 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 586 ~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
.+.+|+.||++.+|++...++..+..+.
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3578999999999999999998887664
No 66
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=58.82 E-value=13 Score=36.83 Aligned_cols=42 Identities=21% Similarity=0.259 Sum_probs=35.2
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 578 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 578 ~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
.||.+.+..+++|.+||++.+|++..-++++|+.|.. -+++.
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~ 56 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVE 56 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--Cccee
Confidence 4666777788999999999999999999999999973 34544
No 67
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=58.57 E-value=17 Score=31.48 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=37.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
....||..+..+...|+.+|++.+|++...+.+.+..|.. .+++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~--~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEE--EGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 3456788888878899999999999999999999999964 46665
No 68
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.57 E-value=8.1 Score=30.69 Aligned_cols=53 Identities=9% Similarity=0.179 Sum_probs=40.2
Q ss_pred hheeeeccccccc--CChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCce
Q 004666 674 DAALVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 734 (738)
Q Consensus 674 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y 734 (738)
+..|...|+.++. ++..+|-.++ ..+...+.+.+..|.++|||.++++.|..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 3456677888776 8877776633 356678999999999999999988665554
No 69
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=58.34 E-value=25 Score=31.78 Aligned_cols=44 Identities=25% Similarity=0.258 Sum_probs=34.5
Q ss_pred HHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 577 AATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 577 ~~iLl~fn~--~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
..+|.++.. .+.+|..||++.+|+|...+.+.|..|. +.+++..
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 344555543 3579999999999999999999999997 4578764
No 70
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=57.60 E-value=2.6e+02 Score=29.75 Aligned_cols=161 Identities=13% Similarity=0.241 Sum_probs=82.6
Q ss_pred hHHHHHhcCcHHHHHHHHHhhccC---CCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhcCCCCCCcchHHHHHHHHHHH
Q 004666 270 GCRALLREDKVEDLSRMYRLYHKI---PKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELH 346 (738)
Q Consensus 270 g~~~ll~~~~~~~L~~ly~L~~~v---~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~ 346 (738)
.|..-+++++.+.+.+.++||-.+ ..|++.....+.+.|......+.+.... ... ++..+.-|+..+..++
T Consensus 15 ~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~---~~~---~~~~~~~~a~~lt~Lf 88 (324)
T smart00762 15 RFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAG---ASD---DTRAAVFYADTLTHLF 88 (324)
T ss_pred HHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhcccc---ccc---cccccchHHHHHHHHH
Confidence 467778889999999999998665 3466666666666555554444332111 000 1122344555555555
Q ss_pred HHH-------HHHHHHhcCCChHH--HHH----HHHHHHHHhcCCCCCCCcHH---HHHHHHHHHhhc-----------C
Q 004666 347 DKY-------MEYVTNCFINHTLF--HKA----LKEAFEIFCNKAVGGSSSSE---LLATFCDNILKK-----------G 399 (738)
Q Consensus 347 ~~~-------~~l~~~~F~~~~~f--~~~----l~~af~~~~n~~~~~~~~~e---~La~y~d~~l~~-----------~ 399 (738)
+.. ..+|..+|+.+... ... .+.-...++..-....++.+ .+..|....+.. +
T Consensus 89 e~ia~ii~~h~~~I~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 168 (324)
T smart00762 89 ENVATIIEQHQPVIEKYYGPDGMLYVITKLQKEADLQGGIILDTFMDERRIDRLISDINSYNHAQLHAGASNDARASSNG 168 (324)
T ss_pred HHHHHHHHhccHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhcccccccccccccccccc
Confidence 544 44667788755322 111 11111111111000011111 122222211111 0
Q ss_pred CCCCCChHHHHHHHHHHhhhhccccChhHHHHHHHHHHHHHhcC
Q 004666 400 GNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLF 443 (738)
Q Consensus 400 ~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~ 443 (738)
....++..+++..|+.+..+.+... .|.+++++|.-.
T Consensus 169 ~~~~~d~revd~lL~Eis~i~~~~~-------lY~rFi~~k~~~ 205 (324)
T smart00762 169 EDEGLDPRELDAILEEISQILSRWE-------LYCRFISRKINE 205 (324)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHhHH-------HHHHHHHHHHhh
Confidence 1123456688888998888876554 899999999774
No 71
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=57.47 E-value=3.9 Score=39.60 Aligned_cols=57 Identities=18% Similarity=0.322 Sum_probs=39.7
Q ss_pred hheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 674 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 674 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
-...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.---+|++.|+||.
T Consensus 101 L~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 334457889999999888765 588899999999999999999888778899999984
No 72
>PRK11569 transcriptional repressor IclR; Provisional
Probab=57.27 E-value=21 Score=37.01 Aligned_cols=47 Identities=17% Similarity=0.173 Sum_probs=39.0
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 576 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 576 Q~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
-+.||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 34578889874 4799999999999999999999999974 57887643
No 73
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=55.98 E-value=25 Score=35.86 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=38.7
Q ss_pred HHHHHhhcCCCC-cCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 577 AATLLLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 577 ~~iLl~fn~~~~-~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+.||.+|..... +++.||++.+|+|...+.+.|..|. ..+++.+.+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 457888887543 7899999999999999999999997 468888765
No 74
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=55.98 E-value=25 Score=36.45 Aligned_cols=46 Identities=26% Similarity=0.326 Sum_probs=38.7
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 577 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 577 ~~iLl~fn~~-~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
..||.+|... ..+|+.||++.+|+|...+-+.|.+|.. .+.|.+.+
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~ 74 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS 74 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 4688899765 4799999999999999999999999974 57786653
No 75
>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=55.05 E-value=23 Score=27.90 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=32.7
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
..|--+.++...+|+.+|++.+|++.+++..+|--|+.
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 45667788888999999999999999999999999875
No 76
>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=54.05 E-value=33 Score=25.01 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=24.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 611 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~ 611 (738)
.+|-+.| ..++|++||++.+|++...+.+....
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3445566 45789999999999999988765543
No 77
>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=53.69 E-value=30 Score=26.70 Aligned_cols=44 Identities=16% Similarity=0.233 Sum_probs=34.0
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 579 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 579 iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
|..+-.+...++..+|++.+|++...+...+..|.. .+++...+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~--~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE--KGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH--CCCEEecC
Confidence 444445778999999999999999999999999963 46776543
No 78
>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=53.65 E-value=29 Score=35.39 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=37.2
Q ss_pred HHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 577 AATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 577 ~~iLl~fn~-~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
+.||.+|.. ..++|+.||++.+|+|...+-+.|..|.. .+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 457888986 45899999999999999999999999974 467764
No 79
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=53.24 E-value=27 Score=26.34 Aligned_cols=36 Identities=17% Similarity=0.216 Sum_probs=30.1
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 586 SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 586 ~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.++.|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeeee
Confidence 56789999999999999999999999973 4666543
No 80
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=52.96 E-value=27 Score=36.00 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=38.2
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 577 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 577 ~~iLl~fn~~~-~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+.||.+|.+.. .+|..||++.+|++...+.+.|..|. ..++|.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 45778887654 59999999999999999999999997 357887654
No 81
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=51.23 E-value=47 Score=30.56 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=32.8
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 583 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 583 fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+..+..+|..+|++.+|+|...+.+.|..|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 3444578999999999999999999999996 467886543
No 82
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=50.93 E-value=30 Score=30.27 Aligned_cols=51 Identities=20% Similarity=0.303 Sum_probs=42.9
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+++.|+.+|......++.+..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le--~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLE--DKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeecC
Confidence 678899999888877766669999999999999999999997 457777653
No 83
>PF13730 HTH_36: Helix-turn-helix domain
Probab=50.69 E-value=38 Score=25.16 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=22.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 590 SYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 590 t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
|.+.|++.+|++...+.+++..|.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 899999999999999999999986
No 84
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=48.90 E-value=15 Score=27.84 Aligned_cols=44 Identities=11% Similarity=0.191 Sum_probs=31.3
Q ss_pred ecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCC
Q 004666 679 RIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENP 731 (738)
Q Consensus 679 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~ 731 (738)
+.+. .+.++..++... +..+...+.+.|+.|.++|++.+..+.+
T Consensus 4 ~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 4 KLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 3444 556676665543 3357788999999999999999876433
No 85
>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=48.90 E-value=24 Score=27.43 Aligned_cols=34 Identities=21% Similarity=0.319 Sum_probs=26.2
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccee
Q 004666 585 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 620 (738)
Q Consensus 585 ~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL 620 (738)
..+..|+.+|.+.|++|.+.++.+|-.|.. .+++
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ--h~~v 57 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQ--HNLV 57 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHH--TTSE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCe
Confidence 345899999999999999999999999874 4554
No 86
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=48.54 E-value=45 Score=27.15 Aligned_cols=39 Identities=10% Similarity=0.208 Sum_probs=28.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
+.-.+|-+.-.+.++|..+|+..+|.+.+++...|..+.
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 344567777888999999999999999999999998774
No 87
>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=46.07 E-value=17 Score=31.56 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=30.4
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 576 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 576 Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
.+.|+..+..++.++-++|+..+|++..++.+.|..|.. .+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 455666666667899999999999999999999999974 35553
No 88
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=45.81 E-value=24 Score=37.59 Aligned_cols=143 Identities=13% Similarity=0.155 Sum_probs=39.1
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCCCCCCcce
Q 004666 571 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRI 648 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~--~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i 648 (738)
.++..+..|.-+..+ ..++-..+|...||++...+.++|..|.. | +++.... +.+++++|+
T Consensus 81 ~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~-k-~lIK~vk---------------sv~~~~rK~ 143 (327)
T PF05158_consen 81 GLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES-K-KLIKSVK---------------SVKNPNRKV 143 (327)
T ss_dssp SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH-T-TSEEEE-----------------SS-SS--E
T ss_pred CCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh-C-CCEEEec---------------CcCCCCeEE
Confidence 456667777766654 45788999999999999999999999975 2 4554221 222334444
Q ss_pred eccCCC--hhhhhh----HHHhHHHhhhhhhhheeeeccccccc-----------------------------CChhHHH
Q 004666 649 KIPLPP--VDERKK----IVEDVDKDRRYAIDAALVRIMKSRKV-----------------------------LGHQQLV 693 (738)
Q Consensus 649 ~i~~~~--~~e~~~----~~~~i~~~r~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 693 (738)
.+...- ..|-.. +..+.+.+=...+...|.+.+.++.. .+.+++.
T Consensus 144 Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~ 223 (327)
T PF05158_consen 144 YMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIA 223 (327)
T ss_dssp EEESSS--------------------------------------------------------------------------
T ss_pred EEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHH
Confidence 332110 000000 11223333334445555555555444 4555555
Q ss_pred HHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCC
Q 004666 694 SECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 730 (738)
Q Consensus 694 ~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d 730 (738)
..+.+.=-..-..+.++|...|+-||=.|-|++-...
T Consensus 224 ~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 224 EFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp -------------------------------------
T ss_pred HHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 5554431113456889999999999999988887643
No 89
>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=44.79 E-value=38 Score=26.14 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=30.3
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 587 DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 587 ~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
..+|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~--~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE--EGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 4799999999999999999999999973 4777654
No 90
>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=44.55 E-value=39 Score=24.98 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=17.5
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHH
Q 004666 587 DRLSYSEIMTQLNLTHDDLVRLLH 610 (738)
Q Consensus 587 ~~~t~~ei~~~~~~~~~~l~~~L~ 610 (738)
+++|+.||++.+|++...++..+.
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 468999999999999999887664
No 91
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.55 E-value=30 Score=35.53 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=40.5
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
-|..|+-+.++++.+++.||++.+|++...+++-|..|. +.++|.+.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEE
Confidence 467889999999999999999999999999999999996 34666554
No 92
>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=43.30 E-value=38 Score=26.66 Aligned_cols=55 Identities=13% Similarity=0.298 Sum_probs=33.2
Q ss_pred hhhhhhheeeecccccc-cCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCC
Q 004666 669 RRYAIDAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 730 (738)
Q Consensus 669 r~~~i~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d 730 (738)
|+..|=.+|...+..++ .-+..||.. .+. +. |..-+...|+.|.++|||+|++.-
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~----~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAE----ALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHH----HHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHH----HhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 44444455555555444 334444433 332 32 577788999999999999999753
No 93
>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=43.19 E-value=26 Score=27.81 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=27.3
Q ss_pred HHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 580 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 580 Ll~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
.-...+++.+|++||+..++++.+.+...|..|..
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33445677899999999999999999999999974
No 94
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=43.15 E-value=63 Score=30.93 Aligned_cols=54 Identities=20% Similarity=0.181 Sum_probs=40.5
Q ss_pred EEEEcHHHHHHHHhhcCCCCc-CHHHHHHHh--CCCHHHHHHHHHHhhhcccceeecCC
Q 004666 569 ELIVSTYQAATLLLFNTSDRL-SYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 569 ~l~~s~~Q~~iLl~fn~~~~~-t~~ei~~~~--~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
++--+.+..+|.-+..-.+.- +.++|++.+ +++.++++.+|..|. +.++|.+..
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 333445566666655544433 899999999 999999999999997 678998764
No 95
>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=43.13 E-value=22 Score=31.26 Aligned_cols=57 Identities=9% Similarity=0.108 Sum_probs=41.9
Q ss_pred eeecccc-cccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceee
Q 004666 677 LVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 736 (738)
Q Consensus 677 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Y 736 (738)
|..+|.. .+.++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4444544 56799999999887642 457888999999999999999987543333444
No 96
>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=43.05 E-value=36 Score=22.66 Aligned_cols=26 Identities=27% Similarity=0.482 Sum_probs=20.8
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 588 RLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 588 ~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
++|-+||++.+|++.+.+-+.|..|.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36889999999999999999998885
No 97
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=42.73 E-value=39 Score=32.05 Aligned_cols=48 Identities=13% Similarity=0.171 Sum_probs=40.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
+.-.-..||-.+.++...|+.+|++.+|++...+.+.++.|.. .+++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~--~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER--QGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeE
Confidence 3456677888899999999999999999999999999999963 45664
No 98
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.20 E-value=53 Score=24.02 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=29.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
|.-+..++.++. .+++..+|++.+|++...+...+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555565553 357999999999999999988887663
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.04 E-value=37 Score=32.73 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=36.0
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 576 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 576 Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
...||.++-.++.+|-++|+..+|++...++++|..|.. -+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e--~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYD--ARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeE
Confidence 445666666667899999999999999999999999974 35665
No 100
>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=41.52 E-value=47 Score=31.34 Aligned_cols=43 Identities=14% Similarity=0.163 Sum_probs=34.4
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 577 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
..|+..+=.++.+|-+||+..+|++..++++.|..|.. .+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 44555444556899999999999999999999999974 46664
No 101
>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=41.46 E-value=43 Score=27.59 Aligned_cols=35 Identities=3% Similarity=-0.031 Sum_probs=30.5
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 610 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~ 610 (738)
-++.|+-+..+ +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988664
No 102
>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=40.55 E-value=36 Score=24.38 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=21.0
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 004666 579 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 610 (738)
Q Consensus 579 iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~ 610 (738)
|+-++.++ +|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 44455554 8999999999999999887664
No 103
>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=40.25 E-value=12 Score=27.09 Aligned_cols=44 Identities=7% Similarity=0.247 Sum_probs=32.5
Q ss_pred hheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhc
Q 004666 674 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLE 725 (738)
Q Consensus 674 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~ 725 (738)
+-.|+..+.....++..+|-..+ ..+.+.+.+.|..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 34456667777788888777643 357888999999999999985
No 104
>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=40.14 E-value=60 Score=23.78 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=27.9
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 574 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 574 ~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
..|..++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 3 ~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 3 PREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444554442 468999999999999999888877653
No 105
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=39.75 E-value=46 Score=33.02 Aligned_cols=49 Identities=24% Similarity=0.318 Sum_probs=41.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
|..-..||-++...+++.+.||++.+|+|...+-.+++.|. +.+++..+
T Consensus 22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le--~aGlirT~ 70 (308)
T COG4189 22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLE--KAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHH--hcCceeee
Confidence 44455688888888899999999999999999999999996 56787643
No 106
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=39.69 E-value=45 Score=31.17 Aligned_cols=48 Identities=13% Similarity=0.225 Sum_probs=40.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
++..--.||..+..+...|+.+|++.+|++...+.+.+..|.. .+++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~--~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ--AGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 4556777888888889999999999999999999999999974 35664
No 107
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=39.57 E-value=17 Score=28.67 Aligned_cols=54 Identities=24% Similarity=0.233 Sum_probs=32.4
Q ss_pred hheeeecccccc-cCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 674 DAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 674 ~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
=|.||..||++. .++.+||..++. +..+ ++.++.|-+.+=|+-|++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 467888999974 588888877553 3333 234566668889999974 47999976
No 108
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=38.76 E-value=72 Score=24.27 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=29.6
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 584 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 584 n~~~~~-t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.....+ |..+|++.+|++...+.++|..|.. .++|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 333344 4999999999999999999999974 4677643
No 109
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=38.44 E-value=31 Score=33.29 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=22.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 588 RLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 588 ~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
.+|+++|++.||+..+++..+|+.|-
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 69999999999999999999999883
No 110
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=37.95 E-value=72 Score=31.38 Aligned_cols=44 Identities=14% Similarity=0.171 Sum_probs=35.1
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 578 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 578 ~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.||......+++|..+|++.+|++...+.++|..|.. .+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~--~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLET--EGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEe
Confidence 3554444556799999999999999999999999974 4777654
No 111
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=37.83 E-value=44 Score=34.25 Aligned_cols=47 Identities=19% Similarity=0.287 Sum_probs=40.5
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
-|-.|+-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 356788899999999999999999999999999999996 34666664
No 112
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=37.56 E-value=1.1e+02 Score=27.73 Aligned_cols=67 Identities=15% Similarity=0.214 Sum_probs=48.2
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCC---CeEEEccCCC
Q 004666 574 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQS---DHFEFNSKFT 642 (738)
Q Consensus 574 ~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~---~~~~~N~~f~ 642 (738)
+--...|-+..+.+..|+.|+++.+|-+.+.+-+.|..|. .++++..+.+|+.-.+. +.+.++-.|.
T Consensus 64 p~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 64 PRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred hhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 3344466677888899999999999999999999999997 47888776544433222 3344555554
No 113
>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=37.39 E-value=53 Score=24.82 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=31.8
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
.|.-+..||.++.. +.+..+|+..+|++...+..++..+.
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 35567778877765 57899999999999999999988885
No 114
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=35.92 E-value=65 Score=31.08 Aligned_cols=64 Identities=16% Similarity=0.179 Sum_probs=48.2
Q ss_pred CceEEeccCCceEEEEeeecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 545 HRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 545 ~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLl~fn~~--~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
.|.-.|.+..|..+++- ...|. ||+.||.-|+.-... ..||.+-||+..+++.++++..|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~-vPkGk----ltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEK-VPKGK----LTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCccc-CCCCc----eeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 34456788888888764 33343 567899888754433 479999999999999999998888774
No 115
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=35.89 E-value=19 Score=31.28 Aligned_cols=46 Identities=11% Similarity=0.223 Sum_probs=38.0
Q ss_pred hhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcc
Q 004666 673 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 726 (738)
Q Consensus 673 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r 726 (738)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|+|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeec
Confidence 45667788888888888887774 45688899999999999999985
No 116
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=35.87 E-value=2.5e+02 Score=26.63 Aligned_cols=59 Identities=22% Similarity=0.241 Sum_probs=42.5
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHh--CCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccC
Q 004666 576 QAATLLLFNTS-DRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 640 (738)
Q Consensus 576 Q~~iLl~fn~~-~~~t~~ei~~~~--~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 640 (738)
...|+-.+... .++|..+|...+ +++...+.++|..|+. +-+|..+. +...-+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~-~g~i~~K~-----~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVE-EGKIVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHh-CCCeeeee-----ecceEEEeeCcc
Confidence 35677777654 599999999998 5889999999999985 33555443 223456777754
No 117
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=35.04 E-value=67 Score=29.72 Aligned_cols=49 Identities=16% Similarity=0.318 Sum_probs=40.9
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
+.-.-.-||-.++++...++.+|++.+|++...+.+.+..|. +.+++..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCceee
Confidence 344567788888888899999999999999999999999996 4567754
No 118
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=34.71 E-value=62 Score=33.11 Aligned_cols=47 Identities=15% Similarity=0.129 Sum_probs=39.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
-|..|+..+++++.+++.||++.+|++...+++-|..|.. .+++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~--~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE--SGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEe
Confidence 4667888899999999999999999999999999999863 4566554
No 119
>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=34.54 E-value=60 Score=25.50 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=34.8
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHHHhhhcccceeecCC
Q 004666 572 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~-----~~~~t~~ei~~~~~~~-~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+|.-|.-||...-+ +-+-|+.||++.+|+. ...+..+|..|. +-+.|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCC
Confidence 35567777655432 2366999999999997 899999999997 347777654
No 120
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=33.84 E-value=2.8e+02 Score=26.52 Aligned_cols=62 Identities=11% Similarity=0.121 Sum_probs=35.7
Q ss_pred HHHHHhhhhccCCCCCc--hHHHHHHHHHHHHHHHHhcccccccccCchHHHHHHHHHHHHHHHHHHHHHHHhchh
Q 004666 42 LYTTIYNMCTQKPPHDY--SQQLYDKYKQAFEEYISSMVLPSLSEKHDEYMLRELVKRWANHKVMVRWLSRFFHYL 115 (738)
Q Consensus 42 lY~~vy~lc~~~~~~~~--~e~LY~~l~~~l~~~l~~~~~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YL 115 (738)
|+..+|++...+|.... -..||++|-+-+++ +...+ =.+..-+.|..|..-+.-|++|+.+|
T Consensus 126 LryDL~tiIsskP~~eK~~L~~LankLFdnvt~-LDyAA-----------R~K~~~eae~yY~~Tv~slddVl~~l 189 (190)
T PLN02999 126 LSQDLTNAMNILPESRRNDYVQAANELVENMSE-LDYYV-----------RTPKVYESYLYYEKTLKSIDNVVELL 189 (190)
T ss_pred HHHHHHHHHhcCCHhhhHHHHHHHHHHhhhHHH-HHHHH-----------hcCChHHHHHHHHHHHHHHHHHHHHh
Confidence 66777777777632111 12355544443332 11111 11224568999999999999999886
No 121
>PRK00215 LexA repressor; Validated
Probab=33.77 E-value=86 Score=30.79 Aligned_cols=51 Identities=20% Similarity=0.227 Sum_probs=39.5
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCC-CHHHHHHHHHHhhhcccceeecCC
Q 004666 572 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNL-THDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~-----~~~~t~~ei~~~~~~-~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
++.-|..||..+.+ ....|..||++.+|+ +...+.+.|..|.. .+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~--~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALER--KGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CCCEEeCC
Confidence 35668888866542 346899999999999 99999999999973 46776654
No 122
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=33.49 E-value=62 Score=30.57 Aligned_cols=50 Identities=30% Similarity=0.343 Sum_probs=37.3
Q ss_pred cCCCceEEeccCCceEEEEeeecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 542 KTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 542 ~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
+++.++|+|.++|- -|+-.+.- +....|+++|+..+|.++..++++|..=
T Consensus 36 ~~~~~~lTWvdSLa--------------------vAAga~ar-ekag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 36 KDPYERLTWVDSLA--------------------VAAGALAR-EKAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred hCcccccchhhHHH--------------------HHHHHHHH-HHccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 56899999987543 22222223 4458999999999999999999988754
No 123
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=32.75 E-value=60 Score=33.20 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=36.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
-|..|+.+.+.++.+++.||++.+|+++..++|-|..|.
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 577899999999999999999999999999999999885
No 124
>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=32.73 E-value=22 Score=27.12 Aligned_cols=26 Identities=12% Similarity=0.332 Sum_probs=20.7
Q ss_pred CCCChhHHHHHHHhhhhhhhhccCCC
Q 004666 704 FKPDIKAIKKRMEDLITRDYLERDKE 729 (738)
Q Consensus 704 F~~~~~~ik~~Ie~Liekeyi~r~~~ 729 (738)
+..+...+.+.|..|.++|||+|..+
T Consensus 31 l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 31 LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 33577889999999999999999754
No 125
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=32.11 E-value=72 Score=28.49 Aligned_cols=48 Identities=19% Similarity=0.221 Sum_probs=37.4
Q ss_pred HHHHHHHHhhcCC--------CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 574 TYQAATLLLFNTS--------DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 574 ~~Q~~iLl~fn~~--------~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.+.-..|+..|.. -+.+.++||..++-+.+.++.+|..|. +++++...
T Consensus 29 I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 29 IWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 4555555555543 479999999999999999999999996 57787643
No 126
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.07 E-value=36 Score=33.86 Aligned_cols=54 Identities=22% Similarity=0.379 Sum_probs=43.7
Q ss_pred eeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 677 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 677 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
-|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.---+|+..|+||.
T Consensus 205 Fv~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 345567788888777765 466677777789999999999998889999999984
No 127
>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=31.68 E-value=17 Score=27.48 Aligned_cols=44 Identities=14% Similarity=0.323 Sum_probs=30.4
Q ss_pred eeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 677 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 677 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
+..++-..+.++..+|-. .+..+...+-+.+..|.++|||+|..
T Consensus 8 iL~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 8 ILRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 334444555566665544 34468888999999999999999864
No 128
>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=31.41 E-value=61 Score=29.06 Aligned_cols=38 Identities=8% Similarity=0.065 Sum_probs=32.0
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 584 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 584 n~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
+..-++|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344589999999999999999999999996 57787653
No 129
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=31.35 E-value=1.5e+02 Score=24.44 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=31.8
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceee
Q 004666 581 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 621 (738)
Q Consensus 581 l~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~ 621 (738)
+..++...+|=++|++.+|++...+-++++.|-...+.|..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 34456668999999999999999999999999643344443
No 130
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=31.19 E-value=24 Score=25.63 Aligned_cols=43 Identities=12% Similarity=0.234 Sum_probs=32.0
Q ss_pred eecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 678 VRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 678 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
.+.+.+++.++..+|... |..+...+.+.|..|.++|+|.+..
T Consensus 6 l~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 6 LELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEee
Confidence 334444556777666663 4568888999999999999999865
No 131
>PRK13239 alkylmercury lyase; Provisional
Probab=30.55 E-value=88 Score=30.83 Aligned_cols=39 Identities=13% Similarity=0.242 Sum_probs=34.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
+...||-++-++...|+.+|+..+|.+.+.+.+.|..|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 566677778888999999999999999999999999884
No 132
>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=29.90 E-value=1.1e+02 Score=21.71 Aligned_cols=39 Identities=26% Similarity=0.367 Sum_probs=28.0
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 573 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 573 s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
+..+..++.++- ..++|..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444555554442 246899999999999999988877654
No 133
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=28.91 E-value=70 Score=31.03 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=36.3
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
-+..|+.+.+.++.+++.+|++.+|++...++|-|..|..
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 5677888899999999999999999999999999999863
No 134
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=28.55 E-value=90 Score=21.70 Aligned_cols=27 Identities=19% Similarity=0.335 Sum_probs=19.8
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 586 SDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 586 ~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
...+|+++|++..|++...+.+..+..
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457999999999999999888877654
No 135
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=28.21 E-value=81 Score=32.27 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=39.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
-+..|+-++++.+.+++.||++.++++...++|-|..|.. .++|.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~--~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAE--QNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4667888888889999999999999999999999999964 4666654
No 136
>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=28.18 E-value=37 Score=34.20 Aligned_cols=33 Identities=9% Similarity=0.235 Sum_probs=28.6
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhccCCCCCCcee
Q 004666 702 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 735 (738)
Q Consensus 702 ~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 735 (738)
.+|..+...++++|+.|++.|+|.|... .++|+
T Consensus 32 ~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 32 DQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 4699999999999999999999999874 56664
No 137
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=28.09 E-value=38 Score=27.54 Aligned_cols=58 Identities=17% Similarity=0.222 Sum_probs=34.7
Q ss_pred hhhhheeeecccccc--cCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhh---ccCCCCCCceeecC
Q 004666 671 YAIDAALVRIMKSRK--VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL---ERDKENPNMFRYLA 738 (738)
Q Consensus 671 ~~i~A~IVRimK~~k--~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi---~r~~~d~~~y~Yia 738 (738)
...=|.||..||++. .++.+||..++.. +... ..+++ .|-+-.-+ +.+.. .++|.|.|
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~-----~d~~-~~~~~---~L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLSL-----LDIG-PKLKE---WLKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHhc-----cCcc-HHHHH---HHHhhhhccCceeccC-CCEEEecc
Confidence 345578999999986 6888888887642 2222 22222 33222333 44443 47999876
No 138
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=28.03 E-value=78 Score=32.74 Aligned_cols=48 Identities=6% Similarity=0.065 Sum_probs=40.5
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 574 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 574 ~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
--+..|+.+.+.++.+++.||++.+|++...++|-|..|.. .+++.+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~--~G~l~r~ 64 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK--QGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh--CCCeEEE
Confidence 35778898999998999999999999999999999999953 3566554
No 139
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.90 E-value=70 Score=29.71 Aligned_cols=30 Identities=13% Similarity=0.207 Sum_probs=27.0
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 585 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 585 ~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
.++.+|-++|++.+|++...|++.|..|..
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 345899999999999999999999999974
No 140
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=27.47 E-value=48 Score=27.67 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=32.7
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhccCCCCCCceeecC
Q 004666 702 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 738 (738)
Q Consensus 702 ~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 738 (738)
.++..+.+.-++.|+.|.++|.|..-..+..+-+|.|
T Consensus 49 erlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 49 SKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 3677889999999999999999988887888999986
No 141
>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=27.41 E-value=66 Score=31.44 Aligned_cols=50 Identities=18% Similarity=0.180 Sum_probs=39.9
Q ss_pred EcHHHHHHHHhhcCC-----CCcCHHHHHHHhCCC-HHHHHHHHHHhhhcccceeecC
Q 004666 572 VSTYQAATLLLFNTS-----DRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~-----~~~t~~ei~~~~~~~-~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
++..|..||....+. -+.|..||++.+|++ ...+.++|..|. +.++|.+.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~ 59 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERD 59 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecC
Confidence 467888888766532 258899999999998 999999999997 45777764
No 142
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=27.35 E-value=78 Score=34.29 Aligned_cols=64 Identities=22% Similarity=0.316 Sum_probs=40.2
Q ss_pred EEeccCCceEEEEeeecCeeEEEEE-------cHHHHHHHHhhcC-C-CCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 548 LTWIYSLGQCNINGKFEQKNIELIV-------STYQAATLLLFNT-S-DRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 548 L~w~~~l~~~~i~~~~~~~~~~l~~-------s~~Q~~iLl~fn~-~-~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
+.+.+.||..|=++ ++...-|+= +-.-..||-++-+ . ..+|+++|++.|||..+++...|++|-
T Consensus 282 IdFSYeLSr~E~~~--GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKI--GSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcC--CCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 46778888766543 332222211 1122234433332 2 239999999999999999999999883
No 143
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=26.97 E-value=89 Score=35.47 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=43.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 571 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
.+|..|..||..+...+.+|..+|++.+|++...+.+.+.+|.. -+++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~--kGlV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEE--KGLVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHh--CCCEEE
Confidence 46789999999998888999999999999999999999999974 356654
No 144
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=26.84 E-value=1e+02 Score=31.95 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=29.5
Q ss_pred HHHHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 576 QAATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 576 Q~~iLl~f-n~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
...|+-.+ +....+|+++|+..|||..+++..+|+.|
T Consensus 210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 34455444 33568999999999999999999999987
No 145
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.83 E-value=44 Score=24.91 Aligned_cols=27 Identities=7% Similarity=0.186 Sum_probs=23.8
Q ss_pred CCCCChhHHHHHHHhhhhhhhhccCCC
Q 004666 703 MFKPDIKAIKKRMEDLITRDYLERDKE 729 (738)
Q Consensus 703 ~F~~~~~~ik~~Ie~Liekeyi~r~~~ 729 (738)
.|..+...+.+.+..|.+.|+|.+.+.
T Consensus 29 ~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 29 QLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 577899999999999999999988753
No 146
>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=26.66 E-value=1.3e+02 Score=22.60 Aligned_cols=31 Identities=16% Similarity=0.411 Sum_probs=25.1
Q ss_pred hhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 582 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 582 ~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
.|+.-...|.+||++.+|++...+-.+|..-
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4555558999999999999999888777643
No 147
>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=26.52 E-value=1.1e+02 Score=25.55 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=35.8
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHh-CCCHHHHHHHHHHhhhcccceeecC
Q 004666 576 QAATLLLFNTSDRLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 576 Q~~iLl~fn~~~~~t~~ei~~~~-~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~--~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEE--AGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHH--cchhhcc
Confidence 3567766666 689999999999 9999999999999973 5788764
No 148
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=26.14 E-value=79 Score=27.79 Aligned_cols=62 Identities=15% Similarity=0.179 Sum_probs=42.2
Q ss_pred hhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCceee
Q 004666 672 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 736 (738)
Q Consensus 672 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Y 736 (738)
.+|+.|.+ -....-.....++.+|+.... .+ ++...+--||+.||+.|.++-.++-.++-+|
T Consensus 48 ~yD~~Il~-~~~~~~~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 48 YYDDFILE-QAPDEFQKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HhhHHHHh-cCCccccHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 34444444 112223456678888988864 34 6778899999999999999988765554443
No 149
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=26.04 E-value=42 Score=34.00 Aligned_cols=33 Identities=21% Similarity=0.287 Sum_probs=28.1
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhccCCCCCCcee
Q 004666 702 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 735 (738)
Q Consensus 702 ~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 735 (738)
..|..+...++++|+.|++.|+|.|... +++|+
T Consensus 41 ~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 41 TQYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 3688899999999999999999999874 56664
No 150
>PHA02591 hypothetical protein; Provisional
Probab=25.94 E-value=84 Score=25.50 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=21.8
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHH
Q 004666 587 DRLSYSEIMTQLNLTHDDLVRLLHS 611 (738)
Q Consensus 587 ~~~t~~ei~~~~~~~~~~l~~~L~~ 611 (738)
.++|.++||+.+|++.+.+.+-|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3799999999999999999887764
No 151
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=25.87 E-value=90 Score=26.76 Aligned_cols=53 Identities=8% Similarity=0.156 Sum_probs=42.7
Q ss_pred hhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcc
Q 004666 673 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 726 (738)
Q Consensus 673 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r 726 (738)
++-+|..++. .+.++=-+|.+++.+...+.+.++...+=..+..|-++|+|++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 3445555665 4678888999999887665578888999999999999999998
No 152
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.79 E-value=74 Score=23.00 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=21.1
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 579 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 579 iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
++.++.+ ..|..+|++.+|++...+.+-+..+
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4444444 7899999999999999988766554
No 153
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=25.70 E-value=39 Score=26.18 Aligned_cols=28 Identities=11% Similarity=0.249 Sum_probs=24.0
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhccCCC
Q 004666 702 RMFKPDIKAIKKRMEDLITRDYLERDKE 729 (738)
Q Consensus 702 ~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 729 (738)
.+|..+..-+.+++..|.+.|+|.+.+.
T Consensus 32 ~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 32 ERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 3688899999999999999999998874
No 154
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=25.50 E-value=65 Score=29.02 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=32.2
Q ss_pred ccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCC
Q 004666 681 MKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 729 (738)
Q Consensus 681 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 729 (738)
|..++.++.++|-+.+ .-+.+-+-+.+.+|++.|.+.|...
T Consensus 37 L~~~~~~tvdelae~l--------nr~rStv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 37 LEENGPLTVDELAEIL--------NRSRSTVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HhhcCCcCHHHHHHHH--------CccHHHHHHHHHHHHHcCCeeeeee
Confidence 3467888888877644 2477889999999999999999753
No 155
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=25.10 E-value=1.2e+02 Score=31.00 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=34.3
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 579 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 579 iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
||++.-+ ++-|++||...++++...+..+|..|. +.+++.+.
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEec
Confidence 5555555 688999999999999999999999996 45677654
No 156
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.87 E-value=1.3e+02 Score=26.96 Aligned_cols=48 Identities=15% Similarity=0.266 Sum_probs=39.3
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 574 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 574 ~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.+.+-|+-+.-+++.+|+.++...||.+-..+++++.-|+. .+-|..+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~ 59 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeC
Confidence 35677888888899999999999999999999999999973 2444443
No 157
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.82 E-value=49 Score=29.61 Aligned_cols=52 Identities=21% Similarity=0.366 Sum_probs=44.5
Q ss_pred hhhhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCC
Q 004666 670 RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 729 (738)
Q Consensus 670 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 729 (738)
...|.+.||-..++++.++..+|... +-.+...+++.+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~--------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAK--------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHH--------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 46788999999999999999999874 44678889999999999999888763
No 158
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.63 E-value=1.7e+02 Score=21.20 Aligned_cols=35 Identities=17% Similarity=0.360 Sum_probs=25.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 611 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~ 611 (738)
+...|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 344455444332 69999999999999999887754
No 159
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=24.59 E-value=63 Score=24.97 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=33.8
Q ss_pred eeecccccccCChhHHHHHHHHH--hccCCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 677 LVRIMKSRKVLGHQQLVSECVEQ--LSRMFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 677 IVRimK~~k~l~~~~L~~~v~~~--l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
|+..+..-..++.+.+.+...-. -...+.++.++++..++.+++.|-|+-++
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~ 55 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSG 55 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--T
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecC
Confidence 34445555677788877765544 23568899999999999999999998874
No 160
>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=24.28 E-value=57 Score=28.46 Aligned_cols=41 Identities=17% Similarity=0.340 Sum_probs=29.9
Q ss_pred ccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhcc--CCCCC
Q 004666 683 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER--DKENP 731 (738)
Q Consensus 683 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r--~~~d~ 731 (738)
..+.++..+|... ...+..-+-+.|+.|.++|||.| ++.|+
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 3456777776663 33567789999999999999997 44444
No 161
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=23.88 E-value=1.1e+02 Score=31.14 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=35.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
-|..|+..+++++.++.+||++.+|++...+++-|..|..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3566888888888999999999999999999999999863
No 162
>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=23.85 E-value=48 Score=33.36 Aligned_cols=33 Identities=15% Similarity=0.373 Sum_probs=28.2
Q ss_pred cCCCCChhHHHHHHHhhhhhhhhccCCCCCCcee
Q 004666 702 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 735 (738)
Q Consensus 702 ~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 735 (738)
.+|..+...+.++|+.|.+.|+|.|... .++|+
T Consensus 40 ~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 40 ERFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 3699999999999999999999999864 56654
No 163
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=23.73 E-value=49 Score=33.49 Aligned_cols=48 Identities=10% Similarity=0.357 Sum_probs=35.3
Q ss_pred cccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCcee
Q 004666 680 IMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 735 (738)
Q Consensus 680 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 735 (738)
.++....+.-+ .+|...|..+...++++|+.|++.|+|.|... +++|+
T Consensus 28 ~~~~G~~LPsE-------~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 28 HYRCGDYLPAE-------QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred ccCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 45655555533 23334699999999999999999999999874 56654
No 164
>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=23.20 E-value=2.8e+02 Score=22.73 Aligned_cols=48 Identities=15% Similarity=0.240 Sum_probs=38.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+++.|=+.-..+.++.-.+|++.++++...++..+..|- ..++|.+.|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 455555666677899999999999999999999999885 467886543
No 165
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=23.19 E-value=1.6e+02 Score=25.01 Aligned_cols=53 Identities=15% Similarity=0.207 Sum_probs=43.7
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 570 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 570 l~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+..+....-||..+...++=...-|+..+++|.+++...|..|. ..++|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 34566788899988887777788899999999999999999997 458887653
No 166
>PRK11050 manganese transport regulator MntR; Provisional
Probab=23.09 E-value=1.6e+02 Score=27.39 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=34.8
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 578 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 578 ~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
.|+.++..++.++..+|++.++++...+.+.|..|.. .+++.+
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~--~GlI~r 83 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLAR--DGLVEM 83 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 3455666777899999999999999999999999964 356654
No 167
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=22.83 E-value=46 Score=30.86 Aligned_cols=50 Identities=12% Similarity=0.232 Sum_probs=42.2
Q ss_pred hhhhheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 671 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 671 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
..+|..|.+++......+..+|-..+= .++..+.++|+.|.++|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeEE
Confidence 456788899999999999998888652 57888999999999999998854
No 168
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=22.68 E-value=1.8e+02 Score=28.08 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=35.5
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 578 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 578 ~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
-++.-++.++..|..+|+..+|++..++.++|=.|. +.+.+.+.
T Consensus 17 ~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~ 60 (183)
T PHA03103 17 KEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMS 60 (183)
T ss_pred HHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecC
Confidence 356667788899999999999999999999999986 34455444
No 169
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=22.29 E-value=1.5e+02 Score=27.22 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=33.8
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 579 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 579 iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
|..+.+.++..++.+|++.++++...+.+.|..|.. .+++..
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~--~Gli~~ 54 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDK--DEYLIY 54 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHH--CCCEEE
Confidence 444556677889999999999999999999999963 466653
No 170
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=22.13 E-value=60 Score=24.19 Aligned_cols=23 Identities=17% Similarity=0.528 Sum_probs=19.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Q 004666 587 DRLSYSEIMTQLNLTHDDLVRLL 609 (738)
Q Consensus 587 ~~~t~~ei~~~~~~~~~~l~~~L 609 (738)
+.+++.||++.+|++..++.+.|
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH
T ss_pred CceEHHHHHHHHCcCHHHHHHHH
Confidence 35789999999999999998877
No 171
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=21.49 E-value=1.6e+02 Score=29.29 Aligned_cols=42 Identities=21% Similarity=0.259 Sum_probs=36.6
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 571 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
.+|+-+..||.+.-+ ++|.+|||+.++++...++.++..+..
T Consensus 143 ~LS~RE~eVL~Lia~--G~SnkEIA~~L~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 143 KVTKYQNDVFILYSF--GFSHEYIAQLLNITVGSSKNKISEILK 184 (217)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 468889999998876 589999999999999999999887753
No 172
>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=21.41 E-value=1.5e+02 Score=24.85 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=34.4
Q ss_pred HHHHHhhcCCCCcCHHHHHHHh--CCCHHHHHHHHHHhhhcccceeecCCC
Q 004666 577 AATLLLFNTSDRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPN 625 (738)
Q Consensus 577 ~~iLl~fn~~~~~t~~ei~~~~--~~~~~~l~~~L~~L~~~k~~iL~~~~~ 625 (738)
+.||...-+++-+|..++++.+ .++...+..++..|. |-+++.++++
T Consensus 19 ~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLI--KkglIEKSGD 67 (96)
T PF09114_consen 19 ANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLI--KKGLIEKSGD 67 (96)
T ss_dssp HHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHH--HTTSEEEETT
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHH--HcCcccccCC
Confidence 4456566667788999999977 788899999999886 5688888743
No 173
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.41 E-value=64 Score=29.59 Aligned_cols=26 Identities=8% Similarity=0.266 Sum_probs=21.7
Q ss_pred CCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 703 MFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 703 ~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 34567778999999999999999964
No 174
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=21.35 E-value=1.2e+02 Score=28.86 Aligned_cols=41 Identities=20% Similarity=0.356 Sum_probs=29.8
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeec
Q 004666 579 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 622 (738)
Q Consensus 579 iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~ 622 (738)
-+|.++. +++|++||++.||++...+-..+.-|.. .++..+
T Consensus 33 gilyls~-~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~--~~lV~~ 73 (177)
T COG1510 33 GILYLSR-KPLTLDEIAEALGMSKSNVSMGLKKLQD--WNLVKK 73 (177)
T ss_pred hhheecC-CCccHHHHHHHHCCCcchHHHHHHHHHh--cchHHh
Confidence 3444554 6999999999999999888777776653 345543
No 175
>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=21.24 E-value=1.3e+02 Score=23.18 Aligned_cols=38 Identities=21% Similarity=0.373 Sum_probs=29.8
Q ss_pred CCCCc-CHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 585 TSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 585 ~~~~~-t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
.++.+ |..+|++..|++...+.++|..|.. .+++...+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~~ 58 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERRP 58 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEEC
Confidence 44678 9999999999999999999999974 57776543
No 176
>PRK14999 histidine utilization repressor; Provisional
Probab=21.08 E-value=56 Score=33.04 Aligned_cols=47 Identities=15% Similarity=0.289 Sum_probs=35.4
Q ss_pred cccccccC-ChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCCCCCCcee
Q 004666 680 IMKSRKVL-GHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 735 (738)
Q Consensus 680 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 735 (738)
.++....+ +-.+|.+ .|..+...|+++|+.|.+.|+|.|... +++|+
T Consensus 29 ~~~~G~~LPsE~eLa~--------~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELVA--------QYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 45555555 4444444 588999999999999999999999874 56664
No 177
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=21.05 E-value=57 Score=32.99 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=29.3
Q ss_pred hccCCCCChhHHHHHHHhhhhhhhhccCCCCCCcee
Q 004666 700 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 735 (738)
Q Consensus 700 l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 735 (738)
|..+|..+...++++|..|.+.|+|.|-.. .++|+
T Consensus 37 La~~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 37 LAEQFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HHHHHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 344799999999999999999999999864 56664
No 178
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=20.94 E-value=1.3e+02 Score=31.31 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=32.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCCCCCCCCCCCeEEEccCC
Q 004666 575 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 641 (738)
Q Consensus 575 ~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 641 (738)
+--.|.-+|.++.-||+.+|.+.|+-|+..|+..|...+ ++.+.+. ....|.|=..|
T Consensus 217 L~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 217 LLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 445677899999999999999999999999999998875 5655432 13456665544
No 179
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.80 E-value=1.8e+02 Score=27.36 Aligned_cols=45 Identities=16% Similarity=0.284 Sum_probs=35.6
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecCC
Q 004666 578 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 624 (738)
Q Consensus 578 ~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~~ 624 (738)
+|..+..+.......+|++.++++...+...++.|. +.+++...+
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 344455567789999999999999999999999996 356776543
No 180
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=20.71 E-value=2.4e+02 Score=21.23 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=35.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004666 571 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 613 (738)
Q Consensus 571 ~~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~ 613 (738)
.+|.-+..++.++.++ .+..||+...|++...+..++....
T Consensus 4 ~Lt~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 4 DLTPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred cCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4577888899888775 7999999999999999998888774
No 181
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=20.49 E-value=1.2e+02 Score=22.03 Aligned_cols=21 Identities=14% Similarity=0.390 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 004666 590 SYSEIMTQLNLTHDDLVRLLH 610 (738)
Q Consensus 590 t~~ei~~~~~~~~~~l~~~L~ 610 (738)
|+.||++..|++...+-+.|.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 689999999999999877765
No 182
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=20.40 E-value=78 Score=26.43 Aligned_cols=47 Identities=13% Similarity=0.224 Sum_probs=34.2
Q ss_pred hheeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccCC
Q 004666 674 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 728 (738)
Q Consensus 674 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 728 (738)
+..|...+...+.++..+|... +.++...+.+.|..|.++|+|++..
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 4455556666667777777553 3456777999999999999998764
No 183
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.24 E-value=2.8e+02 Score=30.34 Aligned_cols=92 Identities=12% Similarity=0.278 Sum_probs=57.6
Q ss_pred HHHhHHHHHHHHHHHHHHhcCCCC-------CCCCHHHHHHHHH-HHhhhhccCCCCCchHHHHHHHHHHHHHHHHhccc
Q 004666 8 LDQGWDYMQKGITKLKRILEGLPE-------SPFSSEEYMMLYT-TIYNMCTQKPPHDYSQQLYDKYKQAFEEYISSMVL 79 (738)
Q Consensus 8 f~~~W~~l~~ai~~i~~~~~~~~~-------~~~s~~~~~~lY~-~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~~~ 79 (738)
=++-|+.|+..++.|.+-.+|-.. +-=|+.+|+.+|. +|-.+|... .|++.++....+ .|+++.+.
T Consensus 22 ~eedw~ai~~fceqinkdp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkn----cGekfH~evgkf--rFLNELIk 95 (594)
T KOG1086|consen 22 DEEDWKAIDGFCEQINKDPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKN----CGEKFHEEVGKF--RFLNELIK 95 (594)
T ss_pred hHHHHHHHHHHHHHHhcCCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHh----hhHHHHHHHHHH--HHHHHHHH
Confidence 478899999999887764443211 1136778999987 567788765 788888876542 23333221
Q ss_pred ccccccCchHHHHHHHHHHHHHHHHHHHHHHHhch
Q 004666 80 PSLSEKHDEYMLRELVKRWANHKVMVRWLSRFFHY 114 (738)
Q Consensus 80 ~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~Y 114 (738)
- .-..|...|..=.....+|.-+|++
T Consensus 96 -v--------vsPKYlG~~tSekvKtkiIelLfsW 121 (594)
T KOG1086|consen 96 -V--------VSPKYLGSRTSEKVKTKIIELLFSW 121 (594)
T ss_pred -H--------hCchhcchhhhHHHHHHHHHHHhhh
Confidence 0 1123556666666777777666653
No 184
>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=20.22 E-value=1.5e+02 Score=23.83 Aligned_cols=48 Identities=15% Similarity=0.180 Sum_probs=38.6
Q ss_pred HHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccceeecC
Q 004666 574 TYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 574 ~~Q~~iLl~fn~--~~~~t~~ei~~~~~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
..|..+|..... ..+++-.+++..+|++...+-..++.|.. .+++.+.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~--~gLI~k~ 51 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEK--KGLIVKQ 51 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHH--CCCEEEE
Confidence 467788877764 35889999999999999999999999963 5677664
No 185
>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=20.21 E-value=1.8e+02 Score=26.66 Aligned_cols=39 Identities=23% Similarity=0.222 Sum_probs=31.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004666 572 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 612 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L 612 (738)
+|.-|..|+.++ ..++|.+||++.+|++...+...+...
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 567788888876 367999999999999998887655443
No 186
>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=20.04 E-value=1.8e+02 Score=24.50 Aligned_cols=33 Identities=12% Similarity=0.319 Sum_probs=22.9
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004666 581 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 614 (738)
Q Consensus 581 l~fn~~~~~t~~ei~~~~~~~~~~l~~~L~~L~~ 614 (738)
.+..+... ++..|.+.||||...++.+|..|..
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~ 47 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPE 47 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGG
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhc
Confidence 34444455 9999999999999999999999974
No 187
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=20.04 E-value=44 Score=34.33 Aligned_cols=45 Identities=18% Similarity=0.222 Sum_probs=39.1
Q ss_pred heeeecccccccCChhHHHHHHHHHhccCCCCChhHHHHHHHhhhhhhhhccC
Q 004666 675 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 727 (738)
Q Consensus 675 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~ 727 (738)
..|...+++++.++.+||.+ .|..+...|.+-|+.|-++|.|.|-
T Consensus 8 ~~Il~~L~~~~~v~v~eLa~--------~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQGKTSVEELAQ--------YFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 45677889999999998877 5788999999999999999999884
No 188
>PRK06474 hypothetical protein; Provisional
Probab=20.02 E-value=2.7e+02 Score=26.74 Aligned_cols=50 Identities=16% Similarity=0.192 Sum_probs=38.7
Q ss_pred EcHHHHHHHHhhcCCC-CcCHHHHHHHh-CCCHHHHHHHHHHhhhcccceeecC
Q 004666 572 VSTYQAATLLLFNTSD-RLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 623 (738)
Q Consensus 572 ~s~~Q~~iLl~fn~~~-~~t~~ei~~~~-~~~~~~l~~~L~~L~~~k~~iL~~~ 623 (738)
.++.-..||..+-..+ .+|..+|++.+ +++...+-++|..|. +.+++...
T Consensus 9 a~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~ 60 (178)
T PRK06474 9 MHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVV 60 (178)
T ss_pred CCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 4556667776665544 49999999999 799999999999997 46787754
Done!