Query 003927
Match_columns 786
No_of_seqs 291 out of 1071
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 14:27:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003927.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003927hhsearch_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 3E-131 6E-136 1136.2 63.8 719 5-784 4-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 1E-121 3E-126 1007.5 61.9 723 7-786 16-773 (773)
3 KOG2284 E3 ubiquitin ligase, C 100.0 4E-115 8E-120 895.0 45.2 684 1-786 1-728 (728)
4 KOG2167 Cullins [Cell cycle co 100.0 3E-113 6E-118 921.1 47.0 646 107-786 2-661 (661)
5 KOG2285 E3 ubiquitin ligase, C 100.0 7E-100 2E-104 788.8 55.0 714 7-786 9-777 (777)
6 PF00888 Cullin: Cullin family 100.0 3.4E-94 7.3E-99 847.7 61.0 584 15-690 1-588 (588)
7 smart00182 CULLIN Cullin. 100.0 2.3E-33 4.9E-38 268.0 18.0 141 470-611 1-142 (142)
8 KOG2165 Anaphase-promoting com 99.9 1.1E-25 2.4E-30 248.3 22.5 299 464-774 442-756 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 2.2E-20 4.7E-25 153.9 1.8 68 713-780 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 95.9 0.14 3E-06 49.5 12.5 101 90-194 38-156 (158)
11 KOG2167 Cullins [Cell cycle co 93.5 4.5 9.8E-05 46.4 18.1 191 69-276 114-324 (661)
12 TIGR01610 phage_O_Nterm phage 92.3 0.4 8.7E-06 42.3 6.4 65 618-690 21-93 (95)
13 PF09339 HTH_IclR: IclR helix- 91.5 0.29 6.3E-06 37.8 4.1 45 625-671 6-51 (52)
14 PF02082 Rrf2: Transcriptional 91.4 0.58 1.3E-05 40.0 6.3 59 623-688 11-70 (83)
15 PF12802 MarR_2: MarR family; 90.0 0.42 9E-06 38.1 3.9 51 620-672 3-55 (62)
16 PF13412 HTH_24: Winged helix- 88.9 0.76 1.7E-05 34.7 4.4 41 621-661 2-42 (48)
17 PF13463 HTH_27: Winged helix 85.9 1.3 2.8E-05 36.0 4.4 51 620-672 1-52 (68)
18 PF01047 MarR: MarR family; I 85.9 0.6 1.3E-05 36.8 2.4 50 621-672 2-51 (59)
19 TIGR02337 HpaR homoprotocatech 84.2 1.8 4E-05 39.5 5.1 52 619-672 25-76 (118)
20 PF12840 HTH_20: Helix-turn-he 83.3 1.6 3.5E-05 34.9 3.8 49 621-671 9-57 (61)
21 PF08220 HTH_DeoR: DeoR-like h 83.1 1.8 4E-05 34.1 4.0 46 624-671 2-47 (57)
22 PF01022 HTH_5: Bacterial regu 81.9 3.4 7.4E-05 31.1 4.9 43 623-668 3-45 (47)
23 PRK11512 DNA-binding transcrip 81.8 2.7 5.7E-05 40.0 5.4 52 619-672 37-88 (144)
24 smart00550 Zalpha Z-DNA-bindin 78.3 3.9 8.5E-05 33.5 4.5 47 623-671 7-55 (68)
25 PF09012 FeoC: FeoC like trans 78.2 0.83 1.8E-05 37.6 0.5 44 726-777 6-49 (69)
26 PRK10857 DNA-binding transcrip 77.1 6.8 0.00015 38.3 6.6 45 624-670 12-57 (164)
27 TIGR01889 Staph_reg_Sar staphy 76.8 5.9 0.00013 35.7 5.7 52 619-672 22-77 (109)
28 PF04492 Phage_rep_O: Bacterio 76.1 8 0.00017 34.4 6.1 61 620-690 30-98 (100)
29 PRK11920 rirA iron-responsive 75.5 7.9 0.00017 37.4 6.5 56 625-687 13-68 (153)
30 smart00346 HTH_ICLR helix_turn 75.4 6 0.00013 34.0 5.3 45 625-671 8-53 (91)
31 smart00347 HTH_MARR helix_turn 74.8 5.3 0.00011 34.7 4.8 53 617-671 5-57 (101)
32 PF08279 HTH_11: HTH domain; 74.3 6.2 0.00013 30.5 4.5 35 627-661 5-40 (55)
33 PF03965 Penicillinase_R: Peni 74.3 3.3 7.1E-05 37.8 3.4 57 725-786 8-64 (115)
34 PRK15090 DNA-binding transcrip 73.4 6.7 0.00015 41.2 6.0 46 625-672 17-62 (257)
35 TIGR02698 CopY_TcrY copper tra 73.0 4.7 0.0001 37.7 4.2 59 723-786 7-65 (130)
36 TIGR02010 IscR iron-sulfur clu 72.8 9.2 0.0002 35.9 6.2 45 624-670 12-57 (135)
37 PF09763 Sec3_C: Exocyst compl 71.4 2.2E+02 0.0049 34.6 19.2 139 243-407 554-701 (701)
38 PF08318 COG4: COG4 transport 71.0 1.7E+02 0.0036 32.1 17.3 164 315-495 15-215 (331)
39 PF01978 TrmB: Sugar-specific 69.3 4.6 0.0001 32.9 2.8 49 621-671 7-55 (68)
40 smart00420 HTH_DEOR helix_turn 68.8 9 0.0002 28.8 4.3 43 626-670 4-46 (53)
41 PRK03573 transcriptional regul 68.8 8.2 0.00018 36.5 4.9 53 618-672 27-80 (144)
42 COG3682 Predicted transcriptio 68.3 4.6 0.0001 37.1 2.8 61 721-786 7-67 (123)
43 PRK13777 transcriptional regul 67.8 10 0.00022 37.8 5.4 53 618-672 41-93 (185)
44 PF04703 FaeA: FaeA-like prote 67.3 11 0.00025 30.3 4.6 56 627-686 5-61 (62)
45 PF13601 HTH_34: Winged helix 67.1 4.7 0.0001 34.3 2.5 43 625-669 3-45 (80)
46 COG1959 Predicted transcriptio 67.0 14 0.00029 35.6 6.0 59 623-688 11-70 (150)
47 PHA00738 putative HTH transcri 65.3 13 0.00029 33.3 5.0 67 617-689 7-73 (108)
48 TIGR00738 rrf2_super rrf2 fami 64.5 16 0.00035 33.9 5.9 46 623-670 11-57 (132)
49 PRK10870 transcriptional repre 63.7 15 0.00034 36.2 5.9 52 619-672 52-105 (176)
50 PF05732 RepL: Firmicute plasm 63.6 8.8 0.00019 37.5 4.0 48 636-692 75-122 (165)
51 PRK11569 transcriptional repre 61.1 15 0.00033 39.0 5.7 47 624-672 30-77 (274)
52 COG1414 IclR Transcriptional r 60.9 16 0.00036 38.1 5.8 46 625-672 7-53 (246)
53 COG3355 Predicted transcriptio 60.4 20 0.00043 33.3 5.4 38 632-671 38-75 (126)
54 cd00090 HTH_ARSR Arsenical Res 59.9 18 0.0004 29.0 4.9 47 621-670 6-52 (78)
55 PF13404 HTH_AsnC-type: AsnC-t 59.5 14 0.00031 27.2 3.5 35 626-660 7-41 (42)
56 PRK10163 DNA-binding transcrip 59.2 18 0.0004 38.3 5.9 47 624-672 27-74 (271)
57 PF05584 Sulfolobus_pRN: Sulfo 59.1 21 0.00046 29.6 4.8 46 621-670 5-50 (72)
58 TIGR02944 suf_reg_Xantho FeS a 58.7 22 0.00047 33.1 5.7 43 626-670 13-57 (130)
59 smart00345 HTH_GNTR helix_turn 58.4 19 0.00042 27.8 4.5 39 631-671 14-53 (60)
60 smart00419 HTH_CRP helix_turn_ 58.3 21 0.00046 26.2 4.5 33 636-670 8-40 (48)
61 smart00762 Cog4 COG4 transport 57.7 2.9E+02 0.0062 30.2 15.1 161 315-491 15-205 (324)
62 PRK09834 DNA-binding transcrip 57.6 18 0.00039 38.1 5.5 46 625-672 14-60 (263)
63 PRK10141 DNA-binding transcrip 56.8 21 0.00045 32.8 5.0 60 623-688 17-76 (117)
64 TIGR01884 cas_HTH CRISPR locus 56.6 16 0.00036 36.8 4.8 52 619-672 140-191 (203)
65 TIGR03879 near_KaiC_dom probab 55.7 14 0.00031 30.8 3.3 34 634-669 30-63 (73)
66 PF08784 RPA_C: Replication pr 55.5 19 0.00042 31.9 4.5 44 619-662 44-91 (102)
67 TIGR02431 pcaR_pcaU beta-ketoa 55.1 24 0.00052 36.8 5.9 44 625-670 12-56 (248)
68 PF08280 HTH_Mga: M protein tr 52.7 17 0.00038 28.7 3.3 37 624-660 7-43 (59)
69 PF10771 DUF2582: Protein of u 52.7 20 0.00044 29.2 3.7 37 626-662 12-48 (65)
70 COG1846 MarR Transcriptional r 51.9 26 0.00057 31.3 5.0 51 620-672 20-70 (126)
71 smart00344 HTH_ASNC helix_turn 50.8 25 0.00055 31.2 4.6 45 623-669 4-48 (108)
72 PF13730 HTH_36: Helix-turn-he 49.8 39 0.00084 26.0 4.9 24 638-661 27-50 (55)
73 smart00418 HTH_ARSR helix_turn 49.4 31 0.00067 26.7 4.5 35 634-670 8-42 (66)
74 PRK11014 transcriptional repre 49.4 44 0.00096 31.5 6.2 40 631-672 20-59 (141)
75 PF08220 HTH_DeoR: DeoR-like h 49.0 7.6 0.00016 30.6 0.7 45 724-776 4-48 (57)
76 PF13463 HTH_27: Winged helix 48.7 13 0.00029 29.8 2.2 50 723-780 6-58 (68)
77 cd00092 HTH_CRP helix_turn_hel 48.2 41 0.00089 26.7 5.0 35 635-671 24-58 (67)
78 PF11994 DUF3489: Protein of u 47.8 40 0.00086 28.0 4.7 47 621-667 9-55 (72)
79 PF01325 Fe_dep_repress: Iron 46.2 40 0.00086 26.9 4.5 45 626-672 12-56 (60)
80 PF01978 TrmB: Sugar-specific 45.7 8.7 0.00019 31.2 0.6 32 754-785 34-65 (68)
81 PF08221 HTH_9: RNA polymerase 45.2 28 0.0006 28.0 3.4 33 634-668 25-57 (62)
82 COG2345 Predicted transcriptio 44.3 29 0.00064 35.4 4.2 62 621-685 11-73 (218)
83 PF04545 Sigma70_r4: Sigma-70, 44.1 51 0.0011 24.8 4.7 33 625-659 11-43 (50)
84 PRK06266 transcription initiat 43.3 36 0.00077 33.8 4.6 44 624-669 24-67 (178)
85 PF14394 DUF4423: Domain of un 42.9 56 0.0012 32.1 5.9 55 616-672 18-75 (171)
86 smart00418 HTH_ARSR helix_turn 42.8 25 0.00054 27.3 2.9 45 726-779 3-47 (66)
87 PF09756 DDRGK: DDRGK domain; 42.7 9.6 0.00021 38.0 0.5 57 722-786 101-157 (188)
88 PF02002 TFIIE_alpha: TFIIE al 41.5 21 0.00045 31.9 2.5 43 624-668 15-57 (105)
89 TIGR02702 SufR_cyano iron-sulf 41.2 55 0.0012 33.0 5.8 44 626-671 5-48 (203)
90 PF01853 MOZ_SAS: MOZ/SAS fami 40.7 28 0.0006 34.6 3.3 27 635-661 149-175 (188)
91 smart00550 Zalpha Z-DNA-bindin 40.0 25 0.00055 28.7 2.5 53 722-782 8-62 (68)
92 cd07153 Fur_like Ferric uptake 39.7 33 0.00072 30.9 3.6 57 725-784 6-63 (116)
93 PF01726 LexA_DNA_bind: LexA D 39.6 50 0.0011 26.9 4.1 24 755-778 39-62 (65)
94 PF12324 HTH_15: Helix-turn-he 39.2 71 0.0015 26.9 5.0 38 624-661 26-63 (77)
95 PF05261 Tra_M: TraM protein, 38.4 1E+02 0.0022 28.4 6.3 57 189-245 8-74 (127)
96 PRK13713 conjugal transfer pro 38.1 79 0.0017 28.8 5.4 38 190-227 2-40 (118)
97 PF00325 Crp: Bacterial regula 37.5 44 0.00096 23.1 2.9 26 636-661 2-27 (32)
98 PF09012 FeoC: FeoC like trans 37.5 38 0.00082 27.7 3.2 32 631-662 9-40 (69)
99 cd07377 WHTH_GntR Winged helix 34.3 84 0.0018 24.5 4.8 38 632-671 20-58 (66)
100 cd06170 LuxR_C_like C-terminal 33.6 84 0.0018 23.6 4.5 37 622-660 3-39 (57)
101 PRK00215 LexA repressor; Valid 33.5 79 0.0017 31.8 5.5 51 620-672 2-58 (205)
102 COG5173 SEC6 Exocyst complex s 33.4 8.4E+02 0.018 28.5 24.5 59 404-485 621-681 (742)
103 TIGR00373 conserved hypothetic 33.2 72 0.0016 30.9 4.9 43 625-669 17-59 (158)
104 smart00421 HTH_LUXR helix_turn 33.1 85 0.0019 23.5 4.5 39 621-661 5-43 (58)
105 PF08281 Sigma70_r4_2: Sigma-7 33.1 71 0.0015 24.3 4.0 24 635-658 25-48 (54)
106 PF07106 TBPIP: Tat binding pr 33.0 2.5E+02 0.0054 27.3 8.8 59 624-688 3-64 (169)
107 PF12802 MarR_2: MarR family; 33.0 20 0.00042 28.2 0.8 26 752-777 31-56 (62)
108 PRK10434 srlR DNA-bindng trans 32.5 53 0.0012 34.5 4.2 47 623-671 6-52 (256)
109 PF06784 UPF0240: Uncharacteri 32.2 71 0.0015 31.7 4.7 64 593-661 96-161 (179)
110 PF02796 HTH_7: Helix-turn-hel 32.1 68 0.0015 23.7 3.6 30 627-658 14-43 (45)
111 COG4189 Predicted transcriptio 31.9 64 0.0014 33.0 4.3 49 621-671 22-70 (308)
112 PRK11169 leucine-responsive tr 31.1 70 0.0015 31.1 4.5 48 620-669 12-59 (164)
113 COG4190 Predicted transcriptio 31.1 1.1E+02 0.0023 28.7 5.1 64 625-690 67-133 (144)
114 PF01047 MarR: MarR family; I 30.2 17 0.00037 28.3 0.0 26 751-776 26-51 (59)
115 PF01726 LexA_DNA_bind: LexA D 30.2 67 0.0015 26.1 3.5 51 620-672 4-60 (65)
116 PRK11179 DNA-binding transcrip 29.1 84 0.0018 30.1 4.6 48 620-669 7-54 (153)
117 TIGR02844 spore_III_D sporulat 28.9 84 0.0018 26.8 3.9 35 623-658 7-41 (80)
118 COG1349 GlpR Transcriptional r 28.0 73 0.0016 33.4 4.3 46 624-671 7-52 (253)
119 KOG2747 Histone acetyltransfer 27.9 71 0.0015 35.5 4.2 64 596-661 282-354 (396)
120 PF05158 RNA_pol_Rpc34: RNA po 27.7 71 0.0015 34.9 4.2 143 619-778 81-260 (327)
121 smart00345 HTH_GNTR helix_turn 27.6 40 0.00086 25.9 1.7 29 749-777 27-55 (60)
122 KOG1020 Sister chromatid cohes 27.4 1.6E+03 0.034 29.9 17.4 49 135-189 915-963 (1692)
123 PF13412 HTH_24: Winged helix- 26.9 28 0.00061 26.0 0.7 44 722-773 5-48 (48)
124 smart00344 HTH_ASNC helix_turn 26.8 35 0.00075 30.4 1.4 47 721-775 4-50 (108)
125 smart00420 HTH_DEOR helix_turn 26.6 35 0.00077 25.4 1.2 44 726-777 6-49 (53)
126 TIGR02404 trehalos_R_Bsub treh 26.4 40 0.00087 34.7 2.0 35 748-783 30-64 (233)
127 PF09681 Phage_rep_org_N: N-te 26.2 76 0.0016 29.3 3.5 50 620-671 27-86 (121)
128 PRK13509 transcriptional repre 26.0 96 0.0021 32.5 4.7 47 623-671 6-52 (251)
129 PF11728 DUF939_C: DUF939 C-te 25.9 3.8E+02 0.0083 26.1 8.6 62 320-399 74-135 (167)
130 PLN03238 probable histone acet 25.5 1E+02 0.0022 32.7 4.7 37 624-660 210-247 (290)
131 PF04967 HTH_10: HTH DNA bindi 25.4 1E+02 0.0022 24.0 3.5 29 631-659 18-46 (53)
132 PF10273 WGG: Pre-rRNA-process 25.4 1.8E+02 0.0039 24.8 5.4 59 59-118 3-66 (82)
133 PRK13239 alkylmercury lyase; P 24.7 1.3E+02 0.0027 30.6 5.0 40 622-661 22-61 (206)
134 COG1522 Lrp Transcriptional re 24.6 1.2E+02 0.0025 28.7 4.8 49 620-670 6-54 (154)
135 TIGR01714 phage_rep_org_N phag 24.5 1E+02 0.0022 28.4 4.0 49 621-671 28-84 (119)
136 PF02186 TFIIE_beta: TFIIE bet 24.5 40 0.00086 27.5 1.2 53 723-786 8-61 (65)
137 PRK04424 fatty acid biosynthes 24.4 83 0.0018 31.3 3.7 46 622-669 7-52 (185)
138 PRK05097 Ter macrodomain organ 24.3 1.6E+02 0.0035 27.5 5.1 72 199-291 17-92 (150)
139 PRK04172 pheS phenylalanyl-tRN 24.2 1E+02 0.0022 35.7 5.0 50 619-670 3-52 (489)
140 PRK09334 30S ribosomal protein 23.8 60 0.0013 28.0 2.2 39 748-786 47-85 (86)
141 PRK11402 DNA-binding transcrip 23.4 49 0.0011 34.2 2.0 33 750-783 41-73 (241)
142 smart00531 TFIIE Transcription 23.4 90 0.002 29.8 3.6 29 634-662 13-41 (147)
143 PF01638 HxlR: HxlR-like helix 23.1 1.3E+02 0.0028 25.9 4.3 44 625-671 8-52 (90)
144 KOG3054 Uncharacterized conser 23.1 61 0.0013 33.2 2.4 54 725-786 205-258 (299)
145 TIGR01889 Staph_reg_Sar staphy 23.0 58 0.0013 29.2 2.1 37 732-776 41-77 (109)
146 TIGR00498 lexA SOS regulatory 22.8 1.5E+02 0.0033 29.6 5.3 50 620-671 4-59 (199)
147 PRK10079 phosphonate metabolis 22.5 53 0.0011 34.0 2.0 48 728-783 28-75 (241)
148 PRK06474 hypothetical protein; 22.1 2.1E+02 0.0045 28.3 6.0 51 619-671 8-60 (178)
149 PF00196 GerE: Bacterial regul 21.9 1.5E+02 0.0032 23.0 4.0 39 621-661 5-43 (58)
150 PRK03573 transcriptional regul 21.9 58 0.0013 30.6 2.0 26 751-776 55-80 (144)
151 cd06171 Sigma70_r4 Sigma70, re 21.9 1.8E+02 0.0039 21.1 4.4 39 621-660 12-50 (55)
152 PRK10681 DNA-binding transcrip 21.6 1.2E+02 0.0026 31.7 4.5 39 623-661 8-46 (252)
153 PF00165 HTH_AraC: Bacterial r 21.4 1.3E+02 0.0027 21.7 3.3 27 634-660 6-32 (42)
154 TIGR02325 C_P_lyase_phnF phosp 21.1 57 0.0012 33.5 1.9 32 751-783 41-72 (238)
155 PF13730 HTH_36: Helix-turn-he 21.0 56 0.0012 25.0 1.4 21 752-772 35-55 (55)
156 COG2996 Predicted RNA-bindinin 20.9 1E+02 0.0022 32.5 3.5 55 613-671 217-279 (287)
157 PF13384 HTH_23: Homeodomain-l 20.6 1E+02 0.0022 22.9 2.8 32 627-660 10-41 (50)
158 PRK10906 DNA-binding transcrip 20.4 1.3E+02 0.0028 31.5 4.4 47 623-671 6-52 (252)
159 PF09904 HTH_43: Winged helix- 20.2 1.2E+02 0.0027 26.3 3.3 32 630-662 16-47 (90)
160 PRK11050 manganese transport r 20.2 1.8E+02 0.0039 27.9 5.0 43 626-670 41-83 (152)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.7e-131 Score=1136.15 Aligned_cols=719 Identities=65% Similarity=1.078 Sum_probs=672.5
Q ss_pred CCCcCCHHHhHHHHHHHHHHHHHHhcCCCCCCCChhhhHHhhhcccccccchhHHHHHHHHhhhhhhhhhhhhhhhhccc
Q 003927 5 ERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQPHLVSAFVNILLLVIHNFFLAFLWYCFFFFFSK 84 (786)
Q Consensus 5 ~~~~~~~~~~W~~~~~~i~~~~~~l~~~~~~~~~~~~ym~~yt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (786)
.+++++++.+|..+++|++++.+++++-+ +.||++|++
T Consensus 4 ~~~~~~~~~~w~~~~~~~~~l~~~~~~~s------~~~~~~~~~------------------------------------ 41 (725)
T KOG2166|consen 4 APKEIDLEVGWSYIETGITKLKRIIEGLS------EPAFEQYQF------------------------------------ 41 (725)
T ss_pred cccccchhccHHHHHHHHHHHHHHHHhhc------cccccHHHH------------------------------------
Confidence 35789999999999999999999776322 556777773
Q ss_pred chhhhHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhh
Q 003927 85 KSVYRTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYF 164 (786)
Q Consensus 85 ~~lY~~vY~~c~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~e~~L~~~~~~W~~~~~~~~~l~~vF~YLdR~y 164 (786)
..+|+++|++|+++.+.+.+++||+++++++.+|+.+.+.+......++.+|+.+++.|.+|+.++++++++|+||||+|
T Consensus 42 ~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~ 121 (725)
T KOG2166|consen 42 MYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPALREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYY 121 (725)
T ss_pred HHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHH
Confidence 36777999999999655556999999999999999998888888888999999999999999999999999999999999
Q ss_pred hhcC-CCCcHHHHH-HHHHHHHHHH-HHHHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhccCcccccHHhhHHHH
Q 003927 165 IARR-SLPPLNEVG-LTCFRDLVYT-ELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAM 241 (786)
Q Consensus 165 v~~~-~~~~i~~l~-l~~fr~~vf~-~l~~~l~~~il~lI~~~R~g~~id~~llk~vi~~l~~lg~~~~~~Y~~~FE~~~ 241 (786)
|+++ +..++++++ +.+|+..+.. ++.+++++++|.+|..+|.|+.||+.+|++++++++.+|.+.+++|..+||++|
T Consensus 122 v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~f 201 (725)
T KOG2166|consen 122 VAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHKEREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKF 201 (725)
T ss_pred HHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHhhcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHH
Confidence 9876 666676666 8888877776 699999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhHhhhc
Q 003927 242 LKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLR 321 (786)
Q Consensus 242 L~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~eE~~r~~~yL~~st~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~ 321 (786)
++.|+.||..++..|+..+++++||.+|+.++.+|..|+..|++..+.+++.+.++..++..|.+.+++.+++||..|+.
T Consensus 202 l~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~ 281 (725)
T KOG2166|consen 202 LQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLN 281 (725)
T ss_pred HHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHh
Confidence 99999999999999999889999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCChhhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHHHHHHHHHHHH
Q 003927 322 DDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYV 401 (786)
Q Consensus 322 ~~~~~dL~~~y~L~~~~~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll~l~~k~~~lv 401 (786)
+++.+||.+||+|++|++.|+++++..|+.|++.+|..++.+..... ..+|+.+|+.+++++++|..++
T Consensus 282 ~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~-----------~~~~~~~v~~~l~~~~~~~~~~ 350 (725)
T KOG2166|consen 282 DDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETA-----------ATNPVEYVQGLLELHDKYKVLV 350 (725)
T ss_pred ccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhc-----------ccchHHHHhccHHHHHHHHHHH
Confidence 99999999999999999999999999999999999988887765432 1579999999999999999999
Q ss_pred HHhcCCChHHHHHHHHHHHHHhhCCCCCCchHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHhhhhccCChhHHHHHH
Q 003927 402 NDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFY 481 (786)
Q Consensus 402 ~~~F~~~~~f~~~l~~af~~~iN~~~~~~~~~e~La~y~D~~lkk~~~~~~~~~e~e~~l~~i~~lf~~l~~KD~F~~~Y 481 (786)
..||++|..|.++++.||..|+|.+..+ .||+||+|||.+||++ ..+.++++++..|++++.+|+|++|||+|+++|
T Consensus 351 ~~~f~~d~~f~~~ld~a~~~fin~n~~~--~~E~la~y~D~~lkk~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Y 427 (725)
T KOG2166|consen 351 KECFANDTLFKKALDAAFEEFINKNVAT--SAELLATYCDDILKKG-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFY 427 (725)
T ss_pred HHHhhccHHHHHHHHHHHHHHHcccCCC--cHHHHHHHhHHHhccc-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHH
Confidence 9999999999999999999999999632 3799999999999995 467889999999999999999999999999999
Q ss_pred HHHHHHHHhCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCC
Q 003927 482 RKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGF 561 (786)
Q Consensus 482 ~~~LakRLL~~~s~s~d~E~~~I~~Lk~~~G~~~t~kl~~M~~D~~~S~~l~~~F~~~~~~~~~~~~~~~f~v~VLt~~~ 561 (786)
+++||||||+++|.|+|+|++||++|+++||.+||+||++||+|+..|++++..|+++ .+.....+++|.|.|||+|+
T Consensus 428 kk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~--~~~~~~~~~df~v~VLt~g~ 505 (725)
T KOG2166|consen 428 KKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY--ANYSANLGIDFTVTVLTTGF 505 (725)
T ss_pred HHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh--hchhccCCCceeEEEeecCC
Confidence 9999999999999999999999999999999999999999999999999999999987 22223457999999999999
Q ss_pred CCCCCCCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHH
Q 003927 562 WPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSE 641 (786)
Q Consensus 562 WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~e 641 (786)
||.+++.++.||++|.++++.|..||.++|+||+|.|+|++|+|+|.++|.+++|+|+|||+|||||++||+.+.+|+++
T Consensus 506 WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~e 585 (725)
T KOG2166|consen 506 WPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEE 585 (725)
T ss_pred cCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHH
Confidence 99998888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCcceEeecCCCchhhhhHHHhHHHHhhhhh
Q 003927 642 IMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPVDEKKKVIEDVDKDRRYAI 721 (786)
Q Consensus 642 i~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~~~~~ki~i~~~~~~e~~~~~~~v~~dR~~~i 721 (786)
|.++|+++.+++.++|+||++.|.+++.+ |.++. +|++.|.+|.+|+++++|+++|.++..|++++.+.+++||+..|
T Consensus 586 I~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i 663 (725)
T KOG2166|consen 586 ILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAI 663 (725)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCchhHHHHHhhhhhHHHHHH
Confidence 99999999999999999999988777766 77777 89999999999999999999998888898999999999999999
Q ss_pred cceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceee
Q 003927 722 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 784 (786)
Q Consensus 722 ~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y 784 (786)
+||||||||+||.|.|++|+.||++|+++||.|++.+||+|||.|||||||+|| +|+++|+|
T Consensus 664 ~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 664 DAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 999999999999999999999999999999999999999999999999999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-121 Score=1007.50 Aligned_cols=723 Identities=31% Similarity=0.534 Sum_probs=644.5
Q ss_pred CcCCHHHhHHHHHHHHHHHHHHhcCCCCCCCChhhhHHhhhcccccccchhHHHHHHHHhhhhhhhhhhhhhhhhcccch
Q 003927 7 KTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQPHLVSAFVNILLLVIHNFFLAFLWYCFFFFFSKKS 86 (786)
Q Consensus 7 ~~~~~~~~W~~~~~~i~~~~~~l~~~~~~~~~~~~ym~~yt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (786)
+..||++.|.+++.||++|..-|. ..++.-.||++||
T Consensus 16 ~~~df~~~W~~i~~~I~~I~~~l~----~~m~~l~~~evY~--------------------------------------- 52 (773)
T COG5647 16 SEEDFESTWEFIERAIGQIFERLY----DSMAILSLMEVYT--------------------------------------- 52 (773)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHH----hhhhhhhHHHHHH---------------------------------------
Confidence 457899999999999999975443 3466777999999
Q ss_pred hhhHHhhhhccCCCCC------------chHHHHHHHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHH
Q 003927 87 VYRTIYNMCTQKPPHD------------YSQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLS 154 (786)
Q Consensus 87 lY~~vY~~c~~~~~~~------------~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~e~~L~~~~~~W~~~~~~~~~l~ 154 (786)
++|++|+++++.- .|..||+++..+.++|+.+.-. .......+.+|..+++.|++|+.++.+++
T Consensus 53 ---~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k~~i~~~~~-~~s~~~~~~fl~~~v~~W~~~~~~~~~i~ 128 (773)
T COG5647 53 ---KIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAKNYIEEYNR-GRSQENMEEFLDELVKFWNRFTKGATMIN 128 (773)
T ss_pred ---HHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHHHHHHHhcc-cccchhHHHHHHHHHHHHHHHHhHHhHHH
Confidence 9999999986531 4889999999999999987532 33333457899999999999999999999
Q ss_pred Hhhcccchhhhh--c---CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhcc--
Q 003927 155 RFFHYLDRYFIA--R---RSLPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGM-- 227 (786)
Q Consensus 155 ~vF~YLdR~yv~--~---~~~~~i~~l~l~~fr~~vf~~l~~~l~~~il~lI~~~R~g~~id~~llk~vi~~l~~lg~-- 227 (786)
++|.||||+|++ + .....++++++..|+.++|.++.+.+.+.+|..+++.|.|+.||+..+..++.|+..+|.
T Consensus 129 ~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s 208 (773)
T COG5647 129 HLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVDSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPS 208 (773)
T ss_pred HHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhHHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccc
Confidence 999999999999 2 345678899999999999999999999999999999999999999999999999999964
Q ss_pred ----CcccccHHhhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHH
Q 003927 228 ----GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSV 303 (786)
Q Consensus 228 ----~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~eE~~r~~~yL~~st~~kl~~~l~~~LI~~ 303 (786)
.++++|.+.|||.||+.|.+||..++++.+..+++.+||.+|+.++++|..+++.|++.+|..+|.++++++||..
T Consensus 209 ~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~ 288 (773)
T COG5647 209 DYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITR 288 (773)
T ss_pred hhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhc
Confidence 3468999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhhhHhhhccCChhhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcc---cccc
Q 003927 304 YANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKR---DVVG 380 (786)
Q Consensus 304 ~~~~ll~~~~s~~~~ll~~~~~~dL~~~y~L~~~~~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~---~~~~ 380 (786)
|.+.|.+.. |||..+++..+.+.|+.||+++++++.|+.+|++.|+.||.+.|.-+ +.....+ ..++.+- ....
T Consensus 289 hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~~~f~~yV~~~g~~~-~i~~~~~-~~~~~~~~~~~~~e 365 (773)
T COG5647 289 HLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQPLQEVFERYVKDEGVLI-NIETNYI-FHCKVDVGFLGSRE 365 (773)
T ss_pred cHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHhhchhh-hhHHhhh-hccchhhcccchhh
Confidence 999997654 89999999999999999999999999999999999999999999221 1111111 0000000 0113
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhCCCC-CCchHHHHHHHHHHHHhcCCCCCCChHHHHH
Q 003927 381 LQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVA-GSSSAELLATFCDNILKKGGSEKLSDEAIEE 459 (786)
Q Consensus 381 ~~~~~~V~~ll~l~~k~~~lv~~~F~~~~~f~~~l~~af~~~iN~~~~-~~~~~e~La~y~D~~lkk~~~~~~~~~e~e~ 459 (786)
..|..|++.++++|+.+..++...|.+|..+.+++++||+.|+|.+.+ ...+||+||+|+|.+||+++ +......++.
T Consensus 366 ~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~-k~s~~~~i~~ 444 (773)
T COG5647 366 CLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDG-KQSFIGKIKD 444 (773)
T ss_pred hcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhccc-cccccccHHH
Confidence 568999999999999999999999999999999999999999999642 35789999999999999975 3333456888
Q ss_pred HHHHHHhhhhccCChhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHH
Q 003927 460 MLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY 539 (786)
Q Consensus 460 ~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~I~~Lk~~~G~~~t~kl~~M~~D~~~S~~l~~~F~~~ 539 (786)
.+.+++.||+|+.+||+|+++|+++||||||+++|+|.++|.+||++||+.||.+||+|+++||+||+.|+++...|++.
T Consensus 445 ~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s 524 (773)
T COG5647 445 LLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHS 524 (773)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999875
Q ss_pred HhcCCCCCCCcceEEEEeecCCCCCCC-CCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEE
Q 003927 540 LSNNPNANPGIDLTVTVLTTGFWPSYK-SFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTEL 618 (786)
Q Consensus 540 ~~~~~~~~~~~~f~v~VLt~~~WP~~~-~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~~~~~~~l 618 (786)
..+ ..+.+||.|.||++.+||..| ...+.||++|.+.++.|++||.+||+||+|.|.|+||+|+|++.|+.+++.+
T Consensus 525 ~~s---~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~ 601 (773)
T COG5647 525 PQS---YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYL 601 (773)
T ss_pred chh---hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccce
Confidence 422 235799999999999999665 4689999999999999999999999999999999999999999998875444
Q ss_pred ---EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCcce
Q 003927 619 ---IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRR 695 (786)
Q Consensus 619 ---~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~~~~~k 695 (786)
+++++|++|+++||+++++|+++|.+.|+++.++++++|+||++.|..+|.+ +++.++|++.|.+|.+|+++..|
T Consensus 602 ~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~r 679 (773)
T COG5647 602 EISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLER 679 (773)
T ss_pred ehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheeeecc--ccccCCCCceEEEccccccccce
Confidence 3668999999999999999999999999999999999999999877666654 47888999999999999999999
Q ss_pred EeecCCCc----hhhhhHHHhHHHHhhhhhcceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhcc
Q 003927 696 IKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDY 771 (786)
Q Consensus 696 i~i~~~~~----~e~~~~~~~v~~dR~~~i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekey 771 (786)
|+++.+.. +++.++++++++||+..+|||||||||+||+|+|++|++||+.|.++||.|++.+||++|+.||||||
T Consensus 680 Iki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeY 759 (773)
T COG5647 680 IKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEY 759 (773)
T ss_pred eeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHH
Confidence 99998754 45667889999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCceeecC
Q 003927 772 LERDKSNPNMFRYLA 786 (786)
Q Consensus 772 l~R~~~d~~~y~Y~a 786 (786)
|+|.++| ..|+|+|
T Consensus 760 LeR~~dd-~iY~YLa 773 (773)
T COG5647 760 LERQADD-EIYVYLA 773 (773)
T ss_pred HHhccCC-ceeeecC
Confidence 9999988 7999997
No 3
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.6e-115 Score=895.04 Aligned_cols=684 Identities=27% Similarity=0.505 Sum_probs=630.0
Q ss_pred CCCCCCCcCCHHHhHHHHHHHHHHHHHHhcCCCCCCCChhhhHHhhhcccccccchhHHHHHHHHhhhhhhhhhhhhhhh
Q 003927 1 MTMNERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQPHLVSAFVNILLLVIHNFFLAFLWYCFFF 80 (786)
Q Consensus 1 ~~~~~~~~~~~~~~W~~~~~~i~~~~~~l~~~~~~~~~~~~ym~~yt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (786)
|.+.+|+.++|+++|..+.+.|..+.. -++++...|-.-|+
T Consensus 1 m~slkp~vv~fd~~w~~l~~si~~ii~------l~~i~~~~w~~~fs--------------------------------- 41 (728)
T KOG2284|consen 1 MYSLKPKVVEFDKVWVQLRPSIIDIIN------LRPITNVQWHHKFS--------------------------------- 41 (728)
T ss_pred CCCCCceeeeHHHHHHHHHHHHHHHHh------ccchhccccccchh---------------------------------
Confidence 667899999999999999999887754 45688888888888
Q ss_pred hcccchhhhHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 003927 81 FFSKKSVYRTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYL 160 (786)
Q Consensus 81 ~~~~~~lY~~vY~~c~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~e~~L~~~~~~W~~~~~~~~~l~~vF~YL 160 (786)
.||.+|.+- |.+-||.||...+.++++|+..+.. .+-..+++.+|..|.+.|+.|..+..++..+|.||
T Consensus 42 ---------dvy~icvs~-p~pl~erly~e~k~~i~~hvrq~~~-~~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yl 110 (728)
T KOG2284|consen 42 ---------DVYDICVSI-PTPLSERLYNEVKACIQEHVRQKRQ-DIVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYL 110 (728)
T ss_pred ---------hHHHHHHhC-CCchhHHHHHHHHHHHHHHHHHHhh-hhhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHH
Confidence 999999996 6778999999999999999986543 33334456799999999999999999999999999
Q ss_pred chhhhhcCC------------------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCC-HHHHHHHHHH
Q 003927 161 DRYFIARRS------------------LPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQID-RALLKNVLDI 221 (786)
Q Consensus 161 dR~yv~~~~------------------~~~i~~l~l~~fr~~vf~~l~~~l~~~il~lI~~~R~g~~id-~~llk~vi~~ 221 (786)
|+.|++.+. +..|-.+||.+||+.+..++...|...+|..|.++|.|+..+ ...+.++|++
T Consensus 111 n~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v~~i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvins 190 (728)
T KOG2284|consen 111 NKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLVKTILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINS 190 (728)
T ss_pred HHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHh
Confidence 999998752 245678899999999999999999999999999999999888 6789999999
Q ss_pred HHHhcc-----------------CcccccHHhhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHcccc
Q 003927 222 FVEIGM-----------------GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYL 284 (786)
Q Consensus 222 l~~lg~-----------------~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~eE~~r~~~yL 284 (786)
|+.+.. ..+.+|++.||.|||.+|..||+++++..+.+.+|++||.+|..+|++|+-||+.||
T Consensus 191 fv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kyl 270 (728)
T KOG2284|consen 191 FVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYL 270 (728)
T ss_pred hhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhc
Confidence 998753 136789999999999999999999999999999999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhHhhhccCChhhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhH
Q 003927 285 HSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLA 364 (786)
Q Consensus 285 ~~st~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~dL~~~y~L~~~~~~~l~~l~~~~~~~I~~~g~~~~~~~ 364 (786)
|+|+..|++..|++.+|..|.+.| +..|..++.+.+..|+..||+|+..+.-||..+...|++||.+.|..+++..
T Consensus 271 h~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~l 346 (728)
T KOG2284|consen 271 HESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENKDLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRL 346 (728)
T ss_pred ChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999999999999877 4469999999999999999999999999999999999999999999999876
Q ss_pred HHHhhhhhhhcccccccchhHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhCCCCC---CchHHHHHHHHH
Q 003927 365 EDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAG---SSSAELLATFCD 441 (786)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~V~~ll~l~~k~~~lv~~~F~~~~~f~~~l~~af~~~iN~~~~~---~~~~e~La~y~D 441 (786)
.+ .+.|..||+.+|.+|.||.+++...|.+|..|..+||+|+...+|...++ .+.||.||+|||
T Consensus 347 t~-------------en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d 413 (728)
T KOG2284|consen 347 TG-------------ENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTD 413 (728)
T ss_pred cc-------------ccchHHHHHHHHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhh
Confidence 43 35799999999999999999999999999999999999999999987642 578999999999
Q ss_pred HHHhcCCCCCCChHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHHHhCChhhHhHHH
Q 003927 442 NILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEG 521 (786)
Q Consensus 442 ~~lkk~~~~~~~~~e~e~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~I~~Lk~~~G~~~t~kl~~ 521 (786)
.+|||+. +++++.++|..|+..+.+|+||+|||+|++||.++||+||+.+.|.|.|.|..||++||+.||++||+++-
T Consensus 414 ~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqacgyefts~~~- 491 (728)
T KOG2284|consen 414 GLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP- 491 (728)
T ss_pred hHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC-
Confidence 9999975 68999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecC
Q 003927 522 MVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYS 601 (786)
Q Consensus 522 M~~D~~~S~~l~~~F~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~ 601 (786)
+.|++.|.+++.+|.+.+. +|.+|.+|+..++.|+.||..+|+||||+|++.
T Consensus 492 -~td~~~s~~lnn~f~~~i~---------------------------nf~~pq~l~~~iq~fe~fyt~~~~grkltwl~~ 543 (728)
T KOG2284|consen 492 -LTDPQLSTNLNNQFAQDIA---------------------------NFHLPQILQPVIQEFEKFYTGKHNGRKLTWLFN 543 (728)
T ss_pred -CCChhhccccchhHHHHHH---------------------------hccchHHHHHHHHHHHHHhccccCCceehhhhh
Confidence 9999999999999987654 278999999999999999999999999999999
Q ss_pred cceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCC
Q 003927 602 LGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTD 681 (786)
Q Consensus 602 l~~~~i~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~ 681 (786)
+|+++++.+|-++.|.-.|.+|||++||+||..+.+++.+|.+.+|++.+.|.+++.++.. .++|.. ++..+..+.
T Consensus 544 ~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tild--v~~~~~--d~~~~~a~s 619 (728)
T KOG2284|consen 544 MSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILD--VTLLTC--DDQNLTADS 619 (728)
T ss_pred hcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCccHHHHHHHHHHHHh--ceeecc--cccccChhh
Confidence 9999999999999999999999999999999999999999999999999999999999974 466754 345777888
Q ss_pred eEEEccCCCCCcceEeecCCCc-----hhhhhHHHhHHHHhhhhhcceeeeccccCCCCChhHHHHHHHHHhCCCCCCCh
Q 003927 682 HFEFNSKFTDKMRRIKIPLPPV-----DEKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDF 756 (786)
Q Consensus 682 ~f~~N~~F~~~~~ki~i~~~~~-----~e~~~~~~~v~~dR~~~i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~ 756 (786)
.|++|.+|+++..|.+|..|.+ +|.+.+...|.+||++.++||||||||+||.+.|+.|++||++|.++||.|++
T Consensus 620 ~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v 699 (728)
T KOG2284|consen 620 LVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDV 699 (728)
T ss_pred hhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCc
Confidence 9999999999999999987654 35566778899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 757 KAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 757 ~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
++||+|||.||+|.||+|.+.+ +.|.|+|
T Consensus 700 ~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 700 PFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred hHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 9999999999999999999876 8999998
No 4
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3e-113 Score=921.05 Aligned_cols=646 Identities=36% Similarity=0.608 Sum_probs=605.7
Q ss_pred HHHHHHHHHHHHHHhcccccccc--cCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhc--CCCCcHHHHHHHHHH
Q 003927 107 LYDKYRESFEEYISSTVLPSIRE--KHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR--RSLPPLNEVGLTCFR 182 (786)
Q Consensus 107 LY~~l~~~l~~~l~~~v~~~l~~--~~~e~~L~~~~~~W~~~~~~~~~l~~vF~YLdR~yv~~--~~~~~i~~l~l~~fr 182 (786)
||+.+++.+++|++..+. .+.+ .+...+|..+.+.|..|+..+.+++.+|.||||.|+.. ..+++++++++.+||
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 899999999999997653 2332 23457999999999999999999999999999999977 367999999999999
Q ss_pred HHHHH----HHHHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhccCcccccHHhhHHHHHHHHHHHHHHHHHHHHh
Q 003927 183 DLVYT----ELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWIL 258 (786)
Q Consensus 183 ~~vf~----~l~~~l~~~il~lI~~~R~g~~id~~llk~vi~~l~~lg~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~ 258 (786)
.+++. .+..++.++++..++++|.|+++|+++|++++.|+..+ .+|.+.|++.|++.+.++|.+++..+.+
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 99998 47788999999999999999999999999999999985 6899999999999999999999999999
Q ss_pred cCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhHhhhccCChhhHHHHHHhhccC
Q 003927 259 EDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKI 338 (786)
Q Consensus 259 ~~s~~eYl~kve~~l~eE~~r~~~yL~~st~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~dL~~~y~L~~~~ 338 (786)
+..+++||++++.++.+|..|+..|++.+|.+.+..++++.|+..|++.++.+ |+..+++.++..|+.+||.|++++
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 799999999999999999999999
Q ss_pred CCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHHHHHHHHHHHHHHhcCCC--hHHHHHHH
Q 003927 339 PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNH--TLFHKSLK 416 (786)
Q Consensus 339 ~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll~l~~k~~~lv~~~F~~~--~~f~~~l~ 416 (786)
.+|...++..|++|+++-|..++.... .++.+|+.+++++++.+-++..||..+ ..|..+++
T Consensus 233 ~~g~l~l~qq~sdylk~~G~KlV~de~----------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~ 296 (661)
T KOG2167|consen 233 QGGQLSLLQQWSDYLKKPGFKLVIDEE----------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMS 296 (661)
T ss_pred hcchHHHHHHHHHHHhcccceeccCch----------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHH
Confidence 989999999999999999999885432 257899999999999999999999988 99999999
Q ss_pred HHHHHHhhCCCCCCchHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHhCCCCCC
Q 003927 417 EAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSAN 496 (786)
Q Consensus 417 ~af~~~iN~~~~~~~~~e~La~y~D~~lkk~~~~~~~~~e~e~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s 496 (786)
+||+.|+|... +++||+||+|.|.+|+.|. +..++++++..++.++.+|+||..||+|+.+|++.||+|||.++|+|
T Consensus 297 ~afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAs 373 (661)
T KOG2167|consen 297 KAFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSAS 373 (661)
T ss_pred HHHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchh
Confidence 99999999774 6899999999999999864 55678889999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHHH
Q 003927 497 DDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEM 576 (786)
Q Consensus 497 ~d~E~~~I~~Lk~~~G~~~t~kl~~M~~D~~~S~~l~~~F~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~~~~~lP~~l 576 (786)
.|+|.+|+++||.+||..||+||++||+||..|++++..|+++..++.....++ +.|.|||.|+||++++.++.||++|
T Consensus 374 vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em 452 (661)
T KOG2167|consen 374 VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEM 452 (661)
T ss_pred hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHH
Confidence 999999999999999999999999999999999999999999865544333455 9999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHH
Q 003927 577 VKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRL 656 (786)
Q Consensus 577 ~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~ 656 (786)
..+++.|..||..+|+||+|.|.+++|+|.+++.|..|+.+|+||++|++|||+||+++.+|++||.++|++.+.+|.++
T Consensus 453 ~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rt 532 (661)
T KOG2167|consen 453 RDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRT 532 (661)
T ss_pred HHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCcceEeecCCCc----hhhhhHHHhHHHHhhhhhcceeeeccccC
Q 003927 657 LHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSR 732 (786)
Q Consensus 657 L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~~~~~ki~i~~~~~----~e~~~~~~~v~~dR~~~i~A~IVRiMK~r 732 (786)
|+||+|+|.++|.+.|.|+.+.++|.|.+|.+|++|..||+|+++.. +|+++|.++|.+||.+.||||||||||+|
T Consensus 533 lqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~r 612 (661)
T KOG2167|consen 533 LQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMR 612 (661)
T ss_pred HHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998764 56777889999999999999999999999
Q ss_pred CCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 733 KVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 733 K~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
|+|+|+.|++|+.+||+ |+..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 613 k~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 613 KTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 99999999999999997 98888 999999999999999999 44 9999998
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.2e-100 Score=788.78 Aligned_cols=714 Identities=26% Similarity=0.458 Sum_probs=640.0
Q ss_pred CcCCHHHhHHHHHHHHHHHHHHhcCCCCCCCChhhhHHhhhcccccccchhHHHHHHHHhhhhhhhhhhhhhhhhcccch
Q 003927 7 KTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQPHLVSAFVNILLLVIHNFFLAFLWYCFFFFFSKKS 86 (786)
Q Consensus 7 ~~~~~~~~W~~~~~~i~~~~~~l~~~~~~~~~~~~ym~~yt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (786)
....||+.|.+..+.+-+|.+ ++++|+..|..||.
T Consensus 9 ~r~qFee~W~~~rpIVlkLLr------Q~sVt~~~WqDLF~--------------------------------------- 43 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLR------QKSVTPAAWQDLFY--------------------------------------- 43 (777)
T ss_pred chhhhhhhccccchHHHHHHh------hccCCHHHHHHHHh---------------------------------------
Confidence 334799999999999999977 78899999999999
Q ss_pred hhhHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhh
Q 003927 87 VYRTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIA 166 (786)
Q Consensus 87 lY~~vY~~c~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~e~~L~~~~~~W~~~~~~~~~l~~vF~YLdR~yv~ 166 (786)
+||..|.+. .....++|+.++..+.+|+...-........+..+|..|..+|.+|-....++...|.-|+..-.-
T Consensus 44 ---~Vh~vclWd--dkGpaKI~d~L~~dI~efi~qAq~rv~s~q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~g 118 (777)
T KOG2285|consen 44 ---HVHKVCLWD--DKGPAKIRDILTRDINEFIHQAQKRVRSLQTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAG 118 (777)
T ss_pred ---hheeeeeec--CCCcHHHHHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhc
Confidence 999999997 335688999999999999987433233334567899999999999999999999999888876443
Q ss_pred cC--------CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhcc---CcccccHH
Q 003927 167 RR--------SLPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGM---GQMDYYEN 235 (786)
Q Consensus 167 ~~--------~~~~i~~l~l~~fr~~vf~~l~~~l~~~il~lI~~~R~g~~id~~llk~vi~~l~~lg~---~~~~~Y~~ 235 (786)
+. .-.+|..+.+..|.+++|..++++|..+.+.++..+|+|+.+|.+++-++-++|+.|+. +.+.+|++
T Consensus 119 k~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmklVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~ 198 (777)
T KOG2285|consen 119 KRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKLVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQ 198 (777)
T ss_pred ccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHH
Confidence 32 12478999999999999999999999999999999999999999999999999999975 56889999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCC--CcHHHHHHHHHHHHHHHHHHHHHHhhh
Q 003927 236 DFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHS--SSEPKLLEKVQHELLSVYANQLLEKEH 313 (786)
Q Consensus 236 ~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~eE~~r~~~yL~~--st~~kl~~~l~~~LI~~~~~~ll~~~~ 313 (786)
.||..||++|.+||+..+..+++++++.+||+.|...|+||+.|+.+||.+ .|..+++++|.++|+.+|.+.|+.
T Consensus 199 nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA--- 275 (777)
T KOG2285|consen 199 NFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA--- 275 (777)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH---
Confidence 999999999999999999999999999999999999999999999999976 678899999999999999999986
Q ss_pred hhhHhhhccCChhhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHHHH
Q 003927 314 SGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIEL 393 (786)
Q Consensus 314 s~~~~ll~~~~~~dL~~~y~L~~~~~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll~l 393 (786)
.|..|+....++-|++||+|+.|++.|++++...+..||+..|.+-+....+.+ +.++..||+.||.+
T Consensus 276 -EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~i-----------ttDsEkYVeqLL~l 343 (777)
T KOG2285|consen 276 -ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENI-----------TTDSEKYVEQLLLL 343 (777)
T ss_pred -HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhc-----------cCCHHHHHHHHHHH
Confidence 589999999999999999999999999999999999999999988776555443 67899999999999
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHHHHHHhhCCC------------------CCCchHHHHHHHHHHHHhcCC-CCCCCh
Q 003927 394 HDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGV------------------AGSSSAELLATFCDNILKKGG-SEKLSD 454 (786)
Q Consensus 394 ~~k~~~lv~~~F~~~~~f~~~l~~af~~~iN~~~------------------~~~~~~e~La~y~D~~lkk~~-~~~~~~ 454 (786)
+++|..+|.++|++|+.|..|-|.||+.++|... +.+++||+||.|||.+||+.. +++++.
T Consensus 344 FnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTS 423 (777)
T KOG2285|consen 344 FNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTS 423 (777)
T ss_pred HHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccH
Confidence 9999999999999999999999999999999864 135789999999999999853 467889
Q ss_pred HHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHHHhCC--hhhHhHHHHHHHHHHhHHH
Q 003927 455 EAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGG--QFTSKMEGMVTDLTLAREN 532 (786)
Q Consensus 455 ~e~e~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~I~~Lk~~~G~--~~t~kl~~M~~D~~~S~~l 532 (786)
+++++.|++|+-+++|+++||+|..|++.||++||+.+.|++.+.|..|+..|+ +||. +|++||.+||+|++.|+++
T Consensus 424 EeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDl 502 (777)
T KOG2285|consen 424 EEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDL 502 (777)
T ss_pred HHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHH
Confidence 999999999999999999999999999999999999999999999999999998 6886 7999999999999999999
Q ss_pred HHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEe
Q 003927 533 QTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKF 611 (786)
Q Consensus 533 ~~~F~~~~~~~~~~~~~~~f~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~ 611 (786)
+..|+..+......++.-.+++.||+.|.|...+. ..+.||.+|+..+-..+.||+++|+||+|.|.|+++.++|++..
T Consensus 503 N~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n 582 (777)
T KOG2285|consen 503 NSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVN 582 (777)
T ss_pred HHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeec
Confidence 99999988776554556678999999999997754 57999999999999999999999999999999999999998766
Q ss_pred cCeeEEEEEcHHHHHHHHhhcCC--CCccHHHHHHHhCCCHHHHHHHHhHhhh---ccccccccCCC----CCCCCCCCe
Q 003927 612 ESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLSDDDVVRLLHSLSC---AKYKILNKEPN----TKTISPTDH 682 (786)
Q Consensus 612 ~~~~~~l~vs~~Q~~ILllFN~~--~~lt~~ei~~~t~l~~~~l~~~L~~L~~---~k~kiL~~~~~----~~~i~~~~~ 682 (786)
+-|.|++.|+|+||+||.+||+. +.+|++.+.-+|.+|+.+|.++|-||+. .|+.||..+|+ .+++.+++.
T Consensus 583 ~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~ 662 (777)
T KOG2285|consen 583 NFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTK 662 (777)
T ss_pred ccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccce
Confidence 55899999999999999999974 6899999999999999999999999985 36788888774 256778899
Q ss_pred EEEccCCCC-----CcceEeecCCCc----hh--hhhHHHhHHHHhhhhhcceeeeccccCCCCChhHHHHHHHHHhCCC
Q 003927 683 FEFNSKFTD-----KMRRIKIPLPPV----DE--KKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRM 751 (786)
Q Consensus 683 f~~N~~F~~-----~~~ki~i~~~~~----~e--~~~~~~~v~~dR~~~i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~ 751 (786)
|.+|.+|.- ..+|.+++.+.. .| .++..+.+-+-|-...|-+||+|||.||+++..+|..|.++.|+..
T Consensus 663 F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnm 742 (777)
T KOG2285|consen 663 FLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNM 742 (777)
T ss_pred EEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHc
Confidence 999999962 223555554321 11 2334567888999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 752 FKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 752 F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
|-|+..+||++||.|||..|++||++|-++|.|+|
T Consensus 743 FlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 743 FLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred cCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 99999999999999999999999999999999997
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=3.4e-94 Score=847.67 Aligned_cols=584 Identities=41% Similarity=0.762 Sum_probs=527.0
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCChhhhHHhhhcccccccchhHHHHHHHHhhhhhhhhhhhhhhhhcccchhhhHHhhh
Q 003927 15 WEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQPHLVSAFVNILLLVIHNFFLAFLWYCFFFFFSKKSVYRTIYNM 94 (786)
Q Consensus 15 W~~~~~~i~~~~~~l~~~~~~~~~~~~ym~~yt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lY~~vY~~ 94 (786)
|+.+++||+.|. ...++...||.+|| +||++
T Consensus 1 W~~l~~~i~~i~-------~~~~~~~~~~~lY~------------------------------------------~vy~l 31 (588)
T PF00888_consen 1 WEILEEAIDQIF-------KKSISKLSYMELYT------------------------------------------CVYNL 31 (588)
T ss_dssp HHHHHHHHHHHH-------TT-GCCSHHHHHHH------------------------------------------HHHHH
T ss_pred ChHHHHHHHHHH-------cCCCChhHHHHHHH------------------------------------------HHHhh
Confidence 999999999986 34588999999999 99999
Q ss_pred hccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhcCCCCcHH
Q 003927 95 CTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLN 174 (786)
Q Consensus 95 c~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~e~~L~~~~~~W~~~~~~~~~l~~vF~YLdR~yv~~~~~~~i~ 174 (786)
|..+ +|++||+++++++.+|+.. +.+.+....++.+|..|.+.|.+|+.++++++++|+||||+|+.++
T Consensus 32 ~~~~----~~~~LY~~l~~~i~~~~~~-~~~~l~~~~~~~~l~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~------ 100 (588)
T PF00888_consen 32 CDNK----YGEQLYDKLKEFISEYLKN-IIESLLSSSDEDLLEEYVQEWEKYKKAIKYISDIFSYLDRNYVKRN------ 100 (588)
T ss_dssp HHTT----THHHHHHHHHHHHHHHHHH-HHHHHCTTTTCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTT------
T ss_pred cCCc----ccHHHHHHHHHHHHHHHHH-HHHHHHhcChhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhh------
Confidence 8887 9999999999999999988 4566666678899999999999999999999999999999999887
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhccCcccccHHhhHHHHHHHHHHHHHHHHH
Q 003927 175 EVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKAS 254 (786)
Q Consensus 175 ~l~l~~fr~~vf~~l~~~l~~~il~lI~~~R~g~~id~~llk~vi~~l~~lg~~~~~~Y~~~FE~~~L~~t~~yY~~~s~ 254 (786)
+|++.|+.++.++++++++.+|.++|.|+.+|..+++++++|++++| ...+|.+.||++||++|.+||+.++
T Consensus 101 -----~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~~~~l~--~~~~y~~~fe~~~l~~t~~yY~~~~- 172 (588)
T PF00888_consen 101 -----LFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLKNVIEMFVELG--SLEVYEEEFEKPFLEETKEYYKSES- 172 (588)
T ss_dssp -----HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHTT--HTHHHHHHTHHHHHHHHHHHHHHHH-
T ss_pred -----hHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhccc--hHHhhHHHHHHHHHHHHHHHHHHHH-
Confidence 99999999999999999999999999999999999999999999998 5789999999999999999999999
Q ss_pred HHHhcCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhHhhhccCChhhHHHHHHh
Q 003927 255 NWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRL 334 (786)
Q Consensus 255 ~~l~~~s~~eYl~kve~~l~eE~~r~~~yL~~st~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~dL~~~y~L 334 (786)
+++.++.+||++|+.++++|.+||+.||+++|..++.++++++||..|.+.| .+|+..|+++++.++|++||+|
T Consensus 173 --i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l 246 (588)
T PF00888_consen 173 --IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRL 246 (588)
T ss_dssp --HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHH
T ss_pred --HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHH
Confidence 6678999999999999999999999999999999999999999999999888 4689999999999999999999
Q ss_pred hccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHHHHHHHHHHHHHHhcCCChHHHHH
Q 003927 335 FSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKS 414 (786)
Q Consensus 335 ~~~~~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll~l~~k~~~lv~~~F~~~~~f~~~ 414 (786)
+++++++++.++..|++||.+.|..+++.... ...|..||+.++++|++|+.++..||++++.|..+
T Consensus 247 ~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~-------------~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~ 313 (588)
T PF00888_consen 247 FSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK-------------SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKA 313 (588)
T ss_dssp HTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC-------------GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHH
T ss_pred hhcccCCCchHHHHHHHHHHHHhHHHHhhccc-------------ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHH
Confidence 99999999999999999999999999876531 34688999999999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCCchHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHhCCCC
Q 003927 415 LKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 494 (786)
Q Consensus 415 l~~af~~~iN~~~~~~~~~e~La~y~D~~lkk~~~~~~~~~e~e~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s 494 (786)
+++||+.++|.+ ...+|++||+|||.+++++. .+.++++++..++.++.+|+|+++||+|+.+|+++||+|||.+++
T Consensus 314 l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~ 390 (588)
T PF00888_consen 314 LDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKS 390 (588)
T ss_dssp HHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-B
T ss_pred HHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccc
Confidence 999999999998 46899999999999999875 567788899999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCC-CCcceEEEEeecCCCCCCCCCC-ccC
Q 003927 495 ANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNAN-PGIDLTVTVLTTGFWPSYKSFD-LNL 572 (786)
Q Consensus 495 ~s~d~E~~~I~~Lk~~~G~~~t~kl~~M~~D~~~S~~l~~~F~~~~~~~~~~~-~~~~f~v~VLt~~~WP~~~~~~-~~l 572 (786)
.+.+.|..||++|+.+||.++|++|++|++|+..|+++++.|++...+.+... ++++|+|.||++|+||..+..+ +.|
T Consensus 391 ~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~l 470 (588)
T PF00888_consen 391 FSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKL 470 (588)
T ss_dssp S-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS----
T ss_pred cccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCccccC
Confidence 99999999999999999999999999999999999999999999987654322 2799999999999999998766 999
Q ss_pred cHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHH
Q 003927 573 PAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDD 652 (786)
Q Consensus 573 P~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~~~~~~~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~ 652 (786)
|++|+.+++.|++||+++|+||+|+|++++|+|+|++++++++++++||++||+||++||+.+++|++||++.||+++++
T Consensus 471 P~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~ 550 (588)
T PF00888_consen 471 PPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEE 550 (588)
T ss_dssp -HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHH
T ss_pred CHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHhhhccccccc--cCCCCCCCCCCCeEEEccCCC
Q 003927 653 VVRLLHSLSCAKYKILN--KEPNTKTISPTDHFEFNSKFT 690 (786)
Q Consensus 653 l~~~L~~L~~~k~kiL~--~~~~~~~i~~~~~f~~N~~F~ 690 (786)
++++|.+|+.. ++|. +.++++.+++++.|.+|.+|+
T Consensus 551 l~~~L~~l~~~--~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 551 LKRALKSLVKS--KILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp HHHHHHCCCTT--TTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHHHHHHHHhC--CcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999854 5554 678889999999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2.3e-33 Score=268.03 Aligned_cols=141 Identities=48% Similarity=0.890 Sum_probs=133.0
Q ss_pred ccCChhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCC
Q 003927 470 YISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPG 549 (786)
Q Consensus 470 ~l~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~I~~Lk~~~G~~~t~kl~~M~~D~~~S~~l~~~F~~~~~~~~~~~~~ 549 (786)
|++|||+|+.+|+++||+|||..++.+.|.|..||++||.+||.++|++|++|++|+..|+++++.|++++.+++ ...+
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 789999999999999999999999999999999999999999999999999999999999999999999876542 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEe
Q 003927 550 IDLTVTVLTTGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKF 611 (786)
Q Consensus 550 ~~f~v~VLt~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~ 611 (786)
++|+|.|||+|+||..+. .++.||++|+.+++.|++||..+|+||+|+|+|++|+|+|+++|
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 899999999999999887 79999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=1.1e-25 Score=248.25 Aligned_cols=299 Identities=24% Similarity=0.320 Sum_probs=232.0
Q ss_pred HHhhhhccCChhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHH--Hh
Q 003927 464 VVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--LS 541 (786)
Q Consensus 464 i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~d~E~~~I~~Lk~~~G~~~t~kl~~M~~D~~~S~~l~~~F~~~--~~ 541 (786)
+-.+...+.+|+.|.+.||.+||.||++....+.|.|..-++.||-++|....+.|++|++|+..|+++++.++.. ..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~ 521 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS 521 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence 3456666799999999999999999999999999999999999999999999999999999999999999999874 22
Q ss_pred cCCCCCCCcceEEEEeecCCCCCCCCCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEc
Q 003927 542 NNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVT 621 (786)
Q Consensus 542 ~~~~~~~~~~f~v~VLt~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~k~~~RkL~W~~~l~~~~i~~~~~~~~~~l~vs 621 (786)
......+.+.+++.||++.+||......+.||.+++..++.|.+-|.+...+|+|.|++++|+|+|.+.|.+++.+++||
T Consensus 522 r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVs 601 (765)
T KOG2165|consen 522 RGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVS 601 (765)
T ss_pred cccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeC
Confidence 21122346888999999999999888889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCcceEeecCC
Q 003927 622 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLP 701 (786)
Q Consensus 622 ~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~~~~~ki~i~~~ 701 (786)
+.||+|+.+|.+.++||++++++.+|+|.+.+.+.|..|+ +.++|..+|. ++++.+|++++.=.+.-+-- .++
T Consensus 602 p~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~~q~~--~~~ 674 (765)
T KOG2165|consen 602 PEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDFDQAE--GTV 674 (765)
T ss_pred HHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeeccccccccccC--CCc
Confidence 9999999999999999999999999999999999999997 5688987653 36778899998533321111 111
Q ss_pred Cc---hhh--hhHHHhHHHHhh--hhhcceeeeccccCCCCChhHHHHHHHHHhCCCCCCCh-------HHHHHHHHhhh
Q 003927 702 PV---DEK--KKVIEDVDKDRR--YAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDF-------KAIKKRIEDLI 767 (786)
Q Consensus 702 ~~---~e~--~~~~~~v~~dR~--~~i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~-------~~iK~~Ie~LI 767 (786)
.. ++. ......+++-+. ..-...||-.+-.-..|+.+-+.+ .|+ .|.|.. +.++.-+..++
T Consensus 675 ~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHn----mLk-mF~~~~~~~~~TlqeL~~fLq~kV 749 (765)
T KOG2165|consen 675 LLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHN----MLK-MFVPPDGSAEITLQELQGFLQRKV 749 (765)
T ss_pred ccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHH----HHe-eeecCCCCCcccHHHHHHHHHHHh
Confidence 11 111 111122222111 122335665555557777776665 333 676544 44555555555
Q ss_pred hhccccc
Q 003927 768 TRDYLER 774 (786)
Q Consensus 768 ekeyl~R 774 (786)
..|-|+-
T Consensus 750 ~e~kL~f 756 (765)
T KOG2165|consen 750 REGKLEF 756 (765)
T ss_pred hccceEE
Confidence 5554443
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=99.79 E-value=2.2e-20 Score=153.89 Aligned_cols=68 Identities=51% Similarity=0.920 Sum_probs=62.7
Q ss_pred HHHHhhhhhcceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCC
Q 003927 713 VDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPN 780 (786)
Q Consensus 713 v~~dR~~~i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~ 780 (786)
|+++|...|+||||||||++|+++|++|+.+|.++++++|.|+..+||++||.||+||||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 46899999999999999999999999999999999999999999999999999999999999999876
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=95.89 E-value=0.14 Score=49.53 Aligned_cols=101 Identities=18% Similarity=0.228 Sum_probs=70.8
Q ss_pred HHhhhhccCCCCCchHHHHHHHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHH-HHHHHHHHhhcccchhhhhc-
Q 003927 90 TIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHK-VMVRWLSRFFHYLDRYFIAR- 167 (786)
Q Consensus 90 ~vY~~c~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~e~~L~~~~~~W~~~~-~~~~~l~~vF~YLdR~yv~~- 167 (786)
.--..|+++. ....+-+.+++.+..-+... ...+.+..++.+|..++..|.-|- ...-++..+|..|++.+-..
T Consensus 38 ~~i~~~~~~~---~~~~~~~dl~elL~tg~~~L-~~~l~~~~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~ 113 (158)
T PF08539_consen 38 FHIKLCIQSF---PPSYFLEDLEELLTTGMYIL-ENQLNEVPDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNG 113 (158)
T ss_pred HHHHHhhccc---chHHHHHHHHHHHHHHHHHH-HHHHhhcchhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccC
Confidence 3345666652 12345556666666554432 345566778899999999999955 66678899999999644322
Q ss_pred ----------------CCCCcHHHHHHHHHHHHHHHHHHHHHH
Q 003927 168 ----------------RSLPPLNEVGLTCFRDLVYTELNGKVR 194 (786)
Q Consensus 168 ----------------~~~~~i~~l~l~~fr~~vf~~l~~~l~ 194 (786)
....+|..++|..|||.|+-+..+++.
T Consensus 114 ~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvLP~y~~l~ 156 (158)
T PF08539_consen 114 KYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVLPYYQRLK 156 (158)
T ss_pred ccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhhcchHhhh
Confidence 244789999999999999988766654
No 11
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=93.53 E-value=4.5 Score=46.37 Aligned_cols=191 Identities=10% Similarity=0.051 Sum_probs=111.4
Q ss_pred hhhhhhhhhhhhhc---------ccchhhhHHhhhhccCCCCCchHHHHHHHHHHHHHHHHhc---c----cccccccCc
Q 003927 69 FFLAFLWYCFFFFF---------SKKSVYRTIYNMCTQKPPHDYSQQLYDKYRESFEEYISST---V----LPSIREKHD 132 (786)
Q Consensus 69 ~~~~~~~~~~~~~~---------~~~~lY~~vY~~c~~~~~~~~~e~LY~~l~~~l~~~l~~~---v----~~~l~~~~~ 132 (786)
|..|++++..+... .+...++.+|+-|..... ...++-+-++.....+..+. + .+. .....
T Consensus 114 rslLrsll~MLsd~~iY~esF~~~fls~f~~lY~aE~~d~~--Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st-~k~l~ 190 (661)
T KOG2167|consen 114 RSLLRSLLKMLSDLQIYKESFELTFLSLFRELYAAEGQDKR--QELEVPEYLEHVEGRLEEENDRVIEYFDSST-KKPLI 190 (661)
T ss_pred HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhcchh--hhcccHHHHHhhhhcccchHHHHHHhccccc-ccchH
Confidence 67777777777654 257888999999998732 22223332322222211110 0 011 11123
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhcCCCCcHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhcCCcC
Q 003927 133 EFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFR--DLVYTELNGKVRDAVITLIDQEREGEQI 210 (786)
Q Consensus 133 e~~L~~~~~~W~~~~~~~~~l~~vF~YLdR~yv~~~~~~~i~~l~l~~fr--~~vf~~l~~~l~~~il~lI~~~R~g~~i 210 (786)
..+...+..+|-....... +++-+|-+ ..++...++.++-..+- ..+....++-+......+|..++.++..
T Consensus 191 atV~~~LL~~hL~~IL~kg----l~~lvDm~--q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~kDk~m 264 (661)
T KOG2167|consen 191 ATVERCLLSRHLDLILTKG----LDSLVDMR--QTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEKDKDM 264 (661)
T ss_pred HHHHHHHHHHHHHHHHhcc----hHHhhhhh--hccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchhhHHH
Confidence 4677788888877644333 33334332 11233456666655552 2223356677777777777777766543
Q ss_pred --CHHHHHHHHHHHHHhccCcccccHHhhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHH
Q 003927 211 --DRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKRE 276 (786)
Q Consensus 211 --d~~llk~vi~~l~~lg~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~eE 276 (786)
+....|.-+++.+.. .++...- .+|+.+++.+|...++ ...+.+.+|+.+....+-.+
T Consensus 265 VqELL~FK~k~Dii~~~-----sF~~~v~-e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 265 VQELLDFKKKVDIIVDE-----SFLKYVA-EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred HHHHHHHHHHhhHHHHH-----HHHHhhH-HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 233467777777763 2333333 7899999999999888 45677899998887655443
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=92.27 E-value=0.4 Score=42.27 Aligned_cols=65 Identities=18% Similarity=0.214 Sum_probs=51.9
Q ss_pred EEEcHHHHHHHHhhc--------CCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCC
Q 003927 618 LIVTTYQASALLLFN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 689 (786)
Q Consensus 618 l~vs~~Q~~ILllFN--------~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F 689 (786)
..++.-|+.+|+..- ..+.+|-.||++.+|++.+.+.++|..|. +-+++.+.. ....|++|.++
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 457788888887554 46789999999999999999999999997 567776532 24679999876
Q ss_pred C
Q 003927 690 T 690 (786)
Q Consensus 690 ~ 690 (786)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 5
No 13
>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=91.54 E-value=0.29 Score=37.81 Aligned_cols=45 Identities=29% Similarity=0.369 Sum_probs=36.5
Q ss_pred HHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 625 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 625 ~~ILllFN~~~-~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
+.||..|.+.+ .+|+.||++.+|+|...+.+.|..|. ..+.+.++
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV--EEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecC
Confidence 46788888765 58999999999999999999999997 45677654
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=91.40 E-value=0.58 Score=40.03 Aligned_cols=59 Identities=15% Similarity=0.215 Sum_probs=42.0
Q ss_pred HHHHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003927 623 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 688 (786)
Q Consensus 623 ~Q~~ILllFN~~~-~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~ 688 (786)
+++.+.+..+..+ .+|.+||++.+++++..+.+.+..|. +.+++...+ | ++..|.++.+
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-G----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCC
Confidence 4555555544444 49999999999999999999999996 678876432 1 4567887765
No 15
>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=89.96 E-value=0.42 Score=38.12 Aligned_cols=51 Identities=25% Similarity=0.385 Sum_probs=42.0
Q ss_pred EcHHHHHHHHhhcCCCC--ccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 620 VTTYQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 620 vs~~Q~~ILllFN~~~~--lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+|+.|+.||......+. +|..||++.++++...+.+.+..|. +.+++.+.+
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 46788999987776665 9999999999999999999999997 557777654
No 16
>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=88.95 E-value=0.76 Score=34.68 Aligned_cols=41 Identities=24% Similarity=0.343 Sum_probs=34.0
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
+..+..||....+++.+|..||++.+|++...+.+.|..|.
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45677788888888889999999999999999999999996
No 17
>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=85.92 E-value=1.3 Score=35.96 Aligned_cols=51 Identities=24% Similarity=0.348 Sum_probs=38.7
Q ss_pred EcHHHHHHHHhhc-CCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 620 VTTYQASALLLFN-SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 620 vs~~Q~~ILllFN-~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+|..|..||.... .....|..+|++.++++...+.+.|..|. ..+++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~--~~glv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLE--EKGLVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEecC
Confidence 3677899998888 77899999999999999999999999997 457776543
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=85.90 E-value=0.6 Score=36.84 Aligned_cols=50 Identities=24% Similarity=0.383 Sum_probs=42.3
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
|..|+.+|....+.+.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 2 t~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 2 TPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp THHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 67889999888888889999999999999999999999997 557776653
No 19
>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=84.16 E-value=1.8 Score=39.54 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=45.2
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 619 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
.++..|+.||......+.+|..+|++.+|++...+-+.+..|. +-+++.+.+
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 4688999999988888899999999999999999999999996 567777654
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=83.30 E-value=1.6 Score=34.86 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=39.8
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
++.-..||..+...++.|+.||++.+|++...+..+|..|. +.+++...
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 45566788778667899999999999999999999999996 56777643
No 21
>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=83.12 E-value=1.8 Score=34.12 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=38.3
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 624 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 624 Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
|..|+-..++.+.+|++||++.+|+++..+.+-|..|. +.+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 44577778888999999999999999999999999997 44556553
No 22
>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=81.92 E-value=3.4 Score=31.05 Aligned_cols=43 Identities=26% Similarity=0.339 Sum_probs=33.6
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 668 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL 668 (786)
...-||.+.-+ ++.++.||++.+|++...+.++|..|. +.+++
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV 45 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLV 45 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCe
Confidence 34556666655 779999999999999999999999986 45555
No 23
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=81.80 E-value=2.7 Score=40.01 Aligned_cols=52 Identities=17% Similarity=0.174 Sum_probs=44.8
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 619 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
.+|..|+.||......+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 4778899998876666789999999999999999999999997 668887764
No 24
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=78.27 E-value=3.9 Score=33.54 Aligned_cols=47 Identities=23% Similarity=0.292 Sum_probs=37.5
Q ss_pred HHHHHHHhhcCCCC--ccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 623 YQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 623 ~Q~~ILllFN~~~~--lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
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 34456777777655 9999999999999999999999996 45666553
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=78.18 E-value=0.83 Score=37.61 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=34.6
Q ss_pred eeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCC
Q 003927 726 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 777 (786)
Q Consensus 726 VRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~ 777 (786)
-.+|+.++.++.++|-. +|..+++.+..-++.|+.+|||++.+.
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 34677888888887766 599999999999999999999998754
No 26
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.14 E-value=6.8 Score=38.26 Aligned_cols=45 Identities=18% Similarity=0.212 Sum_probs=36.5
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 624 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 624 Q~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.+++.+.|+.. ..+|.++|++.+|+|...+.+.|..|. +.+++..
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 34455567654 579999999999999999999999996 6788864
No 27
>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=76.78 E-value=5.9 Score=35.74 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=43.1
Q ss_pred EEcHHHHHHHHhhc----CCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 619 IVTTYQASALLLFN----SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 619 ~vs~~Q~~ILllFN----~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
.+|..|..||.... ..+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45788888886554 55789999999999999999999999997 567887754
No 28
>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=76.06 E-value=8 Score=34.43 Aligned_cols=61 Identities=26% Similarity=0.387 Sum_probs=44.6
Q ss_pred EcHHHHHHHHh-------hcC-CCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCC
Q 003927 620 VTTYQASALLL-------FNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 690 (786)
Q Consensus 620 vs~~Q~~ILll-------FN~-~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~ 690 (786)
+|.-|.-|++. ||. .+.+|..++++.||++...+.+++..|+ +.++|... +..+.+|.+.+
T Consensus 30 ls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 30 LSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred ccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 34445544443 553 4689999999999999999999999997 67888653 35566666543
No 29
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=75.52 E-value=7.9 Score=37.35 Aligned_cols=56 Identities=11% Similarity=0.083 Sum_probs=41.1
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003927 625 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 687 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~ 687 (786)
+.+.|..+..+.+|..+|++..++|...|.+.|..|. |.+++.... | ++..|.++.
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 3444555666678999999999999999999999996 678886432 1 334565544
No 30
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=75.41 E-value=6 Score=33.99 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=37.1
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 625 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 625 ~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
..||..+... +.+|..||++.+|++...+.+.|..|. +.+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeec
Confidence 3466666665 689999999999999999999999996 46788664
No 31
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=74.84 E-value=5.3 Score=34.69 Aligned_cols=53 Identities=28% Similarity=0.326 Sum_probs=44.7
Q ss_pred EEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 617 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 617 ~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
++.++..+..||......+.+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 345778899999888777789999999999999999999999997 45777653
No 32
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=74.35 E-value=6.2 Score=30.51 Aligned_cols=35 Identities=23% Similarity=0.369 Sum_probs=28.1
Q ss_pred HHHhh-cCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 627 ALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 627 ILllF-N~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
||.++ +..+.+|.++|++.+|++...+.+.|..|-
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 44333 666679999999999999999999999885
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=74.26 E-value=3.3 Score=37.80 Aligned_cols=57 Identities=16% Similarity=0.272 Sum_probs=39.1
Q ss_pred eeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 725 IVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 725 IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
|++++=..+.++..+ |.+.+.....+....|+..+..|.+||||+|.... ..|.|-|
T Consensus 8 IM~~lW~~~~~t~~e----I~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p 64 (115)
T PF03965_consen 8 IMEILWESGEATVRE----IHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp HHHHHHHHSSEEHHH----HHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred HHHHHHhCCCCCHHH----HHHHHHhccccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 444444444455444 44566666778899999999999999999998753 4788864
No 34
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=73.40 E-value=6.7 Score=41.22 Aligned_cols=46 Identities=15% Similarity=0.287 Sum_probs=39.5
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 625 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+.||.+|.....+|+.||++.+|+|...+.+.|..|. ..+.|.+.+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~--~~G~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMK--TLGYVAQEG 62 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 4678889887789999999999999999999999997 457776653
No 35
>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=73.00 E-value=4.7 Score=37.74 Aligned_cols=59 Identities=17% Similarity=0.207 Sum_probs=42.9
Q ss_pred ceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 723 ASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 723 A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
..|++++-..+.++..+++. .+..+..+....|...|..|.+||||+|..+. ..|.|-|
T Consensus 7 ~~VM~vlW~~~~~t~~eI~~----~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p 65 (130)
T TIGR02698 7 WEVMRVVWTLGETTSRDIIR----ILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA 65 (130)
T ss_pred HHHHHHHHcCCCCCHHHHHH----HHhhccCCcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence 34666666666676555554 45545667888999999999999999998654 4788854
No 36
>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=72.85 E-value=9.2 Score=35.94 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=35.6
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 624 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 624 Q~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.+++.|.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 34444555544 479999999999999999999999996 6788753
No 37
>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=71.37 E-value=2.2e+02 Score=34.61 Aligned_cols=139 Identities=11% Similarity=0.261 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHh-hhhhhHhhhc
Q 003927 243 KDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEK-EHSGCHALLR 321 (786)
Q Consensus 243 ~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~eE~~r~~~yL~~st~~kl~~~l~~~LI~~~~~~ll~~-~~s~~~~ll~ 321 (786)
+...-||...+.--+ ...+..+.+.|....+++.+..-..+-.....||.+-++. ++.++.. ..+.+....
T Consensus 554 eN~~~~~e~l~~~~~-~~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~~g------ve~l~~~~~~~ei~~~~- 625 (701)
T PF09763_consen 554 ENYHHFYEELSQLKI-NSVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFFEG------VEALLQTVSPEEISYQA- 625 (701)
T ss_pred HHHHHHHHHHhhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHH------HHHHHhccCchhcccch-
Confidence 333344444433222 2455677788887777777654333323333444443321 1111111 000111111
Q ss_pred cCChhhHHHHHHhh--ccCCCChhhHHHHHHHHHHHHHH------HHHHhHHHHhhhhhhhcccccccchhHHHHHHHHH
Q 003927 322 DDKVEDLSRMFRLF--SKIPRGLDPVSNIFKQHVTAEGT------ALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIEL 393 (786)
Q Consensus 322 ~~~~~dL~~~y~L~--~~~~~~l~~l~~~~~~~I~~~g~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll~l 393 (786)
......|+.+-+-+ ..+..|++.|.+.+++|+...+. .++.. .=..+-...++.
T Consensus 626 ~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~------------------vW~~~q~~~i~~ 687 (701)
T PF09763_consen 626 AYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQV------------------VWSAMQEEFIRQ 687 (701)
T ss_pred hccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHH------------------HHHHHHHHHHHH
Confidence 11234454444442 23445777777777777722111 11111 112345678899
Q ss_pred HHHHHHHHHHhcCC
Q 003927 394 HDKYLAYVNDCFQN 407 (786)
Q Consensus 394 ~~k~~~lv~~~F~~ 407 (786)
|.++..|+..|+.|
T Consensus 688 ~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 688 YERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHhCCC
Confidence 99999999999875
No 38
>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=70.99 E-value=1.7e+02 Score=32.10 Aligned_cols=164 Identities=14% Similarity=0.253 Sum_probs=92.7
Q ss_pred hhHhhhccCChhhHHHHHHhhccC---CCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHH
Q 003927 315 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 391 (786)
Q Consensus 315 ~~~~ll~~~~~~dL~~~y~L~~~~---~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll 391 (786)
.|..-.+.++.+.+.|.++||--+ +.||+.....+.+.|.......+........ ++..+.-|+..|.
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~---------~~~~~~~~~~~lt 85 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSS---------DSRSPVFYADALT 85 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhccccc---------cccccccHHHHHH
Confidence 366777788899999988888654 4688888777777777766665544322110 0234555777777
Q ss_pred HHHHHHHH-------HHHHhcCCChH--HHHHHHHHH--------HHHhhCCCCCCchHHHHHHHHHHHHhc--------
Q 003927 392 ELHDKYLA-------YVNDCFQNHTL--FHKSLKEAF--------EVFCNKGVAGSSSAELLATFCDNILKK-------- 446 (786)
Q Consensus 392 ~l~~k~~~-------lv~~~F~~~~~--f~~~l~~af--------~~~iN~~~~~~~~~e~La~y~D~~lkk-------- 446 (786)
.+++.... +|..+|+.... +...|..-| ..|..... -.+....+..|-...+.+
T Consensus 86 ~LFe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~ 164 (331)
T PF08318_consen 86 KLFEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERR-LDRKLQDIQSYNFSFLVKNSGRSSSS 164 (331)
T ss_pred HHHHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-HHHHHHHHHhhhhhhhcccccccccc
Confidence 77766644 56678886532 112222221 11221110 011122233333333322
Q ss_pred ---------CCCCCCChHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHhCCCCC
Q 003927 447 ---------GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSA 495 (786)
Q Consensus 447 ---------~~~~~~~~~e~e~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~ 495 (786)
+.....+.-+++..|+.+..+... -..|.++++.|.-.....
T Consensus 165 ~~~~~~~~~~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~~~ 215 (331)
T PF08318_consen 165 SSRAASSSQSEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFSDP 215 (331)
T ss_pred ccccccccccccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhccccc
Confidence 001223445788888888887764 457999999998875443
No 39
>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=69.25 E-value=4.6 Score=32.90 Aligned_cols=49 Identities=24% Similarity=0.337 Sum_probs=38.6
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
|-.++-|+...-..+..|..||++.+|++...+.+.|..|. +.+++.+.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~--~~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE--EKGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 44566666554466789999999999999999999999997 45676654
No 40
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=68.81 E-value=9 Score=28.79 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=33.8
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 626 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 626 ~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.|+..+.+...+|..+|++.++++...+.+.|..|. +.+++.+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~--~~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLE--EQGLLTR 46 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 455555556679999999999999999999999986 3455544
No 41
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=68.75 E-value=8.2 Score=36.55 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=44.0
Q ss_pred EEEcHHHHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 618 LIVTTYQASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 618 l~vs~~Q~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+.+|..|..||...... +..|..+|++.++++...+.+.+..|. +-+++.+.+
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 35778898888777653 568999999999999999999999997 667887654
No 42
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=68.26 E-value=4.6 Score=37.13 Aligned_cols=61 Identities=20% Similarity=0.316 Sum_probs=50.9
Q ss_pred hcceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 721 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 721 i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
.++.|++||=+++..+..+++.++.. .+.++...|+--|..|..||.|.|.-++ ..|.|-|
T Consensus 7 aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 7 AEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence 56778999999999998888886654 5788999999999999999999998754 5677743
No 43
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=67.76 E-value=10 Score=37.82 Aligned_cols=53 Identities=13% Similarity=0.004 Sum_probs=45.4
Q ss_pred EEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 618 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 618 l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+.+|..|..||......+.+|..+|++.++++...+.+.|..|. +-+++.+.+
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 35778899999988888899999999999999999999999996 557777654
No 44
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=67.29 E-value=11 Score=30.28 Aligned_cols=56 Identities=21% Similarity=0.227 Sum_probs=37.4
Q ss_pred HHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEc
Q 003927 627 ALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFN 686 (786)
Q Consensus 627 ILllFN~-~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N 686 (786)
||-.++. +.++|..||++++|++.......|..|. +.+.+.+.|.++.- ...+.+|
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 3444555 6789999999999999999999999996 55666665543321 1356655
No 45
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=67.15 E-value=4.7 Score=34.30 Aligned_cols=43 Identities=21% Similarity=0.413 Sum_probs=32.5
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 625 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
..||...+..+.+++.+|.+.+|+++..+.++|..|. +.+.+.
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le--~~GyV~ 45 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLE--EAGYVE 45 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEE
Confidence 3455555567889999999999999999999999996 445554
No 46
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=66.98 E-value=14 Score=35.60 Aligned_cols=59 Identities=15% Similarity=0.187 Sum_probs=42.4
Q ss_pred HHHHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003927 623 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 688 (786)
Q Consensus 623 ~Q~~ILllFN~~~-~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~ 688 (786)
+++.+.|.-+..+ ..|.++|++..|+|+..|.+.+..|. |.+++.... | ++.-|.++.+
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 4455555555554 68899999999999999999999996 778886432 1 3445655543
No 47
>PHA00738 putative HTH transcription regulator
Probab=65.35 E-value=13 Score=33.27 Aligned_cols=67 Identities=22% Similarity=0.124 Sum_probs=50.6
Q ss_pred EEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCC
Q 003927 617 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 689 (786)
Q Consensus 617 ~l~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F 689 (786)
++...+.=-.||.+..+++.+++.+|++.++++...+-++|.-|- ..+|+.....|. .-.|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr----~vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGR----TLYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECC----EEEEEECCCc
Confidence 455556666677766677779999999999999999999999996 568887655443 2357777664
No 48
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=64.47 E-value=16 Score=33.91 Aligned_cols=46 Identities=20% Similarity=0.278 Sum_probs=35.1
Q ss_pred HHHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 623 YQASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 623 ~Q~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
+++.+.+.-++. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 344444444433 389999999999999999999999997 5677754
No 49
>PRK10870 transcriptional repressor MprA; Provisional
Probab=63.68 E-value=15 Score=36.18 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=42.5
Q ss_pred EEcHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 619 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~--~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
.+|..|..||..... ..++|..||++.++++...+.+.+..|. +-+++.+.+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe--~kGlV~R~~ 105 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE--KRGWIERRE 105 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecC
Confidence 356778888876653 4579999999999999999999999997 568887764
No 50
>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=63.62 E-value=8.8 Score=37.51 Aligned_cols=48 Identities=25% Similarity=0.331 Sum_probs=40.0
Q ss_pred CccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCC
Q 003927 636 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDK 692 (786)
Q Consensus 636 ~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~~~ 692 (786)
-+|..+|++.+|++...+.+++..|. +.++|.+. ....|.+|++|--+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~-------~~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKI-------RNGAYMINPNFFFK 122 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEc-------cCCeEEECcHHhee
Confidence 47889999999999999999999997 56788765 24589999997644
No 51
>PRK11569 transcriptional repressor IclR; Provisional
Probab=61.05 E-value=15 Score=38.99 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=39.0
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 624 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 624 Q~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
-..||.+|.+. ..+|+.||++.+|++...+.+.|.+|. ..+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 34678889864 579999999999999999999999997 467786653
No 52
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=60.93 E-value=16 Score=38.11 Aligned_cols=46 Identities=28% Similarity=0.447 Sum_probs=39.1
Q ss_pred HHHHHhhcCCCC-ccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 625 ASALLLFNSSDR-LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 625 ~~ILllFN~~~~-lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+.||.+|..... +++.||++.+|+|...+.+.|..|. ..+.+.+++
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 467888887554 7899999999999999999999997 568888765
No 53
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.40 E-value=20 Score=33.27 Aligned_cols=38 Identities=26% Similarity=0.356 Sum_probs=33.5
Q ss_pred cCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 632 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 632 N~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
+.++.+|+++|++.++.+...+.++|+.|. ..+++.++
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~--~~GlV~Re 75 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLL--EAGLVERE 75 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHH--HcCCeeee
Confidence 367899999999999999999999999997 56788765
No 54
>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=59.89 E-value=18 Score=29.02 Aligned_cols=47 Identities=26% Similarity=0.324 Sum_probs=37.4
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
+..+..|+..+.+.+ ++..||++.+|++...+.+.|..|. ..+++..
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~--~~g~i~~ 52 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLE--EAGLVES 52 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHH--HCCCeEE
Confidence 456777777766665 9999999999999999999999986 3456654
No 55
>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=59.51 E-value=14 Score=27.17 Aligned_cols=35 Identities=34% Similarity=0.519 Sum_probs=25.9
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 626 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 626 ~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
.||-...+....|+.+|++.+|++...+.+-+..|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 45666666688999999999999999998877654
No 56
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=59.24 E-value=18 Score=38.32 Aligned_cols=47 Identities=23% Similarity=0.282 Sum_probs=39.0
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 624 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 624 Q~~ILllFN~~-~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
-..||.+|... ..+|+.||++.+|+|...+.+.|.+|. ..+.|.+.+
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~--~~G~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQ--AADFVYQDS 74 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 34688889765 479999999999999999999999997 457776653
No 57
>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=59.12 E-value=21 Score=29.56 Aligned_cols=46 Identities=20% Similarity=0.335 Sum_probs=34.5
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
+..|. ||+..... ..|++||.+.||++.+.|...|.-|. +-+++.+
T Consensus 5 t~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 5 TVTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred hHHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 34454 33334333 89999999999999999999999996 5566654
No 58
>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=58.74 E-value=22 Score=33.05 Aligned_cols=43 Identities=28% Similarity=0.291 Sum_probs=34.1
Q ss_pred HHHHhhc--CCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 626 SALLLFN--SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 626 ~ILllFN--~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.+|..+. ..+.+|..||++.+|++...+.+.|..|. +.+++..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 3444443 34579999999999999999999999997 5678754
No 59
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=58.45 E-value=19 Score=27.76 Aligned_cols=39 Identities=26% Similarity=0.373 Sum_probs=32.1
Q ss_pred hcCCCCc-cHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 631 FNSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 631 FN~~~~l-t~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
+...+.+ |..+|++.+|++...+.++|..|. +.+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 4455567 899999999999999999999997 45777654
No 60
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=58.34 E-value=21 Score=26.24 Aligned_cols=33 Identities=30% Similarity=0.440 Sum_probs=28.7
Q ss_pred CccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 636 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 636 ~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.+|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 57899999999999999999999996 5577764
No 61
>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=57.71 E-value=2.9e+02 Score=30.19 Aligned_cols=161 Identities=15% Similarity=0.270 Sum_probs=85.3
Q ss_pred hhHhhhccCChhhHHHHHHhhccC---CCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHH
Q 003927 315 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 391 (786)
Q Consensus 315 ~~~~ll~~~~~~dL~~~y~L~~~~---~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll 391 (786)
.|..-+++++.+.+.|.++||-.+ ..|++.....+.+.|......+.+..... .. .+..+--|+..|.
T Consensus 15 ~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~---~~------~~~~~~~~a~~lt 85 (324)
T smart00762 15 RFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGA---SD------DTRAAVFYADTLT 85 (324)
T ss_pred HHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccc---cc------cccccchHHHHHH
Confidence 377777888999999999998655 45777777766666666554443322110 00 0223455666666
Q ss_pred HHHHHH-------HHHHHHhcCCChHH------HHHHHHHHHHHhhCCCCCCch---HHHHHHHHHHHHhc---------
Q 003927 392 ELHDKY-------LAYVNDCFQNHTLF------HKSLKEAFEVFCNKGVAGSSS---AELLATFCDNILKK--------- 446 (786)
Q Consensus 392 ~l~~k~-------~~lv~~~F~~~~~f------~~~l~~af~~~iN~~~~~~~~---~e~La~y~D~~lkk--------- 446 (786)
.+++.. ..+|..+|+.+... +...|.-....++.-....+. ...+..|.-..+..
T Consensus 86 ~Lfe~ia~ii~~h~~~I~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~ 165 (324)
T smart00762 86 HLFENVATIIEQHQPVIEKYYGPDGMLYVITKLQKEADLQGGIILDTFMDERRIDRLISDINSYNHAQLHAGASNDARAS 165 (324)
T ss_pred HHHHHHHHHHHhccHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhccccccccccccccc
Confidence 666555 44667778744221 111111121122110000011 11222232222211
Q ss_pred --CCCCCCChHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHhC
Q 003927 447 --GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLF 491 (786)
Q Consensus 447 --~~~~~~~~~e~e~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~ 491 (786)
+...+.+.-+++..|+.+..+... -..|.++++.|.-.
T Consensus 166 ~~~~~~~~d~revd~lL~Eis~i~~~-------~~lY~rFi~~k~~~ 205 (324)
T smart00762 166 SNGEDEGLDPRELDAILEEISQILSR-------WELYCRFISRKINE 205 (324)
T ss_pred cccccCCCCHHHHHHHHHHHHHHHHh-------HHHHHHHHHHHHhh
Confidence 011234556888889988888764 35799999988774
No 62
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=57.60 E-value=18 Score=38.13 Aligned_cols=46 Identities=20% Similarity=0.200 Sum_probs=38.4
Q ss_pred HHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 625 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 625 ~~ILllFN~~~-~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+.||.+|.+.+ .+|..||++.+|++...+.+.|..|. ..++|.+.+
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 45777887654 59999999999999999999999997 567887664
No 63
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=56.75 E-value=21 Score=32.76 Aligned_cols=60 Identities=22% Similarity=0.304 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 688 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~ 688 (786)
.-..||.+.-+.++.++.||++.+|++...+-++|.-|. +.+++.....|+ .-.|++|.+
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~~ 76 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSPH 76 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECch
Confidence 334455544444679999999999999999999999996 578887655432 234677653
No 64
>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=56.60 E-value=16 Score=36.84 Aligned_cols=52 Identities=17% Similarity=0.198 Sum_probs=45.0
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 619 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
.++..|..||..+.+++..+..+|++.+|++...+.+.|..|. +.+++.+.+
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 4678899999988887789999999999999999999999996 567887653
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=55.71 E-value=14 Score=30.78 Aligned_cols=34 Identities=24% Similarity=0.147 Sum_probs=27.2
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 634 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 634 ~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
.+.+|+.||++.+|++...++..+..+. +.++|.
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~ 63 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLV 63 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHH
Confidence 3678999999999999999999888764 344443
No 66
>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=55.51 E-value=19 Score=31.87 Aligned_cols=44 Identities=25% Similarity=0.342 Sum_probs=36.9
Q ss_pred EEcHHHHHHHHhhcC----CCCccHHHHHHHhCCCHHHHHHHHhHhhh
Q 003927 619 IVTTYQASALLLFNS----SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 662 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~----~~~lt~~ei~~~t~l~~~~l~~~L~~L~~ 662 (786)
.++..|-.||-.+.+ .+.+++++|++.++++.++++.+|..|+.
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 578899999988877 45799999999999999999999999975
No 67
>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=55.14 E-value=24 Score=36.76 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=37.0
Q ss_pred HHHHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 625 ASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 625 ~~ILllFN~-~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
+.||.+|.. ...+|+.||++.+|+|...+.+.|..|. ..+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~--~~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLV--ELGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 457888986 4579999999999999999999999997 4566754
No 68
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=52.75 E-value=17 Score=28.74 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=28.4
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 624 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 624 Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
|.-+|-++-+.+.+|+.||++.+|++...++.-+.-|
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L 43 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINEL 43 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 4455544434788999999999999999999888776
No 69
>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=52.74 E-value=20 Score=29.18 Aligned_cols=37 Identities=27% Similarity=0.271 Sum_probs=31.8
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhh
Q 003927 626 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 662 (786)
Q Consensus 626 ~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~ 662 (786)
.|--+.++...+|+.+|+..||++++++..+|..|..
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4556678888999999999999999999999999974
No 70
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=51.92 E-value=26 Score=31.34 Aligned_cols=51 Identities=24% Similarity=0.347 Sum_probs=42.8
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 620 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 620 vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
++..|+.||......+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 788899999877776666659999999999999999999997 567777654
No 71
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=50.84 E-value=25 Score=31.25 Aligned_cols=45 Identities=18% Similarity=0.273 Sum_probs=37.2
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
..-.||..+......|+.+|++.+|++...+.+.+..|. +.+++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~--~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE--EEGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCee
Confidence 345677777777789999999999999999999999996 446664
No 72
>PF13730 HTH_36: Helix-turn-helix domain
Probab=49.81 E-value=39 Score=25.95 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=22.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 638 SYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 638 t~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
|.+.|++.+|++...+.+++..|.
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 73
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=49.43 E-value=31 Score=26.71 Aligned_cols=35 Identities=23% Similarity=0.312 Sum_probs=29.8
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 634 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 634 ~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.+..|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~--~~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR--EAGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 5678999999999999999999999997 4466654
No 74
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=49.39 E-value=44 Score=31.53 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=33.2
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 631 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 631 FN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+..+..+|..+|++.+|+|...+.++|..|. +.+++...+
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 4445578999999999999999999999996 668886543
No 75
>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=48.96 E-value=7.6 Score=30.60 Aligned_cols=45 Identities=16% Similarity=0.324 Sum_probs=39.2
Q ss_pred eeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccC
Q 003927 724 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 776 (786)
Q Consensus 724 ~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~ 776 (786)
.|+..++.++.++..+|.+ .|..+...|.+=+..|-++|.|.|.-
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 4677788889998888877 48889999999999999999999875
No 76
>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=48.70 E-value=13 Score=29.83 Aligned_cols=50 Identities=12% Similarity=0.213 Sum_probs=30.9
Q ss_pred ceeeeccc-cCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhcccccc--CCCCC
Q 003927 723 ASIVRIMK-SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERD--KSNPN 780 (786)
Q Consensus 723 A~IVRiMK-~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~--~~d~~ 780 (786)
..|.+.+. ....++..+|.. .+..+.+.+-+.|+.|+++|||++. +.|+.
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred HHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 34444555 555565555554 3556778889999999999999765 44444
No 77
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=48.24 E-value=41 Score=26.69 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=30.4
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 635 DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 635 ~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
..+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 469999999999999999999999997 45777654
No 78
>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=47.83 E-value=40 Score=28.02 Aligned_cols=47 Identities=19% Similarity=0.175 Sum_probs=38.9
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccc
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKI 667 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~ki 667 (786)
.+=|+.++-++...+.-|+++|+++||.....+.-.|..+...|.++
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 45688899888888889999999999999999999998885434343
No 79
>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=46.24 E-value=40 Score=26.88 Aligned_cols=45 Identities=20% Similarity=0.315 Sum_probs=34.8
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003927 626 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 626 ~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+|..+-.+...++..+|++.+|+++..+...+..|. +.+++..+|
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 344444577899999999999999999999999996 456776544
No 80
>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=45.65 E-value=8.7 Score=31.25 Aligned_cols=32 Identities=16% Similarity=0.429 Sum_probs=26.2
Q ss_pred CChHHHHHHHHhhhhhccccccCCCCCceeec
Q 003927 754 PDFKAIKKRIEDLITRDYLERDKSNPNMFRYL 785 (786)
Q Consensus 754 p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~ 785 (786)
.+...+-+.++.|.++|+++|.++++..|..+
T Consensus 34 i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 34 ISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp SSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred cCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 46788999999999999999998765555543
No 81
>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=45.24 E-value=28 Score=28.01 Aligned_cols=33 Identities=27% Similarity=0.380 Sum_probs=25.8
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 003927 634 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 668 (786)
Q Consensus 634 ~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL 668 (786)
.+..|+.+|...|++|.+.++.+|..|+ +.+++
T Consensus 25 ~G~ltl~~i~~~t~l~~~~Vk~~L~~Li--Qh~~v 57 (62)
T PF08221_consen 25 RGRLTLREIVRRTGLSPKQVKKALVVLI--QHNLV 57 (62)
T ss_dssp C-SEEHHHHHHHHT--HHHHHHHHHHHH--HTTSE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHH--HcCCe
Confidence 4688999999999999999999999997 44554
No 82
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=44.26 E-value=29 Score=35.39 Aligned_cols=62 Identities=23% Similarity=0.284 Sum_probs=43.0
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC-CCCCCCCCCCeEEE
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE-PNTKTISPTDHFEF 685 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~-~~~~~i~~~~~f~~ 685 (786)
+|-+ .||.+.+..++.|.+||++.+|++...++++|..|.. -+++... ..++--.|.-.|.+
T Consensus 11 ~tr~-~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~~~~~~~g~GRP~~~y~L 73 (218)
T COG2345 11 STRE-RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVEVERQQGGRGRPAKLYRL 73 (218)
T ss_pred cHHH-HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--CcceeeeeccCCCCCCceeeee
Confidence 3444 4666677788999999999999999999999999973 3444322 11222345555654
No 83
>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=44.11 E-value=51 Score=24.81 Aligned_cols=33 Identities=27% Similarity=0.392 Sum_probs=24.2
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhH
Q 003927 625 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 659 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~ 659 (786)
.+|-+.| ...+|++||++.+|++...+.+....
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 3444556 45789999999999999988765543
No 84
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.30 E-value=36 Score=33.75 Aligned_cols=44 Identities=16% Similarity=0.181 Sum_probs=35.3
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 624 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 624 Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
...||.+.-.++.+|-++|++.+|++...++++|..|. ..+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~--e~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLY--DARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeE
Confidence 44566555566789999999999999999999999997 345654
No 85
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=42.85 E-value=56 Score=32.12 Aligned_cols=55 Identities=20% Similarity=0.174 Sum_probs=41.7
Q ss_pred EEEEEcHHHHHHHHhhcCCCC-ccHHHHHHHh--CCCHHHHHHHHhHhhhccccccccCC
Q 003927 616 TELIVTTYQASALLLFNSSDR-LSYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 616 ~~l~vs~~Q~~ILllFN~~~~-lt~~ei~~~t--~l~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+++--+.+..+|+-+..-.+. -+.++|++.+ +++.++++.+|..|. +.++|.+..
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 344445666667665554333 2899999999 999999999999997 789998864
No 86
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=42.81 E-value=25 Score=27.29 Aligned_cols=45 Identities=9% Similarity=0.148 Sum_probs=31.4
Q ss_pred eeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCC
Q 003927 726 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNP 779 (786)
Q Consensus 726 VRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~ 779 (786)
++.+. .+.++..++... +..+.+.+.+.|+.|.++|++.+..+.+
T Consensus 3 l~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 33444 556666665443 3356788999999999999999876443
No 87
>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=42.71 E-value=9.6 Score=37.98 Aligned_cols=57 Identities=19% Similarity=0.290 Sum_probs=40.0
Q ss_pred cceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 722 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 722 ~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
=...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.-.-+|++.|+||.
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 344557888999988888766 488889999999999999999999889999999984
No 88
>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=41.52 E-value=21 Score=31.86 Aligned_cols=43 Identities=16% Similarity=0.203 Sum_probs=29.4
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 003927 624 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 668 (786)
Q Consensus 624 Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL 668 (786)
.+.|+..+..++.++-++|++.+|++..++.+.|..|.. .+++
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv 57 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLV 57 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCe
Confidence 345565555567899999999999999999999999974 4555
No 89
>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=41.20 E-value=55 Score=33.00 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=34.9
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 626 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 626 ~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
.||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEe
Confidence 344444445679999999999999999999999997 45777654
No 90
>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=40.73 E-value=28 Score=34.62 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=22.7
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 635 DRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 635 ~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
..+|+++|++.||+..+++..+|+.|-
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 379999999999999999999999883
No 91
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=40.02 E-value=25 Score=28.72 Aligned_cols=53 Identities=11% Similarity=0.197 Sum_probs=39.4
Q ss_pred cceeeeccccCCC--CChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 003927 722 DASIVRIMKSRKV--LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMF 782 (786)
Q Consensus 722 ~A~IVRiMK~rK~--l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y 782 (786)
+..|...||.+.. ++-.+|-.+ .-.+...+.+.+..|.++||+.++++.+..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~--------lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKN--------LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 4456777888766 876666653 3345678999999999999999987665554
No 92
>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=39.70 E-value=33 Score=30.93 Aligned_cols=57 Identities=11% Similarity=0.097 Sum_probs=42.0
Q ss_pred eeecccc-CCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceee
Q 003927 725 IVRIMKS-RKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 784 (786)
Q Consensus 725 IVRiMK~-rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y 784 (786)
|..+|.. .+.++.++|...+.++. ..++...|=+.++.|.+.|.|.+-..+.....|
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 456888999999999999999997643333444
No 93
>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=39.62 E-value=50 Score=26.85 Aligned_cols=24 Identities=17% Similarity=0.494 Sum_probs=20.5
Q ss_pred ChHHHHHHHHhhhhhccccccCCC
Q 003927 755 DFKAIKKRIEDLITRDYLERDKSN 778 (786)
Q Consensus 755 ~~~~iK~~Ie~LIekeyl~R~~~d 778 (786)
++.-+..-++.|.++|||+|+++-
T Consensus 39 S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 39 STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred ChHHHHHHHHHHHHCcCccCCCCC
Confidence 467788899999999999999853
No 94
>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=39.19 E-value=71 Score=26.93 Aligned_cols=38 Identities=13% Similarity=0.224 Sum_probs=28.0
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 624 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 624 Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
.-.+|-+.-....+|.++|+.++|.+.+++...|..+.
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 44566677788999999999999999999999998874
No 95
>PF05261 Tra_M: TraM protein, DNA-binding; InterPro: IPR007925 The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus [].; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3ON0_A 3OMY_B 1DP3_A 2G9E_A 3D8A_B 2G7O_A.
Probab=38.39 E-value=1e+02 Score=28.38 Aligned_cols=57 Identities=14% Similarity=0.464 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCcCC-HHHHHHHHHHHHHhccC---------cccccHHhhHHHHHHHH
Q 003927 189 LNGKVRDAVITLIDQEREGEQID-RALLKNVLDIFVEIGMG---------QMDYYENDFETAMLKDT 245 (786)
Q Consensus 189 l~~~l~~~il~lI~~~R~g~~id-~~llk~vi~~l~~lg~~---------~~~~Y~~~FE~~~L~~t 245 (786)
+++++.+.|-+++++.|..+.-+ ---..++..||.+||+. ...+-+..|-+.+|+.+
T Consensus 8 ~s~~v~~~I~~iVe~r~qeGA~~~dvs~SSv~smLlELGLrVY~~Q~E~k~s~Fnq~eFnk~lLe~v 74 (127)
T PF05261_consen 8 VSNKVLEEINDIVEERRQEGATEKDVSFSSVSSMLLELGLRVYEAQMERKESGFNQEEFNKVLLENV 74 (127)
T ss_dssp --HCHHHHHHHHHHHHHCCT-TTTT--HHHHHHHHHHCCCCHHHHCCHHCSSS--HHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHhHHHHHHHHhhccCCCCHHHHHHHHHHHH
Confidence 35566677778888888765433 23478999999999961 22334444556666554
No 96
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=38.11 E-value=79 Score=28.76 Aligned_cols=38 Identities=13% Similarity=0.448 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHhcCCcCCHH-HHHHHHHHHHHhcc
Q 003927 190 NGKVRDAVITLIDQEREGEQIDRA-LLKNVLDIFVEIGM 227 (786)
Q Consensus 190 ~~~l~~~il~lI~~~R~g~~id~~-llk~vi~~l~~lg~ 227 (786)
++++.+.|-+++++.|..+.-+.+ -+.++..||.+||+
T Consensus 2 s~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELGL 40 (118)
T PRK13713 2 SNEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGL 40 (118)
T ss_pred chHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHhH
Confidence 345667777788888866543322 37889999999995
No 97
>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=37.53 E-value=44 Score=23.12 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=20.7
Q ss_pred CccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 636 RLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 636 ~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
.+|-+||++.+|+..+.+-|.|..|-
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 36789999999999999999998874
No 98
>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=37.49 E-value=38 Score=27.68 Aligned_cols=32 Identities=22% Similarity=0.385 Sum_probs=25.8
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHhHhhh
Q 003927 631 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 662 (786)
Q Consensus 631 FN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~ 662 (786)
..++..+|+.||+..++++++.+...|..|..
T Consensus 9 l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 9 LRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34567899999999999999999999999974
No 99
>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=34.34 E-value=84 Score=24.55 Aligned_cols=38 Identities=26% Similarity=0.385 Sum_probs=29.7
Q ss_pred cCCCCc-cHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 632 NSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 632 N~~~~l-t~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
.....+ |..+|++.+|++...+.++|..|. +.+++...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~--~~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELE--AEGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 333444 499999999999999999999997 45677543
No 100
>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=33.56 E-value=84 Score=23.65 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=27.4
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 622 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 622 ~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
..|.-++.++- +.+|..+|++.+|++...+...+..+
T Consensus 3 ~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 3 PREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34444554442 45799999999999999988877765
No 101
>PRK00215 LexA repressor; Validated
Probab=33.53 E-value=79 Score=31.81 Aligned_cols=51 Identities=25% Similarity=0.309 Sum_probs=39.9
Q ss_pred EcHHHHHHHHhhc-----CCCCccHHHHHHHhCC-CHHHHHHHHhHhhhccccccccCC
Q 003927 620 VTTYQASALLLFN-----SSDRLSYSEIMTQLNL-SDDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 620 vs~~Q~~ILllFN-----~~~~lt~~ei~~~t~l-~~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
++.-|..||.... .....|..||++.+|+ +...+.+.|..|. +.+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCC
Confidence 3567888886554 2446899999999999 9999999999997 456776654
No 102
>COG5173 SEC6 Exocyst complex subunit SEC6 [Intracellular trafficking and secretion]
Probab=33.44 E-value=8.4e+02 Score=28.53 Aligned_cols=59 Identities=17% Similarity=0.327 Sum_probs=36.8
Q ss_pred hcCCChHHHHHHHHHHHHHhhCCCCCCchHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHhhhhccCCh--hHHHHHH
Q 003927 404 CFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDK--DLFAEFY 481 (786)
Q Consensus 404 ~F~~~~~f~~~l~~af~~~iN~~~~~~~~~e~La~y~D~~lkk~~~~~~~~~e~e~~l~~i~~lf~~l~~K--D~F~~~Y 481 (786)
||+++. |.++++.-++. .-++++.|.| .+++...+..|+.+|-.+.+. |.|..+.
T Consensus 621 ~~~~~n-a~~~lksD~~~----------~y~~f~~y~d------------~e~~k~tl~pI~k~~~~m~~~~~d~~~~~~ 677 (742)
T COG5173 621 SIAEEN-ASRTLKSDHTK----------LYEMFSGYGD------------PEDVKTTLSPILKIIPLMDTRNDDLFIVEV 677 (742)
T ss_pred hhcchh-HHHHHHHHHHH----------HHHHHHhhCC------------HHHHHHHHHHHHHHHcccccCCchHHHHHH
Confidence 344444 55666655543 3455555544 356667788899999888655 6788777
Q ss_pred HHHH
Q 003927 482 RKKL 485 (786)
Q Consensus 482 ~~~L 485 (786)
++++
T Consensus 678 ~~lk 681 (742)
T COG5173 678 KSLK 681 (742)
T ss_pred HHHH
Confidence 6543
No 103
>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=33.18 E-value=72 Score=30.91 Aligned_cols=43 Identities=16% Similarity=0.220 Sum_probs=33.6
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 625 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
..|+...=.+..+|-+||++.+|++..++++.|..|. ..+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~--e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALY--DAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCce
Confidence 4455444345689999999999999999999999997 346663
No 104
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=33.13 E-value=85 Score=23.50 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=29.2
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
+.-+..|+.++. ..+|..+|++.+|++...+.+.+..+.
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 445555555553 357999999999999999988887653
No 105
>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=33.05 E-value=71 Score=24.33 Aligned_cols=24 Identities=38% Similarity=0.558 Sum_probs=17.5
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHh
Q 003927 635 DRLSYSEIMTQLNLSDDDVVRLLH 658 (786)
Q Consensus 635 ~~lt~~ei~~~t~l~~~~l~~~L~ 658 (786)
+.+|+.||++.+|++...++..+.
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 468999999999999998887664
No 106
>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=32.99 E-value=2.5e+02 Score=27.32 Aligned_cols=59 Identities=22% Similarity=0.259 Sum_probs=42.4
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHh--CCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003927 624 QASALLLFNSS-DRLSYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 688 (786)
Q Consensus 624 Q~~ILllFN~~-~~lt~~ei~~~t--~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~ 688 (786)
..+|+-.+..+ .++|..+|...+ +++...+.++|..|+. +-+|..+. +...-+|..|.+
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 34667666654 589999999998 5889999999999985 44555443 334457777755
No 107
>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=32.97 E-value=20 Score=28.24 Aligned_cols=26 Identities=12% Similarity=0.308 Sum_probs=20.9
Q ss_pred CCCChHHHHHHHHhhhhhccccccCC
Q 003927 752 FKPDFKAIKKRIEDLITRDYLERDKS 777 (786)
Q Consensus 752 F~p~~~~iK~~Ie~LIekeyl~R~~~ 777 (786)
+..+.+.+.+.|..|+++|||+|..+
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 34567889999999999999999764
No 108
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=32.46 E-value=53 Score=34.50 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=40.2
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
-|..||-+.++.+.+++.||++.+|++...++|-|..|- +.++|.+.
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 467788888988999999999999999999999999996 45666553
No 109
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=32.16 E-value=71 Score=31.67 Aligned_cols=64 Identities=19% Similarity=0.170 Sum_probs=48.2
Q ss_pred CceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 593 HRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 593 ~RkL~W~~~l~~~~i~~~~~~~~~~l~vs~~Q~~ILllFN~--~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
.|.-.|-+.+|..+++-- +.| .||..||.-||.-.. -..||.+.|++..+|+.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~v-PkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEKV-PKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCcccC-CCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 344457788888877643 334 378899988775433 3479999999999999999999888774
No 110
>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=32.13 E-value=68 Score=23.74 Aligned_cols=30 Identities=30% Similarity=0.419 Sum_probs=21.0
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHh
Q 003927 627 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 658 (786)
Q Consensus 627 ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~ 658 (786)
|+-++.++ +|+.+|++.+|++...+.+.|.
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 34455554 8999999999999999888764
No 111
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=31.85 E-value=64 Score=32.98 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=41.4
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
|..-..||-+......+.+.||++++|+|...+..++..|. +.+++..+
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 44555788888888899999999999999999999999996 77888643
No 112
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=31.07 E-value=70 Score=31.08 Aligned_cols=48 Identities=15% Similarity=0.242 Sum_probs=40.3
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 620 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 620 vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
+.-.-..||-...++...|+.+|++.+|++...+.+.++.|. +.+++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~--~~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLE--RQGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeE
Confidence 345566788888888899999999999999999999999996 456664
No 113
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=31.06 E-value=1.1e+02 Score=28.66 Aligned_cols=64 Identities=19% Similarity=0.257 Sum_probs=46.9
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCC---CeEEEccCCC
Q 003927 625 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPT---DHFEFNSKFT 690 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~---~~f~~N~~F~ 690 (786)
...|-+..+.+..|+.|+++.+|-+.+.+.+.|..|. .++|+..+.+|+...|. +.+.++-.|.
T Consensus 67 leLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 67 LELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 3455667788899999999999999999999999996 57888766555544332 3344555554
No 114
>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=30.18 E-value=17 Score=28.34 Aligned_cols=26 Identities=15% Similarity=0.309 Sum_probs=21.5
Q ss_pred CCCCChHHHHHHHHhhhhhccccccC
Q 003927 751 MFKPDFKAIKKRIEDLITRDYLERDK 776 (786)
Q Consensus 751 ~F~p~~~~iK~~Ie~LIekeyl~R~~ 776 (786)
.+..+.+.+-+.|..|.++|||+|..
T Consensus 26 ~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 26 KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 35567889999999999999999864
No 115
>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=30.18 E-value=67 Score=26.08 Aligned_cols=51 Identities=24% Similarity=0.324 Sum_probs=34.3
Q ss_pred EcHHHHHHHHhhcC-----CCCccHHHHHHHhCCC-HHHHHHHHhHhhhccccccccCC
Q 003927 620 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 672 (786)
Q Consensus 620 vs~~Q~~ILllFN~-----~~~lt~~ei~~~t~l~-~~~l~~~L~~L~~~k~kiL~~~~ 672 (786)
+|.-|.-||...-+ +-+-|+.||++.+|+. ...+..+|..|. +-+.|.+.|
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 34556666654322 2356999999999997 899999999996 457777654
No 116
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=29.12 E-value=84 Score=30.08 Aligned_cols=48 Identities=15% Similarity=0.243 Sum_probs=39.9
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 620 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 620 vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
++..--.||..+..+...|+.+|++.+|+++..+.+.+..|.. .+++.
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 4556667888888778999999999999999999999999973 45664
No 117
>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=28.91 E-value=84 Score=26.76 Aligned_cols=35 Identities=9% Similarity=-0.007 Sum_probs=30.0
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHh
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 658 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~ 658 (786)
-|+.|+-.... +.+|+.+|++.+|++...+.+.|.
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 46778877888 899999999999999999988664
No 118
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=28.00 E-value=73 Score=33.42 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=39.4
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 624 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 624 Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
|-.||-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 55788888899999999999999999999999999996 45666653
No 119
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=27.91 E-value=71 Score=35.46 Aligned_cols=64 Identities=20% Similarity=0.252 Sum_probs=39.5
Q ss_pred eEeecCcceEEEEeEecCeeEEEEE-------cHHHHHHHH-hhcCCCC-ccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 596 LTWIYSLGTCNLLGKFESRTTELIV-------TTYQASALL-LFNSSDR-LSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 596 L~W~~~l~~~~i~~~~~~~~~~l~v-------s~~Q~~ILl-lFN~~~~-lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
+.+.|.||+.|-++--+.+ -|.= +-.-..||- +...++. +|+++|++.|||..+++..+|++|-
T Consensus 282 IdFSYeLSr~E~~~GsPEK--PLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSPEK--PLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcCCCCCC--CcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 4566778876665422221 1110 112223332 2332333 9999999999999999999999983
No 120
>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=27.69 E-value=71 Score=34.93 Aligned_cols=143 Identities=12% Similarity=0.142 Sum_probs=39.0
Q ss_pred EEcHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCcceE
Q 003927 619 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRI 696 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~--~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~f~~N~~F~~~~~ki 696 (786)
.++..+..|.-+..+ ...+-..+|...|||+...+.++|.+|.. | ++++... +.+.+++|+
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 456667777766553 45788999999999999999999999974 3 4543211 223344444
Q ss_pred eecCCCc--hhhhh----HHHhHHHHhhhhhcceeeeccccCCC-----------------------------CChhHHH
Q 003927 697 KIPLPPV--DEKKK----VIEDVDKDRRYAIDASIVRIMKSRKV-----------------------------LGHQQLV 741 (786)
Q Consensus 697 ~i~~~~~--~e~~~----~~~~v~~dR~~~i~A~IVRiMK~rK~-----------------------------l~~~~L~ 741 (786)
-+-.... .|-.. +..+.+.+=-..+...|.+.+.++.. .+.+++.
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 4321100 00000 11222333333455555555555544 3333443
Q ss_pred HHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCC
Q 003927 742 LECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSN 778 (786)
Q Consensus 742 ~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d 778 (786)
..+.+.=-..-..++++|...++.|+=-|-|++....
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 3333221112345788999999999988888876543
No 121
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=27.56 E-value=40 Score=25.90 Aligned_cols=29 Identities=7% Similarity=0.177 Sum_probs=24.9
Q ss_pred CCCCCCChHHHHHHHHhhhhhccccccCC
Q 003927 749 GRMFKPDFKAIKKRIEDLITRDYLERDKS 777 (786)
Q Consensus 749 ~~~F~p~~~~iK~~Ie~LIekeyl~R~~~ 777 (786)
..+|..+...+.+.+..|.+.|+|.+.++
T Consensus 27 a~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 27 AAQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 33677889999999999999999998764
No 122
>KOG1020 consensus Sister chromatid cohesion protein SCC2/Nipped-B [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=27.44 E-value=1.6e+03 Score=29.86 Aligned_cols=49 Identities=12% Similarity=0.272 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccchhhhhcCCCCcHHHHHHHHHHHHHHHHH
Q 003927 135 MLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFRDLVYTEL 189 (786)
Q Consensus 135 ~L~~~~~~W~~~~~~~~~l~~vF~YLdR~yv~~~~~~~i~~l~l~~fr~~vf~~l 189 (786)
.|+.+..+..+|...+.++.++.+-.+- .-.+|.+|....|.+.-|.+.
T Consensus 915 Ilrdic~e~pdf~~i~~~cakmlrRv~D------EEg~I~kLv~etf~klWF~p~ 963 (1692)
T KOG1020|consen 915 ILRDICEETPDFSKIVDMCAKMLRRVND------EEGNIKKLVRETFLKLWFTPV 963 (1692)
T ss_pred HHHHHHHhCCChhhHHHHHHHHHHHhcc------chhHHHHHHHHHHHHHhccCC
Confidence 4555666666666555555544432110 123588888888888877754
No 123
>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=26.88 E-value=28 Score=25.95 Aligned_cols=44 Identities=9% Similarity=0.258 Sum_probs=32.0
Q ss_pred cceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhcccc
Q 003927 722 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLE 773 (786)
Q Consensus 722 ~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~ 773 (786)
+-.|+..+.....++..+|-.. +..+.+.+.+.|..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~--------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK--------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH--------hCCCHHHHHHHHHHHHHCcCcC
Confidence 3345666777777887777663 3457888999999999999985
No 124
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.83 E-value=35 Score=30.35 Aligned_cols=47 Identities=13% Similarity=0.197 Sum_probs=38.0
Q ss_pred hcceeeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhcccccc
Q 003927 721 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERD 775 (786)
Q Consensus 721 i~A~IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~ 775 (786)
+|-.|++.+.....++..+|-.. +..+.+.+.++|..|.++|+|+|-
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeece
Confidence 35567788888888888887764 456789999999999999999963
No 125
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=26.65 E-value=35 Score=25.39 Aligned_cols=44 Identities=11% Similarity=0.200 Sum_probs=32.2
Q ss_pred eeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCC
Q 003927 726 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 777 (786)
Q Consensus 726 VRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~ 777 (786)
.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 6 l~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 6 LELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 334444555666666653 45688889999999999999998753
No 126
>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=26.40 E-value=40 Score=34.66 Aligned_cols=35 Identities=11% Similarity=0.230 Sum_probs=29.1
Q ss_pred hCCCCCCChHHHHHHHHhhhhhccccccCCCCCcee
Q 003927 748 LGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 783 (786)
Q Consensus 748 l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~ 783 (786)
|..+|..+...+.++|+.|++.|+|.|..+ +.+|+
T Consensus 30 La~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 30 LMDQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 334699999999999999999999999875 45554
No 127
>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=26.17 E-value=76 Score=29.33 Aligned_cols=50 Identities=14% Similarity=0.151 Sum_probs=38.4
Q ss_pred EcHHHHHHHHh--hc--------CCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 620 VTTYQASALLL--FN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 620 vs~~Q~~ILll--FN--------~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
+..+.-..++. -| +.-++|.++|+..++-+.+.++.+|..|. +.+++...
T Consensus 27 ~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 27 TVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred HHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34555555555 33 44589999999999999999999999996 67887653
No 128
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=25.95 E-value=96 Score=32.48 Aligned_cols=47 Identities=17% Similarity=0.191 Sum_probs=39.3
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
-|..|+-.++++..++..||++.+|++...++|-|..|. +.+++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEe
Confidence 466788888999999999999999999999999999985 34555543
No 129
>PF11728 DUF939_C: DUF939 C-terminal domain; InterPro: IPR021062 This entry represents a C-terminal domain found in a set of bacterial proteins. The proteins are about 160 amino acids in length and are predicted to be multi-pass membrane proteins. ; PDB: 3KMI_B.
Probab=25.94 E-value=3.8e+02 Score=26.14 Aligned_cols=62 Identities=19% Similarity=0.324 Sum_probs=39.4
Q ss_pred hccCChhhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchhHHHHHHHHHHHHHHH
Q 003927 320 LRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLA 399 (786)
Q Consensus 320 l~~~~~~dL~~~y~L~~~~~~~l~~l~~~~~~~I~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~ll~l~~k~~~ 399 (786)
+...+.+-|++|+..+++++.. .+-+..+.+++...|..+-. .+++...++.|-.++..|..
T Consensus 74 MR~~Q~~iL~~M~~~l~~i~~~-~~q~~~ia~~~~~~a~~~~e-----------------~n~~~~ll~~L~~l~~~fr~ 135 (167)
T PF11728_consen 74 MREKQLEILKRMYPNLSKIYMS-PKQAEIIADFLEELAESLHE-----------------NNTAEELLEELEELKEEFRE 135 (167)
T ss_dssp HHHHHHHHHHHHHHHHTT-SS---HHHHHHHHHHHHHHH---------------------TTHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHHhCC-----------------CCcHHHHHHHHHHHHHHHhc
Confidence 4456678899999999999543 34455556666555443321 34677888888888888865
No 130
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=25.47 E-value=1e+02 Score=32.75 Aligned_cols=37 Identities=19% Similarity=0.285 Sum_probs=29.5
Q ss_pred HHHHHHhh-cCCCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 624 QASALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 624 Q~~ILllF-N~~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
...|+-.+ +....+|+++|+..|||..+++..+|+.|
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 33444333 34568999999999999999999999987
No 131
>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=25.40 E-value=1e+02 Score=24.02 Aligned_cols=29 Identities=24% Similarity=0.467 Sum_probs=24.3
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHhH
Q 003927 631 FNSSDRLSYSEIMTQLNLSDDDVVRLLHS 659 (786)
Q Consensus 631 FN~~~~lt~~ei~~~t~l~~~~l~~~L~~ 659 (786)
|+.-...|.+||++.+|++...+..+|..
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 55556899999999999999988777764
No 132
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=25.37 E-value=1.8e+02 Score=24.80 Aligned_cols=59 Identities=12% Similarity=-0.024 Sum_probs=40.0
Q ss_pred HHHHHHHhhhhhhhhhhhhhhhhcc-----cchhhhHHhhhhccCCCCCchHHHHHHHHHHHHHH
Q 003927 59 VNILLLVIHNFFLAFLWYCFFFFFS-----KKSVYRTIYNMCTQKPPHDYSQQLYDKYRESFEEY 118 (786)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~lY~~vY~~c~~~~~~~~~e~LY~~l~~~l~~~ 118 (786)
...|..++..|+.|+.|+.--+... ...+...|..+|+.... ....+|=+.|.+.+.+.
T Consensus 3 ~~~V~~vl~~WtaL~lAVen~wGG~~s~~K~~~l~~~i~~~f~~~~~-~~~~~le~~L~~~m~~e 66 (82)
T PF10273_consen 3 EEGVRLVLNRWTALQLAVENGWGGPDSQEKADWLAEVIVDWFTENKD-PDADDLEDFLEDIMDDE 66 (82)
T ss_pred HHHHHHHHhcCHHHHHHHHhccCCccHHHHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHHHHhH
Confidence 4568899999999999999888764 35777888888877422 23444544444444443
No 133
>PRK13239 alkylmercury lyase; Provisional
Probab=24.73 E-value=1.3e+02 Score=30.61 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=35.0
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 622 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 622 ~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
.+...||.++-++...|.++|++.+|.+.+.+.+.|..|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 3556677778888999999999999999999999999884
No 134
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=24.63 E-value=1.2e+02 Score=28.73 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=39.8
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 620 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 620 vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
+.-.-.-||-........++.+|++.+|++...+.+.+..|. +.+|+..
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 344556678777777789999999999999999999999996 5677753
No 135
>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=24.54 E-value=1e+02 Score=28.35 Aligned_cols=49 Identities=18% Similarity=0.234 Sum_probs=38.0
Q ss_pred cHHHHHHHHhhcCC--------CCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 621 TTYQASALLLFNSS--------DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 621 s~~Q~~ILllFN~~--------~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
..+.-..|+..|.. -++|.++|+..++-+.+.++.+|..|. +++++...
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34555555555543 479999999999999999999999996 77887643
No 136
>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=24.45 E-value=40 Score=27.47 Aligned_cols=53 Identities=26% Similarity=0.271 Sum_probs=30.1
Q ss_pred ceeeeccccCC-CCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 723 ASIVRIMKSRK-VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 723 A~IVRiMK~rK-~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
|.||.-||+|. .++.+||.. .++ +..+ ++.++.|-+.+=|+-|++ .++|.|.|
T Consensus 8 ~~~VeymK~r~~Plt~~eI~d----~l~--~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 8 AKAVEYMKKRDHPLTLEEILD----YLS--LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHH-S-B-HHHHHH----HHT--SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHhcCCCcCHHHHHH----HHc--CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 66888898873 366666655 454 4443 345566668888888874 46999975
No 137
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=24.38 E-value=83 Score=31.31 Aligned_cols=46 Identities=11% Similarity=0.044 Sum_probs=38.6
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003927 622 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 669 (786)
Q Consensus 622 ~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~ 669 (786)
.-+..|+...+.++.+++.+|++.+|++...++|=|..|.. .+++.
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~--~g~~~ 52 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI--PELRE 52 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc--chHHH
Confidence 35677888888899999999999999999999999999963 34444
No 138
>PRK05097 Ter macrodomain organizer matS-binding protein; Provisional
Probab=24.28 E-value=1.6e+02 Score=27.54 Aligned_cols=72 Identities=19% Similarity=0.368 Sum_probs=46.7
Q ss_pred HHHHHHhcCCcC----CHHHHHHHHHHHHHhccCcccccHHhhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 003927 199 TLIDQEREGEQI----DRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLK 274 (786)
Q Consensus 199 ~lI~~~R~g~~i----d~~llk~vi~~l~~lg~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~eYl~kve~~l~ 274 (786)
-+|.+.|+|+.| +.+....+|+.|..+.. +-.....||..+=.|+-..+..+.++
T Consensus 17 YLvkKhreGE~ITry~e~S~~~~aV~~L~~le~---------------------~P~~v~~WI~~hm~p~l~nklkQaIR 75 (150)
T PRK05097 17 YLVKKHREGELITRYIEASAAQEAVDELLKLEN---------------------EPVKVLEWIDKHMNPELVNRMKQTIR 75 (150)
T ss_pred HHHHHhccccchHHHHHhhHHHHHHHHHHHhcc---------------------CcHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 368999999976 56777778888877642 22346779987767777777777775
Q ss_pred HHHHHHccccCCCcHHH
Q 003927 275 REKDRVSHYLHSSSEPK 291 (786)
Q Consensus 275 eE~~r~~~yL~~st~~k 291 (786)
.=..|-=.-=+.+|.+|
T Consensus 76 ArRKRhFNAE~qhTrKK 92 (150)
T PRK05097 76 ARRKRHFNAEHQHTRKK 92 (150)
T ss_pred HHHHccCCccccccccc
Confidence 44443321123456554
No 139
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=24.22 E-value=1e+02 Score=35.71 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=43.0
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 619 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.+|..|..||......+.+|..+|++.+|++...+.+++.+|.. -+++..
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 46789999999998888999999999999999999999999973 355543
No 140
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=23.78 E-value=60 Score=28.02 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=33.9
Q ss_pred hCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 748 LGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 748 l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
++.|+..+.+.-+++|..|.++|-|.....++..-.|.|
T Consensus 47 lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 47 LASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 334788899999999999999999999888888888875
No 141
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.40 E-value=49 Score=34.24 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=27.7
Q ss_pred CCCCCChHHHHHHHHhhhhhccccccCCCCCcee
Q 003927 750 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 783 (786)
Q Consensus 750 ~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~ 783 (786)
..|..+...++++|+.|++.|+|.|..+ +.+|+
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 3588889999999999999999999875 45554
No 142
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.39 E-value=90 Score=29.78 Aligned_cols=29 Identities=10% Similarity=0.188 Sum_probs=26.6
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHhHhhh
Q 003927 634 SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 662 (786)
Q Consensus 634 ~~~lt~~ei~~~t~l~~~~l~~~L~~L~~ 662 (786)
.+.+|-++|++.+|++...+++.|..|..
T Consensus 13 ~~~~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 13 NGCVTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 45799999999999999999999999974
No 143
>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=23.14 E-value=1.3e+02 Score=25.87 Aligned_cols=44 Identities=16% Similarity=0.254 Sum_probs=35.0
Q ss_pred HHHHHhhcCCCCccHHHHHHHh-CCCHHHHHHHHhHhhhccccccccC
Q 003927 625 ASALLLFNSSDRLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 625 ~~ILllFN~~~~lt~~ei~~~t-~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
+.||..... +...+.||.+.+ |+++..|.+.|..|. ..+++.+.
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 456665555 688999999999 999999999999997 46788664
No 144
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.07 E-value=61 Score=33.23 Aligned_cols=54 Identities=22% Similarity=0.332 Sum_probs=43.5
Q ss_pred eeeccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 003927 725 IVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 786 (786)
Q Consensus 725 IVRiMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~Y~a 786 (786)
-|-..|+.|.+..++|-. .|....++.-.+|..|+..|.|.-.-+|+..|+||.
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 345567777777776655 477777777789999999999999999999999984
No 145
>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=22.99 E-value=58 Score=29.20 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=26.9
Q ss_pred CCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccC
Q 003927 732 RKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 776 (786)
Q Consensus 732 rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~ 776 (786)
...++-.+|.. ....+.+.+-+.|+.|.++|||.|..
T Consensus 41 ~~~~t~~eL~~--------~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 41 EGKLTLKEIIK--------EILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred CCcCcHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 34555555554 34456788999999999999999754
No 146
>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=22.81 E-value=1.5e+02 Score=29.57 Aligned_cols=50 Identities=20% Similarity=0.232 Sum_probs=39.7
Q ss_pred EcHHHHHHHHhhcC-----CCCccHHHHHHHhCCC-HHHHHHHHhHhhhccccccccC
Q 003927 620 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 620 vs~~Q~~ILllFN~-----~~~lt~~ei~~~t~l~-~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
++..|..||....+ .-..|..||++.+|++ ...+.++|..|. +-++|.+.
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 46788888866552 2358899999999999 999999999996 55777765
No 147
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.51 E-value=53 Score=34.01 Aligned_cols=48 Identities=13% Similarity=0.366 Sum_probs=34.7
Q ss_pred ccccCCCCChhHHHHHHHHHhCCCCCCChHHHHHHHHhhhhhccccccCCCCCcee
Q 003927 728 IMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 783 (786)
Q Consensus 728 iMK~rK~l~~~~L~~ev~~~l~~~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~ 783 (786)
.++....|.-+ .+|...|..+...|+++|+.|++.|+|.|..+ +.+|+
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 45555555422 23334699999999999999999999999875 45553
No 148
>PRK06474 hypothetical protein; Provisional
Probab=22.12 E-value=2.1e+02 Score=28.28 Aligned_cols=51 Identities=14% Similarity=0.214 Sum_probs=39.4
Q ss_pred EEcHHHHHHHHhhcCCC-CccHHHHHHHh-CCCHHHHHHHHhHhhhccccccccC
Q 003927 619 IVTTYQASALLLFNSSD-RLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 619 ~vs~~Q~~ILllFN~~~-~lt~~ei~~~t-~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
-.++.-..||-.+-..+ .+|..+|++.+ +++...+-++|..|. +.+++...
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~ 60 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVV 60 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34566677776554444 49999999999 799999999999997 67888754
No 149
>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=21.94 E-value=1.5e+02 Score=23.03 Aligned_cols=39 Identities=23% Similarity=0.276 Sum_probs=30.7
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
|.-+..||.++.. +.|..||++..|+++..+..++..+.
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 4566777777765 46899999999999999999988875
No 150
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.91 E-value=58 Score=30.65 Aligned_cols=26 Identities=8% Similarity=0.257 Sum_probs=22.0
Q ss_pred CCCCChHHHHHHHHhhhhhccccccC
Q 003927 751 MFKPDFKAIKKRIEDLITRDYLERDK 776 (786)
Q Consensus 751 ~F~p~~~~iK~~Ie~LIekeyl~R~~ 776 (786)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 45567778999999999999999975
No 151
>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=21.86 E-value=1.8e+02 Score=21.11 Aligned_cols=39 Identities=31% Similarity=0.379 Sum_probs=27.6
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 621 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 621 s~~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
+..+..++.++- .+.+|..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444444554432 245799999999999999988877653
No 152
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=21.55 E-value=1.2e+02 Score=31.73 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=35.7
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhh
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 661 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~ 661 (786)
-|..|+-+.+.++.+++.||++.+|+++..++|=|..|-
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 477889999999999999999999999999999988875
No 153
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=21.39 E-value=1.3e+02 Score=21.69 Aligned_cols=27 Identities=22% Similarity=0.325 Sum_probs=19.6
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 634 SDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 634 ~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
...+|+++|++..|++...+.+.....
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 457999999999999998888877654
No 154
>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=21.11 E-value=57 Score=33.51 Aligned_cols=32 Identities=19% Similarity=0.400 Sum_probs=27.7
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCcee
Q 003927 751 MFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 783 (786)
Q Consensus 751 ~F~p~~~~iK~~Ie~LIekeyl~R~~~d~~~y~ 783 (786)
+|..+...+.++|+.|.+.|||.|..+ +.+|+
T Consensus 41 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 41 RFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 699999999999999999999999875 45554
No 155
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.04 E-value=56 Score=25.01 Aligned_cols=21 Identities=10% Similarity=0.336 Sum_probs=17.9
Q ss_pred CCCChHHHHHHHHhhhhhccc
Q 003927 752 FKPDFKAIKKRIEDLITRDYL 772 (786)
Q Consensus 752 F~p~~~~iK~~Ie~LIekeyl 772 (786)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 345688899999999999987
No 156
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=20.86 E-value=1e+02 Score=32.45 Aligned_cols=55 Identities=22% Similarity=0.298 Sum_probs=38.9
Q ss_pred CeeEEEEEcHHHHHHHHh--------hcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 613 SRTTELIVTTYQASALLL--------FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 613 ~~~~~l~vs~~Q~~ILll--------FN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
...++-....-|++.=.+ ||+ .=|.++|.+..|++....+++|..|. |.+.+..+
T Consensus 217 p~~~E~l~~daq~Il~yL~~~gG~mpf~D--KSsPEdIk~~FgiSKg~FKrAiGgL~--K~g~I~q~ 279 (287)
T COG2996 217 PRAHEMLDEDAQMILTYLESNGGFMPFND--KSSPEDIKATFGISKGQFKRAIGGLM--KAGKIKQD 279 (287)
T ss_pred cccHHhhhhhHHHHHHHHHHcCCccccCC--CCCHHHHHHHhCcCHHHHHHHHHHHH--hCCeEEEc
Confidence 344555555666654322 343 45899999999999999999999997 66666543
No 157
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.65 E-value=1e+02 Score=22.95 Aligned_cols=32 Identities=25% Similarity=0.340 Sum_probs=21.0
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHh
Q 003927 627 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 660 (786)
Q Consensus 627 ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L 660 (786)
|+.++.+ .+|..+|++.+|++...+.+-+..+
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 7899999999999999888766544
No 158
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.40 E-value=1.3e+02 Score=31.53 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=39.1
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003927 623 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 671 (786)
Q Consensus 623 ~Q~~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~~ 671 (786)
-|..|+-..++.+.+++.||++.++++...++|-|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le--~~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLA--EQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 456677778888999999999999999999999999996 44666554
No 159
>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=20.23 E-value=1.2e+02 Score=26.27 Aligned_cols=32 Identities=16% Similarity=0.333 Sum_probs=22.4
Q ss_pred hhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhh
Q 003927 630 LFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 662 (786)
Q Consensus 630 lFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~ 662 (786)
+..+... ++..|.+.||||...++.+|.+|..
T Consensus 16 li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~ 47 (90)
T PF09904_consen 16 LIDSGER-NVPALMEATGMPRRTIQDTIKALPE 47 (90)
T ss_dssp HHHHS-B--HHHHHHHH---HHHHHHHHHGGGG
T ss_pred HHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhc
Confidence 3444455 9999999999999999999999963
No 160
>PRK11050 manganese transport regulator MntR; Provisional
Probab=20.21 E-value=1.8e+02 Score=27.87 Aligned_cols=43 Identities=16% Similarity=0.199 Sum_probs=34.6
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003927 626 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 670 (786)
Q Consensus 626 ~ILllFN~~~~lt~~ei~~~t~l~~~~l~~~L~~L~~~k~kiL~~ 670 (786)
.|+.++...+.++..+|++.++++...+.+.|..|.. .+++.+
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 4455666677899999999999999999999999963 366654
Done!