Query 004376
Match_columns 758
No_of_seqs 206 out of 1083
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 22:23:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004376hhsearch_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 2E-118 4E-123 1016.8 64.9 718 6-756 5-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 8E-111 2E-115 910.3 61.7 724 7-758 16-773 (773)
3 KOG2284 E3 ubiquitin ligase, C 100.0 6E-109 1E-113 836.8 48.2 684 1-758 1-728 (728)
4 KOG2167 Cullins [Cell cycle co 100.0 7E-107 1E-111 859.8 45.6 647 65-758 2-661 (661)
5 PF00888 Cullin: Cullin family 100.0 8.9E-90 1.9E-94 803.3 60.6 586 15-662 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 2.8E-88 6.1E-93 692.3 54.3 716 5-758 7-777 (777)
7 smart00182 CULLIN Cullin. 100.0 3.2E-31 7E-36 249.9 16.5 141 428-583 1-142 (142)
8 KOG2165 Anaphase-promoting com 99.9 3.9E-24 8.4E-29 232.9 39.5 308 422-748 442-758 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 1.8E-19 3.8E-24 146.0 1.5 68 685-752 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 97.0 0.022 4.8E-07 54.1 14.1 137 8-152 2-156 (158)
11 KOG2167 Cullins [Cell cycle co 94.5 0.8 1.7E-05 51.5 14.3 91 8-109 65-158 (661)
12 TIGR01610 phage_O_Nterm phage 92.9 0.29 6.4E-06 42.4 6.2 66 589-662 20-93 (95)
13 PF09339 HTH_IclR: IclR helix- 91.1 0.35 7.7E-06 36.7 4.2 45 597-643 6-51 (52)
14 PF02082 Rrf2: Transcriptional 90.9 0.66 1.4E-05 39.1 6.1 59 595-660 11-70 (83)
15 PF13412 HTH_24: Winged helix- 90.7 0.46 1E-05 35.3 4.4 42 593-634 2-43 (48)
16 PF12802 MarR_2: MarR family; 90.4 0.36 7.9E-06 37.9 3.8 51 592-644 3-55 (62)
17 PF08220 HTH_DeoR: DeoR-like h 88.4 1.1 2.4E-05 34.8 5.0 46 596-643 2-47 (57)
18 PF01047 MarR: MarR family; I 87.3 0.46 9.9E-06 36.9 2.3 51 592-644 1-51 (59)
19 PF13463 HTH_27: Winged helix 86.1 1.2 2.7E-05 35.5 4.4 50 592-643 1-51 (68)
20 TIGR02337 HpaR homoprotocatech 84.8 1.6 3.5E-05 39.4 5.0 52 591-644 25-76 (118)
21 PF01022 HTH_5: Bacterial regu 84.6 2.3 5E-05 31.4 4.8 44 595-641 3-46 (47)
22 PRK11512 DNA-binding transcrip 83.1 2.2 4.8E-05 40.0 5.3 52 591-644 37-88 (144)
23 PF12840 HTH_20: Helix-turn-he 82.8 1.7 3.7E-05 34.1 3.7 49 593-643 9-57 (61)
24 PF09012 FeoC: FeoC like trans 82.0 0.51 1.1E-05 38.2 0.4 43 699-749 7-49 (69)
25 smart00550 Zalpha Z-DNA-bindin 80.6 3 6.6E-05 33.6 4.5 47 595-643 7-55 (68)
26 TIGR02698 CopY_TcrY copper tra 79.0 1.7 3.7E-05 40.1 2.9 60 694-758 6-65 (130)
27 TIGR01889 Staph_reg_Sar staphy 78.9 4.7 0.0001 35.8 5.6 52 591-644 22-77 (109)
28 PF08279 HTH_11: HTH domain; 78.8 4.1 8.9E-05 31.0 4.6 37 598-634 4-41 (55)
29 COG3682 Predicted transcriptio 77.5 1.8 3.9E-05 39.1 2.4 62 692-758 6-67 (123)
30 PRK11920 rirA iron-responsive 76.9 7 0.00015 37.2 6.5 57 597-660 13-69 (153)
31 smart00346 HTH_ICLR helix_turn 76.5 6.3 0.00014 33.4 5.6 45 597-643 8-53 (91)
32 smart00347 HTH_MARR helix_turn 75.7 4.8 0.0001 34.5 4.7 53 589-643 5-57 (101)
33 PRK10857 DNA-binding transcrip 75.1 8.6 0.00019 37.0 6.6 56 597-659 13-69 (164)
34 COG3355 Predicted transcriptio 72.8 7.4 0.00016 35.4 5.1 40 603-644 37-76 (126)
35 PF01978 TrmB: Sugar-specific 72.4 3.6 7.8E-05 33.0 2.8 49 593-643 7-55 (68)
36 PF05732 RepL: Firmicute plasm 72.2 6.5 0.00014 37.8 5.0 48 608-664 75-122 (165)
37 PRK15090 DNA-binding transcrip 72.0 7.6 0.00017 40.3 5.9 45 597-643 17-61 (257)
38 smart00420 HTH_DEOR helix_turn 71.9 7.1 0.00015 28.9 4.3 44 597-642 3-46 (53)
39 TIGR02010 IscR iron-sulfur clu 71.0 11 0.00024 34.9 6.2 56 597-659 13-69 (135)
40 PF03965 Penicillinase_R: Peni 70.9 4.2 9.1E-05 36.5 3.2 60 694-758 5-64 (115)
41 PF05584 Sulfolobus_pRN: Sulfo 70.9 9.5 0.00021 31.0 4.8 43 598-643 9-51 (72)
42 PRK13777 transcriptional regul 70.7 8.2 0.00018 37.9 5.4 53 590-644 41-93 (185)
43 PRK03573 transcriptional regul 69.8 7.5 0.00016 36.3 4.8 53 590-644 27-80 (144)
44 COG1959 Predicted transcriptio 69.5 12 0.00025 35.5 6.0 59 595-660 11-70 (150)
45 PF13404 HTH_AsnC-type: AsnC-t 66.2 8.6 0.00019 27.8 3.4 36 597-632 6-41 (42)
46 PF04492 Phage_rep_O: Bacterio 66.0 17 0.00038 31.7 5.9 62 591-662 29-98 (100)
47 PRK10870 transcriptional repre 64.7 14 0.00031 35.9 5.8 52 591-644 52-105 (176)
48 PF08280 HTH_Mga: M protein tr 63.9 8.9 0.00019 29.9 3.4 38 596-633 7-44 (59)
49 TIGR00738 rrf2_super rrf2 fami 62.5 19 0.00041 32.9 6.0 45 596-642 12-57 (132)
50 PHA00738 putative HTH transcri 62.2 16 0.00035 32.1 4.9 67 589-661 7-73 (108)
51 smart00419 HTH_CRP helix_turn_ 61.8 16 0.00035 26.4 4.4 34 608-643 8-41 (48)
52 PF08784 RPA_C: Replication pr 60.9 14 0.00031 32.3 4.5 44 591-634 44-91 (102)
53 smart00345 HTH_GNTR helix_turn 60.6 17 0.00037 27.6 4.5 39 603-643 14-53 (60)
54 PF04703 FaeA: FaeA-like prote 60.1 11 0.00025 29.7 3.3 45 599-645 5-50 (62)
55 TIGR01884 cas_HTH CRISPR locus 59.9 13 0.00029 37.0 4.7 51 591-643 140-190 (203)
56 COG1414 IclR Transcriptional r 59.1 19 0.0004 37.2 5.7 46 597-644 7-53 (246)
57 PF08220 HTH_DeoR: DeoR-like h 59.0 4.6 9.9E-05 31.3 0.9 45 696-748 4-48 (57)
58 PRK11569 transcriptional repre 58.8 17 0.00037 38.1 5.5 46 596-643 30-76 (274)
59 PF13463 HTH_27: Winged helix 58.7 6.9 0.00015 31.1 2.0 52 695-754 6-60 (68)
60 TIGR03879 near_KaiC_dom probab 57.6 13 0.00028 30.4 3.3 30 604-633 28-57 (73)
61 TIGR02944 suf_reg_Xantho FeS a 57.3 25 0.00054 32.2 5.7 56 597-659 12-69 (130)
62 smart00550 Zalpha Z-DNA-bindin 57.0 8.1 0.00018 31.1 2.1 53 694-754 8-62 (68)
63 PF13601 HTH_34: Winged helix 57.0 11 0.00024 31.4 3.0 44 596-641 2-45 (80)
64 PRK10163 DNA-binding transcrip 56.8 21 0.00045 37.5 5.7 45 597-643 28-73 (271)
65 TIGR02431 pcaR_pcaU beta-ketoa 55.8 22 0.00048 36.6 5.7 44 597-642 12-56 (248)
66 smart00344 HTH_ASNC helix_turn 55.0 20 0.00043 31.5 4.5 45 595-641 4-48 (108)
67 COG2345 Predicted transcriptio 54.9 16 0.00035 36.7 4.2 42 598-641 15-56 (218)
68 PRK09834 DNA-binding transcrip 54.8 22 0.00047 37.1 5.5 46 597-644 14-60 (263)
69 COG1846 MarR Transcriptional r 53.9 23 0.00051 31.3 5.0 51 592-644 20-70 (126)
70 PF01978 TrmB: Sugar-specific 52.0 6.1 0.00013 31.6 0.6 53 697-757 13-65 (68)
71 smart00418 HTH_ARSR helix_turn 51.5 14 0.00031 28.3 2.7 45 698-751 3-47 (66)
72 PRK10141 DNA-binding transcrip 51.3 27 0.00059 31.5 4.7 59 595-659 17-75 (117)
73 PRK11014 transcriptional repre 51.0 42 0.00091 31.2 6.2 49 603-658 20-68 (141)
74 PF08221 HTH_9: RNA polymerase 51.0 20 0.00044 28.3 3.4 34 605-640 24-57 (62)
75 smart00418 HTH_ARSR helix_turn 49.9 30 0.00065 26.4 4.4 35 606-642 8-42 (66)
76 PF09756 DDRGK: DDRGK domain; 49.0 6.9 0.00015 38.4 0.6 57 694-758 101-157 (188)
77 PF13730 HTH_36: Helix-turn-he 49.0 41 0.00089 25.3 4.9 25 610-634 27-51 (55)
78 cd00092 HTH_CRP helix_turn_hel 48.7 39 0.00085 26.4 4.9 35 607-643 24-58 (67)
79 PF10771 DUF2582: Protein of u 47.9 27 0.00058 27.9 3.6 38 597-634 11-48 (65)
80 PF01325 Fe_dep_repress: Iron 47.0 39 0.00084 26.4 4.4 44 599-644 13-56 (60)
81 cd00090 HTH_ARSR Arsenical Res 46.0 37 0.00081 26.8 4.5 47 593-642 6-52 (78)
82 PF11994 DUF3489: Protein of u 45.5 46 0.00099 27.1 4.6 47 593-639 9-55 (72)
83 PF01726 LexA_DNA_bind: LexA D 45.3 35 0.00076 27.2 4.0 55 689-750 7-62 (65)
84 PF04545 Sigma70_r4: Sigma-70, 45.1 49 0.0011 24.4 4.6 33 597-631 11-43 (50)
85 PF02002 TFIIE_alpha: TFIIE al 44.2 18 0.0004 31.7 2.5 45 595-641 14-58 (105)
86 PRK10434 srlR DNA-bindng trans 43.7 28 0.00061 36.1 4.2 47 595-643 6-52 (256)
87 PF09012 FeoC: FeoC like trans 42.5 27 0.00059 28.0 3.0 36 599-634 5-40 (69)
88 PF05158 RNA_pol_Rpc34: RNA po 41.9 19 0.00041 38.8 2.6 143 591-750 81-260 (327)
89 COG1349 GlpR Transcriptional r 40.0 36 0.00078 35.3 4.3 47 595-643 6-52 (253)
90 cd07153 Fur_like Ferric uptake 39.4 34 0.00074 30.4 3.5 57 697-756 6-63 (116)
91 PRK06266 transcription initiat 39.4 41 0.0009 32.8 4.3 45 595-641 23-67 (178)
92 COG4189 Predicted transcriptio 39.3 42 0.0009 33.7 4.2 49 593-643 22-70 (308)
93 PF12324 HTH_15: Helix-turn-he 39.0 73 0.0016 26.3 4.9 40 595-634 25-64 (77)
94 PF13412 HTH_24: Winged helix- 39.0 14 0.00031 27.1 0.9 43 695-745 6-48 (48)
95 PF01853 MOZ_SAS: MOZ/SAS fami 38.9 32 0.00069 33.7 3.4 27 607-633 149-175 (188)
96 smart00421 HTH_LUXR helix_turn 38.7 61 0.0013 24.0 4.5 39 593-633 5-43 (58)
97 TIGR00373 conserved hypothetic 38.6 53 0.0011 31.4 4.8 43 597-641 17-59 (158)
98 COG4190 Predicted transcriptio 38.3 85 0.0018 28.7 5.6 68 593-662 63-133 (144)
99 TIGR02702 SufR_cyano iron-sulf 38.1 63 0.0014 32.1 5.6 44 598-643 5-48 (203)
100 TIGR02844 spore_III_D sporulat 37.8 50 0.0011 27.6 3.9 35 595-630 7-41 (80)
101 PF08281 Sigma70_r4_2: Sigma-7 37.6 56 0.0012 24.5 4.0 37 593-630 12-48 (54)
102 PF09763 Sec3_C: Exocyst compl 37.4 8.1E+02 0.018 29.5 19.2 22 344-365 680-701 (701)
103 cd06170 LuxR_C_like C-terminal 37.4 67 0.0014 23.8 4.5 39 593-633 2-40 (57)
104 PF02796 HTH_7: Helix-turn-hel 37.2 52 0.0011 23.9 3.6 31 598-630 13-43 (45)
105 PF06784 UPF0240: Uncharacteri 36.8 56 0.0012 31.9 4.7 63 566-633 97-161 (179)
106 PRK13509 transcriptional repre 36.2 51 0.0011 34.1 4.7 48 595-644 6-53 (251)
107 PF14394 DUF4423: Domain of un 36.1 83 0.0018 30.5 5.8 55 588-644 18-75 (171)
108 PRK11169 leucine-responsive tr 36.0 52 0.0011 31.5 4.4 48 592-641 12-59 (164)
109 cd07377 WHTH_GntR Winged helix 35.8 80 0.0017 24.3 4.8 38 604-643 20-58 (66)
110 PRK04424 fatty acid biosynthes 35.0 43 0.00092 32.9 3.7 47 594-642 7-53 (185)
111 PF00325 Crp: Bacterial regula 34.9 53 0.0012 22.2 2.9 25 609-633 3-27 (32)
112 PF00196 GerE: Bacterial regul 34.0 61 0.0013 24.8 3.8 41 592-634 4-44 (58)
113 PF04967 HTH_10: HTH DNA bindi 33.7 63 0.0014 24.7 3.6 30 602-631 17-46 (53)
114 smart00344 HTH_ASNC helix_turn 32.4 21 0.00046 31.3 1.0 46 693-746 4-49 (108)
115 PF08318 COG4: COG4 transport 32.1 6.7E+02 0.015 27.0 16.4 163 273-452 15-214 (331)
116 PRK11179 DNA-binding transcrip 32.1 67 0.0015 30.3 4.4 49 591-641 6-54 (153)
117 PRK00215 LexA repressor; Valid 32.0 87 0.0019 31.1 5.5 51 592-644 2-58 (205)
118 PF09681 Phage_rep_org_N: N-te 31.8 68 0.0015 29.1 4.1 38 604-643 49-86 (121)
119 PRK10906 DNA-binding transcrip 31.7 61 0.0013 33.6 4.4 47 595-643 6-52 (252)
120 PRK10681 DNA-binding transcrip 31.7 62 0.0013 33.5 4.5 39 595-633 8-46 (252)
121 smart00420 HTH_DEOR helix_turn 30.7 23 0.00051 26.0 0.8 43 698-748 6-48 (53)
122 COG1522 Lrp Transcriptional re 30.3 81 0.0018 29.5 4.7 49 592-642 6-54 (154)
123 PF01726 LexA_DNA_bind: LexA D 30.2 69 0.0015 25.5 3.5 51 592-644 4-60 (65)
124 TIGR01714 phage_rep_org_N phag 30.0 75 0.0016 28.8 4.0 48 594-643 29-84 (119)
125 COG1654 BirA Biotin operon rep 30.0 1.3E+02 0.0029 25.0 5.2 41 600-640 11-51 (79)
126 PRK09802 DNA-binding transcrip 29.9 65 0.0014 33.7 4.3 48 594-643 17-64 (269)
127 PF12802 MarR_2: MarR family; 29.6 25 0.00053 27.2 0.8 35 707-749 22-56 (62)
128 KOG3054 Uncharacterized conser 29.6 40 0.00088 33.9 2.4 54 697-758 205-258 (299)
129 PRK04172 pheS phenylalanyl-tRN 28.4 79 0.0017 36.3 5.0 50 591-642 3-52 (489)
130 PF02186 TFIIE_beta: TFIIE bet 26.8 28 0.00061 27.8 0.7 54 694-758 7-61 (65)
131 smart00531 TFIIE Transcription 26.8 72 0.0016 30.0 3.6 32 605-636 12-43 (147)
132 KOG2747 Histone acetyltransfer 26.7 79 0.0017 34.6 4.2 26 608-633 329-354 (396)
133 PF01047 MarR: MarR family; I 26.4 22 0.00048 27.2 0.1 42 699-748 10-51 (59)
134 cd06171 Sigma70_r4 Sigma70, re 26.2 1.3E+02 0.0029 21.5 4.4 40 592-632 11-50 (55)
135 PF01638 HxlR: HxlR-like helix 25.6 1.1E+02 0.0024 25.9 4.2 45 596-643 7-52 (90)
136 TIGR00498 lexA SOS regulatory 25.5 72 0.0016 31.5 3.6 50 592-643 4-59 (199)
137 PRK13239 alkylmercury lyase; P 25.2 1.2E+02 0.0026 30.3 4.9 40 594-633 22-61 (206)
138 PF13542 HTH_Tnp_ISL3: Helix-t 24.9 1.6E+02 0.0035 21.7 4.6 35 595-631 16-50 (52)
139 smart00345 HTH_GNTR helix_turn 24.3 50 0.0011 24.9 1.7 27 723-749 29-55 (60)
140 PF00165 HTH_AraC: Bacterial r 24.1 1.1E+02 0.0023 21.7 3.3 28 606-633 6-33 (42)
141 COG3355 Predicted transcriptio 24.0 1.1E+02 0.0023 28.1 3.9 41 701-749 37-77 (126)
142 PLN03238 probable histone acet 23.6 1.2E+02 0.0026 31.8 4.7 37 596-632 210-247 (290)
143 PF13384 HTH_23: Homeodomain-l 23.5 83 0.0018 23.0 2.7 32 599-632 10-41 (50)
144 PHA02591 hypothetical protein; 23.3 97 0.0021 25.5 3.1 24 608-631 59-82 (83)
145 KOG2905 Transcription initiati 23.2 1E+02 0.0023 31.2 4.0 58 595-662 187-244 (254)
146 PF04182 B-block_TFIIIC: B-blo 23.0 1.1E+02 0.0025 24.9 3.7 49 594-644 2-52 (75)
147 PRK09334 30S ribosomal protein 23.0 57 0.0012 27.6 1.8 37 722-758 49-85 (86)
148 PF10007 DUF2250: Uncharacteri 22.7 1.4E+02 0.0031 25.6 4.3 52 590-643 3-54 (92)
149 PRK10411 DNA-binding transcrip 22.5 1.1E+02 0.0025 31.3 4.4 46 595-642 5-50 (240)
150 COG4742 Predicted transcriptio 22.3 1.3E+02 0.0028 31.2 4.6 42 599-643 18-59 (260)
151 TIGR01889 Staph_reg_Sar staphy 22.3 63 0.0014 28.5 2.1 41 703-751 40-82 (109)
152 PF06163 DUF977: Bacterial pro 22.1 55 0.0012 29.7 1.6 54 687-748 7-60 (127)
153 PF02270 TFIIF_beta: Transcrip 21.0 1.1E+02 0.0024 32.1 4.0 57 595-661 217-273 (275)
154 COG1522 Lrp Transcriptional re 21.0 59 0.0013 30.4 1.8 50 691-748 7-56 (154)
155 TIGR03433 padR_acidobact trans 20.9 1.2E+02 0.0026 26.3 3.6 52 694-746 6-57 (100)
156 TIGR02404 trehalos_R_Bsub treh 20.8 60 0.0013 32.9 1.9 33 722-755 32-64 (233)
157 PF00392 GntR: Bacterial regul 20.7 52 0.0011 25.8 1.1 38 717-755 27-64 (64)
158 COG1510 Predicted transcriptio 20.7 1.1E+02 0.0025 29.3 3.6 40 600-642 34-73 (177)
159 PRK11050 manganese transport r 20.3 1.8E+02 0.0039 27.5 4.9 43 598-642 41-83 (152)
160 PF01399 PCI: PCI domain; Int 20.1 1.8E+02 0.0038 24.8 4.6 41 594-634 46-86 (105)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2e-118 Score=1016.81 Aligned_cols=718 Identities=66% Similarity=1.092 Sum_probs=671.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHHHhcccchh
Q 004376 6 RKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSI 85 (758)
Q Consensus 6 ~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~i~~~l~~~v~~~l 85 (758)
+.+.+|+..|+.++++++++.+..++-..+.++.-+++.+|+++|++|+++++.+.+++||+++++++.+|+.+.+.+..
T Consensus 5 ~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~ 84 (725)
T KOG2166|consen 5 PKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPAL 84 (725)
T ss_pred ccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888765444457888999999999999999966656699999999999999998877777
Q ss_pred hccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhcC-CCCcHHHHH-HHHHHHHHhh-hhhHHHHHHHHHHHHHH
Q 004376 86 REKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARR-SLPPLNEVG-LTCFRDLVYT-ELNGKVRDAVITLIDQE 162 (758)
Q Consensus 86 ~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~-~~~~i~~l~-l~~f~~~v~~-~l~~~l~~~ll~~I~~~ 162 (758)
....++.++..+...|.+|+.++.+++++|.||||+||.+. +..++.+++ +.+|+..++. +++++++++++.+|..+
T Consensus 85 ~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~e 164 (725)
T KOG2166|consen 85 REKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHKE 164 (725)
T ss_pred HhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHhh
Confidence 77788899999999999999999999999999999999876 667777766 8888888877 59999999999999999
Q ss_pred hcCCccCHHHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHcccc
Q 004376 163 REGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYL 242 (758)
Q Consensus 163 R~g~~i~~~~l~~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l 242 (758)
|.|+.+|+..|+++++++..+|.+...+|...||++|++.|..||..++++|+...++++|+.+|+.++.+|..|+..|+
T Consensus 165 R~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl 244 (725)
T KOG2166|consen 165 REGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYL 244 (725)
T ss_pred cccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999889999999999999999999999999999988999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhH
Q 004376 243 HSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLA 322 (758)
Q Consensus 243 ~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~dL~~ly~L~~~~~~~l~~l~~~~~~~I~~~g~~i~~~~ 322 (758)
+..+.+++.+.+...++..+++.+++..++|+..|+.+++.++|.+||+|+++++.|++.+++.|+.|++.+|..++.+.
T Consensus 245 ~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~ 324 (725)
T KOG2166|consen 245 HSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARP 324 (725)
T ss_pred hhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888775
Q ss_pred HHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHh
Q 004376 323 EDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNIL 402 (758)
Q Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l 402 (758)
.... ..+|..++..+++++++|..++..||+++..|..+++.||..|+|.+.. ..+|+||+|||.++
T Consensus 325 ~~~~-----------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~l 391 (725)
T KOG2166|consen 325 AETA-----------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDIL 391 (725)
T ss_pred hhhc-----------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHHh
Confidence 5331 1468899999999999999999999999999999999999999999862 23799999999999
Q ss_pred hcCCCCCCCHHHHHHHHHHHHhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhcCchhhHhhhhhcc
Q 004376 403 KKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVS 482 (758)
Q Consensus 403 ~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~ 482 (758)
|++ ..+.++++++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|++.|+.||.+|+++||.+||++|++|+
T Consensus 392 kk~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf- 469 (725)
T KOG2166|consen 392 KKG-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMF- 469 (725)
T ss_pred ccc-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhc-
Confidence 994 467789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccccchhHhhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCCHhHHHHHHHHHHHHhhc
Q 004376 483 FGDYACEFKYLKVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTK 562 (758)
Q Consensus 483 ~~~~~~~~~~~~~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~ 562 (758)
+|+..|++++..|.++ . +.....+++|.|.|||+|+||.+++.++.||++|.++++.|..||..+
T Consensus 470 -------------~D~~~s~~l~~~F~~~-~-~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~k 534 (725)
T KOG2166|consen 470 -------------TDLTLSRELQTAFADY-A-NYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATK 534 (725)
T ss_pred -------------ccHHHHHHHHHHHHhh-h-chhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhc
Confidence 9999999999999987 1 222345799999999999999988888999999999999999999999
Q ss_pred CCCceEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 563 TKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 563 ~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
|+||+|.|+|++|.|+|.++|++++++|+||++||+||++||+.+.+|+++|.+.|+++.+++.++|+||++.|.+++.+
T Consensus 535 h~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~ 614 (725)
T KOG2166|consen 535 HNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK 614 (725)
T ss_pred cCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999888777766
Q ss_pred CCCCCCCCCCCcEEeccCCCCCCceeeccCCCchhhhhHHHhHHHhhhhhhceeeeeccccCCCCChHHHHHHHHHHhcC
Q 004376 643 EPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPVDEKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGR 722 (758)
Q Consensus 643 ~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~ 722 (758)
|.++. ++++.|.+|.+|+++.+|+++++++..+.+++.+.+++||++.|+||||||||+||.|.|++|+.+|.+|+++
T Consensus 615 -~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~ 692 (725)
T KOG2166|consen 615 -PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSE 692 (725)
T ss_pred -ccccC-CCCcEEEeeccccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhh
Confidence 66666 8899999999999999999999888888888899999999999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCCCCCceee
Q 004376 723 MFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 756 (758)
Q Consensus 723 ~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 756 (758)
+|.|++.+||+|||.|||||||+|| +|+++|.|
T Consensus 693 RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 693 RFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 9999999999999999999999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.6e-111 Score=910.35 Aligned_cols=724 Identities=31% Similarity=0.534 Sum_probs=637.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCCCCCC------------cHHHHHHHHHHHHH
Q 004376 7 KTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHD------------YSQQLYDKYRESFE 74 (758)
Q Consensus 7 ~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~------------~~e~LY~~l~~~i~ 74 (758)
+..||++.|..++.||.+|..-+.. .+....||++|+.+|+.|+++++.. .+..||+++....+
T Consensus 16 ~~~df~~~W~~i~~~I~~I~~~l~~----~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li~~L~~~~k 91 (773)
T COG5647 16 SEEDFESTWEFIERAIGQIFERLYD----SMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLIQKLVDYAK 91 (773)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHh----hhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999754433 3566779999999999999985531 37789999999999
Q ss_pred HHHHhcccchhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhc-----CCCCcHHHHHHHHHHHHHhhhhhH
Q 004376 75 EYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR-----RSLPPLNEVGLTCFRDLVYTELNG 149 (758)
Q Consensus 75 ~~l~~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~-----~~~~~i~~l~l~~f~~~v~~~l~~ 149 (758)
+|+...- ...+....+.||..++..|++|..++.+++.+|.||||.|++. .....+.++++..|+..+|.++++
T Consensus 92 ~~i~~~~-~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~ 170 (773)
T COG5647 92 NYIEEYN-RGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVD 170 (773)
T ss_pred HHHHHhc-ccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhH
Confidence 9988642 2222233578999999999999999999999999999999993 233457789999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhcc------CcccccHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhH
Q 004376 150 KVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGM------GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDY 223 (758)
Q Consensus 150 ~l~~~ll~~I~~~R~g~~i~~~~l~~~i~~l~~l~~------~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Y 223 (758)
.+.+.+|..+.+.|.|+.+|+..+..++.|+..++. .++.+|.+.|||+||+.|.+||..++++.+..+++.+|
T Consensus 171 ~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~ey 250 (773)
T COG5647 171 SLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEY 250 (773)
T ss_pred HHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHH
Confidence 999999999999999999999999999999999864 24589999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHHHHHHHHhhccCCCChhhH
Q 004376 224 MLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPV 303 (758)
Q Consensus 224 l~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~dL~~ly~L~~~~~~~l~~l 303 (758)
|.+|..++++|..+++.|++.++..++..+++++||..|.+.+.+.. ||+..+++..+.+.|+.||+++++++.++.++
T Consensus 251 L~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl 329 (773)
T COG5647 251 LEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQPL 329 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhH
Confidence 99999999999999999999999999999999999999999987764 89999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHhhh-hhhhhc-cccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHh
Q 004376 304 SNIFKQHVTAEGTALVKLAEDAASN-KKAEKR-DVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFC 381 (758)
Q Consensus 304 ~~~~~~~I~~~g~~i~~~~~~~~~~-~~~~~~-~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~ 381 (758)
.+.|..||...|.-+ +.....+.. ++.... ......+..+++.++++++.+..++...|.+|..+.+++++||..|+
T Consensus 330 ~~~f~~yV~~~g~~~-~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fi 408 (773)
T COG5647 330 QEVFERYVKDEGVLI-NIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFI 408 (773)
T ss_pred HHHHHHHHHhhchhh-hhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHh
Confidence 999999999999222 222211110 000000 01145688999999999999999999999999999999999999999
Q ss_pred hcCC-CCCChHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHH
Q 004376 382 NKGV-AGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERS 460 (758)
Q Consensus 382 n~~~-~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~ 460 (758)
|.+. +....+|+||+|+|.+||+++ +......++..+..++.||+|+.+||+|+++|+++||||||+++|+|.+.|.+
T Consensus 409 n~~~sa~~~~~e~Laky~D~~lkk~~-k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~ 487 (773)
T COG5647 409 NGNESADSGPSEYLAKYIDGLLKKDG-KQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELK 487 (773)
T ss_pred ccccccccccHHHHHHHhHHHhhccc-cccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHH
Confidence 9964 235789999999999999865 22233467778899999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCchhhHhhhhhcccccccccccccccchhHhhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCC-C
Q 004376 461 ILTKLKQQCGGQFTSKMEGMVSFGDYACEFKYLKVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYK-S 539 (758)
Q Consensus 461 ~i~~Lk~~~G~~~~~kl~~M~~~~~~~~~~~~~~~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~-~ 539 (758)
||++||+.||.+||+|+++|| +||..|+++...|++... + ..+.+++.|.||+..+||..| .
T Consensus 488 mis~LKk~~g~~fT~Kle~Mf--------------~DIsLS~e~~~af~~s~~-s--~~~~~Dl~v~VLt~a~WP~sp~~ 550 (773)
T COG5647 488 MISMLKKVCGQEFTSKLEGMF--------------RDISLSSEFTEAFQHSPQ-S--YNKYLDLFVWVLTQAYWPLSPEE 550 (773)
T ss_pred HHHHHHHHhhhHHHHHHHHHH--------------HhcchhHHHHHHHhhCch-h--hccccchhHHHHHHhcCCCCccc
Confidence 999999999999999999999 999999999999986531 1 235789999999999999665 4
Q ss_pred CCccCCHhHHHHHHHHHHHHhhcCCCceEEeccCcceEEEEeEecCeeEEEE---EcHHHHHHHHhhcCCCCccHHHHHH
Q 004376 540 FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELI---VTTYQASALLLFNSSDRLSYSEIMT 616 (758)
Q Consensus 540 ~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~---~s~~Q~~iLllFn~~~~~t~~ei~~ 616 (758)
..+.||++|.+.++.|++||.+||+||+|.|.++||+|+|++.|+.+++.+. ++++|+.|+++||+++++|+++|.+
T Consensus 551 ~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e 630 (773)
T COG5647 551 VSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILE 630 (773)
T ss_pred cccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHh
Confidence 6899999999999999999999999999999999999999999987754443 6688999999999999999999999
Q ss_pred HhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCCCCCceeeccCCCc----hhhhhHHHhHHHhhhhh
Q 004376 617 QLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYA 692 (758)
Q Consensus 617 ~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~~~~~r~~~ 692 (758)
.|+++..+++++|+||+++|..++.+ +++.+++++.|.+|.+|+++..+|+|+.+.. ++...+++.+++||+..
T Consensus 631 ~T~l~~~dl~~~L~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~ 708 (773)
T COG5647 631 LTKLSTDDLKRVLQSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAE 708 (773)
T ss_pred hcCCChhhHHHHHHHHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHH
Confidence 99999999999999999876655554 3677889999999999999999999997654 34556778899999999
Q ss_pred hceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 693 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 693 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
+|||||||||+||+|.|++|+++|+.+.++||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 709 lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 709 LQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred HHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 9999999999999999999999999999999999999999999999999999999888 8999997
No 3
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.9e-109 Score=836.82 Aligned_cols=684 Identities=27% Similarity=0.510 Sum_probs=627.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHHHhc
Q 004376 1 MTMNERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISST 80 (758)
Q Consensus 1 ~~~~~~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~i~~~l~~~ 80 (758)
||||+|++++||+.|.+|.+.|..|... .++.+.+|..-|+.||.+|..- |++-||+||..++.++++|+.+.
T Consensus 1 m~slkp~vv~fd~~w~~l~~si~~ii~l------~~i~~~~w~~~fsdvy~icvs~-p~pl~erly~e~k~~i~~hvrq~ 73 (728)
T KOG2284|consen 1 MYSLKPKVVEFDKVWVQLRPSIIDIINL------RPITNVQWHHKFSDVYDICVSI-PTPLSERLYNEVKACIQEHVRQK 73 (728)
T ss_pred CCCCCceeeeHHHHHHHHHHHHHHHHhc------cchhccccccchhhHHHHHHhC-CCchhHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999887432 3577888999999999999998 78899999999999999999865
Q ss_pred ccchhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhcCC------------------CCcHHHHHHHHHHHH
Q 004376 81 VLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRS------------------LPPLNEVGLTCFRDL 142 (758)
Q Consensus 81 v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~------------------~~~i~~l~l~~f~~~ 142 (758)
. ......+++.+|..|.+.|+.|..+..++..+|.|||+.|+++++ ...|..+|+.+|++.
T Consensus 74 ~-~~~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~ 152 (728)
T KOG2284|consen 74 R-QDIVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKED 152 (728)
T ss_pred h-hhhhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHH
Confidence 3 233334556799999999999999999999999999999998753 224678899999999
Q ss_pred HhhhhhHHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHHHHhcc-----------------CcccccHHHHHHHHHHHHH
Q 004376 143 VYTELNGKVRDAVITLIDQEREGEQID-RALLKNVLDIFVEIGM-----------------GQMDYYENDFETAMLKDTA 204 (758)
Q Consensus 143 v~~~l~~~l~~~ll~~I~~~R~g~~i~-~~~l~~~i~~l~~l~~-----------------~~~~~Y~~~FE~~~L~~t~ 204 (758)
+..++...|...++..|.++|.|+.++ ...+..++++|+.+.. .+..+|++.||+|||.+|.
T Consensus 153 ~v~~i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~ 232 (728)
T KOG2284|consen 153 LVKTILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTE 232 (728)
T ss_pred HHHHHHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchH
Confidence 999999999999999999999999888 6789999999997753 2467999999999999999
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHH
Q 004376 205 AYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVE 284 (758)
Q Consensus 205 ~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~ 284 (758)
+||+++++..+.+.+|++|+.+|.-++++|+.||+.||+++|..|++-.|++.||.+|.+.| +..|+.++.+.+..
T Consensus 233 ~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~ 308 (728)
T KOG2284|consen 233 QYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENK 308 (728)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999887 45799999999999
Q ss_pred HHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcC
Q 004376 285 DLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQ 364 (758)
Q Consensus 285 dL~~ly~L~~~~~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~ 364 (758)
|++.||.|+..+..|+..+.+.|.+||..+|...++.... .+-|..||+.++.+|.+|.+++...|+
T Consensus 309 d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~-------------en~p~~fve~vl~v~~kf~~~~~~v~~ 375 (728)
T KOG2284|consen 309 DLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTG-------------ENVPQQFVENVLRVYNKFNDMKTAVFM 375 (728)
T ss_pred hHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhcc-------------ccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999998877543 245889999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHhhcCCCC---CChHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhccccChhHHHHHHHH
Q 004376 365 NHTLFHKSLKEAFEVFCNKGVAG---SSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRK 441 (758)
Q Consensus 365 ~~~~f~~~l~~af~~~~n~~~~~---~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~ 441 (758)
+|..|..+++.|+..++|..+++ .+.+|.||+|||.+|+++. +++++.+++..|+..+.+|+|++|||+|.++|.+
T Consensus 376 ~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~ 454 (728)
T KOG2284|consen 376 DDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSK 454 (728)
T ss_pred CchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHH
Confidence 99999999999999999988753 4789999999999999964 6899999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCChHHHHHHHHHHHHhcCchhhHhhhhhcccccccccccccccchhHhhHHHHHHHHHHHhcCCCCCCC
Q 004376 442 KLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVSFGDYACEFKYLKVTDLTLARENQTSFEEYLSNNPNANPG 521 (758)
Q Consensus 442 ~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~~~~~~~~~~~~~~~D~~~S~~~~~~f~~~~~~~~~~~~~ 521 (758)
+||+|||.+.|.|.|.|..||++|++.||.+||+++. + .|+..|.+++++|.+.+.+
T Consensus 455 mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~--------------td~~~s~~lnn~f~~~i~n------- 511 (728)
T KOG2284|consen 455 MLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--L--------------TDPQLSTNLNNQFAQDIAN------- 511 (728)
T ss_pred HHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--C--------------CChhhccccchhHHHHHHh-------
Confidence 9999999999999999999999999999999999987 7 9999999999999887542
Q ss_pred cceEEEEeecCCCCCCCCCCccCCHhHHHHHHHHHHHHhhcCCCceEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHH
Q 004376 522 IDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALL 601 (758)
Q Consensus 522 ~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLl 601 (758)
+.+|.+|++.++.|+.||..+|+||+|+|++.++++++++++-++.|.-.+.++||++||
T Consensus 512 --------------------f~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll 571 (728)
T KOG2284|consen 512 --------------------FHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALL 571 (728)
T ss_pred --------------------ccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCCCCCceeeccCCCc-----h
Q 004376 602 LFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV-----D 676 (758)
Q Consensus 602 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~-----~ 676 (758)
+||..+.+++.||.+.+|++.+.|.+.+.++.+. ++|... +..+..+..|++|.+|+++..+.+|..|.+ +
T Consensus 572 ~f~~~~~i~~k~i~~~~~~~~~~l~kti~tildv--~~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~ 647 (728)
T KOG2284|consen 572 CFERRDAILVKDIGEEIGVSGDYLLKTIRTILDV--TLLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEK 647 (728)
T ss_pred HhcccccchHHhhhhhhCccHHHHHHHHHHHHhc--eeeccc--ccccChhhhhhccccccccceeeEecchhhccccHH
Confidence 9999999999999999999999999999999864 577654 345667888999999999999999987654 3
Q ss_pred hhhhHHHhHHHhhhhhhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceee
Q 004376 677 EKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 756 (758)
Q Consensus 677 e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 756 (758)
|.+.+...+.+||++.++||||||||+||.+.|+.|+.+|++|.++||.|++++||++||.||++.||+|.+.+ +.|.|
T Consensus 648 e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y 726 (728)
T KOG2284|consen 648 EQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQY 726 (728)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchh
Confidence 44556678999999999999999999999999999999999999999999999999999999999999999876 89999
Q ss_pred cC
Q 004376 757 LA 758 (758)
Q Consensus 757 ia 758 (758)
+|
T Consensus 727 ~a 728 (728)
T KOG2284|consen 727 LA 728 (728)
T ss_pred cC
Confidence 97
No 4
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.6e-107 Score=859.76 Aligned_cols=647 Identities=36% Similarity=0.602 Sum_probs=603.5
Q ss_pred HHHHHHHHHHHHHHhcccchhhc-cCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhc--CCCCcHHHHHHHHHHH
Q 004376 65 LYDKYRESFEEYISSTVLPSIRE-KHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR--RSLPPLNEVGLTCFRD 141 (758)
Q Consensus 65 LY~~l~~~i~~~l~~~v~~~l~~-~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~--~~~~~i~~l~l~~f~~ 141 (758)
||+.+++.+++|++..+.+.-.. .+...+|+.+.+.|..|...+.+++.+|.||||.|+.. ...+|+|++++.+||.
T Consensus 2 ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR~ 81 (661)
T KOG2167|consen 2 LYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFRA 81 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHHH
Confidence 79999999999998655322111 23457999999999999999999999999999999987 3578999999999999
Q ss_pred HHhh----hhhHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 004376 142 LVYT----ELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILE 217 (758)
Q Consensus 142 ~v~~----~l~~~l~~~ll~~I~~~R~g~~i~~~~l~~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~ 217 (758)
+++. .+..++.++++..++++|.|+++|+..|+.++.|+.++ ..|.+.|++.|++.+.++|.+++.....+
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~-----~iY~esF~~~fls~f~~lY~aE~~d~~Qe 156 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDL-----QIYKESFELTFLSLFRELYAAEGQDKRQE 156 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH-----HhhhhhhHHHHHHHHHHHHHHHhcchhhh
Confidence 9998 47788899999999999999999999999999999996 57999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHHHHHHHHhhccCC
Q 004376 218 DSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIP 297 (758)
Q Consensus 218 ~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~dL~~ly~L~~~~~ 297 (758)
..+++||++++.++.+|.+|+..+++.+|...+..++.+.|+..|++.++.+ |+..+++.++..++.+||.|++++.
T Consensus 157 l~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~~ 233 (661)
T KOG2167|consen 157 LEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRVQ 233 (661)
T ss_pred cccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHHh
Confidence 9999999999999999999999999998966799999999999999999875 7999999999999999999999998
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCC--hHHHHHHHH
Q 004376 298 RGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNH--TLFHKSLKE 375 (758)
Q Consensus 298 ~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~--~~f~~~l~~ 375 (758)
++...++..|++|+++-|..++.+.. .+...|+.+++++++.+-++..||..+ ..|..++++
T Consensus 234 ~g~l~l~qq~sdylk~~G~KlV~de~----------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~ 297 (661)
T KOG2167|consen 234 GGQLSLLQQWSDYLKKPGFKLVIDEE----------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSK 297 (661)
T ss_pred cchHHHHHHHHHHHhcccceeccCch----------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHH
Confidence 89999999999999999999986532 256899999999999999999999988 999999999
Q ss_pred HHHHHhhcCCCCCChHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHhhhccccChhHHHHHHHHHHHHHhcCCCCCCh
Q 004376 376 AFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSAND 455 (758)
Q Consensus 376 af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~ 455 (758)
||+.|+|... .++|++||+|.|..|+.|. +..++++++..++.++.||+|+..||+|+.+|++.||+|||.++|+|.
T Consensus 298 afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsv 374 (661)
T KOG2167|consen 298 AFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASV 374 (661)
T ss_pred HHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhh
Confidence 9999999775 5799999999999999865 456778899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCchhhHhhhhhcccccccccccccccchhHhhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCC
Q 004376 456 DHERSILTKLKQQCGGQFTSKMEGMVSFGDYACEFKYLKVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWP 535 (758)
Q Consensus 456 ~~E~~~i~~Lk~~~G~~~~~kl~~M~~~~~~~~~~~~~~~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP 535 (758)
|.|++|+.+|+.+||..||+||++|| +|+..|++++..|+++...+.....++ +.+.|+|.|+||
T Consensus 375 dae~~ml~~lk~ecgs~ft~kLegMf--------------kdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWp 439 (661)
T KOG2167|consen 375 DAEKSMLSKLKLECGSAFTYKLEGMF--------------KDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWP 439 (661)
T ss_pred cchhHHHHHhhhhcchHHHHHHHHhh--------------hhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccC
Confidence 99999999999999999999999999 999999999999999966554434455 999999999999
Q ss_pred CCCCCCccCCHhHHHHHHHHHHHHhhcCCCceEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHH
Q 004376 536 SYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIM 615 (758)
Q Consensus 536 ~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~ 615 (758)
++++.++.||++|.++.+.|..||..+|.||+|.|.+++|+|.+++.|..|++++.+|++|++||++||+.+.+|++||.
T Consensus 440 ty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~ 519 (661)
T KOG2167|consen 440 TYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIK 519 (661)
T ss_pred CCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCCCCCceeeccCCCc----hhhhhHHHhHHHhhhh
Q 004376 616 TQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRY 691 (758)
Q Consensus 616 ~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~~~~~r~~ 691 (758)
+.|+|.+.+|.++|+||.|+|.++|.+.|.|+.+.+++.|.+|..|+++..||+|+.+.+ +|.+.+.++|.+||.+
T Consensus 520 ~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy 599 (661)
T KOG2167|consen 520 ESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQY 599 (661)
T ss_pred HhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhH
Confidence 999999999999999999999999999999999999999999999999999999998765 4566788999999999
Q ss_pred hhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 692 AIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 692 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
.|+||||||||+||+|+|+.|+.++.++|+ ||..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 600 ~idaaivrimk~rk~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 600 QIDAAIVRIMKMRKTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HHHHHHHHHHHHHHhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 999999999999999999999999999997 99888 999999999999999999 45 8999998
No 5
>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=8.9e-90 Score=803.33 Aligned_cols=586 Identities=41% Similarity=0.755 Sum_probs=523.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHHHhcccchhhccCcHHHH
Q 004376 15 WEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFML 94 (758)
Q Consensus 15 W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~i~~~l~~~v~~~l~~~~~~~~L 94 (758)
|+.|++||..|. .+ .++..+||++|+.||++|..+ +|+.||+.+++.+.+|+... .+.+.+.+++.+|
T Consensus 1 W~~l~~~i~~i~---~~----~~~~~~~~~lY~~vy~l~~~~----~~~~LY~~l~~~i~~~~~~~-~~~l~~~~~~~~l 68 (588)
T PF00888_consen 1 WEILEEAIDQIF---KK----SISKLSYMELYTCVYNLCDNK----YGEQLYDKLKEFISEYLKNI-IESLLSSSDEDLL 68 (588)
T ss_dssp HHHHHHHHHHHH---TT-----GCCSHHHHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHHH-HHHHCTTTTCHHH
T ss_pred ChHHHHHHHHHH---cC----CCChhHHHHHHHHHHhhcCCc----ccHHHHHHHHHHHHHHHHHH-HHHHHhcChhHHH
Confidence 999999999974 22 467788999999999999877 89999999999999999874 4555555778999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccchhhhhcCCCCcHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhcCCccCHHHHH
Q 004376 95 RELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLK 174 (758)
Q Consensus 95 ~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~i~~l~l~~f~~~v~~~l~~~l~~~ll~~I~~~R~g~~i~~~~l~ 174 (758)
..|...|.+|+.++.+|+++|.||||+|+.++ +|++.|+.++.++++.+++++|.++|.|+.+|...++
T Consensus 69 ~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~-----------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~ 137 (588)
T PF00888_consen 69 EEYVQEWEKYKKAIKYISDIFSYLDRNYVKRN-----------LFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLK 137 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTT-----------HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhh-----------hHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Confidence 99999999999999999999999999999888 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHccccCCCcHHHHHHHH
Q 004376 175 NVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKV 254 (758)
Q Consensus 175 ~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l 254 (758)
++++|++++| +..+|.+.||++||+.|.+||+.++ +...++.+|+.+|+.++++|..|+..|++++|.+++.+.+
T Consensus 138 ~~~~~~~~l~--~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l 212 (588)
T PF00888_consen 138 NVIEMFVELG--SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTL 212 (588)
T ss_dssp HHHHHHHHTT--HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHH
T ss_pred HHHHHHhccc--hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHH
Confidence 9999999988 5689999999999999999999999 5677999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhhhhcCcHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhhc
Q 004376 255 QHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKR 334 (758)
Q Consensus 255 ~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~dL~~ly~L~~~~~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~ 334 (758)
.++||.+|.+.| .+|+..|+.+++.++|++||+|+++++++++.+++.|++||.+.|..+++....
T Consensus 213 ~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~---------- 278 (588)
T PF00888_consen 213 EEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK---------- 278 (588)
T ss_dssp HHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------
T ss_pred HHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------
Confidence 999999999998 469999999999999999999999999999999999999999999999976531
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHhhcCCCCCCCHHH
Q 004376 335 DVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEA 414 (758)
Q Consensus 335 ~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~ 414 (758)
...+..||+.++++|++|+.++.+||++++.|..++++||+.++|.+ ...++++||+|||.++++++ .+.++++
T Consensus 279 ---~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~ 352 (588)
T PF00888_consen 279 ---SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEE 352 (588)
T ss_dssp ---GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCC
T ss_pred ---ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHH
Confidence 23578999999999999999999999999999999999999999998 36899999999999999875 5667788
Q ss_pred HHHHHHHHHhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhcCchhhHhhhhhcccccccccccccc
Q 004376 415 IEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVSFGDYACEFKYLK 494 (758)
Q Consensus 415 ~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~~~~~~~~~~~~~ 494 (758)
++..++.++.||+|+++||+|+.+|+++||+|||.+++.+.+.|+.+|++|+.+||.+++++|++|+
T Consensus 353 ~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~------------- 419 (588)
T PF00888_consen 353 IEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVML------------- 419 (588)
T ss_dssp HHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHH-------------
T ss_pred HHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHH-------------
Confidence 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhHhhHHHHHHHHHHHhcCCCCC-CCcceEEEEeecCCCCCCCCCC-ccCCHhHHHHHHHHHHHHhhcCCCceEEecc
Q 004376 495 VTDLTLARENQTSFEEYLSNNPNAN-PGIDLTVTVLTTGFWPSYKSFD-LNLPAEMVKCVEVFREFYQTKTKHRKLTWIY 572 (758)
Q Consensus 495 ~~D~~~S~~~~~~f~~~~~~~~~~~-~~~~~~~~vLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~ 572 (758)
+|+..|++++++|++...+.+... ++++|+|.||++++||..+..+ +.||++|+.+++.|++||+++|+||+|.|.+
T Consensus 420 -~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~ 498 (588)
T PF00888_consen 420 -KDIKNSKELNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLP 498 (588)
T ss_dssp -HHHHHHHHHHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEG
T ss_pred -HHHhhcHHHHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEec
Confidence 999999999999999987655322 2789999999999999988766 9999999999999999999999999999999
Q ss_pred CcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCC
Q 004376 573 SLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPT 652 (758)
Q Consensus 573 ~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~ 652 (758)
++|+|+|+++++++++++.||++||+||++||+.+++|++||++.||++.++++++|.+|++.+..++.+.+++++++++
T Consensus 499 ~l~~~~i~~~~~~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~ 578 (588)
T PF00888_consen 499 SLSSVEIEFNFNNGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDN 578 (588)
T ss_dssp GGEEEEEEEESSSSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT
T ss_pred ccCcEEEEEEecCCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999986543333366788889999
Q ss_pred CcEEeccCCC
Q 004376 653 DHFEFNSKFT 662 (758)
Q Consensus 653 ~~~~~N~~f~ 662 (758)
+.|.+|.+|+
T Consensus 579 ~~f~~N~~F~ 588 (588)
T PF00888_consen 579 DEFSVNENFT 588 (588)
T ss_dssp -EEEE-TT--
T ss_pred CEEEeCCCCC
Confidence 9999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-88 Score=692.32 Aligned_cols=716 Identities=26% Similarity=0.462 Sum_probs=630.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHHHhcccch
Q 004376 5 ERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPS 84 (758)
Q Consensus 5 ~~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~i~~~l~~~v~~~ 84 (758)
.+....|++.|+...|.+-++.+ ++.+++..|..+|.+||.+|.+. .....++|+.+++.|.+|+.+...+.
T Consensus 7 ~r~r~qFee~W~~~rpIVlkLLr------Q~sVt~~~WqDLF~~Vh~vclWd--dkGpaKI~d~L~~dI~efi~qAq~rv 78 (777)
T KOG2285|consen 7 KRDRDQFEEEWSKARPIVLKLLR------QKSVTPAAWQDLFYHVHKVCLWD--DKGPAKIRDILTRDINEFIHQAQKRV 78 (777)
T ss_pred ccchhhhhhhccccchHHHHHHh------hccCCHHHHHHHHhhheeeeeec--CCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556899999999999988754 24689999999999999999997 23466799999999999998643322
Q ss_pred hhccCcHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhcCC--------CCcHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 004376 85 IREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRS--------LPPLNEVGLTCFRDLVYTELNGKVRDAVI 156 (758)
Q Consensus 85 l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~--------~~~i~~l~l~~f~~~v~~~l~~~l~~~ll 156 (758)
.....+..+|..|..+|.+|-....++...|.-|+..-..+++ -.+|..+.+..|.+.+|..++++|....+
T Consensus 79 ~s~q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAm 158 (777)
T KOG2285|consen 79 RSLQTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAM 158 (777)
T ss_pred HhhccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334566899999999999999999999999999987554321 23688999999999999999999999999
Q ss_pred HHHHHHhcCCccCHHHHHHHHHHHHHhcc---CcccccHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHH
Q 004376 157 TLIDQEREGEQIDRALLKNVLDIFVEIGM---GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKR 233 (758)
Q Consensus 157 ~~I~~~R~g~~i~~~~l~~~i~~l~~l~~---~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~e 233 (758)
.++..+|.|+.+|.+.+-.+-++|+.++. +.+.+|.+.||..||++|.+||+..+..++++.++.+|++.|..-+++
T Consensus 159 klVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~E 238 (777)
T KOG2285|consen 159 KLVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEE 238 (777)
T ss_pred HHHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhH
Confidence 99999999999999999999999999875 567899999999999999999999999999999999999999999999
Q ss_pred HHHHHccccCC--CcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHHHHHHHHhhccCCCChhhHHHHHHHHH
Q 004376 234 EKDRVSHYLHS--SSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHV 311 (758)
Q Consensus 234 E~~r~~~~l~~--~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~dL~~ly~L~~~~~~~l~~l~~~~~~~I 311 (758)
|+.|+.+||.+ .|..+++..+.++|+.++.+.|+. .|..|+....++-|++||+|+.+++.|++++.+.+..||
T Consensus 239 Ee~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI 314 (777)
T KOG2285|consen 239 EEQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHI 314 (777)
T ss_pred HHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHH
Confidence 99999999976 677899999999999999999986 588899999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCC------
Q 004376 312 TAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGV------ 385 (758)
Q Consensus 312 ~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~------ 385 (758)
...|..-+....+.+ +.++..||+.|+.++++|..++.++|++||.|..+-+.||..++|...
T Consensus 315 ~saGLaDM~~aaE~i-----------ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~El 383 (777)
T KOG2285|consen 315 RSAGLADMRNAAENI-----------TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTEL 383 (777)
T ss_pred HhhhHHHHHhhhhhc-----------cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhc
Confidence 999987665443332 567889999999999999999999999999999999999999999863
Q ss_pred ------------CCCChHHHHHHHHHHHhhcCC-CCCCCHHHHHHHHHHHHhhhccccChhHHHHHHHHHHHHHhcCCCC
Q 004376 386 ------------AGSSSAELLATFCDNILKKGG-SEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 452 (758)
Q Consensus 386 ------------~~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~ 452 (758)
+..+.||+||.|||.+||+.. +++++.++++..|++|+-+++|+.+||+|+.+++.+|++|||.+.|
T Consensus 384 p~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~S 463 (777)
T KOG2285|consen 384 PNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMS 463 (777)
T ss_pred cchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcc
Confidence 234679999999999999853 4678889999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHhcCc--hhhHhhhhhcccccccccccccccchhHhhHHHHHHHHHHHhcCCCCCCCcceEEEEee
Q 004376 453 ANDDHERSILTKLKQQCGG--QFTSKMEGMVSFGDYACEFKYLKVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLT 530 (758)
Q Consensus 453 ~~~~~E~~~i~~Lk~~~G~--~~~~kl~~M~~~~~~~~~~~~~~~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~vLt 530 (758)
+..+.|..|+..|+ +||. +|++|+.+|| +|++.|++++..|+..+...+...+.-.+++.||+
T Consensus 464 ADsEkEE~mVewLR-EvGMPaDyVNkLaRMf--------------QDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLN 528 (777)
T KOG2285|consen 464 ADSEKEEMMVEWLR-EVGMPADYVNKLARMF--------------QDIKVSEDLNSSFKKALTGTNNNSIADSINIKILN 528 (777)
T ss_pred cchhHHHHHHHHHH-HcCCcHHHHHHHHHHH--------------hhccccHHHHHHHHHHHhCCCCCCcccceeeeeec
Confidence 99999999999999 5775 7999999999 99999999999999988766555555678999999
Q ss_pred cCCCCCCCC-CCccCCHhHHHHHHHHHHHHhhcCCCceEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--C
Q 004376 531 TGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--D 607 (758)
Q Consensus 531 ~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~--~ 607 (758)
.|.|...+. ..+.||.+|++.+-..++||+++|.||+|.|.|+++.++|++..+-|.|.+.|+++||+||.+||+. +
T Consensus 529 aGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hd 608 (777)
T KOG2285|consen 529 AGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHD 608 (777)
T ss_pred ccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhcccccc
Confidence 999997643 4689999999999999999999999999999999999999887666899999999999999999975 5
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHHhhh---ccccccccCCCC----CCCCCCCcEEeccCCCC-C----CceeeccCCCc
Q 004376 608 RLSYSEIMTQLNLSDDDVVRLLHSLSC---AKYKILNKEPNT----KTISPTDHFEFNSKFTD-K----MRRIKIPLPPV 675 (758)
Q Consensus 608 ~~t~~ei~~~t~i~~~~l~~~L~~L~~---~k~~iL~~~~~~----~~i~~~~~~~~N~~f~~-~----~~~i~i~~~~~ 675 (758)
.+|++.+.-.|.+|+.++.+.|-||+. .|+.||..+|+. +++.++..|.+|.+|.- + .++-+++...-
T Consensus 609 KIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGR 688 (777)
T KOG2285|consen 609 KISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGR 688 (777)
T ss_pred ccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeee
Confidence 899999999999999999999999984 357788877642 45667889999999972 1 12233333211
Q ss_pred ----hh--hhhHHHhHHHhhhhhhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCC
Q 004376 676 ----DE--KKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 749 (758)
Q Consensus 676 ----~e--~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 749 (758)
.| .++..+.+.+-|-...+-+||+|||.||+++..+|-.++++.|+..|-|+..+||++||.|||..|++||++
T Consensus 689 LQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~d 768 (777)
T KOG2285|consen 689 LQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDAD 768 (777)
T ss_pred eeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchh
Confidence 11 122345678889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeecC
Q 004376 750 NPNMFRYLA 758 (758)
Q Consensus 750 ~~~~y~Yia 758 (758)
|-++|+|+|
T Consensus 769 DINtFiYia 777 (777)
T KOG2285|consen 769 DINTFIYIA 777 (777)
T ss_pred hccceeeeC
Confidence 999999997
No 7
>smart00182 CULLIN Cullin.
Probab=99.97 E-value=3.2e-31 Score=249.91 Aligned_cols=141 Identities=48% Similarity=0.890 Sum_probs=132.4
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhcCchhhHhhhhhcccccccccccccccchhHhhHHHHHH
Q 004376 428 YISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVSFGDYACEFKYLKVTDLTLARENQTS 507 (758)
Q Consensus 428 ~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~~~~~~~~~~~~~~~D~~~S~~~~~~ 507 (758)
|+++||+|+.+|+++||+|||..++.+.+.|..+|++|+.+||.+++++|++|+ +|+..|++++++
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml--------------~Di~~S~~l~~~ 66 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMF--------------RDISLSKDLNQS 66 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHH--------------HHHHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999 999999999999
Q ss_pred HHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccCCHhHHHHHHHHHHHHhhcCCCceEEeccCcceEEEEeEe
Q 004376 508 FEEYLSNNPNANPGIDLTVTVLTTGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKF 583 (758)
Q Consensus 508 f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l~~~~ 583 (758)
|++.+.+++ ...+++|+|.|||.++||..+. .++.||++|+.+++.|++||..+|+||+|+|++++|+|+|+++|
T Consensus 67 f~~~~~~~~-~~~~~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 67 FKDMLENNS-NKPIIDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred HHHHHHhcc-CCCCCceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 999876542 2346899999999999998877 78999999999999999999999999999999999999999864
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=3.9e-24 Score=232.88 Aligned_cols=308 Identities=22% Similarity=0.273 Sum_probs=241.4
Q ss_pred HHhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhcCchhhHhhhhhcccccccccccccccchhHhh
Q 004376 422 VVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVSFGDYACEFKYLKVTDLTLA 501 (758)
Q Consensus 422 i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~M~~~~~~~~~~~~~~~~D~~~S 501 (758)
+-.+.+.+.+|+.|.+.||.+||.||+.....+.+.|..-++.||-++|.+..+.|+.|+ +|+..|
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML--------------~Dv~dS 507 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVML--------------NDVIDS 507 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHH--------------Hhhhhh
Confidence 345667789999999999999999999999999999999999999999999999999999 999999
Q ss_pred HHHHHHHHHH--HhcCCCCCCCcceEEEEeecCCCCCCCCCCccCCHhHHHHHHHHHHHHhhcCCCceEEeccCcceEEE
Q 004376 502 RENQTSFEEY--LSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNL 579 (758)
Q Consensus 502 ~~~~~~f~~~--~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~l 579 (758)
+++++.++.. .....-..+.+.+++.+|+..+||......+.||.+++..++.|.+-|.+..++|+|.|++++|.|++
T Consensus 508 ~~id~~i~~~~~~~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Vei 587 (765)
T KOG2165|consen 508 RRIDQSIHNESELSRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEI 587 (765)
T ss_pred hhhhhhhhhhhhhhcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEE
Confidence 9999999873 22212234578899999999999988878899999999999999999999999999999999999999
Q ss_pred EeEecCeeEEEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEecc
Q 004376 580 LGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 659 (758)
Q Consensus 580 ~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 659 (758)
+++|.+++.+++||+.||+|+.+|.+.++||++++++.+|+|.+.+++.|..|++ .++|..+|. ++++++|++++
T Consensus 588 eie~~DRtl~~tVsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iE 662 (765)
T KOG2165|consen 588 EIEFEDRTLVLTVSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIE 662 (765)
T ss_pred EEEEcCeEEEEeeCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeecc
Confidence 9999999999999999999999999999999999999999999999999999984 588987643 36788999988
Q ss_pred CCCCCCceeeccCCCchh-h--hhHHHhHHHhh--hhhhceeeeeccccCCCCChHHHHHHHHHHhcC--CCCCChHHHH
Q 004376 660 KFTDKMRRIKIPLPPVDE-K--KKVIEDVDKDR--RYAIDASIVRIMKSRKVLGHQQLVLECVEQLGR--MFKPDFKAIK 732 (758)
Q Consensus 660 ~f~~~~~~i~i~~~~~~e-~--~~~~~~~~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~--~F~~~~~~ik 732 (758)
+=.+..+--.-+....++ . ......+++-+ -..-...||-.+=.-+.|..+.+.+...-.... ...++-++++
T Consensus 663 se~d~~q~~~~~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~ 742 (765)
T KOG2165|consen 663 SEMDFDQAEGTVLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQ 742 (765)
T ss_pred ccccccccCCCcccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHH
Confidence 543322211111111111 1 11112222211 112334788777777999999988854321111 1223456677
Q ss_pred HHHHhhhhhccccccC
Q 004376 733 KRIEDLITRDYLERDK 748 (758)
Q Consensus 733 ~~Ie~Liereyi~r~~ 748 (758)
..+..++..|-++-.+
T Consensus 743 ~fLq~kV~e~kL~f~~ 758 (765)
T KOG2165|consen 743 GFLQRKVREGKLEFIA 758 (765)
T ss_pred HHHHHHhhccceEEec
Confidence 7777777777665443
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=99.75 E-value=1.8e-19 Score=145.98 Aligned_cols=68 Identities=51% Similarity=0.920 Sum_probs=62.4
Q ss_pred HHHhhhhhhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCC
Q 004376 685 VDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPN 752 (758)
Q Consensus 685 ~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~ 752 (758)
++++|...|+|+||||||++|+++|++|+.+|.++++++|.|+..+||++||.||++|||+||++|+|
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 36799999999999999999999999999999999998999999999999999999999999999875
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=96.98 E-value=0.022 Score=54.14 Aligned_cols=137 Identities=17% Similarity=0.260 Sum_probs=94.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHHHhcccchhhc
Q 004376 8 TIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIRE 87 (758)
Q Consensus 8 ~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~i~~~l~~~v~~~l~~ 87 (758)
.+..++.|..+..++-. +++|+... .+-+..-++-+.--+.|.++. ....+-+.+++.+..-+.. ....++.
T Consensus 2 ~~~~~~~W~~~~~~vl~---lF~g~~l~-~~iEdlN~lv~~~i~~~~~~~---~~~~~~~dl~elL~tg~~~-L~~~l~~ 73 (158)
T PF08539_consen 2 NMSSDDAWNSLCAKVLP---LFQGERLR-LPIEDLNELVRFHIKLCIQSF---PPSYFLEDLEELLTTGMYI-LENQLNE 73 (158)
T ss_pred CCchhhhHHHHHHHHHH---HHcCCCCC-cCHHHHHHHHHHHHHHhhccc---chHHHHHHHHHHHHHHHHH-HHHHHhh
Confidence 35678999999998877 46787654 554444444444455666652 2334445566666555442 2234556
Q ss_pred cCcHHHHHHHHHHHHHH-HHHHHHHHHhhcccchhhhhc-----------------CCCCcHHHHHHHHHHHHHhhhhhH
Q 004376 88 KHDEFMLRELVKRWSNH-KVMVRWLSRFFHYLDRYFIAR-----------------RSLPPLNEVGLTCFRDLVYTELNG 149 (758)
Q Consensus 88 ~~~~~~L~~~~~~W~~~-~~~~~~l~~vf~YLdr~yv~~-----------------~~~~~i~~l~l~~f~~~v~~~l~~ 149 (758)
.+++.++..+...|.-| ..-+-++..+|..|++.+-.. .+..+|..+++..||+.|+-+..+
T Consensus 74 ~~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvLP~y~ 153 (158)
T PF08539_consen 74 VPDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVLPYYQ 153 (158)
T ss_pred cchhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhhcchH
Confidence 67788999999999997 456789999999999644322 234689999999999999988777
Q ss_pred HHH
Q 004376 150 KVR 152 (758)
Q Consensus 150 ~l~ 152 (758)
++.
T Consensus 154 ~l~ 156 (158)
T PF08539_consen 154 RLK 156 (158)
T ss_pred hhh
Confidence 664
No 11
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=94.47 E-value=0.8 Score=51.45 Aligned_cols=91 Identities=9% Similarity=0.062 Sum_probs=54.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHH-hcCCCCCCcHHHHHHHHHHHHHHHHHhccc--ch
Q 004376 8 TIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNM-CTQKPPHDYSQQLYDKYRESFEEYISSTVL--PS 84 (758)
Q Consensus 8 ~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~l-c~~~~~~~~~e~LY~~l~~~i~~~l~~~v~--~~ 84 (758)
-.+..+.|....+++.+.+ + .++.+ +- ....++.++.. |... .|+.++..+-..+...+..... +.
T Consensus 65 np~v~siWem~l~LFR~~f--~-~~~~~-~v---qs~~~N~ll~s~er~r----sgeAvdrslLrsll~MLsd~~iY~es 133 (661)
T KOG2167|consen 65 NPYVLSIWEMGLQLFRAHF--S-QEPQP-FV---QSKTFNGLLKSIERER----SGEAVDRSLLRSLLKMLSDLQIYKES 133 (661)
T ss_pred CCCcCCHHHhhHHHHHHHh--h-ccCCc-hh---hccchHHHHHHHHHHh----hcchhhHHHHHHHHHHHHHHHhhhhh
Confidence 4567789999999998853 2 32221 11 33455666664 4444 5777886666666666654211 11
Q ss_pred hhccCcHHHHHHHHHHHHHHHHHHH
Q 004376 85 IREKHDEFMLRELVKRWSNHKVMVR 109 (758)
Q Consensus 85 l~~~~~~~~L~~~~~~W~~~~~~~~ 109 (758)
......+.|...|..+|.++...+.
T Consensus 134 F~~~fls~f~~lY~aE~~d~~Qel~ 158 (661)
T KOG2167|consen 134 FELTFLSLFRELYAAEGQDKRQELE 158 (661)
T ss_pred hHHHHHHHHHHHHHHHhcchhhhcc
Confidence 2112234577788899999877654
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=92.89 E-value=0.29 Score=42.44 Aligned_cols=66 Identities=18% Similarity=0.206 Sum_probs=53.0
Q ss_pred EEEEcHHHHHHHHhhc--------CCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccC
Q 004376 589 ELIVTTYQASALLLFN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 660 (758)
Q Consensus 589 ~l~~s~~Q~~iLllFn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 660 (758)
...++.-|+.+|+... ....+|-.||++.+|++.+.+.+.|..|. +.++|.+.. ....|.+|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3467888999888765 45689999999999999999999999997 457887542 2367999987
Q ss_pred CC
Q 004376 661 FT 662 (758)
Q Consensus 661 f~ 662 (758)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 64
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=91.12 E-value=0.35 Score=36.67 Aligned_cols=45 Identities=29% Similarity=0.338 Sum_probs=36.7
Q ss_pred HHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 597 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 597 ~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
+.||.+|.+.+ .+|+.||++.+|++...+.+.|..|.. .+.+.+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~--~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE--EGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CcCeecC
Confidence 46788888776 489999999999999999999999974 4666653
No 14
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=90.95 E-value=0.66 Score=39.06 Aligned_cols=59 Identities=15% Similarity=0.215 Sum_probs=41.6
Q ss_pred HHHHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccC
Q 004376 595 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 660 (758)
Q Consensus 595 ~Q~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 660 (758)
+++.+.+..+..+ .+|.+||++.++++...+.+.++.|. +.+++...+ | .++.|.++.+
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 3444445444443 49999999999999999999999997 567876542 1 3577888774
No 15
>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=90.73 E-value=0.46 Score=35.27 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=35.2
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
+..+..||..+.+++.+|..||++.+|++...+.+.|..|..
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456778898888888999999999999999999999999974
No 16
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=90.41 E-value=0.36 Score=37.86 Aligned_cols=51 Identities=25% Similarity=0.385 Sum_probs=42.9
Q ss_pred EcHHHHHHHHhhcCCCC--ccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 592 VTTYQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+|+.|+.||..+...+. +|..||++.++++...+.+.+..|. +.+++.+.+
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 47889999988887776 9999999999999999999999997 457777654
No 17
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=88.39 E-value=1.1 Score=34.77 Aligned_cols=46 Identities=20% Similarity=0.321 Sum_probs=39.4
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 596 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 596 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
|..|+.++++.+.+|++||++.+|++...+++-|..|.. .+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~--~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEK--QGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 456788889999999999999999999999999999974 4666654
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=87.28 E-value=0.46 Score=36.94 Aligned_cols=51 Identities=24% Similarity=0.387 Sum_probs=43.4
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 592 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+|..|+.+|....+.+.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 367899999999988899999999999999999999999997 457777653
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=86.14 E-value=1.2 Score=35.51 Aligned_cols=50 Identities=24% Similarity=0.333 Sum_probs=38.7
Q ss_pred EcHHHHHHHHhhc-CCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 592 VTTYQASALLLFN-SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 592 ~s~~Q~~iLllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
+|..|..||..+. ....+|..+|++.++++...+-+.+..|.. .+++.+.
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~--~glv~~~ 51 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE--KGLVEKE 51 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH--TTSEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEec
Confidence 3678899999998 778999999999999999999999999984 4777654
No 20
>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=84.84 E-value=1.6 Score=39.38 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=45.5
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 591 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
.++..|+.||..+...+.+|..+|++.+|++...+-+.+..|. +.+++.+.+
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 4578999999999888899999999999999999999999997 457887654
No 21
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=84.57 E-value=2.3 Score=31.40 Aligned_cols=44 Identities=25% Similarity=0.307 Sum_probs=34.7
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
...-||.++-+ ++.++.||++.+|++...+.++|..|.. .+++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~--~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLRE--AGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHH--CcCee
Confidence 34567777777 6799999999999999999999999863 45553
No 22
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.09 E-value=2.2 Score=39.99 Aligned_cols=52 Identities=17% Similarity=0.174 Sum_probs=45.5
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 591 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
.++..|+.||......+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 5678999999888777789999999999999999999999997 568887764
No 23
>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=82.80 E-value=1.7 Score=34.07 Aligned_cols=49 Identities=22% Similarity=0.277 Sum_probs=39.7
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
++.-..||.++...++.|+.||++.+|++...+..+|..|.. .+++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEe
Confidence 455667888886777899999999999999999999999974 5777643
No 24
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=82.03 E-value=0.51 Score=38.22 Aligned_cols=43 Identities=19% Similarity=0.324 Sum_probs=34.3
Q ss_pred eccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCC
Q 004376 699 RIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 749 (758)
Q Consensus 699 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 749 (758)
.+|+.++.++..+|-. +|..+++.+...|+.|+.+|||++.+.
T Consensus 7 ~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 7 DYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4678888888888766 699999999999999999999998653
No 25
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=80.62 E-value=3 Score=33.60 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=38.4
Q ss_pred HHHHHHHhhcCCCC--ccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 595 YQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 595 ~Q~~iLllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
..-.||.++.+.+. +|..||++.+|++...+.++|..|.. .+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~--~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK--KGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 44567777877766 99999999999999999999999973 4666654
No 26
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=78.97 E-value=1.7 Score=40.06 Aligned_cols=60 Identities=15% Similarity=0.181 Sum_probs=44.9
Q ss_pred ceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 694 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 694 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
|..|++++-..+.++..+++.... ....+...-+...|..|.+||||+|..+. ..|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~----~~~~~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILA----EKKDWSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHh----hccCCcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence 344677776777787777666543 34567788899999999999999998654 4688854
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=78.88 E-value=4.7 Score=35.81 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=43.7
Q ss_pred EEcHHHHHHHHhhc----CCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 591 IVTTYQASALLLFN----SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 591 ~~s~~Q~~iLllFn----~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
.+|..|..||..+. ..+.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45788888887766 55679999999999999999999999997 457887764
No 28
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=78.80 E-value=4.1 Score=31.01 Aligned_cols=37 Identities=22% Similarity=0.324 Sum_probs=29.4
Q ss_pred HHHHhh-cCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 598 SALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 598 ~iLllF-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
.||.++ +..+.+|.++|++.+|++...+.+.|..|-.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345444 6666799999999999999999999998853
No 29
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=77.55 E-value=1.8 Score=39.06 Aligned_cols=62 Identities=21% Similarity=0.324 Sum_probs=52.4
Q ss_pred hhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 692 AIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 692 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
..++-|+++|=.++..+.+|++.++.. .+.++..-|+.-|..|..||.|.+.-++ ..|.|=|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence 356778999999999999999997774 5788999999999999999999998754 5677743
No 30
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=76.94 E-value=7 Score=37.15 Aligned_cols=57 Identities=11% Similarity=0.078 Sum_probs=42.1
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccC
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 660 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 660 (758)
+.+.|..+..+.+|..+|++..++|...|.+.|..|. +.+++.... | .++.|.++.+
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~~ 69 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGRP 69 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecCC
Confidence 3344444555568999999999999999999999997 568887542 1 3566776553
No 31
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=76.49 E-value=6.3 Score=33.40 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=37.6
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 597 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 597 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
..||..+... +.+|..||++.+|++...+.+.|..|.. .+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeec
Confidence 4567777766 6899999999999999999999999974 5788764
No 32
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=75.75 E-value=4.8 Score=34.55 Aligned_cols=53 Identities=26% Similarity=0.288 Sum_probs=45.3
Q ss_pred EEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 589 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 589 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
++.++..+..||.++...+.+|..+|++.++++...+.+.|..|.. .+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~--~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK--KGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH--CCCeEec
Confidence 3467888999999998878899999999999999999999999974 4777654
No 33
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=75.09 E-value=8.6 Score=36.99 Aligned_cols=56 Identities=16% Similarity=0.207 Sum_probs=41.0
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEecc
Q 004376 597 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 659 (758)
Q Consensus 597 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 659 (758)
+.+.+.|+.. ..+|.++|++.+++|...+.+.|..|. +.+++.... | +++.|.+..
T Consensus 13 ~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~r-G----~~GGy~Lar 69 (164)
T PRK10857 13 AMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVR-G----PGGGYLLGK 69 (164)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCC-C----CCCCeeccC
Confidence 3444556654 479999999999999999999999997 567887431 1 244576654
No 34
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=72.81 E-value=7.4 Score=35.42 Aligned_cols=40 Identities=25% Similarity=0.315 Sum_probs=34.5
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 603 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 603 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
++.++.+|+++|++.++.+...+.+.|+.|.. .+++.+..
T Consensus 37 L~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Rek 76 (126)
T COG3355 37 LEENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVEREK 76 (126)
T ss_pred HhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeeee
Confidence 34677899999999999999999999999984 58888753
No 35
>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=72.35 E-value=3.6 Score=32.97 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=39.5
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
|-.++-|+..+-..+..|..||++.+|++...+.+.|..|.. .+++.+.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~--~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE--KGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 455666666655667899999999999999999999999984 4677654
No 36
>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=72.18 E-value=6.5 Score=37.84 Aligned_cols=48 Identities=25% Similarity=0.302 Sum_probs=39.9
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCCCC
Q 004376 608 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDK 664 (758)
Q Consensus 608 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~ 664 (758)
-+|..+|++.+|++...+.+.+..|.. .++|.+.. .+.|.+|++|-.+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e--~~iI~k~~-------~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEE--KNIIKKIR-------NGAYMINPNFFFK 122 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHh--CCcEEEcc-------CCeEEECcHHhee
Confidence 468899999999999999999999974 57887652 4689999997644
No 37
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=72.00 E-value=7.6 Score=40.32 Aligned_cols=45 Identities=16% Similarity=0.301 Sum_probs=39.3
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
+.||.+|.....+|+.||++.+|+|...+.+.|..|.. .+.|.+.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~ 61 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQE 61 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEc
Confidence 46888898877899999999999999999999999984 5777664
No 38
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=71.93 E-value=7.1 Score=28.92 Aligned_cols=44 Identities=23% Similarity=0.304 Sum_probs=34.9
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
-.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++.+
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 34566666667899999999999999999999999974 355554
No 39
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=71.04 E-value=11 Score=34.90 Aligned_cols=56 Identities=16% Similarity=0.238 Sum_probs=39.6
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEecc
Q 004376 597 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 659 (758)
Q Consensus 597 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 659 (758)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++.... | .++.|.+..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s~~-G----~~Ggy~l~~ 69 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKSVR-G----PGGGYQLGR 69 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEe-C----CCCCEeccC
Confidence 3344445443 379999999999999999999999997 567876421 1 234576544
No 40
>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=70.92 E-value=4.2 Score=36.54 Aligned_cols=60 Identities=12% Similarity=0.225 Sum_probs=42.7
Q ss_pred ceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 694 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 694 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
+..|++++=..+.++..+++..+ .....+...-|...+..|.+||||+|.... ..|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~l----~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEAL----PEERSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHH----CTTSS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHH----HhccccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 33455555566667777766644 445677889999999999999999998754 5788864
No 41
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=70.88 E-value=9.5 Score=30.97 Aligned_cols=43 Identities=16% Similarity=0.346 Sum_probs=34.4
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 598 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 598 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
.||+..... +.|++||.+.||++.+.+...|..|. +-+++.+.
T Consensus 9 ~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~Rk 51 (72)
T PF05584_consen 9 KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIERK 51 (72)
T ss_pred HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeee
Confidence 345555555 89999999999999999999999997 45777653
No 42
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=70.66 E-value=8.2 Score=37.91 Aligned_cols=53 Identities=13% Similarity=0.004 Sum_probs=45.7
Q ss_pred EEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 590 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 590 l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+.++..|+.||..+...+.+|..+|++.++++...+.+.+..|. +-+++.+.+
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 35678999999999988899999999999999999999999996 457887653
No 43
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=69.84 E-value=7.5 Score=36.32 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=44.4
Q ss_pred EEEcHHHHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 590 LIVTTYQASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 590 l~~s~~Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+.++..|..+|...... +..|..+|++.++++...+.+.+..|. +-+++.+.+
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 35778899999888754 468999999999999999999999997 457887764
No 44
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=69.52 E-value=12 Score=35.49 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=43.5
Q ss_pred HHHHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccC
Q 004376 595 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 660 (758)
Q Consensus 595 ~Q~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 660 (758)
+++.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++...+. .++.|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCCC
Confidence 4445555555554 58899999999999999999999996 6688865421 3566777664
No 45
>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=66.20 E-value=8.6 Score=27.75 Aligned_cols=36 Identities=33% Similarity=0.499 Sum_probs=27.2
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 632 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 632 (758)
-.||-.+......++.+|++.+|++...+.+-+..|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 456777777788999999999999999998877654
No 46
>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=66.04 E-value=17 Score=31.72 Aligned_cols=62 Identities=26% Similarity=0.369 Sum_probs=45.6
Q ss_pred EEcHHHHHHHHh-------hcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCC
Q 004376 591 IVTTYQASALLL-------FNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 662 (758)
Q Consensus 591 ~~s~~Q~~iLll-------Fn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~ 662 (758)
.++.-|..|++. ||.. +.+|..++++.||++...+.+++..|+ +.++|... +..+.+|.+.+
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 455666666655 3433 579999999999999999999999998 56888654 34566666543
No 47
>PRK10870 transcriptional repressor MprA; Provisional
Probab=64.70 E-value=14 Score=35.88 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=43.1
Q ss_pred EEcHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 591 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
.+|..|..||..... ..++|..||++.++++...+.+.+..|. +.+++.+.+
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 356778888888764 3578999999999999999999999997 457887764
No 48
>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=63.95 E-value=8.9 Score=29.88 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=29.9
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 596 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 596 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
|.-+|-++-+.+.+|++||++.+|++...++.-+.-|-
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566555557789999999999999999998887764
No 49
>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=62.53 E-value=19 Score=32.92 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=34.2
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 596 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 596 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
++.+.+.-++. ..+|.++|++.+++|...+.+.|..|.. .+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~--~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR--AGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEe
Confidence 33444443333 3799999999999999999999999974 577764
No 50
>PHA00738 putative HTH transcription regulator
Probab=62.19 E-value=16 Score=32.14 Aligned_cols=67 Identities=22% Similarity=0.104 Sum_probs=50.4
Q ss_pred EEEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCC
Q 004376 589 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 661 (758)
Q Consensus 589 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 661 (758)
++...+.=-.||.++.+.+.+++.+|++.++++.+.+-++|.-|.. .+++.....|. .-.|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre--AGLV~srK~Gr----~vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNE--QGYIELYKEGR----TLYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH--CCceEEEEECC----EEEEEECCCc
Confidence 4455566666777777777899999999999999999999999974 57887655442 2346677753
No 51
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=61.83 E-value=16 Score=26.41 Aligned_cols=34 Identities=29% Similarity=0.404 Sum_probs=28.9
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 608 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 608 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
.+|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~--~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK--EGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 478999999999999999999999974 5777643
No 52
>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=60.91 E-value=14 Score=32.26 Aligned_cols=44 Identities=25% Similarity=0.342 Sum_probs=37.2
Q ss_pred EEcHHHHHHHHhhcC----CCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 591 IVTTYQASALLLFNS----SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~----~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
.++..|-.||-.+.. .+.+++++|++.++++.++++.+|..|+.
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 578899999999887 34799999999999999999999999985
No 53
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=60.64 E-value=17 Score=27.60 Aligned_cols=39 Identities=26% Similarity=0.381 Sum_probs=31.9
Q ss_pred hcCCCCc-cHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 603 FNSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 603 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
+.....+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~--~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEA--EGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4445567 8999999999999999999999974 5777654
No 54
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=60.15 E-value=11 Score=29.70 Aligned_cols=45 Identities=24% Similarity=0.220 Sum_probs=33.5
Q ss_pred HHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCC
Q 004376 599 ALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPN 645 (758)
Q Consensus 599 iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~ 645 (758)
||-.++. +.++|..||++.+|++...++..|..|. +.+.+.+.|.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~ 50 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPV 50 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecC
Confidence 4555555 6789999999999999999999999997 4466665543
No 55
>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=59.94 E-value=13 Score=37.00 Aligned_cols=51 Identities=18% Similarity=0.212 Sum_probs=44.9
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 591 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 5678899999999887889999999999999999999999997 45788765
No 56
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=59.11 E-value=19 Score=37.23 Aligned_cols=46 Identities=28% Similarity=0.447 Sum_probs=39.0
Q ss_pred HHHHHhhcCCCC-ccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 597 ASALLLFNSSDR-LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 597 ~~iLllFn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+.||.+|..... +++.||++.+|+|...+.+.|..|. ..+.+...+
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 7899999999999999999999998 468888764
No 57
>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=58.96 E-value=4.6 Score=31.28 Aligned_cols=45 Identities=16% Similarity=0.324 Sum_probs=39.1
Q ss_pred eeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccC
Q 004376 696 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 748 (758)
Q Consensus 696 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 748 (758)
.|+..++.++.++..+|.+ .|..|..-|.+-+..|.++|.|.|.-
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 4667788899999988887 58889999999999999999998853
No 58
>PRK11569 transcriptional repressor IclR; Provisional
Probab=58.79 E-value=17 Score=38.13 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=38.8
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 596 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 596 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
-..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~ 76 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQV 76 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEc
Confidence 34688889875 4799999999999999999999999984 5778654
No 59
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=58.75 E-value=6.9 Score=31.06 Aligned_cols=52 Identities=12% Similarity=0.175 Sum_probs=33.1
Q ss_pred eeeeeccc-cCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhcccccc--CCCCCce
Q 004376 695 ASIVRIMK-SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERD--KSNPNMF 754 (758)
Q Consensus 695 A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~--~~~~~~y 754 (758)
..|.+.+. ..+.++..+|.. .+..+.+.+-+.|+.|+++|||++. +.|+...
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 34455555 566677666655 3566778899999999999999654 4455433
No 60
>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=57.59 E-value=13 Score=30.43 Aligned_cols=30 Identities=20% Similarity=0.203 Sum_probs=25.5
Q ss_pred cCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 604 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 604 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
.....+|+.||++.+|++...++..+..+.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 434578999999999999999999888764
No 61
>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=57.31 E-value=25 Score=32.20 Aligned_cols=56 Identities=21% Similarity=0.249 Sum_probs=39.8
Q ss_pred HHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEecc
Q 004376 597 ASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 659 (758)
Q Consensus 597 ~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 659 (758)
..+|..+.. .+.+|..||++.+|++...+.+.|..|. +.+++..... .++.|.++.
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~~g-----~~ggy~l~~ 69 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSKRG-----VEGGYTLAR 69 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEecCC-----CCCChhhcC
Confidence 344555543 3579999999999999999999999997 4578764321 234566644
No 62
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=57.05 E-value=8.1 Score=31.10 Aligned_cols=53 Identities=11% Similarity=0.197 Sum_probs=40.2
Q ss_pred ceeeeeccccCCC--CChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 004376 694 DASIVRIMKSRKV--LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMF 754 (758)
Q Consensus 694 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 754 (758)
+..|...|+.++. ++-.+|-.+ ...+...+.+.+..|.++|||.+++..+..|
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 3456778888876 887777663 3456678999999999999999987664544
No 63
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=57.00 E-value=11 Score=31.42 Aligned_cols=44 Identities=20% Similarity=0.383 Sum_probs=34.1
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 596 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 596 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
...||..++..+.+++.+|.+.+|+++..+-++|..|.. .+.+.
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~--~GyV~ 45 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE--AGYVE 45 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEE
Confidence 345666677778899999999999999999999999974 35554
No 64
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=56.83 E-value=21 Score=37.46 Aligned_cols=45 Identities=24% Similarity=0.305 Sum_probs=38.5
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 597 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 597 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
..||.+|... ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~ 73 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQD 73 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEc
Confidence 4688899865 4799999999999999999999999985 5777664
No 65
>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=55.81 E-value=22 Score=36.61 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=37.3
Q ss_pred HHHHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 597 ASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 597 ~~iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|.. .+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 468888986 45799999999999999999999999985 467754
No 66
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=55.00 E-value=20 Score=31.49 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=38.1
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
..-.||..+......|+.+|++.+|++...+.+.+..|.. .+++.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~--~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEE--EGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 4456788888888899999999999999999999999974 46665
No 67
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=54.89 E-value=16 Score=36.68 Aligned_cols=42 Identities=26% Similarity=0.311 Sum_probs=35.7
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 598 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 598 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
.||.+.+..++.|.+||++.+|++..-++++|..|.. -+++.
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~ 56 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVE 56 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--Cccee
Confidence 4677778888999999999999999999999999973 35554
No 68
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=54.80 E-value=22 Score=37.06 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=38.4
Q ss_pred HHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 597 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 597 ~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+.||.+|.+.+ .+|..||++.+|++...+.+.|..|.. .+++.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~--~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE--EGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEec
Confidence 45788887654 599999999999999999999999974 57887654
No 69
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=53.92 E-value=23 Score=31.32 Aligned_cols=51 Identities=24% Similarity=0.347 Sum_probs=43.6
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 592 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
++..|+.+|..+...+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 788999999888887776669999999999999999999997 457777654
No 70
>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=52.04 E-value=6.1 Score=31.65 Aligned_cols=53 Identities=11% Similarity=0.251 Sum_probs=37.0
Q ss_pred eeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeec
Q 004376 697 IVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYL 757 (758)
Q Consensus 697 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yi 757 (758)
|-..|-.++.++..+|...+ ..+...+-+.++.|.++|+|+|.+.++..|..+
T Consensus 13 vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 13 VYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 33333355666666665532 456788999999999999999998765555543
No 71
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=51.55 E-value=14 Score=28.32 Aligned_cols=45 Identities=9% Similarity=0.148 Sum_probs=32.0
Q ss_pred eeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCC
Q 004376 698 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNP 751 (758)
Q Consensus 698 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~ 751 (758)
++.+. .+.++..++... +..+...+.+.|+.|.++|++.+....+
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 34444 566777665553 3456788999999999999999876443
No 72
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=51.29 E-value=27 Score=31.49 Aligned_cols=59 Identities=22% Similarity=0.282 Sum_probs=43.0
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEecc
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 659 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 659 (758)
.=..||.++-+.++.++.||++.+|++...+-++|.-|.. .+++.....|. .-.|.+|.
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~--AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE--SGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCceEEEEEcC----EEEEEECc
Confidence 3345665555556799999999999999999999999974 57887654432 23466765
No 73
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=50.99 E-value=42 Score=31.23 Aligned_cols=49 Identities=14% Similarity=0.238 Sum_probs=37.2
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEec
Q 004376 603 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFN 658 (758)
Q Consensus 603 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N 658 (758)
+.....+|..+|++.+|+|...+.+.|..|. +.+++...+. .++.|.+.
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~G-----~~GG~~l~ 68 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVRG-----KNGGIRLG 68 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEecC-----CCCCeeec
Confidence 3344568999999999999999999999997 5688875532 24556654
No 74
>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=50.96 E-value=20 Score=28.27 Aligned_cols=34 Identities=29% Similarity=0.352 Sum_probs=26.3
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccc
Q 004376 605 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 640 (758)
Q Consensus 605 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 640 (758)
..+..|+.+|.+.|++|.+.++..|-.|+. .+++
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ--h~~v 57 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQ--HNLV 57 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHH--TTSE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCe
Confidence 445889999999999999999999999974 4554
No 75
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=49.92 E-value=30 Score=26.39 Aligned_cols=35 Identities=23% Similarity=0.272 Sum_probs=29.8
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 606 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 606 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
.+..|..+|++.+|++...+.+.|..|.. .+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeee
Confidence 56789999999999999999999999974 466654
No 76
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=49.02 E-value=6.9 Score=38.37 Aligned_cols=57 Identities=19% Similarity=0.290 Sum_probs=40.1
Q ss_pred ceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 694 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 694 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
=...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.---+|++.|+||+
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 344557889999999888766 588899999999999999999988778899999984
No 77
>PF13730 HTH_36: Helix-turn-helix domain
Probab=48.97 E-value=41 Score=25.35 Aligned_cols=25 Identities=24% Similarity=0.291 Sum_probs=23.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 610 SYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 610 t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999963
No 78
>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=48.70 E-value=39 Score=26.40 Aligned_cols=35 Identities=26% Similarity=0.326 Sum_probs=30.3
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 607 DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 607 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
..+|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~--~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE--EGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 4689999999999999999999999974 4777654
No 79
>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=47.88 E-value=27 Score=27.93 Aligned_cols=38 Identities=26% Similarity=0.268 Sum_probs=32.8
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
..|--++++...+|+.+|+..|+++.+++..++.-|..
T Consensus 11 G~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 11 GKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 45667889988999999999999999999999998874
No 80
>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=47.03 E-value=39 Score=26.44 Aligned_cols=44 Identities=20% Similarity=0.314 Sum_probs=34.1
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 599 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 599 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
|..+-.+...++..+|++.+|++...+...+..|. +.+++...+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 44444577789999999999999999999999997 346776543
No 81
>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=45.96 E-value=37 Score=26.77 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=38.1
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
+..+..|+..+.+.. ++..||++.+|++...+.+.|..|.. .+++..
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~--~g~i~~ 52 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEE--AGLVES 52 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHH--CCCeEE
Confidence 456777887777766 99999999999999999999999864 356654
No 82
>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=45.55 E-value=46 Score=27.12 Aligned_cols=47 Identities=19% Similarity=0.175 Sum_probs=39.8
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccc
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKI 639 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~i 639 (758)
++=|+.++-++...+.-|+++|++.||-....++-.|..+...|.++
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 45689999999998999999999999999999999998886444444
No 83
>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=45.32 E-value=35 Score=27.23 Aligned_cols=55 Identities=16% Similarity=0.319 Sum_probs=32.5
Q ss_pred hhhhhceeeeeccccCC-CCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCC
Q 004376 689 RRYAIDASIVRIMKSRK-VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSN 750 (758)
Q Consensus 689 r~~~i~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 750 (758)
|+..|=.+|...+..++ .-+..||.. .+. +. |..-+...++.|.++|||+|++.-
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~----~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAE----ALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHH----HHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHH----HhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 34444444555444444 334344333 332 32 577788999999999999999753
No 84
>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=45.14 E-value=49 Score=24.44 Aligned_cols=33 Identities=27% Similarity=0.392 Sum_probs=24.1
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHH
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 631 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 631 (758)
..|-+.| ...+|+.||++.+|++...+.+....
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 3444555 45689999999999999988776543
No 85
>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=44.23 E-value=18 Score=31.75 Aligned_cols=45 Identities=16% Similarity=0.181 Sum_probs=31.4
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
..+.|+..+..++.++-++|+..+|++..++++.|..|.. .+++.
T Consensus 14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 3456676666667899999999999999999999999974 45553
No 86
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.70 E-value=28 Score=36.13 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=41.2
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
-|..||-+.++++.+++.||++.+|++...+++-|..|- +.++|.+.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le--~~g~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILE--HAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEE
Confidence 467889999999999999999999999999999999996 45677664
No 87
>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=42.45 E-value=27 Score=28.03 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=27.9
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 599 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 599 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
|.-...+.+.+|+.||+..++++.+.+...|.-|..
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 334455677899999999999999999999999984
No 88
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=41.88 E-value=19 Score=38.79 Aligned_cols=143 Identities=11% Similarity=0.134 Sum_probs=40.2
Q ss_pred EEcHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCCCCCcee
Q 004376 591 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRI 668 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i 668 (758)
.++..+..|.-+..+ ..++-..+|...||++...+.++|.+|... ++++... +.+.+++|+
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 GLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESK--KLIKSVK---------------SVKNPNRKV 143 (327)
T ss_dssp SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHT--TSEEEE-----------------SS-SS--E
T ss_pred CCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhC--CCEEEec---------------CcCCCCeEE
Confidence 556777777777654 457888999999999999999999999752 4554321 123344454
Q ss_pred eccCCCc--hhhhh----HHHhHHHhhhhhhceeeeeccccCCC-----------------------------CChHHHH
Q 004376 669 KIPLPPV--DEKKK----VIEDVDKDRRYAIDASIVRIMKSRKV-----------------------------LGHQQLV 713 (758)
Q Consensus 669 ~i~~~~~--~e~~~----~~~~~~~~r~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 713 (758)
.+-..-. .|-.. +..+++.+=-..+...|.+.+.++.. .+.+++.
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 4322110 00000 11223333344555555555555554 4445555
Q ss_pred HHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCC
Q 004376 714 LECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSN 750 (758)
Q Consensus 714 ~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 750 (758)
..+.+.=-..-..+.++|...++.||=-|-|++-...
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 5444321112456789999999999999988876543
No 89
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=40.02 E-value=36 Score=35.28 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
-|-.||-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 356789999999999999999999999999999999997 45677764
No 90
>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=39.44 E-value=34 Score=30.42 Aligned_cols=57 Identities=11% Similarity=0.097 Sum_probs=42.0
Q ss_pred eeecccc-CCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceee
Q 004376 697 IVRIMKS-RKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 756 (758)
Q Consensus 697 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 756 (758)
|..+|.. .+.++.++|.+.+.++. ..++..-|=+.|+.|.+.|+|.+-..+.....|
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 4455554 56799999999887642 357888899999999999999986543333444
No 91
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.36 E-value=41 Score=32.79 Aligned_cols=45 Identities=16% Similarity=0.130 Sum_probs=36.9
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
....||.++-.++.+|-++|+..+|++...++++|..|.. .+++.
T Consensus 23 ~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e--~gLv~ 67 (178)
T PRK06266 23 EGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYD--ARLAD 67 (178)
T ss_pred cHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeE
Confidence 3455676666777899999999999999999999999974 45665
No 92
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=39.33 E-value=42 Score=33.70 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=41.7
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
|.+-..||.++...+.+.+.||++.+|+|...+..++..|. +.+++..+
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 44555689999999999999999999999999999999997 56787643
No 93
>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=39.01 E-value=73 Score=26.35 Aligned_cols=40 Identities=13% Similarity=0.186 Sum_probs=29.7
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
+.-.+|-++.....+|..+|+..+|.+.+++...|..+.+
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p~ 64 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMPD 64 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-TT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCCC
Confidence 3455777888889999999999999999999999988753
No 94
>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=39.00 E-value=14 Score=27.07 Aligned_cols=43 Identities=9% Similarity=0.257 Sum_probs=32.5
Q ss_pred eeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhcccc
Q 004376 695 ASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLE 745 (758)
Q Consensus 695 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~ 745 (758)
-.|+..+.....++..+|-.. ...+.+.+.+.|..|.++|||+
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~--------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEK--------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCHHHHHHH--------hCCCHHHHHHHHHHHHHCcCcC
Confidence 346667777888888887764 3567888999999999999985
No 95
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=38.90 E-value=32 Score=33.70 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=22.5
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 607 DRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 607 ~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
..+|+++|++.||+..+++..+|+.|-
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 369999999999999999999999873
No 96
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=38.71 E-value=61 Score=23.96 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=29.7
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
|.-+..++.++. ..+|..+|++.+|++...+...+..+.
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 455555665553 357999999999999999998887664
No 97
>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=38.59 E-value=53 Score=31.36 Aligned_cols=43 Identities=16% Similarity=0.192 Sum_probs=34.8
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 597 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 597 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
..|+..+=.++.+|-+||+..+|++..++++.|..|.. .+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 44565555556899999999999999999999999984 46664
No 98
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=38.34 E-value=85 Score=28.73 Aligned_cols=68 Identities=18% Similarity=0.245 Sum_probs=49.2
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCC---CcEEeccCCC
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPT---DHFEFNSKFT 662 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~---~~~~~N~~f~ 662 (758)
|.--..+|-+..+.+..|+.|+++.+|-+.+.+.+.|..|. .++++..+.+|+...+. +.+.|+-.|.
T Consensus 63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 33444566777888899999999999999999999999997 47888876555433222 3445555554
No 99
>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=38.07 E-value=63 Score=32.12 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=35.8
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 598 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 598 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
.||..+...+.+|..+|++.+|++...+.++|..|.. .+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~--~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLET--EGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEe
Confidence 4555555556799999999999999999999999974 4777654
No 100
>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=37.81 E-value=50 Score=27.60 Aligned_cols=35 Identities=9% Similarity=-0.007 Sum_probs=30.8
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHH
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 630 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 630 (758)
-+..|+-+... +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988764
No 101
>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=37.55 E-value=56 Score=24.47 Aligned_cols=37 Identities=32% Similarity=0.383 Sum_probs=21.9
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHH
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 630 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 630 (758)
|.-+-.++.+.-- ..+|+.||++.+|++...++..+.
T Consensus 12 ~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 12 PERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp -HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3334444433222 357999999999999999887665
No 102
>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=37.42 E-value=8.1e+02 Score=29.50 Aligned_cols=22 Identities=9% Similarity=0.406 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcCC
Q 004376 344 FVRKVIELHDKYLAYVNDCFQN 365 (758)
Q Consensus 344 ~i~~l~~l~~~~~~l~~~~F~~ 365 (758)
+-+..+..|.++..++..|++|
T Consensus 680 ~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 680 MQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHhCCC
Confidence 4466789999999999999875
No 103
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=37.35 E-value=67 Score=23.83 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=28.5
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 593 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 593 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
|..|..++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555554443 457999999999999999988877653
No 104
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=37.24 E-value=52 Score=23.90 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=21.7
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHH
Q 004376 598 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 630 (758)
Q Consensus 598 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 630 (758)
.|+-++.+. .|+.+|++.+|++...+.+.|.
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 344555554 8999999999999999988764
No 105
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=36.77 E-value=56 Score=31.88 Aligned_cols=63 Identities=19% Similarity=0.175 Sum_probs=47.7
Q ss_pred ceEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--CCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 566 RKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 566 R~L~w~~~l~~~~l~~~~~~~~~~l~~s~~Q~~iLllFn~~--~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
|.-.|.+.+|..+++- .+.| .||+.||.-|+.-... ..||.+-|++..+++.+++...|..+.
T Consensus 97 r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 3445778888877753 3334 5788999777654333 379999999999999999999888775
No 106
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=36.19 E-value=51 Score=34.10 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=40.8
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
-|..|+..+++++.+++.||++.+|++...+++-|..|. +.+++.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~ 53 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 466789999999999999999999999999999999986 346666543
No 107
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=36.10 E-value=83 Score=30.45 Aligned_cols=55 Identities=20% Similarity=0.181 Sum_probs=41.6
Q ss_pred EEEEEcHHHHHHHHhhcCCCCc-cHHHHHHHh--CCCHHHHHHHHHHhhhccccccccCC
Q 004376 588 TELIVTTYQASALLLFNSSDRL-SYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 588 ~~l~~s~~Q~~iLllFn~~~~~-t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
+++--+.+..+|+-+..-.+.- +.++|++.+ +++.++++..|..|. +.++|.+..
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 3344455666666666544433 899999999 999999999999997 678998763
No 108
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=36.01 E-value=52 Score=31.53 Aligned_cols=48 Identities=15% Similarity=0.208 Sum_probs=41.2
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 592 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
++-.-..||-.+.++...|+.+|++.+|++...+.+-++.|.. .+++.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~--~GvI~ 59 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER--QGFIQ 59 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeE
Confidence 4556778899999999999999999999999999999999974 46664
No 109
>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=35.82 E-value=80 Score=24.31 Aligned_cols=38 Identities=26% Similarity=0.393 Sum_probs=29.7
Q ss_pred cCCCCc-cHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 604 NSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 604 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
.....+ |..+|++.+|++...+.+.|..|.. .++|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 333334 5999999999999999999999974 4677644
No 110
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=35.00 E-value=43 Score=32.90 Aligned_cols=47 Identities=11% Similarity=0.063 Sum_probs=39.9
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 594 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 594 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
.-+..|+.+.+.++.+++.+|++.+|++...+++-|..|.. .+++.+
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~--~g~~~r 53 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI--PELRER 53 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc--chHHHH
Confidence 35678899999999999999999999999999999999973 355554
No 111
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=34.92 E-value=53 Score=22.24 Aligned_cols=25 Identities=28% Similarity=0.509 Sum_probs=20.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 609 LSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 609 ~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
+|-+||++.+|++.+.+-+.|..|.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 6789999999999999999998875
No 112
>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=34.04 E-value=61 Score=24.80 Aligned_cols=41 Identities=22% Similarity=0.266 Sum_probs=32.2
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 592 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
.|.-+..||.++..+ .|..||++.+|++...+..++..+..
T Consensus 4 LT~~E~~vl~~l~~G--~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 4 LTERELEVLRLLAQG--MSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp S-HHHHHHHHHHHTT--S-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHhc--CCcchhHHhcCcchhhHHHHHHHHHH
Confidence 355677788777774 58999999999999999999988863
No 113
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=33.72 E-value=63 Score=24.68 Aligned_cols=30 Identities=23% Similarity=0.451 Sum_probs=24.9
Q ss_pred hhcCCCCccHHHHHHHhCCCHHHHHHHHHH
Q 004376 602 LFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 631 (758)
Q Consensus 602 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 631 (758)
.|+.....|++||++.+|++...+-.+|..
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 356666899999999999999888777764
No 114
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=32.40 E-value=21 Score=31.32 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=37.9
Q ss_pred hceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccc
Q 004376 693 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER 746 (758)
Q Consensus 693 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 746 (758)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|.|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeec
Confidence 35567788888888998888773 46678889999999999999985
No 115
>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=32.10 E-value=6.7e+02 Score=26.99 Aligned_cols=163 Identities=14% Similarity=0.270 Sum_probs=85.6
Q ss_pred hhhhhhhcCcHHHHHHHHHhhccC---CCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhhccccccchHHHHHHHH
Q 004376 273 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 349 (758)
Q Consensus 273 gl~~ll~~~~~~dL~~ly~L~~~~---~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~ 349 (758)
.|..-.+.++.+.+.|.++||-.+ +.|++...+.+.+.|.......++......+. ...+.-|+..|.
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~---------~~~~~~~~~~lt 85 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSD---------SRSPVFYADALT 85 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc---------ccccccHHHHHH
Confidence 366667788899999999998655 35666666666666666555555433211100 123445666666
Q ss_pred HHHHHHHH-------HHHHhcCCChHHH--HHHHHH--------HHHHhhcCCCCCChHHHHHHHHHHHhhc--------
Q 004376 350 ELHDKYLA-------YVNDCFQNHTLFH--KSLKEA--------FEVFCNKGVAGSSSAELLATFCDNILKK-------- 404 (758)
Q Consensus 350 ~l~~~~~~-------l~~~~F~~~~~f~--~~l~~a--------f~~~~n~~~~~~~~~e~La~y~d~~l~~-------- 404 (758)
.+++..-. +|..+|+...... ..+..- +..|..... -.+....+-.|-...+.+
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 66655544 4566888654221 111111 111111110 001111222333222221
Q ss_pred ---------CCCCCCCHHHHHHHHHHHHhhhccccChhHHHHHHHHHHHHHhcCCCC
Q 004376 405 ---------GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 452 (758)
Q Consensus 405 ---------~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~~ 452 (758)
+.....+.-+++..|+.+..++.. +..|.++++.|.-....
T Consensus 165 ~~~~~~~~~~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 165 SSRAASSSQSEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFSD 214 (331)
T ss_pred ccccccccccccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcccc
Confidence 001223445778888887777643 46799999999887543
No 116
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=32.09 E-value=67 Score=30.33 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=41.6
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004376 591 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 641 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 641 (758)
.++..--.||.++..+...|+.+|++.+|++...+.+-+..|.. .+++.
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~--~GvI~ 54 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ--AGIIT 54 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 34566778888888888999999999999999999999999975 35664
No 117
>PRK00215 LexA repressor; Validated
Probab=31.97 E-value=87 Score=31.10 Aligned_cols=51 Identities=25% Similarity=0.271 Sum_probs=40.1
Q ss_pred EcHHHHHHHHhhcC-----CCCccHHHHHHHhCC-CHHHHHHHHHHhhhccccccccCC
Q 004376 592 VTTYQASALLLFNS-----SDRLSYSEIMTQLNL-SDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 592 ~s~~Q~~iLllFn~-----~~~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
++.-|..||..+.+ ....|+.||++.+|+ +...+.+.|..|.. .+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~--~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALER--KGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CCCEEeCC
Confidence 35678888876652 346899999999999 99999999999973 46776654
No 118
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=31.81 E-value=68 Score=29.15 Aligned_cols=38 Identities=11% Similarity=0.119 Sum_probs=31.9
Q ss_pred cCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 604 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 604 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
+..-+.|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344579999999999999999999999996 67787653
No 119
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=31.71 E-value=61 Score=33.57 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=40.4
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
-+..|+.++++.+.+++.||++.++++...++|-|..|.. .++|.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~--~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAE--QNKILRH 52 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4667888889999999999999999999999999999974 4677665
No 120
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=31.67 E-value=62 Score=33.47 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=36.2
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
-|..|+.+++.++.+++.||++.+|+++..++|-|..|-
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 577899999999999999999999999999999999875
No 121
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=30.74 E-value=23 Score=26.00 Aligned_cols=43 Identities=12% Similarity=0.201 Sum_probs=32.5
Q ss_pred eeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccC
Q 004376 698 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 748 (758)
Q Consensus 698 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 748 (758)
.+.+.+++.++..+|... |..+..-+.+.|..|.++|+|.+..
T Consensus 6 l~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 6 LELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEee
Confidence 344455566777777663 4567888999999999999998865
No 122
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.31 E-value=81 Score=29.48 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=41.2
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 592 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
++-.-.-||..+..+...++.+|++.+|++...+.+.+..|. +.+++..
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 445667788888888889999999999999999999999997 4577764
No 123
>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=30.19 E-value=69 Score=25.55 Aligned_cols=51 Identities=24% Similarity=0.324 Sum_probs=35.2
Q ss_pred EcHHHHHHHHhhcC-----CCCccHHHHHHHhCCC-HHHHHHHHHHhhhccccccccCC
Q 004376 592 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 592 ~s~~Q~~iLllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
++.-|.-||..+-+ .-.-|+.||++.+|+. ...+..+|..|. +-+.|.+.+
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 35567777765533 2256999999999997 899999999997 447777654
No 124
>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=30.01 E-value=75 Score=28.77 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=37.1
Q ss_pred HHHHHHHHhhcCC--------CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 594 TYQASALLLFNSS--------DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 594 ~~Q~~iLllFn~~--------~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
.+.-..|+..|.. -+.|.++|+..++-+.+.++.+|..|. +++++...
T Consensus 29 I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 29 IWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 4555555555543 478999999999999999999999996 67787643
No 125
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=29.96 E-value=1.3e+02 Score=25.04 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=32.1
Q ss_pred HHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccc
Q 004376 600 LLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 640 (758)
Q Consensus 600 LllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 640 (758)
++..++.+.+|-++|++.+|++...+-++++.|-...+.|.
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 34455666899999999999999999999999964334443
No 126
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=29.85 E-value=65 Score=33.70 Aligned_cols=48 Identities=8% Similarity=0.049 Sum_probs=41.1
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 594 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 594 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
--|..|+.+++..+.+|+.||++.+|++...++|-|..|-. .+++.+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~--~G~l~r~ 64 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK--QGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh--CCCeEEE
Confidence 45788999999999999999999999999999999999953 4666654
No 127
>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=29.61 E-value=25 Score=27.20 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=25.5
Q ss_pred CChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCC
Q 004376 707 LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 749 (758)
Q Consensus 707 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 749 (758)
++..+|.. .+..+.+.+.+.|..|.++|||+|..+
T Consensus 22 ~t~~~la~--------~l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 22 LTQSELAE--------RLGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp EEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred cCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 55555555 234567889999999999999998754
No 128
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.55 E-value=40 Score=33.92 Aligned_cols=54 Identities=22% Similarity=0.332 Sum_probs=44.6
Q ss_pred eeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 697 IVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 697 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
-|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.---+|+..|+||.
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 345668888888888765 477777788889999999999999889999999984
No 129
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=28.39 E-value=79 Score=36.26 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=43.6
Q ss_pred EEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 591 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 591 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
.++..|..||..+...+.+|..+|++.+|++...+.+.+.+|.. .+++..
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 46789999999999888999999999999999999999999974 356654
No 130
>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=26.84 E-value=28 Score=27.80 Aligned_cols=54 Identities=24% Similarity=0.193 Sum_probs=32.0
Q ss_pred ceeeeeccccCC-CCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 694 DASIVRIMKSRK-VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 694 ~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
=|.||..||++. .++.+||..++. +..+ ++.++.|-+.+=|+-+++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 367888899864 688888877553 4443 234566668889999975 47899975
No 131
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.82 E-value=72 Score=29.99 Aligned_cols=32 Identities=13% Similarity=0.202 Sum_probs=28.0
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHHHHhhhcc
Q 004376 605 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAK 636 (758)
Q Consensus 605 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 636 (758)
.++.+|-++|++.+|++...|++.|..|...|
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~ 43 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDEK 43 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhh
Confidence 44579999999999999999999999997533
No 132
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=26.71 E-value=79 Score=34.63 Aligned_cols=26 Identities=31% Similarity=0.519 Sum_probs=24.0
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 608 RLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 608 ~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
.+|+++|++.|||..+++...|++|-
T Consensus 329 ~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 329 HISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred cccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 39999999999999999999999883
No 133
>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=26.42 E-value=22 Score=27.21 Aligned_cols=42 Identities=17% Similarity=0.284 Sum_probs=29.1
Q ss_pred eccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccC
Q 004376 699 RIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 748 (758)
Q Consensus 699 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 748 (758)
.++-..+.++..+|-. .+..+...+-+.+..|.++|||+|..
T Consensus 10 ~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 10 RILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 3334455566655544 34567888999999999999998853
No 134
>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=26.19 E-value=1.3e+02 Score=21.52 Aligned_cols=40 Identities=30% Similarity=0.385 Sum_probs=28.8
Q ss_pred EcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004376 592 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 632 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 632 (758)
++..+..++.++-- ..+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34555555555432 45799999999999999998877653
No 135
>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=25.64 E-value=1.1e+02 Score=25.89 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=36.1
Q ss_pred HHHHHHhhcCCCCccHHHHHHHh-CCCHHHHHHHHHHhhhccccccccC
Q 004376 596 QASALLLFNSSDRLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 596 Q~~iLllFn~~~~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~--~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEE--AGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHH--cchhhcc
Confidence 3567766666 688999999999 9999999999999974 5788764
No 136
>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=25.46 E-value=72 Score=31.50 Aligned_cols=50 Identities=20% Similarity=0.228 Sum_probs=40.4
Q ss_pred EcHHHHHHHHhhcCC-----CCccHHHHHHHhCCC-HHHHHHHHHHhhhccccccccC
Q 004376 592 VTTYQASALLLFNSS-----DRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 592 ~s~~Q~~iLllFn~~-----~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
++..|..||....+. -..|+.||++.+|++ ...+.++|..|. +.++|.+.
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 467888888777632 247899999999998 999999999997 45777765
No 137
>PRK13239 alkylmercury lyase; Provisional
Probab=25.18 E-value=1.2e+02 Score=30.31 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=35.4
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 594 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 594 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
.+...||.++.++...|+.+|+..+|.+.+.+.+.|..|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 4666777778888999999999999999999999999885
No 138
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.85 E-value=1.6e+02 Score=21.70 Aligned_cols=35 Identities=23% Similarity=0.344 Sum_probs=25.9
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHH
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 631 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 631 (758)
+...|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 344455444443 69999999999999999987764
No 139
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=24.30 E-value=50 Score=24.91 Aligned_cols=27 Identities=7% Similarity=0.191 Sum_probs=23.8
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCC
Q 004376 723 MFKPDFKAIKKRIEDLITRDYLERDKS 749 (758)
Q Consensus 723 ~F~~~~~~ik~~Ie~Liereyi~r~~~ 749 (758)
+|..+...+.+.+..|.+.|+|.+.+.
T Consensus 29 ~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 29 QLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 577889999999999999999988753
No 140
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=24.06 E-value=1.1e+02 Score=21.66 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.1
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004376 606 SDRLSYSEIMTQLNLSDDDVVRLLHSLS 633 (758)
Q Consensus 606 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 633 (758)
...+|+++|++..|++...+.+......
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4579999999999999998888776543
No 141
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=24.01 E-value=1.1e+02 Score=28.06 Aligned_cols=41 Identities=15% Similarity=0.258 Sum_probs=32.1
Q ss_pred cccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccCC
Q 004376 701 MKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 749 (758)
Q Consensus 701 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 749 (758)
|..++.++.++|-+.+ .-+.+-+-+++.+|++.|.+.|...
T Consensus 37 L~~~~~~tvdelae~l--------nr~rStv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 37 LEENGPLTVDELAEIL--------NRSRSTVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HhhcCCcCHHHHHHHH--------CccHHHHHHHHHHHHHcCCeeeeee
Confidence 4467788888777643 4467889999999999999998643
No 142
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=23.55 E-value=1.2e+02 Score=31.76 Aligned_cols=37 Identities=19% Similarity=0.282 Sum_probs=29.5
Q ss_pred HHHHHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004376 596 QASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSL 632 (758)
Q Consensus 596 Q~~iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L 632 (758)
...|+-.+.+ ...+|+++|+..|||..+++..+|+.|
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 3445544433 568999999999999999999999987
No 143
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.45 E-value=83 Score=23.05 Aligned_cols=32 Identities=25% Similarity=0.340 Sum_probs=21.3
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004376 599 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 632 (758)
Q Consensus 599 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 632 (758)
++.++.+ .+|..+|++.+|++...+.+-+..+
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 7899999999999999998776654
No 144
>PHA02591 hypothetical protein; Provisional
Probab=23.26 E-value=97 Score=25.55 Aligned_cols=24 Identities=29% Similarity=0.340 Sum_probs=21.7
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHH
Q 004376 608 RLSYSEIMTQLNLSDDDVVRLLHS 631 (758)
Q Consensus 608 ~~t~~ei~~~t~i~~~~l~~~L~~ 631 (758)
.+|.++|++.+|++.+.+.+.|.+
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHhc
Confidence 689999999999999999888765
No 145
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=23.21 E-value=1e+02 Score=31.17 Aligned_cols=58 Identities=10% Similarity=0.242 Sum_probs=43.9
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCCC
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 662 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~ 662 (758)
+-..+.-+|.++..||+.+|.+.|+-|...|+.+|..++ ++.+.+. -..+|++-+.|.
T Consensus 187 vld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 187 VLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHh
Confidence 444566789999999999999999999999999999886 4443311 235677766654
No 146
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=23.03 E-value=1.1e+02 Score=24.93 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=39.6
Q ss_pred HHHHHHHHhhcCC--CCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004376 594 TYQASALLLFNSS--DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 644 (758)
Q Consensus 594 ~~Q~~iLllFn~~--~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 644 (758)
..|.++|...... ++++-.+|+..+|++...+-..+..|.. .+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~--~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEK--KGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHH--CCCEEEEE
Confidence 4678888887653 5789999999999999999999999974 57777653
No 147
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=22.99 E-value=57 Score=27.63 Aligned_cols=37 Identities=19% Similarity=0.179 Sum_probs=32.7
Q ss_pred CCCCCChHHHHHHHHhhhhhccccccCCCCCceeecC
Q 004376 722 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 758 (758)
Q Consensus 722 ~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 758 (758)
.++..+.+.-++.|..|-++|.|..-..++.+-+|.|
T Consensus 49 erlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 49 SKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 3678889999999999999999988888888899976
No 148
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.66 E-value=1.4e+02 Score=25.62 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=43.6
Q ss_pred EEEcHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 590 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 590 l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
+..+....-||..+...+.=...-|+..++++.+++...+..|. ..++|.+.
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~ 54 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERV 54 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 34567778899998888777788899999999999999999997 46888765
No 149
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=22.45 E-value=1.1e+02 Score=31.29 Aligned_cols=46 Identities=22% Similarity=0.250 Sum_probs=38.1
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
-|..|+..+++++.++.+||++.+|++...+++-|..|.. .+.|.+
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r 50 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT--QGKILR 50 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEE
Confidence 3567888888888999999999999999999999999864 244444
No 150
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=22.30 E-value=1.3e+02 Score=31.20 Aligned_cols=42 Identities=24% Similarity=0.350 Sum_probs=34.1
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004376 599 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 643 (758)
Q Consensus 599 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 643 (758)
||+++-+ ++.|++||.+.++++...+..+|.-|.. .+++.+.
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~--~~LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKD--KGLVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhh--CCCEEec
Confidence 5566656 6789999999999999999999999973 4676654
No 151
>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=22.29 E-value=63 Score=28.53 Aligned_cols=41 Identities=20% Similarity=0.311 Sum_probs=30.3
Q ss_pred cCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccc--cCCCC
Q 004376 703 SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER--DKSNP 751 (758)
Q Consensus 703 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r--~~~~~ 751 (758)
..+.++..+|... ...+.+-+-+.|..|.++|||.| +++|+
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 4456777777662 34567789999999999999986 55554
No 152
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.06 E-value=55 Score=29.74 Aligned_cols=54 Identities=22% Similarity=0.340 Sum_probs=0.0
Q ss_pred HhhhhhhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccC
Q 004376 687 KDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 748 (758)
Q Consensus 687 ~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 748 (758)
++-...|.+.||...+.++.++..+|.. .+-.+...+++.+..|+++|.|-+.+
T Consensus 7 ~eer~eLk~rIvElVRe~GRiTi~ql~~--------~TGasR~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 7 PEEREELKARIVELVREHGRITIKQLVA--------KTGASRNTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHHHHHHcCCccHHHHHH--------HHCCCHHHHHHHHHHHHHcCCeEeCC
No 153
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=20.99 E-value=1.1e+02 Score=32.11 Aligned_cols=57 Identities=14% Similarity=0.298 Sum_probs=32.1
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCcEEeccCC
Q 004376 595 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 661 (758)
Q Consensus 595 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 661 (758)
+--.|.-+|.++..||+.+|.+.|+-|+..|+.+|...+ ++.+.+. ....|.+=+.|
T Consensus 217 L~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 217 LLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 445677889999999999999999999999999999875 4555421 13556665544
No 154
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.97 E-value=59 Score=30.44 Aligned_cols=50 Identities=16% Similarity=0.240 Sum_probs=41.8
Q ss_pred hhhceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccccC
Q 004376 691 YAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 748 (758)
Q Consensus 691 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 748 (758)
..+|..|.+++.....++..+|-+.| ..+++.+.++|+.|.++|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l--------glS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV--------GLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCceeeEE
Confidence 45677888999999999998888855 357888999999999999998854
No 155
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=20.87 E-value=1.2e+02 Score=26.32 Aligned_cols=52 Identities=10% Similarity=0.118 Sum_probs=42.1
Q ss_pred ceeeeeccccCCCCChHHHHHHHHHHhcCCCCCChHHHHHHHHhhhhhccccc
Q 004376 694 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER 746 (758)
Q Consensus 694 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 746 (758)
+-+|..++. .+.++=-+|.+.+.+.....+.++...+=..+..|-++|+|++
T Consensus 6 ~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 6 DLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 344555665 4678888999999887665678888999999999999999998
No 156
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=20.82 E-value=60 Score=32.95 Aligned_cols=33 Identities=9% Similarity=0.239 Sum_probs=28.0
Q ss_pred CCCCCChHHHHHHHHhhhhhccccccCCCCCcee
Q 004376 722 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 755 (758)
Q Consensus 722 ~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 755 (758)
.+|..+..-+.++|+.|++.|+|.|... +.+|+
T Consensus 32 ~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 32 DQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 3699999999999999999999999764 45554
No 157
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=20.73 E-value=52 Score=25.83 Aligned_cols=38 Identities=13% Similarity=0.263 Sum_probs=0.0
Q ss_pred HHHhcCCCCCChHHHHHHHHhhhhhccccccCCCCCcee
Q 004376 717 VEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 755 (758)
Q Consensus 717 ~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 755 (758)
..++..+|..+..-+.+++..|.+.|+|.+.+. +.+++
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~-~G~~V 64 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLEAEGLIERRPG-RGTFV 64 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT-TEEEE
T ss_pred HHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC-ceEEC
No 158
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=20.71 E-value=1.1e+02 Score=29.35 Aligned_cols=40 Identities=25% Similarity=0.416 Sum_probs=30.0
Q ss_pred HHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 600 LLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 600 LllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
+|.++. +++|++||++.||++...+-..|.-|.. .++..+
T Consensus 34 ilyls~-~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~--~~lV~~ 73 (177)
T COG1510 34 ILYLSR-KPLTLDEIAEALGMSKSNVSMGLKKLQD--WNLVKK 73 (177)
T ss_pred hheecC-CCccHHHHHHHHCCCcchHHHHHHHHHh--cchHHh
Confidence 455555 5899999999999999888777776653 456554
No 159
>PRK11050 manganese transport regulator MntR; Provisional
Probab=20.33 E-value=1.8e+02 Score=27.46 Aligned_cols=43 Identities=16% Similarity=0.199 Sum_probs=34.9
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004376 598 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 642 (758)
Q Consensus 598 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 642 (758)
.|+.++...+.++..+|++.++++...+.+.|..|.. .+++.+
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 4555667777899999999999999999999999974 366654
No 160
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=20.08 E-value=1.8e+02 Score=24.80 Aligned_cols=41 Identities=27% Similarity=0.296 Sum_probs=32.6
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhh
Q 004376 594 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 634 (758)
Q Consensus 594 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 634 (758)
.....+.-++.....+++++|++.++++.+++...+..++.
T Consensus 46 i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~ 86 (105)
T PF01399_consen 46 IRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS 86 (105)
T ss_dssp HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH
Confidence 34445555566788999999999999999999999988874
Done!