Query 004583
Match_columns 744
No_of_seqs 211 out of 1087
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 01:46:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004583.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004583hhsearch_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 4E-120 9E-125 1023.7 65.1 719 5-742 4-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 3E-112 7E-117 914.0 62.6 723 7-744 16-773 (773)
3 KOG2284 E3 ubiquitin ligase, C 100.0 1E-110 2E-115 842.8 46.6 684 1-744 1-728 (728)
4 KOG2167 Cullins [Cell cycle co 100.0 1E-108 3E-113 866.0 45.9 646 65-744 2-661 (661)
5 PF00888 Cullin: Cullin family 100.0 3.8E-91 8.3E-96 810.7 61.9 586 15-648 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 2E-90 4.3E-95 702.8 55.7 716 5-744 7-777 (777)
7 smart00182 CULLIN Cullin. 100.0 1.8E-32 3.9E-37 256.6 17.8 141 428-569 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 1.1E-24 2.3E-29 235.4 39.4 301 421-733 441-757 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 8.6E-20 1.9E-24 146.5 0.7 67 672-738 2-68 (68)
10 PF08539 HbrB: HbrB-like; Int 97.2 0.0092 2E-07 56.2 14.2 137 8-152 2-156 (158)
11 TIGR01610 phage_O_Nterm phage 93.2 0.25 5.4E-06 42.5 6.3 65 576-648 21-93 (95)
12 KOG2167 Cullins [Cell cycle co 92.2 6 0.00013 44.5 16.3 203 13-234 112-324 (661)
13 PF09339 HTH_IclR: IclR helix- 91.6 0.28 6.1E-06 36.9 4.0 45 583-629 6-51 (52)
14 PF13412 HTH_24: Winged helix- 91.4 0.39 8.5E-06 35.3 4.5 42 579-620 2-43 (48)
15 PF02082 Rrf2: Transcriptional 90.8 0.66 1.4E-05 38.8 5.9 58 582-646 12-70 (83)
16 PF12802 MarR_2: MarR family; 90.1 0.4 8.6E-06 37.3 3.7 51 578-630 3-55 (62)
17 PF08220 HTH_DeoR: DeoR-like h 89.1 0.93 2E-05 34.8 5.0 46 582-629 2-47 (57)
18 PF01047 MarR: MarR family; I 87.4 0.43 9.4E-06 36.7 2.3 49 579-629 2-50 (59)
19 PF13463 HTH_27: Winged helix 86.3 1.1 2.5E-05 35.4 4.2 50 578-629 1-51 (68)
20 PF01022 HTH_5: Bacterial regu 85.9 1.8 3.9E-05 31.7 4.7 43 581-626 3-45 (47)
21 PF12840 HTH_20: Helix-turn-he 85.5 1.1 2.4E-05 34.9 3.7 49 579-629 9-57 (61)
22 TIGR02337 HpaR homoprotocatech 85.1 1.6 3.5E-05 39.1 5.1 52 577-630 25-76 (118)
23 PRK11512 DNA-binding transcrip 82.8 2.4 5.1E-05 39.5 5.3 52 577-630 37-88 (144)
24 PF08279 HTH_11: HTH domain; 81.6 2.9 6.3E-05 31.6 4.5 38 583-620 3-41 (55)
25 PF09012 FeoC: FeoC like trans 80.2 1 2.2E-05 36.1 1.6 43 685-735 7-49 (69)
26 smart00550 Zalpha Z-DNA-bindin 79.8 2.8 6E-05 33.5 4.0 47 581-629 7-55 (68)
27 TIGR02698 CopY_TcrY copper tra 79.5 1.3 2.9E-05 40.5 2.3 59 681-744 7-65 (130)
28 COG3682 Predicted transcriptio 79.0 1.3 2.9E-05 39.5 2.0 62 678-744 6-67 (123)
29 TIGR01889 Staph_reg_Sar staphy 78.5 5 0.00011 35.3 5.7 52 577-630 22-77 (109)
30 smart00346 HTH_ICLR helix_turn 77.7 5.7 0.00012 33.4 5.6 45 583-629 8-53 (91)
31 PRK11920 rirA iron-responsive 77.2 6.8 0.00015 36.9 6.4 56 583-645 13-68 (153)
32 smart00347 HTH_MARR helix_turn 76.8 4.4 9.6E-05 34.5 4.8 53 575-629 5-57 (101)
33 PF03965 Penicillinase_R: Peni 76.3 2.3 5.1E-05 37.9 2.9 58 682-744 7-64 (115)
34 PRK10857 DNA-binding transcrip 75.3 8.4 0.00018 36.8 6.5 56 583-645 13-69 (164)
35 smart00420 HTH_DEOR helix_turn 74.7 5.7 0.00012 29.2 4.3 44 583-628 3-46 (53)
36 PF13404 HTH_AsnC-type: AsnC-t 72.6 5.6 0.00012 28.4 3.5 36 583-618 6-41 (42)
37 PF01978 TrmB: Sugar-specific 72.1 3.9 8.4E-05 32.5 2.9 49 579-629 7-55 (68)
38 PRK15090 DNA-binding transcrip 72.1 7.7 0.00017 40.0 6.0 46 583-630 17-62 (257)
39 TIGR02010 IscR iron-sulfur clu 71.0 11 0.00024 34.7 6.1 44 583-628 13-57 (135)
40 PRK13777 transcriptional regul 70.9 8.2 0.00018 37.6 5.4 53 576-630 41-93 (185)
41 PF05732 RepL: Firmicute plasm 70.2 7.8 0.00017 37.0 5.0 48 594-650 75-122 (165)
42 PF04492 Phage_rep_O: Bacterio 70.1 14 0.0003 32.1 6.0 61 577-647 29-97 (100)
43 COG1959 Predicted transcriptio 69.8 11 0.00024 35.3 5.9 58 581-645 11-69 (150)
44 PF05584 Sulfolobus_pRN: Sulfo 69.0 11 0.00025 30.2 4.8 41 585-628 10-50 (72)
45 PRK03573 transcriptional regul 68.9 9.1 0.0002 35.5 5.2 53 576-630 27-80 (144)
46 COG3355 Predicted transcriptio 68.8 7.4 0.00016 35.1 4.2 39 589-629 37-75 (126)
47 PF08280 HTH_Mga: M protein tr 68.2 6.9 0.00015 30.2 3.5 38 582-619 7-44 (59)
48 PHA00738 putative HTH transcri 66.7 12 0.00025 32.7 4.8 67 575-647 7-73 (108)
49 PF08784 RPA_C: Replication pr 66.3 9.6 0.00021 33.0 4.4 44 577-620 44-91 (102)
50 PRK10870 transcriptional repre 64.6 15 0.00032 35.5 5.8 52 577-630 52-105 (176)
51 smart00419 HTH_CRP helix_turn_ 64.4 14 0.0003 26.5 4.4 34 594-629 8-41 (48)
52 PF04703 FaeA: FaeA-like prote 63.5 9 0.0002 30.0 3.3 45 585-631 5-50 (62)
53 TIGR03879 near_KaiC_dom probab 62.6 9.9 0.00021 30.8 3.4 30 590-619 28-57 (73)
54 PF13601 HTH_34: Winged helix 62.2 8.3 0.00018 31.9 3.1 44 582-627 2-45 (80)
55 TIGR00738 rrf2_super rrf2 fami 62.0 19 0.00042 32.6 5.9 45 582-628 12-57 (132)
56 TIGR01884 cas_HTH CRISPR locus 61.8 12 0.00026 37.1 4.7 51 577-629 140-190 (203)
57 PRK11569 transcriptional repre 60.6 16 0.00035 38.1 5.6 46 583-630 31-77 (274)
58 COG1414 IclR Transcriptional r 58.8 19 0.00042 36.8 5.8 46 583-630 7-53 (246)
59 smart00345 HTH_GNTR helix_turn 58.7 18 0.00039 27.3 4.3 39 589-629 14-53 (60)
60 PRK10163 DNA-binding transcrip 58.6 19 0.00042 37.4 5.8 46 583-630 28-74 (271)
61 TIGR02431 pcaR_pcaU beta-ketoa 58.3 20 0.00043 36.7 5.8 44 583-628 12-56 (248)
62 PRK10141 DNA-binding transcrip 57.4 19 0.00042 32.1 4.8 59 581-645 17-75 (117)
63 smart00344 HTH_ASNC helix_turn 57.2 18 0.00039 31.5 4.6 45 581-627 4-48 (108)
64 PF09763 Sec3_C: Exocyst compl 57.1 4.1E+02 0.0089 31.8 18.8 22 344-365 680-701 (701)
65 PF08318 COG4: COG4 transport 56.4 2.8E+02 0.0061 29.7 14.5 163 273-452 15-214 (331)
66 PF08220 HTH_DeoR: DeoR-like h 56.3 5.6 0.00012 30.5 1.0 45 682-734 4-48 (57)
67 TIGR02944 suf_reg_Xantho FeS a 55.5 27 0.00059 31.7 5.6 43 584-628 13-57 (130)
68 COG2345 Predicted transcriptio 55.2 16 0.00035 36.4 4.2 37 584-620 15-51 (218)
69 PF13463 HTH_27: Winged helix 55.2 8.7 0.00019 30.2 2.0 51 682-740 7-60 (68)
70 PRK09834 DNA-binding transcrip 54.8 22 0.00048 36.8 5.5 46 583-630 14-60 (263)
71 PF10771 DUF2582: Protein of u 54.5 20 0.00043 28.4 3.8 38 583-620 11-48 (65)
72 smart00550 Zalpha Z-DNA-bindin 54.4 12 0.00026 29.8 2.7 53 680-740 8-62 (68)
73 PF01978 TrmB: Sugar-specific 53.5 4.9 0.00011 31.9 0.3 47 689-743 19-65 (68)
74 COG1846 MarR Transcriptional r 52.8 26 0.00056 30.9 5.0 51 578-630 20-70 (126)
75 smart00418 HTH_ARSR helix_turn 52.2 26 0.00057 26.5 4.4 36 592-629 8-43 (66)
76 PF04545 Sigma70_r4: Sigma-70, 51.6 35 0.00076 25.0 4.7 33 583-617 11-43 (50)
77 PF13730 HTH_36: Helix-turn-he 50.8 38 0.00081 25.3 4.9 25 596-620 27-51 (55)
78 cd00090 HTH_ARSR Arsenical Res 50.7 29 0.00063 27.2 4.6 47 579-628 6-52 (78)
79 PF02002 TFIIE_alpha: TFIIE al 50.2 14 0.0003 32.3 2.6 44 582-627 15-58 (105)
80 PF08221 HTH_9: RNA polymerase 49.2 23 0.0005 27.6 3.5 30 591-620 24-53 (62)
81 PF05158 RNA_pol_Rpc34: RNA po 48.7 13 0.00027 39.9 2.5 143 577-736 81-260 (327)
82 PRK11014 transcriptional repre 48.3 47 0.001 30.7 6.0 49 589-644 20-68 (141)
83 cd00092 HTH_CRP helix_turn_hel 48.2 39 0.00084 26.2 4.8 35 593-629 24-58 (67)
84 PF01325 Fe_dep_repress: Iron 48.1 35 0.00076 26.4 4.3 44 584-629 12-55 (60)
85 PF11994 DUF3489: Protein of u 47.2 43 0.00093 27.0 4.6 47 579-625 9-55 (72)
86 PF12324 HTH_15: Helix-turn-he 47.0 47 0.001 27.2 4.9 39 581-619 25-63 (77)
87 TIGR00373 conserved hypothetic 46.5 35 0.00075 32.4 4.9 44 582-627 16-59 (158)
88 smart00418 HTH_ARSR helix_turn 45.8 21 0.00045 27.1 2.8 45 684-737 3-47 (66)
89 PF02796 HTH_7: Helix-turn-hel 45.6 27 0.00059 25.2 3.1 31 584-616 13-43 (45)
90 PF14394 DUF4423: Domain of un 45.3 49 0.0011 31.8 5.8 55 574-630 18-75 (171)
91 TIGR02844 spore_III_D sporulat 45.2 35 0.00075 28.3 4.0 35 581-616 7-41 (80)
92 PF08281 Sigma70_r4_2: Sigma-7 44.8 38 0.00082 25.2 4.0 37 579-616 12-48 (54)
93 PF09012 FeoC: FeoC like trans 44.5 25 0.00054 28.0 3.1 36 585-620 5-40 (69)
94 PF01726 LexA_DNA_bind: LexA D 44.4 36 0.00078 26.9 3.9 24 713-736 39-62 (65)
95 COG4189 Predicted transcriptio 44.0 33 0.00072 34.1 4.3 49 579-629 22-70 (308)
96 PF09756 DDRGK: DDRGK domain; 43.8 9.5 0.00021 37.1 0.6 56 681-744 102-157 (188)
97 PRK10434 srlR DNA-bindng trans 43.7 28 0.0006 35.9 4.1 47 581-629 6-52 (256)
98 PRK06266 transcription initiat 43.3 34 0.00073 33.1 4.4 45 581-627 23-67 (178)
99 smart00421 HTH_LUXR helix_turn 43.0 49 0.0011 24.3 4.5 39 579-619 5-43 (58)
100 PF01853 MOZ_SAS: MOZ/SAS fami 42.7 25 0.00054 34.1 3.2 26 594-619 150-175 (188)
101 COG1349 GlpR Transcriptional r 42.0 32 0.00069 35.4 4.2 47 581-629 6-52 (253)
102 cd06170 LuxR_C_like C-terminal 41.8 53 0.0011 24.2 4.5 39 579-619 2-40 (57)
103 COG4190 Predicted transcriptio 41.6 73 0.0016 28.9 5.7 68 579-648 63-133 (144)
104 PRK11169 leucine-responsive tr 39.9 42 0.00091 31.9 4.4 48 578-627 12-59 (164)
105 TIGR02702 SufR_cyano iron-sulf 39.2 62 0.0013 31.9 5.7 44 584-629 5-48 (203)
106 PF00196 GerE: Bacterial regul 38.4 48 0.001 25.2 3.8 40 579-620 5-44 (58)
107 COG1654 BirA Biotin operon rep 38.0 85 0.0018 25.9 5.2 41 587-627 12-52 (79)
108 COG1318 Predicted transcriptio 37.8 48 0.001 31.5 4.2 51 548-619 36-86 (182)
109 PRK11179 DNA-binding transcrip 37.8 49 0.0011 31.0 4.5 49 577-627 6-54 (153)
110 PRK13509 transcriptional repre 37.5 48 0.001 34.0 4.7 48 581-630 6-53 (251)
111 cd07153 Fur_like Ferric uptake 36.0 31 0.00067 30.5 2.7 57 683-742 6-63 (116)
112 PF13412 HTH_24: Winged helix- 35.8 18 0.0004 26.2 1.0 42 682-731 7-48 (48)
113 PRK04424 fatty acid biosynthes 35.2 43 0.00092 32.7 3.7 41 580-620 7-47 (185)
114 PRK00215 LexA repressor; Valid 35.0 74 0.0016 31.4 5.5 51 578-630 2-58 (205)
115 PRK10681 DNA-binding transcrip 34.6 53 0.0012 33.7 4.5 39 581-619 8-46 (252)
116 cd07377 WHTH_GntR Winged helix 34.4 78 0.0017 24.2 4.5 33 595-629 26-58 (66)
117 PF09681 Phage_rep_org_N: N-te 33.7 55 0.0012 29.5 3.8 38 590-629 49-86 (121)
118 COG1522 Lrp Transcriptional re 33.4 68 0.0015 29.8 4.7 49 578-628 6-54 (154)
119 PF04967 HTH_10: HTH DNA bindi 33.1 64 0.0014 24.4 3.5 30 589-618 18-47 (53)
120 PF07393 Sec10: Exocyst comple 32.6 9.4E+02 0.02 28.8 16.0 136 145-296 105-264 (710)
121 PF06784 UPF0240: Uncharacteri 32.5 73 0.0016 30.9 4.7 64 551-619 96-161 (179)
122 PLN03238 probable histone acet 32.2 71 0.0015 33.1 4.8 40 580-619 208-248 (290)
123 smart00531 TFIIE Transcription 31.9 53 0.0012 30.6 3.6 38 585-622 6-43 (147)
124 PF01726 LexA_DNA_bind: LexA D 31.8 96 0.0021 24.5 4.5 51 578-630 4-60 (65)
125 KOG2747 Histone acetyltransfer 31.8 57 0.0012 35.4 4.2 64 554-619 282-354 (396)
126 PF00325 Crp: Bacterial regula 31.6 63 0.0014 21.6 2.8 26 594-619 2-27 (32)
127 PRK13239 alkylmercury lyase; P 31.4 82 0.0018 31.2 4.9 40 580-619 22-61 (206)
128 smart00762 Cog4 COG4 transport 31.3 6.7E+02 0.015 26.7 13.3 161 273-449 15-205 (324)
129 PRK10906 DNA-binding transcrip 31.0 63 0.0014 33.2 4.3 47 581-629 6-52 (252)
130 PLN02999 photosystem II oxygen 30.5 3.1E+02 0.0067 26.4 8.2 62 45-118 126-189 (190)
131 PF13384 HTH_23: Homeodomain-l 30.5 57 0.0012 23.7 2.9 32 585-618 10-41 (50)
132 TIGR01714 phage_rep_org_N phag 30.5 64 0.0014 28.9 3.6 49 579-629 28-84 (119)
133 cd06171 Sigma70_r4 Sigma70, re 30.4 1E+02 0.0022 22.0 4.4 40 578-618 11-50 (55)
134 PRK09802 DNA-binding transcrip 29.9 64 0.0014 33.5 4.2 49 579-629 16-64 (269)
135 PF12802 MarR_2: MarR family; 29.5 23 0.00049 27.2 0.6 35 693-735 22-56 (62)
136 PF00165 HTH_AraC: Bacterial r 29.0 75 0.0016 22.2 3.2 28 592-619 6-33 (42)
137 PHA02591 hypothetical protein; 28.9 67 0.0015 26.2 3.1 25 593-617 58-82 (83)
138 smart00344 HTH_ASNC helix_turn 28.8 26 0.00057 30.4 1.0 46 679-732 4-49 (108)
139 PF02186 TFIIE_beta: TFIIE bet 28.6 21 0.00045 28.3 0.2 53 681-744 8-61 (65)
140 PF13542 HTH_Tnp_ISL3: Helix-t 28.4 1.3E+02 0.0028 22.0 4.6 34 582-617 17-50 (52)
141 PF01047 MarR: MarR family; I 28.3 27 0.00059 26.5 0.8 40 687-734 12-51 (59)
142 PF04182 B-block_TFIIIC: B-blo 27.4 83 0.0018 25.5 3.6 48 580-629 2-51 (75)
143 PRK04172 pheS phenylalanyl-tRN 27.4 85 0.0018 35.7 5.0 50 577-628 3-52 (489)
144 TIGR00498 lexA SOS regulatory 27.3 64 0.0014 31.7 3.5 50 578-629 4-59 (199)
145 TIGR02404 trehalos_R_Bsub treh 25.8 39 0.00085 34.1 1.7 33 708-741 32-64 (233)
146 smart00345 HTH_GNTR helix_turn 25.6 44 0.00095 25.0 1.6 27 709-735 29-55 (60)
147 PF01638 HxlR: HxlR-like helix 25.6 1.1E+02 0.0024 25.7 4.1 45 582-629 7-52 (90)
148 PRK10411 DNA-binding transcrip 25.5 94 0.002 31.7 4.4 40 581-620 5-44 (240)
149 KOG2905 Transcription initiati 24.7 96 0.0021 31.2 4.0 58 581-648 187-244 (254)
150 PRK09334 30S ribosomal protein 24.5 47 0.001 27.9 1.6 36 709-744 50-85 (86)
151 COG3355 Predicted transcriptio 24.5 92 0.002 28.2 3.6 40 687-734 37-76 (126)
152 PF00392 GntR: Bacterial regul 24.2 37 0.0008 26.4 0.9 38 703-741 27-64 (64)
153 COG1510 Predicted transcriptio 24.2 93 0.002 29.7 3.7 40 586-628 34-73 (177)
154 PLN03239 histone acetyltransfe 24.0 1.1E+02 0.0023 32.8 4.5 39 580-618 266-308 (351)
155 PF14947 HTH_45: Winged helix- 24.0 1.4E+02 0.0031 24.2 4.4 43 582-627 8-50 (77)
156 COG4742 Predicted transcriptio 24.0 1.2E+02 0.0027 31.1 4.9 43 584-629 17-59 (260)
157 PRK11402 DNA-binding transcrip 23.7 45 0.00098 33.8 1.7 32 709-741 42-73 (241)
158 KOG3054 Uncharacterized conser 23.6 63 0.0014 32.3 2.5 53 684-744 206-258 (299)
159 PRK13719 conjugal transfer tra 23.5 1.3E+02 0.0029 29.9 4.8 42 577-620 143-184 (217)
160 TIGR01889 Staph_reg_Sar staphy 23.5 55 0.0012 28.6 2.0 42 689-738 40-83 (109)
161 PF06163 DUF977: Bacterial pro 23.3 1.5E+02 0.0031 26.8 4.5 41 580-620 12-52 (127)
162 PF09904 HTH_43: Winged helix- 23.0 1.3E+02 0.0029 25.4 3.9 33 587-620 15-47 (90)
163 PF02270 TFIIF_beta: Transcrip 22.8 1E+02 0.0023 32.1 4.2 59 579-647 215-273 (275)
164 PF10007 DUF2250: Uncharacteri 22.6 1.5E+02 0.0033 25.3 4.3 52 576-629 3-54 (92)
165 PHA03103 double-strand RNA-bin 22.5 1.7E+02 0.0037 28.4 5.2 44 584-629 17-60 (183)
166 TIGR00721 tfx DNA-binding prot 22.4 1.5E+02 0.0033 27.3 4.6 39 578-618 7-45 (137)
167 COG2197 CitB Response regulato 22.3 1.3E+02 0.0029 29.8 4.7 42 577-620 148-189 (211)
168 PRK11050 manganese transport r 22.2 1.7E+02 0.0037 27.4 5.2 43 584-628 41-83 (152)
169 PRK10079 phosphonate metabolis 22.0 52 0.0011 33.4 1.8 48 686-741 28-75 (241)
170 TIGR02325 C_P_lyase_phnF phosp 21.7 52 0.0011 33.2 1.7 32 709-741 41-72 (238)
171 PF04760 IF2_N: Translation in 21.4 62 0.0013 24.2 1.6 22 594-615 3-24 (54)
172 PF06163 DUF977: Bacterial pro 21.3 55 0.0012 29.4 1.5 52 676-735 10-61 (127)
173 PRK15201 fimbriae regulatory p 21.2 1.7E+02 0.0038 28.2 4.8 41 578-620 134-174 (198)
174 PF00356 LacI: Bacterial regul 21.2 1.1E+02 0.0025 22.2 2.9 21 596-616 1-21 (46)
175 TIGR02989 Sig-70_gvs1 RNA poly 21.1 1.5E+02 0.0032 27.5 4.6 39 577-617 111-150 (159)
176 PF01399 PCI: PCI domain; Int 21.0 1.6E+02 0.0036 24.8 4.6 41 580-620 46-86 (105)
177 PF03444 HrcA_DNA-bdg: Winged 20.6 3.1E+02 0.0068 22.6 5.5 48 581-630 10-57 (78)
178 PF13545 HTH_Crp_2: Crp-like h 20.6 1.6E+02 0.0035 23.4 4.2 33 594-628 28-60 (76)
179 PLN00104 MYST -like histone ac 20.5 1.4E+02 0.003 33.2 4.7 37 582-618 361-398 (450)
180 PRK03573 transcriptional regul 20.3 65 0.0014 29.7 1.9 26 709-734 55-80 (144)
181 TIGR03433 padR_acidobact trans 20.3 1.1E+02 0.0023 26.4 3.2 52 680-732 6-57 (100)
182 PRK06474 hypothetical protein; 20.2 2.4E+02 0.0052 27.2 5.9 51 577-629 8-60 (178)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4e-120 Score=1023.68 Aligned_cols=719 Identities=66% Similarity=1.088 Sum_probs=670.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHHHHHHhcccch
Q 004583 5 ERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPS 84 (744)
Q Consensus 5 ~~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~ 84 (744)
.+.+.+|+..|+.++++++++.+..++-+.+.++.-+++.+|+++|++|+++++.+..++||+++++++.+|+.+.+.+.
T Consensus 4 ~~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~ 83 (725)
T KOG2166|consen 4 APKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPA 83 (725)
T ss_pred cccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999988876444445777889999999999999996666669999999999999999987777
Q ss_pred hhccCchHHHHHHHHHHHHHHHHHHHHHHhhchhchhhhhcC-CCCcHHHHH-HHHHHHHHHH-hhhHHHHHHHHHHHHH
Q 004583 85 IREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARR-SLPPLNEVG-LTCFRDLVYT-ELNGKVRDAVITLIDQ 161 (744)
Q Consensus 85 l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~-~~~~i~~l~-l~~f~~~v~~-~l~~~l~~~ll~~I~~ 161 (744)
.....++.+|..+...|.+|+.++.+++++|.||||+||.+. +..++.+++ +.+|+..++. ++.++++++++.+|..
T Consensus 84 ~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~ 163 (725)
T KOG2166|consen 84 LREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHK 163 (725)
T ss_pred HHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHh
Confidence 777788899999999999999999999999999999999876 666777766 8888888877 5999999999999999
Q ss_pred HhcCCccCHHHHHHHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHchh
Q 004583 162 EREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHY 241 (744)
Q Consensus 162 ~R~g~~id~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~ 241 (744)
+|.|+.||+..|+++++++..+|.+..++|...||++|++.|..||..+++.|+...++++|+.+|+.++.+|..|+..|
T Consensus 164 eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~y 243 (725)
T KOG2166|consen 164 EREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHY 243 (725)
T ss_pred hcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999988999999999999999999999999999998899999999999999999999999
Q ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHHHHHHHHHHHHHHHHHHH
Q 004583 242 LHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKL 321 (744)
Q Consensus 242 l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~ 321 (744)
++..+.+++.+.+...++..+++.++++.++|+..|+.+++.++|.+||+|+++++.|++.+++.++.|++.+|..++..
T Consensus 244 l~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r 323 (725)
T KOG2166|consen 244 LHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVAR 323 (725)
T ss_pred hhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999888876
Q ss_pred HHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHH
Q 004583 322 AEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNI 401 (744)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~ 401 (744)
..... ..+|..++..+++++++|..++..||.++..|..+++.||..|+|.+... .+|+||+|||.+
T Consensus 324 ~~~~~-----------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~--~~E~la~y~D~~ 390 (725)
T KOG2166|consen 324 PAETA-----------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVAT--SAELLATYCDDI 390 (725)
T ss_pred hhhhc-----------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCC--cHHHHHHHhHHH
Confidence 54321 14689999999999999999999999999999999999999999998632 279999999999
Q ss_pred hhcCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhhHhHHHHH
Q 004583 402 LKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMV 481 (744)
Q Consensus 402 lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml 481 (744)
+|++ ..+.++++++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|+++|+.||.+|+++||.+||.+|++|+
T Consensus 391 lkk~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf 469 (725)
T KOG2166|consen 391 LKKG-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMF 469 (725)
T ss_pred hccc-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhc
Confidence 9995 467789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHHhcCCCeeEEeccCcc
Q 004583 482 TDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLG 561 (744)
Q Consensus 482 ~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~ 561 (744)
+|+..|++++..|+++. +.....+++|.|.|||.|+||.+++.++.||++|.++++.|..||..+|+||+|.|+|++|
T Consensus 470 ~D~~~s~~l~~~F~~~~--~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~ 547 (725)
T KOG2166|consen 470 TDLTLSRELQTAFADYA--NYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLG 547 (725)
T ss_pred ccHHHHHHHHHHHHhhh--chhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccC
Confidence 99999999999999871 2222357999999999999999888889999999999999999999999999999999999
Q ss_pred eEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeE
Q 004583 562 TCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHF 641 (744)
Q Consensus 562 ~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~ 641 (744)
.|+|.++|.+++++++||++||+||++||+.+.+|+++|.+.|+++.+++.++|+||++.|.+++.. |.++. ++++.|
T Consensus 548 ~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~ 625 (725)
T KOG2166|consen 548 TGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEF 625 (725)
T ss_pred ceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEE
Confidence 9999999999999999999999999999999999999999999999999999999999888777766 66666 789999
Q ss_pred EeccCCCCCCcceeccCCChhhhhhHHHhHHHhhhhhhceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHH
Q 004583 642 EFNSKFTDKMRRIKIPLPPVDEKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRI 721 (744)
Q Consensus 642 ~~N~~f~~~~~~i~i~~~~~~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~I 721 (744)
.+|.+|+++.+|++++.++..+.+++.+.+++||+..|+||||||||+||.+.|++|+.||++|++++|.|++.+||+||
T Consensus 626 ~~N~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~I 705 (725)
T KOG2166|consen 626 AFNSKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRI 705 (725)
T ss_pred EeeccccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence 99999999999999998888888888999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhhhhcccCCCCCCceee
Q 004583 722 EDLITRDYLERDKSNPNMFRY 742 (744)
Q Consensus 722 e~Liekeyi~r~~~d~~~y~Y 742 (744)
|.|||||||+|| +|+++|.|
T Consensus 706 e~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 706 EDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHHHHHhcc-CCCCcccC
Confidence 999999999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-112 Score=914.02 Aligned_cols=723 Identities=31% Similarity=0.534 Sum_probs=636.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCC------------chHHHHHHHHHHHH
Q 004583 7 KTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHD------------YSQQLYDKYRESFE 74 (744)
Q Consensus 7 ~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~------------~~e~LY~~l~~~l~ 74 (744)
+..||+++|..++.||++|..-+.. ++....||++|+.+|+.|+++++.. .+..||+++.....
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 4579999999999999998754433 3556779999999999999985431 36789999999999
Q ss_pred HHHHhcccchhhccCchHHHHHHHHHHHHHHHHHHHHHHhhchhchhhhhc-----CCCCcHHHHHHHHHHHHHHHhhhH
Q 004583 75 EYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR-----RSLPPLNEVGLTCFRDLVYTELNG 149 (744)
Q Consensus 75 ~~l~~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~-----~~~~~i~~l~l~~f~~~v~~~l~~ 149 (744)
+++...- ...+....+.+|..++..|++|..++.+++.+|.||||.|++. .....+.++++..|+.++|.++++
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 9988643 2222233478999999999999999999999999999999992 233467789999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhcc------CchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHH
Q 004583 150 KVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGM------GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDY 223 (744)
Q Consensus 150 ~l~~~ll~~I~~~R~g~~id~~~lk~~i~~l~~l~~------~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Y 223 (744)
.+.+.+|..+.+.|.|+.+|+..+..++.|+..++. .++.+|.+.|||.||+.|.+||..++++.+..+++.+|
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 999999999999999999999999999999999964 24589999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhH
Q 004583 224 MLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPV 303 (744)
Q Consensus 224 l~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l 303 (744)
|.+|.+++++|..++..|++.++..++..+++++||..|.+.+.+.. ||+..+++....+.|+.||+++++++-++.+|
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 HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc---cccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHH
Q 004583 304 SNIFKQHVTAEGTALVKLAEDAASNKKAEKR---DVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVF 380 (744)
Q Consensus 304 ~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~ 380 (744)
.+.|..||...|.-+ +.....+. .++.+. ......+..+++.++++++.+..++...|.+|..+..++++||..|
T Consensus 330 ~~~f~~yV~~~g~~~-~i~~~~~~-~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~f 407 (773)
T COG5647 330 QEVFERYVKDEGVLI-NIETNYIF-HCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTF 407 (773)
T ss_pred HHHHHHHHHhhchhh-hhHHhhhh-ccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHH
Confidence 999999999999322 22221111 001000 0124568899999999999999999999999999999999999999
Q ss_pred hcCCC-CCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHH
Q 004583 381 CNKGV-AGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHER 459 (744)
Q Consensus 381 ~n~~~-~~~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~~~~~E~ 459 (744)
+|.+. +...++|+||+|+|.+||++++ ......++..+.+++.||+|+.+||+|+++|+++||||||+++|.+.+.|.
T Consensus 408 in~~~sa~~~~~e~Laky~D~~lkk~~k-~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~ 486 (773)
T COG5647 408 INGNESADSGPSEYLAKYIDGLLKKDGK-QSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAEL 486 (773)
T ss_pred hccccccccccHHHHHHHhHHHhhcccc-ccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence 99854 2357899999999999998652 222345777889999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcChhhHhHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCC-CCCccCChhHHHHH
Q 004583 460 SILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYK-SFDLNLPAEMVKCV 538 (744)
Q Consensus 460 ~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~-~~~~~lP~~l~~~~ 538 (744)
.||++||+.||.+||+|+++||+||..|+++...|++.. .+ ..+.+++.|.||+..+||..| ...+.||++|.+.+
T Consensus 487 ~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~-~s--~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~l 563 (773)
T COG5647 487 KMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSP-QS--YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPIL 563 (773)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCc-hh--hccccchhHHHHHHhcCCCCccccccCCChHHHHHH
Confidence 999999999999999999999999999999999987643 11 125789999999999999665 46799999999999
Q ss_pred HHHHHHHHhcCCCeeEEeccCcceEEEEeEecCeeEEE---EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHH
Q 004583 539 EVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTEL---IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLL 615 (744)
Q Consensus 539 ~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l---~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L 615 (744)
+.|++||..||+||+|.|.|+||+|+|++.|+.+++.+ +++++|+.|+++||+++++|+++|.+.|+++.++++++|
T Consensus 564 e~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L 643 (773)
T COG5647 564 EGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVL 643 (773)
T ss_pred HHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHH
Confidence 99999999999999999999999999999998775433 367889999999999999999999999999999999999
Q ss_pred hHhhhccccccccCCCCCCCCCCCeEEeccCCCCCCcceeccCCCh----hhhhhHHHhHHHhhhhhhceeeeecccCCC
Q 004583 616 HSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSRK 691 (744)
Q Consensus 616 ~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~~~~~r~~~i~A~IVRimK~~k 691 (744)
+||+++|..++.+ +++.+++++.|.+|.+|+++..+|+++.+.. ++...+++.+++||+..+|||||||||+||
T Consensus 644 ~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk 721 (773)
T COG5647 644 QSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARK 721 (773)
T ss_pred HHHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999877665554 4777889999999999999999999987653 445567788999999999999999999999
Q ss_pred CCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 692 VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 692 ~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
+|.|++|+++|+.+.++||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 722 ~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 722 KLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred cCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999999999999999999999999999999888 8999997
No 3
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-110 Score=842.80 Aligned_cols=684 Identities=27% Similarity=0.505 Sum_probs=626.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHHHHHHhc
Q 004583 1 MTMNERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISST 80 (744)
Q Consensus 1 ~~~~~~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~ 80 (744)
||||+|++++||++|.+|.+.|..+.. ..++.+.+|..-|+.||.+|.+- |.+-||.||..++.++++|+.+.
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 MYSLKPKVVEFDKVWVQLRPSIIDIIN------LRPITNVQWHHKFSDVYDICVSI-PTPLSERLYNEVKACIQEHVRQK 73 (728)
T ss_pred CCCCCceeeeHHHHHHHHHHHHHHHHh------ccchhccccccchhhHHHHHHhC-CCchhHHHHHHHHHHHHHHHHHH
Confidence 899999999999999999999887632 13567788999999999999998 77889999999999999999865
Q ss_pred ccchhhccCchHHHHHHHHHHHHHHHHHHHHHHhhchhchhhhhcCC------------------CCcHHHHHHHHHHHH
Q 004583 81 VLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRS------------------LPPLNEVGLTCFRDL 142 (744)
Q Consensus 81 v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~------------------~~~i~~l~l~~f~~~ 142 (744)
.. .....+++.+|..|.+.|+.|..+..++..+|.|||+.|++.++ ...|..+|+.+|++.
T Consensus 74 ~~-~~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~ 152 (728)
T KOG2284|consen 74 RQ-DIVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKED 152 (728)
T ss_pred hh-hhhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHH
Confidence 32 22233446699999999999999999999999999999998753 234678899999999
Q ss_pred HHHhhhHHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHHHHhcc-----------------CchhchHHHHHHHHHHHHH
Q 004583 143 VYTELNGKVRDAVITLIDQEREGEQID-RALLKNVLDIFVEIGM-----------------GQMDYYENDFETAMLKDTA 204 (744)
Q Consensus 143 v~~~l~~~l~~~ll~~I~~~R~g~~id-~~~lk~~i~~l~~l~~-----------------~~~~~Y~~~FE~~~L~~t~ 204 (744)
+..++...|+..++..|.++|.|+..+ ...+.++|.+|+.+.. -...+|++.||+|||.+|.
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 6789999999998753 1367999999999999999
Q ss_pred HHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHH
Q 004583 205 AYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVE 284 (744)
Q Consensus 205 ~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sg~~~ll~~~~~~ 284 (744)
+||+++++..+.+.+|++|+.+|..++++|+-||+.||++++..|++-.|++.||.+|.+.+ +-.|+.++.+++..
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 99999999999999999999999999999999999999999999999999999999999876 34699999999999
Q ss_pred HHHHHHHhhccCCCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcC
Q 004583 285 DLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQ 364 (744)
Q Consensus 285 ~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~ 364 (744)
|++.||.|+..+..|+..+...|.+||..+|...++.... .+-|..||+.++.+|++|.+++...|+
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 9999999999999999999999999999999998876643 356999999999999999999999999
Q ss_pred CChhHHHHHHHHHHHHhcCCCCC---CCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHH
Q 004583 365 NHTLFHKSLKEAFEVFCNKGVAG---SSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRK 441 (744)
Q Consensus 365 ~~~~f~~~l~~af~~~~n~~~~~---~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~ 441 (744)
+|..|..+++.|+..++|..+++ ++.+|.||+|||.+|+++. +++++.+++..|+..+.+|+|++|||+|.++|.+
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 99999999999999999987642 5789999999999999975 6899999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCChHHHHHHHHHHHHhhcChhhHhHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCC
Q 004583 442 KLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWP 521 (744)
Q Consensus 442 ~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP 521 (744)
+||+||+.+.|.|.|.|+.||++||+.||++||+++- +.|+..|.+++++|.+.+.
T Consensus 455 mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~---------------------- 510 (728)
T KOG2284|consen 455 MLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA---------------------- 510 (728)
T ss_pred HHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH----------------------
Confidence 9999999999999999999999999999999999998 9999999999999987653
Q ss_pred CCCCCCccCChhHHHHHHHHHHHHHhcCCCeeEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHH
Q 004583 522 SYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIM 601 (744)
Q Consensus 522 ~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~ 601 (744)
++.+|.+|+..++.|+.||..+|+||+|+|++.++++++++++-++.|.-.+.++||++||+||..+.+++.||.
T Consensus 511 -----nf~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~ 585 (728)
T KOG2284|consen 511 -----NFHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIG 585 (728)
T ss_pred -----hccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhh
Confidence 278999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCCCCCCcceeccCCCh-----hhhhhHHHhHHHhhh
Q 004583 602 TQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV-----DEKKKVIEDVDKDRR 676 (744)
Q Consensus 602 ~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~-----~e~~~~~~~~~~~r~ 676 (744)
+.+|++.+.|.+++.++.. .++|... +..+..+..|++|.+|+++..+.++..|.+ +|.+.+...+.+||+
T Consensus 586 ~~~~~~~~~l~kti~tild--v~~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk 661 (728)
T KOG2284|consen 586 EEIGVSGDYLLKTIRTILD--VTLLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRK 661 (728)
T ss_pred hhhCccHHHHHHHHHHHHh--ceeeccc--ccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHH
Confidence 9999999999999999985 4677654 345667888999999999999999987654 344566778999999
Q ss_pred hhhceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 677 YAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 677 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
+.++||||||||+||.+.|+.|+++|++|.++||.|++++||+|||.||++.||+|.+.+ +.|.|+|
T Consensus 662 ~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 662 YYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 999999999999999999999999999999999999999999999999999999999876 8999997
No 4
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.4e-108 Score=865.96 Aligned_cols=646 Identities=36% Similarity=0.608 Sum_probs=603.1
Q ss_pred HHHHHHHHHHHHHHhcccchhhc--cCchHHHHHHHHHHHHHHHHHHHHHHhhchhchhhhhc--CCCCcHHHHHHHHHH
Q 004583 65 LYDKYRESFEEYISSTVLPSIRE--KHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR--RSLPPLNEVGLTCFR 140 (744)
Q Consensus 65 LY~~l~~~l~~~l~~~v~~~l~~--~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~--~~~~~i~~l~l~~f~ 140 (744)
||+.++..+.+|++..+. .+.. .+...+|+.+.+.|..|...+.+++.+|.||||.|+.. ...+|+|++|+.+||
T Consensus 2 ly~~l~~~~~~~~~~~~~-q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR 80 (661)
T KOG2167|consen 2 LYKQLRQICEQHIKAQIE-QLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFR 80 (661)
T ss_pred hHHHHHHHHHHHHHHHHh-hCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHH
Confidence 799999999999986543 2222 22346999999999999999999999999999999987 356899999999999
Q ss_pred HHHHH----hhhHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 004583 141 DLVYT----ELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWIL 216 (744)
Q Consensus 141 ~~v~~----~l~~~l~~~ll~~I~~~R~g~~id~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~ 216 (744)
.+++. .+..++.++++..++++|.|+++|+.+|+.++.|+.++ ..|.+.|++.|++.+.++|.+++....+
T Consensus 81 ~~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~-----~iY~esF~~~fls~f~~lY~aE~~d~~Q 155 (661)
T KOG2167|consen 81 AHFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDL-----QIYKESFELTFLSLFRELYAAEGQDKRQ 155 (661)
T ss_pred HHhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH-----HhhhhhhHHHHHHHHHHHHHHHhcchhh
Confidence 99998 47788999999999999999999999999999999986 5899999999999999999999999999
Q ss_pred cCChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccC
Q 004583 217 EDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKI 296 (744)
Q Consensus 217 ~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~ 296 (744)
+..+++||++++.++.+|.+|+..+++.+|...+..++.+.|+..|++.++.+ |+..+++..+..++.+||.|++++
T Consensus 156 el~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~ 232 (661)
T KOG2167|consen 156 ELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRV 232 (661)
T ss_pred hcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHH
Confidence 99999999999999999999999999999966799999999999999999876 899999999999999999999999
Q ss_pred CCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCC--hhHHHHHH
Q 004583 297 PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNH--TLFHKSLK 374 (744)
Q Consensus 297 ~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~--~~f~~~l~ 374 (744)
.++...++..|.+|+++-|..++.+.. .+..+|..+++++++.+-++..||..+ ..|..+++
T Consensus 233 ~~g~l~l~qq~sdylk~~G~KlV~de~----------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~ 296 (661)
T KOG2167|consen 233 QGGQLSLLQQWSDYLKKPGFKLVIDEE----------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMS 296 (661)
T ss_pred hcchHHHHHHHHHHHhcccceeccCch----------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHH
Confidence 889999999999999999999886542 257899999999999999999999988 89999999
Q ss_pred HHHHHHhcCCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCC
Q 004583 375 EAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSAN 454 (744)
Q Consensus 375 ~af~~~~n~~~~~~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~~ 454 (744)
+||+.|+|... .++|++||+|.|..|+.|. +..++++++..++.++.|||||..||+|+.+|++.||+|||.++|++
T Consensus 297 ~afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAs 373 (661)
T KOG2167|consen 297 KAFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSAS 373 (661)
T ss_pred HHHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchh
Confidence 99999999775 5799999999999999865 55678889999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhhcChhhHhHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCChhH
Q 004583 455 DDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEM 534 (744)
Q Consensus 455 ~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l 534 (744)
.|+|..|+.+||.+||..||++|++||+||..|++++..|+++..++.....++ +.+.|+|.|+||++++.++.||++|
T Consensus 374 vdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em 452 (661)
T KOG2167|consen 374 VDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEM 452 (661)
T ss_pred hcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHH
Confidence 999999999999999999999999999999999999999999866555434455 9999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCeeEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHH
Q 004583 535 VKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRL 614 (744)
Q Consensus 535 ~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~ 614 (744)
.++.+.|..||..+|.||+|.|.+++|+|.+++.|..|++++.+|++|++||++||+++.+|++||.+.||+.+.+|.++
T Consensus 453 ~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rt 532 (661)
T KOG2167|consen 453 RDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRT 532 (661)
T ss_pred HHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHhhhccccccccCCCCCCCCCCCeEEeccCCCCCCcceeccCCCh----hhhhhHHHhHHHhhhhhhceeeeecccCC
Q 004583 615 LHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSR 690 (744)
Q Consensus 615 L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~~~~----~e~~~~~~~~~~~r~~~i~A~IVRimK~~ 690 (744)
|+||.|+|.++|.+.|.|+.+.+++.|.+|..|+++..||+|+++.+ +|.+.|.++|.+||.+.||||||||||+|
T Consensus 533 lqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~r 612 (661)
T KOG2167|consen 533 LQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMR 612 (661)
T ss_pred HHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998765 45677889999999999999999999999
Q ss_pred CCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 691 KVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 691 k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
|+|+|+.|+.++.++++ |+..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 613 k~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 613 KTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 99999999999999997 98888 999999999999999999 45 9999998
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=3.8e-91 Score=810.73 Aligned_cols=586 Identities=41% Similarity=0.755 Sum_probs=523.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHHHHHHhcccchhhccCchHHH
Q 004583 15 WEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFML 94 (744)
Q Consensus 15 W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~~~~L 94 (744)
|+.|++||+.|. .+ .++..+||++|+.||++|.++ +|++||+.+++.+.+|+... .+.+.+..++.+|
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 999999999964 32 366778999999999999877 89999999999999999874 4555555778999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhchhchhhhhcCCCCcHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCCccCHHHHH
Q 004583 95 RELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLK 174 (744)
Q Consensus 95 ~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~i~~l~l~~f~~~v~~~l~~~l~~~ll~~I~~~R~g~~id~~~lk 174 (744)
..|...|.+|+.++.+|+++|+||||+|+.++ +|++.|+.++.++++.+++++|.++|.|+.+|..+++
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 HHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHH
Q 004583 175 NVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKV 254 (744)
Q Consensus 175 ~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l 254 (744)
++++|++.+| ...+|.+.||++||++|.+||+.++ +...++.+|+.+|++++++|.+|+..|++++|..++.+.+
T Consensus 138 ~~~~~~~~l~--~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l 212 (588)
T PF00888_consen 138 NVIEMFVELG--SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTL 212 (588)
T ss_dssp HHHHHHHHTT--HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHH
T ss_pred HHHHHHhccc--hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHH
Confidence 9999999998 5689999999999999999999999 5677999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Q 004583 255 QHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKR 334 (744)
Q Consensus 255 ~~~LI~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~ 334 (744)
.++||..|.+.| .+|+..|+++++.++|++||+|+++++++++.+++.|++||.+.|..+++....
T Consensus 213 ~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~---------- 278 (588)
T PF00888_consen 213 EEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK---------- 278 (588)
T ss_dssp HHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------
T ss_pred HHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------
Confidence 999999999988 469999999999999999999999999999999999999999999999876531
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHhhcCCCCCCChHH
Q 004583 335 DVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEA 414 (744)
Q Consensus 335 ~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~lk~~~~~~~~~~~ 414 (744)
...+..||+.+++++++|+.++.+||++++.|..++++||+.++|.. ...++++||+|||.++++++ .+.++++
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 24578999999999999999999999999999999999999999998 36889999999999999875 5667888
Q ss_pred HHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhhHhHHHHHHhHHHHHHHHHHH
Q 004583 415 IEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSF 494 (744)
Q Consensus 415 ~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f 494 (744)
++..++.++.||+|+++||+|+.+|+++||+|||..++.+.+.|..+|++|+.+||.++++++++|++|+..|++++++|
T Consensus 353 ~~~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f 432 (588)
T PF00888_consen 353 IEQKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEF 432 (588)
T ss_dssp HHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCC-CCcceEEEEeecCCCCCCCCCC-ccCChhHHHHHHHHHHHHHhcCCCeeEEeccCcceEEEEeEecCe
Q 004583 495 EEYLSNNPNAN-PGIDLTVTVLTTGFWPSYKSFD-LNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESR 572 (744)
Q Consensus 495 ~~~~~~~~~~~-~~~~~~~~vLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~ 572 (744)
++...+.+... ++++|+|.||++++||..+..+ +.+|++|+.+++.|++||+.+|+||+|.|.+.+|+|+|+++++++
T Consensus 433 ~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~ 512 (588)
T PF00888_consen 433 KQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNG 512 (588)
T ss_dssp HHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSS
T ss_pred HHHhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCC
Confidence 99987665432 2799999999999999998766 999999999999999999999999999999999999999999999
Q ss_pred eEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCCC
Q 004583 573 TTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 648 (744)
Q Consensus 573 ~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~ 648 (744)
+++++||++||+||++||+++++|+++|++.||+++++++++|.+|+..|..++.+.++++.+++++.|.+|.+|+
T Consensus 513 ~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 513 KYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred ceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 9999999999999999999999999999999999999999999999865433333678888999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-90 Score=702.76 Aligned_cols=716 Identities=26% Similarity=0.462 Sum_probs=629.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHHHHHHhcccch
Q 004583 5 ERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPS 84 (744)
Q Consensus 5 ~~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~ 84 (744)
.++...|++.|+...|.+-++.+ +++.++..|..+|.+||..|.+. .....++|+.+...|.+|+.+...+.
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 34456899999999999988754 24688999999999999999997 23466799999999999998753333
Q ss_pred hhccCchHHHHHHHHHHHHHHHHHHHHHHhhchhchhhhhcC--------CCCcHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 004583 85 IREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARR--------SLPPLNEVGLTCFRDLVYTELNGKVRDAVI 156 (744)
Q Consensus 85 l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~--------~~~~i~~l~l~~f~~~v~~~l~~~l~~~ll 156 (744)
.....+..+|..|..+|.+|-....++...|.-|+..-...+ .-.++..+.+..|.+++|..++++|....+
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 333456789999999999999999999999999998755332 124689999999999999999999999999
Q ss_pred HHHHHHhcCCccCHHHHHHHHHHHHHhcc---CchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHH
Q 004583 157 TLIDQEREGEQIDRALLKNVLDIFVEIGM---GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKR 233 (744)
Q Consensus 157 ~~I~~~R~g~~id~~~lk~~i~~l~~l~~---~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~e 233 (744)
.+++.+|+|+.+|.+++-++-++|+.++. +.+.+|+..||..||++|.+||+..+..++++.++.+|++.+..-+++
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 99999999999999999999999999975 567899999999999999999999999999999999999999999999
Q ss_pred HHHHHchhcCC--CcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHHHHHHHHH
Q 004583 234 EKDRVSHYLHS--SSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHV 311 (744)
Q Consensus 234 E~~r~~~~l~~--~t~~kl~~~l~~~LI~~~~~~ll~~~~sg~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i 311 (744)
|+.|+.+||.. .|..+++..+.+.|+.++.+.|+. .|..|+...+++-|++||+|+.+++.|++++...+..||
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 588999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhcCCC------
Q 004583 312 TAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGV------ 385 (744)
Q Consensus 312 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~------ 385 (744)
+..|..-+....+.+ +.++..||+.|+.++++|..++.++|++|+.|..+.+.||..++|...
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 999976554333222 567889999999999999999999999999999999999999999864
Q ss_pred ------------CCCCcHHHHHHHHHHHhhcCC-CCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCC
Q 004583 386 ------------AGSSSAELLATFCDNILKKGG-SEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 452 (744)
Q Consensus 386 ------------~~~~~~e~La~y~d~~lk~~~-~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s 452 (744)
+..+.||+||.|||.+||+.. +++++.++++.+|.+++-+++|+.+||+|+.+++.+|++||+...|
T Consensus 384 p~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~S 463 (777)
T KOG2285|consen 384 PNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMS 463 (777)
T ss_pred cchhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcc
Confidence 124679999999999999853 4678889999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHhhcC--hhhHhHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCcc
Q 004583 453 ANDDHERSILTKLKQQCGG--QFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKS-FDLN 529 (744)
Q Consensus 453 ~~~~~E~~~i~~Lk~~~G~--~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~vLt~~~WP~~~~-~~~~ 529 (744)
++.+.|..|+..|+ +||. +|++++.+||+|++.|++++..|+..+.+.+..++.-.+++.||+.|.|...+. ..+.
T Consensus 464 ADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vS 542 (777)
T KOG2285|consen 464 ADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVS 542 (777)
T ss_pred cchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEe
Confidence 99999999999998 5775 799999999999999999999999988766554555678999999999997643 4589
Q ss_pred CChhHHHHHHHHHHHHHhcCCCeeEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCC
Q 004583 530 LPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLS 607 (744)
Q Consensus 530 lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~--~~~t~~ei~~~t~~~ 607 (744)
||.+|++.+-.-++||+++|.||+|.|.|+++.++|++..+-|.|.+.|+++||+||.+||+. +.+|++.+.-+|.+|
T Consensus 543 LP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELP 622 (777)
T KOG2285|consen 543 LPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELP 622 (777)
T ss_pred CchhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCC
Confidence 999999999999999999999999999999999999877666899999999999999999975 589999999999999
Q ss_pred HHHHHHHHhHhhh---ccccccccCCCC----CCCCCCCeEEeccCCCC-C----CcceeccCCCh----hh--hhhHHH
Q 004583 608 DDDVVRLLHSLSC---AKYKILNKEPNT----KTISPTDHFEFNSKFTD-K----MRRIKIPLPPV----DE--KKKVIE 669 (744)
Q Consensus 608 ~~~l~~~L~~L~~---~k~~iL~~~~~~----~~i~~~~~~~~N~~f~~-~----~~~i~i~~~~~----~e--~~~~~~ 669 (744)
+.++.++|-||+. .|+.||..+|+. +++.++..|.+|.+|.- + .++-+++.+.- .| .++..+
T Consensus 623 DaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeene 702 (777)
T KOG2285|consen 623 DAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENE 702 (777)
T ss_pred CHHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcc
Confidence 9999999999984 367888877642 34667889999999972 1 12223332210 11 122345
Q ss_pred hHHHhhhhhhceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 670 DVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 670 ~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
.+.+-|-...+-+|++|||.||+++..+|-.+..+.|+..|-|+..+||++||.|||..|++||++|-++|+|+|
T Consensus 703 sIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 703 SIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 678889999999999999999999999999999999999999999999999999999999999999999999997
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=1.8e-32 Score=256.59 Aligned_cols=141 Identities=48% Similarity=0.890 Sum_probs=132.6
Q ss_pred cccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhhHhHHHHHHhHHHHHHHHHHHHHHHhcCCCCCCC
Q 004583 428 YISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPG 507 (744)
Q Consensus 428 ~l~~Kd~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 507 (744)
|+++||+|+.+|+++||+|||..++.+.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++.+.+++ ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999876532 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCccCChhHHHHHHHHHHHHHhcCCCeeEEeccCcceEEEEeEe
Q 004583 508 IDLTVTVLTTGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKF 569 (744)
Q Consensus 508 ~~~~~~vLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~ 569 (744)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|.+++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999887 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=1.1e-24 Score=235.43 Aligned_cols=301 Identities=23% Similarity=0.307 Sum_probs=238.9
Q ss_pred HHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhcChhhHhHHHHHHhHHHHHHHHHHHHHH--H
Q 004583 421 KVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--L 498 (744)
Q Consensus 421 ~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~--~ 498 (744)
-+-.+...+.+|+.|++.||.+||.||+.....+.|.|..-++.||-.+|.+..+.|++|++|+..|+++++.+++. .
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 34456677799999999999999999999999999999999999999999999999999999999999999999874 2
Q ss_pred hcCCCCCCCcceEEEEeecCCCCCCCCCCccCChhHHHHHHHHHHHHHhcCCCeeEEeccCcceEEEEeEecCeeEEEEE
Q 004583 499 SNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIV 578 (744)
Q Consensus 499 ~~~~~~~~~~~~~~~vLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~ 578 (744)
.......+.+.+++.+|++.+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|.|+++++|.+++.+++|
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tV 600 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTV 600 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEee
Confidence 22222345688999999999999887778999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCCCCCCcceeccC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPL 658 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i~i~~ 658 (744)
|+.||+|+.+|.+.++||++++++.+|||..-+++.|..|.+ .++|..+|. ++++++|+++++=.+..+- -.+
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iEse~d~~q~--~~~ 673 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIESEMDFDQA--EGT 673 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeecccccccccc--CCC
Confidence 999999999999999999999999999999999999999985 478887642 3678899998854332211 111
Q ss_pred CCh--h-hh--hhHHHhHHHhhh--hhhceeeeecccCCCCCChHHHHHHHHHHhcCCCCC-------ChhHHHHHHHhh
Q 004583 659 PPV--D-EK--KKVIEDVDKDRR--YAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKP-------DFKAIKKRIEDL 724 (744)
Q Consensus 659 ~~~--~-e~--~~~~~~~~~~r~--~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~-------~~~~ik~~Ie~L 724 (744)
+.. + +. ......+++-+. ..-...||-.+=.-+.|..+.+.+... .|.| +-++++.-+..+
T Consensus 674 ~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~k 748 (765)
T KOG2165|consen 674 VLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQRK 748 (765)
T ss_pred cccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHHH
Confidence 111 1 11 111222222111 223347777777779999988888543 4544 345666666666
Q ss_pred hhhhhcccC
Q 004583 725 ITRDYLERD 733 (744)
Q Consensus 725 iekeyi~r~ 733 (744)
+..|-++-.
T Consensus 749 V~e~kL~f~ 757 (765)
T KOG2165|consen 749 VREGKLEFI 757 (765)
T ss_pred hhccceEEe
Confidence 666655544
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=99.76 E-value=8.6e-20 Score=146.49 Aligned_cols=67 Identities=52% Similarity=0.918 Sum_probs=62.0
Q ss_pred HHhhhhhhceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCC
Q 004583 672 DKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPN 738 (744)
Q Consensus 672 ~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~ 738 (744)
+++|...|+|||||+||++|+++|++|+.+|.+.++++|.|+..+||++||.||++|||+||++|+|
T Consensus 2 ~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 2 EQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred cchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 5799999999999999999999999999999999999999999999999999999999999999875
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.24 E-value=0.0092 Score=56.24 Aligned_cols=137 Identities=17% Similarity=0.260 Sum_probs=97.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHHHHHHhcccchhhc
Q 004583 8 TIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIRE 87 (744)
Q Consensus 8 ~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~ 87 (744)
.+..++.|..+..++-. +++|+... .+-+..-++-+.--+.|.++. ....+-+.+++.+..-+.. ....++.
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 35678999999999876 56787764 665555555555556677662 2345556666666665543 2345556
Q ss_pred cCchHHHHHHHHHHHHH-HHHHHHHHHhhchhchhhhhc-----------------CCCCcHHHHHHHHHHHHHHHhhhH
Q 004583 88 KHDEFMLRELVKRWSNH-KVMVRWLSRFFHYLDRYFIAR-----------------RSLPPLNEVGLTCFRDLVYTELNG 149 (744)
Q Consensus 88 ~~~~~~L~~~~~~W~~~-~~~~~~l~~vf~YLdr~yv~~-----------------~~~~~i~~l~l~~f~~~v~~~l~~ 149 (744)
.+++.+|..++..|.-| ..-+-++..+|..|++.+-.. ....+|+.+++..||+.|+-+..+
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 566789999999999644321 234689999999999999987776
Q ss_pred HHH
Q 004583 150 KVR 152 (744)
Q Consensus 150 ~l~ 152 (744)
++.
T Consensus 154 ~l~ 156 (158)
T PF08539_consen 154 RLK 156 (158)
T ss_pred hhh
Confidence 654
No 11
>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=93.24 E-value=0.25 Score=42.50 Aligned_cols=65 Identities=18% Similarity=0.214 Sum_probs=52.4
Q ss_pred EEEcHHHHHHHHhhc--------CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCC
Q 004583 576 LIVTTYQASALLLFN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (744)
Q Consensus 576 l~~s~~Q~~iLllFn--------~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 647 (744)
..++.-|+.+|+..- ....+|-.||++.+|++.+.+.++|..|. +.+++.+.. ....|.+|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~~ 92 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTPL 92 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCCc
Confidence 467888999888665 45689999999999999999999999997 457776542 24779999876
Q ss_pred C
Q 004583 648 T 648 (744)
Q Consensus 648 ~ 648 (744)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 5
No 12
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=92.15 E-value=6 Score=44.46 Aligned_cols=203 Identities=10% Similarity=0.101 Sum_probs=112.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCChHHHHHHHHHHhhhhcCCCCCCchHHHHHHHHHHHHHHHHhc--ccchhh----
Q 004583 13 QGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISST--VLPSIR---- 86 (744)
Q Consensus 13 ~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vy~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~--v~~~l~---- 86 (744)
-.|..|++++.-|... +...+++ ...|-.+++.+|+-|.... -+...+-+.++-....+.... +...+.
T Consensus 112 vdrslLrsll~MLsd~--~iY~esF-~~~fls~f~~lY~aE~~d~--~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~ 186 (661)
T KOG2167|consen 112 VDRSLLRSLLKMLSDL--QIYKESF-ELTFLSLFRELYAAEGQDK--RQELEVPEYLEHVEGRLEEENDRVIEYFDSSTK 186 (661)
T ss_pred hhHHHHHHHHHHHHHH--Hhhhhhh-HHHHHHHHHHHHHHHhcch--hhhcccHHHHHhhhhcccchHHHHHHhcccccc
Confidence 3577777777665332 0000111 2347778889999998772 122223332222211111110 000000
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHHhhchhchhhhhcCCCCcHHHHHHHHHH--HHHHHhhhHHHHHHHHHHHHHHhc
Q 004583 87 EKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFR--DLVYTELNGKVRDAVITLIDQERE 164 (744)
Q Consensus 87 ~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLdr~yv~~~~~~~i~~l~l~~f~--~~v~~~l~~~l~~~ll~~I~~~R~ 164 (744)
......+...+...|-....... +++-+|-. .......++.++-..+- ..+....++.+......++..++.
T Consensus 187 k~l~atV~~~LL~~hL~~IL~kg----l~~lvDm~--q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~k 260 (661)
T KOG2167|consen 187 KPLIATVERCLLSRHLDLILTKG----LDSLVDMR--QTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEEK 260 (661)
T ss_pred cchHHHHHHHHHHHHHHHHHhcc----hHHhhhhh--hccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCchh
Confidence 01123456667777776643322 33333332 11234566676666662 223346677777777778888887
Q ss_pred CCcc--CHHHHHHHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHH
Q 004583 165 GEQI--DRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKRE 234 (744)
Q Consensus 165 g~~i--d~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~~~~~l~~~~~~~Yl~~v~~~l~eE 234 (744)
++.. +....|.-+++.... .++...- .+|+..+++.|...++ .....+.+||.+....+-.+
T Consensus 261 Dk~mVqELL~FK~k~Dii~~~-----sF~~~v~-e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 261 DKDMVQELLDFKKKVDIIVDE-----SFLKYVA-EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred hHHHHHHHHHHHHHhhHHHHH-----HHHHhhH-HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 7643 234577777777763 3444444 8899999999999998 34567889998887765544
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=91.59 E-value=0.28 Score=36.89 Aligned_cols=45 Identities=29% Similarity=0.338 Sum_probs=36.4
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 583 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 583 ~~iLllFn~~~-~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
+.||.+|.+.+ .+|+.||++.+|+|...+.+.|..|.. .+.+.+.
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 46788888775 589999999999999999999999974 4666553
No 14
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=91.36 E-value=0.39 Score=35.31 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=35.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
+..+..||..+.+++.+|..||++.+|++...+.+.|..|..
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 15
>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=90.79 E-value=0.66 Score=38.75 Aligned_cols=58 Identities=16% Similarity=0.218 Sum_probs=40.5
Q ss_pred HHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccC
Q 004583 582 QASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (744)
Q Consensus 582 Q~~iLllFn~~~-~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~ 646 (744)
++.+.+..+..+ .+|.++|++.+++|...+.+.++.|. +.+++...+ | .++.|.++.+
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-G----~~GGy~L~~~ 70 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-G----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCC
Confidence 444444444443 49999999999999999999999997 567776432 2 3677888764
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=90.06 E-value=0.4 Score=37.32 Aligned_cols=51 Identities=24% Similarity=0.346 Sum_probs=42.3
Q ss_pred EcHHHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 578 VTTYQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~--~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|.. .+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~--~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK--KGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEeC
Confidence 47889999988887776 99999999999999999999999974 46776653
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=89.11 E-value=0.93 Score=34.83 Aligned_cols=46 Identities=20% Similarity=0.321 Sum_probs=39.2
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
|..|+.++++++.+|++||++.+|++...+++-|..|.. .+++.+.
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 4566554
No 18
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=87.41 E-value=0.43 Score=36.75 Aligned_cols=49 Identities=22% Similarity=0.356 Sum_probs=42.3
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
|..|+.+|....+.+++|..+|++.++++...+.+.+..|.. .+++.+.
T Consensus 2 t~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~--~g~I~r~ 50 (59)
T PF01047_consen 2 TPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK--KGLIERE 50 (59)
T ss_dssp THHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH--CCCEEec
Confidence 678999999998888999999999999999999999999974 4677654
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=86.26 E-value=1.1 Score=35.40 Aligned_cols=50 Identities=24% Similarity=0.333 Sum_probs=38.4
Q ss_pred EcHHHHHHHHhhc-CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 578 VTTYQASALLLFN-SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 578 ~s~~Q~~iLllFn-~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
+|..|..||..+. ....+|..+|++.++++...+.+.+..|.. .+++.+.
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 3678999999998 778999999999999999999999999984 4677654
No 20
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=85.87 E-value=1.8 Score=31.70 Aligned_cols=43 Identities=26% Similarity=0.307 Sum_probs=34.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 626 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL 626 (744)
...-||.++-+ ++.++.||++.+|++...+.++|..|.. .+++
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~--~glV 45 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLRE--AGLV 45 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHH--CcCe
Confidence 34567777767 6899999999999999999999999863 4554
No 21
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=85.52 E-value=1.1 Score=34.86 Aligned_cols=49 Identities=22% Similarity=0.277 Sum_probs=39.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
++.-..||.++...++.|+.+|++.+|++...+..+|..|.. .+++...
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 455667888887778999999999999999999999999974 5677643
No 22
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=85.06 E-value=1.6 Score=39.06 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=45.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
.++..|+.||..+..++++|..+|++.+|++...+-+.+..|. +-+++.+.+
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 4588899999999888899999999999999999999999997 457777653
No 23
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=82.81 E-value=2.4 Score=39.51 Aligned_cols=52 Identities=17% Similarity=0.174 Sum_probs=45.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
.++..|+.||......+++|..+|++.++++...+.+.+..|. +.+++.+.+
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 5688899999888777789999999999999999999999997 557887654
No 24
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=81.58 E-value=2.9 Score=31.56 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=29.9
Q ss_pred HHHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 583 ASALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 583 ~~iLllF-n~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
..||.++ +..+.+|.++|++.+|++...+.+.|..|..
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3445444 6666799999999999999999999998854
No 25
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=80.19 E-value=1 Score=36.07 Aligned_cols=43 Identities=19% Similarity=0.324 Sum_probs=33.9
Q ss_pred ecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCC
Q 004583 685 RIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 735 (744)
Q Consensus 685 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 735 (744)
.+|+.++.++..+|-. +|..+++.+...|+.|+.+|||++.+.
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 4577888888877766 489999999999999999999998753
No 26
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=79.83 E-value=2.8 Score=33.52 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=38.1
Q ss_pred HHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 581 YQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 581 ~Q~~iLllFn~~~~--~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
..-.||.++.+.+. +|..||++.+|++...+.++|..|.. .+++.+.
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 99999999999999999999999974 4566554
No 27
>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=79.51 E-value=1.3 Score=40.46 Aligned_cols=59 Identities=15% Similarity=0.171 Sum_probs=44.0
Q ss_pred eeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 681 ASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 681 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
..|++++-..+.++..+++... .....+....+...|..|.+||||+|..+. ..|.|-|
T Consensus 7 ~~VM~vlW~~~~~t~~eI~~~l----~~~~~~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p 65 (130)
T TIGR02698 7 WEVMRVVWTLGETTSRDIIRIL----AEKKDWSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA 65 (130)
T ss_pred HHHHHHHHcCCCCCHHHHHHHH----hhccCCcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence 3466677667777777666553 334567888999999999999999998643 5788865
No 28
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=79.04 E-value=1.3 Score=39.54 Aligned_cols=62 Identities=21% Similarity=0.313 Sum_probs=52.1
Q ss_pred hhceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 678 AIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 678 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
..++.||++|=.++..+.+|++.++.. .+.++...|+.-|..|..||.|.|..+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 346778899999999999999987765 478899999999999999999999875 46777754
No 29
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=78.47 E-value=5 Score=35.34 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=43.4
Q ss_pred EEcHHHHHHHHhhc----CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 577 IVTTYQASALLLFN----SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 577 ~~s~~Q~~iLllFn----~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
.+|..|..||..+. ..+++|..+|++.++++...+-+.+..|. +-+++.+.+
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 45888998887766 55689999999999999999999999997 457787654
No 30
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=77.71 E-value=5.7 Score=33.41 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=37.4
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 583 ~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
..||..+... +++|..||++.+|++...+.+.|..|.. .+++.+.
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 5777654
No 31
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=77.15 E-value=6.8 Score=36.93 Aligned_cols=56 Identities=11% Similarity=0.083 Sum_probs=41.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEecc
Q 004583 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (744)
Q Consensus 583 ~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 645 (744)
+.+.|..+..+.+|..+|++..++|...|.+.|..|. +.+++.... | .++.|.++.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~ 68 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGR 68 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecC
Confidence 3344445555678999999999999999999999997 567776542 2 356677654
No 32
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=76.77 E-value=4.4 Score=34.50 Aligned_cols=53 Identities=26% Similarity=0.288 Sum_probs=45.0
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 575 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 575 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
++.++..+..||.++...+.+|..+|++.++++...+.+.|..|.. .+++.+.
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 3457888999999998878899999999999999999999999974 4677654
No 33
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=76.28 E-value=2.3 Score=37.87 Aligned_cols=58 Identities=14% Similarity=0.244 Sum_probs=41.2
Q ss_pred eeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 682 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 682 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
.|++++=..+.++..+++.. +.....+....|...+..|.+||||+|... ...|.|-|
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~----l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEA----LPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHH----HCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHhCCCCCHHHHHHH----HHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 44555555566666666664 444567789999999999999999999875 35788864
No 34
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=75.33 E-value=8.4 Score=36.78 Aligned_cols=56 Identities=16% Similarity=0.207 Sum_probs=40.5
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEecc
Q 004583 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (744)
Q Consensus 583 ~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 645 (744)
+.+.+.|+.. ..+|.++|++.+|+|...+.+.|..|. +.+++.... | +++.|.+..
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 489999999999999999999999997 567776431 1 244566544
No 35
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=74.67 E-value=5.7 Score=29.19 Aligned_cols=44 Identities=23% Similarity=0.304 Sum_probs=34.9
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 583 ~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
-.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++.+
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 34666666667899999999999999999999999874 345543
No 36
>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=72.63 E-value=5.6 Score=28.40 Aligned_cols=36 Identities=33% Similarity=0.499 Sum_probs=27.6
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 583 ~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
-.||-.+.++...++.+|++.+|++...+.+-+..|
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 457777777789999999999999999998877654
No 37
>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=72.14 E-value=3.9 Score=32.52 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=39.4
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
|-.++.|+..+-..+..|..||++.+|++...+.+.|..|.. .+++.+.
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 455666666665777899999999999999999999999984 4666554
No 38
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=72.12 E-value=7.7 Score=40.04 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=39.4
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 583 ~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+.||.+|.....+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 46888898877899999999999999999999999984 46776643
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=70.99 E-value=11 Score=34.66 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=34.4
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 583 ~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 3344545543 479999999999999999999999997 5577764
No 40
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=70.91 E-value=8.2 Score=37.60 Aligned_cols=53 Identities=13% Similarity=0.004 Sum_probs=45.2
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 576 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 576 l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+.++..|+.||..+...+++|..+|++.++++...+.+.+..|. +-+++.+.+
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 35688899999999988899999999999999999999999886 447777653
No 41
>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=70.16 E-value=7.8 Score=37.00 Aligned_cols=48 Identities=25% Similarity=0.302 Sum_probs=39.9
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCCCCC
Q 004583 594 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDK 650 (744)
Q Consensus 594 ~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~ 650 (744)
-+|..+|++.+|++...+.+++..|.. .++|.+.. .+.|.+|++|-.+
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 42
>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=70.06 E-value=14 Score=32.08 Aligned_cols=61 Identities=26% Similarity=0.358 Sum_probs=44.7
Q ss_pred EEcHHHHHHHHh-------hcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCC
Q 004583 577 IVTTYQASALLL-------FNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (744)
Q Consensus 577 ~~s~~Q~~iLll-------Fn~-~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 647 (744)
.++.-|..|++. ||. .+.+|..++++.||++...+.+++..|. +.++|... +..+-+|.+.
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i 97 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNI 97 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeeccc
Confidence 345566666655 343 3579999999999999999999999997 56788654 3445566554
No 43
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=69.81 E-value=11 Score=35.32 Aligned_cols=58 Identities=16% Similarity=0.193 Sum_probs=42.4
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEecc
Q 004583 581 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (744)
Q Consensus 581 ~Q~~iLllFn~~~-~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 645 (744)
+++.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++.... | .++.|.++.
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r-G----~~GGy~Lar 69 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR-G----KGGGYRLAR 69 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec-C----CCCCccCCC
Confidence 3444555555554 68899999999999999999999996 567776432 1 356677655
No 44
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=68.99 E-value=11 Score=30.21 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=33.2
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 585 iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
||+..... ..|++||.+.||++.+.+...|..|. +-+++.+
T Consensus 10 IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 10 ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 44545554 89999999999999999999999996 4567764
No 45
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=68.85 E-value=9.1 Score=35.48 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=44.1
Q ss_pred EEEcHHHHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 576 LIVTTYQASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 576 l~~s~~Q~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+.++..|..||...... ++.|..+|++.+|++...+.+.+..|. +-+++.+.+
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 35688899999888754 468999999999999999999999997 457777654
No 46
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=68.79 E-value=7.4 Score=35.08 Aligned_cols=39 Identities=26% Similarity=0.328 Sum_probs=34.0
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 589 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 589 Fn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.+.+++.|+++|++.++.+...+.++|++|.. .+++.+.
T Consensus 37 L~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Re 75 (126)
T COG3355 37 LEENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVERE 75 (126)
T ss_pred HhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeee
Confidence 34678999999999999999999999999984 5788765
No 47
>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=68.22 E-value=6.9 Score=30.21 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=30.2
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
|.-+|-++-+.+.+|+.+|++.+|++...++..+.-|-
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 55666555557799999999999999999998887764
No 48
>PHA00738 putative HTH transcription regulator
Probab=66.71 E-value=12 Score=32.73 Aligned_cols=67 Identities=22% Similarity=0.104 Sum_probs=51.0
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCC
Q 004583 575 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (744)
Q Consensus 575 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 647 (744)
++...+.=-.||.++.+++.+++.+|++.++|+...+-++|.-|.. .+++.....|. .-.|++|.+.
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 4556666667787777777899999999999999999999999964 57887665443 2346777654
No 49
>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=66.26 E-value=9.6 Score=33.05 Aligned_cols=44 Identities=25% Similarity=0.342 Sum_probs=37.3
Q ss_pred EEcHHHHHHHHhhcC----CCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 577 IVTTYQASALLLFNS----SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~----~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.++..|-.||-.+.. ...+++++|++.++++.++++.+|..|+.
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 578899999998887 35899999999999999999999999985
No 50
>PRK10870 transcriptional repressor MprA; Provisional
Probab=64.62 E-value=15 Score=35.55 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=42.8
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 577 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
-+|..|..||..... ..++|..+|++.++++...+.+.+..|. +-+++.+.+
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 356779988888764 4579999999999999999999999997 457887754
No 51
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=64.42 E-value=14 Score=26.53 Aligned_cols=34 Identities=29% Similarity=0.404 Sum_probs=28.8
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 594 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 594 ~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.+|..+|++.+|++...+.+.|..|.. .+++...
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 578999999999999999999999974 5677643
No 52
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=63.51 E-value=9 Score=29.97 Aligned_cols=45 Identities=22% Similarity=0.175 Sum_probs=33.3
Q ss_pred HHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCC
Q 004583 585 ALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPN 631 (744)
Q Consensus 585 iLllFn~-~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~ 631 (744)
||-.++. +.++|-.||++.+|++...++..|..|.. .+.+.+.|.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~--eG~V~~~~~ 50 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEK--EGKVERSPV 50 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHH--CTSEEEES-
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH--CCCEEEecC
Confidence 4555666 67899999999999999999999999974 455655443
No 53
>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=62.59 E-value=9.9 Score=30.79 Aligned_cols=30 Identities=20% Similarity=0.203 Sum_probs=25.4
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 590 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 590 n~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
.....+|+.||++.+|++...++..+..+.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 334678999999999999999998887664
No 54
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=62.22 E-value=8.3 Score=31.91 Aligned_cols=44 Identities=20% Similarity=0.383 Sum_probs=33.8
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
...||.+++..+.+++.+|.+.+|++...+-++|..|.. .+.+.
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 34444
No 55
>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=61.99 E-value=19 Score=32.63 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=33.9
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 582 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 582 Q~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
++.+.+.-++. ..+|.++|++.+|+|...+.+.|..|.. .+++..
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 33344443333 3899999999999999999999999974 567754
No 56
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=61.80 E-value=12 Score=37.10 Aligned_cols=51 Identities=18% Similarity=0.212 Sum_probs=44.6
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.++..|..||..+.+++..+..+|++.+|++...+.++|..|. +.+++.+.
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 4688899999999887889999999999999999999999997 45777765
No 57
>PRK11569 transcriptional repressor IclR; Provisional
Probab=60.57 E-value=16 Score=38.10 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=38.6
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 583 ~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.+
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 4678889874 4799999999999999999999999984 57776643
No 58
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=58.78 E-value=19 Score=36.81 Aligned_cols=46 Identities=28% Similarity=0.417 Sum_probs=38.8
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 583 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 583 ~~iLllFn~~~-~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+.||.+|.... .+++.||++.+|+|...+.+.|..|.. .+.+...+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~--~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVE--LGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 46888888755 378999999999999999999999984 57887764
No 59
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=58.67 E-value=18 Score=27.26 Aligned_cols=39 Identities=26% Similarity=0.381 Sum_probs=31.7
Q ss_pred hcCCCCc-CHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 589 FNSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 589 Fn~~~~~-t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
+.....+ |..+|++.+|++...+.++|..|.. .+++...
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 4677654
No 60
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=58.62 E-value=19 Score=37.41 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=38.7
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 583 ~~iLllFn~~-~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
..||.+|... ..+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~ 74 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS 74 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 4688889765 4799999999999999999999999985 46776643
No 61
>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=58.27 E-value=20 Score=36.69 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=37.1
Q ss_pred HHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 583 ASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 583 ~~iLllFn~-~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
..||.+|.. ..++|+.||++.+|+|...+.+.|.+|.. .+.|.+
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 45899999999999999999999999985 466654
No 62
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=57.44 E-value=19 Score=32.14 Aligned_cols=59 Identities=22% Similarity=0.305 Sum_probs=43.3
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEecc
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~ 645 (744)
.-..||.++-+.++.++.||++.+|++...+-++|.-|. ..+++.....|. .-.|++|.
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 334566655555679999999999999999999999996 467887655442 23466765
No 63
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=57.17 E-value=18 Score=31.55 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=37.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
..-.||..+..+...|+.+|++.+|++...+.+.+..|.. .+++.
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 3456788888888899999999999999999999999974 35665
No 64
>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=57.12 E-value=4.1e+02 Score=31.82 Aligned_cols=22 Identities=9% Similarity=0.406 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcCC
Q 004583 344 FVRKVIELHDKYLAYVNDCFQN 365 (744)
Q Consensus 344 ~i~~l~~l~~~~~~l~~~~F~~ 365 (744)
+-+..++.|.++..++..|+.|
T Consensus 680 ~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 680 MQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHhCCC
Confidence 4466789999999999999864
No 65
>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=56.41 E-value=2.8e+02 Score=29.72 Aligned_cols=163 Identities=14% Similarity=0.264 Sum_probs=86.3
Q ss_pred hhhhhhhcCcHHHHHHHHHhhccC---CCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHH
Q 004583 273 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 349 (744)
Q Consensus 273 g~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~ 349 (744)
.|..-.+.++.+.+.|.++||-.+ +.|++.....+.+.|.......++.......+ +..+.-|+..|.
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 366667788899999998888654 35777777666666666665555433211100 122444555555
Q ss_pred HHHHHHH-------HHHHHhcCCChhH--HHHHHHHH--------HHHhcCCCCCCCcHHHHHHHHHHHhhc--------
Q 004583 350 ELHDKYL-------AYVNDCFQNHTLF--HKSLKEAF--------EVFCNKGVAGSSSAELLATFCDNILKK-------- 404 (744)
Q Consensus 350 ~l~~~~~-------~l~~~~F~~~~~f--~~~l~~af--------~~~~n~~~~~~~~~e~La~y~d~~lk~-------- 404 (744)
.+++..- .+|..+|+..... ...|..-+ ..|..... -.+....+..|-...+.+
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 5555553 4566788865422 11111111 11111110 001112223333333322
Q ss_pred ---------CCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCC
Q 004583 405 ---------GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 452 (744)
Q Consensus 405 ---------~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~~~s 452 (744)
+.....+.-+++..|+.+..+... ...|.++++.|.-....
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 001223445778888888777744 35799999999887543
No 66
>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=56.27 E-value=5.6 Score=30.48 Aligned_cols=45 Identities=16% Similarity=0.324 Sum_probs=38.8
Q ss_pred eeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004583 682 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 734 (744)
Q Consensus 682 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 734 (744)
.|+..++.++.++..+|.+ .|..+...|.+-+..|-++|.|.|.-
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 4667788889999988877 38889999999999999999999864
No 67
>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=55.46 E-value=27 Score=31.66 Aligned_cols=43 Identities=28% Similarity=0.291 Sum_probs=34.0
Q ss_pred HHHHhhc--CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 584 SALLLFN--SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 584 ~iLllFn--~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
.+|..+. ..+.+|+.||++.+|+|...+.+.|..|. +.+++..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 3455554 33579999999999999999999999997 4577754
No 68
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=55.21 E-value=16 Score=36.38 Aligned_cols=37 Identities=30% Similarity=0.337 Sum_probs=33.4
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.||.+.+..++.|.+||++.+|++..-++++|+.|..
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~ 51 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA 51 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 5677778888999999999999999999999999974
No 69
>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=55.17 E-value=8.7 Score=30.20 Aligned_cols=51 Identities=12% Similarity=0.216 Sum_probs=32.2
Q ss_pred eeeeccc-CCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccC--CCCCCce
Q 004583 682 SIVRIMK-SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERD--KSNPNMF 740 (744)
Q Consensus 682 ~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~--~~d~~~y 740 (744)
.|.+.+. ..+.++..+|... +..+.+.+-+.|+.|+++|||++. +.|+...
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~--------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAER--------LGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHccCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 3444555 5566666666553 556778899999999999999664 4455533
No 70
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=54.78 E-value=22 Score=36.78 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=38.2
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 583 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 583 ~~iLllFn~~~-~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+.||.+|.+.. .+|..||++.+|++...+.+.|..|.. .+++.+.+
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 57787654
No 71
>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=54.46 E-value=20 Score=28.39 Aligned_cols=38 Identities=26% Similarity=0.268 Sum_probs=32.6
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 583 ~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
..|--++++.+.+|+.+|++.||++.+++..++--|..
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 35667788989999999999999999999999998874
No 72
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=54.44 E-value=12 Score=29.81 Aligned_cols=53 Identities=11% Similarity=0.197 Sum_probs=40.0
Q ss_pred ceeeeecccCCCC--CChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCce
Q 004583 680 DASIVRIMKSRKV--LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMF 740 (744)
Q Consensus 680 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y 740 (744)
+..|...|+.++. ++..+|-.+ ...+...+.+.+..|.++|||.+++..+..|
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 3446677888766 887777664 3456678999999999999999987654544
No 73
>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=53.52 E-value=4.9 Score=31.93 Aligned_cols=47 Identities=13% Similarity=0.285 Sum_probs=34.7
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeec
Q 004583 689 SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYL 743 (744)
Q Consensus 689 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yi 743 (744)
.++.++..+|...+ ..+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 19 ~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 19 KNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 55566666665542 456788999999999999999998765555544
No 74
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.81 E-value=26 Score=30.86 Aligned_cols=51 Identities=24% Similarity=0.347 Sum_probs=43.2
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
++..|+.+|..+....+.+..+|++.++++...+.+.+..|. +.+++.+.+
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 688999999888887776669999999999999999999997 457777653
No 75
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=52.22 E-value=26 Score=26.51 Aligned_cols=36 Identities=22% Similarity=0.268 Sum_probs=30.0
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 592 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 592 ~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.++.|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeeee
Confidence 56789999999999999999999999974 4566543
No 76
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=51.58 E-value=35 Score=25.00 Aligned_cols=33 Identities=27% Similarity=0.392 Sum_probs=24.2
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 004583 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 617 (744)
Q Consensus 583 ~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~ 617 (744)
.+|-+.| ..++|+.||++.+|++...+......
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3444556 45789999999999999988876543
No 77
>PF13730 HTH_36: Helix-turn-helix domain
Probab=50.82 E-value=38 Score=25.33 Aligned_cols=25 Identities=24% Similarity=0.291 Sum_probs=23.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 596 SYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 596 t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999863
No 78
>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=50.72 E-value=29 Score=27.22 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=38.0
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
+..+..|+..+.+.. ++..||++.+|++...+.+.|..|.. .+++..
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 456777888777766 99999999999999999999999864 355554
No 79
>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=50.16 E-value=14 Score=32.29 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=31.0
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
.+.|+..+..++.++-++|++.+|++..++++.|..|.. .+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 456776776677899999999999999999999999975 35553
No 80
>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=49.18 E-value=23 Score=27.65 Aligned_cols=30 Identities=33% Similarity=0.364 Sum_probs=24.4
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 591 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 591 ~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.++..|+.+|.+.|++|.+.++..|-.|..
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ 53 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQ 53 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456889999999999999999999999874
No 81
>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=48.74 E-value=13 Score=39.87 Aligned_cols=143 Identities=11% Similarity=0.134 Sum_probs=40.4
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCCCCCCcce
Q 004583 577 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRI 654 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~~~~~~i 654 (744)
.++..+..|.-+..+ ..++-..+|...||++...+.++|.+|... ++++... +.+.+++|+
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 457778888777764 458889999999999999999999999752 4444211 223344444
Q ss_pred eccCCCh--hhhhh----HHHhHHHhhhhhhceeeeecccCCCC-----------------------------CChHHHH
Q 004583 655 KIPLPPV--DEKKK----VIEDVDKDRRYAIDASIVRIMKSRKV-----------------------------LGHQQLV 699 (744)
Q Consensus 655 ~i~~~~~--~e~~~----~~~~~~~~r~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 699 (744)
.+-..-. .+-.. +..+.+.+=-..+...|.+.+.++.. .+.+++.
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 11223333334555555555555554 4444555
Q ss_pred HHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCC
Q 004583 700 LECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSN 736 (744)
Q Consensus 700 ~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d 736 (744)
..+.+.=-..-..+.++|...++.||=-|-|++-...
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 5444331112346789999999999999988886543
No 82
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.31 E-value=47 Score=30.69 Aligned_cols=49 Identities=14% Similarity=0.238 Sum_probs=36.8
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEec
Q 004583 589 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFN 644 (744)
Q Consensus 589 Fn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N 644 (744)
+..+..+|..+|++.+|+|...+.++|..|. +.+++...+. .++.|.+.
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 3344578999999999999999999999997 4577765432 24456654
No 83
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=48.24 E-value=39 Score=26.20 Aligned_cols=35 Identities=26% Similarity=0.326 Sum_probs=30.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 593 DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 593 ~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
..+|..+|++.+|++...+.+.|..|.. .+++...
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 4699999999999999999999999974 4777654
No 84
>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=48.11 E-value=35 Score=26.44 Aligned_cols=44 Identities=18% Similarity=0.233 Sum_probs=34.0
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
+|..+-.+...++..+|++.+|++...+...+..|.. .+++...
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~--~GlV~~~ 55 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE--KGLVEYE 55 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH--CCCEEec
Confidence 3444445778999999999999999999999999974 4666554
No 85
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=47.20 E-value=43 Score=27.00 Aligned_cols=47 Identities=19% Similarity=0.175 Sum_probs=39.4
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccc
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKI 625 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~i 625 (744)
++=|+.++-++...+.-|+++|++.||-..-.++-.|..+...|.++
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 45689999999988899999999999999999998888886444444
No 86
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=47.02 E-value=47 Score=27.16 Aligned_cols=39 Identities=13% Similarity=0.218 Sum_probs=29.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
+.-.+|-++-...++|..+|+..+|.+.+++...|..+.
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 345577778888999999999999999999999998775
No 87
>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=46.46 E-value=35 Score=32.37 Aligned_cols=44 Identities=16% Similarity=0.176 Sum_probs=35.3
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
...|+..+-.++.+|-+||++.+|++..++++.|..|.. .+++.
T Consensus 16 ~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 16 VGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 345666555666899999999999999999999999985 35663
No 88
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=45.78 E-value=21 Score=27.15 Aligned_cols=45 Identities=9% Similarity=0.148 Sum_probs=31.8
Q ss_pred eecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCC
Q 004583 684 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNP 737 (744)
Q Consensus 684 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~ 737 (744)
++.+. .+.++..++... +..+...+.+.|+.|.++|++.+....+
T Consensus 3 l~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 33444 556676665553 3457788999999999999999876433
No 89
>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=45.58 E-value=27 Score=25.17 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=21.6
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 616 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~ 616 (744)
.|+-++.++ +|+.+|++.+|++...+.+.|.
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 90
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=45.26 E-value=49 Score=31.77 Aligned_cols=55 Identities=20% Similarity=0.181 Sum_probs=42.2
Q ss_pred EEEEEcHHHHHHHHhhcCCCCc-CHHHHHHHh--CCCHHHHHHHHhHhhhccccccccCC
Q 004583 574 TELIVTTYQASALLLFNSSDRL-SYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 574 ~~l~~s~~Q~~iLllFn~~~~~-t~~ei~~~t--~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+++--+.+..+|+-+..-.+.- +.++|++.+ +++.++++..|..|. +.++|.+..
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 3444456666777666544433 899999999 999999999999997 678998864
No 91
>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=45.16 E-value=35 Score=28.27 Aligned_cols=35 Identities=9% Similarity=-0.007 Sum_probs=30.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 616 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~ 616 (744)
-++.|+-+..+ +.+|+.+|++.+|++...+.+.|.
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 46788888888 899999999999999999988664
No 92
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=44.79 E-value=38 Score=25.20 Aligned_cols=37 Identities=32% Similarity=0.383 Sum_probs=21.9
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 616 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~ 616 (744)
|..+-.|+.+.- -.++|+.||++.+|++...++..+.
T Consensus 12 ~~~~r~i~~l~~-~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 12 PERQREIFLLRY-FQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp -HHHHHHHHHHH-TS---HHHHHHHCTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHH-HHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 333444443322 2368999999999999999887664
No 93
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=44.50 E-value=25 Score=28.00 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=28.1
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 585 iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
|.-...+++.+|+.||+..++++.+.+...|..|..
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 344455677899999999999999999999999985
No 94
>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=44.40 E-value=36 Score=26.88 Aligned_cols=24 Identities=17% Similarity=0.494 Sum_probs=20.6
Q ss_pred ChhHHHHHHHhhhhhhhcccCCCC
Q 004583 713 DFKAIKKRIEDLITRDYLERDKSN 736 (744)
Q Consensus 713 ~~~~ik~~Ie~Liekeyi~r~~~d 736 (744)
+..-+...++.|.++|||+|++.-
T Consensus 39 S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 39 STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred ChHHHHHHHHHHHHCcCccCCCCC
Confidence 467788889999999999999853
No 95
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=44.01 E-value=33 Score=34.10 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=41.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
|..-..||.++...+++.+.||++.+|+|...+..+++.|. +.+++..+
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 44455789999999999999999999999999999999996 56777643
No 96
>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=43.80 E-value=9.5 Score=37.11 Aligned_cols=56 Identities=20% Similarity=0.319 Sum_probs=39.1
Q ss_pred eeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 681 ASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 681 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.---+|++.|+||.
T Consensus 102 ~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 102 QEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 34457889999998888766 488899999999999999999888778899999984
No 97
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.69 E-value=28 Score=35.92 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
-|..||-+.++++.+++.||++.+|++...+++-|..|- +.+++.+.
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 467899999999999999999999999999999999996 44666654
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.31 E-value=34 Score=33.13 Aligned_cols=45 Identities=16% Similarity=0.130 Sum_probs=36.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
....||.++-.++.+|-++|++.+|++...++++|..|.. .+++.
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 35555
No 99
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.98 E-value=49 Score=24.30 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=30.0
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
+.-+..|+.++. .+++..+|++.+|++...+...+..+.
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 100
>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=42.71 E-value=25 Score=34.14 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=22.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 594 RLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 594 ~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
.+|+++|++.||+..+++..+|+.|-
T Consensus 150 ~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 150 SISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp -EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred eEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 69999999999999999999999883
No 101
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=41.96 E-value=32 Score=35.42 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
-|-.||-+.++++.++++||++.+|+++..+++=|..|. +.++|.+.
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 34666664
No 102
>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=41.76 E-value=53 Score=24.19 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=28.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
+..|..++.++- +++|..+|++.+|++...+...+..+.
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 468999999999999999988877653
No 103
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=41.61 E-value=73 Score=28.87 Aligned_cols=68 Identities=18% Similarity=0.245 Sum_probs=49.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCC---CeEEeccCCC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPT---DHFEFNSKFT 648 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~---~~~~~N~~f~ 648 (744)
|.--..+|-+..+.+..|+.|+++.+|-+.+.|.+.|..|. .++++..+.+|+.-.+. +.+.++-.|.
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 34444567777888899999999999999999999999997 47888776555543322 3344555554
No 104
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=39.89 E-value=42 Score=31.93 Aligned_cols=48 Identities=15% Similarity=0.208 Sum_probs=41.0
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
+.-.-..||-.+.++...|+.+|++.+|++...+.+-++.|.. .+++.
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 4556678899999999999999999999999999999999974 45554
No 105
>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=39.21 E-value=62 Score=31.95 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=35.7
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.||..+...+.+|..+|++.+|++...+.++|..|.. .+++.+.
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 4565555566799999999999999999999999974 4677654
No 106
>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=38.45 E-value=48 Score=25.18 Aligned_cols=40 Identities=23% Similarity=0.246 Sum_probs=31.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
|.-+..||.++.. +.+..+|++.+|+++..+..++..+..
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 5567778877766 468999999999999999999988863
No 107
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=38.01 E-value=85 Score=25.93 Aligned_cols=41 Identities=20% Similarity=0.236 Sum_probs=32.4
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 587 LLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 587 llFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
+..++.+.+|-++|++.+|++...+-++++.|-...+.|..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 34456668999999999999999999999999654444443
No 108
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=37.83 E-value=48 Score=31.47 Aligned_cols=51 Identities=27% Similarity=0.369 Sum_probs=37.8
Q ss_pred cCCCeeEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 548 KTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 548 k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
+++.+.|+|.++|- -|+-.+.- +...+|+++|+..+|.++.+++++|..=.
T Consensus 36 ~~~~~~lTWvdSLa--------------------vAAga~ar-ekag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 36 KDPYERLTWVDSLA--------------------VAAGALAR-EKAGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred hCcccccchhhHHH--------------------HHHHHHHH-HHccCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 56889999987543 22222333 44589999999999999999999887543
No 109
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=37.83 E-value=49 Score=31.02 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=41.4
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
.++..--.||.++..+...|+.+|++.+|++...+.+.+..|.. .+++.
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 34666778898998889999999999999999999999999975 35554
No 110
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=37.48 E-value=48 Score=34.05 Aligned_cols=48 Identities=17% Similarity=0.152 Sum_probs=40.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
-|..|+..+++++.+++.||++.+|++...+++-|..|.. .+++.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~--~g~i~r~~ 53 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE--SGKLKKVR 53 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEec
Confidence 4667899999999999999999999999999999999863 45665543
No 111
>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=36.04 E-value=31 Score=30.48 Aligned_cols=57 Identities=11% Similarity=0.097 Sum_probs=41.9
Q ss_pred eeecccC-CCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceee
Q 004583 683 IVRIMKS-RKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 742 (744)
Q Consensus 683 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Y 742 (744)
|..+|.. .+.++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4444544 55799999999887642 457888999999999999999987543333444
No 112
>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=35.81 E-value=18 Score=26.24 Aligned_cols=42 Identities=10% Similarity=0.240 Sum_probs=31.6
Q ss_pred eeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcc
Q 004583 682 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLE 731 (744)
Q Consensus 682 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~ 731 (744)
.|+..+.....++..+|-..+ ..+.+.+...|..|.++|||+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 455667777788887777653 467888999999999999985
No 113
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=35.19 E-value=43 Score=32.65 Aligned_cols=41 Identities=12% Similarity=0.053 Sum_probs=37.0
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 580 ~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.-+..|+.+.+.++.+++.+|++.+|++...+++-|..|..
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 35678899999999999999999999999999999999874
No 114
>PRK00215 LexA repressor; Validated
Probab=35.01 E-value=74 Score=31.39 Aligned_cols=51 Identities=25% Similarity=0.271 Sum_probs=40.0
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCC-CHHHHHHHHhHhhhccccccccCC
Q 004583 578 VTTYQASALLLFNS-----SDRLSYSEIMTQLNL-SDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 578 ~s~~Q~~iLllFn~-----~~~~t~~ei~~~t~~-~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
++.-|..||..+.+ ....|..||++.+|+ +...+.+.|..|.. .+.+.+.+
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 99999999999974 46676554
No 115
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=34.58 E-value=53 Score=33.72 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=36.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
-|..|+.+++.++.+++.+|++.+|+++..+++-|..|-
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 477899999999999999999999999999999999875
No 116
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=34.36 E-value=78 Score=24.17 Aligned_cols=33 Identities=21% Similarity=0.277 Sum_probs=27.5
Q ss_pred cCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 595 LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 595 ~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.|..+|++.+|++...+.++|..|.. .+++...
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 35999999999999999999999974 4666544
No 117
>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=33.71 E-value=55 Score=29.47 Aligned_cols=38 Identities=11% Similarity=0.119 Sum_probs=32.0
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 590 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 590 n~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
++.-++|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344589999999999999999999999996 67777653
No 118
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.42 E-value=68 Score=29.77 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=41.0
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
++-.-.-||..++++...++.+|++.+|++...+.+.+..|. +.+++..
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 345567788889888899999999999999999999999997 4466653
No 119
>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=33.08 E-value=64 Score=24.40 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=24.7
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 589 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 589 Fn~~~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
|+.-...|++||++.+|++...+-.+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555568999999999999999888877643
No 120
>PF07393 Sec10: Exocyst complex component Sec10; InterPro: IPR009976 This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins [].; GO: 0006887 exocytosis, 0048278 vesicle docking, 0005737 cytoplasm
Probab=32.59 E-value=9.4e+02 Score=28.82 Aligned_cols=136 Identities=16% Similarity=0.307 Sum_probs=75.7
Q ss_pred HhhhHHHHHHHHHHHHH-HhcCCccCHHHHHHHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHH----------HHH
Q 004583 145 TELNGKVRDAVITLIDQ-EREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRK----------ASN 213 (744)
Q Consensus 145 ~~l~~~l~~~ll~~I~~-~R~g~~id~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~----------~~~ 213 (744)
..+.+.+-+.+|+..+. .|.+ |...++.+..+|..++.+. ..=..|++...-|+... ...
T Consensus 105 ~~~~e~fE~~LL~eFe~ay~~~---d~~~M~~~A~vL~~fngg~------~~i~~fi~k~~~f~~~~~~~~~~~~~~~~~ 175 (710)
T PF07393_consen 105 EKYCEIFENALLREFEIAYREG---DYERMKEFAKVLLEFNGGS------SCIDFFINKHEFFIDEDQLDESNGFEDEEI 175 (710)
T ss_pred HHHHHHHHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCc------HHHHHHHHhChhhhhhhhhccccccchhHH
Confidence 35667777777777766 4444 5777999999998886432 01111222222222000 011
Q ss_pred HH-----------hcCChhHHHHHHHHHHHHHHHHHchhcCCCc--HHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhc
Q 004583 214 WI-----------LEDSCPDYMLKAEECLKREKDRVSHYLHSSS--EPKLLEKVQHELLSVYANQLLEKEHSGCHALLRD 280 (744)
Q Consensus 214 ~l-----------~~~~~~~Yl~~v~~~l~eE~~r~~~~l~~~t--~~kl~~~l~~~LI~~~~~~ll~~~~sg~~~ll~~ 280 (744)
|- ...++.+++..+...+++|...+++.+++.. ..++.+.+-..-|..++..+++... ..
T Consensus 176 ~~~l~d~~~~~~~~~~~l~~~~~~i~~~i~~e~~iI~~VFp~~~~Vm~~fiervf~~~I~~~i~~lL~~a~-------~~ 248 (710)
T PF07393_consen 176 WEKLSDPDSHPPINEESLDAFFEDIRDVINEESKIIDRVFPNPEPVMQKFIERVFEQVIQEYIESLLEEAS-------SI 248 (710)
T ss_pred HHhccCcccccccchHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhhc-------cC
Confidence 11 1123568999999999999999999885432 2344455555555666666655431 11
Q ss_pred CcHHHHHHHHHhhccC
Q 004583 281 DKVEDLSRMFRLFSKI 296 (744)
Q Consensus 281 ~~~~~L~~ly~L~~~~ 296 (744)
+...-|+.++.+++.+
T Consensus 249 s~~~YLr~l~~~y~~t 264 (710)
T PF07393_consen 249 STLAYLRTLHGLYSQT 264 (710)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 2233455566555543
No 121
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=32.47 E-value=73 Score=30.86 Aligned_cols=64 Identities=19% Similarity=0.167 Sum_probs=47.8
Q ss_pred CeeEEeccCcceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 551 HRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 551 ~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~--~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
.|.-.|.+.+|..+++- .+.| .||+.||.-|+.-... ..||.+-||+..+++.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 34445788888887763 3334 5688999777654332 479999999999999999998888774
No 122
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=32.22 E-value=71 Score=33.15 Aligned_cols=40 Identities=18% Similarity=0.287 Sum_probs=31.3
Q ss_pred HHHHHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 580 TYQASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 580 ~~Q~~iLllFn~-~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
-+...|+-.+.+ ...+|+++|++.|||..+++..+|++|-
T Consensus 208 YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~ 248 (290)
T PLN03238 208 YWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLN 248 (290)
T ss_pred HHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 344456655443 4689999999999999999999999873
No 123
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.85 E-value=53 Score=30.63 Aligned_cols=38 Identities=13% Similarity=0.159 Sum_probs=30.3
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcc
Q 004583 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAK 622 (744)
Q Consensus 585 iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k 622 (744)
|+..+-.++.+|-++|++.+|++...|++.|..|...|
T Consensus 6 v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~ 43 (147)
T smart00531 6 VLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEK 43 (147)
T ss_pred ehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhh
Confidence 33333345689999999999999999999999997543
No 124
>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=31.80 E-value=96 Score=24.47 Aligned_cols=51 Identities=24% Similarity=0.292 Sum_probs=35.1
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHhHhhhccccccccCC
Q 004583 578 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 578 ~s~~Q~~iLllFn~-----~~~~t~~ei~~~t~~~-~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
++.-|.-||..+-+ +-+-|+.||++.+|+. ...+..+|..|.. -+.|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~--kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALER--KGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH--TTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CcCccCCC
Confidence 35667777765542 2356999999999997 9999999999973 46776654
No 125
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=31.78 E-value=57 Score=35.42 Aligned_cols=64 Identities=20% Similarity=0.277 Sum_probs=41.4
Q ss_pred EEeccCcceEEEEeEecCeeEEEEE-------cHHHHHHHHhhcC-C-CCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 554 LTWIYSLGTCNLLGKFESRTTELIV-------TTYQASALLLFNS-S-DRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 554 L~w~~~l~~~~i~~~~~~~~~~l~~-------s~~Q~~iLllFn~-~-~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
+.+.+.||..|=++--+ .+-|+= +-+-..||-++-+ + ..+|+++|++.|||..+++..+|++|-
T Consensus 282 IdFSYeLSr~E~~~GsP--EKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSP--EKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcCCCC--CCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 56778888766554222 222211 2333344444433 2 239999999999999999999999884
No 126
>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=31.62 E-value=63 Score=21.63 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=20.7
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 594 RLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 594 ~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
.+|-+||++.+|++.+.+-+.|..|.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36789999999999999999998875
No 127
>PRK13239 alkylmercury lyase; Provisional
Probab=31.37 E-value=82 Score=31.19 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=35.4
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 580 ~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
.+...||.++-++...|+.+|++.+|.+.+.+.+.|..|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 4566777778888999999999999999999999999885
No 128
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=31.26 E-value=6.7e+02 Score=26.74 Aligned_cols=161 Identities=14% Similarity=0.276 Sum_probs=79.4
Q ss_pred hhhhhhhcCcHHHHHHHHHhhccC---CCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHH
Q 004583 273 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 349 (744)
Q Consensus 273 g~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~ 349 (744)
.|..-+++++...+.+.++||-.+ +.|++.....+.+.|......+.+.... ... ....+--|+..|.
T Consensus 15 ~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~---~~~------~~~~~~~~a~~lt 85 (324)
T smart00762 15 RFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAG---ASD------DTRAAVFYADTLT 85 (324)
T ss_pred HHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhcccc---ccc------cccccchHHHHHH
Confidence 366677888999999999998765 3466555555555554444333322110 000 0122334555555
Q ss_pred HHHHHH-------HHHHHHhcCCChhH--HHHHHH----HHHHHhcCCCCCCCc---HHHHHHHHHHHhhc---------
Q 004583 350 ELHDKY-------LAYVNDCFQNHTLF--HKSLKE----AFEVFCNKGVAGSSS---AELLATFCDNILKK--------- 404 (744)
Q Consensus 350 ~l~~~~-------~~l~~~~F~~~~~f--~~~l~~----af~~~~n~~~~~~~~---~e~La~y~d~~lk~--------- 404 (744)
.+++.. ..+|..+|+.+... ...|.. -...++..=....++ ...+..|....+..
T Consensus 86 ~Lfe~ia~ii~~h~~~I~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~ 165 (324)
T smart00762 86 HLFENVATIIEQHQPVIEKYYGPDGMLYVITKLQKEADLQGGIILDTFMDERRIDRLISDINSYNHAQLHAGASNDARAS 165 (324)
T ss_pred HHHHHHHHHHHhccHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhccccccccccccccc
Confidence 555444 44667788744322 111111 111111100000011 12222332222211
Q ss_pred --CCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcC
Q 004583 405 --GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLF 449 (744)
Q Consensus 405 --~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~La~RLL~ 449 (744)
+....++..+++..|+.+..+.... ..|.+++++|.-.
T Consensus 166 ~~~~~~~~d~revd~lL~Eis~i~~~~-------~lY~rFi~~k~~~ 205 (324)
T smart00762 166 SNGEDEGLDPRELDAILEEISQILSRW-------ELYCRFISRKINE 205 (324)
T ss_pred cccccCCCCHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHhh
Confidence 0112345568888888888887543 4689999888764
No 129
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=31.02 E-value=63 Score=33.20 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=40.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
-+..|+-++++.+.+++.||++.++++...+++-|..|.. .++|.+.
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 4566654
No 130
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=30.54 E-value=3.1e+02 Score=26.36 Aligned_cols=62 Identities=13% Similarity=0.084 Sum_probs=36.6
Q ss_pred HHHHHhhhhcCCCCCCc--hHHHHHHHHHHHHHHHHhcccchhhccCchHHHHHHHHHHHHHHHHHHHHHHhhchh
Q 004583 45 LYTTIYNMCTQKPPHDY--SQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYL 118 (744)
Q Consensus 45 lY~~vy~lc~~~~~~~~--~e~LY~~l~~~l~~~l~~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YL 118 (744)
|+-.+|++...+|.... -..||+.+-+.+.+.=. .+ =.+..-+.|.-|..-+.-|++|+.+|
T Consensus 126 LryDL~tiIsskP~~eK~~L~~LankLFdnvt~LDy-AA-----------R~K~~~eae~yY~~Tv~slddVl~~l 189 (190)
T PLN02999 126 LSQDLTNAMNILPESRRNDYVQAANELVENMSELDY-YV-----------RTPKVYESYLYYEKTLKSIDNVVELL 189 (190)
T ss_pred HHHHHHHHHhcCCHhhhHHHHHHHHHHhhhHHHHHH-HH-----------hcCChHHHHHHHHHHHHHHHHHHHHh
Confidence 66778887777732111 12355555554433111 00 01124567899999999999999886
No 131
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.52 E-value=57 Score=23.74 Aligned_cols=32 Identities=25% Similarity=0.340 Sum_probs=21.4
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 585 iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
++.++.+ ++|..+|++.+|++...+.+-+..+
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 4444544 7899999999999999988766654
No 132
>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=30.45 E-value=64 Score=28.94 Aligned_cols=49 Identities=18% Similarity=0.234 Sum_probs=37.3
Q ss_pred cHHHHHHHHhhcCC--------CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 579 TTYQASALLLFNSS--------DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 579 s~~Q~~iLllFn~~--------~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
..+.-..|+..|.. -++|.++||..++-+.+.++.+|..|. +++++...
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34444555555543 478999999999999999999999996 67777653
No 133
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=30.43 E-value=1e+02 Score=21.96 Aligned_cols=40 Identities=30% Similarity=0.385 Sum_probs=28.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
++..+..++.++- ..++|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455555555443 246799999999999999988777653
No 134
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=29.90 E-value=64 Score=33.50 Aligned_cols=49 Identities=8% Similarity=0.058 Sum_probs=41.0
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.--|..|+.+++.++.+++.||++.+|++...++|-|..|-. .+++.+.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~--~G~l~r~ 64 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK--QGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh--CCCeEEE
Confidence 345778999999999999999999999999999999999853 3555554
No 135
>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=29.55 E-value=23 Score=27.18 Aligned_cols=35 Identities=14% Similarity=0.302 Sum_probs=25.4
Q ss_pred CChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCC
Q 004583 693 LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 735 (744)
Q Consensus 693 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 735 (744)
++..+|... +..+.+.+.+.|..|+++|||+|..+
T Consensus 22 ~t~~~la~~--------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 22 LTQSELAER--------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp EEHHHHHHH--------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred cCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 555555543 34577889999999999999999753
No 136
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=29.03 E-value=75 Score=22.23 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.2
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 004583 592 SDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (744)
Q Consensus 592 ~~~~t~~ei~~~t~~~~~~l~~~L~~L~ 619 (744)
...+|+++|++..|++...+.+..+...
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 137
>PHA02591 hypothetical protein; Provisional
Probab=28.87 E-value=67 Score=26.18 Aligned_cols=25 Identities=28% Similarity=0.333 Sum_probs=22.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhH
Q 004583 593 DRLSYSEIMTQLNLSDDDVVRLLHS 617 (744)
Q Consensus 593 ~~~t~~ei~~~t~~~~~~l~~~L~~ 617 (744)
.++|.++||+.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3789999999999999999988765
No 138
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=28.83 E-value=26 Score=30.45 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=37.6
Q ss_pred hceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhccc
Q 004583 679 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER 732 (744)
Q Consensus 679 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r 732 (744)
+|-.|++.+.....++..+|-.. +..+.+.+.++|..|.++|+|+|
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 34567778888888888887774 46788899999999999999985
No 139
>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=28.57 E-value=21 Score=28.25 Aligned_cols=53 Identities=25% Similarity=0.231 Sum_probs=30.9
Q ss_pred eeeeecccCCC-CCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 681 ASIVRIMKSRK-VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 681 A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
|.||..||++. .++.+||..++ + +..+ ++.++.|-+.+=|+-|++ .++|.|.|
T Consensus 8 ~~~VeymK~r~~Plt~~eI~d~l----~--~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 8 AKAVEYMKKRDHPLTLEEILDYL----S--LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHH-S-B-HHHHHHHH----T--SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHhcCCCcCHHHHHHHH----c--CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 56788888864 57777777655 3 4443 234566668888999974 47999976
No 140
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=28.45 E-value=1.3e+02 Score=21.99 Aligned_cols=34 Identities=24% Similarity=0.354 Sum_probs=25.3
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 617 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~ 617 (744)
...|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 17 ~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34445444333 69999999999999999987754
No 141
>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=28.26 E-value=27 Score=26.49 Aligned_cols=40 Identities=13% Similarity=0.226 Sum_probs=28.2
Q ss_pred ccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004583 687 MKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 734 (744)
Q Consensus 687 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 734 (744)
+-..+.++..+|-. .+..+...+-+.+..|.++|||+|..
T Consensus 12 l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 12 LYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 33445555555544 34568888999999999999999864
No 142
>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=27.43 E-value=83 Score=25.52 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=39.1
Q ss_pred HHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 580 TYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 580 ~~Q~~iLllFn~--~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
..|.++|...-. ..+++-.+|+..+|++...+-..++.|.. .+++.+.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~--~gLI~k~ 51 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEK--KGLIVKQ 51 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHH--CCCEEEE
Confidence 467888888764 35889999999999999999999999974 5677664
No 143
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=27.39 E-value=85 Score=35.75 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=43.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
.++..|..||..+...+.+|..+|++.+|++...+.+.+.+|.. -+++..
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 46889999999999888999999999999999999999999974 255554
No 144
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=27.26 E-value=64 Score=31.68 Aligned_cols=50 Identities=20% Similarity=0.228 Sum_probs=40.3
Q ss_pred EcHHHHHHHHhhcCC-----CCcCHHHHHHHhCCC-HHHHHHHHhHhhhccccccccC
Q 004583 578 VTTYQASALLLFNSS-----DRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~-----~~~t~~ei~~~t~~~-~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
++..|..||....+. -..|+.||++.+|++ ...+.++|..|. +-++|.+.
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 258899999999998 999999999997 44677764
No 145
>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=25.80 E-value=39 Score=34.08 Aligned_cols=33 Identities=9% Similarity=0.239 Sum_probs=28.3
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004583 708 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 741 (744)
Q Consensus 708 ~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 741 (744)
.+|..+...+.++|+.|++.|+|.|... +++|+
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 3699999999999999999999999864 56664
No 146
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.62 E-value=44 Score=25.03 Aligned_cols=27 Identities=7% Similarity=0.191 Sum_probs=23.8
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCCC
Q 004583 709 MFKPDFKAIKKRIEDLITRDYLERDKS 735 (744)
Q Consensus 709 ~F~~~~~~ik~~Ie~Liekeyi~r~~~ 735 (744)
.|..+...+.+.+..|.+.|+|.+.+.
T Consensus 29 ~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 29 QLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 577889999999999999999988763
No 147
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=25.55 E-value=1.1e+02 Score=25.73 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=35.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHh-CCCHHHHHHHHhHhhhccccccccC
Q 004583 582 QASALLLFNSSDRLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t-~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
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 5777654
No 148
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=25.50 E-value=94 Score=31.66 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=35.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
-|..|+..+++++.++.+||++.+|++...+++-|.-|..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3567888888888999999999999999999999998864
No 149
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=24.69 E-value=96 Score=31.18 Aligned_cols=58 Identities=10% Similarity=0.242 Sum_probs=42.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCCC
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 648 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f~ 648 (744)
+-..+.-+|.++..||+.+|.+.|+-|...|+.+|..++ ++.+.+. ...+|.+-..|.
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 344566788899999999999999999999999999886 3443321 135576655553
No 150
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=24.55 E-value=47 Score=27.87 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=32.4
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 709 MFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 709 ~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
++..+.+.-++.|..|.++|.|+.-..++..-+|.|
T Consensus 50 rlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 50 KYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 678889999999999999999998888888999976
No 151
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=24.52 E-value=92 Score=28.19 Aligned_cols=40 Identities=15% Similarity=0.272 Sum_probs=31.8
Q ss_pred ccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004583 687 MKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 734 (744)
Q Consensus 687 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~ 734 (744)
|..++.++.++|-+.+ .-+.+.+-+++.+|++.|.+.|..
T Consensus 37 L~~~~~~tvdelae~l--------nr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 37 LEENGPLTVDELAEIL--------NRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HhhcCCcCHHHHHHHH--------CccHHHHHHHHHHHHHcCCeeeee
Confidence 3467778887777654 447888999999999999999964
No 152
>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=24.22 E-value=37 Score=26.45 Aligned_cols=38 Identities=13% Similarity=0.263 Sum_probs=0.0
Q ss_pred HHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004583 703 VEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 741 (744)
Q Consensus 703 ~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 741 (744)
..++.++|..+...+.+++..|.+.|+|.+.+ ++.+++
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~-~~G~~V 64 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLEAEGLIERRP-GRGTFV 64 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET-TTEEEE
T ss_pred HHHHHHHhccCCcHHHHHHHHHHHCCcEEEEC-CceEEC
No 153
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=24.21 E-value=93 Score=29.69 Aligned_cols=40 Identities=25% Similarity=0.416 Sum_probs=29.7
Q ss_pred HHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 586 LLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 586 LllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
+|.++. +++|++||++.||++...+-..+.-|.. .++..+
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 444544 6999999999999999888777777753 345543
No 154
>PLN03239 histone acetyltransferase; Provisional
Probab=24.01 E-value=1.1e+02 Score=32.80 Aligned_cols=39 Identities=18% Similarity=0.293 Sum_probs=30.1
Q ss_pred HHHHHHHHhhcCC----CCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 580 TYQASALLLFNSS----DRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 580 ~~Q~~iLllFn~~----~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
-+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
T Consensus 266 YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 266 YWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred HHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 3445566544322 46999999999999999999999988
No 155
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=24.01 E-value=1.4e+02 Score=24.23 Aligned_cols=43 Identities=19% Similarity=0.229 Sum_probs=30.4
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 004583 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (744)
Q Consensus 582 Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~ 627 (744)
-+.||.... .++.+..+|+..++++...+.+.|..|.. .+++.
T Consensus 8 i~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~--~gLI~ 50 (77)
T PF14947_consen 8 IFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEE--KGLIK 50 (77)
T ss_dssp HHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CcCee
Confidence 345676665 56788999999999999999999999974 46664
No 156
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=24.00 E-value=1.2e+02 Score=31.08 Aligned_cols=43 Identities=23% Similarity=0.374 Sum_probs=34.3
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
.||+++-+ ++.|++||...++++...+..+|.-|. +.+++.+.
T Consensus 17 ~lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~ 59 (260)
T COG4742 17 DLLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQE 59 (260)
T ss_pred HHHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEec
Confidence 35565655 688999999999999999999999986 35666654
No 157
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.66 E-value=45 Score=33.85 Aligned_cols=32 Identities=25% Similarity=0.318 Sum_probs=27.6
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004583 709 MFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 741 (744)
Q Consensus 709 ~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 741 (744)
.|..+...++++|+.|++.|+|.|... +++|+
T Consensus 42 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 42 QYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 588899999999999999999999864 56664
No 158
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.57 E-value=63 Score=32.34 Aligned_cols=53 Identities=23% Similarity=0.332 Sum_probs=42.5
Q ss_pred eecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004583 684 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 744 (744)
Q Consensus 684 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~Yia 744 (744)
|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.---+|+..|+||.
T Consensus 206 v~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 206 VEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 44557777777777655 477777777789999999999999889999999984
No 159
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=23.47 E-value=1.3e+02 Score=29.92 Aligned_cols=42 Identities=21% Similarity=0.263 Sum_probs=36.9
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
..|.-+..||.+.-. ++|.+|||+.++++...++.++..+..
T Consensus 143 ~LS~RE~eVL~Lia~--G~SnkEIA~~L~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 143 KVTKYQNDVFILYSF--GFSHEYIAQLLNITVGSSKNKISEILK 184 (217)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 568899999999877 579999999999999999999888763
No 160
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=23.46 E-value=55 Score=28.64 Aligned_cols=42 Identities=19% Similarity=0.306 Sum_probs=30.9
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhccc--CCCCCC
Q 004583 689 SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER--DKSNPN 738 (744)
Q Consensus 689 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r--~~~d~~ 738 (744)
..+.++..+|... ...+.+.+-+.|..|.++|||.| +++|+.
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R 83 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERSEDDER 83 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCCcccCC
Confidence 4456777777664 34567889999999999999997 455543
No 161
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.34 E-value=1.5e+02 Score=26.84 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=36.4
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 580 ~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.+.+-|+-+.-+++.+|+.++...||.+-..+++++.-|+.
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa 52 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA 52 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45677888888899999999999999999999999999874
No 162
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=22.98 E-value=1.3e+02 Score=25.36 Aligned_cols=33 Identities=15% Similarity=0.323 Sum_probs=23.1
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 587 LLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 587 llFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.+..+... ++..|.+.||||...++.+|.+|..
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~ 47 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPE 47 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGG
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhc
Confidence 34445555 9999999999999999999999974
No 163
>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=22.79 E-value=1e+02 Score=32.06 Aligned_cols=59 Identities=14% Similarity=0.290 Sum_probs=32.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEeccCC
Q 004583 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (744)
Q Consensus 579 s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~~~~~i~~~~~~~~N~~f 647 (744)
+-+--.|.-+|.++..||+.+|.+.|+-|+..|+.+|..++ ++.+.+. ....|.|=..|
T Consensus 215 ~eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 215 NELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 33445677889999999999999999999999999999875 4555431 13456654444
No 164
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.55 E-value=1.5e+02 Score=25.27 Aligned_cols=52 Identities=17% Similarity=0.209 Sum_probs=43.1
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 576 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 576 l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
+..+.....||..+...+.=...-|+..+++|.+++...|..|.. .++|.+.
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~--~GLler~ 54 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEE--MGLLERV 54 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEe
Confidence 345677788999888877777788999999999999999999974 5788765
No 165
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=22.48 E-value=1.7e+02 Score=28.38 Aligned_cols=44 Identities=16% Similarity=0.196 Sum_probs=35.4
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
-++.-++.++..|..+|+..+|++..++.++|-.|.. .+.+.+.
T Consensus 17 ~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~--~~~v~~~ 60 (183)
T PHA03103 17 KEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQR--EGMVYMS 60 (183)
T ss_pred HHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHh--cCceecC
Confidence 3566677788999999999999999999999999973 3445444
No 166
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.39 E-value=1.5e+02 Score=27.33 Aligned_cols=39 Identities=26% Similarity=0.233 Sum_probs=31.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
+|.-|..|+.++ ..++|.+||++.+|++...+...+...
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 577788888886 468999999999999998888655543
No 167
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=22.30 E-value=1.3e+02 Score=29.84 Aligned_cols=42 Identities=29% Similarity=0.351 Sum_probs=37.3
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
..|.-|..||.++-+ ++|-+||++.+++++..++.++..+..
T Consensus 148 ~LT~RE~eVL~lla~--G~snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 148 LLTPRELEVLRLLAE--GLSNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 468999999999976 579999999999999999999988864
No 168
>PRK11050 manganese transport regulator MntR; Provisional
Probab=22.16 E-value=1.7e+02 Score=27.36 Aligned_cols=43 Identities=16% Similarity=0.199 Sum_probs=34.7
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 584 ~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
.|+.++..++.++..+|++.++++...+.+.|..|.. .+++.+
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 356654
No 169
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.01 E-value=52 Score=33.45 Aligned_cols=48 Identities=15% Similarity=0.373 Sum_probs=35.6
Q ss_pred cccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004583 686 IMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 741 (744)
Q Consensus 686 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 741 (744)
.++....|.-+. +|...|..+...++++|+.|++.|+|.|... +++|+
T Consensus 28 ~~~~G~~LPsE~-------eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 28 HYRCGDYLPAEQ-------QLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred ccCCCCcCCCHH-------HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 466666665432 2333699999999999999999999999864 46654
No 170
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=21.72 E-value=52 Score=33.24 Aligned_cols=32 Identities=19% Similarity=0.400 Sum_probs=27.7
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004583 709 MFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 741 (744)
Q Consensus 709 ~F~~~~~~ik~~Ie~Liekeyi~r~~~d~~~y~ 741 (744)
+|..+...+.++|+.|++.|+|.|... +++|+
T Consensus 41 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 41 RFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 599999999999999999999999864 46654
No 171
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=21.36 E-value=62 Score=24.25 Aligned_cols=22 Identities=18% Similarity=0.531 Sum_probs=19.0
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 004583 594 RLSYSEIMTQLNLSDDDVVRLL 615 (744)
Q Consensus 594 ~~t~~ei~~~t~~~~~~l~~~L 615 (744)
.+++.||++.+|++..++.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999998877
No 172
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.34 E-value=55 Score=29.44 Aligned_cols=52 Identities=23% Similarity=0.353 Sum_probs=45.0
Q ss_pred hhhhceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCC
Q 004583 676 RYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 735 (744)
Q Consensus 676 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r~~~ 735 (744)
...|.+-||-..++++.++..+|... +..+...+++.+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~--------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAK--------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHH--------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 36788999999999999999999885 45678889999999999999988763
No 173
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.22 E-value=1.7e+02 Score=28.17 Aligned_cols=41 Identities=24% Similarity=0.244 Sum_probs=36.3
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 578 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
+|.-+.-||.+.-+ +.|..||++.++++...++.++..+..
T Consensus 134 LSpRErEVLrLLAq--GkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 134 FSVTERHLLKLIAS--GYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred CCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 68899999998877 578999999999999999998888763
No 174
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.21 E-value=1.1e+02 Score=22.24 Aligned_cols=21 Identities=24% Similarity=0.425 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHh
Q 004583 596 SYSEIMTQLNLSDDDVVRLLH 616 (744)
Q Consensus 596 t~~ei~~~t~~~~~~l~~~L~ 616 (744)
|+.||++..|++...+-+.|.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 689999999999999887775
No 175
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.06 E-value=1.5e+02 Score=27.46 Aligned_cols=39 Identities=21% Similarity=0.260 Sum_probs=29.8
Q ss_pred EEcHHHHHHHHh-hcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 004583 577 IVTTYQASALLL-FNSSDRLSYSEIMTQLNLSDDDVVRLLHS 617 (744)
Q Consensus 577 ~~s~~Q~~iLll-Fn~~~~~t~~ei~~~t~~~~~~l~~~L~~ 617 (744)
.+|..|..|+.+ +- .+++++||++.+|+|...+...+.-
T Consensus 111 ~L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 346667777766 43 4689999999999999998876653
No 176
>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=21.04 E-value=1.6e+02 Score=24.78 Aligned_cols=41 Identities=27% Similarity=0.296 Sum_probs=32.1
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 004583 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (744)
Q Consensus 580 ~~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~ 620 (744)
.....+..++.....+++++|++.++++.+++...+..+..
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 33444555556778999999999999999999998888864
No 177
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.59 E-value=3.1e+02 Score=22.59 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=36.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 004583 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (744)
Q Consensus 581 ~Q~~iLllFn~~~~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~~~ 630 (744)
+++.|=+.-..+..+.-.+|++.++.+...++..+..|- ..++|.+.|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 344444555567789999999999999999999999986 467886543
No 178
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=20.57 E-value=1.6e+02 Score=23.35 Aligned_cols=33 Identities=30% Similarity=0.377 Sum_probs=28.1
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 004583 594 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (744)
Q Consensus 594 ~~t~~ei~~~t~~~~~~l~~~L~~L~~~k~~iL~~ 628 (744)
.+|-++|++.+|++...+.+.|..|.. -+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~--~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKD--EGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHH--TTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 478999999999999999999999963 466654
No 179
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.49 E-value=1.4e+02 Score=33.22 Aligned_cols=37 Identities=22% Similarity=0.339 Sum_probs=29.5
Q ss_pred HHHHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 004583 582 QASALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (744)
Q Consensus 582 Q~~iLllF-n~~~~~t~~ei~~~t~~~~~~l~~~L~~L 618 (744)
-..||-.+ +....+|+++|++.|||..+++..+|+.|
T Consensus 361 ~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 361 TRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 33455333 34468999999999999999999999988
No 180
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=20.30 E-value=65 Score=29.67 Aligned_cols=26 Identities=8% Similarity=0.257 Sum_probs=21.7
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCC
Q 004583 709 MFKPDFKAIKKRIEDLITRDYLERDK 734 (744)
Q Consensus 709 ~F~~~~~~ik~~Ie~Liekeyi~r~~ 734 (744)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 34557778999999999999999964
No 181
>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=20.29 E-value=1.1e+02 Score=26.38 Aligned_cols=52 Identities=10% Similarity=0.118 Sum_probs=41.4
Q ss_pred ceeeeecccCCCCCChHHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhccc
Q 004583 680 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER 732 (744)
Q Consensus 680 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liekeyi~r 732 (744)
+-+|..++. .+.++=-+|.+++.+.....+.++...+=..+..|-++|+|++
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 334455555 4677888999998887665578888999999999999999998
No 182
>PRK06474 hypothetical protein; Provisional
Probab=20.18 E-value=2.4e+02 Score=27.22 Aligned_cols=51 Identities=14% Similarity=0.214 Sum_probs=39.6
Q ss_pred EEcHHHHHHHHhhcCCC-CcCHHHHHHHh-CCCHHHHHHHHhHhhhccccccccC
Q 004583 577 IVTTYQASALLLFNSSD-RLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 629 (744)
Q Consensus 577 ~~s~~Q~~iLllFn~~~-~~t~~ei~~~t-~~~~~~l~~~L~~L~~~k~~iL~~~ 629 (744)
-.++.-..||..+-..+ .+|..+|++.+ +++...+-++|..|. +.+++...
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~ 60 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVV 60 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34566677776665544 49999999999 799999999999997 45777754
Done!