Query 003986
Match_columns 781
No_of_seqs 214 out of 1072
Neff 8.3
Searched_HMMs 46136
Date Thu Mar 28 15:31:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003986.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003986hhsearch_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 5E-118 1E-122 1020.6 64.8 718 6-779 5-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 2E-110 5E-115 913.5 62.2 724 7-781 16-773 (773)
3 KOG2284 E3 ubiquitin ligase, C 100.0 4E-108 1E-112 836.6 46.7 684 1-781 1-728 (728)
4 KOG2167 Cullins [Cell cycle co 100.0 4E-107 8E-112 868.1 46.2 646 65-781 2-661 (661)
5 PF00888 Cullin: Cullin family 100.0 5.9E-90 1.3E-94 809.6 62.6 586 15-648 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 2.3E-88 5E-93 698.0 54.9 715 6-781 8-777 (777)
7 smart00182 CULLIN Cullin. 100.0 8.8E-32 1.9E-36 255.6 17.8 141 428-569 1-142 (142)
8 KOG2165 Anaphase-promoting com 99.9 8.2E-26 1.8E-30 247.6 22.2 222 422-648 442-665 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.7 3.1E-19 6.6E-24 145.8 1.9 68 671-775 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 97.0 0.019 4.1E-07 55.1 14.4 137 8-152 2-156 (158)
11 TIGR01610 phage_O_Nterm phage 92.7 0.35 7.5E-06 42.3 6.4 65 576-648 21-93 (95)
12 KOG2167 Cullins [Cell cycle co 91.4 7.3 0.00016 44.5 16.2 203 13-234 112-324 (661)
13 PF02082 Rrf2: Transcriptional 90.9 0.67 1.4E-05 39.4 6.1 59 581-646 11-70 (83)
14 PF09339 HTH_IclR: IclR helix- 90.6 0.38 8.3E-06 36.8 4.0 45 583-629 6-51 (52)
15 PF13412 HTH_24: Winged helix- 90.6 0.52 1.1E-05 35.3 4.6 42 579-620 2-43 (48)
16 PF12802 MarR_2: MarR family; 89.9 0.44 9.5E-06 37.7 4.0 51 578-630 3-55 (62)
17 PF08220 HTH_DeoR: DeoR-like h 89.0 1 2.2E-05 35.3 5.2 46 582-629 2-47 (57)
18 PF01047 MarR: MarR family; I 86.6 0.55 1.2E-05 36.8 2.5 50 578-629 1-50 (59)
19 PF13463 HTH_27: Winged helix 86.3 1.2 2.6E-05 35.9 4.4 50 578-629 1-51 (68)
20 TIGR02337 HpaR homoprotocatech 83.8 1.9 4.2E-05 39.1 5.1 52 577-630 25-76 (118)
21 PF01022 HTH_5: Bacterial regu 82.5 3.1 6.8E-05 31.0 4.9 43 581-626 3-45 (47)
22 PRK11512 DNA-binding transcrip 81.5 2.9 6.2E-05 39.5 5.5 52 577-630 37-88 (144)
23 PF12840 HTH_20: Helix-turn-he 81.3 2.2 4.8E-05 33.7 3.9 49 579-629 9-57 (61)
24 PF08279 HTH_11: HTH domain; 78.6 4.2 9.1E-05 31.2 4.6 37 584-620 4-41 (55)
25 smart00346 HTH_ICLR helix_turn 77.5 6 0.00013 33.8 5.8 55 583-645 8-63 (91)
26 TIGR01889 Staph_reg_Sar staphy 77.2 5.8 0.00012 35.5 5.7 52 577-630 22-77 (109)
27 PF09012 FeoC: FeoC like trans 76.9 1.4 3E-05 36.0 1.5 44 684-772 6-49 (69)
28 PRK11920 rirA iron-responsive 76.7 7.1 0.00015 37.4 6.5 55 585-646 15-69 (153)
29 smart00550 Zalpha Z-DNA-bindin 76.5 4 8.7E-05 33.2 4.1 47 581-629 7-55 (68)
30 PRK10857 DNA-binding transcrip 75.4 8.2 0.00018 37.4 6.6 57 583-646 13-70 (164)
31 smart00347 HTH_MARR helix_turn 74.0 5.8 0.00013 34.2 4.9 53 575-629 5-57 (101)
32 PF01978 TrmB: Sugar-specific 73.9 2.8 6E-05 34.0 2.5 49 579-629 7-55 (68)
33 PRK15090 DNA-binding transcrip 72.2 7.7 0.00017 40.6 6.1 56 583-646 17-72 (257)
34 TIGR02010 IscR iron-sulfur clu 70.7 11 0.00024 35.1 6.2 55 584-645 14-69 (135)
35 PF04492 Phage_rep_O: Bacterio 70.7 14 0.0003 32.6 6.3 61 577-647 29-97 (100)
36 TIGR02698 CopY_TcrY copper tra 70.5 3.8 8.1E-05 38.1 2.9 32 749-781 34-65 (130)
37 smart00420 HTH_DEOR helix_turn 70.3 8.6 0.00019 28.7 4.5 44 583-628 3-46 (53)
38 PF04703 FaeA: FaeA-like prote 70.2 9.9 0.00021 30.3 4.8 45 585-631 5-50 (62)
39 COG3355 Predicted transcriptio 70.1 10 0.00023 34.8 5.5 38 590-629 38-75 (126)
40 PRK13777 transcriptional regul 69.2 9.5 0.00021 37.8 5.5 53 576-630 41-93 (185)
41 COG1959 Predicted transcriptio 68.7 12 0.00026 35.7 6.0 59 581-646 11-70 (150)
42 PRK03573 transcriptional regul 67.3 10 0.00022 35.6 5.3 53 576-630 27-80 (144)
43 PF05732 RepL: Firmicute plasm 67.1 10 0.00022 36.8 5.1 48 594-650 75-122 (165)
44 PF13404 HTH_AsnC-type: AsnC-t 67.0 8.9 0.00019 28.0 3.6 36 583-618 6-41 (42)
45 smart00419 HTH_CRP helix_turn_ 65.7 13 0.00029 27.2 4.6 33 594-628 8-40 (48)
46 PF13601 HTH_34: Winged helix 64.0 6.2 0.00014 33.2 2.7 44 582-627 2-45 (80)
47 PF08280 HTH_Mga: M protein tr 63.9 9.4 0.0002 30.0 3.6 38 582-619 7-44 (59)
48 PHA00738 putative HTH transcri 63.4 16 0.00035 32.4 5.2 67 575-647 7-73 (108)
49 PF08784 RPA_C: Replication pr 63.3 12 0.00026 33.0 4.5 44 577-620 44-91 (102)
50 PRK10870 transcriptional repre 62.2 18 0.00038 35.6 5.9 52 577-630 52-105 (176)
51 PF03965 Penicillinase_R: Peni 61.6 7.4 0.00016 35.2 2.9 32 749-781 33-64 (115)
52 TIGR03879 near_KaiC_dom probab 61.6 11 0.00024 31.1 3.6 36 590-627 28-63 (73)
53 TIGR00738 rrf2_super rrf2 fami 61.2 20 0.00043 33.0 5.9 45 582-628 12-57 (132)
54 COG3682 Predicted transcriptio 61.2 6.5 0.00014 35.9 2.4 62 678-781 6-67 (123)
55 PF05584 Sulfolobus_pRN: Sulfo 61.1 20 0.00043 29.4 4.9 46 579-628 5-50 (72)
56 PRK11569 transcriptional repre 59.7 17 0.00037 38.4 5.8 54 583-644 31-85 (274)
57 COG1414 IclR Transcriptional r 59.7 19 0.0004 37.5 5.9 46 583-630 7-53 (246)
58 PF09763 Sec3_C: Exocyst compl 59.6 3.9E+02 0.0085 32.4 19.5 22 344-365 680-701 (701)
59 TIGR01884 cas_HTH CRISPR locus 58.7 15 0.00033 36.9 4.9 51 577-629 140-190 (203)
60 cd00090 HTH_ARSR Arsenical Res 58.6 21 0.00045 28.5 5.0 47 579-628 6-52 (78)
61 PRK10163 DNA-binding transcrip 58.0 20 0.00044 37.8 6.0 56 583-646 28-84 (271)
62 PF01978 TrmB: Sugar-specific 57.4 11 0.00023 30.5 2.9 32 749-780 34-65 (68)
63 PRK10141 DNA-binding transcrip 57.4 16 0.00034 33.3 4.2 58 582-645 18-75 (117)
64 TIGR02431 pcaR_pcaU beta-ketoa 55.9 24 0.00051 36.7 6.0 44 583-628 12-56 (248)
65 smart00345 HTH_GNTR helix_turn 55.7 21 0.00045 27.3 4.3 39 589-629 14-53 (60)
66 TIGR02944 suf_reg_Xantho FeS a 55.7 27 0.00058 32.2 5.7 55 584-645 13-69 (130)
67 smart00344 HTH_ASNC helix_turn 55.3 20 0.00044 31.7 4.7 45 581-627 4-48 (108)
68 PRK09834 DNA-binding transcrip 55.0 22 0.00048 37.3 5.7 55 583-645 14-69 (263)
69 smart00550 Zalpha Z-DNA-bindin 51.2 15 0.00033 29.8 2.8 29 749-777 34-62 (68)
70 PF10771 DUF2582: Protein of u 51.0 22 0.00048 28.7 3.6 38 583-620 11-48 (65)
71 COG1846 MarR Transcriptional r 51.0 29 0.00063 30.9 5.1 51 578-630 20-70 (126)
72 PRK11014 transcriptional repre 50.8 40 0.00086 31.7 6.1 50 589-645 20-69 (141)
73 COG2345 Predicted transcriptio 50.6 21 0.00046 36.1 4.3 42 584-627 15-56 (218)
74 PF13730 HTH_36: Helix-turn-he 49.7 40 0.00087 25.6 4.9 25 596-620 27-51 (55)
75 cd00092 HTH_CRP helix_turn_hel 49.6 38 0.00083 26.7 5.0 35 593-629 24-58 (67)
76 PF13463 HTH_27: Winged helix 49.1 16 0.00035 29.1 2.7 27 749-775 30-58 (68)
77 PF11994 DUF3489: Protein of u 46.5 45 0.00097 27.4 4.7 48 579-626 9-56 (72)
78 smart00418 HTH_ARSR helix_turn 46.2 38 0.00083 26.0 4.5 35 592-628 8-42 (66)
79 PF04545 Sigma70_r4: Sigma-70, 45.7 49 0.0011 24.7 4.8 32 584-617 12-43 (50)
80 PF01325 Fe_dep_repress: Iron 45.5 43 0.00092 26.5 4.5 44 585-630 13-56 (60)
81 PF12324 HTH_15: Helix-turn-he 45.1 52 0.0011 27.4 5.0 39 581-619 25-63 (77)
82 PF08220 HTH_DeoR: DeoR-like h 45.0 14 0.00031 28.8 1.7 45 682-771 4-48 (57)
83 PF08221 HTH_9: RNA polymerase 45.0 30 0.00064 27.6 3.6 34 591-626 24-57 (62)
84 PF02002 TFIIE_alpha: TFIIE al 43.3 21 0.00045 31.7 2.7 44 582-627 15-58 (105)
85 PF09012 FeoC: FeoC like trans 42.7 30 0.00065 28.0 3.4 36 585-620 5-40 (69)
86 PRK10434 srlR DNA-bindng trans 42.3 31 0.00067 36.1 4.3 47 581-629 6-52 (256)
87 TIGR02702 SufR_cyano iron-sulf 40.9 59 0.0013 32.6 5.9 44 584-629 5-48 (203)
88 PRK06266 transcription initiat 39.9 37 0.00081 33.4 4.1 45 581-627 23-67 (178)
89 TIGR00373 conserved hypothetic 39.8 51 0.0011 31.7 5.0 43 583-627 17-59 (158)
90 PF02796 HTH_7: Helix-turn-hel 39.3 39 0.00085 24.8 3.2 30 585-616 14-43 (45)
91 TIGR02844 spore_III_D sporulat 39.1 49 0.0011 27.9 4.1 35 581-616 7-41 (80)
92 COG4189 Predicted transcriptio 39.0 44 0.00096 33.8 4.4 49 579-629 22-70 (308)
93 smart00421 HTH_LUXR helix_turn 38.2 66 0.0014 24.0 4.6 39 579-619 5-43 (58)
94 PF08281 Sigma70_r4_2: Sigma-7 37.9 57 0.0012 24.7 4.1 24 593-616 25-48 (54)
95 cd06170 LuxR_C_like C-terminal 37.6 68 0.0015 24.0 4.6 39 579-619 2-40 (57)
96 PRK11169 leucine-responsive tr 37.4 49 0.0011 32.0 4.5 48 578-627 12-59 (164)
97 PF01853 MOZ_SAS: MOZ/SAS fami 36.9 34 0.00074 33.8 3.3 26 594-619 150-175 (188)
98 PF14394 DUF4423: Domain of un 36.8 83 0.0018 30.7 6.0 54 575-630 19-75 (171)
99 PRK04424 fatty acid biosynthes 35.3 44 0.00096 33.1 3.9 46 581-628 8-53 (185)
100 COG1349 GlpR Transcriptional r 35.2 48 0.001 34.6 4.4 46 582-629 7-52 (253)
101 smart00418 HTH_ARSR helix_turn 35.1 41 0.00088 25.8 3.0 26 749-774 22-47 (66)
102 PF01726 LexA_DNA_bind: LexA D 34.2 41 0.00089 27.1 2.8 24 750-773 39-62 (65)
103 PRK11179 DNA-binding transcrip 33.1 66 0.0014 30.6 4.6 49 577-627 6-54 (153)
104 PF06784 UPF0240: Uncharacteri 32.8 69 0.0015 31.5 4.7 63 552-619 97-161 (179)
105 PF09681 Phage_rep_org_N: N-te 32.8 58 0.0013 29.8 3.9 49 579-629 28-86 (121)
106 PRK10681 DNA-binding transcrip 32.6 60 0.0013 33.8 4.6 39 581-619 8-46 (252)
107 PF07393 Sec10: Exocyst comple 32.3 9.9E+02 0.021 29.0 15.7 136 145-296 105-264 (710)
108 PF09756 DDRGK: DDRGK domain; 32.2 26 0.00057 34.7 1.7 58 679-781 100-157 (188)
109 COG4190 Predicted transcriptio 32.2 1.3E+02 0.0027 27.9 5.8 68 579-648 63-133 (144)
110 PF00325 Crp: Bacterial regula 32.0 62 0.0013 22.2 2.9 26 594-619 2-27 (32)
111 PRK13509 transcriptional repre 31.7 69 0.0015 33.4 4.8 47 581-629 6-52 (251)
112 PF00196 GerE: Bacterial regul 31.4 73 0.0016 24.6 3.8 41 578-620 4-44 (58)
113 cd07377 WHTH_GntR Winged helix 31.4 89 0.0019 24.2 4.5 32 596-629 27-58 (66)
114 COG1654 BirA Biotin operon rep 31.0 1.3E+02 0.0028 25.4 5.3 42 586-627 11-52 (79)
115 PRK00215 LexA repressor; Valid 31.0 95 0.0021 31.1 5.6 51 578-630 2-58 (205)
116 PF12802 MarR_2: MarR family; 30.9 37 0.00079 26.4 2.1 24 749-772 33-56 (62)
117 COG1522 Lrp Transcriptional re 30.2 85 0.0018 29.6 4.9 49 578-628 6-54 (154)
118 PF08318 COG4: COG4 transport 29.9 7.5E+02 0.016 26.8 16.0 164 273-452 15-214 (331)
119 PF01726 LexA_DNA_bind: LexA D 29.3 90 0.0019 25.1 4.0 51 578-630 4-60 (65)
120 TIGR01714 phage_rep_org_N phag 29.1 67 0.0015 29.3 3.6 49 579-629 28-84 (119)
121 PRK10906 DNA-binding transcrip 29.0 68 0.0015 33.4 4.3 47 581-629 6-52 (252)
122 PRK13239 alkylmercury lyase; P 28.7 97 0.0021 31.2 5.0 40 580-619 22-61 (206)
123 PF01047 MarR: MarR family; I 28.4 33 0.00071 26.5 1.4 23 749-771 29-51 (59)
124 cd07153 Fur_like Ferric uptake 28.3 55 0.0012 29.3 3.0 57 683-779 6-63 (116)
125 smart00531 TFIIE Transcription 26.9 74 0.0016 30.2 3.7 31 591-621 12-42 (147)
126 cd06171 Sigma70_r4 Sigma70, re 26.8 1.3E+02 0.0028 21.7 4.5 40 578-618 11-50 (55)
127 KOG2747 Histone acetyltransfer 26.4 79 0.0017 34.9 4.2 64 554-619 282-354 (396)
128 smart00344 HTH_ASNC helix_turn 26.2 42 0.0009 29.6 1.8 47 679-770 4-50 (108)
129 TIGR00498 lexA SOS regulatory 25.9 70 0.0015 31.8 3.6 51 578-630 4-60 (199)
130 PF13384 HTH_23: Homeodomain-l 25.5 80 0.0017 23.4 3.0 32 585-618 10-41 (50)
131 PHA02591 hypothetical protein; 24.9 86 0.0019 26.1 3.1 25 593-617 58-82 (83)
132 PF04967 HTH_10: HTH DNA bindi 24.6 1.1E+02 0.0024 23.5 3.6 30 589-618 18-47 (53)
133 KOG2905 Transcription initiati 24.5 97 0.0021 31.7 4.1 59 581-649 187-245 (254)
134 PRK09802 DNA-binding transcrip 24.3 91 0.002 32.8 4.2 48 580-629 17-64 (269)
135 PRK04172 pheS phenylalanyl-tRN 24.3 1.1E+02 0.0023 35.5 5.1 50 577-628 3-52 (489)
136 PLN03238 probable histone acet 24.3 1.2E+02 0.0025 32.1 4.8 38 581-618 209-247 (290)
137 PRK10411 DNA-binding transcrip 24.0 1E+02 0.0023 31.8 4.5 40 581-620 5-44 (240)
138 PF13542 HTH_Tnp_ISL3: Helix-t 23.7 1.8E+02 0.0039 21.6 4.7 35 581-617 16-50 (52)
139 PF02270 TFIIF_beta: Transcrip 23.5 1E+02 0.0022 32.7 4.3 57 581-647 217-273 (275)
140 COG5045 Ribosomal protein S10E 23.3 47 0.001 28.3 1.4 34 730-771 26-59 (105)
141 PF00165 HTH_AraC: Bacterial r 23.2 1.1E+02 0.0024 21.8 3.3 28 592-619 6-33 (42)
142 PF01638 HxlR: HxlR-like helix 23.0 1.3E+02 0.0029 25.6 4.3 45 582-629 7-52 (90)
143 PF05158 RNA_pol_Rpc34: RNA po 23.0 83 0.0018 34.2 3.6 44 577-620 81-126 (327)
144 PF13545 HTH_Crp_2: Crp-like h 21.5 1.6E+02 0.0035 23.8 4.4 33 594-628 28-60 (76)
145 PLN02999 photosystem II oxygen 21.5 6E+02 0.013 24.9 8.5 62 45-118 126-189 (190)
146 PF10007 DUF2250: Uncharacteri 21.0 1.7E+02 0.0037 25.4 4.4 52 576-629 3-54 (92)
147 PF04182 B-block_TFIIIC: B-blo 20.9 1.4E+02 0.003 24.7 3.8 49 580-630 2-52 (75)
148 PF06163 DUF977: Bacterial pro 20.8 1.8E+02 0.0038 26.8 4.6 41 580-620 12-52 (127)
149 PF09904 HTH_43: Winged helix- 20.7 1.6E+02 0.0034 25.4 4.0 33 587-620 15-47 (90)
150 TIGR01889 Staph_reg_Sar staphy 20.7 91 0.002 27.7 2.9 23 749-771 55-77 (109)
151 PF01399 PCI: PCI domain; Int 20.1 1.8E+02 0.0039 24.9 4.7 40 581-620 47-86 (105)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=5.1e-118 Score=1020.63 Aligned_cols=718 Identities=66% Similarity=1.091 Sum_probs=670.7
Q ss_pred CCCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhcccchh
Q 003986 6 RKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSI 85 (781)
Q Consensus 6 ~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l 85 (781)
+.+.+++..|+.+++++.++....++-+.+.++.-+++.+|+++|++|+++++.+..++||+++++++.+|+.+.+.+..
T Consensus 5 ~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~~ 84 (725)
T KOG2166|consen 5 PKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPAL 84 (725)
T ss_pred ccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888764444457778899999999999999966666699999999999999998877777
Q ss_pred hccCcHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhcC-CCCcHHHHH-HHHHHHHHhh-hhHHHHHHHHHHHHHHH
Q 003986 86 REKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARR-SLPPLNEVG-LTCFRDLVYT-ELNGKVRDAVITLIDQE 162 (781)
Q Consensus 86 ~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~-~~~~i~~l~-l~lf~~~v~~-~l~~~l~~~ll~~I~~~ 162 (781)
....++.++..+...|.+|+.++.+++++|.||||+||.+. +..++.+++ +.+|+..++. ++.+.++++++.+|..+
T Consensus 85 ~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~e 164 (725)
T KOG2166|consen 85 REKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHKE 164 (725)
T ss_pred HhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHhh
Confidence 77778899999999999999999999999999999999876 666777766 8889888887 59999999999999999
Q ss_pred hcCCccCHHHHHHHHHHHHHhcCCcccccHHHhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHcccc
Q 003986 163 REGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYL 242 (781)
Q Consensus 163 R~g~~i~~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~eYl~~v~~~l~eE~~r~~~~l 242 (781)
|.|+.+|+..|+++++++..+|.+...+|..+||++|++.|..||..++++|+...++.+|+.+++.++.+|..|+..|+
T Consensus 165 R~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl 244 (725)
T KOG2166|consen 165 REGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYL 244 (725)
T ss_pred cccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999889999999999999999999999999999988999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhH
Q 003986 243 HSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLA 322 (781)
Q Consensus 243 ~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~I~~~g~~i~~~~ 322 (781)
+..+.+++...+..+++..+++.+++..++|+..|+.+++.++|.+||+|+++++.|++.+++.++.|++.+|..++...
T Consensus 245 ~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~ 324 (725)
T KOG2166|consen 245 HSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARP 324 (725)
T ss_pred hhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888776
Q ss_pred HHHhhhhhhhcccccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHHH
Q 003986 323 EDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNIL 402 (781)
Q Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~I~~l~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN~~~~~~~~~e~La~y~D~~l 402 (781)
.... ..+|..++..+++++++|..++..||+++..|..+++.||..|+|.+.. ..+|+||+|||.++
T Consensus 325 ~~~~-----------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~l 391 (725)
T KOG2166|consen 325 AETA-----------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDIL 391 (725)
T ss_pred hhhc-----------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHHh
Confidence 5321 1468899999999999999999999999999999999999999999863 23699999999999
Q ss_pred hcCCCCCCCHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHH
Q 003986 403 KKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVT 482 (781)
Q Consensus 403 k~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~ 482 (781)
|++ ..+.++++++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|++.|+.||.+|+++||.+||++|++|++
T Consensus 392 kk~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~ 470 (725)
T KOG2166|consen 392 KKG-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFT 470 (725)
T ss_pred ccc-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcc
Confidence 994 4677899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcce
Q 003986 483 DLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGT 562 (781)
Q Consensus 483 D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~RkL~w~~~l~~ 562 (781)
|+..|++++..|+++. +.....+++|.|.|||+|+||.+++.++.||++|.++++.|..||..+|+||+|.|+|++|.
T Consensus 471 D~~~s~~l~~~F~~~~--~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~ 548 (725)
T KOG2166|consen 471 DLTLSRELQTAFADYA--NYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGT 548 (725)
T ss_pred cHHHHHHHHHHHHhhh--chhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCc
Confidence 9999999999999871 12223579999999999999998888899999999999999999999999999999999999
Q ss_pred EEEEeEecCeeEEEEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEE
Q 003986 563 CNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFE 642 (781)
Q Consensus 563 ~~i~~~~~~~~~~l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~ 642 (781)
|+|.++|.+++++++||++||+||++||+.+.+|+++|.+.|+++.+++.++|+||++.|.+++.. |.++. ++++.|.
T Consensus 549 ~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~ 626 (725)
T KOG2166|consen 549 GEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFA 626 (725)
T ss_pred eEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEE
Confidence 999999999999999999999999999999999999999999999999999999999888777766 76766 8899999
Q ss_pred EccCCCCCceeEEecCCCchhhhhhHHhHHHhhhhhhcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhh
Q 003986 643 FNSKFTDKMRRIKIPLPPVDEKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFF 722 (781)
Q Consensus 643 lN~~F~~~~~~i~i~~~~~~e~~~~~~~v~~~R~~~I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~ 722 (781)
+|.+|+++++|+++|.++..+.+.+.+.+++||++.|+||||||||+||++.|++|+.||++|++++|.
T Consensus 627 ~N~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~----------- 695 (725)
T KOG2166|consen 627 FNSKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFK----------- 695 (725)
T ss_pred eeccccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcC-----------
Confidence 999999999999999888888888999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHHHHhhhcccccccCCCCCccee
Q 003986 723 FFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 779 (781)
Q Consensus 723 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~Li~~eyl~r~~~~~~~~~Y 779 (781)
|++.+||+|||.|||||||+|| +|+++|+|
T Consensus 696 --------------------------p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 696 --------------------------PDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred --------------------------CCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 9999999999999999999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-110 Score=913.48 Aligned_cols=724 Identities=31% Similarity=0.532 Sum_probs=637.2
Q ss_pred CCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCC------------chHHHHHHHHHHHH
Q 003986 7 KTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHD------------YSQQLYDKYRESFE 74 (781)
Q Consensus 7 ~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~------------~~e~LY~~l~~~l~ 74 (781)
+..||+++|..+++||.+|..-+.. .++...||++|+.+|+.|.++++.. .+..+|+++....+
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 4579999999999999999855543 3556679999999999999985531 37789999999999
Q ss_pred HHHHhcccchhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhc-----CCCCcHHHHHHHHHHHHHhhhhHH
Q 003986 75 EYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR-----RSLPPLNEVGLTCFRDLVYTELNG 149 (781)
Q Consensus 75 ~~l~~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~-----~~~~~i~~l~l~lf~~~v~~~l~~ 149 (781)
+|+...- ........+.+|..++..|++|..++.+++.+|.||||+|++. .....+.++++..|+.++|.++.+
T Consensus 92 ~~i~~~~-~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~ 170 (773)
T COG5647 92 NYIEEYN-RGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVD 170 (773)
T ss_pred HHHHHhc-ccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhH
Confidence 9988642 2222223478999999999999999999999999999999992 233457889999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhcC------CcccccHHHhHHHHHHHHHHHHHHHHHHHHhcCChhHH
Q 003986 150 KVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGM------GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDY 223 (781)
Q Consensus 150 ~l~~~ll~~I~~~R~g~~i~~~~lk~~i~~l~~l~~------~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~eY 223 (781)
.+.+.+|..+.+.|.|+.+|+..+..++.|+..++. .++++|...|||.||+.|.+||..++++.+...++.+|
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 999999999999999999999999999999998854 34579999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHhHHHHHHhhccCCCChhhH
Q 003986 224 MLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPV 303 (781)
Q Consensus 224 l~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l 303 (781)
|.+|..++++|..+++.|++.++..++..+++++||..|.+.+.+.. ||+..+++..+.+.|+.||+++++++.++.+|
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 99999999999999999999999999999999999999999987664 89999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHhhh-hhhhccc-ccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHh
Q 003986 304 SNIFKQHVTAEGTALVKLAEDAASN-KKAEKRD-VVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFC 381 (781)
Q Consensus 304 ~~~~~~~I~~~g~~i~~~~~~~~~~-~~~~~~~-~~~~~~~~~I~~l~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~l 381 (781)
.+.|.+||+..|.-+ +.....+.. +...+.. .....+..+++.++++++.+..++...|.+|..+.+++++||+.++
T Consensus 330 ~~~f~~yV~~~g~~~-~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fi 408 (773)
T COG5647 330 QEVFERYVKDEGVLI-NIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFI 408 (773)
T ss_pred HHHHHHHHHhhchhh-hhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHh
Confidence 999999999999222 222211110 1000000 0134688999999999999999999999999999999999999999
Q ss_pred ccCC-CCCchHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHhcCCCCCChHHHHH
Q 003986 382 NKGV-AGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERS 460 (781)
Q Consensus 382 N~~~-~~~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~~~~~E~~ 460 (781)
|.+. +...+||+||+|+|.+||++++ ..-...++..+.+++.||+|+.+||+|+++|+++||||||+++|.+.+.|..
T Consensus 409 n~~~sa~~~~~e~Laky~D~~lkk~~k-~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~ 487 (773)
T COG5647 409 NGNESADSGPSEYLAKYIDGLLKKDGK-QSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELK 487 (773)
T ss_pred ccccccccccHHHHHHHhHHHhhcccc-ccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHH
Confidence 9954 2357899999999999998753 2223467788889999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCchhHhHHHHHHHHhHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCC-CCCccCcHHHHHHHH
Q 003986 461 ILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYK-SFDLNLPAEMVKCVE 539 (781)
Q Consensus 461 ~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~-~~~~~lP~~l~~~~~ 539 (781)
||++||+.||.+||+|+++||+||..|.++...|++.. ++ ..+.+++.|.||+..+||..| ...+.||++|.+.++
T Consensus 488 mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~-~s--~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le 564 (773)
T COG5647 488 MISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSP-QS--YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILE 564 (773)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCc-hh--hccccchhHHHHHHhcCCCCccccccCCChHHHHHHH
Confidence 99999999999999999999999999999999987643 21 225689999999999999655 468999999999999
Q ss_pred HHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEE---EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 003986 540 VFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELI---VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 616 (781)
Q Consensus 540 ~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~~~~~~~l~---~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 616 (781)
.|++||.+||+||+|.|.|+||+|+|+++|+.+++.+. ++++|+.|+++||+++++|+++|.+.|+++.++++++|+
T Consensus 565 ~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~ 644 (773)
T COG5647 565 GFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQ 644 (773)
T ss_pred HHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHH
Confidence 99999999999999999999999999999988754443 668999999999999999999999999999999999999
Q ss_pred HhhhccccccccCCCCCCCCCCCeEEEccCCCCCceeEEecCCCc----hhhhhhHHhHHHhhhhhhcceeeeecccccc
Q 003986 617 SLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSRKV 692 (781)
Q Consensus 617 sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~I~A~IVRiMK~~k~ 692 (781)
||+++|..+|.+. ++.++|++.|.+|.+|+++..+|+++.+.. ++...+++.+++||+..+|||||||||+||+
T Consensus 645 sl~~ak~~~l~~~--~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~ 722 (773)
T COG5647 645 SLSCAKLVVLLKD--DKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKK 722 (773)
T ss_pred HHHhhheeeeccc--cccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 9998776655543 677899999999999999999999997653 3455677889999999999999999999999
Q ss_pred cChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHHHHhhhcccccccCC
Q 003986 693 LGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRIEDLITRDYLERDKS 772 (781)
Q Consensus 693 ~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~Li~~eyl~r~~~ 772 (781)
|.|++|+++|+.+.+.||. |++.+||++|+.|||||||+|.++
T Consensus 723 l~H~~Lv~e~i~q~~~Rf~-------------------------------------p~vsmvKr~Ie~LiEKeYLeR~~d 765 (773)
T COG5647 723 LKHGDLVKEVIAQHKSRFE-------------------------------------PKVSMVKRAIETLIEKEYLERQAD 765 (773)
T ss_pred CcHHHHHHHHHHHhhccCC-------------------------------------CCHHHHHHHHHHHHHHHHHHhccC
Confidence 9999999999999999999 999999999999999999999988
Q ss_pred CCCcceecC
Q 003986 773 NPNMFRYLA 781 (781)
Q Consensus 773 ~~~~~~Yia 781 (781)
| .+|+|+|
T Consensus 766 d-~iY~YLa 773 (773)
T COG5647 766 D-EIYVYLA 773 (773)
T ss_pred C-ceeeecC
Confidence 8 8999997
No 3
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.4e-108 Score=836.57 Aligned_cols=684 Identities=27% Similarity=0.505 Sum_probs=626.4
Q ss_pred CCCCCCCCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhc
Q 003986 1 MTMNERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISST 80 (781)
Q Consensus 1 ~~~~~~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~ 80 (781)
||||+|++++||++|.+|.+.|..|.. .+++++.+|..-|+.||.+|.+- |.+-||+||..++.++++|+...
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 899999999999999999999988743 23577888999999999999997 78899999999999999999865
Q ss_pred ccchhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhcCC------------------CCcHHHHHHHHHHHH
Q 003986 81 VLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRS------------------LPPLNEVGLTCFRDL 142 (781)
Q Consensus 81 v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~------------------~~~i~~l~l~lf~~~ 142 (781)
.. .+-..+++..|..|.+.|+.|..+..++..+|.||++.|++.++ ...|..+|+.+|++.
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 43 22233456699999999999999999999999999999998753 224678999999999
Q ss_pred HhhhhHHHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHHHHhcC-----------------CcccccHHHhHHHHHHHHH
Q 003986 143 VYTELNGKVRDAVITLIDQEREGEQID-RALLKNVLDIFVEIGM-----------------GQMDYYENDFETAMLKDTA 204 (781)
Q Consensus 143 v~~~l~~~l~~~ll~~I~~~R~g~~i~-~~~lk~~i~~l~~l~~-----------------~~~~~Y~~~FE~~~L~~t~ 204 (781)
+..++...|+..++..|.++|.|+.++ ...+..++..|+.+.. ....+|++.||+|||.+|.
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 6788999999987743 2356899999999999999
Q ss_pred HHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHH
Q 003986 205 AYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVE 284 (781)
Q Consensus 205 ~yY~~~s~~~l~~~~~~eYl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~ 284 (781)
+||+++++..+.+.+|++|+.+|..++++|+.||+.||++++..|++..|++.||.+|.+.+ +..++.++.+.+..
T Consensus 233 ~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~ 308 (728)
T KOG2284|consen 233 QYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENK 308 (728)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999887 34699999999999
Q ss_pred hHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchHHHHHHHHHHHHHHHHHHHHhcC
Q 003986 285 DLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQ 364 (781)
Q Consensus 285 ~L~~ly~L~~~~~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~~l~~~~~~li~~~F~ 364 (781)
|++.||.|+..+..|+..+...|++||..+|...++.... .+-|..||+.++.+|.+|..++...|.
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 9999999999999999999999999999999988876542 346899999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHhccCCCC---CchHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhccCChhHHHHHHHH
Q 003986 365 NHTLFHKSLKEAFEVFCNKGVAG---SSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRK 441 (781)
Q Consensus 365 ~~~~f~~~l~~af~~~lN~~~~~---~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~ 441 (781)
+|..|..+++.|+..++|...++ ++.||.||+|||.+||++. +++++.+++.+|+..+.+|+|++|||+|.++|.+
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 6789999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHhHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCC
Q 003986 442 KLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWP 521 (781)
Q Consensus 442 ~LakRLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP 521 (781)
.||+|||.+.|.|.|.|..||++||+.||++||+++. +.|++.|.+++++|.+.+.
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 CCCCCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhHcCCCCcCHHHHH
Q 003986 522 SYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIM 601 (781)
Q Consensus 522 ~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILllFn~~~~~t~~ei~ 601 (781)
++.+|.+|+..++.|+.||..+|+||+|+|++.++++++++++-++.|.-.+.++||++||+||..+.+++.||.
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 277999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCceeEEecCCCc-----hhhhhhHHhHHHhhh
Q 003986 602 TQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV-----DEKKKVIEDVDKDRR 676 (781)
Q Consensus 602 ~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~~~~~~i~i~~~~~-----~e~~~~~~~v~~~R~ 676 (781)
+.+|++.+.+.+.+.++... ++|.... ..+..+..|++|.+|+++..+.+|..|.+ +|.+.+...|.+||+
T Consensus 586 ~~~~~~~~~l~kti~tildv--~~~~~d~--~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk 661 (728)
T KOG2284|consen 586 EEIGVSGDYLLKTIRTILDV--TLLTCDD--QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRK 661 (728)
T ss_pred hhhCccHHHHHHHHHHHHhc--eeecccc--cccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHH
Confidence 99999999999999999854 5676543 35667888999999999999999988654 345567778999999
Q ss_pred hhhcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHH
Q 003986 677 YAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKK 756 (781)
Q Consensus 677 ~~I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~ 756 (781)
+.++||||||||+||.+.|+.|+.||++|.+.+|. |+.++||+
T Consensus 662 ~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~-------------------------------------p~v~~ikk 704 (728)
T KOG2284|consen 662 YYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFS-------------------------------------PDVPFIKK 704 (728)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCC-------------------------------------CCchHHHH
Confidence 99999999999999999999999999999999999 99999999
Q ss_pred HHHHhhhcccccccCCCCCcceecC
Q 003986 757 RIEDLITRDYLERDKSNPNMFRYLA 781 (781)
Q Consensus 757 ~ie~Li~~eyl~r~~~~~~~~~Yia 781 (781)
|||.||++.||+|.+.+ +.|.|+|
T Consensus 705 ~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 705 SIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHHhhcccc-ccchhcC
Confidence 99999999999999876 8999997
No 4
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.7e-107 Score=868.06 Aligned_cols=646 Identities=36% Similarity=0.609 Sum_probs=603.0
Q ss_pred HHHHHHHHHHHHHHhcccchhhc--cCcHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhcC--CCCcHHHHHHHHHH
Q 003986 65 LYDKYRESFEEYISSTVLPSIRE--KHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARR--SLPPLNEVGLTCFR 140 (781)
Q Consensus 65 LY~~l~~~l~~~l~~~v~~~l~~--~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~--~~~~i~~l~l~lf~ 140 (781)
||+.+++.+++|++..+. .+.. .+...+|+.+.+.|..|+..+.+++.+|.||||.|+... ..+|+|++|+.+||
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 234579999999999999999999999999999999773 56899999999999
Q ss_pred HHHhh----hhHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhcCCcccccHHHhHHHHHHHHHHHHHHHHHHHHh
Q 003986 141 DLVYT----ELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWIL 216 (781)
Q Consensus 141 ~~v~~----~l~~~l~~~ll~~I~~~R~g~~i~~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~ 216 (781)
.+++. .+..++.++++..++++|.|+++|+..|++++.|+.++ ..|.+.|++.|++.+.++|.+++....+
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 46788899999999999999999999999999999986 5899999999999999999999999999
Q ss_pred cCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHhHHHHHHhhccC
Q 003986 217 EDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKI 296 (781)
Q Consensus 217 ~~~~~eYl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~ 296 (781)
+..+++||++++.++.+|.+|+..+++.+|...+..++.+.|+..|++.|+.+ |+..+++.++..++.+||.|++++
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 99999999999999999999999999999966799999999999999999875 799999999999999999999999
Q ss_pred CCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchHHHHHHHHHHHHHHHHHHHHhcCCC--hHHHHHHH
Q 003986 297 PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNH--TLFHKSLK 374 (781)
Q Consensus 297 ~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~~l~~~~~~li~~~F~~~--~~f~~~l~ 374 (781)
.++...++..|.+|++.-|..++.+.. .+...|+.+++++++.+-++..||..+ ..|..+++
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 889899999999999999999986643 266899999999999999999999988 99999999
Q ss_pred HHHHHHhccCCCCCchHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHhcCCCCCC
Q 003986 375 EAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSAN 454 (781)
Q Consensus 375 ~af~~~lN~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~~ 454 (781)
+||+.++|+.. .++||+||+|.|..|+.|. +..++++++..++.++.||+||..||+|+.+|++.||+|||.++|++
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 45678889999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhCCchhHhHHHHHHHHhHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHHH
Q 003986 455 DDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEM 534 (781)
Q Consensus 455 ~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l 534 (781)
.|+|..|+.+||.+||..||++|++|++|+..|++++..|+++..++.....++ +.+.|+|.++||.+++.++.||++|
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 999999999999999999999999999999999999999999866554433445 9999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHH
Q 003986 535 VKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRL 614 (781)
Q Consensus 535 ~~~~~~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~ 614 (781)
.++++.|..||..+|.||+|.|.+++|+|.+++.|+.|++++.+|++|++||++||+++.+|++||.+.|+|.+.+|++.
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 HhHhhhccccccccCCCCCCCCCCCeEEEccCCCCCceeEEecCCCc----hhhhhhHHhHHHhhhhhhcceeeeecccc
Q 003986 615 LHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSR 690 (781)
Q Consensus 615 L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~I~A~IVRiMK~~ 690 (781)
|+||.|+|.++|.+.|.|+.+.+++.|.+|..|+++..||+|+.+.. +|.+.+.++|.+||++.||||||||||+|
T Consensus 533 lqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~r 612 (661)
T KOG2167|consen 533 LQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMR 612 (661)
T ss_pred HHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998764 45677889999999999999999999999
Q ss_pred cccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHHHHhhhccccccc
Q 003986 691 KVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRIEDLITRDYLERD 770 (781)
Q Consensus 691 k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~Li~~eyl~r~ 770 (781)
|+|+|+.|+.++.+||+ || +.+ ++|+|||+||+|||++||
T Consensus 613 k~l~h~~l~~el~~qlk--fp-------------------------------------v~~-d~kkriesli~rey~erd 652 (661)
T KOG2167|consen 613 KTLSHNLLVTELFNQLK--FP-------------------------------------VKP-DLKKRIESLIDREYLERD 652 (661)
T ss_pred HhhchhHHHHHHHHhcC--CC-------------------------------------CCh-hHHHHHHHHHhHHHhccc
Confidence 99999999999999997 98 767 999999999999999999
Q ss_pred CCCCCcceecC
Q 003986 771 KSNPNMFRYLA 781 (781)
Q Consensus 771 ~~~~~~~~Yia 781 (781)
+| +.|.|||
T Consensus 653 -~n-~~y~yva 661 (661)
T KOG2167|consen 653 -DN-NIYNYVA 661 (661)
T ss_pred -cc-ccccccC
Confidence 55 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=5.9e-90 Score=809.60 Aligned_cols=586 Identities=41% Similarity=0.757 Sum_probs=523.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhcccchhhccCcHHHH
Q 003986 15 WEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIREKHDEFML 94 (781)
Q Consensus 15 W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~~~~L 94 (781)
|+.|++||..|. .+ .++..+||++|++||++|..+ +|++||+.+++.+.+|+.. +.+.+.+.+++.+|
T Consensus 1 W~~l~~~i~~i~---~~----~~~~~~~~~lY~~vy~l~~~~----~~~~LY~~l~~~i~~~~~~-~~~~l~~~~~~~~l 68 (588)
T PF00888_consen 1 WEILEEAIDQIF---KK----SISKLSYMELYTCVYNLCDNK----YGEQLYDKLKEFISEYLKN-IIESLLSSSDEDLL 68 (588)
T ss_dssp HHHHHHHHHHHH---TT-----GCCSHHHHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHH-HHHHHCTTTTCHHH
T ss_pred ChHHHHHHHHHH---cC----CCChhHHHHHHHHHHhhcCCc----ccHHHHHHHHHHHHHHHHH-HHHHHHhcChhHHH
Confidence 999999999975 22 366778999999999999887 8999999999999999987 44555555778999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcchhhhhhhcCCCCcHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCccCHHHHH
Q 003986 95 RELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLK 174 (781)
Q Consensus 95 ~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~~~~i~~l~l~lf~~~v~~~l~~~l~~~ll~~I~~~R~g~~i~~~~lk 174 (781)
..|...|.+|+.++.+|+++|+||||+|+.++ +|++.|+.++.++++++++++|.++|.|+.+|...++
T Consensus 69 ~~~~~~w~~~~~~~~~i~~if~yLdr~yv~~~-----------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~ 137 (588)
T PF00888_consen 69 EEYVQEWEKYKKAIKYISDIFSYLDRNYVKRN-----------LFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLK 137 (588)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTT-----------HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhh-----------hHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Confidence 99999999999999999999999999999888 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCcccccHHHhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHccccCCCcHHHHHHHH
Q 003986 175 NVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKV 254 (781)
Q Consensus 175 ~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~eYl~~v~~~l~eE~~r~~~~l~~~t~~kl~~~l 254 (781)
++++|+.++| ...+|.+.||++||++|.+||+.++ +...++.+|+++|++++++|.+|++.|++++|.+++.+.+
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 9999999987 5679999999999999999999999 5677999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhhhhhhhhcCcHHhHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcc
Q 003986 255 QHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKR 334 (781)
Q Consensus 255 ~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~ 334 (781)
.++||.+|.+.| .+|+..|+++++.++|++||+|+++++++++.+.+.|++||.+.|..+++....
T Consensus 213 ~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~---------- 278 (588)
T PF00888_consen 213 EEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK---------- 278 (588)
T ss_dssp HHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------
T ss_pred HHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------
Confidence 999999999988 479999999999999999999999999999999999999999999999976531
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHHHhcCCCCCCCHHH
Q 003986 335 DVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEA 414 (781)
Q Consensus 335 ~~~~~~~~~~I~~l~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~e 414 (781)
...+..||+.+++++++|+.++.+||++++.|..++++||+.++|.+ ...++++||+|||.++++++ .+.++++
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 36899999999999999875 5567788
Q ss_pred HHHHHHHHHhhhhccCChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHhHhHHHHHHH
Q 003986 415 IEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSF 494 (781)
Q Consensus 415 ~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f 494 (781)
++..++.++.||+|+++||+|+.+|+++||+|||.+++.+.+.|..+|++|+.+||.++++++++|++|+..|+++++.|
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-ccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCe
Q 003986 495 EEYLSNNPNAN-PGIDLTVTVLTTGFWPSYKSFD-LNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESR 572 (781)
Q Consensus 495 ~~~~~~~~~~~-~~~~~~~~VLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~~~~ 572 (781)
++.....+... ++++|+|.||++++||..+..+ +.+|++|+.+++.|++||+.+|+||+|+|.+++|+|+|+++++++
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 99987655322 2799999999999999988766 999999999999999999999999999999999999999999999
Q ss_pred eEEEEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCC
Q 003986 573 TTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 648 (781)
Q Consensus 573 ~~~l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~ 648 (781)
+++++||++||+||++||+.+++|+++|++.||+++++++++|.+|+..|..++.+.++++++++++.|.+|.+|+
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=2.3e-88 Score=698.02 Aligned_cols=715 Identities=26% Similarity=0.458 Sum_probs=630.1
Q ss_pred CCCCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhcccchh
Q 003986 6 RKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSI 85 (781)
Q Consensus 6 ~~~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l 85 (781)
++...|++.|+..+|.+.++.+ +++.++..|..+|.+||.+|.+. .....++|+.+.+.|.+|+.+.-.+..
T Consensus 8 r~r~qFee~W~~~rpIVlkLLr------Q~sVt~~~WqDLF~~Vh~vclWd--dkGpaKI~d~L~~dI~efi~qAq~rv~ 79 (777)
T KOG2285|consen 8 RDRDQFEEEWSKARPIVLKLLR------QKSVTPAAWQDLFYHVHKVCLWD--DKGPAKIRDILTRDINEFIHQAQKRVR 79 (777)
T ss_pred cchhhhhhhccccchHHHHHHh------hccCCHHHHHHHHhhheeeeeec--CCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556899999999999988754 24689999999999999999997 335678999999999999986433223
Q ss_pred hccCcHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhcCC--------CCcHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 003986 86 REKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRS--------LPPLNEVGLTCFRDLVYTELNGKVRDAVIT 157 (781)
Q Consensus 86 ~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~--------~~~i~~l~l~lf~~~v~~~l~~~l~~~ll~ 157 (781)
....+..+|..|..+|.+|-....+|...|.-|+..-...++ -.++..+.+.-|.+++|..++.+|....+.
T Consensus 80 s~q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmk 159 (777)
T KOG2285|consen 80 SLQTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMK 159 (777)
T ss_pred hhccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333566899999999999999999999999999987553321 236899999999999999999999999999
Q ss_pred HHHHHhcCCccCHHHHHHHHHHHHHhcC---CcccccHHHhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHH
Q 003986 158 LIDQEREGEQIDRALLKNVLDIFVEIGM---GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKRE 234 (781)
Q Consensus 158 ~I~~~R~g~~i~~~~lk~~i~~l~~l~~---~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~eYl~~v~~~l~eE 234 (781)
++..+|+|+.+|.+.+-.+-+.|+.++. +.+.+|.+.||..||++|.+||+..+..++++.++.+|++.+..-+++|
T Consensus 160 lVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EE 239 (777)
T KOG2285|consen 160 LVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEE 239 (777)
T ss_pred HHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHH
Confidence 9999999999999999999999999975 4678999999999999999999999999999999999999999999999
Q ss_pred HHHHccccCC--CcHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcCcHHhHHHHHHhhccCCCChhhHHHHHHHHHH
Q 003986 235 KDRVSHYLHS--SSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVT 312 (781)
Q Consensus 235 ~~r~~~~l~~--~t~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~I~ 312 (781)
+.|+.+||.+ .|..+++..+.+.|+.++.+.|+. .|..|+....++-|++||+|+.+++.|++++...+..||+
T Consensus 240 e~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~ 315 (777)
T KOG2285|consen 240 EQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIR 315 (777)
T ss_pred HHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHH
Confidence 9999999987 678899999999999999999985 5788999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHHHHhhhhhhhcccccccchHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhccCC-------
Q 003986 313 AEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGV------- 385 (781)
Q Consensus 313 ~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~lN~~~------- 385 (781)
..|..-+....+.+ +.++..||+.|+.++++|..++.++|+.||.|..+.+.||..++|...
T Consensus 316 saGLaDM~~aaE~i-----------ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp 384 (777)
T KOG2285|consen 316 SAGLADMRNAAENI-----------TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELP 384 (777)
T ss_pred hhhHHHHHhhhhhc-----------cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhcc
Confidence 99976664433322 567889999999999999999999999999999999999999999864
Q ss_pred -----------CCCchHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHhcCCCCC
Q 003986 386 -----------AGSSSAELLATFCDNILKKGG-SEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSA 453 (781)
Q Consensus 386 -----------~~~~~~e~La~y~D~~lk~~~-~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~ 453 (781)
+..+.||+||.|||.+||+.. +++++.|+++.+|++++-+++|+.+||+|+.|++.+|++|||.+.|+
T Consensus 385 ~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SA 464 (777)
T KOG2285|consen 385 NSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSA 464 (777)
T ss_pred chhcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhccc
Confidence 124689999999999999852 45678899999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHhCC--chhHhHHHHHHHHhHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccC
Q 003986 454 NDDHERSILTKLKQQCGG--QFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKS-FDLNL 530 (781)
Q Consensus 454 ~~~~E~~~i~~Lk~~~G~--~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~-~~~~l 530 (781)
+.+.|..|+..|+ +||. ++++++.+||+|++.|++++..|+..+...+..++.-.+++.||+.|.|...+. ..+.|
T Consensus 465 DsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSL 543 (777)
T KOG2285|consen 465 DSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSL 543 (777)
T ss_pred chhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeC
Confidence 9999999999998 5774 689999999999999999999999988776555556678999999999997643 46899
Q ss_pred cHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhHcCC--CCcCHHHHHHHhCCCH
Q 003986 531 PAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLSD 608 (781)
Q Consensus 531 P~~l~~~~~~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILllFn~~--~~~t~~ei~~~t~i~~ 608 (781)
|.+|++.+-..++||+++|+||+|.|.|+++.++|++.-+-|.|++.|+++||+||.+||+. +.+|++.+.-.|.+|+
T Consensus 544 P~ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPD 623 (777)
T KOG2285|consen 544 PRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPD 623 (777)
T ss_pred chhHHHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCC
Confidence 99999999999999999999999999999999998876555899999999999999999975 6899999999999999
Q ss_pred HHHHHHHhHhhh---ccccccccCCCC----CCCCCCCeEEEccCCCCC-----ceeEEecCCCc------hhhhhhHHh
Q 003986 609 DDVVRLLHSLSC---AKYKILNKEPNT----KTISPTDHFEFNSKFTDK-----MRRIKIPLPPV------DEKKKVIED 670 (781)
Q Consensus 609 ~~l~~~L~sL~~---~k~kiL~~~~~~----~~i~~~~~f~lN~~F~~~-----~~~i~i~~~~~------~e~~~~~~~ 670 (781)
.++++.|-||+. .|..||..+|+. +++.++..|.+|.+|.-- .++-+++.+.- ...++..+.
T Consensus 624 aELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenes 703 (777)
T KOG2285|consen 624 AELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENES 703 (777)
T ss_pred HHHHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcch
Confidence 999999999984 357888887743 457788999999999731 22333433221 112334466
Q ss_pred HHHhhhhhhcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCC
Q 003986 671 VDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPD 750 (781)
Q Consensus 671 v~~~R~~~I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 750 (781)
+.+-|-...|-+|++|||.||+++..+|-.|.++-|+.+|- |+
T Consensus 704 IVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFl-------------------------------------P~ 746 (777)
T KOG2285|consen 704 IVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFL-------------------------------------PN 746 (777)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccC-------------------------------------Cc
Confidence 78899999999999999999999999999999999999999 99
Q ss_pred hHHHHHHHHHhhhcccccccCCCCCcceecC
Q 003986 751 FKAIKKRIEDLITRDYLERDKSNPNMFRYLA 781 (781)
Q Consensus 751 ~~~ik~~ie~Li~~eyl~r~~~~~~~~~Yia 781 (781)
..+||.+||.|||..|++||++|-++|.|+|
T Consensus 747 kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 747 KKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 9999999999999999999999999999997
No 7
>smart00182 CULLIN Cullin.
Probab=99.98 E-value=8.8e-32 Score=255.65 Aligned_cols=141 Identities=48% Similarity=0.890 Sum_probs=132.5
Q ss_pred ccCChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHhHhHHHHHHHHHHHhcCCCCCCC
Q 003986 428 YISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPG 507 (781)
Q Consensus 428 ~l~~KD~F~~~Y~~~LakRLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 507 (781)
|+++||+|+.+|+++||+|||..++.+.+.|..||++||.+||.+++++|++|++|+..|+++++.|++++.+++ ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999876542 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEe
Q 003986 508 IDLTVTVLTTGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKF 569 (781)
Q Consensus 508 ~~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~ 569 (781)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|++++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999998877 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=8.2e-26 Score=247.64 Aligned_cols=222 Identities=27% Similarity=0.374 Sum_probs=200.7
Q ss_pred HHhhhhccCChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCCchhHhHHHHHHHHhHhHHHHHHHHHH--Hh
Q 003986 422 VVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--LS 499 (781)
Q Consensus 422 i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~--~~ 499 (781)
+-.+...+.+|+.|++.||.+||.||+.....+.|.|..-++.||-++|.+..+.|++|++|+..|+++++.+++. ..
T Consensus 442 ~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~ 521 (765)
T KOG2165|consen 442 FGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELS 521 (765)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence 3456666799999999999999999999999999999999999999999999999999999999999999999874 22
Q ss_pred cCCCCCCCcceEEEEeecCCCCCCCCCCccCcHHHHHHHHHHHHHHhhcCCCceeEeecCcceEEEEeEecCeeEEEEEc
Q 003986 500 NNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVT 579 (781)
Q Consensus 500 ~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~RkL~w~~~l~~~~i~~~~~~~~~~l~~s 579 (781)
......+.+.+++.+||..+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|.|+++++|.+++.+++||
T Consensus 522 r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVs 601 (765)
T KOG2165|consen 522 RGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVS 601 (765)
T ss_pred cccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeC
Confidence 21223356788999999999998888889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCC
Q 003986 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 648 (781)
Q Consensus 580 ~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~ 648 (781)
+.||+|+.+|.+.++||++++++.+|||..-+++.|..|.. .++|..+|. ++++++|+++++=.
T Consensus 602 p~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iEse~ 665 (765)
T KOG2165|consen 602 PEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIESEM 665 (765)
T ss_pred HHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeeccccc
Confidence 99999999999999999999999999999999999999984 588987653 36789999998543
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.75 E-value=3.1e-19 Score=145.83 Aligned_cols=68 Identities=51% Similarity=0.920 Sum_probs=62.4
Q ss_pred HHHhhhhhhcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCC
Q 003986 671 VDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPD 750 (781)
Q Consensus 671 v~~~R~~~I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 750 (781)
|+++|...|+||||||||++|+++|++|+.+|.++++++|+ |+
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~-------------------------------------~~ 43 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFP-------------------------------------PS 43 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS----------------------------------------
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcC-------------------------------------CC
Confidence 36799999999999999999999999999999999999999 99
Q ss_pred hHHHHHHHHHhhhcccccccCCCCC
Q 003986 751 FKAIKKRIEDLITRDYLERDKSNPN 775 (781)
Q Consensus 751 ~~~ik~~ie~Li~~eyl~r~~~~~~ 775 (781)
..+||++||.||+||||+||++|+|
T Consensus 44 ~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 44 VSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred HHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 9999999999999999999999875
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.05 E-value=0.019 Score=55.07 Aligned_cols=137 Identities=18% Similarity=0.263 Sum_probs=96.2
Q ss_pred CCCHHHhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhcccchhhc
Q 003986 8 TIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISSTVLPSIRE 87 (781)
Q Consensus 8 ~~~f~~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~ 87 (781)
.+..++.|..+..++-.+ ++|+... .+-+..-++-+.--+.|.++. ....+-+.+++.+..-+.. ....+..
T Consensus 2 ~~~~~~~W~~~~~~vl~l---F~g~~l~-~~iEdlN~lv~~~i~~~~~~~---~~~~~~~dl~elL~tg~~~-L~~~l~~ 73 (158)
T PF08539_consen 2 NMSSDDAWNSLCAKVLPL---FQGERLR-LPIEDLNELVRFHIKLCIQSF---PPSYFLEDLEELLTTGMYI-LENQLNE 73 (158)
T ss_pred CCchhhhHHHHHHHHHHH---HcCCCCC-cCHHHHHHHHHHHHHHhhccc---chHHHHHHHHHHHHHHHHH-HHHHHhh
Confidence 356789999999998775 5677654 554444445555556677652 2334555666666665543 2334556
Q ss_pred cCcHHHHHHHHHHHHHH-HHHHHHHHHhhcchhhhhhhc-----------------CCCCcHHHHHHHHHHHHHhhhhHH
Q 003986 88 KHDEFMLRELVKRWSNH-KVMVRWLSRFFHYLDRYFIAR-----------------RSLPPLNEVGLTCFRDLVYTELNG 149 (781)
Q Consensus 88 ~~~~~~L~~~~~~W~~~-~~~~~~l~~vf~YLDr~yv~~-----------------~~~~~i~~l~l~lf~~~v~~~l~~ 149 (781)
.+++.+++.++..|.-| ..-+-++..+|..|++.+-.. .+..+|+.+++..|||.|+-+..+
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 67788999999999996 556789999999999644322 234689999999999999987766
Q ss_pred HHH
Q 003986 150 KVR 152 (781)
Q Consensus 150 ~l~ 152 (781)
++.
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=92.65 E-value=0.35 Score=42.34 Aligned_cols=65 Identities=18% Similarity=0.214 Sum_probs=52.5
Q ss_pred EEEcHHHHHHHHhHc--------CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCC
Q 003986 576 LIVTTYQASALLLFN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (781)
Q Consensus 576 l~~s~~Q~~ILllFn--------~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F 647 (781)
..++.-|+.+|+... ....+|-.||++.+|++.+.+.++|..|. +.+++.... ..+.|.+|.++
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 24789999876
Q ss_pred C
Q 003986 648 T 648 (781)
Q Consensus 648 ~ 648 (781)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 4
No 12
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=91.38 E-value=7.3 Score=44.47 Aligned_cols=203 Identities=10% Similarity=0.099 Sum_probs=113.4
Q ss_pred HhHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhc--ccchhh----
Q 003986 13 QGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTTIYNMCTQKPPHDYSQQLYDKYRESFEEYISST--VLPSIR---- 86 (781)
Q Consensus 13 ~~W~~l~~ai~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~e~LY~~l~~~l~~~l~~~--v~~~l~---- 86 (781)
-.|..|++++.-|...- ....++ ...|-.+++.+|+-|..+.. +...+.+.++.....+.... +...+.
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 VDRSLLRSLLKMLSDLQ--IYKESF-ELTFLSLFRELYAAEGQDKR--QELEVPEYLEHVEGRLEEENDRVIEYFDSSTK 186 (661)
T ss_pred hhHHHHHHHHHHHHHHH--hhhhhh-HHHHHHHHHHHHHHHhcchh--hhcccHHHHHhhhhcccchHHHHHHhcccccc
Confidence 45777787776654321 000111 23467788899999998721 22223333322211111110 000010
Q ss_pred ccCcHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhcCCCCcHHHHHHHHHH--HHHhhhhHHHHHHHHHHHHHHHhc
Q 003986 87 EKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFR--DLVYTELNGKVRDAVITLIDQERE 164 (781)
Q Consensus 87 ~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~~~~i~~l~l~lf~--~~v~~~l~~~l~~~ll~~I~~~R~ 164 (781)
......+.+.+...|-....... +++-+|-. .......+++++-..+- ..+....++.++.....++..++.
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 11224566677777777643322 33333332 11233456676666662 223346677777777777888887
Q ss_pred CCcc--CHHHHHHHHHHHHHhcCCcccccHHHhHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHH
Q 003986 165 GEQI--DRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKRE 234 (781)
Q Consensus 165 g~~i--~~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~~~~eYl~~v~~~l~eE 234 (781)
++.. +.-..|..+++.... .++...- .+|+..+++.|...++ .....+.+|+.+....+-.+
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 234577777877764 2333334 7899999999999988 34567889998888765554
No 13
>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=90.88 E-value=0.67 Score=39.38 Aligned_cols=59 Identities=15% Similarity=0.223 Sum_probs=41.4
Q ss_pred HHHHHHHhHcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003986 581 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (781)
Q Consensus 581 ~Q~~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~ 646 (781)
+++.+.+..+..+ .+|.++|++.++++...+.+.++.|. +.+++...+ .+++.|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-----G~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-----GRGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-----STTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-----CCCCceeecCC
Confidence 3444444444443 49999999999999999999999997 567776432 14678888875
No 14
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=90.65 E-value=0.38 Score=36.82 Aligned_cols=45 Identities=29% Similarity=0.338 Sum_probs=36.5
Q ss_pred HHHHHhHcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 583 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 583 ~~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
+.||.+|.+.+ .+|+.||++.+|++...+.+.|..|.. .+.+.++
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 45788888775 589999999999999999999999974 5666654
No 15
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=90.60 E-value=0.52 Score=35.32 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=35.2
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
+..+..||..+.+++.+|..||++.+|++...+.+.|..|..
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 456778898888888999999999999999999999999974
No 16
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=89.93 E-value=0.44 Score=37.70 Aligned_cols=51 Identities=25% Similarity=0.385 Sum_probs=42.6
Q ss_pred EcHHHHHHHHhHcCCCC--cCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 578 VTTYQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~--~~Glv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLE--KKGLVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEeC
Confidence 47889999988887776 9999999999999999999999997 457776653
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=89.03 E-value=1 Score=35.32 Aligned_cols=46 Identities=20% Similarity=0.321 Sum_probs=38.9
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
|..|+.++++++.+|+++|++.+|++...+++-|..|.. .+++.+.
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 456788889899999999999999999999999999974 4556554
No 18
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=86.60 E-value=0.55 Score=36.79 Aligned_cols=50 Identities=24% Similarity=0.400 Sum_probs=42.8
Q ss_pred EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
+|..|+.+|....+.+++|..+|++.++++...+.+.+..|. +.+++.+.
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEec
Confidence 367899999999888899999999999999999999999997 45677654
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=86.31 E-value=1.2 Score=35.87 Aligned_cols=50 Identities=24% Similarity=0.333 Sum_probs=38.5
Q ss_pred EcHHHHHHHHhHc-CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 578 VTTYQASALLLFN-SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 578 ~s~~Q~~ILllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
+|..|..||..+. .....|..+|++.++++...+-+.+..|.. .+++.+.
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 4678999999998 778999999999999999999999999984 4777654
No 20
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=83.85 E-value=1.9 Score=39.12 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=45.2
Q ss_pred EEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
.++..|+.||..+..++++|..+|++.+|++...+-+.+..|. +.+++.+.+
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 4588999999999888899999999999999999999999997 457777653
No 21
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=82.52 E-value=3.1 Score=30.98 Aligned_cols=43 Identities=26% Similarity=0.307 Sum_probs=34.0
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 626 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL 626 (781)
...-||.++-+ ++.++.||++.+|++...+.++|..|.. .+++
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 34567777776 6799999999999999999999999863 4554
No 22
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=81.49 E-value=2.9 Score=39.54 Aligned_cols=52 Identities=17% Similarity=0.174 Sum_probs=45.2
Q ss_pred EEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
.+|..|+.||......+++|..+|++.++++...+-+.+..|. +.+++.+.+
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 5778999999888777789999999999999999999999997 567777654
No 23
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=81.30 E-value=2.2 Score=33.73 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=39.3
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
++.-..||.++...++.|+.+|++.+|++...+..+|..|. +.+++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~--~aGli~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLE--EAGLIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 45556788888667899999999999999999999999997 45676543
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=78.58 E-value=4.2 Score=31.23 Aligned_cols=37 Identities=22% Similarity=0.324 Sum_probs=29.4
Q ss_pred HHHHhH-cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 584 SALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 584 ~ILllF-n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
.||.++ +..+.+|.++|++.+|++...+.+.|..|-.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345444 6666799999999999999999999998853
No 25
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=77.50 E-value=6 Score=33.80 Aligned_cols=55 Identities=18% Similarity=0.358 Sum_probs=42.1
Q ss_pred HHHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003986 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (781)
Q Consensus 583 ~~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~ 645 (781)
..||..+... +++|..||++.+|++...+.+.|..|. +.+++.+.+ .++.|.+..
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~~------~~~~y~l~~ 63 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQDG------QNGRYRLGP 63 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeecC------CCCceeecH
Confidence 4567777766 689999999999999999999999997 357776643 134566544
No 26
>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=77.22 E-value=5.8 Score=35.54 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=43.5
Q ss_pred EEcHHHHHHHHhHc----CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 577 IVTTYQASALLLFN----SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 577 ~~s~~Q~~ILllFn----~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
.+|..|..||..+. ..+++|..+|++.++++...+-+.+..|. +.+.+.+.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le--~kg~I~r~~ 77 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS--KKGYLSKER 77 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEeccC
Confidence 45788888887766 55689999999999999999999999997 457777654
No 27
>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=76.88 E-value=1.4 Score=35.96 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=34.5
Q ss_pred eeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHHHHhhh
Q 003986 684 VRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRIEDLIT 763 (781)
Q Consensus 684 VRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~Li~ 763 (781)
-.+|+.++.++.+||-. +|. .+++.+...++.|+.
T Consensus 6 ~~~l~~~~~~S~~eLa~--------~~~-------------------------------------~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAR--------EFG-------------------------------------ISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHS-SEEHHHHHH--------HTT---------------------------------------HHHHHHHHHHHHC
T ss_pred HHHHHHcCCcCHHHHHH--------HHC-------------------------------------cCHHHHHHHHHHHHH
Confidence 34678888899888853 588 999999999999999
Q ss_pred cccccccCC
Q 003986 764 RDYLERDKS 772 (781)
Q Consensus 764 ~eyl~r~~~ 772 (781)
+|||++.+.
T Consensus 41 kG~I~~~~~ 49 (69)
T PF09012_consen 41 KGYIRKVDM 49 (69)
T ss_dssp CTSCEEEEE
T ss_pred CCcEEEecC
Confidence 999998754
No 28
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=76.75 E-value=7.1 Score=37.41 Aligned_cols=55 Identities=11% Similarity=0.098 Sum_probs=41.4
Q ss_pred HHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003986 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (781)
Q Consensus 585 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~ 646 (781)
+.|..+..+.+|..+|++..++|...|.+.|..|. |.+++.... | +++.|.++..
T Consensus 15 ~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~~ 69 (153)
T PRK11920 15 MYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGRP 69 (153)
T ss_pred HHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecCC
Confidence 34444555678999999999999999999999997 567776432 1 3567877763
No 29
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.46 E-value=4 Score=33.20 Aligned_cols=47 Identities=23% Similarity=0.292 Sum_probs=38.0
Q ss_pred HHHHHHHhHcCCCC--cCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 581 YQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 581 ~Q~~ILllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
..-.||.++.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 44467777777765 9999999999999999999999996 34666554
No 30
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=75.45 E-value=8.2 Score=37.43 Aligned_cols=57 Identities=16% Similarity=0.215 Sum_probs=41.5
Q ss_pred HHHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003986 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (781)
Q Consensus 583 ~~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~ 646 (781)
+.+.+.|+.. ..+|.++|++.+|+|...+.+.|..|. +.+++.... .+++.|.+..+
T Consensus 13 ~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~r-----G~~GGy~Lar~ 70 (164)
T PRK10857 13 AMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVR-----GPGGGYLLGKD 70 (164)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCC-----CCCCCeeccCC
Confidence 3444556654 589999999999999999999999997 567776421 12455766653
No 31
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=73.96 E-value=5.8 Score=34.23 Aligned_cols=53 Identities=26% Similarity=0.288 Sum_probs=45.0
Q ss_pred EEEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 575 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 575 ~l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
++.++..+..||.++...+.+|..+|++.++++...+.+.|..|.. .+++.+.
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 3467888999999988888899999999999999999999999973 4677643
No 32
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=73.93 E-value=2.8 Score=33.96 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=39.4
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
|-.++-|+..+-..+..|..||++.+|++...+.+.|..|.. .+++.+.
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 455666776665677899999999999999999999999974 4666554
No 33
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=72.17 E-value=7.7 Score=40.56 Aligned_cols=56 Identities=14% Similarity=0.311 Sum_probs=44.5
Q ss_pred HHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003986 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (781)
Q Consensus 583 ~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~ 646 (781)
+.||.+|....++|+.||++.+|+|...+.+.|..|.. .+.|.+.+ .++.|.+-..
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~------~~~~Y~lG~~ 72 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG------ESEKYSLTLK 72 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC------CCCcEEecHH
Confidence 46888898877899999999999999999999999984 57776653 2455665543
No 34
>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=70.73 E-value=11 Score=35.12 Aligned_cols=55 Identities=15% Similarity=0.228 Sum_probs=39.2
Q ss_pred HHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003986 584 SALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (781)
Q Consensus 584 ~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~ 645 (781)
.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++.... | .++.|.+..
T Consensus 14 l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s~~-G----~~Ggy~l~~ 69 (135)
T TIGR02010 14 MLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKSVR-G----PGGGYQLGR 69 (135)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEe-C----CCCCEeccC
Confidence 334445443 479999999999999999999999997 567775321 1 234576655
No 35
>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=70.73 E-value=14 Score=32.63 Aligned_cols=61 Identities=26% Similarity=0.358 Sum_probs=45.5
Q ss_pred EEcHHHHHHHHh-------HcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCC
Q 003986 577 IVTTYQASALLL-------FNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (781)
Q Consensus 577 ~~s~~Q~~ILll-------Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F 647 (781)
.++.-|..|+++ ||. .+.+|..++++.||++...+.+++..|+ +.++|... +..+-+|.+.
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 445666666655 343 3589999999999999999999999997 56888654 3556666654
No 36
>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=70.52 E-value=3.8 Score=38.13 Aligned_cols=32 Identities=25% Similarity=0.319 Sum_probs=26.6
Q ss_pred CChHHHHHHHHHhhhcccccccCCCCCcceecC
Q 003986 749 PDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 781 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~~~~~~~~Yia 781 (781)
+....|...|..|.+||||+|..+. ..|.|-|
T Consensus 34 ~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p 65 (130)
T TIGR02698 34 WSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA 65 (130)
T ss_pred CcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence 6788899999999999999998654 4678854
No 37
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=70.26 E-value=8.6 Score=28.68 Aligned_cols=44 Identities=23% Similarity=0.304 Sum_probs=34.8
Q ss_pred HHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 583 ~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
-.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++..
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 34566666667899999999999999999999999974 355543
No 38
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=70.24 E-value=9.9 Score=30.35 Aligned_cols=45 Identities=24% Similarity=0.220 Sum_probs=33.7
Q ss_pred HHHhHcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCC
Q 003986 585 ALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPN 631 (781)
Q Consensus 585 ILllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~ 631 (781)
||-.+++ +.++|..||++.+|++...++..|..|. +.+.+.+.|.
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~ 50 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPV 50 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecC
Confidence 4555666 6789999999999999999999999997 4556665554
No 39
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=70.11 E-value=10 Score=34.77 Aligned_cols=38 Identities=26% Similarity=0.319 Sum_probs=33.5
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 590 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 590 n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
+.+++.|+++|++.++.+...+.++|++|.. .+++.+.
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Re 75 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVERE 75 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeee
Confidence 3678999999999999999999999999984 5777765
No 40
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=69.18 E-value=9.5 Score=37.77 Aligned_cols=53 Identities=13% Similarity=0.004 Sum_probs=45.4
Q ss_pred EEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 576 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 576 l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
+.+|..|+.||.....++++|..+|++.++++...+.+.+..|- +-+++.+.+
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 35678999999999988899999999999999999999999986 457777653
No 41
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=68.74 E-value=12 Score=35.68 Aligned_cols=59 Identities=15% Similarity=0.195 Sum_probs=43.3
Q ss_pred HHHHHHHhHcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003986 581 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (781)
Q Consensus 581 ~Q~~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~ 646 (781)
+.+.+.|.-+..+ ..|.++|++..|+|...|.+.+..|. |.+++..... +++.|.++..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCCC
Confidence 3444455555554 68899999999999999999999996 6677764321 3677887764
No 42
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.31 E-value=10 Score=35.63 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=44.2
Q ss_pred EEEcHHHHHHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 576 LIVTTYQASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 576 l~~s~~Q~~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
+.+|..|..||...... ++.|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le--~~GlV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE--EKGLISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH--HCCCEeeec
Confidence 35778899999888754 468999999999999999999999997 557777654
No 43
>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=67.05 E-value=10 Score=36.85 Aligned_cols=48 Identities=25% Similarity=0.331 Sum_probs=40.1
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCCC
Q 003986 594 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDK 650 (781)
Q Consensus 594 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~~~ 650 (781)
-+|..+|++.+|++...+.+++..|. +.++|.+. ..+.|.+|++|-.+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~-------~~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKI-------RNGAYMINPNFFFK 122 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEc-------cCCeEEECcHHhee
Confidence 46899999999999999999999997 45788765 35789999997554
No 44
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=66.97 E-value=8.9 Score=27.96 Aligned_cols=36 Identities=33% Similarity=0.499 Sum_probs=27.3
Q ss_pred HHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 003986 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (781)
Q Consensus 583 ~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 618 (781)
-.||-.+.+....++.+|++.+|++...+.+-+..|
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 356777777788999999999999999998877654
No 45
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=65.72 E-value=13 Score=27.17 Aligned_cols=33 Identities=30% Similarity=0.440 Sum_probs=28.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 594 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 594 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
++|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 57899999999999999999999997 4577764
No 46
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=63.99 E-value=6.2 Score=33.24 Aligned_cols=44 Identities=20% Similarity=0.383 Sum_probs=33.7
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
...||.+++..+.+++.+|.+.+|++...+-++|..|.. .+.+.
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 345666667778899999999999999999999999974 34443
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=63.94 E-value=9.4 Score=30.00 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=30.0
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
|.-+|-++-+.+.+|+.+|++.+|++...++..+.-|-
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 55566555557789999999999999999999888774
No 48
>PHA00738 putative HTH transcription regulator
Probab=63.40 E-value=16 Score=32.43 Aligned_cols=67 Identities=22% Similarity=0.104 Sum_probs=50.4
Q ss_pred EEEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCC
Q 003986 575 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (781)
Q Consensus 575 ~l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F 647 (781)
++...+.=-.||.++.+++++++.+|++.++++...+-++|.-|-. .+|+.....|. .-.|++|.+-
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 4555565666777777777899999999999999999999999964 57887654432 2357777764
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=63.34 E-value=12 Score=33.02 Aligned_cols=44 Identities=25% Similarity=0.342 Sum_probs=37.3
Q ss_pred EEcHHHHHHHHhHcC----CCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 577 IVTTYQASALLLFNS----SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~----~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
.++..|-.||-.+.+ .+.+++++|++.++++.++++.+|..|+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~ 91 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSN 91 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 578899999999887 35899999999999999999999999985
No 50
>PRK10870 transcriptional repressor MprA; Provisional
Probab=62.17 E-value=18 Score=35.57 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=42.8
Q ss_pred EEcHHHHHHHHhHcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 577 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
.+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+
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 356778888887764 4579999999999999999999999997 457787654
No 51
>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=61.60 E-value=7.4 Score=35.21 Aligned_cols=32 Identities=16% Similarity=0.450 Sum_probs=25.8
Q ss_pred CChHHHHHHHHHhhhcccccccCCCCCcceecC
Q 003986 749 PDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 781 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~~~~~~~~Yia 781 (781)
+....|...+..|.+||||+|.... ..|.|-|
T Consensus 33 ~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p 64 (115)
T PF03965_consen 33 WAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP 64 (115)
T ss_dssp --HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred cchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence 7788999999999999999999754 4677854
No 52
>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=61.60 E-value=11 Score=31.12 Aligned_cols=36 Identities=22% Similarity=0.144 Sum_probs=28.2
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 590 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 590 n~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
.....+|+.||++.+|++...++..+..+. +.++|.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~ 63 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLV 63 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHH
Confidence 334578999999999999999999888764 344554
No 53
>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=61.24 E-value=20 Score=33.05 Aligned_cols=45 Identities=20% Similarity=0.284 Sum_probs=33.9
Q ss_pred HHHHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 582 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 582 Q~~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
++.+.+.-++. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 33344443333 389999999999999999999999997 4567754
No 54
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=61.17 E-value=6.5 Score=35.86 Aligned_cols=62 Identities=21% Similarity=0.324 Sum_probs=51.0
Q ss_pred hhcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHH
Q 003986 678 AIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKR 757 (781)
Q Consensus 678 ~I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ 757 (781)
..++.|++||=.++..+.+|++.++.. .+. ++...|+--
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~e-------------------------------------ws~sTV~TL 44 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DRE-------------------------------------WSYSTVKTL 44 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----ccc-------------------------------------ccHHHHHHH
Confidence 346788999999999999998876655 356 888999999
Q ss_pred HHHhhhcccccccCCCCCcceecC
Q 003986 758 IEDLITRDYLERDKSNPNMFRYLA 781 (781)
Q Consensus 758 ie~Li~~eyl~r~~~~~~~~~Yia 781 (781)
|..|..||.|.|..++ ..|.|-|
T Consensus 45 l~RL~KKg~l~~~kdg-r~~~y~p 67 (123)
T COG3682 45 LNRLVKKGLLTRKKDG-RAFRYSP 67 (123)
T ss_pred HHHHHhccchhhhhcC-Ceeeeec
Confidence 9999999999999754 5677744
No 55
>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=61.08 E-value=20 Score=29.43 Aligned_cols=46 Identities=20% Similarity=0.335 Sum_probs=35.0
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
+..|. ||+..... ..|++||.+.||++.+.+...|..|. +-+++.+
T Consensus 5 t~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 5 TVTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred hHHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 34444 44444444 89999999999999999999999996 4567654
No 56
>PRK11569 transcriptional repressor IclR; Provisional
Probab=59.70 E-value=17 Score=38.39 Aligned_cols=54 Identities=17% Similarity=0.251 Sum_probs=42.5
Q ss_pred HHHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEc
Q 003986 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFN 644 (781)
Q Consensus 583 ~~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN 644 (781)
..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.+ .++.|.+-
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~------~~~~Y~lG 85 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG------ELGHWAIG 85 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC------CCCeEecC
Confidence 4578889874 4799999999999999999999999984 57777653 24556553
No 57
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=59.70 E-value=19 Score=37.50 Aligned_cols=46 Identities=28% Similarity=0.447 Sum_probs=38.9
Q ss_pred HHHHHhHcCCCC-cCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 583 ASALLLFNSSDR-LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 583 ~~ILllFn~~~~-~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
+.||.+|..... +++.||++.+|+|...+.+.|..|. ..+.+.+++
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 467888887554 7899999999999999999999997 467888764
No 58
>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=59.58 E-value=3.9e+02 Score=32.38 Aligned_cols=22 Identities=9% Similarity=0.406 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHhcCC
Q 003986 344 FVRKVIELHDKYLAYVNDCFQN 365 (781)
Q Consensus 344 ~I~~l~~l~~~~~~li~~~F~~ 365 (781)
+-+..+..|.++..|+..|+.|
T Consensus 680 ~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 680 MQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHhCCC
Confidence 3466788999999999999875
No 59
>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=58.67 E-value=15 Score=36.91 Aligned_cols=51 Identities=18% Similarity=0.212 Sum_probs=44.7
Q ss_pred EEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 5678899999999887889999999999999999999999997 45777765
No 60
>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=58.59 E-value=21 Score=28.55 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=38.0
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
+..+..|+..+.+.. ++..||++.+|++...+.+.|..|.. .+++..
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 456777887777666 99999999999999999999999863 355654
No 61
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=58.02 E-value=20 Score=37.75 Aligned_cols=56 Identities=20% Similarity=0.248 Sum_probs=44.0
Q ss_pred HHHHHhHcCC-CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccC
Q 003986 583 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 646 (781)
Q Consensus 583 ~~ILllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~ 646 (781)
..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+++ .++.|.+...
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~------~~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS------QLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC------CCCeEEecHH
Confidence 4688889865 4799999999999999999999999984 57776653 2456665544
No 62
>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=57.41 E-value=11 Score=30.49 Aligned_cols=32 Identities=16% Similarity=0.429 Sum_probs=27.2
Q ss_pred CChHHHHHHHHHhhhcccccccCCCCCcceec
Q 003986 749 PDFKAIKKRIEDLITRDYLERDKSNPNMFRYL 780 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~~~~~~~~Yi 780 (781)
.+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 34 i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 34 ISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp SSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred cCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 67888999999999999999998776666554
No 63
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=57.36 E-value=16 Score=33.30 Aligned_cols=58 Identities=22% Similarity=0.322 Sum_probs=42.4
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003986 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~ 645 (781)
=..||.++-+.++.++.||++.+|++...+-++|.-|. +.+++.....|. .-.|.+|.
T Consensus 18 Rl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 18 RLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 34466555555679999999999999999999999996 457887654332 23466765
No 64
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=55.93 E-value=24 Score=36.67 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=37.0
Q ss_pred HHHHHhHcC-CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 583 ASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 583 ~~ILllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
+.||.+|.. ..++|+.||++.+|+|...+.+.|..|.. .+.|.+
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 458888986 45799999999999999999999999974 466654
No 65
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=55.68 E-value=21 Score=27.34 Aligned_cols=39 Identities=26% Similarity=0.373 Sum_probs=31.7
Q ss_pred HcCCCCc-CHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 589 FNSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 589 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
+.....+ |..+|++.+|++...+.++|..|. +.+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 3445567 899999999999999999999997 45677654
No 66
>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=55.67 E-value=27 Score=32.24 Aligned_cols=55 Identities=22% Similarity=0.250 Sum_probs=39.3
Q ss_pred HHHHhHcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003986 584 SALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (781)
Q Consensus 584 ~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~ 645 (781)
.+|.++.. .+.+|+.||++.+|+|...+.+.|..|. +.+++..... +++.|.++.
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~~~g-----~~ggy~l~~ 69 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTSKRG-----VEGGYTLAR 69 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEecCC-----CCCChhhcC
Confidence 44555543 3579999999999999999999999997 4577754321 234566654
No 67
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=55.34 E-value=20 Score=31.69 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=37.9
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
..-.||.++..+...|+.+|++.+|++...+.+.+..|.. .+++.
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 46665
No 68
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=55.00 E-value=22 Score=37.26 Aligned_cols=55 Identities=20% Similarity=0.247 Sum_probs=42.5
Q ss_pred HHHHHhHcCCC-CcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003986 583 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (781)
Q Consensus 583 ~~ILllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~ 645 (781)
+.||.+|.+.. .+|..||++.+|++...+.+.|..|. ..+.+.+.+. ++.|.+-.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~~------~~~Y~Lg~ 69 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSAS------DDSFRLTL 69 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEecC------CCcEEEcH
Confidence 45788887654 59999999999999999999999997 4577876542 34566543
No 69
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=51.24 E-value=15 Score=29.81 Aligned_cols=29 Identities=10% Similarity=0.226 Sum_probs=24.7
Q ss_pred CChHHHHHHHHHhhhcccccccCCCCCcc
Q 003986 749 PDFKAIKKRIEDLITRDYLERDKSNPNMF 777 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~~~~~~~ 777 (781)
.+...+.+.+..|.++||+.+++++|..|
T Consensus 34 l~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 34 LPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred CCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 67788999999999999999988765544
No 70
>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=51.05 E-value=22 Score=28.68 Aligned_cols=38 Identities=26% Similarity=0.268 Sum_probs=32.6
Q ss_pred HHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 583 ~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
..|-.++++...+|+.+|++.||++++++..++.-|..
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 35667788988999999999999999999999998874
No 71
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=51.03 E-value=29 Score=30.94 Aligned_cols=51 Identities=24% Similarity=0.347 Sum_probs=43.2
Q ss_pred EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
++..|+.+|......++.+..+|++.++++...+.+.+..|. +.+++.+.+
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 788999999888877776669999999999999999999997 457776653
No 72
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=50.78 E-value=40 Score=31.66 Aligned_cols=50 Identities=14% Similarity=0.234 Sum_probs=37.6
Q ss_pred HcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEcc
Q 003986 589 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 645 (781)
Q Consensus 589 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~ 645 (781)
+..+..+|..+|++.+|+|...++++|..|. +.+++...+. .++.|.+..
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~G-----~~GG~~l~~ 69 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVRG-----KNGGIRLGK 69 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEecC-----CCCCeeecC
Confidence 3344578999999999999999999999997 5677765432 245566653
No 73
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=50.57 E-value=21 Score=36.13 Aligned_cols=42 Identities=26% Similarity=0.311 Sum_probs=35.5
Q ss_pred HHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 584 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
.||.+.+...++|..||++.+|++..-++++|+.|.. -+++.
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~ 56 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVE 56 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--Cccee
Confidence 4677778888999999999999999999999999973 34443
No 74
>PF13730 HTH_36: Helix-turn-helix domain
Probab=49.70 E-value=40 Score=25.63 Aligned_cols=25 Identities=24% Similarity=0.291 Sum_probs=23.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 596 SYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 596 t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999963
No 75
>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=49.59 E-value=38 Score=26.69 Aligned_cols=35 Identities=26% Similarity=0.326 Sum_probs=30.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 593 DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 593 ~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
..+|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~--~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE--EGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 4799999999999999999999999973 4777654
No 76
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=49.13 E-value=16 Score=29.14 Aligned_cols=27 Identities=11% Similarity=0.254 Sum_probs=20.3
Q ss_pred CChHHHHHHHHHhhhccccccc--CCCCC
Q 003986 749 PDFKAIKKRIEDLITRDYLERD--KSNPN 775 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~--~~~~~ 775 (781)
.+...+-+.|..|+++|||++. +.|..
T Consensus 30 ~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 30 ISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp --HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred cCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 7788899999999999999664 44444
No 77
>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=46.53 E-value=45 Score=27.44 Aligned_cols=48 Identities=19% Similarity=0.162 Sum_probs=40.2
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 626 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL 626 (781)
++=|+.++-++...+.-|+++|++.||-....++-.|..+...|.++-
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~ 56 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLT 56 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcE
Confidence 466899999999888999999999999999999999998864444433
No 78
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=46.19 E-value=38 Score=25.98 Aligned_cols=35 Identities=23% Similarity=0.272 Sum_probs=29.7
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 592 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 592 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
.++.|..+|++.+|++...+.+.|..|.. .+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeee
Confidence 56789999999999999999999999973 466654
No 79
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=45.73 E-value=49 Score=24.67 Aligned_cols=32 Identities=28% Similarity=0.404 Sum_probs=23.8
Q ss_pred HHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 003986 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 617 (781)
Q Consensus 584 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 617 (781)
.|-+.| ...+|++||++.+|++...+.+....
T Consensus 12 vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 12 VIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 344555 45789999999999999988876543
No 80
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=45.54 E-value=43 Score=26.46 Aligned_cols=44 Identities=20% Similarity=0.314 Sum_probs=34.1
Q ss_pred HHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 585 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
|..+-.+...++..+|++.+|++...+...+..|. +.+++...|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 44444577789999999999999999999999997 456666543
No 81
>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=45.08 E-value=52 Score=27.43 Aligned_cols=39 Identities=13% Similarity=0.218 Sum_probs=29.2
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
+.-.+|-++-...++|..+|+..+|.+.+++...|..+.
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 345577778889999999999999999999999998875
No 82
>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=45.04 E-value=14 Score=28.77 Aligned_cols=45 Identities=16% Similarity=0.324 Sum_probs=38.3
Q ss_pred eeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHHHHh
Q 003986 682 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRIEDL 761 (781)
Q Consensus 682 ~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~L 761 (781)
.|+..++.++.++..+|.+ .|. ++...|++-+..|
T Consensus 4 ~Il~~l~~~~~~s~~ela~--------~~~-------------------------------------VS~~TiRRDl~~L 38 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAE--------EFG-------------------------------------VSEMTIRRDLNKL 38 (57)
T ss_pred HHHHHHHHcCCEEHHHHHH--------HHC-------------------------------------cCHHHHHHHHHHH
Confidence 4667788888999888865 377 9999999999999
Q ss_pred hhcccccccC
Q 003986 762 ITRDYLERDK 771 (781)
Q Consensus 762 i~~eyl~r~~ 771 (781)
-++|.|+|.-
T Consensus 39 ~~~g~i~r~~ 48 (57)
T PF08220_consen 39 EKQGLIKRTH 48 (57)
T ss_pred HHCCCEEEEc
Confidence 9999999864
No 83
>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=44.99 E-value=30 Score=27.56 Aligned_cols=34 Identities=29% Similarity=0.352 Sum_probs=26.1
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccc
Q 003986 591 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 626 (781)
Q Consensus 591 ~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL 626 (781)
.++..|+.+|.+.|++|.+.++.+|-.|.. .+++
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQ--h~~v 57 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQ--HNLV 57 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHH--TTSE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCe
Confidence 356889999999999999999999999973 4444
No 84
>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=43.31 E-value=21 Score=31.68 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=30.5
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
.+.|+.++..++.++-++|++.+|++..++++.|..|.. .+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 455666666667899999999999999999999999974 35553
No 85
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=42.69 E-value=30 Score=28.02 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=28.0
Q ss_pred HHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 585 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
|.-...+++.+|++||+..++++.+.+...|.-|..
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 334455677899999999999999999999999984
No 86
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=42.34 E-value=31 Score=36.11 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=40.5
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
-|..|+-+.++++.+++.||++.+|++...+++-|..|- +.+++.+.
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 467789999999999999999999999999999999996 45666554
No 87
>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=40.93 E-value=59 Score=32.62 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=35.7
Q ss_pred HHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 584 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 584 ~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
.||......+++|..+|++.+|++...+.++|..|.. .+++.+.
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 4555555567799999999999999999999999974 4677654
No 88
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.90 E-value=37 Score=33.36 Aligned_cols=45 Identities=16% Similarity=0.130 Sum_probs=36.6
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
....||.++-.++.+|-++|++.+|++...++++|..|.. .+++.
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 3455666666777899999999999999999999999974 45555
No 89
>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=39.77 E-value=51 Score=31.75 Aligned_cols=43 Identities=16% Similarity=0.192 Sum_probs=34.7
Q ss_pred HHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 583 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 583 ~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
..|+..+=.+..+|-+||++.+|++..++++.|..|.. .+++.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e--~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYD--AGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCce
Confidence 45565555566899999999999999999999999974 45663
No 90
>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=39.34 E-value=39 Score=24.81 Aligned_cols=30 Identities=30% Similarity=0.419 Sum_probs=21.2
Q ss_pred HHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 003986 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 616 (781)
Q Consensus 585 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 616 (781)
|+-++.++ .|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 44455554 8999999999999999988764
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=39.13 E-value=49 Score=27.92 Aligned_cols=35 Identities=9% Similarity=-0.007 Sum_probs=30.6
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHh
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 616 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 616 (781)
-+..|+-+..+ +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988664
No 92
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=39.02 E-value=44 Score=33.83 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=41.3
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
|..-..||-++....++.+.||++.+|+|...+..+++.|. +.+++..+
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 44445688889999999999999999999999999999996 56777643
No 93
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=38.19 E-value=66 Score=24.00 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=29.9
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
|.-+..++.++. .+++..+|++.+|++...+...+..+.
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 94
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=37.85 E-value=57 Score=24.68 Aligned_cols=24 Identities=38% Similarity=0.558 Sum_probs=17.5
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHh
Q 003986 593 DRLSYSEIMTQLNLSDDDVVRLLH 616 (781)
Q Consensus 593 ~~~t~~ei~~~t~i~~~~l~~~L~ 616 (781)
+++|++||++.+|++...++..+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 368999999999999999887765
No 95
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=37.62 E-value=68 Score=23.99 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=28.7
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
|..|..++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555554443 457999999999999999988877653
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=37.38 E-value=49 Score=31.97 Aligned_cols=48 Identities=15% Similarity=0.208 Sum_probs=40.9
Q ss_pred EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
+.-.-..||.++.++...|+.+|++.+|++...+.+-++.|.. .+++.
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 4456677888999999999999999999999999999999973 46664
No 97
>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=36.92 E-value=34 Score=33.76 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=22.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 594 RLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 594 ~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
.+|+++|++.||+..+++..+|+.|-
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 98
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=36.75 E-value=83 Score=30.70 Aligned_cols=54 Identities=20% Similarity=0.191 Sum_probs=40.4
Q ss_pred EEEEcHHHHHHHHhHcCCCC-cCHHHHHHHh--CCCHHHHHHHHhHhhhccccccccCC
Q 003986 575 ELIVTTYQASALLLFNSSDR-LSYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 575 ~l~~s~~Q~~ILllFn~~~~-~t~~ei~~~t--~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
++--+.+..+|+-+..-.+. -+.++|++.+ +++.++++.+|..|. +.++|.+..
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 33344555566665554433 3899999999 999999999999997 678998763
No 99
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=35.30 E-value=44 Score=33.06 Aligned_cols=46 Identities=11% Similarity=0.065 Sum_probs=39.3
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
-+..|+.+.+.++.+++.+|++.+|++...+++-|..|.. .+++.+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~--~g~~~r 53 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI--PELRER 53 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc--chHHHH
Confidence 5677888999999999999999999999999999999973 355543
No 100
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=35.16 E-value=48 Score=34.58 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=40.1
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 582 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
|-.|+-+.++++.++++||++.+|+++..+++=|..|. +.++|.+.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 56788899999999999999999999999999999997 45666664
No 101
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=35.09 E-value=41 Score=25.82 Aligned_cols=26 Identities=8% Similarity=0.179 Sum_probs=21.8
Q ss_pred CChHHHHHHHHHhhhcccccccCCCC
Q 003986 749 PDFKAIKKRIEDLITRDYLERDKSNP 774 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~~~~ 774 (781)
.+...+.+.|+.|.++|++.+....+
T Consensus 22 is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 22 LSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred CCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 66778999999999999999876433
No 102
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=34.19 E-value=41 Score=27.10 Aligned_cols=24 Identities=17% Similarity=0.494 Sum_probs=21.1
Q ss_pred ChHHHHHHHHHhhhcccccccCCC
Q 003986 750 DFKAIKKRIEDLITRDYLERDKSN 773 (781)
Q Consensus 750 ~~~~ik~~ie~Li~~eyl~r~~~~ 773 (781)
+...+...++.|.++|||+|++.-
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 577789999999999999999853
No 103
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=33.09 E-value=66 Score=30.64 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=41.2
Q ss_pred EEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
.++..--.||.++..+...|+.+|++.+|+++..+.+-++.|.. .+++.
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 34566777888888888999999999999999999999999974 35564
No 104
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=32.82 E-value=69 Score=31.52 Aligned_cols=63 Identities=19% Similarity=0.175 Sum_probs=47.9
Q ss_pred ceeEeecCcceEEEEeEecCeeEEEEEcHHHHHHHHhHcCC--CCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 552 RKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 552 RkL~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~ILllFn~~--~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
|.-.|.+.+|..+++- .+.| .||+.||.-|+.-... ..||.+.|++..+++.+++...|..+.
T Consensus 97 r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 3445778888877753 3334 5789999777654433 479999999999999999999888875
No 105
>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=32.77 E-value=58 Score=29.83 Aligned_cols=49 Identities=14% Similarity=0.154 Sum_probs=37.6
Q ss_pred cHHHHHHHHh--Hc--------CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 579 TTYQASALLL--FN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 579 s~~Q~~ILll--Fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
-.+.-..++. .| +.-++|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 28 ~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 28 VIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred HHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 3455555555 33 44589999999999999999999999996 67777653
No 106
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=32.63 E-value=60 Score=33.82 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=36.0
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
-|..|+.+.++++.+++.||++.+|+++..+++-|..|-
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 107
>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=32.29 E-value=9.9e+02 Score=28.99 Aligned_cols=136 Identities=16% Similarity=0.307 Sum_probs=76.1
Q ss_pred hhhHHHHHHHHHHHHHH-HhcCCccCHHHHHHHHHHHHHhcCCcccccHHHhHHHHHHHHHHHHHHH----------HHH
Q 003986 145 TELNGKVRDAVITLIDQ-EREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRK----------ASN 213 (781)
Q Consensus 145 ~~l~~~l~~~ll~~I~~-~R~g~~i~~~~lk~~i~~l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~----------s~~ 213 (781)
..+.+.+-+.+|...+. .|.+ |...++.+..+|..++.+. ..=..|++...-|+... ...
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 35567777777777664 4443 5677899999988875322 11122333333332100 011
Q ss_pred HH-----------hcCChhHHHHHHHHHHHHHHHHHccccCCCc--HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhc
Q 003986 214 WI-----------LEDSCPDYMLKAEECLKREKDRVSHYLHSSS--EPKLLEKVQHELLSVYANQLLEKEHSGCHALLRD 280 (781)
Q Consensus 214 ~l-----------~~~~~~eYl~~v~~~l~eE~~r~~~~l~~~t--~~kl~~~l~~~LI~~~~~~ll~~~~sgl~~ll~~ 280 (781)
|- ...+..+++..+...+++|...+++.+++.. ..++.+.+-...|.+++..+++... ..
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 1123568999999999999999999775532 2344444445555566666655431 11
Q ss_pred CcHHhHHHHHHhhccC
Q 003986 281 DKVEDLSRMFRLFSKI 296 (781)
Q Consensus 281 ~~~~~L~~ly~L~~~~ 296 (781)
+...-|+.++.++..+
T Consensus 249 s~~~YLr~l~~~y~~t 264 (710)
T PF07393_consen 249 STLAYLRTLHGLYSQT 264 (710)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 2233466666666554
No 108
>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=32.24 E-value=26 Score=34.65 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=40.0
Q ss_pred hcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHH
Q 003986 679 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRI 758 (781)
Q Consensus 679 I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~i 758 (781)
+=...|...|.+|.+..++|-. .|. ...+++-.+|
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~--------~f~-------------------------------------l~t~~~i~ri 134 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAA--------EFG-------------------------------------LRTQDVINRI 134 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHH--------HH--------------------------------------S-HHHHHHHH
T ss_pred HHHHHHHHHHHcceeeHHHHHH--------HcC-------------------------------------CCHHHHHHHH
Confidence 3444558889999999988843 488 8889999999
Q ss_pred HHhhhcccccccCCCCCcceecC
Q 003986 759 EDLITRDYLERDKSNPNMFRYLA 781 (781)
Q Consensus 759 e~Li~~eyl~r~~~~~~~~~Yia 781 (781)
..|...|-|.---+|++.|+||+
T Consensus 135 ~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 135 QELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHCCCceeeEcCCCCeEEec
Confidence 99999999988778899999984
No 109
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=32.23 E-value=1.3e+02 Score=27.90 Aligned_cols=68 Identities=18% Similarity=0.245 Sum_probs=49.0
Q ss_pred cHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCC---CeEEEccCCC
Q 003986 579 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPT---DHFEFNSKFT 648 (781)
Q Consensus 579 s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~---~~f~lN~~F~ 648 (781)
|.--...|-+..+.+..|+.|+++.+|-+.+.+.+.|..|. .++++..+.+++...+. +.+.++-.|.
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 33344556777888899999999999999999999999996 57888766555443322 3344555554
No 110
>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=31.95 E-value=62 Score=22.15 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=20.7
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 594 RLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 594 ~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
++|-+||++.+|++.+.+-+.|..|-
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 111
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=31.74 E-value=69 Score=33.36 Aligned_cols=47 Identities=17% Similarity=0.191 Sum_probs=39.8
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
-|..|+..+++++.+++.||++.+|++...+++-|..|. +.+++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEe
Confidence 456788889999999999999999999999999999986 34566554
No 112
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=31.43 E-value=73 Score=24.59 Aligned_cols=41 Identities=22% Similarity=0.255 Sum_probs=32.3
Q ss_pred EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
.|.-+..||.++.. +.|..+|++.+|++...+..++..+..
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 35567778877775 468999999999999999999988863
No 113
>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=31.39 E-value=89 Score=24.23 Aligned_cols=32 Identities=22% Similarity=0.310 Sum_probs=27.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 596 SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 596 t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
|..+|++.+|++...+.++|..|.. .+++...
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 5999999999999999999999974 5676543
No 114
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=31.03 E-value=1.3e+02 Score=25.39 Aligned_cols=42 Identities=21% Similarity=0.262 Sum_probs=32.7
Q ss_pred HHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccc
Q 003986 586 LLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 627 (781)
Q Consensus 586 LllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~ 627 (781)
++..++.+.+|-++|++.+|++...+-++++.|-...+.|..
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 344556678999999999999999999999999644444443
No 115
>PRK00215 LexA repressor; Validated
Probab=30.98 E-value=95 Score=31.06 Aligned_cols=51 Identities=25% Similarity=0.303 Sum_probs=40.2
Q ss_pred EcHHHHHHHHhHcC-----CCCcCHHHHHHHhCC-CHHHHHHHHhHhhhccccccccCC
Q 003986 578 VTTYQASALLLFNS-----SDRLSYSEIMTQLNL-SDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 578 ~s~~Q~~ILllFn~-----~~~~t~~ei~~~t~i-~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
++.-|..||..+.+ ..+.|..||++.+|+ +...+.+.|..|. +.+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCC
Confidence 35678888876652 346899999999999 9999999999997 346776654
No 116
>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=30.94 E-value=37 Score=26.42 Aligned_cols=24 Identities=13% Similarity=0.321 Sum_probs=20.4
Q ss_pred CChHHHHHHHHHhhhcccccccCC
Q 003986 749 PDFKAIKKRIEDLITRDYLERDKS 772 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~~ 772 (781)
.+...+.+.|..|.++|||+|..+
T Consensus 33 ~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 33 ISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred cCHHHHHHHHHHHHHCCCEEEeCC
Confidence 678889999999999999999764
No 117
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.16 E-value=85 Score=29.56 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=40.8
Q ss_pred EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
+.-.-.-||..+++....++.+|++.+|++...+.+.+..|. +.+|+..
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 345566788888888889999999999999999999999997 4566653
No 118
>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=29.86 E-value=7.5e+02 Score=26.83 Aligned_cols=164 Identities=13% Similarity=0.250 Sum_probs=85.5
Q ss_pred hhhhhhhcCcHHhHHHHHHhhccC---CCChhhHHHHHHHHHHHHHHHHHHhHHHHhhhhhhhcccccccchHHHHHHHH
Q 003986 273 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 349 (781)
Q Consensus 273 gl~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~I~~~g~~i~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~ 349 (781)
.|..-.+.++.+.+.|.++||-.+ +.|++.....+.+.|.......++........ ...+.-|+..|.
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 366667788899999999998654 35677777766666666666555443211100 122344555555
Q ss_pred HHHHHHHH-------HHHHhcCCChH--HHHHHHHHHHH----HhccCCCCCch---HHHHHHHHHHHHhc---------
Q 003986 350 ELHDKYLA-------YVNDCFQNHTL--FHKSLKEAFEV----FCNKGVAGSSS---AELLATFCDNILKK--------- 404 (781)
Q Consensus 350 ~l~~~~~~-------li~~~F~~~~~--f~~~l~~af~~----~lN~~~~~~~~---~e~La~y~D~~lk~--------- 404 (781)
.+++..-. +|..+|+.... +...+..-+.. ++..=....++ ...+-.|-...+.+
T Consensus 86 ~LFe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~l~~~~~~i~~~~~~~~~~~~~~~~~~~ 165 (331)
T PF08318_consen 86 KLFEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERRLDRKLQDIQSYNFSFLVKNSGRSSSSS 165 (331)
T ss_pred HHHHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHhhhhhhhccccccccccc
Confidence 55555544 46668885532 11222211111 11110000011 11222333332222
Q ss_pred --------CCCCCCCHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHhcCCCC
Q 003986 405 --------GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 452 (781)
Q Consensus 405 --------~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s 452 (781)
+.....+.-+++..|+.+..+... ...|.++++.|.-....
T Consensus 166 ~~~~~~~~~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 166 SRAASSSQSEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFSD 214 (331)
T ss_pred cccccccccccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcccc
Confidence 001223445678888887777743 45799999999877443
No 119
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=29.27 E-value=90 Score=25.12 Aligned_cols=51 Identities=24% Similarity=0.324 Sum_probs=35.1
Q ss_pred EcHHHHHHHHhHcC-----CCCcCHHHHHHHhCCC-HHHHHHHHhHhhhccccccccCC
Q 003986 578 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 578 ~s~~Q~~ILllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
+|.-|.-||...-+ .-+-|+.||++.+|+. ...+..+|..|. +.+.|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le--~kG~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE--RKGYIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH--HTTSEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCcCccCCC
Confidence 45567777765432 2356999999999997 999999999997 447777654
No 120
>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=29.12 E-value=67 Score=29.31 Aligned_cols=49 Identities=18% Similarity=0.234 Sum_probs=37.8
Q ss_pred cHHHHHHHHhHcCC--------CCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 579 TTYQASALLLFNSS--------DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 579 s~~Q~~ILllFn~~--------~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
..+.-..|+..|.. -+.|.++|+..++-+.+.++.+|..|. +++++...
T Consensus 28 ~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 28 IIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34555555555543 478999999999999999999999996 67777653
No 121
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=29.03 E-value=68 Score=33.43 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=39.6
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
-+..|+-++++++.+++.||++.++++...+++-|..|.. .++|.+.
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 4567888889999999999999999999999999999973 4666554
No 122
>PRK13239 alkylmercury lyase; Provisional
Probab=28.71 E-value=97 Score=31.19 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=35.1
Q ss_pred HHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 580 ~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
.+...+|.++-++.++|+++|+..+|.+.+.+.+.|..|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 4556677778888999999999999999999999999885
No 123
>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=28.39 E-value=33 Score=26.49 Aligned_cols=23 Identities=17% Similarity=0.356 Sum_probs=20.2
Q ss_pred CChHHHHHHHHHhhhcccccccC
Q 003986 749 PDFKAIKKRIEDLITRDYLERDK 771 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~ 771 (781)
.+...+-+.+..|..+|||+|..
T Consensus 29 ~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 29 ISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEE
T ss_pred CChhHHHHHHHHHHHCCCEEecc
Confidence 77899999999999999999864
No 124
>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=28.28 E-value=55 Score=29.25 Aligned_cols=57 Identities=11% Similarity=0.097 Sum_probs=41.2
Q ss_pred eeeeccc-ccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHHHHh
Q 003986 683 IVRIMKS-RKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRIEDL 761 (781)
Q Consensus 683 IVRiMK~-~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~L 761 (781)
|..+|.. .+.++.++|...+.++. .. ++...|=+.++.|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~-------------------------------------i~~~TVYR~L~~L 45 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PS-------------------------------------ISLATVYRTLELL 45 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CC-------------------------------------CCHHHHHHHHHHH
Confidence 4455554 45799999988776542 23 6788899999999
Q ss_pred hhcccccccCCCCCccee
Q 003986 762 ITRDYLERDKSNPNMFRY 779 (781)
Q Consensus 762 i~~eyl~r~~~~~~~~~Y 779 (781)
.+.|.|.+-..+.....|
T Consensus 46 ~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 46 EEAGLVREIELGDGKARY 63 (116)
T ss_pred HhCCCEEEEEeCCCceEE
Confidence 999999997543333444
No 125
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.90 E-value=74 Score=30.17 Aligned_cols=31 Identities=10% Similarity=0.174 Sum_probs=27.6
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHhHhhhc
Q 003986 591 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCA 621 (781)
Q Consensus 591 ~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~ 621 (781)
.++.+|-++|++.+|++...|++.|..|...
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed 42 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDE 42 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhh
Confidence 4457999999999999999999999999753
No 126
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.82 E-value=1.3e+02 Score=21.74 Aligned_cols=40 Identities=30% Similarity=0.385 Sum_probs=28.7
Q ss_pred EcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 003986 578 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 618 (781)
++..+..++.++- ...+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455555554443 245799999999999999998877654
No 127
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=26.43 E-value=79 Score=34.88 Aligned_cols=64 Identities=20% Similarity=0.292 Sum_probs=40.4
Q ss_pred eEeecCcceEEEEeEecCeeEEEEE-------cHHHHHHHHhHcC-C-CCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 554 LTWIYSLGTCNLLGKFESRTTELIV-------TTYQASALLLFNS-S-DRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 554 L~w~~~l~~~~i~~~~~~~~~~l~~-------s~~Q~~ILllFn~-~-~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
+.+.+.||..|=++--+.+ -|+= +-+-..||-++-+ . ..+|+++|++.|||..+++...|++|-
T Consensus 282 IdFSYeLSr~E~~~GsPEK--PLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSPEK--PLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcCCCCCC--CcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 5677888876655322221 1110 2233334433333 2 239999999999999999999999884
No 128
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.25 E-value=42 Score=29.64 Aligned_cols=47 Identities=13% Similarity=0.197 Sum_probs=37.0
Q ss_pred hcceeeeecccccccChHHHHHHHHHHhccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcCCCChHHHHHHH
Q 003986 679 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKVHNTLFSFLFFFFVFVCESFVFLNLTTLALNEMLILQPDFKAIKKRI 758 (781)
Q Consensus 679 I~A~IVRiMK~~k~~~~~~L~~~v~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~i 758 (781)
+|-.|++.+..+..++..+|-.. +. .+...+.++|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~-------------------------------------~s~~tv~~~l 38 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VG-------------------------------------LSPSTVHNRV 38 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HC-------------------------------------cCHHHHHHHH
Confidence 35567777888888888777543 34 7789999999
Q ss_pred HHhhhccccccc
Q 003986 759 EDLITRDYLERD 770 (781)
Q Consensus 759 e~Li~~eyl~r~ 770 (781)
..|.++|+|+|-
T Consensus 39 ~~L~~~g~i~~~ 50 (108)
T smart00344 39 KRLEEEGVIKGY 50 (108)
T ss_pred HHHHHCCCeece
Confidence 999999999953
No 129
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=25.90 E-value=70 Score=31.83 Aligned_cols=51 Identities=22% Similarity=0.273 Sum_probs=40.9
Q ss_pred EcHHHHHHHHhHcCC-----CCcCHHHHHHHhCCC-HHHHHHHHhHhhhccccccccCC
Q 003986 578 VTTYQASALLLFNSS-----DRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 578 ~s~~Q~~ILllFn~~-----~~~t~~ei~~~t~i~-~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
++..|..||....+. -+.|+.||++.+|++ ...+.++|..|. +.++|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecCC
Confidence 467888888777632 358999999999998 999999999997 457777653
No 130
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.47 E-value=80 Score=23.36 Aligned_cols=32 Identities=25% Similarity=0.340 Sum_probs=21.5
Q ss_pred HHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 003986 585 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (781)
Q Consensus 585 ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 618 (781)
++.++.+ .+|..+|++.+|++...+.+-+..+
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 4445554 7899999999999999988876655
No 131
>PHA02591 hypothetical protein; Provisional
Probab=24.87 E-value=86 Score=26.09 Aligned_cols=25 Identities=28% Similarity=0.333 Sum_probs=22.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHhH
Q 003986 593 DRLSYSEIMTQLNLSDDDVVRLLHS 617 (781)
Q Consensus 593 ~~~t~~ei~~~t~i~~~~l~~~L~s 617 (781)
.++|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3689999999999999999988765
No 132
>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=24.60 E-value=1.1e+02 Score=23.54 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=24.2
Q ss_pred HcCCCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 003986 589 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (781)
Q Consensus 589 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~sL 618 (781)
|+.-...|.+||++.+|++...+-.+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 444458999999999999998888777643
No 133
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=24.54 E-value=97 Score=31.65 Aligned_cols=59 Identities=10% Similarity=0.241 Sum_probs=44.4
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCCCC
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTD 649 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F~~ 649 (781)
+-..+.-+|.++..||+.+|.+.|+=|+..|+.+|..++ ++.+.+. ...+|.+-.+|..
T Consensus 187 vld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK~ 245 (254)
T KOG2905|consen 187 VLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYKK 245 (254)
T ss_pred HHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHhh
Confidence 334566788999999999999999999999999999886 3443211 2456777776643
No 134
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=24.32 E-value=91 Score=32.84 Aligned_cols=48 Identities=8% Similarity=0.049 Sum_probs=40.5
Q ss_pred HHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 580 ~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
--|..|+.+++.++.+|+.||++.+|++...++|-|..|-. .+++.+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~--~G~l~r~ 64 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK--QGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh--CCCeEEE
Confidence 45778899999998999999999999999999999999953 4556554
No 135
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=24.30 E-value=1.1e+02 Score=35.47 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=43.2
Q ss_pred EEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 577 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
.+|..|..||..+...+.+|..+|++.+|++...+.+.+.+|.. .+++..
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 355543
No 136
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=24.29 E-value=1.2e+02 Score=32.12 Aligned_cols=38 Identities=18% Similarity=0.310 Sum_probs=30.1
Q ss_pred HHHHHHHhHcC-CCCcCHHHHHHHhCCCHHHHHHHHhHh
Q 003986 581 YQASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSL 618 (781)
Q Consensus 581 ~Q~~ILllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~sL 618 (781)
+...|+-.+.+ ...+|+++|++.|||..+++..+|+.|
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 33445544433 468999999999999999999999987
No 137
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=24.03 E-value=1e+02 Score=31.78 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=35.4
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
-|..|+..+++++.++++||++.+|+++..+++-|..|..
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3566888888888999999999999999999999999863
No 138
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=23.74 E-value=1.8e+02 Score=21.64 Aligned_cols=35 Identities=23% Similarity=0.344 Sum_probs=25.6
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhH
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 617 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~s 617 (781)
+...|+.+.-+. .|+.++++.+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 334444444433 69999999999999999987764
No 139
>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=23.55 E-value=1e+02 Score=32.69 Aligned_cols=57 Identities=14% Similarity=0.298 Sum_probs=32.2
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCCCCCCCCCCCeEEEccCC
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 647 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~~~~~i~~~~~f~lN~~F 647 (781)
+--.|.-+|.++..||+.+|.+.|+-|+..|+.+|..++ ++.+.+. ....|.|=..|
T Consensus 217 L~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-----~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 217 LLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-----VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH-------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----HHhccCC-----cCCcEecchHH
Confidence 445677889999999999999999999999999999886 4554421 23556665555
No 140
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=23.28 E-value=47 Score=28.34 Aligned_cols=34 Identities=18% Similarity=0.195 Sum_probs=23.6
Q ss_pred hhhhhhhhhhhhhhhhcCCCChHHHHHHHHHhhhcccccccC
Q 003986 730 SFVFLNLTTLALNEMLILQPDFKAIKKRIEDLITRDYLERDK 771 (781)
Q Consensus 730 ~~~~~~~~~~~~~~~~~~~~~~~~ik~~ie~Li~~eyl~r~~ 771 (781)
.|+.+|-+.++ ...-.+++.+.+||.+||+++--
T Consensus 26 Dfnl~kH~el~--------ipNL~vika~qsl~S~GYvkt~~ 59 (105)
T COG5045 26 DFNLGKHRELE--------IPNLHVIKAMQSLISYGYVKTIH 59 (105)
T ss_pred hccccCCcccC--------CCchHHHHHHHHHhhcceeEEEe
Confidence 34455555444 33445788889999999999863
No 141
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=23.16 E-value=1.1e+02 Score=21.77 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.1
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHhHhh
Q 003986 592 SDRLSYSEIMTQLNLSDDDVVRLLHSLS 619 (781)
Q Consensus 592 ~~~~t~~ei~~~t~i~~~~l~~~L~sL~ 619 (781)
...+|+++|++..|++...+.+..+...
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 4579999999999999998888776553
No 142
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=23.01 E-value=1.3e+02 Score=25.62 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=35.8
Q ss_pred HHHHHHhHcCCCCcCHHHHHHHh-CCCHHHHHHHHhHhhhccccccccC
Q 003986 582 QASALLLFNSSDRLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 582 Q~~ILllFn~~~~~t~~ei~~~t-~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
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 143
>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=23.00 E-value=83 Score=34.23 Aligned_cols=44 Identities=16% Similarity=0.238 Sum_probs=34.3
Q ss_pred EEcHHHHHHHHhHcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 577 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 577 ~~s~~Q~~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
.++..+..|.-+..+ ..++-..+|...||++...+.++|.+|..
T Consensus 81 ~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~ 126 (327)
T PF05158_consen 81 GLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES 126 (327)
T ss_dssp SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 557777877777664 45788999999999999999999999975
No 144
>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=21.51 E-value=1.6e+02 Score=23.79 Aligned_cols=33 Identities=30% Similarity=0.414 Sum_probs=28.3
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHhHhhhcccccccc
Q 003986 594 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 628 (781)
Q Consensus 594 ~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~ 628 (781)
.+|-++|++.+|++...+.+.|..|. +.+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 57899999999999999999999996 4566654
No 145
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=21.49 E-value=6e+02 Score=24.93 Aligned_cols=62 Identities=13% Similarity=0.084 Sum_probs=36.8
Q ss_pred HHHHHHHHHhcCCCCCc--hHHHHHHHHHHHHHHHHhcccchhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhcch
Q 003986 45 LYTTIYNMCTQKPPHDY--SQQLYDKYRESFEEYISSTVLPSIREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYL 118 (781)
Q Consensus 45 lY~~vY~lc~~~~~~~~--~e~LY~~l~~~l~~~l~~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YL 118 (781)
|+..+|++...+|.... -..||+.+-+.+++.=. .+ =.+..-+.|.-|..-+.-|.+|+.+|
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 67788888887743211 12255554443333110 00 01235568889999999999999886
No 146
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=20.96 E-value=1.7e+02 Score=25.38 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=42.8
Q ss_pred EEEcHHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccC
Q 003986 576 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 629 (781)
Q Consensus 576 l~~s~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~ 629 (781)
+..+....-||..+...+.=...-|+..+++|.+++...|..|. ..++|.+.
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~ 54 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERV 54 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 34566778889888887776778899999999999999999997 45788765
No 147
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=20.87 E-value=1.4e+02 Score=24.68 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=39.3
Q ss_pred HHHHHHHHhHcC--CCCcCHHHHHHHhCCCHHHHHHHHhHhhhccccccccCC
Q 003986 580 TYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 630 (781)
Q Consensus 580 ~~Q~~ILllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~sL~~~k~kiL~~~~ 630 (781)
..|.++|...-. .++++-.+|+..+|++...+-..++.|. +.+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 467888887764 3588999999999999999999999997 456776643
No 148
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.77 E-value=1.8e+02 Score=26.80 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=36.5
Q ss_pred HHHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 580 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 580 ~~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
.+.+-|+-+.-+++.+|+.++...||.+-..+++++.-|+.
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 149
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=20.70 E-value=1.6e+02 Score=25.43 Aligned_cols=33 Identities=15% Similarity=0.323 Sum_probs=23.2
Q ss_pred HhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 587 LLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 587 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
.+..+... ++..|.+.||||...+..+|.+|..
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 34455555 9999999999999999999999974
No 150
>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=20.66 E-value=91 Score=27.71 Aligned_cols=23 Identities=26% Similarity=0.445 Sum_probs=20.2
Q ss_pred CChHHHHHHHHHhhhcccccccC
Q 003986 749 PDFKAIKKRIEDLITRDYLERDK 771 (781)
Q Consensus 749 ~~~~~ik~~ie~Li~~eyl~r~~ 771 (781)
.+...+-+.|..|.++|||.|..
T Consensus 55 ~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 55 IKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred CCHHHHHHHHHHHHHCCCEeccC
Confidence 67888999999999999999743
No 151
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=20.12 E-value=1.8e+02 Score=24.93 Aligned_cols=40 Identities=28% Similarity=0.308 Sum_probs=31.8
Q ss_pred HHHHHHHhHcCCCCcCHHHHHHHhCCCHHHHHHHHhHhhh
Q 003986 581 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 620 (781)
Q Consensus 581 ~Q~~ILllFn~~~~~t~~ei~~~t~i~~~~l~~~L~sL~~ 620 (781)
....+.-+......+++++|++.++++.+++...+..++.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~ 86 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS 86 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH
Confidence 3444455556778999999999999999999999988874
Done!