Query 004648
Match_columns 740
No_of_seqs 241 out of 1073
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 02:50:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004648hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 2E-125 4E-130 1069.2 66.6 719 4-738 5-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 1E-118 2E-123 967.0 63.9 721 5-740 16-773 (773)
3 KOG2167 Cullins [Cell cycle co 100.0 4E-114 8E-119 910.5 46.7 647 67-740 2-661 (661)
4 KOG2284 E3 ubiquitin ligase, C 100.0 1E-110 3E-115 844.3 49.8 680 3-740 5-728 (728)
5 PF00888 Cullin: Cullin family 100.0 1.6E-93 3.5E-98 831.0 62.3 586 13-644 1-588 (588)
6 KOG2285 E3 ubiquitin ligase, C 100.0 1E-92 2.2E-97 721.4 56.6 717 3-740 7-777 (777)
7 smart00182 CULLIN Cullin. 100.0 2.9E-33 6.3E-38 262.5 17.5 141 424-565 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 2.2E-25 4.8E-30 241.3 41.4 306 420-730 444-758 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 4.4E-20 9.5E-25 148.7 1.7 68 667-734 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 97.3 0.0065 1.4E-07 57.4 13.9 137 7-155 3-156 (158)
11 KOG2167 Cullins [Cell cycle co 94.6 2.2 4.8E-05 47.9 18.1 203 11-237 112-324 (661)
12 TIGR01610 phage_O_Nterm phage 92.8 0.27 5.9E-06 42.4 5.9 66 571-644 20-93 (95)
13 PF09339 HTH_IclR: IclR helix- 91.8 0.25 5.4E-06 37.3 3.9 45 579-625 6-51 (52)
14 PF13412 HTH_24: Winged helix- 90.7 0.47 1E-05 35.0 4.4 42 575-616 2-43 (48)
15 PF02082 Rrf2: Transcriptional 90.5 0.71 1.5E-05 38.6 5.9 59 577-642 11-70 (83)
16 PF12802 MarR_2: MarR family; 90.0 0.39 8.4E-06 37.5 3.6 51 574-626 3-55 (62)
17 PF01047 MarR: MarR family; I 86.8 0.47 1E-05 36.7 2.2 50 574-625 1-50 (59)
18 PF13463 HTH_27: Winged helix 86.7 1 2.2E-05 35.8 4.1 50 574-625 1-51 (68)
19 PF08220 HTH_DeoR: DeoR-like h 86.4 1.1 2.3E-05 34.6 3.9 46 578-625 2-47 (57)
20 TIGR02337 HpaR homoprotocatech 85.6 1.4 3.1E-05 39.4 5.0 52 573-626 25-76 (118)
21 PF12840 HTH_20: Helix-turn-he 85.3 1.1 2.3E-05 35.0 3.5 49 575-625 9-57 (61)
22 PF01022 HTH_5: Bacterial regu 84.1 2.4 5.2E-05 31.1 4.7 43 577-622 3-45 (47)
23 PRK11512 DNA-binding transcrip 83.1 2.2 4.9E-05 39.7 5.3 53 572-626 36-88 (144)
24 PF09012 FeoC: FeoC like trans 81.1 0.55 1.2E-05 37.8 0.3 45 679-731 5-49 (69)
25 TIGR02698 CopY_TcrY copper tra 81.0 1.8 4E-05 39.7 3.8 60 676-740 6-65 (130)
26 PF08279 HTH_11: HTH domain; 79.7 3.7 8E-05 31.1 4.5 36 581-616 5-41 (55)
27 smart00550 Zalpha Z-DNA-bindin 79.5 2.8 6.1E-05 33.6 3.9 47 577-625 7-55 (68)
28 TIGR01889 Staph_reg_Sar staphy 78.9 4.7 0.0001 35.6 5.6 52 573-626 22-77 (109)
29 smart00347 HTH_MARR helix_turn 76.6 4.5 9.7E-05 34.5 4.8 53 571-625 5-57 (101)
30 COG3682 Predicted transcriptio 76.0 2.7 5.9E-05 37.7 3.1 62 674-740 6-67 (123)
31 smart00346 HTH_ICLR helix_turn 75.7 6 0.00013 33.3 5.2 45 579-625 8-53 (91)
32 PF03965 Penicillinase_R: Peni 75.5 2.4 5.2E-05 37.9 2.8 60 676-740 5-64 (115)
33 PRK11920 rirA iron-responsive 74.7 8.6 0.00019 36.3 6.4 45 579-625 13-57 (153)
34 PRK10857 DNA-binding transcrip 74.5 9 0.00019 36.7 6.5 45 578-624 12-57 (164)
35 PF01978 TrmB: Sugar-specific 74.4 3.1 6.6E-05 33.2 2.9 50 574-625 6-55 (68)
36 PF08318 COG4: COG4 transport 74.4 1.3E+02 0.0028 32.4 18.6 163 276-448 15-214 (331)
37 PRK15090 DNA-binding transcrip 74.3 6.3 0.00014 40.7 5.9 46 579-626 17-62 (257)
38 PF09763 Sec3_C: Exocyst compl 73.9 1.9E+02 0.0041 34.7 19.1 129 204-361 554-701 (701)
39 PHA00738 putative HTH transcri 73.8 6.3 0.00014 34.4 4.7 67 571-643 7-73 (108)
40 smart00420 HTH_DEOR helix_turn 72.6 6.7 0.00014 28.9 4.2 43 580-624 4-46 (53)
41 PRK13777 transcriptional regul 71.2 7.9 0.00017 37.8 5.4 53 572-626 41-93 (185)
42 PRK03573 transcriptional regul 70.5 7.1 0.00015 36.3 4.8 53 572-626 27-80 (144)
43 TIGR02010 IscR iron-sulfur clu 70.2 11 0.00025 34.6 6.1 44 579-624 13-57 (135)
44 PF04492 Phage_rep_O: Bacterio 70.0 13 0.00028 32.4 5.8 61 574-644 30-98 (100)
45 PF05732 RepL: Firmicute plasm 69.4 5.6 0.00012 38.1 3.9 50 590-648 75-124 (165)
46 PF13404 HTH_AsnC-type: AsnC-t 68.9 7.5 0.00016 27.9 3.5 36 579-614 6-41 (42)
47 COG3355 Predicted transcriptio 68.3 7.5 0.00016 35.2 4.1 39 585-625 37-75 (126)
48 PF04703 FaeA: FaeA-like prote 67.7 10 0.00022 29.8 4.3 56 581-640 5-61 (62)
49 PRK10870 transcriptional repre 66.4 13 0.00028 36.0 5.8 52 573-626 52-105 (176)
50 smart00419 HTH_CRP helix_turn_ 65.5 13 0.00027 26.9 4.3 34 590-625 8-41 (48)
51 PF08784 RPA_C: Replication pr 65.0 11 0.00023 32.8 4.5 44 573-616 44-91 (102)
52 COG1959 Predicted transcriptio 64.8 16 0.00035 34.3 6.0 58 577-641 11-69 (150)
53 PF05584 Sulfolobus_pRN: Sulfo 64.8 15 0.00033 29.6 4.8 46 575-624 5-50 (72)
54 PF08220 HTH_DeoR: DeoR-like h 64.4 3.3 7.2E-05 31.8 1.0 47 677-731 3-49 (57)
55 PRK10141 DNA-binding transcrip 63.1 13 0.00028 33.3 4.7 60 576-641 16-75 (117)
56 COG1414 IclR Transcriptional r 63.0 14 0.00031 37.8 5.7 46 579-626 7-53 (246)
57 PF13601 HTH_34: Winged helix 62.8 8.1 0.00017 32.1 3.1 38 579-616 3-40 (80)
58 smart00345 HTH_GNTR helix_turn 62.4 16 0.00035 27.6 4.7 39 585-625 14-53 (60)
59 PF08280 HTH_Mga: M protein tr 62.4 10 0.00022 29.3 3.5 38 578-615 7-44 (59)
60 PF13463 HTH_27: Winged helix 61.9 6.9 0.00015 30.9 2.5 53 676-736 5-60 (68)
61 PRK11569 transcriptional repre 61.5 14 0.00031 38.5 5.5 46 579-626 31-77 (274)
62 TIGR00738 rrf2_super rrf2 fami 61.5 20 0.00044 32.6 5.9 45 578-624 12-57 (132)
63 PF10771 DUF2582: Protein of u 61.2 11 0.00025 29.8 3.5 38 579-616 11-48 (65)
64 TIGR03879 near_KaiC_dom probab 61.1 11 0.00024 30.6 3.4 30 586-615 28-57 (73)
65 cd00090 HTH_ARSR Arsenical Res 61.0 15 0.00033 29.0 4.5 47 575-624 6-52 (78)
66 TIGR01884 cas_HTH CRISPR locus 60.4 13 0.00028 36.9 4.7 52 573-626 140-191 (203)
67 PRK10163 DNA-binding transcrip 59.8 17 0.00037 37.9 5.7 46 579-626 28-74 (271)
68 TIGR02431 pcaR_pcaU beta-ketoa 58.2 19 0.00041 36.9 5.7 44 579-624 12-56 (248)
69 PRK09834 DNA-binding transcrip 58.2 18 0.00038 37.5 5.5 46 579-626 14-60 (263)
70 smart00550 Zalpha Z-DNA-bindin 57.6 10 0.00022 30.4 2.7 53 676-736 8-62 (68)
71 PF01978 TrmB: Sugar-specific 57.6 3.7 8E-05 32.7 0.2 50 682-739 16-65 (68)
72 smart00344 HTH_ASNC helix_turn 55.5 19 0.00042 31.4 4.5 45 577-623 4-48 (108)
73 TIGR02944 suf_reg_Xantho FeS a 55.5 28 0.0006 31.7 5.7 43 580-624 13-57 (130)
74 COG2345 Predicted transcriptio 55.5 16 0.00034 36.6 4.2 38 579-616 14-51 (218)
75 smart00762 Cog4 COG4 transport 55.2 2.9E+02 0.0064 29.6 16.1 160 276-445 15-205 (324)
76 COG5173 SEC6 Exocyst complex s 54.0 3.8E+02 0.0083 30.5 27.6 59 358-439 621-681 (742)
77 PF13730 HTH_36: Helix-turn-he 53.7 31 0.00067 25.9 4.8 25 592-616 27-51 (55)
78 COG1846 MarR Transcriptional r 53.5 24 0.00053 31.0 5.0 51 574-626 20-70 (126)
79 smart00418 HTH_ARSR helix_turn 52.3 26 0.00056 26.6 4.4 36 588-625 8-43 (66)
80 PF08221 HTH_9: RNA polymerase 50.7 20 0.00043 28.1 3.3 34 587-622 24-57 (62)
81 PF04545 Sigma70_r4: Sigma-70, 50.7 36 0.00078 25.0 4.6 33 578-612 10-42 (50)
82 cd00092 HTH_CRP helix_turn_hel 50.1 35 0.00077 26.5 4.8 35 589-625 24-58 (67)
83 smart00418 HTH_ARSR helix_turn 48.8 15 0.00032 28.1 2.4 45 680-733 3-47 (66)
84 PRK00135 scpB segregation and 48.6 54 0.0012 32.1 6.7 33 583-615 12-45 (188)
85 PF01325 Fe_dep_repress: Iron 47.3 35 0.00076 26.5 4.2 44 581-626 13-56 (60)
86 PF02002 TFIIE_alpha: TFIIE al 47.3 16 0.00035 31.9 2.6 43 578-622 15-57 (105)
87 PF01726 LexA_DNA_bind: LexA D 46.6 32 0.00068 27.3 3.9 24 709-732 39-62 (65)
88 PRK11014 transcriptional repre 45.8 56 0.0012 30.2 6.1 39 585-625 20-58 (141)
89 PF08281 Sigma70_r4_2: Sigma-7 45.2 44 0.00094 24.9 4.4 24 589-612 25-48 (54)
90 PF09756 DDRGK: DDRGK domain; 44.3 7 0.00015 38.1 -0.2 58 675-740 100-157 (188)
91 PF14394 DUF4423: Domain of un 44.1 53 0.0011 31.7 5.8 55 570-626 18-75 (171)
92 cd07153 Fur_like Ferric uptake 44.0 27 0.00057 31.0 3.6 57 679-738 6-63 (116)
93 PF01853 MOZ_SAS: MOZ/SAS fami 43.3 25 0.00054 34.2 3.4 27 589-615 149-175 (188)
94 PF05158 RNA_pol_Rpc34: RNA po 43.2 25 0.00053 37.7 3.7 143 573-732 81-260 (327)
95 PF13412 HTH_24: Winged helix- 41.4 13 0.00028 27.1 0.9 44 676-727 5-48 (48)
96 smart00421 HTH_LUXR helix_turn 40.6 57 0.0012 24.0 4.5 39 575-615 5-43 (58)
97 COG4190 Predicted transcriptio 40.3 60 0.0013 29.5 5.0 64 579-644 67-133 (144)
98 PF02796 HTH_7: Helix-turn-hel 40.0 44 0.00096 24.1 3.5 30 581-612 14-43 (45)
99 TIGR00373 conserved hypothetic 39.7 50 0.0011 31.3 4.8 43 579-623 17-59 (158)
100 PRK10434 srlR DNA-bindng trans 39.5 35 0.00077 35.2 4.1 47 577-625 6-52 (256)
101 PRK06266 transcription initiat 39.5 41 0.00089 32.6 4.3 44 578-623 24-67 (178)
102 cd06170 LuxR_C_like C-terminal 39.1 62 0.0014 23.8 4.5 38 576-615 3-40 (57)
103 PF12324 HTH_15: Helix-turn-he 38.9 75 0.0016 26.1 4.9 39 577-615 25-63 (77)
104 TIGR02702 SufR_cyano iron-sulf 38.9 59 0.0013 32.2 5.5 44 580-625 5-48 (203)
105 smart00344 HTH_ASNC helix_turn 37.9 19 0.00042 31.4 1.7 47 675-729 4-50 (108)
106 PF09012 FeoC: FeoC like trans 37.8 37 0.0008 27.1 3.1 33 584-616 8-40 (69)
107 cd07377 WHTH_GntR Winged helix 37.3 75 0.0016 24.3 4.9 38 586-625 20-58 (66)
108 smart00420 HTH_DEOR helix_turn 37.1 20 0.00042 26.3 1.3 45 679-731 5-49 (53)
109 PF11994 DUF3489: Protein of u 37.1 73 0.0016 25.8 4.5 47 575-621 9-55 (72)
110 PRK00215 LexA repressor; Valid 36.4 67 0.0014 31.8 5.5 51 574-626 2-58 (205)
111 COG1654 BirA Biotin operon rep 36.1 93 0.002 25.8 5.2 41 583-623 12-52 (79)
112 COG1349 GlpR Transcriptional r 35.9 44 0.00096 34.4 4.2 46 578-625 7-52 (253)
113 PRK11169 leucine-responsive tr 35.6 53 0.0011 31.3 4.4 48 574-623 12-59 (164)
114 TIGR02844 spore_III_D sporulat 35.0 60 0.0013 27.0 3.9 35 577-612 7-41 (80)
115 COG4189 Predicted transcriptio 34.2 57 0.0012 32.6 4.3 49 575-625 22-70 (308)
116 PF12802 MarR_2: MarR family; 33.3 19 0.00041 27.7 0.7 26 706-731 31-56 (62)
117 COG1318 Predicted transcriptio 33.1 63 0.0014 30.8 4.2 51 544-615 36-86 (182)
118 smart00345 HTH_GNTR helix_turn 33.1 28 0.00061 26.2 1.7 28 704-731 28-55 (60)
119 TIGR02404 trehalos_R_Bsub treh 33.0 24 0.00053 35.7 1.7 33 704-737 32-64 (233)
120 PF06784 UPF0240: Uncharacteri 32.8 79 0.0017 30.7 5.0 64 547-615 96-161 (179)
121 KOG2747 Histone acetyltransfer 32.8 54 0.0012 35.7 4.2 64 550-615 282-354 (396)
122 PRK04424 fatty acid biosynthes 32.8 51 0.0011 32.2 3.8 46 577-624 8-53 (185)
123 PF00325 Crp: Bacterial regula 32.4 59 0.0013 21.9 2.8 25 591-615 3-27 (32)
124 PRK11179 DNA-binding transcrip 31.9 69 0.0015 30.1 4.5 48 574-623 7-54 (153)
125 PRK13509 transcriptional repre 31.3 68 0.0015 33.0 4.6 47 577-625 6-52 (251)
126 PLN03238 probable histone acet 30.9 75 0.0016 33.1 4.7 40 576-615 208-248 (290)
127 PF01726 LexA_DNA_bind: LexA D 30.6 65 0.0014 25.5 3.3 51 574-626 4-60 (65)
128 PRK09334 30S ribosomal protein 30.3 35 0.00076 28.7 1.8 37 704-740 49-85 (86)
129 KOG1086 Cytosolic sorting prot 29.6 1.7E+02 0.0036 32.2 7.1 92 9-119 22-121 (594)
130 PF01047 MarR: MarR family; I 29.6 26 0.00057 26.6 1.0 43 680-730 9-51 (59)
131 PRK11402 DNA-binding transcrip 29.4 30 0.00066 35.2 1.7 33 704-737 41-73 (241)
132 PF04967 HTH_10: HTH DNA bindi 29.1 84 0.0018 23.8 3.5 29 585-613 18-46 (53)
133 PRK10681 DNA-binding transcrip 28.8 75 0.0016 32.7 4.5 39 577-615 8-46 (252)
134 cd06171 Sigma70_r4 Sigma70, re 28.4 1.2E+02 0.0026 21.7 4.5 39 575-614 12-50 (55)
135 PRK10079 phosphonate metabolis 28.3 33 0.00071 35.0 1.7 53 676-736 22-74 (241)
136 COG1522 Lrp Transcriptional re 27.8 95 0.0021 28.8 4.7 49 574-624 6-54 (154)
137 TIGR02325 C_P_lyase_phnF phosp 27.7 33 0.00072 34.7 1.6 32 705-737 41-72 (238)
138 PF00196 GerE: Bacterial regul 27.6 92 0.002 23.7 3.7 39 575-615 5-43 (58)
139 PF11728 DUF939_C: DUF939 C-te 27.4 3.9E+02 0.0085 25.5 8.8 62 281-353 74-135 (167)
140 KOG2905 Transcription initiati 27.2 80 0.0017 31.8 4.0 58 577-644 187-244 (254)
141 COG5090 TFG2 Transcription ini 27.2 87 0.0019 31.2 4.2 36 580-615 199-234 (297)
142 TIGR00498 lexA SOS regulatory 27.1 1.1E+02 0.0024 30.0 5.2 50 574-625 4-59 (199)
143 PRK04172 pheS phenylalanyl-tRN 27.0 87 0.0019 35.7 5.0 50 573-624 3-52 (489)
144 TIGR03433 padR_acidobact trans 26.7 94 0.002 26.8 4.1 53 675-728 5-57 (100)
145 smart00531 TFIIE Transcription 26.6 74 0.0016 29.7 3.6 32 587-618 12-43 (147)
146 PF00165 HTH_AraC: Bacterial r 26.4 92 0.002 21.9 3.3 28 588-615 6-33 (42)
147 PRK13239 alkylmercury lyase; P 26.4 1.1E+02 0.0024 30.3 4.9 40 576-615 22-61 (206)
148 PF12395 DUF3658: Protein of u 26.0 94 0.002 27.5 4.0 61 675-738 49-109 (111)
149 PRK09802 DNA-binding transcrip 25.8 83 0.0018 32.7 4.2 48 576-625 17-64 (269)
150 PF09681 Phage_rep_org_N: N-te 25.7 83 0.0018 28.4 3.6 50 574-625 27-86 (121)
151 PF13384 HTH_23: Homeodomain-l 25.7 74 0.0016 23.2 2.8 32 581-614 10-41 (50)
152 PRK10906 DNA-binding transcrip 25.5 89 0.0019 32.2 4.3 47 577-625 6-52 (252)
153 TIGR01714 phage_rep_org_N phag 25.4 1E+02 0.0023 27.7 4.1 49 575-625 28-84 (119)
154 TIGR01889 Staph_reg_Sar staphy 25.3 51 0.0011 28.9 2.2 41 685-733 40-82 (109)
155 PF00392 GntR: Bacterial regul 25.0 37 0.00079 26.5 1.0 28 704-731 32-59 (64)
156 PF13730 HTH_36: Helix-turn-he 25.0 44 0.00095 25.0 1.5 21 706-726 35-55 (55)
157 PLN03239 histone acetyltransfe 24.8 1E+02 0.0022 33.1 4.5 40 575-614 265-308 (351)
158 KOG3054 Uncharacterized conser 24.7 52 0.0011 33.0 2.2 54 679-740 205-258 (299)
159 PF13542 HTH_Tnp_ISL3: Helix-t 24.6 1.7E+02 0.0036 21.5 4.6 23 591-613 28-50 (52)
160 PRK14999 histidine utilization 24.5 39 0.00085 34.4 1.5 47 682-737 29-76 (241)
161 PF01638 HxlR: HxlR-like helix 24.4 1.2E+02 0.0025 25.6 4.1 45 578-625 7-52 (90)
162 COG2188 PhnF Transcriptional r 24.0 42 0.0009 34.2 1.5 35 702-737 37-71 (236)
163 PF09904 HTH_43: Winged helix- 23.7 1.2E+02 0.0026 25.7 3.8 33 583-616 15-47 (90)
164 PF02186 TFIIE_beta: TFIIE bet 23.3 40 0.00087 26.8 1.0 54 676-740 7-61 (65)
165 PF02270 TFIIF_beta: Transcrip 23.2 95 0.0021 32.4 4.0 57 577-643 217-273 (275)
166 PRK10434 srlR DNA-bindng trans 23.1 40 0.00086 34.8 1.2 47 676-730 7-53 (256)
167 COG1349 GlpR Transcriptional r 23.0 37 0.00081 35.0 0.9 45 677-729 8-52 (253)
168 cd07377 WHTH_GntR Winged helix 22.9 58 0.0012 25.0 1.8 28 704-731 33-60 (66)
169 PRK06474 hypothetical protein; 22.9 1.8E+02 0.004 28.1 5.7 51 573-625 8-60 (178)
170 PLN00104 MYST -like histone ac 22.7 1.2E+02 0.0025 33.9 4.7 38 577-614 360-398 (450)
171 PHA02591 hypothetical protein; 22.7 1E+02 0.0022 25.3 3.1 25 589-613 58-82 (83)
172 PRK03573 transcriptional regul 22.5 57 0.0012 30.1 2.0 26 705-730 55-80 (144)
173 PHA02943 hypothetical protein; 22.2 1.4E+02 0.003 28.0 4.2 42 581-625 16-57 (165)
174 PF05261 Tra_M: TraM protein, 22.2 2.9E+02 0.0064 24.9 6.1 58 150-207 8-75 (127)
175 PF01399 PCI: PCI domain; Int 22.1 1.5E+02 0.0032 25.1 4.5 40 577-616 47-86 (105)
176 PRK11512 DNA-binding transcrip 22.1 66 0.0014 29.8 2.3 38 685-730 51-88 (144)
177 PF03444 HrcA_DNA-bdg: Winged 21.6 3.1E+02 0.0067 22.7 5.7 48 577-626 10-57 (78)
178 TIGR02989 Sig-70_gvs1 RNA poly 21.6 1.4E+02 0.0031 27.6 4.6 38 574-613 112-150 (159)
179 COG1522 Lrp Transcriptional re 21.6 59 0.0013 30.3 1.9 50 673-730 7-56 (154)
180 cd07977 TFIIE_beta_winged_heli 21.4 60 0.0013 26.6 1.7 26 674-699 9-36 (75)
181 PRK10411 DNA-binding transcrip 21.3 1.3E+02 0.0027 30.8 4.4 39 578-616 6-44 (240)
182 PF04760 IF2_N: Translation in 21.3 63 0.0014 24.3 1.7 22 590-611 3-24 (54)
183 PRK11050 manganese transport r 21.2 1.7E+02 0.0036 27.5 4.9 43 580-624 41-83 (152)
184 smart00347 HTH_MARR helix_turn 21.1 82 0.0018 26.4 2.6 47 676-730 12-58 (101)
185 TIGR02018 his_ut_repres histid 21.0 52 0.0011 33.2 1.5 46 682-736 18-64 (230)
186 PRK09764 DNA-binding transcrip 20.9 56 0.0012 33.2 1.8 46 682-736 22-68 (240)
187 PHA03103 double-strand RNA-bin 20.3 2E+02 0.0043 28.0 5.2 43 581-625 18-60 (183)
188 PRK10906 DNA-binding transcrip 20.3 51 0.0011 33.9 1.3 46 676-729 7-52 (252)
189 PF04182 B-block_TFIIIC: B-blo 20.1 1.4E+02 0.003 24.3 3.5 49 576-626 2-52 (75)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.8e-125 Score=1069.18 Aligned_cols=719 Identities=50% Similarity=0.880 Sum_probs=672.8
Q ss_pred CccCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHHhcc
Q 004648 4 KKKLSFEESWALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQSDV 83 (740)
Q Consensus 4 ~~~~~f~~~W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~~~v 83 (740)
+.+.+|+.+|..++++++++.+..++-+...++.-+|+.+|+++|++|+++.+. +.+++||+++++++.+|+.+.+
T Consensus 5 ~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~----~~~~~lY~~l~~~~~~yl~~~~ 80 (725)
T KOG2166|consen 5 PKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPH----DYSQQLYDKYREVIEEYLIQTV 80 (725)
T ss_pred ccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCC----cchHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888654444577888999999999999999654 4459999999999999999988
Q ss_pred cchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhhcCCCccHHHHH-HHHHHHHHHH-HhHHHHHHHHHHH
Q 004648 84 LPSFEDKRGEFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRSQAGLASLIEVP-VVVFRDRVYK-DLKRDVRDTVIAL 161 (740)
Q Consensus 84 ~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~~~~~i~~l~-l~~f~~~i~~-~~~~~l~~~ll~~ 161 (740)
.+......++.+|..+++.|.+|+.++.+++++|+||||+||++.++..++++++ +.+|+..++. ++++.+.++++.+
T Consensus 81 ~~~~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~l 160 (725)
T KOG2166|consen 81 LPALREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLAL 160 (725)
T ss_pred HHHHHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHH
Confidence 7777777888999999999999999999999999999999999443666676666 9999988877 5999999999999
Q ss_pred HHHHhcCCccCHHHHHHHHHHHHHhCCcchhchHHHHHHHHHHHHHHHHHHHHHhHhhcCChhHHHHHHHHHHHHHHHHH
Q 004648 162 IDEEREGEKIDRALVKKAVDIFVGIGILDMDFYRQDFEEQMIDDAGCYYLRKASSWILNDSCPEYMIKAEECLKKERDRA 241 (740)
Q Consensus 162 I~~~R~g~~id~~~lk~vi~~l~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~s~~eYl~~ve~~l~~E~~r~ 241 (740)
|..+|.|+.||+..|+++++|++.+|.+..++|..+||++|++.|+.||..+++.|+...++++|+.+|+.++.+|..|+
T Consensus 161 I~~eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~ 240 (725)
T KOG2166|consen 161 IHKEREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERV 240 (725)
T ss_pred HHhhcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998899999999999999999999
Q ss_pred ccccCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcCchhhHHHHHHhhhhhcCCcHHHHHHHHHHHHHHHHHH
Q 004648 242 VYYFHTRSESKLIEKVQHELLVVHRNQLLENEKSGCRALISQEKFDDLSRIFRLYDETRTGLEPVAGIFKQYFIDQGKAL 321 (740)
Q Consensus 242 ~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~ 321 (740)
..||+..+.+++.+.++.+++..+.+.+++..++||..|+.+++.++|.+||+|+++++.|++++++.|+.|++.+|..+
T Consensus 241 ~~yl~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l 320 (725)
T KOG2166|consen 241 THYLHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNAL 320 (725)
T ss_pred HhhhhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999888
Q ss_pred HHhhHHhhhhhcccchHHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHhccCCCccCcHHHHHHHHHHHhccC
Q 004648 322 VHQAEEDVRNKTANMEQNLVGKILELHDKFMAYVSICFGDHKLFLMALKEAFEVFCNESIVEISSAEILATFCDNLFKNS 401 (740)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~D~~lk~~ 401 (740)
+........ ..|..+|+.+++++++|..++..||+++..|..+++.||..|+|.+.. ..+|+||+|||.+||++
T Consensus 321 ~~r~~~~~~----~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~lkk~ 394 (725)
T KOG2166|consen 321 VARPAETAA----TNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDILKKG 394 (725)
T ss_pred hhhhhhhcc----cchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHHhccc
Confidence 876654321 468999999999999999999999999999999999999999999863 23699999999999995
Q ss_pred CCCCCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCCchHHhHHHHHHHHH
Q 004648 402 DAEKLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLFDKGGNKDYDKTFLSKLKQHSGGHFTTKMEGMITDVV 481 (740)
Q Consensus 402 ~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~D~~ 481 (740)
. .+.++++++..+++++.+|+|+.+||+|+.+|+++||||||+++|.|+++|+.||++|+++||.+||+||++|++|+.
T Consensus 395 ~-k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~ 473 (725)
T KOG2166|consen 395 S-KKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLT 473 (725)
T ss_pred c-cCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHH
Confidence 4 678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCceEEEEeecCCCCCCCCCCccCCHhHHHHHHHHHHHHhhcCCCceeEeccCccceEE
Q 004648 482 LARENQTALDDWFSSNLNEKPQFDLSVMVLTTGSWPSYKFFGLNLPSEMVKGVESFKKFYGTKTKARKLTWIYSLGNCHV 561 (740)
Q Consensus 482 ~S~~~~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i 561 (740)
.|++++..|+++ .+.....+++|.|.|||+|+||.+++.++.||++|.++++.|..||..+|+||+|.|+|++|+|+|
T Consensus 474 ~s~~l~~~F~~~--~~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei 551 (725)
T KOG2166|consen 474 LSRELQTAFADY--ANYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEI 551 (725)
T ss_pred HHHHHHHHHHhh--hchhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEE
Confidence 999999999987 122224579999999999999998888899999999999999999999999999999999999999
Q ss_pred EEEecCeeEEEEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecc
Q 004648 562 NGKFELKAIELIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNA 641 (740)
Q Consensus 562 ~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 641 (740)
.++|.+++++|+|||+|||||++||+.+.+|+++|.++|+++.+++.++|+||++.|.+++.+ |.++. ++++.|.+|.
T Consensus 552 ~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~ 629 (725)
T KOG2166|consen 552 NGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNS 629 (725)
T ss_pred EEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeec
Confidence 999999999999999999999999999999999999999999999999999999888777766 77777 8899999999
Q ss_pred cCCCCCcceeccCCCcchhhhhHHhHHhhhhhchhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhh
Q 004648 642 KFTDRMRRIRIPLPPVDDRREINEDVGKDRRHNIDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLI 721 (740)
Q Consensus 642 ~F~~~~~~i~i~~~~~~e~~~~~~~v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LI 721 (740)
+|+++.+|+++|.++..+.+++.+.+++||+..|+||||||||+||.|.|++|+.||++|+++||.|++.+||+|||.||
T Consensus 630 ~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LI 709 (725)
T KOG2166|consen 630 KFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLI 709 (725)
T ss_pred cccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHH
Confidence 99999999999988888888899999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccccCCCCCCccee
Q 004648 722 NREFIERDSKDPTMFNY 738 (740)
Q Consensus 722 ereyi~r~~~d~~~y~Y 738 (740)
|||||+|| +|+++|+|
T Consensus 710 EkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 710 EREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHhcc-CCCCcccC
Confidence 99999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.8e-119 Score=966.98 Aligned_cols=721 Identities=29% Similarity=0.485 Sum_probs=642.2
Q ss_pred ccCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCc--------ccHHHHHHHHHHHHH
Q 004648 5 KKLSFEESWALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDC--------SYSQRLYVKYGEVFE 76 (740)
Q Consensus 5 ~~~~f~~~W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~--------~~~e~LY~~l~~~l~ 76 (740)
...||+++|..++.||++|..-|.. +++...||++|+.+|+.|+++.+..+.. ..|..||+++..+.+
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 5679999999999999999854443 2445569999999999999986543211 359999999999999
Q ss_pred HHHHhcccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhhcC-----CCccHHHHHHHHHHHHHHHHhH
Q 004648 77 EHMQSDVLPSFEDKRGEFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRSQA-----GLASLIEVPVVVFRDRVYKDLK 151 (740)
Q Consensus 77 ~~l~~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~-----~~~~i~~l~l~~f~~~i~~~~~ 151 (740)
+++.+.-.. ......+.+|..++..|+++..++.+++.+|.||||+|++ .. ....+.++++..|+..+|.++.
T Consensus 92 ~~i~~~~~~-~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k-~~~~~~~~~~E~~slcl~~~~~~~f~~i~ 169 (773)
T COG5647 92 NYIEEYNRG-RSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLK-KARYDKTLVFEVYSLCLVKEKIESFRLIV 169 (773)
T ss_pred HHHHHhccc-ccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhh-hccCCCccceeeehhhhhHHHHHHHHhhh
Confidence 999875432 2233457899999999999999999999999999999999 32 2345788999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhCC------cchhchHHHHHHHHHHHHHHHHHHHHHhHhhcCChhH
Q 004648 152 RDVRDTVIALIDEEREGEKIDRALVKKAVDIFVGIGI------LDMDFYRQDFEEQMIDDAGCYYLRKASSWILNDSCPE 225 (740)
Q Consensus 152 ~~l~~~ll~~I~~~R~g~~id~~~lk~vi~~l~~l~~------~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~s~~e 225 (740)
+.+.+.+|..+.+.|.|+.+|+..+..++.|+..+|. .++.+|.+.|||.||+.|.+||..+++..+..+++.+
T Consensus 170 ~~lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~e 249 (773)
T COG5647 170 DSLINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTE 249 (773)
T ss_pred HHHHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHH
Confidence 9999999999999999999999999999999999964 2458999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHccccCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcCchhhHHHHHHhhhhhcCCcHH
Q 004648 226 YMIKAEECLKKERDRAVYYFHTRSESKLIEKVQHELLVVHRNQLLENEKSGCRALISQEKFDDLSRIFRLYDETRTGLEP 305 (740)
Q Consensus 226 Yl~~ve~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~ 305 (740)
||.+|+.++++|..+++.|++.++..++.++++++||+.|.+.|.+.. +||..+++....+.|+.||+++++++.|+.+
T Consensus 250 yL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~p 328 (773)
T COG5647 250 YLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQP 328 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhh
Confidence 999999999999999999999999999999999999999999998765 8999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHhhhh-hc--------ccchHHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHH
Q 004648 306 VAGIFKQYFIDQGKALVHQAEEDVRN-KT--------ANMEQNLVGKILELHDKFMAYVSICFGDHKLFLMALKEAFEVF 376 (740)
Q Consensus 306 l~~~~~~~i~~~g~~~~~~~~~~~~~-~~--------~~~~~~~v~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~ 376 (740)
|.+.|..||.+.|.-+ +-....+.. ++ .-.+..+|+.++++++.+..++...|.+|..+..++++||..|
T Consensus 329 l~~~f~~yV~~~g~~~-~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~f 407 (773)
T COG5647 329 LQEVFERYVKDEGVLI-NIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTF 407 (773)
T ss_pred HHHHHHHHHHhhchhh-hhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHH
Confidence 9999999999999222 111111110 11 1148899999999999999999999999999999999999999
Q ss_pred hccCCC-ccCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHhcCCCCCChHHHH
Q 004648 377 CNESIV-EISSAEILATFCDNLFKNSDAEKLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLFDKGGNKDYDK 455 (740)
Q Consensus 377 ~n~~~~-~~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~~~E~ 455 (740)
+|.+.+ ...++|+||+|+|.+||+++ +......++..+.+++.||+|+.+||+|+++|+++||||||+++|+|.++|.
T Consensus 408 in~~~sa~~~~~e~Laky~D~~lkk~~-k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~ 486 (773)
T COG5647 408 INGNESADSGPSEYLAKYIDGLLKKDG-KQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAEL 486 (773)
T ss_pred hccccccccccHHHHHHHhHHHhhccc-cccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence 999642 24689999999999999875 3333446788899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhCCchHHhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCceEEEEeecCCCCCCC-CCCccCCHhHHHHH
Q 004648 456 TFLSKLKQHSGGHFTTKMEGMITDVVLARENQTALDDWFSSNLNEKPQFDLSVMVLTTGSWPSYK-FFGLNLPSEMVKGV 534 (740)
Q Consensus 456 ~~i~~Lk~~~G~~~t~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~-~~~~~lP~~l~~~~ 534 (740)
+||++||+.||.+||+|+++||+||..|.++...|++...+ ..+.+|+.|.||++.+||..| ...++||++|.+.+
T Consensus 487 ~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s---~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~l 563 (773)
T COG5647 487 KMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQS---YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPIL 563 (773)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchh---hccccchhHHHHHHhcCCCCccccccCCChHHHHHH
Confidence 99999999999999999999999999999999999875421 235789999999999999665 46899999999999
Q ss_pred HHHHHHHhhcCCCceeEeccCccceEEEEEecCeeEEEE---ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHH
Q 004648 535 ESFKKFYGTKTKARKLTWIYSLGNCHVNGKFELKAIELI---VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVL 611 (740)
Q Consensus 535 ~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~---~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L 611 (740)
+.|++||.+||+||+|.|.|+||+|+|+++|+.+++.+. ++++|+.|+++||+++++|+++|.+.|+|+.++++++|
T Consensus 564 e~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L 643 (773)
T COG5647 564 EGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVL 643 (773)
T ss_pred HHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHH
Confidence 999999999999999999999999999999998754443 66889999999999999999999999999999999999
Q ss_pred HHhhcccccccccCCCCCCCCCCCceeecccCCCCCcceeccCCCc----chhhhhHHhHHhhhhhchhhheeecccCCC
Q 004648 612 HSLSCSKHKILNKEPNTKTISQSDSFEFNAKFTDRMRRIRIPLPPV----DDRREINEDVGKDRRHNIDAALVRIMKSRK 687 (740)
Q Consensus 612 ~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~i~A~IVRimK~~k 687 (740)
+||+++|..++.+ +++.++|++.|.+|.+|+++..+|+++.+.. +++..+++.+++||+..++||||||||+||
T Consensus 644 ~sl~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk 721 (773)
T COG5647 644 QSLSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARK 721 (773)
T ss_pred HHHHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999877666554 4788999999999999999999999998754 456667889999999999999999999999
Q ss_pred CCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 688 VLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 688 ~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
+|+|++|+++|+.++++||.|++.+||++|+.|||||||+|.++| .+|+|+|
T Consensus 722 ~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 722 KLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred cCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 999999999999999999999999999999999999999999988 8999997
No 3
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.6e-114 Score=910.48 Aligned_cols=647 Identities=32% Similarity=0.539 Sum_probs=606.1
Q ss_pred HHHHHHHHHHHHHHhcccchhhcc--chhhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhh-cCCCccHHHHHHHHHH
Q 004648 67 LYVKYGEVFEEHMQSDVLPSFEDK--RGEFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRS-QAGLASLIEVPVVVFR 143 (740)
Q Consensus 67 LY~~l~~~l~~~l~~~v~~~l~~~--~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~-~~~~~~i~~l~l~~f~ 143 (740)
||+.+++.+++|++..+. .+... +...+|..+.++|..|+..+.+++.+|.||||.|+.+ +..++|+|++|+.+||
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 899999999999986553 23322 3356899999999999999999999999999999996 5678999999999999
Q ss_pred HHHHH----HhHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHHhCCcchhchHHHHHHHHHHHHHHHHHHHHHhHhh
Q 004648 144 DRVYK----DLKRDVRDTVIALIDEEREGEKIDRALVKKAVDIFVGIGILDMDFYRQDFEEQMIDDAGCYYLRKASSWIL 219 (740)
Q Consensus 144 ~~i~~----~~~~~l~~~ll~~I~~~R~g~~id~~~lk~vi~~l~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~ 219 (740)
.+++. .+.....++++..++++|.|+++|+++|+.++.|+.++ .+|.+.|++.|++.+.++|..++....+
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 47788899999999999999999999999999999984 6899999999999999999999999999
Q ss_pred cCChhHHHHHHHHHHHHHHHHHccccCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcCchhhHHHHHHhhhhh
Q 004648 220 NDSCPEYMIKAEECLKKERDRAVYYFHTRSESKLIEKVQHELLVVHRNQLLENEKSGCRALISQEKFDDLSRIFRLYDET 299 (740)
Q Consensus 220 ~~s~~eYl~~ve~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~L~~~~ 299 (740)
+..+++||++++.++.+|..|+..|++.+|...+..+++++|+..|++.++.+ |+..+++..+..++.+||.|++++
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 99999999999999999999999999999977799999999999999999865 799999999999999999999999
Q ss_pred cCCcHHHHHHHHHHHHHHHHHHHHhhHHhhhhhcccchHHHHHHHHHHHHHHHHHHHHhhCCC--HHHHHHHHHHHHHHh
Q 004648 300 RTGLEPVAGIFKQYFIDQGKALVHQAEEDVRNKTANMEQNLVGKILELHDKFMAYVSICFGDH--KLFLMALKEAFEVFC 377 (740)
Q Consensus 300 ~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~~~l~~~~F~~~--~~f~~~l~~af~~~~ 377 (740)
.++...++..|++|+++-|..++.+.. .+..+|+.+++++++.+-++..||..+ ..|..++++||+.|+
T Consensus 233 ~~g~l~l~qq~sdylk~~G~KlV~de~---------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fi 303 (661)
T KOG2167|consen 233 QGGQLSLLQQWSDYLKKPGFKLVIDEE---------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFI 303 (661)
T ss_pred hcchHHHHHHHHHHHhcccceeccCch---------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 889999999999999999999986543 278899999999999999999999988 899999999999999
Q ss_pred ccCCCccCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHhcCCCCCChHHHHHH
Q 004648 378 NESIVEISSAEILATFCDNLFKNSDAEKLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLFDKGGNKDYDKTF 457 (740)
Q Consensus 378 n~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~~~E~~~ 457 (740)
|+.. .++||+||+|.|.+|+.|. +..++++++..+++++.||+|+..||+|+.+|++.||+|||.++|+|.|+|++|
T Consensus 304 nk~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~m 380 (661)
T KOG2167|consen 304 NKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSM 380 (661)
T ss_pred hccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhhcchhHH
Confidence 9775 6799999999999999865 556788899999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCCchHHhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCceEEEEeecCCCCCCCCCCccCCHhHHHHHHHH
Q 004648 458 LSKLKQHSGGHFTTKMEGMITDVVLARENQTALDDWFSSNLNEKPQFDLSVMVLTTGSWPSYKFFGLNLPSEMVKGVESF 537 (740)
Q Consensus 458 i~~Lk~~~G~~~t~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f 537 (740)
+.+||.+||..||+||++||+||..|++++..|+.+..++.....++ +.|.|||.|+||++++.++.||++|..+++.|
T Consensus 381 l~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F 459 (661)
T KOG2167|consen 381 LSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIF 459 (661)
T ss_pred HHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHHHHHHHH
Confidence 99999999999999999999999999999999999855443323344 99999999999999999999999999999999
Q ss_pred HHHHhhcCCCceeEeccCccceEEEEEecCeeEEEEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcc
Q 004648 538 KKFYGTKTKARKLTWIYSLGNCHVNGKFELKAIELIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCS 617 (740)
Q Consensus 538 ~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~ 617 (740)
..||..+|+||+|.|.+++|+|.+++.|+.|+++|.+|++|++||++||+++++|++||.+.|+|.+.+|.|+|+||+|+
T Consensus 460 ~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cg 539 (661)
T KOG2167|consen 460 KKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACG 539 (661)
T ss_pred HHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCCCCCCCCCCceeecccCCCCCcceeccCCCc----chhhhhHHhHHhhhhhchhhheeecccCCCCCChhH
Q 004648 618 KHKILNKEPNTKTISQSDSFEFNAKFTDRMRRIRIPLPPV----DDRREINEDVGKDRRHNIDAALVRIMKSRKVLGYQQ 693 (740)
Q Consensus 618 k~~iL~~~~~~~~~~~~~~~~~N~~F~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~i~A~IVRimK~~k~l~~~~ 693 (740)
|.++|.+.|.|+.+.++|.|.+|..|++|..||+|+++.. +|+++|.++|.+||++.|+||||||||+||+|+|+.
T Consensus 540 r~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~ 619 (661)
T KOG2167|consen 540 RARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNL 619 (661)
T ss_pred cceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhH
Confidence 9999999999999999999999999999999999998765 467788899999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 694 LISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 694 L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
|++++.++|+ ||..+ ++|+|||+||+|||++|| +| +.|.|||
T Consensus 620 l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 620 LVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred HHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 9999999997 99988 999999999999999999 44 9999998
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-110 Score=844.30 Aligned_cols=680 Identities=26% Similarity=0.470 Sum_probs=622.7
Q ss_pred CCccCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHHhc
Q 004648 3 SKKKLSFEESWALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQSD 82 (740)
Q Consensus 3 ~~~~~~f~~~W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~~~ 82 (740)
+|+.++||++|..|.+.|-.+.. ...+.+..|..-|+.||.+|..- |. +.||+||..++.++++|+...
T Consensus 5 kp~vv~fd~~w~~l~~si~~ii~------l~~i~~~~w~~~fsdvy~icvs~-p~----pl~erly~e~k~~i~~hvrq~ 73 (728)
T KOG2284|consen 5 KPKVVEFDKVWVQLRPSIIDIIN------LRPITNVQWHHKFSDVYDICVSI-PT----PLSERLYNEVKACIQEHVRQK 73 (728)
T ss_pred CceeeeHHHHHHHHHHHHHHHHh------ccchhccccccchhhHHHHHHhC-CC----chhHHHHHHHHHHHHHHHHHH
Confidence 78999999999999988877642 23577788999999999999998 45 689999999999999999855
Q ss_pred ccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhhcCC------------------CccHHHHHHHHHHH
Q 004648 83 VLPSFEDKRGEFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRSQAG------------------LASLIEVPVVVFRD 144 (740)
Q Consensus 83 v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~~------------------~~~i~~l~l~~f~~ 144 (740)
.. .....+.+.+|..|.+.|+.|..+..++..+|.|||+.|++ .++ +..|..+|+.+|++
T Consensus 74 ~~-~~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk-~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~ 151 (728)
T KOG2284|consen 74 RQ-DIVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVK-QKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKE 151 (728)
T ss_pred hh-hhhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHh-hhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHH
Confidence 33 23333446699999999999999999999999999999999 432 23577899999999
Q ss_pred HHHHHhHHHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHHHHhCC-----------------cchhchHHHHHHHHHHHH
Q 004648 145 RVYKDLKRDVRDTVIALIDEEREGEKID-RALVKKAVDIFVGIGI-----------------LDMDFYRQDFEEQMIDDA 206 (740)
Q Consensus 145 ~i~~~~~~~l~~~ll~~I~~~R~g~~id-~~~lk~vi~~l~~l~~-----------------~~~~~Y~~~FE~~~l~~t 206 (740)
.+..++...|...++..|.++|.|+..+ ...+.+++++|+.+.. ....+|++.||.|||.+|
T Consensus 152 ~~v~~i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t 231 (728)
T KOG2284|consen 152 DLVKTILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDT 231 (728)
T ss_pred HHHHHHHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccch
Confidence 9999999999999999999999999887 6789999999998853 135799999999999999
Q ss_pred HHHHHHHHHhHhhcCChhHHHHHHHHHHHHHHHHHccccCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcCch
Q 004648 207 GCYYLRKASSWILNDSCPEYMIKAEECLKKERDRAVYYFHTRSESKLIEKVQHELLVVHRNQLLENEKSGCRALISQEKF 286 (740)
Q Consensus 207 ~~yY~~~s~~~l~~~s~~eYl~~ve~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~~~~ 286 (740)
.+||+.+++..+.+.+|++|+.+|..++++|+-||+.|||+++..|++..|++.+|.+|.+.| +..|..++.+++.
T Consensus 232 ~~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~ 307 (728)
T KOG2284|consen 232 EQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEEN 307 (728)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999877 3569999999999
Q ss_pred hhHHHHHHhhhhhcCCcHHHHHHHHHHHHHHHHHHHHhhHHhhhhhcccchHHHHHHHHHHHHHHHHHHHHhhCCCHHHH
Q 004648 287 DDLSRIFRLYDETRTGLEPVAGIFKQYFIDQGKALVHQAEEDVRNKTANMEQNLVGKILELHDKFMAYVSICFGDHKLFL 366 (740)
Q Consensus 287 ~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~~~l~~~~F~~~~~f~ 366 (740)
.||+.||+|+..+..|+..+...|++||.++|...++.... .+.|..||+.++.+|.+|..++...|++|..|.
T Consensus 308 ~d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~------en~p~~fve~vl~v~~kf~~~~~~v~~~d~~f~ 381 (728)
T KOG2284|consen 308 KDLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTG------ENVPQQFVENVLRVYNKFNDMKTAVFMDDGEFS 381 (728)
T ss_pred hhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhcc------ccchHHHHHHHHHHHHHHHHHHHHHhcCchhhh
Confidence 99999999999999999999999999999999998876543 346999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCc---cCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHh
Q 004648 367 MALKEAFEVFCNESIVE---ISSAEILATFCDNLFKNSDAEKLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRL 443 (740)
Q Consensus 367 ~~l~~af~~~~n~~~~~---~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRL 443 (740)
.+++.|+..++|...++ ++.+|.||+|||.+|||+. +++++.++|..|+..+.+|+|++|||+|.++|.++||+||
T Consensus 382 s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~mla~rl 460 (728)
T KOG2284|consen 382 SGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKMLANRL 460 (728)
T ss_pred HHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHHHHHH
Confidence 99999999999987542 5789999999999999975 7899999999999999999999999999999999999999
Q ss_pred cCCCCCChHHHHHHHHHHHHhhCCchHHhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCceEEEEeecCCCCCCCCCC
Q 004648 444 LFDKGGNKDYDKTFLSKLKQHSGGHFTTKMEGMITDVVLARENQTALDDWFSSNLNEKPQFDLSVMVLTTGSWPSYKFFG 523 (740)
Q Consensus 444 L~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~ 523 (740)
+.+.|.|.|.|..||++||+.||++||+++- +.|++.|.+++++|.+.+. +
T Consensus 461 i~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~---------------------------n 511 (728)
T KOG2284|consen 461 IASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA---------------------------N 511 (728)
T ss_pred HhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH---------------------------h
Confidence 9999999999999999999999999999998 9999999999999987654 2
Q ss_pred ccCCHhHHHHHHHHHHHHhhcCCCceeEeccCccceEEEEEecCeeEEEEecHHHHHHHHhhcCCCCccHHHHHHHhCCC
Q 004648 524 LNLPSEMVKGVESFKKFYGTKTKARKLTWIYSLGNCHVNGKFELKAIELIVSTYQAACLMLFNDADRLSFSEILTQLNLN 603 (740)
Q Consensus 524 ~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~ 603 (740)
|.+|.+|+...+.|+.||..+|+||+|+|++.++++++++++-++.|.-.|++|||++||+||..+.+++.+|.+.+|++
T Consensus 512 f~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~~~~~ 591 (728)
T KOG2284|consen 512 FHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEEIGVS 591 (728)
T ss_pred ccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhhhCcc
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCCCCCcceeccCCCc-----chhhhhHHhHHhhhhhchhhh
Q 004648 604 KGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFTDRMRRIRIPLPPV-----DDRREINEDVGKDRRHNIDAA 678 (740)
Q Consensus 604 ~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~~~~~~i~i~~~~~-----~e~~~~~~~v~~~R~~~i~A~ 678 (740)
.++|.+++.++.. .++|... +..+..+..|++|.+|++++.++++..|.. +|.+.+...+.+||++.++||
T Consensus 592 ~~~l~kti~tild--v~~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~a 667 (728)
T KOG2284|consen 592 GDYLLKTIRTILD--VTLLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECA 667 (728)
T ss_pred HHHHHHHHHHHHh--ceeeccc--ccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHH
Confidence 9999999999985 4677654 345667789999999999999999988654 345566778999999999999
Q ss_pred eeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 679 LVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 679 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
||||||+||.+.|+.|++||+.|.++||.|++++||+|||.||+|.||+|.+.+ +.|.|+|
T Consensus 668 ivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 668 IVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 999999999999999999999999999999999999999999999999999876 8999997
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=1.6e-93 Score=831.01 Aligned_cols=586 Identities=37% Similarity=0.670 Sum_probs=523.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHHhcccchhhccch
Q 004648 13 WALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQSDVLPSFEDKRG 92 (740)
Q Consensus 13 W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~l~~~~~ 92 (740)
|+.|++||+.|. .+ .++..+||++|++||++|.++ +|+.||+.+++.+.+|+... .+.+....+
T Consensus 1 W~~l~~~i~~i~---~~----~~~~~~~~~lY~~vy~l~~~~--------~~~~LY~~l~~~i~~~~~~~-~~~l~~~~~ 64 (588)
T PF00888_consen 1 WEILEEAIDQIF---KK----SISKLSYMELYTCVYNLCDNK--------YGEQLYDKLKEFISEYLKNI-IESLLSSSD 64 (588)
T ss_dssp HHHHHHHHHHHH---TT-----GCCSHHHHHHHHHHHHHHTT--------THHHHHHHHHHHHHHHHHHH-HHHHCTTTT
T ss_pred ChHHHHHHHHHH---cC----CCChhHHHHHHHHHHhhcCCc--------ccHHHHHHHHHHHHHHHHHH-HHHHHhcCh
Confidence 999999999975 22 366788999999999998876 79999999999999999885 456665577
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhhcCCCccHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCCccC
Q 004648 93 EFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRSQAGLASLIEVPVVVFRDRVYKDLKRDVRDTVIALIDEEREGEKID 172 (740)
Q Consensus 93 ~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~~~~~i~~l~l~~f~~~i~~~~~~~l~~~ll~~I~~~R~g~~id 172 (740)
+.+|..|...|.+|+.++.+|+++|+||||+|+. +. +|++.++.++.+.+.++++++|.++|.|+.+|
T Consensus 65 ~~~l~~~~~~w~~~~~~~~~i~~if~yLdr~yv~-~~-----------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~ 132 (588)
T PF00888_consen 65 EDLLEEYVQEWEKYKKAIKYISDIFSYLDRNYVK-RN-----------LFREQVFKPLKDKIINALLNLIKNEREGEKID 132 (588)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHTHHHHHTSTT-TT-----------HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-hh-----------hHHHHHHHHHHHHHHHHHHHHHHHHhcCCccc
Confidence 8999999999999999999999999999999999 44 99999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhCCcchhchHHHHHHHHHHHHHHHHHHHHHhHhhcCChhHHHHHHHHHHHHHHHHHccccCcccHHH
Q 004648 173 RALVKKAVDIFVGIGILDMDFYRQDFEEQMIDDAGCYYLRKASSWILNDSCPEYMIKAEECLKKERDRAVYYFHTRSESK 252 (740)
Q Consensus 173 ~~~lk~vi~~l~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~s~~eYl~~ve~~l~~E~~r~~~yL~~~t~~k 252 (740)
+.+++++++|++++| ...+|.+.||++||+.|.+||+.++ +...++.+||.+|+.++++|..|+..||+++|..+
T Consensus 133 ~~~l~~~~~~~~~l~--~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~k 207 (588)
T PF00888_consen 133 RSLLKNVIEMFVELG--SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEK 207 (588)
T ss_dssp HHHHHHHHHHHHHTT--HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHH
T ss_pred HHHHHHHHHHHhccc--hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhh
Confidence 999999999999998 5789999999999999999999999 56779999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcCchhhHHHHHHhhhhhcCCcHHHHHHHHHHHHHHHHHHHHhhHHhhhhh
Q 004648 253 LIEKVQHELLVVHRNQLLENEKSGCRALISQEKFDDLSRIFRLYDETRTGLEPVAGIFKQYFIDQGKALVHQAEEDVRNK 332 (740)
Q Consensus 253 l~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~ 332 (740)
+.+++.++||.+|.+.| .+|+..|+++++.++|++||+|+++++++++.+++.|++||.+.|..+++....
T Consensus 208 i~~~l~~~LI~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~----- 278 (588)
T PF00888_consen 208 IIKTLEEVLISDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK----- 278 (588)
T ss_dssp HHHHHHHHHTGGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC-----
T ss_pred HHHHHHHHHHHHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc-----
Confidence 99999999999999988 368999999999999999999999999999999999999999999999987541
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHhccCCCccCcHHHHHHHHHHHhccCCCCCCChHHHH
Q 004648 333 TANMEQNLVGKILELHDKFMAYVSICFGDHKLFLMALKEAFEVFCNESIVEISSAEILATFCDNLFKNSDAEKLSDETVE 412 (740)
Q Consensus 333 ~~~~~~~~v~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~e~~ 412 (740)
...+..||+.+++++++|+.++..||++++.|..++++||+.++|.+. ..++++||+|||.+|++++ .+.++++++
T Consensus 279 -~~~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~--~~~~e~La~y~d~~l~~~~-~~~~~~~~~ 354 (588)
T PF00888_consen 279 -SSDPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKNN--NKIPELLAKYCDSLLRKSN-KKLSEEEIE 354 (588)
T ss_dssp -GGGCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCST--SHHHHHHHHHHHHHHBSSC-CCS-HCCHH
T ss_pred -ccchHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcCC--cchHHHHHHHhhHhhhhcc-cccchHHHH
Confidence 124789999999999999999999999999999999999999999983 5899999999999999876 567788999
Q ss_pred HHHHHHhHHhccccchHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCCchHHhHHHHHHHHHHHHHHHHHHHH
Q 004648 413 RTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLFDKGGNKDYDKTFLSKLKQHSGGHFTTKMEGMITDVVLARENQTALDD 492 (740)
Q Consensus 413 ~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~D~~~S~~~~~~f~~ 492 (740)
+.++.++.||+|+++||+|+.+|+++||+|||.+++.+.+.|..+|++|+.+||.++|++|++|++|+..|+++++.|++
T Consensus 355 ~~~~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~ 434 (588)
T PF00888_consen 355 QKLDDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQ 434 (588)
T ss_dssp HHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCC-CCCceEEEEeecCCCCCCCCCC-ccCCHhHHHHHHHHHHHHhhcCCCceeEeccCccceEEEEEecCeeE
Q 004648 493 WFSSNLNEK-PQFDLSVMVLTTGSWPSYKFFG-LNLPSEMVKGVESFKKFYGTKTKARKLTWIYSLGNCHVNGKFELKAI 570 (740)
Q Consensus 493 ~~~~~~~~~-~~~~~~~~VLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~ 570 (740)
.....+... ++++|+|.|||+++||..+..+ +.||++|+.+++.|++||..+|+||+|+|.|++|+|+|+++++++++
T Consensus 435 ~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~ 514 (588)
T PF00888_consen 435 KQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKY 514 (588)
T ss_dssp HHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEE
T ss_pred HhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCce
Confidence 987654322 2789999999999999988766 99999999999999999999999999999999999999999999999
Q ss_pred EEEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCC
Q 004648 571 ELIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFT 644 (740)
Q Consensus 571 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~ 644 (740)
+++||++||+||++||+.+++|+++|++.||+++++++++|.+|+..|..++.+.++++++++++.|.+|.+|+
T Consensus 515 ~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 515 ELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred eEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999999999999999999999999999999999865433333678899999999999999996
No 6
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-92 Score=721.41 Aligned_cols=717 Identities=25% Similarity=0.415 Sum_probs=632.0
Q ss_pred CCccCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHHhc
Q 004648 3 SKKKLSFEESWALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQSD 82 (740)
Q Consensus 3 ~~~~~~f~~~W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~~~ 82 (740)
++....||+.|....+.+-++.+ ++++++..|..||.+||..|.+.+. ...++|+.++..+.+|+...
T Consensus 7 ~r~r~qFee~W~~~rpIVlkLLr------Q~sVt~~~WqDLF~~Vh~vclWddk------GpaKI~d~L~~dI~efi~qA 74 (777)
T KOG2285|consen 7 KRDRDQFEEEWSKARPIVLKLLR------QKSVTPAAWQDLFYHVHKVCLWDDK------GPAKIRDILTRDINEFIHQA 74 (777)
T ss_pred ccchhhhhhhccccchHHHHHHh------hccCCHHHHHHHHhhheeeeeecCC------CcHHHHHHHHHHHHHHHHHH
Confidence 34556899999999999999865 3468999999999999999999842 35679999999999999864
Q ss_pred ccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhhcC-------CCccHHHHHHHHHHHHHHHHhHHHHH
Q 004648 83 VLPSFEDKRGEFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRSQA-------GLASLIEVPVVVFRDRVYKDLKRDVR 155 (740)
Q Consensus 83 v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~-------~~~~i~~l~l~~f~~~i~~~~~~~l~ 155 (740)
-........+..+|..|...|.+|.....++...|.-|+..-...+. .-.+|..+.+..|.++||..+++++.
T Consensus 75 q~rv~s~q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq 154 (777)
T KOG2285|consen 75 QKRVRSLQTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQ 154 (777)
T ss_pred HHHHHhhccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 32222223456899999999999999999999999999977443111 12468999999999999999999999
Q ss_pred HHHHHHHHHHhcCCccCHHHHHHHHHHHHHhCC---cchhchHHHHHHHHHHHHHHHHHHHHHhHhhcCChhHHHHHHHH
Q 004648 156 DTVIALIDEEREGEKIDRALVKKAVDIFVGIGI---LDMDFYRQDFEEQMIDDAGCYYLRKASSWILNDSCPEYMIKAEE 232 (740)
Q Consensus 156 ~~ll~~I~~~R~g~~id~~~lk~vi~~l~~l~~---~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~s~~eYl~~ve~ 232 (740)
...+.++..+|+|+.+|.+++-++-++|+.|+. +.+.+|...||..||++|.+||+..+..+++++++.+|++.|+.
T Consensus 155 ~sAmklVhaER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~ 234 (777)
T KOG2285|consen 155 VSAMKLVHAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADK 234 (777)
T ss_pred HHHHHHHHHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHh
Confidence 999999999999999999999999999999986 46789999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHccccCc--ccHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcCchhhHHHHHHhhhhhcCCcHHHHHHH
Q 004648 233 CLKKERDRAVYYFHT--RSESKLIEKVQHELLVVHRNQLLENEKSGCRALISQEKFDDLSRIFRLYDETRTGLEPVAGIF 310 (740)
Q Consensus 233 ~l~~E~~r~~~yL~~--~t~~kl~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~ 310 (740)
.+++|+.|+.+||.+ .|..++++.+.++||.++.+.|+. .|..|+....++.|++||+|..+++.|++++...+
T Consensus 235 KL~EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl 310 (777)
T KOG2285|consen 235 KLEEEEQRAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDL 310 (777)
T ss_pred hhhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHH
Confidence 999999999999876 678899999999999999999985 58899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhHHhhhhhcccchHHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHhccCC---------
Q 004648 311 KQYFIDQGKALVHQAEEDVRNKTANMEQNLVGKILELHDKFMAYVSICFGDHKLFLMALKEAFEVFCNESI--------- 381 (740)
Q Consensus 311 ~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~~--------- 381 (740)
..||+..|.+-+......+. .++..||+.|+.++++|..++.++|++|+.|..|.+.||..++|...
T Consensus 311 ~~HI~saGLaDM~~aaE~it----tDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~ 386 (777)
T KOG2285|consen 311 DTHIRSAGLADMRNAAENIT----TDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNS 386 (777)
T ss_pred HHHHHhhhHHHHHhhhhhcc----CCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccch
Confidence 99999999887755444332 25889999999999999999999999999999999999999999763
Q ss_pred ---------CccCcHHHHHHHHHHHhccCC-CCCCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHhcCCCCCCh
Q 004648 382 ---------VEISSAEILATFCDNLFKNSD-AEKLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLFDKGGNK 451 (740)
Q Consensus 382 ---------~~~~~~e~La~y~D~~lk~~~-~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~ 451 (740)
+..++||+||.|||.+||+.. +++++.||++++|++++-+++|+.+||+|..|++.+|++||+.+.|++.
T Consensus 387 ~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADs 466 (777)
T KOG2285|consen 387 KKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADS 466 (777)
T ss_pred hcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccch
Confidence 124689999999999999853 4678899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhCC--chHHhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCceEEEEeecCCCCCCCC-CCccCCH
Q 004648 452 DYDKTFLSKLKQHSGG--HFTTKMEGMITDVVLARENQTALDDWFSSNLNEKPQFDLSVMVLTTGSWPSYKF-FGLNLPS 528 (740)
Q Consensus 452 ~~E~~~i~~Lk~~~G~--~~t~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~-~~~~lP~ 528 (740)
+.|..|+..|+ +||. +|.+||.+||+|++.|+++++.|++.+..++..++.-.+++.||+.|.|...+. ..+.||.
T Consensus 467 EkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkvseDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ 545 (777)
T KOG2285|consen 467 EKEEMMVEWLR-EVGMPADYVNKLARMFQDIKVSEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPR 545 (777)
T ss_pred hHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccccHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCch
Confidence 99999999998 8886 689999999999999999999999988776554555678999999999997653 4689999
Q ss_pred hHHHHHHHHHHHHhhcCCCceeEeccCccceEEEEEecCeeEEEEecHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHH
Q 004648 529 EMVKGVESFKKFYGTKTKARKLTWIYSLGNCHVNGKFELKAIELIVSTYQAACLMLFND--ADRLSFSEILTQLNLNKGD 606 (740)
Q Consensus 529 ~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~ 606 (740)
+|++.+-..++||+.+|+||+|.|.|+++.++|++.-+-|.|++.|+|+||+||.+||+ ++.+|++.+.-+|.+|+.+
T Consensus 546 ELED~iPdveEfykk~hsgrkl~w~h~msNG~itf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaE 625 (777)
T KOG2285|consen 546 ELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTITFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAE 625 (777)
T ss_pred hHHHhCccHHHHHhcccCccchhhhhhccCCeeEeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHH
Confidence 99999999999999999999999999999999987655589999999999999999997 4689999999999999999
Q ss_pred HHHHHHHhhc---ccccccccCCC----CCCCCCCCceeecccCCC-----CCcceeccCCCc----ch--hhhhHHhHH
Q 004648 607 LIRVLHSLSC---SKHKILNKEPN----TKTISQSDSFEFNAKFTD-----RMRRIRIPLPPV----DD--RREINEDVG 668 (740)
Q Consensus 607 l~~~L~~L~~---~k~~iL~~~~~----~~~~~~~~~~~~N~~F~~-----~~~~i~i~~~~~----~e--~~~~~~~v~ 668 (740)
|.++|-||+. .|+.||..+|+ .+++.++..|.+|.+|.- ..+|-+++.+.. .| .++..+.+-
T Consensus 626 LrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIV 705 (777)
T KOG2285|consen 626 LRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIV 705 (777)
T ss_pred HHHHHHHHHhhhhhhhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhH
Confidence 9999999985 35788887764 245667889999999962 122333443321 11 223345678
Q ss_pred hhhhhchhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 669 KDRRHNIDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 669 ~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
+-|-...+-+|++|||.||+++..+|-.|..+.|+..|-|+..+||+.||.|||..|++||++|-++|+|+|
T Consensus 706 qLRiLRtQEaIikImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 706 QLRILRTQEAIIKIMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 889999999999999999999999999999999999999999999999999999999999999999999997
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=2.9e-33 Score=262.47 Aligned_cols=141 Identities=39% Similarity=0.755 Sum_probs=132.6
Q ss_pred cccchHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCCchHHhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 004648 424 YFKYKDLFAEFYRKKLARRLLFDKGGNKDYDKTFLSKLKQHSGGHFTTKMEGMITDVVLARENQTALDDWFSSNLNEKPQ 503 (740)
Q Consensus 424 ~l~~KD~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~ 503 (740)
|+++||+|+.+|+++||+|||..++.+.+.|..+|++||.+||.++|++|++|++|+..|+++++.|++.+.+++ ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999876532 2346
Q ss_pred CceEEEEeecCCCCCCCC-CCccCCHhHHHHHHHHHHHHhhcCCCceeEeccCccceEEEEEe
Q 004648 504 FDLSVMVLTTGSWPSYKF-FGLNLPSEMVKGVESFKKFYGTKTKARKLTWIYSLGNCHVNGKF 565 (740)
Q Consensus 504 ~~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~ 565 (740)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|+|++|+|+|+++|
T Consensus 80 ~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~RkL~W~~~lg~~~l~~~~ 142 (142)
T smart00182 80 IDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEFEEFYLAKHSGRKLTWLHSLGRGEVKANF 142 (142)
T ss_pred CceEEEECCCCCCCCCCCCCceECCHHHHHHHHHHHHHHHhCCCCCeEEEEcCCceEEEEEEC
Confidence 899999999999999887 78999999999999999999999999999999999999999875
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=2.2e-25 Score=241.30 Aligned_cols=306 Identities=21% Similarity=0.296 Sum_probs=241.9
Q ss_pred HHhccccchHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCCchHHhHHHHHHHHHHHHHHHHHHHHH--hhcC
Q 004648 420 VLLGYFKYKDLFAEFYRKKLARRLLFDKGGNKDYDKTFLSKLKQHSGGHFTTKMEGMITDVVLARENQTALDDW--FSSN 497 (740)
Q Consensus 420 ~lf~~l~~KD~F~~~Y~~~LakRLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~M~~D~~~S~~~~~~f~~~--~~~~ 497 (740)
.|...+.+|+.|.+.||.+||.|||.....+.|.|..-++.||-++|.+..+.|++|++|+..|+++++.+++. ....
T Consensus 444 mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~~r~ 523 (765)
T KOG2165|consen 444 MLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESELSRG 523 (765)
T ss_pred HHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhhhcc
Confidence 34455699999999999999999999999999999999999999999999999999999999999999999884 2222
Q ss_pred CCCCCCCceEEEEeecCCCCCCCCCCccCCHhHHHHHHHHHHHHhhcCCCceeEeccCccceEEEEEecCeeEEEEecHH
Q 004648 498 LNEKPQFDLSVMVLTTGSWPSYKFFGLNLPSEMVKGVESFKKFYGTKTKARKLTWIYSLGNCHVNGKFELKAIELIVSTY 577 (740)
Q Consensus 498 ~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~ 577 (740)
....+.+.+++.+|++.+||......+.||.+++..++.|.+-|.+..++|+|.|.+++|.|++++.|.+++.+++||+.
T Consensus 524 ~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tVsp~ 603 (765)
T KOG2165|consen 524 AEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTVSPE 603 (765)
T ss_pred cccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEeeCHH
Confidence 22334688999999999999887788999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCCCCCcceeccCCCc
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFTDRMRRIRIPLPPV 657 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~~~~~~i~i~~~~~ 657 (740)
||+|+++|.+.++||++++++.+|||...+.|.|..|. +.++|..+|. ++++.+|+++++=.+..+--.-+....
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~~q~~~~~~~e~ 678 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDFDQAEGTVLLEA 678 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeeccccccccccCCCccccc
Confidence 99999999999999999999999999999999999998 4689987653 267889999985443322111111111
Q ss_pred c-hh--hhhHHhHHhhh--hhchhhheeecccCCCCCChhHHHHHHHHHhc--CCCCCChhHHHHHHHhhhhhhccccCC
Q 004648 658 D-DR--REINEDVGKDR--RHNIDAALVRIMKSRKVLGYQQLISECVEMLS--HSFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 658 ~-e~--~~~~~~v~~~R--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~--~~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
+ +. ......+++-+ -..-...||-.+-.-+.|..+.+.+...-... +...++-++++.-+..++..|-|+-.+
T Consensus 679 eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~~ 758 (765)
T KOG2165|consen 679 EEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFIA 758 (765)
T ss_pred ccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEec
Confidence 1 11 11222222211 12345588888888899999888875432111 112234577777777777777666554
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=99.78 E-value=4.4e-20 Score=148.66 Aligned_cols=68 Identities=49% Similarity=0.814 Sum_probs=62.4
Q ss_pred HHhhhhhchhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCC
Q 004648 667 VGKDRRHNIDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPT 734 (740)
Q Consensus 667 v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~ 734 (740)
|+++|...|+|+||||||++|+++|++|+.+|.++++++|+|+..+||++||.||+||||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 36799999999999999999999999999999999999999999999999999999999999999875
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=97.31 E-value=0.0065 Score=57.40 Aligned_cols=137 Identities=14% Similarity=0.232 Sum_probs=96.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHHhcccch
Q 004648 7 LSFEESWALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQSDVLPS 86 (740)
Q Consensus 7 ~~f~~~W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~~~v~~~ 86 (740)
...++.|..++.++-.+ ++|+... ++-++.-++-+.--+.|.++. ....+-+.+++.+..-+... ...
T Consensus 3 ~~~~~~W~~~~~~vl~l---F~g~~l~-~~iEdlN~lv~~~i~~~~~~~-------~~~~~~~dl~elL~tg~~~L-~~~ 70 (158)
T PF08539_consen 3 MSSDDAWNSLCAKVLPL---FQGERLR-LPIEDLNELVRFHIKLCIQSF-------PPSYFLEDLEELLTTGMYIL-ENQ 70 (158)
T ss_pred CchhhhHHHHHHHHHHH---HcCCCCC-cCHHHHHHHHHHHHHHhhccc-------chHHHHHHHHHHHHHHHHHH-HHH
Confidence 45689999999999885 4676554 665555555555556777763 23345555666666554432 344
Q ss_pred hhccchhhHHHHHHHHHHHH-HHHHHHHHHHhchhhhhHHhh----------------cCCCccHHHHHHHHHHHHHHHH
Q 004648 87 FEDKRGEFMLREFVKQWENI-NVMGRWLLRFFEYLDRFYVRS----------------QAGLASLIEVPVVVFRDRVYKD 149 (740)
Q Consensus 87 l~~~~~~~~L~~~~~~W~~~-~~~~~~l~~vf~YLDr~yv~~----------------~~~~~~i~~l~l~~f~~~i~~~ 149 (740)
+....++.+|..++..|.-| ....-++..+|..|++.+-.. .....+|+.++|..||+.|+-|
T Consensus 71 l~~~~~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvLP 150 (158)
T PF08539_consen 71 LNEVPDNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVLP 150 (158)
T ss_pred HhhcchhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhhc
Confidence 55567888999999999996 566788999999999654321 0244789999999999999988
Q ss_pred hHHHHH
Q 004648 150 LKRDVR 155 (740)
Q Consensus 150 ~~~~l~ 155 (740)
..+++.
T Consensus 151 ~y~~l~ 156 (158)
T PF08539_consen 151 YYQRLK 156 (158)
T ss_pred chHhhh
Confidence 777654
No 11
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=94.64 E-value=2.2 Score=47.87 Aligned_cols=203 Identities=12% Similarity=0.089 Sum_probs=117.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCChHhHHHHHHHHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHHhcc--cchhh
Q 004648 11 ESWALMEQGIAKLKKILKGLPEPPFASEECMTLYTIVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQSDV--LPSFE 88 (740)
Q Consensus 11 ~~W~~l~~~i~~i~~il~~~~~~~~s~~~y~~lY~~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~~~v--~~~l~ 88 (740)
-.|..|++++.-|.+.-.-. .++ ..-|-.+.+.+|+-|..+. . +...+.+.++.....+..... ..-+.
T Consensus 112 vdrslLrsll~MLsd~~iY~--esF-~~~fls~f~~lY~aE~~d~-~-----Qel~v~eYl~h~e~~l~~E~~~~i~~~D 182 (661)
T KOG2167|consen 112 VDRSLLRSLLKMLSDLQIYK--ESF-ELTFLSLFRELYAAEGQDK-R-----QELEVPEYLEHVEGRLEEENDRVIEYFD 182 (661)
T ss_pred hhHHHHHHHHHHHHHHHhhh--hhh-HHHHHHHHHHHHHHHhcch-h-----hhcccHHHHHhhhhcccchHHHHHHhcc
Confidence 35788888887755421110 112 1236678889999999873 2 222333333332222222110 00000
Q ss_pred ----ccchhhHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHhhcCCCccHHHHHHHHHHH--HHHHHhHHHHHHHHHHHH
Q 004648 89 ----DKRGEFMLREFVKQWENINVMGRWLLRFFEYLDRFYVRSQAGLASLIEVPVVVFRD--RVYKDLKRDVRDTVIALI 162 (740)
Q Consensus 89 ----~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~YLDr~yv~~~~~~~~i~~l~l~~f~~--~i~~~~~~~l~~~ll~~I 162 (740)
......+.+.+...|-...... ++++-+|-.= ..+...++.++-..+.. .+....++.+......+|
T Consensus 183 ~st~k~l~atV~~~LL~~hL~~IL~k----gl~~lvDm~q---~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV 255 (661)
T KOG2167|consen 183 SSTKKPLIATVERCLLSRHLDLILTK----GLDSLVDMRQ---TSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLV 255 (661)
T ss_pred cccccchHHHHHHHHHHHHHHHHHhc----chHHhhhhhh---ccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceec
Confidence 1112346667777777764333 3344444332 23455677777666632 334467788888888888
Q ss_pred HHHhcCCcc--CHHHHHHHHHHHHHhCCcchhchHHHHHHHHHHHHHHHHHHHHHhHhhcCChhHHHHHHHHHHHHH
Q 004648 163 DEEREGEKI--DRALVKKAVDIFVGIGILDMDFYRQDFEEQMIDDAGCYYLRKASSWILNDSCPEYMIKAEECLKKE 237 (740)
Q Consensus 163 ~~~R~g~~i--d~~~lk~vi~~l~~l~~~~~~~Y~~~FE~~~l~~t~~yY~~~s~~~l~~~s~~eYl~~ve~~l~~E 237 (740)
..++.++.. +....|+-+++.... .+++..- .+|+..++++|...++ ...+.+.+|+.+....+-.+
T Consensus 256 ~de~kDk~mVqELL~FK~k~Dii~~~-----sF~~~v~-e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 256 IDEEKDKDMVQELLDFKKKVDIIVDE-----SFLKYVA-EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred cCchhhHHHHHHHHHHHHHhhHHHHH-----HHHHhhH-HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 888877643 234577777877753 3344333 7899999999999888 45567889998887655444
No 12
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=92.84 E-value=0.27 Score=42.41 Aligned_cols=66 Identities=15% Similarity=0.208 Sum_probs=52.3
Q ss_pred EEEecHHHHHHHHhhc--------CCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeeccc
Q 004648 571 ELIVSTYQAACLMLFN--------DADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAK 642 (740)
Q Consensus 571 ~l~~s~~Q~~iLllFn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 642 (740)
...++.-|+.+|+..- ....+|-.||++.+|++.+.+.++|..|. +.+++.+.. ....|++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3457888998888655 45689999999999999999999999997 457776542 1368999987
Q ss_pred CC
Q 004648 643 FT 644 (740)
Q Consensus 643 F~ 644 (740)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 65
No 13
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=91.84 E-value=0.25 Score=37.30 Aligned_cols=45 Identities=24% Similarity=0.364 Sum_probs=36.3
Q ss_pred HHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 579 AACLMLFNDAD-RLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 579 ~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
+.||..|.+.+ .+|+.||++.+|+|...+.+.|..|.. .+++.+.
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 45778888765 589999999999999999999999974 5666654
No 14
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=90.67 E-value=0.47 Score=34.99 Aligned_cols=42 Identities=19% Similarity=0.301 Sum_probs=34.9
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
+..+..||....+++.+|..||++.+|++...+.+.|..|..
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 456778888888888999999999999999999999999973
No 15
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=90.49 E-value=0.71 Score=38.63 Aligned_cols=59 Identities=14% Similarity=0.235 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeeccc
Q 004648 577 YQAACLMLFNDAD-RLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAK 642 (740)
Q Consensus 577 ~Q~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 642 (740)
+++++.+..+..+ .+|.++|++.+++|+..+.+.++.|. +.+++...+ | +++.|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-G----~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-G----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCC
Confidence 4455555544444 49999999999999999999999997 567876432 2 3567777653
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=89.97 E-value=0.39 Score=37.47 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=42.0
Q ss_pred ecHHHHHHHHhhcCCCC--ccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 574 VSTYQAACLMLFNDADR--LSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
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 57889999988777666 9999999999999999999999997 456776653
No 17
>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=86.81 E-value=0.47 Score=36.66 Aligned_cols=50 Identities=18% Similarity=0.408 Sum_probs=42.4
Q ss_pred ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 574 VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.|..|+.+|....+.+.+|..+|++.++++...+.+.+..|. +.+++.+.
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 367899999888888889999999999999999999999997 45677654
No 18
>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=86.73 E-value=1 Score=35.83 Aligned_cols=50 Identities=18% Similarity=0.313 Sum_probs=38.4
Q ss_pred ecHHHHHHHHhhc-CCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 574 VSTYQAACLMLFN-DADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 574 ~s~~Q~~iLllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
+|..|..||.... .....|..+|++.++++...+.+.+..|.. .+++.+.
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 3678899998888 778999999999999999999999999984 4777654
No 19
>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=86.38 E-value=1.1 Score=34.63 Aligned_cols=46 Identities=17% Similarity=0.341 Sum_probs=38.6
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
|..|+...++.+.+|+++|++.+|+++..+.+-|..|.. .+++.+.
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 446777788889999999999999999999999999974 4556554
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=85.60 E-value=1.4 Score=39.44 Aligned_cols=52 Identities=13% Similarity=0.252 Sum_probs=45.4
Q ss_pred EecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 573 IVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
.++..|+.||..+..++.+|..+|++.+|++...+-+.+..|. +.+++.+.+
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 4688999999988888899999999999999999999999997 457777654
No 21
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=85.29 E-value=1.1 Score=35.05 Aligned_cols=49 Identities=16% Similarity=0.280 Sum_probs=39.6
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
++.-..||.++...++.|+.+|++.+|++...+..+|.-|. +.+++...
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 45666788888777899999999999999999999999997 45677543
No 22
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=84.09 E-value=2.4 Score=31.13 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=33.5
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccc
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKIL 622 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 622 (740)
...-||.++-+ ++.++.||++.+|++...+.++|..|.. .+++
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 34556666666 6799999999999999999999999863 4454
No 23
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.08 E-value=2.2 Score=39.74 Aligned_cols=53 Identities=23% Similarity=0.251 Sum_probs=45.5
Q ss_pred EEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 572 LIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 572 l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
..+|..|+.||......+++|..+|++.++++...+-+.+..|. +.+++.+.+
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le--~~GlI~R~~ 88 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV--CKGWVERLP 88 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEecc
Confidence 35788899999877767789999999999999999999999997 567887764
No 24
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=81.13 E-value=0.55 Score=37.81 Aligned_cols=45 Identities=16% Similarity=0.351 Sum_probs=34.9
Q ss_pred eeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCC
Q 004648 679 LVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 679 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
|-.+|+.++.++..+|-. +|..+++.+...|+.|+.+|||++.+.
T Consensus 5 i~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 334677888888887765 689999999999999999999998754
No 25
>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=81.01 E-value=1.8 Score=39.66 Aligned_cols=60 Identities=15% Similarity=0.226 Sum_probs=45.2
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
+..|++++-..+.++..+++.. +.....+....+...|..|.+||||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 4456777767777777666654 434566788999999999999999999854 35788865
No 26
>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=79.67 E-value=3.7 Score=31.07 Aligned_cols=36 Identities=17% Similarity=0.322 Sum_probs=28.7
Q ss_pred HHHhh-cCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 581 CLMLF-NDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 581 iLllF-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
||.++ +..+.+|.++|++.+|++...+.+.|..|..
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 44434 6666799999999999999999999998863
No 27
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=79.49 E-value=2.8 Score=33.58 Aligned_cols=47 Identities=21% Similarity=0.260 Sum_probs=37.6
Q ss_pred HHHHHHHhhcCCCC--ccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 577 YQAACLMLFNDADR--LSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 577 ~Q~~iLllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
..-.||.++.+.+. +|..||++.+|++...+.++|..|.. .+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~--~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK--KGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 44457777777655 99999999999999999999999973 4566553
No 28
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=78.88 E-value=4.7 Score=35.60 Aligned_cols=52 Identities=23% Similarity=0.429 Sum_probs=43.3
Q ss_pred EecHHHHHHHHhhc----CCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 573 IVSTYQAACLMLFN----DADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 573 ~~s~~Q~~iLllFn----~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
.+|..|..||.... ..+.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 46788888886655 55689999999999999999999999997 557887764
No 29
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=76.55 E-value=4.5 Score=34.53 Aligned_cols=53 Identities=23% Similarity=0.314 Sum_probs=44.9
Q ss_pred EEEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 571 ELIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 571 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
++.++..+..||.+......+|..+|++.++++...+.++|..|.. .+++.+.
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 3457888999998888777899999999999999999999999974 5677653
No 30
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=75.96 E-value=2.7 Score=37.70 Aligned_cols=62 Identities=18% Similarity=0.300 Sum_probs=52.6
Q ss_pred chhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 674 NIDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 674 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
..++.|++||=.++..+.+|++.++.. .+.++...|+.-|..|..||.|.|.-+ ...|.|-|
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~----~~ews~sTV~TLl~RL~KKg~l~~~kd-gr~~~y~p 67 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPA----DREWSYSTVKTLLNRLVKKGLLTRKKD-GRAFRYSP 67 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhh----cccccHHHHHHHHHHHHhccchhhhhc-CCeeeeec
Confidence 357889999999999999999887765 478899999999999999999999875 35677754
No 31
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=75.74 E-value=6 Score=33.34 Aligned_cols=45 Identities=22% Similarity=0.358 Sum_probs=37.0
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 579 AACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 579 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
..||..+... +.+|..+|++.+|++...+.+.|..|.. .+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeec
Confidence 3466667665 6899999999999999999999999973 5777664
No 32
>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=75.46 E-value=2.4 Score=37.88 Aligned_cols=60 Identities=12% Similarity=0.271 Sum_probs=42.8
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
+..|++++=..+.++..+++.. +.....+....|+..+..|.+||||+|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~----l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEA----LPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHH----HCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHH----HHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 4455566656666776666664 444567889999999999999999999875 35788864
No 33
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=74.67 E-value=8.6 Score=36.31 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=35.9
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
+++.|..+..+.+|..+|++..++|...|.+.|+.|. +.+++...
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~ 57 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETV 57 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEee
Confidence 3444555666678999999999999999999999997 56787643
No 34
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=74.50 E-value=9 Score=36.66 Aligned_cols=45 Identities=13% Similarity=0.226 Sum_probs=36.3
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 578 QAACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 578 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
.+++.+.|+.. ..+|.++|++.+++|...+.+.|..|. +.+|+..
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s 57 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSS 57 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEe
Confidence 34445567654 589999999999999999999999997 5678764
No 35
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=74.44 E-value=3.1 Score=33.21 Aligned_cols=50 Identities=20% Similarity=0.327 Sum_probs=39.4
Q ss_pred ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 574 VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.|-.++-|+..+-..+..|..||++.+|+|...+.+.|..|.. .+++.+.
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~--~GlV~~~ 55 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE--KGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH--TTSEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 3455666665555677899999999999999999999999984 4666654
No 36
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=74.43 E-value=1.3e+02 Score=32.36 Aligned_cols=163 Identities=11% Similarity=0.229 Sum_probs=93.2
Q ss_pred hHHHHhhcCchhhHHHHHHhhhhh---cCCcHHHHHHHHHHHHHHHHHHHHhhHHhhhhhcccchHHHHHHHHHHHHHHH
Q 004648 276 GCRALISQEKFDDLSRIFRLYDET---RTGLEPVAGIFKQYFIDQGKALVHQAEEDVRNKTANMEQNLVGKILELHDKFM 352 (740)
Q Consensus 276 ~~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~~ 352 (740)
.|..-.+.++.+.+.+.++||--+ +.|++.....+.+.|.....+.++........ ...+.-|+..|..+++...
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~--~~~~~~~~~~lt~LFe~ia 92 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSD--SRSPVFYADALTKLFEHIA 92 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc--ccccccHHHHHHHHHHHHH
Confidence 477788889999999999999765 35777777777777777777666554322111 1234456666666666654
Q ss_pred H-------HHHHhhCCCHH--HHHHHHHHHHH--------HhccCCCccCcHHHHHHHHHHHhcc---------------
Q 004648 353 A-------YVSICFGDHKL--FLMALKEAFEV--------FCNESIVEISSAEILATFCDNLFKN--------------- 400 (740)
Q Consensus 353 ~-------l~~~~F~~~~~--f~~~l~~af~~--------~~n~~~~~~~~~e~La~y~D~~lk~--------------- 400 (740)
. +|..+|+.... +...|..-+.. |..... -.+....+..|-...+.+
T Consensus 93 ~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (331)
T PF08318_consen 93 TIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERR-LDRKLQDIQSYNFSFLVKNSGRSSSSSSRAASS 171 (331)
T ss_pred HHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-HHHHHHHHHhhhhhhhccccccccccccccccc
Confidence 4 56678887542 11222211111 111110 011222333343333322
Q ss_pred --CCCCCCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHhcCCCC
Q 004648 401 --SDAEKLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLFDKG 448 (740)
Q Consensus 401 --~~~~~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~~~s 448 (740)
+.....+.-+++..|+.+..+... ...|.++++.|.-....
T Consensus 172 ~~~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 172 SQSEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFSD 214 (331)
T ss_pred cccccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcccc
Confidence 001223456788888888887754 35799999999887443
No 37
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=74.28 E-value=6.3 Score=40.74 Aligned_cols=46 Identities=13% Similarity=0.283 Sum_probs=39.4
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+.||.+|.....+|+.||++.+|+|...+.+.|..|.. .+.|.+.+
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 45788898877899999999999999999999999984 57776653
No 38
>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=73.91 E-value=1.9e+02 Score=34.71 Aligned_cols=129 Identities=16% Similarity=0.321 Sum_probs=67.5
Q ss_pred HHHHHHHHHHHHhHhhcCChhHHHHHHHHHHHHHHHHHccccCcccHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhc
Q 004648 204 DDAGCYYLRKASSWILNDSCPEYMIKAEECLKKERDRAVYYFHTRSESKLIEKVQHELLVVHRNQLLENEKSGCRALISQ 283 (740)
Q Consensus 204 ~~t~~yY~~~s~~~l~~~s~~eYl~~ve~~l~~E~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~~~~~~ll~~ 283 (740)
+...-||...+..-. ...+..+.+.|....+++.+..-..+-....+||.+-++ |+..++..
T Consensus 554 eN~~~~~e~l~~~~~-~~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~~-----------------gve~l~~~ 615 (701)
T PF09763_consen 554 ENYHHFYEELSQLKI-NSVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFFE-----------------GVEALLQT 615 (701)
T ss_pred HHHHHHHHHHhhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHH-----------------HHHHHHhc
Confidence 333344444433322 244566777777777777665544333333344443322 22233322
Q ss_pred -----------CchhhHHHHHHhhh--hhcCCcHHHHHHHHHHHHHHH------HHHHHhhHHhhhhhcccchHHHHHHH
Q 004648 284 -----------EKFDDLSRIFRLYD--ETRTGLEPVAGIFKQYFIDQG------KALVHQAEEDVRNKTANMEQNLVGKI 344 (740)
Q Consensus 284 -----------~~~~~L~~ly~L~~--~~~~~l~~l~~~~~~~i~~~g------~~~~~~~~~~~~~~~~~~~~~~v~~l 344 (740)
-....|+.+-+-|. .+..|++.|.+.+..|+...+ ..++... =..+-+..
T Consensus 616 ~~~~ei~~~~~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~v-----------W~~~q~~~ 684 (701)
T PF09763_consen 616 VSPEEISYQAAYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVV-----------WSAMQEEF 684 (701)
T ss_pred cCchhcccchhccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHH-----------HHHHHHHH
Confidence 12455555555532 345577777777777772111 1111111 12344578
Q ss_pred HHHHHHHHHHHHHhhCC
Q 004648 345 LELHDKFMAYVSICFGD 361 (740)
Q Consensus 345 l~l~~~~~~l~~~~F~~ 361 (740)
+..|.++..++..|+.+
T Consensus 685 i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 685 IRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHhCCC
Confidence 89999999999999864
No 39
>PHA00738 putative HTH transcription regulator
Probab=73.75 E-value=6.3 Score=34.43 Aligned_cols=67 Identities=19% Similarity=0.109 Sum_probs=50.9
Q ss_pred EEEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccC
Q 004648 571 ELIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKF 643 (740)
Q Consensus 571 ~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F 643 (740)
++...+.=-.||.++.+++.+++.+|++.++|+...+-++|.-|.. .+|+.....|+. -.|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre--AGLV~srK~Gr~----vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNE--QGYIELYKEGRT----LYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH--CCceEEEEECCE----EEEEECCCc
Confidence 4556666667777777777899999999999999999999999974 578876554432 356777654
No 40
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=72.59 E-value=6.7 Score=28.90 Aligned_cols=43 Identities=21% Similarity=0.322 Sum_probs=34.0
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 580 ACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 580 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++.+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 4555556667799999999999999999999999974 355544
No 41
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=71.16 E-value=7.9 Score=37.81 Aligned_cols=53 Identities=13% Similarity=0.032 Sum_probs=45.6
Q ss_pred EEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 572 LIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 572 l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+.+|..|..||......+++|..+|++.++++...+.+.+..|. +.+++.+.+
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 45778999999999888899999999999999999999999996 457777654
No 42
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.55 E-value=7.1 Score=36.26 Aligned_cols=53 Identities=13% Similarity=0.255 Sum_probs=44.2
Q ss_pred EEecHHHHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 572 LIVSTYQAACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 572 l~~s~~Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+.+|..|..||...... +..|..+|++.++++...+.+.+..|. +.+++.+.+
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 45788899888877654 568999999999999999999999997 567887754
No 43
>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=70.24 E-value=11 Score=34.58 Aligned_cols=44 Identities=14% Similarity=0.225 Sum_probs=34.8
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 579 AACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 579 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
+++.|.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 3444555544 479999999999999999999999997 5677753
No 44
>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=70.01 E-value=13 Score=32.37 Aligned_cols=61 Identities=21% Similarity=0.366 Sum_probs=44.6
Q ss_pred ecHHHHHHHHh-------hcC-CCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCC
Q 004648 574 VSTYQAACLML-------FND-ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFT 644 (740)
Q Consensus 574 ~s~~Q~~iLll-------Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~ 644 (740)
+|.-|.-|++. ||. .+.+|..++++.||++...+.+++..|. +.++|... +..+.+|.+.+
T Consensus 30 ls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 30 LSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred ccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 44555555554 454 3589999999999999999999999997 56788654 34566665543
No 45
>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=69.44 E-value=5.6 Score=38.06 Aligned_cols=50 Identities=20% Similarity=0.308 Sum_probs=41.0
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCCCCCc
Q 004648 590 RLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFTDRMR 648 (740)
Q Consensus 590 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~~~~~ 648 (740)
-.|..+|++.+|++...+.+++..|. +.++|.+.. ...|.+|++|--+-.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG~ 124 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKGD 124 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeCc
Confidence 47889999999999999999999997 457887753 468999999765433
No 46
>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=68.85 E-value=7.5 Score=27.87 Aligned_cols=36 Identities=25% Similarity=0.439 Sum_probs=27.0
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSL 614 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 614 (740)
-.||-.+.+....++.+|++.+|++...+.+-+..|
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 356666777788999999999999999998877654
No 47
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=68.33 E-value=7.5 Score=35.17 Aligned_cols=39 Identities=21% Similarity=0.370 Sum_probs=33.8
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 585 FNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 585 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.+.++.+|+++|++.++.+...+.++|++|.. .+++.+.
T Consensus 37 L~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Re 75 (126)
T COG3355 37 LEENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVERE 75 (126)
T ss_pred HhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeee
Confidence 34678999999999999999999999999984 5788765
No 48
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=67.67 E-value=10 Score=29.81 Aligned_cols=56 Identities=20% Similarity=0.200 Sum_probs=37.1
Q ss_pred HHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeec
Q 004648 581 CLMLFND-ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFN 640 (740)
Q Consensus 581 iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N 640 (740)
||-.++. +.++|..||++.+|++...+...|..|.. .+.+.+.|.++.. ...+.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~--eG~V~~~~~~rG~--~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEK--EGKVERSPVRRGK--STYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHH--CTSEEEES-SSSS--S-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH--CCCEEEecCCCCc--ceeeeec
Confidence 3444555 67899999999999999999999999974 4556655543322 1245555
No 49
>PRK10870 transcriptional repressor MprA; Provisional
Probab=66.36 E-value=13 Score=36.02 Aligned_cols=52 Identities=13% Similarity=0.199 Sum_probs=42.9
Q ss_pred EecHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 573 IVSTYQAACLMLFND--ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
.+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+
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 366778888877654 4579999999999999999999999997 457887764
No 50
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=65.49 E-value=13 Score=26.87 Aligned_cols=34 Identities=29% Similarity=0.449 Sum_probs=28.9
Q ss_pred CccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 590 RLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 590 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 57899999999999999999999997 45677643
No 51
>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=64.98 E-value=11 Score=32.82 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=37.3
Q ss_pred EecHHHHHHHHhhcC----CCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 573 IVSTYQAACLMLFND----ADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~----~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
.++..|-.||-.+.. .+.+++++|++.++++..+++.+|..|+.
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 578899999988887 45899999999999999999999999985
No 52
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=64.81 E-value=16 Score=34.31 Aligned_cols=58 Identities=14% Similarity=0.215 Sum_probs=42.0
Q ss_pred HHHHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecc
Q 004648 577 YQAACLMLFNDAD-RLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNA 641 (740)
Q Consensus 577 ~Q~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 641 (740)
+.+.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++...+ | +++.|.++.
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~r-G----~~GGy~Lar 69 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVR-G----KGGGYRLAR 69 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeec-C----CCCCccCCC
Confidence 4455555555555 68899999999999999999999997 567876432 1 245566554
No 53
>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=64.75 E-value=15 Score=29.63 Aligned_cols=46 Identities=20% Similarity=0.362 Sum_probs=34.3
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
+..|. ||+..... ..|++||.+.||++.+.+...|..|. +-+++.+
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 34444444 89999999999999999999999997 4566654
No 54
>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=64.35 E-value=3.3 Score=31.84 Aligned_cols=47 Identities=15% Similarity=0.337 Sum_probs=40.5
Q ss_pred hheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCC
Q 004648 677 AALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 677 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
..|+..++.++.++..+|.+ .|..|...|++=+..|-++|.|.|.-+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 35677888899999988887 588999999999999999999998653
No 55
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=63.08 E-value=13 Score=33.34 Aligned_cols=60 Identities=15% Similarity=0.262 Sum_probs=43.2
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecc
Q 004648 576 TYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNA 641 (740)
Q Consensus 576 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 641 (740)
+.-..||.+.-+.++.++.||++.+|++...+-++|.-|. ..+++.....|+. -.|++|.
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr~----~~Y~l~~ 75 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGKW----VHYRLSP 75 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcCE----EEEEECc
Confidence 3334555555455679999999999999999999999997 4678876554422 2467665
No 56
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=63.03 E-value=14 Score=37.82 Aligned_cols=46 Identities=28% Similarity=0.458 Sum_probs=39.1
Q ss_pred HHHHHhhcCCCC-ccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 579 AACLMLFNDADR-LSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 579 ~~iLllFn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
..||.+|..... +++.||++.+|+|...+.+.|..|. ..+++...+
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 457888887554 7899999999999999999999998 467888765
No 57
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=62.76 E-value=8.1 Score=32.08 Aligned_cols=38 Identities=32% Similarity=0.465 Sum_probs=30.7
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
..||...+..+.+++.+|.+.+|+++..+.++|..|..
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~ 40 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE 40 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 45666666678899999999999999999999999974
No 58
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=62.38 E-value=16 Score=27.57 Aligned_cols=39 Identities=21% Similarity=0.383 Sum_probs=32.0
Q ss_pred hcCCCCc-cHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 585 FNDADRL-SFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 585 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
+...+.+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~--~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEA--EGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4455567 8999999999999999999999974 4677654
No 59
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=62.37 E-value=10 Score=29.33 Aligned_cols=38 Identities=18% Similarity=0.316 Sum_probs=29.2
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
|.-+|-++-+.+.+|+.+|++.+|++...++.-+.-|-
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 45555444447899999999999999999998887764
No 60
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=61.93 E-value=6.9 Score=30.88 Aligned_cols=53 Identities=13% Similarity=0.199 Sum_probs=33.6
Q ss_pred hhheeeccc-CCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccC--CCCCCcc
Q 004648 676 DAALVRIMK-SRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERD--SKDPTMF 736 (740)
Q Consensus 676 ~A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~--~~d~~~y 736 (740)
+..|.+.+. ....++..+|.. .+..+...+-+.|+.|+++|||++. +.|....
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 344555555 566676666655 3556788899999999999999664 4454433
No 61
>PRK11569 transcriptional repressor IclR; Provisional
Probab=61.48 E-value=14 Score=38.49 Aligned_cols=46 Identities=13% Similarity=0.222 Sum_probs=38.5
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 579 AACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 579 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
..||.+|.+. ..+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQVG 77 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 4577889874 5799999999999999999999999984 57786653
No 62
>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=61.45 E-value=20 Score=32.56 Aligned_cols=45 Identities=18% Similarity=0.269 Sum_probs=34.3
Q ss_pred HHHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 578 QAACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 578 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
++++.+.-++. ..+|.++|++.+++|...+.+.|..|.. .+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~--~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR--AGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH--CCcEEe
Confidence 44444443433 3899999999999999999999999974 567754
No 63
>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=61.25 E-value=11 Score=29.82 Aligned_cols=38 Identities=18% Similarity=0.223 Sum_probs=32.9
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
..|--+.++...+|+.+|++.|++++.++..++-.|+.
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 45666788888999999999999999999999999985
No 64
>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=61.08 E-value=11 Score=30.62 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=25.5
Q ss_pred cCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 586 NDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 586 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
...+.+|+.||++.+|++...++..+..+.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 434678999999999999999999888664
No 65
>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=61.03 E-value=15 Score=28.98 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=37.8
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
+..+..|+..+.+.+ ++..||++.+|++...+.+.|..|.. .+++..
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 456777787766666 99999999999999999999999864 356654
No 66
>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=60.38 E-value=13 Score=36.91 Aligned_cols=52 Identities=17% Similarity=0.211 Sum_probs=44.8
Q ss_pred EecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 573 IVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
.++..|..||..+.+++..+..+|++.+|++...+.++|..|. +.+++.+.+
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~~ 191 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQKG 191 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEEc
Confidence 4678899999999887889999999999999999999999997 457777653
No 67
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=59.84 E-value=17 Score=37.87 Aligned_cols=46 Identities=22% Similarity=0.307 Sum_probs=38.7
Q ss_pred HHHHHhhcCC-CCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 579 AACLMLFNDA-DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 579 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
..||.+|... ..+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~ 74 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS 74 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 4678889865 4799999999999999999999999984 57776653
No 68
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=58.19 E-value=19 Score=36.91 Aligned_cols=44 Identities=18% Similarity=0.264 Sum_probs=37.0
Q ss_pred HHHHHhhcC-CCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 579 AACLMLFND-ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 579 ~~iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
..||.+|.. ...+|+.||++.+|+|...+.+.|.+|.. .+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 457888986 45899999999999999999999999984 466754
No 69
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=58.16 E-value=18 Score=37.55 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=38.2
Q ss_pred HHHHHhhcCCC-CccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 579 AACLMLFNDAD-RLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 579 ~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+.||.+|.+.. .+|..||++.+|+|...+.+.|..|. ..++|.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~--~~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ--EEGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 35777887654 59999999999999999999999997 457887654
No 70
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=57.61 E-value=10 Score=30.35 Aligned_cols=53 Identities=9% Similarity=0.179 Sum_probs=40.6
Q ss_pred hhheeecccCCCC--CChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcc
Q 004648 676 DAALVRIMKSRKV--LGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMF 736 (740)
Q Consensus 676 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y 736 (740)
+..|...|+.++. ++-.+|-.+ ...+...+.+.+..|.++||+.++++.+..|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~--------lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKN--------LGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 4567778888776 887776653 3456778999999999999999988665554
No 71
>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=57.55 E-value=3.7 Score=32.72 Aligned_cols=50 Identities=10% Similarity=0.224 Sum_probs=35.9
Q ss_pred cccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceec
Q 004648 682 IMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYS 739 (740)
Q Consensus 682 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yi 739 (740)
.|-.++.++..+|... ...+...+-+.++.|.++|+++|.++++..|..+
T Consensus 16 ~Ll~~~~~t~~eIa~~--------l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 16 ALLKNGPATAEEIAEE--------LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHCHEEHHHHHHH--------HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHcCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 3335555666665553 2457888999999999999999999766555554
No 72
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=55.55 E-value=19 Score=31.39 Aligned_cols=45 Identities=13% Similarity=0.251 Sum_probs=37.6
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccc
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILN 623 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 623 (740)
..-.||..+..+...|+.+|++.+|++...+.+.+..|.. .+++.
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 3456777787778899999999999999999999999974 45665
No 73
>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=55.54 E-value=28 Score=31.69 Aligned_cols=43 Identities=28% Similarity=0.331 Sum_probs=34.0
Q ss_pred HHHHhhc--CCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 580 ACLMLFN--DADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 580 ~iLllFn--~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
.+|..+. ..+.+|+.||++.+|+|...+.+.|..|. +.+++..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 3444443 34579999999999999999999999997 4577754
No 74
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=55.52 E-value=16 Score=36.56 Aligned_cols=38 Identities=21% Similarity=0.285 Sum_probs=33.5
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
..||.+.+..++.|.+||++.+|++..-++++|+.|..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~ 51 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA 51 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 34666777788999999999999999999999999974
No 75
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=55.24 E-value=2.9e+02 Score=29.56 Aligned_cols=160 Identities=12% Similarity=0.264 Sum_probs=85.6
Q ss_pred hHHHHhhcCchhhHHHHHHhhhhh---cCCcHHHHHHHHHHHHHHHHHHHHhhHHhhhhhcccchHHHHHHHHHHHHHH-
Q 004648 276 GCRALISQEKFDDLSRIFRLYDET---RTGLEPVAGIFKQYFIDQGKALVHQAEEDVRNKTANMEQNLVGKILELHDKF- 351 (740)
Q Consensus 276 ~~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~- 351 (740)
.|..-.++++...+.+.++||.-+ ..|++.....+.+.|......+.+....... ....+.-|+..|..+++..
T Consensus 15 ~F~~Av~~~D~~~i~rffkLFpllg~~eeGL~~Y~~yic~~Ia~~ar~~~~~~~~~~~--~~~~~~~~a~~lt~Lfe~ia 92 (324)
T smart00762 15 RFDEAVKAQDVPELTRFFKLFPLIGMEEEGLELYSKYICDIIADKARSLLNELAGASD--DTRAAVFYADTLTHLFENVA 92 (324)
T ss_pred HHHHHHHcCCHHHHHHHHHhccccCChHhhHHHHHHHHHHHHHHHHHHHhhccccccc--cccccchHHHHHHHHHHHHH
Confidence 477888899999999999999765 3577777776666666665555433221110 0112344555555555544
Q ss_pred ------HHHHHHhhCCCHHH--HHHHHHHH----HHHhc----cCCCccCcHHHHHHHHHHHhcc-----------CCCC
Q 004648 352 ------MAYVSICFGDHKLF--LMALKEAF----EVFCN----ESIVEISSAEILATFCDNLFKN-----------SDAE 404 (740)
Q Consensus 352 ------~~l~~~~F~~~~~f--~~~l~~af----~~~~n----~~~~~~~~~e~La~y~D~~lk~-----------~~~~ 404 (740)
..+|..+|+.+... ...|...+ ..++. ... -.+....+..|.-..+.. +...
T Consensus 93 ~ii~~h~~~I~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (324)
T smart00762 93 TIIEQHQPVIEKYYGPDGMLYVITKLQKEADLQGGIILDTFMDERR-IDRLISDINSYNHAQLHAGASNDARASSNGEDE 171 (324)
T ss_pred HHHHhccHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhh-HHHHHHHHHHhhccccccccccccccccccccC
Confidence 44667778754321 11111111 11111 110 001122233333222211 0112
Q ss_pred CCChHHHHHHHHHHhHHhccccchHHHHHHHHHHHHHHhcC
Q 004648 405 KLSDETVERTMDKVIVLLGYFKYKDLFAEFYRKKLARRLLF 445 (740)
Q Consensus 405 ~~~~~e~~~~l~~i~~lf~~l~~KD~F~~~Y~~~LakRLL~ 445 (740)
..+..+++..|+.+..+.... ..|.+++++|.-.
T Consensus 172 ~~d~revd~lL~Eis~i~~~~-------~lY~rFi~~k~~~ 205 (324)
T smart00762 172 GLDPRELDAILEEISQILSRW-------ELYCRFISRKINE 205 (324)
T ss_pred CCCHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHhh
Confidence 345668899999988887543 4788888888764
No 76
>COG5173 SEC6 Exocyst complex subunit SEC6 [Intracellular trafficking and secretion]
Probab=53.98 E-value=3.8e+02 Score=30.54 Aligned_cols=59 Identities=17% Similarity=0.267 Sum_probs=37.7
Q ss_pred hhCCCHHHHHHHHHHHHHHhccCCCccCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhHHhccccch--HHHHHHH
Q 004648 358 CFGDHKLFLMALKEAFEVFCNESIVEISSAEILATFCDNLFKNSDAEKLSDETVERTMDKVIVLLGYFKYK--DLFAEFY 435 (740)
Q Consensus 358 ~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~D~~lk~~~~~~~~~~e~~~~l~~i~~lf~~l~~K--D~F~~~Y 435 (740)
||+++. +..+++.-++. +.++++.|.| .+++...+..|+.+|..+.+. |.|..+.
T Consensus 621 ~~~~~n-a~~~lksD~~~----------~y~~f~~y~d------------~e~~k~tl~pI~k~~~~m~~~~~d~~~~~~ 677 (742)
T COG5173 621 SIAEEN-ASRTLKSDHTK----------LYEMFSGYGD------------PEDVKTTLSPILKIIPLMDTRNDDLFIVEV 677 (742)
T ss_pred hhcchh-HHHHHHHHHHH----------HHHHHHhhCC------------HHHHHHHHHHHHHHHcccccCCchHHHHHH
Confidence 455444 56666655533 4566777765 356666788888888877654 7787776
Q ss_pred HHHH
Q 004648 436 RKKL 439 (740)
Q Consensus 436 ~~~L 439 (740)
++++
T Consensus 678 ~~lk 681 (742)
T COG5173 678 KSLK 681 (742)
T ss_pred HHHH
Confidence 6543
No 77
>PF13730 HTH_36: Helix-turn-helix domain
Probab=53.71 E-value=31 Score=25.88 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=23.3
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 592 SFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 592 t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999863
No 78
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=53.51 E-value=24 Score=31.04 Aligned_cols=51 Identities=18% Similarity=0.378 Sum_probs=43.0
Q ss_pred ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 574 VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+++.|+.+|......+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 788999999888777766669999999999999999999997 457777654
No 79
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=52.27 E-value=26 Score=26.63 Aligned_cols=36 Identities=17% Similarity=0.255 Sum_probs=30.1
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 588 ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 588 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.+..|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeeee
Confidence 56789999999999999999999999973 4666543
No 80
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=50.73 E-value=20 Score=28.11 Aligned_cols=34 Identities=24% Similarity=0.399 Sum_probs=26.1
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccc
Q 004648 587 DADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKIL 622 (740)
Q Consensus 587 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 622 (740)
..+..|+.+|.+.|++|.+.++.+|-.|.. .+++
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 345889999999999999999999999973 4554
No 81
>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=50.66 E-value=36 Score=25.02 Aligned_cols=33 Identities=18% Similarity=0.424 Sum_probs=24.3
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHH
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLH 612 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 612 (740)
+.+|-+.| ...+|++||++.+|++...+.+...
T Consensus 10 r~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 10 REVIRLRY--FEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 33444566 4578999999999999988877654
No 82
>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=50.07 E-value=35 Score=26.49 Aligned_cols=35 Identities=23% Similarity=0.313 Sum_probs=30.3
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 589 DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 589 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
..+|..+|++.+|++...+.+.|..|.. .+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~--~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE--EGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 4699999999999999999999999974 5777654
No 83
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=48.81 E-value=15 Score=28.06 Aligned_cols=45 Identities=9% Similarity=0.171 Sum_probs=31.8
Q ss_pred eecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCC
Q 004648 680 VRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDP 733 (740)
Q Consensus 680 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~ 733 (740)
++.+. .+.++..++... +..+...+.+.|+.|.++|++.+..+.+
T Consensus 3 l~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 3 LKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 33444 556666665543 3457788999999999999999876433
No 84
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=48.63 E-value=54 Score=32.11 Aligned_cols=33 Identities=24% Similarity=0.488 Sum_probs=29.2
Q ss_pred HhhcCCCC-ccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 583 MLFNDADR-LSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 583 llFn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
++|-..++ +|+++|++.++++..++..+|..|.
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~ 45 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQ 45 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56777776 9999999999999999999998885
No 85
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=47.25 E-value=35 Score=26.51 Aligned_cols=44 Identities=16% Similarity=0.278 Sum_probs=33.9
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 581 CLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 581 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
|..+-.+...++..+|++.+|+++..+...+..|.. .+++...|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~--~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE--KGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH--CCCEEecC
Confidence 444445778999999999999999999999999973 46666543
No 86
>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=47.25 E-value=16 Score=31.94 Aligned_cols=43 Identities=14% Similarity=0.189 Sum_probs=30.0
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccc
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKIL 622 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL 622 (740)
.+.|+..+..++.++-++|++.+|++..++.+.|..|.. .+++
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv 57 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLV 57 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCe
Confidence 455666666667899999999999999999999999974 3455
No 87
>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=46.59 E-value=32 Score=27.30 Aligned_cols=24 Identities=17% Similarity=0.425 Sum_probs=20.8
Q ss_pred ChhHHHHHHHhhhhhhccccCCCC
Q 004648 709 EIKAIKSRIDDLINREFIERDSKD 732 (740)
Q Consensus 709 ~~~~ik~~Ie~LIereyi~r~~~d 732 (740)
|..-+...++.|.++|||+|+++-
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 467778899999999999999864
No 88
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=45.76 E-value=56 Score=30.24 Aligned_cols=39 Identities=13% Similarity=0.335 Sum_probs=32.5
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 585 FNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 585 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
+..+..+|..+|++.+|+|...+.++|..|. +.+++...
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~ 58 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAV 58 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEe
Confidence 4445578999999999999999999999997 46787654
No 89
>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=45.19 E-value=44 Score=24.93 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=17.4
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHH
Q 004648 589 DRLSFSEILTQLNLNKGDLIRVLH 612 (740)
Q Consensus 589 ~~~t~~ei~~~t~i~~~~l~~~L~ 612 (740)
+++|++||++.+|++...++..+.
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 367999999999999998887764
No 90
>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=44.31 E-value=7 Score=38.11 Aligned_cols=58 Identities=19% Similarity=0.300 Sum_probs=40.4
Q ss_pred hhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 675 IDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 675 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
+=...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.-.-+|+..|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 3344457889999998888765 588899999999999999999998888899999984
No 91
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=44.06 E-value=53 Score=31.65 Aligned_cols=55 Identities=20% Similarity=0.154 Sum_probs=41.5
Q ss_pred EEEEecHHHHHHHHhhcCCCCc-cHHHHHHHh--CCCHHHHHHHHHHhhcccccccccCC
Q 004648 570 IELIVSTYQAACLMLFNDADRL-SFSEILTQL--NLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 570 ~~l~~s~~Q~~iLllFn~~~~~-t~~ei~~~t--~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+++--+.+..+|+-+..-.+.- +.++|++.+ +++.++++.+|..|. +.++|.+..
T Consensus 18 ~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 18 FEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 3334455666666665544433 899999999 999999999999997 678998864
No 92
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=44.03 E-value=27 Score=30.95 Aligned_cols=57 Identities=5% Similarity=0.043 Sum_probs=42.5
Q ss_pred eeecccC-CCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCccee
Q 004648 679 LVRIMKS-RKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNY 738 (740)
Q Consensus 679 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Y 738 (740)
|..+|.. .+.++.++|.+.+.++. ..++...|=+.|+.|.+.|.|.+-..+.....|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4445544 56799999999887642 457889999999999999999987543333444
No 93
>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=43.28 E-value=25 Score=34.22 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=22.7
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 589 DRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 589 ~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
..+|+++|++.|||..+++..+|+.|-
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l~ 175 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQLG 175 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHTT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHCC
Confidence 379999999999999999999999883
No 94
>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=43.18 E-value=25 Score=37.74 Aligned_cols=143 Identities=13% Similarity=0.161 Sum_probs=40.1
Q ss_pred EecHHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCCCCCcce
Q 004648 573 IVSTYQAACLMLFND--ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFTDRMRRI 650 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~~~~~~i 650 (740)
.++..+..|.-+..+ ..++-..+|...|+|+...+.++|.+|.. | ++++... +.+.+++|+
T Consensus 81 ~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~-k-~lIK~vk---------------sv~~~~rK~ 143 (327)
T PF05158_consen 81 GLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLES-K-KLIKSVK---------------SVKNPNRKV 143 (327)
T ss_dssp SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHH-T-TSEEEE-----------------SS-SS--E
T ss_pred CCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHh-C-CCEEEec---------------CcCCCCeEE
Confidence 456677777766654 45888999999999999999999999975 3 4554321 222344444
Q ss_pred eccCCCcchhhh------hHHhHHhhhhhchhhheeecccCCCC-----------------------------CChhHHH
Q 004648 651 RIPLPPVDDRRE------INEDVGKDRRHNIDAALVRIMKSRKV-----------------------------LGYQQLI 695 (740)
Q Consensus 651 ~i~~~~~~e~~~------~~~~v~~~R~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 695 (740)
-+-..-.....- ++.+.+.+=-..+...|.+.+.++.. .+.+++.
T Consensus 144 Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~ 223 (327)
T PF05158_consen 144 YMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIA 223 (327)
T ss_dssp EEESSS--------------------------------------------------------------------------
T ss_pred EEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHH
Confidence 432211100000 11223333334455555566555554 3444444
Q ss_pred HHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCC
Q 004648 696 SECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKD 732 (740)
Q Consensus 696 ~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d 732 (740)
.-+.+.=-..-..+.++|...++.||=.|-|++-...
T Consensus 224 ~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 224 EFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp -------------------------------------
T ss_pred HHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 4443321112346889999999999999988887643
No 95
>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=41.42 E-value=13 Score=27.15 Aligned_cols=44 Identities=9% Similarity=0.240 Sum_probs=33.1
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccc
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIE 727 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~ 727 (740)
+-.|+..+.....++..+|-.. ...+.+.+.+.|..|.++|||+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~--------~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK--------LGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH--------HTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHH--------hCCCHHHHHHHHHHHHHCcCcC
Confidence 4456677777788888887764 3467899999999999999985
No 96
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.59 E-value=57 Score=24.00 Aligned_cols=39 Identities=18% Similarity=0.281 Sum_probs=29.3
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
|.-+.-|+.++. .++|..+|++.+|++...+.+.+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555555553 357999999999999999998887653
No 97
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=40.35 E-value=60 Score=29.48 Aligned_cols=64 Identities=16% Similarity=0.220 Sum_probs=48.0
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCC---CceeecccCC
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQS---DSFEFNAKFT 644 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~---~~~~~N~~F~ 644 (740)
-.+|-+..+.+..|+.|+++.+|-+.+.+.+.|..|. .++++..+.+|+...+. +.+.++-.|.
T Consensus 67 leLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 67 LELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 3445667788899999999999999999999999997 47788766556554433 4455666564
No 98
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=40.04 E-value=44 Score=24.13 Aligned_cols=30 Identities=23% Similarity=0.459 Sum_probs=20.9
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHH
Q 004648 581 CLMLFNDADRLSFSEILTQLNLNKGDLIRVLH 612 (740)
Q Consensus 581 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 612 (740)
|+-++.++ .|+.+|++.+|++...+.+.|.
T Consensus 14 i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 14 IKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 34455554 8999999999999999988764
No 99
>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=39.68 E-value=50 Score=31.34 Aligned_cols=43 Identities=14% Similarity=0.169 Sum_probs=34.1
Q ss_pred HHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccc
Q 004648 579 AACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILN 623 (740)
Q Consensus 579 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 623 (740)
..|+..+=.+..+|-+||+..+||+..++++.|..|.. .+++.
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 44555444556899999999999999999999999984 45663
No 100
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=39.52 E-value=35 Score=35.19 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=40.3
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
-|..|+-+.++++.+++.||++.+|++...++|-|..|. +.++|.+.
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 367788889999999999999999999999999999996 45666654
No 101
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.45 E-value=41 Score=32.62 Aligned_cols=44 Identities=14% Similarity=0.143 Sum_probs=35.7
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccc
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILN 623 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 623 (740)
...||.+.-.++.+|-++|++.+||+...++++|..|.. .+++.
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e--~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYD--ARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeE
Confidence 445666566667899999999999999999999999974 45655
No 102
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=39.06 E-value=62 Score=23.85 Aligned_cols=38 Identities=16% Similarity=0.200 Sum_probs=27.7
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 576 TYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 576 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
..|.-++.++- +.+|..+|++.+|++...+...+..+.
T Consensus 3 ~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 3 PREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444554442 467999999999999998888876553
No 103
>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=38.87 E-value=75 Score=26.10 Aligned_cols=39 Identities=10% Similarity=0.193 Sum_probs=28.5
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
+.-.+|-+.-....+|..+|+..+|.+.+++...|..+.
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 344566677788999999999999999999999998774
No 104
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=38.86 E-value=59 Score=32.17 Aligned_cols=44 Identities=14% Similarity=0.200 Sum_probs=35.0
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 580 ACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 580 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.||......+.+|..+|++.+|++...+.++|..|.. .+++.+.
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 4554444556799999999999999999999999974 4677654
No 105
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=37.88 E-value=19 Score=31.37 Aligned_cols=47 Identities=13% Similarity=0.227 Sum_probs=39.0
Q ss_pred hhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccC
Q 004648 675 IDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERD 729 (740)
Q Consensus 675 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~ 729 (740)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|+|-
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeece
Confidence 45678888888888888887763 467889999999999999999963
No 106
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=37.77 E-value=37 Score=27.09 Aligned_cols=33 Identities=15% Similarity=0.326 Sum_probs=26.4
Q ss_pred hhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 584 LFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 584 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
...+...+|+++|+..++++++.+...|.-|..
T Consensus 8 ~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 8 YLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345677899999999999999999999999984
No 107
>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=37.28 E-value=75 Score=24.31 Aligned_cols=38 Identities=21% Similarity=0.395 Sum_probs=29.6
Q ss_pred cCCCCc-cHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 586 NDADRL-SFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 586 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
.....+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 333444 4999999999999999999999974 4666543
No 108
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=37.09 E-value=20 Score=26.28 Aligned_cols=45 Identities=9% Similarity=0.223 Sum_probs=33.2
Q ss_pred eeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCC
Q 004648 679 LVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 679 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
|.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..+
T Consensus 5 il~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 5 ILELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 3344444556777666663 46788999999999999999998763
No 109
>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=37.07 E-value=73 Score=25.82 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=38.7
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccc
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKI 621 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~i 621 (740)
.+=|+.++-++...+.-|+++|++.||-....+.-+|..+...|.++
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl 55 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGL 55 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCc
Confidence 45689999889988899999999999999999998888875333333
No 110
>PRK00215 LexA repressor; Validated
Probab=36.43 E-value=67 Score=31.75 Aligned_cols=51 Identities=20% Similarity=0.249 Sum_probs=39.8
Q ss_pred ecHHHHHHHHhhc-----CCCCccHHHHHHHhCC-CHHHHHHHHHHhhcccccccccCC
Q 004648 574 VSTYQAACLMLFN-----DADRLSFSEILTQLNL-NKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 574 ~s~~Q~~iLllFn-----~~~~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
++.-|..||.... .....|+.||++.+|+ +...+.+.|..|.. .+.+.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~--~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALER--KGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CCCEEeCC
Confidence 3567888886654 2446899999999999 99999999999973 46776654
No 111
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=36.08 E-value=93 Score=25.79 Aligned_cols=41 Identities=12% Similarity=0.193 Sum_probs=32.7
Q ss_pred HhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccc
Q 004648 583 MLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILN 623 (740)
Q Consensus 583 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 623 (740)
+..++.+.+|-++|++.+|++...+-++++.|-...+.|..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEe
Confidence 34556668999999999999999999999999654455554
No 112
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=35.94 E-value=44 Score=34.42 Aligned_cols=46 Identities=17% Similarity=0.304 Sum_probs=39.9
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
|-.|+-+.++.+.++++||++.+|+++..++|=|..|. +.++|.+.
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 55788889999999999999999999999999999997 44666664
No 113
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=35.64 E-value=53 Score=31.31 Aligned_cols=48 Identities=13% Similarity=0.189 Sum_probs=40.5
Q ss_pred ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccc
Q 004648 574 VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILN 623 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 623 (740)
+.-.-..||-.+.++...|+.+|++.+|++...+.+-++.|.. .+++.
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 4456677888899999999999999999999999999999974 45654
No 114
>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=34.96 E-value=60 Score=26.98 Aligned_cols=35 Identities=6% Similarity=0.031 Sum_probs=30.2
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHH
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLH 612 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 612 (740)
=++.|+-+..+ +.+|+.+|++.+|++...+.+.|.
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 36678878888 899999999999999999988764
No 115
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=34.20 E-value=57 Score=32.58 Aligned_cols=49 Identities=24% Similarity=0.341 Sum_probs=41.5
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
|..-..||-+......+.+.||++.+|+|...+..+++.|. +.+++..+
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 45556788888888999999999999999999999999996 56777643
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=33.28 E-value=19 Score=27.70 Aligned_cols=26 Identities=12% Similarity=0.276 Sum_probs=21.0
Q ss_pred CCCChhHHHHHHHhhhhhhccccCCC
Q 004648 706 FKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 706 F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
+..+...+.+.|..|+++|||+|..+
T Consensus 31 l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 31 LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 34677889999999999999999754
No 117
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=33.05 E-value=63 Score=30.76 Aligned_cols=51 Identities=25% Similarity=0.355 Sum_probs=37.8
Q ss_pred cCCCceeEeccCccceEEEEEecCeeEEEEecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 544 KTKARKLTWIYSLGNCHVNGKFELKAIELIVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 544 k~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
+++.+.|+|.++|-. .|.++-. +.-..|+++|++.+|.++..++++|..=.
T Consensus 36 ~~~~~~lTWvdSLav-------------------AAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 36 KDPYERLTWVDSLAV-------------------AAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred hCcccccchhhHHHH-------------------HHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhcch
Confidence 468899999986531 2222322 44578999999999999999999987543
No 118
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.05 E-value=28 Score=26.18 Aligned_cols=28 Identities=7% Similarity=0.198 Sum_probs=24.7
Q ss_pred CCCCCChhHHHHHHHhhhhhhccccCCC
Q 004648 704 HSFKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 704 ~~F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
.+|..+...+.+.+..|.+.|+|.+.++
T Consensus 28 ~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 28 AQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3678899999999999999999998764
No 119
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=32.95 E-value=24 Score=35.66 Aligned_cols=33 Identities=6% Similarity=0.186 Sum_probs=28.3
Q ss_pred CCCCCChhHHHHHHHhhhhhhccccCCCCCCcce
Q 004648 704 HSFKPEIKAIKSRIDDLINREFIERDSKDPTMFN 737 (740)
Q Consensus 704 ~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~ 737 (740)
.+|..+...++++|+.|++.|+|.|..+ +.+|+
T Consensus 32 ~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 32 DQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 3699999999999999999999999876 45543
No 120
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=32.84 E-value=79 Score=30.71 Aligned_cols=64 Identities=14% Similarity=0.143 Sum_probs=48.3
Q ss_pred CceeEeccCccceEEEEEecCeeEEEEecHHHHHHHHhhcCC--CCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 547 ARKLTWIYSLGNCHVNGKFELKAIELIVSTYQAACLMLFNDA--DRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 547 ~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~Q~~iLllFn~~--~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
.|.-.|.+.+|..+++- .+.| .||+.||.-|+.-... ..||.+.|++..+++.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 34456788888888763 3334 3788999877754332 479999999999999999999888775
No 121
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=32.84 E-value=54 Score=35.69 Aligned_cols=64 Identities=22% Similarity=0.284 Sum_probs=41.7
Q ss_pred eEeccCccceEEEEEecCeeEEEEe-------cHHHHHHHHhhcC-CC-CccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 550 LTWIYSLGNCHVNGKFELKAIELIV-------STYQAACLMLFND-AD-RLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 550 L~w~~~l~~~~i~~~~~~~~~~l~~-------s~~Q~~iLllFn~-~~-~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
+.+.|.||..|=.+ ++-.+-|.= +-+-..||-++-+ .+ .+|+++|++.|||..+++..+|++|-
T Consensus 282 IdFSYeLSr~E~~~--GsPEKPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 282 IDFSYELSRREGKI--GSPEKPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhcccCcC--CCCCCCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 56778888766543 222222221 3344445543333 22 39999999999999999999999984
No 122
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=32.77 E-value=51 Score=32.17 Aligned_cols=46 Identities=11% Similarity=0.078 Sum_probs=39.0
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
-+..|+.+.+.++.+++.+|++.+|++...++|-|..|.. .+++.+
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 5677888899999999999999999999999999999974 344443
No 123
>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=32.41 E-value=59 Score=21.86 Aligned_cols=25 Identities=24% Similarity=0.436 Sum_probs=20.3
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 591 LSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 591 ~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
+|-+||++.+|++.+.+-|.|..|.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 6789999999999999999998875
No 124
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=31.87 E-value=69 Score=30.06 Aligned_cols=48 Identities=13% Similarity=0.282 Sum_probs=40.3
Q ss_pred ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccc
Q 004648 574 VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILN 623 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~ 623 (740)
++..--.||.++..+...|+.+|++.+|+++..+.+-+..|.. .+++.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~--~GvI~ 54 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ--AGIIT 54 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCee
Confidence 4556677888888888999999999999999999999999974 35554
No 125
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=31.28 E-value=68 Score=32.98 Aligned_cols=47 Identities=15% Similarity=0.199 Sum_probs=39.6
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
-|..|+-.++++..+++.||++.+|++...++|-|..|.. .+++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~--~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE--SGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEe
Confidence 4567888899999999999999999999999999999863 4566554
No 126
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.92 E-value=75 Score=33.07 Aligned_cols=40 Identities=15% Similarity=0.247 Sum_probs=31.6
Q ss_pred HHHHHHHHhhc-CCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 576 TYQAACLMLFN-DADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 576 ~~Q~~iLllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
-+...|+-.+. ....+|+++|+..|||..+++..+|++|-
T Consensus 208 YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~ 248 (290)
T PLN03238 208 YWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLN 248 (290)
T ss_pred HHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCC
Confidence 34555665443 35689999999999999999999999883
No 127
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=30.58 E-value=65 Score=25.54 Aligned_cols=51 Identities=20% Similarity=0.351 Sum_probs=34.4
Q ss_pred ecHHHHHHHHhhcC-----CCCccHHHHHHHhCCC-HHHHHHHHHHhhcccccccccCC
Q 004648 574 VSTYQAACLMLFND-----ADRLSFSEILTQLNLN-KGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 574 ~s~~Q~~iLllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+|.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.+
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 34556666654332 2356999999999997 899999999997 446777654
No 128
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=30.28 E-value=35 Score=28.71 Aligned_cols=37 Identities=19% Similarity=0.189 Sum_probs=33.2
Q ss_pred CCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 704 HSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 704 ~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
.++..+.+.-+++|..|-++|.|..-..++..-+|.|
T Consensus 49 erlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 49 SKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred HHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 4788899999999999999999998888888999976
No 129
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.65 E-value=1.7e+02 Score=32.17 Aligned_cols=92 Identities=13% Similarity=0.213 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCC-------CCCChHhHHHHHH-HHhHhhhcCCCCCcCcccHHHHHHHHHHHHHHHHH
Q 004648 9 FEESWALMEQGIAKLKKILKGLPE-------PPFASEECMTLYT-IVYDLCSIELPSAQDCSYSQRLYVKYGEVFEEHMQ 80 (740)
Q Consensus 9 f~~~W~~l~~~i~~i~~il~~~~~-------~~~s~~~y~~lY~-~vY~lc~~~~~~~~~~~~~e~LY~~l~~~l~~~l~ 80 (740)
=++.|+.|...+++|.+-.+|-.. +-=|+.+|+.+|. +|-.+|... .|++..+.+..+ .|+.
T Consensus 22 ~eedw~ai~~fceqinkdp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkn--------cGekfH~evgkf--rFLN 91 (594)
T KOG1086|consen 22 DEEDWKAIDGFCEQINKDPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKN--------CGEKFHEEVGKF--RFLN 91 (594)
T ss_pred hHHHHHHHHHHHHHHhcCCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHh--------hhHHHHHHHHHH--HHHH
Confidence 478999999999887554433211 1237889999998 688889875 588888877764 3444
Q ss_pred hcccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhch
Q 004648 81 SDVLPSFEDKRGEFMLREFVKQWENINVMGRWLLRFFEY 119 (740)
Q Consensus 81 ~~v~~~l~~~~~~~~L~~~~~~W~~~~~~~~~l~~vf~Y 119 (740)
+.++ . .-.+|...|..=+...++|.-+|++
T Consensus 92 ELIk-v--------vsPKYlG~~tSekvKtkiIelLfsW 121 (594)
T KOG1086|consen 92 ELIK-V--------VSPKYLGSRTSEKVKTKIIELLFSW 121 (594)
T ss_pred HHHH-H--------hCchhcchhhhHHHHHHHHHHHhhh
Confidence 3321 1 1125667787778888888887776
No 130
>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=29.62 E-value=26 Score=26.65 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=29.6
Q ss_pred eecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCC
Q 004648 680 VRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 680 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
..++-....++..+|-. .+..+...+-+.+..|.++|||+|..
T Consensus 9 L~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 9 LRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 33344445555555444 34568899999999999999999864
No 131
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=29.42 E-value=30 Score=35.19 Aligned_cols=33 Identities=18% Similarity=0.231 Sum_probs=27.8
Q ss_pred CCCCCChhHHHHHHHhhhhhhccccCCCCCCcce
Q 004648 704 HSFKPEIKAIKSRIDDLINREFIERDSKDPTMFN 737 (740)
Q Consensus 704 ~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~ 737 (740)
..|..+...++++|+.|++.|+|.|..+ +.+|+
T Consensus 41 ~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 41 TQYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 3688999999999999999999999876 45543
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=29.11 E-value=84 Score=23.84 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=24.2
Q ss_pred hcCCCCccHHHHHHHhCCCHHHHHHHHHH
Q 004648 585 FNDADRLSFSEILTQLNLNKGDLIRVLHS 613 (740)
Q Consensus 585 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 613 (740)
|+.-...|.+||++.+|++...+..+|..
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 55556899999999999999888877764
No 133
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=28.84 E-value=75 Score=32.68 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=35.9
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
-|..|+-+.+.++.+++.+|++.+|+++..++|-|..|.
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 477899999999999999999999999999999998876
No 134
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=28.36 E-value=1.2e+02 Score=21.67 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=27.9
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSL 614 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 614 (740)
+..+..++.++- ...+|..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444555554432 246799999999999999988877653
No 135
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=28.28 E-value=33 Score=34.97 Aligned_cols=53 Identities=15% Similarity=0.338 Sum_probs=37.6
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcc
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMF 736 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y 736 (740)
.+.|...++....|.-+. +|...|..+...++++|+.|++.|+|.|..+ +.+|
T Consensus 22 ~~~I~~~~~~G~~LPsE~-------eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~Gtf 74 (241)
T PRK10079 22 EQELRQHYRCGDYLPAEQ-------QLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVL 74 (241)
T ss_pred HHHHhcccCCCCcCCCHH-------HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEE
Confidence 333433566666665332 2334699999999999999999999999876 4454
No 136
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.77 E-value=95 Score=28.83 Aligned_cols=49 Identities=16% Similarity=0.364 Sum_probs=40.3
Q ss_pred ecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 574 VSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 574 ~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
+.-.-.-||..+++....++.+|++.+|++...+.+.+..|. +.+|+..
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 344566788888888889999999999999999999999997 4566653
No 137
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=27.74 E-value=33 Score=34.71 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=27.7
Q ss_pred CCCCChhHHHHHHHhhhhhhccccCCCCCCcce
Q 004648 705 SFKPEIKAIKSRIDDLINREFIERDSKDPTMFN 737 (740)
Q Consensus 705 ~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~ 737 (740)
+|..+...++++|+.|.+.|||.|..+ +.+|+
T Consensus 41 ~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 41 RFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 699999999999999999999999876 44543
No 138
>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=27.63 E-value=92 Score=23.66 Aligned_cols=39 Identities=15% Similarity=0.201 Sum_probs=30.6
Q ss_pred cHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 575 STYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 575 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
|.-+..||.++.. +.|..+|++.+|+++..+..++..+.
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 4556677777766 45889999999999999999988875
No 139
>PF11728 DUF939_C: DUF939 C-terminal domain; InterPro: IPR021062 This entry represents a C-terminal domain found in a set of bacterial proteins. The proteins are about 160 amino acids in length and are predicted to be multi-pass membrane proteins. ; PDB: 3KMI_B.
Probab=27.40 E-value=3.9e+02 Score=25.52 Aligned_cols=62 Identities=16% Similarity=0.319 Sum_probs=40.1
Q ss_pred hhcCchhhHHHHHHhhhhhcCCcHHHHHHHHHHHHHHHHHHHHhhHHhhhhhcccchHHHHHHHHHHHHHHHH
Q 004648 281 ISQEKFDDLSRIFRLYDETRTGLEPVAGIFKQYFIDQGKALVHQAEEDVRNKTANMEQNLVGKILELHDKFMA 353 (740)
Q Consensus 281 l~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~v~~ll~l~~~~~~ 353 (740)
+.....+-|++|+..+++++ ....-+..+.+++...+..+... +.+..++..|-.++..|..
T Consensus 74 MR~~Q~~iL~~M~~~l~~i~-~~~~q~~~ia~~~~~~a~~~~e~----------n~~~~ll~~L~~l~~~fr~ 135 (167)
T PF11728_consen 74 MREKQLEILKRMYPNLSKIY-MSPKQAEIIADFLEELAESLHEN----------NTAEELLEELEELKEEFRE 135 (167)
T ss_dssp HHHHHHHHHHHHHHHHTT-S-S--HHHHHHHHHHHHHHH----T----------THHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHHHHHhCCC----------CcHHHHHHHHHHHHHHHhc
Confidence 55677889999999999984 33455666677777766654421 2367778888777777764
No 140
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=27.18 E-value=80 Score=31.77 Aligned_cols=58 Identities=12% Similarity=0.280 Sum_probs=43.5
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccCC
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKFT 644 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~ 644 (740)
+-..+.-+|.++..||+.+|.+.|+-|...|+.+|..++ ++.+.+. -..+|.+-+.|.
T Consensus 187 vld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-----v~NkKg~-----~k~tyeLKPEYK 244 (254)
T KOG2905|consen 187 VLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-----VLNKKGP-----YKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-----HHhccCc-----ccCceecCHHHh
Confidence 344566789999999999999999999999999999886 4544321 135677665554
No 141
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=27.17 E-value=87 Score=31.21 Aligned_cols=36 Identities=8% Similarity=0.092 Sum_probs=32.6
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 580 ACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 580 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
.+.-+|.+.+.||+..|++.+|-|+..|+.+|.+.+
T Consensus 199 ~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~ia 234 (297)
T COG5090 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIA 234 (297)
T ss_pred HHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHH
Confidence 456789999999999999999999999999998875
No 142
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=27.09 E-value=1.1e+02 Score=29.98 Aligned_cols=50 Identities=18% Similarity=0.236 Sum_probs=40.0
Q ss_pred ecHHHHHHHHhhcC-----CCCccHHHHHHHhCCC-HHHHHHHHHHhhcccccccccC
Q 004648 574 VSTYQAACLMLFND-----ADRLSFSEILTQLNLN-KGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 574 ~s~~Q~~iLllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
++..|..||....+ ....|+.||++.+|++ ...+.++|..|. +.+++.+.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~ 59 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERD 59 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecC
Confidence 46788888876653 2358899999999998 999999999997 45777764
No 143
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=27.00 E-value=87 Score=35.71 Aligned_cols=50 Identities=12% Similarity=0.198 Sum_probs=43.4
Q ss_pred EecHHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 573 IVSTYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
.+|..|..||......+.+|..+|++.+|++...+.+++.+|.. .+++..
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 46889999999998888999999999999999999999999974 356554
No 144
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=26.65 E-value=94 Score=26.81 Aligned_cols=53 Identities=11% Similarity=0.164 Sum_probs=43.8
Q ss_pred hhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhcccc
Q 004648 675 IDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIER 728 (740)
Q Consensus 675 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r 728 (740)
++-+|..++. .+.++=-+|.+++.+...+.+.++...+=..+..|-++|+|++
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 4555666666 4678888999999887765678899999999999999999998
No 145
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.56 E-value=74 Score=29.74 Aligned_cols=32 Identities=16% Similarity=0.191 Sum_probs=27.8
Q ss_pred CCCCccHHHHHHHhCCCHHHHHHHHHHhhccc
Q 004648 587 DADRLSFSEILTQLNLNKGDLIRVLHSLSCSK 618 (740)
Q Consensus 587 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k 618 (740)
.++.+|-++|++.+||+...|++.|..|...|
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~ 43 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDEK 43 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhh
Confidence 34579999999999999999999999997533
No 146
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.40 E-value=92 Score=21.86 Aligned_cols=28 Identities=14% Similarity=0.316 Sum_probs=20.3
Q ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 588 ADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 588 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
...+|+++|++..|++..-+.+......
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 4579999999999999988888776553
No 147
>PRK13239 alkylmercury lyase; Provisional
Probab=26.37 E-value=1.1e+02 Score=30.34 Aligned_cols=40 Identities=18% Similarity=0.241 Sum_probs=34.8
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhh
Q 004648 576 TYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLS 615 (740)
Q Consensus 576 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 615 (740)
.+...||.++-++...|+++|+..+|.+.+.+.+.|..|.
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 3556677778888999999999999999999999999885
No 148
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=26.00 E-value=94 Score=27.51 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=42.9
Q ss_pred hhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCccee
Q 004648 675 IDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNY 738 (740)
Q Consensus 675 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Y 738 (740)
+|+.|.+ -....-.....++.+|+.... .+ ++...+--||+.||+.|.++-.++-.++-+|
T Consensus 49 yD~~Il~-~~~~~~~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 49 YDDFILE-QAPDEFQKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred hhHHHHh-cCCccccHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 4555555 112233556688999998874 34 6788999999999999999988765554444
No 149
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=25.83 E-value=83 Score=32.73 Aligned_cols=48 Identities=6% Similarity=0.066 Sum_probs=40.3
Q ss_pred HHHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 576 TYQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 576 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
--|..|+.+.+..+.+|+.||++.+|++...++|-|..|.. .+++.+.
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 45778888899988999999999999999999999999963 3555554
No 150
>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=25.72 E-value=83 Score=28.40 Aligned_cols=50 Identities=8% Similarity=0.078 Sum_probs=38.4
Q ss_pred ecHHHHHHHHh--hc--------CCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 574 VSTYQAACLML--FN--------DADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 574 ~s~~Q~~iLll--Fn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
+-.+.-.+++. .| +.-++|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 27 ~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 27 TVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred HHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34555556665 44 34589999999999999999999999996 67777653
No 151
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.68 E-value=74 Score=23.17 Aligned_cols=32 Identities=19% Similarity=0.365 Sum_probs=21.2
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004648 581 CLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSL 614 (740)
Q Consensus 581 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 614 (740)
++.++.+ .+|..+|++.+|++...+.+-+..+
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4444444 7899999999999999888776554
No 152
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=25.52 E-value=89 Score=32.17 Aligned_cols=47 Identities=15% Similarity=0.237 Sum_probs=39.4
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
-+..|+-+.++.+.+++.||++.++++...++|-|..|.. .++|.+.
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 3566787888889999999999999999999999999974 4566654
No 153
>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=25.40 E-value=1e+02 Score=27.68 Aligned_cols=49 Identities=22% Similarity=0.310 Sum_probs=38.1
Q ss_pred cHHHHHHHHhhcCC--------CCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 575 STYQAACLMLFNDA--------DRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 575 s~~Q~~iLllFn~~--------~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
..+.-..|+..|.. -+.|.++|+..++-+.+.++.+|..|. +++++...
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 34555566655543 479999999999999999999999996 67777653
No 154
>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=25.35 E-value=51 Score=28.92 Aligned_cols=41 Identities=15% Similarity=0.284 Sum_probs=30.4
Q ss_pred CCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhcccc--CCCCC
Q 004648 685 SRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIER--DSKDP 733 (740)
Q Consensus 685 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r--~~~d~ 733 (740)
..+.++..+|.. ....+...+-+.|..|.++|||.| +++|+
T Consensus 40 ~~~~~t~~eL~~--------~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIK--------EILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 345677766665 344577889999999999999997 45554
No 155
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=24.98 E-value=37 Score=26.55 Aligned_cols=28 Identities=14% Similarity=0.268 Sum_probs=24.3
Q ss_pred CCCCCChhHHHHHHHhhhhhhccccCCC
Q 004648 704 HSFKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 704 ~~F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
++|..+...+++++..|.+.|+|.+.++
T Consensus 32 ~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 32 ERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 3688999999999999999999999875
No 156
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.98 E-value=44 Score=25.02 Aligned_cols=21 Identities=14% Similarity=0.339 Sum_probs=18.3
Q ss_pred CCCChhHHHHHHHhhhhhhcc
Q 004648 706 FKPEIKAIKSRIDDLINREFI 726 (740)
Q Consensus 706 F~~~~~~ik~~Ie~LIereyi 726 (740)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 356788999999999999987
No 157
>PLN03239 histone acetyltransferase; Provisional
Probab=24.84 E-value=1e+02 Score=33.06 Aligned_cols=40 Identities=15% Similarity=0.272 Sum_probs=30.8
Q ss_pred cHHHHHHHHhhcCC----CCccHHHHHHHhCCCHHHHHHHHHHh
Q 004648 575 STYQAACLMLFNDA----DRLSFSEILTQLNLNKGDLIRVLHSL 614 (740)
Q Consensus 575 s~~Q~~iLllFn~~----~~~t~~ei~~~t~i~~~~l~~~L~~L 614 (740)
+-+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
T Consensus 265 ~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 265 PYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred HHHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 34555666444222 46999999999999999999999988
No 158
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.71 E-value=52 Score=32.97 Aligned_cols=54 Identities=24% Similarity=0.364 Sum_probs=44.2
Q ss_pred eeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 679 LVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 679 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
-|-..|..|.+..+||-. .|....++.-.+|..|+..|.|.-.-+|+..|+||.
T Consensus 205 Fv~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 345667777777777765 477777778889999999999999999999999984
No 159
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.56 E-value=1.7e+02 Score=21.45 Aligned_cols=23 Identities=17% Similarity=0.387 Sum_probs=20.6
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHH
Q 004648 591 LSFSEILTQLNLNKGDLIRVLHS 613 (740)
Q Consensus 591 ~t~~ei~~~t~i~~~~l~~~L~~ 613 (740)
.|+.+++..+|++...+.+.+..
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 69999999999999999988764
No 160
>PRK14999 histidine utilization repressor; Provisional
Probab=24.54 E-value=39 Score=34.36 Aligned_cols=47 Identities=11% Similarity=0.220 Sum_probs=35.9
Q ss_pred cccCCCCC-ChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcce
Q 004648 682 IMKSRKVL-GYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFN 737 (740)
Q Consensus 682 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~ 737 (740)
..+....| +-.+|.+ .|.++...++++|+.|.+.|+|.|..+ +.+|+
T Consensus 29 ~~~~G~~LPsE~eLa~--------~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELVA--------QYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 55666666 4445554 689999999999999999999999876 45553
No 161
>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=24.42 E-value=1.2e+02 Score=25.60 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=35.4
Q ss_pred HHHHHHhhcCCCCccHHHHHHHh-CCCHHHHHHHHHHhhcccccccccC
Q 004648 578 QAACLMLFNDADRLSFSEILTQL-NLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
-+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
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 3566666656 688999999999 9999999999999974 5777654
No 162
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=23.96 E-value=42 Score=34.17 Aligned_cols=35 Identities=20% Similarity=0.382 Sum_probs=29.0
Q ss_pred hcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcce
Q 004648 702 LSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFN 737 (740)
Q Consensus 702 l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~ 737 (740)
|..+|.++...++++|..|.+.|+|.|..+ +.+|+
T Consensus 37 La~~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 37 LAEQFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HHHHHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 334799999999999999999999999876 45553
No 163
>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=23.74 E-value=1.2e+02 Score=25.73 Aligned_cols=33 Identities=9% Similarity=0.318 Sum_probs=23.1
Q ss_pred HhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 583 MLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 583 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
.+..+... ++..|.+.||||...++.+|.+|..
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~ 47 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPE 47 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGG
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhc
Confidence 34445555 9999999999999999999999974
No 164
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=23.27 E-value=40 Score=26.76 Aligned_cols=54 Identities=24% Similarity=0.231 Sum_probs=31.9
Q ss_pred hhheeecccCCC-CCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcceecC
Q 004648 676 DAALVRIMKSRK-VLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMFNYSA 740 (740)
Q Consensus 676 ~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y~Yia 740 (740)
=|.||..||++. .++.+||..++. +..+ ++.++.|-+.+=|+-+++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 367888999875 588887776553 3333 234556668888999974 47899976
No 165
>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=23.17 E-value=95 Score=32.41 Aligned_cols=57 Identities=16% Similarity=0.326 Sum_probs=31.9
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCCCCCCCCCCCceeecccC
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEPNTKTISQSDSFEFNAKF 643 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F 643 (740)
+--.|.-+|.++..||+.+|.+.|+-|+..|+.+|..++ ++.+.++ -...|.|=..|
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 445677789999999999999999999999999999886 4555431 12456654444
No 166
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=23.08 E-value=40 Score=34.82 Aligned_cols=47 Identities=15% Similarity=0.175 Sum_probs=40.7
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCC
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
...|...+++++.++..||.+ .|.++...|++-|+.|-++|.|.|.-
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~--------~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQ--------YFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 456778889999999998877 58899999999999999999998843
No 167
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=22.98 E-value=37 Score=34.97 Aligned_cols=45 Identities=13% Similarity=0.302 Sum_probs=40.7
Q ss_pred hheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccC
Q 004648 677 AALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERD 729 (740)
Q Consensus 677 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~ 729 (740)
-.|+..+++++.++.++|.+ +|.+|...|++=|..|-++|++.|.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~--------~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKEKGKVSVEELAE--------LFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHH--------HhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 46788899999999998887 6999999999999999999999994
No 168
>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=22.90 E-value=58 Score=24.99 Aligned_cols=28 Identities=11% Similarity=0.261 Sum_probs=24.1
Q ss_pred CCCCCChhHHHHHHHhhhhhhccccCCC
Q 004648 704 HSFKPEIKAIKSRIDDLINREFIERDSK 731 (740)
Q Consensus 704 ~~F~~~~~~ik~~Ie~LIereyi~r~~~ 731 (740)
..|..+...+.+.+..|.++|||.+.++
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 3567789999999999999999998763
No 169
>PRK06474 hypothetical protein; Provisional
Probab=22.89 E-value=1.8e+02 Score=28.11 Aligned_cols=51 Identities=16% Similarity=0.230 Sum_probs=39.4
Q ss_pred EecHHHHHHHHhhcCCC-CccHHHHHHHh-CCCHHHHHHHHHHhhcccccccccC
Q 004648 573 IVSTYQAACLMLFNDAD-RLSFSEILTQL-NLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 573 ~~s~~Q~~iLllFn~~~-~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
-.++.-..||-.+-..+ .+|..+|++.+ +++...+-++|..|. +.+++...
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~ 60 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVV 60 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34566677776555544 49999999999 799999999999997 46787754
No 170
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=22.74 E-value=1.2e+02 Score=33.89 Aligned_cols=38 Identities=18% Similarity=0.324 Sum_probs=30.3
Q ss_pred HHHHHHHh-hcCCCCccHHHHHHHhCCCHHHHHHHHHHh
Q 004648 577 YQAACLML-FNDADRLSFSEILTQLNLNKGDLIRVLHSL 614 (740)
Q Consensus 577 ~Q~~iLll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 614 (740)
+-..|+-. .+....+|+++|++.|||..+++..+|++|
T Consensus 360 W~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 360 WTRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 44455533 344468999999999999999999999988
No 171
>PHA02591 hypothetical protein; Provisional
Probab=22.72 E-value=1e+02 Score=25.30 Aligned_cols=25 Identities=20% Similarity=0.291 Sum_probs=21.9
Q ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Q 004648 589 DRLSFSEILTQLNLNKGDLIRVLHS 613 (740)
Q Consensus 589 ~~~t~~ei~~~t~i~~~~l~~~L~~ 613 (740)
.++|.++|++.+|++.+.+.+-|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3789999999999999999887764
No 172
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=22.51 E-value=57 Score=30.10 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=22.2
Q ss_pred CCCCChhHHHHHHHhhhhhhccccCC
Q 004648 705 SFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 705 ~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 45567788999999999999999964
No 173
>PHA02943 hypothetical protein; Provisional
Probab=22.20 E-value=1.4e+02 Score=28.03 Aligned_cols=42 Identities=21% Similarity=0.191 Sum_probs=31.5
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 581 CLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 581 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
||-.+ ..+..|..||++.+|++-..+.-+|.-|- |-+.+.+.
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV 57 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKV 57 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEE
Confidence 44444 56678899999999999999999888775 44455443
No 174
>PF05261 Tra_M: TraM protein, DNA-binding; InterPro: IPR007925 The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus [].; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3ON0_A 3OMY_B 1DP3_A 2G9E_A 3D8A_B 2G7O_A.
Probab=22.19 E-value=2.9e+02 Score=24.92 Aligned_cols=58 Identities=10% Similarity=0.405 Sum_probs=33.6
Q ss_pred hHHHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHHHHhCCc---------chhchHHHHHHHHHHHHH
Q 004648 150 LKRDVRDTVIALIDEEREGEKID-RALVKKAVDIFVGIGIL---------DMDFYRQDFEEQMIDDAG 207 (740)
Q Consensus 150 ~~~~l~~~ll~~I~~~R~g~~id-~~~lk~vi~~l~~l~~~---------~~~~Y~~~FE~~~l~~t~ 207 (740)
+++.+.+.|-++++..|..+.-+ ---..++..||.+||+. ...+=...|-+.+|+.+.
T Consensus 8 ~s~~v~~~I~~iVe~r~qeGA~~~dvs~SSv~smLlELGLrVY~~Q~E~k~s~Fnq~eFnk~lLe~v~ 75 (127)
T PF05261_consen 8 VSNKVLEEINDIVEERRQEGATEKDVSFSSVSSMLLELGLRVYEAQMERKESGFNQEEFNKVLLENVS 75 (127)
T ss_dssp --HCHHHHHHHHHHHHHCCT-TTTT--HHHHHHHHHHCCCCHHHHCCHHCSSS--HHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHhHHHHHHHHhhccCCCCHHHHHHHHHHHHH
Confidence 34566677777888888765433 23467889999999961 112334456666666553
No 175
>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=22.13 E-value=1.5e+02 Score=25.14 Aligned_cols=40 Identities=23% Similarity=0.229 Sum_probs=31.8
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
...++.-++....++++++|++.++++.+++...+..+..
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 3444555556788999999999999999999999888874
No 176
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=22.08 E-value=66 Score=29.76 Aligned_cols=38 Identities=16% Similarity=0.289 Sum_probs=29.3
Q ss_pred CCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCC
Q 004648 685 SRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 685 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
....++..+|-. .+..+.+.+-+.|+.|.++|||+|.+
T Consensus 51 ~~~~~t~~eLa~--------~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 51 CAACITPVELKK--------VLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HcCCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 345566666655 35567888999999999999999964
No 177
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=21.64 E-value=3.1e+02 Score=22.70 Aligned_cols=48 Identities=10% Similarity=0.226 Sum_probs=37.0
Q ss_pred HHHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 577 YQAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 577 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
+++.|=+.-..+..+.-.+|++.++.+...++..+..|- ..++|.+.|
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~p 57 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQP 57 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCCC
Confidence 444444445566789999999999999999999999996 467886544
No 178
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.62 E-value=1.4e+02 Score=27.63 Aligned_cols=38 Identities=18% Similarity=0.288 Sum_probs=29.0
Q ss_pred ecHHHHHHHHh-hcCCCCccHHHHHHHhCCCHHHHHHHHHH
Q 004648 574 VSTYQAACLML-FNDADRLSFSEILTQLNLNKGDLIRVLHS 613 (740)
Q Consensus 574 ~s~~Q~~iLll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 613 (740)
+|+.|..|+.+ +- .++|++||++.+|+|...+...+.-
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 56666666665 43 4689999999999999988876653
No 179
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=21.55 E-value=59 Score=30.27 Aligned_cols=50 Identities=16% Similarity=0.257 Sum_probs=42.6
Q ss_pred hchhhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCC
Q 004648 673 HNIDAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 673 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
..+|..|.+++....+++..+|-..+- .+++.+.++|+.|.++|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeEE
Confidence 456788999999999999998887653 67889999999999999999854
No 180
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=21.35 E-value=60 Score=26.55 Aligned_cols=26 Identities=23% Similarity=0.249 Sum_probs=20.6
Q ss_pred chhhheeecccCCC--CCChhHHHHHHH
Q 004648 674 NIDAALVRIMKSRK--VLGYQQLISECV 699 (740)
Q Consensus 674 ~i~A~IVRimK~~k--~l~~~~L~~~v~ 699 (740)
..=|.||..||++. .++.+|+..++.
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls 36 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLS 36 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHh
Confidence 34578999999987 688888888765
No 181
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=21.30 E-value=1.3e+02 Score=30.79 Aligned_cols=39 Identities=28% Similarity=0.332 Sum_probs=34.8
Q ss_pred HHHHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhc
Q 004648 578 QAACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSC 616 (740)
Q Consensus 578 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 616 (740)
|..|+..+++++.++.+||++.+|+++..++|-|.-|..
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 556788888888999999999999999999999998864
No 182
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=21.27 E-value=63 Score=24.28 Aligned_cols=22 Identities=23% Similarity=0.507 Sum_probs=19.2
Q ss_pred CccHHHHHHHhCCCHHHHHHHH
Q 004648 590 RLSFSEILTQLNLNKGDLIRVL 611 (740)
Q Consensus 590 ~~t~~ei~~~t~i~~~~l~~~L 611 (740)
.+++.||++.+|++..++.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999998888
No 183
>PRK11050 manganese transport regulator MntR; Provisional
Probab=21.20 E-value=1.7e+02 Score=27.50 Aligned_cols=43 Identities=12% Similarity=0.212 Sum_probs=34.7
Q ss_pred HHHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhccccccccc
Q 004648 580 ACLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNK 624 (740)
Q Consensus 580 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~ 624 (740)
.|+.++...+.++..+|++.++++...+.+.|..|.. .+++.+
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~--~GlI~r 83 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLAR--DGLVEM 83 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 4455666777899999999999999999999999974 356654
No 184
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=21.05 E-value=82 Score=26.42 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=35.1
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCC
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDS 730 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~ 730 (740)
+..|...+...+.++..+|... +.++...+.+.|..|.++|+|++..
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 4556666666667777777653 3456778999999999999998764
No 185
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=21.00 E-value=52 Score=33.19 Aligned_cols=46 Identities=11% Similarity=0.229 Sum_probs=34.2
Q ss_pred cccCCCCC-ChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcc
Q 004648 682 IMKSRKVL-GYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMF 736 (740)
Q Consensus 682 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y 736 (740)
.++....| +-.+|.+ .|..+...++++|+.|.+.|+|.|..+ +.+|
T Consensus 18 ~~~~g~~LPsE~eLa~--------~~~VSR~TVR~Al~~L~~eGli~r~~G-~Gtf 64 (230)
T TIGR02018 18 EWPPGHRIPSEHELVA--------QYGCSRMTVNRALRELTDAGLLERRQG-VGTF 64 (230)
T ss_pred CCCCCCcCcCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEecC-CEEE
Confidence 34444455 4444443 699999999999999999999999876 4444
No 186
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=20.89 E-value=56 Score=33.21 Aligned_cols=46 Identities=13% Similarity=0.251 Sum_probs=34.4
Q ss_pred cccCCCCC-ChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccCCCCCCcc
Q 004648 682 IMKSRKVL-GYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERDSKDPTMF 736 (740)
Q Consensus 682 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~~~d~~~y 736 (740)
.++....| +-.+|.+ .|..+...++++|+.|...|+|.|..+ +.+|
T Consensus 22 ~~~~G~~LPsE~eL~~--------~~~VSR~TvR~Al~~L~~eGli~r~~G-~Gtf 68 (240)
T PRK09764 22 ELKPGDALPTESALQT--------EFGVSRVTVRQALRQLVEQQILESIQG-SGTY 68 (240)
T ss_pred CCCCCCcCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEecC-ceeE
Confidence 44555555 3344444 689999999999999999999999876 3454
No 187
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=20.31 E-value=2e+02 Score=27.98 Aligned_cols=43 Identities=16% Similarity=0.195 Sum_probs=34.3
Q ss_pred HHHhhcCCCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccC
Q 004648 581 CLMLFNDADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKE 625 (740)
Q Consensus 581 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~ 625 (740)
++.-.+.++..|..+|+..+|++..++.++|-.|.. .+.+...
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~--~~~v~~~ 60 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQR--EGMVYMS 60 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHh--cCceecC
Confidence 455566778899999999999999999999999973 3445443
No 188
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.26 E-value=51 Score=33.93 Aligned_cols=46 Identities=20% Similarity=0.415 Sum_probs=40.6
Q ss_pred hhheeecccCCCCCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhccccC
Q 004648 676 DAALVRIMKSRKVLGYQQLISECVEMLSHSFKPEIKAIKSRIDDLINREFIERD 729 (740)
Q Consensus 676 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~r~ 729 (740)
...|..++++++.++..+|.+ +|..+...|.+-+..|-++|.|.|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 456778889999999999887 5789999999999999999999985
No 189
>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=20.10 E-value=1.4e+02 Score=24.30 Aligned_cols=49 Identities=14% Similarity=0.182 Sum_probs=38.9
Q ss_pred HHHHHHHHhhcC--CCCccHHHHHHHhCCCHHHHHHHHHHhhcccccccccCC
Q 004648 576 TYQAACLMLFND--ADRLSFSEILTQLNLNKGDLIRVLHSLSCSKHKILNKEP 626 (740)
Q Consensus 576 ~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~~iL~~~~ 626 (740)
..|.++|...-. ..+++-.+|+..+|++...+-..+..|.. .+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~--~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEK--KGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHH--CCCEEEEE
Confidence 467778877664 45889999999999999999999999973 56776643
Done!