Query 004841
Match_columns 728
No_of_seqs 233 out of 1080
Neff 8.5
Searched_HMMs 46136
Date Thu Mar 28 13:49:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166 Cullins [Cell cycle co 100.0 4E-121 8E-126 1031.9 63.9 703 5-726 4-725 (725)
2 COG5647 Cullin, a subunit of E 100.0 3E-115 6E-120 938.5 60.2 709 7-728 16-773 (773)
3 KOG2167 Cullins [Cell cycle co 100.0 8E-111 2E-115 883.7 46.8 642 54-728 2-661 (661)
4 KOG2284 E3 ubiquitin ligase, C 100.0 1E-109 3E-114 835.7 46.1 670 1-728 1-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 9.6E-93 2.1E-97 720.4 56.5 701 6-728 8-777 (777)
6 PF00888 Cullin: Cullin family 100.0 3.1E-90 6.6E-95 801.5 59.7 575 15-632 1-588 (588)
7 smart00182 CULLIN Cullin. 100.0 4.3E-33 9.3E-38 260.8 17.8 141 412-553 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 6.3E-26 1.4E-30 245.1 41.3 303 405-717 441-757 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 2.7E-20 5.9E-25 149.6 2.0 68 655-722 1-68 (68)
10 PF08539 HbrB: HbrB-like; Int 95.5 0.34 7.5E-06 45.7 13.2 121 9-136 3-156 (158)
11 TIGR01610 phage_O_Nterm phage 92.8 0.31 6.7E-06 42.0 6.2 65 560-632 21-93 (95)
12 PF09339 HTH_IclR: IclR helix- 92.2 0.23 5E-06 37.4 4.1 45 567-613 6-51 (52)
13 PF13412 HTH_24: Winged helix- 90.6 0.49 1.1E-05 34.8 4.4 42 563-604 2-43 (48)
14 PF02082 Rrf2: Transcriptional 90.4 0.76 1.6E-05 38.4 5.9 59 565-630 11-70 (83)
15 PF12802 MarR_2: MarR family; 90.0 0.38 8.2E-06 37.4 3.6 51 562-614 3-55 (62)
16 PF08220 HTH_DeoR: DeoR-like h 88.0 0.76 1.6E-05 35.4 3.9 46 566-613 2-47 (57)
17 PF01047 MarR: MarR family; I 86.8 0.47 1E-05 36.6 2.1 51 562-614 1-51 (59)
18 KOG2167 Cullins [Cell cycle co 86.7 23 0.00049 40.1 15.5 36 181-218 289-324 (661)
19 PF13463 HTH_27: Winged helix 86.6 1.1 2.3E-05 35.6 4.2 50 562-613 1-51 (68)
20 TIGR02337 HpaR homoprotocatech 85.2 1.6 3.4E-05 39.1 5.0 52 561-614 25-76 (118)
21 PF01022 HTH_5: Bacterial regu 84.6 2.2 4.8E-05 31.2 4.7 43 565-610 3-45 (47)
22 PF12840 HTH_20: Helix-turn-he 84.3 1.3 2.8E-05 34.5 3.6 49 563-613 9-57 (61)
23 PRK11512 DNA-binding transcrip 83.1 2.3 4.9E-05 39.6 5.3 53 560-614 36-88 (144)
24 PF09012 FeoC: FeoC like trans 82.7 0.48 1E-05 38.1 0.5 44 668-719 6-49 (69)
25 smart00550 Zalpha Z-DNA-bindin 82.1 2.5 5.5E-05 33.8 4.5 47 565-613 7-55 (68)
26 TIGR02698 CopY_TcrY copper tra 81.6 1.3 2.9E-05 40.5 3.1 60 664-728 6-65 (130)
27 COG3682 Predicted transcriptio 80.8 1.4 3.1E-05 39.4 2.8 62 662-728 6-67 (123)
28 PF08279 HTH_11: HTH domain; 79.3 3.8 8.2E-05 30.9 4.5 37 568-604 4-41 (55)
29 TIGR01889 Staph_reg_Sar staphy 78.8 4.8 0.0001 35.5 5.6 52 561-614 22-77 (109)
30 smart00346 HTH_ICLR helix_turn 77.7 4.9 0.00011 33.8 5.2 45 567-613 8-53 (91)
31 smart00347 HTH_MARR helix_turn 77.0 4.3 9.3E-05 34.6 4.8 53 559-613 5-57 (101)
32 PF03965 Penicillinase_R: Peni 76.7 2.3 5E-05 37.9 3.0 60 664-728 5-64 (115)
33 PRK10857 DNA-binding transcrip 74.7 8.7 0.00019 36.7 6.5 45 566-612 12-57 (164)
34 PRK15090 DNA-binding transcrip 74.4 6.3 0.00014 40.6 6.0 47 566-614 16-62 (257)
35 PRK11920 rirA iron-responsive 74.4 8.9 0.00019 36.2 6.4 56 567-629 13-68 (153)
36 smart00420 HTH_DEOR helix_turn 73.9 6 0.00013 29.1 4.3 43 568-612 4-46 (53)
37 PF01978 TrmB: Sugar-specific 72.8 3.4 7.3E-05 32.9 2.8 49 563-613 7-55 (68)
38 PF04703 FaeA: FaeA-like prote 72.6 7 0.00015 30.6 4.3 56 569-628 5-61 (62)
39 PRK13777 transcriptional regul 70.9 8.1 0.00018 37.7 5.4 53 560-614 41-93 (185)
40 TIGR02010 IscR iron-sulfur clu 70.3 11 0.00025 34.5 6.0 44 567-612 13-57 (135)
41 PF04492 Phage_rep_O: Bacterio 69.7 15 0.00031 32.0 6.1 62 561-632 29-98 (100)
42 PRK03573 transcriptional regul 69.6 8.4 0.00018 35.7 5.1 53 560-614 27-80 (144)
43 COG3355 Predicted transcriptio 68.8 11 0.00024 34.0 5.4 38 574-613 38-75 (126)
44 PHA00738 putative HTH transcri 67.1 11 0.00025 32.8 4.8 67 559-631 7-73 (108)
45 PF13404 HTH_AsnC-type: AsnC-t 66.0 8.8 0.00019 27.5 3.4 36 567-602 6-41 (42)
46 PF05732 RepL: Firmicute plasm 65.9 7.5 0.00016 37.1 3.9 51 578-637 75-125 (165)
47 PRK10870 transcriptional repre 65.3 14 0.0003 35.7 5.8 52 561-614 52-105 (176)
48 smart00345 HTH_GNTR helix_turn 65.1 13 0.00028 28.1 4.5 40 573-614 14-54 (60)
49 COG1959 Predicted transcriptio 64.6 16 0.00034 34.3 5.8 58 565-629 11-69 (150)
50 PF13463 HTH_27: Winged helix 64.4 5.4 0.00012 31.4 2.3 53 665-725 6-61 (68)
51 PF05584 Sulfolobus_pRN: Sulfo 63.7 16 0.00036 29.4 4.8 45 564-612 6-50 (72)
52 PF08784 RPA_C: Replication pr 63.3 12 0.00025 32.5 4.4 44 561-604 44-91 (102)
53 smart00419 HTH_CRP helix_turn_ 62.2 17 0.00036 26.1 4.5 34 578-613 8-41 (48)
54 COG1414 IclR Transcriptional r 62.1 16 0.00034 37.5 5.8 46 567-614 7-53 (246)
55 PF08280 HTH_Mga: M protein tr 62.0 10 0.00022 29.3 3.3 38 566-603 7-44 (59)
56 PRK11569 transcriptional repre 62.0 15 0.00032 38.3 5.7 47 566-614 30-77 (274)
57 TIGR00738 rrf2_super rrf2 fami 61.8 19 0.00041 32.7 5.8 45 566-612 12-57 (132)
58 TIGR01884 cas_HTH CRISPR locus 61.2 12 0.00027 37.0 4.7 52 561-614 140-191 (203)
59 TIGR03879 near_KaiC_dom probab 61.2 10 0.00023 30.7 3.3 36 574-611 28-63 (73)
60 PF13601 HTH_34: Winged helix 61.2 6.7 0.00014 32.5 2.3 43 567-611 3-45 (80)
61 PRK10163 DNA-binding transcrip 60.7 17 0.00037 37.8 5.9 47 566-614 27-74 (271)
62 cd00090 HTH_ARSR Arsenical Res 60.6 17 0.00037 28.6 4.7 48 563-613 6-53 (78)
63 PF08220 HTH_DeoR: DeoR-like h 59.3 4.1 8.8E-05 31.3 0.7 45 666-718 4-48 (57)
64 PRK09834 DNA-binding transcrip 58.8 17 0.00037 37.6 5.5 46 567-614 14-60 (263)
65 PF01978 TrmB: Sugar-specific 57.4 4 8.6E-05 32.5 0.3 51 669-727 15-65 (68)
66 TIGR02431 pcaR_pcaU beta-ketoa 56.3 23 0.0005 36.2 5.9 44 567-612 12-56 (248)
67 TIGR02944 suf_reg_Xantho FeS a 55.6 26 0.00057 31.8 5.5 44 567-612 12-57 (130)
68 smart00550 Zalpha Z-DNA-bindin 55.3 10 0.00022 30.3 2.4 53 664-724 8-62 (68)
69 PRK10141 DNA-binding transcrip 55.2 22 0.00049 31.8 4.8 59 565-629 17-75 (117)
70 PF10771 DUF2582: Protein of u 54.9 16 0.00036 28.9 3.4 38 567-604 11-48 (65)
71 smart00344 HTH_ASNC helix_turn 54.7 20 0.00044 31.2 4.5 45 565-611 4-48 (108)
72 COG1846 MarR Transcriptional r 54.3 23 0.0005 31.1 5.0 51 562-614 20-70 (126)
73 COG2345 Predicted transcriptio 54.1 17 0.00037 36.2 4.2 42 568-611 15-56 (218)
74 smart00418 HTH_ARSR helix_turn 53.5 24 0.00053 26.7 4.4 36 576-613 8-43 (66)
75 PF13730 HTH_36: Helix-turn-he 50.8 37 0.00081 25.4 4.8 24 580-603 27-50 (55)
76 PF01325 Fe_dep_repress: Iron 50.7 30 0.00066 26.8 4.3 44 569-614 13-56 (60)
77 PRK11014 transcriptional repre 49.7 44 0.00096 30.8 6.1 40 573-614 20-59 (141)
78 smart00418 HTH_ARSR helix_turn 49.2 15 0.00032 28.0 2.5 44 669-721 4-47 (66)
79 PF09756 DDRGK: DDRGK domain; 46.9 7.5 0.00016 37.8 0.5 57 664-728 101-157 (188)
80 PF04545 Sigma70_r4: Sigma-70, 46.7 46 0.00099 24.4 4.6 33 567-601 11-43 (50)
81 PF08221 HTH_9: RNA polymerase 46.6 25 0.00054 27.5 3.3 34 575-610 24-57 (62)
82 PF02002 TFIIE_alpha: TFIIE al 46.2 16 0.00035 31.8 2.5 44 566-611 15-58 (105)
83 PF14394 DUF4423: Domain of un 45.2 49 0.0011 31.8 5.8 52 561-614 21-75 (171)
84 PF01726 LexA_DNA_bind: LexA D 44.1 37 0.0008 26.9 3.9 24 697-720 39-62 (65)
85 cd00092 HTH_CRP helix_turn_hel 43.0 38 0.00082 26.3 4.0 35 577-613 24-58 (67)
86 COG1349 GlpR Transcriptional r 42.1 31 0.00067 35.5 4.2 47 565-613 6-52 (253)
87 PRK10434 srlR DNA-bindng trans 42.1 30 0.00065 35.6 4.1 47 565-613 6-52 (256)
88 PF01853 MOZ_SAS: MOZ/SAS fami 41.8 26 0.00056 34.0 3.2 27 577-603 149-175 (188)
89 PF08281 Sigma70_r4_2: Sigma-7 41.5 45 0.00097 24.8 4.0 37 563-600 12-48 (54)
90 PF02796 HTH_7: Helix-turn-hel 40.9 43 0.00092 24.2 3.6 31 568-600 13-43 (45)
91 smart00421 HTH_LUXR helix_turn 40.7 55 0.0012 24.0 4.5 39 563-603 5-43 (58)
92 cd07153 Fur_like Ferric uptake 40.7 29 0.00063 30.6 3.3 57 667-726 6-63 (116)
93 PRK06266 transcription initiat 40.3 40 0.00086 32.7 4.3 44 566-611 24-67 (178)
94 TIGR00373 conserved hypothetic 40.3 48 0.0011 31.4 4.8 43 567-611 17-59 (158)
95 TIGR02702 SufR_cyano iron-sulf 39.8 60 0.0013 32.1 5.7 44 568-613 5-48 (203)
96 PF12324 HTH_15: Helix-turn-he 39.4 72 0.0016 26.2 4.9 38 566-603 26-63 (77)
97 cd06170 LuxR_C_like C-terminal 39.1 61 0.0013 23.9 4.5 39 563-603 2-40 (57)
98 PF11994 DUF3489: Protein of u 39.1 67 0.0015 26.0 4.6 47 563-609 9-55 (72)
99 cd07377 WHTH_GntR Winged helix 39.0 65 0.0014 24.6 4.7 38 574-613 20-58 (66)
100 PF09012 FeoC: FeoC like trans 39.0 32 0.0007 27.4 2.9 33 572-604 8-40 (69)
101 PF13412 HTH_24: Winged helix- 38.4 13 0.00029 27.0 0.6 44 664-715 5-48 (48)
102 PF05158 RNA_pol_Rpc34: RNA po 36.9 29 0.00062 37.2 3.0 143 561-720 81-260 (327)
103 PF08318 COG4: COG4 transport 36.9 5.5E+02 0.012 27.4 16.5 163 257-436 15-214 (331)
104 TIGR02844 spore_III_D sporulat 36.7 54 0.0012 27.2 3.9 35 565-600 7-41 (80)
105 PRK13509 transcriptional repre 36.6 50 0.0011 33.9 4.7 48 565-614 6-53 (251)
106 PRK00215 LexA repressor; Valid 36.4 68 0.0015 31.6 5.5 52 562-615 2-59 (205)
107 PF12802 MarR_2: MarR family; 36.0 15 0.00033 28.2 0.6 26 694-719 31-56 (62)
108 smart00344 HTH_ASNC helix_turn 35.6 19 0.00041 31.4 1.2 47 663-717 4-50 (108)
109 COG4190 Predicted transcriptio 34.5 1.1E+02 0.0024 27.8 5.7 67 564-632 64-133 (144)
110 PF00325 Crp: Bacterial regula 33.7 57 0.0012 21.9 2.9 26 578-603 2-27 (32)
111 PRK11169 leucine-responsive tr 33.6 60 0.0013 30.8 4.4 48 562-611 12-59 (164)
112 PF00196 GerE: Bacterial regul 33.3 63 0.0014 24.5 3.7 40 562-603 4-43 (58)
113 PF01726 LexA_DNA_bind: LexA D 33.0 56 0.0012 25.8 3.4 51 562-614 4-60 (65)
114 smart00420 HTH_DEOR helix_turn 32.8 22 0.00047 26.0 1.0 43 668-718 6-48 (53)
115 PRK04424 fatty acid biosynthes 32.8 48 0.001 32.3 3.6 46 565-612 8-53 (185)
116 COG1654 BirA Biotin operon rep 32.7 1.1E+02 0.0025 25.2 5.2 41 571-611 12-52 (79)
117 PF01047 MarR: MarR family; I 32.4 14 0.0003 28.2 -0.2 43 668-718 9-51 (59)
118 smart00345 HTH_GNTR helix_turn 31.7 30 0.00064 26.0 1.6 28 692-719 28-55 (60)
119 PF06784 UPF0240: Uncharacteri 31.7 75 0.0016 30.8 4.7 63 536-603 97-161 (179)
120 PF04967 HTH_10: HTH DNA bindi 30.6 80 0.0017 23.9 3.7 30 573-602 18-47 (53)
121 PRK11179 DNA-binding transcrip 30.5 75 0.0016 29.8 4.4 48 562-611 7-54 (153)
122 COG4189 Predicted transcriptio 30.4 72 0.0016 31.9 4.2 49 563-613 22-70 (308)
123 PRK09802 DNA-binding transcrip 30.2 62 0.0014 33.6 4.2 48 564-613 17-64 (269)
124 PRK10681 DNA-binding transcrip 30.2 68 0.0015 32.9 4.5 39 565-603 8-46 (252)
125 COG1318 Predicted transcriptio 30.1 74 0.0016 30.3 4.1 50 532-602 36-85 (182)
126 TIGR02404 trehalos_R_Bsub treh 30.1 30 0.00065 34.9 1.8 33 692-725 32-64 (233)
127 KOG2747 Histone acetyltransfer 29.9 64 0.0014 35.1 4.2 65 537-603 281-354 (396)
128 PRK10906 DNA-binding transcrip 29.8 67 0.0015 33.0 4.3 47 565-613 6-52 (252)
129 PF02186 TFIIE_beta: TFIIE bet 29.6 28 0.00061 27.6 1.1 54 664-728 7-61 (65)
130 PF07106 TBPIP: Tat binding pr 29.1 3.2E+02 0.0069 26.0 8.6 59 566-630 3-64 (169)
131 cd06171 Sigma70_r4 Sigma70, re 28.3 1.2E+02 0.0025 21.6 4.4 40 562-602 11-50 (55)
132 COG1522 Lrp Transcriptional re 27.8 96 0.0021 28.7 4.7 49 562-612 6-54 (154)
133 PRK11402 DNA-binding transcrip 27.6 35 0.00076 34.6 1.8 33 692-725 41-73 (241)
134 TIGR00498 lexA SOS regulatory 27.5 64 0.0014 31.6 3.6 51 562-614 4-60 (199)
135 PF09763 Sec3_C: Exocyst compl 27.4 1.1E+03 0.024 28.1 16.6 122 202-349 570-701 (701)
136 smart00531 TFIIE Transcription 27.3 71 0.0015 29.8 3.6 31 575-605 12-42 (147)
137 PF00392 GntR: Bacterial regul 27.2 31 0.00066 26.9 1.0 28 692-719 32-59 (64)
138 PF09681 Phage_rep_org_N: N-te 27.1 73 0.0016 28.7 3.5 38 574-613 49-86 (121)
139 TIGR01889 Staph_reg_Sar staphy 27.0 44 0.00095 29.3 2.0 41 673-721 40-82 (109)
140 PLN03238 probable histone acet 26.8 97 0.0021 32.2 4.7 38 565-602 209-247 (290)
141 PRK04172 pheS phenylalanyl-tRN 26.7 88 0.0019 35.6 4.9 50 561-612 3-52 (489)
142 TIGR01714 phage_rep_org_N phag 26.6 92 0.002 28.0 4.0 48 564-613 29-84 (119)
143 PRK10411 DNA-binding transcrip 26.3 92 0.002 31.7 4.5 46 565-612 5-50 (240)
144 PRK09334 30S ribosomal protein 26.2 47 0.001 27.9 1.9 37 692-728 49-85 (86)
145 PHA03103 double-strand RNA-bin 26.1 1.3E+02 0.0029 29.1 5.2 44 569-614 18-61 (183)
146 PF00165 HTH_AraC: Bacterial r 25.9 94 0.002 21.8 3.3 28 576-603 6-33 (42)
147 PRK13239 alkylmercury lyase; P 25.9 1.2E+02 0.0025 30.2 4.9 40 564-603 22-61 (206)
148 PRK10079 phosphonate metabolis 25.8 40 0.00087 34.2 1.8 48 670-725 28-75 (241)
149 PHA02591 hypothetical protein; 25.8 83 0.0018 25.7 3.1 25 577-601 58-82 (83)
150 PF13384 HTH_23: Homeodomain-l 25.6 72 0.0016 23.2 2.7 32 569-602 10-41 (50)
151 PRK13713 conjugal transfer pro 25.6 4.9E+02 0.011 23.2 10.3 59 132-190 2-70 (118)
152 KOG3054 Uncharacterized conser 25.2 54 0.0012 32.8 2.4 54 667-728 205-258 (299)
153 TIGR02325 C_P_lyase_phnF phosp 25.0 41 0.0009 33.9 1.7 32 693-725 41-72 (238)
154 PF13730 HTH_36: Helix-turn-he 24.7 42 0.00092 25.1 1.3 21 694-714 35-55 (55)
155 PRK03573 transcriptional regul 24.4 48 0.001 30.5 1.9 30 693-722 55-86 (144)
156 cd07377 WHTH_GntR Winged helix 23.6 52 0.0011 25.2 1.7 27 692-718 33-59 (66)
157 PF13542 HTH_Tnp_ISL3: Helix-t 23.3 1.8E+02 0.0039 21.2 4.6 34 566-601 17-50 (52)
158 PF00392 GntR: Bacterial regul 23.1 94 0.002 24.1 3.1 39 574-614 19-58 (64)
159 PRK11050 manganese transport r 22.8 1.6E+02 0.0035 27.5 5.2 43 568-612 41-83 (152)
160 PF10007 DUF2250: Uncharacteri 22.8 1.4E+02 0.0031 25.4 4.2 53 560-614 3-55 (92)
161 PF03444 HrcA_DNA-bdg: Winged 22.8 2.9E+02 0.0062 22.8 5.8 48 565-614 10-57 (78)
162 PRK06474 hypothetical protein; 22.7 2E+02 0.0043 27.8 5.9 52 561-614 8-61 (178)
163 PRK14999 histidine utilization 22.7 47 0.001 33.7 1.6 47 670-725 29-76 (241)
164 TIGR03433 padR_acidobact trans 22.5 1.2E+02 0.0026 26.1 3.9 53 663-716 5-57 (100)
165 PLN03239 histone acetyltransfe 22.3 1.2E+02 0.0026 32.5 4.4 38 565-602 267-308 (351)
166 PF05261 Tra_M: TraM protein, 21.6 6.1E+02 0.013 22.9 10.5 59 131-189 8-76 (127)
167 PF04760 IF2_N: Translation in 21.6 61 0.0013 24.3 1.7 22 578-599 3-24 (54)
168 PF01638 HxlR: HxlR-like helix 21.5 1.4E+02 0.0031 25.0 4.1 45 566-613 7-52 (90)
169 PF09860 DUF2087: Uncharacteri 21.3 1.1E+02 0.0024 24.7 3.1 44 672-724 25-68 (71)
170 COG2188 PhnF Transcriptional r 21.2 53 0.0011 33.3 1.6 35 690-725 37-71 (236)
171 PRK03902 manganese transport t 21.1 1.6E+02 0.0034 27.1 4.6 42 569-612 13-54 (142)
172 PF08073 CHDNT: CHDNT (NUC034) 21.1 1.8E+02 0.004 22.2 4.0 30 61-90 19-52 (55)
173 TIGR02989 Sig-70_gvs1 RNA poly 20.9 1.5E+02 0.0032 27.4 4.6 39 561-601 111-150 (159)
174 PF04182 B-block_TFIIIC: B-blo 20.9 1.3E+02 0.0028 24.4 3.6 49 564-614 2-52 (75)
175 smart00347 HTH_MARR helix_turn 20.8 76 0.0016 26.6 2.3 47 664-718 12-58 (101)
176 KOG2905 Transcription initiati 20.8 1.3E+02 0.0027 30.4 4.0 58 565-632 187-244 (254)
177 PF12395 DUF3658: Protein of u 20.6 1.2E+02 0.0027 26.7 3.6 48 677-726 62-109 (111)
178 PF02270 TFIIF_beta: Transcrip 20.5 1.2E+02 0.0026 31.6 4.1 57 565-631 217-273 (275)
179 TIGR00721 tfx DNA-binding prot 20.5 1.7E+02 0.0037 27.0 4.6 40 561-602 6-45 (137)
180 COG1321 TroR Mn-dependent tran 20.2 1.7E+02 0.0036 27.6 4.6 45 568-614 14-58 (154)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.7e-121 Score=1031.93 Aligned_cols=703 Identities=63% Similarity=1.052 Sum_probs=651.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhcC-----------CchhhHHH-HHHHHHH----H
Q 004841 5 ERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQP-----------HLVSAFVN-ILLLVLP----S 68 (728)
Q Consensus 5 ~~~~~~fe~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~~-----------~~y~~l~~-l~~~v~~----~ 68 (728)
.+.+.+|+.+|..++++++++.+..++-+...++.-+|+.+|+++|+. .+|.++++ +.+++.. .
T Consensus 4 ~~~~~~~~~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~ 83 (725)
T KOG2166|consen 4 APKEIDLEVGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPA 83 (725)
T ss_pred cccccchhccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999988763333346677899999999991 25677887 7777643 3
Q ss_pred HhhhchhhHHHHHHHHHHHHHHHHHHHHHhhchhhhhhhhcC-CCCcHHHHH-HHHHHHHHhh-hhhHHHHHHHHHHHHH
Q 004841 69 IREKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARR-SLPPLNEVG-LTCFRDLVYT-ELNGKVRDAVITLIDQ 145 (728)
Q Consensus 69 l~~~~~~~~L~~~~~~W~~~~~~~~~i~~if~YLdr~yv~~~-~~~~i~~l~-l~~f~~~v~~-~~~~~l~~~ll~~I~~ 145 (728)
.....++.+|+.+.+.|.+|+.++.+++++|+||||+||+++ +..++++++ +.+|+..++. ++++.++++++.+|..
T Consensus 84 ~~~~~~~~~l~~~~~~W~~~~~~~~~~~~i~~YldR~~v~~~~~~~~v~~~~~l~l~r~~v~~~~~~~~~~~all~lI~~ 163 (725)
T KOG2166|consen 84 LREKHDEYMLRELAKRWNNHKVLVRWLSDFFMYLDRYYVAQSRRKLPTLNEVGLTCFRDLVYKFEMQSEAIDALLALIHK 163 (725)
T ss_pred HHhcCcHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcCCCCcccceeeEEeehHHHHHHHHHHHHHHHHHHHHh
Confidence 344567889999999999999999999999999999999976 666777666 8899888877 5999999999999999
Q ss_pred HhcCCcCCHHHHHHHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHchh
Q 004841 146 EREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHY 225 (728)
Q Consensus 146 ~R~g~~id~~~l~~~i~ml~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~~Yl~~v~~~l~eE~~r~~~y 225 (728)
+|.|+.||+..|+++++|+..+|.+..++|...||++|++.|+.||..++++|+...++.+|+.+|+.++.+|..|+..|
T Consensus 164 eR~ge~in~~~i~~~~~~~~~lg~~~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~y 243 (725)
T KOG2166|consen 164 EREGEQIDRELIRNVIDVYVELGMGELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHY 243 (725)
T ss_pred hcccccccHHHHhhHHHHHHhccccchhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999998899999999999999999999999
Q ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHHHHHHHHHHHHHHHHHHH
Q 004841 226 LHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKL 305 (728)
Q Consensus 226 L~~~t~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~ 305 (728)
++..+.+++.+.++..++..+++.+++..++|+..|+.+++.++|.+||+|++++++|++++++.++.|++.+|..++.+
T Consensus 244 l~~~~e~~~~~~le~~~~~~~~~~~~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r 323 (725)
T KOG2166|consen 244 LHSSTEPKLVEVVEDELIVVFADDLEEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVAR 323 (725)
T ss_pred hhhcccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999888876
Q ss_pred HHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHH
Q 004841 306 AEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNI 385 (728)
Q Consensus 306 ~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~ 385 (728)
..... ..+|..+|..+++++++|..++..||++|..|..+++.||..|+|.+.. ..+|+||+|||.+
T Consensus 324 ~~~~~-----------~~~~~~~v~~~l~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~--~~~E~la~y~D~~ 390 (725)
T KOG2166|consen 324 PAETA-----------ATNPVEYVQGLLELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVA--TSAELLATYCDDI 390 (725)
T ss_pred hhhhc-----------ccchHHHHhccHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCC--CcHHHHHHHhHHH
Confidence 55331 1578999999999999999999999999999999999999999999862 2369999999999
Q ss_pred hccCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHH
Q 004841 386 LKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMV 465 (728)
Q Consensus 386 lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~Ml 465 (728)
||++ ..+.++++++..+++++.+|+|+.+||+|+++|+++||||||+++|.|+++|++||++|+++||.+||++|++|+
T Consensus 391 lkk~-~k~~~e~~ie~~l~~v~~l~~yisdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf 469 (725)
T KOG2166|consen 391 LKKG-SKKLSDEAIEDTLEKVVKLLKYISDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMF 469 (725)
T ss_pred hccc-ccCCchhHHHhHhhcceeeeeeccHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhc
Confidence 9995 467889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHhHHHHHHHHHHHHHhcCCCceEEeccCCc
Q 004841 466 TDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLG 545 (728)
Q Consensus 466 ~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg 545 (728)
+|+..|++++..|+++ . +.....+++|.|.|||+|+||.+++.++.||++|..+++.|.+||..+|+||+|.|+|++|
T Consensus 470 ~D~~~s~~l~~~F~~~-~-~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~ 547 (725)
T KOG2166|consen 470 TDLTLSRELQTAFADY-A-NYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLG 547 (725)
T ss_pred ccHHHHHHHHHHHHhh-h-chhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccC
Confidence 9999999999999987 2 2222357999999999999999888889999999999999999999999999999999999
Q ss_pred eEEEEeEEcCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeE
Q 004841 546 TCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHF 625 (728)
Q Consensus 546 ~~~i~~~~~~~~~~l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~ 625 (728)
+|+|.++|.+++++++||++||+||++||+.+.+|+++|.+.|+++.+++.++|+||++.|.+++.+ |.++. ++++.|
T Consensus 548 ~~ei~~~~~~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~ 625 (725)
T KOG2166|consen 548 TGEINGKFDKKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEF 625 (725)
T ss_pred ceEEEEEecCceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEE
Confidence 9999999999999999999999999999999999999999999999999999999999888777766 77766 899999
Q ss_pred EEecCCCCCCcceeccCCChhhhhHHHHhHHHhhhhhhhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHH
Q 004841 626 EFNSKFTDKMRRIKIPLPPVDEKKKVIEDVDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRI 705 (728)
Q Consensus 626 ~~N~~F~~~~~~i~i~~~~~~e~~~~~~~v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~I 705 (728)
.+|.+|+++.+|+++|.++..|.+++.+.+++||+..|+||||||||+||.+.|++|+.||++|+++||.|++.+||+||
T Consensus 626 ~~N~~f~sk~~Rv~i~~~~~~e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~I 705 (725)
T KOG2166|consen 626 AFNSKFTSKMRRVKIPLPPMDERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRI 705 (725)
T ss_pred EeeccccCcceeeccCCCCchhHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence 99999999999999998888888889999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhhhhcccCCCCCCceee
Q 004841 706 EDLITRDYLERDKSNPNMFRY 726 (728)
Q Consensus 706 e~LIereyi~R~~~d~~~y~Y 726 (728)
|.|||||||+|| +|+++|+|
T Consensus 706 e~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 706 EDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred HHHHHHHHHhcc-CCCCcccC
Confidence 999999999999 89999998
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-115 Score=938.49 Aligned_cols=709 Identities=31% Similarity=0.526 Sum_probs=617.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhcC----------Cchh-------------hHHH-HH
Q 004841 7 KTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQP----------HLVS-------------AFVN-IL 62 (728)
Q Consensus 7 ~~~~fe~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~~----------~~y~-------------~l~~-l~ 62 (728)
...||+++|..++.||++|+..+.. .++...||++|+.+||- .++. .+.. ..
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 4579999999999999999865543 24455599999999991 1111 1111 12
Q ss_pred HHHHHHHh---hhchhhHHHHHHHHHHHHHHHHHHHHHhhchhhhhhhhc-----CCCCcHHHHHHHHHHHHHhhhhhHH
Q 004841 63 LLVLPSIR---EKHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR-----RSLPPLNEVGLTCFRDLVYTELNGK 134 (728)
Q Consensus 63 ~~v~~~l~---~~~~~~~L~~~~~~W~~~~~~~~~i~~if~YLdr~yv~~-----~~~~~i~~l~l~~f~~~v~~~~~~~ 134 (728)
+.+...-+ ....+.||..+++.|++|+.++.+++.+|.||||+|++. .....+.++++..|+..+|.++.+.
T Consensus 92 ~~i~~~~~~~s~~~~~~fl~~~v~~W~~~~~~~~~i~~~f~Ymdr~~~k~~~~~~~~~~E~~slcl~~~~~~~f~~i~~~ 171 (773)
T COG5647 92 NYIEEYNRGRSQENMEEFLDELVKFWNRFTKGATMINHLFLYMDRVYLKKARYDKTLVFEVYSLCLVKEKIESFRLIVDS 171 (773)
T ss_pred HHHHHhcccccchhHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHhhhhccCCCccceeeehhhhhHHHHHHHHhhhHH
Confidence 22211100 112368999999999999999999999999999999993 3455678999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhcc------CchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHH
Q 004841 135 VRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGM------GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYM 208 (728)
Q Consensus 135 l~~~ll~~I~~~R~g~~id~~~l~~~i~ml~~l~~------~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~~Yl 208 (728)
+++.+|..+.+.|.|+.+|+..+..++.|+..++. .++++|.+.|||.||+.|.+||..++++.+..+++.+||
T Consensus 172 lin~LL~~~~~~r~~~~id~~yi~~~~~~l~~l~~~s~~~k~~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL 251 (773)
T COG5647 172 LINPLLYYVERYRALQSIDRKYIEDAKDMLESLERPSDYKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYL 251 (773)
T ss_pred HHHHHHHHHHHHHhcCccCchHHHHHHHHHHhhcccchhccccchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHH
Confidence 99999999999999999999999999999999964 245899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHH
Q 004841 209 LKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVS 288 (728)
Q Consensus 209 ~~v~~~l~eE~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~ 288 (728)
.+|+.++++|..+++.|++.++..++..+++++||++|.+.|.+.. ||+..+++....+.|+.||+++++++.|+.+|.
T Consensus 252 ~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~ 330 (773)
T COG5647 252 EKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDLEEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQPLQ 330 (773)
T ss_pred HHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHHHhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHH
Confidence 9999999999999999999999999999999999999999987654 899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhh-hhhhhcc-ccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhc
Q 004841 289 NIFKQHVTAEGTALVKLAEDAASN-KKAEKRD-VVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCN 366 (728)
Q Consensus 289 ~~~~~~i~~~g~~~~~~~~~~~~~-~~~~~~~-~~~~~~~~~i~~ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~N 366 (728)
+.|..||.+.|.-+ +.....+.. +.....- .....+..|++.++.+++.+..++.++|.+|..+..++++||..|+|
T Consensus 331 ~~f~~yV~~~g~~~-~i~~~~~~~~~~~~~~~~~~e~~~~~~~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin 409 (773)
T COG5647 331 EVFERYVKDEGVLI-NIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFIN 409 (773)
T ss_pred HHHHHHHHhhchhh-hhHHhhhhccchhhcccchhhhcHHHHHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhc
Confidence 99999999999221 111111110 0000000 01356889999999999999999999999999999999999999999
Q ss_pred CCC-CCCCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHH
Q 004841 367 KGV-AGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSI 445 (728)
Q Consensus 367 ~~~-~~~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~ 445 (728)
.+. +...+||+||+|+|.+||+++ +.-....++..+.+++.||+|+.+||+|+++|+++||||||+++|+|.+.|.+|
T Consensus 410 ~~~sa~~~~~e~Laky~D~~lkk~~-k~s~~~~i~~~l~~iitLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~m 488 (773)
T COG5647 410 GNESADSGPSEYLAKYIDGLLKKDG-KQSFIGKIKDLLQDIITLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKM 488 (773)
T ss_pred cccccccccHHHHHHHhHHHhhccc-cccccccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHH
Confidence 954 335789999999999999865 222334678889999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCChhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCC-CCCccCcHhHHHHHHH
Q 004841 446 LTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYK-SFDLNLPAEMVKCVEV 524 (728)
Q Consensus 446 i~~Lk~~~G~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~-~~~~~lP~~l~~~~~~ 524 (728)
|++||+.||.+||+|+++||+||..|+++...|++... . ..+.+++.|.||++.+||..| ...+.||++|.+.++.
T Consensus 489 is~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~-s--~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~ 565 (773)
T COG5647 489 ISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQ-S--YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEG 565 (773)
T ss_pred HHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCch-h--hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHH
Confidence 99999999999999999999999999999999886431 1 125789999999999999655 4689999999999999
Q ss_pred HHHHHHhcCCCceEEeccCCceEEEEeEEcCeeEEE---EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004841 525 FREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTEL---IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 601 (728)
Q Consensus 525 f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l---~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 601 (728)
|++||.++|+||+|.|.|+||+|+|++.|+.+.+.+ +++++|+.|+++||+++++|+++|.+.|+++..++++.|+|
T Consensus 566 f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~s 645 (773)
T COG5647 566 FKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQS 645 (773)
T ss_pred HHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHH
Confidence 999999999999999999999999999998775443 46789999999999999999999999999999999999999
Q ss_pred hhhccccccccCCCCCCCCCCCeEEEecCCCCCCcceeccCCCh----hhhhHHHHhHHHhhhhhhhheeeecccccccC
Q 004841 602 LSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSRKVL 677 (728)
Q Consensus 602 L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~i~A~IVRimK~~k~l 677 (728)
|+++|..++.+ +++.++|++.|.+|.+|+++..+|+++.+.. ++...+++.+++||+..+|||||||||+||+|
T Consensus 646 l~~ak~~~l~~--~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l 723 (773)
T COG5647 646 LSCAKLVVLLK--DDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKL 723 (773)
T ss_pred HHhhheeeecc--ccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 99877666654 4788899999999999999999999998754 44556778999999999999999999999999
Q ss_pred ChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 678 GHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 678 ~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
+|++|+++|+.++++||.|++.+||++|+.|||||||+|.++| ..|+|+|
T Consensus 724 ~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa 773 (773)
T COG5647 724 KHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA 773 (773)
T ss_pred cHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence 9999999999999999999999999999999999999999888 8999997
No 3
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7.6e-111 Score=883.73 Aligned_cols=642 Identities=36% Similarity=0.598 Sum_probs=598.2
Q ss_pred chhhHHH-HHHHHHHHHhhh-----chhhHHHHHHHHHHHHHHHHHHHHHhhchhhhhhhhc-C-CCCcHHHHHHHHHHH
Q 004841 54 LVSAFVN-ILLLVLPSIREK-----HDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIAR-R-SLPPLNEVGLTCFRD 125 (728)
Q Consensus 54 ~y~~l~~-l~~~v~~~l~~~-----~~~~~L~~~~~~W~~~~~~~~~i~~if~YLdr~yv~~-~-~~~~i~~l~l~~f~~ 125 (728)
+|..+.. ..+++...+... +...+|+.+.++|..|+..+.+++.+|.||||.|+.. + -.+|+|++|+.+||.
T Consensus 2 ly~~l~~~~~~~~~~~~~q~~~~~~d~~~~l~k~~~~w~~~~~~~~mIRsIfl~lDrt~~~qsnp~v~siWem~l~LFR~ 81 (661)
T KOG2167|consen 2 LYKQLRQICEQHIKAQIEQLRGDELDSVLFLEKIGRCWQPDPKQMIMIRSIFLHLDRTYVLQSNPYVLSIWEMGLQLFRA 81 (661)
T ss_pred hHHHHHHHHHHHHHHHHhhCcCCcchHHHHHHHHhhHhhhhHHhhhhhhheeeecCCcccccCCCCcCCHHHhhHHHHHH
Confidence 4555666 666665544432 2357999999999999999999999999999999999 3 468999999999999
Q ss_pred HHhh----hhhHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHHHHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 004841 126 LVYT----ELNGKVRDAVITLIDQEREGEQIDRALLKNVLDIFVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILE 201 (728)
Q Consensus 126 ~v~~----~~~~~l~~~ll~~I~~~R~g~~id~~~l~~~i~ml~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~ 201 (728)
+++. .+..+..++++..++++|.|+++|+++|+.++.|+.++ ..|.+.|++.|++.+.++|.+++.....+
T Consensus 82 ~f~~~~~~~vqs~~~N~ll~s~er~rsgeAvdrslLrsll~MLsd~-----~iY~esF~~~fls~f~~lY~aE~~d~~Qe 156 (661)
T KOG2167|consen 82 HFSQEPQPFVQSKTFNGLLKSIERERSGEAVDRSLLRSLLKMLSDL-----QIYKESFELTFLSLFRELYAAEGQDKRQE 156 (661)
T ss_pred HhhccCCchhhccchHHHHHHHHHHhhcchhhHHHHHHHHHHHHHH-----HhhhhhhHHHHHHHHHHHHHHHhcchhhh
Confidence 9997 46778899999999999999999999999999999986 58999999999999999999999999999
Q ss_pred CChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCC
Q 004841 202 DSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIP 281 (728)
Q Consensus 202 ~s~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~~L~~ly~L~~~~~ 281 (728)
..+++||++++.++.+|..|+..|++.+|..++..++++.|+..|++.|+.+ |+..+++.++..++.+||.|++++.
T Consensus 157 l~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~IL~k---gl~~lvDm~q~~d~~rly~L~~r~~ 233 (661)
T KOG2167|consen 157 LEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLILTK---GLDSLVDMRQTSDLTRLYMLFSRVQ 233 (661)
T ss_pred cccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHHHhc---chHHhhhhhhccchHhHHHHHHHHh
Confidence 9999999999999999999999999999977799999999999999999875 7999999999999999999999998
Q ss_pred CChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCC--hhHHHHHHH
Q 004841 282 RGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNH--TLFHKSLKE 359 (728)
Q Consensus 282 ~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~li~~~F~~~--~~f~~~l~~ 359 (728)
++...++..|++|+++-|..++.... .+..+|+.+++++++.+-++..||..+ ..|..++++
T Consensus 234 ~g~l~l~qq~sdylk~~G~KlV~de~----------------kDk~mVqELL~FK~k~Dii~~~sF~~~v~e~f~~~~~~ 297 (661)
T KOG2167|consen 234 GGQLSLLQQWSDYLKKPGFKLVIDEE----------------KDKDMVQELLDFKKKVDIIVDESFLKYVAEKFLNSMSK 297 (661)
T ss_pred cchHHHHHHHHHHHhcccceeccCch----------------hhHHHHHHHHHHHHHhhHHHHHHHHHhhHHHHHHHHHH
Confidence 89999999999999999999885532 256799999999999999999999988 899999999
Q ss_pred HHHHHhcCCCCCCCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCCh
Q 004841 360 AFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSAND 439 (728)
Q Consensus 360 af~~~~N~~~~~~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~ 439 (728)
||+.|+|... +++||+||+|.|..|+.|. +..++++++..++.++.||+|+..||+|+.+|++.||+|||.++|+|.
T Consensus 298 afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr~i~gkdvfeA~ykkdLakrLLl~kSAsv 374 (661)
T KOG2167|consen 298 AFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFRFIHGKDVFEAFYKKDLAKRLLLGKSASV 374 (661)
T ss_pred HHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhccchhh
Confidence 9999999774 6799999999999999864 566788899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhCChhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHhHH
Q 004841 440 DHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMV 519 (728)
Q Consensus 440 ~~E~~~i~~Lk~~~G~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~ 519 (728)
|+|.+|+.+||.+||..||+||++|++||..|++++..|+.+...+.....++ +.+.|+|.|+||++++.++.||++|.
T Consensus 375 dae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~l-~~v~vlt~~yWpty~~~ev~Lp~em~ 453 (661)
T KOG2167|consen 375 DAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGNL-LTVNVLTMGYWPTYPPMEVLLPKEMR 453 (661)
T ss_pred cchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCCc-eEEEeecccccCCCCchhccCCHHHH
Confidence 99999999999999999999999999999999999999999865544333455 99999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCCceEEeccCCceEEEEeEEcCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHH
Q 004841 520 KCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLL 599 (728)
Q Consensus 520 ~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L 599 (728)
.+++.|..||..+|+||+|.|.+++|+|.+++.|..|+.++.||++|++||++||+++.+|++||.+.|++.+.+|.++|
T Consensus 454 ~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtl 533 (661)
T KOG2167|consen 454 DCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTL 533 (661)
T ss_pred HHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhccccccccCCCCCCCCCCCeEEEecCCCCCCcceeccCCCh----hhhhHHHHhHHHhhhhhhhheeeecccccc
Q 004841 600 HSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV----DEKKKVIEDVDKDRRYAIDASIVRIMKSRK 675 (728)
Q Consensus 600 ~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~~~~~~i~i~~~~~----~e~~~~~~~v~~~R~~~i~A~IVRimK~~k 675 (728)
+||+|+|.++|.+.|.|+.+.+++.|.+|..|+++..||+|+.+.. +|.++|.++|.+||.+.||||||||||+||
T Consensus 534 qsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk 613 (661)
T KOG2167|consen 534 QSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRK 613 (661)
T ss_pred HHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999998764 466778899999999999999999999999
Q ss_pred cCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 676 VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 676 ~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
+|+|+.|+.++.+||+ |+..+ ++|+|||+||+|||++|| ++ +.|.|||
T Consensus 614 ~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yva 661 (661)
T KOG2167|consen 614 TLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA 661 (661)
T ss_pred hhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence 9999999999999997 99888 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-109 Score=835.70 Aligned_cols=670 Identities=28% Similarity=0.490 Sum_probs=608.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHH----HHHHHHHHhc------CCchhhHHH-HHHHHHHHH
Q 004841 1 MTMNERKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSED----YMMLYTYLFQ------PHLVSAFVN-ILLLVLPSI 69 (728)
Q Consensus 1 ~~~~~~~~~~fe~~W~~l~~ai~~i~~~l~~~~~~~~s~~~----y~~lY~~vy~------~~~y~~l~~-l~~~v~~~l 69 (728)
||||+|++++||++|..|.+.|..+.. |+ ++++.. |.++|..+-. ..+|.+.+. +.+||...+
T Consensus 1 m~slkp~vv~fd~~w~~l~~si~~ii~-l~-----~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~ 74 (728)
T KOG2284|consen 1 MYSLKPKVVEFDKVWVQLRPSIIDIIN-LR-----PITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKR 74 (728)
T ss_pred CCCCCceeeeHHHHHHHHHHHHHHHHh-cc-----chhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHh
Confidence 899999999999999999999988764 32 344444 4555554444 357888888 888887655
Q ss_pred hh---hchhhHHHHHHHHHHHHHHHHHHHHHhhchhhhhhhhcCCC------------------CcHHHHHHHHHHHHHh
Q 004841 70 RE---KHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRSL------------------PPLNEVGLTCFRDLVY 128 (728)
Q Consensus 70 ~~---~~~~~~L~~~~~~W~~~~~~~~~i~~if~YLdr~yv~~~~~------------------~~i~~l~l~~f~~~v~ 128 (728)
.. .+++.+|..|.+.|+.|..+..++..+|.|||..|+++++. ..|..||+.+|++.+.
T Consensus 75 ~~~v~~~p~~~l~~yh~~w~~~~~ga~~~~~l~~yln~qfvk~~~~t~~d~~~~y~~~~~~~~~~eig~lal~~w~~~~v 154 (728)
T KOG2284|consen 75 QDIVDVDPDLLLQEYHKMWRVFHEGAIFIHRLFGYLNKQFVKQKRCTDLDNFAQYAAFLQIPDVKEIGCLALEIWKEDLV 154 (728)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhhcccchhhhhhhcchhcCCcHHHHhHHHHHHHHHHHH
Confidence 44 34567999999999999999999999999999999998642 3467899999999999
Q ss_pred hhhhHHHHHHHHHHHHHHhcCCcCC-HHHHHHHHHHHHHhcc-----------------CchhchHHHHHHHHHHHHHHH
Q 004841 129 TELNGKVRDAVITLIDQEREGEQID-RALLKNVLDIFVEIGM-----------------GQMDYYENDFETAMLKDTAAY 190 (728)
Q Consensus 129 ~~~~~~l~~~ll~~I~~~R~g~~id-~~~l~~~i~ml~~l~~-----------------~~~~~Y~~~FE~~~L~~t~~y 190 (728)
.++...++..++..|.++|.|+..+ ...+.++|.+|+.+.. ....+|++.||.|||.+|.+|
T Consensus 155 ~~i~~~lv~~ll~~i~ndr~g~~p~i~~~v~gvinsfv~~e~tdfdvvpaegaryka~~~~~~fyqe~fe~p~lt~t~~y 234 (728)
T KOG2284|consen 155 KTILPQLVKLLLIAIDNDRKGNFPHIANEVSGVINSFVKMEETDFDVVPAEGARYKARESTTAFYQESFEKPLLTDTEQY 234 (728)
T ss_pred HHHHHHHHHHHHHHhhcccCCCCccHHHHHHHHHHhhhhhhhcccccccccccchhhccccHHHHHHHhccccccchHHH
Confidence 9999999999999999999999887 5689999999998763 135789999999999999999
Q ss_pred HHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHH
Q 004841 191 YSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDL 270 (728)
Q Consensus 191 Y~~~s~~~l~~~s~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~~L 270 (728)
|+++++..+.+.+|++|+.+|..++++|+.||+.|||+++..|++..|++.+|.+|.+.| +..|+.++.+.+..|+
T Consensus 235 y~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~l----ha~ch~~i~~e~~~d~ 310 (728)
T KOG2284|consen 235 YSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDKL----HAVCHDLITNEENKDL 310 (728)
T ss_pred HHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhhH
Confidence 999999999999999999999999999999999999999999999999999999999887 3579999999999999
Q ss_pred HHHHHhhccCCCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCC
Q 004841 271 SRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNH 350 (728)
Q Consensus 271 ~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~li~~~F~~~ 350 (728)
+.||.|+..+..|+..+.+.|++||..+|...++.... ..-|..||+.++.+|.+|..++...|++|
T Consensus 311 ~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~-------------en~p~~fve~vl~v~~kf~~~~~~v~~~d 377 (728)
T KOG2284|consen 311 RNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTG-------------ENVPQQFVENVLRVYNKFNDMKTAVFMDD 377 (728)
T ss_pred HHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhcc-------------ccchHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999999999999999999999999998877643 24588999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHhcCCCCC---CCcHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHH
Q 004841 351 TLFHKSLKEAFEVFCNKGVAG---SSSAELLATFCDNILKKGGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKL 427 (728)
Q Consensus 351 ~~f~~~l~~af~~~~N~~~~~---~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~L 427 (728)
..|..+++.|+..++|...++ .+.||.||+|||.+|+++. +++++.+++..|+..+.+|+|++|||+|.++|.++|
T Consensus 378 ~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~if~yi~dkdifqkfys~ml 456 (728)
T KOG2284|consen 378 GEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVIFRYIEDKDIFQKFYSKML 456 (728)
T ss_pred hhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceeeeeecccHHHHHHHHHHHH
Confidence 999999999999999987643 5789999999999999975 679999999999999999999999999999999999
Q ss_pred HHHhcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCC
Q 004841 428 ARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSY 507 (728)
Q Consensus 428 a~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~ 507 (728)
|+||+.+.|.|.|.|..||++||+.||++||+++- +.|+..|.+++++|.+.+.+
T Consensus 457 a~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~n----------------------- 511 (728)
T KOG2284|consen 457 ANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIAN----------------------- 511 (728)
T ss_pred HHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHHh-----------------------
Confidence 99999999999999999999999999999999998 99999999999999876542
Q ss_pred CCCCccCcHhHHHHHHHHHHHHHhcCCCceEEeccCCceEEEEeEEcCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHH
Q 004841 508 KSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQ 587 (728)
Q Consensus 508 ~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Q~~iLllFn~~~~~t~~ei~~~ 587 (728)
+.+|.+|+...+.|+.||.++|+||+|+|++.++++++++++-++.|.-.|.++||++||+||..+.+++.+|.+.
T Consensus 512 ----f~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ll~f~~~~~i~~k~i~~~ 587 (728)
T KOG2284|consen 512 ----FHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAALLCFERRDAILVKDIGEE 587 (728)
T ss_pred ----ccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHHHHHhcccccchHHhhhhh
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCCCCCcceeccCCCh-----hhhhHHHHhHHHhhhhh
Q 004841 588 LNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPLPPV-----DEKKKVIEDVDKDRRYA 662 (728)
Q Consensus 588 t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~~~~~~i~i~~~~~-----~e~~~~~~~v~~~R~~~ 662 (728)
+|++.++|.+.+.++.. .++|.-. +..+..+..|++|.+|+++..+.++..|.+ +|.+.+...|.+||++.
T Consensus 588 ~~~~~~~l~kti~tild--v~~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y 663 (728)
T KOG2284|consen 588 IGVSGDYLLKTIRTILD--VTLLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYY 663 (728)
T ss_pred hCccHHHHHHHHHHHHh--ceeeccc--ccccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHH
Confidence 99999999999999985 4677643 346677889999999999999999987654 35566778899999999
Q ss_pred hhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 663 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 663 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
++||||||||+||.+.|+.|+.||+.|.++||.|++++||+|||.||++-||+|...+ +.|.|+|
T Consensus 664 ~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a 728 (728)
T KOG2284|consen 664 MECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA 728 (728)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence 9999999999999999999999999999999999999999999999999999999765 8999997
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.6e-93 Score=720.45 Aligned_cols=701 Identities=26% Similarity=0.461 Sum_probs=621.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhcCCchh---------hHHH-HHHHHHHHHh---h-
Q 004841 6 RKTIDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQPHLVS---------AFVN-ILLLVLPSIR---E- 71 (728)
Q Consensus 6 ~~~~~fe~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~~~~y~---------~l~~-l~~~v~~~l~---~- 71 (728)
+....||+.|...+|.+.++.+. +++++..|.++|..||..|+|. .+.+ +.+++.+.-. .
T Consensus 8 r~r~qFee~W~~~rpIVlkLLrQ------~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~qAq~rv~s~ 81 (777)
T KOG2285|consen 8 RDRDQFEEEWSKARPIVLKLLRQ------KSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQAQKRVRSL 81 (777)
T ss_pred cchhhhhhhccccchHHHHHHhh------ccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34458999999999999997652 3589999999999999977774 5555 6666544322 2
Q ss_pred hchhhHHHHHHHHHHHHHHHHHHHHHhhchhhhhhhhcCC--------CCcHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Q 004841 72 KHDEFMLRELVKRWSNHKVMVRWLSRFFHYLDRYFIARRS--------LPPLNEVGLTCFRDLVYTELNGKVRDAVITLI 143 (728)
Q Consensus 72 ~~~~~~L~~~~~~W~~~~~~~~~i~~if~YLdr~yv~~~~--------~~~i~~l~l~~f~~~v~~~~~~~l~~~ll~~I 143 (728)
..+..+|..|..+|.+|.....++...|.-|+..-....+ -.+|..+.+.-|.+++|..++.++..+.+.++
T Consensus 82 q~d~aLL~~YIvEWrkFftQ~niLPlPF~qle~s~~gk~gs~kk~~~eds~vRklMLd~WNe~IF~nIk~rLq~sAmklV 161 (777)
T KOG2285|consen 82 QTDGALLIGYIVEWRKFFTQANILPLPFKQLEESQAGKRGSVKKTPTEDSSVRKLMLDKWNEIIFMNIKERLQVSAMKLV 161 (777)
T ss_pred ccccHHHHHHHHHHHHHHHhcCcCCCcHHHHHHHhhcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2456899999999999999999999999999987544431 24789999999999999999999999999999
Q ss_pred HHHhcCCcCCHHHHHHHHHHHHHhcc---CchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHH
Q 004841 144 DQEREGEQIDRALLKNVLDIFVEIGM---GQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKD 220 (728)
Q Consensus 144 ~~~R~g~~id~~~l~~~i~ml~~l~~---~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~~Yl~~v~~~l~eE~~ 220 (728)
..+|+|+.+|.+++-++-++|+.|+. +.+.+|.+.||..||++|.+||+..+..++++.++.+|++.|...+++|+.
T Consensus 162 haER~G~a~DaQlViGvRESyVnL~snaEDkL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~ 241 (777)
T KOG2285|consen 162 HAERDGNAIDAQLVIGVRESYVNLNSNAEDKLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQ 241 (777)
T ss_pred HHHhccchhhhhhhhhhHHhHhhhccCccccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHH
Confidence 99999999999999999999999975 568899999999999999999999999999999999999999999999999
Q ss_pred HHchhcCC--CcHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHHHHHHHHHHHH
Q 004841 221 RVSHYLHS--SSEPKLLEKVQHELLSVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAE 298 (728)
Q Consensus 221 r~~~yL~~--~t~~kl~~~l~~~LI~~~~~~ll~~~~s~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~ 298 (728)
|+.+||.+ .|..+++..+.++|+.++.+.|+. +|..|+...+.+-|++||+|+.+++.|++++...+..||...
T Consensus 242 RAkRYLE~~~~s~~~lme~~VnaLv~sf~~tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~sa 317 (777)
T KOG2285|consen 242 RAKRYLEMNSPSSGKLMEKAVNALVESFEDTILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSA 317 (777)
T ss_pred HHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhh
Confidence 99999976 678899999999999999999986 588999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhcCCC---------
Q 004841 299 GTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGV--------- 369 (728)
Q Consensus 299 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~N~~~--------- 369 (728)
|..-+....+.+ ++++..||+.|+.++++|..++.++|++|+.|..|.+.||..++|...
T Consensus 318 GLaDM~~aaE~i-----------ttDsEkYVeqLL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~ 386 (777)
T KOG2285|consen 318 GLADMRNAAENI-----------TTDSEKYVEQLLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNS 386 (777)
T ss_pred hHHHHHhhhhhc-----------cCCHHHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccch
Confidence 987765544332 678899999999999999999999999999999999999999999764
Q ss_pred ---------CCCCcHHHHHHHHHHHhccCC-CCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCCh
Q 004841 370 ---------AGSSSAELLATFCDNILKKGG-SEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSAND 439 (728)
Q Consensus 370 ---------~~~~~~e~La~y~d~~lk~~~-~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~ 439 (728)
+..++||+||.|||.+||+.. +++++.++++.+|.+++-+++|+.+||+|..|++.||++||+...|++.
T Consensus 387 ~kgrglkt~pESKCpELLANYCDmLLRkTpLSKkLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADs 466 (777)
T KOG2285|consen 387 KKGRGLKTAPESKCPELLANYCDMLLRKTPLSKKLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADS 466 (777)
T ss_pred hcCCccccCcccccHHHHHHHHHHHHhcCccchhccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccch
Confidence 235799999999999999853 5678899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhCC--hhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCccCcH
Q 004841 440 DHERSILTKLKQQCGG--QFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPGIDLTVTVLTTGFWPSYKS-FDLNLPA 516 (728)
Q Consensus 440 ~~E~~~i~~Lk~~~G~--~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~~~~~VLt~~~WP~~~~-~~~~lP~ 516 (728)
+.|..|+..|+ +||. +|.+|+.+||+|++.|++++..|++.+...+..++.-.+++.||+.|.|...+. ..+.||.
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 5775 799999999999999999999999998876655666778999999999997643 4689999
Q ss_pred hHHHHHHHHHHHHHhcCCCceEEeccCCceEEEEeEEcCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHH
Q 004841 517 EMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSS--DRLSYSEIMTQLNLSDDD 594 (728)
Q Consensus 517 ~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Q~~iLllFn~~--~~~t~~ei~~~t~i~~~~ 594 (728)
+|+..+-..++||+++|+||+|.|.|+++.++|++.-+-|.|++.|+|+||+||.+||+. +.+|++.+.-+|.+|+.+
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 999999999999999999999999999999999987666899999999999999999964 689999999999999999
Q ss_pred HHHHHHHhhh---ccccccccCCCC----CCCCCCCeEEEecCCCC-----CCcceeccCCCh----hh--hhHHHHhHH
Q 004841 595 VVRLLHSLSC---AKYKILNKEPNT----KTISPTDHFEFNSKFTD-----KMRRIKIPLPPV----DE--KKKVIEDVD 656 (728)
Q Consensus 595 l~~~L~~L~~---~k~kiL~~~~~~----~~i~~~~~~~~N~~F~~-----~~~~i~i~~~~~----~e--~~~~~~~v~ 656 (728)
++++|-||+. .|+.||...|+. +++.++..|.+|.+|.- ..+|-+++...- .| .++..+.+.
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 9999999984 357888877642 45667889999999972 123445544321 11 222345678
Q ss_pred HhhhhhhhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 657 KDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 657 ~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
+-|-...|-+||+|||.||+++..+|..|.++.|+..|-|+..+||+.||.|||..|++||++|-++|.|+|
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 6
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=100.00 E-value=3.1e-90 Score=801.51 Aligned_cols=575 Identities=40% Similarity=0.725 Sum_probs=511.1
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhc-------CCchhhHHH-HHHHHHHHHhh---hchhhHHHHHHH
Q 004841 15 WEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQ-------PHLVSAFVN-ILLLVLPSIRE---KHDEFMLRELVK 83 (728)
Q Consensus 15 W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~-------~~~y~~l~~-l~~~v~~~l~~---~~~~~~L~~~~~ 83 (728)
|+.|++||+.|+ .+ .++..+||++|++||+ +.+|..+++ +.+++...... .+++.+|..|..
T Consensus 1 W~~l~~~i~~i~---~~----~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~ 73 (588)
T PF00888_consen 1 WEILEEAIDQIF---KK----SISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQ 73 (588)
T ss_dssp HHHHHHHHHHHH---TT-----GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHH
T ss_pred ChHHHHHHHHHH---cC----CCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHH
Confidence 999999999975 22 3667779999999999 356888888 88887554333 356799999999
Q ss_pred HHHHHHHHHHHHHHhhchhhhhhhhcCCCCcHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhcCCcCCHHHHHHHHHH
Q 004841 84 RWSNHKVMVRWLSRFFHYLDRYFIARRSLPPLNEVGLTCFRDLVYTELNGKVRDAVITLIDQEREGEQIDRALLKNVLDI 163 (728)
Q Consensus 84 ~W~~~~~~~~~i~~if~YLdr~yv~~~~~~~i~~l~l~~f~~~v~~~~~~~l~~~ll~~I~~~R~g~~id~~~l~~~i~m 163 (728)
.|.+|+.++.+|+++|+||||+|+.++ +|++.|+.+++++++.+++.+|.++|.|+.+|..+++++++|
T Consensus 74 ~w~~~~~~~~~i~~if~yLdr~yv~~~-----------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~~~~l~~~~~~ 142 (588)
T PF00888_consen 74 EWEKYKKAIKYISDIFSYLDRNYVKRN-----------LFREQVFKPLKDKIINALLNLIKNEREGEKIDRSLLKNVIEM 142 (588)
T ss_dssp HHHHHHHHHHHHHHHTHHHHHTSTTTT-----------HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHhhhhhh-----------hHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Confidence 999999999999999999999999998 999999999999999999999999999999999999999999
Q ss_pred HHHhccCchhchHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHH
Q 004841 164 FVEIGMGQMDYYENDFETAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELL 243 (728)
Q Consensus 164 l~~l~~~~~~~Y~~~FE~~~L~~t~~yY~~~s~~~l~~~s~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~kl~~~l~~~LI 243 (728)
+.++| ...+|.+.||++||++|.+||+.++ +...++.+|+.+|+.++.+|.+||..||+++|..++.+.+.++||
T Consensus 143 ~~~l~--~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI 217 (588)
T PF00888_consen 143 FVELG--SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLI 217 (588)
T ss_dssp HHHTT--HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHT
T ss_pred Hhccc--hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHH
Confidence 99998 6689999999999999999999999 667799999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhchhhhhhhhhcCcHHHHHHHHHhhccCCCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccccc
Q 004841 244 SVYANQLLEKEHSGCHALLRDDKVEDLSRMFRLFSKIPRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGL 323 (728)
Q Consensus 244 ~~~~~~ll~~~~s~~~~ll~~~~~~~L~~ly~L~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 323 (728)
.+|.+.| .+|+..|+++++.++|++||+|+++++++++.+++.|++||.+.|..+++.... ..
T Consensus 218 ~~~~~~l----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~-------------~~ 280 (588)
T PF00888_consen 218 SDHLDEL----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK-------------SS 280 (588)
T ss_dssp GGGHHHH----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC-------------GG
T ss_pred HHHHHHH----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc-------------cc
Confidence 9999988 479999999999999999999999999999999999999999999999876531 24
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHhccCCCCCCChHHHHHHH
Q 004841 324 QEQVFVRKVIELHDKYLAYVNDCFQNHTLFHKSLKEAFEVFCNKGVAGSSSAELLATFCDNILKKGGSEKLSDEAIEEML 403 (728)
Q Consensus 324 ~~~~~i~~ll~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~N~~~~~~~~~e~La~y~d~~lk~~~~~~~~~~~~~~~l 403 (728)
.+..||+.+++++++|+.++.+||++++.|..++++||+.++|.+ ...+|++||+|||.++++++ .+.++++++..+
T Consensus 281 ~~~~~i~~ll~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~ 357 (588)
T PF00888_consen 281 DPKEFIEDLLELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQKL 357 (588)
T ss_dssp GCHHHHHHHHHHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHHHh
Confidence 578999999999999999999999999999999999999999998 36899999999999999875 567788899999
Q ss_pred HHHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHhHHHhHHHHHHHHHHHh
Q 004841 404 EKVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLS 483 (728)
Q Consensus 404 ~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~ 483 (728)
+.++.||+|+++||+|+.+|+++||+|||.+++.+.+.|..+|++|+.+||.++|++|++|++|+..|+++++.|++...
T Consensus 358 ~~i~~l~~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~ 437 (588)
T PF00888_consen 358 DDIVKLFSYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQS 437 (588)
T ss_dssp HHHHHHHTTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhEEEeeecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred cCCCCC-CCcceEEEEeecCCCCCCCCCC-ccCcHhHHHHHHHHHHHHHhcCCCceEEeccCCceEEEEeEEcCeeEEEE
Q 004841 484 NNPNAN-PGIDLTVTVLTTGFWPSYKSFD-LNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELI 561 (728)
Q Consensus 484 ~~~~~~-~~~~~~~~VLt~~~WP~~~~~~-~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~ 561 (728)
+.+... ++++|+|.|||+++||..+... +.+|++|+.+++.|++||..+|+||+|+|.|++|+|+|++++++++++++
T Consensus 438 ~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~ 517 (588)
T PF00888_consen 438 QNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELT 517 (588)
T ss_dssp TTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEE
T ss_pred hccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEE
Confidence 765432 2799999999999999988766 99999999999999999999999999999999999999999999999999
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCC
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 632 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~ 632 (728)
||++||+||++||+.+++|+++|++.||+++++++++|.+|+..|..++.+.++++.+++++.|.+|.+|+
T Consensus 518 ~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 518 VSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp EEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred eeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 99999999999999999999999999999999999999999865433333778889999999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=4.3e-33 Score=260.76 Aligned_cols=141 Identities=48% Similarity=0.900 Sum_probs=132.8
Q ss_pred cccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHhHHHhHHHHHHHHHHHhcCCCCCCC
Q 004841 412 YISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNPNANPG 491 (728)
Q Consensus 412 ~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 491 (728)
|+++||+|+.+|+++||+|||..++.+.+.|..||++||.+||.++|++|++|++|+..|++++++|++.+.+++. ..+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~~-~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNSN-KPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CCC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999998775432 346
Q ss_pred cceEEEEeecCCCCCCCC-CCccCcHhHHHHHHHHHHHHHhcCCCceEEeccCCceEEEEeEE
Q 004841 492 IDLTVTVLTTGFWPSYKS-FDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKF 553 (728)
Q Consensus 492 ~~~~~~VLt~~~WP~~~~-~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~ 553 (728)
++|+|.|||+++||..+. .++.||++|+.+++.|++||..+|+||+|+|.|++|+|+|+++|
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 78999999999999999999999999999999999999999865
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=6.3e-26 Score=245.07 Aligned_cols=303 Identities=23% Similarity=0.312 Sum_probs=239.1
Q ss_pred HHhhhhccccChHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHhhCChhhHhHHHHHHhHHHhHHHHHHHHHH--H
Q 004841 405 KVVKLLAYISDKDLFAEFYRKKLARRLLFDKSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY--L 482 (728)
Q Consensus 405 ~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s~s~~~E~~~i~~Lk~~~G~~~t~kl~~Ml~D~~~S~~l~~~f~~~--~ 482 (728)
-+-.|...+.+|+.|++.||.+||.||+.....+.+.|..-++.||-++|.+..+.|++|++|+..|+++++.+++. .
T Consensus 441 i~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~~ 520 (765)
T KOG2165|consen 441 IFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESEL 520 (765)
T ss_pred HHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhhh
Confidence 34456666799999999999999999999999999999999999999999999999999999999999999999874 2
Q ss_pred hcCCCCCCCcceEEEEeecCCCCCCCCCCccCcHhHHHHHHHHHHHHHhcCCCceEEeccCCceEEEEeEEcCeeEEEEE
Q 004841 483 SNNPNANPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFREFYQTKTKHRKLTWIYSLGTCNLLGKFESRTTELIV 562 (728)
Q Consensus 483 ~~~~~~~~~~~~~~~VLt~~~WP~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~v 562 (728)
.......+.+.+++.+||+.+||......+.+|.+++..++.|.+-|.+..++|+|.|.+++|+|+|++.|++++.+++|
T Consensus 521 ~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tV 600 (765)
T KOG2165|consen 521 SRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTV 600 (765)
T ss_pred hcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEee
Confidence 22222345688999999999999988888999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCCCCCcceeccC
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRIKIPL 642 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~~~~~~i~i~~ 642 (728)
|+.||+|+.+|.+.++||++++++.+|+|...+++.|..|. +.++|...|. ++++.+|+++++=.+..+--.-+.
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi--~~GvL~e~~~---~s~tgt~T~iEse~d~~q~~~~~~ 675 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWI--QKGVLREEPI---ISDTGTLTVIESEMDFDQAEGTVL 675 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHH--HcCeeecCCC---CCCCceeeeccccccccccCCCcc
Confidence 99999999999999999999999999999999999999998 4688887653 377899999985443322111111
Q ss_pred CChh-hh--hHHHHhHHHhhh--hhhhheeeecccccccCChhHHHHHHHHHhcCCCCCC-------hhHHHHHHHhhhh
Q 004841 643 PPVD-EK--KKVIEDVDKDRR--YAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPD-------FKAIKKRIEDLIT 710 (728)
Q Consensus 643 ~~~~-e~--~~~~~~v~~~R~--~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~-------~~~ik~~Ie~LIe 710 (728)
...+ +. ......+++-+. ..-...||-.+-.-+.|..+.+.+... .|.|. -++++.-+..++.
T Consensus 676 ~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~kV~ 750 (765)
T KOG2165|consen 676 LEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQRKVR 750 (765)
T ss_pred cccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHHHhh
Confidence 1111 11 111222222111 233447777777779999988888432 45443 4556666666665
Q ss_pred hhhcccC
Q 004841 711 RDYLERD 717 (728)
Q Consensus 711 reyi~R~ 717 (728)
.|-|+-.
T Consensus 751 e~kL~f~ 757 (765)
T KOG2165|consen 751 EGKLEFI 757 (765)
T ss_pred ccceEEe
Confidence 5555443
No 9
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.79 E-value=2.7e-20 Score=149.58 Aligned_cols=68 Identities=51% Similarity=0.920 Sum_probs=62.5
Q ss_pred HHHhhhhhhhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCC
Q 004841 655 VDKDRRYAIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPN 722 (728)
Q Consensus 655 v~~~R~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~ 722 (728)
|+++|...|+||||||||++|+++|++|+.+|.++++++|.|+..+||++||+||++|||+||++|+|
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 36799999999999999999999999999999999999999999999999999999999999999876
No 10
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=95.51 E-value=0.34 Score=45.73 Aligned_cols=121 Identities=17% Similarity=0.209 Sum_probs=80.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhc-------CCchh----hHHH-HHHHH---HHHHhhhc
Q 004841 9 IDLEQGWEFMQKGITKLKNILEGLPEPQFSSEDYMMLYTYLFQ-------PHLVS----AFVN-ILLLV---LPSIREKH 73 (728)
Q Consensus 9 ~~fe~~W~~l~~ai~~i~~~l~~~~~~~~s~~~y~~lY~~vy~-------~~~y~----~l~~-l~~~v---~~~l~~~~ 73 (728)
...++.|..+..++-.++ +|+.- .++ -+++=..|-- ....+ .+++ +..-+ ...++..+
T Consensus 3 ~~~~~~W~~~~~~vl~lF---~g~~l-~~~---iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~tg~~~L~~~l~~~~ 75 (158)
T PF08539_consen 3 MSSDDAWNSLCAKVLPLF---QGERL-RLP---IEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTTGMYILENQLNEVP 75 (158)
T ss_pred CchhhhHHHHHHHHHHHH---cCCCC-CcC---HHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 456899999999998864 45432 244 3344333322 11112 3344 33221 12344567
Q ss_pred hhhHHHHHHHHHHHHH-HHHHHHHHhhchhhhhhhhc-----------------CCCCcHHHHHHHHHHHHHhhhhhHHH
Q 004841 74 DEFMLRELVKRWSNHK-VMVRWLSRFFHYLDRYFIAR-----------------RSLPPLNEVGLTCFRDLVYTELNGKV 135 (728)
Q Consensus 74 ~~~~L~~~~~~W~~~~-~~~~~i~~if~YLdr~yv~~-----------------~~~~~i~~l~l~~f~~~v~~~~~~~l 135 (728)
++.+|.+++..|.-|. .-.-++..+|..|++.+-.. ....+|+.++|..|||.|+-+..+++
T Consensus 76 ~~~~l~rL~eiW~~Ff~~VlP~lqavFlPLq~~f~~~~~~~~~~~~~~~~~~~~~~~l~Vr~l~L~~FRD~IvLP~y~~l 155 (158)
T PF08539_consen 76 DNRLLKRLVEIWQFFFTQVLPYLQAVFLPLQLEFQGNGKYMNPSEAREFWGNKAGSELDVRRLLLIAFRDSIVLPYYQRL 155 (158)
T ss_pred hhHHHHHHHHHHHHHhcchHHHHHHHHhhhHHhhcccCccCChhhhhccccccCCCCCcHHHHHHHHHHHHhhhcchHhh
Confidence 7899999999999965 45678999999999654322 24478999999999999998877766
Q ss_pred H
Q 004841 136 R 136 (728)
Q Consensus 136 ~ 136 (728)
.
T Consensus 156 ~ 156 (158)
T PF08539_consen 156 K 156 (158)
T ss_pred h
Confidence 4
No 11
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=92.82 E-value=0.31 Score=41.97 Aligned_cols=65 Identities=18% Similarity=0.214 Sum_probs=52.3
Q ss_pred EEEcHHHHHHHHhhc--------CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCC
Q 004841 560 LIVTTYQASALLLFN--------SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 631 (728)
Q Consensus 560 l~vs~~Q~~iLllFn--------~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F 631 (728)
..++.-|+.+|+..- ....+|-.||++.+|++.+.+.+.|..|. +.+++.+.. ....|.+|.++
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~~ 92 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTPL 92 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCCc
Confidence 467888998888655 46789999999999999999999999997 567776542 24789999876
Q ss_pred C
Q 004841 632 T 632 (728)
Q Consensus 632 ~ 632 (728)
+
T Consensus 93 ~ 93 (95)
T TIGR01610 93 S 93 (95)
T ss_pred c
Confidence 4
No 12
>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=92.15 E-value=0.23 Score=37.42 Aligned_cols=45 Identities=29% Similarity=0.369 Sum_probs=36.6
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 567 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 567 ~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
+.||..|.+.. .+|+.||++.+|+|...+.+.|..|. ..+++.+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~--~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV--EEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCcCeecC
Confidence 46788888775 58999999999999999999999997 35676654
No 13
>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=90.59 E-value=0.49 Score=34.85 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=34.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 604 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 604 (728)
+..+..||....+++.+|..||++.+|++...+.+.|..|..
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 456778888888888999999999999999999999999963
No 14
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=90.39 E-value=0.76 Score=38.39 Aligned_cols=59 Identities=15% Similarity=0.215 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecC
Q 004841 565 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 630 (728)
Q Consensus 565 ~Q~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~ 630 (728)
+++.+.+..+..+ .+|.++|++.+++|+..+.+.++.|. +.+++...+ | +++-|.++.+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-G----~~GGy~L~~~ 70 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-G----RGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCC
Confidence 3444445444443 49999999999999999999999997 567876442 1 3567877664
No 15
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=90.03 E-value=0.38 Score=37.44 Aligned_cols=51 Identities=25% Similarity=0.385 Sum_probs=42.2
Q ss_pred EcHHHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 562 VTTYQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
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 47789999988777666 9999999999999999999999997 457777654
No 16
>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=87.97 E-value=0.76 Score=35.38 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=38.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
|..|+...++++.+|+++|++.+|++...+++-|..|. +.+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~--~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLE--KQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 45677788889999999999999999999999999997 34566554
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=86.80 E-value=0.47 Score=36.58 Aligned_cols=51 Identities=24% Similarity=0.387 Sum_probs=42.9
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+|..|+.+|....+.+.+|..+|++.++++...+.+.+..|. +.+++.+.+
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~~ 51 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERER 51 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEecc
Confidence 367899999888888899999999999999999999999997 457776643
No 18
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=86.72 E-value=23 Score=40.13 Aligned_cols=36 Identities=8% Similarity=0.070 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHH
Q 004841 181 TAMLKDTAAYYSRKASNWILEDSCPDYMLKAEECLKRE 218 (728)
Q Consensus 181 ~~~L~~t~~yY~~~s~~~l~~~s~~~Yl~~v~~~l~eE 218 (728)
.+|+..++++|...++ .....+.+|+.+....+-.+
T Consensus 289 e~f~~~~~~afe~fin--k~~~rpAelIak~~dt~Lr~ 324 (661)
T KOG2167|consen 289 EKFLNSMSKAFETFIN--KRRNRPAELIAKYVDTKLRA 324 (661)
T ss_pred HHHHHHHHHHHHHHHh--cccCCHHHHHHHHHHHHHHh
Confidence 7899999999999988 45667889998887655444
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=86.58 E-value=1.1 Score=35.57 Aligned_cols=50 Identities=24% Similarity=0.333 Sum_probs=38.5
Q ss_pred EcHHHHHHHHhhc-CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 562 VTTYQASALLLFN-SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 562 vs~~Q~~iLllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
+|..|..||.... ....++..+|++.++++...+-+.+..|.. .+++.+.
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 778999999999999999999999999974 5777654
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=85.17 E-value=1.6 Score=39.14 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=45.4
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 561 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
.++..|+.||..+..++.+|..+|++.+|++...+-+.+..|. +.+++.+.+
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 4578899999988888899999999999999999999999997 557887654
No 21
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=84.59 E-value=2.2 Score=31.24 Aligned_cols=43 Identities=26% Similarity=0.339 Sum_probs=33.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccc
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 610 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL 610 (728)
...-||.++-+ ++.++.||++.+|++...+.++|..|. +.+++
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV 45 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLV 45 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCe
Confidence 34567776666 689999999999999999999999986 34554
No 22
>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=84.33 E-value=1.3 Score=34.53 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=39.6
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
++.-..||.++...++.|+.+|++.+|++...+..+|..|. +.+++...
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 45566788888667799999999999999999999999997 45777643
No 23
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.05 E-value=2.3 Score=39.63 Aligned_cols=53 Identities=19% Similarity=0.196 Sum_probs=45.6
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 560 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 560 l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
..+|..|+.||......+.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 35678899999877667789999999999999999999999997 568887764
No 24
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=82.68 E-value=0.48 Score=38.07 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=34.4
Q ss_pred eecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCC
Q 004841 668 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKS 719 (728)
Q Consensus 668 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~ 719 (728)
-.+|+.++.++..+|-. +|..+++.+..-|+.|+.+|||++.+.
T Consensus 6 ~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 34577888888887766 699999999999999999999998653
No 25
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=82.15 E-value=2.5 Score=33.78 Aligned_cols=47 Identities=23% Similarity=0.292 Sum_probs=38.0
Q ss_pred HHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 565 YQASALLLFNSSDR--LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 565 ~Q~~iLllFn~~~~--~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
..-.||.++.+... +|..||++.+|++...+.++|..|. +.+++.+.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~--~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE--KKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 44567777777655 9999999999999999999999996 45666654
No 26
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=81.60 E-value=1.3 Score=40.47 Aligned_cols=60 Identities=17% Similarity=0.203 Sum_probs=44.5
Q ss_pred hheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 664 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 664 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
+..|++++-..+.++..+++.. +.....+....|...|..|.+||||+|..+ ...|.|-|
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 3456667766777777666654 444466788899999999999999999854 45788864
No 27
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=80.76 E-value=1.4 Score=39.37 Aligned_cols=62 Identities=21% Similarity=0.313 Sum_probs=52.3
Q ss_pred hhhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 662 AIDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 662 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
..++.|++||=.++..+.+|++.++.+ .+.++...|+.-|..|..||.|.|.-+ ...|.|-|
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 357788999999999999999987765 478899999999999999999999864 46777744
No 28
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=79.30 E-value=3.8 Score=30.94 Aligned_cols=37 Identities=22% Similarity=0.324 Sum_probs=29.2
Q ss_pred HHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004841 568 SALLLF-NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 604 (728)
Q Consensus 568 ~iLllF-n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 604 (728)
.||.++ +..+.+|.++|++.+|++...+.+.|..|-.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344444 6666799999999999999999999998853
No 29
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=78.83 E-value=4.8 Score=35.47 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=43.4
Q ss_pred EEcHHHHHHHHhhc----CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 561 IVTTYQASALLLFN----SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 561 ~vs~~Q~~iLllFn----~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
.+|..|..||.... ..+.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 45788888887655 55689999999999999999999999997 567887764
No 30
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=77.74 E-value=4.9 Score=33.79 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=37.4
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 567 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 567 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
..||..+... +.+|..+|++.+|++...+.+.|..|. ..+++.+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~--~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ--ELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH--HCCCeeec
Confidence 4466677665 689999999999999999999999997 45788764
No 31
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=77.05 E-value=4.3 Score=34.57 Aligned_cols=53 Identities=28% Similarity=0.326 Sum_probs=45.0
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 559 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 559 ~l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
++.++..+..||.+......+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 5 ~~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~--~~g~v~~~ 57 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLE--KKGLIRRL 57 (101)
T ss_pred ccCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHH--HCCCeEec
Confidence 346778899999888877789999999999999999999999997 45777654
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=76.65 E-value=2.3 Score=37.92 Aligned_cols=60 Identities=13% Similarity=0.243 Sum_probs=43.0
Q ss_pred hheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 664 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 664 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
+..|++++=..+.++..+++. .+.....+....|...+..|.+||||+|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~----~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHE----ALPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHH----HHCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHH----HHHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 344555665666677776666 4444567789999999999999999999864 46888864
No 33
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=74.72 E-value=8.7 Score=36.67 Aligned_cols=45 Identities=18% Similarity=0.212 Sum_probs=36.2
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 566 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 566 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
.+++.+.|+.. ..+|.++|++.+++|...+.+.|..|. +.+++..
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 34444556643 589999999999999999999999997 5678874
No 34
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=74.43 E-value=6.3 Score=40.64 Aligned_cols=47 Identities=15% Similarity=0.266 Sum_probs=40.0
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
-+.||.+|.....+|+.||++.+|+|...+.+.|..|.. .+.|.+.+
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~~ 62 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQEG 62 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 346888898877899999999999999999999999974 57787653
No 35
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=74.35 E-value=8.9 Score=36.16 Aligned_cols=56 Identities=11% Similarity=0.083 Sum_probs=40.8
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEec
Q 004841 567 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 629 (728)
Q Consensus 567 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~ 629 (728)
+.+.|..+....+|..+|++..++|...|.+.|..|. +.+++.... | .++-|.++.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~r-G----~~GGy~La~ 68 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVR-G----RNGGVRLGR 68 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeec-C----CCCCeeecC
Confidence 3344555555678999999999999999999999997 567876542 1 234566544
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=73.88 E-value=6 Score=29.08 Aligned_cols=43 Identities=23% Similarity=0.313 Sum_probs=34.2
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 568 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 568 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
.|+..+.+...+|..+|++.++++...+.+.|..|.. .+++.+
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 4555556667899999999999999999999999974 355544
No 37
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=72.85 E-value=3.4 Score=32.88 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=39.1
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
|-.++.|+..+-..+..|..+|++.+|+|...+.+.|..|.. .+++.+.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~--~GlV~~~ 55 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE--KGLVERE 55 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH--TTSEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 445666665554667899999999999999999999999974 4676654
No 38
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=72.60 E-value=7 Score=30.64 Aligned_cols=56 Identities=23% Similarity=0.231 Sum_probs=37.8
Q ss_pred HHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEe
Q 004841 569 ALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFN 628 (728)
Q Consensus 569 iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N 628 (728)
||-.++. +.++|..||++.+|++...++..|..|. +.+.+.+.|.++.-. ..+.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG~~--~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRGKS--TYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSSSS---EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCCcc--eeeeec
Confidence 3444555 6789999999999999999999999997 456666655443221 346555
No 39
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=70.95 E-value=8.1 Score=37.65 Aligned_cols=53 Identities=13% Similarity=0.004 Sum_probs=45.5
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 560 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 560 l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+.+|..|+.||.....++.+|..+|++.++++...+.+.+..|. +-+++.+.+
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 35678899999999888899999999999999999999999996 457877654
No 40
>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=70.25 E-value=11 Score=34.51 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=34.7
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 567 ASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 567 ~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
+++.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
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 3444555543 479999999999999999999999997 5677764
No 41
>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=69.75 E-value=15 Score=31.96 Aligned_cols=62 Identities=26% Similarity=0.361 Sum_probs=45.7
Q ss_pred EEcHHHHHHHHh-------hcC-CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCC
Q 004841 561 IVTTYQASALLL-------FNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 632 (728)
Q Consensus 561 ~vs~~Q~~iLll-------Fn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~ 632 (728)
.+|.-|..|++. ||. .+.+|..++++.||++...+.+++..|. +.++|... +..+-+|.+.+
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li--~~~vI~~~--------g~~~G~N~~i~ 98 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI--RRGVIIRD--------GKRIGVNKNIS 98 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeC--------CcEEeeecccc
Confidence 445556666655 453 3589999999999999999999999997 57888654 35566666543
No 42
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=69.65 E-value=8.4 Score=35.67 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=44.1
Q ss_pred EEEcHHHHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 560 LIVTTYQASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 560 l~vs~~Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+.+|..|..||...... +..|..+|++.++++...+.+.+..|. +-+++.+.+
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 35678899888877654 568999999999999999999999997 567887764
No 43
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=68.83 E-value=11 Score=33.97 Aligned_cols=38 Identities=26% Similarity=0.319 Sum_probs=33.5
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 574 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 574 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
+.++.+|+++|++.++.+...+.++|+.|.. .+++.+.
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Re 75 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVERE 75 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeee
Confidence 3678999999999999999999999999984 5788765
No 44
>PHA00738 putative HTH transcription regulator
Probab=67.10 E-value=11 Score=32.81 Aligned_cols=67 Identities=22% Similarity=0.124 Sum_probs=50.7
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCC
Q 004841 559 ELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 631 (728)
Q Consensus 559 ~l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F 631 (728)
++...+.=-.||.++.+++.+++.+|++.++++...+-++|.-|- ..+|+.....|.. -.|++|.+-
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr~----vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGRT----LYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECCE----EEEEECCCc
Confidence 455566666677777777789999999999999999999999996 4678876654432 357777653
No 45
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=66.02 E-value=8.8 Score=27.46 Aligned_cols=36 Identities=33% Similarity=0.499 Sum_probs=26.7
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 567 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 567 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
-.||-.+.+....++.+|++.+|++...+.+-+..|
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 346666666688999999999999999998877654
No 46
>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=65.87 E-value=7.5 Score=37.11 Aligned_cols=51 Identities=25% Similarity=0.317 Sum_probs=41.4
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCCCCCcc
Q 004841 578 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRR 637 (728)
Q Consensus 578 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~~~~~~ 637 (728)
-+|..+|++.+|++...+.+++..|. +.++|.+.. .+.|.+|++|--+..+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~--e~~iI~k~~-------~G~Y~iNP~~~~kG~~ 125 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELE--EKNIIKKIR-------NGAYMINPNFFFKGDR 125 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHH--hCCcEEEcc-------CCeEEECcHHheeCcH
Confidence 46889999999999999999999997 457887753 4689999997654433
No 47
>PRK10870 transcriptional repressor MprA; Provisional
Probab=65.34 E-value=14 Score=35.70 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=42.8
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 561 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
.+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+
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 356678888877654 4579999999999999999999999997 567887764
No 48
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=65.07 E-value=13 Score=28.09 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=32.5
Q ss_pred hcCCCCc-CHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 573 FNSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 573 Fn~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+...+.+ |..+|++.+|++...+.++|..|. +.+++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~--~~g~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE--AEGLVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEec
Confidence 4455567 899999999999999999999997 456776543
No 49
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=64.60 E-value=16 Score=34.32 Aligned_cols=58 Identities=16% Similarity=0.202 Sum_probs=41.6
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEec
Q 004841 565 YQASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 629 (728)
Q Consensus 565 ~Q~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~ 629 (728)
+.+.+.|.-+..+ ..|.++|++..|+|+..|.+.|..|. |.+++...+. +++-|.++.
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar 69 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLAR 69 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCC
Confidence 3445555555544 68899999999999999999999996 6788875431 244565554
No 50
>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=64.37 E-value=5.4 Score=31.43 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=33.6
Q ss_pred heeeeccc-ccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccC--CCCCCcee
Q 004841 665 ASIVRIMK-SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERD--KSNPNMFR 725 (728)
Q Consensus 665 A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~--~~d~~~y~ 725 (728)
..|.+.+. ..+.++..+|.. .+..+...+-+.|+.|+++|||++. +.|.....
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~ 61 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKR 61 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEE
T ss_pred HHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeE
Confidence 34455555 566666666655 3566778899999999999999665 45555433
No 51
>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=63.70 E-value=16 Score=29.38 Aligned_cols=45 Identities=18% Similarity=0.324 Sum_probs=34.2
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 564 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 564 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
..|. ||+..... ..|++||.+.||++.+.+...|..|. +-+++.+
T Consensus 6 ~~~~-IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 6 VTQK-ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHH-HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 3444 34444444 89999999999999999999999996 4566654
No 52
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=63.26 E-value=12 Score=32.50 Aligned_cols=44 Identities=25% Similarity=0.342 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHhhcC----CCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004841 561 IVTTYQASALLLFNS----SDRLSYSEIMTQLNLSDDDVVRLLHSLSC 604 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~----~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 604 (728)
.++..|-.||-.+.+ .+.+++++|++.++++..+++.+|..|+.
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 35899999999999999999999999985
No 53
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=62.18 E-value=17 Score=26.12 Aligned_cols=34 Identities=32% Similarity=0.463 Sum_probs=29.0
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 578 RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 578 ~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
.+|..+|++.+|++...+.+.|..|. +.+++.+.
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 45777643
No 54
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=62.06 E-value=16 Score=37.46 Aligned_cols=46 Identities=28% Similarity=0.447 Sum_probs=39.1
Q ss_pred HHHHHhhcCCCC-cCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 567 ASALLLFNSSDR-LSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 567 ~~iLllFn~~~~-~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+.||.+|..... +++.||++.+|+|...+.+.|..|. ..+.+...+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~--~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV--ELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 467888887554 7899999999999999999999997 468888765
No 55
>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=62.00 E-value=10 Score=29.33 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=29.5
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
|.-+|-++-+.+.+|+.+|++.+|++...++..+.-|-
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 55556544447899999999999999999998887764
No 56
>PRK11569 transcriptional repressor IclR; Provisional
Probab=61.97 E-value=15 Score=38.34 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=39.2
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 566 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 566 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
-..||.+|.+. ..+|+.||++.+|+|...+.+.|.+|. ..+.|.+.+
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~--~~G~l~~~~ 77 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQ--QQGFVRQVG 77 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEcC
Confidence 34678889864 579999999999999999999999997 457887653
No 57
>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=61.80 E-value=19 Score=32.70 Aligned_cols=45 Identities=20% Similarity=0.284 Sum_probs=34.2
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 566 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 566 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
++.+.+.-++. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 34444443333 389999999999999999999999997 4567754
No 58
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=61.21 E-value=12 Score=36.98 Aligned_cols=52 Identities=17% Similarity=0.198 Sum_probs=45.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 561 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
.++..|..||..+.+++.++..+|++.+|++...+.+.|..|. +.+++.+.+
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 5678899999999887889999999999999999999999997 457877653
No 59
>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=61.18 E-value=10 Score=30.71 Aligned_cols=36 Identities=22% Similarity=0.144 Sum_probs=27.8
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 574 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 574 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
...+.+|+.||++.+|++...++..+..+. +..+|.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~--~~~~~~ 63 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET--KAGGLV 63 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc--ccchHH
Confidence 333578999999999999999999887764 334443
No 60
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=61.16 E-value=6.7 Score=32.51 Aligned_cols=43 Identities=21% Similarity=0.380 Sum_probs=32.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 567 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 567 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
..||...+..+.+++.+|.+.+|+++..+-++|..|.. .+.+.
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~--~GyV~ 45 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEE--AGYVE 45 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCEE
Confidence 44565556677899999999999999999999999974 34443
No 61
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=60.65 E-value=17 Score=37.76 Aligned_cols=47 Identities=23% Similarity=0.288 Sum_probs=39.2
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 566 QASALLLFNSS-DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 566 Q~~iLllFn~~-~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
-..||.+|... ..+|+.||++.+|+|...+.+.|.+|.. .+.|.+.+
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQDS 74 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEcC
Confidence 34688889765 4799999999999999999999999984 57776653
No 62
>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=60.62 E-value=17 Score=28.62 Aligned_cols=48 Identities=25% Similarity=0.291 Sum_probs=38.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
+..+..|+..+.+.. ++..+|++.+|++...+.+.|..|.. .+++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~--~g~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEE--AGLVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHH--CCCeEEE
Confidence 456777887776666 99999999999999999999999863 4566543
No 63
>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=59.35 E-value=4.1 Score=31.29 Aligned_cols=45 Identities=16% Similarity=0.324 Sum_probs=39.1
Q ss_pred eeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004841 666 SIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 718 (728)
Q Consensus 666 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 718 (728)
.|+..++.++.++..+|.+ .|..+...|.+=+..|-++|.|.|.-
T Consensus 4 ~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 4667788889999888877 58899999999999999999999864
No 64
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=58.81 E-value=17 Score=37.56 Aligned_cols=46 Identities=20% Similarity=0.200 Sum_probs=38.6
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 567 ASALLLFNSSD-RLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 567 ~~iLllFn~~~-~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+.||.+|.++. .+|..||++.+|++...+.+.|..|. ..++|.+.+
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 45778887654 59999999999999999999999997 467887764
No 65
>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=57.37 E-value=4 Score=32.48 Aligned_cols=51 Identities=12% Similarity=0.271 Sum_probs=36.4
Q ss_pred ecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeec
Q 004841 669 RIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYL 727 (728)
Q Consensus 669 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yi 727 (728)
..|-..+.++..+|... ...+...+-+.++.|.++|+++|.+.++..|..+
T Consensus 15 ~~Ll~~~~~t~~eIa~~--------l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 15 LALLKNGPATAEEIAEE--------LGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHCHEEHHHHHHH--------HTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHcCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 33335566666666552 2456788999999999999999998765555544
No 66
>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=56.26 E-value=23 Score=36.19 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=37.2
Q ss_pred HHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 567 ASALLLFNS-SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 567 ~~iLllFn~-~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|.. .+.|.+
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 467888986 45899999999999999999999999974 566754
No 67
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=55.60 E-value=26 Score=31.77 Aligned_cols=44 Identities=27% Similarity=0.289 Sum_probs=34.5
Q ss_pred HHHHHhhc--CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 567 ASALLLFN--SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 567 ~~iLllFn--~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
..+|..+. ..+.+|+.||++.+|+|...+.+.|..|. +.+++..
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 34444443 33579999999999999999999999997 4677764
No 68
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.30 E-value=10 Score=30.32 Aligned_cols=53 Identities=11% Similarity=0.197 Sum_probs=39.8
Q ss_pred hheeeeccccccc--CChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCce
Q 004841 664 DASIVRIMKSRKV--LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMF 724 (728)
Q Consensus 664 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y 724 (728)
+..|...|+.++. ++-.+|-.+ ...+...+.+.+..|.++|||.+++..+..|
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 3456677888766 887766652 3456678999999999999999987664554
No 69
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=55.21 E-value=22 Score=31.77 Aligned_cols=59 Identities=22% Similarity=0.305 Sum_probs=43.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEec
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNS 629 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~ 629 (728)
.-..||.+.-+.++.++.||++.+|++...+-++|.-|. ..+++.....|. .-.|++|.
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 334455555445679999999999999999999999996 467887655432 23477765
No 70
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=54.91 E-value=16 Score=28.86 Aligned_cols=38 Identities=26% Similarity=0.268 Sum_probs=32.8
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004841 567 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 604 (728)
Q Consensus 567 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 604 (728)
..|--+.++...+|+.+|++.|++++.++..+|-.|..
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 45667788888999999999999999999999999974
No 71
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=54.68 E-value=20 Score=31.15 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=37.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
..-.||..+......|+.+|++.+|++...+.+.+..|.. .+++.
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 3456777787778899999999999999999999999973 46665
No 72
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=54.33 E-value=23 Score=31.11 Aligned_cols=51 Identities=24% Similarity=0.347 Sum_probs=43.2
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+++.|+.+|......+..+..+|++.++++...+.+.+..|. +.+++.+.+
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 788899999888777766669999999999999999999997 567777654
No 73
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=54.07 E-value=17 Score=36.23 Aligned_cols=42 Identities=26% Similarity=0.311 Sum_probs=35.1
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 568 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 568 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
.||.+.+...++|.+||++.+|++...++++|..|.. -+++.
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~--~Glv~ 56 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--EGLVE 56 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHh--Cccee
Confidence 4666677788999999999999999999999999973 34444
No 74
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=53.53 E-value=24 Score=26.69 Aligned_cols=36 Identities=22% Similarity=0.268 Sum_probs=30.2
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 576 SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 576 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
.++.|..+|++.+|++...+.+.|..|.. .+++...
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 75
>PF13730 HTH_36: Helix-turn-helix domain
Probab=50.82 E-value=37 Score=25.36 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=22.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 580 SYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 580 t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
|.+.|++.+|++...+.+++..|.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 899999999999999999999986
No 76
>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=50.67 E-value=30 Score=26.83 Aligned_cols=44 Identities=20% Similarity=0.314 Sum_probs=34.2
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 569 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 569 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
|..+-.+...++..+|++.+|+++..+...+..|. +.+++...|
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEecC
Confidence 44444577899999999999999999999999997 456766543
No 77
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=49.71 E-value=44 Score=30.84 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=33.2
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 573 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 573 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+.....+|..+|++.+|+|...+.+.|..|. +.+++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEec
Confidence 4444578999999999999999999999997 567887554
No 78
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=49.19 E-value=15 Score=27.95 Aligned_cols=44 Identities=9% Similarity=0.138 Sum_probs=31.1
Q ss_pred ecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCC
Q 004841 669 RIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNP 721 (728)
Q Consensus 669 RimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~ 721 (728)
+.+. .+.++..++... +..+...+.+.|+.|.++|++.+..+.+
T Consensus 4 ~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~~ 47 (66)
T smart00418 4 KLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREGK 47 (66)
T ss_pred HHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence 3444 556666665542 3457788999999999999999876433
No 79
>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=46.88 E-value=7.5 Score=37.81 Aligned_cols=57 Identities=19% Similarity=0.290 Sum_probs=40.0
Q ss_pred hheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 664 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 664 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
-...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.=--+|++.|+||.
T Consensus 101 L~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 344457889999999888765 588899999999999999999988888899999984
No 80
>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=46.67 E-value=46 Score=24.40 Aligned_cols=33 Identities=27% Similarity=0.392 Sum_probs=24.1
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004841 567 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 601 (728)
Q Consensus 567 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 601 (728)
..|-+.| ...+|++||++.+|++...+.+....
T Consensus 11 ~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 11 EVIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3444556 45789999999999999988776543
No 81
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=46.60 E-value=25 Score=27.50 Aligned_cols=34 Identities=29% Similarity=0.352 Sum_probs=26.2
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccc
Q 004841 575 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKIL 610 (728)
Q Consensus 575 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL 610 (728)
.++..|+.+|.+.|++|.+.++.+|-.|.. .+++
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 346889999999999999999999999973 4554
No 82
>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=46.21 E-value=16 Score=31.82 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=30.6
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
.+.|+..+..++.++-++|++.+|++..++++.|..|.. .+++.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~--~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYE--DGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHH--HSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeE
Confidence 456666666667899999999999999999999999974 45553
No 83
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=45.24 E-value=49 Score=31.81 Aligned_cols=52 Identities=19% Similarity=0.175 Sum_probs=39.2
Q ss_pred EEcHHHHHHHHhhcCCCC-cCHHHHHHHh--CCCHHHHHHHHHHhhhccccccccCC
Q 004841 561 IVTTYQASALLLFNSSDR-LSYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~~~~-~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
--+.+..+|+-+..-.+. -+.++|++.+ +++.++++.+|..|. +.++|.+..
T Consensus 21 ~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~~ 75 (171)
T PF14394_consen 21 YSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKDG 75 (171)
T ss_pred HhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEECC
Confidence 334455556555543332 3899999999 999999999999997 689998864
No 84
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=44.14 E-value=37 Score=26.87 Aligned_cols=24 Identities=17% Similarity=0.494 Sum_probs=21.0
Q ss_pred ChhHHHHHHHhhhhhhhcccCCCC
Q 004841 697 DFKAIKKRIEDLITRDYLERDKSN 720 (728)
Q Consensus 697 ~~~~ik~~Ie~LIereyi~R~~~d 720 (728)
|+.-+...++.|.++|||+|+++-
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 577788999999999999999853
No 85
>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=42.99 E-value=38 Score=26.26 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=30.4
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 577 DRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 577 ~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
..+|..+|++.+|++...+.+.|..|. +.+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~--~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELE--EEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEec
Confidence 479999999999999999999999997 45777654
No 86
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=42.08 E-value=31 Score=35.46 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
-|-.|+-+.++++.++++||++.+|+++..++|=|..|. +.++|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 356788889999999999999999999999999999997 45677664
No 87
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=42.05 E-value=30 Score=35.64 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=40.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
-|..|+-+.++++.+++.||++.+|++...++|-|..|. +.++|.+.
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 467788889999999999999999999999999999996 45666654
No 88
>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=41.78 E-value=26 Score=34.04 Aligned_cols=27 Identities=19% Similarity=0.428 Sum_probs=22.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 577 DRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 577 ~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
..+|+++|++.||+..+++..+|+.|-
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 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=41.51 E-value=45 Score=24.80 Aligned_cols=37 Identities=32% Similarity=0.383 Sum_probs=21.9
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 600 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 600 (728)
|.-+-.++.+.- -+.+|+.||++.+|++...+...+.
T Consensus 12 ~~~~r~i~~l~~-~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 12 PERQREIFLLRY-FQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp -HHHHHHHHHHH-TS---HHHHHHHCTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHH-HHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 333444443322 2468999999999999999887664
No 90
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=40.85 E-value=43 Score=24.16 Aligned_cols=31 Identities=29% Similarity=0.408 Sum_probs=21.6
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 004841 568 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 600 (728)
Q Consensus 568 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 600 (728)
.|+-++.+. +|+.+|++.+|++...+.+.|.
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 344555554 8999999999999999988764
No 91
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.72 E-value=55 Score=24.02 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=29.8
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
|.-+..++.++. ..+|..+|++.+|++...+.+.+..+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 455555665553 357999999999999999998887664
No 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=40.67 E-value=29 Score=30.61 Aligned_cols=57 Identities=11% Similarity=0.097 Sum_probs=42.2
Q ss_pred eeecccc-cccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceee
Q 004841 667 IVRIMKS-RKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 726 (728)
Q Consensus 667 IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 726 (728)
|..+|.. .+.++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 4444544 56799999999887642 457889999999999999999997543333444
No 93
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.27 E-value=40 Score=32.67 Aligned_cols=44 Identities=16% Similarity=0.154 Sum_probs=36.1
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
...||.+.-.+..+|-++|++.+|++...++++|..|.. .+++.
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 455666666667899999999999999999999999974 45655
No 94
>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=40.26 E-value=48 Score=31.37 Aligned_cols=43 Identities=16% Similarity=0.192 Sum_probs=34.6
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 567 ASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 567 ~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
..|+..+-.+..+|-+||+..+|++..++++.|..|.. .+++.
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 44555454566899999999999999999999999974 46664
No 95
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=39.78 E-value=60 Score=32.06 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=35.2
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 568 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 568 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
.||......+.+|..+|++.+|++...+.++|..|. +.+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le--~~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLE--TEGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEe
Confidence 455444445679999999999999999999999997 45777654
No 96
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=39.40 E-value=72 Score=26.18 Aligned_cols=38 Identities=13% Similarity=0.224 Sum_probs=28.1
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
.-.+|-+.-...++|..+|+..+|.+.+++...|..+.
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 44566677788999999999999999999999998774
No 97
>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=39.15 E-value=61 Score=23.86 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=28.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
|..|..++.++- ..+|..+|++.+|++...+...+..+.
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555554443 467999999999999999888877653
No 98
>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=39.14 E-value=67 Score=25.96 Aligned_cols=47 Identities=19% Similarity=0.175 Sum_probs=39.1
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccc
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKI 609 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~ki 609 (728)
.+=|+.++-++...+.-|+++|++.||-....++-.|..+...|.++
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 45689999888888899999999999999999999888886434344
No 99
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=39.03 E-value=65 Score=24.64 Aligned_cols=38 Identities=26% Similarity=0.393 Sum_probs=29.5
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 574 NSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 574 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
.....+ |..+|++.+|++...+.++|..|.. .+++...
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 333344 4999999999999999999999974 5677544
No 100
>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=38.97 E-value=32 Score=27.37 Aligned_cols=33 Identities=21% Similarity=0.373 Sum_probs=26.3
Q ss_pred hhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhh
Q 004841 572 LFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSC 604 (728)
Q Consensus 572 lFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~ 604 (728)
...++..+|+.||+..++++.+.+...|..|..
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 344667899999999999999999999999974
No 101
>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=38.37 E-value=13 Score=27.02 Aligned_cols=44 Identities=9% Similarity=0.258 Sum_probs=32.3
Q ss_pred hheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcc
Q 004841 664 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLE 715 (728)
Q Consensus 664 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~ 715 (728)
+-.|+..+.....++..+|-.. +..+.+.+.+.+..|.++|||+
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 3445666777777888777663 3467889999999999999985
No 102
>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=36.92 E-value=29 Score=37.17 Aligned_cols=143 Identities=13% Similarity=0.167 Sum_probs=39.3
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCCCCCcce
Q 004841 561 IVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFTDKMRRI 638 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~~~~~~i 638 (728)
.++..+..|.-+..+ ...+-..+|...||++...+.++|.+|.. | ++++... +.+.+++|+
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 556778877777654 45788999999999999999999999975 2 4544321 122333333
Q ss_pred eccCC--ChhhhhH----HHHhHHHhhhhhhhheeeeccccccc-----------------------------CChhHHH
Q 004841 639 KIPLP--PVDEKKK----VIEDVDKDRRYAIDASIVRIMKSRKV-----------------------------LGHQQLV 683 (728)
Q Consensus 639 ~i~~~--~~~e~~~----~~~~v~~~R~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 683 (728)
-+-.. +..|-.. +..+.+.+=-..+...|.+.+.++.. .+.+++.
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 32110 0000000 01222223333444455555555444 4444555
Q ss_pred HHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCC
Q 004841 684 LECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSN 720 (728)
Q Consensus 684 ~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d 720 (728)
..+.+.=-..-..+.++|..-++.||=.|-|++-...
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 4444331112346788999999999999988886543
No 103
>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=36.85 E-value=5.5e+02 Score=27.43 Aligned_cols=163 Identities=14% Similarity=0.258 Sum_probs=87.7
Q ss_pred hhhhhhhcCcHHHHHHHHHhhccC---CCChHhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHH
Q 004841 257 GCHALLRDDKVEDLSRMFRLFSKI---PRGLDPVSNIFKQHVTAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVI 333 (728)
Q Consensus 257 ~~~~ll~~~~~~~L~~ly~L~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ll 333 (728)
.|..-.+.++.+.+.+.++||-.+ +.|++...+.+.+.|.......+......... +..+.-|+..|.
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~---------~~~~~~~~~~lt 85 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSD---------SRSPVFYADALT 85 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc---------ccccccHHHHHH
Confidence 466777888999999999988665 35666666666666665555555433211100 123445666666
Q ss_pred HHHHHHHH-------HHHHhcCCChhH--HHHH----HH----HHHHHhcCCCCCCCcHHHHHHHHHHHhcc--------
Q 004841 334 ELHDKYLA-------YVNDCFQNHTLF--HKSL----KE----AFEVFCNKGVAGSSSAELLATFCDNILKK-------- 388 (728)
Q Consensus 334 ~l~~~~~~-------li~~~F~~~~~f--~~~l----~~----af~~~~N~~~~~~~~~e~La~y~d~~lk~-------- 388 (728)
.+++..-. +|..+|+..... ...+ +. -+..|..... -.+....+..|-...+.+
T Consensus 86 ~LFe~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~ 164 (331)
T PF08318_consen 86 KLFEHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERR-LDRKLQDIQSYNFSFLVKNSGRSSSS 164 (331)
T ss_pred HHHHHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-HHHHHHHHHhhhhhhhcccccccccc
Confidence 66666544 566788865422 1111 11 1222222210 001112233343333322
Q ss_pred ---------CCCCCCChHHHHHHHHHHhhhhccccChHHHHHHHHHHHHHHhcCCCC
Q 004841 389 ---------GGSEKLSDEAIEEMLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDKS 436 (728)
Q Consensus 389 ---------~~~~~~~~~~~~~~l~~i~~lf~~l~~KD~F~~~Y~~~La~RLL~~~s 436 (728)
+.....+.-+++..|+.+..++.. ...|.++++.|.-....
T Consensus 165 ~~~~~~~~~~~~~~~d~reld~lL~Eis~i~~~-------w~lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 165 SSRAASSSQSEDEGIDPRELDALLNEISLILQR-------WSLYCRFISRKWNEFSD 214 (331)
T ss_pred ccccccccccccCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcccc
Confidence 001233455788888888777644 34799999999877543
No 104
>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=36.67 E-value=54 Score=27.17 Aligned_cols=35 Identities=9% Similarity=-0.007 Sum_probs=30.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLH 600 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~ 600 (728)
-++.|+-...+ ..+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 46778888888 899999999999999999988664
No 105
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=36.62 E-value=50 Score=33.90 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=40.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
-|..|+..++++..+++.||++.+|++...++|-|..|. +.+++.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~~ 53 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEec
Confidence 466788889999999999999999999999999999986 346666543
No 106
>PRK00215 LexA repressor; Validated
Probab=36.35 E-value=68 Score=31.63 Aligned_cols=52 Identities=25% Similarity=0.306 Sum_probs=40.4
Q ss_pred EcHHHHHHHHhhc-----CCCCcCHHHHHHHhCC-CHHHHHHHHHHhhhccccccccCCC
Q 004841 562 VTTYQASALLLFN-----SSDRLSYSEIMTQLNL-SDDDVVRLLHSLSCAKYKILNKEPN 615 (728)
Q Consensus 562 vs~~Q~~iLllFn-----~~~~~t~~ei~~~t~i-~~~~l~~~L~~L~~~k~kiL~~~~~ 615 (728)
++.-|..||..+. .....|..||++.+|+ +...+.+.|..|. +.+.+.+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~--~~g~i~~~~~ 59 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE--RKGFIRRDPG 59 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH--HCCCEEeCCC
Confidence 3567888886654 2346899999999999 9999999999997 4567766543
No 107
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=35.99 E-value=15 Score=28.16 Aligned_cols=26 Identities=12% Similarity=0.308 Sum_probs=21.0
Q ss_pred CCCChhHHHHHHHhhhhhhhcccCCC
Q 004841 694 FKPDFKAIKKRIEDLITRDYLERDKS 719 (728)
Q Consensus 694 F~~~~~~ik~~Ie~LIereyi~R~~~ 719 (728)
+..+.+.+.+.|..|+++|||+|..+
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 44577889999999999999999754
No 108
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=35.63 E-value=19 Score=31.36 Aligned_cols=47 Identities=13% Similarity=0.197 Sum_probs=38.3
Q ss_pred hhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccC
Q 004841 663 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERD 717 (728)
Q Consensus 663 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~ 717 (728)
+|-.|++.+.....++..+|-.. +..+...+.+++..|.++|+|+|-
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 45567788888888888887763 467889999999999999999953
No 109
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=34.55 E-value=1.1e+02 Score=27.75 Aligned_cols=67 Identities=18% Similarity=0.232 Sum_probs=48.7
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCC---CCeEEEecCCC
Q 004841 564 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISP---TDHFEFNSKFT 632 (728)
Q Consensus 564 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~---~~~~~~N~~F~ 632 (728)
+--..+|-+..+++..|+.|+++.+|-+.+.+.+.|..|. .++++..+.+|+...+ -+.+.++-.|.
T Consensus 64 p~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 64 PRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred hhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 3344556677788899999999999999999999999997 5788876655544332 24455555554
No 110
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=33.67 E-value=57 Score=21.89 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=20.7
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 578 RLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 578 ~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
.+|-+||++.+|++.+.+-|.|..|.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36789999999999999999998875
No 111
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.59 E-value=60 Score=30.81 Aligned_cols=48 Identities=15% Similarity=0.208 Sum_probs=40.5
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
+.-.-..||..+.+....|+.+|++.+|++...+.+-++.|.. .+++.
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 4456677888888889999999999999999999999999973 45654
No 112
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=33.33 E-value=63 Score=24.52 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=31.7
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
.|.-+..||.++.. +.+..+|++.+|+++..+..++..+.
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHH
Confidence 35567777877765 56899999999999999999998886
No 113
>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=33.04 E-value=56 Score=25.82 Aligned_cols=51 Identities=24% Similarity=0.324 Sum_probs=34.9
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHHHhhhccccccccCC
Q 004841 562 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 562 vs~~Q~~iLllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+|.-|.-||...-+ .-+-|+.||++.+|+. ...+..+|..|. +-+.|.+.|
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 35567777655432 2356999999999997 899999999997 457777654
No 114
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=32.83 E-value=22 Score=25.96 Aligned_cols=43 Identities=12% Similarity=0.201 Sum_probs=32.0
Q ss_pred eecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004841 668 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 718 (728)
Q Consensus 668 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 718 (728)
.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..
T Consensus 6 l~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 6 LELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEee
Confidence 334444556766666663 4668888999999999999999865
No 115
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=32.81 E-value=48 Score=32.28 Aligned_cols=46 Identities=11% Similarity=0.065 Sum_probs=38.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
-+..|+.+.+.+..+++.+|++.+|++...++|-|..|.. .+++.+
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 5677888899999999999999999999999999999973 344443
No 116
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=32.73 E-value=1.1e+02 Score=25.20 Aligned_cols=41 Identities=20% Similarity=0.236 Sum_probs=32.1
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 571 LLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 571 llFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
+..++.+.+|-++|++.+|++...+-++++.|-...+.|..
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 34456668999999999999999999999999643444443
No 117
>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=32.42 E-value=14 Score=28.15 Aligned_cols=43 Identities=16% Similarity=0.291 Sum_probs=29.8
Q ss_pred eecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004841 668 VRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 718 (728)
Q Consensus 668 VRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 718 (728)
..++-..+.++..+|-. .+..+...+-+.+..|..+|||+|..
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 33344455555555544 34568889999999999999999864
No 118
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.70 E-value=30 Score=26.00 Aligned_cols=28 Identities=7% Similarity=0.177 Sum_probs=24.5
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCCC
Q 004841 692 RMFKPDFKAIKKRIEDLITRDYLERDKS 719 (728)
Q Consensus 692 ~~F~~~~~~ik~~Ie~LIereyi~R~~~ 719 (728)
.+|..+...+.+.+..|.+.|+|.+.++
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
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=31.68 E-value=75 Score=30.77 Aligned_cols=63 Identities=19% Similarity=0.188 Sum_probs=47.6
Q ss_pred ceEEeccCCceEEEEeEEcCeeEEEEEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 536 RKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 536 R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
|.-.|.+.+|..+++- .+.| .||+.||.-|+.-.. -..||.+-|++..+++.+++...|..+.
T Consensus 97 r~~~~~~~fg~~ep~~-vPkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 97 RDTIPDFEFGFYEPEK-VPKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCcccccccccCccc-CCCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 4445788888888763 3344 567889977765332 2489999999999999999998888775
No 120
>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=30.65 E-value=80 Score=23.89 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=24.6
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 573 FNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 573 Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
|+.-...|.+||++.+|++...+-.+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555568999999999999999888777643
No 121
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=30.55 E-value=75 Score=29.77 Aligned_cols=48 Identities=15% Similarity=0.243 Sum_probs=40.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccc
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILN 611 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~ 611 (728)
++..--.||.++..+...|+.+|++.+|++...+.+-+..|.. .+++.
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 122
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=30.41 E-value=72 Score=31.86 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=40.9
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 563 TTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 563 s~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
|..-..||-+......+.+.||++.+|+|...+..++..|. +.+++..+
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 44555688888888899999999999999999999999996 56777643
No 123
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=30.21 E-value=62 Score=33.58 Aligned_cols=48 Identities=8% Similarity=0.049 Sum_probs=40.7
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 564 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 564 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
--|..|+.+.+.+..+++.||++.+|++...++|-|..|.. .+++.+.
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 45778888999998999999999999999999999999953 4566554
No 124
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=30.20 E-value=68 Score=32.89 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=36.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
-|..|+.+.+.+..+++.+|++.+|+++..++|-|..|.
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 477899999999999999999999999999999999885
No 125
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=30.11 E-value=74 Score=30.27 Aligned_cols=50 Identities=30% Similarity=0.391 Sum_probs=37.3
Q ss_pred cCCCceEEeccCCceEEEEeEEcCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 532 KTKHRKLTWIYSLGTCNLLGKFESRTTELIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 532 ~~~~R~L~w~~~lg~~~i~~~~~~~~~~l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
+++.+.|+|.++|-. -|.+ +.- +....|+++|++.+|.++..++++|..=
T Consensus 36 ~~~~~~lTWvdSLav-------------------AAga-~ar-ekag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 36 KDPYERLTWVDSLAV-------------------AAGA-LAR-EKAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred hCcccccchhhHHHH-------------------HHHH-HHH-HHccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 568899999876531 2222 222 4458899999999999999999998754
No 126
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=30.09 E-value=30 Score=34.89 Aligned_cols=33 Identities=9% Similarity=0.239 Sum_probs=28.5
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004841 692 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 725 (728)
Q Consensus 692 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 725 (728)
.+|..+...+.++|+.|++.|+|.|..+ +++|+
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 4799999999999999999999999874 45654
No 127
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=29.94 E-value=64 Score=35.05 Aligned_cols=65 Identities=20% Similarity=0.264 Sum_probs=41.0
Q ss_pred eEEeccCCceEEEEeEEcCeeEEEEE-------cHHHHHHHHhhcC-C-CCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 537 KLTWIYSLGTCNLLGKFESRTTELIV-------TTYQASALLLFNS-S-DRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 537 ~L~w~~~lg~~~i~~~~~~~~~~l~v-------s~~Q~~iLllFn~-~-~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
-+.+.+.||..|=++--+. +-|+= +-+-..||-++-+ + ..+|+++|++.|||..+++..+|++|-
T Consensus 281 LIdFSYeLSr~E~~~GsPE--KPLSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 281 LIDFSYELSRREGKIGSPE--KPLSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred hhhhhhhhhcccCcCCCCC--CCcchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 3567788887665542222 22211 2233334433332 2 239999999999999999999999983
No 128
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=29.80 E-value=67 Score=32.98 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=39.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
-+..|+.+.+++..+++.||++.++++...++|-|..|.. .++|.+.
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 4567788888889999999999999999999999999973 4666664
No 129
>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=29.58 E-value=28 Score=27.57 Aligned_cols=54 Identities=24% Similarity=0.202 Sum_probs=31.7
Q ss_pred hheeeecccccc-cCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 664 DASIVRIMKSRK-VLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 664 ~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
=|.||.-||++. .++.+||..++ + +..+ ++.++.|-+.+=|+-|++ .++|.|.|
T Consensus 7 l~~~VeymK~r~~Plt~~eI~d~l----~--~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 7 LAKAVEYMKKRDHPLTLEEILDYL----S--LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHH-S-B-HHHHHHHH----T--SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHH----c--CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 367888899875 57777777654 3 4333 345566668888999874 47999975
No 130
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=29.13 E-value=3.2e+02 Score=25.97 Aligned_cols=59 Identities=22% Similarity=0.259 Sum_probs=41.9
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHh--CCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecC
Q 004841 566 QASALLLFNSS-DRLSYSEIMTQL--NLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSK 630 (728)
Q Consensus 566 Q~~iLllFn~~-~~~t~~ei~~~t--~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~ 630 (728)
...|+-.|..+ .++|..+|...+ +++...+.++|..|+. +-+|..|. +...-+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~-~g~i~~K~-----~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVE-EGKIVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHh-CCCeeeee-----ecceEEEeeCcc
Confidence 34566666654 599999999998 5899999999999985 34555543 222456777754
No 131
>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=28.29 E-value=1.2e+02 Score=21.65 Aligned_cols=40 Identities=30% Similarity=0.385 Sum_probs=28.6
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
++..+..++.++- ...+|..+|++.+|++...+.+.+...
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3455555554443 246799999999999999988877653
No 132
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.79 E-value=96 Score=28.73 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=40.2
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 562 VTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 562 vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
+.-.-.-||..+.+....++.+|++.+|++...+.+.+..|. +.+++..
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 344566788888888889999999999999999999999996 4566653
No 133
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=27.62 E-value=35 Score=34.63 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=28.1
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004841 692 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 725 (728)
Q Consensus 692 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 725 (728)
..|..+...++++|+.|++.|+|.|..+ +++|+
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 3688999999999999999999999864 55654
No 134
>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=27.45 E-value=64 Score=31.62 Aligned_cols=51 Identities=22% Similarity=0.277 Sum_probs=40.4
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHHHhhhccccccccCC
Q 004841 562 VTTYQASALLLFNS-----SDRLSYSEIMTQLNLS-DDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 562 vs~~Q~~iLllFn~-----~~~~t~~ei~~~t~i~-~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|. +.++|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecCC
Confidence 46788888876653 2358899999999999 999999999997 457777653
No 135
>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=27.43 E-value=1.1e+03 Score=28.08 Aligned_cols=122 Identities=11% Similarity=0.265 Sum_probs=61.3
Q ss_pred CChhHHHHHHHHHHHHHHHHHchhcCCCcHHHHHHHHHHHHHHHHHHHHHHh-chhhhhhhhhcCcHHHHHHHHHhh--c
Q 004841 202 DSCPDYMLKAEECLKREKDRVSHYLHSSSEPKLLEKVQHELLSVYANQLLEK-EHSGCHALLRDDKVEDLSRMFRLF--S 278 (728)
Q Consensus 202 ~s~~~Yl~~v~~~l~eE~~r~~~yL~~~t~~kl~~~l~~~LI~~~~~~ll~~-~~s~~~~ll~~~~~~~L~~ly~L~--~ 278 (728)
..+..+.+.|...++++.+..-..+-...-+||.+-++. ++.++.. ..+.+.... ......|+.+-.-| +
T Consensus 570 ~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~~g------ve~l~~~~~~~ei~~~~-~ySk~~l~kvl~~y~~k 642 (701)
T PF09763_consen 570 SVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFFEG------VEALLQTVSPEEISYQA-AYSKQELKKVLKSYPSK 642 (701)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHH------HHHHHhccCchhcccch-hccHHHHHHHHHhCChH
Confidence 455677777777777777655443333344444433221 1112111 001111111 11234555554443 2
Q ss_pred cCCCChHhHHHHHHHHH-------HHHHHHHHHHHHHHhhhhhhhhccccccchHHHHHHHHHHHHHHHHHHHHhcCC
Q 004841 279 KIPRGLDPVSNIFKQHV-------TAEGTALVKLAEDAASNKKAEKRDVVGLQEQVFVRKVIELHDKYLAYVNDCFQN 349 (728)
Q Consensus 279 ~~~~~l~~l~~~~~~~i-------~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ll~l~~~~~~li~~~F~~ 349 (728)
.+..|++.|.+.+.+|+ ...+ .++... =..+-+..+..|.++..|+..|+.|
T Consensus 643 ev~k~i~~l~krveKHf~~~~~~~~~~~-~Ll~~v------------------W~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 643 EVRKGIEALYKRVEKHFSRDADDPSFEE-DLLQVV------------------WSAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHcCCccccccchh-hHHHHH------------------HHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 23456666666666666 1111 122111 1234467889999999999999875
No 136
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.30 E-value=71 Score=29.81 Aligned_cols=31 Identities=10% Similarity=0.174 Sum_probs=27.5
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHHhhhc
Q 004841 575 SSDRLSYSEIMTQLNLSDDDVVRLLHSLSCA 605 (728)
Q Consensus 575 ~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~ 605 (728)
.++.+|-++|++.+|++...+++.|..|...
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed 42 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDE 42 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhh
Confidence 3457999999999999999999999999753
No 137
>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=27.22 E-value=31 Score=26.93 Aligned_cols=28 Identities=11% Similarity=0.254 Sum_probs=24.2
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCCC
Q 004841 692 RMFKPDFKAIKKRIEDLITRDYLERDKS 719 (728)
Q Consensus 692 ~~F~~~~~~ik~~Ie~LIereyi~R~~~ 719 (728)
++|..+...+.+++..|.+.|+|.+.+.
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 3688899999999999999999999874
No 138
>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=27.13 E-value=73 Score=28.70 Aligned_cols=38 Identities=11% Similarity=0.119 Sum_probs=32.3
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 574 NSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 574 n~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
++.-+.|.++||..++-+.+.++.+|..|. +.+++...
T Consensus 49 ~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~--k~glIe~~ 86 (121)
T PF09681_consen 49 SGNIPYTAEMLALEFDRPVDTVRLALAVFQ--KLGLIEID 86 (121)
T ss_pred CCCCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 344589999999999999999999999996 67787653
No 139
>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=26.97 E-value=44 Score=29.30 Aligned_cols=41 Identities=17% Similarity=0.266 Sum_probs=30.1
Q ss_pred ccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhccc--CCCCC
Q 004841 673 SRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER--DKSNP 721 (728)
Q Consensus 673 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R--~~~d~ 721 (728)
..+.++..+|.. ....+...+-+.|..|.++|||.| ++.|+
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 345666666665 344567889999999999999997 45554
No 140
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=26.77 E-value=97 Score=32.19 Aligned_cols=38 Identities=18% Similarity=0.297 Sum_probs=30.3
Q ss_pred HHHHHHHhhc-CCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 565 YQASALLLFN-SSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 565 ~Q~~iLllFn-~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
+...|+-.+. ....+|+++|+..|||..+++..+|+.|
T Consensus 209 W~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 209 WTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 3445554443 3568999999999999999999999987
No 141
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=26.74 E-value=88 Score=35.59 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=43.4
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 561 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
.+|..|..||......+.+|..+|++.+|++...+.+.+.+|.. .+++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~--kGlV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEE--KGLVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHh--CCCEEE
Confidence 46789999999998888999999999999999999999999973 356554
No 142
>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=26.55 E-value=92 Score=27.96 Aligned_cols=48 Identities=19% Similarity=0.225 Sum_probs=37.2
Q ss_pred HHHHHHHHhhcC--------CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccC
Q 004841 564 TYQASALLLFNS--------SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 564 ~~Q~~iLllFn~--------~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
.+.-..|+..|. .-+.+.++|+..++-+.+.++.+|..|. +++++...
T Consensus 29 I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~--k~glIe~~ 84 (119)
T TIGR01714 29 IWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLE--SLGLIEKK 84 (119)
T ss_pred HHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 445555555554 3489999999999999999999999996 67887653
No 143
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=26.27 E-value=92 Score=31.71 Aligned_cols=46 Identities=22% Similarity=0.250 Sum_probs=37.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
-|..|+..++++..++.+||++.+|++...+++-|..|.. .+.|.+
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~--~~~l~r 50 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQT--QGKILR 50 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEE
Confidence 3566888888888999999999999999999999999863 234444
No 144
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=26.17 E-value=47 Score=27.86 Aligned_cols=37 Identities=19% Similarity=0.179 Sum_probs=32.9
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 692 RMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 692 ~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
.++..+.+.-++.|..|.++|.|..-..++..-.|.|
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 3688888999999999999999998888888999976
No 145
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=26.13 E-value=1.3e+02 Score=29.15 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=35.3
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 569 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 569 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
++.-.+.++..|..+|+..+|++..++.++|-.|. +.+.+...+
T Consensus 18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~~ 61 (183)
T PHA03103 18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMSD 61 (183)
T ss_pred HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecCC
Confidence 45556677889999999999999999999999997 345555443
No 146
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=25.91 E-value=94 Score=21.75 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.2
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 576 SDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 576 ~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
...+|+++|++..|++...+.+......
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4579999999999999998888776553
No 147
>PRK13239 alkylmercury lyase; Provisional
Probab=25.87 E-value=1.2e+02 Score=30.18 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=34.8
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhh
Q 004841 564 TYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLS 603 (728)
Q Consensus 564 ~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~ 603 (728)
.+...||.++-++...|+.+|++.+|.+.+.+.+.|..|.
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
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=25.80 E-value=40 Score=34.23 Aligned_cols=48 Identities=13% Similarity=0.366 Sum_probs=35.3
Q ss_pred cccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004841 670 IMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 725 (728)
Q Consensus 670 imK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 725 (728)
.++....|.-+ .+|...|..+...|+++|+.|++.|+|.|..+ +++|+
T Consensus 28 ~~~~G~~LPsE-------~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 28 HYRCGDYLPAE-------QQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred ccCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 45655555533 23334799999999999999999999999875 45654
No 149
>PHA02591 hypothetical protein; Provisional
Probab=25.76 E-value=83 Score=25.73 Aligned_cols=25 Identities=28% Similarity=0.333 Sum_probs=22.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHH
Q 004841 577 DRLSYSEIMTQLNLSDDDVVRLLHS 601 (728)
Q Consensus 577 ~~~t~~ei~~~t~i~~~~l~~~L~~ 601 (728)
..+|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3789999999999999999988765
No 150
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.61 E-value=72 Score=23.20 Aligned_cols=32 Identities=25% Similarity=0.340 Sum_probs=21.2
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 569 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 569 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
++.++.+ .+|..+|++.+|++...+.+-+..+
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4444544 7899999999999999888766554
No 151
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=25.56 E-value=4.9e+02 Score=23.24 Aligned_cols=59 Identities=12% Similarity=0.387 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHHHHHhcCCcCCHH-HHHHHHHHHHHhcc---------CchhchHHHHHHHHHHHHHHH
Q 004841 132 NGKVRDAVITLIDQEREGEQIDRA-LLKNVLDIFVEIGM---------GQMDYYENDFETAMLKDTAAY 190 (728)
Q Consensus 132 ~~~l~~~ll~~I~~~R~g~~id~~-~l~~~i~ml~~l~~---------~~~~~Y~~~FE~~~L~~t~~y 190 (728)
+.++.+.|-+++++.|..+.-+.+ -+.++..||.+||. ....+-+..|-+.+|+.+..=
T Consensus 2 s~~v~e~I~~iVe~RrqEGA~~~Dvs~SSv~sMLLELGLRVYeaQ~erkes~Fnq~eFnK~lLE~v~kt 70 (118)
T PRK13713 2 SNEVYEKINAIVEERRQEGAREKDVSFSSVASMLLELGLRVYEAQMERKESGFNQTEFNKLLLECVVKT 70 (118)
T ss_pred chHHHHHHHHHHHHHHHcCCCccCccHHHHHHHHHHHhHHHHHHHHHhhcCcccHHHHHHHHHHHHHHH
Confidence 455667778888888866653322 37889999999994 223455667778888776543
No 152
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.22 E-value=54 Score=32.83 Aligned_cols=54 Identities=22% Similarity=0.332 Sum_probs=44.3
Q ss_pred eeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceeecC
Q 004841 667 IVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRYLA 728 (728)
Q Consensus 667 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Yia 728 (728)
-|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.-.-+|++.|+||.
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 345667788887777765 577777788889999999999999889999999984
No 153
>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=24.99 E-value=41 Score=33.91 Aligned_cols=32 Identities=19% Similarity=0.400 Sum_probs=27.9
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004841 693 MFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 725 (728)
Q Consensus 693 ~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 725 (728)
+|..+...+.++|+.|.+.|||.|..+ +++|+
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 699999999999999999999999864 45654
No 154
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.73 E-value=42 Score=25.06 Aligned_cols=21 Identities=10% Similarity=0.336 Sum_probs=18.2
Q ss_pred CCCChhHHHHHHHhhhhhhhc
Q 004841 694 FKPDFKAIKKRIEDLITRDYL 714 (728)
Q Consensus 694 F~~~~~~ik~~Ie~LIereyi 714 (728)
...+...|.+.|..|.++|||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcCC
Confidence 456788899999999999987
No 155
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.38 E-value=48 Score=30.53 Aligned_cols=30 Identities=10% Similarity=0.265 Sum_probs=23.9
Q ss_pred CCCCChhHHHHHHHhhhhhhhcccCC--CCCC
Q 004841 693 MFKPDFKAIKKRIEDLITRDYLERDK--SNPN 722 (728)
Q Consensus 693 ~F~~~~~~ik~~Ie~LIereyi~R~~--~d~~ 722 (728)
.+..+.+.+.+.|+.|.++|||+|.. +|+.
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR 86 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQTCASDRR 86 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeecCCCCcC
Confidence 45567778999999999999999964 4543
No 156
>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=23.59 E-value=52 Score=25.17 Aligned_cols=27 Identities=11% Similarity=0.241 Sum_probs=23.7
Q ss_pred CCCCCChhHHHHHHHhhhhhhhcccCC
Q 004841 692 RMFKPDFKAIKKRIEDLITRDYLERDK 718 (728)
Q Consensus 692 ~~F~~~~~~ik~~Ie~LIereyi~R~~ 718 (728)
.+|..+...+.+.+..|.++|||.+.+
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 356778899999999999999999875
No 157
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=23.34 E-value=1.8e+02 Score=21.21 Aligned_cols=34 Identities=24% Similarity=0.354 Sum_probs=24.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004841 566 QASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHS 601 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 601 (728)
...|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 17 ~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 17 EQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34444433332 69999999999999999987754
No 158
>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=23.14 E-value=94 Score=24.10 Aligned_cols=39 Identities=26% Similarity=0.402 Sum_probs=30.1
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 574 NSSDRL-SYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 574 n~~~~~-t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
..++.+ |..+|++..|++...++++|..|.. .+++...|
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~~ 58 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERRP 58 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEET
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEEC
Confidence 345688 9999999999999999999999974 57776554
No 159
>PRK11050 manganese transport regulator MntR; Provisional
Probab=22.83 E-value=1.6e+02 Score=27.53 Aligned_cols=43 Identities=16% Similarity=0.199 Sum_probs=34.8
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 568 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 568 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
.|+.++..++.++..+|++.++++...+.+.|..|.. .+++.+
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 160
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.81 E-value=1.4e+02 Score=25.42 Aligned_cols=53 Identities=17% Similarity=0.228 Sum_probs=43.4
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 560 LIVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 560 l~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+..+.....||..+...+.=...-|+..+++|.+++...|..|. ..++|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEec
Confidence 34566778888888877776788899999999999999999997 468887763
No 161
>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=22.80 E-value=2.9e+02 Score=22.82 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=36.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+++.|=+.-.....+.-.+|++.++++...++..+..|- ..++|.+.|
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 344444444566789999999999999999999999996 468887544
No 162
>PRK06474 hypothetical protein; Provisional
Probab=22.74 E-value=2e+02 Score=27.78 Aligned_cols=52 Identities=13% Similarity=0.206 Sum_probs=39.8
Q ss_pred EEcHHHHHHHHhhcCCC-CcCHHHHHHHh-CCCHHHHHHHHHHhhhccccccccCC
Q 004841 561 IVTTYQASALLLFNSSD-RLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~~~-~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
-.++.-..||..+-..+ .+|..+|++.+ +++...+-++|..|. +.+++...+
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~~ 61 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVVK 61 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEee
Confidence 34566667776665444 49999999999 799999999999997 567877543
No 163
>PRK14999 histidine utilization repressor; Provisional
Probab=22.72 E-value=47 Score=33.74 Aligned_cols=47 Identities=15% Similarity=0.275 Sum_probs=36.0
Q ss_pred cccccccC-ChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004841 670 IMKSRKVL-GHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 725 (728)
Q Consensus 670 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 725 (728)
..+....| +-.+|.+ .|..+...|+++|+.|.+.|+|.|..+ +++|+
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 45555556 4555554 689999999999999999999999875 46654
No 164
>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=22.50 E-value=1.2e+02 Score=26.10 Aligned_cols=53 Identities=9% Similarity=0.133 Sum_probs=42.8
Q ss_pred hhheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhccc
Q 004841 663 IDASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLER 716 (728)
Q Consensus 663 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R 716 (728)
++-+|..++. .+.+.=-+|.+++.+.....+.++...+=..+..|-++|+|++
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 3445555665 4678888999998887665678889999999999999999998
No 165
>PLN03239 histone acetyltransferase; Provisional
Probab=22.28 E-value=1.2e+02 Score=32.49 Aligned_cols=38 Identities=18% Similarity=0.317 Sum_probs=29.4
Q ss_pred HHHHHHHhhcCC----CCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 565 YQASALLLFNSS----DRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 565 ~Q~~iLllFn~~----~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
+...|+-.+-+. ..+|+++|+..|||..+++..+|+.|
T Consensus 267 W~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 267 WGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred HHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 444555443222 46999999999999999999999988
No 166
>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=21.65 E-value=6.1e+02 Score=22.94 Aligned_cols=59 Identities=14% Similarity=0.469 Sum_probs=38.9
Q ss_pred hhHHHHHHHHHHHHHHhcCCcCCH-HHHHHHHHHHHHhcc---------CchhchHHHHHHHHHHHHHH
Q 004841 131 LNGKVRDAVITLIDQEREGEQIDR-ALLKNVLDIFVEIGM---------GQMDYYENDFETAMLKDTAA 189 (728)
Q Consensus 131 ~~~~l~~~ll~~I~~~R~g~~id~-~~l~~~i~ml~~l~~---------~~~~~Y~~~FE~~~L~~t~~ 189 (728)
+++++.+.|-++++..|..+.-+. --..++..||.+||. ....+-...|-+.+|+.+..
T Consensus 8 ~s~~v~~~I~~iVe~r~qeGA~~~dvs~SSv~smLlELGLrVY~~Q~E~k~s~Fnq~eFnk~lLe~v~k 76 (127)
T PF05261_consen 8 VSNKVLEEINDIVEERRQEGATEKDVSFSSVSSMLLELGLRVYEAQMERKESGFNQEEFNKVLLENVSK 76 (127)
T ss_dssp --HCHHHHHHHHHHHHHCCT-TTTT--HHHHHHHHHHCCCCHHHHCCHHCSSS--HHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHhHHHHHHHHhhccCCCCHHHHHHHHHHHHHH
Confidence 456677788888888887765433 247889999999995 23345666788888887654
No 167
>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=21.62 E-value=61 Score=24.31 Aligned_cols=22 Identities=18% Similarity=0.531 Sum_probs=19.2
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 004841 578 RLSYSEIMTQLNLSDDDVVRLL 599 (728)
Q Consensus 578 ~~t~~ei~~~t~i~~~~l~~~L 599 (728)
.+++.||++.+|++..++.+.|
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 5789999999999999998887
No 168
>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=21.50 E-value=1.4e+02 Score=24.96 Aligned_cols=45 Identities=16% Similarity=0.248 Sum_probs=35.7
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHh-CCCHHHHHHHHHHhhhccccccccC
Q 004841 566 QASALLLFNSSDRLSYSEIMTQL-NLSDDDVVRLLHSLSCAKYKILNKE 613 (728)
Q Consensus 566 Q~~iLllFn~~~~~t~~ei~~~t-~i~~~~l~~~L~~L~~~k~kiL~~~ 613 (728)
-+.||..... +...+.||.+.+ |++...|.+.|..|. ..+++.+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~--~~GLv~r~ 52 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELE--EAGLVERR 52 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHH--Hcchhhcc
Confidence 3566766665 688999999999 999999999999997 46787764
No 169
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=21.26 E-value=1.1e+02 Score=24.68 Aligned_cols=44 Identities=14% Similarity=0.345 Sum_probs=25.7
Q ss_pred cccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCce
Q 004841 672 KSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMF 724 (728)
Q Consensus 672 K~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y 724 (728)
...+..+-.++-+ +++. +..+...+. ..||+-|||+|+++ .+.|
T Consensus 25 ~~g~~y~E~EVN~-~L~~----~~~D~a~LR---R~LVd~g~L~R~~d-g~~Y 68 (71)
T PF09860_consen 25 EPGREYSEKEVNE-ILKR----FFDDYATLR---RYLVDYGLLERTRD-GSRY 68 (71)
T ss_pred CCCCccCHHHHHH-HHHH----HcccHHHHH---HHHHHcCCeeecCC-CCee
Confidence 4455555555433 2222 334555443 57899999999975 3455
No 170
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=21.16 E-value=53 Score=33.33 Aligned_cols=35 Identities=17% Similarity=0.382 Sum_probs=29.2
Q ss_pred hcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCcee
Q 004841 690 LGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFR 725 (728)
Q Consensus 690 l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~ 725 (728)
|..+|.++...++++|..|.+.|+|.|..+ +++|+
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 444799999999999999999999999864 45654
No 171
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=21.08 E-value=1.6e+02 Score=27.14 Aligned_cols=42 Identities=19% Similarity=0.243 Sum_probs=33.6
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhcccccccc
Q 004841 569 ALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNK 612 (728)
Q Consensus 569 iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~ 612 (728)
|..+.+..+..++.+|++.++++...+.+.|..|.. .+++.+
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~--~Gli~~ 54 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDK--DEYLIY 54 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHH--CCCEEE
Confidence 444556667889999999999999999999999973 466653
No 172
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.06 E-value=1.8e+02 Score=22.19 Aligned_cols=30 Identities=13% Similarity=0.230 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhhc----hhhHHHHHHHHHHHHHH
Q 004841 61 ILLLVLPSIREKH----DEFMLRELVKRWSNHKV 90 (728)
Q Consensus 61 l~~~v~~~l~~~~----~~~~L~~~~~~W~~~~~ 90 (728)
++++|+|.+.+.. ...++.-+...|++|+.
T Consensus 19 Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~ 52 (55)
T PF08073_consen 19 FSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQE 52 (55)
T ss_pred HHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHh
Confidence 8888888776643 24688888999999975
No 173
>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=20.94 E-value=1.5e+02 Score=27.42 Aligned_cols=39 Identities=21% Similarity=0.260 Sum_probs=29.5
Q ss_pred EEcHHHHHHHHh-hcCCCCcCHHHHHHHhCCCHHHHHHHHHH
Q 004841 561 IVTTYQASALLL-FNSSDRLSYSEIMTQLNLSDDDVVRLLHS 601 (728)
Q Consensus 561 ~vs~~Q~~iLll-Fn~~~~~t~~ei~~~t~i~~~~l~~~L~~ 601 (728)
.+|+.|..|+.+ +- .++|++||++.+|+|...+...+.-
T Consensus 111 ~L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 345666666665 43 4789999999999999988876653
No 174
>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=20.89 E-value=1.3e+02 Score=24.36 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=39.0
Q ss_pred HHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 564 TYQASALLLFNS--SDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 564 ~~Q~~iLllFn~--~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
..|.++|...-. ..+++-.+++..+|++...+-..+..|. +.+++.+.+
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~~ 52 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQS 52 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEEE
Confidence 467788877753 3578999999999999999999999997 457777653
No 175
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=20.82 E-value=76 Score=26.57 Aligned_cols=47 Identities=13% Similarity=0.203 Sum_probs=34.1
Q ss_pred hheeeecccccccCChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCC
Q 004841 664 DASIVRIMKSRKVLGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDK 718 (728)
Q Consensus 664 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~ 718 (728)
+..|...+...+.++..+|... +.++...|.+.|..|.++|+|++..
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 4445555666666777776553 3456777999999999999998764
No 176
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=20.81 E-value=1.3e+02 Score=30.39 Aligned_cols=58 Identities=10% Similarity=0.242 Sum_probs=42.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCCC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKFT 632 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F~ 632 (728)
+-..+.-+|.++..||+.+|.+.|+=|...|+.+|..++ ++.+.+. -..+|.+-+.|.
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 334556789999999999999999999999999999886 4443321 235666655553
No 177
>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=20.57 E-value=1.2e+02 Score=26.70 Aligned_cols=48 Identities=19% Similarity=0.155 Sum_probs=37.1
Q ss_pred CChhHHHHHHHHHhcCCCCCChhHHHHHHHhhhhhhhcccCCCCCCceee
Q 004841 677 LGHQQLVLECVEQLGRMFKPDFKAIKKRIEDLITRDYLERDKSNPNMFRY 726 (728)
Q Consensus 677 l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~LIereyi~R~~~d~~~y~Y 726 (728)
.....++.+|+.... .+ ++...+--||+.||+.|.++-.++-.++-+|
T Consensus 62 ~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 62 QKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred cHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 455688999998874 34 6678899999999999999988765554443
No 178
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=20.54 E-value=1.2e+02 Score=31.60 Aligned_cols=57 Identities=14% Similarity=0.298 Sum_probs=31.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCCCCCCCCCCCeEEEecCC
Q 004841 565 YQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEPNTKTISPTDHFEFNSKF 631 (728)
Q Consensus 565 ~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~~~~~i~~~~~~~~N~~F 631 (728)
+--.|.-+|.++.-||+.+|.+.|+=|...|+..|..++ ++.+.+. -...|.|=..|
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 444577789999999999999999999999999999875 4555421 13456654444
No 179
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=20.47 E-value=1.7e+02 Score=26.97 Aligned_cols=40 Identities=25% Similarity=0.236 Sum_probs=31.9
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHh
Q 004841 561 IVTTYQASALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSL 602 (728)
Q Consensus 561 ~vs~~Q~~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L 602 (728)
.+|.-|..|+.++ ...+|.+||++.+|++...+...+...
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 3567788888886 368899999999999998887655543
No 180
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.22 E-value=1.7e+02 Score=27.59 Aligned_cols=45 Identities=20% Similarity=0.338 Sum_probs=36.0
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHHhhhccccccccCC
Q 004841 568 SALLLFNSSDRLSYSEIMTQLNLSDDDVVRLLHSLSCAKYKILNKEP 614 (728)
Q Consensus 568 ~iLllFn~~~~~t~~ei~~~t~i~~~~l~~~L~~L~~~k~kiL~~~~ 614 (728)
+|..++.+.......+|++.+++++..+...++-|. +.+++...|
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~~ 58 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYEP 58 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEec
Confidence 344555567789999999999999999999999996 456776554
Done!