Query 008709
Match_columns 557
No_of_seqs 183 out of 1010
Neff 8.7
Searched_HMMs 46136
Date Thu Mar 28 15:35:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008709hhsearch_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 4.3E-96 9E-101 792.5 53.2 537 3-555 189-725 (725)
2 KOG2167 Cullins [Cell cycle co 100.0 1.5E-96 3E-101 744.7 38.4 530 3-557 126-661 (661)
3 COG5647 Cullin, a subunit of E 100.0 4.1E-93 8.9E-98 736.0 48.2 546 3-557 214-773 (773)
4 KOG2284 E3 ubiquitin ligase, C 100.0 4.3E-87 9.3E-92 647.8 34.2 507 2-557 214-728 (728)
5 KOG2285 E3 ubiquitin ligase, C 100.0 1.9E-76 4.2E-81 578.8 45.5 542 3-557 192-777 (777)
6 PF00888 Cullin: Cullin family 100.0 9.1E-72 2E-76 616.7 46.2 439 3-461 148-588 (588)
7 smart00182 CULLIN Cullin. 100.0 1.8E-33 4E-38 251.7 17.8 141 241-382 1-142 (142)
8 KOG2165 Anaphase-promoting com 100.0 1.3E-28 2.8E-33 255.0 28.2 302 233-546 440-757 (765)
9 PF10557 Cullin_Nedd8: Cullin 99.8 1.4E-20 3.1E-25 144.7 4.3 67 485-551 2-68 (68)
10 TIGR01610 phage_O_Nterm phage 94.4 0.12 2.7E-06 42.4 6.2 66 388-461 20-93 (95)
11 PF02082 Rrf2: Transcriptional 94.2 0.16 3.5E-06 40.5 6.3 60 394-460 11-71 (83)
12 PF13412 HTH_24: Winged helix- 93.1 0.2 4.3E-06 35.2 4.5 42 392-433 2-43 (48)
13 PF09339 HTH_IclR: IclR helix- 92.9 0.18 3.9E-06 36.2 4.1 45 396-442 6-51 (52)
14 PF12802 MarR_2: MarR family; 92.7 0.16 3.4E-06 37.8 3.8 51 391-443 3-55 (62)
15 PF08220 HTH_DeoR: DeoR-like h 92.1 0.41 8.9E-06 35.2 5.3 46 395-442 2-47 (57)
16 PF01047 MarR: MarR family; I 90.7 0.2 4.3E-06 36.9 2.3 50 391-442 1-50 (59)
17 PF13463 HTH_27: Winged helix 90.4 0.47 1E-05 35.9 4.4 50 391-442 1-51 (68)
18 TIGR02698 CopY_TcrY copper tra 89.9 0.71 1.5E-05 40.3 5.6 60 493-557 6-65 (130)
19 COG3682 Predicted transcriptio 89.7 0.71 1.5E-05 39.5 5.1 62 491-557 6-67 (123)
20 TIGR02337 HpaR homoprotocatech 89.4 0.72 1.6E-05 39.4 5.2 51 390-442 25-75 (118)
21 PF01022 HTH_5: Bacterial regu 89.2 1 2.2E-05 31.5 4.8 44 394-440 3-46 (47)
22 PF12840 HTH_20: Helix-turn-he 88.8 0.62 1.3E-05 34.6 3.8 49 392-442 9-57 (61)
23 PRK11512 DNA-binding transcrip 88.2 1 2.2E-05 40.0 5.5 53 389-443 36-88 (144)
24 smart00550 Zalpha Z-DNA-bindin 88.0 1.6 3.4E-05 33.4 5.6 47 394-442 7-55 (68)
25 PRK11920 rirA iron-responsive 87.8 1.7 3.7E-05 39.1 6.6 58 395-459 12-69 (153)
26 PF09012 FeoC: FeoC like trans 87.6 0.44 9.5E-06 36.5 2.4 46 495-548 4-49 (69)
27 PRK10857 DNA-binding transcrip 86.8 2.1 4.6E-05 39.0 6.7 58 395-459 12-70 (164)
28 PF03965 Penicillinase_R: Peni 86.7 0.57 1.2E-05 40.0 2.8 60 493-557 5-64 (115)
29 PF08279 HTH_11: HTH domain; 85.4 1.8 3.8E-05 31.3 4.5 37 397-433 4-41 (55)
30 TIGR01889 Staph_reg_Sar staphy 84.8 2.5 5.4E-05 35.6 5.8 52 390-443 22-77 (109)
31 TIGR02010 IscR iron-sulfur clu 84.7 2.8 6.1E-05 36.8 6.3 45 395-441 12-57 (135)
32 COG1959 Predicted transcriptio 83.7 2.9 6.4E-05 37.4 6.1 59 394-459 11-70 (150)
33 COG3355 Predicted transcriptio 82.3 3.4 7.4E-05 35.6 5.5 37 404-442 39-75 (126)
34 PF01978 TrmB: Sugar-specific 82.0 1.4 3.1E-05 33.4 2.9 49 392-442 7-55 (68)
35 smart00347 HTH_MARR helix_turn 81.9 2.8 6E-05 34.1 4.9 52 389-442 6-57 (101)
36 smart00420 HTH_DEOR helix_turn 81.9 3 6.5E-05 29.3 4.5 43 397-441 4-46 (53)
37 smart00346 HTH_ICLR helix_turn 80.8 3.7 8.1E-05 32.9 5.2 45 396-442 8-53 (91)
38 PF04492 Phage_rep_O: Bacterio 80.0 6.8 0.00015 32.4 6.4 62 390-461 29-98 (100)
39 PRK13777 transcriptional regul 80.0 3.9 8.4E-05 38.0 5.6 52 389-442 41-92 (185)
40 PF04703 FaeA: FaeA-like prote 79.2 4.5 9.7E-05 30.3 4.6 56 398-457 5-61 (62)
41 PRK03573 transcriptional regul 78.9 4.1 8.9E-05 36.0 5.3 53 389-443 27-80 (144)
42 TIGR00738 rrf2_super rrf2 fami 77.7 6.2 0.00014 34.2 6.0 46 394-441 11-57 (132)
43 PF01978 TrmB: Sugar-specific 77.0 1.2 2.5E-05 33.9 1.0 56 493-556 10-65 (68)
44 PRK15090 DNA-binding transcrip 76.9 5.7 0.00012 39.0 6.1 45 396-442 17-61 (257)
45 PF05732 RepL: Firmicute plasm 76.8 3.4 7.4E-05 37.7 4.1 48 407-463 75-122 (165)
46 PF13404 HTH_AsnC-type: AsnC-t 76.3 4.2 9E-05 27.8 3.5 36 396-431 6-41 (42)
47 PF08220 HTH_DeoR: DeoR-like h 75.6 3.3 7.1E-05 30.3 3.0 46 494-547 3-48 (57)
48 PRK10870 transcriptional repre 75.4 7.2 0.00016 36.0 6.0 52 390-443 52-105 (176)
49 smart00419 HTH_CRP helix_turn_ 75.1 7.3 0.00016 26.7 4.7 33 407-441 8-40 (48)
50 smart00345 HTH_GNTR helix_turn 74.9 7.6 0.00017 28.0 5.0 39 402-442 14-53 (60)
51 smart00550 Zalpha Z-DNA-bindin 74.7 7.3 0.00016 29.7 4.9 54 492-553 7-62 (68)
52 PHA00738 putative HTH transcri 74.7 7.4 0.00016 32.4 5.1 67 388-460 7-73 (108)
53 TIGR02944 suf_reg_Xantho FeS a 74.6 7.9 0.00017 33.6 5.8 35 405-441 23-57 (130)
54 PF05584 Sulfolobus_pRN: Sulfo 74.0 8.6 0.00019 29.6 4.9 41 398-441 10-50 (72)
55 PF13463 HTH_27: Winged helix 73.3 7.4 0.00016 29.1 4.7 53 493-553 5-60 (68)
56 PF08784 RPA_C: Replication pr 73.1 6 0.00013 32.7 4.4 44 390-433 44-91 (102)
57 PRK11014 transcriptional repre 72.6 12 0.00026 33.1 6.5 49 402-457 20-68 (141)
58 PF09756 DDRGK: DDRGK domain; 72.5 2.7 5.8E-05 39.0 2.3 58 492-557 100-157 (188)
59 cd00090 HTH_ARSR Arsenical Res 71.8 9.3 0.0002 28.7 5.1 47 392-441 6-52 (78)
60 PF08280 HTH_Mga: M protein tr 71.8 5.2 0.00011 29.5 3.3 38 395-432 7-44 (59)
61 TIGR01884 cas_HTH CRISPR locus 71.2 6.9 0.00015 36.9 4.9 51 390-442 140-190 (203)
62 TIGR03879 near_KaiC_dom probab 68.9 6.1 0.00013 30.6 3.2 30 403-432 28-57 (73)
63 PF13601 HTH_34: Winged helix 68.8 4.6 0.0001 31.9 2.7 43 396-440 3-45 (80)
64 COG1846 MarR Transcriptional r 67.4 11 0.00024 31.6 5.1 50 391-442 20-69 (126)
65 PRK10141 DNA-binding transcrip 67.1 12 0.00027 31.9 5.1 57 396-458 19-75 (117)
66 TIGR02431 pcaR_pcaU beta-ketoa 67.1 13 0.00028 36.3 6.1 44 396-441 12-56 (248)
67 smart00344 HTH_ASNC helix_turn 66.9 10 0.00022 31.5 4.6 45 394-440 4-48 (108)
68 PF13730 HTH_36: Helix-turn-he 66.8 14 0.00031 26.4 4.8 25 409-433 27-51 (55)
69 cd00092 HTH_CRP helix_turn_hel 66.1 16 0.00035 27.1 5.2 35 406-442 24-58 (67)
70 PRK11569 transcriptional repre 66.0 13 0.00028 37.0 5.8 46 395-442 30-76 (274)
71 COG1414 IclR Transcriptional r 65.9 14 0.0003 36.1 5.9 46 396-443 7-53 (246)
72 PF01325 Fe_dep_repress: Iron 65.6 14 0.0003 27.4 4.5 43 398-442 13-55 (60)
73 COG2345 Predicted transcriptio 65.3 9 0.0002 36.4 4.3 42 397-440 15-56 (218)
74 PRK10163 DNA-binding transcrip 64.5 15 0.00033 36.3 6.1 45 396-442 28-73 (271)
75 cd07153 Fur_like Ferric uptake 64.4 15 0.00033 30.9 5.3 58 495-555 5-63 (116)
76 PRK09834 DNA-binding transcrip 62.0 16 0.00035 36.0 5.7 46 396-443 14-60 (263)
77 smart00418 HTH_ARSR helix_turn 61.9 17 0.00036 26.3 4.5 35 405-441 8-42 (66)
78 PF13412 HTH_24: Winged helix- 61.8 11 0.00023 26.2 3.2 45 492-544 4-48 (48)
79 PF04545 Sigma70_r4: Sigma-70, 59.9 24 0.00052 24.7 4.8 32 397-430 12-43 (50)
80 smart00418 HTH_ARSR helix_turn 59.7 16 0.00036 26.3 4.2 45 496-549 2-46 (66)
81 PRK06266 transcription initiat 58.9 15 0.00033 33.9 4.5 44 395-440 24-67 (178)
82 PF02002 TFIIE_alpha: TFIIE al 58.9 8.9 0.00019 31.9 2.8 44 395-440 15-58 (105)
83 cd07377 WHTH_GntR Winged helix 58.0 31 0.00068 25.2 5.5 38 403-442 20-58 (66)
84 PF02186 TFIIE_beta: TFIIE bet 57.2 15 0.00032 27.8 3.3 55 492-557 6-61 (65)
85 PRK10434 srlR DNA-bindng trans 56.9 14 0.00031 36.2 4.3 47 394-442 6-52 (256)
86 PF02796 HTH_7: Helix-turn-hel 56.7 15 0.00033 25.3 3.2 31 397-429 13-43 (45)
87 PF10771 DUF2582: Protein of u 56.6 16 0.00034 27.6 3.4 37 397-433 12-48 (65)
88 COG1318 Predicted transcriptio 56.4 14 0.00031 33.4 3.7 50 361-431 36-85 (182)
89 PF12324 HTH_15: Helix-turn-he 55.4 32 0.0007 26.8 5.0 39 394-432 25-63 (77)
90 PF09012 FeoC: FeoC like trans 55.0 14 0.00029 28.2 3.0 34 400-433 7-40 (69)
91 PF07106 TBPIP: Tat binding pr 54.7 1.7E+02 0.0036 26.6 11.6 59 395-459 3-64 (169)
92 PF05158 RNA_pol_Rpc34: RNA po 54.5 15 0.00032 37.6 4.0 143 390-549 81-260 (327)
93 COG1349 GlpR Transcriptional r 54.1 18 0.00039 35.5 4.4 46 395-442 7-52 (253)
94 TIGR02702 SufR_cyano iron-sulf 52.8 33 0.00072 32.3 5.9 44 397-442 5-48 (203)
95 PF01726 LexA_DNA_bind: LexA D 52.6 31 0.00067 26.0 4.5 56 487-549 6-62 (65)
96 PF11994 DUF3489: Protein of u 52.3 33 0.00071 26.4 4.5 47 392-438 9-55 (72)
97 PF08221 HTH_9: RNA polymerase 51.7 21 0.00045 26.6 3.4 34 404-439 24-57 (62)
98 PRK11169 leucine-responsive tr 51.2 25 0.00053 31.9 4.6 48 391-440 12-59 (164)
99 smart00420 HTH_DEOR helix_turn 51.2 32 0.00069 23.8 4.3 45 495-547 4-48 (53)
100 TIGR00373 conserved hypothetic 51.1 29 0.00063 31.4 4.9 43 396-440 17-59 (158)
101 smart00344 HTH_ASNC helix_turn 50.8 27 0.00059 28.9 4.5 46 492-545 4-49 (108)
102 PF04967 HTH_10: HTH DNA bindi 50.8 25 0.00055 25.3 3.6 30 402-431 18-47 (53)
103 smart00421 HTH_LUXR helix_turn 50.5 35 0.00076 23.9 4.5 39 392-432 5-43 (58)
104 cd07977 TFIIE_beta_winged_heli 50.0 25 0.00054 27.4 3.7 58 490-557 8-70 (75)
105 PF01853 MOZ_SAS: MOZ/SAS fami 49.7 18 0.00039 33.5 3.3 30 402-431 145-174 (188)
106 TIGR02844 spore_III_D sporulat 49.7 28 0.00062 27.5 4.0 35 394-429 7-41 (80)
107 PF12802 MarR_2: MarR family; 49.6 15 0.00032 26.9 2.3 48 493-548 7-56 (62)
108 cd06170 LuxR_C_like C-terminal 49.5 38 0.00082 23.8 4.5 39 392-432 2-40 (57)
109 PF01047 MarR: MarR family; I 49.4 8.4 0.00018 28.0 1.0 47 493-547 5-51 (59)
110 PRK13509 transcriptional repre 49.2 28 0.0006 34.1 4.9 47 394-442 6-52 (251)
111 PRK11179 DNA-binding transcrip 48.6 30 0.00066 30.9 4.7 48 391-440 7-54 (153)
112 PF08281 Sigma70_r4_2: Sigma-7 47.6 35 0.00076 24.2 4.0 23 407-429 26-48 (54)
113 TIGR02404 trehalos_R_Bsub treh 47.5 13 0.00028 35.8 2.3 35 519-554 30-64 (233)
114 PF01726 LexA_DNA_bind: LexA D 47.1 28 0.00061 26.2 3.5 51 391-443 4-60 (65)
115 PF14394 DUF4423: Domain of un 47.1 49 0.0011 30.3 5.9 53 388-442 19-74 (171)
116 PF06784 UPF0240: Uncharacteri 47.1 35 0.00075 31.5 4.8 64 364-432 96-161 (179)
117 COG4189 Predicted transcriptio 46.8 32 0.00069 32.8 4.5 49 392-442 22-70 (308)
118 PF00325 Crp: Bacterial regula 46.7 28 0.0006 22.3 2.8 25 408-432 3-27 (32)
119 PRK00215 LexA repressor; Valid 45.9 44 0.00096 31.4 5.6 51 391-443 2-58 (205)
120 PF00392 GntR: Bacterial regul 45.4 14 0.00031 27.5 1.7 34 519-553 30-63 (64)
121 PF00196 GerE: Bacterial regul 45.3 32 0.0007 24.9 3.6 39 392-432 5-43 (58)
122 PRK10681 DNA-binding transcrip 45.2 31 0.00067 33.8 4.5 39 394-432 8-46 (252)
123 PRK11402 DNA-binding transcrip 44.9 15 0.00033 35.6 2.3 35 519-554 39-73 (241)
124 TIGR03433 padR_acidobact trans 44.1 78 0.0017 26.0 6.1 54 491-545 4-57 (100)
125 COG4190 Predicted transcriptio 43.7 61 0.0013 28.1 5.3 64 396-461 67-133 (144)
126 PF09681 Phage_rep_org_N: N-te 43.3 38 0.00082 29.1 4.2 38 403-442 49-86 (121)
127 PRK10906 DNA-binding transcrip 42.9 35 0.00076 33.4 4.5 47 394-442 6-52 (252)
128 PRK09802 DNA-binding transcrip 42.7 34 0.00073 33.9 4.4 48 393-442 17-64 (269)
129 COG1654 BirA Biotin operon rep 42.7 78 0.0017 25.0 5.5 40 400-439 12-51 (79)
130 TIGR02325 C_P_lyase_phnF phosp 42.4 17 0.00037 35.0 2.2 34 520-554 39-72 (238)
131 PRK10079 phosphonate metabolis 42.4 17 0.00038 35.1 2.3 36 518-554 40-75 (241)
132 KOG3054 Uncharacterized conser 42.1 30 0.00064 33.1 3.6 56 494-557 203-258 (299)
133 PRK04172 pheS phenylalanyl-tRN 42.0 40 0.00087 36.6 5.2 50 390-441 3-52 (489)
134 PF00165 HTH_AraC: Bacterial r 40.8 41 0.00089 22.5 3.3 28 405-432 6-33 (42)
135 PRK04424 fatty acid biosynthes 40.4 38 0.00081 31.5 4.1 46 394-441 8-53 (185)
136 COG1522 Lrp Transcriptional re 40.1 52 0.0011 29.1 4.9 47 392-440 7-53 (154)
137 PRK13239 alkylmercury lyase; P 39.9 54 0.0012 31.0 5.0 39 394-432 23-61 (206)
138 PF00392 GntR: Bacterial regul 39.5 60 0.0013 24.0 4.4 38 403-442 19-57 (64)
139 PF09763 Sec3_C: Exocyst compl 39.5 3E+02 0.0065 31.4 12.0 132 14-178 551-701 (701)
140 PRK14999 histidine utilization 38.1 21 0.00046 34.6 2.1 47 499-554 29-76 (241)
141 cd06171 Sigma70_r4 Sigma70, re 38.0 72 0.0016 21.7 4.5 39 392-431 12-50 (55)
142 TIGR00498 lexA SOS regulatory 37.9 37 0.00081 31.7 3.7 50 391-442 4-59 (199)
143 KOG2747 Histone acetyltransfer 37.9 43 0.00093 34.7 4.3 63 367-431 282-353 (396)
144 COG2188 PhnF Transcriptional r 37.4 22 0.00048 34.4 2.1 36 518-554 36-71 (236)
145 smart00531 TFIIE Transcription 37.4 41 0.00089 29.9 3.7 31 404-434 12-42 (147)
146 PF13384 HTH_23: Homeodomain-l 37.2 38 0.00083 23.5 2.8 32 398-431 10-41 (50)
147 TIGR01714 phage_rep_org_N phag 37.0 50 0.0011 28.3 3.9 48 393-442 29-84 (119)
148 TIGR00122 birA_repr_reg BirA b 36.6 1.3E+02 0.0029 22.4 6.0 34 399-433 6-39 (69)
149 smart00345 HTH_GNTR helix_turn 36.5 27 0.00058 25.0 2.0 28 521-548 28-55 (60)
150 COG1522 Lrp Transcriptional re 36.5 46 0.001 29.4 4.0 50 490-547 7-56 (154)
151 smart00346 HTH_ICLR helix_turn 36.2 88 0.0019 24.7 5.2 45 496-548 10-55 (91)
152 PRK09462 fur ferric uptake reg 35.1 90 0.0019 27.6 5.5 59 494-555 20-80 (148)
153 smart00347 HTH_MARR helix_turn 34.9 95 0.0021 24.7 5.3 48 492-547 11-58 (101)
154 PRK10434 srlR DNA-bindng trans 34.4 37 0.0008 33.3 3.2 46 493-546 7-52 (256)
155 PF13542 HTH_Tnp_ISL3: Helix-t 34.4 1E+02 0.0022 21.5 4.7 35 394-430 16-50 (52)
156 PF09107 SelB-wing_3: Elongati 34.4 83 0.0018 22.4 4.1 41 400-442 3-43 (50)
157 PHA02943 hypothetical protein; 34.3 78 0.0017 28.2 4.7 54 398-458 16-69 (165)
158 PF04760 IF2_N: Translation in 34.2 29 0.00062 24.9 1.8 22 407-428 3-24 (54)
159 PF12395 DUF3658: Protein of u 34.0 92 0.002 26.2 5.1 63 490-555 47-109 (111)
160 TIGR02018 his_ut_repres histid 33.8 28 0.0006 33.4 2.1 33 521-554 33-65 (230)
161 PRK10411 DNA-binding transcrip 33.6 60 0.0013 31.5 4.5 46 394-441 5-50 (240)
162 TIGR01889 Staph_reg_Sar staphy 33.6 75 0.0016 26.5 4.5 41 502-550 40-82 (109)
163 PRK09334 30S ribosomal protein 33.2 35 0.00075 27.3 2.2 37 521-557 49-85 (86)
164 PF09860 DUF2087: Uncharacteri 32.7 62 0.0013 24.9 3.4 49 496-553 20-68 (71)
165 PRK09764 DNA-binding transcrip 32.7 31 0.00067 33.4 2.3 33 521-554 37-69 (240)
166 PLN03238 probable histone acet 32.4 74 0.0016 31.5 4.8 36 396-431 211-247 (290)
167 PF06163 DUF977: Bacterial pro 32.1 92 0.002 26.8 4.6 52 489-548 10-61 (127)
168 PF06163 DUF977: Bacterial pro 32.0 88 0.0019 26.9 4.5 41 393-433 12-52 (127)
169 PF01475 FUR: Ferric uptake re 32.0 70 0.0015 27.1 4.1 60 493-555 10-70 (120)
170 PRK04214 rbn ribonuclease BN/u 31.8 1.2E+02 0.0026 32.1 6.7 39 402-442 305-343 (412)
171 COG1349 GlpR Transcriptional r 31.5 39 0.00084 33.2 2.7 46 493-546 7-52 (253)
172 PF01638 HxlR: HxlR-like helix 31.3 82 0.0018 25.2 4.2 44 396-442 8-52 (90)
173 PRK11169 leucine-responsive tr 31.3 91 0.002 28.2 5.0 48 490-545 13-60 (164)
174 PRK11512 DNA-binding transcrip 31.2 74 0.0016 27.9 4.3 46 494-547 43-88 (144)
175 PHA02591 hypothetical protein; 30.9 64 0.0014 25.2 3.2 24 407-430 59-82 (83)
176 PRK06474 hypothetical protein; 30.8 1.4E+02 0.003 27.5 6.2 51 390-442 8-60 (178)
177 PF09904 HTH_43: Winged helix- 30.8 96 0.0021 25.0 4.3 34 400-434 15-48 (90)
178 PRK03902 manganese transport t 30.8 85 0.0018 27.5 4.6 42 398-441 13-54 (142)
179 PF14947 HTH_45: Winged helix- 30.8 1.1E+02 0.0024 23.7 4.8 43 395-440 8-50 (77)
180 PRK11050 manganese transport r 30.6 1.1E+02 0.0024 27.3 5.4 43 397-441 41-83 (152)
181 PF03444 HrcA_DNA-bdg: Winged 30.4 1.6E+02 0.0034 23.2 5.3 47 394-442 10-56 (78)
182 PF08784 RPA_C: Replication pr 30.3 66 0.0014 26.4 3.6 46 490-543 46-95 (102)
183 PRK10906 DNA-binding transcrip 30.1 50 0.0011 32.3 3.3 46 493-546 7-52 (252)
184 PRK11179 DNA-binding transcrip 29.8 89 0.0019 27.9 4.6 47 491-545 9-55 (153)
185 PF04182 B-block_TFIIIC: B-blo 29.7 84 0.0018 24.3 3.8 48 393-442 2-51 (75)
186 PRK10430 DNA-binding transcrip 29.5 1.3E+02 0.0029 28.6 6.2 46 392-439 160-208 (239)
187 COG1321 TroR Mn-dependent tran 29.5 1E+02 0.0022 27.7 4.8 44 397-442 14-57 (154)
188 PF02270 TFIIF_beta: Transcrip 28.9 78 0.0017 31.5 4.4 57 394-460 217-273 (275)
189 TIGR01610 phage_O_Nterm phage 28.9 96 0.0021 25.2 4.3 38 502-547 44-81 (95)
190 PF10007 DUF2250: Uncharacteri 28.4 1.1E+02 0.0025 24.8 4.4 52 389-442 3-54 (92)
191 PF13545 HTH_Crp_2: Crp-like h 28.1 1.2E+02 0.0026 22.9 4.6 33 407-441 28-60 (76)
192 PF08461 HTH_12: Ribonuclease 27.8 1.1E+02 0.0025 23.0 4.2 50 495-547 2-52 (66)
193 PRK13719 conjugal transfer tra 27.7 1E+02 0.0022 29.3 4.7 42 390-433 143-184 (217)
194 PF08672 APC2: Anaphase promot 27.5 1.1E+02 0.0025 22.6 4.0 56 496-554 2-59 (60)
195 COG3413 Predicted DNA binding 27.0 1E+02 0.0023 29.2 4.8 42 390-431 155-202 (215)
196 TIGR00721 tfx DNA-binding prot 26.9 1.2E+02 0.0026 26.7 4.7 39 391-431 7-45 (137)
197 PF00538 Linker_histone: linke 26.8 1E+02 0.0022 23.9 3.9 56 491-547 8-65 (77)
198 PF00356 LacI: Bacterial regul 26.7 81 0.0018 21.9 2.9 21 409-429 1-21 (46)
199 COG4742 Predicted transcriptio 26.7 1E+02 0.0022 30.3 4.6 42 398-442 18-59 (260)
200 COG2771 CsgD DNA-binding HTH d 26.6 1.7E+02 0.0036 21.1 5.0 41 390-432 4-44 (65)
201 cd07377 WHTH_GntR Winged helix 26.6 51 0.0011 24.0 2.1 27 521-547 33-59 (66)
202 PF04539 Sigma70_r3: Sigma-70 26.2 73 0.0016 24.5 3.0 26 406-431 19-44 (78)
203 KOG2905 Transcription initiati 26.2 92 0.002 29.9 4.0 58 394-461 187-244 (254)
204 TIGR02989 Sig-70_gvs1 RNA poly 26.1 1.1E+02 0.0025 26.9 4.7 38 391-430 112-150 (159)
205 COG2197 CitB Response regulato 26.0 1.1E+02 0.0023 29.1 4.6 42 390-433 148-189 (211)
206 TIGR02337 HpaR homoprotocatech 25.9 1.1E+02 0.0024 25.7 4.4 47 493-547 30-76 (118)
207 PF01399 PCI: PCI domain; Int 25.5 1.3E+02 0.0028 24.2 4.6 40 394-433 47-86 (105)
208 PLN03239 histone acetyltransfe 25.2 1.1E+02 0.0023 31.4 4.5 26 406-431 283-308 (351)
209 PRK03573 transcriptional regul 24.9 54 0.0012 28.7 2.3 26 522-547 55-80 (144)
210 PRK14165 winged helix-turn-hel 24.8 1.4E+02 0.0031 28.5 5.2 45 396-442 10-54 (217)
211 COG0735 Fur Fe2+/Zn2+ uptake r 24.6 1.8E+02 0.0038 25.8 5.5 60 493-555 23-83 (145)
212 PRK00135 scpB segregation and 24.5 2.9E+02 0.0063 25.7 7.1 111 344-461 34-153 (188)
213 COG2865 Predicted transcriptio 24.2 1E+02 0.0022 33.1 4.4 59 491-557 402-460 (467)
214 PF14394 DUF4423: Domain of un 24.2 65 0.0014 29.5 2.7 61 483-554 20-80 (171)
215 PHA03103 double-strand RNA-bin 24.1 1.6E+02 0.0036 27.2 5.2 44 397-442 17-60 (183)
216 PRK15411 rcsA colanic acid cap 24.0 1.2E+02 0.0026 28.6 4.6 42 390-433 137-178 (207)
217 PRK10840 transcriptional regul 23.9 1.3E+02 0.0027 28.2 4.8 41 391-433 151-191 (216)
218 PF13936 HTH_38: Helix-turn-he 23.8 1.4E+02 0.003 20.3 3.7 24 406-429 19-42 (44)
219 PLN00104 MYST -like histone ac 23.8 1.2E+02 0.0026 32.3 4.7 29 403-431 370-398 (450)
220 cd00090 HTH_ARSR Arsenical Res 23.7 1.3E+02 0.0028 22.1 4.0 46 495-549 11-56 (78)
221 PF13551 HTH_29: Winged helix- 23.4 1.5E+02 0.0032 24.3 4.6 35 397-432 3-37 (112)
222 PF04297 UPF0122: Putative hel 23.2 1.5E+02 0.0033 24.5 4.4 38 391-429 18-55 (101)
223 PF08318 COG4: COG4 transport 23.2 8E+02 0.017 24.9 19.1 163 89-265 15-214 (331)
224 smart00526 H15 Domain in histo 23.2 2.5E+02 0.0055 20.8 5.4 53 491-546 10-64 (66)
225 TIGR02983 SigE-fam_strep RNA p 23.0 1.2E+02 0.0025 27.0 4.1 40 391-431 111-150 (162)
226 PRK03975 tfx putative transcri 22.9 1.6E+02 0.0034 26.1 4.7 39 390-430 6-44 (141)
227 TIGR02698 CopY_TcrY copper tra 22.5 2.2E+02 0.0049 24.6 5.6 49 391-441 2-54 (130)
228 PRK00118 putative DNA-binding 22.5 1.4E+02 0.0031 24.9 4.1 37 392-430 19-56 (104)
229 PRK15431 ferrous iron transpor 22.5 75 0.0016 24.9 2.3 31 518-548 21-51 (78)
230 PF08820 DUF1803: Domain of un 22.5 66 0.0014 26.2 2.0 27 519-546 34-60 (93)
231 smart00753 PAM PCI/PINT associ 22.4 1.5E+02 0.0034 23.2 4.3 30 404-433 21-50 (88)
232 smart00088 PINT motif in prote 22.4 1.5E+02 0.0034 23.2 4.3 30 404-433 21-50 (88)
233 PRK00135 scpB segregation and 22.4 1.2E+02 0.0026 28.3 4.1 33 400-432 12-45 (188)
234 PRK15201 fimbriae regulatory p 22.2 1.6E+02 0.0036 27.1 4.7 41 391-433 134-174 (198)
235 PRK11475 DNA-binding transcrip 22.1 1.5E+02 0.0032 28.1 4.7 42 390-433 134-175 (207)
236 COG4367 Uncharacterized protei 22.1 1.1E+02 0.0024 24.4 3.1 24 406-429 22-45 (97)
237 PRK12529 RNA polymerase sigma 22.0 1.1E+02 0.0024 27.8 3.8 37 391-429 128-165 (178)
238 PF09862 DUF2089: Protein of u 21.9 1.8E+02 0.004 24.6 4.7 56 376-433 20-75 (113)
239 PRK09647 RNA polymerase sigma 21.8 1.4E+02 0.003 28.1 4.5 33 396-430 145-177 (203)
240 PF13601 HTH_34: Winged helix 21.7 65 0.0014 25.3 1.9 47 493-547 2-48 (80)
241 PF01418 HTH_6: Helix-turn-hel 21.3 91 0.002 24.2 2.6 34 398-431 25-58 (77)
242 PRK12514 RNA polymerase sigma 21.3 1.2E+02 0.0025 27.6 3.8 36 392-429 131-167 (179)
243 PRK04217 hypothetical protein; 21.1 1.7E+02 0.0037 24.6 4.4 41 390-431 42-82 (110)
244 COG2512 Predicted membrane-ass 21.1 1.3E+02 0.0028 29.6 4.2 47 394-442 197-243 (258)
245 PF10668 Phage_terminase: Phag 21.0 1.4E+02 0.0029 22.3 3.3 23 404-426 19-41 (60)
246 TIGR03859 PQQ_PqqD coenzyme PQ 21.0 1.8E+02 0.0038 22.9 4.2 51 491-544 31-81 (81)
247 PF04079 DUF387: Putative tran 21.0 1.1E+02 0.0024 27.7 3.4 32 400-432 6-37 (159)
248 COG3355 Predicted transcriptio 20.8 77 0.0017 27.4 2.2 48 500-555 37-86 (126)
249 PF02847 MA3: MA3 domain; Int 20.2 1.4E+02 0.0031 24.6 3.9 47 172-218 60-110 (113)
250 PF10007 DUF2250: Uncharacteri 20.2 71 0.0015 26.0 1.8 27 522-548 30-56 (92)
251 PRK12522 RNA polymerase sigma 20.2 1.6E+02 0.0034 26.5 4.4 31 397-429 127-157 (173)
252 KOG3852 Uncharacterized conser 20.1 4E+02 0.0086 26.7 7.1 109 158-289 220-335 (426)
253 PRK09802 DNA-binding transcrip 20.0 99 0.0021 30.6 3.2 47 493-547 19-65 (269)
254 PRK09639 RNA polymerase sigma 20.0 1.7E+02 0.0038 25.9 4.7 32 395-429 118-149 (166)
No 1
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.3e-96 Score=792.54 Aligned_cols=537 Identities=68% Similarity=1.088 Sum_probs=505.1
Q ss_pred CccccHHhhhHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCCCcHhHHHHHHHHHHHHHHHHHH
Q 008709 3 QMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATEL 82 (557)
Q Consensus 3 ~l~~Y~~~fE~~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~l 82 (557)
.+.+|...||++|+..|..||..+++.|+...++.+|+.+++.++.+|.+|+..|++..+..++.+.+...++..+.+.+
T Consensus 189 ~~s~Y~~~Fe~~fl~~t~~~y~~~~~~~l~~~~~~~yl~k~e~~l~~e~~r~~~yl~~~~e~~~~~~le~~~~~~~~~~~ 268 (725)
T KOG2166|consen 189 ELSFYEEDFERKFLQDTASYYSEEASEWLEENSCLDYLKKIEECLKEERERVTHYLHSSTEPKLVEVVEDELIVVFADDL 268 (725)
T ss_pred chhHHHHHhHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhHHHHHHHHHHHHHHH
Confidence 36799999999999999999999999999988999999999999999999999999988888999999999999999999
Q ss_pred HHHhhhHHHHhhccCCHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCccchHHHHHHHH
Q 008709 83 LEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKII 162 (557)
Q Consensus 83 l~~~~~gl~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~ 162 (557)
++..++|+..|+.+++.++|.+||++++++++|++.++..++.|+..+|..++....... ...+..+|..++
T Consensus 269 ~e~~~sgf~~~l~~~~~edl~~my~l~~r~~~gl~~l~~~~~~~~~~eg~~l~~r~~~~~--------~~~~~~~v~~~l 340 (725)
T KOG2166|consen 269 EEMEHSGFRALLNDDKLEDLSRMYRLFRRILPGLEPLASVFKQHVREEGNALVARPAETA--------ATNPVEYVQGLL 340 (725)
T ss_pred HHHhcchHHHHHhccchhHHHHHHHHhhcccccchhHHHHHHHHHHhhHHHHhhhhhhhc--------ccchHHHHhccH
Confidence 999999999999999999999999999999999999999999999999988887664321 046889999999
Q ss_pred HHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHhhhhHhhhhccc
Q 008709 163 ELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYI 242 (557)
Q Consensus 163 ~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l 242 (557)
+++++|..++..||+++..|..+++.||..|+|.+... .+|+||+|||.++|++. .+.++++++..++.++.+|+|+
T Consensus 341 ~~~~~~~~~~~~~f~~d~~f~~~ld~a~~~fin~n~~~--~~E~la~y~D~~lkk~~-k~~~e~~ie~~l~~v~~l~~yi 417 (725)
T KOG2166|consen 341 ELHDKYKVLVKECFANDTLFKKALDAAFEEFINKNVAT--SAELLATYCDDILKKGS-KKLSDEAIEDTLEKVVKLLKYI 417 (725)
T ss_pred HHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHcccCCC--cHHHHHHHhHHHhcccc-cCCchhHHHhHhhcceeeeeec
Confidence 99999999999999999999999999999999998632 26999999999999953 5678999999999999999999
Q ss_pred cChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCCcc
Q 008709 243 SDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPGID 322 (557)
Q Consensus 243 ~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~~~ 322 (557)
.+||+|+.+|++.||+|||+++|.|++.|+.||.+|++.||.+||.+|++|++|+..|+++...|.++ .+....++++
T Consensus 418 sdKdvF~~~Ykk~lakRLl~~~S~sdd~E~~mIsklk~~~g~~~T~kL~~Mf~D~~~s~~l~~~F~~~--~~~~~~~~~d 495 (725)
T KOG2166|consen 418 SDKDVFAEFYKKVLARRLLFDRSASDDHEKSLITKLKNLCGEQFTSKLEGMFTDLTLSRELQTAFADY--ANYSANLGID 495 (725)
T ss_pred cHHHHHHHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHhHHHHHHHhhcccHHHHHHHHHHHHhh--hchhccCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999987 2222345799
Q ss_pred eEEEEeecCCCCCCCCCCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhh
Q 008709 323 LSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLF 402 (557)
Q Consensus 323 f~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Qa~iLl~F 402 (557)
|.|.|||.++||.+++.++.||++|.++++.|..||..+|+||+|.|.|++|.|+|.+++.+++++++||++||+||++|
T Consensus 496 f~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F~~~Y~~kh~gR~L~w~~~l~~~ei~~~~~~~~~~l~vst~Qm~VLlLF 575 (725)
T KOG2166|consen 496 FTVTVLTTGFWPSYKSTDINLPSEMSDCVEMFKGFYATKHNGRRLTWIYSLGTGEINGKFDKKTVELQVSTYQMAVLLLF 575 (725)
T ss_pred eeEEEeecCCcCCccCCCCCCChhHHHHHHHHHHHHhhccCCCeeeeeeccCceEEEEEecCceEEEEEEhHHHHHHHHc
Confidence 99999999999998888899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeecCCCchhhhhhHH
Q 008709 403 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPVDERKKIVE 482 (557)
Q Consensus 403 n~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~~e~~~~~~ 482 (557)
|+.+.+|+++|.+.|+++.+++.++|+||.+.|.+++.. |.+.. ++++.|.+|.+|+++++|++++.++..+.+.+.+
T Consensus 576 N~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~~~~~ 653 (725)
T KOG2166|consen 576 NNTEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMDERKKVVE 653 (725)
T ss_pred cchhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhccC-ccccC-CCCcEEEeeccccCcceeeccCCCCchhHHHHHh
Confidence 999999999999999999999999999998888666666 66666 7899999999999999999999888888888899
Q ss_pred hHHHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 008709 483 DVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 555 (557)
Q Consensus 483 ~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 555 (557)
.+++||+..|+||||||||+||.+.|.+|+.+|.+|++++|.|++.+||+|||.|||||||+|| +|+++|+|
T Consensus 654 ~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y 725 (725)
T KOG2166|consen 654 DVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY 725 (725)
T ss_pred hhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999 89999998
No 2
>KOG2167 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.5e-96 Score=744.69 Aligned_cols=530 Identities=37% Similarity=0.638 Sum_probs=499.3
Q ss_pred CccccHHhhhHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCCCcHhHHHHHHHHHHHHHHHHHH
Q 008709 3 QMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATEL 82 (557)
Q Consensus 3 ~l~~Y~~~fE~~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~l 82 (557)
.+.+|.+.|+..|++.++.+|..+.....++..+++||.+++..+.+|.+++..+++.+|...+..++.+.|+..|++.+
T Consensus 126 d~~iY~esF~~~fls~f~~lY~aE~~d~~Qel~v~eYl~h~e~~l~~E~~~~i~~~D~st~k~l~atV~~~LL~~hL~~I 205 (661)
T KOG2167|consen 126 DLQIYKESFELTFLSLFRELYAAEGQDKRQELEVPEYLEHVEGRLEEENDRVIEYFDSSTKKPLIATVERCLLSRHLDLI 205 (661)
T ss_pred HHHhhhhhhHHHHHHHHHHHHHHHhcchhhhcccHHHHHhhhhcccchHHHHHHhcccccccchHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999999999999999999999999999999999999999977799999999999999999
Q ss_pred HHHhhhHHHHhhccCCHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCccchHHHHHHHH
Q 008709 83 LEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKII 162 (557)
Q Consensus 83 l~~~~~gl~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~ 162 (557)
+.+ |+..+++.++..++.+||.|++++.++...+...|++|+.+.|.+++...+ .+..+|..++
T Consensus 206 L~k---gl~~lvDm~q~~d~~rly~L~~r~~~g~l~l~qq~sdylk~~G~KlV~de~-------------kDk~mVqELL 269 (661)
T KOG2167|consen 206 LTK---GLDSLVDMRQTSDLTRLYMLFSRVQGGQLSLLQQWSDYLKKPGFKLVIDEE-------------KDKDMVQELL 269 (661)
T ss_pred Hhc---chHHhhhhhhccchHhHHHHHHHHhcchHHHHHHHHHHHhcccceeccCch-------------hhHHHHHHHH
Confidence 875 899999999999999999999999888899999999999999999886542 2578999999
Q ss_pred HHHHHHHHHHHHhcCCC--hHHHHHHHHHHHHHhhcCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHhhhhHhhhhc
Q 008709 163 ELHDKYMEYVTNCFINH--TLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLA 240 (557)
Q Consensus 163 ~l~~~~~~li~~~F~~~--~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~ 240 (557)
+++++.+-++..||..+ ..|..++++||+.++|... .++|++||+|.|..|+.|. +..++++++..++.++.||+
T Consensus 270 ~FK~k~Dii~~~sF~~~v~e~f~~~~~~afe~fink~~--~rpAelIak~~dt~Lr~gn-k~~~d~~l~~~~d~i~~lfr 346 (661)
T KOG2167|consen 270 DFKKKVDIIVDESFLKYVAEKFLNSMSKAFETFINKRR--NRPAELIAKYVDTKLRAGN-KETSDEELEFVLDKILVLFR 346 (661)
T ss_pred HHHHHhhHHHHHHHHHhhHHHHHHHHHHHHHHHHhccc--CCHHHHHHHHHHHHHHhcc-ccccchhHHHHHHHHHHHHH
Confidence 99999999999999988 9999999999999999764 5799999999999999765 45678889999999999999
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCC
Q 008709 241 YISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPG 320 (557)
Q Consensus 241 ~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 320 (557)
|+..||+|+.+|++.||+|||.++|++.|+|..|+.+|+.+||..||++|++|++|+..|++++..|+++..++.....+
T Consensus 347 ~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ecgs~ft~kLegMfkdme~sk~i~~~f~~~~~~~~~~~~~ 426 (661)
T KOG2167|consen 347 FIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKLECGSAFTYKLEGMFKDMELSKEINRAFKQSKGANNRLEGN 426 (661)
T ss_pred HHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhhhcchHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999986654433344
Q ss_pred cceEEEEeecCCCCCCCCCCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHH
Q 008709 321 IDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLL 400 (557)
Q Consensus 321 ~~f~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Qa~iLl 400 (557)
+ +.+.|++.++||.+++.++.||++|.++++.|..||..+|.||+|.|.+++|+|++++.|..|++++.||++|++||+
T Consensus 427 l-~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F~~fyl~k~sgrklqW~~~lg~~v~ka~f~~gkkel~~slfq~~vll 505 (661)
T KOG2167|consen 427 L-LTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIFKKFYLGKHSGRKLQWQDSLGHCVLKAEFKEGKKELQVSLFQTLVLL 505 (661)
T ss_pred c-eEEEeecccccCCCCchhccCCHHHHHHHHHHHHhccccccCcceeeecCCcchhhhhhccCCchHHHHHHHHHhHhh
Confidence 5 999999999999999999999999999999999999999999999999999999999999989999999999999999
Q ss_pred hhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeecCCCc----hh
Q 008709 401 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV----DE 476 (557)
Q Consensus 401 ~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~----~e 476 (557)
+||+++.+|++||.+.|++...+|.+.|+||.|+|.++|.++|.|+.+.+++.|.+|..|+++..+|+|+++.. +|
T Consensus 506 ~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee 585 (661)
T KOG2167|consen 506 MFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEE 585 (661)
T ss_pred ccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998764 45
Q ss_pred hhhhHHhHHHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEec
Q 008709 477 RKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 556 (557)
Q Consensus 477 ~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yi 556 (557)
.+.|.++|.+||.+.||||||||||+||+|+|+.|+.++.++++ |+..+ ++|+|||+||+|||++|| +| +.|.||
T Consensus 586 ~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el~~qlk--fpv~~-d~kkriesli~rey~erd-~n-~~y~yv 660 (661)
T KOG2167|consen 586 NKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTELFNQLK--FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYV 660 (661)
T ss_pred hhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHHHHhcC--CCCCh-hHHHHHHHHHhHHHhccc-cc-cccccc
Confidence 67788999999999999999999999999999999999999997 98887 999999999999999999 44 999999
Q ss_pred C
Q 008709 557 A 557 (557)
Q Consensus 557 a 557 (557)
|
T Consensus 661 a 661 (661)
T KOG2167|consen 661 A 661 (661)
T ss_pred C
Confidence 8
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.1e-93 Score=736.02 Aligned_cols=546 Identities=34% Similarity=0.575 Sum_probs=486.9
Q ss_pred CccccHHhhhHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCCCcHhHHHHHHHHHHHHHHHHHH
Q 008709 3 QMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATEL 82 (557)
Q Consensus 3 ~l~~Y~~~fE~~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~l 82 (557)
++.+|.+.||+.||+.|.+||..+++..+...++.+||.+|+.++++|..+++.|++.++..++..+++++||..|.+.|
T Consensus 214 ~l~~y~s~Fep~fL~~t~~fY~~ess~~i~~~~~~eyL~ka~~~~~~E~~~v~~yl~~~~~kpl~~~~edvLi~~hld~l 293 (773)
T COG5647 214 NLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVSTKKPLLEVLEDVLITRHLDDL 293 (773)
T ss_pred cchhhHHhhhHHHHHHhHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhhhhccHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHhhhHHHHhhccCCHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhhHHHhh-hcCC----CCCccchHHH
Q 008709 83 LEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAAT-NQGG----SSGAVQEQVL 157 (557)
Q Consensus 83 l~~~~~gl~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~-~~~~----~~~~~~~~~~ 157 (557)
.+.. +|+..+++..+.+.|..||+++++.+.++..|.+.|..||...|.- ++.....+. +++. ......+..+
T Consensus 294 ~~~~-s~f~~~~d~~~~e~l~~lY~l~se~~~~v~pl~~~f~~yV~~~g~~-~~i~~~~~~~~~~~~~~~~~~e~~~~~~ 371 (773)
T COG5647 294 EEQG-SGFREALDASNLEKLQVLYRLLSETKYGVQPLQEVFERYVKDEGVL-INIETNYIFHCKVDVGFLGSRECLPKLY 371 (773)
T ss_pred Hhch-HHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHhhchh-hhhHHhhhhccchhhcccchhhhcHHHH
Confidence 7754 8999999999999999999999999999999999999999999922 222111111 1110 0012457899
Q ss_pred HHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCCC-CCCcHHHHHHHHHHHhhcCCCCCCChHHHHHhhhhHh
Q 008709 158 IRKIIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVG-GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVV 236 (557)
Q Consensus 158 I~~l~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~n~~~~-~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~ 236 (557)
++.++++++.+..++.+.|.+|..+..++.+||..++|.+.+ ...++|+||+|+|.+|+++++ ..-...++..+.+++
T Consensus 372 ~q~lls~~~~~~~l~~~sf~~D~~~~~~l~~AF~~fin~~~sa~~~~~e~Laky~D~~lkk~~k-~s~~~~i~~~l~~ii 450 (773)
T COG5647 372 VQKLLSCHDLFPSLVNESFEGDGSIVKALGNAFKTFINGNESADSGPSEYLAKYIDGLLKKDGK-QSFIGKIKDLLQDII 450 (773)
T ss_pred HHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHhccccccccccHHHHHHHhHHHhhcccc-ccccccHHHHHHHHH
Confidence 999999999999999999999999999999999999998543 256899999999999998653 222345677888999
Q ss_pred hhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCC
Q 008709 237 KLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQN 316 (557)
Q Consensus 237 ~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~ 316 (557)
.||+|+.+||+|+++|++.||+|||+++|++.+.|..||++|++.||.+||+|+++||+||..|.++...|++.. ..
T Consensus 451 tLfryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~-~s-- 527 (773)
T COG5647 451 TLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSP-QS-- 527 (773)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCc-hh--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997643 11
Q ss_pred CCCCcceEEEEeecCCCCCCC-CCCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEE---Ec
Q 008709 317 AHPGIDLSVTVLTTGFWPSYK-SSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELI---VS 392 (557)
Q Consensus 317 ~~~~~~f~~~VLs~~~WP~~~-~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~---~s 392 (557)
..+.+++.|.||+..+||..| ...+.||++|.+.++.|++||.++|+||+|.|.|+||+|+|++.|+.+++.+. ++
T Consensus 528 ~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~le~f~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s 607 (773)
T COG5647 528 YNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPILEGFKKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFS 607 (773)
T ss_pred hccccchhHHHHHHhcCCCCccccccCCChHHHHHHHHHHHHHHHhccCceEEeeeccccEEEEeeccCCccceehhHHH
Confidence 234689999999999999655 46899999999999999999999999999999999999999999987754443 56
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeecCC
Q 008709 393 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLP 472 (557)
Q Consensus 393 ~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~ 472 (557)
++|+.|+++||+++++|+++|.+.|+++..+++++|+||++.|..++. ++++.++|++.|.+|.+|+++..+|+++.+
T Consensus 608 ~~q~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l~--~~~~~~~p~~~fy~ne~f~~~~~rIki~~~ 685 (773)
T COG5647 608 VYQLLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVLL--KDDKLVSPNTKFYVNENFSSKLERIKINYI 685 (773)
T ss_pred HHHHHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheeeec--cccccCCCCceEEEccccccccceeeeccc
Confidence 789999999999999999999999999999999999999977655554 447778899999999999999999999876
Q ss_pred Cc----hhhhhhHHhHHHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 473 PV----DERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 473 ~~----~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
.. +++.++++.+++||+..+||+||||||++|.|+|++|+++|+.+.+.||.|++.+||++|+.|||||||+|.++
T Consensus 686 ~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~d 765 (773)
T COG5647 686 AESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQAD 765 (773)
T ss_pred ccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccC
Confidence 53 34556778899999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CCCceEecC
Q 008709 549 NPNMFRYLA 557 (557)
Q Consensus 549 ~~~~y~Yia 557 (557)
| .+|+|+|
T Consensus 766 d-~iY~YLa 773 (773)
T COG5647 766 D-EIYVYLA 773 (773)
T ss_pred C-ceeeecC
Confidence 8 8999997
No 4
>KOG2284 consensus E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-87 Score=647.84 Aligned_cols=507 Identities=30% Similarity=0.529 Sum_probs=472.1
Q ss_pred CCccccHHhhhHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCCCcHhHHHHHHHHHHHHHHHHH
Q 008709 2 GQMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATE 81 (557)
Q Consensus 2 ~~l~~Y~~~fE~~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ 81 (557)
+.+.+|.+.||+|||.+|..||+++|+..+.+.+|++|+.+|..++++|+-||+.||++++..+++..|++.+|..|.+.
T Consensus 214 ~~~~fyqe~fe~p~lt~t~~yy~~~a~~~l~~~~cs~yme~vi~~l~~ee~r~~kylh~ss~~kvi~~cq~~mi~~h~~~ 293 (728)
T KOG2284|consen 214 STTAFYQESFEKPLLTDTEQYYSALAQKMLTDLSCSEYMEQVIVLLEQEEMRAKKYLHESSVEKVITLCQKVMIKAHKDK 293 (728)
T ss_pred ccHHHHHHHhccccccchHHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHH
Confidence 35779999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred HHHHhhhHHHHhhccCCHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCccchHHHHHHH
Q 008709 82 LLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKI 161 (557)
Q Consensus 82 ll~~~~~gl~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l 161 (557)
|- -.|..++.+.+..||+.||.|+..+..|+..+.+.|++||..+|...++.... .+.|..||+.+
T Consensus 294 lh----a~ch~~i~~e~~~d~~nmy~ll~~i~~gl~~mv~e~~~~v~~~gl~a~s~lt~----------en~p~~fve~v 359 (728)
T KOG2284|consen 294 LH----AVCHDLITNEENKDLRNMYRLLKPIQAGLSVMVKEFEEYVKKKGLEAVSRLTG----------ENVPQQFVENV 359 (728)
T ss_pred HH----HHHHHHHhhhhhhhHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhcc----------ccchHHHHHHH
Confidence 73 46999999999999999999999999999999999999999999988876632 24689999999
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCCC---CCCcHHHHHHHHHHHhhcCCCCCCChHHHHHhhhhHhhh
Q 008709 162 IELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVG---GSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKL 238 (557)
Q Consensus 162 ~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~n~~~~---~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~l 238 (557)
+.+|.+|.+++...|.+|..|..+++.|+..++|...+ -.+.+|.||+|||.+|+++. .++++.+++.+|+..+.+
T Consensus 360 l~v~~kf~~~~~~v~~~d~~f~s~ldkal~~vvn~~epg~sv~ka~e~la~y~d~llkks~-kg~se~~~e~~l~s~i~i 438 (728)
T KOG2284|consen 360 LRVYNKFNDMKTAVFMDDGEFSSGLDKALQGVVNSKEPGQSVPKASERLARYTDGLLKKST-KGLSETDLEAKLDSAIVI 438 (728)
T ss_pred HHHHHHHHHHHHHHhcCchhhhHHHHHHHHHhhccCCCCccccchHHHHHHHhhhHHhhhh-cCCChhhHHHhhhcceee
Confidence 99999999999999999999999999999999998764 35789999999999999975 578999999999999999
Q ss_pred hccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCC
Q 008709 239 LAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAH 318 (557)
Q Consensus 239 f~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~ 318 (557)
|+|++|||+|.++|.++||+||+.+.|.|.|.|..||++|++.||.+||+++- +-|+..|.+++.+|.+.+.
T Consensus 439 f~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqacgyefts~~~--~td~~~s~~lnn~f~~~i~------ 510 (728)
T KOG2284|consen 439 FRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQACGYEFTSSWP--LTDPQLSTNLNNQFAQDIA------ 510 (728)
T ss_pred eeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHhCceecccCC--CCChhhccccchhHHHHHH------
Confidence 99999999999999999999999999999999999999999999999999998 9999999999999987654
Q ss_pred CCcceEEEEeecCCCCCCCCCCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHH
Q 008709 319 PGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAAT 398 (557)
Q Consensus 319 ~~~~f~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Qa~i 398 (557)
+|.+|.+++...+.|+.||.++|+||+|+|++.++++++++++-++.|.-.+.++||++
T Consensus 511 ---------------------nf~~pq~l~~~iq~fe~fyt~~~~grkltwl~~~~~g~v~~~yl~k~yva~~~~yqma~ 569 (728)
T KOG2284|consen 511 ---------------------NFHLPQILQPVIQEFEKFYTGKHNGRKLTWLFNMSQGDVRLTYLDKQYVAQMYVYQMAA 569 (728)
T ss_pred ---------------------hccchHHHHHHHHHHHHHhccccCCceehhhhhhcccceeeeecCchHHHHHHHHHHHH
Confidence 27899999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeecCCCc----
Q 008709 399 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIPLPPV---- 474 (557)
Q Consensus 399 Ll~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~~~~~---- 474 (557)
||+||..+.+++.||.+.+|++.+.+.+.+.++.+ .++|+- ++..+..+..|++|.+|+++..++++..|.+
T Consensus 570 ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tild--v~~~~~--d~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~ 645 (728)
T KOG2284|consen 570 LLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILD--VTLLTC--DDQNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAV 645 (728)
T ss_pred HHHhcccccchHHhhhhhhCccHHHHHHHHHHHHh--ceeecc--cccccChhhhhhccccccccceeeEecchhhcccc
Confidence 99999999999999999999999999999999975 467753 4456777888999999999999999987654
Q ss_pred -hhhhhhHHhHHHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 008709 475 -DERKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 553 (557)
Q Consensus 475 -~e~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 553 (557)
+|.+.+...+.+||++.++||||||||+||.+.|+.|+.+|+.+.+++|.|++++||++||.||++-||+|.+.+ +.|
T Consensus 646 ~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey 724 (728)
T KOG2284|consen 646 EKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEY 724 (728)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc-ccc
Confidence 344556778999999999999999999999999999999999999999999999999999999999999999875 899
Q ss_pred EecC
Q 008709 554 RYLA 557 (557)
Q Consensus 554 ~Yia 557 (557)
.|+|
T Consensus 725 ~y~a 728 (728)
T KOG2284|consen 725 QYLA 728 (728)
T ss_pred hhcC
Confidence 9998
No 5
>KOG2285 consensus E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.9e-76 Score=578.76 Aligned_cols=542 Identities=29% Similarity=0.505 Sum_probs=481.4
Q ss_pred CccccHHhhhHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCC--CcHhHHHHHHHHHHHHHHHH
Q 008709 3 QMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHS--SSEPKLVEKVQHELLVVYAT 80 (557)
Q Consensus 3 ~l~~Y~~~fE~~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~--~t~~~l~~~l~~~LI~~~~~ 80 (557)
.|.+|.+.||..||+.|.+||+..+..++++.++.+|+..++.-+++|+.|+.+||.. .+..+++..+.+.|+.++.+
T Consensus 192 kL~iYR~nFE~ayl~~T~efYr~~~~~~lqenGVl~YMkYAD~KL~EEe~RAkRYLE~~~~s~~~lme~~VnaLv~sf~~ 271 (777)
T KOG2285|consen 192 KLLIYRQNFERAYLEQTTEFYRKICGNLLQENGVLEYMKYADKKLEEEEQRAKRYLEMNSPSSGKLMEKAVNALVESFED 271 (777)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHhhhhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHH
Confidence 5779999999999999999999999999999999999999999999999999999865 67789999999999999999
Q ss_pred HHHHHhhhHHHHhhccCCHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCccchHHHHHH
Q 008709 81 ELLEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRK 160 (557)
Q Consensus 81 ~ll~~~~~gl~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~I~~ 160 (557)
.|+. .|..|+...+.+.|++||+|+.+++.|++.+.+.+..+|.+.|.+-+....+.+ +.++..||++
T Consensus 272 tIlA----EC~~lI~~~etErL~lmfrLmdrv~~Giepmlkdl~~HI~saGLaDM~~aaE~i--------ttDsEkYVeq 339 (777)
T KOG2285|consen 272 TILA----ECSKLIASKETERLQLMFRLMDRVRSGIEPMLKDLDTHIRSAGLADMRNAAENI--------TTDSEKYVEQ 339 (777)
T ss_pred HHHH----HHHHHHhhhhHHHHHHHHHHHHHhhhcchhHHHHHHHHHHhhhHHHHHhhhhhc--------cCCHHHHHHH
Confidence 9986 588999999999999999999999999999999999999999987665544333 3578899999
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCC------------------CCCCcHHHHHHHHHHHhhcC-CCC
Q 008709 161 IIELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAV------------------GGSSSSELLATFCDNILKKG-GNE 221 (557)
Q Consensus 161 l~~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~n~~~------------------~~~~~~e~La~y~d~~l~~~-~~~ 221 (557)
|+.++++|..++.++|+.|+.|..|-+.||..++|... +..++||+||.|||.+||+. .+.
T Consensus 340 LL~lFnkFS~LVreaF~DDpRfLTARDkAfkaVVNDssiFK~Elp~~~kgrglkt~pESKCpELLANYCDmLLRkTpLSK 419 (777)
T KOG2285|consen 340 LLLLFNKFSSLVREAFCDDPRFLTARDKAFKAVVNDSSIFKTELPNSKKGRGLKTAPESKCPELLANYCDMLLRKTPLSK 419 (777)
T ss_pred HHHHHHHHHHHHHHHhcCChhhhhhhHHHHHHhhcchhhhhhhccchhcCCccccCcccccHHHHHHHHHHHHhcCccch
Confidence 99999999999999999999999999999999999753 23578999999999999984 245
Q ss_pred CCChHHHHHhhhhHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhC--ChhhHhHHHHHHHHHH
Q 008709 222 KLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCG--GQFTSKMEGMVTDLTL 299 (557)
Q Consensus 222 ~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G--~~~~~kl~~Ml~D~~~ 299 (557)
+++.++++.+|++++-+++|+.+||+|+.|++.+|++||+...|++.+.|..|+..|+ +|| .+|++++.+|++|++.
T Consensus 420 kLTSEeIdakL~~VLLVLKYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLR-EvGMPaDyVNkLaRMfQDIkv 498 (777)
T KOG2285|consen 420 KLTSEEIDAKLNQVLLVLKYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLR-EVGMPADYVNKLARMFQDIKV 498 (777)
T ss_pred hccHHHHHHHHHhHhhHhHhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH-HcCCcHHHHHHHHHHHhhccc
Confidence 7889999999999999999999999999999999999999999999999999999998 588 4799999999999999
Q ss_pred hHHHHHHHHHHHhcCCCCCCCcceEEEEeecCCCCCCCC-CCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEE
Q 008709 300 ARENQTSFEEYLSNNQNAHPGIDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNI 378 (557)
Q Consensus 300 S~~l~~~f~~~~~~~~~~~~~~~f~~~VLs~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l 378 (557)
|++++..|+..+...+...+.-.+++.||+.|.|...+. ..+.||.++++.+-.-++||+++|+||+|.|.|+++.++|
T Consensus 499 seDlN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdveEfykk~hsgrkl~w~h~msNG~i 578 (777)
T KOG2285|consen 499 SEDLNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDVEEFYKKKHSGRKLQWYHHMSNGTI 578 (777)
T ss_pred cHHHHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccHHHHHhcccCccchhhhhhccCCee
Confidence 999999999988766544455678999999999997643 4689999999999999999999999999999999999999
Q ss_pred EeEecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHHHHHHHHhhhc---ccceeeecCCCC----CCCC
Q 008709 379 NGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVRLLHSLSC---AKYKILLKEPNT----KTIS 449 (557)
Q Consensus 379 ~~~~~~~~~~l~~s~~Qa~iLl~Fn~~--~~~t~~el~~~~~i~~~~l~~~L~~L~~---~k~~iL~~~~~~----~~~~ 449 (557)
++..+-|.|.+.|+++||+||.+||+. +.+|++.+.-.|.+|..++.+.|-||+. .|+.||...|.. +++.
T Consensus 579 tf~n~~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~k~QiLL~ep~~~~spkDFt 658 (777)
T KOG2285|consen 579 TFVNNFGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKMKYQILLCEPPTTVSPKDFT 658 (777)
T ss_pred EeecccccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhhhhheeeecCcccCCccccc
Confidence 887666899999999999999999975 6899999999999999999999999973 356777766532 3456
Q ss_pred CCCeEEEccCCCCC-----cceeeecCCCc----hh--hhhhHHhHHHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHH
Q 008709 450 QSDHFEFNSKFTDR-----MRRIKIPLPPV----DE--RKKIVEDVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQ 518 (557)
Q Consensus 450 ~~~~~~~N~~f~~~-----~~~i~i~~~~~----~e--~~~~~~~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~ 518 (557)
++..|.+|.+|.-- .++-+++...- .| ..+..+.+.+-|-...+-+||+|||.||+++..+|-.+..+.
T Consensus 659 e~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nAqLq~ELveI 738 (777)
T KOG2285|consen 659 ESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNAQLQMELVEI 738 (777)
T ss_pred ccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 78899999999621 12233332211 11 122346678889999999999999999999999999999999
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 519 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 519 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
|+..|.|+..+||+.||.|||..|++||++|-|+|+|+|
T Consensus 739 LKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia 777 (777)
T KOG2285|consen 739 LKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA 777 (777)
T ss_pred HHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence 999999999999999999999999999999999999997
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=9.1e-72 Score=616.72 Aligned_cols=439 Identities=42% Similarity=0.744 Sum_probs=387.8
Q ss_pred CccccHHhhhHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCCCcHhHHHHHHHHHHHHHHHHHH
Q 008709 3 QMDSYEKDFEEHMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATEL 82 (557)
Q Consensus 3 ~l~~Y~~~fE~~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~l 82 (557)
++.+|.+.||++||+.|.+||+.++ +...++.+|+.+|+.++.+|.+||..|++++|.+++.+.+.++||..|.+.|
T Consensus 148 ~~~~y~~~fe~~~l~~t~~yY~~~~---i~~~~~~~Yl~~v~~~l~~E~~r~~~~l~~~t~~ki~~~l~~~LI~~~~~~l 224 (588)
T PF00888_consen 148 SLEVYEEEFEKPFLEETKEYYKSES---IQENSVSEYLKKVENRLKEEEERVQKYLHPSTKEKIIKTLEEVLISDHLDEL 224 (588)
T ss_dssp HTHHHHHHTHHHHHHHHHHHHHHHH---HHHSHHHHHHHHHHHHHHHHHHHHHHCS-GGGHHHHHHHHHHHHTGGGHHHH
T ss_pred hHHhhHHHHHHHHHHHHHHHHHHHH---HHhcCchhHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999999 5677999999999999999999999999999999999999999999999988
Q ss_pred HHHhhhHHHHhhccCCHHHHHHHHHhhccCCCChhhHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCccchHHHHHHHH
Q 008709 83 LEKEQSGCRALLREDKVEDLSRMYRLYHKIPKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKII 162 (557)
Q Consensus 83 l~~~~~gl~~ll~~~~~~~L~~ly~l~~~~~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~ 162 (557)
.+|+..|+++++.++|++||+|+++++++++.+++.|+++|...|..+++.... ...+..+|+.++
T Consensus 225 ----~~~~~~ll~~~~~~~L~~ly~l~~~~~~~~~~l~~~~~~~i~~~g~~~~~~~~~----------~~~~~~~i~~ll 290 (588)
T PF00888_consen 225 ----SSGFRDLLEEDDKEDLKRLYRLFSRVPNGLESLRDAFKEYIKKEGQNIIDSFEK----------SSDPKEFIEDLL 290 (588)
T ss_dssp ----HTCHHHHHHTT-HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHCC----------GGGCHHHHHHHH
T ss_pred ----HHHHHHHHHhhHHHHHHHHHHHhhcccCCCchHHHHHHHHHHHHhHHHHhhccc----------ccchHHHHHHHH
Confidence 369999999999999999999999999999999999999999999999986531 245789999999
Q ss_pred HHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhcCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHHhhhhHhhhhccc
Q 008709 163 ELHDKYMEYVTNCFINHTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEETLEKVVKLLAYI 242 (557)
Q Consensus 163 ~l~~~~~~li~~~F~~~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~~l~~i~~lf~~l 242 (557)
++|+++..++.+||++++.|..++++||+.++|.. ...++++||+|||.+|++++ .+.++++.+..++.++.+|+|+
T Consensus 291 ~l~~~~~~l~~~~F~~~~~f~~~l~~af~~~~n~~--~~~~~e~La~y~d~~l~~~~-~~~~~~~~~~~~~~i~~l~~~l 367 (588)
T PF00888_consen 291 ELYDKYEKLIQECFDNDSEFKKALDEAFEEFLNKN--NNKIPELLAKYCDSLLRKSN-KKLSEEEIEQKLDDIVKLFSYL 367 (588)
T ss_dssp HHHHHHHHHHHHTTTT-HHHHHHHHHHHHHHHHCS--TSHHHHHHHHHHHHHHBSSC-CCS-HCCHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHhccccHHHHHHHHHhHHHHHHcC--CcchHHHHHHHhhHhhhhcc-cccchHHHHHHhhhhEEEeeec
Confidence 99999999999999999999999999999999988 36899999999999999875 4567788999999999999999
Q ss_pred cChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCC-CCc
Q 008709 243 SDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAH-PGI 321 (557)
Q Consensus 243 ~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~-~~~ 321 (557)
++||+|+.+|+++||+|||.+++.+.+.|..+|++|+.+||.+++++|++|++|+..|+++++.|++.....+... +++
T Consensus 368 ~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~~~g~~~~~kl~~M~~D~~~S~~~~~~f~~~~~~~~~~~~~~~ 447 (588)
T PF00888_consen 368 SDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKKECGSSYTSKLEVMLKDIKNSKELNEEFKQKQSQNNIQLIPPF 447 (588)
T ss_dssp STHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-SS--CC
T ss_pred chhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhcccCchhHHHHHHHHHHHhhcHHHHHHHHHHhhhccccccCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999987655432 279
Q ss_pred ceEEEEeecCCCCCCCCCC-CcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHH
Q 008709 322 DLSVTVLTTGFWPSYKSSD-LNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLL 400 (557)
Q Consensus 322 ~f~~~VLs~~~WP~~~~~~-~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Qa~iLl 400 (557)
+|+|.||++++||..+... +.+|++|+.+++.|++||+.+|+||+|+|.+.+|+|+|++++++++++++||++||+||+
T Consensus 448 ~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~s~~q~~iLl 527 (588)
T PF00888_consen 448 DFNVKVLSKGYWPKYPSENNIKLPPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTVSTLQAAILL 527 (588)
T ss_dssp EEEEEEEETTTS-S-S-SS-----HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEEEHHHHHHHH
T ss_pred ceEEEEecCCCCCCCCCCccccCCHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEeeHHHHHHHH
Confidence 9999999999999988766 999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 008709 401 LFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 461 (557)
Q Consensus 401 ~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 461 (557)
+||+.+++|+++|++.||++.++++++|.+|+..+..++.+.+++.++++++.|.+|.+|+
T Consensus 528 ~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 528 LFNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp GGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEEETTTSSS--TT-EEEE-TT--
T ss_pred HHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceeecCCccCCCCCCCEEEeCCCCC
Confidence 9999999999999999999999999999999865433333678888899999999999996
No 7
>smart00182 CULLIN Cullin.
Probab=100.00 E-value=1.8e-33 Score=251.70 Aligned_cols=141 Identities=48% Similarity=0.896 Sum_probs=132.4
Q ss_pred cccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHHHhcCCCCCCC
Q 008709 241 YISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEYLSNNQNAHPG 320 (557)
Q Consensus 241 ~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~~~~~~~~~~~ 320 (557)
|+++||+|+.+|+++||+|||..++.+.+.|..+|++|+.+||.+++++|++|++|+..|++++++|++.+..++ ...+
T Consensus 1 y~~~Kd~F~~~Y~~~La~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kle~Ml~Di~~S~~l~~~f~~~~~~~~-~~~~ 79 (142)
T smart00182 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLSKDLNQSFKDMLENNS-NKPI 79 (142)
T ss_pred CCCchHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999998876532 2346
Q ss_pred cceEEEEeecCCCCCCCC-CCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEe
Q 008709 321 IDLSVTVLTTGFWPSYKS-SDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKF 382 (557)
Q Consensus 321 ~~f~~~VLs~~~WP~~~~-~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~ 382 (557)
++|+|.|||+++||..+. ..+.||++|+.+++.|++||..+|++|+|+|.+++|+|+|+++|
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 78999999999999999999999999999999999999999864
No 8
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.3e-28 Score=255.04 Aligned_cols=302 Identities=24% Similarity=0.323 Sum_probs=240.5
Q ss_pred hhHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHhHHHHHHHHHHhHHHHHHHHHH--
Q 008709 233 EKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQTSFEEY-- 310 (557)
Q Consensus 233 ~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~kl~~Ml~D~~~S~~l~~~f~~~-- 310 (557)
+-+..|++.+++|+.|++.|+.+||.||+.....+.+.|..-++.||-+||.+..+.|++|++|+..|+++++.++..
T Consensus 440 Di~~mLVsIygSKElfv~EyRnLLAdRLl~~~dy~~E~E~R~leLLKlrFgEt~lq~CevML~Dv~dS~~id~~i~~~~~ 519 (765)
T KOG2165|consen 440 DIFGMLVSIYGSKELFVKEYRNLLADRLLTLTDYDPEKEIRNLELLKLRFGETSLQGCEVMLNDVIDSRRIDQSIHNESE 519 (765)
T ss_pred cHHHHHHHHHcchHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhhhhhhhh
Confidence 345578888999999999999999999999999999999999999999999999999999999999999999999874
Q ss_pred HhcCCCCCCCcceEEEEeecCCCCCCCCCCCcCCHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeEecCeeEEEE
Q 008709 311 LSNNQNAHPGIDLSVTVLTTGFWPSYKSSDLNLPSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGKFEQKNIELI 390 (557)
Q Consensus 311 ~~~~~~~~~~~~f~~~VLs~~~WP~~~~~~~~lP~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~ 390 (557)
........+.+.+++.+||+.+||......+.+|.+++.+++.|.+-|.+..++|+|.|.+++|.|++++.|.+++.+++
T Consensus 520 ~~r~~e~~~~~~i~~~IlS~~fWP~~~~~~~~lP~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~t 599 (765)
T KOG2165|consen 520 LSRGAEEVPDFGISATILSSLFWPPLCDEAFHLPGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLT 599 (765)
T ss_pred hhcccccCCCCchhhhhhhhhcCCccccccccCChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEe
Confidence 32222233468899999999999998888899999999999999999999999999999999999999999999999999
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCcceeeec
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRIKIP 470 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i~i~ 470 (557)
||+.||+|+.+|.+.++||++++++.+|+|...+++.|..|.+ .|+|..+|. ++++..|+++++-.+.-+-- .
T Consensus 600 Vsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~--~GvL~e~~~---~s~tgt~T~iEse~d~~q~~--~ 672 (765)
T KOG2165|consen 600 VSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQ--KGVLREEPI---ISDTGTLTVIESEMDFDQAE--G 672 (765)
T ss_pred eCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHH--cCeeecCCC---CCCCceeeeccccccccccC--C
Confidence 9999999999999999999999999999999999999999984 489987643 36788899988644322111 1
Q ss_pred CCCc--hh-h--hhhHHhHHHhh--HHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCC-------ChHHHHHHHHh
Q 008709 471 LPPV--DE-R--KKIVEDVDKDR--RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKP-------DIKAIKKRMED 536 (557)
Q Consensus 471 ~~~~--~e-~--~~~~~~~~~~r--~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~-------~~~~ik~~Ie~ 536 (557)
.+.. ++ . ......+++-+ -..-...||-.+=.-+.|..+-+.+... .|.| +-++++.-+..
T Consensus 673 ~~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLk-----mF~~~~~~~~~TlqeL~~fLq~ 747 (765)
T KOG2165|consen 673 TVLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLK-----MFVPPDGSAEITLQELQGFLQR 747 (765)
T ss_pred CcccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHe-----eeecCCCCCcccHHHHHHHHHH
Confidence 1111 11 1 11122222211 1233457777777779999998886432 4544 34556666666
Q ss_pred hhhhcccccc
Q 008709 537 LITRDYLERD 546 (557)
Q Consensus 537 Liereyi~r~ 546 (557)
++.-|-++-.
T Consensus 748 kV~e~kL~f~ 757 (765)
T KOG2165|consen 748 KVREGKLEFI 757 (765)
T ss_pred HhhccceEEe
Confidence 6665555544
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=99.81 E-value=1.4e-20 Score=144.75 Aligned_cols=67 Identities=51% Similarity=0.962 Sum_probs=62.0
Q ss_pred HHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCC
Q 008709 485 DKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPN 551 (557)
Q Consensus 485 ~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~ 551 (557)
+++|...|+|+||||||++|+++|++|+.+|.++++++|.|+..+||++||.||++|||+||++|+|
T Consensus 2 ~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 2 EQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred cchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 5789999999999999999999999999999999999999999999999999999999999999876
No 10
>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=94.40 E-value=0.12 Score=42.39 Aligned_cols=66 Identities=17% Similarity=0.229 Sum_probs=52.8
Q ss_pred EEEEcHHHHHHHHhhc--------CCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 008709 388 ELIVSTYQAATLLLFN--------TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 459 (557)
Q Consensus 388 ~l~~s~~Qa~iLl~Fn--------~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 459 (557)
...+++-|+.+|+..- ....+|-.||++.+|++.+.+.++|..|. +.++|.+.. ....|.+|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le--~~GlI~r~~------~~~~~~~n~~ 91 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLA--RRRIIFRQG------MMGIVGVNTP 91 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeeeec------CCceeecCCC
Confidence 3567888998888655 45689999999999999999999999997 457887531 2478999988
Q ss_pred CC
Q 008709 460 FT 461 (557)
Q Consensus 460 f~ 461 (557)
++
T Consensus 92 ~~ 93 (95)
T TIGR01610 92 LS 93 (95)
T ss_pred cc
Confidence 64
No 11
>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=94.16 E-value=0.16 Score=40.55 Aligned_cols=60 Identities=15% Similarity=0.200 Sum_probs=42.7
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCC
Q 008709 394 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 460 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~-~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 460 (557)
+++.+.+..+..+ .+|.++|++.+++++..+.+.++.|. +.+++...+ | +++.|.++.+-
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~--~~Gli~s~~-G----~~GGy~L~~~~ 71 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK--KAGLIESSR-G----RGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEET-S----TTSEEEESS-C
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh--hCCeeEecC-C----CCCceeecCCH
Confidence 4455555544444 49999999999999999999999997 568886542 1 46788887653
No 12
>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=93.05 E-value=0.2 Score=35.24 Aligned_cols=42 Identities=19% Similarity=0.299 Sum_probs=34.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
+..+..||....+++.+|..||++.+|++...+.++|..|..
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 456778888888888899999999999999999999999963
No 13
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=92.88 E-value=0.18 Score=36.25 Aligned_cols=45 Identities=27% Similarity=0.294 Sum_probs=36.6
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 396 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 396 a~iLl~Fn~~~-~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+.||..|.+.+ .+|+.||++.+|++...+.+.|..|.. .+++.+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~--~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE--EGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEC
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CcCeecC
Confidence 46788888765 489999999999999999999999974 4677653
No 14
>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=92.72 E-value=0.16 Score=37.79 Aligned_cols=51 Identities=20% Similarity=0.337 Sum_probs=42.2
Q ss_pred EcHHHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 391 VSTYQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~--~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
+|+.|+.||..+...+. +|..+|++.++++...+.+.+..|. +.+++.+.+
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 46789999988777666 9999999999999999999999997 457877653
No 15
>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=92.14 E-value=0.41 Score=35.17 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=38.8
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
|..|+...++.+.+|+++|++.+|+++..+++-|..|.. .+++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~--~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEK--QGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEE
Confidence 456777788889999999999999999999999999974 4666654
No 16
>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=90.66 E-value=0.2 Score=36.90 Aligned_cols=50 Identities=18% Similarity=0.357 Sum_probs=42.5
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+|..|+.+|....+.+.++..+|++.++++...+.+.+..|. +.+++.+.
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~--~~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE--KKGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH--HCCCEEec
Confidence 367899999888888889999999999999999999999997 44777764
No 17
>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=90.45 E-value=0.47 Score=35.88 Aligned_cols=50 Identities=16% Similarity=0.279 Sum_probs=38.5
Q ss_pred EcHHHHHHHHhhc-CCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 391 VSTYQAATLLLFN-TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn-~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+|..|..||.... ..+.++..+|++.++++...+-+.++.|.. .+++.+.
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 4678899998888 778999999999999999999999999974 4788654
No 18
>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=89.94 E-value=0.71 Score=40.31 Aligned_cols=60 Identities=17% Similarity=0.201 Sum_probs=46.7
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
+..|++++-..+.++..+++... .....+....|...|..|.+||||+|..+ ...|.|-|
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l----~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p 65 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRIL----AEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTA 65 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHH----hhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEe
Confidence 56688888778888877777644 33456778889999999999999999864 45788865
No 19
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=89.75 E-value=0.71 Score=39.45 Aligned_cols=62 Identities=21% Similarity=0.302 Sum_probs=53.4
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
..++.|++||=.++..+.+|++.++.. .+.++...|+--|..|..||.|.+.-+ ...|.|-|
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 457889999999999999999987665 477899999999999999999999874 57788854
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=89.43 E-value=0.72 Score=39.41 Aligned_cols=51 Identities=12% Similarity=0.209 Sum_probs=44.7
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.++..|+.||.....++.+|..+|++.+|++...+-+.+..|. +.+++.+.
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le--~~GlI~r~ 75 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLE--RDGLVTRL 75 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHH--HCCCEEec
Confidence 4578999999988888899999999999999999999999997 45788765
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=89.16 E-value=1 Score=31.55 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=34.4
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
...-||.+.-+ ++.++.||++.+|++...+.++|..|. +.+++.
T Consensus 3 ~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~--~~glV~ 46 (47)
T PF01022_consen 3 TRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLR--EAGLVE 46 (47)
T ss_dssp HHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEE
T ss_pred HHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHH--HCcCee
Confidence 34566766666 679999999999999999999999996 346653
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=88.76 E-value=0.62 Score=34.64 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=39.6
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
++.-..||..+...+++|+.+|++.+|++...+..+|..|. +.+++...
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 45566788888667789999999999999999999999997 45777643
No 23
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=88.20 E-value=1 Score=40.01 Aligned_cols=53 Identities=19% Similarity=0.183 Sum_probs=45.1
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 389 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 389 l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
..++..|+.||......+.+|..+|++.++++...+-+.+..|. +.+++.+.+
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 45677899999877667789999999999999999999999997 558887753
No 24
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=87.98 E-value=1.6 Score=33.38 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=38.0
Q ss_pred HHHHHHHhhcCCCC--cCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 394 YQAATLLLFNTSDR--LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~--~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..-.||..+.+.+. +|..||++.+|++...+.++|..|. +.+++.+.
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 34467777777655 9999999999999999999999996 34677654
No 25
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=87.76 E-value=1.7 Score=39.11 Aligned_cols=58 Identities=10% Similarity=0.087 Sum_probs=42.6
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 459 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 459 (557)
.+.+.|..+..+.+|..+|++..++|...|.+.|+.|. +.+++..... .++.|.++.+
T Consensus 12 r~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~--~aGlv~S~rG-----~~GGy~La~~ 69 (153)
T PRK11920 12 RMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLV--EAGLVETVRG-----RNGGVRLGRP 69 (153)
T ss_pred HHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeecC-----CCCCeeecCC
Confidence 34445555666678999999999999999999999997 5688875421 3455665543
No 26
>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=87.61 E-value=0.44 Score=36.51 Aligned_cols=46 Identities=17% Similarity=0.328 Sum_probs=36.5
Q ss_pred HHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 495 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 495 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
.|-.+|+.++.++.++|-. +|..+++.+...|+.|+.+|||++.+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~--------~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAR--------EFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHH--------HTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 3556788899999888864 588999999999999999999998753
No 27
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=86.82 E-value=2.1 Score=38.99 Aligned_cols=58 Identities=12% Similarity=0.178 Sum_probs=42.1
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 008709 395 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 459 (557)
Q Consensus 395 Qa~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 459 (557)
.+.+.+.|+.. ..+|.++|++.+|+|...+.+.|+.|. +.+++..... +++.|.+..+
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~--~aGLv~s~rG-----~~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR--KNGLVSSVRG-----PGGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEeCCC-----CCCCeeccCC
Confidence 34455567654 579999999999999999999999997 5688875311 2345665444
No 28
>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=86.68 E-value=0.57 Score=39.95 Aligned_cols=60 Identities=10% Similarity=0.197 Sum_probs=46.8
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
+..|++++=..+.++..+++..+ .....+....|...|..|.+||||.|... ...|.|-|
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~~l----~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p 64 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHEAL----PEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSP 64 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHH----CTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEE
T ss_pred HHHHHHHHHhCCCCCHHHHHHHH----HhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEe
Confidence 56788888888888888887644 44456788999999999999999999874 46788864
No 29
>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=85.39 E-value=1.8 Score=31.25 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=29.1
Q ss_pred HHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 397 ATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 397 ~iLl~F-n~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.||..+ +..+.+|.++|++.+|++...+.+.|..|..
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 5666699999999999999999999998853
No 30
>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=84.82 E-value=2.5 Score=35.58 Aligned_cols=52 Identities=25% Similarity=0.367 Sum_probs=43.1
Q ss_pred EEcHHHHHHHHhhc----CCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 390 IVSTYQAATLLLFN----TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn----~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
.+|..|..||.... ..+.+|..+|+..++++...+-+.+..|. +.+++.+.+
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 45788888886655 55689999999999999999999999997 458887653
No 31
>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=84.71 E-value=2.8 Score=36.80 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=35.7
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 395 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 395 Qa~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.+.+.+.++.. ..+|.++|++.+++|...+.+.|..|. +.+++..
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~--~~glv~s 57 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR--KAGLVKS 57 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCceEE
Confidence 34445555544 479999999999999999999999997 5688864
No 32
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=83.74 E-value=2.9 Score=37.44 Aligned_cols=59 Identities=15% Similarity=0.208 Sum_probs=44.3
Q ss_pred HHHHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 008709 394 YQAATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 459 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~-~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 459 (557)
+++.+.|.-+..+ .+|+++|++..|+|+..|.+.|..|. |.+++...+. +++.|.++.+
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~--kaGlV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLR--KAGLVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH--HcCCEEeecC-----CCCCccCCCC
Confidence 4555556555555 68899999999999999999999996 6788875421 3566777665
No 33
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=82.31 E-value=3.4 Score=35.57 Aligned_cols=37 Identities=22% Similarity=0.271 Sum_probs=33.3
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 404 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 404 ~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.++..|+++|++.++.+...+.++|+.|.. .+++.+.
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~--~GlV~Re 75 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLE--AGLVERE 75 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHH--cCCeeee
Confidence 677899999999999999999999999974 5888775
No 34
>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=81.97 E-value=1.4 Score=33.41 Aligned_cols=49 Identities=22% Similarity=0.274 Sum_probs=39.3
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
|-.++.|+...-..+..|..||++.+|++...+.++|..|.. .+++.+.
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 445666665555667899999999999999999999999974 4777654
No 35
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=81.95 E-value=2.8 Score=34.07 Aligned_cols=52 Identities=21% Similarity=0.261 Sum_probs=44.4
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 389 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 389 l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..++..+..||......+.++..+|++.++++...+.++|..|.. .+++.+.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~--~g~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK--KGLIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH--CCCeEec
Confidence 556788899998888777899999999999999999999999973 4777653
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=81.85 E-value=3 Score=29.28 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=34.3
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.|+..+.+...++..+|++.++++...+.+.|..|.. .+++..
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~--~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEE--QGLLTR 46 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEE
Confidence 4555556667799999999999999999999999974 355554
No 37
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=80.83 E-value=3.7 Score=32.89 Aligned_cols=45 Identities=22% Similarity=0.345 Sum_probs=37.0
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 396 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 396 a~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..||..+... +.+|+.||++.+|++...+.+.|..|. ..+++.+.
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 3466667665 689999999999999999999999997 35788654
No 38
>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=80.00 E-value=6.8 Score=32.45 Aligned_cols=62 Identities=24% Similarity=0.393 Sum_probs=46.3
Q ss_pred EEcHHHHHHHHh-------hcC-CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 008709 390 IVSTYQAATLLL-------FNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 461 (557)
Q Consensus 390 ~~s~~Qa~iLl~-------Fn~-~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 461 (557)
.++.-|.-|++. ||. .+.+|..++++.||++...+.+++..|+ +.++|... +..+-+|.+++
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 455566666655 454 3589999999999999999999999997 56888653 45566666553
No 39
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=79.96 E-value=3.9 Score=38.04 Aligned_cols=52 Identities=13% Similarity=-0.008 Sum_probs=44.9
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 389 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 389 l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+.+|..|+.||......+.+|..+|++.++++...+.+.+..|. +-+++.+.
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE--~kGlI~R~ 92 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE--ERGYLTFS 92 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH--HCCCEEec
Confidence 45677899999998888899999999999999999999999996 44788765
No 40
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=79.24 E-value=4.5 Score=30.26 Aligned_cols=56 Identities=21% Similarity=0.206 Sum_probs=37.4
Q ss_pred HHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEc
Q 008709 398 TLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFN 457 (557)
Q Consensus 398 iLl~Fn~-~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N 457 (557)
||-.++. +.+++..||++.+|++...+...|..|. +.+.+.+.|.+... ...|.+|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le--~eG~V~~~~~~rG~--~~~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE--KEGKVERSPVRRGK--STYWRLN 61 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH--HCTSEEEES-SSSS--S-EEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HCCCEEEecCCCCc--ceeeeec
Confidence 4444555 6789999999999999999999999997 44666655443221 1356665
No 41
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=78.90 E-value=4.1 Score=36.01 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=43.9
Q ss_pred EEEcHHHHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 389 LIVSTYQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 389 l~~s~~Qa~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
+.+|..|..+|...... +.+|..+|++.++++...+.+.+..|. +.+++.+.+
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 45677898888877654 568999999999999999999999997 458887653
No 42
>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=77.66 E-value=6.2 Score=34.22 Aligned_cols=46 Identities=20% Similarity=0.272 Sum_probs=35.2
Q ss_pred HHHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 394 YQAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 394 ~Qa~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
+++.+.+.-++. ..+|.++|++.+++|...+.+.|..|. +.++|..
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~--~~gli~~ 57 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLR--RAGLVES 57 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 344444544433 389999999999999999999999997 4577764
No 43
>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=76.97 E-value=1.2 Score=33.92 Aligned_cols=56 Identities=13% Similarity=0.274 Sum_probs=41.5
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEec
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYL 556 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yi 556 (557)
++.|-..|-..+.++..+|...+ ..+...+-+.++.|.++|+|+|.+.++..|..+
T Consensus 10 E~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 10 EAKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 55555555577778877776533 347788999999999999999998766555554
No 44
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=76.95 E-value=5.7 Score=39.05 Aligned_cols=45 Identities=11% Similarity=0.278 Sum_probs=39.2
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+.||.+|.....+|+.||++.+|+|...+.+.|..|.. .+.|.+.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~--~G~l~~~ 61 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT--LGYVAQE 61 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEc
Confidence 46888888877899999999999999999999999974 5788664
No 45
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=76.78 E-value=3.4 Score=37.65 Aligned_cols=48 Identities=19% Similarity=0.282 Sum_probs=39.9
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCC
Q 008709 407 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDR 463 (557)
Q Consensus 407 ~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~ 463 (557)
-+|..+|++.+|++...+.+++..|.. .++|.+. ..+.|.+|++|-.+
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e--~~iI~k~-------~~G~Y~iNP~~~~k 122 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEE--KNIIKKI-------RNGAYMINPNFFFK 122 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHh--CCcEEEc-------cCCeEEECcHHhee
Confidence 478899999999999999999999974 4788765 35689999997543
No 46
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=76.25 E-value=4.2 Score=27.76 Aligned_cols=36 Identities=28% Similarity=0.451 Sum_probs=26.9
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
-.||-........++.+|++.+|+++..+.+.++.|
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 47
>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=75.63 E-value=3.3 Score=30.34 Aligned_cols=46 Identities=13% Similarity=0.334 Sum_probs=40.5
Q ss_pred HHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 494 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 494 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
..|+..++.++.++..+|.+ .|..+...|.+-|..|-++|.|.|.-
T Consensus 3 ~~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 46888899999999999885 47889999999999999999999864
No 48
>PRK10870 transcriptional repressor MprA; Provisional
Probab=75.38 E-value=7.2 Score=35.96 Aligned_cols=52 Identities=13% Similarity=0.185 Sum_probs=42.3
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 390 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~--~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
-+|..|..||..... ..++|..+|++.++++...+.+.+..|. +.+++.+.+
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 355678888877654 4579999999999999999999999997 458887753
No 49
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.12 E-value=7.3 Score=26.74 Aligned_cols=33 Identities=30% Similarity=0.413 Sum_probs=28.7
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 407 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 407 ~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.+|..+|++.+|++...+.+.|..|. +.+++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~--~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLE--KEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 57899999999999999999999997 3577764
No 50
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=74.90 E-value=7.6 Score=27.97 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=32.1
Q ss_pred hcCCCCc-CHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 402 FNTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 402 Fn~~~~~-t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+..++.+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~--~g~i~~~ 53 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEA--EGLVQRR 53 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEe
Confidence 4455567 9999999999999999999999973 4777654
No 51
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=74.70 E-value=7.3 Score=29.67 Aligned_cols=54 Identities=9% Similarity=0.193 Sum_probs=42.2
Q ss_pred HhHHHHHhhccCCC--CChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 008709 492 IDAALVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 553 (557)
Q Consensus 492 i~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 553 (557)
.+..|...|+.++. ++..+|-.++ ..+...+.+.|..|.++|||.+++..|..|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 45678889999877 8887777532 346678999999999999999987665554
No 52
>PHA00738 putative HTH transcription regulator
Probab=74.69 E-value=7.4 Score=32.42 Aligned_cols=67 Identities=18% Similarity=0.090 Sum_probs=49.8
Q ss_pred EEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCC
Q 008709 388 ELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 460 (557)
Q Consensus 388 ~l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 460 (557)
++...+.=-.||.+..+++.+++.+|++.++++...+-++|.-|. ..+|+.....|. .-.|++|.+.
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLr--eAGLV~srK~Gr----~vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILN--EQGYIELYKEGR----TLYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHH--HCCceEEEEECC----EEEEEECCCc
Confidence 345555555677666777779999999999999999999999996 468887654442 3457777664
No 53
>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=74.60 E-value=7.9 Score=33.57 Aligned_cols=35 Identities=29% Similarity=0.301 Sum_probs=30.8
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 405 SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 405 ~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.+.+|+.+|++.+|+|...+.+.|..|. +.+++..
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~--~~Gli~~ 57 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLS--LAGIVTS 57 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHH--HCCcEEe
Confidence 4579999999999999999999999997 4578864
No 54
>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=74.03 E-value=8.6 Score=29.55 Aligned_cols=41 Identities=17% Similarity=0.337 Sum_probs=33.0
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
||+..... ..|+++|.+.||++.+.+...|..|. +-+++.+
T Consensus 10 IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~--k~GiI~R 50 (72)
T PF05584_consen 10 ILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLA--KRGIIER 50 (72)
T ss_pred HHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCeee
Confidence 44444444 89999999999999999999999996 4577764
No 55
>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=73.33 E-value=7.4 Score=29.14 Aligned_cols=53 Identities=9% Similarity=0.187 Sum_probs=35.7
Q ss_pred hHHHHHhhc-cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc--CCCCCce
Q 008709 493 DAALVRIMK-SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD--KENPNMF 553 (557)
Q Consensus 493 ~A~IVRimK-~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~--~~~~~~y 553 (557)
+..|.+.+. ..+.++..+|.. .+..+.+.+-+.|+.|+++|||++. +.|....
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~--------~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~ 60 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAE--------RLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSK 60 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHH--------HTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSE
T ss_pred HHHHHHHHHccCCCcCHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCee
Confidence 566777777 677787777764 3455778889999999999999665 4444433
No 56
>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=73.09 E-value=6 Score=32.73 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHhhcC----CCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 390 IVSTYQAATLLLFNT----SDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~----~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.++..|-.||-.+.+ .+.+++++|++.++++..+++.+|..|+.
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 578899999988877 35799999999999999999999999975
No 57
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=72.63 E-value=12 Score=33.06 Aligned_cols=49 Identities=12% Similarity=0.251 Sum_probs=37.3
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEc
Q 008709 402 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFN 457 (557)
Q Consensus 402 Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N 457 (557)
+..+..+|..+|++.+|+|...+.++|..|. +.+++...+. .+..|.+.
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~--~~Glv~s~~G-----~~GG~~l~ 68 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLS--RAGYVTAVRG-----KNGGIRLG 68 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHH--hCCEEEEecC-----CCCCeeec
Confidence 4455578999999999999999999999997 5688875532 23456554
No 58
>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=72.53 E-value=2.7 Score=39.04 Aligned_cols=58 Identities=17% Similarity=0.332 Sum_probs=40.5
Q ss_pred HhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 492 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 492 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
+=...|...|.+|.+..++|-. .|..+.+++-.+|..|...|-|.---+|.+.|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~--------~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAA--------EFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHH--------HH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHH--------HcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 3444558889999999888764 478888999999999999999998888899999984
No 59
>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=71.84 E-value=9.3 Score=28.73 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=38.1
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
+..+..|+..+.+.+ ++..+|++.+|++...+.+.|..|.. .+++..
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~--~g~i~~ 52 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEE--AGLVES 52 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHH--CCCeEE
Confidence 346777887777666 99999999999999999999999963 366654
No 60
>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=71.84 E-value=5.2 Score=29.49 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=29.3
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
|.-+|-++.+.+.+++.+|++.+|++...++.-+.-|-
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 45555444447789999999999999999999887764
No 61
>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=71.16 E-value=6.9 Score=36.95 Aligned_cols=51 Identities=18% Similarity=0.193 Sum_probs=44.6
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.++..|..||..+.+++.++..+|++.+|++...+.++|..|. +.+++.+.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le--~~GlI~r~ 190 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE--KKGLVEQK 190 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 5678899999999887789999999999999999999999997 45788765
No 62
>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=68.90 E-value=6.1 Score=30.58 Aligned_cols=30 Identities=20% Similarity=0.168 Sum_probs=25.4
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 403 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 403 n~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
...+.+|+.||++.+|++...++..+..+.
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 333578999999999999999999888764
No 63
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=68.77 E-value=4.6 Score=31.89 Aligned_cols=43 Identities=26% Similarity=0.351 Sum_probs=32.4
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
..||...+..+.+++.+|.+.+|++...+-++|..|.. .+.+.
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 34555555667899999999999999999999999974 45554
No 64
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=67.40 E-value=11 Score=31.61 Aligned_cols=50 Identities=20% Similarity=0.315 Sum_probs=42.8
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+++.|+.+|......+..+..+|++.++++...+.+++..|. +.+++.+.
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le--~~glv~r~ 69 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLE--DKGLIERL 69 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeeec
Confidence 778999999888777766669999999999999999999997 45788765
No 65
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=67.13 E-value=12 Score=31.86 Aligned_cols=57 Identities=23% Similarity=0.356 Sum_probs=41.4
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEcc
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 458 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 458 (557)
..||.+.-+.++.++.||++.+|++...+-+||.-|. ..+++.....|. .-.|.+|.
T Consensus 19 l~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~--~AGLV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 19 LGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLR--ESGLLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCceEEEEEcC----EEEEEECc
Confidence 3455544444579999999999999999999999996 468887654431 23466654
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=67.10 E-value=13 Score=36.26 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=37.3
Q ss_pred HHHHHhhcC-CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 396 AATLLLFNT-SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 396 a~iLl~Fn~-~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
..||.+|.. ...+|+.||++.+|+|...+.+.|..|.. .+.|.+
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~--~G~l~~ 56 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE--LGYVTS 56 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEe
Confidence 468888986 45799999999999999999999999974 467764
No 67
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=66.93 E-value=10 Score=31.49 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=37.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
..-.||..+......|+.+|++.+|++...+.+.+..|.. .+++.
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 3456777777778899999999999999999999999974 46665
No 68
>PF13730 HTH_36: Helix-turn-helix domain
Probab=66.77 E-value=14 Score=26.35 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=23.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 409 SYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 409 t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
|.+.|++.+|++...+.+++..|..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999963
No 69
>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=66.11 E-value=16 Score=27.09 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=30.4
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 406 DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 406 ~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..+|..+|++.+|++...+.++|..|.. .+++...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~--~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE--EGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 4699999999999999999999999973 4787654
No 70
>PRK11569 transcriptional repressor IclR; Provisional
Probab=65.97 E-value=13 Score=36.97 Aligned_cols=46 Identities=17% Similarity=0.188 Sum_probs=38.6
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 395 QAATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 395 Qa~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-..||.+|.+. ..+|+.||++.+|++...+.+.|.+|.. .+.|.+.
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~--~G~l~~~ 76 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ--QGFVRQV 76 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEc
Confidence 34678888874 5799999999999999999999999974 5788654
No 71
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=65.93 E-value=14 Score=36.12 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=38.9
Q ss_pred HHHHHhhcCCCC-cCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 396 AATLLLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 396 a~iLl~Fn~~~~-~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
+.||.+|..... +++.||++.+|+|...+.+.|..|+ ..+++.+.+
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 468888887554 7899999999999999999999997 468888764
No 72
>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=65.60 E-value=14 Score=27.36 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=33.7
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
|..+-.+...++..+|++.+|+++..+...+..|. +.+++...
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~--~~GlV~~~ 55 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA--EKGLVEYE 55 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH--HCCCEEec
Confidence 34444477899999999999999999999999996 34777654
No 73
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=65.32 E-value=9 Score=36.44 Aligned_cols=42 Identities=21% Similarity=0.259 Sum_probs=35.6
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
.||.+.+..+++|.+||++.+|++...+++||+.|.. -+++.
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 4666777888999999999999999999999999973 35554
No 74
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=64.51 E-value=15 Score=36.34 Aligned_cols=45 Identities=27% Similarity=0.330 Sum_probs=38.3
Q ss_pred HHHHHhhcCC-CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 396 AATLLLFNTS-DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 396 a~iLl~Fn~~-~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..||.+|... ..+|+.||++.+|++...+.+.|..|.. .+.|.+.
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~--~G~l~~~ 73 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA--ADFVYQD 73 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEc
Confidence 4688889765 4799999999999999999999999974 5778664
No 75
>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=64.44 E-value=15 Score=30.87 Aligned_cols=58 Identities=10% Similarity=0.120 Sum_probs=43.7
Q ss_pred HHHHhhcc-CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 008709 495 ALVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 555 (557)
Q Consensus 495 ~IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 555 (557)
+|..+|.. .+.++.++|...+.++. ..++...|=+.|+.|.+.|+|.+-..+.+...|
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y 63 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGDGKARY 63 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence 45566665 55799999999887652 356888899999999999999997644344444
No 76
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=61.99 E-value=16 Score=35.98 Aligned_cols=46 Identities=17% Similarity=0.150 Sum_probs=38.1
Q ss_pred HHHHHhhcCCC-CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCC
Q 008709 396 AATLLLFNTSD-RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 396 a~iLl~Fn~~~-~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
+.||..|.+.+ .+|..||++.+|++...+.+.|..|.. .++|.+.+
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~--~g~v~~~~ 60 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE--EGYVRRSA 60 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEec
Confidence 45778886654 599999999999999999999999973 57887654
No 77
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=61.87 E-value=17 Score=26.32 Aligned_cols=35 Identities=17% Similarity=0.218 Sum_probs=29.9
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 405 SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 405 ~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.+..|..+|++.+|++...+.++|..|.. .+++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~--~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE--AGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH--CCCeee
Confidence 56789999999999999999999999973 467654
No 78
>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=61.85 E-value=11 Score=26.20 Aligned_cols=45 Identities=7% Similarity=0.237 Sum_probs=35.3
Q ss_pred HhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccc
Q 008709 492 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLE 544 (557)
Q Consensus 492 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~ 544 (557)
.+-.|+..+.....++..+|-..+ ..+.+.+.+.|..|.+.|||+
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 456788888888899998887643 457888999999999999985
No 79
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=59.95 E-value=24 Score=24.70 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=23.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
.|-+.| ...+|++||++.+|++...+......
T Consensus 12 vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 12 VIRLRY--FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 444556 45789999999999999988776543
No 80
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=59.66 E-value=16 Score=26.34 Aligned_cols=45 Identities=11% Similarity=0.226 Sum_probs=32.6
Q ss_pred HHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCC
Q 008709 496 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 549 (557)
Q Consensus 496 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 549 (557)
|++.+. .+.++..++... +..+...+.+.|+.|.++|++.+....
T Consensus 2 il~~l~-~~~~~~~~i~~~--------l~is~~~v~~~l~~L~~~g~i~~~~~~ 46 (66)
T smart00418 2 ILKLLA-EGELCVCELAEI--------LGLSQSTVSHHLKKLREAGLVESRREG 46 (66)
T ss_pred HHHHhh-cCCccHHHHHHH--------HCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence 345555 666777766543 235677899999999999999987643
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=58.90 E-value=15 Score=33.89 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=35.9
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
...||.+.-.++.+|.++|++.+|++...++++|..|.. .+++.
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 345666666667899999999999999999999999974 46665
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=58.89 E-value=8.9 Score=31.91 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=30.2
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
.+.|+..+..++.++-++|++.+|++..++.+.|..|.. .+++.
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 345666666567899999999999999999999999974 35653
No 83
>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=58.04 E-value=31 Score=25.18 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=29.8
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 403 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 403 n~~~~~-t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.....+ |..+|+..+|++...+.++|..|.. .++|...
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~--~G~i~~~ 58 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEA--EGLVERR 58 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEec
Confidence 333444 4999999999999999999999974 4777643
No 84
>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=57.23 E-value=15 Score=27.83 Aligned_cols=55 Identities=24% Similarity=0.218 Sum_probs=33.4
Q ss_pred HhHHHHHhhccCC-CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 492 IDAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 492 i~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
.=|.||..||++. .++.+||..++. +..+ +..++.|-+-+=|+-+++ .++|.|.|
T Consensus 6 ql~~~VeymK~r~~Plt~~eI~d~l~------~d~~----~~~~~~Lk~npKI~~d~~-~~~f~fkp 61 (65)
T PF02186_consen 6 QLAKAVEYMKKRDHPLTLEEILDYLS------LDIG----KKLKQWLKNNPKIEYDPD-GNTFSFKP 61 (65)
T ss_dssp HHHHHHHHHHHH-S-B-HHHHHHHHT------SSS-----HHHHHHHHH-TTEEEE-T-T-CEEE--
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHc------CCCC----HHHHHHHHcCCCEEEecC-CCEEEecc
Confidence 3478999999975 588888886553 4333 335566668889999974 47999976
No 85
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=56.94 E-value=14 Score=36.23 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=40.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-|..||-..++.+.+++.||++.+|++...+++-|..|- +.++|.+.
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 45777654
No 86
>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=56.73 E-value=15 Score=25.29 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=22.0
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
.|+-++.++ +|+.+|++.+|++...+.+.|.
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 344455554 8999999999999999988774
No 87
>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=56.60 E-value=16 Score=27.63 Aligned_cols=37 Identities=19% Similarity=0.204 Sum_probs=31.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.|-.+.++...+|+.+|++.++++..++..++-.|..
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar 48 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR 48 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4566778888999999999999999999999999874
No 88
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=56.37 E-value=14 Score=33.36 Aligned_cols=50 Identities=28% Similarity=0.357 Sum_probs=37.8
Q ss_pred cCCCceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 361 KTKHRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 361 ~~~~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
+++.+.|+|.++|- .-|.++-. +....|+++|+..+|.++.+++++|+.=
T Consensus 36 ~~~~~~lTWvdSLa-------------------vAAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 36 KDPYERLTWVDSLA-------------------VAAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred hCcccccchhhHHH-------------------HHHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 56789999998662 22333333 4457899999999999999999999754
No 89
>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=55.35 E-value=32 Score=26.84 Aligned_cols=39 Identities=10% Similarity=0.208 Sum_probs=28.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
+.-.+|-+.-.+..+|+++|+..+|.+.+++..+|..+.
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 344567777888999999999999999999999998875
No 90
>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=54.99 E-value=14 Score=28.17 Aligned_cols=34 Identities=15% Similarity=0.294 Sum_probs=26.8
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 400 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 400 l~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
-...+++.+|+.||+..++++++.+...|.-|..
T Consensus 7 ~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 7 DYLRERGRVSLAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3345667899999999999999999999999974
No 91
>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=54.72 E-value=1.7e+02 Score=26.59 Aligned_cols=59 Identities=22% Similarity=0.235 Sum_probs=42.1
Q ss_pred HHHHHHhhcCC-CCcCHHHHHHHh--CCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccC
Q 008709 395 QAATLLLFNTS-DRLSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSK 459 (557)
Q Consensus 395 Qa~iLl~Fn~~-~~~t~~el~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~ 459 (557)
...|+-.+... .++|..+|...+ +++...+.++|..|+.. -+|..+. +...-+|..|.+
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 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEE-GKIVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhC-CCeeeee-----ecceEEEeeCcc
Confidence 35677666654 589999999988 68999999999999853 3555443 234566777755
No 92
>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=54.47 E-value=15 Score=37.57 Aligned_cols=143 Identities=12% Similarity=0.144 Sum_probs=38.6
Q ss_pred EEcHHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCCCCccee
Q 008709 390 IVSTYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFTDRMRRI 467 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~--~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~~~~~~i 467 (557)
.++.-+..|+-+.-+ .+++-..+|...+|++...+.++|..|.. | +++.... +.+.+++|+
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 445667777766653 45788999999999999999999999975 3 4554321 122233333
Q ss_pred eecCCCchhhhh------hHHhHHHhhHHhHhHHHHHhhccCCC-----------------------------CChhHHH
Q 008709 468 KIPLPPVDERKK------IVEDVDKDRRYAIDAALVRIMKSRKV-----------------------------LGHQQLV 512 (557)
Q Consensus 468 ~i~~~~~~e~~~------~~~~~~~~r~~~i~A~IVRimK~~k~-----------------------------l~~~~L~ 512 (557)
.+-..-....+. +..+++.+=-..+...|.+.+.++.. .+.+++.
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 332110000000 01122222233444444444444443 4455555
Q ss_pred HHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCC
Q 008709 513 SECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 549 (557)
Q Consensus 513 ~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 549 (557)
..+.+.=-..-..+.++|...|+-|+=.|-|++-...
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 5554331112346789999999999999988887643
No 93
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=54.11 E-value=18 Score=35.52 Aligned_cols=46 Identities=20% Similarity=0.307 Sum_probs=40.2
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
|-.||-+.++.+.++++||++.+|+++..+++=|..|. +.++|.+.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le--~~g~l~R~ 52 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELE--EQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHH--HCCcEEEE
Confidence 56788888999999999999999999999999999996 44777765
No 94
>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=52.82 E-value=33 Score=32.28 Aligned_cols=44 Identities=14% Similarity=0.171 Sum_probs=35.2
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.||......+.+|..+|++.+|++...+.++|..|.. .+++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~--~GlV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLET--EGLIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEe
Confidence 4554444456799999999999999999999999974 4787654
No 95
>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=52.59 E-value=31 Score=26.01 Aligned_cols=56 Identities=13% Similarity=0.309 Sum_probs=37.1
Q ss_pred hhHHhHhHHHHHhhccCC-CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCC
Q 008709 487 DRRYAIDAALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 549 (557)
Q Consensus 487 ~r~~~i~A~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 549 (557)
+|+..|=.+|...+...+ .-+..||.. .+. +. +..-+...|+.|.++|||+|++.-
T Consensus 6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~----~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 6 ERQKEVLEFIREYIEENGYPPTVREIAE----ALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHHHHHHSS---HHHHHH----HHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHH----HhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 455556666776666554 456666654 332 32 577899999999999999999753
No 96
>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=52.28 E-value=33 Score=26.43 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=39.6
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhccccee
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKI 438 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~i 438 (557)
.+=|+.++-++...+.-|+++|++.||-..-.++-+|..+...|.++
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 45689999889888899999999999999999999998886444444
No 97
>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=51.66 E-value=21 Score=26.64 Aligned_cols=34 Identities=21% Similarity=0.319 Sum_probs=26.2
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceee
Q 008709 404 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 439 (557)
Q Consensus 404 ~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL 439 (557)
..+..|+.+|.+.++++...++.+|-.|.+ .+++
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 345899999999999999999999999974 3554
No 98
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=51.24 E-value=25 Score=31.95 Aligned_cols=48 Identities=13% Similarity=0.171 Sum_probs=40.5
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
+.-.-..||....+....|+.+|++.+|++...+.+.++.|.. .+++.
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 3446667888888889999999999999999999999999973 46664
No 99
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=51.21 E-value=32 Score=23.80 Aligned_cols=45 Identities=11% Similarity=0.242 Sum_probs=34.6
Q ss_pred HHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 495 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 495 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
.|.+.+..+..++..+|... |..+...+.+.|..|.++|+|.+..
T Consensus 4 ~il~~l~~~~~~s~~~l~~~--------l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQGKVSVEELAEL--------LGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEEEee
Confidence 35556666667877777754 4568888999999999999999865
No 100
>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=51.07 E-value=29 Score=31.36 Aligned_cols=43 Identities=14% Similarity=0.163 Sum_probs=34.5
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
..|+...-.++.+|-+||++.+|++...+++.|..|.. .+++.
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 44555454556899999999999999999999999974 46664
No 101
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=50.85 E-value=27 Score=28.88 Aligned_cols=46 Identities=11% Similarity=0.223 Sum_probs=39.1
Q ss_pred HhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 008709 492 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 545 (557)
Q Consensus 492 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 545 (557)
+|-.|++.+.....++..+|-.. +..+...+.++|..|.++|+|+|
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~--------l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKK--------VGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeec
Confidence 56788999999888998888763 35688889999999999999985
No 102
>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=50.76 E-value=25 Score=25.32 Aligned_cols=30 Identities=17% Similarity=0.424 Sum_probs=25.2
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 402 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 402 Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
|+.-...|.+||++.+|++...+-.+|..-
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 555568999999999999999988888653
No 103
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=50.51 E-value=35 Score=23.87 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=29.7
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
|.-+..++.++. ..++..+|++.+|++...+...+..+.
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 445555665553 357999999999999999999887664
No 104
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=50.02 E-value=25 Score=27.40 Aligned_cols=58 Identities=17% Similarity=0.243 Sum_probs=35.4
Q ss_pred HhHhHHHHHhhccCC--CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccc---cccCCCCCceEecC
Q 008709 490 YAIDAALVRIMKSRK--VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL---ERDKENPNMFRYLA 557 (557)
Q Consensus 490 ~~i~A~IVRimK~~k--~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi---~r~~~~~~~y~Yia 557 (557)
...=|.||..||++. .++.+||..++.. +... ..+++- |-+-.-+ +.+.. .++|.|.|
T Consensus 8 ~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~-----~d~~-~~~~~~---L~~~~~~~n~~~~~~-~~tf~fkP 70 (75)
T cd07977 8 FTQLAKIVDYMKKRHQHPLTLDEILDYLSL-----LDIG-PKLKEW---LKSEALVNNPKIDPK-DGTFSFKP 70 (75)
T ss_pred hhhHHHHHHHHHhcCCCCccHHHHHHHHhc-----cCcc-HHHHHH---HHhhhhccCceeccC-CCEEEecc
Confidence 445688999999987 5899998886652 2222 222333 3322333 44443 47999975
No 105
>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=49.70 E-value=18 Score=33.55 Aligned_cols=30 Identities=20% Similarity=0.449 Sum_probs=23.7
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 402 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 402 Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
+.....+|+++|++.||+..+++..+|+.|
T Consensus 145 ~~~~~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 145 FKGKKSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp TSSE--EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred cCCCCeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 333337999999999999999999999988
No 106
>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=49.67 E-value=28 Score=27.47 Aligned_cols=35 Identities=3% Similarity=-0.031 Sum_probs=30.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
-++.|+-.... +.+|+.+|++..|++...+.+.|.
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 46678877888 899999999999999999988663
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=49.57 E-value=15 Score=26.91 Aligned_cols=48 Identities=10% Similarity=0.241 Sum_probs=34.1
Q ss_pred hHHHHHhhccCCC--CChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 493 DAALVRIMKSRKV--LGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 493 ~A~IVRimK~~k~--l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
+..|...+..... ++..+|... +..+...+.+.|..|.++|||+|..+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~--------l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAER--------LGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHH--------HTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4556666666665 677666652 33567889999999999999999764
No 108
>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=49.45 E-value=38 Score=23.79 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=28.6
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
|..|..++.++- +.+|..+|++.+|++...+...+..+.
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 344455554443 458999999999999999988887653
No 109
>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=49.36 E-value=8.4 Score=27.99 Aligned_cols=47 Identities=13% Similarity=0.289 Sum_probs=34.7
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
+..+..++-..+.++..+|-. .+..+...+-+.+..|..+|||+|..
T Consensus 5 q~~iL~~l~~~~~~~~~~la~--------~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAE--------KLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHcCCCCHHHHHH--------HHCCChhHHHHHHHHHHHCCCEEecc
Confidence 455666666677777776654 23457888999999999999999964
No 110
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=49.21 E-value=28 Score=34.10 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=40.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-|..|+..+++++.+++.||++.+|++...+++-|..|. +.+++.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le--~~g~i~r~ 52 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLD--ESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEe
Confidence 456788888999999999999999999999999999996 34677654
No 111
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=48.64 E-value=30 Score=30.90 Aligned_cols=48 Identities=13% Similarity=0.225 Sum_probs=40.3
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
++..--.||..+..+...|+.+|++.+|+++..+.+.++.|.. .+++.
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 4556667888888888999999999999999999999999974 35664
No 112
>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=47.58 E-value=35 Score=24.17 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=17.3
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHH
Q 008709 407 RLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 407 ~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
.+|+.||++.+|++...+...+.
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 58999999999999999888764
No 113
>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=47.47 E-value=13 Score=35.78 Aligned_cols=35 Identities=11% Similarity=0.246 Sum_probs=29.9
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 519 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 519 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
|..+|..+...|+++|+.|++.|+|.|... .++|+
T Consensus 30 La~~~gVSR~TVR~Al~~L~~eGli~r~~G-~GTfV 64 (233)
T TIGR02404 30 LMDQYGASRETVRKALNLLTEAGYIQKIQG-KGSIV 64 (233)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEeCC-ceEEE
Confidence 334699999999999999999999999874 57775
No 114
>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=47.13 E-value=28 Score=26.25 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=34.8
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHHhhhcccceeeecCC
Q 008709 391 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~-----~~~~t~~el~~~~~i~-~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
+|.-|.-||...-+ +-.-|+.||++.+|+. ...+..+|..|. +.+.|.+.+
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 347887653
No 115
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=47.09 E-value=49 Score=30.29 Aligned_cols=53 Identities=21% Similarity=0.187 Sum_probs=39.8
Q ss_pred EEEEcHHHHHHHHhhcCCCC-cCHHHHHHHh--CCCHHHHHHHHHhhhcccceeeecC
Q 008709 388 ELIVSTYQAATLLLFNTSDR-LSYSEIMTQL--NLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 388 ~l~~s~~Qa~iLl~Fn~~~~-~t~~el~~~~--~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
++--+.+..+|+-+..-.+. -+.++|++.+ +++.++++.+|..|. +.++|.+.
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~--~~gli~k~ 74 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLE--KLGLIKKD 74 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHH--HCCCeEEC
Confidence 33344555566655544333 3899999999 999999999999997 67999875
No 116
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=47.08 E-value=35 Score=31.55 Aligned_cols=64 Identities=16% Similarity=0.155 Sum_probs=48.3
Q ss_pred CceEEeccCCceEEEEeEecCeeEEEEEcHHHHHHHHhhcCC--CCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 364 HRKLTWIYSLGQCNINGKFEQKNIELIVSTYQAATLLLFNTS--DRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 364 ~R~L~w~~~lg~~~l~~~~~~~~~~l~~s~~Qa~iLl~Fn~~--~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
.|.-.|.+..|..+++-- +.| .||+.||.-|+.-... ..||.+-||+..+++.+++...|..+.
T Consensus 96 ~r~~~~~~~fg~~ep~~v-PkG----kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~ 161 (179)
T PF06784_consen 96 PRDTIPDFEFGFYEPEKV-PKG----KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFK 161 (179)
T ss_pred CCCCcccccccccCcccC-CCC----ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcC
Confidence 344467888888877532 334 4567999988764433 479999999999999999999888774
No 117
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=46.80 E-value=32 Score=32.82 Aligned_cols=49 Identities=24% Similarity=0.318 Sum_probs=41.4
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
|.+-..||-+......+.+.||++.+|+|...+..+++.|. +.+++..+
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 66888644
No 118
>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=46.69 E-value=28 Score=22.27 Aligned_cols=25 Identities=28% Similarity=0.513 Sum_probs=20.4
Q ss_pred cCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 408 LSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 408 ~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
+|-+||+..+|++.+.+-+.|..|.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 6789999999999999999998875
No 119
>PRK00215 LexA repressor; Validated
Probab=45.92 E-value=44 Score=31.38 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=39.9
Q ss_pred EcHHHHHHHHhhc-----CCCCcCHHHHHHHhCC-CHHHHHHHHHhhhcccceeeecCC
Q 008709 391 VSTYQAATLLLFN-----TSDRLSYSEIMTQLNL-THDDLVRLLHSLSCAKYKILLKEP 443 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn-----~~~~~t~~el~~~~~i-~~~~l~~~L~~L~~~k~~iL~~~~ 443 (557)
++.-|..+|.... .....|+.||++.+|+ +...+.+.|..|.. .+++.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~--~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALER--KGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHH--CCCEEeCC
Confidence 3567888886654 2346899999999999 99999999999973 47776653
No 120
>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=45.38 E-value=14 Score=27.48 Aligned_cols=34 Identities=15% Similarity=0.313 Sum_probs=27.0
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 008709 519 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 553 (557)
Q Consensus 519 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 553 (557)
+..+|..+...+.+++..|.+.|+|.+.+. .+++
T Consensus 30 la~~~~vsr~tvr~al~~L~~~g~i~~~~~-~G~~ 63 (64)
T PF00392_consen 30 LAERYGVSRTTVREALRRLEAEGLIERRPG-RGTF 63 (64)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEEETT-TEEE
T ss_pred HHHHhccCCcHHHHHHHHHHHCCcEEEECC-ceEE
Confidence 334688899999999999999999999874 4544
No 121
>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=45.32 E-value=32 Score=24.90 Aligned_cols=39 Identities=15% Similarity=0.236 Sum_probs=31.4
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
|.-+..||.++..+ .+..+|++.+|+++..+..++..+.
T Consensus 5 T~~E~~vl~~l~~G--~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 5 TERELEVLRLLAQG--MSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHHHHTT--S-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhc--CCcchhHHhcCcchhhHHHHHHHHH
Confidence 55677778777764 6899999999999999999998886
No 122
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=45.17 E-value=31 Score=33.77 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=36.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
-|..|+...+.++.+++.||++.+|+++..+++-|..|-
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 477899999999999999999999999999999999875
No 123
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=44.88 E-value=15 Score=35.59 Aligned_cols=35 Identities=23% Similarity=0.310 Sum_probs=29.6
Q ss_pred hccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 519 LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 519 l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
|...|..+...++++|+.|++.|+|.|... +++|+
T Consensus 39 La~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GTfV 73 (241)
T PRK11402 39 LCTQYNVSRITIRKAISDLVADGVLIRWQG-KGTFV 73 (241)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 334688999999999999999999999874 67775
No 124
>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=44.13 E-value=78 Score=25.98 Aligned_cols=54 Identities=7% Similarity=0.157 Sum_probs=44.7
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 545 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 545 (557)
.++-+|..++. .+.++=-+|.+.+.+...+.+.++...+=..+..|-++|+|++
T Consensus 4 ~l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 4 TLDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred hHHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 35567777776 5678889999999877665667888999999999999999998
No 125
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=43.75 E-value=61 Score=28.09 Aligned_cols=64 Identities=16% Similarity=0.212 Sum_probs=47.7
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCC---CCCeEEEccCCC
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTIS---QSDHFEFNSKFT 461 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~---~~~~~~~N~~f~ 461 (557)
..+|-+..+.+..|+.|+++.+|-+...+-+.|..|. .++++..+.+|+.-. .-+.+.++-.|.
T Consensus 67 leLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~--~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 67 LELLELIAQEEPASINELAELVGRDVKNVHRTLSTLA--DLGLIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHH--hcCeEEEecCCcccCceeeccccEEeeecC
Confidence 3466677788899999999999999999999999996 468888765544332 234455666664
No 126
>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=43.33 E-value=38 Score=29.12 Aligned_cols=38 Identities=8% Similarity=0.065 Sum_probs=31.9
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 403 NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 403 n~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+..-+.|.++||..++-+.+.++.+|..|. +.+++...
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 56888653
No 127
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=42.87 E-value=35 Score=33.41 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=39.9
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-+..|+...++.+.+++.||++.++++...+++-|..|.. .++|.+.
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 4567787888889999999999999999999999999963 4677665
No 128
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=42.75 E-value=34 Score=33.90 Aligned_cols=48 Identities=6% Similarity=0.065 Sum_probs=40.7
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 393 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 393 ~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
--|..|+.+.+..+.+++.||++.+|++...++|-|..|-. .+++.+.
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 35778888899988999999999999999999999999953 4666654
No 129
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=42.73 E-value=78 Score=24.96 Aligned_cols=40 Identities=18% Similarity=0.231 Sum_probs=31.8
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceee
Q 008709 400 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 439 (557)
Q Consensus 400 l~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL 439 (557)
+.-++.+.+|=++|++.+|++...+-++++.|-...+.|.
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 4445667899999999999999999999999964334444
No 130
>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=42.42 E-value=17 Score=34.98 Aligned_cols=34 Identities=15% Similarity=0.373 Sum_probs=29.2
Q ss_pred ccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 520 SRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 520 ~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
..+|..+...+.++|+.|.+.|+|.|... .++|+
T Consensus 39 a~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 72 (238)
T TIGR02325 39 AERFGVNRHTVRRAIAALVERGLLRAEQG-RGTFV 72 (238)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 34689999999999999999999999874 57765
No 131
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=42.41 E-value=17 Score=35.14 Aligned_cols=36 Identities=11% Similarity=0.440 Sum_probs=30.4
Q ss_pred HhccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 518 QLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 518 ~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
+|...|..+...|+++|+.|++.|+|.|... +++|+
T Consensus 40 eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 75 (241)
T PRK10079 40 QLAARYEVNRHTLRRAIDQLVEKGWVQRRQG-VGVLV 75 (241)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 4445799999999999999999999999874 57765
No 132
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.15 E-value=30 Score=33.11 Aligned_cols=56 Identities=21% Similarity=0.372 Sum_probs=45.8
Q ss_pred HHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 494 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 494 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
+--|-..|+.|.+..+||-. .|....++.-.+|..|+..|.|.-.-+|++.|+||.
T Consensus 203 ~eFv~YIk~nKvV~ledLas--------~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 203 SEFVEYIKKNKVVPLEDLAS--------EFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHHhcCeeeHHHHHH--------HhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 44567778889888888875 366666777779999999999999888999999984
No 133
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=41.96 E-value=40 Score=36.59 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=43.7
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.+|..|..||......+.+|..+|++.+|++...+.+++.+|.. .+++..
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 46789999999998888999999999999999999999999974 366654
No 134
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=40.80 E-value=41 Score=22.47 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=20.6
Q ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 405 SDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 405 ~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
...+++++|++..|++...+.+.++...
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 4579999999999999999988887553
No 135
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=40.37 E-value=38 Score=31.49 Aligned_cols=46 Identities=11% Similarity=0.049 Sum_probs=39.1
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
-+..|+...+.++.+++.+|++.+|++...+++-|..|.. .+++.+
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 5677888889999999999999999999999999999963 355543
No 136
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=40.14 E-value=52 Score=29.08 Aligned_cols=47 Identities=17% Similarity=0.326 Sum_probs=39.5
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
.-.-.-||.........++.+|++.+|++...+.+.+..|. +.+++.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~--~~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLE--EEGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH--HCCcee
Confidence 44556788888888889999999999999999999999996 457775
No 137
>PRK13239 alkylmercury lyase; Provisional
Probab=39.91 E-value=54 Score=30.97 Aligned_cols=39 Identities=13% Similarity=0.242 Sum_probs=34.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
+...+|.++-++..+|+++|++.+|.+.+.+.+.|+.|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 556677778888999999999999999999999999884
No 138
>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=39.54 E-value=60 Score=24.02 Aligned_cols=38 Identities=18% Similarity=0.299 Sum_probs=29.6
Q ss_pred cCCCCc-CHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 403 NTSDRL-SYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 403 n~~~~~-t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..++.+ |..+|++.+|++...+.++|..|.. .+++...
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~--~g~i~~~ 57 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEA--EGLIERR 57 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHH--CCcEEEE
Confidence 345678 9999999999999999999999974 4777654
No 139
>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=39.45 E-value=3e+02 Score=31.38 Aligned_cols=132 Identities=17% Similarity=0.320 Sum_probs=75.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHccccCCCcHhHHHHHHHHHHHHHHHHHHHHHhhhHHHHh
Q 008709 14 HMLQDTGAYYSRKASNWILEDSCPEYMIKAEECLKKERDRVSHYLHSSSEPKLVEKVQHELLVVYATELLEKEQSGCRAL 93 (557)
Q Consensus 14 ~~L~~t~~yY~~~~~~~i~~~~~~~Yl~~~~~~l~~E~~r~~~~l~~~t~~~l~~~l~~~LI~~~~~~ll~~~~~gl~~l 93 (557)
..++...-||...+..-+ ...+.++.+.+...++++.+.+-..+-.....++.+-+ .|+..+
T Consensus 551 ~~leN~~~~~e~l~~~~~-~~~l~~~~~~A~~~~~~~~~~Y~~~~l~r~~~kL~~F~-----------------~gve~l 612 (701)
T PF09763_consen 551 VLLENYHHFYEELSQLKI-NSVLEEFRKEAKQIYDEHLEAYVTFLLRRPFGKLLDFF-----------------EGVEAL 612 (701)
T ss_pred HHHHHHHHHHHHHhhccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHH-----------------HHHHHH
Confidence 345566666667665443 36678899999999988887665443333333443322 233333
Q ss_pred hcc-----------CCHHHHHHHHHhhc--cCCCChhhHHHHHHHHHHHHH------HHHHHhhHHHhhhcCCCCCccch
Q 008709 94 LRE-----------DKVEDLSRMYRLYH--KIPKGLEPVANVFKQHITAEG------TVLVQQAEDAATNQGGSSGAVQE 154 (557)
Q Consensus 94 l~~-----------~~~~~L~~ly~l~~--~~~~~l~~l~~~~~~~i~~~g------~~~~~~~~~~~~~~~~~~~~~~~ 154 (557)
+.. ..+..|+.+-.-|. .+..+++.+.+.+.+|+...+ ..++... =
T Consensus 613 ~~~~~~~ei~~~~~ySk~~l~kvl~~y~~kev~k~i~~l~krveKHf~~~~~~~~~~~~Ll~~v---------------W 677 (701)
T PF09763_consen 613 LQTVSPEEISYQAAYSKQELKKVLKSYPSKEVRKGIEALYKRVEKHFSRDADDPSFEEDLLQVV---------------W 677 (701)
T ss_pred HhccCchhcccchhccHHHHHHHHHhCChHHHHHHHHHHHHHHHHHcCCccccccchhhHHHHH---------------H
Confidence 332 13556666665542 233456666666666661111 0111111 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC
Q 008709 155 QVLIRKIIELHDKYMEYVTNCFIN 178 (557)
Q Consensus 155 ~~~I~~l~~l~~~~~~li~~~F~~ 178 (557)
..+-+..+..|.++..++..|+.|
T Consensus 678 ~~~q~~~i~~~~~l~~li~~~Y~g 701 (701)
T PF09763_consen 678 SAMQEEFIRQYERLETLIQKCYPG 701 (701)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCC
Confidence 234567788999999999999875
No 140
>PRK14999 histidine utilization repressor; Provisional
Probab=38.06 E-value=21 Score=34.56 Aligned_cols=47 Identities=15% Similarity=0.277 Sum_probs=35.3
Q ss_pred hhccCCCC-ChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 499 IMKSRKVL-GHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 499 imK~~k~l-~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
.++....+ +-.+|. ..|..+...|+++|+.|.+.|+|.|... +++|+
T Consensus 29 ~~~~G~~LPsE~eLa--------~~~gVSR~TVR~Al~~L~~eGli~r~~G-kGTfV 76 (241)
T PRK14999 29 VWQPHDRIPSEAELV--------AQYGFSRMTINRALRELTDEGWLVRLQG-VGTFV 76 (241)
T ss_pred CCCCCCcCCCHHHHH--------HHHCCCHHHHHHHHHHHHHCCCEEEecC-cEEEE
Confidence 34444445 444454 3688999999999999999999999874 57775
No 141
>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=37.96 E-value=72 Score=21.66 Aligned_cols=39 Identities=26% Similarity=0.354 Sum_probs=28.2
Q ss_pred cHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 392 STYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 392 s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
+..+..++.++-- ..+|..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4455555544432 45899999999999999998877654
No 142
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=37.90 E-value=37 Score=31.74 Aligned_cols=50 Identities=18% Similarity=0.184 Sum_probs=39.9
Q ss_pred EcHHHHHHHHhhcC-----CCCcCHHHHHHHhCCC-HHHHHHHHHhhhcccceeeecC
Q 008709 391 VSTYQAATLLLFNT-----SDRLSYSEIMTQLNLT-HDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~-----~~~~t~~el~~~~~i~-~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|. +.++|.+.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~--~~g~i~~~ 59 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALE--RKGYIERD 59 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHH--HCCCEecC
Confidence 46788888876653 2358899999999998 999999999997 45788764
No 143
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=37.87 E-value=43 Score=34.74 Aligned_cols=63 Identities=24% Similarity=0.329 Sum_probs=39.0
Q ss_pred EEeccCCceEEEEeEecCeeEEEEE-------cHHHHHHHHhhcC-C-CCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 367 LTWIYSLGQCNINGKFEQKNIELIV-------STYQAATLLLFNT-S-DRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 367 L~w~~~lg~~~l~~~~~~~~~~l~~-------s~~Qa~iLl~Fn~-~-~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
+.+.+.||..|-.+--+.++ |.= +-.-..+|-.+-+ . ..+|+.+|++.|||..+++...|++|
T Consensus 282 IdFSYeLSr~E~~~GsPEKP--LSDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L 353 (396)
T KOG2747|consen 282 IDFSYELSRREGKIGSPEKP--LSDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSL 353 (396)
T ss_pred hhhhhhhhcccCcCCCCCCC--cchhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhh
Confidence 46777788776554322221 211 1122233322222 2 23999999999999999999999988
No 144
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=37.38 E-value=22 Score=34.41 Aligned_cols=36 Identities=17% Similarity=0.389 Sum_probs=30.5
Q ss_pred HhccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 518 QLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 518 ~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
+|..+|..+...++++|..|.+.|+|.|... .++|+
T Consensus 36 eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G-~GtfV 71 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDELVEEGLIVRRQG-KGTFV 71 (236)
T ss_pred HHHHHHCCcHHHHHHHHHHHHHCCcEEEEec-CeeEE
Confidence 4445799999999999999999999999874 57775
No 145
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=37.36 E-value=41 Score=29.92 Aligned_cols=31 Identities=13% Similarity=0.201 Sum_probs=27.5
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHhhhcc
Q 008709 404 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSCA 434 (557)
Q Consensus 404 ~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~ 434 (557)
.++.+|-++|++.+|++...+++.|..|...
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed 42 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRKILYLLYDE 42 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHHHHHhh
Confidence 4457999999999999999999999999753
No 146
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=37.20 E-value=38 Score=23.48 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=21.6
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
++.++.+ .+|..+|++.+|++...+.+.+..+
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4444444 6899999999999999998877655
No 147
>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=37.04 E-value=50 Score=28.25 Aligned_cols=48 Identities=19% Similarity=0.221 Sum_probs=37.3
Q ss_pred HHHHHHHHhhcCC--------CCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 393 TYQAATLLLFNTS--------DRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 393 ~~Qa~iLl~Fn~~--------~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.+.-..|+..|.. -+.+.++||..++-+.+.++.+|..|. +.+++...
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 4555555555544 378999999999999999999999996 67888653
No 148
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=36.63 E-value=1.3e+02 Score=22.43 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=27.4
Q ss_pred HHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 399 LLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 399 Ll~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
|-...+. ..+..+|++.+|++...+.+++..|..
T Consensus 6 l~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 6 LALLADN-PFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3334443 578999999999999999999999853
No 149
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.53 E-value=27 Score=24.97 Aligned_cols=28 Identities=7% Similarity=0.172 Sum_probs=24.2
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 521 RMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 521 ~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
..|..+...+.+.+..|.+.|+|.+...
T Consensus 28 ~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 28 AQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4577889999999999999999988763
No 150
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.51 E-value=46 Score=29.41 Aligned_cols=50 Identities=12% Similarity=0.247 Sum_probs=42.7
Q ss_pred HhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 490 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 490 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
..+|..|.+++.....++..+|-..+ ..+.+.+..||+.|.+.|.|++-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l--------glS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV--------GLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCceeeEE
Confidence 45788999999999999999988755 257788999999999999998854
No 151
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=36.19 E-value=88 Score=24.66 Aligned_cols=45 Identities=16% Similarity=0.234 Sum_probs=34.7
Q ss_pred HHHhhccC-CCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 496 LVRIMKSR-KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 496 IVRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
|...+... ..++..+|...+ ..+...+.+.+..|.+.|||.+++.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeecCC
Confidence 45555555 679988888754 3467889999999999999999753
No 152
>PRK09462 fur ferric uptake regulator; Provisional
Probab=35.14 E-value=90 Score=27.65 Aligned_cols=59 Identities=3% Similarity=0.113 Sum_probs=43.0
Q ss_pred HHHHHhhcc--CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 008709 494 AALVRIMKS--RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 555 (557)
Q Consensus 494 A~IVRimK~--~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 555 (557)
-+|.+++.. .+-++.++|...+.+.. ..++...|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y 80 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 80 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEE
Confidence 355666664 36899999999887653 356788899999999999999886432233444
No 153
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=34.86 E-value=95 Score=24.65 Aligned_cols=48 Identities=13% Similarity=0.215 Sum_probs=36.8
Q ss_pred HhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 492 IDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 492 i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
.+..|...+...+.++..+|... +.++...+.+.|..|.++|+|++..
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~--------~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKR--------LGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHH--------HCCCchhHHHHHHHHHHCCCeEecC
Confidence 35667777777777888877653 3456777999999999999998764
No 154
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=34.43 E-value=37 Score=33.33 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=40.4
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 546 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 546 (557)
+..|+..+++++.++..||.+ .|..+...|.+-|+.|-++|.|.|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~--------~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQ--------YFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 457888999999999999885 5788999999999999999999884
No 155
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=34.42 E-value=1e+02 Score=21.48 Aligned_cols=35 Identities=17% Similarity=0.360 Sum_probs=25.8
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
+.+.|+.+.-+. .|+.+++..+|++...+.+.+..
T Consensus 16 ~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 344455444332 69999999999999999988764
No 156
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=34.40 E-value=83 Score=22.35 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=32.6
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 400 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 400 l~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-+|.+++.+|+.++-+.+|++-+.....|+-|= +.++..+.
T Consensus 3 ~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD--~~g~T~R~ 43 (50)
T PF09107_consen 3 ELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLD--REGITRRV 43 (50)
T ss_dssp HHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHH--HTTSEEEE
T ss_pred HHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHh--ccCCEEEe
Confidence 457788899999999999999999999888883 45666554
No 157
>PHA02943 hypothetical protein; Provisional
Probab=34.27 E-value=78 Score=28.22 Aligned_cols=54 Identities=22% Similarity=0.240 Sum_probs=36.5
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEcc
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNS 458 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~ 458 (557)
||-.+ ..+..|..||++.+|++...+.-+|.-|- |-|.+.+..-| ....|.+|.
T Consensus 16 ILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLE--rEG~VkrV~~G----~~tyw~l~~ 69 (165)
T PHA02943 16 TLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLA--KEGMVLKVEIG----RAAIWCLDE 69 (165)
T ss_pred HHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHH--HcCceEEEeec----ceEEEEECh
Confidence 44444 55678899999999999999998888774 44555443221 234565555
No 158
>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=34.22 E-value=29 Score=24.87 Aligned_cols=22 Identities=18% Similarity=0.511 Sum_probs=19.3
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 008709 407 RLSYSEIMTQLNLTHDDLVRLL 428 (557)
Q Consensus 407 ~~t~~el~~~~~i~~~~l~~~L 428 (557)
.+++.|||+.+|++..++.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999998888
No 159
>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=33.98 E-value=92 Score=26.19 Aligned_cols=63 Identities=14% Similarity=0.161 Sum_probs=43.6
Q ss_pred HhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 008709 490 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 555 (557)
Q Consensus 490 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 555 (557)
..+|+.|.+ -....=.....++.+|+..+. .+ ++...+--||+.||..|.++-.++-.++-.|
T Consensus 47 d~yD~~Il~-~~~~~~~~~arvIg~vl~~~~-~~-i~D~f~~~Ri~~Li~~G~le~~g~~~~mr~~ 109 (111)
T PF12395_consen 47 DYYDDFILE-QAPDEFQKAARVIGEVLGHSD-QG-IGDWFLEYRIRELISQGVLEIKGDPKDMRHY 109 (111)
T ss_pred HHhhHHHHh-cCCccccHHHHHHHHHHHhcC-cC-CChHHHHHHHHHHHHCCCEEEecCCCccccC
Confidence 345666666 112223556778888888864 34 6678899999999999999988765554443
No 160
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=33.80 E-value=28 Score=33.44 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=28.8
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 521 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 521 ~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
..|..+...|.++|..|.+.|+|.|... +++|+
T Consensus 33 ~~~~VSR~TVR~Al~~L~~eGli~r~~G-~GtfV 65 (230)
T TIGR02018 33 AQYGCSRMTVNRALRELTDAGLLERRQG-VGTFV 65 (230)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-CEEEE
Confidence 4689999999999999999999999874 57764
No 161
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=33.64 E-value=60 Score=31.52 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=37.7
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
-|..|+..+++++.++++||++.+|++...+++-|..|.. .+.|.+
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 244544
No 162
>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=33.64 E-value=75 Score=26.47 Aligned_cols=41 Identities=17% Similarity=0.358 Sum_probs=30.2
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc--CCCC
Q 008709 502 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD--KENP 550 (557)
Q Consensus 502 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~--~~~~ 550 (557)
..+.++..+|... ...+...+-+.|..|.++|||.|. +.|.
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 4466777777753 334677789999999999999974 4443
No 163
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=33.20 E-value=35 Score=27.34 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=32.3
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 521 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 521 ~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
.++......-+++|..|.++|.|..-..+...-+|.|
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 3677888889999999999999998888888899976
No 164
>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=32.75 E-value=62 Score=24.93 Aligned_cols=49 Identities=14% Similarity=0.327 Sum_probs=28.5
Q ss_pred HHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCce
Q 008709 496 LVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMF 553 (557)
Q Consensus 496 IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y 553 (557)
|..-....+..+-.|+=. ++.. +..+...+. ..||+-||++|+++ .+.|
T Consensus 20 l~~~f~~g~~y~E~EVN~-~L~~----~~~D~a~LR---R~LVd~g~L~R~~d-g~~Y 68 (71)
T PF09860_consen 20 LASRFEPGREYSEKEVNE-ILKR----FFDDYATLR---RYLVDYGLLERTRD-GSRY 68 (71)
T ss_pred HHHhCCCCCccCHHHHHH-HHHH----HcccHHHHH---HHHHHcCCeeecCC-CCee
Confidence 333345555666555433 3332 234555443 57899999999974 4555
No 165
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=32.71 E-value=31 Score=33.37 Aligned_cols=33 Identities=12% Similarity=0.264 Sum_probs=28.6
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 521 RMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 521 ~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
..|..+...|+++|+.|...|+|.|... .++|+
T Consensus 37 ~~~~VSR~TvR~Al~~L~~eGli~r~~G-~GtfV 69 (240)
T PRK09764 37 TEFGVSRVTVRQALRQLVEQQILESIQG-SGTYV 69 (240)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEEecC-ceeEE
Confidence 3688999999999999999999999874 57765
No 166
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=32.44 E-value=74 Score=31.55 Aligned_cols=36 Identities=19% Similarity=0.295 Sum_probs=29.0
Q ss_pred HHHHHhh-cCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 396 AATLLLF-NTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 396 a~iLl~F-n~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
..|+-.+ +....+|+++|+..|||..+++..+|+.|
T Consensus 211 ~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 211 RVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 3444333 33568999999999999999999999987
No 167
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=32.05 E-value=92 Score=26.83 Aligned_cols=52 Identities=21% Similarity=0.366 Sum_probs=44.4
Q ss_pred HHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 489 RYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 489 ~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
...|.+.||-..+.++.++..+|... +-.+...++..+..|+++|.|-+.+.
T Consensus 10 r~eLk~rIvElVRe~GRiTi~ql~~~--------TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREHGRITIKQLVAK--------TGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHcCCccHHHHHHH--------HCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 47889999999999999999999863 34577889999999999998888653
No 168
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=32.00 E-value=88 Score=26.94 Aligned_cols=41 Identities=15% Similarity=0.308 Sum_probs=36.3
Q ss_pred HHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 393 TYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 393 ~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.+.+-|+-+--+++.+|+.++...||++-..+.+++.-|+.
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa 52 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA 52 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35667888888889999999999999999999999999974
No 169
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=31.98 E-value=70 Score=27.07 Aligned_cols=60 Identities=10% Similarity=0.171 Sum_probs=43.0
Q ss_pred hHHHHHhhcc-CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 008709 493 DAALVRIMKS-RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 555 (557)
Q Consensus 493 ~A~IVRimK~-~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 555 (557)
.-+|..+|++ .+.++.++|...+.+. ...++...|=+.|+.|.+.|.|.+-..+.+...|
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~---~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKK---GPRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHT---TTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhc---cCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 3455566666 4579999999888743 2456888999999999999999997655444444
No 170
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=31.76 E-value=1.2e+02 Score=32.10 Aligned_cols=39 Identities=23% Similarity=0.252 Sum_probs=33.7
Q ss_pred hcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 402 FNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 402 Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+...+.+|.++|++.++++.+.+.+.|..|. +.+++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~--~agLI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELA--RIGLLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHH--hCCCeEec
Confidence 5667799999999999999999999999997 46888753
No 171
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=31.50 E-value=39 Score=33.15 Aligned_cols=46 Identities=15% Similarity=0.341 Sum_probs=41.2
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 546 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 546 (557)
.-.|+.++++++.++.+||.+ +|..+...|.+=|..|-++|++.|.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~--------~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAE--------LFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHH--------HhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 346899999999999999885 5889999999999999999999994
No 172
>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=31.30 E-value=82 Score=25.21 Aligned_cols=44 Identities=16% Similarity=0.209 Sum_probs=35.1
Q ss_pred HHHHHhhcCCCCcCHHHHHHHh-CCCHHHHHHHHHhhhcccceeeecC
Q 008709 396 AATLLLFNTSDRLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~-~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+.||..... +...+.||.+.+ |++...|.+.|..|.. .+++.+.
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~--~GLv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEE--AGLVERR 52 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHH--TTSEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHH--cchhhcc
Confidence 456666656 688999999999 9999999999999973 5788754
No 173
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=31.26 E-value=91 Score=28.19 Aligned_cols=48 Identities=10% Similarity=0.185 Sum_probs=41.3
Q ss_pred HhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 008709 490 YAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 545 (557)
Q Consensus 490 ~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 545 (557)
..+|-.|.+++.....+++.+|-..| ..+...+.+||..|.+.|.|++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l--------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV--------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEE
Confidence 45788999999999999998887644 3577889999999999999986
No 174
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=31.18 E-value=74 Score=27.94 Aligned_cols=46 Identities=13% Similarity=0.315 Sum_probs=32.1
Q ss_pred HHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 494 AALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 494 A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
..|...+-....++..+|-. .+..+.+.+-+.|+.|.++|||+|..
T Consensus 43 ~~vL~~l~~~~~~t~~eLa~--------~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 43 FKVLCSIRCAACITPVELKK--------VLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HHHHHHHHHcCCCCHHHHHH--------HHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 33344443455677666664 24457788999999999999999964
No 175
>PHA02591 hypothetical protein; Provisional
Probab=30.91 E-value=64 Score=25.17 Aligned_cols=24 Identities=21% Similarity=0.321 Sum_probs=21.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 407 RLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 407 ~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
++|.++||..+|++.+.+.+.|.+
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHhc
Confidence 689999999999999999887765
No 176
>PRK06474 hypothetical protein; Provisional
Probab=30.85 E-value=1.4e+02 Score=27.50 Aligned_cols=51 Identities=16% Similarity=0.207 Sum_probs=39.3
Q ss_pred EEcHHHHHHHHhhcCCC-CcCHHHHHHHh-CCCHHHHHHHHHhhhcccceeeecC
Q 008709 390 IVSTYQAATLLLFNTSD-RLSYSEIMTQL-NLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~-~~t~~el~~~~-~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-.++.-..||..+-..+ .+|..+|++.+ +++...+-++|..|. +.+++...
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~--e~GLI~~~ 60 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV--DSGILHVV 60 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--HCCCEEEe
Confidence 34556667776555544 49999999999 799999999999997 45788754
No 177
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=30.84 E-value=96 Score=25.02 Aligned_cols=34 Identities=12% Similarity=0.298 Sum_probs=23.3
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcc
Q 008709 400 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCA 434 (557)
Q Consensus 400 l~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~ 434 (557)
.+..+... ++..|.+.||||...++.+|.+|...
T Consensus 15 ~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~ 48 (90)
T PF09904_consen 15 YLIDSGER-NVPALMEATGMPRRTIQDTIKALPEL 48 (90)
T ss_dssp HHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGG
T ss_pred HHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcC
Confidence 33444555 99999999999999999999999743
No 178
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=30.80 E-value=85 Score=27.53 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=33.8
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
|..+.+..+..++.+|++.++++...+.+.|..|.. .+++..
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 444456667889999999999999999999999973 366653
No 179
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=30.75 E-value=1.1e+02 Score=23.66 Aligned_cols=43 Identities=21% Similarity=0.220 Sum_probs=30.4
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeee
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILL 440 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~ 440 (557)
-+-||.... .++.+..+|+..+|++...+.+.|..|.. .+++.
T Consensus 8 i~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~--~gLI~ 50 (77)
T PF14947_consen 8 IFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEE--KGLIK 50 (77)
T ss_dssp HHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHH--TTSEE
T ss_pred HHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CcCee
Confidence 345666665 56789999999999999999999999974 46774
No 180
>PRK11050 manganese transport regulator MntR; Provisional
Probab=30.64 E-value=1.1e+02 Score=27.25 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=34.8
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.|+.++...+.++..+|++.++++...+.+.+..|.. .+++.+
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 4555666777899999999999999999999999974 366654
No 181
>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=30.39 E-value=1.6e+02 Score=23.17 Aligned_cols=47 Identities=13% Similarity=0.191 Sum_probs=37.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+++.|=+.-..+..+.-.+|++.++++...++..+..|- ..++|.+.
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le--~lGlve~~ 56 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLE--ELGLVESQ 56 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHH--HCCCccCC
Confidence 444444555667789999999999999999999999995 46888643
No 182
>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=30.32 E-value=66 Score=26.39 Aligned_cols=46 Identities=7% Similarity=0.169 Sum_probs=32.0
Q ss_pred HhHhHHHHHhhcc----CCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccc
Q 008709 490 YAIDAALVRIMKS----RKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYL 543 (557)
Q Consensus 490 ~~i~A~IVRimK~----~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi 543 (557)
..++..|..++|. .-.++.++|.+.+ ..+..+|+++|+.|++.|+|
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeE
Confidence 3445566666676 4457777777533 34789999999999999976
No 183
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=30.12 E-value=50 Score=32.33 Aligned_cols=46 Identities=20% Similarity=0.437 Sum_probs=40.6
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccccc
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERD 546 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~ 546 (557)
...|+.++++++.++..||.+ .|..+...|.+-|..|-++|.|.|-
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 457888899999999999886 4788999999999999999999984
No 184
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=29.79 E-value=89 Score=27.85 Aligned_cols=47 Identities=11% Similarity=0.153 Sum_probs=40.4
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccc
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLER 545 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r 545 (557)
.+|-.|.+.|.....+++.+|-..+ ..+.+.+..||+.|.+.|+|++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l--------glS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF--------GVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeee
Confidence 4677899999999999999988644 3578889999999999999985
No 185
>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=29.68 E-value=84 Score=24.28 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=38.7
Q ss_pred HHHHHHHHhhcC--CCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 393 TYQAATLLLFNT--SDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 393 ~~Qa~iLl~Fn~--~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
..|.++|...-. ..+++-.+|+..+|++...+-..++.|. +.+++.+.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~--~~gLI~k~ 51 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLE--KKGLIVKQ 51 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHH--HCCCEEEE
Confidence 467788877754 4578999999999999999999999997 35777654
No 186
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.50 E-value=1.3e+02 Score=28.65 Aligned_cols=46 Identities=20% Similarity=0.207 Sum_probs=34.6
Q ss_pred cHHHHHHHHhh---cCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceee
Q 008709 392 STYQAATLLLF---NTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKIL 439 (557)
Q Consensus 392 s~~Qa~iLl~F---n~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL 439 (557)
+.-+.-+++.+ +...++|.++|++.+++++..++.++..|++ ++++
T Consensus 160 t~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~--~~~~ 208 (239)
T PRK10430 160 TPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN--CHIL 208 (239)
T ss_pred CHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh--CCEE
Confidence 44444344322 3346899999999999999999999999974 4666
No 187
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=29.49 E-value=1e+02 Score=27.74 Aligned_cols=44 Identities=14% Similarity=0.233 Sum_probs=35.1
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+|..+..+.......+|++.+++++..+...++-|. +.+++...
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~--~~GlV~~~ 57 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLE--RLGLVEYE 57 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHH--HCCCeEEe
Confidence 344455567789999999999999999999999996 44777654
No 188
>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=28.94 E-value=78 Score=31.46 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=32.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKF 460 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f 460 (557)
+--.|.-+|.++..||+.+|.+.|+-|+..|+.+|...+ ++.+.+. ....|.|=..|
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 445677889999999999999999999999999998764 5655421 23567665555
No 189
>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=28.90 E-value=96 Score=25.20 Aligned_cols=38 Identities=8% Similarity=0.073 Sum_probs=29.8
Q ss_pred cCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 502 SRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 502 ~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
....+++.+|... .-.+.+.+.+.|..|.++|+|+|..
T Consensus 44 ~~~~is~~eLa~~--------~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAEL--------TGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHH--------HCcCHHHHHHHHHHHHHCCCeeeec
Confidence 4556787777753 2347778999999999999999876
No 190
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=28.37 E-value=1.1e+02 Score=24.81 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=42.6
Q ss_pred EEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 389 LIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 389 l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+..+.....||..+...+.=...-|+..++++.+++...|..|. ..|+|.+.
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le--~~GLler~ 54 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLE--EMGLLERV 54 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHH--HCCCeEEe
Confidence 44566777888888877766778899999999999999999997 45888875
No 191
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=28.13 E-value=1.2e+02 Score=22.90 Aligned_cols=33 Identities=24% Similarity=0.363 Sum_probs=28.4
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeec
Q 008709 407 RLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 407 ~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
.+|-++|+..+|++...+.+.|..|. +.+++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~--~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLK--DEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHH--HTTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHH--HCCCEEE
Confidence 58999999999999999999999996 3467754
No 192
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=27.83 E-value=1.1e+02 Score=22.96 Aligned_cols=50 Identities=18% Similarity=0.251 Sum_probs=40.7
Q ss_pred HHHHhhccCC-CCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 495 ALVRIMKSRK-VLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 495 ~IVRimK~~k-~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
.|.++++... .++..+|....... -+..+...|..++..|=++||+++..
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~---g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLR---GEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhc---ChhhhHHHHHHHHHHHHHCCCccccC
Confidence 4677787765 59999999877543 37788899999999999999998765
No 193
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=27.65 E-value=1e+02 Score=29.34 Aligned_cols=42 Identities=21% Similarity=0.270 Sum_probs=36.8
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.+|+-+..||.+.-++ .|..|||+.+++++..++.++..+..
T Consensus 143 ~LS~RE~eVL~Lia~G--~SnkEIA~~L~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 143 KVTKYQNDVFILYSFG--FSHEYIAQLLNITVGSSKNKISEILK 184 (217)
T ss_pred CCCHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4688999999988874 79999999999999999999988763
No 194
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=27.54 E-value=1.1e+02 Score=22.58 Aligned_cols=56 Identities=11% Similarity=0.164 Sum_probs=36.1
Q ss_pred HHHhhccCCCCChhHHHHHHHHH--hccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 496 LVRIMKSRKVLGHQQLVSECVEQ--LSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 496 IVRimK~~k~l~~~~L~~~v~~~--l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
|+-.+..-..++.+.+..-..-. -...+.++.++++.-++.+++.|-|+-++ +.|.
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~~---G~Yk 59 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECSG---GSYK 59 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--T---TEEE
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEecC---CEEe
Confidence 45555566677777777765544 23568889999999999999999998873 4553
No 195
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=27.01 E-value=1e+02 Score=29.18 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=33.8
Q ss_pred EEcHHHHHHHHh------hcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 390 IVSTYQAATLLL------FNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 390 ~~s~~Qa~iLl~------Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
..|.-|..+|.. |+.-..++..||++.+||++..+..+|..=
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 678899988843 444458999999999999998888877643
No 196
>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=26.94 E-value=1.2e+02 Score=26.69 Aligned_cols=39 Identities=23% Similarity=0.222 Sum_probs=31.5
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
+|.-|..|+.++ ...+|.+||++.+|++...+...+...
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 567788888876 367999999999999999888665544
No 197
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=26.82 E-value=1e+02 Score=23.93 Aligned_cols=56 Identities=18% Similarity=0.161 Sum_probs=41.4
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCC--ChHHHHHHHHhhhhhccccccC
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKP--DIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~--~~~~ik~~Ie~Liereyi~r~~ 547 (557)
.|-.|| +-|+.++..+...|...+...-.-...| -...++.+|..++++|-|.+..
T Consensus 8 mI~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 8 MILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 444555 6889999999999999888754211222 1356999999999999888864
No 198
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=26.75 E-value=81 Score=21.92 Aligned_cols=21 Identities=14% Similarity=0.390 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 008709 409 SYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 409 t~~el~~~~~i~~~~l~~~L~ 429 (557)
|+.||++..|++...+-++|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 688999999999999988775
No 199
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=26.73 E-value=1e+02 Score=30.28 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=33.5
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
+|++.-+ ++-|++||...++++...+..+|.-|. +.+++.+.
T Consensus 18 lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~--~~~LV~~~ 59 (260)
T COG4742 18 LLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLK--DKGLVVQE 59 (260)
T ss_pred HHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHh--hCCCEEec
Confidence 4454444 678999999999999999999999996 34677654
No 200
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=26.62 E-value=1.7e+02 Score=21.08 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=35.4
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
.+|.-+..++.++..+ .+..+|+..++++...+..++....
T Consensus 4 ~Lt~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 4 DLTPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred cCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4577888889888876 7899999999999999999988775
No 201
>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=26.55 E-value=51 Score=24.01 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=23.3
Q ss_pred cCCCCChHHHHHHHHhhhhhccccccC
Q 008709 521 RMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 521 ~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
..|..+...+.+.|..|.++|||.+.+
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 356678899999999999999998875
No 202
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=26.19 E-value=73 Score=24.48 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=20.5
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 406 DRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 406 ~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
-.-|.+||++.+|++.+.+...+...
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 35699999999999999999988754
No 203
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=26.18 E-value=92 Score=29.95 Aligned_cols=58 Identities=10% Similarity=0.212 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 461 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 461 (557)
+-..+.-+|..+..||+.+|.+.|+-|...|+.+|..++ ++.+.+. -...|.+-..|.
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 444566788899999999999999999999999998875 4443211 235677666653
No 204
>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=26.09 E-value=1.1e+02 Score=26.85 Aligned_cols=38 Identities=21% Similarity=0.288 Sum_probs=28.6
Q ss_pred EcHHHHHHHHh-hcCCCCcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 391 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 391 ~s~~Qa~iLl~-Fn~~~~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
+|+.|..|+.+ +- .+++.+||++.+|++...+...+.-
T Consensus 112 L~~~~r~v~~l~~~--~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 112 LPERQRELLQLRYQ--RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred CCHHHHHHHHHHHh--cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45566666655 43 4689999999999999998877654
No 205
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=25.95 E-value=1.1e+02 Score=29.10 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=37.2
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
..|.-|..||.++-+ ++|..||+..+++++.+++.+...+..
T Consensus 148 ~LT~RE~eVL~lla~--G~snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 148 LLTPRELEVLRLLAE--GLSNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 468899999999887 479999999999999999999988864
No 206
>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=25.91 E-value=1.1e+02 Score=25.67 Aligned_cols=47 Identities=15% Similarity=0.130 Sum_probs=33.1
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
+..|...+.....++..+|... ...+.+.+-..|..|.++|||+|..
T Consensus 30 q~~iL~~l~~~~~~t~~ela~~--------~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLANQ--------ACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHHH--------hCCCchhHHHHHHHHHHCCCEEecc
Confidence 4445555666777777766642 2345556889999999999999954
No 207
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=25.46 E-value=1.3e+02 Score=24.22 Aligned_cols=40 Identities=23% Similarity=0.257 Sum_probs=31.6
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
....+.-.+.....++++++++.++++.+++...+..++.
T Consensus 47 ~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~ 86 (105)
T PF01399_consen 47 RRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLIS 86 (105)
T ss_dssp HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHH
Confidence 3444555556778999999999999999999999888863
No 208
>PLN03239 histone acetyltransferase; Provisional
Probab=25.15 E-value=1.1e+02 Score=31.40 Aligned_cols=26 Identities=27% Similarity=0.406 Sum_probs=24.4
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 406 DRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 406 ~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
..+|+++|+..|||..+++..+|+.|
T Consensus 283 ~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 283 SSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 46999999999999999999999987
No 209
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.90 E-value=54 Score=28.74 Aligned_cols=26 Identities=8% Similarity=0.266 Sum_probs=21.7
Q ss_pred CCCCChHHHHHHHHhhhhhccccccC
Q 008709 522 MFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 522 ~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
.+..+.+.+.+.|+.|.++|||+|..
T Consensus 55 ~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 55 AIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HhCCChhhHHHHHHHHHHCCCEeeec
Confidence 34556777899999999999999964
No 210
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=24.81 E-value=1.4e+02 Score=28.45 Aligned_cols=45 Identities=20% Similarity=0.224 Sum_probs=35.7
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
.+.+-.-++...+|..+|++.++++...+.+.|..|. +.+++.+.
T Consensus 10 iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LE--e~GlI~R~ 54 (217)
T PRK14165 10 LALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLE--DEGYITRT 54 (217)
T ss_pred HHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH--HCCCEEEE
Confidence 3444445566679999999999999999999999996 45787654
No 211
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=24.55 E-value=1.8e+02 Score=25.80 Aligned_cols=60 Identities=15% Similarity=0.141 Sum_probs=45.6
Q ss_pred hHHHHHhhccC-CCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEe
Q 008709 493 DAALVRIMKSR-KVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRY 555 (557)
Q Consensus 493 ~A~IVRimK~~-k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Y 555 (557)
..+|.++|.+. ..++.++|..++.+.- ...+...|=+.++.|.+.|+|.+-....+...|
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~---p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y 83 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEG---PGISLATVYRTLKLLEEAGLVHRLEFEGGKTRY 83 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhC---CCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEE
Confidence 35667777754 4599999999888642 345788899999999999999998754444444
No 212
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=24.47 E-value=2.9e+02 Score=25.73 Aligned_cols=111 Identities=16% Similarity=0.158 Sum_probs=59.3
Q ss_pred CHhHHHHHHHHHHHHhhcCCCceEEeccCCceEEEEeE--e-------cCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHH
Q 008709 344 PSEMVKCVEVFKGFYETKTKHRKLTWIYSLGQCNINGK--F-------EQKNIELIVSTYQAATLLLFNTSDRLSYSEIM 414 (557)
Q Consensus 344 P~~l~~~~~~F~~~Y~~~~~~R~L~w~~~lg~~~l~~~--~-------~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~el~ 414 (557)
|..+..+++....-|.... |-+.-...-|...+..+ + ......-..|...+-+|-..--+.++|-.+|.
T Consensus 34 ~~~v~~~l~~L~~~y~~~~--~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~ 111 (188)
T PRK00135 34 PTEVQQLLEELQEKYEGDD--RGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEID 111 (188)
T ss_pred HHHHHHHHHHHHHHHhhCC--CCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHH
Confidence 3578899999999998653 33333322222222221 0 01111223445555555444444589999999
Q ss_pred HHhCCCHHHHHHHHHhhhcccceeeecCCCCCCCCCCCeEEEccCCC
Q 008709 415 TQLNLTHDDLVRLLHSLSCAKYKILLKEPNTKTISQSDHFEFNSKFT 461 (557)
Q Consensus 415 ~~~~i~~~~l~~~L~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~f~ 461 (557)
+..|++...+ +..|. ..+++...+..........|.++..|-
T Consensus 112 ~irGv~~~~i---i~~L~--~~gLI~e~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 112 EIRGVNSDGA---LQTLL--AKGLIKEVGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred HHHCCCHHHH---HHHHH--HCCCeEEcCcCCCCCCCeeeehhHHHH
Confidence 9999997544 44444 236665432111111334566666653
No 213
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=24.17 E-value=1e+02 Score=33.08 Aligned_cols=59 Identities=14% Similarity=0.284 Sum_probs=49.1
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceEecC
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA 557 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~Yia 557 (557)
.-+.+|++.++..+.++-.+|-+ .|..+...+-+.|..|+.+|++++-.....-+.||.
T Consensus 402 ~~~~~il~~~~en~~~T~~~L~~--------~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~ 460 (467)
T COG2865 402 ERQEKILELIKENGKVTARELRE--------ILGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVK 460 (467)
T ss_pred HHHHHHHHHHhhccccCHHHHHH--------HhCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEec
Confidence 33589999999999999988875 344788899999999999999999887677777763
No 214
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=24.16 E-value=65 Score=29.51 Aligned_cols=61 Identities=15% Similarity=0.151 Sum_probs=38.9
Q ss_pred hHHHhhHHhHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCCCCceE
Q 008709 483 DVDKDRRYAIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFR 554 (557)
Q Consensus 483 ~~~~~r~~~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~~~~y~ 554 (557)
-...|...+|-+ ++.+|.... .... +.+.+.+ ..+.++++++|+.|.+-|+|+++++ +.|+
T Consensus 20 ~~~~W~~~~ir~-l~~l~~~~~--d~~~----iak~l~p--~is~~ev~~sL~~L~~~gli~k~~~--g~y~ 80 (171)
T PF14394_consen 20 YYSSWYHPAIRE-LLPLMPFAP--DPEW----IAKRLRP--KISAEEVRDSLEFLEKLGLIKKDGD--GKYV 80 (171)
T ss_pred HHhhhHHHHHHH-HhhcCCCCC--CHHH----HHHHhcC--CCCHHHHHHHHHHHHHCCCeEECCC--CcEE
Confidence 345566555655 555555543 2222 2233321 4588999999999999999999985 4553
No 215
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=24.11 E-value=1.6e+02 Score=27.19 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=35.1
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-++.-.+.++..|..+|+..+|++..++.++|-.|. +.+.+..+
T Consensus 17 ~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~--~~~~v~~~ 60 (183)
T PHA03103 17 KEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQ--REGMVYMS 60 (183)
T ss_pred HHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHH--hcCceecC
Confidence 355556777889999999999999999999999986 33555444
No 216
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.01 E-value=1.2e+02 Score=28.56 Aligned_cols=42 Identities=12% Similarity=0.149 Sum_probs=37.2
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
..|.-+.-||.+.-++ +|..||++.+++++..++.++..+..
T Consensus 137 ~LT~RE~eVL~lla~G--~snkeIA~~L~iS~~TVk~h~~~I~~ 178 (207)
T PRK15411 137 SLSRTESSMLRMWMAG--QGTIQISDQMNIKAKTVSSHKGNIKR 178 (207)
T ss_pred cCCHHHHHHHHHHHcC--CCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 4789999999988774 78999999999999999999988863
No 217
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=23.91 E-value=1.3e+02 Score=28.20 Aligned_cols=41 Identities=22% Similarity=0.226 Sum_probs=36.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.|.-+.-||.+.-+ +.|..||++.++++...++.++..+..
T Consensus 151 Lt~rE~evl~~~~~--G~s~~eIA~~l~iS~~TV~~h~~~i~~ 191 (216)
T PRK10840 151 LSPKESEVLRLFAE--GFLVTEIAKKLNRSIKTISSQKKSAMM 191 (216)
T ss_pred CCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 68888999988876 489999999999999999999988863
No 218
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.84 E-value=1.4e+02 Score=20.33 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=16.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 406 DRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 406 ~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
..+|..+||+.+|.+...+-+.|.
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 358999999999999998877663
No 219
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.76 E-value=1.2e+02 Score=32.28 Aligned_cols=29 Identities=24% Similarity=0.385 Sum_probs=26.2
Q ss_pred cCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 403 NTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 403 n~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
+....+|+++|+..|||..+++..+|+.|
T Consensus 370 ~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 370 KHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred hcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 44468999999999999999999999988
No 220
>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=23.74 E-value=1.3e+02 Score=22.08 Aligned_cols=46 Identities=13% Similarity=0.273 Sum_probs=32.3
Q ss_pred HHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCC
Q 008709 495 ALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN 549 (557)
Q Consensus 495 ~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~ 549 (557)
.|...+.... ++..+|.. .+..+...+.+.++.|...|+|.+....
T Consensus 11 ~il~~l~~~~-~~~~ei~~--------~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 11 RILRLLLEGP-LTVSELAE--------RLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHHCC-cCHHHHHH--------HHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 3444444444 77777643 2345778899999999999999987543
No 221
>PF13551 HTH_29: Winged helix-turn helix
Probab=23.38 E-value=1.5e+02 Score=24.28 Aligned_cols=35 Identities=23% Similarity=0.364 Sum_probs=27.9
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
.+|+++.++.. |+.+++..+|++...+.+.+..+.
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35566666533 799999999999999999888775
No 222
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=23.25 E-value=1.5e+02 Score=24.51 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=23.8
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
+|--|-.++-++-.. .+|++|||+..|++...+-..+.
T Consensus 18 LT~kQ~~~l~lyy~e-DlSlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 18 LTEKQREILELYYEE-DLSLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp S-HHHHHHHHHHCTS----HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHcc-CCCHHHHHHHHCCCHHHHHHHHH
Confidence 345577777665543 58999999999999976655554
No 223
>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=23.18 E-value=8e+02 Score=24.94 Aligned_cols=163 Identities=12% Similarity=0.231 Sum_probs=84.3
Q ss_pred HHHHhhccCCHHHHHHHHHhhccC---CCChhhHHHHHHHHHHHHHHHHHHhhHHHhhhcCCCCCccchHHHHHHHHHHH
Q 008709 89 GCRALLREDKVEDLSRMYRLYHKI---PKGLEPVANVFKQHITAEGTVLVQQAEDAATNQGGSSGAVQEQVLIRKIIELH 165 (557)
Q Consensus 89 gl~~ll~~~~~~~L~~ly~l~~~~---~~~l~~l~~~~~~~i~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~I~~l~~l~ 165 (557)
.|..-.+.++.+.+.+.++||--+ +.|++...+.+.+.|.....+.+......... +..+.-|+..|..++
T Consensus 15 ~F~~A~~~~D~~~v~rffkLFPlig~~eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~~------~~~~~~~~~~lt~LF 88 (331)
T PF08318_consen 15 KFDEAAQANDVAQVTRFFKLFPLIGQEEEGLDLYSKYLCDIIAEQSRKLLDSATSGSSD------SRSPVFYADALTKLF 88 (331)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc------ccccccHHHHHHHHH
Confidence 466667788999999999988665 34666666666666666665555443211100 112333444444444
Q ss_pred HHH-------HHHHHHhcCCChHHH--HHHHH--------HHHHHhhcCCCCCCcHHHHHHHHHHHhhc-----------
Q 008709 166 DKY-------MEYVTNCFINHTLFH--KALKE--------AFEIFCNKAVGGSSSSELLATFCDNILKK----------- 217 (557)
Q Consensus 166 ~~~-------~~li~~~F~~~~~f~--~~l~~--------af~~~~n~~~~~~~~~e~La~y~d~~l~~----------- 217 (557)
+.. ..+|..||+...... ..+.. -+..|..... -.+....+..|-...+.+
T Consensus 89 e~ia~ii~~h~~lI~~~yG~~~~~~vi~~Lq~E~D~q~~~Ild~f~~~R~-l~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 167 (331)
T PF08318_consen 89 EHIATIIEQHQPLIEKYYGPGYMVYVIEKLQKECDLQAGIILDTFMDERR-LDRKLQDIQSYNFSFLVKNSGRSSSSSSR 167 (331)
T ss_pred HHHHHHHHHccHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-HHHHHHHHHhhhhhhhccccccccccccc
Confidence 444 446778888653211 11111 1111111110 001112222333322222
Q ss_pred ------CCCCCCChHHHHHhhhhHhhhhccccChhHHHHHHHHHHHHHhcCCCC
Q 008709 218 ------GGNEKLSDEAIEETLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRS 265 (557)
Q Consensus 218 ------~~~~~~~~~~~~~~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~ 265 (557)
+.....+.-+++..|+.+..+++.. ..|.++++.|.-....
T Consensus 168 ~~~~~~~~~~~~d~reld~lL~Eis~i~~~w-------~lY~rFi~~k~~~~~~ 214 (331)
T PF08318_consen 168 AASSSQSEDEGIDPRELDALLNEISLILQRW-------SLYCRFISRKWNEFSD 214 (331)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcccc
Confidence 0011233446777888888777643 5799999999887543
No 224
>smart00526 H15 Domain in histone families 1 and 5.
Probab=23.16 E-value=2.5e+02 Score=20.81 Aligned_cols=53 Identities=19% Similarity=0.198 Sum_probs=38.3
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCC--hHHHHHHHHhhhhhcccccc
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPD--IKAIKKRMEDLITRDYLERD 546 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~--~~~ik~~Ie~Liereyi~r~ 546 (557)
.|..||.. |+.++..+...|...+...-. ..|. ...++.+|..++++|-+.+-
T Consensus 10 mI~eAI~~-l~er~GsS~~aI~kyi~~~~~--~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 10 MITEAISA-LKERKGSSLQAIKKYIEANYK--VLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHH-cCCCCCCCHHHHHHHHHHhCC--CChHHHHHHHHHHHHHHHhcCceeec
Confidence 56666665 699999999999988876521 2222 35688889999999987653
No 225
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=23.01 E-value=1.2e+02 Score=26.97 Aligned_cols=40 Identities=18% Similarity=0.204 Sum_probs=28.3
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
++.-|-.++.+.- ..++|.+||++.+|++...++..+..-
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3445555554432 346899999999999999988877543
No 226
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=22.93 E-value=1.6e+02 Score=26.10 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=30.6
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
.+|.-|..||.++. ..+|.+||++.+|++...+......
T Consensus 6 ~Lt~rqreVL~lr~--~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 6 FLTERQIEVLRLRE--RGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45778888887763 5699999999999999776665543
No 227
>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=22.54 E-value=2.2e+02 Score=24.59 Aligned_cols=49 Identities=16% Similarity=0.136 Sum_probs=37.4
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHh----CCCHHHHHHHHHhhhcccceeeec
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQL----NLTHDDLVRLLHSLSCAKYKILLK 441 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~----~i~~~~l~~~L~~L~~~k~~iL~~ 441 (557)
+|..+..|+..+=+.+..|+.||.+.+ +.+...+...|..|.. -+++..
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~--KG~v~~ 54 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD--KGCLTT 54 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH--CCceee
Confidence 456778888766566789999977665 7888999999999974 377754
No 228
>PRK00118 putative DNA-binding protein; Validated
Probab=22.50 E-value=1.4e+02 Score=24.87 Aligned_cols=37 Identities=16% Similarity=0.245 Sum_probs=26.6
Q ss_pred cHHHHHHHHh-hcCCCCcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 392 STYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 392 s~~Qa~iLl~-Fn~~~~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
+.-|-.++.+ +.+ ..|+.+|++.+|++...+.+.+..
T Consensus 19 ~ekqRevl~L~y~e--g~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 19 TEKQRNYMELYYLD--DYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred CHHHHHHHHHHHHc--CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4444444433 333 689999999999999998887754
No 229
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=22.50 E-value=75 Score=24.93 Aligned_cols=31 Identities=19% Similarity=0.192 Sum_probs=26.4
Q ss_pred HhccCCCCChHHHHHHHHhhhhhccccccCC
Q 008709 518 QLSRMFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 518 ~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
+|+.+|..+.+.|..-++.|+.+|-|+|-+.
T Consensus 21 ~Ls~~~~~p~~~VeaMLe~l~~kGkverv~~ 51 (78)
T PRK15431 21 QISQTLNTPQPMINAMLQQLESMGKAVRIQE 51 (78)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCeEeecc
Confidence 3445688899999999999999999999863
No 230
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=22.49 E-value=66 Score=26.21 Aligned_cols=27 Identities=33% Similarity=0.615 Sum_probs=19.4
Q ss_pred hccCCCCChHHHHHHHHhhhhhcccccc
Q 008709 519 LSRMFKPDIKAIKKRMEDLITRDYLERD 546 (557)
Q Consensus 519 l~~~F~~~~~~ik~~Ie~Liereyi~r~ 546 (557)
+++.| |...-+..-||.||.-|||.|+
T Consensus 34 iKk~f-~~qk~~D~fie~li~~GYI~re 60 (93)
T PF08820_consen 34 IKKDF-PKQKRLDIFIEALIKLGYIERE 60 (93)
T ss_pred HHHhh-ccccchhHHHHHHHHcCCeEec
Confidence 33445 3334467789999999999994
No 231
>smart00753 PAM PCI/PINT associated module.
Probab=22.43 E-value=1.5e+02 Score=23.16 Aligned_cols=30 Identities=17% Similarity=0.246 Sum_probs=26.3
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 404 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 404 ~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
....+++++|++.++++.+++...+..++.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~ 50 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIR 50 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 457899999999999999999998888863
No 232
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=22.43 E-value=1.5e+02 Score=23.16 Aligned_cols=30 Identities=17% Similarity=0.246 Sum_probs=26.3
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 404 TSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 404 ~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
....+++++|++.++++.+++...+..++.
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~ 50 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIR 50 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 457899999999999999999998888863
No 233
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=22.40 E-value=1.2e+02 Score=28.27 Aligned_cols=33 Identities=30% Similarity=0.516 Sum_probs=29.3
Q ss_pred HhhcCCCC-cCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 400 LLFNTSDR-LSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 400 l~Fn~~~~-~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
++|-..++ +|+++|++.++++...+..+|..|.
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~ 45 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQ 45 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56777776 9999999999999999999999885
No 234
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=22.19 E-value=1.6e+02 Score=27.10 Aligned_cols=41 Identities=22% Similarity=0.203 Sum_probs=36.1
Q ss_pred EcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 391 VSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 391 ~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
+|+-+.-||.+.-+ +.|..||++.+++++..++.++..+..
T Consensus 134 LSpRErEVLrLLAq--GkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 134 FSVTERHLLKLIAS--GYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred CCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 78899999988877 478999999999999999999888763
No 235
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=22.05 E-value=1.5e+02 Score=28.06 Aligned_cols=42 Identities=14% Similarity=0.166 Sum_probs=37.1
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
..|.-+.-||.++-++ .|..||++.+++++..++.++..+..
T Consensus 134 ~LT~RE~eVL~ll~~G--~snkeIA~~L~iS~~TV~~h~~~I~~ 175 (207)
T PRK11475 134 MLSPTEREILRFMSRG--YSMPQIAEQLERNIKTIRAHKFNVMS 175 (207)
T ss_pred CCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3788999999988874 79999999999999999999988863
No 236
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.05 E-value=1.1e+02 Score=24.40 Aligned_cols=24 Identities=42% Similarity=0.405 Sum_probs=21.9
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 406 DRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 406 ~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
..+|.++|+..+|.++..+.+.|+
T Consensus 22 ~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHH
Confidence 369999999999999999999885
No 237
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.96 E-value=1.1e+02 Score=27.81 Aligned_cols=37 Identities=14% Similarity=0.284 Sum_probs=27.2
Q ss_pred EcHHHHHHHHh-hcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 391 VSTYQAATLLL-FNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 391 ~s~~Qa~iLl~-Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
+|.-|-.|+.+ +- +++|++||++.+|+|...++..|.
T Consensus 128 Lp~~~R~v~~L~~~--~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 128 LRPRVKQAFLMATL--DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44555555544 33 468999999999999999887764
No 238
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.87 E-value=1.8e+02 Score=24.59 Aligned_cols=56 Identities=20% Similarity=0.206 Sum_probs=40.8
Q ss_pred EEEEeEecCeeEEEEEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhc
Q 008709 376 CNINGKFEQKNIELIVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSC 433 (557)
Q Consensus 376 ~~l~~~~~~~~~~l~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~ 433 (557)
.+|+..|.- ..-..++.-|..-+..|=...+ ++.++++.+|+++..++..|..++.
T Consensus 20 t~i~G~F~l-~~~~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 20 TEIEGEFEL-PWFARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred CEEEeeecc-chhhcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 345555542 2334667777777777765433 7899999999999999999998864
No 239
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.82 E-value=1.4e+02 Score=28.05 Aligned_cols=33 Identities=30% Similarity=0.372 Sum_probs=24.3
Q ss_pred HHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHh
Q 008709 396 AATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHS 430 (557)
Q Consensus 396 a~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~ 430 (557)
..++|.+ ...++++||++.+|++...++..|.-
T Consensus 145 ~v~~L~~--~~g~s~~EIA~~Lgis~~tV~~~l~R 177 (203)
T PRK09647 145 AAVVLCD--IEGLSYEEIAATLGVKLGTVRSRIHR 177 (203)
T ss_pred HHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3344444 24689999999999999888776643
No 240
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=21.65 E-value=65 Score=25.30 Aligned_cols=47 Identities=17% Similarity=0.265 Sum_probs=35.7
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
.-+|+-.+.....+++.+|... ...+...+-+.+..|.+.|||++..
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~--------l~lt~g~Ls~hL~~Le~~GyV~~~k 48 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEE--------LGLTDGNLSKHLKKLEEAGYVEVEK 48 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHH--------TT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHH--------hCcCHHHHHHHHHHHHHCCCEEEEE
Confidence 3456777777888888888753 3457888999999999999999864
No 241
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.30 E-value=91 Score=24.16 Aligned_cols=34 Identities=21% Similarity=0.219 Sum_probs=23.5
Q ss_pred HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 398 TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 398 iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
|+....+-..+|+.||++.+|+++..+.|..+.|
T Consensus 25 il~~~~~~~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 25 ILENPDEIAFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp HHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 3333444457999999999999999999887766
No 242
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.28 E-value=1.2e+02 Score=27.56 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=25.9
Q ss_pred cHHHHH-HHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 392 STYQAA-TLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 392 s~~Qa~-iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
+.-+-. +++.|- +++|++||++.+|++...++..|.
T Consensus 131 ~~~~r~i~~l~~~--~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 131 EKDRAAAVRRAYL--EGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHH
Confidence 444444 444443 458999999999999998877664
No 243
>PRK04217 hypothetical protein; Provisional
Probab=21.09 E-value=1.7e+02 Score=24.63 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=28.2
Q ss_pred EEcHHHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhh
Q 008709 390 IVSTYQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSL 431 (557)
Q Consensus 390 ~~s~~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L 431 (557)
.++.-|..++.+.. .+.+|++||++.+|++...+...|...
T Consensus 42 ~Lt~eereai~l~~-~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 42 FMTYEEFEALRLVD-YEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34445544443332 245799999999999999888877643
No 244
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=21.06 E-value=1.3e+02 Score=29.61 Aligned_cols=47 Identities=23% Similarity=0.338 Sum_probs=39.0
Q ss_pred HHHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhhcccceeeecC
Q 008709 394 YQAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLSCAKYKILLKE 442 (557)
Q Consensus 394 ~Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~~~k~~iL~~~ 442 (557)
-|..+-..-+.++.++-.||.+.+|+|+..+-++|+.|- |.+++.+.
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE--k~GlIe~~ 243 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE--KRGLIEKE 243 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH--hCCceEEE
Confidence 455555666777889999999999999999999999996 66888754
No 245
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=21.05 E-value=1.4e+02 Score=22.25 Aligned_cols=23 Identities=9% Similarity=0.403 Sum_probs=19.3
Q ss_pred CCCCcCHHHHHHHhCCCHHHHHH
Q 008709 404 TSDRLSYSEIMTQLNLTHDDLVR 426 (557)
Q Consensus 404 ~~~~~t~~el~~~~~i~~~~l~~ 426 (557)
.++.++..+||+.+|+++..+..
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHH
Confidence 45689999999999999987743
No 246
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=21.02 E-value=1.8e+02 Score=22.88 Aligned_cols=51 Identities=6% Similarity=0.171 Sum_probs=34.7
Q ss_pred hHhHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhcccc
Q 008709 491 AIDAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLE 544 (557)
Q Consensus 491 ~i~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~ 544 (557)
.+=+.|.+.+..++ +..+|+..+.+.... -.+-..++..-|+.|.++++|+
T Consensus 31 ~~g~~Iw~lldg~~--tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 31 DSAGEILELCDGKR--SLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred hHHHHHHHHccCCC--cHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCcC
Confidence 34566777776644 777888877766442 2233577888888888888874
No 247
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=20.98 E-value=1.1e+02 Score=27.69 Aligned_cols=32 Identities=28% Similarity=0.493 Sum_probs=25.1
Q ss_pred HhhcCCCCcCHHHHHHHhCCCHHHHHHHHHhhh
Q 008709 400 LLFNTSDRLSYSEIMTQLNLTHDDLVRLLHSLS 432 (557)
Q Consensus 400 l~Fn~~~~~t~~el~~~~~i~~~~l~~~L~~L~ 432 (557)
++|-..+++|+++|++.++ +...+...|..|.
T Consensus 6 lLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~ 37 (159)
T PF04079_consen 6 LLFASGEPVSIEELAEILG-SEDEVEEALEELQ 37 (159)
T ss_dssp HHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHH
T ss_pred hHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHH
Confidence 5677888899999999999 9999999999885
No 248
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=20.83 E-value=77 Score=27.42 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=34.9
Q ss_pred hccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccCCC--CCceEe
Q 008709 500 MKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKEN--PNMFRY 555 (557)
Q Consensus 500 mK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~~~--~~~y~Y 555 (557)
|..++.++.++|-+.+ .-+.+.+-+.+..|++.|+|.|...+ .+-|.|
T Consensus 37 L~~~~~~tvdelae~l--------nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~y 86 (126)
T COG3355 37 LEENGPLTVDELAEIL--------NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYY 86 (126)
T ss_pred HhhcCCcCHHHHHHHH--------CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeE
Confidence 3467788888877543 34778899999999999999997532 344444
No 249
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=20.25 E-value=1.4e+02 Score=24.64 Aligned_cols=47 Identities=17% Similarity=0.282 Sum_probs=30.5
Q ss_pred HHHhcCCChHHHHHHHHHHHHHhhcCC----CCCCcHHHHHHHHHHHhhcC
Q 008709 172 VTNCFINHTLFHKALKEAFEIFCNKAV----GGSSSSELLATFCDNILKKG 218 (557)
Q Consensus 172 i~~~F~~~~~f~~~l~~af~~~~n~~~----~~~~~~e~La~y~d~~l~~~ 218 (557)
+..+...+......+..||+.++..-+ +.+..++.+|+++..++..+
T Consensus 60 l~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~ 110 (113)
T PF02847_consen 60 LSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADG 110 (113)
T ss_dssp HHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTT
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcC
Confidence 333333444556677777777776532 24578899999999988864
No 250
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=20.25 E-value=71 Score=25.99 Aligned_cols=27 Identities=22% Similarity=0.334 Sum_probs=23.3
Q ss_pred CCCCChHHHHHHHHhhhhhccccccCC
Q 008709 522 MFKPDIKAIKKRMEDLITRDYLERDKE 548 (557)
Q Consensus 522 ~F~~~~~~ik~~Ie~Liereyi~r~~~ 548 (557)
+...+.++|..+++.|.+.|+|+|..+
T Consensus 30 ~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 30 RLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 345678899999999999999999874
No 251
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.23 E-value=1.6e+02 Score=26.55 Aligned_cols=31 Identities=23% Similarity=0.350 Sum_probs=23.4
Q ss_pred HHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 397 ATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 397 ~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
++++.+-+ +++++||++.+|++...++..|.
T Consensus 127 i~~l~~~~--~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 127 VLVLYYYE--QYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHH
Confidence 34444433 57999999999999998887764
No 252
>KOG3852 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.10 E-value=4e+02 Score=26.74 Aligned_cols=109 Identities=14% Similarity=0.193 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCC-------ChHHHHHHHHHHHHHhhcCCCCCCcHHHHHHHHHHHhhcCCCCCCChHHHHH
Q 008709 158 IRKIIELHDKYMEYVTNCFIN-------HTLFHKALKEAFEIFCNKAVGGSSSSELLATFCDNILKKGGNEKLSDEAIEE 230 (557)
Q Consensus 158 I~~l~~l~~~~~~li~~~F~~-------~~~f~~~l~~af~~~~n~~~~~~~~~e~La~y~d~~l~~~~~~~~~~~~~~~ 230 (557)
...|+.+|..-..=+.+||.. ..+|.+|+.---.+.+....+...-.--|-+|||-+.|. .+ ..+..++
T Consensus 220 LD~lL~fy~cs~~~lte~~~ptv~~ESmYGDfqeA~~HL~~rlI~Tr~PEEIRGGGLLKYc~Llvrg-fk-pa~~~ei-- 295 (426)
T KOG3852|consen 220 LDPLLLFYSCSNNPLTECFHPTVTGESMYGDFQEAMTHLQHRLIATRKPEEIRGGGLLKYCHLLVRG-FK-PAKPWEI-- 295 (426)
T ss_pred ehhhhhhhcccCCccchhcCceeeeeeccccHHHHHHHHHHhhhccCCHHHccCchHHHHHHHHHcc-CC-CCCHHHH--
Confidence 455666776666666777754 245777777666666654321111112367999998884 32 1222333
Q ss_pred hhhhHhhhhccccChhHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHhCChhhHh
Q 008709 231 TLEKVVKLLAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSK 289 (557)
Q Consensus 231 ~l~~i~~lf~~l~~Kd~F~~~Y~~~L~~RLL~~~~~~~~~E~~~i~~Lk~~~G~~~~~k 289 (557)
+...+++|.|+.-.-+--.+.++.+=+.|...+|.+...|
T Consensus 296 -------------------k~LeRYMCSRFFIDFpdi~eQqrkle~YL~nHF~g~~~~k 335 (426)
T KOG3852|consen 296 -------------------KALERYMCSRFFIDFPDIIEQQRKLESYLQNHFGGEENRK 335 (426)
T ss_pred -------------------HHHHHHHHhhhcccccHHHHHHHHHHHHHHHhhccccchh
Confidence 2345677888776655445666777777777777554433
No 253
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=20.02 E-value=99 Score=30.59 Aligned_cols=47 Identities=9% Similarity=0.179 Sum_probs=40.8
Q ss_pred hHHHHHhhccCCCCChhHHHHHHHHHhccCCCCChHHHHHHHHhhhhhccccccC
Q 008709 493 DAALVRIMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDK 547 (557)
Q Consensus 493 ~A~IVRimK~~k~l~~~~L~~~v~~~l~~~F~~~~~~ik~~Ie~Liereyi~r~~ 547 (557)
...|+..+++++.++.++|.+ .|.++...|.+=|..|-++|++.|.-
T Consensus 19 ~~~Il~~L~~~~~vtv~eLa~--------~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 19 REQIIQRLRQQGSVQVNDLSA--------LYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHcCCEeHHHHHH--------HHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 567899999999999999885 46789999999999999999998843
No 254
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.01 E-value=1.7e+02 Score=25.88 Aligned_cols=32 Identities=28% Similarity=0.405 Sum_probs=24.6
Q ss_pred HHHHHHhhcCCCCcCHHHHHHHhCCCHHHHHHHHH
Q 008709 395 QAATLLLFNTSDRLSYSEIMTQLNLTHDDLVRLLH 429 (557)
Q Consensus 395 Qa~iLl~Fn~~~~~t~~el~~~~~i~~~~l~~~L~ 429 (557)
+.++.+.+ ..++.+||++.+|++...+...+.
T Consensus 118 r~il~l~~---~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 118 RTVLLLRF---SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred HHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44444555 368999999999999998877664
Done!